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Sample records for amplicon va derived

  1. Functional Overexpression of Vomeronasal Receptors Using a Herpes Simplex Virus Type 1 (HSV-1)-Derived Amplicon.

    Science.gov (United States)

    Stein, Benjamin; Alonso, María Teresa; Zufall, Frank; Leinders-Zufall, Trese; Chamero, Pablo

    2016-01-01

    In mice, social behaviors such as mating and aggression are mediated by pheromones and related chemosignals. The vomeronasal organ (VNO) detects olfactory information from other individuals by sensory neurons tuned to respond to specific chemical cues. Receptors expressed by vomeronasal neurons are implicated in selective detection of these cues. Nearly 400 receptor genes have been identified in the mouse VNO, but the tuning properties of individual receptors remain poorly understood, in part due to the lack of a robust heterologous expression system. Here we develop a herpes virus-based amplicon delivery system to overexpress three types of vomeronasal receptor genes and to characterize cell responses to their proposed ligands. Through Ca2+ imaging in native VNO cells we show that virus-induced overexpression of V1rj2, V2r1b or Fpr3 caused a pronounced increase of responsivity to sulfated steroids, MHC-binding peptide or the synthetic hexapeptide W-peptide, respectively. Other related ligands were not recognized by infected individual neurons, indicating a high degree of selectivity by the overexpressed receptor. Removal of G-protein signaling eliminates Ca2+ responses, indicating that the endogenous second messenger system is essential for observing receptor activation. Our results provide a novel expression system for vomeronasal receptors that should be useful for understanding the molecular logic of VNO ligand detection. Functional expression of vomeronasal receptors and their deorphanization provides an essential requirement for deciphering the neural mechanisms controlling behavior. PMID:27195771

  2. Functional Overexpression of Vomeronasal Receptors Using a Herpes Simplex Virus Type 1 (HSV-1-Derived Amplicon.

    Directory of Open Access Journals (Sweden)

    Benjamin Stein

    Full Text Available In mice, social behaviors such as mating and aggression are mediated by pheromones and related chemosignals. The vomeronasal organ (VNO detects olfactory information from other individuals by sensory neurons tuned to respond to specific chemical cues. Receptors expressed by vomeronasal neurons are implicated in selective detection of these cues. Nearly 400 receptor genes have been identified in the mouse VNO, but the tuning properties of individual receptors remain poorly understood, in part due to the lack of a robust heterologous expression system. Here we develop a herpes virus-based amplicon delivery system to overexpress three types of vomeronasal receptor genes and to characterize cell responses to their proposed ligands. Through Ca2+ imaging in native VNO cells we show that virus-induced overexpression of V1rj2, V2r1b or Fpr3 caused a pronounced increase of responsivity to sulfated steroids, MHC-binding peptide or the synthetic hexapeptide W-peptide, respectively. Other related ligands were not recognized by infected individual neurons, indicating a high degree of selectivity by the overexpressed receptor. Removal of G-protein signaling eliminates Ca2+ responses, indicating that the endogenous second messenger system is essential for observing receptor activation. Our results provide a novel expression system for vomeronasal receptors that should be useful for understanding the molecular logic of VNO ligand detection. Functional expression of vomeronasal receptors and their deorphanization provides an essential requirement for deciphering the neural mechanisms controlling behavior.

  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. CoVaR

    OpenAIRE

    Tobias Adrian; Brunnermeier, Markus K

    2008-01-01

    We define CoVaR as the value at risk (VaR) of financial institutions conditional on other institutions being in distress. The increase of CoVaR relative to VaR measures spillover risk among institutions. We estimate CoVaR using quantile regressions and document significant CoVaR increases among financial institutions. We identify six risk factors that allow institutions to offload tail risk and show that such hedging reduces the wedge between CoVaR and VaR. We argue that financial institution...

  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. VA scandal widens

    Directory of Open Access Journals (Sweden)

    Robbins RA

    2014-05-01

    Full Text Available No abstract available. Article truncated at 150 words. On Memorial Day, which honors those who died in service to the country, the Department of Veterans Affairs (VA Office of Inspector General (OIG is investigating medical facilities in at least 26 cities (1. The scandal started in Phoenix where Sam Foote, a retired VA physician, alleged that up to 40 patients in Arizona died awaiting care in a network where some veterans could not get appointments for more than a year. Foote claimed that Phoenix VA officials were misrepresenting wait times to collect bonus checks while maintaining "secret lists" of patients. These accusations resulted in the suspension of Sharon Helman, the Phoenix VA hospital director, along with her associate director and a another senior unnamed administrator. Dennis Wagner in an article in the Arizona Republic listed many of the accusations made against various VA hospitals outside of Phoenix (1. These include: Chicago: Germaine Clarno, president of a federal ...

  8. 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.

  9. 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.

  10. 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.

  11. Metabarcoding Marine Sediments: Preparation of Amplicon Libraries.

    Science.gov (United States)

    Fonseca, Vera G; Lallias, Delphine

    2016-01-01

    The accurate assessment of community composition and ultimately species identification is of utmost importance in any ecological and evolutionary study. Advances in sequencing technologies have allowed the unraveling of levels of biodiversity never imagined before when applied to large-scale environmental DNA studies (also termed metabarcoding/metagenetics/metasystematics/environmental barcoding). Here, we describe a detailed protocol to assess eukaryotic biodiversity in marine sediments, identifying key steps that should not be neglected when preparing Next-Generation Sequencing (NGS) amplicon libraries: DNA extraction, multiple PCR amplification of DNA barcode markers with index/ tag-primers, and final Illumina MiSeq sequencing library preparation. PMID:27460378

  12. 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...

  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. 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...

  15. 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.

  16. 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

  17. 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...

  18. 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...

  19. Systems consequences of amplicon formation in human breast cancer.

    Science.gov (United States)

    Inaki, Koichiro; Menghi, Francesca; Woo, Xing Yi; Wagner, Joel P; Jacques, Pierre-Étienne; Lee, Yi Fang; Shreckengast, Phung Trang; Soon, Wendy WeiJia; Malhotra, Ankit; Teo, Audrey S M; Hillmer, Axel M; Khng, Alexis Jiaying; Ruan, Xiaoan; Ong, Swee Hoe; Bertrand, Denis; Nagarajan, Niranjan; Karuturi, R Krishna Murthy; Miranda, Alfredo Hidalgo; Liu, Edison T

    2014-10-01

    Chromosomal structural variations play an important role in determining the transcriptional landscape of human breast cancers. To assess the nature of these structural variations, we analyzed eight breast tumor samples with a focus on regions of gene amplification using mate-pair sequencing of long-insert genomic DNA with matched transcriptome profiling. We found that tandem duplications appear to be early events in tumor evolution, especially in the genesis of amplicons. In a detailed reconstruction of events on chromosome 17, we found large unpaired inversions and deletions connect a tandemly duplicated ERBB2 with neighboring 17q21.3 amplicons while simultaneously deleting the intervening BRCA1 tumor suppressor locus. This series of events appeared to be unusually common when examined in larger genomic data sets of breast cancers albeit using approaches with lesser resolution. Using siRNAs in breast cancer cell lines, we showed that the 17q21.3 amplicon harbored a significant number of weak oncogenes that appeared consistently coamplified in primary tumors. Down-regulation of BRCA1 expression augmented the cell proliferation in ERBB2-transfected human normal mammary epithelial cells. Coamplification of other functionally tested oncogenic elements in other breast tumors examined, such as RIPK2 and MYC on chromosome 8, also parallel these findings. Our analyses suggest that structural variations efficiently orchestrate the gain and loss of cancer gene cassettes that engage many oncogenic pathways simultaneously and that such oncogenic cassettes are favored during the evolution of a cancer. PMID:25186909

  20. 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...

  1. Multiplex amplicon sequencing for microbe identification in community-based culture collections.

    Science.gov (United States)

    Armanhi, Jaderson Silveira Leite; de Souza, Rafael Soares Correa; de Araújo, Laura Migliorini; Okura, Vagner Katsumi; Mieczkowski, Piotr; Imperial, Juan; Arruda, Paulo

    2016-01-01

    Microbiome analysis using metagenomic sequencing has revealed a vast microbial diversity associated with plants. Identifying the molecular functions associated with microbiome-plant interaction is a significant challenge concerning the development of microbiome-derived technologies applied to agriculture. An alternative to accelerate the discovery of the microbiome benefits to plants is to construct microbial culture collections concomitant with accessing microbial community structure and abundance. However, traditional methods of isolation, cultivation, and identification of microbes are time-consuming and expensive. Here we describe a method for identification of microbes in culture collections constructed by picking colonies from primary platings that may contain single or multiple microorganisms, which we named community-based culture collections (CBC). A multiplexing 16S rRNA gene amplicon sequencing based on two-step PCR amplifications with tagged primers for plates, rows, and columns allowed the identification of the microbial composition regardless if the well contains single or multiple microorganisms. The multiplexing system enables pooling amplicons into a single tube. The sequencing performed on the PacBio platform led to recovery near-full-length 16S rRNA gene sequences allowing accurate identification of microorganism composition in each plate well. Cross-referencing with plant microbiome structure and abundance allowed the estimation of diversity and abundance representation of microorganism in the CBC. PMID:27404280

  2. 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,...

  3. 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,...

  4. 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,...

  5. 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,...

  6. 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,...

  7. 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,...

  8. 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,...

  9. 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,...

  10. 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,...

  11. 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,...

  12. 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,...

  13. 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,...

  14. 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,...

  15. 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,...

  16. 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,...

  17. 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,...

  18. 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,...

  19. 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,...

  20. 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.

  1. The VA-Medical School Partnership: The Medical School Perspective.

    Science.gov (United States)

    Petersdorf, Robert G.

    1987-01-01

    Issues in the relationship between the Veterans' Administration (VA) and medical schools are discussed, including VA faculty recruitment and retention, ambulatory care in VA teaching hospitals, governance and growth of research within VA medical centers, and effects of cost containment and competition on teaching and training in VA hospitals. (MSE)

  2. 78 FR 62441 - VA Dental Insurance Program-Federalism

    Science.gov (United States)

    2013-10-22

    ... available on VA's Web site at http://www1.va.gov/orpm/ , by following the link for ``VA Regulations... AFFAIRS 38 CFR Part 17 RIN 2900-AO85 VA Dental Insurance Program--Federalism AGENCY: Department of Veterans Affairs. ACTION: Direct final rule. SUMMARY: The Department of Veterans Affairs (VA) is...

  3. 78 FR 32126 - VA Dental Insurance Program

    Science.gov (United States)

    2013-05-29

    ... in the Federal Register (77 FR 12517) a proposed rule to amend VA regulations to establish VADIP, a... coverage capabilities as determined during the Federal contracting process. See 77 FR 12518. Although VA... 510(b). See 77 FR 12520. We will conduct the Federal contracting process anticipating this...

  4. 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...

  5. 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...

  6. SlaVaComp: Konvertierungstool

    OpenAIRE

    Simon Skilevic

    2013-01-01

    В статье сообщается о программе конвертации шрифтов разного формата в формат Юникод, разработанной в рамках фрайбургского проекта по исторической корпусной лингвистике. Программа обеспечивает конвертацию любых шрифтов в формат Юникод без потери информации, содержащейся в исконном файле, то есть с сохранением авторского форматирования. Название программы «SlaVaComp-Konvertierer / SlaVaComp-конвертор». Поскольку программа предназначена для конвертации любых, а не только церковнославянских, шриф...

  7. 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 ...

  8. Agreement Between HEDIS Performance Assessments in the VA and Medicare Advantage

    Directory of Open Access Journals (Sweden)

    Amal N. Trivedi MD, MPH

    2016-03-01

    Full Text Available 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] < 7.0% in diabetes to 54.7% (blood pressure < 140/90 mm Hg in diabetes. The overall agreement between VA and MA HEDIS assessments ranged from 38.5% to 62.6%. 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.

  9. 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...

  10. Women's veteran identity and utilization of VA health services.

    Science.gov (United States)

    Di Leone, Brooke A L; Wang, Joyce M; Kressin, Nancy; Vogt, Dawne

    2016-02-01

    Women have participated in the United States military since its founding. However, until the mid-20th century, there had been limited recognition of women as official members of the military, and women remain a statistical minority within military and veteran populations. It is therefore important to better understand women's veteran identity (which we define here as one's self-concept as derived from their veteran status) and associated implications for service use and experiences in the Department of Veterans Affairs (VA) health care setting. The present research examined the centrality of, and positive regard for, women's veteran identity among 407 female veterans deployed in support of the recent wars in Iraq and Afghanistan. Data were collected via a mailed national survey. Positive regard for veteran identity, but not veteran identity centrality,was positively associated with participants' age and length of time spent in the military. Results also showed that the centrality of women's veteran identity was positively related to their choice to use VA for health care and their feelings of belonging within VA, and that veteran identity centrality and positive regard for veteran identity are differentially associated with participants' military experiences (e.g., combat exposure, deployment sexual harassment) and mental health symptomatology (e.g., depression). PMID:25729892

  11. 78 FR 76061 - Authorization for Non-VA Medical Services

    Science.gov (United States)

    2013-12-16

    .... SUPPLEMENTARY INFORMATION: On November 28, 2012, VA proposed a rule in the Federal Register, at 77 FR 70967, to... for that disability. On the same date, VA published a companion direct final rule at 77 FR 70893 that... analysis are available on VA's Web site at http://www1.va.gov/orpm/ , by following the link for...

  12. 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.

  13. 78 FR 59771 - Proposed Information Collection (Create Payment Request for the VA Funding Fee Payment System (VA...

    Science.gov (United States)

    2013-09-27

    ...), Department of Veterans Affairs, 810 Vermont Avenue NW., Washington, DC 20420 or email nancy.kessinger@va.gov... AFFAIRS Proposed Information Collection (Create Payment Request for the VA Funding Fee Payment System (VA... (VBA), Department of Veterans Affairs (VA), is announcing an opportunity for public comment on...

  14. 75 FR 61859 - Proposed Information Collection (Create Payment Request for the VA Funding Fee Payment System (VA...

    Science.gov (United States)

    2010-10-06

    ....kessinger@va.gov . Please refer to ``OMB Control No. 2900-0474'' in any correspondence. During the comment... AFFAIRS Proposed Information Collection (Create Payment Request for the VA Funding Fee Payment System (VA... (VBA), Department of Veterans Affairs (VA), is announcing an opportunity for public comment on...

  15. 75 FR 61252 - Proposed Information Collection (Create Payment Request for the VA Funding Fee Payment System (VA...

    Science.gov (United States)

    2010-10-04

    ....kessinger@va.gov . Please refer to ``OMB Control No. 2900-0474'' in any correspondence. During the comment... AFFAIRS Proposed Information Collection (Create Payment Request for the VA Funding Fee Payment System (VA... (VBA), Department of Veterans Affairs (VA), is announcing an opportunity for public comment on...

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

    OpenAIRE

    PETRILLO MAURO; ANGERS ALEXANDRE; HENRIKSSON PETER; Bonfini, Laura; PATAK DENNSTEDT Alexandre; 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...

  17. 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.

  18. 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.

  19. 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).

  20. 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

  1. 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/.

  2. 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/. PMID:26424080

  3. 77 FR 47489 - Virginia Disaster #VA-00048

    Science.gov (United States)

    2012-08-08

    ... From the Federal Register Online via the Government Publishing Office SMALL BUSINESS ADMINISTRATION Virginia Disaster VA-00048 AGENCY: Small Business Administration. ACTION: Notice. SUMMARY: This is... State of Virginia (FEMA- 4072-DR), dated 07/27/2012. Incident: Severe Storms and Straight-line...

  4. 77 FR 74908 - Virginia Disaster #VA-00051

    Science.gov (United States)

    2012-12-18

    ... From the Federal Register Online via the Government Publishing Office SMALL BUSINESS ADMINISTRATION Virginia Disaster VA-00051 AGENCY: U.S. Small Business Administration. ACTION: Notice. SUMMARY... INFORMATION CONTACT: A. Escobar, Office of Disaster Assistance, U.S. Small Business Administration, 409...

  5. 77 FR 12517 - VA Dental Insurance Program

    Science.gov (United States)

    2012-03-01

    ... AFFAIRS 38 CFR Part 17 RIN 2900-AN99 VA Dental Insurance Program AGENCY: Department of Veterans Affairs...) proposes to amend its regulations to establish a pilot program to offer premium-based dental insurance to... insurer through the Federal contracting process to offer dental insurance, and the private insurer...

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

    OpenAIRE

    Carlos Eduardo M. Gomes; Osny P. Ferreira

    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. 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.

  8. A flexible and economical barcoding approach for highly multiplexed amplicon sequencing of diverse target genes

    Directory of Open Access Journals (Sweden)

    Craig W. Herbold

    2015-07-01

    Full Text Available High throughput sequencing of phylogenetic and functional gene amplicons provides tremendous insight into the structure and functional potential of complex microbial communities. Here, we introduce a highly adaptable and economical PCR approach to barcoding and pooling libraries of numerous target genes. In this approach, we replace gene- and sequencing platform-specific fusion primers with general, interchangeable barcoding primers, enabling nearly limitless customized barcode-primer combinations. Compared to barcoding with long fusion primers, our multiple-target gene approach is more economical because it overall requires lower number of primers and is based on short primers with generally lower synthesis and purification costs. To highlight our approach, we pooled over 900 different small-subunit rRNA and functional gene amplicon libraries obtained from various environmental or host-associated microbial community samples into a single, paired-end Illumina MiSeq run. Although the amplicon regions ranged in size from approximately 290 to 720 bp, we found no significant systematic sequencing bias related to amplicon length or gene target. Our results indicate that this flexible multiplexing approach produces large, diverse and high quality sets of amplicon sequence data for modern studies in microbial ecology.

  9. Telephone Enrollment in the VA Healthcare System. Interim final rule.

    Science.gov (United States)

    2016-03-16

    This rulemaking amends VA's medical regulations to allow veterans to complete applications for health care enrollment by telephone by providing application information to a VA employee, agreeing to VA's provisions regarding copayment liability and assignment of third-party insurance benefits, and attesting to the accuracy and authenticity of the information provided over the phone. This action will make it easier for veterans to apply to enroll and will speed VA processing of applications. PMID:26987128

  10. Payment for non-VA physician services associated with either outpatient or inpatient care provided at non-VA facilities--VA. Proposed rule.

    Science.gov (United States)

    1997-07-22

    This document proposes to amend Department of Veterans Affairs (VA) medical regulations concerning payment for non-VA physician services that are associated with either outpatient or inpatient care provided to eligible VA beneficiaries at non-VA facilities. We propose that when a service specific reimbursement amount has been calculated under Medicare's Participating Physician Fee Schedule, VA would pay the lesser of the actual billed charge or the calculated amount. We also propose that when an amount has not been calculated, VA would pay the amount calculated under a 75th percentile formula or, in certain limited circumstances, VA would pay the usual and customary rate. In our view, adoption of this proposal would establish reimbursement consistency among federal health benefits programs, would ensure that amounts paid to physicians better represent the relative resource inputs used to furnish a service, and, would, as reflected by a recent VA Office of Inspector General (OIG) audit of the VA fee-basis program, achieve program cost reductions. Further, consistent with statutory requirements, the regulations would continue to specify that VA payment constitutes payment in full.

  11. Functional overexpression of vomeronasal receptors using a Herpes simplex virus type 1 (HSV-1)-derived amplicon

    OpenAIRE

    Benjamin Stein; María Teresa Alonso; Frank Zufall; Trese Leinders-Zufall; Pablo Chamero

    2016-01-01

    In mice, social behaviors such as mating and aggression are mediated by pheromones and related chemosignals. The vomeronasal organ (VNO) detects olfactory information from other individuals by sensory neurons tuned to respond to specific chemical cues. Receptors expressed by vomeronasal neurons are implicated in selective detection of these cues. Nearly 400 receptor genes have been identified in the mouse VNO, but the tuning properties of individual receptors remain poorly understood, in part...

  12. 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

  13. Unlabeled Oligonucleotides as Internal Temperature Controls for Genotyping by Amplicon Melting

    OpenAIRE

    Seipp, Michael T.; Durtschi, Jacob D; Liew, Michael A.; Williams, Jamie; Damjanovich, Kristy; Pont-Kingdon, Genevieve; Lyon, Elaine; Voelkerding, Karl V.; Wittwer, Carl T.

    2007-01-01

    Amplicon melting is a closed-tube method for genotyping that does not require probes, real-time analysis, or allele-specific polymerase chain reaction. However, correct differentiation of homozygous mutant and wild-type samples by melting temperature (Tm) requires high-resolution melting and closely controlled reaction conditions. When three different DNA extraction methods were used to isolate DNA from whole blood, amplicon Tm differences of 0.03 to 0.39°C attributable to the extractions wer...

  14. 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 ...

  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. 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

  17. 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.

  18. Bacterial metabarcoding by 16S rRNA gene ion torrent amplicon sequencing.

    Science.gov (United States)

    Fantini, Elio; Gianese, Giulio; Giuliano, Giovanni; Fiore, Alessia

    2015-01-01

    Ion Torrent is a next generation sequencing technology based on the detection of hydrogen ions produced during DNA chain elongation; this technology allows analyzing and characterizing genomes, genes, and species. Here, we describe an Ion Torrent procedure applied to the metagenomic analysis of 16S rRNA gene amplicons to study the bacterial diversity in food and environmental samples. PMID:25343859

  19. Evaluation of Hybridization Capture Versus Amplicon-Based Methods for Whole-Exome Sequencing.

    Science.gov (United States)

    Samorodnitsky, Eric; Jewell, Benjamin M; Hagopian, Raffi; Miya, Jharna; Wing, Michele R; Lyon, Ezra; Damodaran, Senthilkumar; Bhatt, Darshna; Reeser, Julie W; Datta, Jharna; Roychowdhury, Sameek

    2015-09-01

    Next-generation sequencing has aided characterization of genomic variation. While whole-genome sequencing may capture all possible mutations, whole-exome sequencing remains cost-effective and captures most phenotype-altering mutations. Initial strategies for exome enrichment utilized a hybridization-based capture approach. Recently, amplicon-based methods were designed to simplify preparation and utilize smaller DNA inputs. We evaluated two hybridization capture-based and two amplicon-based whole-exome sequencing approaches, utilizing both Illumina and Ion Torrent sequencers, comparing on-target alignment, uniformity, and variant calling. While the amplicon methods had higher on-target rates, the hybridization capture-based approaches demonstrated better uniformity. All methods identified many of the same single-nucleotide variants, but each amplicon-based method missed variants detected by the other three methods and reported additional variants discordant with all three other technologies. Many of these potential false positives or negatives appear to result from limited coverage, low variant frequency, vicinity to read starts/ends, or the need for platform-specific variant calling algorithms. All methods demonstrated effective copy-number variant calling when evaluated against a single-nucleotide polymorphism array. This study illustrates some differences between whole-exome sequencing approaches, highlights the need for selecting appropriate variant calling based on capture method, and will aid laboratories in selecting their preferred approach. PMID:26110913

  20. 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.

  1. Bacterial metabarcoding by 16S rRNA gene ion torrent amplicon sequencing.

    Science.gov (United States)

    Fantini, Elio; Gianese, Giulio; Giuliano, Giovanni; Fiore, Alessia

    2015-01-01

    Ion Torrent is a next generation sequencing technology based on the detection of hydrogen ions produced during DNA chain elongation; this technology allows analyzing and characterizing genomes, genes, and species. Here, we describe an Ion Torrent procedure applied to the metagenomic analysis of 16S rRNA gene amplicons to study the bacterial diversity in food and environmental samples.

  2. 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...

  3. 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.

  4. Comparison of normalization methods for construction of large, multiplex amplicon pools for next-generation sequencing.

