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Sample records for accelerating epistasis analysis

  1. Accelerating epistasis analysis in human genetics with consumer graphics hardware

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    Cancare Fabio

    2009-07-01

    Full Text Available Abstract Background Human geneticists are now capable of measuring more than one million DNA sequence variations from across the human genome. The new challenge is to develop computationally feasible methods capable of analyzing these data for associations with common human disease, particularly in the context of epistasis. Epistasis describes the situation where multiple genes interact in a complex non-linear manner to determine an individual's disease risk and is thought to be ubiquitous for common diseases. Multifactor Dimensionality Reduction (MDR is an algorithm capable of detecting epistasis. An exhaustive analysis with MDR is often computationally expensive, particularly for high order interactions. This challenge has previously been met with parallel computation and expensive hardware. The option we examine here exploits commodity hardware designed for computer graphics. In modern computers Graphics Processing Units (GPUs have more memory bandwidth and computational capability than Central Processing Units (CPUs and are well suited to this problem. Advances in the video game industry have led to an economy of scale creating a situation where these powerful components are readily available at very low cost. Here we implement and evaluate the performance of the MDR algorithm on GPUs. Of primary interest are the time required for an epistasis analysis and the price to performance ratio of available solutions. Findings We found that using MDR on GPUs consistently increased performance per machine over both a feature rich Java software package and a C++ cluster implementation. The performance of a GPU workstation running a GPU implementation reduces computation time by a factor of 160 compared to an 8-core workstation running the Java implementation on CPUs. This GPU workstation performs similarly to 150 cores running an optimized C++ implementation on a Beowulf cluster. Furthermore this GPU system provides extremely cost effective

  2. Dynamics in Epistasis Analysis.

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    Awdeh, Aseel; Phenix, Hilary; Kaern, Mads; Perkins, Theodore

    2017-01-16

    Finding regulatory relationships between genes, including the direction and nature of influence between them, is a fundamental challenge in the field of molecular genetics. One classical approach to this problem is epistasis analysis. Broadly speaking, epistasis analysis infers the regulatory relationships between a pair of genes in a genetic pathway by considering the patterns of change in an observable trait resulting from single and double deletion of genes. While classical epistasis analysis has yielded deep insights on numerous genetic pathways, it is not without limitations. Here, we explore the possibility of dynamic epistasis analysis, in which, in addition to performing genetic perturbations of a pathway, we drive the pathway by a time-varying upstream signal. We explore the theoretical power of dynamical epistasis analysis by conducting an identifiability analysis of Boolean models of genetic pathways, comparing static and dynamic approaches. We find that even relatively simple input dynamics greatly increases the power of epistasis analysis to discriminate alternative network structures. Further, we explore the question of experiment design, and show that a subset of short time-varying signals, which we call dynamic primitives, allow maximum discriminative power with a reduced number of experiments.

  3. Reconstructability analysis of epistasis.

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    Zwick, Martin

    2011-01-01

    The literature on epistasis describes various methods to detect epistatic interactions and to classify different types of epistasis. Reconstructability analysis (RA) has recently been used to detect epistasis in genomic data. This paper shows that RA offers a classification of types of epistasis at three levels of resolution (variable-based models without loops, variable-based models with loops, state-based models). These types can be defined by the simplest RA structures that model the data without information loss; a more detailed classification can be defined by the information content of multiple candidate structures. The RA classification can be augmented with structures from related graphical modeling approaches. RA can analyze epistatic interactions involving an arbitrary number of genes or SNPs and constitutes a flexible and effective methodology for genomic analysis.

  4. Epistasis analysis using information theory.

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    Moore, Jason H; Hu, Ting

    2015-01-01

    Here we introduce entropy-based measures derived from information theory for detecting and characterizing epistasis in genetic association studies. We provide a general overview of the methods and highlight some of the modifications that have greatly improved its power for genetic analysis. We end with a few published studies of complex human diseases that have used these measures.

  5. Epistasis analysis using artificial intelligence.

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    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.

  6. Epistasis can accelerate adaptive diversification in haploid asexual populations.

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    Griswold, Cortland K

    2015-03-07

    A fundamental goal of the biological sciences is to determine processes that facilitate the evolution of diversity. These processes can be separated into ecological, physiological, developmental and genetic. An ecological process that facilitates diversification is frequency-dependent selection caused by competition. Models of frequency-dependent adaptive diversification have generally assumed a genetic basis of phenotype that is non-epistatic. Here, we present a model that indicates diversification is accelerated by an epistatic basis of phenotype in combination with a competition model that invokes frequency-dependent selection. Our model makes use of a genealogical model of epistasis and insights into the effects of balancing selection on the genealogical structure of a population to understand how epistasis can facilitate diversification. The finding that epistasis facilitates diversification may be informative with respect to empirical results that indicate an epistatic basis of phenotype in experimental bacterial populations that experienced adaptive diversification. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

  7. Dynamic network-based epistasis analysis: Boolean examples

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    Eugenio eAzpeitia

    2011-12-01

    Full Text Available In this review we focus on how the hierarchical and single-path assumptions of epistasis analysis can bias the topologies of gene interactions infered. This has been acknowledged in several previous papers and reviews, but 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 (herein, classical epistasis, defined as the blocking of a particular allelic effect due to the effect of another allele at a different locus. 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 gene interaction topologies are 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 review complements previous accounts, not

  8. A strategy to apply quantitative epistasis analysis on developmental traits.

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    Labocha, Marta K; Yuan, Wang; Aleman-Meza, Boanerges; Zhong, Weiwei

    2017-05-15

    Genetic interactions are keys to understand complex traits and evolution. Epistasis analysis is an effective method to map genetic interactions. Large-scale quantitative epistasis analysis has been well established for single cells. However, there is a substantial lack of such studies in multicellular organisms and their complex phenotypes such as development. Here we present a method to extend quantitative epistasis analysis to developmental traits. In the nematode Caenorhabditis elegans, we applied RNA interference on mutants to inactivate two genes, used an imaging system to quantitatively measure phenotypes, and developed a set of statistical methods to extract genetic interactions from phenotypic measurement. Using two different C. elegans developmental phenotypes, body length and sex ratio, as examples, we showed that this method could accommodate various metazoan phenotypes with performances comparable to those methods in single cell growth studies. Comparing with qualitative observations, this method of quantitative epistasis enabled detection of new interactions involving subtle phenotypes. For example, several sex-ratio genes were found to interact with brc-1 and brd-1, the orthologs of the human breast cancer genes BRCA1 and BARD1, respectively. We confirmed the brc-1 interactions with the following genes in DNA damage response: C34F6.1, him-3 (ortholog of HORMAD1, HORMAD2), sdc-1, and set-2 (ortholog of SETD1A, SETD1B, KMT2C, KMT2D), validating the effectiveness of our method in detecting genetic interactions. We developed a reliable, high-throughput method for quantitative epistasis analysis of developmental phenotypes.

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

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    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.

  10. JBASE: Joint Bayesian Analysis of Subphenotypes and Epistasis

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    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

  11. Epistasis analysis for quantitative traits by functional regression model.

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    Zhang, Futao; Boerwinkle, Eric; Xiong, Momiao

    2014-06-01

    The critical barrier in interaction analysis for rare variants is that most traditional statistical methods for testing interactions were originally designed for testing the interaction between common variants and are difficult to apply to rare variants because of their prohibitive computational time and poor ability. The great challenges for successful detection of interactions with next-generation sequencing (NGS) data are (1) lack of methods for interaction analysis with rare variants, (2) severe multiple testing, and (3) time-consuming computations. To meet these challenges, we shift the paradigm of interaction analysis between two loci to interaction analysis between two sets of loci or genomic regions and collectively test interactions between all possible pairs of SNPs within two genomic regions. In other words, we take a genome region as a basic unit of interaction analysis and use high-dimensional data reduction and functional data analysis techniques to develop a novel functional regression model to collectively test interactions between all possible pairs of single nucleotide polymorphisms (SNPs) within two genome regions. By intensive simulations, we demonstrate that the functional regression models for interaction analysis of the quantitative trait have the correct type 1 error rates and a much better ability to detect interactions than the current pairwise interaction analysis. The proposed method was applied to exome sequence data from the NHLBI's Exome Sequencing Project (ESP) and CHARGE-S study. We discovered 27 pairs of genes showing significant interactions after applying the Bonferroni correction (P-values < 4.58 × 10(-10)) in the ESP, and 11 were replicated in the CHARGE-S study.

  12. Analysis pipeline for the epistasis search – statistical versus biological filtering

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    Xiangqing eSun

    2014-04-01

    Full Text Available Gene-gene interactions may contribute to the genetic variation underlying complex traits but have not always been taken fully into account. Statistical analyses that consider gene-gene interaction may increase the power of detecting associations, especially for low-marginal-effect markers, and may explain in part the missing heritability. Detecting pair-wise and higher-order interactions genome-wide requires enormous computational power. Filtering pipelines increase the computational speed by limiting the number of tests performed. We summarize existing filtering approaches to detect epistasis, after distinguishing the purposes that lead us to search for epistasis. Statistical filtering includes quality control on the basis of single marker statistics to avoid the analysis of bad and least informative data, and limits the search space for finding interactions. Biological filtering includes targeting specific pathways, integrating various databases based on known biological and metabolic pathways, gene function ontology and protein-protein interactions. It is increasingly possible to target single-nucleotide polymorphisms that have defined functions on gene expression, though not belonging to protein-coding genes. Filtering can improve the power of an interaction association study, but also increases the chance of missing important findings.

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

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    Chin Lin

    Full Text Available 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].

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

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    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].

  15. A method for detecting epistasis in genome-wide studies using case-control multi-locus association analysis

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    Galan Jose; Quintas Antonio; Royo Jose; Sáez María; Bermudo Fernando; González-Pérez Antonio; Gayán Javier; Morón Francisco; Ramirez-Lorca Reposo; Real Luis; Ruiz Agustín

    2008-01-01

    Abstract Background The difficulty in elucidating the genetic basis of complex diseases roots in the many factors that can affect the development of a disease. Some of these genetic effects may interact in complex ways, proving undetectable by current single-locus methodology. Results We have developed an analysis tool called Hypothesis Free Clinical Cloning (HFCC) to search for genome-wide epistasis in a case-control design. HFCC combines a relatively fast computing algorithm for genome-wide...

  16. Dissection of complex gene expression using the combined analysis of pleiotropy and epistasis.

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    Philip, Vivek M; Tyler, Anna L; Carter, Gregory W

    2014-01-01

    Global transcript expression experiments are commonly used to investigate the biological processes that underlie complex traits. These studies can exhibit complex patterns of pleiotropy when trans-acting genetic factors influence overlapping sets of multiple transcripts. Dissecting these patterns into biological modules with distinct genetic etiology can provide models of how genetic variants affect specific processes that contribute to a trait. Here we identify transcript modules associated with pleiotropic genetic factors and apply genetic interaction analysis to disentangle the regulatory architecture in a mouse intercross study of kidney function. The method, called the combined analysis of pleiotropy and epistasis (CAPE), has been previously used to model genetic networks for multiple physiological traits. It simultaneously models multiple phenotypes to identify direct genetic influences as well as influences mediated through genetic interactions. We first identify candidate trans expression quantitative trait loci (eQTL) and the transcripts potentially affected. We then clustered the transcripts into modules of co-expressed genes, from which we compute summary module phenotypes. Finally, we applied CAPE to map the network of interacting module QTL (modQTL) affecting the gene modules. The resulting network mapped how multiple modQTL both directly and indirectly affect modules associated with metabolic functions and biosynthetic processes. This work demonstrates how the integration of pleiotropic signals in gene expression data can be used to infer a complex hypothesis of how multiple loci interact to co-regulate transcription programs, thereby providing additional constraints to prioritize validation experiments.

  17. Dynamic QTL and epistasis analysis on seedling root traits in upland cotton.

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    Liang, Qingzhi; Li, Pengbo; Hu, Cheng; Hua, Hua; Li, Zhaohu; Rong, Yihua; Wang, Kunbo; Hua, Jinping

    2014-04-01

    Roots are involved in acquisition of water and nutrients, as well as in providing structural support to plant. The root system provides a dynamic model for developmental analysis. Here, we investigated quantitative trait loci (QTL), dynamic conditional QTL and epistatic interactions for seedling root traits using an upland cotton F2 population and a constructed genetic map. Totally, 37 QTLs for root traits, 35 dynamic conditional QTLs based on the net increased amount of root traits (root tips, forks, length, surface area and volume) (i) after transplanting 10 days compared to 5 days, and (ii) after transplanting 15 days to 10 days were detected. Obvious dynamic characteristic of QTL and dynamic conditional QTL existed at different developmental stages of root because QTL and dynamic conditional QTL had not been detected simultaneously. We further confirmed that additive and dominance effects of QTL qRSA-chr1-1 in interval time 5 to 10 DAT (days after transplant) offset the effects in 10 to 15 DAT. Lots of two-locus interactions for root traits were identified unconditionally or dynamically, and a few epistatic interactions were only detected simultaneously in interval time of 5-10 DAT and 10-15 DAT, suggesting different interactive genetic mechanisms on root development at different stages. Dynamic conditional QTL and epistasis effects provide new attempts to understand the dynamics of roots and provide clues for root architecture selection in upland cotton.

  18. A method for detecting epistasis in genome-wide studies using case-control multi-locus association analysis

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    Galan Jose

    2008-07-01

    Full Text Available Abstract Background The difficulty in elucidating the genetic basis of complex diseases roots in the many factors that can affect the development of a disease. Some of these genetic effects may interact in complex ways, proving undetectable by current single-locus methodology. Results We have developed an analysis tool called Hypothesis Free Clinical Cloning (HFCC to search for genome-wide epistasis in a case-control design. HFCC combines a relatively fast computing algorithm for genome-wide epistasis detection, with the flexibility to test a variety of different epistatic models in multi-locus combinations. HFCC has good power to detect multi-locus interactions simulated under a variety of genetic models and noise conditions. Most importantly, HFCC can accomplish exhaustive genome-wide epistasis search with large datasets as demonstrated with a 400,000 SNP set typed on a cohort of Parkinson's disease patients and controls. Conclusion With the current availability of genetic studies with large numbers of individuals and genetic markers, HFCC can have a great impact in the identification of epistatic effects that escape the standard single-locus association analyses.

  19. Epistasis analysis for estrogen metabolic and signaling pathway genes on young ischemic stroke patients.

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    Yi-Chen Hsieh

    Full Text Available BACKGROUND: Endogenous estrogens play an important role in the overall cardiocirculatory system. However, there are no studies exploring the hormone metabolism and signaling pathway genes together on ischemic stroke, including sulfotransferase family 1E (SULT1E1, catechol-O-methyl-transferase (COMT, and estrogen receptor α (ESR1. METHODS: A case-control study was conducted on 305 young ischemic stroke subjects aged analysis. The logistic regression model also showed there was a significant interaction effect between SULT1E1 -64G/A and COMT Val158Met on ischemic stroke of the young (P for interaction = 0.0171. We further found that lower estradiol level could increase the risk of young ischemic stroke for those who carry either SULT1E1 or COMT risk genotypes, showing a significant interaction effect (P for interaction = 0.0174. CONCLUSIONS: Our findings support that a significant epistasis effect exists among estrogen metabolic and signaling pathway genes and gene-environment interactions on young ischemic stroke subjects.

  20. The causes of epistasis

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    de Visser, J. Arjan G. M.; Cooper, Tim F.; Elena, Santiago F.

    2011-01-01

    Since Bateson's discovery that genes can suppress the phenotypic effects of other genes, gene interactions—called epistasis—have been the topic of a vast research effort. Systems and developmental biologists study epistasis to understand the genotype–phenotype map, whereas evolutionary biologists recognize the fundamental importance of epistasis for evolution. Depending on its form, epistasis may lead to divergence and speciation, provide evolutionary benefits to sex and affect the robustness and evolvability of organisms. That epistasis can itself be shaped by evolution has only recently been realized. Here, we review the empirical pattern of epistasis, and some of the factors that may affect the form and extent of epistasis. Based on their divergent consequences, we distinguish between interactions with or without mean effect, and those affecting the magnitude of fitness effects or their sign. Empirical work has begun to quantify epistasis in multiple dimensions in the context of metabolic and fitness landscape models. We discuss possible proximate causes (such as protein function and metabolic networks) and ultimate factors (including mutation, recombination, and the importance of natural selection and genetic drift). We conclude that, in general, pleiotropy is an important prerequisite for epistasis, and that epistasis may evolve as an adaptive or intrinsic consequence of changes in genetic robustness and evolvability. PMID:21976687

  1. Bayesian analysis of additive epistasis arising from new mutations in mice.

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    Casellas, Joaquim; Gianola, Daniel; Medrano, Juan F

    2014-08-13

    The continuous uploading of polygenic additive mutational variability has been reported in several studies in laboratory species with an inbred genetic background. These studies have focused on the direct contribution of new mutations without considering the possibility of epistatic effects derived from the interaction of new mutations with pre-existing polymorphisms. In this work we focused on this main topic and analysed the statistical and biological relevance of the epistatic variance for 9 week body weight in two populations of inbred mice. We developed a new linear mixed model parameterization where founder-related additive genetic variability, additive mutational variability and the interaction terms between both sources of variation were accounted for under a Bayesian design and without requiring the inversion of a matrix of epistatic genetic covariances. The analyses focused on a six-generations data set from C57BL/6J mice (n = 3736) and a five-generations data set from C57BL/6J(hg/hg) mice (n = 2843). The deviance information criterion (DIC) clearly favoured the model accounting for epistatic variability with reductions larger than 50 DIC units in both populations. Modal estimates for founder related, mutational and epistatic heritabilities were 0·068, 0·011 and 0·095 in C57BL/6J and 0·060, 0·010 and 0·113 in C57BL/6J(hg/hg), ruling out any doubt about the biological relevance of epistasis originating from new mutations in mice. These results contribute new insights on the relevance of epistasis in the genetic architecture of mammals and serve as an important component of an additional source of genetic heterogeneity for inbred strains of laboratory mice.

  2. Biological knowledge-driven analysis of epistasis in human GWAS with application to lipid traits.

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    Ma, Li; Keinan, Alon; Clark, Andrew G

    2015-01-01

    While the importance of epistasis is well established, specific gene-gene interactions have rarely been identified in human genome-wide association studies (GWAS), mainly due to low power associated with such interaction tests. In this chapter, we integrate biological knowledge and human GWAS data to reveal epistatic interactions underlying quantitative lipid traits, which are major risk factors for coronary artery disease. To increase power to detect interactions, we only tested pairs of SNPs filtered by prior biological knowledge, including GWAS results, protein-protein interactions (PPIs), and pathway information. Using published GWAS and 9,713 European Americans (EA) from the Atherosclerosis Risk in Communities (ARIC) study, we identified an interaction between HMGCR and LIPC affecting high-density lipoprotein cholesterol (HDL-C) levels. We then validated this interaction in additional multiethnic cohorts from ARIC, the Framingham Heart Study, and the Multi-Ethnic Study of Atherosclerosis. Both HMGCR and LIPC are involved in the metabolism of lipids and lipoproteins, and LIPC itself has been marginally associated with HDL-C. Furthermore, no significant interaction was detected using PPI and pathway information, mainly due to the stringent significance level required after correcting for the large number of tests conducted. These results suggest the potential of biological knowledge-driven approaches to detect epistatic interactions in human GWAS, which may hold the key to exploring the role gene-gene interactions play in connecting genotypes and complex phenotypes in future GWAS.

  3. The causes of epistasis

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    Visser, de J.A.G.M.; Cooper, T.F.; Elena, S.F.

    2011-01-01

    Since Bateson’s discovery that genes can suppress the phenotypic effects of other genes, gene interactions— called epistasis—have been the topic of a vast research effort. Systems and developmental biologists study epistasis to understand the genotype–phenotype map, whereas evolutionary biologists

  4. Parallel emergence of negative epistasis across experimental lineages.

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    Zee, Peter C; Velicer, Gregory J

    2017-01-27

    Epistatic interactions can greatly impact evolutionary phenomena, particularly the process of adaptation. Here, we leverage four parallel experimentally evolved lineages to study the emergence and trajectories of epistatic interactions in the social bacterium Myxococcus xanthus. A social gene (pilA) necessary for effective group swarming on soft agar had been deleted from the common ancestor of these lineages. During selection for competitiveness at the leading edge of growing colonies, two lineages evolved qualitatively novel mechanisms for greatly increased swarming on soft agar, whereas the other two lineages evolved relatively small increases in swarming. By reintroducing pilA into different genetic backgrounds along the four lineages, we tested whether parallel lineages showed similar patterns of epistasis. In particular, we tested whether a pattern of negative epistasis between accumulating mutations and pilA previously found in the fastest lineage would be found only in the two evolved lineages with the fastest and most striking swarming phenotypes, or rather was due to common epistatic structure across all lineages arising from the generic fixation of adaptive mutations. Our analysis reveals the emergence of negative epistasis across all four independent lineages. Further, we present results showing that the observed negative epistasis is not due exclusively to evolving populations approaching a maximum phenotypic value that inherently limits positive effects of pilA reintroduction, but rather involves direct antagonistic interactions between accumulating mutations and the reintroduced social gene.

  5. Enabling personal genomics with an explicit test of epistasis.

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    Greene, Casey S; Himmelstein, Daniel S; Nelson, Heather H; Kelsey, Karl T; Williams, Scott M; Andrew, Angeline S; Karagas, Margaret R; Moore, Jason H

    2010-01-01

    One goal of personal genomics is to use information about genomic variation to predict who is at risk for various common diseases. Technological advances in genotyping have spawned several personal genetic testing services that market genotyping services directly to the consumer. An important goal of consumer genetic testing is to provide health information along with the genotyping results. This has the potential to integrate detailed personal genetic and genomic information into healthcare decision making. Despite the potential importance of these advances, there are some important limitations. One concern is that much of the literature that is used to formulate personal genetics reports is based on genetic association studies that consider each genetic variant independently of the others. It is our working hypothesis that the true value of personal genomics will only be realized when the complexity of the genotype-to-phenotype mapping relationship is embraced, rather than ignored. We focus here on complexity in genetic architecture due to epistasis or nonlinear gene-gene interaction. We have previously developed a multifactor dimensionality reduction (MDR) algorithm and software package for detecting nonlinear interactions in genetic association studies. In most prior MDR analyses, the permutation testing strategy used to assess statistical significance was unable to differentiate MDR models that captured only interaction effects from those that also detected independent main effects. Statistical interpretation of MDR models required post-hoc analysis using entropy-based measures of interaction information. We introduce here a novel permutation test that allows the effects of nonlinear interactions between multiple genetic variants to be specifically tested in a manner that is not confounded by linear additive effects. We show using simulated nonlinear interactions that the power using the explicit test of epistasis is no different than a standard permutation

  6. A survey about methods dedicated to epistasis detection

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    Clément eNiel

    2015-09-01

    Full Text Available 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 to 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.

  7. Should evolutionary geneticists worry about higher-order epistasis?

    Science.gov (United States)

    Weinreich, Daniel M; Lan, Yinghong; Wylie, C Scott; Heckendorn, Robert B

    2013-12-01

    Natural selection drives evolving populations up the fitness landscape, the projection from nucleotide sequence space to organismal reproductive success. While it has long been appreciated that topographic complexities on fitness landscapes can arise only as a consequence of epistatic interactions between mutations, evolutionary genetics has mainly focused on epistasis between pairs of mutations. Here we propose a generalization to the classical population genetic treatment of pairwise epistasis that yields expressions for epistasis among arbitrary subsets of mutations of all orders (pairwise, three-way, etc.). Our approach reveals substantial higher-order epistasis in almost every published fitness landscape. Furthermore we demonstrate that higher-order epistasis is critically important in two systems we know best. We conclude that higher-order epistasis deserves empirical and theoretical attention from evolutionary geneticists.

  8. A microscopic analysis of shear acceleration

    CERN Document Server

    Rieger, F M; Rieger, Frank M.; Duffy, Peter

    2006-01-01

    A microscopic analysis of the viscous energy gain of energetic particles in (gradual) non-relativistic shear flows is presented. We extend previous work and derive the Fokker-Planck coefficients for the average rate of momentum change and dispersion in the general case of a momentum-dependent scattering time $\\tau(p) \\propto p^{\\alpha}$ with $\\alpha \\geq 0$. We show that in contrast to diffusive shock acceleration the characteristic shear acceleration timescale depends inversely on the particle mean free path which makes the mechanism particularly attractive for high energy seed particles. Based on an analysis of the associated Fokker-Planck equation we show that above the injection momentum $p_0$ power-law differential particle number density spectra $n(p) \\propto p^{-(1+ \\alpha)}$ are generated for $\\alpha >0$ if radiative energy losses are negligible. We discuss the modifications introduced by synchrotron losses and determine the contribution of the accelerated particles to the viscosity of the background ...

  9. Investigating statistical epistasis in complex disorders.

    Science.gov (United States)

    Turton, James C; Bullock, James; Medway, Christopher; Shi, Hui; Brown, Kristelle; Belbin, Olivia; Kalsheker, Noor; Carrasquillo, Minerva M; Dickson, Dennis W; Graff-Radford, Neill R; Petersen, Ronald C; Younkin, Steven G; Morgan, Kevin

    2011-01-01

    The missing heritability exhibited by late-onset Alzheimer's disease is unexplained and has been partly attributed to epistatic interaction. Methods available to explore this are often based on logistic regression and allow for determination of deviation from an expected outcome as a result of statistical epistasis. Three such methodologies including Synergy Factor and the PLINK modules, -epistasis and -fast-epistasis, were applied to study an epistatic interaction between interleukin-6 and interleukin-10. The models analyzed consisted of two synergistic interactions (SF ≈ 4.2 and 1.6) and two antagonistic interactions (SF ≈ 0.9 and 0.6). As with any statistical test, power to detect association is paramount; and most studies will be underpowered for the task. However, the availability of large sample sizes through genome-wide association studies make it feasible to examine approaches for determining epistatic interactions. This study documents the sample sizes needed to achieve a statistically significant outcome from each of the methods examined and discusses the limitations/advantages of the chosen approaches.

  10. Accelerator physics analysis with interactive tools

    Energy Technology Data Exchange (ETDEWEB)

    Holt, J.A.; Michelotti, L.

    1993-05-01

    Work is in progress on interactive tools for linear and nonlinear accelerator design, analysis, and simulation using X-based graphics. The BEAMLINE and MXYZPTLK class libraries, were used with an X Windows graphics library to build a program for interactively editing lattices and studying their properties.

  11. EpiGPU: exhaustive pairwise epistasis scans parallelized on consumer level graphics cards.

    Science.gov (United States)

    Hemani, Gibran; Theocharidis, Athanasios; Wei, Wenhua; Haley, Chris

    2011-06-01

    Hundreds of genome-wide association studies have been performed over the last decade, but as single nucleotide polymorphism (SNP) chip density has increased so has the computational burden to search for epistasis [for n SNPs the computational time resource is O(n(n-1)/2)]. While the theoretical contribution of epistasis toward phenotypes of medical and economic importance is widely discussed, empirical evidence is conspicuously absent because its analysis is often computationally prohibitive. To facilitate resolution in this field, tools must be made available that can render the search for epistasis universally viable in terms of hardware availability, cost and computational time. By partitioning the 2D search grid across the multicore architecture of a modern consumer graphics processing unit (GPU), we report a 92× increase in the speed of an exhaustive pairwise epistasis scan for a quantitative phenotype, and we expect the speed to increase as graphics cards continue to improve. To achieve a comparable computational improvement without a graphics card would require a large compute-cluster, an option that is often financially non-viable. The implementation presented uses OpenCL--an open-source library designed to run on any commercially available GPU and on any operating system. The software is free, open-source, platformindependent and GPU-vendor independent. It can be downloaded from http://sourceforge.net/projects/epigpu/.

  12. Compensatory mutations cause excess of antagonistic epistasis in RNA secondary structure folding

    Directory of Open Access Journals (Sweden)

    Adami Christoph

    2003-02-01

    Full Text Available Background The rate at which fitness declines as an organism's genome accumulates random mutations is an important variable in several evolutionary theories. At an intuitive level, it might seem natural that random mutations should tend to interact synergistically, such that the rate of mean fitness decline accelerates as the number of random mutations is increased. However, in a number of recent studies, a prevalence of antagonistic epistasis (the tendency of multiple mutations to have a mitigating rather than reinforcing effect has been observed. Results We studied in silico the net amount and form of epistatic interactions in RNA secondary structure folding by measuring the fraction of neutral mutants as a function of mutational distance d. We found a clear prevalence of antagonistic epistasis in RNA secondary structure folding. By relating the fraction of neutral mutants at distance d to the average neutrality at distance d, we showed that this prevalence derives from the existence of many compensatory mutations at larger mutational distances. Conclusions Our findings imply that the average direction of epistasis in simple fitness landscapes is directly related to the density with which fitness peaks are distributed in these landscapes.

  13. Applications Toolkit for Accelerator Control and Analysis

    Science.gov (United States)

    Borland, M.

    1997-05-01

    The Advanced Photon Source (APS) has taken a unique approach to creating high-level software applications for accelerator control and analysis. The approach is based on self-describing data, modular program toolkits, and scripts. Self-describing data provides a communication standard that aids the creation of modular program toolkits by allowing compliant programs to be used in essentially arbitrary combinations. These modular programs can be used as part of an arbitrary number of high-level applications. At APS, a group of about 60 data analysis, manipulation, and display tools is used in concert with about 20 control-system-specific tools to implement applications for commissioning and operations. High-level applications are created using scripts, which are relatively simple interpreted programs. The Tcl/Tk script language is used, allowing creation of graphical user interfaces (GUIs) and a library of algorithms that are separate from the interface. This allows greater automation of control by making it easy to take the human out of the loop. Applications of this methodology to accelerator commissioning and operation such as orbit correction, and data archiving and review will be discussed.

  14. Coevolution of robustness, epistasis, and recombination favors asexual reproduction

    OpenAIRE

    MacCarthy, Thomas; Bergman, Aviv

    2007-01-01

    The prevalence of sexual reproduction remains one of the most perplexing phenomena in evolutionary biology. The deterministic mutation hypothesis postulates that sexual reproduction will be advantageous under synergistic epistasis, a condition in which mutations cause a greater reduction in fitness when combined than would be expected from their individual effects. The inverse condition, antagonistic epistasis, correspondingly is predicted to favor asexual reproduction. To assess this hypothe...

  15. Performance analysis of acceleration resolution for radar signal

    Institute of Scientific and Technical Information of China (English)

    ZHAO; Hongzhong; (赵宏钟); FU; Qiang; (付; 强)

    2003-01-01

    The high acceleration of moving targets has brought severe problems in radar signal processing, such as the decrease in output signal-noise-ratio and the deterioration of Doppler resolution. This paper presents an acceleration ambiguity function (AAF) for characterizing the acceleration effects and the acceleration resolution property in radar signal processing. The definition of the acceleration resolution based on AAF is also presented. Using AAF as an analyzing tool, some factors are derived including the loss factor of output SNR, the broadening factor of Doppler resolution, and the optimal accumulative time (OPT) caused by acceleration in linear-phase matched filtering. The convergent property of quadratic-phase matched-filter for searching for and estimating the acceleration is discussed. The results and conclusions are helpful for the quantitative analysis of the acceleration effects on signal processing, and for evaluation of the performance of acceleration in radar signal waveform design.

  16. Genome-wide association analysis identifies new susceptibility loci for Behçet's disease and epistasis between HLA-B*51 and ERAP1

    Science.gov (United States)

    Kirino, Yohei; Bertsias, George; Ishigatsubo, Yoshiaki; Mizuki, Nobuhisa; Tugal-Tutkun, Ilknur; Seyahi, Emire; Ozyazgan, Yilmaz; Sacli, F. Sevgi; Erer, Burak; Inoko, Hidetoshi; Emrence, Zeliha; Cakar, Atilla; Abaci, Neslihan; Ustek, Duran; Satorius, Colleen; Ueda, Atsuhisa; Takeno, Mitsuhiro; Kim, Yoonhee; Wood, Geryl M.; Ombrello, Michael J.; Meguro, Akira; Gül, Ahmet; Remmers, Elaine F.; Kastner, Daniel L.

    2013-01-01

    Patients with Behçet's disease (BD) suffer from episodic inflammation often affecting the orogenital mucosa, skin, and eyes. To discover new BD-susceptibility loci, we performed a genome-wide association study (GWAS) of 779,465 SNPs with imputed genotypes in 1,209 Turkish BD patients and 1,278 controls. We identified novel associations at CCR1, STAT4, and KLRC4. Additionally, two SNPs in ERAP1, encoding ERAP1 p.Asp575Asn and p.Arg725Gln, recessively conferred disease risk. These findings replicated in 1,468 independent Turkish and/or 1,352 Japanese samples (combined meta-analysis p < 2 × 10−9). We also found evidence for interaction between HLA-B*51 and ERAP1 (p = 9 × 10−4). The CCR1 and STAT4 variants were associated with gene expression differences. Three risk loci shared with ankylosing spondylitis and psoriasis (MHC-I, ERAP1, and IL23R, and the MHC-I-ERAP1 interaction), as well as two loci shared with inflammatory bowel disease (IL23R and IL10) implicate shared pathogenic pathways in the spondyloarthritides and BD. PMID:23291587

  17. From classical genetics to quantitative genetics to systems biology: modeling epistasis.

    Directory of Open Access Journals (Sweden)

    David L Aylor

    2008-03-01

    Full Text Available Gene expression data has been used in lieu of phenotype in both classical and quantitative genetic settings. These two disciplines have separate approaches to measuring and interpreting epistasis, which is the interaction between alleles at different loci. We propose a framework for estimating and interpreting epistasis from a classical experiment that combines the strengths of each approach. A regression analysis step accommodates the quantitative nature of expression measurements by estimating the effect of gene deletions plus any interaction. Effects are selected by significance such that a reduced model describes each expression trait. We show how the resulting models correspond to specific hierarchical relationships between two regulator genes and a target gene. These relationships are the basic units of genetic pathways and genomic system diagrams. Our approach can be extended to analyze data from a variety of experiments, multiple loci, and multiple environments.

  18. Coevolution of robustness, epistasis, and recombination favors asexual reproduction.

    Science.gov (United States)

    MacCarthy, Thomas; Bergman, Aviv

    2007-07-31

    The prevalence of sexual reproduction remains one of the most perplexing phenomena in evolutionary biology. The deterministic mutation hypothesis postulates that sexual reproduction will be advantageous under synergistic epistasis, a condition in which mutations cause a greater reduction in fitness when combined than would be expected from their individual effects. The inverse condition, antagonistic epistasis, correspondingly is predicted to favor asexual reproduction. To assess this hypothesis, we introduce a finite population evolutionary process that combines a recombination modifier formalism with a gene-regulatory network model. We demonstrate that when reproductive mode and epistasis are allowed to coevolve, asexual reproduction outcompetes sexual reproduction. In addition, no correlation is found between the level of synergistic epistasis and the fixation time of the asexual mode. However, a significant correlation is found between the level of antagonistic epistasis and asexual mode fixation time. This asymmetry can be explained by the greater reduction in fitness imposed by sexual reproduction as compared with asexual reproduction. Our findings present evidence and suggest plausible explanations that challenge both the deterministic mutation hypothesis and recent arguments asserting the importance of emergent synergistic epistasis in the maintenance of sexual reproduction.

  19. Likelihood Analysis of the Local Group Acceleration

    CERN Document Server

    Schmoldt, I M; Teodoro, L; Efstathiou, G P; Frenk, C S; Keeble, O; Maddox, S J; Oliver, S; Rowan-Robinson, M; Saunders, W J; Sutherland, W; Tadros, H; White, S D M

    1999-01-01

    We compute the acceleration on the Local Group using 11206 IRAS galaxies from the recently completed all-sky PSCz redshift survey. Measuring the acceleration vector in redshift space generates systematic uncertainties due to the redshift space distortions in the density field. We therefore assign galaxies to their real space positions by adopting a non-parametric model for the velocity field that solely relies on the linear gravitational instability and linear biasing hypotheses. Remaining systematic contributions to the measured acceleration vector are corrected for by using PSCz mock catalogues from N-body experiments. The resulting acceleration vector points approx. 15 degrees away from the CMB dipole apex, with a remarkable alignment between small and large scale contributions. A considerable fraction of the measured acceleration is generated within 40 h-1 Mpc with a non-negligible contribution from scales between 90 and 140 h-1 Mpc after which the acceleration amplitude seems to have converged. The local...

  20. Accelerated life models modeling and statistical analysis

    CERN Document Server

    Bagdonavicius, Vilijandas

    2001-01-01

    Failure Time DistributionsIntroductionParametric Classes of Failure Time DistributionsAccelerated Life ModelsIntroductionGeneralized Sedyakin's ModelAccelerated Failure Time ModelProportional Hazards ModelGeneralized Proportional Hazards ModelsGeneralized Additive and Additive-Multiplicative Hazards ModelsChanging Shape and Scale ModelsGeneralizationsModels Including Switch-Up and Cycling EffectsHeredity HypothesisSummaryAccelerated Degradation ModelsIntroductionDegradation ModelsModeling the Influence of Explanatory Varia

  1. Comparison of Multi-field Coupling Analysis of Accelerator Cavity

    Institute of Scientific and Technical Information of China (English)

    LI; Chun-guang; LI; Jin-hai

    2013-01-01

    In the high power accelerator cavity,the joule heat produced by the electromagnetic fields causes the temperature of the cavity rising which leads to frequency changed,called frequency shift.The analysis of the effect of power to the frequency shift is an important task of accelerator cavity design.It involves heat,structure and high frequency analysis.

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

    Science.gov (United States)

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

    2009-02-09

    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.

  3. Acceleration Measurement of Projectile High Velocity Penetrating Concrete Target and Acceleration Signal Analysis

    Institute of Scientific and Technical Information of China (English)

    Peng XU; Jing ZU; Jing-biao FAN

    2010-01-01

    A kind of novel on-boand memory acceleratian measure equipment, self-developed, had been employed in recent field test to obtain the acceleration of projectile penetrating many kinds of concrete target. At the same time, the aluminum foam with different density and pore-diameters had been utilized to protect cirruit modules. Fur-thermore, with the theoretical analysis, computer simulation and field test, the high frequency's impact on the tested acceleration of the projectile had been discussed; At last, the analysis on output signal tested the validity of test data.

  4. Epistasis: Obstacle or Advantage for Mapping Complex Traits?

    NARCIS (Netherlands)

    Verhoeven, K.J.F.; Casella, G.; McIntyre, L.M.

    2010-01-01

    Identification of genetic loci in complex traits has focused largely on one-dimensional genome scans to search for associations between single markers and the phenotype. There is mounting evidence that locus interactions, or epistasis, are a crucial component of the genetic architecture of biologica

  5. Positive epistasis drives the acquisition of multidrug resistance.

    Directory of Open Access Journals (Sweden)

    Sandra Trindade

    2009-07-01

    Full Text Available The evolution of multiple antibiotic resistance is an increasing global problem. Resistance mutations are known to impair fitness, and the evolution of resistance to multiple drugs depends both on their costs individually and on how they interact--epistasis. Information on the level of epistasis between antibiotic resistance mutations is of key importance to understanding epistasis amongst deleterious alleles, a key theoretical question, and to improving public health measures. Here we show that in an antibiotic-free environment the cost of multiple resistance is smaller than expected, a signature of pervasive positive epistasis among alleles that confer resistance to antibiotics. Competition assays reveal that the cost of resistance to a given antibiotic is dependent on the presence of resistance alleles for other antibiotics. Surprisingly we find that a significant fraction of resistant mutations can be beneficial in certain resistant genetic backgrounds, that some double resistances entail no measurable cost, and that some allelic combinations are hotspots for rapid compensation. These results provide additional insight as to why multi-resistant bacteria are so prevalent and reveal an extra layer of complexity on epistatic patterns previously unrecognized, since it is hidden in genome-wide studies of genetic interactions using gene knockouts.

  6. Accelerator mass spectrometry (AMS) in plutonium analysis.

    Science.gov (United States)

    Strumińska-Parulska, Dagmara I

    The paper summarizes the results of the (240)Pu/(239)Pu atomic ratio studies in atmospheric fallout samples collected in 1986 over Gdynia (Poland) as well as three Baltic fish species collected in 1997 using the accelerator mass spectrometry. A new generation of AMS has been developed during last years and this method is an efficient and good technique to measure long-lived radioisotopes in the environment and provides the most accurate determination of the atomic ratios between (240)Pu and (239)Pu. The nuclide compositions of plutonium in filter samples correspond to their means of production. AMS measurements of atmospheric fallout collected in April showed sufficient increase of the (240)Pu/(239)Pu atomic ratio from 0.28 from March to 0.47. Also such high increase of (240)Pu/(239)Pu atomic ratio, close to reactor core (240)Pu/(239)Pu atomic ratio, was observed in September and equaled 0.47.

  7. Analysis of accelerated motion in the theory of relativity

    Science.gov (United States)

    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.

  8. Are Interactions between cis-Regulatory Variants Evidence for Biological Epistasis or Statistical Artifacts?

    Science.gov (United States)

    Fish, Alexandra E; Capra, John A; Bush, William S

    2016-10-06

    The importance of epistasis-or statistical interactions between genetic variants-to the development of complex disease in humans has been controversial. Genome-wide association studies of statistical interactions influencing human traits have recently become computationally feasible and have identified many putative interactions. However, statistical models used to detect interactions can be confounded, which makes it difficult to be certain that observed statistical interactions are evidence for true molecular epistasis. In this study, we investigate whether there is evidence for epistatic interactions between genetic variants within the cis-regulatory region that influence gene expression after accounting for technical, statistical, and biological confounding factors. We identified 1,119 (FDR = 5%) interactions that appear to regulate gene expression in human lymphoblastoid cell lines, a tightly controlled, largely genetically determined phenotype. Many of these interactions replicated in an independent dataset (90 of 803 tested, Bonferroni threshold). We then performed an exhaustive analysis of both known and novel confounders, including ceiling/floor effects, missing genotype combinations, haplotype effects, single variants tagged through linkage disequilibrium, and population stratification. Every interaction could be explained by at least one of these confounders, and replication in independent datasets did not protect against some confounders. Assuming that the confounding factors provide a more parsimonious explanation for each interaction, we find it unlikely that cis-regulatory interactions contribute strongly to human gene expression, which calls into question the relevance of cis-regulatory interactions for other human phenotypes. We additionally propose several best practices for epistasis testing to protect future studies from confounding. Copyright © 2016 American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

  9. The evolution of sex and recombination in response to abiotic or coevolutionary fluctuations in epistasis.

    Science.gov (United States)

    Gandon, Sylvain; Otto, Sarah P

    2007-04-01

    Evolutionary biologists have identified several factors that could explain the widespread phenomena of sex and recombination. One hypothesis is that host-parasite interactions favor sex and recombination because they favor the production of rare genotypes. A problem with many of the early models of this so-called Red Queen hypothesis is that several factors are acting together: directional selection, fluctuating epistasis, and drift. It is thus difficult to identify what exactly is selecting for sex in these models. Is one factor more important than the others or is it the synergistic action of these different factors that really matters? Here we focus on the analysis of a simple model with a single mechanism that might select for sex: fluctuating epistasis. We first analyze the evolution of sex and recombination when the temporal fluctuations are driven by the abiotic environment. We then analyze the evolution of sex and recombination in a two-species coevolutionary model, where directional selection is absent (allele frequencies remain fixed) and temporal variation in epistasis is induced by coevolution with the antagonist species. In both cases we contrast situations with weak and strong selection and derive the evolutionarily stable (ES) recombination rate. The ES recombination rate is most sensitive to the period of the cycles, which in turn depends on the strength of epistasis. In particular, more virulent parasites cause more rapid cycles and consequently increase the ES recombination rate of the host. Although the ES strategy is maximized at an intermediate period, some recombination is favored even when fluctuations are very slow. By contrast, the amplitude of the cycles has no effect on the ES level of sex and recombination, unless sex and recombination are costly, in which case higher-amplitude cycles allow the evolution of higher rates of sex and recombination. In the coevolutionary model, the amount of recombination in the interacting species also has

  10. Accelerator-driven transmutation reactor analysis code system (ATRAS)

    Energy Technology Data Exchange (ETDEWEB)

    Sasa, Toshinobu; Tsujimoto, Kazufumi; Takizuka, Takakazu; Takano, Hideki [Japan Atomic Energy Research Inst., Tokai, Ibaraki (Japan). Tokai Research Establishment

    1999-03-01

    JAERI is proceeding a design study of the hybrid type minor actinide transmutation system which mainly consist of an intense proton accelerator and a fast subcritical core. Neutronics and burnup characteristics of the accelerator-driven system is important from a view point of the maintenance of subcriticality and energy balance during the system operation. To determine those characteristics accurately, it is necessary to involve reactions at high-energy region, which are not treated on ordinary reactor analysis codes. The authors developed a code system named ATRAS to analyze the neutronics and burnup characteristics of accelerator-driven subcritical reactor systems. ATRAS has a function of burnup analysis taking account of the effect of spallation neutron source. ATRAS consists of a spallation analysis code, a neutron transport codes and a burnup analysis code. Utility programs for fuel exchange, pre-processing and post-processing are also incorporated. (author)

  11. Rapid Electromagnetic Analysis of Entire Accelerator Structures

    CERN Document Server

    Cooke, Simon

    2005-01-01

    We present results of a new method for fast, accurate calculation, in 3-D, of the electromagnetic mode spectrum of long, tapered accelerator structures. Instead of discretizing the entire structure directly and solving a huge matrix eigenvalue problem, we use a new two-step technique that scales much better to long, multi-cavity structures. In the first step we compute a small number of eigenmodes of individual cavities, achieving 0.05% frequency accuracy using a new second-order finite-element code. In the second step we use these 3-D mode solutions as field basis functions to obtain a reduced matrix representation of Maxwell's equations for the complete structure. Solving the reduced system takes just a few minutes on a desktop PC even with more than 100 non-identical cavities, and gives the complete mode spectrum in the first few bands of the structure. By judicious choice of the basis modes, we retain 0.05% frequency accuracy for these global solutions, and can reconstruct the complete 3-D field of each m...

  12. Analysis of flame acceleration in open or vented obstructed pipes

    Science.gov (United States)

    Bychkov, Vitaly; Sadek, Jad; Akkerman, V'yacheslav

    2017-01-01

    While flame propagation through obstacles is often associated with turbulence and/or shocks, Bychkov et al. [V. Bychkov et al., Phys. Rev. Lett. 101, 164501 (2008), 10.1103/PhysRevLett.101.164501] have revealed a shockless, conceptually laminar mechanism of extremely fast flame acceleration in semiopen obstructed pipes (one end of a pipe is closed; a flame is ignited at the closed end and propagates towards the open one). The acceleration is devoted to a powerful jet flow produced by delayed combustion in the spaces between the obstacles, with turbulence playing only a supplementary role in this process. In the present work, this formulation is extended to pipes with both ends open in order to describe the recent experiments and modeling by Yanez et al. [J. Yanez et al., arXiv:1208.6453] as well as the simulations by Middha and Hansen [P. Middha and O. R. Hansen, Process Safety Prog. 27, 192 (2008) 10.1002/prs.10242]. It is demonstrated that flames accelerate strongly in open or vented obstructed pipes and the acceleration mechanism is similar to that in semiopen ones (shockless and laminar), although acceleration is weaker in open pipes. Starting with an inviscid approximation, we subsequently incorporate hydraulic resistance (viscous forces) into the analysis for the sake of comparing its role to that of a jet flow driving acceleration. It is shown that hydraulic resistance is actually not required to drive flame acceleration. In contrast, this is a supplementary effect, which moderates acceleration. On the other hand, viscous forces are nevertheless an important effect because they are responsible for the initial delay occurring before the flame acceleration onset, which is observed in the experiments and simulations. Accounting for this effect provides good agreement between the experiments, modeling, and the present theory.

  13. Reverse Pathway Genetic Approach Identifies Epistasis in Autism Spectrum Disorders

    Science.gov (United States)

    Traglia, Michela; Tsang, Kathryn; Bearden, Carrie E.; Rauen, Katherine A.

    2017-01-01

    Although gene-gene interaction, or epistasis, plays a large role in complex traits in model organisms, genome-wide by genome-wide searches for two-way interaction have limited power in human studies. We thus used knowledge of a biological pathway in order to identify a contribution of epistasis to autism spectrum disorders (ASDs) in humans, a reverse-pathway genetic approach. Based on previous observation of increased ASD symptoms in Mendelian disorders of the Ras/MAPK pathway (RASopathies), we showed that common SNPs in RASopathy genes show enrichment for association signal in GWAS (P = 0.02). We then screened genome-wide for interactors with RASopathy gene SNPs and showed strong enrichment in ASD-affected individuals (P < 2.2 x 10−16), with a number of pairwise interactions meeting genome-wide criteria for significance. Finally, we utilized quantitative measures of ASD symptoms in RASopathy-affected individuals to perform modifier mapping via GWAS. One top region overlapped between these independent approaches, and we showed dysregulation of a gene in this region, GPR141, in a RASopathy neural cell line. We thus used orthogonal approaches to provide strong evidence for a contribution of epistasis to ASDs, confirm a role for the Ras/MAPK pathway in idiopathic ASDs, and to identify a convergent candidate gene that may interact with the Ras/MAPK pathway. PMID:28076348

  14. Analyzing the Interdependence Between Some Certain Gene Loci by Epistasis Measures in Fitness Landscapes of Schemata

    Institute of Scientific and Technical Information of China (English)

    李建武; 李敏强

    2003-01-01

    GA-hardness and interdependence between genes in the chromosome are important questions in the study of genetic algorithms(GA). Traditional methods, which are used to measure the interaction between genes, can only reflect the extent of epistasis between all genes in the chromosome. Therefore, the definition of the fitness landscape of schemata is proposed in this paper, and epistasis measures on this landscape of schemata are used to analyze the degree of interdependence between some certain gene loci in study. Some information between these sites can be reflected by some characters of the fitness landscape of schemata which are composed of these fixed sites. The stronger the interaction between these sites, the larger the variation of the fitness of schemata whose fixed sites correspond to those sites in study, and the more rugged the fitness landscape of these schemata. According to the degree of interaction between these given gene loci, building blocks of GA can be analyzed and determined, and further genetic operators and the structure of GA can be designed and adjusted to improve the performance of GA. At last, a lot of experiments including NK-models are done, and results of empirical analysis show that this method is effective.

  15. Detecting High-Order Epistasis in Nonlinear Genotype-Phenotype Maps.

    Science.gov (United States)

    Sailer, Zachary R; Harms, Michael J

    2017-03-01

    High-order epistasis has been observed in many genotype-phenotype maps. These multi-way interactions between mutations may be useful for dissecting complex traits and could have profound implications for evolution. Alternatively, they could be a statistical artifact. High-order epistasis models assume the effects of mutations should add, when they could in fact multiply or combine in some other nonlinear way. A mismatch in the "scale" of the epistasis model and the scale of the underlying map would lead to spurious epistasis. In this article, we develop an approach to estimate the nonlinear scales of arbitrary genotype-phenotype maps. We can then linearize these maps and extract high-order epistasis. We investigated seven experimental genotype-phenotype maps for which high-order epistasis had been reported previously. We find that five of the seven maps exhibited nonlinear scales. Interestingly, even after accounting for nonlinearity, we found statistically significant high-order epistasis in all seven maps. The contributions of high-order epistasis to the total variation ranged from 2.2 to 31.0%, with an average across maps of 12.7%. Our results provide strong evidence for extensive high-order epistasis, even after nonlinear scale is taken into account. Further, we describe a simple method to estimate and account for nonlinearity in genotype-phenotype maps.

  16. Effect of inter- and intragenic epistasis on the heritability of oil content in rapeseed (Brassica napus L.).

    Science.gov (United States)

    Würschum, Tobias; Maurer, Hans Peter; Dreyer, Felix; Reif, Jochen C

    2013-02-01

    The loci detected by association mapping which are involved in the expression of important agronomic traits in crops often explain only a small proportion of the total genotypic variance. Here, 17 SNPs derived from 9 candidate genes from the triacylglycerol biosynthetic pathway were studied in an association analysis in a population of 685 diverse elite rapeseed inbred lines. The 685 lines were evaluated for oil content, as well as for glucosinolates, yield, and thousand-kernel weight in field trials at 4 locations. We detected main effects for most of the studied genes illustrating that genetic diversity for oil content can be exploited by the selection of favorable alleles. In addition to main effects, both intergenic and intragenic epistasis was detected that contributes to a considerable amount to the genotypic variance observed for oil content. The proportion of explained genotypic variance was doubled when in addition to main effects epistasis was considered. Therefore, a knowledge-based improvement of oil content in rapeseed should also take such favorable epistatic interactions into account. Our results suggest, that the observed high contribution of epistasis may to some extent explain the missing heritability in genome-wide association studies.

