Sample records for amplicon va derived

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

    PubMed

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

    2011-01-01

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

  2. Unlabeled oligonucleotides as internal temperature controls for genotyping by amplicon melting.

    PubMed

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

    2007-07-01

    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 degrees C attributable to the extractions were observed. To correct for solution chemistry differences between samples, complementary unlabeled oligonucleotides were included as internal temperature controls to shift and scale the temperature axis of derivative melting plots. This adjustment was applied to a duplex amplicon melting assay for the methylenetetrahydrofolate reductase variants 1298A>C and 677C>T. High- and low-temperature controls bracketing the amplicon melting region decreased the Tm SD within homozygous genotypes by 47 to 82%. The amplicon melting assay was 100% concordant to an adjacent hybridization probe (HybProbe) melting assay when temperature controls were included, whereas a 3% error rate was observed without temperature correction. In conclusion, internal temperature controls increase the accuracy of genotyping by high-resolution amplicon melting and should also improve results on lower resolution instruments.

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

    PubMed Central

    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 were observed. To correct for solution chemistry differences between samples, complementary unlabeled oligonucleotides were included as internal temperature controls to shift and scale the temperature axis of derivative melting plots. This adjustment was applied to a duplex amplicon melting assay for the methylenetetrahydrofolate reductase variants 1298A>C and 677C>T. High- and low-temperature controls bracketing the amplicon melting region decreased the Tm SD within homozygous genotypes by 47 to 82%. The amplicon melting assay was 100% concordant to an adjacent hybridization probe (HybProbe) melting assay when temperature controls were included, whereas a 3% error rate was observed without temperature correction. In conclusion, internal temperature controls increase the accuracy of genotyping by high-resolution amplicon melting and should also improve results on lower resolution instruments. PMID:17591926

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

    NASA Astrophysics Data System (ADS)

    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.

  5. Reproducibility and quantitation of amplicon sequencing-based detection

    PubMed Central

    Zhou, Jizhong; Wu, Liyou; Deng, Ye; Zhi, Xiaoyang; Jiang, Yi-Huei; Tu, Qichao; Xie, Jianping; Van Nostrand, Joy D; He, Zhili; Yang, Yunfeng

    2011-01-01

    To determine the reproducibility and quantitation of the amplicon sequencing-based detection approach for analyzing microbial community structure, a total of 24 microbial communities from a long-term global change experimental site were examined. Genomic DNA obtained from each community was used to amplify 16S rRNA genes with two or three barcode tags as technical replicates in the presence of a small quantity (0.1% wt/wt) of genomic DNA from Shewanella oneidensis MR-1 as the control. The technical reproducibility of the amplicon sequencing-based detection approach is quite low, with an average operational taxonomic unit (OTU) overlap of 17.2%±2.3% between two technical replicates, and 8.2%±2.3% among three technical replicates, which is most likely due to problems associated with random sampling processes. Such variations in technical replicates could have substantial effects on estimating β-diversity but less on α-diversity. A high variation was also observed in the control across different samples (for example, 66.7-fold for the forward primer), suggesting that the amplicon sequencing-based detection approach could not be quantitative. In addition, various strategies were examined to improve the comparability of amplicon sequencing data, such as increasing biological replicates, and removing singleton sequences and less-representative OTUs across biological replicates. Finally, as expected, various statistical analyses with preprocessed experimental data revealed clear differences in the composition and structure of microbial communities between warming and non-warming, or between clipping and non-clipping. Taken together, these results suggest that amplicon sequencing-based detection is useful in analyzing microbial community structure even though it is not reproducible and quantitative. However, great caution should be taken in experimental design and data interpretation when the amplicon sequencing-based detection approach is used for quantitative

  6. DAMe: a toolkit for the initial processing of datasets with PCR replicates of double-tagged amplicons for DNA metabarcoding analyses.

    PubMed

    Zepeda-Mendoza, Marie Lisandra; Bohmann, Kristine; Carmona Baez, Aldo; Gilbert, M Thomas P

    2016-05-03

    DNA metabarcoding is an approach for identifying multiple taxa in an environmental sample using specific genetic loci and taxa-specific primers. When combined with high-throughput sequencing it enables the taxonomic characterization of large numbers of samples in a relatively time- and cost-efficient manner. One recent laboratory development is the addition of 5'-nucleotide tags to both primers producing double-tagged amplicons and the use of multiple PCR replicates to filter erroneous sequences. However, there is currently no available toolkit for the straightforward analysis of datasets produced in this way. We present DAMe, a toolkit for the processing of datasets generated by double-tagged amplicons from multiple PCR replicates derived from an unlimited number of samples. Specifically, DAMe can be used to (i) sort amplicons by tag combination, (ii) evaluate PCR replicates dissimilarity, and (iii) filter sequences derived from sequencing/PCR errors, chimeras, and contamination. This is attained by calculating the following parameters: (i) sequence content similarity between the PCR replicates from each sample, (ii) reproducibility of each unique sequence across the PCR replicates, and (iii) copy number of the unique sequences in each PCR replicate. We showcase the insights that can be obtained using DAMe prior to taxonomic assignment, by applying it to two real datasets that vary in their complexity regarding number of samples, sequencing libraries, PCR replicates, and used tag combinations. Finally, we use a third mock dataset to demonstrate the impact and importance of filtering the sequences with DAMe. DAMe allows the user-friendly manipulation of amplicons derived from multiple samples with PCR replicates built in a single or multiple sequencing libraries. It allows the user to: (i) collapse amplicons into unique sequences and sort them by tag combination while retaining the sample identifier and copy number information, (ii) identify sequences carrying

  7. Induction of humoral responses to BHV-1 glycoprotein D expressed by HSV-1 amplicon vectors

    PubMed Central

    Blanc, Andrea Maria; Berois, Mabel Beatriz; Tomé, Lorena Magalí; Epstein, Alberto L.

    2012-01-01

    Herpes simplex virus type-1 (HSV-1) amplicon vectors are versatile and useful tools for transferring genes into cells that are capable of stimulating a specific immune response to their expressed antigens. In this work, two HSV-1-derived amplicon vectors were generated. One of these expressed the full-length glycoprotein D (gD) of bovine herpesvirus 1 while the second expressed the truncated form of gD (gDtr) which lacked the trans-membrane region. After evaluating gD expression in the infected cells, the ability of both vectors to induce a specific gD immune response was tested in BALB/c mice that were intramuscularly immunized. Specific serum antibody responses were detected in mice inoculated with both vectors, and the response against truncated gD was higher than the response against full-length gD. These results reinforce previous findings that HSV-1 amplicon vectors can potentially deliver antigens to animals and highlight the prospective use of these vectors for treating infectious bovine rhinotracheitis disease. PMID:22437537

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

    PubMed

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

    2014-01-01

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

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

    PubMed

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

    2012-06-25

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

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

    PubMed Central

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

    2014-01-01

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

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

    PubMed Central

    2012-01-01

    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 PMID:22759430

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

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Gardner, S. N.

    2013-08-08

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

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

    PubMed Central

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

    2017-01-01

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

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

    PubMed

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

    2017-01-01

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

  15. Electroanalytical study of proflavine intercalation in 5-methyl or inosine-containing amplicons.

    PubMed

    Alexiadou, Despina K; Ioannou, Andrea K; Kouidou-Andreou, Sofia A; Voulgaropoulos, Anastasios N; Girousi, Stella Th

    2008-10-01

    Amplicons corresponding to the GC-rich p53 exon 5 and its analogues, synthesized by substituting 60% of cytosine by 5-methyl-cytosine, or 60% of guanosine by inosine and GC-poor p53 exon 6 were synthesized and investigated electrochemically, in the presence and absence of proflavine, by differential pulse voltammetry (DPV). Incorporation of base analogues and the thermal stability of the resulting amplicons were tested in the presence of a fluorescent probe (Sybr-Green). Peak current at 1.0 V was lower for methylated than for unmethylated PCR amplicons and was similarly affected by proflavine intercalation. In contrast, considerable peak current differences were observed in the presence of proflavine for unmodified exon 5 v.s. exon 6 or inosine-containing amplicons. Thermal analysis verified the expected shifts in melting temperature (T (m)) due to the base analogue incorporation and GC-content variations. In conclusion, methylated and unmethylated PCR amplicons could be distinguished in model DNA systems using differential pulse voltammetry (DPV) and use of proflavine could serve as an electrochemical probe for identifying different DNA conformations.

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

    PubMed

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

    2013-01-18

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

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

    PubMed Central

    2013-01-01

    Background Demand for dialysis treatment exceeds its supply within the Veterans Health Administration (VA), requiring VA to outsource dialysis care by purchasing private sector dialysis for veterans on a fee-for-service basis. It is unclear whether outcomes are similar for veterans receiving dialysis from VA versus non-VA providers. We assessed the extent of chronic dialysis treatment utilization and differences in all-cause hospitalizations and mortality between veterans receiving dialysis from VA versus VA-outsourced providers. Methods We constructed a retrospective cohort of veterans in 2 VA regions who received chronic dialysis treatment financed by VA between January 2007 and December 2008. From VA administrative data, we identified veterans who received outpatient dialysis in (1) VA, (2) VA-outsourced settings, or (3) both (“dual”) settings. In adjusted analyses, we used two-part and logistic regression to examine associations between dialysis setting and all-cause hospitalization and mortality one-year from veterans’ baseline dialysis date. Results Of 1,388 veterans, 27% received dialysis exclusively in VA, 47% in VA-outsourced settings, and 25% in dual settings. Overall, half (48%) were hospitalized and 12% died. In adjusted analysis, veterans in VA-outsourced settings incurred fewer hospitalizations and shorter hospital stays than users of VA due to favorable selection. Dual-system dialysis patients had lower one-year mortality than veterans receiving VA dialysis. Conclusions VA expenditures for “buying” outsourced dialysis are high and increasing relative to “making” dialysis treatment within its own system. Outcomes comparisons inform future make-or-buy decisions and suggest the need for VA to consider veterans’ access to care, long-term VA savings, and optimal patient outcomes in its placement decisions for dialysis services. PMID:23327632

  18. VA Caregiver Support

    MedlinePlus

    ... Performance VA Plans, Budget, & Performance VA Center for Innovation (VACI) Agency Financial Report ... Management Services Veterans Service Organizations Office of Accountability & Whistleblower ...

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

    PubMed Central

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

    2018-01-01

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

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

    PubMed Central

    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

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

    PubMed

    Petrillo, Mauro; Angers-Loustau, Alexandre; Henriksson, Peter; Bonfini, Laura; Patak, Alex; Kreysa, Joachim

    2015-01-01

    The DNA target sequence is the key element in designing detection methods for genetically modified organisms (GMOs). Unfortunately this information is frequently lacking, especially for unauthorized GMOs. In addition, patent sequences are generally poorly annotated, buried in complex and extensive documentation and hard to link to the corresponding GM event. Here, we present the JRC GMO-Amplicons, a database of amplicons collected by screening public nucleotide sequence databanks by in silico determination of PCR amplification with reference methods for GMO analysis. The European Union Reference Laboratory for Genetically Modified Food and Feed (EU-RL GMFF) provides these methods in the GMOMETHODS database to support enforcement of EU legislation and GM food/feed control. The JRC GMO-Amplicons database is composed of more than 240 000 amplicons, which can be easily accessed and screened through a web interface. To our knowledge, this is the first attempt at pooling and collecting publicly available sequences related to GMOs in food and feed. The JRC GMO-Amplicons supports control laboratories in the design and assessment of GMO methods, providing inter-alia in silico prediction of primers specificity and GM targets coverage. The new tool can assist the laboratories in the analysis of complex issues, such as the detection and identification of unauthorized GMOs. Notably, the JRC GMO-Amplicons database allows the retrieval and characterization of GMO-related sequences included in patents documentation. Finally, it can help annotating poorly described GM sequences and identifying new relevant GMO-related sequences in public databases. The JRC GMO-Amplicons is freely accessible through a web-based portal that is hosted on the EU-RL GMFF website. Database URL: http://gmo-crl.jrc.ec.europa.eu/jrcgmoamplicons/. © The Author(s) 2015. Published by Oxford University Press.

  2. Formation of Linear Amplicons with Inverted Duplications in Leishmania Requires the MRE11 Nuclease

    PubMed Central

    Laffitte, Marie-Claude N.; Genois, Marie-Michelle; Mukherjee, Angana; Légaré, Danielle; Masson, Jean-Yves; Ouellette, Marc

    2014-01-01

    Extrachromosomal DNA amplification is frequent in the protozoan parasite Leishmania selected for drug resistance. The extrachromosomal amplified DNA is either circular or linear, and is formed at the level of direct or inverted homologous repeated sequences that abound in the Leishmania genome. The RAD51 recombinase plays an important role in circular amplicons formation, but the mechanism by which linear amplicons are formed is unknown. We hypothesized that the Leishmania infantum DNA repair protein MRE11 is required for linear amplicons following rearrangements at the level of inverted repeats. The purified LiMRE11 protein showed both DNA binding and exonuclease activities. Inactivation of the LiMRE11 gene led to parasites with enhanced sensitivity to DNA damaging agents. The MRE11−/− parasites had a reduced capacity to form linear amplicons after drug selection, and the reintroduction of an MRE11 allele led to parasites regaining their capacity to generate linear amplicons, but only when MRE11 had an active nuclease activity. These results highlight a novel MRE11-dependent pathway used by Leishmania to amplify portions of its genome to respond to a changing environment. PMID:25474106

  3. 75 FR 78806 - Agency Information Collection (Create Payment Request for the VA Funding Fee Payment System (VA...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-12-16

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

  4. 78 FR 59771 - Proposed Information Collection (Create Payment Request for the VA Funding Fee Payment System (VA...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-09-27

    ... Payment Request for the VA Funding Fee Payment System (VA FFPS); a Computer Generated Funding Fee Receipt.... Title: Create Payment Request for the VA Funding Fee Payment System (VA FFPS); A Computer Generated Funding Fee Receipt, VA Form 26-8986. OMB Control Number: 2900-0474. Type of Review: Revision of a...

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

    PubMed Central

    Herbold, Craig W.; Pelikan, Claus; Kuzyk, Orest; Hausmann, Bela; Angel, Roey; Berry, David; Loy, Alexander

    2015-01-01

    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. PMID:26236305

  6. AmpliVar: mutation detection in high-throughput sequence from amplicon-based libraries.

    PubMed

    Hsu, Arthur L; Kondrashova, Olga; Lunke, Sebastian; Love, Clare J; Meldrum, Cliff; Marquis-Nicholson, Renate; Corboy, Greg; Pham, Kym; Wakefield, Matthew; Waring, Paul M; Taylor, Graham R

    2015-04-01

    Conventional means of identifying variants in high-throughput sequencing align each read against a reference sequence, and then call variants at each position. Here, we demonstrate an orthogonal means of identifying sequence variation by grouping the reads as amplicons prior to any alignment. We used AmpliVar to make key-value hashes of sequence reads and group reads as individual amplicons using a table of flanking sequences. Low-abundance reads were removed according to a selectable threshold, and reads above this threshold were aligned as groups, rather than as individual reads, permitting the use of sensitive alignment tools. We show that this approach is more sensitive, more specific, and more computationally efficient than comparable methods for the analysis of amplicon-based high-throughput sequencing data. The method can be extended to enable alignment-free confirmation of variants seen in hybridization capture target-enrichment data. © 2015 WILEY PERIODICALS, INC.

  7. Microbes in deep marine sediments viewed through amplicon sequencing and metagenomics

    NASA Astrophysics Data System (ADS)

    Biddle, J.; Leon, Z. R.; Russell, J. A., III; Martino, A. J.

    2016-12-01

    Nearly twenty percent of microbial biomass on Earth can be found in the marine subsurface. The majority of this is concentrated on continental margins, which have been investigated by scientific drilling. On the Costa Rica Margin, Iberian Margin and Peru Margins, sediment samples have been investigated through DNA extraction followed by amplicon and metagenomic sequencing. Overall samples show a high degree of microbial diversity, including many lineages of newly defined groups. In this talk, metagenome assembled genomes of unusual lineages will be presented, including their relationships to shallower relatives. From Costa Rica, in particular, we have retrieved deep relatives of Lokiarchaeota and Thorarchaeota, as well as other deeply branching archaeal relatives. We discuss their genome similarities to both other archaea and eukaryotes. From the Iberian Margin, relatives of Atribacteria and Aerophobetes will be discussed. Finally, we will detail the knowledge lost or gained depending on whether samples are studied via amplicon sequencing or total metagenomics, as studies in other environments have shown that up to 15% of microbial diversity is ignored when samples are studied via amplicon sequencing alone.

  8. VA Health Care: Further Action Needed to Address Weaknesses in Management and Oversight of Non-VA Medical Care

    DTIC Science & Technology

    2014-06-18

    medical centers. VA also provides care to veterans in VA-operated community-based outpatient clinics, community living centers ( nursing homes...facility or nursing home up to the point that the veteran can be safely returned to the VA facility following the emergency care treatment at the non-VA... nursing home care, compensation and pension exams, and most pharmacy expenses paid for through the Non-VA Medical Care Program. (See fig. 1.) 8VA

  9. Myosin Va binding to neurofilaments is essential for correct myosin Va distribution and transport and neurofilament density

    PubMed Central

    Rao, Mala V.; Engle, Linda J.; Mohan, Panaiyur S.; Yuan, Aidong; Qiu, Dike; Cataldo, Anne; Hassinger, Linda; Jacobsen, Stephen; Lee, Virginia M-Y.; Andreadis, Athena; Julien, Jean-Pierre; Bridgman, Paul C.; Nixon, Ralph A.

    2002-01-01

    The identification of molecular motors that modulate the neuronal cytoskeleton has been elusive. Here, we show that a molecular motor protein, myosin Va, is present in high proportions in the cytoskeleton of mouse CNS and peripheral nerves. Immunoelectron microscopy, coimmunoprecipitation, and blot overlay analyses demonstrate that myosin Va in axons associates with neurofilaments, and that the NF-L subunit is its major ligand. A physiological association is indicated by observations that the level of myosin Va is reduced in axons of NF-L–null mice lacking neurofilaments and increased in mice overexpressing NF-L, but unchanged in NF-H–null mice. In vivo pulse-labeled myosin Va advances along axons at slow transport rates overlapping with those of neurofilament proteins and actin, both of which coimmunoprecipitate with myosin Va. Eliminating neurofilaments from mice selectively accelerates myosin Va translocation and redistributes myosin Va to the actin-rich subaxolemma and membranous organelles. Finally, peripheral axons of dilute-lethal mice, lacking functional myosin Va, display selectively increased neurofilament number and levels of neurofilament proteins without altering axon caliber. These results identify myosin Va as a neurofilament-associated protein, and show that this association is essential to establish the normal distribution, axonal transport, and content of myosin Va, and the proper numbers of neurofilaments in axons. PMID:12403814

  10. Animals on VA property. Final rule.

    PubMed

    2015-08-17

    The Department of Veterans Affairs (VA) amends its regulation concerning the presence of animals on VA property. This final rule expands the current VA regulation to authorize the presence of service animals consistent with applicable Federal law when these animals accompany individuals with disabilities seeking admittance to property owned or operated by VA.

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

    PubMed

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

    2015-02-03

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

  12. 75 FR 61252 - Proposed Information Collection (Create Payment Request for the VA Funding Fee Payment System (VA...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-10-04

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

  13. 75 FR 61859 - Proposed Information Collection (Create Payment Request for the VA Funding Fee Payment System (VA...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-10-06

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

  14. Determination of VA health care costs.

    PubMed

    Barnett, Paul G

    2003-09-01

    In the absence of billing data, alternative methods are used to estimate the cost of hospital stays, outpatient visits, and treatment innovations in the U.S. Department of Veterans Affairs (VA). The choice of method represents a trade-off between accuracy and research cost. The direct measurement method gathers information on staff activities, supplies, equipment, space, and workload. Since it is expensive, direct measurement should be reserved for finding short-run costs, evaluating provider efficiency, or determining the cost of treatments that are innovative or unique to VA. The pseudo-bill method combines utilization data with a non-VA reimbursement schedule. The cost regression method estimates the cost of VA hospital stays by applying the relationship between cost and characteristics of non-VA hospitalizations. The Health Economics Resource Center uses pseudo-bill and cost regression methods to create an encounter-level database of VA costs. Researchers are also beginning to use the VA activity-based cost allocation system.

  15. 48 CFR 853.215-70 - VA Form 10-1170, Application for Furnishing Nursing Home Care to Beneficiaries of VA.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ..., Application for Furnishing Nursing Home Care to Beneficiaries of VA. 853.215-70 Section 853.215-70 Federal... 853.215-70 VA Form 10-1170, Application for Furnishing Nursing Home Care to Beneficiaries of VA. VA Form 10-1170, Application for Furnishing Nursing Home Care to Beneficiaries of VA, will be used for...

  16. 48 CFR 853.215-70 - VA Form 10-1170, Application for Furnishing Nursing Home Care to Beneficiaries of VA.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ..., Application for Furnishing Nursing Home Care to Beneficiaries of VA. 853.215-70 Section 853.215-70 Federal... 853.215-70 VA Form 10-1170, Application for Furnishing Nursing Home Care to Beneficiaries of VA. VA Form 10-1170, Application for Furnishing Nursing Home Care to Beneficiaries of VA, will be used for...

  17. 48 CFR 853.215-70 - VA Form 10-1170, Application for Furnishing Nursing Home Care to Beneficiaries of VA.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ..., Application for Furnishing Nursing Home Care to Beneficiaries of VA. 853.215-70 Section 853.215-70 Federal... 853.215-70 VA Form 10-1170, Application for Furnishing Nursing Home Care to Beneficiaries of VA. VA Form 10-1170, Application for Furnishing Nursing Home Care to Beneficiaries of VA, will be used for...

  18. 48 CFR 853.215-70 - VA Form 10-1170, Application for Furnishing Nursing Home Care to Beneficiaries of VA.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ..., Application for Furnishing Nursing Home Care to Beneficiaries of VA. 853.215-70 Section 853.215-70 Federal... 853.215-70 VA Form 10-1170, Application for Furnishing Nursing Home Care to Beneficiaries of VA. VA Form 10-1170, Application for Furnishing Nursing Home Care to Beneficiaries of VA, will be used for...

  19. 48 CFR 853.215-70 - VA Form 10-1170, Application for Furnishing Nursing Home Care to Beneficiaries of VA.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ..., Application for Furnishing Nursing Home Care to Beneficiaries of VA. 853.215-70 Section 853.215-70 Federal... 853.215-70 VA Form 10-1170, Application for Furnishing Nursing Home Care to Beneficiaries of VA. VA Form 10-1170, Application for Furnishing Nursing Home Care to Beneficiaries of VA, will be used for...

  20. A fungal mock community control for amplicon sequencing experiments

    USDA-ARS?s Scientific Manuscript database

    The field of microbial ecology has been profoundly advanced by the ability to profile the composition of complex microbial communities by means of high throughput amplicon sequencing of marker genes amplified directly from environmental genomic DNA extracts. However, it has become increasingly clear...

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

    PubMed

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

    2015-07-01

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

  2. Characterizing partial AZFc deletions of the Y chromosome with amplicon-specific sequence markers

    PubMed Central

    Navarro-Costa, Paulo; Pereira, Luísa; Alves, Cíntia; Gusmão, Leonor; Proença, Carmen; Marques-Vidal, Pedro; Rocha, Tiago; Correia, Sónia C; Jorge, Sónia; Neves, António; Soares, Ana P; Nunes, Joaquim; Calhaz-Jorge, Carlos; Amorim, António; Plancha, Carlos E; Gonçalves, João

    2007-01-01

    Background The AZFc region of the human Y chromosome is a highly recombinogenic locus containing multi-copy male fertility genes located in repeated DNA blocks (amplicons). These AZFc gene families exhibit slight sequence variations between copies which are considered to have functional relevance. Yet, partial AZFc deletions yield phenotypes ranging from normospermia to azoospermia, thwarting definite conclusions on their real impact on fertility. Results The amplicon content of partial AZFc deletion products was characterized with novel amplicon-specific sequence markers. Data indicate that partial AZFc deletions are a male infertility risk [odds ratio: 5.6 (95% CI: 1.6–30.1)] and although high diversity of partial deletion products and sequence conversion profiles were recorded, the AZFc marker profiles detected in fertile men were also observed in infertile men. Additionally, the assessment of rearrangement recurrence by Y-lineage analysis indicated that while partial AZFc deletions occurred in highly diverse samples, haplotype diversity was minimal in fertile men sharing identical marker profiles. Conclusion Although partial AZFc deletion products are highly heterogeneous in terms of amplicon content, this plasticity is not sufficient to account for the observed phenotypical variance. The lack of causative association between the deletion of specific gene copies and infertility suggests that AZFc gene content might be part of a multifactorial network, with Y-lineage evolution emerging as a possible phenotype modulator. PMID:17903263

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

    ERIC Educational Resources Information Center

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

    2009-01-01

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

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

    PubMed Central

    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 mutation type, position, and concentration on HRM scores. The impact of amplicon length and G/C content on HRM scores was also evaluated. Different mutation types affected HRM scores to varying degrees (1-bp deletion < 1-bp change < 3-bp insertion < 9-bp insertion). The impact of mutations on HRM scores was influenced by amplicon length and the position of the mutation within the amplicon. Mutations were detected at concentrations of 5% to 95%, with the greatest impact at 50%. The G/C content altered melting temperature values of amplicons but had no impact on HRM scores. These data are relevant to the design of assays that measure genetic diversity using HRM technology. PMID:23178437

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

    PubMed

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

    2017-01-01

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

  6. The Impact of a Change in the Price of VA Health Care on Utilization of VA and Medicare Services.

    PubMed

    Nelson, Richard E; Hicken, Bret; Vanneman, Megan; Liu, Chuan-Fen; Rupper, Randall

    2018-05-15

    The passage of the Veterans Access, Choice, and Accountability Act of 2014 has expanded the non-Veteran Affairs (VA) care options for eligible US Veterans. In order for these new arrangements to provide the best care possible for Veterans, it is important to understand the relationship between VA and non-VA care options. The purpose of this study was to use another recent VA policy change, one that increased the reimbursement rate that eligible Veterans receive for travel for health care to VA, to understand the use of VA and Medicare services among Medicare-enrolled Veterans. We used a difference-in-difference technique to compare inpatient and outpatient utilization and cost in VA and Medicare between Veterans who were eligible for travel reimbursement and those who were not eligible following 2 increases in the travel reimbursement rate. We used generalized estimating equation models and 2-part models when cost outcomes were rare. Our cohort consisted of 110,007 Medicare-enrolled Veterans, including 25,076 under 65 and 84,931 over 65 years old. Following the travel reimbursement rate increases, the number of VA outpatient encounters increased for Veterans in our cohort regardless of age group or whether living in an urban or rural area. The number of non-VA outpatient encounters decreased significantly for Veterans in both age groups living in rural areas following these policy changes. Our estimates suggest that VA outpatient care may be a substitute for Medicare outpatient care for Medicare-enrolled Veterans living in rural areas. These results are important because they indicate how Veteran health care utilization might be affected by future policy changes designed to increase access to VA services. They also indicate the ripple effects that may occur in other health systems due to changes in the VA system.

  7. Managing the human side of change in VA's transformation.

    PubMed

    Backer, T E

    1997-01-01

    Transformational change interventions often fail or short fall of their intended impact on organizations and systems. One main reason is that these interventions frequently do not strategically address the complex human dynamics of change. This happens despite awareness of and commitment to intervening at this level by top management and change leaders. The wisdom that "systems don't change; people change" is widely acknowledged but inadequately applied. These are exactly the conditions the U.S. Department of Veterans Affairs (VA) faces in deploying its new Veterans Integrated Services Networks (VISNs). Applying validated behavioral science strategies that address the human side of change will help VA implement VISNs effectively. Six strategies derived from many years of study and practice in the public and private sectors are discussed, along with suggestions for VISN managers about how to implement them.

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

    PubMed

    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). (c) 2016 APA, all rights reserved).

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

    PubMed Central

    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 amplicon. Retrovirus expression cassettes were used to generate the HSV-EBV-retrovirus hybrid vectors, HERE and HERA, which code for the ecotropic and the amphotropic envelopes, respectively. Retrovirus vector sequences encoding lacZ were cloned downstream from the GPE expression unit. Transfection of 293T/17 cells with amplicon plasmids yielded retrovirus titers between 106 and 107 transducing units/ml, while infection of the same cells with amplicon vectors generated maximum titers 1 order of magnitude lower. Retrovirus titers were dependent on the extent of transduction by amplicon vectors for the same cell line, but different cell lines displayed varying capacities to produce retrovirus vectors even at the same transduction efficiencies. Infection of human and dog primary gliomas with this system resulted in the production of retrovirus vectors for more than 1 week and the long-term retention and increase in transgene activity over time in these cell populations. Although the efficiency of this system still has to be determined in vivo, many applications are foreseeable for this approach to gene delivery. PMID:10559361

  10. Phylogenetic Placement of Exact Amplicon Sequences Improves Associations with Clinical Information

    PubMed Central

    McDonald, Daniel; Gonzalez, Antonio; Navas-Molina, Jose A.; Jiang, Lingjing; Xu, Zhenjiang Zech; Winker, Kevin; Kado, Deborah M.; Orwoll, Eric; Manary, Mark; Mirarab, Siavash

    2018-01-01

    ABSTRACT Recent algorithmic advances in amplicon-based microbiome studies enable the inference of exact amplicon sequence fragments. These new methods enable the investigation of sub-operational taxonomic units (sOTU) by removing erroneous sequences. However, short (e.g., 150-nucleotide [nt]) DNA sequence fragments do not contain sufficient phylogenetic signal to reproduce a reasonable tree, introducing a barrier in the utilization of critical phylogenetically aware metrics such as Faith’s PD or UniFrac. Although fragment insertion methods do exist, those methods have not been tested for sOTUs from high-throughput amplicon studies in insertions against a broad reference phylogeny. We benchmarked the SATé-enabled phylogenetic placement (SEPP) technique explicitly against 16S V4 sequence fragments and showed that it outperforms the conceptually problematic but often-used practice of reconstructing de novo phylogenies. In addition, we provide a BSD-licensed QIIME2 plugin (https://github.com/biocore/q2-fragment-insertion) for SEPP and integration into the microbial study management platform QIITA. IMPORTANCE The move from OTU-based to sOTU-based analysis, while providing additional resolution, also introduces computational challenges. We demonstrate that one popular method of dealing with sOTUs (building a de novo tree from the short sequences) can provide incorrect results in human gut metagenomic studies and show that phylogenetic placement of the new sequences with SEPP resolves this problem while also yielding other benefits over existing methods. PMID:29719869

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

    PubMed

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

    2016-09-01

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

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

    PubMed Central

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

    2015-01-01

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

  13. 77 FR 70893 - Authorization for Non-VA Medical Services

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-11-28

    ... professions, Health records, Homeless, Mental health programs, Nursing homes, Reporting and recordkeeping... restrictive modes of healthcare delivery. Although VA has made great strides to expand the delivery of... expand VA's authority to provide non-VA medical services under the non- VA care authority. As amended...

  14. 77 FR 70967 - Authorization for Non-VA Medical Services

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-11-28

    ... expand the delivery of healthcare to veterans, VA is, like the rest of the healthcare industry...(a)(2)(B) to expand VA's authority to provide non-VA medical services under the non- VA care... furnished hospital care, nursing home care, domiciliary care, or medical services and who requires medical...

  15. 77 FR 67063 - VA Directive 0005 on Scientific Integrity

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-11-08

    ... policies that: Foster a culture of transparency, integrity, and ethical behavior in the development and... provided to the VA's Office of Inspector General (OIG), the Office of Government Ethics, and Congress. VA...: VA has amended Directive 0005, ] 5.b., to state that ``VA policy provides an ethical and accountable...

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

    PubMed Central

    Chandramohan, Daniel; Clark, Samuel J.; Jakob, Robert; Leitao, Jordana; Rao, Chalapati; Riley, Ian; Setel, Philip W.

    2018-01-01

    Background Verbal autopsy (VA) is a practical method for determining probable causes of death at the population level in places where systems for medical certification of cause of death are weak. VA methods suitable for use in routine settings, such as civil registration and vital statistics (CRVS) systems, have developed rapidly in the last decade. These developments have been part of a growing global momentum to strengthen CRVS systems in low-income countries. With this momentum have come pressure for continued research and development of VA methods and the need for a single standard VA instrument on which multiple automated diagnostic methods can be developed. Methods and findings In 2016, partners harmonized a WHO VA standard instrument that fully incorporates the indicators necessary to run currently available automated diagnostic algorithms. The WHO 2016 VA instrument, together with validated approaches to analyzing VA data, offers countries solutions to improving information about patterns of cause-specific mortality. This VA instrument offers the opportunity to harmonize the automated diagnostic algorithms in the future. Conclusions Despite all improvements in design and technology, VA is only recommended where medical certification of cause of death is not possible. The method can nevertheless provide sufficient information to guide public health priorities in communities in which physician certification of deaths is largely unavailable. The WHO 2016 VA instrument, together with validated approaches to analyzing VA data, offers countries solutions to improving information about patterns of cause-specific mortality. PMID:29320495

  17. 78 FR 76064 - Authorization for Non-VA Medical Services; Withdrawal

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-12-16

    ... DEPARTMENT OF VETERANS AFFAIRS 38 CFR Part 17 RIN 2900-AO47 Authorization for Non-VA Medical... November 28, 2012, that would have amended its regulations regarding payment by VA for medical services under VA's statutory authority to provide non-VA medical care. VA sought to remove an outdated...

  18. Gaussian decomposition of high-resolution melt curve derivatives for measuring genome-editing efficiency

    PubMed Central

    Zaboikin, Michail; Freter, Carl

    2018-01-01

    We describe a method for measuring genome editing efficiency from in silico analysis of high-resolution melt curve data. The melt curve data derived from amplicons of genome-edited or unmodified target sites were processed to remove the background fluorescent signal emanating from free fluorophore and then corrected for temperature-dependent quenching of fluorescence of double-stranded DNA-bound fluorophore. Corrected data were normalized and numerically differentiated to obtain the first derivatives of the melt curves. These were then mathematically modeled as a sum or superposition of minimal number of Gaussian components. Using Gaussian parameters determined by modeling of melt curve derivatives of unedited samples, we were able to model melt curve derivatives from genetically altered target sites where the mutant population could be accommodated using an additional Gaussian component. From this, the proportion contributed by the mutant component in the target region amplicon could be accurately determined. Mutant component computations compared well with the mutant frequency determination from next generation sequencing data. The results were also consistent with our earlier studies that used difference curve areas from high-resolution melt curves for determining the efficiency of genome-editing reagents. The advantage of the described method is that it does not require calibration curves to estimate proportion of mutants in amplicons of genome-edited target sites. PMID:29300734

  19. Estimating the costs of VA ambulatory care.

    PubMed

    Phibbs, Ciaran S; Bhandari, Aman; Yu, Wei; Barnett, Paul G

    2003-09-01

    This article reports how we matched Common Procedure Terminology (CPT) codes with Medicare payment rates and aggregate Veterans Affairs (VA) budget data to estimate the costs of every VA ambulatory encounter. Converting CPT codes to encounter-level costs was more complex than a simple match of Medicare reimbursements to CPT codes. About 40 percent of the CPT codes used in VA, representing about 20 percent of procedures, did not have a Medicare payment rate and required other cost estimates. Reconciling aggregated estimated costs to the VA budget allocations for outpatient care produced final VA cost estimates that were lower than projected Medicare reimbursements. The methods used to estimate costs for encounters could be replicated for other settings. They are potentially useful for any system that does not generate billing data, when CPT codes are simpler to collect than billing data, or when there is a need to standardize cost estimates across data sources.

  20. High-Throughput Sequencing of 16S rRNA Gene Amplicons: Effects of Extraction Procedure, Primer Length and Annealing Temperature

    PubMed Central

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

    2012-01-01

    The analysis of 16S-rDNA sequences to assess the bacterial community composition of a sample is a widely used technique that has increased with the advent of high throughput sequencing. Although considerable effort has been devoted to identifying the most informative region of the 16S gene and the optimal informatics procedures to process the data, little attention has been paid to the PCR step, in particular annealing temperature and primer length. To address this, amplicons derived from 16S-rDNA were generated from chicken caecal content DNA using different annealing temperatures, primers and different DNA extraction procedures. The amplicons were pyrosequenced to determine the optimal protocols for capture of maximum bacterial diversity from a chicken caecal sample. Even at very low annealing temperatures there was little effect on the community structure, although the abundance of some OTUs such as Bifidobacterium increased. Using shorter primers did not reveal any novel OTUs but did change the community profile obtained. Mechanical disruption of the sample by bead beating had a significant effect on the results obtained, as did repeated freezing and thawing. In conclusion, existing primers and standard annealing temperatures captured as much diversity as lower annealing temperatures and shorter primers. PMID:22666455

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

    PubMed

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

    2012-01-01

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

  2. VaST: A variability search toolkit

    NASA Astrophysics Data System (ADS)

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

    2018-01-01

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

  3. 38 CFR 77.17 - Recovery of funds by VA.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 38 Pensions, Bonuses, and Veterans' Relief 2 2014-07-01 2014-07-01 false Recovery of funds by VA....17 Recovery of funds by VA. (a) Recovery of funds. VA may recover from the grantee any funds that are... additional adaptive sports grant payments. When VA makes a final decision that action will be taken to...

