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Sample records for amplicon va derived

  1. Herpes simplex virus type 1-derived recombinant and amplicon vectors.

    Science.gov (United States)

    Fraefel, Cornel; Marconi, Peggy; Epstein, Alberto L

    2011-01-01

    Herpes simplex virus type 1 (HSV-1) is a human pathogen whose lifestyle is based on a long-term dual interaction with the infected host, being able to establish both lytic and latent infections. The virus genome is a 153 kbp double-stranded DNA molecule encoding more than 80 genes. The interest of HSV-1 as gene transfer vector stems from its ability to infect many different cell types, both quiescent and proliferating cells, the very high packaging capacity of the virus capsid, the outstanding neurotropic adaptations that this virus has evolved, and the fact that it never integrates into the cellular chromosomes, thus avoiding the risk of insertional mutagenesis. Two types of vectors can be derived from HSV-1, recombinant vectors and amplicon vectors, and different methodologies have been developed to prepare large stocks of each type of vector. This chapter summarizes (1) the two approaches most commonly used to prepare recombinant vectors through homologous recombination, either in eukaryotic cells or in bacteria, and (2) the two methodologies currently used to generate helper-free amplicon vectors, either using a bacterial artificial chromosome (BAC)-based approach or a Cre/loxP site-specific recombination strategy.

  2. Evaluating sequence-derived mtDNA length heteroplasmy by amplicon size analysis

    Science.gov (United States)

    Berger, C.; Hatzer-Grubwieser, P.; Hohoff, C.; Parson, W.

    2011-01-01

    Length heteroplasmy (LH) in mitochondrial (mt)DNA is usually observed in homopolymeric tracts and manifest as mixture of various length variants. The generally used difference-coded annotation to report mtDNA haplotypes does not express the degree of LH variation present in a sample, even more so, it is sometimes difficult to establish which length variants are present and clearly distinguishable from background noise. It has therefore become routine practice for some researchers to call the dominant type, the “major molecule”, which represents the LH variant that is most abundant in a DNA extract. In the majority of cases a clear single dominant variant can be identified. However, in some samples this interpretation is difficult, i.e. when (almost) equally quantitative LH variants are present or when multiple sequencing primers result in the presentation of different dominant types. To better understand those cases we designed amplicon sizing assays for the five most relevant LH regions in the mtDNA control region (around ntps 16,189, 310, 460, 573, and the AC-repeat between 514 and 524) to determine the ratio of the LH variants by fluorescence based amplicon sizing assays. For difficult LH constellations derived by Sanger sequencing (with Big Dye terminators) these assays mostly gave clear and unambiguous results. In the vast majority of cases we found agreement between the results of the sequence and amplicon analyses and propose this alternative method in difficult cases. PMID:21067985

  3. Adenovirus Vector-Derived VA-RNA-Mediated Innate Immune Responses

    Directory of Open Access Journals (Sweden)

    Hiroyuki Mizuguchi

    2011-07-01

    Full Text Available The major limitation of the clinical use of replication-incompetent adenovirus (Ad vectors is the interference by innate immune responses, including induction of inflammatory cytokines and interferons (IFN, following in vivo application of Ad vectors. Ad vector-induced production of inflammatory cytokines and IFNs also results in severe organ damage and efficient induction of acquired immune responses against Ad proteins and transgene products. Ad vector-induced innate immune responses are triggered by the recognition of Ad components by pattern recognition receptors (PRRs. In order to reduce the side effects by Ad vector-induced innate immune responses and to develop safer Ad vectors, it is crucial to clarify which PRRs and which Ad components are involved in Ad vector-induced innate immune responses. Our group previously demonstrated that myeloid differentiating factor 88 (MyD88 and toll-like receptor 9 (TLR9 play crucial roles in the Ad vector-induced inflammatory cytokine production in mouse bone marrow-derived dendritic cells. Furthermore, our group recently found that virus associated-RNAs (VA-RNAs, which are about 160 nucleotide-long non-coding small RNAs encoded in the Ad genome, are involved in IFN production through the IFN-β promoter stimulator-1 (IPS-1-mediated signaling pathway following Ad vector transduction. The aim of this review is to highlight the Ad vector-induced innate immune responses following transduction, especially VA-RNA-mediated innate immune responses. Our findings on the mechanism of Ad vector-induced innate immune responses should make an important contribution to the development of safer Ad vectors, such as an Ad vector lacking expression of VA-RNAs.

  4. Removing Noise From Pyrosequenced Amplicons

    Directory of Open Access Journals (Sweden)

    Davenport Russell J

    2011-01-01

    Full Text Available Abstract Background In many environmental genomics applications a homologous region of DNA from a diverse sample is first amplified by PCR and then sequenced. The next generation sequencing technology, 454 pyrosequencing, has allowed much larger read numbers from PCR amplicons than ever before. This has revolutionised the study of microbial diversity as it is now possible to sequence a substantial fraction of the 16S rRNA genes in a community. However, there is a growing realisation that because of the large read numbers and the lack of consensus sequences it is vital to distinguish noise from true sequence diversity in this data. Otherwise this leads to inflated estimates of the number of types or operational taxonomic units (OTUs present. Three sources of error are important: sequencing error, PCR single base substitutions and PCR chimeras. We present AmpliconNoise, a development of the PyroNoise algorithm that is capable of separately removing 454 sequencing errors and PCR single base errors. We also introduce a novel chimera removal program, Perseus, that exploits the sequence abundances associated with pyrosequencing data. We use data sets where samples of known diversity have been amplified and sequenced to quantify the effect of each of the sources of error on OTU inflation and to validate these algorithms. Results AmpliconNoise outperforms alternative algorithms substantially reducing per base error rates for both the GS FLX and latest Titanium protocol. All three sources of error lead to inflation of diversity estimates. In particular, chimera formation has a hitherto unrealised importance which varies according to amplification protocol. We show that AmpliconNoise allows accurate estimates of OTU number. Just as importantly AmpliconNoise generates the right OTUs even at low sequence differences. We demonstrate that Perseus has very high sensitivity, able to find 99% of chimeras, which is critical when these are present at high

  5. Amplicon-based metagenomic analysis of mixed fungal samples using proton release amplicon sequencing.

    Directory of Open Access Journals (Sweden)

    Daniel P Tonge

    Full Text Available Next generation sequencing technology has revolutionised microbiology by allowing concurrent analysis of whole microbial communities. Here we developed and verified similar methods for the analysis of fungal communities using a proton release sequencing platform with the ability to sequence reads of up to 400 bp in length at significant depth. This read length permits the sequencing of amplicons from commonly used fungal identification regions and thereby taxonomic classification. Using the 400 bp sequencing capability, we have sequenced amplicons from the ITS1, ITS2 and LSU fungal regions to a depth of approximately 700,000 raw reads per sample. Representative operational taxonomic units (OTUs were chosen by the USEARCH algorithm, and identified taxonomically through nucleotide blast (BLASTn. Combination of this sequencing technology with the bioinformatics pipeline allowed species recognition in two controlled fungal spore populations containing members of known identity and concentration. Each species included within the two controlled populations was found to correspond to a representative OTU, and these OTUs were found to be highly accurate representations of true biological sequences. However, the absolute number of reads attributed to each OTU differed among species. The majority of species were represented by an OTU derived from all three genomic regions although in some cases, species were only represented in two of the regions due to the absence of conserved primer binding sites or due to sequence composition. It is apparent from our data that proton release sequencing technologies can deliver a qualitative assessment of the fungal members comprising a sample. The fact that some fungi cannot be amplified by specific "conserved" primer pairs confirms our recommendation that a multi-region approach be taken for other amplicon-based metagenomic studies.

  6. State of the VA

    Directory of Open Access Journals (Sweden)

    Robbins RA

    2016-01-01

    Full Text Available No abstract available. Article truncated at 150 words. Earlier this week, President Obama gave his last State of the Union Address. Although this usually is a speech giving the President the opportunity of flaunt his accomplishments, no mention was made of the VA (1. Given the troubles at the VA, there seems little to tout. Over 70% of the VA medical centers were discovered to have falsified wait times (2. Because of the wait scandal, VA Secretary Eric Shinseki resigned and VA undersecretary, Robert Petzel MD, retired under pressure. Ironically, Shinseki, a retired Army general and member of the Joint Chiefs of Staff, was viewed in a favorable light by the current administration because of a spat with the Bush administration's Secretary of Defense, Donald Rumsfeld, over the number of troops needed to secure Iran and Afghanistan (3. However, during Shinseki's tenure the number of VA "medical troops", doctors and nurses, was insufficient to care for the number …

  7. Association of Myosin Va and Schwann cells-derived RNA in mammal myelinated axons, analyzed by immunocytochemistry and confocal FRET microscopy.

    Science.gov (United States)

    Canclini, Lucía; Wallrabe, Horst; Di Paolo, Andrés; Kun, Alejandra; Calliari, Aldo; Sotelo-Silveira, José Roberto; Sotelo, José Roberto

    2014-03-15

    Evidence from multiple sources supports the hypothesis that Schwann cells in the peripheral nervous system transfer messenger RNA and ribosomes to the axons they ensheath. Several technical and methodological difficulties exist for investigators to unravel this process in myelinated axons - a complex two-cell unit. We present an experimental design to demonstrate that newly synthesized RNA is transferred from Schwann cells to axons in association with Myosin Va. The use of quantitative confocal FRET microscopy to track newly-synthesized RNA and determine the molecular association with Myosin Va, is described in detail.

  8. A quantitative SMRT cell sequencing method for ribosomal amplicons.

    Science.gov (United States)

    Jones, Bethan M; Kustka, Adam B

    2017-04-01

    Advances in sequencing technologies continue to provide unprecedented opportunities to characterize microbial communities. For example, the Pacific Biosciences Single Molecule Real-Time (SMRT) platform has emerged as a unique approach harnessing DNA polymerase activity to sequence template molecules, enabling long reads at low costs. With the aim to simultaneously classify and enumerate in situ microbial populations, we developed a quantitative SMRT (qSMRT) approach that involves the addition of exogenous standards to quantify ribosomal amplicons derived from environmental samples. The V7-9 regions of 18S SSU rDNA were targeted and quantified from protistan community samples collected in the Ross Sea during the Austral summer of 2011. We used three standards of different length and optimized conditions to obtain accurate quantitative retrieval across the range of expected amplicon sizes, a necessary criterion for analyzing taxonomically diverse 18S rDNA molecules from natural environments. The ability to concurrently identify and quantify microorganisms in their natural environment makes qSMRT a powerful, rapid and cost-effective approach for defining ecosystem diversity and function.

  9. Silencing Status Epilepticus-Induced BDNF Expression with Herpes Simplex Virus Type-1 Based Amplicon Vectors.

    Science.gov (United States)

    Falcicchia, Chiara; Trempat, Pascal; Binaschi, Anna; Perrier-Biollay, Coline; Roncon, Paolo; Soukupova, Marie; Berthommé, Hervé; Simonato, Michele

    2016-01-01

    Brain-derived neurotrophic factor (BDNF) has been found to produce pro- but also anti-epileptic effects. Thus, its validity as a therapeutic target must be verified using advanced tools designed to block or to enhance its signal. The aim of this study was to develop tools to silence the BDNF signal. We generated Herpes simplex virus type 1 (HSV-1) derived amplicon vectors, i.e. viral particles containing a genome of 152 kb constituted of concatameric repetitions of an expression cassette, enabling the expression of the gene of interest in multiple copies. HSV-1 based amplicon vectors are non-pathogenic and have been successfully employed in the past for gene delivery into the brain of living animals. Therefore, amplicon vectors should represent a logical choice for expressing a silencing cassette, which, in multiple copies, is expected to lead to an efficient knock-down of the target gene expression. Here, we employed two amplicon-based BDNF silencing strategies. The first, antisense, has been chosen to target and degrade the cytoplasmic mRNA pool of BDNF, whereas the second, based on the convergent transcription technology, has been chosen to repress transcription at the BDNF gene. Both these amplicon vectors proved to be effective in down-regulating BDNF expression in vitro, in BDNF-expressing mesoangioblast cells. However, only the antisense strategy was effective in vivo, after inoculation in the hippocampus in a model of status epilepticus in which BDNF mRNA levels are strongly increased. Interestingly, the knocking down of BDNF levels induced with BDNF-antisense was sufficient to produce significant behavioral effects, in spite of the fact that it was produced only in a part of a single hippocampus. In conclusion, this study demonstrates a reliable effect of amplicon vectors in knocking down gene expression in vitro and in vivo. Therefore, this approach may find broad applications in neurobiological studies.

  10. Silencing Status Epilepticus-Induced BDNF Expression with Herpes Simplex Virus Type-1 Based Amplicon Vectors.

    Directory of Open Access Journals (Sweden)

    Chiara Falcicchia

    Full Text Available Brain-derived neurotrophic factor (BDNF has been found to produce pro- but also anti-epileptic effects. Thus, its validity as a therapeutic target must be verified using advanced tools designed to block or to enhance its signal. The aim of this study was to develop tools to silence the BDNF signal. We generated Herpes simplex virus type 1 (HSV-1 derived amplicon vectors, i.e. viral particles containing a genome of 152 kb constituted of concatameric repetitions of an expression cassette, enabling the expression of the gene of interest in multiple copies. HSV-1 based amplicon vectors are non-pathogenic and have been successfully employed in the past for gene delivery into the brain of living animals. Therefore, amplicon vectors should represent a logical choice for expressing a silencing cassette, which, in multiple copies, is expected to lead to an efficient knock-down of the target gene expression. Here, we employed two amplicon-based BDNF silencing strategies. The first, antisense, has been chosen to target and degrade the cytoplasmic mRNA pool of BDNF, whereas the second, based on the convergent transcription technology, has been chosen to repress transcription at the BDNF gene. Both these amplicon vectors proved to be effective in down-regulating BDNF expression in vitro, in BDNF-expressing mesoangioblast cells. However, only the antisense strategy was effective in vivo, after inoculation in the hippocampus in a model of status epilepticus in which BDNF mRNA levels are strongly increased. Interestingly, the knocking down of BDNF levels induced with BDNF-antisense was sufficient to produce significant behavioral effects, in spite of the fact that it was produced only in a part of a single hippocampus. In conclusion, this study demonstrates a reliable effect of amplicon vectors in knocking down gene expression in vitro and in vivo. Therefore, this approach may find broad applications in neurobiological studies.

  11. VaR BASED RISK MANAGEMENT

    Directory of Open Access Journals (Sweden)

    Mária Bohdalová

    2013-06-01

    Full Text Available In this paper we discuss the Value–at–Risk concept and we analyse the market risk by using EWMA approach. EWMA (exponentially weighted moving average forecasting technique is a popular measure of various risks in financial risk management. We will compare standard EWMA, robust EWMA and skewed EWMA forecast of VaR. JP Morgan standard EWMA is derived from Gaussian distribution. Robust EWMA is based on Laplace distribution and skewed EWMA is a new approach derived from an asymmetric Laplace distribution. Asymmetric Laplace distribution takes into account both skewness and heavy tails in return distribution and the time varying nature of them in practice. Skewed EWMA VaR is a generalization of the standard EWMA method. Using these approaches we will analyse selected financial series (three European market indexes and one exchange rate. We have found andconfirmed that skewed EWMA forecasting of VaR outperforms the standard EWMA method.

  12. PCR Amplicon Prediction from Multiplex Degenerate Primer and Probe Sets

    Energy Technology Data Exchange (ETDEWEB)

    2013-08-08

    Assessing primer specificity and predicting both desired and off-target amplification products is an essential step for robust PCR assay design. Code is described to predict potential polymerase chain reaction (PCR) amplicons in a large sequence database such as NCBI nt from either singleplex or a large multiplexed set of primers, allowing degenerate primer and probe bases, with target mismatch annotates amplicons with gene information automatically downloaded from NCBI, and optionally it can predict whether there are also TaqMan/Luminex probe matches within predicted amplicons.

  13. Fast, accurate and easy-to-pipeline methods for amplicon sequence processing

    Science.gov (United States)

    Antonielli, Livio; Sessitsch, Angela

    2016-04-01

    Next generation sequencing (NGS) technologies established since years as an essential resource in microbiology. While on the one hand metagenomic studies can benefit from the continuously increasing throughput of the Illumina (Solexa) technology, on the other hand the spreading of third generation sequencing technologies (PacBio, Oxford Nanopore) are getting whole genome sequencing beyond the assembly of fragmented draft genomes, making it now possible to finish bacterial genomes even without short read correction. Besides (meta)genomic analysis next-gen amplicon sequencing is still fundamental for microbial studies. Amplicon sequencing of the 16S rRNA gene and ITS (Internal Transcribed Spacer) remains a well-established widespread method for a multitude of different purposes concerning the identification and comparison of archaeal/bacterial (16S rRNA gene) and fungal (ITS) communities occurring in diverse environments. Numerous different pipelines have been developed in order to process NGS-derived amplicon sequences, among which Mothur, QIIME and USEARCH are the most well-known and cited ones. The entire process from initial raw sequence data through read error correction, paired-end read assembly, primer stripping, quality filtering, clustering, OTU taxonomic classification and BIOM table rarefaction as well as alternative "normalization" methods will be addressed. An effective and accurate strategy will be presented using the state-of-the-art bioinformatic tools and the example of a straightforward one-script pipeline for 16S rRNA gene or ITS MiSeq amplicon sequencing will be provided. Finally, instructions on how to automatically retrieve nucleotide sequences from NCBI and therefore apply the pipeline to targets other than 16S rRNA gene (Greengenes, SILVA) and ITS (UNITE) will be discussed.

  14. Detection of immobilized amplicons by ELISA-like techniques.

    Science.gov (United States)

    Oroskar, A A; Rasmussen, S E; Rasmussen, H N; Rasmussen, S R; Sullivan, B M; Johansson, A

    1996-09-01

    The NucleoLink surface is a physically modified, thermostable, optically clear resin. It allows the covalent binding of 5'-phosphorylated oligonucleotides. Target DNA amplification by polymerase chain reaction (PCR) is accomplished by asymmetric amplification on the covalently immobilized primer that develops into immobilized amplicons. A DNA fragment of bovine leukemia virus is used as a model system for the detection of immobilized amplicons by ELISA-like techniques. Covalently bound oligonucleotides are also utilized as capture probe in the hybridization-based signal amplification for detection of an infectious organism.

  15. Geographic Distribution of VA Expenditures Report (GDX)

    Data.gov (United States)

    Department of Veterans Affairs — Geographic Distribution of VA Expenditures Report (GDX) located on the Expenditures page in the Expenditure Tables category. This report details VA expenditures at...

  16. VA National Bed Control System

    Data.gov (United States)

    Department of Veterans Affairs — The VA National Bed Control System records the levels of operating, unavailable and authorized beds at each VAMC, and it tracks requests for changes in these levels....

  17. Barcoded Primers Used in Multiplex Amplicon Pyrosequencing Bias Amplification

    OpenAIRE

    2012-01-01

    “Barcode-tagged” PCR primers used for multiplex amplicon sequencing generate a thus-far-overlooked amplification bias that produces variable terminal restriction fragment length polymorphism (T-RFLP) and pyrosequencing data from the same environmental DNA template. We propose a simple two-step PCR approach that increases reproducibility and consistently recovers higher genetic diversity in pyrosequencing libraries.

  18. The Geometric-VaR Backtesting Method

    DEFF Research Database (Denmark)

    Wei, Wei; Pelletier, Denis

    2014-01-01

    This paper develops a new test to evaluate Value af Risk (VaR) forecasts. VaR is a standard risk measure widely utilized by financial institutions and regulators, yet estimating VaR is a challenging problem, and popular VaR forecast relies on unrealistic assumptions. Hence, assessing the performa...

  19. VA telemental health: suicide assessment.

    Science.gov (United States)

    Godleski, Linda; Nieves, J Edwin; Darkins, Adam; Lehmann, Laurent

    2008-01-01

    The Department of Veterans Affairs (VA) encompasses one of the largest telemental health networks in the world, with over 45,000 videoconferencing and over 5,000 home telemental health encounters annually. Recently, the VA designated suicide prevention as a major priority, with telehealth modalities providing opportunities for remote interventions. Suicide risk assessments, using videoconferencing, are now documented in the literature, as are current studies that find telemental health to be equivalent to face-to-face treatment. Remote assessment of suicidality, however, involves complex legal issues: licensing requirements for remote delivery of care, legal procedures for involuntary detainment and commitment of potentially harmful patients, and liability questions related to the remote nature of the mental health service. VA best practices for remote suicide risk assessment include paradigms for establishing procedures in the context of legal challenges (licensing and involuntary detainment/commitment), for utilizing clinical assessment and triage decision protocols, and for contingency planning to optimize patient care and reduce liability.

  20. Herpes simplex virus type 1-based amplicon vectors for fundamental research in neurosciences and gene therapy of neurological diseases.

    Science.gov (United States)

    Jerusalinsky, Diana; Baez, María Verónica; Epstein, Alberto Luis

    2012-01-01

    Somatic manipulation of the nervous system without the involvement of the germinal line appears as a powerful counterpart of the transgenic strategy. The use of viral vectors to produce specific, transient and localized knockout, knockdown, ectopic expression or overexpression of a gene, leads to the possibility of analyzing both in vitro and in vivo molecular basis of neural function. In this approach, viral particles engineered to carry transgenic sequences are delivered into discrete brain regions, to transduce cells that will express the transgenic products. Amplicons are replication-incompetent helper-dependent vectors derived from herpes simplex virus type 1 (HSV-1), with several advantages that potentiate their use in neurosciences: (1) minimal toxicity: amplicons do not encode any virus proteins, are neither toxic for the infected cells nor pathogenic for the inoculated animals and elicit low levels of adaptive immune responses; (2) extensive transgene capacity to carry up to 150-kb of foreign DNA; i.e., entire genes with regulatory sequences could be delivered; (3) widespread cellular tropism: amplicons can experimentally infect several cell types including glial cells, though naturally the virus infects mainly neurons and epithelial cells; (4) since the viral genome does not integrate into cellular chromosomes there is low probability to induce insertional mutagenesis. Recent investigations on gene transfer into the brain using these vectors, have focused on gene therapy of inherited genetic diseases affecting the nervous system, such as ataxias, or on neurodegenerative disorders using experimental models of Parkinson's or Alzheimer's disease. Another group of studies used amplicons to investigate complex neural functions such as neuroplasticity, anxiety, learning and memory. In this short review, we summarize recent data supporting the potential of HSV-1 based amplicon vector model for gene delivery and modulation of gene expression in primary cultures

  1. 抑郁症患者脑源性神经营养因子Va166Met多态性与血清浓度的关系%Va166Met polymorphism and serum brain-derived neurotrophic factor concentration in depression patients

    Institute of Scientific and Technical Information of China (English)

    杨兆正; 张玉梅; 周宏辉; 周朝昀

    2011-01-01

    目的 探讨脑源性神经营养因子(BDNF)基因Va166Met多态性与抑郁症之间的关系以及Va166Met多态性是否影响血清BDNF浓度.方法 对76例未经药物治疗的抑郁症患者和50例正常人,用限制性片段长度多态性方法分析Va166Met多态性,采用酶联吸附反应方法对血清BDNF浓度进行检测.结果 (1)抑郁症患者血清BDNF浓度(24.7±12.7)ng/ml显著低于正常对照组(36.6±16.4)pg/ml,差异有统计学意义(P<0.01);(2)抑郁症组和对照组之间的Va166Met多态性位点的等位基因频率和基因型分布差异无统计学意义(P>0.05);(3)在押郁症组和对照组,Val/Met+Met/Met基因型组与Val/Val基因型相比,血清BDNF浓度差异无统计学意义(P>0.05).结论 抑郁症患者存在较低的血清BDNF水平,BDNF基因Val66Met多态性与抑郁症之间无相关性,Va166Met多态性对血清BDNF水平浓度无明显影响.%Objective To explore whether the BDNF gene Val66Met polymorphism was associated with depressive disorder and whether the BDNF gene Val66Met polymorphism was correlated with the serum BDNF levels. Methods 76 untreated depressive disorder patients and 50 normal control cases were included in the study. The BDNF gene Val66Met polymorphism was analyzed by using a polymerase chain reaction-based restriction fragment length polymorphism detection assay. The enzyme linked immunoabsorption reaction assay was used to measure the serum BDNF levels. Results Serum BDNF levels were significantly lower in depressive disorder patients (24.7 ± 12.7)ng/ml than that in normal control subjects (36.6± 16.4)pg/ml (P < 0.01). There were no significant differences either in allele or genotype in the Val66Met polymorphism between the depressive disorder and control groups (P > 0. 05).Moreover,there were no significant differences in the serum BDNF levels between the Val/Met+ Met/Met genotype and Val/Val genotype in depressive disorder and control groups. Conclusions There is a

  2. DADA2: High resolution sample inference from Illumina amplicon data

    Science.gov (United States)

    Callahan, Benjamin J; McMurdie, Paul J; Rosen, Michael J; Han, Andrew W; Johnson, Amy Jo A; Holmes, Susan P

    2016-01-01

    We present DADA2, a software package that models and corrects Illumina-sequenced amplicon errors. DADA2 infers sample sequences exactly, without coarse-graining into OTUs, and resolves differences of as little as one nucleotide. In several mock communities DADA2 identified more real variants and output fewer spurious sequences than other methods. We applied DADA2 to vaginal samples from a cohort of pregnant women, revealing a diversity of previously undetected Lactobacillus crispatus variants. PMID:27214047

  3. Multiplex PCR, amplicon size and hybridization efficiency on the NanoChip electronic microarray

    DEFF Research Database (Denmark)

    Børsting, Claus; Sanchez, Juan J; Morling, Niels

    2004-01-01

    . Hybridization to individual amplicons in multiplexes was less efficient suggesting that intramolecular and intermolecular interactions may block access to the target sequence on the NanoChip array. We observed a high risk of contamination with amplicons shorter than 60 bp and therefore, we recommend the use......We tested the SNP typing protocol developed for the NanoChip electronic microarray by analyzing the four Y chromosome loci SRY1532, SRY8299, TAT, and 92R7. Amplicons of different lengths containing the same locus were purified and addressed to the NanoChip array and fluorescently labelled reporter...... probes were hybridized to the amplicons. We demonstrated that as little as 10-30 fmol of 50 bp DNA amplicons was sufficient to obtain strong and reproducible results. The hybridization to 50 bp amplicons was up to 10 times more efficient than the hybridization to 200 bp amplicons containing the same SNP...

  4. Report of VA Medical Training Programs

    Data.gov (United States)

    Department of Veterans Affairs — The Report of VA Medical Training Programs Database is used to track medical center health services trainees and VA physicians serving as faculty. The database also...

  5. Non-VA Hospital System (NVH)

    Data.gov (United States)

    Department of Veterans Affairs — The Veterans Health Administration (VHA) pays for care provided to VA beneficiaries in non-VA hospitals through its contract hospitalization program as mandated by...

  6. Swarm: robust and fast clustering method for amplicon-based studies

    Directory of Open Access Journals (Sweden)

    Frédéric Mahé

    2014-09-01

    Full Text Available Popular de novo amplicon clustering methods suffer from two fundamental flaws: arbitrary global clustering thresholds, and input-order dependency induced by centroid selection. Swarm was developed to address these issues by first clustering nearly identical amplicons iteratively using a local threshold, and then by using clusters’ internal structure and amplicon abundances to refine its results. This fast, scalable, and input-order independent approach reduces the influence of clustering parameters and produces robust operational taxonomic units.

  7. Geographic Distribution of VA Expenditures FY1998

    Data.gov (United States)

    Department of Veterans Affairs — This report details VA expenditures at the state, county, and Congressional District level. It includes categories such as Compensation and Pension, Construction,...

  8. Geographic Distribution of VA Expenditures FY2001

    Data.gov (United States)

    Department of Veterans Affairs — This report details VA expenditures at the state, county, and Congressional District level. It includes categories such as Compensation and Pension, Construction,...

  9. Geographic Distribution of VA Expenditures FY1996

    Data.gov (United States)

    Department of Veterans Affairs — This report details VA expenditures at the state, county, and Congressional District level. It includes categories such as Compensation and Pension, Construction,...

  10. Geographic Distribution of VA Expenditures FY2006

    Data.gov (United States)

    Department of Veterans Affairs — This report details VA expenditures at the state, county, and Congressional District level. It includes categories such as Compensation and Pension, Construction,...

  11. Geographic Distribution of VA Expenditures FY2003

    Data.gov (United States)

    Department of Veterans Affairs — This report details VA expenditures at the state, county, and Congressional District level. It includes categories such as Compensation and Pension, Construction,...

  12. Geographic Distribution of VA Expenditures FY2007

    Data.gov (United States)

    Department of Veterans Affairs — This report details VA expenditures at the state, county, and Congressional District level. It includes categories such as Compensation and Pension, Construction,...

  13. Geographic Distribution of VA Expenditures FY2011

    Data.gov (United States)

    Department of Veterans Affairs — This report details VA expenditures at the state, county, and Congressional District level. It includes categories such as Compensation and Pension, Construction,...

  14. Geographic Distribution of VA Expenditures FY2000

    Data.gov (United States)

    Department of Veterans Affairs — This report details VA expenditures at the state, county, and Congressional District level. It includes categories such as Compensation and Pension, Construction,...

  15. Geographic Distribution of VA Expenditures FY1997

    Data.gov (United States)

    Department of Veterans Affairs — This report details VA expenditures at the state, county, and Congressional District level. It includes categories such as Compensation and Pension, Construction,...

  16. Geographic Distribution of VA Expenditures FY2008

    Data.gov (United States)

    Department of Veterans Affairs — This report details VA expenditures at the state, county, and Congressional District level. It includes categories such as Compensation and Pension, Construction,...

  17. Geographic Distribution of VA Expenditures FY2005

    Data.gov (United States)

    Department of Veterans Affairs — This report details VA expenditures at the state, county, and Congressional District level. It includes categories such as Compensation and Pension, Construction,...

  18. Geographic Distribution of VA Expenditures FY2010

    Data.gov (United States)

    Department of Veterans Affairs — This report details VA expenditures at the state, county, and Congressional District level. It includes categories such as Compensation and Pension, Construction,...

  19. Geographic Distribution of VA Expenditures FY1999

    Data.gov (United States)

    Department of Veterans Affairs — This report details VA expenditures at the state, county, and Congressional District level. It includes categories such as Compensation and Pension, Construction,...

  20. Geographic Distribution of VA Expenditures FY2004

    Data.gov (United States)

    Department of Veterans Affairs — This report details VA expenditures at the state, county, and Congressional District level. It includes categories such as Compensation and Pension, Construction,...

  1. Geographic Distribution of VA Expenditures FY2009

    Data.gov (United States)

    Department of Veterans Affairs — This report details VA expenditures at the state, county, and Congressional District level. It includes categories such as Compensation and Pension, Construction,...

  2. Geographic Distribution of VA Expenditures FY2012

    Data.gov (United States)

    Department of Veterans Affairs — This report details VA expenditures at the state, county, and Congressional District level. It includes categories such as Compensation and Pension, Construction,...

  3. Geographic Distribution of VA Expenditures FY2013

    Data.gov (United States)

    Department of Veterans Affairs — This report details VA expenditures at the state, county, and Congressional District level. It includes categories such as Compensation and Pension, Construction,...

  4. Geographic Distribution of VA Expenditures FY2002

    Data.gov (United States)

    Department of Veterans Affairs — This report details VA expenditures at the state, county, and Congressional District level. It includes categories such as Compensation and Pension, Construction,...

  5. KaVA ESTEMA project

    Science.gov (United States)

    Oyadomari, Miyako; Imai, Hiroshi; Cho, Se-Hyung; Asaki, Yoshiharu; Choi, Yoon-Kyong; Kim, Jaeheon; Yun, Youngjoo; Matsumoto, Naoko; Min, Cheul-Hong; Oyama, Tomoaki; Yoon, Sung-Chul; Yoon, Dong-Hwan; Kim, Dong-Jin; Dodson, Richard; Rioja, Maria; Burns, Ross; Orosz, Gabor; Nakagawa, Akiharu; Chibueze O, James; Nakashima, Jun-ichi; Sobolev, Andrey

    2016-07-01

    The ESTEMA (Expanded Study on Stellar Masers) project is one of three Large Programs of the KaVA (the combined array of the Korean VLBI Network and Japanese VLBI Exploration of Radio Astrometry), and conducted in 2015-2016. It aims to publish a database of the largest sample of VLBI images of circumstellar water (H2O) and silicon-monoxide (SiO) maser sources towards circumstellar envelopes (CSEs) of 80 evolved stars in late AGB to early post-AGB phase. Here we present the specifications of the ESTEMA observations and the planned scientific goals in order to share the basic information of the ESTEMA with astronomical community and encourage future collaborations with the ESTEMA and future follow-up observations for the targeted stars.

  6. Deep amplicon sequencing reveals mixed phytoplasma infection within single grapevine plants

    DEFF Research Database (Denmark)

    Nicolaisen, Mogens; Contaldo, Nicoletta; Makarova, Olga

    2011-01-01

    The diversity of phytoplasmas within single plants has not yet been fully investigated. In this project, deep amplicon sequencing was used to generate 50,926 phytoplasma sequences from 11 phytoplasma-infected grapevine samples from a PCR amplicon in the 5' end of the 16S region. After clustering ...

  7. Construction of a cytomegalovirus-based amplicon: a vector with a unique transfer capacity.

    Science.gov (United States)

    Borst, Eva Maria; Messerle, Martin

    2003-07-01

    Cytomegalovirus (CMV) has a number of interesting properties that qualifies it as a vector for gene transfer. Especially appealing is the ability of the CMV genome to persist in hematopoietic progenitor cells and the packaging capacity of the viral capsid that accommodates a DNA genome of 230 kbp. In order to exploit the packaging capacity of the CMV capsid we investigated whether the principles of an amplicon vector can be applied to CMV. Amplicons are herpesviral vectors, which contain only the cis-active sequences required for replication and packaging of the vector genome. For construction of a CMV amplicon the sequences comprising the lytic origin of replication (orilyt) and the cleavage packaging recognition sites (pac) of human CMV were cloned onto a plasmid. A gene encoding the green fluorescent protein was used as a model transgene. The amplicon plasmid replicated in the presence of a CMV helper virus and was packaged into CMV particles, with replication and packaging being dependent on the presence of the orilyt and pac sequences. The packaged amplicon could be transferred to recipient cells and reisolated from the transduced cells. Analysis of the DNA isolated from CMV capsids revealed that the CMV amplicon was packaged as a concatemer with a size of approximately 210 kbp. The CMV amplicon vector has the potential to transfer therapeutic genes with a size of more than 200 kbp and thus provides a unique transfer capacity among viral vectors.

  8. Technology Reference Model (TRM) Reports: VA Category Framework Count Report

    Data.gov (United States)

    Department of Veterans Affairs — The One VA Enterprise Architecture (OneVA EA) is a comprehensive picture of the Department of Veterans Affairs' (VA) operations, capabilities and services and the...

  9. Technology Reference Model (TRM) Reports: VA Category Mapping Report

    Data.gov (United States)

    Department of Veterans Affairs — The One VA Enterprise Architecture (OneVA EA) is a comprehensive picture of the Department of Veterans Affairs' (VA) operations, capabilities and services and the...

  10. Improved sensitivity of circulating tumor DNA measurement using short PCR amplicons

    DEFF Research Database (Denmark)

    Andersen, Rikke Fredslund; Spindler, Karen-Lise Garm; Brandslund, Ivan

    2015-01-01

    , however, presents a number of challenges that require attention. The amount of DNA is low and highly fragmented and analyses need to be optimized accordingly. KRAS ARMS-qPCR assays with amplicon lengths of 120 and 85 base pairs, respectively, were compared using positive control material (PCR fragments......) and plasma samples from 46 colorectal cancer patients known to harbor a tumor KRAS mutation. KRAS mutated DNA was detected in significantly more clinical samples using the short amplicon assays compared to the long amplicon assays (74% vs. 61%, p=0.03). The level of mutated DNA in plasma was on average three...

  11. Integrated Microfluidic Nucleic Acid Isolation, Isothermal Amplification, and Amplicon Quantification

    Directory of Open Access Journals (Sweden)

    Michael G. Mauk

    2015-10-01

    Full Text Available Microfluidic components and systems for rapid (<60 min, low-cost, convenient, field-deployable sequence-specific nucleic acid-based amplification tests (NAATs are described. A microfluidic point-of-care (POC diagnostics test to quantify HIV viral load from blood samples serves as a representative and instructive example to discuss the technical issues and capabilities of “lab on a chip” NAAT devices. A portable, miniaturized POC NAAT with performance comparable to conventional PCR (polymerase-chain reaction-based tests in clinical laboratories can be realized with a disposable, palm-sized, plastic microfluidic chip in which: (1 nucleic acids (NAs are extracted from relatively large (~mL volume sample lysates using an embedded porous silica glass fiber or cellulose binding phase (“membrane” to capture sample NAs in a flow-through, filtration mode; (2 NAs captured on the membrane are isothermally (~65 °C amplified; (3 amplicon production is monitored by real-time fluorescence detection, such as with a smartphone CCD camera serving as a low-cost detector; and (4 paraffin-encapsulated, lyophilized reagents for temperature-activated release are pre-stored in the chip. Limits of Detection (LOD better than 103 virons/sample can be achieved. A modified chip with conduits hosting a diffusion-mode amplification process provides a simple visual indicator to readily quantify sample NA template. In addition, a companion microfluidic device for extracting plasma from whole blood without a centrifuge, generating cell-free plasma for chip-based molecular diagnostics, is described. Extensions to a myriad of related applications including, for example, food testing, cancer screening, and insect genotyping are briefly surveyed.

  12. Integrated Microfluidic Nucleic Acid Isolation, Isothermal Amplification, and Amplicon Quantification.

    Science.gov (United States)

    Mauk, Michael G; Liu, Changchun; Song, Jinzhao; Bau, Haim H

    2015-10-20

    Microfluidic components and systems for rapid (microfluidic point-of-care (POC) diagnostics test to quantify HIV viral load from blood samples serves as a representative and instructive example to discuss the technical issues and capabilities of "lab on a chip" NAAT devices. A portable, miniaturized POC NAAT with performance comparable to conventional PCR (polymerase-chain reaction)-based tests in clinical laboratories can be realized with a disposable, palm-sized, plastic microfluidic chip in which: (1) nucleic acids (NAs) are extracted from relatively large (~mL) volume sample lysates using an embedded porous silica glass fiber or cellulose binding phase ("membrane") to capture sample NAs in a flow-through, filtration mode; (2) NAs captured on the membrane are isothermally (~65 °C) amplified; (3) amplicon production is monitored by real-time fluorescence detection, such as with a smartphone CCD camera serving as a low-cost detector; and (4) paraffin-encapsulated, lyophilized reagents for temperature-activated release are pre-stored in the chip. Limits of Detection (LOD) better than 10³ virons/sample can be achieved. A modified chip with conduits hosting a diffusion-mode amplification process provides a simple visual indicator to readily quantify sample NA template. In addition, a companion microfluidic device for extracting plasma from whole blood without a centrifuge, generating cell-free plasma for chip-based molecular diagnostics, is described. Extensions to a myriad of related applications including, for example, food testing, cancer screening, and insect genotyping are briefly surveyed.

  13. VA Personal Health Record Sample Data

    Data.gov (United States)

    Department of Veterans Affairs — My HealtheVet (www.myhealth.va.gov) is a Personal Health Record portal designed to improve the delivery of health care services to Veterans, to promote health and...

  14. 77 FR 38179 - Autopsies at VA Expense

    Science.gov (United States)

    2012-06-27

    ..., competition, jobs, the environment, public health or safety, or State, local, or tribal governments or... person in the appropriate class who assumes the right and duty of burial. (e) Death outside a VA...

  15. 76 FR 75509 - Autopsies at VA Expense

    Science.gov (United States)

    2011-12-02

    ... sector of the economy, productivity, competition, jobs, the environment, public health or safety, or... person in the appropriate class who assumes the right and duty of burial. (e) Death outside a VA...

  16. Implementing amplicon-based next generation sequencing in the diagnosis of small cell lung carcinoma metastases.

    Science.gov (United States)

    Meder, Lydia; König, Katharina; Fassunke, Jana; Ozretić, Luka; Wolf, Jürgen; Merkelbach-Bruse, Sabine; Heukamp, Lukas C; Buettner, Reinhard

    2015-12-01

    Small cell lung carcinoma (SCLC) is the most aggressive entity of lung cancer. Rapid cancer progression and early formation of systemic metastases drive the deadly outcome of SCLC. Recent advances in identifying oncogenes by cancer whole genome sequencing improved the understanding of SCLC carcinogenesis. However, tumor material is often limited in the clinic. Thus, it is a compulsive issue to improve SCLC diagnostics by combining established immunohistochemistry and next generation sequencing. We implemented amplicon-based next generation deep sequencing in our routine diagnostics pipeline to analyze RB1, TP53, EP300 and CREBBP, frequently mutated in SCLC. Thereby, our pipeline combined routine SCLC histology and identification of somatic mutations. We comprehensively analyzed fifty randomly collected SCLC metastases isolated from trachea and lymph nodes in comparison to specimens derived from primary SCLC. SCLC lymph node metastases showed enhanced proliferation and frequently a collapsed keratin cytoskeleton compared to SCLC metastases isolated from trachea. We identified characteristic synchronous mutations in RB1 and TP53 and non-synchronous CREBBP and EP300 mutations. Our data showed the benefit of implementing deep sequencing into routine diagnostics. We here identify oncogenic drivers and simultaneously gain further insights into SCLC tumor biology.

  17. Efficient error correction for next-generation sequencing of viral amplicons

    Directory of Open Access Journals (Sweden)

    Skums Pavel

    2012-06-01

    Full Text Available Abstract Background Next-generation sequencing allows the analysis of an unprecedented number of viral sequence variants from infected patients, presenting a novel opportunity for understanding virus evolution, drug resistance and immune escape. However, sequencing in bulk is error prone. Thus, the generated data require error identification and correction. Most error-correction methods to date are not optimized for amplicon analysis and assume that the error rate is randomly distributed. Recent quality assessment of amplicon sequences obtained using 454-sequencing showed that the error rate is strongly linked to the presence and size of homopolymers, position in the sequence and length of the amplicon. All these parameters are strongly sequence specific and should be incorporated into the calibration of error-correction algorithms designed for amplicon sequencing. Results In this paper, we present two new efficient error correction algorithms optimized for viral amplicons: (i k-mer-based error correction (KEC and (ii empirical frequency threshold (ET. Both were compared to a previously published clustering algorithm (SHORAH, in order to evaluate their relative performance on 24 experimental datasets obtained by 454-sequencing of amplicons with known sequences. All three algorithms show similar accuracy in finding true haplotypes. However, KEC and ET were significantly more efficient than SHORAH in removing false haplotypes and estimating the frequency of true ones. Conclusions Both algorithms, KEC and ET, are highly suitable for rapid recovery of error-free haplotypes obtained by 454-sequencing of amplicons from heterogeneous viruses. The implementations of the algorithms and data sets used for their testing are available at: http://alan.cs.gsu.edu/NGS/?q=content/pyrosequencing-error-correction-algorithm

  18. JRC GMO-Amplicons: a collection of nucleic acid sequences related to genetically modified organisms.

    Science.gov (United States)

    Petrillo, Mauro; Angers-Loustau, Alexandre; Henriksson, Peter; Bonfini, Laura; Patak, Alex; Kreysa, Joachim

    2015-01-01

    The DNA target sequence is the key element in designing detection methods for genetically modified organisms (GMOs). Unfortunately this information is frequently lacking, especially for unauthorized GMOs. In addition, patent sequences are generally poorly annotated, buried in complex and extensive documentation and hard to link to the corresponding GM event. Here, we present the JRC GMO-Amplicons, a database of amplicons collected by screening public nucleotide sequence databanks by in silico determination of PCR amplification with reference methods for GMO analysis. The European Union Reference Laboratory for Genetically Modified Food and Feed (EU-RL GMFF) provides these methods in the GMOMETHODS database to support enforcement of EU legislation and GM food/feed control. The JRC GMO-Amplicons database is composed of more than 240 000 amplicons, which can be easily accessed and screened through a web interface. To our knowledge, this is the first attempt at pooling and collecting publicly available sequences related to GMOs in food and feed. The JRC GMO-Amplicons supports control laboratories in the design and assessment of GMO methods, providing inter-alia in silico prediction of primers specificity and GM targets coverage. The new tool can assist the laboratories in the analysis of complex issues, such as the detection and identification of unauthorized GMOs. Notably, the JRC GMO-Amplicons database allows the retrieval and characterization of GMO-related sequences included in patents documentation. Finally, it can help annotating poorly described GM sequences and identifying new relevant GMO-related sequences in public databases. The JRC GMO-Amplicons is freely accessible through a web-based portal that is hosted on the EU-RL GMFF website. Database URL: http://gmo-crl.jrc.ec.europa.eu/jrcgmoamplicons/.

  19. Formation of linear amplicons with inverted duplications in Leishmania requires the MRE11 nuclease.

    Directory of Open Access Journals (Sweden)

    Marie-Claude N Laffitte

    2014-12-01

    Full Text Available Extrachromosomal DNA amplification is frequent in the protozoan parasite Leishmania selected for drug resistance. The extrachromosomal amplified DNA is either circular or linear, and is formed at the level of direct or inverted homologous repeated sequences that abound in the Leishmania genome. The RAD51 recombinase plays an important role in circular amplicons formation, but the mechanism by which linear amplicons are formed is unknown. We hypothesized that the Leishmania infantum DNA repair protein MRE11 is required for linear amplicons following rearrangements at the level of inverted repeats. The purified LiMRE11 protein showed both DNA binding and exonuclease activities. Inactivation of the LiMRE11 gene led to parasites with enhanced sensitivity to DNA damaging agents. The MRE11(-/- parasites had a reduced capacity to form linear amplicons after drug selection, and the reintroduction of an MRE11 allele led to parasites regaining their capacity to generate linear amplicons, but only when MRE11 had an active nuclease activity. These results highlight a novel MRE11-dependent pathway used by Leishmania to amplify portions of its genome to respond to a changing environment.

  20. Pharm GKB: Opium alkaloids and derivatives [PharmGKB

    Lifescience Database Archive (English)

    Full Text Available derivatives (R05DA) Drugs And Small Molecules The following have been classified under this therapeutic category: codeine dextrometho...rphan hydrocodone methadone morphine EvidenceGene VA CHRNA3 VA CHRNA5 No related dr

  1. Agreement Between HEDIS Performance Assessments in the VA and Medicare Advantage: Is Quality in the Eye of the Beholder?

    Science.gov (United States)

    Trivedi, Amal N; Wilson, Ira B; Charlton, Mary E; Kizer, Kenneth W

    2016-01-01

    Medicare Advantage (MA) plans and the Veterans Affairs (VA) health care system assess quality of care using standardized Healthcare Effectiveness Data and Information Set (HEDIS) performance measures. Little is known, however, about the relative accuracy of quality indicators for persons receiving care in more than one health care system. Among Veterans dually enrolled in an MA plan, we examined the agreement between MA and VA HEDIS assessments. Our study tested the hypothesis that private health plans underreport quality of care relative to a fully integrated delivery system utilizing a comprehensive electronic health record. Despite assessing the same individuals using identical measure specifications, reported VA performance was significantly better than reported MA performance for all 12 HEDIS measures. The VA's performance advantage ranged from 9.8% (glycosylated hemoglobin [HbA1c] Performance rates derived from VA and MA aggregate data were 1.6% to 14.3% higher than those reported by VA alone. This analysis suggests that neither MA plans nor the VA fully capture quality of care information for dually enrolled persons. However, the VA's system-wide electronic health record may allow for more complete capture of quality information across multiple providers and settings.

  2. Sex determination in beef by melting curve analysis of PCR amplicons from the amelogenin locus.

    Science.gov (United States)

    Ballin, Nicolai Z; Madsen, Knud G

    2007-11-01

    Sex determination of beef is important to meet the rules of the Commission Regulation (EC) 765/2002 that qualify for export refunds. A SYBR Green sex identification assay based on melting curve analysis of PCR amplicons from the amelogenin locus (AMELX and AMELY) was developed. The PCR amplicons of 130/130 and 130/67 base pairs produced from female and male beef, respectively, are easily distinguished by both melting curve analysis and gel electrophoresis. Results from the melting curve analysis of amplicons are ready in less than three minutes, and requires no additional work in addition to the PCR setup. Applicability of the sex determination assay was studied by analysis of 12 unknown beef samples and the results were compared to an accredited method based on gel electrophoresis. In addition, six different cattle breeds were examined. All test results were correct in respect to sex.

  3. Genetics Home Reference: carbonic anhydrase VA deficiency

    Science.gov (United States)

    ... 19(3):199-229. Review. Citation on PubMed Shah GN, Rubbelke TS, Hendin J, Nguyen H, Waheed A, Shoemaker JD, Sly WS. Targeted mutagenesis of mitochondrial carbonic anhydrases VA and VB implicates both enzymes in ammonia detoxification and glucose ...

  4. The Portfolio Decision Under the VaR Constraint

    Institute of Scientific and Technical Information of China (English)

    ChunfengWang; XinshuTu

    2004-01-01

    The VaR, a new appearing financial risk-manage tool, have been applied widely. Many financial setups have accustomed to measure the risk of a portfolio with the VaR. So it is very necessary to discuss the portfolio choice problem under the VaR constraint. In this paper, by setting and solving the portfolio choice model under the VaR constraint, we illustrate that the use of the VaR constraint reduces the array of choice to a more manageable range. The probability of traget VaR, therefore, can be thought of as a risk tolerance assessment tool (when coupled with another measure of risk).

  5. Use of AmpliWax to optimize amplicon sterilization by isopsoralen.

    Science.gov (United States)

    De la Viuda, M; Fille, M; Ruiz, J; Aslanzadeh, J

    1996-12-01

    The photochemical inactivation of amplicons by isopsoralen (IP-10) has been suggested as a possible means to prevent PCR carryover contamination. To evaluate the technique, serial dilutions of amplicons (10(11) to 10(3)) from the Borrelia burgdorferi OSP A gene were amplified in the presence of 0, 25, 50, and 100 micrograms of IP-10 per ml for 45 cycles. The PCR products were exposed to UV light for 15 min to activate IP-10 and sterilize the amplicons. One microliter of each sterilized sample was reamplified for an additional 45 cycles. The PCR products were then resolved in an agarose gel, blotted onto a nylon membrane, and probed with an alkaline phosphatase-conjugated chemiluminescent probe. Although IP-10 at concentrations of 50 and 100 micrograms/ml effectively sterilized up to 10(11) amplicons, the compound was inhibitory to PCR. IP-10 at a concentration of 25 micrograms/ml had slight inhibitory effect on PCR and did not completely sterilized all of the amplicons. Therefore, in subsequent experiments AmpliWax was substituted for mineral oil, and PCR was performed on 10(9) to 10(3) amplicons as described above. Following the amplification, the PCR tubes were cooled to solidify the AmpliWax and inoculated with various concentrations of IP-10. With this technique, PCR products produced from as many as 10(9) target amplicons were effectively sterilized with 200 micrograms of IP-10 per ml. Similarly, the addition of IP-10 (50 micrograms/ml) before and after PCR was evaluated for the detection of B. burgdorferi in 62 ticks from a region of Southern Connecticut where the organism is highly endemic. PCR performed in the presence of 50 micrograms of IP-10 per ml detected B. burgdorferi-specific DNA in 17 of 62 ticks (27%) following gel electrophoresis and in 34 of 62 ticks (55%) following Southern blot hybridization of the PCR products. In contrast, post-PCR addition of IP-10 detected borrelia-specific DNA in 31 of 62 ticks (50%) following gel electrophoresis and in

  6. Analyses of microstructural properties of VA/VeoVA copolymer modified cement pastes

    OpenAIRE

    Carlos Eduardo M. Gomes; Ferreira,Osny P.

    2005-01-01

    Recently, modern techniques have been applied for analysis of the influence of polymers on microstructural properties of Portland cement, such as Thermogravimetric Analyses (TG), Scanning Electronic Microscopy (SEM), Fourier Transform Infrared Spectroscopy (FT-IR) and Mercury Intrusion Porosimetry (MIP). In this study, thermogravimetric analyses were used to study the influence of vinyl acetate-versatic vinylester copolymer (VA/VeoVA) in seven pastes of 28-day old Portland cement, in which di...

  7. Surface density dependence of PCR amplicon hybridization on PNA/DNA probe layers

    DEFF Research Database (Denmark)

    Yao, Danfeng; Kim, Junyoung; Yu, Fang

    2005-01-01

    at an intermediate sodium concentration (approximately 100 mM). These effects were mainly ascribed to the electrostatic cross talk among the hybridized DNA molecules and the secondary structure of PCR amplicons. For the negatively charged DNA probes, the hybridization reaction was subjected additionally to the DNA...

  8. High-throughput amplicon sequencing reveals distinct communities within a corroding concrete sewer system.

    Science.gov (United States)

    Cayford, Barry I; Dennis, Paul G; Keller, Jurg; Tyson, Gene W; Bond, Philip L

    2012-10-01

    Microbially induced concrete corrosion (MICC) is an important problem in sewers. Here, small-subunit (SSU) rRNA gene amplicon pyrosequencing was used to characterize MICC communities. Microbial community composition differed between wall- and ceiling-associated MICC layers. Acidithiobacillus spp. were present at low abundances, and the communities were dominated by other sulfur-oxidizing-associated lineages.

  9. Amplicon sequencing for the quantification of spoilage microbiota in complex foods including bacterial spores

    NARCIS (Netherlands)

    Boer, de P.; Caspers, M.; Sanders, J.W.; Kemperman, R.; Wijman, J.; Lommerse, G.; Roeselers, G.; Montijn, R.; Abee, T.; Kort, R.

    2015-01-01

    Background
    Spoilage of food products is frequently caused by bacterial spores and lactic acid bacteria. Identification of these organisms by classic cultivation methods is limited by their ability to form colonies on nutrient agar plates. In this study, we adapted and optimized 16S rRNA amplicon

  10. Post-amplification Klenow fragment treatment alleviates PCR bias caused by partially single-stranded amplicons

    NARCIS (Netherlands)

    Egert, M.G.G.; Friedrich, M.W.

    2005-01-01

    Partially single-stranded amplicons, formed during PCR amplification of single and mixed templates, are a potential source of bias in genetic diversity studies. The analysis of 16S rRNA gene diversity in mixed template samples by the fingerprinting technique terminal restriction fragment length poly

  11. Genomic and expression array profiling of chromosome 20q amplicon in human colon cancer cells

    Directory of Open Access Journals (Sweden)

    Carter Jennifer

    2005-01-01

    Full Text Available Background: Gain of the q arm of chromosome 20 in human colorectal cancer has been associated with poorer survival time and has been reported to increase in frequency from adenomas to metastasis. The increasing frequency of chromosome 20q amplification during colorectal cancer progression and the presence of this amplification in carcinomas of other tissue origin has lead us to hypothesize that 20q11-13 harbors one or more genes which, when over expressed promote tumor invasion and metastasis. Aims: Generate genomic and expression profiles of the 20q amplicon in human cancer cell lines in order to identify genes with increased copy number and expression. Materials and Methods: Utilizing genomic sequencing clones and amplification mapping data from our lab and other previous studies, BAC/ PAC tiling paths spanning the 20q amplicon and genomic microarrays were generated. Array-CGH on the custom array with human cancer cell line DNAs was performed to generate genomic profiles of the amplicon. Expression array analysis with RNA from these cell lines using commercial oligo microarrays generated expression profiles of the amplicon. The data were then combined in order to identify genes with increased copy number and expression. Results: Over expressed genes in regions of increased copy number were identified and a list of potential novel genetic tumor markers was assembled based on biological functions of these genes Conclusions: Performing high-resolution genomic microarray profiling in conjunction with expression analysis is an effective approach to identify potential tumor markers.

  12. Overexpressed Genes/ESTs and Characterization of Distinct Amplicons on 17823 in Breast Cancer Cells

    Directory of Open Access Journals (Sweden)

    Ayse E. Erson

    2001-01-01

    Full Text Available 17823 is a frequent site of gene amplification in breast cancer. Several lines of evidence suggest the presence of multiple amplicons on 17823. To characterize distinct amplicons on 17823 and localize putative oncogenes, we screened genes and expressed sequence tags (ESTs in existing physical and radiation hybrid maps for amplification and overexpression in breast cancer cell lines by semiquantitative duplex PCR, semiquantitative duplex RT-PCR, Southern blot, Northern blot analyses. We identified two distinct amplicons on 17823, one including TBX2 and another proximal region including RPS6KB1 (PS6K and MUL. In addition to these previously reported overexpressed genes, we also identified amplification and overexpression of additional uncharacterized genes and ESTs, some of which suggest potential oncogenic activity. In conclusion, we have further defined two distinct regions of gene amplification and overexpression on 17823 with identification of new potential oncogene candidates. Based on the amplification and overexpression patterns of known and as of yet unrecognized genes on 17823, it is likely that some of these genes mapping to the discrete amplicons function as oncogenes and contribute to tumor progression in breast cancer cells.

  13. Troubles continue for the Phoenix VA

    Directory of Open Access Journals (Sweden)

    Robbins RA

    2014-10-01

    Full Text Available No abstract available. Article truncated after 150 words. According to the Joint Commission on the Accreditation of Healthcare Organizations (Joint Commission, JCAHO, an independent organization that reviews hospitals, the Phoenix VA does not comply with U.S. standards for safety, patient care and management (1. The hospital was at the epicenter of the national scandal over the quality of care being afforded to the nation's veterans where the now notorious practice of double-booking patient appointments was first exposed. The hospital's indifferent management provoked congressional investigations that uncovered still more system-wide abuses leading to the removal of the hospital director and the resignation of then VA secretary, Eric Shinseki. The hospital maintains its accreditation but with a follow-up survey in 1-6 months where it must show that it has successfully addressed the 13 identified problems (1. Inspectors who conducted the review in July found that VA employees were unable to report concerns "without retaliatory action from the hospital." Other alarming ...

  14. Simultaneous amplicon sequencing to explore co-occurrence patterns of bacterial, archaeal and eukaryotic microorganisms in rumen microbial communities.

    Science.gov (United States)

    Kittelmann, Sandra; Seedorf, Henning; Walters, William A; Clemente, Jose C; Knight, Rob; Gordon, Jeffrey I; Janssen, Peter H

    2013-01-01

    Ruminants rely on a complex rumen microbial community to convert dietary plant material to energy-yielding products. Here we developed a method to simultaneously analyze the community's bacterial and archaeal 16S rRNA genes, ciliate 18S rRNA genes and anaerobic fungal internal transcribed spacer 1 genes using 12 DNA samples derived from 11 different rumen samples from three host species (Ovis aries, Bos taurus, Cervus elephas) and multiplex 454 Titanium pyrosequencing. We show that the mixing ratio of the group-specific DNA templates before emulsion PCR is crucial to compensate for differences in amplicon length. This method, in contrast to using a non-specific universal primer pair, avoids sequencing non-targeted DNA, such as plant- or endophyte-derived rRNA genes, and allows increased or decreased levels of community structure resolution for each microbial group as needed. Communities analyzed with different primers always grouped by sample origin rather than by the primers used. However, primer choice had a greater impact on apparent archaeal community structure than on bacterial community structure, and biases for certain methanogen groups were detected. Co-occurrence analysis of microbial taxa from all three domains of life suggested strong within- and between-domain correlations between different groups of microorganisms within the rumen. The approach used to simultaneously characterize bacterial, archaeal and eukaryotic components of a microbiota should be applicable to other communities occupying diverse habitats.

