WorldWideScience

Sample records for geminiviral amplicon va

  1. 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

  2. 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 …

  3. Genetics Home Reference: carbonic anhydrase VA deficiency

    Science.gov (United States)

    ... hyperammonemia due to carbonic anhydrase VA deficiency hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency mitochondrial carbonic anhydrase va deficiency Related Information How are ...

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

    Directory of Open Access Journals (Sweden)

    Daniel P Tonge

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

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

    Energy Technology Data Exchange (ETDEWEB)

    2013-08-08

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

  6. Geographic Distribution of VA Expenditures Report (GDX)

    Data.gov (United States)

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

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

    Science.gov (United States)

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

    1996-09-01

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

  8. 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....

  9. Another Phoenix VA director leaves

    Directory of Open Access Journals (Sweden)

    Robbins RA

    2016-08-01

    Full Text Available No abstract available. Article truncated after 150 words. The Arizona Republic reports that the director at the Phoenix VA Medical Center, Deborah Amdur, will retire after only 9 months for health reasons (1. Amdur will be replaced by Barbara Fallen, director of the VA Loma Linda Healthcare System. Fallen will be interim director until a permanent replacement for Amdur can be found. This is the fifth hospital director since former Director Sharon Helman was removed in mid-2014 amid the nationwide veterans health-care scandal that was first exposed at the Phoenix VA. The Veterans Integrated Service Network (VISN in Gilbert, which oversees the VA Medical Center in Arizona, New Mexico and West Texas has also been through a series of 4 directors since Susan Bowers retired under pressure in the wake of the VA scandal. Marie Weldon, current acting regional director, also oversees the Los Angeles-based VA Desert Pacific Healthcare System. Weldon described Fallen as “an experienced leader who ...

  10. Barcoded Primers Used in Multiplex Amplicon Pyrosequencing Bias Amplification

    OpenAIRE

    2012-01-01

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

  11. 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...

  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 performa...

  13. VA telemental health: suicide assessment.

    Science.gov (United States)

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

    2008-01-01

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

  14. 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 ...

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

    Science.gov (United States)

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

    2016-01-01

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

  16. 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...

  17. Report of VA Medical Training Programs

    Data.gov (United States)

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

  18. 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...... to the presence of filamentous microorganisms was monitored weekly over 4 months. Microthrix was identified as a causative filament and suitable control measures were introduced. The level of Microthrix was reduced after 1-2 months but a number of other filamentous species were still present, with most of them...

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

    Science.gov (United States)

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

    2011-01-01

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

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

    Science.gov (United States)

    Jones, Bethan M; Kustka, Adam B

    2017-04-01

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

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

    Directory of Open Access Journals (Sweden)

    Frédéric Mahé

    2014-09-01

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

  2. OneVA EA Vision and Strategy

    Data.gov (United States)

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

  3. Geographic Distribution of VA Expenditures 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,...

  4. 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,...

  5. 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,...

  6. 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,...

  7. 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,...

  8. 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,...

  9. 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,...

  10. 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,...

  11. 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,...

  12. 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,...

  13. 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,...

  14. 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,...

  15. Geographic Distribution of VA Expenditures FY2009

    Data.gov (United States)

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

  16. Geographic Distribution of VA Expenditures 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,...

  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 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,...

  19. 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,...

  20. 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,...

  1. 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,...

  2. 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,...

  3. 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,...

  4. 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,...

  5. 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,...

  6. 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,...

  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 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,...

  9. 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,...

  10. 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,...

  11. 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,...

  12. 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,...

  13. 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,...

  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 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,...

  16. 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,...

  17. 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,...

  18. KaVA ESTEMA project

    Science.gov (United States)

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

    2016-07-01

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

  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. 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 ...

  1. 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...

  2. 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...

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

    Science.gov (United States)

    Borst, Eva Maria; Messerle, Martin

    2003-07-01

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

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

    DEFF Research Database (Denmark)

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

    2015-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Michael G. Mauk

    2015-10-01

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

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

    Science.gov (United States)

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

    2015-10-20

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

  7. 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...

  8. 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...

  9. 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/.

  10. VaR BASED RISK MANAGEMENT

    Directory of Open Access Journals (Sweden)

    Mária Bohdalová

    2013-06-01

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

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

    Directory of Open Access Journals (Sweden)

    Marie-Claude N Laffitte

    2014-12-01

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

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

    Science.gov (United States)

    Ballin, Nicolai Z; Madsen, Knud G

    2007-11-01

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

  13. The Portfolio Decision Under the VaR Constraint

    Institute of Scientific and Technical Information of China (English)

    ChunfengWang; XinshuTu

    2004-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Chiara Falcicchia

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

  15. 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

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

    OpenAIRE

    Carlos Eduardo M. Gomes; Ferreira,Osny P.

    2005-01-01

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

  17. 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

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

    DEFF Research Database (Denmark)

    Yao, Danfeng; Kim, Junyoung; Yu, Fang

    2005-01-01

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

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

    NARCIS (Netherlands)

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

    2005-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Carter Jennifer

    2005-01-01

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

  1. 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

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

    Science.gov (United States)

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

    2012-10-01

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

  3. 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.

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

    DEFF Research Database (Denmark)

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

    2004-01-01

    We tested the SNP typing protocol developed for the NanoChip electronic microarray by analyzing the four Y chromosome loci SRY1532, SRY8299, TAT, and 92R7. Amplicons of different lengths containing the same locus were purified and addressed to the NanoChip array and fluorescently labelled reporter...

  5. 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 ...

  6. 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...

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

    Science.gov (United States)

    Xu, Jiawu; Fonseca, Dina M

    2011-10-01

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

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

    DEFF Research Database (Denmark)

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

    2011-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Claire Rooney

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

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

    OpenAIRE

    2011-01-01

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

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

    Science.gov (United States)

    Lüke, Claudia; Frenzel, Peter

    2011-09-01

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

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

    Science.gov (United States)

    Antonielli, Livio; Sessitsch, Angela

    2016-04-01

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

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

    Science.gov (United States)

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

    2011-01-01

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

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

    Science.gov (United States)

    Bezold, C; Mayer, E; Dighe, A

    1997-01-01

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

  15. Geographic Distribution of VA Expenditures (GDX 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,...

  16. 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.

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

    Directory of Open Access Journals (Sweden)

    Carlos Eduardo M. Gomes

    2005-07-01

    Full Text Available Recently, modern techniques have been applied for analysis of the influence of polymers on microstructural properties of Portland cement, such as Thermogravimetric Analyses (TG, Scanning Electronic Microscopy (SEM, Fourier Transform Infrared Spectroscopy (FT-IR and Mercury Intrusion Porosimetry (MIP. In this study, thermogravimetric analyses were used to study the influence of vinyl acetate-versatic vinylester copolymer (VA/VeoVA in seven pastes of 28-day old Portland cement, in which distinct polymer contents and water/cement ratios were employed. In addition, analyses of FT-IR and MIP on Portland cement pastes modified by the copolymer were employed. The results showed that the addition of polymer interferes significantly in the reduction of Portlandite formation and increases the porosity of the matrices. A possible chemical interaction between the copolymer and hydrated products of Portland cement was also observed.

  18. Proposed comprehensive ototoxicity monitoring program for VA healthcare (COMP-VA)

    Science.gov (United States)

    Konrad-Martin, Dawn; Reavis, Kelly M.; McMillan, Garnett; Helt, Wendy J.; Dille, Marilyn

    2015-01-01

    Prevention and rehabilitation of hearing loss and tinnitus, the two most commonly awarded service-connected disabilities, are high priority initiatives in the Department of Veterans Affairs (VA). At least 4,000 Veterans, most with significant hearing loss, will receive cisplatin this year, with more than half sustaining permanent hearing shift and nearly 40% developing new tinnitus. With improved survivability following cancer treatment, Veterans treated with cisplatin are approached with the dual goals of effective treatment and preserved quality of life. This article describes COMP-VA, a comprehensive ototoxicity monitoring program developed for VA patients receiving cisplatin. The program includes an individualized pretreatment prediction model that identifies the likelihood of hearing shift given cisplatin dose and patient factors. It supports both manual and automated hearing testing with a newly developed portable audiometer capable of performing the recommended procedures on the chemotherapy unit during treatment. It also includes objective methods for identifying outer hair cell changes and predicting audiogram changes using distortion-product otoacoustic emissions. We describe this program of evidence-based ototoxicity monitoring protocols using a case example to give the reader an understanding of how this program would be applied, along with a plan for future work to accomplish the final stages of program development. PMID:24805896

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

    Directory of Open Access Journals (Sweden)

    Robbins RA

    2014-08-01

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

  20. Microcirculatory assessment of patients under VA-ECMO

    NARCIS (Netherlands)

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

    2016-01-01

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

  1. MyHealtheVet (VA's personal health record)

    Science.gov (United States)

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

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

    Science.gov (United States)

    2012-11-08

    ... AFFAIRS VA Directive 0005 on Scientific Integrity AGENCY: Office of Policy and Planning, Department of... Department of Veterans Affairs (VA) Directive 0005 on Scientific Integrity and responds to public comments... Scientific Integrity and the Office of Science and Technology Policy's 2010 guidance memorandum on scientific...

  3. 38 CFR 17.71 - Revocation of VA approval.

    Science.gov (United States)

    2010-07-01

    ... 38 Pensions, Bonuses, and Veterans' Relief 1 2010-07-01 2010-07-01 false Revocation of VA approval... Community Residential Care § 17.71 Revocation of VA approval. (a) If a hearing official determines under... residential care facility and notify the community residential care facility of this revocation. (b)...

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

    Science.gov (United States)

    2007-11-02

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

  5. 78 FR 62441 - VA Dental Insurance Program-Federalism

    Science.gov (United States)

    2013-10-22

    ... AFFAIRS 38 CFR Part 17 RIN 2900-AO85 VA Dental Insurance Program--Federalism AGENCY: Department of... direct final action to amend its regulations related to the VA Dental Insurance Program (VADIP), a pilot program to offer premium-based dental insurance to enrolled veterans and certain survivors and dependents...

  6. 78 FR 63143 - VA Dental Insurance Program-Federalism

    Science.gov (United States)

    2013-10-23

    ... AFFAIRS 38 CFR Part 17 RIN 2900-AO86 VA Dental Insurance Program--Federalism AGENCY: Department of... its regulations related to the VA Dental Insurance Program (VADIP), a pilot program to offer premium-based dental insurance to enrolled veterans and certain survivors and dependents of veterans...

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

    Science.gov (United States)

    2011-08-22

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

  8. Using Amplicon Sequencing To Characterize and Monitor Bacterial Diversity in Drinking Water Distribution Systems

    Science.gov (United States)

    Shaw, Jennifer L. A.; Weyrich, Laura S.; Sawade, Emma; Drikas, Mary; Cooper, Alan J.

    2015-01-01

    Drinking water assessments use a variety of microbial, physical, and chemical indicators to evaluate water treatment efficiency and product water quality. However, these indicators do not allow the complex biological communities, which can adversely impact the performance of drinking water distribution systems (DWDSs), to be characterized. Entire bacterial communities can be studied quickly and inexpensively using targeted metagenomic amplicon sequencing. Here, amplicon sequencing of the 16S rRNA gene region was performed alongside traditional water quality measures to assess the health, quality, and efficiency of two distinct, full-scale DWDSs: (i) a linear DWDS supplied with unfiltered water subjected to basic disinfection before distribution and (ii) a complex, branching DWDS treated by a four-stage water treatment plant (WTP) prior to disinfection and distribution. In both DWDSs bacterial communities differed significantly after disinfection, demonstrating the effectiveness of both treatment regimes. However, bacterial repopulation occurred further along in the DWDSs, and some end-user samples were more similar to the source water than to the postdisinfection water. Three sample locations appeared to be nitrified, displaying elevated nitrate levels and decreased ammonia levels, and nitrifying bacterial species, such as Nitrospira, were detected. Burkholderiales were abundant in samples containing large amounts of monochloramine, indicating resistance to disinfection. Genera known to contain pathogenic and fecal-associated species were also identified in several locations. From this study, we conclude that metagenomic amplicon sequencing is an informative method to support current compliance-based methods and can be used to reveal bacterial community interactions with the chemical and physical properties of DWDSs. PMID:26162884

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

    Directory of Open Access Journals (Sweden)

    Federico M Ibarbalz

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

  10. Using Amplicon Sequencing To Characterize and Monitor Bacterial Diversity in Drinking Water Distribution Systems.

    Science.gov (United States)

    Shaw, Jennifer L A; Monis, Paul; Weyrich, Laura S; Sawade, Emma; Drikas, Mary; Cooper, Alan J

    2015-09-01

    Drinking water assessments use a variety of microbial, physical, and chemical indicators to evaluate water treatment efficiency and product water quality. However, these indicators do not allow the complex biological communities, which can adversely impact the performance of drinking water distribution systems (DWDSs), to be characterized. Entire bacterial communities can be studied quickly and inexpensively using targeted metagenomic amplicon sequencing. Here, amplicon sequencing of the 16S rRNA gene region was performed alongside traditional water quality measures to assess the health, quality, and efficiency of two distinct, full-scale DWDSs: (i) a linear DWDS supplied with unfiltered water subjected to basic disinfection before distribution and (ii) a complex, branching DWDS treated by a four-stage water treatment plant (WTP) prior to disinfection and distribution. In both DWDSs bacterial communities differed significantly after disinfection, demonstrating the effectiveness of both treatment regimes. However, bacterial repopulation occurred further along in the DWDSs, and some end-user samples were more similar to the source water than to the postdisinfection water. Three sample locations appeared to be nitrified, displaying elevated nitrate levels and decreased ammonia levels, and nitrifying bacterial species, such as Nitrospira, were detected. Burkholderiales were abundant in samples containing large amounts of monochloramine, indicating resistance to disinfection. Genera known to contain pathogenic and fecal-associated species were also identified in several locations. From this study, we conclude that metagenomic amplicon sequencing is an informative method to support current compliance-based methods and can be used to reveal bacterial community interactions with the chemical and physical properties of DWDSs. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

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

    Directory of Open Access Journals (Sweden)

    Umberto Rosani

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

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

    Science.gov (United States)

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

    2015-08-01

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

  13. VaR Methodology Application for Banking Currency Portfolios

    Directory of Open Access Journals (Sweden)

    Daniel Armeanu

    2007-02-01

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

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

    DEFF Research Database (Denmark)

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

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

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

    DEFF Research Database (Denmark)

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

    2016-01-01

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

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

    DEFF Research Database (Denmark)

    Nam, Kiwoong; Munch, Kasper; Hobolth, Asger

    2014-01-01

    The unique inheritance pattern of X chromosomes makes them preferential targets of adaptive evolution. We here investigate natural selection on the X chromosome in all species of great apes. We find that diversity is more strongly reduced around genes on the X compared with autosomes......, and that a higher proportion of substitutions results from positive selection. Strikingly, the X exhibits several megabase long regions where diversity is reduced more than five fold. These regions overlap significantly among species, and have a higher singleton proportion, population differentiation...... with ampliconic sequences we propose that intra-genomic conflict between the X and the Y chromosomes is a major driver of X chromosome evolution....