  17. Accelerator human interface. 4. Object analysis by OMT technique

    Energy Technology Data Exchange (ETDEWEB)

    Abe, Isamu; Nakahara, Kazuo [National Lab. for High Energy Physics, Tsukuba, Ibaraki (Japan); Mutoh, Masakatsu; Shibasaki, Yoshinobu

    1995-07-01

    The analysis of the objects of various classes in accelerator domain was carried out by OMT technique, and its summary is reported. By changing the technique from the conventional procedural type to object-oriented type, and reconsidering accelerator control, it becomes possible to give large impact to the development of software and accelerator control. Also the importance of establishing fundamental object system and its outline are described. As to the original objects of accelerators, the change due to age is small as compared with computer environment. Accordingly, by extracting the standard objects as far as possible, and making the objects so as to be able to deal with control system and multi-platform progressing with age, the situation that control systems become out of date can be clearly solved. The establishment of optimal objects shows the possibility of presenting optimal control system, and object analysis brings about many merits. OMT was adopted here. Accelerator control domain is divided into device class and generic task class, and the latter is divided into operation, diagnosis, operation support, simulation, data base, indication system and maintenance classes. The abstracting of data and procedure, the succession between devices and the behavior of objects are described. (K.I.)

  18. Induced acceleration analysis of the hamstrings during standing in crouch

    NARCIS (Netherlands)

    Schrijver, Annemare; Stewart, Caroline; Postans, Neil; Roberts, Andrew

    2009-01-01

    The aim of this study was to use a simple 2D model to calculate the induced accelerations of the hamstring muscles during standing in different degrees of crouch. Comparison was made with previous experimental data and a sensitivity analysis performed.

  19. Accelerated FEM Analysis for Critical Engine Components

    Directory of Open Access Journals (Sweden)

    Leonardo FRIZZIERO

    2014-10-01

    Full Text Available This paper introduces a method to simplify a nonlinear problem in order to use linear finite element analysis. This approach improves calculation time by 2 orders of magnitude. It is then possible to optimize the geometry of the components even without supercomputers. In this paper the method is applied to a very critical component: the aluminium alloy piston of a modern common rail diesel engine. The method consists in the subdivision of the component, in this case the piston, in several volumes, that have approximately a constant temperature. These volumes are then assembled through congruence constraints. To each volume a proper material is then assigned. It is assumed that material behaviour depends on average temperature, load magnitude and load gradient. This assumption is valid since temperatures vary slowly when compared to pressure (load. In fact pressures propagate with the speed of sound. The method is validated by direct comparison with nonlinear simulation of the same component, the piston, taken as an example. In general, experimental tests have confirmed the cost-effectiveness of this approach.

  20. Analysis of lead-acid battery accelerated testing data

    Science.gov (United States)

    Clifford, J. E.; Thomas, R. E.

    1983-06-01

    Battelle conducted an independent review and analysis of the accelerated test procedures and test data obtained by Exide in the 3 year Phase 1 program to develop advanced lead acid batteries for utility load leveling. Of special importance is the extensive data obtained in deep discharge cycling tests on 60 cells at elevated temperatures over a 2-1/2 year period. The principal uncertainty in estimating cell life relates to projecting cycle life data at elevated temperature to the lower operating temperatures. The accelerated positive grid corrosion test involving continuous overcharge at 500C provided some indication of the degree of grid corrosion that might be tolerable before failure. The accelerated positive material shedding test was not examined in any detail. Recommendations are made for additional studies.

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

    Energy Technology Data Exchange (ETDEWEB)

    Uesaka, Mitsuru [Nuclear Engineering Research Laboratory, University of Tokyo, 2-22 Shirakata-Shirane, Tokai, Naka, Ibaraki 319-1188 (Japan)]. E-mail: uesaka@utnl.jp; Sakumi, Akira [Nuclear Engineering Research Laboratory, University of Tokyo, 2-22 Shirakata-Shirane, Tokai, Naka, Ibaraki 319-1188 (Japan); Hosokai, Tomonao [Nuclear Engineering Research Laboratory, University of Tokyo, 2-22 Shirakata-Shirane, Tokai, Naka, Ibaraki 319-1188 (Japan); Kinoshita, Kenichi [National Institute of Radiological Sciences, 4-9-1 Anagawa, Inage, Chiba 263-8555 (Japan); Yamaoka, Nobuaki [Nuclear Engineering Research Laboratory, University of Tokyo, 2-22 Shirakata-Shirane, Tokai, Naka, Ibaraki 319-1188 (Japan); Zhidkov, Alexei [National Institute of Radiological Sciences, 4-9-1 Anagawa, Inage, Chiba 263-8555 (Japan); Ohkubo, Takeru [Nuclear Engineering Research Laboratory, University of Tokyo, 2-22 Shirakata-Shirane, Tokai, Naka, Ibaraki 319-1188 (Japan); Ueda, Toru [Nuclear Engineering Research Laboratory, University of Tokyo, 2-22 Shirakata-Shirane, Tokai, Naka, Ibaraki 319-1188 (Japan); Muroya, Yusa [Nuclear Engineering Research Laboratory, University of Tokyo, 2-22 Shirakata-Shirane, Tokai, Naka, Ibaraki 319-1188 (Japan); Katsumura, Yosuke [Nuclear Engineering Research Laboratory, University of Tokyo, 2-22 Shirakata-Shirane, Tokai, Naka, Ibaraki 319-1188 (Japan); Iijima, Hokuto [Japan Atomic Energy Research Institute, 2-4 Shirane, Tokai, Naka, Ibaraki 319-1195 (Japan); Tomizawa, Hiromitsu [Japan Synchrotron Radiation Research InstituteI, 1-1-1 Kouto, Mikazuki-cho, Sayo-gun, Hyogo 679-5198 (Japan); Kumagai, Noritaka [Japan Synchrotron Radiation Research InstituteI, 1-1-1 Kouto, Mikazuki-cho, Sayo-gun, Hyogo 679-5198 (Japan)

    2005-12-15

    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.

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

    NARCIS (Netherlands)

    Schoustra, Sijmen; Hwang, Sungmin; Krug, Joachim; Visser, de Arjan

    2016-01-01

    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

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

    Energy Technology Data Exchange (ETDEWEB)

    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.

  4. Model independent analysis on the slowing down of cosmic acceleration

    CERN Document Server

    Zhang, Ming-Jian

    2016-01-01

    Possible slowing down of cosmic acceleration has attracted more and more attention. However, most analysis in previous work were commonly imposed in some parametrization models. In the present paper, we investigate this subject using the the Gaussian processes (GP), providing a model-independent analysis. We carry out the reconstruction by abundant data including luminosity distance from Union2, Union2.1 compilation and gamma-ray burst, and Hubble parameter from cosmic chronometer and baryon acoustic oscillation peaks. The GP reconstructions suggest that no slowing down of cosmic acceleration is approved within 95\\% C.L. from current observational data. We also test the influence of spatial curvature and Hubble constant, finding that spatial curvature does not present significant impact on the reconstructions. However, Hubble constant strongly influence the reconstructions especially at low redshift. In order to reveal the reason of inconsistence between our reconstruction and previous parametrization constra...

  5. Maternal-Zygotic Epistasis and the Evolution of Genetic Diseases

    Directory of Open Access Journals (Sweden)

    Nicholas K. Priest

    2010-01-01

    Full Text Available Many birth defects and genetic diseases are expressed in individuals that do not carry the disease causing alleles. Genetic diseases observed in offspring can be caused by gene expression in mothers and by interactions between gene expression in mothers and offspring. It is not clear whether the underlying pattern of gene expression (maternal versus offspring affects the incidence of genetic disease. Here we develop a 2-locus population genetic model with epistatic interactions between a maternal gene and a zygotic gene to address this question. We show that maternal effect genes that affect disease susceptibility in offspring persist longer and at higher frequencies in a population than offspring genes with the same effects. We find that specific forms of maternal-zygotic epistasis can maintain disease causing alleles at high frequencies over a range of plausible values. Our findings suggest that the strength and form of epistasis and the underlying pattern of gene expression may greatly influence the prevalence of human genetic diseases.

  6. Analysis of male pheromones that accelerate female reproductive organ development.

    Science.gov (United States)

    Flanagan, Kelly A; Webb, William; Stowers, Lisa

    2011-02-08

    Male odors can influence a female's reproductive physiology. In the mouse, the odor of male urine results in an early onset of female puberty. Several volatile and protein pheromones have previously been reported to each account for this bioactivity. Here we bioassay inbred BALB/cJ females to study pheromone-accelerated uterine growth, a developmental hallmark of puberty. We evaluate the response of wild-type and mutant mice lacking a specialized sensory transduction channel, TrpC2, and find TrpC2 function to be necessary for pheromone-mediated uterine growth. We analyze the relative effectiveness of pheromones previously identified to accelerate puberty through direct bioassay and find none to significantly accelerate uterine growth in BALB/cJ females. Complementary to this analysis, we have devised a strategy of partial purification of the uterine growth bioactivity from male urine and applied it to purify bioactivity from three different laboratory strains. The biochemical characteristics of the active fraction of all three strains are inconsistent with that of previously known pheromones. When directly analyzed, we are unable to detect previously known pheromones in urine fractions that generate uterine growth. Our analysis indicates that pheromones emitted by males to advance female puberty remain to be identified.

  7. Analysis of male pheromones that accelerate female reproductive organ development.

    Directory of Open Access Journals (Sweden)

    Kelly A Flanagan

    Full Text Available Male odors can influence a female's reproductive physiology. In the mouse, the odor of male urine results in an early onset of female puberty. Several volatile and protein pheromones have previously been reported to each account for this bioactivity. Here we bioassay inbred BALB/cJ females to study pheromone-accelerated uterine growth, a developmental hallmark of puberty. We evaluate the response of wild-type and mutant mice lacking a specialized sensory transduction channel, TrpC2, and find TrpC2 function to be necessary for pheromone-mediated uterine growth. We analyze the relative effectiveness of pheromones previously identified to accelerate puberty through direct bioassay and find none to significantly accelerate uterine growth in BALB/cJ females. Complementary to this analysis, we have devised a strategy of partial purification of the uterine growth bioactivity from male urine and applied it to purify bioactivity from three different laboratory strains. The biochemical characteristics of the active fraction of all three strains are inconsistent with that of previously known pheromones. When directly analyzed, we are unable to detect previously known pheromones in urine fractions that generate uterine growth. Our analysis indicates that pheromones emitted by males to advance female puberty remain to be identified.

  8. Accelerated Gibbs Sampling for Infinite Sparse Factor Analysis

    Energy Technology Data Exchange (ETDEWEB)

    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.

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

    Energy Technology Data Exchange (ETDEWEB)

    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.

  10. Consistency analysis of accelerated degradation mechanism based on gray theory

    Institute of Scientific and Technical Information of China (English)

    Yunxia Chen; Hongxia Chen; Zhou Yang; Rui Kang; Yi Yang

    2014-01-01

    A fundamental premise of an accelerated testing is that the failure mechanism under elevated and normal stress levels should remain the same. Thus, verification of the consistency of failure mechanisms is essential during an accelerated testing. A new consistency analysis method based on the gray theory is pro-posed for complex products. First of al , existing consistency ana-lysis methods are reviewed with a focus on the comparison of the differences among them. Then, the proposed consistency ana-lysis method is introduced. Two effective gray prediction models, gray dynamic model and new information and equal dimensional (NIED) model, are adapted in the proposed method. The process to determine the dimension of NIED model is also discussed, and a decision rule is expanded. Based on that, the procedure of ap-plying the new consistent analysis method is developed. Final y, a case study of the consistency analysis of a reliability enhancement testing is conducted to demonstrate and validate the proposed method.

  11. Predicting epistasis: an experimental test of metabolic control theory with bacterial transcription and translation.

    Science.gov (United States)

    MacLean, R C

    2010-03-01

    Epistatic interactions between mutations are thought to play a crucial role in a number of evolutionary processes, including adaptation and sex. Evidence for epistasis is abundant, but tests of general theoretical models that can predict epistasis are lacking. In this study, I test the ability of metabolic control theory to predict epistasis using a novel experimental approach that combines phenotypic and genetic perturbations of enzymes involved in gene expression and protein synthesis in the bacterium Pseudomonas aeruginosa. These experiments provide experimental support for two key predictions of metabolic control theory: (i) epistasis between genes involved in the same pathway is antagonistic; (ii) epistasis becomes increasingly antagonistic as mutational severity increases. Metabolic control theory is a general theory that applies to any set of genes that are involved in the same linear processing chain, not just metabolic pathways, and I argue that this theory is likely to have important implications for predicting epistasis between functionally coupled genes, such as those involved in antibiotic resistance. Finally, this study highlights the fact that phenotypic manipulations of gene activity provide a powerful method for studying epistasis that complements existing genetic methods.

  12. Acceleration of dynamic fluorescence molecular tomography with principal component analysis.

    Science.gov (United States)

    Zhang, Guanglei; He, Wei; Pu, Huangsheng; Liu, Fei; Chen, Maomao; Bai, Jing; Luo, Jianwen

    2015-06-01

    Dynamic fluorescence molecular tomography (FMT) is an attractive imaging technique for three-dimensionally resolving the metabolic process of fluorescent biomarkers in small animal. When combined with compartmental modeling, dynamic FMT can be used to obtain parametric images which can provide quantitative pharmacokinetic information for drug development and metabolic research. However, the computational burden of dynamic FMT is extremely huge due to its large data sets arising from the long measurement process and the densely sampling device. In this work, we propose to accelerate the reconstruction process of dynamic FMT based on principal component analysis (PCA). Taking advantage of the compression property of PCA, the dimension of the sub weight matrix used for solving the inverse problem is reduced by retaining only a few principal components which can retain most of the effective information of the sub weight matrix. Therefore, the reconstruction process of dynamic FMT can be accelerated by solving the smaller scale inverse problem. Numerical simulation and mouse experiment are performed to validate the performance of the proposed method. Results show that the proposed method can greatly accelerate the reconstruction of parametric images in dynamic FMT almost without degradation in image quality.

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

  16. Robustness and epistasis in mutation-selection models

    Science.gov (United States)

    Wolff, Andrea; Krug, Joachim

    2009-09-01

    We investigate the fitness advantage associated with the robustness of a phenotype against deleterious mutations using deterministic mutation-selection models of a quasispecies type equipped with a mesa-shaped fitness landscape. We obtain analytic results for the robustness effect which become exact in the limit of infinite sequence length. Thereby, we are able to clarify a seeming contradiction between recent rigorous work and an earlier heuristic treatment based on mapping to a Schrödinger equation. We exploit the quantum mechanical analogy to calculate a correction term for finite sequence lengths and verify our analytic results by numerical studies. In addition, we investigate the occurrence of an error threshold for a general class of epistatic landscapes and show that diminishing epistasis is a necessary but not sufficient condition for error threshold behaviour.

  17. Rigorous analysis of trapped modes in accelerating cavities

    Directory of Open Access Journals (Sweden)

    Rolf Schuhmann

    2000-12-01

    Full Text Available We report the development of different algorithms for the calculation of quality factors of eigenmodes in accelerating cavities, which have resonance frequencies above the cutoff frequency of the beam tubes. The analysis is based on a discretization of such cavity structures by the finite integration technique, and the radiation at the open boundaries is systematically taken into account by different approaches in time and frequency domain. Results indicate that even single cell cavities of the TESLA type show Q values of 10^{3} and multicell cavities values in excess of 10^{4}. Thus these modes may cause considerable beam instabilities. Comparison with the conventional method of analyzing closed cavities and identifying modes with little change in frequency as a function of boundary condition shows qualitative differences. Some modes from the closed cavity model do not exist in the open structure and thus would be misinterpreted as trapped modes when only a closed cavity analysis is employed.

  18. Desloratadine analysis: as a pharmaceutical preparation and after accelerating ageing

    Directory of Open Access Journals (Sweden)

    Bober Katarzyna

    2015-09-01

    Full Text Available Desloratadine is a biologically active compound that is not described in the Polish Pharmacopoeia IX, hence, its study is particular important. The aim of this work was to establish a procedure for desloratadine analysis by way of HPTLC in combination with densitometry, so as to be able to ascertain its presence and degree of presence within pharmaceutical preparations. In our work, a mixture of ethyl acetate, n-butanol, ammonia and methanol was used as the mobile phase. Moreover, HPTLC plates precoated with silica gel 60F254 were also employed. The proposed method was tested and subsequently validated. Spectrodensitometric analysis was then performed to determine the optimal wavelength for the quantitative determination (λ=276 nm, and following this, a quantitative analysis of desloratadine within certain pharmaceutical preparations was performed. Our research also took into consideration an analysis of the products of desloratadine decomposition that come about as a result of the accelerated aging of its solutions. The employed procedure for accelerating the aging of such desloratadine solutions consisted of heating these at 40℃ and then irradiating the solution surfaces with UV light. The changing color of these solutions after 2 hours of exposure served to indicate that degradation had occurred. Of note: as a result of irradiation with UV light, desloratadine content was seen to decrease with time, declining to almost zero after 30 hours. However, heating a solution of desloratadine alone did not induce a change in its content. Solutions of desloratadine that had previously undergone irradiation and heating were also analyzed to ascertain whether new substances were present. For this purpose, the GC-MS process was employed. As a result of this procedure, the spectrum of the solution after aging showed the presence of several new peaks that displayed retention several times larger and smaller than the normal desloratadine peak.

  19. On the mechanistic nature of epistasis in a canonical cis-regulatory element

    OpenAIRE

    Lagator, Mato; Paix?o, Tiago; Barton, Nicholas H; Bollback, Jonathan P.; Guet, C?lin C.

    2017-01-01

    eLife digest Mutations are changes to DNA that provide the raw material upon which evolution can act. Therefore, to understand evolution, we need to know the effects of mutations, and how those mutations interact with each other (a phenomenon referred to as epistasis). So far, few mathematical models allow scientists to predict the effects of mutations, and even fewer are able to predict epistasis. Biological systems are complex and consist of many proteins and other molecules. Genes are the ...

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

    Energy Technology Data Exchange (ETDEWEB)

    Lima, J.A.S. [Departamento de Astronomia, Universidade de São Paulo, 55080-900, São Paulo, SP (Brazil); Graef, L.L. [Instituto de Física, Universidade de São Paulo, Rua do Matão travessa R, 05508-090, São Paulo, SP (Brazil); Pavón, D. [Departamento de Física, Universidad Autónoma de Barcelona, 08193 Bellaterra, Barcelona (Spain); Basilakos, Spyros, E-mail: jas.lima@iag.usp.br, E-mail: leilagraef@usp.br, E-mail: diego.pavon@uab.es, E-mail: svasil@academyofathens.gr [Academy of Athens, Research Center for Astronomy and Applied Mathematics, Soranou Efesiou 4, 11527, Athens (Greece)

    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. GPU-ACCELERATED FEM SOLVER FOR THREE DIMENSIONAL ELECTROMAGNETIC ANALYSIS

    Institute of Scientific and Technical Information of China (English)

    Tian Jin; Gong Li; Shi Xiaowei; Le Xu

    2011-01-01

    A new Graphics Processing Unit (GPU) parallelization strategy is proposed to accelerate sparse finite element computation for three dimensional electromagnetic analysis.The parallelization strategy is employed based on a new compression format called sliced ELL Four (sliced ELL-F).The sliced ELL-F format-based parallelization strategy is designed for hastening many addition,dot product,and Sparse Matrix Vector Product (SMVP) operations in the Conjugate Gradient Norm (CGN) calculation of finite element equations.The new implementation of SMVP on GPUs is evaluated.The proposed strategy executed on a GPU can efficiently solve sparse finite element equations,especially when the equations are huge sparse (size of most rows in a coefficient matrix is less than 8).Numerical results show the sliced ELL-F format-based parallelization strategy can reach significant speedups compared to Compressed Sparse Row (CSR) format.

  2. Longitudinal Jitter Analysis of a Linear Accelerator Electron Gun

    Directory of Open Access Journals (Sweden)

    MingShan Liu

    2016-11-01

    Full Text Available We present measurements and analysis of the longitudinal timing jitter of a Beijing Electron Positron Collider (BEPCII linear accelerator electron gun. We simulated the longitudinal jitter effect of the gun using PARMELA to evaluate beam performance, including: beam profile, average energy, energy spread, and XY emittances. The maximum percentage difference of the beam parameters is calculated to be 100%, 13.27%, 42.24% and 65.01%, 86.81%, respectively. Due to this, the bunching efficiency is reduced to 54%. However, the longitudinal phase difference of the reference particle was 9.89°. The simulation results are in agreement with tests and are helpful to optimize the beam parameters by tuning the trigger timing of the gun during the bunching process.

  3. Numerical analysis of flow fields generated by accelerating flames

    Energy Technology Data Exchange (ETDEWEB)

    Kurylo, J.

    1977-12-01

    Presented here is a numerical technique for the analysis of non-steady flow fields generated by accelerating flames in gaseous media. Of particular interest in the study is the evaluation of the non-steady effects on the flow field and the possible transition of the combustion process to detonation caused by an abrupt change in the burning speed of an initially steady flame propagating in an unconfined combustible gas mixture. Optically recorded observations of accelerating flames established that the flow field can be considered to consist of non-steady flow fields associated with an assembly of interacting shock waves, contact discontinuities, deflagration and detonation fronts. In the analysis, these flow fields are treated as spatially one-dimensional, the influence of transport phenomena is considered to be negligible, and unburned and burned substances are assumed to behave as perfect gases with constant, but different, specific heats. The basis of the numerical technique is an explicit, two step, second order accurate, finite difference scheme employed to integrate the flow field equations expressed in divergence form. The burning speed, governing the motion of the deflagration, is expressed in the form of a power law dependence on pressure and temperature immediately ahead of its front. The steady wave solution is obtained by the vector polar interaction technique, that is, by determining the point of intersection between the loci of end states in the plane of the two interaction invariants, pressure and particle velocity. The technique is illustrated by a numerical example in which a steady flame experiences an abrupt change in its burning speed. Solutions correspond either to the eventual reestablishment of a steady state flow field commensurate with the burning speed or to the transition to detonation. The results are in satisfactory agreement with experimental observations.

  4. CAFE: aCcelerated Alignment-FrEe sequence analysis.

    Science.gov (United States)

    Lu, Yang Young; Tang, Kujin; Ren, Jie; Fuhrman, Jed A; Waterman, Michael S; Sun, Fengzhu

    2017-05-03

    Alignment-free genome and metagenome comparisons are increasingly important with the development of next generation sequencing (NGS) technologies. Recently developed state-of-the-art k-mer based alignment-free dissimilarity measures including CVTree, $d_2^*$ and $d_2^S$ are more computationally expensive than measures based solely on the k-mer frequencies. Here, we report a standalone software, aCcelerated Alignment-FrEe sequence analysis (CAFE), for efficient calculation of 28 alignment-free dissimilarity measures. CAFE allows for both assembled genome sequences and unassembled NGS shotgun reads as input, and wraps the output in a standard PHYLIP format. In downstream analyses, CAFE can also be used to visualize the pairwise dissimilarity measures, including dendrograms, heatmap, principal coordinate analysis and network display. CAFE serves as a general k-mer based alignment-free analysis platform for studying the relationships among genomes and metagenomes, and is freely available at https://github.com/younglululu/CAFE. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  5. Transition of Iodine Analysis to Accelerator Mass Spectrometry

    Energy Technology Data Exchange (ETDEWEB)

    Watrous, Matthew George [Idaho National Lab. (INL), Idaho Falls, ID (United States); Adamic, Mary Louise [Idaho National Lab. (INL), Idaho Falls, ID (United States); Olson, John Eric [Idaho National Lab. (INL), Idaho Falls, ID (United States); Baeck, D. L. [Idaho National Lab. (INL), Idaho Falls, ID (United States); Fox, R. V. [Idaho National Lab. (INL), Idaho Falls, ID (United States); Hahn, P. A. [Idaho National Lab. (INL), Idaho Falls, ID (United States); Jenson, D. D. [Idaho National Lab. (INL), Idaho Falls, ID (United States); Lister, T. E. [Idaho National Lab. (INL), Idaho Falls, ID (United States)

    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

  6. An evolutionary perspective on epistasis and the missing heritability.

    Directory of Open Access Journals (Sweden)

    Gibran Hemani

    2013-02-01

    Full Text Available The relative importance between additive and non-additive genetic variance has been widely argued in quantitative genetics. By approaching this question from an evolutionary perspective we show that, while additive variance can be maintained under selection at a low level for some patterns of epistasis, the majority of the genetic variance that will persist is actually non-additive. We propose that one reason that the problem of the "missing heritability" arises is because the additive genetic variation that is estimated to be contributing to the variance of a trait will most likely be an artefact of the non-additive variance that can be maintained over evolutionary time. In addition, it can be shown that even a small reduction in linkage disequilibrium between causal variants and observed SNPs rapidly erodes estimates of epistatic variance, leading to an inflation in the perceived importance of additive effects. We demonstrate that the perception of independent additive effects comprising the majority of the genetic architecture of complex traits is biased upwards and that the search for causal variants in complex traits under selection is potentially underpowered by parameterising for additive effects alone. Given dense SNP panels the detection of causal variants through genome-wide association studies may be improved by searching for epistatic effects explicitly.

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

    Science.gov (United States)

    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 the

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

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

    2016-02-26

    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.

  10. Bridging the Gap between Statistical and Biological Epistasis in Alzheimer’s Disease

    Directory of Open Access Journals (Sweden)

    Mark T. W. Ebbert

    2015-01-01

    Full Text Available Alzheimer’s disease affects millions of people worldwide and incidence is expected to rise as the population ages, but no effective therapies exist despite decades of research and more than 20 known disease markers. Research has shown that Alzheimer’s disease’s missing heritability remains extensive with an estimated 25% of phenotypic variance unexplained by known variants. The missing heritability may be explained by missing variants or by epistasis. Researchers often focus on individual loci rather than epistatic interactions, which is likely an oversimplification of the underlying biology since most phenotypes are affected by multiple genes. Focusing research efforts on epistasis will be critical to resolving Alzheimer’s disease etiology, and a major key to identifying and properly interpreting key epistatic interactions will be bridging the gap between statistical and biological epistasis. This review covers the current state of epistasis research in Alzheimer’s disease and how researchers can bridge the gap between statistical and biological epistasis to help resolve Alzheimer’s disease etiology.

  11. Kinematic analysis of sprinting pickup acceleration versus maximum sprinting speed

    Directory of Open Access Journals (Sweden)

    S. MANZER

    2016-10-01

    Full Text Available Pickup acceleration and maximum sprinting speed are two essential phases of the 100-m sprint with variant sprinting speed, step length, frequency and technique. The aim of the study was to describe and compare the kinematic parameters of both sprint variants. Hypothetically it was assumed to find differences in sprinting speed, step length, flight and contact times as well as between the body angles of different key positions. From 8 female and 8 male (N=16 track and field junior athletes a double stride of both sprint variants was filmed (200 Hz from a sagittal position and the 10-m-sprint time was measured using triple light barriers. Kinematic data for sprinting speed and angles of knee, hip and ankle were compared with an analysis of variance with repeated measures. The sprinting speed was 7.7 m/s and 8.0 m/s (female and 8.4 m/s and 9.2 m/s (male with significantly higher values of step length, flight time and shorter ground contact time during maximum sprinting speed. Because of the longer flight time, it is possible to place the foot closer to the body but with a more extended knee on the ground. These characteristics can be used as orientation for technique training.

  12. Accelerating next generation sequencing data analysis with system level optimizations.

    Science.gov (United States)

    Kathiresan, Nagarajan; Temanni, Ramzi; Almabrazi, Hakeem; Syed, Najeeb; Jithesh, Puthen V; Al-Ali, Rashid

    2017-08-22

    Next generation sequencing (NGS) data analysis is highly compute intensive. In-memory computing, vectorization, bulk data transfer, CPU frequency scaling are some of the hardware features in the modern computing architectures. To get the best execution time and utilize these hardware features, it is necessary to tune the system level parameters before running the application. We studied the GATK-HaplotypeCaller which is part of common NGS workflows, that consume more than 43% of the total execution time. Multiple GATK 3.x versions were benchmarked and the execution time of HaplotypeCaller was optimized by various system level parameters which included: (i) tuning the parallel garbage collection and kernel shared memory to simulate in-memory computing, (ii) architecture-specific tuning in the PairHMM library for vectorization, (iii) including Java 1.8 features through GATK source code compilation and building a runtime environment for parallel sorting and bulk data transfer (iv) the default 'on-demand' mode of CPU frequency is over-clocked by using 'performance-mode' to accelerate the Java multi-threads. As a result, the HaplotypeCaller execution time was reduced by 82.66% in GATK 3.3 and 42.61% in GATK 3.7. Overall, the execution time of NGS pipeline was reduced to 70.60% and 34.14% for GATK 3.3 and GATK 3.7 respectively.

  13. AN ANALYSIS OF IMPORTANT POLICIES FOR ACCELERATING DEVELOPMENT IN NEPAL

    Directory of Open Access Journals (Sweden)

    Sudarshan Neupane

    2015-02-01

    Full Text Available Nepal belongs to one of the least developed countries around the world with HDI 157 out of 187 countries (UNDP 2013. Even though poverty in Nepal has reduced to 24.8% in the latest census, the livelihoods of the poorest people living in the remote communities are still vulnerable. Two third of the population still depends on the subsistence agriculture. Similarly, due to lack of job opportunities, youth migration is escalating and Nepal is facing one of the most critical phases of development in its history (Snellinger 2009. Inadequate infrastructure and poor road connectivity are other constraints for the development (World Bank 2011. It follows that, poor access to electricity is another challenge despite the country’s enormous potential for hydroelectricity. Similarly, Nepal  has huge prospective for tourism due to its unique natural resources (Bhandari 2004. Nonetheless, Nepal has not benefited optimally from the tourism sector for its self-sustained development. Recently Government of Nepal (2011 has announced diverse policies for accelerating development through proper utilization of local resources. This paper critically evaluates the crucial policies such as Agriculture Development Strategy, National Cooperatives Policy, National Youth Policy, and Micro-hydro for Rural Development, and Tourism for Development. The paper discusses each of these policies’ background; critically analyse the likelihood as well as challenges for fast-tracking development; and finally offers some recommendations based discussion and analysis.

  14. Installation of the Ion Accelerator for the Surface Analysis

    Energy Technology Data Exchange (ETDEWEB)

    Kwon, Hyeok-Jung; Kim, Han-Sung; Chung, Bo-Hyun; Ahn, Tae-Sung; Kim, Dae-Il; Kim, Cho-Rong; Cho, Yong-Sub [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of)

    2015-10-15

    In this paper, an introduction to the accelerator, an installation status at KOMAC and the operation plan of the accelerator are discussed. A pelletron, which has been used over 25 years at KIGAM, is moved and installed at KOMAC in order to supply a qualified service to ion beam users. The system will be installed in September and component tests will be carried. The operation of the system starts in 2016 after it gets operation license from Nuclear Safety and Security Commission. Korea Multi-purpose Accelerator Complex (KOMAC) is operating several ion beam accelerators to provide various ion beams to users. Those are a 100 MeV proton linear accelerator, a 220 keV ion implanter for gaseous ion beams, a 150 keV metal ion implanter and a 20 keV high-current ion implanter. All of those are the machine for user service and it is important to qualify the results of the irradiation conditions for user service. For this reason, an electrostatic tandem accelerator, which has been operating over 25 years at Korea Institute of Geoscience and Mineral Resources (KIGAM), is moved to KOMAC in order to supply the qualified and quantified data on the irradiation species.

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

    Science.gov (United States)

    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.

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

    DEFF Research Database (Denmark)

    Immonen, Elina; Collet, Marie; Goenaga, Julieta

    2016-01-01

    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...... 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...... 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...

  17. Feature-Based Analysis of Plasma-Based Particle Acceleration Data

    Energy Technology Data Exchange (ETDEWEB)

    Rubel, Oliver [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Geddes, Cameron G. R. [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Chen, Min [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Cormier-Michel, Estelle [Tech-X Corp., Boulder, CO (United States); Bethel, E. Wes [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)

    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.

  18. Replication and explorations of high-order epistasis using a large advanced intercross line pedigree.

    Directory of Open Access Journals (Sweden)

    Mats Pettersson

    2011-07-01

    Full Text Available Dissection of the genetic architecture of complex traits persists as a major challenge in biology; despite considerable efforts, much remains unclear including the role and importance of genetic interactions. This study provides empirical evidence for a strong and persistent contribution of both second- and third-order epistatic interactions to long-term selection response for body weight in two divergently selected chicken lines. We earlier reported a network of interacting loci with large effects on body weight in an F(2 intercross between these high- and low-body weight lines. Here, most pair-wise interactions in the network are replicated in an independent eight-generation advanced intercross line (AIL. The original report showed an important contribution of capacitating epistasis to growth, meaning that the genotype at a hub in the network releases the effects of one or several peripheral loci. After fine-mapping of the loci in the AIL, we show that these interactions were persistent over time. The replication of five of six originally reported epistatic loci, as well as the capacitating epistasis, provides strong empirical evidence that the originally observed epistasis is of biological importance and is a contributor in the genetic architecture of this population. The stability of genetic interaction mechanisms over time indicates a non-transient role of epistasis on phenotypic change. Third-order epistasis was for the first time examined in this study and was shown to make an important contribution to growth, which suggests that the genetic architecture of growth is more complex than can be explained by two-locus interactions only. Our results illustrate the importance of designing studies that facilitate exploration of epistasis in populations for obtaining a comprehensive understanding of the genetics underlying a complex trait.

  19. Epistasis and Maternal Effect in Resistance to Puccinia coronata Cda.f.sp.avenae Eriks in Oats (Avena sp.)

    Institute of Scientific and Technical Information of China (English)

    Bnejdi F; Hammami I; Allagui M B; Saadoun M; el Gazzah M

    2010-01-01

    The objective of this paper was to investigate the mode of heredity for resistance in oats (Arena sp.) to crown rust caused by Puccinia coronata Cda.f.sp.avenae Eriks.Eight generations of 2 crosses were used to estimate genetic effects and narrow-sense heritability (NSH).Separate generation means analysis (GMA) indicated a complex gene action controlling this trait with additive,dominance,epistatic and maternal effects (ME).The genetic model which assumed no epistasis and no ME did not accurately describe the resistance to P.coronata.In both crosses,the digenic epistatic model with ME epistatic components were negative in most cases,suggesting that gene effects contributed more to the resistance than to the susceptibility.The estimated values of NSH were 15-99% depending upon the cross and isolates.The results indicated that appropriate choice of maternal parent and recurrent selection would increase resistance to crown rust in oats.

  20. Improving power output of inertial energy harvesters by employing principal component analysis of input acceleration

    Science.gov (United States)

    Smilek, Jan; Hadas, Zdenek

    2017-02-01

    In this paper we propose the use of principal component analysis to process the measured acceleration data in order to determine the direction of acceleration with the highest variance on given frequency of interest. This method can be used for improving the power generated by inertial energy harvesters. Their power output is highly dependent on the excitation acceleration magnitude and frequency, but the axes of acceleration measurements might not always be perfectly aligned with the directions of movement, and therefore the generated power output might be severely underestimated in simulations, possibly leading to false conclusions about the feasibility of using the inertial energy harvester for the examined application.

  1. Alignment of Ion Accelerator for Surface Analysis using Theodolite and Laser Tracker

    Energy Technology Data Exchange (ETDEWEB)

    Ahn, Tae Sung; Seo, Dong Hyuk; Kim, Dae Il; Kim, Han Sung; Kwon, Hyeok Jung; Cho, Yong Sub [KAERI, Daejeon (Korea, Republic of)

    2016-05-15

    The method of ion accelerator alignment is used two ways which are a theodolite and laser tracker. For the alignment and maintenance of the proton linear accelerator, the laser tracker is typically used at KOMAC. While the device for alignment by using laser tracker is not installed in all ion accelerator components, it was used in parallel in two methods. In this paper, alignment methods are introduced and the result and comparison of each alignment method are presented. The ion accelerator for surface analysis has aligned using theodolite and laser tracker. The two ways for alignment have advantage as well as weakness. But alignment using laser tracker is stronger than using theodolite. Because it is based on alignment and position data and it is more detailed. Also since the beam distribution is smaller than accelerator component that is direction of beam progress, main component (ex. Magnet, Chamber, Pelletron tank, etc.) alignment using laser tracker is enough to align the ion accelerator.

  2. Trace element analysis in silicon by accelerator SIMS

    Energy Technology Data Exchange (ETDEWEB)

    Ender, R.M.; Suter, M. [Eidgenoessische Technische Hochschule, Zurich (Switzerland); Doebeli, M.; Synal, H.A. [Paul Scherrer Inst. (PSI), Villigen (Switzerland)

    1997-09-01

    The accelerator SIMS technique has been applied to Si samples implanted with different elements. It has been shown that concentrations of several trace elements can be analysed down to about 1 ppb in depth profiling mode. (author) 2 figs., 1 ref.

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

    Energy Technology Data Exchange (ETDEWEB)

    Kononenko, O. [SLAC National Accelerator Lab., Menlo Park, CA (United States)

    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)

  4. eQTL epistasis: detecting epistatic effects and inferring hierarchical relationships of genes in biological pathways.

    Science.gov (United States)

    Kang, Mingon; Zhang, Chunling; Chun, Hyung-Wook; Ding, Chris; Liu, Chunyu; Gao, Jean

    2015-03-01

    Epistasis is the interactions among multiple genetic variants. It has emerged to explain the 'missing heritability' that a marginal genetic effect does not account for by genome-wide association studies, and also to understand the hierarchical relationships between genes in the genetic pathways. The Fisher's geometric model is common in detecting the epistatic effects. However, despite the substantial successes of many studies with the model, it often fails to discover the functional dependence between genes in an epistasis study, which is an important role in inferring hierarchical relationships of genes in the biological pathway. We justify the imperfectness of Fisher's model in the simulation study and its application to the biological data. Then, we propose a novel generic epistasis model that provides a flexible solution for various biological putative epistatic models in practice. The proposed method enables one to efficiently characterize the functional dependence between genes. Moreover, we suggest a statistical strategy for determining a recessive or dominant link among epistatic expression quantitative trait locus to enable the ability to infer the hierarchical relationships. The proposed method is assessed by simulation experiments of various settings and is applied to human brain data regarding schizophrenia. The MATLAB source codes are publicly available at: http://biomecis.uta.edu/epistasis. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  5. Epistasis between calpain 1 and its inhibitor calpastatin within breeds of cattle.

    Science.gov (United States)

    Barendse, W; Harrison, B E; Hawken, R J; Ferguson, D M; Thompson, J M; Thomas, M B; Bunch, R J

    2007-08-01

    The calpain gene family and its inhibitors have diverse effects, many related to protein turnover, which appear to affect a range of phenotypes such as diabetes, exercise-induced muscle injury, and pathological events associated with degenerative neural diseases in humans, fertility, longevity, and postmortem effects on meat tenderness in livestock species. The calpains are inhibited by calpastatin, which binds directly to calpain. Here we report the direct measurement of epistatic interactions of causative mutations for quantitative trait loci (QTL) at calpain 1 (CAPN1), located on chromosome 29, with causative mutations for QTL variation at calpastatin (CAST), located on chromosome 7, in cattle. First we identified potential causative mutations at CAST and then genotyped these along with putative causative mutations at CAPN1 in >1500 cattle of seven breeds. The maximum allele substitution effect on the phenotype of the CAPN1:c.947G>C single nucleotide polymorphism (SNP) was 0.14 sigma(p) (P = 0.0003) and of the CAST:c.155C>T SNP was also 0.14 sigma(p) (P = 0.0011) when measured across breeds. We found significant epistasis between SNPs at CAPN1 and CAST in both taurine and zebu derived breeds. There were more additive x dominance components of epistasis than additive x additive and dominance x dominance components combined. A minority of breed comparisons did not show epistasis, suggesting that genetic variation at other genes may influence the degree of epistasis found in this system.

  6. Advanced multipoles for accelerator magnets theoretical analysis and their measurement

    CERN Document Server

    Schnizer, Pierre

    2017-01-01

    This monograph presents research on the transversal beam dynamics of accelerators and evaluates and describes the respective magnetic field homogeneity.  The widely used cylindrical circular multipoles have disadvantages for elliptical apertures or curved trajectories, and the book also introduces new types of advanced multipole magnets, detailing their application, as well as the numerical data and measurements obtained. The research presented here provides more precise descriptions of the field and better estimates of the beam dynamics. Moreover, the effects of field inhomogeneity can be estimated with higher precision than before. These findings are further elaborated to demonstrate their usefulness for real magnets and accelerator set ups, showing their advantages over cylindrical circular multipoles. The research findings are complemented with data obtained from the new superconducting beam guiding magnet models (SIS100) for the FAIR (Facility for Antiproton and Ion Research) project.  Lastly, the book...

  7. Asymptotic analysis for vanishing acceleration in a thermoviscoelastic system

    Directory of Open Access Journals (Sweden)

    Elena Bonetti

    2005-01-01

    Full Text Available We have investigated a dynamic thermoviscoelastic system (2003, establishing existence and uniqueness results for a related initial and boundary values problem. The aim of the present paper is to study the asymptotic behavior of the solution to the above problem as the power of the acceleration forces goes to zero. In particular, well-posedness and regularity results for the limit (quasistatic problem are recovered.

  8. Likelihood analysis of the Local Group acceleration revisited

    CERN Document Server

    Ciecielag, P

    2004-01-01

    We reexamine likelihood analyzes of the Local Group (LG) acceleration, paying particular attention to nonlinear effects. Under the approximation that the joint distribution of the LG acceleration and velocity is Gaussian, two quantities describing nonlinear effects enter these analyzes. The first one is the coherence function, i.e. the cross-correlation coefficient of the Fourier modes of gravity and velocity fields. The second one is the ratio of velocity power spectrum to gravity power spectrum. To date, in all analyzes of the LG acceleration the second quantity was not accounted for. Extending our previous work, we study both the coherence function and the ratio of the power spectra. With the aid of numerical simulations we obtain expressions for the two as functions of wavevector and \\sigma_8. Adopting WMAP's best determination of \\sigma_8, we estimate the most likely value of the parameter \\beta and its errors. As the observed values of the LG velocity and gravity, we adopt respectively a CMB-based estim...

  9. Linear analysis of active-medium two-beam accelerator

    Directory of Open Access Journals (Sweden)

    Miron Voin

    2015-07-01

    Full Text Available We present detailed development of the linear theory of wakefield amplification by active medium and its possible application to a two-beam accelerator (TBA is discussed. A relativistic train of triggering microbunches traveling along a vacuum channel in an active medium confined by a cylindrical waveguide excites Cherenkov wake in the medium. The wake is a superposition of azimuthally symmetric transverse magnetic modes propagating along a confining waveguide, with a phase velocity equal to the velocity of the triggering bunches. The structure may be designed in such a way that the frequency of one of the modes is close to active-medium resonant frequency, resulting in amplification of the former and domination of a single mode far behind the trigger bunches. Another electron bunch placed in proper phase with the amplified wakefield may be accelerated by the latter. Importantly, the energy for acceleration is provided by the active medium and not the drive bunch as in a traditional TBA. Based on a simplified model, we analyze extensively the impact of various parameters on the wakefield amplification process.

  10. Accelerated testing statistical models, test plans, and data analysis

    CERN Document Server

    Nelson, Wayne B

    2009-01-01

    The Wiley-Interscience Paperback Series consists of selected books that have been made more accessible to consumers in an effort to increase global appeal and general circulation. With these new unabridged softcover volumes, Wiley hopes to extend the lives of these works by making them available to future generations of statisticians, mathematicians, and scientists. "". . . a goldmine of knowledge on accelerated life testing principles and practices . . . one of the very few capable of advancing the science of reliability. It definitely belongs in every bookshelf on engineering.""-Dev G.

  11. Beam Position Monitor and Energy Analysis at the Fermilab Accelerator Science and Technology Facility

    Energy Technology Data Exchange (ETDEWEB)

    Lopez, David Juarez [Univ. of Guanajuato (Mexico)

    2015-08-01

    Fermilab Accelerator Science and Technology Facility has produced its first beam with an energy of 20 MeV. This energy is obtained by the acceleration at the Electron Gun and the Capture Cavity 2 (CC2). When fully completed, the accelerator will consist of a photoinjector, one International Liner Collider (ILC)-type cryomodule, multiple accelerator R&D beamlines, and a downstream beamline to inject 300 MeV electrons into the Integrable Optics Test Accelerator (IOTA). We calculated the total energy of the beam and the corresponding energy to the Electron Gun and CC2. Subsequently, a Beam Position Monitors (BPM) error analysis was done, to calculate the device actual resolution.

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

    Science.gov (United States)

    Chen, Gary K; Guo, Yunfei

    2013-12-03

    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.

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

    Directory of Open Access Journals (Sweden)

    Gary K Chen

    2013-12-01

    Full Text Available 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 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 analyses 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 2,600 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.

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

    Science.gov (United States)

    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

  15. Reactivity determination in accelerator driven reactors using reactor noise analysis

    Directory of Open Access Journals (Sweden)

    Kostić Ljiljana 1

    2002-01-01

    Full Text Available Feynman-alpha and Rossi-alpha methods are used in traditional nuclear reactors to determine the subcritical reactivity of a system. The methods are based on the measurement of the mean value, variance and the covariance of detector counts for different measurement times. Such methods attracted renewed attention recently with the advent of the so-called accelerator driven reactors (ADS proposed some time ago. The ADS systems, intended to be used either in energy generation or transuranium transmutation, will use a subcritical core with a strong spallation source. A spallation source has statistical properties that are different from those traditionally used by radioactive sources. In such reactors the monitoring of the subcritical reactivity is very important, and a statistical method, such as the Feynman-alpha method, is capable of resolving this problem.

  16. Longitudinal jitter analysis of linear accelerator electron gun

    CERN Document Server

    Mingshan, Liu; Iqbal, Munawar

    2015-01-01

    We present measurement and analyses of longitudinal timing jitter of Beijing Electron Positron Collider (BEPCII) linear accelerator electron gun. We simulated longitudinal jitter effect of the gun using PARMELA about beam performance including beam profile, average energy, energy spread, longitudinal phase of reference particle and XY emittance. The maximum percentage difference of the beam parameters are calculated to be; 100%, 13.27%, 42.24%, 7.79% and 65.01%, 86.81%, respectively due to which the bunching efficiency is reduced to 54%. The simulation results are in agreement with test and are helpful to optimize the beam parameters by tuning the trigger timing of the gun during the bunching process.

  17. Control system analysis for the perturbed linear accelerator rf system

    CERN Document Server

    Sung Il Kwon

    2002-01-01

    This paper addresses the modeling problem of the linear accelerator RF system in SNS. Klystrons are modeled as linear parameter varying systems. The effect of the high voltage power supply ripple on the klystron output voltage and the output phase is modeled as an additive disturbance. The cavity is modeled as a linear system and the beam current is modeled as the exogenous disturbance. The output uncertainty of the low level RF system which results from the uncertainties in the RF components and cabling is modeled as multiplicative uncertainty. Also, the feedback loop uncertainty and digital signal processing signal conditioning subsystem uncertainties are lumped together and are modeled as multiplicative uncertainty. Finally, the time delays in the loop are modeled as a lumped time delay. For the perturbed open loop system, the closed loop system performance, and stability are analyzed with the PI feedback controller.

  18. Analysis of cracking in reinforced concrete using accelerated tests

    Energy Technology Data Exchange (ETDEWEB)

    Nguyen, Q.T.; Berthaud, Y. [Univ Paris 06, CNRS, ENSC, LMT, F-94235 Cachan (France); Care, S [CNRS, ENPC, LCPC, Inst Navier, LMSGC, F-77420 Champs Sur Marne (France); Millard, A. [CEA, DEN/DM2S/SEMT/LM2S, F-91191 Gif Sur Yvette (France)

    2007-02-15

    We present in this Note an experimental study-in a laboratory setup-of the mechanical effect (cracking of concrete) of corrosion on plates made of reinforced concrete. Due to the geometry it is possible to use digital image correlation to follow the evolution of strains induced by the corrosion of reinforcement. The corrosion is accelerated by the imposition of current density. Even if the representativeness of this test is still discussed, it allows one to record the entire strain history. The kinetics of cracking has been obtained and compared to a very simple model in which the increase of the corroded layer is modelled by a fictitious thermal load, the reinforcement remaining elastic and the concrete being damageable. (authors)

  19. Epistasis and the temporal change in the additive variance-covariance matrix induced by drift.

    Science.gov (United States)

    López-Fanjul, Carlos; Fernández, Almudena; Toro, Miguel A

    2004-08-01

    The effect of population bottlenecks on the components of the genetic covariance generated by two neutral independent epistatic loci has been studied theoretically (additive, covA; dominance, covD; additive-by-additive, covAA; additive-by-dominance, covAD; and dominance-by-dominance, covDD). The additive-by-additive model and a more general model covering all possible types of marginal gene action at the single-locus level (additive/dominance epistatic model) were considered. The covariance components in an infinitely large panmictic population (ancestral components) were compared with their expected values at equilibrium over replicates randomly derived from the base population, after t consecutive bottlenecks of equal size N (derived components). Formulae were obtained in terms of the allele frequencies and effects at each locus, the corresponding epistatic effects and the inbreeding coefficient Ft. These expressions show that the contribution of nonadditive loci to the derived additive covariance (covAt) does not linearly decrease with inbreeding, as in the pure additive case, and may initially increase or even change sign in specific situations. Numerical examples were also analyzed, restricted for simplicity to the case of all covariance components being positive. For additive-by-additive epistasis, the condition covAt > covA only holds for high frequencies of the allele decreasing the metric traits at each locus (negative allele) if epistasis is weak, or for intermediate allele frequencies if it is strong. For the additive/dominance epistatic model, however, covAt > covA applies for low frequencies of the negative alleles at one or both loci and mild epistasis, but this result can be progressively extended to intermediate frequencies as epistasis becomes stronger. Without epistasis the same qualitative results were found, indicating that marginal dominance induced by epistasis can be considered as the primary cause of an increase of the additive covariance

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

    OpenAIRE

    Li, W; Thorne, RM; Bortnik, J.; Baker, DN; Reeves, GD; Kanekal, SG; Spence, HE; Green, JC

    2015-01-01

    ©2015. American Geophysical Union. All Rights Reserved. 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 c...

  1. Hamiltonian analysis for linearly acceleration-dependent Lagrangians

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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

  3. Superconducting Accelerating Cavity Pressure Sensitivity Analysis and Stiffening

    Energy Technology Data Exchange (ETDEWEB)

    Rodnizki, J [Soreq NRC, Yavne, Israel; Ben Aliz, Y [Soreq NRC, Yavne, Israel; Grin, A [Soreq NRC, Yavne, Israel; Horvitz, Z [Soreq NRC, Yavne, Israel; Perry, A [Soreq NRC, Yavne, Israel; Weissman, L [Soreq NRC, Yavne, Israel; Davis, G Kirk [JLAB; Delayen, Jean R. [Old Dominion Universtiy

    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.

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

    Science.gov (United States)

    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

  5. What’s Downstream? A Set of Classroom Exercises to Help Students Understand Recessive Epistasis

    OpenAIRE

    Jennifer K. Knight; Wood, William B.; Smith, Michelle K.

    2013-01-01

    Undergraduate students in genetics and developmental biology courses often struggle with the concept of epistasis because they are unaware that the logic of gene interactions differs between enzymatic pathways and signaling pathways. If students try to develop and memorize a single simple rule for predicting epistatic relationships without taking into account the nature of the pathway under consideration, they can become confused by cases where the rule does not apply. To remedy this problem,...

  6. What’s Downstream? A Set of Classroom Exercises to Help Students Understand Recessive Epistasis

    Directory of Open Access Journals (Sweden)

    Jennifer K. Knight

    2013-08-01

    Full Text Available Undergraduate students in genetics and developmental biology courses often struggle with the concept of epistasis because they are unaware that the logic of gene interactions differs between enzymatic pathways and signaling pathways. If students try to develop and memorize a single simple rule for predicting epistatic relationships without taking into account the nature of the pathway under consideration, they can become confused by cases where the rule does not apply. To remedy this problem, we developed a short pre-/posttest, an in-class activity for small groups, and a series of clicker questions about recessive epistasis in the context of a signaling pathway that intersects with an enzymatic pathway. We also developed a series of homework problems that provide deliberate practice in applying concepts in epistasis to different pathways and experimental situations. Students show significant improvement from pretest to posttest, and perform well on homework and exam questions following this activity. Here we describe these materials, as well as the formative and summative assessment results from one group of students to show how the activities impact student learning.

  7. Reciprocal sign epistasis between frequently experimentally evolved adaptive mutations causes a rugged fitness landscape.