    Science.gov (United States)

    Harris, J Kirk; Sahl, Jason W; Castoe, Todd A; Wagner, Brandie D; Pollock, David D; Spear, John R

    2010-06-01

    Constructing mixtures of tagged or bar-coded DNAs for sequencing is an important requirement for the efficient use of next-generation sequencers in applications where limited sequence data are required per sample. There are many applications in which next-generation sequencing can be used effectively to sequence large mixed samples; an example is the characterization of microbial communities where management costs associated with construction of multiplex pools are also scalable. One critical step in multiplex pool construction is the normalization process, whereby equimolar amounts of each amplicon are mixed. Here we compare three approaches (spectroscopy, size-restricted spectroscopy, and quantitative binding) for normalization of large, multiplex amplicon pools for performance and efficiency. We found that the quantitative binding approach was superior and represents an efficient scalable process for construction of very large, multiplex pools with hundreds and perhaps thousands of individual amplicons included. We demonstrate the increased sequence diversity identified with higher throughput. Massively parallel sequencing can dramatically accelerate microbial ecology studies by allowing appropriate replication of sequence acquisition to account for temporal and spatial variations. Further, population studies to examine genetic variation, which require even lower levels of sequencing, should be possible where thousands of individual bar-coded amplicons are examined in parallel. PMID:20418443

  5. De novo origin of VCY2 from autosome to Y-transposed amplicon.

    Directory of Open Access Journals (Sweden)

    Peng-Rong Cao

    Full Text Available The formation of new genes is a primary driving force of evolution in all organisms. The de novo evolution of new genes from non-protein-coding genomic regions is emerging as an important additional mechanism for novel gene creation. Y chromosomes underlie sex determination in mammals and contain genes that are required for male-specific functions. In this study, a search was undertaken for Y chromosome de novo genes derived from non-protein-coding sequences. The Y chromosome orphan gene variable charge, Y-linked (VCY2, is an autosome-derived gene that has sequence similarity to large autosomal fragments but lacks an autosomal protein-coding homolog. VCY2 locates in the amplicon containing long DNA fragments that were transposed from autosomes to the Y chromosome before the ape-monkey split. We confirmed that VCY2 cannot be encoded by autosomes due to the presence of multiple disablers that disrupt the open reading frame, such as the absence of start or stop codons and the presence of premature stop codons. Similar observations have been made for homologs in the autosomes of the chimpanzee, gorilla, rhesus macaque, baboon and out-group marmoset, which suggests that there was a non-protein-coding ancestral VCY2 that was common to apes and monkeys that predated the transposition event. Furthermore, while protein-coding orthologs are absent, a putative non-protein-coding VCY2 with conserved disablers was identified in the rhesus macaque Y chromosome male-specific region. This finding implies that VCY2 might have not acquired its protein-coding ability before the ape-monkey split. VCY2 encodes a testis-specific expressed protein and is involved in the pathologic process of male infertility, and the acquisition of this gene might improve male fertility. This is the first evidence that de novo genes can be generated from transposed autosomal non-protein-coding segments, and this evidence provides novel insights into the evolutionary history of the Y

  6. De novo origin of VCY2 from autosome to Y-transposed amplicon.

    Science.gov (United States)

    Cao, Peng-Rong; Wang, Lei; Jiang, Yu-Chao; Yi, Yin-Sha; Qu, Fang; Liu, Tao-Cheng; Lv, Yuan

    2015-01-01

    The formation of new genes is a primary driving force of evolution in all organisms. The de novo evolution of new genes from non-protein-coding genomic regions is emerging as an important additional mechanism for novel gene creation. Y chromosomes underlie sex determination in mammals and contain genes that are required for male-specific functions. In this study, a search was undertaken for Y chromosome de novo genes derived from non-protein-coding sequences. The Y chromosome orphan gene variable charge, Y-linked (VCY)2, is an autosome-derived gene that has sequence similarity to large autosomal fragments but lacks an autosomal protein-coding homolog. VCY2 locates in the amplicon containing long DNA fragments that were transposed from autosomes to the Y chromosome before the ape-monkey split. We confirmed that VCY2 cannot be encoded by autosomes due to the presence of multiple disablers that disrupt the open reading frame, such as the absence of start or stop codons and the presence of premature stop codons. Similar observations have been made for homologs in the autosomes of the chimpanzee, gorilla, rhesus macaque, baboon and out-group marmoset, which suggests that there was a non-protein-coding ancestral VCY2 that was common to apes and monkeys that predated the transposition event. Furthermore, while protein-coding orthologs are absent, a putative non-protein-coding VCY2 with conserved disablers was identified in the rhesus macaque Y chromosome male-specific region. This finding implies that VCY2 might have not acquired its protein-coding ability before the ape-monkey split. VCY2 encodes a testis-specific expressed protein and is involved in the pathologic process of male infertility, and the acquisition of this gene might improve male fertility. This is the first evidence that de novo genes can be generated from transposed autosomal non-protein-coding segments, and this evidence provides novel insights into the evolutionary history of the Y chromosome. PMID

  7. Cuando la ciencia va a la escuela

    OpenAIRE

    Balzarini, A.; Soba, M.; González, E.; Giúdice, L.; Marcomini, C.; Elizalde, A.

    2009-01-01

    A partir de las problemáticas detectadas durante las instancias regional y provincial de La Feria de Ciencias y Tecnología 2006, el Club de Ciencias del Partido de La Costa elaboró una propuesta de alfabetización científica para docentes: las Asesorías "Cuando la ciencia va a la escuela". Ella implica la articulación de la educación formal, no formal (Club de ciencias), la comunidad científica local y el ámbito municipal. Docentes y asesores de ciencia comparten las distintas etapas de una in...

  8. La radio va a la escuela

    OpenAIRE

    Méndiz Rojas, Heleny

    2004-01-01

    Chile, a través de la reforma educativa, y específicamente en el área de lenguaje y comunicación, está propiciando las condiciones para que todas las escuelas y los profesores tengan accesos a las nuevas tecnologías (redes, vídeo, radio, prensa). En este sentido se expone, a continuación, la experiencia «La radio va a la escuela», en la que alumnos de la cátedra de radio de la Escuela de Periodismo de la Universidad Católica del Norte transfieren los conocimientos y significados del medio rad...

  9. 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

    been reported. Subsequently, the vibrational absorption (VA) and vibrational circular dichroism (VCD) and the Raman and Raman Optical Activity (ROA) spectra have been reported. In this work an analysis of the aqueous solution VA, VCD, Raman, and ROA spectra for various isotopomers of LALA are reported....... 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...

  10. What can Medicaid data add to research on VA patients?

    Directory of Open Access Journals (Sweden)

    Ann Hendricks, PhD

    2010-10-01

    Full Text Available This article is the first to describe Department of Veterans Affairs (VA patients' use of Medicaid at a national level. We obtained 1999 national VA enrollment and utilization data, Centers for Medicare and Medicaid Services enrollment and claims, and Medicare information from the VA Information Resource Center. The research team created files for program characteristics and described the VA-Medicaid dually enrolled population, healthcare utilization, and costs. In 1999, VA-Medicaid dual enrollees comprised 10.2% of VA's annual patient load (350,000/3,450,000; 304,000 were veterans. These veterans differed marginally from VA's veteran patients, being on average half a year younger and having 1% fewer males. Dual enrollees with mental health diagnoses and care were almost three times as numerous as long-term care patients; these two groups accounted for ~60% of dual enrollees. Dual enrollees disproportionately included housebound veterans and veterans needing aid and assistance. Half the dual enrollees had 12 months of Medicaid eligibility, and total Federal expenditures per patient not in managed care programs averaged >$18,000 (median >$6,000. Dually enrolled women veterans cost ~55% less than men. Medicaid benefits complement VA and are more accessible in many states. VA researchers need to consider including Medicaid utilization and costs in their studies if they target populations or programs related to long-term care or mental disorders.

  11. Telephone Enrollment in the VA Healthcare System. Final rule.

    Science.gov (United States)

    2016-09-12

    The Department of Veterans Affairs (VA) adopts as final, without change, an interim final rule amending its medical regulations. Specifically, this rule allows veterans to complete applications for health care enrollment by providing application information, agreeing to VA's provisions regarding copayment liability and assignment of third-party insurance benefits, and attesting to the accuracy and authenticity of the information provided to a VA employee over the phone. This action makes it easier for veterans to apply to enroll and speeds VA processing of applications. PMID:27632804

  12. 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.

  13. Comparison of historically simulated VaR: Evidence from oil prices

    Energy Technology Data Exchange (ETDEWEB)

    Costello, Alexandra [Seminole Canada Energy, Calgary, AB (Canada); Asem, Ebenezer; Gardner, Eldon [Faculty of Management, University of Lethbridge, Lethbridge, AB (Canada)

    2008-09-15

    Cabedo and Moya [Cabedo, J.D., Moya, I., 2003. Estimating oil price 'Value at Risk' using the historical simulation approach. Energy Economics 25, 239-253] find that ARMA with historical simulation delivers VaR forecasts that are superior to those from GARCH. We compare the ARMA with historical simulation to the semi-parametric GARCH model proposed by Barone-Adesi et al. [Barone-Adesi, G., Giannopoulos, K., Vosper, L., 1999. VaR without correlations for portfolios of derivative securities. Journal of Futures Markets 19 (5), 583-602]. The results suggest that the semi-parametric GARCH model generates VaR forecasts that are superior to the VaR forecasts from the ARMA with historical simulation. This is due to the fact that GARCH captures volatility clustering. Our findings suggest that Cabedo and Moya's conclusion is mainly driven by the normal distributional assumption imposed on the future risk structure in the GARCH model. (author)

  14. 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......Amplicon pyrosequencing targets a known genetic region and thus inherently produces reads highly anticipated to have certain features, such as conserved nucleotide sequence, and in the case of protein coding DNA, an open reading frame. Pyrosequencing errors, consisting mainly of nucleotide....... This probabilistic approach enables integration of basecalling into a larger model where other parameters can be incorporated, such as the likelihood for observing a full-length open reading frame at the targeted region. We apply the method to 454 amplicon pyrosequencing data obtained from a malaria...

  15. 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...

  16. 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.

  17. 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

    Surface plasmon field-enhanced fluorescence spectroscopy was employed to extensively investigate the hybridization behaviors of polymerase chain reaction (PCR) amplicons on a peptide nucleic acid (PNA) or DNA probe layer that was previously attached on a streptavidin-modified gold surface via...... biotin/streptavidin interaction. Despite the neutral backbone of PNA, the hybridization reactions were strongly influenced by the variation of ionic strength. The association rates exhibited a monotonic decrease with ionic strength increase and the maximum hybridization signal was achieved...... 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/DNA...

  18. Massively parallel sequencing of 17 commonly used forensic autosomal STRs and amelogenin with small amplicons.

    Science.gov (United States)

    Kim, Eun Hye; Lee, Hwan Young; Yang, In Seok; Jung, Sang-Eun; Yang, Woo Ick; Shin, Kyoung-Jin

    2016-05-01

    The next-generation sequencing (NGS) method has been utilized to analyze short tandem repeat (STR) markers, which are routinely used for human identification purposes in the forensic field. Some researchers have demonstrated the successful application of the NGS system to STR typing, suggesting that NGS technology may be an alternative or additional method to overcome limitations of capillary electrophoresis (CE)-based STR profiling. However, there has been no available multiplex PCR system that is optimized for NGS analysis of forensic STR markers. Thus, we constructed a multiplex PCR system for the NGS analysis of 18 markers (13CODIS STRs, D2S1338, D19S433, Penta D, Penta E and amelogenin) by designing amplicons in the size range of 77-210 base pairs. Then, PCR products were generated from two single-sources, mixed samples and artificially degraded DNA samples using a multiplex PCR system, and were prepared for sequencing on the MiSeq system through construction of a subsequent barcoded library. By performing NGS and analyzing the data, we confirmed that the resultant STR genotypes were consistent with those of CE-based typing. Moreover, sequence variations were detected in targeted STR regions. Through the use of small-sized amplicons, the developed multiplex PCR system enables researchers to obtain successful STR profiles even from artificially degraded DNA as well as STR loci which are analyzed with large-sized amplicons in the CE-based commercial kits. In addition, successful profiles can be obtained from mixtures up to a 1:19 ratio. Consequently, the developed multiplex PCR system, which produces small size amplicons, can be successfully applied to STR NGS analysis of forensic casework samples such as mixtures and degraded DNA samples. PMID:26799314

  19. From Benchtop to Desktop: Important Considerations when Designing Amplicon Sequencing Workflows

    OpenAIRE

    Murray, Dáithí C; Megan L Coghlan; Michael Bunce

    2015-01-01

    Amplicon sequencing has been the method of choice in many high-throughput DNA sequencing (HTS) applications. To date there has been a heavy focus on the means by which to analyse the burgeoning amount of data afforded by HTS. In contrast, there has been a distinct lack of attention paid to considerations surrounding the importance of sample preparation and the fidelity of library generation. No amount of high-end bioinformatics can compensate for poorly prepared samples and it is therefore im...

  20. Potential of pmoA Amplicon Pyrosequencing for Methanotroph Diversity Studies ▿†

    OpenAIRE

    Lüke, Claudia; Frenzel, Peter

    2011-01-01

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

    Science.gov (United States)

    Rooney, Claire; Geh, Catherine; Williams, Victoria; Heuckmann, Johannes M; Menon, Roopika; Schneider, Petra; Al-Kadhimi, Katherine; Dymond, Michael; Smith, Neil R; Baker, Dawn; French, Tim; Smith, Paul D; Harrington, Elizabeth A; Barrett, J Carl; Kilgour, Elaine

    2016-01-01

    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. PMID:26905262

  2. 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.

  3. Single genome amplification and direct amplicon sequencing of Plasmodium spp. DNA from ape fecal specimens

    OpenAIRE

    Liu, Weimin; Li, Yingying; Peeters, Martine; Rayner, Julian; Sharp, Paul; Shaw, George; Hahn, Beatrice

    2010-01-01

    Conventional PCR followed by molecular cloning and sequencing of amplified products is commonly used to test clinical specimens for target sequences of interest, such as viral, bacterial or parasite nucleic acids. However, this approach has serious limitations when used to analyze mixtures of genetically divergent templates1–9. This is because Taq polymerase is prone to switch templates during the amplification process, thereby generating recombinants that do not exist in vivo4. When amplicon...

  4. From benchtop to desktop: important considerations when designing amplicon sequencing workflows.

    Directory of Open Access Journals (Sweden)

    Dáithí C Murray

    Full Text Available Amplicon sequencing has been the method of choice in many high-throughput DNA sequencing (HTS applications. To date there has been a heavy focus on the means by which to analyse the burgeoning amount of data afforded by HTS. In contrast, there has been a distinct lack of attention paid to considerations surrounding the importance of sample preparation and the fidelity of library generation. No amount of high-end bioinformatics can compensate for poorly prepared samples and it is therefore imperative that careful attention is given to sample preparation and library generation within workflows, especially those involving multiple PCR steps. This paper redresses this imbalance by focusing on aspects pertaining to the benchtop within typical amplicon workflows: sample screening, the target region, and library generation. Empirical data is provided to illustrate the scope of the problem. Lastly, the impact of various data analysis parameters is also investigated in the context of how the data was initially generated. It is hoped this paper may serve to highlight the importance of pre-analysis workflows in achieving meaningful, future-proof data that can be analysed appropriately. As amplicon sequencing gains traction in a variety of diagnostic applications from forensics to environmental DNA (eDNA it is paramount workflows and analytics are both fit for purpose.

  5. Electrochemical DNA sensor for anthrax toxin activator gene atxA-detection of PCR amplicons.

    Science.gov (United States)

    Das, Ritu; Goel, Ajay K; Sharma, Mukesh K; Upadhyay, Sanjay

    2015-12-15

    We report the DNA probe functionalized electrochemical genosensor for the detection of Bacillus anthracis, specific towards the regulatory gene atxA. The DNA sensor is fabricated on electrochemically deposited gold nanoparticle on self assembled layer of (3-Mercaptopropyl) trimethoxysilane (MPTS) on GC electrode. DNA hybridization is monitored by differential pulse voltammogram (DPV). The modified GC electrode is characterized by atomic force microscopy (AFM), cyclic voltammetry (CV), and electrochemical impedance spectroscopy (EIS) method. We also quantified the DNA probe density on electrode surface by the chronocoulometric method. The detection is specific and selective for atxA gene by DNA probe on the electrode surface. No report is available for the detection of B. anthracis by using atxA an anthrax toxin activator gene. In the light of real and complex sample, we have studied the PCR amplicons of 303, 361 and 568 base pairs by using symmetric and asymmetric PCR approaches. The DNA probe of atxA gene efficiently hybridizes with different base pairs of PCR amplicons. The detection limit is found to be 1.0 pM (S/N ratio=3). The results indicate that the DNA sensor is able to detect synthetic target as well as PCR amplicons of different base pairs. PMID:26257186

  6. Sample Preparation for Fungal Community Analysis by High-Throughput Sequencing of Barcode Amplicons.

    Science.gov (United States)

    Clemmensen, Karina Engelbrecht; Ihrmark, Katarina; Durling, Mikael Brandström; Lindahl, Björn D

    2016-01-01

    Fungal species participate in vast numbers of processes in the landscape around us. However, their often cryptic growth, inside various substrates and in highly diverse species assemblages, has been a major obstacle to thorough analysis of fungal communities, hampering exhaustive description of the fungal kingdom. Recent technological developments allowing rapid, high-throughput sequencing of mixed communities from many samples at once are currently having a tremendous impact in fungal community ecology. Universal DNA extraction followed by amplification and sequencing of fungal species-level barcodes such as the nuclear internal transcribed spacer (ITS) region now enable identification and relative quantification of fungal community members across well-replicated experimental settings. Here, we present the sample preparation procedure presently used in our laboratory for fungal community analysis by high-throughput sequencing of amplified ITS2 markers. We focus on the procedure optimized for studies of total fungal communities in humus-rich soils, wood, and litter. However, this procedure can be applied to other sample types and markers. We focus on the laboratory-based part of sample preparation, that is, the procedure from the point where samples enter the laboratory until amplicons are submitted for sequencing. Our procedure comprises four main parts: (1) universal DNA extraction, (2) optimization of PCR conditions, (3) production of tagged ITS amplicons, and (4) preparation of the multiplexed amplicon mix to be sequenced. The presented procedure is independent of the specific high-throughput sequencing technology used, which makes it highly versatile. PMID:26791497

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

    Directory of Open Access Journals (Sweden)

    Carlos Eduardo M. Gomes

    2005-07-01

    Full Text Available 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 distinct polymer contents and water/cement ratios were employed. In addition, analyses of FT-IR and MIP on Portland cement pastes modified by the copolymer were employed. The results showed that the addition of polymer interferes significantly in the reduction of Portlandite formation and increases the porosity of the matrices. A possible chemical interaction between the copolymer and hydrated products of Portland cement was also observed.

  8. 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...

  9. 77 FR 67063 - VA Directive 0005 on Scientific Integrity

    Science.gov (United States)

    2012-11-08

    ... April 9, 2012 (77 FR 21158). FOR FURTHER INFORMATION CONTACT: Billy E. Jones, M.D., Senior Advisor to... 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...

  10. Using VA Software to Create an Integrated Clinical Information System in Non-VA Medical Facilities

    OpenAIRE

    Kolodner, R.M.; Morton, R.L.; Fowler, D.R.; Cannon, D.S.; Stewart, R S

    1989-01-01

    This paper reports the use of the VA's Decentralized Hospital Computer Program software to integrate clinical data stored on 3 separate computers installed in a public County Hospital. Clinical access to the data on all three systems is currently available only in limited areas in the hospital and requires the use of at least two different terminals. The linking system, written in MUMPS, has been installed on a 80386-based microcomputer located in the Outpatient Psychiatry Clinic in the facil...

  11. DOE Spent Nuclear Fuel Information In Support of TSPA-VA

    Energy Technology Data Exchange (ETDEWEB)

    A. Brewer; D. Cresap; D. Fillmore; H. Loo; M. Ebner; R. McCormack

    1998-09-01

    RW has started the viability assessment (VA) effort to determine the feasibility of Yucca Mountain as the first geologic repository for spent nuclear fuel (SNF) and high-level waste. One component of the viability assessment will be a total system performance assessment (TSPA), based on the design concept and the scientific data and analysis available, describing the repository's probable behavior relative to the overall system performance standards. Thus, all the data collected from the Exploratory Studies Facility to-date have been incorporated into the latest TSPA model. In addition, the Repository Integration Program, an integrated probabilistic simulator, used in the TSPA has also been updated by Golder Associates Incorporated at December 1997. To ensure that the Department of Energy-owned (DOE-owned) SNF continues to be acceptable for disposal in the repository, it will be included in the TSPA-VA evaluation. A number of parameters are needed in the TSPA-VA models to predict the performance of the DOE-owned SNF materials placed into the potential repository. This report documents all of the basis and/or derivation for each of these parameters. A number of properties were not readily available at the time the TSPA-VA data was requested. Thus, expert judgement and opinion was utilized to determine a best property value. The performance of the DOE-owned SNF will be published as part of the TSPA-VA report. Each DOE site will be collecting better data as the DOE SNF program moves closer to repository license application. As required by the RW-0333P, the National Spent Nuclear Fuel Program will be assisting each site in qualifying the information used to support the performance assessment evaluations.

  12. 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 ...

  13. VaR Methodology Application for Banking Currency Portfolios

    Directory of Open Access Journals (Sweden)

    Daniel Armeanu

    2007-02-01

    Full Text Available VaR has become the standard measure that financial analysts use to quantify market risk. VaR measures can have many applications, such as in risk management, to evaluate the performance of risk takers and for regulatory requirements, and hence it is very important to develop methodologies that provide accurate estimates. In particular, the Basel Committee on Banking Supervision at the Bank for International Settlements imposes to financial institutions such as banks and investment firms to meet capital requirements based on VaR estimates. In this paper we determine VaR for a banking currency portfolio and respect rules of National Bank of Romania regarding VaR report.

  14. Impact of Mutation Type and Amplicon Characteristics on Genetic Diversity Measures Generated Using a High-Resolution Melting Diversity Assay

    OpenAIRE

    Cousins, Matthew M.; Donnell, Deborah; Eshleman, Susan H.

    2013-01-01

    We adapted high-resolution melting (HRM) technology to measure genetic diversity without sequencing. Diversity is measured as a single numeric HRM score. Herein, we determined the impact of mutation types and amplicon characteristics on HRM diversity scores. Plasmids were generated with single-base changes, insertions, and deletions. Different primer sets were used to vary the position of mutations within amplicons. Plasmids and plasmid mixtures were analyzed to determine the impact of mutati...

  15. 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.

  16. 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 …

  17. Clinical impact of targeted amplicon sequencing for meningioma as a practical clinical-sequencing system.

    Science.gov (United States)

    Yuzawa, Sayaka; Nishihara, Hiroshi; Yamaguchi, Shigeru; Mohri, Hiromi; Wang, Lei; Kimura, Taichi; Tsuda, Masumi; Tanino, Mishie; Kobayashi, Hiroyuki; Terasaka, Shunsuke; Houkin, Kiyohiro; Sato, Norihiro; Tanaka, Shinya

    2016-07-01

    Recent genetic analyses using next-generation sequencers have revealed numerous genetic alterations in various tumors including meningioma, which is the most common primary brain tumor. However, their use as routine laboratory examinations in clinical applications for tumor genotyping is not cost effective. To establish a clinical sequencing system for meningioma and investigate the clinical significance of genotype, we retrospectively performed targeted amplicon sequencing on 103 meningiomas and evaluated the association with clinicopathological features. We designed amplicon-sequencing panels targeting eight genes including NF2 (neurofibromin 2), TRAF7, KLF4, AKT1, and SMO. Libraries prepared with genomic DNA extracted from PAXgene-fixed paraffin-embedded tissues of 103 meningioma specimens were sequenced using the Illumina MiSeq. NF2 loss in some cases was also confirmed by interphase-fluorescent in situ hybridization. We identified NF2 loss and/or at least one mutation in NF2, TRAF7, KLF4, AKT1, and SMO in 81 out of 103 cases (79%) by targeted amplicon sequencing. On the basis of genetic status, we categorized meningiomas into three genotype groups: NF2 type, TRAKLS type harboring mutation in TRAF7, AKT1, KLF4, and/or SMO, and 'not otherwise classified' type. Genotype significantly correlated with tumor volume, tumor location, and magnetic resonance imaging findings such as adjacent bone change and heterogeneous gadolinium enhancement, as well as histopathological subtypes. In addition, multivariate analysis revealed that genotype was independently associated with risk of recurrence. In conclusion, we established a rapid clinical sequencing system that enables final confirmation of meningioma genotype within 7 days turnaround time. Our method will bring multiple benefits to neuropathologists and neurosurgeons for accurate diagnosis and appropriate postoperative management. PMID:27102344

  18. Shedding Light on the Microbial Community of the Macropod Foregut Using 454-Amplicon Pyrosequencing

    OpenAIRE

    Gulino, Lisa-Maree; Ouwerkerk, Diane; Alicia Y H Kang; Maguire, Anita J.; Kienzle, Marco; Klieve, Athol V.

    2013-01-01

    Twenty macropods from five locations in Queensland, Australia, grazing on a variety of native pastures were surveyed and the bacterial community of the foregut was examined using 454-amplicon pyrosequencing. Specifically, the V3/V4 region of 16S rRNA gene was examined. A total of 5040 OTUs were identified in the data set (post filtering). Thirty-two OTUs were identified as ‘shared’ OTUS (i.e. present in all samples) belonging to either Firmicutes or Bacteroidetes (Clostridiales/Bacteroidales)...