  15. 48 CFR 853.215-70 - VA Form 10-1170, Application for Furnishing Nursing Home Care to Beneficiaries of VA.

    Science.gov (United States)

    2010-10-01

    ..., Application for Furnishing Nursing Home Care to Beneficiaries of VA. 853.215-70 Section 853.215-70 Federal... 853.215-70 VA Form 10-1170, Application for Furnishing Nursing Home Care to Beneficiaries of VA. VA Form 10-1170, Application for Furnishing Nursing Home Care to Beneficiaries of VA, will be used...

  16. Nitrogenase gene amplicons from global marine surface waters are dominated by genes of non-cyanobacteria

    DEFF Research Database (Denmark)

    Farnelid, Hanna; Andersson, Anders F.; Bertilsson, Stefan

    2011-01-01

    analysis of 79,090 nitrogenase (nifH) PCR amplicons encoding 7,468 unique proteins from surface samples (ten DNA samples and two RNA samples) collected at ten marine locations world-wide provides the first in-depth survey of a functional bacterial gene and yield insights into the composition and diversity...... of the nifH gene pool in marine waters. Great divergence in nifH composition was observed between sites. Cyanobacteria-like genes were most frequent among amplicons from the warmest waters, but overall the data set was dominated by nifH sequences most closely related to non-cyanobacteria. Clusters related...... to Alpha-, Beta-, Gamma-, and Delta-Proteobacteria were most common and showed distinct geographic distributions. Sequences related to anaerobic bacteria (nifH Cluster III) were generally rare, but preponderant in cold waters, especially in the Arctic. Although the two transcript samples were dominated...

  17. One-way sequencing of multiple amplicons from tandem repetitive mitochondrial DNA control region.

    Science.gov (United States)

    Xu, Jiawu; Fonseca, Dina M

    2011-10-01

    Repetitive DNA sequences not only exist abundantly in eukaryotic nuclear genomes, but also occur as tandem repeats in many animal mitochondrial DNA (mtDNA) control regions. Due to concerted evolution, these repetitive sequences are highly similar or even identical within a genome. When long repetitive regions are the targets of amplification for the purpose of sequencing, multiple amplicons may result if one primer has to be located inside the repeats. Here, we show that, without separating these amplicons by gel purification or cloning, directly sequencing the mitochondrial repeats with the primer outside repetitive region is feasible and efficient. We exemplify it by sequencing the mtDNA control region of the mosquito Aedes albopictus, which harbors typical large tandem DNA repeats. This one-way sequencing strategy is optimal for population surveys.

  18. Characterization of FGFR1 Locus in sqNSCLC Reveals a Broad and Heterogeneous Amplicon.

    Directory of Open Access Journals (Sweden)

    Claire Rooney

    Full Text Available FGFR1 amplification occurs in ~20% of sqNSCLC and trials with FGFR inhibitors have selected FGFR1 amplified patients by FISH. Lung cancer cell lines were profiled for sensitivity to AZD4547, a potent, selective inhibitor of FGFRs 1-3. Sensitivity to FGFR inhibition was associated with but not wholly predicted by increased FGFR1 gene copy number. Additional biomarker assays evaluating expression of FGFRs and correlation between amplification and expression in clinical tissues are therefore warranted. We validated nanoString for mRNA expression analysis of 194 genes, including FGFRs, from clinical tumour tissue. In a panel of sqNSCLC tumours 14.4% (13/90 were FGFR1 amplified by FISH. Although mean FGFR1 expression was significantly higher in amplified samples, there was significant overlap in the range of expression levels between the amplified and non-amplified cohorts with several non-amplified samples expressing FGFR1 to levels equivalent to amplified samples. Statistical analysis revealed increased expression of FGFR1 neighboring genes on the 8p12 amplicon (BAG4, LSM1 and WHSC1L1 in FGFR1 amplified tumours, suggesting a broad rather than focal amplicon and raises the potential for codependencies. High resolution aCGH analysis of pre-clinical and clinical samples supported the presence of a broad and heterogeneous amplicon around the FGFR1 locus. In conclusion, the range of FGFR1 expression levels in both FGFR1 amplified and non-amplified NSCLC tissues, together with the breadth and intra-patient heterogeneity of the 8p amplicon highlights the need for gene expression analysis of clinical samples to inform the understanding of determinants of response to FGFR inhibitors. In this respect the nanoString platform provides an attractive option for RNA analysis of FFPE clinical samples.

  19. Targeted Amplicon Sequencing (TAS): A Scalable Next-Gen Approach to Multilocus, Multitaxa Phylogenetics

    OpenAIRE

    2011-01-01

    Next-gen sequencing technologies have revolutionized data collection in genetic studies and advanced genome biology to novel frontiers. However, to date, next-gen technologies have been used principally for whole genome sequencing and transcriptome sequencing. Yet many questions in population genetics and systematics rely on sequencing specific genes of known function or diversity levels. Here, we describe a targeted amplicon sequencing (TAS) approach capitalizing on next-gen capacity to sequ...

  20. Potential of pmoA amplicon pyrosequencing for methanotroph diversity studies.

    Science.gov (United States)

    Lüke, Claudia; Frenzel, Peter

    2011-09-01

    We analyzed the potential of pmoA amplicon pyrosequencing compared to that of Sanger sequencing with paddy soils as a model environment. We defined operational taxonomic unit (OTU) cutoff values of 7% and 18%, reflecting methanotrophic species and major phylogenetic pmoA lineages, respectively. Major lineages were already well covered by clone libraries; nevertheless, pyrosequencing provided a higher level of diversity at the species level.

  1. Visionary leadership and the future of VA health system.

    Science.gov (United States)

    Bezold, C; Mayer, E; Dighe, A

    1997-01-01

    As the U.S. Department of Veterans Affairs (VA) makes the change over to Veterans Integrated Service Network (VISNs) the need for new and better leadership is warranted if VA wants to not only survive, but thrive in the emerging twenty-first century healthcare system. VA can prepare for the future and meet the challenges facing them by adopting a system of visionary leadership. The use of scenarios and vision techniques are explained as they relate to VA's efforts to move toward their new system of VISNs. The four scenarios provide snapshots of possible futures for the U.S. healthcare system as well as the possible future role and mission of VA--from VA disappearing to its becoming a premier virtual organization.

  2. Mining environmental high-throughput sequence data sets to identify divergent amplicon clusters for phylogenetic reconstruction and morphotype visualization.

    Science.gov (United States)

    Gimmler, Anna; Stoeck, Thorsten

    2015-08-01

    Environmental high-throughput sequencing (envHTS) is a very powerful tool, which in protistan ecology is predominantly used for the exploration of diversity and its geographic and local patterns. We here used a pyrosequenced V4-SSU rDNA data set from a solar saltern pond as test case to exploit such massive protistan amplicon data sets beyond this descriptive purpose. Therefore, we combined a Swarm-based blastn network including 11 579 ciliate V4 amplicons to identify divergent amplicon clusters with targeted polymerase chain reaction (PCR) primer design for full-length small subunit of the ribosomal DNA retrieval and probe design for fluorescence in situ hybridization (FISH). This powerful strategy allows to benefit from envHTS data sets to (i) reveal the phylogenetic position of the taxon behind divergent amplicons; (ii) improve phylogenetic resolution and evolutionary history of specific taxon groups; (iii) solidly assess an amplicons (species') degree of similarity to its closest described relative; (iv) visualize the morphotype behind a divergent amplicons cluster; (v) rapidly FISH screen many environmental samples for geographic/habitat distribution and abundances of the respective organism and (vi) to monitor the success of enrichment strategies in live samples for cultivation and isolation of the respective organisms.

  3. Viability-qPCR for detecting Legionella: Comparison of two assays based on different amplicon lengths.

    Science.gov (United States)

    Ditommaso, Savina; Giacomuzzi, Monica; Ricciardi, Elisa; Zotti, Carla M

    2015-08-01

    Two different real-time quantitative PCR (PMA-qPCR) assays were applied for quantification of Legionella spp. by targeting a long amplicon (approx 400 bp) of 16S rRNA gene and a short amplicon (approx. 100 bp) of 5S rRNA gene. Purified DNA extracts from pure cultures of Legionella spp. and from environmental water samples were quantified. Application of the two assays to quantify Legionella in artificially contaminated water achieved that both assays were able to detect Legionella over a linear range of 10 to 10(5) cells ml(-1). A statistical analysis of the standard curves showed that both assays were linear with a good correlation coefficient (R(2) = 0.99) between the Ct and the copy number. Amplification with the reference assay was the most effective for detecting low copy numbers (1 bacterium per PCR mixture). Using selective quantification of viable Legionella by the PMA-qPCR method we obtained a greater inhibition of the amplification of the 400-bp 16S gene fragment (Δlog(10) = 3.74 ± 0.39 log(10) GU ml(-1)). A complete inhibition of the PCR signal was obtained when heat-killed cells in a concentration below 1 × 10(5) cells ml(-1) were pretreated with PMA. Analysing short amplicon sizes led to only 2.08 log reductions in the Legionella dead-cell signal. When we tested environmental water samples, the two qPCR assays were in good agreement according to the kappa index (0.741). Applying qPCR combined with PMA treatment, we also obtained a good agreement (kappa index 0.615). The comparison of quantitative results shows that both assays yielded the same quantification sensitivity (mean log = 4.59 vs mean log = 4.31).

  4. The bias associated with amplicon sequencing does not affect the quantitative assessment of bacterial community dynamics.

    Directory of Open Access Journals (Sweden)

    Federico M Ibarbalz

    Full Text Available The performance of two sets of primers targeting variable regions of the 16S rRNA gene V1-V3 and V4 was compared in their ability to describe changes of bacterial diversity and temporal turnover in full-scale activated sludge. Duplicate sets of high-throughput amplicon sequencing data of the two 16S rRNA regions shared a collection of core taxa that were observed across a series of twelve monthly samples, although the relative abundance of each taxon was substantially different between regions. A case in point was the changes in the relative abundance of filamentous bacteria Thiothrix, which caused a large effect on diversity indices, but only in the V1-V3 data set. Yet the relative abundance of Thiothrix in the amplicon sequencing data from both regions correlated with the estimation of its abundance determined using fluorescence in situ hybridization. In nonmetric multidimensional analysis samples were distributed along the first ordination axis according to the sequenced region rather than according to sample identities. The dynamics of microbial communities indicated that V1-V3 and the V4 regions of the 16S rRNA gene yielded comparable patterns of: 1 the changes occurring within the communities along fixed time intervals, 2 the slow turnover of activated sludge communities and 3 the rate of species replacement calculated from the taxa-time relationships. The temperature was the only operational variable that showed significant correlation with the composition of bacterial communities over time for the sets of data obtained with both pairs of primers. In conclusion, we show that despite the bias introduced by amplicon sequencing, the variable regions V1-V3 and V4 can be confidently used for the quantitative assessment of bacterial community dynamics, and provide a proper qualitative account of general taxa in the community, especially when the data are obtained over a convenient time window rather than at a single time point.

  5. VA office of inspector general releases scathing report of Phoenix VA

    Directory of Open Access Journals (Sweden)

    Robbins RA

    2014-08-01

    Full Text Available No abstract available. Article truncated at 150 words. The long-awaited Office of Inspector General’s (OIG report on the Phoenix VA Health Care System (PVAHCS was released on August 27, 2014 (1. The report was scathing in its evaluation of VA practices and leadership. Five questions were investigated: 1.Were there clinically significant delays in care? 2. Did PVAHCS omit the names of veterans waiting for care from its Electronic Wait List (EWL? 3. Were PVAHCS personnel not following established scheduling procedures? 4. Did the PVAHCS culture emphasize goals at the expense of patient care? 5. Are scheduling deficiencies systemic throughout the VA? In each case, the OIG found that the allegations were true. Despite initial denials, the OIG report showed that former PVAHCS director Sharon Helman, associate director Lance Robinson, hospital administration director Brad Curry, chief of staff Darren Deering and other senior executives were aware of delays in care and unofficial wait lists. Perhaps most disturbing is ...

  6. VA INFORMATION TECHNOLOGY: Important Initiatives Begun, Yet Serious Vulnerabilities Persist

    Science.gov (United States)

    2007-11-02

    We appreciate the opportunity to join in today s hearing and share updated information on the Department of Veterans Affairs (VA) information ... technology (IT) program. As you know, IT is essential to VA s ability to effectively serve the veteran population and is the cornerstone of the department’s

  7. 76 FR 52230 - Establishment of Class E Airspace; Forest, VA

    Science.gov (United States)

    2011-08-22

    ... Federal Aviation Administration 14 CFR Part 71 Establishment of Class E Airspace; Forest, VA AGENCY... Airspace at Forest, VA, to accommodate the new Area Navigation (RNAV) Global Positioning System (GPS... published in the Federal Register a notice of proposed rulemaking to establish Class E airspace at...

  8. 77 FR 67063 - VA Directive 0005 on Scientific Integrity

    Science.gov (United States)

    2012-11-08

    ... http://www1.va.gov/vapubs/ . Directive 0005 establishes VA policies that: Foster a culture of... technological information from political or commercial influence; Prohibit suppression or alteration of scientific and technological findings for political purposes; Afford whistleblower protections to...

  9. Microcirculatory assessment of patients under VA-ECMO

    NARCIS (Netherlands)

    Kara, A. (Atila); S. Akin (Sakir); D. dos Reis Miranda (Dinis); A. Struijs (Ard); K. Caliskan (Kadir); R.J. van Thiel (Robert); E.A. Dubois; de Wilde, W. (Wouter); F. Zijlstra (Felix); D.A.M.P.J. Gommers (Diederik); C. Ince (Can)

    2016-01-01

    textabstractBackground: Veno-arterial extracorporeal membrane oxygenation (VA-ECMO) is an effective technique for providing emergency mechanical circulatory support for patients with cardiogenic shock. VA-ECMO enables a rapid restoration of global systemic organ perfusion, but it has not been found

  10. MyHealtheVet (VA's personal health record)

    Science.gov (United States)

    ... Links eBenefits Hearing Aid Batteries (eBenefits) Online Bill Payments VA Mental Health Services Authentication How to Use My Health e Vet VA Dental Insurance Most Requested Forms Women Veterans Health Mobile Apps Privacy & Security | Terms & Conditions | Accessibility | Site Map | ...

  11. Using expected sequence features to improve basecalling accuracy of amplicon pyrosequencing data

    DEFF Research Database (Denmark)

    Rask, Thomas Salhøj; Petersen, Bent; Chen, Donald S.

    2016-01-01

    insertions and deletions, are on the other hand likely to disrupt open reading frames. Such an inverse relationship between errors and expectation based on prior knowledge can be used advantageously to guide the process known as basecalling, i.e. the inference of nucleotide sequence from raw sequencing data...... family, where Multipass generates 20 % more error-free sequences than current state of the art methods, and provides sequence characteristics that allow generation of a set of high confidence error-free sequences. This novel method can be used to increase accuracy of existing and future amplicon...

  12. 38 CFR 1.203 - Information to be reported to VA Police.

    Science.gov (United States)

    2010-07-01

    ... reported to VA Police. 1.203 Section 1.203 Pensions, Bonuses, and Veterans' Relief DEPARTMENT OF VETERANS... be reported to VA Police. Information about actual or possible violations of criminal laws related to... occurs on VA premises, will be reported by VA management officials to the VA police component...

  13. VaR限制下的最优保险投资策略选择%Optimal Portfolio Selection Bounded by VaR for Insurer

    Institute of Scientific and Technical Information of China (English)

    郭文旌; 李心丹

    2009-01-01

    The integral risk of insurance company is measured with VaR. The problem of portfolio selection for insurer is studied under the mean-VaR criterion. To ensure the insurance company is safe in the period of investment, we introduce a safe investment proportion, which the insurer invests in assets. By solving the model, the explicit expressions of optimal investment strategies and efficient frontier are derived. The influence of premium, claim on optimal investment strategies and efficient frontier is discussed. Finally, by real datum the investment procedure is simulated.%以VaR作为保险公司整体风险的测度,建立均值-VaR模型,讨论保险公司最优投资策略的选择问题.为保证保险公司在投资期内的安全,引进一个安全投资比例,保险公司以安全投资比例的资金用于投资.求解模型,得到保险公司的最优投资策略和有效边界的解析形式,讨论了保费、索赔对最优投资策略以及有效边界的影响.最后,用实际数据对保险公司如何选择安全投资比例,如何分配投资资金进行了模拟.

  14. Analysis of the microbiome: Advantages of whole genome shotgun versus 16S amplicon sequencing.

    Science.gov (United States)

    Ranjan, Ravi; Rani, Asha; Metwally, Ahmed; McGee, Halvor S; Perkins, David L

    2016-01-22

    The human microbiome has emerged as a major player in regulating human health and disease. Translational studies of the microbiome have the potential to indicate clinical applications such as fecal transplants and probiotics. However, one major issue is accurate identification of microbes constituting the microbiota. Studies of the microbiome have frequently utilized sequencing of the conserved 16S ribosomal RNA (rRNA) gene. We present a comparative study of an alternative approach using whole genome shotgun sequencing (WGS). In the present study, we analyzed the human fecal microbiome compiling a total of 194.1 × 10(6) reads from a single sample using multiple sequencing methods and platforms. Specifically, after establishing the reproducibility of our methods with extensive multiplexing, we compared: 1) The 16S rRNA amplicon versus the WGS method, 2) the Illumina HiSeq versus MiSeq platforms, 3) the analysis of reads versus de novo assembled contigs, and 4) the effect of shorter versus longer reads. Our study demonstrates that whole genome shotgun sequencing has multiple advantages compared with the 16S amplicon method including enhanced detection of bacterial species, increased detection of diversity and increased prediction of genes. In addition, increased length, either due to longer reads or the assembly of contigs, improved the accuracy of species detection.

  15. Analysis of the microbiome: Advantages of whole genome shotgun versus 16S amplicon sequencing

    Science.gov (United States)

    Ranjan, Ravi; Rani, Asha; Metwally, Ahmed; McGee, Halvor S.; Perkins, David L.

    2016-01-01

    The human microbiome has emerged as a major player in regulating human health and disease. Translation studies of the microbiome have the potential to indicate clinical applications such as fecal transplants and probiotics. However, one major issue is accurate identification of microbes constituting the microbiota. Studies of the microbiome have frequently utilized sequencing of the conserved 16S ribosomal RNA (rRNA) gene. We present a comparative study of an alternative approach using shotgun whole genome sequencing (WGS). In the present study, we analyzed the human fecal microbiome compiling a total of 194.1×106 reads from a single sample using multiple sequencing methods and platforms. Specifically, after establishing the reproducibility of our methods with extensive multiplexing, we compared: 1) The 16S rRNA amplicon versus the WGS method, 2) the Illumina HiSeq versus MiSeq platforms, 3) the analysis of reads versus de novo assembled contigs, and 4) the effect of shorter versus longer reads. Our study demonstrates that shotgun whole genome sequencing has multiple advantages compared with the 16S amplicon method including enhanced detection of bacterial species, increased detection of diversity and increased prediction of genes. In addition, increased length, either due to longer reads or the assembly of contigs, improved the accuracy of species detection. PMID:26718401

  16. AMPLISAS: a web server for multilocus genotyping using next-generation amplicon sequencing data.

    Science.gov (United States)

    Sebastian, Alvaro; Herdegen, Magdalena; Migalska, Magdalena; Radwan, Jacek

    2016-03-01

    Next-generation sequencing (NGS) technologies are revolutionizing the fields of biology and medicine as powerful tools for amplicon sequencing (AS). Using combinations of primers and barcodes, it is possible to sequence targeted genomic regions with deep coverage for hundreds, even thousands, of individuals in a single experiment. This is extremely valuable for the genotyping of gene families in which locus-specific primers are often difficult to design, such as the major histocompatibility complex (MHC). The utility of AS is, however, limited by the high intrinsic sequencing error rates of NGS technologies and other sources of error such as polymerase amplification or chimera formation. Correcting these errors requires extensive bioinformatic post-processing of NGS data. Amplicon Sequence Assignment (AMPLISAS) is a tool that performs analysis of AS results in a simple and efficient way, while offering customization options for advanced users. AMPLISAS is designed as a three-step pipeline consisting of (i) read demultiplexing, (ii) unique sequence clustering and (iii) erroneous sequence filtering. Allele sequences and frequencies are retrieved in excel spreadsheet format, making them easy to interpret. AMPLISAS performance has been successfully benchmarked against previously published genotyped MHC data sets obtained with various NGS technologies.

  17. ICO amplicon NGS data analysis: a Web tool for variant detection in common high-risk hereditary cancer genes analyzed by amplicon GS Junior next-generation sequencing.

    Science.gov (United States)

    Lopez-Doriga, Adriana; Feliubadaló, Lídia; Menéndez, Mireia; Lopez-Doriga, Sergio; Morón-Duran, Francisco D; del Valle, Jesús; Tornero, Eva; Montes, Eva; Cuesta, Raquel; Campos, Olga; Gómez, Carolina; Pineda, Marta; González, Sara; Moreno, Victor; Capellá, Gabriel; Lázaro, Conxi

    2014-03-01

    Next-generation sequencing (NGS) has revolutionized genomic research and is set to have a major impact on genetic diagnostics thanks to the advent of benchtop sequencers and flexible kits for targeted libraries. Among the main hurdles in NGS are the difficulty of performing bioinformatic analysis of the huge volume of data generated and the high number of false positive calls that could be obtained, depending on the NGS technology and the analysis pipeline. Here, we present the development of a free and user-friendly Web data analysis tool that detects and filters sequence variants, provides coverage information, and allows the user to customize some basic parameters. The tool has been developed to provide accurate genetic analysis of targeted sequencing of common high-risk hereditary cancer genes using amplicon libraries run in a GS Junior System. The Web resource is linked to our own mutation database, to assist in the clinical classification of identified variants. We believe that this tool will greatly facilitate the use of the NGS approach in routine laboratories.

  18. COPD, COOP and BREATH at the VA

    Directory of Open Access Journals (Sweden)

    Robbins RA

    2011-02-01

    Full Text Available No abstract available. Article truncated at 150 words. The February 2011 Pulmonary Journal Club reviews a study by Rice and colleagues (1 of high-risk COPD patients (click here for Pulmonary Journal Club. This review was authored by Kevin Park who also authored an ACP Journal Club review (2. In Rice’s study a single educational session, an individualized care plan, and monthly case-manager telephone calls, resulted in a 41% decrease in hospitalizations and emergency room visits and a nonsignficant trend toward decreased mortality.Rice’s study was supported and conducted in the Veterans Integrated Service Network (VISN 23 (Minnesota, Iowa, Nebraska and the Dakotas. The COPD patients in this study were recruited and followed primarily using the VA computer system. The study represents a potential model of data-based management leading to improved patient outcomes. The authors; Robert Petzel MD, then VISN 23 Director (now Veterans Healthcare Administration Undersecretary; and Janet Murphy, then VISN Primary Care Service Line CEO (now VISN …

  19. Optimizing multi-period portfolio decision model with mean-VaR risk control%基于均值-VaR的多周期最优投资组合决策模型

    Institute of Scientific and Technical Information of China (English)

    李蕊

    2011-01-01

    文中考虑了基于均值-VaR风险的最优投资组合决策问题,在存在无风险资产和交易费用的情形下,建立了基于均值-VaR风险控制的多周期最优投资组合决策模型。应用遗传算法对模型进行了求解,对求解结果进行了比较分析,并结合单周期的情形进行了比较分析,结果表明基于均值-VaR风险控制的多周期最优投资组合决策模型相对于单周期最优投资组合决策模型有明显的改进效果。%Optimal portfolio decision-making with mean-VaR risk was considered in this paper.Multi-period and portfolio decision model were established with the risk-free assets and transaction costs.The solutions of the model were derived by numerical simulation of genetic algorithm,and a comparative analysis with the single-period portfolio decision model was conducted.The results show that the multi-period portfolio decision model improves the single-period portfolio decision model with mean-VaR risk control.

  20. Parallel tagged amplicon sequencing of relatively long PCR products using the Illumina HiSeq platform and transcriptome assembly.

    Science.gov (United States)

    Feng, Yan-Jie; Liu, Qing-Feng; Chen, Meng-Yun; Liang, Dan; Zhang, Peng

    2016-01-01

    In phylogenetics and population genetics, a large number of loci are often needed to accurately resolve species relationships. Normally, loci are enriched by PCR and sequenced by Sanger sequencing, which is expensive when the number of amplicons is large. Next-generation sequencing (NGS) techniques are increasingly used for parallel amplicon sequencing, which reduces sequencing costs tremendously, but has not reduced preparation costs very much. Moreover, for most current NGS methods, amplicons need to be purified and quantified before sequencing and their lengths are also restricted (normally HiSeq paired-end 90-bp data. Overall, we validate a rapid, cost-effective and scalable approach to sequence a large number of targeted loci from a large number of samples that is particularly suitable for both phylogenetics and population genetics studies that require a modest scale of data.

  1. Ultra-Deep Pyrosequencing (UDPS) Data Treatment to Study Amplicon HCV Minor Variants

    Science.gov (United States)

    Gregori, Josep; Esteban, Juan I.; Cubero, María; Garcia-Cehic, Damir; Perales, Celia; Casillas, Rosario; Alvarez-Tejado, Miguel; Rodríguez-Frías, Francisco; Guardia, Jaume; Domingo, Esteban; Quer, Josep

    2013-01-01

    We have investigated the reliability and reproducibility of HCV viral quasispecies quantification by ultra-deep pyrosequencing (UDPS) methods. Our study has been divided in two parts. First of all, by UDPS sequencing of clone mixes samples we have established the global noise level of UDPS and fine tuned a data treatment workflow previously optimized for HBV sequence analysis. Secondly, we have studied the reproducibility of the methodology by comparing 5 amplicons from two patient samples on three massive sequencing platforms (FLX+, FLX and Junior) after applying the error filters developed from the clonal/control study. After noise filtering the UDPS results, the three replicates showed the same 12 polymorphic sites above 0.7%, with a mean CV of 4.86%. Two polymorphic sites below 0.6% were identified by two replicates and one replicate respectively. A total of 25, 23 and 26 haplotypes were detected by GS-Junior, GS-FLX and GS-FLX+. The observed CVs for the normalized Shannon entropy (Sn), the mutation frequency (Mf), and the nucleotidic diversity (Pi) were 1.46%, 3.96% and 3.78%. The mean absolute difference in the two patients (5 amplicons each), in the GS-FLX and GS-FLX+, were 1.46%, 3.96% and 3.78% for Sn, Mf and Pi. No false polymorphic site was observed above 0.5%. Our results indicate that UDPS is an optimal alternative to molecular cloning for quantitative study of HCV viral quasispecies populations, both in complexity and composition. We propose an UDPS data treatment workflow for amplicons from the RNA viral quasispecies which, at a sequencing depth of at least 10,000 reads per strand, enables to obtain sequences and frequencies of consensus haplotypes above 0.5% abundance with no erroneous mutations, with high confidence, resistant mutants as minor variants at the level of 1%, with high confidence that variants are not missed, and highly confident measures of quasispecies complexity. PMID:24391758

  2. Quantitative characterization of cell transduction by HSV-1 amplicons using flow cytometry and real-time PCR.

    Science.gov (United States)

    El-Sherbini, Yasser M; Stevenson, Mark M; Seymour, Leonard W; Wade-Martins, Richard

    2009-08-01

    Herpes simplex virus type 1 (HSV-1) amplicon preparations are usually quantified as transducing units/ml (TU/ml), with little information on genomic copy/TU ratios. In the present study, two HSV-1 amplicons expressing enhanced green fluorescent protein (EGFP) were analysed by quantitative PCR (qPCR) and transducing activity to obtain genomic copy/TU ratios. One vector (pHSV-GL) contains the HSV-1 packaging signal (pac) and origin of replication (oriS) and the other (pHSV/EBV-GL) includes Epstein-Barr virus (EBV) episomal maintenance elements. The pHSV-GL and pHSV/EBV-GL amplicons were prepared at titres of 7.55x10(7) and 7.24x10(7)TU/ml, containing 2.56x10(9) and 1.33x10(9) genomic copies/ml respectively. This produced preliminary estimates of genomic copy/TU ratios of 34:1 and 18:1. However standard transduction conditions did not deplete fully the supernatant of transducing particles since the same supernatant was subsequently able to achieve 25% the initial transduction efficiency, although centrifugation of amplicon particles onto cells improved infectivity by 1.8-fold. Finally, qPCR analysis of FACS-purified EGFP-expressing cells showed the presence of approximately 3 amplicon genomes/transduced cell, independent of the infection dose. Accordingly, the initial estimated genomic copy/TU ratio for pHSV-GL was revised to 6.3:1. Measuring the genomic copy/TU ratios is an important parameter for comparing the quality of amplicon preparations and standardizing experimental conditions.

  3. Vibrational analysis of various irotopes of L-alanyl-L-alanine in aqueous solution: Vibrational Absorption (VA), Vibrational Circular Dichroism (VCD), Raman and Raman Optical Activity (ROA) Spectra

    DEFF Research Database (Denmark)

    Jalkanen, Karl J.; Nieminen, R.M.; Knapp-Mohammady, M.;

    2003-01-01

    . DFT Becke3LYP/6-31G* theory has been used to determine the geometry, Hessian, atomic polar tensors (APT), and atomic axial tensors (AAT), and the electric dipole-electric dipole polarizability derivatives (EDEDPD), which are required for us to simulate the VA, VCD, and Raman spectra. The electric...... dipole-magnetic dipole polarizability derivatives (EDMDPD) and the electric dipole-electric cluadrapole polarizability derivatives (EDEQPD) have been calculated at the RHF/6-31G* level of theory, The VA, VCD, Raman, and ROA spectral simulations for the various isotoporners are compared...

  4. VA Facilities by Congressional District (FY2011): Overview

    Data.gov (United States)

    Department of Veterans Affairs — Maps are organized by state and depict the Veteran population using VetPop2011 data as of 9/30/2013 and VA facilities using Veteran Affairs Site Tracking (VAST) data...

  5. Service Utilization of Veterans Dually Eligible for VA...

    Data.gov (United States)

    U.S. Department of Health & Human Services — Service Utilization of Veterans Dually Eligible for VA and Medicare Fee-For-Service, 1999-2004 According to findings in Service Utilization of Veterans Dually...

  6. Key Science Observations of AGNs with KaVA Array

    CERN Document Server

    Kino, Motoki; Zhao, Guang-Yao; Sohn, Bong Won

    2015-01-01

    KaVA (KVN and VERA Array) is a new combined VLBI array with KVN (Korean VLBI Network) and VERA (VLBI Exploration of Radio Astrometry). First, we briefly review the imaging capabilities of KaVA array which actually achieves more than three times better dynamic range than that achieved by VERA alone. The KaVA images clearly show detailed structures of extended radio jets in AGNs. Next, we represent the key science program to be led by KaVA AGN sub working group. We will conduct the monitoring observations of Sgr A* and M87 because of the largeness of their central super-massive black hole angular sizes. The main science goals of the program are (i) testing magnetically-driven-jet paradigm by mapping velocity fields of the M87 jet, and (ii) obtaining tight constraints on physical properties of radio emitting region in Sgr A*.

  7. VA Homeless Grant and Per Diem FY09

    Data.gov (United States)

    Department of Veterans Affairs — VA's Homeless Providers Grant and Per Diem Program is offered annually (as funding permits) by the Department of Veterans Affairs Health Care for Homeless Veterans...

  8. 78 FR 71041 - VA Compensation and Pension Regulation Rewrite Project

    Science.gov (United States)

    2013-11-27

    ... ``Report to the Secretary of Veterans Affairs'' and to criticisms by the U.S. Court of Appeals for Veterans... and in the absence of historical information that VA ever implemented the regulations differently....

  9. VA Enterprise Design Patters - 2.5 (Enterprise Architecture)

    Data.gov (United States)

    Department of Veterans Affairs — Enterprise architectural guidelines and constraints that provide references to the use of enterprise capabilities that will enable the VA to access and exchange data...

  10. VA Enterprise Design Patterns - 5.1 (Mobility) Mobile

    Data.gov (United States)

    Department of Veterans Affairs — First of a set of guidance documents that establish the architectural foundation for mobile computing in the VA. This document outlines the enterprise capabilities...

  11. High‑throughput sequencing of amplicons for monitoring yeast biodiversity in must and during alcoholic fermentation.

    Science.gov (United States)

    David, Vanessa; Terrat, Sébastien; Herzine, Khaled; Claisse, Olivier; Rousseaux, Sandrine; Tourdot-Maréchal, Raphaëlle; Masneuf-Pomarede, Isabelle; Ranjard, Lionel; Alexandre, Hervé

    2014-05-01

    We compared pyrosequencing technology with the PCR-ITS-RFLP analysis of yeast isolates and denaturing gradient gel electrophoresis (DGGE). These methods gave divergent findings for the yeast population. DGGE was unsuitable for the quantification of biodiversity and its use for species detection was limited by the initial abundance of each species. The isolates identified by PCR-ITSRFLP were not fully representative of the true population. For population dynamics, high-throughput sequencing technology yielded results differing in some respects from those obtained with other approaches. This study demonstrates that 454 pyrosequencing of amplicons is more relevant than other methods for studying the yeast community on grapes and during alcoholic fermentation. Indeed, this high-throughput sequencing method detected larger numbers of species on grapes and identified species present during alcoholic fermentation that were undetectable with the other techniques.

  12. Amplicon restriction patterns associated with nitrogenase activity of root nodules for selection of superior Myrica seedlings

    Indian Academy of Sciences (India)

    Mhathung Yanthan; Arvind K Misran

    2013-11-01

    Trees of Myrica sp. grow abundantly in the forests of Meghalaya, India. These trees are actinorhizal and harbour nitrogen-fixing Frankia in their root nodules and contribute positively towards the enhancement of nitrogen status of forest areas. They can be used in rejuvenation of mine spoils and nitrogen-depleted fallow lands generated due to slash and burn agriculture practiced in the area. We have studied the association of amplicon restriction patterns (ARPs) of Myrica ribosomal RNA gene and internal transcribed spacer (ITS) region and nitrogenase activity of its root nodules. We found that ARPs thus obtained could be used as markers for early screening of seedlings that could support strains of Frankia that fix atmospheric nitrogen more efficiently.

  13. Swarm v2: highly-scalable and high-resolution amplicon clustering.

    Science.gov (United States)

    Mahé, Frédéric; Rognes, Torbjørn; Quince, Christopher; de Vargas, Colomban; Dunthorn, Micah

    2015-01-01

    Previously we presented Swarm v1, a novel and open source amplicon clustering program that produced fine-scale molecular operational taxonomic units (OTUs), free of arbitrary global clustering thresholds and input-order dependency. Swarm v1 worked with an initial phase that used iterative single-linkage with a local clustering threshold (d), followed by a phase that used the internal abundance structures of clusters to break chained OTUs. Here we present Swarm v2, which has two important novel features: (1) a new algorithm for d = 1 that allows the computation time of the program to scale linearly with increasing amounts of data; and (2) the new fastidious option that reduces under-grouping by grafting low abundant OTUs (e.g., singletons and doubletons) onto larger ones. Swarm v2 also directly integrates the clustering and breaking phases, dereplicates sequencing reads with d = 0, outputs OTU representatives in fasta format, and plots individual OTUs as two-dimensional networks.

  14. Similar diversity of Alphaproteobacteria and nitrogenase gene amplicons on two related Sphagnum mosses

    Directory of Open Access Journals (Sweden)

    Anastasia eBragina

    2012-01-01

    Full Text Available Sphagnum mosses represent a main component in ombrotrophic wetlands. They harbor a specific and diverse microbial community with essential functions for the host. To understand extend and degree of host specificity, Sphagnum fallax and S. angustifolium, two phylogenetically closely related species, which show distinct habitat preference with respect to the nutrient level, were analyzed by a multifaceted approach. Microbial fingerprints obtained by PCR-SSCP (single-strand conformation polymorphism using universal, group-specific and functional primers were highly similar. Similarity was confirmed for colonization patterns obtained by fluorescence in situ hybridization (FISH coupled with confocal laser scanning microscopy (CLSM: Alphaproteobacteria were the main colonizers inside the hyaline cells of Sphagnum leaves. A deeper survey of Alphaproteobacteria by 16S rRNA gene amplicon sequencing reveals a high diversity with Acidocella, Acidisphaera, Rhodopila and Phenylobacterium as major genera for both mosses. Pathogen defense and nitrogen fixation are important functions of Sphagnum-associated bacteria, which are fulfilled by microbial communities of both Sphagna in a similar way. NifH libraries of Sphagnum-associated microbial communities were characterized by high diversity and abundance of Alphaproteobacteria but contained also diverse amplicons of other taxa, e.g. Cyanobacteria, Geobacter and Spirochaeta. Statistically significant differences between the microbial communities of both Sphagnum species could not be discovered in any of the experimental approach. Our results show that the same close relationship, which exists between the physical, morphological and chemical characteristics of Sphagnum mosses and the ecology and function of bog ecosystems, also connects moss plantlets with their associated bacterial communities.

  15. Nitrogenase gene amplicons from global marine surface waters are dominated by genes of non-cyanobacteria.

    Directory of Open Access Journals (Sweden)

    Hanna Farnelid

    Full Text Available Cyanobacteria are thought to be the main N(2-fixing organisms (diazotrophs in marine pelagic waters, but recent molecular analyses indicate that non-cyanobacterial diazotrophs are also present and active. Existing data are, however, restricted geographically and by limited sequencing depths. Our analysis of 79,090 nitrogenase (nifH PCR amplicons encoding 7,468 unique proteins from surface samples (ten DNA samples and two RNA samples collected at ten marine locations world-wide provides the first in-depth survey of a functional bacterial gene and yield insights into the composition and diversity of the nifH gene pool in marine waters. Great divergence in nifH composition was observed between sites. Cyanobacteria-like genes were most frequent among amplicons from the warmest waters, but overall the data set was dominated by nifH sequences most closely related to non-cyanobacteria. Clusters related to Alpha-, Beta-, Gamma-, and Delta-Proteobacteria were most common and showed distinct geographic distributions. Sequences related to anaerobic bacteria (nifH Cluster III were generally rare, but preponderant in cold waters, especially in the Arctic. Although the two transcript samples were dominated by unicellular cyanobacteria, 42% of the identified non-cyanobacterial nifH clusters from the corresponding DNA samples were also detected in cDNA. The study indicates that non-cyanobacteria account for a substantial part of the nifH gene pool in marine surface waters and that these genes are at least occasionally expressed. The contribution of non-cyanobacterial diazotrophs to the global N(2 fixation budget cannot be inferred from sequence data alone, but the prevalence of non-cyanobacterial nifH genes and transcripts suggest that these bacteria are ecologically significant.

  16. Developing de novo human artificial chromosomes in embryonic stem cells using HSV-1 amplicon technology.

    Science.gov (United States)

    Moralli, Daniela; Monaco, Zoia L

    2015-02-01

    De novo artificial chromosomes expressing genes have been generated in human embryonic stem cells (hESc) and are maintained following differentiation into other cell types. Human artificial chromosomes (HAC) are small, functional, extrachromosomal elements, which behave as normal chromosomes in human cells. De novo HAC are generated following delivery of alpha satellite DNA into target cells. HAC are characterized by high levels of mitotic stability and are used as models to study centromere formation and chromosome organisation. They are successful and effective as gene expression vectors since they remain autonomous and can accommodate larger genes and regulatory regions for long-term expression studies in cells unlike other viral gene delivery vectors currently used. Transferring the essential DNA sequences for HAC formation intact across the cell membrane has been challenging for a number of years. A highly efficient delivery system based on HSV-1 amplicons has been used to target DNA directly to the ES cell nucleus and HAC stably generated in human embryonic stem cells (hESc) at high frequency. HAC were detected using an improved protocol for hESc chromosome harvesting, which consistently produced high-quality metaphase spreads that could routinely detect HAC in hESc. In tumour cells, the input DNA often integrated in the host chromosomes, but in the host ES genome, it remained intact. The hESc containing the HAC formed embryoid bodies, generated teratoma in mice, and differentiated into neuronal cells where the HAC were maintained. The HAC structure and chromatin composition was similar to the endogenous hESc chromosomes. This review will discuss the technological advances in HAC vector delivery using HSV-1 amplicons and the improvements in the identification of de novo HAC in hESc.

  17. Whistle-blower accuses VA inspector general of a "whitewash"

    Directory of Open Access Journals (Sweden)

    Robbins RA

    2014-09-01

    Full Text Available No abstract available. Article truncated after 150 words. Yesterday, Dr. Sam Foote, the initial whistle-blower at the Phoenix VA, criticized the Department of Veterans Affairs inspector general's (VAOIG report on delays in healthcare at the Phoenix VA at a hearing before the House Committee of Veterans Affairs (1,2. Foote accused the VAOIG of minimizing bad patient outcomes and deliberately confusing readers, downplaying the impact of delayed health care at Phoenix VA facilities. "At its best, this report is a whitewash. At its worst, it is a feeble attempt at a cover-up," said Foote. Foote earlier this year revealed that as many as 40 Phoenix patients died while awaiting care and that the Phoenix VA maintained secret waiting lists while under-reporting patient wait times for appointments. His disclosures triggered the national VA scandal. Richard Griffin, the acting VAOIG, said that nearly 300 patients died while on backlogged wait lists in the Phoenix VA Health Care System, a much higher ...

  18. Long amplicon (LA)-qPCR for the discrimination of infectious and noninfectious phix174 bacteriophages after UV inactivation.

    Science.gov (United States)

    Ho, Johannes; Seidel, Michael; Niessner, Reinhard; Eggers, Jutta; Tiehm, Andreas

    2016-10-15

    Waterborne viruses are increasingly being considered in risk assessment schemes. In general, virus detection by culture methods is time consuming. In contrast, detection by quantitative polymerase chain reaction (qPCR) is more rapid and therefore, more suitable for monitoring. At present, qPCR lacks the essential ability for discriminating between infectious and non-infectious viruses, thus limiting its applicability for monitoring disinfection processes. In this study, a method was developed to quantify UV inactivation by long amplicon (LA)-qPCR. Bacteriophage phiX174 was used as a surrogate for human pathogenic viruses. A qPCR protocol was developed with new sets of primers, resulting in amplicon lengths of 108, 250, 456, 568, 955, 1063, 1544, and 1764 nucleotides. The log reduction of gene copies increased with increasing amplicon length. Additional treatment with the intercalating dye, PMA, had no effect, indicating that the bacteriophage capsids were not damaged by low pressure UV irradiation. A qPCR of nearly the complete genome (approx. 5000 nucleotides) showed similar results to the plaque assay. The log reduction in qPCR correlates with [specific amplicon length x UV dose]. The normalized DNA effect constant can be applied to calculate phiX174 inactivation based on qPCR detection.

  19. Next-generation sequencing of multiple individuals per barcoded library by deconvolution of sequenced amplicons using endonuclease fragment analysis

    DEFF Research Database (Denmark)

    Andersen, Jeppe D; Pereira, Vania; Pietroni, Carlotta

    2014-01-01

    digestion of PCR amplicons prior to library preparation, creating a specific fragment pattern for each individual that can be resolved after sequencing. By using both barcodes and restriction fragment patterns, we demonstrate the ability to sequence the human melanocortin 1 receptor (MC1R) genes from 72...... individuals using only 24 barcoded libraries....

  20. 75 FR 3970 - Fund Availability Under the VA Homeless Providers Grant and Per Diem Program

    Science.gov (United States)

    2010-01-25

    ... FURTHER INFORMATION CONTACT: Ms. Chelsea Watson, VA Homeless Providers Grant and Per Diem Program... per diem-funded program will participate in VA's national program monitoring and evaluation system administered by VA's Northeast Program Evaluation Center (NEPEC). It is the intention of VA to develop...

  1. U.S. Dept. Veterans Affairs (VA) SMEC-bio Reporting for Leadership Decision Support

    OpenAIRE

    2013-01-01

    Objective To assess Reports sent from the United States VA Subject Matter Expertise Center for Biological Events (SMEC-bio) – a proof-of-concept decision support initiative – to the VA Integrated Operations Center (VA IOC). Introduction VA is the U.S. federal agency responsible for providing services to America’s Veterans. Within VA, VHA is the organization responsible for administration of health care services. VHA, with 152 Medical Centers and over 900 outpatient clinics located throughout ...

  2. Extracellular DNA amplicon sequencing reveals high levels of benthic eukaryotic diversity in the central Red Sea

    KAUST Repository

    Pearman, John K.

    2015-11-01

    The present study aims to characterize the benthic eukaryotic biodiversity patterns at a coarse taxonomic level in three areas of the central Red Sea (a lagoon, an offshore area in Thuwal and a shallow coastal area near Jeddah) based on extracellular DNA. High-throughput amplicon sequencing targeting the V9 region of the 18S rRNA gene was undertaken for 32 sediment samples. High levels of alpha-diversity were detected with 16,089 operational taxonomic units (OTUs) being identified. The majority of the OTUs were assigned to Metazoa (29.2%), Alveolata (22.4%) and Stramenopiles (17.8%). Stramenopiles (Diatomea) and Alveolata (Ciliophora) were frequent in a lagoon and in shallower coastal stations, whereas metazoans (Arthropoda: Maxillopoda) were dominant in deeper offshore stations. Only 24.6% of total OTUs were shared among all areas. Beta-diversity was generally lower between the lagoon and Jeddah (nearshore) than between either of those and the offshore area, suggesting a nearshore–offshore biodiversity gradient. The current approach allowed for a broad-range of benthic eukaryotic biodiversity to be analysed with significantly less labour than would be required by other traditional taxonomic approaches. Our findings suggest that next generation sequencing techniques have the potential to provide a fast and standardised screening of benthic biodiversity at large spatial and temporal scales.

  3. Extracellular DNA amplicon sequencing reveals high levels of benthic eukaryotic diversity in the central Red Sea.

    Science.gov (United States)

    Pearman, John K; Irigoien, Xabier; Carvalho, Susana

    2016-04-01

    The present study aims to characterize the benthic eukaryotic biodiversity patterns at a coarse taxonomic level in three areas of the central Red Sea (a lagoon, an offshore area in Thuwal and a shallow coastal area near Jeddah) based on extracellular DNA. High-throughput amplicon sequencing targeting the V9 region of the 18S rRNA gene was undertaken for 32 sediment samples. High levels of alpha-diversity were detected with 16,089 operational taxonomic units (OTUs) being identified. The majority of the OTUs were assigned to Metazoa (29.2%), Alveolata (22.4%) and Stramenopiles (17.8%). Stramenopiles (Diatomea) and Alveolata (Ciliophora) were frequent in a lagoon and in shallower coastal stations, whereas metazoans (Arthropoda: Maxillopoda) were dominant in deeper offshore stations. Only 24.6% of total OTUs were shared among all areas. Beta-diversity was generally lower between the lagoon and Jeddah (nearshore) than between either of those and the offshore area, suggesting a nearshore-offshore biodiversity gradient. The current approach allowed for a broad-range of benthic eukaryotic biodiversity to be analysed with significantly less labour than would be required by other traditional taxonomic approaches. Our findings suggest that next generation sequencing techniques have the potential to provide a fast and standardised screening of benthic biodiversity at large spatial and temporal scales.

  4. The development of reduced size STR amplicons as tools for analysis of degraded DNA.

    Science.gov (United States)

    Butler, John M; Shen, Yin; McCord, Bruce R

    2003-09-01

    New multiplex PCR sets of commonly used short tandem repeat (STR) markers have been developed to produce PCR products that are reduced in size when compared to standard commercial STR kits. The reduction in size of these amplicons can facilitate the examination and analysis of degraded DNA evidence by improving amplification efficiency. This "miniSTR" approach will permit current forensic practitioners to use STR markers and instrumentation already present in their laboratories and to generate genotyping data that is directly comparable to reference samples and searchable through the FBI's Combined DNA Index System (CODIS) databases. This paper discusses the development of these new primer sets and presents some initial results in the analysis of degraded and aged DNA samples. A method for removal of problematic fluorescent dye artifacts is also described. Comparison studies in over 100 samples have verified that these miniSTR primers can provide fully concordant results to commercial STR kits and can provide improved signal from degraded DNA specimens. These miniplex sets should prove valuable in the analysis of samples where allele dropout and reduced sensitivity of larger STR alleles occurs.

  5. Accuracy of the high-throughput amplicon sequencing to identify species within the genus Aspergillus.

    Science.gov (United States)

    Lee, Seungeun; Yamamoto, Naomichi

    2015-12-01

    This study characterized the accuracy of high-throughput amplicon sequencing to identify species within the genus Aspergillus. To this end, we sequenced the internal transcribed spacer 1 (ITS1), β-tubulin (BenA), and calmodulin (CaM) gene encoding sequences as DNA markers from eight reference Aspergillus strains with known identities using 300-bp sequencing on the Illumina MiSeq platform, and compared them with the BLASTn outputs. The identifications with the sequences longer than 250 bp were accurate at the section rank, with some ambiguities observed at the species rank due to mostly cross detection of sibling species. Additionally, in silico analysis was performed to predict the identification accuracy for all species in the genus Aspergillus, where 107, 210, and 187 species were predicted to be identifiable down to the species rank based on ITS1, BenA, and CaM, respectively. Finally, air filter samples were analysed to quantify the relative abundances of Aspergillus species in outdoor air. The results were reproducible across biological duplicates both at the species and section ranks, but not strongly correlated between ITS1 and BenA, suggesting the Aspergillus detection can be taxonomically biased depending on the selection of the DNA markers and/or primers.

  6. Targeted amplicon sequencing (TAS): a scalable next-gen approach to multilocus, multitaxa phylogenetics.

    Science.gov (United States)

    Bybee, Seth M; Bracken-Grissom, Heather; Haynes, Benjamin D; Hermansen, Russell A; Byers, Robert L; Clement, Mark J; Udall, Joshua A; Wilcox, Edward R; Crandall, Keith A

    2011-01-01

    Next-gen sequencing technologies have revolutionized data collection in genetic studies and advanced genome biology to novel frontiers. However, to date, next-gen technologies have been used principally for whole genome sequencing and transcriptome sequencing. Yet many questions in population genetics and systematics rely on sequencing specific genes of known function or diversity levels. Here, we describe a targeted amplicon sequencing (TAS) approach capitalizing on next-gen capacity to sequence large numbers of targeted gene regions from a large number of samples. Our TAS approach is easily scalable, simple in execution, neither time-nor labor-intensive, relatively inexpensive, and can be applied to a broad diversity of organisms and/or genes. Our TAS approach includes a bioinformatic application, BarcodeCrucher, to take raw next-gen sequence reads and perform quality control checks and convert the data into FASTA format organized by gene and sample, ready for phylogenetic analyses. We demonstrate our approach by sequencing targeted genes of known phylogenetic utility to estimate a phylogeny for the Pancrustacea. We generated data from 44 taxa using 68 different 10-bp multiplexing identifiers. The overall quality of data produced was robust and was informative for phylogeny estimation. The potential for this method to produce copious amounts of data from a single 454 plate (e.g., 325 taxa for 24 loci) significantly reduces sequencing expenses incurred from traditional Sanger sequencing. We further discuss the advantages and disadvantages of this method, while offering suggestions to enhance the approach.

  7. Nitrogenase gene amplicons from global marine surface waters are dominated by genes of non-cyanobacteria

    DEFF Research Database (Denmark)

    Farnelid, Hanna; Andersson, Anders F.; Bertilsson, Stefan;

    2011-01-01

    Cyanobacteria are thought to be the main N2-fixing organisms (diazotrophs) in marine pelagic waters, but recent molecular analyses indicate that non-cyanobacterial diazotrophs are also present and active. Existing data are, however, restricted geographically and by limited sequencing depths. Our ...... occasionally expressed. The contribution of non-cyanobacterial diazotrophs to the global N2 fixation budget cannot be inferred from sequence data alone, but the prevalence of non-cyanobacterial nifH genes and transcripts suggest that these bacteria are ecologically significant.......Cyanobacteria are thought to be the main N2-fixing organisms (diazotrophs) in marine pelagic waters, but recent molecular analyses indicate that non-cyanobacterial diazotrophs are also present and active. Existing data are, however, restricted geographically and by limited sequencing depths. Our...... analysis of 79,090 nitrogenase (nifH) PCR amplicons encoding 7,468 unique proteins from surface samples (ten DNA samples and two RNA samples) collected at ten marine locations world-wide provides the first in-depth survey of a functional bacterial gene and yield insights into the composition and diversity...

  8. Swarm v2: highly-scalable and high-resolution amplicon clustering

    Directory of Open Access Journals (Sweden)

    Frédéric Mahé

    2015-12-01

    Full Text Available Previously we presented Swarm v1, a novel and open source amplicon clustering program that produced fine-scale molecular operational taxonomic units (OTUs, free of arbitrary global clustering thresholds and input-order dependency. Swarm v1 worked with an initial phase that used iterative single-linkage with a local clustering threshold (d, followed by a phase that used the internal abundance structures of clusters to break chained OTUs. Here we present Swarm v2, which has two important novel features: (1 a new algorithm for d = 1 that allows the computation time of the program to scale linearly with increasing amounts of data; and (2 the new fastidious option that reduces under-grouping by grafting low abundant OTUs (e.g., singletons and doubletons onto larger ones. Swarm v2 also directly integrates the clustering and breaking phases, dereplicates sequencing reads with d = 0, outputs OTU representatives in fasta format, and plots individual OTUs as two-dimensional networks.

  9. Differential amplicons (ΔAmp—a new molecular method to assess RNA integrity

    Directory of Open Access Journals (Sweden)

    J. Björkman

    2016-01-01

    Full Text Available Integrity of the mRNA in clinical samples has major impact on the quality of measured expression levels. This is independent of the measurement technique being next generation sequencing (NGS, Quantitative real-time PCR (qPCR or microarray profiling. If mRNA is highly degraded or damaged, measured data will be very unreliable and the whole study is likely a waste of time and money. It is therefore common strategy to test the quality of RNA in samples before conducting large and costly studies. Most methods today to assess the quality of RNA are ignorant to the nature of the RNA and, therefore, reflect the integrity of ribosomal RNA, which is the dominant species, rather than of mRNAs, microRNAs and long non-coding RNAs, which usually are the species of interest. Here, we present a novel molecular approach to assess the quality of the targeted RNA species by measuring the differential amplification (ΔAmp of an Endogenous RNase Resistant (ERR marker relative to a reference gene, optionally combined with the measurement of two amplicons of different lengths. The combination reveals any mRNA degradation caused by ribonucleases as well as physical, chemical or UV damage. ΔAmp has superior sensitivity to common microfluidic electrophoretic methods, senses the integrity of the actual targeted RNA species, and allows for a smoother and more cost efficient workflow.

  10. Tolerance of VA Mycorrhizal Fungi to Soil Acidity

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    A 45-day greenhouse experiment was carried out to determine effect of vesicular-arbuscular (VA) mycorrhizai fungi on colonization rate,plant height, plant growth,hyphae length,total Al in the plants,exchangeable A1 in the soil and soil pH by comparison at soil pH 3.5,4.5 and 6.0.Plant mung bean (Phaseolus radiatus L.) and crotalaria (Crotalaria mucronata Desv.) were grown with and without VA mycorrhizal fungi in pots with red soil.Ten VA mycorrhizal fungi strains were tested,including Glomus epigaeum (No.90001),Glomus caledonium (No.90036),Glomus mosseae (No.90107), Acaulospora spp.(No.34),Scutellospora heterogama (No.36),Scutellospora calospora (No. 37),Glomus manihotis (No.38),Gigaspora spp.(No.47),Glomus manihotis (No.49),and Acaulospora spp.(No.53).Being the most tolerant to acidity,strain 34 and strain 38 showed quicker and higher-rated colonization without lagging,three to four times more in number of nodules,two to four times more in plant dry weight,30% to 60% more in hyphae length,lower soil exchangeable Al,and higher soil pH than without VA mycorrhizal fungi (CK).Other strains also could improve plant growth and enhance plant tolerance to acidity,but their effects were not marked.This indicated that VA mycorrhizal fungi differed in the tolerance to soil acidity and so did their inoculation effects.In the experiment,acidic soil could be remedied by inoculation of promising VA mycorrhizal fungi tolerant of acidity.

  11. Polymicrobial nature of chronic diabetic foot ulcer biofilm infections determined using bacterial tag encoded FLX amplicon pyrosequencing (bTEFAP.

    Directory of Open Access Journals (Sweden)

    Scot E Dowd

    Full Text Available BACKGROUND: Diabetic extremity ulcers are associated with chronic infections. Such ulcer infections are too often followed by amputation because there is little or no understanding of the ecology of such infections or how to control or eliminate this type of chronic infection. A primary impediment to the healing of chronic wounds is biofilm phenotype infections. Diabetic foot ulcers are the most common, disabling, and costly complications of diabetes. Here we seek to derive a better understanding of the polymicrobial nature of chronic diabetic extremity ulcer infections. METHODS AND FINDINGS: Using a new bacterial tag encoded FLX amplicon pyrosequencing (bTEFAP approach we have evaluated the bacterial diversity of 40 chronic diabetic foot ulcers from different patients. The most prevalent bacterial genus associated with diabetic chronic wounds was Corynebacterium spp. Findings also show that obligate anaerobes including Bacteroides, Peptoniphilus, Fingoldia, Anaerococcus, and Peptostreptococcus spp. are ubiquitous in diabetic ulcers, comprising a significant portion of the wound biofilm communities. Other major components of the bacterial communities included commonly cultured genera such as Streptococcus, Serratia, Staphylococcus and Enterococcus spp. CONCLUSIONS: In this article, we highlight the patterns of population diversity observed in the samples and introduce preliminary evidence to support the concept of functional equivalent pathogroups (FEP. Here we introduce FEP as consortia of genotypically distinct bacteria that symbiotically produce a pathogenic community. According to this hypothesis, individual members of these communities when they occur alone may not cause disease but when they coaggregate or consort together into a FEP the synergistic effect provides the functional equivalence of well-known pathogens, such as Staphylococcus aureus, giving the biofilm community the factors necessary to maintain chronic biofilm infections

  12. Stratigraphic-structural characteristics of Mačva basin

    Directory of Open Access Journals (Sweden)

    Carević Ivana

    2009-01-01

    Full Text Available The analysis of stratigraphic-structural features of Mačva basin had been conducted in this paper on the basis of data obtained with deep exploratory boring performed for the needs of hydrogeothermal research project for the purpose of identifying the reserves of geothermal energy of Mačva. The research has been carried out with the aim of finding out the relation between the Tertiary and its Triassic bedrock (Ladinian and Carnian stages in which process the considerable realistic image of paleorelief (the bedrock of Tertiary deposits was obtained.

