WorldWideScience

Sample records for amplicon va derived

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

    Science.gov (United States)

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

    2011-01-01

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

  2. 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.

  3. Small RNA sequence analysis of adenovirus VA RNA-derived miRNAs reveals an unexpected serotype-specific difference in structure and abundance.

    Directory of Open Access Journals (Sweden)

    Wael Kamel

    Full Text Available Human adenoviruses (HAds encode for one or two highly abundant virus-associated RNAs, designated VA RNAI and VA RNAII, which fold into stable hairpin structures resembling miRNA precursors. Here we show that the terminal stem of the VA RNAs originating from Ad4, Ad5, Ad11 and Ad37, all undergo Dicer dependent processing into virus-specific miRNAs (so-called mivaRNAs. We further show that the mivaRNA duplex is subjected to a highly asymmetric RISC loading with the 3'-strand from all VA RNAs being the favored strand, except for the Ad37 VA RNAII, where the 5'-mivaRNAII strand was preferentially assembled into RISC. Although the mivaRNA seed sequences are not fully conserved between the HAds a bioinformatics prediction approach suggests that a large fraction of the VA RNAII-, but not the VA RNAI-derived mivaRNAs still are able to target the same cellular genes. Using small RNA deep sequencing we demonstrate that the Dicer processing event in the terminal stem of the VA RNAs is not unique and generates 3'-mivaRNAs with a slight variation of the position of the 5' terminal nucleotide in the RISC loaded guide strand. Also, we show that all analyzed VA RNAs, except Ad37 VA RNAI and Ad5 VA RNAII, utilize an alternative upstream A start site in addition to the classical +1 G start site. Further, the 5'-mivaRNAs with an A start appears to be preferentially incorporated into RISC. Although the majority of mivaRNA research has been done using Ad5 as the model system our analysis demonstrates that the mivaRNAs expressed in Ad11- and Ad37-infected cells are the most abundant mivaRNAs associated with Ago2-containing RISC. Collectively, our results show an unexpected variability in Dicer processing of the VA RNAs and a serotype-specific loading of mivaRNAs into Ago2-based RISC.

  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. OneVA Pharmacy

    Data.gov (United States)

    Department of Veterans Affairs — The OneVA Pharmacy application design consists of 3 main components: VistA Medication Profile screen, Health Data Record Clinical Data Service (HDR/CDS), and OneVA...

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

    Science.gov (United States)

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

    2014-03-15

    Evidence from multiple sources supports the hypothesis that Schwann cells in the peripheral nervous system transfer messenger RNA and ribosomes to the axons they ensheath. Several technical and methodological difficulties exist for investigators to unravel this process in myelinated axons - a complex two-cell unit. We present an experimental design to demonstrate that newly synthesized RNA is transferred from Schwann cells to axons in association with Myosin Va. The use of quantitative confocal FRET microscopy to track newly-synthesized RNA and determine the molecular association with Myosin Va, is described in detail. Copyright © 2013 Elsevier Inc. All rights reserved.

  7. Has the VA Become a White Elephant?

    Directory of Open Access Journals (Sweden)

    Robbins RA

    2016-11-01

    Full Text Available No abstract available. Article truncated at 150 words. As I write this Dennis Wagner is publishing a series of articles in the Arizona Republic describing his quest to find out if care at VA hospitals have improved over the last 2 years (1. To begin the article Wagner describes the fable of the King of Siam who presented albino pachyderms to his enemies knowing they would be bankrupted because the cost of food and care outweighed all usefulness. A modern expression derives from this parable: the white elephant. The Department of Veterans Affairs (VA has prided itself on being a leader in healthcare. It is the largest healthcare system in the US, implemented the first electronic medical record, and more than 70 percent of all US doctors have received training in the VA healthcare system (2. This year the VA is celebrating the 70th anniversary of its partnership with US medical schools. Beginning in 1946, the VA partnered ...

  8. Imaging Herpes Simplex Virus Type 1 Amplicon Vector–Mediated Gene Expression in Human Glioma Spheroids

    OpenAIRE

    Christine Kaestle; Alexandra Winkeler; Raphaela Richter; Heinrich Sauer; Jürgen Hescheler; Cornel Fraefel; Maria Wartenberg; Andreas H. Jacobs

    2011-01-01

    Vectors derived from herpes simplex virus type 1 (HSV-1) have great potential for transducing therapeutic genes into the central nervous system; however, inefficient distribution of vector particles in vivo may limit their therapeutic potential in patients with gliomas. This study was performed to investigate the extent of HSV-1 amplicon vector–mediated gene expression in a three-dimensional glioma model of multicellular spheroids by imaging highly infectious HSV-1 virions expressing green fl...

  9. Optimal Activation of Isopsoralen To Prevent Amplicon Carryover

    OpenAIRE

    Fahle, Gary A.; Gill, Vee J.; Fischer, Steven H.

    1999-01-01

    We compared the efficiencies of activation of the photochemical isopsoralen compound 10 and its resulting amplicon neutralizations under conditions with a UV transilluminator box at room temperature (RT) and a HRI-300 UV photothermal reaction chamber at RT and at 5°C. Our data suggest that use of the HRI-300 reaction chamber at 5°C results in a statistically significantly higher degree of amplicon neutralization.

  10. BioMaS: a modular pipeline for Bioinformatic analysis of Metagenomic AmpliconS.

    Science.gov (United States)

    Fosso, Bruno; Santamaria, Monica; Marzano, Marinella; Alonso-Alemany, Daniel; Valiente, Gabriel; Donvito, Giacinto; Monaco, Alfonso; Notarangelo, Pasquale; Pesole, Graziano

    2015-07-01

    Substantial advances in microbiology, molecular evolution and biodiversity have been carried out in recent years thanks to Metagenomics, which allows to unveil the composition and functions of mixed microbial communities in any environmental niche. If the investigation is aimed only at the microbiome taxonomic structure, a target-based metagenomic approach, here also referred as Meta-barcoding, is generally applied. This approach commonly involves the selective amplification of a species-specific genetic marker (DNA meta-barcode) in the whole taxonomic range of interest and the exploration of its taxon-related variants through High-Throughput Sequencing (HTS) technologies. The accessibility to proper computational systems for the large-scale bioinformatic analysis of HTS data represents, currently, one of the major challenges in advanced Meta-barcoding projects. BioMaS (Bioinformatic analysis of Metagenomic AmpliconS) is a new bioinformatic pipeline designed to support biomolecular researchers involved in taxonomic studies of environmental microbial communities by a completely automated workflow, comprehensive of all the fundamental steps, from raw sequence data upload and cleaning to final taxonomic identification, that are absolutely required in an appropriately designed Meta-barcoding HTS-based experiment. In its current version, BioMaS allows the analysis of both bacterial and fungal environments starting directly from the raw sequencing data from either Roche 454 or Illumina HTS platforms, following two alternative paths, respectively. BioMaS is implemented into a public web service available at https://recasgateway.ba.infn.it/ and is also available in Galaxy at http://galaxy.cloud.ba.infn.it:8080 (only for Illumina data). BioMaS is a friendly pipeline for Meta-barcoding HTS data analysis specifically designed for users without particular computing skills. A comparative benchmark, carried out by using a simulated dataset suitably designed to broadly represent

  11. High throughput 16S rRNA gene amplicon sequencing

    DEFF Research Database (Denmark)

    Nierychlo, Marta; Larsen, Poul; Jørgensen, Mads Koustrup

    S rRNA gene amplicon sequencing has been developed over the past few years and is now ready to use for more comprehensive studies related to plant operation and optimization thanks to short analysis time, low cost, high throughput, and high taxonomic resolution. In this study we show how 16S r......RNA gene amplicon sequencing can be used to reveal factors of importance for the operation of full-scale nutrient removal plants related to settling problems and floc properties. Using optimized DNA extraction protocols, indexed primers and our in-house Illumina platform, we prepared multiple samples...... be correlated to the presence of the species that are regarded as “strong” and “weak” floc formers. In conclusion, 16S rRNA gene amplicon sequencing provides a high throughput approach for a rapid and cheap community profiling of activated sludge that in combination with multivariate statistics can be used...

  12. VA National Bed Control System

    Data.gov (United States)

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

  13. 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...

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

    Science.gov (United States)

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

    2014-01-01

    Popular de novo amplicon clustering methods suffer from two fundamental flaws: arbitrary global clustering thresholds, and input-order dependency induced by centroid selection. Swarm was developed to address these issues by first clustering nearly identical amplicons iteratively using a local threshold, and then by using clusters’ internal structure and amplicon abundances to refine its results. This fast, scalable, and input-order independent approach reduces the influence of clustering parameters and produces robust operational taxonomic units. PMID:25276506

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

    Directory of Open Access Journals (Sweden)

    Frédéric Mahé

    2014-09-01

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

  16. 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...

  17. 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...

  18. 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 ...

  19. Comparison of outcomes for veterans receiving dialysis care from VA and non-VA providers

    Directory of Open Access Journals (Sweden)

    Wang Virginia

    2013-01-01

    Full Text Available Abstract Background Demand for dialysis treatment exceeds its supply within the Veterans Health Administration (VA, requiring VA to outsource dialysis care by purchasing private sector dialysis for veterans on a fee-for-service basis. It is unclear whether outcomes are similar for veterans receiving dialysis from VA versus non-VA providers. We assessed the extent of chronic dialysis treatment utilization and differences in all-cause hospitalizations and mortality between veterans receiving dialysis from VA versus VA-outsourced providers. Methods We constructed a retrospective cohort of veterans in 2 VA regions who received chronic dialysis treatment financed by VA between January 2007 and December 2008. From VA administrative data, we identified veterans who received outpatient dialysis in (1 VA, (2 VA-outsourced settings, or (3 both (“dual” settings. In adjusted analyses, we used two-part and logistic regression to examine associations between dialysis setting and all-cause hospitalization and mortality one-year from veterans’ baseline dialysis date. Results Of 1,388 veterans, 27% received dialysis exclusively in VA, 47% in VA-outsourced settings, and 25% in dual settings. Overall, half (48% were hospitalized and 12% died. In adjusted analysis, veterans in VA-outsourced settings incurred fewer hospitalizations and shorter hospital stays than users of VA due to favorable selection. Dual-system dialysis patients had lower one-year mortality than veterans receiving VA dialysis. Conclusions VA expenditures for “buying” outsourced dialysis are high and increasing relative to “making” dialysis treatment within its own system. Outcomes comparisons inform future make-or-buy decisions and suggest the need for VA to consider veterans’ access to care, long-term VA savings, and optimal patient outcomes in its placement decisions for dialysis services.

  20. Comparison of outcomes for veterans receiving dialysis care from VA and non-VA providers.

    Science.gov (United States)

    Wang, Virginia; Maciejewski, Matthew L; Patel, Uptal D; Stechuchak, Karen M; Hynes, Denise M; Weinberger, Morris

    2013-01-18

    Demand for dialysis treatment exceeds its supply within the Veterans Health Administration (VA), requiring VA to outsource dialysis care by purchasing private sector dialysis for veterans on a fee-for-service basis. It is unclear whether outcomes are similar for veterans receiving dialysis from VA versus non-VA providers. We assessed the extent of chronic dialysis treatment utilization and differences in all-cause hospitalizations and mortality between veterans receiving dialysis from VA versus VA-outsourced providers. We constructed a retrospective cohort of veterans in 2 VA regions who received chronic dialysis treatment financed by VA between January 2007 and December 2008. From VA administrative data, we identified veterans who received outpatient dialysis in (1) VA, (2) VA-outsourced settings, or (3) both ("dual") settings. In adjusted analyses, we used two-part and logistic regression to examine associations between dialysis setting and all-cause hospitalization and mortality one-year from veterans' baseline dialysis date. Of 1,388 veterans, 27% received dialysis exclusively in VA, 47% in VA-outsourced settings, and 25% in dual settings. Overall, half (48%) were hospitalized and 12% died. In adjusted analysis, veterans in VA-outsourced settings incurred fewer hospitalizations and shorter hospital stays than users of VA due to favorable selection. Dual-system dialysis patients had lower one-year mortality than veterans receiving VA dialysis. VA expenditures for "buying" outsourced dialysis are high and increasing relative to "making" dialysis treatment within its own system. Outcomes comparisons inform future make-or-buy decisions and suggest the need for VA to consider veterans' access to care, long-term VA savings, and optimal patient outcomes in its placement decisions for dialysis services.

  1. Amplicon sequencing of bacterial microbiota in abortion material from cattle.

    Science.gov (United States)

    Vidal, Sara; Kegler, Kristel; Posthaus, Horst; Perreten, Vincent; Rodriguez-Campos, Sabrina

    2017-10-10

    Abortions in cattle have a significant economic impact on animal husbandry and require prompt diagnosis for surveillance of epizootic infectious agents. Since most abortions are not epizootic but sporadic with often undetected etiologies, this study examined the bacterial community present in the placenta (PL, n = 32) and fetal abomasal content (AC, n = 49) in 64 cases of bovine abortion by next generation sequencing (NGS) of the 16S rRNA gene. The PL and AC from three fetuses of dams that died from non-infectious reasons were included as controls. All samples were analyzed by bacterial culture, and 17 were examined by histopathology. We observed 922 OTUs overall and 267 taxa at the genus level. No detectable bacterial DNA was present in the control samples. The microbial profiles of the PL and AC differed significantly, both in their composition (PERMANOVA), species richness and Chao-1 (Mann-Whitney test). In both organs, Pseudomonas was the most abundant genus. The combination of NGS and culture identified opportunistic pathogens of interest in placentas with lesions, such as Vibrio metschnikovii, Streptococcus uberis, Lactococcus lactis and Escherichia coli. In placentas with lesions where culturing was unsuccessful, Pseudomonas and unidentified Aeromonadaceae were identified by NGS displaying high number of reads. Three cases with multiple possible etiologies and placentas presenting lesions were detected by NGS. Amplicon sequencing has the potential to uncover unknown etiological agents. These new insights on cattle abortion extend our focus to previously understudied opportunistic abortive bacteria.

  2. OneVA EA Vision and Strategy

    Data.gov (United States)

    Department of Veterans Affairs — The outcomes/goals supported by effective use of an EA are: Improved Service Delivery, Functional Integration, Resource Optimization and Authoritative Reference. VA...

  3. Geographic Distribution of VA Expenditures FY 2016

    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 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,...

  5. 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,...

  6. 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,...

  7. Geographic Distribution of VA Expenditures FY1998

    Data.gov (United States)

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

  8. Geographic Distribution of VA Expenditures 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,...

  9. 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,...

  10. 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,...

  11. Dynamic Copy Number Evolution of X- and Y-Linked Ampliconic Genes in Human Populations

    DEFF Research Database (Denmark)

    Lucotte, Elise A; Skov, Laurits; Jensen, Jacob Malte

    2018-01-01

    we explore the evolution of human X- and Y-linked ampliconic genes by investigating copy number variation (CNV) and coding variation between populations using the Simons Genome Diversity Project. We develop a method to assess CNVs using the read-depth on modified X and Y chromosome targets containing...... related Y haplogroups, that diversified less than 50,000 years ago. Moreover, X and Y-linked ampliconic genes seem to have a faster amplification dynamic than autosomal multicopy genes. Looking at expression data from another study, we also find that XY-linked ampliconic genes with extensive copy number...

  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. Canary: an atomic pipeline for clinical amplicon assays.

    Science.gov (United States)

    Doig, Kenneth D; Ellul, Jason; Fellowes, Andrew; Thompson, Ella R; Ryland, Georgina; Blombery, Piers; Papenfuss, Anthony T; Fox, Stephen B

    2017-12-15

    High throughput sequencing requires bioinformatics pipelines to process large volumes of data into meaningful variants that can be translated into a clinical report. These pipelines often suffer from a number of shortcomings: they lack robustness and have many components written in multiple languages, each with a variety of resource requirements. Pipeline components must be linked together with a workflow system to achieve the processing of FASTQ files through to a VCF file of variants. Crafting these pipelines requires considerable bioinformatics and IT skills beyond the reach of many clinical laboratories. Here we present Canary, a single program that can be run on a laptop, which takes FASTQ files from amplicon assays through to an annotated VCF file ready for clinical analysis. Canary can be installed and run with a single command using Docker containerization or run as a single JAR file on a wide range of platforms. Although it is a single utility, Canary performs all the functions present in more complex and unwieldy pipelines. All variants identified by Canary are 3' shifted and represented in their most parsimonious form to provide a consistent nomenclature, irrespective of sequencing variation. Further, proximate in-phase variants are represented as a single HGVS 'delins' variant. This allows for correct nomenclature and consequences to be ascribed to complex multi-nucleotide polymorphisms (MNPs), which are otherwise difficult to represent and interpret. Variants can also be annotated with hundreds of attributes sourced from MyVariant.info to give up to date details on pathogenicity, population statistics and in-silico predictors. Canary has been used at the Peter MacCallum Cancer Centre in Melbourne for the last 2 years for the processing of clinical sequencing data. By encapsulating clinical features in a single, easily installed executable, Canary makes sequencing more accessible to all pathology laboratories. Canary is available for download as source

  14. Hi-Plex for Simple, Accurate, and Cost-Effective Amplicon-based Targeted DNA Sequencing.

    Science.gov (United States)

    Pope, Bernard J; Hammet, Fleur; Nguyen-Dumont, Tu; Park, Daniel J

    2018-01-01

    Hi-Plex is a suite of methods to enable simple, accurate, and cost-effective highly multiplex PCR-based targeted sequencing (Nguyen-Dumont et al., Biotechniques 58:33-36, 2015). At its core is the principle of using gene-specific primers (GSPs) to "seed" (or target) the reaction and universal primers to "drive" the majority of the reaction. In this manner, effects on amplification efficiencies across the target amplicons can, to a large extent, be restricted to early seeding cycles. Product sizes are defined within a relatively narrow range to enable high-specificity size selection, replication uniformity across target sites (including in the context of fragmented input DNA such as that derived from fixed tumor specimens (Nguyen-Dumont et al., Biotechniques 55:69-74, 2013; Nguyen-Dumont et al., Anal Biochem 470:48-51, 2015), and application of high-specificity genetic variant calling algorithms (Pope et al., Source Code Biol Med 9:3, 2014; Park et al., BMC Bioinformatics 17:165, 2016). Hi-Plex offers a streamlined workflow that is suitable for testing large numbers of specimens without the need for automation.

  15. Imaging Herpes Simplex Virus Type 1 Amplicon Vector–Mediated Gene Expression in Human Glioma Spheroids

    Directory of Open Access Journals (Sweden)

    Christine Kaestle

    2011-05-01

    Full Text Available Vectors derived from herpes simplex virus type 1 (HSV-1 have great potential for transducing therapeutic genes into the central nervous system; however, inefficient distribution of vector particles in vivo may limit their therapeutic potential in patients with gliomas. This study was performed to investigate the extent of HSV-1 amplicon vector–mediated gene expression in a three-dimensional glioma model of multicellular spheroids by imaging highly infectious HSV-1 virions expressing green fluorescent protein (HSV-GFP. After infection or microscopy-guided vector injection of glioma spheroids at various spheroid sizes, injection pressures and injection times, the extent of HSV-1 vector–mediated gene expression was investigated via laser scanning microscopy. Infection of spheroids with HSV-GFP demonstrated a maximal depth of vector-mediated GFP expression at 70 to 80 μm. A > 80% transduction efficiency was reached only in small spheroids with a diameter of 90%. The results demonstrated that vector-mediated gene expression in glioma spheroids was strongly dependent on the mode of vector application—injection pressure and injection time being the most important parameters. The assessment of these vector application parameters in tissue models will contribute to the development of safe and efficient gene therapy protocols for clinical application.

  16. KENO-VA-PVM KENO-VA-SM, KENO5A for Parallel Processors

    International Nuclear Information System (INIS)

    Ramon, Javier; Pena, Jorge

    2002-01-01

    1 - Description of program or function: This package contains versions KENO-Va-SM (Shared Memory version) and KENO-Va-PVM (Parallel Virtual Machine version) based on SCALE-4.1. KENO-Va three-dimensional Boltzmann transport equation for neutron multiplying systems. The primary purpose of KENO-Va is to determine k-effective. Other calculated quantities include lifetime and generation time, energy-dependent leakages, energy- and region-dependent absorptions, fissions, fluxes, and fission densities. 2 - Method of solution: KENO-Va employs the Monte Carlo technique

  17. 75 FR 78806 - Agency Information Collection (Create Payment Request for the VA Funding Fee Payment System (VA...

    Science.gov (United States)

    2010-12-16

    ... Payment Request for the VA Funding Fee Payment System (VA FFPS); a Computer Generated Funding Fee Receipt.... 2900-0474.'' SUPPLEMENTARY INFORMATION: Title: Create Payment Request for the VA Funding Fee Payment System (VA FFPS); a Computer Generated Funding Fee Receipt, VA Form 26-8986. OMB Control Number: 2900...

  18. 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...

  19. 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...

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

    Science.gov (United States)

    Skums, Pavel; Dimitrova, Zoya; Campo, David S; Vaughan, Gilberto; Rossi, Livia; Forbi, Joseph C; Yokosawa, Jonny; Zelikovsky, Alex; Khudyakov, Yury

    2012-06-25

    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. 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. 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/. © The Author(s) 2015. Published by Oxford University Press.

  2. VA Veterans Health Administration Access Data

    Data.gov (United States)

    Department of Veterans Affairs — At the Department of Veterans Affairs (VA), our most important mission is to provide the high quality health care and benefits Veterans have earned and deserve —...

  3. 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...

  4. Generic Amplicon Deep Sequencing to Determine Ilarvirus Species Diversity in Australian Prunus.

    Science.gov (United States)

    Kinoti, Wycliff M; Constable, Fiona E; Nancarrow, Narelle; Plummer, Kim M; Rodoni, Brendan

    2017-01-01

    The distribution of Ilarvirus species populations amongst 61 Australian Prunus trees was determined by next generation sequencing (NGS) of amplicons generated using a genus-based generic RT-PCR targeting a conserved region of the Ilarvirus RNA2 component that encodes the RNA dependent RNA polymerase (RdRp) gene. Presence of Ilarvirus sequences in each positive sample was further validated by Sanger sequencing of cloned amplicons of regions of each of RNA1, RNA2 and/or RNA3 that were generated by species specific PCRs and by metagenomic NGS. Prunus necrotic ringspot virus (PNRSV) was the most frequently detected Ilarvirus , occurring in 48 of the 61 Ilarvirus -positive trees and Prune dwarf virus (PDV) and Apple mosaic virus (ApMV) were detected in three trees and one tree, respectively. American plum line pattern virus (APLPV) was detected in three trees and represents the first report of APLPV detection in Australia. Two novel and distinct groups of Ilarvirus -like RNA2 amplicon sequences were also identified in several trees by the generic amplicon NGS approach. The high read depth from the amplicon NGS of the generic PCR products allowed the detection of distinct RNA2 RdRp sequence variant populations of PNRSV, PDV, ApMV, APLPV and the two novel Ilarvirus -like sequences. Mixed infections of ilarviruses were also detected in seven Prunus trees. Sanger sequencing of specific RNA1, RNA2, and/or RNA3 genome segments of each virus and total nucleic acid metagenomics NGS confirmed the presence of PNRSV, PDV, ApMV and APLPV detected by RNA2 generic amplicon NGS. However, the two novel groups of Ilarvirus -like RNA2 amplicon sequences detected by the generic amplicon NGS could not be associated to the presence of sequence from RNA1 or RNA3 genome segments or full Ilarvirus genomes, and their origin is unclear. This work highlights the sensitivity of genus-specific amplicon NGS in detection of virus sequences and their distinct populations in multiple samples, and the

  5. Generic Amplicon Deep Sequencing to Determine Ilarvirus Species Diversity in Australian Prunus

    Directory of Open Access Journals (Sweden)

    Wycliff M. Kinoti

    2017-06-01

    Full Text Available The distribution of Ilarvirus species populations amongst 61 Australian Prunus trees was determined by next generation sequencing (NGS of amplicons generated using a genus-based generic RT-PCR targeting a conserved region of the Ilarvirus RNA2 component that encodes the RNA dependent RNA polymerase (RdRp gene. Presence of Ilarvirus sequences in each positive sample was further validated by Sanger sequencing of cloned amplicons of regions of each of RNA1, RNA2 and/or RNA3 that were generated by species specific PCRs and by metagenomic NGS. Prunus necrotic ringspot virus (PNRSV was the most frequently detected Ilarvirus, occurring in 48 of the 61 Ilarvirus-positive trees and Prune dwarf virus (PDV and Apple mosaic virus (ApMV were detected in three trees and one tree, respectively. American plum line pattern virus (APLPV was detected in three trees and represents the first report of APLPV detection in Australia. Two novel and distinct groups of Ilarvirus-like RNA2 amplicon sequences were also identified in several trees by the generic amplicon NGS approach. The high read depth from the amplicon NGS of the generic PCR products allowed the detection of distinct RNA2 RdRp sequence variant populations of PNRSV, PDV, ApMV, APLPV and the two novel Ilarvirus-like sequences. Mixed infections of ilarviruses were also detected in seven Prunus trees. Sanger sequencing of specific RNA1, RNA2, and/or RNA3 genome segments of each virus and total nucleic acid metagenomics NGS confirmed the presence of PNRSV, PDV, ApMV and APLPV detected by RNA2 generic amplicon NGS. However, the two novel groups of Ilarvirus-like RNA2 amplicon sequences detected by the generic amplicon NGS could not be associated to the presence of sequence from RNA1 or RNA3 genome segments or full Ilarvirus genomes, and their origin is unclear. This work highlights the sensitivity of genus-specific amplicon NGS in detection of virus sequences and their distinct populations in multiple samples

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

    International Nuclear Information System (INIS)

    Costello, Alexandra; Asem, Ebenezer; Gardner, Eldon

    2008-01-01

    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)

  7. Genes encoded within 8q24 on the amplicon of a large extrachromosomal element are selectively repressed during the terminal differentiation of HL-60 cells.

    Science.gov (United States)

    Hirano, Tetsuo; Ike, Fumio; Murata, Takehide; Obata, Yuichi; Utiyama, Hiroyasu; Yokoyama, Kazunari K

    2008-04-02

    Human acute myeloblastic leukemia HL-60 cells become resistant to differentiation during long-term cultivation. After 150 passages, double minute chromosomes (dmins) found in early-passaged cells are replaced by large extrachromosomal elements (LEEs). In a DNA library derived from a purified fraction of LEEs, 12.6% (23/183) of clones were assigned to 8q24 and 9.2% (17/183) were assigned to 14q11 in the human genome. Fluorescence in situ hybridization (FISH) revealed a small aberrant chromosome, which had not been found in early-passaged cells, in addition to the purified LEEs. We determined that each LEE consisted of six discontinuous segments in a region that extended for 4.4Mb over the 8q24 locus. Five genes, namely, Myc (a proto-oncogene), NSMCE2 (for a SUMO ligase), CCDC26 (for a retinoic acid-dependent modulator of myeloid differentiation), TRIB1 (for a regulator of MAPK kinase) and LOC389637 (for a protein of unknown function), were encoded by the amplicon. Breaks in the chromosomal DNA within the amplicon were found in the NSMCE2 and CCDC26 genes. The discontinuous structure of the amplicon unit of the LEEs was identical with that of dmins in HL-60 early-passaged cells. The difference between them seemed, predominantly, to be the number (10-15 copies per LEE versus 2 or 3 copies per dmin) of constituent units. Expression of the Myc, NSMCE2, CCDC26 and LOC389637 and TRIB1 genes was constitutive in all lines of HL-60 cells and that of the first four genes was repressed during the terminal differentiation of early-passaged HL-60 cells. We also detected abnormal transcripts of CCDC26. Our results suggest that these genes were selected during the development of amplicons. They might be amplified and, sometimes, truncated to contribute to the maintenance of HL-60 cells in an undifferentiated state.

  8. Do Older Rural and Urban Veterans Experience Different Rates of Unplanned Readmission to VA and Non-VA Hospitals?

    Science.gov (United States)

    Weeks, William B.; Lee, Richard E.; Wallace, Amy E.; West, Alan N.; Bagian, James P.

    2009-01-01

    Context: Unplanned readmission within 30 days of discharge is an indicator of hospital quality. Purpose: We wanted to determine whether older rural veterans who were enrolled in the VA had different rates of unplanned readmission to VA or non-VA hospitals than their urban counterparts. Methods: We used the combined VA/Medicare dataset to examine…

  9. 75 FR 61252 - Proposed Information Collection (Create Payment Request for the VA Funding Fee Payment System (VA...

    Science.gov (United States)

    2010-10-04

    ... Payment Request for the VA Funding Fee Payment System (VA FFPS); A Computer Generated Funding Fee Receipt... Payment Request for the VA Funding Fee Payment System (VA FFPS); A Computer Generated Funding Fee Receipt... information through the Federal Docket Management System (FDMS) at http://www.Regulations.gov or to Nancy J...

  10. 78 FR 59771 - Proposed Information Collection (Create Payment Request for the VA Funding Fee Payment System (VA...

    Science.gov (United States)

    2013-09-27

    ... Payment Request for the VA Funding Fee Payment System (VA FFPS); a Computer Generated Funding Fee Receipt.... Title: Create Payment Request for the VA Funding Fee Payment System (VA FFPS); A Computer Generated... through the Federal Docket Management System (FDMS) at www.Regulations.gov or to Nancy J. Kessinger...

  11. 75 FR 61859 - Proposed Information Collection (Create Payment Request for the VA Funding Fee Payment System (VA...

    Science.gov (United States)

    2010-10-06

    ... Payment Request for the VA Funding Fee Payment System (VA FFPS); A Computer Generated Funding Fee Receipt... Payment Request for the VA Funding Fee Payment System (VA FFPS); A Computer Generated Funding Fee Receipt... information through the Federal Docket Management System (FDMS) at http://www.Regulations.gov or to Nancy J...

  12. VaST: A variability search toolkit

    Science.gov (United States)

    Sokolovsky, K. V.; Lebedev, A. A.

    2018-01-01

    Variability Search Toolkit (VaST) is a software package designed to find variable objects in a series of sky images. It can be run from a script or interactively using its graphical interface. VaST relies on source list matching as opposed to image subtraction. SExtractor is used to generate source lists and perform aperture or PSF-fitting photometry (with PSFEx). Variability indices that characterize scatter and smoothness of a lightcurve are computed for all objects. Candidate variables are identified as objects having high variability index values compared to other objects of similar brightness. The two distinguishing features of VaST are its ability to perform accurate aperture photometry of images obtained with non-linear detectors and handle complex image distortions. The software has been successfully applied to images obtained with telescopes ranging from 0.08 to 2.5 m in diameter equipped with a variety of detectors including CCD, CMOS, MIC and photographic plates. About 1800 variable stars have been discovered with VaST. It is used as a transient detection engine in the New Milky Way (NMW) nova patrol. The code is written in C and can be easily compiled on the majority of UNIX-like systems. VaST is free software available at http://scan.sai.msu.ru/vast/.

  13. 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

  14. Poincare group, SU(3) and V-A in leptonic decay

    International Nuclear Information System (INIS)

    Boehm, A.

    1975-07-01

    From as few assumptions as possible about the relations between the Poincare group, the particle classifying SU(3) and V-A we derive properties of the K/sub l 3 / and K/sub L 2 / decays. From the assumed relation between SU(3) and the Poincare group and the first class condition it follows that the formfactor ratio Xi of K/sub l 3 / decay is Xi = --0.57, and that a value of Xi = 0 is in disagreement with very general and well accepted theoretical assumptions. Assuming universality of V-A, the Cabibbo suppression is derived from the relations between SU(3) and V-A as a consequence of the brokenness of SU(3). (U.S.)

  15. 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

  16. 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.

  17. 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...

  18. Polyadenylated Sequencing Primers Enable Complete Readability of PCR Amplicons Analyzed by Dideoxynucleotide Sequencing

    Directory of Open Access Journals (Sweden)

    Martin Beránek

    2012-01-01

    Full Text Available Dideoxynucleotide DNA sequencing is one of the principal procedures in molecular biology. Loss of an initial part of nucleotides behind the 3' end of the sequencing primer limits the readability of sequenced amplicons. We present a method which extends the readability by using sequencing primers modified by polyadenylated tails attached to their 5' ends. Performing a polymerase chain reaction, we amplified eight amplicons of six human genes (AMELX, APOE, HFE, MBL2, SERPINA1 and TGFB1 ranging from 106 bp to 680 bp. Polyadenylation of the sequencing primers minimized the loss of bases in all amplicons. Complete sequences of shorter products (AMELX 106 bp, SERPINA1 121 bp, HFE 208 bp, APOE 244 bp, MBL2 317 bp were obtained. In addition, in the case of TGFB1 products (366 bp, 432 bp, and 680 bp, respectively, the lengths of sequencing readings were significantly longer if adenylated primers were used. Thus, single strand dideoxynucleotide sequencing with adenylated primers enables complete or near complete readability of short PCR amplicons.

  19. 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

    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 reporte...

  20. Absolute estimation of initial concentrations of amplicon in a real-time RT-PCR process

    Directory of Open Access Journals (Sweden)

    Kohn Michael

    2007-10-01

    Full Text Available Abstract Background Since real time PCR was first developed, several approaches to estimating the initial quantity of template in an RT-PCR reaction have been tried. While initially only the early thermal cycles corresponding to exponential duplication were used, lately there has been an effort to use all of the cycles in a PCR. The efforts have included both fitting empirical sigmoid curves and more elaborate mechanistic models that explore the chemical reactions taking place during each cycle. The more elaborate mechanistic models require many more parameters than can be fit from a single amplification, while the empirical models provide little insight and are difficult to tailor to specific reactants. Results We directly estimate the initial amount of amplicon using a simplified mechanistic model based on chemical reactions in the annealing step of the PCR. The basic model includes the duplication of DNA with the digestion of Taqman probe and the re-annealing between previously synthesized DNA strands of opposite orientation. By modelling the amount of Taqman probe digested and matching that with the observed fluorescence, the conversion factor between the number of fluorescing dye molecules and observed fluorescent emission can be estimated, along with the absolute initial amount of amplicon and the rate parameter for re-annealing. The model is applied to several PCR reactions with known amounts of amplicon and is shown to work reasonably well. An expanded version of the model allows duplication of amplicon without release of fluorescent dye, by adding 1 more parameter to the model. The additional process is helpful in most cases where the initial primer concentration exceeds the initial probe concentration. Software for applying the algorithm to data may be downloaded at http://www.niehs.nih.gov/research/resources/software/pcranalyzer/ Conclusion We present proof of the principle that a mechanistically based model can be fit to observations

  1. Does universal 16S rRNA gene amplicon sequencing of environmental communities provide an accurate description of nitrifying guilds?

    DEFF Research Database (Denmark)

    Diwan, Vaibhav; Albrechtsen, Hans-Jørgen; Smets, Barth F.

    2018-01-01

    amplicon sequencing and from guild targeted approaches. The universal amplicon sequencing provided 1) accurate estimates of nitrifier composition, 2) clustering of the samples based on these compositions consistent with sample origin, 3) estimates of the relative abundance of the guilds correlated...

  2. The VA mission act: Funding to fail?

    Directory of Open Access Journals (Sweden)

    Robbins RA

    2018-06-01

    Full Text Available No abstract available. Article truncated after 150 words. Yesterday on D-Day, the 74th anniversary of the invasion of Normandy, President Trump signed the VA Mission Act. The law directs the VA to combine a number of existing private-care programs, including the so-called Choice program, which was created in 2014 after veterans died waiting for appointments at the Phoenix VA (1. During the signing Trump touted the new law saying “there has never been anything like this in the history of the VA” and saying that veterans “can go right outside [the VA] to a private doctor”-but can they? Although the bill authorizes private care, it appropriates no money to pay for it. Although a bipartisan plan to fund the expansion is proposed in the House, the White House has been lobbying Republicans to vote the plan down (2. Instead Trump has been asking Congress to pay for veteran’s programs by cutting spending elsewhere (2. We in Arizona are …

  3. Assessing the quality of VA Human Research Protection Programs: VA vs. affiliated University Institutional Review Board.

    Science.gov (United States)

    Tsan, Min-Fu; Nguyen, Yen; Brooks, Robert

    2013-04-01

    We compared the Human Research Protection Program (HRPP) quality indicator data of the Department of Veterans Affairs (VA) facilities using their own VA institutional review boards (IRBs) with those using affiliated university IRBs. From a total of 25 performance metrics, 13 did not demonstrate statistically significant differences, while 12 reached statistically significance differences. Among the 12 with statistically significant differences, facilities using their own VA IRBs performed better on four of the metrics, while facilities using affiliate IRBs performed better on eight. However, the absolute difference was small (0.2-2.7%) in all instances, suggesting that they were of no practical significance. We conclude that it is acceptable for facilities to use their own VA IRBs or affiliated university IRBs as their IRBs of record.

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

    KAUST Repository

    Wang, Yong; Qian, Pei-Yuan

    2009-01-01

    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

  5. 38 CFR 74.27 - How will VA store information?

    Science.gov (United States)

    2010-07-01

    ... (CONTINUED) VETERANS SMALL BUSINESS REGULATIONS Records Management § 74.27 How will VA store information? VA... examination visits will be scanned onto portable media and fully secured in the Center for Veterans Enterprise...

  6. 77 FR 67063 - VA Directive 0005 on Scientific Integrity

    Science.gov (United States)

    2012-11-08

    ... in multiple areas, including data integrity, ethics, privacy, and human research protections, as well... replace the Association for the Accreditation of Human Research Protection Programs (AAHRPP) with Alion... human research protection programs. VA Response: VA is currently reviewing its accreditation...

  7. Accessing VA Healthcare During Large-Scale Natural Disasters.

    Science.gov (United States)

    Der-Martirosian, Claudia; Pinnock, Laura; Dobalian, Aram

    2017-01-01

    Natural disasters can lead to the closure of medical facilities including the Veterans Affairs (VA), thus impacting access to healthcare for U.S. military veteran VA users. We examined the characteristics of VA patients who reported having difficulty accessing care if their usual source of VA care was closed because of natural disasters. A total of 2,264 veteran VA users living in the U.S. northeast region participated in a 2015 cross-sectional representative survey. The study used VA administrative data in a complex stratified survey design with a multimode approach. A total of 36% of veteran VA users reported having difficulty accessing care elsewhere, negatively impacting the functionally impaired and lower income VA patients.

  8. pyAmpli: an amplicon-based variant filter pipeline for targeted resequencing data.

    Science.gov (United States)

    Beyens, Matthias; Boeckx, Nele; Van Camp, Guy; Op de Beeck, Ken; Vandeweyer, Geert

    2017-12-14

    Haloplex targeted resequencing is a popular method to analyze both germline and somatic variants in gene panels. However, involved wet-lab procedures may introduce false positives that need to be considered in subsequent data-analysis. No variant filtering rationale addressing amplicon enrichment related systematic errors, in the form of an all-in-one package, exists to our knowledge. We present pyAmpli, a platform independent parallelized Python package that implements an amplicon-based germline and somatic variant filtering strategy for Haloplex data. pyAmpli can filter variants for systematic errors by user pre-defined criteria. We show that pyAmpli significantly increases specificity, without reducing sensitivity, essential for reporting true positive clinical relevant mutations in gene panel data. pyAmpli is an easy-to-use software tool which increases the true positive variant call rate in targeted resequencing data. It specifically reduces errors related to PCR-based enrichment of targeted regions.

  9. 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

    . The new basecalling method described here, named Multipass, implements a probabilistic framework for working with the raw flowgrams obtained by pyrosequencing. For each sequence variant Multipass calculates the likelihood and nucleotide sequence of several most likely sequences given the flowgram data....... 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 virulence gene...... family, where Multipass generates 20 % more error-free sequences than current state of the art methods, and provides sequence characteristics that allow generation of a set of high confidence error-free sequences. This novel method can be used to increase accuracy of existing and future amplicon...

  10. Strong selective sweeps associated with ampliconic regions in great ape X chromosomes

    DEFF Research Database (Denmark)

    Nam, Kiwoong; Munch, Kasper; Hobolth, Asger

    2014-01-01

    The unique inheritance pattern of X chromosomes makes them preferential targets of adaptive evolution. We here investigate natural selection on the X chromosome in all species of great apes. We find that diversity is more strongly reduced around genes on the X compared with autosomes...... with ampliconic sequences we propose that intra-genomic conflict between the X and the Y chromosomes is a major driver of X chromosome evolution....

  11. 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 ...

  12. VA announces aggressive new approach to produce rapid improvements in VA medical centers

    Directory of Open Access Journals (Sweden)

    Robbins RA

    2018-02-01

    Full Text Available No abstract available. Article truncated at 150 words. The U.S. Department of Veterans Affairs (VA announced steps that it is taking as part of an aggressive new approach to produce rapid improvements at VA’s low-performing medical facilities nationwide (1. VA defines its low-performing facilities as those medical centers that receive the lowest score in its Strategic Analytics for Improvement and Learning (SAIL star rating system, or a one-star rating out of five. The SAIL star rating was initiated in 2016 and uses a variety of measures including mortality, length of hospital stay, readmission rates, hospital complications, physician productivity and efficiency. A complete listing of the VA facilities, their star ratings and the metrics used to determine the ratings is available through the end of fiscal year 2017 (2. Based on the latest ratings, the VA currently has 15 one-star facilities including Denver, Loma Linda, and Phoenix in the Southwest (Table 1. Table 1. VA facilities with one-star ratings …

  13. Ultra-high resolution HLA genotyping and allele discovery by highly multiplexed cDNA amplicon pyrosequencing

    Directory of Open Access Journals (Sweden)

    Lank Simon M

    2012-08-01

    Full Text Available Abstract Background High-resolution HLA genotyping is a critical diagnostic and research assay. Current methods rarely achieve unambiguous high-resolution typing without making population-specific frequency inferences due to a lack of locus coverage and difficulty in exon-phase matching. Achieving high-resolution typing is also becoming more challenging with traditional methods as the database of known HLA alleles increases. Results We designed a cDNA amplicon-based pyrosequencing method to capture 94% of the HLA class I open-reading-frame with only two amplicons per sample, and an analogous method for class II HLA genes, with a primary focus on sequencing the DRB loci. We present a novel Galaxy server-based analysis workflow for determining genotype. During assay validation, we performed two GS Junior sequencing runs to determine the accuracy of the HLA class I amplicons and DRB amplicon at different levels of multiplexing. When 116 amplicons were multiplexed, we unambiguously resolved 99%of class I alleles to four- or six-digit resolution, as well as 100% unambiguous DRB calls. The second experiment, with 271 multiplexed amplicons, missed some alleles, but generated high-resolution, concordant typing for 93% of class I alleles, and 96% for DRB1 alleles. In a third, preliminary experiment we attempted to sequence novel amplicons for other class II loci with mixed success. Conclusions The presented assay is higher-throughput and higher-resolution than existing HLA genotyping methods, and suitable for allele discovery or large cohort sampling. The validated class I and DRB primers successfully generated unambiguously high-resolution genotypes, while further work is needed to validate additional class II genotyping amplicons.

  14. High-throughput sequencing of 16S rRNA gene amplicons: effects of extraction procedure, primer length and annealing temperature.

    Science.gov (United States)

    Sergeant, Martin J; Constantinidou, Chrystala; Cogan, Tristan; Penn, Charles W; Pallen, Mark J

    2012-01-01

    The analysis of 16S-rDNA sequences to assess the bacterial community composition of a sample is a widely used technique that has increased with the advent of high throughput sequencing. Although considerable effort has been devoted to identifying the most informative region of the 16S gene and the optimal informatics procedures to process the data, little attention has been paid to the PCR step, in particular annealing temperature and primer length. To address this, amplicons derived from 16S-rDNA were generated from chicken caecal content DNA using different annealing temperatures, primers and different DNA extraction procedures. The amplicons were pyrosequenced to determine the optimal protocols for capture of maximum bacterial diversity from a chicken caecal sample. Even at very low annealing temperatures there was little effect on the community structure, although the abundance of some OTUs such as Bifidobacterium increased. Using shorter primers did not reveal any novel OTUs but did change the community profile obtained. Mechanical disruption of the sample by bead beating had a significant effect on the results obtained, as did repeated freezing and thawing. In conclusion, existing primers and standard annealing temperatures captured as much diversity as lower annealing temperatures and shorter primers.

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

    Science.gov (United States)

    Gimmler, Anna; Stoeck, Thorsten

    2015-08-01

    Environmental high-throughput sequencing (envHTS) is a very powerful tool, which in protistan ecology is predominantly used for the exploration of diversity and its geographic and local patterns. We here used a pyrosequenced V4-SSU rDNA data set from a solar saltern pond as test case to exploit such massive protistan amplicon data sets beyond this descriptive purpose. Therefore, we combined a Swarm-based blastn network including 11 579 ciliate V4 amplicons to identify divergent amplicon clusters with targeted polymerase chain reaction (PCR) primer design for full-length small subunit of the ribosomal DNA retrieval and probe design for fluorescence in situ hybridization (FISH). This powerful strategy allows to benefit from envHTS data sets to (i) reveal the phylogenetic position of the taxon behind divergent amplicons; (ii) improve phylogenetic resolution and evolutionary history of specific taxon groups; (iii) solidly assess an amplicons (species') degree of similarity to its closest described relative; (iv) visualize the morphotype behind a divergent amplicons cluster; (v) rapidly FISH screen many environmental samples for geographic/habitat distribution and abundances of the respective organism and (vi) to monitor the success of enrichment strategies in live samples for cultivation and isolation of the respective organisms. © 2015 Society for Applied Microbiology and John Wiley & Sons Ltd.

  16. VA Vascular Injury Study (VAVIS): VA-DoD extremity injury outcomes collaboration.

    Science.gov (United States)

    Shireman, Paula K; Rasmussen, Todd E; Jaramillo, Carlos A; Pugh, Mary Jo

    2015-02-03

    Limb injuries comprise 50-60% of U.S. Service member's casualties of wars in Afghanistan and Iraq. Combat-related vascular injuries are present in 12% of this cohort, a rate 5 times higher than in prior wars. Improvements in medical and surgical trauma care, including initial in-theatre limb salvage approaches (IILS) have resulted in improved survival and fewer amputations, however, the long-term outcomes such as morbidity, functional decline, and risk for late amputation of salvaged limbs using current process of care have not been studied. The long-term care of these injured warfighters poses a significant challenge to the Department of Defense (DoD) and Department of Veterans Affairs (VA). The VA Vascular Injury Study (VAVIS): VA-DoD Extremity Injury Outcomes Collaborative, funded by the VA, Health Services Research and Development Service, is a longitudinal cohort study of Veterans with vascular extremity injuries. Enrollment will begin April, 2015 and continue for 3 years. Individuals with a validated extremity vascular injury in the Department of Defense Trauma Registry will be contacted and will complete a set of validated demographic, social, behavioral, and functional status measures during interview and online/ mailed survey. Primary outcome measures will: 1) Compare injury, demographic and geospatial characteristics of patients with IILS and identify late vascular surgery related limb complications and health care utilization in Veterans receiving VA vs. non-VA care, 2) Characterize the preventive services received by individuals with vascular repair and related outcomes, and 3) Describe patient-reported functional outcomes in Veterans with traumatic vascular limb injuries. This study will provide key information about the current process of care for Active Duty Service members and Veterans with polytrauma/vascular injuries at risk for persistent morbidity and late amputation. The results of this study will be the first step for clinicians in VA and

  17. 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 for...

  18. SlaVaComp Fonts Converter

    Directory of Open Access Journals (Sweden)

    Simon Skilevic

    2013-12-01

    Full Text Available This paper presents a fonts converter that was developed as a part of the Freiburg project on historical corpus linguistics. The tool named SlaVaComp-Konvertierer converts Church Slavonic texts digitized with non-Unicode fonts into the Unicode format without any loss of information contained in the original file and without damage to the original formatting. It is suitable for the conversion of all idiosyncratic fonts—not only Church Slavonic—and therefore can be used not only in Palaeoslavistic, but also in all historical and philological studies.