  19. Analysis and Visualization Tool for Targeted Amplicon Bisulfite Sequencing on Ion Torrent Sequencers.

    Science.gov (United States)

    Pabinger, Stephan; Ernst, Karina; Pulverer, Walter; Kallmeyer, Rainer; Valdes, Ana M; Metrustry, Sarah; Katic, Denis; Nuzzo, Angelo; Kriegner, Albert; Vierlinger, Klemens; Weinhaeusel, Andreas

    2016-01-01

    Targeted sequencing of PCR amplicons generated from bisulfite deaminated DNA is a flexible, cost-effective way to study methylation of a sample at single CpG resolution and perform subsequent multi-target, multi-sample comparisons. Currently, no platform specific protocol, support, or analysis solution is provided to perform targeted bisulfite sequencing on a Personal Genome Machine (PGM). Here, we present a novel tool, called TABSAT, for analyzing targeted bisulfite sequencing data generated on Ion Torrent sequencers. The workflow starts with raw sequencing data, performs quality assessment, and uses a tailored version of Bismark to map the reads to a reference genome. The pipeline visualizes results as lollipop plots and is able to deduce specific methylation-patterns present in a sample. The obtained profiles are then summarized and compared between samples. In order to assess the performance of the targeted bisulfite sequencing workflow, 48 samples were used to generate 53 different Bisulfite-Sequencing PCR amplicons from each sample, resulting in 2,544 amplicon targets. We obtained a mean coverage of 282X using 1,196,822 aligned reads. Next, we compared the sequencing results of these targets to the methylation level of the corresponding sites on an Illumina 450k methylation chip. The calculated average Pearson correlation coefficient of 0.91 confirms the sequencing results with one of the industry-leading CpG methylation platforms and shows that targeted amplicon bisulfite sequencing provides an accurate and cost-efficient method for DNA methylation studies, e.g., to provide platform-independent confirmation of Illumina Infinium 450k methylation data. TABSAT offers a novel way to analyze data generated by Ion Torrent instruments and can also be used with data from the Illumina MiSeq platform. It can be easily accessed via the Platomics platform, which offers a web-based graphical user interface along with sample and parameter storage. TABSAT is freely

  20. Amplicon-based metagenomics identified candidate organisms in soils that caused yield decline in strawberry

    OpenAIRE

    Xiangming Xu; Thomas Passey; Feng Wei; Robert Saville; Harrison, Richard J.

    2015-01-01

    A phenomenon of yield decline due to weak plant growth in strawberry was recently observed in non-chemo-fumigated soils, which was not associated with the soil fungal pathogen Verticillium dahliae, the main target of fumigation. Amplicon-based metagenomics was used to profile soil microbiota in order to identify microbial organisms that may have caused the yield decline. A total of 36 soil samples were obtained in 2013 and 2014 from four sites for metagenomic studies; two of the four sites ha...

  1. 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...

  2. 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...

  3. 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...

  4. 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*.

  5. 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 ...

  6. 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.

  7. 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.

  8. Amplicon-based metagenomics identified candidate organisms in soils that caused yield decline in strawberry.

    Science.gov (United States)

    Xu, Xiangming; Passey, Thomas; Wei, Feng; Saville, Robert; Harrison, Richard J

    2015-01-01

    A phenomenon of yield decline due to weak plant growth in strawberry was recently observed in non-chemo-fumigated soils, which was not associated with the soil fungal pathogen Verticillium dahliae, the main target of fumigation. Amplicon-based metagenomics was used to profile soil microbiota in order to identify microbial organisms that may have caused the yield decline. A total of 36 soil samples were obtained in 2013 and 2014 from four sites for metagenomic studies; two of the four sites had a yield-decline problem, the other two did not. More than 2000 fungal or bacterial operational taxonomy units (OTUs) were found in these samples. Relative abundance of individual OTUs was statistically compared for differences between samples from sites with or without yield decline. A total of 721 individual comparisons were statistically significant - involving 366 unique bacterial and 44 unique fungal OTUs. Based on further selection criteria, we focused on 34 bacterial and 17 fungal OTUs and found that yield decline resulted probably from one or more of the following four factors: (1) low abundance of Bacillus and Pseudomonas populations, which are well known for their ability of supressing pathogen development and/or promoting plant growth; (2) lack of the nematophagous fungus (Paecilomyces species); (3) a high level of two non-specific fungal root rot pathogens; and (4) wet soil conditions. This study demonstrated the usefulness of an amplicon-based metagenomics approach to profile soil microbiota and to detect differential abundance in microbes. PMID:26504572

  9. 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. PMID:26257385

  10. 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.

  11. Deriving Derivatives

    OpenAIRE

    Soklakov, Andrei N.

    2013-01-01

    Quantitative Structuring is a rigorous framework for the design of financial products. We show how it incorporates traditional investment ideas while supporting a more accurate expression of clients' views on the market. We briefly touch upon adjacent topics regarding the safety of financial derivatives and the role of pricing models in product design.

  12. 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.

  13. The Adjustment of VaR to the Empirical Distribution of Returns

    Directory of Open Access Journals (Sweden)

    Radu Lupu

    2006-06-01

    Full Text Available Basel II Recommendations concerning internal rating based models approach for financial institutions and the success of RiskMetrics made Value-at-Risk (VaR is the most important risk measurement instrument at international level. The objective of this paper is to address the problem of adapting this method to the statistical properties of the returns for portfolios that include derivatives in the form of options too. We assume that the returns for the analyzed portfolios are not normally distributed. The methodologies presented are the ones used to capture the percentile when returns follow the features of the empirical distributions reviewed in Cont (2001.

  14. Drug and drug-related supply promotion by pharmaceutical company representatives at VA facilities. Final rule.

    Science.gov (United States)

    2012-03-01

    This final rule amends the Department of Veterans Affairs (VA) regulations regarding access to VA facilities by 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 provide pharmaceutical company representatives with a consistent standard of permissible business practice at VA facilities. The amendments will facilitate mutually beneficial relationships between VA and pharmaceutical company representatives. PMID:22420057

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

    OpenAIRE

    Gamage, Shantini D.; Simbartl, Loretta A.; Kralovic, Stephen M.; Wallace, Katherine S.; Roselle, Gary A.

    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 ...

  16. 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.

  17. 16S rRNA amplicon sequencing dataset for conventionalized and conventionally raised zebrafish larvae.

    Science.gov (United States)

    Davis, Daniel J; Bryda, Elizabeth C; Gillespie, Catherine H; Ericsson, Aaron C

    2016-09-01

    Data presented here contains metagenomic analysis regarding the sequential conventionalization of germ-free zebrafish embryos. Zebrafish embryos that underwent a germ-free sterilization process immediately after fertilization were promptly exposed to and raised to larval stage in conventional fish water. At 6 days postfertilization (dpf), these "conventionalized" larvae were compared to zebrafish larvae that were raised in conventional fish water never undergoing the initial sterilization process. Bacterial 16S rRNA amplicon sequencing was performed on DNA isolated from homogenates of the larvae revealing distinct microbiota variations between the two groups. The dataset described here is also related to the research article entitled "Microbial modulation of behavior and stress responses in zebrafish larvae" (Davis et al., 2016) [1]. PMID:27508247

  18. Rare amplicons implicate frequent deregulation of cell fate specification pathways in oral squamous cell carcinoma.

    Science.gov (United States)

    Snijders, Antoine M; Schmidt, Brian L; Fridlyand, Jane; Dekker, Nusi; Pinkel, Daniel; Jordan, Richard C K; Albertson, Donna G

    2005-06-16

    Genomes of solid tumors are characterized by gains and losses of regions, which may contribute to tumorigenesis by altering gene expression. Often the aberrations are extensive, encompassing whole chromosome arms, which makes identification of candidate genes in these regions difficult. Here, we focused on narrow regions of gene amplification to facilitate identification of genetic pathways important in oral squamous cell carcinoma (SCC) development. We used array comparative genomic hybridization (array CGH) to define minimum common amplified regions and then used expression analysis to identify candidate driver genes in amplicons that spanned LAMA3, MMP7), as well as members of the hedgehog (GLI2) and notch (JAG1, RBPSUH, FJX1) pathways to be amplified and overexpressed. Deregulation of these and other members of the hedgehog and notch pathways (HHIP, SMO, DLL1, NOTCH4) implicates deregulation of developmental and differentiation pathways, cell fate misspecification, in oral SCC development. PMID:15824737

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

    Science.gov (United States)

    Yanthan, Mhathung; Misra, Arvind K

    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. PMID:24287658

  20. 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.

  1. The cost of hospital readmissions: evidence from the VA.

    Science.gov (United States)

    Carey, Kathleen; Stefos, Theodore

    2016-09-01

    This paper is an examination of hospital 30-day readmission costs using data from 119 acute care hospitals operated by the U.S. Veterans Administration (VA) in fiscal year 2011. We applied a two-part model that linked readmission probability to readmission cost to obtain patient level estimates of expected readmission cost for VA patients overall, and for patients discharged for three prevalent conditions with relatively high readmission rates. Our focus was on the variable component of direct patient cost. Overall, managers could expect to save $2140 for the average 30-day readmission avoided. For heart attack, heart failure, and pneumonia patients, expected readmission cost estimates were $3432, $2488 and $2278. Patient risk of illness was the dominant driver of readmission cost in all cases. The VA experience has implications for private sector hospitals that treat a high proportion of chronically ill and/or low income patients, or that are contemplating adopting bundled payment mechanisms. PMID:25576391

  2. 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.

  3. 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.

  4. 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...

  5. 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.

  6. 78 FR 42455 - Medications Prescribed by Non-VA Providers

    Science.gov (United States)

    2013-07-16

    ....019, Veterans Rehabilitation Alcohol and Drug Dependence; and 64.022, Veterans Home Based Primary Care....S.C. 1712(d), VA is required to furnish prescription drugs and medicine ordered by a duly licensed... affected by this final rule are 64.007, Blind Rehabilitation Centers; 64.008, Veterans Domiciliary Care;...

  7. 78 FR 2708 - Virginia Disaster Number VA-00052

    Science.gov (United States)

    2013-01-14

    ... From the Federal Register Online via the Government Publishing Office SMALL BUSINESS 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...

  8. 78 FR 63143 - VA Dental Insurance Program-Federalism

    Science.gov (United States)

    2013-10-23

    ... insurer is then responsible for the administration of the dental insurance plan. VA's role under VADIP is.... U.S. Const. art. VI, cl. 2; Gade v. Nat'l Solid Wastes Mgmt. Ass'n, 505 U.S. 88, 98 (1992); M...(d) N/A. Plan benefits 510(f) Sec. 17.169(c)(2). Enrollment periods 510(g) Sec....

  9. 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...

  10. 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…

  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. 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...

  13. 38 CFR 1.9 - Description, use, and display of VA seal and flag.

    Science.gov (United States)

    2010-07-01

    ... audiovisual media prepared by or for VA and attributed thereto. (F) Official prestige publications which... audiovisual media prepared by and for VA and attributed thereto. (H) For other similar official purposes....

  14. 77 FR 2348 - Agency Information Collection (VA Enrollment Certification): Activity Under OMB Review

    Science.gov (United States)

    2012-01-17

    ... or email denise.mclamb@va.gov . Please refer to ``OMB Control No. 2900-0073.'' SUPPLEMENTARY... AFFAIRS Agency Information Collection (VA Enrollment Certification): Activity Under OMB Review AGENCY..., 2012. ADDRESSES: Submit written comments on the collection of information through...

  15. Digital fragment analysis of short tandem repeats by high-throughput amplicon sequencing.

    Science.gov (United States)

    Darby, Brian J; Erickson, Shay F; Hervey, Samuel D; Ellis-Felege, Susan N

    2016-07-01

    High-throughput sequencing has been proposed as a method to genotype microsatellites and overcome the four main technical drawbacks of capillary electrophoresis: amplification artifacts, imprecise sizing, length homoplasy, and limited multiplex capability. The objective of this project was to test a high-throughput amplicon sequencing approach to fragment analysis of short tandem repeats and characterize its advantages and disadvantages against traditional capillary electrophoresis. We amplified and sequenced 12 muskrat microsatellite loci from 180 muskrat specimens and analyzed the sequencing data for precision of allele calling, propensity for amplification or sequencing artifacts, and for evidence of length homoplasy. Of the 294 total alleles, we detected by sequencing, only 164 alleles would have been detected by capillary electrophoresis as the remaining 130 alleles (44%) would have been hidden by length homoplasy. The ability to detect a greater number of unique alleles resulted in the ability to resolve greater population genetic structure. The primary advantages of fragment analysis by sequencing are the ability to precisely size fragments, resolve length homoplasy, multiplex many individuals and many loci into a single high-throughput run, and compare data across projects and across laboratories (present and future) with minimal technical calibration. A significant disadvantage of fragment analysis by sequencing is that the method is only practical and cost-effective when performed on batches of several hundred samples with multiple loci. Future work is needed to optimize throughput while minimizing costs and to update existing microsatellite allele calling and analysis programs to accommodate sequence-aware microsatellite data. PMID:27386092

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. Shedding light on the microbial community of the macropod foregut using 454-amplicon pyrosequencing.

    Directory of Open Access Journals (Sweden)

    Lisa-Maree Gulino

    Full Text Available Twenty macropods from five locations in Queensland, Australia, grazing on a variety of native pastures were surveyed and the bacterial community of the foregut was examined using 454-amplicon pyrosequencing. Specifically, the V3/V4 region of 16S rRNA gene was examined. A total of 5040 OTUs were identified in the data set (post filtering. Thirty-two OTUs were identified as 'shared' OTUS (i.e. present in all samples belonging to either Firmicutes or Bacteroidetes (Clostridiales/Bacteroidales. These phyla predominated the general microbial community in all macropods. Genera represented within the shared OTUs included: unclassified Ruminococcaceae, unclassified Lachnospiraceae, unclassified Clostridiales, Peptococcus sp. Coprococcus spp., Streptococcus spp., Blautia sp., Ruminoccocus sp., Eubacterium sp., Dorea sp., Oscillospira sp. and Butyrivibrio sp. The composition of the bacterial community of the foregut samples of each the host species (Macropus rufus, Macropus giganteus and Macropus robustus was significantly different allowing differentiation between the host species based on alpha and beta diversity measures. Specifically, eleven dominant OTUs that separated the three host species were identified and classified as: unclassified Ruminococcaceae, unclassified Bacteroidales, Prevotella spp. and a Syntrophococcus sucromutans. Putative reductive acetogens and fibrolytic bacteria were also identified in samples. Future work will investigate the presence and role of fibrolytics and acetogens in these ecosystems. Ideally, the isolation and characterization of these organisms will be used for enhanced feed efficiency in cattle, methane mitigation and potentially for other industries such as the biofuel industry.

  1. Flow cytometry community fingerprinting and amplicon sequencing for the assessment of landfill leachate cellulolytic bioaugmentation.

    Science.gov (United States)

    Kinet, R; Dzaomuho, P; Baert, J; Taminiau, B; Daube, G; Nezer, C; Brostaux, Y; Nguyen, F; Dumont, G; Thonart, P; Delvigne, F

    2016-08-01

    Flow cytometry (FCM) is a high throughput single cell technology that is actually becoming widely used for studying phenotypic and genotypic diversity among microbial communities. This technology is considered in this work for the assessment of a bioaugmentation treatment in order to enhance cellulolytic potential of landfill leachate. The experimental results reveal the relevant increase of leachate cellulolytic potential due to bioaugmentation. Cytometric monitoring of microbial dynamics along these assays is then realized. The flow FP package is used to establish microbial samples fingerprint from initial 2D cytometry histograms. This procedure allows highlighting microbial communities' variation along the assays. Cytometric and 16S rRNA gene sequencing fingerprinting methods are then compared. The two approaches give same evidence about microbial dynamics throughout digestion assay. There are however a lack of significant correlation between cytometric and amplicon sequencing fingerprint at genus or species level. Same phenotypical profiles of microbiota during assays matched to several 16S rRNA gene sequencing ones. Flow cytometry fingerprinting can thus be considered as a promising routine on-site method suitable for the detection of stability/variation/disturbance of complex microbial communities involved in bioprocesses. PMID:27160955

  2. Amplicon pyrosequencing reveals the soil microbial diversity associated with invasive Japanese barberry (Berberis thunbergii DC.).

    Science.gov (United States)

    Coats, V C; Pelletreau, K N; Rumpho, M E

    2014-03-01

    The soil microbial community acts as a reservoir of microbes that directly influences the structure and composition of the aboveground plant community, promotes plant growth, increases stress tolerance and mediates local patterns of nutrient cycling. Direct interactions between plants and rhizosphere-dwelling microorganisms occur at, or near, the surface of the root. Upon introduction and establishment, invasive plants modify the soil microbial communities and soil biochemistry affecting bioremediation efforts and future plant communities. Here, we used tag-encoded FLX amplicon 454 pyrosequencing (TEFAP) to characterize the bacterial and fungal community diversity in the rhizosphere of Berberis thunbergii DC. (Japanese barberry) from invasive stands in coastal Maine to investigate effects of soil type, soil chemistry and surrounding plant cover on the soil microbial community structure. Acidobacteria, Actinobacteria, Proteobacteria and Verrucomicrobia were the dominant bacterial phyla, whereas fungal communities were comprised mostly of Ascomycota and Basidiomycota phyla members, including Agaricomycetes and Sordariomycetes. Bulk soil chemistry had more effect on the bacterial community structure than the fungal community. An effect of geographic location was apparent in the rhizosphere microbial communities, yet it was less significant than the effect of surrounding plant cover. These data demonstrate a high degree of spatial variation in the rhizosphere microbial communities of Japanese barberry with apparent effects of soil chemistry, location and canopy cover on the microbial community structure. PMID:24118303

  3. Comparative analyses of amplicon migration behavior in differing denaturing gradient gel electrophoresis (DGGE) systems

    Science.gov (United States)

    Thornhill, D. J.; Kemp, D. W.; Sampayo, E. M.; Schmidt, G. W.

    2010-03-01

    Denaturing gradient gel electrophoresis (DGGE) is commonly utilized to identify and quantify microbial diversity, but the conditions required for different electrophoretic systems to yield equivalent results and optimal resolution have not been assessed. Herein, the influence of different DGGE system configuration parameters on microbial diversity estimates was tested using Symbiodinium, a group of marine eukaryotic microbes that are important constituents of coral reef ecosystems. To accomplish this, bacterial clone libraries were constructed and sequenced from cultured isolates of Symbiodinium for the ribosomal DNA internal transcribed spacer 2 (ITS2) region. From these, 15 clones were subjected to PCR with a GC clamped primer set for DGGE analyses. Migration behaviors of the resulting amplicons were analyzed using a range of conditions, including variation in the composition of the denaturing gradient, electrophoresis time, and applied voltage. All tests were conducted in parallel on two commercial DGGE systems, a C.B.S. Scientific DGGE-2001, and the Bio-Rad DCode system. In this context, identical nucleotide fragments exhibited differing migration behaviors depending on the model of apparatus utilized, with fragments denaturing at a lower gradient concentration and applied voltage on the Bio-Rad DCode system than on the C.B.S. Scientific DGGE-2001 system. Although equivalent PCR-DGGE profiles could be achieved with both brands of DGGE system, the composition of the denaturing gradient and application of electrophoresis time × voltage must be appropriately optimized to achieve congruent results across platforms.

  4. 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

  5. 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...

  6. 78 FR 6849 - Agency Information Collection (Verification of VA Benefits) Activity Under OMB Review

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    2013-01-31

    ... AFFAIRS Agency Information Collection (Verification of VA Benefits) Activity Under OMB Review AGENCY... abstracted below to the Office of Management and Budget (OMB) for review and comment. The PRA submission... VA Benefits, VA Form 26-8937. OMB Control Number: 2900-0406. ] Type of Review: Extension of...

  7. 38 CFR 21.1032 - VA has a duty to assist claimants in obtaining evidence.

    Science.gov (United States)

    2010-07-01

    ... 38 Pensions, Bonuses, and Veterans' Relief 2 2010-07-01 2010-07-01 false VA has a duty to assist claimants in obtaining evidence. 21.1032 Section 21.1032 Pensions, Bonuses, and Veterans' Relief DEPARTMENT... Educational Assistance Claims § 21.1032 VA has a duty to assist claimants in obtaining evidence. (a) VA's...

  8. 38 CFR 21.33 - VA has a duty to assist claimants in obtaining evidence.

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    2010-07-01

    ... 38 Pensions, Bonuses, and Veterans' Relief 2 2010-07-01 2010-07-01 false VA has a duty to assist... Employment Under 38 U.S.C. Chapter 31 Claims § 21.33 VA has a duty to assist claimants in obtaining evidence... claimant either orally or in writing when VA: (i) Has made reasonable efforts to obtain relevant...

  9. 76 FR 24570 - Proposed Information Collection (Application for VA Education Benefits) Activity; Comment Request

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    2011-05-02

    ...., Washington, DC 20420 or email to nancy.kessinger@va.gov . Please refer to ``OMB Control No. 2900-0154'' in... AFFAIRS Proposed Information Collection (Application for VA Education Benefits) Activity; Comment Request... Veterans Benefits Administration (VBA), Department of Veterans Affairs (VA), is announcing an...

  10. 76 FR 67557 - Proposed Information Collection (Survey of Veteran Enrollees' Health and Reliance Upon VA...

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    2011-11-01

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  11. 78 FR 53506 - Agency Information Collection (HUD/VA Addendum to Uniform Residential Loan Application) Activity...

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    2013-08-29

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  12. 78 FR 59773 - Proposed Information Collection (VA Request for Determination of Reasonable Value) Activity...

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    2013-09-27

    ... Avenue NW., Washington, DC 20420 or email nancy.kessinger@va.gov . Please refer to ``OMB Control No. 2900... AFFAIRS Proposed Information Collection (VA Request for Determination of Reasonable Value) Activity.... SUMMARY: The Veterans Benefits Administration (VBA), Department of Veterans Affairs (VA), is announcing...

  13. 77 FR 20889 - Proposed Information Collection (Request One-VA Identification Verification Card) Activity...

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    2012-04-06

    ... of Veterans Affairs, 810 Vermont Avenue NW., Washington, DC 20420 or email: john.hancock@va.gov... AFFAIRS Proposed Information Collection (Request One-VA Identification Verification Card) Activity... Veterans Affairs (VA), is announcing an opportunity for public comment on the proposed collection...

  14. 76 FR 40452 - Agency Information Collection (VA MATIC Authorization) Activity Under OMB Review

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    2011-07-08

    ...: Submit written comments on the collection of information through http://www.Regulations.gov ; or to VA's... denise.mclamb@va.gov . Please refer to ``OMB Control No. 2900-0492.'' SUPPLEMENTARY INFORMATION: Title... AFFAIRS Agency Information Collection (VA MATIC Authorization) Activity Under OMB Review AGENCY:...

  15. 76 FR 27381 - Proposed Information Collection (Notice of Waiver of VA Compensation or Pension To Receive...

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    2011-05-11

    ...., Washington, DC 20420 or e-mail to nancy.kessinger@va.gov . Please refer to ``OMB Control No. 2900-0463'' in... AFFAIRS Proposed Information Collection (Notice of Waiver of VA Compensation or Pension To Receive... of Veterans Affairs (VA), is announcing an opportunity for public comment on the proposed...

  16. 78 FR 29436 - Proposed Information Collection (HUD/VA Addendum to Uniform Residential Loan Application...

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    2013-05-20

    ...), Department of Veterans Affairs, 810 Vermont Avenue NW., Washington, DC 20420 or email nancy.kessinger@va.gov... AFFAIRS Proposed Information Collection (HUD/VA Addendum to Uniform Residential Loan Application) Activity.... SUMMARY: The Veterans Benefits Administration (VBA), Department of Veterans Affairs (VA), is announcing...

  17. 75 FR 61249 - Proposed Information Collection (VA Request for Determination of Reasonable Value) Activity...

    Science.gov (United States)

    2010-10-04

    ...., Washington, DC 20420 or e-mail nancy.kessinger@va.gov . Please refer to ``OMB Control No. 2900-0045'' in any... AFFAIRS Proposed Information Collection (VA Request for Determination of Reasonable Value) Activity.... SUMMARY: The Veterans Benefits Administration (VBA), Department of Veterans Affairs (VA), is announcing...

  18. 75 FR 54965 - Proposed Information Collection (Statement of Purchaser or Owner Assuming Seller's Loans, VA Form...

    Science.gov (United States)

    2010-09-09

    ...., Washington, DC 20420 or e-mail nancy.kessinger@va.gov . Please refer to ``OMB Control No. 2900-0111'' in any... AFFAIRS Proposed Information Collection (Statement of Purchaser or Owner Assuming Seller's Loans, VA Form... Affairs (VA), is announcing an opportunity for public comment on the proposed collection of...

  19. 78 FR 36642 - Proposed Information Collection (VA Loan Electronic Reporting Interface (VALERI) System) Activity...