  17. 38 CFR 1.203 - Information to be reported to VA Police.

    Science.gov (United States)

    2010-07-01

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

  18. COPD, COOP and BREATH at the VA

    Directory of Open Access Journals (Sweden)

    Robbins RA

    2011-02-01

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

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

    Science.gov (United States)

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

    2014-03-01

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

  20. Unscheduled DNA replication origin activation at inserted HPV 18 sequences in a HPV-18/MYC amplicon.

    Science.gov (United States)

    Conti, Chiara; Herrick, John; Bensimon, Aaron

    2007-08-01

    Oncogene amplification is a critical step leading to tumorigenesis, but the underlying mechanisms are still poorly understood. Despite data suggesting that DNA replication is a major source of genomic instability, little is known about replication origin usage and replication fork progression in rearranged regions. Using a single DNA molecule approach, we provide here the first study of replication kinetics on a previously characterized MYC/papillomavirus (HPV18) amplicon in a cervical cancer. Using this amplicon as a model, we investigated the role DNA replication control plays in generating amplifications in human cancers. The data reveal severely perturbed DNA replication kinetics in the amplified region when compared with other regions of the same genome. It was found that DNA replication is initiated from both genomic and viral sequences, resulting in a higher median frequency of origin firings. In addition, it was found that the higher initiation frequency was associated with an equivalent increase in the number of stalled replication forks. These observations raise the intriguing possibility that unscheduled replication origin activation at inserted HPV-18 viral DNA sequences triggers DNA amplification in this cancer cell line and the subsequent overexpression of the MYC oncogene.

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

    Science.gov (United States)

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

    2016-01-01

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

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

    Science.gov (United States)

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

    2016-01-22

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

  3. 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.

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

    Science.gov (United States)

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

    2016-03-01

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

  5. 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 ...

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

    Science.gov (United States)

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

    2016-01-01

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

  7. 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.

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

    Science.gov (United States)

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

    2013-01-01

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

  9. 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...

  10. 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...

  11. Key Science Observations of AGNs with KaVA Array

    CERN Document Server

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

    2015-01-01

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

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

    Science.gov (United States)

    2013-11-27

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

  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. 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...

  16. VA Homeless Grant and Per Diem FY09

    Data.gov (United States)

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

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

    Science.gov (United States)

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

    2009-08-01

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

  18. A VA medical center's PTSD residential recovery program.

    Science.gov (United States)

    Devaney, Donald E

    2010-01-01

    With the influx of military veterans with Post Traumatic Stress Disorder (PTSD) increasingly affecting all healthcare facilities, including acute care and long term, learning from the experience of VA hospitals in treating those with PTSD may prove valuable. In this article, Tripler/VA Provost Marshal Donald E. Delaney describes a program that has been in operation since 1994. He may be contacted for further in formation at (808) 433-4465 or Donald.devaney@amedd.army .mil

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

    Directory of Open Access Journals (Sweden)

    Robbins RA

    2014-09-01

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

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

    Science.gov (United States)

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

    2014-05-01

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

  1. 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.

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

    Indian Academy of Sciences (India)

    Mhathung Yanthan; Arvind K Misran

    2013-11-01

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

  3. Genotyping common FSHR polymorphisms based on competitive amplification of differentially melting amplicons (CADMA)

    DEFF Research Database (Denmark)

    Borgbo, Tanni; Sommer Kristensen, Lasse; Lindgren, Ida

    2014-01-01

    PURPOSE: To provide an improved platform for simple, reliable, and cost-effective genotyping. BACKGROUND: Modern fertility treatments are becoming increasingly individualized in an attempt to optimise the follicular response and reproductive outcome, following controlled ovarian stimulation....... As the field of pharmacogenetics evolve, genetic biomarkers such as polymorphisms of the follicle stimulating hormone receptor (FSHR) may be included as a predictive tool for individualized fertility treatment. However, the currently available genotyping methods are expensive, time-consuming or have a limited...... analytical sensitivity. Here, we present a novel version of "competitive amplification of differentially melting amplicons" (CADMA), providing an improved platform for simple, reliable, and cost-effective genotyping. METHODS: Two CADMA based assays were designed for the two common polymorphisms of the FSHR...

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

    Directory of Open Access Journals (Sweden)

    Hanna Farnelid

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

  5. 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.

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

    Science.gov (United States)

    Moralli, Daniela; Monaco, Zoia L

    2015-02-01

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

  7. 75 FR 3970 - Fund Availability Under the VA Homeless Providers Grant and Per Diem Program

    Science.gov (United States)

    2010-01-25

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

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

    DEFF Research Database (Denmark)

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

    2014-01-01

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

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

    Science.gov (United States)

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

    2016-10-15

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

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

    OpenAIRE

    2013-01-01

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

  12. 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, Ptherapy (odds ratio=1.16, P=0.033), although they had fewer average therapy days (coefficient=-1.53±0.11, Prehabilitation therapy days (both unadjusted and adjusted), but they were significantly more likely to receive restorative nursing care both before and after risk adjustment.

  13. Tolerance of VA Mycorrhizal Fungi to Soil Acidity

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

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

  14. Stratigraphic-structural characteristics of Mačva basin

    Directory of Open Access Journals (Sweden)

    Carević Ivana

    2009-01-01

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

  15. ROM Simulation: Applications to Stress Testing and VaR

    OpenAIRE

    Carol Alexander; Daniel Ledermann

    2012-01-01

    Most banks employ historical simulation for Value-at-Risk (VaR) calculations, where VaR is computed from a lower quantile of a forecast distribution for the portfolio’s profit and loss (P&L) that is constructed from a single, multivariate historical sample on the portfolio’s risk factors. The implicit assumption is that history will repeat itself for certain over the forecast horizon. Until now, the only alternative is to assume the historical sample is generated by a multivariate, parametric...

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

    Science.gov (United States)

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

    2011-01-01

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

  17. 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.

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

    Science.gov (United States)

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

    2016-04-01

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

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

    DEFF Research Database (Denmark)

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

    2011-01-01

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

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

    Science.gov (United States)

    Lee, Seungeun; Yamamoto, Naomichi

    2015-12-01

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

  1. 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.

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

    Science.gov (United States)

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

    2003-09-01

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

  3. 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.

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

    Science.gov (United States)

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

    2015-12-01

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

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

    Science.gov (United States)

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

    2014-03-01

    The soil microbial community acts as a reservoir of microbes that directly influences the structure and composition of the aboveground plant community, promotes plant growth, increases stress tolerance and mediates local patterns of nutrient cycling. Direct interactions between plants and rhizosphere-dwelling microorganisms occur at, or near, the surface of the root. Upon introduction and establishment, invasive plants modify the soil microbial communities and soil biochemistry affecting bioremediation efforts and future plant communities. Here, we used tag-encoded FLX amplicon 454 pyrosequencing (TEFAP) to characterize the bacterial and fungal community diversity in the rhizosphere of Berberis thunbergii DC. (Japanese barberry) from invasive stands in coastal Maine to investigate effects of soil type, soil chemistry and surrounding plant cover on the soil microbial community structure. Acidobacteria, Actinobacteria, Proteobacteria and Verrucomicrobia were the dominant bacterial phyla, whereas fungal communities were comprised mostly of Ascomycota and Basidiomycota phyla members, including Agaricomycetes and Sordariomycetes. Bulk soil chemistry had more effect on the bacterial community structure than the fungal community. An effect of geographic location was apparent in the rhizosphere microbial communities, yet it was less significant than the effect of surrounding plant cover. These data demonstrate a high degree of spatial variation in the rhizosphere microbial communities of Japanese barberry with apparent effects of soil chemistry, location and canopy cover on the microbial community structure. © 2013 John Wiley & Sons Ltd.

  6. 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.

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

    Science.gov (United States)

    ... confidential Homeless Veterans Chat and see resources for homeless Veterans . Network of Support The Veterans Crisis Line can put you in touch with VA ... Expect Resource Locator Veterans Live Chat Veterans Text Homeless Veterans Live Chat Military Live Chat Deaf - Hard ... Suicide The Veterans Crisis Line ...

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

    Science.gov (United States)

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

    2002-01-01

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

  9. VA contracts give unfair advantage to Picker--study.

    Science.gov (United States)

    Wagner, M

    1991-08-19

    Service contracts for computed tomography scanners in Dept. of Veterans Affairs hospitals have given an unfair advantage to Picker International, according to a study by the VA's inspector general's office. The report is the latest round in a controversy that has pitted Picker against at least two independent service organizations and enmeshed it in a $1.65 billion lawsuit.

  10. 78 FR 2708 - Virginia Disaster Number VA-00052

    Science.gov (United States)

    2013-01-14

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

  11. 77 FR 51100 - Virginia Disaster No. VA-00048

    Science.gov (United States)

    2012-08-23

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

  12. 48 CFR 833.103 - Protests to VA.

    Science.gov (United States)

    2010-10-01

    ... REQUIREMENTS PROTESTS, DISPUTES, AND APPEALS Protests 833.103 Protests to VA. (a) Filing of protests. (1) An... (DAS for A&MM), or for solicitations issued by the Director, Office of Construction and Facilities Management. A protest filed with the DAS for A&MM or the Director, Office of Construction and Facilities...

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

    Institute of Scientific and Technical Information of China (English)

    舒跃龙; 吴小兵; 杨天忠; 贡惠宇; 侯云德; 颜子颖

    1999-01-01

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

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

    Science.gov (United States)

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

    2007-04-01

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

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

    OpenAIRE

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

    2012-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Charles K Lee

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

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

    Science.gov (United States)

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

    2012-01-01

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

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

    Science.gov (United States)

    Damiati, E; Borsani, G; Giacopuzzi, Edoardo

    2016-05-01

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

  19. 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.

  20. HSV-1 amplicon-mediated post-transcriptional inhibition of Rad51 sensitizes human glioma cells to ionizing radiation.

    Science.gov (United States)

    Saydam, O; Saydam, N; Glauser, D L; Pruschy, M; Dinh-Van, V; Hilbe, M; Jacobs, A H; Ackermann, M; Fraefel, C

    2007-08-01

    Standard treatment for glioblastoma multiforme and other brain tumors consists of surgical resection followed by combined radio-/chemotherapy. However, radiation resistance of tumor cells limits the success of this treatment, and the tumors invariably recur. Therefore, the selective inhibition of molecular mediators of radiation resistance may provide therapeutic benefit to the patient. One of these targets is the Rad51 protein, which is a key component of the homologous recombinational repair of DNA double-strand breaks. Here, we investigated whether post-transcriptional silencing of Rad51 by herpes simplex virus-type 1 (HSV-1) amplicon vector-mediated short interfering RNA expression can enhance the antitumor effect of radiation therapy. We demonstrate that these vectors specifically and efficiently inhibited the radiation-induced recruitment of Rad51 into nuclear foci in human glioma cells. The combination of vector-mediated silencing of Rad51 expression and treatment with ionizing radiation resulted in a pronounced reduction of the survival of human glioma cells in culture. In athymyc mice, a single intratumoral injection of Rad51-specific HSV-1 amplicon vector followed by a single radiation treatment resulted in a significant decrease in tumor size. In control animals, including mice that received an intratumoral injection of Rad51-specific amplicon vector but no radiation treatment, the tumor sizes increased.

  1. 75 FR 33216 - Payment or Reimbursement for Emergency Treatment Furnished by Non-VA Providers in Non-VA...

    Science.gov (United States)

    2010-06-11

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

  2. 75 FR 25321 - Agency Information Collection (VA National Rehabilitation Special Events, Event Registration...

    Science.gov (United States)

    2010-05-07

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

  3. 78 FR 55777 - Proposed Information Collection (VA, National Veterans Sports Programs and Special Events, Event...

    Science.gov (United States)

    2013-09-11

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

  4. 78 FR 77204 - Proposed Information Collection (VA National Veterans Sports Programs and Special Event Surveys...

    Science.gov (United States)

    2013-12-20

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

  5. 78 FR 76412 - Agency Information Collection (VA National Rehabilitation Special Events, Event Registration...

    Science.gov (United States)

    2013-12-17

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

  6. 77 FR 74279 - Agency Information Collection (VA/DOD Joint Disability Evaluation Board Claim): Activity under...

    Science.gov (United States)

    2012-12-13

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

  7. 38 CFR 1.9 - Description, use, and display of VA seal and flag.

    Science.gov (United States)

    2010-07-01

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

  8. 38 CFR 26.9 - Information on and public participation in VA environmental process.

    Science.gov (United States)

    2010-07-01

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

  9. The Impact of VA's Geriatric Research, Education and Clinical Centers on Academic Affiliates

    Science.gov (United States)

    Bragg, Elizabeth J.; Meganathan, Karthikeyan; Shay, Kenneth; Gilman, Stuart C.; Zeiss, Robert A.; Hettler, Debbie L.

    2011-01-01

    The education mission of the Department of Veterans Affairs (VA) is to train health professionals to benefit VA and the United States. One approach for achieving that mission, along with VA's research and clinical missions, was the establishment of Geriatric Research, Education and Clinical Centers (GRECCs) in 1975. These were developed at VA…

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

    Science.gov (United States)

    2011-11-21

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

  11. 48 CFR 803.7000 - Display of the VA Hotline poster.

    Science.gov (United States)

    2010-10-01

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

  12. 38 CFR 74.26 - What types of business information will VA collect?

    Science.gov (United States)

    2010-07-01

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

  13. 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.

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

    Directory of Open Access Journals (Sweden)

    Linda Resnik, PT, PhD

    2010-05-01

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

  15. Cosmological bounds in MaVaN models

    Energy Technology Data Exchange (ETDEWEB)

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

    2012-08-15

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

  16. VaR without correlations for portfolio of derivative securities

    OpenAIRE

    Barone-Adesi, Giovanni; Giannopoulos, Kostas; Vosper, Les

    2008-01-01

    We propose filtering historical simulation by GARCH processes to model the future distribution of assets and swap values. Options’ price changes are computed by full reevaluation on the changing prices of underlying assets. Our methodology takes implicitly into account assets’ correlations without restricting their values over time or computing them explicitly. VaR values for portfolios of derivative securities are obtained without linearising them. Historical simulation assigns equal probabi...