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

    Directory of Open Access Journals (Sweden)

    Federico M Ibarbalz

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

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

    Science.gov (United States)

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

    2015-08-01

    Two different real-time quantitative PCR (PMA-qPCR) assays were applied for quantification of Legionella spp. by targeting a long amplicon (approx 400 bp) of 16S rRNA gene and a short amplicon (approx. 100 bp) of 5S rRNA gene. Purified DNA extracts from pure cultures of Legionella spp. and from environmental water samples were quantified. Application of the two assays to quantify Legionella in artificially contaminated water achieved that both assays were able to detect Legionella over a linear range of 10 to 10(5) cells ml(-1). A statistical analysis of the standard curves showed that both assays were linear with a good correlation coefficient (R(2) = 0.99) between the Ct and the copy number. Amplification with the reference assay was the most effective for detecting low copy numbers (1 bacterium per PCR mixture). Using selective quantification of viable Legionella by the PMA-qPCR method we obtained a greater inhibition of the amplification of the 400-bp 16S gene fragment (Δlog(10) = 3.74 ± 0.39 log(10) GU ml(-1)). A complete inhibition of the PCR signal was obtained when heat-killed cells in a concentration below 1 × 10(5) cells ml(-1) were pretreated with PMA. Analysing short amplicon sizes led to only 2.08 log reductions in the Legionella dead-cell signal. When we tested environmental water samples, the two qPCR assays were in good agreement according to the kappa index (0.741). Applying qPCR combined with PMA treatment, we also obtained a good agreement (kappa index 0.615). The comparison of quantitative results shows that both assays yielded the same quantification sensitivity (mean log = 4.59 vs mean log = 4.31). Copyright © 2015 Elsevier Ltd. All rights reserved.

  1. Massively parallel amplicon sequencing reveals isotype-specific variability of antimicrobial peptide transcripts in Mytilus galloprovincialis.

    Directory of Open Access Journals (Sweden)

    Umberto Rosani

    Full Text Available BACKGROUND: Effective innate responses against potential pathogens are essential in the living world and possibly contributed to the evolutionary success of invertebrates. Taken together, antimicrobial peptide (AMP precursors of defensin, mytilin, myticin and mytimycin can represent about 40% of the hemocyte transcriptome in mussels injected with viral-like and bacterial preparations, and unique profiles of myticin C variants are expressed in single mussels. Based on amplicon pyrosequencing, we have ascertained and compared the natural and Vibrio-induced diversity of AMP transcripts in mussel hemocytes from three European regions. METHODOLOGY/PRINCIPAL FINDINGS: Hemolymph was collected from mussels farmed in the coastal regions of Palavas (France, Vigo (Spain and Venice (Italy. To represent the AMP families known in M. galloprovincialis, nine transcript sequences have been selected, amplified from hemocyte RNA and subjected to pyrosequencing. Hemolymph from farmed (offshore and wild (lagoon Venice mussels, both injected with 10(7 Vibrio cells, were similarly processed. Amplicon pyrosequencing emphasized the AMP transcript diversity, with Single Nucleotide Changes (SNC minimal for mytilin B/C and maximal for arthropod-like defensin and myticin C. Ratio of non-synonymous vs. synonymous changes also greatly differed between AMP isotypes. Overall, each amplicon revealed similar levels of nucleotidic variation across geographical regions, with two main sequence patterns confirmed for mytimycin and no substantial changes after immunostimulation. CONCLUSIONS/SIGNIFICANCE: Barcoding and bidirectional pyrosequencing allowed us to map and compare the transcript diversity of known mussel AMPs. Though most of the genuine cds variation was common to the analyzed samples we could estimate from 9 to 106 peptide variants in hemolymph pools representing 100 mussels, depending on the AMP isoform and sampling site. In this study, no prevailing SNC patterns related

  2. Gene Fusions Associated with Recurrent Amplicons Represent a Class of Passenger Aberrations in Breast Cancer

    Directory of Open Access Journals (Sweden)

    Shanker Kalyana-Sundaram

    2012-08-01

    Full Text Available Application of high-throughput transcriptome sequencing has spurred highly sensitive detection and discovery of gene fusions in cancer, but distinguishing potentially oncogenic fusions from random, “passenger” aberrations has proven challenging. Here we examine a distinctive group of gene fusions that involve genes present in the loci of chromosomal amplifications—a class of oncogenic aberrations that are widely prevalent in breast cancers. Integrative analysis of a panel of 14 breast cancer cell lines comparing gene fusions discovered by high-throughput transcriptome sequencing and genome-wide copy number aberrations assessed by array comparative genomic hybridization, led to the identification of 77 gene fusions, of which more than 60% were localized to amplicons including 17q12, 17q23, 20q13, chr8q, and others. Many of these fusions appeared to be recurrent or involved highly expressed oncogenic drivers, frequently fused with multiple different partners, but sometimes displaying loss of functional domains. As illustrative examples of the “amplicon-associated” gene fusions, we examined here a recurrent gene fusion involving the mediator of mammalian target of rapamycin signaling, RPS6KB1 kinase in BT-474, and the therapeutically important receptor tyrosine kinase EGFR in MDA-MB-468 breast cancer cell line. These gene fusions comprise a minor allelic fraction relative to the highly expressed full-length transcripts and encode chimera lacking the kinase domains, which do not impart dependence on the respective cells. Our study suggests that amplicon-associated gene fusions in breast cancer primarily represent a by-product of chromosomal amplifications, which constitutes a subset of passenger aberrations and should be factored accordingly during prioritization of gene fusion candidates.

  3. SEED 2: a user-friendly platform for amplicon high-throughput sequencing data analyses.

    Science.gov (United States)

    Vetrovský, Tomáš; Baldrian, Petr; Morais, Daniel; Berger, Bonnie

    2018-02-14

    Modern molecular methods have increased our ability to describe microbial communities. Along with the advances brought by new sequencing technologies, we now require intensive computational resources to make sense of the large numbers of sequences continuously produced. The software developed by the scientific community to address this demand, although very useful, require experience of the command-line environment, extensive training and have steep learning curves, limiting their use. We created SEED 2, a graphical user interface for handling high-throughput amplicon-sequencing data under Windows operating systems. SEED 2 is the only sequence visualizer that empowers users with tools to handle amplicon-sequencing data of microbial community markers. It is suitable for any marker genes sequences obtained through Illumina, IonTorrent or Sanger sequencing. SEED 2 allows the user to process raw sequencing data, identify specific taxa, produce of OTU-tables, create sequence alignments and construct phylogenetic trees. Standard dual core laptops with 8 GB of RAM can handle ca. 8 million of Illumina PE 300 bp sequences, ca. 4GB of data. SEED 2 was implemented in Object Pascal and uses internal functions and external software for amplicon data processing. SEED 2 is a freeware software, available at http://www.biomed.cas.cz/mbu/lbwrf/seed/ as a self-contained file, including all the dependencies, and does not require installation. Supplementary data contain a comprehensive list of supported functions. daniel.morais@biomed.cas.cz. Supplementary data are available at Bioinformatics online. © The Author(s) 2018. Published by Oxford University Press.

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

    DEFF Research Database (Denmark)

    Yao, Danfeng; Kim, Junyoung; Yu, Fang

    2005-01-01

    at an intermediate sodium concentration (approximately 100 mM). These effects were mainly ascribed to the electrostatic cross talk among the hybridized DNA molecules and the secondary structure of PCR amplicons. For the negatively charged DNA probes, the hybridization reaction was subjected additionally to the DNA....../DNA electrostatic barrier, particularly in lower ionic strength range (e.g., 10 approximately 150 mM Na(+)). The electrostatic cross talk was shown to be largely reduced if the PNA probe layer was sufficiently diluted by following a strategic templated immobilization method. As a consequence, a pseudo...

  5. 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...... by unicellular cyanobacteria, 42% of the identified non-cyanobacterial nifH clusters from the corresponding DNA samples were also detected in cDNA. The study indicates that non-cyanobacteria account for a substantial part of the nifH gene pool in marine surface waters and that these genes are at least...

  6. Global Perspectives on Activated Sludge Community Composition analyzed using 16S rRNA amplicon sequencing

    DEFF Research Database (Denmark)

    Nierychlo, Marta; Saunders, Aaron Marc; Albertsen, Mads

    communities, and in this study activated sludge sampled from 32 Wastewater Treatment Plants (WWTPs) around the world was described and compared. The top abundant bacteria in the global activated sludge ecosystem were found and the core population shared by multiple samples was investigated. The results......Activated sludge is the most commonly applied bioprocess throughout the world for wastewater treatment. Microorganisms are key to the process, yet our knowledge of their identity and function is still limited. High-througput16S rRNA amplicon sequencing can reliably characterize microbial...

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

    Directory of Open Access Journals (Sweden)

    Stephan Pabinger

    Full Text Available 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

  8. Medical Student Psychiatry Examination Performance at VA and Non-VA Clerkship Sites

    Science.gov (United States)

    Tucker, Phebe; von Schlageter, Margo Shultes; Park, EunMi; Rosenberg, Emily; Benjamin, Ashley B.; Nawar, Ola

    2009-01-01

    Objective: The authors examined the effects of medical student assignment to U.S. Department of Veterans Affairs (VA) Medical Center inpatient and outpatient psychiatry clerkship sites versus other university and community sites on the performance outcome measure of National Board of Medical Examiners (NBME) subject examination scores. Methods:…

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

    Science.gov (United States)

    Bezold, C; Mayer, E; Dighe, A

    1997-01-01

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

  10. A priori Considerations When Conducting High-Throughput Amplicon-Based Sequence Analysis

    Directory of Open Access Journals (Sweden)

    Aditi Sengupta

    2016-03-01

    Full Text Available Amplicon-based sequencing strategies that include 16S rRNA and functional genes, alongside “meta-omics” analyses of communities of microorganisms, have allowed researchers to pose questions and find answers to “who” is present in the environment and “what” they are doing. Next-generation sequencing approaches that aid microbial ecology studies of agricultural systems are fast gaining popularity among agronomy, crop, soil, and environmental science researchers. Given the rapid development of these high-throughput sequencing techniques, researchers with no prior experience will desire information about the best practices that can be used before actually starting high-throughput amplicon-based sequence analyses. We have outlined items that need to be carefully considered in experimental design, sampling, basic bioinformatics, sequencing of mock communities and negative controls, acquisition of metadata, and in standardization of reaction conditions as per experimental requirements. Not all considerations mentioned here may pertain to a particular study. The overall goal is to inform researchers about considerations that must be taken into account when conducting high-throughput microbial DNA sequencing and sequences analysis.

  11. Insight into biases and sequencing errors for amplicon sequencing with the Illumina MiSeq platform.

    Science.gov (United States)

    Schirmer, Melanie; Ijaz, Umer Z; D'Amore, Rosalinda; Hall, Neil; Sloan, William T; Quince, Christopher

    2015-03-31

    With read lengths of currently up to 2 × 300 bp, high throughput and low sequencing costs Illumina's MiSeq is becoming one of the most utilized sequencing platforms worldwide. The platform is manageable and affordable even for smaller labs. This enables quick turnaround on a broad range of applications such as targeted gene sequencing, metagenomics, small genome sequencing and clinical molecular diagnostics. However, Illumina error profiles are still poorly understood and programs are therefore not designed for the idiosyncrasies of Illumina data. A better knowledge of the error patterns is essential for sequence analysis and vital if we are to draw valid conclusions. Studying true genetic variation in a population sample is fundamental for understanding diseases, evolution and origin. We conducted a large study on the error patterns for the MiSeq based on 16S rRNA amplicon sequencing data. We tested state-of-the-art library preparation methods for amplicon sequencing and showed that the library preparation method and the choice of primers are the most significant sources of bias and cause distinct error patterns. Furthermore we tested the efficiency of various error correction strategies and identified quality trimming (Sickle) combined with error correction (BayesHammer) followed by read overlapping (PANDAseq) as the most successful approach, reducing substitution error rates on average by 93%. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  12. Direct recovery of infectious Pestivirus from a full-length RT-PCR amplicon

    DEFF Research Database (Denmark)

    Rasmussen, Thomas Bruun; Reimann, Ilona; Hoffmann, Bernd

    2008-01-01

    This study describes the use of a novel and rapid long reverse transcription (RT)-PCR for the generation of infectious full-length cDNA of pestiviruses. To produce rescued viruses, full-length RT-PCR amplicons of 12.3 kb, including a T7-promotor, were transcribed directly in vitro, and the result......This study describes the use of a novel and rapid long reverse transcription (RT)-PCR for the generation of infectious full-length cDNA of pestiviruses. To produce rescued viruses, full-length RT-PCR amplicons of 12.3 kb, including a T7-promotor, were transcribed directly in vitro......, and the resulting RNA transcripts were electroporated into ovine cells. Infectious virus was obtained after one cell culture passage. The rescued viruses had a phenotype similar to the parental Border Disease virus strain. Therefore, direct generation of infectious pestiviruses from full-length RT-PCR cDNA products...

  13. Development of a parallelization method for KENO V.a

    International Nuclear Information System (INIS)

    Basoglu, B.; Bentley, C.; Dunn, M.

    1995-01-01

    The KENO V.a codes is a widely used Monte carlo codes that is part of the SCALE modular codes system for performing standardized computer analysis of nuclear systems for licensing evaluation. In the past few years, attempts have been made to speed up KENO V.a using new generation computers. In this paper we report on the initial development of a parallel version of KENO V.a for the Kendall Square Research supercomputer (KSRI) at ORNL. Investigations thus far have shown that the parallel code provides accurate results with significantly reduced computation times relative to the conventional KENO V.a code

  14. 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)

  15. Comparing Catheter-associated Urinary Tract Infection Prevention Programs Between VA and Non-VA Nursing Homes

    Science.gov (United States)

    Mody, Lona; Greene, M. Todd; Saint, Sanjay; Meddings, Jennifer; Trautner, Barbara W.; Wald, Heidi L.; Crnich, Christopher; Banaszak-Holl, Jane; McNamara, Sara E.; King, Beth J.; Hogikyan, Robert; Edson, Barbara; Krein, Sarah L.

    2018-01-01

    OBJECTIVE The impact of healthcare system integration on infection prevention programs is unknown. Using catheter-associated urinary tract infection (CAUTI) prevention as an example, we hypothesize that U.S. Department of Veterans Affairs (VA) nursing homes have a more robust infection prevention infrastructure due to integration and centralization compared with non-VA nursing homes. SETTING VA and non-VA nursing homes participating in the “AHRQ Safety Program for Long-term Care” collaborative. METHODS Nursing homes provided baseline information about their infection prevention programs to assess strengths and gaps related to CAUTI prevention. RESULTS A total of 353 (71%; 47 VA, 306 non-VA) of 494 nursing homes from 41 states responded. VA nursing homes reported more hours/week devoted to infection prevention-related activities (31 vs. 12 hours, P<.001), and were more likely to have committees that reviewed healthcare-associated infections. Compared with non-VA facilities, a higher percentage of VA nursing homes reported tracking CAUTI rates (94% vs. 66%, P<.001), sharing CAUTI data with leadership (94% vs. 70%, P=.014) and nursing personnel (85% vs. 56%, P=.003). However, fewer VA nursing homes reported having policies for appropriate catheter use (64% vs. 81%, P=.004) and catheter insertion (83% vs. 94%, P=.004). CONCLUSIONS Among nursing homes participating in an AHRQ-funded collaborative, VA and non-VA nursing homes differed in their approach to CAUTI prevention. Best practices from both settings should be applied universally to create an optimal infection prevention program within emerging integrated healthcare systems. PMID:27917728

  16. Identification and Evaluation of Single-Nucleotide Polymorphisms in Allotetraploid Peanut (Arachis hypogaea L.) Based on Amplicon Sequencing Combined with High Resolution Melting (HRM) Analysis.

    Science.gov (United States)

    Hong, Yanbin; Pandey, Manish K; Liu, Ying; Chen, Xiaoping; Liu, Hong; Varshney, Rajeev K; Liang, Xuanqiang; Huang, Shangzhi

    2015-01-01

    The cultivated peanut (Arachis hypogaea L.) is an allotetraploid (AABB) species derived from the A-genome (Arachis duranensis) and B-genome (Arachis ipaensis) progenitors. Presence of two versions of a DNA sequence based on the two progenitor genomes poses a serious technical and analytical problem during single nucleotide polymorphism (SNP) marker identification and analysis. In this context, we have analyzed 200 amplicons derived from expressed sequence tags (ESTs) and genome survey sequences (GSS) to identify SNPs in a panel of genotypes consisting of 12 cultivated peanut varieties and two diploid progenitors representing the ancestral genomes. A total of 18 EST-SNPs and 44 genomic-SNPs were identified in 12 peanut varieties by aligning the sequence of A. hypogaea with diploid progenitors. The average frequency of sequence polymorphism was higher for genomic-SNPs than the EST-SNPs with one genomic-SNP every 1011 bp as compared to one EST-SNP every 2557 bp. In order to estimate the potential and further applicability of these identified SNPs, 96 peanut varieties were genotyped using high resolution melting (HRM) method. Polymorphism information content (PIC) values for EST-SNPs ranged between 0.021 and 0.413 with a mean of 0.172 in the set of peanut varieties, while genomic-SNPs ranged between 0.080 and 0.478 with a mean of 0.249. Total 33 SNPs were used for polymorphism detection among the parents and 10 selected lines from mapping population Y13Zh (Zhenzhuhei × Yueyou13). Of the total 33 SNPs, nine SNPs showed polymorphism in the mapping population Y13Zh, and seven SNPs were successfully mapped into five linkage groups. Our results showed that SNPs can be identified in allotetraploid peanut with high accuracy through amplicon sequencing and HRM assay. The identified SNPs were very informative and can be used for different genetic and breeding applications in peanut.

  17. Ultra-deep pyrosequencing (UDPS data treatment to study amplicon HCV minor variants.

    Directory of Open Access Journals (Sweden)

    Josep Gregori

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

  18. Evaluation of the reproducibility of amplicon sequencing with Illumina MiSeq platform.

    Science.gov (United States)

    Wen, Chongqing; Wu, Liyou; Qin, Yujia; Van Nostrand, Joy D; Ning, Daliang; Sun, Bo; Xue, Kai; Liu, Feifei; Deng, Ye; Liang, Yuting; Zhou, Jizhong

    2017-01-01

    Illumina's MiSeq has become the dominant platform for gene amplicon sequencing in microbial ecology studies; however, various technical concerns, such as reproducibility, still exist. To assess reproducibility, 16S rRNA gene amplicons from 18 soil samples of a reciprocal transplantation experiment were sequenced on an Illumina MiSeq. The V4 region of 16S rRNA gene from each sample was sequenced in triplicate with each replicate having a unique barcode. The average OTU overlap, without considering sequence abundance, at a rarefaction level of 10,323 sequences was 33.4±2.1% and 20.2±1.7% between two and among three technical replicates, respectively. When OTU sequence abundance was considered, the average sequence abundance weighted OTU overlap was 85.6±1.6% and 81.2±2.1% for two and three replicates, respectively. Removing singletons significantly increased the overlap for both (~1-3%, pdeep sequencing increased OTU overlap both when sequence abundance was considered (95%) and when not (44%). However, if singletons were not removed the overlap between two technical replicates (not considering sequence abundance) plateaus at 39% with 30,000 sequences. Diversity measures were not affected by the low overlap as α-diversities were similar among technical replicates while β-diversities (Bray-Curtis) were much smaller among technical replicates than among treatment replicates (e.g., 0.269 vs. 0.374). Higher diversity coverage, but lower OTU overlap, was observed when replicates were sequenced in separate runs. Detrended correspondence analysis indicated that while there was considerable variation among technical replicates, the reproducibility was sufficient for detecting treatment effects for the samples examined. These results suggest that although there is variation among technical replicates, amplicon sequencing on MiSeq is useful for analyzing microbial community structure if used appropriately and with caution. For example, including technical replicates

  19. 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 ...

  20. VA Dental Insurance Program--federalism. Direct final rule.

    Science.gov (United States)

    2013-10-22

    The Department of Veterans Affairs (VA) is taking direct final action to amend its regulations related to the VA Dental Insurance Program (VADIP), a pilot program to offer premium-based dental insurance to enrolled veterans and certain survivors and dependents of veterans. Specifically, this rule will add language to clarify the limited preemptive effect of certain criteria in the VADIP regulations.

  1. 76 FR 52230 - Establishment of Class E Airspace; Forest, VA

    Science.gov (United States)

    2011-08-22

    ...-0378; Airspace Docket No. 11-AEA-11] Establishment of Class E Airspace; Forest, VA AGENCY: Federal... at Forest, VA, to accommodate the new Area Navigation (RNAV) Global Positioning System (GPS) Standard... published in the Federal Register a notice of proposed rulemaking to establish Class E airspace at Forest...

  2. ESTIMASI NILAI VaR PORTOFOLIO MENGGUNAKAN FUNGSI ARCHIMEDEAN COPULA

    Directory of Open Access Journals (Sweden)

    AULIA ATIKA PRAWIBTA SUHARTO

    2017-01-01

    Full Text Available Value at Risk explains the magnitude of the worst losses occurred in financial products investments with a certain level of confidence and time interval. The purpose of this study is to estimate the VaR of portfolio using Archimedean Copula family. The methods for calculating the VaR are as follows: (1 calculating the stock return; (2 calculating descriptive statistics of return; (3 checking for the nature of autocorrelation and heteroscedasticity effects on stock return data; (4 checking for the presence of extreme value by using Pareto tail; (5 estimating the parameters of Achimedean Copula family; (6 conducting simulations of Archimedean Copula; (7 estimating the value of the stock portfolio VaR. This study uses the closing price of TLKM and GGRM. At 90% the VaR obtained using Clayton, Gumbel, Frank copulas are 0.9562%, 1.0189%, 0.9827% respectively. At 95% the VaR obtained using Clayton, Gumbel, Frank copulas are 1.2930%, 1.2522%, 1.3152% respectively. At 99% the VaR obtained using Clayton, Gumbel, Frank copulas are 2.0327%, 1.9164%, is 1.8678% respectively. In conclusion estimation of VaR using Clayton copula yields the highest VaR.

  3. 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 with...

  4. Home Health Care and Patterns of Subsequent VA and Medicare Health Care Utilization for Veterans

    Science.gov (United States)

    Van Houtven, Courtney Harold; Jeffreys, Amy S.; Coffman, Cynthia J.

    2008-01-01

    Purpose: The Veterans Affairs or VA health care system is in the process of significantly expanding home health care (HOC) nationwide. We describe VA HHC use in 2003 for all VA HHC users from 2002; we examine whether VA utilization across a broad spectrum of services differed for a sample of VA HHC users and their propensity-score-matched…

  5. 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.

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

    Science.gov (United States)

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

    2015-01-01

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

  7. Photochemical immobilization of anthraquinone conjugated oligonucleotides and PCR amplicons on solid surfaces

    DEFF Research Database (Denmark)

    Koch, T.; Jacobsen, N.; Fensholdt, J.

    2000-01-01

    Ligand immobilization on solid surfaces is an essential step in fields such as diagnostics, bio sensor manufacturing, and new material sciences in general. In this paper a photochemical approach based on anthraquinone as the chromophore is presented. Photochemical procedures offer special...... advantages as they are able to generate highly reactive species in an orientation specific manner. As presented here, anthraquinone (AQ) mediated covalent DNA immobilization appears to be superior to currently known procedures. A synthetic procedure providing AQ-phosphoramidites is presented. These reagents...... facilitate AQ conjugation during routine DNA synthesis, thus enabling the AQ-oligonucleotides to be immobilized in a very convenient and efficient manner. AQ-conjugated PCR primers can be used directly in PCR. When the PCR is performed in solution, the amplicons can be immobilized after the PCR. Moreover...

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

    Science.gov (United States)

    Moralli, Daniela; Monaco, Zoia L

    2015-02-01

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

  9. Implementation of Amplicon Parallel Sequencing Leads to Improvement of Diagnosis and Therapy of Lung Cancer Patients.

    Science.gov (United States)

    König, Katharina; Peifer, Martin; Fassunke, Jana; Ihle, Michaela A; Künstlinger, Helen; Heydt, Carina; Stamm, Katrin; Ueckeroth, Frank; Vollbrecht, Claudia; Bos, Marc; Gardizi, Masyar; Scheffler, Matthias; Nogova, Lucia; Leenders, Frauke; Albus, Kerstin; Meder, Lydia; Becker, Kerstin; Florin, Alexandra; Rommerscheidt-Fuss, Ursula; Altmüller, Janine; Kloth, Michael; Nürnberg, Peter; Henkel, Thomas; Bikár, Sven-Ernö; Sos, Martin L; Geese, William J; Strauss, Lewis; Ko, Yon-Dschun; Gerigk, Ulrich; Odenthal, Margarete; Zander, Thomas; Wolf, Jürgen; Merkelbach-Bruse, Sabine; Buettner, Reinhard; Heukamp, Lukas C

    2015-07-01

    The Network Genomic Medicine Lung Cancer was set up to rapidly translate scientific advances into early clinical trials of targeted therapies in lung cancer performing molecular analyses of more than 3500 patients annually. Because sequential analysis of the relevant driver mutations on fixated samples is challenging in terms of workload, tissue availability, and cost, we established multiplex parallel sequencing in routine diagnostics. The aim was to analyze all therapeutically relevant mutations in lung cancer samples in a high-throughput fashion while significantly reducing turnaround time and amount of input DNA compared with conventional dideoxy sequencing of single polymerase chain reaction amplicons. In this study, we demonstrate the feasibility of a 102 amplicon multiplex polymerase chain reaction followed by sequencing on an Illumina sequencer on formalin-fixed paraffin-embedded tissue in routine diagnostics. Analysis of a validation cohort of 180 samples showed this approach to require significantly less input material and to be more reliable, robust, and cost-effective than conventional dideoxy sequencing. Subsequently, 2657 lung cancer patients were analyzed. We observed that comprehensive biomarker testing provided novel information in addition to histological diagnosis and clinical staging. In 2657 consecutively analyzed lung cancer samples, we identified driver mutations at the expected prevalence. Furthermore we found potentially targetable DDR2 mutations at a frequency of 3% in both adenocarcinomas and squamous cell carcinomas. Overall, our data demonstrate the utility of systematic sequencing analysis in a clinical routine setting and highlight the dramatic impact of such an approach on the availability of therapeutic strategies for the targeted treatment of individual cancer patients.

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

    Directory of Open Access Journals (Sweden)

    Hanna Farnelid

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

  11. 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.

  12. 1000-kVA arc power supply

    International Nuclear Information System (INIS)

    Wright, R.E.; Barber, G.C.; Ponte, N.S.

    1979-01-01

    Because of ever-increasing power demands for the development of the Oak Ridge duoPIGatron ion source, a continuous-duty arc power supply was constructed for the Medium Energy Test Facility (METF) to furnish power for the plasma generator of experimental ion sources. The power supply utilizes 12-pulse rectification with half-wave switching in a delta and wye full-wave bridge that may be connected in series or parallel. It will deliver 340 V dc, 2500 A to an ion source when series connected and 170 V dc, 5000 A when paralleled connected. Silicon-controlled rectifiers (SCR) in each rectifier bridge can be switched for pulses as short as 10 ms through continuous duty. The filter section that reduces the ripple in the output consists of an inductor-to-capacitor (L-C) filter to smooth the 720-Hz pulses. The power transformer serves as an isolation transformer allowing the secondary to be elevated to the accelerating potential of the ion source. The dc output level is controlled with a 1000-kVA auto transformer connected to the primary of the power transformer. All elevated voltages and currents are monitored at ground potential with an optical telemetry system. This paper describes the power supply in detail, including block diagrams, component specifications, and waveforms when supplying power to an ion source

  13. 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 …

  14. 76 FR 40453 - Agency Information Collection (Application for VA Education Benefits) Activity Under OMB Review

    Science.gov (United States)

    2011-07-08

    ... (Application for VA Education Benefits) Activity Under OMB Review AGENCY: Veterans Benefits Administration... Education Benefits, VA Form 22-1990. b. Application for Family Member to Use Transferred Benefits, VA Form 22-1990E. [[Page 40454

  15. VA INFORMATION SYSTEMS: Computer Security Weaknesses Persist at the Veterans Health Administration

    National Research Council Canada - National Science Library

    2000-01-01

    .... To determine the status of computer security within VHA, we (1) evaluated information system general controls at the VA Maryland Health Cafe System, the New Mexico VA Health Care System, and the VA North Texas Health Care System and (2...

  16. Function of the EGR-1/TIS8 radiation inducible promoter in a minimal HSV-1 amplicon system

    International Nuclear Information System (INIS)

    Spear, M.A.; Sakamoto, K.M.; Herrlinger, U.; Pechan, P.; Breakefield, X.O.

    1997-01-01

    Purpose: To evaluate function of the EGR-1/TIS8 promoter region in minimal HSV-1 amplicon system in order to determine the feasibility of using the system to regulate vector replication with radiation. Materials and Methods: A 600-base pair 5' upstream region of the EGR-1 promoter linked to chloramphenicol acetyltransferase (CAT) was recombined into a minimal HSV-1 amplicon vector system (pONEC). pONEC or a control plasmid was transfected into U87 glioma cells using the Lipofectamine method. Thirty-six hours later one aliquot of cells from each transfection was irradiated to a dose of 20 Gy and another identical aliquot served as a control. CAT activity was assayed 8 hours after irradiation. Results: pONEC transfected cells irradiated with 20 Gy demonstrated 2.0 fold increase in CAT activity compared to non-irradiated cells. Cells transfected with control plasmid showed no change in CAT activity. Unirradiated pONEC cells had CAT activity 1.3 times those transfected with control plasmid. Conclusion: We have previously created HSV-1 gene therapy amplicon vector systems which allow virus-amplicon interdependent replication, with the intent of regulating replication. The above data demonstrates that a minimal amplicon system will allow radiation dependent regulation by the EGR-1 promoter, thus indicating the possibility of using this system to regulate onsite, spatially and temporally regulated vector production. Baseline CAT activity was higher and relative induction lower than other reported expression constructs, which raises concern for the ability of the system to produce a differential in transcription levels sufficient for this purpose. This is possibly the result of residual promoter/enhancer elements remaining in the HSV-1 sequences. We are attempting to create constructs lacking these elements. Addition of secondary promoter sequences may also be of use. We are also currently evaluating the efficacy of the putative IEX-1 radiation inducible promoter region in

  17. SlaVaComp: Konvertierungstool (= SlaVaComp Fonts Converter

    Directory of Open Access Journals (Sweden)

    Simon Skilevic

    2013-12-01

    Full Text Available Der vorliegende Beitrag informiert über ein Tool, das im Rahmen eines Freiburger Projekts zur historischen Korpuslinguistik entwickelt wurde und dazu dient, kirchenslavische Texte, die ohne Einsatz von Unicode digitalisiert wurden, ohne Verlust von Information bzw. Formatierung ins Unicode-Format zu überführen. Das Tool heißt SlaVaComp-Konvertierer. Es eignet sich für die Konvertierung aller idiosynkratischen Fonts und kann somit nicht nur in der Paläoslavistik, sondern in allen historisch arbeitenden Philologien eingesetzt werden. ____________________ This paper presents a fonts converter that was developed as a part of the Freiburg project on historical corpus linguistics. The tool named SlaVaComp-Konvertierer converts Church Slavonic texts digitized with non-Unicode fonts into the Unicode format without any loss of information contained in the original file and without damage to the original formatting. It is suitable for the conversion of all idiosyncratic fonts—not only Church Slavonic—and therefore can be used not only in Palaeoslavistic, but also in all historical and philological studies.

  18. An academic-VA partnership: Student interprofessional teams integrated with VA PACT teams.

    Science.gov (United States)

    Swenty, Constance L; Schaar, Gina L; Butler, Ryan M

    2016-12-01

    Veterans are challenged with multiple unique healthcare issues related to their military service environment. Likewise, health care providers must understand the special concerns associated with military conflict and recognize how the veteran's care can be optimized by interprofessional care delivery. Little is taught didactically or clinically that supports nursing students in addressing the unique issues of the veteran or the student's need to work collaboratively with allied health team members to enhance the veteran's care. Because of limited exposure to the veteran's special conditions, nursing students who may seek a career with the veteran population often face challenges in rendering appropriate care. The VA offers an invaluable opportunity for health profession students to collaborate with VA interprofessional Patient Aligned Care Teams (PACT) ultimately optimizing veteran health outcomes. This academic partnership, that implements an interprofessional model, will prepare students to better embrace the veteran population. This article describes the immersion of health profession students in interprofessional collaborative practice (IPCP) using PACT team principles which ultimately promotes the students' ability to link theory content to patient care delivery. Copyright © 2016 Elsevier Ltd. All rights reserved.

  19. Maximum power per VA control of vector controlled interior ...

    Indian Academy of Sciences (India)

    Thakur Sumeet Singh

    2018-04-11

    Apr 11, 2018 ... Department of Electrical Engineering, Indian Institute of Technology Delhi, New ... The MPVA operation allows maximum-utilization of the drive-system. ... Permanent magnet motor; unity power factor; maximum VA utilization; ...

  20. 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...

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

    Data.gov (United States)

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

  2. 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 ...

  3. 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

  4. Differential amplicons (ΔAmp)-a new molecular method to assess RNA integrity.

    Science.gov (United States)

    Björkman, J; Švec, D; Lott, E; Kubista, M; Sjöback, R

    2016-01-01

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

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

    Directory of Open Access Journals (Sweden)

    J. Björkman

    2016-01-01

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

  6. 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.

  7. 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.

  8. 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.

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

    Directory of Open Access Journals (Sweden)

    Frédéric Mahé

    2015-12-01

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

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

    Science.gov (United States)

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

    2011-01-01

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

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

    Science.gov (United States)

    Gulino, Lisa-Maree; Ouwerkerk, Diane; Kang, Alicia Y H; 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). 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.

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

    Science.gov (United States)

    2010-03-01

    ... Sports Clinic Application, VA Form 0924--233 hours. b. National Veterans Wheelchair Games Application, VA.... National Veterans TEE Tournament Application, VA Form 0927--133 hours. e. National Veterans Summer Sports... Form 0929--67 hours. OMB Control Number: 2900-New (VA Form 0924). Type of Review: Existing collection...

  13. 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

    to link sludge and floc properties to the microbial communities. All data was subjected to extensive network analysis and multivariate statistics through R. The 16S amplicon results confirmed the findings of relatively few core groups of organism shared by all the wastewater treatment plants......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...... a year, totaling over 400 samples. All samples were subjected to 16S rDNA amplicon sequencing using V13 primers on the Illumina MiSeq platform (2x300bp) to a depth of at least 20.000 quality filtered reads per sample. The OTUs were assigned taxonomy based on a manually curated version of the greengenes...

  14. VaR and CVaR Implied in Option Prices

    Directory of Open Access Journals (Sweden)

    Giovanni Barone Adesi

    2016-02-01

    Full Text Available VaR (Value at Risk and CVaR (Conditional Value at Risk are implied by option prices. Their relationships to option prices are derived initially under the pricing measure. It does not require assumptions about the distribution of portfolio returns. The effects of changes of measure are modest at the short horizons typically used in applications. The computation of CVaR from option price is very convenient, because this measure is not elicitable, making direct comparisons of statistical inferences from market data problematic.

  15. 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.

  16. 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.

  17. Prerequisites for Amplicon Pyrosequencing of Microbial Methanol Utilizers in the Environment

    Directory of Open Access Journals (Sweden)

    Steffen eKolb

    2013-09-01

    Full Text Available The commercial availability of next generation sequencing (NGS technologies facilitated the assessment of functional groups of microorganisms in the environment with high coverage, resolution, and reproducibility. Soil methylotrophs were among the first microorganisms in the environment that were assessed with molecular tools, and nowadays, as well with NGS technologies. Studies in the past years re-attracted notice to the pivotal role of methylotrophs in global conversions of methanol, which mainly originates from plants, and is involved in oxidative reactions and ozone formation in the atmosphere. Aerobic methanol utilizers belong to Bacteria, yeasts, Ascomycota, and molds. Numerous bacterial methylotrophs are facultatively aerobic, and also contribute to anaerobic methanol oxidation in the environment, whereas strict anaerobic methanol utilizers belong to methanogens and acetogens. The diversity of enzymes catalyzing the initial oxidation of methanol is considerable, and comprises at least five different enzyme types in aerobes, and one in strict anaerobes. Only the gene of the large subunit of PQQ-dependent methanol dehydrogenase (mxaF has been analyzed by environmental pyrosequencing. To enable a comprehensive assessment of methanol utilizers in the environment, new primers targeting genes of the PQQ MDH in Methylibium (mdh2, of the NAD-dependent MDH (mdh, of the methanol oxidoreductase of Actinobacteria (mdo, of the fungal FAD-dependent alcohol oxidase (mod1, mod2, and homologues, and of the gene of the large subunit of the methanol:corrinoid methyltransferases (mtaC in methanogens and acetogens need to be developed. Combined stable isotope probing of nucleic acids or proteins with amplicon-based NGS are straightforward approaches to reveal insights into functions of certain methylotrophic taxa in the global methanol cycle.

  18. A Role for Myosin Va in Human Cytomegalovirus Nuclear Egress.

    Science.gov (United States)

    Wilkie, Adrian R; Sharma, Mayuri; Pesola, Jean M; Ericsson, Maria; Fernandez, Rosio; Coen, Donald M

    2018-03-15

    Herpesviruses replicate and package their genomes into capsids in replication compartments within the nuclear interior. Capsids then move to the inner nuclear membrane for envelopment and release into the cytoplasm in a process called nuclear egress. We previously found that nuclear F-actin is induced upon infection with the betaherpesvirus human cytomegalovirus (HCMV) and is important for nuclear egress and capsid localization away from replication compartment-like inclusions toward the nuclear rim. Despite these and related findings, it has not been shown that any specific motor protein is involved in herpesvirus nuclear egress. In this study, we have investigated whether the host motor protein, myosin Va, could be fulfilling this role. Using immunofluorescence microscopy and coimmunoprecipitation, we observed associations between a nuclear population of myosin Va and the viral major capsid protein, with both concentrating at the periphery of replication compartments. Immunoelectron microscopy showed that nearly 40% of assembled nuclear capsids associate with myosin Va. We also found that myosin Va and major capsid protein colocalize with nuclear F-actin. Importantly, antagonism of myosin Va with RNA interference or a dominant negative mutant revealed that myosin Va is important for the efficient production of infectious virus, capsid accumulation in the cytoplasm, and capsid localization away from replication compartment-like inclusions toward the nuclear rim. Our results lead us to suggest a working model whereby human cytomegalovirus capsids associate with myosin Va for movement from replication compartments to the nuclear periphery during nuclear egress. IMPORTANCE Little is known regarding how newly assembled and packaged herpesvirus capsids move from the nuclear interior to the periphery during nuclear egress. While it has been proposed that an actomyosin-based mechanism facilitates intranuclear movement of alphaherpesvirus capsids, a functional role for

  19. Patient deaths blamed on long waits at the Phoenix VA

    Directory of Open Access Journals (Sweden)

    Robbins RA

    2014-04-01

    Full Text Available No abstract available. Article truncated at 150 words. This morning the lead article in the Arizona Republic was a report blaming as many as 40 deaths at the Phoenix VA on long waits (1. Yesterday, Rep. Jeff Miller, the chairman of the House Committee on Veterans Affairs, held a hearing titled “A Continued Assessment of Delays in VA Medical Care and Preventable Veteran Deaths.” “It appears as though there could be as many as 40 veterans whose deaths could be related to delays in care,” Miller announced to a stunned audience. The committee has spent months investigating patient-care scandals and allegations at VA facilities in Pittsburgh, Atlanta, Miami and other cities. said that dozens of VA hospital patients in Phoenix may have died while awaiting medical care. He went on to say that staff investigators have evidence that the Phoenix VA Health Care System keeps two sets of records to conceal prolonged waits that patients must endure for ...

  20. VA's National PTSD Brain Bank: a National Resource for Research.

    Science.gov (United States)

    Friedman, Matthew J; Huber, Bertrand R; Brady, Christopher B; Ursano, Robert J; Benedek, David M; Kowall, Neil W; McKee, Ann C

    2017-08-25

    The National PTSD Brain Bank (NPBB) is a brain tissue biorepository established to support research on the causes, progression, and treatment of PTSD. It is a six-part consortium led by VA's National Center for PTSD with participating sites at VA medical centers in Boston, MA; Durham, NC; Miami, FL; West Haven, CT; and White River Junction, VT along with the Uniformed Services University of Health Sciences. It is also well integrated with VA's Boston-based brain banks that focus on Alzheimer's disease, ALS, chronic traumatic encephalopathy, and other neurological disorders. This article describes the organization and operations of NPBB with specific attention to: tissue acquisition, tissue processing, diagnostic assessment, maintenance of a confidential data biorepository, adherence to ethical standards, governance, accomplishments to date, and future challenges. Established in 2014, NPBB has already acquired and distributed brain tissue to support research on how PTSD affects brain structure and function.

  1. Poststroke Rehabilitation and Restorative Care Utilization: A Comparison Between VA Community Living Centers and VA-contracted Community Nursing Homes.

    Science.gov (United States)

    Jia, Huanguang; Pei, Qinglin; Sullivan, Charles T; Cowper Ripley, Diane C; Wu, Samuel S; Bates, Barbara E; Vogel, W Bruce; Bidelspach, Douglas E; Wang, Xinping; Hoffman, Nannette

    2016-03-01

    Effective poststroke rehabilitation care can speed patient recovery and minimize patient functional disabilities. Veterans affairs (VA) community living centers (CLCs) and VA-contracted community nursing homes (CNHs) are the 2 major sources of institutional long-term care for Veterans with stroke receiving care under VA auspices. This study compares rehabilitation therapy and restorative nursing care among Veterans residing in VA CLCs versus those Veterans in VA-contracted CNHs. Retrospective observational. All Veterans diagnosed with stroke, newly admitted to the CLCs or CNHs during the study period who completed at least 2 Minimum Data Set assessments postadmission. The outcomes were numbers of days for rehabilitation therapy and restorative nursing care received by the Veterans during their stays in CLCs or CNHs as documented in the Minimum Data Set databases. For rehabilitation therapy, the CLC Veterans had lower user rates (75.2% vs. 76.4%, P=0.078) and fewer observed therapy days (4.9 vs. 6.4, Pcare, CLC Veterans had higher user rates (33.5% vs. 30.6%, Pcare days (9.4 vs. 5.9, Pcare (coefficient=5.48±0.37, Pcare both before and after risk adjustment.

  2. VA Telemedicine: An Analysis of Cost and Time Savings.

    Science.gov (United States)

    Russo, Jack E; McCool, Ryan R; Davies, Louise

    2016-03-01

    The Veterans Affairs (VA) healthcare system provides beneficiary travel reimbursement ("travel pay") to qualifying patients for traveling to appointments. Travel pay is a large expense for the VA and hence the U.S. Government, projected to cost nearly $1 billion in 2015. Telemedicine in the VA system has the potential to save money by reducing patient travel and thus the amount of travel pay disbursed. In this study, we quantify this savings and also report trends in VA telemedicine volumes over time. All telemedicine visits based at the VA Hospital in White River Junction, VT between 2005 and 2013 were reviewed (5,695 visits). Travel distance and time saved as a result of telemedicine were calculated. Clinical volume in the mental health department, which has had the longest participation in telemedicine, was analyzed. Telemedicine resulted in an average travel savings of 145 miles and 142 min per visit. This led to an average travel payment savings of $18,555 per year. Telemedicine volume grew significantly over the study period such that by the final year the travel pay savings had increased to $63,804, or about 3.5% of the total travel pay disbursement for that year. The number of mental health telemedicine visits rose over the study period but remained small relative to the number of face-to-face visits. A higher proportion of telemedicine visits involved new patients. Telemedicine at the VA saves travel distance and time, although the reduction in travel payments remains modest at current telemedicine volumes.

  3. The WHO 2016 verbal autopsy instrument: An international standard suitable for automated analysis by InterVA, InSilicoVA, and Tariff 2.0.

    Directory of Open Access Journals (Sweden)

    Erin K Nichols

    2018-01-01

    Full Text Available Verbal autopsy (VA is a practical method for determining probable causes of death at the population level in places where systems for medical certification of cause of death are weak. VA methods suitable for use in routine settings, such as civil registration and vital statistics (CRVS systems, have developed rapidly in the last decade. These developments have been part of a growing global momentum to strengthen CRVS systems in low-income countries. With this momentum have come pressure for continued research and development of VA methods and the need for a single standard VA instrument on which multiple automated diagnostic methods can be developed.In 2016, partners harmonized a WHO VA standard instrument that fully incorporates the indicators necessary to run currently available automated diagnostic algorithms. The WHO 2016 VA instrument, together with validated approaches to analyzing VA data, offers countries solutions to improving information about patterns of cause-specific mortality. This VA instrument offers the opportunity to harmonize the automated diagnostic algorithms in the future.Despite all improvements in design and technology, VA is only recommended where medical certification of cause of death is not possible. The method can nevertheless provide sufficient information to guide public health priorities in communities in which physician certification of deaths is largely unavailable. The WHO 2016 VA instrument, together with validated approaches to analyzing VA data, offers countries solutions to improving information about patterns of cause-specific mortality.

  4. 78 FR 62441 - VA Dental Insurance Program-Federalism

    Science.gov (United States)

    2013-10-22

    ...--Federalism AGENCY: Department of Veterans Affairs. ACTION: Direct final rule. SUMMARY: The Department of... that they are submitted in response to ``RIN 2900-AO85-VA Dental Insurance Program-- Federalism... add preemption language in accordance with the discussion above. Executive Order 13132, Federalism...

  5. 78 FR 63143 - VA Dental Insurance Program-Federalism

    Science.gov (United States)

    2013-10-23

    ...--Federalism AGENCY: Department of Veterans Affairs. ACTION: Proposed rule. SUMMARY: The Department of Veterans... that they are submitted in response to ``RIN 2900-AO86-VA Dental Insurance Program-- Federalism... Order 13132, Federalism Section 6(c) of Executive Order 13132 (entitled ``Federalism'') requires an...

  6. VA Library Service--Today's look at Tomorrow's Library.

    Science.gov (United States)

    Veterans Administration, Washington, DC.

    The Conference Poceedings are divided into three broad topics: systems planning, audiovisuals in biomedical communication, and automation and networking. Speakers from within the Veterans Administration (VA), from the National Medical Audiovisual Center, and the Lister Hill National Center for Biomedical Communications, National Library of…

  7. What does Shulkin's firing mean for the VA?

    Directory of Open Access Journals (Sweden)

    Robbins RA

    2018-03-01

    Full Text Available No abstract available. Article truncated at 150 words. David Shulkin MD, Secretary for Veterans Affairs (VA was finally fired by President Donald Trump ending long speculation (1. Trump nominated his personal physician, Ronny Jackson MD, to fill Shulkin’s post. The day after his firing, Shulkin criticized his firing in a NY Times op-ed claiming pro-privatization factions within the Trump administration led to his ouster (2. “They saw me as an obstacle to privatization who had to be removed,” Dr. Shulkin wrote. “That is because I am convinced that privatization is a political issue aimed at rewarding select people and companies with profits, even if it undermines care for veterans.” Former Secretary Shulkin’s tenure at the VA has had several controversies. First, as undersecretary of Veterans Healthcare and later as secretary money appropriated to the VA to obtain private care under the Veterans Access, Choice, and Accountability Acts of 2014 and the VA Choice and Quality Employment Act of …

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

    DEFF Research Database (Denmark)

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

    2003-01-01

    . DFT Becke3LYP/6-31G* theory has been used to determine the geometry, Hessian, atomic polar tensors (APT), and atomic axial tensors (AAT), and the electric dipole-electric dipole polarizability derivatives (EDEDPD), which are required for us to simulate the VA, VCD, and Raman spectra. The electric...

  9. Unraveling Core Functional Microbiota in Traditional Solid-State Fermentation by High-Throughput Amplicons and Metatranscriptomics Sequencing.

