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Sample records for genotype 5a failure

  1. Highly Efficient JFH1-Based Cell-Culture System for Hepatitis C Virus Genotype 5a: Failure of Homologous Neutralizing-Antibody Treatment to Control Infection

    DEFF Research Database (Denmark)

    Jensen, Tanja B; Gottwein, Judith Margarete; Scheel, Troels Kasper Høyer

    2008-01-01

    was to adapt the system to employ genotype 5. Methods. @nbsp; Huh7.5 cells infected with SA13/JFH1, containing Core-NS2 of strain SA13 (genotype 5a), were monitored for Core expression and for supernatant infectivity and HCV-RNA titers. Adaptive mutations of SA13/JFH1 were identified by sequence analysis...

  2. Hepatitis C virus genotyping in Greece: unexpected high prevalence of genotype 5a in a Greek island.

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    Karatapanis, Stylianos; Tsoplou, Panagiota; Papastergiou, Vasilios; Vasiageorgi, Aggeliki; Stampori, Maria; Saitis, Ioannis; Tsitsopoulos, Eustathios; Lisgos, Phillipos; Skorda, Lamprini; Ketikoglou, Ioannis; Goulis, Ioannis

    2012-02-01

    Hepatitis C virus (HCV) genotype 5 (G5) is a rare genotype reported mainly in South Africa. However, increasing data suggest the sporadic presence of this genotype in different European countries. To assess the epidemiology of HCV-G5 in Greece, genotyping was performed in 973 consecutive patients infected with HCV, referred to 7 hepatology centers throughout Greece, from January 2005 to December 2009. Genotype 5a (19 patients, 1.9%) was the fifth most prevalent genotype after genotype 1 (408 patients, 41.9%), genotype 3 (318 patients, 32.7%), genotype 4 (158 patients, 16.2%), and genotype 2 (70 patients, 7.2%). The majority of patients infected with G5 (16/19,84.2%) were referred to the General Hospital of Rhodes, an island in south-east Greece. The HCV genotype distribution in that particular island, indicates a particularly high G5 prevalence of 12.8%, after genotype 1 (40%), genotype 3 (28%), and genotype 4 (15%). Among the patients from Rhodes infected with G5 (n = 16), 13 (81.2%) were females. The mean age was 62.3 ± 6.5 years, significantly older than the patients infected with other HCV genotypes (mean age 40.6 ± 7.2, P < 0.0001). Nine out of the 16 cases (56.2%) presented features of high pre-treatment viral loads. Advanced liver fibrosis (Metavir F3-F4) was found in four out of five performed liver biopsies. Ten patients received treatment with pegylated interferon plus ribavirin and a sustained viral response were achieved in six cases. The source of infection is unknown but parenteral iatrogenic routes of transmission seem to have contributed significantly to the spread of genotype 5a in this region.

  3. An autochthonous case of hepatitis C virus genotype 5a in Brazil: phylogenetic analysis

    DEFF Research Database (Denmark)

    Ribeiro, L.C.; Souto, F.J.D.; do Espirito-Santo, M.P.

    2009-01-01

    Genotype 5 of hepatitis C virus (HCV) has been rarely identified in South America. A female of African descent who never left Brazil was found to be infected by this genotype in Mato Grosso state, Central Brazil. The patient denied drug injections and revealed that she had received blood...... transfusions several years before. One of her blood donors was identified and tested negative for anti-HCV and HCV RNA, as were her husband and offspring. Phylogenetic analysis of the E1 and NS5B regions confirmed that this HCV strain belonged to genotype 5a. However, the E1 region analysis indicates that our...

  4. Efficient cell culture system for hepatitis C virus genotype 5A

    DEFF Research Database (Denmark)

    2013-01-01

    The present inventors developed 5a/2a intergenotypic recombinants in which the JFH1 structural genes (Core, E1 and E2), p7 and all of or part of NS2 were replaced by the corresponding genes of the genotype 5a reference strain SA13. Compared to the J6/JFH control virus, after transfection of in vi......The present inventors developed 5a/2a intergenotypic recombinants in which the JFH1 structural genes (Core, E1 and E2), p7 and all of or part of NS2 were replaced by the corresponding genes of the genotype 5a reference strain SA13. Compared to the J6/JFH control virus, after transfection...

  5. Recombinant HCV variants with NS5A from genotypes 1-7 have different sensitivities to an NS5A inhibitor but not interferon-a

    DEFF Research Database (Denmark)

    Scheel, Troels K H; Gottwein, Judith M; Mikkelsen, Lotte S;

    2011-01-01

    Heterogeneity in the hepatitis C virus (HCV) protein NS5A influences its sensitivity to interferon-based therapy. Furthermore, NS5A is an important target for development of HCV-specific inhibitors. We aimed to develop recombinant infectious cell culture systems that express NS5A from isolates...... of the 7 major HCV genotypes, and determining their sensitivity to a specific NS5A inhibitor and to interferon-a....

  6. Differential sensitivity of 5'UTR-NS5A recombinants of hepatitis C virus genotypes 1-6 to protease and NS5A inhibitors

    DEFF Research Database (Denmark)

    Li, Yi-Ping; Ramirez, Santseharay; Humes, Daryl

    2014-01-01

    BACKGROUND & AIMS: Hepatitis C virus (HCV) therapy will benefit from the preclinical evaluation of direct-acting antiviral (DAA) agents in infectious culture systems that test the effects on different virus genotypes. We developed HCV recombinants comprising the 5' untranslated region-NS5A (5-5A)...

  7. Genotypic resistance tests in the management of the HIV-infected patient at virological failure.

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    Aceti, Antonio; Carosi, Giampiero

    2003-01-01

    Witness for the prosecution: The IAS-USA and Euro-Resistance Group HIV guidelines recommend the use of resistance testing for all patients experiencing treatment failure for whom therapy change is being considered. However, these assays suffer from several limitations (problems in sensitivity, specificity, complexity of interpretation, cost) and the results of the prospective studies evaluating genotype-guided treatment in HIV patients failing antiretroviral treatment are inconclusive and partially contrasting (virological benefit is short-term). On this basis, incorporating genotypic resistance assays into the clinical management of HIV patients experiencing first treatment failure is not a sufficiently evidence-based practice. Witness for the defence: Highly active antiretroviral therapy (HAART) has markedly improved the prognosis of HIV-infected patients by controlling HIV replication. However, HAART fails to control HIV replication in an increasing number of patients as a result of a complex array of causes. There is now substantial evidence that the emergence of drug resistance is a leading cause (as well as consequence) of antiretroviral therapy failure. Moreover, HIV drug resistance can be transmitted and this can favour initial treatment failure. Several retrospective and prospective studies have indicated that both genotypic and phenotypic HIV-1 drug resistance testing results are associated with, or predictive of, the virological outcome. As a consequence, international guidelines have soundly recommended the use of resistance testing to guide treatment choices after virological failure. The rationale and advantages of using such testing after first virological failure will be discussed.