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

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-10-22

    ... DEPARTMENT OF VETERANS AFFAIRS 38 CFR Part 17 RIN 2900-AO85 VA Dental Insurance Program... Veterans Affairs (VA) is taking direct final action to amend its regulations related to the VA Dental Insurance Program (VADIP), a pilot program to offer premium-based dental insurance to enrolled veterans and...

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

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-10-23

    ... DEPARTMENT OF VETERANS AFFAIRS 38 CFR Part 17 RIN 2900-AO86 VA Dental Insurance Program... Affairs (VA) proposes to amend its regulations related to the VA Dental Insurance Program (VADIP), a pilot program to offer premium-based dental insurance to enrolled veterans and certain survivors and dependents...

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

    PubMed

    Bezold, C; Mayer, E; Dighe, A

    1997-01-01

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

  7. A universal procedure for primer labelling of amplicons.

    PubMed Central

    Neilan, B A; Wilton, A N; Jacobs, D

    1997-01-01

    Detection and visualisation of nucleic acids is integral to genome analyses. Exponential amplification procedures have provided the means for the manipulation of nucleic acid sequences, which were otherwise inaccessible. We describe the development and application of a universal method for the labelling of any PCR product using a single end-labelled primer. Amplification was performed in a single reaction with the resulting amplicon labelled to a high specific activity. The method was adapted to a wide range of PCRs and significantly reduced the expense of such analyses. PMID:9207046

  8. Targeted RNA-Sequencing with Competitive Multiplex-PCR Amplicon Libraries

    PubMed Central

    Blomquist, Thomas M.; Crawford, Erin L.; Lovett, Jennie L.; Yeo, Jiyoun; Stanoszek, Lauren M.; Levin, Albert; Li, Jia; Lu, Mei; Shi, Leming; Muldrew, Kenneth; Willey, James C.

    2013-01-01

    Whole transcriptome RNA-sequencing is a powerful tool, but is costly and yields complex data sets that limit its utility in molecular diagnostic testing. A targeted quantitative RNA-sequencing method that is reproducible and reduces the number of sequencing reads required to measure transcripts over the full range of expression would be better suited to diagnostic testing. Toward this goal, we developed a competitive multiplex PCR-based amplicon sequencing library preparation method that a) targets only the sequences of interest and b) controls for inter-target variation in PCR amplification during library preparation by measuring each transcript native template relative to a known number of synthetic competitive template internal standard copies. To determine the utility of this method, we intentionally selected PCR conditions that would cause transcript amplification products (amplicons) to converge toward equimolar concentrations (normalization) during library preparation. We then tested whether this approach would enable accurate and reproducible quantification of each transcript across multiple library preparations, and at the same time reduce (through normalization) total sequencing reads required for quantification of transcript targets across a large range of expression. We demonstrate excellent reproducibility (R2 = 0.997) with 97% accuracy to detect 2-fold change using External RNA Controls Consortium (ERCC) reference materials; high inter-day, inter-site and inter-library concordance (R2 = 0.97–0.99) using FDA Sequencing Quality Control (SEQC) reference materials; and cross-platform concordance with both TaqMan qPCR (R2 = 0.96) and whole transcriptome RNA-sequencing following “traditional” library preparation using Illumina NGS kits (R2 = 0.94). Using this method, sequencing reads required to accurately quantify more than 100 targeted transcripts expressed over a 107-fold range was reduced more than 10,000-fold, from 2.3×109 to 1

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

    PubMed Central

    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

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

    PubMed

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

    2017-12-14

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

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

    PubMed

    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. Copyright © 2015 Elsevier B.V. All rights reserved.

  12. 48 CFR 819.7109 - VA review of application.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... SOCIOECONOMIC PROGRAMS SMALL BUSINESS PROGRAMS VA Mentor-Protégé Program 819.7109 VA review of application. (a) VA OSDBU will review the information to establish the mentor and protégé eligibility and to ensure... charge to apply for the Mentor-Protégé Program. (b) After OSDBU completes its review and provides written...

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

    PubMed

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

    2014-10-01

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

  14. 38 CFR 1.203 - Information to be reported to VA Police.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

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

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

    PubMed

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

    2014-03-15

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

  16. Adenovirus virus-associated RNAII-derived small RNAs are efficiently incorporated into the rna-induced silencing complex and associate with polyribosomes.

    PubMed

    Xu, Ning; Segerman, Bo; Zhou, Xiaofu; Akusjärvi, Göran

    2007-10-01

    Adenovirus type 5 encodes two highly structured short RNAs, the virus-associated (VA) RNAI and RNAII. Both are processed by Dicer into small RNAs that are incorporated into the RNA-induced silencing complex (RISC). We show here, by cloning of small RNAs, that approximately 80% of Ago2-containing RISC immunopurified from late-infected cells is associated with VA RNA-derived small RNAs (mivaRNAs). Most surprisingly, VA RNAII, which is expressed at 20-fold lower levels compared to that of VA RNAI, appears to be the preferred substrate for Dicer and accounts for approximately 60% of all small RNAs in RISC. The mivaRNAs are derived from the 3' strand of the terminal stems of the VA RNAs, with the major fraction of VA RNAII starting at position 138. The small RNAs derived from VA RNAI were more heterogeneous in size, with the two predominant small RNAs starting at positions 137 and 138. Collectively, our results suggest that the mivaRNAs are efficiently used for RISC assembly in late-infected cells. Potentially, they function as miRNAs, regulating translation of cellular mRNAs. In support of this hypothesis, we detected a fraction of the VA RNAII-derived mivaRNAs on polyribosomes.

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

    PubMed

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

    2016-03-01

    Effective poststroke rehabilitation care can speed patient recovery and minimize patient functional disabilities. Veterans affairs (VA) community living centers (CLCs) and VA-contracted community nursing homes (CNHs) are the 2 major sources of institutional long-term care for Veterans with stroke receiving care under VA auspices. This study compares rehabilitation therapy and restorative nursing care among Veterans residing in VA CLCs versus those Veterans in VA-contracted CNHs. Retrospective observational. All Veterans diagnosed with stroke, newly admitted to the CLCs or CNHs during the study period who completed at least 2 Minimum Data Set assessments postadmission. The outcomes were numbers of days for rehabilitation therapy and restorative nursing care received by the Veterans during their stays in CLCs or CNHs as documented in the Minimum Data Set databases. For rehabilitation therapy, the CLC Veterans had lower user rates (75.2% vs. 76.4%, P=0.078) and fewer observed therapy days (4.9 vs. 6.4, P<0.001) than CNH Veterans. However, the CLC Veterans had higher adjusted odds for therapy (odds ratio=1.16, P=0.033), although they had fewer average therapy days (coefficient=-1.53±0.11, P<0.001). For restorative nursing care, CLC Veterans had higher user rates (33.5% vs. 30.6%, P<0.001), more observed average care days (9.4 vs. 5.9, P<0.001), higher adjusted odds (odds ratio=2.28, P<0.001), and more adjusted days for restorative nursing care (coefficient=5.48±0.37, P<0.001). Compared with their counterparts at VA-contracted CNHs, Veterans at VA CLCs had fewer average rehabilitation therapy days (both unadjusted and adjusted), but they were significantly more likely to receive restorative nursing care both before and after risk adjustment.

  18. Veterans' experiences initiating VA-based mental health care.

    PubMed

    Bovin, Michelle J; Miller, Christopher J; Koenig, Christopher J; Lipschitz, Jessica M; Zamora, Kara A; Wright, Patricia B; Pyne, Jeffrey M; Burgess, James F

    2018-05-21

    Military veterans who could benefit from mental health services often do not access them. Research has revealed a range of barriers associated with initiating United States Department of Veterans Affairs (VA) care, including those specific to accessing mental health care (e.g., fear of stigmatization). More work is needed to streamline access to VA mental health-care services for veterans. In the current study, we interviewed 80 veterans from 9 clinics across the United States about initiation of VA mental health care to identify barriers to access. Results suggested that five predominant factors influenced veterans' decisions to initiate care: (a) awareness of VA mental health services; (b) fear of negative consequences of seeking care; (c) personal beliefs about mental health treatment; (d) input from family and friends; and (e) motivation for treatment. Veterans also spoke about the pathways they used to access this care. The four most commonly reported pathways included (a) physical health-care appointments; (b) the service connection disability system; (c) non-VA care; and (d) being mandated to care. Taken together, these data lend themselves to a model that describes both modifiers of, and pathways to, VA mental health care. The model suggests that interventions aimed at the identified pathways, in concert with efforts designed to reduce barriers, may increase initiation of VA mental health-care services by veterans. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

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

    PubMed

    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. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  20. Adenovirus Virus-Associated RNAII-Derived Small RNAs Are Efficiently Incorporated into the RNA-Induced Silencing Complex and Associate with Polyribosomes▿ §

    PubMed Central

    Xu, Ning; Segerman, Bo; Zhou, Xiaofu; Akusjärvi, Göran

    2007-01-01

    Adenovirus type 5 encodes two highly structured short RNAs, the virus-associated (VA) RNAI and RNAII. Both are processed by Dicer into small RNAs that are incorporated into the RNA-induced silencing complex (RISC). We show here, by cloning of small RNAs, that approximately 80% of Ago2-containing RISC immunopurified from late-infected cells is associated with VA RNA-derived small RNAs (mivaRNAs). Most surprisingly, VA RNAII, which is expressed at 20-fold lower levels compared to that of VA RNAI, appears to be the preferred substrate for Dicer and accounts for approximately 60% of all small RNAs in RISC. The mivaRNAs are derived from the 3′ strand of the terminal stems of the VA RNAs, with the major fraction of VA RNAII starting at position 138. The small RNAs derived from VA RNAI were more heterogeneous in size, with the two predominant small RNAs starting at positions 137 and 138. Collectively, our results suggest that the mivaRNAs are efficiently used for RISC assembly in late-infected cells. Potentially, they function as miRNAs, regulating translation of cellular mRNAs. In support of this hypothesis, we detected a fraction of the VA RNAII-derived mivaRNAs on polyribosomes. PMID:17652395

  1. Functional characterization of the 19q12 amplicon in grade III breast cancers

    PubMed Central

    2012-01-01

    Introduction The 19q12 locus is amplified in a subgroup of oestrogen receptor (ER)-negative grade III breast cancers. This amplicon comprises nine genes, including cyclin E1 (CCNE1), which has been proposed as its 'driver'. The aim of this study was to identify the genes within the 19q12 amplicon whose expression is required for the survival of cancer cells harbouring their amplification. Methods We investigated the presence of 19q12 amplification in a series of 313 frozen primary breast cancers and 56 breast cancer cell lines using microarray comparative genomic hybridisation (aCGH). The nine genes mapping to the smallest region of amplification on 19q12 were silenced using RNA interference in phenotypically matched breast cancer cell lines with (MDA-MB-157 and HCC1569) and without (Hs578T, MCF7, MDA-MB-231, ZR75.1, JIMT1 and BT474) amplification of this locus. Genes whose silencing was selectively lethal in amplified cells were taken forward for further validation. The effects of cyclin-dependent kinase 2 (CDK2) silencing and chemical inhibition were tested in cancer cells with and without CCNE1 amplification. Results 19q12 amplification was identified in 7.8% of ER-negative grade III breast cancer. Of the nine genes mapping to this amplicon, UQCRFS1, POP4, PLEKHF1, C19ORF12, CCNE1 and C19ORF2 were significantly over-expressed when amplified in primary breast cancers and/or breast cancer cell lines. Silencing of POP4, PLEKHF1, CCNE1 and TSZH3 selectively reduced cell viability in cancer cells harbouring their amplification. Cancer cells with CCNE1 amplification were shown to be dependent on CDK2 expression and kinase activity for their survival. Conclusions The 19q12 amplicon may harbour more than a single 'driver', given that expression of POP4, PLEKHF1, CCNE1 and TSZH3 is required for the survival of cancer cells displaying their amplification. The observation that cancer cells harbouring CCNE1 gene amplification are sensitive to CDK2 inhibitors provides a

  2. 78 FR 32126 - VA Dental Insurance Program

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-05-29

    ... DEPARTMENT OF VETERANS AFFAIRS 38 CFR Part 17 RIN 2900-AN99 VA Dental Insurance Program AGENCY... its regulations to establish rules and procedures for the VA Dental Insurance Program (VADIP), a pilot program that offers premium-based dental insurance to enrolled veterans and certain survivors and...

  3. 77 FR 12517 - VA Dental Insurance Program

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-03-01

    ... DEPARTMENT OF VETERANS AFFAIRS 38 CFR Part 17 RIN 2900-AN99 VA Dental Insurance Program AGENCY... dental insurance to enrolled veterans and certain survivors and dependents of veterans. VA would contract with a private insurer through the Federal contracting process to offer dental insurance, and the...

  4. Release of VA Records Relating to HIV. Final rule.

    PubMed

    2017-03-23

    The Department of Veterans Affairs (VA) is amending its medical regulations governing the release of VA medical records. Specifically, VA is eliminating the restriction on sharing a negative test result for the human immunodeficiency virus (HIV) with veterans' outside providers. HIV testing is a common practice today in healthcare and the stigma of testing that may have been seen in the 1980s when HIV was first discovered is no longer prevalent. Continuing to protect negative HIV tests causes delays and an unnecessary burden on veterans when VA tries to share electronic medical information with the veterans' outside providers through electronic health information exchanges. For this same reason, VA will also eliminate restrictions on negative test results of sickle cell anemia. This final rule eliminates the current barriers to electronic medical information exchange.

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

    PubMed

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

    2018-01-01

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

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

    PubMed

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

    2008-04-02

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

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

    PubMed

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

    2018-02-14

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

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

    PubMed

    Rask, Thomas S; Petersen, Bent; Chen, Donald S; Day, Karen P; Pedersen, Anders Gorm

    2016-04-22

    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 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. The new basecalling method described here, named Multipass, implements a probabilistic framework for working with the raw flowgrams obtained by pyrosequencing. For each sequence variant Multipass calculates the likelihood and nucleotide sequence of several most likely sequences given the flowgram data. This probabilistic approach enables integration of basecalling into a larger model where other parameters can be incorporated, such as the likelihood for observing a full-length open reading frame at the targeted region. We apply the method to 454 amplicon pyrosequencing data obtained from a malaria virulence gene family, where Multipass generates 20 % more error-free sequences than current state of the art methods, and provides sequence characteristics that allow generation of a set of high confidence error-free sequences. This novel method can be used to increase accuracy of existing and future amplicon sequencing data, particularly where extensive prior knowledge is available about the obtained sequences, for example in analysis of the immunoglobulin VDJ region where Multipass can be combined with a model for the known recombining germline genes. Multipass is available for Roche 454 data at http://www.cbs.dtu.dk/services/MultiPass-1.0 , and the concept can potentially be implemented for other sequencing technologies as well.

  9. 2. Perspective Map of Buena Vista (In Buena Vista, VA, ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    2. Perspective Map of Buena Vista (In Buena Vista, VA, NY:South Publishing Co., 1891 n.p.) (copy on file at Virginia State Library, Richmond, VA) - North River Canal System, West side of Buena Vista, Buena Vista, Roanoke City, VA

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

    PubMed

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

    2015-04-01

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

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

    PubMed

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

    2017-07-28

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

  12. The NO vA simulation chain

    DOE PAGES

    Aurisano, A.; Backhouse, C.; Hatcher, R.; ...

    2015-12-23

    The NO vA experiment is a two-detector, long-baseline neutrino experiment operating in the recently upgraded NuMI muon neutrino beam. Simulating neutrino interactions and backgrounds requires many steps including: the simulation of the neutrino beam flux using FLUKA and the FLUGG interface, cosmic ray generation using CRY, neutrino interaction modeling using GENIE, and a simulation of the energy deposited in the detector using GEANT4. To shorten generation time, the modeling of detector-specific aspects, such as photon transport, detector and electronics noise, and readout electronics, employs custom, parameterized simulation applications. We will describe the NO vA simulation chain, and present details onmore » the techniques used in modeling photon transport near the ends of cells, and in developing a novel data-driven noise simulation. Due to the high intensity of the NuMI beam, the Near Detector samples a high rate of muons originating in the surrounding rock. In addition, due to its location on the surface at Ash River, MN, the Far Detector collects a large rate ((˜) 140 kHz) of cosmic muons. Furthermore, we will discuss the methods used in NO vA for overlaying rock muons and cosmic ray muons with simulated neutrino interactions and show how realistically the final simulation reproduces the preliminary NO vA data.« less

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

    PubMed

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

    2016-02-01

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

  14. 78 FR 48609 - Safety Zone; James River; Newport News, VA

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-08-09

    ...-AA00 Safety Zone; James River; Newport News, VA AGENCY: Coast Guard, DHS. ACTION: Temporary final rule...-0670 to read as follows: Sec. 165.T05-0670 Safety Zone, James River, Newport News, VA. (a) Definitions...'11'' N longitude 076[deg]38'40'' W, located near Fort Eustis in Newport News, VA. (c) Regulations. (1...

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

    PubMed Central

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

    2015-01-01

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

  16. 33 CFR 80.510 - Chesapeake Bay Entrance, VA.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 33 Navigation and Navigable Waters 1 2014-07-01 2014-07-01 false Chesapeake Bay Entrance, VA. 80.510 Section 80.510 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Fifth District § 80.510 Chesapeake Bay Entrance, VA. A...

  17. 38 CFR 74.27 - How will VA store information?

    Code of Federal Regulations, 2010 CFR

    2010-07-01

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

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

    ERIC Educational Resources Information Center

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

    2009-01-01

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

  19. FACILITIES FOR EDUCATION IN VA HOSPITALS. FINAL REPORT.

    ERIC Educational Resources Information Center

    GREEN, ALAN C.; AND OTHERS

    THIS STUDY WAS AUTHORIZED BY THE VA DEPARTMENT OF MEDICINE AND SURGERY FOR THE PURPOSE OF IDENTIFYING AND DETERMINING THE FACILITIES NEEDED TO PROPERLY HOUSE AND SUPPORT EDUCATION ACTIVITIES IN EXISTING AND FUTURE VA HOSPITALS AND TO PRODUCE ARCHITECTURAL GUIDANCE IN THE DESIGN OF THE FACILITIES. CURRENT PRACTICES AND SIGNIFICANT TRENDS IN MEDICAL…

  20. High-Throughput Amplicon Sequencing Reveals Distinct Communities within a Corroding Concrete Sewer System

    PubMed Central

    Dennis, Paul G.; Keller, Jurg; Tyson, Gene W.

    2012-01-01

    Microbially induced concrete corrosion (MICC) is an important problem in sewers. Here, small-subunit (SSU) rRNA gene amplicon pyrosequencing was used to characterize MICC communities. Microbial community composition differed between wall- and ceiling-associated MICC layers. Acidithiobacillus spp. were present at low abundances, and the communities were dominated by other sulfur-oxidizing-associated lineages. PMID:22843532

  1. 48 CFR 852.219-71 - VA mentor-protégé program.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

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

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

    PubMed

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

    2015-09-01

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

  3. Empirical analysis on future-cash arbitrage risk with portfolio VaR

    NASA Astrophysics Data System (ADS)

    Chen, Rongda; Li, Cong; Wang, Weijin; Wang, Ze

    2014-03-01

    This paper constructs the positive arbitrage position by alternating the spot index with Chinese Exchange Traded Fund (ETF) portfolio and estimating the arbitrage-free interval of futures with the latest trade data. Then, an improved Delta-normal method was used, which replaces the simple linear correlation coefficient with tail dependence correlation coefficient, to measure VaR (Value-at-risk) of the arbitrage position. Analysis of VaR implies that the risk of future-cash arbitrage is less than that of investing completely in either futures or spot market. Then according to the compositional VaR and the marginal VaR, we should increase the futures position and decrease the spot position appropriately to minimize the VaR, which can minimize risk subject to certain revenues.

  4. Monitoring therapy responses at the leukemic subclone level by ultra-deep amplicon resequencing in acute myeloid leukemia.

    PubMed

    Ojamies, P N; Kontro, M; Edgren, H; Ellonen, P; Lagström, S; Almusa, H; Miettinen, T; Eldfors, S; Tamborero, D; Wennerberg, K; Heckman, C; Porkka, K; Wolf, M; Kallioniemi, O

    2017-05-01

    In our individualized systems medicine program, personalized treatment options are identified and administered to chemorefractory acute myeloid leukemia (AML) patients based on exome sequencing and ex vivo drug sensitivity and resistance testing data. Here, we analyzed how clonal heterogeneity affects the responses of 13 AML patients to chemotherapy or targeted treatments using ultra-deep (average 68 000 × coverage) amplicon resequencing. Using amplicon resequencing, we identified 16 variants from 4 patients (frequency 0.54-2%) that were not detected previously by exome sequencing. A correlation-based method was developed to detect mutation-specific responses in serial samples across multiple time points. Significant subclone-specific responses were observed for both chemotherapy and targeted therapy. We detected subclonal responses in patients where clinical European LeukemiaNet (ELN) criteria showed no response. Subclonal responses also helped to identify putative mechanisms underlying drug sensitivities, such as sensitivity to azacitidine in DNMT3A mutated cell clones and resistance to cytarabine in a subclone with loss of NF1 gene. In summary, ultra-deep amplicon resequencing method enables sensitive quantification of subclonal variants and their responses to therapies. This approach provides new opportunities for designing combinatorial therapies blocking multiple subclones as well as for real-time assessment of such treatments.

  5. Haemophilia utilization group study - Part Va (HUGS Va): design, methods and baseline data.

    PubMed

    Zhou, Z-Y; Wu, J; Baker, J; Curtis, R; Forsberg, A; Huszti, H; Koerper, M; Lou, M; Miller, R; Parish, K; Riske, B; Shapiro, A; Ullman, M; Johnson, K

    2011-09-01

    To describe the study design, procedures and baseline characteristics of the Haemophilia Utilization Group Study - Part Va (HUGS Va), a US multi-center observational study evaluating the cost of care and burden of illness in persons with factor VIII deficiency. Patients with factor VIII level ≤ 30%, age 2-64 years, receiving treatment at one of six federally supported haemophilia treatment centres (HTCs) were enrolled in the study. Participants completed an initial interview including questions on socio-demographical characteristics, health insurance status, co-morbidities, access to care, haemophilia treatment regimen, factor utilization, self-reported joint pain and motion limitation and health-related quality of life. A periodic follow-up survey collected data regarding time lost from usual activities, disability days, health care utilization and outcomes of care. HTC clinicians documented participants' baseline clinical characteristics and pharmacy dispensing records for 2 years. Between July 2005 and July 2007, 329 participants were enrolled. Average age was 9.7 years for children and 33.5 years for adults; two-thirds had severe haemophilia. The distributions of age, marital status, education level and barriers to haemophilia care were relatively consistent across haemophilic severity categories. Differences were found in participants' employment status, insurance status and income. Overall, children with haemophilia had quality of life scores comparable to healthy counterparts. Adults had significantly lower physical functioning than the general US population. As one of the largest economic studies of haemophilia care, HUGS Va will provide detailed information regarding the burden of illness and health care utilization in the US haemophilia A population. © 2011 Blackwell Publishing Ltd.

  6. Use of VA and Medicare Services By Dually Eligible Veterans with Psychiatric Problems

    PubMed Central

    Carey, Kathleen; Montez-Rath, Maria E; Rosen, Amy K; Christiansen, Cindy L; Loveland, Susan; Ettner, Susan L

    2008-01-01

    Objective To examine how service accessibility measured by geographic distance affects service sector choices for veterans who are dually eligible for veterans affairs (VA) and Medicare services and who are diagnosed with mental health and/or substance abuse (MH/SA) disorders. Data Sources Primary VA data sources were the Patient Treatment (acute care), Extended Care (long-term care), and Outpatient Clinic files. VA cost data were obtained from (1) inpatient and outpatient cost files developed by the VA Health Economics and Resource Center and (2) outpatient VA Decision Support System files. Medicare data sources were the denominator, Medicare Provider Analysis Review (MEDPAR), Provider-of-Service, Outpatient Standard Analytic and Physician/Supplier Standard Analytic files. Additional sources included the Area Resource File and Census Bureau data. Study Design We identified dually eligible veterans who had either an inpatient or outpatient MH/SA diagnosis in the VA system during fiscal year (FY)'99. We then estimated one- and two-part regression models to explain the effects of geographic distance on both VA and Medicare total and MH/SA costs. Principal Findings Results provide evidence for substitution between the VA and Medicare, demonstrating that poorer geographic access to VA inpatient and outpatient clinics decreased VA expenditures but increased Medicare expenditures, while poorer access to Medicare-certified general and psychiatric hospitals decreased Medicare expenditures but increased VA expenditures. Conclusions As geographic distance to VA medical facility increases, Medicare plays an increasingly important role in providing mental health services to veterans. PMID:18355256

  7. Greening America's Capitals - Richmond, VA

    EPA Pesticide Factsheets

    Report from the Greening America's Capitals project in Richmond, VA, to help the city develop design options to protect pedestrians, bicyclists, transit users, and drivers; improve stormwater management; and spur revitalization.

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

    PubMed

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

    2016-03-01

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

  9. 77 FR 58773 - Drawbridge Operation Regulations; James River, Newport News, VA

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-09-24

    ... Operation Regulations; James River, Newport News, VA AGENCY: Coast Guard, DHS. ACTION: Notice of temporary... schedule that governs the US 17/258 Bridge across the James River, mile 5.0, at Newport News, VA. The... 17/258 Bridge over the James River, mile 5.0, at Newport News, VA opens on signal as required by 33...

  10. Community Veterans' Decision to Use VA Services: A Multimethod Veteran Health Partnership Study.

    PubMed

    Franco, Zeno E; Logan, Clinton; Flower, Mark; Curry, Bob; Ruffalo, Leslie; Brazauskas, Ruta; Whittle, Jeff

    2016-01-01

    Ensuring veterans' access to healthcare is a national priority. Prior studies of veterans' use of Veterans Health Administration (VA) healthcare have had limited success in evaluating barriers to access for certain vulnerable veteran subpopulations. Our coalition of researchers and veteran community members sought to understand factors affecting use of VA, particularly for those less likely to participate in traditional survey studies. We recruited 858 veterans to complete a collaboratively designed survey at community events or via social media. We compared our results regarding VA use with the 2010 National Survey of Veterans (NSV) using chi-square tests, multiple logistic regression to identify predictors of VA use, and content analysis for open-ended descriptions of barriers to VA use. Veterans in our study were more likely than NSV respondents to report using VA healthcare ever (76% vs. 28%; p<0.0001). Within this group, more veterans in our sample were current VA users (83% vs. 68%; p<0.0001). In multivariable analysis, VA use was predicted by self-reported physical problems (comparing "a lot" vs. "none" for each variable, adjusted odds ratio [OR], 8.35), thinking problems (OR, 1.14), need for smoking cessation (OR, 1.54), need for pain management (OR, 1.65), and need for other mental health services (OR, 3.04). We identified 15 themes summarizing veterans' perceived barriers to VA use. Persistent actual and perceived barriers prevent some veterans from using VA services. The VA can better understand and address these issues through community-academic partnerships with veterans' organizations.

  11. 38 CFR 74.27 - How will VA store information?

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... information? 74.27 Section 74.27 Pensions, Bonuses, and Veterans' Relief DEPARTMENT OF VETERANS AFFAIRS (CONTINUED) VETERANS SMALL BUSINESS REGULATIONS Records Management § 74.27 How will VA store information? VA intends to store records provided to complete the VetBiz Vendor Information Pages registration fully...

  12. 38 CFR 74.27 - How will VA store information?

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... information? 74.27 Section 74.27 Pensions, Bonuses, and Veterans' Relief DEPARTMENT OF VETERANS AFFAIRS (CONTINUED) VETERANS SMALL BUSINESS REGULATIONS Records Management § 74.27 How will VA store information? VA intends to store records provided to complete the VetBiz Vendor Information Pages registration fully...

  13. 38 CFR 74.27 - How will VA store information?

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... information? 74.27 Section 74.27 Pensions, Bonuses, and Veterans' Relief DEPARTMENT OF VETERANS AFFAIRS (CONTINUED) VETERANS SMALL BUSINESS REGULATIONS Records Management § 74.27 How will VA store information? VA intends to store records provided to complete the VetBiz Vendor Information Pages registration fully...

  14. 38 CFR 74.27 - How will VA store information?

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... information? 74.27 Section 74.27 Pensions, Bonuses, and Veterans' Relief DEPARTMENT OF VETERANS AFFAIRS (CONTINUED) VETERANS SMALL BUSINESS REGULATIONS Records Management § 74.27 How will VA store information? VA intends to store records provided to complete the VetBiz Vendor Information Pages registration fully...

  15. A VaR Algorithm for Warrants Portfolio

    NASA Astrophysics Data System (ADS)

    Dai, Jun; Ni, Liyun; Wang, Xiangrong; Chen, Weizhong

    Based on Gamma Vega-Cornish Fish methodology, this paper propose the algorithm for calculating VaR via adjusting the quantile under the given confidence level using the four moments (e.g. mean, variance, skewness and kurtosis) of the warrants portfolio return and estimating the variance of portfolio by EWMA methodology. Meanwhile, the proposed algorithm considers the attenuation of the effect of history return on portfolio return of future days. Empirical study shows that, comparing with Gamma-Cornish Fish method and standard normal method, the VaR calculated by Gamma Vega-Cornish Fish can improve the effectiveness of forecasting the portfolio risk by virture of considering the Gamma risk and the Vega risk of the warrants. The significance test is conducted on the calculation results by employing two-tailed test developed by Kupiec. Test results show that the calculated VaRs of the warrants portfolio all pass the significance test under the significance level of 5%.

  16. The depiction of Alboran Sea Gyre during Donde Va? using remote sensing and conventional data

    NASA Technical Reports Server (NTRS)

    Laviolette, P. E.

    1984-01-01

    Experienced oceanographic investigators have come to realize that remote sensing techniques are most successful when applied as part of programs of integrated measurements aimed at solving specific oceanographic problems. A good example of such integration occurred during the multi-platform international experiment, Donde Va? in the Alboran Sea during the period June through October, 1982. The objective of Donde Va? was to derive the interrelationship of the Atlantic waters entering the Mediterranean Sea and the Alboran Sea Gyre. The experimental plan conceived solely with this objective in mind consisted of a variety of remote sensing and conventional platforms: three ships, three aircraft, five current moorings, two satellites and a specialized beach radar (CODAR). Integrated analyses of these multiple-data sets are still being conducted. However, the initial results show detailed structure of the incoming Atlantic jet and Alboran Sea Gyre that would not have been possible by conventional means.

  17. Factors related to attrition from VA healthcare use: findings from the National Survey of Women Veterans.

    PubMed

    Hamilton, Alison B; Frayne, Susan M; Cordasco, Kristina M; Washington, Donna L

    2013-07-01

    While prior research characterizes women Veterans' barriers to accessing and using Veterans Health Administration (VA) care, there has been little attention to women who access VA and use services, but then discontinue use. Recent data suggest that among women Veterans, there is a 30 % attrition rate within 3 years of initial VA use. To compare individual characteristics and perceptions about VA care between women Veteran VA attriters (those who discontinue use) and non-attriters (those who continue use), and to compare recent versus remote attriters. Cross-sectional, population-based 2008-2009 national telephone survey. Six hundred twenty-six attriters and 2,065 non-attriters who responded to the National Survey of Women Veterans. Population weighted demographic, military and health characteristics; perceptions about VA healthcare; length of time since last VA use; among attriters, reasons for no longer using VA care. Fifty-four percent of the weighted VA ever user population reported that they no longer use VA. Forty-five percent of attrition was within the past ten years. Attriters had better overall health (p = 0.007), higher income (p < 0.001), and were more likely to have health insurance (p < 0.001) compared with non-attriters. Attriters had less positive perceptions of VA than non-attriters, with attriters having lower ratings of VA quality and of gender-specific features of VA care (p < 0.001). Women Veterans who discontinued VA use since 2001 did not differ from those with more remote VA use on most measures of VA perceptions. Overall, among attriters, distance to VA sites of care and having alternate insurance coverage were the most common reasons for discontinuing VA use. We found high VA attrition despite recent advances in VA care for women Veterans. Women's attrition from VA could reduce the critical mass of women Veterans in VA and affect current system-wide efforts to provide high-quality care for women Veterans. An understanding of reasons for

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

    PubMed

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

    2017-05-01

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

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

    PubMed

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

    2012-02-01

    Healthcare for end-stage renal disease (ESRD) is intensive, expensive, and provided in both the public and private sector. Using a societal perspective, we examined healthcare costs and health outcomes for Department of Veterans Affairs (VA) ESRD patients comparing those who received hemodialysis care at VA versus private sector facilities. Dialysis patients were recruited from 8 VA medical centers from 2001 through 2003 and followed for 12 months in a prospective cohort study. Patient demographics, clinical characteristics, quality of life, healthcare use, and cost data were collected. Healthcare data included utilization (VA), claims (Medicare), and patient self-report. Costs included VA calculated costs, Medicare dialysis facility reports and reimbursement rates, and patient self-report. Multivariable regression was used to compare costs between patients receiving dialysis at VA versus private sector facilities. The cohort comprised 334 patients: 170 patients in the VA dialysis group and 164 patients in the private sector group. The VA dialysis group had more comorbidities at baseline, outpatient and emergency visits, prescriptions, and longer hospital stays; they also had more conservative anemia management and lower baseline urea reduction ratio (67% vs. 72%; P<0.001), although levels were consistent with guidelines (Kt/V≥1.2). In adjusted analysis, the VA dialysis group had $36,431 higher costs than those in the private sector dialysis group (P<0.001). Continued research addressing costs and effectiveness of care across public and private sector settings is critical in informing health policy options for patients with complex chronic illnesses such as ESRD.

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

    PubMed Central

    Van Nostrand, Joy D.; Ning, Daliang; Sun, Bo; Xue, Kai; Liu, Feifei; Deng, Ye; Liang, Yuting; Zhou, Jizhong

    2017-01-01

    Illumina’s MiSeq has become the dominant platform for gene amplicon sequencing in microbial ecology studies; however, various technical concerns, such as reproducibility, still exist. To assess reproducibility, 16S rRNA gene amplicons from 18 soil samples of a reciprocal transplantation experiment were sequenced on an Illumina MiSeq. The V4 region of 16S rRNA gene from each sample was sequenced in triplicate with each replicate having a unique barcode. The average OTU overlap, without considering sequence abundance, at a rarefaction level of 10,323 sequences was 33.4±2.1% and 20.2±1.7% between two and among three technical replicates, respectively. When OTU sequence abundance was considered, the average sequence abundance weighted OTU overlap was 85.6±1.6% and 81.2±2.1% for two and three replicates, respectively. Removing singletons significantly increased the overlap for both (~1–3%, p<0.001). Increasing the sequencing depth to 160,000 reads by deep sequencing increased OTU overlap both when sequence abundance was considered (95%) and when not (44%). However, if singletons were not removed the overlap between two technical replicates (not considering sequence abundance) plateaus at 39% with 30,000 sequences. Diversity measures were not affected by the low overlap as α-diversities were similar among technical replicates while β-diversities (Bray-Curtis) were much smaller among technical replicates than among treatment replicates (e.g., 0.269 vs. 0.374). Higher diversity coverage, but lower OTU overlap, was observed when replicates were sequenced in separate runs. Detrended correspondence analysis indicated that while there was considerable variation among technical replicates, the reproducibility was sufficient for detecting treatment effects for the samples examined. These results suggest that although there is variation among technical replicates, amplicon sequencing on MiSeq is useful for analyzing microbial community structure if used appropriately

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

    PubMed

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

    2017-01-01

    Illumina's MiSeq has become the dominant platform for gene amplicon sequencing in microbial ecology studies; however, various technical concerns, such as reproducibility, still exist. To assess reproducibility, 16S rRNA gene amplicons from 18 soil samples of a reciprocal transplantation experiment were sequenced on an Illumina MiSeq. The V4 region of 16S rRNA gene from each sample was sequenced in triplicate with each replicate having a unique barcode. The average OTU overlap, without considering sequence abundance, at a rarefaction level of 10,323 sequences was 33.4±2.1% and 20.2±1.7% between two and among three technical replicates, respectively. When OTU sequence abundance was considered, the average sequence abundance weighted OTU overlap was 85.6±1.6% and 81.2±2.1% for two and three replicates, respectively. Removing singletons significantly increased the overlap for both (~1-3%, p<0.001). Increasing the sequencing depth to 160,000 reads by deep sequencing increased OTU overlap both when sequence abundance was considered (95%) and when not (44%). However, if singletons were not removed the overlap between two technical replicates (not considering sequence abundance) plateaus at 39% with 30,000 sequences. Diversity measures were not affected by the low overlap as α-diversities were similar among technical replicates while β-diversities (Bray-Curtis) were much smaller among technical replicates than among treatment replicates (e.g., 0.269 vs. 0.374). Higher diversity coverage, but lower OTU overlap, was observed when replicates were sequenced in separate runs. Detrended correspondence analysis indicated that while there was considerable variation among technical replicates, the reproducibility was sufficient for detecting treatment effects for the samples examined. These results suggest that although there is variation among technical replicates, amplicon sequencing on MiSeq is useful for analyzing microbial community structure if used appropriately and

  2. 32 CFR 105.10 - SARC and SAPR VA procedures.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... CIVILIAN SEXUAL ASSAULT PREVENTION AND RESPONSE PROGRAM PROCEDURES § 105.10 SARC and SAPR VA procedures. (a) SARC procedures. The SARC shall: (1) Serve as the single point of contact to coordinate sexual assault response when a sexual assault is reported. All SARCs shall be authorized to perform VA duties in...