    Directory of Open Access Journals (Sweden)

    Daniel J Kvitek

    2011-04-01

    Full Text Available The fitness landscape captures the relationship between genotype and evolutionary fitness and is a pervasive metaphor used to describe the possible evolutionary trajectories of adaptation. However, little is known about the actual shape of fitness landscapes, including whether valleys of low fitness create local fitness optima, acting as barriers to adaptive change. Here we provide evidence of a rugged molecular fitness landscape arising during an evolution experiment in an asexual population of Saccharomyces cerevisiae. We identify the mutations that arose during the evolution using whole-genome sequencing and use competitive fitness assays to describe the mutations individually responsible for adaptation. In addition, we find that a fitness valley between two adaptive mutations in the genes MTH1 and HXT6/HXT7 is caused by reciprocal sign epistasis, where the fitness cost of the double mutant prohibits the two mutations from being selected in the same genetic background. The constraint enforced by reciprocal sign epistasis causes the mutations to remain mutually exclusive during the experiment, even though adaptive mutations in these two genes occur several times in independent lineages during the experiment. Our results show that epistasis plays a key role during adaptation and that inter-genic interactions can act as barriers between adaptive solutions. These results also provide a new interpretation on the classic Dobzhansky-Muller model of reproductive isolation and display some surprising parallels with mutations in genes often associated with tumors.

  8. Reciprocal sign epistasis between frequently experimentally evolved adaptive mutations causes a rugged fitness landscape.

    Directory of Open Access Journals (Sweden)

    Daniel J Kvitek

    2011-04-01

    Full Text Available The fitness landscape captures the relationship between genotype and evolutionary fitness and is a pervasive metaphor used to describe the possible evolutionary trajectories of adaptation. However, little is known about the actual shape of fitness landscapes, including whether valleys of low fitness create local fitness optima, acting as barriers to adaptive change. Here we provide evidence of a rugged molecular fitness landscape arising during an evolution experiment in an asexual population of Saccharomyces cerevisiae. We identify the mutations that arose during the evolution using whole-genome sequencing and use competitive fitness assays to describe the mutations individually responsible for adaptation. In addition, we find that a fitness valley between two adaptive mutations in the genes MTH1 and HXT6/HXT7 is caused by reciprocal sign epistasis, where the fitness cost of the double mutant prohibits the two mutations from being selected in the same genetic background. The constraint enforced by reciprocal sign epistasis causes the mutations to remain mutually exclusive during the experiment, even though adaptive mutations in these two genes occur several times in independent lineages during the experiment. Our results show that epistasis plays a key role during adaptation and that inter-genic interactions can act as barriers between adaptive solutions. These results also provide a new interpretation on the classic Dobzhansky-Muller model of reproductive isolation and display some surprising parallels with mutations in genes often associated with tumors.

  9. Pervasive sign epistasis between conjugative plasmids and drug-resistance chromosomal mutations.

    Science.gov (United States)

    Silva, Rui F; Mendonça, Sílvia C M; Carvalho, Luís M; Reis, Ana M; Gordo, Isabel; Trindade, Sandra; Dionisio, Francisco

    2011-07-01

    Multidrug-resistant bacteria arise mostly by the accumulation of plasmids and chromosomal mutations. Typically, these resistant determinants are costly to the bacterial cell. Yet, recently, it has been found that, in Escherichia coli bacterial cells, a mutation conferring resistance to an antibiotic can be advantageous to the bacterial cell if another antibiotic-resistance mutation is already present, a phenomenon called sign epistasis. Here we study the interaction between antibiotic-resistance chromosomal mutations and conjugative (i.e., self-transmissible) plasmids and find many cases of sign epistasis (40%)--including one of reciprocal sign epistasis where the strain carrying both resistance determinants is fitter than the two strains carrying only one of the determinants. This implies that the acquisition of an additional resistance plasmid or of a resistance mutation often increases the fitness of a bacterial strain already resistant to antibiotics. We further show that there is an overall antagonistic interaction between mutations and plasmids (52%). These results further complicate expectations of resistance reversal by interdiction of antibiotic use.

  10. Pervasive sign epistasis between conjugative plasmids and drug-resistance chromosomal mutations.

    Directory of Open Access Journals (Sweden)

    Rui F Silva

    2011-07-01

    Full Text Available Multidrug-resistant bacteria arise mostly by the accumulation of plasmids and chromosomal mutations. Typically, these resistant determinants are costly to the bacterial cell. Yet, recently, it has been found that, in Escherichia coli bacterial cells, a mutation conferring resistance to an antibiotic can be advantageous to the bacterial cell if another antibiotic-resistance mutation is already present, a phenomenon called sign epistasis. Here we study the interaction between antibiotic-resistance chromosomal mutations and conjugative (i.e., self-transmissible plasmids and find many cases of sign epistasis (40%--including one of reciprocal sign epistasis where the strain carrying both resistance determinants is fitter than the two strains carrying only one of the determinants. This implies that the acquisition of an additional resistance plasmid or of a resistance mutation often increases the fitness of a bacterial strain already resistant to antibiotics. We further show that there is an overall antagonistic interaction between mutations and plasmids (52%. These results further complicate expectations of resistance reversal by interdiction of antibiotic use.

  11. Accelerating DNA Sequence Analysis using Intel Xeon Phi

    OpenAIRE

    Memeti, Suejb; Pllana, Sabri

    2015-01-01

    Genetic information is increasing exponentially, doubling every 18 months. Analyzing this information within a reasonable amount of time requires parallel computing resources. While considerable research has addressed DNA analysis using GPUs, so far not much attention has been paid to the Intel Xeon Phi coprocessor. In this paper we present an algorithm for large-scale DNA analysis that exploits thread-level and the SIMD parallelism of the Intel Xeon Phi. We evaluate our approach for various ...

  12. Survival dimensionality reduction (SDR: development and clinical application of an innovative approach to detect epistasis in presence of right-censored data

    Directory of Open Access Journals (Sweden)

    Beretta Lorenzo

    2010-08-01

    Full Text Available Abstract Background Epistasis is recognized as a fundamental part of the genetic architecture of individuals. Several computational approaches have been developed to model gene-gene interactions in case-control studies, however, none of them is suitable for time-dependent analysis. Herein we introduce the Survival Dimensionality Reduction (SDR algorithm, a non-parametric method specifically designed to detect epistasis in lifetime datasets. Results The algorithm requires neither specification about the underlying survival distribution nor about the underlying interaction model and proved satisfactorily powerful to detect a set of causative genes in synthetic epistatic lifetime datasets with a limited number of samples and high degree of right-censorship (up to 70%. The SDR method was then applied to a series of 386 Dutch patients with active rheumatoid arthritis that were treated with anti-TNF biological agents. Among a set of 39 candidate genes, none of which showed a detectable marginal effect on anti-TNF responses, the SDR algorithm did find that the rs1801274 SNP in the FcγRIIa gene and the rs10954213 SNP in the IRF5 gene non-linearly interact to predict clinical remission after anti-TNF biologicals. Conclusions Simulation studies and application in a real-world setting support the capability of the SDR algorithm to model epistatic interactions in candidate-genes studies in presence of right-censored data. Availability: http://sourceforge.net/projects/sdrproject/

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

    Science.gov (United States)

    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.

  14. Desloratadine analysis: as a pharmaceutical preparation and after accelerating ageing

    OpenAIRE

    Bober Katarzyna; Płonka Marlena; Miszczyk Marek

    2015-01-01

    Desloratadine is a biologically active compound that is not described in the Polish Pharmacopoeia IX, hence, its study is particular important. The aim of this work was to establish a procedure for desloratadine analysis by way of HPTLC in combination with densitometry, so as to be able to ascertain its presence and degree of presence within pharmaceutical preparations. In our work, a mixture of ethyl acetate, n-butanol, ammonia and methanol was used as the mobile phase. Moreover, HPTLC plate...

  15. Vibration isolation analysis of clutches based on trouble shooting of vehicle accelerating noise

    Science.gov (United States)

    Liu, Xue-Lai; Shangguan, Wen-Bin; Jing, Xingjian; Ahmed, Waizuddin

    2016-11-01

    Vehicle accelerating noise is a troublesome issue commonly existing in automobiles, leading to negative passenger experience. Considering real experimental results and practical issues, a nonlinear 3-degree of freedom (DOF) torsional model of the clutch system is developed for reducing abnormal noise during vehicle accelerating. In this model, the nonlinear characteristics of the multi-staged clutch damper and the gear backlash are carefully studied. This greatly facilitates the analysis of the vibration transmission characteristics of the clutch and helps understanding of the influence of each critical physical parameter on noise generation. To reduce the accelerating noise, an optimization method for the clutch dynamics is proposed, based on the parameter analysis results, and the effectiveness is validated both in simulations and experiments.

  16. WarpIV: In Situ Visualization and Analysis of Ion Accelerator Simulations.

    Science.gov (United States)

    Rubel, Oliver; Loring, Burlen; Vay, Jean-Luc; Grote, David P; Lehe, Remi; Bulanov, Stepan; Vincenti, Henri; Bethel, E Wes

    2016-01-01

    The generation of short pulses of ion beams through the interaction of an intense laser with a plasma sheath offers the possibility of compact and cheaper ion sources for many applications--from fast ignition and radiography of dense targets to hadron therapy and injection into conventional accelerators. To enable the efficient analysis of large-scale, high-fidelity particle accelerator simulations using the Warp simulation suite, the authors introduce the Warp In situ Visualization Toolkit (WarpIV). WarpIV integrates state-of-the-art in situ visualization and analysis using VisIt with Warp, supports management and control of complex in situ visualization and analysis workflows, and implements integrated analytics to facilitate query- and feature-based data analytics and efficient large-scale data analysis. WarpIV enables for the first time distributed parallel, in situ visualization of the full simulation data using high-performance compute resources as the data is being generated by Warp. The authors describe the application of WarpIV to study and compare large 2D and 3D ion accelerator simulations, demonstrating significant differences in the acceleration process in 2D and 3D simulations. WarpIV is available to the public via https://bitbucket.org/berkeleylab/warpiv. The Warp In situ Visualization Toolkit (WarpIV) supports large-scale, parallel, in situ visualization and analysis and facilitates query- and feature-based analytics, enabling for the first time high-performance analysis of large-scale, high-fidelity particle accelerator simulations while the data is being generated by the Warp simulation suite. This supplemental material https://extras.computer.org/extra/mcg2016030022s1.pdf provides more details regarding the memory profiling and optimization and the Yee grid recentering optimization results discussed in the main article.

  17. Status of MAPA (Modular Accelerator Physics Analysis) and the Tech-X Object-Oriented Accelerator Library

    Science.gov (United States)

    Cary, J. R.; Shasharina, S.; Bruhwiler, D. L.

    1998-04-01

    The MAPA code is a fully interactive accelerator modeling and design tool consisting of a GUI and two object-oriented C++ libraries: a general library suitable for treatment of any dynamical system, and an accelerator library including many element types plus an accelerator class. The accelerator library inherits directly from the system library, which uses hash tables to store any relevant parameters or strings. The GUI can access these hash tables in a general way, allowing the user to invoke a window displaying all relevant parameters for a particular element type or for the accelerator class, with the option to change those parameters. The system library can advance an arbitrary number of dynamical variables through an arbitrary mapping. The accelerator class inherits this capability and overloads the relevant functions to advance the phase space variables of a charged particle through a string of elements. Among other things, the GUI makes phase space plots and finds fixed points of the map. We discuss the object hierarchy of the two libraries and use of the code.

  18. Role of epistasis on the fixation probability of a non-mutator in an adapted asexual population.

    Science.gov (United States)

    James, Ananthu

    2016-10-21

    The mutation rate of a well adapted population is prone to reduction so as to have a lower mutational load. We aim to understand the role of epistatic interactions between the fitness affecting mutations in this process. Using a multitype branching process, the fixation probability of a single non-mutator emerging in a large asexual mutator population is analytically calculated here. The mutator population undergoes deleterious mutations at constant, but at a much higher rate than that of the non-mutator. We find that antagonistic epistasis lowers the chances of mutation rate reduction, while synergistic epistasis enhances it. Below a critical value of epistasis, the fixation probability behaves non-monotonically with variation in the mutation rate of the background population. Moreover, the variation of this critical value of the epistasis parameter with the strength of the mutator is discussed in the appendix. For synergistic epistasis, when selection is varied, the fixation probability reduces overall, with damped oscillations. Copyright © 2016 Elsevier Ltd. All rights reserved.

  19. Analysis of output trends from Varian 2100C/D and 600C/D accelerators.

    Science.gov (United States)

    Grattan, M W D; Hounsell, A R

    2011-01-07

    Analysis of Varian linear accelerator output trends is reported. Two groups, consisting of four matched Varian 2100C/D and four matched Varian 600C/D accelerators, with different designs of monitor chamber, have been investigated and the data acquired from regular calibrated ion chamber/electrometer measurements of the output performance of the eight accelerators analysed. The trend of machine output with time, having removed the effect of adjusting the monitor chamber response, was compared on a monthly and annual basis for monitor chambers with ages ranging between 1 year and 7 years. The results indicate that the response is generally consistent within each set of accelerators with different monitor chamber designs. Those used in a Varian 600C/D machine result in a reduction in measured output over time, with an average monthly reduction of 0.35 ± 0.09% over the course of the first 4 years of use. The chambers used in a 2100C/D accelerator result in an increase in measured output over time, with an average monthly increase of 0.26 ± 0.09% over the course of the first 4 years of use. The output increase then reduces towards the end of this period of time, with the average monthly change falling to -0.03 ± 0.02% for the following 3 years. The output response trend was similar for all clinical energies used on the 2100C/D accelerators--6, 15 MV x-ray beams, and 4, 6, 9, 12, 16 and 20 MeV electron beams. By tracking these changes it has been possible to predict the response over time to allow appropriate adjustments in monitor chamber response to maintain a measured accelerator output within tolerance and give confidence in performance. It has also provided data to indicate the need for planned preventative intervention and indicate if the monitor chamber response is behaving as expected.

  20. The stability analysis of the full velocity and acceleration velocity model

    Science.gov (United States)

    Xiaomei, Zhao; Ziyou, Gao

    2007-03-01

    The stability analysis is one of the important problems in the traffic flow theory, since the congestion phenomena can be regarded as the instability and the phase transition of a dynamical system. Theoretically, we analyze the stable conditions of the full velocity and acceleration difference model (FVADM), which is proposed by introducing the acceleration difference term based on the previous car-following models (the optimal velocity model and the full velocity difference model, OVM and FVDM). By numerical simulations, it is found that when the traffic flow is unstable, the traffic jam in the FVADM is weaker than that in the FVDM. Also it is observed that the spreading speed of the jam is slower in the FVADM than that in the FVDM and the fluctuations of vehicles in the FVADM are smaller than those in the FVDM. Therefore, the acceleration difference term has strong effects on traffic dynamics and plays an important role in stabilizing the traffic flow.

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

    Science.gov (United States)

    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.

  2. Synergistic interaction between ankle and knee during hopping revealed through induced acceleration analysis.

    Science.gov (United States)

    João, Filipa; Veloso, António; Cabral, Sílvia; Moniz-Pereira, Vera; Kepple, Thomas

    2014-02-01

    The forces produced by the muscles can deliver energy to a target segment they are not attached to, by transferring this energy throughout the other segments in the chain. This is a synergistic way of functioning, which allows muscles to accelerate or decelerate segments in order to reach the target one. The purpose of this study was to characterize the contribution of each lower extremity joint to the vertical acceleration of the body's center of mass during a hopping exercise. To accomplish this, an induced acceleration analysis was performed using a model with eight segments. The results indicate that the strategies produced during a hopping exercise rely on the synergy between the knee and ankle joints, with most of the vertical acceleration being produced by the knee extensors, while the ankle plantar flexors act as stabilizers of the foot. This synergy between the ankle and the knee is perhaps a mechanism that allows the transfer of power from the knee muscles to the ground, and we believe that in this particular task the net action of the foot and ankle moments is to produce a stable foot with little overall acceleration.

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

    Energy Technology Data Exchange (ETDEWEB)

    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.

  4. Statistical epistasis and functional brain imaging support a role of voltage-gated potassium channels in human memory.

    Directory of Open Access Journals (Sweden)

    Angela Heck

    Full Text Available Despite the current progress in high-throughput, dense genome scans, a major portion of complex traits' heritability still remains unexplained, a phenomenon commonly termed "missing heritability." The negligence of analytical approaches accounting for gene-gene interaction effects, such as statistical epistasis, is probably central to this phenomenon. Here we performed a comprehensive two-way SNP interaction analysis of human episodic memory, which is a heritable complex trait, and focused on 120 genes known to show differential, memory-related expression patterns in rat hippocampus. Functional magnetic resonance imaging was also used to capture genotype-dependent differences in memory-related brain activity. A significant, episodic memory-related interaction between two markers located in potassium channel genes (KCNB2 and KCNH5 was observed (P(nominal combined=0.000001. The epistatic interaction was robust, as it was significant in a screening (P(nominal=0.0000012 and in a replication sample (P(nominal=0.01. Finally, we found genotype-dependent activity differences in the parahippocampal gyrus (P(nominal=0.001 supporting the behavioral genetics finding. Our results demonstrate the importance of analytical approaches that go beyond single marker statistics of complex traits.

  5. A developmental systems perspective on epistasis: computational exploration of mutational interactions in model developmental regulatory networks.

    Directory of Open Access Journals (Sweden)

    Jayson Gutiérrez

    Full Text Available The way in which the information contained in genotypes is translated into complex phenotypic traits (i.e. embryonic expression patterns depends on its decoding by a multilayered hierarchy of biomolecular systems (regulatory networks. Each layer of this hierarchy displays its own regulatory schemes (i.e. operational rules such as +/- feedback and associated control parameters, resulting in characteristic variational constraints. This process can be conceptualized as a mapping issue, and in the context of highly-dimensional genotype-phenotype mappings (GPMs epistatic events have been shown to be ubiquitous, manifested in non-linear correspondences between changes in the genotype and their phenotypic effects. In this study I concentrate on epistatic phenomena pervading levels of biological organization above the genetic material, more specifically the realm of molecular networks. At this level, systems approaches to studying GPMs are specially suitable to shed light on the mechanistic basis of epistatic phenomena. To this aim, I constructed and analyzed ensembles of highly-modular (fully interconnected networks with distinctive topologies, each displaying dynamic behaviors that were categorized as either arbitrary or functional according to early patterning processes in the Drosophila embryo. Spatio-temporal expression trajectories in virtual syncytial embryos were simulated via reaction-diffusion models. My in silico mutational experiments show that: 1 the average fitness decay tendency to successively accumulated mutations in ensembles of functional networks indicates the prevalence of positive epistasis, whereas in ensembles of arbitrary networks negative epistasis is the dominant tendency; and 2 the evaluation of epistatic coefficients of diverse interaction orders indicates that, both positive and negative epistasis are more prevalent in functional networks than in arbitrary ones. Overall, I conclude that the phenotypic and fitness effects of

  6. Delayed resonator with acceleration feedback - Complete stability analysis by spectral methods and vibration absorber design

    Science.gov (United States)

    Vyhlídal, Tomáš; Olgac, Nejat; Kučera, Vladimír

    2014-12-01

    This paper deals with the problem of active vibration suppression using the concept of delayed resonator (DR) absorber with acceleration feedback. A complete dynamic analysis of DR and its coupling with a single degree of freedom mechanical system are performed. Due to the presence of a delay in the acceleration feedback, the dynamics of the resonator itself, as well as the dynamics of combined system are of ‘neutral' character. On this system, spectral methods are applied to perform a complete stability analysis. Particularly, the method of cluster treatment of characteristic roots is used to determine stability boundaries in the space of the resonator parameters. Based on this analysis, a methodology to select the resonator parameters is proposed in order to guarantee desirable suppression characteristics and to provide safe stability margins. An example case study is included to demonstrate these analytical results.

  7. Determination of the radionuclide inventory in accelerator waste using calculation and radiochemical analysis

    Energy Technology Data Exchange (ETDEWEB)

    Schumann, D.; Neuhausen, J.; Weinreich, R. [Paul Scherrer Institut, CH-5232 Villigen PSI (Switzerland); Atchison, F. [Paul Scherrer Institut, CH-5232 Villigen PSI (Switzerland)], E-mail: francis.atchison@psi.ch; Kubik, P.; Synal, H.-A. [Paul Scherrer Institut, c/o Institute of Particle Physics, ETH Zuerich, CH-8093 Zurich (Switzerland); Korschinek, G.; Faestermann, Th.; Rugel, G. [Technische Universitaet Muenchen, D-85747 Garching (Germany)

    2007-11-15

    We use a description of the work carried out to determine the radioactive inventory for a redundant beam-dump from the PSI accelerator complex, as an illustration of techniques for the classification and characterisation of accelerator waste and how some difficulties can be circumvented. The work has been carried out using a combination of calculation and sample analysis: The inventory calculation effectively involves a large scale Monte-Carlo transport calculation of a medium-sized spallation facility and for the sample analysis, standard radiochemical analysis techniques have had to be extended to include AMS measurements so as to allow measurement of some of the long half-life, waste disposal relevant, nuclides.

  8. QTL Mapping and Epistasis Analysis for Phytic Acid Concentration in Rice Grain by Using the Bayesian Model Selection%利用贝叶斯法进行水稻籽粒植酸含量性状的QTL定位及互作分析

    Institute of Scientific and Technical Information of China (English)

    李茂柏; 王慧; 张建明; 李丁鲁; 杨润清; 周宇琼; 朴钟泽

    2009-01-01

    Main QTL and epistasis interaction effects for phytic acid concentration in rice grain were investigated by using a F_2 population consisted of 172 lines derived from the cross between an indica rice LPA(the grain phytic acid concentration was 7.11 mg/g) and a japonica rice Zhonghua 11(the phytic acid concentration was 11.92 mg/g) with the Bayesian model selection. A genetic linkage map including 126 SSR and 4 STS markers was constructed with the F_2 population. Three main QTLs related to phytic acid concentration in rice grain were detected. They were located on chromosomes 3, 5, and 6, explaining 5.38%, 8.02%, and 4.62% of phenotypic variation, respectively. The three alleles for reducing the phytic aid concentration were from the parent LPA. Ten pairs of epistatic interaction were detected on chromosomes 1, 3, 5, 6, and 11, with the interaction effects from 1.69 to 5.18 and the percentages of phenotypic variance ranged from 8.67% to 24.73%.%利用水稻植酸含量差异较大的品种中花11(粳型)和LPA(籼型)为亲本杂交获得F_2群体的172个单株,构建了含126个SSR和4个STS标记的遗传连锁图谱,利用贝叶斯(Bayesian)法对水稻籽粒植酸含量性状进行了主效应QTL定位和上位性互作分析.共检测到 3 个与水稻籽粒植酸含量性状有关的主效QTL,分布在第3、5和6 染色体的相应区间内,表型贡献率分别为5.38%、8.02%和4.62%,降低籽粒植酸含量的等位基因均来自亲本LPA.检测到10对上位性互作影响籽粒植酸含量, 分布于水稻第1、3、5、6、11染色体上,互作效应值为1.69~5.18,其表型变异的解释率为8.67%~24.73%.

  9. Proton and Helium Injection Into First Order Fermi Acceleration at Shocks: Hybrid Simulation and Analysis

    Science.gov (United States)

    Dudnikova, Galina; Malkov, Mikhail; Sagdeev, Roald; Liseykina, Tatjana; Hanusch, Adrian

    2016-10-01

    Elemental composition of galactic cosmic rays (CR) probably holds the key to their origin. Most likely, they are accelerated at collisionless shocks in supernova remnants, but the acceleration mechanism is not entirely understood. One complicated problem is ``injection'', a process whereby the shock selects a tiny fraction of particles to keep on crossing its front and gain more energy. Comparing the injection rates of particles with different mass to charge ratio is a powerful tool for studying this process. Recent advances in measurements of CR He/p ratio have provided particularly important new clues. We performed a series of hybrid simulations and analyzed a joint injection of protons and Helium, in conjunction with upstream waves they generate. The emphasis of this work is on the bootstrap aspects of injection manifested in particle confinement to the shock and, therefore, their continuing acceleration by the self-driven waves. The waves are initially generated by He and protons in separate spectral regions, and their interaction plays a crucial role in particle acceleration. The work is ongoing and new results will be reported along with their analysis and comparison with the latest data from the AMS-02 space-based spectrometer. Work supported Grant RFBR 16-01-00209, NASA ATP-program under Award NNX14AH36G, and by the US Department of Energy under Award No. DE-FG02-04ER54738.

  10. Epistasis in tomato color mutations involves regulation of phytoene synthase 1 expression by cis-carotenoids.

    Science.gov (United States)

    Kachanovsky, David E; Filler, Shdema; Isaacson, Tal; Hirschberg, Joseph

    2012-11-13

    Tomato (Solanum lycopersicum) fruit accumulate the red carotenoid pigment lycopene. The recessive mutation yellow-flesh (locus r) in tomato eliminates fruit carotenoids by disrupting the activity of the fruit-specific phytoene synthase (PSY1), the first committed step in the carotenoid biosynthesis pathway. Fruits of the recessive mutation tangerine (t) appear orange due to accumulation of 7,9,7',9'-tetra-cis-lycopene (prolycopene) as a result of a mutation in the carotenoid cis-trans isomerase. It was established 60 y ago that tangerine is epistatic to yellow-flesh. This uncharacteristic epistasis interaction defies a paradigm in biochemical genetics arguing that mutations that disrupt enzymes acting early in a biosynthetic pathway are epistatic to other mutations that block downstream steps in the same pathway. To explain this conundrum, we have investigated the interaction between tangerine and yellow-flesh at the molecular level. Results presented here indicate that allele r(2997) of yellow-flesh eliminates transcription of PSY1 in fruits. In a genetic background of tangerine, transcription of PSY1 is partially restored to a level sufficient for producing phytoene and downstream carotenoids. Our results revealed the molecular mechanism underlying the epistasis of t over r and suggest the involvement of cis-carotenoid metabolites in a feedback regulation of PSY1 gene expression.

  11. Epistasis among Drosophila persimilis factors conferring hybrid male sterility with D. pseudoobscura bogotana.

    Directory of Open Access Journals (Sweden)

    Audrey S Chang

    Full Text Available The Bateson-Dobzhansky-Muller model posits that hybrid incompatibilities result from genetic changes that accumulate during population divergence. Indeed, much effort in recent years has been devoted to identifying genes associated with hybrid incompatibilities, often with limited success, suggesting that hybrid sterility and inviability are frequently caused by complex interactions between multiple loci and not by single or a small number of gene pairs. Our previous study showed that the nature of epistasis between sterility-conferring QTL in the Drosophila persimilis-D. pseudoobscura bogotana species pair is highly specific. Here, we further dissect one of the three QTL underlying hybrid male sterility between these species and provide evidence for multiple factors within this QTL. This result indicates that the number of loci thought to contribute to hybrid dysfunction may have been underestimated, and we discuss how linkage and complex epistasis may be characteristic of the genetics of hybrid incompatibilities. We further pinpoint the location of one locus that confers hybrid male sterility when homozygous, dubbed "mule-like", to roughly 250 kilobases.

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

    Science.gov (United States)

    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.

  13. Epistasis among Drosophila persimilis factors conferring hybrid male sterility with D. pseudoobscura bogotana.

    Science.gov (United States)

    Chang, Audrey S; Bennett, Sarah M; Noor, Mohamed A F

    2010-10-27

    The Bateson-Dobzhansky-Muller model posits that hybrid incompatibilities result from genetic changes that accumulate during population divergence. Indeed, much effort in recent years has been devoted to identifying genes associated with hybrid incompatibilities, often with limited success, suggesting that hybrid sterility and inviability are frequently caused by complex interactions between multiple loci and not by single or a small number of gene pairs. Our previous study showed that the nature of epistasis between sterility-conferring QTL in the Drosophila persimilis-D. pseudoobscura bogotana species pair is highly specific. Here, we further dissect one of the three QTL underlying hybrid male sterility between these species and provide evidence for multiple factors within this QTL. This result indicates that the number of loci thought to contribute to hybrid dysfunction may have been underestimated, and we discuss how linkage and complex epistasis may be characteristic of the genetics of hybrid incompatibilities. We further pinpoint the location of one locus that confers hybrid male sterility when homozygous, dubbed "mule-like", to roughly 250 kilobases.

  14. Epistasis modifies the dominance of loci causing hybrid male sterility in the Drosophila pseudoobscura species group.

    Science.gov (United States)

    Chang, Audrey S; Noor, Mohamed A F

    2010-01-01

    Speciation, the evolution of reproductive isolation between populations, serves as the driving force for generating biodiversity. Postzygotic barriers to gene flow, such as F(1) hybrid sterility and inviability, play important roles in the establishment and maintenance of biological species. F(1) hybrid incompatibilities in taxa that obey Haldane's rule, the observation that the heterogametic sex suffers greater hybrid fitness problems than the homogametic sex, are thought to often result from interactions between recessive-acting X-linked loci and dominant-acting autosomal loci. Because they play such prominent roles in producing hybrid incompatibilities, we examine the dominance and nature of epistasis between alleles derived from Drosophila persimilis that confer hybrid male sterility in the genetic background of its sister species, D. pseudoobscura bogotana. We show that epistasis elevates the apparent dominance of individually recessive-acting QTL such that they can contribute to F(1) hybrid sterility. These results have important implications for assumptions underlying theoretical models of hybrid incompatibilities and may offer a possible explanation for why, to date, identification of dominant-acting autosomal "speciation genes" has been challenging.

  15. Epistasis and maternal effects in experimental adaptation to chronic nutritional stress in Drosophila.

    Science.gov (United States)

    Vijendravarma, R K; Kawecki, T J

    2013-12-01

    Based on ecological and metabolic arguments, some authors predict that adaptation to novel, harsh environments should involve alleles showing negative (diminishing return) epistasis and/or that it should be mediated in part by evolution of maternal effects. Although the first prediction has been supported in microbes, there has been little experimental support for either prediction in multicellular eukaryotes. Here we use a line-cross design to study the genetic architecture of adaptation to chronic larval malnutrition in a population of Drosophila melanogaster that evolved on an extremely nutrient-poor larval food for 84 generations. We assayed three fitness-related traits (developmental rate, adult female weight and egg-to-adult viability) under the malnutrition conditions in 14 crosses between this selected population and a nonadapted control population originally derived from the same base population. All traits showed a pattern of negative epistasis between alleles improving performance under malnutrition. Furthermore, evolutionary changes in maternal traits accounted for half of the 68% increase in viability and for the whole of 8% reduction in adult female body weight in the selected population (relative to unselected controls). These results thus support both of the above predictions and point to the importance of nonadditive effects in adaptive microevolution.

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

    Science.gov (United States)

    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.

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

    Directory of Open Access Journals (Sweden)

    Hiroaki Miyagawa

    2013-07-01

    Full Text Available 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.

  18. Stepwise Distributed Open Innovation Contests for Software Development: Acceleration of Genome-Wide Association Analysis.

    Science.gov (United States)

    Hill, Andrew; Loh, Po-Ru; Bharadwaj, Ragu B; Pons, Pascal; Shang, Jingbo; Guinan, Eva; Lakhani, Karim; Kilty, Iain; Jelinsky, Scott A

    2017-05-01

    The association of differing genotypes with disease-related phenotypic traits offers great potential to both help identify new therapeutic targets and support stratification of patients who would gain the greatest benefit from specific drug classes. Development of low-cost genotyping and sequencing has made collecting large-scale genotyping data routine in population and therapeutic intervention studies. In addition, a range of new technologies is being used to capture numerous new and complex phenotypic descriptors. As a result, genotype and phenotype datasets have grown exponentially. Genome-wide association studies associate genotypes and phenotypes using methods such as logistic regression. As existing tools for association analysis limit the efficiency by which value can be extracted from increasing volumes of data, there is a pressing need for new software tools that can accelerate association analyses on large genotype-phenotype datasets. Using open innovation (OI) and contest-based crowdsourcing, the logistic regression analysis in a leading, community-standard genetics software package (PLINK 1.07) was substantially accelerated. OI allowed us to do this in computational, numeric, and algorithmic approaches was identified that accelerated the logistic regression in PLINK 1.07 by 18- to 45-fold. Combining contest-derived logistic regression code with coarse-grained parallelization, multithreading, and associated changes to data initialization code further developed through distributed innovation, we achieved an end-to-end speedup of 591-fold for a data set size of 6678 subjects by 645 863 variants, compared to PLINK 1.07's logistic regression. This represents a reduction in run time from 4.8 hours to 29 seconds. Accelerated logistic regression code developed in this project has been incorporated into the PLINK2 project. Using iterative competition-based OI, we have developed a new, faster implementation of logistic regression for genome-wide association

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

    Energy Technology Data Exchange (ETDEWEB)

    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.

  20. RF-thermal-structural-RF coupled analysis on a travelling wave disk-loaded accelerating structure

    Institute of Scientific and Technical Information of China (English)

    PEI Shi-Lun; CHI Yun-Long; ZHANG Jing-Ru; HOU Mi; LI Xiao-Ping

    2012-01-01

    The travelling wave (TW) disk-loaded accelerating structure is one of the key components in normal conducting (NC) linear accelerators,and has been studied for many years.In the design process,usually after the dimensions of each cell and the two couplers are finalized,the structure is fabricated and tuned,and then the whole structure RF characteristics are measured by using a vector network analyzer.Before fabrication,the whole structure characteristics (including RF,thermal and structural ones) are less simulated due to the limited capability of currently available computers.In this paper,we described a method for performing RF-thermal-structural-RF coupled analysis on a TW disk-loaded structure using only one PC.In order to validate our method,we first analyzed and compared our RF simulation results on the 3 m long BEPC Ⅱ structure with the corresponding experimental results,which shows very good consistency.Finally,the RF-thermal-structure-RF coupled analysis results on the 1.35 m long NSC KIPT linac accelerating structure are presented.

  1. Negative Epistasis and Evolvability in TEM-1 ß-Lactamase- The Thin Line between an Enzyme's Conformational Freedom and Disorder

    NARCIS (Netherlands)

    Dellus-Gur, E.; Elias, M.; Caselli, E.; Prati, F.; Salverda, M.L.M.; Visser, de J.A.G.M.; Fraser, J.S.; Tawfik, D.S.

    2015-01-01

    Epistasis is a key factor in evolution since it determines which combinations of mutations provide adaptive solutions and which mutational pathways toward these solutions are accessible by natural selection. There is growing evidence for the pervasiveness of sign epistasis—a complete reversion of mu

  2. Multiphysics Analysis of Frequency Detuning in Superconducting RF Cavities for Proton Particle Accelerators

    Energy Technology Data Exchange (ETDEWEB)

    Awida, M. H. [Fermilab; Gonin, I. [Fermilab; Passarelli, D. [Fermilab; Sukanov, A. [Fermilab; Khabiboulline, T. [Fermilab; Yakovlev, V. [Fermilab

    2016-01-22

    Multiphysics analyses for superconducting cavities are essential in the course of cavity design to meet stringent requirements on cavity frequency detuning. Superconducting RF cavities are the core accelerating elements in modern particle accelerators whether it is proton or electron machine, as they offer extremely high quality factors thus reducing the RF losses per cavity. However, the superior quality factor comes with the challenge of controlling the resonance frequency of the cavity within few tens of hertz bandwidth. In this paper, we investigate how the multiphysics analysis plays a major role in proactively minimizing sources of frequency detuning, specifically; microphonics and Lorentz Force Detuning (LFD) in the stage of RF design of the cavity and mechanical design of the niobium shell and the helium vessel.

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

    Energy Technology Data Exchange (ETDEWEB)

    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

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

    Science.gov (United States)

    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

  5. Benchmarking study and its application for shielding analysis of large accelerator facilities

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Hee-Seock; Kim, Dong-hyun; Oranj, Leila Mokhtari; Oh, Joo-Hee; Lee, Arim; Jung, Nam-Suk [POSTECH, Pohang (Korea, Republic of)

    2015-10-15

    Shielding Analysis is one of subjects which are indispensable to construct large accelerator facility. Several methods, such as the Monte Carlo, discrete ordinate, and simplified calculation, have been used for this purpose. The calculation precision is overcome by increasing the trial (history) numbers. However its accuracy is still a big issue in the shielding analysis. To secure the accuracy in the Monte Carlo calculation, the benchmarking study using experimental data and the code comparison are adopted fundamentally. In this paper, the benchmarking result for electrons, protons, and heavy ions are presented as well as the proper application of the results is discussed. The benchmarking calculations, which are indispensable in the shielding analysis were performed for different particles: proton, heavy ion and electron. Four different multi-particle Monte Carlo codes, MCNPX, FLUKA, PHITS, and MARS, were examined for higher energy range equivalent to large accelerator facility. The degree of agreement between the experimental data including the SINBAD database and the calculated results were estimated in the terms of secondary neutron production and attenuation through the concrete and iron shields. The degree of discrepancy and the features of Monte Carlo codes were investigated and the application way of the benchmarking results are discussed in the view of safety margin and selecting the code for the shielding analysis. In most cases, the tested Monte Carlo codes give proper credible results except of a few limitation of each codes.

  6. Analysis of the Chirplet Transform-Based Algorithm for Radar Detection of Accelerated Targets

    Science.gov (United States)

    Galushko, V. G.; Vavriv, D. M.

    2017-06-01

    Purpose: Efficiency analysis of an optimal algorithm of chirp signal processing based on the chirplet transform as applied to detection of radar targets in uniformly accelerated motion. Design/methodology/approach: Standard methods of the optimal filtration theory are used to investigate the ambiguity function of chirp signals. Findings: An analytical expression has been derived for the ambiguity function of chirp signals that is analyzed with respect to detection of radar targets moving at a constant acceleration. Sidelobe level and characteristic width of the ambiguity function with respect to the coordinates frequency and rate of its change have been estimated. The gain in the signal-to-noise ratio has been assessed that is provided by the algorithm under consideration as compared with application of the standard Fourier transform to detection of chirp signals against a “white” noise background. It is shown that already with a comparatively small (block diagram of implementation of the algorithm under consideration is suggested on the basis of a multichannel weighted Fourier transform. Recommendations as for selection of the detection algorithm parameters have been developed. Conclusions: The obtained results testify to efficiency of application of the algorithm under consideration to detection of radar targets moving at a constant acceleration. Nevertheless, it seems expedient to perform computer simulations of its operability with account for the noise impact along with trial measurements in real conditions.

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

    Energy Technology Data Exchange (ETDEWEB)

    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.

  8. OncoSimulR: genetic simulation with arbitrary epistasis and mutator genes in asexual populations.

    Science.gov (United States)

    Diaz-Uriarte, Ramon

    2017-06-15

    OncoSimulR implements forward-time genetic simulations of biallelic loci in asexual populations with special focus on cancer progression. Fitness can be defined as an arbitrary function of genetic interactions between multiple genes or modules of genes, including epistasis, restrictions in the order of accumulation of mutations, and order effects. Mutation rates can differ among genes, and can be affected by (anti)mutator genes. Also available are sampling from simulations (including single-cell sampling), plotting the genealogical relationships of clones and generating and plotting fitness landscapes. Implemented in R and C ++, freely available from BioConductor for Linux, Mac and Windows under the GNU GPL license. Version 2.5.9 or higher available from: http://www.bioconductor.org/packages/devel/bioc/html/OncoSimulR.html . GitHub repository at: https://github.com/rdiaz02/OncoSimul. ramon.diaz@iib.uam.es. Supplementary data are available at Bioinformatics online.

  9. Conservation and Rewiring of Functional Modules Revealed by an Epistasis Map in Fission Yeast

    Science.gov (United States)

    Roguev, Assen; Bandyopadhyay, Sourav; Zofall, Martin; Zhang, Ke; Fischer, Tamas; Collins, Sean R.; Qu, Hongjing; Shales, Michael; Park, Han-Oh; Hayles, Jacqueline; Hoe, Kwang-Lae; Kim, Dong-Uk; Ideker, Trey; Grewal, Shiv I.; Weissman, Jonathan S.; Krogan, Nevan J.

    2009-01-01

    An epistasis map (E-MAP) was constructed in the fission yeast, Schizosaccharomyces pombe, by systematically measuring the phenotypes associated with pairs of mutations. This high-density, quantitative genetic interaction map focused on various aspects of chromosome function, including transcription regulation and DNA repair/replication. The E-MAP uncovered a previously unidentified component of the RNA interference (RNAi) machinery (rsh1) and linked the RNAi pathway to several other biological processes. Comparison of the S. pombe E-MAP to an analogous genetic map from the budding yeast revealed that, whereas negative interactions were conserved between genes involved in similar biological processes, positive interactions and overall genetic profiles between pairs of genes coding for physically associated proteins were even more conserved. Hence, conservation occurs at the level of the functional module (protein complex), but the genetic cross talk between modules can differ substantially. PMID:18818364

  10. Analysis of longitudinal bunching in an FEL driven two-beam accelerator

    Energy Technology Data Exchange (ETDEWEB)

    Lidia, S.; Gardelle, J.; Lefevre, T.; Donohue, J.T.; Gouard, P.; Rullier, J.L.; Vermare, C.

    2000-08-01

    Recent experiments have explored the use of a free-electron laser (FEL) as a buncher for a microwave two-beam accelerator, and the subsequent driving of a standing-wave rf output cavity. Here the authors present a deeper analysis of the longitudinal dynamics of the electron bunches as they are transported from the end of the FEL and through the output cavity. In particular, the authors examine the effect of the transport region and cavity aperture to filter the bunched portion of the beam.

  11. Characterizing gene-gene interactions in a statistical epistasis network of twelve candidate genes for obesity.

    Science.gov (United States)

    De, Rishika; Hu, Ting; Moore, Jason H; Gilbert-Diamond, Diane

    2015-01-01

    Recent findings have reemphasized the importance of epistasis, or gene-gene interactions, as a contributing factor to the unexplained heritability of obesity. Network-based methods such as statistical epistasis networks (SEN), present an intuitive framework to address the computational challenge of studying pairwise interactions between thousands of genetic variants. In this study, we aimed to analyze pairwise interactions that are associated with Body Mass Index (BMI) between SNPs from twelve genes robustly associated with obesity (BDNF, ETV5, FAIM2, FTO, GNPDA2, KCTD15, MC4R, MTCH2, NEGR1, SEC16B, SH2B1, and TMEM18). We used information gain measures to identify all SNP-SNP interactions among and between these genes that were related to obesity (BMI > 30 kg/m(2)) within the Framingham Heart Study Cohort; interactions exceeding a certain threshold were used to build an SEN. We also quantified whether interactions tend to occur more between SNPs from the same gene (dyadicity) or between SNPs from different genes (heterophilicity). We identified a highly connected SEN of 709 SNPs and 1241 SNP-SNP interactions. Combining the SEN framework with dyadicity and heterophilicity analyses, we found 1 dyadic gene (TMEM18, P-value = 0.047) and 3 heterophilic genes (KCTD15, P-value = 0.045; SH2B1, P-value = 0.003; and TMEM18, P-value = 0.001). We also identified a lncRNA SNP (rs4358154) as a key node within the SEN using multiple network measures. This study presents an analytical framework to characterize the global landscape of genetic interactions from genome-wide arrays and also to discover nodes of potential biological significance within the identified network.

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

    Science.gov (United States)

    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.

  13. GPU-accelerated analysis and visualization of large structures solved by molecular dynamics flexible fitting.

    Science.gov (United States)

    Stone, John E; McGreevy, Ryan; Isralewitz, Barry; Schulten, Klaus

    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-à-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.

  14. Dynamical analysis of an accelerator-based fluid-fueled subcritical radioactive waste burning system

    Science.gov (United States)

    Woosley, Michael Louis, Jr.

    The recent revival of interest in accelerator-driven subcritical fluid-fueled systems is documented. Several important applications of these systems are mentioned. In particular, new applications have focused on the destruction of high-level radioactive waste. Systems can be designed to quickly destroy the actinides and long-lived fission products from light water reactor fuel, weapons plutonium, and other high-level defense wastes. The proposed development of these systems is used to motivate the need for the development of dynamic analysis methods for their nuclear kinetics. A physical description of the Los Alamos 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 three 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 which 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. Specific transients which 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. Modest initiating events can cause significant swings in system temperature and power. The circulation of the fluid fuel can lead to oscillations on the relatively short scale of the loop circulation time. The system responds quickly to reactivity changes because the large neutron source overwhelms the damping effect of delayed

  15. Accelerating policy decisions to adopt haemophilus influenzae type B vaccine: a global, multivariable analysis.

    Directory of Open Access Journals (Sweden)

    Jessica C Shearer

    2010-03-01

    Full Text Available 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.

  16. Relevance Epistasis Network of Gastritis for Intra-chromosomes in the Korea Associated Resource (KARE Cohort Study

    Directory of Open Access Journals (Sweden)

    Hyun-hwan Jeong

    2014-12-01

    Full Text Available Gastritis is a common but a serious disease with a potential risk of developing carcinoma. Helicobacter pylori infection is reported as the most common cause of gastritis, but other genetic and genomic factors exist, especially single-nucleotide polymorphisms (SNPs. Association studies between SNPs and gastritis disease are important, but results on epistatic interactions from multiple SNPs are rarely found in previous genome-wide association (GWA studies. In this study, we performed computational GWA case-control studies for gastritis in Korea Associated Resource (KARE data. By transforming the resulting SNP epistasis network into a gene-gene epistasis network, we also identified potential gene-gene interaction factors that affect the susceptibility to gastritis.

  17. First Results from a Principal Component Analysis of Tycho's SNR: Evidence for Cosmic Ray Ion Acceleration

    Science.gov (United States)

    Warren, J. S.; Hughes, J. P.; Badenes, C.

    2005-12-01

    We present results from a Principal Component Analysis (PCA) of Tycho's supernova remnant (SNR). PCA is a statistical technique we implemented to characterize X-ray spectra extracted from distinct spatial regions across the entire image of the remnant. We used the PCA to determine the location of the contact discontinuity (CD) in Tycho, which marks the boundary between shocked ejecta and shocked interstellar material, and found an azimuthal-angle-averaged radius of 241". For the average radius of the outer blast wave (BW) we found 251". Taking account of projection effects, the ratio of BW:CD is 1:0.93, which is inconsistent with adiabatic hydrodynamic models of SNR evolution. The BW:CD ratio can be explained if cosmic ray acceleration of ions is occurring at the forward shock. Such a scenario is further supported by evidence from the morphology and spectral nature of the BW emission for the acceleration of cosmic ray electrons. We also present PCA results regarding the ranges in Si and Fe composition in Tycho, and a newly uncovered spectral variation in the form of a low energy excess that has not been previously noted.

  18. Calculation and Spectra Analysis of Horizontal Acceleration Correction (HACC) for Airborne Gravimetry

    Institute of Scientific and Technical Information of China (English)

    SHI Pan; SUN Zhongmiao; XIAO Yun

    2004-01-01

    On the basis of a sinusoidal model of the disturbed horizontal acceleration, the spectrum characteristics of misaligned angle and horizontal acceleration correction are analyzed. In an airborne gravimetry test, the misaligned angle of platform and horizontal acceleration correction are calculated. They are 5'and 3 mGal, respectively, when the flight is stable.

  19. Role of sugammadex in accelerating postoperative discharge: A meta-analysis.

    Science.gov (United States)

    Carron, Michele; Zarantonello, Francesco; Lazzarotto, Nadia; Tellaroli, Paola; Ori, Carlo

    2017-06-01

    Sugammadex has been introduced for reversal of neuromuscular blockade (NMB) induced by rocuronium (or vecuronium). Although its efficacy and safety have been established, data are conflicting as to whether it accelerates discharge to the surgical ward compared with neostigmine, which is traditionally used for reversing NMB. The object of this systematic review and meta-analysis was to review the research comparing sugammadex and neostigmine in the context of patient discharge after general anesthesia. Systematic review and meta-analysis. University medical hospital. Five-hundred eighteen patients from six studies were included. A comprehensive search was conducted using PubMed, Web of Science, Google Scholar, and Cochrane Library electronic databases to identify randomized controlled trials written in English. Two reviewers independently selected the studies, extracted data regarding postoperative discharge, and assessed the trials' methodological quality and evidence level. Postoperative discharge time was determined from the operating room (OR) to the postanesthesia care unit (PACU) and from the PACU to the surgical ward. This study was conducted using PRISMA methodology. Time to discharge after NMB reversal with sugammadex or neostigmine. Compared with neostigmine, sugammadex was associated with a significantly faster discharge from the OR to the PACU (mean difference [MD]=22.14min, 95% CI (14.62, 29.67), Psugammadex than for neostigmine from the OR to the PACU (MD=5.58min, 95% CI (3.03, 8.14), P≤0.0001, I(2)=0%). However, discharge-readiness was similar in both groups for patients moving from the PACU to the surgical ward (MD=-1.10min, 95% CI (-5.69, 3.50), P=0.6394, I(2)=25.3%). Results from this meta-analysis suggest that sugammadex accelerates postoperative discharge of patients after general anesthesia compared with neostigmine. Copyright © 2017 Elsevier Inc. All rights reserved.

  20. FADTTSter: accelerating hypothesis testing with functional analysis of diffusion tensor tract statistics

    Science.gov (United States)

    Noel, Jean; Prieto, Juan C.; Styner, Martin

    2017-03-01

    Functional Analysis of Diffusion Tensor Tract Statistics (FADTTS) is a toolbox for analysis of white matter (WM) fiber tracts. It allows associating diffusion properties along major WM bundles with a set of covariates of interest, such as age, diagnostic status and gender, and the structure of the variability of these WM tract properties. However, to use this toolbox, a user must have an intermediate knowledge in scripting languages (MATLAB). FADTTSter was created to overcome this issue and make the statistical analysis accessible to any non-technical researcher. FADTTSter is actively being used by researchers at the University of North Carolina. FADTTSter guides non-technical users through a series of steps including quality control of subjects and fibers in order to setup the necessary parameters to run FADTTS. Additionally, FADTTSter implements interactive charts for FADTTS' outputs. This interactive chart enhances the researcher experience and facilitates the analysis of the results. FADTTSter's motivation is to improve usability and provide a new analysis tool to the community that complements FADTTS. Ultimately, by enabling FADTTS to a broader audience, FADTTSter seeks to accelerate hypothesis testing in neuroimaging studies involving heterogeneous clinical data and diffusion tensor imaging. This work is submitted to the Biomedical Applications in Molecular, Structural, and Functional Imaging conference. The source code of this application is available in NITRC.

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

    Science.gov (United States)

    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

  2. Negative Epistasis and Evolvability in TEM-1 β-Lactamase--The Thin Line between an Enzyme's Conformational Freedom and Disorder.

    Science.gov (United States)

    Dellus-Gur, Eynat; Elias, Mikael; Caselli, Emilia; Prati, Fabio; Salverda, Merijn L M; de Visser, J Arjan G M; Fraser, James S; Tawfik, Dan S

    2015-07-17

    Epistasis is a key factor in evolution since it determines which combinations of mutations provide adaptive solutions and which mutational pathways toward these solutions are accessible by natural selection. There is growing evidence for the pervasiveness of sign epistasis--a complete reversion of mutational effects, particularly in protein evolution--yet its molecular basis remains poorly understood. We describe the structural basis of sign epistasis between G238S and R164S, two adaptive mutations in TEM-1 β-lactamase--an enzyme that endows antibiotics resistance. Separated by 10 Å, these mutations initiate two separate trajectories toward increased hydrolysis rates and resistance toward second and third-generation cephalosporins antibiotics. Both mutations allow the enzyme's active site to adopt alternative conformations and accommodate the new antibiotics. By solving the corresponding set of crystal structures, we found that R164S causes local disorder whereas G238S induces discrete conformations. When combined, the mutations in 238 and 164 induce local disorder whereby nonproductive conformations that perturb the enzyme's catalytic preorganization dominate. Specifically, Asn170 that coordinates the deacylating water molecule is misaligned, in both the free form and the inhibitor-bound double mutant. This local disorder is not restored by stabilizing global suppressor mutations and thus leads to an evolutionary cul-de-sac. Conformational dynamism therefore underlines the reshaping potential of protein's structures and functions but also limits protein evolvability because of the fragility of the interactions networks that maintain protein structures.

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

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    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

  4. High-performance liquid chromatography accelerator mass spectrometry: correcting for losses during analysis by internal standardization.

    Science.gov (United States)

    Lappin, G; Simpson, M; Shishikura, Y; Garner, C

    2008-07-01

    A method was developed to account for analytical losses of (14)C-analyte when determining the concentration in biological samples using chromatographic separation and analysis by accelerator mass spectrometry. From the equations of J. Vogel and A.H. Love (in: A.L. Burlingame (Ed.), Methods in Enzymology, Academic Press, New York, 2005), new equations were derived to describe the isotopic dilution of a chromatographically isolated (14)C-analyte. The analytical recovery for each sample was determined by the use of the UV response for nonlabeled analyte, as an internal standard against a standard curve. The slope of the curve was substituted into the equations to provide a method of accurately determining the analyte concentration.

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

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    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.