    Science.gov (United States)

    Song, Zhewei; Du, Hai; Zhang, Yan; Xu, Yan

    2017-01-01

    Fermentation microbiota is specific microorganisms that generate different types of metabolites in many productions. In traditional solid-state fermentation, the structural composition and functional capacity of the core microbiota determine the quality and quantity of products. As a typical example of food fermentation, Chinese Maotai-flavor liquor production involves a complex of various microorganisms and a wide variety of metabolites. However, the microbial succession and functional shift of the core microbiota in this traditional food fermentation remain unclear. Here, high-throughput amplicons (16S rRNA gene amplicon sequencing and internal transcribed space amplicon sequencing) and metatranscriptomics sequencing technologies were combined to reveal the structure and function of the core microbiota in Chinese soy sauce aroma type liquor production. In addition, ultra-performance liquid chromatography and headspace-solid phase microextraction-gas chromatography-mass spectrometry were employed to provide qualitative and quantitative analysis of the major flavor metabolites. A total of 10 fungal and 11 bacterial genera were identified as the core microbiota. In addition, metatranscriptomic analysis revealed pyruvate metabolism in yeasts (genera Pichia, Schizosaccharomyces, Saccharomyces , and Zygosaccharomyces ) and lactic acid bacteria (genus Lactobacillus ) classified into two stages in the production of flavor components. Stage I involved high-level alcohol (ethanol) production, with the genus Schizosaccharomyces serving as the core functional microorganism. Stage II involved high-level acid (lactic acid and acetic acid) production, with the genus Lactobacillus serving as the core functional microorganism. The functional shift from the genus Schizosaccharomyces to the genus Lactobacillus drives flavor component conversion from alcohol (ethanol) to acid (lactic acid and acetic acid) in Chinese Maotai-flavor liquor production. Our findings provide insight into

  10. Unraveling Core Functional Microbiota in Traditional Solid-State Fermentation by High-Throughput Amplicons and Metatranscriptomics Sequencing

    Directory of Open Access Journals (Sweden)

    Zhewei Song

    2017-07-01

    Full Text Available Fermentation microbiota is specific microorganisms that generate different types of metabolites in many productions. In traditional solid-state fermentation, the structural composition and functional capacity of the core microbiota determine the quality and quantity of products. As a typical example of food fermentation, Chinese Maotai-flavor liquor production involves a complex of various microorganisms and a wide variety of metabolites. However, the microbial succession and functional shift of the core microbiota in this traditional food fermentation remain unclear. Here, high-throughput amplicons (16S rRNA gene amplicon sequencing and internal transcribed space amplicon sequencing and metatranscriptomics sequencing technologies were combined to reveal the structure and function of the core microbiota in Chinese soy sauce aroma type liquor production. In addition, ultra-performance liquid chromatography and headspace-solid phase microextraction-gas chromatography-mass spectrometry were employed to provide qualitative and quantitative analysis of the major flavor metabolites. A total of 10 fungal and 11 bacterial genera were identified as the core microbiota. In addition, metatranscriptomic analysis revealed pyruvate metabolism in yeasts (genera Pichia, Schizosaccharomyces, Saccharomyces, and Zygosaccharomyces and lactic acid bacteria (genus Lactobacillus classified into two stages in the production of flavor components. Stage I involved high-level alcohol (ethanol production, with the genus Schizosaccharomyces serving as the core functional microorganism. Stage II involved high-level acid (lactic acid and acetic acid production, with the genus Lactobacillus serving as the core functional microorganism. The functional shift from the genus Schizosaccharomyces to the genus Lactobacillus drives flavor component conversion from alcohol (ethanol to acid (lactic acid and acetic acid in Chinese Maotai-flavor liquor production. Our findings provide

  11. 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

    The simultaneous sequencing of samples from multiple individuals increases the efficiency of next-generation sequencing (NGS) while also reducing costs. Here we describe a novel and simple approach for sequencing DNA from multiple individuals per barcode. Our strategy relies on the endonuclease...... digestion of PCR amplicons prior to library preparation, creating a specific fragment pattern for each individual that can be resolved after sequencing. By using both barcodes and restriction fragment patterns, we demonstrate the ability to sequence the human melanocortin 1 receptor (MC1R) genes from 72...... individuals using only 24 barcoded libraries....

  12. Analysis of intra-host genetic diversity of Prunus necrotic ringspot virus (PNRSV) using amplicon next generation sequencing.

    Science.gov (United States)

    Kinoti, Wycliff M; Constable, Fiona E; Nancarrow, Narelle; Plummer, Kim M; Rodoni, Brendan

    2017-01-01

    PCR amplicon next generation sequencing (NGS) analysis offers a broadly applicable and targeted approach to detect populations of both high- or low-frequency virus variants in one or more plant samples. In this study, amplicon NGS was used to explore the diversity of the tripartite genome virus, Prunus necrotic ringspot virus (PNRSV) from 53 PNRSV-infected trees using amplicons from conserved gene regions of each of PNRSV RNA1, RNA2 and RNA3. Sequencing of the amplicons from 53 PNRSV-infected trees revealed differing levels of polymorphism across the three different components of the PNRSV genome with a total number of 5040, 2083 and 5486 sequence variants observed for RNA1, RNA2 and RNA3 respectively. The RNA2 had the lowest diversity of sequences compared to RNA1 and RNA3, reflecting the lack of flexibility tolerated by the replicase gene that is encoded by this RNA component. Distinct PNRSV phylo-groups, consisting of closely related clusters of sequence variants, were observed in each of PNRSV RNA1, RNA2 and RNA3. Most plant samples had a single phylo-group for each RNA component. Haplotype network analysis showed that smaller clusters of PNRSV sequence variants were genetically connected to the largest sequence variant cluster within a phylo-group of each RNA component. Some plant samples had sequence variants occurring in multiple PNRSV phylo-groups in at least one of each RNA and these phylo-groups formed distinct clades that represent PNRSV genetic strains. Variants within the same phylo-group of each Prunus plant sample had ≥97% similarity and phylo-groups within a Prunus plant sample and between samples had less ≤97% similarity. Based on the analysis of diversity, a definition of a PNRSV genetic strain was proposed. The proposed definition was applied to determine the number of PNRSV genetic strains in each of the plant samples and the complexity in defining genetic strains in multipartite genome viruses was explored.

  13. Analysis of intra-host genetic diversity of Prunus necrotic ringspot virus (PNRSV using amplicon next generation sequencing.

    Directory of Open Access Journals (Sweden)

    Wycliff M Kinoti

    Full Text Available PCR amplicon next generation sequencing (NGS analysis offers a broadly applicable and targeted approach to detect populations of both high- or low-frequency virus variants in one or more plant samples. In this study, amplicon NGS was used to explore the diversity of the tripartite genome virus, Prunus necrotic ringspot virus (PNRSV from 53 PNRSV-infected trees using amplicons from conserved gene regions of each of PNRSV RNA1, RNA2 and RNA3. Sequencing of the amplicons from 53 PNRSV-infected trees revealed differing levels of polymorphism across the three different components of the PNRSV genome with a total number of 5040, 2083 and 5486 sequence variants observed for RNA1, RNA2 and RNA3 respectively. The RNA2 had the lowest diversity of sequences compared to RNA1 and RNA3, reflecting the lack of flexibility tolerated by the replicase gene that is encoded by this RNA component. Distinct PNRSV phylo-groups, consisting of closely related clusters of sequence variants, were observed in each of PNRSV RNA1, RNA2 and RNA3. Most plant samples had a single phylo-group for each RNA component. Haplotype network analysis showed that smaller clusters of PNRSV sequence variants were genetically connected to the largest sequence variant cluster within a phylo-group of each RNA component. Some plant samples had sequence variants occurring in multiple PNRSV phylo-groups in at least one of each RNA and these phylo-groups formed distinct clades that represent PNRSV genetic strains. Variants within the same phylo-group of each Prunus plant sample had ≥97% similarity and phylo-groups within a Prunus plant sample and between samples had less ≤97% similarity. Based on the analysis of diversity, a definition of a PNRSV genetic strain was proposed. The proposed definition was applied to determine the number of PNRSV genetic strains in each of the plant samples and the complexity in defining genetic strains in multipartite genome viruses was explored.

  14. Sequence-specific validation of LAMP amplicons in real-time optomagnetic detection of Dengue serotype 2 synthetic DNA

    DEFF Research Database (Denmark)

    Minero, Gabriel Khose Antonio; Nogueira, Catarina; Rizzi, Giovanni

    2017-01-01

    We report on an optomagnetic technique optimised for real-time molecular detection of Dengue fever virus under ideal as well as non-ideal laboratory conditions using two different detection approaches. The first approach is based on the detection of the hydrodynamic volume of streptavidin coated...... magnetic nanoparticles attached to biotinylated LAMP amplicons. We demonstrate detection of sub-femtomolar Dengue DNA target concentrations in the ideal contamination-free lab environment within 20 min. The second detection approach is based on sequence-specific binding of functionalised magnetic...... claim detection of down to 100 fM of Dengue target after 20 min of LAMP with a contamination background....

  15. 76 FR 79067 - Payment or Reimbursement for Emergency Treatment Furnished by Non-VA Providers in Non-VA...

    Science.gov (United States)

    2011-12-21

    ... DEPARTMENT OF VETERANS AFFAIRS 38 CFR Part 17 RIN 2900-AN49 Payment or Reimbursement for Emergency..., authorize the Secretary of Veterans Affairs to reimburse eligible veterans for costs related to non-VA.... Specifically, section 1725 authorizes reimbursement for emergency treatment for eligible veterans with...

  16. 75 FR 33216 - Payment or Reimbursement for Emergency Treatment Furnished by Non-VA Providers in Non-VA...

    Science.gov (United States)

    2010-06-11

    ... health care services for veterans).'' Proposed Sec. 17.121(a) would establish the clinical decision maker... practice to utilize the services of health care professionals, such as nurses, for purposes of clinical review. For this reason, establishing the clinical decision maker as a ``designated VA clinician'' would...

  17. 78 FR 77204 - Proposed Information Collection (VA National Veterans Sports Programs and Special Event Surveys...

    Science.gov (United States)

    2013-12-20

    ... AGENCY: Office of Public & Intergovernmental Affairs, Department of Veterans Affairs. ACTION: Notice. SUMMARY: The Office of Public Affairs (OPA), Department of Veterans Affairs (VA), is announcing an... DEPARTMENT OF VETERANS AFFAIRS [OMB Control No. 2900-NEW] Proposed Information Collection (VA...

  18. 48 CFR 852.219-71 - VA mentor-protégé program.

    Science.gov (United States)

    2010-10-01

    ... 48 Federal Acquisition Regulations System 5 2010-10-01 2010-10-01 false VA mentor-protégÃ....219-71 VA mentor-protégé program. As prescribed in 819.7115(a), insert the following clause: VA Mentor-Protégé Program (DEC 2009) (a) Large businesses are encouraged to participate in the VA Mentor-Protégé...

  19. 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.

  20. 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.

  1. 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.

  2. 38 CFR 26.7 - VA environmental decision making and documents.

    Science.gov (United States)

    2010-07-01

    ... 38 Pensions, Bonuses, and Veterans' Relief 2 2010-07-01 2010-07-01 false VA environmental decision making and documents. 26.7 Section 26.7 Pensions, Bonuses, and Veterans' Relief DEPARTMENT OF VETERANS AFFAIRS (CONTINUED) ENVIRONMENTAL EFFECTS OF THE DEPARTMENT OF VETERANS AFFAIRS (VA) ACTIONS § 26.7 VA environmental decision making and document...

  3. 76 FR 24570 - Proposed Information Collection (Application for VA Education Benefits) Activity; Comment Request

    Science.gov (United States)

    2011-05-02

    ... (Application for VA Education Benefits) Activity; Comment Request AGENCY: Veterans Benefits Administration, Department of Veterans Affairs. ACTION: Notice. SUMMARY: The Veterans Benefits Administration (VBA... Under the Montgomery GI Bill, VA Form 22-1990E. c. Application for VA Education Benefits Under the...

  4. 78 FR 18425 - Proposed Information Collection VA Police Officer Pre-Employment Screening Checklist); Comment...

    Science.gov (United States)

    2013-03-26

    ... techniques or the use of other forms of information technology. Title: VA Police Officer Pre-Employment... Police Officer Pre-Employment Screening Checklist); Comment Request AGENCY: Office of Operations... approved collection. Abstract: VA personnel complete VA Form 0120 to document pre- employment history and...

  5. 48 CFR 852.219-9 - VA Small business subcontracting plan minimum requirements.

    Science.gov (United States)

    2010-10-01

    ... 48 Federal Acquisition Regulations System 5 2010-10-01 2010-10-01 false VA Small business... 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...

  6. 76 FR 71920 - Payment for Home Health Services and Hospice Care by Non-VA Providers

    Science.gov (United States)

    2011-11-21

    ... concerning the billing methodology for non-VA providers of home health services and hospice care. The proposed rulemaking would include home health services and hospice care under the VA regulation governing... to ``RIN 2900-AN98--Payment for home health and services and hospice care by non-VA providers...

  7. 78 FR 56271 - FY 2014-2020 Draft VA Strategic Plan

    Science.gov (United States)

    2013-09-12

    ... DEPARTMENT OF VETERANS AFFAIRS FY 2014-2020 Draft VA Strategic Plan AGENCY: Department of Veterans... Affairs (VA) is announcing the availability of the FY 2014-2020 Draft VA Strategic Plan (Strategic Plan... Act of 2010 (GPRAMA) (Pub. L. 111-352). The Strategic Plan provides the Department's long-term...

  8. 78 FR 76412 - Agency Information Collection (VA National Rehabilitation Special Events, Event Registration...

    Science.gov (United States)

    2013-12-17

    ... INFORMATION: Titles: a. National Disabled Veterans Winter Sports Clinic Application, VA Form 0924a, c, d and..., c, e. j. Voluntary Service Application, VA Form 0927f. k. National Veterans Summer sports Clinic... Festival Event Application, VA0929a, b, c, d, e, f, g, h. Type of Review: Revision of an already approved...

  9. 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.

  10. QCD sum-rules for V-A spectral functions

    International Nuclear Information System (INIS)

    Chakrabarti, J.; Mathur, V.S.

    1980-01-01

    The Borel transformation technique of Shifman et al is used to obtain QCD sum-rules for V-A spectral functions. In contrast to the situation in the original Weinberg sum-rules and those of Bernard et al, the problem of saturating the sum-rules by low lying resonances is brought under control. Furthermore, the present sum-rules, on saturation, directly determine useful phenomenological parameters

  11. CoVaCS: a consensus variant calling system.

    Science.gov (United States)

    Chiara, Matteo; Gioiosa, Silvia; Chillemi, Giovanni; D'Antonio, Mattia; Flati, Tiziano; Picardi, Ernesto; Zambelli, Federico; Horner, David Stephen; Pesole, Graziano; Castrignanò, Tiziana

    2018-02-05

    The advent and ongoing development of next generation sequencing technologies (NGS) has led to a rapid increase in the rate of human genome re-sequencing data, paving the way for personalized genomics and precision medicine. The body of genome resequencing data is progressively increasing underlining the need for accurate and time-effective bioinformatics systems for genotyping - a crucial prerequisite for identification of candidate causal mutations in diagnostic screens. Here we present CoVaCS, a fully automated, highly accurate system with a web based graphical interface for genotyping and variant annotation. Extensive tests on a gold standard benchmark data-set -the NA12878 Illumina platinum genome- confirm that call-sets based on our consensus strategy are completely in line with those attained by similar command line based approaches, and far more accurate than call-sets from any individual tool. Importantly our system exhibits better sensitivity and higher specificity than equivalent commercial software. CoVaCS offers optimized pipelines integrating state of the art tools for variant calling and annotation for whole genome sequencing (WGS), whole-exome sequencing (WES) and target-gene sequencing (TGS) data. The system is currently hosted at Cineca, and offers the speed of a HPC computing facility, a crucial consideration when large numbers of samples must be analysed. Importantly, all the analyses are performed automatically allowing high reproducibility of the results. As such, we believe that CoVaCS can be a valuable tool for the analysis of human genome resequencing studies. CoVaCS is available at: https://bioinformatics.cineca.it/covacs .

  12. Validation of KENO V.a: Comparison with critical experiments

    International Nuclear Information System (INIS)

    Jordan, W.C.; Landers, N.F.; Petrie, L.M.

    1986-12-01

    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. Sections 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/. 48 refs., 19 figs., 19 tabs

  13. Vectorization of the KENO V.a criticality safety code

    International Nuclear Information System (INIS)

    Hollenbach, D.F.; Dodds, H.L.; Petrie, L.M.

    1991-01-01

    The development of the vector processor, which is used in the current generation of supercomputers and is beginning to be used in workstations, provides the potential for dramatic speed-up for codes that are able to process data as vectors. Unfortunately, the stochastic nature of Monte Carlo codes prevents the old scalar version of these codes from taking advantage of the vector processors. New Monte Carlo algorithms that process all the histories undergoing the same event as a batch are required. Recently, new vectorized Monte Carlo codes have been developed that show significant speed-ups when compared to the scalar version of themselves or equivalent codes. This paper discusses the vectorization of an already existing and widely used criticality safety code, KENO V.a All the changes made to KENO V.a are transparent to the user making it possible to upgrade from the standard scalar version of KENO V.a to the vectorized version without learning a new code

  14. Identification of novel candidate target genes in amplicons of Glioblastoma multiforme tumors detected by expression and CGH microarray profiling

    Directory of Open Access Journals (Sweden)

    Hernández-Moneo Jose-Luis

    2006-09-01

    Full Text Available Abstract Background Conventional cytogenetic and comparative genomic hybridization (CGH studies in brain malignancies have shown that glioblastoma multiforme (GBM is characterized by complex structural and numerical alterations. However, the limited resolution of these techniques has precluded the precise identification of detailed specific gene copy number alterations. Results We performed a genome-wide survey of gene copy number changes in 20 primary GBMs by CGH on cDNA microarrays. A novel amplicon at 4p15, and previously uncharacterized amplicons at 13q32-34 and 1q32 were detected and are analyzed here. These amplicons contained amplified genes not previously reported. Other amplified regions containg well-known oncogenes in GBMs were also detected at 7p12 (EGFR, 7q21 (CDK6, 4q12 (PDGFRA, and 12q13-15 (MDM2 and CDK4. In order to identify the putative target genes of the amplifications, and to determine the changes in gene expression levels associated with copy number change events, we carried out parallel gene expression profiling analyses using the same cDNA microarrays. We detected overexpression of the novel amplified genes SLA/LP and STIM2 (4p15, and TNFSF13B and COL4A2 (13q32-34. Some of the candidate target genes of amplification (EGFR, CDK6, MDM2, CDK4, and TNFSF13B were tested in an independent set of 111 primary GBMs by using FISH and immunohistological assays. The novel candidate 13q-amplification target TNFSF13B was amplified in 8% of the tumors, and showed protein expression in 20% of the GBMs. Conclusion This high-resolution analysis allowed us to propose novel candidate target genes such as STIM2 at 4p15, and TNFSF13B or COL4A2 at 13q32-34 that could potentially contribute to the pathogenesis of these tumors and which would require futher investigations. We showed that overexpression of the amplified genes could be attributable to gene dosage and speculate that deregulation of those genes could be important in the development

  15. 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.

  16. VA Health Care: VA Spends Millions on Post-Traumatic Stress Disorder Research and Incorporates Research Outcomes into Guidelines and Policy for Post-Traumatic Stress Disorder Services

    Science.gov (United States)

    2011-01-01

    post - traumatic stress disorder ( PTSD ) and...Veterans Affairs (VA) Intramural Post - Traumatic Stress Disorder ( PTSD ) Research Funding and VA’s Medical and Prosthetic Research Appropriation...Table 6: Department of Veterans Affairs (VA) Research Centers and Programs That Conduct or Support Post - Traumatic Stress Disorder ( PTSD ) Research

  17. Building capacity in VA to provide emergency gynecology services for women.

    Science.gov (United States)

    Cordasco, Kristina M; Huynh, Alexis K; Zephyrin, Laurie; Hamilton, Alison B; Lau-Herzberg, Amy E; Kessler, Chad S; Yano, Elizabeth M

    2015-04-01

    Visits to Veterans Administration (VA) emergency departments (EDs) are increasingly being made by women. A 2011 national inventory of VA emergency services for women revealed that many EDs have gaps in their resources and processes for gynecologic emergency care. To guide VA in addressing these gaps, we sought to understand factors acting as facilitators and/or barriers to improving VA ED capacity for, and quality of, emergency gynecology care. Semistructured interviews with VA emergency and women's health key informants. ED directors/providers (n=14), ED nurse managers (n=13), and Women Veteran Program Managers (n=13) in 13 VA facilities. Leadership, staff, space, demand, funding, policies, and community were noted as important factors influencing VA EDs building capacity and improving emergency gynecologic care for women Veterans. These factors are intertwined and cross multiple organizational levels so that each ED's capacity is a reflection not only of its own factors, but also those of its local medical center and non-VA community context as well as VA regional and national trends and policies. Policies and quality improvement initiatives aimed at building VA's emergency gynecologic services for women need to be multifactorial and aimed at multiple organizational levels. Policies need to be flexible to account for wide variations across EDs and their medical center and community contexts. Approaches that build and encourage local leadership engagement, such as evidence-based quality improvement methodology, are likely to be most effective.

  18. Can reported VaR be used as an indicator of the volatility of share prices? Evidence from UK banks.

    OpenAIRE

    Ou, Shian Kao

    2006-01-01

    Value at Risk (VaR) is used as an indicator to measure the risks contained in a firm. With the uprising development of VaR theory and computational techniques, the VaR is nowadays adopted by banks and reported in annual reports. Since the method to calculate VaR is questioned, and the reported VaR can not be thoroughly audited, this paper attempts to find the relationship between the reported VaR and the volatility of share price for UK listed banks. This paper reviews literature about VaR an...

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

    DEFF Research Database (Denmark)

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

    2016-01-01

    BACKGROUND: There is an immense scientific interest in the human microbiome and its effects on human physiology, health, and disease. A common approach for examining bacterial communities is high-throughput sequencing of 16S rRNA gene hypervariable regions, aggregating sequence-similar amplicons...

  20. Prostate-Specific and Tumor-Specific Targeting of an Oncolytic HSV-1 Amplicon/Helper Virus for Prostate Cancer Treatment

    Science.gov (United States)

    2009-11-01

    regulation HSV-1 amplicon and recombinant viruses Molecular cloning Cell culture/gene transfection Xenograft mouse model Histology 20...no herpetic lesions were seen in CMV-ICP4-143T–treated and CMV-ICP4-145T– treated animals, although some gastritis developed 28 days after the viral

  1. A need for standardization in drinking water analysis – an investigation of DNA extraction procedure, primer choice and detection limit of 16S rRNA amplicon sequencing

    DEFF Research Database (Denmark)

    Brandt, Jakob; Nielsen, Per Halkjær; Albertsen, Mads

    have been made to illuminate the effects specifically related to bacterial communities in drinking water. In this study, we investigated the impact of the DNA extraction and primer choice on the observed community structure, and we also estimated the detection limit of the 16S rRNA amplicon sequencing...

  2. V.A. Gorodtsov and Kazan: tour 1920

    Directory of Open Access Journals (Sweden)

    Kuzminykh Sergey V.

    2014-12-01

    Full Text Available A fragment of an archival document is published, that is connected to the September 8-12, 1920, stay in Kazan of V.A. Gorodtsov, who headed the Archaeological Subdepartment with the Museum Department of the RSFSR People’s Commissariat for Education, in the framework of his inspecting tour around the towns of the Volga and Urals region. The document is a diary, and its entries reflect information about the tour and its results that had not been exhaustively reflected in official documentation. It narrates about meetings, polemic exchanges, Gorodtsov’s addresses to scientists and the public, his impressions of the archaeological investigations in the regions, and the state of the museums and collections. V.A. Gorodtsov’s encounters and personal contacts with B.F. Adler, N.F. Katanov, M.G. Hudyakov and other researchers had played a positive role in archaeology development in the Volga-Kama region during the hardest times after the revolution.

  3. 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.

  4. Characteristics Associated With Utilization of VA and Non-VA Care Among Iraq and Afghanistan Veterans With Post-Traumatic Stress Disorder.

    Science.gov (United States)

    Finley, Erin P; Mader, Michael; Bollinger, Mary J; Haro, Elizabeth K; Garcia, Hector A; Huynh, Alexis K; Pugh, Jacqueline A; Pugh, Mary Jo

    2017-11-01

    Post-traumatic stress disorder (PTSD) affects nearly one-fifth of Iraq and Afghanistan Veterans (IAV). The Department of Veterans Affairs (VA) has invested in making evidence-based psychotherapies for PTSD available at every VA facility nationwide; however, an unknown number of veterans opt to receive care in the community rather than with VA. We compared PTSD care utilization patterns among Texas IAV with PTSD, an ethnically, geographically, and economically diverse group. To identify IAV in Texas with service-connected disability for PTSD, we used a crosswalk of VA administrative data from the Operation Enduring Freedom/Operation Iraqi Freedom Roster and service-connected disability data from the Veterans Benefits Administration. We then surveyed a random sample of 1,128 veterans from the cohort, stratified by sex, rurality, and past use/nonuse of any VA care. Respondents were classified into current utilization groups (VA only, non-VA only, dual care, and no professional PTSD treatment) on the basis of reported PTSD care in the prior 12 months. Responses were weighted to account for sample stratification and for response rate within each strata. Utilization group characteristics were compared to the population mean using the one sample Z-test for proportions, or the t-test for means. A multinomial logistic regression model was used to identify survey variables significantly associated with current utilization group. 249 IAV completed the survey (28.4% response rate). Respondents reported receiving PTSD care: in the VA only (58.3%); in military or community-based settings (including private practitioners) (non-VA only, 8.7%); and in both VA and non-VA settings (dual care, 14.5%). The remainder (18.5%) reported no professional PTSD care in the prior year. Veterans ineligible for Department of Defense care, uncomfortable talking about their problems, and opposed to medication were more likely to receive non-VA care only, whereas those with lower household income

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

    International Nuclear Information System (INIS)

    Busch, R.D.

    2003-01-01

    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

  6. Job satisfaction and burnout among VA and community mental health workers.

    Science.gov (United States)

    Salyers, Michelle P; Rollins, Angela L; Kelly, Yu-Fan; Lysaker, Paul H; Williams, Jane R

    2013-03-01

    Building on two independent studies, we compared burnout and job satisfaction of 66 VA staff and 86 community mental health center staff in the same city. VA staff reported significantly greater job satisfaction and accomplishment, less emotional exhaustion and lower likelihood of leaving their job. Sources of work satisfaction were similar (primarily working with clients, helping/witnessing change). VA staff reported fewer challenges with job-related aspects (e.g. flexibility, pay) but more challenges with administration. Community mental health administrators and policymakers may need to address job-related concerns (e.g. pay) whereas VA administrators may focus on reducing, and helping workers navigate, administrative policies.

  7. 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…

  8. 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.

  9. 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.

  10. 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. Copyright © 2016 Elsevier B.V. All rights reserved.

  11. 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.

  12. Evolution of MHC class I genes in the endangered loggerhead sea turtle (Caretta caretta) revealed by 454 amplicon sequencing.

    Science.gov (United States)

    Stiebens, Victor A; Merino, Sonia E; Chain, Frédéric J J; Eizaguirre, Christophe

    2013-04-30

    In evolutionary and conservation biology, parasitism is often highlighted as a major selective pressure. To fight against parasites and pathogens, genetic diversity of the immune genes of the major histocompatibility complex (MHC) are particularly important. However, the extensive degree of polymorphism observed in these genes makes it difficult to conduct thorough population screenings. We utilized a genotyping protocol that uses 454 amplicon sequencing to characterize the MHC class I in the endangered loggerhead sea turtle (Caretta caretta) and to investigate their evolution at multiple relevant levels of organization. MHC class I genes revealed signatures of trans-species polymorphism across several reptile species. In the studied loggerhead turtle individuals, it results in the maintenance of two ancient allelic lineages. We also found that individuals carrying an intermediate number of MHC class I alleles are larger than those with either a low or high number of alleles. Multiple modes of evolution seem to maintain MHC diversity in the loggerhead turtles, with relatively high polymorphism for an endangered species.

  13. PipeCraft: Flexible open-source toolkit for bioinformatics analysis of custom high-throughput amplicon sequencing data.

    Science.gov (United States)

    Anslan, Sten; Bahram, Mohammad; Hiiesalu, Indrek; Tedersoo, Leho

    2017-11-01

    High-throughput sequencing methods have become a routine analysis tool in environmental sciences as well as in public and private sector. These methods provide vast amount of data, which need to be analysed in several steps. Although the bioinformatics may be applied using several public tools, many analytical pipelines allow too few options for the optimal analysis for more complicated or customized designs. Here, we introduce PipeCraft, a flexible and handy bioinformatics pipeline with a user-friendly graphical interface that links several public tools for analysing amplicon sequencing data. Users are able to customize the pipeline by selecting the most suitable tools and options to process raw sequences from Illumina, Pacific Biosciences, Ion Torrent and Roche 454 sequencing platforms. We described the design and options of PipeCraft and evaluated its performance by analysing the data sets from three different sequencing platforms. We demonstrated that PipeCraft is able to process large data sets within 24 hr. The graphical user interface and the automated links between various bioinformatics tools enable easy customization of the workflow. All analytical steps and options are recorded in log files and are easily traceable. © 2017 John Wiley & Sons Ltd.

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

    Science.gov (United States)

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

    2017-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Ilias Lagkouvardos

    2017-01-01

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

  16. Fireworks algorithm for mean-VaR/CVaR models

    Science.gov (United States)

    Zhang, Tingting; Liu, Zhifeng

    2017-10-01

    Intelligent algorithms have been widely applied to portfolio optimization problems. In this paper, we introduce a novel intelligent algorithm, named fireworks algorithm, to solve the mean-VaR/CVaR model for the first time. The results show that, compared with the classical genetic algorithm, fireworks algorithm not only improves the optimization accuracy and the optimization speed, but also makes the optimal solution more stable. We repeat our experiments at different confidence levels and different degrees of risk aversion, and the results are robust. It suggests that fireworks algorithm has more advantages than genetic algorithm in solving the portfolio optimization problem, and it is feasible and promising to apply it into this field.

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

    International Nuclear Information System (INIS)

    Thiele, R.; Horn, B.; Coates, C.W.; Stainback, J.R.

    2001-01-01

    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)

  18. Archetypal Analysis of "Almalek and Albrahmh” from Kalila va Demna

    Directory of Open Access Journals (Sweden)

    Ali Noori

    2016-12-01

    Full Text Available Archetype Theory, has been raised from Carl Gustav Young’s Psychoanalytical School. Young knows mental images and Sediments and Hereditary information which there are in the collective unconscious as Archetype. In other word, archetype is general type of repeated experiences and behaviors of human forefathers which rooted in collective unconscious. the most important Archetypes are "Anima"," Animus", "old wise man", "shadow", "mask", "rebirth" ,and "self" and "individuality". Kalila va Demna is the book which is full of allegorical stories, which because of their mythical aspect, are researchable from Archetypal Analytic criticism. One of this stories which Archetypal color is Dominant in it, is "Almalek and Albrahmh” from 16th chapter of Kalila va Demna. In this study, some archetypes such as "shadow", "Anima", "mask", "old wise man", " self " and "individuality" in the story of "Almalek and Albrahmh" from sixteenth chapter of book, has been analyzed. Since either this tale because of being legendary, and consisting of series of dreams – which have given it mythical, symbolic and interpretable nature – has capacity for archetypal analysis, or archetypal approach has high capacity and power to analyze such narrations. The story was investigated on mentioned view, and it was found that king Heblar which has stricken to a kind of Psychosis, Finds its way into the subconscious through dreams and After a confrontation with his anima, under guidance of old wise meets his self (true self and reach to his individuality and Is rescued from distress. It can be said that the king starts his path of the individual process with a dream.  He, in the bigining of the story, with the help of Iran Dokht and at the end of the story, with the help of minister is released of grief and psychosis.

  19. Development of a continuous energy version of KENO V.a

    International Nuclear Information System (INIS)

    Dunn, M.E.; Bentley, C.L.; Goluoglu, S.; Paschal, L.S.; Dodds, H.L.

    1997-01-01

    KENO V.a is a multigroup Monte Carlo code that solves the Boltzmann transport equation and is used extensively in the nuclear criticality safety community to calculate the effective multiplication factor k eff of systems containing fissile material. Because of the smaller amount of disk storage and CPU time required in calculations, multigroup approaches have been preferred over continuous energy (point) approaches in the past to solve the transport equation. With the advent of high-performance computers, storage and CPU limitations are less restrictive, thereby making continuous energy methods viable for transport calculations. Moreover, continuous energy methods avoid many of the assumptions and approximations inherent in multigroup methods. Because a continuous energy version of KENO V.a does not exist, the objective of the work is to develop a new version of KENO V.a that utilizes continuous energy cross sections. Currently, a point cross-section library, which is based on a raw continuous energy cross-section library such as ENDF/B-V is not available for implementation in KENO V.a; however, point cross-section libraries are available for MCNP, another widely used Monte Carlo transport code. Since MCNP cross sections are based on ENDF data and are readily available, a new version of KENO V.a named PKENO V.a has been developed that performs the random walk using MCNP cross sections. To utilize point cross sections, extensive modifications have been made to KENO V.a. At this point in the research, testing of the code is underway. In particular, PKENO V.a, KENO V.a, and MCNP have been used to model nine critical experiments and one subcritical problem. The results obtained with PKENO V.a are in excellent agreement with MCNP, KENO V.a, and experiments

  20. A quantitative and qualitative comparison of illumina MiSeq and 454 amplicon sequencing for genotyping the highly polymorphic major histocompatibility complex (MHC) in a non-model species.

    Science.gov (United States)

    Razali, Haslina; O'Connor, Emily; Drews, Anna; Burke, Terry; Westerdahl, Helena

    2017-07-28

    High-throughput sequencing enables high-resolution genotyping of extremely duplicated genes. 454 amplicon sequencing (454) has become the standard technique for genotyping the major histocompatibility complex (MHC) genes in non-model organisms. However, illumina MiSeq amplicon sequencing (MiSeq), which offers a much higher read depth, is now superseding 454. The aim of this study was to quantitatively and qualitatively evaluate the performance of MiSeq in relation to 454 for genotyping MHC class I alleles using a house sparrow (Passer domesticus) dataset with pedigree information. House sparrows provide a good study system for this comparison as their MHC class I genes have been studied previously and, consequently, we had prior expectations concerning the number of alleles per individual. We found that 454 and MiSeq performed equally well in genotyping amplicons with low diversity, i.e. amplicons from individuals that had fewer than 6 alleles. Although there was a higher rate of failure in the 454 dataset in resolving amplicons with higher diversity (6-9 alleles), the same genotypes were identified by both 454 and MiSeq in 98% of cases. We conclude that low diversity amplicons are equally well genotyped using either 454 or MiSeq, but the higher coverage afforded by MiSeq can lead to this approach outperforming 454 in amplicons with higher diversity.

  1. 76 FR 38302 - Safety Zone; Cape Charles Fireworks, Cape Charles Harbor, Cape Charles, VA

    Science.gov (United States)

    2011-06-30

    ... the Town of Cape Charles will sponsor a fireworks display on the shoreline of the navigable waters of...-AA00 Safety Zone; Cape Charles Fireworks, Cape Charles Harbor, Cape Charles, VA AGENCY: Coast Guard... navigable waters of Cape Charles City Harbor in Cape Charles, VA in support of the Fourth of July Fireworks...

  2. 76 FR 27970 - Safety Zone; Cape Charles Fireworks, Cape Charles Harbor, Cape Charles, VA.

    Science.gov (United States)

    2011-05-13

    ... Charles will sponsor a fireworks display on the shoreline of the navigable waters of Cape Charles City...[deg]01'30'' W (NAD 1983). This safety zone will be established in the vicinity of Cape Charles, VA...-AA00 Safety Zone; Cape Charles Fireworks, Cape Charles Harbor, Cape Charles, VA. AGENCY: Coast Guard...

  3. 77 FR 29929 - Safety Zone; Town of Cape Charles Fireworks, Cape Charles Harbor, Cape Charles, VA

    Science.gov (United States)

    2012-05-21

    ... section of this notice. Basis and Purpose On July 4, 2012 the Town of Cape Charles will sponsor a...-AA00 Safety Zone; Town of Cape Charles Fireworks, Cape Charles Harbor, Cape Charles, VA AGENCY: Coast... temporary safety zone on the waters of Cape Charles City Harbor in Cape Charles, VA in support of the Fourth...

  4. 77 FR 60746 - Proposed Information Collection (VA/DOD Joint Disability Evaluation Board Claim) Activity...

    Science.gov (United States)

    2012-10-04

    ... burden of the collection of information on respondents, including through the use of automated collection techniques or the use of other forms of information technology. Title: VA/DOD Joint Disability Evaluation... War on Terror Heroes, VA and the Department of Defense (DOD) have agreed to develop a joint process in...

  5. 76 FR 44288 - Establishment of Class E Airspace; New Market, VA

    Science.gov (United States)

    2011-07-25

    ...-380; Airspace Docket No. 11-AEA-12] Establishment of Class E Airspace; New Market, VA AGENCY: Federal... proposes to establish Class E Airspace at New Market, VA, to accommodate the additional airspace needed for the Standard Instrument Approach Procedures developed for New Market Airport. This action would...

  6. 38 CFR 1.9 - Description, use, and display of VA seal and flag.

    Science.gov (United States)

    2010-07-01

    ... stars represent the five branches of military service. The crossed flags represent our nation's history... employees. (D) Official VA signs. (E) Official publications or graphics issued by and attributed to VA, or...) Souvenir or novelty items. (iii) Toys or commercial gifts or premiums. (iv) Letterhead design, except on...

  7. 78 FR 31840 - Safety Zone; USO Patriotic Festival Air Show, Atlantic Ocean; Virginia Beach, VA

    Science.gov (United States)

    2013-05-28

    ...-AA00 Safety Zone; USO Patriotic Festival Air Show, Atlantic Ocean; Virginia Beach, VA AGENCY: Coast... provide for the safety of life on navigable waters during the USO Patriotic Festival Air Show. This action... Patriotic Festival Air Show, Atlantic Ocean; Virginia Beach, VA. (a) Regulated Area. The following area is a...

  8. 77 FR 74279 - Agency Information Collection (VA/DOD Joint Disability Evaluation Board Claim): Activity under...

    Science.gov (United States)

    2012-12-13

    ... Joint Disability Evaluation Board Claim): Activity under OMB Review AGENCY: Veterans Benefits... . Please refer to ``OMB Control No. 2900-0704.'' SUPPLEMENTARY INFORMATION: Title: VA/DOD Joint Disability Evaluation Board Claim, VA Form 21- 0819. OMB Control Number: 2900-0704. Type of Review: Extension of a...

  9. 75 FR 25321 - Agency Information Collection (VA National Rehabilitation Special Events, Event Registration...

    Science.gov (United States)

    2010-05-07

    ... Winter Sports Clinic Application, VA Form 0924a series. b. National Veterans Wheelchair Games Application.... National Veterans TEE Tournament Application, VA Form 0927a series. e. National Veterans Summer Sports... Form 0929a series. Type of Review: Existing collection in use without an OMB control number. Abstract...

  10. 48 CFR 853.236-70 - VA Form 10-6298, Architect-Engineer Fee Proposal.

    Science.gov (United States)

    2010-10-01

    ... 48 Federal Acquisition Regulations System 5 2010-10-01 2010-10-01 false VA Form 10-6298, Architect-Engineer Fee Proposal. 853.236-70 Section 853.236-70 Federal Acquisition Regulations System DEPARTMENT OF...-Engineer Fee Proposal. VA Form 10-6298, Architect-Engineer Fee Proposal, shall be used as prescribed in 836...

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

    NARCIS (Netherlands)

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

    2015-01-01

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

  12. 38 CFR 3.2130 - Will VA accept a signature by mark or thumbprint?

    Science.gov (United States)

    2010-07-01

    ... signature by mark or thumbprint? 3.2130 Section 3.2130 Pensions, Bonuses, and Veterans' Relief DEPARTMENT OF... of This Title General § 3.2130 Will VA accept a signature by mark or thumbprint? VA will accept signatures by mark or thumbprint if: (a) They are witnessed by two people who sign their names and give their...

  13. 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...

  14. 38 CFR 74.26 - What types of business information will VA collect?

    Science.gov (United States)

    2010-07-01

    ... VETERANS AFFAIRS (CONTINUED) VETERANS SMALL BUSINESS REGULATIONS Records Management § 74.26 What types of business information will VA collect? VA will examine a variety of business records. See § 74.12, “What is... 38 Pensions, Bonuses, and Veterans' Relief 2 2010-07-01 2010-07-01 false What types of business...

  15. 77 FR 21158 - VA Directive 0005 on Scientific Integrity: Availability for Review and Comment

    Science.gov (United States)

    2012-04-09

    ... Draft VA Directive 0005 on Scientific Integrity: [square] Fosters a culture of transparency, integrity, and ethical behavior in the development and application of scientific and technological findings in VA... information from inappropriate political or commercial influence; [square] Ensures that selection and...

  16. 48 CFR 803.7000 - Display of the VA Hotline poster.

    Science.gov (United States)

    2010-10-01

    ... poster. 803.7000 Section 803.7000 Federal Acquisition Regulations System DEPARTMENT OF VETERANS AFFAIRS... Improper Business Practices 803.7000 Display of the VA Hotline poster. (a) Under the circumstances described in paragraph (b) of this section, a contractor must display prominently a VA Hotline poster...

  17. 76 FR 27381 - Proposed Information Collection (Notice of Waiver of VA Compensation or Pension To Receive...

    Science.gov (United States)

    2011-05-11

    ... waive VA benefits for the number of days equal to the number of days in which they received training pay... of Waiver of VA Compensation or Pension To Receive Military Pay and Allowances) Activity; Comment... currently approved collection, and allow 60 days for public comment in response to the notice. This notice...

  18. 78 FR 66265 - Drawbridge Operation Regulation; Elizabeth River, Eastern Branch, Norfolk, VA

    Science.gov (United States)

    2013-11-05

    ... Operation Regulation; Elizabeth River, Eastern Branch, Norfolk, VA AGENCY: Coast Guard, DHS. ACTION: Notice... Elizabeth River Eastern Branch, mile 1.1, at Norfolk, VA. This deviation is necessary to facilitate... maintenance. The Norfolk Southern 5 railroad Bridge, at mile 1.1, across the Elizabeth River (Eastern Branch...

  19. 78 FR 55777 - Proposed Information Collection (VA, National Veterans Sports Programs and Special Events, Event...

    Science.gov (United States)

    2013-09-11

    ... techniques or the use of other forms of information technology. Titles: a. National Disabled Veterans Winter... Form 0928h. m. Surfing Personnel Application, VA Form 0928i. n. Venue Personnel Application, VA Form... Creative Arts Festival, National Veterans TEE Tournament, National Disabled Veterans Winter Sports Clinic...

  20. Comparing VA and private sector healthcare costs for end-stage renal disease.

    Science.gov (United States)

    Hynes, Denise M; Stroupe, Kevin T; Fischer, Michael J; Reda, Domenic J; Manning, Willard; Browning, Margaret M; Huo, Zhiping; Saban, Karen; Kaufman, James S

    2012-02-01

    Healthcare for end-stage renal disease (ESRD) is intensive, expensive, and provided in both the public and private sector. Using a societal perspective, we examined healthcare costs and health outcomes for Department of Veterans Affairs (VA) ESRD patients comparing those who received hemodialysis care at VA versus private sector facilities. Dialysis patients were recruited from 8 VA medical centers from 2001 through 2003 and followed for 12 months in a prospective cohort study. Patient demographics, clinical characteristics, quality of life, healthcare use, and cost data were collected. Healthcare data included utilization (VA), claims (Medicare), and patient self-report. Costs included VA calculated costs, Medicare dialysis facility reports and reimbursement rates, and patient self-report. Multivariable regression was used to compare costs between patients receiving dialysis at VA versus private sector facilities. The cohort comprised 334 patients: 170 patients in the VA dialysis group and 164 patients in the private sector group. The VA dialysis group had more comorbidities at baseline, outpatient and emergency visits, prescriptions, and longer hospital stays; they also had more conservative anemia management and lower baseline urea reduction ratio (67% vs. 72%; Pprivate sector dialysis group (Pprivate sector settings is critical in informing health policy options for patients with complex chronic illnesses such as ESRD.

  1. 75 FR 34934 - Safety Zone; Fireworks for the Virginia Lake Festival, Buggs Island Lake, Clarksville, VA

    Science.gov (United States)

    2010-06-21

    ...-AA00 Safety Zone; Fireworks for the Virginia Lake Festival, Buggs Island Lake, Clarksville, VA AGENCY... Fireworks for the Virginia Lake Festival event. This action is intended to restrict vessel traffic movement... Virginia Lake Festival, Buggs Island Lake, Clarksville, VA (a) Regulated Area. The following area is a...

  2. MODEL NON LINIER GARCH (NGARCH UNTUK MENGESTIMASI NILAI VALUE at RISK (VaR PADA IHSG

    Directory of Open Access Journals (Sweden)

    I KOMANG TRY BAYU MAHENDRA

    2015-06-01

    Full Text Available In investment, risk measurement is important. One of risk measure is Value at Risk (VaR. There are many methods that can be used to estimate risk based on VaR framework. One of them Non Linier GARCH (NGARCH model. In this research, determination of VaR used NGARCH model. NGARCH model allowed for asymetric behaviour in the volatility such that “good news” or positive return and “bad news” or negative return. Based on calculations of VaR, the higher of the confidence level and the longer the investment period, the risk was greater. Determination of VaR using NGARCH model was less than GARCH model.

  3. 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.

  4. 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.

  5. Using surface-enhanced Raman spectroscopy and electrochemically driven melting to discriminate Yersinia pestis from Y. pseudotuberculosis based on single nucleotide polymorphisms within unpurified polymerase chain reaction amplicons.

    Science.gov (United States)

    Papadopoulou, Evanthia; Goodchild, Sarah A; Cleary, David W; Weller, Simon A; Gale, Nittaya; Stubberfield, Michael R; Brown, Tom; Bartlett, Philip N

    2015-02-03

    The development of sensors for the detection of pathogen-specific DNA, including relevant species/strain level discrimination, is critical in molecular diagnostics with major impacts in areas such as bioterrorism and food safety. Herein, we use electrochemically driven denaturation assays monitored by surface-enhanced Raman spectroscopy (SERS) to target single nucleotide polymorphisms (SNPs) that distinguish DNA amplicons generated from Yersinia pestis, the causative agent of plague, from the closely related species Y. pseudotuberculosis. Two assays targeting SNPs within the groEL and metH genes of these two species have been successfully designed. Polymerase chain reaction (PCR) was used to produce Texas Red labeled single-stranded DNA (ssDNA) amplicons of 262 and 251 bases for the groEL and metH targets, respectively. These amplicons were used in an unpurified form to hybridize to immobilized probes then subjected to electrochemically driven melting. In all cases electrochemically driven melting was able to discriminate between fully homologous DNA and that containing SNPs. The metH assay was particularly challenging due to the presence of only a single base mismatch in the middle of the 251 base long PCR amplicon. However, manipulation of assay conditions (conducting the electrochemical experiments at 10 °C) resulted in greater discrimination between the complementary and mismatched DNA. Replicate data were collected and analyzed for each duplex on different days, using different batches of PCR product and different sphere segment void (SSV) substrates. Despite the variability introduced by these differences, the assays are shown to be reliable and robust providing a new platform for strain discrimination using unpurified PCR samples.