  17. VA/DoD Joint Executive Council Fiscal Year 2010

    Science.gov (United States)

    2010-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

    Jordan, W.C.

    1999-01-01

    Section 1 of this report documents the validation of KENO V.a against 258 critical experiments. Experiments considered were primarily high or low enriched uranium systems. The results indicate that the KENO V.a Monte Carlo Criticality Program accurately calculates a broad range of critical experiments. A substantial number of the calculations showed a positive or negative bias in excess of 1 1/2% in k-effective (k{sub eff}). Classes of criticals which show a bias include 3% enriched green blocks, highly enriched uranyl fluoride slab arrays, and highly enriched uranyl nitrate arrays. If these biases are properly taken into account, the KENO V.a code can be used with confidence for the design and criticality safety analysis of uranium-containing systems. Section 2 of this report documents the results of investigation into the cause of the bias observed in Sect. 1. The results of this study indicate that the bias seen in Sect. 1 is caused by code bias, cross-section bias, reporting bias, and modeling bias. There is evidence that many of the experiments used in this validation and in previous validations are not adequately documented. The uncertainty in the experimental parameters overshadows bias caused by the code and cross sections and prohibits code validation to better than about 1% in k{sub eff}.

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

    Science.gov (United States)

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

    2015-07-01

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

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

    Directory of Open Access Journals (Sweden)

    Jan Zietsch

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

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

    Science.gov (United States)

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

    2017-01-01

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

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

    DEFF Research Database (Denmark)

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

    2017-01-01

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

  4. Impact of the REACH II and REACH VA Dementia Caregiver Interventions on Healthcare Costs.

    Science.gov (United States)

    Nichols, Linda O; Martindale-Adams, Jennifer; Zhu, Carolyn W; Kaplan, Erin K; Zuber, Jeffrey K; Waters, Teresa M

    2017-05-01

    Examine caregiver and care recipient healthcare costs associated with caregivers' participation in Resources for Enhancing Alzheimer's Caregivers Health (REACH II or REACH VA) behavioral interventions to improve coping skills and care recipient management. RCT (REACH II); propensity-score matched, retrospective cohort study (REACH VA). Five community sites (REACH II); 24 VA facilities (REACH VA). Care recipients with Alzheimer's disease and related dementias (ADRD) and their caregivers who participated in REACH II study (analysis sample of 110 caregivers and 197 care recipients); care recipients whose caregivers participated in REACH VA and a propensity matched control group (analysis sample of 491). Previously collected data plus Medicare expenditures (REACH II) and VA costs plus Medicare expenditures (REACH VA). There was no increase in VA or Medicare expenditures for care recipients or their caregivers who participated in either REACH intervention. For VA care recipients, REACH was associated with significantly lower total VA costs of care (33.6%). VA caregiver cost data was not available. In previous research, both REACH II and REACH VA have been shown to provide benefit for dementia caregivers at a cost of less than $5/day; however, concerns about additional healthcare costs may have hindered REACH's widespread adoption. Neither REACH intervention was associated with additional healthcare costs for caregivers or patients; in fact, for VA patients, there were significantly lower healthcare costs. The VA costs savings may be related to the addition of a structured format for addressing the caregiver's role in managing complex ADRD care to an existing, integrated care system. These findings suggest that behavioral interventions are a viable mechanism to support burdened dementia caregivers without additional healthcare costs. © 2017, Copyright the Authors Journal compilation © 2017, The American Geriatrics Society.

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

    Institute of Scientific and Technical Information of China (English)

    万晓; 闫琳

    2007-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Shah Mukim Uddin

    2015-03-01

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

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

    Science.gov (United States)

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

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

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

    Directory of Open Access Journals (Sweden)

    Axel Poulet

    2016-01-01

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

  9. A comprehensive method for amplicon-based and metagenomic characterization of viruses, bacteria, and eukaryotes in freshwater samples.

    Science.gov (United States)

    Uyaguari-Diaz, Miguel I; Chan, Michael; Chaban, Bonnie L; Croxen, Matthew A; Finke, Jan F; Hill, Janet E; Peabody, Michael A; Van Rossum, Thea; Suttle, Curtis A; Brinkman, Fiona S L; Isaac-Renton, Judith; Prystajecky, Natalie A; Tang, Patrick

    2016-07-19

    Studies of environmental microbiota typically target only specific groups of microorganisms, with most focusing on bacteria through taxonomic classification of 16S rRNA gene sequences. For a more holistic understanding of a microbiome, a strategy to characterize the viral, bacterial, and eukaryotic components is necessary. We developed a method for metagenomic and amplicon-based analysis of freshwater samples involving the concentration and size-based separation of eukaryotic, bacterial, and viral fractions. Next-generation sequencing and culture-independent approaches were used to describe and quantify microbial communities in watersheds with different land use in British Columbia. Deep amplicon sequencing was used to investigate the distribution of certain viruses (g23 and RdRp), bacteria (16S rRNA and cpn60), and eukaryotes (18S rRNA and ITS). Metagenomic sequencing was used to further characterize the gene content of the bacterial and viral fractions at both taxonomic and functional levels. This study provides a systematic approach to separate and characterize eukaryotic-, bacterial-, and viral-sized particles. Methodologies described in this research have been applied in temporal and spatial studies to study the impact of land use on watershed microbiomes in British Columbia.

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

    Directory of Open Access Journals (Sweden)

    Shalchian-Tabrizi Kamran

    2011-05-01

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

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

    Science.gov (United States)

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

    2016-06-01

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

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

    Science.gov (United States)

    Koch, Edward F

    2012-05-01

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

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

    Science.gov (United States)

    Veludandi, Vineel K.; Vasudevan, K.

    2017-01-01

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

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

    Science.gov (United States)

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

    2015-06-01

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

  15. The KaVA and KVN Pulsar Project

    CERN Document Server

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

    2014-01-01

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

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

    Science.gov (United States)

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

    1975-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Vesa Hongisto

    2014-12-01

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

  18. Factors determining medical students' and residents' satisfaction during VA-based training: findings from the VA Learners' Perceptions Survey.

    Science.gov (United States)

    Cannon, Grant W; Keitz, Sheri A; Holland, Gloria J; Chang, Barbara K; Byrne, John M; Tomolo, Anne; Aron, David C; Wicker, Annie B; Kashner, T Michael

    2008-06-01

    To compare medical students' and physician residents' satisfaction with Veterans Affairs (VA) training to determine the factors that were most strongly associated with trainee satisfaction ratings. Each year from 2001 to 2006, all medical students and residents in VA teaching facilities were invited to complete the Learners' Perceptions Survey. Participants rated their overall training satisfaction on a 100-point scale and ranked specific satisfaction in four separate educational domains (learning environment, clinical faculty, working environment, and physical environment) on a five-point Likert scale. Each domain was composed of unique items. A total of 6,527 medical students and 16,583 physician residents responded to the survey. The overall training satisfaction scores for medical students and physician residents were 84 and 79, respectively (P training continuum. For both medical students and residents, the rating of each of the four educational domains was statistically significantly associated with the overall training satisfaction score (P training satisfaction score, followed by the clinical preceptor, working environment, and physical environment domains; no significant differences were found between medical students and physician residents in the rank order. Satisfaction with quality of care and faculty teaching contributed significantly to training satisfaction. Factors that influence training satisfaction were similar for residents and medical students. The domain with the highest association was the learning environment; quality of care was a key item within this domain.

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

    Institute of Scientific and Technical Information of China (English)

    黄翀; 许国栋; 杨玮枫; 吴永俊

    2015-01-01

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

  20. 沪深300指数极值VaR的分析与计算

    Institute of Scientific and Technical Information of China (English)

    周孝华; 唐秋燕

    2008-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Robbins RA

    2013-04-01

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

  2. Codex Alimentarius - značenje i važnost

    OpenAIRE

    1998-01-01

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

  3. 75 FR 41577 - VBA/VHA Musculoskeletal Forum: Improving VA's Disability Evaluation Criteria

    Science.gov (United States)

    2010-07-16

    ...The Department of Veterans Affairs (VA) will hold the Veterans Benefits Administration (VBA)/Veterans Health Administration (VHA) Musculoskeletal Forum: Improving VA's Disability Criteria to capture public comment and current medical science information from presentations made by subject matter experts. VA plans to use this information to update the sections of VA's Schedule for Rating Disabilities (VASRD) that pertain to diseases and injuries of the musculoskeletal system. See 38 CFR 4.40-4.73. Specifically, diagnostic code descriptors and evaluation criteria will be discussed. Contingent upon available capacity and time, individuals wishing to make oral statements will be accommodated on a first-come, first-served basis.

  4. 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.

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

    Directory of Open Access Journals (Sweden)

    L.S. Brinn

    2010-09-01

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

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

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

    Institute of Scientific and Technical Information of China (English)

    张则斌; 黄智猛

    2000-01-01

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

  12. 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.

  13. 76 FR 26607 - Safety Zone; Air Power Over Hampton Roads, Back River, Hampton, VA

    Science.gov (United States)

    2011-05-09

    ... vicinity of Willoughby Point, VA to protect mariners from the hazards associated with air show events... host an air show event in the vicinity of Willoughby Point, VA immediately above the Back River...'' N/ 076 20'18'' W (NAD 1983), in the vicinity of Willoughby Point on the Back River, Hampton...

  14. 33 CFR 334.350 - Chesapeake Bay off Fort Monroe, Va.; firing range danger zone.

    Science.gov (United States)

    2010-07-01

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

  15. 33 CFR 334.130 - Atlantic Ocean off Wallops Island and Chincoteague Inlet, Va.; danger zone.

    Science.gov (United States)

    2010-07-01

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

  16. 76 FR 44288 - Establishment of Class E Airspace; New Market, VA

    Science.gov (United States)

    2011-07-25

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

  17. 75 FR 76082 - Agency Information Collection (Credit Underwriting Standards and Procedures for Processing VA...

    Science.gov (United States)

    2010-12-07

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

  18. 78 FR 26250 - Payment for Home Health Services and Hospice Care to Non-VA Providers

    Science.gov (United States)

    2013-05-06

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

  19. 76 FR 3017 - VA Veteran-Owned Small Business Verification Guidelines

    Science.gov (United States)

    2011-01-19

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

  20. 33 CFR 334.220 - Chesapeake Bay, south of Tangier Island, Va.; naval firing range.

    Science.gov (United States)

    2010-07-01

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

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

    Science.gov (United States)

    2012-06-01

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

  2. 48 CFR 819.602-3 - Resolving differences between VA and the Small Business Administration.

    Science.gov (United States)

    2010-10-01

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

  3. 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...

  4. 78 FR 28949 - Fund Availability Under VA's Homeless Providers Grant and Per Diem Program (Rehabilitation)

    Science.gov (United States)

    2013-05-16

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

  5. 77 FR 27120 - Safety Zone; Virginia Beach Oceanfront Air Show, Atlantic Ocean, Virginia Beach, VA

    Science.gov (United States)

    2012-05-09

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

  6. 78 FR 56151 - Safety Zone, North Atlantic Ocean; Virginia Beach, VA

    Science.gov (United States)

    2013-09-12

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

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

    NARCIS (Netherlands)

    Maly, Ico

    2015-01-01

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

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

    NARCIS (Netherlands)

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

    2015-01-01

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

  9. 38 CFR 74.25 - What types of personally identifiable information will VA collect?

    Science.gov (United States)

    2010-07-01

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

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

    Science.gov (United States)

    2011-07-08

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

  11. 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...

  12. 75 FR 20774 - Establishment of Class E Airspace; Fort A.P. Hill, VA

    Science.gov (United States)

    2010-04-21

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

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

    Science.gov (United States)

    2010-07-01

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

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

    Science.gov (United States)

    2010-03-01

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

  15. 30 CFR 57.22605 - Blasting from the surface (V-A mines).

    Science.gov (United States)

    2010-07-01

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

  16. Analysis of amplicon-based NGS data from neurological disease gene panels: a new method for allele drop-out management.

    Science.gov (United States)

    Zucca, Susanna; Villaraggia, Margherita; Gagliardi, Stella; Grieco, Gaetano Salvatore; Valente, Marialuisa; Cereda, Cristina; Magni, Paolo

    2016-11-08

    Amplicon-based targeted resequencing is a commonly adopted solution for next-generation sequencing applications focused on specific genomic regions. The reliability of such approaches rests on the high specificity and deep coverage, although sequencing artifacts attributable to PCR-like amplification can be encountered. Between these artifacts, allele drop-out, which is the preferential amplification of one allele, causes an artificial increase in homozygosity when heterozygous mutations fall on a primer pairing region. Here, a procedure to manage such artifacts, based on a pipeline composed of two steps of alignment and variant calling, is proposed. This methodology has been compared to the Illumina Custom Amplicon workflow, available on Illumina MiSeq, on the analysis of data obtained with four newly designed TruSeq Custom Amplicon gene panels. Four gene panels, specific for Parkinson disease, for Intracerebral Hemorrhage Diseases (COL4A1 and COL4A2 genes) and for Familial Hemiplegic Migraine (CACNA1A and ATP1A2 genes) were designed. A total of 119 samples were re-sequenced with Illumina MiSeq sequencer and panel characterization in terms of coverage, number of variants found and allele drop-out potential impact has been carried out. Results show that 14 % of identified variants is potentially affected by allele drop-out artifacts and that both the Custom Amplicon workflow and the procedure proposed here could correctly identify them. Furthermore, a more complex configuration in presence of two mutations was simulated in silico. In this configuration, our proposed methodology outperforms Custom Amplicon workflow, being able to correctly identify two mutations in all the studied configurations. Allele drop-out plays a crucial role in amplicon-based targeted re-sequencing and specific procedures in data analysis of amplicon data should be adopted. Although a consensus has been established in the elimination of primer sequences from aligned data (e.g., via primer

  17. 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.

  18. 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.

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

    Directory of Open Access Journals (Sweden)

    I KOMANG TRY BAYU MAHENDRA

    2015-06-01

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

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

    Directory of Open Access Journals (Sweden)

    Kleiboeker Steven B

    2005-04-01

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

  1. 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.

