WorldWideScience

Sample records for amplicon va derived

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

    Directory of Open Access Journals (Sweden)

    Benjamin Stein

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

  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. (SELAX strain) B2 amplicon

    African Journals Online (AJOL)

    USER

    2010-07-12

    Jul 12, 2010 ... Restriction enzyme digests of the clones suggested that the cloned portion of the B2 amplicon was 16 kb. Key words: B2 gene, A2B2 esterase, insecticide resistance. INTRODUCTION. Organophosphate resistance in Culex pipiens complex mosquitoes has been shown to be correlated with the presence of ...

  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. Cooperative Epigenetic Modulation by Cancer Amplicon Genes

    Science.gov (United States)

    Rui, Lixin; Tolga Emre, N. C.; Kruhlak, Michael J.; Chung, Hye-Jung; Steidl, Christian; Slack, Graham; Wright, George W.; Lenz, Georg; Ngo, Vu N.; Shaffer, Arthur L.; Xu, Weihong; Zhao, Hong; Yang, Yandan; Lamy, Laurence; Davis, R. Eric; Xiao, Wenming; Powell, John; Maloney, David; Thomas, Craig J.; Möller, Peter; Rosenwald, Andreas; Ott, German; Muller-Hermelink, Hans Konrad; Savage, Kerry; Connors, Joseph M.; Rimsza, Lisa M.; Campo, Elias; Jaffe, Elaine S.; Delabie, Jan; Smeland, Erlend B.; Weisenburger, Dennis D.; Chan, Wing C.; Gascoyne, Randy D.; Levens, David; Staudt, Louis M.

    2010-01-01

    Chromosome band 9p24 is frequently amplified in primary mediastinal B-cell lymphoma (PMBL) and Hodgkin lymphoma (HL). To identify oncogenes in this amplicon, we screened an RNA interference library targeting amplicon genes and thereby identified JAK2 and the histone demethylase JMJD2C as essential genes in these lymphomas. Inhibition of JAK2 and JMJD2C cooperated in killing these lymphomas by decreasing tyrosine 41 phosphorylation and increasing lysine 9 trimethylation of histone H3, promoting heterochromatin formation. MYC, a major target of JAK2-mediated histone phosphorylation, was silenced following JAK2 and JMJD2C inhibition, with a corresponding increase in repressive chromatin. Hence, JAK2 and JMJD2C cooperatively remodel the PMBL and HL epigenome, offering a mechanistic rationale for the development of JAK2 and JMJD2C inhibitors in these diseases. PMID:21156283

  6. 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...

  7. State of the VA

    Directory of Open Access Journals (Sweden)

    Robbins RA

    2016-01-01

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

  8. 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.

  9. 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...

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

    Science.gov (United States)

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

    2012-01-01

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

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

    Science.gov (United States)

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

    2016-07-12

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

  12. The Geometric-VaR Backtesting Method

    DEFF Research Database (Denmark)

    Wei, Wei; Pelletier, Denis

    2014-01-01

    This paper develops a new test to evaluate Value af Risk (VaR) forecasts. VaR is a standard risk measure widely utilized by financial institutions and regulators, yet estimating VaR is a challenging problem, and popular VaR forecast relies on unrealistic assumptions. Hence, assessing...... the performance of VaR is of great importance. We propose the geometric-VaR test which utilizes the duration between the violations of VaR as well as the value of VaR. We conduct a Monte Carlo study based on desk-level data and we find that our test has high power against various alternatives....

  13. 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....

  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. FlowClus: efficiently filtering and denoising pyrosequenced amplicons.

    Science.gov (United States)

    Gaspar, John M; Thomas, W Kelley

    2015-03-27

    Reducing the effects of sequencing errors and PCR artifacts has emerged as an essential component in amplicon-based metagenomic studies. Denoising algorithms have been designed that can reduce error rates in mock community data, but they change the sequence data in a manner that can be inconsistent with the process of removing errors in studies of real communities. In addition, they are limited by the size of the dataset and the sequencing technology used. FlowClus uses a systematic approach to filter and denoise reads efficiently. When denoising real datasets, FlowClus provides feedback about the process that can be used as the basis to adjust the parameters of the algorithm to suit the particular dataset. When used to analyze a mock community dataset, FlowClus produced a lower error rate compared to other denoising algorithms, while retaining significantly more sequence information. Among its other attributes, FlowClus can analyze longer reads being generated from all stages of 454 sequencing technology, as well as from Ion Torrent. It has processed a large dataset of 2.2 million GS-FLX Titanium reads in twelve hours; using its more efficient (but less precise) trie analysis option, this time was further reduced, to seven minutes. Many of the amplicon-based metagenomics datasets generated over the last several years have been processed through a denoising pipeline that likely caused deleterious effects on the raw data. By using FlowClus, one can avoid such negative outcomes while maintaining control over the filtering and denoising processes. Because of its efficiency, FlowClus can be used to re-analyze multiple large datasets together, thereby leading to more standardized conclusions. FlowClus is freely available on GitHub (jsh58/FlowClus); it is written in C and supported on Linux.

  16. Performance of amplicon-based next generation DNA sequencing for diagnostic gene mutation profiling in oncopathology.

    Science.gov (United States)

    Sie, Daoud; Snijders, Peter J F; Meijer, Gerrit A; Doeleman, Marije W; van Moorsel, Marinda I H; van Essen, Hendrik F; Eijk, Paul P; Grünberg, Katrien; van Grieken, Nicole C T; Thunnissen, Erik; Verheul, Henk M; Smit, Egbert F; Ylstra, Bauke; Heideman, Daniëlle A M

    2014-10-01

    Next generation DNA sequencing (NGS) holds promise for diagnostic applications, yet implementation in routine molecular pathology practice requires performance evaluation on DNA derived from routine formalin-fixed paraffin-embedded (FFPE) tissue specimens. The current study presents a comprehensive analysis of TruSeq Amplicon Cancer Panel-based NGS using a MiSeq Personal sequencer (TSACP-MiSeq-NGS) for somatic mutation profiling. TSACP-MiSeq-NGS (testing 212 hotspot mutation amplicons of 48 genes) and a data analysis pipeline were evaluated in a retrospective learning/test set approach (n = 58/n = 45 FFPE-tumor DNA samples) against 'gold standard' high-resolution-melting (HRM)-sequencing for the genes KRAS, EGFR, BRAF and PIK3CA. Next, the performance of the validated test algorithm was assessed in an independent, prospective cohort of FFPE-tumor DNA samples (n = 75). In the learning set, a number of minimum parameter settings was defined to decide whether a FFPE-DNA sample is qualified for TSACP-MiSeq-NGS and for calling mutations. The resulting test algorithm revealed 82% (37/45) compliance to the quality criteria and 95% (35/37) concordant assay findings for KRAS, EGFR, BRAF and PIK3CA with HRM-sequencing (kappa = 0.92; 95% CI = 0.81-1.03) in the test set. Subsequent application of the validated test algorithm to the prospective cohort yielded a success rate of 84% (63/75), and a high concordance with HRM-sequencing (95% (60/63); kappa = 0.92; 95% CI = 0.84-1.01). TSACP-MiSeq-NGS detected 77 mutations in 29 additional genes. TSACP-MiSeq-NGS is suitable for diagnostic gene mutation profiling in oncopathology.

  17. VA administrators breahe a sigh of relief

    Directory of Open Access Journals (Sweden)

    Robbins RA

    2014-06-01

    Full Text Available No abstract available. Article truncated at 150 words. On May 30, Eric Shinseki, the Secretary for Veterans Affairs (VA, resigned under pressure amidst a growing scandal regarding falsification of patient wait times at nearly 40 VA medical centers. Before leaving office Shinseki fired Sharon Helman, the former hospital director at the Phoenix VA, where the story first broke, along with her deputy and another unnamed administrator. In addition, Susan Bowers, director of VA Veterans Integrated Service Network (VISN 18 and Helman’s boss, resigned. Robert Petzel, undersecretary for the Veterans Health Administration (VHA, head of the VA hospitals and clinics, had resigned earlier. You could hear the sigh of relief from the VA administrators. With their bosses resigning left and right, the VA leadership in shambles and the reputation of the VA soiled for many years to come, why are the VA administrators relieved? The simple answer is that nothing has really changed. There for a moment it looked ...

  18. Probabilistic methods for verbal autopsy interpretation: InterVA robustness in relation to variations in a priori probabilities.

    Directory of Open Access Journals (Sweden)

    Edward Fottrell

    Full Text Available InterVA is a probabilistic method for interpreting verbal autopsy (VA data. It uses a priori approximations of probabilities relating to diseases and symptoms to calculate the probability of specific causes of death given reported symptoms recorded in a VA interview. The extent to which InterVA's ability to characterise a population's mortality composition might be sensitive to variations in these a priori probabilities was investigated.A priori InterVA probabilities were changed by 1, 2 or 3 steps on the logarithmic scale on which the original probabilities were based. These changes were made to a random selection of 25% and 50% of the original probabilities, giving six model variants. A random sample of 1,000 VAs from South Africa, were used as a basis for experimentation and were processed using the original InterVA model and 20 random instances of each of the six InterVA model variants. Rank order of cause of death and cause-specific mortality fractions (CSMFs from the original InterVA model and the mean, maximum and minimum results from the 20 randomly modified InterVA models for each of the six variants were compared.CSMFs were functionally similar between the original InterVA model and the models with modified a priori probabilities such that even the CSMFs based on the InterVA model with the greatest degree of variation in the a priori probabilities would not lead to substantially different public health conclusions. The rank order of causes were also similar between all versions of InterVA.InterVA is a robust model for interpreting VA data and even relatively large variations in a priori probabilities do not affect InterVA-derived results to a great degree. The original physician-derived a priori probabilities are likely to be sufficient for the global application of InterVA in settings without routine death certification.

  19. 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 ...

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

    DEFF Research Database (Denmark)

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

    2004-01-01

    . Hybridization to individual amplicons in multiplexes was less efficient suggesting that intramolecular and intermolecular interactions may block access to the target sequence on the NanoChip array. We observed a high risk of contamination with amplicons shorter than 60 bp and therefore, we recommend the use...

  1. Metatranscriptomics and Amplicon Sequencing Reveal Mutualisms in Seagrass Microbiomes

    Directory of Open Access Journals (Sweden)

    Byron C. Crump

    2018-03-01

    Full Text Available Terrestrial plants benefit from many well-understood mutualistic relationships with root- and leaf-associated microbiomes, but relatively little is known about these relationships for seagrass and other aquatic plants. We used 16S rRNA gene amplicon sequencing and metatranscriptomics to assess potential mutualisms between microorganisms and the seagrasses Zostera marina and Zostera japonica collected from mixed beds in Netarts Bay, OR, United States. The phylogenetic composition of leaf-, root-, and water column-associated bacterial communities were strikingly different, but these communities were not significantly different between plant species. Many taxa present on leaves were related to organisms capable of consuming the common plant metabolic waste product methanol, and of producing agarases, which can limit the growth of epiphytic algae. Taxa present on roots were related to organisms capable of oxidizing toxic sulfur compounds and of fixing nitrogen. Metatranscriptomic sequencing identified expression of genes involved in all of these microbial metabolic processes at levels greater than typical water column bacterioplankton, and also identified expression of genes involved in denitrification and in bacterial synthesis of the plant growth hormone indole-3-acetate. These results provide the first evidence using metatranscriptomics that seagrass microbiomes carry out a broad range of functions that may benefit their hosts, and imply that microbe–plant mutualisms support the health and growth of aquatic plants.

  2. 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...

  3. 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...

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

    OpenAIRE

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

    1996-01-01

    The photochemical inactivation of amplicons by isopsoralen (IP-10) has been suggested as a possible means to prevent PCR carryover contamination. To evaluate the technique, serial dilutions of amplicons (10(11) to 10(3)) from the Borrelia burgdorferi OSP A gene were amplified in the presence of 0, 25, 50, and 100 micrograms of IP-10 per ml for 45 cycles. The PCR products were exposed to UV light for 15 min to activate IP-10 and sterilize the amplicons. One microliter of each sterilized sample...

  5. Characterization of Novel Genes With 8p11-12 Amplicon in Breast Cancer

    National Research Council Canada - National Science Library

    Yang, Zeng-Quan

    2004-01-01

    ...% of human breast cancer (HBC). Using chromosome comparative genomic hybridization (CGH) and array CGH, overlapping amplicons were found to be centered around chromosome 8p11-p12 in 3 breast cancer cell lines developed in Dr...

  6. 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.

  7. 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.

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

    Directory of Open Access Journals (Sweden)

    Skums Pavel

    2012-06-01

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

  9. Geographic Distribution of VA Expenditures FY2008

    Data.gov (United States)

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

  10. Geographic Distribution of VA Expenditures FY2006

    Data.gov (United States)

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

  11. Geographic Distribution of VA Expenditures 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,...

  12. 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,...

  13. 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,...

  14. Geographic Distribution of VA Expenditures FY1999

    Data.gov (United States)

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

  15. Geographic Distribution of VA Expenditures FY2001

    Data.gov (United States)

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

  16. Geographic Distribution of VA Expenditures FY2011

    Data.gov (United States)

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

  17. Geographic Distribution of VA Expenditures FY1998

    Data.gov (United States)

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

  18. Geographic Distribution of VA Expenditures FY2000

    Data.gov (United States)

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

  19. 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...

  20. Geographic Distribution of VA Expenditures FY2007

    Data.gov (United States)

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

  1. Geographic Distribution of VA Expenditures FY2003

    Data.gov (United States)

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

  2. Geographic Distribution of VA Expenditures FY1996

    Data.gov (United States)

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

  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 FY2005

    Data.gov (United States)

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

  5. 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,...

  6. 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,...

  7. Geographic Distribution of VA Expenditures FY1997

    Data.gov (United States)

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

  8. 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,...

  9. VA Dental Insurance Program. Final rule.

    Science.gov (United States)

    2013-05-29

    The Department of Veterans Affairs (VA) amends its regulations to establish rules and procedures for the VA Dental Insurance Program (VADIP), a pilot program that offers premium-based dental insurance to enrolled veterans and certain survivors and dependents of veterans. Under the pilot program, VA will contract with a private insurer, through the Federal contracting process, to offer dental insurance to eligible individuals. The private insurer will be responsible for the administration of the dental insurance plan. VA will form the contract and verify the eligibility of individuals who apply for the private dental insurance.

  10. 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

  11. Genome editing using FACS enrichment of nuclease-expressing cells and indel detection by amplicon analysis

    DEFF Research Database (Denmark)

    Lonowski, Lindsey A; Narimatsu, Yoshiki; Riaz, Anjum

    2017-01-01

    ). First, Indel Detection by Amplicon Analysis (IDAA) determines the size and frequency of insertions and deletions elicited by nucleases in cells, tissues or embryos through analysis of fluorophore-labeled PCR amplicons covering the nuclease target site by capillary electrophoresis in a sequenator. Second...... the testing of new nuclease reagents and the generation of edited cell pools or clonal cell lines, reducing the number of clones that need to be generated and increasing the ease with which they are screened. The pipeline shortens the time line, but it most prominently reduces the workload of cell...

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

    Science.gov (United States)

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

    1996-12-01

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

  13. Multitracer Positron Emission Tomographic Imaging of Exogenous Gene Expression Mediated by a Universal Herpes Simplex Virus 1 Amplicon Vector

    Directory of Open Access Journals (Sweden)

    Christiane Kummer

    2007-05-01

    Full Text Available To develop efficient and safe gene therapy approaches, the herpes simplex virus type 1 thymidine kinase gene (HSV-1-tk has been shown to function as a marker gene for the direct noninvasive in vivo localization of thymidine kinase (TK expression by positron emission tomography (PET using radiolabeled nucleoside analogues as specific TK substrates. Moreover, the gene encoding dopamine type 2 receptor (d2r could be used as a PET marker gene using specific radiolabeled receptor binding compounds. Here we describe the quantitative colocalization of d2r and HSV-1-tk gene expression mediated from a universal HSV-1 amplicon vector in a subcutaneous human Gli36dEGFR glioma model by PET. The HSV-1 amplicon vector was constructed using a bicistronic gene cassette to contain (1 the d2r80A mutant, which is able to bind its ligand racloprid but unable to activate downstream signal transduction pathways, and (2 the tk39 mutant with enhanced enzymatic activity toward guanosine analogues fused to the green fluorescent protein gene (tk39gfp serving as a marker gene in cell culture. After infection of human Gli36dEGFR glioma cells with the HSV-d2r80AIREStk39gfp (HSV-DITG amplicon vector in cell culture, D2 receptor expression and its targeting to the cell surface were determined by Western blotting and immunolabeling. Vector application in vivo served for quantitative colocalization of d2r80A- and tk39gfp-derived PET signals employing the specific D2 receptor binding compound [11C]racloprid and the specific TK39 substrate 9-(4-[18F]fluoro-3-hydroxymethylbutylguanine. Our results demonstrate that for the range of gene expression studied in vivo, both enzymatic and receptor binding assays give comparable quantitative information on the level of vector-mediated gene expression in vivo. The d2r80A in combination with a specific binding compound passing the intact blood-brain barrier might be an alternative marker gene for the noninvasive assessment of vector

  14. 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...

  15. 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...

  16. Geographic Distribution of VA Expenditures Report FY2015

    Data.gov (United States)

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

  17. 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

  18. 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

  19. 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.

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

    DEFF Research Database (Denmark)

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

    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...

  1. 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...

  2. Characterization of the 17p amplicon in human sarcomas: microsatellite marker analysis

    NARCIS (Netherlands)

    Wolf, M.; Tarkkanen, M.; Hulsebos, T.; Larramendy, M. L.; Forus, A.; Myklebost, O.; Aaltonen, L. A.; Elomaa, I.; Knuutila, S.

    1999-01-01

    The structure of the 17p amplicon from 9 human sarcoma specimens evaluated by comparative genomic hybridization (CGH) has been studied by analyzing 28 microsatellite markers by PCR. Eleven sarcoma specimens showing no DNA copy number increases at 17p by CGH were analyzed as control samples. Five

  3. The influence of amplicon length on real-time PCR results

    Directory of Open Access Journals (Sweden)

    Debode, F.

    2017-01-01

    Full Text Available Description of the subject. This paper discusses the influence of amplicon length on real-time PCR results. Objectives. The aim of the experiments was to show that amplicon size has an influence on detection. Method. Tests were performed on genomic and plasmid DNA. Double-dye probes and SYBR® Green were used for detection by real-time PCR. Primers were selected in order to produce fragments with increasing sizes. Experiments dealt with two targets: an endogenous target for soybean (part of the lectin gene and a transgenic target (junction P35S-CTP of the MON40-3-2 soybean. Results. The results show that the kinetics of amplification curves evolve as a function of amplicon length, and smaller amplicons yield a higher level of fluorescence for the plateau phase. DNA degradation within the sample as well as the principles of fluorescence acquisition as a function of the chemistry used can also be factors. Conclusions. It was experimentally shown that the observed effect is linked to the suboptimal elongation temperature used in real-time PCR. Detection using SYBR® Green is less impacted as the loss of efficiency is partially compensated by the greater integration of SYBR® Green molecules in the larger fragments.

  4. 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.

  5. 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)

  6. A failure of oversight at the VA

    Directory of Open Access Journals (Sweden)

    Robbins RA

    2014-09-01

    Full Text Available No abstract available. Article truncated at 150 words. On September 8, 2014 the Washington Examiner reported that the Central Office of the VA was allowed to change language in the VA Office of Inspector General (VAOIG report on delays in patient care at the Phoenix VA Medical Center (1. Crucial language that the VAOIG could not “conclusively” prove that delays in care caused patient deaths at a Phoenix hospital was added to its final report after a draft version was sent to agency administrators for comment. Rep. Jeff Miller, chairman of the House veterans' committee, said "there are significant differences between the final IG report and the draft version ...". The following day Richard Griffin, the acting VAOIG, vigorously defended the independence of his office and bristled at the allegations that the VA was allowed to alter his office's report. However, his denials and indignance seem disingenuous. To understand why, we need to go back a few years. ...

  7. 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...

  8. Genetics Home Reference: carbonic anhydrase VA deficiency

    Science.gov (United States)

    ... bicarbonate. Bicarbonate is necessary to maintain the proper acid-base balance in the body, which is necessary for most biological reactions to proceed properly. The carbonic anhydrase VA enzyme ...

  9. Bacterial and viral identification and differentiation by amplicon sequencing on the MinION nanopore sequencer.

    Science.gov (United States)

    Kilianski, Andy; Haas, Jamie L; Corriveau, Elizabeth J; Liem, Alvin T; Willis, Kristen L; Kadavy, Dana R; Rosenzweig, C Nicole; Minot, Samuel S

    2015-01-01

    The MinION™ nanopore sequencer was recently released to a community of alpha-testers for evaluation using a variety of sequencing applications. Recent reports have tested the ability of the MinION™ to act as a whole genome sequencer and have demonstrated that nanopore sequencing has tremendous potential utility. However, the current nanopore technology still has limitations with respect to error-rate, and this is problematic when attempting to assemble whole genomes without secondary rounds of sequencing to correct errors. In this study, we tested the ability of the MinION™ nanopore sequencer to accurately identify and differentiate bacterial and viral samples via directed sequencing of characteristic genes shared broadly across a target clade. Using a 6 hour sequencing run time, sufficient data were generated to identify an E. coli sample down to the species level from 16S rDNA amplicons. Three poxviruses (cowpox, vaccinia-MVA, and vaccinia-Lister) were identified and differentiated down to the strain level, despite over 98% identity between the vaccinia strains. The ability to differentiate strains by amplicon sequencing on the MinION™ was accomplished despite an observed per-base error rate of approximately 30%. While nanopore sequencing, using the MinION™ platform from Oxford Nanopore in particular, continues to mature into a commercially available technology, practical uses are sought for the current versions of the technology. This study offers evidence of the utility of amplicon sequencing by demonstrating that the current versions of MinION™ technology can accurately identify and differentiate both viral and bacterial species present within biological samples via amplicon sequencing.

  10. Pregnancy-associated glycoprotein (PAG) family: transcripts and gene amplicons in camelids.

    Science.gov (United States)

    Majewska, Marta; Panasiewicz, Grzegorz; Klisch, Karl; Olivera, Louis V M; Mamani, Javier M; Abd-Elnaeim, Mahmoud M; Szafranska, Bozena

    2009-07-01

    In this study, the placental localization of PAG-like transcripts and genomic existence of PAG-like amplicons in new-world (Lp, Lama pacos, alpaca) and old-world camelids (Cb, Camelus bactrianus, bactrian; Cd, Camelus dromedarius; dromedary) are reported for the first time. Sections of Lp (150-347 days post coitum), Cd (43-90 cm crown-rump length) and Cb (term) placentas were used for heterologous (ht; cross-species) autoradiographic in situ hybridization (aISH) with single-stranded diagnostic (antisense) or control (sense) [alpha-(35)S]dATP-labeled 323 nt porcine PAG8 (pPAG8) cDNA probes produced by asymmetric PCRs. The aISH with antisense (35)S-pPAG8 probe identified camelid PAG-like (LpPAG, CbPAG and CdPAG) mRNA expression restricted to chorionic epithelium cells within placentas of camelids. In addition, genomic DNA (gDNA), isolated from placental sections were used as templates for camelid PAG-like gene amplicon production by PCR. Specificity of the obtained multiple camelid gDNA PAG-like amplicons was confirmed by double ht-Southern hybridizations with [alpha-(32)P]dATP-labeled 611 bp pPAG5 and pPAG10 double-stranded cDNA probes. The double ht-Southern hybridizations of camelid gDNA amplicons (with pPAG5 and -10 probes) allowed the identification of length-polymorphism of LpPAG, CbPAG and CdPAG genes, coding catalytically active and potentially inactive forms. Such an application of porcine PAG probes may be advantageous for future identification of still undiscovered PAG-like families in other eutherian species.

  11. 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/.

  12. Analysing 454 amplicon resequencing experiments using the modular and database oriented Variant Identification Pipeline

    Directory of Open Access Journals (Sweden)

    Deforce Dieter

    2010-05-01

    Full Text Available Abstract Background Next-generation amplicon sequencing enables high-throughput genetic diagnostics, sequencing multiple genes in several patients together in one sequencing run. Currently, no open-source out-of-the-box software solution exists that reliably reports detected genetic variations and that can be used to improve future sequencing effectiveness by analyzing the PCR reactions. Results We developed an integrated database oriented software pipeline for analysis of 454/Roche GS-FLX amplicon resequencing experiments using Perl and a relational database. The pipeline enables variation detection, variation detection validation, and advanced data analysis, which provides information that can be used to optimize PCR efficiency using traditional means. The modular approach enables customization of the pipeline where needed and allows researchers to adopt their analysis pipeline to their experiments. Clear documentation and training data is available to test and validate the pipeline prior to using it on real sequencing data. Conclusions We designed an open-source database oriented pipeline that enables advanced analysis of 454/Roche GS-FLX amplicon resequencing experiments using SQL-statements. This modular database approach allows easy coupling with other pipeline modules such as variant interpretation or a LIMS system. There is also a set of standard reporting scripts available.

  13. Simultaneous analysis of multiple PCR amplicons enhances capillary SSCP discrimination of MHC alleles.

    Science.gov (United States)

    Alcaide, Miguel; López, Lidia; Tanferna, Alessandro; Blas, Julio; Sergio, Fabrizio; Hiraldo, Fernando

    2010-04-01

    Major histocompatibility complex (MHC) genotyping still remains one of the most challenging issues for evolutionary ecologists. To date, none of the proposed methods have proven to be perfect, and all provide both important pros and cons. Although denaturing capillary electrophoresis has become a popular alternative, allele identification commonly relies upon conformational polymorphisms of two single-stranded DNA molecules at the most. Using the MHC class II (beta chain, exon 2) of the black kite (Aves: Accipitridae) as our model system, we show that the simultaneous analysis of overlapping PCR amplicons from the same target region substantially enhances allele discrimination. To cover this aim, we designed a multiplex PCR capable to generate four differentially sized and labeled amplicons from the same allele. Informative peaks to assist allele calling then fourfold those generated by the analysis of single PCR amplicons. Our approach proved successful to differentiate all the alleles (N=13) isolated from eight unrelated birds at a single optimal run temperature and electrophoretic conditions. In particular, we emphasize that this approach may constitute a straightforward and cost-effective alternative for the genotyping of single or duplicated MHC genes displaying low to moderate sets of divergent alleles.

  14. Comparison of somatic mutation calling methods in amplicon and whole exome sequence data.

    Science.gov (United States)

    Xu, Huilei; DiCarlo, John; Satya, Ravi Vijaya; Peng, Quan; Wang, Yexun

    2014-03-28

    High-throughput sequencing is rapidly becoming common practice in clinical diagnosis and cancer research. Many algorithms have been developed for somatic single nucleotide variant (SNV) detection in matched tumor-normal DNA sequencing. Although numerous studies have compared the performance of various algorithms on exome data, there has not yet been a systematic evaluation using PCR-enriched amplicon data with a range of variant allele fractions. The recently developed gold standard variant set for the reference individual NA12878 by the NIST-led "Genome in a Bottle" Consortium (NIST-GIAB) provides a good resource to evaluate admixtures with various SNV fractions. Using the NIST-GIAB gold standard, we compared the performance of five popular somatic SNV calling algorithms (GATK UnifiedGenotyper followed by simple subtraction, MuTect, Strelka, SomaticSniper and VarScan2) for matched tumor-normal amplicon and exome sequencing data. We demonstrated that the five commonly used somatic SNV calling methods are applicable to both targeted amplicon and exome sequencing data. However, the sensitivities of these methods vary based on the allelic fraction of the mutation in the tumor sample. Our analysis can assist researchers in choosing a somatic SNV calling method suitable for their specific needs.

  15. Insured Veterans' Use of VA and Non-VA Health Care in a Rural State.

    Science.gov (United States)

    West, Alan N; Charlton, Mary E

    2016-09-01

    To understand how working-age VA-enrolled veterans with commercial insurance use both VA and non-VA outpatient care, and how rural residence affects dual use, for common diagnoses and procedures. We analyzed VA and non-VA outpatient treatment records for any months during 2005-2010 that New Hampshire veterans ages health care and commercial insurance (per NH's mandatory claims database). Controlling for covariates, we used analysis of variance to compare urban and rural VA users, non-VA users, and dual users on travel burden, diagnosis counts, duration in outpatient care, and visit frequencies, and logistic regressions to assess whether rural veterans were as likely to be seen for common conditions and procedures. More than half of patients were non-VA users and another third were dual users; rural residents were slightly more likely than urban residents to be dual users. For nearly any common diagnosis or procedure, dual users were more likely to have it at some time during treatment than other patients in either VA or non-VA care, but they seldom had it listed in both care systems. Dual users also were seen most often overall, although within either care system they were seen less often than other patients, particularly if they were rural residents living far from care. Rural residence reduced chances of treatment for a wide variety of conditions, though it also was associated with more musculoskeletal and connective tissue diagnoses. It also reduced chances that patients had some diagnostic and treatment procedures but increased the odds of others that may require fewer visits. Dual users living in rural areas may have less continuity in their health care. Ensuring that rural dual users are identified in primary care should improve access and care coordination. © 2016 National Rural Health Association.

  16. Detection of double-stranded PCR amplicons at the attomole level electrosprayed from low nanomolar solutions using FT-ICR mass spectrometry.