    Science.gov (United States)

    2013-06-18

    ... nancy.kessinger@va.gov . Please refer to ``OMB Control No. 2900-0021'' in any correspondence. During the... AFFAIRS Proposed Information Collection (VA Loan Electronic Reporting Interface (VALERI) System) Activity.... SUMMARY: The Veterans Benefits Administration (VBA), Department of Veterans Affairs (VA), is announcing...

  20. 76 FR 67561 - Proposed Information Collection (VA Enrollment Certification) Activity: Comment Request

    Science.gov (United States)

    2011-11-01

    ..., 810 Vermont Avenue NW., Washington, DC 20420 or email to nancy.kessinger@va.gov . Please refer to... AFFAIRS Proposed Information Collection (VA Enrollment Certification) Activity: Comment Request AGENCY... Benefits Administration (VBA), Department of Veterans Affairs (VA), is announcing an opportunity for...

  1. 75 FR 61858 - Proposed Information Collection (VA Request for Determination of Reasonable Value) Activity...

    Science.gov (United States)

    2010-10-06

    ...., Washington, DC 20420 or e-mail nancy.kessinger@va.gov . Please refer to ``OMB Control No. 2900-0045'' in any... AFFAIRS Proposed Information Collection (VA Request for Determination of Reasonable Value) Activity.... SUMMARY: The Veterans Benefits Administration (VBA), Department of Veterans Affairs (VA), is announcing...

  2. 77 FR 56711 - Proposed Information Collection (VA MATIC Enrollment/Change); Comment Request

    Science.gov (United States)

    2012-09-13

    ... Affairs, 810 Vermont Avenue NW., Washington, DC 20420 or email nancy.kessinger@va.gov . Please refer to... AFFAIRS Proposed Information Collection (VA MATIC Enrollment/Change); Comment Request AGENCY: Veterans... Administration (VBA), Department of Veterans Affairs (VA), is announcing an opportunity for public comment on...

  3. 77 FR 56709 - Proposed Information Collection (VA Subcontracting Report for Service Disabled Veteran-Owned...

    Science.gov (United States)

    2012-09-13

    ....taylor@va.gov . Please refer to ``OMB Control No. 2900-0741'' in any correspondence. During the comment... AFFAIRS Proposed Information Collection (VA Subcontracting Report for Service Disabled Veteran-Owned Small... and Disadvantaged Business Utilization (OSDBU), Department of Veterans Affairs (VA), is announcing...

  4. 78 FR 52085 - VA Veteran-Owned Small Business Verification Guidelines

    Science.gov (United States)

    2013-08-22

    ... (77 FR 38181) an interim final rule that revised the requirement for re-verification of SDVOSB/VOSB... analysis are available on VA's Web site at http://www1.va.gov/orpm/ , by following the link for ``VA... rule amending 38 CFR part 74, which was published on June 27, 2012, at 77 FR 38181, is adopted...

  5. 75 FR 17832 - Proposed Information Collection (VA Loan Electronic Reporting Interface (VALERI) System) Activity...

    Science.gov (United States)

    2010-04-07

    ... nancy.kessinger@va.gov . Please refer to ``OMB Control No. 2900-0021'' in any correspondence. During the... AFFAIRS Proposed Information Collection (VA Loan Electronic Reporting Interface (VALERI) System) Activity.... SUMMARY: The Veterans Benefits Administration (VBA), Department of Veterans Affairs (VA), is announcing...

  6. 77 FR 38396 - Agency Information Collection (One-VA Identification Verification Card) Activities Under OMB Review

    Science.gov (United States)

    2012-06-27

    ... information through www.Regulations.gov or to VA's OMB Desk Officer, Office of Information and Regulatory... 20420, (202) 632-7479, Fax (202) 632-7583 or email denise.mclamb@va.gov . Please refer to ``OMB Control... AFFAIRS Agency Information Collection (One-VA Identification Verification Card) Activities Under...

  7. 75 FR 48413 - Agency Information Collection (HUD/VA Addendum to Uniform Residential Loan Application) Activity...

    Science.gov (United States)

    2010-08-10

    ... information through www.Regulations.gov ; or to VA's OMB Desk Officer, OMB Human Resources and Housing Branch..., (202) 461-7485, FAX (202) 273-0443 or e-mail denise.mclamb@va.gov . Please refer to ``OMB Control No... AFFAIRS Agency Information Collection (HUD/VA Addendum to Uniform Residential Loan Application)...

  8. 76 FR 63357 - VA National Academic Affiliations Council; Notice of Establishment

    Science.gov (United States)

    2011-10-12

    ... Avenue, NW., Washington, DC, or e-mail at Gloria.Holland@va.gov ; or phone at (202) 461-9584. Dated... AFFAIRS VA National Academic Affiliations Council; Notice of Establishment As required by Section 9(a)(2... establishment of the Department of Veterans Affairs (VA) National Academic Affiliations Council. The...

  9. 75 FR 33898 - Agency Information Collection (VA Loan Electronic Reporting Interface (VALERI) System) Activity...

    Science.gov (United States)

    2010-06-15

    ... through http://www.Regulations.gov ; or to VA's OMB Desk Officer, OMB Human Resources and Housing Branch..., (202) 461-7485, FAX (202) 273-0443 or e-mail denise.mclamb@va.gov . Please refer to ``OMB Control No... AFFAIRS Agency Information Collection (VA Loan Electronic Reporting Interface (VALERI) System)...

  10. 77 FR 30050 - VA National Academic Affiliations Council, Notice of meeting

    Science.gov (United States)

    2012-05-21

    ... 20420, or by email to Gloria.Holland@va.gov . Any member of the public wishing to attend or seeking... AFFAIRS VA National Academic Affiliations Council, Notice of meeting The Department of Veterans Affairs (VA) gives notice under Public Law 92-463 (Federal Advisory Committee Act) that the second meeting...

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

    Science.gov (United States)

    2013-09-11

    ... 20420 or email: matt.bristol@va.gov . Please refer to ``OMB Control No. 2900-0759'' in any... AFFAIRS Proposed Information Collection (VA, National Veterans Sports Programs and Special Events, Event... Programs and Special Events (NVSP), Department of Veterans Affairs (VA), is announcing an opportunity...

  12. 75 FR 9277 - Proposed Information Collection (VA National Rehabilitation Special Events, Event Registration...

    Science.gov (United States)

    2010-03-01

    ...), Department of Veterans Affairs, 810 Vermont Avenue, NW., Washington, DC 20420 or e-mail: matt.bristol@va.gov... AFFAIRS Proposed Information Collection (VA National Rehabilitation Special Events, Event Registration... Veterans Affairs (VA), is announcing an opportunity for public comment on the proposed collection...

  13. 77 FR 24268 - Agency Information Collection (Dependents' Application for VA Educational Benefits) Activity...

    Science.gov (United States)

    2012-04-23

    ....Regulations.gov or to VA's OMB Desk Officer, OMB Human Resources and Housing Branch, New Executive Office...-7583 or email denise.mclamb@va.gov . Please refer to ``OMB Control No. 2900-0098.'' SUPPLEMENTARY... AFFAIRS Agency Information Collection (Dependents' Application for VA Educational Benefits) Activity...

  14. 77 FR 70210 - Agency Information Collection (VA Subcontracting Report for Service Disabled Veteran-owned Small...

    Science.gov (United States)

    2012-11-23

    ... through www.Regulations.gov ; or to VA's OMB Desk Officer, OMB Human Resources and Housing Branch, New...-7492, fax (202) 632-7583 or email crystal.rennie@va.gov . Please refer to ``OMB Control No. 2900-0741... AFFAIRS Agency Information Collection (VA Subcontracting Report for Service Disabled Veteran-owned...

  15. 78 FR 77204 - Proposed Information Collection (VA National Veterans Sports Programs and Special Event Surveys...

    Science.gov (United States)

    2013-12-20

    ... Affairs, 810 Vermont Avenue NW., Washington, DC 20420; or email: crystal.rennie@va.gov . Please refer to... AFFAIRS Proposed Information Collection (VA National Veterans Sports Programs and Special Event Surveys... Veterans Affairs (VA), is announcing an opportunity for public comment on the proposed collection...

  16. 75 FR 78808 - Agency Information Collection (VA Request for Determination of Reasonable Value) Activity Under...

    Science.gov (United States)

    2010-12-16

    ....Regulations.gov or to VA's OMB Desk Officer, OMB Human Resources and Housing Branch, New Executive Office...-0966 or e-mail denise.mclamb@va.gov . Please refer to ``OMB Control No. 2900-0045.'' SUPPLEMENTARY... AFFAIRS Agency Information Collection (VA Request for Determination of Reasonable Value) Activity...

  17. 78 FR 76412 - Agency Information Collection (VA National Rehabilitation Special Events, Event Registration...

    Science.gov (United States)

    2013-12-17

    ... the collection of information through www.Regulations.gov or to VA's OMB Desk Officer, OMB Human...., Washington, DC 20420, (202) 632-7492 or email crystal.rennie@va.gov . Please refer to ``OMB Control No. 2900... AFFAIRS Agency Information Collection (VA National Rehabilitation Special Events, Event...

  18. 75 FR 41577 - VBA/VHA Musculoskeletal Forum: Improving VA's Disability Evaluation Criteria

    Science.gov (United States)

    2010-07-16

    ... Mr. Tuttle at (202) 461-9037 or Bradley.Tuttle2@va.gov , or Thomas Kniffen at (202) 461-9725 or Thomas.Kniffen@va.gov . Dated: July 8, 2010. John R. Gingrich, Chief of Staff, Department of Veterans... AFFAIRS VBA/VHA Musculoskeletal Forum: Improving VA's Disability Evaluation Criteria AGENCY: Department...

  19. 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.

  20. Analysis of the mouse gut microbiome using full-length 16S rRNA amplicon sequencing.

    Science.gov (United States)

    Shin, Jongoh; Lee, Sooin; Go, Min-Jeong; Lee, Sang Yup; Kim, Sun Chang; Lee, Chul-Ho; Cho, Byung-Kwan

    2016-01-01

    Demands for faster and more accurate methods to analyze microbial communities from natural and clinical samples have been increasing in the medical and healthcare industry. Recent advances in next-generation sequencing technologies have facilitated the elucidation of the microbial community composition with higher accuracy and greater throughput than was previously achievable; however, the short sequencing reads often limit the microbial composition analysis at the species level due to the high similarity of 16S rRNA amplicon sequences. To overcome this limitation, we used the nanopore sequencing platform to sequence full-length 16S rRNA amplicon libraries prepared from the mouse gut microbiota. A comparison of the nanopore and short-read sequencing data showed that there were no significant differences in major taxonomic units (89%) except one phylotype and three taxonomic units. Moreover, both sequencing data were highly similar at all taxonomic resolutions except the species level. At the species level, nanopore sequencing allowed identification of more species than short-read sequencing, facilitating the accurate classification of the bacterial community composition. Therefore, this method of full-length 16S rRNA amplicon sequencing will be useful for rapid, accurate and efficient detection of microbial diversity in various biological and clinical samples. PMID:27411898

  1. 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.

  2. 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.

  3. ANTIAMNESIC EFFECT OF THE TWO NOVEL K-OPIOID AGONISTS, VA-100 AND VA-101, IN THE MOUSE PASSIVE AVOIDANCE TEST

    OpenAIRE

    Ghelardini, C; Galeotti, N; Di Cesare Mannelli, L.; A. Cappelli; M.ANZINI; Bartolini, A.

    2001-01-01

    The effects of the administration of the two novel k-opioid agonists (VA-100, VA-101) on memory processes were evaluated with the mouse passive avoidance test. The administration of VA-100 (50–100 mg kg–1 p.o.) and VA-101 (100 mg kg–1 p.o.) administered 20 min before the training session prevented nor-binaltorphimine (4.9 mg per mouse i.c.v.), scopolamine (1.5 mg kg–1 i.p.), mecamylamine (20 mg kg–1 i.p.), diphenhydramine (20 mg kg–1 i.p.), and baclofen (2 mg kg–1 i.p.) amnesia. A...

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

    OpenAIRE

    Linda Resnik, PT, PhD

    2010-01-01

    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 agreem...

  5. 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.

  6. Voltammetric detection of sequence-selective DNA hybridization related to Toxoplasma gondii in PCR amplicons.

    Science.gov (United States)

    Gokce, Gultekin; Erdem, Arzum; Ceylan, Cagdas; Akgöz, Muslum

    2016-03-01

    This work describes the single-use electrochemical DNA biosensor technology developed for voltammetric detection of sequence selective DNA hybridization related to important human and veterinary pathogen; Toxoplasma gondii. In the principle of electrochemical label-free detection assay, the duplex of DNA hybrid formation was detected by measuring guanine oxidation signal occured in the presence of DNA hybridization. The biosensor design consisted of the immobilization of an inosine-modified (guanine-free) probe onto the surface of pencil graphite electrode (PGE), and the detection of the duplex formation in connection with the differential pulse voltammetry(DPV) by measuring the guanine signal. Toxoplasma gondii capture probe was firstly immobilized onto the surface of the activated PGE by wet adsorption. The extent of hybridization at PGE surface between the probe and the target was then determined by measuring the guanine signal observed at +1.0V. The electrochemical monitoring of optimum DNA hybridization has been performed in the target concentration of 40µg/mL in 50min of hybridization time. The specificity of the electrochemical biosensor was then tested using non-complementary, or mismatch short DNA sequences. Under the optimum conditions, the guanine oxidation signal indicating full hybridization was measured in various target concentration from 0.5 to 25µg/mL and a detection limit was found to be 1.78µg/mL. This single-use biosensor platform was successfully applied for the voltammetric detection of DNA hybridization related to Toxoplasma gondii in PCR amplicons. PMID:26717837

  7. 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.

  8. 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. PMID:27003585

  9. Analysis of a Drosophila amplicon in follicle cells highlights the diversity of metazoan replication origins.

    Science.gov (United States)

    Kim, Jane C; Orr-Weaver, Terry L

    2011-10-01

    To investigate the properties of metazoan replication origins, recent studies in cell culture have adopted the strategy of identifying origins using genome-wide approaches and assessing correlations with such features as transcription and histone modifications. Drosophila amplicon in follicle cells (DAFCs), genomic regions that undergo repeated rounds of DNA replication to increase DNA copy number, serve as powerful in vivo model replicons. Because there are six DAFCs, compared with thousands of origins activated in the typical S phase, close molecular characterization of all DAFCs is possible. To determine the extent to which the six DAFCs are different or similar, we investigated the developmental and replication properties of the newly identified DAFC-34B. DAFC-34B contains two genes expressed in follicle cells, although the timing and spatial patterns of expression suggest that amplification is not a strategy to promote high expression at this locus. Like the previously characterized DAFC-62D, DAFC-34B displays origin activation at two separate stages of development. However, unlike DAFC-62D, amplification at the later stage is not transcription-dependent. We mapped the DAFC-34B amplification origin to 1 kb by nascent strand analysis and delineated cis requirements for origin activation, finding that a 6-kb region, but not the 1-kb origin alone, is sufficient for amplification. We analyzed the developmental localization of the origin recognition complex (ORC) and the minichromosome maintenance (MCM)2-7 complex, the replicative helicase. Intriguingly, the final round of origin activation at DAFC-34B occurs in the absence of detectable ORC, although MCMs are present, suggesting a new amplification initiation mechanism. PMID:21933960

  10. 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.

  11. Validation of KENO V.a Comparison with Critical Experiments

    Energy Technology Data Exchange (ETDEWEB)

    Jordan, W.C.

    1999-01-01

    Section 1 of this report documents the validation of KENO V.a against 258 critical experiments. Experiments considered were primarily high or low enriched uranium systems. The results indicate that the KENO V.a Monte Carlo Criticality Program accurately calculates a broad range of critical experiments. A substantial 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 which 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, the KENO V.a code can be used with confidence for the design and criticality safety analysis of uranium-containing systems. Section 2 of this report documents the results of investigation into the cause of the bias observed in Sect. 1. The results of this study indicate that the bias seen in Sect. 1 is caused by code bias, cross-section bias, reporting bias, and modeling bias. There is evidence that many of the experiments used in this validation and in previous validations are not adequately documented. The uncertainty in the experimental parameters overshadows bias caused by the code and cross sections and prohibits code validation to better than about 1% in k{sub eff}.

  12. Gene-specific amplicons from metagenomes as an alternative to directed evolution for enzyme screening: a case study using phenylacetaldehyde reductases.

    Science.gov (United States)

    Itoh, Nobuya; Kazama, Miki; Takeuchi, Nami; Isotani, Kentaro; Kurokawa, Junji

    2016-06-01

    Screening gene-specific amplicons from metagenomes (S-GAM) is a highly promising technique for the isolation of genes encoding enzymes for biochemical and industrial applications. From metagenomes, we isolated phenylacetaldehyde reductase (par) genes, which code for an enzyme that catalyzes the production of various Prelog's chiral alcohols. Nearly full-length par genes were amplified by PCR from metagenomic DNA, the products of which were fused with engineered par sequences at both terminal regions of the expression vector to ensure proper expression and then used to construct Escherichia coli plasmid libraries. Sequence- and activity-based screening of these libraries identified different homologous par genes, Hpar-001 to -036, which shared more than 97% amino acid sequence identity with PAR. Comparative characterization of these active homologs revealed a wide variety of enzymatic properties including activity, substrate specificity, and thermal stability. Moreover, amino acid substitutions in these genes coincided with those of Sar268 and Har1 genes, which were independently engineered by error-prone PCR to exhibit increased activity in the presence of concentrated 2-propanol. The comparative data from both approaches suggest that sequence information from homologs isolated from metagenomes is quite useful for enzyme engineering. Furthermore, by examining the GAM-based sequence dataset derived from soil metagenomes, we easily found amino acid substitutions that increase the thermal stability of PAR/PAR homologs. Thus, GAM-based approaches can provide not only useful homologous enzymes but also an alternative to directed evolution methodologies. PMID:27419059

  13. 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.

  14. 77 FR 64388 - Agency Information Collection (Former POW Medical History), VA Form 10-0048 Activities Under OMB...

    Science.gov (United States)

    2012-10-19

    ... AFFAIRS Agency Information Collection (Former POW Medical History), VA Form 10-0048 Activities Under OMB....'' SUPPLEMENTARY INFORMATION: Title: Former POW Medical History, VA Form 10-0048. OMB Control Number: 2900-0427... a VA physician during a medical examination of a Former Prisoner of War veteran. VA will use...

  15. 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.

  16. 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.

  17. The cytological manifestation of gene amplification in multidrug-resistant mouse leukemia P388 sublines is correlated with amplicon content

    Energy Technology Data Exchange (ETDEWEB)

    Il`inskaya, G.V.; Kopnin, B.P. [Institute of Carcinogenesis, Moscow (Russian Federation); Demidova, N.S. [Institute of Chemical Physics, Moscow (Russian Federation)

    1995-10-01

    Previously, we showed that development of multidrug resistance (MDR) in mouse P388 leukemia cells is often associated with the appearance of newly-formed chromosomelike structures that contain amplified copies of the mdr1 gene. In the present study, we compared amplicon content in P388 sublines showing different types of these structures. A strong correlation between the formation of specific acentric markers consisting of two identical arms and the absence of the sorcin gene coamplification was found. In all the sublines containing other types of chromosomelike structures, the sorcin gene is coamplified. 9 refs., 2 figs., 1 tab.

  18. 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...

  19. Integration of Women Veterans into VA Quality Improvement Research Efforts: What Researchers Need to Know

    OpenAIRE

    Yano, Elizabeth M.; Hayes, Patricia; Wright, Steven; Schnurr, Paula P.; Lipson, Linda; Bean-Mayberry, Bevanne; Washington, Donna L

    2010-01-01

    The Department of Veterans Affairs (VA) and other federal agencies require funded researchers to include women in their studies. Historically, many researchers have indicated they will include women in proportion to their VA representation or pointed to their numerical minority as justification for exclusion. However, women’s participation in the military—currently 14% of active military—is rapidly changing veteran demographics, with women among the fastest growing segments of new VA users. T...

  20. KENO V.a Primer: A Primer for Criticality Calculations with SCALE/KENO V.a Using CSPAN for Input

    Energy Technology Data Exchange (ETDEWEB)

    Busch, R.D.

    2003-01-17

    The SCALE (Standardized Computer Analyses for Licensing Evaluation) computer software system developed at Oak Ridge National Laboratory (ORNL) is widely used and accepted around the world for criticality safety analyses. The well-known KENO V.a three-dimensional Monte Carlo criticality computer code is the primary criticality safety analysis tool in SCALE. The KENO V.a primer is designed to help a new user understand and use the SCALE/KENO V.a Monte Carlo code for nuclear criticality safety analyses. It assumes that the user has a college education in a technical field. There is no assumption of familiarity with Monte Carlo codes in general or with SCALE/KENO V.a in particular. The primer is designed to teach by example, with each example illustrating two or three features of SCALE/KENO V.a that are useful in criticality analyses. The primer is based on SCALE 4.4a, which includes the Criticality Safety Processor for Analysis (CSPAN) input processor for Windows personal computers (PCs). A second edition of the primer, which uses the new KENO Visual Editor, is currently under development at ORNL and is planned for publication in late 2003. Each example in this first edition of the primer uses CSPAN to provide the framework for data input. Starting with a Quickstart section, the primer gives an overview of the basic requirements for SCALE/KENO V.a input and allows the user to quickly run a simple criticality problem with SCALE/KENO V.a. The sections that follow Quickstart include a list of basic objectives at the beginning that identifies the goal of the section and the individual SCALE/KENO V.a features which are covered in detail in the example problems in that section. Upon completion of the primer, a new user should be comfortable using CSPAN to set up criticality problems in SCALE/KENO V.a.

  1. 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.

  2. 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.

  3. 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.

  4. 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…

  5. 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.

  6. RiboFR-Seq: a novel approach to linking 16S rRNA amplicon profiles to metagenomes.

    Science.gov (United States)

    Zhang, Yanming; Ji, Peifeng; Wang, Jinfeng; Zhao, Fangqing

    2016-06-01

    16S rRNA amplicon analysis and shotgun metagenome sequencing are two main culture-independent strategies to explore the genetic landscape of various microbial communities. Recently, numerous studies have employed these two approaches together, but downstream data analyses were performed separately, which always generated incongruent or conflict signals on both taxonomic and functional classifications. Here we propose a novel approach, RiboFR-Seq (Ribosomal RNA gene flanking region sequencing), for capturing both ribosomal RNA variable regions and their flanking protein-coding genes simultaneously. Through extensive testing on clonal bacterial strain, salivary microbiome and bacterial epibionts of marine kelp, we demonstrated that RiboFR-Seq could detect the vast majority of bacteria not only in well-studied microbiomes but also in novel communities with limited reference genomes. Combined with classical amplicon sequencing and shotgun metagenome sequencing, RiboFR-Seq can link the annotations of 16S rRNA and metagenomic contigs to make a consensus classification. By recognizing almost all 16S rRNA copies, the RiboFR-seq approach can effectively reduce the taxonomic abundance bias resulted from 16S rRNA copy number variation. We believe that RiboFR-Seq, which provides an integrated view of 16S rRNA profiles and metagenomes, will help us better understand diverse microbial communities. PMID:26984526

  7. 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.

  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. PMID:27008882

  10. 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; Viala, Sandrine; Decousus, Stephanie; Perin, Axel; Lafarge, Laurence; Ollier, Marie; El Saghir, Nagi S.

    2016-01-01

    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.

  11. 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.

  12. Penn/VA center for studies of addiction.

    Science.gov (United States)

    O'Brien, Charles P; McLellan, A Thomas; Childress, Anna Rose; Woody, George E

    2009-01-01

    The Penn/VA Center was founded in 1971 because of great concern over the number of Vietnam veterans returning home addicted to heroin. At that time little was known about the science of addiction, so our program from the very beginning was designed to gather data about the nature of addiction and measure the effects of available treatments. In other words, the goals were always a combination of treatment and research. This combination has continued to the present day. A human laboratory for the study of addiction phenomena such as conditioned responses was also founded in 1971. The key clinician investigators in this group have remained in the Center since the 1970s with most of the research staff continuing to work together. Important new investigators have been added over the years. Treatment was empirically based with randomized, controlled clinical trials as the gold standard for determining evidence-based treatment. The patients coming to treatment do not distinguish between abuse of alcohol and other drugs, so the treatment and research programs have always focused on all drugs including ethyl alcohol and the combination of ethyl alcohol with other drugs such as cocaine and opioids. Most of the patients coming for treatment also suffered from additional psychiatric disorders such as depression, anxiety, bipolar disorder or schizophrenia. Thus, the addiction treatment program in 1980 absorbed the rest of the VA Psychiatry Service into the Substance Abuse Program forming a new Behavioral Health Service with responsibility for over 9000 patients. The integration of substance abuse treatment with overall mental health care was the most efficient way to handle patients with complicated combinations of disorders. While this continues to be the best way to treat patients, it has proven difficult in practice. The main reason for this difficulty is that most mental health therapists whether they are psychiatrists, psychologists or social workers feel very inadequate

  13. 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.