  2. The use of VA Disability Compensation and Social Security Disability Insurance among working-aged veterans.

    Science.gov (United States)

    Wilmoth, Janet M; London, Andrew S; Heflin, Colleen M

    2015-07-01

    Although there is substantial disability among veterans, relatively little is known about working-aged veterans' uptake of Department of Veterans Affairs (VA) Disability Compensation and Social Security Disability Insurance (DI). This study identifies levels of veteran participation in VA disability and/or DI benefit programs, examines transitions into and out of VA and DI programs among veterans, and estimates the size and composition of the veteran population receiving VA and/or DI benefits over time. Data from the 1992, 1993, 1996, 2001, 2004, and 2008 Survey of Income and Program Participation (SIPP) are used to describe VA and DI program participation among veterans under the age of 65. The majority of working-aged veterans do not receive VA or DI benefits and joint participation is low, but use of these programs has increased over time. A higher percentage of veterans receive VA compensation, which ranges from 4.9% in 1992 to 13.2% in 2008, than DI compensation, which ranges from 2.9% in 1992 to 6.7% in 2008. The rate of joint participation ranges from less than 1% in 1992 to 3.6% in 2008. Veterans experience few transitions between VA and DI programs during the 36-48 months they are observed. The number of veterans receiving benefits from VA and/or DI nearly doubled between 1992 and 2008. There have been substantial shifts in the composition of veterans using these programs, as cohorts who served prior to 1964 are replaced by those who served after 1964. The findings suggest potential gaps in veterans' access to disability programs that might be addressed through improved coordination of VA and DI benefits. Copyright © 2015 Elsevier Inc. All rights reserved.

  3. 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.

  4. COPULA BASED VaR APPROACH FOR EUROPEAN STOCKS PORTFOLIO

    Directory of Open Access Journals (Sweden)

    Mária Bohdalová

    2013-06-01

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

  5. 75 FR 26160 - Drug and Drug-Related Supply Promotion by Pharmaceutical Company Sales Representatives at VA...

    Science.gov (United States)

    2010-05-11

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

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

    Science.gov (United States)

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

    2016-04-01

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

  7. Analysis of black fungal biofilms occurring at domestic water taps. I: compositional analysis using Tag-Encoded FLX Amplicon Pyrosequencing.

    Science.gov (United States)

    Heinrichs, Guido; Hübner, Iris; Schmidt, Carsten K; de Hoog, G Sybren; Haase, Gerhard

    2013-06-01

    Mass growth of dark fungal biofilms on water taps and associated habitats was observed in various German drinking water distribution systems recently. Customers of affected drinking water systems are anxious about potential and unknown health risks. These environments are known to harbour a fungal flora also comprising a variety of fungal opportunists that are well known to cause superficial mycoses in humans (Exophiala equina, Exophiala lecanii-corni) but are not known to establish dark biofilms so far. To gain profound insight on composition of respective biofilms, a metagenomic approach using Tag-Encoded FLX Amplicon Pyrosequencing (TEFAP) of the ribosomal internal transcribed spacer 2 region in comparison with a classical cultivation approach using Sabouraud agar with chloramphenicol and erythritol-chloramphenicol-agar was performed. E. lecanii-corni was found to be the major component in 10 of 13 biofilms analysed independently of the method used. Alternaria sp., E. equina, Fusarium spp. and Ochroconis spp. were also relatively abundant. As expected, TEFAP usually revealed a higher diversity than the cultivation approaches. For example, opportunistic species like Candida albicans or Exophiala dermatitidis were detected in very low amounts. In conclusion, TEFAP turned out to be a promising and powerful tool for the semi-quantitative analysis of fungal biofilms. Referring to relevant literature, potential biological hazards caused by fungi of the dark biofilms can be regarded as low.

  8. 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.

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

    Science.gov (United States)

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

    2015-09-01

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

  10. 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.

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

    Science.gov (United States)

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

    2013-01-01

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

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

    Science.gov (United States)

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

    2017-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Ilias Lagkouvardos

    2017-01-01

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

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

    Science.gov (United States)

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

    2016-12-15

    The currently available nucleic acid amplification tests (NAATs) for trichomoniasis are accurate, quick and confirmative with superior sensitivity than traditional culture-based microbiology assays. However, these assays are associated with problems of carry over contamination, false positive results, requirement of technical expertise for performance and detection of end product. Hence, a diagnostic assay with easy visualization of the amplified product will be profitable. An in-house, rapid, sensitive, specific molecular-beacon-based PCR assay, using primers against pfoB gene of Trichomonas vaginalis, was developed and evaluated using dry ectocervical swabs (n=392) from symptomatic females with vaginal discharge. Total DNA was isolated and used as template for the PCR assays. The performance and reproducibility of PCR assay was evaluated by composite reference standard (CRS). For easy visualization of the amplified product, molecular-beacon was designed and amplicons were visualized directly using fluorescent handheld dark reader or by Micro-Plate Reader. Molecular-beacons are single-stranded hairpin shaped nucleic acid probes composed of a stem, with fluorophore/quencher pair and a loop region complementary to the desired DNA. The beacon-based PCR assay designed in the present study is highly specific as confirmed by competition experiments and extremely sensitive with detection limit of 20fg of genomic DNA (3-4 pathogens). The minimum infrastructure requirement and ease to perform the assay makes this method highly useful for resource poor countries for better disease management. Copyright © 2016 Elsevier B.V. All rights reserved.

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

    Directory of Open Access Journals (Sweden)

    De Paepe Anne

    2004-02-01

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

  16. 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.

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

    Science.gov (United States)

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

    2017-03-01

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

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

    Science.gov (United States)

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

    2017-01-01

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

  19. 76 FR 3209 - West Los Angeles VA Medical Center Veterans Programs Enhancement Act of 1998; Draft Master Plan

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    2011-01-19

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

  20. 38 CFR 17.1000 - Payment or reimbursement for emergency services for nonservice-connected conditions in non-VA...

    Science.gov (United States)

    2010-07-01

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

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

    Institute of Scientific and Technical Information of China (English)

    方毅; 张屹山

    2007-01-01

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

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

    Science.gov (United States)

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

    2017-07-28

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

  3. 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.

  4. 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

  5. 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)

    Šlapeta, Jan; Linares, Marjorie C.

    2013-01-01

    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 environments, it is

  6. 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

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

    Science.gov (United States)

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

    2016-03-01

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

  8. 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.

  9. 77 FR 12647 - Fund Availability Under VA's Homeless Providers Grant and Per Diem Program

    Science.gov (United States)

    2012-03-01

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

  10. 77 FR 70212 - Agency Information Collection Activities Under OMB Review: VA MATIC Enrollment/Change

    Science.gov (United States)

    2012-11-23

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

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

    Science.gov (United States)

    2012-08-08

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

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

    Science.gov (United States)

    ... Care Apply Online Application Process Veteran Eligibility Active Duty Families of Veterans Women Veterans Determine Costs Copays ... VHA Forms & Publications Quality & Safety Quality of Care Ethics VA/DOD Clinical Practice Guidelines Access and Quality ...

  13. 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...

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

    Directory of Open Access Journals (Sweden)

    Marc Gregory Dumont

    2014-02-01

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

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

    Science.gov (United States)

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

    2017-02-01

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

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

    Science.gov (United States)

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

    2017-01-15

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

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

    Science.gov (United States)

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

    2015-01-01

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

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

    Science.gov (United States)

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

    2016-04-01

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

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

    Directory of Open Access Journals (Sweden)

    Lin eChen

    2015-10-01

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

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

    Science.gov (United States)

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

    2015-12-01

    Compared to Sanger sequencing, next-generation sequencing offers advantages for high resolution HLA genotyping including increased throughput, lower cost, and reduced genotype ambiguity. Here we describe an enhancement of the Roche 454 GS GType HLA genotyping assay to provide very high resolution (VHR) typing, by the addition of 8 primer pairs to the original 14, to genotype 11 HLA loci. These additional amplicons help resolve common and well-documented alleles and exclude commonly found null alleles in genotype ambiguity strings. Simplification of workflow to reduce the initial preparation effort using early pooling of amplicons or the Fluidigm Access Array™ is also described. Performance of the VHR assay was evaluated on 28 well characterized cell lines using Conexio Assign MPS software which uses genomic, rather than cDNA, reference sequence. Concordance was 98.4%; 1.6% had no genotype assignment. Of concordant calls, 53% were unambiguous. To further assess the assay, 59 clinical samples were genotyped and results compared to unambiguous allele assignments obtained by prior sequence-based typing supplemented with SSO and/or SSP. Concordance was 98.7% with 58.2% as unambiguous calls; 1.3% could not be assigned. Our results show that the amplicon-based VHR assay is robust and can replace current Sanger methodology. Together with software enhancements, it has the potential to provide even higher resolution HLA typing. Copyright © 2015. Published by Elsevier Inc.

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

    Science.gov (United States)

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

    2017-02-23

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

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

    Directory of Open Access Journals (Sweden)

    Dariush Etemadmoghadam

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

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

    Science.gov (United States)

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

    2010-11-12

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

  4. 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...

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

    Science.gov (United States)

    2015-10-27

    ELECTRONIC HEALTH RECORDS VA and DOD Need to Establish Goals and Metrics for Their Interoperability Efforts Statement of...COVERED 00-00-2015 to 00-00-2015 4. TITLE AND SUBTITLE Electronic Health Records : VA and DOD Need to Establish Goals and Metrics for Their...Subcommittee on Oversight and Investigations, Committee on Veterans’ Affairs, House of Representatives October 27, 2015 ELECTRONIC HEALTH RECORDS

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

    Science.gov (United States)

    2016-04-01

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

  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. 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.

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

    DEFF Research Database (Denmark)

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

    2004-01-01

    Conformational determination of [Leu]enkephalin in DMSO-d6 is carried out using VA and VCD spectral analyses. Conformational energies, vibrational frequencies and VA and VCD intensities are calculated using DFT at B3LYP/6-31G* level of theory. Comparison between the measured spectra and the spect......Conformational determination of [Leu]enkephalin in DMSO-d6 is carried out using VA and VCD spectral analyses. Conformational energies, vibrational frequencies and VA and VCD intensities are calculated using DFT at B3LYP/6-31G* level of theory. Comparison between the measured spectra...... and the spectral simulations of the low energy conformations of the neutral species enable conformational determination of the molecule. In an earlier study, based only on VA spectroscopy, the results led to the conclusion that [Leu]enkephalin had only a single b-bend conformation of the neutral species in DMSO-d6...... . The present work shows the importance of using VCD in addition to VA in determining the conformation of chiral molecules and which one of the examined three single b-bend structures is the most stable in DMSO-d6 ....

  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. 金融风险管理的VaR方法及其应用

    Institute of Scientific and Technical Information of China (English)

    何弟

    2012-01-01

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

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

    Science.gov (United States)

    Geoffroy, Véronique; Pizot, Cécile; Redin, Claire; Piton, Amélie; Vasli, Nasim; Stoetzel, Corinne; Blavier, André; Laporte, Jocelyn; Muller, Jean

    2015-01-01

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

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

    Institute of Scientific and Technical Information of China (English)

    李明; 刘喜波; 何慧; 姚沛

    2013-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Amy A. Gravely, MA

    2011-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Rosenstiel Philip

    2010-04-01

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

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

    Science.gov (United States)

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

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

  20. 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

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

    Institute of Scientific and Technical Information of China (English)

    邹新月

    2005-01-01

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

  2. 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 …

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

    Science.gov (United States)

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

    2014-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2009-01-12

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

  6. 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.

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

    Science.gov (United States)

    2012-09-01

    Entrance to the Base That Houses Tripler Army Medical Center in Honolulu, Hawaii 25 Contents Page ii GAO-12-992 VA and DOD...Collaboration Figure 5: Traffic Approaching the Entrance to the Base That Houses Tripler Army Medical Center in Honolulu, Hawaii, with the Medical Center...Army, the Navy, and the Air Force. The VA and DOD partners at the Honolulu joint venture are Tripler Army Medical Center and the VA Pacific Islands

  8. 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

    requirement to include two more reports, resulting in GAO reports in 2011, 2012, and 2016. 5GAO, VA and DOD Health Care: First Federal Health ...FEDERAL HEALTH CARE CENTER VA and DOD Need to Develop Better Information to Monitor Operations and Improve Efficiency...Government Accountability Office Highlights of GAO-17-197, a report to congressional committees January 2017 FEDERAL HEALTH CARE CENTER VA and DOD

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

    Science.gov (United States)

    2003-11-14

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

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

    Directory of Open Access Journals (Sweden)

    Beatriz Vaz de Melo Mendes

    2005-12-01

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

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

    Directory of Open Access Journals (Sweden)

    A.G. KHAN

    1995-01-01

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

  12. Performance-based budgeting in the public sector: an illustration from the VA health care system.

    Science.gov (United States)

    Yaisawarng, Suthathip; Burgess, James F

    2006-03-01

    This paper estimates frontier cost functions for US Department of Veterans Affairs (VA) hospitals in FY2000 that are consistent with economic theory and explicitly account for cost differences across patients' risk, level of access to care, quality of care, and hospital-specific characteristics. Results indicate that on average VA hospitals in FY2000 operate at efficiency levels of 94%, as compared to previous studies on US private sector hospitals that average closer to 90% efficient. Using these cost frontiers, management systems potentially could be implemented to enhance the equitable allocation of the VA medical care global budget and systematically distribute funds across hospitals and networks. The paper also provides recommendations to improve the efficiency of delivering health care services applicable to public sector organizations. Copyright 2005 John Wiley & Sons, Ltd.

  13. VaR RAROC与投资组合问题探讨

    Institute of Scientific and Technical Information of China (English)

    陈学华; 杨辉耀; 唐珂

    2004-01-01

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

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

    Science.gov (United States)

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

    2006-07-26

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

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

    Institute of Scientific and Technical Information of China (English)

    郭文旌; 李心丹

    2009-01-01

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

  16. 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.

  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. Variations in the Use of mHealth Tools: The VA Mobile Health Study.