    Science.gov (United States)

    Hannis, J C; Muddiman, D C

    2001-02-01

    An 82-base-pair polymerase chain reaction (PCR) product was amplified from the tetranucleotide short tandem repeat locus within the human tyrosine hydroxylase gene. PCR amplification was carried out using 100 ng of human nuclear DNA obtained from an individual who is homozygotic for the 9.3 allele resulting in a 50.5 kDa amplicon. To generate sufficient material for these investigations, several reactions were pooled and subsequently purified and quantified using UV-vis spectrophotometry. A serial dilution was carried out from a 2 microM stock solution providing solution concentrations down to 5 nM. Measurements were made using hexapole accumulation and gated trapping strategies in a 4.7 Telsa Fourier transform ion cyclotron resonance mass spectrometer (FTICR-MS) which facilitated detection of the amplicon at the attomole level when electrosprayed from a 5 nM solution with a single acquisition! The signal-to-noise ratio was determined to be 8.3 for the spectrum derived from the 5 nM solution using the magnitude-mode mass spectral peak height for the most abundant charge-state. This remarkable sensitivity for large PCR amplicons will dramatically improve the ability of electrospray ionization mass spectrometry to address important genetic questions for low copy number genes or when the amount of initial template is limited; the latter issue is commonly encountered in DNA forensics. Furthermore, these data represents over 2 orders of magnitude decrease in detection limits over other existing ESI-MS reports concerning PCR products, including those conducted using FTICR-MS.

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

    Science.gov (United States)

    de Boer, Paulo; Caspers, Martien; Sanders, Jan-Willem; Kemperman, Robèr; Wijman, Janneke; Lommerse, Gijs; Roeselers, Guus; Montijn, Roy; Abee, Tjakko; Kort, Remco

    2015-01-01

    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 sequencing for quantification of bacterial spores in a canned food matrix and for monitoring the outgrowth of spoilage microbiota in a ready-to-eat food matrix. The detection limit of bar-coded 16S rRNA amplicon sequencing was determined for the number of bacterial spores in a canned food matrix. Analysis of samples from a canned food matrix spiked with a mixture of equinumerous spores from the thermophiles, Geobacillus stearothermophilus and Geobacillus thermoglucosidans, and the mesophiles, Bacillus sporothermodurans, Bacillus cereus, and Bacillus subtilis, led to the detection of these spores with an average limit of 2 × 10(2) spores ml(-1). The data were normalized by setting the number of sequences resulting from DNA of an inactivated bacterial species, present in the matrix at the same concentration in all samples, to a fixed value for quantitative sample-to-sample comparisons. The 16S rRNA amplicon sequencing method was also employed to monitor population dynamics in a ready-to-eat rice meal, incubated over a period of 12 days at 7 °C. The most predominant outgrowth was observed by the genera Leuconostoc, Bacillus, and Paenibacillus. Analysis of meals pre-treated with weak acids showed inhibition of outgrowth of these three genera. The specificity of the amplicon synthesis was improved by the design of oligonucleotides that minimize the amplification of 16S rRNA genes from chloroplasts originating from plant-based material present in the food. This study shows that the composition of complex spoilage populations, including bacterial spores, can be monitored in complex food matrices by bar-coded amplicon sequencing in a quantitative manner. In order to allow sample

  18. 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

    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...... nanoparticles to loops of LAMP amplicons. Melting studies reveal that true positive and spurious amplicons have different melting points and this allows us to discriminate between them. This is found to be in a good agreement with subsequent studies on real-time sequence-specific discrimination of LAMP...... amplicons. The specific binding causes clustering of magnetic nanoparticles via binding to multiple sites (loops) emerging in the elongation phase of LAMP. Formation of nanoclusters is monitored via the depletion of the optomagnetic signal due to free nanoparticles. After sequence-specific validation, we...

  19. 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.

  20. 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.

  1. 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.

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

    OpenAIRE

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

    2015-01-01

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

  3. 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

  4. Determinants of National Guard Mental Health Service Utilization in VA versus Non-VA Settings.

    Science.gov (United States)

    Gorman, Lisa A; Sripada, Rebecca K; Ganoczy, Dara; Walters, Heather M; Bohnert, Kipling M; Dalack, Gregory W; Valenstein, Marcia

    2016-10-01

    To determine associations between need, enabling, and predisposing factors with mental health service use among National Guard soldiers in the first year following a combat deployment to Iraq or Afghanistan. Primary data were collected between 2011 and 2013 from 1,426 Guard soldiers representing 36 units. Associations between Guard soldier factors and any mental health service use were assessed using multivariable logistic regression models in a cross-sectional study. Further analysis among service users (N = 405) assessed VA treatment versus treatment in other settings. Fifty-six percent of Guard soldiers meeting cutoffs on symptom scales received mental health services with 81 percent of those reporting care from the VA. Mental health service use was associated with need (mental health screens and physical health) and residing in micropolitan communities. Among service users, predisposing factors (middle age range and female gender) and enabling factors (employment, income above $50,000, and private insurance) were associated with greater non-VA services use. Overall service use was strongly associated with need, whereas sector of use (non-VA vs. VA) was insignificantly associated with need but strongly associated with enabling factors. These findings have implications for the recent extension of veteran health coverage to non-VA providers. © Health Research and Educational Trust.

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

    Science.gov (United States)

    2016-03-16

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

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

    Science.gov (United States)

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

    2015-01-01

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

  7. 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.

  8. 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.

  9. CASPER: context-aware scheme for paired-end reads from high-throughput amplicon sequencing.

    Science.gov (United States)

    Kwon, Sunyoung; Lee, Byunghan; Yoon, Sungroh

    2014-01-01

    Merging the forward and reverse reads from paired-end sequencing is a critical task that can significantly improve the performance of downstream tasks, such as genome assembly and mapping, by providing them with virtually elongated reads. However, due to the inherent limitations of most paired-end sequencers, the chance of observing erroneous bases grows rapidly as the end of a read is approached, which becomes a critical hurdle for accurately merging paired-end reads. Although there exist several sophisticated approaches to this problem, their performance in terms of quality of merging often remains unsatisfactory. To address this issue, here we present a context-aware scheme for paired-end reads (CASPER): a computational method to rapidly and robustly merge overlapping paired-end reads. Being particularly well suited to amplicon sequencing applications, CASPER is thoroughly tested with both simulated and real high-throughput amplicon sequencing data. According to our experimental results, CASPER significantly outperforms existing state-of-the art paired-end merging tools in terms of accuracy and robustness. CASPER also exploits the parallelism in the task of paired-end merging and effectively speeds up by multithreading. CASPER is freely available for academic use at http://best.snu.ac.kr/casper.

  10. 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...

  11. 76 FR 79067 - Payment or Reimbursement for Emergency Treatment Furnished by Non-VA Providers in Non-VA...

    Science.gov (United States)

    2011-12-21

    ... document amends the Department of Veterans Affairs (VA) medical regulations concerning emergency hospital.... We received three comments related to the transfer of veterans from non-VA hospitals. The commenters... VA setting. If the veteran who has an accident on a military installation is personally financially...

  12. 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 ...

  13. 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 …

  14. 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...

  15. 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...

  16. 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.

  17. 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

    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......Cyanobacteria are thought to be the main N2-fixing organisms (diazotrophs) in marine pelagic waters, but recent molecular analyses indicate that non-cyanobacterial diazotrophs are also present and active. Existing data are, however, restricted geographically and by limited sequencing depths. Our...... 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...

  18. Amplicon Sequencing Reveals Microbiological Signatures in Spent Nuclear Fuel Storage Basins

    Directory of Open Access Journals (Sweden)

    Christopher E. Bagwell

    2018-03-01

    Full Text Available Water quality is an important determinant for the structural integrity of alloy cladded fuels and assemblies during long-term wet storage. Detailed characterization of a water filled storage basin for spent nuclear reactor fuel was performed following the formation and proliferation of an amorphous white flocculent. White precipitant was sampled throughout the storage basin for chemical and spectroscopic characterization, and environmental DNA was extracted for 454 pyrosequencing of bacterial 16S rRNA gene diversity. Accordingly, spectroscopic analyses indicated the precipitant to be primarily amorphous to crystalline aluminum (oxy hydroxides with minor associated elemental components including Fe, Si, Ti, and U. High levels of organic carbon were co-localized with the precipitant relative to bulk dissolved organic concentrations. Bacterial densities were highly variable between sampling locations and with depth within the water filled storage basin; cell numbers ranged from 4 × 103to 4 × 104 cells/mL. Bacterial diversity that was physically associated with the aluminum (oxy hydroxide complexes exceeded an estimated 4,000 OTUs/amplicon library (3% cutoff and the majority of sequences were aligned to the families Burkholderiaceae (23%, Nitrospiraceae (23%, Hyphomicrobiaceae (17%, and Comamonadaceae (6%. We surmise that episodic changes in the physical and chemical properties of the basin contribute to the polymerization of aluminum (oxy hydroxides, which in turn can chemisorb nutrients, carbon ligands and bacterial cells from the surrounding bulk aqueous phase. As such, these precipitants should establish favorable microhabitats for bacterial colonization and growth. Comparative analyses of 16S rRNA gene amplicon libraries across a selection of natural and engineered aquatic ecosystems were performed and microbial community and taxonomic signatures unique to the spent nuclear fuel (SNF storage basin environment were revealed. These insights

  19. 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.

  20. 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:…

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

    Science.gov (United States)

    Minero, Gabriel Antonio S; Nogueira, Catarina; Rizzi, Giovanni; Tian, Bo; Fock, Jeppe; Donolato, Marco; Strömberg, Mattias; Hansen, Mikkel F

    2017-09-08

    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 nanoparticles to loops of LAMP amplicons. Melting studies reveal that true positive and spurious amplicons have different melting points and this allows us to discriminate between them. This is found to be in a good agreement with subsequent studies on real-time sequence-specific discrimination of LAMP amplicons. The specific binding causes clustering of magnetic nanoparticles via binding to multiple sites (loops) emerging in the elongation phase of LAMP. Formation of nanoclusters is monitored via the depletion of the optomagnetic signal due to free nanoparticles. After sequence-specific validation, we claim detection of down to 100 fM of Dengue target after 20 min of LAMP with a contamination background.

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

    Science.gov (United States)

    2016-09-12

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

  3. 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

  4. 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

  5. 16S rRNA Amplicon Sequencing for Epidemiological Surveys of Bacteria in Wildlife.

    Science.gov (United States)

    Galan, Maxime; Razzauti, Maria; Bard, Emilie; Bernard, Maria; Brouat, Carine; Charbonnel, Nathalie; Dehne-Garcia, Alexandre; Loiseau, Anne; Tatard, Caroline; Tamisier, Lucie; Vayssier-Taussat, Muriel; Vignes, Helene; Cosson, Jean-François

    2016-01-01

    The human impact on natural habitats is increasing the complexity of human-wildlife interactions and leading to the emergence of infectious diseases worldwide. Highly successful synanthropic wildlife species, such as rodents, will undoubtedly play an increasingly important role in transmitting zoonotic diseases. We investigated the potential for recent developments in 16S rRNA amplicon sequencing to facilitate the multiplexing of the large numbers of samples needed to improve our understanding of the risk of zoonotic disease transmission posed by urban rodents in West Africa. In addition to listing pathogenic bacteria in wild populations, as in other high-throughput sequencing (HTS) studies, our approach can estimate essential parameters for studies of zoonotic risk, such as prevalence and patterns of coinfection within individual hosts. However, the estimation of these parameters requires cleaning of the raw data to mitigate the biases generated by HTS methods. We present here an extensive review of these biases and of their consequences, and we propose a comprehensive trimming strategy for managing these biases. We demonstrated the application of this strategy using 711 commensal rodents, including 208 Mus musculus domesticus , 189 Rattus rattus , 93 Mastomys natalensis , and 221 Mastomys erythroleucus , collected from 24 villages in Senegal. Seven major genera of pathogenic bacteria were detected in their spleens: Borrelia , Bartonella , Mycoplasma , Ehrlichia , Rickettsia , Streptobacillus , and Orientia . Mycoplasma , Ehrlichia , Rickettsia , Streptobacillus , and Orientia have never before been detected in West African rodents. Bacterial prevalence ranged from 0% to 90% of individuals per site, depending on the bacterial taxon, rodent species, and site considered, and 26% of rodents displayed coinfection. The 16S rRNA amplicon sequencing strategy presented here has the advantage over other molecular surveillance tools of dealing with a large spectrum of

  6. 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.

  7. 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.

  8. 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.

  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. 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.

  11. High-Throughput Analysis of DNA Break-Induced Chromosome Rearrangements by Amplicon Sequencing.

    Science.gov (United States)

    Brown, Alexander J; Al-Soodani, Aneesa T; Saul, Miles; Her, Stephanie; Garcia, Juan C; Ramsden, Dale A; Her, Chengtao; Roberts, Steven A

    2018-01-01

    The mechanistic understanding of how DNA double-strand breaks (DSB) are repaired is rapidly advancing in part due to the advent of inducible site-specific break model systems as well as the employment of next-generation sequencing (NGS) technologies to sequence repair junctions at high depth. Unfortunately, the sheer volume of data produced by these methods makes it difficult to analyze the structure of repair junctions manually or with other general-purpose software. Here, we describe methods to produce amplicon libraries of DSB repair junctions for sequencing, to map the sequencing reads, and then to use a robust, custom python script, Hi-FiBR, to analyze the sequence structure of mapped reads. The Hi-FiBR analysis processes large data sets quickly and provides information such as number and type of repair events, size of deletion, size of insertion and inserted sequence, microhomology usage, and whether mismatches are due to sequencing error or biological effect. The analysis also corrects for common alignment errors generated by sequencing read mapping tools, allowing high-throughput analysis of DSB break repair fidelity to be accurately conducted regardless of which suite of NGS analysis software is available. © 2018 Elsevier Inc. All rights reserved.

  12. Species tree estimation of North American chorus frogs (Hylidae: Pseudacris) with parallel tagged amplicon sequencing.

    Science.gov (United States)

    Barrow, Lisa N; Ralicki, Hannah F; Emme, Sandra A; Lemmon, Emily Moriarty

    2014-06-01

    The field of phylogenetics is changing rapidly with the application of high-throughput sequencing to non-model organisms. Cost-effective use of this technology for phylogenetic studies, which often include a relatively small portion of the genome but several taxa, requires strategies for genome partitioning and sequencing multiple individuals in parallel. In this study we estimated a multilocus phylogeny for the North American chorus frog genus Pseudacris using anonymous nuclear loci that were recently developed using a reduced representation library approach. We sequenced 27 nuclear loci and three mitochondrial loci for 44 individuals on 1/3 of an Illumina MiSeq run, obtaining 96.5% of the targeted amplicons at less than 20% of the cost of traditional Sanger sequencing. We found heterogeneity among gene trees, although four major clades (Trilling Frog, Fat Frog, crucifer, and West Coast) were consistently supported, and we resolved the relationships among these clades for the first time with strong support. We also found discordance between the mitochondrial and nuclear datasets that we attribute to mitochondrial introgression and a possible selective sweep. Bayesian concordance analysis in BUCKy and species tree analysis in (*)BEAST produced largely similar topologies, although we identify taxa that require additional investigation in order to clarify taxonomic and geographic range boundaries. Overall, we demonstrate the utility of a reduced representation library approach for marker development and parallel tagged sequencing on an Illumina MiSeq for phylogenetic studies of non-model organisms. Copyright © 2014 Elsevier Inc. All rights reserved.

  13. 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.

  14. 33 CFR 80.510 - Chesapeake Bay Entrance, VA.

    Science.gov (United States)

    2010-07-01

    ... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Chesapeake Bay Entrance, VA. 80.510 Section 80.510 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Fifth District § 80.510 Chesapeake Bay Entrance, VA. A...

  15. 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...

  16. 78 FR 76061 - Authorization for Non-VA Medical Services

    Science.gov (United States)

    2013-12-16

    ... INFORMATION CONTACT: Lisa Brown, Chief, Policy Management Department, Department of Veterans Affairs, Chief..., even though the services are in theory available from the VA at other than a `local' VA facility... whether this rulemaking would result in additional administrative burdens for veterans to obtain referrals...

  17. Tropomyosin isoforms bias actin track selection by vertebrate myosin Va

    Science.gov (United States)

    Sckolnick, Maria; Krementsova, Elena B.; Warshaw, David M.; Trybus, Kathleen M.

    2016-01-01

    Tropomyosin (Tpm) isoforms decorate actin with distinct spatial and temporal localization patterns in cells and thus may function to sort actomyosin processes by modifying the actin track affinity for specific myosin isoforms. We examined the effect of three Tpm isoforms on the ability of myosin Va (myoVa) to engage with actin in vitro in the absence or presence of the cargo adapter melanophilin (Mlph), which links myoVa to Rab27a-melanosomes for in vivo transport. We show that both the myosin motor domain and the cargo adapter Mlph, which has an actin-binding domain that acts as a tether, are sensitive to the Tpm isoform. Actin–Tpm3.1 and actin–Tpm1.8 were equal or better tracks compared to bare actin for myoVa-HMM based on event frequency, run length, and speed. The full-length myoVa-Mlph complex showed high-frequency engagement with actin-Tpm3.1 but not with actin-Tpm1.8. Actin–Tpm4.2 excluded both myoVa-HMM and full-length myoVa-Mlph from productive interactions. Of importance, Tpm3.1 is enriched in the dendritic protrusions and cortical actin of melanocytes, where myoVa-Mlph engages in melanosome transport. These results support the hypothesis that Tpm isoforms constitute an “actin–Tpm code” that allows for spatial and temporal sorting of actomyosin function in the cell. PMID:27535431

  18. Microcirculatory assessment of patients under VA-ECMO

    NARCIS (Netherlands)

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

    2016-01-01

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

  19. Microcirculatory assessment of patients under VA-ECMO

    NARCIS (Netherlands)

    Kara, Atila; Akin, Sakir; Dos Reis Miranda, Dinis; Struijs, Ard; Caliskan, Kadir; van Thiel, Robert J.; Dubois, Eric A.; de Wilde, Wouter; Zijlstra, Felix; Gommers, Diederik; Ince, Can

    2016-01-01

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

  20. 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.

  1. 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

  2. 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 ...

  3. 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.

  4. 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...

  5. DNA Methylation Analysis by Bisulfite Conversion Coupled to Double Multiplexed Amplicon-Based Next-Generation Sequencing (NGS).

    Science.gov (United States)

    Bashtrykov, Pavel; Jeltsch, Albert

    2018-01-01

    Methylation of cytosine bases in DNA is one of the main epigenetic signals regulating gene expression and chromatin structure. The distribution of DNA methylation in the genome has a cell-type-specific pattern and can be modulated by internal or external stimuli. One of the most powerful approaches to investigate DNA methylation patterns is bisulfite conversion of the DNA followed by DNA sequencing, which allows to determine methylation patterns at a single-cytosine resolution. Here, we present a protocol for bisulfite DNA methylation analysis of targeted genomic regions using amplicon-based next-generation sequencing (NGS) on an Illumina sequencing system. We use a PCR-free library generation approach and implement a nested strategy for double molecular barcoding of samples (combining indexing of adapters and in-line barcoding of individual amplicons) which allows highly multiplexed sequencing. Also, we discuss the main limitations of this technology in particular in relation to clonal DNA amplification and other PCR artifacts.

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

    DEFF Research Database (Denmark)

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

    Wastewater treatment is the world’s largest biotechnological processes and a perfect model system for microbial ecology as the habitat is well defined and replicated all over the world. Extensive investigations on Danish wastewater treatment plants using fluorescent in situ hybridization have...... the existing knowledge on core genera with high-throughput amplicon sequencing, plant design and process data in order to identify interactions and community shaping factors. We investigated 25 Danish full-scale wastewater treatment plants with nutrient removal over a period of 7 years with two to four samples...... 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...

  7. 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.

  8. Time for the VA to clean up its act

    Directory of Open Access Journals (Sweden)

    Robbins RA

    2015-06-01

    Full Text Available No abstract available. Article truncated after 150 words. One year after a Veterans Affairs (VA scandal was ignited here in Phoenix, the number of veterans on wait lists is 50 percent higher than at the same time last year, according to VA data (1. The VA is also facing a nearly $3 billion budget shortfall. VA Secretary Bob McDonald has asked for “flexibility” to reallocate billions of dollars in clinical funds to cover the shortfall. Since the scandal broke last year, VA providers have increased their workloads, adding 2.7 million more appointments than the previous year. However, the VA has played "games" with patient eligibility for years. When money was plentiful VA administrators would open the doors to patients since the following years' budgets were based on the number of patients seen. However, when money was tight, the doors would be slammed shut leaving many patients in the lurch scrambling to obtain health care elsewhere. Now it appears ...

  9. 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

  10. 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 …

  11. 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...

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

    Data.gov (United States)

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

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

    Data.gov (United States)

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

  14. 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...

  15. Evaluating the accuracy of amplicon-based microbiome computational pipelines on simulated human gut microbial communities.

    Science.gov (United States)

    Golob, Jonathan L; Margolis, Elisa; Hoffman, Noah G; Fredricks, David N

    2017-05-30

    Microbiome studies commonly use 16S rRNA gene amplicon sequencing to characterize microbial communities. Errors introduced at multiple steps in this process can affect the interpretation of the data. Here we evaluate the accuracy of operational taxonomic unit (OTU) generation, taxonomic classification, alpha- and beta-diversity measures for different settings in QIIME, MOTHUR and a pplacer-based classification pipeline, using a novel software package: DECARD. In-silico we generated 100 synthetic bacterial communities approximating human stool microbiomes to be used as a gold-standard for evaluating the colligative performance of microbiome analysis software. Our synthetic data closely matched the composition and complexity of actual healthy human stool microbiomes. Genus-level taxonomic classification was correctly done for only 50.4-74.8% of the source organisms. Miscall rates varied from 11.9 to 23.5%. Species-level classification was less successful, (6.9-18.9% correct); miscall rates were comparable to those of genus-level targets (12.5-26.2%). The degree of miscall varied by clade of organism, pipeline and specific settings used. OTU generation accuracy varied by strategy (closed, de novo or subsampling), reference database, algorithm and software implementation. Shannon diversity estimation accuracy correlated generally with OTU-generation accuracy. Beta-diversity estimates with Double Principle Coordinate Analysis (DPCoA) were more robust against errors introduced in processing than Weighted UniFrac. The settings suggested in the tutorials were among the worst performing in all outcomes tested. Even when using the same classification pipeline, the specific OTU-generation strategy, reference database and downstream analysis methods selection can have a dramatic effect on the accuracy of taxonomic classification, and alpha- and beta-diversity estimation. Even minor changes in settings adversely affected the accuracy of the results, bringing them far from the

  16. 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.

  17. 76 FR 61150 - Enhanced-Use Lease (EUL) of Department of Veterans Affairs (VA) Real Property at the VA...

    Science.gov (United States)

    2011-10-03

    ... Affairs. ACTION: Notice of Intent to Enter into an Enhanced-Use Lease. SUMMARY: The Secretary of VA... homelessness; and provide a supportive services program that guides resident Veterans toward attaining long...

  18. 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.

  19. 77 FR 60746 - Proposed Information Collection (VA/DOD Joint Disability Evaluation Board Claim) Activity...

    Science.gov (United States)

    2012-10-04

    ... participation in a joint DOD/VA Disability Evaluation Board and VA compensation after separation from service... retirement, and VA disability compensation. VA Form 21- 0819 will be used to gather the necessary information... Secretary. Denise McLamb, Program Analyst, Enterprise Records Service. BILLING CODE 8320-01-P ...

  20. 78 FR 76412 - Agency Information Collection (VA National Rehabilitation Special Events, Event Registration...

    Science.gov (United States)

    2013-12-17

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF VETERANS... Application, VA Form 0924t. e. National Veterans Wheelchair Games Event Application, VA Form 0925b. f. Voluntary Service Application, VA Form 0925d. g. National Veteran Golden Age Games Application, VA Form 0926...

  1. 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

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

    DEFF Research Database (Denmark)

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

    RNA gene amplicon sequencing is rapid, cheap, high throughput, and has high taxonomic resolution. However, biases are introduced in multiple steps of this approach, including non-representative DNA extraction and uneven taxonomic coverage of selected PCR primers, potentially giving a skewed view...... parameters involving harsher lysis conditions than recommended for the commercial kit, and appeared to be similar for both the mesophilic and thermophilic reactor biomass samples. The community profiling was found to be greatly influenced by the selected PCR primers, and showed that in silico designed...

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

    Science.gov (United States)

    Andersen, Jeppe D; Pereira, Vania; Pietroni, Carlotta; Mikkelsen, Martin; Johansen, Peter; Børsting, Claus; Morling, Niels

    2014-08-01

    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.

  4. 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.

  5. 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

  6. |SE|S|AM|E| Barcode: NGS-oriented software for amplicon characterization--application to species and environmental barcoding.

    Science.gov (United States)

    Piry, S; Guivier, E; Realini, A; Martin, J-F

    2012-11-01

    Progress in NGS technologies has opened up new opportunities for characterizing biodiversity, both for individual specimen identification and for environmental barcoding. Although the amount of data available to biologist is increasing, user-friendly tools to facilitate data analysis have yet to be developed. Our aim, with |SE|S|AM|E| Barcode, is to provide such support through a unified platform. The sequences are analysed through a pipeline that (i) processes NGS amplicon runs, filtering markers and samples, (ii) builds reference libraries and finally (iii) identifies (barcodes) the sequences in each amplicon from the reference library. We use a simulated data set for specimen identification and a recently published data set for environmental barcoding to validate the method. The results obtained are consistent with the expected characterizations (in silico and previously published, respectively). |SE|S|AM|E| Barcode and its documentation are freely available under the Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported Licence for Windows and Linux from http://www1.montpellier.inra.fr/CBGP/NGS/. © 2012 Blackwell Publishing Ltd.

  7. 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.

  8. A Systematic Assessment of Accuracy in Detecting Somatic Mosaic Variants by Deep Amplicon Sequencing: Application to NF2 Gene.

    Directory of Open Access Journals (Sweden)

    Elisa Contini

    Full Text Available The accurate detection of low-allelic variants is still challenging, particularly for the identification of somatic mosaicism, where matched control sample is not available. High throughput sequencing, by the simultaneous and independent analysis of thousands of different DNA fragments, might overcome many of the limits of traditional methods, greatly increasing the sensitivity. However, it is necessary to take into account the high number of false positives that may arise due to the lack of matched control samples. Here, we applied deep amplicon sequencing to the analysis of samples with known genotype and variant allele fraction (VAF followed by a tailored statistical analysis. This method allowed to define a minimum value of VAF for detecting mosaic variants with high accuracy. Then, we exploited the estimated VAF to select candidate alterations in NF2 gene in 34 samples with unknown genotype (30 blood and 4 tumor DNAs, demonstrating the suitability of our method. The strategy we propose optimizes the use of deep amplicon sequencing for the identification of low abundance variants. Moreover, our method can be applied to different high throughput sequencing approaches to estimate the background noise and define the accuracy of the experimental design.

  9. 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.

  10. 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.

  11. 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, Prestorative nursing care, CLC Veterans had higher user rates (33.5% vs. 30.6%, Prestorative nursing care (coefficient=5.48±0.37, Prestorative nursing care both before and after risk adjustment.

  12. REACH VA: Moving from Translation to System Implementation.

    Science.gov (United States)

    Nichols, Linda O; Martindale-Adams, Jennifer; Burns, Robert; Zuber, Jeffrey; Graney, Marshall J

    2016-02-01

    Resources for Enhancing All Caregivers Health in the Department of Veterans Affairs (REACH VA) has been implemented in the VA system as a national program for caregivers. We describe the trajectory of REACH VA from national randomized clinical trial through translation to national implementation. The implementation is examined through the six stages of the Fixsen and Blasé implementation process model: exploration and adoption, program installation, initial implementation, full operation, innovation, and sustainability. Different drivers that move the implementation process forward are important at each stage, including staff selection, staff training, consultation and coaching, staff evaluation, administrative support, program evaluation/fidelity, and systems interventions. Caregivers in the REACH VA 4 session intervention currently implemented in the VA had similar outcomes to longer REACH interventions, including Resources for Enhancing Alzheimer's Caregivers Health (REACH II). Caregivers experienced significant decreases in burden, depression, anxiety, number of troubling patient behaviors reported, caregiving frustrations, stress symptoms (feeling overwhelmed, feeling like crying, being frustrated as a result of caregiving, being lonely), and general stress. Effect sizes (Cohen's d) for these significant variables were between small and medium ranging from .24 to .46. The implementation of REACH VA provides a road map for implementation of other behavioral interventions in health care delivery settings. Lessons learned include the importance of implementing a proven, needed intervention, support from both leadership and clinical staff, willingness to respond to staff and organization needs and modify the intervention while preserving its integrity, and fitting the intervention into ongoing routines and practices. Published by Oxford University Press on behalf of the Gerontological Society of America 2014.

  13. Algorithm for post-clustering curation of DNA amplicon data yields reliable biodiversity estimates

    DEFF Research Database (Denmark)

    Froslev, Tobias Guldberg; Kjoller, Rasmus; Bruun, Hans Henrik

    2017-01-01

    DNA metabarcoding is promising for cost-effective biodiversity monitoring, but reliable diversity estimates are difficult to achieve and validate. Here we present and validate a method, called LULU, for removing erroneous molecular operational taxonomic units (OTUs) from community data derived by...

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

    Science.gov (United States)

    Nichols, Erin K; Byass, Peter; Chandramohan, Daniel; Clark, Samuel J; Flaxman, Abraham D; Jakob, Robert; Leitao, Jordana; Maire, Nicolas; Rao, Chalapati; Riley, Ian; Setel, Philip W

    2018-01-01

    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.

  15. Hospital Distance and Readmissions Among VA-Medicare Dual-Enrolled Veterans.

    Science.gov (United States)

    Wong, Edwin S; Rinne, Seppo T; Hebert, Paul L; Cook, Meredith A; Liu, Chuan-Fen

    2016-09-01

    Geographic access to inpatient care at the Veterans Affairs (VA) Health Care System is challenging for many veterans with chronic obstructive pulmonary disease (COPD) given relatively few VA hospitals nationwide. Veterans with lengthy travel distances may obtain non-VA care, particularly those dually enrolled in Medicare. Our primary objective was to assess whether distance from VA patients' residence to the nearest VA and non-VA hospitals was associated with 30-day all-cause readmission and the system where patients were readmitted (VA or Medicare). Using VA and Medicare administrative data, we identified 21,273 patients hospitalized for COPD between October 2008 and September 2011 and dually enrolled in VA and fee-for-service Medicare. Outcome variables were dichotomous measures denoting readmission for any cause within 30 days following discharge and whether the readmission occurred in a non-VA hospital through Medicare. Distance to the nearest hospital was defined as the number of miles between patients' residence ZIP code and the ZIP code of the nearest VA and non-VA hospital accepting Medicare, respectively. Probit models with sample selection were applied to examine the relationship between hospital distance and outcome measures. Respective distances to the nearest VA and non-VA hospital were not associated with 30-day all-cause readmission. Greater distance to the nearest VA hospital was associated with a greater conditional probability of choosing non-VA hospitals for readmission. COPD patients with poor geographic access to VA hospitals did not forgo subsequent inpatient care following their index hospitalization, but they were more likely to seek non-VA substitutes. © 2016 National Rural Health Association.