  14. The SAPPHIRE and 50 MT projects at BWXT, Lynchburg, VA

    International Nuclear Information System (INIS)

    When the SAPPHIRE project for the down-blending of HEU material of Khazak origin was initiated in 1996 at BWX Technologies (BWXT) formally Babcock and Wilcox in Lynchburg, VA and the Agency was requested to apply its specially designed safeguards measures to the process with a view to provide assurance to the international community that down-blending had actually taken place as stipulated in the USA-Khazak agreement a learning process was initiated from this effort culminating in the current 50 MT downblending process at the same facility with BWXT, the USA Authorities, and the Agency as partners in this technologically advanced enterprise aimed at the downgrading of a substantial quantity of weapons grade material. In the present paper an overview is provided of the road leading to an effective, and mutually agreeable safeguards approach for carrying out verifications in the sensitive environment of a facility devoted to HEU uranium processing. (author)

  15. The SAPPHIRE and 50 MT projects at BWXT, Lynchburg, VA

    International Nuclear Information System (INIS)

    Full text: When the SAPPHIRE project for the down-blending of HEU material of Khazak origin was initiated in 1996 at BWX Technologies (BWXT) formally Babcock and Wilcox in Lynchburg, VA and the Agency was requested to apply its specially designed safeguards measures to the process with a view to provide assurance to the international community that down-blending had actually taken place as stipulated in the USA-Khazak agreement a learning process was initiated from this effort culminating in the current 50 MT downblending process at the same facility with BWXT, the USA Authorities, and the Agency as partners in this technologically advanced enterprise aimed at the downgrading of a substantial quantity of weapons grade material. In the present paper an overview is provided of the road leading to an effective, and mutually agreeable safeguards approach for carrying out verifications in the sensitive environment of a facility devoted to HEU uranium processing. (author)

  16. 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.

  17. 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.

  18. 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...

  19. 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...

  20. 77 FR 33089 - OPSAIL 2012 Virginia, Port of Hampton Roads, VA

    Science.gov (United States)

    2012-06-05

    ...) entitled ``OPSAIL 2012 Virginia, Port of Hampton Roads, VA'' in the Federal Register (77 FR 19957). We... Acronyms DHS Department of Homeland Security FR Federal Register NPRM Notice of Proposed Rulemaking A... Hampton Roads, VA AGENCY: Coast Guard, DHS. ACTION: Temporary final rule. SUMMARY: The Coast Guard...

  1. 30 CFR 57.22309 - Methane monitors (V-A mines).

    Science.gov (United States)

    2010-07-01

    ... 30 CFR part 18, and prevent starting of such equipment when methane levels reach 1.5 percent; and (3... 30 Mineral Resources 1 2010-07-01 2010-07-01 false Methane monitors (V-A mines). 57.22309 Section... Standards for Methane in Metal and Nonmetal Mines Equipment § 57.22309 Methane monitors (V-A mines)....

  2. 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...

  3. 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...

  4. 78 FR 56271 - FY 2014-2020 Draft VA Strategic Plan

    Science.gov (United States)

    2013-09-12

    ... partners; and developing our workforce with the skills, tools, and leadership to meet our clients' needs... through integration within VA and with our partners; and developing our workforce with the skills, tools, and leadership to meet our clients' needs and expectations. DATES: Comments must be received by VA...

  5. 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:...

  6. 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...

  7. 77 FR 13519 - Safety Zone; Virginia Beach Oceanfront Air Show, Atlantic Ocean, Virginia Beach, VA

    Science.gov (United States)

    2012-03-07

    ... 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: Notice of proposed rulemaking. SUMMARY... Virginia Beach, VA. This action is necessary to provide for the safety of life on navigable waters...

  8. 38 CFR 74.25 - What types of personally identifiable information will VA collect?

    Science.gov (United States)

    2010-07-01

    ... What types of personally identifiable information will VA collect? In order to establish owner... 38 Pensions, Bonuses, and Veterans' Relief 2 2010-07-01 2010-07-01 false What types of personally identifiable information will VA collect? 74.25 Section 74.25 Pensions, Bonuses, and Veterans'...

  9. 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......

  10. 76 FR 40453 - Agency Information Collection (Application for VA Education Benefits) Activity Under OMB Review

    Science.gov (United States)

    2011-07-08

    ... AFFAIRS Agency Information Collection (Application for VA Education Benefits) Activity Under OMB Review... of information abstracted below to the Office of Management and Budget (OMB) for review and comment... Review: Extension of a currently approved collection. Abstract: a. Claimants complete VA Form 22-1990...

  11. ‘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

  12. 77 FR 23204 - VA Acquisition Regulation: Electronic Submission of Payment Requests

    Science.gov (United States)

    2012-04-18

    ... reflect the increased use of electronic commerce in the Federal Government and in the private sector... part 1315 by requiring the use of electronic commerce. Electronic invoice submission replaces payment... using under VA's current interim electronic invoicing clause. See 74 FR 32223. VA's Electronic...

  13. 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…

  14. 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...

  15. 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...

  16. 30 CFR 57.22605 - Blasting from the surface (V-A mines).

    Science.gov (United States)

    2010-07-01

    ... applicable requirements of 30 CFR parts 18 through 36. (e) This standard applies only to mines blasting... 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...

  17. 78 FR 59099 - Agency Information Collection (VA Loan Electronic Reporting Interface (VALERI) System) Activity...

    Science.gov (United States)

    2013-09-25

    ... Affairs, 810 Vermont Avenue NW., Washington, DC 20420, (202) 632-7492 or email crystal.rennie@va.gov... AFFAIRS Agency Information Collection (VA Loan Electronic Reporting Interface (VALERI) System) Activity... through www.Regulations.gov , or to Office of Information and Regulatory Affairs, Office of Management...

  18. 76 FR 70831 - Proposed Information Collection (Survey of Veteran Enrollees (Quality and Efficiency of VA Health...

    Science.gov (United States)

    2011-11-15

    ..., 810 Vermont Avenue NW., Washington, DC 20420; or email: cynthia.harvey-pryor@va.gov . Please refer to... AFFAIRS Proposed Information Collection (Survey of Veteran Enrollees (Quality and Efficiency of VA Health.... ACTION: Notice. SUMMARY: The Veterans Health Administration (VHA), Department of Veterans Affairs...

  19. 77 FR 39346 - Proposed Information Collection (Statement of Accredited Representative in Appealed Case, VA Form...

    Science.gov (United States)

    2012-07-02

    ... Affairs, 810 Vermont Avenue NW., Washington, DC 20420 or email Sue.Hamlin@mail.va.gov . Please refer to... AFFAIRS Proposed Information Collection (Statement of Accredited Representative in Appealed Case, VA Form... Affairs. ACTION: Notice. SUMMARY: The Board of Veterans' Appeals (BVA), Department of Veterans Affairs...

  20. The Latest Development of Approaches to Calculate VaR%VaR计算方法的最新进展

    Institute of Scientific and Technical Information of China (English)

    郑冲

    2003-01-01

    自20世纪90年代以来,VaR(Value at Risk)方法发展迅速,并在风险管理、绩效评价、金融监管等方面获得广泛应用.最初用来计算V8R的方法主要有历史模拟、分析方法和Monte Carlo模拟三种.近年来,针对实际应用中出现的问题,这三类方法得到进一步改进并取得较大进展.

  1. 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.

  2. Optimisation of 16S rDNA amplicon sequencing protocols for microbial community profiling of anaerobic digesters

    DEFF Research Database (Denmark)

    Kirkegaard, Rasmus Hansen; McIlroy, Simon Jon; Larsen, Poul;

    of the community composition. As such sample specific optimisation and standardisation of DNA extraction, as well PCR primer selection, are essential to minimising the potential for such biases. The aim of this study was to develop a protocol for optimized community profiling of anaerobic digesters. The FastDNA......RNA gene amplicon sequencing is rapid, cheap, high throughput, and has high taxonomic resolution. However, biases are introduced in multiple steps of this approach, including non-representative DNA extraction and uneven taxonomic coverage of selected PCR primers, potentially giving a skewed view...... SPIN kit was selected and the mechanical lysis parameters optimised for extraction of genomic DNA from mesophilic and thermophilic anaerobic digester samples. Different primer sets were compared for targeting the archaea and bacteria, both together and individually. Shotgun sequencing of a TruSeq PCR...

  3. Obtaining representative community profiles of anaerobic digesters through optimisation of 16S rRNA amplicon sequencing protocols

    DEFF Research Database (Denmark)

    Kirkegaard, Rasmus Hansen; McIlroy, Simon Jon; Karst, Søren Michael;

    of the community composition . As such sample specific optimisation and standardisation of DNA extraction, as well PCR primer selection, are essential to minimising the potential for such biases. The aim of this study was to develop a protocol for optimized community profiling of anaerobic digesters. The FastDNA......RNA gene amplicon sequencing is rapid, cheap, high throughput, and has high taxonomic resolution. However, biases are introduced in multiple steps of this approach, including non-representative DNA extraction and uneven taxonomic coverage of selected PCR primers, potentially giving a skewed view...... SPIN kit was selected and the mechanical lysis parameters optimised for extraction of genomic DNA from mesophilic and thermophilic anaerobic digester samples. Different primer sets were compared for targeting the archaea and bacteria, both together and individually . Shotgun sequencing...

  4. 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...

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

    Directory of Open Access Journals (Sweden)

    Rachel Peterson

    Full Text Available 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.

  6. Shotgun metagenomes and multiple primer pair-barcode combinations of amplicons reveal biases in metabarcoding analyses of fungi

    Directory of Open Access Journals (Sweden)

    Leho Tedersoo

    2015-05-01

    Full Text Available Rapid development of high-throughput (HTS molecular identification methods has revolutionized our knowledge about taxonomic diversity and ecology of fungi. However, PCR-based methods exhibit multiple technical shortcomings that may bias our understanding of the fungal kingdom. This study was initiated to quantify potential biases in fungal community ecology by comparing the relative performance of amplicon-free shotgun metagenomics and amplicons of nine primer pairs over seven nuclear ribosomal DNA (rDNA regions often used in metabarcoding analyses. The internal transcribed spacer (ITS barcodes ITS1 and ITS2 provided greater taxonomic and functional resolution and richness of operational taxonomic units (OTUs at the 97% similarity threshold compared to barcodes located within the ribosomal small subunit (SSU and large subunit (LSU genes. All barcode-primer pair combinations provided consistent results in ranking taxonomic richness and recovering the importance of floristic variables in driving fungal community composition in soils of Papua New Guinea. The choice of forward primer explained up to 2.0% of the variation in OTU-level analysis of the ITS1 and ITS2 barcode data sets. Across the whole data set, barcode-primer pair combination explained 37.6–38.1% of the variation, which surpassed any environmental signal. Overall, the metagenomics data set recovered a similar taxonomic overview, but resulted in much lower fungal rDNA sequencing depth, inability to infer OTUs, and high uncertainty in identification. We recommend the use of ITS2 or the whole ITS region for metabarcoding and we advocate careful choice of primer pairs in consideration of the relative proportion of fungal DNA and expected dominant groups.

  7. Short-read assembly of full-length 16S amplicons reveals bacterial diversity in subsurface sediments.

    Directory of Open Access Journals (Sweden)

    Christopher S Miller

    Full Text Available In microbial ecology, a fundamental question relates to how community diversity and composition change in response to perturbation. Most studies have had limited ability to deeply sample community structure (e.g. Sanger-sequenced 16S rRNA libraries, or have had limited taxonomic resolution (e.g. studies based on 16S rRNA hypervariable region sequencing. Here, we combine the higher taxonomic resolution of near-full-length 16S rRNA gene amplicons with the economics and sensitivity of short-read sequencing to assay the abundance and identity of organisms that represent as little as 0.01% of sediment bacterial communities. We used a new version of EMIRGE optimized for large data size to reconstruct near-full-length 16S rRNA genes from amplicons sheared and sequenced with Illumina technology. The approach allowed us to differentiate the community composition among samples acquired before perturbation, after acetate amendment shifted the predominant metabolism to iron reduction, and once sulfate reduction began. Results were highly reproducible across technical replicates, and identified specific taxa that responded to the perturbation. All samples contain very high alpha diversity and abundant organisms from phyla without cultivated representatives. Surprisingly, at the time points measured, there was no strong loss of evenness, despite the selective pressure of acetate amendment and change in the terminal electron accepting process. However, community membership was altered significantly. The method allows for sensitive, accurate profiling of the "long tail" of low abundance organisms that exist in many microbial communities, and can resolve population dynamics in response to environmental change.

  8. 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.

  9. Molecular identification of CTX-M and blaOXY/K1 β-lactamase genes in Enterobacteriaceae by sequencing of universal M13-sequence tagged PCR-amplicons

    Directory of Open Access Journals (Sweden)

    Tärnberg Maria

    2009-01-01

    Full Text Available Abstract Background Plasmid encoded blaCTX-M enzymes represent an important sub-group of class A β-lactamases causing the ESBL phenotype which is increasingly found in Enterobacteriaceae including Klebsiella spp. Molecular typing of clinical ESBL-isolates has become more and more important for prevention of the dissemination of ESBL-producers among nosocomial environment. Methods Multiple displacement amplified DNA derived from 20 K. pneumoniae and 34 K. oxytoca clinical isolates with an ESBL-phenotype was used in a universal CTX-M PCR amplification assay. Identification and differentiation of blaCTX-M and blaOXY/K1 sequences was obtained by DNA sequencing of M13-sequence-tagged CTX-M PCR-amplicons using a M13-specific sequencing primer. Results Nine out of 20 K. pneumoniae clinical isolates had a blaCTX-M genotype. Interestingly, we found that the universal degenerated primers also amplified the chromosomally located K1-gene in all 34 K. oxytoca clinical isolates. Molecular identification and differentiation between blaCTX-M and blaOXY/K1-genes could only been achieved by sequencing of the PCR-amplicons. In silico analysis revealed that the universal degenerated CTX-M primer-pair used here might also amplify the chromosomally located blaOXY and K1-genes in Klebsiella spp. and K1-like genes in other Enterobacteriaceae. Conclusion The PCR-based molecular typing method described here enables a rapid and reliable molecular identification of blaCTX-M, and blaOXY/K1-genes. The principles used in this study could also be applied to any situation in which antimicrobial resistance genes would need to be sequenced.

  10. 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.

  11. 75 FR 24510 - Drug and Drug-Related Supply Promotion by Pharmaceutical Company Sales Representatives at VA...

    Science.gov (United States)

    2010-05-05

    ...), regarding soliciting, vending, and debt collection on VA property, VA would allow promotion in VA medical... benefits (including potential economic, environmental, public health and safety, and other advantages.... Sponsorship includes any contribution, whether in the form of staple goods, personnel, or financing,...

  12. Homeless and nonhomeless VA service users likely eligible for Medicaid expansion

    Directory of Open Access Journals (Sweden)

    Jack Tsai, PhD

    2014-09-01

    Full Text Available Administrative data on the population of Department of Veterans Affairs (VA service users in 2010 under the age of 65 yr (n = 3,841,225 were analyzed to identify the number and characteristics of homeless and nonhomeless VA service users who are likely to be eligible for the Medicaid expansion (LEME option under the Affordable Care Act. Results showed that, estimating conservatively, about 1.2 million (21% current VA users are LEME if all states implement the expansion. Homeless service users were twice as likely to be eligible than nonhomeless users (64% vs 30%. VA service users who are LEME, regardless of housing status, were physically healthier than those not LEME but were more likely to have substance use disorders and posttraumatic stress disorder. These findings suggest that many VA service users are LEME, particularly those who are homeless and/or have mental health needs. Cross-system use of VA and Medicaid-funded services may be advantageous for veterans with extensive medical and psychiatric needs but also risks fragmented care. Information and education for VA clinicians and their patients about possible implications of the Affordable Care Act may be important.

  13. 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.

  14. Effects of inspired CO2, hyperventilation, and time on VA/Q inequality in the dog

    Science.gov (United States)

    Tsukimoto, K.; Arcos, J. P.; Schaffartzik, W.; Wagner, P. D.; West, J. B.

    1992-01-01

    In a recent study by Tsukimoto et al. (J. Appl. Physiol. 68: 2488-2493, 1990), CO2 inhalation appeared to reduce the size of the high ventilation-perfusion ratio (VA/Q) mode commonly observed in anesthetized mechanically air-ventilated dogs. In that study, large tidal volumes (VT) were used during CO2 inhalation to preserve normocapnia. To separate the influences of CO2 and high VT on the VA/Q distribution in the present study, we examined the effect of inspired CO2 on the high VA/Q mode using eight mechanically ventilated dogs (4 given CO2, 4 controls). The VA/Q distribution was measured first with normal VT and then with increased VT. In the CO2 group at high VT, data were collected before, during, and after CO2 inhalation. With normal VT, there was no difference in the size of the high VA/Q mode between groups [10.5 +/- 3.5% (SE) of ventilation in the CO2 group, 11.8 +/- 5.2% in the control group]. Unexpectedly, the size of the high VA/Q mode decreased similarly in both groups over time, independently of the inspired PCO2, at a rate similar to the fall in cardiac output over time. The reduction in the high VA/Q mode together with a simultaneous increase in alveolar dead space (estimated by the difference between inert gas dead space and Fowler dead space) suggests that poorly perfused high VA/Q areas became unperfused over time. A possible mechanism is that elevated alveolar pressure and decreased cardiac output eliminate blood flow from corner vessels in nondependent high VA/Q regions.

  15. Grad u postindustrijsko doba: važnija ekonomska obilježja suvremenog grada

    OpenAIRE

    Majetić, Filip

    2014-01-01

    Temeljni cilj ovog rada je sustavan prikaz važnijih obilježja grada u postindustrijsko doba1, tj. važnijih ekonomskih obilježja suvremenog grada. Kritičkim pregledom relevantne literature s područja sociologije i urbane geografije kao važnija obilježja grada u postindustrijsko doba izdvojeni su i raspravljeni sljedeći procesi: deindustrijalizacija, tercijarizacija, ekonomska polarizacija stanovništva, rast udjela kućnih proizvodnih pogona i „znojnica“, rast udjela neslužbene ekonomije, gentri...

  16. Coagulation factor Va binds to human umbilical vein endothelial cells and accelerates protein C activation.

    OpenAIRE

    Maruyama, I.; Salem, H H; Majerus, P W

    1984-01-01

    In vitro the rate of protein C activation by thrombin is significantly accelerated by two distinct cofactors (a) the endothelial cell surface protein, thrombomodulin, and (b) human coagulation Factor Va. We have recently reported that the activity of Factor Va is contained in the 78,000-D light chain. In this study we have investigated the effects of Factor Va and its light chain on the activation of protein C in the presence of cultured endothelial cells. Thrombin-catalyzed protein C activat...

  17. 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.

  18. 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.

  19. 78 FR 26250 - Payment for Home Health Services and Hospice Care to Non-VA Providers

    Science.gov (United States)

    2013-05-06

    ... rule that may result in expenditure by State, local, and tribal governments, in the aggregate, or by... November 21, 2011 (76 FR 71920), VA proposed to amend its regulations concerning the billing...

  20. 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...

  1. 77 FR 74279 - Agency Information Collection (VA/DOD Joint Disability Evaluation Board Claim): Activity under...

    Science.gov (United States)

    2012-12-13

    ... President Bush's Interagency Task Force on Returning Global War on Terror Heroes, VA and the Department of Defense (DOD) have agreed to develop a joint process in which Global War on Terror (GWOT) service...

  2. 77 FR 60746 - Proposed Information Collection (VA/DOD Joint Disability Evaluation Board Claim) Activity...

    Science.gov (United States)

    2012-10-04

    ... Interagency Task Force on Returning Global War on Terror Heroes, VA and the Department of Defense (DOD) have agreed to develop a joint process in which Global War on Terror (GWOT) service members are evaluated...

  3. 76 FR 582 - Elizabeth Hartwell Mason Neck National Wildlife Refuge, Fairfax County, VA, and Featherstone...

    Science.gov (United States)

    2011-01-05

    ... notice of intent to prepare a CCP in the Federal Register on May 18, 2007 (72 FR 28066). Mason Neck and..., Woodbridge, VA 22191-2716. FOR FURTHER INFORMATION CONTACT: Greg Weiler, Refuge Manager, Potomac River...

  4. 78 FR 34892 - Drawbridge Operation Regulation; Elizabeth River, Eastern Branch, Norfolk, VA

    Science.gov (United States)

    2013-06-11

    ..., VA. This deviation is necessary to facilitate thermite welding on rail joints on the Norfolk Southern... 33 CFR 117.5 to facilitate thermite welding on the rails. Under the regular operating schedule,...

  5. 77 FR 12647 - Fund Availability Under VA's Homeless Providers Grant and Per Diem Program

    Science.gov (United States)

    2012-03-01

    ... Department places special emphasis on addressing the needs of underserved populations, including homeless women veterans with or without the care of dependent children. 2. Funding Priority 2--VA is offering...

  6. 30 CFR 57.22240 - Actions at 2.0 percent methane (V-A mines).

    Science.gov (United States)

    2010-07-01

    ... 30 Mineral Resources 1 2010-07-01 2010-07-01 false Actions at 2.0 percent methane (V-A mines). 57... MINES Safety Standards for Methane in Metal and Nonmetal Mines Ventilation § 57.22240 Actions at 2.0 percent methane (V-A mines). If methane reaches 2.0 percent in the mine atmosphere, all persons other...

  7. VaR and Liquidity Risk.Impact on Market Behaviour and Measurement Issues.

    OpenAIRE

    Erzegovesi, Luca

    2002-01-01

    Current trends in international banking supervision following the 1996 Amendment to the Basel Accord emphasise market risk control based upon internal Value-at-risk (VaR) models. This paper discusses the merits and drawbacks of VaR models in the light of their impact on market liquidity. After a preliminary review of basic concepts and measures regarding market risk, market friction and liquidity risk, the arguments supporting the internal models approach to supervision on market risk are dis...

  8. 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)

  9. 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.

  10. 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/.

  11. 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.

  12. 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.

  13. 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.

  14. 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. PMID:26476551

  15. 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.

  16. 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.

  17. 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. PMID:27318568

  18. 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.

  19. 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.

  20. Fungi Sailing the Arctic Ocean: Speciose Communities in North Atlantic Driftwood as Revealed by High-Throughput Amplicon Sequencing.

    Science.gov (United States)

    Rämä, Teppo; Davey, Marie L; Nordén, Jenni; Halvorsen, Rune; Blaalid, Rakel; Mathiassen, Geir H; Alsos, Inger G; Kauserud, Håvard

    2016-08-01

    High amounts of driftwood sail across the oceans and provide habitat for organisms tolerating the rough and saline environment. Fungi have adapted to the extremely cold and saline conditions which driftwood faces in the high north. For the first time, we applied high-throughput sequencing to fungi residing in driftwood to reveal their taxonomic richness, community composition, and ecology in the North Atlantic. Using pyrosequencing of ITS2 amplicons obtained from 49 marine logs, we found 807 fungal operational taxonomic units (OTUs) based on clustering at 97 % sequence similarity cut-off level. The phylum Ascomycota comprised 74 % of the OTUs and 20 % belonged to Basidiomycota. The richness of basidiomycetes decreased with prolonged submersion in the sea, supporting the general view of ascomycetes being more extremotolerant. However, more than one fourth of the fungal OTUs remained unassigned to any fungal class, emphasising the need for better DNA reference data from the marine habitat. Different fungal communities were detected in coniferous and deciduous logs. Our results highlight that driftwood hosts a considerably higher fungal diversity than currently known. The driftwood fungal community is not a terrestrial relic but a speciose assemblage of fungi adapted to the stressful marine environment and different kinds of wooden substrates found in it. PMID:27147245

  1. 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...

  2. 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.

  3. 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.

  4. 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

  5. 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.

  6. 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. PMID:26976467

  7. 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.