    Science.gov (United States)

    Frisbee, Kathleen L

    2016-07-19

    Mobile health (mHealth) technologies exhibit promise for offering patients and their caregivers point-of-need tools for health self-management. This research study involved the dissemination of iPads containing a suite of mHealth apps to family caregivers of veterans who receive care from the Veterans Affairs (VA) Health Administration and have serious physical or mental injuries. The goal of the study was to identify factors and characteristics of veterans and their family caregivers that predict the use of mHealth apps. Veteran/family caregiver dyads (N=882) enrolled in VA's Comprehensive Assistance for Family Caregivers program were recruited to participate in an mHealth pilot program. Veterans and caregivers who participated and received an iPad agreed to have their use of the apps monitored and were asked to complete a survey assessing Caregiver Preparedness, Caregiver Traits, and Caregiver Zarit Burden Inventory baseline surveys. Of the 882 dyads, 94.9% (837/882) of caregivers were women and 95.7% (844/882) of veteran recipients were men. Mean caregiver age was 40 (SD 10.2) years and mean veteran age was 39 (SD 9.15) years, and 39.8% (351/882) lived in rural locations. Most (89%, 788/882) of the caregivers were spouses. Overall, the most frequently used app was Summary of Care, followed by RX Refill, then Journal, Care4Caregivers, VA Pain Coach, and last, VA PTSD Coach. App use was significantly predicted by the caregiver being a spouse, increased caregiver computer skills, a rural living location, lower levels of caregiver preparedness, veteran mental health diagnosis (other than posttraumatic stress disorder), and veteran age. This mHealth Family Caregiver pilot project effectively establishes the VA's first patient-facing mHealth apps that are integrated within the VA data system. Use varied considerably, and apps that were most used were those that assisted them in their caregiving responsibilities.

  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. 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.

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

    Institute of Scientific and Technical Information of China (English)

    陈守东; 孔繁利; 胡铮洋

    2007-01-01

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

  2. RAROC基于VaR的封闭式基金业绩评估

    Institute of Scientific and Technical Information of China (English)

    张晓彬; 黄志勇

    2006-01-01

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

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

    OpenAIRE

    WAYAN ARTHINI; KOMANG DHARMAWAN; LUH PUTU IDA HARINI

    2012-01-01

    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 simul...

  4. 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.

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

    Science.gov (United States)

    Pandey, Neeti; Rajagopal, Raman

    2016-10-01

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

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

    Directory of Open Access Journals (Sweden)

    Laurent Houzet

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

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

    Science.gov (United States)

    Wang, Yong; Qian, Pei-Yuan

    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 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.

  9. 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.

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

    Institute of Scientific and Technical Information of China (English)

    魏红刚; 孟英玉

    2010-01-01

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

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

    Institute of Scientific and Technical Information of China (English)

    刘用明; 贺薇

    2011-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Komang Dharmawan

    2013-10-01

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

  13. 77 FR 60746 - Proposed Information Collection (VA/DOD Joint Disability Evaluation Board Claim) Activity...

    Science.gov (United States)

    2012-10-04

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

  14. 75 FR 69032 - Naval Surface Warfare Center, Potomac River, Dahlgren, VA; Danger Zone

    Science.gov (United States)

    2010-11-10

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

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

    Science.gov (United States)

    2016-12-01

    end to homelessness does not mean that no one will ever experience a housing crisis again, but that every community will have a systematic response...focuses on short-term, crisis intervention when providing homeless prevention and rapid rehousing; both of these programs also provide supportive... HOMELESS VETERANS Management Improvements Could Help VA Better Identify Supportive-Housing Projects Report to

  16. Racial and ethnic disparities in the VA health care system: a systematic review.

    Science.gov (United States)

    Saha, Somnath; Freeman, Michele; Toure, Joahd; Tippens, Kimberly M; Weeks, Christine; Ibrahim, Said

    2008-05-01

    To better understand the causes of racial disparities in health care, we reviewed and synthesized existing evidence related to disparities in the "equal access" Veterans Affairs (VA) health care system. We systematically reviewed and synthesized evidence from studies comparing health care utilization and quality by race within the VA. Racial disparities in the VA exist across a wide range of clinical areas and service types. Disparities appear most prevalent for medication adherence and surgery and other invasive procedures, processes that are likely to be affected by the quantity and quality of patient-provider communication, shared decision making, and patient participation. Studies indicate a variety of likely root causes of disparities including: racial differences in patients' medical knowledge and information sources, trust and skepticism, levels of participation in health care interactions and decisions, and social support and resources; clinician judgment/bias; the racial/cultural milieu of health care settings; and differences in the quality of care at facilities attended by different racial groups. Existing evidence from the VA indicates several promising targets for interventions to reduce racial disparities in the quality of health care.

  17. 75 FR 33273 - Final Environmental Impact Statement (FEIS) for Disposal and Reuse of Fort Monroe, VA

    Science.gov (United States)

    2010-06-11

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

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

    Science.gov (United States)

    2016-09-01

    VA HEALTH CARE Processes to Evaluate, Implement, and Monitor Organizational Structure Changes Needed Report to...Monitor Organizational Structure Changes Needed What GAO Found Recent internal and external reviews of Veterans Health Administration (VHA...operations have identified deficiencies in its organizational structure and recommended changes that would require significant restructuring to address

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

    NARCIS (Netherlands)

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

    2015-01-01

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

  20. 76 FR 24567 - Proposed Information Collection (VA MATIC Authorization); Comment Request

    Science.gov (United States)

    2011-05-02

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

  1. 78 FR 79563 - Proposed Information Collection (VA MATIC Authorization); Comment Request

    Science.gov (United States)

    2013-12-30

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

  2. 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

    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...

  3. Use of a cost accounting system to evaluate costs of a VA special program.

    Science.gov (United States)

    Menke, T J; Wray, N P

    1999-04-01

    The Department of Veterans Affairs (VA) established six mobile clinics to provide care for rural veterans. Each was operated by a parent VA Medical Center (VAMC). To describe the use of a cost-accounting system which does not provide costs at the service or patient level to determine the costs of the mobile clinics. Costs per visit were compared among the mobile clinics with the parent VAMCs and with simulated fixed-location clinics. Cost data came from VA's Centralized Accounting for Local Management (CALM) data. Utilization data came from VA's outpatient file. Information was obtained from the VAMCs' fiscal services to reallocate costs among the CALM subaccounts to generate cost data that was comparable among the mobile clinics. Costs per visit for the mobile clinics were twice as high as those of the parent VAMCs. Costs per visit would be lower at fixed-location clinics unless the volume were substantially less than that provided by the mobile clinics. Differences between cost allocations for accounting purposes and research are likely to necessitate adjusting cost accounting data for research purposes. Fortunately, information from the accountants or primary data can lead to a cost database which is appropriate for research evaluations. In the mobile clinics study, the analysis of cost accounting data led to the conclusion that mobile clinics were not a cost-effective way in which to provide care to rural veterans.

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

    Institute of Scientific and Technical Information of China (English)

    袁晓俭; 陈难先; 申江

    2011-01-01

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

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

    Institute of Scientific and Technical Information of China (English)

    Xiao-Yuan Chen; Jian-Xun Jin

    2008-01-01

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

  6. 78 FR 38452 - Agency Information Collection (VA Police Officer Pre-Employment Screening Checklist) Activities...

    Science.gov (United States)

    2013-06-26

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    1987-01-01

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

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

    NARCIS (Netherlands)

    Garandeau, Claire F.|info:eu-repo/dai/nl/380715066; 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

  9. 77 FR 38396 - Agency Information Collection (One-VA Identification Verification Card) Activities Under OMB Review

    Science.gov (United States)

    2012-06-27

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

  10. 75 FR 48413 - Agency Information Collection (HUD/VA Addendum to Uniform Residential Loan Application) Activity...

    Science.gov (United States)

    2010-08-10

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

  11. 76 FR 27967 - Safety Zone; Shore Thing and Independence Day Fireworks, Chesapeake Bay, Norfolk, VA

    Science.gov (United States)

    2011-05-13

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

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

    Science.gov (United States)

    2010-06-17

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

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

    Science.gov (United States)

    2010-05-11

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

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

    Science.gov (United States)

    2011-06-30

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

  15. 75 FR 3968 - Fund Availability Under the VA Homeless Providers Grant and Per Diem Program

    Science.gov (United States)

    2010-01-25

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

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

    NARCIS (Netherlands)

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

    2011-01-01

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

  17. 76 FR 67557 - Proposed Information Collection (Survey of Veteran Enrollees' Health and Reliance Upon VA...

    Science.gov (United States)

    2011-11-01

    ... use of other forms of information technology. Title: Survey of Veteran Enrollees' Health and Reliance... on population-based budget formulation, policy scenario testing, and strategic planning. Affected... AFFAIRS Proposed Information Collection (Survey of Veteran Enrollees' Health and Reliance Upon VA...

  18. 77 FR 13519 - Safety Zone; Virginia Beach Oceanfront Air Show, Atlantic Ocean, Virginia Beach, VA

    Science.gov (United States)

    2012-03-07

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

  19. 77 FR 70708 - VA Acquisition Regulation: Electronic Submission of Payment Requests

    Science.gov (United States)

    2012-11-27

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

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

    Science.gov (United States)

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

    2012-05-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2008-09-15

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

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

    Lifescience Database Archive (English)

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

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

    Science.gov (United States)

    2013-09-12

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

  5. 75 FR 54965 - Proposed Information Collection (Statement of Purchaser or Owner Assuming Seller's Loans, VA Form...

    Science.gov (United States)

    2010-09-09

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

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

    NARCIS (Netherlands)

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

    2016-01-01

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

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

    NARCIS (Netherlands)

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

    2015-01-01

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

  8. 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).

  9. 75 FR 15721 - Back Bay National Wildlife Refuge, City of Virginia Beach, VA

    Science.gov (United States)

    2010-03-30

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

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

    Science.gov (United States)

    2011-07-25

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

  11. 77 FR 1500 - Plum Tree Island National Wildlife Refuge, Poquoson, VA

    Science.gov (United States)

    2012-01-10

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

  12. 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.

  13. Review and Evaluation of the VA Enrollee Health Care Projection Model

    Science.gov (United States)

    2008-01-01

    to be less healthy and less well-off financially than the general civilian population (Ahga et al., 2000). The health needs of VA patients with...Glied S, Remler DK, Zivin JG. Inside the sausage factory: Improving estimates of the effects of health insurance expansion proposals. Milbank Q

  14. 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.

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

    Science.gov (United States)

    2012-02-08

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

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

    Lifescience Database Archive (English)

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

  17. Genome Sequence of Borrelia chilensis VA1, a South American Member of the Lyme Borreliosis Group.

    Science.gov (United States)

    Huang, Weihua; Ojaimi, Caroline; Fallon, John T; Travisany, Dante; Maass, Alejandro; Ivanova, Larisa; Tomova, Alexandra; González-Acuña, Daniel; Godfrey, Henry P; Cabello, Felipe C

    2015-02-12

    Borrelia chilensis strain VA1 is a recently described South American member of the Borrelia burgdorferi sensu lato complex from Chile. Whole-genome sequencing analysis determined its linear chromosome and plasmids lp54 and cp26, confirmed its membership in the Lyme borreliosis group, and will open new research avenues regarding its pathogenic potential. Copyright © 2015 Huang et al.

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

    Lifescience Database Archive (English)

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

  19. 78 FR 48314 - Drawbridge Operation Regulation; Milford Haven Inlet, Hudgins, VA

    Science.gov (United States)

    2013-08-08

    ... SECURITY Coast Guard 33 CFR Part 117 Drawbridge Operation Regulation; Milford Haven Inlet, Hudgins, VA... Bridge (Gwynn's Island) across the Milford Haven Inlet, mile 0.1, at Hudgins, Virginia. The deviation is... Milford Haven Inlet near Hudgins, Virginia. VDOT requested a deviation from the requirement to open on...

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

    CERN Multimedia

    2002-01-01

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

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

    Science.gov (United States)

    2013-10-01

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

  2. 75 FR 60171 - Proposed Information Collection (Credit Underwriting Standards and Procedures for Processing VA...

    Science.gov (United States)

    2010-09-29

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

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

    DEFF Research Database (Denmark)

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

    2013-01-01

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

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

    Science.gov (United States)

    2013-03-26

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

  5. 78 FR 12600 - VA Homeless Providers Grant and Per Diem Program

    Science.gov (United States)

    2013-02-25

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

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

    NARCIS (Netherlands)

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

    2014-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

    Fox, P.B.

    2002-05-06

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

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

    Science.gov (United States)

    2007-11-02

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

  9. 38 CFR 1.218 - Security and law enforcement at VA facilities.

    Science.gov (United States)

    2010-07-01

    ... VETERANS AFFAIRS GENERAL PROVISIONS Security and Law Enforcement at Department of Veterans Affairs Facilities § 1.218 Security and law enforcement at VA facilities. (a) Authority and rules of conduct... or concealed, whether loaded or unloaded (except by Federal or State law enforcement officers on...

  10. 78 FR 46497 - Amendment of Class D and E Airspace, and Establishment of Class E Airspace; Oceana NAS, VA

    Science.gov (United States)

    2013-08-01

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

  11. 78 FR 21084 - Proposed Amendment of Class D and E Airspace, and Establishment of Class E Airspace; Oceana NAS, VA

    Science.gov (United States)

    2013-04-09

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

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

    Science.gov (United States)

    2014-11-01

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

  13. 78 FR 68364 - Payment for Home Health Services and Hospice Care to Non-VA Providers; Delay of Effective Date

    Science.gov (United States)

    2013-11-14

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

  14. 75 FR 32240 - Draft Tier II Environmental Impact Statement: Southeast High Speed Rail Corridor-Richmond, VA...

    Science.gov (United States)

    2010-06-07

    ... Planning District Commission, 200 S. Mecklenburg Avenue, South Hill, VA. Norlina Town Hall, 101 Main Street... bridges/ overpasses, will create a fully grade-separated system to ensure the safety of both passengers... Franklin Street, Richmond, VA. Richmond Regional Planning District Commission, 9211 Forest Hill Avenue...

  15. VA Health Care: Improvements Needed in Monitoring Antidepressant Use for Major Depressive Disorder and in Increasing Accuracy of Suicide Data

    Science.gov (United States)

    2014-11-01

    VA HEALTH CARE Improvements Needed in Monitoring Antidepressant Use for Major Depressive Disorder and in Increasing...00-2014 4. TITLE AND SUBTITLE VA Health Care: Improvements Needed in Monitoring Antidepressant Use for Major Depressive Disorder and in Increasing... disorder with mixed anxiety and depressed mood. 29American Psychiatric Association: Diagnostic and Statistical Manual. Depression not otherwise

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

    Science.gov (United States)

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

    2016-01-01

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

  17. 76 FR 30598 - Payment or Reimbursement for Emergency Services for Nonservice-Connected Conditions in Non-VA...

    Science.gov (United States)

    2011-05-26

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

  18. 77 FR 23615 - Payment or Reimbursement for Emergency Services for Nonservice-Connected Conditions in Non-VA...