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

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    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

  7. Accelerated design and quality control of impact modifiers for plastics through atomic force microscopy (AFM) analysis

    Science.gov (United States)

    Moeller, Gunter

    2011-03-01

    Standard polymer resins are often too brittle or do not meet other mechanical property requirements for typical polymer applications. To achieve desired properties it is common to disperse so called ``impact modifiers'', which are spherical latex particles with diameters of much less than one micrometer, into the pure resin. Understanding and control of the entire process from latex particle formation to subsequent dispersion into polymer resins are necessary to accelerate the development of new materials that meet specific application requirements. In this work AFM imaging and nanoindentation techniques in combination with AFM-based spectroscopic techniques were applied to assess latex formation and dispersion. The size and size distribution of the latex particles can be measured based on AFM amplitude modulation images. AFM phase images provide information about the chemical homogeneity of individual particles. Nanoindentation may be used to estimate their elastic and viscoelastic properties. Proprietary creep and nanoscale Dynamic Mechanical Analysis (DMA) tests that we have developed were used to measure these mechanical properties. The small size of dispersed latex inclusions requires local mechanical and spectroscopic analysis techniques with high lateral and spatial resolution. We applied the CRAVE AFM method, developed at NIST, to perform mechanical analysis of individual latex inclusions and compared results with those obtained using nanoscale DMA. NanoIR, developed by Anasys Inc., and principal component confocal Raman were used for spectroscopic analysis and results from both techniques compared.

  8. Reliability of segmental accelerations measured using a new wireless gait analysis system.

    Science.gov (United States)

    Kavanagh, Justin J; Morrison, Steven; James, Daniel A; Barrett, Rod

    2006-01-01

    The purpose of this study was to determine the inter- and intra-examiner reliability, and stride-to-stride reliability, of an accelerometer-based gait analysis system which measured 3D accelerations of the upper and lower body during self-selected slow, preferred and fast walking speeds. Eight subjects attended two testing sessions in which accelerometers were attached to the head, neck, lower trunk, and right shank. In the initial testing session, two different examiners attached the accelerometers and performed the same testing procedures. A single examiner repeated the procedure in a subsequent testing session. All data were collected using a new wireless gait analysis system, which features near real-time data transmission via a Bluetooth network. Reliability for each testing condition (4 locations, 3 directions, 3 speeds) was quantified using a waveform similarity statistic known as the coefficient of multiple determination (CMD). CMD's ranged from 0.60 to 0.98 across all test conditions and were not significantly different for inter-examiner (0.86), intra-examiner (0.87), and stride-to-stride reliability (0.86). The highest repeatability for the effect of location, direction and walking speed were for the shank segment (0.94), the vertical direction (0.91) and the fast walking speed (0.91), respectively. Overall, these results indicate that a high degree of waveform repeatability was obtained using a new gait system under test-retest conditions involving single and dual examiners. Furthermore, differences in acceleration waveform repeatability associated with the reapplication of accelerometers were small in relation to normal motor variability.

  9. Thermal-hydraulic analysis of LBE spallation target for accelerator-driven systems

    Indian Academy of Sciences (India)

    Aniseh Ahmed Atef Abdalla; Jiyang Yu; Yongwel Yang

    2013-01-01

    In an accelerator-driven subcritical system (ADS), a high-performance spallation neutron source is used to feed the subcritical reactor. Neutron generation depends on the proton beam intensity. If the beam intensity is increased by a given factor, the number of generated neutrons will increase. The mechanism yielding a high rate of neutron production per energy is the spallation process, and this mechanism produces very high-energy deposition in the spallation target material. Producing a high rate of neutrons is accompanied by creation of problems of decay heat cooling and radiological protection. As a first step in designing a full-scale industrial ADS, a small-scale experimental ADS, which is similar to the European experimental ADS (XADS) is analysed. The analysis presented in this paper is based on lead–bismuth eutectic (LBE) cooled XADS-type experimental reactors, designed during the European experimental (PDS-XADS) project. Computational fluid dynamics analysis has been carried out for the spallation target. Steady-state behaviour and shear stress transport turbulence model with the automatic wall treatment were applied in the present analysis.

  10. The L(1/2) regularization approach for survival analysis in the accelerated failure time model.

    Science.gov (United States)

    Chai, Hua; Liang, Yong; Liu, Xiao-Ying

    2015-09-01

    The analysis of high-dimensional and low-sample size microarray data for survival analysis of cancer patients is an important problem. It is a huge challenge to select the significantly relevant bio-marks from microarray gene expression datasets, in which the number of genes is far more than the size of samples. In this article, we develop a robust prediction approach for survival time of patient by a L(1/2) regularization estimator with the accelerated failure time (AFT) model. The L(1/2) regularization could be seen as a typical delegate of L(q)(0regularization methods and it has shown many attractive features. In order to optimize the problem of the relevant gene selection in high-dimensional biological data, we implemented the L(1/2) regularized AFT model by the coordinate descent algorithm with a renewed half thresholding operator. The results of the simulation experiment showed that we could obtain more accurate and sparse predictor for survival analysis by the L(1/2) regularized AFT model compared with other L1 type regularization methods. The proposed procedures are applied to five real DNA microarray datasets to efficiently predict the survival time of patient based on a set of clinical prognostic factors and gene signatures.

  11. Automated Bearing Fault Diagnosis Using 2D Analysis of Vibration Acceleration Signals under Variable Speed Conditions

    Directory of Open Access Journals (Sweden)

    Sheraz Ali Khan

    2016-01-01

    Full Text Available Traditional fault diagnosis methods of bearings detect characteristic defect frequencies in the envelope power spectrum of the vibration signal. These defect frequencies depend upon the inherently nonstationary shaft speed. Time-frequency and subband signal analysis of vibration signals has been used to deal with random variations in speed, whereas design variations require retraining a new instance of the classifier for each operating speed. This paper presents an automated approach for fault diagnosis in bearings based upon the 2D analysis of vibration acceleration signals under variable speed conditions. Images created from the vibration signals exhibit unique textures for each fault, which show minimal variation with shaft speed. Microtexture analysis of these images is used to generate distinctive fault signatures for each fault type, which can be used to detect those faults at different speeds. A k-nearest neighbor classifier trained using fault signatures generated for one operating speed is used to detect faults at all the other operating speeds. The proposed approach is tested on the bearing fault dataset of Case Western Reserve University, and the results are compared with those of a spectrum imaging-based approach.

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

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    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.

  13. Congenic mice reveal genetic epistasis and overlapping disease loci for autoimmune diabetes and listeriosis.

    Science.gov (United States)

    Wang, Nancy; Elso, Colleen M; Mackin, Leanne; Mannering, Stuart I; Strugnell, Richard A; Wijburg, Odilia L; Brodnicki, Thomas C

    2014-08-01

    The nonobese diabetic (NOD) mouse strain serves as a genomic standard for assessing how allelic variation for insulin-dependent diabetes (Idd) loci affects the development of autoimmune diabetes. We previously demonstrated that C57BL/6 (B6) mice harbor a more diabetogenic allele than NOD mice for the Idd14 locus when introduced onto the NOD genetic background. New congenic NOD mouse strains, harboring smaller B6-derived intervals on chromosome 13, now localize Idd14 to an ~18-Mb interval and reveal a new locus, Idd31. Notably, the B6 allele for Idd31 confers protection against diabetes, but only in the absence of the diabetogenic B6 allele for Idd14, indicating genetic epistasis between these two loci. Moreover, congenic mice that are more susceptible to diabetes are more resistant to Listeria monocytogenes infection. This result co-localizes Idd14 and Listr2, a resistance locus for listeriosis, to the same genomic interval and indicates that congenic NOD mice may also be useful for localizing resistance loci for infectious disease.

  14. Quantification of various APP-mRNA isoforms and epistasis in Lesch-Nyhan disease.

    Science.gov (United States)

    Nguyen, Khue Vu; Nyhan, William L

    2017-03-16

    The present work is the development of a simple and specific kinetic method based on RT-PCR technique coupled with direct sequencing for quantification of various amyloid precursor protein-mRNA isoforms (APP-mRNA isoforms) in biological samples, especially for identifying the most abundant one that may decisive for the normal status or disease risk. Application of this kinetic method to the Lesch-Nyhan disease (LND) was performed and results indicated an epistasis between mutated hypoxanthine phosphoribosyltransferase1 (HPRT1) and APP genes. APP-mRNA isoform of 624bp, with a deletion starting after 49bp of the 5' end of exon 3 followed by a complete deletion of exons 4-15, mutations in exon 1: c.22C>T, p.L18F, and exon 3: c.269A>G, p.Q90R encoding APP207 isoform, was the most abundant one in most of the LND patients and would be responsible for the neurobehavioral syndrome in these patients. The method is useful for identifying the defective APP-mRNA isoform in LND patients, and in neurodevelopmental and neurodegenerative disorders in which the APP gene is involved in the pathogenesis of diseases such as autism, fragile X syndrome, amyotrophic lateral sclerosis, and Alzheimer's disease, and may pave the way for new strategies applicable to rational antisense drugs design. Copyright © 2017 Elsevier B.V. All rights reserved.

  15. Epistasis as a determinant of the HIV-1 protease's robustness to mutation.

    Directory of Open Access Journals (Sweden)

    Elena Capel

    Full Text Available The robustness of phenotypes to mutation is critical to protein evolution; robustness may be an adaptive trait if it promotes evolution. We hypothesised that native proteins subjected to natural selection in vivo should be more robust than proteins generated in vitro in the absence of natural selection. We compared the mutational robustness of two human immunodeficiency virus type 1 (HIV-1 proteases with comparable catalytic efficiencies, one isolated from an infected individual and the second generated in vitro via random mutagenesis. Single mutations in the protease (82 and 60 in the wild-type and mutant backgrounds, respectively were randomly generated in vitro and the catalytic efficiency of each mutant was determined. No differences were observed between these two protease variants when lethal, neutral, and deleterious mutations were compared (P = 0.8025, chi-squared test. Similarly, average catalytic efficiency (-72.6% and -64.5%, respectively did not significantly differ between protease mutant libraries (P = 0.3414, Mann Whitney test. Overall, the two parental proteins displayed similar mutational robustness. Importantly, strong and widespread epistatic interactions were observed when the effect of the same mutation was compared in both proteases, suggesting that epistasis can be a key determinant of the robustness displayed by the in vitro generated protease.

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

    Science.gov (United States)

    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.

  17. Steady-state responses of axially accelerating viscoelastic beams: Approximate analysis and numerical confirmation

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    Nonlinear parametric vibration of axially accelerating viscoelastic beams is inves-tigated via an approximate analytical method with numerical confirmations. Based on nonlinear models of a finite-small-stretching slender beam moving at a speed with a periodic fluctuation, a solvability condition is established via the method of multiple scales for subharmonic resonance. Therefore, the amplitudes of steady-state periodic responses and their existence conditions are derived. The amplitudes of stable steady-state responses increase with the amplitude of the axial speed fluctuation, and decrease with the viscosity coefficient and the nonlinear coefficient. The minimum of the detuning parameter which causes the existence of a stable steady-state periodic response decreases with the amplitude of the axial speed fluctuation, and increases with the viscosity coefficient. Nu-merical solutions are sought via the finite difference scheme for a nonlinear par-tial-differential equation and a nonlinear integro-partial-differential equation. The calculation results qualitatively confirm the effects of the related parameters pre-dicted by the approximate analysis on the amplitude and the existence condition of the stable steady-state periodic responses. Quantitative comparisons demonstrate that the approximate analysis results have rather high precision.

  18. Multiphysics Analysis of the 2.5 MeV BNCT RFQ Accelerator

    CERN Document Server

    Xiaowen, Zhu; Kun, Zhu

    2016-01-01

    Boron Neutron Capture Therapy (BNCT), is an advanced cancer therapy that destroys the cancer tumors using the well-known Li(p,n)Be . Because of the highly selectively reaction between a boron and a neutron, BNCT is effective for rapidly spreading cancer, invasive carcinoma, such as head and neck cancer, melanoma, malignant brain tumors and so on. The PKU RFQ group proposes an RFQ based neutron source for BNCT application. The 162.5 MHz four-vane RFQ will accelerate 20-mA H+ from 35.0 keV to 2.50 MeV in CW mode, and delivers a neutron yield of 1.73*10^13 n/sec/cm^2. The thermal management will become the most important issues. The detailed multiphysics analysis of the BNCT RFQ will be studied, and the RFQ frequency shift during nominal operating condition is also predicted. The multiphysics analysis is performed by using the CST Multiphysics Model and verified with ANSYS Multiphysics.

  19. Hyperfractionated or accelerated radiotherapy in head and neck cancer: a meta-analysis

    DEFF Research Database (Denmark)

    Bourhis, J.; Overgaard, Jens; Audry, H.

    2006-01-01

    -specified categories: hyperfractionated, accelerated, and accelerated with total dose reduction. FINDINGS: 15 trials with 6515 patients were included. The median follow-up was 6 years. Tumours sites were mostly oropharynx and larynx; 5221 (74%) patients had stage III-IV disease (International Union Against Cancer...

  20. Statistical analysis of data from accelerated ageing tests of PES UF membranes

    NARCIS (Netherlands)

    Zondervan, Edwin; Zwijnenburg, Arie; Roffel, Brian

    2007-01-01

    In this research, membrane life-time was evaluated by means of accelerated ageing experiments. A pressure pulse unit was used to perform the ageing experiments in an accelerated way. An experimental design has been set up and four ageing factors were varied at two levels. The four ageing factors stu

  1. Statistical analysis of data from accelerated ageing tests of PES UF membranes

    NARCIS (Netherlands)

    Zondervan, E.; Zwijnenburg, A.; Roffel, B.

    2007-01-01

    In this research, membrane life-time was evaluated by means of accelerated ageing experiments. A pressure pulse unit was used to perform the ageing experiments in an accelerated way. An experimental design has been set up and four ageing factors were varied at two levels. The four ageing factors

  2. Intuitional experiment and numerical analysis of flow characteristics affected by flow accelerated corrosion in elbow pipe system

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Hyung Joon [School of Mechanical and Aerospace Engineering, Seoul National University, Gwanak-gu, Seoul 151-744 (Korea, Republic of); Kim, Kyung Hoon, E-mail: kimkh@khu.ac.kr [Department of Mechanical Engineering, Kyung Hee University, Seochun 1, Yongin, Gyeonggi 446-701 (Korea, Republic of)

    2016-05-15

    Highlights: • Wall-thinning erosion of pipelines in plants leads to fatal accidents unexpectedly. • Flow Acceleration Corrosion (FAC) is a main reason of wall-thinning. • For industrial safety, it is necessary to verify the tendency of FAC. • We focused on local wall thinning by FAC with intuitional visualization experiment and numerical analysis in elbow pipe.

  3. Linear to non linear analysis for positron acceleration in plasma hollow channel wakefields

    Science.gov (United States)

    Amorim, Ligia Diana; An, Weiming; Mori, Warren B.; Vieira, Jorge

    2016-10-01

    Plasma wakefield accelerators are promising candidates for future generation compact accelerators. The standard regime of operation, non-linear or blowout regime, is reached when a particle bunch space charge or laser pulse ponderomotive force radially expels plasma electrons forming a bucket of ions that defocus positron bunches, thus preventing their acceleration. To avoid defocusing, hollow plasma channels have been considered. The corresponding wakefields have been examined in the linear and non-linear excitation regimes for electrons. It is therefore important to extend the theory for positron acceleration, particularly in the nonlinear regime where the wakefields strongly differ. In this work we explore the wakefield structure, examine the differences between the electron and positron beam cases, and explore positron acceleration in nonlinear regimes. We support our findings with multi-dimensional particle-in-cell simulations performed with OSIRIS and quasi-3D and QuickPIC.

  4. Nuclear techniques for the analysis and dating of cultural heritage with the tandetron accelerator at the CEDAD

    OpenAIRE

    Lucio Calcagnile

    2014-01-01

    The Accelerator Mass Spectrometry technique for measuring carbon isotopes and dating artifacts, together with nuclear techniques of ion beam analysis are widely used in the field of cultural heritage owing to the great advantage of their being non-destructive. In Italy, CEDAD - CEntro Di DAtazione e Diagnostica of the University of Salento, with its tandetron accelerator of 3MV, has played a major role for over ten years, in studying materials of cultural assets requiring the determination of...

  5. A new convergence analysis and perturbation resilience of some accelerated proximal forward-backward algorithms with errors

    CERN Document Server

    Reem, Daniel

    2015-01-01

    Many problems in science and engineering involve, as part of their solution process, the consideration of a separable function which is the sum of two convex functions, one of them possibly non-smooth. Recently a few works have discussed inexact versions of several accelerated proximal methods aiming at solving this minimization problem. This paper shows that inexact versions of a method of Beck and Teboulle (FISTA) preserve, in a Hilbert space setting, the same (non-asymptotic) rate of convergence under some assumptions on the decay rate of the error terms. The notion of inexactness discussed here seems to be rather simple, but, interestingly, when comparing to related works, similar decay rates of the errors terms yield similar convergence rates. The derivation sheds some light on the somewhat mysterious origin of some parameters which appear in various accelerated methods. A consequence of the analysis is that the accelerated method is perturbation resilient, making it suitable, in principle, for the super...

  6. CFD Analysis and Design of Detailed Target Configurations for an Accelerator-Driven Subcritical System

    Energy Technology Data Exchange (ETDEWEB)

    Kraus, Adam; Merzari, Elia; Sofu, Tanju; Zhong, Zhaopeng; Gohar, Yousry

    2016-08-01

    High-fidelity analysis has been utilized in the design of beam target options for an accelerator driven subcritical system. Designs featuring stacks of plates with square cross section have been investigated for both tungsten and uranium target materials. The presented work includes the first thermal-hydraulic simulations of the full, detailed target geometry. The innovative target cooling manifold design features many regions with complex flow features, including 90 bends and merging jets, which necessitate three-dimensional fluid simulations. These were performed using the commercial computational fluid dynamics code STAR-CCM+. Conjugate heat transfer was modeled between the plates, cladding, manifold structure, and fluid. Steady-state simulations were performed but lacked good residual convergence. Unsteady simulations were then performed, which converged well and demonstrated that flow instability existed in the lower portion of the manifold. It was established that the flow instability had little effect on the peak plate temperatures, which were well below the melting point. The estimated plate surface temperatures and target region pressure were shown to provide sufficient margin to subcooled boiling for standard operating conditions. This demonstrated the safety of both potential target configurations during normal operation.

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

    Science.gov (United States)

    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

  8. Statistical analysis of the acceleration of Baltic mean sea-level rise, 1900-2012

    Directory of Open Access Journals (Sweden)

    Birgit Hünicke

    2016-07-01

    Full Text Available We analyse annual mean sea-level records from tide-gauges located in the Baltic and parts of the North Sea with the aim of detecting an acceleration of sea-level rise over the 20textsuperscript{th} and 21textsuperscript{st} centuries. The acceleration is estimated as a (1 fit to a polynomial of order two in time, (2 a long-term linear increase in the rates computed over gliding overlapping decadal time segments, and (3 a long-term increase of the annual increments of sea level.The estimation methods (1 and (2 prove to be more powerful in detecting acceleration when tested with sea-level records produced in global climate model simulations. These methods applied to the Baltic-Sea tide-gauges are, however, not powerful enough to detect a significant acceleration in most of individual records, although most estimated accelerations are positive. This lack of detection of statistically significant acceleration at the individual tide-gauge level can be due to the high-level of local noise and not necessarily to the absence of acceleration.The estimated accelerations tend to be stronger in the north and east of the Baltic Sea. Two hypothesis to explain this spatial pattern have been explored. One is that this pattern reflects the slow-down of the Glacial Isostatic Adjustment. However, a simple estimation of this effect suggests that this slow-down cannot explain the estimated acceleration. The second hypothesis is related to the diminishing sea-ice cover over the 20textsuperscript{th} century. The melting o of less saline and colder sea-ice can lead to changes in sea-level. Also, the melting of sea-ice can reduce the number of missing values in the tide-gauge records in winter, potentially influencing the estimated trends and acceleration of seasonal mean sea-level This hypothesis cannot be ascertained either since the spatial pattern of acceleration computed for winter and summer separately are very similar. The all-station-average-record displays an

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

    Energy Technology Data Exchange (ETDEWEB)

    Takamura, Yota, E-mail: takamura@spin.pe.titech.ac.jp [Imaging Science and Engineering Laboratory, Tokyo Institute of Technology, Yokohama (Japan); Department of Physical Electronics, Tokyo Institute of Technology, Tokyo (Japan); Akushichi, Taiju; Shuto, Yusuke; Sugahara, Satoshi, E-mail: sugahara@isl.titech.ac.jp [Imaging Science and Engineering Laboratory, Tokyo Institute of Technology, Yokohama (Japan)

    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.

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

    Science.gov (United States)

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

    2015-05-01

    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.

  11. Replication by the Epistasis Project of the interaction between the genes for IL-6 and IL-10 in the risk of Alzheimer's disease

    Directory of Open Access Journals (Sweden)

    Alvarez Victoria

    2009-08-01

    Full Text Available Abstract Background Chronic inflammation is a characteristic of Alzheimer's disease (AD. An interaction associated with the risk of AD has been reported between polymorphisms in the regulatory regions of the genes for the pro-inflammatory cytokine, interleukin-6 (IL-6, gene: IL6, and the anti-inflammatory cytokine, interleukin-10 (IL-10, gene: IL10. Methods We examined this interaction in the Epistasis Project, a collaboration of 7 AD research groups, contributing DNA samples from 1,757 cases of AD and 6,295 controls. Results We replicated the interaction. For IL6 rs2069837 AA × IL10 rs1800871 CC, the synergy factor (SF was 1.63 (95% confidence interval: 1.10–2.41, p = 0.01, controlling for centre, age, gender and apolipoprotein E ε4 (APOEε4 genotype. Our results are consistent between North Europe (SF = 1.7, p = 0.03 and North Spain (SF = 2.0, p = 0.09. Further replication may require a meta-analysis. However, association due to linkage disequilibrium with other polymorphisms in the regulatory regions of these genes cannot be excluded. Conclusion We suggest that dysregulation of both IL-6 and IL-10 in some elderly people, due in part to genetic variations in the two genes, contributes to the development of AD. Thus, inflammation facilitates the onset of sporadic AD.

  12. An end to endless forms: epistasis, phenotype distribution bias, and nonuniform evolution.

    Directory of Open Access Journals (Sweden)

    Elhanan Borenstein

    2008-10-01

    Full Text Available Studies of the evolution of development characterize the way in which gene regulatory dynamics during ontogeny constructs and channels phenotypic variation. These studies have identified a number of evolutionary regularities: (1 phenotypes occupy only a small subspace of possible phenotypes, (2 the influence of mutation is not uniform and is often canalized, and (3 a great deal of morphological variation evolved early in the history of multicellular life. An important implication of these studies is that diversity is largely the outcome of the evolution of gene regulation rather than the emergence of new, structural genes. Using a simple model that considers a generic property of developmental maps-the interaction between multiple genetic elements and the nonlinearity of gene interaction in shaping phenotypic traits-we are able to recover many of these empirical regularities. We show that visible phenotypes represent only a small fraction of possibilities. Epistasis ensures that phenotypes are highly clustered in morphospace and that the most frequent phenotypes are the most similar. We perform phylogenetic analyses on an evolving, developmental model and find that species become more alike through time, whereas higher-level grades have a tendency to diverge. Ancestral phenotypes, produced by early developmental programs with a low level of gene interaction, are found to span a significantly greater volume of the total phenotypic space than derived taxa. We suggest that early and late evolution have a different character that we classify into micro- and macroevolutionary configurations. These findings complement the view of development as a key component in the production of endless forms and highlight the crucial role of development in constraining biotic diversity and evolutionary trajectories.

  13. Converging evidence for epistasis between ANK3 and potassium channel gene KCNQ2 in bipolar disorder

    Directory of Open Access Journals (Sweden)

    Jennifer Toolan Judy

    2013-05-01

    Full Text Available 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 x 10-8. A total of 31 pairwise interactions involving combinations between two SNPs from KCNQ2 and 16 different SNPs in ANK3 were significant after permutation. Of these, 28 pairwise 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 5 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.

  14. FAM-MDR: a flexible family-based multifactor dimensionality reduction technique to detect epistasis using related individuals.

    Directory of Open Access Journals (Sweden)

    Tom Cattaert

    Full Text Available 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.

  15. Fluid-structure-interaction analysis for welded pipes with flow-accelerated corrosion wall thinning

    Energy Technology Data Exchange (ETDEWEB)

    Sun, L.; Ding, Y., E-mail: lan.sun@cnl.ca [Canadian Nuclear Laboratories, Chalk River, Ontario (Canada)

    2016-06-15

    The flow-accelerated corrosion (FAC) entrance effect results in enhanced wall thinning immediately downstream of a weld if the weld connects an upstream FAC-resistant material with a downstream less resistant material. The weld regions, especially those with local repairs, are susceptible to cracking due to the high residual stresses induced by fabrication. The combined effects of the FAC entrance effect and high stresses at a weld might compromise the structural integrity of the piping and lead to a failure. Weld degradation by FAC entrance effect has been observed at nuclear and fossil power plants. This paper describes an application using fluid-structure-interaction (FSI) modelling to study the combined effects of FAC wall thinning, weld residual stresses, and in-service loads on welded structures. Simplified cases analyzed were based on CANDU outlet feeder conditions. The analysis includes the flow and mass transfer modelling of the FAC entrance effect using computational fluid dynamics (CFD) and nonlinear structural analyses of the welded structures with wall thinning and an assumed weld residual stress and strain distribution. The FSI analyses were performed using ANSYS Workbench, an integrated platform that enables the coupling of CFD and structural analysis solutions. The obtained results show that the combination of FAC, weld residual stresses, in-service loads (including the internal pressure) and (or) extreme loads could cause high stresses and affect the integrity of the welded pipes. The present work demonstrated that the FSI modelling can be used as an effective approach to assess the integrity of welded structures. (author)

  16. Analysis of flame acceleration induced by wall friction in open tubes

    CERN Document Server

    Akkerman, V'yacheslav; Bychkov, Vitaly; Eriksson, Lars-Erik; 10.1063/1.3425646

    2012-01-01

    Spontaneous flame acceleration leading to explosion triggering in open tubes/channels due to wall friction was analytically and computationally studied. It was first demonstrated that the acceleration is effected when the thermal expansion across the flame exceeds a critical value depending on the combustion configuration. For the axisymmetric flame propagation in cylindrical tubes with both ends open, a theory of the initial (exponential) stage of flame acceleration in the quasi-isobaric limit was developed and substantiated by extensive numerical simulation of the hydrodynamics and combustion with an Arrhenius reaction. The dynamics of the flame shape, velocity, and acceleration rate, as well as the velocity profile ahead and behind the flame, have been determined.

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

    Energy Technology Data Exchange (ETDEWEB)

    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.

  18. A Reliability Accelerated Test of High-speed Punch Based on Failure Analysis

    Directory of Open Access Journals (Sweden)

    Chen Lan

    2016-01-01

    Full Text Available By analyzing the maintainability data of a certain high-speed punch, its main fault modes, such as oil/gas parts damage, parts damage and leakages, were identified. According to the fault signal measurability and the accelerated failure mechanism, the content and scheme of a reliability accelerated test (RAT were planned specifically, which was partly verified by some tests on a high-speed punch. This paper provides a basis for the RAT of high-speed punch.

  19. Accelerated Degradation Process Analysis Based on the Nonlinear Wiener Process with Covariates and Random Effects

    Directory of Open Access Journals (Sweden)

    Li Sun

    2016-01-01

    Full Text Available It is assumed that the drift parameter is dependent on the acceleration variables and the diffusion coefficient remains the same across the whole accelerated degradation test (ADT in most of the literature based on Wiener process. However, the diffusion coefficient variation would also become obvious in some applications with the stress increasing. Aiming at the phenomenon, the paper concludes that both the drift parameter and the diffusion parameter depend on stress variables based on the invariance principle of failure mechanism and Nelson assumption. Accordingly, constant stress accelerated degradation process (CSADP and step stress accelerated degradation process (SSADP with random effects are modeled. The unknown parameters in the established model are estimated based on the property of degradation and degradation increment, separately for CASDT and SSADT, by the maximum likelihood estimation approach with measurement error. In addition, the simulation steps of accelerated degradation data are provided and simulated step stress accelerated degradation data is designed to validate the proposed model compared to other models. Finally, a case study of CSADT is conducted to demonstrate the benefits of our model in the practical engineering.

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

    Science.gov (United States)

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

    2014-08-05

    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.

  1. Comprehensive transcriptome analysis reveals accelerated genic evolution in a Tibet fish, Gymnodiptychus pachycheilus.

    Science.gov (United States)

    Yang, Liandong; Wang, Ying; Zhang, Zhaolei; He, Shunping

    2014-12-26

    Elucidating the genetic mechanisms of organismal adaptation to the Tibetan Plateau at a genomic scale can provide insights into the process of adaptive evolution. Many highland species have been investigated and various candidate genes that may be responsible for highland adaptation have been identified. However, we know little about the genomic basis of adaptation to Tibet in fishes. Here, we performed transcriptome sequencing of a schizothoracine fish (Gymnodiptychus pachycheilus) and used it to identify potential genetic mechanisms of highland adaptation. We obtained totally 66,105 assembled unigenes, of which 7,232 were assigned as putative one-to-one orthologs in zebrafish. Comparative gene annotations from several species indicated that at least 350 genes lost and 41 gained since the divergence between G. pachycheilus and zebrafish. An analysis of 6,324 orthologs among zebrafish, fugu, medaka, and spotted gar identified consistent evidence for genome-wide accelerated evolution in G. pachycheilus and only the terminal branch of G. pachycheilus had an elevated Ka/Ks ratio than the ancestral branch. Many functional categories related to hypoxia and energy metabolism exhibited rapid evolution in G. pachycheilus relative to zebrafish. Genes showing signature of rapid evolution and positive selection in the G. pachycheilus lineage were also enriched in functions associated with energy metabolism and hypoxia. The first genomic resources for fish in the Tibetan Plateau and evolutionary analyses provided some novel insights into highland adaptation in fishes and served as a foundation for future studies aiming to identify candidate genes underlying the genetic bases of adaptation to Tibet in fishes.

  2. Problems and pit-falls in testing for G × E and epistasis in candidate gene studies of human behavior.

    Science.gov (United States)

    Eaves, Lindon; Verhulst, Brad

    2014-11-01

    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.

  3. The Statistical Power of Inclusive Composite Interval Mapping in Detecting Digenic Epistasis Showing Common F2 Segregation Ratios

    Institute of Scientific and Technical Information of China (English)

    Luyan Zhang; Huihui Li; Jiankang Wang

    2012-01-01

    Epistasis is a commonly observed genetic phenomenon and an important source of variation of complex traits,which could maintain additive variance and therefore assure the long-term genetic gain in breeding.Inclusive composite interval mapping (ICIM) is able to identify epistatic quantitative trait loci (QTLs) no matter whether the two interacting QTLs have any additive effects.In this article,we conducted a simulation study to evaluate detection power and false discovery rate (FDR) of ICIM epistatic mapping,by considering F2 and doubled haploid (DH) populations,different F2 segregation ratios and population sizes.Results indicated that estimations of QTL locations and effects were unbiased,and the detection power of epistatic mapping was largely affected by population size,heritability of epistasis,and the amount and distribution of genetic effects.When the same likelihood of odd (LOD) threshold was used,detection power of QTL was higher in F2 population than power in DH population; meanwhile FDR in F2 was also higher than that in DH.The increase of marker density from 10 cM to 5 cM led to similar detection power but higher FDR.In simulated populations,ICIM achieved better mapping results than multiple interval mapping (MIM) in estimation of QTL positions and effect.At the end,we gave epistatic mapping results of ICIM in one actual population in rice (Oryza sativa L.).

  4. Nuclear techniques for the analysis and dating of cultural heritage with the tandetron accelerator at the CEDAD

    Directory of Open Access Journals (Sweden)

    Lucio Calcagnile

    2014-12-01

    Full Text Available The Accelerator Mass Spectrometry technique for measuring carbon isotopes and dating artifacts, together with nuclear techniques of ion beam analysis are widely used in the field of cultural heritage owing to the great advantage of their being non-destructive. In Italy, CEDAD - CEntro Di DAtazione e Diagnostica of the University of Salento, with its tandetron accelerator of 3MV, has played a major role for over ten years, in studying materials of cultural assets requiring the determination of their elemental composition and determination of absolute chronology using radiocarbon. This study describes the Accelerator Mass Spectrometry technique used with the accelerator at CEDAD to determine age by means of radiocarbon and PIXE-PIGE techniques, and to determine elements, even in traces, present in materials. Some case studies carried out at CEDAD are reported, including those on the Riace Bronzes and Capitoline Wolf. The latter has been definitively dated to the Middle Ages, 17 centuries later than the previously attributed dating by historians. In addition, an important technical innovation is described, achieved within the framework of the IT@CHA Project enabling organic materials to be dated using only 10 μg of carbon.

  5. Monte Carlo analysis of the accelerator-driven system at Kyoto University Research Reactor Institute

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Won Kyeong; Lee, Deok Jung [Nuclear Engineering Division, Ulsan National Institute of Science and Technology, Ulsan (Korea, Republic of); Lee, Hyun Chul [VHTR Technology Development Division, Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of); Pyeon, Cheol Ho [Nuclear Engineering Science Division, Kyoto University Research Reactor Institute, Osaka (Japan); Shin, Ho Cheol [Core and Fuel Analysis Group, Korea Hydro and Nuclear Power Central Research Institute, Daejeon (Korea, Republic of)

    2016-04-15

    An accelerator-driven system consists of a subcritical reactor and a controllable external neutron source. The reactor in an accelerator-driven system can sustain fission reactions in a subcritical state using an external neutron source, which is an intrinsic safety feature of the system. The system can provide efficient transmutations of nuclear wastes such as minor actinides and long-lived fission products and generate electricity. Recently at Kyoto University Research Reactor Institute (KURRI; Kyoto, Japan), a series of reactor physics experiments was conducted with the Kyoto University Critical Assembly and a Cockcroft-Walton type accelerator, which generates the external neutron source by deuterium-tritium reactions. In this paper, neutronic analyses of a series of experiments have been re-estimated by using the latest Monte Carlo code and nuclear data libraries. This feasibility study is presented through the comparison of Monte Carlo simulation results with measurements.

  6. Monte Carlo Analysis of the Accelerator-Driven System at Kyoto University Research Reactor Institute

    Directory of Open Access Journals (Sweden)

    Wonkyeong Kim

    2016-04-01

    Full Text Available An accelerator-driven system consists of a subcritical reactor and a controllable external neutron source. The reactor in an accelerator-driven system can sustain fission reactions in a subcritical state using an external neutron source, which is an intrinsic safety feature of the system. The system can provide efficient transmutations of nuclear wastes such as minor actinides and long-lived fission products and generate electricity. Recently at Kyoto University Research Reactor Institute (KURRI; Kyoto, Japan, a series of reactor physics experiments was conducted with the Kyoto University Critical Assembly and a Cockcroft–Walton type accelerator, which generates the external neutron source by deuterium–tritium reactions. In this paper, neutronic analyses of a series of experiments have been re-estimated by using the latest Monte Carlo code and nuclear data libraries. This feasibility study is presented through the comparison of Monte Carlo simulation results with measurements.

  7. Calcium isolation from large-volume human urine samples for 41Ca analysis by accelerator mass spectrometry.

    Science.gov (United States)

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

    2013-08-01

    Calcium oxalate precipitation is the first step in preparation of biological samples for (41)Ca 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 (41)Ca administration during which human samples, collected over a lifetime, provide (41)Ca:Ca ratios that are significantly above background.

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

    Science.gov (United States)

    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

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

    Energy Technology Data Exchange (ETDEWEB)

    Chitarin, Giuseppe, E-mail: chitarin@igi.cnr.it; Aprile, Daniele [Consorzio RFX, (CNR, ENEA, INFN, Università di Padova, Acciaierie Venete SpA), Corso Stati Uniti 4, 35127 Padova (Italy); Department of Management and Engineering, University of Padova, Strad. S. Nicola 3, 36100 Vicenza (Italy); Agostinetti, Piero; Marconato, Nicolò; Marcuzzi, Diego; Serianni, Gianluigi; Veltri, Pierluigi; Zaccaria, Pierluigi [Consorzio RFX, (CNR, ENEA, INFN, Università di Padova, Acciaierie Venete SpA), Corso Stati Uniti 4, 35127 Padova (Italy)

    2016-02-15

    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.

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    White, Jonathan R.; Adams, Douglas E.; Rumsey, Mark A.

    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.ADAMSThe benefit of using a simulation model as opposed

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

    Science.gov (United States)

    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.

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

    NARCIS (Netherlands)

    Duijn, E. van; Sandman, H.; Grossouw, D.; Mocking, J.A.J.; Coulier, L.; Vaes, W.H.J.

    2014-01-01

    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.

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

    NARCIS (Netherlands)

    Duijn, E. van; Sandman, H.; Grossouw, D.; Mocking, J.A.J.; Coulier, L.; Vaes, W.H.J.

    2014-01-01

    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. H

  15. Analysis of radionuclide inventory in accelerator wastes; Analytische Bestimmung des Radionuklidinventars in Beschleunigerabfaellen

    Energy Technology Data Exchange (ETDEWEB)

    Schumann, D.; Weinreich, R.; Atchison, F.; Beer, H.F. [Paul Scherrer Inst., Villigen (Switzerland)

    2005-07-01

    For the determination of the radionuclide inventory of a PSI beam dump {gamma}-spectroscopic as well as -after chemical separation - AMS (Accelerator mass spectrometry) measurements were performed. The results serve as a validation of a calculation code which predict the radionuclide content of the waste for disposal. The chemical separation techniques necessary for isolation of several element fractions are described. (orig.)

  16. The Effects of Acceleration on High-Ability Learners: A Meta-Analysis

    Science.gov (United States)

    Steenbergen-Hu, Saiying; Moon, Sidney M.

    2011-01-01

    Current empirical research about the effects of acceleration on high-ability learners' academic achievement and social-emotional development were synthesized using meta-analytic techniques. A total of 38 primary studies conducted between 1984 and 2008 were included. The results were broken down by developmental level (P-12 and postsecondary) and…

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

    Science.gov (United States)

    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.

  18. Discovery by the Epistasis Project of an epistatic interaction between the GSTM3 gene and the HHEX/IDE/KIF11 locus in the risk of Alzheimer's disease

    NARCIS (Netherlands)

    J.M. Bullock (James); C. Medway (Christopher); M. Cortina-Borja (Mario); J.C. Turton (James); J.A. Prince (Jonathan); C.A. Ibrahim-Verbaas (Carla); M. Schuur (Maaike); M.M.B. Breteler (Monique); C.M. van Duijn (Cock); P.G. Kehoe (Patrick); R. Barber (Rachel); E. Coto (Eliecer); V. Alvarez (Victoria); P. Deloukas (Panagiotis); N. Hammond (Naomi); O. Combarros (Onofre); I. Mateo (Ignacio); D.R. Warden (Donald); M.G. Lehmann (Michael); O. Belbin (Olivia); K. Brown (Kristelle); G.K. Wilcock (Gordon); R. Heun (Reinhard); H. Kölsch (Heike); A.D. Smith; D.J. Lehmann (Donald); K. Morgan (Kevin)

    2013-01-01

    textabstractDespite recent discoveries in the genetics of sporadic Alzheimer's disease, there remains substantial " hidden heritability." It is thought that some of this missing heritability may be because of gene-gene, i.e., epistatic, interactions. We examined potential epistasis between 110 candi

  19. SHEsisEpi, a GPU-enhanced genome-wide SNP-SNP interaction scanning algorithm, efficiently reveals the risk genetic epistasis in bipolar disorder

    Institute of Scientific and Technical Information of China (English)

    Xiaohan Hu; Qiang Liu; Zhao Zhang; Zhiqiang Li; Shilin Wang; Lin He; Yongyong Shi

    2010-01-01

    @@ Dear Editor, We developed a GPU-based analytical method, named as SHEsisEpi, which purely focuses on risk epistasis in a genome-wide association study (GWAS) of complex traits, excluding the contamination of marginal effects caused by single-locus association. We analyzed the Wellcome Trust Case Control Consortium's (WTCCC)GWAS data of bipolar disorder (BPD) with 500K SNPs.

  20. Ultra-trace analysis of (41)Ca in urine by accelerator mass spectrometry: an inter-laboratory comparison.

    Science.gov (United States)

    Jackson, George S; Hillegonds, Darren J; Muzikar, Paul; Goehring, Brent

    2013-10-15

    A (41)Ca interlaboratory comparison between Lawrence Livermore National Laboratory (LLNL) and the Purdue Rare Isotope Laboratory (PRIME Lab) has been completed. Analysis of the ratios assayed by accelerator mass spectrometry (AMS) shows that there is no statistically significant difference in the ratios. Further, Bayesian analysis shows that the uncertainties reported by both facilities are correct with the possibility of a slight under-estimation by one laboratory. Finally, the chemistry procedures used by the two facilities to produce CaF2 for the cesium sputter ion source are robust and don't yield any significant differences in the final result.

  1. Future accelerators (?)

    Energy Technology Data Exchange (ETDEWEB)

    John Womersley

    2003-08-21

    I describe the future accelerator facilities that are currently foreseen for electroweak scale physics, neutrino physics, and nuclear structure. I will explore the physics justification for these machines, and suggest how the case for future accelerators can be made.

  2. Analysis of Uncertainties in Protection Heater Delay Time Measurements and Simulations in Nb$_{3}$Sn High-Field Accelerator Magnets

    CERN Document Server

    Salmi, Tiina; Marchevsky, Maxim; Bajas, Hugo; Felice, Helene; Stenvall, Antti

    2015-01-01

    The quench protection of superconducting high-field accelerator magnets is presently based on protection heaters, which are activated upon quench detection to accelerate the quench propagation within the winding. Estimations of the heater delay to initiate a normal zone in the coil are essential for the protection design. During the development of Nb3Sn magnets for the LHC luminosity upgrade, protection heater delays have been measured in several experiments, and a new computational tool CoHDA (Code for Heater Delay Analysis) has been developed for heater design. Several computational quench analyses suggest that the efficiency of the present heater technology is on the borderline of protecting the magnets. Quantifying the inevitable uncertainties related to the measured and simulated delays is therefore of pivotal importance. In this paper, we analyze the uncertainties in the heater delay measurements and simulations using data from five impregnated high-field Nb3Sn magnets with different heater geometries. ...

  3. High power beam dump project for the accelerator prototype LIPAc: cooling design and analysis

    Energy Technology Data Exchange (ETDEWEB)

    Parro Albeniz, M.

    2015-07-01

    In the nuclear fusion field running in parallel to ITER (International Thermonuclear Experimental Reactor) as one of the complementary activities headed towards solving the technological barriers, IFMIF (International Fusion Material Irradiation Facility) project aims to provide an irradiation facility to qualify advanced materials resistant to extreme conditions like the ones expected in future fusion reactors like DEMO (DEMOnstration Power Plant). IFMIF consists of two constant wave deuteron accelerators delivering a 125 mA and 40 MeV beam each that will collide on a lithium target producing an intense neutron fluence (1017 neutrons/s) with a similar spectra to that of fusion neutrons [1], [2]. This neutron flux is employed to irradiate the different material candidates to be employed in the future fusion reactors, and the samples examined after irradiation at the so called post-irradiative facilities. As a first step in such an ambitious project, an engineering validation and engineering design activity phase called IFMIF-EVEDA (Engineering Validation and Engineering Design Activities) is presently going on. One of the activities consists on the construction and operation of an accelerator prototype named LIPAc (Linear IFMIF Prototype Accelerator). It is a high intensity deuteron accelerator identical to the low energy part of the IFMIF accelerators. The LIPAc components, which will be installed in Japan, are delivered by different european countries. The accelerator supplies a 9 MeV constant wave beam of deuterons with a power of 1.125 MW, which after being characterized by different instruments has to be stopped safely. For such task a beam dump to absorb the beam energy and take it to a heat sink is needed. Spain has the compromise of delivering such device and CIEMAT (Centro de Investigaciones Energéticas Medioambientales y Tecnológicas) is responsible for such task. The central piece of the beam dump, where the ion beam is stopped, is a copper cone with

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

    Science.gov (United States)

    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

  5. Dynamic Analysis of a Timoshenko Beam Subjected to an Accelerating Mass Using Spectral Element Method

    Directory of Open Access Journals (Sweden)

    Guangsong Chen

    2014-01-01

    Full Text Available This paper presents formulations for a Timoshenko beam subjected to an accelerating mass using spectral element method in time domain (TSEM. Vertical displacement and bending rotation of the beam were interpolated by Lagrange polynomials supported on the Gauss-Lobatto-Legendre (GLL points. By using GLL integration rule, the mass matrix was diagonal and the dynamic responses can be obtained efficiently and accurately. The results were compared with those obtained in the literature to verify the correctness. The variation of the vibration frequencies of the Timoshenko and moving mass system was researched. The effects of inertial force, centrifugal force, Coriolis force, and tangential force on a Timoshenko beam subjected to an accelerating mass were investigated.

  6. Varying alpha and cosmic acceleration in Brans-Dicke-BSBM theory: stability analysis and observational tests

    CERN Document Server

    Farajollahi, H

    2012-01-01

    By integration of generalized BSBM and Brans-Dicke cosmological models, in this article, we investigate the theoretical framework of fine structure constant variation and current cosmic acceleration. We first develop a mathematical formalism to analyze the stability of the model. By employing observational data to constrain the model parameters, phase space description is performed and the attractor solutions of the model are detected. We then examine the model against observational data such as Hubble parameter dataset and quasar absorption spectra. The results confirms current universe acceleration and also predicts fine structure constant variation. Furthermore, extrapolation of the best fitted model in high redshift ($z> 15$) shows a significantly larger variation of fine structure constant in earlier epoch of the universe.

  7. A cosmographic analysis of the transition to acceleration using SN-Ia and BAO

    CERN Document Server

    Muthukrishna, Daniel

    2016-01-01

    We explore the distance-redshift relation using a cosmographic methodology, and show how the cosmographic parameters can be used to determine the redshift of transition from deceleration to acceleration. Such a transition at a low redshift occupies only a small region of the available parameter space, and the prior assumption of an early period of deceleration can significantly change the posterior constraints. We use available type Ia Supernovae (SN-Ia) and Baryon Acoustic Oscillation (BAO) data sets to determine the cosmographic deceleration $q_0$, jerk $j_0$, snap $s_0$ and lerk $l_0$ parameters. The parameters are consistent with the $\\Lambda$CDM model for a flat universe within 2-sigma. We derive constraints on the redshift of transition from deceleration to acceleration for the different expansions, and find $z_{\\rm acc} > 0.14$ at 95% confidence in the most conservative case.

  8. Harmonic analysis and field quality improvement of an HTS quadrupole magnet for a heavy ion accelerator

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Zhan; Wei, Shaoqing; Lee, Sang Jin [Uiduk University, Gyeongju (Korea, Republic of); Jo, Hyun Chul; Kim, Do Gyun; Kim, Jong Won [Rare Isotope Science Project, Institute for Basic Science, Daejeon (Korea, Republic of)

    2016-06-15

    In recent years, the iron-dominated high-temperature superconductor (HTS) quadrupole magnets are being developed for heavy ion accelerators. Field analyses for iron-dominated quadrupole magnets were based on the normal-conducting (NC) quadrupole magnet early in the development for accelerators. Some conclusions are still in use today. However, the magnetic field of iron-dominated HTS quadrupole magnets cannot fully follow these conclusions. This study established an HTS quadrupole magnet model and an NC quadrupole magnet model, respectively. The harmonic characteristics of two magnets were analyzed and compared. According to the comparison, the conventional iron-dominated quadrupole magnets can be designed for maximum field gradient; the HTS quadrupole magnet, however, should be considered with varying field gradient. Finally, the HTS quadrupole magnet was designed for the changing field gradient. The field quality of the design was improved comparing with the result of the previous study. The new design for the HTS quadrupole magnet has been suggested.

  9. Quantitative elemental analysis of an industrial mineral talc, using accelerator-based analytical technique

    Energy Technology Data Exchange (ETDEWEB)

    Olabanji, S.O. [Istituto Nazionale di Fisica Nucleare (INFN), Laboratori Nazionali di Legnaro, viale dell' Universita 2, 35020 Legnaro (Padova) (Italy) and Centre for Energy Research and Development, Obafemi Awolowo University, Ile-Ife (Nigeria)]. E-mail: skayode2002@yahoo.co.uk; Ige, A.O. [Natural History Museum, Obafemi Awolowo University, Ile-Ife (Nigeria); Mazzoli, C. [Dipartimento di Mineralogia e Petrologia, Universita di Padova, 35100 Padova (Italy); Ceccato, D. [Istituto Nazionale di Fisica Nucleare (INFN), Laboratori Nazionali di Legnaro, viale dell' Universita 2, 35020 Legnaro (Padova) (Italy); Dipartimento di Fisica, Universita di Padova, via Marzolo 8, 35100 Padova (Italy); Ajayi, E.O.B. [Department of Physics, Obafemi Awolowo University, Ile-Ife (Nigeria); De Poli, M. [Istituto Nazionale di Fisica Nucleare (INFN), Laboratori Nazionali di Legnaro, viale dell' Universita 2, 35020 Legnaro (Padova) (Italy); Moschini, G. [Istituto Nazionale di Fisica Nucleare (INFN), Laboratori Nazionali di Legnaro, viale dell' Universita 2, 35020 Legnaro (Padova) (Italy); Dipartimento di Fisica, Universita di Padova, via Marzolo 8, 35100 Padova (Italy)

    2005-10-15

    Accelerator-based technique of PIXE was employed for the determination of the elemental concentration of an industrial mineral, talc. Talc is a very versatile mineral in industries with several applications. Due to this, there is a need to know its constituents to ensure that the workers are not exposed to health risks. Besides, microscopic tests on some talc samples in Nigeria confirm that they fall within the BP British Pharmacopoeia standard for tablet formation. However, for these samples to become a local source of raw material for pharmaceutical grade talc, the precise elemental compositions should be established which is the focus of this work. Proton beam produced by the 2.5 MV AN 2000 Van de Graaff accelerator at INFN, LNL, Legnaro, Padova, Italy was used for the PIXE measurements. The results which show the concentration of different elements in the talc samples, their health implications and metabolic roles are presented and discussed.

  10. Performance analysis of superconducting rf cavities for the CERN rare isotope accelerator

    Science.gov (United States)

    Calatroni, S.; Miyazaki, A.; Rosaz, G.; Sublet, A.; Venturini Delsolaro, W.; Vaglio, R.; Palmieri, V.

    2016-09-01

    The first cryomodule of the new HIE-ISOLDE rare isotope accelerator has recently been commissioned with beam at CERN, with the second cryomodule ready for installation. Each cryomodule contains five superconducting low-beta quarter wave cavities, produced with the technology of sputtering a thin niobium film onto the copper substrate (Nb /Cu ). This technology has several benefits compared to the bulk niobium solution, but also drawbacks among which the most relevant is the increase of surface resistance with accelerating field. Recent work has established the possible connection of this phenomenon to local defects in the Nb /Cu interface, which may lead to increased thermal impedance and thus local thermal runaway. We have analyzed the performance of the HIE-ISOLDE cavities series production, as well as of a few prototypes', in terms of this model, and found a strong correlation between the rf properties and one of the model characteristic quantities, namely the total surface having increased interface thermal impedance.

  11. Analysis of a Fossil Bone from the Archaeological Settlement Malu Rosu, Romania by Accelerator Mass Spectrometry

    CERN Document Server

    Olariu, A; Hellborg, R; Stenström, K; Faarinen, M P; Persson, P; Erlandsson, B; Skog, G; Alexandrescu, E; Olariu, Agata; Popescu, Ion V.; Hellborg, Ragnar; Stenstr\\"om, Kristina; Faarinen, Mikko; Persson, Per; Erlandsson, Bengt; Alexandrescu, Emilian

    2001-01-01

    A fossil bone from the archaeological site Malu Rosu Giurgiu, in Romania has been analyzed by accelerator mass spectrometry to estimate its age by determining its $^{14}$C content. The radiocarbon age of the bone is in agreement with the date obtained by the method for age determination, based on fluorine content. This is the first radiocarbon dating for the final Neolithic period, for this archaeological settlement in the Romanian region.

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

    Energy Technology Data Exchange (ETDEWEB)

    Fredrickson, C.D.

    1977-11-15

    Various resource data are presented showing that geothermal energy has the potential of satisfying a significant 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 prospect in the state directed at timely on-line power are given. Specific actions required to realize each of these individual scenarios are identified.

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

    Science.gov (United States)

    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.

  14. An Economic Analysis of Electron Accelerators and Cobalt-60 for Irradiating Food

    OpenAIRE

    Morrison, Rosanna Mentzer

    1989-01-01

    Average costs per pound of irradiating food are similar for the electron accelerator and cobalt-60 irradiators analyzed in this study, but initial investment costs can vary by $1 million. Irradiation costs range from 0.5 to 7 cents per pound and decrease as annual volumes treated increase. Cobalt-60 is less expensive than electron beams for annual volumes below 50 million pounds. For radiation source requirements above the equivalent of 1 million curies of cobalt-60, electron beams are more e...