  16. 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

  17. Community analysis of picocyanobacteria in an oligotrophic lake by cloning 16S rRNA gene and 16S rRNA gene amplicon sequencing.

    Science.gov (United States)

    Fujimoto, Naoshi; Mizuno, Keigo; Yokoyama, Tomoki; Ohnishi, Akihiro; Suzuki, Masaharu; Watanabe, Satoru; Komatsu, Kenji; Sakata, Yoichi; Kishida, Naohiro; Akiba, Michihiro; Matsukura, Satoko

    2015-01-01

    In this study, the picocyanobacterial species composition of Lake Miyagase was examined by analyzing the 16S rRNA gene in a clone library and by amplicon sequencing using a benchtop next-generation sequencer. Five separate samples were analyzed from different days over a ten-month period. In the picocyanobacterial lineage, 9 and 12 OTUs were identified from a clone library and by amplicon sequencing, respectively. Both analyses suggested that a picocyanobacterium related to Synechococcus sp. MW6B4 was dominant in Lake Miyagase. Our findings suggest that 16S rRNA gene amplicon sequencing enables detailed evaluation of picocyanobacteria composition. One OTU identified was found to be a novel cluster that does not group with any of the known freshwater picocyanobacteria.

  18. 77 FR 70893 - Authorization for Non-VA Medical Services

    Science.gov (United States)

    2012-11-28

    ... INFORMATION: Over the past two decades, the healthcare industry has increasingly emphasized providing care in... healthcare to veterans, VA is, like the rest of the healthcare industry, economically unable to provide all... procedure, Alcohol abuse, Alcoholism, Claims, Day care, Dental health, Drug abuse, Government contracts...

  19. 77 FR 70967 - Authorization for Non-VA Medical Services

    Science.gov (United States)

    2012-11-28

    .... SUPPLEMENTARY INFORMATION: Over the past two decades, the healthcare industry has increasingly emphasized... expand the delivery of healthcare to veterans, VA is, like the rest of the healthcare industry... Subjects in 38 CFR Part 17 Administrative practice and procedure, Alcohol abuse, Alcoholism, Claims, Day...

  20. VA Is Here for the People Who Support Our Veterans

    Science.gov (United States)

    ... Expect Resource Locator Veterans Live Chat Veterans Text Homeless Veterans Live Chat Military Live Chat Deaf - Hard of Hearing Contact Us About About the Veterans Crisis Line FAQs Veteran Suicide VA is here for the people who support our Veterans. Whether you’re a ...

  1. 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 …

  2. 77 FR 67063 - VA Directive 0005 on Scientific Integrity

    Science.gov (United States)

    2012-11-08

    ... 20420. Call (202) 461-4902 for an appointment. Comments A. Purpose, Responsibilities, and Definitions... policies that: Foster a culture of transparency, integrity, and ethical behavior in the development and... ``inappropriate influence.'' The definition of ``inappropriate influence'' should be more explicit. VA Response...

  3. HPV Genotyping of Modified General Primer-Amplicons Is More Analytically Sensitive and Specific by Sequencing than by Hybridization.

    Science.gov (United States)

    Meisal, Roger; Rounge, Trine Ballestad; Christiansen, Irene Kraus; Eieland, Alexander Kirkeby; Worren, Merete Molton; Molden, Tor Faksvaag; Kommedal, Øyvind; Hovig, Eivind; Leegaard, Truls Michael; Ambur, Ole Herman

    2017-01-01

    Sensitive and specific genotyping of human papillomaviruses (HPVs) is important for population-based surveillance of carcinogenic HPV types and for monitoring vaccine effectiveness. Here we compare HPV genotyping by Next Generation Sequencing (NGS) to an established DNA hybridization method. In DNA isolated from urine, the overall analytical sensitivity of NGS was found to be 22% higher than that of hybridization. NGS was also found to be the most specific method and expanded the detection repertoire beyond the 37 types of the DNA hybridization assay. Furthermore, NGS provided an increased resolution by identifying genetic variants of individual HPV types. The same Modified General Primers (MGP)-amplicon was used in both methods. The NGS method is described in detail to facilitate implementation in the clinical microbiology laboratory and includes suggestions for new standards for detection and calling of types and variants with improved resolution.

  4. HPV Genotyping of Modified General Primer-Amplicons Is More Analytically Sensitive and Specific by Sequencing than by Hybridization.

    Directory of Open Access Journals (Sweden)

    Roger Meisal

    Full Text Available Sensitive and specific genotyping of human papillomaviruses (HPVs is important for population-based surveillance of carcinogenic HPV types and for monitoring vaccine effectiveness. Here we compare HPV genotyping by Next Generation Sequencing (NGS to an established DNA hybridization method. In DNA isolated from urine, the overall analytical sensitivity of NGS was found to be 22% higher than that of hybridization. NGS was also found to be the most specific method and expanded the detection repertoire beyond the 37 types of the DNA hybridization assay. Furthermore, NGS provided an increased resolution by identifying genetic variants of individual HPV types. The same Modified General Primers (MGP-amplicon was used in both methods. The NGS method is described in detail to facilitate implementation in the clinical microbiology laboratory and includes suggestions for new standards for detection and calling of types and variants with improved resolution.

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

    Directory of Open Access Journals (Sweden)

    Leho Tedersoo

    2015-05-01

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

  6. Bacterial diversity in Solenopsis invicta and Solenopsis geminata ant colonies characterized by 16S amplicon 454 pyrosequencing.

    Science.gov (United States)

    Ishak, Heather D; Plowes, Rob; Sen, Ruchira; Kellner, Katrin; Meyer, Eli; Estrada, Dora A; Dowd, Scot E; Mueller, Ulrich G

    2011-05-01

    Social insects harbor diverse assemblages of bacterial microbes, which may play a crucial role in the success or failure of biological invasions. The invasive fire ant Solenopsis invicta (Formicidae, Hymenoptera) is a model system for understanding the dynamics of invasive social insects and their biological control. However, little is known about microbes as biotic factors influencing the success or failure of ant invasions. This pilot study is the first attempt to characterize and compare microbial communities associated with the introduced S. invicta and the native Solenopsis geminata in the USA. Using 16S amplicon 454 pyrosequencing, bacterial communities of workers, brood, and soil from nest walls were compared between neighboring S. invicta and S. geminata colonies at Brackenridge Field Laboratory, Austin, Texas, with the aim of identifying potential pathogenic, commensal, or mutualistic microbial associates. Two samples of S. geminata workers showed high counts of Spiroplasma bacteria, a known pathogen or mutualist of other insects. A subsequent analysis using PCR and sequencing confirmed the presence of Spiroplasma in additional colonies of both Solenopsis species. Wolbachia was found in one alate sample of S. geminata, while one brood sample of S. invicta had a high count of Lactococcus. As expected, ant samples from both species showed much lower microbial diversity than the surrounding soil. Both ant species had similar overall bacterial diversities, although little overlap in specific microbes. To properly characterize a single bacterial community associated with a Solenopsis ant sample, rarefaction analyses indicate that it is necessary to obtain 5,000-10,000 sequences. Overall, 16S amplicon 454 pyrosequencing appears to be a cost-effective approach to screen whole microbial diversity associated with invasive ant species.

  7. 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.

  8. Algorithm for post-clustering curation of DNA amplicon data yields reliable biodiversity estimates

    DEFF Research Database (Denmark)

    Frøslev, Tobias Guldberg; Kjøller, Rasmus; Bruun, Hans Henrik

    2017-01-01

    DNA metabarcoding is promising for cost-effective biodiversity monitoring, but reliable diversity estimates are difficult to achieve and validate. Here we present and validate a method, called LULU, for removing erroneous molecular operational taxonomic units (OTUs) from community data derived...... soil from 130 sites in Denmark spanning major environmental gradients. OTU tables are produced with several different OTU definition algorithms and subsequently curated with LULU, and validated against field survey data. LULU curation consistently improves α-diversity estimates and other biodiversity...... metrics, and does not require a sequence reference database; thus, it represents a promising method for reliable biodiversity estimation....

  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

    .... The only exceptions are loans made to veterans receiving VA compensation for service-connected disabilities, (or veterans whom, but for receipt of retirement pay, would be entitled to receive compensation...: September 29, 2010. By direction of the Secretary. Denise McLamb, Program Analyst, Enterprise Records...

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    Science.gov (United States)

    2010-10-06

    .... The only exceptions are loans made to veterans receiving VA compensation for service-connected disabilities, (or veterans whom, but for receipt of retirement pay, would be entitled to receive compensation...: September 29, 2010. By direction of the Secretary. Denise McLamb, Program Analyst, Enterprise Records...

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    Science.gov (United States)

    2010-12-16

    ... guaranteed. The only exceptions are loans made to veterans receiving VA compensation for service-connected disabilities, (or veterans whom, but for receipt of retirement pay, would be entitled to receive compensation...,000. Dated: December 10, 2010. By direction of the Secretary. Denise McLamb, Program Analyst...

  12. 75 FR 33216 - Payment or Reimbursement for Emergency Treatment Furnished by Non-VA Providers in Non-VA...

    Science.gov (United States)

    2010-06-11

    ... grammatical errors and updating obsolete citations. DATES: Comments must be received by VA on or before August... amendments made to 38 U.S.C. 1725 and 1728, and would make technical changes such as correcting grammatical errors and updating obsolete regulatory citations: 38 CFR 17.120, 17.121, 17.1002, 17.1005, 17.1006, and...

  13. VA Health Care. Additional Efforts to Better Assess Joint Ventures Needed

    National Research Council Canada - National Science Library

    2008-01-01

    .... VA has maintained eight joint ventures with DOD across the country. VA has also developed partnerships, or affiliations, with university medical schools to obtain health care services for veterans and provide training to medical residents...

  14. Number of Veterans who Used VA Benefits by State FY2016

    Data.gov (United States)

    Department of Veterans Affairs — This file shows the number of Veterans in each state who used each of 7 VA benefits during fiscal year 2016. It also shows the unique count of users across all VA...

  15. 78 FR 39599 - Safety Zone; Fort Monroe Fireworks Display, Chesapeake Bay, Hampton, VA

    Science.gov (United States)

    2013-07-02

    ...-AA00 Safety Zone; Fort Monroe Fireworks Display, Chesapeake Bay, Hampton, VA AGENCY: Coast Guard, DHS... navigable waters of the Chesapeake Bay in Hampton, VA to support the Fort Monroe Fireworks. This action is... Authority will host a fireworks display in the Chesapeake Bay off of Fort Monroe in Hampton, VA. The...

  16. 77 FR 35308 - Proposed Amendment of Restricted Area R-6601; Fort A.P. Hill, VA

    Science.gov (United States)

    2012-06-13

    ...-0561; Airspace Docket No. 12-AEA-7] Proposed Amendment of Restricted Area R-6601; Fort A.P. Hill, VA..., Fort A.P. Hill, VA. The U. S. Army requested this action to provide the additional airspace needed to... Garrison, Fort A.P. Hill, VA 22427; telephone: (804) 633-8223. FOR FURTHER INFORMATION CONTACT: Paul...

  17. 75 FR 3968 - Fund Availability Under the VA Homeless Providers Grant and Per Diem Program

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    2010-01-25

    ... Capital Grant component of VA's Homeless Providers Grant and Per Diem Program. This Notice contains... announces the availability of capital funds for assistance under VA's Homeless Providers Grant and Per Diem... DEPARTMENT OF VETERANS AFFAIRS Fund Availability Under the VA Homeless Providers Grant and Per...

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    Science.gov (United States)

    2010-03-01

    ... techniques or the use of other forms of information technology. Titles: a. National Disabled Veterans Winter 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...

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    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...

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

    OpenAIRE

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

    2016-01-01

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

  1. VaR: Exchange Rate Risk and Jump Risk

    Directory of Open Access Journals (Sweden)

    Fen-Ying Chen

    2010-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Brittany Turner-Ivey

    2014-08-01

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

  3. VA/DoD Collaboration Guidebook for Healthcare Research

    Science.gov (United States)

    2011-01-24

    Research Unit (NMRU), San Antonio, Texas, conducts dental research, directed energy effects, and combat casualty care research. Naval Medical...Healthcare System has been a presence at the VA-sponsored National Veterans Wheelchair Games (NVWG) since 2000, the National Disabled Veterans Winter...an opportunity to disseminate research results, educate wheelchair users on their work, and recruit wheelchair users to participate in studies. Dr

  4. 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

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

    Directory of Open Access Journals (Sweden)

    Viviana Kozina

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

  6. Simultaneous Whole Mitochondrial Genome Sequencing with Short Overlapping Amplicons Suitable for Degraded DNA Using the Ion Torrent Personal Genome Machine.

    Science.gov (United States)

    Chaitanya, Lakshmi; Ralf, Arwin; van Oven, Mannis; Kupiec, Tomasz; Chang, Joseph; Lagacé, Robert; Kayser, Manfred

    2015-12-01

    Whole mitochondrial (mt) genome analysis enables a considerable increase in analysis throughput, and improves the discriminatory power to the maximum possible phylogenetic resolution. Most established protocols on the different massively parallel sequencing (MPS) platforms, however, invariably involve the PCR amplification of large fragments, typically several kilobases in size, which may fail due to mtDNA fragmentation in the available degraded materials. We introduce a MPS tiling approach for simultaneous whole human mt genome sequencing using 161 short overlapping amplicons (average 200 bp) with the Ion Torrent Personal Genome Machine. We illustrate the performance of this new method by sequencing 20 DNA samples belonging to different worldwide mtDNA haplogroups. Additional quality control, particularly regarding the potential detection of nuclear insertions of mtDNA (NUMTs), was performed by comparative MPS analysis using the conventional long-range amplification method. Preliminary sensitivity testing revealed that detailed haplogroup inference was feasible with 100 pg genomic input DNA. Complete mt genome coverage was achieved from DNA samples experimentally degraded down to genomic fragment sizes of about 220 bp, and up to 90% coverage from naturally degraded samples. Overall, we introduce a new approach for whole mt genome MPS analysis from degraded and nondegraded materials relevant to resolve and infer maternal genetic ancestry at complete resolution in anthropological, evolutionary, medical, and forensic applications. © 2015 The Authors. **Human Mutation published by Wiley Periodicals, Inc.

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

    Directory of Open Access Journals (Sweden)

    Teresita M Porter

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

  8. Multilocus amplicon sequencing of Pseudomonas aeruginosa cystic fibrosis airways isolates collected prior to and after early antipseudomonal chemotherapy.

    Science.gov (United States)

    Fischer, Sebastian; Greipel, Leonie; Klockgether, Jens; Dorda, Marie; Wiehlmann, Lutz; Cramer, Nina; Tümmler, Burkhard

    2017-05-01

    Early antimicrobial chemotherapy can prevent or at least delay chronic cystic fibrosis (CF) airways infections with Pseudomonas aeruginosa. During a 10-year study period P. aeruginosa was detected for the first time in 54 CF patients regularly seen at the CF centre Hannover. Amplicon sequencing of 34 loci of the P. aeruginosa core genome was performed in baseline and post-treatment isolates of the 15 CF patients who had remained P. aeruginosa - positive after the first round of antipseudomonal chemotherapy. Deep sequencing uncovered coexisting alternative nucleotides at in total 33 of 55,284 examined genome positions including six non-synonymous polymorphisms in the lasR gene, a key regulator of quorum sensing. After early treatment 42 of 50 novel nucleotide substitutions had emerged in exopolysaccharide biosynthesis, efflux pump and porin genes. Early treatment selects pathoadaptive mutations in P. aeruginosa that are typical for chronic infections of CF lungs. Copyright © 2016 European Cystic Fibrosis Society. Published by Elsevier B.V. All rights reserved.

  9. 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.

  10. 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.

  11. Synthetic spike-in standards for high-throughput 16S rRNA gene amplicon sequencing.

    Science.gov (United States)

    Tourlousse, Dieter M; Yoshiike, Satowa; Ohashi, Akiko; Matsukura, Satoko; Noda, Naohiro; Sekiguchi, Yuji

    2017-02-28

    High-throughput sequencing of 16S rRNA gene amplicons (16S-seq) has become a widely deployed method for profiling complex microbial communities but technical pitfalls related to data reliability and quantification remain to be fully addressed. In this work, we have developed and implemented a set of synthetic 16S rRNA genes to serve as universal spike-in standards for 16S-seq experiments. The spike-ins represent full-length 16S rRNA genes containing artificial variable regions with negligible identity to known nucleotide sequences, permitting unambiguous identification of spike-in sequences in 16S-seq read data from any microbiome sample. Using defined mock communities and environmental microbiota, we characterized the performance of the spike-in standards and demonstrated their utility for evaluating data quality on a per-sample basis. Further, we showed that staggered spike-in mixtures added at the point of DNA extraction enable concurrent estimation of absolute microbial abundances suitable for comparative analysis. Results also underscored that template-specific Illumina sequencing artifacts may lead to biases in the perceived abundance of certain taxa. Taken together, the spike-in standards represent a novel bioanalytical tool that can substantially improve 16S-seq-based microbiome studies by enabling comprehensive quality control along with absolute quantification. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  12. Fluorescent duplex allele-specific PCR and amplicon melting for rapid homogeneous mtDNA haplogroup H screening and sensitive mixture detection.

    Directory of Open Access Journals (Sweden)

    Harald Niederstätter

    Full Text Available BACKGROUND: For large scale studies aiming at a better understanding of mitochondrial DNA (mtDNA, sequence variation in particular mt haplogroups (hgs and population structure, reliable low-cost high-throughput genotyping assays are needed. Furthermore, methods facilitating sensitive mixture detection and relative quantification of allele proportions are indispensable for the study of heteroplasmy, mitochondrial sequence evolution, and mitochondrial disorders. Here the properties of a homogeneous competitive duplex allele specific PCR (ARMS assay were scrutinized in the light of these requirements. METHODOLOGY/PRINCIPAL FINDINGS: A duplex ARMS assay amplifying either the ancestral mtDNA 2706G allele (non-hg H samples or the derived 7028C allele (hg H samples in the presence of SYBR Green fluorescent reporter dye was developed and characterized. Product detection, allele calling, and hg inference were based on the amplicon-characteristic melting-point temperatures obtained with on-line post-PCR fluorescent dissociation curve analysis (DCA. The analytical window of the assay covered at least 5 orders of magnitude of template DNA input with a detection limit in the low picogram range of genomic DNA. A set of forensically relevant test specimens was analyzed successfully. The presence of mtDNA mixtures was detected over a broad range of input DNA amounts and mixture ratios, and the estimation of allele proportions in samples with known total mtDNA content was feasible with limitations. A qualified DNA analyst successfully analyzed approximately 2,200 DNA extracts within three regular working days, without using robotic lab-equipment. By performing the amplification on-line, the assay also facilitated absolute mtDNA quantification. CONCLUSIONS: Although this assay was developed just for a particular purpose, the approach is general in that it is potentially suitable in a broad variety of assay-layouts for many other applications, including the

  13. 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...

  14. Combined amplicon pyrosequencing assays reveal presence of the apicomplexan "type-N" (cf. Gemmocystis cylindrus and Chromera velia on the Great Barrier Reef, Australia.

    Directory of Open Access Journals (Sweden)

    Jan Slapeta

    Full Text Available BACKGROUND: The coral is predominantly composed of the metabolically dependent coral host and the photosynthetic dinoflagellate Symbiodinium sp. The system as a whole interacts with symbiotic eukaryotes, bacteria and viruses. Gemmocystiscylindrus (cf. "type-N" symbiont belonging to the obligatory parasitic phylum Apicomplexa (Alveolata is ubiquitous in the Caribbean coral, but its presence in the Great Barrier Reef coral has yet to be documented. Approaches allowing identification of the healthy community from the pathogenic or saprobic organisms are needed for sustainable coral reef monitoring. METHODS & PRINCIPAL FINDINGS: We investigated the diversity of eukaryotes associated with a common reef-building corals from the southern Great Barrier Reef. We used three tag encoded 454 amplicon pyrosequencing assays targeting eukaryote small-subunit rRNA gene to demonstrate the presence of the apicomplexan type-N and a photosynthetic sister species to Apicomplexa-Chromeravelia. Amplicon pyrosequencing revealed presence of the small-subunit rRNA genes of known eukaryotic pathogens (Cryptosporidium and Cryptococcus. We therefore conducted bacterial tag encoded amplicon pyrosequencing assay for small-subunit rRNA gene to support effluent exposure of the coral. Bacteria of faecal origin (Enterobacteriales formed 41% of total sequences in contrast to 0-2% of the coral-associated bacterial communities with and without C. velia, respectively. SIGNIFICANCE: This is the first time apicomplexan type-N has been detected in the Great Barrier Reef. Eukaryote tag encoded amplicon pyrosequencing assays demonstrate presence of apicomplexan type-N and C. Velia in total coral DNA. The data highlight the need for combined approaches for eukaryotic diversity studies coupled with bacterial community assessment to achieve a more realistic goals of defining the holobiont community and assessing coral disease. With increasing evidence of Apicomplexa in coral reef

  15. Bacterial community in naturally fermented milk products of Arunachal Pradesh and Sikkim of India analysed by high-throughput amplicon sequencing

    OpenAIRE

    Shangpliang, H. Nakibapher Jones; Rai, Ranjita; Keisam, Santosh; Jeyaram, Kumaraswamy; Tamang, Jyoti Prakash

    2018-01-01

    Naturally fermented milk (NFM) products are popular ethnic fermented foods in Arunachal Pradesh and Sikkim states of India. The present study is the first to have documented the bacterial community in 54 samples of NFM products viz. chhurpi, churkam, dahi and gheu/mar by high-throughput Illumina amplicon sequencing. Metagenomic investigation showed that Firmicutes (Streptococcaceae, Lactobacillaceae) and Proteobacteria (Acetobacteraceae) were the two predominant members of the bacterial commu...

  16. 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.

  17. 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.

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

    Science.gov (United States)

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

    2016-02-25

    Microbial diversity in geothermal waters of the Unkeshwar hot springs in Maharashtra, India, was studied using 16S rRNA amplicon metagenomic sequencing. Taxonomic analysis revealed the presence of Bacteroidetes, Proteobacteria, Cyanobacteria, Actinobacteria, Archeae, and OD1 phyla. Metabolic function prediction analysis indicated a battery of biological information systems indicating rich and novel microbial diversity, with potential biotechnological applications in this niche. Copyright © 2016 Mehetre et al.

  19. Combined amplicon pyrosequencing assays reveal presence of the apicomplexan "type-N" (cf. Gemmocystis cylindrus) and Chromera velia on the Great Barrier Reef, Australia.

    Science.gov (United States)

    Slapeta, Jan; Linares, Marjorie C

    2013-01-01

    The coral is predominantly composed of the metabolically dependent coral host and the photosynthetic dinoflagellate Symbiodinium sp. The system as a whole interacts with symbiotic eukaryotes, bacteria and viruses. Gemmocystiscylindrus (cf. "type-N" symbiont) belonging to the obligatory parasitic phylum Apicomplexa (Alveolata) is ubiquitous in the Caribbean coral, but its presence in the Great Barrier Reef coral has yet to be documented. Approaches allowing identification of the healthy community from the pathogenic or saprobic organisms are needed for sustainable coral reef monitoring. We investigated the diversity of eukaryotes associated with a common reef-building corals from the southern Great Barrier Reef. We used three tag encoded 454 amplicon pyrosequencing assays targeting eukaryote small-subunit rRNA gene to demonstrate the presence of the apicomplexan type-N and a photosynthetic sister species to Apicomplexa-Chromeravelia. Amplicon pyrosequencing revealed presence of the small-subunit rRNA genes of known eukaryotic pathogens (Cryptosporidium and Cryptococcus). We therefore conducted bacterial tag encoded amplicon pyrosequencing assay for small-subunit rRNA gene to support effluent exposure of the coral. Bacteria of faecal origin (Enterobacteriales) formed 41% of total sequences in contrast to 0-2% of the coral-associated bacterial communities with and without C. velia, respectively. This is the first time apicomplexan type-N has been detected in the Great Barrier Reef. Eukaryote tag encoded amplicon pyrosequencing assays demonstrate presence of apicomplexan type-N and C. Velia in total coral DNA. The data highlight the need for combined approaches for eukaryotic diversity studies coupled with bacterial community assessment to achieve a more realistic goals of defining the holobiont community and assessing coral disease. With increasing evidence of Apicomplexa in coral reef environments, it is important not only to understand the evolution of these

  20. A One-Step Real-Time Multiplex PCR for Screening Y-Chromosomal Microdeletions without Downstream Amplicon Size Analysis

    Science.gov (United States)

    Kozina, Viviana; Cappallo-Obermann, Heike; Gromoll, Jörg; Spiess, Andrej-Nikolai

    2011-01-01

    Backgound Y-chromosomal microdeletions (YCMD) are one of the major genetic causes for non-obstructive azoospermia. Genetic testing for YCMD by multiplex polymerase chain reaction (PCR) is an established method for quick and robust screening of deletions in the AZF regions of the Y-chromosome. Multiplex PCRs have the advantage of including a control gene in every reaction and significantly reducing the number of reactions needed to screen the relevant genomic markers. Principal Findings The widely established “EAA/EMQN best practice guidelines for molecular diagnosis of Y-chromosomal microdeletions (2004)” were used as a basis for designing a real-time multiplex PCR system, in which the YCMD can simply be identified by their melting points. For this reason, some AZF primers were substituted by primers for regions in their genomic proximity, and the ZFX/ZFY control primer was exchanged by the AMELX/AMELY control primer. Furthermore, we substituted the classical SybrGreen I dye by the novel and high-performing DNA-binding dye EvaGreen™ and put substantial effort in titrating the primer combinations in respect to optimal melting peak separation and peak size. Significance With these changes, we were able to develop a platform-independent and robust real-time based multiplex PCR, which makes the need for amplicon identification by electrophoretic sizing expendable. By using an open-source system for real-time PCR analysis, we further demonstrate the applicability of automated melting point and YCMD detection. PMID:21887237

  1. Redefining the Human Oral Mycobiome with Improved Practices in Amplicon-based Taxonomy: Discovery of Malassezia as a Prominent Commensal

    Science.gov (United States)

    Dupuy, Amanda K.; David, Marika S.; Li, Lu; Heider, Thomas N.; Peterson, Jason D.; Montano, Elizabeth A.; Dongari-Bagtzoglou, Anna; Diaz, Patricia I.; Strausbaugh, Linda D.

    2014-01-01

    Fungi are a large, complex group, increasingly recognized as emerging threats. Their roles as modifiers of health mandate accurate portrayals of fungal communities in humans. As an entry point into the airways and gastrointestinal tract, fungi in the mouth are relevant to several biocompartments. We have revised current practices in sequence-based taxonomy assignments and employed the improvements to address the question of the fungal genera present in the healthy human mouth. The human oral mycobiome was surveyed using massively parallel, high throughput sequencing of internal transcribed spacer 1 (ITS1) amplicons from saliva following robust extraction methods. Taxonomy was assigned by comparison to a curated reference dataset, followed by filtering with an empirically determined BLAST E-value match statistic (10−42). Nomenclature corrections further refined results by conjoining redundant names for a single fungal genus. Following these curation steps, about two-thirds of the initially identified genera were eliminated. In comparison with the one similar metagenomic study and several earlier culture-based ones, our findings change the current conception of the oral mycobiome, especially with the discovery of the high prevalence and abundance of the genus Malassezia. Previously identified as an important pathogen of the skin, and recently reported as the predominant fungal genus at the nostril and backs of the head and ear, this is the first account of Malassezia in the human mouth. Findings from this study were in good agreement with others on the existence of many consensus members of the core mycobiome, and on unique patterns for individual subjects. This research offered a cautionary note about unconditional acceptance of lengthy lists of community members produced by automated assignments, provided a roadmap for enhancing the likely biological relevance of sequence-based fungal surveys, and built the foundation for understanding the role of fungi in health

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

    Directory of Open Access Journals (Sweden)

    Franck Curk

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

  3. Microbial community composition and diversity via 16S rRNA gene amplicons: evaluating the illumina platform.

    Directory of Open Access Journals (Sweden)

    Lucas Sinclair

    Full Text Available As new sequencing technologies become cheaper and older ones disappear, laboratories switch vendors and platforms. Validating the new setups is a crucial part of conducting rigorous scientific research. Here we report on the reliability and biases of performing bacterial 16S rRNA gene amplicon paired-end sequencing on the MiSeq Illumina platform. We designed a protocol using 50 barcode pairs to run samples in parallel and coded a pipeline to process the data. Sequencing the same sediment sample in 248 replicates as well as 70 samples from alkaline soda lakes, we evaluated the performance of the method with regards to estimates of alpha and beta diversity. Using different purification and DNA quantification procedures we always found up to 5-fold differences in the yield of sequences between individually barcodes samples. Using either a one-step or a two-step PCR preparation resulted in significantly different estimates in both alpha and beta diversity. Comparing with a previous method based on 454 pyrosequencing, we found that our Illumina protocol performed in a similar manner - with the exception for evenness estimates where correspondence between the methods was low. We further quantified the data loss at every processing step eventually accumulating to 50% of the raw reads. When evaluating different OTU clustering methods, we observed a stark contrast between the results of QIIME with default settings and the more recent UPARSE algorithm when it comes to the number of OTUs generated. Still, overall trends in alpha and beta diversity corresponded highly using both clustering methods. Our procedure performed well considering the precisions of alpha and beta diversity estimates, with insignificant effects of individual barcodes. Comparative analyses suggest that 454 and Illumina sequence data can be combined if the same PCR protocol and bioinformatic workflows are used for describing patterns in richness, beta-diversity and taxonomic

  4. 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/

  5. 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.