  13. Inhibition of adenovirus replication by the E1A antisense transcript initiated from hsp70 and VA-1 promoters.

    Science.gov (United States)

    Miroshnichenko, O I; Borisenko, A S; Ponomareva, T I; Tikhonenko, T I

    1990-03-01

    The E1A region of the adenoviral genome, important for initiation of virus infection and activation of other viral genes, was chosen as a target for engineering antisense RNA (asRNA) to inhibit adenovirus 5 (Ad5) replication in COS-1 cell culture in vitro. The hsp70 promoter, taken from the appropriate heat-shock-protein gene of Drosophila melanogaster, and the VA-1 RNA promoter, derived from the Ad5 gene coding for low-molecular-mass VA-1 RNA and recognized by RNA polymerase III were used as regulatory elements of transcription. The two types of recombinant constructs contained E1A fragments of 710 bp (hsp70 constructs) or 380 or 740 bp (VA-1 RNA constructs) in reverse orientation relative to the promoter position, as well as a transcription termination signal, the SV40 ori, and the gene controlling Geneticin (antibiotic G418) resistance (G418R). After selection of transfected COS-1 cells in the presence of G418, a number of stable G418R cell lines were raised which expressed engineered asRNAs. Plating of Ad5 suspensions of known titre on monolayers of transfected COS-1 cells clearly showed strong inhibition of adenovirus replication by asRNAs: 75% with the hsp70 promoter and 90% with the VA-1 RNA promoter.

  14. Effects of ERBB2 amplicon size and genomic alterations of chromosomes 1, 3, and 10 on patient response to trastuzumab in metastatic breast cancer.

    Science.gov (United States)

    Morrison, Larry E; Jewell, Susan S; Usha, Lydia; Blondin, Beth A; Rao, Ruta D; Tabesh, Bita; Kemper, Matthew; Batus, Marta; Coon, John S

    2007-04-01

    Trastuzumab is widely used for advanced breast cancer patients with ERBB2-amplified tumors. Nevertheless, over half of these patients do not have an objective response. One reason may be altered expression of genes that might compensate for ERBB2 inhibition. We previously mapped the gene-rich region of chromosome 17 telomeric to ERBB2, and reported considerable variability in the telomeric extent of the ERBB2 amplicon. Here we examined whether the variable amplicon size may be associated with patient response to trastuzumab. In addition, we looked at associations between response and several signaling pathway-related genes unrelated to the ERBB2 amplicon, including AKT3, PTEN, PIK3CA, and PTGS2. In 35 patients with ERBB2-amplified metastatic breast cancer, with 40% overall response to trastuzumab, fluorescence in situ hybridization identified the telomeric extent of the ERBB2 amplicon and the status of the several pathway-related genes. Objective response strongly correlated with the telomeric amplicon size, with 62% of patients with shorter amplicons responding, compared with only 7% of patients with longer amplicons (P = 0.0015). Abnormal copy number of PTGS2 was marginally associated with objective response (P = 0.066), while abnormal copy numbers of two reference loci, 1q25 and the chromosome 10 centromere, were significantly associated with response. Pairwise combinations of copy number status of these loci and ERBB2 amplicon size provided stronger associations and identified a group of patients without responders. These results suggest that patient selection for trastuzumab may be improved by considering ERBB2 amplicon size and genomic status of the 1q25, PTGS2, and centromere 10 loci.

  15. A novel recombinant adeno-associated virus vector packaging system with HSV-1 amplicon providing helper functions

    Institute of Scientific and Technical Information of China (English)

    舒跃龙; 吴小兵; 杨天忠; 贡惠宇; 侯云德; 颜子颖

    1999-01-01

    A novel packaging system for producing recombinant adeno-associated virus (rAAV) vector was described. Instead of the conventional method for rAAV production by two-plasmid co-transfection followed by superinfection with adenovirus 5, an HSV-1 amplicon system expressing AAV-2 rep and cap genes from their native promoters was used to provide complete helper functions for rAAV replicating and packaging. This HSV-1 ampticon stock consisted of two kinds of infectious HSV-1 virions, a replicating-defective HSV-1 amplicon pseudovirus harboring multi-copies of AAV-2 rep and cap gene and a temperature-sensitive HSV-1 mutant strain ts-KOS. High-titer rAAV was generated with this new packaging system. This packaging system gives a simple and scaleable process for rAAV production.

  16. Groundtruthing next-gen sequencing for microbial ecology-biases and errors in community structure estimates from PCR amplicon pyrosequencing.

    Directory of Open Access Journals (Sweden)

    Charles K Lee

    Full Text Available Analysis of microbial communities by high-throughput pyrosequencing of SSU rRNA gene PCR amplicons has transformed microbial ecology research and led to the observation that many communities contain a diverse assortment of rare taxa-a phenomenon termed the Rare Biosphere. Multiple studies have investigated the effect of pyrosequencing read quality on operational taxonomic unit (OTU richness for contrived communities, yet there is limited information on the fidelity of community structure estimates obtained through this approach. Given that PCR biases are widely recognized, and further unknown biases may arise from the sequencing process itself, a priori assumptions about the neutrality of the data generation process are at best unvalidated. Furthermore, post-sequencing quality control algorithms have not been explicitly evaluated for the accuracy of recovered representative sequences and its impact on downstream analyses, reducing useful discussion on pyrosequencing reads to their diversity and abundances. Here we report on community structures and sequences recovered for in vitro-simulated communities consisting of twenty 16S rRNA gene clones tiered at known proportions. PCR amplicon libraries of the V3-V4 and V6 hypervariable regions from the in vitro-simulated communities were sequenced using the Roche 454 GS FLX Titanium platform. Commonly used quality control protocols resulted in the formation of OTUs with >1% abundance composed entirely of erroneous sequences, while over-aggressive clustering approaches obfuscated real, expected OTUs. The pyrosequencing process itself did not appear to impose significant biases on overall community structure estimates, although the detection limit for rare taxa may be affected by PCR amplicon size and quality control approach employed. Meanwhile, PCR biases associated with the initial amplicon generation may impose greater distortions in the observed community structure.

  17. Groundtruthing next-gen sequencing for microbial ecology-biases and errors in community structure estimates from PCR amplicon pyrosequencing.

    Science.gov (United States)

    Lee, Charles K; Herbold, Craig W; Polson, Shawn W; Wommack, K Eric; Williamson, Shannon J; McDonald, Ian R; Cary, S Craig

    2012-01-01

    Analysis of microbial communities by high-throughput pyrosequencing of SSU rRNA gene PCR amplicons has transformed microbial ecology research and led to the observation that many communities contain a diverse assortment of rare taxa-a phenomenon termed the Rare Biosphere. Multiple studies have investigated the effect of pyrosequencing read quality on operational taxonomic unit (OTU) richness for contrived communities, yet there is limited information on the fidelity of community structure estimates obtained through this approach. Given that PCR biases are widely recognized, and further unknown biases may arise from the sequencing process itself, a priori assumptions about the neutrality of the data generation process are at best unvalidated. Furthermore, post-sequencing quality control algorithms have not been explicitly evaluated for the accuracy of recovered representative sequences and its impact on downstream analyses, reducing useful discussion on pyrosequencing reads to their diversity and abundances. Here we report on community structures and sequences recovered for in vitro-simulated communities consisting of twenty 16S rRNA gene clones tiered at known proportions. PCR amplicon libraries of the V3-V4 and V6 hypervariable regions from the in vitro-simulated communities were sequenced using the Roche 454 GS FLX Titanium platform. Commonly used quality control protocols resulted in the formation of OTUs with >1% abundance composed entirely of erroneous sequences, while over-aggressive clustering approaches obfuscated real, expected OTUs. The pyrosequencing process itself did not appear to impose significant biases on overall community structure estimates, although the detection limit for rare taxa may be affected by PCR amplicon size and quality control approach employed. Meanwhile, PCR biases associated with the initial amplicon generation may impose greater distortions in the observed community structure.

  18. Groundtruthing Next-Gen Sequencing for Microbial Ecology–Biases and Errors in Community Structure Estimates from PCR Amplicon Pyrosequencing

    OpenAIRE

    Lee, Charles K.; Craig W. Herbold; Polson, Shawn W.; K Eric Wommack; Williamson, Shannon J.; McDonald, Ian R.; S. Craig Cary

    2012-01-01

    Analysis of microbial communities by high-throughput pyrosequencing of SSU rRNA gene PCR amplicons has transformed microbial ecology research and led to the observation that many communities contain a diverse assortment of rare taxa-a phenomenon termed the Rare Biosphere. Multiple studies have investigated the effect of pyrosequencing read quality on operational taxonomic unit (OTU) richness for contrived communities, yet there is limited information on the fidelity of community structure est...

  19. 78 FR 2708 - Virginia Disaster Number VA-00052

    Science.gov (United States)

    2013-01-14

    ... ADMINISTRATION Virginia Disaster Number VA-00052 AGENCY: U.S. Small Business Administration. ACTION: Amendment 1... completed loan applications to: U.S. Small Business Administration, Processing and Disbursement Center... Disaster Assistance, U.S. Small Business Administration, 409 3rd Street SW., Suite 6050, Washington,...

  20. 77 FR 51100 - Virginia Disaster No. VA-00048

    Science.gov (United States)

    2012-08-23

    ... ADMINISTRATION Virginia Disaster No. VA-00048 AGENCY: U.S. Small Business Administration. ACTION: Amendment 1.... ADDRESSES: Submit completed loan applications to: U.S. Small Business Administration, Processing and..., Office of Disaster Assistance, U.S. Small Business Administration, 409 3rd Street, SW., Suite...

  1. VA/DoD Collaboration Guidebook for Healthcare Research

    Science.gov (United States)

    2011-01-24

    Fort Hood, TX Reynolds Army Community Hospital, Fort Sill, OK Bayne Jones Army Community Hospital, Fort Polk, LA VA/DoD Research Collaboration...www.rach.sill.amedd.army.mil/ Bayne Jones Army Community Hospital, Fort Polk, LA http://www.polk.amedd.army.mil/ 50 (IRB) Dwight D. Eisenhower AMC, Fort

  2. Military and VA General Dentistry Training: A National Resource.

    Science.gov (United States)

    Atchison, Kathryn A.; Bachand, William; Buchanan, C. Richard; Lefever, Karen H.; Lin, Sylvia; Engelhardt, Rita

    2002-01-01

    Compared the program characteristics of the postgraduate general dentistry (PGD) training programs sponsored by the military and the Veterans Health Administration (VA). Gathered information on program infrastructure and emphasis, resident preparation prior to entering the program, and patients served and types of services provided. Programs…

  3. Amplicon-based semiconductor sequencing of human exomes: performance evaluation and optimization strategies.

    Science.gov (United States)

    Damiati, E; Borsani, G; Giacopuzzi, Edoardo

    2016-05-01

    The Ion Proton platform allows to perform whole exome sequencing (WES) at low cost, providing rapid turnaround time and great flexibility. Products for WES on Ion Proton system include the AmpliSeq Exome kit and the recently introduced HiQ sequencing chemistry. Here, we used gold standard variants from GIAB consortium to assess the performances in variants identification, characterize the erroneous calls and develop a filtering strategy to reduce false positives. The AmpliSeq Exome kit captures a large fraction of bases (>94 %) in human CDS, ClinVar genes and ACMG genes, but with 2,041 (7 %), 449 (13 %) and 11 (19 %) genes not fully represented, respectively. Overall, 515 protein coding genes contain hard-to-sequence regions, including 90 genes from ClinVar. Performance in variants detection was maximum at mean coverage >120×, while at 90× and 70× we measured a loss of variants of 3.2 and 4.5 %, respectively. WES using HiQ chemistry showed ~71/97.5 % sensitivity, ~37/2 % FDR and ~0.66/0.98 F1 score for indels and SNPs, respectively. The proposed low, medium or high-stringency filters reduced the amount of false positives by 10.2, 21.2 and 40.4 % for indels and 21.2, 41.9 and 68.2 % for SNP, respectively. Amplicon-based WES on Ion Proton platform using HiQ chemistry emerged as a competitive approach, with improved accuracy in variants identification. False-positive variants remain an issue for the Ion Torrent technology, but our filtering strategy can be applied to reduce erroneous variants.

  4. Competitive amplification of differentially melting amplicons (CADMA improves KRAS hotspot mutation testing in colorectal cancer

    Directory of Open Access Journals (Sweden)

    Kristensen Lasse

    2012-11-01

    Full Text Available Abstract Background Cancer is an extremely heterogeneous group of diseases traditionally categorized according to tissue of origin. However, even among patients with the same cancer subtype the cellular alterations at the molecular level are often very different. Several new therapies targeting specific molecular changes found in individual patients have initiated the era of personalized therapy and significantly improved patient care. In metastatic colorectal cancer (mCRC a selected group of patients with wild-type KRAS respond to antibodies against the epidermal growth factor receptor (EGFR. Testing for KRAS mutations is now required prior to anti-EGFR treatment, however, less sensitive methods based on conventional PCR regularly fail to detect KRAS mutations in clinical samples. Methods We have developed sensitive and specific assays for detection of the seven most common KRAS mutations based on a novel methodology named Competitive Amplification of Differentially Melting Amplicons (CADMA. The clinical applicability of these assays was assessed by analyzing 100 colorectal cancer samples, for which KRAS mutation status has been evaluated by the commercially available TheraScreen® KRAS mutation kit. Results The CADMA assays were sensitive to at least 0.5% mutant alleles in a wild-type background when using 50 nanograms of DNA in the reactions. Consensus between CADMA and the TheraScreen kit was observed in 96% of the colorectal cancer samples. In cases where disagreement was observed the CADMA result could be confirmed by a previously published assay based on TaqMan probes and by fast COLD-PCR followed by Sanger sequencing. Conclusions The high analytical sensitivity and specificity of CADMA may increase diagnostic sensitivity and specificity of KRAS mutation testing in mCRC patients.

  5. 75 FR 33216 - Payment or Reimbursement for Emergency Treatment Furnished by Non-VA Providers in Non-VA...

    Science.gov (United States)

    2010-06-11

    ... amendments made to 38 U.S.C. 1725 and 1728, and would make technical changes such as correcting grammatical... authorized. In addition, these amendments would make nonsubstantive technical changes such as correcting grammatical errors and updating obsolete citations. DATES: Comments must be received by VA on or before...

  6. 75 FR 25321 - Agency Information Collection (VA National Rehabilitation Special Events, Event Registration...

    Science.gov (United States)

    2010-05-07

    ... therapeutic rehabilitation programs such as the National Veterans Wheelchair Games, National Veterans Golden... AFFAIRS Agency Information Collection (VA National Rehabilitation Special Events, Event Registration... Wheelchair Games Application, VA Form 0925a series. c. National Veterans Golden Age Games Application,...

  7. Rights and Responsibilities of VA Patients and Residents of Community Living Centers

    Science.gov (United States)

    ... Community Living Centers Veterans Health Administration Rights and Responsibilities of VA Patients and Residents of Community Living ... email vaoighotline@va.gov . 5. Additional Rights and Responsibilities of Community Living Center Residents Because the CLC ...

  8. 48 CFR 803.7000 - Display of the VA Hotline poster.

    Science.gov (United States)

    2010-10-01

    ... 48 Federal Acquisition Regulations System 5 2010-10-01 2010-10-01 false Display of the VA Hotline... Improper Business Practices 803.7000 Display of the VA Hotline poster. (a) Under the circumstances described in paragraph (b) of this section, a contractor must display prominently a VA Hotline...

  9. 38 CFR 74.26 - What types of business information will VA collect?

    Science.gov (United States)

    2010-07-01

    ... 38 Pensions, Bonuses, and Veterans' Relief 2 2010-07-01 2010-07-01 false What types of business information will VA collect? 74.26 Section 74.26 Pensions, Bonuses, and Veterans' Relief DEPARTMENT OF... business information will VA collect? VA will examine a variety of business records. See § 74.12, “What...

  10. 76 FR 71920 - Payment for Home Health Services and Hospice Care by Non-VA Providers

    Science.gov (United States)

    2011-11-21

    ... AFFAIRS 38 CFR Part 17 RIN 2900-AN98 Payment for Home Health Services and Hospice Care by Non-VA Providers... methodology for non-VA providers of home health services and hospice care. The proposed rulemaking would include home health services and hospice care under the VA regulation governing payment for other...

  11. 78 FR 55777 - Proposed Information Collection (VA, National Veterans Sports Programs and Special Events, Event...

    Science.gov (United States)

    2013-09-11

    ... AFFAIRS Proposed Information Collection (VA, National Veterans Sports Programs and Special Events, Event... Events, Department of Veterans Affairs. ACTION: Notice. SUMMARY: The Office of National Veterans Sports... Service Application, VA Form 0927f. k. National Veterans Summer sports Clinic Event Application, VA...

  12. 78 FR 77204 - Proposed Information Collection (VA National Veterans Sports Programs and Special Event Surveys...

    Science.gov (United States)

    2013-12-20

    ... AFFAIRS Proposed Information Collection (VA National Veterans Sports Programs and Special Event Surveys... ``OMB Control No. 2900-NEW (VA National Veterans Sports Programs and Special Event Surveys)'' in any... National Veterans Sports Programs and Special Event Surveys. OMB Control Number: 2900-NEW (VA...

  13. 78 FR 76412 - Agency Information Collection (VA National Rehabilitation Special Events, Event Registration...

    Science.gov (United States)

    2013-12-17

    ... sports Clinic Event Application, VA Form 0928a, c. l. Volunteer Application, VA Form 0928h. m. Surfing... AFFAIRS Agency Information Collection (VA National Rehabilitation Special Events, Event Registration Applications) Activities Under OMB Review AGENCY: Office of National Programs and Special Events, Department...

  14. 38 CFR 26.9 - Information on and public participation in VA environmental process.

    Science.gov (United States)

    2010-07-01

    ... participation in VA environmental process. 26.9 Section 26.9 Pensions, Bonuses, and Veterans' Relief DEPARTMENT...) ACTIONS § 26.9 Information on and public participation in VA environmental process. (a) During the..., the Office of Environmental Affairs, or a VA element, information is available by writing to...

  15. 77 FR 74279 - Agency Information Collection (VA/DOD Joint Disability Evaluation Board Claim): Activity under...

    Science.gov (United States)

    2012-12-13

    ... AFFAIRS Agency Information Collection (VA/DOD Joint Disability Evaluation Board Claim): Activity under OMB....'' SUPPLEMENTARY INFORMATION: Title: VA/DOD Joint Disability Evaluation Board Claim, VA Form 21- 0819. OMB Control... collection of information abstracted below to the Office of Management and Budget (OMB) for review...

  16. 38 CFR 1.9 - Description, use, and display of VA seal and flag.

    Science.gov (United States)

    2010-07-01

    ... employees. (D) Official VA signs. (E) Official publications or graphics issued by and attributed to VA, or... furtherance of the VA mission. (e) Distinguishing flag. (1) Description of distinguishing flag. (i) The base...) Souvenir or novelty items. (iii) Toys or commercial gifts or premiums. (iv) Letterhead design, except...

  17. VaR: Exchange Rate Risk and Jump Risk

    Directory of Open Access Journals (Sweden)

    Fen-Ying Chen

    2010-01-01

    Full Text Available Incorporating the Poisson jumps and exchange rate risk, this paper provides an analytical VaR to manage market risk of international portfolios over the subprime mortgage crisis. There are some properties in the model. First, different from past studies in portfolios valued only in one currency, this model considers portfolios not only with jumps but also with exchange rate risk, that is vital for investors in highly integrated global financial markets. Second, in general, the analytical VaR solution is more accurate than historical simulations in terms of backtesting and Christoffersen's independence test (1998 for small portfolios and large portfolios. In other words, the proposed model is reliable not only for a portfolio on specific stocks but also for a large portfolio. Third, the model can be regarded as the extension of that of Kupiec (1999 and Chen and Liao (2009.

  18. Guest Editorial: Research update: VA study to optimize DEKA Arm

    Directory of Open Access Journals (Sweden)

    Linda Resnik, PT, PhD

    2010-05-01

    Full Text Available In 2005, the Defense Advanced Research Projects Agency (DARPA announced its Revolutionizing Prosthetics program and funded the development of the DEKA prosthetic arm. The DEKA Arm System incorporates major technological advances such as flexible socket design, innovative control features, software, and hardware that together enable enhanced functionality that promises to surpass any currently available prosthetic device. In 2008, the Department of Veterans Affairs (VA entered into an agreement with DARPA to conduct clinical evaluations of the prototype DEKA Arm System, a prosthetic device system still under development and not yet available commercially. Studies of the DEKA Arm System have been underway at VA sites since late 2008, with the first subject fitted with a DEKA Arm in early 2009.

  19. VA/DoD Joint Executive Council Fiscal Year 2010

    Science.gov (United States)

    2010-01-01

    patient context management, and an Integration Platform (Common Service Broker (Enterprise Service Bus) capability). IT development activities are...and DoD transitioned over $16.8 million in customer buys from less efficient local purchase processes to more beneficial eCommerce venues. Figure...eZSAVe application is now merged into one Web platform . As a result, both VA and DoD customers at these sites have access to multiple MEDPDB

  20. Cosmological bounds in MaVaN models

    Energy Technology Data Exchange (ETDEWEB)

    Boriero, D.F.; Holanda, P.C. de [Instituto de Fisica ' Gleb Wataghin' , Universidade Estadual de Campinas, UNICAMP, 13083-859, Campinas, Sao Paulo (Brazil)

    2012-08-15

    Mass varying neutrino (MaVaN) is a class of models which in cosmology try to explain the coincidence of dark energy density through a tracking mechanism related with neutrinos. This special model couples the quintessential scalar field with neutrino generating an effective mass which becomes variable. Furthermore, it has been shown that an additional coupling among the quintessential field and baryons could generate specific dependences of neutrino mass with baryonic density.

  1. The 4q12 amplicon in malignant peripheral nerve sheath tumors: consequences on gene expression and implications for sunitinib treatment.

    Directory of Open Access Journals (Sweden)

    Jan Zietsch

    Full Text Available BACKGROUND: Malignant peripheral nerve sheath tumors (MPNST are highly aggressive tumors which originate from Schwann cells and develop in about 10% of neurofibromatosis type 1 (NF1 patients. The five year survival rate is poor and more effective therapies are needed. Sunitinib is a drug targeting receptor tyrosine kinases (RTK like PDGFRalpha, c-Kit and VEGFR-2. These genes are structurally related and cluster on chromosomal segment 4q12. METHODOLOGY/PRINCIPAL FINDINGS: Here we characterize this region by multiplex ligation-dependent probe amplification (MLPA in MPNST. Our probe set encompasses the 3 adjacent RTK genes (PDGFRA, KIT, KDR and 6 flanking genes. We found amplification of several genes within this region in a subset of MPNST and MPNST cell lines. Transcript and protein expression of PDGFRA matched well with its increased copy number suggesting a central role of PDGFRA within the amplicon. Studying the effect of sunitinib on 5 MPNST cell lines revealed that cell line S462 harboring the 4q12 amplicon was extremely sensitive to the drug with an IC50 below 1.0 microM. Moreover, sunitinib induced apoptosis and prevented PDGF-AA induced signaling via PDGFRalpha as determined by western blotting. Co-expression of VEGF and its receptor VEGFR-2 (KDR was present in MPNST cell lines suggesting an autocrine loop. We show that VEGF triggered signal transduction via the MAPK pathway, which could be blocked by sunitinib. CONCLUSIONS/SIGNIFICANCE: Since multiple receptors targeted by sunitinib are expressed or over-expressed by MPNST cells sunitinib appears as an attractive drug for treatment of MPNST patients. Presence of the 4q12 amplicon and subsequent over-expression of PDGFRA might serve as predictive markers for efficacy of sunitinib.

  2. Genotyping-in-Thousands by sequencing (GT-seq): A cost effective SNP genotyping method based on custom amplicon sequencing.

    Science.gov (United States)

    Campbell, Nathan R; Harmon, Stephanie A; Narum, Shawn R

    2015-07-01

    Genotyping-in-Thousands by sequencing (GT-seq) is a method that uses next-generation sequencing of multiplexed PCR products to generate genotypes from relatively small panels (50-500) of targeted single-nucleotide polymorphisms (SNPs) for thousands of individuals in a single Illumina HiSeq lane. This method uses only unlabelled oligos and PCR master mix in two thermal cycling steps for amplification of targeted SNP loci. During this process, sequencing adapters and dual barcode sequence tags are incorporated into the amplicons enabling thousands of individuals to be pooled into a single sequencing library. Post sequencing, reads from individual samples are split into individual files using their unique combination of barcode sequences. Genotyping is performed with a simple perl script which counts amplicon-specific sequences for each allele, and allele ratios are used to determine the genotypes. We demonstrate this technique by genotyping 2068 individual steelhead trout (Oncorhynchus mykiss) samples with a set of 192 SNP markers in a single library sequenced in a single Illumina HiSeq lane. Genotype data were 99.9% concordant to previously collected TaqMan(™) genotypes at the same 192 loci, but call rates were slightly lower with GT-seq (96.4%) relative to Taqman (99.0%). Of the 192 SNPs, 187 were genotyped in ≥90% of the individual samples and only 3 SNPs were genotyped in <70% of samples. This study demonstrates amplicon sequencing with GT-seq greatly reduces the cost of genotyping hundreds of targeted SNPs relative to existing methods by utilizing a simple library preparation method and massive efficiency of scale.

  3. EURRECA—Principles and Future for Deriving Micronutrient Recommendations

    NARCIS (Netherlands)

    Claessens, M.; Contor, L.; Dhonukshe-Rutten, R.; Groot, L.C.P.Q.M. de; Fairweather-Tait, S.J.; Gurinovic, M.; Koletzko, B.; Ommen, B. van; Raats, M.M.; Veer, P. van 't

    2013-01-01

    The EURopean micronutrient RECommendations Aligned (EURRECA) Network of Excellence (NoE) explored an approach for settingmicronutrient recommendations, which would address the variation in recommendations across Europe. Therefore, a framework for deriving and using micronutrient Dietary Reference Va

  4. 基于动态VaR约束与随机波动率模型的最优投资策略%Optimal investment strategy with stochastic volatility and dynamic VaR constraint

    Institute of Scientific and Technical Information of China (English)

    伊博; 李仲飞; 曾燕

    2012-01-01

    This paper considers an optimal portfolio choice problem under Stein-Stein stochastic volatility model and dynamic VaR constraint. The investor aims to maximize the expected power utility of the terminal wealth, and the financial market consists of one risk-free asset and one risky asset whose price process is described by Stein-Stein stochastic volatility model. At the same time, the investor hopes to limit the potential risk over investment horizon by a dynamic VaR constraint. Adopting the stochastic dynamic programming approach and Lagrange multiple method, we derive the closed-form expressions of the optimal strategy as well as the optimal value function in a special case. Moreover, economic implications and numerical analysis are proposed to illustrate the impacts of stochastic volatility and dynamic VaR constraint on the investor's optimal strategy.%研究Stein-Stein随机波动率模型下带动态VaR约束的最优投资组合选择问题.假设投资者的目标是最大化终端财富的期望幂效用,可投资于无风险资产和一种风险资产,风险资产的价格过程由Stein-Stein随机波动率模型刻画.同时,投资者期望能在投资过程中利用动态VaR约束控制所面对的风险.运用Bellman动态规划方法和Lagrange乘子法,得到了该约束问题最优策略的解析式及特殊情形下最优值函数的解析式;并通过理论分析和数值算例,阐述了动态VaR约束与随机波动率对最优投资策略的影响.

  5. CLOTU: An online pipeline for processing and clustering of 454 amplicon reads into OTUs followed by taxonomic annotation

    Directory of Open Access Journals (Sweden)

    Shalchian-Tabrizi Kamran

    2011-05-01

    Full Text Available Abstract Background The implementation of high throughput sequencing for exploring biodiversity poses high demands on bioinformatics applications for automated data processing. Here we introduce CLOTU, an online and open access pipeline for processing 454 amplicon reads. CLOTU has been constructed to be highly user-friendly and flexible, since different types of analyses are needed for different datasets. Results In CLOTU, the user can filter out low quality sequences, trim tags, primers, adaptors, perform clustering of sequence reads, and run BLAST against NCBInr or a customized database in a high performance computing environment. The resulting data may be browsed in a user-friendly manner and easily forwarded to downstream analyses. Although CLOTU is specifically designed for analyzing 454 amplicon reads, other types of DNA sequence data can also be processed. A fungal ITS sequence dataset generated by 454 sequencing of environmental samples is used to demonstrate the utility of CLOTU. Conclusions CLOTU is a flexible and easy to use bioinformatics pipeline that includes different options for filtering, trimming, clustering and taxonomic annotation of high throughput sequence reads. Some of these options are not included in comparable pipelines. CLOTU is implemented in a Linux computer cluster and is freely accessible to academic users through the Bioportal web-based bioinformatics service (http://www.bioportal.uio.no.

  6. A Portable Automatic Endpoint Detection System for Amplicons of Loop Mediated Isothermal Amplification on Microfluidic Compact Disk Platform

    Directory of Open Access Journals (Sweden)

    Shah Mukim Uddin

    2015-03-01

    Full Text Available In recent years, many improvements have been made in foodborne pathogen detection methods to reduce the impact of food contamination. Several rapid methods have been developed with biosensor devices to improve the way of performing pathogen detection. This paper presents an automated endpoint detection system for amplicons generated by loop mediated isothermal amplification (LAMP on a microfluidic compact disk platform. The developed detection system utilizes a monochromatic ultraviolet (UV emitter for excitation of fluorescent labeled LAMP amplicons and a color sensor to detect the emitted florescence from target. Then it processes the sensor output and displays the detection results on liquid crystal display (LCD. The sensitivity test has been performed with detection limit up to 2.5 × 10−3 ng/µL with different DNA concentrations of Salmonella bacteria. This system allows a rapid and automatic endpoint detection which could lead to the development of a point-of-care diagnosis device for foodborne pathogens detection in a resource-limited environment.

  7. Improved Efficiency and Reliability of NGS Amplicon Sequencing Data Analysis for Genetic Diagnostic Procedures Using AGSA Software.

    Science.gov (United States)

    Poulet, Axel; Privat, Maud; Ponelle, Flora; Viala, Sandrine; Decousus, Stephanie; Perin, Axel; Lafarge, Laurence; Ollier, Marie; El Saghir, Nagi S; Uhrhammer, Nancy; Bignon, Yves-Jean; Bidet, Yannick

    Screening for BRCA mutations in women with familial risk of breast or ovarian cancer is an ideal situation for high-throughput sequencing, providing large amounts of low cost data. However, 454, Roche, and Ion Torrent, Thermo Fisher, technologies produce homopolymer-associated indel errors, complicating their use in routine diagnostics. We developed software, named AGSA, which helps to detect false positive mutations in homopolymeric sequences. Seventy-two familial breast cancer cases were analysed in parallel by amplicon 454 pyrosequencing and Sanger dideoxy sequencing for genetic variations of the BRCA genes. All 565 variants detected by dideoxy sequencing were also detected by pyrosequencing. Furthermore, pyrosequencing detected 42 variants that were missed with Sanger technique. Six amplicons contained homopolymer tracts in the coding sequence that were systematically misread by the software supplied by Roche. Read data plotted as histograms by AGSA software aided the analysis considerably and allowed validation of the majority of homopolymers. As an optimisation, additional 250 patients were analysed using microfluidic amplification of regions of interest (Access Array Fluidigm) of the BRCA genes, followed by 454 sequencing and AGSA analysis. AGSA complements a complete line of high-throughput diagnostic sequence analysis, reducing time and costs while increasing reliability, notably for homopolymer tracts.

  8. Improved Efficiency and Reliability of NGS Amplicon Sequencing Data Analysis for Genetic Diagnostic Procedures Using AGSA Software

    Directory of Open Access Journals (Sweden)

    Axel Poulet

    2016-01-01

    Full Text Available Screening for BRCA mutations in women with familial risk of breast or ovarian cancer is an ideal situation for high-throughput sequencing, providing large amounts of low cost data. However, 454, Roche, and Ion Torrent, Thermo Fisher, technologies produce homopolymer-associated indel errors, complicating their use in routine diagnostics. We developed software, named AGSA, which helps to detect false positive mutations in homopolymeric sequences. Seventy-two familial breast cancer cases were analysed in parallel by amplicon 454 pyrosequencing and Sanger dideoxy sequencing for genetic variations of the BRCA genes. All 565 variants detected by dideoxy sequencing were also detected by pyrosequencing. Furthermore, pyrosequencing detected 42 variants that were missed with Sanger technique. Six amplicons contained homopolymer tracts in the coding sequence that were systematically misread by the software supplied by Roche. Read data plotted as histograms by AGSA software aided the analysis considerably and allowed validation of the majority of homopolymers. As an optimisation, additional 250 patients were analysed using microfluidic amplification of regions of interest (Access Array Fluidigm of the BRCA genes, followed by 454 sequencing and AGSA analysis. AGSA complements a complete line of high-throughput diagnostic sequence analysis, reducing time and costs while increasing reliability, notably for homopolymer tracts.

  9. A Method for Amplicon Deep Sequencing of Drug Resistance Genes in Plasmodium falciparum Clinical Isolates from India.

    Science.gov (United States)

    Rao, Pavitra N; Uplekar, Swapna; Kayal, Sriti; Mallick, Prashant K; Bandyopadhyay, Nabamita; Kale, Sonal; Singh, Om P; Mohanty, Akshaya; Mohanty, Sanjib; Wassmer, Samuel C; Carlton, Jane M

    2016-06-01

    A major challenge to global malaria control and elimination is early detection and containment of emerging drug resistance. Next-generation sequencing (NGS) methods provide the resolution, scalability, and sensitivity required for high-throughput surveillance of molecular markers of drug resistance. We have developed an amplicon sequencing method on the Ion Torrent PGM platform for targeted resequencing of a panel of six Plasmodium falciparum genes implicated in resistance to first-line antimalarial therapy, including artemisinin combination therapy, chloroquine, and sulfadoxine-pyrimethamine. The protocol was optimized using 12 geographically diverse P. falciparum reference strains and successfully applied to multiplexed sequencing of 16 clinical isolates from India. The sequencing results from the reference strains showed 100% concordance with previously reported drug resistance-associated mutations. Single-nucleotide polymorphisms (SNPs) in clinical isolates revealed a number of known resistance-associated mutations and other nonsynonymous mutations that have not been implicated in drug resistance. SNP positions containing multiple allelic variants were used to identify three clinical samples containing mixed genotypes indicative of multiclonal infections. The amplicon sequencing protocol has been designed for the benchtop Ion Torrent PGM platform and can be operated with minimal bioinformatics infrastructure, making it ideal for use in countries that are endemic for the disease to facilitate routine large-scale surveillance of the emergence of drug resistance and to ensure continued success of the malaria treatment policy.

  10. Procurement Risk Management Model Based on VaR%基于VaR的采购风险度量模型

    Institute of Scientific and Technical Information of China (English)

    万晓; 闫琳

    2007-01-01

    探讨将VaR风险价值法这一新型风险管理工具引入采购风险管理之中,利用VaR方法中的RiskMetrics模型对价格收益率序列方差进行拟合,建立采购风险度量模型.

  11. Upregulated, 7q21-22 amplicon candidate gene SHFM1 confers oncogenic advantage by suppressing p53 function in gastric cancer.

    Science.gov (United States)

    Tamilzhalagan, Sembulingam; Muthuswami, Muthulakshmi; Periasamy, Jayaprakash; Lee, Ming Hui; Rha, Sun Young; Tan, Patrick; Ganesan, Kumaresan

    2015-06-01

    Chromosomal aberrations are hallmarks of cancers and the locus of frequent genomic amplifications often harbors key cancer driver genes. Many genomic amplicons remain larger with hundreds of genes and the key drivers remain to be identified by an amplification-wide systematic analysis. The 7q21.12-q22.3 genomic amplification is frequent in gastric cancers which occur in ~10% of the patients and multiple cell lines. This 7q21.12-q22.3 amplicon has not yet been completely analyzed towards identifying the driver genes and their functional contribution in oncogenesis. The amplitude and prevalence indicate the important role conferred by this amplicon in gastric cancers. Among the 159 genes of this amplicon, 12 genes are found over-expressed in primary gastric tumors and cell lines. Many of the over-expressed genes show negative association with p53 transcriptional activity. RNAi based functional screening of the genes reveal, SHFM1 as key gastric cancer driver gene. SHFM1 confers cell cycle progression and resistance to p53 stabilizing drugs in gastric cancer cells. SHFM1 also activates Src, MAPK/ERK and PI3K/Akt signaling pathways. This is the first integrative genomic investigation of 7q21.12-q22.3 amplicon revealing the potential oncogenic candidacy of 12 genes. The oncogenic contribution of SHFM1, mediated by the p53 suppressive feature has been demonstrated in gastric cancer cells.

  12. The VA Maryland Health Care System's telemental health program.

    Science.gov (United States)

    Koch, Edward F

    2012-05-01

    The VA Maryland Health Care System introduced videoconferencing technology to provide psychiatry, evidenced-based psychotherapy, case management, and patient education at rural clinics where it was difficult to recruit providers. Telemental health services enable rural clinics to offer additional services, such as case management and patient education. Services have been expanded to urban outpatient clinics where a limited number of mental health clinic hours are available. This technology expands the availability of mental health providers and services, allowing patients to receive services from providers located at distant medical centers.

  13. Noncoherent detection of DQPSK in OFDM systems using predictive VA

    Science.gov (United States)

    Veludandi, Vineel K.; Vasudevan, K.

    2017-01-01

    Noncoherent detection of differential quaternary phase shift keying (DQPSK) signals in OFDM systems is efficiently implemented using a predictive Viterbi algorithm (VA) operating on a trellis with just S T = MP‑1 states instead of M P states, where M denotes an M-ary PSK constellation and P denotes the order of the prediction filter. The prediction filter coefficients are generated based on the channel DFT alone making a high SNR approximation, since the estimation of the noise-variance using training symbols results in loss of throughput.

  14. The HER2 amplicon includes several genes required for the growth and survival of HER2 positive breast cancer cells — A data description

    Directory of Open Access Journals (Sweden)

    Vesa Hongisto

    2014-12-01

    Full Text Available A large number of breast cancers are characterized by amplification and overexpression of the chromosome segment surrounding the HER2 (ERBB2 oncogene. As the HER2 amplicon at 17q12 contains multiple genes, we have systematically explored the role of the HER2 co-amplified genes in breast cancer cell growth and their relation to trastuzumab resistance. We integrated array comparative genomic hybridization (aCGH data of the HER2 amplicon from 71 HER2 positive breast tumors and 10 cell lines with systematic functional RNA interference analysis of 23 core amplicon genes with several phenotypic endpoints in a panel of trastuzumab responding and non-responding HER2 positive breast cancer cells. In this Data in Brief we give a detailed description of the experimental procedures and the data analysis methods used in the study (1.

  15. The KaVA and KVN Pulsar Project

    CERN Document Server

    Dodson, Richard; Sohn, Bongwon; Rioja, Mar\\'\\ia J; Jung, Taehyun; Seymour, Andrew; Raja, Wasim

    2014-01-01

    We present our work towards using the Korean VLBI (Very Long Baseline Interferometer) Network (KVN) and VLBI Exploration of Radio Astronomy (VERA) arrays combined into the KVN and VERA Array (KaVA) for observations of radio pulsars at high frequencies ($\\simeq$22-GHz). Pulsar astronomy is generally focused at frequencies approximately 0.3 to several GHz and pulsars are usually discovered and monitored with large, single-dish, radio telescopes. For most pulsars, reduced radio flux is expected at high frequencies due to their steep spectrum, but there are exceptions where high frequency observations can be useful. Moreover, some pulsars are observable at high frequencies only, such as those close to the Galactic Center. The discoveries of a radio-bright magnetar and a few dozen extended Chandra sources within 15 arc-minute of the Galactic Center provide strong motivations to make use of the KaVA frequency band for searching pulsars in this region. Here, we describe the science targets and report progresses made...

  16. Clinical application study of externally powered upper-limb prosthetics systems: the VA elbow, the VA hand, and the VA/NU myoelectric hand systems.

    Science.gov (United States)

    Lewis, E A; Sheredos, C R; Sowell, T T; Houston, V L

    1975-01-01

    The results have been presented of a 2-year survey designed to determine whether external power systems offer a significant contribution to the needs of the upper-limb amputee or whether they represent novelties duplicating the functions of conventional mechanical components. The following conclusions have been drawn: 1. External power does offer advantages to the arm amputee. Myoelectric control, especially combined with a self-suspending socket, offers an otherwise normal partial forearm amputee better function without the necessity of a harness. External power, especially for the short partial or total arm amputee and others with limited excursion, brings increased function with less effort. For these patients the advantages of such components as the electric elbow outweigh the recent disadvantages. 2. The components evaluated in this Study are not without limitations. Maintenance requirements of the VA Elbow were excessive. The VA Elbow should not be prescribed for patients who do heavy work with their prostheses because the flexspline may break. Regarding such concerns as lack of sensory feedback, noise, weight, and flexion/extension speed, the advantages of each unit must be weighed against the disadvantages with preference to the individual amputee. 3. The endoskeletal forearm with soft cover is an advantage because of its lightness and cosmesis. 4. Because of the many malfunctions attributed to prosthetist errors, the need is evident for thorough specialized education in the field of external power. A few centralized fabrication facilities may be desirable as opposed to fabrication by many facilities with limited experience. Modular components that are interchangeable and field repairable would be desirable. The systems should be fitted, installed and repaired only by trained prosthetists who have successfully completed a course in externally powered upper-limb prostheses. All members of the Clinic Team should be thoroughly educated in external power as it

  17. Mixed-Methods Research in a Complex Multisite VA Health Services Study: Variations in the Implementation and Characteristics of Chiropractic Services in VA

    Directory of Open Access Journals (Sweden)

    Raheleh Khorsan

    2013-01-01

    Full Text Available Maximizing the quality and benefits of newly established chiropractic services represents an important policy and practice goal for the US Department of Veterans Affairs’ healthcare system. Understanding the implementation process and characteristics of new chiropractic clinics and the determinants and consequences of these processes and characteristics is a critical first step in guiding quality improvement. This paper reports insights and lessons learned regarding the successful application of mixed methods research approaches—insights derived from a study of chiropractic clinic implementation and characteristics, Variations in the Implementation and Characteristics of Chiropractic Services in VA (VICCS. Challenges and solutions are presented in areas ranging from selection and recruitment of sites and participants to the collection and analysis of varied data sources. The VICCS study illustrates the importance of several factors in successful mixed-methods approaches, including (1 the importance of a formal, fully developed logic model to identify and link data sources, variables, and outcomes of interest to the study’s analysis plan and its data collection instruments and codebook and (2 ensuring that data collection methods, including mixed-methods, match study aims. Overall, successful application of a mixed-methods approach requires careful planning, frequent trade-offs, and complex coding and analysis.

  18. Network analysis of the microorganism in 25 Danish wastewater treatment plants over 7 years using high-throughput amplicon sequencing

    DEFF Research Database (Denmark)

    Albertsen, Mads; Larsen, Poul; Saunders, Aaron Marc;

    Wastewater treatment is the world’s largest biotechnological processes and a perfect model system for microbial ecology as the habitat is well defined and replicated all over the world. Extensive investigations on Danish wastewater treatment plants using fluorescent in situ hybridization have...... identified 38 probe-defined core genera, which are shared among all investigated Danish plants. A large body of knowledge exists on many of the core genera, however few attempts have been made to integrate the knowledge on a system-level understanding of the process. In this work we aimed to integrate...... the existing knowledge on core genera with high-throughput amplicon sequencing, plant design and process data in order to identify interactions and community shaping factors. We investigated 25 Danish full-scale wastewater treatment plants with nutrient removal over a period of 7 years with two to four samples...

  19. Codex Alimentarius - značenje i važnost

    OpenAIRE

    1998-01-01

    Codex Alimentarius dugi je niz godina važan zakonodavni akt u području prehrambene industrije. Zbog važnosti mlijeka i mliječnih proizvoda utemeljen je "Codex Odbor" za mlijeko i mliječne proizvode, koji je integriran u cjeloviti Codex sustav. Posebno je važna povezanost između Codex-a i WTO (World Trade Organization -Svjetska trgovinska organizacija). Za Hrvatsku je od posebne važnosti skori ulazak u WTO. Valja naglasiti daje "Pravilnik o kvaliteti mlijeka i mliječnih proizvoda", koji će kak...

  20. 沪深300指数极值VaR的分析与计算

    Institute of Scientific and Technical Information of China (English)

    周孝华; 唐秋燕

    2008-01-01

    文章将GARCH模型和EVT理论相结合,对沪深300指数的风险价值进行分析与计算,并将其与传统基于正态分布假设计算的VaR、GARCH模型计算的VaR以及基于EVT理论计算的VaR进行比较,发现采用GARCH模型和EVT理论相结合而得到的极值VaR能更好地反应沪深300指数的风险.

  1. Helman defends decision to pull VA sponsorship of Veterans day parade

    Directory of Open Access Journals (Sweden)

    Robbins RA

    2013-04-01

    Full Text Available No abstract available. Article truncated after 150 words. Sharon Helman, Phoenix VA Director, defended her decision to cancel VA sponsorship of the annual Phoenix Veterans Day Parade in a 4/10/13 email to VA employees. Helman said that VA sponsorship was cancelled because of “…priorities in the organization (specifically access, and heightened awareness over liability concerns which VA Legal Counsel brought forward”. She concluded her letter by warning “… that all media inquiries should be forwarded to Paul Coupaud, Acting Public Affairs Officer”. VA officials initially said fear of litigation prompted the review of VA support. Last year, a float carrying wounded Veterans in a Midland, Texas, parade collided with a freight train, killing four and injuring 17. Crash victims and their families filed lawsuits in Texas against Union Pacific Railroad and the float owner. The VA was not a defendant, and the VA has not issued any national directives on liability as a result of the tragedy.In…

  2. Differential patterns of myosin Va expression during the ontogenesis of the rat hippocampus

    Directory of Open Access Journals (Sweden)

    L.S. Brinn

    2010-09-01

    Full Text Available Myosin Va is an actin-based, processive molecular motor protein highly enriched in the nervous tissue of vertebrates. It has been associated with processes of cellular motility, which include organelle transport and neurite outgrowth. The in vivo expression of myosin Va protein in the developing nervous system of mammals has not yet been reported. We describe here the immunolocalization of myosin Va in the developing rat hippocampus. Coronal sections of the embryonic and postnatal rat hippocampus were probed with an affinity-purified, polyclonal anti-myosin Va antibody. Myosin Va was localized in the cytoplasm of granule cells in the dentate gyrus and of pyramidal cells in Ammon's horn formation. Myosin Va expression changed during development, being higher in differentiating rather than already differentiated granule and pyramidal cells. Some of these cells presented a typical migratory profile, while others resembled neurons that were in the process of differentiation. Myosin Va was also transiently expressed in fibers present in the fimbria. Myosin Va was not detected in germinative matrices of the hippocampus proper or of the dentate gyrus. In conclusion, myosin Va expression in both granule and pyramidal cells showed both position and time dependency during hippocampal development, indicating that this motor protein is under developmental regulation.

  3. Analysis of 16S rRNA amplicon sequencing options on the Roche/454 next-generation titanium sequencing platform.

    Directory of Open Access Journals (Sweden)

    Hideyuki Tamaki

    Full Text Available BACKGROUND: 16S rRNA gene pyrosequencing approach has revolutionized studies in microbial ecology. While primer selection and short read length can affect the resulting microbial community profile, little is known about the influence of pyrosequencing methods on the sequencing throughput and the outcome of microbial community analyses. The aim of this study is to compare differences in output, ease, and cost among three different amplicon pyrosequencing methods for the Roche/454 Titanium platform METHODOLOGY/PRINCIPAL FINDINGS: The following three pyrosequencing methods for 16S rRNA genes were selected in this study: Method-1 (standard method is the recommended method for bi-directional sequencing using the LIB-A kit; Method-2 is a new option designed in this study for unidirectional sequencing with the LIB-A kit; and Method-3 uses the LIB-L kit for unidirectional sequencing. In our comparison among these three methods using 10 different environmental samples, Method-2 and Method-3 produced 1.5-1.6 times more useable reads than the standard method (Method-1, after quality-based trimming, and did not compromise the outcome of microbial community analyses. Specifically, Method-3 is the most cost-effective unidirectional amplicon sequencing method as it provided the most reads and required the least effort in consumables management. CONCLUSIONS: Our findings clearly demonstrated that alternative pyrosequencing methods for 16S rRNA genes could drastically affect sequencing output (e.g. number of reads before and after trimming but have little effect on the outcomes of microbial community analysis. This finding is important for both researchers and sequencing facilities utilizing 16S rRNA gene pyrosequencing for microbial ecological studies.

  4. Research on Viewing Angle Characteristics of Negative VA-LCD%负性VA-LCD视角特性研究

    Institute of Scientific and Technical Information of China (English)

    黄翀; 许国栋; 杨玮枫; 吴永俊

    2015-01-01

    Liquid crystal material has birefringence effect, so the polarized light occurs at different levels of bi⁃refringence in all directions in liquid crystal material, which determines the viewing angle characteristic and the contrast of LCD are different along with the change of viewing angles. The electro-optical characteristics of the nega⁃tive VA-LCD under different driving voltages and the electro-optical characteristics along with the change of view⁃ing angles are tested by a grating spectrograph to analyze electro-optical characteristics and viewing angles of the three primary colors of the negative VA-LCD. The results show that the transmittance of three primary colors is low under 2.2 V driving voltage, when the driving voltage exceeds 2.2 V, the transmittance increases with the increase of the voltage. The transmittance of red and green primary color increases all along, and reach 5.0 V are leveling off, but the transmittance of blue primary color is the maximum at 3.7 V, then become smaller, and then tends to a sta⁃ble value at 6.0 V. In the viewing angles of the three primary colors of the negative VA-LCD, the viewing angle cov⁃erage of the red primary color is the widest, and the viewing angle coverage of the green primary color is wider and the viewing angle coverage of the red primary color is the narrowest.%液晶材料具有双折射效应,因此偏振光在液晶材料中各个方向上发生双折射的程度不同,这决定了LCD的视角特性和对比度随视角的变化有所不同。用光栅光谱仪测量在不同电压驱动下负性VA-LCD的电光特性,以及测量其电光特性随视角的变化;并对其三基色的电光特性和视角特性进行分析。结果表明,三基色的透过率在驱动电压2.2 V之前很小;在2.2 V后,透过率随电压的升高而增大;其中红基色和绿基色的透过率是一直升高,在电压达到5.0 V后,就是趋于平缓,而蓝基色的透过率是在3.7 V左

  5. Personalities, Cultural Identity, Intercultural Dialogue: V.A. Urechia

    Directory of Open Access Journals (Sweden)

    Anişoara Popa

    2014-12-01

    Full Text Available Considering, as Tzvetan Todorov does, that “the intercultural dimension is part of the cultural dimension” and that personalities assumed different roles, according to the historic circumstances, the ideative sphere of the time, and the specific internal mechanisms of generating elites that each culture has, the goal of this paper is to provide a few comments on the personalities‟ contribution in the intercultural dialogue, starting from the critical examination of the role that V.A. Urechia (1834-1901 - historian, politician and man of letters – had in redefining the national Romanian identity and in the development of the Romanian-Spanish cultural relations at the end of the 19th century. Applying the classical Freudian psychodynamic pattern of the personality structure to the culture, we propose a new point of view on the personalities‟ role in intercultural dialog.

  6. Calculations on various total cross-sections of electron impact on group VA - atoms-threshold to 2000 eV

    Energy Technology Data Exchange (ETDEWEB)

    Joshipura, K N; Gangopadhyay, Sumona; Kothari, Harshit N [Department of Physics, Sardar Patel University, Vallabh Vidyanagar - 388 120 (India); Shelat, Foram A, E-mail: knjoshipura@yahoo.co, E-mail: sumona_013@yahoo.co.i [GCET Engineering college, Sardar Patel University, Vallabh Vidyanagar - 388 120 (India)

    2009-11-01

    In this paper we have calculated various total cross-sections of Nitrogen, Phosphorus, Arsenic, Antimony and Bismuth (Group VA-atoms) in the energy range of 15 to 2000 eV. Spherical Complex potential formalism is used to derive total as well as inelastic cross-sections. We have developed CSP-ic method by which we can extract ionization cress-section from the inelastic cross-section. Our results are compared with available theoretical and experimental data.

  7. Myosin Va is developmentally regulated and expressed in the human cerebellum from birth to old age

    Directory of Open Access Journals (Sweden)

    C.C.R. Souza

    2013-02-01

    Full Text Available Myosin Va functions as a processive, actin-based motor molecule highly enriched in the nervous system, which transports and/or tethers organelles, vesicles, and mRNA and protein translation machinery. Mutation of myosin Va leads to Griscelli disease that is associated with severe neurological deficits and a short life span. Despite playing a critical role in development, the expression of myosin Va in the central nervous system throughout the human life span has not been reported. To address this issue, the cerebellar expression of myosin Va from newborns to elderly humans was studied by immunohistochemistry using an affinity-purified anti-myosin Va antibody. Myosin Va was expressed at all ages from the 10th postnatal day to the 98th year of life, in molecular, Purkinje and granular cerebellar layers. Cerebellar myosin Va expression did not differ essentially in localization or intensity from childhood to old age, except during the postnatal developmental period. Structures resembling granules and climbing fibers in Purkinje cells were deeply stained. In dentate neurons, long processes were deeply stained by anti-myosin Va, as were punctate nuclear structures. During the first postnatal year, myosin Va was differentially expressed in the external granular layer (EGL. In the EGL, proliferating prospective granule cells were not stained by anti-myosin Va antibody. In contrast, premigratory granule cells in the EGL stained moderately. Granule cells exhibiting a migratory profile in the molecular layer were also moderately stained. In conclusion, neuronal myosin Va is developmentally regulated, and appears to be required for cerebellar function from early postnatal life to senescence.

  8. Risk Capital and the Modification to VaR Capital Allocation Method%风险资本与VaR资本分配方法修正

    Institute of Scientific and Technical Information of China (English)

    张则斌; 黄智猛

    2000-01-01

    本文认为VaR资本分配方法由于没有考虑对债权人的利息补偿,可能严重低估风险(权益)资本的要求。我们引入Merton模型,对VaR资本分配方法进行了修正。

  9. Investigation of Microbial Diversity in Geothermal Hot Springs in Unkeshwar, India, Based on 16S rRNA Amplicon Metagenome Sequencing.

    Science.gov (United States)

    Mehetre, Gajanan T; Paranjpe, Aditi; Dastager, Syed G; Dharne, Mahesh S

    2016-02-25

    Microbial diversity in geothermal waters of the Unkeshwar hot springs in Maharashtra, India, was studied using 16S rRNA amplicon metagenomic sequencing. Taxonomic analysis revealed the presence of Bacteroidetes, Proteobacteria, Cyanobacteria, Actinobacteria, Archeae, and OD1 phyla. Metabolic function prediction analysis indicated a battery of biological information systems indicating rich and novel microbial diversity, with potential biotechnological applications in this niche.

  10. ‘Scientific’ nationalism : N-VA and the discursive battle for the Flemish nation

    NARCIS (Netherlands)

    Maly, Ico

    2015-01-01

    This paper investigates how the discursive battle for the Flemish nation is waged in the Flemish mass media by politicians of the Flemish nationalist party, the New Flemish Alliance (N-VA). I focus on the ‘new nationalism’ that N-VA politicians advocate as a means to ‘banalise’ a hot Flemish nationa

  11. 78 FR 28949 - Fund Availability Under VA's Homeless Providers Grant and Per Diem Program (Rehabilitation)

    Science.gov (United States)

    2013-05-16

    ... AFFAIRS Fund Availability Under VA's Homeless Providers Grant and Per Diem Program (Rehabilitation) AGENCY... announces the availability of rehabilitation funds under VA's Homeless Providers Grant and Per Diem Program... local or state codes. Each rehabilitation funded program will submit quarterly reports to the Grant...

  12. 48 CFR 852.219-9 - VA Small business subcontracting plan minimum requirements.

    Science.gov (United States)

    2010-10-01

    ... Provisions and Clauses 852.219-9 VA Small business subcontracting plan minimum requirements. As prescribed in subpart 819.709, insert the following clause: VA Small Business Subcontracting Plan Minimum Requirements... plan, the minimum goals for award of subcontracts to service-disabled veteran-owned small...

  13. 48 CFR 819.602-3 - Resolving differences between VA and the Small Business Administration.

    Science.gov (United States)

    2010-10-01

    ... between VA and the Small Business Administration. 819.602-3 Section 819.602-3 Federal Acquisition Regulations System DEPARTMENT OF VETERANS AFFAIRS SOCIOECONOMIC PROGRAMS SMALL BUSINESS PROGRAMS Certificates... Small Business Administration. The Director, OSDBU, is the VA liaison with the SBA. Information...

  14. 38 CFR 58.16 - VA Form 10-0144-Certification Regarding Lobbying.

    Science.gov (United States)

    2010-07-01

    ... 38 Pensions, Bonuses, and Veterans' Relief 2 2010-07-01 2010-07-01 false VA Form 10-0144-Certification Regarding Lobbying. 58.16 Section 58.16 Pensions, Bonuses, and Veterans' Relief DEPARTMENT OF VETERANS AFFAIRS (CONTINUED) FORMS § 58.16 VA Form 10-0144—Certification Regarding Lobbying. ER06JA00.013...

  15. 76 FR 1190 - Back Bay National Wildlife Refuge, City of Virginia Beach, VA; Final Comprehensive Conservation...

    Science.gov (United States)

    2011-01-07

    ... Fish and Wildlife Service Back Bay National Wildlife Refuge, City of Virginia Beach, VA; Final... National Wildlife Refuge (NWR). In this final CCP, we describe how we will manage this refuge for the next... CONTACT: Jared Brandwein, Refuge Manager, Back Bay NWR, 4005 Sandpiper Road, Virginia Beach, VA......

  16. 33 CFR 334.220 - Chesapeake Bay, south of Tangier Island, Va.; naval firing range.

    Science.gov (United States)

    2010-07-01

    ... Island, Va.; naval firing range. 334.220 Section 334.220 Navigation and Navigable Waters CORPS OF....220 Chesapeake Bay, south of Tangier Island, Va.; naval firing range. (a) The danger zone. Beginning... the range will be conducted intermittently by one or more vessels, depending on weather and...

  17. A Stochastic Dominance Approach to the Basel III Dilemma: Expected Shortfall or VaR?

    NARCIS (Netherlands)

    C-L. Chang (Chia-Lin); J.A. Jiménez-Martín (Juan-Ángel); E. Maasoumi (Esfandiar); M.J. McAleer (Michael); T. Pérez-Amaral (Teodosio)

    2015-01-01

    markdownabstract__Abstract__ The Basel Committee on Banking Supervision (BCBS) (2013) recently proposed shifting the quantitative risk metrics system from Value-at-Risk (VaR) to Expected Shortfall (ES). The BCBS (2013) noted that “a number of weaknesses have been identified with using VaR for deter

  18. 38 CFR 74.25 - What types of personally identifiable information will VA collect?