  8. Genetic diversity of NS5A protein from hepatitis C virus genotype 3a and its relationship to therapy response

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    Rahal Paula

    2010-02-01

    Full Text Available Abstract Background The quasispecies nature of HCV may have important implications for viral persistence, pathogenicity and resistance to antiviral agents. The variability of one of the viral proteins, NS5A, is believed to be related to the response to IFN therapy, the standard treatment for infection. In this study we analyzed the quasispecies composition of NS5A protein in patients infected with HCV genotype 3a, before IFN therapy. Methods Viral RNA was isolated from samples of 12 patients: four sustained virological responders (SVR, four non-responders (NR, and four end-of-treatment responders (ETR. cDNA was synthesized, the NS5A region was amplified and the fragments obtained were cloned. Fifteen clones from each patient were sequenced with eight primers, generating 179 contigs. Results Higher values for substitution (either synonymous or non-synonymous and for distance were found in the SVR group. However, the NR group showed relatively more non-synonymous mutations than the other groups, owing to the higher values of dN/dS in complete NS5A and most specific regions. Overall, NS5A protein is undergoing purifying selection, since all dN/dS ratios values are below 0.5. Conclusions Our study provides an overview of the genetic variability of complete NS5A protein in HCV genotype 3a.

  9. Hereditary Hemochromatosis (HFE genotypes in heart failure: Relation to etiology and prognosis

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    Torp-Pedersen Christian

    2010-07-01

    Full Text Available Abstract Background It is believed that hereditary hemochromatosis (HH might play a role in cardiac disease (heart failure (HF and ischemia. Mutations within several genes are HH-associated, the most common being the HFE gene. In a large cohort of HF patients, we sought to determine the etiological role and the prognostic significance of HFE genotypes. Methods We studied 667 HF patients (72.7% men with depressed systolic function, enrolled in a multicentre trial with a follow-up period of up to 5 years. All were genotyped for the known HFE variants C282Y, H63D and S65C. Results The genotype and allele frequencies in the HF group were similar to the frequencies determined in the general Danish population. In multivariable analysis mortality was not predicted by C282Y-carrier status (HR 1.2, 95% CI: 0.8-1.7; H63D-carrier status (HR 1.0, 95% CI: 0.7-1.3; nor S65C-carrier status (HR 1.2, 95% CI: 0.7-2.0. We identified 27 (4.1% homozygous or compound heterozygous carriers of HFE variants. None of these carriers had a clinical presentation suggesting hemochromatosis, but hemoglobin and ferritin levels were higher than in the rest of the cohort. Furthermore, a trend towards reduced mortality was seen in this group in univariate analyses (HR 0.4, 95% CI: 0.2-0.9, p = 0.03, but not in multivariate (HR 0.5, 95% CI: 0.2-1.2. Conclusion HFE genotypes do not seem to be a significant contributor to the etiology of heart failure in Denmark. HFE variants do not affect mortality in HF.

  10. Regulation of the Production of Infectious Genotype 1a Hepatitis C Virus by NS5A Domain III▿

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    Kim, Seungtaek; Welsch, Christoph; Yi, MinKyung; Lemon, Stanley M.

    2011-01-01

    Although hepatitis C virus (HCV) assembly remains incompletely understood, recent studies with the genotype 2a JFH-1 strain suggest that it is dependent upon the phosphorylation of Ser residues near the C terminus of NS5A, a multifunctional nonstructural protein. Since genotype 1 viruses account for most HCV disease yet differ substantially in sequence from that of JFH-1, we studied the role of NS5A in the production of the H77S virus. While less efficient than JFH-1, genotype 1a H77S RNA produces infectious virus when transfected into permissive Huh-7 cells. The exchange of complete NS5A sequences between these viruses was highly detrimental to replication, while exchanges of the C-terminal domain III sequence (46% amino acid sequence identity) were well tolerated, with little effect on RNA synthesis. Surprisingly, the placement of the H77S domain III sequence into JFH-1 resulted in increased virus yields; conversely, H77S yields were reduced by the introduction of domain III from JFH-1. These changes in infectious virus yield correlated well with changes in the abundance of NS5A in RNA-transfected cells but not with RNA replication or core protein expression levels. Alanine replacement mutagenesis of selected Ser and Thr residues in the C-terminal domain III sequence revealed no single residue to be essential for infectious H77S virus production. However, virus production was eliminated by Ala substitutions at multiple residues and could be restored by phosphomimetic Asp substitutions at these sites. Thus, despite low overall sequence homology, the production of infectious virus is regulated similarly in JFH-1 and H77S viruses by a conserved function associated with a C-terminal Ser/Thr cluster in domain III of NS5A. PMID:21525356

  11. Discovery of ravidasvir (PPI-668) as a potent pan-genotypic HCV NS5A inhibitor.

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    Zhong, Min; Peng, Eric; Huang, Ningwu; Huang, Qi; Huq, Anja; Lau, Meiyen; Colonno, Richard; Li, Leping

    2016-09-15

    This Letter describes the synthesis, representative structure activity relationship (SAR), activity and PK profiles of a series of functionalized benzimidazole-naphthylene-imidazole derivatives as HCV NS5A inhibitors. This effort successfully led to the discovery of ravidasvir (PPI-668), which has been well tolerated and shown high sustained viral response rates as a key component in all-oral combination regimens in multiple human clinical trials.