  6. Cost-Effectiveness of Treatments for Genotype 1 Hepatitis C Virus Infection in Non-VA and VA Populations

    Directory of Open Access Journals (Sweden)

    Shan Liu PhD

    2016-09-01

    Full Text Available Background: Chronic hepatitis C viral (HCV infection affects millions of Americans. Health care systems face complex choices between highly efficacious, costly treatments. This study assessed the cost-effectiveness of treatments for chronic, genotype 1 HCV monoinfected, treatment-naïve individuals in the Department of Veterans Affairs (VA and general US health care systems. Methods: The study used a decision-analytic Markov model, employing appropriate payer perspectives and time horizons, and discounting benefits and costs at 3% annually. Interventions included the following: sofosbuvir/ledipasvir (SOF-LDV; ombitasvir/paritaprevir/ritonavir/dasabuvir (3D; sofosbuvir/simeprevir (SOF-SMV; sofosbuvir/pegylated interferon/ribavirin (SOF-RBV-PEG; boceprevir/pegylated interferon/ribavirin (BOC-RBV-PEG; and pegylated interferon/ribavirin (PEG-RBV. Outcomes were sustained virologic response (SVR, advanced liver disease, costs, quality adjusted life years (QALYs, and incremental cost-effectiveness. Results: SOF-LDV and 3D achieve high SVR rates, reducing advanced liver disease (>20% relative to no treatment, and increasing QALYs by >2 years per person. For the non-VA population, at current prices ($5040 per week for SOF-LDV; $4796 per week for 3D, SOF-LDV’s lifetime cost ($293,370 is $18,000 lower than 3D’s because of its shorter duration in subgroups. SOF-LDV costs $17,100 per QALY gained relative to no treatment. 3D costs $208,000 per QALY gained relative to SOF-LDV. Both dominate other treatments and are even more cost-effective for the VA, though VA aggregate treatment costs still exceed $4 billion at SOF-LDV prices of $3308 per week. Drug prices strongly determine relative cost-effectiveness for SOF-LDV and 3D; with price reductions of 20% to 30% depending on health system, 3D could be cost-effective relative to SOF-LDV. We currently lack head-to-head regimen effectiveness trials. Conclusions: New HCV treatments are cost-effective in multiple

  7. V-A hadronic tau decays : a QCD laboratory

    Energy Technology Data Exchange (ETDEWEB)

    Narison, Stephan E-mail: narison@lpm.univ-montp2.fr

    2001-04-01

    Recent ALEPH/OPAL data on the V-A spectral functions from hadronic {tau} decays are used for fixing the QCD continuum threshold at which the first and second Weinberg sum rules should be satisfied in the chiral limit, and for predicting the values of the low-energy constants f{sub {pi}}, m{sub {pi}{sup +}} - m{sub {pi}{sup 0}} and L{sub 10}. Some DMO-like sum rules and the {tau}-total hadronic widths R{sub {tau}}{sub ,V-A} are also used for extracting the values of the D = 6, 8 QCD vacuum condensates and the corresponding (in the chiral limit) electroweak kaon penguin matrix elements {sub 2{pi}}, where a deviation from the vacuum saturation estimate has been obtained. Combining these results with the one of the QCD penguin matrix element {sub 2{pi}} obtained from a (maximal) q-barq-gluonium mixing scheme from the scalar meson sum rules, we deduce, in the Electroweak Standard Model (ESM), the conservative upper bound for the CP-violating ratio: {epsilon}'/{epsilon} {<=} (22 {+-} 9)10{sup -4}, in agreement with the present measurements.

  8. The use of yoga in specialized VA PTSD treatment programs.

    Science.gov (United States)

    Libby, Daniel J; Reddy, Felice; Pilver, Corey E; Desai, Rani A

    2012-01-01

    Posttraumatic stress disorder (PTSD) is a chronic, debilitating anxiety disorder that is highly prevalent among U.S. military veterans. Yoga, defined to include physical postures (asana) and mindfulness and meditation, is being increasingly used as an adjunctive treatment for PTSD and other psychological disorders. No research or administrative data have detailed the use of these services in Department of Veterans Affairs' (VA) 170 PTSD treatment programs. One hundred twenty-five program coordinators or designated staff completed an 81-item survey of their program's use of complementary and alternative medicine modalities in the past year. This report describes data from a subset of 30 questions used to assess the prevalence, nature, and context of the use of yoga, mindfulness, and meditation other than mindfulness practices. Results revealed that these practices are widely offered in VA specialized PTSD treatment programs and that there is great variability in the context and nature of how they are delivered. Understanding how yoga is used by these programs may inform ongoing efforts to define and distinguish yoga therapy as a respected therapeutic discipline and to create patient-centered care models that mindfully fulfill the unmet needs of individuals with mental health issues, including veterans with PTSD.

  9. 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.

  10. 78 FR 21817 - Amendment of Restricted Area R-6601; Fort A.P. Hill, VA

    Science.gov (United States)

    2013-04-12

    ...; Airspace Docket No. 12-AEA-7] RIN 2120-AA66 Amendment of Restricted Area R-6601; Fort A.P. Hill, VA AGENCY... limits and time of designation of restricted area R-6601, Fort A.P. Hill, VA. The U.S. Army requested... limits and increase the time of designation of restricted area R-6601, Fort A.P. Hill, VA, (77 FR 35308...

  11. VA-Index: Quantifying Assortativity Patterns in Networks with Multidimensional Nodal Attributes (Open Access)

    Science.gov (United States)

    2016-01-27

    RESEARCH ARTICLE VA- Index : Quantifying Assortativity Patterns in Networks with Multidimensional Nodal Attributes Konstantinos Pelechrinis*, DongWei...treatment of this problem. In this study we develop a metric, the vector assortativity index (VA- index for short), based on network randomization and...extensive experimental results on synthetic network data show that the VA- index outperforms a baseline extension of the assortativity coeffi- cient, which

  12. 75 FR 70351 - Termination of Environmental Review Process Cities of Chesapeake and Virginia Beach, VA

    Science.gov (United States)

    2010-11-17

    ... Virginia Beach, VA AGENCY: Federal Highway Administration (FHWA), DOT. ACTION: Termination of environmental... the Cities of Chesapeake and Virginia Beach, Virginia, is terminated. FOR FURTHER INFORMATION CONTACT...

  13. 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…

  14. Neuroimaging overuse is more common in Medicare compared with the VA.

    Science.gov (United States)

    Burke, James F; Kerr, Eve A; McCammon, Ryan J; Holleman, Rob; Langa, Kenneth M; Callaghan, Brian C

    2016-08-23

    To inform initiatives to reduce overuse, we compared neuroimaging appropriateness in a large Medicare cohort with a Department of Veterans Affairs (VA) cohort. Separate retrospective cohorts were established in Medicare and in VA for headache and neuropathy from 2004 to 2011. The Medicare cohorts included all patients enrolled in the Health and Retirement Study (HRS) with linked Medicare claims (HRS-Medicare; n = 1,244 for headache and 998 for neuropathy). The VA cohorts included all patients receiving services in the VA (n = 93,755 for headache and 183,642 for neuropathy). Inclusion criteria were age over 65 years and an outpatient visit for incident neuropathy or a primary headache. Neuroimaging use was measured with Current Procedural Terminology codes and potential overuse was defined using published criteria for use with administrative data. Increasingly specific appropriateness criteria excluded nontarget conditions for which neuroimaging may be appropriate. For both peripheral neuropathy and headache, potentially inappropriate imaging was more common in HRS-Medicare compared with the VA. Forty-nine percentage of all headache patients received neuroimaging in HRS-Medicare compared with 22.1% in the VA (p neuroimaging compared with 9.0% in the VA (p neuroimaging is likely less common in the VA than in a Medicare population. Better understanding the reasons for the more selective use of neuroimaging in the VA could help inform future initiatives to reduce overuse of diagnostic testing. © 2016 American Academy of Neurology.

  15. 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

  16. 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

  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. 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

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

    Directory of Open Access Journals (Sweden)

    C.C.R. Souza

    2013-02-01

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

  20. Adenovirus VA RNA: An essential pro-viral non-coding RNA.

    Science.gov (United States)

    Vachon, Virginia K; Conn, Graeme L

    2016-01-02

    Adenovirus (AdV) 'virus-associated' RNAs (VA RNAs) are exceptionally abundant (up to 10(8)copies/cell), heterogeneous, non-coding RNA transcripts (∼ 150-200 nucleotides). The predominant species, VA RNAI, is best recognized for its essential function in relieving the cellular anti-viral blockade of protein synthesis through inhibition of the double-stranded RNA-activated protein kinase (PKR). More recent evidence has revealed that VA RNAs also interfere with several other host cell processes, in part by virtue of the high level to which they accumulate. Following transcription by cellular RNA polymerase III, VA RNAs saturate the nuclear export protein Exportin 5 (Exp5) and the cellular endoribonculease Dicer, interfering with pre-micro (mi)RNA export and miRNA biogenesis, respectively. Dicer-processed VA RNA fragments are incorporated into the RNA-induced silencing complex (RISC) as 'mivaRNAs', where they may specifically target cellular genes. VA RNAI also interacts with other innate immune proteins, including OAS1. While intact VA RNAI has the paradoxical effect of activating OAS1, a non-natural VA RNAI construct lacking the entire Terminal Stem has been reported to be a pseudoinhibitor of OAS1. Here, we show that a VA RNAI construct corresponding to an authentic product of Dicer processing similarly fails to activate OAS1 but also retains only a modest level of inhibitory activity against PKR in contrast to the non-natural deletion construct. These findings underscore the complexity of the arms race between virus and host, and highlight the need for further exploration of the impact of VA RNAI interactions with host defenses on the outcome of AdV infection beyond that of well-established PKR inhibition. Additional contributions of VA RNAI heterogeneity resulting from variations in transcription initiation and termination to each of these functions remain open questions that are discussed here. Copyright © 2015 Elsevier B.V. All rights reserved.

  1. 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.

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

    Directory of Open Access Journals (Sweden)

    Anişoara Popa

    2014-12-01

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

  3. 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.

  4. Expanded Access to Non-VA Care Through the Veterans Choice Program. Interim final rule.

    Science.gov (United States)

    2015-12-01

    The Department of Veterans Affairs (VA) revises its medical regulations that implement section 101 of the Veterans Access, Choice, and Accountability Act of 2014 (hereafter referred to as "the Choice Act"), which requires VA to establish a program to furnish hospital care and medical services through eligible non-VA health care providers to eligible veterans who either cannot be seen within the wait-time goals of the Veterans Health Administration (VHA) or who qualify based on their place of residence (hereafter referred to as the "Veterans Choice Program" or the "Program"). These regulatory revisions are required by the most recent amendments to the Choice Act made by the Construction Authorization and Choice Improvement Act of 2014, and by the Surface Transportation and Veterans Health Care Choice Improvement Act of 2015. The Construction Authorization and Choice Improvement Act of 2014 amended the Choice Act to define additional criteria that VA may use to determine that a veteran's travel to a VA medical facility is an "unusual or excessive burden," and the Surface Transportation and Veterans Health Care Choice Improvement Act of 2015 amended the Choice Act to cover all veterans enrolled in the VA health care system, remove the 60-day limit on an episode of care, modify the wait-time and 40-mile distance eligibility criteria, and expand provider eligibility based on criteria as determined by VA. This interim final rule revises VA regulations consistent with the changes made to the Choice Act as described above.

  5. 78 FR 56151 - Safety Zone, North Atlantic Ocean; Virginia Beach, VA

    Science.gov (United States)

    2013-09-12

    ... SECURITY Coast Guard 33 CFR Part 165 RIN 1625-AA00 Safety Zone, North Atlantic Ocean; Virginia Beach, VA... zone on the navigable waters of the North Atlantic Ocean in Virginia Beach, VA to support the Virginia... Delegation No. 0170.1. ] On September 12, 2013 the City of Virginia Beach will host a fireworks display...

  6. 77 FR 27120 - Safety Zone; Virginia Beach Oceanfront Air Show, Atlantic Ocean, Virginia Beach, VA

    Science.gov (United States)

    2012-05-09

    ... SECURITY Coast Guard 33 CFR Part 165 RIN 1625-AA00 Safety Zone; Virginia Beach Oceanfront Air Show, Atlantic Ocean, Virginia Beach, VA AGENCY: Coast Guard, DHS. ACTION: Temporary final rule. SUMMARY: The... Beach, VA to support the Virginia Beach Oceanfront Air Show. This action is necessary to provide for the...

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

    Science.gov (United States)

    2012-03-07

    ... SECURITY Coast Guard 33 CFR Part 165 RIN 1625-AA00 Safety Zone; Virginia Beach Oceanfront Air Show, Atlantic Ocean, Virginia Beach, VA AGENCY: Coast Guard, DHS. ACTION: Notice of proposed rulemaking. SUMMARY... Virginia Beach, VA. This action is necessary to provide for the safety of life on navigable waters during...

  8. 48 CFR 852.219-9 - VA Small business subcontracting plan minimum requirements.

    Science.gov (United States)

    2010-10-01

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

  9. 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

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

    Science.gov (United States)

    2010-07-01

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

  11. 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...

  12. 75 FR 34367 - Safety Zone; Shore Thing & Independence Day Fireworks, Chesapeake Bay, Norfolk, VA

    Science.gov (United States)

    2010-06-17

    ...-AA00 Safety Zone; Shore Thing & Independence Day Fireworks, Chesapeake Bay, Norfolk, VA AGENCY: Coast... zone on the Chesapeake Bay in the vicinity of Ocean View Beach Park, Norfolk, VA in support of the... movement on the Chesapeake Bay [[Page 34368

  13. 75 FR 26155 - Safety Zone; Shore Thing & Independence Day Fireworks, Chesapeake Bay, Norfolk, VA

    Science.gov (United States)

    2010-05-11

    ...-AA00 Safety Zone; Shore Thing & Independence Day Fireworks, Chesapeake Bay, Norfolk, VA AGENCY: Coast... temporary safety zone on the Chesapeake Bay in the vicinity of Ocean View Beach Park, Norfolk, VA in support... traffic movement on the Chesapeake Bay to protect mariners from the hazards associated with fireworks...

  14. 76 FR 38300 - Safety Zone; Shore Thing and Independence Day Fireworks, Chesapeake Bay, Norfolk, VA

    Science.gov (United States)

    2011-06-30

    ...-AA00 Safety Zone; Shore Thing and Independence Day Fireworks, Chesapeake Bay, Norfolk, VA AGENCY: Coast... zone on the Chesapeake Bay in the vicinity of Ocean View Beach Park, Norfolk, VA in support of the... intended to restrict vessel traffic movement on the Chesapeake Bay to protect mariners from the hazards...

  15. 33 CFR 334.350 - Chesapeake Bay off Fort Monroe, Va.; firing range danger zone.

    Science.gov (United States)

    2010-07-01

    ... 33 Navigation and Navigable Waters 3 2010-07-01 2010-07-01 false Chesapeake Bay off Fort Monroe, Va.; firing range danger zone. 334.350 Section 334.350 Navigation and Navigable Waters CORPS OF....350 Chesapeake Bay off Fort Monroe, Va.; firing range danger zone. (a) The danger zone. All of the...

  16. 76 FR 27967 - Safety Zone; Shore Thing and Independence Day Fireworks, Chesapeake Bay, Norfolk, VA

    Science.gov (United States)

    2011-05-13

    ...-AA00 Safety Zone; Shore Thing and Independence Day Fireworks, Chesapeake Bay, Norfolk, VA AGENCY: Coast... temporary safety zone on the Chesapeake Bay in the vicinity of Ocean View Beach Park, Norfolk, VA in support... action is intended to restrict vessel traffic movement on the Chesapeake Bay to protect mariners from the...

  17. 75 FR 20774 - Establishment of Class E Airspace; Fort A.P. Hill, VA

    Science.gov (United States)

    2010-04-21

    ... DEPARTMENT OF TRANSPORTATION Federal Aviation Administration 14 CFR Part 71 [Docket No. FAA-2009-0739; Airspace Docket No. 09-AEA-14] Establishment of Class E Airspace; Fort A.P. Hill, VA AGENCY... December 7, 2009 that establishes Class E airspace at Fort A.P. Hill, VA. DATES: Effective Date: 0901 UTC...

  18. 77 FR 63734 - Security Zone; James River, Kingsmill Resort, Williamsburg, VA

    Science.gov (United States)

    2012-10-17

    ...-AA00 Security Zone; James River, Kingsmill Resort, Williamsburg, VA AGENCY: Coast Guard, DHS. ACTION... River in the vicinity of Kingsmill Resort Marina, Williamsburg, VA during a visit by The President of... Docket Management Facility in Room W12-140 on the ground floor of the Department of Transportation West...

  19. 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...

  20. 48 CFR 803.7000 - Display of the VA Hotline poster.

    Science.gov (United States)

    2010-10-01

    ... GENERAL IMPROPER BUSINESS PRACTICES AND PERSONAL CONFLICTS OF INTEREST Contractor Responsibility to Avoid Improper Business Practices 803.7000 Display of the VA Hotline poster. (a) Under the circumstances... prepared by the VA Office of Inspector General in a common work area within a business segment performing...

  1. 38 CFR 17.52 - Hospital care and medical services in non-VA facilities.

    Science.gov (United States)

    2010-07-01

    .... 19012, Pub. L. 99-272) (10) For any disability of a veteran receiving VA contract nursing home care. The veteran is receiving contract nursing home care and requires emergency treatment in non-VA facilities... provisions of this section. When demand is only for infrequent use, individual authorizations may be used...

  2. 38 CFR 17.96 - Medication prescribed by non-VA physicians.

    Science.gov (United States)

    2010-07-01

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

  3. 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... navigable waters of the Back River in the vicinity of Hampton, VA. This action is necessary to provide for the safety of life on navigable waters during the Air Power Over Hampton Roads Air Show. This action...

  4. 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...

  5. 77 FR 72816 - Foreign-Trade Zone 20-Suffolk, VA; Authorization of Production Activity; Usui International...

    Science.gov (United States)

    2012-12-06

    ... Foreign-Trade Zones Board Foreign-Trade Zone 20--Suffolk, VA; Authorization of Production Activity; Usui International Corporation (Diesel Engine Fuel Lines); Chesapeake, VA On June 28, 2012, the Virginia Port Authority, grantee of FTZ 20, submitted a notification of proposed production activity to the Foreign-Trade...

  6. 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...

  7. 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...

  8. 76 FR 3017 - VA Veteran-Owned Small Business Verification Guidelines

    Science.gov (United States)

    2011-01-19

    ... that greatly affect today's business climate and put an unnecessary burden on certain business owners... DEPARTMENT OF VETERANS AFFAIRS 38 CFR Part 74 RIN 2900-AM78 VA Veteran-Owned Small Business... Veterans Affairs (VA) to verify ownership and control of veteran-owned small businesses, including service...

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

    Science.gov (United States)

    2013-08-20

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

  10. 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.

  11. Comparing the health status of VA and non-VA ambulatory patients: the veterans' health and medical outcomes studies.

    Science.gov (United States)

    Rogers, William H; Kazis, Lewis E; Miller, Donald R; Skinner, Katherine M; Clark, Jack A; Spiro, Avron; Fincke, R Graeme

    2004-01-01

    The purpose of this study was to compare health status and disease profiles of ambulatory patients in specific Veterans Administration (VA) and civilian healthcare settings. A random sample of 2425 male veterans seeking care at 4 Boston-area VA outpatient clinics, who took part in the Veterans Health Study (VHS) in 1993-1995, were compared to 1318 male patients seeking civilian outpatient care in 3 major metropolitan areas covered in the Medical Outcomes Study (MOS) in 1986. The MOS sampled patients who had 1 of 5 conditions--hypertension, noninsulin-dependent diabetes, recent myocardial infarction, congestive heart failure, or depression. These 2 samples were age adjusted and compared in terms of the SF-36 Health Status/Quality of Life measures, and a list of 100 clinical variables (diagnostic, symptom, and medical event reports) collected with comparable instruments by a trained clinical observer. Individual odds ratios (VHS to MOS) were calculated for each measure and clinical variables. SF-36 measures of patient health in the VHS were lower than those in the MOS by more than one half of a standard deviation (SD) on 4 of 8 scales, by more than one quarter of a SD on the other 4, by 58% of a SD on the physical health summary scale, and by 37% of a SD on the mental health summary scale (P illness burden than did patients in the MOS. Current economic condition and service-connected disability explain most, if not all, of the differences. The differences were clinically and socially meaningful and would be consistent with substantially higher expected healthcare use.

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

    Science.gov (United States)

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

    2017-06-01

    The 16S rRNA gene amplicon and whole-genome shotgun metagenomic (WGSM) sequencing approaches were used to investigate wide-spectrum profiles of microbial composition and metabolic diversity from a full-scale UASB reactor applied to poultry slaughterhouse wastewater treatment. The data were generated by using MiSeq 2 × 250 bp and HiSeq 2 × 150 bp Illumina sequencing platforms for 16S amplicon and WGSM sequencing, respectively. Each approach revealed a distinct microbial community profile, with Pseudomonas and Psychrobacter as predominant genus for the WGSM dataset and Clostridium and Methanosaeta for the 16S rRNA gene amplicon dataset. The virome characterization revealed the presence of two viral families with Bacteria and Archaea as host, Myoviridae, and Siphoviridae. A wide functional diversity was found with predominance of genes involved in the metabolism of acetone, butanol, and ethanol synthesis; and one-carbon metabolism (e.g., methanogenesis). Genes related to the acetotrophic methanogenesis pathways were more abundant than methylotrophic and hydrogenotrophic, corroborating the taxonomic results that showed the prevalence of the acetotrophic genus Methanosaeta. Moreover, the dataset indicated a variety of metabolic genes involved in sulfur, nitrogen, iron, and phosphorus cycles, with many genera able to act in all cycles. BLAST analysis against Antibiotic Resistance Genes Database (ARDB) revealed that microbial community contained 43 different types of antibiotic resistance genes, some of them were associated with growth chicken promotion (e.g., bacitracin, tetracycline, and polymyxin). © 2017 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.

  13. Assessment of Capture and Amplicon-Based Approaches for the Development of a Targeted Next-Generation Sequencing Pipeline to Personalize Lymphoma Management.

    Science.gov (United States)

    Hung, Stacy S; Meissner, Barbara; Chavez, Elizabeth A; Ben-Neriah, Susana; Ennishi, Daisuke; Jones, Martin R; Shulha, Hennady P; Chan, Fong Chun; Boyle, Merrill; Kridel, Robert; Gascoyne, Randy D; Mungall, Andrew J; Marra, Marco A; Scott, David W; Connors, Joseph M; Steidl, Christian

    2018-03-01

    Targeted next-generation sequencing panels are increasingly used to assess the value of gene mutations for clinical diagnostic purposes. For assay development, amplicon-based methods have been preferentially used on the basis of short preparation time and small DNA input amounts. However, capture sequencing has emerged as an alternative approach because of high testing accuracy. We compared capture hybridization and amplicon sequencing approaches using fresh-frozen and formalin-fixed, paraffin-embedded tumor samples from eight lymphoma patients. Next, we developed a targeted sequencing pipeline using a 32-gene panel for accurate detection of actionable mutations in formalin-fixed, paraffin-embedded tumor samples of the most common lymphocytic malignancies: chronic lymphocytic leukemia, diffuse large B-cell lymphoma, and follicular lymphoma. We show that hybrid capture is superior to amplicon sequencing by providing deep more uniform coverage and yielding higher sensitivity for variant calling. Sanger sequencing of 588 variants identified specificity limits of thresholds for mutation calling, and orthogonal validation on 66 cases indicated 93% concordance with whole-genome sequencing. The developed pipeline and assay identified at least one actionable mutation in 91% of tumors from 219 lymphoma patients and revealed subtype-specific mutation patterns and frequencies consistent with the literature. This pipeline is an accurate and sensitive method for identifying actionable gene mutations in routinely acquired biopsy materials, suggesting further assessment of capture-based assays in the context of personalized lymphoma management. Copyright © 2018 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.

  14. 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

  15. 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.

  16. Associations between sex hormones and cognitive and neuropsychiatric manifestations in vascular dementia (VaD).

    Science.gov (United States)

    Xing, Yi; Qin, Wei; Li, Fang; Jia, Xiang-Fei; Jia, Jianping

    2013-01-01

    Although numerous studies have been carried out to determine the effects of sex hormones on Alzheimer's disease (AD), little is known about the associations between sex hormones and VaD. The aim of this study was to compare serum sex hormone levels between VaD patients and normal controls, and to further determine the link between sex hormones and cognitive and neuropsychiatric manifestations of VaD. Serum levels of total estradiol (TE2), total testosterone (TT), luteinizing hormone (LH), and sex hormone binding globulin (SHBG) were measured in 87 VaD patients and 110 cognitive normal controls. The levels of bioavailable estradiol (BE2) and bioavailable testosterone (BT) were calculated. The VaD patients underwent the tests of global cognitive function, verbal memory, and visuospatial, and executive ability. The Neuropsychiatric Inventory (NPI) was used to assess neuropsychiatric symptoms. Compared to controls, the testosterone and SHBG levels were lower in male VaD patients, and the estradiol levels were higher in female VaD patients. The hormones levels were not correlated with cognitive functions among either male or female VaD patients. There were no associations between hormone levels and neuropsychiatric symptoms among male patients, while the TE2 and TT levels were positively associated with apathy and anxiety, respectively among female patients. Our findings suggested there were sex hormone level changes in VaD patients in comparison with cognitive normal controls. Sex hormones were associated with neuropsychiatric symptoms among female but not male VaD patients. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

  17. 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.

  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. Variation in Utilization of Health Care Services for Rural VA Enrollees With Mental Health-Related Diagnoses.

    Science.gov (United States)

    Johnson, Christopher E; Bush, Ruth L; Harman, Jeffrey; Bolin, Jane; Evans Hudnall, Gina; Nguyen, Ann M

    2015-01-01

    Rural-dwelling Department of Veterans Affairs (VA) enrollees are at high risk for a wide variety of mental health-related disorders. The objective of this study is to examine the variation in the types of mental and nonmental health services received by rural VA enrollees who have a mental health-related diagnosis. The Andersen and Aday behavioral model of health services use and the Agency for Healthcare Research and Quality Medical Expenditure Panel Survey (MEPS) data were used to examine how VA enrollees with mental health-related diagnoses accessed places of care from 1999 to 2009. Population survey weights were applied to the MEPS data, and logit regression was conducted to model how predisposing, enabling, and need factors influence rural veteran health services use (measured by visits to different places of care). Analyses were performed on the subpopulations: rural VA, rural non-VA, urban VA, and urban non-VA enrollees. For all types of care, both rural and urban VA enrollees received care from inpatient, outpatient, office-based, and emergency room settings at higher odds than urban non-VA enrollees. Rural VA enrollees also received all types of care from inpatient, office-based, and emergency room settings at higher odds than urban VA enrollees. Rural VA enrollees had higher odds of a mental health visit of any kind compared to urban VA and non-VA enrollees. Based on these variations, the VA may want to develop strategies to increase screening efforts in inpatient settings and emergency rooms to further capture rural VA enrollees who have undiagnosed mental health conditions. © 2015 National Rural Health Association.

  20. VA Pipeline for Future Nurse Leaders: an Exploration of Current Nurse Leadership Development in the Veteran’s Health Administration

    Science.gov (United States)

    2016-06-10

    chaotic, complex VA landscape is the balance between national and field leadership, the overall VA leadership crisis, and public concern that the...employees and 4.7 million Veterans from World War I, the Spanish American War, and even some Veterans of the Civil War. In 1988, President 15...service to our Nation’s Veterans. With the shifting, expanding, and more complex VA healthcare landscape , this increases the demands for VA leaders to fill

  1. 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

    ... DEPARTMENT OF VETERANS AFFAIRS 38 CFR Part 17 RIN 2900-AN98 Payment for Home Health Services and... Federal Register on May 6, 2013 (78 FR 26250) a final rule to change the billing methodology for non-VA... INFORMATION: This rulemaking makes the VA regulation governing payments for certain non-VA health care, 38 CFR...

  2. 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.

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

    Directory of Open Access Journals (Sweden)

    Yong Wang

    Full Text Available 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.

  4. 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

  5. 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.

  6. 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.

  7. National comparison of literally homeless male and female VA service users: entry characteristics, clinical needs, and service patterns.

    Science.gov (United States)

    Tsai, Jack; Kasprow, Wesley J; Kane, Vincent; Rosenheck, Robert A

    2014-01-01

    Although there are growing numbers of homeless female U.S. veterans, the U.S. Department of Veterans Affairs (VA) has traditionally served a predominantly male population; thus, it is important to examine differences between homeless female and male veterans in their service needs and the current provision of VA homeless services. A national registry of 119,947 users of VA homeless services from 2011 to 2012 was used to 1) estimate the proportion of female veterans among VA homeless service users, 2) examine the proportion of VA homeless service users who are literally homeless by gender, and 3) report differences between female and male VA homeless service users who are literally homeless on sociodemographic and clinical characteristics, as well as on outreach, referral, and admission patterns for an array of specialized VA services. Of VA homeless service users, 8% were female compared with 7% among all homeless veterans, 6% among all VA service users, and 7% among all veterans. Of female VA homeless service users, 54% were literally homeless, slightly fewer than the 59% of male VA homeless service users. Comparing literally homeless VA service users, females were younger, 21% more had dependent children, 8% more were diagnosed with non-military-related posttraumatic stress disorder, and 19% to 20% more were referred and admitted to VA's supported housing program than males. Female veterans use VA homeless services at a rate similar to their use of general VA services and they have unique needs, especially for child care, which may require additional specialized resources. Published by Elsevier Inc.

  8. 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.

  9. 75 FR 52989 - Specialty Minerals, Inc., Franklin, VA; Notice of Negative Determination Regarding Application...