    Science.gov (United States)

    2012-04-20

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

  19. 76 FR 72045 - Enhanced-Use Lease (EUL) of Department of Veterans Affairs (VA) Real Property for the Development...

    Science.gov (United States)

    2011-11-21

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

  20. 76 FR 72047 - Enhanced-Use Lease (EUL) of Department of Veterans Affairs (VA) Real Property for the Development...

    Science.gov (United States)

    2011-11-21

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

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

    Science.gov (United States)

    2011-11-21

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

  2. Modulation of cytochrome C oxidase-va is possibly involved in metallothionein protection from doxorubicin cardiotoxicity.

    Science.gov (United States)

    Merten, Kevyn E; Feng, Wenke; Zhang, Li; Pierce, William; Cai, Jian; Klein, Jon B; Kang, Y James

    2005-12-01

    Previous studies using a cardiac-specific metallothionein (MT)-overexpressing transgenic (MT-TG) mouse model have demonstrated that MT protects from doxorubicin (DOX)-induced oxidative heart injury. The molecular mechanisms that underlie this cardioprotection, however, have yet to be defined. In the present study, we tested the hypothesis that MT overexpression activates cytoprotective mechanisms, leading to cardiac protection from DOX toxicity. MT-TG mice and nontransgenic wild-type (WT) controls were treated i.p. with DOX at a single dose of 20 mg/kg and sacrificed on the third day after the treatment. An expression proteomic analysis involving two-dimensional gel electrophoresis and matrix-assisted laser desorption ionization time-of-flight mass spectrometry was used to identify MT-induced changes in cytoprotection-related proteins. We identified 18 proteins that were modified by DOX treatment in the heart. These proteins included those involved in cellular antioxidant defense, enzymes of the mitochondrial electron transport chain, enzymes involved in beta-oxidation of fatty acids and glycolysis, and proteins involved in regulation of cardiac muscle contraction. However, the most dominant modification by MT is the cytochrome c oxidase subunit Va (CCO-Va). In response to DOX treatment, a specific isoform of CCO-Va was enhanced in the MT-TG but not in the WT mouse hearts. Because CCO-Va is a critical component in the mitochondrial electron transport chain, the results suggest that the cardioprotective effect of MT may be related to an increased expression or a differential modification of CCO-Va.

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

    Science.gov (United States)

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

    2014-04-01

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

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

    Directory of Open Access Journals (Sweden)

    Liu Chuan-Fen

    2012-03-01

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

  5. 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.

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

    DEFF Research Database (Denmark)

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

    2016-01-01

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

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

    Institute of Scientific and Technical Information of China (English)

    高莹; 周鑫; 金秀

    2008-01-01

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

  8. RAROC基于VaR的封闭式基金业绩评估

    Institute of Scientific and Technical Information of China (English)

    张晓彬; 黄志勇

    2006-01-01

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

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

    Science.gov (United States)

    Salmivalli, Christina; Poskiparta, Elisa

    2012-01-01

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

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

    Science.gov (United States)

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

    2011-01-01

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

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

    Science.gov (United States)

    2014-09-01

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

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

    Science.gov (United States)

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

    2016-11-15

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

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

    Directory of Open Access Journals (Sweden)

    Katsuyuki Shiroguchi

    2011-04-01

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

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

    CERN Document Server

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

    2013-01-01

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

  15. Pitfalls of converting practice guidelines into quality measures: lessons learned from a VA performance measure.

    Science.gov (United States)

    Walter, Louise C; Davidowitz, Natalie P; Heineken, Paul A; Covinsky, Kenneth E

    2004-05-26

    The Department of Veterans Affairs (VA) manages the largest health care system in the United States, and the Institute of Medicine has recommended that many practices of VA quality measurement be applied to the US health care system as a whole. The VA measures quality of care at all of its sites by assessing adherence rates to performance measures, which generally are derived from evidence-based practice guidelines. Higher adherence rates are used as evidence of better quality of care. However, there are problems with converting practice guidelines, intended to offer guidance to clinicians, into performance measures that are meant to identify poor-quality care. We suggest a more balanced perspective on the use of performance measures to define quality by delineating conceptual problems with the conversion of practice guidelines into quality measures. Focusing on colorectal cancer screening, we use a case study at 1 VA facility to illustrate pitfalls that can cause adherence rates to guideline-based performance measures to be poor indicators of the quality of cancer screening. Pitfalls identified included (1) not properly considering illness severity of the sample population audited for adherence to screening, (2) not distinguishing screening from diagnostic procedures when setting achievable target screening rates, and (3) not accounting for patient preferences or clinician judgment when scoring performance measures. For many patients with severe comorbid illnesses or strong preferences against screening, the risks of colorectal cancer screening outweigh the benefits, and the decision to not screen may reflect good quality of care. Performance measures require more thoughtful specification and interpretation to avoid defining high testing rates as good quality of care regardless of who received the test, why it was performed, or whether the patient wanted it.

  16. 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.

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

    Science.gov (United States)

    2015-10-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    1980-04-01

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

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

    Science.gov (United States)

    2009-11-01

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

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

    NARCIS (Netherlands)

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

    2013-01-01

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

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

    Science.gov (United States)

    2016-12-01

    Health Care Letter 1 Background 6 VHA Lacks Complete and Accurate Data on VAMC Compliance with Environment of Care Requirements for Women Veterans...of Care Requirements 40 Appendix IV Veterans Health Administration (VHA) Gynecologist Availability 44 Appendix V Veterans Affairs (VA) Clinics...Veterans Health Administration (VHA) Requirements Related to the Outpatient Environment of Care for Women Veterans, December 2015-March 2016 40 Table

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

    Institute of Scientific and Technical Information of China (English)

    WANG Chun-feng; LI Gang

    2001-01-01

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

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

    NARCIS (Netherlands)

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

    2000-01-01

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

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

    Science.gov (United States)

    2011-01-26

    AUTHOR(S) 5d. PROJECT NUMBER 5e. TASK NUMBER 5f. WORK UNIT NUMBER 7. PERFORMING ORGANIZATION NAME(S) AND ADDRESS(ES) Defense Centers of Excellence for...Psychological Health & Traumatic Brain Injury,2345 Crystal Drive,Crystal park 4, Suite 120,Arlington,VA,22202 8. PERFORMING ORGANIZATION REPORT...restructuring; or stress inoculation training B •Imagery Rehearsal Therapy C •Patient Education •Psychodynamic Therapy • Hypnosis •Relaxation

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

    Science.gov (United States)

    2015-03-01

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

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

    Directory of Open Access Journals (Sweden)

    Elisama Azevedo

    2012-01-01

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

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

    KAUST Repository

    Gojobori, Takashi

    2016-12-24

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

  8. VA's expansion of supportive housing: successes and challenges on the path toward Housing First.

    Science.gov (United States)

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

    2014-05-01

    The U.S. Department of Veterans Affairs (VA) is transitioning to a Housing First approach to placement of veterans in permanent supportive housing through the use of rental vouchers, an ambitious organizational transformation. This qualitative study examined the experiences of eight VA facilities undertaking this endeavor in 2012. A multidisciplinary team interviewed facility leadership, midlevel managers, and frontline staff (N=95 individuals) at eight VA facilities representing four U.S. regions. The team used a semistructured interview protocol and the constant comparative method to explore how individuals throughout the organizations experienced and responded to the challenges of transitioning to a Housing First approach. Frontline staff faced challenges in rapidly housing homeless veterans because of difficult rental markets, the need to coordinate with local public housing authorities, and a lack of available funds for move-in costs. Staff sought to balance their time spent on housing activities with intensive case management of highly vulnerable veterans. Finding low-demand sheltering options (that is, no expectations regarding sobriety or treatment participation, as in the Housing First model) for veterans waiting for housing presented a significant challenge to implementation of Housing First. Facility leadership supported Housing First implementation through resource allocation, performance monitoring, and reliance on midlevel managers to understand and meet the challenges of implementation. The findings highlight the considerable practical challenges and innovative solutions arising from a large-scale effort to implement Housing First, with particular attention to the experiences of individuals at all levels within an organization.

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

    Science.gov (United States)

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

    2015-04-01

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

  10. 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.

  11. The effect of standardized, computer-guided templates on quality of VA disability exams.

    Science.gov (United States)

    Fielstein, Elliot M; Brown, Steven H; McBrine, Caroll S; Clark, Terry K; Hardenbrook, Shawn P; Speroff, Ted

    2006-01-01

    The costs and limitations of clinical encounter documentation using dictation/transcription have provided impetus for increased use of computerized structured data entry to enforce standardization and improve quality. The purpose of the present study is to compare exam report quality of Veterans Affairs (VA) disability exams documented by computerized protocol-guided templates with exams documented in the usual fashion (dictation). Exam report quality for 17,490 VA compensation and pension (C&P) disability exams reviewed in 2005 was compared for exam reports completed by template and exam reports completed in routine fashion (dictation). An additional set of 2,903 exams reviewed for quality the last three months of 2004 were used for baseline comparison. Mean template quality scores of 91 (95% CI 89, 92) showed significant improvement over routine exams conducted during the study period 78 (95% CI 77, 78) and at baseline 73 (95% CI 72, 75). The quality difference among examination types is presented. The results of the present study suggest that use of the standardized, guided documentation templates in VA disability exams produces significant improvement in quality compared with routinely completed exams (dictation). The templates demonstrate the opportunity and capacity for informatics tools to enhance delivery of care when operating in a health system with a sophisticated electronic medical record.

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

    Institute of Scientific and Technical Information of China (English)

    张胜杰; 张敏敏

    2011-01-01

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

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

    Science.gov (United States)

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

    2016-01-01

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

  14. 76 FR 71440 - Enhanced-Use Lease (EUL) of Department of Veterans Affairs (VA) Real Property for the Development...

    Science.gov (United States)

    2011-11-17

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

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

    Directory of Open Access Journals (Sweden)

    Xu Zijian

    2015-01-01

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

  16. 75 FR 30915 - Computer Matching Program Between the Department of Veterans Affairs (VA) and the Department of...

    Science.gov (United States)

    2010-06-02

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

  17. 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.

  18. 30 CFR 57.22101 - Smoking (I-A, II-A, III, and V-A mines).

    Science.gov (United States)

    2010-07-01

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

  19. 30 CFR 57.22212 - Air flow (I-C, II-A, and V-A mines).

    Science.gov (United States)

    2010-07-01

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

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

    Institute of Scientific and Technical Information of China (English)

    赵利锋; 张崇岐

    2009-01-01

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

  1. Structural and biochemical characterisation of VaF1, a P-IIIa fibrinogenolytic metalloproteinase from Vipera ammodytes ammodytes venom.

    Science.gov (United States)

    Leonardi, Adrijana; Sajevic, Tamara; Latinović, Zorica; Pungerčar, Jože; Balija, Maja Lang; Bakija, Alenka Trampuš; Vidmar, Robert; Halassy, Beata; Križaj, Igor

    2015-02-01

    A high molecular mass metalloproteinase with α-fibrinogenolytic activity, termed VaF1, was purified from nose-horned viper (Vipera ammodytes ammodytes) venom. Subcutaneous injection of 9 μg of VaF1 did not induce bleeding in rats. Nevertheless, in vitro it degraded collagen IV, nidogen and fibronectin, components of the extracellular matrix, although with low efficacy and narrow specificity. VaF1 would be expected to exert anti-coagulant action, due to its hydrolysis of fibrinogen, factor X, prothrombin and plasminogen, plasma proteins involved in blood coagulation. The enzyme is a single-chain glycoprotein with a molecular mass of 49.7 kDa, as determined by mass spectrometry, and multiple isoelectric points centred at pH 5.8. The complete amino acid sequence of the precursor of VaF1 was deduced by cloning and sequencing its cDNA. Composed of metalloproteinase, disintegrin-like and cysteine-rich domains, VaF1 is a typical P-IIIa subclass snake venom metalloproteinase. Although it possesses a collagen-binding sequence in its disintegrin-like domain, VaF1 displayed no effect on collagen-induced platelet aggregation in vitro. Two consensus N-glycosylation sites are present in the sequence of VaF1, however, the extent of its glycosylation is low, only 5.2% of the total molecular mass. Interestingly, in standard experimental conditions VaF1 is not recognised by antiserum against the whole venom, so it can contribute to post-serotherapy complications, such as ineffective blood coagulation, in the envenomed patient. Copyright © 2014 Elsevier B.V. and Société française de biochimie et biologie Moléculaire (SFBBM). All rights reserved.

  2. 30 CFR 57.22608 - Secondary blasting (I-A, II-A, and V-A mines).

    Science.gov (United States)

    2010-07-01

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

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

    Directory of Open Access Journals (Sweden)

    Evelyne Oppermann-Marsaux

    2011-07-01

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

  4. Effect of VA and MWNT contents on the rheological and physical properties of EVA

    Science.gov (United States)

    Kim, Jong-Ho; Lee, Seungwon; Kim, Byoung Chul; Shin, Bong-Seob; Jeon, Jong-Young; Chae, Dong Wook

    2016-02-01

    Ethylene vinyl acetate (EVA) copolymers with two different VA contents (15 and 33 wt.%, denoted by EVA15 and EVA33, respectively) were melt compounded with multi-walled carbon nanotubes (MWNTs) and the effect of VA and nanotube contents on the rheological, thermal and morphological properties was investigated. The addition of nanotubes into both EVAs increased the onset temperature of crystallization and broadened the peak, but further addition from 3 wt.% slightly decreased the temperature with increasing nanotube contents. In the wide angle X-ray diffraction patterns the peak of EVA15 was little affected by the presence of nanotubes but that of EVA33 slightly shifted to higher degree and became sharper with increasing nanotube contents. Dynamic viscosity (η') increased with nanotube contents giving abrupt increase at 2 wt.% nanotubes. Loss tangent decreased with increasing nanotube contents exhibiting the plateau-like behavior over most of the frequency range from 2 wt.% nanotubes. In the Casson plot, yield stress increased with nanotube content and its increasing extent was more notable for more VA content. In the Cole-Cole plot, the presence of nanotubes from 2 wt.% gave rise to the deviation from the single master curve by decreasing the slope. The deviated extent of EVA33 became more remarkable with increasing nanotube contents than that of EVA15. The stress-strain curve showed that more improved tensile modulus and yield stress were achieved by the introduction of MWNTs for EVA 33 than for EVA15. Tensile strength of EVA33 increased with increasing nanotube contents, while that of EVA15 decreased.