  3. 32 CFR 105.10 - SARC and SAPR VA procedures.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... CIVILIAN SEXUAL ASSAULT PREVENTION AND RESPONSE PROGRAM PROCEDURES § 105.10 SARC and SAPR VA procedures. (a) SARC procedures. The SARC shall: (1) Serve as the single point of contact to coordinate sexual assault response when a sexual assault is reported. All SARCs shall be authorized to perform VA duties in...

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

    PubMed

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

    2013-03-01

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

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

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 48 Federal Acquisition Regulations System 5 2010-10-01 2010-10-01 false VA Small business... Provisions and Clauses 852.219-9 VA Small business subcontracting plan minimum requirements. As prescribed in subpart 819.709, insert the following clause: VA Small Business Subcontracting Plan Minimum Requirements...

  6. 48 CFR 852.219-9 - VA Small business subcontracting plan minimum requirements.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 48 Federal Acquisition Regulations System 5 2013-10-01 2013-10-01 false VA Small business... Provisions and Clauses 852.219-9 VA Small business subcontracting plan minimum requirements. As prescribed in subpart 819.709, insert the following clause: VA Small Business Subcontracting Plan Minimum Requirements...

  7. 48 CFR 852.219-9 - VA Small business subcontracting plan minimum requirements.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 48 Federal Acquisition Regulations System 5 2011-10-01 2011-10-01 false VA Small business... Provisions and Clauses 852.219-9 VA Small business subcontracting plan minimum requirements. As prescribed in subpart 819.709, insert the following clause: VA Small Business Subcontracting Plan Minimum Requirements...

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

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 48 Federal Acquisition Regulations System 5 2012-10-01 2012-10-01 false VA Small business... Provisions and Clauses 852.219-9 VA Small business subcontracting plan minimum requirements. As prescribed in subpart 819.709, insert the following clause: VA Small Business Subcontracting Plan Minimum Requirements...

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

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 48 Federal Acquisition Regulations System 5 2014-10-01 2014-10-01 false VA Small business... Provisions and Clauses 852.219-9 VA Small business subcontracting plan minimum requirements. As prescribed in subpart 819.709, insert the following clause: VA Small Business Subcontracting Plan Minimum Requirements...

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

    PubMed Central

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

    2017-01-01

    PCR amplicon next generation sequencing (NGS) analysis offers a broadly applicable and targeted approach to detect populations of both high- or low-frequency virus variants in one or more plant samples. In this study, amplicon NGS was used to explore the diversity of the tripartite genome virus, Prunus necrotic ringspot virus (PNRSV) from 53 PNRSV-infected trees using amplicons from conserved gene regions of each of PNRSV RNA1, RNA2 and RNA3. Sequencing of the amplicons from 53 PNRSV-infected trees revealed differing levels of polymorphism across the three different components of the PNRSV genome with a total number of 5040, 2083 and 5486 sequence variants observed for RNA1, RNA2 and RNA3 respectively. The RNA2 had the lowest diversity of sequences compared to RNA1 and RNA3, reflecting the lack of flexibility tolerated by the replicase gene that is encoded by this RNA component. Distinct PNRSV phylo-groups, consisting of closely related clusters of sequence variants, were observed in each of PNRSV RNA1, RNA2 and RNA3. Most plant samples had a single phylo-group for each RNA component. Haplotype network analysis showed that smaller clusters of PNRSV sequence variants were genetically connected to the largest sequence variant cluster within a phylo-group of each RNA component. Some plant samples had sequence variants occurring in multiple PNRSV phylo-groups in at least one of each RNA and these phylo-groups formed distinct clades that represent PNRSV genetic strains. Variants within the same phylo-group of each Prunus plant sample had ≥97% similarity and phylo-groups within a Prunus plant sample and between samples had less ≤97% similarity. Based on the analysis of diversity, a definition of a PNRSV genetic strain was proposed. The proposed definition was applied to determine the number of PNRSV genetic strains in each of the plant samples and the complexity in defining genetic strains in multipartite genome viruses was explored. PMID:28632759

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

    PubMed

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

    2017-01-01

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

  12. 33 CFR 110.166 - York River, Va., naval anchorage.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... ANCHORAGES ANCHORAGE REGULATIONS Anchorage Grounds § 110.166 York River, Va., naval anchorage. (a) The anchorage grounds. Between Yorktown and the Naval Mine Depot, beginning at latitude 37°15′34″, longitude 76... 33 Navigation and Navigable Waters 1 2014-07-01 2014-07-01 false York River, Va., naval anchorage...

  13. 33 CFR 110.166 - York River, Va., naval anchorage.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... ANCHORAGES ANCHORAGE REGULATIONS Anchorage Grounds § 110.166 York River, Va., naval anchorage. (a) The anchorage grounds. Between Yorktown and the Naval Mine Depot, beginning at latitude 37°15′34″, longitude 76... 33 Navigation and Navigable Waters 1 2013-07-01 2013-07-01 false York River, Va., naval anchorage...

  14. 33 CFR 110.166 - York River, Va., naval anchorage.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... ANCHORAGES ANCHORAGE REGULATIONS Anchorage Grounds § 110.166 York River, Va., naval anchorage. (a) The anchorage grounds. Between Yorktown and the Naval Mine Depot, beginning at latitude 37°15′34″, longitude 76... 33 Navigation and Navigable Waters 1 2012-07-01 2012-07-01 false York River, Va., naval anchorage...

  15. 33 CFR 110.166 - York River, Va., naval anchorage.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... ANCHORAGES ANCHORAGE REGULATIONS Anchorage Grounds § 110.166 York River, Va., naval anchorage. (a) The anchorage grounds. Between Yorktown and the Naval Mine Depot, beginning at latitude 37°15′34″, longitude 76... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false York River, Va., naval anchorage...

  16. 33 CFR 110.166 - York River, Va., naval anchorage.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... ANCHORAGES ANCHORAGE REGULATIONS Anchorage Grounds § 110.166 York River, Va., naval anchorage. (a) The anchorage grounds. Between Yorktown and the Naval Mine Depot, beginning at latitude 37°15′34″, longitude 76... 33 Navigation and Navigable Waters 1 2011-07-01 2011-07-01 false York River, Va., naval anchorage...

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

    PubMed

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

    2015-01-01

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

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed

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

    2018-03-15

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

  20. (4015) 1979 VA: 'Missing Link' Discovered

    NASA Technical Reports Server (NTRS)

    Helin, Eleanor F.

    1993-01-01

    Apollo Asteroid (4015) 1979 VA was discovered in November of 1979 by Helin at Palomar with the 0.46m Schmidt Telescope. It's orbital elements immediately indicated a possible cometary origin. With an extremely eccentric orbit, it approaches the orbit of Jupiter (at the time, the largest 'Q', aphelion, of any known near-Earth asteroid). Physical observations acquired during the discovery apparition suggested that it was carbonaceous in nature. Research into prediscovery observations of Near-Earth Asteroids (Bowell et. al., 1992) has located Palomar Sky Survey photographic plates taken in 1949 observations of (4015) 1979 VA, not as an asteroid, but rather a small cometary image (IAU Circular Nos. 5585 and 5586, August 13, 1992)...

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

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 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). (a) Methane monitors shall be installed on continuous mining machines used in or beyond the last open crosscut...

  2. 30 CFR 57.22309 - Methane monitors (V-A mines).

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 30 Mineral Resources 1 2011-07-01 2011-07-01 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). (a) Methane monitors shall be installed on continuous mining machines used in or beyond the last open crosscut...

  3. First and second energy derivative analyses for open-shell self-consistent field wavefunctions

    NASA Astrophysics Data System (ADS)

    Yamaguchi, Yukio; Schaefer, Henry F., III; Frenking, Gernot

    A study of first and second derivatives of the orbital, electronic, nuclear and total energies for the self-consistent field (SCF) wavefunction has been applied to general open-shell SCF systems. The diagonal elements of the Lagrangian matrix for the general open-shell SCF wavefunction are adapted as the 'oŕbital' energies. The first and second derivatives of the orbital energies in terms of the normal coordinates are determined via the finite difference method, while those of the electronic, nuclear and total energies are obtained by analytical techniques. Using three low lying states of the CH2 and H2CO molecules as examples, it is demonstrated that the derivatives of the SCF energetic quantities with respect to the normal coordinates provide useful chemical information concerning the respective molecular structures and reactivities. The conventional concept of the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) has been extended to the molecular vibrational motion, and the terminology of vibrationally active MOs (va-MOs), va-HOMO and va-LUMO has been introduced for each normal coordinate. The energy derivative analysis method may be used as a powerful semi-quantitative modelin understanding and interpreting various chemical phenomena.

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

    PubMed Central

    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

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

    PubMed

    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.

  6. Home health care and patterns of subsequent VA and medicare health care utilization for veterans.

    PubMed

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

    2008-10-01

    The Veterans Affairs or VA health care system is in the process of significantly expanding home health care (HHC) nationwide. We describe VA HHC use in 2003 for all VA HHC users from 2002; we examine whether VA utilization across a broad spectrum of services differed for a sample of VA HHC users and their propensity-score-matched controls. We also consider crossover between the VA and Medicare. This is a retrospective study using propensity score and stratified analysis to control for selection bias on observable characteristics. We examined the full cohort of 2002 VA HHC users (n = 24,169) and a 2:1 sample of age- and race-based nonusers (n = 53,356). Utilization measures included VA and Medicare outpatient, inpatient, nursing home, and hospice use, as well as VA home-based primary care, respite care, and adult day health care. VA HHC users had a higher absolute probability of outpatient use by around 3%, of inpatient use by 12%, and nursing home use by 6% than their propensity-score-matched controls. Veterans who used HHC services had a higher rate of VA service use in the subsequent year than controls did, even after we adjusted for differences in observed health status, eligibility advantages, and supplemental insurance status. High utilization for VA home health users spilled over into high Medicare utilization.

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

    ERIC Educational Resources Information Center

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

    2008-01-01

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

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

    PubMed

    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. © 2015 John Wiley & Sons Ltd.

  9. Inhibition of adenovirus replication by the E1A antisense transcript initiated from hsp70 and VA-1 promoters.

    PubMed

    Miroshnichenko, O I; Borisenko, A S; Ponomareva, T I; Tikhonenko, T I

    1990-03-01

    The E1A region of the adenoviral genome, important for initiation of virus infection and activation of other viral genes, was chosen as a target for engineering antisense RNA (asRNA) to inhibit adenovirus 5 (Ad5) replication in COS-1 cell culture in vitro. The hsp70 promoter, taken from the appropriate heat-shock-protein gene of Drosophila melanogaster, and the VA-1 RNA promoter, derived from the Ad5 gene coding for low-molecular-mass VA-1 RNA and recognized by RNA polymerase III were used as regulatory elements of transcription. The two types of recombinant constructs contained E1A fragments of 710 bp (hsp70 constructs) or 380 or 740 bp (VA-1 RNA constructs) in reverse orientation relative to the promoter position, as well as a transcription termination signal, the SV40 ori, and the gene controlling Geneticin (antibiotic G418) resistance (G418R). After selection of transfected COS-1 cells in the presence of G418, a number of stable G418R cell lines were raised which expressed engineered asRNAs. Plating of Ad5 suspensions of known titre on monolayers of transfected COS-1 cells clearly showed strong inhibition of adenovirus replication by asRNAs: 75% with the hsp70 promoter and 90% with the VA-1 RNA promoter.

  10. 48 CFR 803.7000 - Display of the VA Hotline poster.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

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

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

    Code of Federal Regulations, 2012 CFR

    2012-10-01

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

  12. 48 CFR 803.7000 - Display of the VA Hotline poster.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

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

  13. 48 CFR 803.7000 - Display of the VA Hotline poster.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

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

  14. 48 CFR 803.7000 - Display of the VA Hotline poster.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

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

  15. 77 FR 38181 - VA Veteran-Owned Small Business Verification Guidelines

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-06-27

    ... DEPARTMENT OF VETERANS AFFAIRS 38 CFR Part 74 RIN 2900-AO49 VA Veteran-Owned Small Business... small businesses (VOSBs), including service-disabled veteran-owned small businesses (SDVOSBs) in order...- AO49--VA Veteran-Owned Small Business Verification Guidelines.'' All comments received will be...

  16. 78 FR 56271 - FY 2014-2020 Draft VA Strategic Plan

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-09-12

    ... and access to benefits and services through integration within VA and with our partners; and... integration within VA and with our partners; and developing our workforce with the skills, tools, and... program to coordination and integration across programs and organizations, measuring performance by the...

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

    PubMed

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

    2015-08-01

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

  18. 38 CFR 26.7 - VA environmental decision making and documents.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... environmental decision making and documents. (a) Relevant environmental documents shall accompany other decision documents as they proceed through the decision-making process. (b) The major decision points for VA actions... 38 Pensions, Bonuses, and Veterans' Relief 2 2010-07-01 2010-07-01 false VA environmental decision...

  19. 38 CFR 26.9 - Information on and public participation in VA environmental process.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... participation in VA environmental process. 26.9 Section 26.9 Pensions, Bonuses, and Veterans' Relief DEPARTMENT OF VETERANS AFFAIRS (CONTINUED) ENVIRONMENTAL EFFECTS OF THE DEPARTMENT OF VETERANS AFFAIRS (VA) ACTIONS § 26.9 Information on and public participation in VA environmental process. (a) During the...

  20. Case-mix groups for VA hospital-based home care.

    PubMed

    Smith, M E; Baker, C R; Branch, L G; Walls, R C; Grimes, R M; Karklins, J M; Kashner, M; Burrage, R; Parks, A; Rogers, P

    1992-01-01

    The purpose of this study is to group hospital-based home care (HBHC) patients homogeneously by their characteristics with respect to cost of care to develop alternative case mix methods for management and reimbursement (allocation) purposes. Six Veterans Affairs (VA) HBHC programs in Fiscal Year (FY) 1986 that maximized patient, program, and regional variation were selected, all of which agreed to participate. All HBHC patients active in each program on October 1, 1987, in addition to all new admissions through September 30, 1988 (FY88), comprised the sample of 874 unique patients. Statistical methods include the use of classification and regression trees (CART software: Statistical Software; Lafayette, CA), analysis of variance, and multiple linear regression techniques. The resulting algorithm is a three-factor model that explains 20% of the cost variance (R2 = 20%, with a cross validation R2 of 12%). Similar classifications such as the RUG-II, which is utilized for VA nursing home and intermediate care, the VA outpatient resource allocation model, and the RUG-HHC, utilized in some states for reimbursing home health care in the private sector, explained less of the cost variance and, therefore, are less adequate for VA home care resource allocation.

  1. Semi-nonparametric VaR forecasts for hedge funds during the recent crisis

    NASA Astrophysics Data System (ADS)

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

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-11-27

    ...The Department of Veterans Affairs (VA) proposes to reorganize and rewrite its compensation and pension regulations in a logical, claimant-focused, and user-friendly format. The intended effect of the proposed revisions is to assist claimants, beneficiaries, veterans' representatives, and VA personnel in locating and understanding these regulations.

  3. 38 CFR 17.66 - Notice of noncompliance with VA standards.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... AFFAIRS MEDICAL Community Residential Care § 17.66 Notice of noncompliance with VA standards. If the hearing official determines that an approved community residential care facility does not comply with the... standards must be met in order to avoid revocation of VA approval; (c) The community residential care...

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

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Wen, Chongqing; Wu, Liyou; Qin, Yujia

    Illumina's MiSeq has become the dominant platform for gene amplicon sequencing in microbial ecology studies; however, various technical concerns, such as reproducibility, still exist. To assess reproducibility, 16S rRNA gene amplicons from 18 soil samples of a reciprocal transplantation experiment were sequenced on an Illumina MiSeq. The V4 region of 16S rRNA gene from each sample was sequenced in triplicate with each replicate having a unique barcode. The average OTU overlap, without considering sequence abundance, at a rarefaction level of 10,323 sequences was 33.4±2.1% and 20.2±1.7% between two and among three technical replicates, respectively. When OTU sequence abundance was considered,more » the average sequence abundance weighted OTU overlap was 85.6±1.6% and 81.2±2.1% for two and three replicates, respectively. Removing singletons significantly increased the overlap for both (~1-3%, p<0.001). Increasing the sequencing depth to 160,000 reads by deep sequencing increased OTU overlap both when sequence abundance was considered (95%) and when not (44%). However, if singletons were not removed the overlap between two technical replicates (not considering sequence abundance) plateaus at 39% with 30,000 sequences. Diversity measures were not affected by the low overlap as α-diversities were similar among technical replicates while β-diversities (Bray-Curtis) were much smaller among technical replicates than among treatment replicates (e.g., 0.269 vs. 0.374). Higher diversity coverage, but lower OTU overlap, was observed when replicates were sequenced in separate runs. Detrended correspondence analysis indicated that while there was considerable variation among technical replicates, the reproducibility was sufficient for detecting treatment effects for the samples examined. These results suggest that although there is variation among technical replicates, amplicon sequencing on MiSeq is useful for analyzing microbial community structure if used

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

    DOE PAGES

    Wen, Chongqing; Wu, Liyou; Qin, Yujia; ...

    2017-04-28

    Illumina's MiSeq has become the dominant platform for gene amplicon sequencing in microbial ecology studies; however, various technical concerns, such as reproducibility, still exist. To assess reproducibility, 16S rRNA gene amplicons from 18 soil samples of a reciprocal transplantation experiment were sequenced on an Illumina MiSeq. The V4 region of 16S rRNA gene from each sample was sequenced in triplicate with each replicate having a unique barcode. The average OTU overlap, without considering sequence abundance, at a rarefaction level of 10,323 sequences was 33.4±2.1% and 20.2±1.7% between two and among three technical replicates, respectively. When OTU sequence abundance was considered,more » the average sequence abundance weighted OTU overlap was 85.6±1.6% and 81.2±2.1% for two and three replicates, respectively. Removing singletons significantly increased the overlap for both (~1-3%, p<0.001). Increasing the sequencing depth to 160,000 reads by deep sequencing increased OTU overlap both when sequence abundance was considered (95%) and when not (44%). However, if singletons were not removed the overlap between two technical replicates (not considering sequence abundance) plateaus at 39% with 30,000 sequences. Diversity measures were not affected by the low overlap as α-diversities were similar among technical replicates while β-diversities (Bray-Curtis) were much smaller among technical replicates than among treatment replicates (e.g., 0.269 vs. 0.374). Higher diversity coverage, but lower OTU overlap, was observed when replicates were sequenced in separate runs. Detrended correspondence analysis indicated that while there was considerable variation among technical replicates, the reproducibility was sufficient for detecting treatment effects for the samples examined. These results suggest that although there is variation among technical replicates, amplicon sequencing on MiSeq is useful for analyzing microbial community structure if used

  6. 78 FR 26250 - Payment for Home Health Services and Hospice Care to Non-VA Providers

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-05-06

    ... Hospice Care to Non-VA Providers AGENCY: Department of Veterans Affairs. ACTION: Final rule. SUMMARY: The Department of Veterans Affairs (VA) amends its regulations concerning the billing methodology for non-VA... billing methodology for non-VA providers of home health services and hospice care. The proposed rulemaking...

  7. Characterization of Novel Genes Within 8P11-12 Amplicon in Breast Cancer

    DTIC Science & Technology

    2007-06-01

    C-myc amplification in breast cancer: a meta - analysis of its occurrence and prognostic relevance. Br J Cancer, 83: 1688-1695, 2000. 2. Hui, R...Nass SJ, Dickson RB, Trock BJ. C-myc amplification in breast cancer: a meta - analysis of its occurrence and prognostic relevance. Br J Cancer 2000;83...a detailed genomic and expression analysis of the 8p11-p12 amplicon in breast cancer cell lines and identified several novel candidate genes

  8. Identification of VaD and AD prodromes: the Cache County Study.

    PubMed

    Hayden, K M; Warren, L H; Pieper, C F; Østbye, T; Tschanz, J T; Norton, M C; Breitner, J C S; Welsh-Bohmer, K A

    2005-07-01

    It is unclear whether vascular dementia (VaD) has a cognitive prodrome, akin to the mild cognitive impairment (MCI) prodrome to Alzheimer's dementia (AD). To evaluate whether VaD has a cognitive prodrome, and if it can be differentiated from prodromal AD, we examined neuropsychological test performance of participants in a nested case-control study within a population-based cohort aged 65 or older. Participants (n = 485) were identified from the Cache County Study, a large population-based study of aging and dementia. After an average of 3 years of follow-up, a total of 62 incident dementia cases were identified (14 VaD, 48 AD). We identified a number of neuropsychological tests (executive and memory) that discriminated between diagnosed VaD and AD cases. Multivariate analyses sought to differentiate between these same groups 3 years before clinical diagnosis. The Consortium to Establish a Registry for Alzheimer's Disease Word List Recognition Test correct recognition of foils (mean difference, 1.25; 95% confidence interval [CI], 0.42 to 2.07; p < 0.01), Logical Memory I (mean difference, 7.16; 95% CI, 0.78 to 13.55, p < 0.05), Logical Memory II delayed recall (mean difference, 8.67; 95% CI, 1.59 to 15.74, p < 0.05), and percent savings (mean difference, 51.07; 95% CI, 32.58 to 69.56, p < 0.0001) differentiated VaD from AD cases after adjustment for age, sex, education, and dementia severity. Three years before dementia diagnosis, word list recognition ("no" responses mean difference, 1.40; 95% CI, 0.64 to 2.17; p < 0.001, and "yes" responses mean difference, -1.14; 95% CI, -2.14 to -0.13; p < 0.03) discriminated between prodromal VaD and AD. These results suggest that VaD has a prodromal syndrome, the cognitive features of which are distinguishable from the cognitive prodrome of AD.

  9. 76 FR 63357 - VA National Academic Affiliations Council; Notice of Establishment

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-10-12

    ... DEPARTMENT OF VETERANS AFFAIRS VA National Academic Affiliations Council; Notice of Establishment... Academic Affiliations Council. The Secretary of Veterans Affairs has determined that establishing the... Secretary for Health on matters affecting partnerships between VA and its academic affiliates. The Council...

  10. An overview of patient safety climate in the VA.

    PubMed

    Hartmann, Christine W; Rosen, Amy K; Meterko, Mark; Shokeen, Priti; Zhao, Shibei; Singer, Sara; Falwell, Alyson; Gaba, David M

    2008-08-01

    To assess variation in safety climate across VA hospitals nationally. Data were collected from employees at 30 VA hospitals over a 6-month period using the Patient Safety Climate in Healthcare Organizations survey. We sampled 100 percent of senior managers and physicians and a random 10 percent of other employees. At 10 randomly selected hospitals, we sampled an additional 100 percent of employees working in units with intrinsically higher hazards (high-hazard units [HHUs]). Data were collected using an anonymous survey design. We received 4,547 responses (49 percent response rate). The percent problematic response--lower percent reflecting higher levels of patient safety climate--ranged from 12.0-23.7 percent across hospitals (mean=17.5 percent). Differences in safety climate emerged by management level, clinician status, and workgroup. Supervisors and front-line staff reported lower levels of safety climate than senior managers; clinician responses reflected lower levels of safety climate than those of nonclinicians; and responses of employees in HHUs reflected lower levels of safety climate than those of workers in other areas. This is the first systematic study of patient safety climate in VA hospitals. Findings indicate an overall positive safety climate across the VA, but there is room for improvement.

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

    DTIC Science & Technology

    2011-01-01

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

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

    PubMed

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

    2016-03-15

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

  13. High-resolution mapping of the 11q13 amplicon and identification of a gene, TAOS1, that is amplified and overexpressed in oral cancer cells

    PubMed Central

    Huang, Xin; Gollin, Susanne M.; Raja, Siva; Godfrey, Tony E.

    2002-01-01

    Amplification of chromosomal band 11q13 is a common event in human cancer. It has been reported in about 45% of head and neck carcinomas and in other cancers including esophageal, breast, liver, lung, and bladder cancer. To understand the mechanism of 11q13 amplification and to identify the potential oncogene(s) driving it, we have fine-mapped the structure of the amplicon in oral squamous cell carcinoma cell lines and localized the proximal and distal breakpoints. A 5-Mb physical map of the region has been prepared from which sequence is available. We quantified copy number of sequence-tagged site markers at 42–550 kb intervals along the length of the amplicon and defined the amplicon core and breakpoints by using TaqMan-based quantitative microsatellite analysis. The core of the amplicon maps to a 1.5-Mb region. The proximal breakpoint localizes to two intervals between sequence-tagged site markers, 550 kb and 160 kb in size, and the distal breakpoint maps to a 250 kb interval. The cyclin D1 gene maps to the amplicon core, as do two new expressed sequence tag clusters. We have analyzed one of these expressed sequence tag clusters and now report that it contains a previously uncharacterized gene, TAOS1 (tumor amplified and overexpressed sequence 1), which is both amplified and overexpressed in oral cancer cells. The data suggest that TAOS1 may be an amplification-dependent candidate oncogene with a role in the development and/or progression of human tumors, including oral squamous cell carcinomas. The approach described here should be useful for characterizing amplified genomic regions in a wide variety of tumors. PMID:12172009

  14. 77 FR 12697 - VA Homeless Providers Grant and Per Diem Program

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-03-01

    ...We propose to revise and reorganize regulations which contain the Department of Veterans Affairs' (VA) Homeless Providers Grant and Per Diem Program. This rulemaking would update our current regulations, implement and authorize new VA policies, and generally improve the clarity of part 61.

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

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-05-02

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

  16. Isolation of cultivation-resistant oomycetes, first detected as amplicon sequences, from roots of herbicide-terminated winter rye

    USDA-ARS?s Scientific Manuscript database

    The dynamics of microbial communities associated with dying cover crops are of interest because of potential impacts on disease in a subsequent crop, and because of the importance of microbial activity on plant residue to soil organic matter dynamics and nutrient cycling. High throughput amplicon se...

  17. Participation of Myosin Va and Pka Type I in the Regeneration of Neuromuscular Junctions

    PubMed Central

    Röder, Ira Verena; Strack, Siegfried; Reischl, Markus; Dahley, Oliver; Khan, Muzamil Majid; Kassel, Olivier; Zaccolo, Manuela; Rudolf, Rüdiger

    2012-01-01

    Background The unconventional motor protein, myosin Va, is crucial for the development of the mouse neuromuscular junction (NMJ) in the early postnatal phase. Furthermore, the cooperative action of protein kinase A (PKA) and myosin Va is essential to maintain the adult NMJ. We here assessed the involvement of myosin Va and PKA in NMJ recovery during muscle regeneration. Methodology/Principal Findings To address a putative role of myosin Va and PKA in the process of muscle regeneration, we used two experimental models the dystrophic mdx mouse and Notexin-induced muscle degeneration/regeneration. We found that in both systems myosin Va and PKA type I accumulate beneath the NMJs in a fiber maturation-dependent manner. Morphologically intact NMJs were found to express stable nicotinic acetylcholine receptors and to accumulate myosin Va and PKA type I in the subsynaptic region. Subsynaptic cAMP signaling was strongly altered in dystrophic muscle, particularly in fibers with severely subverted NMJ morphology. Conclusions/Significance Our data show a correlation between the subsynaptic accumulation of myosin Va and PKA type I on the one hand and NMJ regeneration status and morphology, AChR stability and specificity of subsynaptic cAMP handling on the other hand. This suggests an important role of myosin Va and PKA type I for the maturation of NMJs in regenerating muscle. PMID:22815846

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

    PubMed Central

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

    2017-01-01

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

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

    PubMed

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

    2017-01-01

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

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

    PubMed

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

    2013-01-01

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

  1. [Experimental and calculated spectra of the amplicons UBC-85 and UBC-126 (RAPD-PCR)].

    PubMed

    Glazko, G V; Rogozin, I B; Glazko, V I; Zelenaia, L B; Sozinov, A A

    1997-01-01

    The comparative analysis of experimental amplification spectrum in 13 Ungulata species and counting ones in DNA sequences of different taxa in GenBank (mammalian, other vertebrate, invertebrate, viruses, prokaryote) with the uses of RAPD-PCR primers UBC-85 and UBC-126 was carried out. The particularities of the distribution of amplicons' frequencies in experimental and counting spectrums were revealed, for some of them the similar increased frequencies in mammalian and prokaryotic species were observed.

  2. 78 FR 6849 - Agency Information Collection (Verification of VA Benefits) Activity Under OMB Review

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-01-31

    ... (Verification of VA Benefits) Activity Under OMB Review AGENCY: Veterans Benefits Administration, Department of... ``OMB Control No. 2900-0406.'' SUPPLEMENTARY INFORMATION: Title: Verification of VA Benefits, VA Form 26... eliminate unlimited versions of lender- designed forms. The form also informs the lender whether or not the...

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

    PubMed

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

    2017-12-01

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

  4. CoVaCS: a consensus variant calling system.

    PubMed

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

    2018-02-05

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

  5. Enhancing Cross-Cultural Collaboration between DoD and VA

    DTIC Science & Technology

    2012-04-27

    James A. Lovell Federal Health Care Center ( FHCC ). The NDAA 2010 authorized the DoD and VA to establish a five-year demonstration project...integrating the North Chicago VA Medical Center and the Naval Health Clinic Great Lakes.50 The FHCC is named in 15 honor of retired U.S. Naval officer...and Illinois resident, Captain James A. Lovell , who was an astronaut on Apollo 13. The joint facility serves the medical needs of active duty service

  6. 76 FR 44288 - Establishment of Class E Airspace; New Market, VA

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-07-25

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

  7. 77 FR 30050 - VA National Academic Affiliations Council, Notice of meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-05-21

    ... DEPARTMENT OF VETERANS AFFAIRS VA National Academic Affiliations Council, Notice of meeting The...) that the second meeting of the National Academic Affiliations Council will be held on June 5-6, 2012... the Secretary on matters affecting partnerships between VA and its academic affiliates. On June 5, the...

  8. 76 FR 40453 - Agency Information Collection (Application for VA Education Benefits) Activity Under OMB Review

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-07-08

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

  9. An Overview of Patient Safety Climate in the VA

    PubMed Central

    Hartmann, Christine W; Rosen, Amy K; Meterko, Mark; Shokeen, Priti; Zhao, Shibei; Singer, Sara; Falwell, Alyson; Gaba, David M

    2008-01-01

    Objective To assess variation in safety climate across VA hospitals nationally. Study Setting Data were collected from employees at 30 VA hospitals over a 6-month period using the Patient Safety Climate in Healthcare Organizations survey. Study Design We sampled 100 percent of senior managers and physicians and a random 10 percent of other employees. At 10 randomly selected hospitals, we sampled an additional 100 percent of employees working in units with intrinsically higher hazards (high-hazard units [HHUs]). Data Collection Data were collected using an anonymous survey design. Principal Findings We received 4,547 responses (49 percent response rate). The percent problematic response—lower percent reflecting higher levels of patient safety climate—ranged from 12.0–23.7 percent across hospitals (mean=17.5 percent). Differences in safety climate emerged by management level, clinician status, and workgroup. Supervisors and front-line staff reported lower levels of safety climate than senior managers; clinician responses reflected lower levels of safety climate than those of nonclinicians; and responses of employees in HHUs reflected lower levels of safety climate than those of workers in other areas. Conclusions This is the first systematic study of patient safety climate in VA hospitals. Findings indicate an overall positive safety climate across the VA, but there is room for improvement. PMID:18355257

  10. Military and VA general dentistry training: a national resource.

    PubMed

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

    2002-06-01

    In 1999, HRSA contracted with the UCLA School of Dentistry to evaluate the postgraduate general dentistry (PDG) training programs. The purpose of this article is to compare the program characteristics of the PGD training programs sponsored by the Armed Services (military) and VA. Surveys mailed to sixty-six VA and forty-two military program directors in fall 2000 sought information regarding the infrastructure of the program, the program emphasis, resident preparation prior to entering the program, and a description of patients served and types of services provided. Of the eighty-one returned surveys (75 percent response rate), thirty were received from military program directors and fifty-one were received from VA program directors. AEGDs reported treating a higher proportion of children patients and GPRs more medically intensive, disadvantaged and HIV/AIDS patients. Over half of the directors reported increases in curriculum emphasis in implantology. The program directors reported a high level of inadequate preparation among incoming dental residents. Having a higher ratio of residents to total number of faculty predicted inadequate preparation (p=.022) although the model was weak. Although HRSA doesn't financially support federally sponsored programs, their goal of improved dental training to care for medically compromised individuals is facilitated through these programs, thus making military and VA general dentistry programs a national resource.

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

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Bagwell, Christopher E.; Noble, Peter A.; Milliken, Charles E.

    Water quality is an important determinant for the structural integrity of alloy cladded fuels and assemblies during long-term wet storage. Detailed characterization of a water filled storage basin for spent nuclear reactor fuel was performed following the formation and proliferation of an amorphous white flocculent. White precipitant was sampled throughout the storage basin for chemical and spectroscopic characterization, and eDNA was extracted for pyrosequencing of bacterial rRNA gene diversity. Accordingly, spectroscopic analyses indicated the precipitant to be primarily amorphous to crystalline aluminum (oxy) hydroxides with minor associated elemental components including Fe, Si, Ti, and U. High levels of dissolved carbonmore » were co-localized with the precipitant relative to bulk water. Bacterial densities were highly variable between sampling locations and with depth; cell numbers (log scale) ranged from 5.6 to 4.89 cells / mL. Bacterial diversity that was physically associated with the aluminum (oxy) hydroxide complexes exceeded an estimated 4,000 OTUs / amplicon library (3% cutoff) and the greatest percent majority of sequences were aligned to the families Burkholderiales (23%), Nitrospiraceae (23%), Hyphomicrobiaceae (17%), and Comamonadaceae (6%). We surmise that episodic changes in the physical and chemical properties of the basin contribute to the polymerization of aluminum (oxy) hydroxides, which in turn can chemisorb nutrients, carbon ligands and bacterial cells from the surrounding bulk aqueous phase. As such, these precipitants should establish favorable microhabitats for bacterial colonization and growth. Comparative analyses of 16S rRNA gene amplicon libraries across diverse environmental landscapes were performed and microbiological signatures unique to the spent nuclear fuel storage basin environment were revealed. These insights could spur the development of tractable bioindicators that are specific of and diagnostic for water quality at

  12. MyHealtheVet (VA's personal health record)

    MedlinePlus

    ... Overview Site Map Help & User Guides FAQ Privacy & Security Terms and Conditions Policies Privacy Policy Web Policies FOIA Accessibility System Use Important Links VA Home White House USA.gov Inspector ...