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

    Science.gov (United States)

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

    2015-01-01

    Researchers at the U.S. Department of Veterans Affairs (VA) have used administrative criteria to identify homelessness among U.S. Veterans. Our objective was to explore the use of these codes in VA health care facilities. We examined VA health records (2002-2012) of Veterans recently separated from the military and identified as homeless using VA conventional identification criteria (ICD-9-CM code V60.0, VA specific codes for homeless services), plus closely allied V60 codes indicating housing instability. Logistic regression analyses examined differences between Veterans who received these codes. Health care services and co-morbidities were analyzed in the 90 days post-identification of homelessness. VA conventional criteria identified 21,021 homeless Veterans from Operations Enduring Freedom, Iraqi Freedom, and New Dawn (rate 2.5%). Adding allied V60 codes increased that to 31,260 (rate 3.3%). While certain demographic differences were noted, Veterans identified as homeless using conventional or allied codes were similar with regards to utilization of homeless, mental health, and substance abuse services, as well as co-morbidities. Differences were noted in the pattern of usage of homelessness-related diagnostic codes in VA facilities nation-wide. Creating an official VA case definition for homelessness, which would include additional ICD-9-CM and other administrative codes for VA homeless services, would likely allow improved identification of homeless and at-risk Veterans. This also presents an opportunity for encouraging uniformity in applying these codes in VA facilities nationwide as well as in other large health care organizations. PMID:26172386

  7. 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.

  8. 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. Copyright © 2015. Published by Elsevier Inc.

  9. HeurAA: accurate and fast detection of genetic variations with a novel heuristic amplicon aligner program for next generation sequencing.

    Directory of Open Access Journals (Sweden)

    Lőrinc S Pongor

    Full Text Available Next generation sequencing (NGS of PCR amplicons is a standard approach to detect genetic variations in personalized medicine such as cancer diagnostics. Computer programs used in the NGS community often miss insertions and deletions (indels that constitute a large part of known human mutations. We have developed HeurAA, an open source, heuristic amplicon aligner program. We tested the program on simulated datasets as well as experimental data from multiplex sequencing of 40 amplicons in 12 oncogenes collected on a 454 Genome Sequencer from lung cancer cell lines. We found that HeurAA can accurately detect all indels, and is more than an order of magnitude faster than previous programs. HeurAA can compare reads and reference sequences up to several thousand base pairs in length, and it can evaluate data from complex mixtures containing reads of different gene-segments from different samples. HeurAA is written in C and Perl for Linux operating systems, the code and the documentation are available for research applications at http://sourceforge.net/projects/heuraa/

  10. 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

  11. Recombinant adeno-associated virus type 2 replication and packaging is entirely supported by a herpes simplex virus type 1 amplicon expressing Rep and Cap.

    Science.gov (United States)

    Conway, J E; Zolotukhin, S; Muzyczka, N; Hayward, G S; Byrne, B J

    1997-11-01

    Recombinant adeno-associated virus (AAV) type 2 (rAAV) vectors have recently been shown to have great utility as gene transfer agents both in vitro and in vivo. One of the problems associated with the use of rAAV vectors has been the difficulty of large-scale vector production. Low-efficiency plasmid transfection of the rAAV vector and complementing AAV type 2 (AAV-2) functions (rep and cap) followed by superinfection with adenovirus has been the standard approach to rAAV production. The objectives of this study were to demonstrate the ability of a recombinant herpes simplex virus type 1 (HSV-1) amplicon expressing AAV-2 Rep and Cap to support replication and packaging of rAAV vectors. HSV-1 amplicon vectors were constructed which contain the AAV-2 rep and cap genes under control of their native promoters (p5, p19, and p40). An HSV-1 amplicon vector, HSV-RC/KOS or HSV-RC/d27, was generated by supplying helper functions with either wild-type HSV-1 (KOS strain) or the ICP27-deleted mutant of HSV-1, d27-1, respectively. Replication of the amplicon stocks is not inhibited by the presence of AAV-2 Rep proteins, which highlights important differences between HSV-1 and adenovirus replication and the mechanism of providing helper function for productive AAV infection. Coinfection of rAAV and HSV-RC/KOS resulted in the replication and amplification of rAAV genomes. Similarly, rescue and replication of rAAV genomes occurred when rAAV vector plasmids were transfected into cells followed by HSV-RC/KOS infection and when two rAAV proviral cell lines were infected with HSV-RC/KOS or HSV-RC/d27. Production of infectious rAAV by rescue from two rAAV proviral cell lines has also been achieved with HSV-RC/KOS and HSV-RC/d27. The particle titer of rAAV produced with HSV-RC/d27 is equal to that achieved by supplying rep and cap by transfection followed by adenovirus superinfection. Importantly, no detectable wild-type AAV-2 is generated with this approach. These results demonstrate

  12. Cytomegalovirus sequence variability, amplicon length, and DNase-sensitive non-encapsidated genomes are obstacles to standardization and commutability of plasma viral load results.

    Science.gov (United States)

    Naegele, Klaudia; Lautenschlager, Irmeli; Gosert, Rainer; Loginov, Raisa; Bir, Katia; Helanterä, Ilkka; Schaub, Stefan; Khanna, Nina; Hirsch, Hans H

    2018-04-22

    Cytomegalovirus (CMV) management post-transplantation relies on quantification in blood, but inter-laboratory and inter-assay variability impairs commutability. An international multicenter study demonstrated that variability is mitigated by standardizing plasma volumes, automating DNA extraction and amplification, and calibration to the 1st-CMV-WHO-International-Standard as in the FDA-approved Roche-CAP/CTM-CMV. However, Roche-CAP/CTM-CMV showed under-quantification and false-negative results in a quality assurance program (UK-NEQAS-2014). To evaluate factors contributing to quantification variability of CMV viral load and to develop optimized CMV-UL54-QNAT. The UL54 target of the UK-NEQAS-2014 variant was sequenced and compared to 329 available CMV GenBank sequences. Four Basel-CMV-UL54-QNAT assays of 361 bp, 254 bp, 151 bp, and 95 bp amplicons were developed that only differed in reverse primer positions. The assays were validated using plasmid dilutions, UK-NEQAS-2014 sample, as well as 107 frozen and 69 prospectively collected plasma samples from transplant patients submitted for CMV QNAT, with and without DNase-digestion prior to nucleic acid extraction. Eight of 43 mutations were identified as relevant in the UK-NEQAS-2014 target. All Basel-CMV-UL54 QNATs quantified the UK-NEQAS-2014 but revealed 10-fold increasing CMV loads as amplicon size decreased. The inverse correlation of amplicon size and viral loads was confirmed using 1st-WHO-International-Standard and patient samples. DNase pre-treatment reduced plasma CMV loads by >90% indicating the presence of unprotected CMV genomic DNA. Sequence variability, amplicon length, and non-encapsidated genomes obstruct standardization and commutability of CMV loads needed to develop thresholds for clinical research and management. Besides regular sequence surveys, matrix and extraction standardization, we propose developing reference calibrators using 100 bp amplicons. Copyright © 2018 Elsevier B.V. All

  13. Continuation of Iranshahri Thoughts in Kalileh va Demne

    Directory of Open Access Journals (Sweden)

    Bijan Zahirinav

    2010-10-01

    Full Text Available In this essay, Iranshahri’s thoughts such as ideal king, divine charisma, togetherness of religion and kingdom, justice, truth etc in kalileh va Demneh are investigated. In Kalileh and Demneh, kingdom is a divine gift and the king is at the center of the state affairs. Therefore, affection and kindness must be imprinted on his forehead, otherwise he would be a devilish creature who disturbs governing orders of the universe. He must metaphysically be supported in the circus of governmental affairs, and this is possible only by divine charisma. Such a king must be decorated with justice ornament, so that every body does his best in his own special class and approaches the salvation of soul. The king must also be decorated with accomplishments such as battle assistance and with virtues such as religion assistance. He must strengthen the social connection by “truth”. Basically, without truth life has no harmony because falsehood diverts life form its regular direction. But finally, with the dominance of divine forces over devilish ones, utopia, which is a secure place for releasing from disorder and injustice is proven to be true. Therefore, we conclude that Kalileh and Demneh has a contribution to the continuation of Iranshahri’s thoughts and also to the historical and cultural continuation of Iran in transition to the Islamic period.

  14. Methods for estimating and comparing VA outpatient drug benefits with the private sector.

    Science.gov (United States)

    Render, Marta L; Nowak, John; Hammond, Emmett K; Roselle, Gary

    2003-06-01

    To estimate and compare Veterans Health Administration (VA) expenditures for outpatient pharmaceuticals for veterans at six VA facilities with hypothetical private sector costs. Using the VA Pharmacy Benefits Management Strategic Health Care Group (PBM) database, we extracted data for all dispensed outpatient prescriptions from the six study sites over federal fiscal year 1999. After extensive data validation, we converted prescriptions to the same units and merged relevant VA pricing information by National Drug Code to Redbook listed average wholesale price and the Medicaid maximal allowable charge, where available. We added total VA drug expenditures to personnel cost from the pharmacy portion of that medical center's cost distribution report. Hypothetical private sector payments were $200.8 million compared with an aggregate VA budget of $118.8 million. Using National Drug Code numbers, 97% of all items dispensed from the six facilities were matched to private sector price data. Nonmatched pharmaceuticals were largely generic over-the-counter pain relievers and commodities like alcohol swabs. The most commonly prescribed medications reflect the diseases and complaints of an older male population: pain, cardiovascular problems, diabetes, and depression or other psychiatric disorders. Use of the VA PBM database permits researchers to merge expenditure and prescription data to patient diagnoses and sentinel events. A critical element in its use is creating similar units among the systems. Such data sets permit a deeper view of the variability in drug expenditures, an important sector of health care whose inflation has been disproportionate to that of the economy and even health care.

  15. Flexural Stiffness of Myosin Va Subdomains as Measured from Tethered Particle Motion

    Science.gov (United States)

    Michalek, Arthur J.; Kennedy, Guy G.; Warshaw, David M.; Ali, M. Yusuf

    2015-01-01

    Myosin Va (MyoVa) is a processive molecular motor involved in intracellular cargo transport on the actin cytoskeleton. The motor's processivity and ability to navigate actin intersections are believed to be governed by the stiffness of various parts of the motor's structure. Specifically, changes in calcium may regulate motor processivity by altering the motor's lever arm stiffness and thus its interhead communication. In order to measure the flexural stiffness of MyoVa subdomains, we use tethered particle microscopy, which relates the Brownian motion of fluorescent quantum dots, which are attached to various single- and double-headed MyoVa constructs bound to actin in rigor, to the motor's flexural stiffness. Based on these measurements, the MyoVa lever arm and coiled-coil rod domain have comparable flexural stiffness (0.034 pN/nm). Upon addition of calcium, the lever arm stiffness is reduced 40% as a result of calmodulins potentially dissociating from the lever arm. In addition, the flexural stiffness of the full-length MyoVa construct is an order of magnitude less stiff than both a single lever arm and the coiled-coil rod. This suggests that the MyoVa lever arm-rod junction provides a flexible hinge that would allow the motor to maneuver cargo through the complex intracellular actin network. PMID:26770194

  16. 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.

  17. RNA-Based Amplicon Sequencing Reveals Microbiota Development during Ripening of Artisanal versus Industrial Lard d'Arnad.

    Science.gov (United States)

    Ferrocino, Ilario; Bellio, Alberto; Romano, Angelo; Macori, Guerrino; Rantsiou, Kalliopi; Decastelli, Lucia; Cocolin, Luca

    2017-08-15

    Valle d'Aosta Lard d'Arnad is a protected designation of origin (PDO) product produced from fat of the shoulder and back of heavy pigs. Its manufacturing process can be very diverse, especially regarding the maturation temperature and the NaCl concentration used for the brine; thereby, the main goal of this study was to investigate the impact of those parameters on the microbiota developed during curing and ripening. Three farms producing Lard d'Arnad were selected. Two plants, reflecting the industrial process characterized either by low maturation temperature (plant A [10% NaCl, 2°C]) or by using a low NaCl concentration (plant B [2.5% NaCl, 4°C]), were selected, while the third was characterized by an artisanal process (plant C [30% NaCl, 8°C]). Lard samples were obtained at time 0 and after 7, 15, 30, 60, and 90 days of maturation. From each plant, 3 independent lots were analyzed. The diversity of live microbiota was evaluated by using classical plate counts and amplicon target sequencing of small subunit (SSU) rRNA. The main taxa identified by sequencing were Acinetobacter johnsonii , Psychrobacter , Staphylococcus equorum , Staphylococcus sciuri , Pseudomonas fragi , Brochothrix , Halomonas , and Vibrio , and differences in their relative abundances distinguished samples from the individual plants. The composition of the microbiota was more similar among plants A and B, and it was characterized by the higher presence of taxa recognized as undesired bacteria in food-processing environments. Oligotype analysis of Halomonas and Acinetobacter revealed the presence of several characteristic oligotypes associated with A and B samples. IMPORTANCE Changes in the food production process can drastically affect the microbial community structure, with a possible impact on the final characteristics of the products. The industrial processes of Lard d'Arnad production are characterized by a reduction in the salt concentration in the brines to address a consumer demand

  18. Analysis of VaR on Stock Investing%股票投资的风险价值VaR分析

    Institute of Scientific and Technical Information of China (English)

    张江红; 唐泉

    2011-01-01

    VaR is a tool to measure financial risk,which is supported and recognized by the international financial community in recent years.For equity portfolios consisting of different market factors or different financial instruments,VaR can reliably evaluate the market risks.In the paper the basic principle and calculation of VaR is introduced,the company stock value at risk has been analyzed using normal method,which company has issued convertible bond and stock.Meanwhile the affect that the issuance of convertible bond to the underlying stock fluctuation has been taken into account in order to provide reference for the different types of investors.%VaR是近年来受到国际金融界广泛支持和认可的一种度量金融风险的工具.对于不同市场因子和不同金融工具的投资组合,VaR可以相对可靠地衡量其市场风险.本文介绍了VaR的基本原理和计算方法,并用正态分布对发行有可转债的上市公司股票的风险价值进行分析,考虑了可转债的发行对标的股票波动的影响,以期为资本市场不同类型的投资者在进行资本投资前估计风险提供参考.

  19. Validation of KENO V.a for the Portsmouth Gaseous Diffusion Plant

    International Nuclear Information System (INIS)

    Felsher, H.D.; Fentiman, A.W.; Tayloe, R.W.; D'Aquila, D.

    1992-01-01

    At the Portsmouth Gaseous Diffusion Plant, KENO V.a is used to make criticality calculations for complex configurations and a wide range of 235 U enrichments. It is essential that the calculated critical conditions either accurately reflect the true critical state or that the bias from the true critical conditions are well known. Accordingly, a study has been initiated to validate KENO V.a over the ranges of parameters expected to be used when modeling equipment and processes at Portsmouth. Preliminary results of that study are reported in this paper. The ultimate goal of this study is to identify a set of data from existing critical experiments that will exercise all KENO V.a parameters commonly used by Portsmouth's criticality safety personnel. A second goal is to identify a relatively small subset of those experiments that may be run frequently to ensure that KENO V.a provides consistent results

  20. ESTIMATING RISK ON THE CAPITAL MARKET WITH VaR METHOD

    Directory of Open Access Journals (Sweden)

    Sinisa Bogdan

    2015-06-01

    Full Text Available The two basic questions that every investor tries to answer before investment are questions about predicting return and risk. Risk and return are generally considered two positively correlated sizes, during the growth of risk it is expected increase of return to compensate the higher risk. The quantification of risk in the capital market represents the current topic since occurrence of securities. Together with estimated future returns it represents starting point of any investment. In this study it is described the history of the emergence of VaR methods, usefulness in assessing the risks of financial assets. Three main Value at Risk (VaR methodologies are decribed and explained in detail: historical method, parametric method and Monte Carlo method. After the theoretical review of VaR methods it is estimated risk of liquid stocks and portfolio from the Croatian capital market with historical and parametric VaR method, after which the results were compared and explained.

  1. 77 FR 12647 - Fund Availability Under VA's Homeless Providers Grant and Per Diem Program

    Science.gov (United States)

    2012-03-01

    ... women veterans with or without the care of dependent children. 2. Funding Priority 2--VA is offering the... homeless veterans (i.e., veterans who are not incarcerated but are involved in the criminal justice system...

  2. Electronic Health Records: DOD's and VA's Sharing of Information Could Benefit from Improved Management

    National Research Council Canada - National Science Library

    2009-01-01

    ...) and the Department of Veterans Affairs (VA) are required to accelerate the exchange of health information between the departments and to develop systems or capabilities that allow for interoperability...

  3. 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...

  4. VA Construction: Improved Processes Needed to Monitor Contract Modifications, Develop Schedules, and Estimate Costs

    Science.gov (United States)

    2017-03-01

    the Handbook.36 VA headquarters officials told us that regional CFM offices monitor change- order - processing time frames for projects in their...visited collected different types of data on change orders. Because VA lacks the data on the change order processing timeframes required by the Handbook...goals of processing change orders in a timelier manner, especially given our previous findings that change- order - processing time frames caused

  5. Feasibility and acceptability of interventions to delay gun access in VA mental health settings.

    Science.gov (United States)

    Walters, Heather; Kulkarni, Madhur; Forman, Jane; Roeder, Kathryn; Travis, Jamie; Valenstein, Marcia

    2012-01-01

    The majority of VA patient suicides are completed with firearms. Interventions that delay patients' gun access during high-risk periods may reduce suicide, but may not be acceptable to VA stakeholders or may be challenging to implement. Using qualitative methods, stakeholders' perceptions about gun safety and interventions to delay gun access during high-risk periods were explored. Ten focus groups and four individual interviews were conducted with key stakeholders, including VA mental health patients, mental health clinicians, family members and VA facility leaders (N=60). Transcripts were consensus-coded by two independent coders, and structured summaries were developed and reviewed using a consensus process. All stakeholder groups indicated that VA health system providers had a role in increasing patient safety and emphasized the need for providers to address gun access with their at-risk patients. However, VA mental health patients and clinicians reported limited discussion regarding gun access in VA mental health settings during routine care. Most, although not all, patients and clinicians indicated that routine screening for gun access was acceptable, with several noting that it was more acceptable for mental health patients. Most participants suggested that family and friends be involved in reducing gun access, but expressed concerns about potential family member safety. Participants generally found distribution of trigger locks acceptable, but were skeptical about its effectiveness. Involving Veteran Service Organizations or other individuals in temporarily holding guns during high-risk periods was acceptable to many participants but only with numerous caveats. Patients, clinicians and family members consider the VA health system to have a legitimate role in addressing gun safety. Several measures to delay gun access during high-risk periods for suicide were seen as acceptable and feasible if implemented thoughtfully. Published by Elsevier Inc.

  6. 46 CFR 7.55 - Cape Henry, VA to Cape Fear, NC.

    Science.gov (United States)

    2010-10-01

    ... 46 Shipping 1 2010-10-01 2010-10-01 false Cape Henry, VA to Cape Fear, NC. 7.55 Section 7.55 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY PROCEDURES APPLICABLE TO THE PUBLIC BOUNDARY LINES Atlantic Coast § 7.55 Cape Henry, VA to Cape Fear, NC. (a) A line drawn from Rudee Inlet Jetty Light “2” to...

  7. 46 CFR 7.45 - Cape Henlopen, DE to Cape Charles, VA.

    Science.gov (United States)

    2010-10-01

    ... 46 Shipping 1 2010-10-01 2010-10-01 false Cape Henlopen, DE to Cape Charles, VA. 7.45 Section 7.45... Atlantic Coast § 7.45 Cape Henlopen, DE to Cape Charles, VA. (a) A line drawn from the easternmost extremity of Indian River Inlet North Jetty to latitude 38°36.5′ N. longitude 75°02.8′ W. (Indian River...

  8. Employment status, employment functioning, and barriers to employment among VA primary care patients.

    Science.gov (United States)

    Zivin, Kara; Yosef, Matheos; Levine, Debra S; Abraham, Kristen M; Miller, Erin M; Henry, Jennifer; Nelson, C Beau; Pfeiffer, Paul N; Sripada, Rebecca K; Harrod, Molly; Valenstein, Marcia

    2016-03-15

    Prior research found lower employment rates among working-aged patients who use the VA than among non-Veterans or Veterans who do not use the VA, with the lowest reported employment rates among VA patients with mental disorders. This study assessed employment status, employment functioning, and barriers to employment among VA patients treated in primary care settings, and examined how depression and anxiety were associated with these outcomes. The sample included 287 VA patients treated in primary care in a large Midwestern VA Medical Center. Bivariate and multivariable analyses were conducted examining associations between socio-demographic and clinical predictors of six employment domains, including: employment status, job search self-efficacy, work performance, concerns about job loss among employed Veterans, and employment barriers and likelihood of job seeking among not employed Veterans. 54% of respondents were employed, 36% were not employed, and 10% were economically inactive. In adjusted analyses, participants with depression or anxiety (43%) were less likely to be employed, had lower job search self-efficacy, had lower levels of work performance, and reported more employment barriers. Depression and anxiety were not associated with perceived likelihood of job loss among employed or likelihood of job seeking among not employed. Single VA primary care clinic; cross-sectional study. Employment rates are low among working-aged VA primary care patients, particularly those with mental health conditions. Offering primary care interventions to patients that address mental health issues, job search self-efficacy, and work performance may be important in improving health, work, and economic outcomes. Published by Elsevier B.V.

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

    Science.gov (United States)

    2017-03-01

    must manually review and correct most incoming cases due to issues with labeling, mismatched dates, and missing files. Via an internal study, VA...individuals acclimate to their jobs —and factored this into the modeling assumptions used to project the number of Board staff needed. More...Needed to Promote Increased User Satisfaction . GAO-15-582 (Washington, D.C.: September 1, 2015). Page 29 GAO-17-234 VA Disability

  10. Biphasic Study to Characterize Agricultural Biogas Plants by High-Throughput 16S rRNA Gene Amplicon Sequencing and Microscopic Analysis.

    Science.gov (United States)

    Maus, Irena; Kim, Yong Sung; Wibberg, Daniel; Stolze, Yvonne; Off, Sandra; Antonczyk, Sebastian; Pühler, Alfred; Scherer, Paul; Schlüter, Andreas

    2017-02-28

    Process surveillance within agricultural biogas plants (BGPs) was concurrently studied by high-throughput 16S rRNA gene amplicon sequencing and an optimized quantitative microscopic fingerprinting (QMF) technique. In contrast to 16S rRNA gene amplicons, digitalized microscopy is a rapid and cost-effective method that facilitates enumeration and morphological differentiation of the most significant groups of methanogens regarding their shape and characteristic autofluorescent factor 420. Moreover, the fluorescence signal mirrors cell vitality. In this study, four different BGPs were investigated. The results indicated stable process performance in the mesophilic BGPs and in the thermophilic reactor. Bacterial subcommunity characterization revealed significant differences between the four BGPs. Most remarkably, the genera Defluviitoga and Halocella dominated the thermophilic bacterial subcommunity, whereas members of another taxon, Syntrophaceticus , were found to be abundant in the mesophilic BGP. The domain Archaea was dominated by the genus Methanoculleus in all four BGPs, followed by Methanosaeta in BGP1 and BGP3. In contrast, Methanothermobacter members were highly abundant in the thermophilic BGP4. Furthermore, a high consistency between the sequencing approach and the QMF method was shown, especially for the thermophilic BGP. The differences elucidated that using this biphasic approach for mesophilic BGPs provided novel insights regarding disaggregated single cells of Methanosarcina and Methanosaeta species. Both dominated the archaeal subcommunity and replaced coccoid Methanoculleus members belonging to the same group of Methanomicrobiales that have been frequently observed in similar BGPs. This work demonstrates that combining QMF and 16S rRNA gene amplicon sequencing is a complementary strategy to describe archaeal community structures within biogas processes.

  11. The application of amplicon length heterogeneity PCR (LH-PCR) for monitoring the dynamics of soil microbial communities associated with cadaver decomposition.

    Science.gov (United States)

    Moreno, Lilliana I; Mills, DeEtta; Fetscher, Jill; John-Williams, Krista; Meadows-Jantz, Lee; McCord, Bruce

    2011-03-01

    The placement of cadavers in shallow, clandestine graves may alter the microbial and geochemical composition of the underlying and adjacent soils. Using amplicon length heterogeneity-PCR (LH-PCR) the microbial community changes in these soils can be assessed. In this investigation, nine different grave sites were examined over a period of 16weeks. The results indicated that measurable changes occurred in the soil bacterial community during the decomposition process. In this study, amplicons corresponding to anaerobic bacteria, not indigenous to the soil, were shown to produce differences between grave sites and control soils. Among the bacteria linked to these amplicons are those that are most often part of the commensal flora of the intestines, mouth and skin. In addition, over the 16week sampling interval, the level of indicator organisms (i.e., nitrogen fixing bacteria) dropped as the body decomposed and after four weeks of environmental exposure they began to increase again; thus differences in the abundance of nitrogen fixing bacteria were also found to contribute to the variation between controls and grave soils. These results were verified using primers that specifically targeted the nifH gene coding for nitrogenase reductase. LH-PCR provides a fast, robust and reproducible method to measure microbial changes in soil and could be used to determine potential cadaveric contact in a given area. The results obtained with this method could ultimately provide leads to investigators in criminal or missing person scenarios and allow for further analysis using human specific DNA assays to establish the identity of the buried body. Copyright © 2010 Elsevier B.V. All rights reserved.

  12. Microbial community profiling of fresh basil and pitfalls in taxonomic assignment of enterobacterial pathogenic species based upon 16S rRNA amplicon sequencing.

    Science.gov (United States)

    Ceuppens, Siele; De Coninck, Dieter; Bottledoorn, Nadine; Van Nieuwerburgh, Filip; Uyttendaele, Mieke

    2017-09-18

    Application of 16S rRNA (gene) amplicon sequencing on food samples is increasingly applied for assessing microbial diversity but may as unintended advantage also enable simultaneous detection of any human pathogens without a priori definition. In the present study high-throughput next-generation sequencing (NGS) of the V1-V2-V3 regions of the 16S rRNA gene was applied to identify the bacteria present on fresh basil leaves. However, results were strongly impacted by variations in the bioinformatics analysis pipelines (MEGAN, SILVAngs, QIIME and MG-RAST), including the database choice (Greengenes, RDP and M5RNA) and the annotation algorithm (best hit, representative hit and lowest common ancestor). The use of pipelines with default parameters will lead to discrepancies. The estimate of microbial diversity of fresh basil using 16S rRNA (gene) amplicon sequencing is thus indicative but subject to biases. Salmonella enterica was detected at low frequencies, between 0.1% and 0.4% of bacterial sequences, corresponding with 37 to 166 reads. However, this result was dependent upon the pipeline used: Salmonella was detected by MEGAN, SILVAngs and MG-RAST, but not by QIIME. Confirmation of Salmonella sequences by real-time PCR was unsuccessful. It was shown that taxonomic resolution obtained from the short (500bp) sequence reads of the 16S rRNA gene containing the hypervariable regions V1-V3 cannot allow distinction of Salmonella with closely related enterobacterial species. In conclusion 16S amplicon sequencing, getting the status of standard method in microbial ecology studies of foods, needs expertise on both bioinformatics and microbiology for analysis of results. It is a powerful tool to estimate bacterial diversity but amenable to biases. Limitations concerning taxonomic resolution for some bacterial species or its inability to detect sub-dominant (pathogenic) species should be acknowledged in order to avoid overinterpretation of results. Copyright © 2017 Elsevier B

  13. 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.

  14. 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/.

  15. 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.

  16. Enhanced dissolution rate of dronedarone hydrochloride via preparation of solid dispersion using vinylpyrrolidone-vinyl acetate copolymer (Kollidone® VA 64)

    Energy Technology Data Exchange (ETDEWEB)

    Jung, Hyuck Jun; Kang, Myung Joo [College of Pharmacy, Dankook University, Cheonan (Korea, Republic of); Han, Sang Duk [Dong-A ST Rese arch Institute, Pharmaceutical Product Research Laboratories, Yongin (Korea, Republic of)

    2015-09-15

    Solid dispersion (SD) systems have been widely used to increase the dissolution rate and oral absorption of poorly water-soluble compounds. In order to enhance the dissolution rate of dronedarone hydrochloride (DRN), a recent antiarrhythmic agent, SDs of DRN were formulated using conventional solvent evaporation method with amorphous polymers including hydroxypropyl methyl cellulose (HPMC), poly(vinyl pyrrolidone) (PVP), and vinylpyrrolidone-vinyl acetate copolymer (VA64). The prepared SDs were characterized in terms of drug crystallinity, morphology, and in vitro dissolution profile in aqueous medium. The physical characterization using differential scanning calorimetry and X-ray powder diffraction revealed that the active compound was molecularly dispersed in all polymeric carriers tested, in a stable amorphous form in drug to polymer ratios ranging from 1:0.5 to 1:2. The dissolution rates of DRN in all SDs were much higher than those from the corresponding physical mixture and drug powder alone. In particular, the greatest dissolution enhancement was obtained from the VA64-based SD in a drug to polymer weight ratio of 1:1, achieving almost complete drug release after 120 min at pH 1.2. Thus, VA64-based SD with higher drug dissolution rate along with a simple preparation process is suggested as an alternative for the oral formulation of the benzofuran derivative.

  17. A novel ultra high-throughput 16S rRNA gene amplicon sequencing library preparation method for the Illumina HiSeq platform.

    Science.gov (United States)

    de Muinck, Eric J; Trosvik, Pål; Gilfillan, Gregor D; Hov, Johannes R; Sundaram, Arvind Y M

    2017-07-06

    Advances in sequencing technologies and bioinformatics have made the analysis of microbial communities almost routine. Nonetheless, the need remains to improve on the techniques used for gathering such data, including increasing throughput while lowering cost and benchmarking the techniques so that potential sources of bias can be better characterized. We present a triple-index amplicon sequencing strategy to sequence large numbers of samples at significantly lower c ost and in a shorter timeframe compared to existing methods. The design employs a two-stage PCR protocol, incorpo rating three barcodes to each sample, with the possibility to add a fourth-index. It also includes heterogeneity spacers to overcome low complexity issues faced when sequencing amplicons on Illumina platforms. The library preparation method was extensively benchmarked through analysis of a mock community in order to assess biases introduced by sample indexing, number of PCR cycles, and template concentration. We further evaluated the method through re-sequencing of a standardized environmental sample. Finally, we evaluated our protocol on a set of fecal samples from a small cohort of healthy adults, demonstrating good performance in a realistic experimental setting. Between-sample variation was mainly related to batch effects, such as DNA extraction, while sample indexing was also a significant source of bias. PCR cycle number strongly influenced chimera formation and affected relative abundance estimates of species with high GC content. Libraries were sequenced using the Illumina HiSeq and MiSeq platforms to demonstrate that this protocol is highly scalable to sequence thousands of samples at a very low cost. Here, we provide the most comprehensive study of performance and bias inherent to a 16S rRNA gene amplicon sequencing method to date. Triple-indexing greatly reduces the number of long custom DNA oligos required for library preparation, while the inclusion of variable length

  18. Illumina MiSeq 16S amplicon sequence analysis of bovine respiratory disease associated bacteria in lung and mediastinal lymph node tissue.

    Science.gov (United States)

    Johnston, Dayle; Earley, Bernadette; Cormican, Paul; Murray, Gerard; Kenny, David Anthony; Waters, Sinead Mary; McGee, Mark; Kelly, Alan Kieran; McCabe, Matthew Sean

    2017-05-02

    Bovine respiratory disease (BRD) is caused by growth of single or multiple species of pathogenic bacteria in lung tissue following stress and/or viral infection. Next generation sequencing of 16S ribosomal RNA gene PCR amplicons (NGS 16S amplicon analysis) is a powerful culture-independent open reference method that has recently been used to increase understanding of BRD-associated bacteria in the upper respiratory tract of BRD cattle. However, it has not yet been used to examine the microbiome of the bovine lower respiratory tract. The objective of this study was to use NGS 16S amplicon analysis to identify bacteria in post-mortem lung and lymph node tissue samples harvested from fatal BRD cases and clinically healthy animals. Cranial lobe and corresponding mediastinal lymph node post-mortem tissue samples were collected from calves diagnosed as BRD cases by veterinary laboratory pathologists and from clinically healthy calves. NGS 16S amplicon libraries, targeting the V3-V4 region of the bacterial 16S rRNA gene were prepared and sequenced on an Illumina MiSeq. Quantitative insights into microbial ecology (QIIME) was used to determine operational taxonomic units (OTUs) which corresponded to the 16S rRNA gene sequences. Leptotrichiaceae, Mycoplasma, Pasteurellaceae, and Fusobacterium were the most abundant OTUs identified in the lungs and lymph nodes of the calves which died from BRD. Leptotrichiaceae, Fusobacterium, Mycoplasma, Trueperella and Bacteroides had greater relative abundances in post-mortem lung samples collected from fatal cases of BRD in dairy calves, compared with clinically healthy calves without lung lesions. Leptotrichiaceae, Mycoplasma and Pasteurellaceae showed higher relative abundances in post-mortem lymph node samples collected from fatal cases of BRD in dairy calves, compared with clinically healthy calves without lung lesions. Two Leptotrichiaceae sequence contigs were subsequently assembled from bacterial DNA-enriched shotgun sequences

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

    Directory of Open Access Journals (Sweden)

    Fu Juanjuan

    2011-07-01

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

  20. 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

  1. Two-stage clustering (TSC: a pipeline for selecting operational taxonomic units for the high-throughput sequencing of PCR amplicons.

    Directory of Open Access Journals (Sweden)

    Xiao-Tao Jiang

    Full Text Available Clustering 16S/18S rRNA amplicon sequences into operational taxonomic units (OTUs is a critical step for the bioinformatic analysis of microbial diversity. Here, we report a pipeline for selecting OTUs with a relatively low computational demand and a high degree of accuracy. This pipeline is referred to as two-stage clustering (TSC because it divides tags into two groups according to their abundance and clusters them sequentially. The more abundant group is clustered using a hierarchical algorithm similar to that in ESPRIT, which has a high degree of accuracy but is computationally costly for large datasets. The rarer group, which includes the majority of tags, is then heuristically clustered to improve efficiency. To further improve the computational efficiency and accuracy, two preclustering steps are implemented. To maintain clustering accuracy, all tags are grouped into an OTU depending on their pairwise Needleman-Wunsch distance. This method not only improved the computational efficiency but also mitigated the spurious OTU estimation from 'noise' sequences. In addition, OTUs clustered using TSC showed comparable or improved performance in beta-diversity comparisons compared to existing OTU selection methods. This study suggests that the distribution of sequencing datasets is a useful property for improving the computational efficiency and increasing the clustering accuracy of the high-throughput sequencing of PCR amplicons. The software and user guide are freely available at http://hwzhoulab.smu.edu.cn/paperdata/.

  2. 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.

  3. Cowpea mosaic virus RNA-1 acts as an amplicon whose effects can be counteracted by a RNA-2-encoded suppressor of silencing

    International Nuclear Information System (INIS)

    Liu Li; Grainger, Jef; Canizares, M. Carmen; Angell, Susan M.; Lomonossoff, George P.

    2004-01-01

    Lines of Nicotiana benthamiana transgenic for full-length copies of both Cowpea mosaic virus (CPMV) genomic RNAs, either singly or together, have been produced. Plants transgenic for both RNAs developed symptoms characteristic of a CPMV infection. When plants transgenic for RNA-1 were agro-inoculated with RNA-2, no infection developed and the plants were also resistant to challenge with CPMV. By contrast, plants transgenic for RNA-2 became infected when agro-inoculated with RNA-1 and were fully susceptible to CPMV infection. The resistance of RNA-1 transgenic plants was shown to be related to the ability of RNA-1 to self-replicate and act as an amplicon. The ability of transgenically expressed RNA-2 to counteract the amplicon effect suggested that it encodes a suppressor of posttranscriptional gene silencing (PTGS). By examining the ability of portions of RNA-2 to reverse PTGS in N. benthamiana, we have identified the small (S) coat protein as the CPMV RNA-2-encoded suppressor of PTGS

  4. 'Mitominis': multiplex PCR analysis of reduced size amplicons for compound sequence analysis of the entire mtDNA control region in highly degraded samples.

    Science.gov (United States)

    Eichmann, Cordula; Parson, Walther

    2008-09-01

    The traditional protocol for forensic mitochondrial DNA (mtDNA) analyses involves the amplification and sequencing of the two hypervariable segments HVS-I and HVS-II of the mtDNA control region. The primers usually span fragment sizes of 300-400 bp each region, which may result in weak or failed amplification in highly degraded samples. Here we introduce an improved and more stable approach using shortened amplicons in the fragment range between 144 and 237 bp. Ten such amplicons were required to produce overlapping fragments that cover the entire human mtDNA control region. These were co-amplified in two multiplex polymerase chain reactions and sequenced with the individual amplification primers. The primers were carefully selected to minimize binding on homoplasic and haplogroup-specific sites that would otherwise result in loss of amplification due to mis-priming. The multiplexes have successfully been applied to ancient and forensic samples such as bones and teeth that showed a high degree of degradation.

  5. Interaction of blood coagulation factor Va with phospholipid vesicles examined by using lipophilic photoreagents

    International Nuclear Information System (INIS)

    Krieg, U.C.; Isaacs, B.S.; Yemul, S.S.; Esmon, C.T.; Bayley, H.; Johnson, A.E.

    1987-01-01

    Two different lipophilic photoreagents, [ 3 H]adamantane diazirine and 3-(trifluoromethyl)-3-(m-[ 125 I]iodophenyl)diazirine (TID), have been utilized to examine the interactions of blood coagulation factor Va with calcium, prothrombin, factor Xa, and, in particular, phospholipid vesicles. With each of these structurally dissimilar reagents, the extent of photolabeling of factor Va was greater when the protein was bound to a membrane surface than when it was free in solution. Specifically, the covalent photoreaction with Vl, the smaller subunit of factor Va, was 2-fold higher in the presence of phosphatidylcholine/phosphatidylserine (PC/PS, 3:1) vesicles, to which factor Va binds, than in the presence of 100% PC vesicles, to which the protein does not bind. However, the magnitude of the PC/PS-dependent photolabeling was much less than has been observed previously with integral membrane proteins. It therefore appears that the binding of factor Va to the membrane surface exposes Vl to the lipid core of the bilayer, but that only a small portion of the Vl polypeptide is exposed to, or embedded in, the bilayer core. Addition of either prothrombin or active-site-blocked factor Xa to PC/PS-bound factor Va had little effect on the photolabeling of Vl with TID, but reduced substantially the covalent labeling of Vh, the larger subunit of factor Va. This indicates that prothrombin and factor Xa each cover nonpolar surfaces on Vh when the macromolecules associate on the PC/PS surface. It therefore seems likely that the formation of the prothrombinase complex involves a direct interaction between Vh and factor Xa and between Vh and prothrombin.(ABSTRACT TRUNCATED AT 250 WORDS)

  6. Electroencephalogram (EEG spectral features discriminate between Alzheimer’s (AD and Vascular dementia (VaD

    Directory of Open Access Journals (Sweden)

    Emanuel eNeto

    2015-02-01

    Full Text Available Alzheimer’s disease (AD and vascular dementia (VaD present with similar clinical symptoms of cognitive decline, but the underlying pathophysiological mechanisms differ. To determine whether clinical electroencephalography (EEG can provide information relevant to discriminate between these diagnoses, we used quantitative EEG analysis to compare the spectra between non-medicated patients with AD (n=77 and VaD (n=77 and healthy elderly normal controls (NC (n=77. We use curve-fitting with a combination of a power loss and Gaussian function to model the averaged resting-state spectra of each EEG channel extracting six parameters. We assessed the performance of our model and tested the extracted parameters for group differentiation. We performed regression analysis in a MANCOVA with group, age, gender, and number of epochs as predictors and further explored the topographical group differences with pair-wise contrasts. Significant topographical differences between the groups were found in several of the extracted features. Both AD and VaD groups showed increased delta power when compared to NC, whereas the AD patients showed a decrease in alpha power for occipital and temporal regions when compared with NC. The VaD patients had higher alpha power than NC and AD. The AD and VaD groups showed slowing of the alpha rhythm. Variability of the alpha frequency was wider for both AD and VaD groups. There was a general decrease in beta power for both AD and VaD. The proposed model is a useful to parameterize spectra which allowed extracting relevant clinical EEG key features that move towards simple and interpretable diagnostic criteria.

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

    Science.gov (United States)

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

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

  8. 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

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

    Directory of Open Access Journals (Sweden)

    Robbins RA

    2013-03-01

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

  10. Value at risk (VaR in uncertainty: Analysis with parametric method and black & scholes simulations

    Directory of Open Access Journals (Sweden)

    Humberto Banda Ortiz

    2014-07-01

    Full Text Available VaR is the most accepted risk measure worldwide and the leading reference in any risk management assessment. However, its methodology has important limitations which makes it unreliable in contexts of crisis or high uncertainty. For this reason, the aim of this work is to test the VaR accuracy when is employed in contexts of volatility, for which we compare the VaR outcomes in scenarios of both stability and uncertainty, using the parametric method and a historical simulation based on data generated with the Black & Scholes model. VaR main objective is the prediction of the highest expected loss for any given portfolio, but even when it is considered a useful tool for risk management under conditions of markets stability, we found that it is substantially inaccurate in contexts of crisis or high uncertainty. In addition, we found that the Black & Scholes simulations lead to underestimate the expected losses, in comparison with the parametric method and we also found that those disparities increase substantially in times of crisis. In the first section of this work we present a brief context of risk management in finance. In section II we present the existent literature relative to the VaR concept, its methods and applications. In section III we describe the methodology and assumptions used in this work. Section IV is dedicated to expose the findings. And finally, in Section V we present our conclusions.

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

    International Nuclear Information System (INIS)

    Dunn, Michael E.; Greene, N. Maurice; Petrie, Lester M.

    2003-01-01

    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)

  12. Effectiveness of Expanded Implementation of STAR-VA for Managing Dementia-Related Behaviors Among Veterans.

    Science.gov (United States)

    Karel, Michele J; Teri, Linda; McConnell, Eleanor; Visnic, Stephanie; Karlin, Bradley E

    2016-02-01

    Nonpharmacological, psychosocial approaches are first-line treatments for managing behavioral symptoms in dementia, but they can be challenging to implement in long-term care settings. The Veterans Health Administration implemented STAR-VA, an interdisciplinary behavioral approach for managing challenging dementia-related behaviors in its Community Living Center (CLCs, nursing home care) settings. This study describes how the program was implemented and provides an evaluation of Veteran clinical outcomes and staff feedback on the intervention. One mental health professional and registered nurse team from 17 CLCs completed STAR-VA training, which entailed an experiential workshop followed by 6 months of expert consultation as they worked with their teams to implement STAR-VA with Veterans identified to have challenging dementia-related behaviors. The frequency and severity of target behaviors and symptoms of depression, anxiety, and agitation were evaluated at baseline and at intervention completion. Staff provided feedback regarding STAR-VA feasibility and impact. Seventy-one Veterans completed the intervention. Behaviors clustered into 6 types: care refusal or resistance, agitation, aggression, vocalization, wandering, and other. Frequency and severity of target behaviors and symptoms of depression, anxiety, and agitation all significantly decreased, with overall effect sizes of 1 or greater. Staff rated both benefits for Veterans and program feasibility favorably. This evaluation supports the feasibility and effectiveness of STAR-VA, an interdisciplinary, behavioral intervention for managing challenging behaviors among residents with dementia in CLCs. Published by Oxford University Press on behalf of the Gerontological Society of America 2015.

  13. Isolation and characterization of specific bacteriophage Va1 to Vibrio alginolyticus

    Directory of Open Access Journals (Sweden)

    Carla Fernández Espinel

    2017-04-01

    Full Text Available Vibrio alginolyticus is associated with diseases in aquaculture. The misuse of antibiotics has led to the search for alternatives in the treatment of bacterial diseases, among them the application of bacteriophages that infect and destroy bacteria selectively. In this way, a highly lytic V. alginolyticus bacteriophage, termed Va1, was isolated, with the aim to evaluate its physical chemical parameters. For this purpose, different temperature, pH, chloroform exposure and host range conditions were evaluated. The temperature stability of phage Va1 showed higher titers at 20 and 30 °C decreasing from 40 °C. With respect to pH, the highest titers for the bacteriophage were between 5 and 8, and chloroform exposure reduced viability of the Va1 phage by 25%. The one-step curve determined that the latency period and the burst size were 20 minutes and 192 PFU / infective center respectively. Under the transmission electron microscope, the Va1 phage showed an icosahedral head and a non-contractile tail, belonging to the Podoviridae family. In conclusion, Va1 phage presents potential characteristics for use in phage therapy.

  14. Testing popular VaR models in EU new member and candidate states

    Directory of Open Access Journals (Sweden)

    Saša Žiković

    2007-12-01

    Full Text Available The impact of allowing banks to calculate their capital requirement based on their internal VaR models, and the impact of regulation changes on banks in transitional countries has not been well studied. This paper examines whether VaR models that are created and suited for developed markets apply to the volatile stock markets of EU new member and candidate states (Bulgaria, Romania, Croatia and Turkey. Nine popular VaR models are tested on five stock indexes from EU new member and candidate states. Backtesting results show that VaR models commonly used in developed stock markets are not well suited for measuring market risk in these markets. Presented findings bear very important implications that have to be addressed by regulators and risk practitioners operating in EU new member andcandidate states. Risk managers have to start thinking outside the frames set by their parent companies or else investors present in these markets may find themselves in serious trouble, dealing with losses that they have not been expecting. National regulators have to take into consideration that simplistic VaR models that are widely used in some developed countries are not well suited for these illiquid and developing stock markets.

  15. Cloning, Characterization, and Functional Investigation of VaHAESA from Vitis amurensis Inoculated with Plasmopara viticola

    Directory of Open Access Journals (Sweden)

    Shaoli Liu

    2018-04-01

    Full Text Available Plant pattern recognition receptors (PRRs are essential for immune responses and establishing symbiosis. Plants detect invaders via the recognition of pathogen-associated molecular patterns (PAMPs by PRRs. This phenomenon is termed PAMP-triggered immunity (PTI. We investigated disease resistance in Vitis amurensis to identify PRRs that are important for resistance against downy mildew, analyzed the PRRs that were upregulated by incompatible Plasmopara viticola infection, and cloned the full-length cDNA of the VaHAESA gene. We then analyzed the structure, subcellular localization, and relative disease resistance of VaHAESA. VaHAESA and PRR-receptor-like kinase 5 (RLK5 are highly similar, belonging to the leucine-rich repeat (LRR-RLK family and localizing to the plasma membrane. The expression of PRR genes changed after the inoculation of V. amurensis with compatible and incompatible P. viticola; during early disease development, transiently transformed V. vinifera plants expressing VaHAESA were more resistant to pathogens than those transformed with the empty vector and untransformed controls, potentially due to increased H2O2, NO, and callose levels in the transformants. Furthermore, transgenic Arabidopsis thaliana showed upregulated expression of genes related to the PTI pathway and improved disease resistance. These results show that VaHAESA is a positive regulator of resistance against downy mildew in grapevines.

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

    Science.gov (United States)

    2014-11-01

    servicemembers to civilian life. For its part, VA’s agency priority goals are to (1) ensure access to VA benefits and services, (2) eliminate the disability...transfer their benefits to dependents. VA – Veterans Benefit Administration ( VBA ) Spinal Cord Injury and Disorders Centers Disability; Physical...who are temporarily residing in a home owned by a family member to help adapt the home to meet his or her special needs. VA - VBA Yellow Ribbon

  17. 48 CFR 852.219-72 - Evaluation factor for participation in the VA mentor-protégé program.

    Science.gov (United States)

    2010-10-01

    ... participation in the VA mentor-protégé program. 852.219-72 Section 852.219-72 Federal Acquisition Regulations... Texts of Provisions and Clauses 852.219-72 Evaluation factor for participation in the VA mentor-protégé... the VA Mentor-Protégé Program (DEC2009) This solicitation contains an evaluation factor or sub-factor...

  18. 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.

  19. VA Dental Insurance Program--federalism. Direct final rule; confirmation of effective date.

    Science.gov (United States)

    2014-03-20

    The Department of Veterans Affairs (VA) published a direct final rule in the Federal Register on October 22, 2013, amending its regulations related to the VA Dental Insurance Program (VADIP), a pilot program to offer premium-based dental insurance to enrolled veterans and certain survivors and dependents of veterans. Specifically, this rule adds language to clarify the limited preemptive effect of certain criteria in the VADIP regulations. VA received no comments concerning this rule or its companion substantially identical proposed rule published in the Federal Register on October 23, 2013. This document confirms that the direct final rule became effective on December 23, 2013. In a companion document in this issue of the Federal Register, we are withdrawing as unnecessary the proposed rule.

