WorldWideScience

Sample records for amplicon va derived

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

    Science.gov (United States)

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

    2016-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Benjamin Stein

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

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

    Directory of Open Access Journals (Sweden)

    Hiroyuki Mizuguchi

    2011-07-01

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

  4. Removing Noise From Pyrosequenced Amplicons

    Directory of Open Access Journals (Sweden)

    Davenport Russell J

    2011-01-01

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

  5. A Novel Ligustrazine Derivative T-VA Prevents Neurotoxicity in Differentiated PC12 Cells and Protects the Brain against Ischemia Injury in MCAO Rats

    Directory of Open Access Journals (Sweden)

    Guoling Li

    2015-09-01

    Full Text Available Broad-spectrum drugs appear to be more promising for the treatment of acute ischemic stroke. In our previous work, a new ligustrazine derivative (3,5,6-trimethylpyrazin-2-yl methyl 3-methoxy-4-[(3,5,6-trimethylpyrazin-2-ylmethoxy]benzoate (T-VA showed neuroprotective effect on injured PC12 cells (EC50 = 4.249 µM. In the current study, we show that this beneficial effect was due to the modulation of nuclear transcription factor-κB/p65 (NF-κB/p65 and cyclooxygenase-2 (COX-2 expressions. We also show that T-VA exhibited neuroprotective effect in a rat model of ischemic stroke with concomitant improvement of motor functions. We propose that the protective effect observed in vivo is owing to increased vascular endothelial growth factor (VEGF expression, decreased oxidative stress, and up-regulation of Ca2+–Mg2+ ATP enzyme activity. Altogether, our results warrant further studies on the utility of T-VA for the potential treatment of ischemic brain injuries, such as stroke.

  6. CoVaR

    OpenAIRE

    Tobias Adrian; Brunnermeier, Markus K

    2008-01-01

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

  7. State of the VA

    Directory of Open Access Journals (Sweden)

    Robbins RA

    2016-01-01

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

  8. VA scandal widens

    Directory of Open Access Journals (Sweden)

    Robbins RA

    2014-05-01

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

  9. 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.

  10. Chesapeake Bay, VA/MD (M130) Bathymetric Digital ElevationModel (30 meter resolution) Derived From Source Hydrographic SurveySoundings Collected by NOAA

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Bathymetry for Chesapeake Bay was derived from two hundred ninety-sevensurveys containing 3,178,509 soundings. Thirty-five older, lessaccurate, overlapping surveys...

  11. 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.

  12. Geographic Distribution of VA Expenditures Report (GDX)

    Data.gov (United States)

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

  13. 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...

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

    Science.gov (United States)

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

    2014-10-01

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

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

    Science.gov (United States)

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

    2016-01-01

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

  16. Report of VA Medical Training Programs

    Data.gov (United States)

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

  17. Non-VA Hospital System (NVH)

    Data.gov (United States)

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

  18. 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...... belonging to the phylum Chloroflexi. Based on knowledge about their ecophysiology, other control measures were introduced and the bulking problem was reduced after 2 months. Besides changes in the filament abundance and composition also other changes in the microbial community were observed that likely...... correlated with the bacterial species composition in 25 Danish full-scale WWTPs with nutrient removal. Examples of properties were SVI, filament index, floc size, floc strength, content of cations and amount of extracellular polymeric substances. Multivariate statistics provided several important insights...

  19. 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,...

  20. 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,...

  1. Geographic Distribution of VA Expenditures FY2003

    Data.gov (United States)

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

  2. Geographic Distribution of VA Expenditures 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,...

  3. 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,...

  4. 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,...

  5. 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,...

  6. 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,...

  7. 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,...

  8. 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,...

  9. 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,...

  10. 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,...

  11. 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,...

  12. Geographic Distribution of VA Expenditures FY2007

    Data.gov (United States)

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

  13. Geographic Distribution of VA Expenditures FY2011

    Data.gov (United States)

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

  14. Geographic Distribution of VA Expenditures 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 FY1997

    Data.gov (United States)

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

  16. Geographic Distribution of VA Expenditures 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,...

  17. 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...

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

    OpenAIRE

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

    1996-01-01

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

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

    Science.gov (United States)

    Petersdorf, Robert G.

    1987-01-01

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

  20. 78 FR 62441 - VA Dental Insurance Program-Federalism

    Science.gov (United States)

    2013-10-22

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

  1. 78 FR 32126 - VA Dental Insurance Program

    Science.gov (United States)

    2013-05-29

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

  2. 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.

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

    OpenAIRE

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

    2015-01-01

    The DNA target sequence is the key element in designing detection methods for genetically modified organisms (GMOs). Unfortunately this information is frequently lacking, especially for unauthorized GMOs. In addition, patent sequences are generally poorly annotated, buried in complex and extensive documentation and hard to link to the corresponding GM event. Here, we present the JRC GMO-Amplicons, a database of amplicons collected by screening public nucleotide sequence databanks by in silico...

  4. Multi-factor data normalization enables the detection of copy number aberrations in amplicon sequencing data

    OpenAIRE

    Boeva, Valentina; Popova, Tatiana; Lienard, Maxime; Toffoli, Sebastien; Kamal, Maud; Le Tourneau, Christophe; Gentien, David; Servant, Nicolas; Gestraud, Pierre; Rio Frio, Thomas; Hupé, Philippe; Barillot, Emmanuel; Laes, Jean-François

    2014-01-01

    Motivation: Because of its low cost, amplicon sequencing, also known as ultra-deep targeted sequencing, is now becoming widely used in oncology for detection of actionable mutations, i.e. mutations influencing cell sensitivity to targeted therapies. Amplicon sequencing is based on the polymerase chain reaction amplification of the regions of interest, a process that considerably distorts the information on copy numbers initially present in the tumor DNA. Therefore, additional experiments such...

  5. 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...

  6. 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...

  7. SlaVaComp: Konvertierungstool

    OpenAIRE

    Simon Skilevic

    2013-01-01

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

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

    International Nuclear Information System (INIS)

    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)

  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/. PMID:26424080

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

    Directory of Open Access Journals (Sweden)

    Skums Pavel

    2012-06-01

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

  11. 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...

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

    Science.gov (United States)

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

    2016-02-01

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

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

    Directory of Open Access Journals (Sweden)

    Craig W. Herbold

    2015-07-01

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

  14. Integration of complete chloroplast genome sequences with small amplicon datasets improves phylogenetic resolution in Acacia.

    Science.gov (United States)

    Williams, Anna V; Miller, Joseph T; Small, Ian; Nevill, Paul G; Boykin, Laura M

    2016-03-01

    Combining whole genome data with previously obtained amplicon sequences has the potential to increase the resolution of phylogenetic analyses, particularly at low taxonomic levels or where recent divergence, rapid speciation or slow genome evolution has resulted in limited sequence variation. However, the integration of these types of data for large scale phylogenetic studies has rarely been investigated. Here we conduct a phylogenetic analysis of the whole chloroplast genome and two nuclear ribosomal loci for 65 Acacia species from across the most recent Acacia phylogeny. We then combine this data with previously generated amplicon sequences (four chloroplast loci and two nuclear ribosomal loci) for 508 Acacia species. We use several phylogenetic methods, including maximum likelihood bootstrapping (with and without constraint) and ExaBayes, in order to determine the success of combining a dataset of 4000bp with one of 189,000bp. The results of our study indicate that the inclusion of whole genome data gave a far better resolved and well supported representation of the phylogenetic relationships within Acacia than using only amplicon sequences, with the greatest support observed when using a whole genome phylogeny as a constraint on the amplicon sequences. Our study therefore provides methods for optimal integration of genomic and amplicon sequences. PMID:26702955

  15. 78 FR 76061 - Authorization for Non-VA Medical Services

    Science.gov (United States)

    2013-12-16

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

  16. 78 FR 59771 - Proposed Information Collection (Create Payment Request for the VA Funding Fee Payment System (VA...

    Science.gov (United States)

    2013-09-27

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

  17. 75 FR 61859 - Proposed Information Collection (Create Payment Request for the VA Funding Fee Payment System (VA...

    Science.gov (United States)

    2010-10-06

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

  18. 75 FR 61252 - Proposed Information Collection (Create Payment Request for the VA Funding Fee Payment System (VA...

    Science.gov (United States)

    2010-10-04

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

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

    OpenAIRE

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

    2007-01-01

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

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

    OpenAIRE

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

    2016-01-01

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

  1. 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.

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

    Science.gov (United States)

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

    2015-09-01

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

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

    Directory of Open Access Journals (Sweden)

    Carter Jennifer

    2005-01-01

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

  4. The Portfolio Decision Under the VaR Constraint

    Institute of Scientific and Technical Information of China (English)

    ChunfengWang; XinshuTu

    2004-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Kohn Michael

    2007-10-01

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

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

    Directory of Open Access Journals (Sweden)

    Peng-Rong Cao

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

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

    Science.gov (United States)

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

    2015-01-01

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

  8. 77 FR 47489 - Virginia Disaster #VA-00048

    Science.gov (United States)

    2012-08-08

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

  9. 77 FR 74908 - Virginia Disaster #VA-00051

    Science.gov (United States)

    2012-12-18

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

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

    OpenAIRE

    Carlos Eduardo M. Gomes; Osny P. Ferreira

    2005-01-01

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

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

    Science.gov (United States)

    2016-03-16

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

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

    DEFF Research Database (Denmark)

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

    2016-01-01

    insertions and deletions, are on the other hand likely to disrupt open reading frames. Such an inverse relationship between errors and expectation based on prior knowledge can be used advantageously to guide the process known as basecalling, i.e. the inference of nucleotide sequence from raw sequencing data......Amplicon pyrosequencing targets a known genetic region and thus inherently produces reads highly anticipated to have certain features, such as conserved nucleotide sequence, and in the case of protein coding DNA, an open reading frame. Pyrosequencing errors, consisting mainly of nucleotide....... This probabilistic approach enables integration of basecalling into a larger model where other parameters can be incorporated, such as the likelihood for observing a full-length open reading frame at the targeted region. We apply the method to 454 amplicon pyrosequencing data obtained from a malaria...

  13. Troubles continue for the Phoenix VA

    OpenAIRE

    Robbins RA

    2014-01-01

    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...

  14. Web Data Mining Using FiVaTech

    OpenAIRE

    V Naveen Kumar

    2012-01-01

    In this paper, we proposed a new approach, called FiVaTech for the problem of Web data extraction. FiVaTech is a page-level data extraction system which deduces the data schema and templates for the input pages generated from a CGI program. FiVaTech uses tree templates to model the generation of dynamic Web pages. FiVaTech can deduce the schema and templates for each individual Deep Web site, which contains either singleton or multiple data records in one Web page. FiVaTech applies tree match...

  15. 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 ...

  16. 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

    2016-07-01

    We present the open-source software package DADA2 for modeling and correcting Illumina-sequenced amplicon errors (https://github.com/benjjneb/dada2). DADA2 infers sample sequences exactly and resolves differences of as little as 1 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

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

    Science.gov (United States)

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

    2016-05-01

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

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

    OpenAIRE

    Murray, Dáithí C; Megan L Coghlan; Michael Bunce

    2015-01-01

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

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

    OpenAIRE

    Lüke, Claudia; Frenzel, Peter

    2011-01-01

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

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

    OpenAIRE

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

    2010-01-01

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

  1. Single-stranded positive-sense RNA viruses generated in days using infectious subgenomic amplicons

    OpenAIRE

    Aubry, Fabien; Nougairède, Antoine; de Fabritus, Lauriane; Querat, Gilles; Gould, Ernest A.; de Lamballerie, Xavier

    2014-01-01

    Reverse genetics is a key methodology for producing genetically modified RNA viruses and deciphering cellular and viral biological properties, but methods based on the preparation of plasmid-based complete viral genomes are laborious and unpredictable. Here, both wild-type and genetically modified infectious RNA viruses were generated in days using the newly described ISA (infectious-subgenomic-amplicons) method. This new versatile and simple procedure may enhance our capacity to obtain infec...

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

    Directory of Open Access Journals (Sweden)

    Dáithí C Murray

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

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

    Science.gov (United States)

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

    2016-01-01

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

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

    Science.gov (United States)

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

    2015-12-15

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

  5. 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...

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

    OpenAIRE

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

    2013-01-01

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

  7. Application of PCR amplicon sequencing using a single primer pair in PCR amplification to assess variations in Helicobacter pylori CagA EPIYA tyrosine phosphorylation motifs

    Directory of Open Access Journals (Sweden)

    Karlsson Anneli

    2010-02-01

    Full Text Available Abstract Background The presence of various EPIYA tyrosine phosphorylation motifs in the CagA protein of Helicobacter pylori has been suggested to contribute to pathogenesis in adults. In this study, a unique PCR assay and sequencing strategy was developed to establish the number and variation of cagA EPIYA motifs. Findings MDA-DNA derived from gastric biopsy specimens from eleven subjects with gastritis was used with M13- and T7-sequence-tagged primers for amplification of the cagA EPIYA motif region. Automated capillary electrophoresis using a high resolution kit and amplicon sequencing confirmed variations in the cagA EPIYA motif region. In nine cases, sequencing revealed the presence of AB, ABC, or ABCC (Western type cagA EPIYA motif, respectively. In two cases, double cagA EPIYA motifs were detected (ABC/ABCC or ABC/AB, indicating the presence of two H. pylori strains in the same biopsy. Conclusion Automated capillary electrophoresis and Amplicon sequencing using a single, M13- and T7-sequence-tagged primer pair in PCR amplification enabled a rapid molecular typing of cagA EPIYA motifs. Moreover, the techniques described allowed for a rapid detection of mixed H. pylori strains present in the same biopsy specimen.

  8. La radio va a la escuela

    OpenAIRE

    Méndiz Rojas, Heleny

    2004-01-01

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

  9. Cuando la ciencia va a la escuela

    OpenAIRE

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

    2009-01-01

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

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

    Science.gov (United States)

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

    2016-07-01

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

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

    OpenAIRE

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

    2013-01-01

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

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

    Science.gov (United States)

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

    2016-01-01

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

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

    OpenAIRE

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

    2015-01-01

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

  14. 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

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

  15. Immigrants at retirement: stay/return or 'va-et-vient'?

    OpenAIRE

    de Coulon, Augustin; wolff, François-Charles

    2005-01-01

    where labour considerations no longer matter, the location decisions are expected to depend not only on a comparison of standard-of-living between the origin and host countries, but should also be affected by the strength of family relationships. Assuming that migrants derive some satisfaction from contact and visits with other family members, we suggest that migrants may choose a third type of migration move beyond the standard stay/return decision called the ‘va-et-vient’ where individuals ...

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

    Science.gov (United States)

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

    2015-01-01

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

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

    Science.gov (United States)

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

    2016-03-01

    Next-generation sequencing (NGS) technologies are revolutionizing the fields of biology and medicine as powerful tools for amplicon sequencing (AS). Using combinations of primers and barcodes, it is possible to sequence targeted genomic regions with deep coverage for hundreds, even thousands, of individuals in a single experiment. This is extremely valuable for the genotyping of gene families in which locus-specific primers are often difficult to design, such as the major histocompatibility complex (MHC). The utility of AS is, however, limited by the high intrinsic sequencing error rates of NGS technologies and other sources of error such as polymerase amplification or chimera formation. Correcting these errors requires extensive bioinformatic post-processing of NGS data. Amplicon Sequence Assignment (AMPLISAS) is a tool that performs analysis of AS results in a simple and efficient way, while offering customization options for advanced users. AMPLISAS is designed as a three-step pipeline consisting of (i) read demultiplexing, (ii) unique sequence clustering and (iii) erroneous sequence filtering. Allele sequences and frequencies are retrieved in excel spreadsheet format, making them easy to interpret. AMPLISAS performance has been successfully benchmarked against previously published genotyped MHC data sets obtained with various NGS technologies. PMID:26257385

  18. 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. PMID:26718401

  19. Analysis of β-Subunit-dependent GABAA Receptor Modulation and Behavioral Effects of Valerenic Acid Derivatives.

    Science.gov (United States)

    Khom, S; Hintersteiner, J; Luger, D; Haider, M; Pototschnig, G; Mihovilovic, M D; Schwarzer, C; Hering, S

    2016-06-01

    Valerenic acid (VA)-a β2/3-selective GABA type A (GABAA) receptor modulator-displays anxiolytic and anticonvulsive effects in mice devoid of sedation, making VA an interesting drug candidate. Here we analyzed β-subunit-dependent enhancement of GABA-induced chloride currents (IGABA) by a library of VA derivatives and studied their effects on pentylenetetrazole (PTZ)-induced seizure threshold and locomotion. Compound-induced IGABA enhancement was determined in oocytes expressing α1β1γ2S, α1β2γ2S, or α1β3γ2S receptors. Effects on seizure threshold and locomotion were studied using C57BL/6N mice and compared with saline-treated controls. β2/3-selective VA derivatives such as VA-amide (VA-A) modulating α1β3γ2S (VA-A: Emax = 972 ± 69%, n = 6, P tetrazole (α1β3γ2S: VA-TET: EC50 = 6.0 ± 1.0 μM, P < 0.05; VA-TET: 0.3 mg/kg: 47.3 ± 0.5 mg/kg PTZ versus VA: 10 mg/kg: 49.0 ± 1.8 mg/kg PTZ, P < 0.05). At higher doses (≥10 mg/kg), VA-A, VA-MA, and VA-TET reduced locomotion. In contrast, unselective VA derivatives induced anticonvulsive effects only at high doses (30 mg/kg) or did not display any behavioral effects. Our data indicate that the β2/3-selective compounds VA-A, VA-MA, and VA-TET induce anticonvulsive effects at low doses (≤10 mg/kg), whereas impairment of locomotion was observed at doses ≥10 mg/kg. PMID:27190170

  20. 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. PMID:24227591

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

    Science.gov (United States)

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

    2015-01-01

    The cultivated peanut (Arachis hypogaea L.) is an allotetraploid (AABB) species derived from the A-genome (Arachis duranensis) and B-genome (Arachis ipaensis) progenitors. Presence of two versions of a DNA sequence based on the two progenitor genomes poses a serious technical and analytical problem during single nucleotide polymorphism (SNP) marker identification and analysis. In this context, we have analyzed 200 amplicons derived from expressed sequence tags (ESTs) and genome survey sequences (GSS) to identify SNPs in a panel of genotypes consisting of 12 cultivated peanut varieties and two diploid progenitors representing the ancestral genomes. A total of 18 EST-SNPs and 44 genomic-SNPs were identified in 12 peanut varieties by aligning the sequence of A. hypogaea with diploid progenitors. The average frequency of sequence polymorphism was higher for genomic-SNPs than the EST-SNPs with one genomic-SNP every 1011 bp as compared to one EST-SNP every 2557 bp. In order to estimate the potential and further applicability of these identified SNPs, 96 peanut varieties were genotyped using high resolution melting (HRM) method. Polymorphism information content (PIC) values for EST-SNPs ranged between 0.021 and 0.413 with a mean of 0.172 in the set of peanut varieties, while genomic-SNPs ranged between 0.080 and 0.478 with a mean of 0.249. Total 33 SNPs were used for polymorphism detection among the parents and 10 selected lines from mapping population Y13Zh (Zhenzhuhei × Yueyou13). Of the total 33 SNPs, nine SNPs showed polymorphism in the mapping population Y13Zh, and seven SNPs were successfully mapped into five linkage groups. Our results showed that SNPs can be identified in allotetraploid peanut with high accuracy through amplicon sequencing and HRM assay. The identified SNPs were very informative and can be used for different genetic and breeding applications in peanut. PMID:26697032

  2. 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.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    1998-09-01

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

  4. 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...

  5. 77 FR 67063 - VA Directive 0005 on Scientific Integrity

    Science.gov (United States)

    2012-11-08

    ....(1), to clarify that VA employees who conduct research independently determine the content of... as training in specific content areas relevant to their research. Consequently, no changes were made.... Conflict of interest policies should apply to research staff as well as research investigators. VA...

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

    OpenAIRE

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

    1989-01-01

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

  7. 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 ...

  8. Web Data Mining Using FiVaTech

    Directory of Open Access Journals (Sweden)

    V Naveen Kumar

    2012-08-01

    Full Text Available In this paper, we proposed a new approach, called FiVaTech for the problem of Web data extraction. FiVaTech is a page-level data extraction system which deduces the data schema and templates for the input pages generated from a CGI program. FiVaTech uses tree templates to model the generation of dynamic Web pages. FiVaTech can deduce the schema and templates for each individual Deep Web site, which contains either singleton or multiple data records in one Web page. FiVaTech applies tree matching, tree alignment, and mining techniques to achieve the challenging task. The experiments show an encouraging result for the test pages used in many state-of-the-art Web data extraction works.

  9. 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.

  10. 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. PMID:25959587

  11. Development of microsatellite and amplicon length polymorphism markers for Camellia japonica L. from tea plant (Camellia sinensis) expressed sequence tags.

    Science.gov (United States)

    Ueno, Saneyoshi; Tsumura, Yoshihiko

    2009-05-01

    Simple sequence repeats and amplicon length polymorphism markers for Camellia japonica were developed, based on Camellia sinensis sequences in the National Center for Biotechnology Information database. In total, 2495 gene sequences were used to design 216 primer pairs. To identify amplicon length polymorphism markers, 61 gene loci in 16 Camellia individuals were re-sequenced. In total, 10 markers (three expressed sequence tags-simple sequence repeats and seven amplicon length polymorphisms) yielded polymerase chain reaction products with clear polymorphic patterns and were used for genotyping 22 C. japonica individuals from a population. Numbers of alleles and expected heterozygosity ranged from two to 13 and from 0.28 to 0.90, respectively. PMID:21564753

  12. Single-Step Conversion of Cells to Retrovirus Vector Producers with Herpes Simplex Virus–Epstein-Barr Virus Hybrid Amplicons

    OpenAIRE

    Sena-Esteves, Miguel; Saeki, Yoshinaga; Camp, Sara M.; Chiocca, E. Antonio; Breakefield, Xandra O.

    1999-01-01

    We report here on the development and characterization of a novel herpes simplex virus type 1 (HSV-1) amplicon-based vector system which takes advantage of the host range and retention properties of HSV–Epstein-Barr virus (EBV) hybrid amplicons to efficiently convert cells to retrovirus vector producer cells after single-step transduction. The retrovirus genes gag-pol and env (GPE) and retroviral vector sequences were modified to minimize sequence overlap and cloned into an HSV-EBV hybrid amp...

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

    Science.gov (United States)

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

    2005-06-16

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

  14. 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.

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

    DEFF Research Database (Denmark)

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

    2011-01-01

    Cyanobacteria are thought to be the main N2-fixing organisms (diazotrophs) in marine pelagic waters, but recent molecular analyses indicate that non-cyanobacterial diazotrophs are also present and active. Existing data are, however, restricted geographically and by limited sequencing depths. Our...... of the nifH gene pool in marine waters. Great divergence in nifH composition was observed between sites. Cyanobacteria-like genes were most frequent among amplicons from the warmest waters, but overall the data set was dominated by nifH sequences most closely related to non-cyanobacteria. Clusters related...... 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...

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

    Science.gov (United States)

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

    2016-09-01

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

  17. 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 ...... ampliconic sequences we propose that intra-genomic conflict between the X and the Y chromosomes is a major driver of X chromosome evolution.......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, and...