  15. From tracking code to analysis generalised Courant-Snyder theory for any accelerator model

    CERN Document Server

    Forest, Etienne

    2016-01-01

    This book illustrates a theory well suited to tracking codes, which the author has developed over the years. Tracking codes now play a central role in the design and operation of particle accelerators. The theory is fully explained step by step with equations and actual codes that the reader can compile and run with freely available compilers. In this book, the author pursues a detailed approach based on finite “s”-maps, since this is more natural as long as tracking codes remain at the center of accelerator design. The hierarchical nature of software imposes a hierarchy that puts map-based perturbation theory above any other methods. This is not a personal choice: it follows logically from tracking codes overloaded with a truncated power series algebra package. After defining abstractly and briefly what a tracking code is, the author illustrates most of the accelerator perturbation theory using an actual code: PTC. This book may seem like a manual for PTC; however, the reader is encouraged to explore...

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

    Science.gov (United States)

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

    2009-03-01

    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 (˜4-40 g/cm2, or ˜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.

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

    Energy Technology Data Exchange (ETDEWEB)

    Lypsch, F. [Institute for Safety Research and Reactor Technology, Juelich GmbH (Germany); Hill, R.N. [Argonne National Lab., IL (United States)

    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. Acceleration of Plasma Flows in the Solar Atmosphere Due to Magnetofluid Coupling - Simulation and Analysis

    CERN Document Server

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

    2005-01-01

    Within the framework of a two-fluid description possible pathways for the generation of fast flows (dynamical as well as steady) in the lower solar atmosphere is established. It is shown that a primary plasma flow (locally sub-Alfv\\'enic) is accelerated when interacting with emerging/ambient arcade--like closed field structures. The acceleration implies a conversion of thermal and field energies to kinetic energy of the flow. The time-scale for creating reasonably fast flows ($\\gtrsim 100$ km/s) is dictated by the initial ion skin depth while the amplification of the flow depends on local $\\beta $. It is shown, for the first time, that distances over which the flows become "fast" are $\\sim 0.01 R_s$ from the interaction surface; later the fast flow localizes (with dimensions $\\lesssim 0.05 R_S$) in the upper central region of the original arcade. For fixed initial temperature the final speed ($\\gtrsim 500 km/s$) of the accelerated flow, and the modification of the field structure are independent of the time-d...

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

    Science.gov (United States)

    Lypsch, F.; Hill, R. N.

    1995-09-01

    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 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.

  20. A new convergence analysis and perturbation resilience of some accelerated proximal forward–backward algorithms with errors

    Science.gov (United States)

    Reem, Daniel; De Pierro, Alvaro

    2017-04-01

    Many problems in science and engineering involve, as part of their solution process, the consideration of a separable function which is the sum of two convex functions, one of them possibly non-smooth. Recently a few works have discussed inexact versions of several accelerated proximal methods aiming at solving this minimization problem. This paper shows that inexact versions of a method of Beck and Teboulle (fast iterative shrinkable tresholding algorithm) preserve, in a Hilbert space setting, the same (non-asymptotic) rate of convergence under some assumptions on the decay rate of the error terms The notion of inexactness discussed here seems to be rather simple, but, interestingly, when comparing to related works, closely related decay rates of the errors terms yield closely related convergence rates. The derivation sheds some light on the somewhat mysterious origin of some parameters which appear in various accelerated methods. A consequence of the analysis is that the accelerated method is perturbation resilient, making it suitable, in principle, for the superiorization methodology. By taking this into account, we re-examine the superiorization methodology and significantly extend its scope. This work was supported by FAPESP 2013/19504-9. The second author was supported also by CNPq grant 306030/2014-4.

  1. The dopamine β-hydroxylase -1021C/T polymorphism is associated with the risk of Alzheimer's disease in the Epistasis Project

    Directory of Open Access Journals (Sweden)

    Arias-Vásquez Alejandro

    2010-11-01

    Full Text Available Abstract Background The loss of noradrenergic neurones of the locus coeruleus is a major feature of Alzheimer's disease (AD. Dopamine β-hydroxylase (DBH catalyses the conversion of dopamine to noradrenaline. Interactions have been reported between the low-activity -1021T allele (rs1611115 of DBH and polymorphisms of the pro-inflammatory cytokine genes, IL1A and IL6, contributing to the risk of AD. We therefore examined the associations with AD of the DBH -1021T allele and of the above interactions in the Epistasis Project, with 1757 cases of AD and 6294 elderly controls. Methods We genotyped eight single nucleotide polymorphisms (SNPs in the three genes, DBH, IL1A and IL6. We used logistic regression models and synergy factor analysis to examine potential interactions and associations with AD. Results We found that the presence of the -1021T allele was associated with AD: odds ratio = 1.2 (95% confidence interval: 1.06-1.4, p = 0.005. This association was nearly restricted to men DBH -1021T and the -889TT genotype (rs1800587 of IL1A: synergy factor = 1.9 (1.2-3.1, 0.005. All these results were consistent between North Europe and North Spain. Conclusions Extensive, previous evidence (reviewed here indicates an important role for noradrenaline in the control of inflammation in the brain. Thus, the -1021T allele with presumed low activity may be associated with misregulation of inflammation, which could contribute to the onset of AD. We suggest that such misregulation is the predominant mechanism of the association we report here.

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

    Directory of Open Access Journals (Sweden)

    David M. Cauvi

    2014-01-01

    Full Text Available 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.

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

    Science.gov (United States)

    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

  4. Accelerating Value Creation with Accelerators

    DEFF Research Database (Denmark)

    Jonsson, Eythor Ivar

    2015-01-01

    accelerator programs. Microsoft runs accelerators in seven different countries. Accelerators have grown out of the infancy stage and are now an accepted approach to develop new ventures based on cutting-edge technology like the internet of things, mobile technology, big data and virtual reality. It is also...... with the traditional audit and legal universes and industries are examples of emerging potentials both from a research and business point of view to exploit and explore further. The accelerator approach may therefore be an Idea Watch to consider, no matter which industry you are in, because in essence accelerators...

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

    Energy Technology Data Exchange (ETDEWEB)

    Gupta, Ramesh Chandra [Univ. of Rajasthan, Jaipur (India). Dept. of Physics

    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. Application of accelerated solvent extraction in the analysis of organic contaminants, bioactive and nutritional compounds in food and feed.

    Science.gov (United States)

    Sun, Hanwen; Ge, Xusheng; Lv, Yunkai; Wang, Anbang

    2012-05-11

    Accelerated solvent extraction (ASE) has become a popular green extraction technology for different classes of organic contaminants present in numerous kinds of food and feed for food safety. The parameters affecting ASE efficiency and application advancement of ASE in the analysis of organic contaminants, natural toxins compounds as well as bioactive and nutritional compounds in animal origin food, plant origin food and animal feed are reviewed in detail. ASE is a fully automated and reliable extraction technique with many advantages over traditional extraction techniques, so it could be especially useful for routine analyses of pollutants in food and feed.

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

    Energy Technology Data Exchange (ETDEWEB)

    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

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

    Energy Technology Data Exchange (ETDEWEB)

    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

  9. Monte Carlo analysis of accelerator-driven systems studies on spallation neutron yield and energy gain

    CERN Document Server

    Hashemi-Nezhad, S R; Westmeier, W; Bamblevski, V P; Krivopustov, M I; Kulakov, B A; Sosnin, A N; Wan, J S; Odoj, R

    2001-01-01

    The neutron yield in the interaction of protons with lead and uranium targets has been studied using the LAHET code system. The dependence of the neutron multiplicity on target dimensions and proton energy has been calculated and the dependence of the energy amplification on the proton energy has been investigated in an accelerator-driven system of a given effective multiplication coefficient. Some of the results are compared with experimental findings and with similar calculations by the DCM/CEM code of Dubna and the FLUKA code system used in CERN. (14 refs).

  10. Photoneutron Flux Measurement via Neutron Activation Analysis in a Radiotherapy Bunker with an 18 MV Linear Accelerator

    Directory of Open Access Journals (Sweden)

    Çeçen Yiğit

    2017-01-01

    Full Text Available In cancer treatment, high energy X-rays are used which are produced by linear accelerators (LINACs. If the energy of these beams is over 8 MeV, photonuclear reactions occur between the bremsstrahlung photons and the metallic parts of the LINAC. As a result of these interactions, neutrons are also produced as secondary radiation products (γ,n which are called photoneutrons. The study aims to map the photoneutron flux distribution within the LINAC bunker via neutron activation analysis (NAA using indium-cadmium foils. Irradiations made at different gantry angles (0°, 90°, 180° and 270° with a total of 91 positions in the Philips SLI-25 linear accelerator treatment room and location-based distribution of thermal neutron flux was obtained. Gamma spectrum analysis was carried out with high purity germanium (HPGe detector. Results of the analysis showed that the maximum neutron flux in the room occurred at just above of the LINAC head (1.2x105 neutrons/cm2.s which is compatible with an americium-beryllium (Am-Be neutron source. There was a 90% decrease of flux at the walls and at the start of the maze with respect to the maximum neutron flux. And, just in front of the LINAC door, inside the room, neutron flux was measured less than 1% of the maximum.

  11. Accelerating Value Creation with Accelerators

    DEFF Research Database (Denmark)

    Jonsson, Eythor Ivar

    2015-01-01

    Accelerators can help to accelerate value creation. Accelerators are short-term programs that have the objective of creating innovative and fast growing ventures. They have gained attraction as larger corporations like Microsoft, Barclays bank and Nordea bank have initiated and sponsored accelera......Accelerators can help to accelerate value creation. Accelerators are short-term programs that have the objective of creating innovative and fast growing ventures. They have gained attraction as larger corporations like Microsoft, Barclays bank and Nordea bank have initiated and sponsored...... an approach to facilitate implementation and realization of business ideas and is a lucrative approach to transform research into ventures and to revitalize regions and industries in transition. Investors have noticed that the accelerator approach is a way to increase the possibility of success by funnelling...

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

    Science.gov (United States)

    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.

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

    Energy Technology Data Exchange (ETDEWEB)

    Hassan, Md. Taufique, E-mail: thassan@tulane.edu [Department of Physics, University of Dhaka (Bangladesh); Shariff, Md. Asad [Tandem Accelerator Facilities division, INST, AERE, Savar (Bangladesh); Hossein, Amzad; Abedin, Md. Joynal [Accelerator Facilities division, AECD (Bangladesh); Fazlul Hoque, A.K.M. [Daffodil International University, Dhaka (Bangladesh); Chowdhuri, M.S. [Department of Physics, University of Dhaka (Bangladesh)

    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.

  14. Comparison of spectral analysis of vibration using commercial knock sensor and 3-axis acceleration sensor

    Science.gov (United States)

    Zieliński, Ł.; Walczak, D.; Szczurowski, K.; Radkowski, S.

    2016-09-01

    With the development of internal combustion engines, engineers attempt to reduce the noise and vibration generated. Due to the high cost of fuel, are increasingly looking for new sources of power in order to reduce costs. In diesel engines, an increasingly popular method is the admixture of propane-butane. This follows because of the price of the fuel as well as to improve the efficiency of combustion. With the development of this type of dual fuel power seems to be a reasonable study of the effects of LPG to generate noise and vibration, as well as an attempt to evaluate the combustion process. Unfortunately, too much addition of LPG causes a phenomenon called knock consisting in abnormal, uneven, explosive combustion of fuels in reciprocating engines. This phenomenon may lead to a reduction in engine performance and permanent damage. Control of the knock detection uses vibration acceleration sensors recording the high frequency ranges. Within the framework of the research conducted by the team of authors, an attempt was made to compare the vibroacoustic signals originating from the commercial knocking sensor with a three-axis acceleration sensor. These signals were subject to a quick Fourier transform in the purpose of analysing the amplitude spectra.

  15. Performance analysis and acceleration of explicit integration for large kinetic networks using batched GPU computations

    Energy Technology Data Exchange (ETDEWEB)

    Shyles, Daniel [University of Tennessee (UT); Dongarra, Jack J. [University of Tennessee, Knoxville (UTK); Guidry, Mike W. [ORNL; Tomov, Stanimire Z. [ORNL; Billings, Jay Jay [ORNL; Brock, Benjamin A. [ORNL; Haidar Ahmad, Azzam A. [ORNL

    2016-09-01

    Abstract—We demonstrate the systematic implementation of recently-developed fast explicit kinetic integration algorithms that solve efficiently N coupled ordinary differential equations (subject to initial conditions) on modern GPUs. We take representative test cases (Type Ia supernova explosions) and demonstrate two or more orders of magnitude increase in efficiency for solving such systems (of realistic thermonuclear networks coupled to fluid dynamics). This implies that important coupled, multiphysics problems in various scientific and technical disciplines that were intractable, or could be simulated only with highly schematic kinetic networks, are now computationally feasible. As examples of such applications we present the computational techniques developed for our ongoing deployment of these new methods on modern GPU accelerators. We show that similarly to many other scientific applications, ranging from national security to medical advances, the computation can be split into many independent computational tasks, each of relatively small-size. As the size of each individual task does not provide sufficient parallelism for the underlying hardware, especially for accelerators, these tasks must be computed concurrently as a single routine, that we call batched routine, in order to saturate the hardware with enough work.

  16. Comparative Analysis of Torque and Acceleration of Pre- and Post-Transmission Parallel Hybrid Drivetrains

    Directory of Open Access Journals (Sweden)

    Zulkifli Saiful A.

    2016-01-01

    Full Text Available Parallel hybrid electric vehicles (HEV can be classified according to the location of the electric motor with respect to the transmission unit for the internal combustion engine (ICE: they can be pre-transmission or posttransmission parallel hybrid. A split-axle parallel HEV – in which the ICE and electric motor provide propulsion power to different axles – is a sub-type of the post-transmission hybrid, since addition of torque and power from the two power sources occurs after the vehicle’s transmission. The term ‘through-the-road’ (TTR hybrid is also used for the split-parallel HEV, since power coupling between the ICE and electric motor is not through some mechanical device but through the vehicle itself, its wheels and the road on which it moves. The present work presents torquespeed relationship of the split-parallel hybrid and analyses simulation results of torque profiles and acceleration performance of pre-transmission and post-transmission hybrid configurations, using three different sizes of electric motor. Different operating regions of the pre-trans and post-trans motors are observed, leading to different speed and torque profiles. Although ICE average efficiency in the post-trans hybrid is slightly lower than in the pre-trans hybrid, the post-trans hybrid vehicle has better fuel economy and acceleration performance than the pre-trans hybrid vehicle.

  17. Analysis of Samples Treated by Resistance Test Method Exposed to Accelerated Aging

    Directory of Open Access Journals (Sweden)

    Irena Bates

    2015-09-01

    Full Text Available Global awareness that packaging has to be fully adequate and of high quality, is gradually increasing. That is why printing inks and substrates, which have no detrimental effect on packed products, should be considered a compulsory precondition for food and tobacco packaging. Printing inks that have been developed in the recent years, especially for food and tobacco packaging, have low-odour and low migration into the printing substrate during the drying process. Their migration into the printing substrate is within the acceptable limits and has no detrimental effect in terms of food safety. Another extremely important element of prints in high quality food and tobacco packaging is their stability, as they have to be resistant to liquids and chemicals, which are a part of packed product. The selection of an appropriate printing substrate is also extremely relevant, since the interaction of substrate with printing inks should have zero effect on the packed product and should not change the physical appearance of packaging. This paper presents the results of analysing the stability of laboratory samples printed with low-migration inks, observed immediately after the printing (unaged and two treatments of accelerated aging. The accelerated aging of prints was conducted in order to simulate conditions in which food and tobacco packaging can be found due to the prolonged indoors storage. The stability of prints was analysed based on optical characteristics by observing the prints’ relative reflectance curves.

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

    Science.gov (United States)

    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.

  19. Structural Performance Assessment Based on Statistical and Wavelet Analysis of Acceleration Measurements of a Building during an Earthquake

    Directory of Open Access Journals (Sweden)

    Mosbeh R. Kaloop

    2016-01-01

    Full Text Available This study introduces the analysis of structural health monitoring (SHM system based on acceleration measurements during an earthquake. The SHM system is applied to assess the performance investigation of the administration building in Seoul National University of Education, South Korea. The statistical and wavelet analysis methods are applied to investigate and assess the performance of the building during an earthquake shaking which took place on March 31, 2014. The results indicate that (1 the acceleration, displacement, and torsional responses of the roof recording point on the top floor of the building are more dominant in the X direction; (2 the rotation of the building has occurred at the base recording point; (3 95% of the energy content of the building response is shown in the dominant frequency range (6.25–25 Hz; (4 the wavelet spectrum illustrates that the roof vibration is more obvious and dominant during the shaking; and (5 the wavelet spectrum reveals the elasticity responses of the structure during the earthquake shaking.

  20. Ultra-trace analysis of 36Cl by accelerator mass spectrometry: an interlaboratory study.

    Science.gov (United States)

    Merchel, S; Bremser, W; Alfimov, V; Arnold, M; Aumaître, G; Benedetti, L; Bourlès, D L; Caffee, M; Fifield, L K; Finkel, R C; Freeman, S P H T; Martschini, M; Matsushi, Y; Rood, D H; Sasa, K; Steier, P; Takahashi, T; Tamari, M; Tims, S G; Tosaki, Y; Wilcken, K M; Xu, S

    2011-07-01

    A first international (36)Cl interlaboratory comparison has been initiated. Evaluation of the final results of the eight participating accelerator mass spectrometry (AMS) laboratories on three synthetic AgCl samples with (36)Cl/Cl ratios at the 10(-11), 10(-12), and 10(-13) level shows no difference in the sense of simple statistical significance. However, more detailed statistical analyses demonstrate certain interlaboratory bias and underestimation of uncertainties by some laboratories. Following subsequent remeasurement and reanalysis of the data from some AMS facilities, the round-robin data indicate that (36)Cl/Cl data from two individual AMS laboratories can differ by up to 17%. Thus, the demand for further work on harmonising the (36)Cl-system on a worldwide scale and enlarging the improvement of measurements is obvious.

  1. Cost-benefit analysis on radiotherapy services for cancer treatment, with LINAC type equipments (linear accelerators

    Directory of Open Access Journals (Sweden)

    Luiz Alberto Blois

    2014-12-01

    Full Text Available This work consists in analyzing the economic feasibility of the investment to implement a Radiotherapy sector for radiological of cancer treatment by type linear accelerators equipments, based on the case of a public hospital in São Paulo. From technical and financial details of the project and the survey reference values for health care to their procedures, the statistical outcome of treatment on patients' life expectancy and average income indicators of the state's population, were estimated to income (private and social and expenses of this health service and other elements that make up the flow of the investment project box. From these estimates we evaluated public and private investment return, ie, if it fits only on the public sector or if private sector could also implement this projects geared exclusively to free admittance.

  2. Application software of the CERN PS accelerator controls system - analysis of its cost and resources

    Energy Technology Data Exchange (ETDEWEB)

    Benincasa, G.; Daneels, A.; Heymans, P.; Serre, C.

    1986-06-01

    The CERN PS accelerators have evolved into one of the world's most sophisticated high energy physics facility. The variety of beams and their high repetition rate means that a most sophisticated controls system is required. This reflects on the application software. At the time of the completion of the new control system, nearly 1000 programs, amounting to around 450 000 lines of code, have been developed at the cost of approximately 120 man-years. The span of this software ranges from real-time application programs to special purpose development and management tools. This paper documents the cost, resources and production of this software project. These are analyzed in terms of the structure of the application software. Rules-of-thumb are suggested for estimating the required effort at various phases of the project and to define the implementation strategy.

  3. Sensitivity Analysis of Core Neutronic Parameters in Electron Accelerator-driven Subcritical Advanced Liquid Metal Reactor

    Directory of Open Access Journals (Sweden)

    Marziye Ebrahimkhani

    2016-02-01

    Full Text Available Calculation of the core neutronic parameters is one of the key components in all nuclear reactors. In this research, the energy spectrum and spatial distribution of the neutron flux in a uranium target have been calculated. In addition, sensitivity of the core neutronic parameters in accelerator-driven subcritical advanced liquid metal reactors, such as electron beam energy (Ee and source multiplication coefficient (ks, has been investigated. A Monte Carlo code (MCNPX_2.6 has been used to calculate neutronic parameters such as effective multiplication coefficient (keff, net neutron multiplication (M, neutron yield (Yn/e, energy constant gain (G0, energy gain (G, importance of neutron source (φ∗, axial and radial distributions of neutron flux, and power peaking factor (Pmax/Pave in two axial and radial directions of the reactor core for four fuel loading patterns. According to the results, safety margin and accelerator current (Ie have been decreased in the highest case of ks, but G and φ∗ have increased by 88.9% and 21.6%, respectively. In addition, for LP1 loading pattern, with increasing Ee from 100 MeV up to 1 GeV, Yn/e and G improved by 91.09% and 10.21%, and Ie and Pacc decreased by 91.05% and 10.57%, respectively. The results indicate that placement of the Np–Pu assemblies on the periphery allows for a consistent keff because the Np–Pu assemblies experience less burn-up.

  4. RECIRCULATING ACCELERATION

    Energy Technology Data Exchange (ETDEWEB)

    BERG,J.S.; GARREN,A.A.; JOHNSTONE,C.

    2000-04-07

    This paper compares various types of recirculating accelerators, outlining the advantages and disadvantages of various approaches. The accelerators are characterized according to the types of arcs they use: whether there is a single arc for the entire recirculator or there are multiple arcs, and whether the arc(s) are isochronous or non-isochronous.

  5. LIBO accelerates

    CERN Multimedia

    2002-01-01

    The prototype module of LIBO, a linear accelerator project designed for cancer therapy, has passed its first proton-beam acceleration test. In parallel a new version - LIBO-30 - is being developed, which promises to open up even more interesting avenues.

  6. The use of electrostatic accelerator for material analysis; Uso de un acelerador electrostatico para el analisis de materiales

    Energy Technology Data Exchange (ETDEWEB)

    Climet, A.; Agullo, F.; Espejo, O.; Pascual, C.

    2001-07-01

    An electrostatic accelerator is a very versatile tool for the analysis of the elemental composition of materials by means of ion-beam based analytical techniques. These techniques known as IBA (ion beam analysis) are widely used as a quantitative and non destructive characterization of almost any material down to depth of 10{mu}m below the surface and with a depth resolution at the surface from 2 to 20 nm. Their applications cover a wide range of areas such as: materials science, microelectronics, corrosion studies, polymer science, environmental studies, biomedical sciences and art and archaeology. In this work the general physical principles of IBA are reviewed and its capabilities are illustrated with a selection of examples. (Author) 21 refs.

  7. Accelerating Inspire

    CERN Document Server

    AUTHOR|(CDS)2266999

    2017-01-01

    CERN has been involved in the dissemination of scientific results since its early days and has continuously updated the distribution channels. Currently, Inspire hosts catalogues of articles, authors, institutions, conferences, jobs, experiments, journals and more. Successful orientation among this amount of data requires comprehensive linking between the content. Inspire has lacked a system for linking experiments and articles together based on which accelerator they were conducted at. The purpose of this project has been to create such a system. Records for 156 accelerators were created and all 2913 experiments on Inspire were given corresponding MARC tags. Records of 18404 accelerator physics related bibliographic entries were also tagged with corresponding accelerator tags. Finally, as a part of the endeavour to broaden CERN's presence on Wikipedia, existing Wikipedia articles of accelerators were updated with short descriptions and links to Inspire. In total, 86 Wikipedia articles were updated. This repo...

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

    Energy Technology Data Exchange (ETDEWEB)

    Able, CM; Baydush, AH; Nguyen, C; Munley, MT [Wake Forest School of Medicine, Department of Radiation Oncology, Winston Salem, NC (United States); Gersh, J [Gibbs Cancer Center and Research Institute, Spartenburg Regional Medical Ce, Spartenburg, SC (United States); Ndlovu, A; Rebo, I [John Theuer Cancer Center, Hackensack University Medical Center, Hackensack, NJ (United States); Booth, J; Perez, M [North Sydney Cancer Center, Royal North Shore Hospital, Sydney, St Leonards (Australia); Sintay, B [Cone Health Cancer Center, Greensboro, NC (United States)

    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. Pharmacokinetic analysis of 14C-ursodiol in newborn infants using accelerator mass spectrometry.

    Science.gov (United States)

    Gordi, Toufigh; Baillie, Rebecca; Vuong, Le T; Abidi, Saira; Dueker, Stephen; Vasquez, Herbert; Pegis, Priscilla; Hopper, Andrew O; Power, Gordon G; Blood, Arlin B

    2014-09-01

    Pharmacokinetic studies in the neonatal population are often limited by the small volume of blood that can be collected. The high sensitivity of (14) C-accelerator mass spectrometry (AMS) enables pharmacokinetic studies to be conducted with greatly reduced sample volumes. We demonstrated the utility of AMS in infants by studying the plasma pharmacokinetic behavior of nanogram doses of (14) C-ursodiol administered as a non-perturbing microdose or as a microtracer with therapeutic doses of non-labeled ursodiol in infants. Five non-cholestatic infants were administered 3 consecutive oral microdoses of (14) C-ursodiol: 8 ng (1.0 nCi), 26 ng (3.3 nCi), and 80 ng (10 nCi) 48 hours apart. Three additional infants with cholestasis were administered a single 80 ng (10.0 nCi) oral dose of (14) C-ursodiol together with a therapeutic dose of 40 mg/kg of non-labeled ursodiol. A pharmacokinetic model describing ursodiol concentrations was developed using nonlinear mixed-effects modeling. The pharmacokinetics of ursodiol in this pilot study were best described by a two-compartment model with first-order elimination. This study demonstrates the feasibility and utility of microdose and microtrace methodology in pediatric research.

  10. Analysis of accelerated death benefit claims at a Japanese life insurance company.

    Science.gov (United States)

    Kobayashi, Miyoharu; Kudomi, Hiroyuki

    2002-01-01

    We studied accelerated death benefit (ADB) claims at the Dai-ichi Mutual Life Insurance Company (Dai-ichi Life). The ADB provision is designed to pay all or a portion of the death benefit if the insured is expected to die within 6 months. Dai-ichi Life paid 243 ADB claims and did not pay 17 ADB claims between December 1994 and March 1998. Of the 260 ADB claims, 253 (97.3%) were caused by malignant neoplasm, 2 by intracranial hemorrhage, 2 by angina pectoris, 1 by dilated cardiomyopathy, 1 by hepatic cirrhosis, and 1 by bleeding gastric ulcer. The age range of the 243 paid claims at the time when the attendant physician predicted a life expectancy below 6 months was 21.6-72.6 years (48.7 +/- 8.7 years [Mean +/- SD]). By the end of March 2000, 236 cases were followed up among the above 243 paid ADB claims. Of the 236 followed-up cases, 149 (63.1%) died within 6 months and 203 (86.0%) died within 1 year. The range of survival periods of these 236 cases was 6-1516 days (210 +/- 237 days). Of the 217 dead cases due to malignant neoplasm, 45 (20.7%) died of gastric cancer, 44 (20.3%) of lung cancer, 24 (11.1%) of liver cancer, 16 (7.4%) of colon cancer, 13 (6.0%) of rectum cancer, and 12 (5.5%) of pancreatic cancer.

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

    Science.gov (United States)

    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.

  12. Optimisation analysis and improvement of the effective beam sizes in Accelerator Test Facility 2

    CERN Document Server

    AUTHOR|(CDS)2082063; Kisiel, Adam

    2016-10-20

    A lepton linear collider is considered by the accelerator and particle physics communities as an appropriate machine to perform high precision particle physics research in the TeV energy regime. There are two proposals for the future e+e- linear collider: the Compact Linear Collider (CLIC) and the International Linear Collider (ILC), both developed by two wide international collaborations with strong overlap between them. Both designs satisfy the particle physics requirements. At the TeV energy regime the cross sections of many processes of interest are small, therefore large luminosities on the order of 10^{34} cm^{-2}s^{-1} at the interaction point (IP) are required to deliver the required event rates. The luminosity inversely depends on the transverse size of the colliding beams which restricts the beam sizes at the IP to the nanometer level. The strong focusing of the beams occurs in the final focus system (FFS), the most inner part of a linear collider, where the beams are focused at the IP by means of t...

  13. Analysis and comparison between electric and magnetic power couplers for accelerators in Free Electron Lasers (FEL)

    Science.gov (United States)

    Serpico, C.; Grudiev, A.; Vescovo, R.

    2016-10-01

    Free-electron lasers represent a new and exciting class of coherent optical sources possessing broad wavelength tunability and excellent optical-beam quality. The FERMI seeded free-electron laser (FEL), located at the Elettra laboratory in Trieste, is driven by a 200 m long, S-band linac: the high energy part of the linac is equipped with 6 m long backward traveling wave (BTW) structures. The structures have small iris radius and a nose cone geometry which allows for high gradient operation. Development of new high-gradient, S-band accelerating structures for the replacement of the existing BTWs is under consideration. This paper investigates two possible solutions for the RF power couplers suitable for a linac driven FEL which require reduced wakefields effects, high operating gradient and very high reliability. The first part of the manuscript focuses on the reduction of residual field asymmetries, while in the second analyzes RF performances, the peak surface fields and the expected breakdown rate. In the conclusion, two solutions are compared and pros and cons are highlighted.

  14. An analysis of spatially varying turbulent Prandtl number in a flow with local acceleration and deceleration

    Science.gov (United States)

    Jung, Eunbum; Lee, Wook; Kang, Seongwon; Iaccarino, Gianluca

    2015-11-01

    The turbulent Prandtl number (Prt) is an important parameter in turbulent flows used in many engineering models for heat transfer. In the present study, spatial variation of Prt in a wall-bounded turbulent flow is investigated using DNS. We derived a form of Prt applicable to a general flow configuration, using the least-square method in a manner consistent with the turbulent viscosity model in LES. For a flow subject to local acceleration and deceleration induced by the wall geometry, we performed a parametric study for the Reynolds number, Prandtl number and a geometric factor using DNS. A comparison of the data from DNS and RANS with a constant Prt indicates the potential of improved RANS predictions using the present variable Prt subject to the local flow field. Also, it is observed that the local pressure gradient has an important effect on the Prt field. From the flow statistics, a few flow variables showing higher correlations with Prt are identified. An elementary model for Prt is devised, and used for RANS prediction producing a more accurate prediction of the heat transfer rate. Corresponding author

  15. Accelerated stress testing and diagnostic analysis of degradation in CdTe solar cells

    Science.gov (United States)

    Albin, David S.

    2008-08-01

    Solar cell module reliability is inextricably linked to cell-level reliability. This is particularly so with thin-film technologies. In CdTe, reliability issues historically associate with back contact stability and the use of Cu as an extrinsic dopant. Using a simple approach by which identical cells are heated under open-circuit bias and 1-sun illumination, degradation activation energies of 0.63 and 2.94 eV in laboratory-scale CdS/CdTe devices were identified in the accelerated stress temperature range of 60 to 120 °C. At lower stress temperatures, cell performance changes were linearly correlated with changes in both fill factor (FF) and short-circuit current (Jsc). At higher stress temperatures, changes in efficiency were correlated with changes in FF and open-circuit voltage (Voc). The measured activation energy of 0.63 is associated with Cu-diffusion. During the early stage of stress testing, which may provide additional back contact annealing, improvements in FF were due to Cu-diffusion. Decreased performance observed at longer stress times (decreased FF and Voc), according to a two-diode Pspice model, were due to both increased space-charge recombination (near the junction) and decreased recombination in the bulk. Kirkendall void formation (S-outdiffusion) at the CdS/CdTe interface is given as responsible for the 2.9 eV degradation mechanism.

  16. Economic analysis of opportunities to accelerate Alzheimer's disease research and development.

    Science.gov (United States)

    Scott, Troy J; O'Connor, Alan C; Link, Albert N; Beaulieu, Travis J

    2014-04-01

    The development of disease-modifying treatments for Alzheimer's disease (AD) faces a number of barriers. Among these are the lack of surrogate biomarkers, the exceptional size and duration of clinical trials, difficulties in identifying appropriate populations for clinical trials, and the limitations of monotherapies in addressing such a complex multifactorial disease. This study sets out to first estimate the consequent impact on the expected cost of developing disease-modifying treatments for AD and then to estimate the potential benefits of bringing together industry, academic, and government stakeholders to co-invest in, for example, developing better biomarkers and cognitive assessment tools, building out advanced registries and clinical trial-readiness cohorts, and establishing clinical trial platforms to investigate combinations of candidate drugs and biomarkers from the portfolios of multiple companies. Estimates based on interviews with experts on AD research and development suggest that the cost of one new drug is now $5.7 billion (95% confidence interval (CI) $3.7-9.5 billion) and could be reduced to $2.0 billion (95% CI $1.5-2.9 billion). The associated acceleration in the arrival of disease-modifying treatments could reduce the number of case years of dementia by 7.0 million (95% CI 4.4-9.4 million) in the United States from 2025 through 2040.

  17. A Bayesian approach to joint analysis of multivariate longitudinal data and parametric accelerated failure time.

    Science.gov (United States)

    Luo, Sheng

    2014-02-20

    Impairment caused by Parkinson's disease (PD) is multidimensional (e.g., sensoria, functions, and cognition) and progressive. Its multidimensional nature precludes a single outcome to measure disease progression. Clinical trials of PD use multiple categorical and continuous longitudinal outcomes to assess the treatment effects on overall improvement. A terminal event such as death or dropout can stop the follow-up process. Moreover, the time to the terminal event may be dependent on the multivariate longitudinal measurements. In this article, we consider a joint random-effects model for the correlated outcomes. A multilevel item response theory model is used for the multivariate longitudinal outcomes and a parametric accelerated failure time model is used for the failure time because of the violation of proportional hazard assumption. These two models are linked via random effects. The Bayesian inference via MCMC is implemented in 'BUGS' language. Our proposed method is evaluated by a simulation study and is applied to DATATOP study, a motivating clinical trial to determine if deprenyl slows the progression of PD. © 2013 The authors. Statistics in Medicine published by John Wiley & Sons, Ltd.

  18. Analysis of efficient ion acceleration with multi-picosecond LFEX laser

    Science.gov (United States)

    Iwata, Natsumi; Yogo, Akifumi; Mima, Kunioki; Tosaki, Shota; Koga, Keisuke; Nagatomo, Hideo; Kishimoto, Yasuaki; Nishimura, Hiroaki; Azechi, Horishi

    2016-10-01

    We demonstrate an efficient proton acceleration reaching 30 MeV by using high contrast, kilojoule, picosecond laser LFEX at the peak intensity of 2.3 ×1018 W/cm2. Owing to the large spot size of 70 μm FWHM, the target foil expands one-dimensionally during the multi-picosecond pulse duration time, which yields the electron heating beyond the ponderomotive scaling observed in the experiment. We present by a 1D PIC simulation that the electron temperature evolves in time while the electrons recirculate between the front and rear surfaces of the expanding plasma. A theoretical calculation for the ion maximum energy that takes the temperature evolution into account agrees with the experimental result quantitatively. Being supported by the experiment and simulation, our theoretical model for the non-isothermal plasma expansion dynamics will provide an important basis for understanding the multi-picosecond high intensity laser-plasma interactions and for various applications such as energetic ion beam generation for medical applications and fast ignition-based laser fusion.

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

    Science.gov (United States)

    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.

  20. Confronting Twin Paradox Acceleration

    Science.gov (United States)

    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 .

  1. Analysis of breakdown on thermal and electrical measurements for SPIDER accelerating grids

    Energy Technology Data Exchange (ETDEWEB)

    Pesce, Alberto, E-mail: alberto.pesce@igi.cnr.it [Consorzio RFX - Associazione EURATOM-ENEA per la fusione, Corso Stati Uniti 4, 35127 Padova (Italy); Pomaro, Nicola [Consorzio RFX - Associazione EURATOM-ENEA per la fusione, Corso Stati Uniti 4, 35127 Padova (Italy)

    2011-10-15

    The PRIMA test facility, under realization in Padova, includes a full size plasma source prototype for ITER, called SPIDER (Source for the Production of Ions of Deuterium Extracted from Radio Frequency plasma). The effects of breakdown in the electrical insulation inside the ion source are analyzed with particular care to the embedded diagnostic system, i.e. the thermal and electrical measurements installed on the grids and ion source case and transferred by multipolar cables to the acquisition system, located inside the 100 kV insulated deck and hosting the ion source power supply, the signal conditioning and the acquisition cubicles. The breakdown affects strongly the measurements, so it has to be mitigated in order to guarantee adequate reliability of the whole measurement set. A parametric study has been carried out on a detailed circuital model for fast transients, implemented using SimPowerSystems{sup TM} tool of Matlab Simulink code. The model includes all the relevant conductors of the subsystems downstream the insulating transformer of the Accelerating Grids Power Supply (AGPS), i.e. the AGPS rectifier, the multipolar transmission line, the 100 kV High Voltage Deck, the ion source power supply and the ion source itself. In particular all the magnetic and capacitive couplings have been computed by a proper 2D fem model. The optimization of the cabling layout, of the wire screening and of the protection devices, like surge arresters and resistors, has been carried out through the accurate modeling of the circuit. The energy dissipated on each ion source surge arrester is estimated and adequate TSD (transient suppression devices) are selected. A peculiar and difficult to satisfy requirement is the high number of surges that the TSD has to withstand. Breakdowns between components polarized at different voltages have been considered, in order to inspect the worst condition during a breakdown.

  2. Mediation Analysis with Survival Outcomes: Accelerated Failure Time Versus Proportional Hazards Models

    Directory of Open Access Journals (Sweden)

    Lois A Gelfand

    2016-03-01

    Full Text Available 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.

  3. Horizontal Accelerator

    Data.gov (United States)

    Federal Laboratory Consortium — The Horizontal Accelerator (HA) Facility is a versatile research tool available for use on projects requiring simulation of the crash environment. The HA Facility is...

  4. Three-dimensional multi-physics analysis and commissioning frequency tuning strategy of a radio-frequency quadrupole accelerator

    Science.gov (United States)

    Ma, Wei; Lu, Liang; Liu, Ting; Xu, Xianbo; Sun, Liepeng; Li, Chenxing; Shi, Longbo; Wang, Wenbin; He, Yuan; Zhao, Hongwei

    2017-09-01

    The resonant frequency stability of the radio frequency quadrupole (RFQ) is an important concern during commissioning. The power dissipated on the RFQ internal surface will heat the cavity and lead to a temperature rise and a structural deformation, especially in the continuous wave (CW) RFQs, which will cause the resonant frequency shifts. It is important to simulate the temperature rise, the deformation and the frequency shift of the RFQ cavity. The cooling water takes away the power to maintain the frequency stability. Meanwhile, the RFQ resonant frequency can be tuned by adjusting the water temperature. In this paper, a detailed three-dimensional multi-physics analysis of the Low Energy Accelerator Facility (LEAF) RFQ will be presented and a commissioning frequency tuning strategy will be studied.

  5. Monitoring the FLASH Cryomodule Transportation from DESY Hamburg to CEA Saclay: Coupler Contact, Vacuum, Acceleration and Vibration Analysis

    Energy Technology Data Exchange (ETDEWEB)

    Barbanotti, S.; Bosotti, A.; Fusetti, M.; Michelato, P.; /INFN, Milan /LASA, Segrate; Bertolini, A.; /Hannover, Max Planck Inst. Grav.; Berry, S.; Dorlot, M.; Madec, C.; Napoly, O.; /Saclay; Amirikas, R.; Boehnert, M.; /DESY /Fermilab

    2009-05-01

    With a view to the series production of one hundred, 12 m long XFEL 1.3 GHz cryomodules and their transportation from the assembly site at CEA Saclay (F) to the installation site at DESY Hamburg (D) a test transportation of a FLASH cryomodule has been performed, in the condition foreseen for the mass transportation. The present study examines the stresses induced on the module and verifies the damping capabilities of the transport frame in order to minimize risk of damage to the most critical components. During the transportation, acceleration and vibration have been monitored as well as coupler antenna contacts and vacuum performances. This paper describes the analysis performed and compares those results to the data of a similar transportation study at Fermilab for the CM1 cryomodule.

  6. Error analysis of linear optics measurements via turn-by-turn beam position data in circular accelerators

    CERN Document Server

    Franchi, Andrea

    2016-01-01

    Many advanced techniques have been developed, tested and implemented in the last decades in almost all circular accelerators across the world to measure the linear optics. However, the greater availability and accuracy of beam diagnostics and the ever better correction of linear magnetic lattice imperfections (beta beating at 1% level and coupling at 0.1%) are reaching what seems to be the intrinsic accuracy and precision of different measurement techniques. This paper aims to highlight and quantify, when possible, the limitations of one standard method, the harmonic analysis of turn-by-turn beam position data. To this end, new analytic formulas for the evaluation of lattice parameters modified by focusing errors are derived. The unexpected conclusion of this study is that for the ESRF storage ring (and possibly for any third generation light source operating at ultra-low coupling and with similar diagnostics), measurement and correction of linear optics via orbit beam position data are to be preferred to the...

  7. Future accelerators

    CERN Document Server

    Hübner, K

    1999-01-01

    An overview of the various schemes for electron-positron linear colliders is given and the status of the development of key components and the various test facilities is given. The present studies of muon-muon colliders and very large hadron colliders are summarized including the plans for component development and tests. Accelerator research and development to achieve highest gradients in linear accelerators is outlined. (44 refs).

  8. Time-Stretch Accelerated Processor for Real-time, In-service, Signal Analysis

    DEFF Research Database (Denmark)

    Lonappan, Cejo K.; Buckley, Brandon W.; Adam, Jost

    2014-01-01

    We demonstrate real-time, in-service, digital signal analysis of 10 Gbit/s data using a 1.2 Tbit/s burst-mode digital processor. The processor comprises a time-stretch front-end and a custom data acquisition and real-time signal processing back- end. Experimental demonstration of real-time, in-service......, signal integrity analysis of streaming video packets at 10 Gbit/s is presented....

  9. Accelerated partial-breast irradiation with interstitial implants. Analysis of factors affecting cosmetic outcome

    Energy Technology Data Exchange (ETDEWEB)

    Ott, Oliver J.; Lotter, Michael; Fietkau, Rainer; Strnad, Vratislav [University Hospital Erlangen (Germany). Dept. of Radiation Oncology

    2009-03-15

    Purpose: To analyze patient-, disease-, and treatment-related factors for their impact on cosmetic outcome (CO) after interstitial multicatheter accelerated partial-breast irradiation (APBI). Patients and Methods: Between April 2001 and January 2005, 171 patients with early breast cancer were recruited in Erlangen for this subanalysis of the German-Austrian APBI phase II-trial. 58% (99/171) of the patients received pulsed-dose-rate (PDR), and 42% (72/171) high-dose-rate (HDR) brachytherapy. Prescribed reference dose for HDR brachytherapy was 32 Gy in eight fractions of 4 Gy, twice daily. Prescribed reference dose in PDR brachytherapy was 49.8 Gy in 83 consecutive fractions of 0.6 Gy each hour. Total treatment time was 3-4 days. Endpoint of this evaluation was the CO, graded as excellent, good, fair, or poor. Patients were divided in two groups with an excellent (n = 102) or nonexcellent (n = 69) cosmetic result. Various factors were analyzed for their impact on excellent CO. Results: The median follow-up time was 52 months (range: 21-91 months). Cosmetic results were rated as excellent in 59.6% (102/171), good in 29.8% (51/171), fair in 9.9% (17/171), and poor in 0.6% (1/171). The initial cosmetic status was significantly worse for the nonexcellent CO group (p = 0.000). The percentage of patients who received PDR brachytherapy APBI was higher in the nonexcellent CO group (68.1% vs. 51%; p = 0.026). Acute toxicity was higher in the nonexcellent CO group (24.6% vs. 12.7%; p = 0.045). Furthermore, the presence of any late toxicity was found to be associated with a worse cosmetic result (65.2% vs. 18.6%; p = 0.000). In detail, the appearance of skin hyperpigmentation (p = 0.034), breast tissue fibrosis (p = 0.000), and telangiectasia (p = 0.000) had a negative impact on CO. Conclusion: The initial, surgery-associated cosmetic status, brachytherapy modality, and the presence of acute and late toxicities were found to have an impact on overall CO. Our data have proven

  10. Statistical epistasis and progressive brain change in schizophrenia: an approach for examining the relationships between multiple genes.

    Science.gov (United States)

    Andreasen, N C; Wilcox, M A; Ho, B-C; Epping, E; Ziebell, S; Zeien, E; Weiss, B; Wassink, T

    2012-11-01

    Although schizophrenia is generally considered to occur as a consequence of multiple genes that interact with one another, very few methods have been developed to model epistasis. Phenotype definition has also been a major challenge for research on the genetics of schizophrenia. In this report, we use novel statistical techniques to address the high dimensionality of genomic data, and we apply a refinement in phenotype definition by basing it on the occurrence of brain changes during the early course of the illness, as measured by repeated magnetic resonance scans (i.e., an 'intermediate phenotype.') The method combines a machine-learning algorithm, the ensemble method using stochastic gradient boosting, with traditional general linear model statistics. We began with 14 genes that are relevant to schizophrenia, based on association studies or their role in neurodevelopment, and then used statistical techniques to reduce them to five genes and 17 single nucleotide polymorphisms (SNPs) that had a significant statistical interaction: five for PDE4B, four for RELN, four for ERBB4, three for DISC1 and one for NRG1. Five of the SNPs involved in these interactions replicate previous research in that, these five SNPs have previously been identified as schizophrenia vulnerability markers or implicate cognitive processes relevant to schizophrenia. This ability to replicate previous work suggests that our method has potential for detecting a meaningful epistatic relationship among the genes that influence brain abnormalities in schizophrenia.

  11. Negative epistasis between the malaria-protective effects of alpha+-thalassemia and the sickle cell trait.

    Science.gov (United States)

    Williams, Thomas N; Mwangi, Tabitha W; Wambua, Sammy; Peto, Timothy E A; Weatherall, David J; Gupta, Sunetra; Recker, Mario; Penman, Bridget S; Uyoga, Sophie; Macharia, Alex; Mwacharo, Jedidah K; Snow, Robert W; Marsh, Kevin

    2005-11-01

    The hemoglobinopathies, disorders of hemoglobin structure and production, protect against death from malaria. In sub-Saharan Africa, two such conditions occur at particularly high frequencies: presence of the structural variant hemoglobin S and alpha(+)-thalassemia, a condition characterized by reduced production of the normal alpha-globin component of hemoglobin. Individually, each is protective against severe Plasmodium falciparum malaria, but little is known about their malaria-protective effects when inherited in combination. We investigated this question by studying a population on the coast of Kenya and found that the protection afforded by each condition inherited alone was lost when the two conditions were inherited together, to such a degree that the incidence of both uncomplicated and severe P. falciparum malaria was close to baseline in children heterozygous with respect to the mutation underlying the hemoglobin S variant and homozygous with respect to the mutation underlying alpha(+)-thalassemia. Negative epistasis could explain the failure of alpha(+)-thalassemia to reach fixation in any population in sub-Saharan Africa.

  12. Sex-specific mitonuclear epistasis and the evolution of mitochondrial bioenergetics, ageing, and life history in seed beetles.

    Science.gov (United States)

    Đorđević, Mirko; Stojković, Biljana; Savković, Uroš; Immonen, Elina; Tucić, Nikola; Lazarević, Jelica; Arnqvist, Göran

    2017-02-01

    The role of mitochondrial DNA for the evolution of life-history traits remains debated. We examined mitonuclear effects on the activity of the multisubunit complex of the electron transport chain (ETC) involved in oxidative phosphorylation (OXPHOS) across lines of the seed beetle Acanthoscelides obtectus selected for a short (E) or a long (L) life for more than >160 generations. We constructed and phenotyped mitonuclear introgression lines, which allowed us to assess the independent effects of the evolutionary history of the nuclear and the mitochondrial genome. The nuclear genome was responsible for the largest share of divergence seen in ageing. However, the mitochondrial genome also had sizeable effects, which were sex-specific and expressed primarily as epistatic interactions with the nuclear genome. The effects of mitonuclear disruption were largely consistent with mitonuclear coadaptation. Variation in ETC activity explained a large proportion of variance in ageing and life-history traits and this multivariate relationship differed somewhat between the sexes. In conclusion, mitonuclear epistasis has played an important role in the laboratory evolution of ETC complex activity, ageing, and life histories and these are closely associated. The mitonuclear architecture of evolved differences in life-history traits and mitochondrial bioenergetics was sex-specific.

  13. Data Streaming for Metabolomics: Accelerating Data Processing and Analysis from Days to Minutes.

    Science.gov (United States)

    Montenegro-Burke, J Rafael; Aisporna, Aries E; Benton, H Paul; Rinehart, Duane; Fang, Mingliang; Huan, Tao; Warth, Benedikt; Forsberg, Erica; Abe, Brian T; Ivanisevic, Julijana; Wolan, Dennis W; Teyton, Luc; Lairson, Luke; Siuzdak, Gary

    2017-01-17

    The speed and throughput of analytical platforms has been a driving force in recent years in the "omics" technologies and while great strides have been accomplished in both chromatography and mass spectrometry, data analysis times have not benefited at the same pace. Even though personal computers have become more powerful, data transfer times still represent a bottleneck in data processing because of the increasingly complex data files and studies with a greater number of samples. To meet the demand of analyzing hundreds to thousands of samples within a given experiment, we have developed a data streaming platform, XCMS Stream, which capitalizes on the acquisition time to compress and stream recently acquired data files to data processing servers, mimicking just-in-time production strategies from the manufacturing industry. The utility of this XCMS Online-based technology is demonstrated here in the analysis of T cell metabolism and other large-scale metabolomic studies. A large scale example on a 1000 sample data set demonstrated a 10 000-fold time savings, reducing data analysis time from days to minutes. Further, XCMS Stream has the capability to increase the efficiency of downstream biochemical dependent data acquisition (BDDA) analysis by initiating data conversion and data processing on subsets of data acquired, expanding its application beyond data transfer to smart preliminary data decision-making prior to full acquisition.

  14. Data Streaming for Metabolomics: Accelerating Data Processing and Analysis from Days to Minutes

    Science.gov (United States)

    2016-01-01

    The speed and throughput of analytical platforms has been a driving force in recent years in the “omics” technologies and while great strides have been accomplished in both chromatography and mass spectrometry, data analysis times have not benefited at the same pace. Even though personal computers have become more powerful, data transfer times still represent a bottleneck in data processing because of the increasingly complex data files and studies with a greater number of samples. To meet the demand of analyzing hundreds to thousands of samples within a given experiment, we have developed a data streaming platform, XCMS Stream, which capitalizes on the acquisition time to compress and stream recently acquired data files to data processing servers, mimicking just-in-time production strategies from the manufacturing industry. The utility of this XCMS Online-based technology is demonstrated here in the analysis of T cell metabolism and other large-scale metabolomic studies. A large scale example on a 1000 sample data set demonstrated a 10 000-fold time savings, reducing data analysis time from days to minutes. Further, XCMS Stream has the capability to increase the efficiency of downstream biochemical dependent data acquisition (BDDA) analysis by initiating data conversion and data processing on subsets of data acquired, expanding its application beyond data transfer to smart preliminary data decision-making prior to full acquisition. PMID:27983788

  15. Time-Stretch Accelerated Processor for Real-time, In-service, Signal Analysis

    DEFF Research Database (Denmark)

    Lonappan, Cejo K.; Buckley, Brandon W.; Adam, Jost

    2014-01-01

    We demonstrate real-time, in-service, digital signal analysis of 10 Gbit/s data using a 1.2 Tbit/s burst-mode digital processor. The processor comprises a time-stretch front-end and a custom data acquisition and real-time signal processing back- end. Experimental demonstration of real-time, in...

  16. A comparative study of an accelerated life-test model and a toxicokinetics-based model for the analysis of Porcellio scaber survival data.

    Science.gov (United States)

    Ren, Shijin

    2004-01-01

    Statistical models have long been used for reliability analysis and risk assessment. In the present study, an accelerated life-test model was used to analyze a set of dose-time-response data obtained with the terrestrial isopod Porcellio scaber. Survival data were experimentally obtained by exposing P. scaber to diazinon (a nonpersistent insecticide) at six concentrations between 2 and 11.31 microg/g (toxicant/soil). Survival data are presented on a weekly basis. The accelerated life-test model assumed a log-normal distribution and constant variance across all diazinon concentrations. Model parameters were obtained by maximum likelihood estimation. The accelerated life-test model was compared to a toxicokinetics-based model reported in the literature. Survival predictions made by both models were compared with the observed data. Both the accelerated life-test model and the toxicokinetics-based model underestimated toxicity at a diazinon concentration of 8 microg/g. Overall, however, the accelerated life-test model outperformed the toxicokinetics-based model, with survival predictions closer to the observed data in most cases and a stronger correlation between predicted and observed survivals. However, as a statistical model, the accelerated life-test model did not reveal mechanistic information, and only statistical and distributional interpretations of its model parameters could be made.

  17. Data Streaming for Metabolomics: Accelerating Data Processing and Analysis from Days to Minutes

    OpenAIRE

    Montenegro-Burke, J. Rafael; Aisporna, Aries E.; Benton, H. Paul; Rinehart, Duane; Fang, Mingliang; Huan, Tao; Warth, Benedikt; Forsberg, Erica; Abe, Brian T.; Ivanisevic, Julijana; Wolan, Dennis W.; Teyton, Luc; Lairson, Luke; Siuzdak, Gary

    2016-01-01

    The speed and throughput of analytical platforms has been a driving force in recent years in the “omics” technologies and while great strides have been accomplished in both chromatography and mass spectrometry, data analysis times have not benefited at the same pace. Even though personal computers have become more powerful, data transfer times still represent a bottleneck in data processing because of the increasingly complex data files and studies with a greater number of samples. To meet th...