  8. Absence of platelet phenotype in mice lacking the motor protein myosin Va.

    Directory of Open Access Journals (Sweden)

    Matthew T Harper

    Full Text Available BACKGROUND: The motor protein myosin Va plays an important role in the trafficking of intracellular vesicles. Mutation of the Myo5a gene causes Griscelli syndrome type 1 in humans and the dilute phenotype in mice, which are both characterised by pigment dilution and neurological defects as a result of impaired vesicle transport in melanocytes and neuroendocrine cells. The role of myosin Va in platelets is currently unknown. Rab27 has been shown to be associated with myosin Va cargo vesicles and is known to be important in platelet dense granule biogenesis and secretion, a crucial event in thrombus formation. Therefore, we hypothesised that myosin Va may regulate granule secretion or formation in platelets. METHODOLOGY/PRINCIPAL FINDINGS: Platelet function was studied in vitro using a novel Myo5a gene deletion mouse model. Myo5a(-/- platelets were devoid of myosin Va, as determined by immunoblotting, and exhibited normal expression of surface markers. We assessed dense granule, α-granule and lysosomal secretion, integrin α(IIbβ(3 activation, Ca(2+ signalling, and spreading on fibrinogen in response to collagen-related peptide or the PAR4 agonist, AYPGKF in washed mouse platelets lacking myosin Va or wild-type platelets. Surprisingly, Myo5a(-/- platelets showed no significant functional defects in these responses, or in the numbers of dense and α-granules expressed. CONCLUSION: Despite the importance of myosin Va in vesicle transport in other cells, our data demonstrate this motor protein has no non-redundant role in the secretion of dense and α-granules or other functional responses in platelets.

  9. Very high resolution single pass HLA genotyping using amplicon sequencing on the 454 next generation DNA sequencers: Comparison with Sanger sequencing.

    Science.gov (United States)

    Yamamoto, F; Höglund, B; Fernandez-Vina, M; Tyan, D; Rastrou, M; Williams, T; Moonsamy, P; Goodridge, D; Anderson, M; Erlich, H A; Holcomb, C L

    2015-12-01

    Compared to Sanger sequencing, next-generation sequencing offers advantages for high resolution HLA genotyping including increased throughput, lower cost, and reduced genotype ambiguity. Here we describe an enhancement of the Roche 454 GS GType HLA genotyping assay to provide very high resolution (VHR) typing, by the addition of 8 primer pairs to the original 14, to genotype 11 HLA loci. These additional amplicons help resolve common and well-documented alleles and exclude commonly found null alleles in genotype ambiguity strings. Simplification of workflow to reduce the initial preparation effort using early pooling of amplicons or the Fluidigm Access Array™ is also described. Performance of the VHR assay was evaluated on 28 well characterized cell lines using Conexio Assign MPS software which uses genomic, rather than cDNA, reference sequence. Concordance was 98.4%; 1.6% had no genotype assignment. Of concordant calls, 53% were unambiguous. To further assess the assay, 59 clinical samples were genotyped and results compared to unambiguous allele assignments obtained by prior sequence-based typing supplemented with SSO and/or SSP. Concordance was 98.7% with 58.2% as unambiguous calls; 1.3% could not be assigned. Our results show that the amplicon-based VHR assay is robust and can replace current Sanger methodology. Together with software enhancements, it has the potential to provide even higher resolution HLA typing. PMID:26037172

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

    Directory of Open Access Journals (Sweden)

    Franck Curk

    Full Text Available 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

  11. 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

  12. 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.

  13. 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.  

  14. 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

  15. 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.

  16. 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. PMID:27033205

  17. 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

  18. 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

  19. Improving Memory Subsystem Performance Using ViVA: Virtual Vector Architecture

    Energy Technology Data Exchange (ETDEWEB)

    Gebis, Joseph; Oliker, Leonid; Shalf, John; Williams, Samuel; Yelick, Katherine

    2009-01-12

    The disparity between microprocessor clock frequencies and memory latency is a primary reason why many demanding applications run well below peak achievable performance. Software controlled scratchpad memories, such as the Cell local store, attempt to ameliorate this discrepancy by enabling precise control over memory movement; however, scratchpad technology confronts the programmer and compiler with an unfamiliar and difficult programming model. In this work, we present the Virtual Vector Architecture (ViVA), which combines the memory semantics of vector computers with a software-controlled scratchpad memory in order to provide a more effective and practical approach to latency hiding. ViVA requires minimal changes to the core design and could thus be easily integrated with conventional processor cores. To validate our approach, we implemented ViVA on the Mambo cycle-accurate full system simulator, which was carefully calibrated to match the performance on our underlying PowerPC Apple G5 architecture. Results show that ViVA is able to deliver significant performance benefits over scalar techniques for a variety of memory access patterns as well as two important memory-bound compact kernels, corner turn and sparse matrix-vector multiplication -- achieving 2x-13x improvement compared the scalar version. Overall, our preliminary ViVA exploration points to a promising approach for improving application performance on leading microprocessors with minimal design and complexity costs, in a power efficient manner.

  20. 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 …

  1. Continuous-energy version of KENO V.a for criticality safety applications

    International Nuclear Information System (INIS)

    KENO V.a is a multigroup Monte Carlo code that solves the Boltzmann transport equation and is used extensively in the criticality safety community to calculate the effective multiplication factor of systems with fissionable material. In this work, a continuous-energy or pointwise version of KENO V.a has been developed by first designing a new continuous-energy cross-section format and then by developing the appropriate Monte Carlo transport procedures to sample the new cross-section format. In order to generate pointwise cross sections for a test library, a series of cross-section processing modules were developed and used to process 50 ENDF/B-6 Release 7 nuclides for the test library. Once the cross-section processing procedures were in place, a continuous-energy version of KENO V.a was developed and tested by calculating 21 critical benchmark experiments. The point KENO-calculated results for the 21 benchmarks are in agreement with calculated results obtained with the multigroup version of KENO V.a using the 238-group ENDF/B-5 and 199-group ENDF/B-6 Release 3 libraries. Based on the calculated results with the prototypic cross-section library, a continuous-energy version of the KENO V.a code has been successfully developed and demonstrated for modeling systems with fissionable material. (author)

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

    OpenAIRE

    Christina Salmivalli; Elisa Poskiparta

    2012-01-01

    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 l...

  3. HS300指数收益波动性及VaR度量研究

    Institute of Scientific and Technical Information of China (English)

    姜全; 刘孟

    2008-01-01

    本文分别运用EGARCH和ComisH-Fisher扩展的VaR模型对中国股票市场(以沪深300指教作为代表)的期望收益率以及市场风险进行实证比较研究,发现结合条件异方差的Comish-Fish-er扩展的VaR模型与仅用波动率描述的VaR计量方法比较具有较好的修正作用.同时对中国股市波动的成因进行初步的探讨,并提出一些建议.

  4. 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......-less viruses replicated with higher efficiency in Ras-mutant cells, as compared to cell lines without Ras mutation. However, several exceptions to this rule were observed, arguing against a direct inhibition of PKR by mutant Ras. Phosphorylation of the PKR-substrate eIF2alpha was observed regardless of the Ras...

  5. Computing Conditional VaR using Time-varying CopulasComputing Conditional VaR using Time-varying Copulas

    Directory of Open Access Journals (Sweden)

    Beatriz Vaz de Melo Mendes

    2005-12-01

    Full Text Available It is now widespread the use of Value-at-Risk (VaR as a canonical measure at risk. Most accurate VaR measures make use of some volatility model such as GARCH-type models. However, the pattern of volatility dynamic of a portfolio follows from the (univariate behavior of the risk assets, as well as from the type and strength of the associations among them. Moreover, the dependence structure among the components may change conditionally t past observations. Some papers have attempted to model this characteristic by assuming a multivariate GARCH model, or by considering the conditional correlation coefficient, or by incorporating some possibility for switches in regimes. In this paper we address this problem using time-varying copulas. Our modeling strategy allows for the margins to follow some FIGARCH type model while the copula dependence structure changes over time.

  6. 基于EVT-BM-FIGARCH的动态VaR风险测度%Dynamic VaR Risk Measures Based on EVT-BM-FIGARCH

    Institute of Scientific and Technical Information of China (English)

    肖智; 傅肖肖; 钟波

    2008-01-01

    对金融资产回报,用FIGARCH模型捕捉波动的异方差性和长期记忆性的同时,将回报序列转化为标准残差序列、通过用EVT-BM方法拟合标准残差的尾部分布来处理回报序列的厚尾性,建立了金融风险度量模型--基于EVT-BM-FIGARCH的动态VaR模型.并用该模型对上证综合指数进行实证分析,结果表明模型能够更精确、合理地度量上证综合指数回报的VaR风险.

  7. 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.

  8. 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.

  9. KiVa Koulu -oppituntien vaikutus neljäsluokkalaisten vertaissuhteisiin koulussa

    OpenAIRE

    Kähönen, Loviisa

    2015-01-01

    TIIVISTELMÄ Kähönen, Loviisa. KiVa Koulu -oppituntien vaikutus neljäsluokkalaisten vertaissuhteisiin koulussa. Diak Helsinki, kevät 2015, 77 s., 4 liitettä. Diakonia-ammattikorkeakoulu, Sosiaalialan koulutusohjelma, sosionomi (AMK). Opinnäytetyössä tutkittiin KiVa Koulu -toimenpideohjelmaan kuuluvien kiusaamisen vastaisten oppituntien vaikutusta erään helsinkiläisen ala-asteen koulun neljäsluokkalaisten vertaissuhteisiin. Työn keskiössä olivat luokan ryhmärakenteen, luokkalaisten v...

  10. Comparison of Friction Characteristics on TN and VA Mode Alignment Films with Friction Force Microscopy

    Science.gov (United States)

    Kwak, Musun; Chung, Hanrok; Kwon, Hyukmin; Kim, Jehyun; Han, Daekyung; Yi, Yoonseon; Lee, Sangmun; Lee, Chulgu; Cha, Sooyoul

    Using frictional force microscopy (FFM), the friction surface characteristics were compared between twisted nematic (TN) mode and vertical alignment (VA) mode alignment films (AFs). The friction asymmetry was detected depending on temperature conditions on TN mode AF, but not on VA mode AF. The difference between two modes was explained by leaning intermolecular repulsion caused by the pre-tilt angle uniformity and the density of side chain. No level difference according to temperature conditions appeared when the pre-tilt angle were measured after liquid crystal (LC) injection.

  11. 33 CFR 165.501 - Chesapeake Bay entrance and Hampton Roads, VA and adjacent waters-Regulated Navigation Area.

    Science.gov (United States)

    2010-07-01

    ... Hampton Roads, VA and adjacent waters-Regulated Navigation Area. 165.501 Section 165.501 Navigation and... Areas Fifth Coast Guard District § 165.501 Chesapeake Bay entrance and Hampton Roads, VA and adjacent... Sector Hampton Roads. Designated representative of the Captain of the Port means a person, including...

  12. 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 ...

  13. 75 FR 32240 - Draft Tier II Environmental Impact Statement: Southeast High Speed Rail Corridor-Richmond, VA...

    Science.gov (United States)

    2010-06-07

    ... Federal Railroad Administration Draft Tier II Environmental Impact Statement: Southeast High Speed Rail... Draft Environmental Impact Statement and public hearings for the Southeast High Speed Rail, Richmond, VA... availability of the Southeast High Speed Rail, Richmond, VA to Raleigh, NC Project Draft Tier II...

  14. 75 FR 51331 - Draft Tier II Environmental Impact Statement: Southeast High Speed Rail Corridor-Richmond, VA...

    Science.gov (United States)

    2010-08-19

    ... Federal Railroad Administration Draft Tier II Environmental Impact Statement: Southeast High Speed Rail... the Tier II Draft Environmental Impact Statement for the Southeast High Speed Rail, Richmond, VA to... the Draft Tier II Environmental Impact Statement for the Southeast High Speed Rail, Richmond, VA...

  15. Gastrointestinal Bacterial and Methanogenic Archaea Diversity Dynamics Associated with Condensed Tannin-Containing Pine Bark Diet in Goats Using 16S rDNA Amplicon Pyrosequencing

    OpenAIRE

    Min, Byeng R.; Sandra Solaiman; Raymon Shange; Jong-Su Eun

    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 elucida...

  16. 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:...

  17. 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

  18. 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

  19. 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.

  20. 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.

  1. 77 FR 61721 - Atlantic Ocean off Wallops Island and Chincoteague Inlet, VA; Danger Zone

    Science.gov (United States)

    2012-10-11

    ... below. The proposed rule was published in the October 11, 2011, issue of the Federal Register (76 FR... Inlet, VA; Danger Zone AGENCY: U.S. Army Corps of Engineers, Department of Defense. ACTION: Final rule. ] SUMMARY: The U.S. Army Corps of Engineers (Corps) is amending an existing permanent danger zone in...

  2. 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...

  3. 77 FR 12697 - VA Homeless Providers Grant and Per Diem Program

    Science.gov (United States)

    2012-03-01

    ... unexpected problems. Therefore, we are returning to this former definition because it is standard for the... applicant takes measures to protect the capital securing VA's grant investment. We would remove the... supportive housing, health care, and social services programs, have more successful outcomes. We...

  4. 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...

  5. 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...

  6. 76 FR 3017 - VA Veteran-Owned Small Business Verification Guidelines

    Science.gov (United States)

    2011-01-19

    ... that single business participation restricts business growth and limits participation in global markets... AFFAIRS 38 CFR Part 74 RIN 2900-AM78 VA Veteran-Owned Small Business Verification Guidelines AGENCY... verify ownership and control of veteran-owned small businesses, including service- disabled...

  7. 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.

  8. 75 FR 30782 - Reorganization/Expansion of Foreign-Trade Zone 20; Hampton Roads, VA, Area

    Science.gov (United States)

    2010-06-02

    ... inviting public comment was given in the Federal Register (74 FR 20927, 5/6/09) and the application has... Foreign-Trade Zones Board Reorganization/Expansion of Foreign-Trade Zone 20; Hampton Roads, VA, Area..., and to add six new sites (proposed Sites 19- 24) in the Hampton Roads, Virginia, area within...

  9. 77 FR 19957 - OPSAIL 2012 Virginia, Port of Hampton Roads, VA

    Science.gov (United States)

    2012-04-03

    ... Federal Register (73 FR 3316). Public Meeting We do not now plan to hold a public meeting. But you may... Virginia, Port of Hampton Roads, VA AGENCY: Coast Guard, DHS. ACTION: Notice of proposed rulemaking. SUMMARY: The Coast Guard proposes establishing temporary regulations in the Port of Hampton...

  10. Possible deviations from (V-A) charged currents: precise measurement of muon decay parameters

    International Nuclear Information System (INIS)

    This short review examines the experimental limits on possible deviations from (V-A) charged weak currents, as would occur at some mass scale, for example, in manifestly left-right-symmetric electro-weak theories. Both present and anticipated limits are considered, emphasizing muon-decay experiments but including other experimental input where convenient

  11. The Effect of Increased Travel Reimbursement Rates on Health Care Utilization in the VA

    Science.gov (United States)

    Nelson, Richard E.; Hicken, Bret; West, Alan; Rupper, Randall

    2012-01-01

    Purpose: The reimbursement rate that eligible veterans receive for travel to Department of Veterans Affairs (VA) facilities increased from 11 to 28.5 cents per mile on February 1, 2008. We examined the effect of this policy change on utilization of outpatient, inpatient, and pharmacy services, stratifying veterans based on distance from a VA…

  12. Implementing the KiVa Antibullying Program: Recognition of Stable Victims

    Science.gov (United States)

    Haataja, Anne; Sainio, Miia; Turtonen, Mira; Salmivalli, Christina

    2016-01-01

    Teachers do not always recognise students who are victimised by their peers. In this study, we examined the recognition of stable victims in 76 schools beginning to implement the KiVa antibullying programme. We focused on 348 victims (9-15 years) who reported victimisation at the pretest and still at wave 2, after five months of programme…

  13. 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...

  14. 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...

  15. 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...

  16. 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...

  17. 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.

  18. 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 VETERANS AFFAIRS (CONTINUED) VETERANS SMALL BUSINESS REGULATIONS Records Management § 74.26 What types...

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

    CERN Document Server

    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).

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

    CERN Document Server

    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).

  1. 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......

  2. 78 FR 51067 - VA Health Professional Scholarship and Visual Impairment and Orientation and Mobility...

    Science.gov (United States)

    2013-08-20

    ... additional regulations necessary to implement the new VIOMPSP. This will eliminate redundancies between the... Federal Register on December 26, 2012 (77 FR 75918), VA proposed to amend part 17 of 38 CFR by amending... economy, a sector of the economy, productivity, competition, jobs, the environment, public health...

  3. 78 FR 60379 - Proposed Information Collection (Credit Underwriting Standards and Procedures for Processing VA...

    Science.gov (United States)

    2013-10-01

    ... specific information concerning a Veteran's credit history in order to properly underwrite the veteran's loan. VA loans may not be guaranteed unless the Veteran is a satisfactory credit risk. The data... AFFAIRS Proposed Information Collection (Credit Underwriting Standards and Procedures for Processing...

  4. 75 FR 60171 - Proposed Information Collection (Credit Underwriting Standards and Procedures for Processing VA...

    Science.gov (United States)

    2010-09-29

    ... specific information concerning a veteran's credit history in order to properly underwrite the veteran's loan. VA loans may not be guaranteed unless the veteran is a satisfactory credit risk. The data... AFFAIRS Proposed Information Collection (Credit Underwriting Standards and Procedures for Processing...

  5. 75 FR 76082 - Agency Information Collection (Credit Underwriting Standards and Procedures for Processing VA...

    Science.gov (United States)

    2010-12-07

    ... a veteran's credit history in order to properly underwrite the veteran's loan. VA loans may not be guaranteed unless the veteran is a satisfactory credit risk. The data collected on the following forms are... AFFAIRS Agency Information Collection (Credit Underwriting Standards and Procedures for Processing...

  6. 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... income, but only so long as such veteran's annual income does not exceed the maximum annual...

  7. For Children Only? Effects of the KiVa Antibullying Program on Teachers

    Science.gov (United States)

    Ahtola, Annarilla; Haataja, Anne; Karna, Antti; Poskiparta, Elisa; Salmivalli, Christina

    2012-01-01

    The effects of an antibullying program, KiVa, on Grade 1-3 teachers' perceptions of bullying were investigated. Data were gathered from 128 teachers in 33 intervention schools and 110 teachers in 29 control schools. Two-level regression models showed that, at the end of the intervention year, self-evaluated competence to tackle bullying was at a…

  8. A Large-Scale Evaluation of the KiVa Antibullying Program: Grades 4-6

    Science.gov (United States)

    Karna, 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…

  9. 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

  10. 75 FR 61417 - South River Watershed Dam No. 10A, Augusta County, VA

    Science.gov (United States)

    2010-10-05

    ... Natural Resources Conservation Service South River Watershed Dam No. 10A, Augusta County, VA AGENCY... not being prepared for the rehabilitation of South River Watershed Dam No. 10A, Augusta County... Register. [This activity is listed in the Catalog of Federal Domestic Assistance under 10.904,...

  11. Study of cancer cell lines with Fourier transform infrared (FTIR)/vibrational absorption (VA) spectroscopy

    DEFF Research Database (Denmark)

    Uceda Otero, E. P.; Eliel, G. S. N.; Fonseca, E. J. S.;

    2013-01-01

    In this work we have used Fourier transform infrared (FTIR) / vibrational absorption (VA) spectroscopy to study two cancer cell lines: the Henrietta Lacks (HeLa) human cervix carcinoma and 5637 human bladder carcinoma cell lines. Our goal is to experimentally investigate biochemical changes and d...

  12. 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....

  13. 77 FR 6587 - Startek USA, Inc. Alexandria, LA; Startek USA, Inc., Collinsville, VA; Amended Certification...

    Science.gov (United States)

    2012-02-08

    ... published in the Federal Register on February 10, 2011 (76 FR 7587). On its own motion, the Department... 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...

  14. 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...

  15. 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

  16. Scholar and teacher: V.A. Kitaev at the history department of Volgograd State University

    Directory of Open Access Journals (Sweden)

    Kuznetsov Oleg Viktorovich

    2013-11-01

    Full Text Available Vladimir A. Kitaev was born 1941. He was the first dean of the Faculty of History and the first head of the Department of History of the USSR (now the Department of History of Russia of Volgograd State University, reputable scientist, recognized expert in the history of the Russian social thought. The article shows the role of V.A. Kitaev in the formation and development of the faculty and the department. A characteristic of V.A. Kitaev’ sresearch and teaching activities is given. Kitaev’s featuresas a scholar and teacher such as great erudition, science scrupulosity, exactingness to himself andto his disciples, are marked. V.A. Kitaev worked at Volgograd State University for 16 years. All the while, he headed the Department andwas the dean for the first four years. The main thing is what he wanted in those positions – along with their colleagues was to lay and develop the traditions of the classical university, university atmosphere of the faculty and the university. The major scientific issues that are developed by V.A. Kitaev were: the history of liberalism and the fate of liberal reforms (modernization in Russia, the history of the Russian conservative thought, the problem of revolutionary violence as an inevitable result of the practical realization of socialist ideas. As an advocate of “establishing full-fledged liberal order”, V.A. Kitaev had, in essence, to ascertain: in Russia XIX – early XX century did not yet develop the historical conditions for the triumph of liberal ideas. The weakness and indecision of Russian liberals and their fear of the revolutionary movement, the constant fluctuation between the reform and reaction did not allow them to become independent of the political force that would determine the fate of the country in the end.

  17. 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.

  18. 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.

  19. 3D digitalizacija in vizualizacija situle z Vač: 3D digitisation and visualisation of the Vače situla:

    OpenAIRE

    Vidmar, Gregor

    2012-01-01

    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 3D 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, ...

  20. 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.

  1. 76 FR 44087 - Agency Information Collection (Supplement to VA Forms 21-526, 21-534, and 21-535 (For Philippine...

    Science.gov (United States)

    2011-07-22

    ... collection of information through http://www.Regulations.gov or to VA's OMB Desk Officer, OMB Human Resources..., NW., Washington, DC 20420, (202) 461-7485, fax (202) 461-0966 or e-mail denise.mclamb@va.gov . Please... AFFAIRS Agency Information Collection (Supplement to VA Forms 21-526, 21- 534, and 21-535 (For...

  2. 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.

  3. Dynamic VaR Risk Measures Based on EVT-POT-FIGARCH%基于EVT-POT-FIGARCH的动态VaR风险测度

    Institute of Scientific and Technical Information of China (English)

    肖智; 傅肖肖; 钟波

    2008-01-01

    金融实践中,金融资产回报不仅具有厚尾性、波动的异方差性两大特点,而且其波动表现出明显的长期记忆性.本文利用FIGARCH模型处理波动异方差性和长期记忆性、EVT-POT方法捕捉回报分布厚尾的优势,提出了能反映厚尾性、异方差性和长期记忆性的金融风险度量模型--基于EVT-POT-FIGARCH的动态VaR模型,并用中国股票市场的沪深300指数和上证综合指数的每日收盘价进行实证分析.结果表明,模型能较好地处理这两个指数回报序列的三大特点,更准确地度量其VaR风险.

  4. Effects of VA mycorrhizas fungus on phosphorus and potassium uptake in tea seedlings

    International Nuclear Information System (INIS)

    Tea (Camellia sinensis) seeds were sown on sterilized acidic yellow soil (pH 5.6) in a pot experiment and treated as follows: 1) inoculated with VA mycorrhizas fungus (Glomus citricolum), 2) nonmycorrhizal as control, top dressed with 32P-single superphosphate (M-32P) and 86Rb-rubidium chloride (M-86Rb). The results showed that the percentage of VA mycorrhizas infection was 52.6% for M-32P and 56.7% for M-86Rb. Plant height, dry weight and the uptake of phosphorus and potassium were 2.1 and 1.8 times, 2.4 and 2.5 times, 5.6 and 4.1 times as that of control respectively. The utilization rate of phosphorus and potassium were raised by 14.10% and 17.13% respectively

  5. Development of a 3 MJ/750 kVA SMES system

    Energy Technology Data Exchange (ETDEWEB)

    Hae-Jong Kim; Ki-Chul Seong; Jeon-Wook Cho [Korea Electrotechnology Research Institute, Changwon (KR). Applied Superconductivity Group] (and others)

    2006-05-15

    Research and development on superconducting magnetic energy storage (SMES) system have been carried out to realize efficient electric power management for several decades. Korea Electrotechnology Research Institute (KERI) has developed a 3 MJ/750 kVA SMES system to improve power quality in sensitive electric loads. It consists of an IGBT based power converter, NbTi mixed matrix Rutherford cable superconducting magnet and a cryostat with HTS current leads. A computer code was developed to find the parameters of the SMES magnet which used minimum amount of superconductors for the same energy storage capability, and the 3 MJ SMES magnet was designed based upon that. This paper describes the fabrication and experimental results of the 3 MJ/750 kVA SMES system. (author)

  6. Evaluation of an implementation model: a national investigation of VA residential programs.

    Science.gov (United States)

    Cook, Joan M; Dinnen, Stephanie; Coyne, James C; Thompson, Richard; Simiola, Vanessa; Ruzek, Josef; Schnurr, Paula P

    2015-03-01

    This national investigation utilizes qualitative data to evaluate an implementation model regarding factors influencing provider use of two evidence-based treatments for posttraumatic stress disorder (PTSD). Semi-structured qualitative interviews with 198 mental health providers from 38 Department of Veterans Affairs' (VA) residential treatment programs were used to explore these issues regarding prolonged exposure (PE) and cognitive processing therapy (CPT) in VA residential PTSD programs. Several unique and some overlapping predictors emerged. Leadership was viewed as an influence on implementation for both CPT and PE, while a lack of dedicated time and resources was viewed as a deterrent for both. Compatibility of CPT with providers' existing practices and beliefs, the ability to observe noticeable patient improvement, a perceived relative advantage of CPT over alternative treatments, and the presence of a supportive peer network emerged as influential on CPT implementation. Leadership was associated with PE implementation. Implications for the design and improvement of training and implementation efforts are discussed. PMID:24817625

  7. KENO3D Visualization Tool for KENO V.a and KENO-VI Geometry Models

    Energy Technology Data Exchange (ETDEWEB)

    Horwedel, J.E.; Bowman, S.M.