  12. Association of I/D angiotensin-converting enzyme genotype with erythropoietin stimulation in kidney failure

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    Savin Marina

    2017-01-01

    Full Text Available Angiotensin-converting enzyme (ACE-gene polymorphism is a possible predisposing factor of erythropoietin response under hypoxic conditions. However, it is not completely clear whether the ACE insertion/deletion (I/D genotype has an impact on anemia in patients with permanent kidney failure. A 9-month prospective trial was conducted on 53 patients on hemodialysis aimed at determining the beneficial effect of oral vs intravenous iron in anemia management with recombinant human erythropoietin (rHuEpo, and identifying a possible association of the ACE gene I/D polymorphism with the response to rHuEpo. Patients were randomly allocated to receive 50-100 mg daily of ferrous gluconate orally (N=26 or intravenously every two weeks (N=27, together with rHuEpo-beta (200 IU/kg subcutaneously, to achieve a hemoglobin increase to 105 g/L; subsequently the rHuEpo dose was adjusted at one or two week intervals. In 34 patients who regularly received ACE-inhibitor (ACEi medication, genotyping for ACE-gene I/D polymorphism was performed using PCR, gel analysis and appropriate restriction digestion. After prolonged rHuEpo treatment, 24.5% of patients attained the targeted 9th-month hemoglobin concentration (105 g/L. Of these, 6/26 of patients received elemental iron orally and 7/27 received it intravenously. We observed an association between homozygous DD (deletion of the ACE gene and a remarkable early increase in blood hemoglobin (p=0.028, erythrocyte count (p=0.020 and hematocrit (p=0.043 after reduction of the dose of rHuEpo (F=3.95; p=0.029, irrespective of the iron repletion mode (p=0.960. This is the first report on DD genotype as a linkage marker for the optimization of rHuEpo dose for anemia management in hemodialysis patients.

  13. Emergence of occult minority genotype 2b hepatitis C infection in an HIV-1-co-infected patient treated for genotype 5a HCV infection with 48 weeks of pegylated-interferon-alpha 2b and ribavirin.

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    Buckton, A J; Kulasegaram, R; Ngui, S L; Fisher, M; James, R; Rangarajan, S; Teo, C G

    2007-09-01

    An HIV-1/hepatitis C virus (HCV) co-infected patient with haemophilia received a 48-week course of pegylated interferon-alpha-2b and ribavirin therapy for genotype 5a HCV infection. Virological response was achieved at week 24. At the end of treatment, HCV RNA in serum was detected and identified to belong to genotype 2b, rather than genotype 5a. A sensitive method for identifying minority HCV genotypes in pre-treatment serum showed genotype 2b HCV carriage prior to treatment. Sequencing the interferon sensitivity-determining region of the HCV NS5A gene obtained from pre-, intra- and post-treatment sera revealed emergence of quasispecies bearing R-->K and M-->A/T mutations at codons 2222 and 2223, respectively. Occult presence of minority HCV subpopulations and their acquisition of mutations following therapy can result in poor treatment outcome.

  14. Transient replication of a hepatitis C virus genotype 1b replicon chimera encoding NS5A-5B from genotype 3a.

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    Kylefjord, Helen; Danielsson, Axel; Sedig, Susanne; Belda, Oscar; Wiktelius, Daniel; Vrang, Lotta; Targett-Adams, Paul

    2014-01-01

    Although hepatitis C virus (HCV) is a pathogen of global significance, experimental therapies in current clinical development include highly efficacious all-oral combinations of HCV direct-acting antivirals (DAAs). If approved for use, these new treatment regimens will impact dramatically upon our capacity to eradicate HCV in the majority of virus-infected patients. However, recent data from late-stage clinical evaluations demonstrated that individuals infected with HCV genotype (GT) 3 responded less well to all-oral DAA combinations than patients infected with other HCV GTs. In light of these observations, the present study sought to expand the number of molecular tools available to investigate small molecule-mediated inhibition of HCV GT3 NS5A and NS5B proteins in preclinical tissue-culture systems. Accordingly, a novel subgenomic HCV replicon chimera was created by utilizing a GT1b backbone modified to produce NS5A and NS5B proteins from a consensus sequence generated from HCV GT3a genomic sequences deposited online at the European Hepatitis C Virus database. This approach avoided the need to isolate and amplify HCV genomes from sera derived from HCV-infected patients. The replicon chimera, together with a version engineered to express NS5A encoding a Y93H mutation, demonstrated levels of replication in transient assays robust enough to assess accurate antiviral activities of inhibitors representing different HCV DAA classes. Thus, the replicon chimera represents a new simple molecular tool suitable for drug discovery programmes aimed at investigating, understanding, and improving GT3a activities of HCV DAAs targeting NS5A or NS5B.

  15. Analysis of hepatitis C virus core/NS5A protein co-localization using novel cell culture systems expressing core-NS2 and NS5A of genotypes 1-7

    DEFF Research Database (Denmark)

    Galli, Andrea; Scheel, Troels K H; Prentoe, Jannick C

    2013-01-01

    JFH1-based recombinants expressing core-NS2 and NS5A from genotypes 1-7, and analysed core and NS5A co-localization in infected cells. Huh7.5 cells were transfected with RNA of core-NS2/NS5A recombinants and putative adaptive mutations were analysed by reverse genetics. Adapted core-NS2/NS5A...

  16. The Clinical and Economic Impact of Genotype Testing at First-line Antiretroviral Therapy Failure for HIV-Infected Patients in South Africa

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    Levison, Julie H.; Wood, Robin; Scott, Callie A.; Ciaranello, Andrea L.; Martinson, Neil A.; Rusu, Corina; Losina, Elena; Freedberg, Kenneth A.; Walensky, Rochelle P.

    2013-01-01

    Background. In resource-limited settings, genotype testing at virologic failure on first-line antiretroviral therapy (ART) may identify patients with wild-type (WT) virus. After adherence counseling, these patients may safely and effectively continue first-line ART, thereby delaying more expensive second-line ART. Methods. We used the Cost-Effectiveness of Preventing AIDS Complications International model of human immunodeficiency virus (HIV) disease to simulate a South African cohort of HIV-infected adults at first-line ART failure. Two strategies were examined: no genotype vs genotype, assuming availability of protease inhibitor–based second-line ART. Model inputs at first-line ART failure were mean age 38 years, mean CD4 173/µL, and WT virus prevalence 20%; genotype cost was $300 per test and delay to results, 3 months. Outcomes included life expectancy, per-person costs (2010 US dollars), and incremental cost-effectiveness ratios (dollars per years of life saved [YLS]). Results. No genotype had a projected life expectancy of 106.1 months, which with genotype increased to 108.3 months. Per-person discounted lifetime costs were $16 360 and $16 540, respectively. Compared to no genotype, genotype was very cost-effective, by international guidance, at $900/YLS. The cost-effectiveness of genotype was sensitive to prevalence of WT virus (very cost-effective when prevalence ≥12%), CD4 at first-line ART failure, and ART efficacy. Genotype-associated delays in care ≥5 months decreased survival and made no genotype the preferred strategy. When the test cost was ART failure is very cost-effective in South Africa. The cost-effectiveness of this strategy will depend on prevalence of WT virus and timely response to genotype results. PMID:23087386

  17. Mutation in mitochondrial complex IV subunit COX5A causes pulmonary arterial hypertension, lactic acidemia, and failure to thrive.