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

    Science.gov (United States)

    Yanthan, Mhathung; Misra, Arvind K

    2013-11-01

    Trees of Myrica sp. grow abundantly in the forests of Meghalaya, India. These trees are actinorhizal and harbour nitrogen-fixing Frankia in their root nodules and contribute positively towards the enhancement of nitrogen status of forest areas. They can be used in rejuvenation of mine spoils and nitrogen-depleted fallow lands generated due to slash and burn agriculture practiced in the area. We have studied the association of amplicon restriction patterns (ARPs) of Myrica ribosomal RNA gene and internal transcribed spacer (ITS) region and nitrogenase activity of its root nodules. We found that ARPs thus obtained could be used as markers for early screening of seedlings that could support strains of Frankia that fix atmospheric nitrogen more efficiently. PMID:24287658

  19. 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

    -based genotyping results. Comparing the CADMA-based assays to (AS-PCR) and Sanger sequencing, the CADMA based assays showed an improved analytical sensitivity and a wider applicability. CONCLUSIONS: The new assays provide a reliable, fast and user-friendly genotyping method facilitating a wider implication...... 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...... gene: rs6165 (c.919A > G, p. Thr307Ala, FSHR 307) and rs6166 (c.2039A > G, p. Asn680Ser, FSHR 680). To evaluate the reliability of the new CADMA-based assays, the genotyping results were compared with two conventional PCR based genotyping methods; allele-specific PCR (AS-PCR) and Sanger sequencing...

  20. 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 ...

  1. 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 …

  2. 1000-kVA arc power supply

    International Nuclear Information System (INIS)

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

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

    DEFF Research Database (Denmark)

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

    2003-01-01

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

  4. Deriving Derivatives

    OpenAIRE

    Soklakov, Andrei N.

    2013-01-01

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

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

    International Nuclear Information System (INIS)

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

  6. Key Science Observations of AGNs with KaVA Array

    CERN Document Server

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

    2015-01-01

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

  7. VA 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...

  8. 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...

  9. Virginia Tech sponsors conservation course in Blackstone, Va.

    OpenAIRE

    Davis, Lynn

    2007-01-01

    The Virginia Forest Landowner Education Program's (VFLEP) Short Course Series now includes a course, Forest and Farmland Conservation Strategies. It will be held on June 15 at the Southern Piedmont Virginia Agricultural Experiment Station in Blackstone, Va.

  10. 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...

  11. The VA Computerized Patient Record — A First Look

    OpenAIRE

    Anderson, Curtis L.; Meldrum, Kevin C.

    1994-01-01

    In support of its in-house DHCP Physician Order Entry/Results Reporting application, the VA is developing the first edition of a Computerized Patient Record. The system will feature a physician-oriented interface with real time, expert system-based order checking, a controlled vocabulary, a longitudinal repository of patient data, HL7 messaging support, a clinical reminder and warning system, and full integration with existing VA applications including lab, pharmacy, A/D/T, radiology, dieteti...

  12. "Women's Veteran Identity and Utilization of VA Health Services": Correction to Di Leone et al. (2015).

    Science.gov (United States)

    2016-02-01

    Reports an error in "Women's Veteran Identity and Utilization of VA Health Services" by Brooke A. L. Di Leone, Joyce M. Wang, Nancy Kressin and Dawne Vogt (Psychological Services, Advanced Online Publication, Mar 2, 2015, np). In the article, the institutional affiliation in the byline of Dawne Vogt did not include the National Center for PTSD. All versions of this article have been corrected. (The following abstract of the original article appeared in record 2015-09317-001.) Women have participated in the United States military since its founding. However, until the mid-20th century, there had been limited recognition of women as official members of the military, and women remain a statistical minority within military and veteran populations. It is therefore important to better understand women's veteran identity (which we define here as one's self-concept as derived from their veteran status) and associated implications for service use and experiences in the Department of Veterans Affairs (VA) health care setting. The present research examined the centrality of, and positive regard for, women's veteran identity among 407 female veterans deployed in support of the recent wars in Iraq and Afghanistan. Data were collected via a mailed national survey. Positive regard for veteran identity, but not veteran identity centrality, was positively associated with participants' age and length of time spent in the military. Results also showed that the centrality of women's veteran identity was positively related to their choice to use VA for health care and their feelings of belonging within VA, and that veteran identity centrality and positive regard for veteran identity are differentially associated with participants' military experiences (e.g., combat exposure, deployment sexual harassment) and mental health symptomatology (e.g., depression). (PsycINFO Database Record PMID:25938857

  13. 78 FR 28947 - Fund Availability Under VA's Homeless Providers Grant and Per Diem Program (VANS)

    Science.gov (United States)

    2013-05-16

    ... Application Package: Download directly from VA's Grant and Per Diem Program Web page at: http://www.va.gov... AFFAIRS Fund Availability Under VA's Homeless Providers Grant and Per Diem Program (VANS) AGENCY: Department of Veterans Affairs. ACTION: Notice. SUMMARY: The Department of Veterans Affairs (VA)...

  14. 78 FR 28949 - Fund Availability Under VA's Homeless Providers Grant and Per Diem Program (Rehabilitation)

    Science.gov (United States)

    2013-05-16

    ... Diem Program Web page at: http://www.va.gov/HOMELESS/GPD.asp or http://www.grants.gov/ . Questions... certifications and will be provided by VA on the Grant and Per Diem Web site at http://www.va.gov/HOMELESS/GPD... AFFAIRS Fund Availability Under VA's Homeless Providers Grant and Per Diem Program (Rehabilitation)...

  15. 75 FR 3970 - Fund Availability Under the VA Homeless Providers Grant and Per Diem Program

    Science.gov (United States)

    2010-01-25

    ... Application Package: Download directly from VA's Grant and Per Diem Program Web page at: http://www.va.gov... AFFAIRS Fund Availability Under the VA Homeless Providers Grant and Per Diem Program AGENCY: Department of Veterans Affairs. ACTION: Notice. SUMMARY: The Department of Veterans Affairs (VA) is announcing...

  16. 75 FR 3968 - Fund Availability Under the VA Homeless Providers Grant and Per Diem Program

    Science.gov (United States)

    2010-01-25

    ... Application Package: Download directly from VA's Grant and Per Diem Program Web page at: http://www.va.gov... AFFAIRS Fund Availability Under the VA Homeless Providers Grant and Per Diem Program AGENCY: Department of Veterans Affairs. ACTION: Notice. SUMMARY: The Department of Veterans Affairs (VA) is announcing...

  17. 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

  18. 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.

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

    Science.gov (United States)

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

    2016-08-01

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

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

    Science.gov (United States)

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

    2016-07-01

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

  1. 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.

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

    Science.gov (United States)

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

    2014-03-01

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

  3. 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. PMID:26525270

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

    Science.gov (United States)

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

    2010-03-01

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

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

    Directory of Open Access Journals (Sweden)

    J. Björkman

    2016-01-01

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

  6. 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.

  7. VaR and CVaR Implied in Option Prices

    Directory of Open Access Journals (Sweden)

    Giovanni Barone Adesi

    2016-02-01

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

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

    Science.gov (United States)

    2012-03-01

    This final rule amends the Department of Veterans Affairs (VA) regulations regarding access to VA facilities by pharmaceutical company representatives. The purposes of the rule are to reduce or eliminate any potential for disruption in the patient care environment, manage activities and promotions at VA facilities, and provide pharmaceutical company representatives with a consistent standard of permissible business practice at VA facilities. The amendments will facilitate mutually beneficial relationships between VA and pharmaceutical company representatives. PMID:22420057

  9. High-Throughput Identification and Quantification of Candida Species Using High Resolution Derivative Melt Analysis of Panfungal Amplicons

    OpenAIRE

    Mandviwala, Tasneem; Shinde, Rupali; Kalra, Apoorv; Jack D. Sobel; Akins, Robert A.

    2010-01-01

    Fungal infections pose unique challenges to molecular diagnostics; fungal molecular diagnostics consequently lags behind bacterial and viral counterparts. Nevertheless, fungal infections are often life-threatening, and early detection and identification of species is crucial to successful intervention. A high throughput PCR-based method is needed that is independent of culture, is sensitive to the level of one fungal cell per milliliter of blood or other tissue types, and is capable of detect...

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

    DEFF Research Database (Denmark)

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

    the existing knowledge on core genera with high-throughput amplicon sequencing, plant design and process data in order to identify interactions and community shaping factors. We investigated 25 Danish full-scale wastewater treatment plants with nutrient removal over a period of 7 years with two to four samples...... database, which integrates the current knowledge of the core species in wastewater treatment plants (www.midasfieldguide.org). For each sample the wastewater treatment plants provided operational data, and selected samples were subjected to extensive physio-chemical analysis and shear tests in order...... to link sludge and floc properties to the microbial communities. All data was subjected to extensive network analysis and multivariate statistics through R. The 16S amplicon results confirmed the findings of relatively few core groups of organism shared by all the wastewater treatment plants...

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

    Science.gov (United States)

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

    2016-01-01

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

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

    Science.gov (United States)

    Carey, Kathleen; Stefos, Theodore

    2016-09-01

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

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

    Science.gov (United States)

    Kim, Jane C; Orr-Weaver, Terry L

    2011-10-01

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

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

    Science.gov (United States)

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

    2016-03-01

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

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

    Science.gov (United States)

    Damiati, E; Borsani, G; Giacopuzzi, Edoardo

    2016-05-01

    The Ion Proton platform allows to perform whole exome sequencing (WES) at low cost, providing rapid turnaround time and great flexibility. Products for WES on Ion Proton system include the AmpliSeq Exome kit and the recently introduced HiQ sequencing chemistry. Here, we used gold standard variants from GIAB consortium to assess the performances in variants identification, characterize the erroneous calls and develop a filtering strategy to reduce false positives. The AmpliSeq Exome kit captures a large fraction of bases (>94 %) in human CDS, ClinVar genes and ACMG genes, but with 2,041 (7 %), 449 (13 %) and 11 (19 %) genes not fully represented, respectively. Overall, 515 protein coding genes contain hard-to-sequence regions, including 90 genes from ClinVar. Performance in variants detection was maximum at mean coverage >120×, while at 90× and 70× we measured a loss of variants of 3.2 and 4.5 %, respectively. WES using HiQ chemistry showed ~71/97.5 % sensitivity, ~37/2 % FDR and ~0.66/0.98 F1 score for indels and SNPs, respectively. The proposed low, medium or high-stringency filters reduced the amount of false positives by 10.2, 21.2 and 40.4 % for indels and 21.2, 41.9 and 68.2 % for SNP, respectively. Amplicon-based WES on Ion Proton platform using HiQ chemistry emerged as a competitive approach, with improved accuracy in variants identification. False-positive variants remain an issue for the Ion Torrent technology, but our filtering strategy can be applied to reduce erroneous variants. PMID:27003585

  17. 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.

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

    Directory of Open Access Journals (Sweden)

    SteffenKolb

    2013-09-01

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

  19. 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.

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

    Science.gov (United States)

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

    2016-06-01

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

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

    Science.gov (United States)

    2011-08-22

    ..., VA (76 FR 34196) Docket No. FAA-2011-0378. Interested parties were invited to participate in this... Procedures (44 FR 11034; February 26, 1979); and (3) does not warrant preparation of a Regulatory Evaluation.... 106(g); 40103, 40113, 40120; E.O. 10854, 24 FR 9565, 3 CFR, 1959-1963 Comp., p. 389. Sec. 71.1 0...

  2. 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...

  3. 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,...

  4. 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…

  5. EURRECA—Principles and Future for Deriving Micronutrient Recommendations

    NARCIS (Netherlands)

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

    2013-01-01

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

  6. Exploring the Gastrointestinal "Nemabiome": Deep Amplicon Sequencing to Quantify the Species Composition of Parasitic Nematode Communities.

    Science.gov (United States)

    Avramenko, Russell W; Redman, Elizabeth M; Lewis, Roy; Yazwinski, Thomas A; Wasmuth, James D; Gilleard, John S

    2015-01-01

    Parasitic helminth infections have a considerable impact on global human health as well as animal welfare and production. Although co-infection with multiple parasite species within a host is common, there is a dearth of tools with which to study the composition of these complex parasite communities. Helminth species vary in their pathogenicity, epidemiology and drug sensitivity and the interactions that occur between co-infecting species and their hosts are poorly understood. We describe the first application of deep amplicon sequencing to study parasitic nematode communities as well as introduce the concept of the gastro-intestinal "nemabiome". The approach is analogous to 16S rDNA deep sequencing used to explore microbial communities, but utilizes the nematode ITS-2 rDNA locus instead. Gastro-intestinal parasites of cattle were used to develop the concept, as this host has many well-defined gastro-intestinal nematode species that commonly occur as complex co-infections. Further, the availability of pure mono-parasite populations from experimentally infected cattle allowed us to prepare mock parasite communities to determine, and correct for, species representation biases in the sequence data. We demonstrate that, once these biases have been corrected, accurate relative quantitation of gastro-intestinal parasitic nematode communities in cattle fecal samples can be achieved. We have validated the accuracy of the method applied to field-samples by comparing the results of detailed morphological examination of L3 larvae populations with those of the sequencing assay. The results illustrate the insights that can be gained into the species composition of parasite communities, using grazing cattle in the mid-west USA as an example. However, both the technical approach and the concept of the 'nemabiome' have a wide range of potential applications in human and veterinary medicine. These include investigations of host-parasite and parasite-parasite interactions during co

  7. 77 FR 21158 - VA Directive 0005 on Scientific Integrity: Availability for Review and Comment

    Science.gov (United States)

    2012-04-09

    ...; Encourages the full participation of employees in scientific and professional societies, publication and... AFFAIRS VA Directive 0005 on Scientific Integrity: Availability for Review and Comment AGENCY: Office of... (VA) Directive 0005 on Scientific Integrity. The Draft Directive incorporates the principles...

  8. 77 FR 2348 - Agency Information Collection (VA Enrollment Certification): Activity Under OMB Review

    Science.gov (United States)

    2012-01-17

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

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

    DEFF Research Database (Denmark)

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

    2014-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    1995-10-01

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

  11. 77 FR 23204 - VA Acquisition Regulation: Electronic Submission of Payment Requests

    Science.gov (United States)

    2012-04-18

    ... using under VA's current interim electronic invoicing clause. See 74 FR 32223. VA's Electronic Invoice... INFORMATION: On July 7, 2009, VA published a notice, in the Federal Register at 74 FR 32223, of a class... interchange (EDI) formats; or (3) another electronic form as prescribed by the contract administration...

  12. 38 CFR 21.1032 - VA has a duty to assist claimants in obtaining evidence.

    Science.gov (United States)

    2010-07-01

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

  13. 38 CFR 21.33 - VA has a duty to assist claimants in obtaining evidence.

    Science.gov (United States)

    2010-07-01

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

  14. 78 FR 6849 - Agency Information Collection (Verification of VA Benefits) Activity Under OMB Review

    Science.gov (United States)

    2013-01-31

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

  15. 76 FR 24570 - Proposed Information Collection (Application for VA Education Benefits) Activity; Comment Request

    Science.gov (United States)

    2011-05-02

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

  16. 76 FR 67557 - Proposed Information Collection (Survey of Veteran Enrollees' Health and Reliance Upon VA...

    Science.gov (United States)

    2011-11-01

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

  17. 78 FR 53506 - Agency Information Collection (HUD/VA Addendum to Uniform Residential Loan Application) Activity...

    Science.gov (United States)

    2013-08-29

    ....rennie@va.gov . Please refer to ``OMB Control No. 2900-0144.'' SUPPLEMENTARY INFORMATION: Title: HUD/VA... AFFAIRS Agency Information Collection (HUD/VA Addendum to Uniform Residential Loan Application) Activity... information through www.Regulations.gov , or to Office of Information and Regulatory Affairs, Office...

  18. 78 FR 59773 - Proposed Information Collection (VA Request for Determination of Reasonable Value) Activity...

    Science.gov (United States)

    2013-09-27

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

  19. 78 FR 60379 - Proposed Information Collection (Credit Underwriting Standards and Procedures for Processing VA...

    Science.gov (United States)

    2013-10-01

    ...., Washington, DC 20420 or email nancy.kessinger@va.gov . Please refer to ``OMB Control No. 2900-0521'' in any... AFFAIRS Proposed Information Collection (Credit Underwriting Standards and Procedures for Processing VA... Affairs (VA), is announcing an opportunity for public comment on the proposed collection of...

  20. 77 FR 20889 - Proposed Information Collection (Request One-VA Identification Verification Card) Activity...

    Science.gov (United States)

    2012-04-06

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

  1. 76 FR 40452 - Agency Information Collection (VA MATIC Authorization) Activity Under OMB Review

    Science.gov (United States)

    2011-07-08

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

  2. 76 FR 27381 - Proposed Information Collection (Notice of Waiver of VA Compensation or Pension To Receive...

    Science.gov (United States)

    2011-05-11

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

  3. 78 FR 29436 - Proposed Information Collection (HUD/VA Addendum to Uniform Residential Loan Application...

    Science.gov (United States)

    2013-05-20

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

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

    Science.gov (United States)

    2012-10-04

    ... 20420 or email to ] nancy.kessinger@va.gov . Please refer to ``OMB Control No. 2900-0704'' in any... AFFAIRS Proposed Information Collection (VA/DOD Joint Disability Evaluation Board Claim) Activity: Comment...: The Veterans Benefits Administration (VBA), Department of Veterans Affairs (VA), is announcing...

  5. 75 FR 61249 - Proposed Information Collection (VA Request for Determination of Reasonable Value) Activity...

    Science.gov (United States)

    2010-10-04

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

  6. 75 FR 54965 - Proposed Information Collection (Statement of Purchaser or Owner Assuming Seller's Loans, VA Form...

    Science.gov (United States)

    2010-09-09

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

  7. 78 FR 36642 - Proposed Information Collection (VA Loan Electronic Reporting Interface (VALERI) System) Activity...

    Science.gov (United States)

    2013-06-18

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

  8. 76 FR 67561 - Proposed Information Collection (VA Enrollment Certification) Activity: Comment Request

    Science.gov (United States)

    2011-11-01

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

  9. 75 FR 61858 - Proposed Information Collection (VA Request for Determination of Reasonable Value) Activity...

    Science.gov (United States)

    2010-10-06

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

  10. 77 FR 56711 - Proposed Information Collection (VA MATIC Enrollment/Change); Comment Request

    Science.gov (United States)

    2012-09-13

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

  11. 77 FR 56709 - Proposed Information Collection (VA Subcontracting Report for Service Disabled Veteran-Owned...

    Science.gov (United States)

    2012-09-13

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

  12. 78 FR 52085 - VA Veteran-Owned Small Business Verification Guidelines

    Science.gov (United States)

    2013-08-22

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

  13. 75 FR 60171 - Proposed Information Collection (Credit Underwriting Standards and Procedures for Processing VA...

    Science.gov (United States)

    2010-09-29

    ...., Washington, DC 20420 or e-mail nancy.kessinger@va.gov . Please refer to ``OMB Control No. 2900-0521'' in any... AFFAIRS Proposed Information Collection (Credit Underwriting Standards and Procedures for Processing VA... Affairs (VA), is announcing an opportunity for public comment on the proposed collection of...

  14. 75 FR 17832 - Proposed Information Collection (VA Loan Electronic Reporting Interface (VALERI) System) Activity...

    Science.gov (United States)

    2010-04-07

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

  15. 77 FR 38396 - Agency Information Collection (One-VA Identification Verification Card) Activities Under OMB Review

    Science.gov (United States)

    2012-06-27

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

  16. 75 FR 48413 - Agency Information Collection (HUD/VA Addendum to Uniform Residential Loan Application) Activity...

    Science.gov (United States)

    2010-08-10

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

  17. 76 FR 63357 - VA National Academic Affiliations Council; Notice of Establishment

    Science.gov (United States)

    2011-10-12

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

  18. 75 FR 33898 - Agency Information Collection (VA Loan Electronic Reporting Interface (VALERI) System) Activity...

    Science.gov (United States)

    2010-06-15

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

  19. 77 FR 30050 - VA National Academic Affiliations Council, Notice of meeting

    Science.gov (United States)

    2012-05-21

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

  20. 78 FR 55777 - Proposed Information Collection (VA, National Veterans Sports Programs and Special Events, Event...

    Science.gov (United States)

    2013-09-11

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

  1. 75 FR 9277 - Proposed Information Collection (VA National Rehabilitation Special Events, Event Registration...

    Science.gov (United States)

    2010-03-01

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

  2. 77 FR 24268 - Agency Information Collection (Dependents' Application for VA Educational Benefits) Activity...

    Science.gov (United States)

    2012-04-23

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

  3. 78 FR 48543 - Veterans Health Administration Fund Availability Under the VA's Homeless Providers Grant and Per...

    Science.gov (United States)

    2013-08-08

    ... initial announcement will be made via news release, which will be posted on the GPD Web site at www.va.gov... AFFAIRS Veterans Health Administration Fund Availability Under the VA's Homeless Providers Grant and Per...). SUMMARY: Funding Opportunity Title: VA Grant and Per Diem (GPD) Special Needs Renewal. The Department...

  4. 77 FR 70210 - Agency Information Collection (VA Subcontracting Report for Service Disabled Veteran-owned Small...

    Science.gov (United States)

    2012-11-23

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

  5. 78 FR 77204 - Proposed Information Collection (VA National Veterans Sports Programs and Special Event Surveys...

    Science.gov (United States)

    2013-12-20

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

  6. 78 FR 79563 - Proposed Information Collection (VA MATIC Authorization); Comment Request

    Science.gov (United States)

    2013-12-30

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

  7. 75 FR 78808 - Agency Information Collection (VA Request for Determination of Reasonable Value) Activity Under...

    Science.gov (United States)

    2010-12-16

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

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

    Science.gov (United States)

    2013-12-17

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

  9. 75 FR 41577 - VBA/VHA Musculoskeletal Forum: Improving VA's Disability Evaluation Criteria

    Science.gov (United States)

    2010-07-16

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

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

    OpenAIRE

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

    2001-01-01

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

  11. 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.

  12. 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.

  13. American Indian veterans and VA services in three tribes.

    Science.gov (United States)

    Kaufman, Carol E; Kaufman, L Jeanne; Shangreau, Carly; Dailey, Nancy; Blair, Byron; Shore, Jay

    2016-01-01

    The purpose of this project was to describe experiences of reservation-based American Indian (AI) veterans with the Department of Veterans Affairs (VA), and to identify opportunities for improving care and services. Focus group discussions and individual interviews were conducted with AI veterans, family members, and community members in three diverse tribes. Results showed that many veterans in tribal communities experienced challenges receiving services and benefits from the VA, including lack of culturally competent care, transportation problems, and difficulties navigating the system. Family members, often main caregivers for AI veterans, lacked necessary resources, including sources for information, support services, and financial means to procure adequate care. A number of strengths also were identified, including local leadership and a strong community commitment to improve care for veterans. PMID:27115133

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

    Science.gov (United States)

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

    2016-06-01

    A major challenge to global malaria control and elimination is early detection and containment of emerging drug resistance. Next-generation sequencing (NGS) methods provide the resolution, scalability, and sensitivity required for high-throughput surveillance of molecular markers of drug resistance. We have developed an amplicon sequencing method on the Ion Torrent PGM platform for targeted resequencing of a panel of six Plasmodium falciparum genes implicated in resistance to first-line antimalarial therapy, including artemisinin combination therapy, chloroquine, and sulfadoxine-pyrimethamine. The protocol was optimized using 12 geographically diverse P. falciparum reference strains and successfully applied to multiplexed sequencing of 16 clinical isolates from India. The sequencing results from the reference strains showed 100% concordance with previously reported drug resistance-associated mutations. Single-nucleotide polymorphisms (SNPs) in clinical isolates revealed a number of known resistance-associated mutations and other nonsynonymous mutations that have not been implicated in drug resistance. SNP positions containing multiple allelic variants were used to identify three clinical samples containing mixed genotypes indicative of multiclonal infections. The amplicon sequencing protocol has been designed for the benchtop Ion Torrent PGM platform and can be operated with minimal bioinformatics infrastructure, making it ideal for use in countries that are endemic for the disease to facilitate routine large-scale surveillance of the emergence of drug resistance and to ensure continued success of the malaria treatment policy. PMID:27008882

  15. 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.