  20. LIFE JOURNEY: MEDICAL AND SCIENTIFIC WORK OF PROFESSOR V.A. SOKOLOV

    Directory of Open Access Journals (Sweden)

    P. A. Ivanov

    2017-01-01

    Full Text Available The article is dedicated to doctor of medicine, professor V.A. Sokolov. In 2017 he celebrates his eightieth birthday. Professor V.A. .Sokolov is one of the founders of polytrauma treatment in USSR and Russia. For a long time he had been heading polytrauma department at the N.V. Sklifosovsky Research Institute for Emergency Medicine. Due to his work, algorithms of life sustaining and recovery of serious patients were developed. Professor V.A. Sokolov is the author of 6 monographies and about 300 periodical papers. Besides, he is the holder of 32 patents. Some of his inventions were popularized and manufactured. He had been leading active scientific work, which resulted in 6 doctoral dissertations and 15 candidate theses. The staff of N.V. Sklifosovsky Research Institute for Emergency Medicine congratulates on the anniversary.

  1. Waves from the Sun: to the 100th anniversary of V.A. Troitskaya's birth

    Science.gov (United States)

    Guglielmi, Anatol; Potapov, Alexander

    2017-09-01

    It has been one hundred years since the birth of the outstanding scientist Professor V.A. Troitskaya. Her remarkable achievements in solar-terrestrial physics are widely known. For many years, Valeria A. Troitskaya was the President of the International Association of Geomagnetism and Aeronomy. This article deals with only one aspect of the multifaceted creative activity of V.A. Troitskaya. It relates to the problem of sources of ultra-low frequency (ULF) electromagnetic oscillations and waves outside Earth’s magnetosphere. We were fortunate to work under the leadership of V.A. Troitskaya on this problem. In this paper, we briefly describe the history from the emergence of the idea of the extramagnetospheric origin of dayside permanent ULF oscillations in the late 1960s to the modern quest made by ground and satellite means for ULF waves excited by solar surface oscillations propagating in the interplanetary medium and reaching Earth.

  2. The Burr X Pareto Distribution: Properties, Applications and VaR Estimation

    Directory of Open Access Journals (Sweden)

    Mustafa Ç. Korkmaz

    2017-12-01

    Full Text Available In this paper, a new three-parameter Pareto distribution is introduced and studied. We discuss various mathematical and statistical properties of the new model. Some estimation methods of the model parameters are performed. Moreover, the peaks-over-threshold method is used to estimate Value-at-Risk (VaR by means of the proposed distribution. We compare the distribution with a few other models to show its versatility in modelling data with heavy tails. VaR estimation with the Burr X Pareto distribution is presented using time series data, and the new model could be considered as an alternative VaR model against the generalized Pareto model for financial institutions.

  3. EFFECTS OF VARIOUS SOIL ENVIRONMENTAL STRESSES ON THE OCCURRENCE, DISTRIBUTION AND EFFECTIVENESS OF VA MYCORRHIZAE

    Directory of Open Access Journals (Sweden)

    A.G. KHAN

    1995-01-01

    Full Text Available The vesicular - arbuscular (VA mycorrhizal fungi are geographically ubiquitous soil inhabitants and form universal symbiotic relationship with plants from every phylum. These fungi link host plants with host soils and their biota in the mycorrhizosphere and play an important role in plant health, productivity and soil structure. Although VA mycorrhizal fungi do not show any host specificity, there is increasing evidence that various climatic and edaphic environmental factors such as land use and management practices, physical, chemical and biological properties of host soils and host plant characteristics influence their occurrence, taxonomic distribution and effectiveness. The interaction of these factors with vesicular-arbuscular mycorrhizae (VAM is poorly understood except in a few cases. It is now very clear that VA mycorrhizal associations are ecologically significant factors that require more attention than previously accorded. This paper discusses the occurrence, distribution and significance of VAM in environmentally stressed soil conditions that limit plant growth such as drought, waterlogging and salinity.

  4. VA Disability Compensation and Money Spent on Substance Use Among Homeless Veterans: A Controversial Association.

    Science.gov (United States)

    Tsai, Jack; Rosenheck, Robert A

    2015-06-01

    There has long been concern that public support payments are used to support addictive behaviors. This study examined the amount of money homeless veterans spend on alcohol and drugs and the association between public support income, including VA disability compensation, and expenditures on alcohol and drugs. Data were from 1,160 veterans from 19 sites on entry into the Housing and Urban Development-Veterans Affairs Supportive Housing program. Descriptive statistics and nonparametric analyses were conducted. About 33% of veterans reported spending money on alcohol and 22% reported spending money on drugs in the past month. No significant association was found between public support income, VA disability compensation, and money spent on alcohol and drugs. A substantial proportion of homeless veterans spend some income on alcohol and drugs, but disability income, including VA compensation, does not seem to be related to substance use or money spent on addictive substances.

  5. Information Technology: DOD and VA Have Increased Their Sharing of Health Information, but Further Actions Are Needed

    National Research Council Canada - National Science Library

    Melvin, Valerie C

    2008-01-01

    ...) and the Department of Veterans Affairs (VA) to accelerate the exchange of health information between the departments and to develop systems or capabilities that allow for full interoperability...

  6. Malaria epidemiology in the Pakaanóva (Wari') Indians, Brazilian Amazon.

    Science.gov (United States)

    Sá, D Ribeiro; Souza-Santos, R; Escobar, A L; Coimbra, C E A

    2005-04-01

    This paper reports the results of a longitudinal study of malaria incidence (1998-2002) among the Pakaanóva (Wari') Indians, Brazilian southwest Amazon region, based on data routinely gathered by Brazilian National Health Foundation outposts network in conjunction with the Indian health service. Malaria is present yearlong in the Pakaanóva. Statistically significant differences between seasons or months were not noticed. A total of 1933 cases of malaria were diagnosed in the Pakaanóva during this period. The P. vivax / P. falciparum ratio was 3.4. P. vivax accounted for 76.5% of the cases. Infections with P. malariae were not recorded. Incidence rates did not differ by sex. Most malaria cases were reported in children < 10 years old (45%). About one fourth of all cases were diagnosed on women 10-40 years old. An entomological survey carried out at two Pakaanóva villages yielded a total of 3.232 specimens of anophelines. Anopheles darlingi predominated (94.4%). Most specimens were captured outdoors and peak activity hours were noted at early evening and just before sunrise. It was observed that Pakaanóva cultural practices may facilitate outdoor exposure of individuals of both sexes and all age groups during peak hours of mosquito activities (e.g., coming to the river early in the morning for bathing or to draw water, fishing, engaging in hunting camps, etc). In a context in which anophelines are ubiquitous and predominantly exophilic, and humans of both sexes and all ages are prone to outdoor activities during peak mosquito activity hours, malaria is likely to remain endemic in the Pakaanóva, thus requiring the development of alternative control strategies that are culturally and ecologically sensitive.

  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. Validity testing and neuropsychology practice in the VA healthcare system: results from recent practitioner survey (.).

    Science.gov (United States)

    Young, J Christopher; Roper, Brad L; Arentsen, Timothy J

    2016-05-01

    A survey of neuropsychologists in the Veterans Health Administration examined symptom/performance validity test (SPVT) practices and estimated base rates for patient response bias. Invitations were emailed to 387 psychologists employed within the Veterans Affairs (VA), identified as likely practicing neuropsychologists, resulting in 172 respondents (44.4% response rate). Practice areas varied, with 72% at least partially practicing in general neuropsychology clinics and 43% conducting VA disability exams. Mean estimated failure rates were 23.0% for clinical outpatient, 12.9% for inpatient, and 39.4% for disability exams. Failure rates were the highest for mTBI and PTSD referrals. Failure rates were positively correlated with the number of cases seen and frequency and number of SPVT use. Respondents disagreed regarding whether one (45%) or two (47%) failures are required to establish patient response bias, with those administering more measures employing the more stringent criterion. Frequency of the use of specific SPVTs is reported. Base rate estimates for SPVT failure in VA disability exams are comparable to those in other medicolegal settings. However, failure in routine clinical exams is much higher in the VA than in other settings, possibly reflecting the hybrid nature of the VA's role in both healthcare and disability determination. Generally speaking, VA neuropsychologists use SPVTs frequently and eschew pejorative terms to describe their failure. Practitioners who require only one SPVT failure to establish response bias may overclassify patients. Those who use few or no SPVTs may fail to identify response bias. Additional clinical and theoretical implications are discussed.

  9. Kritika važećeg i prijedlog novog pravnog uređenja vađenja i uklanjanja podrtina i potonulih stvari

    Directory of Open Access Journals (Sweden)

    Vesna Skorupan Wolff

    2012-12-01

    Full Text Available Glavni cilj rada je ponuditi i prikazati rješenja koja predstavljaju prijedlog novog pravnog uređenja instituta vađenja i uklanjanja podrtina i potonulih stvari. Prije toga, autorice u radu prikazuju genezu pravnih izvora u povijesti i ranijem domaćem zakonodavstvu te proučavaju sva relevantna pitanja i sve odredbe važećeg Pomorskog zakonika (u nastavku PZ o ovoj materiji. Analizira se značenje i uporaba pojedinih izraza, sistematizacija zakonske građe unutar strukture zakona te sadržaj i domašaj pojedinih odredbi. Autorice preispituju razinu usklađenosti pozitivnog PZ-a sa suvremenom međunarodnom regulativom u ovom području. Ukazuje se na važne probleme koji mogu nastati zbog manjkavosti odredbi pozitivnog PZ-a i nepostojanja sustavne regulacije svih relevantnih pitanja koja se mogu pojaviti u praksi. U okviru istraživanja provodi se i poredbena analiza ovih instituta u drugim nacionalnim zakonodavstvima. Predložena zakonska rješenja odlikuju se cjelovitošću i sustavnošću u normiranju svih relevantnih pitanja. Uređivanje ovih instituta specijalnim odredbama pružit će viši stupanj pravne sigurnosti te viši stupanj sigurnosti plovidbe Jadranom, zaštite okoliša, njegovih prirodnih bogatstava i drugih povezanih interesa.

  10. Bacterial tag encoded FLX titanium amplicon pyrosequencing (bTEFAP based assessment of prokaryotic diversity in metagenome of Lonar soda lake, India

    Directory of Open Access Journals (Sweden)

    Pravin Dudhagara

    2015-06-01

    Full Text Available Bacterial diversity and archaeal diversity in metagenome of the Lonar soda lake sediment were assessed by bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP. Metagenome comprised 5093 sequences with 2,531,282 bp and 53 ± 2% G + C content. Metagenome sequence data are available at NCBI under the Bioproject database with accession no. PRJNA218849. Metagenome sequence represented the presence of 83.1% bacterial and 10.5% archaeal origin. A total of 14 different bacteria demonstrating 57 species were recorded with dominating species like Coxiella burnetii (17%, Fibrobacter intestinalis (12% and Candidatus Cloacamonas acidaminovorans (11%. Occurrence of two archaeal phyla representing 24 species, among them Methanosaeta harundinacea (35%, Methanoculleus chikugoensis (12% and Methanolinea tarda (11% were dominating species. Significant presence of 11% sequences as an unclassified indicated the possibilities for unknown novel prokaryotes from the metagenome.

  11. 16S rRNA Amplicon Sequencing Demonstrates that Indoor-Reared Bumblebees (Bombus terrestris Harbor a Core Subset of Bacteria Normally Associated with the Wild Host.

    Directory of Open Access Journals (Sweden)

    Ivan Meeus

    Full Text Available A MiSeq multiplexed 16S rRNA amplicon sequencing of the gut microbiota of wild and indoor-reared Bombus terrestris (bumblebees confirmed the presence of a core set of bacteria, which consisted of Neisseriaceae (Snodgrassella, Orbaceae (Gilliamella, Lactobacillaceae (Lactobacillus, and Bifidobacteriaceae (Bifidobacterium. In wild B. terrestris we detected several non-core bacteria having a more variable prevalence. Although Enterobacteriaceae are unreported by non next-generation sequencing studies, it can become a dominant gut resident. Furthermore the presence of some non-core lactobacilli were associated with the relative abundance of bifidobacteria. This association was not observed in indoor-reared bumblebees lacking the non-core bacteria, but having a more standardized microbiota compared to their wild counterparts. The impact of the bottleneck microbiota of indoor-reared bumblebees when they are used in the field for pollination purpose is discussed.

  12. Modeling of human factor Va inactivation by activated protein C

    Directory of Open Access Journals (Sweden)

    Bravo Maria

    2012-05-01

    Full Text Available Abstract Background Because understanding of the inventory, connectivity and dynamics of the components characterizing the process of coagulation is relatively mature, it has become an attractive target for physiochemical modeling. Such models can potentially improve the design of therapeutics. The prothrombinase complex (composed of the protease factor (FXa and its cofactor FVa plays a central role in this network as the main producer of thrombin, which catalyses both the activation of platelets and the conversion of fibrinogen to fibrin, the main substances of a clot. A key negative feedback loop that prevents clot propagation beyond the site of injury is the thrombin-dependent generation of activated protein C (APC, an enzyme that inactivates FVa, thus neutralizing the prothrombinase complex. APC inactivation of FVa is complex, involving the production of partially active intermediates and “protection” of FVa from APC by both FXa and prothrombin. An empirically validated mathematical model of this process would be useful in advancing the predictive capacity of comprehensive models of coagulation. Results A model of human APC inactivation of prothrombinase was constructed in a stepwise fashion by analyzing time courses of FVa inactivation in empirical reaction systems with increasing number of interacting components and generating corresponding model constructs of each reaction system. Reaction mechanisms, rate constants and equilibrium constants informing these model constructs were initially derived from various research groups reporting on APC inactivation of FVa in isolation, or in the presence of FXa or prothrombin. Model predictions were assessed against empirical data measuring the appearance and disappearance of multiple FVa degradation intermediates as well as prothrombinase activity changes, with plasma proteins derived from multiple preparations. Our work integrates previously published findings and through the cooperative

  13. 78 FR 44881 - Drawbridge Operation Regulation; York River, Between Yorktown and Gloucester Point, VA

    Science.gov (United States)

    2013-07-25

    ... deviation from the operating schedule that governs the operation of the Coleman Memorial Bridge (US 17/George P. Coleman Memorial Swing Bridge) across the York River, mile 7.0, between Gloucester Point and Yorktown, VA. This deviation is necessary to facilitate maintenance work on the moveable spans on the...

  14. 77 FR 76451 - Designation for the West Sacramento, CA; Frankfort, IN; and Richmond, VA Areas.

    Science.gov (United States)

    2012-12-28

    ... DEPARTMENT OF AGRICULTURE Grain Inspection, Packers and Stockyards Administration Designation for the West Sacramento, CA; Frankfort, IN; and Richmond, VA Areas. AGENCY: Grain Inspection, Packers and...-Agri West Sacramento, CA(916) 374-9700.. 1/1/2013 12/31/2015 Frankfort Frankfort, IN(765) 258-3624...

  15. 77 FR 6587 - Startek USA, Inc. Alexandria, LA; Startek USA, Inc., Collinsville, VA; Amended Certification...

    Science.gov (United States)

    2012-02-08

    ... DEPARTMENT OF LABOR Employment and Training Administration [TA-W-75,089; TA-W-75,089A] Startek USA, Inc. Alexandria, LA; Startek USA, Inc., Collinsville, VA; Amended Certification Regarding Eligibility... for Worker Adjustment Assistance on January 26, 2011, applicable to workers of StarTek USA, Inc...

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

    NARCIS (Netherlands)

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

    2016-01-01

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

  17. 76 FR 34248 - Equestrian Stables at Meadowood Special Recreation Management Area, VA; Information Sharing Meeting

    Science.gov (United States)

    2011-06-13

    ...), located in Lorton, VA, and collect comments, suggestions and ideas from the public pertaining to the... individual during normal business hours. The FIRS is available 24 hours a day, 7 days a week, to leave a message or question with the above individual. You will receive a reply during normal business hours...

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

    CERN Multimedia

    2002-01-01

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

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

    CERN Multimedia

    2002-01-01

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

  20. 75 FR 60171 - Proposed Information Collection (Credit Underwriting Standards and Procedures for Processing VA...

    Science.gov (United States)

    2010-09-29

    ... DEPARTMENT OF VETERANS AFFAIRS [OMB Control No. 2900-0521] Proposed Information Collection (Credit Underwriting Standards and Procedures for Processing VA Guaranteed Loans) Activity: Comment Request AGENCY... comment on the proposed collection of certain information by the agency. Under the Paperwork Reduction Act...

  1. 78 FR 60379 - Proposed Information Collection (Credit Underwriting Standards and Procedures for Processing VA...

    Science.gov (United States)

    2013-10-01

    ... DEPARTMENT OF VETERANS AFFAIRS [OMB Control No. 2900-0521] Proposed Information Collection (Credit Underwriting Standards and Procedures for Processing VA Guaranteed Loans) Activity: Comment Request AGENCY... comment on the proposed collection of certain information by the agency. Under the Paperwork Reduction Act...

  2. 75 FR 76082 - Agency Information Collection (Credit Underwriting Standards and Procedures for Processing VA...

    Science.gov (United States)

    2010-12-07

    ... DEPARTMENT OF VETERANS AFFAIRS [OMB Control No. 2900-0521] Agency Information Collection (Credit Underwriting Standards and Procedures for Processing VA Guaranteed Loans) Activity Under OMB Review AGENCY... information abstracted below to the Office of Management and Budget (OMB) for review and comment. The PRA...

  3. 76 FR 48204 - Fund Availability Under VA's Homeless Providers Grant and Per Diem Program

    Science.gov (United States)

    2011-08-08

    ... programs addressing emotional, social, spiritual, and generative needs. Terminally Ill (1) Help... optimize reintegration such as life-skills education, recreational activities, and follow up case..., and medication education. Through this NOFA, VA seeks to renew the FY 2009 previous grant and per diem...

  4. 75 FR 52989 - Specialty Minerals, Inc., Franklin, VA; Notice of Negative Determination Regarding Application...

    Science.gov (United States)

    2010-08-30

    ... DEPARTMENT OF LABOR Employment and Training Administration [TA-W-74,057] Specialty Minerals, Inc., Franklin, VA; Notice of Negative Determination Regarding Application for Reconsideration By applications dated July 9, 2010 and July 16, 2010 (filed by a company official and a worker, respectively...

  5. 77 FR 70805 - Presquile National Wildlife Refuge, Chesterfield County, VA; Final Comprehensive Conservation...

    Science.gov (United States)

    2012-11-27

    .... Mail: Andy Hofmann, Project Leader, Eastern Virginia Rivers NWR Complex, U.S. Fish and Wildlife Service, P.O. Box 1030, 335 Wilna Road, Warsaw, VA 22572. Fax: Attention: Andy Hofmann, 804-333-1470. In-Person Viewing or Pickup: Call Andy Hofmann, Project Leader, at 804-333-1470 extension 112 during regular...

  6. VA Health Care: Processes to Evaluate, Implement, and Monitor Organizational Structure Changes Needed

    Science.gov (United States)

    2016-09-01

    their families , such as medallions and markers for headstones that signify veterans’ service. Page 3 GAO-16-803 VHA Organizational ... Research Oversight, and Chief Nursing Page 8 GAO-16-803 VHA Organizational Structure Officer. Also, the Chief Financial Officer and...VA HEALTH CARE Processes to Evaluate, Implement, and Monitor Organizational Structure Changes Needed Report to

  7. 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

    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

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

    Science.gov (United States)

    2010-07-01

    ... DEPARTMENT OF VETERANS AFFAIRS (CONTINUED) VETERANS SMALL BUSINESS REGULATIONS Records Management § 74.25 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...

  9. 77 FR 1716 - James River National Wildlife Refuge, Prince George County, VA

    Science.gov (United States)

    2012-01-11

    ... River National Wildlife Refuge, Prince George County, VA AGENCY: Fish and Wildlife Service, Interior... (the refuge, NWR), which is located in Prince George County, Virginia. We provide this notice in... River NWR, in Prince George County, Virginia. This notice complies with our CCP policy to advise other...

  10. Intra-Operative Indocyanine Green-Videoangiography (ICG-VA) in ...

    African Journals Online (AJOL)

    Methods: Fifteen consecutive patients with anterior circulation aneurysms who underwent craniotomy and clipping of the aneurysms were included in this study. Intraoperative ICG-VA was performed in all cases after exposure of the aneurysm and the branches in the vicinity of the aneurysm or the parent vessel before ...

  11. 76 FR 582 - Elizabeth Hartwell Mason Neck National Wildlife Refuge, Fairfax County, VA, and Featherstone...

    Science.gov (United States)

    2011-01-05

    ...] Elizabeth Hartwell Mason Neck National Wildlife Refuge, Fairfax County, VA, and Featherstone National... comprehensive conservation plan and the environmental assessment (CCP/EA) for Elizabeth Hartwell Mason Neck (Mason Neck) National Wildlife Refuge (NWR) and Featherstone NWR for a 45-day public review and comment...

  12. 76 FR 59153 - Elizabeth Hartwell Mason Neck National Wildlife Refuge, Fairfax County, VA, and Featherstone...

    Science.gov (United States)

    2011-09-23

    ...] Elizabeth Hartwell Mason Neck National Wildlife Refuge, Fairfax County, VA, and Featherstone National... plan (CCP) and finding of no significant impact (FONSI) for Elizabeth Hartwell Mason Neck (Mason Neck...: Download a copy of the document at http://www.fws.gov/northeast/planning/MasonNeck_Featherstone/ccphome...

  13. 33 CFR 80.505 - Cape Henlopen, DE to Cape Charles, VA.

    Science.gov (United States)

    2010-07-01

    ... to Cape Charles, VA. (a) A line drawn from the seaward extremity of Indian River Inlet North Jetty to Indian River Inlet South Jetty Light. (b) A line drawn from Ocean City Inlet Light 6, 225° true across... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Cape Henlopen, DE to Cape Charles...

  14. 78 FR 27882 - VA Veteran-Owned Small Business (VOSB) Verification Guidelines

    Science.gov (United States)

    2013-05-13

    ... Verification Self-Assessment Tool that walks the veteran through the regulation and how it applies to the...) Verification Guidelines AGENCY: Department of Veterans Affairs. ACTION: Advanced notice of proposed rulemaking... regulations governing the Department of Veterans Affairs (VA) Veteran-Owned Small Business (VOSB) Verification...

  15. 75 FR 28295 - Parkdale Mills (Formerly Hanesbrands, Inc.) Galax, VA; Notice of Affirmative Determination...

    Science.gov (United States)

    2010-05-20

    ... DEPARTMENT OF LABOR Employment and Training Administration [TA-W-72,695] Parkdale Mills (Formerly Hanesbrands, Inc.) Galax, VA; Notice of Affirmative Determination Regarding Application for Reconsideration By application dated February 2, 2010, petitioners requested administrative reconsideration of the negative...

  16. 77 FR 19975 - VA Acquisition Regulation: Simplified Acquisition Procedures for Health-Care Resources (Section...

    Science.gov (United States)

    2012-04-03

    ... to which technology, economic conditions, or other factors have changed in the area affected by the... comments on factors described in the Supplementary Information. DATES: Comments must be received by VA on... (003A2A), Office of Acquisition, Logistics and Construction, Department of Veterans Affairs, 810 Vermont...

  17. The VA and VCD spectra of various isotopomers of L-alanine in aqueous solution

    DEFF Research Database (Denmark)

    Abdali, Salim; Jalkanen, Karl J.; Bohr, Henrik

    2002-01-01

    Density functional theory (DFT) at the Becke 3LYP level has been used to calculate the vibrational absorption (VA) and vibrational circular dichroism (VCD) spectra of various deuterated species Of L-alanine. The effect of replacing the methine hydrogen, CH1, the methyl group, CH3, and both...

  18. 77 FR 70708 - VA Acquisition Regulation: Electronic Submission of Payment Requests

    Science.gov (United States)

    2012-11-27

    ... electronic data interchange (EDI) formats; or (3) another electronic form as prescribed by the contract....fsc.va.gov/einvoice.asp .); or, (b) A system that conforms to the X12 electronic data interchange (EDI... Institute (ANSI). The X12 EDI Web site ( http://www.x12.org ) includes additional information on EDI 810 and...

  19. 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...

  20. 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

  1. 76 FR 70345 - Drawbridge Operation Regulations; Elizabeth River, Eastern Branch, Norfolk, VA

    Science.gov (United States)

    2011-11-14

    ... DEPARTMENT OF HOMELAND SECURITY Coast Guard 33 CFR Part 117 [Docket No. USCG-2011-1022] Drawbridge Operation Regulations; Elizabeth River, Eastern Branch, Norfolk, VA AGENCY: Coast Guard, DHS. ACTION: Notice... periodic maintenance. The Norfolk Southern 5 Bridge, at mile 1.1, across the Elizabeth River (Eastern...

  2. 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.

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

    Science.gov (United States)

    2016-12-01

    Congressional Requesters December 2016 GAO-17-52 United States Government Accountability Office United States Government Accountability Office...VHA officials said not all facilities require onsite gynecologists and facilities may authorize gynecological services from non-VA providers. They...including previously closed combat positions, which could contribute to the increase in the women veteran population. See GAO, Military Personnel: DOD Is

  4. 76 FR 26607 - Safety Zone; Air Power Over Hampton Roads, Back River, Hampton, VA

    Science.gov (United States)

    2011-05-09

    ...-AA00 Safety Zone; Air Power Over Hampton Roads, Back River, Hampton, VA AGENCY: Coast Guard, DHS... the safety of life on navigable waters during the Air Power Over Hampton Roads Air Show. This action... Division Chief, Sector Hampton Roads, Coast Guard; telephone 757-668- 5581, e-mail [email protected

  5. 77 FR 33089 - OPSAIL 2012 Virginia, Port of Hampton Roads, VA

    Science.gov (United States)

    2012-06-05

    ...] RIN 1625-AA00, AA08, AA11 OPSAIL 2012 Virginia, Port of Hampton Roads, VA AGENCY: Coast Guard, DHS... of Hampton Roads, Virginia for Operation Sail (OPSAIL) 2012 Virginia activities. This regulation is..., Hampton Roads, the James River and Elizabeth River. DATES: This rule is effective from June 6, 2012 to...

  6. 77 FR 19957 - OPSAIL 2012 Virginia, Port of Hampton Roads, VA

    Science.gov (United States)

    2012-04-03

    ...-0174] RIN 1625-AA00, AA01, AA08, AA11, AA87 OPSAIL 2012 Virginia, Port of Hampton Roads, VA AGENCY... temporary regulations in the Port of Hampton Roads, Virginia for Operation Sail (OPSAIL) 2012 Virginia... portions of Chesapeake Bay, Hampton Roads, the James River and Elizabeth River. DATES: Comments and related...

  7. 75 FR 30782 - Reorganization/Expansion of Foreign-Trade Zone 20; Hampton Roads, VA, Area

    Science.gov (United States)

    2010-06-02

    ... DEPARTMENT OF COMMERCE Foreign-Trade Zones Board [Order No. 1683] Reorganization/Expansion of Foreign-Trade Zone 20; Hampton Roads, VA, Area Pursuant to its authority under the Foreign-Trade Zones Act...) in the Hampton Roads, Virginia, area within the Norfolk Customs and Border Protection port of entry...

  8. 76 FR 44279 - Radio Broadcasting Services; Clinchco, VA, and Coal Run, KY

    Science.gov (United States)

    2011-07-25

    ...] Radio Broadcasting Services; Clinchco, VA, and Coal Run, KY AGENCY: Federal Communications Commission... Station WPKE-FM, Coal Run Kentucky, from Channel 276A to Channel 221C3. DATES: Effective August 1, 2011... 221C3 at Coal Run, Kentucky, are 37-23-57 NL and 82-23-42 WL, and for Channel 276A at Clinchco, Virginia...

  9. 38 CFR 17.96 - Medication prescribed by non-VA physicians.

    Science.gov (United States)

    2010-07-01

    ... AFFAIRS MEDICAL Outpatient Treatment § 17.96 Medication prescribed by non-VA physicians. Any prescription... and medicines ordered by a private or non-Department of Veterans Affairs doctor of medicine or doctor of osteopathy duly licensed to practice in the jurisdiction where the prescription is written, shall...

  10. 38 CFR 17.1000 - Payment or reimbursement for emergency services for nonservice-connected conditions in non-VA...

    Science.gov (United States)

    2010-07-01

    ... for emergency services for nonservice-connected conditions in non-VA facilities. 17.1000 Section 17.1000 Pensions, Bonuses, and Veterans' Relief DEPARTMENT OF VETERANS AFFAIRS MEDICAL Payment Or Reimbursement for Emergency Services for Nonservice-Connected Conditions in Non-Va Facilities § 17.1000 Payment...

  11. 75 FR 44720 - Safety Zone; Live-Fire Gun Exercise, M/V Del Monte, James River, VA

    Science.gov (United States)

    2010-07-29

    ... DEPARTMENT OF HOMELAND SECURITY Coast Guard 33 CFR Part 165 [Docket No. USCG-2010-0585] RIN 1625-AA00 Safety Zone; Live-Fire Gun Exercise, M/V Del Monte, James River, VA AGENCY: Coast Guard, DHS... follows: Sec. 165.T05-0585 Safety Zone; Live-Fire Gun Exercise, M/V Del Monte, James River, VA (a...

  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. 76 FR 44086 - Agency Information Collection (Notice of Waiver of VA Compensation or Pension To Receive Military...

    Science.gov (United States)

    2011-07-22

    ... number of days equal to the number of days in which they received training pay. An agency may not conduct... of Waiver of VA Compensation or Pension To Receive Military Pay and Allowances) Activity Under OMB....'' SUPPLEMENTARY INFORMATION: Title: Notice of Waiver of VA Compensation or Pension to Receive Military Pay and...

  14. On Setting Day-Ahead Equity Trading Risk Limits: VaR Prediction at Market Close or Open?

    Directory of Open Access Journals (Sweden)

    Ana-Maria Fuertes

    2016-09-01

    Full Text Available This paper investigates the information content of the ex post overnight return for one-day-ahead equity Value-at-Risk (VaR forecasting. To do so, we deploy a univariate VaR modeling approach that constructs the forecast at market open and, accordingly, exploits the available overnight close-to-open price variation. The benchmark is the bivariate VaR modeling approach proposed by Ahoniemi et al. that constructs the forecast at the market close instead and, accordingly, it models separately the daytime and overnight return processes and their covariance. For a small cap portfolio, the bivariate VaR approach affords superior predictive ability than the ex post overnight VaR approach whereas for a large cap portfolio the results are reversed. The contrast indicates that price discovery at the market open is less efficient for small capitalization, thinly traded stocks.

  15. 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.

  16. Access to mental health care among women Veterans: is VA meeting women's needs?

    Science.gov (United States)

    Kimerling, Rachel; Pavao, Joanne; Greene, Liberty; Karpenko, Julie; Rodriguez, Allison; Saweikis, Meghan; Washington, Donna L

    2015-04-01

    Patient-centered access to mental health describes the fit between patient needs and resources of the system. To date, little data are available to guide implementation of services to women veterans, an underrepresented minority within Department of Veteran Affairs (VA) health care. The current study examines access to mental health care among women veterans, and identifies gender-related indicators of perceived access to mental health care. A population-based sample of 6287 women veterans using VA primary care services participated in a survey of past year perceived need for mental health care, mental health utilization, and gender-related mental health care experiences. Subjective rating of how well mental health care met their needs was used as an indicator of perceived access. Half of all women reported perceived mental health need; 84.3% of those women received care. Nearly all mental health users (90.9%) used VA services, although only about half (48.8%) reported that their mental health care met their needs completely or very well. Gender related experiences (availability of female providers, women-only treatment settings, women-only treatment groups, and gender-related comfort) were each associated with 2-fold increased odds of perceived access, and associations remained after adjusting for ease of getting care. Women VA users demonstrate very good objective access to mental health services. Desire for, and access to specialized mental health services for women varies across the population and are important aspects of shared decision making in referral and treatment planning for women using VA primary care.

  17. Global Derivatives

    DEFF Research Database (Denmark)

    Andersen, Torben Juul

    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......" provides comprehensive coverage of different types of derivatives, including exchange traded contracts and over-the-counter instruments as well as real options. There is an equal emphasis on the practical application of derivatives and their actual uses in business transactions and corporate risk...... management situations. Its key features include: derivatives are introduced in a global market perspective; describes major derivative pricing models for practical use, extending these principles to valuation of real options; practical applications of derivative instruments are richly illustrated...

  18. Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons

    Science.gov (United States)

    Haas, Brian J.; Gevers, Dirk; Earl, Ashlee M.; Feldgarden, Mike; Ward, Doyle V.; Giannoukos, Georgia; Ciulla, Dawn; Tabbaa, Diana; Highlander, Sarah K.; Sodergren, Erica; Methé, Barbara; DeSantis, Todd Z.; Petrosino, Joseph F.; Knight, Rob; Birren, Bruce W.

    2011-01-01

    Bacterial diversity among environmental samples is commonly assessed with PCR-amplified 16S rRNA gene (16S) sequences. Perceived diversity, however, can be influenced by sample preparation, primer selection, and formation of chimeric 16S amplification products. Chimeras are hybrid products between multiple parent sequences that can be falsely interpreted as novel organisms, thus inflating apparent diversity. We developed a new chimera detection tool called Chimera Slayer (CS). CS detects chimeras with greater sensitivity than previous methods, performs well on short sequences such as those produced by the 454 Life Sciences (Roche) Genome Sequencer, and can scale to large data sets. By benchmarking CS performance against sequences derived from a controlled DNA mixture of known organisms and a simulated chimera set, we provide insights into the factors that affect chimera formation such as sequence abundance, the extent of similarity between 16S genes, and PCR conditions. Chimeras were found to reproducibly form among independent amplifications and contributed to false perceptions of sample diversity and the false identification of novel taxa, with less-abundant species exhibiting chimera rates exceeding 70%. Shotgun metagenomic sequences of our mock community appear to be devoid of 16S chimeras, supporting a role for shotgun metagenomics in validating novel organisms discovered in targeted sequence surveys. PMID:21212162

  19. Vađenje podrtina i potonulih stvari u svjetlu novele Pomorskog zakonika iz 2013. godine

    Directory of Open Access Journals (Sweden)

    Vesna Skorupan Wolff

    2017-11-01

    Full Text Available Materiju vađenja podrtina i potonulih stvari uređuju odredbe upravnopravne prirode koje reguliraju odnose između vlasnika podrtine ili potonule stvari, odnosno ovlaštene osobe i upravnih tijela, a kojima se uređuju razni pravni aspekti postupka vađenja. Pravo vaditi podrtinu ili potonulu stvar primarno ima njezin vlasnik odnosno ovlaštena osoba. Zakon vlasnicima podrtina i potonulih stvari, odnosno ovlaštenim osobama, ostavlja primjeren rok u kojem mogu pokrenuti upravni postupak za dobivanje dozvole za vađenje podrtine ili potonule stvari. Na taj način jamči se nepovredivost vlasništva i utvrđuje načelo prema kojem činjenica da je stvar potonula ili se nasukala ne utječe izravno na vlasnička prava njezina dotadašnjeg vlasnika. Međutim, ako vlasnik, odnosno ovlaštena osoba ne zatraži odobrenje za vađenje podrtine ili potonule stvari, ili kad bez opravdanog razloga prekine ili napusti započeto vađenje kao i u slučaju ako je ovlaštena osoba nepoznata, PZ nudi pravni okvir i omogućuje da vađenje podrtine ili potonule stvari poduzme pošteni nalaznik ili lučka kapetanija. U okviru instituta vađenja podrtina i potonulih stvari uvodi se posebno pravno uređenje za nalaz stvari u moru te se precizno normiraju svi segmenti postupka vađenja kada ga poduzima pošteni nalaznik ili lučka kapetanija. Uređuju se i sva relevantna pitanja u svezi postupanja s izvađenim stvarima kao što su njihovo čuvanje te u propisanim slučajevima mogućnost prodaje na javnoj dražbi. PZ-om se precizno uređuju obvezni odnosi koji nastaju između vlasnika, odnosno ovlaštene osobe i poštenog nalaznika te vlasnika, odnosno ovlaštene osobe i lučke kapetanije, ovisno o tome tko je poduzeo vađenje, a koji se odnose na plaćanje naknade za vađenje, čuvanje, nalazninu i druge tražbine koje zakon priznaje poštenim nalaznicima i lučkim kapetanijama. U okviru toga, uređuje se i posebno stvarnopravno uređenje za stjecanje prava vlasni

  20. Headache diagnoses among Iraq and Afghanistan war veterans enrolled in VA: a gender comparison.

    Science.gov (United States)

    Carlson, Kathleen F; Taylor, Brent C; Hagel, Emily M; Cutting, Andrea; Kerns, Robert; Sayer, Nina A

    2013-01-01

    To examine the prevalence and correlates of headache diagnoses, by gender, among Iraq and Afghanistan War Veterans who use Department of Veterans Affairs (VA) health care. Understanding the health care needs of recent Veterans, and how these needs differ between women and men, is a priority for the VA. The potential for a large burden of headache disorders among Veterans seeking VA services exists but has not been examined in a representative sample. We conducted a historical cohort study using national VA inpatient and outpatient data from fiscal year 2011. Participants were all (n = 470,215) Iraq and Afghanistan War Veteran VA users in 2011; nearly 13% were women. We identified headache diagnoses using International Classification of Diseases (ICD-9) diagnosis codes assigned during one or more VA inpatient or outpatient encounters. Descriptive analyses included frequencies of patient characteristics, prevalence and types of headache diagnoses, and prevalence of comorbid diagnoses. Prevalence ratios (PR) with 95% confidence intervals (CI) were used to estimate associations between gender and headache diagnoses. Multivariate models adjusted for age and race. Additional models also adjusted for comorbid diagnoses. In 2011, 56,300 (11.9%) Veterans received a headache-related diagnosis. While controlling for age and race, headache diagnoses were 1.61 times more prevalent (95% CI = 1.58-1.64) among women (18%) than men (11%). Most of this difference was associated with migraine diagnoses, which were 2.66 times more prevalent (95% CI = 2.59-2.73) among women. Cluster and post-traumatic headache diagnoses were less prevalent in women than in men. These patterns remained the same when also controlling for comorbid diagnoses, which were common among both women and men with headache diagnoses. The most prevalent comorbid diagnoses examined were depression (46% of women with headache diagnoses vs 40% of men), post-traumatic stress disorder (38% vs 58%), and back

  1. 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 inherently static, capital itself is unprecedentedly mobile, fluid and fungible. As such derivatives raise the specter of ‘financial weapons of mass destruction’....

  2. Financial Derivatives

    OpenAIRE

    Janečková, Alena

    2011-01-01

    1 Abstract/ Financial derivatives The purpose of this thesis is to provide an introduction to financial derivatives which has been, from the legal perspective, described in a not satisfactory manner as quite little literature that can be found about this topic. The main objectives of this thesis are to define the term "financial derivatives" and its particular types and to analyse legal nature of these financial instruments. The last objective is to try to draft future law regulation of finan...

  3. Tuberculin reactivity and tuberculosis epidemiology in the Pakaanóva (Wari') Indians of Rondônia, south-western Brazilian Amazon.

    Science.gov (United States)

    Escobar, A L; Coimbra, C E A; Camacho, L A B; Santos, R V

    2004-01-01

    To investigate the characteristics of tuberculin skin test reactivity in the Pakaanóva Indians, in Amazonia, Brazil, after revaccination of all study participants with bacille Calmette-Guerin (BCG). The investigation was designed as a post-BCG vaccination purified protein derivative (PPD) survey. Data included PPD readings, age, sex, nutritional status, place of residence, previous tuberculosis, physical examinations and BCG status. Bivariate and multivariate logistic regression analyses were conducted. About 90% (n = 505) of the total population participated. One third (32.1%) of the subjects presented induration > or = 10 mm at 72 h. Induration sizes showed weak linear correlation with age; differences between sexes were not observed. Skin reaction was not associated with nutritional status. Individuals with a history of tuberculosis were six times more likely to test positive. History of tuberculosis, age, and previous BCG vaccination were significantly associated with PPD reactivity in the multivariate analyses. The Pakaanóva showed a high proportion (58.4%) of non-reactors, even with a recent BCG booster. Sex differences in PPD reactivity were either not present or could not be demonstrated. The association between age and PPD reactivity resembles that observed in other Amazonian populations. The authors discuss the potential of PPD testing as a screening tool to enhance tuberculosis detection, especially in indigenous populations in Amazonia with limited access to health services.

  4. VA Student Financial Aid. Opportunity To Reduce Overlap in Approving Education and Training Programs. Report to the Committee on Veterans' Affairs, U.S. Senate.

    Science.gov (United States)

    General Accounting Office, Washington, DC. Health, Education, and Human Services Div.

    The Department of Veterans Affairs (VA) contracts with state approving agencies (SAAs) to assess whether schools and training programs offer education of sufficient quality for veterans to receive VA education assistance benefits when attending them. The General Accounting Office examined the gatekeeping activities of the VA and the Department of…

  5. Dynamic VaR Measurement of Gold Market with SV-T-MN Model

    Directory of Open Access Journals (Sweden)

    Fenglan Li

    2017-01-01

    Full Text Available VaR (Value at Risk in the gold market was measured and predicted by combining stochastic volatility (SV model with extreme value theory. Firstly, for the fat tail and volatility persistence characteristics in gold market return series, the gold price return volatility was modeled by SV-T-MN (SV-T with Mixture-of-Normal distribution model based on state space. Secondly, future sample volatility prediction was realized by using approximate filtering algorithm. Finally, extreme value theory based on generalized Pareto distribution was applied to measure dynamic risk value (VaR of gold market return. Through the proposed model on the price of gold, empirical analysis was investigated; the results show that presented combined model can measure and predict Value at Risk of the gold market reasonably and effectively and enable investors to further understand the extreme risk of gold market and take coping strategies actively.

  6. Strategies from a nationwide health information technology implementation: the VA CART story.

    Science.gov (United States)

    Box, Tamára L; McDonell, Mary; Helfrich, Christian D; Jesse, Robert L; Fihn, Stephan D; Rumsfeld, John S

    2010-01-01

    The VA Cardiovascular Assessment, Reporting, and Tracking (CART) system is a customized electronic medical record system which provides standardized report generation for cardiac catheterization procedures, serves as a national data repository, and is the centerpiece of a national quality improvement program. Like many health information technology projects, CART implementation did not proceed without some barriers and resistance. We describe the nationwide implementation of CART at the 77 VA hospitals which perform cardiac catheterizations in three phases: (1) strategic collaborations; (2) installation; and (3) adoption. Throughout implementation, success required a careful balance of technical, clinical, and organizational factors. We offer strategies developed through CART implementation which are broadly applicable to technology projects aimed at improving the quality, reliability, and efficiency of health care.

  7. The use of genus-specific amplicon pyrosequencing to assess phytophthora species diversity using eDNA from soil and water in Northern Spain.

    Science.gov (United States)

    Català, Santiago; Pérez-Sierra, Ana; Abad-Campos, Paloma

    2015-01-01

    Phytophthora is one of the most important and aggressive plant pathogenic genera in agriculture and forestry. Early detection and identification of its pathways of infection and spread are of high importance to minimize the threat they pose to natural ecosystems. eDNA was extracted from soil and water from forests and plantations in the north of Spain. Phytophthora-specific primers were adapted for use in high-throughput Sequencing (HTS). Primers were tested in a control reaction containing eight Phytophthora species and applied to water and soil eDNA samples from northern Spain. Different score coverage threshold values were tested for optimal Phytophthora species separation in a custom-curated database and in the control reaction. Clustering at 99% was the optimal criteria to separate most of the Phytophthora species. Multiple Molecular Operational Taxonomic Units (MOTUs) corresponding to 36 distinct Phytophthora species were amplified in the environmental samples. Pyrosequencing of amplicons from soil samples revealed low Phytophthora diversity (13 species) in comparison with the 35 species detected in water samples. Thirteen of the MOTUs detected in rivers and streams showed no close match to sequences in international sequence databases, revealing that eDNA pyrosequencing is a useful strategy to assess Phytophthora species diversity in natural ecosystems.

  8. A performance evaluation of Nextera XT and KAPA HyperPlus for rapid Illumina library preparation of long-range mitogenome amplicons.

    Science.gov (United States)

    Ring, Joseph D; Sturk-Andreaggi, Kimberly; Peck, Michelle A; Marshall, Charla

    2017-07-01

    Next-generation sequencing (NGS) facilitates the rapid and high-throughput generation of human mitochondrial genome (mitogenome) data to build population and reference databases for forensic comparisons. To this end, long-range amplification provides an effective method of target enrichment that is amenable to library preparation assays employing DNA fragmentation. This study compared the Nextera XT DNA Library Preparation Kit (Illumina, San Diego, CA) and the KAPA HyperPlus Library Preparation Kit (Kapa Biosystems, Wilmington, MA) for enzymatic fragmentation and indexing of ∼8500bp mitogenome amplicons for Illumina sequencing. The Nextera XT libraries produced low-coverage regions that were consistent across all samples, while the HyperPlus libraries resulted in uniformly high coverage across the mitogenome, even with reduced-volume reaction conditions. The balanced coverage observed from KAPA HyperPlus libraries enables not only low-level variant calling across the mitogenome but also increased sample multiplexing for greater processing efficiency. Copyright © 2017 Elsevier B.V. All rights reserved.

  9. Microfluidic PCR Amplification and MiSeq Amplicon Sequencing Techniques for High-Throughput Detection and Genotyping of Human Pathogenic RNA Viruses in Human Feces, Sewage, and Oysters

    Directory of Open Access Journals (Sweden)

    Mamoru Oshiki

    2018-04-01

    Full Text Available Detection and genotyping of pathogenic RNA viruses in human and environmental samples are useful for monitoring the circulation and prevalence of these pathogens, whereas a conventional PCR assay followed by Sanger sequencing is time-consuming and laborious. The present study aimed to develop a high-throughput detection-and-genotyping tool for 11 human RNA viruses [Aichi virus; astrovirus; enterovirus; norovirus genogroup I (GI, GII, and GIV; hepatitis A virus; hepatitis E virus; rotavirus; sapovirus; and human parechovirus] using a microfluidic device and next-generation sequencer. Microfluidic nested PCR was carried out on a 48.48 Access Array chip, and the amplicons were recovered and used for MiSeq sequencing (Illumina, Tokyo, Japan; genotyping was conducted by homology searching and phylogenetic analysis of the obtained sequence reads. The detection limit of the 11 tested viruses ranged from 100 to 103 copies/μL in cDNA sample, corresponding to 101–104 copies/mL-sewage, 105–108 copies/g-human feces, and 102–105 copies/g-digestive tissues of oyster. The developed assay was successfully applied for simultaneous detection and genotyping of RNA viruses to samples of human feces, sewage, and artificially contaminated oysters. Microfluidic nested PCR followed by MiSeq sequencing enables efficient tracking of the fate of multiple RNA viruses in various environments, which is essential for a better understanding of the circulation of human pathogenic RNA viruses in the human population.

  10. Size Matters: Assessing Optimum Soil Sample Size for Fungal and Bacterial Community Structure Analyses Using High Throughput Sequencing of rRNA Gene Amplicons

    Directory of Open Access Journals (Sweden)

    Christopher Ryan Penton

    2016-06-01

    Full Text Available We examined the effect of different soil sample sizes obtained from an agricultural field, under a single cropping system uniform in soil properties and aboveground crop responses, on bacterial and fungal community structure and microbial diversity indices. DNA extracted from soil sample sizes of 0.25, 1, 5 and 10 g using MoBIO kits and from 10 and 100 g sizes using a bead-beating method (SARDI were used as templates for high-throughput sequencing of 16S and 28S rRNA gene amplicons for bacteria and fungi, respectively, on the Illumina MiSeq and Roche 454 platforms. Sample size significantly affected overall bacterial and fungal community structure, replicate dispersion and the number of operational taxonomic units (OTUs retrieved. Richness, evenness and diversity were also significantly affected. The largest diversity estimates were always associated with the 10 g MoBIO extractions with a corresponding reduction in replicate dispersion. For the fungal data, smaller MoBIO extractions identified more unclassified Eukaryota incertae sedis and unclassified glomeromycota while the SARDI method retrieved more abundant OTUs containing unclassified Pleosporales and the fungal genera Alternaria and Cercophora. Overall, these findings indicate that a 10 g soil DNA extraction is most suitable for both soil bacterial and fungal communities for retrieving optimal diversity while still capturing rarer taxa in concert with decreasing replicate variation.