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    Baertling, Fabian; Al-Murshedi, Fathiya; Sánchez-Caballero, Laura; Al-Senaidi, Khalfan; Joshi, Niranjan P; Venselaar, Hanka; van den Brand, Mariël Am; Nijtmans, Leo Gj; Rodenburg, Richard Jt

    2017-03-01

    COX5A is a nuclear-encoded subunit of mitochondrial respiratory chain complex IV (cytochrome c oxidase). We present patients with a homozygous pathogenic variant in the COX5A gene. Clinical details of two affected siblings suffering from early-onset pulmonary arterial hypertension, lactic acidemia, failure to thrive, and isolated complex IV deficiency are presented. We show that the variant lies within the evolutionarily conserved COX5A/COX4 interface domain, suggesting that it alters the interaction between these two subunits during complex IV biogenesis. In patient skin fibroblasts, the enzymatic activity and protein levels of complex IV and several of its subunits are reduced. Lentiviral complementation rescues complex IV deficiency. The monomeric COX1 assembly intermediate accumulates demonstrating a function of COX5A in complex IV biogenesis. A potential therapeutic lead is demonstrated by showing that copper supplementation leads to partial rescue of complex IV deficiency in patient fibroblasts.

  18. Analysis of functional differences between hepatitis C virus NS5A of genotypes 1-7 in infectious cell culture systems

    DEFF Research Database (Denmark)

    Scheel, Troels K H; Prentoe, Jannick; Carlsen, Thomas H R

    2012-01-01

    directly-acting antiviral compounds. NS5A is important for replication and virus production, but has not been studied for most HCV genotypes. We studied the function of NS5A using infectious NS5A genotype 1-7 cell culture systems, and through reverse genetics demonstrated a universal importance...... of the amphipathic alpha-helix, domain I and II and the low-complexity sequence (LCS) I for HCV replication; the replicon-enhancing LCSI mutation S225P attenuated all genotypes. Mutation of conserved prolines in LCSII led to minor reductions in virus production for the JFH1(genotype 2a) NS5A recombinant, but had...... greater effects on other isolates; replication was highly attenuated for ED43(4a) and QC69(7a) recombinants. Deletion of the conserved residues 414-428 in domain III reduced virus production for most recombinants but not JFH1(2a). Reduced virus production was linked to attenuated replication in all cases...

  19. Sequence-based in silico analysis of well studied Hepatitis C Virus epitopes and their variants in other genotypes (particularly genotype 5a against South African human leukocyte antigen backgrounds

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    Prabdial-Sing Nishi

    2012-12-01

    Full Text Available Abstract Background Host genetics influence the outcome of HCV disease. HCV is also highly mutable and escapes host immunity. HCV genotypes are geographically distributed and HCV subtypes have been shown to have distinct repertoires of HLA-restricted viral epitopes which explains the lack of cross protection across genotypes observed in some studies. Despite this, immune databases and putative epitope vaccines concentrate almost exclusively on HCV genotype 1 class I-epitopes restricted by the HLA-A*02 allele. While both genotype and allele predominate in developed countries, we hypothesise that HCV variation and population genetics will affect the efficacy of proposed epitope vaccines in South Africa. This in silico study investigates HCV viral variability within well-studied epitopes identified in genotype 1 and uses algorithms to predict the immunogenicity of their variants from other less studied genotypes and thus rate the most promising vaccine candidates for the South African population. Six class I- and seven class II- restricted epitope sequences within the core, NS3, NS4B and NS5B regions were compared across the six HCV genotypes using local genotype 5a sequence data together with global data. Common HLA alleles in the South African population are A30:01, A02:01, B58:02, B07:02; DRB1*13:01 and DRB1*03:01. Epitope binding to 13 class I- and 8 class –II alleles were described using web-based prediction servers, Immune Epitope Database, (IEDB and Propred. Online population coverage tools were used to assess vaccine efficacy. Results Despite the homogeneity of genotype 1 and genotype 5 over the epitopes, there was limited promiscuity to local HLA-alleles.Host differences will make a putative vaccine less effective in South Africa. Of the 6 well-characterized class I- epitopes, only 2 class I- epitopes were promiscuous and 3 of the 7 class-II epitopes were better conserved and promiscuous. By fine tuning the putative vaccine using an

  20. Hereditary hemochromatosis (HFE) genotypes in heart failure: relation to etiology and prognosis

    DEFF Research Database (Denmark)

    Møller, Daniel Vega; Pecini, Redi; Gustafsson, Finn;

    2010-01-01

    It is believed that hereditary hemochromatosis (HH) might play a role in cardiac disease (heart failure (HF) and ischemia). Mutations within several genes are HH-associated, the most common being the HFE gene. In a large cohort of HF patients, we sought to determine the etiological role and the p......It is believed that hereditary hemochromatosis (HH) might play a role in cardiac disease (heart failure (HF) and ischemia). Mutations within several genes are HH-associated, the most common being the HFE gene. In a large cohort of HF patients, we sought to determine the etiological role...

  1. Genotypic drug resistance and long-term mortality in patients with triple-class antiretroviral drug failure

    DEFF Research Database (Denmark)

    Lohse, Nicolai; Jørgensen, Louise B; Kronborg, Gitte

    2007-01-01

    OBJECTIVE: To examine the prevalence of drug-resistance-associated mutations in HIV patients with triple-drug class virological failure (TCF) and their association with long-term mortality. DESIGN: Population-based study from the Danish HIV Cohort Study (DHCS). METHODS: We included all patients...... with increased mortality (mortality rate ratio [MRR] 2.3 [95% confidence interval (CI) 1.1-4.8]), as were the individual mutations T215Y (MRR 3.4 [95% CI 1.6-7.0]), G190A/S (MRR 3.2 [95% CI 1.6-6.6]) and V82F/A/T/S (MRR 2.5 [95% CI 1.2-5.3]). CONCLUSIONS: In HIV patients with TCF, the total number of genotypic...

  2. Retreatment with direct-acting antivirals of genotypes 1-3-4 hepatitis C patients who failed an anti-NS5A regimen in real world.