    Science.gov (United States)

    2010-07-01

    ... identifiable information will VA collect? 74.25 Section 74.25 Pensions, Bonuses, and Veterans' Relief... What types of personally identifiable information will VA collect? In order to establish owner eligibility, the Department will collect individual names and Social Security numbers for veterans,...

  19. 76 FR 40453 - Agency Information Collection (Application for VA Education Benefits) Activity Under OMB Review

    Science.gov (United States)

    2011-07-08

    ... any correspondence. FOR FURTHER INFORMATION CONTACT: Denise McLamb, Enterprise Records Service (005R1B... INFORMATION: Titles: a. Application for VA Education Benefits, VA Form 22-1990. b. Application for Family... of the Secretary. Denise McLamb, Program Analyst, Enterprise Records Service. BILLING CODE 8320-01-P...

  20. 75 FR 20774 - Establishment of Class E Airspace; Fort A.P. Hill, VA

    Science.gov (United States)

    2010-04-21

    ... Federal Aviation Administration 14 CFR Part 71 Establishment of Class E Airspace; Fort A.P. Hill, VA... Register December 7, 2009 that establishes Class E airspace at Fort A.P. Hill, VA. DATES: Effective Date..., Eastern Service Center, Federal Aviation Administration, P.O. Box 20636, Atlanta, Georgia 30320;...

  1. 77 FR 27120 - Safety Zone; Virginia Beach Oceanfront Air Show, Atlantic Ocean, Virginia Beach, VA

    Science.gov (United States)

    2012-05-09

    ..., Virginia Beach, VA in the Federal Register (76 FR 13519). We received one comment on the proposed rule. No... SECURITY Coast Guard 33 CFR Part 165 RIN 1625-AA00 Safety Zone; Virginia Beach Oceanfront Air Show, Atlantic Ocean, Virginia Beach, VA AGENCY: Coast Guard, DHS. ACTION: Temporary final rule. SUMMARY:...

  2. 78 FR 56151 - Safety Zone, North Atlantic Ocean; Virginia Beach, VA

    Science.gov (United States)

    2013-09-12

    ... SECURITY Coast Guard 33 CFR Part 165 RIN 1625-AA00 Safety Zone, North Atlantic Ocean; Virginia Beach, VA... zone on the navigable waters of the North Atlantic Ocean in Virginia Beach, VA to support the Virginia... Acronyms DHS Department of Homeland Security FR Federal Register NPRM Notice of Proposed Rulemaking...

  3. 78 FR 26250 - Payment for Home Health Services and Hospice Care to Non-VA Providers

    Science.gov (United States)

    2013-05-06

    ... AFFAIRS 38 CFR Part 17 RIN 2900-AN98 Payment for Home Health Services and Hospice Care to Non-VA Providers... services and hospice care. Because the newly applicable methodology cannot supersede rates for which VA has specifically contracted, this rulemaking will only affect home health and hospice care providers who do...

  4. 78 FR 51067 - VA Health Professional Scholarship and Visual Impairment and Orientation and Mobility...

    Science.gov (United States)

    2013-08-20

    ... AFFAIRS 38 CFR Part 17 RIN 2900-AO34 VA Health Professional Scholarship and Visual Impairment and Orientation and Mobility Professional Scholarship Programs AGENCY: Department of Veterans Affairs. ACTION... Scholarship Program (HPSP) regulations. VA is also establishing regulations for a new program, the...

  5. 76 FR 3017 - VA Veteran-Owned Small Business Verification Guidelines

    Science.gov (United States)

    2011-01-19

    ... to one business has no foundation in law and that there is no compelling reason to limit... AFFAIRS 38 CFR Part 74 RIN 2900-AM78 VA Veteran-Owned Small Business Verification Guidelines AGENCY..., and Information Technology Act of 2006. This law requires the Department of Veterans Affairs (VA)...

  6. 30 CFR 57.22605 - Blasting from the surface (V-A mines).

    Science.gov (United States)

    2010-07-01

    ... 30 Mineral Resources 1 2010-07-01 2010-07-01 false Blasting from the surface (V-A mines). 57.22605... Standards for Methane in Metal and Nonmetal Mines Explosives § 57.22605 Blasting from the surface (V-A mines). (a) All development and production blasting shall be initiated from the surface after all persons...

  7. Conformational determination of [Leu]enkephalin based on theoretical and experimental VA and VCD spectral analyses

    DEFF Research Database (Denmark)

    Abdali, Salim; Jalkanen, Karl J.; Cao, X.;

    2004-01-01

    Conformational determination of [Leu]enkephalin in DMSO-d6 is carried out using VA and VCD spectral analyses. Conformational energies, vibrational frequencies and VA and VCD intensities are calculated using DFT at B3LYP/6-31G* level of theory. Comparison between the measured spectra and the spect...

  8. VA Disability Benefits: Additional Planning Would Enhance Efforts to Improve the Timeliness of Appeals Decisions

    Science.gov (United States)

    2017-03-01

    accompanied by draft legislation for the Congress’ consideration . If enacted into law , the draft legislation would make process changes that...recent available) on appeals decision timeliness and workloads; reviewed relevant federal laws , regulations, and planning documents; and interviewed VA...matter for congressional consideration . VA should: apply sensitivity analyses when projecting staff needs, develop a more timely and detailed

  9. VA/DOD Federal Health Care Center: Costly Information Technology Delays Continue and Evaluation Plan Lacking

    Science.gov (United States)

    2012-06-01

    portability, which would allow VA and DOD clinicians to place, manage, and update clinical orders from either VA or DOD electronic health records systems...on, which includes five dedicated, full-time pharmacists to conduct manual checks of patient records to reconcile allergy information and identify

  10. 33 CFR 334.350 - Chesapeake Bay off Fort Monroe, Va.; firing range danger zone.

    Science.gov (United States)

    2010-07-01

    ..., Va.; firing range danger zone. 334.350 Section 334.350 Navigation and Navigable Waters CORPS OF ENGINEERS, DEPARTMENT OF THE ARMY, DEPARTMENT OF DEFENSE DANGER ZONE AND RESTRICTED AREA REGULATIONS § 334.350 Chesapeake Bay off Fort Monroe, Va.; firing range danger zone. (a) The danger zone. All of...

  11. 33 CFR 334.130 - Atlantic Ocean off Wallops Island and Chincoteague Inlet, Va.; danger zone.

    Science.gov (United States)

    2010-07-01

    ... and Chincoteague Inlet, Va.; danger zone. 334.130 Section 334.130 Navigation and Navigable Waters CORPS OF ENGINEERS, DEPARTMENT OF THE ARMY, DEPARTMENT OF DEFENSE DANGER ZONE AND RESTRICTED AREA REGULATIONS § 334.130 Atlantic Ocean off Wallops Island and Chincoteague Inlet, Va.; danger zone. (a) The...

  12. 76 FR 44288 - Establishment of Class E Airspace; New Market, VA

    Science.gov (United States)

    2011-07-25

    ... Federal Aviation Administration 14 CFR Part 71 Establishment of Class E Airspace; New Market, VA AGENCY... action proposes to establish Class E Airspace at New Market, VA, to accommodate the additional airspace needed for the Standard Instrument Approach Procedures developed for New Market Airport. This...

  13. 38 CFR 17.96 - Medication prescribed by non-VA physicians.

    Science.gov (United States)

    2010-07-01

    ... 38 Pensions, Bonuses, and Veterans' Relief 1 2010-07-01 2010-07-01 false Medication prescribed by non-VA physicians. 17.96 Section 17.96 Pensions, Bonuses, and Veterans' Relief DEPARTMENT OF VETERANS AFFAIRS MEDICAL Outpatient Treatment § 17.96 Medication prescribed by non-VA physicians. Any...

  14. 75 FR 9277 - Proposed Information Collection (VA National Rehabilitation Special Events, Event Registration...

    Science.gov (United States)

    2010-03-01

    ... techniques or the use of other forms of information technology. Titles: a. National Disabled Veterans Winter... . Please refer to ``OMB Control No. 2900-New (VA Form 0924)'' in any ] correspondence. During the comment... Form 0929--67 hours. OMB Control Number: 2900-New (VA Form 0924). Type of Review: Existing...

  15. Quantitative assessment of the effect of uracil-DNA glycosylase on amplicon DNA degradation and RNA amplification in reverse transcription-PCR

    Directory of Open Access Journals (Sweden)

    Kleiboeker Steven B

    2005-04-01

    Full Text Available Abstract Although PCR and RT-PCR provided a valuable approach for detection of pathogens, the high level of sensitivity of these assays also makes them prone to false positive results. In addition to cross-contamination with true positive samples, false positive results are also possible due to "carry-over" contamination of samples with amplicon DNA generated by previous reactions. To reduce this source of false positives, amplicon generated by reactions in which dUTP was substituted for dTTP can be degraded by uracil DNA glycosylase (UNG. UNG does not degrade RNA but will cleave contaminating uracil-containing DNA while leaving thymine-containing DNA intact. The availability of heat-labile UNG makes use of this approach feasible for RT-PCR. In this study, real-time RT-PCR was used to quantify UNG degradation of amplicon DNA and the effect of UNG on RNA detection. Using the manufacturers' recommended conditions, complete degradation of DNA was not observed for samples containing 250 copies of amplicon DNA. Doubling the UNG concentration resulted in degradation of the two lowest concentrations of DNA tested, but also resulted in an increase of 1.94 cycles in the CT for RNA detection. To improve DNA degradation while minimizing the effect on RNA detection, a series of time, temperature and enzyme concentrations were evaluated. Optimal conditions were found to be 0.25 U UNG per 25 μl reaction with a 20 min, 30°C incubation prior to RT-PCR. Under these conditions, high concentrations of amplicon DNA could be degraded while the CT for RNA detection was increased by 1.2 cycles.

  16. KAT6A, a Chromatin Modifier from the 8p11-p12 Amplicon is a Candidate Oncogene in Luminal Breast Cancer

    Directory of Open Access Journals (Sweden)

    Brittany Turner-Ivey

    2014-08-01

    Full Text Available The chromosome 8p11-p12 amplicon is present in 12% to 15% of breast cancers, resulting in an increase in copy number and expression of several chromatin modifiers in these tumors, including KAT6A. Previous analyses in SUM-52 breast cancer cells showed amplification and overexpression of KAT6A, and subsequent RNAi screening identified KAT6A as a potential driving oncogene. KAT6A is a histone acetyltransferase previously identified as a fusion partner with CREB binding protein in acute myeloid leukemia. Knockdown of KAT6A in SUM-52 cells, a luminal breast cancer cell line harboring the amplicon, resulted in reduced growth rate compared to non-silencing controls and profound loss of clonogenic capacity both in mono-layer and in soft agar. The normal cell line MCF10A, however, did not exhibit slower growth with knockdown of KAT6A. SUM-52 cells with KAT6A knockdown formed fewer mammospheres in culture compared to controls, suggesting a possible role for KAT6A in self-renewal. Previous data from our laboratory identified FGFR2 as a driving oncogene in SUM-52 cells. The colony forming efficiency of SUM-52 KAT6A knockdown cells in the presence of FGFR inhibition was significantly reduced compared to cells with KAT6A knockdown only. These data suggest that KAT6A may be a novel oncogene in breast cancers bearing the 8p11-p12 amplicon. While there are other putative oncogenes in the amplicon, the identification of KAT6A as a driving oncogene suggests that chromatin-modifying enzymes are a key class of oncogenes in these cancers, and play an important role in the selection of this amplicon in luminal B breast cancers.

  17. Empirical analysis on future-cash arbitrage risk with portfolio VaR

    Science.gov (United States)

    Chen, Rongda; Li, Cong; Wang, Weijin; Wang, Ze

    2014-03-01

    This paper constructs the positive arbitrage position by alternating the spot index with Chinese Exchange Traded Fund (ETF) portfolio and estimating the arbitrage-free interval of futures with the latest trade data. Then, an improved Delta-normal method was used, which replaces the simple linear correlation coefficient with tail dependence correlation coefficient, to measure VaR (Value-at-risk) of the arbitrage position. Analysis of VaR implies that the risk of future-cash arbitrage is less than that of investing completely in either futures or spot market. Then according to the compositional VaR and the marginal VaR, we should increase the futures position and decrease the spot position appropriately to minimize the VaR, which can minimize risk subject to certain revenues.

  18. VA Health Professional Scholarship and Visual Impairment and Orientation and Mobility Professional Scholarship Programs. Final rule.

    Science.gov (United States)

    2013-08-20

    The Department of Veterans Affairs (VA) is amending its VA Health Professional Scholarship Program (HPSP) regulations. VA is also establishing regulations for a new program, the Visual Impairment and Orientation and Mobility Professional Scholarship Program (VIOMPSP). These regulations comply with and implement sections 302 and 603 of the Caregivers and Veterans Omnibus Health Services Act of 2010 (the 2010 Act). Section 302 of the 2010 Act established the VIOMPSP, which authorizes VA to provide financial assistance to certain students seeking a degree in visual impairment or orientation or mobility, in order to increase the supply of qualified blind rehabilitation specialists for VA and the United States. Section 603 of the 2010 Act reauthorized and modified HPSP, a program that provides scholarships for education or training in certain health care occupations.

  19. Targeting the central nervous system with herpes simplex virus / Sleeping Beauty hybrid amplicon vectors.

    Science.gov (United States)

    de Silva, Suresh; Bowers, William J

    2011-10-01

    The pursuits of sustainable treatments for diseases and disorders that afflict the central nervous system (CNS) have proven challenging for the field of viral vector-based gene therapy. However, recent advances in viral vector technology coupled with efficient delivery methods have opened up new avenues that show promise at the preclinical testing stage. The development of the Herpes Simplex Virus/Sleeping Beauty (HSV/SB) hybrid vector represents such an advance for devising treatments targeting the CNS with its potential for stably integrating large transgenomic segments of DNA within the genomes of transduced cells. In utero administration of this hybrid vector into the embryonic mouse brain has revealed the capacity for widespread transgene dissemination due to the targeting of a neuronal precursor cell population. This unique feature has provided the means to stably express a transgene throughout the brain for prolonged periods, which is a prerequisite for the treatment of progressive CNS disorders. In this review we provide a comprehensive breakdown of the characteristics of the HSV/SB vector system and how it can be efficiently employed in the derivation of CNS-targeted gene therapeutic strategies.

  20. Identifying Homelessness among Veterans Using VA Administrative Data: Opportunities to Expand Detection Criteria.

    Science.gov (United States)

    Peterson, Rachel; Gundlapalli, Adi V; Metraux, Stephen; Carter, Marjorie E; Palmer, Miland; Redd, Andrew; Samore, Matthew H; Fargo, Jamison D

    2015-01-01

    Researchers at the U.S. Department of Veterans Affairs (VA) have used administrative criteria to identify homelessness among U.S. Veterans. Our objective was to explore the use of these codes in VA health care facilities. We examined VA health records (2002-2012) of Veterans recently separated from the military and identified as homeless using VA conventional identification criteria (ICD-9-CM code V60.0, VA specific codes for homeless services), plus closely allied V60 codes indicating housing instability. Logistic regression analyses examined differences between Veterans who received these codes. Health care services and co-morbidities were analyzed in the 90 days post-identification of homelessness. VA conventional criteria identified 21,021 homeless Veterans from Operations Enduring Freedom, Iraqi Freedom, and New Dawn (rate 2.5%). Adding allied V60 codes increased that to 31,260 (rate 3.3%). While certain demographic differences were noted, Veterans identified as homeless using conventional or allied codes were similar with regards to utilization of homeless, mental health, and substance abuse services, as well as co-morbidities. Differences were noted in the pattern of usage of homelessness-related diagnostic codes in VA facilities nation-wide. Creating an official VA case definition for homelessness, which would include additional ICD-9-CM and other administrative codes for VA homeless services, would likely allow improved identification of homeless and at-risk Veterans. This also presents an opportunity for encouraging uniformity in applying these codes in VA facilities nationwide as well as in other large health care organizations.

  1. 75 FR 26160 - Drug and Drug-Related Supply Promotion by Pharmaceutical Company Sales Representatives at VA...

    Science.gov (United States)

    2010-05-11

    ... Representatives at VA Facilities AGENCY: Department of Veterans Affairs. ACTION: Proposed rule; republication... a convenience to the public, instead of merely publishing a correction document, we are republishing... VA facilities, and provide sales representatives with a consistent standard of permissible...

  2. COPULA BASED VaR APPROACH FOR EUROPEAN STOCKS PORTFOLIO

    Directory of Open Access Journals (Sweden)

    Mária Bohdalová

    2013-06-01

    Full Text Available The paper gives stochastic assessments of the financial crisis and discusses the Value at Risk European stocks from the point of view of copula based approach. Copula techniques can be based on the connection between rank correlation and certain one–parameter bivariate copulas. This relation allows easy calibration of the parameters. We use more general numerical calibration techniques that are based on maximum likelihood estimation (MLE. Using this approach we want to estimate VaR of the EU stocks portfolio using Monte Carlo simulation. The focus will be on modelling the interdependence between two risk factor returns. We suppose that the risk factor returns have some assumed marginal distributions, which need not be identical, and their dependency is modelled with copulas. We find that standard parametric copula functions (such as Gaussian are not able to provide a good fit to the data. This is especially true when one or more of the marginal distributions has fat tails. We overcome this problem by fitting a t–copula with different marginal which can approximate any possible shape for the joint density.

  3. A molecular-beacon-based asymmetric PCR assay for easy visualization of amplicons in the diagnosis of trichomoniasis.

    Science.gov (United States)

    Sonkar, Subash C; Sachdev, Divya; Mishra, Prashant K; Kumar, Anita; Mittal, Pratima; Saluja, Daman

    2016-12-15

    The currently available nucleic acid amplification tests (NAATs) for trichomoniasis are accurate, quick and confirmative with superior sensitivity than traditional culture-based microbiology assays. However, these assays are associated with problems of carry over contamination, false positive results, requirement of technical expertise for performance and detection of end product. Hence, a diagnostic assay with easy visualization of the amplified product will be profitable. An in-house, rapid, sensitive, specific molecular-beacon-based PCR assay, using primers against pfoB gene of Trichomonas vaginalis, was developed and evaluated using dry ectocervical swabs (n=392) from symptomatic females with vaginal discharge. Total DNA was isolated and used as template for the PCR assays. The performance and reproducibility of PCR assay was evaluated by composite reference standard (CRS). For easy visualization of the amplified product, molecular-beacon was designed and amplicons were visualized directly using fluorescent handheld dark reader or by Micro-Plate Reader. Molecular-beacons are single-stranded hairpin shaped nucleic acid probes composed of a stem, with fluorophore/quencher pair and a loop region complementary to the desired DNA. The beacon-based PCR assay designed in the present study is highly specific as confirmed by competition experiments and extremely sensitive with detection limit of 20fg of genomic DNA (3-4 pathogens). The minimum infrastructure requirement and ease to perform the assay makes this method highly useful for resource poor countries for better disease management.

  4. Rhea: a transparent and modular R pipeline for microbial profiling based on 16S rRNA gene amplicons.

    Science.gov (United States)

    Lagkouvardos, Ilias; Fischer, Sandra; Kumar, Neeraj; Clavel, Thomas

    2017-01-01

    The importance of 16S rRNA gene amplicon profiles for understanding the influence of microbes in a variety of environments coupled with the steep reduction in sequencing costs led to a surge of microbial sequencing projects. The expanding crowd of scientists and clinicians wanting to make use of sequencing datasets can choose among a range of multipurpose software platforms, the use of which can be intimidating for non-expert users. Among available pipeline options for high-throughput 16S rRNA gene analysis, the R programming language and software environment for statistical computing stands out for its power and increased flexibility, and the possibility to adhere to most recent best practices and to adjust to individual project needs. Here we present the Rhea pipeline, a set of R scripts that encode a series of well-documented choices for the downstream analysis of Operational Taxonomic Units (OTUs) tables, including normalization steps, alpha- and beta-diversity analysis, taxonomic composition, statistical comparisons, and calculation of correlations. Rhea is primarily a straightforward starting point for beginners, but can also be a framework for advanced users who can modify and expand the tool. As the community standards evolve, Rhea will adapt to always represent the current state-of-the-art in microbial profiles analysis in the clear and comprehensive way allowed by the R language. Rhea scripts and documentation are freely available at https://lagkouvardos.github.io/Rhea.

  5. Rhea: a transparent and modular R pipeline for microbial profiling based on 16S rRNA gene amplicons

    Directory of Open Access Journals (Sweden)

    Ilias Lagkouvardos

    2017-01-01

    Full Text Available The importance of 16S rRNA gene amplicon profiles for understanding the influence of microbes in a variety of environments coupled with the steep reduction in sequencing costs led to a surge of microbial sequencing projects. The expanding crowd of scientists and clinicians wanting to make use of sequencing datasets can choose among a range of multipurpose software platforms, the use of which can be intimidating for non-expert users. Among available pipeline options for high-throughput 16S rRNA gene analysis, the R programming language and software environment for statistical computing stands out for its power and increased flexibility, and the possibility to adhere to most recent best practices and to adjust to individual project needs. Here we present the Rhea pipeline, a set of R scripts that encode a series of well-documented choices for the downstream analysis of Operational Taxonomic Units (OTUs tables, including normalization steps, alpha- and beta-diversity analysis, taxonomic composition, statistical comparisons, and calculation of correlations. Rhea is primarily a straightforward starting point for beginners, but can also be a framework for advanced users who can modify and expand the tool. As the community standards evolve, Rhea will adapt to always represent the current state-of-the-art in microbial profiles analysis in the clear and comprehensive way allowed by the R language. Rhea scripts and documentation are freely available at https://lagkouvardos.github.io/Rhea.

  6. Amplicon Resequencing Identified Parental Mosaicism for Approximately 10% of "de novo" SCN1A Mutations in Children with Dravet Syndrome.

    Science.gov (United States)

    Xu, Xiaojing; Yang, Xiaoxu; Wu, Qixi; Liu, Aijie; Yang, Xiaoling; Ye, Adam Yongxin; Huang, August Yue; Li, Jiarui; Wang, Meng; Yu, Zhe; Wang, Sheng; Zhang, Zhichao; Wu, Xiru; Wei, Liping; Zhang, Yuehua

    2015-09-01

    The majority of children with Dravet syndrome (DS) are caused by de novo SCN1A mutations. To investigate the origin of the mutations, we developed and applied a new method that combined deep amplicon resequencing with a Bayesian model to detect and quantify allelic fractions with improved sensitivity. Of 174 SCN1A mutations in DS probands which were considered "de novo" by Sanger sequencing, we identified 15 cases (8.6%) of parental mosaicism. We identified another five cases of parental mosaicism that were also detectable by Sanger sequencing. Fraction of mutant alleles in the 20 cases of parental mosaicism ranged from 1.1% to 32.6%. Thirteen (65% of 20) mutations originated paternally and seven (35% of 20) maternally. Twelve (60% of 20) mosaic parents did not have any epileptic symptoms. Their mutant allelic fractions were significantly lower than those in mosaic parents with epileptic symptoms (P = 0.016). We identified mosaicism with varied allelic fractions in blood, saliva, urine, hair follicle, oral epithelium, and semen, demonstrating that postzygotic mutations could affect multiple somatic cells as well as germ cells. Our results suggest that more sensitive tools for detecting low-level mosaicism in parents of families with seemingly "de novo" mutations will allow for better informed genetic counseling.

  7. Factors that affect large subunit ribosomal DNA amplicon sequencing studies of fungal communities: classification method, primer choice, and error.

    Directory of Open Access Journals (Sweden)

    Teresita M Porter

    Full Text Available Nuclear large subunit ribosomal DNA is widely used in fungal phylogenetics and to an increasing extent also amplicon-based environmental sequencing. The relatively short reads produced by next-generation sequencing, however, makes primer choice and sequence error important variables for obtaining accurate taxonomic classifications. In this simulation study we tested the performance of three classification methods: 1 a similarity-based method (BLAST + Metagenomic Analyzer, MEGAN; 2 a composition-based method (Ribosomal Database Project naïve bayesian classifier, NBC; and, 3 a phylogeny-based method (Statistical Assignment Package, SAP. We also tested the effects of sequence length, primer choice, and sequence error on classification accuracy and perceived community composition. Using a leave-one-out cross validation approach, results for classifications to the genus rank were as follows: BLAST + MEGAN had the lowest error rate and was particularly robust to sequence error; SAP accuracy was highest when long LSU query sequences were classified; and, NBC runs significantly faster than the other tested methods. All methods performed poorly with the shortest 50-100 bp sequences. Increasing simulated sequence error reduced classification accuracy. Community shifts were detected due to sequence error and primer selection even though there was no change in the underlying community composition. Short read datasets from individual primers, as well as pooled datasets, appear to only approximate the true community composition. We hope this work informs investigators of some of the factors that affect the quality and interpretation of their environmental gene surveys.

  8. A one-step real-time multiplex PCR for screening Y-chromosomal microdeletions without downstream amplicon size analysis.

    Directory of Open Access Journals (Sweden)

    Viviana Kozina

    Full Text Available BACKGROUND: Y-chromosomal microdeletions (YCMD are one of the major genetic causes for non-obstructive azoospermia. Genetic testing for YCMD by multiplex polymerase chain reaction (PCR is an established method for quick and robust screening of deletions in the AZF regions of the Y-chromosome. Multiplex PCRs have the advantage of including a control gene in every reaction and significantly reducing the number of reactions needed to screen the relevant genomic markers. PRINCIPAL FINDINGS: The widely established "EAA/EMQN best practice guidelines for molecular diagnosis of Y-chromosomal microdeletions (2004" were used as a basis for designing a real-time multiplex PCR system, in which the YCMD can simply be identified by their melting points. For this reason, some AZF primers were substituted by primers for regions in their genomic proximity, and the ZFX/ZFY control primer was exchanged by the AMELX/AMELY control primer. Furthermore, we substituted the classical SybrGreen I dye by the novel and high-performing DNA-binding dye EvaGreen™ and put substantial effort in titrating the primer combinations in respect to optimal melting peak separation and peak size. SIGNIFICANCE: With these changes, we were able to develop a platform-independent and robust real-time based multiplex PCR, which makes the need for amplicon identification by electrophoretic sizing expendable. By using an open-source system for real-time PCR analysis, we further demonstrate the applicability of automated melting point and YCMD detection.

  9. Amplicon-Based Pyrosequencing Reveals High Diversity of Protistan Parasites in Ships' Ballast Water: Implications for Biogeography and Infectious Diseases.

    Science.gov (United States)

    Pagenkopp Lohan, K M; Fleischer, R C; Carney, K J; Holzer, K K; Ruiz, G M

    2016-04-01

    Ships' ballast water (BW) commonly moves macroorganisms and microorganisms across the world's oceans and along coasts; however, the majority of these microbial transfers have gone undetected. We applied high-throughput sequencing methods to identify microbial eukaryotes, specifically emphasizing the protistan parasites, in ships' BW collected from vessels calling to the Chesapeake Bay (Virginia and Maryland, USA) from European and Eastern Canadian ports. We utilized tagged-amplicon 454 pyrosequencing with two general primer sets, amplifying either the V4 or V9 domain of the small subunit (SSU) of the ribosomal RNA (rRNA) gene complex, from total DNA extracted from water samples collected from the ballast tanks of bulk cargo vessels. We detected a diverse group of protistan taxa, with some known to contain important parasites in marine systems, including Apicomplexa (unidentified apicomplexans, unidentified gregarines, Cryptosporidium spp.), Dinophyta (Blastodinium spp., Euduboscquella sp., unidentified syndinids, Karlodinium spp., Syndinium spp.), Perkinsea (Parvilucifera sp.), Opisthokonta (Ichthyosporea sp., Pseudoperkinsidae, unidentified ichthyosporeans), and Stramenopiles (Labyrinthulomycetes). Further characterization of groups with parasitic taxa, consisting of phylogenetic analyses for four taxa (Cryptosporidium spp., Parvilucifera spp., Labyrinthulomycetes, and Ichthyosporea), revealed that sequences were obtained from both known and novel lineages. This study demonstrates that high-throughput sequencing is a viable and sensitive method for detecting parasitic protists when present and transported in the ballast water of ships. These data also underscore the potential importance of human-aided dispersal in the biogeography of these microbes and emerging diseases in the world's oceans.

  10. High-throughput amplicon sequencing and stream benthic bacteria: identifying the best taxonomic level for multiple-stressor research

    Science.gov (United States)

    Salis, R. K.; Bruder, A.; Piggott, J. J.; Summerfield, T. C.; Matthaei, C. D.

    2017-03-01

    Disentangling the individual and interactive effects of multiple stressors on microbial communities is a key challenge to our understanding and management of ecosystems. Advances in molecular techniques allow studying microbial communities in situ and with high taxonomic resolution. However, the taxonomic level which provides the best trade-off between our ability to detect multiple-stressor effects versus the goal of studying entire communities remains unknown. We used outdoor mesocosms simulating small streams to investigate the effects of four agricultural stressors (nutrient enrichment, the nitrification inhibitor dicyandiamide (DCD), fine sediment and flow velocity reduction) on stream bacteria (phyla, orders, genera, and species represented by Operational Taxonomic Units with 97% sequence similarity). Community composition was assessed using amplicon sequencing (16S rRNA gene, V3-V4 region). DCD was the most pervasive stressor, affecting evenness and most abundant taxa, followed by sediment and flow velocity. Stressor pervasiveness was similar across taxonomic levels and lower levels did not perform better in detecting stressor effects. Community coverage decreased from 96% of all sequences for abundant phyla to 28% for species. Order-level responses were generally representative of responses of corresponding genera and species, suggesting that this level may represent the best compromise between stressor sensitivity and coverage of bacterial communities.

  11. Metagenomic Analysis of Slovak Bryndza Cheese Using Next-Generation 16S rDNA Amplicon Sequencing

    Directory of Open Access Journals (Sweden)

    Planý Matej

    2016-06-01

    Full Text Available Knowledge about diversity and taxonomic structure of the microbial population present in traditional fermented foods plays a key role in starter culture selection, safety improvement and quality enhancement of the end product. Aim of this study was to investigate microbial consortia composition in Slovak bryndza cheese. For this purpose, we used culture-independent approach based on 16S rDNA amplicon sequencing using next generation sequencing platform. Results obtained by the analysis of three commercial (produced on industrial scale in winter season and one traditional (artisanal, most valued, produced in May Slovak bryndza cheese sample were compared. A diverse prokaryotic microflora composed mostly of the genera Lactococcus, Streptococcus, Lactobacillus, and Enterococcus was identified. Lactococcus lactis subsp. lactis and Lactococcus lactis subsp. cremoris were the dominant taxons in all tested samples. Second most abundant species, detected in all bryndza cheeses, were Lactococcus fujiensis and Lactococcus taiwanensis, independently by two different approaches, using different reference 16S rRNA genes databases (Greengenes and NCBI respectively. They have been detected in bryndza cheese samples in substantial amount for the first time. The narrowest microbial diversity was observed in a sample made with a starter culture from pasteurised milk. Metagenomic analysis by high-throughput sequencing using 16S rRNA genes seems to be a powerful tool for studying the structure of the microbial population in cheeses.

  12. Combined subtractive cDNA cloning and array CGH: an efficient approach for identification of overexpressed genes in DNA amplicons

    Directory of Open Access Journals (Sweden)

    De Paepe Anne

    2004-02-01

    Full Text Available Abstract Background Activation of proto-oncogenes by DNA amplification is an important mechanism in the development and maintenance of cancer cells. Until recently, identification of the targeted genes relied on labour intensive and time consuming positional cloning methods. In this study, we outline a straightforward and efficient strategy for fast and comprehensive cloning of amplified and overexpressed genes. Results As a proof of principle, we analyzed neuroblastoma cell line IMR-32, with at least two amplification sites along the short arm of chromosome 2. In a first step, overexpressed cDNA clones were isolated using a PCR based subtractive cloning method. Subsequent deposition of these clones on a custom microarray and hybridization with IMR-32 DNA, resulted in the identification of clones that were overexpressed due to gene amplification. Using this approach, amplification of all previously reported amplified genes in this cell line was detected. Furthermore, four additional clones were found to be amplified, including the TEM8 gene on 2p13.3, two anonymous transcripts, and a fusion transcript, resulting from 2p13.3 and 2p24.3 fused sequences. Conclusions The combinatorial strategy of subtractive cDNA cloning and array CGH analysis allows comprehensive amplicon dissection, which opens perspectives for improved identification of hitherto unknown targeted oncogenes in cancer cells.

  13. The molecular motor Myosin Va interacts with the cilia-centrosomal protein RPGRIP1L

    Science.gov (United States)

    Assis, L. H. P.; Silva-Junior, R. M. P.; Dolce, L. G.; Alborghetti, M. R.; Honorato, R. V.; Nascimento, A. F. Z.; Melo-Hanchuk, T. D.; Trindade, D. M.; Tonoli, C. C. C.; Santos, C. T.; Oliveira, P. S. L.; Larson, R. E.; Kobarg, J.; Espreafico, E. M.; Giuseppe, P. O.; Murakami, M. T.

    2017-01-01

    Myosin Va (MyoVa) is an actin-based molecular motor abundantly found at the centrosome. However, the role of MyoVa at this organelle has been elusive due to the lack of evidence on interacting partners or functional data. Herein, we combined yeast two-hybrid screen, biochemical studies and cellular assays to demonstrate that MyoVa interacts with RPGRIP1L, a cilia-centrosomal protein that controls ciliary signaling and positioning. MyoVa binds to the C2 domains of RPGRIP1L via residues located near or in the Rab11a-binding site, a conserved site in the globular tail domain (GTD) from class V myosins. According to proximity ligation assays, MyoVa and RPGRIP1L can interact near the cilium base in ciliated RPE cells. Furthermore, we showed that RPE cells expressing dominant-negative constructs of MyoVa are mostly unciliated, providing the first experimental evidence about a possible link between this molecular motor and cilia-related processes. PMID:28266547

  14. 38 CFR 17.1000 - Payment or reimbursement for emergency services for nonservice-connected conditions in non-VA...

    Science.gov (United States)

    2010-07-01

    ... for emergency services for nonservice-connected conditions in non-VA facilities. 17.1000 Section 17... Reimbursement for Emergency Services for Nonservice-Connected Conditions in Non-Va Facilities § 17.1000 Payment or reimbursement for emergency services for nonservice-connected conditions in non-VA...

  15. 76 FR 3209 - West Los Angeles VA Medical Center Veterans Programs Enhancement Act of 1998; Draft Master Plan

    Science.gov (United States)

    2011-01-19

    ... AFFAIRS West Los Angeles VA Medical Center Veterans Programs Enhancement Act of 1998; Draft Master Plan... an opportunity for public comment on the West Los Angeles (WLA) Department of Veterans Affairs (VA... is part of the larger VA Greater Los Angeles (GLA) Healthcare System, serving Veterans in Los...

  16. RAROC: Using CVaR and Using VaR%CVaR、VaR应用在RAROC的比较研究

    Institute of Scientific and Technical Information of China (English)

    方毅; 张屹山

    2007-01-01

    本文将CVaR引入到RAROC(Risk-Adjusted Return on Capital)中,进行绩效评价.而且,将CVaR与VaR的结果进行了比较.在正态分布的情况下,CVaR与VaR的RAPM(Risk-Adjusted Performance Measure)对于绩效评价都是充分的、可靠的、有效的,且两者是等价的.但在非正态的情况下,CVaR的RAPM相对于VaR的RAPM更加充分、谨慎、可靠、有效.我们运用Bootstrap方法进行了实证研究.

  17. Development of a control region-based mtDNA SNaPshot™ selection tool, integrated into a mini amplicon sequencing method.

    Science.gov (United States)

    Weiler, Natalie E C; de Vries, Gerda; Sijen, Titia

    2016-03-01

    Mitochondrial DNA (mtDNA) analysis is regularly applied to forensic DNA samples with limited amounts of nuclear DNA (nDNA), such as hair shafts and bones. Generally, this mtDNA analysis involves examination of the hypervariable control region by Sanger sequencing of amplified products. When samples are severely degraded, small-sized amplicons can be applied and an earlier described mini-mtDNA method by Eichmann et al. [1] that accommodates ten mini amplicons in two multiplexes is found to be a very robust approach. However, in cases with large numbers of samples, like when searching for hairs with an mtDNA profile deviant from that of the victim, the method is time (and cost) consuming. Previously, Chemale et al. [2] described a SNaPshot™-based screening tool for a Brazilian population that uses standard-size amplicons for HVS-I and HVS-II. Here, we describe a similar tool adapted to the full control region and compatible with mini-mtDNA amplicons. Eighteen single nucleotide polymorphisms (SNPs) were selected based on their relative frequencies in a European population. They showed a high discriminatory power in a Dutch population (97.2%). The 18 SNPs are assessed in two SNaPshot™ multiplexes that pair to the two mini-mtDNA amplification multiplexes. Degenerate bases are included to limit allele dropout due to SNPs at primer binding site positions. Three SNPs provide haplogroup information. Reliability testing showed no differences with Sanger sequencing results. Since mini-mtSNaPshot screening uses only a small portion of the same PCR products used for Sanger sequencing, no additional DNA extract is consumed, which is forensically advantageous.

  18. FasL and FADD delivery by a glioma-specific and cell cycle-dependent HSV-1 amplicon virus enhanced apoptosis in primary human brain tumors

    Directory of Open Access Journals (Sweden)

    Lam Paula Y

    2010-10-01

    Full Text Available Abstract Background Glioblastoma multiforme is the most malignant cancer of the brain and is notoriously difficult to treat due to the highly proliferative and infiltrative nature of the cells. Herein, we explored the combination treatment of pre-established human glioma xenograft using multiple therapeutic genes whereby the gene expression is regulated by both cell-type and cell cycle-dependent transcriptional regulatory mechanism conferred by recombinant HSV-1 amplicon vectors. Results We demonstrated for the first time that Ki67-positive proliferating primary human glioma cells cultured from biopsy samples were effectively induced into cell death by the dual-specific function of the pG8-FasL amplicon vectors. These vectors were relatively stable and exhibited minimal cytotoxicity in vivo. Intracranial implantation of pre-transduced glioma cells resulted in better survival outcome when compared with viral vectors inoculated one week post-implantation of tumor cells, indicating that therapeutic efficacy is dependent on the viral spread and mode of viral vectors administration. We further showed that pG8-FasL amplicon vectors are functional in the presence of commonly used treatment regimens for human brain cancer. In fact, the combined therapies of pG8-FasL and pG8-FADD in the presence of temozolomide significantly improved the survival of mice bearing intracranial high-grade gliomas. Conclusion Taken together, our results showed that the glioma-specific and cell cycle-dependent HSV-1 amplicon vector is potentially useful as an adjuvant therapy to complement the current gene therapy strategy for gliomas.

  19. Amplicon-dependent CCNE1 expression is critical for clonogenic survival after cisplatin treatment and is correlated with 20q11 gain in ovarian cancer.

    Directory of Open Access Journals (Sweden)

    Dariush Etemadmoghadam

    Full Text Available Genomic amplification of 19q12 occurs in several cancer types including ovarian cancer where it is associated with primary treatment failure. We systematically attenuated expression of genes within the minimally defined 19q12 region in ovarian cell lines using short-interfering RNAs (siRNA to identify driver oncogene(s within the amplicon. Knockdown of CCNE1 resulted in G1/S phase arrest, reduced cell viability and apoptosis only in amplification-carrying cells. Although CCNE1 knockdown increased cisplatin resistance in short-term assays, clonogenic survival was inhibited after treatment. Gain of 20q11 was highly correlated with 19q12 amplification and spanned a 2.5 Mb region including TPX2, a centromeric protein required for mitotic spindle function. Expression of TPX2 was highly correlated with gene amplification and with CCNE1 expression in primary tumors. siRNA inhibition of TPX2 reduced cell viability but this effect was not amplicon-dependent. These findings demonstrate that CCNE1 is a key driver in the 19q12 amplicon required for survival and clonogenicity in cells with locus amplification. Co-amplification at 19q12 and 20q11 implies the presence of a cooperative mutational network. These observations have implications for the application of targeted therapies in CCNE1 dependent ovarian cancers.

  20. Amplicon-dependent CCNE1 expression is critical for clonogenic survival after cisplatin treatment and is correlated with 20q11 gain in ovarian cancer.

    Science.gov (United States)

    Etemadmoghadam, Dariush; George, Joshy; Cowin, Prue A; Cullinane, Carleen; Kansara, Maya; Gorringe, Kylie L; Smyth, Gordon K; Bowtell, David D L

    2010-11-12

    Genomic amplification of 19q12 occurs in several cancer types including ovarian cancer where it is associated with primary treatment failure. We systematically attenuated expression of genes within the minimally defined 19q12 region in ovarian cell lines using short-interfering RNAs (siRNA) to identify driver oncogene(s) within the amplicon. Knockdown of CCNE1 resulted in G1/S phase arrest, reduced cell viability and apoptosis only in amplification-carrying cells. Although CCNE1 knockdown increased cisplatin resistance in short-term assays, clonogenic survival was inhibited after treatment. Gain of 20q11 was highly correlated with 19q12 amplification and spanned a 2.5 Mb region including TPX2, a centromeric protein required for mitotic spindle function. Expression of TPX2 was highly correlated with gene amplification and with CCNE1 expression in primary tumors. siRNA inhibition of TPX2 reduced cell viability but this effect was not amplicon-dependent. These findings demonstrate that CCNE1 is a key driver in the 19q12 amplicon required for survival and clonogenicity in cells with locus amplification. Co-amplification at 19q12 and 20q11 implies the presence of a cooperative mutational network. These observations have implications for the application of targeted therapies in CCNE1 dependent ovarian cancers.

  1. Microbial diversity of a full-scale UASB reactor applied to poultry slaughterhouse wastewater treatment: integration of 16S rRNA gene amplicon and shotgun metagenomic sequencing.

    Science.gov (United States)

    Delforno, Tiago Palladino; Lacerda Júnior, Gileno Vieira; Noronha, Melline F; Sakamoto, Isabel K; Varesche, Maria Bernadete A; Oliveira, Valéria M

    2017-02-23

    The 16S rRNA gene amplicon and whole-genome shotgun metagenomic (WGSM) sequencing approaches were used to investigate wide-spectrum profiles of microbial composition and metabolic diversity from a full-scale UASB reactor applied to poultry slaughterhouse wastewater treatment. The data were generated by using MiSeq 2 × 250 bp and HiSeq 2 × 150 bp Illumina sequencing platforms for 16S amplicon and WGSM sequencing, respectively. Each approach revealed a distinct microbial community profile, with Pseudomonas and Psychrobacter as predominant genus for the WGSM dataset and Clostridium and Methanosaeta for the 16S rRNA gene amplicon dataset. The virome characterization revealed the presence of two viral families with Bacteria and Archaea as host, Myoviridae, and Siphoviridae. A wide functional diversity was found with predominance of genes involved in the metabolism of acetone, butanol, and ethanol synthesis; and one-carbon metabolism (e.g., methanogenesis). Genes related to the acetotrophic methanogenesis pathways were more abundant than methylotrophic and hydrogenotrophic, corroborating the taxonomic results that showed the prevalence of the acetotrophic genus Methanosaeta. Moreover, the dataset indicated a variety of metabolic genes involved in sulfur, nitrogen, iron, and phosphorus cycles, with many genera able to act in all cycles. BLAST analysis against Antibiotic Resistance Genes Database (ARDB) revealed that microbial community contained 43 different types of antibiotic resistance genes, some of them were associated with growth chicken promotion (e.g., bacitracin, tetracycline, and polymyxin).

  2. Amplicon-based profiling of bacteria in raw and secondary treated wastewater from treatment plants across Australia.

    Science.gov (United States)

    Ahmed, Warish; Staley, Christopher; Sidhu, Jatinder; Sadowsky, Michael; Toze, Simon

    2017-02-01

    In this study, we investigated the use of Illumina high-throughput sequencing of 16S ribosomal RNA (rRNA) amplicons to explore microbial diversity and community structure in raw and secondary treated wastewater (WW) samples from four municipal wastewater treatment plants (WWTPs A-D) across Australia. Sequence reads were analyzed to determine the abundance and diversity of bacterial communities in raw and secondary treated WW samples across the four WWTPs. In addition, sequence reads were also characterized to phenotypic features and to estimate the abundance of potential pathogenic bacterial genera and antibiotic-resistant genes in total bacterial communities. The mean coverage, Shannon diversity index, observed richness (S obs), and abundance-based coverage estimate (ACE) of richness for raw and secondary treated WW samples did not differ significantly (P > 0.05) among the four WWTPs examined. Generally, raw and secondary treated WW samples were dominated by members of the genera Pseudomonas, Arcobacter, and Bacteroides. Evaluation of source contributions to secondary treated WW, done using SourceTracker, revealed that 8.80-61.4% of the bacterial communities in secondary treated WW samples were attributed to raw WW. Twenty-five bacterial genera were classified as containing potential bacterial pathogens. The abundance of potentially pathogenic genera in raw WW samples was higher than that found in secondary treated WW samples. Among the pathogenic genera identified, Pseudomonas and Arcobacter had the greatest percentage of the sequence reads. The abundances of antibiotic resistance genes were generally low (treated WW samples from four WWTPs across Australia and demonstrated that Illumina high-throughput sequencing can be an alternative approach for monitoring WW quality in order to protect environmental and human health.

  3. Uncultured bacterial diversity in a seawater recirculating aquaculture system revealed by 16S rRNA gene amplicon sequencing.

    Science.gov (United States)

    Lee, Da-Eun; Lee, Jinhwan; Kim, Young-Mog; Myeong, Jeong-In; Kim, Kyoung-Ho

    2016-04-01

    Bacterial diversity in a seawater recirculating aquaculture system (RAS) was investigated using 16S rRNA amplicon sequencing to understand the roles of bacterial communities in the system. The RAS was operated at nine different combinations of temperature (15°C, 20°C, and 25°C) and salinity (20‰, 25‰, and 32.5‰). Samples were collected from five or six RAS tanks (biofilters) for each condition. Fifty samples were analyzed. Proteobacteria and Bacteroidetes were most common (sum of both phyla: 67.2% to 99.4%) and were inversely proportional to each other. Bacteria that were present at an average of ≥ 1% included Actinobacteria (2.9%) Planctomycetes (2.0%), Nitrospirae (1.5%), and Acidobacteria (1.0%); they were preferentially present in packed bed biofilters, mesh biofilters, and maturation biofilters. The three biofilters showed higher diversity than other RAS tanks (aerated biofilters, floating bed biofilters, and fish tanks) from phylum to operational taxonomic unit (OTU) level. Samples were clustered into several groups based on the bacterial communities. Major taxonomic groups related to family Rhodobacteraceae and Flavobacteriaceae were distributed widely in the samples. Several taxonomic groups like [Saprospiraceae], Cytophagaceae, Octadecabacter, and Marivita showed a cluster-oriented distribution. Phaeobacter and Sediminicola-related reads were detected frequently and abundantly at low temperature. Nitrifying bacteria were detected frequently and abundantly in the three biofilters. Phylogenetic analysis of the nitrifying bacteria showed several similar OTUs were observed widely through the biofilters. The diverse bacterial communities and the minor taxonomic groups, except for Proteobacteria and Bacteroidetes, seemed to play important roles and seemed necessary for nitrifying activity in the RAS, especially in packed bed biofilters, mesh biofilters, and maturation biofilters.

  4. Nuclear species-diagnostic SNP markers mined from 454 amplicon sequencing reveal admixture genomic structure of modern citrus varieties.

    Science.gov (United States)

    Curk, Franck; Ancillo, Gema; Ollitrault, Frédérique; Perrier, Xavier; Jacquemoud-Collet, Jean-Pierre; Garcia-Lor, Andres; Navarro, Luis; Ollitrault, Patrick

    2015-01-01

    Most cultivated Citrus species originated from interspecific hybridisation between four ancestral taxa (C. reticulata, C. maxima, C. medica, and C. micrantha) with limited further interspecific recombination due to vegetative propagation. This evolution resulted in admixture genomes with frequent interspecific heterozygosity. Moreover, a major part of the phenotypic diversity of edible citrus results from the initial differentiation between these taxa. Deciphering the phylogenomic structure of citrus germplasm is therefore essential for an efficient utilization of citrus biodiversity in breeding schemes. The objective of this work was to develop a set of species-diagnostic single nucleotide polymorphism (SNP) markers for the four Citrus ancestral taxa covering the nine chromosomes, and to use these markers to infer the phylogenomic structure of secondary species and modern cultivars. Species-diagnostic SNPs were mined from 454 amplicon sequencing of 57 gene fragments from 26 genotypes of the four basic taxa. Of the 1,053 SNPs mined from 28,507 kb sequence, 273 were found to be highly diagnostic for a single basic taxon. Species-diagnostic SNP markers (105) were used to analyse the admixture structure of varieties and rootstocks. This revealed C. maxima introgressions in most of the old and in all recent selections of mandarins, and suggested that C. reticulata × C. maxima reticulation and introgression processes were important in edible mandarin domestication. The large range of phylogenomic constitutions between C. reticulata and C. maxima revealed in mandarins, tangelos, tangors, sweet oranges, sour oranges, grapefruits, and orangelos is favourable for genetic association studies based on phylogenomic structures of the germplasm. Inferred admixture structures were in agreement with previous hypotheses regarding the origin of several secondary species and also revealed the probable origin of several acid citrus varieties. The developed species-diagnostic SNP

  5. Classification of pmoA amplicon pyrosequences using BLAST and the lowest common ancestor method in MEGAN

    Directory of Open Access Journals (Sweden)

    Marc Gregory Dumont

    2014-02-01

    Full Text Available The classification of high-throughput sequencing data of protein-encoding genes is not as well established as for 16S rRNA. The objective of this work was to develop a simple and accurate method of classifying large datasets of pmoA sequences, a common marker for methanotrophic bacteria. A taxonomic system for pmoA was developed based on a phylogenetic analysis of available sequences. The taxonomy incorporates the known diversity of pmoA present in public databases, including both sequences from cultivated and uncultivated organisms. Representative sequences from closely related genes, such as those encoding the bacterial ammonia monooxygenase, were also included in the pmoA taxonomy. In total, 53 low-level taxa (genus-level are included. Using previously published datasets of high-throughput pmoA amplicon sequence data, we tested two approaches for classifying pmoA: a naïve Bayesian classifier and BLAST. Classification of pmoA sequences based on BLAST analyses was performed using the lowest common ancestor (LCA algorithm in MEGAN, a software program commonly used for the analysis of metagenomic data. Both the naïve Bayesian and BLAST methods were able to classify pmoA sequences and provided similar classifications; however, the naïve Bayesian classifier was prone to misclassifying contaminant sequences present in the datasets. Another advantage of the BLAST/LCA method was that it provided a user-interpretable output and enabled novelty detection at various levels, from highly divergent pmoA sequences to genus-level novelty.  

  6. Amplicon-based taxonomic characterization of bacteria in urban and peri-urban roof-harvested rainwater stored in tanks.

    Science.gov (United States)

    Ahmed, W; Staley, C; Hamilton, K A; Beale, D J; Sadowsky, M J; Toze, S; Haas, C N

    2017-01-15

    Overall, 26% of Australian households use rainwater tanks as a source of potable and nonpotable water. Limited information is available on the total bacterial communities in tank water. Therefore, identification of dominant bacterial communities, diversity, and their distribution is important in understanding the microbial quality of tank water. In this study, the abundance and diversity of bacterial communities in 88 tank water samples collected from the urban areas of Brisbane (n=44) and the peri-urban center of Currumbin (n=44) in Southeast Queensland, Australia were determined using amplicon-based Illumina next-generation sequencing. In addition, the SourceTracker program was used to identify the sources of fecal contamination in tank water samples. Sequence reads were also analyzed to detect potential bacterial pathogenic genera in the tank water samples collected. Differences in sample coverage, alpha diversity, and richness did not differ significantly between the Brisbane and Currumbin tank water samples. Comamonadaceae and Planctomycetaceae were the most abundant families in all tank water samples. Curvibacter was the most abundant genus in all tank water samples. SourceTracker revealed that around 34% (Brisbane) and 43% (Currumbin) of tank water samples had a signature for bird fecal contamination. The potential opportunistic pathogenic genera including Burkholderia, Chromobacterium, Clostridium, Legionella, Mycobacterium, Nocardia, and Pseudomonas were most prevalent in tank water samples. Next-generation sequencing can be used as an initial screening tool to identify a wide array of potential pathogenic genera in tank water samples followed by quantifying specific pathogen(s) of interest using more sensitive molecular assays such as quantitative PCR (qPCR).

  7. Responses of soil microeukaryotic communities to short-term fumigation-incubation revealed by MiSeq amplicon sequencing

    Directory of Open Access Journals (Sweden)

    Lin eChen

    2015-10-01

    Full Text Available In soil microbiology, there is a ‘paradox’ of soil organic carbon (SOC mineralization, which is that even though chloroform fumigation destroys majority of the soil microbial biomass, SOC mineralization continues at the same rate as in the non-fumigated soil during the incubation period. Soil microeukaryotes as important SOC decomposers, however, their community-level responses to chloroform fumigation are not well understood. Using the 18S rRNA gene amplicon sequencing, we analyzed the composition, diversity and C-metabolic functions of a grassland soil and an arable soil microeukaryotic community in response to fumigation followed by a 30-day incubation. The grassland and arable soil microeukaryotic communities were dominated by the fungal Ascomycota (80.5–93.1% of the fungal sequences, followed by the protistan Cercozoa and Apicomplexa. In the arable soil fungal community, the predominance of the class Sordariomycetes was replaced by the class Eurotiomycetes after fumigation at days 7 and 30 of the incubation. Fumigation changed the microeukaryotic α-diversity in the grassland soil at days 0 and 7, and β-diversity in the arable soil at days 7 and 30. Network analysis indicated that after fumigation fungi were important groups closely related to other taxa. Most phylotypes (especially Sordariomycetes, Dothideomycetes, Coccidia and uncultured Chytridiomycota were inhibited, and only a few were positively stimulated by fumigation. Despite the inhibited Sordariomycetes, the fumigated communities mainly consisted of Eurotiomycetes and Sordariomycetes (21.9% and 36.5% relative frequency, respectively, which are able to produce hydrolytic enzymes associated with SOC mineralization. Our study suggests that fumigation not only decreases biomass size, but modulates the composition and diversity of the soil microeukaryotic communities, which are capable of driving SOC mineralization by release of hydrolytic enzymes during short-term fumigation-incubation.

  8. Influence of PVP/VA copolymer composition on drug-polymer solubility

    DEFF Research Database (Denmark)

    Rask, Malte Bille; Knopp, Matthias Manne; Olesen, Niels Erik

    2016-01-01

    In this study, the influence of copolymer composition on drug-polymer solubility was investigated. The solubility of the model drug celecoxib (CCX) in various polyvinylpyrrolidone/vinyl acetate (PVP/VA) copolymer compositions (70/30, 60/40, 50/50 and 30/70 w/w) and the pure homopolymers...... polyvinylpyrrolidone (PVP) and polyvinyl acetate (PVA) was predicted at 25 °C using a thermal analysis method based on the recrystallization of a supersaturated amorphous dispersion (recrystallization method). These solubilities were compared with a prediction based on the solubility of CCX in the liquid monomeric...... precursors of PVP/VA, N-vinylpyrrolidone (NVP) and vinyl acetate (VA), using the Flory-Huggins lattice theory (liquid monomer solubility approach). The solubilities predicted from the liquid monomer solubility approach increased linearly with increasing VP/VA ratio from 0.03-0.60 w/w. Even though...

  9. Activating Ras mutations fail to ensure efficient replication of adenovirus mutants lacking VA-RNA

    DEFF Research Database (Denmark)

    Schümann, Michael; Dobbelstein, Matthias

    2006-01-01

    Adenoviruses lacking their PKR-antagonizing VA RNAs replicate poorly in primary cells. It has been suggested that these virus recombinants still replicate efficiently in tumor cells with Ras mutations and might therefore be useful in tumor therapy. The ability of interferon-sensitive viruses...... to grow in Ras-mutant tumor cells is generally ascribed to a postulated inhibitory effect of mutant Ras on PKR. We have constructed a set of isogenic adenoviruses that lack either or both VA RNA species, and tested virus replication in a variety of cell species with different Ras status. In tendency, VA...... mutational status, upon infection with VA-less adenoviruses in the presence of interferon, but also upon addition of the PKR activator polyIC to cells. When comparing two isogenic cell lines that differ solely with regard to the presence or absence of mutant Ras, no difference was observed concerning...

  10. 77 FR 12647 - Fund Availability Under VA's Homeless Providers Grant and Per Diem Program

    Science.gov (United States)

    2012-03-01

    ... than 4 p.m. Eastern Time on Wednesday, May 30, 2012. FOR FURTHER INFORMATION CONTACT: Chelsea Watson... program monitoring and evaluation system. It is the intent of VA to develop specific performance...

  11. 77 FR 47433 - Presquile National Wildlife Refuge, Chesterfield County, VA; Comprehensive Conservation Plan and...

    Science.gov (United States)

    2012-08-08

    ... Fish and Wildlife Service Presquile National Wildlife Refuge, Chesterfield County, VA; Comprehensive Conservation Plan and Environmental Assessment AGENCY: Fish and Wildlife Service, Interior. ACTION: Notice of..., consistent with sound principles of fish and wildlife management conservation, legal mandates, and...

  12. 77 FR 70212 - Agency Information Collection Activities Under OMB Review: VA MATIC Enrollment/Change

    Science.gov (United States)

    2012-11-23

    ... MATIC or change their financial institution from which VA currently deducts his/her Government Life Insurance premium. An agency may not conduct or sponsor, and a person is not required to respond to...