  13. Mapping and characterization of the amplicon near APOA2 in 1q23 in human sarcomas by FISH and array CGH

    PubMed Central

    Kresse, Stine H; Berner, Jeanne-Marie; Meza-Zepeda, Leonardo A; Gregory, Simon G; Kuo, Wen-Lin; Gray, Joe W; Forus, Anne; Myklebost, Ola

    2005-01-01

    Background Amplification of the q21-q23 region on chromosome 1 is frequently found in sarcomas and a variety of other solid tumours. Previous analyses of sarcomas have indicated the presence of at least two separate amplicons within this region, one located in 1q21 and one located near the apolipoprotein A-II (APOA2) gene in 1q23. In this study we have mapped and characterized the amplicon in 1q23 in more detail. Results We have used fluorescence in situ hybridisation (FISH) and microarray-based comparative genomic hybridisation (array CGH) to map and define the borders of the amplicon in 10 sarcomas. A subregion of approximately 800 kb was identified as the core of the amplicon. The amplification patterns of nine possible candidate target genes located to this subregion were determined by Southern blot analysis. The genes activating transcription factor 6 (ATF6) and dual specificity phosphatase 12 (DUSP12) showed the highest level of amplification, and they were also shown to be over-expressed by quantitative real-time reverse transcription PCR (RT-PCR). In general, the level of expression reflected the level of amplification in the different tumours. DUSP12 was expressed significantly higher than ATF6 in a subset of the tumours. In addition, two genes known to be transcriptionally activated by ATF6, glucose-regulated protein 78 kDa and -94 kDa (GRP78 and GRP94), were shown to be over-expressed in the tumours that showed over-expression of ATF6. Conclusion ATF6 and DUSP12 seem to be the most likely candidate target genes for the 1q23 amplification in sarcomas. Both genes have possible roles in promoting cell growth, which makes them interesting candidate targets. PMID:16274472

  14. Mapping and characterization of the amplicon near APOA2 in 1q23 in human sarcomas by FISH and array CGH.

    PubMed

    Kresse, Stine H; Berner, Jeanne-Marie; Meza-Zepeda, Leonardo A; Gregory, Simon G; Kuo, Wen-Lin; Gray, Joe W; Forus, Anne; Myklebost, Ola

    2005-11-07

    Amplification of the q21-q23 region on chromosome 1 is frequently found in sarcomas and a variety of other solid tumours. Previous analyses of sarcomas have indicated the presence of at least two separate amplicons within this region, one located in 1q21 and one located near the apolipoprotein A-II (APOA2) gene in 1q23. In this study we have mapped and characterized the amplicon in 1q23 in more detail. We have used fluorescence in situ hybridisation (FISH) and microarray-based comparative genomic hybridisation (array CGH) to map and define the borders of the amplicon in 10 sarcomas. A subregion of approximately 800 kb was identified as the core of the amplicon. The amplification patterns of nine possible candidate target genes located to this subregion were determined by Southern blot analysis. The genes activating transcription factor 6 (ATF6) and dual specificity phosphatase 12 (DUSP12) showed the highest level of amplification, and they were also shown to be over-expressed by quantitative real-time reverse transcription PCR (RT-PCR). In general, the level of expression reflected the level of amplification in the different tumours. DUSP12 was expressed significantly higher than ATF6 in a subset of the tumours. In addition, two genes known to be transcriptionally activated by ATF6, glucose-regulated protein 78 kDa and -94 kDa (GRP78 and GRP94), were shown to be over-expressed in the tumours that showed over-expression of ATF6. ATF6 and DUSP12 seem to be the most likely candidate target genes for the 1q23 amplification in sarcomas. Both genes have possible roles in promoting cell growth, which makes them interesting candidate targets.

  15. What the VA can teach us about geriatric care.

    PubMed

    Ratner, Edward R; West, Melissa; Hartwig, Kristopher N; Meyer, Bruce C

    2013-01-01

    The innovation now being demanded by Medicare is creating new opportunities for health care organizations to redesign how they deliver care for elderly people. For many years, the VA Health System has experimented with ways to deliver care more effectively and efficiently. Hospital-based postacute and palliative care and home-based primary care are two examples of successful approaches that non-VA providers should be looking at as they move away from fee-for-service reimbursement and invent new care-delivery models.

  16. 76 FR 27381 - Proposed Information Collection (Notice of Waiver of VA Compensation or Pension To Receive...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-05-11

    ... of Waiver of VA Compensation or Pension To Receive Military Pay and Allowances) Activity; Comment... Pension to Receive Military Pay and Allowances, VA Form 21-8951 and VA Form 21-8951-2. OMB Control Number... to waive VA disability benefits in order to receive active or inactive duty training pay are required...

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

    PubMed Central

    Liu, Shan; Barnett, Paul G.; Holodniy, Mark; Lo, Jeanie; Joyce, Vilija R.; Gidwani, Risha; Asch, Steven M.; Owens, Douglas K.; Goldhaber-Fiebert, Jeremy D.

    2018-01-01

    Background Chronic hepatitis C viral (HCV) infection affects millions of Americans. Healthcare systems face complex choices between multiple highly efficacious, costly treatments. This study assessed the cost-effectiveness of HCV treatments for chronic, genotype 1 HCV monoinfected, treatment-naïve individuals in the Department of Veterans Affairs (VA) and general U.S. healthcare systems. Methods We conducted a decision-analytic Markov model-based cost-effectiveness analysis, employing appropriate payer perspectives and time horizons, and discounting benefits and costs at 3% annually. Interventions included: Sofosbuvir/ledipasvir (SOF-LDV); ombitasvir/paritaprevir/ritonavir/dasabuvir (3D); sofosbuvir/simeprevir (SOF-SMV); sofosbuvir/pegylated interferon/ribavirin (SOF-RBV-PEG); boceprevir/pegylated interferon/ribavirin (BOC-RBV-PEG); and pegylated interferon/ribavirin (PEG-RBV). Outcomes were sustained virologic response (SVR), advanced liver disease, costs, quality adjusted life years (QALYs), and incremental cost-effectiveness. Results SOF-LDV and 3D achieve higher SVR rates compared to older regimens and reduce advanced liver disease (>20% relative to no treatment), increasing QALYs by over 2 years per person. For the non-VA population, at current prices ($5,040 per week for SOF-LDV and $4,796 per week for 3D), SOF-LDV’s lifetime cost ($293,370) is $18,000 lower than 3D’s because of its shorter treatment duration in subgroups. SOF-LDV costs $17,100 per QALY gained relative to no treatment. 3D costs $208,000 per QALY gained relative to SOF-LDV. Both dominate other treatments and are even more cost-effective for the VA, though VA aggregate treatment costs still exceed $4 billion at SOF-LDV prices of $3,308 per week. Drug prices strongly determine relative cost-effectiveness for SOF-LDV and 3D; With sufficient price reductions (approximately 20–30% depending on the health system), 3D could be cost-effective relative to SOF-LDV. Limitations include the lack of

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

    NASA Technical Reports Server (NTRS)

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

    1992-01-01

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

  19. 30 CFR 57.22315 - Self-contained breathing apparatus (V-A mines).

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 30 Mineral Resources 1 2010-07-01 2010-07-01 false Self-contained breathing apparatus (V-A mines... NONMETAL MINES Safety Standards for Methane in Metal and Nonmetal Mines Equipment § 57.22315 Self-contained breathing apparatus (V-A mines). Self-contained breathing apparatus of a duration to allow for escape from...

  20. 30 CFR 57.22315 - Self-contained breathing apparatus (V-A mines).

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 30 Mineral Resources 1 2011-07-01 2011-07-01 false Self-contained breathing apparatus (V-A mines... NONMETAL MINES Safety Standards for Methane in Metal and Nonmetal Mines Equipment § 57.22315 Self-contained breathing apparatus (V-A mines). Self-contained breathing apparatus of a duration to allow for escape from...

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

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-03-01

    ... Clinic Application, VA Form 0928--53 hours. f. National Veterans Creative Arts Festival Application, VA... Games, National Veterans Golden Age Games, National Veterans Creative Arts Festival, National Veterans...

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

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-05-07

    ... Clinic Application, VA Form 0928a series. f. National Veterans Creative Arts Festival Application, VA... Veterans Creative Arts Festival, National Veterans TEE Tournament, National Disabled Veterans Winter Sports...

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

    PubMed

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

    2015-07-01

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

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

    PubMed

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

    2005-04-01

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

  5. 46 CFR 7.45 - Cape Henlopen, DE to Cape Charles, VA.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 46 Shipping 1 2011-10-01 2011-10-01 false Cape Henlopen, DE to Cape Charles, VA. 7.45 Section 7.45 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY PROCEDURES APPLICABLE TO THE PUBLIC BOUNDARY LINES Atlantic Coast § 7.45 Cape Henlopen, DE to Cape Charles, VA. (a) A line drawn from the easternmost...

  6. ViVaMBC: estimating viral sequence variation in complex populations from illumina deep-sequencing data using model-based clustering.

    PubMed

    Verbist, Bie; Clement, Lieven; Reumers, Joke; Thys, Kim; Vapirev, Alexander; Talloen, Willem; Wetzels, Yves; Meys, Joris; Aerssens, Jeroen; Bijnens, Luc; Thas, Olivier

    2015-02-22

    Deep-sequencing allows for an in-depth characterization of sequence variation in complex populations. However, technology associated errors may impede a powerful assessment of low-frequency mutations. Fortunately, base calls are complemented with quality scores which are derived from a quadruplet of intensities, one channel for each nucleotide type for Illumina sequencing. The highest intensity of the four channels determines the base that is called. Mismatch bases can often be corrected by the second best base, i.e. the base with the second highest intensity in the quadruplet. A virus variant model-based clustering method, ViVaMBC, is presented that explores quality scores and second best base calls for identifying and quantifying viral variants. ViVaMBC is optimized to call variants at the codon level (nucleotide triplets) which enables immediate biological interpretation of the variants with respect to their antiviral drug responses. Using mixtures of HCV plasmids we show that our method accurately estimates frequencies down to 0.5%. The estimates are unbiased when average coverages of 25,000 are reached. A comparison with the SNP-callers V-Phaser2, ShoRAH, and LoFreq shows that ViVaMBC has a superb sensitivity and specificity for variants with frequencies above 0.4%. Unlike the competitors, ViVaMBC reports a higher number of false-positive findings with frequencies below 0.4% which might partially originate from picking up artificial variants introduced by errors in the sample and library preparation step. ViVaMBC is the first method to call viral variants directly at the codon level. The strength of the approach lies in modeling the error probabilities based on the quality scores. Although the use of second best base calls appeared very promising in our data exploration phase, their utility was limited. They provided a slight increase in sensitivity, which however does not warrant the additional computational cost of running the offline base caller. Apparently

  7. 75 FR 41577 - VBA/VHA Musculoskeletal Forum: Improving VA's Disability Evaluation Criteria

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-07-16

    ... medical science information from presentations made by subject matter experts. VA plans to use this information to update the sections of VA's Schedule for Rating Disabilities (VASRD) that pertain to diseases... FURTHER INFORMATION CONTACT: Mr. Brad Tuttle, VASRD Coordinator, Compensation and Pension Service...

  8. 75 FR 33216 - Payment or Reimbursement for Emergency Treatment Furnished by Non-VA Providers in Non-VA...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-06-11

    ... treatment of eligible veterans at non-VA facilities and expand the circumstances under which payment for..., potentially eligible veterans would be appropriately afforded ample opportunity to qualify for this expanded...; 64.010, Veterans Nursing Home Care; and 64.011, Veterans Dental Care. Signing Authority The Secretary...

  9. CloVR-ITS: Automated internal transcribed spacer amplicon sequence analysis pipeline for the characterization of fungal microbiota

    PubMed Central

    2013-01-01

    Background Besides the development of comprehensive tools for high-throughput 16S ribosomal RNA amplicon sequence analysis, there exists a growing need for protocols emphasizing alternative phylogenetic markers such as those representing eukaryotic organisms. Results Here we introduce CloVR-ITS, an automated pipeline for comparative analysis of internal transcribed spacer (ITS) pyrosequences amplified from metagenomic DNA isolates and representing fungal species. This pipeline performs a variety of steps similar to those commonly used for 16S rRNA amplicon sequence analysis, including preprocessing for quality, chimera detection, clustering of sequences into operational taxonomic units (OTUs), taxonomic assignment (at class, order, family, genus, and species levels) and statistical analysis of sample groups of interest based on user-provided information. Using ITS amplicon pyrosequencing data from a previous human gastric fluid study, we demonstrate the utility of CloVR-ITS for fungal microbiota analysis and provide runtime and cost examples, including analysis of extremely large datasets on the cloud. We show that the largest fractions of reads from the stomach fluid samples were assigned to Dothideomycetes, Saccharomycetes, Agaricomycetes and Sordariomycetes but that all samples were dominated by sequences that could not be taxonomically classified. Representatives of the Candida genus were identified in all samples, most notably C. quercitrusa, while sequence reads assigned to the Aspergillus genus were only identified in a subset of samples. CloVR-ITS is made available as a pre-installed, automated, and portable software pipeline for cloud-friendly execution as part of the CloVR virtual machine package (http://clovr.org). Conclusion The CloVR-ITS pipeline provides fungal microbiota analysis that can be complementary to bacterial 16S rRNA and total metagenome sequence analysis allowing for more comprehensive studies of environmental and host-associated microbial

  10. 48 CFR 833.103 - Protests to VA.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... encouraged to use alternative dispute resolution (ADR) procedures to resolve protests at any stage in the protest process. If ADR is used, VA will not furnish any documentation in an ADR proceeding beyond what is...

  11. 78 FR 21817 - Amendment of Restricted Area R-6601; Fort A.P. Hill, VA

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-04-12

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

  12. The VA Computerized Patient Record — A First Look

    PubMed Central

    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, dietetics, surgery, vitals, allergy tracking, discharge summary, problem list, progress notes, consults, and online physician order entry. PMID:7949886

  13. 76 FR 71920 - Payment for Home Health Services and Hospice Care by Non-VA Providers

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-11-21

    ... concerning the billing methodology for non-VA providers of home health services and hospice care. The proposed rulemaking would include home health services and hospice care under the VA regulation governing payment for other non-VA health care providers. Because the newly applicable methodology cannot supersede...

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

    NASA Technical Reports Server (NTRS)

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

    1992-01-01

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

  15. RadNet Air Data From Richmond, VA

    EPA Pesticide Factsheets

    This page presents radiation air monitoring and air filter analysis data for Richmond, VA from EPA's RadNet system. RadNet is a nationwide network of monitoring stations that measure radiation in air, drinking water and precipitation.

  16. RadNet Air Data From Harrisonburg, VA

    EPA Pesticide Factsheets

    This page presents radiation air monitoring and air filter analysis data for Harrisonburg, VA from EPA's RadNet system. RadNet is a nationwide network of monitoring stations that measure radiation in air, drinking water and precipitation.

  17. 78 FR 66265 - Drawbridge Operation Regulation; Elizabeth River, Eastern Branch, Norfolk, VA

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-11-05

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

  18. 78 FR 36715 - VA Veteran-Owned Small Business (VOSB) Verification Guidelines; Correction

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-06-19

    ... DEPARTMENT OF VETERANS AFFAIRS 38 CFR Part 74 RIN 2900-AO63 VA Veteran-Owned Small Business (VOSB... Department of Veterans Affairs (VA) amended its Veteran-Owned Small Business (VOSB) Verification Guidelines... Office of Small and Disadvantaged Business Utilization (00SB), Department of Veterans Affairs, 810...

  19. Simultaneous Amplicon Sequencing to Explore Co-Occurrence Patterns of Bacterial, Archaeal and Eukaryotic Microorganisms in Rumen Microbial Communities

    PubMed Central

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

    2013-01-01

    Ruminants rely on a complex rumen microbial community to convert dietary plant material to energy-yielding products. Here we developed a method to simultaneously analyze the community's bacterial and archaeal 16S rRNA genes, ciliate 18S rRNA genes and anaerobic fungal internal transcribed spacer 1 genes using 12 DNA samples derived from 11 different rumen samples from three host species (Ovis aries, Bos taurus, Cervus elephas) and multiplex 454 Titanium pyrosequencing. We show that the mixing ratio of the group-specific DNA templates before emulsion PCR is crucial to compensate for differences in amplicon length. This method, in contrast to using a non-specific universal primer pair, avoids sequencing non-targeted DNA, such as plant- or endophyte-derived rRNA genes, and allows increased or decreased levels of community structure resolution for each microbial group as needed. Communities analyzed with different primers always grouped by sample origin rather than by the primers used. However, primer choice had a greater impact on apparent archaeal community structure than on bacterial community structure, and biases for certain methanogen groups were detected. Co-occurrence analysis of microbial taxa from all three domains of life suggested strong within- and between-domain correlations between different groups of microorganisms within the rumen. The approach used to simultaneously characterize bacterial, archaeal and eukaryotic components of a microbiota should be applicable to other communities occupying diverse habitats. PMID:23408926

  20. 46 CFR 7.55 - Cape Henry, VA to Cape Fear, NC.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

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

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

    PubMed

    Ibarbalz, Federico M; Pérez, María Victoria; Figuerola, Eva L M; Erijman, Leonardo

    2014-01-01

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

  2. The Bias Associated with Amplicon Sequencing Does Not Affect the Quantitative Assessment of Bacterial Community Dynamics

    PubMed Central

    Figuerola, Eva L. M.; Erijman, Leonardo

    2014-01-01

    The performance of two sets of primers targeting variable regions of the 16S rRNA gene V1–V3 and V4 was compared in their ability to describe changes of bacterial diversity and temporal turnover in full-scale activated sludge. Duplicate sets of high-throughput amplicon sequencing data of the two 16S rRNA regions shared a collection of core taxa that were observed across a series of twelve monthly samples, although the relative abundance of each taxon was substantially different between regions. A case in point was the changes in the relative abundance of filamentous bacteria Thiothrix, which caused a large effect on diversity indices, but only in the V1–V3 data set. Yet the relative abundance of Thiothrix in the amplicon sequencing data from both regions correlated with the estimation of its abundance determined using fluorescence in situ hybridization. In nonmetric multidimensional analysis samples were distributed along the first ordination axis according to the sequenced region rather than according to sample identities. The dynamics of microbial communities indicated that V1–V3 and the V4 regions of the 16S rRNA gene yielded comparable patterns of: 1) the changes occurring within the communities along fixed time intervals, 2) the slow turnover of activated sludge communities and 3) the rate of species replacement calculated from the taxa–time relationships. The temperature was the only operational variable that showed significant correlation with the composition of bacterial communities over time for the sets of data obtained with both pairs of primers. In conclusion, we show that despite the bias introduced by amplicon sequencing, the variable regions V1–V3 and V4 can be confidently used for the quantitative assessment of bacterial community dynamics, and provide a proper qualitative account of general taxa in the community, especially when the data are obtained over a convenient time window rather than at a single time point. PMID:24923665

  3. Who pays when VA users are hospitalized in the private sector? Evidence from three data sources.

    PubMed

    West, Alan N; Weeks, William B

    2007-10-01

    Older veterans enrolled in VA healthcare receive much of their medical care in the private sector, through Medicare. Less is known about younger VA enrollees' use of the private sector, or its funding. We compare payers for younger and older enrollees' private sector use in 3 hospitalization datasets. From 1998 to 2000, using private sector discharge data for VA enrollees in New York State, we categorized hospitalizations according to payer (self/family, private insurance, Medicare, Medicaid, other sources). We compared this payer distribution to population-weighted national Medical Expenditure Panel Survey (MEPS) data from 1996-2003 for veterans in VA healthcare. We also compared Medicare utilization in either dataset to hospitalizations for New York veterans from 1998-2000 in the VA-Medicare dataset. Analyses separated patients younger than age 65 from those age 65 or older. VA enrollees under age 65 obtain roughly half their hospitalizations in the private sector; older enrollees use the private sector at least twice as often as the VA. Datasets generally agree on payer distributions. Although older enrollees rely heavily on Medicare, they also use commercial insurance and self/family payments substantially. Half of younger enrollees' non-VA hospitalizations are paid by private insurance, but Medicare, Medicaid, and self/family each pay for one-quarter to one-third of admissions. VA enrollees use the private sector for most of their inpatient care, which is funded by multiple sources. Developing a national UB-92/VA dataset would be critical to understanding veterans' use of the private sector for specific diagnoses and procedures, particularly for the fast growing population of younger veterans.

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

    PubMed

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

    2017-08-25

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

  5. Competitive amplification of differentially melting amplicons (CADMA) enables sensitive and direct detection of all mutation types by high-resolution melting analysis.

    PubMed

    Kristensen, Lasse S; Andersen, Gitte B; Hager, Henrik; Hansen, Lise Lotte

    2012-01-01

    Sensitive and specific mutation detection is of particular importance in cancer diagnostics, prognostics, and individualized patient treatment. However, the majority of molecular methodologies that have been developed with the aim of increasing the sensitivity of mutation testing have drawbacks in terms of specificity, convenience, or costs. Here, we have established a new method, Competitive Amplification of Differentially Melting Amplicons (CADMA), which allows very sensitive and specific detection of all mutation types. The principle of the method is to amplify wild-type and mutated sequences simultaneously using a three-primer system. A mutation-specific primer is designed to introduce melting temperature decreasing mutations in the resulting mutated amplicon, while a second overlapping primer is designed to amplify both wild-type and mutated sequences. When combined with a third common primer very sensitive mutation detection becomes possible, when using high-resolution melting (HRM) as detection platform. The introduction of melting temperature decreasing mutations in the mutated amplicon also allows for further mutation enrichment by fast coamplification at lower denaturation temperature PCR (COLD-PCR). For proof-of-concept, we have designed CADMA assays for clinically relevant BRAF, EGFR, KRAS, and PIK3CA mutations, which are sensitive to, between 0.025% and 0.25%, mutated alleles in a wild-type background. In conclusion, CADMA enables highly sensitive and specific mutation detection by HRM analysis. © 2011 Wiley Periodicals, Inc.

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

    DTIC Science & Technology

    2017-03-01

    address challenges in managing projects to build medical facilities. In response to statutory requirements and additional congressional direction, VA...is outsourcing management of certain such projects to the U.S. Army Corps of Engineers (USACE). As of October 2016, VA had 23 ongoing projects...costing $100 million or more. VA and USACE have entered into interagency agreements for 12 of these 23 projects. The agreements entail USACE’s managing

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

    PubMed

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

    2012-01-01

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

  8. 33 CFR 334.290 - Elizabeth River, Southern Branch, Va., naval restricted areas.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ..., Va., naval restricted areas. 334.290 Section 334.290 Navigation and Navigable Waters CORPS OF....290 Elizabeth River, Southern Branch, Va., naval restricted areas. (a) The areas—(1) St. Helena Annex Area. Beginning at a point at St. Helena Annex of the Norfolk Naval Shipyard, on the eastern shore of...

  9. 33 CFR 334.290 - Elizabeth River, Southern Branch, Va., naval restricted areas.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ..., Va., naval restricted areas. 334.290 Section 334.290 Navigation and Navigable Waters CORPS OF....290 Elizabeth River, Southern Branch, Va., naval restricted areas. (a) The areas—(1) St. Helena Annex Area. Beginning at a point at St. Helena Annex of the Norfolk Naval Shipyard, on the eastern shore of...

  10. 77 FR 3844 - Proposed Information Collection (Dependents' Application for VA Educational Benefits) Activity...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-01-25

    ... use of other forms of information technology. Title: Dependents' Application for VA Educational... (Dependents' Application for VA Educational Benefits) Activity; Comment Request AGENCY: Veterans Benefits...' Educational Assistance and Fry Scholarship benefits. DATES: Written comments and recommendations on the...

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

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-05-05

    ... VA facilities and the business relationships between VA staff and sales representatives promoting..., and provide sales representatives with a consistent standard of permissible business practice at VA... include suspension of a sales representative's access privileges, or, in extreme cases, denying access to...

  12. Myosin Va Bound to Phagosomes Binds to F-Actin and Delays Microtubule-dependent Motility

    PubMed Central

    Al-Haddad, Ahmed; Shonn, Marion A.; Redlich, Bärbel; Blocker, Ariel; Burkhardt, Janis K.; Yu, Hanry; Hammer, John A.; Weiss, Dieter G.; Steffen, Walter; Griffiths, Gareth; Kuznetsov, Sergei A.

    2001-01-01

    We established a light microscopy-based assay that reconstitutes the binding of phagosomes purified from mouse macrophages to preassembled F-actin in vitro. Both endogenous myosin Va from mouse macrophages and exogenous myosin Va from chicken brain stimulated the phagosome–F-actin interaction. Myosin Va association with phagosomes correlated with their ability to bind F-actin in an ATP-regulated manner and antibodies to myosin Va specifically blocked the ATP-sensitive phagosome binding to F-actin. The uptake and retrograde transport of phagosomes from the periphery to the center of cells in bone marrow macrophages was observed in both normal mice and mice homozygous for the dilute-lethal spontaneous mutation (myosin Va null). However, in dilute-lethal macrophages the accumulation of phagosomes in the perinuclear region occurred twofold faster than in normal macrophages. Motion analysis revealed saltatory phagosome movement with temporarily reversed direction in normal macrophages, whereas almost no reversals in direction were observed in dilute-lethal macrophages. These observations demonstrate that myosin Va mediates phagosome binding to F-actin, resulting in a delay in microtubule-dependent retrograde phagosome movement toward the cell center. We propose an “antagonistic/cooperative mechanism” to explain the saltatory phagosome movement toward the cell center in normal macrophages. PMID:11553713

  13. Overlapping buprenorphine, opioid, and benzodiazepine prescriptions among Veterans dually enrolled in VA and Medicare Part D

    PubMed Central

    Gellad, Walid F.; Zhao, Xinhua; Thorpe, Carolyn T.; Thorpe, Joshua M.; Sileanu, Florentina E.; Cashy, John P.; Mor, Maria; Hale, Jennifer A.; Radomski, Thomas; Hausmann, Leslie R. M.; Fine, Michael J.; Good, Chester B.

    2016-01-01

    Background Buprenorphine is a key tool in the management of opioid use disorder, but there are growing concerns about abuse, diversion and safety. These concerns are amplified for the Department of Veterans Affairs (VA), whose patients may receive care concurrently from multiple prescribers within and outside VA. To illustrate the extent of this challenge, we examined overlapping prescriptions for buprenorphine, opioids, and benzodiazepines among Veterans dually enrolled in VA and Medicare Part D. Methods We constructed a cohort of all Veterans dually enrolled in VA and Part D who filled an opioid prescription in 2012. We identified patients who received tablet or film buprenorphine products from either source. We calculated the proportion of buprenorphine recipients with any overlapping prescription (based on days supply) for a non-buprenorphine opioid or benzodiazepine, focusing on Veterans who received overlapping prescriptions from a different system than their buprenorphine prescription (Part D buprenorphine recipients receiving overlapping opioids or benzodiazepines from VA and vice versa). Results We identified 1,790 dually enrolled Veterans with buprenorphine prescriptions, including 760 (43%) from VA and 1,091 (61%) from Part D (61 Veterans with buprenorphine from both systems were included in each group). Among VA buprenorphine recipients, 199 (26%) received an overlapping opioid prescription and 11 (1%) received an overlapping benzodiazepine prescription from Part D. Among Part D buprenorphine recipients, 208 (19%) received an overlapping opioid prescription and 178 (16%) received an overlapping benzodiazepine prescription from VA. Among VA and Part D buprenorphine recipients with cross-system opioid overlap, 25% (49/199) and 35% (72/208), respectively, had >90 days of overlap. Conclusions Many buprenorphine recipients receive overlapping prescriptions for opioids and benzodiazepines from a different health care system than the one in which their

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

    PubMed Central

    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

  15. 38 CFR 74.26 - What types of business information will VA collect?

    Code of Federal Regulations, 2010 CFR

    2010-07-01

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

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

    DOE PAGES

    Bagwell, Christopher E.; Noble, Peter A.; Milliken, Charles E.; ...

    2018-03-09

    Water quality is an important determinant for the structural integrity of alloy cladded fuels and assemblies during long-term wet storage. Detailed characterization of a water filled storage basin for spent nuclear reactor fuel was performed following the formation and proliferation of an amorphous white flocculent. White precipitant was sampled throughout the storage basin for chemical and spectroscopic characterization, and environmental DNA was extracted for 454 pyrosequencing of bacterial 16S rRNA gene diversity. Accordingly, spectroscopic analyses indicated the precipitant to be primarily amorphous to crystalline aluminum (oxy) hydroxides with minor associated elemental components including Fe, Si, Ti, and U. High levelsmore » of organic carbon were co-localized with the precipitant relative to bulk dissolved organic concentrations. Bacterial densities were highly variable between sampling locations and with depth within the water filled storage basin; cell numbers ranged from 4 × 10 3to 4 × 104 cells/mL. Bacterial diversity that was physically associated with the aluminum (oxy) hydroxide complexes exceeded an estimated 4,000 OTUs/amplicon library (3% cutoff) and the majority of sequences were aligned to the families Burkholderiaceae (23%), Nitrospiraceae (23%), Hyphomicrobiaceae (17%), and Comamonadaceae (6%). We surmise that episodic changes in the physical and chemical properties of the basin contribute to the polymerization of aluminum (oxy) hydroxides, which in turn can chemisorb nutrients, carbon ligands and bacterial cells from the surrounding bulk aqueous phase. As such, these precipitants should establish favorable microhabitats for bacterial colonization and growth. Comparative analyses of 16S rRNA gene amplicon libraries across a selection of natural and engineered aquatic ecosystems were performed and microbial community and taxonomic signatures unique to the spent nuclear fuel (SNF) storage basin environment were revealed. These insights could

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

    PubMed

    Bagwell, Christopher E; Noble, Peter A; Milliken, Charles E; Li, Dien; Kaplan, Daniel I

    2018-01-01

    Water quality is an important determinant for the structural integrity of alloy cladded fuels and assemblies during long-term wet storage. Detailed characterization of a water filled storage basin for spent nuclear reactor fuel was performed following the formation and proliferation of an amorphous white flocculent. White precipitant was sampled throughout the storage basin for chemical and spectroscopic characterization, and environmental DNA was extracted for 454 pyrosequencing of bacterial 16S rRNA gene diversity. Accordingly, spectroscopic analyses indicated the precipitant to be primarily amorphous to crystalline aluminum (oxy) hydroxides with minor associated elemental components including Fe, Si, Ti, and U. High levels of organic carbon were co-localized with the precipitant relative to bulk dissolved organic concentrations. Bacterial densities were highly variable between sampling locations and with depth within the water filled storage basin; cell numbers ranged from 4 × 10 3 to 4 × 10 4 cells/mL. Bacterial diversity that was physically associated with the aluminum (oxy) hydroxide complexes exceeded an estimated 4,000 OTUs/amplicon library (3% cutoff) and the majority of sequences were aligned to the families Burkholderiaceae (23%), Nitrospiraceae (23%), Hyphomicrobiaceae (17%), and Comamonadaceae (6%). We surmise that episodic changes in the physical and chemical properties of the basin contribute to the polymerization of aluminum (oxy) hydroxides, which in turn can chemisorb nutrients, carbon ligands and bacterial cells from the surrounding bulk aqueous phase. As such, these precipitants should establish favorable microhabitats for bacterial colonization and growth. Comparative analyses of 16S rRNA gene amplicon libraries across a selection of natural and engineered aquatic ecosystems were performed and microbial community and taxonomic signatures unique to the spent nuclear fuel (SNF) storage basin environment were revealed. These insights could spur

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

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Bagwell, Christopher E.; Noble, Peter A.; Milliken, Charles E.

    Water quality is an important determinant for the structural integrity of alloy cladded fuels and assemblies during long-term wet storage. Detailed characterization of a water filled storage basin for spent nuclear reactor fuel was performed following the formation and proliferation of an amorphous white flocculent. White precipitant was sampled throughout the storage basin for chemical and spectroscopic characterization, and environmental DNA was extracted for 454 pyrosequencing of bacterial 16S rRNA gene diversity. Accordingly, spectroscopic analyses indicated the precipitant to be primarily amorphous to crystalline aluminum (oxy) hydroxides with minor associated elemental components including Fe, Si, Ti, and U. High levelsmore » of organic carbon were co-localized with the precipitant relative to bulk dissolved organic concentrations. Bacterial densities were highly variable between sampling locations and with depth within the water filled storage basin; cell numbers ranged from 4 × 10 3to 4 × 104 cells/mL. Bacterial diversity that was physically associated with the aluminum (oxy) hydroxide complexes exceeded an estimated 4,000 OTUs/amplicon library (3% cutoff) and the majority of sequences were aligned to the families Burkholderiaceae (23%), Nitrospiraceae (23%), Hyphomicrobiaceae (17%), and Comamonadaceae (6%). We surmise that episodic changes in the physical and chemical properties of the basin contribute to the polymerization of aluminum (oxy) hydroxides, which in turn can chemisorb nutrients, carbon ligands and bacterial cells from the surrounding bulk aqueous phase. As such, these precipitants should establish favorable microhabitats for bacterial colonization and growth. Comparative analyses of 16S rRNA gene amplicon libraries across a selection of natural and engineered aquatic ecosystems were performed and microbial community and taxonomic signatures unique to the spent nuclear fuel (SNF) storage basin environment were revealed. These insights could

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

    PubMed Central

    Bagwell, Christopher E.; Noble, Peter A.; Milliken, Charles E.; Li, Dien; Kaplan, Daniel I.

    2018-01-01

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

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

    DTIC Science & Technology

    2016-12-01

    HOMELESS VETERANS Management Improvements Could Help VA Better Identify Supportive-Housing Projects Report to...VETERANS Management Improvements Could Help VA Better Identify Supportive-Housing Projects What GAO Found As of September 2016, for veterans who...disabled veterans. These supportive-housing EULs receive project -based HUD-VASH vouchers, which provide housing subsidies, on-site case management

  1. The Impact of VA and Navy Hospital Collaboration on Medical School Education

    ERIC Educational Resources Information Center

    Atre-Vaidya, Nutan; Ross, Arthur, III; Sandu, Ioana C.; Hassan, Tariq

    2009-01-01

    Objective: The U.S. Department of Veterans Affairs (VA) is the largest single provider of medical education in the United States and is often the preferred training site for medical students and residents. However, changing priorities of patients and the marketplace are forcing medical schools and the VA to consider new ways of practicing medicine…

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

    DTIC Science & Technology

    2016-12-01

    November 2014. VHA officials also said that after reviewing information from sources such as veteran surveys and feedback from regional VA business...authorizations for care (of both men and women) from early calendar year 2016. In one case, almost a month and a half elapsed from the time of the...veteran’s initial pregnancy confirmation appointment at VA (when she was 6 weeks pregnant) to when the Choice authorization was sent by the VA facility to

  3. 76 FR 70831 - Proposed Information Collection (Survey of Veteran Enrollees (Quality and Efficiency of VA Health...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-11-15

    ... of Veteran Enrollees (Quality and Efficiency of VA Health Care)) Activity; Comment Request AGENCY... of Veteran Enrollees (Quality and Efficiency of VA Health Care), VA Form 10-21088. OMB Control Number... will be used to collect data that is necessary to promote quality and efficient delivery of health care...

  4. Microbial community analysis of the hypersaline water of the Dead Sea using high-throughput amplicon sequencing.

    PubMed

    Jacob, Jacob H; Hussein, Emad I; Shakhatreh, Muhamad Ali K; Cornelison, Christopher T

    2017-10-01

    Amplicon sequencing using next-generation technology (bTEFAP ® ) has been utilized in describing the diversity of Dead Sea microbiota. The investigated area is a well-known salt lake in the western part of Jordan found in the lowest geographical location in the world (more than 420 m below sea level) and characterized by extreme salinity (approximately, 34%) in addition to other extreme conditions (low pH, unique ionic composition different from sea water). DNA was extracted from Dead Sea water. A total of 314,310 small subunit RNA (SSU rRNA) sequences were parsed, and 288,452 sequences were then clustered. For alpha diversity analysis, sample was rarefied to 3,000 sequences. The Shannon-Wiener index curve plot reached a plateau at approximately 3,000 sequences indicating that sequencing depth was sufficient to capture the full scope of microbial diversity. Archaea was found to be dominating the sequences (52%), whereas Bacteria constitute 45% of the sequences. Altogether, prokaryotic sequences (which constitute 97% of all sequences) were found to predominate. The findings expand on previous studies by using high-throughput amplicon sequencing to describe the microbial community in an environment which in recent years has been shown to hide some interesting diversity. © 2017 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.

  5. 76 FR 59765 - Virginia Disaster # VA-00036

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-09-27

    ... SMALL BUSINESS ADMINISTRATION [Disaster Declaration 12843 and 12844] Virginia Disaster VA-00036 AGENCY: U.S. Small Business Administration. ACTION: Notice SUMMARY: This is a notice of an Administrative declaration of a disaster for the Commonwealth of Virginia dated 09/21/2011. Incident: Hurricane Irene...

  6. 77 FR 3841 - Proposed Information Collection (Survey of Veteran Enrollees (Quality and Efficiency of VA Health...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-01-25

    ... of Veteran Enrollees (Quality and Efficiency of VA Health Care)) Activities Under OMB Review AGENCY... of Veteran Enrollees (Quality and Efficiency of VA Health Care), VA Form 10-21088. OMB Control Number... will be used to collect data that is necessary to promote quality and efficient delivery of health care...

  7. 78 FR 18425 - Proposed Information Collection VA Police Officer Pre-Employment Screening Checklist); Comment...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-03-26

    ... enhance the quality, utility, and clarity of the information to be collected; and (4) ways to minimize the... approved collection. Abstract: VA personnel complete VA Form 0120 to document pre- employment history and...