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    Halfon, Philippe; Scholtès, Caroline; Izopet, Jacques; Larrat, Sylvie; Trimoulet, Pascale; Zoulim, Fabien; Alric, Laurent; Métivier, Sophie; Leroy, Vincent; Ouzan, Denis; de Lédinghen, Victor; Mohamed, Sofiane; Pénaranda, Guillaume; Khiri, Hacène; Thélu, Marie-Ange; Plauzolles, Anne; Chiche, Laurent; Bourlière, Marc; Abravanel, Florence

    2017-10-04

    The aim was to study retreatment according to baseline nonstructural protein 5A (NS5A) resistance-associated substitutions (RASs) after the failure of first-line DAA-based treatment. From January 2014 to March 2016, 2995 HCV-infected patients were treated with NS5A inhibitors in six French liver referral centers; 80 (2.7%) patients relapsed. This "real-world" study included 24 of those 80 patients who had failed to achieve sustained virological response (SVR) on previous NS5A-based therapy. These 24 patients were re-treated with different regimen combinations. Antiviral efficacy was evaluated using the primary endpoints of SVR at weeks 4 and 12 post-treatment (SVR4, SVR12). The presence of NS5A RASs/polymorphisms was found in 20 (80%) patients at baseline of retreatment. All patients achieved SVR with HCV RNA below the lower limit of quantification (<15 IU/mL) by the end of treatment. SVR4 and SVR12 were achieved in 23/24 patients (96%), and the remaining patient relapsed four weeks post-treatment. Based on these results, retreatment of patients after the failure of a first-line NS5A regimen is effective (96% SVR). In the future, either dual or triple therapy regimens may have similar results with shorter treatment duration. Copyright © 2017. Published by Elsevier B.V.

  3. Genotypic and phenotypic nevirapine resistance correlates with virological failure during salvage therapy including abacavir and nevirapine

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    Jørgensen, L B; Katzenstein, T L; Gerstoft, J;

    2000-01-01

    OBJECTIVE: To study the development of resistance during 8 weeks of salvage therapy with abacavir and nevirapine in combination with other reverse transcriptase inhibitors (RTIs) and protease inhibitors (PIs). METHODS: Samples obtained at baseline and after 8 weeks of therapy from 16 heavily...... and after 2, 4 and 8 weeks of therapy. RESULTS: The majority of patients was genotypically and phenotypically resistant to lamivudine, abacavir, zidovudine and PIs, whereas 50% of the patients showed resistance to nevirapine at baseline in at least one of the methods used. After 8 weeks of salvage therapy...... higher transient reduction in viral load was observed in patients with nevirapine-sensitive HIV at baseline compared to patients with resistant HIV at baseline. CONCLUSION: The transient effect of salvage therapy including abacavir and nevirapine was due to the effect of nevirapine. The lack of effect...

  4. Elevated Lipoprotein(a) Levels, LPA Risk Genotypes, and Increased Risk of Heart Failure in the General Population

    DEFF Research Database (Denmark)

    Kamstrup, Pia R; Nordestgaard, Børge G

    2016-01-01

    OBJECTIVES: This study sough to test whether elevated lipoprotein(a) levels and corresponding LPA risk genotypes (low number of kringle IV type 2 repeats, rs3798220 and rs10455872, minor allele carriers) are associated with an increased risk of heart failure (HF). BACKGROUND: Elevated lipoprotein......(a) levels represent a genetically determined risk factor for myocardial infarction (MI) and aortic valve stenosis (AVS). It is presently unknown whether elevated lipoprotein(a) levels also cause heart failure (HF). METHODS: We combined 2 general population studies, the Copenhagen City Heart Study (n = 10...... mediation analyses. RESULTS: Elevated lipoprotein(a) levels were associated with multivariable adjusted hazard ratios for HF of 1.10 (95% CI: 0.97 to 1.25) for the 34th to 66th percentiles (8 to 19 mg/dl), 1.24 (95% CI: 1.08 to 1.42) for the 67th to 90th percentiles (20 to 67 mg/dl), 1.57 (95% CI: 1.32 to 1...

  5. Genotypic drug resistance and long-term mortality in patients with triple-class antiretroviral drug failure

    DEFF Research Database (Denmark)

    Lohse, Nicolai; Jørgensen, Louise B; Kronborg, Gitte

    2007-01-01

    OBJECTIVE: To examine the prevalence of drug-resistance-associated mutations in HIV patients with triple-drug class virological failure (TCF) and their association with long-term mortality. DESIGN: Population-based study from the Danish HIV Cohort Study (DHCS). METHODS: We included all patients...... with increased mortality (mortality rate ratio [MRR] 2.3 [95% confidence interval (CI) 1.1-4.8]), as were the individual mutations T215Y (MRR 3.4 [95% CI 1.6-7.0]), G190A/S (MRR 3.2 [95% CI 1.6-6.6]) and V82F/A/T/S (MRR 2.5 [95% CI 1.2-5.3]). CONCLUSIONS: In HIV patients with TCF, the total number of genotypic...... resistance mutations and specific single mutations predicted mortality.OBJECTIVE: To examine the prevalence of drug-resistance-associated mutations in HIV patients with triple-drug class virological failure (TCF) and their association with long-term mortality. DESIGN: Population-based study from the Danish...

  6. Quasispecies evolution in NS5A region of hepatitis C virus genotype 1b during interferon or combined interferon-ribavirin therapy

    Institute of Scientific and Technical Information of China (English)

    Pascal Veillon; Christopher Payan; Hélène Le Guillou-Guillemette; Catherine Gaudy; Fran(c)oise Lunel

    2007-01-01

    AIM: To evaluate the implication of substitutions in the hepatitis C virus (HCV) non-structural 5A (NS5A) protein in the resistance of HCV during mono-interferon (IFN)or combined IFN-ribavirin (IFN-R) therapy. Although NS5A has been reported to interact with the HCV RNA-dependent RNA polymerase, NS5B, as well as with many cellular proteins, the function of NS5A in the life cycle of HCV remains unclear.METHODS: HCV quasispecies were studied by cloning and sequencing of sequential isolates from patients infected by HCV genotype 1b. Patients were treated by IFN-α2b for 3 mo followed by IFN-α2b alone or combined IFN-R therapy for 9 additional months. Patients were categorized intro two groups based on their response to the treatments: 7 with sustained virological response (SVR) (quasispecies = 150) and 3 non-responders (NR) to IFN-R (quasispecies = 106).RESULTS: Prior to treatment, SVR patients displayed a lower complexity of quasispecies than NR patients. Most patients had a decrease in the complexity of quasispecies during therapy. Analysis of amino acids substitutions showed that the degree of the complexity of the interferon sensitivity-determining region (ISDR) and the V3 domain of NS5A protein was able to discriminate the two groups of patients. Moreover, SVR patients displayed more variability in the NS5A region than NR patients.CONCLUSION: These results suggest that detailed molecular analysis of the NS5A region may be important for understanding its function in IFN response during HCV 1b infection.