  13. VA Health Care: Improved Monitoring Needed for Effective Oversight of Care for Women Veterans

    Science.gov (United States)

    2016-12-01

    Congressional Requesters December 2016 GAO-17-52 United States Government Accountability Office United States Government Accountability Office...2VA health care systems are made up of multiple VAMCs. Established under the Veterans Access, Choice, and Accountability Act of 2014, Choice...on VA’s Provision of Health Care Services to Women Veterans, GAO-09-884T (Washington, D.C.: July 14, 2009) and VA Health Care: Preliminary Findings

  14. Veterans Justice Outreach Program: VA Could Improve Management by Establishing Performance Measures and Fully Assessing Risks

    Science.gov (United States)

    2016-04-01

    the Computerized Patient Record System. Once the veteran’s information is entered into VA’s databases, it is accessible to other VA clinicians... Computerized Patient Record System, which contains the medical records of veterans that VA is serving. Appendix I: Objectives, Scope, and...MasterCard, Visa, check, or money order. Call for additional information. Connect with GAO on Facebook , Flickr, Twitter, and YouTube. Subscribe to our RSS

  15. Report on the evaluation of the VA/Seattle below-knee prosthesis.

    Science.gov (United States)

    Ellepola, W; Sheredos, S J

    1993-01-01

    The Department of Veterans Affairs (VA), Rehabilitation Research and Development (Rehab R&D) Service, Technology Transfer Section (TTS) with collaboration from the Prosthetic and Sensory Aids Service (PSAS) managed clinical trials to evaluate the VA/Seattle Below-Knee (BK) Prosthetic System. The clinical trials were held at the Prosthetic Treatment Center (PTC), VA Medical Center, Hines, Illinois. Five other VA medical centers participated in the outreach program of the trials as satellite stations, with PTC Hines as the central fabrication facility. The VA/Seattle BK system is the first complete prosthetic system designed and developed by the Department of Veterans Affairs. It consists of a socket designed and fabricated using computer-aided, automated technology, and off-the-shelf modular components: a lightweight pylon and an ankle unit, and a lightweight, energy-storing foot. The computer-based socket design software, the modular components, and the prosthetic foot were developed with funds from the VA Rehab R&D Service. The evaluation trials were conducted to determine the efficacy of the VA/Seattle prosthesis, its reliability, and acceptance by veterans. The clinical trials began in April 1991 and were completed in August 1992. Forty-six BK amputee veterans were fitted with the VA/Seattle prosthesis. Their progress with the prosthesis was followed for a period of 6 months and data were gathered at intervals of 2 weeks, 3 months, and 6 months. Forty sets of subject data instruments were collected. In order to maintain the accuracy of the results, TTS used the 22 sets that were complete for data analysis.(ABSTRACT TRUNCATED AT 250 WORDS)

  16. CITY OF RADFORD TERRAIN, CITY OF RADFORD, VA, USA

    Data.gov (United States)

    Federal Emergency Management Agency, Department of Homeland Security — Terrain data includes digital elevation models, LIDAR derived contours, LIDAR three-dimensional spot elevations and breaklines, field surveyed ground elevations and...

  17. 金融风险管理的VaR方法及其应用

    Institute of Scientific and Technical Information of China (English)

    何弟

    2012-01-01

    近年来,巴林银行、长期资本管理公司等一系列因承担市场风险而发生巨额损失甚至倒闭的案例,使得无论金融机构还是监管当局都日益重视对市场风险的管理.与传统风险测量技术相比,VaR模型体现了更大地适应性和科学性,并且已得到大多数金融机构的认可.文章主要对VaR模型的概念、VaR模型的计算方法和VaR模型的应用进行了介绍,并借助于Excel、Matlab、SAS等软件,通过实例,详细介绍了VaR模型的两种计算方法,即历史模拟法和蒙特卡罗模拟法;另外,也借助该实例,阐述了VaR模型在风险度量和业绩评价中的实际运用.

  18. PERHITUNGAN VaR PORTOFOLIO SAHAM MENGGUNAKAN DATA HISTORIS DAN DATA SIMULASI MONTE CARLO

    Directory of Open Access Journals (Sweden)

    WAYAN ARTHINI

    2012-09-01

    Full Text Available Value at Risk (VaR is the maximum potential loss on a portfolio based on the probability at a certain time.  In this research, portfolio VaR values calculated from historical data and Monte Carlo simulation data. Historical data is processed so as to obtain stock returns, variance, correlation coefficient, and variance-covariance matrix, then the method of Markowitz sought proportion of each stock fund, and portfolio risk and return portfolio. The data was then simulated by Monte Carlo simulation, Exact Monte Carlo Simulation and Expected Monte Carlo Simulation. Exact Monte Carlo simulation have same returns and standard deviation  with historical data, while the Expected Monte Carlo Simulation satistic calculation similar to historical data. The results of this research is the portfolio VaR  with time horizon T=1, T=10, T=22 and the confidence level of 95 %, values obtained VaR between historical data and Monte Carlo simulation data with the method exact and expected. Value of VaR from both Monte Carlo simulation is greater than VaR historical data.

  19. VaRank: a simple and powerful tool for ranking genetic variants

    Directory of Open Access Journals (Sweden)

    Véronique Geoffroy

    2015-03-01

    Full Text Available Background. Most genetic disorders are caused by single nucleotide variations (SNVs or small insertion/deletions (indels. High throughput sequencing has broadened the catalogue of human variation, including common polymorphisms, rare variations or disease causing mutations. However, identifying one variation among hundreds or thousands of others is still a complex task for biologists, geneticists and clinicians. Results. We have developed VaRank, a command-line tool for the ranking of genetic variants detected by high-throughput sequencing. VaRank scores and prioritizes variants annotated either by Alamut Batch or SnpEff. A barcode allows users to quickly view the presence/absence of variants (with homozygote/heterozygote status in analyzed samples. VaRank supports the commonly used VCF input format for variants analysis thus allowing it to be easily integrated into NGS bioinformatics analysis pipelines. VaRank has been successfully applied to disease-gene identification as well as to molecular diagnostics setup for several hundred patients. Conclusions. VaRank is implemented in Tcl/Tk, a scripting language which is platform-independent but has been tested only on Unix environment. The source code is available under the GNU GPL, and together with sample data and detailed documentation can be downloaded from http://www.lbgi.fr/VaRank/.

  20. Semi-nonparametric VaR forecasts for hedge funds during the recent crisis

    Science.gov (United States)

    Del Brio, Esther B.; Mora-Valencia, Andrés; Perote, Javier

    2014-05-01

    The need to provide accurate value-at-risk (VaR) forecasting measures has triggered an important literature in econophysics. Although these accurate VaR models and methodologies are particularly demanded for hedge fund managers, there exist few articles specifically devoted to implement new techniques in hedge fund returns VaR forecasting. This article advances in these issues by comparing the performance of risk measures based on parametric distributions (the normal, Student’s t and skewed-t), semi-nonparametric (SNP) methodologies based on Gram-Charlier (GC) series and the extreme value theory (EVT) approach. Our results show that normal-, Student’s t- and Skewed t- based methodologies fail to forecast hedge fund VaR, whilst SNP and EVT approaches accurately success on it. We extend these results to the multivariate framework by providing an explicit formula for the GC copula and its density that encompasses the Gaussian copula and accounts for non-linear dependences. We show that the VaR obtained by the meta GC accurately captures portfolio risk and outperforms regulatory VaR estimates obtained through the meta Gaussian and Student’s t distributions.

  1. Beta coefficient based on value-at-risk: estimation methods and empirical analysis%VaR风险度量下的β系数:估计方法和实证研究

    Institute of Scientific and Technical Information of China (English)

    姚京; 袁子甲; 李仲飞; 李端

    2009-01-01

    In the traditional Capital Asset Pricing Model (CAPM), the β coefficient is estimated with an implicit normality assumption. To reduce the gap to the reality, this paper studies the issue of estimating VaR-β, an alternative type of β coefficient based on Value-at-Risk (VaR) with a distribution-free specification.Based on some common VaR calculation models, we propose three different estimation methods for VaR-β: kernel density method, higher moments method and copula method. And we also derive analytical expressions for the VaR-βs under these estimation methods. Finally, an empirical analysis of kernel density method is given for Hong Kong stock market, in which we demonstrate that the confidence level can be taken as a measurement of investors' sentiment.%传统资本资产定价模型得出的β系数受到正态分布假设的约束.为了更好地反映金融现实,对VaR-β系数的估计问题(VaR-β系数是一种在Value-at-Risk风险度量下的β系数,可以在各种概率分布假设下应用)进行了研究.在一些常用VaR估计方法的基础上,发展了三种VaR-β系数估计方法:核密度方法、高阶矩方法和Copula方法,并得出了相应的解析表达式.最后,使用香港证券市场中的数据对核密度方法的应用进行了实证研究,并论证了置信度水平可以做为反映投资者情绪的一个指标.

  2. Haplotyping and copy number estimation of the highly polymorphic human beta-defensin locus on 8p23 by 454 amplicon sequencing

    Directory of Open Access Journals (Sweden)

    Rosenstiel Philip

    2010-04-01

    Full Text Available Abstract Background The beta-defensin gene cluster (DEFB at chromosome 8p23.1 is one of the most copy number (CN variable regions of the human genome. Whereas individual DEFB CNs have been suggested as independent genetic risk factors for several diseases (e.g. psoriasis and Crohn's disease, the role of multisite sequence variations (MSV is less well understood and to date has only been reported for prostate cancer. Simultaneous assessment of MSVs and CNs can be achieved by PCR, cloning and Sanger sequencing, however, these methods are labour and cost intensive as well as prone to methodological bias introduced by bacterial cloning. Here, we demonstrate that amplicon sequencing of pooled individual PCR products by the 454 technology allows in-depth determination of MSV haplotypes and estimation of DEFB CNs in parallel. Results Six PCR products spread over ~87 kb of DEFB and harbouring 24 known MSVs were amplified from 11 DNA samples, pooled and sequenced on a Roche 454 GS FLX sequencer. From ~142,000 reads, ~120,000 haplotype calls (HC were inferred that identified 22 haplotypes ranging from 2 to 7 per amplicon. In addition to the 24 known MSVs, two additional sequence variations were detected. Minimal CNs were estimated from the ratio of HCs and compared to absolute CNs determined by alternative methods. Concordance in CNs was found for 7 samples, the CNs differed by one in 2 samples and the estimated minimal CN was half of the absolute in one sample. For 7 samples and 2 amplicons, the 454 haplotyping results were compared to those by cloning/Sanger sequencing. Intrinsic problems related to chimera formation during PCR and differences between haplotyping by 454 and cloning/Sanger sequencing are discussed. Conclusion Deep amplicon sequencing using the 454 technology yield thousands of HCs per amplicon for an affordable price and may represent an effective method for parallel haplotyping and CN estimation in small to medium-sized cohorts. The

  3. 基于Clayton Copula-GARCH模型投资组合VaR的度量%Estimation of Portfolio VaR under Clayton Copula-GARCH model

    Institute of Scientific and Technical Information of China (English)

    李明; 刘喜波; 何慧; 姚沛

    2013-01-01

    运用Copula方法研究了含股指期货的投资组合的风险度量问题.首先采用不同的GARCH模型对单个资产收益率建模,然后选择Clayton Copula函数来描述投资组合各资产之间的相关结构,建立联合分布模型,进而采用Monte Carlo方法模拟产生各资产的收益率序列,计算出投资组合的VaR.Kupiec检验表明,ClaytonCopula-GARCH模型在投资组合风险度量上具有较高的准确性.%In this paper,we use Copula method to measure VaR of portfolio which contain stock index futures.First,choose different GARCH models to fit each asset return series,second,select Clayton Copula function to describe the relational structure between each asset of the portfolio and build joint distribution model,third,use Monte Carlo method to produce each return sequence of the assets,and then calculate VaR of the portfolio.Kupiec inspection showed that the VaR measure method based on Clayton Copula-GARCH model is effective.

  4. Validity of PTSD diagnoses in VA administrative data: Comparison of VA administrative PTSD diagnoses to self-reported PTSD Checklist scores

    Directory of Open Access Journals (Sweden)

    Amy A. Gravely, MA

    2011-01-01

    Full Text Available Little research has been done on the validity of posttraumatic stress disorder (PTSD diagnoses that are found in Department of Veterans Affairs (VA administrative data, even though they are often used in VA research. We compared PTSD diagnoses found in VA administrative data with PTSD Checklist (PCL scores self-reported by 4,777 newly diagnosed participants in a national postal survey study. Using PCL scores of at least 50 as the gold standard, we compared positive predictive values (PPVs for at least one versus at least two PTSD diagnoses (found within 4 months of the first in VA administrative data overall and by subgroups of interest: age, sex, and clinic where first diagnosed. The overall PPV was 75% for at least one PTSD diagnosis and 82% for at least two PTSD diagnoses. Similarly, the PPV significantly increased for all subgroup analyses when at least two PTSD diagnoses were used. The increase in PPV was greatest for those first diagnosed in primary care and for those older than 65. To select a sample of veterans with more definitive PTSD from administrative data, researchers should select those veterans with at least two PTSD diagnoses as opposed to at least one.

  5. VA/Q distribution during heavy exercise and recovery in humans: implications for pulmonary edema

    Science.gov (United States)

    Schaffartzik, W.; Poole, D. C.; Derion, T.; Tsukimoto, K.; Hogan, M. C.; Arcos, J. P.; Bebout, D. E.; Wagner, P. D.

    1992-01-01

    Ventilation-perfusion (VA/Q) inequality has been shown to increase with exercise. Potential mechanisms for this increase include nonuniform pulmonary vasoconstriction, ventilatory time constant inequality, reduced large airway gas mixing, and development of interstitial pulmonary edema. We hypothesized that persistence of VA/Q mismatch after ventilation and cardiac output subside during recovery would be consistent with edema; however, rapid resolution would suggest mechanisms related to changes in ventilation and blood flow per se. Thirteen healthy males performed near-maximal cycle ergometry at an inspiratory PO2 of 91 Torr (because hypoxia accentuates VA/Q mismatch on exercise). Cardiorespiratory variables and inert gas elimination patterns were measured at rest, during exercise, and between 2 and 30 min of recovery. Two profiles of VA/Q distribution behavior emerged during heavy exercise: in group 1 an increase in VA/Q mismatch (log SDQ of 0.35 +/- 0.02 at rest and 0.44 +/- 0.02 at exercise; P less than 0.05, n = 7) and in group 2 no change in VA/Q mismatch (n = 6). There were no differences in anthropometric data, work rate, O2 uptake, or ventilation during heavy exercise between groups. Group 1 demonstrated significantly greater VA/Q inequality, lower vital capacity, and higher forced expiratory flow at 25-75% of forced vital capacity for the first 20 min during recovery than group 2. Cardiac index was higher in group 1 both during heavy exercise and 4 and 6 min postexercise. However, both ventilation and cardiac output returned toward baseline values more rapidly than did VA/Q relationships. Arterial pH was lower in group 1 during exercise and recovery. We conclude that greater VA/Q inequality in group 1 and its persistence during recovery are consistent with the hypothesis that edema occurs and contributes to the increase in VA/Q inequality during exercise. This is supported by observation of greater blood flows and acidosis and, presumably therefore

  6. Topiramate Protects Pericytes from Glucotoxicity: Role for Mitochondrial CA VA in Cerebromicrovascular Disease in Diabetes.

    Science.gov (United States)

    Patrick, Ping; Price, Tulin O; Diogo, Ana L; Sheibani, Nader; Banks, William A; Shah, Gul N

    Hyperglycemia in diabetes mellitus causes oxidative stress and pericyte depletion from the microvasculature of the brain thus leading to the Blood-Brain Barrier (BBB) disruption. The compromised BBB exposes the brain to circulating substances, resulting in neurotoxicity and neuronal cell death. The decline in pericyte numbers in diabetic mouse brain and pericyte apoptosis in high glucose cultures are caused by excess superoxide produced during enhanced respiration (mitochondrial oxidative metabolism of glucose). Superoxide is precursor to all Reactive Oxygen Species (ROS) which, in turn, cause oxidative stress. The rate of respiration and thus the ROS production is regulated by mitochondrial carbonic anhydrases (mCA) VA and VB, the two isoforms expressed in the mitochondria. Inhibition of both mCA: decreases the oxidative stress and restores the pericyte numbers in diabetic brain; and reduces high glucose-induced respiration, ROS, oxidative stress, and apoptosis in cultured brain pericytes. However, the individual role of the two isoforms has not been established. To investigate the contribution of mCA VA in ROS production and apoptosis, a mCA VA overexpressing brain pericyte cell line was engineered. These cells were exposed to high glucose and analyzed for the changes in ROS and apoptosis. Overexpression of mCA VA significantly increased pericyte ROS and apoptosis. Inhibition of mCA VA with topiramate prevented increases both in glucose-induced ROS and pericyte death. These results demonstrate, for the first time, that mCA VA regulates the rate of pericyte respiration. These findings identify mCA VA as a novel and specific therapeutic target to protect the cerebromicrovascular bed in diabetes.

  7. The Application of VaR Method to Risk Evaluation of Bank Loans%VaR方法在银行贷款风险评估中的应用

    Institute of Scientific and Technical Information of China (English)

    邹新月

    2005-01-01

    Value-at-Risk model developed recently is a mathemetical medol to measure and monitor market risk. The article focuses on discussing calculate procedure and calculate method about applying VaR means for the bank loan risk in evaluation, we make clear differentiate both the Bank for International Settlements draw credit risk reserve and VaR means calculate bank loan risk value, find VaR means in application practicality value and extensity perspective in our bank loan risk for evaluation

  8. User and clinician perspectives on DEKA arm: results of VA study to optimize DEKA arm.

    Science.gov (United States)

    Resnik, Linda; Klinger, Shana Lieberman; Etter, Katherine

    2014-01-01

    This article summarizes feedback from Department of Veterans Affairs (VA) subjects and clinicians gathered during the VA optimization study of the DEKA Arm. VA subjects and clinicians tested two DEKA Arm prototypes (second-generation [gen 2] and third-generation [gen 3]). Features of the prototypes in three configurations are described. DEKA used feedback from the VA optimization study and from their own subjects to refine the gen 2 prototype. Thirty-three unique subjects participated in the VA evaluation; 26 participated in the gen 2 evaluation (1 subject participated twice), 13 participated in the gen 3 evaluation, and 5 participated in both gen 2 and gen 3 evaluations. Subject data were gathered through structured and open-ended surveys, interviews, and audio- and videotaped sessions. Study prosthetists and therapists provided ongoing feedback and completed surveys at the end of each subject's protocol. Eleven categories of feedback were identified: weight, cosmesis, hand grips, wrist design, elbow design, end-point control, foot controls, batteries and chargers, visual notifications, tactor, and socket features. Final feedback on the gen 3 was generally positive, particularly regarding improvements in wrist design, visual notifications, foot controls, end-point control, and cosmesis. Additional refinements to make the device lighter in weight, eliminate external wires and cables, and eliminate the external battery may further enhance its perceived usability and acceptability.

  9. In aftermath of financial investigation Phoenix VA employee demoted after her testimony

    Directory of Open Access Journals (Sweden)

    Robbins RA

    2013-03-01

    Full Text Available No abstract available. Article truncated after 150 words. A previous Southwest Journal of Pulmonary and Critical Care Journal editorial commented on fiscal mismanagement at the Department of Veterans Affairs (VA Medical Center in Phoenix (1. Now Paula Pedene, the former Phoenix VA public affairs officer, claims she was demoted for testimony she gave to the VA Inspector General’s Office (OIG regarding that investigation (2. In 2011, the OIG investigated the Phoenix VA for excess spending on private care of patients (3. The report blamed systemic failures for controls so weak that $56 million in medical fees were paid during 2010 without adequate review. The report particularly focused on one clinician assigned by the Chief of Staff to review hundreds of requests per week and the intensive care unit physicians for transferring patients to chronic ventilator units (1,3. After the investigation, the director and one of the associate directors left the VA and the chief of staff was promoted …

  10. Large-scale benchmarking reveals false discoveries and count transformation sensitivity in 16S rRNA gene amplicon data analysis methods used in microbiome studies

    DEFF Research Database (Denmark)

    Thorsen, Jonathan; Brejnrod, Asker Daniel; Mortensen, Martin Steen

    2016-01-01

    BACKGROUND: There is an immense scientific interest in the human microbiome and its effects on human physiology, health, and disease. A common approach for examining bacterial communities is high-throughput sequencing of 16S rRNA gene hypervariable regions, aggregating sequence-similar amplicons...... analysis and (2) beta-diversity-based sample separation, using a rigorous benchmarking framework based on large clinical 16S microbiome datasets from different sources. RESULTS: Running more than 380,000 full differential relative abundance tests on real datasets with permuted case/control assignments...... should be interpreted with caution. We provide an easily extensible framework for benchmarking of new methods and future microbiome datasets....

  11. Case Study of the Capital Asset Realignment for Enhanced Services as Applied to the Wyoming VA Healthcare Market

    Science.gov (United States)

    2003-11-14

    Capital Asset Realignment 1 Running Head: Capital Asset Realignment U.S. Army – Baylor University Graduate Program in Healthcare Administration Case...restructure the Veterans Health Administration ” (1995) and “Prescription for Change: The Guiding Principles and Strategic Objective Underlying the...assets to meet the VA mission (1998). With the evidence mounting on the need to realign the VA infrastructure, VA Secretary Anthony Principi launched

  12. Efficient transfer of a VA-SWNT film by a flip-over technique.

    Science.gov (United States)

    Kim, Myung Jong; Nicholas, Nolan; Kittrell, Carter; Haroz, Erik; Shan, Hongwei; Wainerdi, T J; Lee, Sungbae; Schmidt, Howard K; Smalley, Richard E; Hauge, Robert H

    2006-07-26

    A transfer of a VA-SWNT film onto a conductive surface has been achieved using a novel "flip-over" technique. The top surface of a VA-SWNT film was covered by entangled bundles in an as-grown sample. When a VA-SWNT film was flipped over, an optically flat surface consisting of the tips of very well aligned, clean bundles from the bottom of the film are exposed while the top of the film is well contacted to the substrate. Thus, we expect this technique to provide us with means to prepare carbon nanotube electrodes for device applications such as super capacitors, thermo-electric devices, fuel cells, and field emission filaments.

  13. VaR RAROC与投资组合问题探讨

    Institute of Scientific and Technical Information of China (English)

    陈学华; 杨辉耀; 唐珂

    2004-01-01

    VaR为风险度量工具、以RAROC作为目标函数的投资决策模型.利用资产回报分布的偏度和峰度,对VaR进行调整,使它可以应用于非正态分布时的资产组合风险价值估计,而不增加计算的复杂性;同时又对RARAOC作了修正,使之克服了RAROC的缺点.应用此模型,使投资组合经理在受到内外部施加VaR限额约束时,在上级以RAROC作为投资业绩评估工具的情形下,可以有效地实现资产组合的优化配置.

  14. Physical stability of solid dispersions with respect to thermodynamic solubility of tadalafil in PVP-VA.

    Science.gov (United States)

    Wlodarski, K; Sawicki, W; Kozyra, A; Tajber, L

    2015-10-01

    The aim of this paper was to evaluate physical stability of solid dispersions in respect to the drug, tadalafil (Td), in vinylpyrrolidone and vinyl acetate block copolymer (PVP-VA). Nine solid dispersions of Td in PVP-VA (Td/PVP-VA) varied in terms of quantitative composition (1:9-9:1, w/w) were successfully produced by spray-drying. Their amorphous nature, supersaturated character and molecular level of mixing (a solid solution structure) were subsequently confirmed using DSC, PXRD, SEM and calculation of Hansen total solubility parameters. Due to thermal degradation of both components before the melting point of Td (302.3°C), an approach based on the drug crystallization from the supersaturated solid dispersion was selected to calculate the solubility of Td in the polymer. Annealing of the Td/PVP-VA solid dispersion (1:1, w/w) at selected temperatures above its Tg resulted in different stable solid dispersions. According to the Gordon-Taylor equation their new Tgs gave the information about the quantitative composition which corresponded to the thermodynamic solubility of Td in PVP-VA at given temperatures of annealing. The obtained relationship was fitted to the exponential function, with the calculated solubility of Td of 20.5% at 25°C. This value was in accordance with the results of hot stage polarizing light microscopy as well as stability tests carried out at 80°C and 0% RH, in which Td solid dispersions containing 10-20% of the drug were the only systems that did not crystallize within two months. A thermal analysis protocol utilizing a fast heating rate was shown to generate Td solubility data complementing the solid dispersion method. The Flory-Huggins model applied for the Td/PVP-VA system yielded the solubility value of 0.1% at 25°C, showing the lack of applicability in this case.

  15. Effects of the KiVa antibullying program on cyberbullying and cybervictimization frequency among Finnish youth.

    Science.gov (United States)

    Williford, Anne; Elledge, L Christian; Boulton, Aaron J; DePaolis, Kathryn J; Little, Todd D; Salmivalli, Christina

    2013-01-01

    Cyberbullying among school-aged children has received increased attention in recent literature. However, no empirical evidence currently exists on whether existing school-based antibullying programs are effective in targeting the unique aspects of cyberbullying. To address this important gap, the present study investigates the unique effects of the KiVa Antibullying Program on the frequency of cyberbullying and cybervictimization among elementary and middle school youth. Using data from a group randomized controlled trial, multilevel ordinal regression analyses were used to examine differences in the frequencies of cyberbullying and cybervictimization between intervention (N = 9,914) and control students (N = 8,498). The effects of age and gender on frequencies of cyber behaviors were also assessed across conditions. Results revealed a significant intervention effect on the frequency of cybervictimization; KiVa students reported lower frequencies of cybervictimization at posttest than students in a control condition. The effect of condition on the perpetration of cyberbullying was moderated by age. When student age was below the sample mean, KiVa students reported lower frequencies of cyberbullying than students in the control condition. We also found evidence of classroom level variation in cyberbullying and cybervictimization, suggesting cyberbullying is in part a classroom-level phenomenon. KiVa appears to be an efficacious program to address cyber forms of bullying and victimization. We discuss several unique aspects of KiVa that may account for the significant intervention effects. Results suggest that KiVa is an intervention option for schools concerned with reducing cyberbullying behavior and its deleterious effects on children's adjustment.

  16. BMP-2 Overexpression Augments Vascular Smooth Muscle Cell Motility by Upregulating Myosin Va via Erk Signaling

    Directory of Open Access Journals (Sweden)

    Ming Zhang

    2014-01-01

    Full Text Available Background. The disruption of physiologic vascular smooth muscle cell (VSMC migration initiates atherosclerosis development. The biochemical mechanisms leading to dysfunctional VSMC motility remain unknown. Recently, cytokine BMP-2 has been implicated in various vascular physiologic and pathologic processes. However, whether BMP-2 has any effect upon VSMC motility, or by what manner, has never been investigated. Methods. VSMCs were adenovirally transfected to genetically overexpress BMP-2. VSMC motility was detected by modified Boyden chamber assay, confocal time-lapse video assay, and a colony wounding assay. Gene chip array and RT-PCR were employed to identify genes potentially regulated by BMP-2. Western blot and real-time PCR detected the expression of myosin Va and the phosphorylation of extracellular signal-regulated kinases 1/2 (Erk1/2. Immunofluorescence analysis revealed myosin Va expression locale. Intracellular Ca2+ oscillations were recorded. Results. VSMC migration was augmented in VSMCs overexpressing BMP-2 in a dose-dependent manner. siRNA-mediated knockdown of myosin Va inhibited VSMC motility. Both myosin Va mRNA and protein expression significantly increased after BMP-2 administration and were inhibited by Erk1/2 inhibitor U0126. BMP-2 induced Ca2+ oscillations, generated largely by a “cytosolic oscillator”. Conclusion. BMP-2 significantly increased VSMCs migration and myosin Va expression, via the Erk signaling pathway and intracellular Ca2+ oscillations. We provide additional insight into the pathophysiology of atherosclerosis, and inhibition of BMP-2-induced myosin Va expression may represent a potential therapeutic strategy.

  17. Computing VaR and ES Based-on EVT%基于极值分布理论的VaR与ES度量

    Institute of Scientific and Technical Information of China (English)

    陈守东; 孔繁利; 胡铮洋

    2007-01-01

    本文应用极值分布理论对金融收益序列的尾部进行估计,计算收益序列的在险价值VaR和预期不足ES来度量市场风险.通过伪最大似然估计方法估计的GARCH模型对收益数据进行拟合,应用极值理论中的GPD对新息分布的尾部建模,得到了基于尾部估计产生收益序列的VaR和ES值.采用上证指数日对数收益数据为样本,得到了度量条件极值和无条件极值下VaR和ES的结果.实证研究表明:在置信水平很高(如99%)的条件下,采用极值方法度量风险值效果更好.而置信水平在95%下,其他方法和极值方法结合效果会很好.用ES度量风险能够使我们了解不利情况发生时风险的可能情况.

  18. Glycoprotein is enough for sindbis virus-derived DNA vector to express heterogenous genes.

    Science.gov (United States)

    Zhu, Wuyang; Li, Jiangjiao; Tang, Li; Wang, Huanqin; Li, Jia; Fu, Juanjuan; Liang, Guodong

    2011-07-10

    To investigate the necessity and potential application of structural genes for expressing heterogenous genes from Sindbis virus-derived vector, the DNA-based expression vector pVaXJ was constructed by placing the recombinant genome of sindbis-like virus XJ-160 under the control of the human cytomegalovirus (CMV) promoter of the plasmid pVAX1, in which viral structural genes were replaced by a polylinker cassette to allow for insertion of heterologous genes. The defect helper plasmids pVaE or pVaC were developed by cloning the gene of glycoprotein E3E26KE1 or capsid protein of XJ-160 virus into pVAX1, respectively. The report gene cassette pVaXJ-EGFP or pV-Gluc expressing enhanced green fluorescence protein (EGFP) or Gaussia luciferase (G.luc) were constructed by cloning EGFP or G.luc gene into pVaXJ. EGFP or G.luc was expressed in the BHK-21 cells co-transfected with report gene cassettes and pVaE at levels that were comparable to those produced by report gene cassettes, pVaC and pVaE and were much higher than the levels produced by report gene cassette and pVaC, suggesting that glycoprotein is enough for Sindbis virus-derived DNA vector to express heterogenous genes in host cells. The method of gene expression from Sindbis virus-based DNA vector only co-transfected with envelop E gene increase the conveniency and the utility of alphavirus-based vector systems in general.

  19. Glycoprotein is enough for sindbis virus-derived DNA vector to express heterogenous genes

    Directory of Open Access Journals (Sweden)

    Fu Juanjuan

    2011-07-01

    Full Text Available Abstract To investigate the necessity and potential application of structural genes for expressing heterogenous genes from Sindbis virus-derived vector, the DNA-based expression vector pVaXJ was constructed by placing the recombinant genome of sindbis-like virus XJ-160 under the control of the human cytomegalovirus (CMV promoter of the plasmid pVAX1, in which viral structural genes were replaced by a polylinker cassette to allow for insertion of heterologous genes. The defect helper plasmids pVaE or pVaC were developed by cloning the gene of glycoprotein E3E26KE1 or capsid protein of XJ-160 virus into pVAX1, respectively. The report gene cassette pVaXJ-EGFP or pV-Gluc expressing enhanced green fluorescence protein (EGFP or Gaussia luciferase (G.luc were constructed by cloning EGFP or G.luc gene into pVaXJ. EGFP or G.luc was expressed in the BHK-21 cells co-transfected with report gene cassettes and pVaE at levels that were comparable to those produced by report gene cassettes, pVaC and pVaE and were much higher than the levels produced by report gene cassette and pVaC, suggesting that glycoprotein is enough for Sindbis virus-derived DNA vector to express heterogenous genes in host cells. The method of gene expression from Sindbis virus-based DNA vector only co-transfected with envelop E gene increase the conveniency and the utility of alphavirus-based vector systems in general.

  20. RAROC基于VaR的封闭式基金业绩评估

    Institute of Scientific and Technical Information of China (English)

    张晓彬; 黄志勇

    2006-01-01

    介绍了基于VaR的证券投资基金绩效评估方法--RAROC方法,通过该方法对我国封闭式基金投资绩效的分析来揭示投资风险,结果表明:引进VaR风险度量模型,把经风险调整后的绩效评估方法RAROC应用到投资基金绩效评估中,能更客观、准确地反映封闭式基金的投资绩效.

  1. Molecular characterization and diversity analysis of bacterial communities associated with Dialeurolonga malleswaramensis (Hemiptera: Aleyrodidae) adults using 16S rDNA amplicon pyrosequencing and FISH.

    Science.gov (United States)

    Pandey, Neeti; Rajagopal, Raman

    2016-10-01

    Dialeurolonga malleswaramensis Sundararaj (Hemiptera: Aleyrodidae) is a phytophagous sap sucking insect. It infests Polyalthia longifolia, an important avenue tree of India, effective in alleviating noise pollution and having immense medicinal importance. Samples of this insect were collected from Polyalthia longifolia. The cytochrome c oxidase subunit I gene (mtCO1) helped in the molecular characterization of the insect. This study reports the bacterial diversity in D. malleswaramensis adults by high throughput 16S rDNA amplicon pyrosequencing. The major genera identified were Portiera and Arsenophonus. Other bacterial genera detected were uncultured alpha proteobacterium, Sphingopyxis and Methylobacterium. We also employed fluorescence in situ hybridization (FISH) in whole mount samples to confirm the presence of dominant endosymbionts Portiera and Arsenophonus to the bacteriocyte of D. malleswaramensis. This study concludes that combining techniques like 16S rDNA amplicon pyrosequencing and FISH reveal both dominant and rare bacteria. The data also predict the evolutionary position of this pest with respect to other whitefly species using a mitochondrial marker.

  2. A New Method for Rapid Screening of End-Point PCR Products: Application to Single Genome Amplified HIV and SIV Envelope Amplicons.

    Directory of Open Access Journals (Sweden)

    Laurent Houzet

    Full Text Available PCR is the most widely applied technique for large scale screening of bacterial clones, mouse genotypes, virus genomes etc. A drawback of large PCR screening is that amplicon analysis is usually performed using gel electrophoresis, a step that is very labor intensive, tedious and chemical waste generating. Single genome amplification (SGA is used to characterize the diversity and evolutionary dynamics of virus populations within infected hosts. SGA is based on the isolation of single template molecule using limiting dilution followed by nested PCR amplification and requires the analysis of hundreds of reactions per sample, making large scale SGA studies very challenging. Here we present a novel approach entitled Long Amplicon Melt Profiling (LAMP based on the analysis of the melting profile of the PCR reactions using SYBR Green and/or EvaGreen fluorescent dyes. The LAMP method represents an attractive alternative to gel electrophoresis and enables the quick discrimination of positive reactions. We validate LAMP for SIV and HIV env-SGA, in 96- and 384-well plate formats. Because the melt profiling allows the screening of several thousands of PCR reactions in a cost-effective, rapid and robust way, we believe it will greatly facilitate any large scale PCR screening.

  3. Conservative fragments in bacterial 16S rRNA genes and primer design for 16S ribosomal DNA amplicons in metagenomic studies

    KAUST Repository

    Wang, Yong

    2009-10-09

    Bacterial 16S ribosomal DNA (rDNA) amplicons have been widely used in the classification of uncultured bacteria inhabiting environmental niches. Primers targeting conservative regions of the rDNAs are used to generate amplicons of variant regions that are informative in taxonomic assignment. One problem is that the percentage coverage and application scope of the primers used in previous studies are largely unknown. In this study, conservative fragments of available rDNA sequences were first mined and then used to search for candidate primers within the fragments by measuring the coverage rate defined as the percentage of bacterial sequences containing the target. Thirty predicted primers with a high coverage rate (>90%) were identified, which were basically located in the same conservative regions as known primers in previous reports, whereas 30% of the known primers were associated with a coverage rate of <90%. The application scope of the primers was also examined by calculating the percentages of failed detections in bacterial phyla. Primers A519-539, E969- 983, E1063-1081, U515 and E517, are highly recommended because of their high coverage in almost all phyla. As expected, the three predominant phyla, Firmicutes, Gemmatimonadetes and Proteobacteria, are best covered by the predicted primers. The primers recommended in this report shall facilitate a comprehensive and reliable survey of bacterial diversity in metagenomic studies. © 2009 Wang, Qian.

  4. The Simultaneous VaR Calculation of Exchange Rate Risk Based on Panel-GARCH Model%基于面板GARCH模型的汇率风险联动VaR测算

    Institute of Scientific and Technical Information of China (English)

    刘用明; 贺薇

    2011-01-01

    为弥补现有VaR测算模型在同时测算多汇率风险因子VaR值过程中的不足,笔者将面板CARCH模型应用于汇率风险的VaR测算中,通过与一元GARCH模型、多元GARCH模型中的BEKK模型和DCC模型相对比,发现其联动VaR测算的结果优于后三种模型.基于残差项正态分布假设下的面板GARCH模型能够较好地捕获汇率的波动,其运用能提高VaR测算的精度,增强金融机构或企业的汇率风险管理水平.

  5. Study on the Estimation and Analysis of VaR with Bootstrap Simulation Technology%应用Bootstrap模拟技术的VaR计算与分析研究

    Institute of Scientific and Technical Information of China (English)

    魏红刚; 孟英玉

    2010-01-01

    比较估计VaR的方差-协方差方法、历史模拟法和Monte Carlo模拟方法,提出估计VaR的新模型和新方法.新模型把随机收益率分解成刻画收益率二阶矩特征的部分和刻画随机均值的正态部分.新方法使用Bootstrap模拟技术和Monte Carlo模拟技术计算VaR.实证分析表明,新方法计算的VaR在传统方法计算的VaR参考范围内.

  6. 77 FR 13519 - Safety Zone; Virginia Beach Oceanfront Air Show, Atlantic Ocean, Virginia Beach, VA

    Science.gov (United States)

    2012-03-07

    ..., Atlantic Ocean, Virginia Beach, VA AGENCY: Coast Guard, DHS. ACTION: Notice of proposed rulemaking. SUMMARY: The Coast Guard proposes establishing a safety zone on the navigable waters of the Atlantic Ocean in..., which will then become highlighted in blue. In the ``Document Type'' drop down menu select...

  7. 77 FR 70708 - VA Acquisition Regulation: Electronic Submission of Payment Requests

    Science.gov (United States)

    2012-11-27

    ... System; (2) American National Standards Institute (ANSI) X12 electronic data interchange (EDI) formats....fsc.va.gov/einvoice.asp .); or, (b) A system that conforms to the X12 electronic data interchange (EDI... Institute (ANSI). The X12 EDI Web site ( http://www.x12.org ) includes additional information on EDI 810...

  8. VA Puget Sound Telemental Health Service to rural veterans: a growing program.

    Science.gov (United States)

    Barnwell, Sara V Smucker; Juretic, Meghan A; Hoerster, Katherine D; Van de Plasch, Richard; Felker, Bradford L

    2012-05-01

    The VA Puget Sound Health Care System Telemental Health program connects veterans with psychologists, psychiatrists, and social workers via live clinical video teleconferencing. Providers deliver care to veterans in rural Veteran Affairs medical centers, community-based outpatient clinics and residences, and thus, increase access to specialty mental health care for rural and medically underserved veteran communities.

  9. 77 FR 1500 - Plum Tree Island National Wildlife Refuge, Poquoson, VA

    Science.gov (United States)

    2012-01-10

    ... Fish and Wildlife Service Plum Tree Island National Wildlife Refuge, Poquoson, VA AGENCY: Fish and...), intend to prepare a comprehensive conservation plan (CCP) and environmental assessment (EA) for Plum Tree..._evrnwr@fws.gov . Include ``Plum Tree Island CCP'' in the subject line of the message. Fax: Attn:...

  10. 76 FR 44279 - Radio Broadcasting Services; Clinchco, VA, and Coal Run, KY

    Science.gov (United States)

    2011-07-25

    ... COMMISSION 47 CFR Part 73 Radio Broadcasting Services; Clinchco, VA, and Coal Run, KY AGENCY: Federal...''), upgrading its Station WPKE-FM, Coal Run Kentucky, from Channel 276A to Channel 221C3. DATES: Effective... 221C3 at Coal Run, Kentucky, are 37-23-57 NL and 82-23-42 WL, and for Channel 276A at Clinchco,...

  11. 75 FR 15721 - Back Bay National Wildlife Refuge, City of Virginia Beach, VA

    Science.gov (United States)

    2010-03-30

    ... Fish and Wildlife Service Back Bay National Wildlife Refuge, City of Virginia Beach, VA AGENCY: Fish... environmental assessment (EA) for Back Bay National Wildlife Refuge (NWR) for a 30-day public review and comment... by the National Wildlife Refuge System Improvement Act of 1997 (Improvement......

  12. 77 FR 38396 - Agency Information Collection (One-VA Identification Verification Card) Activities Under OMB Review

    Science.gov (United States)

    2012-06-27

    ... ``OMB Control No. 2900-0673'' in any correspondence. FOR FURTHER INFORMATION CONTACT: Denise McLamb... 20420, (202) 632-7479, Fax (202) 632-7583 or email denise.mclamb@va.gov . Please refer to ``OMB Control.... Denise McLamb, Program Analyst, Enterprise Records Service. BILLING CODE 8320-01-P...

  13. 75 FR 48413 - Agency Information Collection (HUD/VA Addendum to Uniform Residential Loan Application) Activity...

    Science.gov (United States)

    2010-08-10

    ... Control No. 2900-0144'' in any correspondence. FOR FURTHER INFORMATION CONTACT: Denise McLamb, Enterprise..., (202) 461-7485, FAX (202) 273-0443 or e-mail denise.mclamb@va.gov . Please refer to ``OMB Control No... Respondents: 200,000. Dated: August 5, 2010. By direction of the Secretary. Denise McLamb, Program...

  14. 75 FR 76082 - Agency Information Collection (Credit Underwriting Standards and Procedures for Processing VA...

    Science.gov (United States)

    2010-12-07

    ...: Denise McLamb, Enterprise Records Service (005R1B), Department of Veterans Affairs, 810 Vermont Avenue, NW., Washington, DC 20420, (202) 461-7485, FAX (202) 273-0443 or e-mail denise.mclamb@.va.gov. Please... direction of the Secretary. Denise McLamb, Program Analyst, Enterprise Records Service. BILLING CODE...

  15. 78 FR 38452 - Agency Information Collection (VA Police Officer Pre-Employment Screening Checklist) Activities...

    Science.gov (United States)

    2013-06-26

    ... AFFAIRS Agency Information Collection (VA Police Officer Pre-Employment Screening Checklist) Activities Under OMB Review AGENCY: Office of Policy, Planning and Preparedness, Department of Veterans Affairs... Management and Budget (OMB) for review and comment. The PRA submission describes the nature of...

  16. Choosing Expected Shortfall Over VaR in Basel III Using Stochastic Dominance

    NARCIS (Netherlands)

    C-L. Chang (Chia-Lin); J.A. Jiménez-Martín (Juan-Ángel); E. Maasoumi (Esfandiar); M.J. McAleer (Michael); T. Pérez-Amaral (Teodosio)

    2016-01-01

    textabstractWe compare Value at Risk (VaR) and Expected Shortfall (ES) following a Stochastic Dominance (SD) approach frequently used to order distributions in terms of welfare and in portfolio selection. Basel Committee on Banking Supervision (BCBS) recommends bank risk managers to shift the curren

  17. Choosing Expected Shortfall over VaR in Basel III Using Stochastic Dominance

    NARCIS (Netherlands)

    C-L. Chang (Chia-Lin); J.A. Jiménez-Martín (Juan-Ángel); E. Maasoumi (Esfandiar); M.J. McAleer (Michael)

    2015-01-01

    textabstractBank risk managers follow the Basel Committee on Banking Supervision (BCBS) recommendations that recently proposed shifting the quantitative risk metrics system from Value-at-Risk (VaR) to Expected Shortfall (ES). The Basel Committee on Banking Supervision (2013, p. 3) noted that: “a num

  18. Forecasting VaR and ES of stock index portfolio: A Vine copula method

    Science.gov (United States)

    Zhang, Bangzheng; Wei, Yu; Yu, Jiang; Lai, Xiaodong; Peng, Zhenfeng

    2014-12-01

    Risk measurement has both theoretical and practical significance in risk management. Using daily sample of 10 international stock indices, firstly this paper models the internal structures among different stock markets with C-Vine, D-Vine and R-Vine copula models. Secondly, the Value-at-Risk (VaR) and Expected Shortfall (ES) of the international stock markets portfolio are forecasted using Monte Carlo method based on the estimated dependence of different Vine copulas. Finally, the accuracy of VaR and ES measurements obtained from different statistical models are evaluated by UC, IND, CC and Posterior analysis. The empirical results show that the VaR forecasts at the quantile levels of 0.9, 0.95, 0.975 and 0.99 with three kinds of Vine copula models are sufficiently accurate. Several traditional methods, such as historical simulation, mean-variance and DCC-GARCH models, fail to pass the CC backtesting. The Vine copula methods can accurately forecast the ES of the portfolio on the base of VaR measurement, and D-Vine copula model is superior to other Vine copulas.

  19. 76 FR 27967 - Safety Zone; Shore Thing and Independence Day Fireworks, Chesapeake Bay, Norfolk, VA

    Science.gov (United States)

    2011-05-13

    ... View Beach Park, Norfolk, VA in support of the Shore Thing and Independence Day Fireworks event. This action is necessary to provide for the safety of life on navigable waters during the Shore Thing and... SECURITY Coast Guard 33 CFR Part 165 RIN 1625-AA00 Safety Zone; Shore Thing and Independence Day...

  20. 75 FR 34367 - Safety Zone; Shore Thing & Independence Day Fireworks, Chesapeake Bay, Norfolk, VA

    Science.gov (United States)

    2010-06-17

    ... SECURITY Coast Guard 33 CFR Part 165 RIN 1625-AA00 Safety Zone; Shore Thing & Independence Day Fireworks... is establishing a temporary safety zone on the Chesapeake Bay in the vicinity of Ocean View Beach Park, Norfolk, VA in support of the Shore Thing & Independence Day Fireworks event. This action...

  1. 75 FR 26155 - Safety Zone; Shore Thing & Independence Day Fireworks, Chesapeake Bay, Norfolk, VA

    Science.gov (United States)

    2010-05-11

    ... View Beach Park, Norfolk, VA in support of the Shore Thing & Independence Day Fireworks event. This... SECURITY Coast Guard 33 CFR Part 165 RIN 1625-AA00 Safety Zone; Shore Thing & Independence Day Fireworks... Federal Register (73 FR 3316). Public Meeting We do not now plan to hold a public meeting. But you...

  2. 76 FR 38300 - Safety Zone; Shore Thing and Independence Day Fireworks, Chesapeake Bay, Norfolk, VA

    Science.gov (United States)

    2011-06-30

    ... SECURITY Coast Guard 33 CFR Part 165 RIN 1625-AA00 Safety Zone; Shore Thing and Independence Day Fireworks... is establishing a temporary safety zone on the Chesapeake Bay in the vicinity of Ocean View Beach Park, Norfolk, VA in support of the Shore Thing and Independence Day Fireworks event. This action...

  3. Data of evolutionary structure change: 1A4VA-1JKBA [Confc[Archive

    Lifescience Database Archive (English)

    Full Text Available 1A4VA-1JKBA 1A4V 1JKB A A KQFTKCELSQLLKDI--DGYGGIALPELICTMFHTSGYD...line> 1JKB A 1JK...CA 299 GLU CA 390 1JKB A 1JK...line> ASP CA 274 TYR CA 329 1JKB ...A 1JKBA RVVRDPQGIRA

  4. 77 FR 6587 - Startek USA, Inc. Alexandria, LA; Startek USA, Inc., Collinsville, VA; Amended Certification...

    Science.gov (United States)

    2012-02-08

    ... Employment and Training Administration Startek USA, Inc. Alexandria, LA; Startek USA, Inc., Collinsville, VA..., applicable to workers of StarTek USA, Inc., Alexandria, Louisiana. The workers are engaged in the supply of..., Virginia location of StarTek USA, Inc. supplied call center services such as sales and technical...

  5. Processing and Characterization of High Density Polyethylene/Ethylene Vinyl Acetate Blends with Different VA Contents

    Directory of Open Access Journals (Sweden)

    Othman Y. Alothman

    2012-01-01

    Full Text Available Different series of high density Polyethylene/Ethylene Vinyl Acetate (HDPE/EVA blends were prepared via melt blending in a corotating intermeshing twin screw extruder. The effects of VA percentage and EVA loading ratio on the thermal, rheological viscoelastic, mechanical, and fracture toughness of the blends were analyzed. The results showed that the addition of EVA to HDPE reduces the thermal, elastic, and viscoelastic properties of the blends. The microscopic examination of the fracture surface confirmed the ductile fracture of HDPE/EVA blends for all blend ratios and VA percentages. Increasing the EVA ratio and VA content caused a significant reduction in the blend crystallinity but had no significant effect on melting temperature. The complex viscosity increased with increasing the percentage of EVA due to the restriction of molecular mobility and reduction of free volume, induced by the addition of EVA. The storage modulus decreased with increasing the EVA ratio and temperature, while it increased with increasing the frequency. Young’s modulus, yield strength, and fracture strain decreased with increasing the EVA ratio. Similarly, the fracture toughness decreased proportional to the EVA percentage. Finally the results indicated that the VA content has significant effects on the mechanical, thermal, and dynamic properties of HDPE/EVA blends.

  6. Estimasi Nilai VaR Dinamis Indeks Saham Menggunakan Peak-Over Threshold dan Block Maxima

    Directory of Open Access Journals (Sweden)

    Komang Dharmawan

    2013-10-01

    Full Text Available Kejadian ekstrim pada bidang finansial pada periode 2008/2009  telah menyadarkan para praktisi maupun peneliti di bidang finansial untuk mengevaluasi kembali teknik-teknik pemodelan risiko finansial.  Ini menegaskan bahwa diperlukan model-model matematika atau teknik pemodelan yang lebih baik di bidang manajemen risiko finansial yang dapat mengatisipasi adanya kejadian-kejadian yang jarang muncul seperti pada periode tahun tersebut di atas. Metode yang paling sesuai dalam menangani kejadian kejadian ekstrim seperti ini adalah Extreme Value Theory (EVT. Dalam pemodelan Value at Risk(VaR, tingkat pengembalian (return suatu data finansial biasanya ditaksir menggunakan suatu pendekatan yang mengasumsikan bahwa data tersebut terdistrubusi secara normal. Namun asumsi ini tidak merefleksikan perilaku nilai return yang sesungguhnya, sebab distribusi data finansial menunjukkan adanya ekor distribusi yang lebih gemuk (heavy-tail, yaitu ekor distribusi turun lebih pelan dibandingkan dengan ekor distribusi normal.  Ini berarti peluang munculnya nilai ekstrim lebih besar. Sehingga pendekatan secara konvensional dianggap mengabaikan nilai-nilai ekstrim ini. Paper ini membahas penerapkan EVT pada data finansial. Kemudian menghitung nilai VaR dinamis dari nilai indeks IHSG (Jakarta Stock Exchange periode 28 Desember 2007-28 Desembar 2012. EVT dipakai untuk memprediksi VaR statis dan EVT-GARCH(1,1 dipakai untuk memprediksi VaR dinamis.

  7. VA AND DoD Health Care: Factors Contributing to Reduced Pharmacy Costs and Continuing Challenges

    Science.gov (United States)

    2007-11-02

    of the Congressional Commission on Servicemembers and Veterans Transition Assistance, Anthony J. Principi , Chairman (Arlington, Va. Congressional...and Drug Administration that are tested against a standard of bioequivalence to the original brand name version. a38 U.S.C. § 8126(a)(4). bThe

  8. A large-scale evaluation of the KiVa Antibullying Program: Grades 4-6

    NARCIS (Netherlands)

    Kärnä, A.; Voeten, M.J.M.; Little, T.D.; Poskiparta, E.H.; Salmivalli, C.

    2011-01-01

    This study demonstrates the effectiveness of the KiVa antibullying program using a large sample of 8,237 youth from Grades 4-6 (10-12 years). Altogether, 78 schools were randomly assigned to intervention (39 schools, 4,207 students) and control conditions (39 schools, 4,030 students). Multilevel reg

  9. Le CERN va devoir supprimer quelques 600 postes d'ici a 2007

    CERN Multimedia

    2002-01-01

    "Le Laboratoire europeen pour la physique des particules (CERN) qui procede actuellement a la construction du LHC (Large Hadron Collider) , le plus grand accelerateur de particules du monde, va devoir supprimer, comme cela avait ete evoque en juin, quelques 600 postes d'ici a 2007" (1 paragraph).

  10. 78 FR 56271 - FY 2014-2020 Draft VA Strategic Plan

    Science.gov (United States)

    2013-09-12

    ... defining success by Veterans' outcomes; enhancing the quality of and access to benefits and services..., and leadership to meet our clients' needs and expectations. DATES: Comments must be received by VA on... a more defined performance framework by defining a governance structure and by better...

  11. 75 FR 3968 - Fund Availability Under the VA Homeless Providers Grant and Per Diem Program

    Science.gov (United States)

    2010-01-25

    ... throughout by an approved automatic sprinkler system unless a facility is specifically exempted under the... requirements of the current edition of the Life Safety Code of the National Fire Protection Association as it...-funded program will participate in VA's National Program Monitoring and Evaluation System administered...

  12. Data of evolutionary structure change: 1A4VA-1IOTA [Confc[Archive

    Lifescience Database Archive (English)

    Full Text Available 1A4VA-1IOTA 1A4V 1IOT A A KQFTKCELSQLLKDI--DGYGGIALPELICTMFHTSGYD.../n14> 1IOT A 1IOTA.../y> -8.890999794006348 tion> 0.9589999914169312 -0.21400000154972076 0.9139999747276306 0.3440000116825104 ...dbID> A 1IOTA KKIVSDGNGMN

  13. 75 FR 54965 - Proposed Information Collection (Statement of Purchaser or Owner Assuming Seller's Loans, VA Form...

    Science.gov (United States)

    2010-09-09

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF VETERANS... correspondence. During the comment period, comments may be viewed online through FDMS. FOR FURTHER INFORMATION... determinations for substitution of entitlement. If a veteran chooses to sell his or her VA guaranteed home,...

  14. Findings of VA/DoD CPG on CAM Therapies for PTSD

    Science.gov (United States)

    2011-01-26

    The Quadruple Aim: Working Together, Achieving Success 2011 Military Health System Conference Defense Centers of Excellence for Psychological Health... Psychological Health & Traumatic Brain Injury,2345 Crystal Drive,Crystal park 4, Suite 120,Arlington,VA,22202 8. PERFORMING ORGANIZATION REPORT...breathing exercises, massage therapy, meditation, naturopathy, and yoga 2011 MHS Conference Complementary and Alternative Medicine White House

  15. Belowground-system development of VA mycorrhiza in a restored tallgrass prairie community

    Energy Technology Data Exchange (ETDEWEB)

    Cook, B.D.; Jastrow, J.D.; Miller, R.M.; McGraw, A.C.

    1987-01-01

    This study was conducted to determine the relationship between root and VA mycorrhizal fungus development in a tallgrass prairie restoration chronosequence. Emphasis is placed on characterizing the relationship of root length, colonized root length, and percentage of root length occupied by the mycorrhizal fungus by differing root size classes. Mycorrhizal fungus composition and populations along the restoration chronosequence was determined. 3 refs., 1 fig.

  16. Lattice-Inversion Embedded-Atom-Method Interatomic Potentials for Group-VA Transition Metals

    Institute of Scientific and Technical Information of China (English)

    袁晓俭; 陈难先; 申江

    2011-01-01

    The lattice-inversion embedded-atom-method (LI-EAM) interatomic potential we developed previously [J. Phys.: Condens. Matter 22 (2010) 375503] is extended to group- VA transition metals (V, Nb and Ta). It is found that considering interatomic interactions up to appropriate-distance-neighbor atoms is crucial to constructing accurate EAM potentials, especially for the prediction of surface energy. The LI-EAM interatomic potentials for group-VA transition metals are successfully built by considering interatomic interactions up to the fifth neighbor atoms. These angular-independent potentials drastically promote the accuracy of the predicted surface energies, which match the experimental resuits well.%The lattice-inversion embedded-atom-method(LI-EAM)interatomic potential we developed previously[J.Phys.:Condens.Matter 22(2010)375503]is extended to group-VA transition metals(V,Nb and Ta).It is found that considering interatomic interactions up to appropriate-distance-neighbor atoms is crucial to constructing accurate EAM potentials,especially for the prediction of surface energy.The LI-EAM interatomic potentials for group-VA transition metals are successfully built by considering interatomic interactions up to the fifth neighbor atoms.These angular-independent potentials drastically promote the accuracy of the predicted surface energies,which match the experimental results well.

  17. Development of HTS Transformers and a 10 kVA HTS Transformer Prototype Design

    Institute of Scientific and Technical Information of China (English)

    Xiao-Yuan Chen; Jian-Xun Jin

    2008-01-01

    With the improvement of high temperature superconductor (HTS) practical performance, research and development concerning the applications of HTS transformers have been progressed actively worldwide. This paper provides a comprehensive summary on various HTS transformers, and studies the design of a single-phase 10 kVA (220V/24V) HTS trans- former prototype to verify HTS for practical transformer applications.

  18. 77 FR 60746 - Proposed Information Collection (VA/DOD Joint Disability Evaluation Board Claim) Activity...

    Science.gov (United States)

    2012-10-04

    ... AFFAIRS Proposed Information Collection (VA/DOD Joint Disability Evaluation Board Claim) Activity: Comment... opportunity for public comment on the proposed collection of certain information by the agency. Under the... Register concerning each proposed collection of information, including each proposed extension of...

  19. Validation and Comparison of KENO V.a and KENO-VI

    Energy Technology Data Exchange (ETDEWEB)

    Fox, P.B.

    2002-05-06

    This report documents the validation and comparison of KENO V.a and KENO-VI using the SCALE 27-group ENDF/B-IV and 238-group ENDF/B-V cross-section libraries against critical experiments. Experiments considered were primarily high- or low-enriched uranium systems. The results indicate that KENO V.a and KENO-VI Monte Carlo Criticality Programs accurately calculate a broad range of critical experiments. A number of the calculations showed a positive or negative bias in excess of 1 1/2% in k-effective (k{sub eff}). Classes of criticals that show a bias include 3% enriched green blocks, highly-enriched uranyl fluoride slab arrays, and highly-enriched uranyl nitrate arrays. If these biases are properly taken into account, KENO V.a and KENO-VI can be used with confidence for the design and criticality safety analysis of uranium-containing systems. KENO V.a and KENO-VI calculate the same k{sub eff} for a system within statistics and thus may be used interchangeably as long as the geometry of the problem can be modeled.

  20. 75 FR 69032 - Naval Surface Warfare Center, Potomac River, Dahlgren, VA; Danger Zone

    Science.gov (United States)

    2010-11-10

    ..., Dahlgren, VA; Danger Zone AGENCY: United States Army Corps of Engineers, Department of Defense. ACTION... amend an existing permanent danger zone in the waters of the Upper Machodoc Creek and the Potomac River... River Test Range. Many of the tests are hazardous operations presenting a danger to persons or...

  1. 75 FR 33273 - Final Environmental Impact Statement (FEIS) for Disposal and Reuse of Fort Monroe, VA

    Science.gov (United States)

    2010-06-11

    ... Department of the Army Final Environmental Impact Statement (FEIS) for Disposal and Reuse of Fort Monroe, VA... socioeconomic impacts associated with the disposal and reuse of Fort Monroe, Virginia. DATES: The waiting period... reuse of Fort Monroe. The 2005 BRAC Commission Report directed the closure of Fort Monroe and...

  2. 76 FR 24567 - Proposed Information Collection (VA MATIC Authorization); Comment Request

    Science.gov (United States)

    2011-05-02

    ... needed to deduct insurance premiums from policyholder's bank account. DATES: Written comments and.... Abstract: Veteran policyholders complete VA Form 29-0532-1 to authorize deduction of Government Life Insurance premiums from their bank account. Affected Public: Individuals or households. Estimated...