    2016-01-01

    A major challenge to global malaria control and elimination is early detection and containment of emerging drug resistance. Next-generation sequencing (NGS) methods provide the resolution, scalability, and sensitivity required for high-throughput surveillance of molecular markers of drug resistance. We have developed an amplicon sequencing method on the Ion Torrent PGM platform for targeted resequencing of a panel of six Plasmodium falciparum genes implicated in resistance to first-line antimalarial therapy, including artemisinin combination therapy, chloroquine, and sulfadoxine-pyrimethamine. The protocol was optimized using 12 geographically diverse P. falciparum reference strains and successfully applied to multiplexed sequencing of 16 clinical isolates from India. The sequencing results from the reference strains showed 100% concordance with previously reported drug resistance-associated mutations. Single-nucleotide polymorphisms (SNPs) in clinical isolates revealed a number of known resistance-associated mutations and other nonsynonymous mutations that have not been implicated in drug resistance. SNP positions containing multiple allelic variants were used to identify three clinical samples containing mixed genotypes indicative of multiclonal infections. The amplicon sequencing protocol has been designed for the benchtop Ion Torrent PGM platform and can be operated with minimal bioinformatics infrastructure, making it ideal for use in countries that are endemic for the disease to facilitate routine large-scale surveillance of the emergence of drug resistance and to ensure continued success of the malaria treatment policy. PMID:27008882

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

    Science.gov (United States)

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

    2016-01-01

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

  17. 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.

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

    Science.gov (United States)

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

    2016-06-01

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

  19. 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.

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

    OpenAIRE

    Linda Resnik, PT, PhD

    2010-01-01

    In 2005, the Defense Advanced Research Projects Agency (DARPA) announced its Revolutionizing Prosthetics program and funded the development of the DEKA prosthetic arm. The DEKA Arm System incorporates major technological advances such as flexible socket design, innovative control features, software, and hardware that together enable enhanced functionality that promises to surpass any currently available prosthetic device. In 2008, the Department of Veterans Affairs (VA) entered into an agreem...

  1. VA paradigm shift in care of veterans with limb loss

    Directory of Open Access Journals (Sweden)

    Gayle E. Reiber, PhD, MPH

    2010-08-01

    Full Text Available Traumatic limb loss results in pain and discomfort in addition to the loss of an important part of the body and its function. The mental health challengesaccompanying limb loss include issues of frustration and body image, role in life, and feelings of not being whole. Many servicemembers and veteranswith limb loss need to prove to themselves that they can still accomplishphysical feats, such as those with lower-limb loss returning to running or those with upper-limb loss working with tools. If our servicemembers and veterans let these activities go, they again feel a loss. Therefore, Department of Veterans Affairs (VA services are available to help individuals meet their physical and recreational goals, whether they be running, walking, or masteringcomplex upper-limb activities. Veterans with limb loss need ongoing clinical care, prosthetic devices, and mobility assistance. As their prosthetic devices are repaired, replaced, and updated, they need corresponding educationand training. Too often in the past, the VA has taken a narrow view of amputation care, focusing only on managing prosthetic devices. Prosthetic care is one small but important aspect of the complex rehabilitation partnershipbetween the veteran with limb loss and the VA.

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

    International Nuclear Information System (INIS)

    Section 1 of this report documents the validation of KENO V.a against 258 critical experiments. Experiments considered were primarily high or low enriched uranium systems. The results indicate that the KENO V.a Monte Carlo Criticality Program accurately calculates a broad range of critical experiments. A substantial number of the calculations showed a positive or negative bias in excess of 1 1/2% in k-effective (k/sub eff/). Classes of criticals which show a bias include 3% enriched green blocks, highly enriched uranyl fluoride slab arrays, and highly enriched uranyl nitrate arrays. If these biases are properly taken into account, the KENO V.a code can be used with confidence for the design and criticality safety analysis of uranium-containing systems. Sections 2 of this report documents the results of investigation into the cause of the bias observed in Sect. 1. The results of this study indicate that the bias seen in Sect. 1 is caused by code bias, cross-section bias, reporting bias, and modeling bias. There is evidence that many of the experiments used in this validation and in previous validations are not adequately documented. The uncertainty in the experimental parameters overshadows bias caused by the code and cross sections and prohibits code validation to better than about 1% in k/sub eff/. 48 refs., 19 figs., 19 tabs

  3. 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}.

  4. 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.

  5. 77 FR 64388 - Agency Information Collection (Former POW Medical History), VA Form 10-0048 Activities Under OMB...

    Science.gov (United States)

    2012-10-19

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

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

    Directory of Open Access Journals (Sweden)

    Leho Tedersoo

    2015-05-01

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

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

    Directory of Open Access Journals (Sweden)

    Hideyuki Tamaki

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

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

    Directory of Open Access Journals (Sweden)

    Christopher S Miller

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

  9. Managing market risk with VaR (Value At Risk)

    OpenAIRE

    Angelovska, Julijana

    2013-01-01

    Market risk estimates the uncertainty of future earnings, due to the changes in market conditions. Value at Risk has become the standard measure that financial analysts use to quantify market risk. For estimating risk, the issue is that different ways to estimate volatility can lead to very different VaR calculations. The performance of SMA with rolling windows of 100 and EWMA using 0.94 (proposed by RiskMetrics) as smoothing constant λ and rolling window of 100 days, perhaps the most widely ...

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

    Directory of Open Access Journals (Sweden)

    Tärnberg Maria

    2009-01-01

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

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

    OpenAIRE

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

    2016-01-01

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

  12. 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...

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

    OpenAIRE

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

    2010-01-01

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

  14. Dental health status of an aging VA population: implications for a preventive dental health care program.

    OpenAIRE

    Morhart, R E; Davis, M. E.; D. G. Weiss; Fitzgerald, R. J.; Rhyne, R R

    1986-01-01

    The purpose of this study was to describe the sociodemographic characteristics and dental health status of the largest eligible class of veterans (Class IV) within the Greater Miami catchment area. Only 43 percent of 4,882 Class IV patients within this area have sought VA dental care. Sociodemographic data were obtained from a randomized sample of both the VA-treated and non-VA-treated groups. The prevalence and incidence of dental diseases and actual dental treatment procedures completed for...

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

    Energy Technology Data Exchange (ETDEWEB)

    Busch, R.D.

    2003-01-17

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

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

    Directory of Open Access Journals (Sweden)

    Raheleh Khorsan

    2013-01-01

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

  17. 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.

  18. 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.

  19. Mean-VaR Models and Algorithms for Fuzzy Portfolio Selection

    Science.gov (United States)

    Dong, Wen; Peng, Jin

    In this paper, value-at-risk (VaR for short) is used as the measure of risk. Based on the concept of VaR, a fuzzy mean-VaR model is proposed. Firstly, we recall some definitions and results of value-at-risk in credibilistic risk analysis. Secondly, we propose the fuzzy mean- VaR model of fuzzy programming, or more precisely, credibilistic programming. Thirdly, a hybrid intelligent algorithm is provided to give a general solution of the optimization problem. Finally, numerical examples are also presented to illustrate the effectiveness of the proposed algorithm.

  20. A Probabilistic Simulation Based VaR Computation and Sensitivity Analysis Method

    OpenAIRE

    Li, Wendy

    2015-01-01

    This paper presents a new method to compute VaR (value at risk) and perform corresponding variance based sensitivity analysis. VaR has a long history of being applied in stock price prediction and investment portfolio analysis. Traditional method, however, is mainly analytical, and has certain limitations. The VaR simulation, on the other hand, provides more realistic analysis but is very slow which affects the applications. This study proposes a new VaR computation method based on a probabil...

  1. Penn/VA center for studies of addiction.

    Science.gov (United States)

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

    2009-01-01

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

  2. 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.

  3. Development of 30 kVA class fully superconducting generator

    International Nuclear Information System (INIS)

    This paper reports that the authors are developing a 4 poles 30 kVA class fully superconducting generator to investigate the characteristics of superconducting armature winding subject to the rotating magnetic field produced by the superconducting rotor and behavior of a superconducting generator connected to an electric power utility grid. A static test of the armature winding have been performed by applying 50 Hz AC current. AC quench currents of the armature windings have reached to 200 Arms after several quenches which was well over the rated current. A static test of the field windings have been also performed to verify its rated performance. In the paper, detailed configurations and electrical test results of the generator are shown

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

    International Nuclear Information System (INIS)

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

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

    International Nuclear Information System (INIS)

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

  6. ‘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

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

    Science.gov (United States)

    2010-07-01

    ... display of VA seal and flag. 1.9 Section 1.9 Pensions, Bonuses, and Veterans' Relief DEPARTMENT OF VETERANS AFFAIRS GENERAL PROVISIONS Department of Veterans Affairs Official Seal and Distinguishing Flag § 1.9 Description, use, and display of VA seal and flag. (a) General. This section describes...

  8. 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...

  9. 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... eliminate veteran homelessness within 5 years. The VA Homeless Providers Grant and Per Diem Program is one... practice and procedure, Alcohol abuse, Alcoholism, Day care, Dental health, Drug abuse,...

  10. 30 CFR 57.22309 - Methane monitors (V-A mines).

    Science.gov (United States)

    2010-07-01

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

  11. 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...

  12. 76 FR 40453 - Agency Information Collection (Application for VA Education Benefits) Activity Under OMB Review

    Science.gov (United States)

    2011-07-08

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

  13. 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...

  14. 78 FR 51067 - VA Health Professional Scholarship and Visual Impairment and Orientation and Mobility...

    Science.gov (United States)

    2013-08-20

    ... Federal Register on December 26, 2012 (77 FR 75918), VA proposed to amend part 17 of 38 CFR by amending... a participant may continue to attend school under the standards and practices of the school at which... doctorate degree in another health care discipline needed by VA. (2) VIOMPSP. For the purposes of...

  15. 76 FR 34248 - Equestrian Stables at Meadowood Special Recreation Management Area, VA; Information Sharing Meeting

    Science.gov (United States)

    2011-06-13

    ... Equestrian Stables at Meadowood Special Recreation Management Area, VA; Information Sharing Meeting AGENCY... equestrian stables at Meadowood Special Recreation Management Area (SRMA), located in Lorton, VA, and collect... will begin with an overview of the status of equestrian activities at the Meadowood SRMA....

  16. 78 FR 59099 - Agency Information Collection (VA Loan Electronic Reporting Interface (VALERI) System) Activity...

    Science.gov (United States)

    2013-09-25

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

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

    Science.gov (United States)

    2010-12-07

    ... collection of information through http://www.Regulations.gov or to VA's OMB Desk Officer, OMB Human Resources..., NW., Washington, DC 20420, (202) 461-7485, FAX (202) 273-0443 or e-mail denise.mclamb@.va.gov. Please... AFFAIRS Agency Information Collection (Credit Underwriting Standards and Procedures for Processing...

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

    Science.gov (United States)

    2011-11-15

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

  19. 77 FR 70212 - Agency Information Collection Activities Under OMB Review: VA MATIC Enrollment/Change

    Science.gov (United States)

    2012-11-23

    ... or email crystal.rennie@va.gov . Please refer to ``OMB Control No. 2900-0525.'' SUPPLEMENTARY... AFFAIRS Agency Information Collection Activities Under OMB Review: VA MATIC Enrollment/Change AGENCY..., 2012. ADDRESSES: Submit written comments on the collection of information through...

  20. 77 FR 39346 - Proposed Information Collection (Statement of Accredited Representative in Appealed Case, VA Form...

    Science.gov (United States)

    2012-07-02

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

  1. 30 CFR 57.22605 - Blasting from the surface (V-A mines).

    Science.gov (United States)

    2010-07-01

    ... applicable requirements of 30 CFR parts 18 through 36. (e) This standard applies only to mines blasting... 30 Mineral Resources 1 2010-07-01 2010-07-01 false Blasting from the surface (V-A mines). 57.22605... Standards for Methane in Metal and Nonmetal Mines Explosives § 57.22605 Blasting from the surface (V-A...

  2. 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…

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

    Science.gov (United States)

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

    2016-04-01

    Ships' ballast water (BW) commonly moves macroorganisms and microorganisms across the world's oceans and along coasts; however, the majority of these microbial transfers have gone undetected. We applied high-throughput sequencing methods to identify microbial eukaryotes, specifically emphasizing the protistan parasites, in ships' BW collected from vessels calling to the Chesapeake Bay (Virginia and Maryland, USA) from European and Eastern Canadian ports. We utilized tagged-amplicon 454 pyrosequencing with two general primer sets, amplifying either the V4 or V9 domain of the small subunit (SSU) of the ribosomal RNA (rRNA) gene complex, from total DNA extracted from water samples collected from the ballast tanks of bulk cargo vessels. We detected a diverse group of protistan taxa, with some known to contain important parasites in marine systems, including Apicomplexa (unidentified apicomplexans, unidentified gregarines, Cryptosporidium spp.), Dinophyta (Blastodinium spp., Euduboscquella sp., unidentified syndinids, Karlodinium spp., Syndinium spp.), Perkinsea (Parvilucifera sp.), Opisthokonta (Ichthyosporea sp., Pseudoperkinsidae, unidentified ichthyosporeans), and Stramenopiles (Labyrinthulomycetes). Further characterization of groups with parasitic taxa, consisting of phylogenetic analyses for four taxa (Cryptosporidium spp., Parvilucifera spp., Labyrinthulomycetes, and Ichthyosporea), revealed that sequences were obtained from both known and novel lineages. This study demonstrates that high-throughput sequencing is a viable and sensitive method for detecting parasitic protists when present and transported in the ballast water of ships. These data also underscore the potential importance of human-aided dispersal in the biogeography of these microbes and emerging diseases in the world's oceans. PMID:26476551

  4. 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.

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

    Science.gov (United States)

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

    2016-08-01

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

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

    Science.gov (United States)

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

    2015-12-01

    Whole mitochondrial (mt) genome analysis enables a considerable increase in analysis throughput, and improves the discriminatory power to the maximum possible phylogenetic resolution. Most established protocols on the different massively parallel sequencing (MPS) platforms, however, invariably involve the PCR amplification of large fragments, typically several kilobases in size, which may fail due to mtDNA fragmentation in the available degraded materials. We introduce a MPS tiling approach for simultaneous whole human mt genome sequencing using 161 short overlapping amplicons (average 200 bp) with the Ion Torrent Personal Genome Machine. We illustrate the performance of this new method by sequencing 20 DNA samples belonging to different worldwide mtDNA haplogroups. Additional quality control, particularly regarding the potential detection of nuclear insertions of mtDNA (NUMTs), was performed by comparative MPS analysis using the conventional long-range amplification method. Preliminary sensitivity testing revealed that detailed haplogroup inference was feasible with 100 pg genomic input DNA. Complete mt genome coverage was achieved from DNA samples experimentally degraded down to genomic fragment sizes of about 220 bp, and up to 90% coverage from naturally degraded samples. Overall, we introduce a new approach for whole mt genome MPS analysis from degraded and nondegraded materials relevant to resolve and infer maternal genetic ancestry at complete resolution in anthropological, evolutionary, medical, and forensic applications. PMID:26387877

  7. 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.

  8. 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.

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

    Science.gov (United States)

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

    2016-03-01

    Mitochondrial DNA (mtDNA) analysis is regularly applied to forensic DNA samples with limited amounts of nuclear DNA (nDNA), such as hair shafts and bones. Generally, this mtDNA analysis involves examination of the hypervariable control region by Sanger sequencing of amplified products. When samples are severely degraded, small-sized amplicons can be applied and an earlier described mini-mtDNA method by Eichmann et al. [1] that accommodates ten mini amplicons in two multiplexes is found to be a very robust approach. However, in cases with large numbers of samples, like when searching for hairs with an mtDNA profile deviant from that of the victim, the method is time (and cost) consuming. Previously, Chemale et al. [2] described a SNaPshot™-based screening tool for a Brazilian population that uses standard-size amplicons for HVS-I and HVS-II. Here, we describe a similar tool adapted to the full control region and compatible with mini-mtDNA amplicons. Eighteen single nucleotide polymorphisms (SNPs) were selected based on their relative frequencies in a European population. They showed a high discriminatory power in a Dutch population (97.2%). The 18 SNPs are assessed in two SNaPshot™ multiplexes that pair to the two mini-mtDNA amplification multiplexes. Degenerate bases are included to limit allele dropout due to SNPs at primer binding site positions. Three SNPs provide haplogroup information. Reliability testing showed no differences with Sanger sequencing results. Since mini-mtSNaPshot screening uses only a small portion of the same PCR products used for Sanger sequencing, no additional DNA extract is consumed, which is forensically advantageous. PMID:26976467

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

    Science.gov (United States)

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

    2016-01-01

    Microbial diversity in geothermal waters of the Unkeshwar hot springs in Maharashtra, India, was studied using 16S rRNA amplicon metagenomic sequencing. Taxonomic analysis revealed the presence of Bacteroidetes, Proteobacteria, Cyanobacteria, Actinobacteria, Archeae, and OD1 phyla. Metabolic function prediction analysis indicated a battery of biological information systems indicating rich and novel microbial diversity, with potential biotechnological applications in this niche. PMID:26950332

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

    Science.gov (United States)

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

    2015-12-01

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

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

    Directory of Open Access Journals (Sweden)

    Jack Tsai, PhD

    2014-09-01

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

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

    Science.gov (United States)

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

    2015-01-01

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

  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. 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

  16. The Histone Variant H3.3 Is Enriched at Drosophila Amplicon Origins but Does Not Mark Them for Activation.

    Science.gov (United States)

    Paranjape, Neha P; Calvi, Brian R

    2016-01-01

    Eukaryotic DNA replication begins from multiple origins. The origin recognition complex (ORC) binds origin DNA and scaffolds assembly of a prereplicative complex (pre-RC), which is subsequently activated to initiate DNA replication. In multicellular eukaryotes, origins do not share a strict DNA consensus sequence, and their activity changes in concert with chromatin status during development, but mechanisms are ill-defined. Previous genome-wide analyses in Drosophila and other organisms have revealed a correlation between ORC binding sites and the histone variant H3.3. This correlation suggests that H3.3 may designate origin sites, but this idea has remained untested. To address this question, we examined the enrichment and function of H3.3 at the origins responsible for developmental gene amplification in the somatic follicle cells of the Drosophila ovary. We found that H3.3 is abundant at these amplicon origins. H3.3 levels remained high when replication initiation was blocked, indicating that H3.3 is abundant at the origins before activation of the pre-RC. H3.3 was also enriched at the origins during early oogenesis, raising the possibility that H3.3 bookmarks sites for later amplification. However, flies null mutant for both of the H3.3 genes in Drosophila did not have overt defects in developmental gene amplification or genomic replication, suggesting that H3.3 is not essential for the assembly or activation of the pre-RC at origins. Instead, our results imply that the correlation between H3.3 and ORC sites reflects other chromatin attributes that are important for origin function. PMID:27172191

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

    Science.gov (United States)

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

    2016-04-01

    Bacterial diversity in a seawater recirculating aquaculture system (RAS) was investigated using 16S rRNA amplicon sequencing to understand the roles of bacterial communities in the system. The RAS was operated at nine different combinations of temperature (15°C, 20°C, and 25°C) and salinity (20‰, 25‰, and 32.5‰). Samples were collected from five or six RAS tanks (biofilters) for each condition. Fifty samples were analyzed. Proteobacteria and Bacteroidetes were most common (sum of both phyla: 67.2% to 99.4%) and were inversely proportional to each other. Bacteria that were present at an average of ≥ 1% included Actinobacteria (2.9%) Planctomycetes (2.0%), Nitrospirae (1.5%), and Acidobacteria (1.0%); they were preferentially present in packed bed biofilters, mesh biofilters, and maturation biofilters. The three biofilters showed higher diversity than other RAS tanks (aerated biofilters, floating bed biofilters, and fish tanks) from phylum to operational taxonomic unit (OTU) level. Samples were clustered into several groups based on the bacterial communities. Major taxonomic groups related to family Rhodobacteraceae and Flavobacteriaceae were distributed widely in the samples. Several taxonomic groups like [Saprospiraceae], Cytophagaceae, Octadecabacter, and Marivita showed a cluster-oriented distribution. Phaeobacter and Sediminicola-related reads were detected frequently and abundantly at low temperature. Nitrifying bacteria were detected frequently and abundantly in the three biofilters. Phylogenetic analysis of the nitrifying bacteria showed several similar OTUs were observed widely through the biofilters. The diverse bacterial communities and the minor taxonomic groups, except for Proteobacteria and Bacteroidetes, seemed to play important roles and seemed necessary for nitrifying activity in the RAS, especially in packed bed biofilters, mesh biofilters, and maturation biofilters. PMID:27033205

  18. 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

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

    Science.gov (United States)

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

    1992-01-01

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

  20. 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

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

    OpenAIRE

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

    2015-01-01

    Myosin Va (MyoVa) is a processive molecular motor involved in intracellular cargo transport on the actin cytoskeleton. The motor’s processivity and ability to navigate actin intersections are believed to be governed by the stiffness of various parts of the motor’s structure. Specifically, changes in calcium may regulate motor processivity by altering the motor’s lever arm stiffness and thus its interhead communication. In order to measure the flexural stiffness of MyoVa subdomains, we use tet...

  2. Važnost oca za zdrav duhovni život

    OpenAIRE

    Szentmartoni, Mihály

    1999-01-01

    Rasprava o važnosti oca za djetetov psihički razvoj dobiva svoju aktualnost od sve nejasnije uloge oca u obiteljskom sustavu. U ovoj se studiji promatra važnost očeve prisutnosti u djetetovu životu uz opasku da iako je njegova uloga važna za formiranje djetetova identiteta, ipak nije njegov temelj. Takav iznijansirani pristup vrijedi i za razvoj religioznosti. Očeva slika ne utemeljuje sliku o Bogu, nego samo simbolizira, a razvoj religioznosti slijedi psihički proces diferencijacije i razluč...

  3. Melanophilin and myosin Va track the microtubule plus end on EB1

    OpenAIRE

    Wu, Xufeng S.; Tsan, Grace L.; Hammer, John A.

    2005-01-01

    In mouse melanocytes, myosin Va is recruited onto the surface of melanosomes by a receptor complex containing Rab27a that is present in the melanosome membrane and melanophilin (Mlp), which links myosin Va to Rab27a. In this study, we show that Mlp is also a microtubule plus end–tracking protein or +TIP. Moreover, myosin Va tracks the plus end in a Mlp-dependent manner. Data showing that overexpression and short inhibitory RNA knockdown of the +TIP EB1 have opposite effects on Mlp–microtubule...

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

    OpenAIRE

    Majetić, Filip

    2014-01-01

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

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

    DEFF Research Database (Denmark)

    Abdali, Salim; Jalkanen, Karl J.; Bohr, Henrik; Suhai, S.; Nieminen, R.M.