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

    PubMed

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

    2014-05-01

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

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

    PubMed

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

    2017-02-28

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

  10. 78 FR 11094 - Drawbridge Operation Regulation; James River, Between Isle of Wight and Newport News, VA

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-02-15

    ... Operation Regulation; James River, Between Isle of Wight and Newport News, VA AGENCY: Coast Guard, DHS... River, mile 5.0, between Isle of Wight and Newport News, VA. This deviation is necessary to facilitate... Isle of Isle and Newport News, VA opens on signal. The James River Bridge has vertical clearances in...

  11. 75 FR 8005 - Safety Zone; Wicomico Community Fireworks, Great Wicomico River, Mila, VA

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-02-23

    ...-AA00 Safety Zone; Wicomico Community Fireworks, Great Wicomico River, Mila, VA AGENCY: Coast Guard, DHS... the Great Wicomico River in the vicinity of Mila, VA in support of the Wicomico Community Fireworks... protect mariners from the hazards associated with fireworks displays. DATES: Comments and related material...

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

    PubMed

    2013-08-20

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

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

    PubMed Central

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

    2015-01-01

    Previously we presented Swarm v1, a novel and open source amplicon clustering program that produced fine-scale molecular operational taxonomic units (OTUs), free of arbitrary global clustering thresholds and input-order dependency. Swarm v1 worked with an initial phase that used iterative single-linkage with a local clustering threshold (d), followed by a phase that used the internal abundance structures of clusters to break chained OTUs. Here we present Swarm v2, which has two important novel features: (1) a new algorithm for d = 1 that allows the computation time of the program to scale linearly with increasing amounts of data; and (2) the new fastidious option that reduces under-grouping by grafting low abundant OTUs (e.g., singletons and doubletons) onto larger ones. Swarm v2 also directly integrates the clustering and breaking phases, dereplicates sequencing reads with d = 0, outputs OTU representatives in fasta format, and plots individual OTUs as two-dimensional networks. PMID:26713226

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

    PubMed

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

    2015-01-01

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

  15. 75 FR 29660 - Safety Zone; Wicomico Community Fireworks, Great Wicomico River, Mila, VA

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-05-27

    ...-AA00 Safety Zone; Wicomico Community Fireworks, Great Wicomico River, Mila, VA AGENCY: Coast Guard, DHS... the Great Wicomico River in the vicinity of Mila, VA in support of the Wicomico Community Fireworks... protect mariners from the hazards associated with fireworks displays. DATES: This rule is effective from 9...

  16. VA and HRS Local Coordination of Florida's Home-Based Services to the Elderly.

    ERIC Educational Resources Information Center

    Bradham, Douglas D.; Chico, Innette Mary

    Florida's District 12 Veterans Administration (VA) wanted to deliver medical case-management services to veterans not receiving home-based services due to the geographic restrictions of the VA's Hospital-Based Home Care Program. The Florida Department of Health and Rehabilitative Services (HRS) desired to demonstrate the effectiveness of nurse…

  17. Implementation of online suicide-specific training for VA providers.

    PubMed

    Marshall, Elizabeth; York, Janet; Magruder, Kathryn; Yeager, Derik; Knapp, Rebecca; De Santis, Mark L; Burriss, Louisa; Mauldin, Mary; Sulkowski, Stan; Pope, Charlene; Jobes, David A

    2014-10-01

    Due to the gap in suicide-specific intervention training for mental health students and professionals, e-learning is one solution to improving provider skills in the Veterans Affairs (VA) health system. This study focused on the development and evaluation of an equivalent e-learning alternative to the Collaborative Assessment and Management of Suicidality (CAMS) in-person training approach at a Veteran Health Affairs medical center. The study used a multicenter, randomized, cluster, and three group design. the development of e-CAMS was an iterative process and included pilot testing. Eligible and consenting mental health providers, who completed a CAMS pre-survey, were randomized. Provider satisfaction was assessed using the standard VA evaluation of training consisting of 20 items. Two post training focus groups, divided by learning conditions, were conducted to assess practice adoption using a protocol focused on experiences with training and delivery of CAMS. A total of 215 providers in five sites were randomized to three conditions: 69 to e-learning, 70 to in-person, 76 to the control. The providers were primarily female, Caucasian, midlife providers. Based on frequency scores of satisfaction items, both learning groups rated the trainings positively. In focus groups representing divided by learning conditions, participants described positive reactions to CAMS training and similar individual and institutional barriers to full implementation of CAMS. This is the first evaluation study of a suicide-specific e-learning training within the VA. The e-CAMS appears equivalent to the in-person CAMS in terms of provider satisfaction with training and practice adoption, consistent with other comparisons of training deliveries across specialty areas. Additional evaluation of provider confidence and adoption and patient outcomes is in progress. The e-CAMS has the potential to provide ongoing training for VA and military mental health providers and serve as a tutorial for

  18. 16S rRNA Amplicon Sequencing for Epidemiological Surveys of Bacteria in Wildlife

    PubMed Central

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

    2016-01-01

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

  19. 75 FR 20774 - Establishment of Class E Airspace; Fort A.P. Hill, VA

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-04-21

    ...-0739; Airspace Docket No. 09-AEA-14] Establishment of Class E Airspace; Fort A.P. Hill, VA AGENCY... December 7, 2009 that establishes Class E airspace at Fort A.P. Hill, VA. DATES: Effective Date: 0901 UTC... Service Center, Federal Aviation Administration, P.O. Box 20636, Atlanta, Georgia 30320; telephone (404...

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

    PubMed

    Li, Yongcheng; Lu, Ming; Wu, Chuanbin

    2017-11-10

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

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

    PubMed

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

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

  2. 78 FR 36642 - Proposed Information Collection (VA Loan Electronic Reporting Interface (VALERI) System) Activity...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-06-18

    ... DEPARTMENT OF VETERANS AFFAIRS [OMB Control No. 2900-0021] Proposed Information Collection (VA Loan Electronic Reporting Interface (VALERI) System) Activity: Comment Request AGENCY: Veterans... techniques or the use of other forms of information technology. Title: VA Loan Electronic Reporting Interface...

  3. RadNet Air Data From Virginia Beach, VA

    EPA Pesticide Factsheets

    This page presents radiation air monitoring and air filter analysis data for Virginia Beach, VA from EPA's RadNet system. RadNet is a nationwide network of monitoring stations that measure radiation in air, drinking water and precipitation.

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

    PubMed

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

    2015-03-31

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

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

    PubMed

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

    2017-07-06

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

  6. 48 CFR 853.236-70 - VA Form 10-6298, Architect-Engineer Fee Proposal.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 48 Federal Acquisition Regulations System 5 2014-10-01 2014-10-01 false VA Form 10-6298, Architect-Engineer Fee Proposal. 853.236-70 Section 853.236-70 Federal Acquisition Regulations System DEPARTMENT OF...-Engineer Fee Proposal. VA Form 10-6298, Architect-Engineer Fee Proposal, shall be used as prescribed in 836...

  7. 48 CFR 853.236-70 - VA Form 10-6298, Architect-Engineer Fee Proposal.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

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

  8. 48 CFR 819.602-3 - Resolving differences between VA and the Small Business Administration.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 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 copies...

  9. 78 FR 59099 - Agency Information Collection (VA Loan Electronic Reporting Interface (VALERI) System) Activity...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-09-25

    ... Information and Regulatory Affairs, Office of Management and Budget, Attn: VA Desk Officer; 725 17th St. NW....'' SUPPLEMENTARY INFORMATION: Title: VA Loan Electronic Reporting Interface (VALERI) System. OMB Control Number... information submitted through the VALERI system to perform supplemental servicing, determination on...

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

    DTIC Science & Technology

    2016-09-01

    VA HEALTH CARE Processes to Evaluate , Implement, and Monitor Organizational Structure Changes Needed Report to...Accountability Office Highlights of GAO-16-803, a report to congressional requesters September 2016 VA HEALTH CARE Processes to Evaluate , Implement, and...recommended organizational structure changes are evaluated to determine appropriate actions and implemented. This is inconsistent with federal standards

  11. Military and VA telemedicine systems for patients with traumatic brain injury.

    PubMed

    Girard, Philip

    2007-01-01

    Telemedicine plays a critical role within the Department of Veterans Affairs (VA) Veterans Health Administration by allowing the surveillance and care of patients who are isolated by geography, poverty, and disability. In military settings, telemedicine is being widely used to identify injury and illness and aid in the treatment, rehabilitation, and recovery of combat-wounded soldiers in theater. Rapid advances in both domains are transforming the way clinicians provide care, education, and support to patients with traumatic brain injury (TBI) and their families. This article discusses the military and VA telemedicine capabilities that are supporting the care of service members and veterans with TBI. These capabilities include new technologies that enhance the identification of TBI, management of symptoms in theater, and application of proven technologies (interactive video, Internet, and World Wide Web) to improve overall care coordination throughout military and VA systems. The impact of distance learning, teleconsultation, telerehabilitation, and home telehealth programs is also described within this context.

  12. Iraq and Afghanistan Veterans: National Findings from VA Residential Treatment Programs

    PubMed Central

    Cook, Joan M.; Dinnen, Stephanie; O’Donnell, Casey; Bernardy, Nancy; Rosenheck, Robert; Desai, Rani

    2013-01-01

    A quality improvement effort was undertaken in Department of Veterans Affairs’ (VA) residential treatment programs for Posttraumatic Stress Disorder (PTSD) across the United States. Qualitative interviews were conducted with over 250 directors, providers, and staff during site visits of 38 programs. The aims of this report are to describe clinical issues and distinctive challenges in working with veterans from Iraq and Afghanistan and approaches to addressing their needs. Providers indicated that the most commonly reported problems were: acute PTSD symptomotology; other complex mental health symptom presentations; broad readjustment problems; and difficulty with time demands of and readiness for intensive treatment. Additional concerns included working with active duty personnel and mixing different eras in therapy. Programmatic solutions address structure (e.g., blended versus era-specific therapy), content (e.g., physical activity), and adaptations (e.g., inclusion of family; shortened length of stay). Clinical implications for VA managers and policy makers as well as non-VA health care systems and individual health care providers are noted. PMID:23458113

  13. 76 FR 44086 - Agency Information Collection (Notice of Waiver of VA Compensation or Pension To Receive Military...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-07-22

    ... of Waiver of VA Compensation or Pension To Receive Military Pay and Allowances) Activity Under OMB....'' SUPPLEMENTARY INFORMATION: Title: Notice of Waiver of VA Compensation or Pension to Receive Military Pay and... order to receive active or inactive duty training pay are required to complete VA Forms 21-8951 and 21...

  14. MyRIP interaction with MyoVa on secretory granules is controlled by the cAMP-PKA pathway.

    PubMed

    Brozzi, Flora; Lajus, Sophie; Diraison, Frederique; Rajatileka, Shavanthi; Hayward, Katy; Regazzi, Romano; Molnár, Elek; Váradi, Anikó

    2012-11-01

    Myosin- and Rab-interacting protein (MyRIP), which belongs to the protein kinase A (PKA)-anchoring family, is implicated in hormone secretion. However, its mechanism of action is not fully elucidated. Here we investigate the role of MyRIP in myosin Va (MyoVa)-dependent secretory granule (SG) transport and secretion in pancreatic beta cells. These cells solely express the brain isoform of MyoVa (BR-MyoVa), which is a key motor protein in SG transport. In vitro pull-down, coimmunoprecipitation, and colocalization studies revealed that MyRIP does not interact with BR-MyoVa in glucose-stimulated pancreatic beta cells, suggesting that, contrary to previous notions, MyRIP does not link this motor protein to SGs. Glucose-stimulated insulin secretion is augmented by incretin hormones, which increase cAMP levels and leads to MyRIP phosphorylation, its interaction with BR-MyoVa, and phosphorylation of the BR-MyoVa receptor rabphilin-3A (Rph-3A). Rph-3A phosphorylation on Ser-234 was inhibited by small interfering RNA knockdown of MyRIP, which also reduced cAMP-mediated hormone secretion. Demonstrating the importance of this phosphorylation, nonphosphorylatable and phosphomimic Rph-3A mutants significantly altered hormone release when PKA was activated. These data suggest that MyRIP only forms a functional protein complex with BR-MyoVa on SGs when cAMP is elevated and under this condition facilitates phosphorylation of SG-associated proteins, which in turn can enhance secretion.

  15. Intelligent walkers for the elderly: performance and safety testing of VA-PAMAID robotic walker.

    PubMed

    Rentschler, Andrew J; Cooper, Rory A; Blasch, Bruce; Boninger, Michael L

    2003-01-01

    A walker that could help navigate and avoid collisions with obstacles could help reduce health costs and increase the quality of care and independence of thousands of people. This study evaluated the safety and performance of the Veterans Affairs Personal Adaptive Mobility Aid (VA-PAMAID). We performed engineering tests on the VA-PAMAID to determine safety factors, including stability, energy consumption, fatigue life, and sensor and control malfunctions. The VA-PAMAID traveled 10.9 km on a full charge and avoided obstacles while traveling at a speed of up to 1.2 m/s. No failures occurred during static stability, climatic, or fatigue testing. Some problems were encountered during obstacle climbing and sensor and control testing. The VA-PAMAID has good range, has adequate reaction time, and is structurally sound. Clinical trials are planned to compare the device to other low-technical adaptive mobility devices.

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

    NASA Astrophysics Data System (ADS)

    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.

  17. 75 FR 35511 - Virginia Disaster Number VA-00028

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-06-22

    ... SMALL BUSINESS ADMINISTRATION [Disaster Declaration 12040 and 12041] Virginia Disaster Number VA-00028 AGENCY: Small Business Administration. ACTION: Amendment 3. SUMMARY: This is an amendment of the... declaration remains unchanged. (Catalog of Federal Domestic Assistance Numbers 59002 and 59008) Roger B...

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

    DTIC Science & Technology

    2012-06-01

    Lovell Federal Health Care Center ( FHCC ). Although DOD and VA have shared resources at some level since the 1980s,1 the FHCC is unique in that it is...establish a 5-year demonstration to integrate VA and DOD medical care into a first-of- its-kind FHCC in North Chicago, Illinois. Expectations for the... FHCC are outlined in the Executive Agreement signed by VA and DOD in April 2010. The NDAA for Fiscal Year 2010, as amended by the NDAA for

  19. 38 CFR 3.2130 - Will VA accept a signature by mark or thumbprint?

    Code of Federal Regulations, 2010 CFR

    2010-07-01

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

  20. 30 CFR 57.22240 - Actions at 2.0 percent methane (V-A mines).

    Code of Federal Regulations, 2010 CFR

    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 than...

  1. Making Bullying Prevention a Priority in Finnish Schools: The KiVa Antibullying Program

    ERIC Educational Resources Information Center

    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…

  2. 30 CFR 57.22240 - Actions at 2.0 percent methane (V-A mines).

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 30 Mineral Resources 1 2011-07-01 2011-07-01 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 than...

  3. One in vitro model for visceral adipose-derived fibroblasts in chronic inflammation

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Yue Guiping; Du Lirui; Xia Tao

    2005-08-05

    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 themore » 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.« less

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

    PubMed

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

    2015-02-03

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

  5. Using average cost methods to estimate encounter-level costs for medical-surgical stays in the VA.

    PubMed

    Wagner, Todd H; Chen, Shuo; Barnett, Paul G

    2003-09-01

    The U.S. Department of Veterans Affairs (VA) maintains discharge abstracts, but these do not include cost information. This article describes the methods the authors used to estimate the costs of VA medical-surgical hospitalizations in fiscal years 1998 to 2000. They estimated a cost regression with 1996 Medicare data restricted to veterans receiving VA care in an earlier year. The regression accounted for approximately 74 percent of the variance in cost-adjusted charges, and it proved to be robust to outliers and the year of input data. The beta coefficients from the cost regression were used to impute costs of VA medical-surgical hospital discharges. The estimated aggregate costs were reconciled with VA budget allocations. In addition to the direct medical costs, their cost estimates include indirect costs and physician services; both of these were allocated in proportion to direct costs. They discuss the method's limitations and application in other health care systems.

  6. 77 FR 7229 - Virginia Disaster Number VA-00037

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-02-10

    ... SMALL BUSINESS ADMINISTRATION [Disaster Declaration 12909 and 12910] Virginia Disaster Number VA-00037 AGENCY: U.S. Small Business Administration. ACTION: Amendment 3. SUMMARY: This is an amendment of... remains unchanged. (Catalog of Federal Domestic Assistance Numbers 59002 and 59008.) Jane M. D. Pease...

  7. 76 FR 62132 - Virginia Disaster Number VA-00038

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-10-06

    ... SMALL BUSINESS ADMINISTRATION [Disaster Declaration 12805 and 12806] Virginia Disaster Number VA-00038 AGENCY: U.S. Small Business Administration. ACTION: Amendment 2. SUMMARY: This is an amendment of... Federal Domestic Assistance Numbers 59002 and 59008) James E. Rivera, Associate Administrator for Disaster...

  8. VA-086 methacrylate gelatine photopolymerizable hydrogels: A parametric study for highly biocompatible 3D cell embedding.

    PubMed

    Occhetta, Paola; Visone, Roberta; Russo, Laura; Cipolla, Laura; Moretti, Matteo; Rasponi, Marco

    2015-06-01

    The ability to replicate in vitro the native extracellular matrix (ECM) features and to control the three-dimensional (3D) cell organization plays a fundamental role in obtaining functional engineered bioconstructs. In tissue engineering (TE) applications, hydrogels have been successfully implied as biomatrices for 3D cell embedding, exhibiting high similarities to the natural ECM and holding easily tunable mechanical properties. In the present study, we characterized a promising photocrosslinking process to generate cell-laden methacrylate gelatin (GelMA) hydrogels in the presence of VA-086 photoinitiator using a ultraviolet LED source. We investigated the influence of prepolymer concentration and light irradiance on mechanical and biomimetic properties of resulting hydrogels. In details, the increasing of gelatin concentration resulted in enhanced rheological properties and shorter polymerization time. We then defined and validated a reliable photopolymerization protocol for cell embedding (1.5% VA-086, LED 2 mW/cm2) within GelMA hydrogels, which demonstrated to support bone marrow stromal cells viability when cultured up to 7 days. Moreover, we showed how different mechanical properties, derived from different crosslinking parameters, strongly influence cell behavior. In conclusion, this protocol can be considered a versatile tool to obtain biocompatible cell-laden hydrogels with properties easily adaptable for different TE applications. © 2014 Wiley Periodicals, Inc.

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

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-03-01

    ... Affairs (VA) is announcing the availability of funds for applications for assistance under the Per Diem..., application process, and amount of funding available. DATES: Applications must be received in accordance with... Providers Grant and Per Diem Program for eligible entities. VA will award only one application for funding...

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

    ERIC Educational Resources Information Center

    Veterans Administration, Washington, DC.

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

  11. Solution behavior of PVP-VA and HPMC-AS-based amorphous solid dispersions and their bioavailability implications.

    PubMed

    Qian, Feng; Wang, Jennifer; Hartley, Ruiling; Tao, Jing; Haddadin, Raja; Mathias, Neil; Hussain, Munir

    2012-10-01

    To identify the mechanism behind the unexpected bio-performance of two amorphous solid dispersions: BMS-A/PVP-VA and BMS-A/HPMC-AS. Solubility of crystalline BMS-A in PVP-VA and HPMC-AS was measured by DSC. Drug-polymer interaction parameters were obtained by Flory-Huggins model fitting. Drug dissolution kinetics of spray-dried dispersions were studied under sink and non-sink conditions. BMS-A supersaturation was studied in the presence of pre-dissolved PVP-VA and HPMC-AS. Potency and crystallinity of undissolved solid dispersions were determined by HPLC and DSC. Polymer dissolution kinetics were obtained by mass balance calculation. Bioavailability of solid dispersions was assessed in dogs. In solid state, both polymers are miscible with BMS-A, while PVP-VA solublizes the drug better. BMS-A dissolves similarly from both solid dispersions in vitro regardless of dissolution method, while the HPMC-AS dispersion performed much better in vivo. At the same concentration, HPMC-AS is more effective in prolonging BMS-A supersaturation; this effect was negated by the slow dissolution rate of HPMC-AS. Further study revealed that fast PVP-VA dissolution resulted in elevated drug loading in undissolved dispersions and facilitated drug recrystallization before complete release. In contrast, the hydrophobicity and slower HPMC-AS dissolution prevented BMS-A recrystallization within the HPMC-AS matrix for >24 h. The lower bioavailability of PVP-VA dispersion was attributed to BMS-A recrystallization within the undissolved dispersion, due to hydrophilicity and fast PVP-VA dissolution rate. Polymer selection for solid dispersion development has significant impact on in vivo performance besides physical stability.

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

    PubMed

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

    2009-01-01

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

  13. Integrating metagenomic and amplicon databases to resolve the phylogenetic and ecological diversity of the Chlamydiae

    PubMed Central

    Lagkouvardos, Ilias; Weinmaier, Thomas; Lauro, Federico M; Cavicchioli, Ricardo; Rattei, Thomas; Horn, Matthias

    2014-01-01

    In the era of metagenomics and amplicon sequencing, comprehensive analyses of available sequence data remain a challenge. Here we describe an approach exploiting metagenomic and amplicon data sets from public databases to elucidate phylogenetic diversity of defined microbial taxa. We investigated the phylum Chlamydiae whose known members are obligate intracellular bacteria that represent important pathogens of humans and animals, as well as symbionts of protists. Despite their medical relevance, our knowledge about chlamydial diversity is still scarce. Most of the nine known families are represented by only a few isolates, while previous clone library-based surveys suggested the existence of yet uncharacterized members of this phylum. Here we identified more than 22 000 high quality, non-redundant chlamydial 16S rRNA gene sequences in diverse databases, as well as 1900 putative chlamydial protein-encoding genes. Even when applying the most conservative approach, clustering of chlamydial 16S rRNA gene sequences into operational taxonomic units revealed an unexpectedly high species, genus and family-level diversity within the Chlamydiae, including 181 putative families. These in silico findings were verified experimentally in one Antarctic sample, which contained a high diversity of novel Chlamydiae. In our analysis, the Rhabdochlamydiaceae, whose known members infect arthropods, represents the most diverse and species-rich chlamydial family, followed by the protist-associated Parachlamydiaceae, and a putative new family (PCF8) with unknown host specificity. Available information on the origin of metagenomic samples indicated that marine environments contain the majority of the newly discovered chlamydial lineages, highlighting this environment as an important chlamydial reservoir. PMID:23949660

  14. Racial and Ethnic Disparities in the VA Health Care System: A Systematic Review

    PubMed Central

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

    2008-01-01

    Objectives To better understand the causes of racial disparities in health care, we reviewed and synthesized existing evidence related to disparities in the “equal access” Veterans Affairs (VA) health care system. Methods We systematically reviewed and synthesized evidence from studies comparing health care utilization and quality by race within the VA. Results Racial disparities in the VA exist across a wide range of clinical areas and service types. Disparities appear most prevalent for medication adherence and surgery and other invasive procedures, processes that are likely to be affected by the quantity and quality of patient–provider communication, shared decision making, and patient participation. Studies indicate a variety of likely root causes of disparities including: racial differences in patients’ medical knowledge and information sources, trust and skepticism, levels of participation in health care interactions and decisions, and social support and resources; clinician judgment/bias; the racial/cultural milieu of health care settings; and differences in the quality of care at facilities attended by different racial groups. Conclusions Existing evidence from the VA indicates several promising targets for interventions to reduce racial disparities in the quality of health care. PMID:18301951

  15. Evaluation of VA Women's Health Fellowships: developing leaders in academic women's health.

    PubMed

    Tilstra, Sarah A; Kraemer, Kevin L; Rubio, Doris M; McNeil, Melissa A

    2013-07-01

    The Department of Veterans Affairs (VA) instituted the VA Women's Health Fellowship (VAWHF) Program in 1994, to accommodate the health needs of increasing numbers of female veterans and to develop academic leaders in women's health. Despite the longevity of the program, it has never been formally evaluated. To describe the training environments of VAWHFs and career outcomes of female graduates. Cross-sectional web-based surveys of current program directors (2010-2011) and VAWHF graduates (1995-2011). Responses were received from six of seven program directors (86 %) and 42 of 74 graduates (57 %). The mean age of graduates was 41.2 years, and mean time since graduation was 8.5 years. Of the graduates, 97 % were female, 74 % trained in internal medicine, and 64 % obtained an advanced degree. Those with an advanced degree were more likely than those without an advanced degree to pursue an academic career (82 % vs. 60 %; P<0.01). Of the female graduates, 76 % practice clinical women's health and spend up to 66 % of their time devoted to women's health issues. Thirty percent have held a VA faculty position. Seventy-nine percent remain in academics, with 39 % in the tenure stream. Overall, 94 % had given national presentations, 88 % had received grant funding, 79 % had published in peer-reviewed journals, 64 % had developed or evaluated curricula, 51 % had received awards for teaching or research, and 49 % had held major leadership positions. At 11 or more years after graduation, 33 % of the female graduates in academics had been promoted to the rank of associate professor and 33 % to the rank of full professor. The VAWHF Program has been successful in training academic leaders in women's health. Finding ways to retain graduates in the VA system would ensure continued clinical, educational, and research success for the VA women veteran's healthcare program.

  16. Collaboration in health services research: on developing relationships between VA researchers and those in other institutions.

    PubMed Central

    Greenlick, M R; Freeborn, D K

    1986-01-01

    This article explores the potential for collaboration between investigators in institutions outside of the VA and those engaged in research within the VA. The focus is on the potential for collaborative work in health services research; our perspective is that of researchers in a freestanding HMO research center affiliated with the Veterans Administration's Northwest Health Services Research and Development Field Program. The paper begins with a review of the reasons that make collaboration between VA researchers and other health services researchers so appropriate at this time. An example of collaboration is presented, drawing on the experience of the Northwest Field Program and the Kaiser Permanente Center for Health Research. Finally, some difficulties inherent in collaboration between VA and other health services researchers are discussed. PMID:3512485

  17. Quality Of End-Of-Life Care Is Higher In The VA Compared To Care Paid For By Traditional Medicare.

    PubMed

    Gidwani-Marszowski, Risha; Needleman, Jack; Mor, Vincent; Faricy-Anderson, Katherine; Boothroyd, Derek B; Hsin, Gary; Wagner, Todd H; Lorenz, Karl A; Patel, Manali I; Joyce, Vilija R; Murrell, Samantha S; Ramchandran, Kavitha; Asch, Steven M

    2018-01-01

    Congressional and Veterans Affairs (VA) leaders have recommended the VA become more of a purchaser than a provider of health care. Fee-for-service Medicare provides an example of how purchased care differs from the VA's directly provided care. Using established indicators of overly intensive end-of-life care, we compared the quality of care provided through the two systems to veterans dying of cancer in fiscal years 2010-14. The Medicare-reliant veterans were significantly more likely to receive high-intensity care, in the form of chemotherapy, hospital stays, admission to the intensive care unit, more days spent in the hospital, and death in the hospital. However, they were significantly less likely than VA-reliant patients to have multiple emergency department visits. Higher-intensity end-of-life care may be driven by financial incentives present in fee-for-service Medicare but not in the VA's integrated system. To avoid putting VA-reliant veterans at risk of receiving lower-quality care, VA care-purchasing programs should develop coordination and quality monitoring programs to guard against overly intensive end-of-life care.

  18. Geropsychology Training in a VA Nursing Home Setting

    ERIC Educational Resources Information Center

    Karel, Michele J.; Moye, Jennifer

    2005-01-01

    There is a growing need for professional psychology training in nursing home settings, and nursing homes provide a rich environment for teaching geropsychology competencies. We describe the nursing home training component of our Department of Veterans Affairs (VA) Predoctoral Internship and Geropsychology Postdoctoral Fellowship programs. Our…

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

    PubMed

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

    2015-04-01

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

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

    PubMed

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

    2011-03-01

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

  1. 76 FR 27970 - Safety Zone; Cape Charles Fireworks, Cape Charles Harbor, Cape Charles, VA.

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-05-13

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

  2. 76 FR 38302 - Safety Zone; Cape Charles Fireworks, Cape Charles Harbor, Cape Charles, VA

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-06-30

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

  3. 76 FR 67557 - Proposed Information Collection (Survey of Veteran Enrollees' Health and Reliance Upon VA...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-11-01

    ... of Veteran Enrollees' Health and Reliance Upon VA) Activity: Comment Request AGENCY: Veterans Health... enrollees' health status and reliance on VA's health care services. DATES: Written comments and... of automated collection techniques or the use of other forms of information technology. Title: Survey...

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

    PubMed

    Barnett, P G; Rodgers, J H

    1999-04-01

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

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

    PubMed Central

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

    2013-01-01

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

  6. Herpes simplex virus amplicon delivery of a hypoxia-inducible soluble vascular endothelial growth factor receptor (sFlk-1) inhibits angiogenesis and tumor growth in pancreatic adenocarcinoma.

    PubMed

    Reinblatt, Maura; Pin, Richard H; Bowers, William J; Federoff, Howard J; Fong, Yuman

    2005-12-01

    Tumor hypoxia induces vascular endothelial growth factor (VEGF) expression, which stimulates angiogenesis and tumor proliferation. The VEGF signaling pathway is inhibited by soluble VEGF receptors (soluble fetal liver kinase 1; sFlk-1), which bind VEGF and block its interaction with endothelial cells. Herpes simplex virus (HSV) amplicons are replication-incompetent viruses used for gene delivery. We attempted to attenuate angiogenesis and inhibit pancreatic tumor growth through HSV amplicon-mediated expression of sFlk-1 under hypoxic control. A multimerized hypoxia-responsive enhancer (10 x HRE) was cloned upstream of the sFlk-1 gene (10 x HRE/sFlk-1). A novel HSV amplicon expressing 10 x HRE/sFlk-1 was genetically engineered (HSV10 x HRE/sFlk-1).Human pancreatic adenocarcinoma cells (AsPC1) were transduced with HSV10 x HRE/sFlk-1 and incubated in normoxia (21% oxygen) or hypoxia (1% oxygen). Capillary inhibition was evaluated by human umbilical vein endothelial cell assay. Western blot assessed sFlk-1 expression. AsPC1 flank tumor xenografts (n = 24) were transduced with HSV10 x HRE/sFlk-1. Media from normoxic AsPC1 transduced with HSV10 x HRE/sFlk-1 yielded a 36% reduction in capillary formation versus controls (P < .05), whereas hypoxic AsPC1 yielded a 76% reduction (P < .005). Western blot of AsPC1 transduced with HSV10 x HRE/sFlk-1 demonstrated greater sFlk-1 expression in hypoxia versus normoxia. AsPC1 flank tumors treated with HSV10 x HRE/sFlk-1 exhibited a 59% reduction in volume versus controls (P < .000001). HSV amplicon delivery of a hypoxia-inducible soluble VEGF receptor significantly reduces new vessel formation and tumor growth. Tumor hypoxia can thus be used to direct antiangiogenic therapy to pancreatic adenocarcinoma.

  7. Comparative Analysis of VaR Estimation of Double Long-Memory GARCH Models: Empirical Analysis of China's Stock Market

    NASA Astrophysics Data System (ADS)

    Cao, Guangxi; Guo, Jianping; Xu, Lin

    GARCH models are widely used to model the volatility of financial assets and measure VaR. Based on the characteristics of long-memory and lepkurtosis and fat tail of stock market return series, we compared the ability of double long-memory GARCH models with skewed student-t-distribution to compute VaR, through the empirical analysis of Shanghai Composite Index (SHCI) and Shenzhen Component Index (SZCI). The results show that the ARFIMA-HYGARCH model performance better than others, and at less than or equal to 2.5 percent of the level of VaR, double long-memory GARCH models have stronger ability to evaluate in-sample VaRs in long position than in short position while there is a diametrically opposite conclusion for ability of out-of-sample VaR forecast.

  8. 12 CFR 217.205 - VaR-based measure.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... requirements. The Board-regulated institution must update data sets at least monthly or more frequently as... year. Data used to determine the VaR-based measure must be relevant to the Board-regulated institution.... A Board-regulated institution using this option must update its data more frequently than monthly...

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

    PubMed

    Nocentini, Annalaura; Menesini, Ersilia

    2016-11-01

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

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

    PubMed

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

    2016-05-01

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

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

    PubMed

    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.

  12. Using policy to increase prescribing of smoking cessation medications in the VA healthcare system.

    PubMed

    Smith, Mark W; Chen, Shuo; Siroka, Andrew M; Hamlett-Berry, Kim

    2010-12-01

    Since 2002 the US Veterans Affairs (VA) healthcare system has initiated national policies and programmes to reduce smoking among its patients and to increase evidence-based treatment for smoking. To document changes in dispensing rates of cessation-related medications in VA from 2004 to 2008. Retrospective analysis of VA administrative data. Prescription fills for nicotine replacement therapy (NRT), and for bupropion among NRT users, each grew more than 60% in four years. The increase stemmed primarily from treating more people rather than from filling more prescriptions per person. The results provide strong support for the efficacy of these policies and illustrate how healthcare systems can successfully employ multiple strategies to increase evidence-based smoking-cessation treatment.

  13. 30 CFR 57.22218 - Seals and stoppings (III, V-A, and V-B mines).

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 30 Mineral Resources 1 2011-07-01 2011-07-01 false Seals and stoppings (III, V-A, and V-B mines... NONMETAL MINES Safety Standards for Methane in Metal and Nonmetal Mines Ventilation § 57.22218 Seals and stoppings (III, V-A, and V-B mines). (a) All seals, and those stoppings that separate main intake from main...

  14. 30 CFR 57.22218 - Seals and stoppings (III, V-A, and V-B mines).

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 30 Mineral Resources 1 2010-07-01 2010-07-01 false Seals and stoppings (III, V-A, and V-B mines... NONMETAL MINES Safety Standards for Methane in Metal and Nonmetal Mines Ventilation § 57.22218 Seals and stoppings (III, V-A, and V-B mines). (a) All seals, and those stoppings that separate main intake from main...

  15. 30 CFR 57.22608 - Secondary blasting (I-A, II-A, and V-A mines).

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 30 Mineral Resources 1 2011-07-01 2011-07-01 false Secondary blasting (I-A, II-A, and V-A mines). 57.22608 Section 57.22608 Mineral Resources MINE SAFETY AND HEALTH ADMINISTRATION, DEPARTMENT OF... blasting (I-A, II-A, and V-A mines). Prior to secondary blasting, tests for methane shall be made in the...

  16. 30 CFR 57.22608 - Secondary blasting (I-A, II-A, and V-A mines).

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 30 Mineral Resources 1 2010-07-01 2010-07-01 false Secondary blasting (I-A, II-A, and V-A mines). 57.22608 Section 57.22608 Mineral Resources MINE SAFETY AND HEALTH ADMINISTRATION, DEPARTMENT OF... blasting (I-A, II-A, and V-A mines). Prior to secondary blasting, tests for methane shall be made in the...

  17. 30 CFR 57.22101 - Smoking (I-A, II-A, III, and V-A mines).

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 30 Mineral Resources 1 2012-07-01 2012-07-01 false Smoking (I-A, II-A, III, and V-A mines). 57.22101 Section 57.22101 Mineral Resources MINE SAFETY AND HEALTH ADMINISTRATION, DEPARTMENT OF LABOR... Smoking (I-A, II-A, III, and V-A mines). Persons shall not smoke or carry smoking materials, matches, or...

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

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 30 Mineral Resources 1 2014-07-01 2014-07-01 false Smoking (I-A, II-A, III, and V-A mines). 57.22101 Section 57.22101 Mineral Resources MINE SAFETY AND HEALTH ADMINISTRATION, DEPARTMENT OF LABOR... Smoking (I-A, II-A, III, and V-A mines). Persons shall not smoke or carry smoking materials, matches, or...

  19. 30 CFR 57.22101 - Smoking (I-A, II-A, III, and V-A mines).

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 30 Mineral Resources 1 2013-07-01 2013-07-01 false Smoking (I-A, II-A, III, and V-A mines). 57.22101 Section 57.22101 Mineral Resources MINE SAFETY AND HEALTH ADMINISTRATION, DEPARTMENT OF LABOR... Smoking (I-A, II-A, III, and V-A mines). Persons shall not smoke or carry smoking materials, matches, or...

  20. 30 CFR 57.22101 - Smoking (I-A, II-A, III, and V-A mines).

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 30 Mineral Resources 1 2011-07-01 2011-07-01 false Smoking (I-A, II-A, III, and V-A mines). 57.22101 Section 57.22101 Mineral Resources MINE SAFETY AND HEALTH ADMINISTRATION, DEPARTMENT OF LABOR... Smoking (I-A, II-A, III, and V-A mines). Persons shall not smoke or carry smoking materials, matches, or...