  5. Effects of VA Facility Dog on Hospitalized Veterans Seen by a Palliative Care Psychologist.

    Science.gov (United States)

    Krause-Parello, Cheryl A; Levy, Cari; Holman, Elizabeth; Kolassa, John E

    2016-01-01

    The United States is home to 23 million veterans. In many instances, veterans with serious illness who seek healthcare at the VA receive care from a palliative care service. Animal-assisted intervention (AAI) is gaining attention as a therapeutic stress reducing modality; however, its effects have not been well studied in veterans receiving palliative care in an acute care setting. A crossover repeated-measures study was conducted to examine the effects of an animal-assisted intervention (AAI) in the form of a therapy dog on stress indicators in 25 veterans on the palliative care service at the VA Eastern Colorado Healthcare System in Denver, CO. Veterans had a visit from a therapy dog and the dog's handler, a clinical psychologist (experimental condition) and an unstructured visit with the clinical psychologist alone (control condition). Blood pressure, heart rate, and the salivary biomarkers cortisol, alpha-amylase, and immunoglobulin A were collected before, after, and 30-minutes after both the experimental and control conditions. Significant decreases in cortisol were found when the before time period was compared to the 30-minutes after time period for both the experimental ( p = 0.007) and control condition ( p = 0.036). A significant decrease in HR was also found when the before time period was compared to the 30-minutes after time period for both the experimental ( p = 0.0046) and control ( p = 0.0119) condition. Results of this study supported that a VA facility dog paired with a palliative care psychologist had a measurable impact on salivary cortisol levels and HR in veterans.

  6. 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

  7. 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.

  8. Analysis of low energy arc discharge characteristics based on dynamic V-A characteristics model

    Institute of Scientific and Technical Information of China (English)

    JING Li-nan; WANG Li-gong

    2006-01-01

    Low energy arc discharge characteristics was analyzed based on dynamic V-A characteristics model. It draws conclusions that discharge time relates to the source voltage and the product of inductance and stable current, discharge time will increase when the source voltage increases; current reduce rate is in inverse proportion to the value of inductance; arc resistance when the arc occurs is the ratio of minimum arcing voltage to stable current. It also gains the expressions of arc resistance and arc power, arc resistance and arc power both increase as the source voltage increases and decrease as the value of inductance increases. Conclusions above mentioned are helpful to design intrinsically safe circuits.

  9. Què va ser primer en l'origen de la vida?

    OpenAIRE

    Santos, Mauro

    2010-01-01

    Una recerca publicada a "Proceedings of the National Academy of Sciences" rebutja la teoria de què l'origen de la vida es va originar com un sistema de molècules autocatalític capaç d'experimentar evolució darwiniana sense la necessitat d'ARN o d'ADN i de la seva replicació. L'estudi, en què ha participat Mauro Santos, investigador del Departament de Genètica i de Microlobiologia de la UAB, ha demostrat, analitzant el que alguns investigadors han anomenat "genomes compostos", que aquestes xar...

  10. Toxicidad de VA-DIFTET® por administración a dosis repetida en ratones

    OpenAIRE

    Pablo González; Enrique Muñoz; Anait Martínez; Mildrey Fariñas; Reynaldo Oliva; Osmany Marrero

    2000-01-01

    Una vez estudiada la toxicidad de la vacuna VA-DIFTET® (vacuna antidiftérica antitetánica) por administración a dosis única en dos especies de animales, se impone la evaluación a dosis repetida, teniendo en cuenta que el esquema de inmunización en humanos prevé la aplicación de tres dosis cuando el componente pertusis de la DPT está contraindicado. Se emplearon 210 ratones OF-1 de ambos sexos. Los grupos experimentales fueron similares a los de la prueba a dosis única con la vacuna dúplex, an...

  11. 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.

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

    Directory of Open Access Journals (Sweden)

    Radu Lupu

    2006-06-01

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

  13. [Theory of V.A. dogiel on polymerization and oligomerization as a general integration concept].

    Science.gov (United States)

    Makmaev, Iu V

    2010-01-01

    The theory of V.A. Dogiel on the significance of polymerization and ligomerization processes in the evolution of Protozoa and Metazoa is compared with the paper of I.I. Schmalhauisen (1972) on factors and steps of aromorph evolution. Dogiel's theory is considered as a general integration conception. Four steps are distinguished in the evolution of biological systems: (1) formation of morphofunctional system by units of the lower structural level, (2) polymerization of morphofunctional units of a system, (3) oligomerization of morphofunctional units of system by means of their reduction, uniting, or differentiation, (4) integration and stabilization of a system owing to development of morphofunctional connections between its parts.

  14. va le travail à l’ère du numérique ?

    OpenAIRE

    Bercot, Régine; Blanc, Martine; Durampart, Michel; Grenier, Corinne; Guyot, Brigitte; Hassanaly, Parina; Le Bis, Isabelle; Metzger, Jean-Luc; Moatty, Frédéric; Peyrard, Catherine; Pierson, Françoise; Rouard, Françoise; Saint Laurent-Kogan (de), Anne-France; Teiger, Catherine; Vacher, Béatrice

    2013-01-01

    va le travail ? Les technologies de l’information ont envahi massivement les sphères professionnelles, et ont soumis le travail des salariés à des bouleversements tant techniques, qu’organisationnels et identitaires, encore peu étudiés aujourd’hui. L’ouvrage se concentre sur trois changements majeurs. Il montre : 1) comment s’associent désormais les salariés au travail ; 2) quels apprentissages sont désormais requis, quand les savoirs sont dès leur acquisition considérés comme obsolètes ;...

  15. 3kVA UPS for residential application with interface for solar panels and microprocessor control

    Directory of Open Access Journals (Sweden)

    André Luiz Batista Ferreira

    2014-05-01

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

  16. STUDY ON DETERMINATION OF TRACE Fe BY Fe(Ⅱ)-VA THIN LAYER RESIN PHASE SPECTROPHOTOMETRY

    Institute of Scientific and Technical Information of China (English)

    SONG Huanyu; YAN Yongsheng; WANG Yun

    2006-01-01

    A new method for the determination of Fe by thin layer resin phase spectrophotometry in alkali condition was reported. The complex anion formed by Fe(Ⅱ) and VA was absorbed on the 717#resin and Fe was determined by making thin layer. This method had a high sensitivity (ε620=3.0×105 L/mol·cm), which was 15 times higher than that of liquid phase spectrophotometry. It had been proved a satisfactory precision (5.0μg Fe, n=6, RSD=1.8%). The trace Fe in natural water was determined and the recovery was 97%.

  17. 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.

  18. Crisis convulsiva en hemodi??lisis con compromiso de la v??a a??rea

    OpenAIRE

    2014-01-01

    La aparici??n de crisis convulsivas en los pacientes sometidos a hemodi??lisis son m??s frecuentes que en la poblaci??n general y son debidas por diversas causas siendo las metab??licas las m??s frecuentes. Estos pacientes tienen mayor incidencia de coagulopat??as y junto al uso de heparina durante la hemodi??lisis pueden desarrollar hemorragias cerebrales que a su vez pueden ser la causa de crisis convulsivas. Ante una crisis convulsiva es imprescindible mantener una v??a a??rea ...

  19. Efficient PCR-Based Amplification of Diverse Alcohol Dehydrogenase Genes from Metagenomes for Improving Biocatalysis: Screening of Gene-Specific Amplicons from Metagenomes

    Science.gov (United States)

    Kariya, Satomi; Kurokawa, Junji

    2014-01-01

    Screening of gene-specific amplicons from metagenomes (S-GAM) has tremendous biotechnological potential. We used this approach to isolate alcohol dehydrogenase (adh) genes from metagenomes based on the Leifsonia species adh gene (lsadh), the enzyme product of which can produce various chiral alcohols. A primer combination was synthesized by reference to homologs of lsadh, and PCR was used to amplify nearly full-length adh genes from metagenomic DNAs. All adh preparations were fused with lsadh at the terminal region and used to construct Escherichia coli plasmid libraries. Of the approximately 2,000 colonies obtained, 1,200 clones were identified as adh positive (∼60%). Finally, 40 adh genes, Hladh-001 to Hladh-040 (for homologous Leifsonia adh), were identified from 223 clones with high efficiency, which were randomly sequenced from the 1,200 clones. The Hladh genes obtained via this approach encoded a wide variety of amino acid sequences (8 to 99%). After screening, the enzymes obtained (HLADH-012 and HLADH-021) were confirmed to be superior to LSADH in some respects for the production of anti-Prelog chiral alcohols. PMID:25085492

  20. Characterization of bacterial community associated with phytoplankton bloom in a eutrophic lake in South Norway using 16S rRNA gene amplicon sequence analysis.

    Science.gov (United States)

    Parulekar, Niranjan Nitin; Kolekar, Pandurang; Jenkins, Andrew; Kleiven, Synne; Utkilen, Hans; Johansen, Anette; Sawant, Sangeeta; Kulkarni-Kale, Urmila; Kale, Mohan; Sæbø, Mona

    2017-01-01

    Interactions between different phytoplankton taxa and heterotrophic bacterial communities within aquatic environments can differentially support growth of various heterotrophic bacterial species. In this study, phytoplankton diversity was studied using traditional microscopic techniques and the bacterial communities associated with phytoplankton bloom were studied using High Throughput Sequencing (HTS) analysis of 16S rRNA gene amplicons from the V1-V3 and V3-V4 hypervariable regions. Samples were collected from Lake Akersvannet, a eutrophic lake in South Norway, during the growth season from June to August 2013. Microscopic examination revealed that the phytoplankton community was mostly represented by Cyanobacteria and the dinoflagellate Ceratium hirundinella. The HTS results revealed that Proteobacteria (Alpha, Beta, and Gamma), Bacteriodetes, Cyanobacteria, Actinobacteria and Verrucomicrobia dominated the bacterial community, with varying relative abundances throughout the sampling season. Species level identification of Cyanobacteria showed a mixed population of Aphanizomenon flos-aquae, Microcystis aeruginosa and Woronichinia naegeliana. A significant proportion of the microbial community was composed of unclassified taxa which might represent locally adapted freshwater bacterial groups. Comparison of cyanobacterial species composition from HTS and microscopy revealed quantitative discrepancies, indicating a need for cross validation of results. To our knowledge, this is the first study that uses HTS methods for studying the bacterial community associated with phytoplankton blooms in a Norwegian lake. The study demonstrates the value of considering results from multiple methods when studying bacterial communities.

  1. The Influence of DNA Extraction Procedure and Primer Set on the Bacterial Community Analysis by Pyrosequencing of Barcoded 16S rRNA Gene Amplicons.

    Science.gov (United States)

    Starke, Ingo C; Vahjen, Wilfried; Pieper, Robert; Zentek, Jürgen

    2014-01-01

    In this study, the effect of different DNA extraction procedures and primer sets on pyrosequencing results regarding the composition of bacterial communities in the ileum of piglets was investigated. Ileal chyme from piglets fed a diet containing different amounts of zinc oxide was used to evaluate a pyrosequencing study with barcoded 16S rRNA PCR products. Two DNA extraction methods (bead beating versus silica gel columns) and two primer sets targeting variable regions of bacterial 16S rRNA genes (8f-534r versus 968f-1401r) were considered. The SEED viewer software of the MG-RAST server was used for automated sequence analysis. A total of 5.2 × 10(5) sequences were used for analysis after processing for read length (150 bp), minimum sequence occurrence (5), and exclusion of eukaryotic and unclassified/uncultured sequences. DNA extraction procedures and primer sets differed significantly in total sequence yield. The distribution of bacterial order and main bacterial genera was influenced significantly by both parameters. However, this study has shown that the results of pyrosequencing studies using barcoded PCR amplicons of bacterial 16S rRNA genes depend on DNA extraction and primer choice, as well as on the manner of downstream sequence analysis.

  2. The Influence of DNA Extraction Procedure and Primer Set on the Bacterial Community Analysis by Pyrosequencing of Barcoded 16S rRNA Gene Amplicons

    Directory of Open Access Journals (Sweden)

    Ingo C. Starke

    2014-01-01

    Full Text Available In this study, the effect of different DNA extraction procedures and primer sets on pyrosequencing results regarding the composition of bacterial communities in the ileum of piglets was investigated. Ileal chyme from piglets fed a diet containing different amounts of zinc oxide was used to evaluate a pyrosequencing study with barcoded 16S rRNA PCR products. Two DNA extraction methods (bead beating versus silica gel columns and two primer sets targeting variable regions of bacterial 16S rRNA genes (8f-534r versus 968f-1401r were considered. The SEED viewer software of the MG-RAST server was used for automated sequence analysis. A total of 5.2×105 sequences were used for analysis after processing for read length (150 bp, minimum sequence occurrence (5, and exclusion of eukaryotic and unclassified/uncultured sequences. DNA extraction procedures and primer sets differed significantly in total sequence yield. The distribution of bacterial order and main bacterial genera was influenced significantly by both parameters. However, this study has shown that the results of pyrosequencing studies using barcoded PCR amplicons of bacterial 16S rRNA genes depend on DNA extraction and primer choice, as well as on the manner of downstream sequence analysis.

  3. Detection of Clavibacter michiganensis subsp. sepedonicus by AmpliDet RNA, a new technology based on real time monitoring of NASBA amplicons with a molecular beacon.

    Science.gov (United States)

    van Beckhoven, J R C M; Stead, D E; van der Wolf, J M

    2002-01-01

    To develop a procedure for direct detection of viable cells of Clavibacter michiganensis subsp. sepedonicus (Cms), the causal organism of bacterial ring rot in potato, based on AmpliDet RNA, in which amplicons generated by nucleic acid sequence based amplification (NASBA) are monitored in real time with a molecular beacon. Five methods were evaluated and fine-tuned for extraction of RNA from Cms. The most efficient non-commercial RNA extraction method included an enzymatic breakdown of the cell wall followed by a phenol extraction. AmpliDet RNA enabled detection of 10,000 molecules of purified rRNA per reaction and 100 cfu of Cms per reaction in more complex samples. Two primer pairs were tested with DNA and RNA purified from Cms. One primer pair was able to distinguish live from dead cells. An AmpliDet RNA was developed which enabled fast and specific detection of viable cells of Cms in complex substrates at a detection limit of 100 cfu per reaction. This novel AmpliDet RNA is carried out in sealed tubes, thus reducing the risk of carry-over contamination. The method will be particularly suitable for studies on the epidemiology of Cms in which viable cells should be exclusively detected.

  4. The utility of diversity profiling using Illumina 18S rRNA gene amplicon deep sequencing to detect and discriminate Toxoplasma gondii among the cyst-forming coccidia.