    2002-01-01

    Density functional theory (DFT) at the Becke 3LYP level has been used to calculate the vibrational absorption (VA) and vibrational circular dichroism (VCD) spectra of various deuterated species Of L-alanine. The effect of replacing the methine hydrogen, CH1, the methyl group, CH3, and both the...... changes in the VA and VCD spectra are used as a check of the Becke 3LYP hybrid model to successfully reproduce these fine features in the VA and VCD intensities. Furthermore, several aspects of the isotopomers and the isotope effects on vibrational spectra are discussed in the light of the approximation...

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

    OpenAIRE

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

    1984-01-01

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

  7. The Impact of Merger and Acquisition on Value at Risk (VaR): A Case Study of China Eastern Airline

    OpenAIRE

    Fung, Ka Wai Terence; Wan, Wilson

    2013-01-01

    This paper attempts to examine the impact of merger and acquisition on Value at Risk (VaR) of China Eastern Airline. The VaR is estimated for the whole sample and pre-merger periods by three methods: RiskMetrics , AR-GARCH and Generalized Extreme Value (GEV). The regression-based model reports the highest VaR followed by RiskMetrics and GEV. All models report a low VaR after the 11 June, 2009 merger, indicating a negative impact of merger and acquisition on VaR.

  8. ESTIMATING RISK ON THE CAPITAL MARKET WITH VaR METHOD

    Directory of Open Access Journals (Sweden)

    Sinisa Bogdan

    2015-06-01

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

  9. 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...... 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 ....

  10. 78 FR 34892 - Drawbridge Operation Regulation; Elizabeth River, Eastern Branch, Norfolk, VA

    Science.gov (United States)

    2013-06-11

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

  11. 77 FR 12647 - Fund Availability Under VA's Homeless Providers Grant and Per Diem Program

    Science.gov (United States)

    2012-03-01

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

  12. 38 CFR 17.96 - Medication prescribed by non-VA physicians.

    Science.gov (United States)

    2010-07-01

    ..., which is not part of authorized Department of Veterans Affairs hospital or outpatient care, for drugs... be filled by a Department of Veterans Affairs pharmacy or a non-VA pharmacy in a state home...

  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 the...

  14. Sexual Victimization, Health Status, and VA Healthcare Utilization Among Lesbian and Bisexual OEF/OIF Veterans

    OpenAIRE

    Mattocks, Kristin M.; Sadler, Anne; Yano, Elizabeth M.; Krebs, Erin E.; Zephyrin, Laurie; Brandt, Cynthia; Kimerling, Rachel; Sandfort, Theo; Dichter, Melissa E.; Weiss, Jeffrey J.; Allison, Jeroan; Haskell, Sally

    2013-01-01

    ABSTRACT Background Many lesbian and bisexual (LB) women veterans may have been targets of victimization in the military based on their gender and presumed sexual orientation, and yet little is known regarding the health or mental health of LB veterans, nor the degree to which they feel comfortable receiving care in the VA. Objective The purpose of this study was to examine the prevalence of mental health and gender-specific conditions, VA healthcare satisfaction and trauma exposure among LB ...

  15. Risikomessung mit VaR für Portfolios: Diskussion und empirischer Vergleich verschiedener Berechnungsmethoden

    OpenAIRE

    Böhmer, Ekkehart; Sperlich, Stefan

    1997-01-01

    In dieser Arbeit werden zwei Methoden zur Ermittlung der Eigenkapitalunterlegung von Risikopositionen und die Auswirkungen unterschiedlicher Verteilungsannahmen auf das Value-at-Risk (VaR) untersucht. Die empirischen Ergebnisse basieren auf zwei Beispielportfolios aus DAX-Aktien und einer Simulationsstudie. Wir zeigen, daß sich Verteilungen, die sich gut zur Beschreibung von Aktienrenditen eignen, nicht unbedingt zur Kalkulation des VaR für Portfolios verwendet werden sollten. Dieses Ergebnis...

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

    OpenAIRE

    Erzegovesi, Luca

    2002-01-01

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

  17. 30 CFR 57.22240 - Actions at 2.0 percent methane (V-A mines).

    Science.gov (United States)

    2010-07-01

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

  18. Evaluation of an Implementation Model: A National Investigation of VA Residential Programs

    OpenAIRE

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

    2015-01-01

    This national investigation utilizes qualitative data to evaluate an implementation model regarding factors influencing provider use of two evidence-based treatments for posttraumatic stress disorder (PTSD). Semi-structured qualitative interviews with 198 mental health providers from 38 Department of Veterans Affairs’ (VA) residential treatment programs were used to explore these issues regarding prolonged exposure (PE) and cognitive processing therapy (CPT) in VA residential PTSD programs. S...

  19. The VA's use of DICOM to integrate image data seamlessly into the online patient record.

    OpenAIRE

    Kuzmak, P. M.; Dayhoff, R. E.

    1999-01-01

    The US Department of Veterans Affairs (VA) is using the Digital Imaging and Communications in Medicine (DICOM) standard to integrate image data objects from multiple systems for use across the healthcare enterprise. DICOM uses a structured representation of image data and a communication mechanism that allows the VA to easily acquire radiology images and store them directly into the online patient record. Images can then be displayed on low-cost clinician's workstations throughout the medical...

  20. Exploring the Gastrointestinal “Nemabiome”: Deep Amplicon Sequencing to Quantify the Species Composition of Parasitic Nematode Communities

    Science.gov (United States)

    Avramenko, Russell W.; Redman, Elizabeth M.; Lewis, Roy; Yazwinski, Thomas A.; Wasmuth, James D.; Gilleard, John S.

    2015-01-01

    Parasitic helminth infections have a considerable impact on global human health as well as animal welfare and production. Although co-infection with multiple parasite species within a host is common, there is a dearth of tools with which to study the composition of these complex parasite communities. Helminth species vary in their pathogenicity, epidemiology and drug sensitivity and the interactions that occur between co-infecting species and their hosts are poorly understood. We describe the first application of deep amplicon sequencing to study parasitic nematode communities as well as introduce the concept of the gastro-intestinal “nemabiome”. The approach is analogous to 16S rDNA deep sequencing used to explore microbial communities, but utilizes the nematode ITS-2 rDNA locus instead. Gastro-intestinal parasites of cattle were used to develop the concept, as this host has many well-defined gastro-intestinal nematode species that commonly occur as complex co-infections. Further, the availability of pure mono-parasite populations from experimentally infected cattle allowed us to prepare mock parasite communities to determine, and correct for, species representation biases in the sequence data. We demonstrate that, once these biases have been corrected, accurate relative quantitation of gastro-intestinal parasitic nematode communities in cattle fecal samples can be achieved. We have validated the accuracy of the method applied to field-samples by comparing the results of detailed morphological examination of L3 larvae populations with those of the sequencing assay. The results illustrate the insights that can be gained into the species composition of parasite communities, using grazing cattle in the mid-west USA as an example. However, both the technical approach and the concept of the ‘nemabiome’ have a wide range of potential applications in human and veterinary medicine. These include investigations of host-parasite and parasite-parasite interactions

  1. 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.

  2. 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.

  3. 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/.

  4. Contribution of Amino Acid Region 659−663 of Factor Va Heavy Chain to the Activity of Factor Xa within Prothrombinase†,‡

    Science.gov (United States)

    2010-01-01

    Factor Va, the cofactor of prothrombinase, is composed of heavy and light chains associated noncovalently in the presence of divalent metal ions. The COOH-terminal region of the heavy chain contains acidic amino acid clusters that are important for cofactor activity. In this work, we have investigated the role of amino acid region 659−663, which contains five consecutive acidic amino acid residues, by site-directed mutagenesis. We have generated factor V molecules in which all residues were mutated to either lysine (factor V5K) or alanine (factor V5A). We have also constructed a mutant molecule with this region deleted (factor VΔ659−663). The recombinant molecules along with wild-type factor V (factor VWT) were transiently expressed in mammalian cells, purified, and assessed for cofactor activity. Two-stage clotting assays revealed that the mutant molecules had reduced clotting activities compared to that of factor VaWT. Kinetic analyses of prothrombinase assembled with the mutant molecules demonstrated diminished kcat values, while the affinity of all mutant molecules for factor Xa was similar to that for factor VaWT. Gel electrophoresis analyses of plasma-derived and recombinant mutant prothrombin activation demonstrated delayed cleavage of prothrombin at both Arg320 and Arg271 by prothrombinase assembled with the mutant molecules, resulting in meizothrombin lingering throughout the activation process. These results were confirmed after analysis of the cleavage of FPR-meizothrombin. Our findings provide new insights into the structural contribution of the acidic COOH-terminal region of factor Va heavy chain to factor Xa activity within prothrombinase and demonstrate that amino acid region 659−663 from the heavy chain of the cofactor contributes to the regulation of the rate of cleavage of prothrombin by prothrombinase. PMID:20722419

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

    Science.gov (United States)

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

    1992-01-01

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

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

    OpenAIRE

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

    2014-01-01

    Eighteen Kiko-cross meat goats (n=6) were used to collect gastrointestinal (GI) bacteria and methanogenic archaea for diversity measures when fed condensed tannin-containing pine bark (PB). Three dietary treatments were tested: control diet (0% PB and 30% wheat straw (WS); 0.17% condensed tannins (CT) dry matter (DM)); 15% PB and 15% WS (1.6% CT DM), and 30% PB and 0% WS (3.2% CT DM). A 16S rDNA bacterial tag-encoded FLX amplicon pyrosequencing technique was used to characterize and elucida...

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

    Directory of Open Access Journals (Sweden)

    Matthew T Harper

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

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

    International Nuclear Information System (INIS)

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

  9. 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

  10. 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.

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

    International Nuclear Information System (INIS)

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

  12. 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 …

  13. 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.

  14. Point KENO V.a: A continuous-energy Monte Carlo code for transport applications

    International Nuclear Information System (INIS)

    KENO V.a is a multigroup Monte Carlo code that solves the Boltzmann transport equation and is used extensively in the criticality safety community to calculate the effective multiplication factor of systems with fissionable material. In this work, a continuous-energy or pointwise version of KENO V.a has been developed by first designing a new continuous-energy cross-section format and then by developing the appropriate Monte Carlo transport procedures to sample the new cross-section format. In order to generate pointwise cross sections for a test library, a series of cross-section processing modules were developed and used to process 50 ENDF/B-VI Release 7 nuclides for the test library. Once the cross-section processing procedures were in place, a continuous-energy version of KENO V.a was developed and tested by calculating 46 test cases that include critical and calculational benchmark problems. The Point KENO-calculated results for the test problems are in agreement with calculated results obtained with the multigroup version of KENO V.a and MCNP4C. Based on the calculated results with the prototypic cross-section library, a continuous-energy version of the KENO V.a code has been successfully developed and demonstrated for modeling systems with fissionable material. (authors)

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

    International Nuclear Information System (INIS)

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

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

    OpenAIRE

    Christina Salmivalli; Elisa Poskiparta

    2012-01-01

    The effects of a Finnish national school-based antibullying program (KiVa) were evaluated in a randomized controlled trial (2007–2009) and during nationwide implementation (since 2009). The KiVa program is been found to reduce bullying and victimization and increase empathy towards victimized peers and self-efficacy to support and defend them. KiVa increases school liking and motivation and contributes to significant reductions in anxiety, depression, and negative peer perceptions. Somewhat l...

  17. Structure refinements of the layered intergrowth phases SbIIISbxVA1-xTiO6 (x ≅0, A=Ta, Nb) using synchrotron X-ray powder diffraction data

    International Nuclear Information System (INIS)

    The structures of the layered intergrowth phases SbIIISbxVA1-xTiO6 (x≅0, A = Ta, Nb) have been refined by the Rietveld method, using X-ray diffraction data obtained using a synchrotron source. The starting models for these structures were derived from those of Sb3IIISbxVA3-xTiO14 (x=1.26, A = Ta and x = 0.89, A = Nb), previously solved by single crystal X-ray diffraction. There were no significant differences between the derived models and the final structures, validating the approach used to obtain the models and confirming that the n = 1 and n = 3 members of the family SbnIIISbxVAn-xTiO4n+2 are part of a structurally homologous series. (orig.)

  18. Improvements in the vectorization of the KENO V.a criticality safety code

    International Nuclear Information System (INIS)

    A version of KENO V.a that takes advantage of the potential speedup inherent in vector processors is being developed at Oak Ridge National Laboratory (ORNL). The current version of KENO V.a tracks an individual particle history from source generation until it either leaks from the system or is killed, at which time the next particle history is processed. A vectorized Monte Carlo code tracks multiple particle histories simultaneously. Several new vectorized Monte Carlo particle-tracking codes have been developed, proving that significant speedups are possible, however, these new codes are either proprietary or not widely used. All new vectorized Monte Carlo Codes use an event-based algorithm in which all the particles undergoing a particular event are processed simultaneously. The vectorized version of KENO V.a currently being developed employs an event-based, event-driven, all-zone, tagged-particle algorithm

  19. 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.

  20. HS300指数收益波动性及VaR度量研究

    Institute of Scientific and Technical Information of China (English)

    姜全; 刘孟

    2008-01-01

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

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

    Institute of Scientific and Technical Information of China (English)

    肖智; 傅肖肖; 钟波

    2008-01-01

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

  2. 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.

  3. 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.

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

    Science.gov (United States)

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

    2015-10-01

    The aim of this paper was to evaluate physical stability of solid dispersions in respect to the drug, tadalafil (Td), in vinylpyrrolidone and vinyl acetate block copolymer (PVP-VA). Nine solid dispersions of Td in PVP-VA (Td/PVP-VA) varied in terms of quantitative composition (1:9-9:1, w/w) were successfully produced by spray-drying. Their amorphous nature, supersaturated character and molecular level of mixing (a solid solution structure) were subsequently confirmed using DSC, PXRD, SEM and calculation of Hansen total solubility parameters. Due to thermal degradation of both components before the melting point of Td (302.3°C), an approach based on the drug crystallization from the supersaturated solid dispersion was selected to calculate the solubility of Td in the polymer. Annealing of the Td/PVP-VA solid dispersion (1:1, w/w) at selected temperatures above its Tg resulted in different stable solid dispersions. According to the Gordon-Taylor equation their new Tgs gave the information about the quantitative composition which corresponded to the thermodynamic solubility of Td in PVP-VA at given temperatures of annealing. The obtained relationship was fitted to the exponential function, with the calculated solubility of Td of 20.5% at 25°C. This value was in accordance with the results of hot stage polarizing light microscopy as well as stability tests carried out at 80°C and 0% RH, in which Td solid dispersions containing 10-20% of the drug were the only systems that did not crystallize within two months. A thermal analysis protocol utilizing a fast heating rate was shown to generate Td solubility data complementing the solid dispersion method. The Flory-Huggins model applied for the Td/PVP-VA system yielded the solubility value of 0.1% at 25°C, showing the lack of applicability in this case. PMID:26247119

  5. 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. PMID:23659182

  6. Computation of VaR and CVaR using stochastic approximations and unconstrained importance sampling.

    OpenAIRE

    Bardou, Olivier; Frikha, Noufel; Pagès, G

    2009-01-01

    Value-at-Risk (VaR) and Conditional Value-at-Risk (CVaR) are two risk measures which are widely used in the practice of risk management. This paper deals with the problem of computing both VaR and CVaR using stochastic approximation (with decreasing steps): we propose a first Robbins-Monro procedure based on Rockaffelar-Uryasev's identity for the CVaR. The convergence rate of this algorithm to its target satisfies a Gaussian Central Limit Theorem. As a second step, in order to speed up the in...

  7. Two questions of L. Va${\\rm \\check{\\textbf{s}}}$ on *-clean rings

    OpenAIRE

    Chen, Jianlong; Cui, Jian

    2011-01-01

    A ring $R$ with an involution * is called (strongly) *-clean if every element of $R$ is the sum of a unit and a projection (that commute). All *-clean rings are clean. Va${\\rm \\check{s}}$ [L. Va${\\rm \\check{s}}$, *-Clean rings; some clean and almost clean Baer *-rings and von Neumann algebras, J. Algebra 324 (12) (2010) 3388-3400] asked whether there exists a *-ring that is clean but not *-clean and whether a unit regular and *-regular ring is strongly *-clean. In this paper, we answer both q...

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

    Science.gov (United States)

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

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

  9. KiVa Koulu -oppituntien vaikutus neljäsluokkalaisten vertaissuhteisiin koulussa

    OpenAIRE

    Kähönen, Loviisa

    2015-01-01

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

  10. Contribution of Amino Acid Region 334−335 from Factor Va Heavy Chain to the Catalytic Efficiency of Prothrombinase†

    Science.gov (United States)

    2008-01-01

    We have demonstrated that amino acids E323, Y324, E330, and V331 from the factor Va heavy chain are required for the interaction of the cofactor with factor Xa and optimum rates of prothrombin cleavage. We have also shown that amino acid region 332−336 contains residues that are important for cofactor function. Using overlapping peptides, we identified amino acids D334 and Y335 as contributors to cofactor activity. We constructed recombinant factor V molecules with the mutations D334 → K and Y335 → F (factor VKF) and D334 → A and Y335 → A (factor VAA). Kinetic studies showed that while factor VaKF and factor VaAA had a KD for factor Xa similar to the KD observed for wild-type factor Va (factor VaWT), the clotting activities of the mutant molecules were impaired and the kcat of prothrombinase assembled with factor VaKF and factor VaAA was reduced. The second-order rate constant of prothrombinase assembled with factor VaKF or factor VaAA for prothrombin activation was ∼10-fold lower than the second-order rate constant for the same reaction catalyzed by prothrombinase assembled with factor VaWT. We also created quadruple mutants combining mutations in the amino acid region 334–335 with mutations at the previously identified amino acids that are important for factor Xa binding (i.e., E323Y324 and E330V331). Prothrombinase assembled with the quadruple mutant molecules displayed a second-order rate constant up to 400-fold lower than the values obtained with prothrombinase assembled with factor VaWT. The data demonstrate that amino acid region 334–335 is required for the rearrangement of enzyme and substrate necessary for efficient catalysis of prothrombin by prothrombinase. PMID:18537263

  11. Cooperative Regulation of the Activity of Factor Xa within Prothrombinase by Discrete Amino Acid Regions from Factor Va Heavy Chain†

    Science.gov (United States)

    2008-01-01

    The prothrombinase complex catalyzes the activation of prothrombin to α-thrombin. We have repetitively shown that amino acid region 695DYDY698 from the COOH terminus of the heavy chain of factor Va regulates the rate of cleavage of prothrombin at Arg271 by prothrombinase. We have also recently demonstrated that amino acid region 334DY335 is required for the optimal activity of prothrombinase. To assess the effect of these six amino acid residues on cofactor activity, we created recombinant factor Va molecules combining mutations at amino acid regions 334–335 and 695−698 as follows: factor V3K (334DY335 → KF and 695DYDY698 → KFKF), factor VKF/4A (334DY335 → KF and 695DYDY698 → AAAA), and factor V6A (334DY335 → AA and 695DYDY698 → AAAA). The recombinant factor V molecules were expressed and purified to homogeneity. Factor Va3K, factor VaK4/4A, and factor Va6A had reduced affinity for factor Xa, when compared to the affinity of the wild-type molecule (factor VaWt) for the enzyme. Prothrombinase assembled with saturating concentrations of factor Va3K had a 6-fold reduced second-order rate constant for prothrombin activation compared to the value obtained with prothrombinase assembled with factor VaWt, while prothrombinase assembled with saturating concentrations of factor VaKF/4A and factor Va6A had approximately 1.5-fold reduced second-order rate constants. Overall, the data demonstrate that amino acid region 334–335 together with amino acid region 695−698 from factor Va heavy chain are part of a cooperative mechanism within prothrombinase regulating cleavage and activation of prothrombin by factor Xa. PMID:18991406

  12. 75 FR 24510 - Drug and Drug-Related Supply Promotion by Pharmaceutical Company Sales Representatives at VA...

    Science.gov (United States)

    2010-05-05

    ... control the promotion of drugs and drug-related supplies at VA facilities and the business relationships... standard of permissible business practice at VA facilities. It would also facilitate mutually beneficial... terms to be inclusive of all items typically promoted by pharmaceutical sales representatives....

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

    Science.gov (United States)

    2010-06-07

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

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

    Science.gov (United States)

    2010-08-19

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

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

    Science.gov (United States)

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

    2016-09-01

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

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

    Science.gov (United States)

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

    2015-11-01

    Next generation sequencing (NGS) platforms are replacing traditional molecular biology protocols like cloning and Sanger sequencing. However, accuracy of NGS platforms has rarely been measured when quantifying relative frequencies of genotypes or taxa within populations. Here we developed a new bioinformatic pipeline (QRS) that pools similar sequence variants and estimates their frequencies in NGS data sets from populations or communities. We tested whether the estimated frequency of representative sequences, generated by 454 amplicon sequencing, differs significantly from that obtained by Sanger sequencing of cloned PCR products. This was performed by analysing sequence variation of the highly variable first internal transcribed spacer (ITS1) of the ichthyosporean Caullerya mesnili, a microparasite of cladocerans of the genus Daphnia. This analysis also serves as a case example of the usage of this pipeline to study within-population variation. Additionally, a public Illumina data set was used to validate the pipeline on community-level data. Overall, there was a good correspondence in absolute frequencies of C. mesnili ITS1 sequences obtained from Sanger and 454 platforms. Furthermore, analyses of molecular variance (amova) revealed that population structure of C. mesnili differs across lakes and years independently of the sequencing platform. Our results support not only the usefulness of amplicon sequencing data for studies of within-population structure but also the successful application of the QRS pipeline on Illumina-generated data. The QRS pipeline is freely available together with its documentation under GNU Public Licence version 3 at http://code.google.com/p/quantification-representative-sequences. PMID:25728529

  17. 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.

  18. 78 FR 56271 - FY 2014-2020 Draft VA Strategic Plan

    Science.gov (United States)

    2013-09-12

    ...; enhancing the quality of and access to benefits and services through integration within VA and with our... focus from improvements within a service or benefit delivery program to coordination and integration... defining success by Veterans' outcomes; enhancing the quality of and access to benefits and...

  19. 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

  20. 38 CFR 1.218 - Security and law enforcement at VA facilities.

    Science.gov (United States)

    2010-07-01

    ... not reside in quarters on the property, is prohibited. Acts of prostitution or solicitation for acts of prostitution on VA property is prohibited. For the purposes of this paragraph, an act of prostitution is defined as the performance or the offer or agreement to perform any sexual act for money...

  1. 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...

  2. 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:...

  3. 77 FR 33089 - OPSAIL 2012 Virginia, Port of Hampton Roads, VA

    Science.gov (United States)

    2012-06-05

    ... Acronyms DHS Department of Homeland Security FR Federal Register NPRM Notice of Proposed Rulemaking A...) entitled ``OPSAIL 2012 Virginia, Port of Hampton Roads, VA'' in the Federal Register (77 FR 19957). We... events. Vessel operators should expect significant congestion along the OPSAIL parade route and...

  4. 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

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

    Science.gov (United States)

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

    2014-12-01

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

  6. 75 FR 61417 - South River Watershed Dam No. 10A, Augusta County, VA

    Science.gov (United States)

    2010-10-05

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

  7. Nederogovatelná lidská práva a terorismus

    Czech Academy of Sciences Publication Activity Database

    Balaš, Vladimír

    Praha: Vysoká škola aplikovaného práva, s.r.o, 2008 - (Blahož, J.), s. 135-147 ISBN 978-80-86775-20-3 R&D Projects: GA AV ČR IAA700680702 Institutional research plan: CEZ:AV0Z70680506 Keywords : human rights * terrorism Subject RIV: AG - Legal Sciences

  8. 77 FR 6587 - Startek USA, Inc. Alexandria, LA; Startek USA, Inc., Collinsville, VA; Amended Certification...