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

    DTIC Science & Technology

    2009-11-01

    that differentially expressed tumor suppressor miRNAs can be utilized to control the replication of an oncolytic DNA virus in a tumor-specific...demonstrated that the utilization of the tissue-specific promoter and the miRNA-mediated 3’UTRs in a targeted virotherapy is a viable approach with...elements into the whole HSV-1 viral genome should increase the safety margin substantially. The major advantage of the amplicon/helper system is its

  2. Initiating an ophthalmic laser program for VA outpatients.

    PubMed

    Newcomb, R D

    1995-08-01

    Administrative and clinical considerations for the establishment of an ophthalmic laser program at a VA Outpatient Clinic are discussed. Outcomes of the first 320 patients treated over a 3-year period of time are presented. The program is evaluated from the perspectives of patient care, safety, maintenance, education, and economics.

  3. 77 FR 39346 - Proposed Information Collection (Statement of Accredited Representative in Appealed Case, VA Form...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-07-02

    ... in Appealed Case, VA Form 646. OMB Control Number: 2900-0042. Type of Review: Extension of a... (Statement of Accredited Representative in Appealed Case, VA Form 646) Activity: Comment Request AGENCY: The Board of Veterans' Appeals (BVA), Department of Veterans Affairs. ACTION: Notice. SUMMARY: The Board of...

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

    PubMed

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

    2016-02-01

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

  5. Testing V-A in Top Decay at CDF at √s = 1.8 TeV

    NASA Astrophysics Data System (ADS)

    Kilminster, Ben

    2004-02-01

    The structure of the tbW vertex can be probed by measuring the polarization of the W in t → W + b → l + ν + b. The invariant mass of the the lepton and b quark measures the W decay angle which in turn allows a comparison with polarizations expected from a V-A and V+A tbW vertex. We measure the fraction by rate of Ws produced with a V+A coupling in lieu of the Standard Model V-A to be fV+A = -0.21-0.24+0.42 (stat) ± 0.21 (sys). We assign a limit of fV+A < 0.80 @ 95% CL. By combining this result with a complementary observable in the same data, we assign a limit of fV+A < 0.61 @ 95% CL. From this CDF Run I preliminary result, we find no evidence for a non-standard Model tbW vertex.

  6. 77 FR 48127 - Foreign-Trade Zone 20-Suffolk, VA; Notification of Proposed Production Activity, Usui...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-08-13

    ... DEPARTMENT OF COMMERCE Foreign-Trade Zones Board [B-53-2012] Foreign-Trade Zone 20--Suffolk, VA; Notification of Proposed Production Activity, Usui International Corporation, (Diesel Engine Fuel Lines), Chesapeake, VA The Virginia Port Authority, grantee of FTZ 20, submitted a notification of proposed production activity on behalf of Usui...

  7. 76 FR 59153 - Elizabeth Hartwell Mason Neck National Wildlife Refuge, Fairfax County, VA, and Featherstone...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-09-23

    ... DEPARTMENT OF THE INTERIOR Fish and Wildlife Service [FWS-R5-R-2011-N128; BAC-4311-K9-S3] Elizabeth Hartwell Mason Neck National Wildlife Refuge, Fairfax County, VA, and Featherstone National Wildlife Refuge, Prince William County, VA AGENCY: Fish and Wildlife Service, Interior. ACTION: Notice of...

  8. 48 CFR 852.219-72 - Evaluation factor for participation in the VA mentor-protégé program.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

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

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

    DTIC Science & Technology

    2017-01-01

    delivery of health care that would be more accessible and less expensive than operating two federal medical centers serving VA and DOD beneficiaries in...departments—including DOD’s operational readiness mission—by integrating services previously provided by the former North Chicago VA Medical Center...1VA beneficiaries include veterans of military service and certain dependents and survivors. DOD beneficiaries include active duty

  10. Correspondence of the Boston Assessment of Traumatic Brain Injury-Lifetime (BAT-L) clinical interview and the VA TBI screen.

    PubMed

    Fortier, Catherine Brawn; Amick, Melissa M; Kenna, Alexandra; Milberg, William P; McGlinchey, Regina E

    2015-01-01

    Mild traumatic brain injury is the signature injury of Operation Enduring Freedom (OEF), Operation Iraqi Freedom (OIF), and Operation New Dawn (OND), yet its identification and diagnosis is controversial and fraught with challenges. In 2007, the Department of Veterans Affairs (VA) implemented a policy requiring traumatic brain injury (TBI) screening on all individuals returning from deployment in the OEF/OIF/OND theaters of operation that lead to the rapid and widespread use of the VA TBI screen. The Boston Assessment of TBI-Lifetime (BAT-L) is the first validated, postcombat semistructured clinical interview to characterize head injuries and diagnose TBIs throughout the life span, including prior to, during, and post-military service. Community-dwelling convenience sample of 179 OEF/OIF/OND veterans. BAT-L, VA TBI screen. Based on BAT-L diagnosis of military TBI, the VA TBI screen demonstrated similar sensitivity (0.85) and specificity (0.82) when administered by research staff. When BAT-L diagnosis was compared with historical clinician-administered VA TBI screen in a subset of participants, sensitivity was reduced. The specificity of the research-administered VA TBI screen was more than adequate. The sensitivity of the VA TBI screen, although relatively high, suggests that it does not oversample or "catch all" possible military TBIs. Traumatic brain injuries identified by the BAT-L, but not identified by the VA TBI screen, were predominantly noncombat military injuries. There is potential concern regarding the validity and reliability of the clinician administered VA TBI screen, as we found poor correspondence between it and the BAT-L, as well as low interrater reliability between the clinician-administered and research-administered screen.

  11. 12 CFR 324.205 - VaR-based measure.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... risk-based capital requirements. The FDIC-supervised institution must update data sets at least monthly... observation period of at least one year. Data used to determine the VaR-based measure must be relevant to the... portfolio over a full business cycle. An FDIC-supervised institution using this option must update its data...

  12. 12 CFR 3.205 - VaR-based measure.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... bank or Federal savings association must update data sets at least monthly or more frequently as... be based on a historical observation period of at least one year. Data used to determine the VaR... using this option must update its data more frequently than monthly and in a manner appropriate for the...

  13. 30 CFR 57.22212 - Air flow (I-C, II-A, and V-A mines).

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 30 Mineral Resources 1 2011-07-01 2011-07-01 false Air flow (I-C, II-A, and V-A mines). 57.22212 Section 57.22212 Mineral Resources MINE SAFETY AND HEALTH ADMINISTRATION, DEPARTMENT OF LABOR METAL AND... Standards for Methane in Metal and Nonmetal Mines Ventilation § 57.22212 Air flow (I-C, II-A, and V-A mines...

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

    NASA Astrophysics Data System (ADS)

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

    2017-04-01

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

  15. Multi-locus and long amplicon sequencing approach to study microbial diversity at species level using the MinION™ portable nanopore sequencer

    PubMed Central

    Sanz, Yolanda

    2017-01-01

    Abstract The miniaturized and portable DNA sequencer MinION™ has demonstrated great potential in different analyses such as genome-wide sequencing, pathogen outbreak detection and surveillance, human genome variability, and microbial diversity. In this study, we tested the ability of the MinION™ platform to perform long amplicon sequencing in order to design new approaches to study microbial diversity using a multi-locus approach. After compiling a robust database by parsing and extracting the rrn bacterial region from more than 67000 complete or draft bacterial genomes, we demonstrated that the data obtained during sequencing of the long amplicon in the MinION™ device using R9 and R9.4 chemistries were sufficient to study 2 mock microbial communities in a multiplex manner and to almost completely reconstruct the microbial diversity contained in the HM782D and D6305 mock communities. Although nanopore-based sequencing produces reads with lower per-base accuracy compared with other platforms, we presented a novel approach consisting of multi-locus and long amplicon sequencing using the MinION™ MkIb DNA sequencer and R9 and R9.4 chemistries that help to overcome the main disadvantage of this portable sequencing platform. Furthermore, the nanopore sequencing library, constructed with the last releases of pore chemistry (R9.4) and sequencing kit (SQK-LSK108), permitted the retrieval of the higher level of 1D read accuracy sufficient to characterize the microbial species present in each mock community analysed. Improvements in nanopore chemistry, such as minimizing base-calling errors and new library protocols able to produce rapid 1D libraries, will provide more reliable information in the near future. Such data will be useful for more comprehensive and faster specific detection of microbial species and strains in complex ecosystems. PMID:28605506

  16. 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.

    PubMed

    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.

  17. 77 FR 72816 - Foreign-Trade Zone 20-Suffolk, VA; Authorization of Production Activity; Usui International...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-12-06

    ... DEPARTMENT OF COMMERCE Foreign-Trade Zones Board [B-53-2012] Foreign-Trade Zone 20--Suffolk, VA; Authorization of Production Activity; Usui International Corporation (Diesel Engine Fuel Lines); Chesapeake, VA On June 28, 2012, the Virginia Port Authority, grantee of FTZ 20, submitted a notification of proposed production activity to the...

  18. 78 FR 31840 - Safety Zone; USO Patriotic Festival Air Show, Atlantic Ocean; Virginia Beach, VA

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-05-28

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

  19. 77 FR 39404 - Safety Zone; Wicomico Community Fireworks Rain Date, Great Wicomico River, Mila, VA

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-07-03

    ...-AA00 Safety Zone; Wicomico Community Fireworks Rain Date, Great Wicomico River, Mila, VA AGENCY: Coast... zone on the Great Wicomico River in the vicinity of Mila, VA in support of the Wicomico Community Rain... as follows: Sec. 165.T05-0425 Safety Zone; Wicomico Community Fireworks Rain Date, Great Wicomico...

  20. 38 CFR 17.71 - Revocation of VA approval.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... Community Residential Care § 17.71 Revocation of VA approval. (a) If a hearing official determines under § 17.70 of this part that a community residential care facility does not comply with the standards set forth in § 17.63 of this part and determines that the community residential care facility shall not have...

  1. ENTRANCE TO CEMETERY FROM VA MEDICAL CENTER CAMPUS, WITH ADMINISTRATION ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    ENTRANCE TO CEMETERY FROM VA MEDICAL CENTER CAMPUS, WITH ADMINISTRATION BUILDING IN BACKGROUND. VIEW TO NORTH. - Bath National Cemetery, Department of Veterans Affairs Medical Center, San Juan Avenue, Bath, Steuben County, NY

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

    PubMed

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

    2015-07-01

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

  3. Toward a VA Women's Health Research Agenda: setting evidence-based priorities to improve the health and health care of women veterans.

    PubMed

    Yano, Elizabeth M; Bastian, Lori A; Frayne, Susan M; Howell, Alexandra L; Lipson, Linda R; McGlynn, Geraldine; Schnurr, Paula P; Seaver, Margaret R; Spungen, Ann M; Fihn, Stephan D

    2006-03-01

    The expansion of women in the military is reshaping the veteran population, with women now constituting the fastest growing segment of eligible VA health care users. In recognition of the changing demographics and special health care needs of women, the VA Office of Research & Development recently sponsored the first national VA Women's Health Research Agenda-setting conference to map research priorities to the needs of women veterans and position VA as a national leader in Women's Health Research. This paper summarizes the process and outcomes of this effort, outlining VA's research priorities for biomedical, clinical, rehabilitation, and health services research.

  4. Toward a VA Women's Health Research Agenda: Setting Evidence-based Priorities to Improve the Health and Health Care of Women Veterans

    PubMed Central

    Yano, Elizabeth M; Bastian, Lori A; Frayne, Susan M; Howell, Alexandra L; Lipson, Linda R; McGlynn, Geraldine; Schnurr, Paula P; Seaver, Margaret R; Spungen, Ann M; Fihn, Stephan D

    2006-01-01

    The expansion of women in the military is reshaping the veteran population, with women now constituting the fastest growing segment of eligible VA health care users. In recognition of the changing demographics and special health care needs of women, the VA Office of Research & Development recently sponsored the first national VA Women's Health Research Agenda-setting conference to map research priorities to the needs of women veterans and position VA as a national leader in Women's Health Research. This paper summarizes the process and outcomes of this effort, outlining VA's research priorities for biomedical, clinical, rehabilitation, and health services research. PMID:16637953

  5. Functional evaluation of sublingual microcirculation indicates successful weaning from VA-ECMO in cardiogenic shock.

    PubMed

    Akin, Sakir; Dos Reis Miranda, Dinis; Caliskan, Kadir; Soliman, Osama I; Guven, Goksel; Struijs, Ard; van Thiel, Robert J; Jewbali, Lucia S; Lima, Alexandre; Gommers, Diederik; Zijlstra, Felix; Ince, Can

    2017-10-26

    Veno-arterial extracorporeal membrane oxygenation (VA-ECMO) is increasingly adopted for the treatment of cardiogenic shock (CS). However, a marker of successful weaning remains largely unknown. Our hypothesis was that successful weaning is associated with sustained microcirculatory function during ECMO flow reduction. Therefore, we sought to test the usefulness of microcirculatory imaging in the same sublingual spot, using incident dark field (IDF) imaging in assessing successful weaning from VA-ECMO and compare IDF imaging with echocardiographic parameters. Weaning was performed by decreasing the VA-ECMO flow to 50% (F 50 ) from the baseline. The endpoint of the study was successful VA-ECMO explantation within 48 hours after weaning. The response of sublingual microcirculation to a weaning attempt (WA) was evaluated. Microcirculation was measured in one sublingual area (single spot (ss)) using CytoCam IDF imaging during WA. Total vessel density (TVDss) and perfused vessel density (PVDss) of the sublingual area were evaluated before and during 50% flow reduction (TVDss F50 , PVDss F50 ) after a WA and compared to conventional echocardiographic parameters as indicators of the success or failure of the WA. Patients (n = 13) aged 49 ± 18 years, who received VA-ECMO for the treatment of refractory CS due to pulmonary embolism (n = 5), post cardiotomy (n = 3), acute coronary syndrome (n = 2), myocarditis (n = 2) and drug intoxication (n = 1), were included. TVDss F50 (21.9 vs 12.9 mm/mm 2 , p = 0.001), PVDss F50 (19.7 vs 12.4 mm/mm 2 , p = 0.01) and aortic velocity-time integral (VTI) at 50% flow reduction (VTI F50 ) were higher in patients successfully weaned vs not successfully weaned. The area under the curve (AUC) was 0.99 vs 0.93 vs 0.85 for TVDss F50 (small vessels) >12.2 mm/mm 2 , left ventricular ejection fraction (LVEF) >15% and aortic VTI >11 cm. Likewise, the AUC was 0.91 vs 0.93 vs 0.85 for the PVDss F50 (all vessels) >14

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

    ERIC Educational Resources Information Center

    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…

  7. 78 FR 76061 - Authorization for Non-VA Medical Services

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-12-16

    ..., Health professions, Health records, Homeless, Mental health programs, Nursing homes, Reporting and... final rule adopts the proposed rule without changes. We received several comments urging VA to expand....009, Veterans Medical Care Benefits; 64.010, Veterans Nursing Home Care; 64.011, Veterans Dental Care...

  8. Characteristics and service utilization of homeless veterans entering VA substance use treatment.

    PubMed

    Cox, Koriann B; Malte, Carol A; Saxon, Andrew J

    2017-05-01

    This article compares characteristics and health care utilization patterns of homeless veterans entering substance use disorder (SUD) treatment. Baseline self-report and medical record data were collected from 181 homeless veterans participating in a randomized trial of SUD/housing case management. Veterans, categorized as newly (n = 45), episodically (n = 61), or chronically homeless (n = 75), were compared on clinical characteristics and health care utilization in the year prior to baseline. Between-groups differences were seen in stimulant use, bipolar, and depressive disorders. A significant majority accessed VA emergency department services, and nearly half accessed inpatient services, with more utilization among chronically versus newly homeless. A majority in all groups attended VA primary care (73.5%) and mental health (56.9%) visits, and 26.7% newly, 32.8% episodically, and 56.0% chronically homeless veterans initiated multiple SUD treatment episodes (p = .002). A significant proportion of veterans struggling with homelessness and SUDs appear to remain unstable despite high utilization of VA acute and preventative services. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

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

    PubMed Central

    Mehetre, Gajanan T.; Paranjpe, Aditi; Dastager, Syed G.

    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

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

    PubMed

    Eichmann, Cordula; Parson, Walther

    2008-09-01

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

  11. Chernobyl Doses. Volume 2. Conifer Stress near Chernobyl Derived from Landsat Imagery

    DTIC Science & Technology

    1992-12-01

    Defense Nuclear Agency Alexandria, VA 22310-3398 AD-A259 085 S.... IiilII|IlH~l D.A-TR-92-3,,.v2 Chernobyl Doses Volume 2-Conifer Stress Near... Chernobyl Derived from Landsat Imagery Gene E. McClellan Terrence H. Hemmer Ronald N. DeWitt Pacific-Sierra Research Corporation 12340 Santa Monica Boulevard...870929 - 920228 4. TITLE AND SUBTITLE 5. FUNDING NUMBERS Chernobyl Doses C - DNA 001-87-C-0104 Volume 2- Conifer Stress Near Chernobyl Derived from

  12. 30 CFR 57.22208 - Auxiliary fans (I-A, II-A, III, and V-A mines).

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 30 Mineral Resources 1 2011-07-01 2011-07-01 false Auxiliary fans (I-A, II-A, III, and V-A mines). 57.22208 Section 57.22208 Mineral Resources MINE SAFETY AND HEALTH ADMINISTRATION, DEPARTMENT OF... fans (I-A, II-A, III, and V-A mines). (a) Auxiliary fans, except fans used in shops and other areas...

  13. 30 CFR 57.22103 - Open flames (I-A, II-A, III, and V-A mines).

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 30 Mineral Resources 1 2011-07-01 2011-07-01 false Open flames (I-A, II-A, III, and V-A mines). 57.22103 Section 57.22103 Mineral Resources MINE SAFETY AND HEALTH ADMINISTRATION, DEPARTMENT OF LABOR... Open flames (I-A, II-A, III, and V-A mines). Open flames shall not be permitted underground except for...

  14. 30 CFR 57.22207 - Booster fans (I-A, II-A, III, and V-A mines).

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 30 Mineral Resources 1 2014-07-01 2014-07-01 false Booster fans (I-A, II-A, III, and V-A mines... NONMETAL MINES Safety Standards for Methane in Metal and Nonmetal Mines Ventilation § 57.22207 Booster fans (I-A, II-A, III, and V-A mines). (a) Booster fans shall be approved by MSHA under the applicable...

  15. 30 CFR 57.22207 - Booster fans (I-A, II-A, III, and V-A mines).

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 30 Mineral Resources 1 2011-07-01 2011-07-01 false Booster fans (I-A, II-A, III, and V-A mines... NONMETAL MINES Safety Standards for Methane in Metal and Nonmetal Mines Ventilation § 57.22207 Booster fans (I-A, II-A, III, and V-A mines). (a) Booster fans shall be approved by MSHA under the applicable...

  16. 30 CFR 57.22207 - Booster fans (I-A, II-A, III, and V-A mines).

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 30 Mineral Resources 1 2013-07-01 2013-07-01 false Booster fans (I-A, II-A, III, and V-A mines... NONMETAL MINES Safety Standards for Methane in Metal and Nonmetal Mines Ventilation § 57.22207 Booster fans (I-A, II-A, III, and V-A mines). (a) Booster fans shall be approved by MSHA under the applicable...

  17. 30 CFR 57.22207 - Booster fans (I-A, II-A, III, and V-A mines).

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 30 Mineral Resources 1 2012-07-01 2012-07-01 false Booster fans (I-A, II-A, III, and V-A mines... NONMETAL MINES Safety Standards for Methane in Metal and Nonmetal Mines Ventilation § 57.22207 Booster fans (I-A, II-A, III, and V-A mines). (a) Booster fans shall be approved by MSHA under the applicable...

  18. VA/DoD Joint Executive Council FY 2009: Joint Strategic Plan FY 2010-2012

    DTIC Science & Technology

    2009-01-01

    through the Military Health System (MHS) Population Health Portal . HEC Traumatic Brain Injury and Psychological Health In FY 2009, VA and DoD made...available using the Deployment Occupational and Environmental Health Surveillance Portal . TBI and MH assessment tools were evaluated and monitored through...with increased access, VA maintained the frequency of encounters for treatment of PTSD and other MH conditions in Veterans of prior eras. To forecast

  19. Metatranscriptomics and Amplicon Sequencing Reveal Mutualisms in Seagrass Microbiomes

    PubMed Central

    Crump, Byron C.; Wojahn, John M.; Tomas, Fiona; Mueller, Ryan S.

    2018-01-01

    Terrestrial plants benefit from many well-understood mutualistic relationships with root- and leaf-associated microbiomes, but relatively little is known about these relationships for seagrass and other aquatic plants. We used 16S rRNA gene amplicon sequencing and metatranscriptomics to assess potential mutualisms between microorganisms and the seagrasses Zostera marina and Zostera japonica collected from mixed beds in Netarts Bay, OR, United States. The phylogenetic composition of leaf-, root-, and water column-associated bacterial communities were strikingly different, but these communities were not significantly different between plant species. Many taxa present on leaves were related to organisms capable of consuming the common plant metabolic waste product methanol, and of producing agarases, which can limit the growth of epiphytic algae. Taxa present on roots were related to organisms capable of oxidizing toxic sulfur compounds and of fixing nitrogen. Metatranscriptomic sequencing identified expression of genes involved in all of these microbial metabolic processes at levels greater than typical water column bacterioplankton, and also identified expression of genes involved in denitrification and in bacterial synthesis of the plant growth hormone indole-3-acetate. These results provide the first evidence using metatranscriptomics that seagrass microbiomes carry out a broad range of functions that may benefit their hosts, and imply that microbe–plant mutualisms support the health and growth of aquatic plants. PMID:29599758

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

    PubMed

    Moralli, Daniela; Monaco, Zoia L

    2015-02-01

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

  1. Derivative Free Optimization of Complex Systems with the Use of Statistical Machine Learning Models

    DTIC Science & Technology

    2015-09-12

    AFRL-AFOSR-VA-TR-2015-0278 DERIVATIVE FREE OPTIMIZATION OF COMPLEX SYSTEMS WITH THE USE OF STATISTICAL MACHINE LEARNING MODELS Katya Scheinberg...COMPLEX SYSTEMS WITH THE USE OF STATISTICAL MACHINE LEARNING MODELS 5a.  CONTRACT NUMBER 5b.  GRANT NUMBER FA9550-11-1-0239 5c.  PROGRAM ELEMENT...developed, which has been the focus of our research. 15. SUBJECT TERMS optimization, Derivative-Free Optimization, Statistical Machine Learning 16. SECURITY

  2. 77 FR 27118 - Safety Zone; Rocketts Red Glare Fireworks, Ancarrows Landing Park, James River, Richmond, VA

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-05-09

    ... DEPARTMENT OF HOMELAND SECURITY Coast Guard 33 CFR Part 165 [Docket No. USCG-2012-0114] RIN 1625-AA00 Safety Zone; Rocketts Red Glare Fireworks, Ancarrows Landing Park, James River, Richmond, VA... Glare Fireworks, Ancarrows Landing Park, James River, Richmond, VA in the Federal Register (76 FR 13525...

  3. 38 CFR 21.4216 - Review of decision of Director of VA Regional Processing Office of jurisdiction.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... Director of VA Regional Processing Office of jurisdiction. 21.4216 Section 21.4216 Pensions, Bonuses, and... Administration of Educational Assistance Programs Schools § 21.4216 Review of decision of Director of VA Regional Processing Office of jurisdiction. (a) Decision is subject to review by the Director, Education Service. At...

  4. 75 FR 34934 - Safety Zone; Fireworks for the Virginia Lake Festival, Buggs Island Lake, Clarksville, VA

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-06-21

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

  5. National Dam Safety Program. Upper Apple Mountain & Lower Apple Mountain. Dam (Inventory Number VA 18711 and VA 18709), Potomac River Basin, Warren County, Virginia. Phase I Inspection Report.

    DTIC Science & Technology

    1981-03-01

    pt 3349 tIto . %. 0- Z 20a Z US It - r.422 j - oil too I - i n IN IU w-nj 1.t 1-1 1 1 Uzi bp- r* 93 I .- -CL US0 (1syOWSW!)C 91 00A o Z z 49 W, x _jW4~0...UNCLASSIFIED .’mollIIEIEEIIII l//lEEBhE/h//E IIIEEIIIlIIIII I hhhhhhhhhhhhl POTOAC RIVER BASIN Name Of Dam: UPPER APPLE MTN. 6 LOWER ALE Mt. Location...WARREN COUNTY Inventory Number: VA. 48711 S VA. 16709 PHASE I INSPECTION REPORT NATIONAL DAM SAFETY PROGRAM + I + - SEP3 tell. "=: ~~t PUMP, -We"* li

  6. VA Education Benefits: VA Should Strengthen Its Efforts to Help Veterans Make Informed Education Choices. Report to Congressional Requesters. GAO-14-324

    ERIC Educational Resources Information Center

    Emrey-Arras, Melissa

    2014-01-01

    In fiscal year 2013, VA provided over $12 billion in benefits for veterans' postsecondary education; however, questions have been raised as to whether some schools are receiving these funds as a result of inappropriate recruiting practices. GAO was asked to examine issues related to schools' recruitment of veterans. This report examines (1) how…

  7. Microbial Diversity in Commercial Bee Pollen from Europe, Chile, and Mexico, Based on 16S rRNA Gene Amplicon Metagenome Sequencing

    PubMed Central

    Moreno Andrade, Vicente D.; Saldaña Gutiérrez, Carlos; Calvillo Medina, Rosa P.; Cruz Hérnandez, Andrés; Vázquez Cruz, Moisés A.; Torres Ruíz, Alfonso; Romero Gómez, Sergio; Ramos López, Miguel A.; Álvarez-Hidalgo, Erika; López-Gaytan, Silvia B.; Ramírez, Natanahel Salvador; Jones, George H.

    2018-01-01

    ABSTRACT Bee pollen is a highly nutritive natural foodstuff. Because of its use as a comestible, the association of bacteria with bee pollen is commercially and biologically important. We report here the bacterial diversity of seven bee pollen samples (five from Europe, one from Chile, and one from Mexico) based on 16S rRNA gene amplicon metagenome sequencing. PMID:29773615

  8. VA/DoD Collaboration Guidebook for Healthcare Research

    DTIC Science & Technology

    2011-01-24

    specific time periods. The VA has academic affiliates that, in some instances, may supplement a researcher’s income and provide tenure and academic ...Clinical care dollars only Career Scientist and Research Scientist Research efforts paid by research funds Academic Researcher Research or...their graduate medical education (GME) program training director. DoD researchers may have scientific academic affiliations with the Uniformed

  9. Automated Tumor Registry for Oncology. A VA-DHCP MUMPS application.

    PubMed

    Richie, S

    1992-01-01

    The VA Automated Tumor Registry for Oncology, Version 2, is a multifaceted, completely automated user-friendly cancer database. Easy to use modules include: Automatic Casefinding; Suspense Files; Abstracting and Printing; Follow-up; Annual Reports; Statistical Reports; Utility Functions.

  10. 77 FR 12997 - Drug and Drug-Related Supply Promotion by Pharmaceutical Company Representatives at VA Facilities

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-03-05

    ... reduce or eliminate any potential for disruption in the patient care environment, manage activities and... activities that VA staff would otherwise perform during duty hours, including patient care and other... important that VA be able to limit the effects of such promotion on patient care. Again, we make no changes...

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

    PubMed

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

    2009-02-01

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

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

    PubMed

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

    2016-02-25

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

  13. The Integrated Care Team Approach of the Department of Veterans Affairs (VA): Geriatric Primary Care.

    PubMed

    Rasin-Waters, Donna; Abel, Valerie; Kearney, Lisa K; Zeiss, Antonette

    2018-05-01

    Historically, integrated mental and behavioral healthcare in the Department of Veterans Affairs (VA) commenced with initiatives in geriatrics. Innovation and system-wide expansion has occurred over decades and culminated in a unified vision for training and practice in the VA medical home model: Patient Aligned Care Team or PACT approach. In one VA hospital, the integration of neuropsychological services in geriatric primary care is pivotal and increases access for patients, as well as contributing to timely and effective care on an interprofessional team. The development and innovative use of an algorithm to identify problems with cognition, health literacy, and mental and behavioral health has been pragmatic and provides useful information for collaborative treatment planning in GeriPACT, VA geriatric primary care. Use of the algorithm also assists with decision-making regarding brief versus comprehensive neuropsychological assessment in the primary care setting. The model presented here was developed by supervising neuropsychologists as part of a postdoctoral residency program in geropsychology. However, postdoctoral residency programs in neuropsychology, as well as neuropsychological clinics, can also use this model to integrate neuropsychological assessment and interventions in geriatric primary care settings.

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

    PubMed

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

    2017-08-01

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

  15. 76 FR 59502 - Establishment of Class E Airspace; Gordonsville, VA

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-09-27

    ... at Gordonsville, VA, to accommodate the new Standard Instrument Approach Procedures serving Gordonsville Municipal Airport. This action enhances the safety and airspace management of Instrument Flight... approach procedures developed for Gordonsville Municipal Airport. This action is necessary for the safety...

  16. Automated Tumor Registry for Oncology. A VA-DHCP MUMPS application.

    PubMed Central

    Richie, S.

    1992-01-01

    The VA Automated Tumor Registry for Oncology, Version 2, is a multifaceted, completely automated user-friendly cancer database. Easy to use modules include: Automatic Casefinding; Suspense Files; Abstracting and Printing; Follow-up; Annual Reports; Statistical Reports; Utility Functions. PMID:1482866

  17. Exploring the role narrative free-text plays in discrepancies between physician coding and the InterVA regarding determination of malaria as cause of death, in a malaria holo-endemic region.

    PubMed

    Rankin, Johanna C; Lorenz, Eva; Neuhann, Florian; Yé, Maurice; Sié, Ali; Becher, Heiko; Ramroth, Heribert

    2012-02-21

    In countries where tracking mortality and clinical cause of death are not routinely undertaken, gathering verbal autopsies (VA) is the principal method of estimating cause of death. The most common method for determining probable cause of death from the VA interview is Physician-Certified Verbal Autopsy (PCVA). A recent alternative method to interpret Verbal Autopsy (InterVA) is a computer model using a Bayesian approach to derive posterior probabilities for causes of death, given an a priori distribution at population level and a set of interview-based indicators. The model uses the same input information as PCVA, with the exception of narrative text information, which physicians can consult but which were not inputted into the model. Comparing the results of physician coding with the model, large differences could be due to difficulties in diagnosing malaria, especially in holo-endemic regions. Thus, the aim of the study was to explore whether physicians' access to electronically unavailable narrative text helps to explain the large discrepancy in malaria cause-specific mortality fractions (CSMFs) in physician coding versus the model. Free-texts of electronically available records (N = 5,649) were summarised and incorporated into the InterVA version 3 (InterVA-3) for three sub-groups: (i) a 10%-representative subsample (N = 493) (ii) records diagnosed as malaria by physicians and not by the model (N = 1035), and (iii) records diagnosed by the model as malaria, but not by physicians (N = 332). CSMF results before and after free-text incorporation were compared. There were changes of between 5.5-10.2% between models before and after free-text incorporation. No impact on malaria CSMFs was seen in the representative sub-sample, but the proportion of malaria as cause of death increased in the physician sub-sample (2.7%) and saw a large decrease in the InterVA subsample (9.9%). Information on 13/106 indicators appeared at least once in the free-texts that had not been

  18. Chaplains' Engagement with Suicidality among Their Service Users: Findings from the VA/DoD Integrated Mental Health Strategy.

    PubMed

    Kopacz, Marek S; Nieuwsma, Jason A; Jackson, George L; Rhodes, Jeffrey E; Cantrell, William C; Bates, Mark J; Meador, Keith G

    2016-04-01

    Chaplains play an important role in supporting the mental health of current and former military personnel; in this study, the engagement of Department of Veterans Affairs (VA), Army, Navy, and Air Force chaplains with suicidality among their service users were examined. An online survey was used to collect data from 440 VA and 1,723 Department of Defense (DoD) chaplains as part of the VA/DoD Integrated Mental Health Strategy. Differences were noted for demographics, work setting characteristics, encountering suicidality, and self-perceived preparation for dealing with suicidality. Compared to DoD chaplains, VA chaplains encounter more at-risk service users, yet feel less prepared for dealing with suicidality. Published 2015. This article is a U.S. Government work and is in the public domain in the USA.

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

    NASA Astrophysics Data System (ADS)

    Guglielmi, Anatol; Potapov, Alexander

    2017-09-01

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

  20. Contraceptive Provision in the VA Healthcare System to Women Who Report Military Sexual Trauma

    PubMed Central

    Mattocks, Kristin; Schwarz, Eleanor Bimla; Borrero, Sonya; Skanderson, Melissa; Zephyrin, Laurie; Brandt, Cynthia; Haskell, Sally

    2014-01-01

    Abstract Background: Women Veterans who suffered military sexual trauma (MST) may be at high risk for unintended pregnancy and benefit from contraceptive services. The objective of this study is to compare documented provision of contraceptives to women Veterans using the Department of Veterans Affairs (VA) health system who report or deny MST. Methods: This retrospective cohort study included women Veterans aged 18–45 years who served in Operation Enduring or Iraqi Freedom and had at least one visit to a VA medical center between 2002 and 2010. Data were obtained from VA administrative and clinical databases. Chi-squared tests and logistic regression were conducted to evaluate the association between MST, ascertained by routine clinical screening, and first documented receipt of hormonal or long-acting contraception. Results: Of 68,466 women Veterans, 13% reported, 59% denied and 28% had missing data for the MST screen. Among the entire study cohort, 30% of women had documented receipt of a contraceptive method. Women reporting MST were significantly more likely than those denying MST to receive a method of contraception (adjusted odds ratio [aOR] 1.12, 95% confidence interval [CI] 1.07–1.18) including an intrauterine device (odds ratio [OR] 1.29, 95% CI 1.17–1.41) or contraceptive injection (OR 1.17, 95% CI 1.05–1.29). Women who were younger, unmarried, seen at a women's health clinic, or who had more than one visit were more likely to receive contraception. Conclusions: A minority of women Veterans of reproductive age receive contraceptive services from the VA. Women Veterans who report MST, and particularly those who seek care at VA women's health clinics, are more likely to receive contraception. PMID:24787680

  1. Insights into the complex association of bovine factor Va with acidic-lipid-containing synthetic membranes.

    PubMed Central

    Cutsforth, G A; Koppaka, V; Krishnaswamy, S; Wu, J R; Mann, K G; Lentz, B R

    1996-01-01

    The mechanism of binding of blood coagulation cofactor factor Va to acidic-lipid-containing membranes has been addressed. Binding isotherms were generated at room temperature using the change in fluorescence anisotropy of pyrene-labeled bovine factor Va to detect binding to sonicated membrane vesicles containing either bovine brain phosphatidylserine (PS) or 1,2-dioleoyl-3-sn-phosphatidylglycerol (DOPG) in combination with 1-palmitoyl-2-oleoyl-3-sn-phosphatidylcholine (POPC). The composition of the membranes was varied from 0 to 40 mol% for PS/POPC and from 0 to 65 mol % for DOPG/POPC membranes. Fitting the data to a classical Langmuir adsorption model yielded estimates of the dissociation constant (Kd) and the stoichiometry of binding. The values of Kd defined in this way displayed a maximum at low acidic lipid content but were nearly constant at intermediate to high fractions of acidic lipid. Fitting the binding isotherms to a two-process binding model (nonspecific adsorption in addition to binding of acidic lipids to sites on the protein) suggested a significant acidic-lipid-independent binding affinity in addition to occupancy of three protein sites that bind PS in preference to DOPG. Both analyses indicated that interaction of factor Va with an acidic-lipid-containing membrane is much more complex than those of factor Xa or prothrombin. Furthermore, a change in the conformation of bound pyrene-labeled factor Va with surface concentration of acidic lipid was implied by variation of both the saturating fluorescence anisotropy and the binding parameters with the acidic lipid content of the membrane. Finally, the results cannot support the contention that binding occurs through nonspecific adsorption to a patch or domain of acidic lipids in the membrane. Factor Va is suggested to associate with membranes by a complex process that includes both acidic-lipid-specific and acidic-lipid-independent sites and a protein structure change induced by occupancy of acidic

  2. 38 CFR 17.1000 - Payment or reimbursement for emergency services for nonservice-connected conditions in non-VA...

    Code of Federal Regulations, 2010 CFR

    2010-07-01

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

  3. 38 CFR 17.169 - VA Dental Insurance Program for veterans and survivors and dependents of veterans (VADIP).