  3. 78 FR 79563 - Proposed Information Collection (VA MATIC Authorization); Comment Request

    Science.gov (United States)

    2013-12-30

    ... needed to deduct insurance premiums from policyholder's bank account. DATES: Written comments and.... Abstract: Veteran policyholders complete VA Form 29-0532-1 to authorize deduction of Government Life Insurance premiums from their bank account. Affected Public: Individuals or households. Estimated...

  4. Le CERN va supprimer 600 postes d'ici a 2007

    CERN Multimedia

    2002-01-01

    "Le Laboratoire europeen pour la physique des particules (CERN), qui doit economiser quelque 340 millions d'euros jusqu'en 2008, va reduire ses effectifs de 600 postes d'ici a 2007, a annonce jeudi son porte-parole, James Gillies" (1/2/ page).

  5. Non-intubated recovery from refractory cardiogenic shock on percutaneous VA-extracorporeal membrane oxygenation

    NARCIS (Netherlands)

    van Houte, J; Donker, D W; Wagenaar, L J; Slootweg, A P; Kirkels, J H; van Dijk, D

    2015-01-01

    We report on the use of percutaneous femoral veno-arterial extracorporeal membrane oxygenation (VA-ECMO) in a fully awake, non-intubated and spontaneously breathing patient suffering from acute, severe and refractory cardiogenic shock due to a (sub)acute anterior myocardial infarction. Intensified h

  6. Data of evolutionary structure change: 1DUIA-2G4VA [Confc[Archive

    Lifescience Database Archive (English)

    Full Text Available 1DUIA-2G4VA 1DUI 2G4V A A --AKCVSYGVSQIKAPALHS-----QGYTGSNVKVAVID...H - HHHHHHHHHH EEE - 0 1DUI... A 1DUIA GTVLA----VAPSA ALA CA 375 ARG CA 304 ASN CA 261 1DUI... A 1DUIA AGNEGTSGSSSTV

  7. 78 FR 18425 - Proposed Information Collection VA Police Officer Pre-Employment Screening Checklist); Comment...

    Science.gov (United States)

    2013-03-26

    ... qualification and suitability to be hired as a VA police officer. Affected Public: State, Local, or Tribal... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF VETERANS... Request AGENCY: Office of Operations, Security, and Preparedness, Department of Veterans Affairs....

  8. 78 FR 60379 - Proposed Information Collection (Credit Underwriting Standards and Procedures for Processing VA...

    Science.gov (United States)

    2013-10-01

    ... AFFAIRS Proposed Information Collection (Credit Underwriting Standards and Procedures for Processing VA... information by the agency. Under the Paperwork Reduction Act (PRA) of 1995, Federal agencies are required to publish notice in the Federal Register concerning each proposed collection of information, including...

  9. 75 FR 60171 - Proposed Information Collection (Credit Underwriting Standards and Procedures for Processing VA...

    Science.gov (United States)

    2010-09-29

    ... AFFAIRS Proposed Information Collection (Credit Underwriting Standards and Procedures for Processing VA... information by the agency. Under the Paperwork Reduction Act (PRA) of 1995, Federal agencies are required to publish notice in the Federal Register concerning each proposed collection of information, including...

  10. Differential effects of the KiVa anti-bullying program on popular and unpopular bullies

    NARCIS (Netherlands)

    Garandeau, Claire F.; Lee, Ihno A.; Salmivalli, Christina

    2014-01-01

    This study utilized data from the evaluation of the Finnish KiVa program in testing the prediction that school bullies' high perceived popularity would impede the success of anti-bullying interventions. Multiple-group structural equation modeling (SEM) analyses were conducted on a subsample of 911 t

  11. 78 FR 12600 - VA Homeless Providers Grant and Per Diem Program

    Science.gov (United States)

    2013-02-25

    ... the Federal Register on March 1, 2012 (77 FR 12698), VA proposed to amend its regulations concerning... recuperating from an acute injury or illness. The commenter noted that homeless adults are hospitalized more.... Capital lease is defined by Sec. 61.4. Chronically mentally ill means a condition of schizophrenia...

  12. 76 FR 30598 - Payment or Reimbursement for Emergency Services for Nonservice-Connected Conditions in Non-VA...

    Science.gov (United States)

    2011-05-26

    ... AFFAIRS 38 CFR Part 17 RIN 2900-AN86 Payment or Reimbursement for Emergency Services for Nonservice... Reimbursement for Emergency Services for Nonservice-Connected Conditions in Non-VA Facilities'' regulations to... reimbursement to veterans who receive emergency services in non-VA facilities, and would establish...

  13. 77 FR 23615 - Payment or Reimbursement for Emergency Services for Nonservice-Connected Conditions in Non-VA...

    Science.gov (United States)

    2012-04-20

    ... AFFAIRS 38 CFR Part 17 RIN 2900-AN86 Payment or Reimbursement for Emergency Services for Nonservice... Emergency Services for Nonservice- Connected Conditions in Non-VA Facilities'' regulations to conform with a... Reimbursement for Emergency Services for Nonservice-Connected Conditions in Non-VA Facilities.'' This final...

  14. 76 FR 72045 - Enhanced-Use Lease (EUL) of Department of Veterans Affairs (VA) Real Property for the Development...

    Science.gov (United States)

    2011-11-21

    ... finance, design, develop, construct, maintain and operate the EUL development. The lessee will also be... AFFAIRS Enhanced-Use Lease (EUL) of Department of Veterans Affairs (VA) Real Property for the Development... to enter into an Enhanced-Use Lease (EUL). SUMMARY: The Secretary of VA intends to enter into an...

  15. 76 FR 72047 - Enhanced-Use Lease (EUL) of Department of Veterans Affairs (VA) Real Property for the Development...

    Science.gov (United States)

    2011-11-21

    ... lease, the lessee will be required to finance, design, develop, construct, manage, operate, and maintain... AFFAIRS Enhanced-Use Lease (EUL) of Department of Veterans Affairs (VA) Real Property for the Development... Enhanced-Use Lease (EUL). SUMMARY: The Secretary of VA intends to enter into an EUL on an approximately...

  16. 76 FR 72046 - Enhanced-Use Lease (EUL) of Department of Veterans Affairs (VA) Real Property for the Development...

    Science.gov (United States)

    2011-11-21

    ..., the lessee will be required to finance, design, develop, renovate, operate, and maintain one building... AFFAIRS Enhanced-Use Lease (EUL) of Department of Veterans Affairs (VA) Real Property for the Development.... ACTION: Notice of intent to enter into an Enhanced-Use Lease (EUL). SUMMARY: The Secretary of VA...

  17. A configurational and conformational study of aframodial and its diasteriomers via experimental and theoretical VA and VCD spectroscopies

    DEFF Research Database (Denmark)

    Jalkanen, Karl J.; Gale, J.D.; Lassen, Peter Rygaard;

    2008-01-01

    In this work we present the experimental and theoretical vibrational absorption (VA) and the theoretical vibrational circular dichroism (VCD) spectra for aframodial. In addition, we present the theoretical VA and VCD spectra for the diasteriomers of aframodial. Aframodial has four chiral centers ...

  18. 78 FR 68364 - Payment for Home Health Services and Hospice Care to Non-VA Providers; Delay of Effective Date

    Science.gov (United States)

    2013-11-14

    ... AFFAIRS 38 CFR Part 17 RIN 2900-AN98 Payment for Home Health Services and Hospice Care to Non-VA Providers... services and hospice care. The preamble of that final rule stated the effective date was November 15, 2013..., applicable to non-VA home health services and hospice care. Section 17.56 provides, among other things,...

  19. 78 FR 46497 - Amendment of Class D and E Airspace, and Establishment of Class E Airspace; Oceana NAS, VA

    Science.gov (United States)

    2013-08-01

    ... Establishment of Class E Airspace; Oceana NAS, VA AGENCY: Federal Aviation Administration (FAA), DOT. ACTION... establishes Class E surface airspace at Oceana Naval Air Station, (NAS), VA, due to the Air Traffic Control Tower at Oceana NAS (Apollo Soucek Field) now operating on a part time basis. This action enhances...

  20. 78 FR 21084 - Proposed Amendment of Class D and E Airspace, and Establishment of Class E Airspace; Oceana NAS, VA

    Science.gov (United States)

    2013-04-09

    ... Establishment of Class E Airspace; Oceana NAS, VA AGENCY: Federal Aviation Administration (FAA), DOT. ACTION... operating hours, and establish Class E Airspace at Oceana Naval Air Station, (NAS), VA, due to the Air Traffic Control Tower at Oceana NAS (Apollo Soucek Field) operating on a part time basis. This...

  1. Military and Veteran Support: DOD and VA Programs That Address the Effects of Combat and Transition to Civilian Life

    Science.gov (United States)

    2014-11-01

    TBI, amputations , burns, spinal cord injuries, visual impairment, and PTSD. Over a third of the 99 programs that we identified...recovering servicemember or veteran through recovery, rehabilitation , and reintegration. DOD and VA We Identified 87 DOD and VA Programs That Help...health Provides veterans with spinal cord injury with specialized rehabilitative services at one of the 24 Spinal Cord Injury Centers available

  2. MGC9753 gene, located within PPP1R1B-STARD3-ERBB2-GRB7 amplicon on human chromosome 17q12, encodes the seven-transmembrane receptor with extracellular six-cystein domain.

    Science.gov (United States)

    Katoh, Masuko; Katoh, Masaru

    2003-06-01

    MYC, ERBB2, MET, FGFR2, CCNE1, MYCN, WNT2, CD44, MDM2, NCOA3, IQGAP1 and STK6 loci are amplified in human gastric cancer. It has been reported that the gene corresponding to EST H16094 is co-amplified with ERBB2 gene in human gastric cancer. Here, we identified and characterized the gene corresponding to EST H16094 by using bioinformatics. BLAST programs revealed that EST H16094 was derived from the uncharacterized MGC9753 gene. Two ORFs were predicted within human MGC9753 mRNA, and ORF1 (nucleotide position 18-980 of NM_033419.1) was predicted as the coding region of human MGC9753 mRNA based on comparative genomics. Nucleotide sequence of mouse Mgc9753 mRNA was next determined in silico by modification of AK052486 cDNA (deleting C at the nucleotide position 37). Human MGC9753 and mouse Mgc9753 proteins were 320-amino-acid seven-transmembrane receptors with the N-terminal six-cysteine domain and an N-glycosylation site (85.0% total-amino-acid identity). Human MGC9753 protein showed 90.6% total-amino-acid identity with human CAB2 aberrant protein, which lacked the third-transmembrane domain of MGC9753 due to frame shifts within ORF. Human MGC9753 gene, consisting of eight exons, were clustered with PPP1R1B, STARD3, TCAP, PNMT, ERBB2, MGC14832 and GRB7 genes within the 120-kb region. PPP1R1B, STARD3, MGC9753, ERBB2 and GRB7 genes are co-amplified in several cases of gastric cancer. This is the first report on comprehensive characterization of the amplicon around the PPP1R1B-STARD3-TCAP-PNMT-MGC9753-ERBB2-MGC14832-GRB7 locus on human chromosome 17q12.

  3. Myosin Va mediates Rab8A-regulated GLUT4 vesicle exocytosis in insulin-stimulated muscle cells.

    Science.gov (United States)

    Sun, Yi; Chiu, Tim T; Foley, Kevin P; Bilan, Philip J; Klip, Amira

    2014-04-01

    Rab-GTPases are important molecular switches regulating intracellular vesicle traffic, and we recently showed that Rab8A and Rab13 are activated by insulin in muscle to mobilize GLUT4-containing vesicles to the muscle cell surface. Here we show that the unconventional motor protein myosin Va (MyoVa) is an effector of Rab8A in this process. In CHO-IR cell lysates, a glutathione S-transferase chimera of the cargo-binding COOH tail (CT) of MyoVa binds Rab8A and the related Rab10, but not Rab13. Binding to Rab8A is stimulated by insulin in a phosphatidylinositol 3-kinase-dependent manner, whereas Rab10 binding is insulin insensitive. MyoVa-CT preferentially binds GTP-locked Rab8A. Full-length green fluorescent protein (GFP)-MyoVa colocalizes with mCherry-Rab8A in perinuclear small puncta, whereas GFP-MyoVa-CT collapses the GTPase into enlarged perinuclear depots. Further, GFP-MyoVa-CT blocks insulin-stimulated translocation of exofacially myc-tagged GLUT4 to the surface of muscle cells. Mutation of amino acids in MyoVa-CT predicted to bind Rab8A abrogates both interaction with Rab8A (not Rab10) and inhibition of insulin-stimulated GLUT4myc translocation. Of importance, small interfering RNA-mediated MyoVa silencing reduces insulin-stimulated GLUT4myc translocation. Rab8A colocalizes with GLUT4 in perinuclear but not submembrane regions visualized by confocal total internal reflection fluorescence microscopy. Hence insulin signaling to the molecular switch Rab8A connects with the motor protein MyoVa to mobilize GLUT4 vesicles toward the muscle cell plasma membrane.

  4. Use of outpatient care in VA and Medicare among disability-eligible and age-eligible veteran patients

    Directory of Open Access Journals (Sweden)

    Liu Chuan-Fen

    2012-03-01

    Full Text Available Abstract Background More than half of veterans who use Veterans Health Administration (VA care are also eligible for Medicare via disability or age, but no prior studies have examined variation in use of outpatient services by Medicare-eligible veterans across health system, type of care or time. Objectives To examine differences in use of VA and Medicare outpatient services by disability-eligible or age-eligible veterans among veterans who used VA primary care services and were also eligible for Medicare. Methods A retrospective cohort study of 4,704 disability- and 10,816 age-eligible veterans who used VA primary care services in fiscal year (FY 2000. We tracked their outpatient utilization from FY2001 to FY2004 using VA administrative and Medicare claims data. We examined utilization differences for primary care, specialty care, and mental health outpatient visits using generalized estimating equations. Results Among Medicare-eligible veterans who used VA primary care, disability-eligible veterans had more VA primary care visits (p p p p p p Conclusions Greater use of primary care and specialty care visits by disability-eligible veterans is most likely related to greater health needs not captured by the patient characteristics we employed and eligibility for VA care at no cost. Outpatient care patterns of disability-eligible veterans may foreshadow care patterns of veterans returning from Afghanistan and Iraq wars, who are entering the system in growing numbers. This study provides an important baseline for future research assessing utilizations among returning veterans who use both VA and Medicare systems. Establishing effective care coordination protocols between VA and Medicare providers can help ensure efficient use of taxpayer resources and high quality care for disabled veterans.

  5. Large-scale benchmarking reveals false discoveries and count transformation sensitivity in 16S rRNA gene amplicon data analysis methods used in microbiome studies

    DEFF Research Database (Denmark)

    Thorsen, Jonathan; Brejnrod, Asker Daniel; Mortensen, Martin Steen;

    2016-01-01

    BACKGROUND: There is an immense scientific interest in the human microbiome and its effects on human physiology, health, and disease. A common approach for examining bacterial communities is high-throughput sequencing of 16S rRNA gene hypervariable regions, aggregating sequence-similar amplicons ...... should be interpreted with caution. We provide an easily extensible framework for benchmarking of new methods and future microbiome datasets....... into operational taxonomic units (OTUs). Strategies for detecting differential relative abundance of OTUs between sample conditions include classical statistical approaches as well as a plethora of newer methods, many borrowing from the related field of RNA-seq analysis. This effort is complicated by unique data...... characteristics, including sparsity, sequencing depth variation, and nonconformity of read counts to theoretical distributions, which is often exacerbated by exploratory and/or unbalanced study designs. Here, we assess the robustness of available methods for (1) inference in differential relative abundance...

  6. The Quantification of Representative Sequences pipeline for amplicon sequencing: case study on within-population ITS1 sequence variation in a microparasite infecting Daphnia.

    Science.gov (United States)

    González-Tortuero, E; Rusek, J; Petrusek, A; Gießler, S; Lyras, D; Grath, S; Castro-Monzón, F; Wolinska, J

    2015-11-01

    Next generation sequencing (NGS) platforms are replacing traditional molecular biology protocols like cloning and Sanger sequencing. However, accuracy of NGS platforms has rarely been measured when quantifying relative frequencies of genotypes or taxa within populations. Here we developed a new bioinformatic pipeline (QRS) that pools similar sequence variants and estimates their frequencies in NGS data sets from populations or communities. We tested whether the estimated frequency of representative sequences, generated by 454 amplicon sequencing, differs significantly from that obtained by Sanger sequencing of cloned PCR products. This was performed by analysing sequence variation of the highly variable first internal transcribed spacer (ITS1) of the ichthyosporean Caullerya mesnili, a microparasite of cladocerans of the genus Daphnia. This analysis also serves as a case example of the usage of this pipeline to study within-population variation. Additionally, a public Illumina data set was used to validate the pipeline on community-level data. Overall, there was a good correspondence in absolute frequencies of C. mesnili ITS1 sequences obtained from Sanger and 454 platforms. Furthermore, analyses of molecular variance (amova) revealed that population structure of C. mesnili differs across lakes and years independently of the sequencing platform. Our results support not only the usefulness of amplicon sequencing data for studies of within-population structure but also the successful application of the QRS pipeline on Illumina-generated data. The QRS pipeline is freely available together with its documentation under GNU Public Licence version 3 at http://code.google.com/p/quantification-representative-sequences.

  7. GARCH-EVT模型在动态VaR中的应用%Application of GARCH-EVT Model in Dynamic VaR

    Institute of Scientific and Technical Information of China (English)

    高莹; 周鑫; 金秀

    2008-01-01

    在综合考虑金融资产收益数据分布的波动集群性和厚尾特征,尤其是波动的条件异方差对动态VaR估计的影响的基础上,运用极值理论(EVT),建立了GARCH-EVT模型,计算了上海证券市场综合指数的动态VaR,并且将GARCH-EVT模型与GARCH-NORMAL模型进行比较.通过实证分析,并利用后验测试,结果表明GARCH-EVT模型优于GARCH-NORMAL模型.GARCH-EVT模型很好地解决了波动集群性和厚尾现象,为管理者和投资者提供了一个控制风险、预测收益的量化工具.

  8. RAROC基于VaR的封闭式基金业绩评估

    Institute of Scientific and Technical Information of China (English)

    张晓彬; 黄志勇

    2006-01-01

    介绍了基于VaR的证券投资基金绩效评估方法——RAROC方法,通过该方法对我国封闭式基金投资绩效的分析来揭示投资风险,结果表明:引进VaR风险度量模型,把经风险调整后的绩效评估方法RAROC应用到投资基金绩效评估中,能更客观、准确地反映封闭式基金的投资绩效。

  9. Making bullying prevention a priority in Finnish schools: the KiVa antibullying program.

    Science.gov (United States)

    Salmivalli, Christina; Poskiparta, Elisa

    2012-01-01

    The KiVa antibullying program has been widely implemented in Finnish comprehensive schools since 2009. The program is predicated on the idea that a positive change in the behaviors of classmates can reduce the rewards gained by the perpetrators of bullying and consequently their motivation to bully in the first place. KiVa involves both universal and bullying specific actions to prevent the emergence of new cases of bullying, stop ongoing bullying, and reduce the negative consequences of victimization. The program has been evaluated in a randomized controlled trial involving 234 Finnish schools and during broad dissemination across Finnish schools (the evaluation involving almost one thousand schools) with positive findings. The program content and the implementation model are presented in this article, and the findings from the evaluation studies are summarized.

  10. A large-scale evaluation of the KiVa antibullying program: grades 4-6.

    Science.gov (United States)

    Kärnä, Antti; Voeten, Marinus; Little, Todd D; Poskiparta, Elisa; Kaljonen, Anne; Salmivalli, Christina

    2011-01-01

    This study demonstrates the effectiveness of the KiVa antibullying program using a large sample of 8,237 youth from Grades 4-6 (10-12 years). Altogether, 78 schools were randomly assigned to intervention (39 schools, 4,207 students) and control conditions (39 schools, 4,030 students). Multilevel regression analyses revealed that after 9 months of implementation, the intervention had consistent beneficial effects on 7 of the 11 dependent variables, including self- and peer-reported victimization and self-reported bullying. The results indicate that the KiVa program is effective in reducing school bullying and victimization in Grades 4-6. Despite some evidence against school-based interventions, the results suggest that well-conceived school-based programs can reduce victimization.

  11. VA Health Care: Actions Needed to Address Higher-Than-Expected Demand for the Family Caregiver Program

    Science.gov (United States)

    2014-09-01

    155 1:78 8 North Florida / South Georgia VA HCS Gainesville and Lake City, FL 2 162 1:81 3 VA New Jersey HCS East Orange and Lyons, NJ 2 162 1:81...2 79 1:40 3 James J. Peters VAMC Bronx, NY 3 123 1:41 8 West Palm Beach VAMC West Palm Beach, FL 2 82 1:41 8 C.W. Bill Young VAMC Bay Pines, FL 3...8 Orlando VAMC Orlando, FL 3 472 1:157 20 VA Puget Sound HCS Lakewood and Seattle, WA 2 331 1:166 17 South Texas Veterans HCS Kerrville and San

  12. VA Mental Health: Clearer Guidance on Access Policies and Wait-Time Data Needed

    Science.gov (United States)

    2015-10-01

    which assess VAMC performance across 25 quality measures, including death and medical complication rates, customer satisfaction , and access (based on...care, for our purposes, refers to the delivery of services by providers that are respectful of and responsive to the experiences, views, and needs... Services , Directorate for Information Operations and Reports, 1215 Jefferson Davis Highway, Suite 1204, Arlington VA 22202-4302. Respondents should be

  13. Cargo Transport by Two Coupled Myosin Va Motors on Actin Filaments and Bundles.

    Science.gov (United States)

    Ali, M Yusuf; Vilfan, Andrej; Trybus, Kathleen M; Warshaw, David M

    2016-11-15

    Myosin Va (myoVa) is a processive, actin-based molecular motor essential for intracellular cargo transport. When a cargo is transported by an ensemble of myoVa motors, each motor faces significant physical barriers and directional challenges created by the complex actin cytoskeleton, a network of actin filaments and actin bundles. The principles that govern the interaction of multiple motors attached to the same cargo are still poorly understood. To understand the mechanical interactions between multiple motors, we developed a simple in vitro model in which two individual myoVa motors labeled with different-colored Qdots are linked via a third Qdot that acts as a cargo. The velocity of this two-motor complex was reduced by 27% as compared to a single motor, whereas run length was increased by only 37%, much less than expected from multimotor transport models. Therefore, at low ATP, which allowed us to identify individual motor steps, we investigated the intermotor dynamics within the two-motor complex. The randomness of stepping leads to a buildup of tension in the linkage between motors-which in turn slows down the leading motor-and increases the frequency of backward steps and the detachment rate. We establish a direct relationship between the velocity reduction and the distribution of intermotor distances. The analysis of run lengths and dwell times for the two-motor complex, which has only one motor engaged with the actin track, reveals that half of the runs are terminated by almost simultaneous detachment of both motors. This finding challenges the assumptions of conventional multimotor models based on consecutive motor detachment. Similar, but even more drastic, results were observed with two-motor complexes on actin bundles, which showed a run length that was even shorter than that of a single motor.

  14. Direct observation of the myosin Va recovery stroke that contributes to unidirectional stepping along actin.

    Directory of Open Access Journals (Sweden)

    Katsuyuki Shiroguchi

    2011-04-01

    Full Text Available Myosins are ATP-driven linear molecular motors that work as cellular force generators, transporters, and force sensors. These functions are driven by large-scale nucleotide-dependent conformational changes, termed "strokes"; the "power stroke" is the force-generating swinging of the myosin light chain-binding "neck" domain relative to the motor domain "head" while bound to actin; the "recovery stroke" is the necessary initial motion that primes, or "cocks," myosin while detached from actin. Myosin Va is a processive dimer that steps unidirectionally along actin following a "hand over hand" mechanism in which the trailing head detaches and steps forward ∼72 nm. Despite large rotational Brownian motion of the detached head about a free joint adjoining the two necks, unidirectional stepping is achieved, in part by the power stroke of the attached head that moves the joint forward. However, the power stroke alone cannot fully account for preferential forward site binding since the orientation and angle stability of the detached head, which is determined by the properties of the recovery stroke, dictate actin binding site accessibility. Here, we directly observe the recovery stroke dynamics and fluctuations of myosin Va using a novel, transient caged ATP-controlling system that maintains constant ATP levels through stepwise UV-pulse sequences of varying intensity. We immobilized the neck of monomeric myosin Va on a surface and observed real time motions of bead(s attached site-specifically to the head. ATP induces a transient swing of the neck to the post-recovery stroke conformation, where it remains for ∼40 s, until ATP hydrolysis products are released. Angle distributions indicate that the post-recovery stroke conformation is stabilized by ≥ 5 k(BT of energy. The high kinetic and energetic stability of the post-recovery stroke conformation favors preferential binding of the detached head to a forward site 72 nm away. Thus, the recovery

  15. Improving the Estimations of VaR-GARCH Using Genetic Algorithm

    Institute of Scientific and Technical Information of China (English)

    WANG Chun-feng; LI Gang

    2001-01-01

    In this paper, genetic algorithm (GA) is put forward to improve the accuracy and robustness of the parameters estimation in GARCH models, and the results are applied to calculate value at risk. The computing examples of Dow Jones Index and exchange rate are presented, and the computation results indicate that VaR-GARCH model based on GA outperformed the conventional numerical method on the aspect of computational robustness and accuracy.

  16. Effectiveness of the KiVa Antibullying Program: Grades 1-3 and 7-9

    NARCIS (Netherlands)

    Kärnä, A.; Voeten, M.J.M.; Little, T.D.; Alanen, E.; Poskiparta, E.H.; Salmivalli, C.

    2013-01-01

    This study investigated the effectiveness of the KiVa Antibullying Program in two samples of students, one from Grades 1-3 (7-9 years old, N = 6,927) and the other from Grades 7-9 (13-15 years old, N = 16, 503). The Grades 1-3 students were located in 74 schools and Grades 7-9 students in 73 schools

  17. Military and Veterans’ Benefits: Analysis of VA Compensation Levels for Survivors of Veterans and Servicemembers

    Science.gov (United States)

    2009-11-01

    pensions , and life insurance. Lastly, GAO interviewed officials from VA and groups representing veterans, servicemembers, and their survivors. GAO is...in our analysis other sources of income survivors may receive, such as Social Security, private pensions , or life insurance. For additional context...with survivors receiving a percentage of the employee’s calculated retirement annuity .31 FERS offers similar survivor benefits, but the maximum is 50

  18. Effects of topsoil storage during surface mining on the viability of VA mycorrhiza

    Energy Technology Data Exchange (ETDEWEB)

    Rives, C.S. (Illinois State Univ., Normal); Bajwa, M.I.; Liberta, A.E.; Miller, R.M.

    1980-04-01

    Storing topsoil for 3 years was shown to reduce substantially the levels of viable inocula relative to levels in adjacent, undisturbed prairie soils. The detrimental effect of storage on VA mycorrhiza is associated with the loss of viability of mycorrhizal fragments occurring in the stored soil. Data are also presented supporting an interaction between infected root segments and roots of uninfected plants as a major means of spreading mycorrhiza in these soils.

  19. Low-energy constants and condensates from the V-A spectrum

    CERN Document Server

    Boito, D; Jamin, M; Maltman, K; Peris, S

    2013-01-01

    We present an analysis of the isospin-one V-A correlator based on our successful simultaneous description of the OPAL V and A non-strange tau spectral data. We discuss the values obtained for the Chiral Perturbation Theory low-energy constants L_10 and C_87 as well as the dimension-six and eight condensates and compare them with those in the literature.

  20. VA Health Care: Actions Needed to Improve Newly Enrolled Veterans Access to Primary Care

    Science.gov (United States)

    2015-03-01

    primary care provider and support staff—a nurse care manager, clinical associate, and administrative clerk. Letter Page 2 GAO-16-328...Health Eligibility Center, VHA central office—VHA’s Health Resource Center, Office of Primary Care, and Access and Clinical Administration Program ...newly enrolled veterans were able to access primary care from the Department of Veterans Affairs’ (VA) Veterans Health Administration (VHA), and others

  1. VaProS: a database-integration approach for protein/genome information retrieval

    KAUST Repository

    Gojobori, Takashi

    2016-12-24

    Life science research now heavily relies on all sorts of databases for genome sequences, transcription, protein three-dimensional (3D) structures, protein–protein interactions, phenotypes and so forth. The knowledge accumulated by all the omics research is so vast that a computer-aided search of data is now a prerequisite for starting a new study. In addition, a combinatory search throughout these databases has a chance to extract new ideas and new hypotheses that can be examined by wet-lab experiments. By virtually integrating the related databases on the Internet, we have built a new web application that facilitates life science researchers for retrieving experts’ knowledge stored in the databases and for building a new hypothesis of the research target. This web application, named VaProS, puts stress on the interconnection between the functional information of genome sequences and protein 3D structures, such as structural effect of the gene mutation. In this manuscript, we present the notion of VaProS, the databases and tools that can be accessed without any knowledge of database locations and data formats, and the power of search exemplified in quest of the molecular mechanisms of lysosomal storage disease. VaProS can be freely accessed at http://p4d-info.nig.ac.jp/vapros/.

  2. Matching prosthetics order records in VA National Prosthetics Patient Database to healthcare utilization databases.

    Science.gov (United States)

    Smith, Mark W; Su, Pon; Phibbs, Ciaran S

    2010-01-01

    The National Prosthetics Patient Database (NPPD) is the national Department of Veterans Affairs (VA) dataset that records characteristics of individual prosthetic and assistive devices. It remains unknown how well NPPD records can be matched to encounter records for the same individuals in major VA utilization databases. We compared the count of prosthetics records in the NPPD with the count of prosthetics-related procedures for the same individuals recorded in major VA utilization databases. We then attempted to match the NPPD records to the utilization records by person and date. In general, 40% to 60% of the NPPD records could be matched to outpatient utilization records within a 14-day window around the NPPD dataset entry date. Match rates for inpatient data were lower: 10% to 16% within a 14-day window. The NPPD will be particularly important for studies of certain veteran groups, such as those with spinal cord injury or blast-related polytraumatic injury. Health services researchers should use both the NPPD and utilization databases to develop a full understanding of prosthetics use by individual patients.

  3. The hypothalamic photoreceptors regulating seasonal reproduction in birds: a prime role for VA opsin.

    Science.gov (United States)

    García-Fernández, José M; Cernuda-Cernuda, Rafael; Davies, Wayne I L; Rodgers, Jessica; Turton, Michael; Peirson, Stuart N; Follett, Brian K; Halford, Stephanie; Hughes, Steven; Hankins, Mark W; Foster, Russell G

    2015-04-01

    Extraretinal photoreceptors located within the medio-basal hypothalamus regulate the photoperiodic control of seasonal reproduction in birds. An action spectrum for this response describes an opsin photopigment with a λmax of ∼ 492 nm. Beyond this however, the specific identity of the photopigment remains unresolved. Several candidates have emerged including rod-opsin; melanopsin (OPN4); neuropsin (OPN5); and vertebrate ancient (VA) opsin. These contenders are evaluated against key criteria used routinely in photobiology to link orphan photopigments to specific biological responses. To date, only VA opsin can easily satisfy all criteria and we propose that this photopigment represents the prime candidate for encoding daylength and driving seasonal breeding in birds. We also show that VA opsin is co-expressed with both gonadotropin-releasing hormone (GnRH) and arginine-vasotocin (AVT) neurons. These new data suggest that GnRH and AVT neurosecretory pathways are endogenously photosensitive and that our current understanding of how these systems are regulated will require substantial revision.

  4. Interactions between Leishmania braziliensis and Macrophages Are Dependent on the Cytoskeleton and Myosin Va

    Directory of Open Access Journals (Sweden)

    Elisama Azevedo

    2012-01-01

    Full Text Available Leishmaniasis is a neglected tropical disease with no effective vaccines. Actin, microtubules and the actin-based molecular motor myosin Va were investigated for their involvement in Leishmania braziliensis macrophage interactions. Results showed a decrease in the association index when macrophages were without F-actin or microtubules regardless of the activation state of the macrophage. In the absence of F-actin, the production of NO in non-activated cells increased, while in activated cells, the production of NO was reduced independent of parasites. The opposite effect of an increased NO production was observed in the absence of microtubules. In activated cells, the loss of cytoskeletal components inhibited the release of IL-10 during parasite interactions. The production of IL-10 also decreased in the absence of actin or microtubules in non-activated macrophages. Only the disruption of actin altered the production of TNF-α in activated macrophages. The expression of myosin Va tail resulted in an acute decrease in the association index between transfected macrophages and L. braziliensis promastigotes. These data reveal the importance of F-actin, microtubules, and myosin-Va suggesting that modulation of the cytoskeleton may be a mechanism used by L. braziliensis to overcome the natural responses of macrophages to establish infections.

  5. 基于时变VaR的动态套期保值策略研究%A Research on Dynamic Hedging Strategy Based on Minimized Time-varying VaR

    Institute of Scientific and Technical Information of China (English)

    张胜杰; 张敏敏

    2011-01-01

    套期保值可以规避股市系统性风险,文章研究动态套保策略,以VaR最小化为目标,弥补了现有研究的两点不足.文章建立了ECM—BGARCH模型来拟合市场波动,椎导了基于时变VaR的动态套保比模型,满足每日VaR最小且有效;然后,对我国股指期货的实证研究反映出,相比静态模型,动态模型体现出较好的应用效果:(1)提高了套保绩效;(2)降低了平均VaR,意味着需要更少的风险准备金,节约了套保者的资金成本,也更容易达到资金监管要求;(3)取得了更准确的VaR失效率,时变VaR更准确反映了市场异常.%Systemic risk of stock market can be evaded by hedging, and this paper researches the dynamic hedging strategy, solving two existing researching inadequacies. This paper, based on minimized VaR, establi- shes ECM-BGARCH model to fit the volatility of market, and deduces the optimal dynamic hedging ratio, which meanwhile makes daily VaR minimized and effective. After empirical studies of China's stock index fu- tures market , compared with the original static model, the dynamic model has a good performance in applica- tion: ( 1 ) improving the hedging effectiveness ; (2) reducing the average VaR, which means less risk reserve fund is required saving the capital cost which achieves capital regulatory requirements more likely; (3)getting more accurate VaR failure rate, which means that the time-varying VaR reflects the market exceptions more accurately.

  6. 76 FR 71440 - Enhanced-Use Lease (EUL) of Department of Veterans Affairs (VA) Real Property for the Development...

    Science.gov (United States)

    2011-11-17

    ... into an EUL on an approximately 5.2-acre parcel of land at the Edward Hines, Jr. VA Hospital in Hines, Illinois. The selected lessee will finance, design, develop, construct, manage, maintain and operate...

  7. 75 FR 30915 - Computer Matching Program Between the Department of Veterans Affairs (VA) and the Department of...

    Science.gov (United States)

    2010-06-02

    ... eligibility status of Veterans, Servicemembers, and reservists, and eligible dependents who have applied for... is to enable VA to verify that individuals meet the conditions of military service and...

  8. Research on the Hedging of CSI300 Stock Index Future Based on VaR and CVaR Model

    Directory of Open Access Journals (Sweden)

    Xu Zijian

    2015-01-01

    Full Text Available Hedging function is one of the most significant functions of stock index futures, and it received extensive public attention. This article set VaR and CVaR as hedging objective function of the hedging model in China and proposed the hedging effect measurement method based on VaR and CVaR. It also used the actual data of CSI300 stock index future to calculate its hedging effect. It is found from the result that the hedging model of stock index future based on VaR and CVaR can effectively reduce the risk of portfolio, and a relatively good accumulated income rate will be obtained. By comparison, the hedging model of stock index future based on CVaR will do better in controlling the risk of portfolio, while the hedging model of stock index future based on VaR will obtain a better accumulated income rate.

  9. The VA Point-of-Care Precision Oncology Program: Balancing Access with Rapid Learning in Molecular Cancer Medicine.

    Science.gov (United States)

    Fiore, Louis D; Brophy, Mary T; Turek, Sara; Kudesia, Valmeek; Ramnath, Nithya; Shannon, Colleen; Ferguson, Ryan; Pyarajan, Saiju; Fiore, Melissa A; Hornberger, John; Lavori, Philip

    2016-01-01

    The Department of Veterans Affairs (VA) recognized the need to balance patient-centered care with responsible creation of generalizable knowledge on the effectiveness of molecular medicine tools. Embracing the principles of the rapid learning health-care system, a new clinical program called the Precision Oncology Program (POP) was created in New England. The POP integrates generalized knowledge about molecular medicine in cancer with a database of observations from previously treated veterans. The program assures access to modern genomic oncology practice in the veterans affairs (VA), removes disparities of access across the VA network of clinical centers, disseminates the products of learning that are generalizable to non-VA settings, and systematically presents opportunities for patients to participate in clinical trials of targeted therapeutics.

  10. KiVa Antibullying Program: Overview of Evaluation Studies Based on a Randomized Controlled Trial and National Rollout in Finland

    Directory of Open Access Journals (Sweden)

    Christina Salmivalli

    2012-12-01

    Full Text Available The effects of a Finnish national school-based antibullying program (KiVa were evaluated in a randomized controlled trial (2007–2009 and during nationwide implementation (since 2009. The KiVa program is been found to reduce bullying and victimization and increase empathy towards victimized peers and self-efficacy to support and defend them. KiVa increases school liking and motivation and contributes to significant reductions in anxiety, depression, and negative peer perceptions. Somewhat larger reductions in bullying and victimization were found in the randomized controlled trial than in the broad rollout, and the largest effects were obtained in primary school (grades 1–6. The uptake of the KiVa program is remarkable, with 90 percent of Finnish comprehensive schools currently registered as program users.

  11. Estimating Value at Risk with the Generalized Kalman Filter%基于Generalized Kalman Filter的VaR估计

    Institute of Scientific and Technical Information of China (English)

    赵利锋; 张崇岐

    2009-01-01

    在应用Kalman Filter方法估计时变风险β系数的基础上,引入Generalized Kalman Filter方法来估计时变卢系数,再通过Sharp对角线模型计算投资组合的VaR,并运用Backtesting检验判断两方法估计VaR的精确度.

  12. 30 CFR 57.22212 - Air flow (I-C, II-A, and V-A mines).

    Science.gov (United States)

    2010-07-01

    ... 30 Mineral Resources 1 2010-07-01 2010-07-01 false Air flow (I-C, II-A, and V-A mines). 57.22212... Standards for Methane in Metal and Nonmetal Mines Ventilation § 57.22212 Air flow (I-C, II-A, and V-A mines). Air flow across each working face shall be sufficient to carry away any accumulation of methane,...

  13. 30 CFR 57.22608 - Secondary blasting (I-A, II-A, and V-A mines).

    Science.gov (United States)

    2010-07-01

    ... 30 Mineral Resources 1 2010-07-01 2010-07-01 false Secondary blasting (I-A, II-A, and V-A mines... blasting (I-A, II-A, and V-A mines). Prior to secondary blasting, tests for methane shall be made in the mine atmosphere at blast sites by a competent person. Secondary blasting shall not be done when...

  14. 30 CFR 57.22101 - Smoking (I-A, II-A, III, and V-A mines).

    Science.gov (United States)

    2010-07-01

    ... 30 Mineral Resources 1 2010-07-01 2010-07-01 false Smoking (I-A, II-A, III, and V-A mines). 57.22101 Section 57.22101 Mineral Resources MINE SAFETY AND HEALTH ADMINISTRATION, DEPARTMENT OF LABOR... Smoking (I-A, II-A, III, and V-A mines). Persons shall not smoke or carry smoking materials, matches,...

  15. Les emplois du marqueur discursif « di va » en ancien français

    Directory of Open Access Journals (Sweden)

    Evelyne Oppermann-Marsaux

    2011-07-01

    Full Text Available Cet article porte sur les différents emplois du marqueur discursif « di va » en ancien français. Il s’intéresse plus particulièrement à trois aspects : le figement de la séquence « di va » en comparaison avec les occurrences de « va + di », la pragmaticalisation de l’impératif « di » ainsi que la position et la fonction de « di va » à l’intérieur du discours rapporté. L’étude permet de définir « di va » comme un marqueur discursif polysémique, en distinguant entre les emplois de « di va 1 », dans lesquels le sémantisme premier du verbe « dire » reste présent, et ceux de « di va 2 », où ce sémantisme s’efface. Dans ce dernier cas, « di va » devient compatible avec des contextes injonctifs et déclaratifs. Toujours employé en position initiale (« Di va, P », il traduit souvent une réaction de la part du locuteur face au comportement – verbal ou non verbal – de son allocutaire et peut alors prendre des valeurs expressives différentes, allant de l’opposition à la bienveillance et à l’incrédulité. « Di va 1 » en revanche, figure exclusivement dans le contexte immédiat d’une interrogation (qu’il ne précède pas obligatoirement et se comporte alors « seulement » comme une interjection d’appel, qui attire l’attention de l’allocutaire sur la question posée.This paper deals with the different uses of the discourse marker “di va” in Old French. It focuses on three main points: the fixation of the sequence “di va” compared to the occurrences of “va + di”, the pragmaticalization of the imperative “di”, and the position and the function of “di va” within reported speech. The study defines “di va” as a polysemic discourse marker, and distinguishes between the uses of “di va 1”, where the primary lexical meaning of the verb “dire” is still present, and those of “di va 2”, where this lexical meaning has disappeared

  16. Enhanced detection of polymorphic DNA by multiple arbitrary amplicon profiling of endonuclease-digested DNA: identification of markers tightly linked to the supernodulation locus in soybean.

    Science.gov (United States)

    Caetano-Anollés, G; Bassam, B J; Gresshoff, P M

    1993-10-01

    Multiple endonuclease digestion of template DNA or amplification products can increase significantly the detection of polymorphic DNA in fingerprints generated by multiple arbitrary amplicon profiling (MAAP). This coupling of endonuclease cleavage and amplification of arbitrary stretches of DNA, directed by short oligonucleotide primers, readily allowed distinction of closely related fungal and bacterial isolates and plant cultivars. MAAP analysis of cleaved template DNA enabled the identification of molecular markers linked to a developmental locus of soybean (Glycine max L. Merrill). Ethyl methane sulfonate (EMS)-induced supernodulating, near-isogenic lines altered in the nts locus, which controls nodule formation, could be distinguished from each other and from the parent cultivar by amplification of template pre-digested with 2-3 restriction enzymes. A total of 42 DNA polymorphisms were detected using only 19 octamer primers. In the absence of digestion, 25 primers failed to differentiate these soybean genotypes. Several polymorphic products co-segregated tightly with the nts locus in F2 families from crosses between the allelic mutants nts382 and nts1007 and the ancestral G. soja Sieb. & Succ. PI468.397. Our results suggest that EMS is capable of inducing extensive DNA alterations, probably around discrete mutational hot-spots. EMS-induced DNA polymorphisms may constitute sequence-tagged markers diagnostic of specific genomic regions.

  17. The utility of diversity profiling using Illumina 18S rRNA gene amplicon deep sequencing to detect and discriminate Toxoplasma gondii among the cyst-forming coccidia.

    Science.gov (United States)

    Cooper, Madalyn K; Phalen, David N; Donahoe, Shannon L; Rose, Karrie; Šlapeta, Jan

    2016-01-30

    Next-generation sequencing (NGS) has the capacity to screen a single DNA sample and detect pathogen DNA from thousands of host DNA sequence reads, making it a versatile and informative tool for investigation of pathogens in diseased animals. The technique is effective and labor saving in the initial identification of pathogens, and will complement conventional diagnostic tests to associate the candidate pathogen with a disease process. In this report, we investigated the utility of the diversity profiling NGS approach using Illumina small subunit ribosomal RNA (18S rRNA) gene amplicon deep sequencing to detect Toxoplasma gondii in previously confirmed cases of toxoplasmosis. We then tested the diagnostic approach with species-specific PCR genotyping, histopathology and immunohistochemistry of toxoplasmosis in a Risso's dolphin (Grampus griseus) to systematically characterise the disease and associate causality. We show that the Euk7A/Euk570R primer set targeting the V1-V3 hypervariable region of the 18S rRNA gene can be used as a species-specific assay for cyst-forming coccidia and discriminate T. gondii. Overall, the approach is cost-effective and improves diagnostic decision support by narrowing the differential diagnosis list with more certainty than was previously possible. Furthermore, it supplements the limitations of cryptic protozoan morphology and surpasses the need for species-specific PCR primer combinations.

  18. Gastrointestinal Bacterial and Methanogenic Archaea Diversity Dynamics Associated with Condensed Tannin-Containing Pine Bark Diet in Goats Using 16S rDNA Amplicon Pyrosequencing

    Directory of Open Access Journals (Sweden)

    Byeng R. Min

    2014-01-01

    Full Text Available Eighteen Kiko-cross meat goats (n=6 were used to collect gastrointestinal (GI bacteria and methanogenic archaea for diversity measures when fed condensed tannin-containing pine bark (PB. Three dietary treatments were tested: control diet (0% PB and 30% wheat straw (WS; 0.17% condensed tannins (CT dry matter (DM; 15% PB and 15% WS (1.6% CT DM, and 30% PB and 0% WS (3.2% CT DM. A 16S rDNA bacterial tag-encoded FLX amplicon pyrosequencing technique was used to characterize and elucidate changes in GI bacteria and methanogenic archaea diversity among the diets. Proteobacteria was the most dominant phylum in goats with mean relative abundance values ranging from 39.7 (30% PB to 46.5% (control and 47.1% (15% PB. Other phyla individually accounted for fewer than 25% of the relative abundance observed. Predominant methanogens were Methanobrevibacter (75, 72, and 49%, Methanosphaera (3.3, 2.3, and 3.4%, and Methanobacteriaceae (1.2, 0.6, and 0.7% population in control, 15, and 30% PB, respectively. Among methanogens, Methanobrevibacter was linearly decreased (P=0.05 with increasing PB supplementation. These results indicate that feeding PB selectively altered bacteria and methanogenic archaeal populations in the GI tract of goats.

  19. Gastrointestinal Bacterial and Methanogenic Archaea Diversity Dynamics Associated with Condensed Tannin-Containing Pine Bark Diet in Goats Using 16S rDNA Amplicon Pyrosequencing.

    Science.gov (United States)

    Min, Byeng R; Solaiman, Sandra; Shange, Raymon; Eun, Jong-Su

    2014-01-01

    Eighteen Kiko-cross meat goats (n = 6) were used to collect gastrointestinal (GI) bacteria and methanogenic archaea for diversity measures when fed condensed tannin-containing pine bark (PB). Three dietary treatments were tested: control diet (0% PB and 30% wheat straw (WS); 0.17% condensed tannins (CT) dry matter (DM)); 15% PB and 15% WS (1.6% CT DM), and 30% PB and 0% WS (3.2% CT DM). A 16S rDNA bacterial tag-encoded FLX amplicon pyrosequencing technique was used to characterize and elucidate changes in GI bacteria and methanogenic archaea diversity among the diets. Proteobacteria was the most dominant phylum in goats with mean relative abundance values ranging from 39.7 (30% PB) to 46.5% (control) and 47.1% (15% PB). Other phyla individually accounted for fewer than 25% of the relative abundance observed. Predominant methanogens were Methanobrevibacter (75, 72, and 49%), Methanosphaera (3.3, 2.3, and 3.4%), and Methanobacteriaceae (1.2, 0.6, and 0.7%) population in control, 15, and 30% PB, respectively. Among methanogens, Methanobrevibacter was linearly decreased (P = 0.05) with increasing PB supplementation. These results indicate that feeding PB selectively altered bacteria and methanogenic archaeal populations in the GI tract of goats.

  20. The use of genus-specific amplicon pyrosequencing to assess phytophthora species diversity using eDNA from soil and water in Northern Spain.

    Science.gov (United States)

    Català, Santiago; Pérez-Sierra, Ana; Abad-Campos, Paloma

    2015-01-01

    Phytophthora is one of the most important and aggressive plant pathogenic genera in agriculture and forestry. Early detection and identification of its pathways of infection and spread are of high importance to minimize the threat they pose to natural ecosystems. eDNA was extracted from soil and water from forests and plantations in the north of Spain. Phytophthora-specific primers were adapted for use in high-throughput Sequencing (HTS). Primers were tested in a control reaction containing eight Phytophthora species and applied to water and soil eDNA samples from northern Spain. Different score coverage threshold values were tested for optimal Phytophthora species separation in a custom-curated database and in the control reaction. Clustering at 99% was the optimal criteria to separate most of the Phytophthora species. Multiple Molecular Operational Taxonomic Units (MOTUs) corresponding to 36 distinct Phytophthora species were amplified in the environmental samples. Pyrosequencing of amplicons from soil samples revealed low Phytophthora diversity (13 species) in comparison with the 35 species detected in water samples. Thirteen of the MOTUs detected in rivers and streams showed no close match to sequences in international sequence databases, revealing that eDNA pyrosequencing is a useful strategy to assess Phytophthora species diversity in natural ecosystems.

  1. The Influence of DNA Extraction Procedure and Primer Set on the Bacterial Community Analysis by Pyrosequencing of Barcoded 16S rRNA Gene Amplicons.

    Science.gov (United States)

    Starke, Ingo C; Vahjen, Wilfried; Pieper, Robert; Zentek, Jürgen

    2014-01-01

    In this study, the effect of different DNA extraction procedures and primer sets on pyrosequencing results regarding the composition of bacterial communities in the ileum of piglets was investigated. Ileal chyme from piglets fed a diet containing different amounts of zinc oxide was used to evaluate a pyrosequencing study with barcoded 16S rRNA PCR products. Two DNA extraction methods (bead beating versus silica gel columns) and two primer sets targeting variable regions of bacterial 16S rRNA genes (8f-534r versus 968f-1401r) were considered. The SEED viewer software of the MG-RAST server was used for automated sequence analysis. A total of 5.2 × 10(5) sequences were used for analysis after processing for read length (150 bp), minimum sequence occurrence (5), and exclusion of eukaryotic and unclassified/uncultured sequences. DNA extraction procedures and primer sets differed significantly in total sequence yield. The distribution of bacterial order and main bacterial genera was influenced significantly by both parameters. However, this study has shown that the results of pyrosequencing studies using barcoded PCR amplicons of bacterial 16S rRNA genes depend on DNA extraction and primer choice, as well as on the manner of downstream sequence analysis.

  2. The Influence of DNA Extraction Procedure and Primer Set on the Bacterial Community Analysis by Pyrosequencing of Barcoded 16S rRNA Gene Amplicons

    Directory of Open Access Journals (Sweden)

    Ingo C. Starke

    2014-01-01

    Full Text Available In this study, the effect of different DNA extraction procedures and primer sets on pyrosequencing results regarding the composition of bacterial communities in the ileum of piglets was investigated. Ileal chyme from piglets fed a diet containing different amounts of zinc oxide was used to evaluate a pyrosequencing study with barcoded 16S rRNA PCR products. Two DNA extraction methods (bead beating versus silica gel columns and two primer sets targeting variable regions of bacterial 16S rRNA genes (8f-534r versus 968f-1401r were considered. The SEED viewer software of the MG-RAST server was used for automated sequence analysis. A total of 5.2×105 sequences were used for analysis after processing for read length (150 bp, minimum sequence occurrence (5, and exclusion of eukaryotic and unclassified/uncultured sequences. DNA extraction procedures and primer sets differed significantly in total sequence yield. The distribution of bacterial order and main bacterial genera was influenced significantly by both parameters. However, this study has shown that the results of pyrosequencing studies using barcoded PCR amplicons of bacterial 16S rRNA genes depend on DNA extraction and primer choice, as well as on the manner of downstream sequence analysis.

  3. Effect of VA and MWNT contents on the rheological and physical properties of EVA

    Science.gov (United States)

    Kim, Jong-Ho; Lee, Seungwon; Kim, Byoung Chul; Shin, Bong-Seob; Jeon, Jong-Young; Chae, Dong Wook

    2016-02-01

    Ethylene vinyl acetate (EVA) copolymers with two different VA contents (15 and 33 wt.%, denoted by EVA15 and EVA33, respectively) were melt compounded with multi-walled carbon nanotubes (MWNTs) and the effect of VA and nanotube contents on the rheological, thermal and morphological properties was investigated. The addition of nanotubes into both EVAs increased the onset temperature of crystallization and broadened the peak, but further addition from 3 wt.% slightly decreased the temperature with increasing nanotube contents. In the wide angle X-ray diffraction patterns the peak of EVA15 was little affected by the presence of nanotubes but that of EVA33 slightly shifted to higher degree and became sharper with increasing nanotube contents. Dynamic viscosity (η') increased with nanotube contents giving abrupt increase at 2 wt.% nanotubes. Loss tangent decreased with increasing nanotube contents exhibiting the plateau-like behavior over most of the frequency range from 2 wt.% nanotubes. In the Casson plot, yield stress increased with nanotube content and its increasing extent was more notable for more VA content. In the Cole-Cole plot, the presence of nanotubes from 2 wt.% gave rise to the deviation from the single master curve by decreasing the slope. The deviated extent of EVA33 became more remarkable with increasing nanotube contents than that of EVA15. The stress-strain curve showed that more improved tensile modulus and yield stress were achieved by the introduction of MWNTs for EVA 33 than for EVA15. Tensile strength of EVA33 increased with increasing nanotube contents, while that of EVA15 decreased.

  4. [Theory of V.A. dogiel on polymerization and oligomerization as a general integration concept].

    Science.gov (United States)

    Makmaev, Iu V

    2010-01-01

    The theory of V.A. Dogiel on the significance of polymerization and ligomerization processes in the evolution of Protozoa and Metazoa is compared with the paper of I.I. Schmalhauisen (1972) on factors and steps of aromorph evolution. Dogiel's theory is considered as a general integration conception. Four steps are distinguished in the evolution of biological systems: (1) formation of morphofunctional system by units of the lower structural level, (2) polymerization of morphofunctional units of a system, (3) oligomerization of morphofunctional units of system by means of their reduction, uniting, or differentiation, (4) integration and stabilization of a system owing to development of morphofunctional connections between its parts.

  5. va le travail à l’ère du numérique ?

    OpenAIRE

    Bercot, Régine; Blanc, Martine; Durampart, Michel; Grenier, Corinne; Guyot, Brigitte; Hassanaly, Parina; Le Bis, Isabelle; Metzger, Jean-Luc; Moatty, Frédéric; Peyrard, Catherine; Pierson, Françoise; Rouard, Françoise; Saint Laurent-Kogan (de), Anne-France; Teiger, Catherine; Vacher, Béatrice

    2013-01-01

    va le travail ? Les technologies de l’information ont envahi massivement les sphères professionnelles, et ont soumis le travail des salariés à des bouleversements tant techniques, qu’organisationnels et identitaires, encore peu étudiés aujourd’hui. L’ouvrage se concentre sur trois changements majeurs. Il montre : 1) comment s’associent désormais les salariés au travail ; 2) quels apprentissages sont désormais requis, quand les savoirs sont dès leur acquisition considérés comme obsolètes ;...

  6. STUDY ON DETERMINATION OF TRACE Fe BY Fe(Ⅱ)-VA THIN LAYER RESIN PHASE SPECTROPHOTOMETRY

    Institute of Scientific and Technical Information of China (English)

    SONG Huanyu; YAN Yongsheng; WANG Yun

    2006-01-01

    A new method for the determination of Fe by thin layer resin phase spectrophotometry in alkali condition was reported. The complex anion formed by Fe(Ⅱ) and VA was absorbed on the 717#resin and Fe was determined by making thin layer. This method had a high sensitivity (ε620=3.0×105 L/mol·cm), which was 15 times higher than that of liquid phase spectrophotometry. It had been proved a satisfactory precision (5.0μg Fe, n=6, RSD=1.8%). The trace Fe in natural water was determined and the recovery was 97%.

  7. Toxicidad de VA-DIFTET® por administración a dosis repetida en ratones

    OpenAIRE

    Pablo González; Enrique Muñoz; Anait Martínez; Mildrey Fariñas; Reynaldo Oliva; Osmany Marrero

    2000-01-01

    Una vez estudiada la toxicidad de la vacuna VA-DIFTET® (vacuna antidiftérica antitetánica) por administración a dosis única en dos especies de animales, se impone la evaluación a dosis repetida, teniendo en cuenta que el esquema de inmunización en humanos prevé la aplicación de tres dosis cuando el componente pertusis de la DPT está contraindicado. Se emplearon 210 ratones OF-1 de ambos sexos. Los grupos experimentales fueron similares a los de la prueba a dosis única con la vacuna dúplex, an...

  8. The Orbital Evolution of 2007 VA85, an Amor-type Asteroid on a Retrograde Orbit.

    Science.gov (United States)

    Kankiewicz, P.; Włodarczyk, I.

    2010-06-01

    Among the known population of asteroids on retrograde orbits (i > 90°) we found an object classified as an Amor-type asteroid. During the analysis of the first results of astrometry, we found some possible Earth-impact solutions for this asteroid. After taking into account the latest observations, we excluded any significant impact solution. However, this asteroid is the first known example of potentially hazardous object on a retrograde orbit. We also investigated the orbital evolution of 2007 VA85 (1 My in the past), obtaining possible scenarios of its dynamical origin.

  9. Què va ser primer en l'origen de la vida?

    OpenAIRE

    Santos, Mauro

    2010-01-01

    Una recerca publicada a "Proceedings of the National Academy of Sciences" rebutja la teoria de què l'origen de la vida es va originar com un sistema de molècules autocatalític capaç d'experimentar evolució darwiniana sense la necessitat d'ARN o d'ADN i de la seva replicació. L'estudi, en què ha participat Mauro Santos, investigador del Departament de Genètica i de Microlobiologia de la UAB, ha demostrat, analitzant el que alguns investigadors han anomenat "genomes compostos", que aquestes xar...

  10. Social work in the Veterans Health Administration (VA) System: rewards, challenges, roles and interventions.

    Science.gov (United States)

    Beder, Joan; Postiglione, Paul

    2013-01-01

    For the social worker in the Veterans Health Administration (VA) System, numerous challenges are faced and met while serving the nation's Veterans. As part of the multidisciplinary team, social workers perform a variety of tasks and function in diverse roles. The qualitative survey research reported in this article sought to detail what social workers identified about the impact and rewards of their work and what they saw as the challenges and frustrations. In addition the social workers were asked to clarify their role with the patient and the family. Intervention strategies used in the course of the social workers interaction with the Veterans was also ascertained.

  11. Analysis of low energy arc discharge characteristics based on dynamic V-A characteristics model

    Institute of Scientific and Technical Information of China (English)

    JING Li-nan; WANG Li-gong

    2006-01-01

    Low energy arc discharge characteristics was analyzed based on dynamic V-A characteristics model. It draws conclusions that discharge time relates to the source voltage and the product of inductance and stable current, discharge time will increase when the source voltage increases; current reduce rate is in inverse proportion to the value of inductance; arc resistance when the arc occurs is the ratio of minimum arcing voltage to stable current. It also gains the expressions of arc resistance and arc power, arc resistance and arc power both increase as the source voltage increases and decrease as the value of inductance increases. Conclusions above mentioned are helpful to design intrinsically safe circuits.