    Science.gov (United States)

    2012-02-08

    ... published in the Federal Register on February 10, 2011 (76 FR 7587). On its own motion, the Department... Employment and Training Administration Startek USA, Inc. Alexandria, LA; Startek USA, Inc., Collinsville, VA..., applicable to workers of StarTek USA, Inc., Alexandria, Louisiana. The workers are engaged in the supply...

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

    International Nuclear Information System (INIS)

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

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

    Science.gov (United States)

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

    2012-01-01

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

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

    DEFF Research Database (Denmark)

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

    2013-01-01

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

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

    Science.gov (United States)

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

    2016-01-01

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

  13. 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).

  14. 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).

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

    Science.gov (United States)

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

    2012-01-01

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

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

    Science.gov (United States)

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

    2011-01-01

    This study demonstrates the effectiveness of the KiVa antibullying program using a large sample of 8,237 youth from Grades 4-6 (10-12 years). Altogether, 78 schools were randomly assigned to intervention (39 schools, 4,207 students) and control conditions (39 schools, 4,030 students). Multilevel regression analyses revealed that after 9 months of…

  17. 76 FR 64236 - Establishment of Class E Airspace; New Market, VA

    Science.gov (United States)

    2011-10-18

    ... establish Class E airspace at New Market, VA (76 FR 44288). Interested parties were invited to participate... ``significant rule'' under DOT Regulatory Policies and Procedures (44 FR 11034; February 26, 1979); and (3) does... continues to read as follows: Authority: 49 U.S.C. 106(g); 40103, 40113, 40120; E.O. 10854, 24 FR 9565,...

  18. 76 FR 44288 - Establishment of Class E Airspace; New Market, VA

    Science.gov (United States)

    2011-07-25

    ...; (2) is not a ``significant rule'' under DOT Regulatory Policies and Procedures (44 FR 11034; February...: Authority: 49 U.S.C. 106(g); 40103, 40113, 40120; E.O. 10854, 24 FR 9565, 3 CFR, 1959-1963 Comp., p. 389... Federal Aviation Administration 14 CFR Part 71 Establishment of Class E Airspace; New Market, VA...

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

    Directory of Open Access Journals (Sweden)

    Kuznetsov Oleg Viktorovich

    2013-11-01

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

  20. 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.

  1. 3D digitalizacija in vizualizacija situle z Vač: 3D digitisation and visualisation of the Vače situla:

    OpenAIRE

    Vidmar, Gregor

    2012-01-01

    The project of 3D digitisation and visualisation of the Vače situla was implemented at the beginning of 2011 in cooperation with the National Museum of Slovenia where the situla is kept and the company MFC.2 which, among other services, develops and implements 3D digitisation and visualisation projects. The purpose of the project was to digitise and visualise a famous and precious piece of cultural heritage and to 1. show what modern 3D shape and texture scanning technologies allow us to do, ...

  2. 76 FR 44087 - Agency Information Collection (Supplement to VA Forms 21-526, 21-534, and 21-535 (For Philippine...

    Science.gov (United States)

    2011-07-22

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

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

    Institute of Scientific and Technical Information of China (English)

    肖智; 傅肖肖; 钟波

    2008-01-01

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

  4. 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.

  5. Multivariate modelling of 10-day-ahead VaR and dynamic correlation for worldwide real estate and stock indices

    OpenAIRE

    Stavros Degiannakis; Apostolos Kiohos

    2014-01-01

    Purpose – The Basel Committee regulations require the estimation of value-at-risk (VaR) at 99 percent confidence level for a ten-trading-day-ahead forecasting horizon. The paper provides a multivariate modelling framework for multi-period VaR estimates for leptokurtic and asymmetrically distributed real estate portfolio returns. The purpose of the paper is to estimate accurate ten-day-ahead 99%VaR forecasts for real estate markets along with stock markets for seven countries across the world ...

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

    OpenAIRE

    Bridget M. Smith, PhD; Charlesnika T. Evans, MPH, PhD; Philip Ullrich, PhD; Stephen Burns, MD; Marylou Guihan, PhD; Scott Miskevics, MS; Sherri L. LaVela, PhD, MPH, MBA; Suparna Rajan, PhD; Frances M. Weaver, PhD

    2010-01-01

    The Department of Veterans Affairs (VA) provides integrated services to more than 25,000 veterans with spinal cord injuries and disorders (SCI/D). VA data offer great potential for providing insights into healthcare utilization and morbidity, and these capabilities are central to efforts to improve healthcare for veterans with SCI/D. The objective of this article is to introduce researchers to the use of VA data to examine questions related to SCI/D using examples from Spinal Cord Injury (SCI...

  7. Važnost modernoga katastra u zaštiti okoliša

    OpenAIRE

    Blagonić, Boris; Prosen, Anton

    2007-01-01

    U radu je obrađena uloga katastra u zaštiti okoliša, te naglašena važnost modernizacije katastarskih sustava radi učinkovitije zaštite okoliša. Dan je pregled bitnih međunarodnih konvencija i instrumenata zemljišne politike u svrhu zaštite okoliša. Posebno je naglašena važnost katastarske infrastrukture pri evidentiranju i registraciji prirodnih dobara kao što su vode, šume i druga prirodna područja. Na kraju se navode prostorne baze podataka relevantne za zaštitu čovjekova okoliša, koje su p...

  8. Multichannel spectroscopy system based on VA2TA front-end self-triggered chip

    International Nuclear Information System (INIS)

    An experimental prototype of a spectroscopy system that is based on 128-channel self-triggered VA2TA chip has been created. Software which allows registering and analyzing events in a multistrip silicon sensor has been developed. Main parameters of the measurement are defined in a program window and they control how the information from the connected channels is being processed. Low noise silicon planar and multistrip sensors have been bonded to the VA2TA chip and the energy resolution of the system has been tested. Spectra from 241Am, 57Co and characteristic X-ray radiation have been measured to test the energy resolution which was approximately 3.6...3.9 keV for a planar sensor for the energies in a range of 26...122 keV

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

    International Nuclear Information System (INIS)

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

  10. A single phase model 9 kVA high-temperature superconducting power transformer

    International Nuclear Information System (INIS)

    A model 9 kVA (240 V/9.6 V) single-phase HTS transformer has been developed and tested with and without a cold iron core at 77 K. The primary and secondary windings were wound by transposed conductors, which are made from stainless steel-reinforced multifilamentary Bi2223/Ag tapes. The structures of the primary and secondary windings are helical and double-pancake, respectively. Primarily characteristics of the transformer are obtained through no-load tests, and short circuit tests. The iron cores are made of the common laminated Fe-Si steel plates and operate at nitrogen temperature 77 K. Based on the results of this transformer, we will develop a 630 kVA HTS transformer with the same rating currents in the near future

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2006-05-15

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

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

    Science.gov (United States)

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

    2015-03-01

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

  13. Oncogenic Role of miR-15a-3p in 13q Amplicon-Driven Colorectal Adenoma-to-Carcinoma Progression.

    Science.gov (United States)

    de Groen, Florence L M; Timmer, Lisette M; Menezes, Renee X; Diosdado, Begona; Hooijberg, Erik; Meijer, Gerrit A; Steenbergen, Renske D M; Carvalho, Beatriz

    2015-01-01

    Progression from colorectal adenoma to carcinoma is strongly associated with an accumulation of genomic alterations, including gain of chromosome 13. This gain affects the whole q arm and is present in 40%-60% of all colorectal cancers (CRCs). Several genes located at this amplicon are known to be overexpressed in carcinomas due to copy number dosage. A subset of these genes, including the mir-17~92 cluster, are functionally involved in CRC development. The present study set out to explore whether apart from mir-17~92, other miRNAs located at the 13q amplicon show a copy number dependent dosage effect that may contribute to 13q-driven colorectal adenoma-to-carcinoma progression. Integration of publically available miRNA expression, target mRNA expression and DNA copy number data from 125 CRCs yielded three miRNAs, miR-15a, -17, and -20a, of which high expression levels were significantly correlated with a 13q gain and which influenced target mRNA expression. These results could be confirmed by qRT-PCR in a series of 100 colon adenomas and carcinomas.Functional analysis of both mature miRNAs encoded by mir-15a, i.e. miR-15a-5p and miR-15a-3p, showed that silencing of miR-15a-3p significantly inhibited viability of CRC cells. Integration of miR-15a expression levels with mRNA expression data of predicted target genes identified mitochondrial uncoupling protein 2 (UCP2) and COP9 signalosome subunit 2 (COPS2) as candidates with significantly decreased expression in CRCs with 13q gain. Upon silencing of miR-15a-3p, mRNA expression of both genes increased in CRC cells, supporting miR-15a-3p mediated regulation of UPC2 and COPS2 expression. In conclusion, significant overexpression of miR-15a-3p due to gain of 13q is functionally relevant in CRC, with UCP2 and COPS2 as candidate target genes. Taken together our findings suggest that miR-15a-3p may contribute to adenoma-to-carcinoma progression. PMID:26148070

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

    International Nuclear Information System (INIS)

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

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

    Institute of Scientific and Technical Information of China (English)

    WANG Chun-feng; LI Gang

    2001-01-01

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

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

    OpenAIRE

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

    2015-01-01

    Extraretinal photoreceptors located within the medio-basal hypothalamus regulate the photoperiodic control of seasonal reproduction in birds. An action spectrum for this response describes an opsin photopigment with a λmax of ∼492nm. Beyond this however, the specific identity of the photopigment remains unresolved. Several candidates have emerged including rod-opsin; melanopsin (OPN4); neuropsin (OPN5); and vertebrate ancient (VA) opsin. These contenders are evaluated against key criteria use...

  17. Landslide Hazard Zonation in Ardal County (CHaharmahal va Bakhtiari Province, Iran) Using Analytical Hierarchy Process (AHP)

    OpenAIRE

    H. Basiri Dehkordi; M Naderi Khorasgani; J.Mohammadi

    2014-01-01

    Landslide as a global disaster causes great human and financial damages. Identification of landslide causes and zonation assist in instability control and construction projects siting. This study aimed to identify landslide causes and instability zonation in Ardal county, Chaharmahal va Bakhtiari province, Iran, using Analytical Hierarchy Process (AHP). Current landslides were delineated through field survey and interpretation of Earth Google images and geologic maps. By using Digital Elevati...

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

    International Nuclear Information System (INIS)

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

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

    NARCIS (Netherlands)

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

    2000-01-01

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

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

    OpenAIRE

    Zikovic, Sasa; Filer, Randall

    2012-01-01

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

  1. Health care informatics research implementation of the VA-DHCP Spanish version for Latin America.

    Science.gov (United States)

    Samper, R.; Marin, C. J.; Ospina, J. A.; Varela, C. A.

    1992-01-01

    The VA DHCP, hospital computer program represents an integral solution to the complex clinical and administrative functions of any hospital world wide. Developed by the Department of Veterans Administration, it has until lately run exclusively in mainframe platforms. The recent implementation in PCs opens the opportunity for use in Latinamerica. Detailed description of the strategy for Spanish, local implementation in Colombia is made. PMID:1482994

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

    Science.gov (United States)

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

    2013-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2000-06-01

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

  4. Fundamental risk analysis and VaR forecasts of the Nord Pool system price

    OpenAIRE

    Lundby, Martin; Uppheim, Kristoffer

    2011-01-01

    This paper compares the Value at Risk (VaR) forecasting performance of different quantile regression models to conventional GARCH specifications on the Nord Pool system price. The sample covers hourly data from 2005-2011. In order to identify significant explanatory variables, we use a linear quantile regression to characterize the effects of fundamental factors on the system price formations. From our analysis we are able to show how the sensitivity of the variables change over the range of ...

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

    Directory of Open Access Journals (Sweden)

    Konstantinos Pelechrinis

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

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

    Science.gov (United States)

    Pelechrinis, Konstantinos; Wei, Dong

    2016-01-01

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

  7. 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.

  8. Jan Křtitel Vaňhal and the Bohemian and Moravian collections of Brothers Hospitallers

    Czech Academy of Sciences Publication Activity Database

    Freemanová, Michaela

    2014-01-01

    Roč. 25, - (2014), s. 159-168. ISSN 1848-7890 Institutional support: RVO:68378076 Keywords : Jan Křtitel Vaňhal * music collections * Brothers Hospitallers Subject RIV: AL - Art, Architecture, Cultural Heritage

  9. Allele discovery of ten candidate drought-response genes in Austrian oak using a systematically informatics approach based on 454 amplicon sequencing

    Directory of Open Access Journals (Sweden)

    Homolka Andreas

    2012-04-01

    Full Text Available Abstract Background Rise of temperatures and shortening of available water as result of predicted climate change will impose significant pressure on long-lived forest tree species. Discovering allelic variation present in drought related genes of two Austrian oak species can be the key to understand mechanisms of natural selection and provide forestry with key tools to cope with future challenges. Results In the present study we have used Roche 454 sequencing and developed a bioinformatic pipeline to process multiplexed tagged amplicons in order to identify single nucleotide polymorphisms and allelic sequences of ten candidate genes related to drought/osmotic stress from sessile oak (Quercus robur and sessile oak (Q. petraea individuals. Out of these, eight genes of 336 oak individuals growing in Austria have been detected with a total number of 158 polymorphic sites. Allele numbers ranged from ten to 52 with observed heterozygosity ranging from 0.115 to 0.640. All loci deviated from Hardy-Weinberg equilibrium and linkage disequilibrium was found among six combinations of loci. Conclusions We have characterized 183 alleles of drought related genes from oak species and detected first evidences of natural selection. Beside the potential for marker development, we have created an expandable bioinformatic pipeline for the analysis of next generation sequencing data.

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

    Directory of Open Access Journals (Sweden)

    Eng Wee eChua

    2016-01-01

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

  11. Cross-Comparison of Exome Analysis, Next-Generation Sequencing of Amplicons, and the iPLEX® ADME PGx Panel for Pharmacogenomic Profiling

    Science.gov (United States)

    Chua, Eng Wee; Cree, Simone L.; Ton, Kim N. T.; Lehnert, Klaus; Shepherd, Phillip; Helsby, Nuala; Kennedy, Martin A.

    2016-01-01

    Whole-exome sequencing (WES) has been widely used for analysis of human genetic diseases, but its value for the pharmacogenomic profiling of individuals is not well studied. Initially, we performed an in-depth evaluation of the accuracy of WES variant calling in the pharmacogenes CYP2D6 and CYP2C19 by comparison with MiSeq® amplicon sequencing data (n = 36). This analysis revealed that the concordance rate between WES and MiSeq® was high, achieving 99.60% for variants that were called without exceeding the truth-sensitivity threshold (99%), defined during variant quality score recalibration (VQSR). Beyond this threshold, the proportion of discordant calls increased markedly. Subsequently, we expanded our findings beyond CYP2D6 and CYP2C19 to include more genes genotyped by the iPLEX® ADME PGx Panel in the subset of twelve samples. WES performed well, agreeing with the genotyping panel in approximately 99% of the selected pass-filter variant calls. Overall, our results have demonstrated WES to be a promising approach for pharmacogenomic profiling, with an estimated error rate of lower than 1%. Quality filters, particularly VQSR, are important for reducing the number of false variants. Future studies may benefit from examining the role of WES in the clinical setting for guiding drug therapy. PMID:26858644

  12. Cross-Comparison of Exome Analysis, Next-Generation Sequencing of Amplicons, and the iPLEX(®) ADME PGx Panel for Pharmacogenomic Profiling.

    Science.gov (United States)

    Chua, Eng Wee; Cree, Simone L; Ton, Kim N T; Lehnert, Klaus; Shepherd, Phillip; Helsby, Nuala; Kennedy, Martin A

    2016-01-01

    Whole-exome sequencing (WES) has been widely used for analysis of human genetic diseases, but its value for the pharmacogenomic profiling of individuals is not well studied. Initially, we performed an in-depth evaluation of the accuracy of WES variant calling in the pharmacogenes CYP2D6 and CYP2C19 by comparison with MiSeq(®) amplicon sequencing data (n = 36). This analysis revealed that the concordance rate between WES and MiSeq(®) was high, achieving 99.60% for variants that were called without exceeding the truth-sensitivity threshold (99%), defined during variant quality score recalibration (VQSR). Beyond this threshold, the proportion of discordant calls increased markedly. Subsequently, we expanded our findings beyond CYP2D6 and CYP2C19 to include more genes genotyped by the iPLEX(®) ADME PGx Panel in the subset of twelve samples. WES performed well, agreeing with the genotyping panel in approximately 99% of the selected pass-filter variant calls. Overall, our results have demonstrated WES to be a promising approach for pharmacogenomic profiling, with an estimated error rate of lower than 1%. Quality filters, particularly VQSR, are important for reducing the number of false variants. Future studies may benefit from examining the role of WES in the clinical setting for guiding drug therapy. PMID:26858644

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

    Science.gov (United States)

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

    2016-01-30

    Next-generation sequencing (NGS) has the capacity to screen a single DNA sample and detect pathogen DNA from thousands of host DNA sequence reads, making it a versatile and informative tool for investigation of pathogens in diseased animals. The technique is effective and labor saving in the initial identification of pathogens, and will complement conventional diagnostic tests to associate the candidate pathogen with a disease process. In this report, we investigated the utility of the diversity profiling NGS approach using Illumina small subunit ribosomal RNA (18S rRNA) gene amplicon deep sequencing to detect Toxoplasma gondii in previously confirmed cases of toxoplasmosis. We then tested the diagnostic approach with species-specific PCR genotyping, histopathology and immunohistochemistry of toxoplasmosis in a Risso's dolphin (Grampus griseus) to systematically characterise the disease and associate causality. We show that the Euk7A/Euk570R primer set targeting the V1-V3 hypervariable region of the 18S rRNA gene can be used as a species-specific assay for cyst-forming coccidia and discriminate T. gondii. Overall, the approach is cost-effective and improves diagnostic decision support by narrowing the differential diagnosis list with more certainty than was previously possible. Furthermore, it supplements the limitations of cryptic protozoan morphology and surpasses the need for species-specific PCR primer combinations. PMID:26801593

  14. Volatility Derivatives

    OpenAIRE

    Peter Carr; Roger Lee

    2009-01-01

    Volatility derivatives are a class of derivative securities where the payoff explicitly depends on some measure of the volatility of an underlying asset. Prominent examples of these derivatives include variance swaps and VIX futures and options. We provide an overview of the current market for these derivatives. We also survey the early literature on the subject. Finally, we provide relatively simple proofs of some fundamental results related to variance swaps and volatility swaps.

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

    OpenAIRE

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

    2008-01-01

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

  16. Persistence of an intact endometrial matrix and vessels structure in women exposed to VA-2914, a selective progesterone receptor modulator.

    OpenAIRE

    Ravet, Stéphanie; Munaut, Carine; Blacher, Silvia; Brichant, Géraldine; Labied, Soraya; Beliard, Aude; Chabbert-Buffet, N.; Bouchard, P.; Foidart, Jean-Michel; PINTIAUX, Axelle

    2008-01-01

    Background: VA-2914 is a selective progesterone receptor modulator with potential contraceptive activity that induces amenorrhea, whereas progestins cause endometrial spotting and bleeding. This abnormal bleeding due to progestins is a consequence of focal stromal proteolysis by an increase in naked vessel size and density. Objective: Our objective was to quantify the effects of VA-2914 on endometrial vascularization, fibrillar matrix, and vascular endothelial growth factor (VEGF)-A expr...

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

    OpenAIRE

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

    2010-01-01

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

  18. 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...

  19. 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.

  20. A randomized trial of the cost effectiveness of VA hospital-based home care for the terminally ill.

    OpenAIRE

    Hughes, S. L.; Cummings, J.; Weaver, F; Manheim, L; Braun, B.; Conrad, K

    1992-01-01

    All admissions to a 1,100-bed Department of Veterans Affairs (VA) hospital were screened to identify 171 terminally ill patients with informal caregivers who were then randomly assigned to VA hospital-based team home care (HBHC, N = 85) or customary care (N = 86). Patient functioning, and patient and caregiver morale and satisfaction with care were measured at baseline, one month, and six months. Health services utilization was monitored over the six-month study period and converted to cost. ...

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

    Directory of Open Access Journals (Sweden)

    Bridget M. Smith, PhD

    2010-10-01

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

  2. Analytical derivation of traffic patterns in cache-coherent shared-memory systems

    DEFF Research Database (Denmark)

    Stuart, Matthias Bo; Sparsø, Jens

    2011-01-01

    This paper presents an analytical method to derive the worst-case traffic pattern caused by a task graph mapped to a cache-coherent shared-memory system. Our analysis allows designers to rapidly evaluate the impact of different mappings of tasks to IP cores on the traffic pattern. The accuracy va...

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

    Science.gov (United States)

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

    2016-02-01

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

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

    Science.gov (United States)

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

    2016-08-01

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

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

    Science.gov (United States)

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

    2016-01-01

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

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

    International Nuclear Information System (INIS)

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

  7. 3D Digitisation and Visualisation of the Vače Situla

    OpenAIRE

    Gregor Vidmar

    2013-01-01

    EXTENDED ABSTRACT:The project of 3D digitisation and visualisation of the Vače situla was implemented at the beginning of 2011 in cooperation with the National Museum of Slovenia where the situla is kept and the company MFC.2 which, among other services, develops and implements 3 D digitisation and visualisation projects. The purpose of the project was to digitise and visualise a famous and precious piece of cultural heritage and to  1. show what modern 3D shape and texture scanning technolog...

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

    OpenAIRE

    Shirokova Natalya Olegovna

    2012-01-01

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

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

    International Nuclear Information System (INIS)

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

  10. 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...