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 38 Pensions, Bonuses, and Veterans' Relief 1 2013-07-01 2013-07-01 false VA Dental Insurance..., Bonuses, and Veterans' Relief DEPARTMENT OF VETERANS AFFAIRS MEDICAL Dental Services § 17.169 VA Dental... Dental Insurance Program (VADIP) provides premium-based dental insurance coverage through which...

  4. 38 CFR 17.169 - VA Dental Insurance Program for veterans and survivors and dependents of veterans (VADIP).

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 38 Pensions, Bonuses, and Veterans' Relief 1 2014-07-01 2014-07-01 false VA Dental Insurance..., Bonuses, and Veterans' Relief DEPARTMENT OF VETERANS AFFAIRS MEDICAL Dental Services § 17.169 VA Dental... Dental Insurance Program (VADIP) provides premium-based dental insurance coverage through which...

  5. 38 CFR 17.120 - Payment or reimbursement for emergency treatment furnished by non-VA providers to certain...

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... for emergency treatment furnished by non-VA providers to certain veterans with service-connected... Payment or reimbursement for emergency treatment furnished by non-VA providers to certain veterans with... emergency treatment, not previously authorized, in a private or public (or Federal) hospital not operated by...

  6. 38 CFR 17.120 - Payment or reimbursement for emergency treatment furnished by non-VA providers to certain...

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... for emergency treatment furnished by non-VA providers to certain veterans with service-connected... Payment or reimbursement for emergency treatment furnished by non-VA providers to certain veterans with... emergency treatment, not previously authorized, in a private or public (or Federal) hospital not operated by...

  7. 38 CFR 17.120 - Payment or reimbursement for emergency treatment furnished by non-VA providers to certain...

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... for emergency treatment furnished by non-VA providers to certain veterans with service-connected... Payment or reimbursement for emergency treatment furnished by non-VA providers to certain veterans with... emergency treatment, not previously authorized, in a private or public (or Federal) hospital not operated by...

  8. 30 CFR 57.22206 - Main ventilation failure (I-A, II-A, III, and V-A mines).

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 30 Mineral Resources 1 2011-07-01 2011-07-01 false Main ventilation failure (I-A, II-A, III, and V-A mines). 57.22206 Section 57.22206 Mineral Resources MINE SAFETY AND HEALTH ADMINISTRATION... Main ventilation failure (I-A, II-A, III, and V-A mines). (a) When there has been a main ventilation...

  9. Microbial Diversity in Commercial Bee Pollen from Europe, Chile, and Mexico, Based on 16S rRNA Gene Amplicon Metagenome Sequencing.

    PubMed

    Moreno Andrade, Vicente D; Saldaña Gutiérrez, Carlos; Calvillo Medina, Rosa P; Cruz Hérnandez, Andrés; Vázquez Cruz, Moisés A; Torres Ruíz, Alfonso; Romero Gómez, Sergio; Ramos López, Miguel A; Álvarez-Hidalgo, Erika; López-Gaytan, Silvia B; Ramírez, Natanahel Salvador; Jones, George H; Hernandez-Flores, Jose Luis; Campos-Guillén, Juan

    2018-05-17

    Bee pollen is a highly nutritive natural foodstuff. Because of its use as a comestible, the association of bacteria with bee pollen is commercially and biologically important. We report here the bacterial diversity of seven bee pollen samples (five from Europe, one from Chile, and one from Mexico) based on 16S rRNA gene amplicon metagenome sequencing. Copyright © 2018 Moreno Andrade et al.

  10. 76 FR 27379 - Proposed Information Collection (Supplement to VA Forms 21-526, 21-534, and 21-535 (For...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-05-11

    ... information technology. Title: Supplement to VA Forms 21-526, 21-534, and 21-535 (For Philippine Claims), VA... residence, proof of service, and whether the applicant was a member of pro-Japanese, pro-German, or anti...

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

    PubMed

    Menke, T J; Wray, N P

    1999-04-01

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

  12. 76 FR 34576 - Amendment of Class E Airspace; Waynesboro, VA

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-06-14

    ... Waynesboro, VA, to accommodate the additional airspace need for the Standard Instrument Approach Procedures developed for Eagle's Nest Airport. This action enhances the safety and management of Instrument Flight... upward from 700 feet above the surface to accommodate new standard instrument approach procedures...

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

    DTIC Science & Technology

    2014-11-01

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

  14. 77 FR 29929 - Safety Zone; Town of Cape Charles Fireworks, Cape Charles Harbor, Cape Charles, VA

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-05-21

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

  15. 30 CFR 57.22214 - Changes in ventilation (I-A, II-A, III, and V-A mines).

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 30 Mineral Resources 1 2011-07-01 2011-07-01 false Changes in ventilation (I-A, II-A, III, and V-A mines). 57.22214 Section 57.22214 Mineral Resources MINE SAFETY AND HEALTH ADMINISTRATION, DEPARTMENT OF... ventilation (I-A, II-A, III, and V-A mines). (a) Changes in ventilation which affect the main air current or...

  16. 30 CFR 57.22214 - Changes in ventilation (I-A, II-A, III, and V-A mines).

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 30 Mineral Resources 1 2010-07-01 2010-07-01 false Changes in ventilation (I-A, II-A, III, and V-A mines). 57.22214 Section 57.22214 Mineral Resources MINE SAFETY AND HEALTH ADMINISTRATION, DEPARTMENT OF... ventilation (I-A, II-A, III, and V-A mines). (a) Changes in ventilation which affect the main air current or...

  17. 38 CFR 17.101 - Collection or recovery by VA for medical care or services provided or furnished to a veteran for...

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... VA for medical care or services provided or furnished to a veteran for a nonservice-connected... MEDICAL Charges, Waivers, and Collections § 17.101 Collection or recovery by VA for medical care or... section covers collection or recovery by VA, under 38 U.S.C. 1729, for medical care or services provided...

  18. Astrovirus VA1/HMO-C: An Increasingly Recognized Neurotropic Pathogen in Immunocompromised Patients

    PubMed Central

    Brown, Julianne R.; Morfopoulou, Sofia; Hubb, Jonathan; Emmett, Warren A.; Ip, Winnie; Shah, Divya; Brooks, Tony; Paine, Simon M. L.; Anderson, Glenn; Virasami, Alex; Tong, C. Y. William; Clark, Duncan A.; Plagnol, Vincent; Jacques, Thomas S.; Qasim, Waseem; Hubank, Mike; Breuer, Judith

    2015-01-01

    Background. An 18-month-old boy developed encephalopathy, for which extensive investigation failed to identify an etiology, 6 weeks after stem cell transplant. To exclude a potential infectious cause, we performed high-throughput RNA sequencing on brain biopsy. Methods. RNA-Seq was performed on an Illumina Miseq, generating 20 million paired-end reads. Nonhost data were checked for similarity to known organisms using BLASTx. The full viral genome was sequenced by primer walking. Results. We identified an astrovirus, HAstV-VA1/HMO-C-UK1(a), which was highly divergent from human astrovirus (HAstV 1–8) genotypes, but closely related to VA1/HMO-C astroviruses, including one recovered from a case of fatal encephalitis in an immunosuppressed child. The virus was detected in stool and serum, with highest levels in brain and cerebrospinal fluid (CSF). Immunohistochemistry of the brain biopsy showed positive neuronal staining. A survey of 680 stool and 349 CSF samples identified a related virus in the stool of another immunosuppressed child. Conclusions. The discovery of HAstV-VA1/HMO-C-UK1(a) as the cause of encephalitis in this case provides further evidence that VA1/HMO-C viruses, unlike HAstV 1–8, are neuropathic, particularly in immunocompromised patients, and should be considered in the differential diagnosis of encephalopathy. With a turnaround from sample receipt to result of <1 week, we confirm that RNA-Seq presents a valuable diagnostic tool in unexplained encephalitis. PMID:25572899

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

    DTIC Science & Technology

    2014-11-01

    VA HEALTH CARE Improvements Needed in Monitoring Antidepressant Use for Major Depressive Disorder and in Increasing...00-2014 4. TITLE AND SUBTITLE VA Health Care: Improvements Needed in Monitoring Antidepressant Use for Major Depressive Disorder and in Increasing...Use for Major Depressive Disorder and in Increasing Accuracy of Suicide Data Why GAO Did This Study In 2013, VA estimated that about 1.5 million

  20. 78 FR 52085 - VA Veteran-Owned Small Business Verification Guidelines

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-08-22

    ... DEPARTMENT OF VETERANS AFFAIRS 38 CFR Part 74 RIN 2900-AO49 VA Veteran-Owned Small Business Verification Guidelines AGENCY: Department of Veterans Affairs. ACTION: Final rule. SUMMARY: This document... Domestic Assistance This final rule affects the verification guidelines of veteran- owned small businesses...

  1. 75 FR 54771 - Safety Zone; Thunder on the Bay, Chesapeake Bay, Buckroe Beach Park, Hampton, VA

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-09-09

    ...-AA00 Safety Zone; Thunder on the Bay, Chesapeake Bay, Buckroe Beach Park, Hampton, VA AGENCY: Coast... safety zone on the navigable waters of Chesapeake Bay in Hampton, VA in support of the Thunder on the Bay.... 0 2. Add Sec. 165.T05-0755 to read as follows: Sec. 165.T05-0755 Safety Zone; Thunder on the Bay...

  2. 33 CFR 334.293 - Elizabeth River, Craney Island Refueling Pier Restricted Area, Portsmouth VA; naval restricted area.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... Refueling Pier Restricted Area, Portsmouth VA; naval restricted area. 334.293 Section 334.293 Navigation and... RESTRICTED AREA REGULATIONS § 334.293 Elizabeth River, Craney Island Refueling Pier Restricted Area, Portsmouth VA; naval restricted area. (a) The area. (1) The waters within an area beginning at a point on the...

  3. 33 CFR 334.293 - Elizabeth River, Craney Island Refueling Pier Restricted Area, Portsmouth VA; naval restricted area.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... Refueling Pier Restricted Area, Portsmouth VA; naval restricted area. 334.293 Section 334.293 Navigation and... RESTRICTED AREA REGULATIONS § 334.293 Elizabeth River, Craney Island Refueling Pier Restricted Area, Portsmouth VA; naval restricted area. (a) The area. (1) The waters within an area beginning at a point on the...

  4. 33 CFR 334.293 - Elizabeth River, Craney Island Refueling Pier Restricted Area, Portsmouth VA; naval restricted area.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... Refueling Pier Restricted Area, Portsmouth VA; naval restricted area. 334.293 Section 334.293 Navigation and... RESTRICTED AREA REGULATIONS § 334.293 Elizabeth River, Craney Island Refueling Pier Restricted Area, Portsmouth VA; naval restricted area. (a) The area. (1) The waters within an area beginning at a point on the...

  5. 33 CFR 334.293 - Elizabeth River, Craney Island Refueling Pier Restricted Area, Portsmouth VA; naval restricted area.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... Refueling Pier Restricted Area, Portsmouth VA; naval restricted area. 334.293 Section 334.293 Navigation and... RESTRICTED AREA REGULATIONS § 334.293 Elizabeth River, Craney Island Refueling Pier Restricted Area, Portsmouth VA; naval restricted area. (a) The area. (1) The waters within an area beginning at a point on the...

  6. 33 CFR 334.293 - Elizabeth River, Craney Island Refueling Pier Restricted Area, Portsmouth VA; naval restricted area.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... Refueling Pier Restricted Area, Portsmouth VA; naval restricted area. 334.293 Section 334.293 Navigation and... RESTRICTED AREA REGULATIONS § 334.293 Elizabeth River, Craney Island Refueling Pier Restricted Area, Portsmouth VA; naval restricted area. (a) The area. (1) The waters within an area beginning at a point on the...

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

    PubMed

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

    2016-12-01

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

  8. 78 FR 20846 - Proposed Establishment of Class E Airspace; Leesburg, VA

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-04-08

    ... action proposes to establish Class E surface airspace at Leesburg, VA, to aid Potomac TRACON in the safe... airspace required to aid Potomac TRACON in the safe and orderly flow of air traffic at Leesburg Executive...

  9. 77 FR 25592 - Drawbridge Operation Regulations; James River, Hopewell, VA

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-05-01

    ..., at Hopewell, VA. This deviation is necessary to facilitate mechanical repairs to the vertical lift.... SUPPLEMENTARY INFORMATION: The Virginia Department of Transportation, who owns and operates this vertical-lift... position to facilitate repairs to the skew couplings that keep the vertical lift portion of the bridge...

  10. Synthesis and tyrosinase inhibitory properties of some novel derivatives of kojic acid.

    PubMed

    Saghaie, L; Pourfarzam, M; Fassihi, A; Sartippour, B

    2013-10-01

    Tyrosinase is a multifunctional oxidase that is widely distributed in nature. It is a key enzyme in melanin biosynthesis and is involved in determining the color of mammalian skin and hair. In addition it is responsible for the undesirable enzymatic browning that occurs in plant-derived foods, limiting the shelf-life of fresh-cut products with the resultant economic loss. In recent years there has been considerable interest to study the inhibitory activity of tyrosinase and a number of inhibitory compounds derived from natural sources or partly/fully synthetic have been described. However, the current conventional methods to control tyrosinase action are inadequate. Considering the significant industrial and economic impact of the inhibitors of tyrosinase, this study was set to seek new potent inhibitors of this enzyme. A series of 3-hydroxypyridine-4-one derivatives were prepared in high yield and evaluated for their inhibitory activity on tyrosinase enzyme using dopachrome method. Our results show that all synthesized compounds have inhibitory effect on tyrosinase activity for the oxidation of L-DOPA. Among compounds studied those containing two free hydroxyl group (ie Va and V'a) were more potent than their analogues with one hydroxyl group (ie Vb and V'b). Also substitution of a methyl group on position N(1) of the hydroxypyridinone ring seems to confer more inhibitory potency.

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

    PubMed

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

    2013-01-01

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

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

    PubMed

    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.

  13. A Prospective Study of Racial and Ethnic Variation in VA Psychotherapy Services for PTSD.

    PubMed

    Spoont, Michele R; Sayer, Nina A; Kehle-Forbes, Shannon M; Meis, Laura A; Nelson, David B

    2017-03-01

    To determine whether there are racial or ethnic disparities in receipt of U.S. Department of Veterans Affairs (VA) psychotherapy services for veterans with posttraumatic stress disorder (PTSD), the authors examined the odds of receipt of any psychotherapy and of individual psychotherapy among self-identified racial and ethnic groups for six months after individuals were diagnosed as having PTSD. Data were from a national prospective cohort study of 6,884 veterans with PTSD. Patients with no mental health care in the prior year were surveyed immediately following receipt of a PTSD diagnosis. VA databases were used to determine mental health service use. Analyses controlled for treatment need, access to services, and treatment beliefs. Among veterans with PTSD initially seen in VA mental health treatment settings, Latino veterans were less likely than white veterans to receive any psychotherapy, after the analyses controlled for treatment need, access, and beliefs. Among those initially seen in mental health settings who received some psychotherapy services, Latinos, African Americans, and Asian/Pacific Islanders were less likely than white veterans to receive any individual therapy. These racial-ethnic differences in psychotherapy receipt were due to factors occurring between VA health care networks as well as factors occurring within networks. Drivers of disparities differed across racial and ethnic groups. Inequity in psychotherapy services for some veterans from racial and ethnic minority groups with PTSD were due to factors operating both within and between health care networks.

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

    PubMed Central

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

    2014-01-01

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

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

    PubMed Central

    Houzet, Laurent; Deleage, Claire; Satie, Anne-Pascale; Merlande, Laetitia; Mahe, Dominique; Dejucq-Rainsford, Nathalie

    2015-01-01

    PCR is the most widely applied technique for large scale screening of bacterial clones, mouse genotypes, virus genomes etc. A drawback of large PCR screening is that amplicon analysis is usually performed using gel electrophoresis, a step that is very labor intensive, tedious and chemical waste generating. Single genome amplification (SGA) is used to characterize the diversity and evolutionary dynamics of virus populations within infected hosts. SGA is based on the isolation of single template molecule using limiting dilution followed by nested PCR amplification and requires the analysis of hundreds of reactions per sample, making large scale SGA studies very challenging. Here we present a novel approach entitled Long Amplicon Melt Profiling (LAMP) based on the analysis of the melting profile of the PCR reactions using SYBR Green and/or EvaGreen fluorescent dyes. The LAMP method represents an attractive alternative to gel electrophoresis and enables the quick discrimination of positive reactions. We validate LAMP for SIV and HIV env-SGA, in 96- and 384-well plate formats. Because the melt profiling allows the screening of several thousands of PCR reactions in a cost-effective, rapid and robust way, we believe it will greatly facilitate any large scale PCR screening. PMID:26053379

  16. 38 CFR 74.29 - When will VA dispose of records?

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... (CONTINUED) VETERANS SMALL BUSINESS REGULATIONS Records Management § 74.29 When will VA dispose of records? The records, including those pertaining to businesses not determined to be eligible for the program... of the last Notice of Verified Status Approval letter. Longer retention will not be required unless a...

  17. 30 CFR 57.22221 - Overcast and undercast construction (I-A, II-A, III, and V-A mines).

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 30 Mineral Resources 1 2011-07-01 2011-07-01 false Overcast and undercast construction (I-A, II-A, III, and V-A mines). 57.22221 Section 57.22221 Mineral Resources MINE SAFETY AND HEALTH ADMINISTRATION... Overcast and undercast construction (I-A, II-A, III, and V-A mines). Overcasts and undercasts shall be— (a...

  18. 30 CFR 57.22228 - Preshift examination (I-A, I-C, II-A, III, and V-A mines).

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 30 Mineral Resources 1 2010-07-01 2010-07-01 false Preshift examination (I-A, I-C, II-A, III, and V-A mines). 57.22228 Section 57.22228 Mineral Resources MINE SAFETY AND HEALTH ADMINISTRATION... Preshift examination (I-A, I-C, II-A, III, and V-A mines). (a) Preshift examinations shall be conducted...

  19. 30 CFR 57.22221 - Overcast and undercast construction (I-A, II-A, III, and V-A mines).

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 30 Mineral Resources 1 2010-07-01 2010-07-01 false Overcast and undercast construction (I-A, II-A, III, and V-A mines). 57.22221 Section 57.22221 Mineral Resources MINE SAFETY AND HEALTH ADMINISTRATION... Overcast and undercast construction (I-A, II-A, III, and V-A mines). Overcasts and undercasts shall be— (a...

  20. 30 CFR 57.22228 - Preshift examination (I-A, I-C, II-A, III, and V-A mines).

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 30 Mineral Resources 1 2011-07-01 2011-07-01 false Preshift examination (I-A, I-C, II-A, III, and V-A mines). 57.22228 Section 57.22228 Mineral Resources MINE SAFETY AND HEALTH ADMINISTRATION... Preshift examination (I-A, I-C, II-A, III, and V-A mines). (a) Preshift examinations shall be conducted...

  1. A Survey of Physicians' Attitudes toward Decision-Making Authority for Initiating and Withdrawing VA-ECMO: Results and Ethical Implications for Shared Decision Making.

    PubMed

    Meltzer, Ellen C; Ivascu, Natalia S; Stark, Meredith; Orfanos, Alexander V; Acres, Cathleen A; Christos, Paul J; Mangione, Thomas; Fins, Joseph J

    2016-01-01

    Although patients exercise greater autonomy than in the past, and shared decision making is promoted as the preferred model for doctor-patient engagement, tensions still exist in clinical practice about the primary locus of decision-making authority for complex, scarce, and resource-intensive medical therapies: patients and their surrogates, or physicians. We assessed physicians' attitudes toward decisional authority for adult venoarterial extracorporeal membrane oxygenation (VA-ECMO), hypothesizing they would favor a medical locus. A survey of resident/fellow physicians and internal medicine attendings at an academic medical center, May to August 2013. We used a 24-item, internet-based survey assessing physician-respondents' demographic characteristics, knowledge, and attitudes regarding decisional authority for adult VA-ECMO. Qualitative narratives were also collected. A total of 179 physicians completed the survey (15 percent response rate); 48 percent attendings and 52 percent residents/fellows. Only 32 percent of the respondents indicated that a surrogate's consent should be required to discontinue VA-ECMO; 56 percent felt that physicians should have the right to discontinue VA-ECMO over a surrogate's objection. Those who self-reported as "knowledgeable" about VA-ECMO, compared to those who did not, more frequently replied that there should not be presumed consent for VA-ECMO (47.6 percent versus 33.3 percent, p = 0.007), that physicians should have the right to discontinue VA-ECMO over a surrogate's objection (76.2 percent versus 50 percent, p = 0.02) and that, given its cost, the use of VA-ECMO should be restricted (81.0 percent versus 54.4 percent, p = 0.005). Surveyed physicians, especially those who self-reported as knowledgeable about VA-ECMO and/or were specialists in pulmonary/critical care, favored a medical locus of decisional authority for VA-ECMO. VA-ECMO is complex, and the data may (1) reflect physicians' hesitance to cede authority to presumably

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

    PubMed

    Tsai, Jack; Rosenheck, Robert A

    2015-06-01

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

  3. Multimethod evaluation of the VA's peer-to-peer Toolkit for patient-centered medical home implementation.

    PubMed

    Luck, Jeff; Bowman, Candice; York, Laura; Midboe, Amanda; Taylor, Thomas; Gale, Randall; Asch, Steven

    2014-07-01

    Effective implementation of the patient-centered medical home (PCMH) in primary care practices requires training and other resources, such as online toolkits, to share strategies and materials. The Veterans Health Administration (VA) developed an online Toolkit of user-sourced tools to support teams implementing its Patient Aligned Care Team (PACT) medical home model. To present findings from an evaluation of the PACT Toolkit, including use, variation across facilities, effect of social marketing, and factors influencing use. The Toolkit is an online repository of ready-to-use tools created by VA clinic staff that physicians, nurses, and other team members may share, download, and adopt in order to more effectively implement PCMH principles and improve local performance on VA metrics. Multimethod evaluation using: (1) website usage analytics, (2) an online survey of the PACT community of practice's use of the Toolkit, and (3) key informant interviews. Survey respondents were PACT team members and coaches (n = 544) at 136 VA facilities. Interview respondents were Toolkit users and non-users (n = 32). For survey data, multivariable logistic models were used to predict Toolkit awareness and use. Interviews and open-text survey comments were coded using a "common themes" framework. The Consolidated Framework for Implementation Research (CFIR) guided data collection and analyses. The Toolkit was used by 6,745 staff in the first 19 months of availability. Among members of the target audience, 80 % had heard of the Toolkit, and of those, 70 % had visited the website. Tools had been implemented at 65 % of facilities. Qualitative findings revealed a range of user perspectives from enthusiastic support to lack of sufficient time to browse the Toolkit. An online Toolkit to support PCMH implementation was used at VA facilities nationwide. Other complex health care organizations may benefit from adopting similar online peer-to-peer resource libraries.

  4. 76 FR 72046 - Enhanced-Use Lease (EUL) of Department of Veterans Affairs (VA) Real Property for the Development...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-11-21

    ... Point VA Medical Center--VA Maryland Health Care System in Perryville. As consideration for the lease... their families, and a supportive services program. FOR FURTHER INFORMATION CONTACT: Edward Bradley... consideration under such a lease for the provision of medical care and services would result in a demonstrable...

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

    PubMed

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

    2010-01-01

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

  6. 30 CFR 57.22205 - Doors on main fans (I-A, II-A, III, and V-A mines).

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 30 Mineral Resources 1 2011-07-01 2011-07-01 false Doors on main fans (I-A, II-A, III, and V-A mines). 57.22205 Section 57.22205 Mineral Resources MINE SAFETY AND HEALTH ADMINISTRATION, DEPARTMENT OF... main fans (I-A, II-A, III, and V-A mines). In mines ventilated by multiple main fans, each main fan...

  7. 30 CFR 57.22220 - Air passing unsealed areas (I-A, II-A, III, and V-A mines).

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 30 Mineral Resources 1 2011-07-01 2011-07-01 false Air passing unsealed areas (I-A, II-A, III, and V-A mines). 57.22220 Section 57.22220 Mineral Resources MINE SAFETY AND HEALTH ADMINISTRATION... passing unsealed areas (I-A, II-A, III, and V-A mines). Air that has passed by or through unsealed...

  8. 30 CFR 57.22220 - Air passing unsealed areas (I-A, II-A, III, and V-A mines).

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 30 Mineral Resources 1 2010-07-01 2010-07-01 false Air passing unsealed areas (I-A, II-A, III, and V-A mines). 57.22220 Section 57.22220 Mineral Resources MINE SAFETY AND HEALTH ADMINISTRATION... passing unsealed areas (I-A, II-A, III, and V-A mines). Air that has passed by or through unsealed...

  9. 76 FR 77270 - Board Meeting; January 9, 2012, Arlington, VA

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-12-12

    ... NUCLEAR WASTE TECHNICAL REVIEW BOARD Board Meeting; January 9, 2012, Arlington, VA The U.S. Nuclear Waste Technical Review Board will meet to discuss integration efforts undertaken by DOE-NE and DOE... Amendments Act of 1987, the U.S. Nuclear Waste Technical Review Board will hold a public meeting in Arlington...

  10. Exploring the role narrative free-text plays in discrepancies between physician coding and the InterVA regarding determination of malaria as cause of death, in a malaria holo-endemic region

    PubMed Central

    2012-01-01

    Background In countries where tracking mortality and clinical cause of death are not routinely undertaken, gathering verbal autopsies (VA) is the principal method of estimating cause of death. The most common method for determining probable cause of death from the VA interview is Physician-Certified Verbal Autopsy (PCVA). A recent alternative method to interpret Verbal Autopsy (InterVA) is a computer model using a Bayesian approach to derive posterior probabilities for causes of death, given an a priori distribution at population level and a set of interview-based indicators. The model uses the same input information as PCVA, with the exception of narrative text information, which physicians can consult but which were not inputted into the model. Comparing the results of physician coding with the model, large differences could be due to difficulties in diagnosing malaria, especially in holo-endemic regions. Thus, the aim of the study was to explore whether physicians' access to electronically unavailable narrative text helps to explain the large discrepancy in malaria cause-specific mortality fractions (CSMFs) in physician coding versus the model. Methods Free-texts of electronically available records (N = 5,649) were summarised and incorporated into the InterVA version 3 (InterVA-3) for three sub-groups: (i) a 10%-representative subsample (N = 493) (ii) records diagnosed as malaria by physicians and not by the model (N = 1035), and (iii) records diagnosed by the model as malaria, but not by physicians (N = 332). CSMF results before and after free-text incorporation were compared. Results There were changes of between 5.5-10.2% between models before and after free-text incorporation. No impact on malaria CSMFs was seen in the representative sub-sample, but the proportion of malaria as cause of death increased in the physician sub-sample (2.7%) and saw a large decrease in the InterVA subsample (9.9%). Information on 13/106 indicators appeared at least once in the

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

    PubMed

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

    2016-06-01

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

  12. Statistical Match of the VA 1979-1980 Recipient File against the 1979-1980 Basic Grant Recipient File. Revised.

    ERIC Educational Resources Information Center

    Applied Management Sciences, Inc., Silver Spring, MD.

    The amount of misreporting of Veterans Administration (VA) benefits was assessed, along with the impact of misreporting on the Basic Educational Opportunity Grant (BEOG) program. Accurate financial information is need to determine appropriate awards. The analysis revealed: over 97% of VA beneficiaries misreported benefits; the total net loss to…

  13. 33 CFR 334.330 - Atlantic Ocean and connecting waters in vicinity of Myrtle Island, Va.; Air Force practice...

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 33 Navigation and Navigable Waters 3 2014-07-01 2014-07-01 false Atlantic Ocean and connecting waters in vicinity of Myrtle Island, Va.; Air Force practice bombing, rocket firing, and gunnery range... waters in vicinity of Myrtle Island, Va.; Air Force practice bombing, rocket firing, and gunnery range...

  14. 33 CFR 334.330 - Atlantic Ocean and connecting waters in vicinity of Myrtle Island, Va.; Air Force practice...

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 33 Navigation and Navigable Waters 3 2012-07-01 2012-07-01 false Atlantic Ocean and connecting waters in vicinity of Myrtle Island, Va.; Air Force practice bombing, rocket firing, and gunnery range... waters in vicinity of Myrtle Island, Va.; Air Force practice bombing, rocket firing, and gunnery range...

  15. 33 CFR 334.330 - Atlantic Ocean and connecting waters in vicinity of Myrtle Island, Va.; Air Force practice...

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 33 Navigation and Navigable Waters 3 2013-07-01 2013-07-01 false Atlantic Ocean and connecting waters in vicinity of Myrtle Island, Va.; Air Force practice bombing, rocket firing, and gunnery range... waters in vicinity of Myrtle Island, Va.; Air Force practice bombing, rocket firing, and gunnery range...

  16. 33 CFR 334.330 - Atlantic Ocean and connecting waters in vicinity of Myrtle Island, Va.; Air Force practice...

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 33 Navigation and Navigable Waters 3 2011-07-01 2011-07-01 false Atlantic Ocean and connecting waters in vicinity of Myrtle Island, Va.; Air Force practice bombing, rocket firing, and gunnery range... waters in vicinity of Myrtle Island, Va.; Air Force practice bombing, rocket firing, and gunnery range...

  17. 33 CFR 334.330 - Atlantic Ocean and connecting waters in vicinity of Myrtle Island, Va.; Air Force practice...

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 33 Navigation and Navigable Waters 3 2010-07-01 2010-07-01 false Atlantic Ocean and connecting waters in vicinity of Myrtle Island, Va.; Air Force practice bombing, rocket firing, and gunnery range... waters in vicinity of Myrtle Island, Va.; Air Force practice bombing, rocket firing, and gunnery range...

  18. Factors Related to Attrition from VA Healthcare Use: Findings from the National Survey of Women Veterans

    DTIC Science & Technology

    2013-01-01

    present analysis we draw on aspects of the Andersen Behavioral Model,21 particularly need characteristics (e.g., mental health), as determinants of...converted to number of years ago. Number of years since last VA use was grouped into five-year increments. Statistical Analysis The analytic sample was...healthcare several decades ago. A limitation of our study is that recollections about the decision to discontinue VA care are subject to recall bias

  19. Aerosol Vacuum-Assisted Plasma Ionization (Aero-VaPI) Coupled to Ion Mobility-Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Blair, Sandra L.; Ng, Nga L.; Zambrzycki, Stephen C.; Li, Anyin; Fernández, Facundo M.

    2018-02-01

    In this communication, we report on the real-time analysis of organic aerosol particles by Vacuum-assisted Plasma Ionization-Mass Spectrometry (Aero-VaPI-MS) using a home-built VaPI ion source coupled to a Synapt G2-S HDMS ion mobility-mass spectrometry (IM-MS) system. Standards of organic molecules of interest in prebiotic chemistry were used to generate aerosols. Monocaprin and decanoic acid aerosol particles were successfully detected in both the positive and negative ion modes, respectively. A complex aerosol mixture of different sizes of polymers of L-malic acid was also examined through ion mobility (IM) separations, resulting in the detection of polymers of up to eight monomeric units. This noncommercial plasma ion source is proposed as a low cost alternative to other plasma ionization platforms used for aerosol analysis, and a higher-performance alternative to more traditional aerosol mass spectrometers. VaPI provides robust online ionization of organics in aerosols without extensive ion activation, with the coupling to IM-MS providing higher peak capacity and excellent mass accuracy. [Figure not available: see fulltext.

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

    NASA Astrophysics Data System (ADS)

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

    2017-03-01

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

  1. 30 CFR 57.22205 - Doors on main fans (I-A, II-A, III, and V-A mines).

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 30 Mineral Resources 1 2010-07-01 2010-07-01 false Doors on main fans (I-A, II-A, III, and V-A... main fans (I-A, II-A, III, and V-A mines). In mines ventilated by multiple main fans, each main fan... reversal through the fan. The doors shall be located so that they are not in direct line with explosive...

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

    PubMed

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

    2006-06-01

    Inappropriate prescribing in the elderly is common, but rates across different health care systems and the impact of formulary restrictions are not well described. To determine if rates of inappropriate medication use in the elderly differ between the Veterans Affairs (VA) health care system and the private sector Medicare health maintenance organization (HMO) patients. A cross-sectional study design compared administrative pharmacy claims from 10 distinct geographic regions in the United States in the VA health care system and 10 analogous regions for patients enrolled in Medicare HMOs. The cohorts included 123,633 VA and 157,517 Medicare HMO patients aged 65 years and older. Inappropriate medication use was identified using the Zhan modification of the Beers criteria, which categorizes 33 potentially inappropriate drugs into 3 major classifications: "always avoid," "rarely appropriate," and "some indications." Comparisons between the VA health care system and the private sector Medicare HMO were performed for overall differences and stratified by gender and age. The drug formulary status of the Zhan-criteria drugs was known for the VA health system but not for the Medicare HMO patients. Compared with private sector patients, VA patients were less likely to receive any inappropriate medication (21% vs. 29%, P <0.001), and in each classification: always avoid (2% vs. 5%, P <0.001), rarely appropriate (8% vs. 13%, P<0.001), and some indications (15% vs. 17%, P <0.001). The rate of inappropriate drug use was lower in the VA compared with the private sector for males (21% vs. 24%, P <0.001) and females (28% vs. 32%, P <0.001). Differences were consistent when stratified by age. Compared with private sector Medicare HMOs, elderly VA patients were less likely to receive medications defined by the Zhan criteria as potentially inappropriate. A restrictive formulary that excludes 12 of the 33 Zhan criteria drugs may be a factor in the reduction of undesired prescribing

  3. Amplicon-Based Sequencing of Soil Fungi from Wood Preservative Test Sites

    PubMed Central

    Kirker, Grant T.; Bishell, Amy B.; Jusino, Michelle A.; Palmer, Jonathan M.; Hickey, William J.; Lindner, Daniel L.

    2017-01-01

    Soil samples were collected from field sites in two AWPA (American Wood Protection Association) wood decay hazard zones in North America. Two field plots at each site were exposed to differing preservative chemistries via in-ground installations of treated wood stakes for approximately 50 years. The purpose of this study is to characterize soil fungal species and to determine if long term exposure to various wood preservatives impacts soil fungal community composition. Soil fungal communities were compared using amplicon-based DNA sequencing of the internal transcribed spacer 1 (ITS1) region of the rDNA array. Data show that soil fungal community composition differs significantly between the two sites and that long-term exposure to different preservative chemistries is correlated with different species composition of soil fungi. However, chemical analyses using ICP-OES found levels of select residual preservative actives (copper, chromium and arsenic) to be similar to naturally occurring levels in unexposed areas. A list of indicator species was compiled for each treatment-site combination; functional guild analyses indicate that long-term exposure to wood preservatives may have both detrimental and stimulatory effects on soil fungal species composition. Fungi with demonstrated capacity to degrade industrial pollutants were found to be highly correlated with areas that experienced long-term exposure to preservative testing. PMID:29093702

  4. Racial Differences in Satisfaction with VA Health Care: A Mixed Methods Pilot Study.

    PubMed

    Zickmund, Susan L; Burkitt, Kelly H; Gao, Shasha; Stone, Roslyn A; Rodriguez, Keri L; Switzer, Galen E; Shea, Judy A; Bayliss, Nichole K; Meiksin, Rebecca; Walsh, Mary B; Fine, Michael J

    2015-09-01

    As satisfied patients are more adherent and play a more active role in their own care, a better understanding of factors associated with patient satisfaction is important. In response to a United States Veterans Administration (VA) Hospital Report Card that revealed lower levels of satisfaction with health care for African Americans compared to Whites, we conducted a mixed methods pilot study to obtain preliminary qualitative and quantitative information about possible underlying reasons for these racial differences. We conducted telephone interviews with 30 African American and 31 White veterans with recent inpatient and/or outpatient health care visits at three urban VA Medical Centers. We coded the qualitative interviews in terms of identified themes within defined domains. We summarized racial differences using ordinal logistic regression for Likert scale outcomes and used random effects logistic regression to assess racial differences at the domain level. Compared to Whites, African Americans were younger (p < 0.001) and better educated (p = 0.04). Qualitatively, African Americans reported less satisfaction with trust/confidence in their VA providers and healthcare system and less satisfaction with patient-provider communication. Quantitatively, African Americans reported less satisfaction with outpatient care (odds ratio = 0.28; 95 % confidence interval (CI) 0.10-0.82), but not inpatient care. At the domain level, African Americans were significantly less likely than Whites to express satisfaction themes in the domain of trust/confidence (odds ratio = 0.36; 95 % CI 0.18-0.73). The current pilot study demonstrates racial differences in satisfaction with outpatient care and identifies some specific sources of dissatisfaction. Future research will include a large national cohort, including Hispanic veterans, in order to gain further insight into the sources of racial and ethnic differences in satisfaction with VA care and inform future

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

    NASA Astrophysics Data System (ADS)

    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.