  12. Crisis convulsiva en hemodi??lisis con compromiso de la v??a a??rea

    OpenAIRE

    2014-01-01

    La aparici??n de crisis convulsivas en los pacientes sometidos a hemodi??lisis son m??s frecuentes que en la poblaci??n general y son debidas por diversas causas siendo las metab??licas las m??s frecuentes. Estos pacientes tienen mayor incidencia de coagulopat??as y junto al uso de heparina durante la hemodi??lisis pueden desarrollar hemorragias cerebrales que a su vez pueden ser la causa de crisis convulsivas. Ante una crisis convulsiva es imprescindible mantener una v??a a??rea ...

  13. 投资组合行业配置的动态VaR研究--基于时变Copula-GJR-Skewed-t模型

    Institute of Scientific and Technical Information of China (English)

    刘澄; 张玲

    2013-01-01

    用时变Copula-GJR-Skewed-t模型研究了深证22个行业分类指数中任意两个投资组合的动态VaR,并与静态VaR比较。实证结果表明,时变t-Copula函数在众多Copula函数中对行业投资组合的拟合效果最优,给出了模型估计出的VaR最大和最小的5对行业组合,不同行业组合的动态VaR在股市周期各阶段关系相对稳定,同一行业组合的动态VaR和静态VaR关系相对稳定,且略高于静态VaR。%Based on time-varying Copula-GJR-Skewed-t model, portfolio dynamical VaR of any two industrial indexes among 22 industrial indexes of Shenzhen stock exchanges is analyzed and compared to corresponding static VaR. The empirical result shows that among several Copulas, time-varying t-Copula is the most suitable for the industrial portfolios. Industrial portfolios of the 5 biggest and 5 smallest VaR are given. The relationship of dynamical VaR of different portfolios keeps stable in all phases of stock market cycle. The relationship of dynamical VaR and static VaR of a portfolio keeps stable, the former is a little bigger than the latter.

  14. Hemoglobin derivatives

    Science.gov (United States)

    ... this page: //medlineplus.gov/ency/article/003371.htm Hemoglobin derivatives To use the sharing features on this page, please enable JavaScript. Hemoglobin derivatives are altered forms of hemoglobin . Hemoglobin is ...

  15. SiO Masers around WX Psc Mapped with the KVN and VERA Array (KaVA)

    Science.gov (United States)

    Yun, Youngjoo; Cho, Se-Hyung; Imai, Hiroshi; Kim, Jaeheon; Asaki, Yoshiharu; Chibueze, James O.; Choi, Yoon Kyung; Dodson, Richard; Kim, Dong-Jin; Kusuno, Kozue; Matsumoto, Naoko; Min, Cheulhong; Oyadomari, Miyako; Rioja, María J.; Yoon, Dong-Hwan; Byun, Do-Young; Chung, Hyunsoo; Chung, Moon-Hee; Hagiwara, Yoshiaki; Han, Myoung-Hee; Han, Seog-Tae; Hirota, Tomoya; Honma, Mareki; Hwang, Jung-Wook; Je, Do-Heung; Jike, Takaaki; Jung, Dong-Kyu; Jung, Taehyun; Kang, Ji-Hyun; Kang, Jiman; Kang, Yong-Woo; Kan-ya, Yukitoshi; Kanaguchi, Masahiro; Kawaguchi, Noriyuki; Kim, Bong Gyu; Ryoung Kim, Hyo; Kim, Hyun-Goo; Kim, Jongsoo; Kim, Kee-Tae; Kim, Mikyoung; Kobayashi, Hideyuki; Kono, Yusuke; Kurayama, Tomoharu; Lee, Changhoon; Lee, Jeewon; Lee, Jeong Ae; Lee, Jung-Won; Lee, Sang Hyun; Lee, Sang-Sung; Lyo, A.-Ran; Minh, Young Chol; Oh, Chungsik; Oh, Se-Jin; Oyama, Tomoaki; Roh, Duk-Gyoo; Sawada-Satoh, Satoko; Shibata, Katsunori M.; Sohn, Bong Won; Song, Min-Gyu; Tamura, Yoshiaki; Wi, Seog-Oh; Yeom, Jae-Hwan

    2016-05-01

    We present the first images of the v = 1 and v = 2 J = 1 → 0 SiO maser lines taken with KaVA, i.e., the combined array of the Korean Very Long Baseline Interferometry (VLBI) Network and the VLBI Exploration of Radio Astrometry (VERA), toward the OH/IR star WX Psc. The combination of long and short antenna baselines enabled us to detect a large number of maser spots, which exhibit a typical ring-like structure in both the v = 1 and v = 2 J = 1 → 0 SiO masers as those that have been found in previous VLBI observational results of WX Psc. The relative alignment of the v = 1 and v = 2 SiO maser spots are precisely derived from astrometric analysis, due to the absolute coordinates of the reference maser spot that were well determined in an independent astrometric observation with VERA. The superposition of the v = 1 and v = 2 maser spot maps shows a good spatial correlation between the v = 1 and v = 2 SiO maser features. Nevertheless, it is also shown that the v = 2 SiO maser spot is distributed in an inner region compared to the v = 1 SiO maser by about 0.5 mas on average. These results provide good support for the recent theoretical studies of the SiO maser pumping, in which both the collisional and the radiative pumping predict the strong spatial correlation and the small spatial discrepancy between the v = 1 and v = 2 SiO maser.

  16. Measurement to stock market liquidity risk based on GARCH-VaR model%基于GARCH-VaR模型的股票流动性风险度量

    Institute of Scientific and Technical Information of China (English)

    刘晓青; 杨一文

    2015-01-01

    Based on investigation to liquidity risk before, this paper focuses more on the heterogeneity of stock market. Firstly, it does MODWT to the liquidity scale data, then calculates VaR of each scale using GARCH-VaR model, finally tests the effectiveness of the model. The paper proves risk capacity varies with capital scale, and the various risk pressure long-term and short-term investors face.%在原有流动性风险研究的基础上,充分考虑股票市场异质性,对流动性指标数据进行了最大重复离散小波变换(MODWT),然后运用GARCH-VaR模型分别计算各尺度上的VaR值,并对其进行了有效性检验。通过对各尺度VaR值的统计结果进行分析,验证所投资市场资本规模对风险容纳能力的不同以及长期投资者与短期投资者面对的不同流动性压力。

  17. Morphological alteration of the Dráva as the result of human impact

    Directory of Open Access Journals (Sweden)

    Tímea Kiss

    2011-10-01

    Full Text Available The Croatian-Hungarian border section of the Dráva River has been undisturbed for almost a century, and it is characterised by unique fluvial morphology (braided pattern and islands supporting rich habitats and wildlife. However, during the last decades human impact became more and moreintensive. Between 1975 and 1989 three water reservoirs were built on the Croatian section of the river, just 16 km from the beginning of the border-section, altering the hydrology and the sediment characteristics of the river. On a local scale cut-offs, revetments and groynes were built. The aim of the study was to evaluate the effect of these human interventions. As the result of the alteration of the hydrology the channel pattern of the Dráva has been changing from braided to meandering, though on the upstream meandering part the territory and number of islands increased due to the drop of water stages. A cut-off and a groyne influenced only the morphology of a short section. As the result of the cut-off braided pattern became more pronounced, and the groyne caused intensive channel aggradation and gave way to lateral island development.

  18. The KiVa antibullying curriculum and outcome: does fidelity matter?

    Science.gov (United States)

    Haataja, Anne; Voeten, Marinus; Boulton, Aaron J; Ahtola, Annarilla; Poskiparta, Elisa; Salmivalli, Christina

    2014-10-01

    Research on school-based prevention suggests that the success of prevention programs depends on whether they are implemented as intended. In antibullying program evaluations, however, limited attention has been paid to implementation fidelity. The present study fills in this gap by examining the link between the implementation of the KiVa antibullying program and outcome. With a large sample of 7413 students (7-12years) from 417 classrooms within 76 elementary schools, we tested whether the degree of implementation of the student lessons in the KiVa curriculum was related to the effectiveness of the program in reducing bullying problems in classrooms. Results of multilevel structural equation modeling revealed that after nine months of implementation, lesson adherence as well as lesson preparation time (but not duration of lessons) were associated with reductions in victimization at the classroom level. No statistically significant effects, however, were found for classroom-level bullying. The different outcomes for victimization and bullying as well as the importance of documenting program fidelity are discussed.

  19. Necessity of Recension, Correction and Analysis of Bostan ol-Arefin va Tohfat ol-Moridin

    Directory of Open Access Journals (Sweden)

    سعید بزرگ بیگدلی

    2013-06-01

    Full Text Available Bostan ol-Arefin va Tohfat ol-Moridin is one of the mystical prose texts of the Khorasan area in the fifth century A.H. Among the many Persian literary texts, it is considered as a precious ancient source for many of the anecdotes, miracles and sayings of the Sufis. Furthermore, the linguistic features of this book such as numerous special vocabularies, stylistic aspects and prose similar to the spoken language of the fifth century are among the other values of this book. Bostan ol-Arefin va Tohfat ol-Moridin, Montakhab-e Ronaq ol-Majalis and the attachments whose second edition has recently been released was published by Dr. Ahmad Ali Rajai Bukharaee in 1354 Š (1975. In this article the author is going to investigate this printed text by using the known and accessible manuscripts of Bostan ol-Arefin and other ancient sources to point to numerous errors in the text calling for a new recension.

  20. The process of implementing a rural VA wound care program for diabetic foot ulcer patients.

    Science.gov (United States)

    Reiber, Gayle E; Raugi, Gregory J; Rowberg, Donald

    2007-10-01

    Delivering and documenting evidence-based treatment to all Department of Veterans Affairs (VA) foot ulcer patients has wide appeal. However, primary and secondary care medical centers where 52% of these patients receive care are at a disadvantage given the frequent absence of trained specialists to manage diabetic foot ulcers. A retrospective review of diabetic foot ulcer patient records and a provider survey were conducted to document the foot ulcer problem and to assess practitioner needs. Results showed of the 125 persons with foot ulcers identified through administrative data, only, 21% of diabetic foot patients were correctly coded. Chronic Care and Microsystem models were used to prepare a tailored intervention in a VA primary care medical center. The site Principal Investigators, a multidisciplinary site wound care team, and study investigators jointly implemented a diabetic foot ulcer program. Intervention components include wound care team education and training, standardized good wound care practices based on strong scientific evidence, and a wound care template embedded in the electronic medical record to facilitate data collection, clinical decision making, patient ordering, and coding. A strategy for delivering offloading pressure devices, regular case management support, and 24/7 emergency assistance also was developed. It took 9 months to implement the model. Patients were enrolled and followed for 1 year. Process and outcome evaluations are on-going.

  1. Measuring the risk of an Iranian banking system using Value at Risk (VaR Model

    Directory of Open Access Journals (Sweden)

    Sudabeh Morshedian Rafiee

    2012-10-01

    Full Text Available Measuring risk of financial institutes and banks plays an important role on managing them. Recent financial turmoil in United States banking system has motivated banking industry to monitor risk factors more closely. In this paper, we present an empirical study to measure the risk of some private banks in Iran called Bank Mellat using Value at Risk (VaR method. The proposed study collects the necessary information for the fiscal year of 2010 and analyses them using regression analysis. The study divides the financial data into two groups where the financial data of the first half of year is considered in the first group and the remaining information for the second half of year 2010 is considered in the second group. The implementation of VaR method indicates that financial risks increase during the time horizon. The study also uses linear regression method where independent variable is time, dependent variable is the financial risk, and the results confirm what we have found in the previous part of the survey.

  2. Model of dynamic VaR estimation and empirical study%动态VaR估计模型及实证

    Institute of Scientific and Technical Information of China (English)

    马玉林; 赵静

    2009-01-01

    为了准确描述金融收益率序列的波动率聚集,异方差、厚尾等特性,研究我国证券市场的时变风险,本文利用极值理论和GARCH模型在处理金融数据上的优点,构造了基于GARCH-EVT的条件VaR模型,并对沪市综合指数收益率进行实证研究,结果表明,上海股市存在ARCH效应j收益率序列具有较强的自相关性;以GARCH模型为基础的条件极值方法比GARCH-正态和GARCH-t模型更好地消除了厚尾性对估计结果的影响,能更准确地捕捉风险的时交特性.

  3. VLBI observations of bright AGN jets with KVN and VERA Array (KaVA): Evaluation of Imaging Capability

    CERN Document Server

    Niinuma, Kotaro; Kino, Motoki; Sohn, Bong Won; Akiyama, Kazunori; Zhao, Guang-Yao; Sawada-Satoh, Satoko; Trippe, Sascha; Hada, Kazuhiro; Jung, Taehyun; Hagiwara, Yoshiaki; Dodson, Richard; Koyama, Shoko; Honma, Mareki; Nagai, Hiroshi; Chung, Aeree; Doi, Akihiro; Fujisawa, Kenta; Han, Myoung-Hee; Kim, Joeng-Sook; Lee, Jeewon; Lee, Jeong Ae; Miyazaki, Atsushi; Oyama, Tomoaki; Sorai, Kazuo; Wajima, Kiyoaki; Bae, Jaehan; Byun, Do-Young; Cho, Se-Hyung; Choi, Yoon Kyung; Chung, Hyunsoo; Chung, Moon-Hee; Han, Seog-Tae; Hirota, Tomoya; Hwang, Jung-Wook; Je, Do-Heung; Jike, Takaaki; Jung, Dong-Kyu; Jung, Jin-Seung; Kang, Ji-Hyun; Kang, Jiman; Kang, Yong-Woo; Kan-ya, Yukitoshi; Kanaguchi, Masahiro; Kawaguchi, Noriyuki; Kim, Bong Gyu; Kim, Hyo Ryoung; Kim, Hyun-Goo; Kim, Jaeheon; Kim, Jongsoo; Kim, Kee-Tae; Kim, Mikyoung; Kobayashi, Hideyuki; Kono, Yusuke; Kurayama, Tomoharu; Lee, Changhoon; Lee, Jung-Won; Lee, Sang Hyun; Minh, Young Chol; Matsumoto, Naoko; Nakagawa, Akiharu; Oh, Chung Sik; Oh, Se-Jin; Park, Sun-Youp; Roh, Duk-Gyoo; Sasao, Tetsuo; Shibata, Katsunori M; Song, Min-Gyu; Tamura, Yoshiaki; Wi, Seog-Oh; Yeom, Jae-Hwan; Yun, Young Joo

    2014-01-01

    The Korean very-long-baseline interferometry (VLBI) network (KVN) and VLBI Exploration of Radio Astrometry (VERA) Array (KaVA) is the first international VLBI array dedicated to high-frequency (23 and 43 GHz bands) observations in East Asia. Here, we report the first imaging observations of three bright active galactic nuclei (AGNs) known for their complex morphologies: 4C 39.25, 3C 273, and M 87. This is one of the initial result of KaVA early science. Our KaVA images reveal extended outflows with complex substructure such as knots and limb brightening, in agreement with previous Very Long Baseline Array (VLBA) observations. Angular resolutions are better than 1.4 and 0.8 milliarcsecond at 23 GHz and 43 GHz, respectively. KaVA achieves a high dynamic range of ~1000, more than three times the value achieved by VERA. We conclude that KaVA is a powerful array with a great potential for the study of AGN outflows, at least comparable to the best existing radio interferometric arrays.

  4. Enhanced T-lymphocyte blastogenic response to tuberculin (PPD) in children of northeast (NE) Thailand supplemented with vitamin A (VA) and zinc (Zn)

    Energy Technology Data Exchange (ETDEWEB)

    Kramer, T.R.; Udomkesmalee, E.; Dhanamitta, S.; Sirisinha, S.; Charoenkiatkul, S.; Tantipopipat, S.; Banjong, O.; Rojroongwasinkul, N.; Smith, J.C. Jr. (Dept. of Agriculture, Beltsville, MD (United States) Mahidol Univ., Nakhon Pathom (Thailand))

    1991-03-15

    Beneficial effects of Va and/or Zn supplementation of children in NE Thailand are described in a companion abstract. In the same study, blastogenic response (BR) of T-lymphocytes to concanavalin-A (ConA) and PPD were assayed in cultures containing mononuclear cells (MNC) or whole blood (WB). Methods were previously described. Children were previously vaccinated with BCG. BR to ConA of MNC or WB from children supplemented with VA, Zn, VA + Zn or placebo were similar. BR to PPD of MNC was higher in children receiving VA + Zn than placebo, but not in children supplemented with VA or Zn alone. Data indicate that children with suboptimal VA and Zn nutriture supplemented with < 2 times RDA of these nutrients showed enhanced cellular immunity to PPD. This observation is relevant to BCG immunization program and thus may benefit public health.

  5. A Comparative Study of VaR Model and Its Demonstration Based on Monte Carlo Simulation%基于蒙特卡洛模拟的VaR模型及其模拟实证对比研究

    Institute of Scientific and Technical Information of China (English)

    喻为民

    2014-01-01

    在对VaR模型基本思想介绍基础上,构建基于蒙特卡洛模拟的VaR计算模型,并结合Matlab2012a计算软件,分别计算基于随机模拟和历史模拟的金融市场VaR数值,并在同类型模拟方法下进行横向对比分析。研究结果表明:t分布模型在高置信水平条件下较标准正态分布模型具有更高的精度要求和优势,且对于金融收益率数据的表征更为合理科学;2013年我国股指期货市场结构较2012年发生较大程度变化,且系统风险有进一步扩大趋势。%Based on the introduction of VaR Model, this paper builds a VaR calculation model with Monte Carlo Simulation, calculates the VaR values in financial market by random simulation and historical simulation combining with Matlab 2012a calculation software and makes a lateral comparative analysis through the same type simulation. The result shows that, compared to the standardized normal distribution model, t distribution model has high precision requirement and advantage in the condition of the high confidence level and the characterization of financial returns is more reasonable. The structure of stock index futures market in 2013 has changed a lot and the system risk has the trend of being enlarged.

  6. Comprehensive analysis of human endogenous retrovirus group HERV-W locus transcription in multiple sclerosis brain lesions by high-throughput amplicon sequencing.

    Science.gov (United States)

    Schmitt, Katja; Richter, Christin; Backes, Christina; Meese, Eckart; Ruprecht, Klemens; Mayer, Jens

    2013-12-01

    Human endogenous retroviruses (HERVs) of the HERV-W group comprise hundreds of loci in the human genome. Deregulated HERV-W expression and HERV-W locus ERVWE1-encoded Syncytin-1 protein have been implicated in the pathogenesis of multiple sclerosis (MS). However, the actual transcription of HERV-W loci in the MS context has not been comprehensively analyzed. We investigated transcription of HERV-W in MS brain lesions and white matter brain tissue from healthy controls by employing next-generation amplicon sequencing of HERV-W env-specific reverse transcriptase (RT) PCR products, thus revealing transcribed HERV-W loci and the relative transcript levels of those loci. We identified more than 100 HERV-W loci that were transcribed in the human brain, with a limited number of loci being predominantly transcribed. Importantly, relative transcript levels of HERV-W loci were very similar between MS and healthy brain tissue samples, refuting deregulated transcription of HERV-W env in MS brain lesions, including the high-level-transcribed ERVWE1 locus encoding Syncytin-1. Quantitative RT-PCR likewise did not reveal differences in MS regarding HERV-W env general transcript or ERVWE1- and ERVWE2-specific transcript levels. However, we obtained evidence for interindividual differences in HERV-W transcript levels. Reporter gene assays indicated promoter activity of many HERV-W long terminal repeats (LTRs), including structurally incomplete LTRs. Our comprehensive analysis of HERV-W transcription in the human brain thus provides important information on the biology of HERV-W in MS lesions and normal human brain, implications for study design, and mechanisms by which HERV-W may (or may not) be involved in MS.

  7. Analytical derivation of traffic patterns in cache-coherent shared-memory systems

    DEFF Research Database (Denmark)

    Stuart, Matthias Bo; Sparsø, Jens

    2011-01-01

    This paper presents an analytical method to derive the worst-case traffic pattern caused by a task graph mapped to a cache-coherent shared-memory system. Our analysis allows designers to rapidly evaluate the impact of different mappings of tasks to IP cores on the traffic pattern. The accuracy va...

  8. Modeling Daily VaR and CVaR by Integrating CARR and EVT Models%基于CARR—EVT整体方法的动态日VaR和CVaR模型研究

    Institute of Scientific and Technical Information of China (English)

    赵树然; 任培民; 赵昕

    2012-01-01

    Using daily VaR and CVaR simultaneously can doubly control mar ket risks. Their estimations are the key point of risk management. The rapid devel opment of science and technology makes it possible to obtain high frequent data. Because they have much information about volatility, scholars begin to study daily VaR and CVaR based on high frequent data. In the paper, we are to estimate daily VaR and CVaR by integrating the CARR model and extreme value theory. The em pirical analysis on Shanghai and Shenzhen composite indexes showes that, com pared with type of GARCH models based on daily data and CARR model not in tegrating extreme value theory, our method remarkably improves the accuracy of VaR and CVaR estimators. Moreover, the two estimators are robust to the distribu tion of new information.%本文同时使用日VaR和CVaR模型可实现对市场风险的双重监控,其估计一直是风险管理的重点。科技的发展使获得高频数据成为可能,由于其包含丰富波动信息,学者们开始利用它来研究日VaR和CVaR的估计问题。本文通过整合基于高频数据的CARR模型和非参数的极值理论EVT,实现对日VaR和CVaR的动态估计。上证和深圳综指的实证结果表明,与基于日度数据GARCH类模型和未与极值理论整合的CARR模型的VaR和CVaR相比,本文方法极大提高了估计拍维确.悻.同时所得仕讳豇右茱,辛新自-奔右尉响柏籀馇.件

  9. 基于均值-VaR-熵的证券投资组合应用研究%The Research of Application in Portfolio Based on Mean-VaR-Entropy

    Institute of Scientific and Technical Information of China (English)

    印凡成; 陈瑞冰; 黄健元

    2013-01-01

    In order to research the optimal portfolio problem, the article starts from the risk measurement of portfolio theory, uses the VaR and entropy to measure risk, and proposes a new risk measurement model; mean-VaR-entropy model. In the context of abnormal distribution return rate, using the linear combination of VaR and cross-entropy function as the minimum objective function, expected return rate as a constraint, based on the mean-VaR-entropy, we build the portfolio model without short sales, considering transaction costs, constraints, and discuss the selection of investment and the allocation of investment ratio. And we use the actual data to obtain the optimal solution of the model and the allocation ratio. The results show that diversification is the inevitable choice for investors facing the minimum risk to achieve the purpose of expected return.%为研究证券最优投资组合问题,从投资组合理论的风险度量着手,用VaR和熵来共同度量风险,提出新的风险度量模型:均值-VaR-熵模型.在证券收益率服从非正态分布的假设下,以VaR和叉熵的线性组合为最小目标函数,预期收益率为约束条件,构建考虑交易成本、不允许卖空的基于均值-VaR-熵的证券投资组合模型,探讨证券投资选择及比例分配问题,并利用实际数据求得该模型的最优解及各证券的分配比例.结果表明,多元化投资是证券投资者在风险最小的情况下实现预期收益目标的必然选择.

  10. The Application Study of VaR and TCE in Efficiency Used in Risk Management%风险管理测度VaR和TCE的实证研究

    Institute of Scientific and Technical Information of China (English)

    王苹

    2005-01-01

    针对单一金融产品和由多种资产组成的投资组合两种情况,用几只股票的历史收盘数据实证比较了两种先进的度量金融市场风险测度--风险值(VaR)和尾部条件期望(TCE)的有效性.结果显示, TCE比VaR更有效.

  11. Global financial crisis and VaR performance in emerging markets: A case of EU candidate states - Turkey and Croatia

    Directory of Open Access Journals (Sweden)

    Bora Aktan

    2009-06-01

    Full Text Available We investigate the relative performance of a wide array of Value at Risk (VaR models with the daily returns of Turkish (XU100 and Croatian (CROBEX stock index prior to and during the ongoing financial crisis. In addition to widely used VaR models, we also study the behaviour of conditional and unconditional extreme value theory (EVT and hybrid historical simulation (HHS models to generate 95, 99 and 99.5% confidence level estimates. Results indicate that during the crisis period all tested VaR model except EVT and HHS models seriously underpredict the true level of risk, with EVT models doing so at a higher cost of capital compared to HHS model

  12. Financial Derivatives

    DEFF Research Database (Denmark)

    Wigan, Duncan

    2013-01-01

    Contemporary derivatives mark the development of capital and constitute a novel form of ownership. By reconfiguring the temporal, spatial and legal character of ownership derivatives present a substantive challenge to the tax collecting state. While fiscal systems are nationally bounded and inheren...... and inherently static, capital itself is unprecedentedly mobile, fluid and fungible. As such derivatives raise the specter of ‘financial weapons of mass destruction’....

  13. KiVa Anti-Bullying Program in Italy: Evidence of Effectiveness in a Randomized Control Trial.

    Science.gov (United States)

    Nocentini, Annalaura; Menesini, Ersilia

    2016-11-01

    The present study aims to evaluate the effectiveness of the KiVa anti-bullying program in Italy through a randomized control trial of students in grades 4 and 6. The sample involved 2042 students (51 % female; grade 4, mean age = 8.85; ds = 0.43; grade 6, mean age = 10.93; ds = 0.50); 13 comprehensive schools were randomly assigned into intervention (KiVa) or control (usual school provision) conditions. Different outcomes (bullying, victimization, pro-bullying attitudes, pro-victim attitudes, empathy toward victims), analyses (longitudinal mixed model with multiple-item scales; longitudinal prevalence of bullies and victims using Olweus' single question), and estimates of effectiveness (Cohen's d; odds ratios) were considered in order to compare the Italian results with those from other countries. Multilevel models showed that KiVa reduced bullying and victimization and increased pro-victim attitudes and empathy toward the victim in grade 4, with effect sizes from 0.24 to 0.40. In grade 6, KiVa reduced bullying, victimization, and pro-bullying attitudes; the effects were smaller as compared to grade 4, yet significant (d ≥ 0.20). Finally, using Olweus dichotomous definition of bullies and victims, results showed that the odds of being a victim were 1.93 times higher for a control student than for a KiVa student in grade 4. Overall, the findings provide evidence of the effectiveness of the program in Italy; the discussion will focus on factors that influenced successfully the transportability of the KiVa program in Italy.

  14. Childhood cause-specific mortality in rural Western Kenya: application of the InterVA-4 model

    Directory of Open Access Journals (Sweden)

    Nyaguara O. Amek

    2014-10-01

    Full Text Available Background: Assessing the progress in achieving the United Nation's Millennium Development Goals in terms of population health requires consistent and reliable information on cause-specific mortality, which is often rare in resource-constrained countries. Health and demographic surveillance systems (HDSS have largely used medical personnel to review and assign likely causes of death based on the information gathered from standardized verbal autopsy (VA forms. However, this approach is expensive and time consuming, and it may lead to biased results based on the knowledge and experience of individual clinicians. We assessed the cause-specific mortality for children under 5 years old (under-5 deaths in Siaya County, obtained from a computer-based probabilistic model (InterVA-4. Design: Successfully completed VA interviews for under-5 deaths conducted between January 2003 and December 2010 in the Kenya Medical Research Institute/US Centers for Disease Control and Prevention HDSS were extracted from the VA database and processed using the InterVA-4 (version 4.02 model for interpretation. Cause-specific mortality fractions were then generated from the causes of death produced by the model. Results: A total of 84.33% (6,621 childhood deaths had completed VA data during the study period. Children aged 1–4 years constituted 48.53% of all cases, and 42.50% were from infants. A single cause of death was assigned to 89.18% (5,940 of cases, 8.35% (556 of cases were assigned two causes, and 2.10% (140 were assigned ‘indeterminate’ as cause of death by the InterVA-4 model. Overall, malaria (28.20% was the leading cause of death, followed by acute respiratory infection including pneumonia (25.10%, in under-5 children over the study period. But in the first 5 years of the study period, acute respiratory infection including pneumonia was the main cause of death, followed by malaria. Similar trends were also reported in infants (29 days–11 months and

  15. AVTA Federal Fleet PEV Readiness Data Logging and Characterization Study for Department of Veterans Affairs – VA Manhattan Campus

    Energy Technology Data Exchange (ETDEWEB)

    Stephen Schey; Jim Francfort

    2014-10-01

    This report focuses on the Department of Veterans Affairs, VA Manhattan Campus (VA- Manhattan) fleet to identify the daily operational characteristics of select vehicles and report findings on vehicle and mission characterizations to support successful introduction of plug-in electric vehicles (PEVs) into the agency’s fleet. Individual observations of these selected vehicles provide the basis for recommendations related to electric vehicle adoption and whether a battery electric vehicle or plug-in hybrid electric vehicle (collectively called PEVs) can fulfill the mission requirements.

  16. Elektromiografsko ispitivanje aktivnosti žvačnih mišića u ispitanika s temporomandibularnom disfunkcijom

    OpenAIRE

    Alajbeg, Iva; Valentić-Peruzović, Melita; Alajbeg, Ivan; Ileš, Davor; Knezović-Zlatarić, Dubravka; Katunarić, Marina

    2003-01-01

    Pojam temporomandibularna disfunkcija (TMD) obuhvaća mnoge poremećaje u vezi sa žvačnim mišićima i temporomandibularnim zglobovima. U vezu s nastankom TMD-a najčešće se dovode okluzalni, traumatski, psihosocijalni i sustavski čimbenici. Svrha ovoga istraživanja bila je ustanoviti postoji li promijenjena aktivnost žvačnih mišića u ispitanika s poremećajem te utvrditi mogućnosti dijagnostike temporomandibularnih poremećaja metodom elektromiografije. U ispitivanju je sudjelovalo 40 ispitanika: 1...

  17. VaR方法在银行信用风险管理中的应用

    Institute of Scientific and Technical Information of China (English)

    钱诗曼

    2009-01-01

    风险价值(VaR)是目前国际金融风险管理领域广泛使用的工具,也是度量信用风险的一种新的技术标准.本文介绍了VAR度量风险的含义,并通过借鉴信用计量模型(Credit Metrics),指出Credit Metrics模型在我国的应用前景以及应用VaR方法强化信用风险管理建议和措施.

  18. An Analysis of Exchange Rate Risk Exposure Related to the Public Debt Portfolio of Tunisia: Beyond VaR Approach

    OpenAIRE

    Omrane Samia

    2012-01-01

    The aim of this study is to assess the exchange rate risk associated with the Tunisian public debt portfolio through Value-at-Risk (VaR) methodology. We use daily spot exchange rates of the Tunisian dinar against the three main debt currencies, the dollar, the euro and the yen. Our period of interest is from 02/01/2004 to 31/12/2008. Thetas and Marginal VaR analysis reveal that Japanese yen is the most risky currency constituting the Tunisian public debt portfolio. American dollar appea...

  19. VaR方法与投资风险管理

    Institute of Scientific and Technical Information of China (English)

    黄宁宁

    2004-01-01

    随着中国金融市场的不断发展,投资风险也日益成为各种金融机构不能回避的重要问题,运用科学的风险管理手段控制风险已经成为中国各个金融机构的紧迫任务.在各种投资风险管理手段中,VaR方法以其科学性和较广的适用性脱颖而出,成为目前投资管理的流行方法.本文通过一个具体的实例,采用中国股票市场的数据,运用Matlab程序,说明如何通过Var方法进行投资风险管理.

  20. Long-term monitoring of Sgr A* at 7 mm with VERA and KaVA

    CERN Document Server

    Akiyama, Kazunori; Sohn, Bong Won; Lee, Sang Sung; Trippe, Sascha; Honma, Mareki

    2013-01-01

    We present the results of radio monitoring observations of Sgr A* at 7 mm (i.e. 43 GHz) with VLBI Exploration of Radio Astrometry (VERA), which is a VLBI array in Japan. VERA provides angular resolutions on millisecond scales, resolving structure within ~100 Schwarzschild radii of Sgr A* similar to Very Large Baseline Array (VLBA). We performed multi-epoch observations of Sgr A* in 2005 - 2008, and started monitoring it again with VERA from January 2013 for tracing the current G2 encounter event. Our preliminary results in 2013 show that Sgr A* on mas scales has been in ordinary state as of August 2013, although some fraction of the G2 cloud already passed pericenter of Sgr A* in April 2013. We will continue on monitoring Sgr A* with VERA and newly developed KaVA (KVN and VERA Array).

  1. Multiyear slant-path rain fade statistics at 28.56 GHz for Wallops Island, Va.

    Science.gov (United States)

    Goldhirsh, J.

    1980-01-01

    The multiyear rain fade statistics collected in the Wallops Island, Va., area at 28.56 GHz during 1977 through 1979 showed that the overall fade distributions for the individual years showed small differences. Exceedance time variations were observed in the monthly and time of day fade data from year to year, but the second year fades relative to the first year had less than 20% rms deviation. These results are useful to designers of earth-satellite communications systems which require reliable fade statistics for establishing link-margin requirements. The Wallops Island fade distribution had an rms decibel deviation of less than 14% when compared with the International Radio Consultative Committee prediction model.

  2. 3D Digitisation and Visualisation of the Vače Situla

    Directory of Open Access Journals (Sweden)

    Gregor Vidmar

    2013-09-01

    Full Text Available EXTENDED ABSTRACT:The project of 3D digitisation and visualisation of the Vače situla was implemented at the beginning of 2011 in cooperation with the National Museum of Slovenia where the situla is kept and the company MFC.2 which, among other services, develops and implements 3 D digitisation and visualisation projects. The purpose of the project was to digitise and visualise a famous and precious piece of cultural heritage and to  1. show what modern 3D shape and texture scanning technologies allow us to do,  2. show how to ensure safety and reach high quality in digitising cultural heritage objects.  3. measure the added value of the 3 D visualisation of cultural heritage as a powerful tool for preservation, conservation, research, education, knowledge sharing and promotion of cultural heritage objects. Furthermore, the aims of the project were:  1. 3D capture of the shape and texture of the situla using the 3D scanning method.  2. 3D image of the situla and its details with expert descriptions.  3. 3D stereoscopic projection of the situla viewed with 3D glasses and with the possibility of controlling it remotely.  4. 3D animation giving professional interpretation of certain facts about the situla.  5. Public presentation of the project results on Slovenian cultural holiday, 8th February 2011, at the National Museum of Slovenia. The 3D capture of the shape and texture of the situla was carried out using the white light 3D scanning method followed by 3D flesh animation to show the object and its details. A touch screen was used to provide user access to the content. Reality based model enabled vertical rotation of the situla as well as the interactive display of individual engravings. By clicking a situla detail a photo with an extensive professional explanation of the scene was displayed in a new browser window. For attractive public presentation of the exhibition a 3D stereoscopic animation of the situla rotating and seemingly

  3. Myosin-Va-dependent cell-to-cell transfer of RNA from Schwann cells to axons.

    Science.gov (United States)

    Sotelo, José R; Canclini, Lucía; Kun, Alejandra; Sotelo-Silveira, José R; Xu, Lei; Wallrabe, Horst; Calliari, Aldo; Rosso, Gonzalo; Cal, Karina; Mercer, John A

    2013-01-01

    To better understand the role of protein synthesis in axons, we have identified the source of a portion of axonal RNA. We show that proximal segments of transected sciatic nerves accumulate newly-synthesized RNA in axons. This RNA is synthesized in Schwann cells because the RNA was labeled in the complete absence of neuronal cell bodies both in vitro and in vivo. We also demonstrate that the transfer is prevented by disruption of actin and that it fails to occur in the absence of myosin-Va. Our results demonstrate cell-to-cell transfer of RNA and identify part of the mechanism required for transfer. The induction of cell-to-cell RNA transfer by injury suggests that interventions following injury or degeneration, particularly gene therapy, may be accomplished by applying them to nearby glial cells (or implanted stem cells) at the site of injury to promote regeneration.

  4. Retention for Stoploss reinsurance to minimize VaR in compound Poisson-Lognormal distribution

    Science.gov (United States)

    Soleh, Achmad Zanbar; Noviyanti, Lienda; Nurrahmawati, Irma

    2015-12-01

    Automobile insurance is one of the emerging general insurance's product in Indonesia. Fluctuation in total premium revenues and total claim expenses leads to a risk that insurance company can not be able to pay consumer's claims, thus reinsurance is needeed. Reinsurance is a risk transfer mechanism from the insurance company to another company called reinsurer, one of the reinsurance type is Stoploss. Because reinsurer charges premium to the insurance company, it is important to determine the retention or the total claims to be retain solely by the insurance company. Thus, retention is determined using Value at Risk (VaR) which minimize the total risk of the insurance company in the presence of Stoploss reinsurance. Retention depends only on the distribution of total claims and reinsurance loading factor. We use the compound Poisson distribution and the Log-Normal Distribution to illustrate the retention value in a collective risk model.

  5. The efficacy of Focused Acceptance and Commitment Therapy in VA primary care.

    Science.gov (United States)

    Glover, Natalie G; Sylvers, Patrick D; Shearer, Erika M; Kane, Mary-Catherine; Clasen, Peter C; Epler, Amee J; Plumb-Vilardaga, Jennifer C; Bonow, Jordan T; Jakupcak, Matthew

    2016-05-01

    Focused Acceptance & Commitment Therapy (FACT) is a brief intervention based on traditional Acceptance and Commitment Therapy (ACT). Although there is a growing body of research on the efficacy of ACT for a variety of populations and disorders, there is little research to date on the use of FACT in group settings. This project is 1 of the first of its kind, as it examines data on psychological flexibility, health and mental health status, and symptom reduction from a 4-week FACT group. Participants in this study were 51 patients who attended this group as part of routine clinical care in a VA integrated primary care and mental health setting. They completed pre- and posttreatment measures of well-being, depression, anxiety, stress, psychological flexibility, and perceptions of physical and mental health functioning. Pre- to posttreatment analyses of variance demonstrated large effects for quality of life, F(1, 51) = 21.29, p < .001, η2 = 0.30, moderate effects for depressive symptoms, F(1, 51) = 11.47, p < .001, η2 = 0.08, and perceptions of mental health functioning (MCS scale), F(1, 51) = 9.67, p = .003, η2 = 0.11, and small effects for perceptions of perceived stress, F(1, 51) = 4.08, p = .04, η2 = 0.03, and physical health functioning (PCS scale), F(1, 51) = 6.60, p = .01, η2 = 0.08. There was a statistical trend for reductions in anxiety, F(1, 51) = 3.29, p = .07, η2 = 0.01, and a nonsignificant effect for psychological flexibility, F(1, 51) = 2.05, p = .16, η2 = 0.04. These data provide initial support for the implementation of a group-based FACT protocol within a VA primary care setting and help to lay a foundation for further, more controlled studies on Group FACT in future research. (PsycINFO Database Record

  6. Continuity in a VA patient-centered medical home reduces emergency department visits.

    Directory of Open Access Journals (Sweden)

    Krisda H Chaiyachati

    Full Text Available One major goal of the Patient-Centered Medical Home (PCMH is to improve continuity of care between patients and providers and reduce the utilization of non-primary care services like the emergency department (ED.To characterize continuity under the Veterans Health Administration's PCMH model--the Patient Aligned Care Team (PACT, at one large Veterans Affair's (VA's primary care clinic, determine the characteristics associated with high levels of continuity, and assess the association between continuity and ED visits.Retrospective, observational cohort study of patients at the West Haven VA (WHVA Primary Care Clinic from March 2011 to February 2012.The 13,495 patients with established care at the Clinic, having at least one visit, one year before March 2011.Our exposure variable was continuity of care--a patient seeing their assigned primary care provider (PCP at each clinic visit. The outcome of interest was having an ED visit.The patients encompassed 42,969 total clinic visits, and 3185 (24% of them had 15,458 ED visits. In a multivariable logistic regression analysis, patients with continuity of care--at least one visit with their assigned PCP--had lower ED utilization compared to individuals without continuity (adjusted odds ratio [AOR] 0.54; 95% CI: 0.41, 0.71, controlling for frequency of primary care visits, comorbidities, insurance, distance from the ED, and having a trainee PCP assigned. Likewise, the adjusted rate of ED visits was 544/1000 person-year (PY for patients with continuity vs. 784/1000 PY for patients without continuity (p = 0.001. Compared to patients with low continuity (50% continuity were less likely to utilize the ED.Strong continuity of care is associated with decreased ED utilization in a PCMH model and improving continuity may help reduce the utilization of non-primary care services.

  7. A fast video clip retrieval algorithm based on VA-file

    Science.gov (United States)

    Liu, Fangjie; Dong, DaoGuo; Miao, Xiaoping; Xue, XiangYang

    2003-12-01

    Video clip retrieval is a significant research topic of content-base multimedia retrieval. Generally, video clip retrieval process is carried out as following: (1) segment a video clip into shots; (2) extract a key frame from each shot as its representative; (3) denote every key frame as a feature vector, and thus a video clip can be denoted as a sequence of feature vectors; (4) retrieve match clip by computing the similarity between the feature vector sequence of a query clip and the feature vector sequence of any clip in database. To carry out fast video clip retrieval the index structure is indispensable. According to our literature survey, S2-tree [17] is the one and only index structure having been applied to support video clip retrieval, which combines the characteristics of both X-tree and Suffix-tree and converts the series vectors retrieval to string matching. But S2-tree structure will not be applicable if the feature vector's dimension is beyond 20, because the X-tree itself cannot be used to sustain similarity query effectively when dimensions of vectors are beyond 20. Furthermore, it cannot support flexible similarity definitions between two vector sequences. VA-file represents the vector approximately by compressing the original data and it maintains the original order when representing vectors in a sequence, which is a very valuable merit for vector sequences matching. In this paper, a new video clip similarity model as well as video clip retrieval algorithm based on VA-File are proposed. The experiments show that our algorithm incredibly shortened the retrieval time compared to sequential scanning without index structure.

  8. 两类多元GARCH模型的预测绩效和组合VaR的研究%The Forecast Performance of Two Style GARCH Models and Portfolio VaR Computation

    Institute of Scientific and Technical Information of China (English)

    吕轶; 陈荣达; 刘剑波

    2009-01-01

    运用VaR模型对股票组合进行风险测度的关键之一是得到组合条件协方差矩阵.而经典的多元GARCH模型来求解波动率面临着估计参数过多,计算量庞大的问题.因此,使用正交GARCH模型和CCC模型来估算波动率,并以沪深两市A股市场上四个行业的65只股票为样本,使用RMSE和MAD指标比较这些模型的预测能力,求得股票组合的VaR,得出前者效率高和后者预测能力略高的结论.%The conditional covariance matrix plays a critical role in portfolio VaR computation. However, in the classical multivariate GARCH model large-scale portfolio is highly parameterized and difficult to estimate in practice. So this paper uses O-GARCH model and CCC model to calculate the volatilities of portfolio. Then 65 samples of stocks in A stock market of Shanghai and Shenzhen is examined by these models. Finally, we follow two criteria to judge the quality of the volatility forcasts and compute portfolio VaR by the conditional covariance matrix.

  9. A Monter Carlo optimize calculation of credit risk VaR for loan portfolio%贷款组合信用风险VaR仿真计算的一种优化方法

    Institute of Scientific and Technical Information of China (English)

    邓云胜; 任若恩

    2003-01-01

    This paper presents the principle of Monte Carlo optimize calculation of credit risk VaR for loanportfolio using Importance Sampling technique. Based on Matlab language, simulation experiments arecarried out and the result shows this approach can effectively reduce the numher of simulation runs andimprove the precision of parameter estimation.

  10. Risk Evaluation in Fuel Oil Futures Market Based on VaR-GARCH Dynamic Model%基于VaR-GARCH族动态模型的燃料油期货市场风险测量

    Institute of Scientific and Technical Information of China (English)

    戴毓; 周德群

    2009-01-01

    In this paper,we build a dynamic VaR-GARCHs evaluation model of the single futures contract in Shanghai fuel oil futures market was given.Based on VaR,the dynamic VaR-GARCH evaluation model can effectively forecast the range of volatility in the future well and truly.Furthermore,it is workable in forewarning and monitoring market risks.Considering actual futures margin rate in Shanghai fuel oil futures market,a new rate setting model(RCM)was obtained with corrected futures margin rate.RCM absorbs the advantages of margin rate setting techniques used at home and aborad.As a result,it can effectively control and avoid market risks,thus increasing the efficiency of fund utilization.%针对上海燃料油期货市场,基于VaR方法,建立了单个期货合约的VaR-GARCH族动态测量模型.实证结果表明,该模型可以较准确地预测未来价格波动范围,并具有较好的风险预警、风险监控作用.针对燃料油期货的现行保证金比例,本文给出修正后的保证金比例井提出了一种新型的保证金设定模型,该模型结合了国内、外确定期货保证金方法的优点,在有效地控制和规避市场风险的基础上提高了资金使用效率.

  11. Predicting Glycerophosphoinositol Identities in Lipidomic Datasets Using VaLID (Visualization and Phospholipid Identification—An Online Bioinformatic Search Engine

    Directory of Open Access Journals (Sweden)

    Graeme S. V. McDowell

    2014-01-01

    Full Text Available The capacity to predict and visualize all theoretically possible glycerophospholipid molecular identities present in lipidomic datasets is currently limited. To address this issue, we expanded the search-engine and compositional databases of the online Visualization and Phospholipid Identification (VaLID bioinformatic tool to include the glycerophosphoinositol superfamily. VaLID v1.0.0 originally allowed exact and average mass libraries of 736,584 individual species from eight phospholipid classes: glycerophosphates, glyceropyrophosphates, glycerophosphocholines, glycerophosphoethanolamines, glycerophosphoglycerols, glycerophosphoglycerophosphates, glycerophosphoserines, and cytidine 5′-diphosphate 1,2-diacyl-sn-glycerols to be searched for any mass to charge value (with adjustable tolerance levels under a variety of mass spectrometry conditions. Here, we describe an update that now includes all possible glycerophosphoinositols, glycerophosphoinositol monophosphates, glycerophosphoinositol bisphosphates, and glycerophosphoinositol trisphosphates. This update expands the total number of lipid species represented in the VaLID v2.0.0 database to 1,473,168 phospholipids. Each phospholipid can be generated in skeletal representation. A subset of species curated by the Canadian Institutes of Health Research Training Program in Neurodegenerative Lipidomics (CTPNL team is provided as an array of high-resolution structures. VaLID is freely available and responds to all users through the CTPNL resources web site.

  12. Uus trend - süvaõpe ülikoolis / Kalle Tammemäe ; intervjueerinud Raivo Juurak

    Index Scriptorium Estoniae

    Tammemäe, Kalle, 1958-

    2011-01-01

    Intervjuu TTÜ õppeprorektori Kalle Tammemäega kavandatavast süvaõppesüsteemist, mis hakkab toetama eelkõige teadustööst huvitatud üliõpilasi, aidates mõnelgi neist aja jooksul õppejõuks-teaduriks kasvada

  13. VA Community Mental Health Service Providers' Utilization of and Attitudes toward Telemental Health Care: The Gatekeeper's Perspective

    Science.gov (United States)

    Jameson, John Paul; Farmer, Mary Sue; Head, Katharine J.; Fortney, John; Teal, Cayla R.

    2011-01-01

    Context: Mental health (MH) providers in community-based outpatient clinics (CBOCs) are important stakeholders in the development of the Veterans Health Administration (VA) telemental health (TMH) system, but their perceptions of these technologies have not been systematically examined. Purpose: The purpose of this study was to investigate the…

  14. 76 FR 36955 - West Los Angeles VA Medical Center Veterans Programs Enhancement Act of 1998; Master Plan

    Science.gov (United States)

    2011-06-23

    ...- centered care, recreation therapy and mental health programs and staff. The area will have limited public... commenters wanted to see the development of more outdoor sports facilities for veterans, such as a fitness... coordination with VA patient-centered care, recreation therapy and mental health programs and staff. An...

  15. 76 FR 71442 - Enhanced-Use Lease (EUL) of Department of Veterans Affairs (VA) Real Property for the Development...

    Science.gov (United States)

    2011-11-17

    ... Veterans. FOR FURTHER INFORMATION CONTACT: Edward Bradley, Office of Asset Enterprise Management (044... of Permanent Supportive Housing Facility in St. Cloud, MN AGENCY: Department of Veterans Affairs... to enter into an EUL on an approximately 6.0-acre parcel of land at the VA St. Cloud Health...

  16. Electronic Health Records: DOD and VA Have Increased Their Sharing of Health Information, but More Work Remains

    Science.gov (United States)

    2008-07-01

    participating in recent initiatives ed by the Office of the National Coordinator for Health Information echnology (within the Department of Health...veterans, many DOD and VA patients tend to be highly mobile and may have health records residing at multiple medical facilities within

  17. 75 FR 35846 - In the Matter of Babcock & Wilcox Nuclear Operations Group, Inc., Lynchburg, VA; Order Imposing...

    Science.gov (United States)

    2010-06-23

    ... From the Federal Register Online via the Government Publishing Office NUCLEAR REGULATORY COMMISSION In the Matter of Babcock & Wilcox Nuclear Operations Group, Inc., Lynchburg, VA; Order Imposing Civil Monetary Penalty I Babcock & Wilcox Nuclear Operations Group, Inc., (Licensee) is the holder...

  18. Going to scale: A nonrandomized nationwide trial of the KiVa Antibullying Program for Grades 1-9

    NARCIS (Netherlands)

    Kärnä, A.; Voeten, M.J.M.; Little, T.D.; Poskiparta, E.H.; Alanen, E.; Salmivalli, C.

    2011-01-01

    Objective: The effects of school-based antibullying programs have typically been examined on small samples, with number of schools ranging from 1 to 78 (Farrington & Ttofi, 2009). This study investigated the effectiveness of the KiVa antibullying program in the beginning of its nationwide implementa

  19. 76 FR 54770 - Public Meeting: Notification by Capital One Financial Corporation, McLean, VA, To Acquire ING...

    Science.gov (United States)

    2011-09-02

    ... Public Meeting: Notification by Capital One Financial Corporation, McLean, VA, To Acquire ING Bank, FSB, Wilmington, DE, and Indirectly To Acquire Shares of Sharebuilder Advisors, LLC and ING Direct Investing, Inc... Financial Corporation, McLean, Virginia, to acquire ING Bank, FSB, Wilmington, Delaware, and indirectly...

  20. 77 FR 12997 - Drug and Drug-Related Supply Promotion by Pharmaceutical Company Representatives at VA Facilities

    Science.gov (United States)

    2012-03-05

    ... AFFAIRS 38 CFR Part 1 RIN 2900-AN42 Drug and Drug-Related Supply Promotion by Pharmaceutical Company... pharmaceutical company representatives. The purposes of the rule are to reduce or eliminate any potential for disruption in the patient care environment, manage activities and promotions at VA facilities, and...

  1. 75 FR 24510 - Drug and Drug-Related Supply Promotion by Pharmaceutical Company Sales Representatives at VA...

    Science.gov (United States)

    2010-05-05

    ... ethical conduct. Pharmaceutical sales representatives have heavy interaction with local VA staff each year... marketing of drugs and drug-related supplies. The proposed rule would generally deny sales representatives... de minimis value set forth in the standards of ethical conduct for Federal employees, and...

  2. VA and DOD Health Care: First Federal Health Care Center Established, but Implementation Concerns Need to Be Addressed

    Science.gov (United States)

    2011-07-01

    develop the automated orders portability capability. This interim process necessitated the hiring of five full-time pharmacists to conduct manual...planning, VA and DOD have not yet fully provided clinicians at the FHCC with the IT capabilities the Executive Agreement identified as needed upon opening

  3. Two Cases of Type Va Extrahepatic Bile Duct Duplication With Distal Klatskin Tumor Surgically Treated with Whipple Procedure and Hepaticojejunostomy.

    Science.gov (United States)

    Hammad, Tariq A; Alastal, Yaseen; Khan, Muhammad Ali; Hammad, Mohammad; Alaradi, Osama; Nigam, Ankesh; Sodeman, Thomas C; Nawras, Ali

    2015-10-01

    We describe the diagnostic and therapeutic challenges of a type Va extrahepatic bile duct duplication coexistent with distally located hilar cholangiocarcinoma (Klatskin tumor). We present 2 cases that were diagnosed preoperatively and treated with a modified surgical technique of a combined pylorus-preserving Whipple procedure and hepaticojejunostomy.

  4. Predicting glycerophosphoinositol identities in lipidomic datasets using VaLID (Visualization and Phospholipid Identification)--an online bioinformatic search engine.

    Science.gov (United States)

    McDowell, Graeme S V; Blanchard, Alexandre P; Taylor, Graeme P; Figeys, Daniel; Fai, Stephen; Bennett, Steffany A L

    2014-01-01

    The capacity to predict and visualize all theoretically possible glycerophospholipid molecular identities present in lipidomic datasets is currently limited. To address this issue, we expanded the search-engine and compositional databases of the online Visualization and Phospholipid Identification (VaLID) bioinformatic tool to include the glycerophosphoinositol superfamily. VaLID v1.0.0 originally allowed exact and average mass libraries of 736,584 individual species from eight phospholipid classes: glycerophosphates, glyceropyrophosphates, glycerophosphocholines, glycerophosphoethanolamines, glycerophosphoglycerols, glycerophosphoglycerophosphates, glycerophosphoserines, and cytidine 5'-diphosphate 1,2-diacyl-sn-glycerols to be searched for any mass to charge value (with adjustable tolerance levels) under a variety of mass spectrometry conditions. Here, we describe an update that now includes all possible glycerophosphoinositols, glycerophosphoinositol monophosphates, glycerophosphoinositol bisphosphates, and glycerophosphoinositol trisphosphates. This update expands the total number of lipid species represented in the VaLID v2.0.0 database to 1,473,168 phospholipids. Each phospholipid can be generated in skeletal representation. A subset of species curated by the Canadian Institutes of Health Research Training Program in Neurodegenerative Lipidomics (CTPNL) team is provided as an array of high-resolution structures. VaLID is freely available and responds to all users through the CTPNL resources web site.

  5. 76 FR 10522 - Naval Surface Warfare Center, Upper Machodoc Creek and the Potomac River, Dahlgren, VA; Danger Zone

    Science.gov (United States)

    2011-02-25

    ... and the Potomac River, Dahlgren, VA; Danger Zone AGENCY: U.S. Army Corps of Engineers, DoD. ACTION... danger zone in the vicinity of Naval Surface Warfare Center, Dahlgren, in King George County, Virginia..., and expands the boundaries of a portion of the danger zone. The amendment is necessary to protect...

  6. 78 FR 59861 - VA Acquisition Regulation: Service-Disabled Veteran-Owned and Veteran-Owned Small Business Status...

    Science.gov (United States)

    2013-09-30

    ... (definition service-disabled Veteran)''. Upon rendering a decision, new VAAR 819.307(g) provides that the... AFFAIRS 48 CFR Part 819 RIN 2900-AM92 VA Acquisition Regulation: Service-Disabled Veteran-Owned and... Service-Disabled Veteran-Owned Small Businesses (SDVOSB) and Veteran-Owned Small Businesses (VOSB)...

  7. Derivative Free Optimization of Complex Systems with the Use of Statistical Machine Learning Models

    Science.gov (United States)

    2015-09-12

    AFRL-AFOSR-VA-TR-2015-0278 DERIVATIVE FREE OPTIMIZATION OF COMPLEX SYSTEMS WITH THE USE OF STATISTICAL MACHINE LEARNING MODELS Katya Scheinberg...COMPLEX SYSTEMS WITH THE USE OF STATISTICAL MACHINE LEARNING MODELS 5a.  CONTRACT NUMBER 5b.  GRANT NUMBER FA9550-11-1-0239 5c.  PROGRAM ELEMENT...developed, which has been the focus of our research. 15. SUBJECT TERMS optimization, Derivative-Free Optimization, Statistical Machine Learning 16. SECURITY

  8. Derivative Chameleons

    CERN Document Server

    Noller, Johannes

    2012-01-01

    We consider generalized chameleon models where the conformal coupling between matter and gravitational geometries is not only a function of the chameleon field \\phi, but also of its derivatives via higher order co-ordinate invariants. Specifically we consider the first such non-trivial conformal factor A(\\phi,X), where X is the canonical kinetic term for \\phi. The associated phenomenology is investigated and we show that such theories have a new generic mass-altering mechanism, potentially assisting the generation of a sufficiently large chameleon mass in dense environments. The most general effective potential is derived for such derivative chameleon setups and explicit examples are given. Interestingly this points us to the existence of a purely derivative chameleon protected by a shift symmetry for \\phi. We also discuss potential ghost-like instabilities associated with mass-lifting mechanisms and find another, mass-lowering and instability-free, branch of solutions. This suggests that, barring fine-tuning...

  9. VaSP1, catalytically active serine proteinase from Vipera ammodytes ammodytes venom with unconventional active site triad.

    Science.gov (United States)

    Kurtović, Tihana; Brgles, Marija; Leonardi, Adrijana; Lang Balija, Maja; Sajevic, Tamara; Križaj, Igor; Allmaier, Günter; Marchetti-Deschmann, Martina; Halassy, Beata

    2014-01-01

    VaSP1, a serine proteinase from Vipera ammodytes ammodytes venom, is a glycosylated monomer of 31.5 kDa, as determined by MALDI mass spectrometry, showing multiple isoelectric points between pH 6.5 and pH 8.5. Partial amino acid sequencing of VaSP1 by Edman degradation and MS/MS analysis identified sequences which allowed its classification among the so-called snake venom serine proteinase homologues, members of the peptidase S1 family, however being devoid of the canonical catalytic triad. Only few representatives of this group have been identified so far with just two of them characterised in detail at the protein level. Despite substitution of His57 with Arg, VaSP1 possesses proteolytic activity which can be inhibited by Pefabloc, benzamidine, Zn²⁺ ions, DTT and trypsin inhibitor II, a Kunitz/BPTI group member. It hydrolyses N(α)-benzoyl-Phe-Val-Arg-p-NA, exhibiting Michaelis-Menten behaviour with K(m) = 48.2 μM and V(m) = 0.019 nM s⁻¹. The pH for optimal activity on tested substrate is around 9.0. VaSP1 also cleaves insulin B-chain, digesting it at positions His¹⁰-Leu¹¹, Ala¹⁴-Leu¹⁵ and Tyr¹⁶-Leu¹⁷. Furthermore, the novel serine proteinase is active towards wide array of proteins involved in haemostasis where its degradation of fibrinogen, fibrin, prothrombin, factor X and plasminogen in vivo probably results in depletion of coagulation factors in blood circulation. The possibility that VaSP1 possesses anticoagulant properties has been further indicated by its ability to prolong prothrombin time and activated partial thromboplastin time.