    2000-06-01

    Criticality safety analyses often require detailed modeling of complex geometries. Effective visualization tools can enhance checking the accuracy of these models. This report describes the KENO3D visualization tool developed at the Oak Ridge National Laboratory (ORNL) to provide visualization of KENO V.a and KENO-VI criticality safety models. The development of KENO3D is part of the current efforts to enhance the SCALE (Standardized Computer Analyses for Licensing Evaluations) computer software system.

  8. Ranking of VaR and ES Models: Performance in developed and emerging markets

    OpenAIRE

    Zikovic, Sasa; Filer, Randall

    2012-01-01

    An inherent problem with comparing and ranking competing Value at Risk (VaR) and Expected shortfall (ES) models is that they measure only a single realization of the underlying data generation process. The question is whether there is any significant statistical difference in the performance of different models. Is it only a matter of chance that in a particular market and in particular time period a certain model performs better than some other? It all comes down to a question whether someth...

  9. The hypothalamic photoreceptors regulating seasonal reproduction in birds: A prime role for VA opsin.

    OpenAIRE

    Garcia-Fernandez, JM; Cernuda-Cernuda, R.; Davies, WL; Rodgers, J.; Turton, M.; Peirson, SN; Follett, BK; Halford, S; Hughes, S.; Hankins, MW; Foster, RG

    2015-01-01

    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 ∼492nm. 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 use...

  10. 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.

  11. 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.

  12. 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.

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

    Science.gov (United States)

    Karna, Antti; Voeten, Marinus; Little, Todd D.; Alanen, Erkki; Poskiparta, Elisa; Salmivalli, Christina

    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 that were randomly assigned to intervention and…

  14. C4b-binding protein protects coagulation factor Va from inactivation by activated protein C

    NARCIS (Netherlands)

    van de Poel, RHL; Meijers, JCM; Rosing, J; Tans, G; Bouma, Bonno N.

    2000-01-01

    We investigated the effect of C4BP on APC-mediated inactivation of factor Va (FVa) in the absence and presence of protein S. FVa inactivation was biphasic (k(506) = 4.4 x 10(8) M-1 s(-1), k(306) = 2.7 x 10(7) M-1 s(-1)), and protein S accelerated Arg(306) cleavage approximately 10-fold. Preincubatio

  15. VA-Index: Quantifying Assortativity Patterns in Networks with Multidimensional Nodal Attributes.

    Directory of Open Access Journals (Sweden)

    Konstantinos Pelechrinis

    Full Text Available Network connections have been shown to be correlated with structural or external attributes of the network vertices in a variety of cases. Given the prevalence of this phenomenon network scientists have developed metrics to quantify its extent. In particular, the assortativity coefficient is used to capture the level of correlation between a single-dimensional attribute (categorical or scalar of the network nodes and the observed connections, i.e., the edges. Nevertheless, in many cases a multi-dimensional, i.e., vector feature of the nodes is of interest. Similar attributes can describe complex behavioral patterns (e.g., mobility of the network entities. To date little attention has been given to this setting and there has not been a general and formal treatment of this problem. In this study we develop a metric, the vector assortativity index (VA-index for short, based on network randomization and (empirical statistical hypothesis testing that is able to quantify the assortativity patterns of a network with respect to a vector attribute. Our extensive experimental results on synthetic network data show that the VA-index outperforms a baseline extension of the assortativity coefficient, which has been used in the literature to cope with similar cases. Furthermore, the VA-index can be calibrated (in terms of parameters fairly easy, while its benefits increase with the (co-variance of the vector elements, where the baseline systematically over(underestimate the true mixing patterns of the network.

  16. VA-Index: Quantifying Assortativity Patterns in Networks with Multidimensional Nodal Attributes.

    Science.gov (United States)

    Pelechrinis, Konstantinos; Wei, Dong

    2016-01-01

    Network connections have been shown to be correlated with structural or external attributes of the network vertices in a variety of cases. Given the prevalence of this phenomenon network scientists have developed metrics to quantify its extent. In particular, the assortativity coefficient is used to capture the level of correlation between a single-dimensional attribute (categorical or scalar) of the network nodes and the observed connections, i.e., the edges. Nevertheless, in many cases a multi-dimensional, i.e., vector feature of the nodes is of interest. Similar attributes can describe complex behavioral patterns (e.g., mobility) of the network entities. To date little attention has been given to this setting and there has not been a general and formal treatment of this problem. In this study we develop a metric, the vector assortativity index (VA-index for short), based on network randomization and (empirical) statistical hypothesis testing that is able to quantify the assortativity patterns of a network with respect to a vector attribute. Our extensive experimental results on synthetic network data show that the VA-index outperforms a baseline extension of the assortativity coefficient, which has been used in the literature to cope with similar cases. Furthermore, the VA-index can be calibrated (in terms of parameters) fairly easy, while its benefits increase with the (co-)variance of the vector elements, where the baseline systematically over(under)estimate the true mixing patterns of the network. PMID:26816262

  17. 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.

  18. 银行系统性风险度量——基于动态CoVaR方法的分析%Banking Systemic Risk Based on Dynamic CoVaR Estimation

    Institute of Scientific and Technical Information of China (English)

    高国华; 潘英丽

    2011-01-01

    以测量金融机构溢出风险的条件CoVaR模型为基础,应用股价数据对我国14家上市商业银行的系统性风险贡献度及其影响因素进行测算分析.实证结果表明:银行系统性风险贡献度与其自身VaR之间并无显著线性关系,对我国银行体系而言,系统重要性银行主要是四大国有银行,尤其以建设银行、中国银行和工商银行的系统性影响最为显著,其他股份制银行的风险溢出和传染效应远小于这3家银行;银行的溢出风险ΔCoVaR、自身风险VaR水平、不良贷款率以及宏观经济波动对于预测银行系统性风险的边际贡献具有显著影响.%This paper estimated banking systemic risk based on CoVaR measure discussed by Adrian and Brunnermeier(2009).Our conclusions are: ① banking systemic risk has no linear relationship with its VaR.In China the four state-owned banks have most systemic risk.② CoVaR,VaR and non-performing loans ratio are significant to predict future marginal systemic risk of banks.

  19. 基于t Copula的中国股市指数组合VaR估计及其评价%Estimate and Evaluation on VaR of China Stock Indices Portfolio Based on t Copula

    Institute of Scientific and Technical Information of China (English)

    李宝良

    2012-01-01

    The assumption of traditional joint normal distribution can not describe tail dependence condition of finance market,which cause low estimation on VaR.This paper uses t Copula to overcome this problem and to test 95 percent and 99 percent of VaR of equal weight investment portfolio of the composition of Shanghai stock indices and Shenzhen stock indices and the results show that the performance of VaR based on t Copula Model is better than traditional variance-covariance analysis method,historic simulation method,Monte Carlo simulation method and estimation method of correlative coefficient model based on dynamic condition%传统的联合正态分布假设无法刻画金融市场尾部相依情况,导致投资组合VaR的低估。采用tCopula克服了这一问题;并对上证指数和深证指数构成的等权重投资组合的95%和99%VaR进行了验证;结果表明,基于t Copula模型的VaR表现要优于传统的方差-协方差分析法、历史模拟法和蒙特卡罗模拟法以及基于动态条件相关系数模型的估计方法。

  20. 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.

  1. A new amplicon based approach of whole mitogenome sequencing for phylogenetic and phylogeographic analysis: An example of East African white-eyes (Aves, Zosteropidae).

    Science.gov (United States)

    Meimberg, Harald; Schachtler, Christina; Curto, Manuel; Husemann, Martin; Habel, Jan Christian

    2016-09-01

    Classical Sanger sequencing is still frequently used to generate sequence data for phylogenetic and phylogeographic inference. In this contribution we present a novel approach to genotype whole mitogenomic haplotypes using Illumina MiSeq reads from indexed amplicons. Our new approach reduces preparation time by multiplexing loci within a single or few PCR reactions and by plate format library construction. The use of paired-end reads allows covering amplicons of about 0.5kb and thus no nebulisation and assembly are necessary. We tested the power and effectiveness of this technique by analysing the mitogenomic diversity of East African white-eye bird species (Zosteropidae), a taxonomically highly diverse and complex species flock found in various ecosystems spread across major parts of Africa. We compare the newly generated mitogenomic data set with published data of three mitochondrial genes for a similar set of populations and taxa. The comparison demonstrates that our new procedure represents a cost effective use of NGS for medium throughput phylogenetic analyses. Using this method, we were able to increase the amount of phylogenetic information significantly, while reducing the costs and effort in the laboratory. The mitogenomic data show a higher resolution than previous studies providing higher support and new insights in the relationships of Zosterops species. Our data suggest to split Z. poliogaster into four distinct species, three of which had previously been proposed: Z. silvanus, Z. mbulensis, Z. kikyuensis and Z. kulalensis. Our approach allows the genotyping of whole mitogenomes for a large number of individuals and thus allows more reliable reconstruction of phylogenetic and phylogeographic relationships - also for non-model organisms. PMID:27233440

  2. 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.

  3. 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,...

  4. 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.

  5. Mechanism and regulation of the Two-component FMN-dependent monooxygenase ActVA-ActVB from Streptomyces coelicolor.

    OpenAIRE

    Valton, Julien; Mathevon, Carole; Fontecave, Marc; Nivière, Vincent; Ballou, David P.

    2008-01-01

    International audience The ActVA-ActVB system from Streptomyces coelicolor is a two-component flavin-dependent monooxygenase involved in the antibiotic actinorhodin biosynthesis. ActVB is a NADH:flavin oxidoreductase that provides a reduced FMN to ActVA, the monooxygenase that catalyzes the hydroxylation of dihydrokalafungin, the precursor of actinorhodin. In this work, using stopped-flow spectrophotometry, we investigated the mechanism of hydroxylation of dihydrokalafungin catalyzed by Ac...

  6. 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,...

  7. 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...

  8. Using VA data for research in persons with spinal cord injuries and disorders: Lessons from SCI QUERI

    Directory of Open Access Journals (Sweden)

    Bridget M. Smith, PhD

    2010-10-01

    Full Text Available The Department of Veterans Affairs (VA provides integrated services to more than 25,000 veterans with spinal cord injuries and disorders (SCI/D. VA data offer great potential for providing insights into healthcare utilization and morbidity, and these capabilities are central to efforts to improve healthcare for veterans with SCI/D. The objective of this article is to introduce researchers to the use of VA data to examine questions related to SCI/D using examples from Spinal Cord Injury (SCI Quality Enhancement Research Initiative studies. Sources of VA data available to investigators interested in SCI/D-related research include national-level VA administrative and clinical databases and primary data (medical record review, patient surveys. Methods used to identify veterans with SCI/D include the Allocation Resource Center cohort, the Spinal Cord Dysfunction (SCD Registry, and the VA inpatient SCI flag; only 33% of veterans were included in all three groups (n = 12,306. While neurological level of SCI was unknown for approximately a third of veterans (from SCD Registry data alone, the percent decreased to 13% when augmented with diagnostic codes. Primary data can be used to augment other missing SCI data and to provide more detailed information about complications commonly associated with SCI/D.

  9. 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

  10. 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.

  11. 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.

  12. 3D Digitisation and Visualisation of the Vače Situla

    OpenAIRE

    Gregor Vidmar

    2013-01-01

    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 technolog...

  13. 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%.

  14. THE THEATRE AND V.A. SEROV’S ARTISTIC WORLD

    OpenAIRE

    Shirokova Natalya Olegovna

    2012-01-01

    The article is devoted to the theatre theme in V.A. Serov’s artistic world, the article studies the stage actors’ and the ballet dancers’ portraits, the scenic canvas for “Shekherazada“ ballet performance, which the artist created the different times. The Serov’s characters interpretation is based on the personality concept proper and the wide spread in the Silver Age the “disguise” image peculiar treatment. The canvas analysis demonstrates the two culture layers (that of the Silver Age and o...

  15. V.A. Baraboj. Chernobyl: ten years later. Medical consequences of radiation accidents

    International Nuclear Information System (INIS)

    Review of the book - Chernobyl: ten years later. Medical consequences of radiation accidents (Kiev, Chernobylinterinform, 1996) by V.A. Baraboj - is presented. The book is based on experimental data obtained by author and available data of other scientists. It is shown that experiments on rats irradiation demonstrate the same combination of symptoms as persons participated in Chernobyl accident response. Attention is paid to the dosimetric, genetic, phenotypic features of exposed persons. Contributions of chemical hazardous pollutants and psychoemotional stress to the general pattern were also accounted. The importance of the book for specialists and public is accentuated

  16. [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.

  17. 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...

  18. Uloga i važnost brendiranja tradicijske izvedbene umjetnosti na primjeru Ansambla Lado

    OpenAIRE

    Dabo, Krešimir

    2012-01-01

    U današnjem globaliziranom svijetu u kojem se komunikacijski i marketinški stručnjaci bore za pozornost javnosti, u svijetu opterećenom informacijama do tolike mjere da se javlja efekt apatije na poruke oglašivača, brendiranje postaje jednim od ključnih faktora uspjeha tvrtki, proizvoda i usluga, među koje ubrajamo i kulturne sadržaje. Tema rada vezana je uz važnost implementacije brendiranja tradicijske umjetnosti kao kulturnog proizvoda na ovome tržištu na primjeru jedinog...

  19. Development and test of a 100 kVA superconducting transformer operated at 77 K

    International Nuclear Information System (INIS)

    High-temperature superconducting (HTS) transformers are very promising candidates for application in electrical power engineering. Their main advantages are reduced size, weight, better efficiency and reduced potential fire and environmental hazards. We have designed, constructed and tested a 100 kVA HTS power transformer operated at 77 K. The nominal primary and secondary currents (voltages) are 18 A (5.6 kV) and 92 A (1.1 kV), respectively. No-load tests, short-circuit tests and load tests proved repeatedly that the transformer has the rated capacity. HTS winding losses of 20.6 W and iron losses of 403 W were measured. (author)

  20. "Va, vis et deviens!": le passage de l'école obligatoire à la formation professionnelle

    OpenAIRE

    Londino, Noémie; Zittoun, Tania; Gilomen, Heinz

    2012-01-01

    Ce travail examine la période du passage de l’école obligatoire à la formation professionnelle initiale de type dual dans le cadre du système de formation suisse. Une jeune personne qui doit effectuer ce passage et qui commence sa formation professionnelle va devoir traverser plusieurs étapes, ainsi que s’engager dans de nouvelles expériences au sein d’une entreprise. Plus spécifiquement, ce travail choisit d’intégrer la perspective de ces jeunes personnes afin de mieux comprendre la manière ...

  1. 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.

  2. 3kVA UPS for residential application with interface for solar panels and microprocessor control

    Directory of Open Access Journals (Sweden)

    André Luiz Batista Ferreira

    2014-05-01

    Full Text Available This paper presents a complete design of a UPS 3kVA for residential applications and it is an important contribution to the academic and commercial environment. It also allows the use of solar panels, can make the load in question less dependent on the grid, and the use of clean energy. To this end we implemented a prototype in the field with battery bank of 150V, using as general control a digital signal controller (DSC family of DSP56F800E FreescaleTM.

  3. 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...

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. Prevalence and correlates of cannabis use in an outpatient VA posttraumatic stress disorder clinic.

    Science.gov (United States)

    Gentes, Emily L; Schry, Amie R; Hicks, Terrell A; Clancy, Carolina P; Collie, Claire F; Kirby, Angela C; Dennis, Michelle F; Hertzberg, Michael A; Beckham, Jean C; Calhoun, Patrick S

    2016-05-01

    Recent research has documented high rates of comorbidity between cannabis use disorders and posttraumatic stress disorder (PTSD) in veterans. However, despite possible links between PTSD and cannabis use, relatively little is known about cannabis use in veterans who present for PTSD treatment, particularly among samples not diagnosed with a substance use disorder. This study examined the prevalence of cannabis use and the psychological and functional correlates of cannabis use among a large sample of veterans seeking treatment at a Veterans Affairs (VA) PTSD specialty clinic. Male veterans (N = 719) who presented at a VA specialty outpatient PTSD clinic completed measures of demographic variables, combat exposure, alcohol, cannabis and other drug use, and PTSD and depressive symptoms. The associations among demographic, psychological, and functional variables were estimated using logistic regressions. Overall, 14.6% of participants reported using cannabis in the past 6 months. After controlling for age, race, service era, and combat exposure, past 6-month cannabis use was associated with unmarried status, use of tobacco products, other drug use, hazardous alcohol use, PTSD severity, depressive symptom severity, and suicidality. The present findings show that cannabis use is quite prevalent among veterans seeking PTSD specialty treatment and is associated with poorer mental health and use of other substances. It may be possible to identify and treat individuals who use cannabis in specialty clinics (e.g., PTSD clinics) where they are likely to present for treatment of associated mental health issues. (PsycINFO Database Record PMID:27214172

  9. Effectiveness of a social robot, "Paro," in a VA long-term care setting.

    Science.gov (United States)

    Lane, Geoffrey W; Noronha, Delilah; Rivera, Alexandra; Craig, Kathy; Yee, Christina; Mills, Brent; Villanueva, Eimee

    2016-08-01

    Interest in animal assisted interventions (AAI) has grown over the years, but acceptance of AAI by the clinical and research community has been hampered by safety, hygiene, and logistical concerns. Advances in the field of social robotics have provided a promising route to deliver AAI while avoiding these aforementioned obstacles. Although there has been promising initial research on social robotics in older adults, to date there has been no such research conducted with a veteran population. The present pilot study followed 23 veteran residents of a Veterans Affairs (VA) geropsychiatric long-term care facility over the span of approximately a year and a half. It was found that use of Paro, a social robot, resulted in increased observed positive affective and behavioral indicators, with concomitant decreases observed in negative affective and behavioral indicators. The authors concluded that Paro is likely an effective nonpharmacological approach for managing dementia-related mood and behavior problems with veterans in VA long term care facilities. They additionally observed that Paro is best presented to residents who are relatively calm and approachable, as opposed to actively exhibiting behavior or mood problems. Future research directions are discussed in light of both the positive results noted and the inherent limitations of our pilot study. (PsycINFO Database Record PMID:27195530

  10. 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. PMID:25267170

  11. Using GIS to profile health-care costs of VA Quality-Enhancement Research Initiative diseases.

    Science.gov (United States)

    Yu, Wei; Cowper, Diane; Berger, Magdalena; Kuebeler, Mark; Kubal, Joe; Manheim, Larry

    2004-06-01

    The Health Services Research and Development (HSR&D) Service at the Department of Veterans Affairs (VA) Health Care System launched a Quality Enhancement Research Initiative (QUERI) in 1998. This study estimated health-care costs of nine diseases under the QUERI project and analyzed geographic differences in health-care costs and utilization across 22 VA Integrated Service Networks (VISNs), using a geographic information system (GIS). Patients with these diseases were identified from diagnoses recorded between October 1999 and September 2000. Annual health-care costs for each disease were estimated in four categories: inpatient medical or surgical, other inpatient, outpatient, and outpatient pharmacy. Geographic differences of costs and health-care utilization across the 22 VISNs for chronic heart failure, diabetes, and spinal-cord injury were mapped using a GIS package. Average costs and patterns of health-care utilization varied substantially across the 22 VISNs. The observed differences in health-care utilization across geographic regions raised questions for further investigation. PMID:15446617

  12. Validity Assessment of Referral Decisions at a VA Health Care System Polytrauma System of Care.

    Science.gov (United States)

    Chung, Joyce; Aguila, Fatima; Harris, Odette

    2015-01-01

    There has been intensive interest to ensure equitable and appropriate access to the specialized rehabilitative services of the VA Polytrauma System of Care (PSC) for patients sustaining polytrauma and traumatic brain injuries (TBI). A retrospective cohort study with prospective data acquisition was conducted to assess validity and objectivity of the acceptance decision algorithm to the VA Palo Alto Health Care System (VAPAHCS) PSC. Our hypotheses are (1) VAPAHCS PSC referral decisions were appropriate and without bias and (2) the identified needs of redirected referrals were addressed. This analysis included 1,025 referrals (906 patients); 813 patients (89.7%) were accepted, and 93 (10.3%) were redirected. Redirected cases were older, were more often active duty service members, and were not from the West Coast. There were more females redirected due to concomitant spinal cord injury. These are rationale differences. In redirected patients, the most commonly identified rehabilitation needs were psychological support, mobility/physical therapy, and communication/speech services; >75% of patients had these services offered elsewhere outside of the PSC resources. While balancing financial stewardship and meeting our mission to provide outstanding rehabilitative care to veterans and service members, we demonstrated that acceptance decisions were valid and without bias, and redirected patients received appropriate alternate resources. PMID:26180664

  13. VaR的计算方式及其回测检验——基于计算机产业股票的实证研究%The VaR Calculation Method and its Back Measured Test——An Empirical Study Based on Computer Industry Stock

    Institute of Scientific and Technical Information of China (English)

    张顺

    2012-01-01

    VaR自上个世纪90年代起,已经成为了主流的度量风险的方式,但是,VaR模型的计算方式有十多种,哪一种VaR模型是最优模型,甚至于构建什么样的比较框架才能选择出最优模型,仍然没有一个统一的标准。采取比较主流的方式对VaR在股票中的计算以及对VaR模型的回测,是呈现VaR作为现阶段最为流行的风险度量工具的计算和回测检验的方式。%since the 1990s of the last century,VaR has become a mainstream way to measure risk,but there are dozens of calculation methods of VaR model.There is no unified standard as for what kind of VaR model is the best one and what comparative framework can help to select the best model.To take a more mainstream way to calculate the VaR in stock and backtest VaR model is very useful.

  14. An aromatic hydroxylation reaction catalyzed by a two-component FMN-dependent Monooxygenase. The ActVA-ActVB system from Streptomyces coelicolor.

    OpenAIRE

    Valton, Julien; Fontecave, Marc; Douki, Thierry; Kendrew, Steven G; Nivière, Vincent

    2006-01-01

    International audience The ActVA-ActVB system from Streptomyces coelicolor isatwo-component flavin-dependent monooxygenase that belongs to an emerging class of enzymes involved in various oxidation reactions in microorganisms. The ActVB component is a NADH:flavin oxidoreductase that provides a reduced FMN to the second component, ActVA the proper monooxygenase. In this work, we demonstrate that the ActVA-ActVB system catalyzes the aromatic monohydroxylation of dihydrokalafungin by molecula...

  15. 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.

  16. 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......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...

  17. 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

  18. 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.

  19. 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.

  20. 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

  1. 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.

  2. Cross-comparison of exome analysis, next-generation sequencing of amplicons, and the iPLEX® ADME PGx Panel for pharmacogenomic profiling

    Directory of Open Access Journals (Sweden)

    Eng Wee eChua

    2016-01-01

    Full Text Available Whole-exome sequencing (WES has been widely used for analysis of human genetic diseases, but its value for the pharmacogenomic profiling of individuals is not well studied. Initially, we performed an in-depth evaluation of the accuracy of WES variant calling in the pharmacogenes CYP2D6 and CYP2C19 by comparison with MiSeq® amplicon sequencing data (n = 36. This analysis revealed that the concordance rate between WES and MiSeq® was high, achieving 99.60% for variants that were called without exceeding the truth-sensitivity threshold (99%, defined during variant quality score recalibration. Beyond this threshold, the proportion of discordant calls increased markedly. Subsequently, we expanded our findings beyond CYP2D6 and CYP2C19 to include more genes genotyped by the iPLEX® ADME PGx Panel in the subset of twelve samples. WES performed well, agreeing with the genotyping panel in approximately 99% of the selected pass-filter variant calls. Overall, our results have demonstrated WES to be a promising approach for pharmacogenomic profiling, with an estimated error rate of lower than 1%. Quality filters, particularly variant quality score recalibration, are important for reducing the number of false variants. Future studies may benefit from examining the role of WES in the clinical setting for guiding drug therapy.

  3. 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. PMID:26801593

  4. 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.

  5. 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.