    Science.gov (United States)

    2010-08-30

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF LABOR Employment and Training Administration Specialty Minerals, Inc., Franklin, VA; Notice of Negative Determination Regarding Application for Reconsideration By applications dated July 9, 2010 and July 16, 2010...

  10. 75 FR 41577 - VBA/VHA Musculoskeletal Forum: Improving VA's Disability Evaluation Criteria

    Science.gov (United States)

    2010-07-16

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF VETERANS AFFAIRS VBA/VHA Musculoskeletal Forum: Improving VA's Disability Evaluation Criteria AGENCY: Department of... Veterans Benefits Administration (VBA)/Veterans Health Administration (VHA) Musculoskeletal Forum...

  11. DoD-VA Health Care: A Case Study in Interagency Reform

    National Research Council Canada - National Science Library

    Cho, John M

    2008-01-01

    .... Examination of the DoD-VA health care partnership in the aftermath of Walter Reed provides new insight into the timing, proportion, and necessity of IAR legislation for improving interagency collaboration...

  12. 48 CFR 852.219-71 - VA mentor-protégé program.

    Science.gov (United States)

    2010-10-01

    ... increase their participation as VA prime contractors and as subcontractors. (b) The program consists of: (1... calculated on a dollar-for-dollar basis and reported by the large business prime contractor via the...

  13. 77 FR 12647 - Fund Availability Under VA's Homeless Providers Grant and Per Diem Program

    Science.gov (United States)

    2012-03-01

    ... Providers Grant and Per Diem Program as a part of the effort to end homelessness among our Nation's veterans... ``Transition in Place'' housing model to aid in VA's efforts to end homelessness among veterans. The...

  14. 75 FR 3970 - Fund Availability Under the VA Homeless Providers Grant and Per Diem Program

    Science.gov (United States)

    2010-01-25

    ... Homeless Providers Grant and Per Diem Program as a part of the effort to end chronic homelessness among our... effort to end chronic homelessness among all veterans. It is important to be aware that VA places great...

  15. 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...

  16. 78 FR 12600 - VA Homeless Providers Grant and Per Diem Program

    Science.gov (United States)

    2013-02-25

    ... between 2009 and 2011 VA and the Department of Housing and Urban Development had successfully housed a... post-traumatic stress disorder (PTSD), based on a diagnosis from a licensed mental health professional... that remain in development; [[Page 12607

  17. 78 FR 38452 - Agency Information Collection (VA Police Officer Pre-Employment Screening Checklist) Activities...

    Science.gov (United States)

    2013-06-26

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF VETERANS AFFAIRS Agency Information Collection (VA Police Officer Pre-Employment Screening Checklist) Activities Under OMB Review AGENCY: Office of Policy, Planning and Preparedness, Department of Veterans Affairs...

  18. Combined Analysis of the VA and DOD Gulf War Clinical Registries

    National Research Council Canada - National Science Library

    Kang, Han

    2002-01-01

    .... Merging of VA PGR and CCEP with linkage to other data resources, 2. General descriptive report on the demographic and military characteristics, overall symptom and diagnosis reporting, and self-reported exposures of the combined data, 3...

  19. 78 FR 51067 - VA Health Professional Scholarship and Visual Impairment and Orientation and Mobility...

    Science.gov (United States)

    2013-08-20

    ... Visual Impairment and Orientation and Mobility Professional Scholarship Programs AGENCY: Department of... program, the Visual Impairment and Orientation and Mobility Professional Scholarship Program (VIOMPSP... orientation or mobility, in order to increase the supply of qualified blind rehabilitation specialists for VA...

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

    DEFF Research Database (Denmark)

    Schümann, Michael; Dobbelstein, Matthias

    2006-01-01

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

  1. 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...

  2. On Conditional Value at Risk (CoVaR for tail-dependent copulas

    Directory of Open Access Journals (Sweden)

    Jaworski Piotr

    2017-01-01

    Full Text Available The paper deals with Conditional Value at Risk (CoVaR for copulas with nontrivial tail dependence. We show that both in the standard and the modified settings, the tail dependence function determines the limiting properties of CoVaR as the conditioning event becomes more extreme. The results are illustrated with examples using the extreme value, conic and truncation invariant families of bivariate tail-dependent copulas.

  3. 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.

  4. Electronic Health Records: VA and DOD Need to Establish Goals and Metrics for Their Interoperability Efforts

    Science.gov (United States)

    2015-10-27

    systems. What GAO Recommends In its August 2015 report, GAO recommended that VA and DOD, working with the IPO , establish a time frame for...Veterans Affairs (VA) and Defense (DOD), with guidance from the Interagency Program Office ( IPO ) tasked with facilitating the departments’ efforts to...In accordance with its responsibilities, the IPO issued guidance outlining the technical approach for achieving interoperability between the

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

    Science.gov (United States)

    Ellepola, W; Sheredos, S J

    1993-01-01

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

  7. 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...

  8. 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...

  9. 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/.

  10. Teacher factors contributing to dosage of the KiVa anti-bullying program.

    Science.gov (United States)

    Swift, Lauren E; Hubbard, Julie A; Bookhout, Megan K; Grassetti, Stevie N; Smith, Marissa A; Morrow, Michael T

    2017-12-01

    The KiVa Anti-Bullying Program (KiVa) seeks to meet the growing need for anti-bullying programming through a school-based, teacher-led intervention for elementary school children. The goals of this study were to examine how intervention dosage impacts outcomes of KiVa and how teacher factors influence dosage. Participants included 74 teachers and 1409 4th- and 5th-grade students in nine elementary schools. Teachers and students completed data collection at the beginning and end of the school year, including measures of bullying and victimization, correlates of victimization (depression, anxiety, peer rejection, withdrawal, and school avoidance), intervention cognitions/emotions (anti-bullying attitudes, and empathy toward victims), bystander behaviors, and teacher factors thought to relate to dosage (self-efficacy for teaching, professional burnout, perceived principal support, expected effectiveness of KiVa, perceived feasibility of KiVa). The dosage of KiVa delivered to classrooms was measured throughout the school year. Results highlight dosage as an important predictor of change in bullying, victimization, correlates of victimization, bystander behavior, and intervention cognitions/emotions. Of the teacher factors, professional burnout uniquely predicted intervention dosage. A comprehensive structural equation model linking professional burnout to dosage and then to child-level outcomes demonstrated good fit. Implications for intervention design and implementation are discussed. Copyright © 2017 Society for the Study of School Psychology. Published by Elsevier Ltd. All rights reserved.

  11. Partnership to improve quality care for veterans: the VA Nursing Academy.

    Science.gov (United States)

    Harper, Doreen C; Selleck, Cynthia S; Eagerton, Gregory; Froelich, Kimberly

    2015-01-01

    More than 22 million living veterans reside in the United States. In fact, understanding military culture and the experiences of these veterans is important to their ongoing health care and the unique challenges faced by many. The Veterans Affairs (VA) Nursing Academy began in 2007 to fund pilot partnerships between schools of nursing and local VA health care facilities to better serve our veteran population. Fifteen academic/service partnerships were selected for funding between 2007 and 2009 with the goals of expanding faculty and professional development, increasing nursing student enrollment, providing opportunities for educational and practice innovations, and increasing the recruitment and retention of VA nurses. This article details critical components of the partnership developed between the Birmingham VA Medical Center and the University of Alabama at Birmingham School of Nursing, a VA Nursing Academy partnership funded in the 2009 cohort. Site-specific goals of the partnership are described along with a discussion of the framework used to develop the Birmingham VA Nursing Academy, which includes relationship building, engagement, governance, evaluation of outcomes, and sustainability. The logic model developed for the partnership is included, and the interim outputs and outcomes of this practice-academic partnership are detailed, a number of which can be replicated by VAs and schools of nursing across the country. Copyright © 2015 Elsevier Inc. All rights reserved.

  12. 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.

  13. 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.

  14. 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....... The PowerWater DNA Isolation Kit resulted in significantly higher amounts of isolated DNA compared to the FastDNA SPIN Kit for Soil. Furthermore, extraction with the PowerWater kit lead to detection of a significantly higher number of OTUs. Likewise, the primer experiment revealed great discrepancies in OTU....... coli could be detected in all samples. However, samples with 101 cells/mL had several contaminating OTUs, constituting approximately 8% of the read abundances. For 16S rRNA gene analysis in drinking water samples, we recommend using the PowerWater DNA Isolation Kit for DNA extraction in combination...

  15. 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.

  16. 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

    detection power. For beta-diversity-based sample separation, we show that library size normalization has very little effect and that the distance metric is the most important factor in terms of separation power. CONCLUSIONS: Our results, generalizable to datasets from different sequencing platforms......, demonstrate how the choice of method considerably affects analysis outcome. Here, we give recommendations for tools that exhibit low false positive rates, have good retrieval power across effect sizes and case/control proportions, and have low sparsity bias. Result output from some commonly used methods......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...

  17. Simplified strategy for rapid first-line screening of fragile X syndrome: closed-tube triplet-primed PCR and amplicon melt peak analysis.

    Science.gov (United States)

    Rajan-Babu, Indhu-Shree; Law, Hai-Yang; Yoon, Chui-Sheun; Lee, Caroline G; Chong, Samuel S

    2015-05-04

    Premutation and full-mutation hyperexpansion of CGG-triplets in the X-linked Fragile X Mental Retardation 1 (FMR1) gene have been implicated in fragile X-associated tremor/ataxia syndrome, fragile X-associated primary ovarian insufficiency, and fragile X syndrome (FXS), respectively. The currently available molecular diagnostic tests are either costly or labour-intensive, which prohibits their application as a first-line FMR1 test in large-scale population-based screening programs. In this study, we demonstrate the utility of a simplified closed-tube strategy for rapid first-line screening of FXS based on melt peak temperature (Tm) analysis of direct triplet-primed polymerase chain reaction amplicons (dTP-PCR MCA). In addition, we also evaluated the correlation between Tm and CGG-repeat size based on capillary electrophoresis (CE) of dTP-PCR amplicons. The assays were initially tested on 29 FMR1 reference DNA samples, followed by a blinded validation on 107 previously characterised patient DNA samples. The dTP-PCR MCA produced distinct melt profiles of higher Tm for samples carrying an expanded allele. Among the samples tested, we also observed a good correlation between Tm and CGG-repeat size. In the blinded validation study, dTP-PCR MCA accurately classified all normal and expansion carriers, and the FMR1 genotypic classification of all samples was completely concordant with the previously determined genotypes as well as the dTP-PCR CE results. This simple and cost-effective MCA-based assay may be useful as a first-line FXS screening tool that could rapidly screen out the large majority of unaffected individuals, thus minimising the number of samples that need to be analysed by Southern blot analysis.

  18. 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

  19. 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)

  20. GeneX Va: VBC open source microarray database and analysis software.

    Science.gov (United States)

    Lee, Jae K; Laudeman, Tom; Kanter, Jodi; James, Teela; Siadaty, Mir S; Knaus, William A; Prorok, Alyson; Bao, Yongde; Freeman, Brad; Puiu, Daniela; Wen, Li Min; Buck, Gregory A; Schlauch, Karen; Weller, Jennifer; Fox, Jay W

    2004-04-01

    Developed by the Virginia Bioinformatics Consortium (VBC), GeneX Va is an open source, freeware database and bioinformatics analysis software for archiving and analyzing Affymetrix GeneChip data. It provides an integrated framework for management, documentation, and analysis of microarray experiments and data to support a range of users, from individual research laboratories to institutional microarray facilities. GeneX Va also provides web-based access to a PostgreSQL relational database system with a comprehensive security system. Data can be extracted from the database and delivered to interactive or scriptable statistical analysis protocols. The security system allows each investigator to manage their own array data and analysis output files and also provides custom access privileges for other users, groups, and internal/external collaborators. The analysis interface uses "Analysis Trees," an innovative user interface that allows researchers to interactively create a tree-structured flow chart of analysis routines. The latest GeneX Va software is available from and can be freely downloaded at the Sourceforge web site http://va-genex.sourceforge.net. To allow researchers to access the database and analysis capabilities of the GeneX Va system, microarray data from many VBC GeneChip experiments have been deposited into a public section of the GeneX Va system at the University of Virginia. The VBC GeneX Va sites, which include documentation, are at http://genes.med.virginia.edu/ of the University of Virginia and at http://genex.csbc.vcu.edu/ of the Virginia Commonwealth University.

  1. 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 …

  2. 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.

  3. 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.

  4. 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)

  5. 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.

  6. Implementing brief Dynamic Interpersonal Therapy (DIT) in a VA Medical Center.

    Science.gov (United States)

    Chen, Cory K; Ingenito, Christine P; Kehn, Michelle M; Nehrig, Nicole; Abraham, Karen S

    2017-07-12

    Given increasing mental health needs in the VA, identifying strategies to deliver new services is critical. This paper describes the process of navigating provider, patient and systems barriers of an initiative to increase choice, access and quality of psychotherapy at the VA by incorporating an evidence-based short-term, psychodynamic psychotherapy. Brief Dynamic Interpersonal Therapy (DIT) was selected as a viable model for implementation. Data were gathered on the process of implementation, barriers, Veterans seen, and access to psychodynamic psychotherapy. Nine psychologists and 22 masters level pre-doctoral psychology externs have delivered DIT to 73 Veterans. Veterans referred for psychodynamic psychotherapy annually increased 360%. Furthermore, DIT has become the dominant form of psychodynamic psychotherapy requested of the psychology service representing 70.1% of psychodynamic psychotherapy referrals. Strategies are presented for addressing: (1) provider ability, flexibility and motivation, (2) Veteran perception of relevance, distinctiveness and adaptability to complex presenting issues and (3) administrative support. Implementing an evidence-based short-term psychodynamic treatment option in the VA is feasible. VA mental health providers can be trained in brief psychodynamic psychotherapy and can successfully implement those approaches in VA settings. Finally, psychodynamic treatment approaches may serve as a promising alternative to currently available treatments.

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

    Science.gov (United States)

    2014-09-01

    benefit for veterans who require assistance from a caregiver. It can be added to a veteran’s existing pension if the veteran requires assistance with...AL 2 241 1:121 22 VA Long Beach HCS Long Beach, CA 2 245 1:123 22 VA Loma Linda HCS Loma Linda, CA 3 375 1:125 18 New Mexico VA HCS Albuquerque, NM

  8. Hemoglobin derivatives

    Science.gov (United States)

    ... this page: //medlineplus.gov/ency/article/003371.htm Hemoglobin derivatives To use the sharing features on this page, please enable JavaScript. Hemoglobin derivatives are altered forms of hemoglobin . Hemoglobin is ...

  9. 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...

  10. 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.

  11. 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.

  12. Calculating operational value-at-risk (OpVaR in a retail bank

    Directory of Open Access Journals (Sweden)

    Ja'nel Esterhuysen

    2012-05-01

    Full Text Available The management of operational value-at-risk (OpVaR in financial institutions is presented by means of a novel, robust calculation technique and the influence of this value on the capital held by a bank for operational risk. A clear distinction between economic and regulatory capital is made, as well as the way OpVaR models may be used to calculate both types of capital. Under the Advanced Measurement Approach (AMA, banks may employ OpVaR models to calculate regulatory capital; this article therefore illustrates the differences in regulatory capital when using the AMA and the Standardised Approach (SA, by means of an example. Economic capital is found to converge with regulatory capital using the AMA, but not if the SA is used.

  13. 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.

  14. 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.

  15. VA health service utilization for homeless and low-income Veterans: a spotlight on the VA Supportive Housing (VASH) program in greater Los Angeles.

    Science.gov (United States)

    Gabrielian, Sonya; Yuan, Anita H; Andersen, Ronald M; Rubenstein, Lisa V; Gelberg, Lillian

    2014-05-01

    The US Department of Housing and Urban Development (HUD)-VA Supportive Housing (VASH) program-the VA's Housing First effort-is central to efforts to end Veteran homelessness. Yet, little is known about health care utilization patterns associated with achieving HUD-VASH housing. We compare health service utilization at the VA Greater Los Angeles among: (1) formerly homeless Veterans housed through HUD-VASH (HUD-VASH Veterans); (2) currently homeless Veterans; (3) housed, low-income Veterans not in HUD-VASH; and (4) housed, not low-income Veterans. We performed a secondary database analysis of Veterans (n=62,459) who received VA Greater Los Angeles care between October 1, 2010 and September 30, 2011. We described medical/surgical and mental health utilization [inpatient, outpatient, and emergency department (ED)]. We controlled for demographics, need, and primary care use in regression analyses of utilization data by housing and income status. HUD-VASH Veterans had more inpatient, outpatient, and ED use than currently homeless Veterans. Adjusting for demographics and need, HUD-VASH Veterans and the low-income housed Veterans had similar likelihoods of medical/surgical inpatient and outpatient utilization, compared with the housed, not low-income group. Adjusting first for demographics and need (model 1), then also for primary care use (model 2), HUD-VASH Veterans had the greatest decrease in incident rates of specialty medical/surgical, mental health, and ED care from models 1 to 2, becoming similar to the currently homeless, compared with the housed, not low-income group. Our findings suggest that currently homeless Veterans underuse health care relative to housed Veterans. HUD-VASH may address this disparity by providing housing and linkages to primary care.

  16. Myosin-Va and Dynamic Actin Oppose Microtubules to Drive Long-Range Organelle Transport

    Science.gov (United States)

    Evans, Richard D.; Robinson, Christopher; Briggs, Deborah A.; Tooth, David J.; Ramalho, Jose S.; Cantero, Marta; Montoliu, Lluis; Patel, Shyamal; Sviderskaya, Elena V.; Hume, Alistair N.

    2014-01-01

    Summary In animal cells, microtubule and actin tracks and their associated motors (dynein, kinesin, and myosin) are thought to regulate long- and short-range transport, respectively [1–8]. Consistent with this, microtubules extend from the perinuclear centrosome to the plasma membrane and allow bidirectional cargo transport over long distances (>1 μm). In contrast, actin often comprises a complex network of short randomly oriented filaments, suggesting that myosin motors move cargo short distances. These observations underpin the “highways and local roads” model for transport along microtubule and actin tracks [2]. The “cooperative capture” model exemplifies this view and suggests that melanosome distribution in melanocyte dendrites is maintained by long-range transport on microtubules followed by actin/myosin-Va-dependent tethering [5, 9]. In this study, we used cell normalization technology to quantitatively examine the contribution of microtubules and actin/myosin-Va to organelle distribution in melanocytes. Surprisingly, our results indicate that microtubules are essential for centripetal, but not centrifugal, transport. Instead, we find that microtubules retard a centrifugal transport process that is dependent on myosin-Va and a population of dynamic F-actin. Functional analysis of mutant proteins indicates that myosin-Va works as a transporter dispersing melanosomes along actin tracks whose +/barbed ends are oriented toward the plasma membrane. Overall, our data highlight the role of myosin-Va and actin in transport, and not tethering, and suggest a new model in which organelle distribution is determined by the balance between microtubule-dependent centripetal and myosin-Va/actin-dependent centrifugal transport. These observations appear to be consistent with evidence coming from other systems showing that actin/myosin networks can drive long-distance organelle transport and positioning [10, 11]. PMID:25065759

  17. 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.

  18. 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.

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

    Science.gov (United States)

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

    2013-01-01

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

  20. Analisis del VaR en crisis y estabilidad: El caso de Mexico y Argentina

    Directory of Open Access Journals (Sweden)

    Cortez, K.A.

    2008-07-01

    Full Text Available The present analysis shows the possible effects of the risk to which the economies of Mexico and Argentina are exposed. The article studies the methodology of the VaR using the parametric model of average variance in individual in the type of change of the economies of Mexico and Argentina. The types from changes of the two economies are taken and the evolution of the VaR at time of crisis and exchange stability is analyzed. The main disadvantages of the Bar like metric are explained of measurement of risk.

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

    Science.gov (United States)

    Rask, Malte Bille; Knopp, Matthias Manne; Olesen, Niels Erik; Holm, René; Rades, Thomas

    2016-03-31

    In this study, the influence of copolymer composition on drug-polymer solubility was investigated. The solubility of the model drug celecoxib (CCX) in various polyvinylpyrrolidone/vinyl acetate (PVP/VA) copolymer compositions (70/30, 60/40, 50/50 and 30/70 w/w) and the pure homopolymers polyvinylpyrrolidone (PVP) and polyvinyl acetate (PVA) was predicted at 25 °C using a thermal analysis method based on the recrystallization of a supersaturated amorphous dispersion (recrystallization method). These solubilities were compared with a prediction based on the solubility of CCX in the liquid monomeric precursors of PVP/VA, N-vinylpyrrolidone (NVP) and vinyl acetate (VA), using the Flory-Huggins lattice theory (liquid monomer solubility approach). The solubilities predicted from the liquid monomer solubility approach increased linearly with increasing VP/VA ratio from 0.03-0.60 w/w. Even though the solubilities predicted from the recrystallization method also increased with increasing VP/VA ratio from 0.02-0.40 w/w, the predicted solubility seemed to approach a plateau at high VP/VA ratios. Increasing positive deviations from the Gordon-Taylor equation with increasing VP/VA ratio indicated strong interactions between CCX and the VP repeat unit, which was in accordance with the relatively high solubilities predicted using both methods. As the solubility plateau may be a consequence of steric hindrance caused by the size differences between CCX and the VP repeat units, it is likely that a CCX molecule interacting with a VP repeat unit hinders another CCX molecule from binding to the neighboring repeat units in the polymer chain. Therefore, it is possible that replacing these neighboring hygroscopic VP repeat units with hydrophobic VA repeat units, could increase the physical stability of an amorphous solid dispersion without compromising the drug-polymer solubility. This knowledge could be used advantageously in future development of amorphous drug delivery systems as

  2. Myosin Va participates in acrosomal formation and nuclear morphogenesis during spermatogenesis of Chinese mitten crab Eriocheir sinensis.

    Directory of Open Access Journals (Sweden)

    Xiao Sun

    Full Text Available BACKGROUND: The Chinese mitten crab Eriocheir sinensis belongs to the Class Crustacea, Decapoda, Brachyura. The spermatozoon of this species is of aflagellated type, it has a spherical acrosome surrounded by the cup-shaped nucleus, which are unique to brachyurans. For the past several decades, studies on the spermatogenesis of the mitten crab mainly focus on the morphology. Compared with the extensive study of molecular mechanism of spermatogenesis in mammals, relatively less information is available in crustacean species. Myosin Va, a member of Class V myosin, has been implicated in acrosome biogenesis and vesicle transport during spermatogenesis in mammals. In the present study we demonstrate the expression and cellular localization of myosin Va during spermatogenesis in E. sinensis. METHODOLOGY/PRINCIPAL FINDINGS: Western blot demonstrated that myosin Va is expressed during spermatogenesis. Immunocytochemical and ultrastructural analyses showed that myosin Va mainly localizes in the cytoplasm in spermatocytes. At the early stage of spermiogenesis, myosin Va binds to the endoplasmic reticulum vesicle (EV and proacrosomal granule (PG. Subsequently, myosin Va localizes within the proacrosomal vesicle (PV formed by PG and EV fusion and locates in the membrane complex (MC at the mid spermatid stage. At the late spermatid stage, myosin Va is associated with the shaping nucleus and mitochondria. In mature spermatozoon, myosin Va predominates in acrosomal tubule (AT and nucleus. CONCLUSIONS/SIGNIFICANCE: Our study demonstrates that myosin Va may be involved in acrosome biogenesis and nuclear morphogenesis during spermatogenesis in E. sinensis. Considering the distribution and molecular characteristics of myosin Va, we also propose a hypothesis of AT formation in this species. It is the first time to uncover the role of myosin Va in crustacean spermatogenesis.

  3. 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.

  4. Tandem multiplication of the IS26-flanked amplicon with the bla(SHV-5) gene within plasmid p1658/97.

    Science.gov (United States)

    Zienkiewicz, Maksymilian; Kern-Zdanowicz, Izabela; Carattoli, Alessandra; Gniadkowski, Marek; Cegłowski, Piotr

    2013-04-01

    The IncF plasmid p1658/97 (c. 125 kb) from Escherichia coli isolates recovered during a clonal outbreak in a hospital in Warsaw, Poland, in 1997 contains the extended-spectrum β-lactamase (ESBL) gene bla(SHV-5), originated from the Klebsiella pneumoniae chromosome. A region containing the bla(SHV-5) gene is flanked by two IS26 copies and its copy number multiplies spontaneously within p1658/97 and RecA-deficient E. coli strains. Here, we demonstrate that the amplified IS26-bla(SHV-5) units were arranged in tandems, containing up to more than 10 units, which could raise ceftazidime MICs for host strains from 4 μg mL(-1) to more than 128 μg mL(-1). Successive deletions within p1658/97, located outside the amplifiable module and encompassing even as little as c. 15% of the plasmid, blocked the amplification. Moreover, the complementing re-introduction of the deleted fragments in trans did not restore the process. Similarly, insertions of a 1-kb DNA fragment into the amplicon inhibited its self-multiplication ability. The module was able to transmit into another IS26-containing plasmid by recombination. The results prompted us to speculate that local DNA structure, especially favorable in p1658/97, might have been responsible for the IS26-bla(SHV-5) multiplication ability. © 2013 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

  5. Application of long amplicon propidium monoazide-PCR to assess the effects of temperature and background microbiota on pathogens in river water.

    Science.gov (United States)

    Banihashemi, Avid; Van Dyke, Michele I; Huck, Peter M

    2017-06-01

    The decay rates of enteric waterborne pathogens were evaluated following the introduction of Yersinia enterocolitica, Salmonella enterica, Campylobacter jejuni and Arcobacter butzleri into river water at different temperatures (5, 15 and 25°C) for a period of 28 days. To improve the accuracy of the results a molecular viability assay, long amplicon propidium monoazide-polymerase chain reaction (PMA-PCR), was used to quantify the viable cell concentration and results from PCR with and without PMA were compared. As well, the effect of background microbiota was assessed for Y. enterocolitica and S. enterica by inoculating cells into sterile and non-sterile river water. Cell persistence was improved by up to 4 log for Y. enterocolitica and 4.5 log for S. enterica in sterile river water compared to natural river water, showing that the autochthonous biological activity in river water can accelerate the die-off of introduced bacteria. Results also showed that low temperature significantly improved the persistence of all four target bacteria in non-sterile river water. There was a more rapid decline in cell concentration in samples with PMA pretreatment; therefore using PMA-PCR analysis can provide more reliable data on viable/active enteric bacteria in aquatic microcosms and allows for improved assessment of pathogens in the environment.

  6. Identification of active denitrifiers by DNA-stable isotope probing and amplicon sequencing reveals Betaproteobacteria as responsible for attenuation of nitrate contamination in a low impacted aquifer.

    Science.gov (United States)

    Bellini, M Inés; Kumaresan, Deepak; Tarlera, Silvana; Murrell, J Colin; Fernández-Scavino, Ana

    2018-02-01

    Groundwater reservoirs constitute important freshwater resources. However, these ecosystems are highly vulnerable to contamination and have to rely on the resident microbiota to attenuate the impact of this contamination. Nitrate is one of the main contaminants found in groundwater, and denitrification is the main process that removes the compound. In this study, the response to nutrient load on indigenous microbial communities in groundwater from a low impacted aquifer in Uruguay was evaluated. Denitrification rates were measured in groundwater samples from three different sites with nitrate, acetate and pyrite amendments. Results showed that denitrification is feasible under in situ nitrate and electron donor concentrations, although the lack of readily available organic energy source would limit the attenuation of higher nitrate concentrations. DNA-stable isotope probing, combined with amplicon sequencing of 16S rRNA, nirS and nirK genes, was used to identify the active denitrifiers. Members of the phylum Betaproteobacteria were the dominant denitrifiers in two of three sites, with different families being observed; members of the genus Vogesella (Neisseriaceae) were key denitrifiers at one site, while the genera Dechloromonas (Rhodocyclaceae) and Comamonas (Comamonadaceae) were the main denitrifiers detected at the other sites. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

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

    Science.gov (United States)

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

    2014-01-01

    Eighteen Kiko-cross meat goats (n = 6) were used to collect gastrointestinal (GI) bacteria and methanogenic archaea for diversity measures when fed condensed tannin-containing pine bark (PB). Three dietary treatments were tested: control diet (0% PB and 30% wheat straw (WS); 0.17% condensed tannins (CT) dry matter (DM)); 15% PB and 15% WS (1.6% CT DM), and 30% PB and 0% WS (3.2% CT DM). A 16S rDNA bacterial tag-encoded FLX amplicon pyrosequencing technique was used to characterize and elucidate changes in GI bacteria and methanogenic archaea diversity among the diets. Proteobacteria was the most dominant phylum in goats with mean relative abundance values ranging from 39.7 (30% PB) to 46.5% (control) and 47.1% (15% PB). Other phyla individually accounted for fewer than 25% of the relative abundance observed. Predominant methanogens were Methanobrevibacter (75, 72, and 49%), Methanosphaera (3.3, 2.3, and 3.4%), and Methanobacteriaceae (1.2, 0.6, and 0.7%) population in control, 15, and 30% PB, respectively. Among methanogens, Methanobrevibacter was linearly decreased (P = 0.05) with increasing PB supplementation. These results indicate that feeding PB selectively altered bacteria and methanogenic archaeal populations in the GI tract of goats.

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

    Directory of Open Access Journals (Sweden)

    Byeng R. Min

    2014-01-01

    Full Text Available Eighteen Kiko-cross meat goats (n=6 were used to collect gastrointestinal (GI bacteria and methanogenic archaea for diversity measures when fed condensed tannin-containing pine bark (PB. Three dietary treatments were tested: control diet (0% PB and 30% wheat straw (WS; 0.17% condensed tannins (CT dry matter (DM; 15% PB and 15% WS (1.6% CT DM, and 30% PB and 0% WS (3.2% CT DM. A 16S rDNA bacterial tag-encoded FLX amplicon pyrosequencing technique was used to characterize and elucidate changes in GI bacteria and methanogenic archaea diversity among the diets. Proteobacteria was the most dominant phylum in goats with mean relative abundance values ranging from 39.7 (30% PB to 46.5% (control and 47.1% (15% PB. Other phyla individually accounted for fewer than 25% of the relative abundance observed. Predominant methanogens were Methanobrevibacter (75, 72, and 49%, Methanosphaera (3.3, 2.3, and 3.4%, and Methanobacteriaceae (1.2, 0.6, and 0.7% population in control, 15, and 30% PB, respectively. Among methanogens, Methanobrevibacter was linearly decreased (P=0.05 with increasing PB supplementation. These results indicate that feeding PB selectively altered bacteria and methanogenic archaeal populations in the GI tract of goats.