  7. Highly efficient infectious cell culture of three HCV genotype 2b strains and sensitivity to lead protease, NS5A, and polymerase inhibitors

    DEFF Research Database (Denmark)

    Ramirez, Santseharay; Li, Yi-Ping; Brun Jensen, Sanne;

    2014-01-01

    , we succeeded in generating DH8, J8, and DH10 viruses with authentic sequences in the regions targeted by lead direct acting antivirals. NS5B inhibitors Sofosbuvir, Mericitabine, and BI207127 had activity against 1a (strain TN), 2a (strains JFH1 and J6), and the 2b strains, whereas VX-222...... systems can be established by using consensus clones with defined mutations. Lead protease and NS5A inhibitors, as well as polymerase inhibitors Sofosbuvir, Mericitabine, and BI207127, show cross-activity against full-length 1a, 2a, and 2b viruses, but important sensitivity differences exist......Hepatitis C virus (HCV) is a genetically diverse virus with multiple genotypes exhibiting remarkable differences, particularly in drug susceptibility. Drug and vaccine development will benefit from high-titer HCV cultures mimicking the complete viral life cycle, but such systems only exist...

  8. Differential efficacy of protease inhibitors against HCV genotypes 2a, 3a, 5a, and 6a NS3/4A protease recombinant viruses

    DEFF Research Database (Denmark)

    Gottwein, Judith M; Scheel, Troels K H; Jensen, Tanja B;

    2011-01-01

    The hepatitis C virus (HCV) genotype influences efficacy of interferon (IFN)-based therapy. HCV protease inhibitors are being licensed for treatment of genotype 1 infection. Because there are limited or no data on efficacy against HCV genotypes 2-7, we aimed at developing recombinant infectious c...

  9. Screening and familial characterization of copy-number variations in NR5A1 in 46,XY disorders of sex development and premature ovarian failure.

    Science.gov (United States)

    Harrison, Steven M; Campbell, Ian M; Keays, Melise; Granberg, Candace F; Villanueva, Carlos; Tannin, Grace; Zinn, Andrew R; Castrillon, Diego H; Shaw, Chad A; Stankiewicz, Pawel; Baker, Linda A

    2013-10-01

    The NR5A1 gene encodes for steroidogenic factor 1, a nuclear receptor that regulates proper adrenal and gonadal development and function. Mutations identified by NR5A1 sequencing have been associated with disorders of sex development (DSD), ranging from sex reversal to severe hypospadias in 46,XY patients and premature ovarian failure (POF) in 46,XX patients. Previous reports have identified four families with a history of both 46,XY DSD and 46,XX POF carrying segregating NR5A1 sequence mutations. Recently, three 46,XY DSD sporadic cases with NR5A1 microdeletions have been reported. Here, we identify the first NR5A1 microdeletion transmitted in a pedigree with both 46,XY DSD and 46,XX POF. A 46,XY individual with DSD due to gonadal dysgenesis was born to a young mother who developed POF. Array CGH analysis revealed a maternally inherited 0.23 Mb microdeletion of chromosome 9q33.3, including the NR5A1 gene. Based on this finding, we screened patients with unexplained 46,XY DSD (n = 11), proximal hypospadias (n = 21) and 46,XX POF (n = 36) for possible NR5A1 copy-number variations (CNVs) via multiplex ligation-dependent probe amplification (MLPA), but did not identify any additional CNVs involving NR5A1. These data suggest that NR5A1 CNVs are an infrequent cause of these disorders but that array CGH and MLPA are useful genomic screening tools to uncover the genetic basis of such unexplained cases. This case is the first report of a familial NR5A1 CNV transmitting in a pedigree, causing both the male and female phenotypes associated with NR5A1 mutations, and the first report of a NR5A1 CNV associated with POF.

  10. Nucleotide mismatches between the VP7 gene and the primer are associated with genotyping failure of a specific lineage from G1 rotavirus strains

    Directory of Open Access Journals (Sweden)

    Espinola Emilio E

    2006-05-01

    Full Text Available Abstract In recent years it was reported that the accumulation of point mutations in VP4 and VP7 genes of rotavirus strains was the main cause of the failure of the G or P-typing. Failures in the correct genotyping of G1, G2, G8, G9 and G10 rotavirus strains were reported in the most commonly used reverse transcription (RT-PCR strategies. Collecting VP7 gene sequences of G1 rotavirus strains from databases we found that 74 (61.2 % out of 121 G1 strains from lineage I showed the four specific mismatches at the 5' end of the 9T1-1 primer, previously associated with the failure of G1-typing. Thus, a great percentage of the G1 strains from lineage I worldwide reported could not have been typed if the Das's RT-PCR strategy were used. This analysis shows that the failure on the detection of the G1 strains could be due to the diversification of rotavirus strains in phylogenetic lineages. Therefore, the use of different RT-PCR strategies with different primer binding locations on the VP7 gene or new typing methodologies -like microarrays procedures- could be a better option to avoid the failure of the G-typing of rotavirus strains detected during surveillance programs.

  11. Combination treatment with hepatitis C virus protease and NS5A inhibitors is effective against recombinant genotype 1a, 2a, and 3a viruses

    DEFF Research Database (Denmark)

    Gottwein, Judith M; Jensen, Sanne B; Li, Yi-Ping

    2013-01-01

    -FL) recombinants relying only on the JFH1 NS3 helicase, NS5B, and the 3' untranslated region. With identified adaptive mutations, semi-FL recombinants of genotypes(isolates) 1a(TN) and 3a(S52) produced supernatant infectivity titers of ~4 log(10) focus-forming units/ml in Huh7.5 cells. Genotype 1a(TN) adaptive...

  12. An investigation of CYP2D6 genotype and response to metoprolol CR/XL during dose titration in patients with heart failure: a MERIT-HF substudy.

    Science.gov (United States)

    Batty, J A; Hall, A S; White, H L; Wikstrand, J; de Boer, R A; van Veldhuisen, D J; van der Harst, P; Waagstein, F; Hjalmarson, Å; Kjekshus, J; Balmforth, A J

    2014-03-01

    To explore the pharmacogenetic effects of the cytochrome P450 (CYP)2D6 genotype in patients with systolic heart failure treated using controlled/extended-release (CR/XL) metoprolol, this study assessed the CYP2D6 locus for the nonfunctional *4 allele (1846G>A; rs3892097) in the Metoprolol CR/XL Randomised Intervention Trial in Congestive Heart Failure (MERIT-HF; n = 605). Participants were characterized as extensive, intermediate, or poor metabolizers (EMs, IMs, or PMs, respectively), based on the presence of the CYP2D6*4 allele (EM: *1*1, 60.4%; IM: *1*4, 35.8%; and PM: *4*4, 3.8%). Plasma metoprolol concentrations were 2.1-/4.6-fold greater in the IM/PM groups as compared with the EM group (P Metoprolol induced significantly lower heart rates and diastolic blood pressures during early titration, indicating a CYP2D6*4 allele dose-response effect (P metoprolol pharmacokinetics/pharmacodynamics during early titration; however, the MERIT-HF-defined titration schedule remains recommended for all patients, regardless of genotype.