  10. 基于VaR和ES调整的Sharpe比率及在基金评价中的实证研究%Adjusting Sharpe Ratio by VaR or ES and Its Appliacation in Fund Performance

    Institute of Scientific and Technical Information of China (English)

    刘沛欣; 田军; 周勇

    2012-01-01

    传统Sharpe比率将投资收益的标准差作为风险的度量,而实证研究中更关注基金的损失风险而非全部风险,这是收益标准差所无法准确刻画的。针对传统Sharpe比率的这一缺点,本文考虑了用于度量下方风险的指标风险价值VaR(Value at Risk)和预期不足ES(Expected Shortfall)来替代投资收益的标准差,从而对传统Sharpe比率进行了调整。这里对VaR和ES进行计算时,运用了经验非参数估计和非参数平滑核估计两种方法。此外,本文还考虑了基金收益随时间波动的动态性,用广义自回归异方差GARCH模型对收益波动进行模拟,考察动态的VaR和ES,在实践中以动态的VaR和ES评价风险收益更加灵活。在实证研究中,本文用传统的Sharpe比率、基于VaR和ES的Sharpe比率以及基于条件VaR和条件ES的条件Sharpe比率对国内证券市场上所有26只封闭式基金在2005-2009年间的业绩进行了实证分析,分析了基金在不同指标下所体现的风险控制能力和收益水平的差别,并基于不同指标对所有基金进行了排名。此外,本文还运用协整检验考察基金收益率与市场基准指数是否存在联动关系,检验证明两者并不存在长期的均衡关系。%Sharpe ratio, the extra yield adjusted by investment risk, is one of the most popular fund performance evaluation indexes in fiannce. Traditional Sharpe ratio takes investment standard deviation as the risk measure, however, it is more interested to focus on the downside risk instead of whole investment risk. So standard deviation is no longer appropriate. We adjust the way of evaluating risk by VaR (Value at Risk) and ES (Expected Shortfall) with empirical nonparametric and nonparametric smooth kernel estimating method. Besides, we also consider the time-varying of return volatility and simulated the volatility by GARCH model, then we get time-varying VaR and ES that are more appealing and powerful in

  11. 国际有色金属期货市场VaR和ES风险度量功效的比较%Comparative research between VaR and ES on international nonferrous metals futures market

    Institute of Scientific and Technical Information of China (English)

    杨娴; 陆凤彬; 汪寿阳

    2011-01-01

    采用历史模拟法、蒙特卡罗模拟法、指数加权法、等权重法、GARCH法和极值理论法六种参数方法和非参数方法对国际有色金属期货市场风险值VaR建模,并引入基于极值理论的预期不足ES对风险度量进行补充.在利用返回检验对实证结果的功效进行比较研究的基础之上,得出结论:从对ES和VaR的检验结果比较而言,当有色金属期货市场价格出现大幅跌涨时,ES比VaR更能准确地度量市场风险;从对各种方法VaR的检验结果比较而言,在95%的置信度下,GARCH法和指数加权法能够更加有效地度量市场风险,在99%的置信度下,指数加权法、GARCH法和历史模拟法能够更好地估计市场风险.%In view that the volatility of International Nonferrous Metals Market has direct and profound impact on the cost of production and the development of economy in China, we estimated the VaR of the futures market using Historical Simulation (HS), Monte Carlo method (MC), Exponentially Weighted Moving Average approach (EWMA), Equally Weighted approach (EWA), GARCH and Extreme Value Theory (EVT) separately. Then, we estimated the ES of the futures market based on EVT. Finally, we adopted backtest to evaluate the power of each method. Our findings indicate that ES is better than VaR in evaluating market risks when there is a sharp fall or rise in commodity prices; GARCH and EWMA gain an advantage over the other four methods with a 95% level of confidence; EWMA, GARCH and HS gain an advantage over the other three methods with a 99% level of confidence.

  12. Derivative chameleons

    Science.gov (United States)

    Noller, Johannes

    2012-07-01

    We consider generalized chameleon models where the conformal coupling between matter and gravitational geometries is not only a function of the chameleon field phi, but also of its derivatives via higher order co-ordinate invariants (such as ∂μphi∂μphi,squphi,...). Specifically we consider the first such non-trivial conformal factor A(phi,∂μphi∂μphi). The associated phenomenology is investigated and we show that such theories have a new generic mass-altering mechanism, potentially assisting the generation of a sufficiently large chameleon mass in dense environments. The most general effective potential is derived for such derivative chameleon setups and explicit examples are given. Interestingly this points us to the existence of a purely derivative chameleon protected by a shift symmetry for phi → phi+c. We also discuss potential ghost-like instabilities associated with mass-lifting mechanisms and find another, mass-lowering and instability-free, branch of solutions. This suggests that, barring fine-tuning, stable derivative models are in fact typically anti-chameleons that suppress the field's mass in dense environments. Furthermore we investigate modifications to the thin-shell regime and prove a no-go theorem for chameleon effects in non-conformal geometries of the disformal type.

  13. Global Derivatives

    DEFF Research Database (Denmark)

    Andersen, Torben Juul

    ." - Steen Parsholt, Chairman and CEO, Aon Nordic Region. "Andersen has done a wonderful job of developing a comprehensive text that deals with risk management in global markets. I would recommend this book to any student or businessman who has a need to better understand the risks and risk management...... management practice. Of particular note is the global and integrated approach chosen in this book which should be of special interest to aspiring managers active in global and international markets." - Dr Jean-Pierre Zigrand, Lecturer in Finance, London School of Economics, UK. More than 90 per cent...... management situations. Its key features include: derivatives are introduced in a global market perspective; describes major derivative pricing models for practical use, extending these principles to valuation of real options; practical applications of derivative instruments are richly illustrated...

  14. Electricity derivatives

    CERN Document Server

    Aïd, René

    2015-01-01

    Offering a concise but complete survey of the common features of the microstructure of electricity markets, this book describes the state of the art in the different proposed electricity price models for pricing derivatives and in the numerical methods used to price and hedge the most prominent derivatives in electricity markets, namely power plants and swings. The mathematical content of the book has intentionally been made light in order to concentrate on the main subject matter, avoiding fastidious computations. Wherever possible, the models are illustrated by diagrams. The book should allow prospective researchers in the field of electricity derivatives to focus on the actual difficulties associated with the subject. It should also offer a brief but exhaustive overview of the latest techniques used by financial engineers in energy utilities and energy trading desks.

  15. Spectroscopic and MD simulation studies on unfolding processes of mitochondrial carbonic anhydrase VA induced by urea.

    Science.gov (United States)

    Idrees, Danish; Prakash, Amresh; Haque, Md Anzarul; Islam, Asimul; Ahmad, Faizan; Hassan, Md Imtaiyaz

    2016-09-01

    Carbonic anhydrase VA (CAVA) is primarily expressed in the mitochondria and involved in numerous physiological processes including lipogenesis, insulin secretion from pancreatic cells, ureagenesis, gluconeogenesis and neuronal transmission. To understand the biophysical properties of CAVA, we carried out a reversible urea-induced isothermal denaturation at pH 7.0 and 25°C. Spectroscopic probes, [θ]222 (mean residue ellipticity at 222 nm), F344 (Trp-fluorescence emission intensity at 344 nm) and Δε280 (difference absorption at 280 nm) were used to monitor the effect of urea on the structure and stability of CAVA. The urea-induced reversible denaturation curves were used to estimate [Formula: see text], Gibbs free energy in the absence of urea; Cm, the mid-point of the denaturation curve, i.e. molar urea concentration ([urea]) at which ΔGD = 0; and m, the slope (=∂ΔGD/∂[urea]). Coincidence of normalized transition curves of all optical properties suggests that unfolding/refolding of CAVA is a two-state process. We further performed 40 ns molecular dynamics simulation of CAVA to see the dynamics at different urea concentrations. An excellent agreement was observed between in silico and in vitro studies.

  16. Do hassles and uplifts change with age? Longitudinal findings from the VA normative aging study.

    Science.gov (United States)

    Aldwin, Carolyn M; Jeong, Yu-Jin; Igarashi, Heidi; Spiro, Avron

    2014-03-01

    To examine emotion regulation in later life, we contrasted the modified hedonic treadmill theory with developmental theories, using hassles and uplifts to assess emotion regulation in context. The sample was 1,315 men from the VA Normative Aging Study aged 53 to 85 years, who completed 3,894 observations between 1989 and 2004. We computed 3 scores for both hassles and uplifts: intensity (ratings reflecting appraisal processes), exposure (count), and summary (total) scores. Growth curves over age showed marked differences in trajectory patterns for intensity and exposure scores. Although exposure to hassles and uplifts decreased in later life, intensity scores increased. Group-based modeling showed individual differences in patterns of hassles and uplifts intensity and exposure, with relative stability in uplifts intensity, normative nonlinear changes in hassles intensity, and complex patterns of individual differences in exposure for both hassles and uplifts. Analyses with the summary scores showed that emotion regulation in later life is a function of both developmental change and contextual exposure, with different patterns emerging for hassles and uplifts. Thus, support was found for both hedonic treadmill and developmental change theories, reflecting different aspects of emotion regulation in late life.

  17. Manassantin B inhibits melanosome transport in melanocytes by disrupting the melanophilin-myosin Va interaction.

    Science.gov (United States)

    Chang, Huikyoung; Choi, Hyunjung; Joo, Kyung-Mi; Kim, Daegun; Lee, Tae Ryong

    2012-11-01

    Human skin hyperpigmentation disorders occur when the synthesis and/or distribution of melanin increases. The distribution of melanin in the skin is achieved by melanosome transport and transfer. The transport of melanosomes, the organelles where melanin is made, in a melanocyte precedes the transfer of the melanosomes to a keratinocyte. Therefore, hyperpigmentation can be regulated by decreasing melanosome transport. In this study, we found that an extract of Saururus chinensis Baill (ESCB) and one of its components, manassantin B, inhibited melanosome transport in Melan-a melanocytes and normal human melanocytes (NHMs). Manassantin B disturbed melanosome transport by disrupting the interaction between melanophilin and myosin Va. Manassantin B is neither a direct nor an indirect inhibitor of tyrosinase. The total melanin content was not reduced when melanosome transport was inhibited in a Melan-a melanocyte monoculture by manassantin B. Manassantin B decreased melanin content only when Melan-a melanocytes were co-cultured with SP-1 keratinocytes or stimulated by α-MSH. Therefore, we propose that specific inhibitors of melanosome transport, such as manassantin B, are potential candidate or lead compounds for the development of agents to treat undesirable hyperpigmentation of the skin.

  18. Branching Ratios and Polarization in B-> VV,VA,AA Decays

    CERN Document Server

    Cheng, Hai-Yang

    2008-01-01

    We present a detailed study of charmless two-body B decays into final states involving two vector mesons (VV) or two axial-vector mesons (AA) or one vector and one axial-vector meson (VA), within the framework of QCD factorization, where $A$ is either a $^3P_1$ or $^1P_1$ axial-vector meson. The main results are as follows. (i) In the presence of NLO nonfactorizable corrections, effective Wilson coefficients $a_i^h$ are helicity dependent. For some modes, the constructive (destructive) interference in the negative-helicity (longitudinal-helicity) amplitude of the $\\bar B\\to VV$ decay will render the former comparable to the latter and bring up the transverse polarization. (ii) The measured rates and the longitudinal polarization fraction $f_L$ of penguin-dominated charmless $VV$ modes can be {\\it accommodated} in QCD factorization by allowing for sizable penguin annihilation contributions, though the parameters $\\rho_A$ and $\\phi_A$ fit to the data of $K^*\\phi$ and $K^*\\rho$ are not the same. (iii) The predic...

  19. A spatial exploration of informal trail networks within Great Falls Park, VA

    Science.gov (United States)

    Wimpey, Jeremy; Marion, Jeffrey L.

    2011-01-01

    Informal (visitor-created) trails represent a threat to the natural resources of protected natural areas around the globe. These trails can remove vegetation, displace wildlife, alter hydrology, alter habitat, spread invasive species, and fragment landscapes. This study examines informal and formal trails within Great Falls Park, VA, a sub-unit of the George Washington Memorial Parkway, managed by the U.S. National Park Service. This study sought to answer three specific questions: 1) Are the physical characteristics and topographic alignments of informal trails significantly different from formal trails, 2) Can landscape fragmentation metrics be used to summarize the relative impacts of formal and informal trail networks on a protected natural area? and 3) What can we learn from examining the spatial distribution of the informal trails within protected natural areas? Statistical comparisons between formal and informal trails in this park indicate that informal trails have less sustainable topographic alignments than their formal counterparts. Spatial summaries of the lineal and areal extent and fragmentation associated with the trail networks by park management zones compare park management goals to the assessed attributes. Hot spot analyses highlight areas of high trail density within the park and findings provide insights regarding potential causes for development of dense informal trail networks.

  20. Building strong research partnerships between public health and researchers: a VA case study.

    Science.gov (United States)

    Midboe, Amanda M; Elwy, A Rani; Durfee, Janet M; Gifford, Allen L; Yakovchenko, Vera; Martinello, Richard A; Ross, David; Czarnogorski, Maggie; Goetz, Matthew B; Asch, Steven M

    2014-12-01

    We are in a new era of partner-based implementation research, and we need clear strategies for how to navigate this new era. Drawing on principles from community-based participatory research, the Clinical Public Health group of the Department of Veterans Affairs and the HIV/Hepatitis Quality Enhancement Research Initiative (HHQUERI) forged a longstanding partnership that has improved the care of Veterans with Human Immunodeficiency Virus (HIV) and Hepatitis C Virus. An exemplar HIV testing project epitomizes this partnership and is discussed in terms of the lessons learned as a result of our high level of collaboration around design, analysis, implementation, and dissemination across projects over the past several years. Lessons learned through this partnered testing program involve respecting different time horizons among the partners, identifying relevant research questions for both parties, designing flexible studies, engaging all partners throughout the research, and placing an emphasis on relationship building at all times. These lessons and strategies can benefit others conducting partner-based research both within the Veterans Health Administration (VA) and in other integrated healthcare systems.

  1. A spatial exploration of informal trail networks within Great Falls Park, VA.

    Science.gov (United States)

    Wimpey, Jeremy; Marion, Jeffrey L

    2011-03-01

    Informal (visitor-created) trails represent a threat to the natural resources of protected natural areas around the globe. These trails can remove vegetation, displace wildlife, alter hydrology, alter habitat, spread invasive species, and fragment landscapes. This study examines informal and formal trails within Great Falls Park, VA, a sub-unit of the George Washington Memorial Parkway, managed by the U.S. National Park Service. This study sought to answer three specific questions: 1) Are the physical characteristics and topographic alignments of informal trails significantly different from formal trails, 2) Can landscape fragmentation metrics be used to summarize the relative impacts of formal and informal trail networks on a protected natural area? and 3) What can we learn from examining the spatial distribution of the informal trails within protected natural areas? Statistical comparisons between formal and informal trails in this park indicate that informal trails have less sustainable topographic alignments than their formal counterparts. Spatial summaries of the lineal and areal extent and fragmentation associated with the trail networks by park management zones compare park management goals to the assessed attributes. Hot spot analyses highlight areas of high trail density within the park and findings provide insights regarding potential causes for development of dense informal trail networks.

  2. 大屏来临,“视”不可挡——优派两款22英寸宽屏VA2216w/VA2226w新上市

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    随着大屏液晶显示器的逐渐普及,22英寸宽屏显示器渐渐成为市场和消费者关注的焦点。近日,全球视讯科技的领导品牌优派(ViewSonic)两款全新外观的新CASA系列22英寸宽屏新品VA2216w、VA2226w上市,继20英寸CASA新品之后,优派两款22英寸宽屏再度引爆市场,成为消费者游戏、电影、娱乐的首选产品。

  3. Assessment of Fund Performance Using Sharpe Ratio Adjusted by VaR%基于VaR的Ssharpe指标在基金业绩评价中的应用

    Institute of Scientific and Technical Information of China (English)

    彭海伟; 吴启芳

    2004-01-01

    针对标准差衡量风险中的缺陷,本文考虑下方风险和收益波动的时变性,对计算Shapre值时的风险测度进行了调整.实证部分,应用传统的Shrpe比率、基于VaR的Sharpe比例和基于条件VaR的条件Sharpe值对中国证券市场上运作满3年的33只封闭式基金在2001-2003年间的业绩进行了检验,分析了基金控制风险和实现收益水平上的差异.

  4. 基于VaR和RAROC的保险基金最优投资研究%Research on the Optimization Model of Insurance Funds Investment Based on VaR and RAROC

    Institute of Scientific and Technical Information of China (English)

    陈学华; 韩兆洲; 唐珂

    2006-01-01

    本文从保险基金的有效运用所应遵循的安全性、盈利性和流动性的基本原则出发,把VaR、RAROC纳入到保险基金投资的研究中来,建立了一个考虑承保风险、VaR限额约束和追求风险调整的资本收益率最大化的保险基金投资优化模型,并给出了模型的求解方法和计算实例.

  5. Influence of amplicon size on the polymerase chain reaction of Parvovirus B19 genome in formalin-fixed specimens Influência do tamanho do amplicon na reação em cadeia da polimerase na detecção do genoma do PB19 em amostras fixadas em formalina

    Directory of Open Access Journals (Sweden)

    Paulo Roberto Veiga Quemelo

    2009-04-01

    Full Text Available The polymerase chain reaction (PCR has provided diagnosis of archival material, but some fixation methods such as formalin damage DNA and, subsequently, affect PCR analysis, particularly paraffin-embedded tissues. PCR is known due to its high specificity and sensitivity, although some difficulties arise when formalinfixed and paraffin-embedded tissue is used. Not only does this occur due to protein cross-linking, which increases with longer fixation time, but it also happens due to the direct damage that formalin causes in the DNA itself. PCR was used to analyze placenta and fetal organs from 34 samples with suspected Parvovirus B19 infection. It was not possible to amplify Parvovirus B19 DNA using nested-PCR, probably due to the size of the amplicon generated with the first set of primers. We approached this problem by using only the second set of primers. Two out of 34 tissue samples (5,9% were positive by PCR. However, PCR performed on corresponding fetal organs was negative in one of the two. We also observed a negative relation between the thickness of the tissue fragment and the positivity of the samples. In conclusion, although PCR is highly specific and sensitive in fresh or ideally fixed material, a careful standardization of PCR assays is necessary when using formalin fixed paraffin-embedded tissues by applying primers that require smaller DNA fragments for amplification.A reação em cadeia da polimerase (PCR tem fornecido diagnóstico de material de arquivo, mas alguns métodos de fixação, tais como formalina, provocam danos ao DNA e subsequentemente afetam sua análise, particularmente tecidos embebidos em parafina. A PCR é conhecida pela sua alta especificidade e sensibilidade, embora algumas dificuldades ocorram quando o material utilizado foi fixado em formalina e embebido em parafina. Isso não se deve somente pela formação de cross-linkings com proteínas, a qual aumenta com o maior tempo de fixação, mas também pelo

  6. 基于动态极值VaR股指分析的中国行业风险研究%Study of Chinese industry risk based on stock index analysis of dynamic EVT-VaR

    Institute of Scientific and Technical Information of China (English)

    刘庆斌; 姜薇

    2009-01-01

    应用动态极值VaR模型分析中国行业股票价格指数,对不同市场条件下中国行业风险进行实证研究.在McNeil等提出的GARCH模型与极值理论基础上,运用Huisman等提出的VaR法修正上述风险值估计方法,构建了动态极值VaR模型.在该模型的构建中考虑了风险因子的时变特性,采用EVT方法对风险因子的厚尾特性进行建模,简化了风险值的估计过程,并提高了估计的准确性.动态极值VaR模型能够较好地刻画风险尾部分布特性,同时能够比较准确地度量所研究时间段内的市场风险和行业风险.研究结果表明,不同市场条件下各行业的风险特性具有显著的变化.最后利用Kruskal-Wallis一致性检验对上述结论进行了验证.据此,在资产组合管理过程中,有必要依据市场环境和行业风险特性对资产配置比例进行调整.

  7. Intramanchette transport during primate spermiogenesis:expression of dynein, myosin Va, motor recruiter myosin Va,Ⅶa-Rab27a/b interacting protein, and Rab27b in the manchette during human and monkey spermiogenesis

    Institute of Scientific and Technical Information of China (English)

    Shinichi Hayasaka; Yukihiro Terada; Kichiya Suzuki; Haruo Murakawa; Ikuo Tachibana; Tadashi Sankai; Takashi Murakami; Nobuo Yaegashi; Kunihiro Okamura

    2008-01-01

    Aim: To show whether molecular motor dynein on a microtubule track, molecular motor myosin Va, motor recruiter myosin Va, Ⅶa-Rab27a/b interacting protein (MyRIP), and vesicle receptor Rab27b on an F-actin track were present during human and monkey spermiogenesis involving intramanchette transport (IMT). Methods: Spermiogenic cells were obtained from three men with obstructive azoospermia and normal adult cynomolgus monkey (Macaca fascieularis). Immunocytochemical detection and reverse transcription-polymerase chain reaction (RT-PCR) analysis of the pro- teins were carried out. Samples were analyzed by light microscope. Results: Using RT-PCR, we found that dynein, myosin Va, MyRIP and Rab27b were expressed in monkey testis. These proteins were localized to the manchette, as shown by immunofluorescence, particularly during human and monkey spermiogenesis. Conclusion: We speculate that during primate spermiogenesis, those proteins that compose microtubule-based and actin-based vesicle transport systems are actually present in the manchette and might possibly be involved in intramanchette transport. (Asian J Androl 2008 Jul; 10: 561-568)

  8. 基于GARCH-EVT-VaR模型的碳市场风险计量实证研究%Value-at-Risk Estimation of Carbon Spot Markets Based on an Integrated GARCH-EVT-VaR Model

    Institute of Scientific and Technical Information of China (English)

    蒋晶晶; 叶斌; 马晓明

    2015-01-01

    对欧盟碳市场风险进行实证研究,在分析碳市场价格波动特征基础上,将条件方差和极值理论纳入VaR计量框架,建立量化碳市场价格波动风险的GARCH-EVT-VaR模型.应用该模型对欧盟碳排放交易市场(EU ETS)进行实证研究,结果显示:碳市场价格波动具有尖峰、厚尾、自相关、波动性聚类和条件方差等典型特征,EUA和CER价格波动呈现显著同步性;碳市场存在显著的极端价格波动风险,GARCH-EVT-VaR模型能够更准确地量化碳市场风险,从而为应对极端事件预留充足的风险储备.

  9. 基于VaR的房地产市场风险分析——以浙江省为例%Risk analysis of real estate market based on VaR:empirical research on Zhejiang,China

    Institute of Scientific and Technical Information of China (English)

    吴燕华; 罗乐勤

    2011-01-01

    采用VaR方法构建房地产市场风险的测量模型,通过收集1991—2010年浙江省房地产业发展数据,应用SPSS17.0和Matlab软件进行回归分析和蒙特卡洛仿真,定量分析房地产市场风险累积程度的大小,为房地产政策制订和市场监管提供直观量化的决策依据。%This paper uses value at risk(VaR) model to predict the risk of real estate market.By collecting the real estate data of Zhejiang province from 1991 to 2009,multinomial-regression analysis and Monte Carlo simulation were made by using SPSS 17.0 and Matlab software respectively quantitatively analyzing how big the accumulation level of the market risk is.VaR method can offer reference index for the government to control the market risk and make effective policies.

  10. Važiavimo dviračiu kaip aktyvios laisvalaikio formos nauda sveikatinimui: Kauno miesto gyventojų atvejis

    OpenAIRE

    Solnyškinaitė, Neringa

    2014-01-01

    Apklaustieji teigiamai vertina važiavimą dviračiu kaip aktyvaus laisvalaikio formą, labiausiai džiaugiasi pagerėjusia emocine būsena ir teigia, kad dviratis puiki transporto priemonė, nes yra sutaupoma pinigų už transportą. Respondentai tai pat pastebėjo tokius pokyčius kaip padidėjusią raumeninę masę, sumažėjusį svorį, sustiprėjusią širdį ir kaulus. Galima daryti išvadą, kad anot respondentų važiavimas dviračiu labiausiai gerina emocinę būseną, galbūt jiems pavyko atsikratyti slogių minčių i...

  11. Fast-response liquid crystal display by the VA-IPS display mode with nematic liquid crystal and polymer networks

    Science.gov (United States)

    Chen, Tien-Jung; Lin, Guan-Jhong; Chen, Bo-Yu; Wu, Jin-Jei; Yang, Ying-Jay

    2012-10-01

    To improve electrooptical characteristics of the vertical aligned (VA) liquid crystal displays (LCDs), the monomer material and in-plane switching (IPS) field produced by interdigital electrodes are employed in LC cells. The fast switching response and well optical transmittance of the VA-IPS display mode are successfully achieved by mixing the nematic LC with polymer networks, attributed to the surface anchoring, and the molecular orientation of the LC cell will be further governed, especially under the greater applied voltage. Furthermore, the high concentration doping of the monomer can effectively improve the response behavior, but it also results in the transmittance sacrificed due to the light scattering, and the threshold voltage (Vth) increased.

  12. Effects of the KiVa anti-bullying program on adolescents' depression, anxiety, and perception of peers.

    Science.gov (United States)

    Williford, Anne; Boulton, Aaron; Noland, Brian; Little, Todd D; Kärnä, Antti; Salmivalli, Christina

    2012-02-01

    The present study investigated the effects of the KiVa antibullying program on students' anxiety, depression, and perception of peers in Grades 4-6. Furthermore, it was investigated whether reductions in peer-reported victimization predicted changes in these outcome variables. The study participants included 7,741 students from 78 schools who were randomly assigned to either intervention or control condition, and the program effects were tested with structural equation modeling. A cross-lagged panel model suggested that the KiVa program is effective for reducing students' internalizing problems and improving their peer-group perceptions. Finally, changes in anxiety, depression, and positive peer perceptions were found to be predicted by reductions in victimization. Implications of the findings and future directions for research are discussed.

  13. Integrating a modern knowledge-based system architecture with a legacy VA database: the ATHENA and EON projects at Stanford.

    Science.gov (United States)

    Advani, A; Tu, S; O'Connor, M; Coleman, R; Goldstein, M K; Musen, M

    1999-01-01

    We present a methodology and database mediator tool for integrating modern knowledge-based systems, such as the Stanford EON architecture for automated guideline-based decision-support, with legacy databases, such as the Veterans Health Information Systems & Technology Architecture (VISTA) systems, which are used nation-wide. Specifically, we discuss designs for database integration in ATHENA, a system for hypertension care based on EON, at the VA Palo Alto Health Care System. We describe a new database mediator that affords the EON system both physical and logical data independence from the legacy VA database. We found that to achieve our design goals, the mediator requires two separate mapping levels and must itself involve a knowledge-based component.

  14. An analysis of exchange rate risk exposure related to the public debt portfolio of Tunisia: Beyond VaR approach

    Directory of Open Access Journals (Sweden)

    Omrane Samia

    2012-01-01

    Full Text Available The aim of this study is to assess the exchange rate risk associated with the Tunisian public debt portfolio through Value-at-Risk (VaR methodology. We use daily spot exchange rates of the Tunisian dinar against the three main debt currencies, the dollar, the euro and the yen. Our period of interest is from 02/01/2004 to 31/12/2008. Thetas and Marginal VaR analysis reveal that Japanese yen is the most risky currency constituting the Tunisian public debt portfolio. American dollar appears as a source of risk for the Tunisian external debt but remains less risky than the yen, while, the euro constitutes a hedge currency for exchange risk management associated with the Tunisian public debt portfolio.

  15. Risk Measure of Portfolio Based on Pattern Comparison VaR with CVaR%投资组合的风险度量问题研究

    Institute of Scientific and Technical Information of China (English)

    应可慧

    2010-01-01

    本文研究CVaR模型对投资组合的风险度量问题,将VaR与CVaR两个风险度量模型进行比较,指出当今流行的风险管理模型VaR的缺陷,分析了CVaR模型进行风险管理的优势,以及用CVaR模型来代替VaR模型作为金融机构风险管理主要工具的重要性.

  16. VA (Veterans Administration) can Reduce Excess Disability Payments by Improving Pay Data Exchange with the Military Services.

    Science.gov (United States)

    2014-09-26

    Recoup the additional $385,000 on the 64 separation payment cases GAO identified where the recoupment balance was understated. -- Follow Agency appeal...D-R157 613 Vfi (VETERANS ADMINISTRATION) CAN REDUCE EXCESS / DI SRILITY PAYMENTS BY IMP..(UL) GENERAL ACCOUNTING U U LASI E OFFIC WASHINGTON DC...Affairs < VA Can Reduce Excess Disability Payments By Improving Pay Data * Exchange With The Military Services Federal law requires that the Veterans

  17. ’n Interpretasie van die ruimtestruktuur in na ’va (Etienne le Roux: enkele riglyne

    Directory of Open Access Journals (Sweden)

    P. H. Swanepoel

    1977-03-01

    Full Text Available Na ’va is die afsluitende werk van die derde trilogie in Leroux se romansiklus van nege dele. In hierdie roman vind daar op meer as een vlak ’n sametrekking plaas van die romans van die derde trilogie, maar dit bied ook retrospektief ’n blik op die agt romans wat dit voorafgaan. Hier word egter slegs aandag gegee aan aspekte van die ruimte.

  18. Military Sexual Trauma: Improvements Made, but VA Can Do More to Track and Improve the Consistency of Disability Claim Decisions

    Science.gov (United States)

    2014-06-01

    which in the judgment of a mental health professional employed by the Department, resulted from a physical assault of a sexual nature, battery of...a sexual nature, or sexual harassment which occurred while the veteran was serving on active duty or active duty for training.”12 While MST is not...MILITARY SEXUAL TRAUMA Improvements Made, but VA Can Do More to Track and Improve the Consistency of Disability

  19. Changing Patterns of Glucose-Lowering Medication Use in VA Nursing Home Residents with Diabetes, 2005 – 2011

    Science.gov (United States)

    Lee, Sei J.; Stijacic-Cenzer, Irena; Barnhart, Caroline; McClymont, Keelan; Steinman, Michael A

    2015-01-01

    Objective Although nursing home (NH) residents make up a large and growing proportion of Americans with diabetes mellitus, little is known about how glucose-lowering medications are used in this population. We sought to examine glucose-lowering medication use in Veterans Affairs (VA) NH residents with diabetes between 2005–2011. Research Design and Methods Retrospective cohort study, utilizing linked laboratory, pharmacy, administrative and NH Minimum Dataset (MDS) 2.0 databases in 123 VA NHs. A total of 9,431 long-stay (>90 days) VA NH residents over age 65 followed for 52,313 person-quarters. We identified receipt of glucose lowering medications including insulin, metformin, sulfonylureas, thiazolidinediones and others (alpha-glucosidase inhibitors, meglitinides, glucagon like peptide-1 analogs, dipeptidyl peptidase-4 inhibitors and amylin analogues) per quarter. Results The rates of sulfonylurea use in long-stay NH residents dropped dramatically from 24% in 2005 to 12% in 2011 (p<0.001), driven in large part by the dramatic decrease in glyburide use (10% to 2%, p<0.001). There was sharp drop in thiazolidinedione use in 2007 (4% to <1%, p<0.001). Metformin use was stable, ranging between 7% to 9% (p=0.24). Insulin use increased slightly from 30% to 32% (p<0.001). Use of other classes of glucose-lowering medications was stable (p=0.22) and low, remaining below 1.3%. Conclusions and Relevance Between 2005 and 2011, there were dramatic declines in use of sulfonylureas and thiazolidinediones in VA NH residents, suggesting that prescribing practices can be quickly changed in this setting. PMID:26272298

  20. Estimation of Dynamic VaR in Chinese Stock Markets Based on Time Scale and Extreme Value Theory

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    The accuracy and time scale invariance of value-at-risk (VaR) measurement methods for different stock indices and at different confidence levels are tested. Extreme value theory (EVT) is applied to model the extreme tail of standardized residual series of daily/weekly indices losses, and parametric and nonparametric methods are used to estimate parameters of the general Pareto distribution (GPD), and dynamic VaR for indices of three stock markets in China. The accuracy and time scale invariance of risk measurement methods through back-testing approach are also examined. Results show that not all the indices accept time scale invariance; there are some differences in accuracy between different indices at various confidence levels. The most powerful dynamic VaR estimation methods are EVT-GJR-Hill at 97.5% level for weekly loss to Shanghai stock market, and EVT-GARCH-MLE (Hill) at 99.0% level for weekly loss to Taiwan and Hong Kong stock markets, respectively.

  1. Review of VA/DOD Clinical Practice Guideline on management of acute stress and interventions to prevent posttraumatic stress disorder

    Directory of Open Access Journals (Sweden)

    William P. Nash, MD

    2012-06-01

    Full Text Available This article summarizes the recommendations of the Department of Veterans Affairs (VA/Department of Defense (DOD VA/DOD Clinical Practice Guideline for Management of Post-Traumatic Stress that pertain to acute stress and the prevention of posttraumatic stress disorder, including screening and early interventions for acute stress states in various settings. Recommended interventions during the first 4 days after a potentially traumatic event include attending to safety and basic needs and providing access to physical, emotional, and social resources. Psychological first aid is recommended for management of acute stress, while psychological debriefing is discouraged. Further medical and psychiatric assessment and provision of brief, trauma-focused cognitive-behavioral therapy are warranted if clinically significant distress or functional impairment persists or worsens after 2 days or if the criteria for a diagnosis of acute stress disorder are met. Follow-up monitoring and rescreening are endorsed for at least 6 months for everyone who experiences significant acute posttraumatic stress. Four interventions that illustrate early intervention principles contained in the VA/DOD Clinical Practice Guideline are described.

  2. Managing Challenging Behaviors of Dementia in Veterans: Identifying and Changing Activators and Consequences Using STAR-VA.

    Science.gov (United States)

    Curyto, Kim J; McCurry, Sue M; Luci, Katherine; Karlin, Bradley E; Teri, Linda; Karel, Michele J

    2017-02-01

    One of the most challenging clinical issues for long-term care staff is the management of dementia-related behavioral symptoms. STAR-VA is an interdisciplinary intervention for managing challenging behaviors of Veterans with dementia in Community Living Centers (CLCs) within the U.S. Department of Veterans Affairs. The goals of the current article are to delineate categories of challenging behaviors found in CLCs, the context in which behaviors occurred, and the interventions used by CLC clinical teams when implementing STAR-VA. In 2013, 17 CLC teams completed STAR-VA training, enrolling 71 Veteran participants. Four independent raters identified common assessment and intervention themes for six behavior categories, coding activators, consequences, goal behaviors, and care plans for each category. Successful care plans included staff changes in communication approaches, incorporation of pleasant events into care, and individualized environmental modifications. Findings illustrate the range of interventions that CLC teams may apply as a result of systematic behavioral assessment informing an understanding of activators and consequences of dementia-related behaviors. [Journal of Gerontological Nursing, 43(2), 33-43.].

  3. Implementation outcomes of evidence-based quality improvement for depression in VA community based outpatient clinics

    Directory of Open Access Journals (Sweden)

    Fortney John

    2012-04-01

    Full Text Available Abstract Background Collaborative-care management is an evidence-based practice for improving depression outcomes in primary care. The Department of Veterans Affairs (VA has mandated the implementation of collaborative-care management in its satellite clinics, known as Community Based Outpatient Clinics (CBOCs. However, the organizational characteristics of CBOCs present added challenges to implementation. The objective of this study was to evaluate the effectiveness of evidence-based quality improvement (EBQI as a strategy to facilitate the adoption of collaborative-care management in CBOCs. Methods This nonrandomized, small-scale, multisite evaluation of EBQI was conducted at three VA Medical Centers and 11 of their affiliated CBOCs. The Plan phase of the EBQI process involved the localized tailoring of the collaborative-care management program to each CBOC. Researchers ensured that the adaptations were evidence based. Clinical and administrative staff were responsible for adapting the collaborative-care management program for local needs, priorities, preferences and resources. Plan-Do-Study-Act cycles were used to refine the program over time. The evaluation was based on the RE-AIM (Reach, Effectiveness, Adoption, Implementation, Maintenance Framework and used data from multiple sources: administrative records, web-based decision-support systems, surveys, and key-informant interviews. Results Adoption: 69.0% (58/84 of primary care providers referred patients to the program. Reach: 9.0% (298/3,296 of primary care patients diagnosed with depression who were not already receiving specialty care were enrolled in the program. Fidelity: During baseline care manager encounters, education/activation was provided to 100% (298/298 of patients, barriers were assessed and addressed for 100% (298/298 of patients, and depression severity was monitored for 100% (298/298 of patients. Less than half (42.5%, 681/1603 of follow-up encounters during the acute

  4. Geochemical and Petrologic Constraints on the Source of Eocene Volcanism at Mole Hill, Rockingham County, VA

    Science.gov (United States)

    Johnson, E. A.; Beard, J. S.

    2010-12-01

    Mole Hill is an Eocene (48 Ma) basaltic volcanic neck located west of Harrisonburg, VA, and provides a unique opportunity to probe the mantle beneath the Shenandoah Valley. It lies on the northeastern edge of a swarm of alkaline-series volcanic plugs, dikes, and diatremes extending through Rockingham and Highland Counties, VA, and Pendleton County, WV. The Eocene volcanics are thought to have exploited extensive basement fracture systems originally formed during the Alleghenian Orogeny and subsequent rifting. The Eocene volcanism may have been triggered by reactivation of faults due to global shifts in relative plate motions (Southworth 1993, USGS Bull, B1839-I) but the source material and magmatic processes for the Eocene volcanism are largely unknown. Compositional and texture analyses of xenocrystic and groundmass clinopyroxene, olivine, and spinel were completed either at Virginia Tech on the Cameca SX-50 electron microprobe in the Dept of Geological Sciences, or in the Dept of Mineral Sciences, Smithsonian Institution, Washington, D.C using the JEOL JXA-8900R WD/EDS microanalyzer or the FEI NOVA nanoSEM600 FEG Variable Pressure Scanning Electron Microscope. Xenocrysts up to 2cm in diameter are distributed throughout the volcanic neck, with clinopyroxene >>spinel>olivine. The clinopyroxene and olivine xenocrysts show undulatory extinction in cross-polarized light and are found as individual crystals or as aggregates. Clinopyroxene xenocryst cores are high-Al, low-Cr augite ( ˜Wo44En46Fs10) with Mg# 78.5-85.9. The clinopyroxene xenocrysts have compositionally zoned rims 100-250 μm-wide containing abundant plagioclase inclusions and sparse melt inclusions in a sieve texture. The outer edges of xenocrysts approach the compositions of groundmass and microphenocryst clinopyroxenes ( ˜Wo47En38Fs15; Mg# 67.9-74.5). Olivine xenocrysts contain sulfide inclusions and Cr-rich spinel and have Mg-rich ( ˜Fo86-90) cores with more Fe- and Ca-rich rims (Fo70

  5. Toxicidad de VA-DIFTET® por administración a dosis repetida en ratones

    Directory of Open Access Journals (Sweden)

    Pablo González

    2000-06-01

    Full Text Available Una vez estudiada la toxicidad de la vacuna VA-DIFTET® (vacuna antidiftérica antitetánica por administración a dosis única en dos especies de animales, se impone la evaluación a dosis repetida, teniendo en cuenta que el esquema de inmunización en humanos prevé la aplicación de tres dosis cuando el componente pertusis de la DPT está contraindicado. Se emplearon 210 ratones OF-1 de ambos sexos. Los grupos experimentales fueron similares a los de la prueba a dosis única con la vacuna dúplex, anatoxina diftérica, anatoxina tetánica, adyuvante, tiomersal, solución salina fisiológica y un grupo control no tratado. Un grupo de hembras y otro de machos fue asignado aleatoriamente a cada tratamiento y para recibir 1, 2 ó 3 dosis por vía intramuscular. Tras cada aplicación se evaluó la aparición de síntomas clínicos, el incremento de peso, el consumo de agua y alimento y la dinámica de la respuesta inmune contra las anatoxinas tetánica y diftérica, específicamente de tipo IgG, mediante ELISA indirecto. Al término de las observaciones los animales fueron sacrificados y se realizaron estudios anatomopatológicos. Además, durante el sacrificio se evaluó el índice relativo de bazo y timo, así como la relación bazo/timo. No se comprobaron alteraciones que evidenciaran toxicidad por parte de la vacuna y sus componentes. Asimismo, se demostró una marcada respuesta inmune en los grupos vacunales e inoculados con las anatoxinas. Se considera que los resultados de la prueba fueron satisfactorios.

  6. Comparing the Planform Morphologies of a Freely Meandering Channel and the Bedrock- Controlled South River, VA.

    Science.gov (United States)

    Narinesingh, P.; Pizzuto, J.

    2008-12-01

    The planforms of the lithologically controlled South River, VA, and the freely meandering Teklanika River, AK were investigated using two statistical methods as well as fractal and spectral analyses. The lithologic controls along the South River include riverbanks consisting of pre-Holocene terraces and alluvial fans, and highly resistant bedrock that frequently crops out both in the bed and along the banks. A statistical analysis of bends composed of single arcs shows that the average radius of curvature is six times greater and the average bend length is 25 percent smaller for the South River relative to the meandering river, indicating that lithologically controlled bends are less curved and shorter than freely-formed meander bends. Fractal analysis reveals that the meandering river displays a smaller range in length scales than the South River, which exhibits a wider range in length scales that reflect a wider distribution of bend sizes. The method of Lancaster and Bras, (2002), which identifies bends of different complexity, indicates that the meandering river displays bends composed of single arcs, complex arcs and multiple complex arcs. Unlike the freely meandering Teklanika River, the lithologically controlled South River does not display bends composed of multiple complex arcs, though bends composed of single and complex arcs are common. Spectral analysis reveals that the meandering river's pattern is composed of a relatively narrow range of dominant wavelengths with the most prominent wavelength being the longest, while the lithologically controlled river displays dominant wavelengths over a relatively wide range and the most prominent wavelength is not the longest. This analysis demonstrates that lithological controls increase the range of bend lengths, increase radii of curvature, simplify bend shapes, and increase the distribution of wavelengths of sinuous rivers.

  7. 基于Monte Carlo-CoVaR的金融机构风险外溢效应研究

    Institute of Scientific and Technical Information of China (English)

    张凡

    2015-01-01

    金融机构之间的风险外溢则通过两两之间的Co-VaR值加以分析,文章通过Monte-Carlo模拟出动态VaR值,并以回归分析计算出Co-VaR值.在风险价值VaR=-Rt-2(eu+σ×F-1(a)-1)的基础上,通过随机模拟法历史数据构造出目标收益分布函数F-1(a),这就将不确定性的风险价值通过最大程度的随机模拟与随机游走方法来计算得到,以减少人为主观因素对风险价值的影响.

  8. Verbal autopsy interpretation: a comparative analysis of the InterVA model versus physician review in determining causes of death in the Nairobi DSS

    OpenAIRE

    2010-01-01

    Abstract Background Developing countries generally lack complete vital registration systems that can produce cause of death information for health planning in their populations. As an alternative, verbal autopsy (VA) - the process of interviewing family members or caregivers on the circumstances leading to death - is often used by Demographic Surveillance Systems to generate cause of death data. Physician review (PR) is the most common method of interpreting VA, but this method is a time- and...

  9. Employing external facilitation to implement cognitive behavioral therapy in VA clinics: a pilot study

    Directory of Open Access Journals (Sweden)

    Blevins Dean

    2010-10-01

    Full Text Available Abstract Background Although for more than a decade healthcare systems have attempted to provide evidence-based mental health treatments, the availability and use of psychotherapies remains low. A significant need exists to identify simple but effective implementation strategies to adopt complex practices within complex systems of care. Emerging evidence suggests that facilitation may be an effective integrative implementation strategy for adoption of complex practices. The current pilot examined the use of external facilitation for adoption of cognitive behavioral therapy (CBT in 20 Department of Veteran Affairs (VA clinics. Methods The 20 clinics were paired on facility characteristics, and 23 clinicians from these were trained in CBT. A clinic in each pair was randomly selected to receive external facilitation. Quantitative methods were used to examine the extent of CBT implementation in 10 clinics that received external facilitation compared with 10 clinics that did not, and to better understand the relationship between individual providers' characteristics and attitudes and their CBT use. Costs of external facilitation were assessed by tracking the time spent by the facilitator and therapists in activities related to implementing CBT. Qualitative methods were used to explore contextual and other factors thought to influence implementation. Results Examination of change scores showed that facilitated therapists averaged an increase of 19% [95% CI: (2, 36] in self-reported CBT use from baseline, while control therapists averaged a 4% [95% CI: (-14, 21] increase. Therapists in the facilitated condition who were not providing CBT at baseline showed the greatest increase (35% compared to a control therapist who was not providing CBT at baseline (10% or to therapists in either condition who were providing CBT at baseline (average 3%. Increased CBT use was unrelated to prior CBT training. Barriers to CBT implementation were therapists' lack of

  10. Mean-VaR Portfolio Selection Based on Particle Swarm Optimization Algorithm%基于粒子群优化算法的均值-VaR投资组合选择

    Institute of Scientific and Technical Information of China (English)

    曾艳姗; 李仲飞

    2012-01-01

    在现实市场中,①为防止由卖空交易引起市场操纵等问题的出现,即使在发达的证券市场,交易仍受到一定的卖空限制;②由于市场相关规定与投资者自身风险控制的需要,在某些资产上的投资比例受到一定限制;③交易过程中需支付印花税等交易成本.故结合这三方面,采用Value-at-Risk(VaR)度量风险,在收益率服从正态和非正态分布两种假设下,构建了带有限卖空约束、投资比例约束和交易成本的均值-VaR投资组合模型.首先,给出了该模型的粒子群优化(PSO)算法;其次采用A股市场的实际数据进行了数值实验;最后分析了有效前沿的特征及有限卖空约束对投资决策的影响.%In the real market, ( i) in order to prevent market manipulation and other problems caused by short selling, transaction is still subject to some short selling restrictions even in developed markets; (ii) due to the market's relevant regulations and investors' requirement of risk control, the proportions invested in some assets have certain limits; (iii) investors must pay stamp duty and other transaction costs during transaction. Considering these three aspects, Value-at-Risk (VaR) as risk measure is adopted, and a mean-VaR portfolio model is constructed with limited short selling, proportion of investment limits and transaction cost under two assumptions that the rate of return is normal and non-normal distribution. Firstly, a particle swarm optimization (PSO) algorithm is presented for the model; secondly, numerical experiments are provided by using the test data from A stock market of China; finally, the characteristics of the portfolio efficient frontier and the influences on investors' decision-making under the limited short selling constraints are discussed.

  11. The Effect of VAc-VeoVa10 Latex Powder on Mechanical Properties of Modified Mortar%VAc-VeoVa10乳胶粉对改性水泥砂浆力学性能的影响

    Institute of Scientific and Technical Information of China (English)

    程祥龙; 班倩; 滕朝辉; 夏大寒; 申迎华

    2012-01-01

    According to the bad caking property and flexibility of cement mortar used in external thermal insulation system, Vac-VeoVa10 latex powder was used to modify the cement mortar. The effect of dosage of Vac-VeoVa10 latex powder on mechanical properties of modified mortar was studied. The results show that with the increase of dosage of latex powder, both the bond strength between modified mortar and expanded polystyrene boards (EPS), and the strength between modified mortar and cement mortar block increased; the flexural strength and flexibility were improved, but the compressive strength decreased. At the same time, the influence of cement/sand ratio, dosage of Vac-VeoVa10 and dosage of water retaining agent on mortar performance was analyzed by orthogonal test, including the bond strength between modified mortar and expanded polystyrene boards (EPS), the strength between modified mortar and cement mortar block by compressive strength,flexural strength,and ratio of compressive strength to flexural strength. By comprehensive consideration, at the cement/sand ratio 1:1, the mass fraction of polymer powder 4% ,and the mass fraction of water retaining agent 0. 2%, the properties of modified mortar was the best.%针对目前膨胀聚苯板(EPS)外墙外保温系统用水泥砂浆粘结性差、柔韧性差等问题,用醋酸乙烯酯(VAc)与叔碳酸乙烯酯(VeoVa10)共聚乳胶粉对其进行改性.研究了乳胶粉用量对改性水泥砂浆力学性能的影响.结果表明,随着乳胶粉用量的增加,砂浆的粘结强度增加、抗折强度提高、抗压强度降低、柔韧性提高.通过正交试验研究了灰砂质量比、乳胶粉用量、保水剂用量等因素对改性水泥砂浆与EPS以及与基础砂浆粘结强度、抗折强度、抗压强度以及压折比的影响,得出改性水泥砂浆的最优配比为:水泥与石英砂的质量比1∶1,乳胶粉质量分数4%,保水剂质量分数0.2%.

  12. Construction of recombinant pseudorabies viruses by using PRV BACs deficient in IE180 or pac sequences: Application of vBAC90D recombinant virus to production of PRV amplicons.

    Science.gov (United States)

    Lerma, L; Muñoz, A L; Wagner, S; Dinu, M; Martín, B; Tabarés, E

    2016-02-02

    We describe a simple and efficient method to obtain recombinant pseudorabies virus (PRV) in mammalian cells by using the PRV BACs, PBAC80 deficient in pac sequences and PBAC90 deficient in the IE180 gene. These essential viral sequences were used as targets to obtain viable recombinant viruses. PBAC80 was constructed, confirmed to encode a copy of the IE180 gene regulated by the inducible Ptet promoter, and used to obtain recombinant attenuated PRV viruses that express the EGFP protein (PRV-BT80GF virus). PBAC90 was used to obtain the vBAC90D virus, deficient in IE180 and free of replication-competent revertants, and which can be used as a helper in the production of PRV amplicons.

  13. Targeted Amplicon Sequencing for Single-Nucleotide-Polymorphism Genotyping of Attaching and Effacing Escherichia coli O26:H11 Cattle Strains via a High-Throughput Library Preparation Technique.

    Science.gov (United States)

    Ison, Sarah A; Delannoy, Sabine; Bugarel, Marie; Nagaraja, Tiruvoor G; Renter, David G; den Bakker, Henk C; Nightingale, Kendra K; Fach, Patrick; Loneragan, Guy H

    2015-11-13

    Enterohemorrhagic Escherichia coli (EHEC) O26:H11, a serotype within Shiga toxin-producing E. coli (STEC) that causes severe human disease, has been considered to have evolved from attaching and effacing E. coli (AEEC) O26:H11 through the acquisition of a Shiga toxin-encoding gene. Targeted amplicon sequencing using next-generation sequencing technology of 48 phylogenetically informative single-nucleotide polymorphisms (SNPs) and three SNPs differentiating Shiga toxin-positive (stx-positive) strains from Shiga toxin-negative (stx-negative) strains were used to infer the phylogenetic relationships of 178 E. coli O26:H11 strains (6 stx-positive strains and 172 stx-negative AEEC strains) from cattle feces to 7 publically available genomes of human clinical strains. The AEEC cattle strains displayed synonymous SNP genotypes with stx2-positive sequence type 29 (ST29) human O26:H11 strains, while stx1 ST21 human and cattle strains clustered separately, demonstrating the close phylogenetic relatedness of these Shiga toxin-negative AEEC cattle strains and human clinical strains. With the exception of seven stx-negative strains, five of which contained espK, three stx-related SNPs differentiated the STEC strains from non-STEC strains, supporting the hypothesis that these AEEC cattle strains could serve as a potential reservoir for new or existing pathogenic human strains. Our results support the idea that targeted amplicon sequencing for SNP genotyping expedites strain identification and genetic characterization of E. coli O26:H11, which is important for food safety and public health.

  14. Transfer factor (diffusing capacity) standardized for alveolar volume: validation, reference values and applications of a new linear model to replace KCO (TL/VA)

    Science.gov (United States)

    Chinn, D J; Cotes, J E; Flowers, R; Marks, A M; Reed, J W

    1996-06-01

    Transfer factor (TL) varies with alveolar volume (VA), but not in the manner implied by the carbon monoxide transfer coefficient (KCO (TL/VA)). This paper considers two other simple models (one linear and one exponential) which might standardize TL for VA, and asks the questions: 1) Is either model valid? 2) What are appropriate reference values? and 3) Will the model be useful? The relationship of TL to VA within subjects at different depths of inspiration, and between subjects having lungs of different sizes, were measured and compared. The subjects were asymptomatic, nonsmoking, Caucasian adults, including 31 males assessed in the laboratory and 503 male and female participants in population studies. The linear partial regression coefficients of TL on VA (L corrected for body temperature, atmospheric pressure and water saturation (BTPS)) standardized for height (H) in metres, were similar within- and between-subjects; the coefficients applied over a wide range of values for VA. This was not the case for the exponential model. The resulting reference equations in SI units for males and females were: TL = 11.52 H + 2.72 VA.H-2 - 0.051 Age -12.35. RSD 1.17; and TL = 4.87 H + 2.29 VA.H-2 - 0.019 Age -3.03. RSD 0.92, respectively. The residual standard deviations (RSD) about the new relationships were less than in other series. The new linear model could account for much of the variation between different published reference values for TL; it could be useful clinically, in circumstances when VA deviates from the norm. The model does not explain differences in TL associated with gender. Inclusion of VA.H-2 as a covariate in the reference equation for transfer factor, in addition to age and height, improves the accuracy of prediction of normal transfer factor compared with current reference values; its use suggests that some of the differences between published values is due to the volume term. The equations can be used clinically, and eliminate the need for carbon

  15. Performance of InterVA for assigning causes of death to verbal autopsies: multisite validation study using clinical diagnostic gold standards

    Directory of Open Access Journals (Sweden)

    Flaxman Abraham D

    2011-08-01

    Full Text Available Abstract Background InterVA is a widely disseminated tool for cause of death attribution using information from verbal autopsies. Several studies have attempted to validate the concordance and accuracy of the tool, but the main limitation of these studies is that they compare cause of death as ascertained through hospital record review or hospital discharge diagnosis with the results of InterVA. This study provides a unique opportunity to assess the performance of InterVA compared to physician-certified verbal autopsies (PCVA and alternative automated methods for analysis. Methods Using clinical diagnostic gold standards to select 12,542 verbal autopsy cases, we assessed the performance of InterVA on both an individual and population level and compared the results to PCVA, conducting analyses separately for adults, children, and neonates. Following the recommendation of Murray et al., we randomly varied the cause composition over 500 test datasets to understand the performance of the tool in different settings. We also contrasted InterVA with an alternative Bayesian method, Simplified Symptom Pattern (SSP, to understand the strengths and weaknesses of the tool. Results Across all age groups, InterVA performs worse than PCVA, both on an individual and population level. On an individual level, InterVA achieved a chance-corrected concordance of 24.2% for adults, 24.9% for children, and 6.3% for neonates (excluding free text, considering one cause selection. On a population level, InterVA achieved a cause-specific mortality fraction accuracy of 0.546 for adults, 0.504 for children, and 0.404 for neonates. The comparison to SSP revealed four specific characteristics that lead to superior performance of SSP. Increases in chance-corrected concordance are attained by developing cause-by-cause models (2%, using all items as opposed to only the ones that mapped to InterVA items (7%, assigning probabilities to clusters of symptoms (6%, and using empirical

  16. Suicide-related behaviors in older patients with new anti-epileptic drug use: data from the VA hospital system

    Directory of Open Access Journals (Sweden)

    Dersh Jeffrey J

    2010-01-01

    Full Text Available Abstract Background The U.S. Food and Drug Administration (FDA recently linked antiepileptic drug (AED exposure to suicide-related behaviors based on meta-analysis of randomized clinical trials. We examined the relationship between suicide-related behaviors and different AEDs in older veterans receiving new AED monotherapy from the Veterans Health Administration (VA, controlling for potential confounders. Methods VA and Medicare databases were used to identify veterans 66 years and older, who received a care from the VA between 1999 and 2004, and b an incident AED (monotherapy prescription. Previously validated ICD-9-CM codes were used to identify suicidal ideation or behavior (suicide-related behaviors cases, epilepsy, and other conditions previously associated with suicide-related behaviors. Each case was matched to controls based on prior history of suicide-related behaviors, year of AED prescription, and epilepsy status. Results The strongest predictor of suicide-related behaviors (N = 64; Controls N = 768 based on conditional logistic regression analysis was affective disorder (depression, anxiety, or post-traumatic stress disorder (PTSD; Odds Ratio 4.42, 95% CI 2.30 to 8.49 diagnosed before AED treatment. Increased suicide-related behaviors were not associated with individual AEDs, including the most commonly prescribed AED in the US - phenytoin. Conclusion Our extensive diagnostic and treatment data demonstrated that the strongest predictor of suicide-related behaviors for older patients newly treated with AED monotherapy was a previous diagnosis of affective disorder. Additional, research using a larger sample is needed to clearly determine the risk of suicide-related behaviors among less commonly used AEDs.

  17. Appalachian region oilfield reservoir investigations, Gordon Stray, Gordon, and fourth sands, Smithfield field, Grant District, Wetzel County, W. Va

    Energy Technology Data Exchange (ETDEWEB)

    Whildon, C.E. Jr.; Overbey, W.K. Jr.

    1965-09-01

    The U.S. Bureau of Mines is investigating the susceptibility of selected pressure-depleted Appalachian region oil reservoirs to more intensive oil recovery methods. A map shows the well locations, formation samples and published reports of wells cored under the current reservoir evaluation program. Also, a map shows a part of Wetzel County, W. Va., showing oil-productive areas, the location of the cored well and geologic structure. A columnar section is given of the geological formations in the vicinity of the cored wells. Well logs were taken to supplement core information. Core analysis, well logs, geology, field development, and production history are presented. (19 refs.)

  18. Paralelismos entre el ajedrez y la novela La vida que se va de Vicente Leñero

    OpenAIRE

    2010-01-01

    En este estudio analizo cómo el autor mexicano Vicente Leñero escribe su novela La vida que se va estableciendo un paralelismo entre la creación de su novela y el juego de ajedrez. La novela cuenta la historia de una anciana ajedrecista que al final de su vida aprovecha su encuentro con un periodista para contarle las diferentes vidas que hubiera podido vivir si en vez de haber tomado una decisión hubiera optado por otra contraria. Esencialmente, el estudio está dividido en dos par...

  19. Efectividad de la vacuna VA-MENGOC-BC® contra cepas heterólogas de meningococo B

    Directory of Open Access Journals (Sweden)

    Rolando Ochoa-Azze

    2016-08-01

    Full Text Available La efectividad de las vacunas de vesículas de membrana externa de Neisseria meningitidis serogrupo B ha sido cuestionada por algunos investigadores, limitándola a la cepa vacunal. VA-MENGOC-BC® es una vacuna antimeningocócica basada en dicha tecnología. Presentamos un metaanálisis de estudios realizados en diferentes contextos epidemiológicos, evaluando su efectividad contra cepas heterólogas de meningococo B en varios grupos de edades. Se demuestra que la vacuna es efectiva contra cepas homólogas, heterólogas y de diferentes complejos clonales.

  20. Application of PCR amplicon sequencing using a single primer pair in PCR amplification to assess variations in Helicobacter pylori CagA EPIYA tyrosine phosphorylation motifs

    OpenAIRE

    Karlsson Anneli; Monstein Hans-Jürg; Ryberg Anna; Borch Kurt

    2010-01-01

    Background The presence of various EPIYA tyrosine phosphorylation motifs in the CagA protein of Helicobacter pylori has been suggested to contribute to pathogenesis in adults. In this study, a unique PCR assay and sequencing strategy was developed to establish the number and variation of cagA EPIYA motifs. Findings MDA-DNA derived from gastric biopsy specimens from eleven subjects with gastritis was used with M13- and T7- sequence-tagged primers for amplification of the cagA EPIYA motif regio...