  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. Financial derivatives

    OpenAIRE

    Koutný, Ondřej

    2012-01-01

    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...

  12. Financial Derivatives

    DEFF Research Database (Denmark)

    Wigan, Duncan

    2013-01-01

    Contemporary derivatives mark the development of capital and constitute a novel form of ownership. By reconfiguring the temporal, spatial and legal character of ownership derivatives present a substantive challenge to the tax collecting state. While fiscal systems are nationally bounded and inheren......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...

  13. 33 CFR 334.280 - James River between the entrance to Skiffes Creek and Mulberry Point, Va.; army training and...

    Science.gov (United States)

    2010-07-01

    ... to Skiffes Creek and Mulberry Point, Va.; army training and small craft testing area. 334.280 Section... Creek and Mulberry Point, Va.; army training and small craft testing area. (a) The restricted area... regulations of the Department of the Army, nor will the passage of fishing vessels to or from authorized traps...

  14. 75 FR 23800 - Notice of Intent to Repatriate a Cultural Item: Virginia Museum of Fine Arts, Richmond, VA

    Science.gov (United States)

    2010-05-04

    ...). Records from the Portland Art Museum read as follows: ``Purchase, Indian Collection Subscription Fund. To...: Virginia Museum of Fine Arts, Richmond, VA AGENCY: National Park Service, Interior. ACTION: Notice. Notice... of Fine Arts, Richmond, VA, that meets the definition of ``object of cultural patrimony'' under 25 U...

  15. 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...

  16. 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 ...

  17. 77 FR 12997 - Drug and Drug-Related Supply Promotion by Pharmaceutical Company Representatives at VA Facilities

    Science.gov (United States)

    2012-03-05

    ... it would be inappropriate to allow, as a general rule, drug marketing to target health professional...,'' ``promotional materials,'' ``patient education materials,'' and ``individual departments.'' We disagree with the... representatives and VA staff. Commenters also suggested that VA define the term ``marketing activities'' as used...

  18. 75 FR 15721 - Back Bay National Wildlife Refuge, City of Virginia Beach, VA

    Science.gov (United States)

    2010-03-30

    ... Fish and Wildlife Service Back Bay National Wildlife Refuge, City of Virginia Beach, VA AGENCY: Fish... will also hold public meetings in Virginia Beach, Virginia during the 30-day review period to receive... Back Bay NWR, 4005 Sandpiper Road, Virginia Beach, Virginia. U.S. Postal Service: Thomas Bonetti...

  19. 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...

  20. 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 ...

  1. 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

  2. 76 FR 2148 - Specialty Minerals, Inc., Franklin, VA; Notice of Revised Determination on Reconsideration

    Science.gov (United States)

    2011-01-12

    ... Employment and Training Administration Specialty Minerals, Inc., Franklin, VA; Notice of Revised... Minerals, Inc., Franklin, Virginia (the subject firm). The Notice was published ] in the Federal Register... reconsideration, I determine that workers of Specialty Minerals, Inc., Franklin, Virginia, who are engaged in...

  3. DOD and VA Health Care: Actions Needed to Help Ensure Appropriate Medication Continuation and Prescribing Practices

    Science.gov (United States)

    2016-01-01

    GAO-16-158 DOD and VA Health Care medications.56 When we discussed the concept of a single formulary with officials, VHA officials expressed concern...Director; Jennie F. Apter; Pamela Dooley; Joshua D. Ferencik; Jacquelyn Hamilton; Toni Harrison; Katie McConnell ; and Daniel Ries made key

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

    Science.gov (United States)

    2016-12-01

    Coalition for Homeless Veterans, and Vietnam Veterans of America . We also interviewed officials in select locations that either have large populations of... homelessness : The National Alliance to End Homelessness , National Coalition for Homeless Veterans, U.S. Vets, Vietnam Veterans of America , and the... HOMELESS VETERANS Management Improvements Could Help VA Better Identify Supportive-Housing Projects Report to

  5. 78 FR 56271 - FY 2014-2020 Draft VA Strategic Plan

    Science.gov (United States)

    2013-09-12

    ... developing our workforce with the skills, tools, and leadership to meet our clients' needs and expectations... requires agencies require more frequent reporting and reviews (quarterly instead of annually) that are... leadership to meet our clients' needs and expectations. VA's FY 2014-2020 strategic goals are to: (1) Empower...

  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... health services and hospice care. The reasons that we would make the billing methodology in Sec. 17.56... could be interpreted as providing an alternate billing methodology applicable only to these services...

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

    CERN Document Server

    2002-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Othman Y. Alothman

    2012-01-01

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

  9. 76 FR 34248 - Equestrian Stables at Meadowood Special Recreation Management Area, VA; Information Sharing Meeting

    Science.gov (United States)

    2011-06-13

    ... DEPARTMENT OF THE INTERIOR Equestrian Stables at Meadowood Special Recreation Management Area, VA; Information Sharing Meeting AGENCY: Bureau of Land Management, Interior. ACTION: Notice of public meeting... about the condition of the equestrian stables at Meadowood Special Recreation Management Area (SRMA...

  10. 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...

  11. Note from North America: "Linda, VA AG 2013 and Knitting Needles" and "Words"

    Science.gov (United States)

    Alper, Paul

    2014-01-01

    This article is comprised of two essays by Paul Alper. The first essay, "Linda VA AG 2013 and Knitting Needles," provides examples of how a natural language does not necessarily work the way of logic. The second essay, "Words," discusses how the words of winners tend to become what we call the enduring historical record. The…

  12. 30 CFR 57.22229 - Weekly testing (I-A, III, and V-A mines).

    Science.gov (United States)

    2010-07-01

    ... METAL AND NONMETAL MINE SAFETY AND HEALTH SAFETY AND HEALTH STANDARDS-UNDERGROUND METAL AND NONMETAL MINES Safety Standards for Methane in Metal and Nonmetal Mines Ventilation § 57.22229 Weekly testing (I... 30 Mineral Resources 1 2010-07-01 2010-07-01 false Weekly testing (I-A, III, and V-A mines). 57...

  13. 77 FR 21158 - VA Directive 0005 on Scientific Integrity: Availability for Review and Comment

    Science.gov (United States)

    2012-04-09

    ... Friday (except holidays). Call (202) 461-4902 for an appointment. Those without computer access may call..., and ethical behavior in the development and application of scientific and technological findings in VA... research, including the protection of human subjects, laboratory animal welfare, research safety and...

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

    NARCIS (Netherlands)

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

    2014-01-01

    This study utilized data from the evaluation of the Finnish KiVa program in testing the prediction that school bullies' high perceived popularity would impede the success of anti-bullying interventions. Multiple-group structural equation modeling (SEM) analyses were conducted on a subsample of 911

  15. 38 CFR 1.9 - Description, use, and display of VA seal and flag.

    Science.gov (United States)

    2010-07-01

    ... 38 Pensions, Bonuses, and Veterans' Relief 1 2010-07-01 2010-07-01 false Description, use, and display of VA seal and flag. 1.9 Section 1.9 Pensions, Bonuses, and Veterans' Relief DEPARTMENT OF... stars represent the five branches of military service. The crossed flags represent our nation's history...

  16. 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...

  17. 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...

  18. 75 FR 76953 - Foreign-Trade Zone 238-Dublin, VA Site Renumbering Notice

    Science.gov (United States)

    2010-12-10

    ... DEPARTMENT OF COMMERCE Foreign-Trade Zones Board Foreign-Trade Zone 238--Dublin, VA Site Renumbering Notice Foreign-Trade Zone 238 was approved by the Foreign-Trade Zones Board on August 5, 1999... Boulevard, Pulaski. For further information, contact Maureen Hinman at [email protected]trade.gov or (202) 482...

  19. 75 FR 76953 - Foreign-Trade Zone 207-Richmond, VA Site Renumbering Notice

    Science.gov (United States)

    2010-12-10

    ... DEPARTMENT OF COMMERCE Foreign-Trade Zones Board Foreign-Trade Zone 207--Richmond, VA Site Renumbering Notice Foreign-Trade Zone 207 was approved by the Foreign-Trade Zones Board on March 31, 1995... [email protected]trade.gov or (202) 482-0627. Dated: December 1, 2010. Andrew McGilvray, Executive Secretary...

  20. 77 FR 56709 - Proposed Information Collection (VA Subcontracting Report for Service Disabled Veteran-Owned...

    Science.gov (United States)

    2012-09-13

    ... Subcontracting Report for Service Disabled Veteran-Owned Small Business and Veteran-Owned Small Business Concerns... use of other forms of information technology. Title: VA Subcontracting Report for Service Disabled... direction of the Secretary. Denise McLamb, Program Analyst, Enterprise Records Service. [FR Doc. 2012-22488...

  1. 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

  2. 77 FR 48127 - Foreign-Trade Zone 20-Suffolk, VA; Notification of Proposed Production Activity, Usui...

    Science.gov (United States)

    2012-08-13

    ..., Usui International Corporation, (Diesel Engine Fuel Lines), Chesapeake, VA The Virginia Port Authority... is located within Site 9 of FTZ 20. The facility is used for the production of diesel engine fuel lines. Production under FTZ procedures could exempt Usui from customs duty payments on foreign status...

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

    Science.gov (United States)

    2010-10-01

    ... 48 Federal Acquisition Regulations System 5 2010-10-01 2010-10-01 false Resolving differences between VA and the Small Business Administration. 819.602-3 Section 819.602-3 Federal Acquisition Regulations System DEPARTMENT OF VETERANS AFFAIRS SOCIOECONOMIC PROGRAMS SMALL BUSINESS PROGRAMS Certificates of Competency and Determinations of...

  4. 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...

  5. 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.

  6. 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).

  7. Exploring the Relevance and Quality of the VaRemba Initiation ...

    African Journals Online (AJOL)

    district in Zimbabwe as well as assess its impact on formal schooling. When exploring issues ... to analyse the impact of the VaRemba initiation curriculum on formal education; and. • to suggest possible ..... towards men, including their male teachers, and a negative attitude towards female teachers. One teacher described ...

  8. 38 CFR 58.10 - VA Form 10-3567-State Home Inspection Staffing Profile.

    Science.gov (United States)

    2010-07-01

    ... 38 Pensions, Bonuses, and Veterans' Relief 2 2010-07-01 2010-07-01 false VA Form 10-3567-State Home Inspection Staffing Profile. 58.10 Section 58.10 Pensions, Bonuses, and Veterans' Relief... Profile. ER06JA00.000 ER06JA00.001 ER06JA00.002 ...

  9. 78 FR 77204 - Proposed Information Collection (VA National Veterans Sports Programs and Special Event Surveys...

    Science.gov (United States)

    2013-12-20

    ... use of other forms of information technology. Titles: VA National Veterans Sports Programs and Special... National Veterans Sports Programs and Special Event Surveys Data Collection) Activity: Comment Request... needed to evaluate the National Veterans Sports Programs and Special Event Surveys Data Collection is...

  10. Data of evolutionary structure change: 1A4VA-1GFUA [Confc[Archive

    Lifescience Database Archive (English)

    Full Text Available 1A4VA-1GFUA 1A4V 1GFU A A KQFTKCELSQLLKDI--DGYGGIALPELICTMFHTSGYD...ine> 1GFU A 1GFU...A 390 TYR CA 428 1GFU A 1GFU...e> TYR CA 329 1GFU A 1GFU...ine> GLU CA 184 GLN CA 218 TRP CA 302 1GFU

  11. 75 FR 60171 - Proposed Information Collection (Credit Underwriting Standards and Procedures for Processing VA...

    Science.gov (United States)

    2010-09-29

    ... credit history in order to properly underwrite the veteran's loan. VA loans may not be guaranteed unless the veteran is a satisfactory credit risk. The data collected on the following forms will be used to... DEPARTMENT OF VETERANS AFFAIRS [OMB Control No. 2900-0521] Proposed Information Collection (Credit...

  12. 75 FR 76082 - Agency Information Collection (Credit Underwriting Standards and Procedures for Processing VA...

    Science.gov (United States)

    2010-12-07

    ... must obtain specific information concerning a veteran's credit history in order to properly underwrite the veteran's loan. VA loans may not be guaranteed unless the veteran is a satisfactory credit risk... DEPARTMENT OF VETERANS AFFAIRS [OMB Control No. 2900-0521] Agency Information Collection (Credit...

  13. 78 FR 60379 - Proposed Information Collection (Credit Underwriting Standards and Procedures for Processing VA...

    Science.gov (United States)

    2013-10-01

    ... credit history in order to properly underwrite the veteran's loan. VA loans may not be guaranteed unless the Veteran is a satisfactory credit risk. The data collected on the following forms will be used to... DEPARTMENT OF VETERANS AFFAIRS [OMB Control No. 2900-0521] Proposed Information Collection (Credit...

  14. 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...

  15. 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

  16. Quantifying risks with exact analytical solutions of derivative pricing distribution

    Science.gov (United States)

    Zhang, Kun; Liu, Jing; Wang, Erkang; Wang, Jin

    2017-04-01

    Derivative (i.e. option) pricing is essential for modern financial instrumentations. Despite of the previous efforts, the exact analytical forms of the derivative pricing distributions are still challenging to obtain. In this study, we established a quantitative framework using path integrals to obtain the exact analytical solutions of the statistical distribution for bond and bond option pricing for the Vasicek model. We discuss the importance of statistical fluctuations away from the expected option pricing characterized by the distribution tail and their associations to value at risk (VaR). The framework established here is general and can be applied to other financial derivatives for quantifying the underlying statistical distributions.

  17. 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.

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

    Directory of Open Access Journals (Sweden)

    Liu Chuan-Fen

    2012-03-01

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

  19. The Characters’ Transactional Analysis in Shir-va-Gav (lion and cow Story (one of Kelile-va-Demne stories

    Directory of Open Access Journals (Sweden)

    a razi

    2012-05-01

    The results of the analysis of the components of transactional analysis in Shir-va-Gav story show that the characters' relations have continuity, and among triple aspects of the character's structure, Kelile’s, Demne’s, and Shir's behaviors are assessable in the form of adult, parent, and child, respectively. Transactions among characters are of complementary kind in the beginning but throughout the story they turn into interaction of crossed kind and cause disorder in behavior.

  20. 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

  1. Improving the genotyping resolution of Cryptosporidium hominis subtype IbA10G2 using one step PCR-based amplicon sequencing.

    Science.gov (United States)

    Beser, Jessica; Hallström, Björn M; Advani, Abdolreza; Andersson, Sofia; Östlund, Gabriel; Winiecka-Krusnell, Jadwiga; Lebbad, Marianne; Alm, Erik; Troell, Karin; Arrighi, Romanico B G

    2017-11-01

    Cryptosporidium hominis gp60 subtype IbA10G2 is a common cause of cryptosporidiosis. This subtype is responsible for many waterborne outbreaks as well as sporadic cases and is considered virulent and highly important in the epidemiology of cryptosporidiosis. Due to low heterogeneity within the genome of C. hominis it has been difficult to identify epidemiological markers with higher resolution than gp60. However, new markers are required in order to improve outbreak investigations and studies of the transmission dynamics of this clinically important subtype. Based on the whole genome sequences of 17 C. hominis isolates, we have identified several differential loci and developed a new sequence based typing panel with higher resolution than gp60. An amplicon sequencing method was also developed which is based on a one-step PCR which can be sequenced using a Next Generation Sequencing (NGS) platform. Such a system provides a rapid and high-throughput workflow. A panel of nine loci with 10 single nucleotide variants (SNV) was selected and evaluated using clinical IbA10G2 isolates from sporadic, cluster and outbreak associated cases. The specimens were separated into 10 different genetic profiles named sequence types (STs). All isolates within an outbreak or cluster belonged to the same ST, including several samples from the two large waterborne outbreaks which occurred in Sweden between 2010 and 2011 indicating that these outbreaks might be linked. The results demonstrate the methods suitability for improved genotyping of C. hominis IbA10G2. Copyright © 2017 Elsevier B.V. All rights reserved.

  2. Global Derivatives

    DEFF Research Database (Denmark)

    Andersen, Torben Juul

    ." - Steen Parsholt, Chairman and CEO, Aon Nordic Region. "Andersen has done a wonderful job of developing a comprehensive text that deals with risk management in global markets. I would recommend this book to any student or businessman who has a need to better understand the risks and risk management......""In Global Derivatives: A Strategic Risk Management Perspective", Torben Juul Andersen has succeeded to gather in one book a complete and thorough summary and an easy-to-read explanation of all types of derivative instruments and their background, and their use in modern management of risk...... approaches to dealing in the global business environment." - Sharon Brown-Hruska, Commissioner, Commodity Futures Trading Commission, USA. "This comprehensive survey of modern risk management using derivative securities is a fine demonstration of the practical relevance of modern derivatives theory to risk...

  3. 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

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

    Science.gov (United States)

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

    2015-10-01

    The aim of this paper was to evaluate physical stability of solid dispersions in respect to the drug, tadalafil (Td), in vinylpyrrolidone and vinyl acetate block copolymer (PVP-VA). Nine solid dispersions of Td in PVP-VA (Td/PVP-VA) varied in terms of quantitative composition (1:9-9:1, w/w) were successfully produced by spray-drying. Their amorphous nature, supersaturated character and molecular level of mixing (a solid solution structure) were subsequently confirmed using DSC, PXRD, SEM and calculation of Hansen total solubility parameters. Due to thermal degradation of both components before the melting point of Td (302.3°C), an approach based on the drug crystallization from the supersaturated solid dispersion was selected to calculate the solubility of Td in the polymer. Annealing of the Td/PVP-VA solid dispersion (1:1, w/w) at selected temperatures above its Tg resulted in different stable solid dispersions. According to the Gordon-Taylor equation their new Tgs gave the information about the quantitative composition which corresponded to the thermodynamic solubility of Td in PVP-VA at given temperatures of annealing. The obtained relationship was fitted to the exponential function, with the calculated solubility of Td of 20.5% at 25°C. This value was in accordance with the results of hot stage polarizing light microscopy as well as stability tests carried out at 80°C and 0% RH, in which Td solid dispersions containing 10-20% of the drug were the only systems that did not crystallize within two months. A thermal analysis protocol utilizing a fast heating rate was shown to generate Td solubility data complementing the solid dispersion method. The Flory-Huggins model applied for the Td/PVP-VA system yielded the solubility value of 0.1% at 25°C, showing the lack of applicability in this case. Copyright © 2015 Elsevier B.V. All rights reserved.

  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. Perceptions of homelessness in older homeless veterans, VA homeless program staff liaisons, and housing intervention providers.

    Science.gov (United States)

    Molinari, Victor A; Brown, Lisa M; Frahm, Kathryn A; Schinka, John A; Casey, Roger

    2013-05-01

    To understand the needs and challenges encountered by older homeless veterans. We conducted six focus groups of older veterans, two focus groups, and one semi-structured interview of VA staff liaisons, and two focus groups and one semi-structured interview of housing intervention providers. Major themes for older veterans: 1) negative homelessness experience; 2) benefits of the structured transitional housing program; 3) importance of peer outreach; and 4) need for age-tailored job placement programs. Major themes for VA staff liaison/housing intervention providers: 1) belief that the transitional housing program has made a positive change; 2) need for individualized criteria to address the unique needs of veterans; 3) distinct differences between older and younger homeless veterans; 4) outreach services; 5) permanent housing issues; and 6) coordination of services. Compared with younger veterans, older veterans have less social support, greater employment and health challenges, and, perhaps greater motivation to change.

  7. 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

  8. 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

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

    Science.gov (United States)

    2016-04-01

    stakeholders, such as VA homeless and mental health program officials; as well as external stakeholders, such as representatives from the National ...others face difficulties, such as mental illness, substance abuse, unemployment, homelessness , and other serious issues. For some veterans, these...Program in 2009. The VJO Program is designed to connect veterans to supports and services to reduce and prevent re- incarceration and homelessness .2

  10. Suppression of Antifolate Resistance by Targeting the Myosin Va Trafficking Pathway in Melanoma

    Directory of Open Access Journals (Sweden)

    María Piedad Fernández-Pérez

    2013-07-01

    Full Text Available Human melanoma is a significant clinical problem. As most melanoma patients relapse with lethal drug-resistant disease, understanding and preventing mechanism(s of resistance is one of the highest priorities to improve melanoma therapy. Melanosomal sequestration and the cellular exportation of cytotoxic drugs have been proposed to be important melanoma-specific mechanisms that contribute to multidrug resistance in melanoma. Concretely, we found that treatment of melanoma with methotrexate (MTX altered melanogenesis and accelerated the exportation of melanosomes; however, the cellular and molecular processes by which MTX is trapped into melanosomes and exported out of cells have not been elucidated. In this study, we identified myosin Va (MyoVa as a possible mediator of these cellular processes. The results demonstrated that melanoma treatment with MTX leads to Akt2- dependent MyoVa phosphorylation, which enhances its ability to interact with melanosomes and accelerates their exportation. To understand the mechanism(s by which MTX activates Akt2, we examined the effects of this drug on the activity of protein phosphatase 2A, an Akt inhibitor activated by the methylation of its catalytic subunit. Taken together, this study identified a novel trafficking pathway in melanoma that promotes tumor resistance through Akt2/MyoVa activation. Because of these findings, we explored several MTX combination therapies to increase the susceptibility of melanoma to this drug. By avoiding MTX exportation, we observed that the E2F1 apoptotic pathway is functional in melanoma, and its induction activates p73 and apoptosis protease-activating factor 1 following a p53-autonomous proapoptotic signaling event.

  11. 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.

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

    Science.gov (United States)

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

    2013-01-01

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

  13. 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...

  14. 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 ...

  15. 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.

  16. 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.

  17. Sediment as a Regional Resource in the Low-Commercial-Use Navigation Program, Mathews County, VA

    Science.gov (United States)

    2013-09-01

    Commercial fishing, boat repair, marine construction, ecotourism , and other marine activities are important economic endeavors that provide sources of...to subside, future damages will likely worsen and begin impacting new areas. The mean sea level trend at Gloucester Point, VA (16 miles south of...Mathews County), is 3.81 millimeters per year (mm/year) rise with a 95% confidence interval of +/- 0.47 mm/year rise based on monthly mean sea level data

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

    Science.gov (United States)

    2016-12-01

    clerk stations and a lack of privacy curtains in examination rooms, as required by VHA policy. GAO also found weaknesses in VHA’s oversight of the...VHA officials said not all facilities require onsite gynecologists and facilities may authorize gynecological services from non-VA providers. They...does not have such measures for women veterans’ sex-specific care, such as mammography, maternity care, or gynecology . VHA’s data show poor

  19. Prothrombotic skeletal muscle myosin directly enhances prothrombin activation by binding factors Xa and Va

    Science.gov (United States)

    Deguchi, Hiroshi; Sinha, Ranjeet K.; Marchese, Patrizia; Ruggeri, Zaverio M.; Zilberman-Rudenko, Jevgenia; McCarty, Owen J. T.; Cohen, Mitchell J.

    2016-01-01

    To test the hypothesis that skeletal muscle myosins can directly influence blood coagulation and thrombosis, ex vivo studies of the effects of myosin on thrombogenesis in fresh human blood were conducted. Addition of myosin to blood augmented the thrombotic responses of human blood flowing over collagen-coated surfaces (300 s−1 shear rate). Perfusion of human blood over myosin-coated surfaces also caused fibrin and platelet deposition, evidencing myosin’s thrombogenicity. Myosin markedly enhanced thrombin generation in both platelet-rich plasma and platelet-poor plasma, indicating that myosin promoted thrombin generation in plasma primarily independent of platelets. In purified reaction mixtures composed only of factor Xa, factor Va, prothrombin, and calcium ions, myosin greatly enhanced prothrombinase activity. The Gla domain of factor Xa was not required for myosin’s prothrombinase enhancement. When binding of purified clotting factors to immobilized myosin was monitored using biolayer interferometry, factors Xa and Va each showed favorable binding interactions. Factor Va reduced by 100-fold the apparent Kd of myosin for factor Xa (Kd ∼0.48 nM), primarily by reducing koff, indicating formation of a stable ternary complex of myosin:Xa:Va. In studies to assess possible clinical relevance for this discovery, we found that antimyosin antibodies inhibited thrombin generation in acute trauma patient plasmas more than in control plasmas (P = .0004), implying myosin might contribute to acute trauma coagulopathy. We posit that myosin enhancement of thrombin generation could contribute either to promote hemostasis or to augment thrombosis risk with consequent implications for myosin’s possible contributions to pathophysiology in the setting of acute injuries. PMID:27421960

  20. DoD/VA Health Information Technology (IT) Data Sharing to Benefit Our Patients

    Science.gov (United States)

    2011-01-25

    GRISCOM. MISS Q Oemograpi-Ocs -U~H:::: Alergy Wetness l lrnrru1izations V•ol Signs Review PKC Couplers Readineu Patient Questionnaires l =~otes...Authorization Act (NDAA) FY 2008, Section 1635 required DoD and VA to “ develop and implement electronic health record (EHR) systems or... developed and funded 36 2011 MHS Conference 37 Recruitment Accession/Training Routine Care Readiness/ Pre-Deployment Deployed/Theater CareCare in

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

    OpenAIRE

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

    2015-01-01

    We report on the use of percutaneous femoral veno-arterial extracorporeal membrane oxygenation (VA-ECMO) in a fully awake, non-intubated and spontaneously breathing patient suffering from acute, severe and refractory cardiogenic shock due to a (sub)acute anterior myocardial infarction. Intensified heart failure therapy was closely monitored with a pulmonary artery catheter and allowed gradual weaning off the ECMO support without additional invasive measures, notably without mechanical ventila...

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

    Science.gov (United States)

    2017-03-01

    2017, VA officials also noted the agency is in the process of developing additional components, including document review software for VLJs and...average time taken to recruit, and skills needed in recruits, or identified metrics (other than hiring goals) against which it would measure the... Tester Ranking Member Committee on Veterans’ Affairs United States Senate The Honorable Jerry Moran Chairman The Honorable Brian Schatz Ranking

  3. Global Derivatives

    DEFF Research Database (Denmark)

    Andersen, Torben Juul

    , postgraduate qualification or MBA programme. This book also caters for practicing managers and executives who need to understand current developments in global derivatives markets and require cutting-edge insight on strategic risk management issues. Dr Torben Juul Andersen is currently Associate Professor...... approaches to dealing in the global business environment." - Sharon Brown-Hruska, Commissioner, Commodity Futures Trading Commission, USA. "This comprehensive survey of modern risk management using derivative securities is a fine demonstration of the practical relevance of modern derivatives theory to risk...... management practice. Of particular note is the global and integrated approach chosen in this book which should be of special interest to aspiring managers active in global and international markets." - Dr Jean-Pierre Zigrand, Lecturer in Finance, London School of Economics, UK. More than 90 per cent...

  4. 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.

  5. 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.

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

    Science.gov (United States)

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

    2010-01-01

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

  7. Evaluation of a simplified version of KENO V.a on a parallel processors computer

    International Nuclear Information System (INIS)

    Ugolini, D.; Petrie, L.M.; Dodds, H.L. Jr.

    1987-01-01

    KENO V.a is a widely used Monte Carlo criticality code developed by Oak Ridge National Laboratory for use primarily on large single processor mainframe computers. The code can be very costly to use if a large number of histories is required because the histories are performed sequentially via the single processor. With the advent of parallel processor computers, it should be possible to reduce computing costs (i.e., computer run time) by performing the histories in parallel. The purposes of this work is to implement KENO V.a on a parallel processor computer, specifically the NCUBE and then to compare results obtained on the NCUBE (i.e., accuracy and computing time) with results obtained on a large mainframe computer (IBM 3033). The NCUBE is a message-passing machine with no shared memory. A simplified version of KENO V.a was developed for this study because the standard version was too large to compile on the NCUBE. In addition, a special 1-group cross-section library, reduced from the standard 16-group Hansen Roach Library, was also used. The sample problem used in this study was an 18-cm-diam sphere of 235 U at 0.05 atom/b x cm

  8. Treatment of veterans with mental health symptoms in VA primary care prior to suicide.

    Science.gov (United States)

    Denneson, Lauren M; Williams, Holly B; Kaplan, Mark S; McFarland, Bentson H; Dobscha, Steven K

    2016-01-01

    We describe Veterans Affairs (VA) primary care received by veterans with mental health symptoms in the year prior to suicide to identify opportunities to improve care. Death certificate data from 11 states were linked to VA national patient care data for veterans who died by suicide in 2009 and had received VA care. We identified 118 age-, sex- and clinician-matched case-control pairs (suicide decedents and living controls) with mental health symptoms. Using McNemar's chi-square and paired t tests, we compare primary care follow-up received during the year prior to death. Cases and controls received similar primary care clinician follow-up and treatment for mental health symptoms. Cases were less likely than controls to fill 90 or more total days of an antidepressant during the year (P=.02), despite no differences in prescription orders from clinicians (P=.05). Cases and controls were equally likely to fill 90 or more consecutive days of an antidepressant (P=.47). Across both groups, 48% (n=113) received assessment for suicidal ideation in primary care. We identified two areas to improve primary care for veterans at risk for suicide: monitoring antidepressant treatment adherence and improving suicidal ideation assessment and follow-up for veterans with mental health symptoms. Published by Elsevier Inc.

  9. 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.

  10. 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/.

  11. 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.

  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. 76 FR 60965 - Enhanced-Use Lease (EUL) of Department of Veterans Affairs (VA) Real Property for the Development...