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

    PubMed Central

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

    2016-01-01

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

  7. 33 CFR 334.260 - York River, Va.; naval restricted areas.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ....; naval restricted areas. (a) The areas—(1) Naval mine service-testing area (prohibited). A rectangular... 76°31′50″ W.; and thence along the shore line to the point of beginning. (2) Naval mine service... 33 Navigation and Navigable Waters 3 2012-07-01 2012-07-01 false York River, Va.; naval restricted...

  8. 33 CFR 334.260 - York River, Va.; naval restricted areas.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ....; naval restricted areas. (a) The areas—(1) Naval mine service-testing area (prohibited). A rectangular... 76°31′50″ W.; and thence along the shore line to the point of beginning. (2) Naval mine service... 33 Navigation and Navigable Waters 3 2011-07-01 2011-07-01 false York River, Va.; naval restricted...

  9. 33 CFR 334.260 - York River, Va.; naval restricted areas.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ....; naval restricted areas. (a) The areas—(1) Naval mine service-testing area (prohibited). A rectangular... 76°31′50″ W.; and thence along the shore line to the point of beginning. (2) Naval mine service... 33 Navigation and Navigable Waters 3 2010-07-01 2010-07-01 false York River, Va.; naval restricted...

  10. 38 CFR 17.106 - VA collection rules; third-party payers.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... a veteran who is also a beneficiary under the third-party payer's plan. VA's right to recover or... prosecute legal proceedings against a third-party payer to enforce a right of the United States under 38 U.S... the terms and conditions of the third-party payer's plan. Patient care records will not be made...

  11. 38 CFR 17.106 - VA collection rules; third-party payers.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... a veteran who is also a beneficiary under the third-party payer's plan. VA's right to recover or... prosecute legal proceedings against a third-party payer to enforce a right of the United States under 38 U.S... the terms and conditions of the third-party payer's plan. Patient care records will not be made...

  12. A simple method for semi-random DNA amplicon fragmentation using the methylation-dependent restriction enzyme MspJI.

    PubMed

    Shinozuka, Hiroshi; Cogan, Noel O I; Shinozuka, Maiko; Marshall, Alexis; Kay, Pippa; Lin, Yi-Han; Spangenberg, German C; Forster, John W

    2015-04-11

    Fragmentation at random nucleotide locations is an essential process for preparation of DNA libraries to be used on massively parallel short-read DNA sequencing platforms. Although instruments for physical shearing, such as the Covaris S2 focused-ultrasonicator system, and products for enzymatic shearing, such as the Nextera technology and NEBNext dsDNA Fragmentase kit, are commercially available, a simple and inexpensive method is desirable for high-throughput sequencing library preparation. MspJI is a recently characterised restriction enzyme which recognises the sequence motif CNNR (where R = G or A) when the first base is modified to 5-methylcytosine or 5-hydroxymethylcytosine. A semi-random enzymatic DNA amplicon fragmentation method was developed based on the unique cleavage properties of MspJI. In this method, random incorporation of 5-methyl-2'-deoxycytidine-5'-triphosphate is achieved through DNA amplification with DNA polymerase, followed by DNA digestion with MspJI. Due to the recognition sequence of the enzyme, DNA amplicons are fragmented in a relatively sequence-independent manner. The size range of the resulting fragments was capable of control through optimisation of 5-methyl-2'-deoxycytidine-5'-triphosphate concentration in the reaction mixture. A library suitable for sequencing using the Illumina MiSeq platform was prepared and processed using the proposed method. Alignment of generated short reads to a reference sequence demonstrated a relatively high level of random fragmentation. The proposed method may be performed with standard laboratory equipment. Although the uniformity of coverage was slightly inferior to the Covaris physical shearing procedure, due to efficiencies of cost and labour, the method may be more suitable than existing approaches for implementation in large-scale sequencing activities, such as bacterial artificial chromosome (BAC)-based genome sequence assembly, pan-genomic studies and locus-targeted genotyping-by-sequencing.

  13. 75 FR 57215 - Proposed Establishment of Class E Airspace; Crewe, VA

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-09-20

    ... submitted in triplicate to the Docket Management System (see ADDRESSES section for address and phone number... action proposes to establish Class E Airspace at Crewe, VA, to accommodate the additional airspace needed for the Standard Instrument Approach Procedures (SIAPs) developed for Crewe Municipal Airport. This...

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

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-05-13

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

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

    NASA Technical Reports Server (NTRS)

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

    2010-01-01

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

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

    PubMed

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

    2017-09-18

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

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

    ERIC Educational Resources Information Center

    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…

  18. 38 CFR 17.107 - VA response to disruptive behavior of patients.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 38 Pensions, Bonuses, and Veterans' Relief 1 2014-07-01 2014-07-01 false VA response to disruptive behavior of patients. 17.107 Section 17.107 Pensions, Bonuses, and Veterans' Relief DEPARTMENT OF VETERANS AFFAIRS MEDICAL Disciplinary Control of Beneficiaries Receiving Hospital, Domiciliary Or Nursing Home Care...

  19. 38 CFR 17.107 - VA response to disruptive behavior of patients.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 38 Pensions, Bonuses, and Veterans' Relief 1 2013-07-01 2013-07-01 false VA response to disruptive behavior of patients. 17.107 Section 17.107 Pensions, Bonuses, and Veterans' Relief DEPARTMENT OF VETERANS AFFAIRS MEDICAL Disciplinary Control of Beneficiaries Receiving Hospital, Domiciliary Or Nursing Home Care...

  20. 38 CFR 17.107 - VA response to disruptive behavior of patients.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 38 Pensions, Bonuses, and Veterans' Relief 1 2012-07-01 2012-07-01 false VA response to disruptive behavior of patients. 17.107 Section 17.107 Pensions, Bonuses, and Veterans' Relief DEPARTMENT OF VETERANS AFFAIRS MEDICAL Disciplinary Control of Beneficiaries Receiving Hospital, Domiciliary Or Nursing Home Care...

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

    PubMed

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

    2017-10-10

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

  2. 38 CFR 58.17 - VA Form 10-0144A-Statement of Assurance of Compliance with Equal Opportunity Laws.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 38 Pensions, Bonuses, and Veterans' Relief 2 2010-07-01 2010-07-01 false VA Form 10-0144A-Statement of Assurance of Compliance with Equal Opportunity Laws. 58.17 Section 58.17 Pensions, Bonuses, and Veterans' Relief DEPARTMENT OF VETERANS AFFAIRS (CONTINUED) FORMS § 58.17 VA Form 10-0144A—Statement of Assurance of Compliance with Equal...

  3. 30 CFR 57.22204 - Main fan operation and inspection (I-A, II-A, III, and V-A mines).

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 30 Mineral Resources 1 2011-07-01 2011-07-01 false Main fan operation and inspection (I-A, II-A, III, and V-A mines). 57.22204 Section 57.22204 Mineral Resources MINE SAFETY AND HEALTH ADMINISTRATION... Main fan operation and inspection (I-A, II-A, III, and V-A mines). Main fans shall be— (a) Provided...

  4. Computer-Based Patient Records: Better Planning and Oversight by VA, DOD, and IHS Would Enhance Health Data Sharing

    DTIC Science & Technology

    2001-04-01

    IHS), could share information technology (IT) and patient medical information to provide greater continuity of care, accelerate VA eligibility... patient medical information to provide greater continuity of care, accelerate VA eligibility determinations, and save software development costs.1 In...system, which primarily includes information on patient hospital admission and discharge, patient medications , laboratory results, and radiology

  5. 30 CFR 57.22204 - Main fan operation and inspection (I-A, II-A, III, and V-A mines).

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 30 Mineral Resources 1 2010-07-01 2010-07-01 false Main fan operation and inspection (I-A, II-A, III, and V-A mines). 57.22204 Section 57.22204 Mineral Resources MINE SAFETY AND HEALTH ADMINISTRATION... Main fan operation and inspection (I-A, II-A, III, and V-A mines). Main fans shall be— (a) Provided...

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

    PubMed

    Walker, F J

    1992-10-05

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

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

    PubMed

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

    2004-01-01

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

  8. Evaluating and improving pressure ulcer care: the VA experience with administrative data.

    PubMed

    Berlowitz, D R; Halpern, J

    1997-08-01

    A number of state initiatives are using databases originally developed for nursing home reimbursements to assess the quality of care. Since 1991 the Department of Veterans Affairs (VA; Washington, DC) has been using a long term care administrative database to calculate facility-specific rates of pressure ulcer development. This information is disseminated to all 140 long term care facilities as part of a quality assessment and improvement program. Assessments are performed on all long term care residents on April 1 and October 1, as well as at the time of admission or transfer to a long term care unit. Approximately 18,000 long term care residents are evaluated in each six-month period; the VA rate of pressure ulcer development is approximately 3.5%. Reports of the rates of pressure ulcer development are then disseminated to all facilities, generally within two months of the assessment date. The VA's more than five years' experience in using administrative data to assess outcomes for long term care highlights several important issues that should be considered when using outcome measures based on administrative data. These include the importance of carefully selecting the outcome measure, the need to consider the structure of the database, the role of case-mix adjustment, strategies for reporting rates to small facilities, and methods for information dissemination. Attention to these issues will help ensure that results from administrative databases lead to improvements in the quality of care.

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

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Il`inskaya, G.V.; Kopnin, B.P.; Demidova, N.S.

    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.

  10. 77 FR 24268 - Agency Information Collection (Dependents' Application for VA Educational Benefits) Activity...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-04-23

    .../11 GI Bill Marine Gunnery Sergeant John David Fry Scholarship (Fry Scholarship) benefits. VA will use the information collected to determine whether a claimant qualifies for DEA or Fry Scholarship...

  11. [Amplicon density-weighted algorithms for analyzing dissimilarity and dynamic alterations of RAPD polymorphisms of Cordyceps sinensis].

    PubMed

    Yao, Yi-sang; Gao, Ling; Li, Yu-ling; Ma, Shao-li; Wu, Zi-mei; Tan, Ning-zhi; Wu, Jian-yong; Ni, Lu-qun; Zhu, Jia-shi

    2014-08-18

    To examine the dynamic maturational alterations of random amplified polymorphic DNA (RAPD) molecular marker polymorphism resulted from differential expressions of multiple fungi in the caterpillar body, stroma and ascocarp portion of Cordyceps sinensis (Cs). Used the fuzzy, integral RAPD molecular marker polymorphism method with 20 random primers; used density-weighted cluster algorithms and ZUNIX similarity equations; compared RAPD polymorphisms of the caterpillar body, stroma and ascocarp of Cs during maturation; and compared RAPD polymorphisms of Cs and Hirsutella sinensis (Hs). Density-unweighted algorithms neglected the differences in density of the DNA amplicons. Use of the density-weighted ZUNIX similarity equations and the clustering method integrated components of the amplicon density differences in similarity computations and clustering construction and prevented from the loss of the information of fungal genomes. An overall similarity 0.42 (< the overall dissimilarity 0.58) was observed for all compartments of Cs at different maturation stages. The similarities for the stromata or caterpillar bodies of Cs at 3 maturational stages were 0.57 or 0.50, respectively. During Cs maturation, there were dynamic Low→High→Low alterations of the RAPD polymorphisms between stromata and caterpillar bodies dissected from the same pieces of Cs. The polymorphic similarity was the highest (0.87) between the ascocarp and mature stroma, forming a clustering clade, while the premature stroma and caterpillar body formed another clade. These 2 clades merged into one cluster. Another clade containing the maturing stroma and caterpillar body merged with mature caterpillar body, forming another cluster. The RAPD polymorphic similarities between Hs and Cs samples were 0.55-0.69. Hs were separated from Cs clusters by the out-group control Paecilomyces militaris. The wealthy RAPD polymorphisms change dynamically in the Cs compartments with maturation. The different RAPD

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

    ERIC Educational Resources Information Center

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

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

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

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 33 Navigation and Navigable Waters 1 2011-07-01 2011-07-01 false Cape Henlopen, DE to Cape Charles, VA. 80.505 Section 80.505 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Fifth District § 80.505 Cape Henlopen, DE...

  14. 33 CFR 334.280 - James River between the entrance to Skiffes Creek and Mulberry Point, Va.; army training and...

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... to Skiffes Creek and Mulberry Point, Va.; army training and small craft testing area. 334.280 Section... DEFENSE DANGER ZONE AND RESTRICTED AREA REGULATIONS § 334.280 James River between the entrance to Skiffes Creek and Mulberry Point, Va.; army training and small craft testing area. (a) The restricted area...

  15. NPDES Permit for Eastern Colorado Health Care System (VA Hospital) in Colorado

    EPA Pesticide Factsheets

    Under NPDES permit CO-0034991, the U.S. Department of Veterans Affairs (VA) is authorized to discharge from its wastewater treatment facility in Adams County, Colorado, to a storm sewer to Toll Gate Creek, a tributary of Sand Creek.

  16. ST09, a Novel Thioester Derivative of Tacrine, Alleviates Cognitive Deficits and Enhances Glucose Metabolism in Vascular Dementia Rats.

    PubMed

    Liu, Jian-Min; Wu, Peng-Fei; Rao, Jing; Zhou, Jun; Shen, Zu-Cheng; Luo, Han; Huang, Jian-Geng; Liang, Xiao; Long, Li-Hong; Xie, Qing-Guo; Jiang, Feng-Chao; Wang, Fang; Chen, Jian-Guo

    2016-03-01

    Chemical entities containing mercapto group have been increasingly attractive in the therapy of central nerve system (CNS) diseases. In the recent study, we screened a series of mercapto-tacrine derivatives with synergistic neuropharmacological profiles in vitro. We investigated the effect and mechanism of ST09, a thioester derivative of tacrine containing a potential mercapto group, on the vascular dementia (VaD) model of rat induced by bilateral common carotid arteries occlusion (2-VO). ST09 and its active metabolite ST10 retained excellent inhibition on acetylcholinesterase (AChE) activity. ST09 significantly attenuated the 2-VO-induced impairment in spatial acquisition performance and inhibited the 2-VO-induced rise of AChE activity. In the VaD model, ST09 attenuated the oxidative stress and decreased the apoptosis in the cortex and hippocampus. Compared with donepezil, ST09 exhibited a better effect on the regeneration of free thiols in 2-VO rats. Interestingly, ST09, not donepezil, greatly improved glucose metabolism in various brain regions of 2-VO rats using functional imaging of (18) F-labeled fluoro-deoxyglucose (FDG) positron emission tomography (PET). ST09 may serve as a more promising agent for the therapy of VaD than tacrine owing to the introduction of a potential mercapto group into the parent skeleton. © 2016 John Wiley & Sons Ltd.

  17. Making the connection: the VA-Regenstrief project.

    PubMed

    Martin, D K

    1992-01-01

    The Regenstrief Automated Medical Record System is a well-established clinical information system with powerful facilities for querying and decision support. My colleagues and I introduced this system into the Indianapolis Veterans Affairs (VA) Medical Center by interfacing it to the institution's automated data-processing system, the Decentralized Hospital Computer Program (DHCP), using a recently standardized method for clinical data interchange. This article discusses some of the challenges encountered in that process, including the translation of vocabulary terms and maintenance of the software interface. Efforts such as these demonstrate the importance of standardization in medical informatics and the need for data standards at all levels of information exchange.

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

    PubMed

    Ravet, S; Munaut, C; Blacher, S; Brichant, G; Labied, S; Beliard, A; Chabbert-Buffet, N; Bouchard, P; Foidart, J-M; Pintiaux, A

    2008-11-01

    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. Our objective was to quantify the effects of VA-2914 on endometrial vascularization, fibrillar matrix, and vascular endothelial growth factor (VEGF)-A expression in endometrial biopsies from 41 women before and after 12 wk daily treatment with a placebo, or 2.5, 5, or 10 mg VA-2914. Collagen fibrillar network was stained by silver impregnation. Vessel area, density, and structure were quantified with a computer-assisted image analysis system after double immunostaining using an anti-von Willebrand factor (endothelial cells) and an anti-alpha smooth muscle actin (vascular smooth muscle cells) marker antibody. VEGF-A mRNAs were quantified by RT-PCR and localized by immunohistochemistry. The endometrial vessels, collagen network, and mRNA levels of VEGF-A were identical during the luteal phase at baseline and in VA-2914 treated women. VEGF-A distribution was unchanged. VA-2914 does not alter the endometrial matrix and cells, and does not modify the endometrial vessel morphology as compared with baseline biopsies.

  19. Canary: an atomic pipeline for clinical amplicon assays.

    PubMed

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

    2017-12-15

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

  20. Predicting glycerophosphoinositol identities in lipidomic datasets using VaLID (Visualization and Phospholipid Identification)--an online bioinformatic search engine.

    PubMed

    McDowell, Graeme S V; Blanchard, Alexandre P; Taylor, Graeme P; Figeys, Daniel; Fai, Stephen; 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 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.

  1. Amplicon-based next-generation sequencing of plasma cell-free DNA for detection of driver and resistance mutations in advanced non-small cell lung cancer.

    PubMed

    Guibert, N; Hu, Y; Feeney, N; Kuang, Y; Plagnol, V; Jones, G; Howarth, K; Beeler, J F; Paweletz, C P; Oxnard, G R

    2018-04-01

    Genomic analysis of plasma cell-free DNA is transforming lung cancer care; however, available assays are limited by cost, turnaround time, and imperfect accuracy. Here, we study amplicon-based plasma next-generation sequencing (NGS), rather than hybrid-capture-based plasma NGS, hypothesizing this would allow sensitive detection and monitoring of driver and resistance mutations in advanced non-small cell lung cancer (NSCLC). Plasma samples from patients with NSCLC and a known targetable genotype (EGFR, ALK/ROS1, and other rare genotypes) were collected while on therapy and analyzed blinded to tumor genotype. Plasma NGS was carried out using enhanced tagged amplicon sequencing of hotspots and coding regions from 36 genes, as well as intronic coverage for detection of ALK/ROS1 fusions. Diagnostic accuracy was compared with plasma droplet digital PCR (ddPCR) and tumor genotype. A total of 168 specimens from 46 patients were studied. Matched plasma NGS and ddPCR across 120 variants from 80 samples revealed high concordance of allelic fraction (R2 = 0.95). Pretreatment, sensitivity of plasma NGS for the detection of EGFR driver mutations was 100% (30/30), compared with 87% for ddPCR (26/30). A full spectrum of rare driver oncogenic mutations could be detected including sensitive detection of ALK/ROS1 fusions (8/9 detected, 89%). Studying 25 patients positive for EGFR T790M that developed resistance to osimertinib, 15 resistance mechanisms could be detected including tertiary EGFR mutations (C797S, Q791P) and mutations or amplifications of non-EGFR genes, some of which could be detected pretreatment or months before progression. This blinded analysis demonstrates the ability of amplicon-based plasma NGS to detect a full range of targetable genotypes in NSCLC, including fusion genes, with high accuracy. The ability of plasma NGS to detect a range of preexisting and acquired resistance mechanisms highlights its potential value as an alternative to single mutation

  2. 78 FR 76412 - Agency Information Collection (VA National Rehabilitation Special Events, Event Registration...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-12-17

    ... Festival Event Application, VA0929a, b, c, d, e, f, g, h. Type of Review: Revision of an already approved... Age Games, National Veterans Creative Arts Festival, National Veterans TEE Tournament, National...

  3. Two Major Bile Acids in the Hornbills, (24R,25S)-3α,7α,24-Trihydroxy-5β-cholestan-27-oyl Taurine and Its 12α-Hydroxy Derivative.

    PubMed

    Satoh, Rika; Ogata, Hiroaki; Saito, Tetsuya; Zhou, Biao; Omura, Kaoru; Kurabuchi, Satoshi; Mitamura, Kuniko; Ikegawa, Shigeo; Hagey, Lee R; Hofmann, Alan F; Iida, Takashi

    2016-06-01

    Two major bile acids were isolated from the gallbladder bile of two hornbill species from the Bucerotidae family of the avian order Bucerotiformes Buceros bicornis (great hornbill) and Penelopides panini (Visayan tarictic hornbill). Their structures were determined to be 3α,7α,24-dihydroxy-5β-cholestan-27-oic acid and its 12α-hydroxy derivative, 3α,7α,12α,24-tetrahydroxy-5β-cholestan-27-oic acid (varanic acid, VA), both present in bile as their corresponding taurine amidates. The four diastereomers of varanic acid were synthesized and their assigned structures were confirmed by X-ray crystallographic analysis. VA and its 12-deoxy derivative were found to have a (24R,25S)-configuration. 13 additional hornbill species were also analyzed by HPLC and showed similar bile acid patterns to B. bicornis and P. panini. The previous stereochemical assignment for (24R,25S)-VA isolated from the bile of varanid lizards and the Gila monster should now be revised to the (24S,25S)-configuration.

  4. Inter-rater reliability and review of the VA unresolved narratives.

    PubMed Central

    Eagon, J. C.; Hurdle, J. F.; Lincoln, M. J.

    1996-01-01

    To better understand how VA clinicians use medical vocabulary in every day practice, we set out to characterize terms generated in the Problem List module of the VA's DHCP system that were not mapped to terms in the controlled-vocabulary lexicon of DHCP. When entered terms fail to match those in the lexicon, a note is sent to a central repository. When our study started, the volume in that repository had reached 16,783 terms. We wished to characterize the potential reasons why these terms failed to match terms in the lexicon. After examining two small samples of randomly selected terms, we used group consensus to develop a set of rating criteria and a rating form. To be sure that the results of multiple reviewers could be confidently compared, we analyzed the inter-rater agreement of our rating process. Two rates used this form to rate the same 400 terms. We found that modifiers and numeric data were common and consistent reasons for failure to match, while others such as use of synonyms and absence of the concept from the lexicon were common but less consistently selected. PMID:8947642

  5. Inter-rater reliability and review of the VA unresolved narratives.

    PubMed

    Eagon, J C; Hurdle, J F; Lincoln, M J

    1996-01-01

    To better understand how VA clinicians use medical vocabulary in every day practice, we set out to characterize terms generated in the Problem List module of the VA's DHCP system that were not mapped to terms in the controlled-vocabulary lexicon of DHCP. When entered terms fail to match those in the lexicon, a note is sent to a central repository. When our study started, the volume in that repository had reached 16,783 terms. We wished to characterize the potential reasons why these terms failed to match terms in the lexicon. After examining two small samples of randomly selected terms, we used group consensus to develop a set of rating criteria and a rating form. To be sure that the results of multiple reviewers could be confidently compared, we analyzed the inter-rater agreement of our rating process. Two rates used this form to rate the same 400 terms. We found that modifiers and numeric data were common and consistent reasons for failure to match, while others such as use of synonyms and absence of the concept from the lexicon were common but less consistently selected.

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

    PubMed

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

    2011-01-01

    This study demonstrates the effectiveness of the KiVa antibullying program using a large sample of 8,237 youth from Grades 4-6 (10-12 years). Altogether, 78 schools were randomly assigned to intervention (39 schools, 4,207 students) and control conditions (39 schools, 4,030 students). Multilevel regression analyses revealed that after 9 months of implementation, the intervention had consistent beneficial effects on 7 of the 11 dependent variables, including self- and peer-reported victimization and self-reported bullying. The results indicate that the KiVa program is effective in reducing school bullying and victimization in Grades 4-6. Despite some evidence against school-based interventions, the results suggest that well-conceived school-based programs can reduce victimization. © 2011 The Authors. Child Development © 2011 Society for Research in Child Development, Inc.

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

    PubMed

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

    2018-03-01

    Ethylene response factor (ERF) transcription factors play important roles in regulating immune responses in plants. In our study, we characterized a member of the ERF transcription factor family, VaERF20 , from the Chinese wild Vitis genotype, V. amurensis Rupr "Shuangyou". Phylogenetic analysis indicated that VaERF20 belongs to group IXc of the ERF family, in which many members are known to contribute to fighting pathogen infection. Consistent with this, expression of VaERF20 was induced by treatment with the necrotrophic fungal pathogen Botrytis cinerea (B. cinerea ) in "Shuangyou" and V. vinifera "Red Globe". Arabidopsis thaliana plants over-expressing VaERF20 displayed enhanced resistance to B. cinerea and the bacterium Pseudomonas syringae pv. tomato ( Pst ) DC3000. Patterns of pathogen-induced reactive oxygen species (ROS) accumulation were entirely distinct in B. cinerea and Pst DC3000 inoculated plants. Examples of both salicylic acid (SA) and jasmonic acid/ethylene (JA/ET) responsive defense genes were up-regulated after B. cinerea and Pst DC3000 inoculation of the VaERF20 -overexpressing transgenic A. thaliana plants. Evidence of pattern-triggered immunity (PTI), callose accumulation and stomatal defense, together with increased expression of PTI genes, was also greater in the transgenic lines. These data indicate that VaERF20 participates in various signal transduction pathways and acts as an inducer of immune responses.

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

    PubMed Central

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

    2018-01-01

    Ethylene response factor (ERF) transcription factors play important roles in regulating immune responses in plants. In our study, we characterized a member of the ERF transcription factor family, VaERF20, from the Chinese wild Vitis genotype, V. amurensis Rupr “Shuangyou”. Phylogenetic analysis indicated that VaERF20 belongs to group IXc of the ERF family, in which many members are known to contribute to fighting pathogen infection. Consistent with this, expression of VaERF20 was induced by treatment with the necrotrophic fungal pathogen Botrytis cinerea (B. cinerea) in “Shuangyou” and V. vinifera “Red Globe”. Arabidopsis thaliana plants over-expressing VaERF20 displayed enhanced resistance to B. cinerea and the bacterium Pseudomonas syringae pv. tomato (Pst) DC3000. Patterns of pathogen-induced reactive oxygen species (ROS) accumulation were entirely distinct in B. cinerea and PstDC3000 inoculated plants. Examples of both salicylic acid (SA) and jasmonic acid/ethylene (JA/ET) responsive defense genes were up-regulated after B. cinerea and PstDC3000 inoculation of the VaERF20-overexpressing transgenic A. thaliana plants. Evidence of pattern-triggered immunity (PTI), callose accumulation and stomatal defense, together with increased expression of PTI genes, was also greater in the transgenic lines. These data indicate that VaERF20 participates in various signal transduction pathways and acts as an inducer of immune responses. PMID:29494485

  9. The business case for the reduction of surgical complications in VA hospitals.

    PubMed

    Vaughan-Sarrazin, Mary; Bayman, Levent; Rosenthal, Gary; Henderson, William; Hendricks, Ann; Cullen, Joseph J

    2011-04-01

    Surgical complications contribute substantially to costs. Most important, surgical complications contribute to morbidity and mortality, and some may be preventable. This study estimates costs of specific surgical complications for patients undergoing general surgery in VA hospitals using merged data from the VA Surgical Quality Improvement Program and VA Decision Support System. Costs associated with 19 potentially preventable complications within 6 broader categories were estimated using generalized, linear mixed regression models to control for patient-level determinants of costs (eg, type of operation, demographics, comorbidity, severity) and hospital-level variation in costs. Costs included costs of the index hospitalization and subsequent 30-day readmissions. In 14,639 patients undergoing general surgical procedures from 10/2005 through 9/2006, 20% of patients developed postoperative surgical complications. The presence of any complication significantly increased unadjusted costs nearly 3-fold ($61,083 vs $22,000), with the largest cost differential attributed to respiratory complications. Patients who developed complications had several markers for greater preoperative severity, including increased age and a lesser presurgery functional health status. After controlling for differences in patient severity, costs for patients with any complication were 1.89 times greater compared to costs for patients with no complications (P < .0001). Within major complication categories, adjusted costs were significantly greater for patients with respiratory, cardiac, central nervous system, urinary, wound, or other complications. Surgical complications contribute markedly to costs of inpatient operations. Investment in quality improvement that decreases the incidence of surgical complications could decrease costs. Copyright © 2011 Mosby, Inc. All rights reserved.

  10. Addressing the Health Concerns of VA Women with Sexual Trauma

    DTIC Science & Technology

    2017-10-01

    AWARD NUMBER: W81XWH-14-1-0368 TITLE: Addressing the Health Concerns of VA Women with Sexual Trauma PRINCIPAL INVESTIGATOR: Caron Zlotnick, PhD...develop and assess a computer-delivered intervention (Safety and Health Experiences Program; SHE) that will provide a screening and brief behavior...intervention for women veterans with any lifetime ST. More specifically, the intervention, SHE, will address interrelated health concerns for women

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

    PubMed Central

    Azevedo, Elisama; Oliveira, Leandro Teixeira; Castro Lima, Ana Karina; Terra, Rodrigo; Dutra, Patrícia Maria Lourenço; Salerno, Verônica P.

    2012-01-01

    Leishmaniasis is a neglected tropical disease with no effective vaccines. Actin, microtubules and the actin-based molecular motor myosin Va were investigated for their involvement in Leishmania braziliensis macrophage interactions. Results showed a decrease in the association index when macrophages were without F-actin or microtubules regardless of the activation state of the macrophage. In the absence of F-actin, the production of NO in non-activated cells increased, while in activated cells, the production of NO was reduced independent of parasites. The opposite effect of an increased NO production was observed in the absence of microtubules. In activated cells, the loss of cytoskeletal components inhibited the release of IL-10 during parasite interactions. The production of IL-10 also decreased in the absence of actin or microtubules in non-activated macrophages. Only the disruption of actin altered the production of TNF-α in activated macrophages. The expression of myosin Va tail resulted in an acute decrease in the association index between transfected macrophages and L. braziliensis promastigotes. These data reveal the importance of F-actin, microtubules, and myosin-Va suggesting that modulation of the cytoskeleton may be a mechanism used by L. braziliensis to overcome the natural responses of macrophages to establish infections. PMID:22792440

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

    PubMed

    Azevedo, Elisama; Oliveira, Leandro Teixeira; Castro Lima, Ana Karina; Terra, Rodrigo; Dutra, Patrícia Maria Lourenço; Salerno, Verônica P

    2012-01-01

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

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

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Begoli, Edmon; Bates, Jack; Kistler, Derek E

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

  14. The KiVa antibullying program in primary schools in Chile, with and without the digital game component: study protocol for a randomized controlled trial.

    PubMed

    Gaete, Jorge; Valenzuela, Daniela; Rojas-Barahona, Cristian; Valenzuela, Eduardo; Araya, Ricardo; Salmivalli, Christina

    2017-02-20

    Bullying is a major problem worldwide and Chile is no exception. Bullying is defined as a systematic aggressive behavior against a victim who cannot defend him or herself. Victims suffer social isolation and psychological maladjustment, while bullies have a higher risk for conduct problems and substance use disorders. These problems appear to last over time. The KiVa antibullying program has been evaluated in Finland and other European countries, showing preventive effects on victimization and self-reported bullying. The aims of this study are (1) to develop a culturally appropriate version of the KiVa material and (2) to test the effectiveness of the KiVa program, with and without the online game, on reducing experiences of victimization and bullying behavior among vulnerable primary schools in Santiago (Chile), using a cluster randomized controlled trial (RCT) design with three arms: (1) full KiVa program group, (2) partial KiVa (without online game) program group and (3) control group. This is a three-arm, single-blind, cluster randomized controlled trial (RCT) with a target enrolment of 1495 4th and 5th graders attending 13 vulnerable schools per arm. Students in the full and partial KiVa groups will receive universal actions: ten 2-h lessons delivered by trained teachers during 1 year; they will be exposed to posters encouraging them to support victims and behave constructively when witnessing bullying; and a person designated by the school authorities will be present in all school breaks and lunchtimes using a visible KiVa vest to remind everybody that they are in a KiVa school. KiVa schools also will have indicated actions, which consist of a set of discussion groups with the victims and with the bullies, with proper follow-up. Only full KiVa schools will also receive an online game which has the aim to raise awareness of the role of the group in bullying, increase empathy and promote strategies to support victimized peers. Self-reported victimization

  15. The distribution of low and high-risk HPV types in vulvar and vaginal intraepithelial neoplasia (VIN and VaIN).

    PubMed

    Srodon, Monica; Stoler, Mark H; Baber, Gwen B; Kurman, Robert J

    2006-12-01

    It has been proposed that low-grade vulvar and vaginal lesions (VIN 1 and VaIN 1) are flat condylomas and should be designated as such. Moreover, their relationship to high-grade lesions (VIN 3 and VaIN 3) is unclear. Accordingly, this study was undertaken to address these issues by comparing the distribution of human papillomavirus (HPV) types in vulvar and vaginal intraepithelial lesions. We identified 33 cases of VIN 1, 34 cases of VIN 3, 17 cases of VaIN 1, and 16 cases of VaIN 3. In addition, 36 cases of low-grade squamous intraepithelial lesion (LSIL) in the cervix and 116 cases of cervical high-grade squamous intraepithelial lesion were used for comparison. Polymerase chain reaction analysis was performed using both the Roche PGMY and DDL SPF 10 systems. In cases where HPV was detected, the majority of low-grade and high-grade lesions contained a single HPV type. However, a minority of cases were found to have multiple HPV types. Of the VIN 1 cases, a low-risk virus was seen in 22 (67%), with HPV 6 or 11 accounting for 14 (42%). A high-risk virus was detected in 14 (42%) of cases of which 2 (6%) contained HPV 16. Of the VIN 3 cases, all had high-risk HPV of which 31 (91%) were found to have HPV 16. Of the VaIN 1 cases, 6 (35%) were found to have low-risk HPV types. HPV 6 or 11 were not found in these cases. High-risk virus was seen in 13 (76%) VaIN 1 cases, with 1 (6%) containing HPV 16. HPV was detected in 15 of 16 (94%) VaIN 3 lesions, all of which had high-risk types. HPV 16 was found in 8 (50%). In contrast, 2 (6%) of cervical LSIL had low-risk HPV (HPV 6 and 11), whereas 34 (94%) of LSIL cases had high-risk HPVs. Of the cervical high-grade squamous intraepithelial lesion cases, 100% had high-risk HPVs of which 87 (75%) were found to have HPV 16. The findings demonstrate that a significant number of low-grade vulvar and vaginal lesions contain high-risk HPV types, supporting their designation as low-grade intraepithelial lesions rather than flat

  16. 77 FR 33089 - OPSAIL 2012 Virginia, Port of Hampton Roads, VA

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-06-05

    ... of Hampton Roads. The Coast Guard will establish safety zones as a part of these regulations to... other time deemed necessary for safety and security by the Captain of the Port, Hampton Roads, vessels...] RIN 1625-AA00, AA08, AA11 OPSAIL 2012 Virginia, Port of Hampton Roads, VA AGENCY: Coast Guard, DHS...

  17. Sediment dynamics over multiple time scales in Dyke Marsh Preserve (Potomac River, VA)

    NASA Astrophysics Data System (ADS)

    Palinkas, C. M.; Walters, D.

    2010-12-01

    Tidal freshwater marshes are critical components of fluvial and estuarine ecosystems, yet sediment dynamics within them have not received as much attention as their saltwater counterparts. This study examines sedimentation in Dyke Marsh Preserve, located on the Potomac River (VA), focusing on understanding the spatial variability present over multiple time scales. Bimonthly sediment data were collected using ceramic tiles, and seasonal- and decadal-scale sedimentation was determined via 7Be (half-life 53.3 days) and 210Pb (half-life 22.3 years), respectively. Results were also compared to SET data collected by the National Park Service since 2006. Preliminary data indicate that sites at lower elevations have higher sedimentation rates, likely related to their close proximity to the sediment source. Mass accumulation rates generally decreased with increasing time scale, such that the seasonal rates were greater than the SET-derived accretion rates, which were in turn greater than the decadal-scale rates. However, the bimonthly rates were the lowest observed, probably because the sampling period (May-October 2010) did not include the main depositional period of the year, which would be integrated by the other techniques.

  18. 77 FR 74586 - Drawbridge Operation Regulation; Elizabeth River, Eastern Branch, Norfolk, VA

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-12-17

    ... DEPARTMENT OF HOMELAND SECURITY Coast Guard 33 CFR Part 117 [Docket No. USCG-2012-1052] Drawbridge Operation Regulation; Elizabeth River, Eastern Branch, Norfolk, VA AGENCY: Coast Guard, DHS. ACTION: Notice...-2012-1052 and are available online at www.regulations.gov , inserting USCG-2012-1052 in the ``Search...

  19. 77 FR 20716 - Drawbridge Operation Regulation; Blackwater River, South Quay, VA

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-04-06

    ... passage of vessels. There have been no requests for openings in 11 years. DATES: This rule is effective... S189 Bridge across Blackwater River, mile 9.2, at South Quay VA. There has been no request for openings since the year 2000. The only industrial waterway user to request openings left the area in 2000. Since...

  20. 30 CFR 57.22605 - Blasting from the surface (V-A mines).

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... Standards for Methane in Metal and Nonmetal Mines Explosives § 57.22605 Blasting from the surface (V-A mines). (a) All development and production blasting shall be initiated from the surface after all persons are... methane in the mine is less than 1.0 percent, persons may enter the mine, and all places blasted shall be...

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