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

    International Nuclear Information System (INIS)

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

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

    OpenAIRE

    Londino, Noémie; Zittoun, Tania; Gilomen, Heinz

    2012-01-01

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

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

    OpenAIRE

    Dabo, Krešimir

    2012-01-01

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

  14. SiO Masers around WX Psc Mapped with the KVN and VERA Array (KaVA)

    Science.gov (United States)

    Yun, Youngjoo; Cho, Se-Hyung; Imai, Hiroshi; Kim, Jaeheon; Asaki, Yoshiharu; Chibueze, James O.; Choi, Yoon Kyung; Dodson, Richard; Kim, Dong-Jin; Kusuno, Kozue; Matsumoto, Naoko; Min, Cheulhong; Oyadomari, Miyako; Rioja, María J.; Yoon, Dong-Hwan; Byun, Do-Young; Chung, Hyunsoo; Chung, Moon-Hee; Hagiwara, Yoshiaki; Han, Myoung-Hee; Han, Seog-Tae; Hirota, Tomoya; Honma, Mareki; Hwang, Jung-Wook; Je, Do-Heung; Jike, Takaaki; Jung, Dong-Kyu; Jung, Taehyun; Kang, Ji-Hyun; Kang, Jiman; Kang, Yong-Woo; Kan-ya, Yukitoshi; Kanaguchi, Masahiro; Kawaguchi, Noriyuki; Kim, Bong Gyu; Ryoung Kim, Hyo; Kim, Hyun-Goo; Kim, Jongsoo; Kim, Kee-Tae; Kim, Mikyoung; Kobayashi, Hideyuki; Kono, Yusuke; Kurayama, Tomoharu; Lee, Changhoon; Lee, Jeewon; Lee, Jeong Ae; Lee, Jung-Won; Lee, Sang Hyun; Lee, Sang-Sung; Lyo, A.-Ran; Minh, Young Chol; Oh, Chungsik; Oh, Se-Jin; Oyama, Tomoaki; Roh, Duk-Gyoo; Sawada-Satoh, Satoko; Shibata, Katsunori M.; Sohn, Bong Won; Song, Min-Gyu; Tamura, Yoshiaki; Wi, Seog-Oh; Yeom, Jae-Hwan

    2016-05-01

    We present the first images of the v = 1 and v = 2 J = 1 → 0 SiO maser lines taken with KaVA, i.e., the combined array of the Korean Very Long Baseline Interferometry (VLBI) Network and the VLBI Exploration of Radio Astrometry (VERA), toward the OH/IR star WX Psc. The combination of long and short antenna baselines enabled us to detect a large number of maser spots, which exhibit a typical ring-like structure in both the v = 1 and v = 2 J = 1 → 0 SiO masers as those that have been found in previous VLBI observational results of WX Psc. The relative alignment of the v = 1 and v = 2 SiO maser spots are precisely derived from astrometric analysis, due to the absolute coordinates of the reference maser spot that were well determined in an independent astrometric observation with VERA. The superposition of the v = 1 and v = 2 maser spot maps shows a good spatial correlation between the v = 1 and v = 2 SiO maser features. Nevertheless, it is also shown that the v = 2 SiO maser spot is distributed in an inner region compared to the v = 1 SiO maser by about 0.5 mas on average. These results provide good support for the recent theoretical studies of the SiO maser pumping, in which both the collisional and the radiative pumping predict the strong spatial correlation and the small spatial discrepancy between the v = 1 and v = 2 SiO maser.

  15. Financial Derivatives

    DEFF Research Database (Denmark)

    Wigan, Duncan

    2013-01-01

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

  16. VLBI observations of bright AGN jets with KVN and VERA Array (KaVA): Evaluation of Imaging Capability

    CERN Document Server

    Niinuma, Kotaro; Kino, Motoki; Sohn, Bong Won; Akiyama, Kazunori; Zhao, Guang-Yao; Sawada-Satoh, Satoko; Trippe, Sascha; Hada, Kazuhiro; Jung, Taehyun; Hagiwara, Yoshiaki; Dodson, Richard; Koyama, Shoko; Honma, Mareki; Nagai, Hiroshi; Chung, Aeree; Doi, Akihiro; Fujisawa, Kenta; Han, Myoung-Hee; Kim, Joeng-Sook; Lee, Jeewon; Lee, Jeong Ae; Miyazaki, Atsushi; Oyama, Tomoaki; Sorai, Kazuo; Wajima, Kiyoaki; Bae, Jaehan; Byun, Do-Young; Cho, Se-Hyung; Choi, Yoon Kyung; Chung, Hyunsoo; Chung, Moon-Hee; Han, Seog-Tae; Hirota, Tomoya; Hwang, Jung-Wook; Je, Do-Heung; Jike, Takaaki; Jung, Dong-Kyu; Jung, Jin-Seung; Kang, Ji-Hyun; Kang, Jiman; Kang, Yong-Woo; Kan-ya, Yukitoshi; Kanaguchi, Masahiro; Kawaguchi, Noriyuki; Kim, Bong Gyu; Kim, Hyo Ryoung; Kim, Hyun-Goo; Kim, Jaeheon; Kim, Jongsoo; Kim, Kee-Tae; Kim, Mikyoung; Kobayashi, Hideyuki; Kono, Yusuke; Kurayama, Tomoharu; Lee, Changhoon; Lee, Jung-Won; Lee, Sang Hyun; Minh, Young Chol; Matsumoto, Naoko; Nakagawa, Akiharu; Oh, Chung Sik; Oh, Se-Jin; Park, Sun-Youp; Roh, Duk-Gyoo; Sasao, Tetsuo; Shibata, Katsunori M; Song, Min-Gyu; Tamura, Yoshiaki; Wi, Seog-Oh; Yeom, Jae-Hwan; Yun, Young Joo

    2014-01-01

    The Korean very-long-baseline interferometry (VLBI) network (KVN) and VLBI Exploration of Radio Astrometry (VERA) Array (KaVA) is the first international VLBI array dedicated to high-frequency (23 and 43 GHz bands) observations in East Asia. Here, we report the first imaging observations of three bright active galactic nuclei (AGNs) known for their complex morphologies: 4C 39.25, 3C 273, and M 87. This is one of the initial result of KaVA early science. Our KaVA images reveal extended outflows with complex substructure such as knots and limb brightening, in agreement with previous Very Long Baseline Array (VLBA) observations. Angular resolutions are better than 1.4 and 0.8 milliarcsecond at 23 GHz and 43 GHz, respectively. KaVA achieves a high dynamic range of ~1000, more than three times the value achieved by VERA. We conclude that KaVA is a powerful array with a great potential for the study of AGN outflows, at least comparable to the best existing radio interferometric arrays.

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

    Science.gov (United States)

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

    2016-08-01

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

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

    Science.gov (United States)

    Chung, Joyce; Aguila, Fatima; Harris, Odette

    2015-01-01

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

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

    Science.gov (United States)

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

    2004-06-01

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

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

    Directory of Open Access Journals (Sweden)

    Sudabeh Morshedian Rafiee

    2012-10-01

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

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

    Science.gov (United States)

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

    2016-05-01

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

  2. The KiVa antibullying curriculum and outcome: does fidelity matter?

    Science.gov (United States)

    Haataja, Anne; Voeten, Marinus; Boulton, Aaron J; Ahtola, Annarilla; Poskiparta, Elisa; Salmivalli, Christina

    2014-10-01

    Research on school-based prevention suggests that the success of prevention programs depends on whether they are implemented as intended. In antibullying program evaluations, however, limited attention has been paid to implementation fidelity. The present study fills in this gap by examining the link between the implementation of the KiVa antibullying program and outcome. With a large sample of 7413 students (7-12years) from 417 classrooms within 76 elementary schools, we tested whether the degree of implementation of the student lessons in the KiVa curriculum was related to the effectiveness of the program in reducing bullying problems in classrooms. Results of multilevel structural equation modeling revealed that after nine months of implementation, lesson adherence as well as lesson preparation time (but not duration of lessons) were associated with reductions in victimization at the classroom level. No statistically significant effects, however, were found for classroom-level bullying. The different outcomes for victimization and bullying as well as the importance of documenting program fidelity are discussed. PMID:25267170

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

    OpenAIRE

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

    2006-01-01

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

  4. The Application Study of VaR and TCE in Efficiency Used in Risk Management%风险管理测度VaR和TCE的实证研究

    Institute of Scientific and Technical Information of China (English)

    王苹

    2005-01-01

    针对单一金融产品和由多种资产组成的投资组合两种情况,用几只股票的历史收盘数据实证比较了两种先进的度量金融市场风险测度--风险值(VaR)和尾部条件期望(TCE)的有效性.结果显示, TCE比VaR更有效.

  5. Derivative Chameleons

    CERN Document Server

    Noller, Johannes

    2012-01-01

    We consider generalized chameleon models where the conformal coupling between matter and gravitational geometries is not only a function of the chameleon field \\phi, but also of its derivatives via higher order co-ordinate invariants. Specifically we consider the first such non-trivial conformal factor A(\\phi,X), where X is the canonical kinetic term for \\phi. The associated phenomenology is investigated and we show that such theories have a new generic mass-altering mechanism, potentially assisting the generation of a sufficiently large chameleon mass in dense environments. The most general effective potential is derived for such derivative chameleon setups and explicit examples are given. Interestingly this points us to the existence of a purely derivative chameleon protected by a shift symmetry for \\phi. We also discuss potential ghost-like instabilities associated with mass-lifting mechanisms and find another, mass-lowering and instability-free, branch of solutions. This suggests that, barring fine-tuning...

  6. Financial derivatives

    OpenAIRE

    Simon Gray and Joanna Place

    2006-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Bora Aktan

    2009-06-01

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

  8. Myosin Va plays a role in nitrergic smooth muscle relaxation in gastric fundus and corpora cavernosa of penis.

    Directory of Open Access Journals (Sweden)

    Arun Chaudhury

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

  9. An analysis of exchange rate risk exposure related to the public debt portfolio of Tunisia: Beyond VaR approach

    OpenAIRE

    Omrane Samia

    2012-01-01

    The aim of this study is to assess the exchange rate risk associated with the Tunisian public debt portfolio through Value-at-Risk (VaR) methodology. We use daily spot exchange rates of the Tunisian dinar against the three main debt currencies, the dollar, the euro and the yen. Our period of interest is from 02/01/2004 to 31/12/2008. Thetas and Marginal VaR analysis reveal that Japanese yen is the most risky currency constituting the Tunisian public debt portfolio. American dollar appea...

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

    Energy Technology Data Exchange (ETDEWEB)

    Stephen Schey; Jim Francfort

    2014-10-01

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

  11. Is Value-at-Risk (VaR) a Fair Proxy for Market Risk Under Conditions of Market Leverage?

    OpenAIRE

    Lang, Todd M.

    2000-01-01

    Ex-post intraday market-risk extrema are compared with ex-ante standard RiskMetrics parametric Value-at-Risk (VaR) limits for three foreign currency futures markets (British Pound, Japanese Yen, Swiss Frank) to determine whether forecasted volatility of market returns based on settlement price data provides a valid proxy for short-term market risk independent of market leverage. Intraday violations of ex-ante one-day VaR limits at the 95% confidence level should occur for less than 5% of m...

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

    Directory of Open Access Journals (Sweden)

    Nyaguara O. Amek

    2014-10-01

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

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

    Science.gov (United States)

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

    2015-07-30

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

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

    Science.gov (United States)

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

    2016-03-01

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

  15. Electricity derivatives

    CERN Document Server

    Aïd, René

    2015-01-01

    Offering a concise but complete survey of the common features of the microstructure of electricity markets, this book describes the state of the art in the different proposed electricity price models for pricing derivatives and in the numerical methods used to price and hedge the most prominent derivatives in electricity markets, namely power plants and swings. The mathematical content of the book has intentionally been made light in order to concentrate on the main subject matter, avoiding fastidious computations. Wherever possible, the models are illustrated by diagrams. The book should allow prospective researchers in the field of electricity derivatives to focus on the actual difficulties associated with the subject. It should also offer a brief but exhaustive overview of the latest techniques used by financial engineers in energy utilities and energy trading desks.

  16. Kontrola pravorijeka i važnost novootkrivenih činjenica

    OpenAIRE

    Várady, Tibor

    2012-01-01

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

  17. TaVa -havaintojen hyödyntäminen työturvallisuuden parantamisessa

    OpenAIRE

    Huttunen, Tatu

    2011-01-01

    Työ tehtiin oppilastyönä NCC Rakennus Oy:lle kevään 2011 aikana. Tapaturmat ja vaaratilanteet (TaVa) on NCC:n ylläpitämä tietopankki, johon kerätään työmailta työturvallisuuteen liittyviä havaintoja, läheltä piti -tilanteita, parannusehdotuksia sekä kirjataan sattuneet tapaturmat. Työssä käytiin läpi ja luokiteltiin järjestelmään kirjattuja havaintoja ja pyrittiin keräämään tietoa, jota olisi mahdollisuus siirtää esimerkiksi tehtäväsuunnitelmiin ja työturvallisuuden kehittämiseen. Periaatteen...

  18. 20 kHz, 25 kVA node power transformer

    Science.gov (United States)

    Hussey, S.

    1989-01-01

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

  19. 3D Digitisation and Visualisation of the Vače Situla

    Directory of Open Access Journals (Sweden)

    Gregor Vidmar

    2013-09-01

    Full Text Available EXTENDED ABSTRACT:The project of 3D digitisation and visualisation of the Vače situla was implemented at the beginning of 2011 in cooperation with the National Museum of Slovenia where the situla is kept and the company MFC.2 which, among other services, develops and implements 3 D digitisation and visualisation projects. The purpose of the project was to digitise and visualise a famous and precious piece of cultural heritage and to  1. show what modern 3D shape and texture scanning technologies allow us to do,  2. show how to ensure safety and reach high quality in digitising cultural heritage objects.  3. measure the added value of the 3 D visualisation of cultural heritage as a powerful tool for preservation, conservation, research, education, knowledge sharing and promotion of cultural heritage objects. Furthermore, the aims of the project were:  1. 3D capture of the shape and texture of the situla using the 3D scanning method.  2. 3D image of the situla and its details with expert descriptions.  3. 3D stereoscopic projection of the situla viewed with 3D glasses and with the possibility of controlling it remotely.  4. 3D animation giving professional interpretation of certain facts about the situla.  5. Public presentation of the project results on Slovenian cultural holiday, 8th February 2011, at the National Museum of Slovenia. The 3D capture of the shape and texture of the situla was carried out using the white light 3D scanning method followed by 3D flesh animation to show the object and its details. A touch screen was used to provide user access to the content. Reality based model enabled vertical rotation of the situla as well as the interactive display of individual engravings. By clicking a situla detail a photo with an extensive professional explanation of the scene was displayed in a new browser window. For attractive public presentation of the exhibition a 3D stereoscopic animation of the situla rotating and seemingly

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

    OpenAIRE

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

    2014-01-01

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

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

    Science.gov (United States)

    Magon, Navneet; Alinsod, Red

    2016-08-01

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

  2. Internal Model Validation in Brazil: Analysis of VaR Backtesting Methodologies

    Directory of Open Access Journals (Sweden)

    Myrian Beatriz Eiras das Neves

    2006-06-01

    Full Text Available The purpose of this paper is to analyze backtesting methodologies of VaR, focusing on aspects as suitability to volatile markets and limited data set. We verify, from regulatory standpoint, tests to complement the Basel traffic light results, using simulated and real data. The results indicate that tests based on failures proportion are not adequate for small samples even fro 1,000 observations. The Basel criterion is conservative and has low power, which does not invalidate its application, as the criterion is only one of the procedures adopted in internal model validation process. Thus, it is suggested using tests that capture the shape of returns distribution, as the Kuiper test, in addition to the Basel criterion.

  3. Retention for Stoploss reinsurance to minimize VaR in compound Poisson-Lognormal distribution

    Science.gov (United States)

    Soleh, Achmad Zanbar; Noviyanti, Lienda; Nurrahmawati, Irma

    2015-12-01

    Automobile insurance is one of the emerging general insurance's product in Indonesia. Fluctuation in total premium revenues and total claim expenses leads to a risk that insurance company can not be able to pay consumer's claims, thus reinsurance is needeed. Reinsurance is a risk transfer mechanism from the insurance company to another company called reinsurer, one of the reinsurance type is Stoploss. Because reinsurer charges premium to the insurance company, it is important to determine the retention or the total claims to be retain solely by the insurance company. Thus, retention is determined using Value at Risk (VaR) which minimize the total risk of the insurance company in the presence of Stoploss reinsurance. Retention depends only on the distribution of total claims and reinsurance loading factor. We use the compound Poisson distribution and the Log-Normal Distribution to illustrate the retention value in a collective risk model.

  4. The efficacy of Focused Acceptance and Commitment Therapy in VA primary care.

    Science.gov (United States)

    Glover, Natalie G; Sylvers, Patrick D; Shearer, Erika M; Kane, Mary-Catherine; Clasen, Peter C; Epler, Amee J; Plumb-Vilardaga, Jennifer C; Bonow, Jordan T; Jakupcak, Matthew

    2016-05-01

    Focused Acceptance & Commitment Therapy (FACT) is a brief intervention based on traditional Acceptance and Commitment Therapy (ACT). Although there is a growing body of research on the efficacy of ACT for a variety of populations and disorders, there is little research to date on the use of FACT in group settings. This project is 1 of the first of its kind, as it examines data on psychological flexibility, health and mental health status, and symptom reduction from a 4-week FACT group. Participants in this study were 51 patients who attended this group as part of routine clinical care in a VA integrated primary care and mental health setting. They completed pre- and posttreatment measures of well-being, depression, anxiety, stress, psychological flexibility, and perceptions of physical and mental health functioning. Pre- to posttreatment analyses of variance demonstrated large effects for quality of life, F(1, 51) = 21.29, p scale), F(1, 51) = 9.67, p = .003, η2 = 0.11, and small effects for perceptions of perceived stress, F(1, 51) = 4.08, p = .04, η2 = 0.03, and physical health functioning (PCS scale), F(1, 51) = 6.60, p = .01, η2 = 0.08. There was a statistical trend for reductions in anxiety, F(1, 51) = 3.29, p = .07, η2 = 0.01, and a nonsignificant effect for psychological flexibility, F(1, 51) = 2.05, p = .16, η2 = 0.04. These data provide initial support for the implementation of a group-based FACT protocol within a VA primary care setting and help to lay a foundation for further, more controlled studies on Group FACT in future research. (PsycINFO Database Record PMID:27148950

  5. Predicción de betas y VaR de portafolios de acciones mediante el filtro de Kalman y los modelos GARCH Beta and VaR prediction for stock portfolios using Kalman's filter and Garch models

    Directory of Open Access Journals (Sweden)

    Norman Giraldo Gómez

    2005-06-01

    Full Text Available En este trabajo se estudió el desempeño de un estimador del VaR de portafolios de acciones basado en el cálculo de los coeficientes beta de las acciones que lo conforman, conocido como el VaR factorial. Para ello se proyectaron tales betas recursivamente, por medio del filtro de Kalman y modelando el término, que depende de la volatilidad de los rendimientos del mercado, de acuerdo con modelos condicionalmente heterocedásticos del tipo GARCH, EGARCH y GJR. A partir de simulaciones basadas en un modelo de baja oscilación para las betas, se compararon (con la metodología media-varianza de RiskMetrics los resultados de estos modelos con el VaR calculado y se introdujeron dos pruebas de hipótesis para realizar tal comparación. La conclusión es que tanto el estimador propuesto como el de RiskMetrics pronostican correctamente el número de casos en los cuales los rendimientos extremos negativos de un portafolio superan el margen del VaR. No obstante, el estimador propuesto calcula de forma más precisa que el método de RiskMetrics el valor mediante el cual se supera tal margen.This paper studies the performance of an estimator used to calculate VaR for a stock portfolio using stock Beta coefficients. Such coefficients are recursively projected using Kalman's filter and modelling the market-volatility restrained term according to conditionally heteroscedastic GARCH, EGARCH and GJR models. A low Beta oscillation model is used to carry out diverse simulations and the results are compared with RiskMetrics mean-variance. Two hypothesis tests were introduced. We conclude that the new estimator is as effective as the one used by RiskMetrics to foresee those cases in which extremely negative yields overflow the VaR margin. However, our estimator is a better predictor of the excess amount on VaR margin than the one used by RiskMetrics.

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

    Science.gov (United States)

    2011-05-11

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

  7. 77 FR 17086 - Section 8 Housing Choice Vouchers: Revised Implementation of the HUD-VA Supportive Housing Program

    Science.gov (United States)

    2012-03-23

    ... 6, 2008 (73 FR 25026). The appropriations acts funding the HUD-VASH program authorize the HUD... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF HOUSING AND URBAN DEVELOPMENT Section 8 Housing Choice Vouchers: Revised Implementation of the HUD-VA...

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

    International Nuclear Information System (INIS)

    32P labelled fertilizer and five synthetic phosphates (dicalcium phosphate, octocalcium phosphate, iron phosphate, aluminium phosphate and apatite), which were used to simulate inorganic phosphates such as Ca2-P, Ca8-P, FeP, Al-P and Ca10-P in calcareous soil, were applied to corn plants inoculating with and without vesicular-arbuscular (VA) mycorrhizal fungi in a calcareous soil. The results showed that VA mycorrhizal fungi and dicalcium phosphate, octocalcium phosphate, iron phosphate, aluminium phosphate promoted growth and increased phosphorus content of corn plant. The four synthetic phosphates except apatite had higher contributions to corn plant growth than VA mycorrhizal fungi. Contributions of fertilizer-P, soil-P and synthetic phosphates to phosphorus nutrition of corn plant were in order of synthetic phosphates (except apatite) > soil- P > fertilizer-P. Inoculating with VA mycorrhizal fungi increased the contribution of soil-P and decreased the contribution of synthetic phosphates, but did not affect the contribution of fertilizer-P

  9. Predicting Glycerophosphoinositol Identities in Lipidomic Datasets Using VaLID (Visualization and Phospholipid Identification—An Online Bioinformatic Search Engine

    Directory of Open Access Journals (Sweden)

    Graeme S. V. McDowell

    2014-01-01

    Full Text Available The capacity to predict and visualize all theoretically possible glycerophospholipid molecular identities present in lipidomic datasets is currently limited. To address this issue, we expanded the search-engine and compositional databases of the online Visualization and Phospholipid Identification (VaLID bioinformatic tool to include the glycerophosphoinositol superfamily. VaLID v1.0.0 originally allowed exact and average mass libraries of 736,584 individual species from eight phospholipid classes: glycerophosphates, glyceropyrophosphates, glycerophosphocholines, glycerophosphoethanolamines, glycerophosphoglycerols, glycerophosphoglycerophosphates, glycerophosphoserines, and cytidine 5′-diphosphate 1,2-diacyl-sn-glycerols to be searched for any mass to charge value (with adjustable tolerance levels under a variety of mass spectrometry conditions. Here, we describe an update that now includes all possible glycerophosphoinositols, glycerophosphoinositol monophosphates, glycerophosphoinositol bisphosphates, and glycerophosphoinositol trisphosphates. This update expands the total number of lipid species represented in the VaLID v2.0.0 database to 1,473,168 phospholipids. Each phospholipid can be generated in skeletal representation. A subset of species curated by the Canadian Institutes of Health Research Training Program in Neurodegenerative Lipidomics (CTPNL team is provided as an array of high-resolution structures. VaLID is freely available and responds to all users through the CTPNL resources web site.

  10. 77 FR 75628 - STS Hydropower, Ltd., Dan River, Inc., and City of Danville, VA; Notice of Application for...

    Science.gov (United States)

    2012-12-21

    ... Energy Regulatory Commission STS Hydropower, Ltd., Dan River, Inc., and City of Danville, VA; Notice of..., 2012, Jeoffrey L. Burtch, as Chapter 7 Bankruptcy Trustee for Dan River, Inc. and STS Hydropower, Ltd... the license for the Schoolfield Hydroelectric Project from Dan River, Inc. and STS Hydropower, Ltd....

  11. 78 FR 59861 - VA Acquisition Regulation: Service-Disabled Veteran-Owned and Veteran-Owned Small Business Status...

    Science.gov (United States)

    2013-09-30

    ... the Federal Register on December 8, 2009 (74 FR 64619), VA revised 48 CFR parts 802, 804, 808, 809... (definition service-disabled Veteran)''. Upon rendering a decision, new VAAR 819.307(g) provides that the... bears the risk that the delivery method chosen will not result in timely receipt by the...