  11. Color perception differentiates Alzheimer's Disease (AD) from Vascular Dementia (VaD) patients.

    Science.gov (United States)

    Arnaoutoglou, N A; Arnaoutoglou, M; Nemtsas, P; Costa, V; Baloyannis, S J; Ebmeier, K P

    2017-08-01

    Alzheimer's Disease (AD) and Vascular Dementia (VaD) are the most common causes of dementia in older people. Both diseases appear to have similar clinical symptoms, such as deficits in attention and executive function, but specific cognitive domains are affected. Current cohort studies have shown a close relationship between αβ deposits and age-related macular degeneration (Johnson et al., 2002; Ratnayaka et al., 2015). Additionally, a close link between the thinning of the retinal nerve fiber (RNFL) and AD patients has been described, while it has been proposed that AD patients suffer from a non-specific type of color blindness (Pache et al., 2003). Our study included 103 individuals divided into three groups: A healthy control group (n = 35), AD (n = 32) according to DSM-IV-TR, NINCDS-ADRDA criteria, and VaD (n = 36) based on ΝΙΝDS-AIREN, as well as Magnetic Resonance Imaging (MRI) results. The severity of patient's cognitive impairment, was measured with the Mini-Mental State Examination (MMSE) and was classified according to the Reisberg global deterioration scale (GDS). Visual perception was examined using the Ishihara plates: "Ishihara Color Vision Test - 38 Plate." The three groups were not statistically different for demographic data (age, gender, and education). The Ishihara color blindness test has a sensitivity of 80.6% and a specificity of 87.5% to discriminate AD and VaD patients when an optimal (32.5) cut-off value of performance is used. Ishihara Color Vision Test - 38 Plate is a promising potential method as an easy and not time-consuming screening test for the differential diagnosis of dementia between AD and VaD.

  12. A Survey on Power and Political Culture in Kalile va Demne

    Directory of Open Access Journals (Sweden)

    J Dehghanian

    2011-04-01

    Postmodernist thinkers, especially Michel Foucault, make it clear that power and political culture are so complicated and affect private and social life. It is possible to claim that there is a meaningful relationship between people’s deed and power in each society. In this article, we take a look at political culture and power in Kalile va Demne and will analyze its effects on people’s thoughts and deeds.

  13. KENO3D, Visualisation Tool for KENO V.A and KENO-VI Geometry Models

    International Nuclear Information System (INIS)

    2008-01-01

    1 - Description of program or function: The KENO3D Visualization Tool for KENO Geometry Models is a powerful state-of-the-art visualization tool that enables KENO V.a users and KENO-VI to interactively display their three-dimensional geometry models. The KENO3D interactive options include: - Shaded or wire-frame images ; - Standard views such as top view, side view, front view, and isometric(3-D) view; - Rotating the model ; - Zooming in on selected locations ; - Selecting parts of the model to display ; - Editing colors and displaying legends ; - Displaying properties of any unit in the model ; - Creating cut-away views ; - Removing units from the model; - Printing image or saving image to a common graphics formats. KENO3D was developed for use by criticality safety specialists that use the KENO three-dimensional Monte Carlo criticality computer code. KENO V.a and KENO-VI are part of the SCALE (Standardized Computer Analyses for Licensing Evaluations) computer software system developed at Ridge National Laboratory (ORNL) that is widely used and accepted around the world for criticality safety analyses. 2 - Methods: KENO3D reads CSAS, KENO V.a, or KENO-VI input files. It attempts to verify that the KENO geometry input is 'legal', i.e., it conforms to the code input guidelines. KENO3D prints a warning message for illegal geometry input, and if possible, it displays the illegal KENO geometry to facilitate debugging of the input. Problems with more than 300,000 KENO V.a bodies have been successfully tested and displayed. KENO3D has the look and feel of a typical PC Windows application. Toolbar buttons are included for all major menu options. There is a setup dialog that allows the user to specify toolbars that should be displayed

  14. Homeless Veterans: Management Improvements Could Help VA Better Identify Supportive Housing Projects

    Science.gov (United States)

    2016-12-01

    of the country. The Fair Market Rent is the cost of standard, non- luxury housing in the community. The payment standard is the maximum subsidy a...access that can be particularly beneficial for those located in high-rent markets . According to the VA’s Fiscal Year 2017 “EUL Consideration...during fiscal year 2017. The draft that VA shared with us requires an analysis of the local market , including current and anticipated supply and

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

    International Nuclear Information System (INIS)

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

    2000-01-01

    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

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

    Science.gov (United States)

    2010-07-01

    ... ENGINEERS, DEPARTMENT OF THE ARMY, DEPARTMENT OF DEFENSE DANGER ZONE AND RESTRICTED AREA REGULATIONS § 334.220 Chesapeake Bay, south of Tangier Island, Va.; naval firing range. (a) The danger zone. Beginning... to latitude 37°45′00″, longitude 76°09′48″; thence to latitude 37°45′00″, longitude 76°08′51″; and...

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

    Directory of Open Access Journals (Sweden)

    Katsuyuki Shiroguchi

    2011-04-01

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

  18. Calculation of criticality of the AP600 reactor with KENO V.a code

    Energy Technology Data Exchange (ETDEWEB)

    Krumbein, A; Caner, M; Shapira, M [Israel Atomic Energy Commission, Yavne (Israel). Soreq Nuclear Research Center

    1996-12-01

    The Westinghouse AP600 PWR has been modeled using the KENO V.a three dimensional Monte Carlo criticality program of the SCALE-PC code system. These calculations and the use of a Monte Carlo neutron transport code such as KENO will provide us with an independent check on our WIMS/CITATION calculations for the AP600 as well as for other reactors. It will also enable us to model more complicated geometries. (authors).

  19. 5kVa power inverter design and simulation based on boost ...

    African Journals Online (AJOL)

    Five (5) kVA power inverter was designed and simulated base on two topologies; Boost converter and Half-bridge inverter topology. A 555 timer IC was used as the control at fixed frequencies of 25 kHz and 50 Hz for the two stages. The results of the simulation were obtained. The graphs for both stages were plotted and the ...

  20. Use of the Decision Support System for VA cost-effectiveness research.

    Science.gov (United States)

    Barnett, P G; Rodgers, J H

    1999-04-01

    The Department of Veterans Affairs is adopting the Decision Support System (DSS), computer software and databases which include a cost-accounting system which determines the cost of health care products and patient encounters. A system for providing cost data for cost-effectiveness analysis should be provide valid, detailed, and comprehensive data that can be aggregated. The design of DSS is described and compared with those criteria. Utilization data from DSS was compared with other VA utilization data. Aggregate DSS cost data from 35 medical centers was compared with relative resource weights developed for the Medicare program. Data on hospital stays at 3 facilities found that 3.7% of the stays in DSS were not in the VA discharge database, whereas 7.6% of the stays in the discharge data were not in DSS. DSS reported between 68.8% and 97.1% of the outpatient encounters reported by six facilities in the ambulatory care data base. Relative weights for each Diagnosis Related Group based on DSS data from 35 VA facilities correlated with Medicare weights (correlation coefficient of .853). DSS will be useful for research if certain problems are overcome. It is difficult to distinguish long-term from acute hospital care. VA does not have a complete database of all inpatient procedures, so DSS has not assigned them a specific cost. The authority to access encounter-level DSS data needs to be centralized. Researchers can provide the feedback needed to improve DSS cost estimates. A comprehensive encounter-level extract would facilitate use of DSS for research.

  1. VA OpenNotes: exploring the experiences of early patient adopters with access to clinical notes.

    Science.gov (United States)

    Nazi, Kim M; Turvey, Carolyn L; Klein, Dawn M; Hogan, Timothy P; Woods, Susan S

    2015-03-01

    To explore the experience of early patient adopters who accessed their clinical notes online using the Blue Button feature of the My HealtheVet portal. A web-based survey of VA patient portal users from June 22 to September 15, 2013. 33.5% of respondents knew that clinical notes could be viewed, and nearly one in four (23.5%) said that they had viewed their notes at least once. The majority of VA Notes users agreed that accessing their notes will help them to do a better job of taking medications as prescribed (80.1%) and be better prepared for clinic visits (88.6%). Nine out of 10 users agreed that use of visit notes will help them understand their conditions better (91.8%), and better remember the plan for their care (91.9%). In contrast, 87% disagreed that VA Notes will make them worry more, and 88.4% disagreed that access to VA Notes will be more confusing than helpful. Users who had either contacted their provider or healthcare team (11.9%) or planned to (13.5%) primarily wanted to learn more about a health issue, medication, or test results (53.7%). Initial assessment of the patient experience within the first 9 months of availability provides evidence that patients both value and benefit from online access to clinical notes. These findings are congruent with OpenNotes study findings on a broader scale. Additional outreach and education is needed to enhance patient awareness. Healthcare professionals should author notes keeping in mind the opportunity patient access presents for enhanced communication. © The Author 2014. Published by Oxford University Press on behalf of the American Medical Informatics Association. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  2. Comparison of Comet Enflow and VA One Acoustic-to-Structure Power Flow Predictions

    Science.gov (United States)

    Grosveld, Ferdinand W.; Schiller, Noah H.; Cabell, Randolph H.

    2010-01-01

    Comet Enflow is a commercially available, high frequency vibroacoustic analysis software based on the Energy Finite Element Analysis (EFEA). In this method the same finite element mesh used for structural and acoustic analysis can be employed for the high frequency solutions. Comet Enflow is being validated for a floor-equipped composite cylinder by comparing the EFEA vibroacoustic response predictions with Statistical Energy Analysis (SEA) results from the commercial software program VA One from ESI Group. Early in this program a number of discrepancies became apparent in the Enflow predicted response for the power flow from an acoustic space to a structural subsystem. The power flow anomalies were studied for a simple cubic, a rectangular and a cylindrical structural model connected to an acoustic cavity. The current investigation focuses on three specific discrepancies between the Comet Enflow and the VA One predictions: the Enflow power transmission coefficient relative to the VA One coupling loss factor; the importance of the accuracy of the acoustic modal density formulation used within Enflow; and the recommended use of fast solvers in Comet Enflow. The frequency region of interest for this study covers the one-third octave bands with center frequencies from 16 Hz to 4000 Hz.

  3. Phenomenology of MaVaN’s Models in Reactor Neutrino Data

    Directory of Open Access Journals (Sweden)

    M. F. Carneiro

    2013-01-01

    Full Text Available Mass Varying Neutrinos (MaVaN’s mechanisms were proposed to link the neutrino mass scale with the dark energy density, addressing the coincidence problem. In some scenarios, this mass can present a dependence on the baryonic density felt by neutrinos, creating an effective neutrino mass that depends both on the neutrino and baryonic densities. In this work, we study the phenomenological consequence of MaVaN’s scenarios in which the matter density dependence is induced by Yukawa interactions of a light neutral scalar particle which couples to neutrinos and matter. Under the assumption of one mass scale dominance, we perform an analysis of KamLAND neutrino data which depends on 4 parameters: the two standard oscillation parameters, Δm0,212 and tan2θ12, and two new coefficients which parameterize the environment dependence of neutrino mass. We introduce an Earth’s crust model to compute precisely the density in each point along the neutrino trajectory. We show that this new description of density does not affect the analysis with the standard model case. With the MaVaN model, we observe a first order effect in lower density, which leads to an improvement on the data description.

  4. GeVaDSs – decision support system for novel Genetic Vaccine development process

    Directory of Open Access Journals (Sweden)

    Blazewicz Jacek

    2012-05-01

    Full Text Available Abstract Background The lack of a uniform way for qualitative and quantitative evaluation of vaccine candidates under development led us to set up a standardized scheme for vaccine efficacy and safety evaluation. We developed and implemented molecular and immunology methods, and designed support tools for immunization data storage and analyses. Such collection can create a unique opportunity for immunologists to analyse data delivered from their laboratories. Results We designed and implemented GeVaDSs (Genetic Vaccine Decision Support system an interactive system for efficient storage, integration, retrieval and representation of data. Moreover, GeVaDSs allows for relevant association and interpretation of data, and thus for knowledge-based generation of testable hypotheses of vaccine responses. Conclusions GeVaDSs has been tested by several laboratories in Europe, and proved its usefulness in vaccine analysis. Case study of its application is presented in the additional files. The system is available at: http://gevads.cs.put.poznan.pl/preview/(login: viewer, password: password.

  5. Trade in Value Added (TiVA in EU New Member States (EU NMS

    Directory of Open Access Journals (Sweden)

    Ines Kersan-Škabić

    2017-01-01

    Full Text Available Contemporary trade analysis indicates the necessity of calculating trade in value added (TiVA which is created through global value chains (GVCs. This paper aims to determine the characteristics and importance of GVC trade in the EU new member states (EU NMS with special emphasis placed on the industry level. The results demonstrate different levels of GVC participation of the EU NMS, where Hungary is the most integrated country and Croatia the least integrated. Regional GVCs exist because a huge part of value added (VA comes from EU member states, as in gross export as well as in final demand (Europe as a hub. The most important source countries are Germany and Italy and there is also evidence of geographical and historical relations between the countries. The domination of backward participation has been found in the analysis made on the industrial level, i.e. the EU NMS are highly dependent on the import of intermediates for the production and export of final products. Strong interconnections between imports of intermediate products and exports of final products have been found in the manufacture of computers, electronics and optical products; manufacture of wood, paper, printing and reproduction. This research has contributed to the scarce literature concerning GVC (TiVA in EU NMS and has opened up new possibilities for further research and analysis.

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

    KAUST Repository

    Gojobori, Takashi; Ikeo, Kazuho; Katayama, Yukie; Kawabata, Takeshi; Kinjo, Akira R.; Kinoshita, Kengo; Kwon, Yeondae; Migita, Ohsuke; Mizutani, Hisashi; Muraoka, Masafumi; Nagata, Koji; Omori, Satoshi; Sugawara, Hideaki; Yamada, Daichi; Yura, Kei

    2016-01-01

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

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

    KAUST Repository

    Gojobori, Takashi

    2016-12-24

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

  8. Characterization of the interaction between the heavy and light chains of bovine factor Va.

    Science.gov (United States)

    Walker, F J

    1992-10-05

    Bovine factor Va has been previously been shown to consist of heavy (M(r) = 94,000) and light chains (M(r) = 81,000), that interact in a manner dependent upon the presence of either calcium or manganese ions. In an attempt to understand the mechanism of subunit interaction we have studied the effects of temperature and ions on factor Va stability. The rates of formation of factor Va from isolated chains and dissociation were temperature-dependent with an energy of activation of 6.2 and 1.3 kcal mol-1, respectively. The yield of factor Va from isolated chains was inversely related to the amount of time the chains were incubated at 4 degrees C. Incubation of individual chains revealed that the heavy chain is cold-labile, an effect that is reversible. Manganese ion was observed to prevent the conversion to the inactive form. High salt tends to stabilize the two-chain structure of factor Va, but is inhibitory to its formation from isolated chains. High concentrations of either manganese or calcium ions also inhibited reconstitution of activity. The light chain, in particular, was sensitive to the presence of manganese or calcium ion. Heavy chain that had been cleaved by activated protein C had a weakened interaction with the light chain, and the resulting complex had no procoagulant activity. Cooling of the heavy chain to 4 degrees C enhanced its intrinsic fluorescence. Manganese ion prevented some of this enhancement. The heavy chain fluorescence returned to the room temperature value with a half-life of approximately 10 min. In the presence of manganese ion relaxation was accelerated. The intrinsic fluorescence of activated protein C-cleaved heavy chain was not increased when the temperature was decreased. These data suggest that the heavy chain can exist in two forms. Elevated temperature converts it to a form that can bind ions and have a productive interaction with the light chain. However, conditions that prevent the heavy chain from combining with the light

  9. Definition of the Radionuclide Inventory for the DOE Spent Nuclear Fuel Used in the TSPA-VA Base Case

    International Nuclear Information System (INIS)

    A.J. Smith

    1998-01-01

    The purpose of this document is to present the details of the calculations used to define the radionuclide inventory for the Department of Energy (DOE) spent nuclear fuel (SNF) used in the TSPA-VA calculations

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

    Directory of Open Access Journals (Sweden)

    Christina Salmivalli

    2012-12-01

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

  11. Electronic Health Records: DOD and VA Have Increased Their Sharing of Health Information, but More Work Remains

    National Research Council Canada - National Science Library

    Melvin, Valerie C; Oliver, Barbara S; Collier, Barbara; Shaw, Kelly; Williams, Jr, Robert

    2008-01-01

    ...) and the Department of Veterans Affairs (VA) are required to accelerate the exchange of health information between the departments and to develop systems or capabilities that allow for full interoperability...

  12. Revenue Based Budgeting at VA Northern California Health Care System: A Model for Financially Aligning Organizational Incentives and Operations

    National Research Council Canada - National Science Library

    Stockwell, David

    1999-01-01

    .... Changes in sharing agreement regulations, TRICARE, and Medical Care Cost Recovery (MCCR) also provided each network with the ability to generate revenue from sources outside the traditional VA appropriation...

  13. Creating a sampling frame for population-based veteran research: Representativeness and overlap of VA and Department of Defense databases

    OpenAIRE

    Donna L. Washington, MD, MPH; Su Sun, MPH; Mark Canning, BA

    2010-01-01

    Most veteran research is conducted in Department of Veterans Affairs (VA) healthcare settings, although most veterans obtain healthcare outside the VA. Our objective was to determine the adequacy and relative contributions of Veterans Health Administration (VHA), Veterans Benefits Administration (VBA), and Department of Defense (DOD) administrative databases for representing the U.S. veteran population, using as an example the creation of a sampling frame for the National Survey of Women Vete...

  14. 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.

  15. 30 CFR 57.22208 - Auxiliary fans (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 Auxiliary fans (I-A, II-A, III, and V-A mines... fans (I-A, II-A, III, and V-A mines). (a) Auxiliary fans, except fans used in shops and other areas... applicable requirements of 30 CFR part 18, and be operated so that recirculation is minimized. Auxiliary fans...

  16. Research on Interval Forecast For Metal Futures Market′s VaR Based on Bootstrap%基于Bootstrap的金属期货市场风险VaR区间预测

    Institute of Scientific and Technical Information of China (English)

    沈盟; 王璐

    2016-01-01

    金属期货市场风险VaR的准确测度对防范期货交易风险及保持市场健康平稳运行有重要作用.传统的VaR测度方法主要以点预测为主,无法反映预测近似值的精确程度及范围. 因此,提出了一种基于Bootstrap的金属期货市场风险VaR区间预测方法,同时引入LR检验区间预测的有效性,最后利用我国铜和铝期货市场数据进行了VaR风险的区间预测. 结果表明,新的VaR区间预测方法能克服点预测的不足,准确有效地描述VaR的估计风险,同时置信区间上下限可用于风险的预警及控制.%The accurate measurement on metal futures market′s VaR is important to prevent the futures′transaction risk and maintain the market healthy and stable operation.The traditional methods measuring VaR focus on point forecast which can't re-flect the accuracy of the predictive value.A new method to measure the interval forecast for metal futures market's VaR based on bootstrap is put forward.LR test is used to test the effectiveness of interval forecast.Finally,we empirical study the interval fore-cast of copper and aluminum futures market's VaR in China.The results show that the new method can overcome the lack of point forecast,while the upper and lower confidence interval can be used for early warning and control financial risks.

  17. Influence of heavy metals on rhizosphere microbial communities of Siam weed (Chromolaena odorata (L. using a 16S rRNA gene amplicon sequencing approach

    Directory of Open Access Journals (Sweden)

    Thanyaporn Ruangdech

    2017-06-01

    Full Text Available A 16S rRNA amplicon sequencing approach was used to assess the impacts of cadmium (Cd and zinc (Zn contamination on populations of rhizobacteria on Siam weed (Chromolaena odorata (L.. Bacterial communities were characterized using the Illumina MiSeq platform and the V6 hypervariable region of the 16S rRNA gene. Among the 54,026 unique operational taxonomic units (OTUs identified, 99.7% were classified as bacteria and the rest were classified as archaea. Several dominant bacterial phyla were observed in all samples—Proteobacteria, Actinobacteria, Acidobacteria, Firmicutes and Bacteroidetes. These five phyla accounted for 89.2% of all OTUs identified among all sites, and only two OTUs could not be classified to a phylum. Comparison among samples containing low and high levels of Cd contamination using nonparametric Shannon and Shannon diversity indices showed that soils with low levels of diversity had a higher level of Cd (p < 0.05. These results indicated that levels of Cd may significantly alter bacterial species selection. The Cd- and Zn-resistant bacteria from each sample were subjected to heavy-metal minimum inhibitory concentration (MIC analyses. The MIC values obtained from 1152 isolates were used to individually analyze the pattern of gene function using the BioNumerics software. The results of this analysis showed that 26.7% of the bacteria were resistant to Cd concentrations up to 320 mg/L and only 2.3% of bacteria were resistant to Zn at concentrations up to 3200 mg/L. The MIC analyses indicated that the number of resistant bacteria decreased with increasing metal concentrations and those bacteria resistant to Cd and Zn may contain more than one group of metal-resistance genes.

  18. Lactococcus lactis Diversity in Undefined Mixed Dairy Starter Cultures as Revealed by Comparative Genome Analyses and Targeted Amplicon Sequencing of epsD.

    Science.gov (United States)

    Frantzen, Cyril A; Kleppen, Hans Petter; Holo, Helge

    2018-02-01

    Undefined mesophilic mixed (DL) starter cultures are used in the production of continental cheeses and contain unknown strain mixtures of Lactococcus lactis and leuconostocs. The choice of starter culture affects the taste, aroma, and quality of the final product. To gain insight into the diversity of Lactococcus lactis strains in starter cultures, we whole-genome sequenced 95 isolates from three different starter cultures. Pan-genomic analyses, which included 30 publically available complete genomes, grouped the strains into 21 L. lactis subsp . lactis and 28 L. lactis subsp. cremoris lineages. Only one of the 95 isolates grouped with previously sequenced strains, and the three starter cultures showed no overlap in lineage distributions. The culture diversity was assessed by targeted amplicon sequencing using purR , a core gene, and epsD , present in 93 of the 95 starter culture isolates but absent in most of the reference strains. This enabled an unprecedented discrimination of starter culture Lactococcus lactis and revealed substantial differences between the three starter cultures and compositional shifts during the cultivation of cultures in milk. IMPORTANCE In contemporary cheese production, standardized frozen seed stock starter cultures are used to ensure production stability, reproducibility, and quality control of the product. The dairy industry experiences significant disruptions of cheese production due to phage attacks, and one commonly used countermeasure to phage attack is to employ a starter rotation strategy, in which two or more starters with minimal overlap in phage sensitivity are used alternately. A culture-independent analysis of the lactococcal diversity in complex undefined starter cultures revealed large differences between the three starter cultures and temporal shifts in lactococcal composition during the production of bulk starters. A better understanding of the lactococcal diversity in starter cultures will enable the development of

  19. Derivative chameleons

    International Nuclear Information System (INIS)

    Noller, Johannes

    2012-01-01

    We consider generalized chameleon models where the conformal coupling between matter and gravitational geometries is not only a function of the chameleon field φ, but also of its derivatives via higher order co-ordinate invariants (such as ∂ μ φ∂ μ φ,□φ,...). Specifically we consider the first such non-trivial conformal factor A(φ,∂ μ φ∂ μ φ). The associated phenomenology is investigated and we show that such theories have a new generic mass-altering mechanism, potentially assisting the generation of a sufficiently large chameleon mass in dense environments. The most general effective potential is derived for such derivative chameleon setups and explicit examples are given. Interestingly this points us to the existence of a purely derivative chameleon protected by a shift symmetry for φ → φ+c. We also discuss potential ghost-like instabilities associated with mass-lifting mechanisms and find another, mass-lowering and instability-free, branch of solutions. This suggests that, barring fine-tuning, stable derivative models are in fact typically anti-chameleons that suppress the field's mass in dense environments. Furthermore we investigate modifications to the thin-shell regime and prove a no-go theorem for chameleon effects in non-conformal geometries of the disformal type

  20. Derivative chameleons

    Energy Technology Data Exchange (ETDEWEB)

    Noller, Johannes, E-mail: johannes.noller08@imperial.ac.uk [Theoretical Physics, Blackett Laboratory, Imperial College London, Prince Consort Road, London, SW7 2BZ (United Kingdom)

    2012-07-01

    We consider generalized chameleon models where the conformal coupling between matter and gravitational geometries is not only a function of the chameleon field φ, but also of its derivatives via higher order co-ordinate invariants (such as ∂{sub μ}φ∂{sup μ}φ,□φ,...). Specifically we consider the first such non-trivial conformal factor A(φ,∂{sub μ}φ∂{sup μ}φ). The associated phenomenology is investigated and we show that such theories have a new generic mass-altering mechanism, potentially assisting the generation of a sufficiently large chameleon mass in dense environments. The most general effective potential is derived for such derivative chameleon setups and explicit examples are given. Interestingly this points us to the existence of a purely derivative chameleon protected by a shift symmetry for φ → φ+c. We also discuss potential ghost-like instabilities associated with mass-lifting mechanisms and find another, mass-lowering and instability-free, branch of solutions. This suggests that, barring fine-tuning, stable derivative models are in fact typically anti-chameleons that suppress the field's mass in dense environments. Furthermore we investigate modifications to the thin-shell regime and prove a no-go theorem for chameleon effects in non-conformal geometries of the disformal type.

  1. (SELAX strain) B2 amplicon

    African Journals Online (AJOL)

    USER

    2010-07-12

    Jul 12, 2010 ... enzyme was inactivated by heating at 75°C for 10 min after the addition of 2 µl of ... material of the vector DNA and the partial genomic digests were packaged in ... tubes. The tubes were incubated for 15 min at 37°C. Molten LB ... Plaque transfer was carried out for 2 min with ink markings made on the agar ...

  2. 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.

  3. Brand-Name Prescription Drug Use Among Diabetes Patients in the VA and Medicare Part D: A National Comparison

    Science.gov (United States)

    Gellad, Walid F.; Donohue, Julie M.; Zhao, Xinhua; Mor, Maria K.; Thorpe, Carolyn T.; Smith, Jeremy; Good, Chester B.; Fine, Michael J.; Morden, Nancy E.

    2013-01-01

    Background Medicare Part D and the Department of Veterans Affairs (VA) use different approaches to manage prescription drug benefits, with implications for spending. Medicare relies on private plans with distinct formularies, whereas VA administers its own benefit using a national formulary. Objective To compare overall and regional rates of brand-name drug use among older adults with diabetes in Medicare and VA. Design Retrospective cohort Setting Medicare and VA Patients National sample in 2008 of 1,061,095 Part D beneficiaries and 510,485 Veterans age 65+ with diabetes. Measurements Percent of patients on oral hypoglycemics, statins, and angiotensin-converting-enzyme inhibitors/angiotensin-receptor-blockers who filled brand-name drugs and percent of patients on long-acting insulin who filled analogues. We compared sociodemographic and health-status adjusted hospital referral region (HRR) brand-name use to examine local practice patterns, and calculated changes in spending if each system’s brand-name use mirrored the other. Results Brand-name use in Medicare was 2–3 times that of VA: 35.3% vs. 12.7% for oral hypoglycemics, 50.7% vs. 18.2% for statins, 42.5% vs. 20.8% for angiotensin-converting-enzyme inhibitors/angiotensin-receptor-blockers, and 75.1% vs. 27.0% for insulin analogues. Adjusted HRR brand-name statin use ranged (5th to 95th percentile) from 41.0%–58.3% in Medicare and 6.2%–38.2% in VA. For each drug group, the HRR at the 95th percentile in VA had lower brand-name use than the 5th percentile HRR in Medicare. Medicare spending in this population would have been $1.4 billion less if brand-name use matched the VA for these medications. Limitation This analysis cannot fully describe the factors underlying differences in brand-name use. Conclusions Medicare beneficiaries with diabetes use 2–3 times more brand-name drugs than a comparable group within VA, at substantial excess cost. Primary Funding Sources VA; NIH; RWJF PMID:23752663

  4. HIGH PREVALENCE OF AGENT ORANGE EXPOSURE AMONG THYROID CANCER PATIENTS IN THE NATIONAL VA HEALTHCARE SYSTEM.

    Science.gov (United States)

    Le, Karen T; Sawicki, Mark P; Wang, Marilene B; Hershman, Jerome M; Leung, Angela M

    2016-06-01

    Thyroid cancer is the most common endocrine malignancy and the most rapidly increasing cancer in the U.S. Little is known regarding the epidemiology and characteristics of patients with thyroid cancer within the national Veterans Health Administration (VHA) integrated healthcare system. The aim of this study was to further understand the characteristics of thyroid cancer patients in the VHA population, particularly in relation to Agent Orange exposure. This is a descriptive analysis of the VA (Veterans Affairs) Corporate Data Warehouse database from all U.S. VHA healthcare sites from October1, 1999, to December 31, 2013. Information was extracted for all thyroid cancer patients based on International Classification of Diseases-ninth revision diagnosis codes; histologic subtypes of thyroid cancer were not available. There were 19,592 patients (86% men, 76% white, 58% married, 42% Vietnam-era Veteran) in the VHA system with a diagnosis of thyroid cancer within this 14-year study period. The gender-stratified prevalence rates of thyroid cancer among the Veteran population during the study period were 1:1,114 (women) and 1:1,023 (men), which were lower for women but similar for men, when compared to the U.S. general population in 2011 (1:350 for women and 1:1,219 for men). There was a significantly higher proportion of self-reported Agent Orange exposure among thyroid cancer patients (10.0%), compared to the general VHA population (6.2%) (PAgent Orange exposure compared to the overall national VA patient population. T4 = thyroxine TCDD = 2, 3, 7, 8-tetrachlorodibenzo-p-dioxin TSH = thyroid-stimulating hormone VA = Veterans Affairs VHA = Veterans Health Administration.

  5. Making housing first happen: organizational leadership in VA's expansion of permanent supportive housing.

    Science.gov (United States)

    Kertesz, Stefan G; Austin, Erika Laine; Holmes, Sally K; Pollio, David E; Schumacher, Joseph E; White, Bert; Lukas, Carol VanDeusen

    2014-12-01

    While most organizational literature has focused on initiatives that transpire inside the hospital walls, the redesign of American health care increasingly asks that health care institutions address matters outside their walls, targeting the health of populations. The US Department of Veterans Affairs (VA)'s national effort to end Veteran homelessness represents an externally focused organizational endeavor. Our aim was to evaluate the role of organizational practices in the implementation of Housing First (HF), an evidence-based homeless intervention for chronically homeless individuals. This was an interview-based comparative case study conducted across eight VA Medical Centers (VAMCs). Front line staff, mid-level managers, and senior leaders at VA Medical Centers were interviewed between February and December 2012. Using a structured narrative and numeric scoring, we assessed the correlation between successful HF implementation and organizational practices devised according to the organizational transformation model (OTM). Scoring results suggested a strong association between HF implementation and OTM practice. Strong impetus to house Veterans came from national leadership, reinforced by Medical Center directors closely tracking results. More effective Medical Center leaders differentiated themselves by joining front-line staff in the work (at public events and in process improvement exercises), by elevating homeless-knowledgeable persons into senior leadership, and by exerting themselves to resolve logistic challenges. Vertical alignment and horizontal integration advanced at sites that fostered work groups cutting across service lines and hierarchical levels. By contrast, weak alignment from top to bottom typically also hindered cooperation across departments. Staff commitment to ending homelessness was high, though sustainability planning was limited in this baseline year of observation. Key organizational practices correlated with more successful

  6. Fermion number non-conservation and cold neutral fermionic matter in (V-A) gauge theories

    International Nuclear Information System (INIS)

    Matveev, V.A.; Rubakov, V.A.; Tavkhelidze, A.N.; Tokarev, V.F.

    1987-01-01

    It is shown that in four-dimensional abelian (V-A) theories, the ground state of cold neutral fermionic matter is an anomalous state containing domains of abnormal phase surrounded by the normal vacuum. Inside these domains, there exists a gauge field condensate which makes real fermions disappear both inside and outside the domains. In non-abelian theories, the abnormal matter is unstable in its turn, and the system rolls back down into the normal state with a small number of fermions above the topologically non-trivial vacuum. Thus, in several non-abelian gauge theories, the fermion number density of cold neutral matter cannot exceed some critical value. (orig.)

  7. Radioiodination of the protein complex of the VA-MENGOC-BC vaccine

    International Nuclear Information System (INIS)

    Caso, R.; Lastre, M.; Alvarez, L.

    1996-01-01

    In this work was made the labelling of the protein complex of the vaccine VA-MEMGOC-BC with I-125 in order to study its immunological responses. These proteins were in both forms: dissolved and conjugated with polisacarids of the C-group. There were used three methods of iodination: chloramine-T iodogen and lactoperoxidase. Was found out that dissolved proteins can be iodinated using these methods with 0,1 mCi of I-125, and the obtained specific activities were similar

  8. 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.

  9. The electrical characteristics of copper slags in a 270 kVA DC arc furnace

    International Nuclear Information System (INIS)

    Derin, Bora; Sahin, Filiz Cinar; Yucel, Onuralp

    2003-01-01

    The electrical resistance of slags is the main criteria to determine the design and the operation conditions of slag resistance furnace (SRF) depending on temperature and composition. In this study, a 270 kVA DC electric arc furnace were used to determine the electrical characteristic of molten ancient copper slags. The specific conductivity of the slag was estimated by using furnace geometric factor given in the literature as an empirical formula and by using furnace resistance measured during smelting of the copper slag with or without different additives such as coke, CaO and Al 2 O 3 . (Original)

  10. SiO MASERS AROUND WX PSC MAPPED WITH THE KVN AND VERA ARRAY (KaVA)

    Energy Technology Data Exchange (ETDEWEB)

    Yun, Youngjoo; Cho, Se-Hyung; Kim, Jaeheon; Choi, Yoon Kyung; Kim, Dong-Jin; Yoon, Dong-Hwan; Byun, Do-Young; Chung, Hyunsoo; Chung, Moon-Hee; Han, Myoung-Hee [Korea Astronomy and Space Science Institute, 776 Daedeok-daero, Yuseong, Daejeon 305-348 (Korea, Republic of); Imai, Hiroshi; Oyadomari, Miyako [Graduate School of Science and Engineering, Kagoshima University, 1-21-35 Korimoto, Kagoshima 890-0065 (Japan); Asaki, Yoshiharu [National Astronomical Observatory of Japan (NAOJ) Chile Observatory/Joint ALMA Observatory (JAO), Alonso de Cordova 3107, Vitacura 763 0355, Santiago (Chile); Chibueze, James O. [Department of Physics and Astronomy, Faculty of Physical Sciences, University of Nigeria, Carver Building, 1 University Road, Nsukka (Nigeria); Dodson, Richard; Rioja, María J. [International Centre for Radio Astronomy Research, M468, The University of Western Australia, 35 Stirling Hwy, Crawley, Western Australia 6009 (Australia); Kusuno, Kozue [Department of Space and Astronautical Science, School of Physical Sciences, The Graduate University for Advanced Studies (SOKENDAI), 3-1-1 Yoshinodai, Chuou-Ku, Sagamihara, Kanagawa 252-5210 (Japan); Matsumoto, Naoko; Hagiwara, Yoshiaki [Mizusawa VLBI Observatory, National Astronomical Observatory of Japan, 2-21-1 Osawa, Mitaka, Tokyo 181-8588 (Japan); Min, Cheulhong, E-mail: yjyun@kasi.re.kr, E-mail: cho@kasi.re.kr [Department of Astronomical Sciences, The Graduate University for Advanced Studies (SOKENDAI), 2-21-1 Osawa, Mitaka, Tokyo 181-8588 (Japan); and others

    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.

  11. Comparison of rates of potentially inappropriate medication use according to the Zhan criteria for VA versus private sector medicare HMOs.

    Science.gov (United States)

    Barnett, Mitchell J; Perry, Paul J; Langstaff, Jodi D; Kaboli, Peter J

    2006-06-01

    Inappropriate prescribing in the elderly is common, but rates across different health care systems and the impact of formulary restrictions are not well described. To determine if rates of inappropriate medication use in the elderly differ between the Veterans Affairs (VA) health care system and the private sector Medicare health maintenance organization (HMO) patients. A cross-sectional study design compared administrative pharmacy claims from 10 distinct geographic regions in the United States in the VA health care system and 10 analogous regions for patients enrolled in Medicare HMOs. The cohorts included 123,633 VA and 157,517 Medicare HMO patients aged 65 years and older. Inappropriate medication use was identified using the Zhan modification of the Beers criteria, which categorizes 33 potentially inappropriate drugs into 3 major classifications: "always avoid," "rarely appropriate," and "some indications." Comparisons between the VA health care system and the private sector Medicare HMO were performed for overall differences and stratified by gender and age. The drug formulary status of the Zhan-criteria drugs was known for the VA health system but not for the Medicare HMO patients. Compared with private sector patients, VA patients were less likely to receive any inappropriate medication (21% vs. 29%, P private sector for males (21% vs. 24%, P private sector Medicare HMOs, elderly VA patients were less likely to receive medications defined by the Zhan criteria as potentially inappropriate. A restrictive formulary that excludes 12 of the 33 Zhan criteria drugs may be a factor in the reduction of undesired prescribing patterns in elderly populations.

  12. The Analysis of The Starting Pattern in Nezami’s Khosrow va Shirin, Leili va Majnoun and Haft Peykar

    Directory of Open Access Journals (Sweden)

    Tayebe Ja’fari

    2016-05-01

    Full Text Available AbstractAccording to what Nezami states in his versified story Khosro va Shirin, King Hormoz is a fair and peasant-supporter monarch and everything is alright in his time. The only matter which bothers the King’s mind and feelings is the sadness of having no child. But this piteous sadness is removed after vowing, sacrificing and being born a boy as a result. This boy is totally different from his age children because of his unique characteristics.    Leili va Majnoon’s starting pattern can be Khosro va Shirin’s starting pattern simply by having some changes in characters. In this poem, the memoir related to the chieftain of Amer, who was one of the Arab grandees and has a settled land, is expressed. He is an artist who has a significant reputation in hospitality and being mendicant-adherent, but the sadness of having no child makes him like King Hormoz, so he decides to vow and sacrifice and asks God to give him a child.   Based on an archetypal approach, the boy who has been requested by prayer in Khosrow va Shirin, Leili va Majnoon, and other myths is an archetypal item that these literary works’ starting patterns are the expression of common conditions before, during, and after his birth. He is the heavenly child who has been born to make a great upheaval.   Based on an archetypal approach, the heavenly child can be considered as the best form of emanation of the potential aspect of Ego in dreams and myths in which the king, as the actual aspect of this archetype, wishes this child’s birth; to reach his perfect ideal. With this paraphastic approach, Khosrow Parviz and King Hormoz are respectively the potential and the actual aspect of Ego. Hormoz is the actual part that is almost perfect. He is an ideal, fair and peasant-supporter king. But this perfect person is only some parts of his talent who has reached the actuality and can be manifest. This potential aspect is the child whom the king is

  13. Morphological alteration of the Dráva as the result of human impact

    Directory of Open Access Journals (Sweden)

    Tímea Kiss

    2011-10-01

    Full Text Available The Croatian-Hungarian border section of the Dráva River has been undisturbed for almost a century, and it is characterised by unique fluvial morphology (braided pattern and islands supporting rich habitats and wildlife. However, during the last decades human impact became more and moreintensive. Between 1975 and 1989 three water reservoirs were built on the Croatian section of the river, just 16 km from the beginning of the border-section, altering the hydrology and the sediment characteristics of the river. On a local scale cut-offs, revetments and groynes were built. The aim of the study was to evaluate the effect of these human interventions. As the result of the alteration of the hydrology the channel pattern of the Dráva has been changing from braided to meandering, though on the upstream meandering part the territory and number of islands increased due to the drop of water stages. A cut-off and a groyne influenced only the morphology of a short section. As the result of the cut-off braided pattern became more pronounced, and the groyne caused intensive channel aggradation and gave way to lateral island development.

  14. KENO3D visualization tool for KENO V.a geometry models

    International Nuclear Information System (INIS)

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

    1999-01-01

    The standardized computer analyses for licensing evaluations (SCALE) computer software system developed at Oak Ridge National Laboratory (ORNL) is widely used and accepted around the world for criticality safety analyses. SCALE includes the well-known KENO V.a three-dimensional Monte Carlo criticality computer code. Criticality safety analysis often require detailed modeling of complex geometries. Checking the accuracy of these models can be enhanced by effective visualization tools. To address this need, ORNL has recently developed a powerful state-of-the-art visualization tool called KENO3D that enables KENO V.a users to interactively display their three-dimensional geometry models. The interactive options include the following: (1) having shaded or wireframe images; (2) showing standard views, such as top view, side view, front view, and isometric three-dimensional view; (3) rotating the model; (4) zooming in on selected locations; (5) selecting parts of the model to display; (6) editing colors and displaying legends; (7) displaying properties of any unit in the model; (8) creating cutaway views; (9) removing units from the model; and (10) printing image or saving image to common graphics formats

  15. 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.

  16. Measuring the risk of an Iranian banking system using Value at Risk (VaR Model

    Directory of Open Access Journals (Sweden)

    Sudabeh Morshedian Rafiee

    2012-10-01

    Full Text Available Measuring risk of financial institutes and banks plays an important role on managing them. Recent financial turmoil in United States banking system has motivated banking industry to monitor risk factors more closely. In this paper, we present an empirical study to measure the risk of some private banks in Iran called Bank Mellat using Value at Risk (VaR method. The proposed study collects the necessary information for the fiscal year of 2010 and analyses them using regression analysis. The study divides the financial data into two groups where the financial data of the first half of year is considered in the first group and the remaining information for the second half of year 2010 is considered in the second group. The implementation of VaR method indicates that financial risks increase during the time horizon. The study also uses linear regression method where independent variable is time, dependent variable is the financial risk, and the results confirm what we have found in the previous part of the survey.

  17. Characteristics of MHC class I genes in house sparrows Passer domesticus as revealed by long cDNA transcripts and amplicon sequencing.

    Science.gov (United States)

    Karlsson, Maria; Westerdahl, Helena

    2013-08-01

    In birds the major histocompatibility complex (MHC) organization differs both among and within orders; chickens Gallus gallus of the order Galliformes have a simple arrangement, while many songbirds of the order Passeriformes have a more complex arrangement with larger numbers of MHC class I and II genes. Chicken MHC genes are found at two independent loci, classical MHC-B and non-classical MHC-Y, whereas non-classical MHC genes are yet to be verified in passerines. Here we characterize MHC class I transcripts (α1 to α3 domain) and perform amplicon sequencing using a next-generation sequencing technique on exon 3 from house sparrow Passer domesticus (a passerine) families. Then we use phylogenetic, selection, and segregation analyses to gain a better understanding of the MHC class I organization. Trees based on the α1 and α2 domain revealed a distinct cluster with short terminal branches for transcripts with a 6-bp deletion. Interestingly, this cluster was not seen in the tree based on the α3 domain. 21 exon 3 sequences were verified in a single individual and the average numbers within an individual were nine and five for sequences with and without a 6-bp deletion, respectively. All individuals had exon 3 sequences with and without a 6-bp deletion. The sequences with a 6-bp deletion have many characteristics in common with non-classical MHC, e.g., highly conserved amino acid positions were substituted compared with the other alleles, low nucleotide diversity and just a single site was subject to positive selection. However, these alleles also have characteristics that suggest they could be classical, e.g., complete linkage and absence of a distinct cluster in a tree based on the α3 domain. Thus, we cannot determine for certain whether or not the alleles with a 6-bp deletion are non-classical based on our present data. Further analyses on segregation patterns of these alleles in combination with dating the 6-bp deletion through MHC characterization across the

  18. 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.

  19. Validation of the Monte Carlo Criticality Program KENO V.a for highly-enriched uranium systems

    International Nuclear Information System (INIS)

    Knight, J.R.

    1984-11-01

    A series of calculations based on critical experiments have been performed using the KENO V.a Monte Carlo Criticality Program for the purpose of validating KENO V.a for use in evaluating Y-12 Plant criticality problems. The experiments were reflected and unreflected systems of single units and arrays containing highly enriched uranium metal or uranium compounds. Various geometrical shapes were used in the experiments. The SCALE control module CSAS25 with the 27-group ENDF/B-4 cross-section library was used to perform the calculations. Some of the experiments were also calculated using the 16-group Hansen-Roach Library. Results are presented in a series of tables and discussed. Results show that the criteria established for the safe application of the KENO IV program may also be used for KENO V.a results

  20. Waves from the Sun: to the 100th anniversary of V.A. Troitskaya’s birth

    Directory of Open Access Journals (Sweden)

    Guglielmi A.V.

    2017-09-01

    Full Text Available It has been one hundred years since the birth of the outstanding scientist Professor V.A. Troitskaya. Her remarkable achievements in solar-terrestrial physics are widely known. For many years, Valeria A. Troitskaya was the President of the International Association of Geomagnetism and Aeronomy. This article deals with only one aspect of the multifaceted creative activity of V.A. Troitskaya. It relates to the problem of sources of ultra-low frequency (ULF electromagnetic oscillations and waves outside Earth’s magnetosphere. We were fortunate to work under the leadership of V.A. Troitskaya on this problem. In this paper, we briefly describe the history from the emergence of the idea of the extramagnetospheric origin of dayside permanent ULF oscillations in the late 1960s to the modern quest made by ground and satellite means for ULF waves excited by solar surface oscillations propagating in the interplanetary medium and reaching Earth.

  1. Validation of KENO V.a for criticality safety calculations involving WR-1 fast-neutron fuel arrangements

    Energy Technology Data Exchange (ETDEWEB)

    Gauld, I. C.

    1991-07-15

    The KENO V.a criticality safety code, used with the SCALE 27-energy-group ENDF/B-IV-based cross-section library, has been validated for low-enriched uranium carbide (UC) WR-1 fast-neutron (FN) fuel arrangements. Because of a lack of relevant experimental data for UC fuel in the published literature, the validation is based primarily on calculational comparisons with critical experiments for fuel types with a range of enrichments and densities that cover those of the FN UC fuel. The ability of KENO V.a to handle the unique annular pin arrangement of the WR-1 FN fuel bundle was established using a comparison with the MCNP3B code used with a continuous-energy ENDF/B-V-based cross-section library. This report is part of the AECL--10146 report series documenting the validation of the KENO V.a criticality safety code.

  2. Comparison of topical fixed-combination fortified vancomycin-amikacin (VA solution) to conventional separate therapy in the treatment of bacterial corneal ulcer.

    Science.gov (United States)

    Chiang, C-C; Lin, J-M; Chen, W-L; Chiu, Y-T; Tsai, Y-Y

    2009-02-01

    In an in vitro study, fixed-combination fortified vancomycin and amikacin ophthalmic solutions (VA solution) had the same potency and stable physical properties as the separate components. In this retrospective clinical study, we evaluated the efficacy of the topical VA solution in the treatment of bacterial corneal ulcer and comparison with separate topical fortified vancomycin and amikacin. Separate topical fortified eye drops was used prior to January 2004 and switched to the VA solution afterwards in the treatment of bacterial corneal ulcer. The medical records of 223 patients diagnosed with bacterial corneal ulcers between January 2002 and December 2005 were reviewed retrospectively. There were 122 patients in the VA group and 101 in the separate group. Cure was defined as complete healing of the ulcer accompanied by a nonprogressive stromal infiltrate on two consecutive visits. No significant difference was found between the VA and separate therapy group. The mean treatment duration was 15.4 days in the VA group and 16.1 days in the separate therapy group. The average hospital stay was 5.4 days (VA) and 7.2 days (separate antibiotics). Stromal infiltration regressed significantly without further expansion in both groups. All corneal ulcers completely re-epithelialized without complications related to drugs. VA solution provided similar efficacy to the conventional separate therapy in the treatment of bacterial corneal ulcers; however, it is more convenient and tolerable, promotes patient's compliance, avoids the washout effect, and reduces nurse utilization. Hence, VA solution is a good alternative to separate therapy.