    Science.gov (United States)

    2011-09-30

    .... SUMMARY: The Secretary of VA intends to enter into an EUL on a 1.9-acre parcel of land at the Canandaigua... homelessness and their families; and provide a supportive services program that guides resident Veterans toward...

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

    Science.gov (United States)

    2011-11-21

    ... Affairs. ACTION: Notice of intent to enter into an Enhanced-Use Lease (EUL). SUMMARY: The Secretary of VA... homelessness, and provide on-site supportive services. FOR FURTHER INFORMATION CONTACT: Edward Bradley, Office...

  15. 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.

  16. 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...

  17. Electricity derivatives

    OpenAIRE

    Barone-Adesi, Giovanni; Gigli, Andrea

    2006-01-01

    In this paper we propose an algorithm for pricing derivatives written on electricity in an incomplete market setting. A discrete time model for price dynamics which embodies the main features of electricity price revealed by simple time series analysis is considered. We use jointly Binomial and Monte Carlo methods for pricing under a risk-neutral measure of which we prove the existence.

  18. dione derivatives

    Indian Academy of Sciences (India)

    dione derivatives via de-Boc and cyclization reaction in modest yield. Spectroscopic (1H, 13C NMR, and Mass) and analytical techniques have been used to identify and confirm the structure of the products. Keywords. Triflic anhydride; Boc anhydride; Negishi coupling; acid-amine coupling; cyclization reaction; cytotoxicity ...

  19. 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...

  20. A measurement of the V-A x V-A structure of the weak charged current in semileptonic b decays and missing energy measurements

    CERN Document Server

    Behner, Frank

    1995-01-01

    The polarization of the W-propagator in semileptonic b decays is measured with the 13 experiment at LEP via simultaneous observation of the charged lepton and the neutrino spectrum. The polarization is seen with more than 3 standard deviations and found to be in agreement with the V-AxV-A structure. The measurement excludes the V+Ax V-A polarization with more than 6 standard deviations. Furthermore, the branching ratio in B_, vX is measured and found to be 22.7%±0.8%(stat.)±l.5%(syst.) which corresponds to a branching ratio of B_,evX of 10.1%±0.8%.

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

    International Nuclear Information System (INIS)

    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; Imai, Hiroshi; Oyadomari, Miyako; Asaki, Yoshiharu; Chibueze, James O.; Dodson, Richard; Rioja, María J.; Kusuno, Kozue; Matsumoto, Naoko; Hagiwara, Yoshiaki; Min, Cheulhong

    2016-01-01

    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.

  2. Rural women veterans demographic report: defining VA users' health and health care access in rural areas.

    Science.gov (United States)

    Brooks, Elizabeth; Dailey, Nancy; Bair, Byron; Shore, Jay

    2014-01-01

    While many women choose to live in rural areas after retiring from active military duty, a paucity of studies examine rural women veterans' health care needs. This report is the first of its kind to describe the population demographics and health care utilization of rural female veteran patients enrolled in the Department of Veterans Affairs (VA). Using the National Patient Care Datasets (n = 327,785), we ran adjusted regression analyses to examine service utilization between (1) urban and rural and (2) urban and highly rural women veterans. Rural and highly rural women veterans were older and more likely to be married than their urban counterparts. Diagnostic rates were generally similar between groups for several mental health disorders, hypertension, and diabetes, with the exception of nonposttraumatic stress anxiety that was significantly lower for highly rural women veterans. Rural and highly rural women veterans were less likely to present to the VA for women's specific care than urban women veterans; highly rural women veterans were less likely to present for mental health care compared to urban women veterans. Among the users of primary care, mental health, women's specific, and all outpatient services, patients' annual utilization rates were similar. Improved service options for women's specific care and mental health visits may help rural women veterans access care. Telehealth technologies and increased outreach, perhaps peer-based, should be considered. Other recommendations for VA policy and planning include increasing caregiver support options, providing consistency for mental health services, and revising medical encounter coding procedures. © 2013 National Rural Health Association.

  3. VA Health Service Utilization for Homeless and Low-income Veterans

    Science.gov (United States)

    Gabrielian, Sonya; Yuan, Anita H.; Andersen, Ronald M.; Rubenstein, Lisa V.; Gelberg, Lillian

    2016-01-01

    Background The US Department of Housing and Urban Development (HUD)-VA Supportive Housing (VASH) program—the VA’s Housing First effort—is central to efforts to end Veteran homelessness. Yet, little is known about health care utilization patterns associated with achieving HUD-VASH housing. Objectives We compare health service utilization at the VA Greater Los Angeles among: (1) formerly homeless Veterans housed through HUD-VASH (HUD-VASH Veterans); (2) currently homeless Veterans; (3) housed, low-income Veterans not in HUD-VASH; and (4) housed, not low-income Veterans. Research Design We performed a secondary database analysis of Veterans (n = 62,459) who received VA Greater Los Angeles care between October 1, 2010 and September 30, 2011. We described medical/surgical and mental health utilization [inpatient, outpatient, and emergency department (ED)]. We controlled for demographics, need, and primary care use in regression analyses of utilization data by housing and income status. Results HUD-VASH Veterans had more inpatient, outpatient, and ED use than currently homeless Veterans. Adjusting for demographics and need, HUD-VASH Veterans and the low-income housed Veterans had similar likelihoods of medical/surgical inpatient and outpatient utilization, compared with the housed, not low-income group. Adjusting first for demographics and need (model 1), then also for primary care use (model 2), HUD-VASH Veterans had the greatest decrease in incident rates of specialty medical/surgical, mental health, and ED care from models 1 to 2, becoming similar to the currently homeless, compared with the housed, not low-income group. Conclusions Our findings suggest that currently homeless Veterans underuse health care relative to housed Veterans. HUD-VASH may address this disparity by providing housing and linkages to primary care. PMID:24714583

  4. 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

  5. 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.

  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. The Orbital Evolution of 2007 VA85, an Amor-type Asteroid on a Retrograde Orbit.

    Science.gov (United States)

    Kankiewicz, P.; Włodarczyk, I.

    2010-06-01

    Among the known population of asteroids on retrograde orbits (i > 90°) we found an object classified as an Amor-type asteroid. During the analysis of the first results of astrometry, we found some possible Earth-impact solutions for this asteroid. After taking into account the latest observations, we excluded any significant impact solution. However, this asteroid is the first known example of potentially hazardous object on a retrograde orbit. We also investigated the orbital evolution of 2007 VA85 (1 My in the past), obtaining possible scenarios of its dynamical origin.

  8. Določanje meje naselja na primeru strnjenih vaških naselij

    OpenAIRE

    Vidic, Nina

    2015-01-01

    Namen diplomske naloge je določitev meje strnjenih vaških naselij glede na različne kazalnike na podlagi razpoložljivih prostorskih podatkov. V teoretičnem delu so predstavljene različne definicije meje naselja od slovenske prostorske zakonodaje do različnih avtorjev, ki so se ukvarjali s proučevanjem naselij. Na podlagi razpoložljivih podatkov in izbranih kazalnikov smo na primeru treh testnih naseljih Gorica in Studenčice v Občini Radovljica ter Kočna v Občini Jesenice, določili mejo naselj...

  9. 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

  10. Uloga i važnost interne revizije u upravljanju poduzećem

    OpenAIRE

    Kostelac, Ivan

    2016-01-01

    Za uspješnost svakog poslovanja veoma je važna politika poslovanja te ciljevi i misije kako bi poduzeće moglo poslovati efikasno i efektivno. Kako bi se što bolje postavili ciljevi i misije te samim time izveo i uspješan poslovan plan veoma je bitna interna revizija. Interna revizija je veoma bitna zato što prije svega pomaže u kvalitetnijem ispunjenju ciljeva i misija uz smanjenje eventualnih pogrešaka te otkrivanje mogućih rizika koji bi mogli nastati i naštetiti cjelokupnom poslovnom pl...

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

    DEFF Research Database (Denmark)

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

    2016-01-01

    In this study, the influence of copolymer composition on drug-polymer solubility was investigated. The solubility of the model drug celecoxib (CCX) in various polyvinylpyrrolidone/vinyl acetate (PVP/VA) copolymer compositions (70/30, 60/40, 50/50 and 30/70 w/w) and the pure homopolymers...... dispersion without compromising the drug-polymer solubility. This knowledge could be used advantageously in future development of amorphous drug delivery systems as copolymers could be customized to provide optimal drug-polymer solubility and physical stability....

  12. 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)

  13. 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

  14. Variations in the implementation and characteristics of chiropractic services in VA.

    Science.gov (United States)

    Lisi, Anthony J; Khorsan, Raheleh; Smith, Monica M; Mittman, Brian S

    2014-12-01

    In 2004, the US Department of Veterans Affairs expanded its delivery of chiropractic care by establishing onsite chiropractic clinics at select facilities across the country. Systematic information regarding the planning and implementation of these clinics and describing their features and performance is lacking. To document the planning, implementation, key features and performance of VA chiropractic clinics, and to identify variations and their underlying causes and key consequences as well as their implications for policy, practice, and research on the introduction of new clinical services into integrated health care delivery systems. Comparative case study of 7 clinics involving site visit-based and telephone-based interviews with 118 key stakeholders, including VA clinicians, clinical leaders and administrative staff, and selected external stakeholders, as well as reviews of key documents and administrative data on clinic performance and service delivery. Interviews were recorded, transcribed, and analyzed using a mixed inductive (exploratory) and deductive approach. Interview data revealed considerable variations in clinic planning and implementation processes and clinic features, as well as perceptions of clinic performance and quality. Administrative data showed high variation in patterns of clinic patient care volume over time. A facility's initial willingness to establish a chiropractic clinic, along with a higher degree of perceived evidence-based and collegial attributes of the facility chiropractor, emerged as key factors associated with higher and more consistent delivery of chiropractic services and higher perceived quality of those services.

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

    Science.gov (United States)

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

    2016-05-01

    Recent research has documented high rates of comorbidity between cannabis use disorders and posttraumatic stress disorder (PTSD) in veterans. However, despite possible links between PTSD and cannabis use, relatively little is known about cannabis use in veterans who present for PTSD treatment, particularly among samples not diagnosed with a substance use disorder. This study examined the prevalence of cannabis use and the psychological and functional correlates of cannabis use among a large sample of veterans seeking treatment at a Veterans Affairs (VA) PTSD specialty clinic. Male veterans (N = 719) who presented at a VA specialty outpatient PTSD clinic completed measures of demographic variables, combat exposure, alcohol, cannabis and other drug use, and PTSD and depressive symptoms. The associations among demographic, psychological, and functional variables were estimated using logistic regressions. Overall, 14.6% of participants reported using cannabis in the past 6 months. After controlling for age, race, service era, and combat exposure, past 6-month cannabis use was associated with unmarried status, use of tobacco products, other drug use, hazardous alcohol use, PTSD severity, depressive symptom severity, and suicidality. The present findings show that cannabis use is quite prevalent among veterans seeking PTSD specialty treatment and is associated with poorer mental health and use of other substances. It may be possible to identify and treat individuals who use cannabis in specialty clinics (e.g., PTSD clinics) where they are likely to present for treatment of associated mental health issues. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

  16. 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

  17. RESPONSE OF TWO SUNFLOWER (HELIANTHUS ANNUUS L. GENOTYPES TO VA-MYCORRHIZAL INOCULATION AND PHOSPHORUS LEVELS

    Directory of Open Access Journals (Sweden)

    C.P. CHANDRASHEKARA, V.C. PATIL

    1995-01-01

    Full Text Available The performance of two sunflower genotypes (Morden and MSFH-8 with and without VA-mycorrhizal fungi at three P levels (38, 56 and 75 kg P2O5 ha-1 in vertisol of Dharwad was studied to determine the effect of mycorrhizal inoculation on plant growth, yield and P uptake. The results showed that the VAM inoculation increased sunflower yield (14%, total biomass (16%, oil content (3.1% and P uptake (30.5% over uninoculated control. The percent root colonization and chlamydo-spore count decreased with increasing P levels. The total biomass production, seed yield and P uptake of mycorrhizal plants at 38 kg P2O5 ha-1 more than the non-mycorrhizal plants at 75 kg P2O5 ha-1. The biomass and seed yield of mycorrhizal plants at same P level were more than the non-mycorrhizal plants. Mycorrhizal plants of Morden at 38 kg P2O5 ha-1 and MSFH-8 at 56 kg P2O5 ha-1 produced higher seed yield, oil content and total biomass than non-mycorrhizal plants supplied with 75 kg P2O5 ha-1. The results indicated that, VA-mycorrhizal inoculation helps in saving 25 and 50 percent of recommended dose of phosphatic fertilizer (75 kg P2O5 ha-1 in MSFH-8 (single cross hybrid and Morden (open pollinated variety, respectively.

  18. VA nursing home residents with substance use disorders: Mental health comorbidities, functioning, and problem behaviors.

    Science.gov (United States)

    Lemke, Sonne; Schaefer, Jeanne A

    2010-07-01

    This research addresses whether residents with substance use disorders (SUDs) in VA nursing homes (VANHs) are distinctive in terms of their demographic characteristics, medical and mental health comorbidities, functioning, and problem behaviors. Residents over age 55 admitted to VANHs (n = 27,002) were identified in VA administrative files, and SUD and non-SUD residents were compared. Compared with other residents, the residents with SUDs (18% of admissions over age 55) were more likely to be younger, male, African-American, unmarried, have low income and a tobacco use disorder. Controlling for demographic factors and smoking, SUD residents were more likely to have mental health comorbidities (dementia, serious mental illness, depressive disorders, and post-traumatic stress disorder), as well as AIDS/hepatitis, pulmonary disease, gastro-intestinal disorders, and injuries. SUD residents were less likely to have cancer, diabetes, neurological disorders, heart failure, and renal failure. SUD residents were more independent in activities of daily living, such as mobility and toileting. They were more likely to engage in verbal disruption but not in other problem behaviors such as aggression. With demographic factors and comorbidities controlled, the functioning differences were diminished, and SUD and non-SUD residents did not differ in the levels of problem behaviors. VANH residents with SUDs have distinctive patterns of comorbidities and functioning. SUD appears to represent a separate risk factor for VANH admission. Residents with SUDs present challenges but may have good potential for positive discharge outcomes if their substance use problems and limited resources can be addressed.

  19. Validating physician-certified verbal autopsy and probabilistic modeling (InterVA approaches to verbal autopsy interpretation using hospital causes of adult deaths

    Directory of Open Access Journals (Sweden)

    Tsofa Benjamin

    2011-08-01

    Full Text Available Abstract Background The most common method for determining cause of death is certification by physicians based either on available medical records, or where such data are not available, through verbal autopsy (VA. The physician-certification approach is costly and inconvenient; however, recent work shows the potential of a computer-based probabilistic model (InterVA to interpret verbal autopsy data in a more convenient, consistent, and rapid way. In this study we validate separately both physician-certified verbal autopsy (PCVA and the InterVA probabilistic model against hospital cause of death (HCOD in adults dying in a district hospital on the coast of Kenya. Methods Between March 2007 and June 2010, VA interviews were conducted for 145 adult deaths that occurred at Kilifi District Hospital. The VA data were reviewed by a physician and the cause of death established. A range of indicators (including age, gender, physical signs and symptoms, pregnancy status, medical history, and the circumstances of death from the VA forms were included in the InterVA for interpretation. Cause-specific mortality fractions (CSMF, Cohen's kappa (κ statistic, receiver operating characteristic (ROC curves, sensitivity, specificity, and positive predictive values were applied to compare agreement between PCVA, InterVA, and HCOD. Results HCOD, InterVA, and PCVA yielded the same top five underlying causes of adult deaths. The InterVA overestimated tuberculosis as a cause of death compared to the HCOD. On the other hand, PCVA overestimated diabetes. Overall, CSMF for the five major cause groups by the InterVA, PCVA, and HCOD were 70%, 65%, and 60%, respectively. PCVA versus HCOD yielded a higher kappa value (κ = 0.52, 95% confidence interval [CI]: 0.48, 0.54 than the InterVA versus HCOD which yielded a kappa (κ value of 0.32 (95% CI: 0.30, 0.38. Overall, (κ agreement across the three methods was 0.41 (95% CI: 0.37, 0.48. The areas under the ROC curves were 0

  20. 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.

  1. VaCPK20 gene overexpression significantly increased resveratrol content and expression of stilbene synthase genes in cell cultures of Vitis amurensis Rupr.

    Science.gov (United States)

    Aleynova-Shumakova, O A; Dubrovina, A S; Manyakhin, A Y; Karetin, Y A; Kiselev, K V

    2014-06-01

    Resveratrol, a naturally occurring plant phenol, has been reported to exhibit a wide range of valuable biological and pharmacological properties. In the present investigation, we show that transformation of a Vitis amurensis Rupr. cell suspension with the gene VaCPK20 for a calcium-dependent protein kinase (CDPK) under the control of double CaMV 35S promoter increased resveratrol production in five independently transformed cell lines in 9-68 times compared with control cells. The VaCPK20-transformed calli were capable of producing 0.04-0.42 % dry wt. of resveratrol, while the control calli produced up to 0.008 % dry wt. of resveratrol Also, we characterized expression of stilbene synthase (STS) genes in the five VaCPK20-transgenic cell lines of V. amurensis. In all VaCPK20-transgenic cell lines, expression of VaSTS7 increased; while expression of VaSTS1 decreased. We suggest that transformation of V. amurensis calli with the VaCPK20 gene induced resveratrol accumulation via enhancement of expression of the VaSTS7 gene involved in resveratrol biosynthesis. The obtained data first demonstrate that overexpression of a CDPK gene resulted in increased accumulation of a stilbenoid phytoalexine in transgenic plant cells. We propose that the VaCPK20 gene could play an important role in the regulation of resveratrol biosynthesis in grape cells.

  2. Global financial crisis and VaR performance in emerging markets: A case of EU candidate states - Turkey and Croatia

    Directory of Open Access Journals (Sweden)

    Bora Aktan

    2009-06-01

    Full Text Available We investigate the relative performance of a wide array of Value at Risk (VaR models with the daily returns of Turkish (XU100 and Croatian (CROBEX stock index prior to and during the ongoing financial crisis. In addition to widely used VaR models, we also study the behaviour of conditional and unconditional extreme value theory (EVT and hybrid historical simulation (HHS models to generate 95, 99 and 99.5% confidence level estimates. Results indicate that during the crisis period all tested VaR model except EVT and HHS models seriously underpredict the true level of risk, with EVT models doing so at a higher cost of capital compared to HHS model

  3. Towards a Heterogeneous, Polystore-like Data Architecture for the US Department of Veteran Affairs (VA) Enterprise Analytics

    Energy Technology Data Exchange (ETDEWEB)

    Begoli, Edmon [ORNL; Bates, Jack [Veterans Administration; Kistler, Derek E [ORNL

    2016-01-01

    The Polystore architecture revisits the federated approach to access and querying of the standalone, independent databases in the uniform and optimized fashion, but this time in the context of heterogeneous data and specialized analyses. In the light of this architectural philosophy, and in the light of the major data architecture development efforts at the US Department of Veterans Administration (VA), we discuss the need for the heterogeneous data store consisting of the large relational data warehouse, an image and text datastore, and a peta-scale genomic repository. The VA's heterogeneous datastore would, to a larger or smaller degree, follow the architectural blueprint proposed by the polystore architecture. To this end, we discuss the current state of the data architecture at VA, architectural alternatives for development of the heterogeneous datastore, the anticipated challenges, and the drawbacks and benefits of adopting the polystore architecture.

  4. 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.

  5. A new formulation for minimum input volt-ampere (VA-slip relationship of three-phase induction motors

    Directory of Open Access Journals (Sweden)

    Haroon Ashfaq

    2017-07-01

    Full Text Available The magnetization component of input current of low-rating three-phase induction motor is large which results in poor power factor particularly at low-load conditions. The situation becomes critical when motor is fed from a distributed generating (DG system. In this paper, the performance analysis of induction motor is carried out for minimum input VA. A distinct novel slip is found at which the input VA is minimum independent of the load conditions. This optimum slip is expressed in terms of motor per-phase equivalent circuit parameters. This novel relationship is valid for every induction motor. As compared to rated conditions, a drastic reduction in VA with a large improvement in power factor is observed. Although, a marginal change in output power and efficiency is recorded. All the analytical, simulated and experimental results match each other with a very fair degree of accuracy.

  6. 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

  7. 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.

  8. 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.

  9. AVTA Federal Fleet PEV Readiness Data Logging and Characterization Study for Department of Veterans Affairs – VA Manhattan Campus

    Energy Technology Data Exchange (ETDEWEB)

    Stephen Schey; Jim Francfort

    2014-10-01

    This report focuses on the Department of Veterans Affairs, VA Manhattan Campus (VA- Manhattan) fleet to identify the daily operational characteristics of select vehicles and report findings on vehicle and mission characterizations to support successful introduction of plug-in electric vehicles (PEVs) into the agency’s fleet. Individual observations of these selected vehicles provide the basis for recommendations related to electric vehicle adoption and whether a battery electric vehicle or plug-in hybrid electric vehicle (collectively called PEVs) can fulfill the mission requirements.

  10. 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.

  11. Childhood cause-specific mortality in rural Western Kenya: application of the InterVA-4 model

    Directory of Open Access Journals (Sweden)

    Nyaguara O. Amek

    2014-10-01

    Full Text Available Background: Assessing the progress in achieving the United Nation's Millennium Development Goals in terms of population health requires consistent and reliable information on cause-specific mortality, which is often rare in resource-constrained countries. Health and demographic surveillance systems (HDSS have largely used medical personnel to review and assign likely causes of death based on the information gathered from standardized verbal autopsy (VA forms. However, this approach is expensive and time consuming, and it may lead to biased results based on the knowledge and experience of individual clinicians. We assessed the cause-specific mortality for children under 5 years old (under-5 deaths in Siaya County, obtained from a computer-based probabilistic model (InterVA-4. Design: Successfully completed VA interviews for under-5 deaths conducted between January 2003 and December 2010 in the Kenya Medical Research Institute/US Centers for Disease Control and Prevention HDSS were extracted from the VA database and processed using the InterVA-4 (version 4.02 model for interpretation. Cause-specific mortality fractions were then generated from the causes of death produced by the model. Results: A total of 84.33% (6,621 childhood deaths had completed VA data during the study period. Children aged 1–4 years constituted 48.53% of all cases, and 42.50% were from infants. A single cause of death was assigned to 89.18% (5,940 of cases, 8.35% (556 of cases were assigned two causes, and 2.10% (140 were assigned ‘indeterminate’ as cause of death by the InterVA-4 model. Overall, malaria (28.20% was the leading cause of death, followed by acute respiratory infection including pneumonia (25.10%, in under-5 children over the study period. But in the first 5 years of the study period, acute respiratory infection including pneumonia was the main cause of death, followed by malaria. Similar trends were also reported in infants (29 days–11 months and

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

    Science.gov (United States)

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

    2015-07-30

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

  13. PVP VA64 as a novel release-modifier for sustained-release mini-matrices prepared via hot melt extrusion.

    Science.gov (United States)

    Li, Yongcheng; Lu, Ming; Wu, Chuanbin

    2017-11-10

    The purpose of this study was to explore poly(vinylpyrrolidone-co-vinyl acetate) (PVP VA64) as a novel release-modifier to tailor the drug release from ethylcellulose (EC)-based mini-matrices prepared via hot melt extrusion (HME). Quetiapine fumarate (QF) was selected as model drug. QF/EC/PVP VA64 mini-matrices were extruded with 30% drug loading. The physical state of QF in extruded mini-matrices was characterized using differential scanning calorimetry, X-ray powder diffraction, and confocal Raman microscopy. The release-controlled ability of PVP VA64 was investigated and compared with that of xanthan gum, crospovidone, and low-substituted hydroxypropylcellulose. The influences of PVP VA64 content and processing temperature on QF release behavior and mechanism were also studied. The results indicated QF dispersed as the crystalline state in all mini-matrices. The release of QF from EC was very slow as only 4% QF was released in 24 h. PVP VA64 exhibited the best ability to enhance the drug release as compared with other three release-modifiers. The drug release increased to 50-100% in 24 h with the addition of 20-40% PVP VA64. Increasing processing temperature slightly slowed down the drug release by decreasing free volume and pore size. The release kinetics showed good fit with the Ritger-Peppas model. The values of release exponent (n) increased as PVP VA64 is added (0.14 for pure EC, 0.41 for 20% PVP VA64, and 0.61 for 40% PVP VA64), revealing that the addition of PVP VA64 enhanced the erosion mechanism. This work presented a new polymer blend system of EC with PVP VA64 for sustained-release prepared via HME.

  14. ¿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.

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

    DEFF Research Database (Denmark)

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

    2013-01-01

    In this work we have used Fourier transform infrared (FTIR) / vibrational absorption (VA) spectroscopy to study two cancer cell lines: the Henrietta Lacks (HeLa) human cervix carcinoma and 5637 human bladder carcinoma cell lines. Our goal is to experimentally investigate biochemical changes...... and differences in these cells lines utilizing FTIR spectroscopy. We have used the chemometrical and statistical method principal component analysis (PCA) to investigate the spectral differences. We have been able to identify certain bands in the spectra which are so-called biomarkers for two types of cell lines......, three groups for the 5637 human bladder carcinoma cell line (5637A, 5637B and 5637C), and another one for the HeLa human cervix carcinoma cell line. The vibrational modes can be assigned to specific bands involving characteristic motions of the protein backbone. This work shows that infrared vibrational...

  16. Myosin Va becomes a low duty ratio motor in the inhibited form.

    Science.gov (United States)

    Sato, Osamu; Li, Xiang-Dong; Ikebe, Mitsuo

    2007-05-04

    Vertebrate myosin Va is a typical processive motor with high duty ratio. Recent studies have revealed that the actin-activated ATPase activity of the full-length myosin Va (M5aFull) is inhibited at a low [Ca(2+)], which is due to the formation of a folded conformation of M5aFull. To clarify the underlying inhibitory mechanism, we analyzed the actin-activated ATP hydrolysis mechanism of the M5aFull at the inhibited and the activated states, respectively. Marked differences were found in the hydrolysis, P(i) release, and ADP release steps between the activated and the inhibited states. The kinetic constants of these steps of the activated state were similar to those of the unregulated S1 construct, in which the rate-limiting step was the ADP release step. On the other hand, the P(i) release rate from acto-M5aFull was decreased in EGTA by >1,000-fold, which makes this step the rate-limiting step for the actin-activated ATP hydrolysis cycle of M5aFull. The ADP off rate from acto-M5aFull was decreased by approximately 10-fold, and the equilibrium between the prehydrolysis state and the post hydrolysis state was shifted toward the former state in the inhibited state of M5aFull. Because of these changes, M5aFull spends a majority of the ATP hydrolysis cycling time in the weak actin binding state. The present results indicate that M5aFull molecules at a low [Ca(2+)] is inhibited as a cargo transporter not only due to the decrease in the cross-bridge cycling rate but also due to the decrease in the duty ratio thus being dissociated from actin.

  17. Continuity in a VA patient-centered medical home reduces emergency department visits.

    Directory of Open Access Journals (Sweden)

    Krisda H Chaiyachati

    Full Text Available One major goal of the Patient-Centered Medical Home (PCMH is to improve continuity of care between patients and providers and reduce the utilization of non-primary care services like the emergency department (ED.To characterize continuity under the Veterans Health Administration's PCMH model--the Patient Aligned Care Team (PACT, at one large Veterans Affair's (VA's primary care clinic, determine the characteristics associated with high levels of continuity, and assess the association between continuity and ED visits.Retrospective, observational cohort study of patients at the West Haven VA (WHVA Primary Care Clinic from March 2011 to February 2012.The 13,495 patients with established care at the Clinic, having at least one visit, one year before March 2011.Our exposure variable was continuity of care--a patient seeing their assigned primary care provider (PCP at each clinic visit. The outcome of interest was having an ED visit.The patients encompassed 42,969 total clinic visits, and 3185 (24% of them had 15,458 ED visits. In a multivariable logistic regression analysis, patients with continuity of care--at least one visit with their assigned PCP--had lower ED utilization compared to individuals without continuity (adjusted odds ratio [AOR] 0.54; 95% CI: 0.41, 0.71, controlling for frequency of primary care visits, comorbidities, insurance, distance from the ED, and having a trainee PCP assigned. Likewise, the adjusted rate of ED visits was 544/1000 person-year (PY for patients with continuity vs. 784/1000 PY for patients without continuity (p = 0.001. Compared to patients with low continuity (50% continuity were less likely to utilize the ED.Strong continuity of care is associated with decreased ED utilization in a PCMH model and improving continuity may help reduce the utilization of non-primary care services.