  18. Throughput Analysis for a High-Performance FPGA-Accelerated Real-Time Search Application

    Directory of Open Access Journals (Sweden)

    Wim Vanderbauwhede

    2012-01-01

    Full Text Available We propose an FPGA design for the relevancy computation part of a high-throughput real-time search application. The application matches terms in a stream of documents against a static profile, held in off-chip memory. We present a mathematical analysis of the throughput of the application and apply it to the problem of scaling the Bloom filter used to discard nonmatches.

  19. Spectral Analysis of Acceleration Data for Detection of Generalized Tonic-Clonic Seizures

    Science.gov (United States)

    Joo, Hyo Sung; Han, Su-Hyun; Lee, Jongshill; Jang, Dong Pyo; Kang, Joong Koo; Woo, Jihwan

    2017-01-01

    Generalized tonic-clonic seizures (GTCSs) can be underestimated and can also increase mortality rates. The monitoring devices used to detect GTCS events in daily life are very helpful for early intervention and precise estimation of seizure events. Several studies have introduced methods for GTCS detection using an accelerometer (ACM), electromyography, or electroencephalography. However, these studies need to be improved with respect to accuracy and user convenience. This study proposes the use of an ACM banded to the wrist and spectral analysis of ACM data to detect GTCS in daily life. The spectral weight function dependent on GTCS was used to compute a GTCS-correlated score that can effectively discriminate between GTCS and normal movement. Compared to the performance of the previous temporal method, which used a standard deviation method, the spectral analysis method resulted in better sensitivity and fewer false positive alerts. Finally, the spectral analysis method can be implemented in a GTCS monitoring device using an ACM and can provide early alerts to caregivers to prevent risks associated with GTCS. PMID:28264522

  20. A massively parallel GPU-accelerated model for analysis of fully nonlinear free surface waves

    DEFF Research Database (Denmark)

    Engsig-Karup, Allan Peter; Madsen, Morten G.; Glimberg, Stefan Lemvig

    2011-01-01

    -throughput co-processors to the CPU. We describe and demonstrate how this approach makes it possible to do fast desktop computations for large nonlinear wave problems in numerical wave tanks (NWTs) with close to 50/100 million total grid points in double/ single precision with 4 GB global device memory...... space dimensions and is useful for fast analysis and prediction purposes in coastal and offshore engineering. A dedicated numerical model based on the proposed algorithm is executed in parallel by utilizing affordable modern special purpose graphics processing unit (GPU). The model is based on a low...

  1. Analysis of lead-acid battery deep-cycle accelerated testing data

    Science.gov (United States)

    Clifford, J. E.; Thomas, R. E.

    1984-06-01

    Battelle conducted a detailed analysis of the deep cycle, acclerated test data (at a nominal 70 C) obtained by Exide in the three-year, Phase 1 program to develop advanced lead-acid batteries for utility load leveling. Cycle life results for 60 lead-acid cells in three fractional factorial experiments were analyzed to develop quantitative relationships for real-time cycles to failure as a function of cell design variables. Important factors affecting cycle life were depth of discharge with respect to plate active material and acid within the plate stack, acid specific gravity, separator system design, and additives in the active material.

  2. BALSA: integrated secondary analysis for whole-genome and whole-exome sequencing, accelerated by GPU

    Directory of Open Access Journals (Sweden)

    Ruibang Luo

    2014-06-01

    Full Text Available 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.

  3. A Comprehensive Analysis on Wearable Acceleration Sensors in Human Activity Recognition

    Directory of Open Access Journals (Sweden)

    Majid Janidarmian

    2017-03-01

    Full Text Available Sensor-based motion recognition integrates the emerging area of wearable sensors with novel machine learning techniques to make sense of low-level sensor data and provide rich contextual information in a real-life application. Although Human Activity Recognition (HAR problem has been drawing the attention of researchers, it is still a subject of much debate due to the diverse nature of human activities and their tracking methods. Finding the best predictive model in this problem while considering different sources of heterogeneities can be very difficult to analyze theoretically, which stresses the need of an experimental study. Therefore, in this paper, we first create the most complete dataset, focusing on accelerometer sensors, with various sources of heterogeneities. We then conduct an extensive analysis on feature representations and classification techniques (the most comprehensive comparison yet with 293 classifiers for activity recognition. Principal component analysis is applied to reduce the feature vector dimension while keeping essential information. The average classification accuracy of eight sensor positions is reported to be 96.44% ± 1.62% with 10-fold evaluation, whereas accuracy of 79.92% ± 9.68% is reached in the subject-independent evaluation. This study presents significant evidence that we can build predictive models for HAR problem under more realistic conditions, and still achieve highly accurate results.

  4. SU-E-T-627: Failure Modes and Effect Analysis for Monthly Quality Assurance of Linear Accelerator

    Energy Technology Data Exchange (ETDEWEB)

    Xie, J [Fudan University shanghai cancer center, Shanghai, Shanghai (China); Xiao, Y [Thomas Jefferson UniversityHospital, Philadelphia, PA (United States); Wang, J; Peng, J; Lu, S [Fudan University Shanghai Cancer Center, Shanghai, Shanghai (China); Hu, W [Fudan University Shanghai Caner Center, Shanghai, Shanghai (China)

    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.

  5. Thin Layer Chromatography-Autography-High Resolution Mass Spectrometry Analysis: Accelerating the Identification of Acetylcholinesterase Inhibitors.

    Science.gov (United States)

    Ramallo, I Ayelen; Salazar, Mario O; Furlan, Ricardo L E

    2015-01-01

    The prevailing treatment for Alzheimer's disease is the use of acetylcholinesterase (AChE) inhibitors. Natural extracts are the principal source of AChE's inhibitors. However, their chemical complexity demands for simple, selective and rapid assays. To develop a strategy for identification of AChE inhibitors present in mixtures employing high resolution mass spectrometry (HRMS) and thin layer chromatography (TLC)-biological staining. The strategy uses an autographic assay based on the α-naphthyl acetate - fast blue B system for the detection of AChE activity. The immobilisation of AChE in agar allowed the extraction of the compounds for analysis by HRMS. Three TLC experiments employing different solvent systems were used in parallel and the mass spectra of the compounds extracted from the inhibition halos, were compared. The analysis was performed under MatLab environment. The strategy was used to detect the presence of physostigmine in an extract of Brassica rapa L. spiked with the inhibitor. Similarly, caffeine was straightforwardly spotted as responsible for the inhibitory properties of an extract of Ilex paraguariensis Saint-Hilaire. Comparison of the HRMS profiles lead to the facile identification of the [M+H](+) and [M+Na](+) of the compounds responsible for the inhibition. The proposed methodology, coupling TLC-AChE autography-HRMS, illustrates the feasibility of assigning molecular formulas of active compounds present in complex mixtures directly from autography. The new AChE agar-immobilised assay presented a more homogenous colour and a better definition than direct spraying methods, reducing the cost of the assay and improving its sensitivity. Copyright © 2015 John Wiley & Sons, Ltd.

  6. Using "Short" Interrupted Time-Series Analysis To Measure the Impacts of Whole-School Reforms: With Applications to a Study of Accelerated Schools.

    Science.gov (United States)

    Bloom, Howard S.

    2002-01-01

    Introduces an new approach for measuring the impact of whole school reforms. The approach, based on "short" interrupted time-series analysis, is explained, its statistical procedures are outlined, and how it was used in the evaluation of a major whole-school reform, Accelerated Schools is described (H. Bloom and others, 2001). (SLD)

  7. Accelerated Unification

    OpenAIRE

    Arkani-Hamed, Nima; Cohen, Andrew; Georgi, Howard

    2001-01-01

    We construct four dimensional gauge theories in which the successful supersymmetric unification of gauge couplings is preserved but accelerated by N-fold replication of the MSSM gauge and Higgs structure. This results in a low unification scale of $10^{13/N}$ TeV.

  8. Modelling, analysis, and acceleration of a printed circuit board fabrication process

    Indian Academy of Sciences (India)

    K S Aithal; Y Narahari; E Manjunath

    2001-10-01

    Product design and fabrication constitute an important business activity in any manufacturing firm. Designing an optimized product fabrication process is an important problem in itself and is of significant practical and research interest. In this paper, we look into a printed circuit board (PCB) fabrication process and investigate ways in which the fabrication cycle time can be minimized. Single class queueing networks constitute the modelling framework for our study. The model developed in this paper and the analysis experiments carried out are based on extensive data collected on a PCB fabrication company located in Bangalore, India. This is a representative PCB fabrication company involving multiple, concurrent fabrication works with contention for human/technical resources. Our model seeks to capture faithfully the flow of the fabrication process in this company and such other organisations, using queueing networks. Using the model developed, we explore how the cycle times can be reduced using input control, load balancing, and variability reduction. The model presented is sufficiently generic and conceptual; its scope extends beyond that of a PCB fabrication organization.

  9. Comprehensive analysis of animal TALE homeobox genes: new conserved motifs and cases of accelerated evolution.

    Science.gov (United States)

    Mukherjee, Krishanu; Bürglin, Thomas R

    2007-08-01

    TALE homeodomain proteins are an ancient subgroup within the group of homeodomain transcription factors that play important roles in animal, plant, and fungal development. We have extracted the full complement of TALE superclass homeobox genes from the genome projects of seven protostomes, seven deuterostomes, and Nematostella. This was supplemented with TALE homeobox genes from additional species and phylogenetic analyses were carried out with 276 sequences. We found 20 homeobox genes and 4 pseudogenes in humans, 21 genes in mouse, 8 genes in Drosophila, and 5 genes plus one truncated gene in Caenorhabditis elegans. Apart from the previously identified TALE classes MEIS, PBC, IRO, and TGIF, a novel class is identified, termed MOHAWK (MKX). Further, we show that the MEIS class can be divided into two families, PREP and MEIS. Prep genes have previously only been described in vertebrates but are lacking in Drosophila. Here we identify orthologues in other insect taxa as well as in the cnidarian Nematostella. In C. elegans, a divergent Prep protein has lost the homeodomain. Full-length multiple sequence alignment of the protostome and deuterostome sequences allowed us to identify several novel conserved motifs within the MKX, TGIF, and MEIS classes. Phylogenetic analyses revealed fast-evolving PBC class genes; in particular, some X-linked PBC genes in nematodes are subject to rapid evolution. In addition, several instances of gene loss were identified. In conclusion, our comprehensive analysis provides a defining framework for the classification of animal TALE homeobox genes and the understanding of their evolution.

  10. GPU加速的多边形叠加分析%Accelerating polygon overlay analysis by GPU

    Institute of Scientific and Technical Information of China (English)

    赵斯思; 周成虎

    2013-01-01

    叠加分析是地理信息系统最重要的分析功能之一,对多边形图层进行叠加分析要花费大量时间.为此,将GPU用于多边形叠加分析过程中的MBR过滤及多边形剪裁两个阶段.对MBR过滤阶段,提出了基于GPU的通过直方图及并行前置和实现的MBR过滤算法.对多边形剪裁阶段,通过改进Weiler-Atherton算法,使用新的焦点插入方法和简化的出入点标记算法,并结合并行前置和算法,提出了基于GPU的多边形剪裁算法.对实现过程中可能出现的负载不均衡情况,给出了基于动态规划的负载均衡方法.通过对这些算法的应用,实现对过滤阶段及精炼阶段的加速.实验结果表明,基于GPU的MBR过滤方法相对CPU实现的加速比为3.8,而基于GPU的多边形剪裁的速度比CPU实现快3.4倍.整体上,与CPU实现相比,GPU加速的多边形叠加提供了3倍以上的加速比.%Overlay analysis is one of the most important analysis capabilities of geographic information systems. Overlay analysis with polygon layers is a time-intensive process. To improve time efficiency, modern approaches of overlay analysis are generally divided into two stages, filtering and refinement (also known as polygon clipping). A great deal of effort has been taken to significantly reduce the number of candidates in the first stage (filtering) in order to alleviate the workload of the second stage (refinement). However, the second stage is still the most time-consuming part of the process. In this paper we applied GPGPU (General-purpose Graphics Processing Unit) computing to the two key stages of overlay analysis: MBR filtering (part of the filtering) and polygon clipping, and restricted the search area to polygon intersection analysis. We proposed GPU-based MBR filtering algorithm by combining histogram and parallel prefix-sum algorithms, and introduced GPU-based polygon clipping algorithm by improving Weiler-Atherton algorithm. There are two differences

  11. Biomedical accelerator mass spectrometry

    Science.gov (United States)

    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.

  12. The potential of accelerating early detection of autism through content analysis of YouTube videos.

    Directory of Open Access Journals (Sweden)

    Vincent A Fusaro

    Full Text Available 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.

  13. High-throughput GC-ECD analysis of PCBs in food by accelerated solvent extraction. Method validation

    Energy Technology Data Exchange (ETDEWEB)

    Piersanti, A.; Fioroni, L.; Paoloni, A.; Tavoloni, T.; Pecorelli, I.; Galarini, R. [Istituto Zooprofilattico Sperimentale dell' Umbria e delle Marche, Perugia (Italy)

    2004-09-15

    In the year 2000 the determination of the PCBs in food commodities was introduced in the Italian national residue control plan in which government labs were requested to estimate the total PCB content as sum of seven more representative congeners. Later on, in 2001, it was decided that a more appropriate estimation of the total PCBs was possible through analysis of eighteen rather than seven congeners. Therefore the need for simple and validated analytical methods arose. In this work a method for the analysis of the PCBs 18-congeners (T{sub 3}CB-28, T{sub 4}CB-52, P{sub 5}CB-95, P{sub 5}CB-99, P{sub 5}CB-101, P{sub 5}CB-105, P{sub 5}CB-110, P{sub 5}CB-118, H{sub 6}CB-138, H{sub 6}CB-146, H{sub 6}CB-149, H{sub 6}CB-151, H{sub 6}CB-153, H{sub 7}CB-170, H{sub 7}CB-177, H{sub 7}CB-180, H{sub 7}CB-183, H{sub 7}CB-187) is reported. This has been set up taking in account the advantages of the automated and high efficient Accelerated Solvent Extraction together with good purification achieved by a one-step acidic-extrelut/silica chromatography. The instrumental analysis is performed by capillary-GC equipped with an ECD detector. An in-house validation study has been made on swine muscle assessing the method performances in terms of limit of detection, response linearity range, trueness and precision.

  14. Analysis of heterogeneity and epistasis in physiological mixed populations by combined structural equation modelling and latent class analysis

    DEFF Research Database (Denmark)

    Fenger, Mogens; Linneberg, A.; Werge, Thomas Mears

    2008-01-01

    and genetic variations of such networks. METHODS: In this study on type 2 diabetes mellitus, heterogeneity was resolved in a latent class framework combined with structural equation modelling using phenotypic indicators of distinct physiological processes. We modelled the clinical condition "the metabolic...

  15. GAMUT: GPU accelerated microRNA analysis to uncover target genes through CUDA-miRanda.

    Science.gov (United States)

    Wang, Shuang; Kim, Jihoon; Jiang, Xiaoqian; Brunner, Stefan F; Ohno-Machado, Lucila

    2014-01-01

    datasets. 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/.

  16. Recombination accelerates adaptation on a large-scale empirical fitness landscape in HIV-1.

    Science.gov (United States)

    Moradigaravand, Danesh; Kouyos, Roger; Hinkley, Trevor; Haddad, Mojgan; Petropoulos, Christos J; Engelstädter, Jan; Bonhoeffer, Sebastian

    2014-06-01

    Recombination has the potential to facilitate adaptation. In spite of the substantial body of theory on the impact of recombination on the evolutionary dynamics of adapting populations, empirical evidence to test these theories is still scarce. We examined the effect of recombination on adaptation on a large-scale empirical fitness landscape in HIV-1 based on in vitro fitness measurements. Our results indicate that recombination substantially increases the rate of adaptation under a wide range of parameter values for population size, mutation rate and recombination rate. The accelerating effect of recombination is stronger for intermediate mutation rates but increases in a monotonic way with the recombination rates and population sizes that we examined. We also found that both fitness effects of individual mutations and epistatic fitness interactions cause recombination to accelerate adaptation. The estimated epistasis in the adapting populations is significantly negative. Our results highlight the importance of recombination in the evolution of HIV-I.

  17. Zebrafish scales respond differently to in vitro dynamic and static acceleration: analysis of interaction between osteoblasts and osteoclasts.

    Science.gov (United States)

    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.

  18. Accelerated Aging of BKC 44306-10 Rigid Polyurethane Foam: FT-IR Spectroscopy, Dimensional Analysis, and Micro Computed Tomography

    Energy Technology Data Exchange (ETDEWEB)

    Gilbertson, Robert D. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Patterson, Brian M. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Smith, Zachary [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    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.

  19. Structural dynamics of the monoamine transporter homologue LeuT from accelerated conformational sampling and channel analysis

    Science.gov (United States)

    Thomas, James R.; Gedeon, Patrick C.; Madura, Jeffry D.

    2014-01-01

    The bacterial leucine transporter LeuT retains significant secondary structure similarities to the human monoamine transporters (MAT) such as the dopamine and serotonin reuptake proteins. The primary method of computational study of the MATs has been through the use of the crystallized LeuT structure. Different conformations of LeuT can give insight into mechanistic details of the MAT family. A conformational sampling performed through accelerated molecular dynamics (aMD) simulations testing different combinations of the leucine substrate and bound sodium ions revealed seven distinct conformational clusters. Further analysis has been performed to target salt-bridge residues R30–D404, Y108–F253, and R5–D369 and transmembrane domains on both the seven isolated structures and the total trajectories. In addition, solvent accessibility of LeuT and its substrate binding pockets has been analyzed using a program for calculating channel radii. Occupation of the Na2 site stabilizes the outward conformation and should bind to the open outward conformation before the leucine and Na1 sodium while two possible pathways were found to be available for intracellular transport. PMID:24753369

  20. Structural dynamics of the monoamine transporter homolog LeuT from accelerated conformational sampling and channel analysis.

    Science.gov (United States)

    Thomas, James R; Gedeon, Patrick C; Madura, Jeffry D

    2014-10-01

    The bacterial leucine transporter LeuT retains significant secondary structure similarities to the human monoamine transporters (MAT) such as the dopamine and serotonin reuptake proteins. The primary method of computational study of the MATs has been through the use of the crystallized LeuT structure. Different conformations of LeuT can give insight into mechanistic details of the MAT family. A conformational sampling performed through accelerated molecular dynamics simulations testing different combinations of the leucine substrate and bound sodium ions revealed seven distinct conformational clusters. Further analysis has been performed to target salt-bridge residues R30-D404, Y108-F253, and R5-D369 and transmembrane domains on both the seven isolated structures and the total trajectories. In addition, solvent accessibility of LeuT and its substrate binding pockets has been analyzed using a program for calculating channel radii. Occupation of the Na2 site stabilizes the outward conformation and should bind to the open outward conformation before the leucine and Na1 sodium while two possible pathways were found to be available for intracellular transport.

  1. Arrhenius time-scaled least squares: a simple, robust approach to accelerated stability data analysis for bioproducts.

    Science.gov (United States)

    Rauk, Adam P; Guo, Kevin; Hu, Yanling; Cahya, Suntara; Weiss, William F

    2014-08-01

    Defining a suitable product presentation with an acceptable stability profile over its intended shelf-life is one of the principal challenges in bioproduct development. Accelerated stability studies are routinely used as a tool to better understand long-term stability. Data analysis often employs an overall mass action kinetics description for the degradation and the Arrhenius relationship to capture the temperature dependence of the observed rate constant. To improve predictive accuracy and precision, the current work proposes a least-squares estimation approach with a single nonlinear covariate and uses a polynomial to describe the change in a product attribute with respect to time. The approach, which will be referred to as Arrhenius time-scaled (ATS) least squares, enables accurate, precise predictions to be achieved for degradation profiles commonly encountered during bioproduct development. A Monte Carlo study is conducted to compare the proposed approach with the common method of least-squares estimation on the logarithmic form of the Arrhenius equation and nonlinear estimation of a first-order model. The ATS least squares method accommodates a range of degradation profiles, provides a simple and intuitive approach for data presentation, and can be implemented with ease. © 2014 Wiley Periodicals, Inc. and the American Pharmacists Association.

  2. Particle Accelerators in China

    Science.gov (United States)

    Zhang, Chuang; Fang, Shouxian

    As the special machines that can accelerate charged particle beams to high energy by using electromagnetic fields, particle accelerators have been widely applied in scientific research and various areas of society. The development of particle accelerators in China started in the early 1950s. After a brief review of the history of accelerators, this article describes in the following sections: particle colliders, heavy-ion accelerators, high-intensity proton accelerators, accelerator-based light sources, pulsed power accelerators, small scale accelerators, accelerators for applications, accelerator technology development and advanced accelerator concepts. The prospects of particle accelerators in China are also presented.

  3. MUON ACCELERATION

    Energy Technology Data Exchange (ETDEWEB)

    BERG,S.J.

    2003-11-18

    One of the major motivations driving recent interest in FFAGs is their use for the cost-effective acceleration of muons. This paper summarizes the progress in this area that was achieved leading up to and at the FFAG workshop at KEK from July 7-12, 2003. Much of the relevant background and references are also given here, to give a context to the progress we have made.

  4. Laser acceleration

    Science.gov (United States)

    Tajima, T.; Nakajima, K.; Mourou, G.

    2017-02-01

    The fundamental idea of Laser Wakefield Acceleration (LWFA) is reviewed. An ultrafast intense laser pulse drives coherent wakefield with a relativistic amplitude robustly supported by the plasma. While the large amplitude of wakefields involves collective resonant oscillations of the eigenmode of the entire plasma electrons, the wake phase velocity ˜ c and ultrafastness of the laser pulse introduce the wake stability and rigidity. A large number of worldwide experiments show a rapid progress of this concept realization toward both the high-energy accelerator prospect and broad applications. The strong interest in this has been spurring and stimulating novel laser technologies, including the Chirped Pulse Amplification, the Thin Film Compression, the Coherent Amplification Network, and the Relativistic Mirror Compression. These in turn have created a conglomerate of novel science and technology with LWFA to form a new genre of high field science with many parameters of merit in this field increasing exponentially lately. This science has triggered a number of worldwide research centers and initiatives. Associated physics of ion acceleration, X-ray generation, and astrophysical processes of ultrahigh energy cosmic rays are reviewed. Applications such as X-ray free electron laser, cancer therapy, and radioisotope production etc. are considered. A new avenue of LWFA using nanomaterials is also emerging.

  5. Precision and accuracy in the quantitative analysis of biological samples by accelerator mass spectrometry: application in microdose absolute bioavailability studies.

    Science.gov (United States)

    Gao, Lan; Li, Jing; Kasserra, Claudia; Song, Qi; Arjomand, Ali; Hesk, David; Chowdhury, Swapan K

    2011-07-15

    Determination of the pharmacokinetics and absolute bioavailability of an experimental compound, SCH 900518, following a 89.7 nCi (100 μg) intravenous (iv) dose of (14)C-SCH 900518 2 h post 200 mg oral administration of nonradiolabeled SCH 900518 to six healthy male subjects has been described. The plasma concentration of SCH 900518 was measured using a validated LC-MS/MS system, and accelerator mass spectrometry (AMS) was used for quantitative plasma (14)C-SCH 900518 concentration determination. Calibration standards and quality controls were included for every batch of sample analysis by AMS to ensure acceptable quality of the assay. Plasma (14)C-SCH 900518 concentrations were derived from the regression function established from the calibration standards, rather than directly from isotopic ratios from AMS measurement. The precision and accuracy of quality controls and calibration standards met the requirements of bioanalytical guidance (U.S. Department of Health and Human Services, Food and Drug Administration, Center for Drug Evaluation and Research, Center for Veterinary Medicine. Guidance for Industry: Bioanalytical Method Validation (ucm070107), May 2001. http://www.fda.gov/downloads/Drugs/GuidanceCompilanceRegulatoryInformation/Guidances/ucm070107.pdf ). The AMS measurement had a linear response range from 0.0159 to 9.07 dpm/mL for plasma (14)C-SCH 900158 concentrations. The CV and accuracy were 3.4-8.5% and 94-108% (82-119% for the lower limit of quantitation (LLOQ)), respectively, with a correlation coefficient of 0.9998. The absolute bioavailability was calculated from the dose-normalized area under the curve of iv and oral doses after the plasma concentrations were plotted vs the sampling time post oral dose. The mean absolute bioavailability of SCH 900518 was 40.8% (range 16.8-60.6%). The typical accuracy and standard deviation in AMS quantitative analysis of drugs from human plasma samples have been reported for the first time, and the impact of these

  6. Photon activation analysis of the scraper in a 200-MeV electron accelerator using gamma-spectrometry depth profiling

    CERN Document Server

    Lijuan, He; Guobing, Yu; Guangyi, Ren; Zongjin, Duan

    2014-01-01

    For a high energy electron facility, the estimates of induced radioactivity in materials are of major importance to keep exposure to personnel and to the environment as low as reasonably achievable. In addition, an accurate prediction of induced radioactivity is also essential for the design, operation and decommissioning of a high energy electron linear accelerator. The research of induced radioactivity focuses on the photonuclear reaction, whose giant resonance response in the copper is ranging from 10 MeV to 28 MeV. The 200 MeV electron linac of NSRL is one of the earliest high-energy electron linear accelerators in P. R. China. The electrons are accelerated to 200 MeV by five acceleration tubes and collimated by the scrapers made of copper. At present, it is the first retired high-energy electron linear accelerator in domestic. Its decommissioning provides an efficient way for the induced radioactivity research of such accelerators, and is a matter of great significance to the accumulation of the induced ...

  7. Accelerators and the Accelerator Community

    Energy Technology Data Exchange (ETDEWEB)

    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.

  8. GPU-accelerated nonparametric kinetic analysis of DCE-MRI data from glioblastoma patients treated with bevacizumab.

    Science.gov (United States)

    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

  9. Electrostatic accelerators fundamentals and applications

    CERN Document Server

    2005-01-01

    Electrostatic accelerators are an important and widespread subgroup within the broad spectrum of modern, large particle acceleration devices. They are specifically designed for applications that require high-quality ion beams in terms of energy stability and emittance at comparatively low energies (a few MeV). Their ability to accelerate virtually any kind of ion over a continuously tunable range of energies make them a highly versatile tool for investigations in many research fields including, but not limited to, atomic and nuclear spectroscopy, heavy ion reactions, accelerator mass spectroscopy as well as ion-beam analysis and modification. The book is divided into three parts. The first part concisely introduces the field of accelerator technology and techniques that emphasize their major modern applications. The second part treats the electrostatic accelerator per se: its construction and operational principles as well as its maintenance. The third part covers all relevant applications in which electrosta...

  10. preparation of microgram samples on iron wool for radiocarbon analysis via accelerator mass spectrometry: A closed-system approach

    Science.gov (United States)

    Verkouteren, R. Michael; Klouda, George A.; Currie, Lloyd A.; Donahue, Douglas J.; Jull, A. J. Timothy; Linick, T. W.

    1987-11-01

    A technique has been developed at NBS for the production of high quality targets for radiocarbon analysis by accelerator mass spectrometry (AMS). Our process optimizes chemical yields, ion currents and characterizes the chemical blank. The approach encompasses sample combustion to CO 2, catalytic reduction of CO 2 by Zn to CO, reduction to graphitic carbon on high-purity iron wool and in situ formation of a homogeneous iron-carbon bead; all steps are performed in a closed system. The total measurement system blank and variability are considered in the light of contributions from combustion, iron wool, reduction, bead formation and instrument blank. Additionally, use of this approach provides an increase in throughput, i.e. the effective management of large numbers of samples. Chemical yields for 50-800 μg C samples deposited on 15 mg iron wool were greater than 90%. Integrated 12C - ion currents observed were significant, being 4-64% of those observed in pure graphite. These currents are about an order of magnitude greater than those expected from dilution of graphite with an inert substrate. Isotopic accuracy, precision and blank were assessed by measuring the {14C }/{13C } ratios of a series of targets prepared from dead carbon and oxalic acid (SRM 4990C). Each target was typically measured for one hour; bead consumption was estimated at 5% to 10%. System blank subsequent to combustion was equivalent to (2.2 ± 0.5) μg modern carbon (chemistry + instrument); combustion blank currently stands at (0.4 ± 0.1) (SE, n = 6) μg C.

  11. accelerating cavity

    CERN Multimedia

    On the inside of the cavity there is a layer of niobium. Operating at 4.2 degrees above absolute zero, the niobium is superconducting and carries an accelerating field of 6 million volts per metre with negligible losses. Each cavity has a surface of 6 m2. The niobium layer is only 1.2 microns thick, ten times thinner than a hair. Such a large area had never been coated to such a high accuracy. A speck of dust could ruin the performance of the whole cavity so the work had to be done in an extremely clean environment.

  12. Impact accelerations

    Science.gov (United States)

    Vongierke, H. E.; Brinkley, J. W.

    1975-01-01

    The degree to which impact acceleration is an important factor in space flight environments depends primarily upon the technology of capsule landing deceleration and the weight permissible for the associated hardware: parachutes or deceleration rockets, inflatable air bags, or other impact attenuation systems. The problem most specific to space medicine is the potential change of impact tolerance due to reduced bone mass and muscle strength caused by prolonged weightlessness and physical inactivity. Impact hazards, tolerance limits, and human impact tolerance related to space missions are described.

  13. Mapping epistasis and environment × QTX interaction based on four -omics genotypes for the detected QTX loci controlling complex traits in tobacco

    Directory of Open Access Journals (Sweden)

    Liyuan Zhou

    2013-12-01

    Full Text Available Using newly developed methods and software, association mapping was conducted for chromium content and total sugar in tobacco leaf, based on four -omics datasets. Our objective was to collect data on genotype and phenotype for 60 leaf samples at four developmental stages, from three plant architectural positions and for three cultivars that were grown in two locations. Association mapping was conducted to detect genetic variants at quantitative trait SNP (QTS loci, quantitative trait transcript (QTT differences, quantitative trait protein (QTP variability, and quantitative trait metabolite (QTM changes, which can be summarized as QTX locus variation. The total heritabilities of the four -omics loci for both traits tested were 23.60% for epistasis and 15.26% for treatment interaction. Epistasis and environment × treatment interaction had important impacts on complex traits at all -omics levels. For decreasing chromium content and increasing total sugar in tobacco leaf, six methylated loci can be directly used for marker-assisted selection, and expression of ten QTTs, seven QTPs and six QTMs can be modified by selection or cultivation.

  14. Mapping epistasis and environment × QTX interaction based on four-omics genotypes for the detected QTX loci controlling complex traits in tobacco

    Institute of Scientific and Technical Information of China (English)

    Liyuan; Zhou; Ruiyuan; Li; Longjiang; Fan; Yuewei; Shi; Zhihong; Wang; Shengdong; Xie; Yijie; Gui; Xueliang; Ren; Jun; Zhu

    2013-01-01

    Using newly developed methods and software, association mapping was conducted for chromium content and total sugar in tobacco leaf, based on four-omics datasets. Our objective was to collect data on genotype and phenotype for 60 leaf samples at four developmental stages, from three plant architectural positions and for three cultivars that were grown in two locations. Association mapping was conducted to detect genetic variants at quantitative trait SNP(QTS) loci, quantitative trait transcript(QTT) differences,quantitative trait protein(QTP) variability, and quantitative trait metabolite(QTM) changes,which can be summarized as QTX locus variation. The total heritabilities of the four-omics loci for both traits tested were 23.60% for epistasis and 15.26% for treatment interaction.Epistasis and environment × treatment interaction had important impacts on complex traits at all-omics levels. For decreasing chromium content and increasing total sugar in tobacco leaf, six methylated loci can be directly used for marker-assisted selection, and expression of ten QTTs, seven QTPs and six QTMs can be modified by selection or cultivation.

  15. Modeling and Analysis of Radio Frequency Structures Using AN Equivalent Circuit Methodology with Application to Charged Particle Accelerator RF Resonators

    Science.gov (United States)

    Vincent, John J.

    The delineation of analysis techniques for high power radio frequency resonators, used as a fundamental component of particle accelerators, receives little attention in the literature. This dissertation reviews, describes, and develops techniques for resolving a transmission line mode rf resonator into an approximate equivalent circuit. Specifically, it presents a toolbox of techniques used to model and represent rf structures. One technique develops models of transmission lines with varying characteristic impedance (referred to as non-uniform) using multiple series connected circuits consisting of lumped elements and constant impedance transmission lines based on a conserved energy approach. This technique is tested for exponentially tapered and linearly tapered quarter-wave resonators. Another technique developed, maps transmission lines with arbitrary cross-sections (referred to as nonstandard) to a standard structure that preserves the characteristic impedance and loss properties of the original line. The techniques developed are applied to the analysis of the complex K1200 Superconducting Cyclotron rf resonators at the National Superconducting Cyclotron Laboratory (NSCL). The results predicted from the model are compared to measurements. The K1200 rf resonators are tunable over the frequency range of 9.5 to 27 MHz with tuning stems that vary from 300 cm to 11 cm respectively. The resonators are operated in the continuos wave (cw) mode and sustain peak voltages of up to 180 kV requiring drive power of up to 250 kW. Using the techniques developed, the resonant frequency versus tuning stem position was predicted to within a positioning error that varied from 1 to 3.5 cm over the tuning range of 9.5 to 27 Mhz. The discrepancy between model predictions and the experimental data for the resonator power dissipation is postulated to be due to high surface resistance in regions where the rf surfaces were heavily worked or welded. After adjusting the surface resistance

  16. A model for family-based case–control studies of genetic imprinting and epistasis

    Science.gov (United States)

    Li, Xin; Sui, Yihan; Liu, Tian; Wang, Jianxin; Li, Yongci; Lin, Zhenwu; Hegarty, John; Koltun, Walter A.; Wang, Zuoheng

    2014-01-01

    Genetic imprinting, or called the parent-of-origin effect, has been recognized to play an important role in the formation and pathogenesis of human diseases. Although the epigenetic mechanisms that establish genetic imprinting have been a focus of many genetic studies, our knowledge about the number of imprinting genes and their chromosomal locations and interactions with other genes is still scarce, limiting precise inference of the genetic architecture of complex diseases. In this article, we present a statistical model for testing and estimating the effects of genetic imprinting on complex diseases using a commonly used case–control design with family structure. For each subject sampled from a case and control population, we not only genotype its own single nucleotide polymorphisms (SNPs) but also collect its parents’ genotypes. By tracing the transmission pattern of SNP alleles from parental to offspring generation, the model allows the characterization of genetic imprinting effects based on Pearson tests of a 2 × 2 contingency table. The model is expanded to test the interactions between imprinting effects and additive, dominant and epistatic effects in a complex web of genetic interactions. Statistical properties of the model are investigated, and its practical usefulness is validated by a real data analysis. The model will provide a useful tool for genome-wide association studies aimed to elucidate the picture of genetic control over complex human diseases. PMID:23887693

  17. Cytonuclear Epistasis Controls the Density of Symbiont Wolbachia pipientis in Nongonadal Tissues of Mosquito Culex quinquefasciatus.

    Science.gov (United States)

    Emerson, Kevin J; Glaser, Robert L

    2017-08-07

    Wolbachia pipientis, a bacterial symbiont infecting arthropods and nematodes, is vertically transmitted through the female germline and manipulates its host's reproduction to favor infected females. Wolbachia also infects somatic tissues where it can cause nonreproductive phenotypes in its host, including resistance to viral pathogens. Wolbachia-mediated phenotypes are strongly associated with the density of Wolbachia in host tissues. Little is known, however, about how Wolbachia density is regulated in native or heterologous hosts. Here, we measure the broad-sense heritability of Wolbachia density among families in field populations of the mosquito Culex pipiens, and show that densities in ovary and nongonadal tissues of females in the same family are not correlated, suggesting that Wolbachia density is determined by distinct mechanisms in the two tissues. Using introgression analysis between two different strains of the closely related species C. quinquefasciatus, we show that Wolbachia densities in ovary tissues are determined primarily by cytoplasmic genotype, while densities in nongonadal tissues are determined by both cytoplasmic and nuclear genotypes and their epistatic interactions. Quantitative-trait-locus mapping identified two major-effect quantitative-trait loci in the C. quinquefasciatus genome explaining a combined 23% of variance in Wolbachia density, specifically in nongonadal tissues. A better understanding of how Wolbachia density is regulated will provide insights into how Wolbachia density can vary spatiotemporally in insect populations, leading to changes in Wolbachia-mediated phenotypes such as viral pathogen resistance. Copyright © 2017 Emerson, Glaser.

  18. Epistasis between microRNAs 155 and 146a during T cell-mediated antitumor immunity

    Science.gov (United States)

    Huffaker, Thomas B.; Hu, Ruozhen; Runtsch, Marah C.; Bake, Erin; Chen, Xinjian; Zhao, Jimmy; Round, June L.; Baltimore, David; O’Connell, Ryan M.

    2012-01-01

    SUMMARY An increased understanding of antitumor immunity is necessary to improve cell-based immunotherapies against human cancers. Here, we investigated the roles of two immune system-expressed microRNAs (miRNAs), miR-155 and miR-146a, in the regulation of antitumor immune responses. Our results indicate that miR-155 promotes and miR-146a inhibits IFNγ responses by T cells and reduced solid tumor growth in vivo. Using a novel double knockout (DKO) mouse strain deficient in both miR-155 and miR-146a, we have also identified an epistatic relationship between these two miRNAs. DKO mice had defective T cell responses and tumor growth phenotypes similar to miR-155−/− mice. Further analysis of the T cell compartment revealed that miR-155 modulates IFNγ expression through a mechanism involving repression of Ship1. Our work reveals critical roles for miRNAs in the reciprocal regulation of CD4+ and CD8+ T cell-mediated antitumor immunity, and demonstrates the dominant nature of miR-155 during its promotion of immune responses. PMID:23200854

  19. Epistasis between MicroRNAs 155 and 146a during T Cell-Mediated Antitumor Immunity

    Directory of Open Access Journals (Sweden)

    Thomas B. Huffaker

    2012-12-01

    Full Text Available An increased understanding of antitumor immunity is necessary for improving cell-based immunotherapies against human cancers. Here, we investigated the roles of two immune system-expressed microRNAs (miRNAs, miR-155 and miR-146a, in the regulation of antitumor immune responses. Our results indicate that miR-155 promotes and miR-146a inhibits interferon γ (IFNγ responses by T cells and reduces solid tumor growth in vivo. Using a double-knockout (DKO mouse strain deficient in both miR-155 and miR-146a, we have also identified an epistatic relationship between these two miRNAs. DKO mice had defective T cell responses and tumor growth phenotypes similar to miR-155−/− mice. Further analysis of the T cell compartment revealed that miR-155 modulates IFNγ expression through a mechanism involving repression of Ship1. Our work reveals critical roles for miRNAs in the reciprocal regulation of CD4+ and CD8+ T cell-mediated antitumor immunity and demonstrates the dominant nature of miR-155 during its promotion of immune responses.

  20. Performance analysis of GPU-accelerated filter-based source finding for HI spectral line image data

    Science.gov (United States)

    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.

  1. Performance Analysis of GPU-Accelerated Filter-Based Source Finding for HI Spectral Line Image Data

    CERN Document Server

    Westerlund, Stefan

    2015-01-01

    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.

  2. Epistasis and inheritance of plant habit and fruit quality traits in ornamental pepper (Capsicum annuum L.).

    Science.gov (United States)

    Santos, R M C; do Rêgo, E R; Borém, A; Nascimento, M F; Nascimento, N F F; Finger, F L; Rêgo, M M

    2014-10-31

    Two accessions of ornamental pepper Capsicum annuum L., differing in most of the characters studied, were crossed, resulting in the F1 generation, and the F2 generation was obtained through self-fertilization of the F1 generation. The backcross generations RC1 and RC2 were obtained through crossing between F1 and the parents P1 and P2, respectively. Morpho-agronomic characterization was performed based on the 19 quantitative descriptors of Capsicum. The data obtained were subjected to generation analysis, in which the means and additive variance (σa(2)), variance due to dominance deviation (σd(2)), phenotypic variance (σf(2)), genetic variance (σg(2)) and environmental variance (σm(2)) were calculated. For the full model, we estimated the mean effects of all possible homozygotes, additives, dominants, and epistatics: additive-additive, additive-dominant, and dominant-dominant. For the additive-dominant model, we estimated the additive effects, dominant effects and mean effects of possible homozygotes. The character fruit dry matter had the lowest value for broad sense heritability (0.42), and the highest values were found for fresh matter and fruit weight, 0.91 and 0.92, respectively. The lowest value for narrow sense heritability was for the minor fruit diameter character (0.33), and the highest values were found for seed yield per fruit and fresh matter, 0.87 and 0.84, respectively. The additive-dominant model explained only the variation found in plant height, canopy width, stem length, corolla diameter, leaf width, and pedicel length, but in the other characters, the epistatic effects showed significant values.

  3. Using a commercial mathematics software package for on-line analysis at the BNL Accelerator Test Facility

    Energy Technology Data Exchange (ETDEWEB)

    Malone, R.; Wang, X.J.

    1999-06-14

    BY WRITING BOTH A CUSTOM WINDOWS(NTTM) DYNAMIC LINK LIBRARY AND GENERIC COMPANION SERVER SOFTWARE, THE INTRINSIC FUNCTIONS OF MATHSOFT MATHCAD(TM) HAVE BEEN EXTENDED WITH NEW CAPABILITIES WHICH PERMIT DIRECT ACCESS TO THE CONTROL SYSTEM DATABASES OF BROOKHAVEN NATIONAL LABORATORY ACCELERATOR TEST FACILITY. UNDER THIS SCHEME, A MATHCAD WORKSHEET EXECUTING ON A PERSONAL COMPUTER BECOMES A CLIENT WHICH CAN BOTH IMPORT AND EXPORT DATA TO A CONTROL SYSTEM SERVER VIA A NETWORK STREAM SOCKET CONNECTION. THE RESULT IS AN ALTERNATIVE, MATHEMATICALLY ORIENTED VIEW OF CONTROLLING THE ACCELERATOR INTERACTIVELY.

  4. Two - three loci control scleral ossicle formation via epistasis in the cavefish Astyanax mexicanus.

    Science.gov (United States)

    Lyon, Anastasia; Powers, Amanda K; Gross, Joshua B; O'Quin, Kelly E

    2017-01-01

    The sclera is the protective outer layer of the eye. In fishes, birds, and reptiles, the sclera may be reinforced with additional bony elements called scleral ossicles. Teleost fish vary in the number and size of scleral ossicles; however, the genetic mechanisms responsible for this variation remain poorly understood. In this study, we examine the inheritance of scleral ossicles in the Mexican tetra, Astyanax mexicanus, which exhibits both a cave morph and a surface fish morph. As these morphs and their hybrids collectively exhibit zero, one, and two scleral ossicles, they represent a microcosm of teleost scleral ossicle diversity. Our previous research in F2 hybrids of cavefish from Pachón cave and surface fish from Texas suggested that three genes likely influence the formation of scleral ossicles in this group through an epistatic threshold model of inheritance, though our sample size was small. In this study, we expand our sample size using additional hybrids of Pachón cavefish and Mexican surface fish to (1) confirm the threshold model of inheritance, (2) refine the number of genes responsible for scleral ossicle formation, and (3) increase our power to detect quantitative trait loci (QTL) for this trait. To answer these three questions, we scored surface fish and cavefish F2 hybrids for the presence of zero, one, or two scleral ossicles. We then analyzed their distribution among the F2 hybrids using a chi-square (χ2) test, and used a genetic linkage map of over 100 microsatellite markers to identify QTL responsible for scleral ossicle number. We found that inheritance of scleral ossicles follows an epistatic threshold model of inheritance controlled by two genes, which contrasts the three-locus model estimated from our previous study. Finally, the combined analysis of hybrids from both crosses identified two strong QTL for scleral ossicle number on linkage groups 4.2 and 21, and a weaker QTL on linkage group 4.1. Scleral ossification remains a complex

  5. Two – three loci control scleral ossicle formation via epistasis in the cavefish Astyanax mexicanus

    Science.gov (United States)

    Lyon, Anastasia; Powers, Amanda K.; Gross, Joshua B.; O’Quin, Kelly E.

    2017-01-01

    The sclera is the protective outer layer of the eye. In fishes, birds, and reptiles, the sclera may be reinforced with additional bony elements called scleral ossicles. Teleost fish vary in the number and size of scleral ossicles; however, the genetic mechanisms responsible for this variation remain poorly understood. In this study, we examine the inheritance of scleral ossicles in the Mexican tetra, Astyanax mexicanus, which exhibits both a cave morph and a surface fish morph. As these morphs and their hybrids collectively exhibit zero, one, and two scleral ossicles, they represent a microcosm of teleost scleral ossicle diversity. Our previous research in F2 hybrids of cavefish from Pachón cave and surface fish from Texas suggested that three genes likely influence the formation of scleral ossicles in this group through an epistatic threshold model of inheritance, though our sample size was small. In this study, we expand our sample size using additional hybrids of Pachón cavefish and Mexican surface fish to (1) confirm the threshold model of inheritance, (2) refine the number of genes responsible for scleral ossicle formation, and (3) increase our power to detect quantitative trait loci (QTL) for this trait. To answer these three questions, we scored surface fish and cavefish F2 hybrids for the presence of zero, one, or two scleral ossicles. We then analyzed their distribution among the F2 hybrids using a chi-square (χ2) test, and used a genetic linkage map of over 100 microsatellite markers to identify QTL responsible for scleral ossicle number. We found that inheritance of scleral ossicles follows an epistatic threshold model of inheritance controlled by two genes, which contrasts the three-locus model estimated from our previous study. Finally, the combined analysis of hybrids from both crosses identified two strong QTL for scleral ossicle number on linkage groups 4.2 and 21, and a weaker QTL on linkage group 4.1. Scleral ossification remains a complex

  6. Analysis of simple step-stress accelerated life test data from Lindley distribution under type-I censoring

    OpenAIRE

    Varghese A. Sharon; V S Vaidyanathan

    2016-01-01

    This article introduces step-stress accelerated life time model with Lindley lifetime under type-I censoring. The corresponding likelihood function is developed and parameter estimation by maximum likelihood approach is discussed. Also, parametric bootstrap confidence intervals are constructed for the unknown parameters. Simulation study is carried out to evaluate performance of the estimators of the proposed model.

  7. Analysis of x-ray emission and electron dynamics in a capillary-guided laser wakefield accelerator

    Directory of Open Access Journals (Sweden)

    J. Ju

    2014-05-01

    Full Text Available The dynamics of electron acceleration driven by laser wakefield inside a 30.5 mm long dielectric capillary tube is analyzed using radiation emitted in the x-ray range. 3D particle-in-cell simulations, performed with parameters close to the experimental ones, show that in long plasmas, the accelerated electrons catch up and finally overrun the driving laser owing to a higher velocity of the electrons in the plasma. The electrons are then transversely scattered by the laser pulse, and penetrate the capillary wall where they generate bremsstrahlung radiation, modeled using geant4 simulations. The signature of bremsstrahlung radiation is detected using an x-ray camera, together with the betatron radiation emitted during electron acceleration in the plasma bubble. The reflection of betatron radiation from the inner capillary surface also accounts for a fraction of the observed signal on the x-ray camera. The simulation results are in agreement with the experimental ones and provide a detailed description of the electron and radiation properties, useful for the design of laser wakefield accelerators or radiation sources using long plasma media.

  8. Analysis of x-ray emission and electron dynamics in a capillary-guided laser wakefield accelerator

    Science.gov (United States)

    Ju, J.; Genoud, G.; Ferrari, H. E.; Dadoun, O.; Paradkar, B.; Svensson, K.; Wojda, F.; Burza, M.; Persson, A.; Lundh, O.; Andreev, N. E.; Wahlström, C.-G.; Cros, B.

    2014-05-01

    The dynamics of electron acceleration driven by laser wakefield inside a 30.5 mm long dielectric capillary tube is analyzed using radiation emitted in the x-ray range. 3D particle-in-cell simulations, performed with parameters close to the experimental ones, show that in long plasmas, the accelerated electrons catch up and finally overrun the driving laser owing to a higher velocity of the electrons in the plasma. The electrons are then transversely scattered by the laser pulse, and penetrate the capillary wall where they generate bremsstrahlung radiation, modeled using geant4 simulations. The signature of bremsstrahlung radiation is detected using an x-ray camera, together with the betatron radiation emitted during electron acceleration in the plasma bubble. The reflection of betatron radiation from the inner capillary surface also accounts for a fraction of the observed signal on the x-ray camera. The simulation results are in agreement with the experimental ones and provide a detailed description of the electron and radiation properties, useful for the design of laser wakefield accelerators or radiation sources using long plasma media.

  9. Bottleneck analysis approach to accelerate newborn care services in two regions in Ghana: implications for national newborn care.

    Science.gov (United States)

    Yawson, A E; Awoonor-Williams, J K; Sagoe-Moses, I; Aboagye, P K; Yawson, A O; Senaya, L K; Bonsu, G; Eleeza, J B; Agongo, E E A; Banskota, H K

    2016-12-01

    The aim of this work is to describe application of a data-driven approach (bottleneck analysis [BNA] approach process) to accelerate newborn care services in two regions and what effect it had on national-level newborn care interventions in Ghana. A mixed-method approach was used for the study. The BNA tool generated quantitative data and group discussions provided phenomenological explanations to identified service gaps. Regional newborn care health service assessments were conducted in November 2013 through desk reviews, field and health facility visits and coaching/mentorship. The BNA tool (an excel-based tool) directly utilized service coverage data and programme monitoring and review reports in Ghana. Outputs were generated based on service coverage indicators: supply side/health system factors (commodities, human resource and access), demand side (service utilization) and quality/effective coverage. National targets were used as benchmarks to assess gaps in coverage indicators. Key health system bottlenecks included absence/stock-out of essential newborn care commodities/resuscitation kits and absence of updated policies at services delivery points. In both regions, less than 55% of health facilities had at least 80% of midwives trained to provide essential obstetric and newborn care, management of preterm babies, resuscitation and inpatient paediatric care. In addition, less than 35% of pregnant women were assisted by a skilled birth attendant (midwife) and monitored with a partograph in the two regions. Demand-side bottlenecks included cultural preference for home deliveries, limited knowledge on importance of postnatal care and poor community involvement.The BNA approach in the two regions resulted in the development of national and other regional operational plans and monitoring and evaluation framework for newborn care services in Ghana over the period 2012-2016, and a relative improvement in neonatal mortality at the regional and national level. The BNA

  10. Simulation and characterization of the RF system and global stability analysis at the REGAE linear electron accelerator

    Energy Technology Data Exchange (ETDEWEB)

    Mayet, Frank

    2012-12-15

    LAOLA (LAboratory for Laser- and beam-driven plasma Acceleration), is a collaboration between groups from DESY and the University of Hamburg. Its mission is to complement basic research in the relatively new field of plasma wakefield acceleration (PWA) by an explicit combination with DESY's conventional, modern accelerators. The linear electron accelerator REGAE is designed to produce sub 10 fs low charge electron bunches with ultra-low emittance at a repetition rate of 50 Hz. The planned experiments include femtosecond electron diffraction (R.J. Dwayne Miller), as well as the probing of laser induced plasma wakefields with well characterized bunches (LAOLA). They all require high bunch time of flight stability down to 10 fs. The REGAE machine consists of two RF cavities, both fed by a single klystron. While the first one - the gun cavity - is used for acceleration of the electrons, the second one - the buncher cavity - can be used to reduce the electron bunch length. This scheme only works for a specific RF phase relation between the two cavities. This thesis is split into two parts. In the first one the implications of the unique two cavity design on day-to-day machine operation are analyzed. To this end an analytical model of the RF system is developed, which is necessary for understanding how to individually adjust the cavity phases. In the second part the influence of the setup on time of flight stability is discussed with an emphasis on phase jitter compensation. RF phase stability measurements reveal that the current machine setup allows for a time of flight stability down to 50 fs right after the gun.

  11. Fundamental principles, measurement techniques and data analysis in a ion accelerator; Principios fundamentales, tecnicas de medicion y analisis de datos en un acelerador de iones

    Energy Technology Data Exchange (ETDEWEB)

    Gonzalez M, O. [Facultad de Ciencias, UNAM, Ciudad Universitaria, 04510 Mexico D. F. (Mexico); Gleason, C. [Facultad de Ciencias, Universidad Autonoma del Estado de Morelos, Cuernavaca, Morelos (Mexico); Hinojosa, G. [Instituto de Ciencias Fisicas, UNAM, Ciudad Universitaria, 04510 Mexico D. F. (Mexico)]. e-mail: hinojosa@fis.unam.mx

    2008-07-01

    The present work is intended to be a general reference for students and professionals interested in the field. Here, we present an introduction to the analysis techniques and fundamental principles for data processing and operation of a typical ion accelerator that operates in the low energy range. We also present a detailed description of the apparatus and propose new analysis methods for the results. In addition, we introduce illustrative simulations of the ion's trajectories in the different components of the apparatus performed with specialized software and, a new computer data acquisition and control interface. (Author)

  12. SHORT ACCELERATION TIMES FROM SUPERDIFFUSIVE SHOCK ACCELERATION IN THE HELIOSPHERE

    Energy Technology Data Exchange (ETDEWEB)

    Perri, S.; Zimbardo, G., E-mail: silvia.perri@fis.unical.it [Dipartimento di Fisica, Università della Calabria, Ponte P. Bucci, I-87036 Rende (Italy)

    2015-12-10

    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.