    Science.gov (United States)

    Cooper, Madalyn K; Phalen, David N; Donahoe, Shannon L; Rose, Karrie; Šlapeta, Jan

    2016-01-30

    Next-generation sequencing (NGS) has the capacity to screen a single DNA sample and detect pathogen DNA from thousands of host DNA sequence reads, making it a versatile and informative tool for investigation of pathogens in diseased animals. The technique is effective and labor saving in the initial identification of pathogens, and will complement conventional diagnostic tests to associate the candidate pathogen with a disease process. In this report, we investigated the utility of the diversity profiling NGS approach using Illumina small subunit ribosomal RNA (18S rRNA) gene amplicon deep sequencing to detect Toxoplasma gondii in previously confirmed cases of toxoplasmosis. We then tested the diagnostic approach with species-specific PCR genotyping, histopathology and immunohistochemistry of toxoplasmosis in a Risso's dolphin (Grampus griseus) to systematically characterise the disease and associate causality. We show that the Euk7A/Euk570R primer set targeting the V1-V3 hypervariable region of the 18S rRNA gene can be used as a species-specific assay for cyst-forming coccidia and discriminate T. gondii. Overall, the approach is cost-effective and improves diagnostic decision support by narrowing the differential diagnosis list with more certainty than was previously possible. Furthermore, it supplements the limitations of cryptic protozoan morphology and surpasses the need for species-specific PCR primer combinations.

  5. DNA extraction protocols cause differences in 16S rRNA amplicon sequencing efficiency but not in community profile composition or structure.

    Science.gov (United States)

    Rubin, Benjamin E R; Sanders, Jon G; Hampton-Marcell, Jarrad; Owens, Sarah M; Gilbert, Jack A; Moreau, Corrie S

    2014-12-01

    The recent development of methods applying next-generation sequencing to microbial community characterization has led to the proliferation of these studies in a wide variety of sample types. Yet, variation in the physical properties of environmental samples demands that optimal DNA extraction techniques be explored for each new environment. The microbiota associated with many species of insects offer an extraction challenge as they are frequently surrounded by an armored exoskeleton, inhibiting disruption of the tissues within. In this study, we examine the efficacy of several commonly used protocols for extracting bacterial DNA from ants. While bacterial community composition recovered using Illumina 16S rRNA amplicon sequencing was not detectably biased by any method, the quantity of bacterial DNA varied drastically, reducing the number of samples that could be amplified and sequenced. These results indicate that the concentration necessary for dependable sequencing is around 10,000 copies of target DNA per microliter. Exoskeletal pulverization and tissue digestion increased the reliability of extractions, suggesting that these steps should be included in any study of insect-associated microorganisms that relies on obtaining microbial DNA from intact body segments. Although laboratory and analysis techniques should be standardized across diverse sample types as much as possible, minimal modifications such as these will increase the number of environments in which bacterial communities can be successfully studied. © 2014 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.

  6. 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.

  7. 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.

  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. Evaluation of the bacterial diversity in the feces of cattle using 16S rDNA bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP

    Directory of Open Access Journals (Sweden)

    Sun Yan

    2008-07-01

    Full Text Available Abstract Background The microbiota of an animal's intestinal tract plays important roles in the animal's overall health, productivity and well-being. There is still a scarcity of information on the microbial diversity in the gut of livestock species such as cattle. The primary reason for this lack of data relates to the expense of methods needed to generate such data. Here we have utilized a bacterial tag-encoded FLX 16s rDNA amplicon pyrosequencing (bTEFAP approach that is able to perform diversity analyses of gastrointestinal populations. bTEFAP is relatively inexpensive in terms of both time and labor due to the implementation of a novel tag priming method and an efficient bioinformatics pipeline. We have evaluated the microbiome from the feces of 20 commercial, lactating dairy cows. Results Ubiquitous bacteria detected from the cattle feces included Clostridium, Bacteroides, Porpyhyromonas, Ruminococcus, Alistipes, Lachnospiraceae, Prevotella, Lachnospira, Enterococcus, Oscillospira, Cytophage, Anaerotruncus, and Acidaminococcus spp. Foodborne pathogenic bacteria were detected in several of the cattle, a total of 4 cows were found to be positive for Salmonella spp (tentative enterica and 6 cows were positive for Campylobacter spp. (tentative lanienae. Conclusion Using bTEFAP we have examined the microbiota in the feces of cattle. As these methods continue to mature we will better understand the ecology of the major populations of bacteria the lower intestinal tract. This in turn will allow for a better understanding of ways in which the intestinal microbiome contributes to animal health, productivity and wellbeing.

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

    Science.gov (United States)

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

    1993-10-01

    Multiple endonuclease digestion of template DNA or amplification products can increase significantly the detection of polymorphic DNA in fingerprints generated by multiple arbitrary amplicon profiling (MAAP). This coupling of endonuclease cleavage and amplification of arbitrary stretches of DNA, directed by short oligonucleotide primers, readily allowed distinction of closely related fungal and bacterial isolates and plant cultivars. MAAP analysis of cleaved template DNA enabled the identification of molecular markers linked to a developmental locus of soybean (Glycine max L. Merrill). Ethyl methane sulfonate (EMS)-induced supernodulating, near-isogenic lines altered in the nts locus, which controls nodule formation, could be distinguished from each other and from the parent cultivar by amplification of template pre-digested with 2-3 restriction enzymes. A total of 42 DNA polymorphisms were detected using only 19 octamer primers. In the absence of digestion, 25 primers failed to differentiate these soybean genotypes. Several polymorphic products co-segregated tightly with the nts locus in F2 families from crosses between the allelic mutants nts382 and nts1007 and the ancestral G. soja Sieb. & Succ. PI468.397. Our results suggest that EMS is capable of inducing extensive DNA alterations, probably around discrete mutational hot-spots. EMS-induced DNA polymorphisms may constitute sequence-tagged markers diagnostic of specific genomic regions.

  11. 投资组合行业配置的动态VaR研究--基于时变Copula-GJR-Skewed-t模型

    Institute of Scientific and Technical Information of China (English)

    刘澄; 张玲

    2013-01-01

    用时变Copula-GJR-Skewed-t模型研究了深证22个行业分类指数中任意两个投资组合的动态VaR,并与静态VaR比较。实证结果表明,时变t-Copula函数在众多Copula函数中对行业投资组合的拟合效果最优,给出了模型估计出的VaR最大和最小的5对行业组合,不同行业组合的动态VaR在股市周期各阶段关系相对稳定,同一行业组合的动态VaR和静态VaR关系相对稳定,且略高于静态VaR。%Based on time-varying Copula-GJR-Skewed-t model, portfolio dynamical VaR of any two industrial indexes among 22 industrial indexes of Shenzhen stock exchanges is analyzed and compared to corresponding static VaR. The empirical result shows that among several Copulas, time-varying t-Copula is the most suitable for the industrial portfolios. Industrial portfolios of the 5 biggest and 5 smallest VaR are given. The relationship of dynamical VaR of different portfolios keeps stable in all phases of stock market cycle. The relationship of dynamical VaR and static VaR of a portfolio keeps stable, the former is a little bigger than the latter.

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

    Institute of Scientific and Technical Information of China (English)

    李蕊

    2011-01-01

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

  13. Measurement to stock market liquidity risk based on GARCH-VaR model%基于GARCH-VaR模型的股票流动性风险度量

    Institute of Scientific and Technical Information of China (English)

    刘晓青; 杨一文

    2015-01-01

    Based on investigation to liquidity risk before, this paper focuses more on the heterogeneity of stock market. Firstly, it does MODWT to the liquidity scale data, then calculates VaR of each scale using GARCH-VaR model, finally tests the effectiveness of the model. The paper proves risk capacity varies with capital scale, and the various risk pressure long-term and short-term investors face.%在原有流动性风险研究的基础上,充分考虑股票市场异质性,对流动性指标数据进行了最大重复离散小波变换(MODWT),然后运用GARCH-VaR模型分别计算各尺度上的VaR值,并对其进行了有效性检验。通过对各尺度VaR值的统计结果进行分析,验证所投资市场资本规模对风险容纳能力的不同以及长期投资者与短期投资者面对的不同流动性压力。

  14. Necessity of Recension, Correction and Analysis of Bostan ol-Arefin va Tohfat ol-Moridin

    Directory of Open Access Journals (Sweden)

    سعید بزرگ بیگدلی

    2013-06-01

    Full Text Available Bostan ol-Arefin va Tohfat ol-Moridin is one of the mystical prose texts of the Khorasan area in the fifth century A.H. Among the many Persian literary texts, it is considered as a precious ancient source for many of the anecdotes, miracles and sayings of the Sufis. Furthermore, the linguistic features of this book such as numerous special vocabularies, stylistic aspects and prose similar to the spoken language of the fifth century are among the other values of this book. Bostan ol-Arefin va Tohfat ol-Moridin, Montakhab-e Ronaq ol-Majalis and the attachments whose second edition has recently been released was published by Dr. Ahmad Ali Rajai Bukharaee in 1354 Š (1975. In this article the author is going to investigate this printed text by using the known and accessible manuscripts of Bostan ol-Arefin and other ancient sources to point to numerous errors in the text calling for a new recension.

  15. The process of implementing a rural VA wound care program for diabetic foot ulcer patients.

    Science.gov (United States)

    Reiber, Gayle E; Raugi, Gregory J; Rowberg, Donald

    2007-10-01

    Delivering and documenting evidence-based treatment to all Department of Veterans Affairs (VA) foot ulcer patients has wide appeal. However, primary and secondary care medical centers where 52% of these patients receive care are at a disadvantage given the frequent absence of trained specialists to manage diabetic foot ulcers. A retrospective review of diabetic foot ulcer patient records and a provider survey were conducted to document the foot ulcer problem and to assess practitioner needs. Results showed of the 125 persons with foot ulcers identified through administrative data, only, 21% of diabetic foot patients were correctly coded. Chronic Care and Microsystem models were used to prepare a tailored intervention in a VA primary care medical center. The site Principal Investigators, a multidisciplinary site wound care team, and study investigators jointly implemented a diabetic foot ulcer program. Intervention components include wound care team education and training, standardized good wound care practices based on strong scientific evidence, and a wound care template embedded in the electronic medical record to facilitate data collection, clinical decision making, patient ordering, and coding. A strategy for delivering offloading pressure devices, regular case management support, and 24/7 emergency assistance also was developed. It took 9 months to implement the model. Patients were enrolled and followed for 1 year. Process and outcome evaluations are on-going.

  16. 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.

  17. The KiVa antibullying curriculum and outcome: does fidelity matter?

    Science.gov (United States)

    Haataja, Anne; Voeten, Marinus; Boulton, Aaron J; Ahtola, Annarilla; Poskiparta, Elisa; Salmivalli, Christina

    2014-10-01

    Research on school-based prevention suggests that the success of prevention programs depends on whether they are implemented as intended. In antibullying program evaluations, however, limited attention has been paid to implementation fidelity. The present study fills in this gap by examining the link between the implementation of the KiVa antibullying program and outcome. With a large sample of 7413 students (7-12years) from 417 classrooms within 76 elementary schools, we tested whether the degree of implementation of the student lessons in the KiVa curriculum was related to the effectiveness of the program in reducing bullying problems in classrooms. Results of multilevel structural equation modeling revealed that after nine months of implementation, lesson adherence as well as lesson preparation time (but not duration of lessons) were associated with reductions in victimization at the classroom level. No statistically significant effects, however, were found for classroom-level bullying. The different outcomes for victimization and bullying as well as the importance of documenting program fidelity are discussed.

  18. Patient-provider secure messaging in VA: variations in adoption and association with urgent care utilization.

    Science.gov (United States)

    Shimada, Stephanie L; Hogan, Timothy P; Rao, Sowmya R; Allison, Jeroan J; Quill, Ann L; Feng, Hua; Phillips, Barrett D; Nazi, Kim M; Haidary, Susan T; Houston, Thomas K

    2013-03-01

    The Veterans Health Administration has implemented patient to clinical team electronic asynchronous secure messaging (SM). This disruptive technology has the potential to support continuous, coordinated quality care, but limited evidence supports this connection. The objective of this paper is to (1) measure SM implementation and identify facility characteristics associated with higher rates of adoption and (2) understand the association of SM use and noncontinuity care [ie, urgent care (UC)] utilization rates. We conducted a retrospective cohort study of 132 VA facilities implementing SM in primary care. We used a combination of cross-sectional survey data on predictors of SM implementation and longitudinal data (July 2010-June 2012) on use of SM and UC. Human resources (coordinator and staff/volunteer availability to directly assist Veterans), computer resources (computers and computer rooms for Veterans), and leadership support for coordinators were associated with increased SM adoption rates. Higher SM use was associated with lower UC rates; early adopters of SM achieved a greater decrease in UC utilization over time than later adopters. In this exploratory analysis of early SM implementation in VA, we found a path of associations linking SM and reductions in UC utilization. These results suggest a need for further examination of the relationship between SM and its effects on health care utilization patterns.

  19. LINKAGE DISEQUILIBRIUM AND A CONTACT ZONE IN PLETHODON CINEREUS ON THE DEL-MAR-VA PENINSULA.

    Science.gov (United States)

    Wynn, Addison H

    1986-01-01

    A contact zone between two electrophoretically differentiated forms of Plethodon cinereus extends across the Del-Mar-Va Peninsula. Based on the presumed nature of regional climates during the late Pleistocene, it is suggested that the climate was inhospitable for P. cinereus on the Del-Mar-Va Peninsula at the Wisconsin maximum. It is postulated that, after the Laurentide ice sheet receded about 14,000 years BP, the peninsula was invaded by populations of P. cinereus from the north and south. When the two forms of P. cinereus met, a secondary zone of contact was produced. This contact zone is now apparent in an area in which six electrophoretic loci have concordant clinal changes in allele frequency. The lack of evidence for heterozygote deficiencies, the broad width of the contact zone, and the overall symmetry of introgression suggest that fusion of the populations is occurring freely. Two esterase loci are in linkage disequilibrium in four of eight populations to the north of the contact zone. As all populations of P. cinereus studied to date have disequilibrium coefficients of similar sign, selection is likely important in the maintenance of this linkage disequilibrium. Within the contact zone, the incidence of the linkage disequilibrium increases, but exchange of genes between the two introgressing populations may account for the higher incidence of linkage disequilibrium. © 1986 The Society for the Study of Evolution.

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

    Directory of Open Access Journals (Sweden)

    Tímea Kiss

    2011-10-01

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