  3. The impact of the Department of Veterans Affairs Health Care Personnel Enhancement Act of 2004 on VA physicians' salaries and retention.

    Science.gov (United States)

    Weeks, William B; Wallace, Tanner A; Wallace, Amy E

    2009-01-01

    To determine whether the Department of Veterans Affairs Health Care Personnel Enhancement Act (the Act), which was designed to achieve VA physician salary parity with American Academy of Medical Colleges (AAMC) Associate Professors and enacted in 2006, had achieved its goal. Using VA human resources datasets and data from the AAMC, we calculated mean VA physician salaries, with 95 percent confidence intervals, for 15 different medical specialties. For each specialty, we compared VA salaries to the median, 25th, and 75th percentile of AAMC Associate Professors' incomes. The Act's passage resulted in a $20,000 annual increase in VA physicians' salaries. VA primary care physicians, medical subspecialists, and psychiatrists had salaries that were comparable to their AAMC counterparts prior to and after enactment of the Act. However, VA surgical specialists', anesthesiologists', and radiologists' salaries lagged their AAMC counterparts both before and after the Act's enactment. Income increases were negatively correlated with full-time workforce changes. VA does not appear to provide comparable salaries for physicians necessary for surgical care. In certain cases, VA should consider outsourcing surgical services.

  4. Myosin Va Plays a Role in Nitrergic Smooth Muscle Relaxation in Gastric Fundus and Corpora Cavernosa of Penis

    Science.gov (United States)

    Carew, Josephine A.; Goyal, Raj K.; Sullivan, Maryrose P.

    2014-01-01

    The intracellular motor protein myosin Va is involved in nitrergic neurotransmission possibly by trafficking of neuronal nitric oxide synthase (nNOS) within the nerve terminals. In this study, we examined the role of myosin Va in the stomach and penis, proto-typical smooth muscle organs in which nitric oxide (NO) mediated relaxation is critical for function. We used confocal microscopy and co-immunoprecipitation of tissue from the gastric fundus (GF) and penile corpus cavernosum (CCP) to localize myosin Va with nNOS and demonstrate their molecular interaction. We utilized in vitro mechanical studies to test whether smooth muscle relaxations during nitrergic neuromuscular neurotransmission is altered in DBA (dilute, brown, non-agouti) mice which lack functional myosin Va. Myosin Va was localized in nNOS-positive nerve terminals and was co-immunoprecipitated with nNOS in both GF and CCP. In comparison to C57BL/6J wild type (WT) mice, electrical field stimulation (EFS) of precontracted smooth muscles of GF and CCP from DBA animals showed significant impairment of nitrergic relaxation. An NO donor, Sodium nitroprusside (SNP), caused comparable levels of relaxation in smooth muscles of WT and DBA mice. These normal postjunctional responses to SNP in DBA tissues suggest that impairment of smooth muscle relaxation resulted from inhibition of NO synthesis in prejunctional nerve terminals. Our results suggest that normal physiological processes of relaxation of gastric and cavernosal smooth muscles that facilitate food accommodation and penile erection, respectively, may be disrupted under conditions of myosin Va deficiency, resulting in complications like gastroparesis and erectile dysfunction. PMID:24516539

  5. KiVa Anti-Bullying Program in Italy: Evidence of Effectiveness in a Randomized Control Trial.

    Science.gov (United States)

    Nocentini, Annalaura; Menesini, Ersilia

    2016-11-01

    The present study aims to evaluate the effectiveness of the KiVa anti-bullying program in Italy through a randomized control trial of students in grades 4 and 6. The sample involved 2042 students (51 % female; grade 4, mean age = 8.85; ds = 0.43; grade 6, mean age = 10.93; ds = 0.50); 13 comprehensive schools were randomly assigned into intervention (KiVa) or control (usual school provision) conditions. Different outcomes (bullying, victimization, pro-bullying attitudes, pro-victim attitudes, empathy toward victims), analyses (longitudinal mixed model with multiple-item scales; longitudinal prevalence of bullies and victims using Olweus' single question), and estimates of effectiveness (Cohen's d; odds ratios) were considered in order to compare the Italian results with those from other countries. Multilevel models showed that KiVa reduced bullying and victimization and increased pro-victim attitudes and empathy toward the victim in grade 4, with effect sizes from 0.24 to 0.40. In grade 6, KiVa reduced bullying, victimization, and pro-bullying attitudes; the effects were smaller as compared to grade 4, yet significant (d ≥ 0.20). Finally, using Olweus dichotomous definition of bullies and victims, results showed that the odds of being a victim were 1.93 times higher for a control student than for a KiVa student in grade 4. Overall, the findings provide evidence of the effectiveness of the program in Italy; the discussion will focus on factors that influenced successfully the transportability of the KiVa program in Italy.

  6. Physicochemical properties of direct compression tablets with spray dried and ball milled solid dispersions of tadalafil in PVP-VA.

    Science.gov (United States)

    Wlodarski, K; Tajber, L; Sawicki, W

    2016-12-01

    The aim of this research was to develop immediate release tablets comprising solid dispersion (IRSDTs) of tadalafil (Td) in a vinylpyrrolidone and vinyl acetate block copolymer (PVP-VA), characterized by improved dissolution profiles. The solid dispersion of Td in PVP-VA (Td/PVP-VA) in a weight ratio of 1:1 (w/w) was prepared using two different processes i.e. spray drying and ball milling. While the former process has been well established in the formulation of IRSDTs the latter has not been exploited in these systems yet. Regardless of the preparation method, both Td/PVP-VA solid dispersions were amorphous as confirmed by PXRD, DSC and FTIR. However, different morphology of particles (SEM) resulted in differences in water apparent solubility and disk intrinsic dissolution rate (DIDR). Both solid dispersions and crystalline Td were successfully made into directly compressible tablets at three doses of Td, i.e. 2.5mg, 10mgand20mg, yielding nine different formulations (D 1 -D 9 ). Each of the lots met the requirements set by Ph.Eur. and was evaluated with respect to appearance, diameter, thickness, mass, hardness, friability, disintegration time and content of Td. IRSDTs performed as supersaturable formulations and had significantly improved water dissolution profiles in comparison with equivalent tablets containing crystalline Td and the marketed formulations. Tablets with both spray dried and ball milled Td/PVP-VA revealed the greatest improvement in dissolution depending on the investigated doses, i.e. 2.5mgand20mg, respectively. Also, dissolution of Td from Td/PVP-VA delivered in different forms occurred in the following order: powders>tablets>capsules. Copyright © 2016 Elsevier B.V. All rights reserved.

  7. High users of VA emergency room facilities: are outpatients abusing the system or is the system abusing them?

    Science.gov (United States)

    Schneider, K C; Dove, H G

    1983-01-01

    A phenomenon well known to emergency room personnel is the high use of ER facilities by a small number of patients. In this study of 335 patients followed in outpatient specialty clinics at a university-affiliated VA medical center, 23% of the patients accounted for 73% of the ER visits. Although some patients may be abusing the system, the problem is difficult to correct because of congressional legislation that deters the VA from providing primary care. Thus, a small subset of patients with chronic medical problems who live close to the hospital are likely to continue to consume a disproportionate amount of ER resources.

  8. 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.

  9. Tail dependence between oil and stocks of major oil-exporting countries using the CoVaR approach

    Directory of Open Access Journals (Sweden)

    Nader Trabelsi

    2017-12-01

    Full Text Available This paper investigates the negative tail risk dependence between oil shocks and stock indices (at aggregated and desegregated levels for Saudi Arabia (KSA, United Arab Emirates (UAE and Russia, over the period between 2007 and 2016. DCC-MGARCH approach and CoVaR measure are employed to assess the oil shock exposure. The results show that the tail dependence is significant and depends on the origin of the oil shocks, with intensity that varies across countries and sectors. Keywords: Oil price shocks, Oil-exporting countries, Conditional VaR, JEL Classification: C58, G11, Q4

  10. ¿Hacia dónde va la integración?

    Directory of Open Access Journals (Sweden)

    Alberto Acosta

    2015-01-01

    Full Text Available La ola integracionista se filtra por todas partes, en especial, en la formación de bloques económicos. Los periodistas juegan un papel importante como agentes dinamizadores. Aborda el Plan Bush vs. Integración, la crisis de la hegemonía a la integración, limitaciones del desarrollo dependiente. Responde a la pregunta de ¿Hacia donde va la integración en América latina? Advierte que la integración deberá construirse sobre una movilización ideológica en tormo a la definición de objetivos y metas que hagan posible las transformaciones en todas las sociedades involucradas.

  11. Myosin-Va-dependent cell-to-cell transfer of RNA from Schwann cells to axons.

    Directory of Open Access Journals (Sweden)

    José R Sotelo

    Full Text Available To better understand the role of protein synthesis in axons, we have identified the source of a portion of axonal RNA. We show that proximal segments of transected sciatic nerves accumulate newly-synthesized RNA in axons. This RNA is synthesized in Schwann cells because the RNA was labeled in the complete absence of neuronal cell bodies both in vitro and in vivo. We also demonstrate that the transfer is prevented by disruption of actin and that it fails to occur in the absence of myosin-Va. Our results demonstrate cell-to-cell transfer of RNA and identify part of the mechanism required for transfer. The induction of cell-to-cell RNA transfer by injury suggests that interventions following injury or degeneration, particularly gene therapy, may be accomplished by applying them to nearby glial cells (or implanted stem cells at the site of injury to promote regeneration.

  12. Myosin-Va-dependent cell-to-cell transfer of RNA from Schwann cells to axons.

    Science.gov (United States)

    Sotelo, José R; Canclini, Lucía; Kun, Alejandra; Sotelo-Silveira, José R; Xu, Lei; Wallrabe, Horst; Calliari, Aldo; Rosso, Gonzalo; Cal, Karina; Mercer, John A

    2013-01-01

    To better understand the role of protein synthesis in axons, we have identified the source of a portion of axonal RNA. We show that proximal segments of transected sciatic nerves accumulate newly-synthesized RNA in axons. This RNA is synthesized in Schwann cells because the RNA was labeled in the complete absence of neuronal cell bodies both in vitro and in vivo. We also demonstrate that the transfer is prevented by disruption of actin and that it fails to occur in the absence of myosin-Va. Our results demonstrate cell-to-cell transfer of RNA and identify part of the mechanism required for transfer. The induction of cell-to-cell RNA transfer by injury suggests that interventions following injury or degeneration, particularly gene therapy, may be accomplished by applying them to nearby glial cells (or implanted stem cells) at the site of injury to promote regeneration.

  13. Benchmark calculations by KENO-Va using the JEF 2.2 library

    Energy Technology Data Exchange (ETDEWEB)

    Markova, L.

    1994-12-01

    This work has to be a contribution to the validation of the JEF2.2 neutron cross-section libarary, following the earlier published benchmark calculations having been performed to validate the previous version JEF1.1 of the libarary. Several simple calculational problems and one experimental problem were chosen for a criticality calculations. In addition also a realistic hexagonal arrangement of the VVER-440 fuel assemblies in a spent fuel cask were analyzed in a partly cylindrized model. All criticality calculations, carried out by the KENO-Va code using the JEF2.2 neutron cross-section library in 172 energy groups, resulted in multiplication factors (k{sub eff}) which were tabulated and compared with the results of other available calculations of the same problems. (orig.).

  14. 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

  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. Long-term monitoring of Sgr A* at 7 mm with VERA and KaVA

    Science.gov (United States)

    Akiyama, K.; Kino, M.; Sohn, B.; Lee, S.; Trippe, S.; Honma, M.

    2014-05-01

    We present the results of radio monitoring observations of Sgr A* at 7 mm (i.e. 43 GHz) with the VLBI Exploration of Radio Astrometry (VERA), which is a VLBI array in Japan. VERA provides angular resolution on millisecond scales, resolving structures within 100 Schwarzschild radii of Sgr A* , similar to the Very Large Baseline Array (VLBA). We performed multi-epoch observations of Sgr A* in 2005 - 2008, and started monitoring it again with VERA from 2013 January to trace the current G2 encounter event. Our preliminary results in 2013 show that Sgr A* on mas scales has been in an ordinary state as of August 2013, although some fraction of the G2 cloud already passed the pericenter of Sgr A* in April 2013. We will continue monitoring Sgr A* with VERA and the newly developed KaVA (KVN and VERA Array).

  17. The results of studies on clinical dosemeters type VA-J-18. Pt.1

    International Nuclear Information System (INIS)

    Penchev, V.; Buchakliev, Z.; Popits, R.; Konstantinov, B.

    1982-01-01

    A description is submitted of standard instruments used to detect and measure exposure to low and medium energy X-ray and gamma rays ( 137 Cs and 60 Co), designed for the control and calibration of dosimeters. The studies performed on clinical dosimeters, type VA-J-18, are reported. To secure exact exposure measurement, correction coefficients for non-linearity of the readings and for inaccuracy of the range factors are introduced. Non-linearity does not exceed 5 per cent of the begining of the scale, and in the range 30 to 100 scale divisions, it is within the +- 1 per cent limits. Usually, the inaccuracy of the range factors amounts to +- 3 per cent, but in isolated cases it may reach up to 10 per cent, and for that reason the second correction coefficient should be introduced as a routine in all measurements. (author)

  18. Drug use and HIV risks among migrant workers on the DelMarVa Peninsula.

    Science.gov (United States)

    Inciardi, J A; Surratt, H L; Colón, H M; Chitwood, D D; Rivers, J E

    1999-01-01

    Because high rates of drug use have been documented in the migrant farm worker population, the National Institute on Drug Abuse funded the Migrant Health Study to examine HIV risk behaviors among drug-using farm workers and their sexual partners. Many of these individuals were home-based in South Florida and migrated during the work season to various points along the Eastern Migratory Stream. The focus of this paper is a description of the characteristics and behaviors of the 151 respondents contacted on the DelMarVa Peninsula during 1994 and 1995. The data indicate that drug use was widespread in this population, a significant proportion were at risk for HIV infection, and 6% were HIV positive. As a result of these findings, public health agencies on the peninsula have instituted HIV education programs in those clinics utilized by both local and transient agricultural workers.

  19. 77 FR 75628 - STS Hydropower, Ltd., Dan River, Inc., and City of Danville, VA; Notice of Application for...

    Science.gov (United States)

    2012-12-21

    ..., Ltd., Dan River, Inc., and City of Danville, VA; Notice of Application for Partial Transfer of License... Bankruptcy Trustee for Dan River, Inc. and STS Hydropower, Ltd (co-licensees) transferors and the City of... Project from Dan River, Inc. and STS Hydropower, Ltd. to STS Hydropower, Ltd. and the City of Danville...

  20. 76 FR 54770 - Public Meeting: Notification by Capital One Financial Corporation, McLean, VA, To Acquire ING...

    Science.gov (United States)

    2011-09-02

    ... FEDERAL RESERVE SYSTEM Public Meeting: Notification by Capital One Financial Corporation, McLean, VA, To Acquire ING Bank, FSB, Wilmington, DE, and Indirectly To Acquire Shares of Sharebuilder... Reserve System. ACTION: Notice of public meeting. SUMMARY: Three public meetings will be held regarding...

  1. 76 FR 72046 - Enhanced-Use Lease (EUL) of Department of Veterans Affairs (VA) Real Property for the Development...

    Science.gov (United States)

    2011-11-21

    ... DEPARTMENT OF VETERANS AFFAIRS Enhanced-Use Lease (EUL) of Department of Veterans Affairs (VA) Real Property for the Development of Space for Community Services and Parking in Memphis, TN AGENCY... property is located. This project meets this requirement. Approved: November 14, 2011. Eric K. Shinseki...

  2. 76 FR 72048 - Enhanced-Use Lease (EUL) of Department of Veterans Affairs (VA) Real Property for the Development...

    Science.gov (United States)

    2011-11-21

    ... DEPARTMENT OF VETERANS AFFAIRS Enhanced-Use Lease (EUL) of Department of Veterans Affairs (VA) Real Property for the Development of Permanent Housing in Grand Island, NE AGENCY: Department of... property is located. This project meets this requirement. Approved: November 14, 2011. Eric K. Shinseki...

  3. Modeling of Mean-VaR portfolio optimization by risk tolerance when the utility function is quadratic

    Science.gov (United States)

    Sukono, Sidi, Pramono; Bon, Abdul Talib bin; Supian, Sudradjat

    2017-03-01

    The problems of investing in financial assets are to choose a combination of weighting a portfolio can be maximized return expectations and minimizing the risk. This paper discusses the modeling of Mean-VaR portfolio optimization by risk tolerance, when square-shaped utility functions. It is assumed that the asset return has a certain distribution, and the risk of the portfolio is measured using the Value-at-Risk (VaR). So, the process of optimization of the portfolio is done based on the model of Mean-VaR portfolio optimization model for the Mean-VaR done using matrix algebra approach, and the Lagrange multiplier method, as well as Khun-Tucker. The results of the modeling portfolio optimization is in the form of a weighting vector equations depends on the vector mean return vector assets, identities, and matrix covariance between return of assets, as well as a factor in risk tolerance. As an illustration of numeric, analyzed five shares traded on the stock market in Indonesia. Based on analysis of five stocks return data gained the vector of weight composition and graphics of efficient surface of portfolio. Vector composition weighting weights and efficient surface charts can be used as a guide for investors in decisions to invest.

  4. 78 FR 54571 - Special Local Regulation for Marine Event Hampton Bay Days Festival, Hampton River; Hampton, VA

    Science.gov (United States)

    2013-09-05

    ...-AA08 Special Local Regulation for Marine Event Hampton Bay Days Festival, Hampton River; Hampton, VA... Fifth Coast Guard District. This regulation applies only to the Hampton Bay Days Festival, which... Purpose Hampton Bay Days is sponsoring the three days Hampton Bay Days Festival, which includes a...

  5. 77 FR 17086 - Section 8 Housing Choice Vouchers: Revised Implementation of the HUD-VA Supportive Housing Program

    Science.gov (United States)

    2012-03-23

    ... Housing g. Mobility and Portability of HUD-VASH Vouchers h. Case Management Requirements i. Turnover of... veterans with case management and clinical services provided by the VA through its community medical... services sites and Community-Based Outpatient Clinics (CBOCs) across the nation. The HUD- VASH program is a...

  6. Federal Health Care Center: VA and DOD Need to Develop Better Information to Monitor Operations and Improve Efficiency

    Science.gov (United States)

    2017-01-01

    Defense (DOD) responsibility for contracting support Quality assurance Accreditation and oversight from external entities and credentialing and...MTF designation would introduce additional operational requirements and challenges to the FHCC, including financial management and quality assurance...departments—including DOD’s operational readiness mission—by integrating services previously provided by the former North Chicago VA Medical Center

  7. 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

  8. 78 FR 68364 - Payment for Home Health Services and Hospice Care to Non-VA Providers; Delay of Effective Date

    Science.gov (United States)

    2013-11-14

    ... providers of home health services and hospice care. The preamble of that final rule stated the effective... 17.56, applicable to non-VA home health services and hospice care. Section 17.56 provides, among... DEPARTMENT OF VETERANS AFFAIRS 38 CFR Part 17 RIN 2900-AN98 Payment for Home Health Services and...

  9. VA and DOD Health Care: Department-Level Actions Needed to Assess Collaboration Performance, Address Barriers, and Identify Opportunities

    Science.gov (United States)

    2012-09-01

    approximately 150 hospitals, 130 nursing homes, 800 community-based outpatient clinics, as well as other facilities to provide care to veterans. VA also...receive care and have to return for rescheduled appointments. Such missed appointments can lead to lost revenue for the military treatment facility

  10. 76 FR 59166 - Parkdale America, LLC, a Division of Parkdale Mills, Inc., Plant #22, Galax, VA; Notice of...

    Science.gov (United States)

    2011-09-23

    ... DEPARTMENT OF LABOR Employment and Training Administration [TA-W-80,089] Parkdale America, LLC, a Division of Parkdale Mills, Inc., Plant 22, Galax, VA; Notice of Affirmative Determination Regarding... of Parkdale Mills, Inc., Plant 22, Galax, Virginia (subject firm). The determination was issued on...

  11. 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…

  12. Federal Health Care Center: VA and DOD Need to Address Ongoing Difficulties and Better Prepare for Future Integrations

    Science.gov (United States)

    2016-02-01

    related documentation, performing data reliability checks (such as examining the data for missing values), and interviewing FHCC officials. After taking...and personnel Staffing, training, and the transfer of DOD civilian personnel to VA Xa Property Construction, transfer of property, and physical ...29For example, geriatric and mental health clinical areas were initially grouped with other

  13. 77 FR 18984 - Special Local Regulation for Marine Events; Yorktown Parade of Sail, York River; Yorktown, VA

    Science.gov (United States)

    2012-03-29

    ...-AA08 Special Local Regulation for Marine Events; Yorktown Parade of Sail, York River; Yorktown, VA... proposes to establish special local regulation during the Yorktown Parade of Sail, a parade of five tall... sponsor the ``Yorktown Parade of Sail'' on the waters of York River. The event will consist of...

  14. 76 FR 30598 - Payment or Reimbursement for Emergency Services for Nonservice-Connected Conditions in Non-VA...

    Science.gov (United States)

    2011-05-26

    ... DEPARTMENT OF VETERANS AFFAIRS 38 CFR Part 17 RIN 2900-AN86 Payment or Reimbursement for Emergency...) ``Payment or Reimbursement for Emergency Services for Nonservice-Connected Conditions in Non-VA Facilities... Reimbursement Act. Some of the revisions in this proposed rule are purely technical, matching the language of...

  15. Contribution of soil-32P, fertilizer-32P and VA mycorrhizal fungi to phosphorus nutrition of corn plant

    International Nuclear Information System (INIS)

    Feng Gu; Yang Maoqiu; Bai Dengsha; Huang Quansheng

    1997-01-01

    32 P labelled fertilizer and five synthetic phosphates (dicalcium phosphate, octocalcium phosphate, iron phosphate, aluminium phosphate and apatite), which were used to simulate inorganic phosphates such as Ca 2 -P, Ca 8 -P, Fe P , Al-P and Ca 10 -P in calcareous soil, were applied to corn plants inoculating with and without vesicular-arbuscular (VA) mycorrhizal fungi in a calcareous soil. The results showed that VA mycorrhizal fungi and dicalcium phosphate, octocalcium phosphate, iron phosphate, aluminium phosphate promoted growth and increased phosphorus content of corn plant. The four synthetic phosphates except apatite had higher contributions to corn plant growth than VA mycorrhizal fungi. Contributions of fertilizer-P, soil-P and synthetic phosphates to phosphorus nutrition of corn plant were in order of synthetic phosphates (except apatite) > soil- P > fertilizer-P. Inoculating with VA mycorrhizal fungi increased the contribution of soil-P and decreased the contribution of synthetic phosphates, but did not affect the contribution of fertilizer-P

  16. Changing Patterns of Glucose-Lowering Medication Use in VA Nursing Home Residents With Diabetes, 2005 to 2011.

    Science.gov (United States)

    Lee, Sei J; Stijacic-Cenzer, Irena; Barnhart, Caroline; McClymont, Keelan; Steinman, Michael A

    2015-10-01

    Although nursing home (NH) residents make up a large and growing proportion of Americans with diabetes mellitus, little is known about how glucose-lowering medications are used in this population. We sought to examine glucose-lowering medication use in Veterans Affairs (VA) NH residents with diabetes between 2005 and 2011. Retrospective cohort study, using linked laboratory, pharmacy, administrative, and NH Minimum Dataset (MDS) 2.0 databases in 123 VA NHs. A total of 9431 long-stay (>90 days) VA NH residents older than 65 followed for 52,313 person-quarters. We identified receipt of glucose-lowering medications, including insulin, metformin, sulfonylureas, thiazolidinediones, and others (alpha-glucosidase inhibitors, meglitinides, glucagonlike peptide-1 analogs, dipeptidyl peptidase-4 inhibitors and amylin analogs) per quarter. The rates of sulfonylurea use in long-stay NH residents dropped dramatically from 24% in 2005 to 12% in 2011 (P use (10% to 2%, P use in 2007 (4% to Metformin use was stable, ranging between 7% and 9% (P = .24). Insulin use increased slightly from 30% to 32% (P Use of other classes of glucose-lowering medications was stable (P = .22) and low, remaining below 1.3%. Between 2005 and 2011, there were dramatic declines in use of sulfonylureas and thiazolidinediones in VA NH residents, suggesting that prescribing practices can be quickly changed in this setting. Published by Elsevier Inc.

  17. 75 FR 26160 - Drug and Drug-Related Supply Promotion by Pharmaceutical Company Sales Representatives at VA...

    Science.gov (United States)

    2010-05-11

    ... ward areas where patients may be encountered; (ii) Clinic examination rooms; (iii) Nurses stations; (iv... access to VA medical facilities by sales representatives (including account managers and clinical... would require the Chief of Pharmacy or other official responsible for such decisions to approve...

  18. Kollidon VA64, a membrane-resealing agent, reduces histopathology and improves functional outcome after controlled cortical impact in mice.

    Science.gov (United States)

    Mbye, Lamin H; Keles, Eyup; Tao, Luyang; Zhang, Jimmy; Chung, Joonyong; Larvie, Mykol; Koppula, Rajani; Lo, Eng H; Whalen, Michael J

    2012-03-01

    Loss of plasma membrane integrity is a feature of acute cellular injury/death in vitro and in vivo. Plasmalemma-resealing agents are protective in acute central nervous system injury models, but their ability to reseal cell membranes in vivo has not been reported. Using a mouse controlled cortical impact (CCI) model, we found that propidium iodide-positive (PI+) cells pulse labeled at 6, 24, or 48 hours maintained a degenerative phenotype and disappeared from the injured brain by 7 days, suggesting that plasmalemma permeability is a biomarker of fatal cellular injury after CCI. Intravenous or intracerebroventricular administration of Kollidon VA64, poloxamer P188, or polyethylene glycol 8000 resealed injured cell membranes in vivo (P<0.05 versus vehicle or poloxamer P407). Kollidon VA64 (1 mmol/L, 500 μL) administered intravenously to mice 1  hour after CCI significantly reduced acute cellular degeneration, chronic brain tissue damage, brain edema, blood-brain barrier damage, and postinjury motor deficits (all P<0.05 versus vehicle). However, VA64 did not rescue pulse-labeled PI+ cells from eventual demise. We conclude that PI permeability within 48 hours of CCI is a biomarker of eventual cell death/loss. Kollidon VA64 reduces secondary damage after CCI by mechanisms other than or in addition to resealing permeable cells.

  19. Two Cases of Type Va Extrahepatic Bile Duct Duplication With Distal Klatskin Tumor Surgically Treated with Whipple Procedure and Hepaticojejunostomy.

    Science.gov (United States)

    Hammad, Tariq A; Alastal, Yaseen; Khan, Muhammad Ali; Hammad, Mohammad; Alaradi, Osama; Nigam, Ankesh; Sodeman, Thomas C; Nawras, Ali

    2015-10-01

    We describe the diagnostic and therapeutic challenges of a type Va extrahepatic bile duct duplication coexistent with distally located hilar cholangiocarcinoma (Klatskin tumor). We present 2 cases that were diagnosed preoperatively and treated with a modified surgical technique of a combined pylorus-preserving Whipple procedure and hepaticojejunostomy.

  20. VA and DOD Health Care: First Federal Health Care Center Established, but Implementation Concerns Need to Be Addressed

    Science.gov (United States)

    2011-07-01

    procedures for the reporting of information security incidents. However, VA and DOD did not meet designated deadlines for the three capabilities that were...addition to the contact named above, Marcia A. Mann, Assistant Director; Jill K. Center; Kaycee M. Glavich; E. Jane Whipple ; and Malissa G. Winograd

  1. Comparisons and Characterizations of the Mean-Variance, Mean-VaR, Mean-CVaR Models for Portfolio Selection With Background Risk

    OpenAIRE

    Xu, Guo; Wing-Keung, Wong; Lixing, Zhu

    2013-01-01

    This paper investigates the impact of background risk on an investor’s portfolio choice in a mean-VaR, mean-CVaR and mean-variance framework, and analyzes the characterizations of the mean-variance boundary and mean-VaR efficient frontier in the presence of background risk. We also consider the case with a risk-free security.

  2. High-Level Heat Resistance of Spores of Bacillus amyloliquefaciens and Bacillus licheniformis Results from the Presence of a spoVA Operon in a Tn1546 Transposon

    NARCIS (Netherlands)

    Berendsen, Erwin M; Koning, Rosella A; Boekhorst, Jos; de Jong, Anne; Kuipers, Oscar P; Wells-Bennik, Marjon H J

    2016-01-01

    Bacterial endospore formers can produce spores that are resistant to many food processing conditions, including heat. Some spores may survive heating processes aimed at production of commercially sterile foods. Recently, it was shown that a spoVA operon, designated spoVA(2mob), present on a Tn1546

  3. Two populations of double minute chromosomes harbor distinct amplicons, the MYC locus at 8q24.2 and a 0.43-Mb region at 14q24.1, in the SW613-S human carcinoma cell line.

    Science.gov (United States)

    Guillaud-Bataille, M; Brison, O; Danglot, G; Lavialle, C; Raynal, B; Lazar, V; Dessen, P; Bernheim, A

    2009-01-01

    High-level amplifications observed in tumor cells are usually indicative of genes involved in oncogenesis. We report here a high resolution characterization of a new amplified region in the SW613-S carcinoma cell line. This cell line contains tumorigenic cells displaying high-level MYC amplification in the form of double minutes (DM(+) cells) and non tumorigenic cells exhibiting low-level MYC amplification in the form of homogeneously staining regions (DM(-) cells). Both cell types were studied at genomic and functional levels. The DM(+) cells display a second amplification, corresponding to the 14q24.1 region, in a distinct population of DMs. The 0.43-Mb amplified and overexpressed region contains the PLEK2, PIGH, ARG2, VTI1B, RDH11, and ZFYVE26 genes. Both amplicons were stably maintained upon in vitro and in vivo propagation. However, the 14q24.1 amplicon was not found in cells with high-level MYC amplification in the form of HSRs, either obtained after spontaneous integration of endogenous DM MYC copies or after transfection of DM(-) cells with a MYC gene expression vector. These HSR-bearing cells are highly tumorigenic. The 14q24.1 amplification may not play a role in malignancy per se but might contribute to maintaining the amplification in the form of DMs. Copyright 2009 S. Karger AG, Basel.

  4. Multimethod evaluation of the VA's peer-to-peer Toolkit for patient-centered medical home implementation.

    Science.gov (United States)

    Luck, Jeff; Bowman, Candice; York, Laura; Midboe, Amanda; Taylor, Thomas; Gale, Randall; Asch, Steven

    2014-07-01

    Effective implementation of the patient-centered medical home (PCMH) in primary care practices requires training and other resources, such as online toolkits, to share strategies and materials. The Veterans Health Administration (VA) developed an online Toolkit of user-sourced tools to support teams implementing its Patient Aligned Care Team (PACT) medical home model. To present findings from an evaluation of the PACT Toolkit, including use, variation across facilities, effect of social marketing, and factors influencing use. The Toolkit is an online repository of ready-to-use tools created by VA clinic staff that physicians, nurses, and other team members may share, download, and adopt in order to more effectively implement PCMH principles and improve local performance on VA metrics. Multimethod evaluation using: (1) website usage analytics, (2) an online survey of the PACT community of practice's use of the Toolkit, and (3) key informant interviews. Survey respondents were PACT team members and coaches (n = 544) at 136 VA facilities. Interview respondents were Toolkit users and non-users (n = 32). For survey data, multivariable logistic models were used to predict Toolkit awareness and use. Interviews and open-text survey comments were coded using a "common themes" framework. The Consolidated Framework for Implementation Research (CFIR) guided data collection and analyses. The Toolkit was used by 6,745 staff in the first 19 months of availability. Among members of the target audience, 80 % had heard of the Toolkit, and of those, 70 % had visited the website. Tools had been implemented at 65 % of facilities. Qualitative findings revealed a range of user perspectives from enthusiastic support to lack of sufficient time to browse the Toolkit. An online Toolkit to support PCMH implementation was used at VA facilities nationwide. Other complex health care organizations may benefit from adopting similar online peer-to-peer resource libraries.

  5. Geochemical and Petrologic Constraints on the Source of Eocene Volcanism at Mole Hill, Rockingham County, VA

    Science.gov (United States)

    Johnson, E. A.; Beard, J. S.

    2010-12-01

    Mole Hill is an Eocene (48 Ma) basaltic volcanic neck located west of Harrisonburg, VA, and provides a unique opportunity to probe the mantle beneath the Shenandoah Valley. It lies on the northeastern edge of a swarm of alkaline-series volcanic plugs, dikes, and diatremes extending through Rockingham and Highland Counties, VA, and Pendleton County, WV. The Eocene volcanics are thought to have exploited extensive basement fracture systems originally formed during the Alleghenian Orogeny and subsequent rifting. The Eocene volcanism may have been triggered by reactivation of faults due to global shifts in relative plate motions (Southworth 1993, USGS Bull, B1839-I) but the source material and magmatic processes for the Eocene volcanism are largely unknown. Compositional and texture analyses of xenocrystic and groundmass clinopyroxene, olivine, and spinel were completed either at Virginia Tech on the Cameca SX-50 electron microprobe in the Dept of Geological Sciences, or in the Dept of Mineral Sciences, Smithsonian Institution, Washington, D.C using the JEOL JXA-8900R WD/EDS microanalyzer or the FEI NOVA nanoSEM600 FEG Variable Pressure Scanning Electron Microscope. Xenocrysts up to 2cm in diameter are distributed throughout the volcanic neck, with clinopyroxene >>spinel>olivine. The clinopyroxene and olivine xenocrysts show undulatory extinction in cross-polarized light and are found as individual crystals or as aggregates. Clinopyroxene xenocryst cores are high-Al, low-Cr augite ( ˜Wo44En46Fs10) with Mg# 78.5-85.9. The clinopyroxene xenocrysts have compositionally zoned rims 100-250 μm-wide containing abundant plagioclase inclusions and sparse melt inclusions in a sieve texture. The outer edges of xenocrysts approach the compositions of groundmass and microphenocryst clinopyroxenes ( ˜Wo47En38Fs15; Mg# 67.9-74.5). Olivine xenocrysts contain sulfide inclusions and Cr-rich spinel and have Mg-rich ( ˜Fo86-90) cores with more Fe- and Ca-rich rims (Fo70

  6. One in vitro model for visceral adipose-derived fibroblasts in chronic inflammation

    International Nuclear Information System (INIS)

    Yue Guiping; Du Lirui; Xia Tao; He Xianhui; Qiu Huan; Xu Lihui; Chen Xiaodong; Feng Shengqiu; Yang Zaiqing

    2005-01-01

    One pathogenesis of the obesity-associated complications is that consistent with increased body fat mass, the elevation of adipose tissue-derived cytokines inflicts a low-grade chronic inflammation, which ultimately leads to metabolic disorders. Adipocytes and macrophages in visceral adipose (VA) have been confirmed to contribute to the chronic inflammation; however, the role of the resident fibroblasts is still unknown. We established one VA fibroblast cell line, termed VAFC. Morphological analysis indicated that there were large numbers of pits at the cell plasma membrane. In vitro VAFC cells promoted bone marrow cells to differentiate into macrophages and protected them from apoptosis in the serum-free conditions. Additionally, they also interfered in lymphocytes proliferation. On the basis of these results, this cell line might be an in vitro model for understanding the role of adipose-derived fibroblasts in obesity-associated chronic inflammation

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

    International Nuclear Information System (INIS)

    Bowen, O.N.; Lawson, J.Q.

    1977-01-01

    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

  8. 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. (c) 2014 APA, all rights reserved.

  9. 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.

  10. Facility management - efektivní správa stavebních objektů

    OpenAIRE

    Helekalová, Denisa

    2013-01-01

    Diplomová práce „ Facility management – efektivní správa stavebních objektů“ je zaměřena na stavební objekty a přínos pro ně při využívání služeb facility managementu. Práce se snaží přiblížit, co je facility management kdo ho poskytuje v České republice a jak přispívá k úsporám. Zmíněny jsou také informační technologie využívané ve facility managementu, protože bez těch se v dnešní době téměř žádný obor neobejde. První část je též zaměřena na stavbu, její životní cyklus a náklady s ním spoje...

  11. Improving Patient Safety: Avoiding Unread Imaging Exams in the National VA Enterprise Electronic Health Record.

    Science.gov (United States)

    Bastawrous, Sarah; Carney, Benjamin

    2017-06-01

    In the current digital and filmless age of radiology, rates of unread radiology exams remain low, however, may still exist in unique environments. Veterans Affairs (VA) health care systems may experience higher rates of unread exams due to coexistence of Veterans Health Information Systems and Technology Architecture (VistA) imaging and commercial picture archiving and communication systems (PACS). The purpose of this patient safety initiative was to identify any unread exams and causes leading to unread exams. Following approval by departmental quality assurance committee, a comprehensive review was performed of all radiology exams within VistA imaging from July 1, 2009 to June 30, 2014 to identify unread radiology exams. Over the 5-year period, the total unread exam rate was calculated to be 0.17%, with the highest yearly unread exam rate of 0.25%. The leading majority of unread exam type was plain radiographs. Analysis revealed unfinished dictations, unassociated accession numbers, technologist errors, and inefficient radiologist work lists as top contributors to unread exams. Once unread radiology exams were discovered and the causes identified, valuable process changes were implemented within our department to ensure simultaneous tracking of all unread exams in VistA imaging as well as the commercial PACS.

  12. A PC [personal computer]-based version of KENO V.a

    International Nuclear Information System (INIS)

    Nigg, D.A.; Atkinson, C.A.; Briggs, J.B.; Taylor, J.T.

    1990-01-01

    The use of personal computers (PCs) and engineering workstations for complex scientific computations has expanded rapidly in the last few years. This trend is expected to continue in the future with the introduction of increasingly sophisticated microprocessors and microcomputer systems. For a number of reasons, including security, economy, user convenience, and productivity, an integrated system of neutronics and radiation transport software suitable for operation in an IBM PC-class environment has been under development at the Idaho National Engineering Laboratory (INEL) for the past 3 yr. Nuclear cross-section data and resonance parameters are preprocessed from the Evaluated Nuclear Data Files Version 5 (ENDF/B-V) and supplied in a form suitable for use in a PC-based spectrum calculation and multigroup cross-section generation module. This module produces application-specific data libraries that can then be used in various neutron transport and diffusion theory code modules. This paper discusses several details of the Monte Carlo criticality module, which is based on the well-known highly-sophisticated KENO V.a package developed at Oak Ridge National Laboratory and previously released in mainframe form by the Radiation Shielding Information Center (RSIC). The conversion process and a variety of benchmarking results are described

  13. The VA Ostomy Health-Related Quality of Life Study: objectives, methods, and patient sample.

    Science.gov (United States)

    Krouse, Robert S; Mohler, M Jane; Wendel, Christopher S; Grant, Marcia; Baldwin, Carol M; Rawl, Susan M; McCorkle, Ruth; Rosenfeld, Kenneth E; Ko, Clifford Y; Schmidt, C Max; Coons, Stephen Joel

    2006-04-01

    To present the design and methods of a multisite study of health-related quality of life (HR-QOL) in veterans living with ostomies. Veterans from Tucson, Indianapolis, and Los Angeles VA Medical Centers were surveyed using the validated City of Hope ostomy-specific tool (mCOH-QOL-Ostomy) and the SF-36V. Cases (ostomates) had a major gastrointestinal procedure that required an intestinal stoma, while controls had similar procedures for which an ostomy was not required. Ostomy subjects were recruited for four focus groups in each of two sites divided by ostomy type (colostomy versus ileostomy) and overall mCOH-QOL-Ostomy HR-QOL score (highest versus lowest quartile). The focus groups further evaluated barriers, concerns, and adaptation methods and skills. This report presents recruitment results, reliability of survey instruments, and demographic characteristics of the sample. The overall response (i.e., recruitment) rate across all sites was 48% and by site was 53%, 57%, and 37%, respectively (p ostomies had significantly longer time since surgery than controls (p ostomies is an illustration of a successful mixed methods approach to HR-QOL research. We collected meaningful quantitative and qualitative data that will be used in the development of new approaches to care that will lead to improved functioning and well-being in persons living with ostomies. Subsequent reports will provide the results of this research project.

  14. Katalonijas autonomijas prasības pamatojums normatīva perspektīvā

    OpenAIRE

    Beluza, Veronika

    2014-01-01

    Darba nosaukums ir- „Katalonijas autonomijas prasības pamatojums normatīva perspektīvā” un šī darba uzdevums ir noskaidrot, vai katalāņu vēlme gūt neatkarību ir pamatota, balstoties uz pašnoteikšanās tiesībām. Katalonijas valdību neapmierina Spānijas centrālas varas politika, tāpēc tā vairākus gadus cenšas pieradīt, ka Katalonija ir tiesīga uz secesiju. Darba mērķi ir: noteikt katalāņu nacionālo identitāti, secesijas pieprasījuma vērtīgumu un pašnoteikšanās tiesību izmantošanas ierobežojumu i...

  15. The Effect of Mantram Repetition on Burnout and Stress Among VA Staff.

    Science.gov (United States)

    Leary, Sheryl; Weingart, Kimberly; Topp, Robert; Bormann, Jill

    2018-03-01

    In this study, the authors determined the effect of a structured Internet-delivered Mantram Repetition Program (MRP) on burnout and stress of conscience (SOC), stress related to ambiguity from ethical or moral conflicts among health care workers (HCWs) within the Veteran Affairs (VA) Healthcare System. A secondary purpose was to determine whether practicing meditation prior to the study combined with MRP affected burnout or SOC. The MRP teaches the mindful practices of repeating a mantram, slowing down, and one-pointed attention for managing stress. Thirty-nine HCW volunteers who provided direct patient care completed the Internet-delivered MRP. The outcomes of burnout (i.e., exhaustion, cynicism, and professional efficacy) and SOC (i.e., frequency of stressful events and troubled conscience about those events) were measured at baseline (T1), postintervention (T2), and 3-months postintervention (T3). Repeated measures ANOVA indicated that exhaustion significantly ( p stressful events significantly declined between T1 and T2 and troubled conscience declined between T1 and T3. Secondary analysis demonstrated that individuals who did not practice meditation at baseline ( n = 16, 41%) significantly decreased exhaustion, frequency of stressful events, and troubled conscience between T1 and T3, and improved professional efficacy between T1 and T2. Individuals who practiced meditation at baseline ( n = 23, 59%) did not demonstrate significant change on any study outcomes. An MRP intervention may reduce burnout and SOC in those individuals who are naïve to practicing meditation.

  16. GdnHCl-induced unfolding intermediate in the mitochondrial carbonic anhydrase VA.

    Science.gov (United States)

    Idrees, Danish; Prakash, Amresh; Haque, Md Anzarul; Islam, Asimul; Hassan, Md Imtaiyaz; Ahmad, Faizan

    2016-10-01

    Carbonic anhydrase VA (CAVA) is a mitochondrial enzyme belonging to the α-family of CAs, which is involved in several physiological processes including ureagenesis, lipogenesis, gluconeogenesis and neuronal transmission. Here, we have tried to understand the folding mechanism of CAVA using guanidine hydrochloride (GdnHCl)-induced denaturation at pH 8.0 and 25°C. The conformational stability was measured from the GdnHCl-induced denaturation study of CAVA monitored by circular dichroism (CD) and fluorescence measurements. On increasing the concentration of GdnHCl up to 5.0, a stable intermediate was observed between the concentrations 3.25M to 3.40M of the denaturant. However, CAVA gets completely denatured at 4.0M GdnHCl. The existence of a stable intermediate state was validated by 1-anilinonaphthalene-8-sulfonic acid (ANS binding) fluorescence and near-UV CD measurements. In silico studies were also performed to analyse the effect of GdnHCl on the structure and stability of CAVA under explicit conditions. Molecular dynamics simulations for 40ns were carried out and a well-defined correlation was established for both in vitro and in silico studies. Copyright © 2016 Elsevier B.V. All rights reserved.

  17. Correspondence of the Boston Assessment of Traumatic Brain Injury-Lifetime (BAT-L) clinical interview and the VA TBI screen.

    Science.gov (United States)

    Fortier, Catherine Brawn; Amick, Melissa M; Kenna, Alexandra; Milberg, William P; McGlinchey, Regina E

    2015-01-01

    Mild traumatic brain injury is the signature injury of Operation Enduring Freedom (OEF), Operation Iraqi Freedom (OIF), and Operation New Dawn (OND), yet its identification and diagnosis is controversial and fraught with challenges. In 2007, the Department of Veterans Affairs (VA) implemented a policy requiring traumatic brain injury (TBI) screening on all individuals returning from deployment in the OEF/OIF/OND theaters of operation that lead to the rapid and widespread use of the VA TBI screen. The Boston Assessment of TBI-Lifetime (BAT-L) is the first validated, postcombat semistructured clinical interview to characterize head injuries and diagnose TBIs throughout the life span, including prior to, during, and post-military service. Community-dwelling convenience sample of 179 OEF/OIF/OND veterans. BAT-L, VA TBI screen. Based on BAT-L diagnosis of military TBI, the VA TBI screen demonstrated similar sensitivity (0.85) and specificity (0.82) when administered by research staff. When BAT-L diagnosis was compared with historical clinician-administered VA TBI screen in a subset of participants, sensitivity was reduced. The specificity of the research-administered VA TBI screen was more than adequate. The sensitivity of the VA TBI screen, although relatively high, suggests that it does not oversample or "catch all" possible military TBIs. Traumatic brain injuries identified by the BAT-L, but not identified by the VA TBI screen, were predominantly noncombat military injuries. There is potential concern regarding the validity and reliability of the clinician administered VA TBI screen, as we found poor correspondence between it and the BAT-L, as well as low interrater reliability between the clinician-administered and research-administered screen.

  18. Night and day in the VA: associations between night shift staffing, nurse workforce characteristics, and length of stay.

    Science.gov (United States)

    de Cordova, Pamela B; Phibbs, Ciaran S; Schmitt, Susan K; Stone, Patricia W

    2014-04-01

    In hospitals, nurses provide patient care around the clock, but the impact of night staff characteristics on patient outcomes is not well understood. The aim of this study was to examine the association between night nurse staffing and workforce characteristics and the length of stay (LOS) in 138 veterans affairs (VA) hospitals using panel data from 2002 through 2006. Staffing in hours per patient day was higher during the day than at night. The day nurse workforce had more educational preparation than the night workforce. Nurses' years of experience at the unit, facility, and VA level were greater at night. In multivariable analyses controlling for confounding variables, higher night staffing and a higher skill mix were associated with reduced LOS. © 2014 Wiley Periodicals, Inc.

  19. Analisis Risiko Investasi Saham Syariah Dengan Model Value AT Risk-Asymmetric Power Autoregressive Conditional Heterocedasticity (VaR-APARCH

    Directory of Open Access Journals (Sweden)

    Syarif Hidayatullah

    2017-04-01

    Full Text Available Penelitian ini membahas analisis risiko data runtun waktu dengan model Value at Risk- Asymmetric Power Autoregressive Conditional Heteroscedasticity (VaR-APARCHdalam pasar modal syariah. Metode yang digunakan dalam penelitian ini adalah penerapan kasus.Data yang digunakan adalah harga penutupan harian saham dalam Jakarta Islamic Index (JIIperiode 4 Maret 2013 sampai 8 April 2015.Model APARCH yang dipilih berdasarkan nilai Schwarz Criterion (SC.Langkah-langkah dalam penelitian ini adalah menguji kestasioneran data, mengidentifikasi model ARIMA,mengestimasi parameter model ARIMA, menguji diagnostik model ARIMA, mendeteksi ada tidaknya unsur ARCH atau unsur heteroskedastisitas, uji asimetris data saham, mengestimasi model APARCH, menguji diagnostik model APARCH, dan menghitung risiko dengan VaR-APARCH.Model terbaik yang dipilih adalah ARIMA ((3,0,0 dan APARCH (1,1. Model ini valid untuk menganalisis besar risiko investasi dalam jangka waktu 10 hari ke depan.