  13. BiForce Toolbox: powerful high-throughput computational analysis of gene-gene interactions in genome-wide association studies.

    Science.gov (United States)

    Gyenesei, Attila; Moody, Jonathan; Laiho, Asta; Semple, Colin A M; Haley, Chris S; Wei, Wen-Hua

    2012-07-01

    Genome-wide association studies (GWAS) have discovered many loci associated with common disease and quantitative traits. However, most GWAS have not studied the gene-gene interactions (epistasis) that could be important in complex trait genetics. A major challenge in analysing epistasis in GWAS is the enormous computational demands of analysing billions of SNP combinations. Several methods have been developed recently to address this, some using computers equipped with particular graphical processing units, most restricted to binary disease traits and all poorly suited to general usage on the most widely used operating systems. We have developed the BiForce Toolbox to address the demand for high-throughput analysis of pairwise epistasis in GWAS of quantitative and disease traits across all commonly used computer systems. BiForce Toolbox is a stand-alone Java program that integrates bitwise computing with multithreaded parallelization and thus allows rapid full pairwise genome scans via a graphical user interface or the command line. Furthermore, BiForce Toolbox incorporates additional tests of interactions involving SNPs with significant marginal effects, potentially increasing the power of detection of epistasis. BiForce Toolbox is easy to use and has been applied in multiple studies of epistasis in large GWAS data sets, identifying interesting interaction signals and pathways.

  14. Analysis of recombination QTLs, segregation distortion, and epistasis for fitness in maize multiple populations using ultra-high-density markers

    Science.gov (United States)

    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...

  15. Inertia coupling analysis of a self-decoupled wheel force transducer under multi-axis acceleration fields.

    Directory of Open Access Journals (Sweden)

    Lihang Feng

    Full Text Available 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.

  16. Inertia coupling analysis of a self-decoupled wheel force transducer under multi-axis acceleration fields.

    Science.gov (United States)

    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.

  17. Fisher's geometric model of adaptation meets the functional synthesis: data on pairwise epistasis for fitness yields insights into the shape and size of phenotype space.

    Science.gov (United States)

    Weinreich, Daniel M; Knies, Jennifer L

    2013-10-01

    The functional synthesis uses experimental methods from molecular biology, biochemistry and structural biology to decompose evolutionarily important mutations into their more proximal mechanistic determinants. However these methods are technically challenging and expensive. Noting strong formal parallels between R.A. Fisher's geometric model of adaptation and a recent model for the phenotypic basis of protein evolution, we sought to use the former to make inferences into the latter using data on pairwise fitness epistasis between mutations. We present an analytic framework for classifying pairs of mutations with respect to similarity of underlying mechanism on this basis, and also show that these data can yield an estimate of the number of mutationally labile phenotypes underlying fitness effects. We use computer simulations to explore the robustness of our approach to violations of analytic assumptions and analyze several recently published datasets. This work provides a theoretical complement to the functional synthesis as well as a novel test of Fisher's geometric model.

  18. Time-motion analysis of acceleration demands of 4v4 small-sided soccer games played on different pitch sizes.

    Science.gov (United States)

    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. Copyright © 2013 Elsevier B.V. All rights reserved.

  19. Accelerated Parallel Texture Optimization

    Institute of Scientific and Technical Information of China (English)

    Hao-Da Huang; Xin Tong; Wen-Cheng Wang

    2007-01-01

    Texture optimization is a texture synthesis method that can efficiently reproduce various features of exemplar textures. However, its slow synthesis speed limits its usage in many interactive or real time applications. In this paper, we propose a parallel texture optimization algorithm to run on GPUs. In our algorithm, k-coherence search and principle component analysis (PCA) are used for hardware acceleration, and two acceleration techniques are further developed to speed up our GPU-based texture optimization. With a reasonable precomputation cost, the online synthesis speed of our algorithm is 4000+ times faster than that of the original texture optimization algorithm and thus our algorithm is capable of interactive applications. The advantages of the new scheme are demonstrated by applying it to interactive editing of flow-guided synthesis.

  20. Speciation analysis of 129I in seawater by carrier-free AgI-AgCl coprecipitation and accelerator mass spectrometric measurement

    DEFF Research Database (Denmark)

    Luo, Maoyi; Hou, Xiaolin; He, Chaohui;

    2013-01-01

    A rapid and simple method was developed for speciation analysis of 129I in seawater by selective coprecipitation of carrier-free iodide and accelerator mass spectrometry (AMS) measurement of 129I. Iodide was separated from seawater and other species of iodine by coprecipitation of AgI with Ag2SO3...... is higher than 70%. Six seawater samples collected from the Norwegian Sea were analyzed by this method as well as a conventional anion-exchange chromatographic method; the results from the two methods show no significant difference (p = 0.05). Because only one separation step and fewer chemicals...... are involved in the procedure, this method is suitable for operation on board sampling vessels, as it avoids the transport of samples to the laboratory and storage for a longer time before analysis, therefore significantly improving the analytical capacity and reliability of speciation analysis of 129I...

  1. Accelerated Degradation Test and Predictive Failure Analysis of B10 Copper-Nickel Alloy under Marine Environmental Conditions

    Directory of Open Access Journals (Sweden)

    Bo Sun

    2015-09-01

    Full Text Available This paper studies the corrosion behavior of B10 copper-nickel alloy in marine environment. Accelerated degradation test under marine environmental conditions was designed and performed based on the accelerated testing principle and the corrosion degradation mechanism. With the prolongation of marine corrosion time, the thickness of Cu2O film increased gradually. Its corrosion product was Cu2(OH3Cl, which increased in quantity over time. Cl− was the major factor responsible for the marine corrosion of copper and copper alloy. Through the nonlinear fitting of corrosion rate and corrosion quantity (corrosion weight loss, degradation data of different corrosion cycles, the quantitative effects of two major factors, i.e., dissolved oxygen (DO and corrosion medium temperature, on corrosion behavior of copper alloy were analyzed. The corrosion failure prediction models under different ambient conditions were built. One-day corrosion weight loss under oxygenated stirring conditions was equivalent to 1.31-day weight loss under stationary conditions, and the corrosion rate under oxygenated conditions was 1.31 times higher than that under stationary conditions. In addition, corrosion medium temperature had a significant effect on the corrosion of B10 copper sheet.

  2. Stochastic Analysis and Forecasts of the Patterns of Speed, Acceleration, and Levels of Material Stock Accumulation in Society.

    Science.gov (United States)

    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.

  3. Design and analysis of a piezoelectric material based touch screen with additional pressure and its acceleration measurement functions

    Science.gov (United States)

    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.

  4. The statistical analysis of failure of a MEVATRON77 DX67 linear accelerator over a ten year period

    CERN Document Server

    Aoyama, H; Tahara, S; Uno, H; Kadohisa, S; Azuma, Y; Nakagiri, Y; Hiraki, Y

    2003-01-01

    A linear accelerator (linac) takes a leading role in radiation therapy. A linac consists of complicated main parts and systems and it is required that highly accurate operational procedures should be maintained. Operational failure occurs for various reasons. In this report, the failure occurrences of one linac over a ten year period were recorded and analyzed. The subject model was a MEVATRON77 DX67 (Siemens, Inc). The failure rate for each system, the form classification of the contents of failure, the operation situation at the time of failure, and the average performance life of the main parts were totaled. Moreover, the relation between the number of therapies that patients received (operating efficiency) and the failure rate within that number and the relation between environment (temperature and humidity) and the failure rate attributed to other systems were analyzed. In this report, irradiation interruption was also included with situations where treatment was unable to begin in total for the number o...

  5. The Real-Time Data Analysis and Decision System for Particle Flux Detection in the LHC Accelerator at CERN.

    CERN Document Server

    Zamantzas, C; Dehning, B

    2006-01-01

    The superconducting Large Hadron Collider (LHC) under construction at the European Organisation for Nuclear Research (CERN) is an accelerator unprecedented in terms of beam energy, particle production rate and also in the potential of self-destruction. Its operation requires a large variety of instrumentation, not only for the control of the beams, but also for the protection of the complex hardware systems. The Beam Loss Monitoring (BLM) system has to prevent the superconducting magnets from becoming normal conducting and protect the machine components against damages making it one of the most critical elements for the protection of the LHC. For its operation, the system requires 3600 detectors to be placed at various locations around the 27 km ring. The measurement system is sub-divided to the tunnel electronics, which are responsible for acquiring, digitising and transmitting the data, and the surface electronics, which receive the data via 2 km optical data links, process, analyze, store and issue warning...

  6. The application software of the CERN PS accelerator controls system — analysis of its cost and resources

    Science.gov (United States)

    Benincasa, Gianpaolo; Daneels, Axel; Heymans, Paul; Serre, Christian

    1986-06-01

    The CERN PS accelerators have evolved into one of the world's most sophisticated high energy physics facility. The variety of beams and their high repetition rate means that a most sophisticated controls system is required. This reflects on the application software. At the time of the completion of the new control system, nearly 1000 programs, amounting to around 450 000 lines of code, have been developed at the cost of approximately 120 man-years. The span of this software ranges from real-time application programs to special purpose development and management tools. This paper documents the cost, resources and production of this software project. These are analyzed in terms of the structure of the application software. Rules-of-thumb are suggested for estimating the required effort at various phases of the project and to define the implementation strategy.

  7. The Use of Integrated Electronic Data Capture and Analysis for Accelerator Construction and Commissioning Pansophy from the SNS Towards the ILC

    CERN Document Server

    Ozelis, Joseph P; Madre, Bonnie D; Reece, Charles E

    2005-01-01

    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.

  8. Combined analysis of νμ disappearance and νμ→νe appearance in MINOS using accelerator and atmospheric neutrinos.

    Science.gov (United States)

    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.

  9. Piezoelectric particle accelerator

    Energy Technology Data Exchange (ETDEWEB)

    Kemp, Mark A.; Jongewaard, Erik N.; Haase, Andrew A.; Franzi, Matthew

    2017-08-29

    A particle accelerator is provided that includes a piezoelectric accelerator element, where the piezoelectric accelerator element includes a hollow cylindrical shape, and an input transducer, where the input transducer is disposed to provide an input signal to the piezoelectric accelerator element, where the input signal induces a mechanical excitation of the piezoelectric accelerator element, where the mechanical excitation is capable of generating a piezoelectric electric field proximal to an axis of the cylindrical shape, where the piezoelectric accelerator is configured to accelerate a charged particle longitudinally along the axis of the cylindrical shape according to the piezoelectric electric field.

  10. Development and application of compact and on-chip electron linear accelerators for dynamic tracking cancer therapy and DNA damage/repair analysis

    Science.gov (United States)

    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.

  11. Acceleration without Horizons

    CERN Document Server

    Doria, Alaric

    2015-01-01

    We derive the metric of an accelerating observer moving with non-constant proper acceleration in flat spacetime. With the exception of a limiting case representing a Rindler observer, there are no horizons. In our solution, observers can accelerate to any desired terminal speed $v_{\\infty} < c$. The motion of the accelerating observer is completely determined by the distance of closest approach and terminal velocity or, equivalently, by an acceleration parameter and terminal velocity.

  12. Accelerating flight: Edge with arbitrary acceleration

    CSIR Research Space (South Africa)

    Gledhill, Irvy MA

    2011-11-01

    Full Text Available ? temporal scales ? Euler ? convection ? Reynolds ? translational viscous ? Ekman ? rotational viscous ? Translational acceleration ? related to g ? Rotational accleration ? Rossby ? Coriolis ? Centrifugal ? Gravitational ? CSIR 2009...

  13. Microwave View on Particle Acceleration in Flares

    CERN Document Server

    Fleishman, Gregory D

    2013-01-01

    The thermal-to-nonthermal partition was found to vary greatly from one flare to another resulting in a broad variety of cases from 'heating without acceleration' to 'acceleration without heating'. Recent analysis of microwave data of these differing cases suggests that a similar acceleration mechanism, forming a power-law nonthermal tail up to a few MeV or even higher, operates in all the cases. However, the level of this nonthermal spectrum compared to the original thermal distribution differs significantly from one case to another, implying a highly different thermal-to-nonthermal energy partition in various cases. This further requires a specific mechanism capable of extracting the charged particles from the thermal pool and supplying them to a bulk acceleration process to operate in flares \\textit{in addition} to the bulk acceleration process itself, which, in contrast, efficiently accelerates the seed particles, while cannot accelerate the thermal particles. Within this 'microwave' view on the flare ener...

  14. Accelerator Mass Spectrometry of Actinides in Ground- and Seawater: An Innovative Method Allowing for the Simultaneous Analysis of U, Np, Pu, Am, and Cm Isotopes below ppq Levels.

    Science.gov (United States)

    Quinto, Francesca; Golser, Robin; Lagos, Markus; Plaschke, Markus; Schäfer, Thorsten; Steier, Peter; Geckeis, Horst

    2015-06-02

    (236)U, (237)Np, and Pu isotopes and (243)Am were determined in ground- and seawater samples at levels below ppq (fg/g) with a maximum sample size of 250 g. Such high sensitivity was possible by using accelerator mass spectrometry (AMS) at the Vienna Environmental Research Accelerator (VERA) with extreme selectivity and recently improved efficiency and a significantly simplified separation chemistry. The use of nonisotopic tracers was investigated in order to allow for the determination of (237)Np and (243)Am, for which isotopic tracers either are rarely available or suffer from various isobaric mass interferences. In the present study, actinides were concentrated from the sample matrix via iron hydroxide coprecipitation and measured sequentially without previous chemical separation from each other. The analytical method was validated by the analysis of the Reference Material IAEA 443 and was applied to groundwater samples from the Colloid Formation and Migration (CFM) project at the deep underground rock laboratory of the Grimsel Test Site (GTS) and to natural water samples affected solely by global fallout. While the precision of the presented analytical method is somewhat limited by the use of nonisotopic spikes, the sensitivity allows for the determination of ∼10(5) atoms in a sample. This provides, e.g., the capability to study the long-term release and retention of actinide tracers in field experiments as well as the transport of actinides in a variety of environmental systems by tracing contamination from global fallout.

  15. Accelerated Analyte Uptake on Single Beads in Microliter-scale Batch Separations using Acoustic Streaming: Plutonium Uptake by Anion Exchange for Analysis by Mass Spectrometry

    Energy Technology Data Exchange (ETDEWEB)

    Paxton, Walter F.; O' Hara, Matthew J.; Peper, Shane M.; Petersen, Steven L.; Grate, Jay W.

    2008-06-01

    The use of acoustic streaming as a non-contact mixing platform to accelerate mass transport-limited diffusion processes in small volume heterogeneous reactions has been investigated. Single bead anion exchange of plutonium at nanomolar and sub-picomolar concentrations in 20 microliter liquid volumes was used to demonstrate the effect of acoustic mixing. Pu uptake rates on individual ~760 micrometer diameter AG 1x4 anion exchange resin beads were determined using acoustic mixing and compared with Pu uptake rates achieved by static diffusion alone. An 82 MHz surface acoustic wave (SAW) device was placed in contact with the underside of a 384-well microplate containing flat-bottomed semiconical wells. Acoustic energy was coupled into the solution in the well, inducing acoustic streaming. Pu uptake rates were determined by the plutonium remaining in solution after specific elapsed time intervals, using liquid scintillation counting (LSC) for nanomolar concentrations and thermal ionization mass spectrometry (TIMS) analysis for the sub-picomolar concentration experiments. It was found that this small batch uptake reaction could be accelerated by a factor of about five-fold or more, depending on the acoustic power applied.

  16. Analysis and Management of Accelerated Aging of Relay in NPPs%核电厂继电器加速老化分析及管理研究

    Institute of Scientific and Technical Information of China (English)

    张圣; 马沂荩; 江虹; 陈世均; 黄立军; 莫春铌

    2013-01-01

    This paper reveals the main factors of accelerated the aging of relay through statistical analysis of aging and failure data of intermediate relay and output relay for MV distribution board in Daya Bay nuclear power plant and Ling'ao nuclear power plant The factors of accelerating relay aging are operation context including humidity, temperature, vibration impact, and etc., and aging mechanism including oxidation corrosion, mechanical wear, electrical wear, organic gas corrosion, insulation aging, electromagnetic interference, and etc. The suggested measures are the classified management, relay replacement, periodic check, and periodic replacement or maintenance.%通过对大亚湾和岭澳核电站中压配电盘的中间和出口继电器老化与失效数据进行统计,分析核电厂继电器加速老化的主要因素.继电器加速老化的影响因素为运行环境,主要是湿度、温度和振动冲击;老化机理为氧化腐蚀、机械磨损、电磨损、有机气体腐蚀、绝缘老化和电磁干扰.建议对继电器分类管理、替代使用,进行周期检测、更换或维护.

  17. 浅谈固定资产加速折旧法的应用%Analysis on the Application of the Accelerated Depreciation Method of Fixed Asset

    Institute of Scientific and Technical Information of China (English)

    王晓东

    2013-01-01

    Following the development of the market economy, enterprise financial management is also in constant change. This paper mainly discusses the deepening of the market competitiveness of enterprises in the process of operation. Analysis on influence of using the accelerated depreciation method of fixed asset to count and draw the depreciation of fixed assets of industrial accounting data and business income tax is given. lastly, the important significance of the accelerated depreciation of fixed assets is expounded.%  随着市场经济发展不断加快,企业财务管理也在不断的变化之中。本文主要讨论企业在运行过程中对市场竞争力不断加深,其在使用加速折旧法计提固定资产折旧对企业会计信息、企业所得税的影响进行了分析,并阐述了对固定资产进行加速折旧的重要意义。

  18. Analysis of accelerated degradation of a HT-PEM fuel cell caused by cell reversal in fuel starvation condition

    DEFF Research Database (Denmark)

    Zhou, Fan; Andreasen, Søren Juhl; Kær, Søren Knudsen;

    2015-01-01

    This paper reports an accelerated degradation test of a high temperature PEM fuel cell under repeated H2 starvation condition. The H2 stoichiometry is cycled between 3.0 and 0.8 every 2 min during the test. The experimental results show that the polarity of the fuel cell is reversed under H2...... starvation condition, and the cell performance indicated by cell voltage at H2 stoichiometry of 3.0 declines from 0.59 V to 0.41 V in 19 cycles. Since CO2 is detected in anode exhaust under H2 starvation condition, carbon corrosion is believed to be the reason for the degradation in this test. After the test......, there is only a slight decrease in open circuit voltage of the fuel cell which implies the membrane is not affected by the test. The electrochemical impedance spectrum measurement shows that the H2 starvation can cause significant increase in the ohmic resistance and charge transfer resistance. By looking...

  19. Vol. 34 - Optimization of quench protection heater performance in high-field accelerator magnets through computational and experimental analysis

    CERN Document Server

    Salmi, Tiina

    2016-01-01

    Superconducting accelerator magnets with increasingly hi gh magnetic fields are being designed to improve the performance of the Large Hadron Collider (LHC) at CERN. One of the technical challenges is the magnet quench p rotection, i.e., preventing damage in the case of an unexpected loss of superc onductivity and the heat generation related to that. Traditionally this is d one by disconnecting the magnet current supply and using so-called protection he aters. The heaters suppress the superconducting state across a large fraction of the winding thus leading to a uniform dissipation of the stored energy. Preli minary studies suggested that the high-field Nb 3 Sn magnets under development for the LHC luminosity upgrade (HiLumi) could not be reliably protected using the existing heaters. In this thesis work I analyzed in detail the present state-of-the-art protection heater technology, aiming to optimize its perfo rmance and evaluate the prospects in high-field magnet protection. The heater efficiency analyses ...

  20. CARAT-GxG: CUDA-Accelerated Regression Analysis Toolkit for Large-Scale Gene-Gene Interaction with GPU Computing System.

    Science.gov (United States)

    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.

  1. High-Intensity Proton Accelerator

    Energy Technology Data Exchange (ETDEWEB)

    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.

  2. Speciation analysis of 129I in seawater using coprecipitation and accelerator mass spectrometry and its applications

    DEFF Research Database (Denmark)

    Xing, Shan; Hou, Xiaolin; Aldahan, Ala

    2017-01-01

    Speciation analysis of long-lived 129I in seawater can provide useful information on the source of water masses. This paper presents an improved method for speciation analysis of 129I based on coprecipitation of iodide as AgI with Ag2SO3 and AgCl. By adding a small amount of 127I carrier, the sep...

  3. The new external ion beam analysis setup at the Demokritos Tandem accelerator and first applications in cultural heritage

    Science.gov (United States)

    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.

  4. Analysis of tetragonal to monoclinic phase transformation caused by accelerated artificial aging and the effects of microstructure in stabilized zirconia

    Science.gov (United States)

    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

    Energy Technology Data Exchange (ETDEWEB)

    Sokaras, Dimosthenis, E-mail: dsokaras@inp.demokritos.g [Institute of Nuclear Physics, N.C.S.R. ' Demokritos' , Aghia Paraskevi, 15310 Athens (Greece); Bistekos, Euthimios; Georgiou, Lambros [Philon Models, 18541 Piraeus (Greece); Salomon, Joseph [Laboratoire du C2RMF, Centre de Rechereche et de Restauration des Musees du France, 75001 Paris (France); Bogovac, Mladen [Institute Ruder Boskovic, 10002 Zagreb (Croatia); Aloupi-Siotis, Eleni [Thetis Authentics Ltd., 11636 Athens (Greece); Paschalis, Vasilis [Benaki Museum, 10674 Athens (Greece); Aslani, Ioanna [Thetis Authentics Ltd., 11636 Athens (Greece); Karabagia, Sofia; Lagoyannis, Anastasios; Harissopulos, Sotirios; Kantarelou, Vasiliki [Institute of Nuclear Physics, N.C.S.R. ' Demokritos' , Aghia Paraskevi, 15310 Athens (Greece); Karydas, Andreas-Germanos [Institute of Nuclear Physics, N.C.S.R. ' Demokritos' , Aghia Paraskevi, 15310 Athens (Greece); Nuclear Spectrometry and Applications Laboratory, International Atomic Energy Agency (IAEA), 2444 Seibersdorf (Austria)

    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{sup 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, {gamma}-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. 2014 CERN Accelerator Schools: Plasma Wake Acceleration

    CERN Multimedia

    2014-01-01

    A specialised school on Plasma Wake Acceleration will be held at CERN, Switzerland from 23-29 November, 2014.   This course will be of interest to staff and students in accelerator laboratories, university departments and companies working in or having an interest in the field of new acceleration techniques. Following introductory lectures on plasma and laser physics, the course will cover the different components of a plasma wake accelerator and plasma beam systems. An overview of the experimental studies, diagnostic tools and state of the art wake acceleration facilities, both present and planned, will complement the theoretical part. Topical seminars and a visit of CERN will complete the programme. Further information can be found at: http://cas.web.cern.ch/cas/PlasmaWake2014/CERN-advert.html http://indico.cern.ch/event/285444/

  7. Using "short" interrupted time-series analysis to measure the impacts of whole-school reforms. With applications to a study of accelerated schools.

    Science.gov (United States)

    Bloom, Howard S

    2003-02-01

    The present article introduces a new approach for measuring the impacts of whole-school reforms. The approach is based on "short" interrupted time-series analysis, which has been used to evaluate programs in many fields. The approach is used to measure impacts on three facets of student performance: (a) average (mean) test scores, which summarize impacts on total performance; (b) the distribution of scores across specific ranges, which helps to identify where in the distribution of student performance impacts were experienced; and (c) the variation (standard deviation) of scores, which indicates how the disparity in student performance was affected. To help researchers use the approach, the article lays out its conceptual rationale, describes its statistical procedures, explains how to interpret its findings, indicates its strengths and limitations, and illustrates how it was used to evaluate a major whole-school reform--Accelerated Schools.

  8. Production yield of produced radioisotopes from 100 MeV proton beam on lead target for shielding analysis of large accelerator

    Energy Technology Data Exchange (ETDEWEB)

    Oranj, Leila Mokhtari; Oh, Joo Hee; Jung, Nam Suk; Bae, O Ryun; Lee, Hee Seock [Div. of Advanced Nuclear Engineering, POSTECH, Pohang (Korea, Republic of)

    2014-11-15

    In this work, the production yield of major shielding material, a lead, was investigated using 100 MeV protons of KOMAC accelerator facility. For the analysis of the experimental data, the activity has been calculated using the FLUKA Monte Carlo code and analytical methods. The cross section data and the stopping power in the irradiated assembly were calculated by TALYS and SRIM codes in the analytical method, respectively. Consequently, the experimental production yield of produced radioisotopes was compared with the data that are based on Monte Carlo calculations and analytical studies. In this research, the {sup nat}Pb(p, x) reaction was studied using experimental measurements, Monte Carlo simulations and analytical methods. Rereading to the experimental measurements, we demonstrate that both Monte Carlo simulation and analytical methods could be useful tools for the estimation of production yield of this reaction.

  9. Qualitative analysis of multi-disciplinary round-table discussions on the acceleration of benefits and data analytics through hospital electronic prescribing (ePrescribing) systems.

    Science.gov (United States)

    Cresswell, Kathrin; Coleman, Jamie; Smith, Pam; Swainson, Charles; Slee, Ann; Sheikh, Aziz

    2016-07-04

    Electronic systems that facilitate prescribing, administration and dispensing of medicines (ePrescribing systems) are at the heart of international efforts to improve the safety, quality and efficiency of medicine management. Considering the initial costs of procuring and maintaining ePrescribing systems, there is a need to better understand how to accelerate and maximise the financial benefits associated with these systems. We sought to investigate how different sectors are approaching the realisation of returns on investment from ePrescribing systems in U.K. hospitals and what lessons can be learned for future developments and implementation strategies within healthcare settings. We conducted international, multi-disciplinary, round-table discussions with 21 participants from different backgrounds including policy makers, healthcare organisations, academic researchers, vendors and patient representatives. The discussions were audio-recorded, transcribed and then thematically analysed with the qualitative analysis software NVivo10. There was an over-riding concern that realising financial returns from ePrescribing systems was challenging. The underlying reasons included substantial fixed costs of care provision, the difficulties in radically changing the medicines management process and the lack of capacity within NHS hospitals to analyse and exploit the digital data being generated. Any future data strategy should take into account the need to collect and analyse local and national data (i.e. within and across hospitals), setting comparators to measure progress (i.e. baseline measurements) and clear standards guiding data management so that data are comparable across settings. A more coherent national approach to realising financial benefits from ePrescribing systems is needed as implementations progress and the range of tools to collect information will lead to exponential data growth. The move towards more sophisticated closed-loop systems that integrate

  10. Accelerated partial breast irradiation using once-daily fractionation: analysis of 312 cases with four years median follow-up

    Directory of Open Access Journals (Sweden)

    Shaikh Arif Y

    2012-02-01

    Full Text Available Abstract 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

  11. High Energy Particle Accelerators

    CERN Multimedia

    Audio Productions, Inc, New York

    1960-01-01

    Film about the different particle accelerators in the US. Nuclear research in the US has developed into a broad and well-balanced program.Tour of accelerator installations, accelerator development work now in progress and a number of typical experiments with high energy particles. Brookhaven, Cosmotron. Univ. Calif. Berkeley, Bevatron. Anti-proton experiment. Negative k meson experiment. Bubble chambers. A section on an electron accelerator. Projection of new accelerators. Princeton/Penn. build proton synchrotron. Argonne National Lab. Brookhaven, PS construction. Cambridge Electron Accelerator; Harvard/MIT. SLAC studying a linear accelerator. Other research at Madison, Wisconsin, Fixed Field Alternate Gradient Focusing. (FFAG) Oakridge, Tenn., cyclotron. Two-beam machine. Comments : Interesting overview of high energy particle accelerators installations in the US in these early years. .

  12. Improved plasma accelerator

    Science.gov (United States)

    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.

  13. Accelerator Technology Division

    Science.gov (United States)

    1992-04-01

    In fiscal year (FY) 1991, the Accelerator Technology (AT) division continued fulfilling its mission to pursue accelerator science and technology and to develop new accelerator concepts for application to research, defense, energy, industry, and other areas of national interest. This report discusses the following programs: The Ground Test Accelerator Program; APLE Free-Electron Laser Program; Accelerator Transmutation of Waste; JAERI, OMEGA Project, and Intense Neutron Source for Materials Testing; Advanced Free-Electron Laser Initiative; Superconducting Super Collider; The High-Power Microwave Program; (Phi) Factory Collaboration; Neutral Particle Beam Power System Highlights; Accelerator Physics and Special Projects; Magnetic Optics and Beam Diagnostics; Accelerator Design and Engineering; Radio-Frequency Technology; Free-Electron Laser Technology; Accelerator Controls and Automation; Very High-Power Microwave Sources and Effects; and GTA Installation, Commissioning, and Operations.

  14. Accelerators, Colliders, and Snakes

    Science.gov (United States)

    Courant, Ernest D.

    2003-12-01

    The author traces his involvement in the evolution of particle accelerators over the past 50 years. He participated in building the first billion-volt accelerator, the Brookhaven Cosmotron, which led to the introduction of the "strong-focusing" method that has in turn led to the very large accelerators and colliders of the present day. The problems of acceleration of spin-polarized protons are also addressed, with discussions of depolarizing resonances and "Siberian snakes" as a technique for mitigating these resonances.

  15. The CERN Accelerator School

    CERN Multimedia

    2016-01-01

    Introduction to accelerator physics The CERN Accelerator School: Introduction to Accelerator Physics, which should have taken place in Istanbul, Turkey, later this year has now been relocated to Budapest, Hungary.  Further details regarding the new hotel and dates will be made available as soon as possible on a new Indico site at the end of May.

  16. Accelerators and Dinosaurs

    CERN Multimedia

    Turner, Michael Stanley

    2003-01-01

    Using naturally occuring particles on which to research might have made accelerators become extinct. But in fact, results from astrophysics have made accelerator physics even more important. Not only are accelerators used in hospitals but they are also being used to understand nature's inner workings by searching for Higgs bosons, CP violation, neutrino mass and dark matter (2 pages)

  17. Far field acceleration

    Energy Technology Data Exchange (ETDEWEB)

    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.

  18. Acceleration: It's Elementary

    Science.gov (United States)

    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. An effective method of UV-oxidation of dissolved organic carbon in natural waters for radiocarbon analysis by accelerator mass spectrometry

    Science.gov (United States)

    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.

  20. Accelerated solvent extraction and analysis of tea polyphenols%茶多酚的加速溶剂萃取与分析

    Institute of Scientific and Technical Information of China (English)

    赵敏; 唐美华; 张之翼; 吕凤兰; 陈国松

    2012-01-01

    以毛尖茶叶为原料,用加速溶剂萃取法提取茶多酚粗品.用单因素试验研究和正交试验考察乙醇体积分数、温度和循环次数对萃取率的影响.用二极管阵列-高效液相色谱( DAD - HPLC)对照测定加速溶剂萃取的萘多酚粗品、微波辅助提取的萘多酚粗品和商品荼多酚.结果表明:茶多酚粗品的制备最佳条件为萃取温度160℃、乙醇体积分数60%、循环萃取2次.高温加速溶剂萃取法对茶多酚的粗提率较高,但其中儿茶素的总量却显著下降.降低提取温度,则茶多酚中的主要功能成分儿茶素的含量显著高于微波辅助提取法.%The gross tea polyphenols were extracted from Maojian tea by the accelerated solvent method. Single factor test and orthogonal design were used to explore the effects of ethanol volume fraction, temperature and cycle times on the extraction ratio. The comparison of gross polyphenols got from accelerated solvent extraction, microwave-assisted extraction and commodity was made by diode array detector-high performance liquid chromatography (DAD-HPLC) analysis. Results showed that the optimum operation conditions for gross polyphenlos extraction are 160 ℃ , 2 times, and 60% ethanol. The accelerated solvent extraction ratio at a high temperature was higher for the gross tea polyphenols and lower for the cate-chin. If the extraction temperature was dropped down to 40℃, the content of catechin was much higher than that from microwave-assisted extraction.

  1. Phase-plane analysis of gaze stabilization to high acceleration head thrusts: a continuum across normal subjects and patients with loss of vestibular function.

    Science.gov (United States)

    Peng, Grace C Y; Zee, David S; Minor, Lloyd B

    2004-04-01

    We investigated the vestibulo-ocular reflex (VOR) during high-acceleration, yaw-axis, head rotations in 12 normals and 15 patients with vestibular loss [7 unilateral vestibular deficient (UVD) and 8 bilateral vestibular deficient (BVD)]. We analyzed gaze stabilization within a 200-ms window after head rotation began, using phase planes, which allowed simultaneous analysis of gaze velocity and gaze position. These "gaze planes" revealed critical dynamic information not easily gleaned from traditional gain measurements. We found linear relationships between peak gaze-velocity and peak gaze-position error when normalized to peak head speed and position, respectively. Values fell on a continuum, increasing from normals, to normals tested with very high acceleration (VHA = 10,000-20,000 degrees/s2), to UVD patients during rotations toward the intact side, to UVD patients during rotations toward the lesioned side, to BVD patients. We classified compensatory gaze corrections as gaze-position corrections (GPCs) or gaze-velocity error corrections (GVCs). We defined patients as better-compensated when the value of their end gaze position was low relative to peak gaze position. In the gaze plane this criterion corresponded to relatively stereotyped patterns over many rotations, and appearance of high velocity (100-400 degrees/s) GPCs in the gaze plane ending quadrant (150-200 ms after head movement onset). In less-compensated patients, and normals at VHA, more GVCs were generated, and GPCs were generated only after gaze-velocity error was minimized. These findings suggest that challenges to compensatory vestibular function can be from vestibular deficiency or novel stimuli not previously experienced. Similar patterns of challenge and compensation were observed in both patients with vestibular loss and normal subjects.

  2. An investigation of the neutron flux in bone-fluorine phantoms comparing accelerator based in vivo neutron activation analysis and FLUKA simulation data

    Energy Technology Data Exchange (ETDEWEB)

    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.

  3. The Accelerator Reliability Forum

    CERN Document Server

    Lüdeke, Andreas; Giachino, R

    2014-01-01

    A high reliability is a very important goal for most particle accelerators. The biennial Accelerator Reliability Workshop covers topics related to the design and operation of particle accelerators with a high reliability. In order to optimize the over-all reliability of an accelerator one needs to gather information on the reliability of many different subsystems. While a biennial workshop can serve as a platform for the exchange of such information, the authors aimed to provide a further channel to allow for a more timely communication: the Particle Accelerator Reliability Forum [1]. This contribution will describe the forum and advertise it’s usage in the community.

  4. 核电关键设备加速老化分析与维修策略研究%Analysis and Maintenance Policy on Accelerated Aging of Nuclear Power Critical Equipments

    Institute of Scientific and Technical Information of China (English)

    张圣; 李继

    2011-01-01

    Key equipments for nuclear power plants appeared accelerated aging problem, the paper gives the accelerated aging factor, the establishment of technical routes, the aging of the equipment status, to do an assessment of the reliability analysis. As well as accelerated aging mechanism analysis and countermeasures have done a study on maintenance of equipment for the next lay the foundation for the formulation of strategy.%针对核电站关键设备出现的加速老化问题,给出了加速老化的因素,制定了技术路线,对设备的老化状态、可靠性做了评估分析.并对加速老化机理分析和对策做了研究,为下一步设备维修策略的制定奠定基础.

  5. Acceleration profiles in elite Australian soccer.

    Science.gov (United States)

    Varley, M C; Aughey, R J

    2013-01-01

    We quantified the acceleration and high-velocity running of elite Australian soccer players. We hypothesised that high-intensity activity would be underestimated when excluding acceleration during match analysis given its high metabolic demand and occurrence at low velocities. Player movements were observed from 29 players (forwards and central and wide defenders and midfielders) during domestic Australian competition using 5-Hz global positioning system. Effort occurrence were determined for high-velocity running, sprinting and maximal accelerations. The commencement and final velocity of maximal accelerations were also identified. Players undertook an 8~fold greater number of maximal accelerations than sprints per game (65±21 vs. 8±5). Of maximal accelerations ~98% commenced from a starting velocity lower than what would be considered high-velocity running while ~85% did not cross the high-velocity running threshold. The number of efforts performed in all categories were position dependent (Psprints compared to all other positions (Pdrills.

  6. Industrial Application of Accelerators

    CERN Document Server

    CERN. Geneva

    2017-01-01

    At CERN, we are very familiar with large, high energy particle accelerators. However, in the world outside CERN, there are more than 35000 accelerators which are used for applications ranging from treating cancer, through making better electronics to removing harmful micro-organisms from food and water. These are responsible for around $0.5T of commerce each year. Almost all are less than 20 MeV and most use accelerator types that are somewhat different from what is at CERN. These lectures will describe some of the most common applications, some of the newer applications in development and the accelerator technology used for them. It will also show examples of where technology developed for particle physics is now being studied for these applications. Rob Edgecock is a Professor of Accelerator Science, with a particular interest in the medical applications of accelerators. He works jointly for the STFC Rutherford Appleton Laboratory and the International Institute for Accelerator Applications at the Univer...

  7. Industrial Application of Accelerators

    CERN Document Server

    CERN. Geneva

    2017-01-01

    At CERN, we are very familiar with large, high energy particle accelerators. However, in the world outside CERN, there are more than 35000 accelerators which are used for applications ranging from treating cancer, through making better electronics to removing harmful micro-organisms from food and water. These are responsible for around $0.5T of commerce each year. Almost all are less than 20 MeV and most use accelerator types that are somewhat different from what is at CERN. These lectures will describe some of the most common applications, some of the newer applications in development and the accelerator technology used for them. It will also show examples of where technology developed for particle physics is now being studied for these applications. Rob Edgecock is a Professor of Accelerator Science, with a particular interest in the medical applications of accelerators. He works jointly for the STFC Rutherford Appleton Laboratory and the International Institute for Accelerator Applications at the Uni...

  8. Dynamics of pyroelectric accelerators

    Energy Technology Data Exchange (ETDEWEB)

    Ghaderi, R.; Davani, F. Abbasi, E-mail: fabbasi@sbu.ac.ir [Radiation Application Department, Shahid Beheshti University, Tehran (Iran, Islamic Republic of)

    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.

  9. Analysis of insulation resistance degradation in Ni–BaTiO3 multilayer ceramic capacitors under highly accelerated life test

    Science.gov (United States)

    Sada, Takao; Fujikawa, Nobuyoshi

    2017-10-01

    The degradation mechanism of electrical breakdown in Ni–BaTiO3 multilayer ceramic capacitors (MLCCs) was studied by visualizing degraded areas in early failure and wear-out failure modes. The visualization was achieved by the fabrication of electrically degraded MLCCs just before electrical breakdown and by detection of the degraded area by infrared-optical-beam-induced resistance change (IR-OBIRCH) analysis. In the case of our prototype MLCCs, a thinner dielectric layer caused early failure and microstructural abnormalities in the dielectric layer caused wear-out failure. Such a visualization method directly demonstrates the causes of electrical breakdown in MLCCs.

  10. Acceleration in astrophysics

    Energy Technology Data Exchange (ETDEWEB)

    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.

  11. Quantitative analysis of results of quality control tests in linear accelerators used in radiotherapy; Analise quantitativa dos resultados de testes de controle de qualidade em aceleradores lineares usados em radioterapia

    Energy Technology Data Exchange (ETDEWEB)

    Passaro, Bruno M.; Rodrigues, Laura N. [Instituto de Pesquisas Energeticas e Nucleares (IPEN/CNEN-SP), Sao Paulo, SP (Brazil); Videira, Heber S., E-mail: bruno.passaro@gmail.com [Universidade de Sao Paulo (HCFMRP/USP), Sao Paulo, SP (Brazil). Faculdade de Medicina. Hospital das Clinicas

    2013-04-15

    The aim of this study is to assess and analyze the stability of the calibration factor of three linear accelerators, as well as the other dosimetric parameters normally included in a program of quality control in radiotherapy. The average calibration factors of the accelerators for the period of approximately four years for the Clinac 600C and Clinac 6EX were (0.998±0.012) and (0.996±0.014), respectively. For the Clinac 2100CD 6 MV and 15 MV was (1.008±0.009) and (1.006±0.010), respectively, in a period of approximately four years. The data of the calibration factors were divided into four subgroups for a more detailed analysis of behavior over the years. Through statistical analysis of calibration factors, we found that for the 600C and Clinacs 2100CD, is an expected probability that more than 90% of cases the values are within acceptable ranges according to TG-142, while for the Clinac 6EX is expected around 85% since this had several exchanges of accelerator components. The values of TPR20,10 of three accelerators are practically constant and within acceptable limits according to the TG-142. It can be concluded that a detailed study of data from the calibration factor of the accelerators and TPR{sub 20},{sub 10} from a quantitative point of view, is extremely useful in a quality assurance program. (author)

  12. Exploratory Data Analysis of Acceleration Signals to Select Light-Weight and Accurate Features for Real-Time Activity Recognition on Smartphones

    Directory of Open Access Journals (Sweden)

    Seok-Won Lee

    2013-09-01

    Full Text Available Smartphone-based activity recognition (SP-AR recognizes users’ activities using the embedded accelerometer sensor. Only a small number of previous works can be classified as online systems, i.e., the whole process (pre-processing, feature extraction, and classification is performed on the device. Most of these online systems use either a high sampling rate (SR or long data-window (DW to achieve high accuracy, resulting in short battery life or delayed system response, respectively. This paper introduces a real-time/online SP-AR system that solves this problem. Exploratory data analysis was performed on acceleration signals of 6 activities, collected from 30 subjects, to show that these signals are generated by an autoregressive (AR process, and an accurate AR-model in this case can be built using a low SR (20 Hz and a small DW (3 s. The high within class variance resulting from placing the phone at different positions was reduced using kernel discriminant analysis to achieve position-independent recognition. Neural networks were used as classifiers. Unlike previous works, true subject-independent evaluation was performed, where 10 new subjects evaluated the system at their homes for 1 week. The results show that our features outperformed three commonly used features by 40% in terms of accuracy for the given SR and DW.

  13. Particle-accelerator decommissioning

    Energy Technology Data Exchange (ETDEWEB)

    Opelka, J.H.; Mundis, R.L.; Marmer, G.J.; Peterson, J.M.; Siskind, B.; Kikta, M.J.

    1979-12-01

    Generic considerations involved in decommissioning particle accelerators are examined. There are presently several hundred accelerators operating in the United States that can produce material containing nonnegligible residual radioactivity. Residual radioactivity after final shutdown is generally short-lived induced activity and is localized in hot spots around the beam line. The decommissioning options addressed are mothballing, entombment, dismantlement with interim storage, and dismantlement with disposal. The recycle of components or entire accelerators following dismantlement is a definite possibility and has occurred in the past. Accelerator components can be recycled either immediately at accelerator shutdown or following a period of storage, depending on the nature of induced activation. Considerations of cost, radioactive waste, and radiological health are presented for four prototypic accelerators. Prototypes considered range from small accelerators having minimal amounts of radioactive mmaterial to a very large accelerator having massive components containing nonnegligible amounts of induced activation. Archival information on past decommissionings is presented, and recommendations concerning regulations and accelerator design that will aid in the decommissioning of an accelerator are given.

  14. Epistasis between COMT Val158Met and DRD3 Ser9Gly polymorphisms and cognitive function in schizophrenia: genetic influence on dopamine transmission

    Directory of Open Access Journals (Sweden)

    Alexandre A. Loch

    2015-09-01

    Full Text Available Objective:To assess the relationship between cognitive function, a proposed schizophrenia endophenotype, and two genetic polymorphisms related to dopamine function, catechol-O-methyl transferase (COMT Val158Met and dopamine receptor 3 (DRD3 Ser9Gly.Methods:Fifty-eight outpatients with schizophrenia/schizoaffective disorder and 88 healthy controls underwent neurocognitive testing and genotyping. Analyses of covariance (ANCOVAs using age, sex, and years of education as covariates compared cognitive performance for the proposed genotypes in patients and controls. ANCOVAs also tested for the epistatic effect of COMT and DRD3 genotype combinations on cognitive performance.Results:For executive functioning, COMT Val/Val patients performed in a similar range as controls (30.70-33.26 vs. 35.53-35.67, but as COMT Met allele frequency increased, executive functioning worsened. COMT Met/Met patients carrying the DRD3 Ser/Ser genotype performed poorest (16.184 vs. 27.388-31.824. Scores of carriers of this COMT/DRD3 combination significantly differed from all DRD3 Gly/Gly combinations (p < 0.05, from COMT Val/Met DRD3 Ser/Gly (p = 0.02, and from COMT Val/Val DRD3 Ser/Ser (p = 0.01 in patients. It also differed significantly from all control scores (p < 0.001.Conclusion:Combined genetic polymorphisms related to dopamine neurotransmission might influence executive function in schizophrenia. Looking at the effects of multiple genes on a single disease trait (epistasis provides a comprehensive and more reliable way to determine genetic effects on endophenotypes.

  15. Patient-Specific Electric Field Simulations and Acceleration Measurements for Objective Analysis of Intraoperative Stimulation Tests in the Thalamus.

    Science.gov (United States)

    Hemm, Simone; Pison, Daniela; Alonso, Fabiola; Shah, Ashesh; Coste, Jérôme; Lemaire, Jean-Jacques; Wårdell, Karin

    2016-01-01

    Despite an increasing use of deep brain stimulation (DBS) the fundamental mechanisms of action remain largely unknown. Simulation of electric entities has previously been proposed for chronic DBS combined with subjective symptom evaluations, but not for intraoperative stimulation tests. The present paper introduces a method for an objective exploitation of intraoperative stimulation test data to identify the optimal implant position of the chronic DBS lead by relating the electric field (EF) simulations to the patient-specific anatomy and the clinical effects quantified by accelerometry. To illustrate the feasibility of this approach, it was applied to five patients with essential tremor bilaterally implanted in the ventral intermediate nucleus (VIM). The VIM and its neighborhood structures were preoperatively outlined in 3D on white matter attenuated inversion recovery MR images. Quantitative intraoperative clinical assessments were performed using accelerometry. EF simulations (n = 272) for intraoperative stimulation test data performed along two trajectories per side were set-up using the finite element method for 143 stimulation test positions. The resulting EF isosurface of 0.2 V/mm was superimposed to the outlined anatomical structures. The percentage of volume of each structure's overlap was calculated and related to the corresponding clinical improvement. The proposed concept has been successfully applied to the five patients. For higher clinical improvements, not only the VIM but as well other neighboring structures were covered by the EF isosurfaces. The percentage of the volumes of the VIM, of the nucleus intermediate lateral of the thalamus and the prelemniscal radiations within the prerubral field of Forel increased for clinical improvements higher than 50% compared to improvements lower than 50%. The presented new concept allows a detailed and objective analysis of a high amount of intraoperative data to identify the optimal stimulation target. First

  16. Bayes Analysis and Reliability Implications of Stress-Rupture Testing a Kevlar/Epoxy COPV Using Temperature and Pressure Acceleration

    Science.gov (United States)

    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.

  17. Leaky Fermi accelerators

    CERN Document Server

    Shah, Kushal; Rom-Kedar, Vered; Turaev, Dmitry

    2015-01-01

    A Fermi accelerator is a billiard with oscillating walls. A leaky accelerator interacts with an environment of an ideal gas at equilibrium by exchange of particles through a small hole on its boundary. Such interaction may heat the gas: we estimate the net energy flow through the hole under the assumption that the particles inside the billiard do not collide with each other and remain in the accelerator for sufficiently long time. The heat production is found to depend strongly on the type of the Fermi accelerator. An ergodic accelerator, i.e. one which has a single ergodic component, produces a weaker energy flow than a multi-component accelerator. Specifically, in the ergodic case the energy gain is independent of the hole size, whereas in the multi-component case the energy flow may be significantly increased by shrinking the hole size.

  18. Accelerator reliability workshop

    Energy Technology Data Exchange (ETDEWEB)

    Hardy, L.; Duru, Ph.; Koch, J.M.; Revol, J.L.; Van Vaerenbergh, P.; Volpe, A.M.; Clugnet, K.; Dely, A.; Goodhew, D

    2002-07-01

    About 80 experts attended this workshop, which brought together all accelerator communities: accelerator driven systems, X-ray sources, medical and industrial accelerators, spallation sources projects (American and European), nuclear physics, etc. With newly proposed accelerator applications such as nuclear waste transmutation, replacement of nuclear power plants and others. Reliability has now become a number one priority for accelerator designers. Every part of an accelerator facility from cryogenic systems to data storage via RF systems are concerned by reliability. This aspect is now taken into account in the design/budget phase, especially for projects whose goal is to reach no more than 10 interruptions per year. This document gathers the slides but not the proceedings of the workshop.

  19. Accelerator and radiation physics

    CERN Document Server

    Basu, Samita; Nandy, Maitreyee

    2013-01-01

    "Accelerator and radiation physics" encompasses radiation shielding design and strategies for hadron therapy accelerators, neutron facilities and laser based accelerators. A fascinating article describes detailed transport theory and its application to radiation transport. Detailed information on planning and design of a very high energy proton accelerator can be obtained from the article on radiological safety of J-PARC. Besides safety for proton accelerators, the book provides information on radiological safety issues for electron synchrotron and prevention and preparedness for radiological emergencies. Different methods for neutron dosimetry including LET based monitoring, time of flight spectrometry, track detectors are documented alongwith newly measured experimental data on radiation interaction with dyes, polymers, bones and other materials. Design of deuteron accelerator, shielding in beam line hutches in synchrotron and 14 MeV neutron generator, various radiation detection methods, their characteriza...

  20. Power Converters for Accelerators

    CERN Document Server

    Visintini, R

    2015-01-01

    Particle accelerators use a great variety of power converters for energizing their sub-systems; while the total number of power converters usually depends on the size of the accelerator or combination of accelerators (including the experimental setup), the characteristics of power converters depend on their loads and on the particle physics requirements: this paper aims to provide an overview of the magnet power converters in use in several facilities worldwide.

  1. Miniaturization Techniques for Accelerators

    Energy Technology Data Exchange (ETDEWEB)

    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.

  2. FFAGS for rapid acceleration

    Energy Technology Data Exchange (ETDEWEB)

    Carol J. Johnstone and Shane Koscielniak

    2002-09-30

    When large transverse and longitudinal emittances are to be transported through a circular machine, extremely rapid acceleration holds the advantage that the beam becomes immune to nonlinear resonances because there is insufficient time for amplitudes to build up. Uncooled muon beams exhibit large emittances and require fast acceleration to avoid decay losses and would benefit from this style of acceleration. The approach here employs a fixed-field alternating gradient or FFAG magnet structure and a fixed frequency acceleration system. Acceptance is enhanced by the use only of linear lattice elements, and fixed-frequency rf enables the use of cavities with large shunt resistance and quality factor.

  3. FFAGS FOR MUON ACCELERATION.

    Energy Technology Data Exchange (ETDEWEB)

    BERG,J.S.KAHN,S.PALMER,R.TRBOJEVIC,D.JOHNSTONE,C.KEIL,Y.OGITSU,T.OHMORI,C.SESSLER,A.KOSCIELNIAK,S.

    2003-06-26

    Due to their finite lifetime, muons must be accelerated very rapidly. It is challenging to make the magnets ramp fast enough to accelerate in a synchrotron, and accelerating in a linac is very expensive. One can use a recirculating accelerator (like CEBAF), but one needs a different arc for each turn, and this limits the number of turns one can use to accelerate, and therefore requires significant amounts of RF to achieve the desired energy gain. An alternative method for muon acceleration is using a fixed field alternating gradient (FFAG) accelerator. Such an accelerator has a very large energy acceptance (a factor of two or three), allowing one to use the same arc with a magnetic field that is constant over time. Thus, one can in principle make as many turns as one can tolerate due to muon decay, therefore reducing the RF cost without increasing the arc cost. This paper reviews the current status of research into the design of FFAGs for muon acceleration. Several current designs are described and compared. General design considerations are also discussed.