  12. Mitochondrial Carbonic Anhydrase VA Deficiency Resulting from CA5A Alterations Presents with Hyperammonemia in Early Childhood

    Science.gov (United States)

    van Karnebeek, Clara D.; Sly, William S.; Ross, Colin J.; Salvarinova, Ramona; Yaplito-Lee, Joy; Santra, Saikat; Shyr, Casper; Horvath, Gabriella A.; Eydoux, Patrice; Lehman, Anna M.; Bernard, Virginie; Newlove, Theresa; Ukpeh, Henry; Chakrapani, Anupam; Preece, Mary Anne; Ball, Sarah; Pitt, James; Vallance, Hilary D.; Coulter-Mackie, Marion; Nguyen, Hien; Zhang, Lin-Hua; Bhavsar, Amit P.; Sinclair, Graham; Waheed, Abdul; Wasserman, Wyeth W.; Stockler-Ipsiroglu, Sylvia

    2014-01-01

    Four children in three unrelated families (one consanguineous) presented with lethargy, hyperlactatemia, and hyperammonemia of unexplained origin during the neonatal period and early childhood. We identified and validated three different CA5A alterations, including a homozygous missense mutation (c.697T>C) in two siblings, a homozygous splice site mutation (c.555G>A) leading to skipping of exon 4, and a homozygous 4 kb deletion of exon 6. The deleterious nature of the homozygous mutation c.697T>C (p.Ser233Pro) was demonstrated by reduced enzymatic activity and increased temperature sensitivity. Carbonic anhydrase VA (CA-VA) was absent in liver in the child with the homozygous exon 6 deletion. The metabolite profiles in the affected individuals fit CA-VA deficiency, showing evidence of impaired provision of bicarbonate to the four enzymes that participate in key pathways in intermediary metabolism: carbamoylphosphate synthetase 1 (urea cycle), pyruvate carboxylase (anaplerosis, gluconeogenesis), propionyl-CoA carboxylase, and 3-methylcrotonyl-CoA carboxylase (branched chain amino acids catabolism). In the three children who were administered carglumic acid, hyperammonemia resolved. CA-VA deficiency should therefore be added to urea cycle defects, organic acidurias, and pyruvate carboxylase deficiency as a treatable condition in the differential diagnosis of hyperammonemia in the neonate and young child. PMID:24530203

  13. 75 FR 61621 - Charges Billed to Third Parties for Prescription Drugs Furnished by VA to a Veteran for a...

    Science.gov (United States)

    2010-10-06

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

  14. Design and conditioning of a 50-kVA power-conditioning unit for photovoltaic power systems. Final report

    Energy Technology Data Exchange (ETDEWEB)

    Stechschulte, D.L.; Shuey, K.C.; Vonderembse, J.F.; Shireman, D.W.; Niederjohn, W.M.

    1981-07-01

    A 50-kVA power conditioning unit is described including its operation, mechanical layout, factory tests results, and recommendations for future work. The appendixes include a description of the microprocessor controller for the power system, applicable drawings, and a summary of the design specifications for the power conditioning unit.

  15. 75 FR 35846 - In the Matter of Babcock & Wilcox Nuclear Operations Group, Inc., Lynchburg, VA; Order Imposing...

    Science.gov (United States)

    2010-06-23

    ... under 10 CFR 2.315(c), must be filed in accordance with the NRC E-Filing rule (72 FR 49139, August 28... COMMISSION In the Matter of Babcock & Wilcox Nuclear Operations Group, Inc., Lynchburg, VA; Order Imposing Civil Monetary Penalty I Babcock & Wilcox Nuclear Operations Group, Inc., (Licensee) is the holder...

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

    Science.gov (United States)

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

    2011-01-01

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

  17. Effects of the KiVa Anti-bullying Program on Adolescents' Depression, Anxiety, and Perception of Peers

    Science.gov (United States)

    Williford, Anne; Boulton, Aaron; Noland, Brian; Little, Todd D.; Karna, Antti; Salmivalli, Christina

    2012-01-01

    The present study investigated the effects of the KiVa antibullying program on students' anxiety, depression, and perception of peers in Grades 4-6. Furthermore, it was investigated whether reductions in peer-reported victimization predicted changes in these outcome variables. The study participants included 7,741 students from 78 schools who were…

  18. 大豆小片段法HRM基因分型体系优化%Optimization of small amplicon of HRM genotyping system in soybean

    Institute of Scientific and Technical Information of China (English)

    2015-01-01

    SNP genotyping by High Resolution Melting Curve( HRM)is a simple and effective,higher sensi-tivity and stronger specificity method. Optimization and establishment of soybean HRM-based SNP genotyping sys-tem is the precondition and basis for soybean SNP research in future. In this study,small amplicon after adding the internal calibration was used to optimize and establish SNP genotyping system. The results showed that it was better to make PCR product length 50 -80bp,the melting temperature at 72 -82℃ and Tm value between 55 -62℃when designing a SNP primer. A total of 10μL PCR reaction system should contain 25ng DNA template,0. 6pmol SNP primers and 1μL LC Green dye. After PCR reaction,3 pmol high and low temperature internal calibration should be added to each wells,and then denatured for HRM analysis. Moreover,the optimized SNP genotyping system was used to genotyping a recombinant inbred lines( RILs)population,and the results demonstrated that the RILs could be completely divided into 2 genotypes of their parents by the optimized system,with improved accuracy and efficiency. The optimized SNP genotyping system established in this study will provide a useful foundation for developing SNP markers,constructing high density genetic maps,QTL identification in the future.%应用高分辨率熔解曲线( high resolution melting curve,HRM)技术进行基因分型简单有效,灵敏度高、特异性强。优化并建立基于HRM的大豆SNP基因分型体系,是准确进行SNP研究的前提和基础。本研究利用添加内标后的小片段法进行SNP基因分型体系优化研究,结果表明在设计SNP引物时,最好使其PCR产物长度为50~80bp,熔解温度在72~82℃,Tm值介于55~62℃之间;10μL PCR反应体系中应包含25ng DNA模板,0.6pmol SNP引物,1μL LC Green染料;PCR反应后,应在各点样孔分别加入3pmol的高、低温内标,然后进行变性处理和HRM分析。同时利用建立的基因分型体

  19. Influence of amplicon size on the polymerase chain reaction of Parvovirus B19 genome in formalin-fixed specimens Influência do tamanho do amplicon na reação em cadeia da polimerase na detecção do genoma do PB19 em amostras fixadas em formalina

    Directory of Open Access Journals (Sweden)

    Paulo Roberto Veiga Quemelo

    2009-04-01

    Full Text Available The polymerase chain reaction (PCR has provided diagnosis of archival material, but some fixation methods such as formalin damage DNA and, subsequently, affect PCR analysis, particularly paraffin-embedded tissues. PCR is known due to its high specificity and sensitivity, although some difficulties arise when formalinfixed and paraffin-embedded tissue is used. Not only does this occur due to protein cross-linking, which increases with longer fixation time, but it also happens due to the direct damage that formalin causes in the DNA itself. PCR was used to analyze placenta and fetal organs from 34 samples with suspected Parvovirus B19 infection. It was not possible to amplify Parvovirus B19 DNA using nested-PCR, probably due to the size of the amplicon generated with the first set of primers. We approached this problem by using only the second set of primers. Two out of 34 tissue samples (5,9% were positive by PCR. However, PCR performed on corresponding fetal organs was negative in one of the two. We also observed a negative relation between the thickness of the tissue fragment and the positivity of the samples. In conclusion, although PCR is highly specific and sensitive in fresh or ideally fixed material, a careful standardization of PCR assays is necessary when using formalin fixed paraffin-embedded tissues by applying primers that require smaller DNA fragments for amplification.A reação em cadeia da polimerase (PCR tem fornecido diagnóstico de material de arquivo, mas alguns métodos de fixação, tais como formalina, provocam danos ao DNA e subsequentemente afetam sua análise, particularmente tecidos embebidos em parafina. A PCR é conhecida pela sua alta especificidade e sensibilidade, embora algumas dificuldades ocorram quando o material utilizado foi fixado em formalina e embebido em parafina. Isso não se deve somente pela formação de cross-linkings com proteínas, a qual aumenta com o maior tempo de fixação, mas também pelo

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

    Science.gov (United States)

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

    2016-01-01

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

  1. Role of the Acidic Hirudin-like COOH-Terminal Amino Acid Region of Factor Va Heavy Chain in the Enhanced Function of Prothrombinase†‡

    Science.gov (United States)

    2008-01-01

    Prothrombinase activates prothrombin through initial cleavage at Arg320 followed by cleavage at Arg271. This pathway is characterized by the generation of an enzymatically active, transient intermediate, meizothrombin, that has increased chromogenic substrate activity but poor clotting activity. The heavy chain of factor Va contains an acidic region at the COOH terminus (residues 680−709). We have shown that a pentapeptide from this region (DYDYQ) inhibits prothrombin activation by prothrombinase by inhibiting meizothrombin generation. To ascertain the function of these regions, we have created a mutant recombinant factor V molecule that is missing the last 30 amino acids from the heavy chain (factor VΔ680−709) and a mutant molecule with the 695DYDY698 → AAAA substitutions (factor V4A). The clotting activities of both recombinant mutant factor Va molecules were impaired compared to the clotting activity of wild-type factor Va (factor VaWt). Using an assay employing purified reagents, we found that prothrombinase assembled with factor VaΔ680−709 displayed an ∼39% increase in kcat, while prothrombinase assembled with factor Va4A exhibited an ∼20% increase in kcat for the activation of prothrombin as compared to prothrombinase assembled with factor VaWt. Gel electrophoresis analyzing prothrombin activation by prothrombinase assembled with the mutant molecules revealed a delay in prothrombin activation with persistence of meizothrombin. Our data demonstrate that the COOH-terminal region of factor Va heavy chain is indeed crucial for coordinated prothrombin activation by prothrombinase because it regulates meizothrombin cleavage at Arg271 and suggest that this portion of factor Va is partially responsible for the enhanced procoagulant function of prothrombinase. PMID:18590276

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

    Science.gov (United States)

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

    2000-01-01

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

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

    International Nuclear Information System (INIS)

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

  4. Do hassles and uplifts change with age? Longitudinal findings from the VA normative aging study.

    Science.gov (United States)

    Aldwin, Carolyn M; Jeong, Yu-Jin; Igarashi, Heidi; Spiro, Avron

    2014-03-01

    To examine emotion regulation in later life, we contrasted the modified hedonic treadmill theory with developmental theories, using hassles and uplifts to assess emotion regulation in context. The sample was 1,315 men from the VA Normative Aging Study aged 53 to 85 years, who completed 3,894 observations between 1989 and 2004. We computed 3 scores for both hassles and uplifts: intensity (ratings reflecting appraisal processes), exposure (count), and summary (total) scores. Growth curves over age showed marked differences in trajectory patterns for intensity and exposure scores. Although exposure to hassles and uplifts decreased in later life, intensity scores increased. Group-based modeling showed individual differences in patterns of hassles and uplifts intensity and exposure, with relative stability in uplifts intensity, normative nonlinear changes in hassles intensity, and complex patterns of individual differences in exposure for both hassles and uplifts. Analyses with the summary scores showed that emotion regulation in later life is a function of both developmental change and contextual exposure, with different patterns emerging for hassles and uplifts. Thus, support was found for both hedonic treadmill and developmental change theories, reflecting different aspects of emotion regulation in late life. PMID:24660796

  5. A spatial exploration of informal trail networks within Great Falls Park, VA

    Science.gov (United States)

    Wimpey, Jeremy; Marion, Jeffrey L.

    2011-01-01

    Informal (visitor-created) trails represent a threat to the natural resources of protected natural areas around the globe. These trails can remove vegetation, displace wildlife, alter hydrology, alter habitat, spread invasive species, and fragment landscapes. This study examines informal and formal trails within Great Falls Park, VA, a sub-unit of the George Washington Memorial Parkway, managed by the U.S. National Park Service. This study sought to answer three specific questions: 1) Are the physical characteristics and topographic alignments of informal trails significantly different from formal trails, 2) Can landscape fragmentation metrics be used to summarize the relative impacts of formal and informal trail networks on a protected natural area? and 3) What can we learn from examining the spatial distribution of the informal trails within protected natural areas? Statistical comparisons between formal and informal trails in this park indicate that informal trails have less sustainable topographic alignments than their formal counterparts. Spatial summaries of the lineal and areal extent and fragmentation associated with the trail networks by park management zones compare park management goals to the assessed attributes. Hot spot analyses highlight areas of high trail density within the park and findings provide insights regarding potential causes for development of dense informal trail networks.

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

    Institute of Scientific and Technical Information of China (English)

    傅强; 邢琳琳

    2009-01-01

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

  7. 基于GARCH-EVT-VaR模型的碳市场风险计量实证研究%Value-at-Risk Estimation of Carbon Spot Markets Based on an Integrated GARCH-EVT-VaR Model

    Institute of Scientific and Technical Information of China (English)

    蒋晶晶; 叶斌; 马晓明

    2015-01-01

    对欧盟碳市场风险进行实证研究,在分析碳市场价格波动特征基础上,将条件方差和极值理论纳入VaR计量框架,建立量化碳市场价格波动风险的GARCH-EVT-VaR模型.应用该模型对欧盟碳排放交易市场(EU ETS)进行实证研究,结果显示:碳市场价格波动具有尖峰、厚尾、自相关、波动性聚类和条件方差等典型特征,EUA和CER价格波动呈现显著同步性;碳市场存在显著的极端价格波动风险,GARCH-EVT-VaR模型能够更准确地量化碳市场风险,从而为应对极端事件预留充足的风险储备.

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

    Institute of Scientific and Technical Information of China (English)

    范伟锋; 陈衍尧; 区健毅; 朱秋贤; 李锦塘

    2014-01-01

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

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

    Institute of Scientific and Technical Information of China (English)

    李杰辉

    2007-01-01

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

  10. One in vitro model for visceral adipose-derived fibroblasts in chronic inflammation

    International Nuclear Information System (INIS)

    One pathogenesis of the obesity-associated complications is that consistent with increased body fat mass, the elevation of adipose tissue-derived cytokines inflicts a low-grade chronic inflammation, which ultimately leads to metabolic disorders. Adipocytes and macrophages in visceral adipose (VA) have been confirmed to contribute to the chronic inflammation; however, the role of the resident fibroblasts is still unknown. We established one VA fibroblast cell line, termed VAFC. Morphological analysis indicated that there were large numbers of pits at the cell plasma membrane. In vitro VAFC cells promoted bone marrow cells to differentiate into macrophages and protected them from apoptosis in the serum-free conditions. Additionally, they also interfered in lymphocytes proliferation. On the basis of these results, this cell line might be an in vitro model for understanding the role of adipose-derived fibroblasts in obesity-associated chronic inflammation

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

    OpenAIRE

    Škevin, Petra

    2012-01-01

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

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

    Science.gov (United States)

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

    2016-03-01

    Health care systems are increasingly burdened by the large numbers of safety measures currently being reported. Within the Veterans Administration (VA), most safety reporting occurs within organizational silos, with little involvement by the frontline users of these measures. To provide a more integrated picture of patient safety, the study team partnered with multiple VA stakeholders and engaged potential frontline users at 2 hospitals to develop a Guiding Patient Safety (GPS) tool. The GPS is currently in its fourth generation; once approval is obtained from senior leadership, implementation will begin. Stakeholders were enthusiastic about the GPS's user-friendly format, comprehensive content, and potential utility for improving safety. These findings suggest that stakeholder engagement is a critical first step in the development of tools that will more likely be used by frontline users. Policy makers and researchers may consider adopting this innovative partnered-research model in developing future national initiatives to deliver meaningful programs to frontline users. PMID:25500716

  13. Telephone care coordination for smokers in VA mental health clinics: protocol for a hybrid type-2 effectiveness-implementation trial

    OpenAIRE

    Rogers, Erin; Fernandez, Senaida; Gillespie, Colleen; Smelson, David; Hagedorn, Hildi J; Elbel, Brian; Kalman, David; Axtmayer, Alfredo; Kurowski, Karishma; Sherman, Scott E

    2013-01-01

    Background This paper describes an innovative protocol for a type-II hybrid effectiveness-implementation trial that is evaluating a smoking cessation telephone care coordination program for Veterans Health Administration (VA) mental-health clinic patients. As a hybrid trial, the protocol combines implementation science and clinical trial methods and outcomes that can inform future cessation studies and the implementation of tobacco cessation programs into routine care. The primary objectives ...

  14. Influence of Copolymer Composition on In Vitro and In Vivo Performance of Celecoxib-PVP/VA Amorphous Solid Dispersions.

    Science.gov (United States)

    Knopp, Matthias Manne; Nguyen, Julia Hoang; Mu, Huiling; Langguth, Peter; Rades, Thomas; Holm, René

    2016-03-01

    Previous studies suggested that an amorphous solid dispersion with a copolymer consisting of both hydrophobic and hydrophilic monomers could improve the dissolution profile of a poorly water-soluble drug compared to the crystalline form. Therefore, this study investigated the influence of the copolymer composition of polyvinylpyrrolidone/vinyl acetate (PVP/VA) on the non-sink in vitro dissolution behavior and in vivo performance of celecoxib (CCX) amorphous solid dispersions. The study showed that the hydrophilic monomer vinylpyrrolidone (VP) was responsible for the generation of CCX supersaturation whereas the hydrophobic monomer vinyl acetate (VA) was responsible for the stabilization of the supersaturated solution. For CCX, there was an optimal copolymer composition around 50-60% VP content where further replacement of VP monomers with VA monomers did not have any biopharmaceutical advantages. A linear relationship was found between the in vitro AUC0-4h and in vivo AUC0-24h for the CCX:PVP/VA systems, indicating that the non-sink in vitro dissolution method applied in this study was useful in predicting the in vivo performance. These results indicated that when formulating a poorly water-soluble drug as an amorphous solid dispersion using a copolymer, the copolymer composition has a significant influence on the dissolution profile and in vivo performance. Thus, the dissolution profile of a drug can theoretically be tailored by changing the monomer ratio of a copolymer with respect to the required in vivo plasma-concentration profile. As this ratio is likely to be drug dependent, determining the optimal ratio between the hydrophilic (dissolution enhancing) and hydrophobic (crystallization inhibiting) monomers for a given drug is imperative. PMID:26769250

  15. Performance testing of the neutron probe VA-S-20.1 for soil moisture measurements in forests

    International Nuclear Information System (INIS)

    The neutron probe VA-S-20.1 was tested for application in forestry. The probe should be only applied if a large number of measurements has to be carried out through long periods because of following disadvantages: 1) the heaviness of the devices and shielding container, 2) low sensitivity of the counter during field operation, and 3) the determination of the calibration curve is material and time consuming

  16. Household adaptation strategies to floods.The case study of the Bečva river basin, the Czech Republic

    Czech Academy of Sciences Publication Activity Database

    Duží, Barbora; Vikhrov, Dmytro; Stojanov, Robert; Jakubínský, Jiří

    Brno: Global change research centre, Academy of Sciences of the Czech Republic, v. v. i, 2013 - (Stojanov, R.; Žalud, Z.; Cudlín, P.; Farda, A.; Urban, O.; Trnka, M.), s. 77-82 ISBN 978-80-904351-8-6. [Global Change and Resilience. Brno (CZ), 22.05.2013-24.05.2013] Institutional support: RVO:67179843 Keywords : climate extremes * floods * adaptation * coping * Bečva basin * local knowledge Subject RIV: EH - Ecology, Behaviour

  17. Molecular Survey of Toxoplasma gondii in Sheep, Cattle and Meat Products in Chaharmahal va Bakhtiari Province, Southwest of Iran

    OpenAIRE

    Hamidreza Azizi; Behrouz Shiran; Arash Borjian Boroujeni; Milad Jafari

    2014-01-01

    Background Toxoplasmosis is a worldwide spread disease. The present study examined the prevalence of Toxoplasma gondii infection among animals of edible meat (cattle and sheep) in Chaharmahal va Bakhtiari Province (Southwest of Iran) in 2012. Furthermore, we attempted for the first time to identify this parasite from the meat products in the province. Methods The tongue, brain, femur muscle and liver of 50 sheep and 70 cattle as well as 50 samples of meat products were selected and collected ...

  18. Cooperative Regulation of the Activity of Factor Xa within Prothrombinase by Discrete Amino Acid Regions from Factor Va Heavy Chain†

    OpenAIRE

    Barhoover, Melissa A.; Orban, Tivadar; Bukys, Michael A.; Kalafatis, Michael

    2008-01-01

    The prothrombinase complex catalyzes the activation of prothrombin to α-thrombin. We have repetitively shown that amino acid region 695DYDY698 from the COOH terminus of the heavy chain of factor Va regulates the rate of cleavage of prothrombin at Arg271 by prothrombinase. We have also recently demonstrated that amino acid region 334DY335 is required for the optimal activity of prothrombinase. To assess the effect of these six amino acid residues on cofactor activity, we created recombinant fa...

  19. Risk Measures and Contagion Matrix: an Application of CoVaR for the Brazilian Financial Market

    Directory of Open Access Journals (Sweden)

    Aléssio Tony Cavalcanti de Almeida

    2012-12-01

    Full Text Available The main point of this work is to assess how a financial distress in return series of the major Brazilian companies assets and relevant domestic market (Ibovespa and main international index (Dow Jones interact with each other, in an attempt to capture spillover effects. We try to capture the systemic risk, the contagion effect and the stress test. This paper uses the methodology CoVaR, described in the Adrian and Brunnermeier (2011 which use quantile regression. The main innovation of this work is the construction and estimation of the contagion matrix to domestic capital market. The results show that there is no relationship between risk measurements given by Value at Risk (VaR and CoVaR, moreover the systemic risk shows those assets that generate more negative externalities for the domestic financial market. The stress test indicates that a distress in domestic market indicator returns have more spillover effects on domestic papers than a distress in the international market returns. Finally, the contagion matrix reveals that the interrelationships of contagion between the firms’ returns are relevant sectorial evidence for assessment and management of risks.

  20. Training satisfaction for subspecialty fellows in internal medicine: Findings from the Veterans Affairs (VA Learners' Perceptions Survey

    Directory of Open Access Journals (Sweden)

    Byrne John M

    2011-05-01

    Full Text Available Abstract Background Learner satisfaction assessment is critical in the design and improvement of training programs. However, little is known about what influences satisfaction and whether trainee specialty is correlated. A national comparison of satisfaction among internal medicine subspecialty fellows in the Department of Veterans Affairs (VA provides a unique opportunity to examine educational factors associated with learner satisfaction. We compared satisfaction across internal medicine fellows by subspecialty and compared factors associated with satisfaction between procedural versus non-procedural subspecialty fellows, using data from the Learners' Perceptions Survey (LPS, a validated survey tool. Methods We surveyed 2,221 internal medicine subspecialty fellows rotating through VA between 2001 and 2008. Learners rated their overall training satisfaction on a 100-point scale, and on a five-point Likert scale ranked satisfaction with items within six educational domains: learning, clinical, working and physical environments; personal experience; and clinical faculty/preceptor. Results Procedural and non-procedural fellows reported similar overall satisfaction scores (81.2 and 81.6. Non-procedural fellows reported higher satisfaction with 79 of 81 items within the 6 domains and with the domain of physical environment (4.06 vs. 3.85, p Conclusions Internal medicine fellows are highly satisfied with their VA training. Nonprocedural fellows reported higher satisfaction with most items. For both procedural and non-procedural fellows, clinical faculty/preceptor and personal experience have the strongest impact on overall satisfaction.

  1. Estimation of Dynamic VaR in Chinese Stock Markets Based on Time Scale and Extreme Value Theory

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    The accuracy and time scale invariance of value-at-risk (VaR) measurement methods for different stock indices and at different confidence levels are tested. Extreme value theory (EVT) is applied to model the extreme tail of standardized residual series of daily/weekly indices losses, and parametric and nonparametric methods are used to estimate parameters of the general Pareto distribution (GPD), and dynamic VaR for indices of three stock markets in China. The accuracy and time scale invariance of risk measurement methods through back-testing approach are also examined. Results show that not all the indices accept time scale invariance; there are some differences in accuracy between different indices at various confidence levels. The most powerful dynamic VaR estimation methods are EVT-GJR-Hill at 97.5% level for weekly loss to Shanghai stock market, and EVT-GARCH-MLE (Hill) at 99.0% level for weekly loss to Taiwan and Hong Kong stock markets, respectively.