  20. VA-LCP anterior clavicle plate: the anatomically precontoured fixation system with angular stability for clavicle shaft.

    Science.gov (United States)

    van Olden, G D J

    2014-12-01

    The aim of this investigation was to evaluate the introduction of the VA-LCP anterior clavicle plate in the treatment of clavicle fractures. From March 2011 to March 2013, 42 clavicle fractures were treated; 40 were middle-third and 2 lateral-third, and 13/42 (31 %) patients were treated due to painful nonunion. Patient age ranged from 16 to 81 years. Complications were screw placement through the AC-joint, one superficial wound infection and one neuropraxia of the nervus radialis with dropping hand. We had some difficulties prebending both lateral to low and lateral to high but without clinical consequences. In all cases, the fracture healed with full functionality. After 1 year, 4 patients underwent a removal of the hardware. The VA-LCP anterior plate showed good reliability and sufficient stability with both middle-third, lateral and nonunion fractures of the clavicle.

  1. VA Health Care: Improvements Needed in Monitoring Antidepressant Use for Major Depressive Disorder and in Increasing Accuracy of Suicide Data

    Science.gov (United States)

    2014-11-01

    2009-2013 13 Contents Page ii GAO-15-55 VA Psychiatric Medications and Suicide Data Table 2: Number of Veterans in GAO’s Sample...anxiety, depressed mood, ruminations , suicidal ideation, sleep problems, intrusive memories, drug seeking behaviors, flashbacks, guilt/remorse...recommendation, with estimated completion dates in calendar year 2015. As agreed with your office, unless you publicly announce the contents of this

  2. Annotated bibliography for liquid metal surface tensions of groups III-A, IV-A, and V-A metals

    International Nuclear Information System (INIS)

    Murtha, M.J.; Burnet, G.

    1976-04-01

    An annotated bibliography has been prepared which includes summaries of 82 publications dating from 1920 and dealing with the measurement of the surface tensions of Groups III-A, IV-A, and V-A metals in the liquid state. The bibliography is organized by key element investigated, and contains a tabulation of correlations for surface tension as a function of temperature. A brief discussion dealing with variables and methods has been included

  3. Effects of a pain education program in Complementary and Alternative Medicine treatment utilization at a VA medical center.

    Science.gov (United States)

    Cosio, David; Lin, Erica H

    2015-06-01

    Past studies have shown that U.S. Veterans are consumers of CAM. However, more than 75% of Veteran non-users report they would utilize these treatment options if made available. Thus, Veterans may not be fully aware of the CAM options currently available to them in the current U.S. VA health care system. The current study tested the hypothesis that Veterans would report an increase in CAM utilization after completing a formal pain education program in a VA medical center. The study used a quasi-experimental, one-group, pre/post-test design. Midwestern, U.S. VA Medical Center. The responses from 103 Veterans who elected to participate in the program and the assessment measures were included in the outcome analyses. "Pain Education School" is a 12-week, educational program that is open to all Veterans and their families. It is a comprehensive program that introduces patients to 23 different disciplines at the VA Medical Center that deal with chronic, non-cancer pain. An adaptation of the Complementary and Alternative Medicine Questionnaire(©), SECTION A: Use of Alternative Health Care Providers. There was a significant difference found in overall utilization of CAM after completing the pain education program. The most utilized CAM modality was the chiropractor; the least utilized were hypnosis and aromatherapy. Not all health care systems or providers may have access to an education-focused, professionally driven program as an amenity. However, lessons can be learned from this study in terms of what pain providers may be able to accomplish in their practice. Published by Elsevier Ltd.

  4. Creating a sampling frame for population-based veteran research: representativeness and overlap of VA and Department of Defense databases.

    Science.gov (United States)

    Washington, Donna L; Sun, Su; Canning, Mark

    2010-01-01

    Most veteran research is conducted in Department of Veterans Affairs (VA) healthcare settings, although most veterans obtain healthcare outside the VA. Our objective was to determine the adequacy and relative contributions of Veterans Health Administration (VHA), Veterans Benefits Administration (VBA), and Department of Defense (DOD) administrative databases for representing the U.S. veteran population, using as an example the creation of a sampling frame for the National Survey of Women Veterans. In 2008, we merged the VHA, VBA, and DOD databases. We identified the number of unique records both overall and from each database. The combined databases yielded 925,946 unique records, representing 51% of the 1,802,000 U.S. women veteran population. The DOD database included 30% of the population (with 8% overlap with other databases). The VHA enrollment database contributed an additional 20% unique women veterans (with 6% overlap with VBA databases). VBA databases contributed an additional 2% unique women veterans (beyond 10% overlap with other databases). Use of VBA and DOD databases substantially expands access to the population of veterans beyond those in VHA databases, regardless of VA use. Adoption of these additional databases would enhance the value and generalizability of a wide range of studies of both male and female veterans.

  5. Risk Measures and Contagion Matrix: an Application of CoVaR for the Brazilian Financial Market

    Directory of Open Access Journals (Sweden)

    Aléssio Tony Cavalcanti de Almeida

    2012-12-01

    Full Text Available The main point of this work is to assess how a financial distress in return series of the major Brazilian companies assets and relevant domestic market (Ibovespa and main international index (Dow Jones interact with each other, in an attempt to capture spillover effects. We try to capture the systemic risk, the contagion effect and the stress test. This paper uses the methodology CoVaR, described in the Adrian and Brunnermeier (2011 which use quantile regression. The main innovation of this work is the construction and estimation of the contagion matrix to domestic capital market. The results show that there is no relationship between risk measurements given by Value at Risk (VaR and CoVaR, moreover the systemic risk shows those assets that generate more negative externalities for the domestic financial market. The stress test indicates that a distress in domestic market indicator returns have more spillover effects on domestic papers than a distress in the international market returns. Finally, the contagion matrix reveals that the interrelationships of contagion between the firms’ returns are relevant sectorial evidence for assessment and management of risks.

  6. Aerosol Vacuum-Assisted Plasma Ionization (Aero-VaPI) Coupled to Ion Mobility-Mass Spectrometry

    Science.gov (United States)

    Blair, Sandra L.; Ng, Nga L.; Zambrzycki, Stephen C.; Li, Anyin; Fernández, Facundo M.

    2018-02-01

    In this communication, we report on the real-time analysis of organic aerosol particles by Vacuum-assisted Plasma Ionization-Mass Spectrometry (Aero-VaPI-MS) using a home-built VaPI ion source coupled to a Synapt G2-S HDMS ion mobility-mass spectrometry (IM-MS) system. Standards of organic molecules of interest in prebiotic chemistry were used to generate aerosols. Monocaprin and decanoic acid aerosol particles were successfully detected in both the positive and negative ion modes, respectively. A complex aerosol mixture of different sizes of polymers of L-malic acid was also examined through ion mobility (IM) separations, resulting in the detection of polymers of up to eight monomeric units. This noncommercial plasma ion source is proposed as a low cost alternative to other plasma ionization platforms used for aerosol analysis, and a higher-performance alternative to more traditional aerosol mass spectrometers. VaPI provides robust online ionization of organics in aerosols without extensive ion activation, with the coupling to IM-MS providing higher peak capacity and excellent mass accuracy. [Figure not available: see fulltext.

  7. Implementation outcomes of evidence-based quality improvement for depression in VA community based outpatient clinics

    Directory of Open Access Journals (Sweden)

    Fortney John

    2012-04-01

    Full Text Available Abstract Background Collaborative-care management is an evidence-based practice for improving depression outcomes in primary care. The Department of Veterans Affairs (VA has mandated the implementation of collaborative-care management in its satellite clinics, known as Community Based Outpatient Clinics (CBOCs. However, the organizational characteristics of CBOCs present added challenges to implementation. The objective of this study was to evaluate the effectiveness of evidence-based quality improvement (EBQI as a strategy to facilitate the adoption of collaborative-care management in CBOCs. Methods This nonrandomized, small-scale, multisite evaluation of EBQI was conducted at three VA Medical Centers and 11 of their affiliated CBOCs. The Plan phase of the EBQI process involved the localized tailoring of the collaborative-care management program to each CBOC. Researchers ensured that the adaptations were evidence based. Clinical and administrative staff were responsible for adapting the collaborative-care management program for local needs, priorities, preferences and resources. Plan-Do-Study-Act cycles were used to refine the program over time. The evaluation was based on the RE-AIM (Reach, Effectiveness, Adoption, Implementation, Maintenance Framework and used data from multiple sources: administrative records, web-based decision-support systems, surveys, and key-informant interviews. Results Adoption: 69.0% (58/84 of primary care providers referred patients to the program. Reach: 9.0% (298/3,296 of primary care patients diagnosed with depression who were not already receiving specialty care were enrolled in the program. Fidelity: During baseline care manager encounters, education/activation was provided to 100% (298/298 of patients, barriers were assessed and addressed for 100% (298/298 of patients, and depression severity was monitored for 100% (298/298 of patients. Less than half (42.5%, 681/1603 of follow-up encounters during the acute

  8. Applying the High Reliability Health Care Maturity Model to Assess Hospital Performance: A VA Case Study.

    Science.gov (United States)

    Sullivan, Jennifer L; Rivard, Peter E; Shin, Marlena H; Rosen, Amy K

    2016-09-01

    The lack of a tool for categorizing and differentiating hospitals according to their high reliability organization (HRO)-related characteristics has hindered progress toward implementing and sustaining evidence-based HRO practices. Hospitals would benefit both from an understanding of the organizational characteristics that support HRO practices and from knowledge about the steps necessary to achieve HRO status to reduce the risk of harm and improve outcomes. The High Reliability Health Care Maturity (HRHCM) model, a model for health care organizations' achievement of high reliability with zero patient harm, incorporates three major domains critical for promoting HROs-Leadership, Safety Culture, and Robust Process Improvement ®. A study was conducted to examine the content validity of the HRHCM model and evaluate whether it can differentiate hospitals' maturity levels for each of the model's components. Staff perceptions of patient safety at six US Department of Veterans Affairs (VA) hospitals were examined to determine whether all 14 HRHCM components were present and to characterize each hospital's level of organizational maturity. Twelve of the 14 components from the HRHCM model were detected; two additional characteristics emerged that are present in the HRO literature but not represented in the model-teamwork culture and system-focused tools for learning and improvement. Each hospital's level of organizational maturity could be characterized for 9 of the 14 components. The findings suggest the HRHCM model has good content validity and that there is differentiation between hospitals on model components. Additional research is needed to understand how these components can be used to build the infrastructure necessary for reaching high reliability.

  9. The Multiple-component Binary Hyad, vA 351 - a Progress Report

    Science.gov (United States)

    Benedict, George Fritz; Franz, Otto G.; Wasserman, Lawrence H.

    2017-06-01

    We extend results first announced by Franz et al. (1998) in the abstract, http://adsabs.harvard.edu/abs/1998AAS...19310207F ,that identified vA 351 = H346 in the Hyades as a multiple star system containing a white dwarf. With HST/FGS fringe tracking and scanning, spanning four years, we establish a parallax, relative orbit, and mass fraction for the A-B components, with a period, P~5.47y. With ground-based radial velocities from the McDonald Observatory Struve 2.1m telescope and Sandiford Spectrograph, spanning 14 years, we find that component B consists of BC, two M dwarf stars orbiting with a very short period (P(BC)~0.75 days), having a mass ratio C/B~0.94. We confirm that the total mass of the system can only be reconciled with the distance and component photometry by including a fainter, higher mass component, proposed to be a ~0.8Msun white dwarf. Thus, the quadruple system consists of three M dwarfs (A,B,C) and one white dwarf (D). The M dwarf masses and absolute magnitudes are consistent with the Benedict et al. (2016, http://adsabs.harvard.edu/abs/2016AJ....152..141B) lower Main Sequence Mass-Luminosity Relation. The radial velocity signal has so far yielded a signature only for the short-period BC orbital motion. Velocities from H-α and He I emission lines confirm the BC period from absorption lines, with similar (He I) and higher (H-α) velocity amplitudes.

  10. Toxicidad de VA-DIFTET® por administración a dosis repetida en ratones

    Directory of Open Access Journals (Sweden)

    Pablo González

    2000-06-01

    Full Text Available Una vez estudiada la toxicidad de la vacuna VA-DIFTET® (vacuna antidiftérica antitetánica por administración a dosis única en dos especies de animales, se impone la evaluación a dosis repetida, teniendo en cuenta que el esquema de inmunización en humanos prevé la aplicación de tres dosis cuando el componente pertusis de la DPT está contraindicado. Se emplearon 210 ratones OF-1 de ambos sexos. Los grupos experimentales fueron similares a los de la prueba a dosis única con la vacuna dúplex, anatoxina diftérica, anatoxina tetánica, adyuvante, tiomersal, solución salina fisiológica y un grupo control no tratado. Un grupo de hembras y otro de machos fue asignado aleatoriamente a cada tratamiento y para recibir 1, 2 ó 3 dosis por vía intramuscular. Tras cada aplicación se evaluó la aparición de síntomas clínicos, el incremento de peso, el consumo de agua y alimento y la dinámica de la respuesta inmune contra las anatoxinas tetánica y diftérica, específicamente de tipo IgG, mediante ELISA indirecto. Al término de las observaciones los animales fueron sacrificados y se realizaron estudios anatomopatológicos. Además, durante el sacrificio se evaluó el índice relativo de bazo y timo, así como la relación bazo/timo. No se comprobaron alteraciones que evidenciaran toxicidad por parte de la vacuna y sus componentes. Asimismo, se demostró una marcada respuesta inmune en los grupos vacunales e inoculados con las anatoxinas. Se considera que los resultados de la prueba fueron satisfactorios.

  11. The work of V.A. Snegirev: an historical and psychological study

    Directory of Open Access Journals (Sweden)

    Mazilov V.A.

    2017-03-01

    Full Text Available In the history of psychology there are many scientists whose names and contributions have been forgotten. One poorly studied area in the history of psychology is the psychological views of theologians. Among these is Veniamin Alekseevich Snegirev, a psychologist and theologian at Kazan Theological Academy, whose contributions are not fully appreciated today. The authors identify V.A. Snegirev’s contribution to several fields of psychological science at the end of the 19th century: methodology, theory, general psychology, and the psychology of dreams. The research is based on archival materials, encyclopedia articles, reviews of the activity of Kazan Theological Academy in the 19th century, works of Snegirev and other researchers who have studied his contributions. The authors describe the scientist’s childhood, his student period, and work as a professor. his work at the Kazan Theological Academy and the University of Kazan is discussed in detail: he taught courses on psychology, logic, and metaphysics, was a member of the Academy Council, took part in the functioning of the library, was recognized with several awards and honors. Snegirev’s teaching activity is described by the recollections of his student, the famous philosopher Viktor I. Nesmelov. Snegirev considered psychology to be based in philosophy, because philosophical problems represent the content of human consciousness. A bibliography of Snegirev’s scientific works is provided. The psychological and philosophical views of the Russian scientist are signifi- cant: his main points are to recognize the object of science – the human being – as a “living person”, thinking, feeling, and exercising his will; and the rejection of the idea that a person can be reduced to a sum of mental phenomena. There are several common concepts in the works of Snegirev and European and American philosophers, such as Wilhelm Dilthey and William James. Snegirev participated in the

  12. Effect of pH on structure, function, and stability of mitochondrial carbonic anhydrase VA.

    Science.gov (United States)

    Idrees, Danish; Shahbaaz, Mohd; Bisetty, Krishna; Islam, Asimul; Ahmad, Faizan; Hassan, Md Imtaiyaz

    2017-02-01

    Mitochondrial carbonic anhydrase VA (CAVA) catalyzes the hydration of carbon dioxide to produce proton and bicarbonate which is primarily expressed in the mitochondrial matrix of liver, and involved in numerous physiological processes including lipogenesis, insulin secretion from pancreatic cells, ureagenesis, gluconeogenesis, and neuronal transmission. To understand the effect of pH on the structure, function, and stability of CAVA, we employed spectroscopic techniques such as circular dichroism, fluorescence, and absorbance measurements in wide range of pH (from pH 2.0 to pH 11.5). CAVA showed an aggregation at acidic pH range from pH 2.0 to pH 5.0. However, it remains stable and maintains its secondary structure in the pH range, pH 7.0-pH 11.5. Furthermore, this enzyme has an appreciable activity at more than pH 7.0 (7.0 < pH ≤ 11.5) with maximum activity at pH 9.0. The maximal values of k cat and k cat /K m at pH 9.0 are 3.7 × 10 6  s -1 and 5.5 × 10 7  M -1  s -1 , respectively. However, this enzyme loses its activity in the acidic pH range. We further performed 20-ns molecular dynamics simulation of CAVA to see the dynamics at different pH values. An excellent agreement was observed between in silico and in vitro studies. This study provides an insight into the activity of CAVA in the pH range of subcellular environment.

  13. Genes encoded within 8q24 on the amplicon of a large extrachromosomal element are selectively repressed during the terminal differentiation of HL-60 cells

    OpenAIRE

    Hirano, Tetsuo; Ike, Fumio; Murata, Takehide; Obata, Yuichi; Utiyama, Hiroyasu; Yokoyama, Kazunari K.

    2008-01-01

    Human acute myeloblastic leukemia HL-60 cells become resistant to differentiation during long­term cultivation. After 150 passages, double minute chromosomes (dmins) found in early­-passaged cells are replaced by large extrachromosomal elements (LEEs). In a DNA library derived from a purified fraction of LEEs, 12.6% (23/183) of clones were assigned to 8q24 and 9.2% (17/183) were assigned to 14q11 in the human genome. Fluorescence in situ hybridization (FISH) revealed a small aberrant chromos...

  14. The KiVa antibullying program in primary schools in Chile, with and without the digital game component: study protocol for a randomized controlled trial.

    Science.gov (United States)

    Gaete, Jorge; Valenzuela, Daniela; Rojas-Barahona, Cristian; Valenzuela, Eduardo; Araya, Ricardo; Salmivalli, Christina

    2017-02-20

    Bullying is a major problem worldwide and Chile is no exception. Bullying is defined as a systematic aggressive behavior against a victim who cannot defend him or herself. Victims suffer social isolation and psychological maladjustment, while bullies have a higher risk for conduct problems and substance use disorders. These problems appear to last over time. The KiVa antibullying program has been evaluated in Finland and other European countries, showing preventive effects on victimization and self-reported bullying. The aims of this study are (1) to develop a culturally appropriate version of the KiVa material and (2) to test the effectiveness of the KiVa program, with and without the online game, on reducing experiences of victimization and bullying behavior among vulnerable primary schools in Santiago (Chile), using a cluster randomized controlled trial (RCT) design with three arms: (1) full KiVa program group, (2) partial KiVa (without online game) program group and (3) control group. This is a three-arm, single-blind, cluster randomized controlled trial (RCT) with a target enrolment of 1495 4th and 5th graders attending 13 vulnerable schools per arm. Students in the full and partial KiVa groups will receive universal actions: ten 2-h lessons delivered by trained teachers during 1 year; they will be exposed to posters encouraging them to support victims and behave constructively when witnessing bullying; and a person designated by the school authorities will be present in all school breaks and lunchtimes using a visible KiVa vest to remind everybody that they are in a KiVa school. KiVa schools also will have indicated actions, which consist of a set of discussion groups with the victims and with the bullies, with proper follow-up. Only full KiVa schools will also receive an online game which has the aim to raise awareness of the role of the group in bullying, increase empathy and promote strategies to support victimized peers. Self-reported victimization

  15. 38 CFR 58.17 - VA Form 10-0144A-Statement of Assurance of Compliance with Equal Opportunity Laws.

    Science.gov (United States)

    2010-07-01

    ... 38 Pensions, Bonuses, and Veterans' Relief 2 2010-07-01 2010-07-01 false VA Form 10-0144A-Statement of Assurance of Compliance with Equal Opportunity Laws. 58.17 Section 58.17 Pensions, Bonuses, and Veterans' Relief DEPARTMENT OF VETERANS AFFAIRS (CONTINUED) FORMS § 58.17 VA Form 10-0144A—Statement of Assurance of Compliance with Equal...

  16. 30 CFR 57.22204 - Main fan operation and inspection (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 Main fan operation and inspection (I-A, II-A, III, and V-A mines). 57.22204 Section 57.22204 Mineral Resources MINE SAFETY AND HEALTH ADMINISTRATION... Main fan operation and inspection (I-A, II-A, III, and V-A mines). Main fans shall be— (a) Provided...

  17. 30 CFR 57.22205 - Doors on main fans (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 Doors on main fans (I-A, II-A, III, and V-A... main fans (I-A, II-A, III, and V-A mines). In mines ventilated by multiple main fans, each main fan... reversal through the fan. The doors shall be located so that they are not in direct line with explosive...

  18. 30 CFR 57.22202 - Main fans (I-A, I-B, I-C, II-A, III, V-A, and V-B mines).

    Science.gov (United States)

    2010-07-01

    ... 30 Mineral Resources 1 2010-07-01 2010-07-01 false Main fans (I-A, I-B, I-C, II-A, III, V-A, and V... Main fans (I-A, I-B, I-C, II-A, III, V-A, and V-B mines). (a) Main fans shall be— (1) Installed on the... mines, provided with an automatic signal device to give an alarm when the fan stops. The signal device...

  19. RİSK ÖLÇÜMÜNDE ALTERNATİF YAKLAŞIMLAR: RİSKE MARUZ DEĞER (VaR ve BEKLENEN KAYIP (ES UYGULAMALARI

    Directory of Open Access Journals (Sweden)

    SEZER BOZKUŞ

    2013-06-01

    Full Text Available This article shows that Value-at-Risk (VaR, the most popular risk measure in practice, has a considerable positive bias when used for a portfolio with fat-tail distribution. Numerical examples, i.e. USD/Euro daily prices and ISE-100 Index monthly returns, are given to demonstrate the use of our method. In the search for a suitable alternative to VaR, Expected Shortfall (ES or conditional VaR has been characterized as the coherent risk measure to dominate VaR. We discuss properties of VaR and ES and compare them in terms of consistency with elimination of tail risk, strengths and weaknesses. We conclude that ES is more applicable than VaR since ES is free of tail risk and consistent under more lenient conditions than VaR is.

  20. Expression of Vitis amurensis VaERF20 in Arabidopsis thaliana Improves Resistance to Botrytis cinerea and Pseudomonas syringae pv. Tomato DC3000

    Directory of Open Access Journals (Sweden)

    Mengnan Wang

    2018-03-01

    Full Text Available Ethylene response factor (ERF transcription factors play important roles in regulating immune responses in plants. In our study, we characterized a member of the ERF transcription factor family, VaERF20, from the Chinese wild Vitis genotype, V. amurensis Rupr “Shuangyou”. Phylogenetic analysis indicated that VaERF20 belongs to group IXc of the ERF family, in which many members are known to contribute to fighting pathogen infection. Consistent with this, expression of VaERF20 was induced by treatment with the necrotrophic fungal pathogen Botrytis cinerea (B. cinerea in “Shuangyou” and V. vinifera “Red Globe”. Arabidopsis thaliana plants over-expressing VaERF20 displayed enhanced resistance to B. cinerea and the bacterium Pseudomonas syringae pv. tomato (Pst DC3000. Patterns of pathogen-induced reactive oxygen species (ROS accumulation were entirely distinct in B. cinerea and PstDC3000 inoculated plants. Examples of both salicylic acid (SA and jasmonic acid/ethylene (JA/ET responsive defense genes were up-regulated after B. cinerea and PstDC3000 inoculation of the VaERF20-overexpressing transgenic A. thaliana plants. Evidence of pattern-triggered immunity (PTI, callose accumulation and stomatal defense, together with increased expression of PTI genes, was also greater in the transgenic lines. These data indicate that VaERF20 participates in various signal transduction pathways and acts as an inducer of immune responses.

  1. Solar Terminator Waves in the Ionosphere Measured by the Wallops Island, VA Dynasonde

    Science.gov (United States)

    Zabotin, N. A.; Song, H.; Bullett, T. W.

    2017-12-01

    Solar terminator represents a unique source of atmospheric waves possessing of near-ideal coherent properties: its geometry and magnitude of the impact changes very little from day to day. This feature has been used in [Forbes et al., GRL, 2008] to obtain "snapshots" of terminator waves in the neutral atmosphere at the altitude 400 km by averaging CHAMP accelerometer data over relatively long sequences of the satellite passes. The results were represented in the geographic latitude vs local time coordinates. We apply a similar approach averaging time series of Wallops Island, VA Dynasonde Doppler data to obtain "snapshots" of terminator waves in the ionosphere in the true altitude vs local "terminator time" coordinates. The averaging is performed independently for every month of the yearlong observation period from May 2013 to April 2014. The altitude range covered is 90 km to 400 km with 2 km resolution, representing the entire bottom-side ionosphere. Individual local time segments used for the averaging were 12 hours long and all centered at the times of the sunrise or sunset terminator passing at every specific altitude. This procedure effectively suppresses all kinds of incoherent wave activity and allows one to reveal the perturbation phenomenon mainly caused by the solar terminator. This is an important advantage of this technique compared to multiple "terminator wave" studies based on simple time coincidence. Both sunrise and sunset terminator waves are easily visualized in all of the monthly images. Our results confirm observations of [Forbes et al., GRL, 2008] of the wave structures existing on both sides of the terminator. The phase fronts of the sunset terminator wave are propagating downward indicating upward movement of the terminator-related disturbance and of the wave energy generated by it. The phase fronts of the sunrise terminator waves are propagating upward indicating downward movement of the terminator-related disturbance and of the wave energy

  2. Employing external facilitation to implement cognitive behavioral therapy in VA clinics: a pilot study

    Directory of Open Access Journals (Sweden)

    Blevins Dean

    2010-10-01

    Full Text Available Abstract Background Although for more than a decade healthcare systems have attempted to provide evidence-based mental health treatments, the availability and use of psychotherapies remains low. A significant need exists to identify simple but effective implementation strategies to adopt complex practices within complex systems of care. Emerging evidence suggests that facilitation may be an effective integrative implementation strategy for adoption of complex practices. The current pilot examined the use of external facilitation for adoption of cognitive behavioral therapy (CBT in 20 Department of Veteran Affairs (VA clinics. Methods The 20 clinics were paired on facility characteristics, and 23 clinicians from these were trained in CBT. A clinic in each pair was randomly selected to receive external facilitation. Quantitative methods were used to examine the extent of CBT implementation in 10 clinics that received external facilitation compared with 10 clinics that did not, and to better understand the relationship between individual providers' characteristics and attitudes and their CBT use. Costs of external facilitation were assessed by tracking the time spent by the facilitator and therapists in activities related to implementing CBT. Qualitative methods were used to explore contextual and other factors thought to influence implementation. Results Examination of change scores showed that facilitated therapists averaged an increase of 19% [95% CI: (2, 36] in self-reported CBT use from baseline, while control therapists averaged a 4% [95% CI: (-14, 21] increase. Therapists in the facilitated condition who were not providing CBT at baseline showed the greatest increase (35% compared to a control therapist who was not providing CBT at baseline (10% or to therapists in either condition who were providing CBT at baseline (average 3%. Increased CBT use was unrelated to prior CBT training. Barriers to CBT implementation were therapists' lack of

  3. p53 levels, cell cycle kinetics and radiosensitivity in two SV40 transformed Wi38VA13 fibroblast strains

    International Nuclear Information System (INIS)

    Werner, F.; Zoelzer, F.; Streffer, C.

    2001-01-01

    Background: The tumor suppressor protein p53 which can mediate an ionizing radiation-induced G 1 arrest in mammalian cells, forms complexes with SV40 large T antigen (l-T-Ag). We have analyzed the p53 levels, the capability to undergo a G 1 arrest and the radiosensitivity of two SV40 transformed fibroblast strains differing in their large T antigen expression. Material and Methods: One of the two strains (VA13F) is the commercially available form of Wi38VA13, the other (VA13E) arose spontaneously from the original one in our laboratory. Their p53 levels were measured by means of flow cytometry (FCM) and Western blot (WB) with two p53 antibodies (Ab-3, clone PAb240; Ab-6, clone DO-1; both Oncogene Science). Cell cycle distributions were determined flow cytometrically after BrdU labeling at regular time intervals after exposure to 250 kV X-rays. Radiosensitivity was assessed in a clonogenicity assay. Results: The p53 levels of the two strains corresponded to their large T antigen expression, presumably due to complex formation between the two proteins. The strain with a high p53 level did not show a G 1 arrest and had a relatively high radiosensitivity, whereas the strain with a low p53 level showed a significant G 1 arrest and a lower radiosensitivity. Conclusion: These results suggest that 1. complex formation between the large T antigen and p53 reduces the latter's functionality; 2. in these two strains the G 1 arrest is one of the factors determining radiosensitivity. (orig.) [de

  4. Suicide-related behaviors in older patients with new anti-epileptic drug use: data from the VA hospital system

    Directory of Open Access Journals (Sweden)

    Dersh Jeffrey J

    2010-01-01

    Full Text Available Abstract Background The U.S. Food and Drug Administration (FDA recently linked antiepileptic drug (AED exposure to suicide-related behaviors based on meta-analysis of randomized clinical trials. We examined the relationship between suicide-related behaviors and different AEDs in older veterans receiving new AED monotherapy from the Veterans Health Administration (VA, controlling for potential confounders. Methods VA and Medicare databases were used to identify veterans 66 years and older, who received a care from the VA between 1999 and 2004, and b an incident AED (monotherapy prescription. Previously validated ICD-9-CM codes were used to identify suicidal ideation or behavior (suicide-related behaviors cases, epilepsy, and other conditions previously associated with suicide-related behaviors. Each case was matched to controls based on prior history of suicide-related behaviors, year of AED prescription, and epilepsy status. Results The strongest predictor of suicide-related behaviors (N = 64; Controls N = 768 based on conditional logistic regression analysis was affective disorder (depression, anxiety, or post-traumatic stress disorder (PTSD; Odds Ratio 4.42, 95% CI 2.30 to 8.49 diagnosed before AED treatment. Increased suicide-related behaviors were not associated with individual AEDs, including the most commonly prescribed AED in the US - phenytoin. Conclusion Our extensive diagnostic and treatment data demonstrated that the strongest predictor of suicide-related behaviors for older patients newly treated with AED monotherapy was a previous diagnosis of affective disorder. Additional, research using a larger sample is needed to clearly determine the risk of suicide-related behaviors among less commonly used AEDs.

  5. Efectividad de la vacuna VA-MENGOC-BC® contra cepas heterólogas de meningococo B

    Directory of Open Access Journals (Sweden)

    Rolando Ochoa-Azze

    2016-08-01

    Full Text Available La efectividad de las vacunas de vesículas de membrana externa de Neisseria meningitidis serogrupo B ha sido cuestionada por algunos investigadores, limitándola a la cepa vacunal. VA-MENGOC-BC® es una vacuna antimeningocócica basada en dicha tecnología. Presentamos un metaanálisis de estudios realizados en diferentes contextos epidemiológicos, evaluando su efectividad contra cepas heterólogas de meningococo B en varios grupos de edades. Se demuestra que la vacuna es efectiva contra cepas homólogas, heterólogas y de diferentes complejos clonales.

  6. Communications and Collaboration Keep San Francisco VA Medical Center Project on Track

    International Nuclear Information System (INIS)

    Federal Energy Management Program

    2001-01-01

    This case study about energy saving performance contacts (ESPCs) presents an overview of how the Veterans Affairs Medical Center in San Francisco established an ESPC contract and the benefits derived from it. The Federal Energy Management Program instituted these special contracts to help federal agencies finance energy-saving projects at their facilities

  7. Interest rate derivatives

    DEFF Research Database (Denmark)

    Svenstrup, Mikkel

    This Ph.D. thesis consists of four self-contained essays on valuation of interest rate derivatives. In particular derivatives related to management of interest rate risk care are considered.......This Ph.D. thesis consists of four self-contained essays on valuation of interest rate derivatives. In particular derivatives related to management of interest rate risk care are considered....

  8. Evaluation of velvet antler total protein effect on bone marrow-derived endothelial progenitor cells

    OpenAIRE

    Xiao, Xiang; Li, Lin; Xu, Shuqiang; Mao, Min; Pan, Ruiyan; Li, Yanjun; Wu, Jiayun; Huang, Li; Zheng, Xiaoyun

    2017-01-01

    Lu Rong, velvet antler (VA), is a traditional Chinese medicine, which is used as a food supplement and therapeutic drug in China, Japan, Russia, New Zealand and Southeast Asia. The regenerative characteristics of VA have resulted in great research interest, particularly regarding the fields of organ grafting and stem cell differentiation. Various VA proteomic studies verified that proteins act as the primary bioactive components of VA. The present study aimed to investigate if VA proteins (VA...

  9. Assessing the Health-Care Risk: The Clinical-VaR, a Key Indicator for Sound Management.

    Science.gov (United States)

    Jiménez-Rodríguez, Enrique; Feria-Domínguez, José Manuel; Sebastián-Lacave, Alonso

    2018-03-30

    Clinical risk includes any undesirable situation or operational factor that may have negative consequences for patient safety or capable of causing an adverse event (AE). The AE, intentional or unintentionally, may be related to the human factor, that is, medical errors (MEs). Therefore, the importance of the health-care risk management is a current and relevant issue on the agenda of many public and private institutions. The objective of the management has been evolving from the identification of AE to the assessment of cost-effective and efficient measures that improve the quality control through monitoring. Consequently, the goal of this paper is to propose a Key Risk Indicator (KRI) that enhances the advancement of the health-care management system. Thus, the application of the Value at Risk (VaR) concept in combination to the Loss Distribution Approach (LDA) is proved to be a proactive tool, within the frame of balanced scorecard (BSC), in health organizations. For this purpose, the historical events recorded in the Algo-OpData ® database (Algorithmics Inc., Toronto, ON, Canada, IBM, Armonk, NY, USA) have been used. The analysis highlights the importance of risk in the financials outcomes of the sector. The results of paper show the usefulness of the Clinical-VaR to identify and monitor the risk and sustainability of the implemented controls.

  10. Assessing the Health-Care Risk: The Clinical-VaR, a Key Indicator for Sound Management

    Directory of Open Access Journals (Sweden)

    Enrique Jiménez-Rodríguez

    2018-03-01

    Full Text Available Clinical risk includes any undesirable situation or operational factor that may have negative consequences for patient safety or capable of causing an adverse event (AE. The AE, intentional or unintentionally, may be related to the human factor, that is, medical errors (MEs. Therefore, the importance of the health-care risk management is a current and relevant issue on the agenda of many public and private institutions. The objective of the management has been evolving from the identification of AE to the assessment of cost-effective and efficient measures that improve the quality control through monitoring. Consequently, the goal of this paper is to propose a Key Risk Indicator (KRI that enhances the advancement of the health-care management system. Thus, the application of the Value at Risk (VaR concept in combination to the Loss Distribution Approach (LDA is proved to be a proactive tool, within the frame of balanced scorecard (BSC, in health organizations. For this purpose, the historical events recorded in the Algo-OpData® database (Algorithmics Inc., Toronto, ON, Canada, IBM, Armonk, NY, USA have been used. The analysis highlights the importance of risk in the financials outcomes of the sector. The results of paper show the usefulness of the Clinical-VaR to identify and monitor the risk and sustainability of the implemented controls.

  11. Tout va bien ! méthode de français : cahier d'exercices 2

    CERN Document Server

    Augé, H; Marlhens, C; Martin, L

    2005-01-01

    Tout va bien ! est une méthode de français destinée aux grands adolescents et adultes débutants ou faux-débutants. Ses objectifs respectent scrupuleusement les recommandations du Cadre européen commun de référence pour les langues, comme en témoigne le portfolio qui accompagne le livre de l'élève. Tout va bien ! propose : Des supports et des situations de communication authentiques ou proches de l'authentique, permettant à l'élève de se sensibiliser aux différents registres et de découvrir certains aspects de la culture francophone tout autant que la langue. De très nombreuses activités visant l'acquisition des quatre compétences de communication et l'utilisation de stratégies spécifiques. Un travail sur la grammaire et le vocabulaire associés aux situations et au service de la communication faisant une large place à l'observation et à la réflexion. Une invitation régulière à l'évaluation, au travail an autonomie et à l'auto-évaluation.

  12. Tout va bien ! méthode de français : cahier d'exercices 1

    CERN Document Server

    Augé, H; Marlhens, C; Martin, L

    2005-01-01

    Tout va bien ! est une méthode de français destinée aux grands adolescents et adultes débutants ou faux-débutants. Ses objectifs respectent scrupuleusement les recommandations du Cadre européen commun de référence pour les langues, comme en témoigne le portfolio qui accompagne le livre de l'élève. Tout va bien ! propose : Des supports et des situations de communication authentiques ou proches de l'authentique, permettant à l'élève de se sensibiliser aux différents registres et de découvrir certains aspects de la culture francophone tout autant que la langue. De très nombreuses activités visant l'acquisition des quatre compétences de communication et l'utilisation de stratégies spécifiques. Un travail sur la grammaire et le vocabulaire associés aux situations et au service de la communication faisant une large place à l'observation et à la réflexion. Une invitation régulière à l'évaluation, au travail an autonomie et à l'auto-évaluation.

  13. Assessing the Health-Care Risk: The Clinical-VaR, a Key Indicator for Sound Management

    Science.gov (United States)

    Jiménez-Rodríguez, Enrique; Sebastián-Lacave, Alonso

    2018-01-01

    Clinical risk includes any undesirable situation or operational factor that may have negative consequences for patient safety or capable of causing an adverse event (AE). The AE, intentional or unintentionally, may be related to the human factor, that is, medical errors (MEs). Therefore, the importance of the health-care risk management is a current and relevant issue on the agenda of many public and private institutions. The objective of the management has been evolving from the identification of AE to the assessment of cost-effective and efficient measures that improve the quality control through monitoring. Consequently, the goal of this paper is to propose a Key Risk Indicator (KRI) that enhances the advancement of the health-care management system. Thus, the application of the Value at Risk (VaR) concept in combination to the Loss Distribution Approach (LDA) is proved to be a proactive tool, within the frame of balanced scorecard (BSC), in health organizations. For this purpose, the historical events recorded in the Algo-OpData® database (Algorithmics Inc., Toronto, ON, Canada, IBM, Armonk, NY, USA) have been used. The analysis highlights the importance of risk in the financials outcomes of the sector. The results of paper show the usefulness of the Clinical-VaR to identify and monitor the risk and sustainability of the implemented controls. PMID:29601529

  14. Validation of KENO V.a for highly enriched uranium systems with hydrogen and/or carbon moderation

    International Nuclear Information System (INIS)

    Elliott, E.P.; Vornehm, R.G.; Dodds, H.L. Jr.

    1993-01-01

    This paper describes the validation in accordance with ANSI/ANS-8.1-1983(R1988) of KENO V.a using the 27-group ENDF/B-IV cross-section library for systems containing highly-enriched uranium, carbon, and hydrogen and for systems containing highly-enriched uranium and carbon with high carbon to uranium (C/U) atomic ratios. The validation has been performed for two separate computational platforms: an IBM 3090 mainframe and an HP 9000 Model 730 workstation, both using the Oak Ridge Y-12 Plant Nuclear Criticality Safety Software (NCSS) code package. Critical experiments performed at the Oak Ridge Critical Experiments Facility, in support of the Rover reactor program, and at the Pajarito site at Los Alamos National Laboratory were identified as having the constituents desired for this validation as well as sufficient experimental detail to allow accurate construction of KENO V.a calculational models. Calculated values of k eff for the Rover experiments, which contain uranium, carbon, and hydrogen, are between 1.0012 ± 0.0026 and 1.0245 ± 0.0023. Calculation of the Los Alamos experiments, which contain uranium and carbon at high C/U ratios, yields values of k eff between 0.9746 ± 0.0028 and 0.9983 ± 0.0027. Safety criteria can be established using this data for both types of systems

  15. The Feasibility of Using Large-Scale Text Mining to Detect Adverse Childhood Experiences in a VA-Treated Population.

    Science.gov (United States)

    Hammond, Kenric W; Ben-Ari, Alon Y; Laundry, Ryan J; Boyko, Edward J; Samore, Matthew H

    2015-12-01

    Free text in electronic health records resists large-scale analysis. Text records facts of interest not found in encoded data, and text mining enables their retrieval and quantification. The U.S. Department of Veterans Affairs (VA) clinical data repository affords an opportunity to apply text-mining methodology to study clinical questions in large populations. To assess the feasibility of text mining, investigation of the relationship between exposure to adverse childhood experiences (ACEs) and recorded diagnoses was conducted among all VA-treated Gulf war veterans, utilizing all progress notes recorded from 2000-2011. Text processing extracted ACE exposures recorded among 44.7 million clinical notes belonging to 243,973 veterans. The relationship of ACE exposure to adult illnesses was analyzed using logistic regression. Bias considerations were assessed. ACE score was strongly associated with suicide attempts and serious mental disorders (ORs = 1.84 to 1.97), and less so with behaviorally mediated and somatic conditions (ORs = 1.02 to 1.36) per unit. Bias adjustments did not remove persistent associations between ACE score and most illnesses. Text mining to detect ACE exposure in a large population was feasible. Analysis of the relationship between ACE score and adult health conditions yielded patterns of association consistent with prior research. Copyright © 2015 International Society for Traumatic Stress Studies.

  16. Transient characteristics of parallel running of the 20kVA superconducting synchronous generator and a conventional one

    International Nuclear Information System (INIS)

    Nitta, T.; Okada, T.

    1989-01-01

    This paper describes electrical transient characteristics of parallel running of the 20kVA superconducting synchronous generator and a conventional one. In the experimental power system, the superconducting generator is connected through reactors (artificial transmission lines) to a regional power system (infinite bus) and the conventional generator (20kVA) is connected to the terminal of the superconducting generator. Several tests were performed in order to consider the transient behavior of superconducting generator (SCG) in the power system. The items of the tests are synchronous closing test, loss of synchronism test and disconnecting and reclosing test. From the experimental results, it can be said that by installing SCG in power systems, voltage stability and power system stability can be improved in transient states as well as in steady states and the variation of armature current of SCG during a transient period is extremely larger than that of the conventional one. The transient analysis by a computer simulation was also carried out for the experiments. The simulation results are in good agreement with the experimental ones

  17. Educational system factors that engage resident physicians in an integrated quality improvement curriculum at a VA hospital: a realist evaluation.

    Science.gov (United States)

    Ogrinc, Greg; Ercolano, Ellyn; Cohen, Emily S; Harwood, Beth; Baum, Karyn; van Aalst, Robertus; Jones, Anne C; Davies, Louise

    2014-10-01

    Learning about quality improvement (QI) in resident physician training is often relegated to elective or noncore clinical activities. The authors integrated teaching, learning, and doing QI into the routine clinical work of inpatient internal medicine teams at a Veterans Affairs (VA) hospital. This study describes the design factors that facilitated and inhibited the integration of a QI curriculum-including real QI work-into the routine work of inpatient internal medicine teams. A realist evaluation framework used three data sources: field notes from QI faculty; semistructured interviews with resident physicians; and a group interview with QI faculty and staff. From April 2011 to July 2012, resident physician teams at the White River Junction VA Medical Center used the Model for Improvement for their QI work and analyzed data using statistical process control charts. Three domains affected the delivery of the QI curriculum and engagement of residents in QI work: setting, learner, and teacher. The constant presence of the QI material on a public space in the team workroom was a facilitating mechanism in the setting. Explicit sign-out of QI work to the next resident team formalized the handoff in the learner domain. QI teachers who were respected clinical leaders with QI expertise provided role modeling and local system knowledge. Integrating QI teaching into the routine clinical and educational systems of an inpatient service is challenging. Identifiable, concrete strategies in the setting, learner, and teacher domains helped integrate QI into the clinical and educational systems.

  18. Bacterial diversity of the Colombian fermented milk "Suero Costeño" assessed by culturing and high-throughput sequencing and DGGE analysis of 16S rRNA gene amplicons.

    Science.gov (United States)

    Motato, Karina Edith; Milani, Christian; Ventura, Marco; Valencia, Francia Elena; Ruas-Madiedo, Patricia; Delgado, Susana

    2017-12-01

    "Suero Costeño" (SC) is a traditional soured cream elaborated from raw milk in the Northern-Caribbean coast of Colombia. The natural microbiota that characterizes this popular Colombian fermented milk is unknown, although several culturing studies have previously been attempted. In this work, the microbiota associated with SC from three manufacturers in two regions, "Planeta Rica" (Córdoba) and "Caucasia" (Antioquia), was analysed by means of culturing methods in combination with high-throughput sequencing and DGGE analysis of 16S rRNA gene amplicons. The bacterial ecosystem of SC samples was revealed to be composed of lactic acid bacteria belonging to the Streptococcaceae and Lactobacillaceae families; the proportions and genera varying among manufacturers and region of elaboration. Members of the Lactobacillus acidophilus group, Lactocococcus lactis, Streptococcus infantarius and Streptococcus salivarius characterized this artisanal product. In comparison with culturing, the use of molecular in deep culture-independent techniques provides a more realistic picture of the overall bacterial communities residing in SC. Besides the descriptive purpose, these approaches will facilitate a rational strategy to follow (culture media and growing conditions) for the isolation of indigenous strains that allow standardization in the manufacture of SC. Copyright © 2017 Elsevier Ltd. All rights reserved.

  19. Derivatives in emerging markets

    OpenAIRE

    Dubravko Mihaljek; Frank Packer

    2010-01-01

    Turnover of derivatives has grown more rapidly in emerging markets than in developed countries. Foreign exchange derivatives are the most commonly traded of all risk categories, with increasingly frequent turnover in emerging market currencies and a growing share of cross-border transactions. As the global reach of the financial centres in emerging Asia has expanded, the offshore trading of many emerging market currency derivatives has risen as well. Growth in derivatives turnover is positive...

  20. Tailoring an educational program on the AHRQ Patient Safety Indicators to meet stakeholder needs: lessons learned in the VA.

    Science.gov (United States)

    Shin, Marlena H; Rivard, Peter E; Shwartz, Michael; Borzecki, Ann; Yaksic, Enzo; Stolzmann, Kelly; Zubkoff, Lisa; Rosen, Amy K

    2018-02-14

    Given that patient safety measures are increasingly used for public reporting and pay-for performance, it is important for stakeholders to understand how to use these measures for improvement. The Agency for Healthcare Research and Quality (AHRQ) Patient Safety Indicators (PSIs) are one particularly visible set of measures that are now used primarily for public reporting and pay-for-performance among both private sector and Veterans Health Administration (VA) hospitals. This trend generates a strong need for stakeholders to understand how to interpret and use the PSIs for quality improvement (QI). The goal of this study was to develop an educational program and tailor it to stakeholders' needs. In this paper, we share what we learned from this program development process. Our study population included key VA stakeholders involved in reviewing performance reports and prioritizing and initiating quality/safety initiatives. A pre-program formative evaluation through telephone interviews and web-based surveys assessed stakeholders' educational needs/interests. Findings from the formative evaluation led to development and implementation of a cyberseminar-based program, which we tailored to stakeholders' needs/interests. A post-program survey evaluated program participants' perceptions about the PSI educational program. Interview data confirmed that the concepts we had developed for the interviews could be used for the survey. Survey results informed us on what program delivery mode and content topics were of high interest. Six cyberseminars were developed-three of which focused on two content areas that were noted of greatest interest: learning how to use PSIs for monitoring trends and understanding how to interpret PSIs. We also used snapshots of VA PSI reports so that participants could directly apply learnings. Although initial interest in the program was high, actual attendance was low. However, post-program survey results indicated that perceptions about the