  6. 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

  7. The prevalence of body dysmorphic disorder and its clinical correlates in a VA primary care behavioral health clinic.

    Science.gov (United States)

    Kelly, Megan M; Zhang, Jinxin; Phillips, Katharine A

    2015-07-30

    We examined the prevalence of body dysmorphic disorder (BDD) in a Veterans Affairs (VA) primary care behavioral health clinic. Of 100 Veterans, 11% (95% CI = 6.3-18.6%) had current BDD and 12% (95% CI = 7.0-19.8%) had lifetime BDD. However, only 8.3% of these Veterans had been diagnosed with BDD. BDD was significantly associated with a substantially elevated rate of suicide attempts, major depression, and obsessive-compulsive disorder. This severe disorder appears to be underdiagnosed in VA settings. PMID:25935375

  8. 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.

  9. 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.

  10. Indomethacin-Kollidon VA64 Extrudates: A Mechanistic Study of pH-Dependent Controlled Release.

    Science.gov (United States)

    Tres, Francesco; Treacher, Kevin; Booth, Jonathan; Hughes, Leslie P; Wren, Stephen A C; Aylott, Jonathan W; Burley, Jonathan C

    2016-03-01

    Because of its weakly acidic nature (pKa of 4.5), indomethacin presents an aqueous solubility that significantly increases when changing from acidic to neutral/alkaline pH (1.5 μg/mL at pH 1.2 and 105.2 μg/mL at pH 7.4). We have therefore investigated the impact of the dissolution medium pH on the dissolution performance of indomethacin:Kollidon VA64 extrudates. The impact of the drug loading on the dissolution properties of these systems was also examined (5%, 15%, 30%, 50%, 70%, and 90% drug loading). Time-resolved Raman spectroscopy along with in-line UV-vis spectrophotometry was employed to directly relate changes in dissolution behavior to physicochemical changes that occur to the extrudate during the test. The dissolution tests were performed in pH 2 HCl (to mimic the stomach conditions), and this was then switched during the experiment to pH 6.8 phosphate buffer (to simulate the poststomach conditions). The rotating disc dissolution rate test was also used to simultaneously measure the dissolution rate of both the drug and the polymer. We found that in pH 2 HCl buffer, for the 15% or higher drug-loaded extrudates, Kollidon VA64 preferentially dissolves from the exterior of the compact leaving an amorphous drug-rich hydrophobic shell, which, similarly to an enteric coating, inhibits the drug release. The in situ formation of an enteric coating has been previously hypothesized, and this has been the first time that is directly observed in a pH-variable dissolution test. The dissolution medium switch to pH 6.8 phosphate buffer, due to the large increase of the aqueous solubility of indomethacin at this pH, leads to rapid dissolution of the material forming the coating and therefore total drug release. In contrast, the 5% extrudate is fully hydrated and quickly dissolves at low pH pointing to a dissolution performance dependent on highly water-soluble Kollidon VA64. PMID:26845251

  11. 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.

  12. Prirast i indeks kondicije – dva važna čimbenika u uzgoju dagnji

    OpenAIRE

    Župan, Dr.sc. Ivan; Šarić, dr.med.vet., mr. Tomislav

    2014-01-01

    Proizvodnja dagnje zastupljena je u većini mediteranskih zemalja, a najveći proizvođači su Španjolska i Grčka. Hrvatska proizvodnja je u odnosu na ukupnu količinu vrlo mala i već desetljećima konstantno iznosi oko 3.000 tona godišnje. Tehnologija uzgoja dagnji je relativno jednostavna, a cijeli sektor karakterizira neorganiziranost tržišta i nepovezanost proizvođača. Prirast i indeks kondicije dagnji važni su čimbenici u proizvodnji dagnji, zbog što bržeg postizanja tržišne veličine te...

  13. 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

  14. ThermiVa: The Revolutionary Technology for Vulvovaginal Rejuvenation and Noninvasive Management of Female SUI.

    Science.gov (United States)

    Magon, Navneet; Alinsod, Red

    2016-08-01

    Addressing vaginal laxity, atrophic vaginitis, stress urinary incontinence (SUI), and different manifestations of sexual dysfunction has always been problematic due to women's traditional difficulty discussing these issues with doctors as well as the societal attitude of resignation toward these conditions. The recent rise of non-invasive feminine rejuvenation using energy-based modalities to vaginal tissue has its origins in aesthetic medicine. Transcutaneous temperature-controlled radiofrequency therapy at the vulvovaginal region has shown promising results in giving a more youthful appearing vulva, restoration of vaginal elasticity and 'tightness', considerable improvement in SUI, reduction in overactive bladder symptoms, and reduction in sexual dysfunction. It is also emerging as the non-invasive treatment modality for mild to moderate SUI. It seems that the time has come, when women shall ever be grateful to their gynecologist for management of SUI with ThermiVa without an incision. PMID:27382227

  15. 20 kHz, 25 kVA node power transformer

    Science.gov (United States)

    Hussey, S.

    1989-01-01

    The electrical and mechanical design information and the electrical and thermal testing performed on the 440-208-V rms, 20-kHz, 25-kVa prototype node transformer are summarized. The calculated efficiency of the node transformer is 99.3 percent based on core loss and copper loss test data, and its maximum calculated load regulation is 0.7 percent. The node transformer has a weight of 19.7 lb and has a power density of 0.8 lb/kW. The hot-spot temperature rise is estimated to be 33 C above the cold plate mounting base. This proof-of-concept transformer design is a viable candidate for the space station Freedom application.

  16. Kontrola pravorijeka i važnost novootkrivenih činjenica

    OpenAIRE

    Várady, Tibor

    2012-01-01

    Uvijek je bilo i bit će slučajeva u kojima istina o nekim važnim činjenicama ostaje nepoznata i nakon donošenja konačne odluke. Događa se da se istina otkrije, ali tek u vrijeme kada više ne postoji mogućnost oslanjanja na redovite pravne lijekove. Prema ovom problemu zauzeta su različita stajališta. Uvođenje trećeg pravnog sredstva (pored poništaja i protivljenja priznanju arbitražnog pravorijeka) otvara složena pitanja. Izbor između suprotstavljenih opcija nije jednostavan. Treće pravno sre...

  17. 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.

  18. 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.

  19. 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.

  20. Global Derivatives

    DEFF Research Database (Denmark)

    Andersen, Torben Juul

    ""In Global Derivatives: A Strategic Risk Management Perspective", Torben Juul Andersen has succeeded to gather in one book a complete and thorough summary and an easy-to-read explanation of all types of derivative instruments and their background, and their use in modern management of risk...... approaches to dealing in the global business environment." - Sharon Brown-Hruska, Commissioner, Commodity Futures Trading Commission, USA. "This comprehensive survey of modern risk management using derivative securities is a fine demonstration of the practical relevance of modern derivatives theory to risk...... 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...

  1. 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 PMID:27148950

  2. 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

  3. 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.

  4. 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.

  5. Financial derivatives

    OpenAIRE

    Simon Gray and Joanna Place

    2006-01-01

    Derivatives, ranging from relatively simple forward contracts to complicated options products, are an increasingly important feature of financial markets worldwide. They are already being used in many emerging markets, and as the financial sector becomes deeper and more stable, their use is certain to grow. This Handbook provides a basic guide to the different types of derivatives traded, including the pricing and valuation of the products, and accounting and statistical treatment. Also, it a...

  6. 76 FR 27379 - Proposed Information Collection (Supplement to VA Forms 21-526, 21-534, and 21-535 (For...

    Science.gov (United States)

    2011-05-11

    ... to nancy.kessinger@va.gov . Please refer to ``OMB Control No. 2900-0094'' in any correspondence... AFFAIRS Proposed Information Collection (Supplement to VA Forms 21-526, 21-534, and 21-535 (For Philippine.... ACTION: Notice. SUMMARY: The Veterans Benefits Administration (VBA), Department of Veterans Affairs...

  7. 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…

  8. 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

    ... Federal Register (75 FR 69033) with the docket number COE-2010-0038 and no comments were received... 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,...

  9. 75 FR 61621 - Charges Billed to Third Parties for Prescription Drugs Furnished by VA to a Veteran for a...

    Science.gov (United States)

    2010-10-06

    ... may: (1) Have an annual effect on the economy of $100 million or more or adversely affect in a material way the economy, a sector of the economy, productivity, competition, jobs, the environment, public...), prior to the effective date of this document, VA billed $51 for each prescription filled (see 70...

  10. 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

  11. 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

    ... at the Chillicothe VA Medical Center in Chillicothe, Ohio. As consideration for the EUL, the lessee... placement for senior, disabled, homeless and/or at-risk Veterans and their families. FOR FURTHER INFORMATION... consideration under such a lease for the provision of medical care and services would result in a...

  12. 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.

  13. 77 FR 17086 - Section 8 Housing Choice Vouchers: Revised Implementation of the HUD-VA Supportive Housing Program

    Science.gov (United States)

    2012-03-23

    ... for homeless veterans authorized by section 8(o)(19) of the United States Housing Act of 1937 (1937... homelessness among veterans outlined in the Administration's Federal Strategy to Prevent and End Homelessness... states, the District of Columbia, Puerto Rico, and Guam. HUD, in consultation with the VA, and...

  14. Going to Scale: A Nonrandomized Nationwide Trial of the KiVa Antibullying Program for Grades 1-9

    Science.gov (United States)

    Karna, Antti; Voeten, Marinus; Little, Todd D.; Poskiparta, Elisa; Alanen, Erkki; Salmivalli, Christina

    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 implementation in Finland. Method: At each time point, the…

  15. 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.; Karna, Antti; Salmivalli, Christina

    2012-01-01

    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…

  16. Rapid Drug Susceptibility Testing of Drug-Resistant Mycobacterium tuberculosis Isolates Directly from Clinical Samples by Use of Amplicon Sequencing: a Proof-of-Concept Study

    Science.gov (United States)

    Anderson, Julia; Lemmer, Darrin; Lehmkuhl, Erik; Georghiou, Sophia B.; Heaton, Hannah; Wiggins, Kristin; Gillece, John D.; Schupp, James M.; Catanzaro, Donald G.; Crudu, Valeriu; Cohen, Ted; Rodwell, Timothy C.; Engelthaler, David M.

    2016-01-01

    Increasingly complex drug-resistant tuberculosis (DR-TB) is a major global health concern and one of the primary reasons why TB is now the leading infectious cause of death worldwide. Rapid characterization of a DR-TB patient's complete drug resistance profile would facilitate individualized treatment in place of empirical treatment, improve treatment outcomes, prevent amplification of resistance, and reduce the transmission of DR-TB. The use of targeted next-generation sequencing (NGS) to obtain drug resistance profiles directly from patient sputum samples has the potential to enable comprehensive evidence-based treatment plans to be implemented quickly, rather than in weeks to months, which is currently needed for phenotypic drug susceptibility testing (DST) results. In this pilot study, we evaluated the performance of amplicon sequencing of Mycobacterium tuberculosis DNA from patient sputum samples using a tabletop NGS technology and automated data analysis to provide a rapid DST solution (the Next Gen-RDST assay). One hundred sixty-six out of 176 (94.3%) sputum samples from the Republic of Moldova yielded complete Next Gen-RDST assay profiles for 7 drugs of interest. We found a high level of concordance of our Next Gen-RDST assay results with phenotypic DST (97.0%) and pyrosequencing (97.8%) results from the same clinical samples. Our Next Gen-RDST assay was also able to estimate the proportion of resistant-to-wild-type alleles down to mixtures of ≤1%, which demonstrates the ability to detect very low levels of resistant variants not detected by pyrosequencing and possibly below the threshold for phenotypic growth methods. The assay as described here could be used as a clinical or surveillance tool. PMID:27225403

  17. Rapid Drug Susceptibility Testing of Drug-Resistant Mycobacterium tuberculosis Isolates Directly from Clinical Samples by Use of Amplicon Sequencing: a Proof-of-Concept Study.

    Science.gov (United States)

    Colman, Rebecca E; Anderson, Julia; Lemmer, Darrin; Lehmkuhl, Erik; Georghiou, Sophia B; Heaton, Hannah; Wiggins, Kristin; Gillece, John D; Schupp, James M; Catanzaro, Donald G; Crudu, Valeriu; Cohen, Ted; Rodwell, Timothy C; Engelthaler, David M

    2016-08-01

    Increasingly complex drug-resistant tuberculosis (DR-TB) is a major global health concern and one of the primary reasons why TB is now the leading infectious cause of death worldwide. Rapid characterization of a DR-TB patient's complete drug resistance profile would facilitate individualized treatment in place of empirical treatment, improve treatment outcomes, prevent amplification of resistance, and reduce the transmission of DR-TB. The use of targeted next-generation sequencing (NGS) to obtain drug resistance profiles directly from patient sputum samples has the potential to enable comprehensive evidence-based treatment plans to be implemented quickly, rather than in weeks to months, which is currently needed for phenotypic drug susceptibility testing (DST) results. In this pilot study, we evaluated the performance of amplicon sequencing of Mycobacterium tuberculosis DNA from patient sputum samples using a tabletop NGS technology and automated data analysis to provide a rapid DST solution (the Next Gen-RDST assay). One hundred sixty-six out of 176 (94.3%) sputum samples from the Republic of Moldova yielded complete Next Gen-RDST assay profiles for 7 drugs of interest. We found a high level of concordance of our Next Gen-RDST assay results with phenotypic DST (97.0%) and pyrosequencing (97.8%) results from the same clinical samples. Our Next Gen-RDST assay was also able to estimate the proportion of resistant-to-wild-type alleles down to mixtures of ≤1%, which demonstrates the ability to detect very low levels of resistant variants not detected by pyrosequencing and possibly below the threshold for phenotypic growth methods. The assay as described here could be used as a clinical or surveillance tool. PMID:27225403

  18. Utilization and expenditures of veterans obtaining primary care in community clinics and VA medical centers: an observational cohort study

    Directory of Open Access Journals (Sweden)

    Chapko Michael

    2007-04-01

    Full Text Available Abstract Background To compare VA inpatient and outpatient utilization and expenditures of veterans seeking primary care in community-based outpatient clinics (CBOCs and VA medical centers (VAMCs in fiscal years 2000 (FY00 and 2001. Methods The sample included 25,092 patients who obtained primary care exclusively from 108 CBOCs in FY00, 26,936 patients who obtained primary care exclusively from 72 affiliated VAMCs in FY00, and 11,450 "crossover" patients who obtained primary care in CBOCs and VAMCs in FY00. VA utilization and expenditure data were drawn from the VA's system-wide cost accounting system. Veteran demographic characteristics and a 1999 Diagnostic Cost Group risk score were obtained from VA administrative files. Outpatient utilization (primary care, specialty care, mental health, pharmacy, radiology and laboratory and inpatient utilization were estimated using count data models and expenditures were estimated using one-part or two-part models. The second part of two-part models was estimated using generalized linear regressions. Results CBOC patients had a slightly more primary care visits per year than VAMC patients (p Conclusion CBOCs provided veterans improved access to primary care and other services, but expenditures were contained because CBOC patients who sought health care had fewer visits and hospital stays than comparable VAMC patients. These results suggest a more complex pattern of health care utilization and expenditures by CBOC patients than has been found in prior studies. This study also illustrates that CBOCs continue to be a critical primary care and mental health access point for veterans.

  19. 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.

  20. 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.

  1. 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

  2. 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.

  3. Morphological research on radio loud AGN 4C39.25 using KaVA observations

    Science.gov (United States)

    Yoo, Hyemin; Sohn, Bong Won; Yi, Sukyoung; KaVA AGN WG members

    2016-01-01

    4C39.25 (0923+392) is a distant radio loud AGN placed at redshift 0.695. Its kilo-parsec scale jet observed by VLBA(Kollgaard et al. 1990) and parsec scale jet observed by VLBA(Kellermann et al. 1998) are misaligned. This might indicate episodic-jet activity which recently turned on. This object currently shows two stationary compact parsec-scale components:a bright jet component on the east and less luminous core on the west. Also, it is known that there have been superluminal jet components which are flowing from the core toward east, and then merging with the bright jet component (Marscher et al. 1991, Alberdi et al. 2000, Lister et al. 2013). Including the detection of broad emission lines(SDSS), its viewing angle was concluded to be small. However, the jet component being more luminous than the core is abnormal for a source with a small viewing angle. Furthermore, it has young radio galaxy-like properties such as non-variation in total flux(Alberdi et al. 1997, 2000, MOJAVE database) and a high frequency peak in the spectral energy distribution(Orienti et al 2007). In this case, it is more reliable to think that viewing angle of 4C39.25 is large. Korean VLBI Network (KVN) and VLBI Exploration of Radio Astronomy (VERA) Array (KaVA) is a cooperated VLBI system of Korea and Japan which provides high-frequency (23GHz and 43GHz) and high spatial resolution(1.2mas and 0.6mas). Their advantages of multi-wavelength and relatively high S/N ratio relative to its number of baseline allow us to discover the central region and dim structures of 4C39.25. We present results of several epochs observed during 2013 to 2014, focusing on morphological changes of 4C39.25 using KaVA images. According to these results, we were able to find a recently emitted counter-jet component for images of first 6 epochs. Also the counter-jet component propagates along a curved trajectory, and it shows an extreme superluminal motion. This might indicate a necessity of relatively large viewing

  4. Illumina MiSeq Phylogenetic Amplicon Sequencing Shows a Large Reduction of an Uncharacterised Succinivibrionaceae and an Increase of the Methanobrevibacter gottschalkii Clade in Feed Restricted Cattle.

    Directory of Open Access Journals (Sweden)

    Matthew Sean McCabe

    Full Text Available Periodic feed restriction is used in cattle production to reduce feed costs. When normal feed levels are resumed, cattle catch up to a normal weight by an acceleration of normal growth rate, known as compensatory growth, which is not yet fully understood. Illumina Miseq Phylogenetic marker amplicon sequencing of DNA extracted from rumen contents of 55 bulls showed that restriction of feed (70% concentrate, 30% grass silage for 125 days, to levels that caused a 60% reduction of growth rate, resulted in a large increase of relative abundance of Methanobrevibacter gottschalkii clade (designated as OTU-M7, and a large reduction of an uncharacterised Succinivibrionaceae species (designated as OTU-S3004. There was a strong negative Spearman correlation (ρ = -0.72, P = <1x10(-20 between relative abundances of OTU-3004 and OTU-M7 in the liquid rumen fraction. There was also a significant increase in acetate:propionate ratio (A:P in feed restricted animals that showed a negative Spearman correlation (ρ = -0.69, P = <1x10(-20 with the relative abundance of OTU-S3004 in the rumen liquid fraction but not the solid fraction, and a strong positive Spearman correlation with OTU-M7 in the rumen liquid (ρ = 0.74, P = <1x10(-20 and solid (ρ = 0.69, P = <1x10(-20 fractions. Reduced A:P ratios in the rumen are associated with increased feed efficiency and reduced production of methane which has a global warming potential (GWP 100 years of 28. Succinivibrionaceae growth in the rumen was previously suggested to reduce methane emissions as some members of this family utilise hydrogen, which is also utilised by methanogens for methanogenesis, to generate succinate which is converted to propionate. Relative abundance of OTU-S3004 showed a positive Spearman correlation with propionate (ρ = 0.41, P = <0.01 but not acetate in the liquid rumen fraction.

  5. 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.

  6. 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。

  7. 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.

  8. Development of robots for rehabilitation therapy: the Palo Alto VA/Stanford experience.

    Science.gov (United States)

    Burgar, C G; Lum, P S; Shor, P C; Machiel Van der Loos, H F

    2000-01-01

    For over 25 years, personal assistant robots for severely disabled individuals have been in development. More recently, using robots to deliver rehabilitation therapy has been proposed. This paper summarizes the development and clinical testing of three mechatronic systems for post-stroke therapy conducted at the VA Palo Alto in collaboration with Stanford University. We describe the philosophy and experiences that guided their evolution. Unique to the Palo Alto approach is provision for bimanual, mirror-image, patient-controlled therapeutic exercise. Proof-of-concept was established with a 2-degree-of-freedom (DOF) elbow/forearm manipulator. Tests of a second-generation therapy robot producing planar forearm movements in 19 hemiplegic and control subjects confirmed the validity and reliability of interaction forces during mechanically assisted upper-limb movements. Clinical trials comparing 3-D robot-assisted therapy to traditional therapy in 21 chronic stroke subjects showed significant improvement in the Fugl-Meyer (FM) measure of motor recovery in the robot group, which exceeded improvements in the control group. PMID:11321002

  9. 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. PMID:24660796

  10. 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...

  11. 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.

  12. 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.

  13. Enhancing the power output of the VA-955 UHF-TV klystron

    International Nuclear Information System (INIS)

    The Varian VA-955 UHF-TV klystron is rated at 50 kW CW, and four of these klystrons were used to provide 200 kW of RF power for lower hybrid heating experiments on the ATC machine at 800 MHz. These proven, production-type tubes were wanted to generate more power for larger type machines, such as the PDX. Varian was asked whether the tubes were capable of higher-power operation in pulsed applications. They replied that they had no experimental data but felt that the tubes were capable of greatly enhanced performance under pulsed conditions. By using cathode modulation instead of modulating anode control of the klystron, and thus limiting the time that high voltage is applied to the cathode, it was shown that the tube is capable of an output power of 200 kW for tens of milliseconds compared to its normal CW rating of 50 kW. A description is given of the experimental results, the required modifications to the klystron and output transmission circuit, the details of operation of the regulating modulator used to perform the experiment. Upgrade kits are now being fabricated to allow 200 kW operation of the two 50 kW units which were lent to General Atomic for Doublet II experiments

  14. 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.

  15. 基于极值理论和Copula函数的条件VaR计算%Calculate the condition VaR by extreme value theory and Copula function

    Institute of Scientific and Technical Information of China (English)

    傅强; 邢琳琳

    2009-01-01

    Aiming at the non-linear and non-symmetrical tail characteristics of different risk of certain aasset,this paper applies the extreme value theory and Copula function to risk assets research and VaR calculation.The empirical result of Shenzhen Component Index shows that the extreme theory can better fit the edge distribution of the daily earnings rate and daily volatility which have thick tail.And Gumbel Copula function can also better reflect the relationship between them.The market risk VaR calculated by the joint distributions fitted with Gumbel Copula function can provide the investors in the risk analysis whih useful information.%针对金融市场中某种资产不同风险的非线性和非对称尾部的特性,将极值理论和Copula函数应用于资产风险的研究以及条件VaR的估计.经过对深证成指的实证研究表明,极值理论能更好地拟合具有厚尾分布的收益率和日内波幅的边缘分布,Gumbel Copula函数也能更好地反映两者之间的相关关系.由Gumbel Copu-la函数拟合的联合分布计算出的在一定日内波幅条件下的市场风险VaR能给投资者在进行风险分析以及构建投资组合时提供有用的信息.

  16. VA-LCP治疗桡骨远端不稳定性骨折的疗效观察%Effectiveness of VA-LCP on unstable distal radius fractures

    Institute of Scientific and Technical Information of China (English)

    范伟锋; 陈衍尧; 区健毅; 朱秋贤; 李锦塘

    2014-01-01

    目的 观察方向锁定加压接骨板VA-LCP治疗桡骨远端不稳定性骨折的临床疗效.方法 采用掌侧入路VA-LCP内固定术治疗22例桡骨远端不稳定性骨折患者.结果 患者均获随访,时间6~16个月,骨折均愈合.根据Garland and Werley标准进行功能评价:优11例,良10例,可1例,优良率为95.5%;根据Batra放射学评分法评定:优10例,良10例,优良率为90.9%.结论 VA-LCP治疗桡骨远端不稳定性骨折,内固定更牢固,避免复位丢失,可早期功能锻炼,是治疗桡骨远端粉碎性骨折的理想选择.

  17. 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.

  18. The Application of VAR Model in the Risk Management of Life Insurance Fund%VaR模型与寿险投资风险管理

    Institute of Scientific and Technical Information of China (English)

    李杰辉

    2007-01-01

    本文基于VaR法对我国寿险投资的风险管理进行研究.先对寿险资金的投资组合可能面临的风险进行分析,然后通过对风险价值(即VaR)的介绍,提出采用VaR对寿险投资组合风险进行度量和管理,并给以实际例子加以说明.

  19. Marketing komercijalnih nekretnina – važnost lokacije uredskog prostora za imidž poduzeća

    OpenAIRE

    Škevin, Petra

    2012-01-01

    U ovome se radu istražuju važni aspekti marketinga komercijalnih nekretnina na imidž poduzeća, a to su mišljenja poslovnih ljudi - menadžera o važnosti i utjecaju lokacije te ostalih čimbenika uredskog prostora, kao što su interijer ureda, prometna povezanost, arhitektura zgrade i sl. Istražene su i druge pojave i pitanja koji se javljaju kod izbora uredskog prostora. Rezultati su pokazali da većina ispitivane populacije menadžera smatra da uredski prostor utječe na imidž poduzeća, i to prije...

  20. 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...