  13. Novel NR5A1 missense mutation in premature ovarian failure: detection in han chinese indicates causation in different ethnic groups.

    Directory of Open Access Journals (Sweden)

    Xue Jiao

    Full Text Available BACKGROUND: The etiology of most premature ovarian failure (POF cases is usually elusive. Although genetic causes clearly exist and a likely susceptible region of 8q22.3 has been discovered, no predominant explanation exists for POF. More recently, evidences have indicated that mutations in NR5A1 gene could be causative for POF. We therefore screened for mutations in the NR5A1 gene in a large cohort of Chinese women with non-syndromic POF. METHODS: Mutation screening of NR5A1 gene was performed in 400 Han Chinese women with well-defined 46,XX idiopathic non-syndromic POF and 400 controls. Subsequently, functional characterization of the novel mutation identified was evaluated in vitro. RESULTS: A novel heterozygous missense mutation [c.13T>G (p.Tyr5Asp] in NR5A1 was identified in 1 of 384 patients (0.26%. This mutation impaired transcriptional activation on Amh, Inhibin-a, Cyp11a1 and Cyp19a1 gene, as shown by transactivation assays. However, no dominant negative effect was observed, nor was there impact on protein expression and nuclear localization. CONCLUSIONS: This novel mutation p.Tyr5Asp, in a novel non-domain region, is presumed to result in haploinsufficiency. Irrespectively, perturbation in NR5A1 is not a common explanation for POF in Chinese.

  14. Genotypic drug resistance and long-term mortality in patients with triple-class antiretroviral drug failure

    DEFF Research Database (Denmark)

    Lohse, Nicolai; Jørgensen, Louise B; Kronborg, Gitte

    2007-01-01

    in the DHCS who experienced TCF between January 1995 and November 2004, and we performed genotypic resistance tests for International AIDS Society (IAS)-USA primary mutations on virus from plasma samples taken around the date of TCF. We computed time to all-cause death from date of TCF. The relative risk...... with increased mortality (mortality rate ratio [MRR] 2.3 [95% confidence interval (CI) 1.1-4.8]), as were the individual mutations T215Y (MRR 3.4 [95% CI 1.6-7.0]), G190A/S (MRR 3.2 [95% CI 1.6-6.6]) and V82F/A/T/S (MRR 2.5 [95% CI 1.2-5.3]). CONCLUSIONS: In HIV patients with TCF, the total number of genotypic...

  15. Genotypic drug resistance and long-term mortality in patients with triple-class antiretroviral drug failure

    DEFF Research Database (Denmark)

    Lohse, Nicolai; Jørgensen, Louise B; Kronborg, Gitte

    2007-01-01

    in the DHCS who experienced TCF between January 1995 and November 2004, and we performed genotypic resistance tests for International AIDS Society (IAS)-USA primary mutations on virus from plasma samples taken around the date of TCF. We computed time to all-cause death from date of TCF. The relative risk...... with increased mortality (mortality rate ratio [MRR] 2.3 [95% confidence interval (CI) 1.1-4.8]), as were the individual mutations T215Y (MRR 3.4 [95% CI 1.6-7.0]), G190A/S (MRR 3.2 [95% CI 1.6-6.6]) and V82F/A/T/S (MRR 2.5 [95% CI 1.2-5.3]). CONCLUSIONS: In HIV patients with TCF, the total number of genotypic...... HIV Cohort Study (DHCS). METHODS: We included all patients in the DHCS who experienced TCF between January 1995 and November 2004, and we performed genotypic resistance tests for International AIDS Society (IAS)-USA primary mutations on virus from plasma samples taken around the date of TCF. We...

  16. Prevalence of relevant NS5A resistance-associated substitutions to elbasvir in genotype 1a hepatitis C virus patients in Spain.

    Science.gov (United States)

    Palladino, Claudia; Esteban-Cartelle, Beatriz; Mate-Cano, Irene; Sánchez-Carrillo, Marta; Resino, Salvador; Briz, Verónica

    2017-05-15

    Resistance-associated substitutions (RASs) to the new HCV NS5A inhibitor elbasvir may limit its efficacy and lead to virological failure in HCV-GT1a-infected patients. There are no data outside clinical trials evaluating their prevalence and impact in grazoprevir/elbasvir in GT1a-infected patients in Spain. A multicentre cross-sectional study of 632 initial patients was conducted. In 13 of these patients, the sample could not be amplified or a consensus sequence by Sanger sequencing could not be performed. Ultimately, 617 HCV-G1a-infected individuals treated at 84 Spanish hospitals from the 17 autonomous communities plus the 2 autonomous cities of Spain were analysed. HCV population sequencing was used to identify RAS to elbasvir and the mutational pattern and drug sensitivity were confirmed by geno2pheno[HCV]. Viruses bearing RASs to elbasvir were present in 6.2% of HCV-G1a infected patients. The most common RASs were the Y93C/H/N and Q30E/H/R (2.4% and 2.3%, respectively). Only 3.4% of the identified RASs to elbasvir conferred reduced susceptibility to elbasvir by geno2pheno[HCV], which exclusively identified the positions Q30H/R (n=7) and Y93C/H/N (n=8) as single mutations and Q30H+Y93H (n=4) and Q30R+Y93H (n=2) as double mutations as the major RASs to elbasvir. A lower prevalence of RASs to elbasvir was observed in our HCV-G1a Spanish cohort than reported previously in clinical trials evaluating patients from the USA. This information may be essential to guide the implementation of grazoprevir/elbasvir in Spain and to manage G1a-infected patients. Copyright © 2017 Elsevier España, S.L.U. and Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica. All rights reserved.