  4. High Gradient Accelerator Research

    Energy Technology Data Exchange (ETDEWEB)

    Temkin, Richard [Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States). Dept. of Physics. Plasma Science and Fusion Center

    2016-07-12

    The goal of the MIT program of research on high gradient acceleration is the development of advanced acceleration concepts that lead to a practical and affordable next generation linear collider at the TeV energy level. Other applications, which are more near-term, include accelerators for materials processing; medicine; defense; mining; security; and inspection. The specific goals of the MIT program are: • Pioneering theoretical research on advanced structures for high gradient acceleration, including photonic structures and metamaterial structures; evaluation of the wakefields in these advanced structures • Experimental research to demonstrate the properties of advanced structures both in low-power microwave cold test and high-power, high-gradient test at megawatt power levels • Experimental research on microwave breakdown at high gradient including studies of breakdown phenomena induced by RF electric fields and RF magnetic fields; development of new diagnostics of the breakdown process • Theoretical research on the physics and engineering features of RF vacuum breakdown • Maintaining and improving the Haimson / MIT 17 GHz accelerator, the highest frequency operational accelerator in the world, a unique facility for accelerator research • Providing the Haimson / MIT 17 GHz accelerator facility as a facility for outside users • Active participation in the US DOE program of High Gradient Collaboration, including joint work with SLAC and with Los Alamos National Laboratory; participation of MIT students in research at the national laboratories • Training the next generation of Ph. D. students in the field of accelerator physics.

  5. Accelerated Aging in Electrolytic Capacitors for Prognostics

    Data.gov (United States)

    National Aeronautics and Space Administration — The focus of this work is the analysis of different degradation phenomena based on thermal overstress and electrical overstress accelerated aging systems and the use...

  6. Accelerated Stem Growth Rates and Improved Fiber Properties of Loblolly Pine: Functional Analysis Of CyclinD from Pinus taeda

    Energy Technology Data Exchange (ETDEWEB)

    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. (Scion Research.)

    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

  7. Measurement of \\Omega_m, \\Omega_{\\Lambda} from a blind analysis of Type Ia supernovae with CMAGIC: Using color information to verify the acceleration of the Universe

    CERN Document Server

    Conley, A; Amanullah, R; Commins, E D; Fadeev, V; Folatelli, G; Garavini, G; Gibbons, R; Goldhaber, G; Goobar, A; Groom, D E; Hook, I; Howell, D A; Kim, A G; Knop, R A; Kowalski, M; Kuznetsova, N; Lidman, C; Nobili, S; Nugent, P; Pain, R; Perlmutter, S; Smith, E; Spadafora, A L; Stanishev, V; Strovink, M; Thomas, R C; Wang, L; Wood-Vasey, W M

    2006-01-01

    We present measurements of \\Omega_m and \\Omega_{\\Lambda} from a blind analysis of 21 high-redshift supernovae using a new technique (CMAGIC) for fitting the multi-color lightcurves of Type Ia supernovae, first introduced in Wang et al. (2003). CMAGIC takes advantage of the remarkably simple behavior of Type Ia supernovae on color-magnitude diagrams, and has several advantages over current techniques based on maximum magnitudes. Among these are a reduced sensitivity to host galaxy dust extinction, a shallower luminosity-width relation, and the relative simplicity of the fitting procedure. This allows us to provide a cross check of previous supernova cosmology results, despite the fact that current data sets were not observed in a manner optimized for CMAGIC. We describe the details of our novel blindness procedure, which is designed to prevent experimenter bias. The data are broadly consistent with the picture of an accelerating Universe, and agree with a flat Universe within 1.7\\sigma, including systematics. ...

  8. Analysis and determination of susceptibility Risk from slope instability at Colima State Mexico due to the accelerators factors of rain and seismicity

    Science.gov (United States)

    Ramirez-Ruiz, J. J.

    2016-12-01

    Slope instability is presented each year in the mountain region of the Colima State, Mexico. It occurs due to the combination of different factors existing in this area as: Precipitation, topography contrast, type and mechanical properties of deposits that constitute the rocks and soils of the region and the erosion due to the elimination of vegetation deck to develop and grow urban areas. To these geological factors we can extend the tectonic activity of the Western part of Mexico that originate high seismicity by the interaction of Cocos plate and North America plate forming the region of Graben de Colima, were is located our study area. Here we will present a Zonification and determination of the Susceptibility maps of slope instability due to the rain and seismicity accelerators factors. The North part of the State Colima is covered by deposits of the Volcan de Colima with an elevation of 3860 masl. It is the area of major precipitation yearly with more than 1200 mm in comparison to the average precipitation of about 900 mm of the State of Colima. Using a SIG system and the mapping of more than 30 sites we realize a zonification and analysis of the Risk using a methodology developed by CENAPRED. The susceptibility map developed in this area in combination with erosion factors permit us to determine an approximation of the Risk considering some limitations that will be present in this study.

  9. Sampling and analysis plan for the Bear Creek Valley Boneyard/Burnyard Accelerated Action Project, Oak Ridge Y-12 Plant, Oak Ridge, Tennessee

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    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.

  10. Repair of overheating linear accelerator

    Energy Technology Data Exchange (ETDEWEB)

    Barkley, Walter; Baldwin, William; Bennett, Gloria; Bitteker, Leo; Borden, Michael; Casados, Jeff; Fitzgerald, Daniel; Gorman, Fred; Johnson, Kenneth; Kurennoy, Sergey; Martinez, Alberto; O’Hara, James; Perez, Edward; Roller, Brandon; Rybarcyk, Lawrence; Stark, Peter; Stockton, Jerry

    2004-01-01

    Los Alamos Neutron Science Center (LANSCE) is a proton accelerator that produces high energy particle beams for experiments. These beams include neutrons and protons for diverse uses including radiography, isotope production, small feature study, lattice vibrations and material science. The Drift Tube Linear Accelerator (DTL) is the first portion of a half mile long linear section of accelerator that raises the beam energy from 750 keV to 100 MeV. In its 31st year of operation (2003), the DTL experienced serious issues. The first problem was the inability to maintain resonant frequency at full power. The second problem was increased occurrences of over-temperature failure of cooling hoses. These shortcomings led to an investigation during the 2003 yearly preventative maintenance shutdown that showed evidence of excessive heating: discolored interior tank walls and coper oxide deposition in the cooling circuits. Since overheating was suspected to be caused by compromised heat transfer, improving that was the focus of the repair effort. Investigations revealed copper oxide flow inhibition and iron oxide scale build up. Acid cleaning was implemented with careful attention to protection of the base metal, selection of components to clean and minimization of exposure times. The effort has been very successful in bringing the accelerator through a complete eight month run cycle allowing an incredible array of scientific experiments to be completed this year (2003-2004). This paper will describe the systems, investigation analysis, repair, return to production and conclusion.

  11. Asia honours accelerator physicists

    CERN Multimedia

    2010-01-01

    "Steve Meyers of Cern and Jie Wei of Beijing's Tsinghua University are the first recipients of a new prize for particle physics. The pair were honoured for their contributions to numerous particle-accelerator projects - including Cern's Large Hadron Collider - by the Asian Committee for Future Accelerators (ACFA)..." (1 paragraph)

  12. COLLECTIVE-FIELD ACCELERATION

    Energy Technology Data Exchange (ETDEWEB)

    Sessler, Andrew M.

    1969-07-04

    Diverse methods proposed for the acceleration of particles by means of collective fields are reviewed. A survey is made of the various currently active experimental programs devoted to investigating collective acceleration, and the present status of the research is briefly noted.

  13. Accelerators Beyond The Tevatron?

    Energy Technology Data Exchange (ETDEWEB)

    Lach, Joseph; /Fermilab

    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?

  14. KEK digital accelerator

    Science.gov (United States)

    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.

  15. KEK digital accelerator

    Directory of Open Access Journals (Sweden)

    T. Iwashita

    2011-07-01

    Full Text Available 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.

  16. On the Analysis Method of the Triple Tesh Cross Design

    Institute of Scientific and Technical Information of China (English)

    JinYi

    1995-01-01

    The analysis method of the triple test cross design has been discussed carefully form the two factor experiment design and the genetic models of additive-dominant effect and of epistasis effect-Two points different from the previous reprots have been concluded:(1)both the degrees of freedom of the orthogonal terms C2 and C3 are m;(2) the denominator in the F test to C2 and C3 is the error mean of square between plots.

  17. Accelerating Around an Unbanked Curve

    Science.gov (United States)

    Mungan, Carl E.

    2006-02-01

    The December 2004 issue of TPT presented a problem concerning how a car should accelerate around an unbanked curve of constant radius r starting from rest if it is to avoid skidding. Interestingly enough, two solutions were proffered by readers.2 The purpose of this note is to compare and contrast the two approaches. Further experimental investigation of various turning strategies using a remote-controlled car and overhead video analysis could make for an interesting student project.

  18. An analysis of airspeed, altitude, and acceleration data obtained from a twin-engine transport airplane operated over a feeder-line route in the Rocky Mountains

    Science.gov (United States)

    Copp, Martin R; Fetner, Mary W

    1956-01-01

    Time-history data of airspeed, altitude, and acceleration obtained with the NACA VGH recorder from a twin-engine airplane operated by a regional feeder airline in the Rocky Mountains are evaluated to determine the magnitude and frequency of occurrence of gusts and gust accelerations and the operating airspeeds and altitudes. The results obtained are compared with the results previously obtained from a representative short-haul and long-haul operation.

  19. Cache-based memory copy hardware accelerator for multicore systems

    NARCIS (Netherlands)

    Duarte, F.; Wong, S.

    2010-01-01

    In this paper, we present a new architecture of the cache-based memory copy hardware accelerator in a multicore system supporting message passing. The accelerator is able to accelerate memory data movements, in particular memory copies. We perform an analytical analysis based on open-queuing theory

  20. Accelerators, Beams And Physical Review Special Topics - Accelerators And Beams

    Energy Technology Data Exchange (ETDEWEB)

    Siemann, R.H.; /SLAC

    2011-10-24

    Accelerator science and technology have evolved as accelerators became larger and important to a broad range of science. Physical Review Special Topics - Accelerators and Beams was established to serve the accelerator community as a timely, widely circulated, international journal covering the full breadth of accelerators and beams. The history of the journal and the innovations associated with it are reviewed.

  1. The Accelerated Kepler Problem

    CERN Document Server

    Namouni, Fathi

    2007-01-01

    The accelerated Kepler problem is obtained by adding a constant acceleration to the classical two-body Kepler problem. This setting models the dynamics of a jet-sustaining accretion disk and its content of forming planets as the disk loses linear momentum through the asymmetric jet-counterjet system it powers. The dynamics of the accelerated Kepler problem is analyzed using physical as well as parabolic coordinates. The latter naturally separate the problem's Hamiltonian into two unidimensional Hamiltonians. In particular, we identify the origin of the secular resonance in the accelerated Kepler problem and determine analytically the radius of stability boundary of initially circular orbits that are of particular interest to the problem of radial migration in binary systems as well as to the truncation of accretion disks through stellar jet acceleration.

  2. On Accelerated Black Holes

    CERN Document Server

    Letelier, P S; Letelier, Patricio S.; Oliveira, Samuel R.

    1998-01-01

    The C-metric is revisited and global interpretation of some associated spacetimes are studied in some detail. Specially those with two event horizons, one for the black hole and another for the acceleration. We found that the spacetime fo an accelerated Schwarzschild black hole is plagued by either conical singularities or lack of smoothness and compactness of the black hole horizon. By using standard black hole thermodynamics we show that accelerated black holes have higher Hawking temperature than Unruh temperature. We also show that the usual upper bound on the product of the mass and acceleration parameters (<1/sqrt(27)) is just a coordinate artifact. The main results are extended to accelerated Kerr black holes. We found that they are not changed by the black hole rotation.

  3. Accelerated large-scale multiple sequence alignment

    Directory of Open Access Journals (Sweden)

    Lloyd Scott

    2011-12-01

    Full Text Available Abstract Background Multiple sequence alignment (MSA is a fundamental analysis method used in bioinformatics and many comparative genomic applications. Prior MSA acceleration attempts with reconfigurable computing have only addressed the first stage of progressive alignment and consequently exhibit performance limitations according to Amdahl's Law. This work is the first known to accelerate the third stage of progressive alignment on reconfigurable hardware. Results We reduce subgroups of aligned sequences into discrete profiles before they are pairwise aligned on the accelerator. Using an FPGA accelerator, an overall speedup of up to 150 has been demonstrated on a large data set when compared to a 2.4 GHz Core2 processor. Conclusions Our parallel algorithm and architecture accelerates large-scale MSA with reconfigurable computing and allows researchers to solve the larger problems that confront biologists today. Program source is available from http://dna.cs.byu.edu/msa/.

  4. Boundary-projection acceleration: A new approach to synthetic acceleration of transport calculations

    Energy Technology Data Exchange (ETDEWEB)

    Adams, M.L.; Martin, W.R.

    1987-01-01

    We present a new class of synthetic acceleration methods which can be applied to transport calculations regardless of geometry, discretization scheme, or mesh shape. Unlike other synthetic acceleration methods which base their acceleration on P1 equations, these methods use acceleration equations obtained by projecting the transport solution onto a coarse angular mesh only on cell boundaries. We demonstrate, via Fourier analysis of a simple model problem as well as numerical calculations of various problems, that the simplest of these methods are unconditionally stable with spectral radius less than or equal toc/3 (c being the scattering ratio), for several different discretization schemes in slab geometry. 28 refs., 4 figs., 3 tabs.

  5. Layers of epistasis: genome-wide regulatory networks and network approaches to genome-wide association studies

    Science.gov (United States)

    Cowper-Sal·lari, Richard; Cole, Michael D.; Karagas, Margaret R.; Lupien, Mathieu; Moore, Jason H.

    2010-01-01

    The conceptual foundation of the genome-wide association study (GWAS) has advanced unchecked since its conception. A revision might seem premature as the potential of GWAS has not been fully realized. Multiple technical and practical limitations need to be overcome before GWAS can be fairly criticized. But with the completion of hundreds of studies and a deeper understanding of the genetic architecture of disease, warnings are being raised. The results compiled to date indicate that risk-associated variants lie predominantly in non-coding regions of the genome. Additionally, alternative methodologies are uncovering large and heterogeneous sets of rare variants underlying disease. The fear is that, even in its fulfilment, the current GWAS paradigm might be incapable of dissecting all kinds of phenotypes. In the following text we review several initiatives that aim to overcome these limitations. The overarching theme of these studies is the inclusion of biological knowledge to both the analysis and interpretation of genotyping data. GWAS is uninformed of biology by design and although there is some virtue in its simplicity it is also its most conspicuous deficiency. We propose a framework in which to integrate these novel approaches, both empirical and theoretical, in the form of a genome-wide regulatory network (GWRN). By processing experimental data into networks, emerging data types based on chromatin-immunoprecipitation are made computationally tractable. This will give GWAS re-analysis efforts the most current and relevant substrates, and root them firmly on our knowledge of human disease. PMID:21197657

  6. Use of combination of accelerator-based ion-beam analysis techniques to the investigation of the corrosion behavior of CoCrMo alloy

    Energy Technology Data Exchange (ETDEWEB)

    Noli, F., E-mail: noli@chem.auth.gr [Department of Chemistry, Aristotle University, GR-54124 Thessaloniki (Greece); Misaelides, P. [Department of Chemistry, Aristotle University, GR-54124 Thessaloniki (Greece); Lagoyannis, A. [Tandem Accelerator Laboratory, Nuclear Physics Institute, NCSR Demokritos, GR-15310 Aghia Paraskevi, Attiki (Greece); Pichon, L. [Institut P’ UPR 3346 Université de Poitiers, CNRS F-86960 Futuroscope, Cedex (France); Ozturk, O. [Department of Physics, Izmir Institute of Technology, Gulbahce-Urla, 35430 Izmir (Turkey)

    2014-07-15

    Highlights: •Effect of plasma nitriding-oxidizing on the corrosion and mechanical properties of CoCrMo alloy. •The double treatment (nitriding+oxidizing) led to higher improvement. •This effect is attributed to the presence of a stable nitride layer. -- Abstract: Nuclear Reaction Analysis – NRA in combination with d-RBS (E{sub d}: 1.35 MeV) was applied in order to investigate the corrosion behavior of CoCrMo alloy. The corrosion resistance of the alloy was compared to that of modified CoCrMo samples by several techniques as plasma nitriding and oxidizing at moderate temperature (∼400 °C). Electrochemical techniques in simulated body fluid 0.9% NaCl (37 °C) were applied in order to accelerate the corrosion process. The nitrogen depth distribution before and after the corrosion was determined using the {sup 14}N(d,α){sup 12}C and the {sup 14}N(d,p){sup 15}N nuclear reactions whereas the oxygen by the {sup 16}O(d,p){sup 17}O. The surface morphology and microstructure was investigated using microscopy techniques. It was found that surface treatments produce thick nitrided layers (5–6 μm) consisting of a supersaturated nitrogen solution (nitrogen concentration is ∼30 at.%) in the matrix (expanded phase γ{sub N}) and a thin oxygen solution (0.3 μm). The samples subjected to plasma nitridation and oxidation exhibited the lowest deterioration and better resistance to corrosion compared to the single nitrided or single oxidized and the untreated material. This could be attributed to the modified surface region with the high nitrogen content and the presence of oxygen.

  7. Time-Dependent Neutronic Analysis of a Power-Flattened Gas Cooled Accelerator Driven System Fuelled with Thorium, Uranium, Plutonium, and Curium Dioxides TRISO Particles

    Directory of Open Access Journals (Sweden)

    Gizem Bakır

    2016-01-01

    Full Text Available This study presents the power flattening and time-dependent neutronic analysis of a conceptual helium gas cooled Accelerator Driven System (ADS loaded with TRISO (tristructural-isotropic fuel particles. Target material is lead-bismuth eutectic (LBE. ThO2, UO2, PuO2, and CmO2 TRISO particles are used as fuel. PuO2 and CmO2 fuels are extracted from PWR-MOX spent fuel. Subcritical core is radially divided into 10 equidistant subzones in order to flatten the power produced in the core. Tens of thousands of these TRISO fuel particles are embedded in the carbon matrix fuel pebbles as five different cases. The high-energy Monte Carlo code MCNPX 2.7 with the LA150 library is used for the neutronic calculations. Time-dependent burnup calculations are carried out for thermal fission power (Pth of 1000 MW using the BURN card. The energy gain of the ADS is in the range of 99.98–148.64 at the beginning of a cycle. Furthermore, the peak-to-average fission power density ratio is obtained between 1.021 and 1.029 at the beginning of the cycle. These ratios show a good quasi-uniform power density for each case. Furthermore, up to 155.1 g 233U and 103.6 g 239Pu per day can be produced. The considered system has a high neutronic capability in terms of energy multiplication, fissile breeding, and spent fuel transmutation with thorium utilization.

  8. Particle acceleration by plasma

    CERN Document Server

    Ogata, A

    2002-01-01

    Plasma acceleration is carried out by using potential of plasma wave. It is classified by generation method of plasma wave such as the laser wake-field acceleration and the beat wave acceleration. Other method using electron beam is named the plasma wake-field acceleration (or beam wake-field acceleration). In this paper, electron acceleration by laser wake-field in gas plasma, ion source by laser radiation of solid target and nanoion beam generation by one component of plasma in trap are explained. It is an applicable method that ions, which run out from the solid target irradiated by laser, are used as ion source of accelerator. The experimental system using 800 nm laser, 50 mJ pulse energy and 50 fs pulse width was studied. The laser intensity is 4x10 sup 1 sup 6 Wcm sup - sup 2 at the focus. The target film of metal and organic substance film was used. When laser irradiated Al target, two particles generated, in front and backward. It is new fact that the neutral particle was obtained in front, because it...

  9. The miniature accelerator

    CERN Multimedia

    Antonella Del Rosso

    2015-01-01

    The image that most people have of CERN is of its enormous accelerators and their capacity to accelerate particles to extremely high energies. But thanks to some cutting-edge studies on beam dynamics and radiofrequency technology, along with innovative construction techniques, teams at CERN have now created the first module of a brand-new accelerator, which will be just 2 metres long. The potential uses of this miniature accelerator will include deployment in hospitals for the production of medical isotopes and the treatment of cancer. It’s a real David-and-Goliath story.   Serge Mathot, in charge of the construction of the "mini-RFQ", pictured with the first of the four modules that will make up the miniature accelerator. The miniature accelerator consists of a radiofrequency quadrupole (RFQ), a component found at the start of all proton accelerator chains around the world, from the smallest to the largest. The LHC is designed to produce very high-intensity beams ...

  10. Cosmic particle acceleration

    Energy Technology Data Exchange (ETDEWEB)

    Zimbardo, Gaetano; Perri, Silvia [Universita della Calabria, Dipartimento di Fisica, 87036 Rende (Italy)

    2014-07-01

    The most popular mechanism for the acceleration of cosmic rays, which is thought to operate in supernova remnant shocks as well as at heliospheric shocks, is the diffusive shock acceleration, which is a Fermi mechanism based on normal diffusion. On the other hand, in the last few years it has been shown that the transport of plasma particles in the presence of electric and magnetic turbulence can be superdiffusive rather than normal diffusive. The term 'superdiffusive' refers to the mean square displacement of particle positions growing superlinearly with time, as compared to the normal linear growth. In particular, superdiffusion is characterized by a non Gaussian statistical process called Levy random walk. We show how diffusive shock acceleration is modified by superdiffusion, and how this yields new predictions for the cosmic ray spectral index, for the acceleration time, and for the spatial profile of energetic particles. A comparison with observations of particle acceleration at heliospheric shocks and at supernova remnant shocks is done. We discuss how superdiffusive shock acceleration allows to explain the observations of hard ion spectra at the solar wind termination shock detected by Voyager 2, of hard radio spectra due to synchrotron emission of electrons accelerated at supernova remnant shocks, and how it can help to explain the observations of 'thin rims' in the X-ray synchrotron emission.

  11. Multicavity proton cyclotron accelerator

    Directory of Open Access Journals (Sweden)

    J. L. Hirshfield

    2002-08-01

    Full Text Available A mechanism for acceleration of protons is described, in which energy gain occurs near cyclotron resonance as protons drift through a sequence of rotating-mode TE_{111} cylindrical cavities in a strong nearly uniform axial magnetic field. Cavity resonance frequencies decrease in sequence from one another with a fixed frequency interval Δf between cavities, so that synchronism can be maintained between the rf fields and proton bunches injected at intervals of 1/Δf. An example is presented in which a 122 mA, 1 MeV proton beam is accelerated to 961 MeV using a cascade of eight cavities in an 8.1 T magnetic field, with the first cavity resonant at 120 MHz and with Δf=8 MHz. Average acceleration gradient exceeds 40 MV/m, average effective shunt impedance is 223 MΩ/m, but maximum surface field in the cavities does not exceed 7.2 MV/m. These features occur because protons make many orbital turns in each cavity and thus experience acceleration from each cavity field many times. Longitudinal and transverse stability appear to be intrinsic properties of the acceleration mechanism, and an example to illustrate this is presented. This acceleration concept could be developed into a proton accelerator for a high-power neutron spallation source, such as that required for transmutation of nuclear waste or driving a subcritical fission burner, provided a number of significant practical issues can be addressed.

  12. 上位性及其对家养动物复杂经济性状形成的遗传学影响%Epistasis and its genetic influence on phenotype shaping of complex economic traits in domestic animals

    Institute of Scientific and Technical Information of China (English)

    户国; 王守志; 李辉

    2012-01-01

    Bateson于1909年最早将上位性(Epistasis)这个概念引入遗传学领域,在1918年,Fisher将不同位点上的非等位基因相互作用定义为上位性,非等位基因间的交互作用而产生的基因效应定位为上位效应( Epistatic effect).自此,在相当长的时期内,受到试验方法及技术手段的限制,研究者多采用以数量遗传学为主的研究方法对上位性开展研究.近年来,伴随着分子数量遗传学与功能基因组学的飞速发展,人们现在已获得大量的理论和实验证据支持上位效应对家养动物复杂性状的表型塑造以及复杂遗传系统演化机制存在重要的遗传学影响.文章拟对目前使用较为广泛的上位性概念、类型及主要的学术观点加以评述,着重介绍了这些概念的产生的背景、原理以及差别之处,并对上位性对家养动物复杂经济性状的遗传学影响给予简要介绍,以期能够为相关领域的研究者提供参考.%Epistasis was first introduced into genetics by Bateson in 1909. The genetic interpretation of epistasis by Fisher in 1918 was generally defined as the interaction between two or more allele on different loci to influence a single trait. The factors participated in the mechanism of phenotype shaping in domestic animals are very complex. It often involvea the additive effect, dominant effect of the single locus, and the epistatic effect caused by the interaction among the alleles on different loci. The interaction between genes and the environment is an important factor, too. In recent years, with the rapid development of molecular quantitative genetics and functional genomics, a lot of theoretical and experimental evidence has been obtained, which could support the epistatic effect with the fundamentally important influence on the structure and function of genetic pathways of complex phenotype in domestic animals and the evolutionary dynamics of complex genetic systems. This paper tried to introduce

  13. Application of Accelerators and Storage Rings: Accelerators in Medicine

    CERN Document Server

    Amaldi, U

    2013-01-01

    This document is part of Subvolume C 'Accelerators and Colliders' of Volume 21 'Elementary Particles' of Landolt-Börnstein - Group I 'Elementary Particles, Nuclei and Atoms'. It contains the the Section '11.3 Accelerators in Medicine' of the Chapter '11 Application of Accelerators and Storage Rings' with the content: 11.3 Accelerators in Medicine 11.3.1 Accelerators and Radiopharmaceuticals 11.3.2 Accelerators and Cancer Therapy

  14. Analysis of Acceleration, Airspeed, and Gust-Velocity Data From a Four-Engine Transport Airplane Operating Over a Northwestern United States Alaska Route

    Science.gov (United States)

    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.

  15. Analysis of thickness measurements on secondary lines in EDF PWRs to evaluate the accuracy of the flow accelerated corrosion monitoring software: BRT-CICERO

    Energy Technology Data Exchange (ETDEWEB)

    Persoz, Matthieu [CAP AMPERE, 1 place Pleyel, 93282 Saint Denis (France); Bouvier, Jean-Baptiste [CNEN, 165-173 av. Pierre Brossolette, 92542 Montrouge Cedex (France); Ardillon, Emmanuel [R and D Division, EDF, 6 quai Watier, 78401 Chatou Cedex (France); Trevin, Stephane [SEPTEN, 12 - 14 av. Dutrievoz, 69628 Villeurbanne Cedex (France)

    2006-09-15

    The surveillance of Flow Accelerated Corrosion (FAC) on secondary pipes is a major concern for every nuclear power plant operator. After the Surry accident in 1986, EDF launched a computer code development program to monitor this degradation phenomenon. A chemical corrosion model has been developed, based on laboratory test results obtained by EDF R and D since the late 70's. This model enables to compute the wall thickness loss of pipes submitted to FAC, with respect to the thermo-hydraulic conditions, the fluid chemistry, the material chromium content, the pipe geometry and the cycles duration. The computer code, called BRT-CICERO(TM), has first been tested on a few plants in the years 1993-1995. Most of the EDF NPPs began to use it afterwards. In 2001, after the discovery of a severe damage on a 4'' x 6'' reducer at Fessenheim unit 2, that was correctly predicted by BRT-CICERO(TM), the EDF corporate level made its use mandatory for each of its 58 Pressurized Water Reactors (PWR). Several years of operation and experience feedback have enabled to carry out different improvements on the BRT-CICERO(TM) software. Since 2003, EDF NPPs are using the 2.2 version. At the beginning of year 2005, the 58 BRT-CICERO(TM) input-databases were gathered and structured in a form such that statistical treatments could be made. A very great number of data were collected from BRT-CICERO(TM) input-databases by a specific modification of a tool integrated into the software. It appears that a statistical approach could allow an effective analysis of these data. The first goal of this study was to give the degree of confidence in the application and this approach appeared effective. The second goal was to prove that a part of the conservatism is due to the FAC kinetics calculation algorithm implemented in BRT-CICERO(TM). The investigation of the relative difference between measured and calculated thicknesses shows that a part of the conservatism should be due

  16. Transient cosmic acceleration from interacting fluids

    CERN Document Server

    Fabris, Julio C; Pinto-Neto, Nelson; Zimdahl, Winfried

    2009-01-01

    Recent investigations seem to favor a cosmological dynamics according to which the accelerated expansion of the Universe may have already peaked and is now slowing down again \\cite{sastaro}. As a consequence, the cosmic acceleration may be a transient phenomenon. We investigate a toy model that reproduces such a background behavior as the result of a time-dependent coupling in the dark sector which implies a cancelation of the "bare" cosmological constant. With the help of a statistical analysis of Supernova Type Ia (SNIa) data we demonstrate that for a certain parameter combination a transient accelerating phase emerges as a pure interaction effect.

  17. ATHENA: A knowledge-based hybrid backpropagation-grammatical evolution neural network algorithm for discovering epistasis among quantitative trait Loci

    Directory of Open Access Journals (Sweden)

    Turner Stephen D

    2010-09-01

    Full Text Available Abstract Background Growing interest and burgeoning technology for discovering genetic mechanisms that influence disease processes have ushered in a flood of genetic association studies over the last decade, yet little heritability in highly studied complex traits has been explained by genetic variation. Non-additive gene-gene interactions, which are not often explored, are thought to be one source of this "missing" heritability. Methods Stochastic methods employing evolutionary algorithms have demonstrated promise in being able to detect and model gene-gene and gene-environment interactions that influence human traits. Here we demonstrate modifications to a neural network algorithm in ATHENA (the Analysis Tool for Heritable and Environmental Network Associations resulting in clear performance improvements for discovering gene-gene interactions that influence human traits. We employed an alternative tree-based crossover, backpropagation for locally fitting neural network weights, and incorporation of domain knowledge obtainable from publicly accessible biological databases for initializing the search for gene-gene interactions. We tested these modifications in silico using simulated datasets. Results We show that the alternative tree-based crossover modification resulted in a modest increase in the sensitivity of the ATHENA algorithm for discovering gene-gene interactions. The performance increase was highly statistically significant when backpropagation was used to locally fit NN weights. We also demonstrate that using domain knowledge to initialize the search for gene-gene interactions results in a large performance increase, especially when the search space is larger than the search coverage. Conclusions We show that a hybrid optimization procedure, alternative crossover strategies, and incorporation of domain knowledge from publicly available biological databases can result in marked increases in sensitivity and performance of the ATHENA

  18. A new procedure combining GC-MS with accelerated solvent extraction for the analysis of phthalic acid esters in contaminated soils

    Institute of Scientific and Technical Information of China (English)

    Tingting MA; Ying TENG; Peter CHRISTIE; Yongming LUO; Yongshan CHEN; Mao YE

    2013-01-01

    An optimized procedure based on gas chromatography-mass spectrometry (GC-MS) combined with accelerated solvent extraction (ASE) is developed for the analysis of six phthalic acid esters (PAEs), which are priority soil pollutants nominated by United States Environmental Protection Agency (USEPA). Quantification of PAEs in soil employs ultrasonic extraction (UE) (USEPA 3550) and ASE (USEPA 3545), followed by clean up procedures involving three different chromatography columns and two combined elution methods. GC-MS conditions under selected ion monitoring (SIM) mode are described and quality assurance and quality control (QA/ QC) criteria with high accuracy and sensitivity for target analytes were achieved. Method reliability is assured with the use of an isotopically labeled PAE, di-n-butyl phthalate-d4 (DnBP-D4), as a surrogate, and benzyl benzoate (BB) as an internal standard, and with the analysis of certified reference materials (CRM). QA/QC for the developed procedure was tested in four PAE-spiked soils and one PAE-contaminated soil. The four spiked soils were originated from typical Chinese agricultural fields and the contaminated soil was obtained from an electronic waste dismantling area. Instrument detection limits (IDLs) for the six PAEs ranged 0.10-0.31 μg·L-1 and method detection limits (MDLs) of the four spiked soils varied from a range of 20-70 μg· kg -1 to a range of 90-290 μg· kg-1. Lineal-iVy of response between 20 μg· L-1 and 2mg.L~ was also established and the correlation coefficients (R) were a11〉0.998. Spiked soil matrix showed relative recovery rates between 75 and 120% for the six target compounds and about 93% for the surrogate substance. The developed procedure is anticipated to be highly applicable for field surveys of soil PAE pollution in China.

  19. Vibration control in accelerators

    Energy Technology Data Exchange (ETDEWEB)

    Montag, C.

    2011-01-01

    In the vast majority of accelerator applications, ground vibration amplitudes are well below tolerable magnet jitter amplitudes. In these cases, it is necessary and sufficient to design a rigid magnet support structure that does not amplify ground vibration. Since accelerator beam lines are typically installed at an elevation of 1-2m above ground level, special care has to be taken in order to avoid designing a support structure that acts like an inverted pendulum with a low resonance frequency, resulting in untolerable lateral vibration amplitudes of the accelerator components when excited by either ambient ground motion or vibration sources within the accelerator itself, such as cooling water pumps or helium flow in superconducting magnets. In cases where ground motion amplitudes already exceed the required jiter tolerances, for instance in future linear colliders, passive vibration damping or active stabilization may be considered.

  20. Compact particle accelerator

    Energy Technology Data Exchange (ETDEWEB)

    Elizondo-Decanini, Juan M.

    2017-08-29

    A compact particle accelerator having an input portion configured to receive power to produce particles for acceleration, where the input portion includes a switch, is provided. In a general embodiment, a vacuum tube receives particles produced from the input portion at a first end, and a plurality of wafer stacks are positioned serially along the vacuum tube. Each of the plurality of wafer stacks include a dielectric and metal-oxide pair, wherein each of the plurality of wafer stacks further accelerate the particles in the vacuum tube. A beam shaper coupled to a second end of the vacuum tube shapes the particles accelerated by the plurality of wafer stacks into a beam and an output portion outputs the beam.

  1. Rejuvenating CERN's Accelerators

    CERN Multimedia

    2004-01-01

    In the coming years and especially in 2005, CERN's accelerators are going to receive an extensive renovation programme to ensure they will perform reliably and effectively when the LHC comes into service.

  2. Joint International Accelerator School

    CERN Multimedia

    CERN Accelerator School

    2014-01-01

    The CERN and US Particle Accelerator Schools recently organised a Joint International Accelerator School on Beam Loss and Accelerator Protection, held at the Hyatt Regency Hotel, Newport Beach, California, USA from 5-14 November 2014. This Joint School was the 13th in a series of such schools, which started in 1985 and also involves the accelerator communities in Japan and Russia.   Photo courtesy of Alfonse Pham, Michigan State University.   The school attracted 58 participants representing 22 different nationalities, with around half from Europe and the other half from Asia and the Americas. The programme comprised 26 lectures, each of 90 minutes, and 13 hours of case study. The students were given homework each day and had an opportunity to sit a final exam, which counted towards university credit. Feedback from the participants was extremely positive, praising the expertise and enthusiasm of the lecturers, as well as the high standard and quality of their lectures. Initial dis...

  3. Dielectric assist accelerating structure

    Science.gov (United States)

    Satoh, D.; Yoshida, M.; Hayashizaki, N.

    2016-01-01

    A higher-order TM02 n mode accelerating structure is proposed based on a novel concept of dielectric loaded rf cavities. This accelerating structure consists of ultralow-loss dielectric cylinders and disks with irises which are periodically arranged in a metallic enclosure. Unlike conventional dielectric loaded accelerating structures, most of the rf power is stored in the vacuum space near the beam axis, leading to a significant reduction of the wall loss, much lower than that of conventional normal-conducting linac structures. This allows us to realize an extremely high quality factor and a very high shunt impedance at room temperature. A simulation of a 5 cell prototype design with an existing alumina ceramic indicates an unloaded quality factor of the accelerating mode over 120 000 and a shunt impedance exceeding 650 M Ω /m at room temperature.

  4. Origin of Nonthermal Emission from the Fermi Bubbles and Mechanisms of Particle Acceleration There

    CERN Document Server

    Dogiel, V A; Chernyshov, D O; Ko, C -M

    2013-01-01

    We analyse processes of particle acceleration in the Fermi Bubbles. The goal of our investigations is to obtain restrictions for acceleration mechanisms. Our analysis of the three processes: acceleration from background plasma, re-acceleration of relativistic electrons emitted by supernova remnants, and acceleration by shocks generated by processes of star tidal disruption in the Galactic Center, showed that the model of multi-shock acceleration does not have serious objections at present and therefore seems us more attractive than others.

  5. LHCb GPU Acceleration Project

    CERN Document Server

    AUTHOR|(SzGeCERN)744808; Campora Perez, Daniel Hugo; Neufeld, Niko; Vilasis Cardona, Xavier

    2016-01-01

    The LHCb detector is due to be upgraded for processing high-luminosity collisions, which will increase the load on its computation infrastructure from 100 GB/s to 4 TB/s, encouraging us to look for new ways of accelerating the Online reconstruction. The Coprocessor Manager is our new framework for integrating LHCb’s existing computation pipelines with massively parallel algorithms running on GPUs and other accelerators. This paper describes the system and analyzes its performance.

  6. Accelerating News Issue 2

    CERN Document Server

    Kahle, K; Wildner, E

    2012-01-01

    In this summer issue we look at how developments in collimator materials could have applications in aerospace and beyond, and how Polish researchers are harnessing accelerators for medical and industrial uses. We see how the LHC luminosity upgrade is linking with European industry and US researchers, and how the neutrino oscillation community is progressing. We find out the mid-term status of TIARA-PP and how it is mapping European accelerator education resources.

  7. Accelerating Cosmologies from Compactification

    CERN Document Server

    Townsend, P K; Townsend, Paul K.; Wohlfarth, Mattias N.R.

    2003-01-01

    A solution of the (4+n)-dimensional vacuum Einstein equations is found for which spacetime is compactified on a compact hyperbolic manifold of time-varying volume to a flat four-dimensional FLRW cosmology undergoing accelerated expansion in Einstein conformal frame. This shows that the `no-go' theorem forbidding acceleration in `standard' (time-independent) compactifications of string/M-theory does not apply to `cosmological' (time-dependent) hyperbolic compactifications.

  8. Accelerators for America's Future

    Science.gov (United States)

    Bai, Mei

    2016-03-01

    Particle accelerator, a powerful tool to energize beams of charged particles to a desired speed and energy, has been the working horse for investigating the fundamental structure of matter and fundermental laws of nature. Most known examples are the 2-mile long Stanford Linear Accelerator at SLAC, the high energy proton and anti-proton collider Tevatron at FermiLab, and Large Hadron Collider that is currently under operation at CERN. During the less than a century development of accelerator science and technology that led to a dazzling list of discoveries, particle accelerators have also found various applications beyond particle and nuclear physics research, and become an indispensible part of the economy. Today, one can find a particle accelerator at almost every corner of our lives, ranging from the x-ray machine at the airport security to radiation diagnostic and therapy in hospitals. This presentation will give a brief introduction of the applications of this powerful tool in fundermental research as well as in industry. Challenges in accelerator science and technology will also be briefly presented

  9. Detection of linear ego-acceleration from optic flow.

    Science.gov (United States)

    Festl, Freya; Recktenwald, Fabian; Yuan, Chunrong; Mallot, Hanspeter A

    2012-07-20

    Human observers are able to estimate various ego-motion parameters from optic flow, including rotation, translational heading, time-to-collision (TTC), time-to-passage (TTP), etc. The perception of linear ego-acceleration or deceleration, i.e., changes of translational velocity, is less well understood. While time-to-passage experiments indicate that ego-acceleration is neglected, subjects are able to keep their (perceived) speed constant under changing conditions, indicating that some sense of ego-acceleration or velocity change must be present. In this paper, we analyze the relation of ego-acceleration estimates and geometrical parameters of the environment using simulated flights through cylindrical and conic (narrowing or widening) corridors. Theoretical analysis shows that a logarithmic ego-acceleration parameter, called the acceleration rate ρ, can be calculated from retinal acceleration measurements. This parameter is independent of the geometrical layout of the scene; if veridical ego-motion is known at some instant in time, acceleration rate allows updating of ego-motion without further depth-velocity calibration. Results indicate, however, that subjects systematically confuse ego-acceleration with corridor narrowing and ego-deceleration with corridor widening, while veridically judging ego-acceleration in straight corridors. We conclude that judgments of ego-acceleration are based on first-order retinal flow and do not make use of acceleration rate or retinal acceleration.

  10. Diffusive Shock Acceleration and Reconnection Acceleration Processes

    Science.gov (United States)

    Zank, G. P.; Hunana, P.; Mostafavi, P.; Le Roux, J. A.; Li, Gang; Webb, G. M.; Khabarova, O.; Cummings, A.; Stone, E.; Decker, R.

    2015-12-01

    Shock waves, as shown by simulations and observations, can generate high levels of downstream vortical turbulence, including magnetic islands. We consider a combination of diffusive shock acceleration (DSA) and downstream magnetic-island-reconnection-related processes as an energization mechanism for charged particles. Observations of electron and ion distributions downstream of interplanetary shocks and the heliospheric termination shock (HTS) are frequently inconsistent with the predictions of classical DSA. We utilize a recently developed transport theory for charged particles propagating diffusively in a turbulent region filled with contracting and reconnecting plasmoids and small-scale current sheets. Particle energization associated with the anti-reconnection electric field, a consequence of magnetic island merging, and magnetic island contraction, are considered. For the former only, we find that (i) the spectrum is a hard power law in particle speed, and (ii) the downstream solution is constant. For downstream plasmoid contraction only, (i) the accelerated spectrum is a hard power law in particle speed; (ii) the particle intensity for a given energy peaks downstream of the shock, and the distance to the peak location increases with increasing particle energy, and (iii) the particle intensity amplification for a particular particle energy, f(x,c/{c}0)/f(0,c/{c}0), is not 1, as predicted by DSA, but increases with increasing particle energy. The general solution combines both the reconnection-induced electric field and plasmoid contraction. The observed energetic particle intensity profile observed by Voyager 2 downstream of the HTS appears to support a particle acceleration mechanism that combines both DSA and magnetic-island-reconnection-related processes.

  11. 摆角、摆长及周期数对测重力加速度的影响分析%Influence and Analysis of Pendulum Angle, Pendulum Length and Periodicity on the Acceleration of Gravity

    Institute of Scientific and Technical Information of China (English)

    翟凤瑞; 李宇赤; 易中周; 张黎黎; 王丹

    2011-01-01

    用单摆法测量重力加速度是普通物理实验中常用的方法,但在实验中,摆角、摆长和周期数常常对重力加速度的测量误差产生一定的影响.文章主要分析不同摆角、摆长及周期数三个条件对测重力加速度的影响,最终由处理分析结果可知,在普通物理实验室里,取摆角、摆长=47或55cm、周期数次,处理得到的重力加速度与本地的理论计算值很接近.%It is an ordinary method to measure acceleration of gravity with a pendulum in physical experiments.But in the experiment,the pendulum angle,pendulum length and periodicity often have some influences on measurement errors of acceleration of gravity.This paper mainly analyzes the influences of pendulum angle,pendulum length and periodicity on the acceleration of gravity.It can be seen from the processing and analysis results that the value of acceleration of gravity by experiments is very close to the local acceleration theoretical value when the swing angle is 3.8 degrees,pendulum length is 47 cm or 55 cm and periodicity is 37 times.

  12. Secular Acceleration of Barnard's Star

    Science.gov (United States)

    Bartlett, Jennifer L.; Ianna, P. A.

    2009-01-01

    Barnard's Star should have significant secular acceleration because it lies close to the Sun and has the highest known proper motion along with a large radial velocity. It will pass within about 1.4 pc in another 9,750 years. Secular changes in proper motion and radial velocity are essentially the Coriolis and centrifugal accelerations, respectively, arising from use of a rotating coordinate system defined by the Sun-star radius vector. Although stellar space velocities measured with respect to the Sun are essentially constant, these perspective effects arise with changing distance and viewing angle. Hipparcos-2 plus Nidever et al. (2002) predict a perspective change in the proper motion of 1.285±0.006 mas yr-2 for Barnard's Star. Recent analysis of 900+ photographic plates between 1968 and 1998 with the 26.25-in (0.67-m) McCormick refractor detected a secular acceleration of 1.25±0.04 mas yr-2, which agrees with the predicted value within the measurement errors. Earlier, Benedict et al. (1999) measured its secular acceleration to be 1.2±0.2 mas yr-2 using 3 years of HST FGS observations. Similarly, a perspective change in radial velocity of 4.50±0.01 m s-1 yr-1 can be predicted for Barnard's Star. Kürster et al. (2003) detected variations in their observations of it that are largely attributable to secular acceleration along the line of sight with some contribution from stellar activity. Although secular acceleration effects have been limited for past studies of stellar motions, they can be significant for observations extending over decades or for high-precision measurements required to detect extrasolar planets. Future studies will need to consider this factor for the nearest stars and for those with large proper motions or radial velocities. NSF grant AST 98-20711; Litton Marine Systems; Peninsula Community Foundation Levinson Fund; UVa Governor's Fellowship, Dean's F&A Fellowship, and Graduate School of Arts and Sciences; and, US Naval Observatory

  13. A study of the ASR of an aggregate with high chert content by means of ultra-accelerated mortar bar test and pore fluid analysis

    NARCIS (Netherlands)

    Larbi, J.A.; Visser, J.H.M.

    2002-01-01

    Various studies have indicated that the use of some ultra-accelerated mortar bar expansion test methods for assessing the alkali-silica reactivity of concrete aggregates (particularly those using 1 M NaOH solution at 80 oC) can give rise to misleading results causing certain types of aggregates to b

  14. Is the Tail Wagging the Dog? An Analysis of Accelerated Reader and the Influence of Reading Rewards on Learning and Library Media Centers

    Science.gov (United States)

    McCarthy, Cheryl A.

    2003-01-01

    Accelerated Reader (AR) is a computerized reading reward program by Renaissance Learning Inc. (RLI) that offers schools management software with computer quizzes of books identified by reading level (RL) and assigned points in order for children to read books, take quizzes, and earn points. Schools or teachers decide whether to offer prizes in…

  15. The connection between supernova remnants and the Galactic magnetic field: An analysis of quasi-parallel and quasi-perpendicular cosmic ray acceleration for the axisymmetric sample

    CERN Document Server

    West, J L; Ferrand, G

    2016-01-01

    The mechanism for acceleration of cosmic rays in supernova remnants (SNRs) is an outstanding question in the field. We model a sample of 32 axisymmetric SNRs using the quasi-perpendicular and quasi-parallel cosmic-ray-electron (CRE) acceleration cases. The axisymmetric sample is defined to include SNRs with a double-sided, bilateral morphology, and also those with a one-sided morphology where one limb is much brighter than the other. Using a coordinate transformation technique, we insert a bubble-like model SNR into a model of the Galactic magnetic field. Since radio emission of SNRs is dominated by synchrotron emission and since this emission depends on the magnetic field and CRE distribution, we are able to simulate the SNRs emission and compare this to data. We find that the quasi-perpendicular CRE acceleration case is much more consistent with the data than the quasi-parallel CRE acceleration case, with G327.6+14.6 (SN1006) being a notable exception. We propose that SN1006 may be a case where both quasi-p...

  16. Accelerated partial breast irradiation using intensity-modulated radiotherapy versus whole breast irradiation: 5-year survival analysis of a phase 3 randomised controlled trial.

    Science.gov (United States)

    Livi, Lorenzo; Meattini, Icro; Marrazzo, Livia; Simontacchi, Gabriele; Pallotta, Stefania; Saieva, Calogero; Paiar, Fabiola; Scotti, Vieri; De Luca Cardillo, Carla; Bastiani, Paolo; Orzalesi, Lorenzo; Casella, Donato; Sanchez, Luis; Nori, Jacopo; Fambrini, Massimiliano; Bianchi, Simonetta

    2015-03-01

    Accelerated partial breast irradiation (APBI) has been introduced as an alternative treatment method for selected patients with early stage breast cancer (BC). Intensity-modulated radiotherapy (IMRT) has the theoretical advantage of a further increase in dose conformity compared with three-dimensional techniques, with more normal tissue sparing. The aim of this randomised trial is to compare the local recurrence and survival of APBI using the IMRT technique after breast-conserving surgery to conventional whole-breast irradiation (WBI) in early stage BC. This study was performed at the University of Florence (Florence, Italy). Women aged more than 40years affected by early BC, with a maximum pathological tumour size of 25mm, were randomly assigned in a 1:1 ratio to receive either WBI or APBI using IMRT. Patients in the APBI arm received a total dose of 30 Gy to the tumour bed in five daily fractions. The WBI arm received 50Gy in 25 fractions, followed by a boost on the tumour bed of 10Gy in five fractions. The primary end-point was occurrence of ipsilateral breast tumour recurrences (IBTRs); the main analysis was by intention-to-treat. This trial is registered with ClinicalTrials.gov, number NCT02104895. A total of 520 patients were randomised (260 to external WBI and 260 to APBI with IMRT) between March 2005 and June 2013. At a median follow-up of 5.0 years (Interquartile Range (IQR) 3.4-7.0), the IBTR rate was 1.5% (three cases) in the APBI group (95% confidence interval (CI) 0.1-3.0) and in the WBI group (three cases; 95% CI 0.0-2.8). No significant difference emerged between the two groups (log rank test p=0.86). We identified seven deaths in the WBI group and only one in the APBI group (p=0.057). The 5-year overall survival was 96.6% for the WBI group and 99.4% for the APBI group. The APBI group presented significantly better results considering acute (p=0.0001), late (p=0.004), and cosmetic outcome (p=0.045). To our knowledge, this is the first randomised

  17. 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

    Directory of Open Access Journals (Sweden)

    Sprague Lisa D

    2006-12-01

    Full Text Available Abstract 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 10.5 g/dl and for patients who completed the protocol. Conclusion The SCHARC protocol was effective in patients diagnosed with advanced head and neck cancer. It led to long-term disease control and survival in about 50 % of the patients with significant but acceptable toxicity. Most patients

  18. Accelerating DSMC data extraction.

    Energy Technology Data Exchange (ETDEWEB)

    Gallis, Michail A.; Piekos, Edward Stanley

    2006-10-01

    In many direct simulation Monte Carlo (DSMC) simulations, the majority of computation time is consumed after the flowfield reaches a steady state. This situation occurs when the desired output quantities are small compared to the background fluctuations. For example, gas flows in many microelectromechanical systems (MEMS) have mean speeds more than two orders of magnitude smaller than the thermal speeds of the molecules themselves. The current solution to this problem is to collect sufficient samples to achieve the desired resolution. This can be an arduous process because the error is inversely proportional to the square root of the number of samples so we must, for example, quadruple the samples to cut the error in half. This work is intended to improve this situation by employing more advanced techniques, from fields other than solely statistics, for determining the output quantities. Our strategy centers on exploiting information neglected by current techniques, which collect moments in each cell without regard to one another, values in neighboring cells, nor their evolution in time. Unlike many previous acceleration techniques that modify the method itself, the techniques examined in this work strictly post-process so they may be applied to any DSMC code without affecting its fidelity or generality. Many potential methods are drawn from successful applications in a diverse range of areas, from ultrasound imaging to financial market analysis. The most promising methods exploit relationships between variables in space, which always exist in DSMC due to the absence of shocks. Disparate techniques were shown to produce similar error reductions, suggesting that the results shown in this report may be typical of what is possible using these methods. Sample count reduction factors of approximately three to five were found to be typical, although factors exceeding ten were shown on some variables under some techniques.

  19. 固定资产新加速折旧政策影响分析%New Accelerated Depreciation of Fixed Assets Policy Impact Analysis

    Institute of Scientific and Technical Information of China (English)

    罗鉴益; 徐伟

    2016-01-01

    2014年10月财政部、国家税务总局联合发布了关于固定资产新加速折旧政策的通知。新政策旨在推动我国经济转型,加速促进传统企业的技术改造,鼓励扶持中小企业创业创新,提高国际竞争能力。为帮助企业正确选择加速折旧政策从而实现减税负,对固定资产加速折旧方法的设计、新加速折旧政策及存在的问题进行了分析,对固定资产的认定标准、折旧方法和年限的确定、研发费用的加计扣除,以及加速折旧的选择时机等进行了探讨。%In October 2014,the Ministry of Finance and the State Administration of Taxation jointly issued a notice about the policy of new accelerated depreciation of fixed assets.New policy aimed at promoting China ’s economic and the traditional enterprise ’s technological transformation, encouraging and supporting small and medium-sized enterprises business innovation and improving the international competitiveness.This paper analyzed the design of accelerated depreciation of fixed assets,new accelerated depreciation policy and existing problems.The judging standard of fixed assets,depreciation method,depreciation life confirmation,research and development costs deduction and timing of accelerated depreciation aspects,that choosing accelerated depreciation policy to help enterprise reduce tax incidence and so on were discussed.

  20. Small type accelerator. Try for accelerator driven system

    CERN Document Server

    Mori, Y

    2003-01-01

    FFAG (Fixed-field alternating gradient) accelerator for accelerator driven subcritical reactor, which aims to change from long-lived radioactive waste to short-lived radioactivity, is introduced. It is ring accelerator. The performance needed is proton as accelerator particle, 10MW (total) beam power, about 1GeV beam energy, >30% power efficiency and continuous beam. The feature of FFAG accelerator is constant magnetic field. PoP (Proof-of-principle)-FFAG accelerator, radial type, was run at first in Japan in 2000. The excursion is about some ten cm. In principle, beam can be injected and extracted at any place of ring. The 'multi-fish' acceleration can accelerate beams to 100% duty by repeating acceleration. 150MeV-FFAG accelerator has been started since 2001. It tried to practical use, for example, treatment of cancer. (S.Y.)