  18. Exploring end-of-residency transitions in a VA Patient Aligned Care Team.

    Science.gov (United States)

    Wang, Emily S; Conde, Michelle V; Simon, Bret; Leykum, Luci K

    2014-07-01

    End-of-residency transitions create disruptions in primary care continuity. The national implementation of Patient Aligned Care Teams (PACT) in Veterans Health Administration (VA) primary care clinics creates an opportunity to mitigate this discontinuity through the provision of team-based care. To identify team-based solutions to end-of-residency transitions in a resident PACT continuity clinic by assessing the knowledge, attitudes, and perceptions of non-physician PACT members and resident PACT physicians. Cross-sectional survey of 27 resident physicians and 24 non-physician PACT members in the Internal Medicine Clinic at the Audie L. Murphy VA Hospital in the South Texas Veterans Health Care System. Twenty-seven residents and 24 non-physician PACT members completed the survey, with response rates of 90 % and 100 %, respectively. All residents and 96 % of non-physician PACT members agreed or strongly agreed that the residents were responsible for informing patients about end-of-residency transitions. Only 38 % of non-physician PACT members versus 52 % of residents indicated that non-physician PACT members should be responsible for this transition. Approximately 80 % of resident physicians and non-physician PACT members agreed there should be a formalized approach to these transitions; 67 % of non-physician PACT members were willing to support this transition. Potential barriers to team-based care transitions were identified. Major themes of write-in suggestions for improving the transition focused on communication and relationships between the patient and PACT and among the PACT members. PACT implementation changes the roles and relationship structures among all team members. While end-of-residency transitions create a disruption in the relationship system, the remainder of the PACT may bridge this transition. Our results demonstrate the importance of a team-based solution that engages all PACT members by improving communication and fostering effective team

  19. Huddle up!: The adoption and use of structured team communication for VA medical home implementation.

    Science.gov (United States)

    Rodriguez, Hector P; Meredith, Lisa S; Hamilton, Alison B; Yano, Elizabeth M; Rubenstein, Lisa V

    2015-01-01

    Daily clinical team meetings (i.e., "huddles") may be helpful in implementing new roles and responsibilities for patient care because they provide a regular opportunity for member learning and feedback. We examined how huddles were implemented in the context of the VA patient-centered medical home (PCMH) transformation, including assessing barriers and facilitators to regular huddling among small teams ("teamlets"). We assessed the extent to which teamlet members that huddled had higher self-efficacy for PCMH changes, reported better teamwork experiences, and perceived more supportive practice environments. We used a convergent mixed-methods approach to analyze 79 teamlet member interviews from six VA primary care practices and 418 clinician and staff PCMH survey responses from the six interviewed practices and 13 additional practices in the same region. Most members reported participating in teamlet huddles when asked in surveys (85%). A minority of interview participants, however, described routine huddling focused on previsit planning that included all members. When members reported routine teamlet huddling, activities included (a) previsit planning, (b) strategizing treatment plans for patients with special or complex needs, (c) addressing daily workflow and communication issues through collective problem solving, and (d) ensuring awareness of what team members do and what actions are happening on the teamlet and in the practice. Primary care providers (PCPs) were least likely to report routine huddling. PCP huddlers reported greater self-efficacy for implementing PCMH changes. All huddlers, irrespective of role, reported better teamwork and more supportive practice climates. The most common barriers to teamlet huddling were limited time and operational constraints. In order to improve the impact of huddles on patient care, practice leaders should clearly communicate the goals, requirements, and benefits of huddling and provide adequate time and resources to

  20. 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

  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. VA Benefits: Increasing Outreach and Measuring Outcomes Would Improve the Post-9/11 GI Bill On-the-Job Training and Apprenticeship Programs

    Science.gov (United States)

    2015-11-01

    provide case- management to veterans with significant barriers to employment, such as homelessness or disabilities.40...determined that the data were sufficiently reliable for the purposes of this report. The summary statistics that VA provided from its LTS data...analyzed them. In addition, VA provided summary information from the WEAMS dataset as of March 23, 2015 on the number of facilities (employers or

  3. 76 FR 44087 - Agency Information Collection (Supplement to VA Forms 21-526, 21-534, and 21-535 (For Philippine...

    Science.gov (United States)

    2011-07-22

    ... AFFAIRS Agency Information Collection (Supplement to VA Forms 21-526, 21- 534, and 21-535 (For Philippine..., 21-534, and 21-535 (For Philippine Claims), VA Form 21-4169. OMB Control Number: 2900-0094. Type of... Philippines or recognized guerrilla services. An agency may not conduct or sponsor, and a person is not...

  4. 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

  5. Targeted Amplicon Sequencing for Single-Nucleotide-Polymorphism Genotyping of Attaching and Effacing Escherichia coli O26:H11 Cattle Strains via a High-Throughput Library Preparation Technique.

    Science.gov (United States)

    Ison, Sarah A; Delannoy, Sabine; Bugarel, Marie; Nagaraja, Tiruvoor G; Renter, David G; den Bakker, Henk C; Nightingale, Kendra K; Fach, Patrick; Loneragan, Guy H

    2016-01-15

    Enterohemorrhagic Escherichia coli (EHEC) O26:H11, a serotype within Shiga toxin-producing E. coli (STEC) that causes severe human disease, has been considered to have evolved from attaching and effacing E. coli (AEEC) O26:H11 through the acquisition of a Shiga toxin-encoding gene. Targeted amplicon sequencing using next-generation sequencing technology of 48 phylogenetically informative single-nucleotide polymorphisms (SNPs) and three SNPs differentiating Shiga toxin-positive (stx-positive) strains from Shiga toxin-negative (stx-negative) strains were used to infer the phylogenetic relationships of 178 E. coli O26:H11 strains (6 stx-positive strains and 172 stx-negative AEEC strains) from cattle feces to 7 publically available genomes of human clinical strains. The AEEC cattle strains displayed synonymous SNP genotypes with stx2-positive sequence type 29 (ST29) human O26:H11 strains, while stx1 ST21 human and cattle strains clustered separately, demonstrating the close phylogenetic relatedness of these Shiga toxin-negative AEEC cattle strains and human clinical strains. With the exception of seven stx-negative strains, five of which contained espK, three stx-related SNPs differentiated the STEC strains from non-STEC strains, supporting the hypothesis that these AEEC cattle strains could serve as a potential reservoir for new or existing pathogenic human strains. Our results support the idea that targeted amplicon sequencing for SNP genotyping expedites strain identification and genetic characterization of E. coli O26:H11, which is important for food safety and public health. Copyright © 2016 Ison et al.

  6. A pilot study of a heuristic algorithm for novel template identification from VA electronic medical record text.

    Science.gov (United States)

    Redd, Andrew M; Gundlapalli, Adi V; Divita, Guy; Carter, Marjorie E; Tran, Le-Thuy; Samore, Matthew H

    2017-07-01

    Templates in text notes pose challenges for automated information extraction algorithms. We propose a method that identifies novel templates in plain text medical notes. The identification can then be used to either include or exclude templates when processing notes for information extraction. The two-module method is based on the framework of information foraging and addresses the hypothesis that documents containing templates and the templates within those documents can be identified by common features. The first module takes documents from the corpus and groups those with common templates. This is accomplished through a binned word count hierarchical clustering algorithm. The second module extracts the templates. It uses the groupings and performs a longest common subsequence (LCS) algorithm to obtain the constituent parts of the templates. The method was developed and tested on a random document corpus of 750 notes derived from a large database of US Department of Veterans Affairs (VA) electronic medical notes. The grouping module, using hierarchical clustering, identified 23 groups with 3 documents or more, consisting of 120 documents from the 750 documents in our test corpus. Of these, 18 groups had at least one common template that was present in all documents in the group for a positive predictive value of 78%. The LCS extraction module performed with 100% positive predictive value, 94% sensitivity, and 83% negative predictive value. The human review determined that in 4 groups the template covered the entire document, with the remaining 14 groups containing a common section template. Among documents with templates, the number of templates per document ranged from 1 to 14. The mean and median number of templates per group was 5.9 and 5, respectively. The grouping method was successful in finding like documents containing templates. Of the groups of documents containing templates, the LCS module was successful in deciphering text belonging to the template

  7. Towards Predicting Street-Level Inundation: using Operational Forecast Modeling Techniques during 2011 Hurricane Irene in Hampton Roads, VA

    Science.gov (United States)

    Loftis, D.; Loftis, J. D.; Stiles, W. A.

    2016-02-01

    Storm surge-induced coastal inundation poses numerous personal, commercial, industrial, and sociopolitical challenges for society. Flooding can be caused by the combination of storm surge and river-induced inland flooding in many locations throughout the coastal plain. The cross-disciplinary nature of the hydrodynamics involved (hydraulics, oceanography, and hydrology), coupled with the complexity of the atmospheric forcing, makes a numerical model the best approach for a comprehensive study of the dynamics of coastal inundation. This study builds upon the lessons learned from forecast modeling experiences during 2011 Hurricane Irene in Tidewater Virginia, to ascertain the most effective way to approach predicting street-level inundation. During the storm event, an open-source large-scale ocean model, SCHISM, was provided atmospheric forcing from the National Oceanic and Atmospheric Administration's Global Forecast System, updated every 6 hours to simulate 9 separate 30-hour simulations, which were provided to emergency managers and the National Weather Service in Wakefield, VA. To accurately predict street-level inundation, water elevations at key points near the mouths of vulnerable tributaries can be used to drive a separate street-level high-resolution sub-grid model (UnTRIM) to simulate localized flooding events on the scale of 5-meter resolution. To this end, high-resolution Digital Elevation Models including building and roadway infrastructure were developed from Lidar-derived topography for the Hampton Roads Region of Virginia, and used to accurately predict flooding in low-lying areas of the Cities of Norfolk, Portsmouth, and Chesapeake along the Elizabeth and Lafayette Rivers, the City of Virginia Beach along the Lynnhaven River, and along Hampton, York, and Poquoson along the Back River. Tropical storm surge flood heights were validated via temporal comparison with water level observations from NOAA, the USGS, and NASA aggregated to an average R2

  8. Serving homeless veterans in the VA Desert Pacific Healthcare Network: a needs assessment to inform quality improvement endeavors.

    Science.gov (United States)

    Gabrielian, Sonya; Yuan, Anita; Rubenstein, Lisa; Andersen, Ronald M; Gelberg, Lillian

    2013-08-01

    This report describes a needs assessment of VA programs for homeless Veterans in Southern California and Nevada, the geographic region with the most homeless Veterans in the nation. The assessment was formulated through key informant interviews. Current service provisions are discussed, along with salient unmet needs for this vulnerable population.

  9. 48 CFR 852.219-11 - VA notice of total veteran-owned small business set-aside.

    Science.gov (United States)

    2010-10-01

    ... representations: That it is a veteran-owned small business concern, and that it is a small business concern under...-owned small business set-aside. 852.219-11 Section 852.219-11 Federal Acquisition Regulations System... Provisions and Clauses 852.219-11 VA notice of total veteran-owned small business set-aside. As prescribed in...

  10. 33 CFR 334.340 - Chesapeake Bay off Plumtree Island, Hampton, Va.; Air Force precision test area.

    Science.gov (United States)

    2010-07-01

    ... 33 Navigation and Navigable Waters 3 2010-07-01 2010-07-01 false Chesapeake Bay off Plumtree... REGULATIONS § 334.340 Chesapeake Bay off Plumtree Island, Hampton, Va.; Air Force precision test area. (a) The danger zone. The waters of Chesapeake Bay and connecting waters within an area bounded as follows...

  11. 77 FR 23615 - Payment or Reimbursement for Emergency Services for Nonservice-Connected Conditions in Non-VA...

    Science.gov (United States)

    2012-04-20

    ....'' The 2010 Act removed ``or in part'' from this exclusion. In order to remove this partial payment exclusion from VA regulations, we are removing the clause ``or in part'' from Sec. 17.1002(g) to parallel... revises Sec. Sec. 17.1001, 17.1002, 17.1004, and 17.1005. These revisions eliminate certain exclusions...

  12. Uus trend - süvaõpe ülikoolis / Kalle Tammemäe ; intervjueerinud Raivo Juurak

    Index Scriptorium Estoniae

    Tammemäe, Kalle, 1958-

    2011-01-01

    Intervjuu TTÜ õppeprorektori Kalle Tammemäega kavandatavast süvaõppesüsteemist, mis hakkab toetama eelkõige teadustööst huvitatud üliõpilasi, aidates mõnelgi neist aja jooksul õppejõuks-teaduriks kasvada

  13. 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

    managers , who supervise active duty staff on the West Campus, on how to effectively utilize such staff, particularly Navy hospital corpsmen. General...MTF designation would introduce additional operational requirements and challenges to the FHCC, including financial management and quality assurance... manage their operations with separate governance structures, workforces, and budgets. VA and DOD’s joint review team concluded that converting the

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

    Science.gov (United States)

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

    2011-01-01

    Objective: The effects of school-based antibullying programs have typically been examined on small samples, with number of schools ranging from 1 to 78 (Farrington & Ttofi, 2009). This study investigated the effectiveness of the KiVa antibullying program in the beginning of its nationwide implementation in Finland. Method: At each time point,…

  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. 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…

  17. 75 FR 24510 - Drug and Drug-Related Supply Promotion by Pharmaceutical Company Sales Representatives at VA...

    Science.gov (United States)

    2010-05-05

    ... those programs and materials focus on clinician education as opposed to marketing of drugs and drug... that the proposed rule allow VA medical professionals to become educated through the promotion of such... financing, intended to support the program. (2) Marketing activities cannot be conducted during an...

  18. 75 FR 26160 - Drug and Drug-Related Supply Promotion by Pharmaceutical Company Sales Representatives at VA...

    Science.gov (United States)

    2010-05-11

    ... those programs and materials focus on clinician education as opposed to marketing of drugs and drug... that the proposed rule allow VA medical professionals to become educated through the promotion of such...) Marketing activities cannot be conducted during an educational program. (3) Promotional materials are not to...

  19. 75 FR 38979 - Expansion/Reorganization of Foreign-Trade Zone 204, Tri-Cities Area, TN/VA

    Science.gov (United States)

    2010-07-07

    ... DEPARTMENT OF COMMERCE Foreign-Trade Zones Board [Order No. 1691] Expansion/Reorganization of Foreign-Trade Zone 204, Tri-Cities Area, TN/VA Pursuant to its authority under the Foreign-Trade Zones Act of June 18, 1934, as amended (19 U.S.C. 81a-81u), the Foreign-Trade Zones Board (the Board) adopts...

  20. 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...

  1. 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.

  2. Dimension and deriving manner for derived quantities

    International Nuclear Information System (INIS)

    Zhao Zhixiang

    1993-01-01

    Most physical quantities we are interested in are derived from some directly measured physical quantities. To obtain correct least-square result in derived quantity space, one must pay attention to inconsistencies problem to avoid ppp phenomenon in generating derived quantities and their covariance matrix. The situation is complicated by the problems of dimension and deriving manner for derived quantities. Some more general problems, which are independent of ppp, are discussed

  3. Three-Dimensional Echocardiography-Derived Right Ventricular Ejection Fraction Correlates with Success of Decannulation and Prognosis in Patients Stabilized by Venoarterial Extracorporeal Life Support.

    Science.gov (United States)

    Huang, Kuan-Chih; Lin, Lian-Yu; Chen, Yih-Sharng; Lai, Chien-Heng; Hwang, Juey-Jen; Lin, Lung-Chun

    2018-02-01

    Venoarterial extracorporeal membrane oxygenation (VA-ECMO) has been proved to effectively rescue patients from refractory cardiogenic shock. The role of the right ventricle in VA-ECMO has been emphasized, but quantitative right ventricular (RV) analysis in this population has been lacking. Three-dimensional echocardiography (3DE) is currently suggested for RV volumetric analysis. The aims of this study were to assess 3DE-derived RV ejection fraction (RVEF) in patients with refractory cardiogenic shock stabilized by VA-ECMO and to explore the association between 3DE-derived RVEF and weaning success as well as the prognosis after the first intent of decannulation. Three-dimensional echocardiographic data sets before the first intent of decannulation were retrospectively selected and analyzed in 46 patients who underwent VA-ECMO for refractory acute circulatory collapse. Twenty-eight of the 46 patients had protocol-defined success in weaning from VA-ECMO. In the success group, both ventricles were smaller and had better pumping function. By stepwise multivariate linear regression, RV free wall strain, left ventricular ejection fraction, RV fractional area change, and central venous pressure were found to be independently associated with RVEF. Receiver operating characteristic curve analysis showed that RVEF had the highest area under the curve (0.90, P  24.6% was associated with higher weaning success and lower 30-day mortality after the first intent of decannulation. Copyright © 2017 American Society of Echocardiography. Published by Elsevier Inc. All rights reserved.

  4. Association of substance use and VA service-connected disability benefits with risk of homelessness among veterans.

    Science.gov (United States)

    Edens, Ellen L; Kasprow, Wes; Tsai, Jack; Rosenheck, Robert A

    2011-01-01

    Recent public attention on homelessness has shifted beyond emergency services and supportive housing to primary prevention. This study compares a national sample of homeless and nonhomeless Veterans Affairs (VA) mental health services users to determine risk and protective factors for homelessness. Using VA administrative data, veterans were identified as homeless (ie, used VA homeless services or received a diagnostic code for "lack of housing") or nonhomeless and compared using logistic regression. Additional analyses were conducted for two low-risk subgroups: veterans who served in current Middle East wars (Operation Enduring Freedom [OEF]/Operation Iraqi Freedom [OIF]) and veterans with ≥50% service-connected disability. Among all VA mental health users, OEF/OIF (odds ratio [OR]) = 0.4) and ≥50% service-connected (OR = .3) veterans were less likely to be homeless. In the overall and subgroup analyses, illicit drug use (OR = 3.3-4.7) was by far the strongest predictor of homelessness, followed by pathological gambling (PG) (OR = 2.0-2.4), alcohol use disorder (OR = 1.8-2.0), and having a personality disorder (OR = 1.6-2.2). In both low-risk groups, severe mental illness (schizophrenia or bipolar disorder), along with substance use disorders, PG, and personality disorders, increased homelessness risk. Substance use, PG, and personality disorders confer the greatest modifiable risk of homelessness among veterans using VA services, while service-connected disability conferred reduced risk. Clinical prevention efforts could focus on these factors.  © American Academy of Addiction Psychiatry.

  5. 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.

  6. Priority setting and the ethics of resource allocation within VA healthcare facilities: results of a survey.

    Science.gov (United States)

    Foglia, Mary Beth; Pearlman, Robert A; Bottrell, Melissa M; Altemose, Jane A; Fox, Ellen

    2008-01-01

    Setting priorities and the subsequent allocation of resources is a major ethical issue facing healthcare facilities, including the Veterans Health Administration (VHA), the largest integrated healthcare delivery network in the United States. Yet despite the importance of priority setting and its impact on those who receive and those who provide care, we know relatively little about how clinicians and managers view allocation processes within their facilities. The purpose of this secondary analysis of survey data was to characterize staff members' perceptions regarding the fairness of healthcare ethics practices related to resource allocation in Veterans Administration (VA) facilities. The specific aim of the study was to compare the responses of clinicians, clinician managers, and non-clinician managers with respect to these survey items. We utilized a paper and web-based survey and a cross-sectional design of VHA clinicians and managers. Our sample consisted of a purposive stratified sample of 109 managers and a stratified random sample of 269 clinicians employed 20 or more hours per week in one of four VA medical centers. The four medical centers were participating as field sites selected to test the logistics of administering and reporting results of the Integrated Ethics Staff Survey, an assessment tool aimed at characterizing a broad range of ethical practices within a healthcare organization. In general, clinicians were more critical than clinician managers or non-clinician managers of the institutions' allocation processes and of the impact of resource decisions on patient care. Clinicians commonly reported that they did not (a) understand their facility's decision-making processes, (b) receive explanations from management regarding the reasons behind important allocation decisions, or (b) perceive that they were influential in allocation decisions. In addition, clinicians and managers both perceived that education related to the ethics of resource

  7. Prevalence and trends of selected urologic conditions for VA healthcare users

    Directory of Open Access Journals (Sweden)

    Fischer Michael J

    2006-11-01

    Full Text Available Abstract Background Conducted as part of the Urologic Diseases in America project whose aim was to quantify the burden of urologic diseases on the American public, this study focuses on Veterans Health Administration (VHA users as a special population to supplement data on overall prevalence rates and trends in the United States. Veterans comprise 25% of the male population 18 years or older and contribute substantially to the overall burden of urologic conditions. The objective of this study is to describe the prevalence rates and trends of urologic cancers and selected benign conditions from 1999 to 2002 for VHA users. Methods VHA administrative files for 1999 – 2002 and Medicare claims files for the same years were used to identify those who had a diagnosis of qualifying urologic conditions. Results Among the conditions evaluated, prostate cancer was listed as a primary diagnosis for 5.4% of VHA users in 2002, followed in decreasing prevalence by erectile dysfunction (2.9%, renal mass (1.5%, interstitial cystitis (1.4%, and prostatitis (1.1%. Age-adjusted rates showed significant increases for renal mass (31%, interstitial cystitis (14%, and erectile dysfunction (8% between 1999 and 2002. Systematic variations in prevalence rates and trends were observed by age, race/ethnicity, and region. Those in the Western region generally had lower age-adjusted prevalence rates and their increases were also slower than other regions. Addition of Medicare data resulted in large increases (21 to 489% in prevalence among VHA users, suggesting substantial amount of non-VA urological care provided to VHA users. Conclusion Prevalence rates for many urologic diseases increased between 1999 and 2002, which were not entirely attributable to the aging of veterans. This changing urologic disease burden has substantial implications for access to urologic care and treatment capacity, especially in light of the level of urologic care delivered to veterans by

  8. Joint action of benzoxazinone derivatives and phenolic acids.

    Science.gov (United States)

    Jia, Chunhong; Jia, Chunghong; Kudsk, Per; Mathiassen, Solvejg K

    2006-02-22

    The joint action of binary and ternary mixtures of benzoxazinone derivatives and phenolic acids was studied using the additive dose model (ADM) as reference model. The activity of fixed-ratio mixtures of phenolic acids [ferulic acid (FA), p-coumaric acid (CA), vanillic acid (VA), and p-hydroxybenzoic acid (HBA)] and benzoxazinone derivatives [2,4-dihydroxy-7-methoxy-1,4-benzoxazin-3-one (DIMBOA), 6-methoxybenzoxazolin-2-one (MBOA), benzoxazolin-2-one (BOA), 2-aminophenol (AP), and N-(2-hydroxyphenyl)acetamide (HPAA)] on Lolium perenne and Myosotis arvensis root growth was assessed in Petri dishes. Root length was recorded 6 days after seeding, and EC(50) and EC(90) values were estimated using nonlinear regression analyses. The benzoxazinone derivatives were found to be more phytotoxic than the phenolic acids, particularly on M. arvensis. Binary mixtures of phenolic acids responded predominantly additively on both plant species. Deviations from additivity were species-specific with antagonistic responses on L. perenne and synergistic responses on M. arvensis. Similarly, binary mixtures of benzoxazinone derivatives also followed the ADM, although synergistic responses were observed for BOA + AP and BOA + HPAA. Binary and ternary mixtures of benzoxazinone derivatives and phenolic acids responded primarily antagonistically; however, a significant synergistic performance was observed with DIMBOA + FA and DIMBOA + VA on L. perenne. These results do not support the assumption that allelopathic effects of wheat can be attributed to synergistic effects of otherwise weakly active allelopathic compounds, and it is suggested that future research be directed toward identifying and studying the effects of other potential allelochemicals including the degradation products of the most abundant wheat allelochemicals.

  9. Multiclonal methicillin-resistant Staphylococcus aureus (MRSA) outbreak and its control after use of the Veterans Affairs (VA) MRSA bundle in a VA long-term care facility, 2004-2014.

    Science.gov (United States)

    Webb, Risa M; Denton, Carmelita; Spruill, Emily; Henson, Gay; Bruce, Lisa; Woods, Gail L; Swiatlo, Andrea; Walker, Erica D; Peel, Chere; Sullivan, Donna

    2016-06-01

    A multiclonal methicillin-resistant Staphylococcus aureus (MRSA) outbreak with 91 infections occurred in our Veterans Affairs (VA) community living center over 46 months. Both similar and unique strains were shown by repetitive polymerase chain reaction to contribute to the outbreak, including 1 strain causing infections over a 33-month period. Most infections were soft tissue infections (67%). For 21 months after the initiation of the VA MRSA bundle, no infections were identified, and low rates of infection have been sustained an additional 4 years. The average annual rate of MRSA infection decreased by 62% (P < .001) from 0.6 per 1,000 resident days for 4 years prior to the bundle implementation to 0.09 per 1,000 resident days for 4 years after the bundle implementation. Published by Elsevier Inc.

  10. Air pollution and DNA methylation: interaction by psychological factors in the VA Normative Aging Study.

    Science.gov (United States)

    Madrigano, Jaime; Baccarelli, Andrea; Mittleman, Murray A; Sparrow, David; Spiro, Avron; Vokonas, Pantel S; Cantone, Laura; Kubzansky, Laura; Schwartz, Joel

    2012-08-01

    DNA methylation is a potential pathway linking air pollution to disease. Studies indicate that psychological functioning modifies the association between pollution and morbidity. The authors estimated the association of DNA methylation with ambient particulate matter less than 2.5 µm in diameter (PM(2.5)) and black carbon, using mixed models. DNA methylation of the inducible nitric oxide synthase gene, iNOS, and the glucocorticoid receptor gene, GCR, was measured by quantitative polymerase chain reaction pyrosequencing of 1,377 blood samples from 699 elderly male participants in the VA Normative Aging Study (1999-2009). The authors also investigated whether this association was modified by psychological factors including optimism or pessimism, anxiety, and depression. iNOS methylation was decreased after acute exposure to both black carbon and PM(2.5). A 1-μg/m(3) increase in exposure to black carbon in the 4 hours preceding the clinical examination was associated with a 0.9% decrease in 5-methylcytosine (95% CI: 0.4, 1.4) in iNOS, and a 10-μg/m(3) increase in exposure to PM(2.5) was associated with a 0.6% decrease in 5-methylcytosine (95% CI: 0.03, 1.1) in iNOS. Participants with low optimism and high anxiety had associations that were 3-4 times larger than those with high optimism or low anxiety. GCR methylation was not associated with particulate air pollution exposure.

  11. 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

  12. 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.

  13. 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

  14. Expression of Vitis amurensis VaERF20 in Arabidopsis thaliana Improves Resistance to Botrytis cinerea and Pseudomonas syringae pv. Tomato DC3000

    OpenAIRE

    Mengnan Wang; Yanxun Zhu; Rui Han; Wuchen Yin; Chunlei Guo; Zhi Li; Xiping Wang

    2018-01-01

    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 t...

  15. Partnering With VA Stakeholders to Develop a Comprehensive Patient Safety Data Display: Lessons Learned From the Field.

    Science.gov (United States)

    Chen, Qi; Shin, Marlena H; Chan, Jeffrey A; Sullivan, Jennifer L; Borzecki, Ann M; Shwartz, Michael; Rivard, Peter E; Hatoun, Jonathan; Rosen, Amy K

    2016-01-01

    Health care systems are increasingly burdened by the large numbers of safety measures currently being reported. Within the Veterans Administration (VA), most safety reporting occurs within organizational silos, with little involvement by the frontline users of these measures. To provide a more integrated picture of patient safety, the study team partnered with multiple VA stakeholders and engaged potential frontline users at 2 hospitals to develop a Guiding Patient Safety (GPS) tool. The GPS is currently in its fourth generation; once approval is obtained from senior leadership, implementation will begin. Stakeholders were enthusiastic about the GPS's user-friendly format, comprehensive content, and potential utility for improving safety. These findings suggest that stakeholder engagement is a critical first step in the development of tools that will more likely be used by frontline users. Policy makers and researchers may consider adopting this innovative partnered-research model in developing future national initiatives to deliver meaningful programs to frontline users. © The Author(s) 2014.

  16. Definitive differentiation between single and mixed mycobacterial infections in red deer (Cervus elaphus) by a combination of duplex amplification of p34 and f57 sequences and Hpy188I enzymatic restriction of duplex amplicons.

    Science.gov (United States)

    Godfroid, Jacques; Delcorps, Cathy; Irenge, Leonid M; Walravens, Karl; Marché, Sylvie; Gala, Jean-Luc

    2005-09-01

    Severe emaciation and mortalities suggestive of mycobacterial infections were recently reported for both adult and young wild red deer (Cervus elaphus) in the southeastern part of Belgium. In deer, tuberculous lesions are not pathognomonic of Mycobacterium bovis infection due to gross and microscopic similarities with lesions caused by Mycobacterium avium subsp. paratuberculosis or M. avium subsp. avium. The aim of this study was to improve molecular methods for the species-specific identification of M. bovis, M. avium subsp. avium, and M. avium subsp. paratuberculosis in mycobacterial infections of deer. DNA banding patterns were assessed prior to and after Hpy188I restriction of f57-upstream (us)-p34 duplex amplicons. The duplex f57-us-p34 PCR differentiated M. bovis from M. avium subsp. paratuberculosis and M. avium subsp. avium infections, whereas the restriction step differentiated single M. avium subsp. paratuberculosis or M. avium subsp. avium infections from mixed M. avium subsp. paratuberculosis/M. avium subsp. avium infections. The endonuclease Hpy188I cleaves DNA between nucleotides N and G in the unique TCNGA sequence. This restriction site was found at position 168 upstream of the us-p34 initiation codon in all M. avium subsp. avium strains tested, regardless of their origin and the results of IS901 PCR. In contrast, the restriction site was abrogated in all M. avium subsp. paratuberculosis strains tested, independent of their origin, Mycobactin J dependency, and IS900 PCR results. Consequently, a two-step strategy, i.e., duplex us-p34-f57 PCR and Hpy188I restriction, allowed us to exclude M. bovis infection and to identify single (M. avium subsp. paratuberculosis or M. avium subsp. avium) or mixed (M. avium subsp. paratuberculosis/M. avium subsp. avium) infections in wild red deer in Belgium. Accordingly, we propose to integrate, in a functional molecular definition of M. avium subsp. paratuberculosis, the absence of the Hpy188I restriction site from

  17. 30 CFR 57.22212 - Air flow (I-C, II-A, and V-A mines).

    Science.gov (United States)

    2010-07-01

    ... 30 Mineral Resources 1 2010-07-01 2010-07-01 false Air flow (I-C, II-A, and V-A mines). 57.22212 Section 57.22212 Mineral Resources MINE SAFETY AND HEALTH ADMINISTRATION, DEPARTMENT OF LABOR METAL AND NONMETAL MINE SAFETY AND HEALTH SAFETY AND HEALTH STANDARDS-UNDERGROUND METAL AND NONMETAL MINES Safety Standards for Methane in Metal and Nonmeta...

  18. Demonstration of Electro-Osmotic Pulse Technology in Earth-Covered Magazines at Fort A.P. Hill, VA

    Science.gov (United States)

    2009-08-01

    damage, and growth of pathogens such as mold and microorganisms. At Fort A.P. Hill, VA, large amounts of water seep through the concrete walls...to the walls using galvanized steel angles. The an- gles were held in place using screws going through the wall and base with nuts to keep them...between them at the apex of the arch and held in place using nuts . Figure C-10 shows the completed model under testing. Prior to assembling the

  19. 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

  20. 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.