  2. Implementation outcomes of evidence-based quality improvement for depression in VA community based outpatient clinics

    Directory of Open Access Journals (Sweden)

    Fortney John

    2012-04-01

    Full Text Available Abstract Background Collaborative-care management is an evidence-based practice for improving depression outcomes in primary care. The Department of Veterans Affairs (VA has mandated the implementation of collaborative-care management in its satellite clinics, known as Community Based Outpatient Clinics (CBOCs. However, the organizational characteristics of CBOCs present added challenges to implementation. The objective of this study was to evaluate the effectiveness of evidence-based quality improvement (EBQI as a strategy to facilitate the adoption of collaborative-care management in CBOCs. Methods This nonrandomized, small-scale, multisite evaluation of EBQI was conducted at three VA Medical Centers and 11 of their affiliated CBOCs. The Plan phase of the EBQI process involved the localized tailoring of the collaborative-care management program to each CBOC. Researchers ensured that the adaptations were evidence based. Clinical and administrative staff were responsible for adapting the collaborative-care management program for local needs, priorities, preferences and resources. Plan-Do-Study-Act cycles were used to refine the program over time. The evaluation was based on the RE-AIM (Reach, Effectiveness, Adoption, Implementation, Maintenance Framework and used data from multiple sources: administrative records, web-based decision-support systems, surveys, and key-informant interviews. Results Adoption: 69.0% (58/84 of primary care providers referred patients to the program. Reach: 9.0% (298/3,296 of primary care patients diagnosed with depression who were not already receiving specialty care were enrolled in the program. Fidelity: During baseline care manager encounters, education/activation was provided to 100% (298/298 of patients, barriers were assessed and addressed for 100% (298/298 of patients, and depression severity was monitored for 100% (298/298 of patients. Less than half (42.5%, 681/1603 of follow-up encounters during the acute

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

    Directory of Open Access Journals (Sweden)

    Pablo González

    2000-06-01

    Full Text Available Una vez estudiada la toxicidad de la vacuna VA-DIFTET® (vacuna antidiftérica antitetánica por administración a dosis única en dos especies de animales, se impone la evaluación a dosis repetida, teniendo en cuenta que el esquema de inmunización en humanos prevé la aplicación de tres dosis cuando el componente pertusis de la DPT está contraindicado. Se emplearon 210 ratones OF-1 de ambos sexos. Los grupos experimentales fueron similares a los de la prueba a dosis única con la vacuna dúplex, anatoxina diftérica, anatoxina tetánica, adyuvante, tiomersal, solución salina fisiológica y un grupo control no tratado. Un grupo de hembras y otro de machos fue asignado aleatoriamente a cada tratamiento y para recibir 1, 2 ó 3 dosis por vía intramuscular. Tras cada aplicación se evaluó la aparición de síntomas clínicos, el incremento de peso, el consumo de agua y alimento y la dinámica de la respuesta inmune contra las anatoxinas tetánica y diftérica, específicamente de tipo IgG, mediante ELISA indirecto. Al término de las observaciones los animales fueron sacrificados y se realizaron estudios anatomopatológicos. Además, durante el sacrificio se evaluó el índice relativo de bazo y timo, así como la relación bazo/timo. No se comprobaron alteraciones que evidenciaran toxicidad por parte de la vacuna y sus componentes. Asimismo, se demostró una marcada respuesta inmune en los grupos vacunales e inoculados con las anatoxinas. Se considera que los resultados de la prueba fueron satisfactorios.

  4. Strength of the pnicogen bond in complexes involving group Va elements N, P, and As.

    Science.gov (United States)

    Setiawan, Dani; Kraka, Elfi; Cremer, Dieter

    2015-03-01

    A set of 36 pnicogen homo- and heterodimers, R3E···ER3 and R3E···E′R′3, involving differently substituted group Va elements E = N, P, and As has been investigated at the ωB97X-D/aug-cc-pVTZ level of theory to determine the strength of the pnicogen bond with the help of the local E···E′ stretching force constants k(a). The latter are directly related to the amount of charge transferred from an E donor lone pair orbital to an E′ acceptor σ* orbital, in the sense of a through-space anomeric effect. This leads to a buildup of electron density in the intermonomer region and a distinct pnicogen bond strength order quantitatively assessed via k(a). However, the complex binding energy ΔE depends only partly on the pnicogen bond strength as H,E-attractions, H-bonding, dipole-dipole, or multipole-multipole attractions also contribute to the stability of pnicogen bonded dimers. A variation from through-space anomeric to second order hyperonjugative, and skewed π,π interactions is observed. Charge transfer into a π* substituent orbital of the acceptor increases the absolute value of ΔE by electrostatic effects but has a smaller impact on the pnicogen bond strength. A set of 10 dimers obtains its stability from covalent pnicogen bonding whereas all other dimers are stabilized by electrostatic interactions. The latter are quantified by the magnitude of the local intermonomer bending force constants XE···E′. Analysis of the frontier orbitals of monomer and dimer in connection with the investigation of electron difference densities, and atomic charges lead to a simple rationalization of the various facets of pnicogen bonding. The temperature at which a given dimer is observable under experimental conditions is provided. PMID:25325889

  5. Predicting Glycerophosphoinositol Identities in Lipidomic Datasets Using VaLID (Visualization and Phospholipid Identification)—An Online Bioinformatic Search Engine

    OpenAIRE

    McDowell, Graeme S. V.; Blanchard, Alexandre P.; Taylor, Graeme P.; Daniel Figeys; Stephen Fai; Bennett, Steffany A. L.

    2014-01-01

    The capacity to predict and visualize all theoretically possible glycerophospholipid molecular identities present in lipidomic datasets is currently limited. To address this issue, we expanded the search-engine and compositional databases of the online Visualization and Phospholipid Identification (VaLID) bioinformatic tool to include the glycerophosphoinositol superfamily. VaLID v1.0.0 originally allowed exact and average mass libraries of 736,584 individual species from eight phospholipid c...

  6. Discriminating between the effect of shunt and reduced VA/Q on arterial oxygen saturation is particularly useful in clinical practice.

    Science.gov (United States)

    Jones, J G; Jones, S E

    2000-01-01

    There is an extensive literature on methods for discriminating between an increased shunt and a reduced ratio of ventilation to perfusion. In this review we prefer the terms "VA/Q" and "reduced or low VA/Q" rather than "V/Q inequality" to refer to the effects on arterial oxygenation of reducing V/Q below 0.8 to about 0.1. Almost without exception the conventional methods for measuring shunt and reduced VA/Q are invasive as well as technically complex. For most clinicians who are dealing with a hypoxemic patient the relevance of these entities is not so obvious as to justify the time and difficulty in either understanding or measuring them. However this review shows that, while an increased shunt and a decreased VA/Q both reduce arterial oxygen saturation (SaO2) at a particular inspired oxygen concentration (PIO2), the effect of shunt and reduced VA/Q have important clinical differences on the relationship between PIO2 and SaO2. The review also outlines a simple non-invasive method for measuring shunt and reduced VA/Q which illustrates the value of discriminating between them in clinical practice. PMID:12580217

  7. On $n$-derivations

    Directory of Open Access Journals (Sweden)

    Mohammad Hossein Sattari

    2016-06-01

    Full Text Available In this article, the notion of $n-$derivation is introduced for all integers $ngeq 2$. Although all derivations are $n-$derivations,  in general these notions are not equivalent. Some properties of ordinary derivations are  investigated for $n-$derivations. Also, we show that under certain mild condition  $n-$derivations are derivations.

  8. Synthesis and biological evaluation of some novel furan derivatives.

    Science.gov (United States)

    Sen, Sandip; De, Biplab; Easwari, T S

    2014-11-01

    The present work involved cyclization of Schiff bases to azetidine-2-one and thiazolidine 4-one derivatives. The schiff bases (IIIa-j) were obtained upon reaction between electrophillic carbon atom of furfuraldehyde and nucleophillic nitrogen atom of amines. Azetidine-2-one derivatives (IVa-j) were obtained by reaction between imines and monochloro acetyl chloride in the presence of triethyl amine and 1, 4 dioxan. On the other hand, preparations of thiazolidine-4-ones (Va-j) were preceded by nucleophilic attack of sulphur of thioglycolic acid on imine carbon followed by intramolecular cyclization in the presence of SnCl2. The structures of the compounds were confirmed by spectral and elemental analysis. The biological evaluation of the compounds like anti-microbial, antioxidant, analgesic, CNS depressant and anti-diabetic activity were determined. From the pharmacological investigation it was found that out of all the compounds IVa, IVb, IVe, IVf, IVh,Va, Vb, Ve, Vf, Vh had shown more potent activity. PMID:25362600

  9. Performance of InterVA for assigning causes of death to verbal autopsies: multisite validation study using clinical diagnostic gold standards

    Directory of Open Access Journals (Sweden)

    Flaxman Abraham D

    2011-08-01

    Full Text Available Abstract Background InterVA is a widely disseminated tool for cause of death attribution using information from verbal autopsies. Several studies have attempted to validate the concordance and accuracy of the tool, but the main limitation of these studies is that they compare cause of death as ascertained through hospital record review or hospital discharge diagnosis with the results of InterVA. This study provides a unique opportunity to assess the performance of InterVA compared to physician-certified verbal autopsies (PCVA and alternative automated methods for analysis. Methods Using clinical diagnostic gold standards to select 12,542 verbal autopsy cases, we assessed the performance of InterVA on both an individual and population level and compared the results to PCVA, conducting analyses separately for adults, children, and neonates. Following the recommendation of Murray et al., we randomly varied the cause composition over 500 test datasets to understand the performance of the tool in different settings. We also contrasted InterVA with an alternative Bayesian method, Simplified Symptom Pattern (SSP, to understand the strengths and weaknesses of the tool. Results Across all age groups, InterVA performs worse than PCVA, both on an individual and population level. On an individual level, InterVA achieved a chance-corrected concordance of 24.2% for adults, 24.9% for children, and 6.3% for neonates (excluding free text, considering one cause selection. On a population level, InterVA achieved a cause-specific mortality fraction accuracy of 0.546 for adults, 0.504 for children, and 0.404 for neonates. The comparison to SSP revealed four specific characteristics that lead to superior performance of SSP. Increases in chance-corrected concordance are attained by developing cause-by-cause models (2%, using all items as opposed to only the ones that mapped to InterVA items (7%, assigning probabilities to clusters of symptoms (6%, and using empirical

  10. Employing external facilitation to implement cognitive behavioral therapy in VA clinics: a pilot study

    Directory of Open Access Journals (Sweden)

    Blevins Dean

    2010-10-01

    Full Text Available Abstract Background Although for more than a decade healthcare systems have attempted to provide evidence-based mental health treatments, the availability and use of psychotherapies remains low. A significant need exists to identify simple but effective implementation strategies to adopt complex practices within complex systems of care. Emerging evidence suggests that facilitation may be an effective integrative implementation strategy for adoption of complex practices. The current pilot examined the use of external facilitation for adoption of cognitive behavioral therapy (CBT in 20 Department of Veteran Affairs (VA clinics. Methods The 20 clinics were paired on facility characteristics, and 23 clinicians from these were trained in CBT. A clinic in each pair was randomly selected to receive external facilitation. Quantitative methods were used to examine the extent of CBT implementation in 10 clinics that received external facilitation compared with 10 clinics that did not, and to better understand the relationship between individual providers' characteristics and attitudes and their CBT use. Costs of external facilitation were assessed by tracking the time spent by the facilitator and therapists in activities related to implementing CBT. Qualitative methods were used to explore contextual and other factors thought to influence implementation. Results Examination of change scores showed that facilitated therapists averaged an increase of 19% [95% CI: (2, 36] in self-reported CBT use from baseline, while control therapists averaged a 4% [95% CI: (-14, 21] increase. Therapists in the facilitated condition who were not providing CBT at baseline showed the greatest increase (35% compared to a control therapist who was not providing CBT at baseline (10% or to therapists in either condition who were providing CBT at baseline (average 3%. Increased CBT use was unrelated to prior CBT training. Barriers to CBT implementation were therapists' lack of

  11. Suicide-related behaviors in older patients with new anti-epileptic drug use: data from the VA hospital system

    Directory of Open Access Journals (Sweden)

    Dersh Jeffrey J

    2010-01-01

    Full Text Available Abstract Background The U.S. Food and Drug Administration (FDA recently linked antiepileptic drug (AED exposure to suicide-related behaviors based on meta-analysis of randomized clinical trials. We examined the relationship between suicide-related behaviors and different AEDs in older veterans receiving new AED monotherapy from the Veterans Health Administration (VA, controlling for potential confounders. Methods VA and Medicare databases were used to identify veterans 66 years and older, who received a care from the VA between 1999 and 2004, and b an incident AED (monotherapy prescription. Previously validated ICD-9-CM codes were used to identify suicidal ideation or behavior (suicide-related behaviors cases, epilepsy, and other conditions previously associated with suicide-related behaviors. Each case was matched to controls based on prior history of suicide-related behaviors, year of AED prescription, and epilepsy status. Results The strongest predictor of suicide-related behaviors (N = 64; Controls N = 768 based on conditional logistic regression analysis was affective disorder (depression, anxiety, or post-traumatic stress disorder (PTSD; Odds Ratio 4.42, 95% CI 2.30 to 8.49 diagnosed before AED treatment. Increased suicide-related behaviors were not associated with individual AEDs, including the most commonly prescribed AED in the US - phenytoin. Conclusion Our extensive diagnostic and treatment data demonstrated that the strongest predictor of suicide-related behaviors for older patients newly treated with AED monotherapy was a previous diagnosis of affective disorder. Additional, research using a larger sample is needed to clearly determine the risk of suicide-related behaviors among less commonly used AEDs.

  12. p53 levels, cell cycle kinetics and radiosensitivity in two SV40 transformed Wi38VA13 fibroblast strains

    International Nuclear Information System (INIS)

    Background: The tumor suppressor protein p53 which can mediate an ionizing radiation-induced G1 arrest in mammalian cells, forms complexes with SV40 large T antigen (l-T-Ag). We have analyzed the p53 levels, the capability to undergo a G1 arrest and the radiosensitivity of two SV40 transformed fibroblast strains differing in their large T antigen expression. Material and Methods: One of the two strains (VA13F) is the commercially available form of Wi38VA13, the other (VA13E) arose spontaneously from the original one in our laboratory. Their p53 levels were measured by means of flow cytometry (FCM) and Western blot (WB) with two p53 antibodies (Ab-3, clone PAb240; Ab-6, clone DO-1; both Oncogene Science). Cell cycle distributions were determined flow cytometrically after BrdU labeling at regular time intervals after exposure to 250 kV X-rays. Radiosensitivity was assessed in a clonogenicity assay. Results: The p53 levels of the two strains corresponded to their large T antigen expression, presumably due to complex formation between the two proteins. The strain with a high p53 level did not show a G1 arrest and had a relatively high radiosensitivity, whereas the strain with a low p53 level showed a significant G1 arrest and a lower radiosensitivity. Conclusion: These results suggest that 1. complex formation between the large T antigen and p53 reduces the latter's functionality; 2. in these two strains the G1 arrest is one of the factors determining radiosensitivity. (orig.)

  13. Effect of Health-Related Quality of Life on Women and Men’s Veterans Affairs (VA) Health Care Utilization and Mortality

    Science.gov (United States)

    Murdoch, Maureen

    2007-01-01

    Introduction Although women will account for almost 11% of veterans by 2040, we know little about their health and functioning, particularly compared to men. Objective To compare women and men veterans’ health-related quality of life (HRQOL) and VA health care utilization and to see if previously described associations between HRQOL, subsequent VA health care utilization, and mortality in male veterans would generalize to women veterans. Methods Prospective cohort study of all veterans who received medical care from an Upper Midwest Veterans Affairs facility between 10/1/96 and 3/31/98 and returned a mailed questionnaire. Results Women’s effective survey response rate was 52% (n = 1,500); men’s, 58% (n = 35,000). In the following year, 9% of women and 12% of men had at least one hospitalization. One percent of women and 3% of men died in the post-survey year. After adjustment, women’s HRQOL was higher than men’s; for every 10-point decrement in overall physical or mental functioning, women and men had similarly increased risk/odds of subsequently dying, being hospitalized at a VA facility, or making a VA outpatient stop. Among younger women and women who received VA care outside of the Twin City metro area, poorer overall mental or physical health functioning was associated with fewer primary care stops; among their male counterparts, it was associated with more primary care stops. Conclusion Compared to men, women veterans receiving VA health care in the upper Midwest catchment area had better HRQOL and used fewer health services. Although VA health care utilization was similar across gender after adjusting for HRQOL, poorer mental or physical health was associated with fewer primary care stops for selected subgroups of women. PMID:17610020

  14. Un juego serio en que se va la vida. Fragmentos, citas, reescrituras en Zettel, de Héctor Libertella

    OpenAIRE

    Agustina Pérez

    2015-01-01

    Los papeles sueltos de Zettel, último libro Héctor Libertella, tienen algo de la tarea obstinada que Antoine Compagnon encuentra en niños y ancianos, trabajo del papel como cortar y pegar, juego serio en que se va la vida, o llega. Se revisará Zettel a la luz de otros textos de Libertella para indagar su vínculo con el fragmento como tipo de exposición que no aspira a la exhaustividad sino a lo inacabado, siendo siempre en germen (Lacoue-Labarthe y Nancy) y con el trabajo de la citación (Comp...

  15. Maximum Likelihood Analysis of Neutron Beta Decay Observables to Resolve the Limits of the V-A Law

    CERN Document Server

    Gardner, S

    2013-01-01

    We assess the ability of future neutron beta decay measurements of up to O(10^{-4}) precision to falsify the standard model, particularly the V-A law, and to identify the dynamics beyond it. To do this, we employ a maximum likelihood statistical framework which incorporates both experimental and theoretical uncertainties. Using illustrative combined global fits to Monte Carlo pseudodata, we also quantify the importance of experimental measurements of the energy dependence of the angular correlation coefficients as input to such efforts, and we determine the precision to which ill-known "second-class" hadronic matrix elements must be determined in order to exact such tests.

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

    DEFF Research Database (Denmark)

    Jalkanen, Karl J.; Gale, J.D.; Lassen, Peter Rygaard; Hemmingsen, Lars Bo Stegeager; Rodarte, A.; Degtyarenko, I.M.; Nieminen, R.M.; Christensen, S.B.; Knapp-Mohammady, M.; Suhai, S.

    -chiral' chromophores in the molecule, since one has two contributions; one due to the inherent chirality at the four chiral centers, and one due to the chirality of the side chain groups in specific conformers, that is, its helicity. Theoretical simulations for various levels of theory are compared to the experimental...... VA recorded to date. The VCD spectra simulations are presented, but no experimental VCD and Raman spectra have been reported to date, though some preliminary VCD measurements have been made in Stephens' lab in Los Angeles. The flexible side chain is proposed to be responsible for the small size of...

  17. Contribution of Amino Acid Region 334−335 from Factor Va Heavy Chain to the Catalytic Efficiency of Prothrombinase†

    OpenAIRE

    Barhoover, Melissa A.; Orban, Tivadar; Beck, Daniel O.; Bukys, Michael A.; Kalafatis, Michael

    2008-01-01

    We have demonstrated that amino acids E323, Y324, E330, and V331 from the factor Va heavy chain are required for the interaction of the cofactor with factor Xa and optimum rates of prothrombin cleavage. We have also shown that amino acid region 332−336 contains residues that are important for cofactor function. Using overlapping peptides, we identified amino acids D334 and Y335 as contributors to cofactor activity. We constructed recombinant factor V molecules with the mutations D334 → K and ...

  18. Multiple mental account portfolio's VaR model and fund risk management based on Copula theory%基于Copula理论的多心理帐户组合VaR模型与基金风险管理

    Institute of Scientific and Technical Information of China (English)

    李平; 黄光东; 路阳

    2011-01-01

    We improve the VaR model based on Copula theory and Shefrin and Statman's behavior portfolio theory and multiple mental account theory, adding the subjective parameters reflecting risk manager's expectation and risk attitude, such that risk measurement and management can be built on the "New 3P"— Probability, Prospect and Preference. Then we give a new approach to risk forecasting and optimizing of investment weight for fund portfolios.%在Shefrin和Statman的行为投资组合和多心理帐户理论的基础上,结合Copula理论对传统的VaR计算模型进行了改进,加入了反映人们预期和风险态度的主观参数,从而使风险度量能够建立在概率(probability)、前景(prospect)和偏好(preference)("新3P")的基础之上.然后在此基础上给出了基金投资组合风险预警和投资比例优化的方法.

  19. Fuzzy NPV model with VaR method and its hybrid intelligent algo-rithm%带有VaR方法的模糊NPV模型及其混合智能算法

    Institute of Scientific and Technical Information of China (English)

    袁国强; 刘晓俊; 朱建林

    2015-01-01

    Based on credibility theory, this paper establishes a class of NPV model with fuzzy VaR method and designs hybrid intelligent algorithm, which contains approximation approach, neuron network and genetic algorithm, to solve the proposed model. A numerical example is presented to illustrate the effectiveness of the model and algorithm. The sensitivity analysis of optimal solution will be done through changing the credibility level of the objective function and credibility constraint.%基于可信性理论建立一类带有模糊VaR方法的NPV模型,并设计含有逼近方法、神经网络和遗传算法的混合智能算法对提出的模型进行求解。给出一个数值例子表明模型和算法的有效性。通过改变目标函数和可信性约束中的可信性水平对最优解进行灵敏度分析。

  20. The interdependence of mental health service systems: the effects of VA mental health funding on veterans' use of state mental health inpatient facilities.

    Science.gov (United States)

    Desai, Rani A.; Rosenheck, Robert A.

    2000-06-01

    BACKGROUND: There are relatively few published data on how the financial structures of different health systems affect each other. With increasing financial restrictions in both public and private healthcare systems, it is important to understand how changes in one system (e.g. VA mental healthcare) affect utilization of other systems (e.g. state hospitals). AIMS OF THE STUDY: This study utilizes data from state hospitals in eight states to examine the relationship of VA per capita mental health funding and state per capita mental health expenditures to veterans' use of state hospitals, adjusting for other determinants of utilization. METHODS: This study utilized a large database that included records from all male inpatient admissions to state hospitals between 1984 and 1989 in eight states (n = 152541). Funding levels for state hospitals and VA mental health systems were examined as alternative enabling factors for veterans' use of state hospital care. Logistic regression models were adjusted for other determinants of utilization such as socio-economic status, diagnosis, travel distances to VA and non-VA facilities and the proportion of veterans in the population. RESULTS: The single strongest predictor of whether a state hospital patient would be a veteran was the level of VA mental healthcare funding (OR = 0.81 per $10 of funding per veteran in the population, p = 0.0001), with higher VA funding associated with less use of state hospitals by veterans. Higher per capita state funding, reciprocally, increased veterans' use of state hospitals. We also calculated elasticities for state hospital use with respect to VA mental healthcare funding and with respect to state hospital per capita funding. A 50% increase in VA per capita mental health spending was associated with a 30% decrease in veterans' use of state hospitals (elasticity of -0.6). Conversely, a 50% increase in state hospital per capita funding was associated with only an 11% increase in veterans' use of