  17. Development and application of hepatitis C reporter viruses with genotype 1 to 7 core-nonstructural protein 2 (NS2) expressing fluorescent proteins or luciferase in modified JFH1 NS5A

    DEFF Research Database (Denmark)

    Gottwein, Judith M; Jensen, Tanja B; Mathiesen, Christian K

    2011-01-01

    To facilitate genotype-specific high-throughput studies of hepatitis C virus (HCV), we have developed reporter viruses using JFH1-based recombinants expressing core-nonstructural protein 2 (NS2) of genotype 1 to 7 prototype isolates. We introduced enhanced green fluorescent protein (EGFP) into NS5A...... domain III of the genotype 2a virus J6/JFH1 [2a(J6)]. During Huh7.5 cell culture adaptation, 2a(J6)-EGFP acquired a 40-amino-acid (aa) (¿40) or 25-aa (¿25) deletion in NS5A domain II, rescuing the impairment of viral assembly caused by the EGFP insertion. ¿40 conferred efficient growth characteristics...... deletions in EGFP, while 2a(J6)¿40 did not show an impaired viability. We further developed panels of JFH1-based genotype 1 to 7 core-NS2 recombinants expressing EGFP- or RLuc-NS5A¿40 fusion proteins. In cell culture, the different EGFP recombinants showed growth characteristics comparable to those...

  18. Diversity of Enterococcus faecalis Genotypes from Multiple Oral Sites Associated with Endodontic Failure Using Repetitive Sequence-based Polymerase Chain Reaction and Arbitrarily Primed Polymerase Chain Reaction.

    Science.gov (United States)

    Delboni, Maraísa G; Gomes, Brenda P F A; Francisco, Priscila A; Teixeira, Fabrício B; Drake, David

    2017-03-01

    The aim of this study was to evaluate the diversity and similarity of Enterococcus faecalis genotype isolates from multiple oral sites using repetitive sequence-based polymerase chain reaction and arbitrarily primed polymerase chain reaction (AP-PCR). Forty-two endodontically treated teeth with apical periodontitis were selected. A total of 126 microbial samples were collected from 3 different sites (saliva, pulp chamber, and root canals, all n = 42) during the nonsurgical retreatment procedures. After growth on m-Enterococcus agar, the colonies were isolated, characterized as gram-positive catalase negative cocci, and identified using an API 20 Strep kit (bioMérieux, Marcy-l'Etoile, France). Seventy-four colonies from 10 patients were confirmed as E. faecalis by polymerase chain reaction (16S ribosomal RNA). Repetitive sequence-based polymerase chain reactions using ERIC and AP-PCR using RW3A primers were performed in all 74 colonies. Fingerprints were analyzed and separated into genotypic groups based on the Dice coefficient percentage of similarity (82% or greater) as determined by ERIC reproducibility assays involving E. faecalis controls. Seven different E. faecalis genotypes (GTs) (GT1 = 27%, GT2 = 17.6%, GT3 = 1.3%, GT4 = 18.9%, GT5 = 9.5%, GT6 = 14.9%, and GT7 = 10.8%) were observed in different subjects and oral sites associated with endodontic failure. Remarkably, in 4 of 5 patients, the same GTs present in the infected root canals were also isolated from either the pulp chamber or the saliva samples. In particular, GT6 was detected in all 3 oral sites of patient 37. E. faecalis GTs isolated from saliva, the pulp chamber, and the root canal were similar using the Rep-PCR and AP-PCR methods. These findings suggest that coronal microleakage is a conceivable cause of endodontic failure. Copyright © 2016 American Association of Endodontists. Published by Elsevier Inc. All rights reserved.

  19. Development and application of hepatitis C reporter viruses with genotype 1 to 7 core-nonstructural protein 2 (NS2) expressing fluorescent proteins or luciferase in modified JFH1 NS5A.

    Science.gov (United States)

    Gottwein, Judith M; Jensen, Tanja B; Mathiesen, Christian K; Meuleman, Philip; Serre, Stephanie B N; Lademann, Jacob B; Ghanem, Lubna; Scheel, Troels K H; Leroux-Roels, Geert; Bukh, Jens

    2011-09-01

    To facilitate genotype-specific high-throughput studies of hepatitis C virus (HCV), we have developed reporter viruses using JFH1-based recombinants expressing core-nonstructural protein 2 (NS2) of genotype 1 to 7 prototype isolates. We introduced enhanced green fluorescent protein (EGFP) into NS5A domain III of the genotype 2a virus J6/JFH1 [2a(J6)]. During Huh7.5 cell culture adaptation, 2a(J6)-EGFP acquired a 40-amino-acid (aa) (Δ40) or 25-aa (Δ25) deletion in NS5A domain II, rescuing the impairment of viral assembly caused by the EGFP insertion. Δ40 conferred efficient growth characteristics to 2a(J6) tagged with EGFP, DsRed-Express2, mCherry, or Renilla luciferase (RLuc), yielding peak supernatant infectivity titers of 4 to 5 log(10) focus-forming units (FFU)/ml. 2a(J6) with Δ40 or Δ25 was fully viable in Huh7.5 cells. In human liver chimeric mice, 2a(J6)-EGFPΔ40 acquired various deletions in EGFP, while 2a(J6)Δ40 did not show an impaired viability. We further developed panels of JFH1-based genotype 1 to 7 core-NS2 recombinants expressing EGFP- or RLuc-NS5AΔ40 fusion proteins. In cell culture, the different EGFP recombinants showed growth characteristics comparable to those of the nontagged recombinants, with peak infectivity titers of 4 to 5 log(10) FFU/ml. RLuc recombinants showed slightly less efficient growth characteristics, with peak infectivity titers up to 10-fold lower. Overall, the EGFP and RLuc recombinants were genetically stable after one viral passage. The usefulness of these reporter viruses for high-throughput fluorescence- and luminescence-based studies of HCV-receptor interactions and serum-neutralizing antibodies was demonstrated. Finally, using RLuc viruses, we showed that the genotype-specific core-NS2 sequence did not influence the response to alfa-2b interferon (IFN-alfa-2b) and that genotype 1 to 7 viruses all responded to treatment with p7 ion channel inhibitors.

  20. Genetic markers associated with dihydroartemisinin-piperaquine failure in Plasmodium falciparum malaria in Cambodia: a genotype-phenotype association study.

    Science.gov (United States)

    Amato, Roberto; Lim, Pharath; Miotto, Olivo; Amaratunga, Chanaki; Dek, Dalin; Pearson, Richard D; Almagro-Garcia, Jacob; Neal, Aaron T; Sreng, Sokunthea; Suon, Seila; Drury, Eleanor; Jyothi, Dushyanth; Stalker, Jim; Kwiatkowski, Dominic P; Fairhurst, Rick M

    2017-02-01

    As the prevalence of artemisinin-resistant Plasmodium falciparum malaria increases in the Greater Mekong subregion, emerging resistance to partner drugs in artemisinin combination therapies seriously threatens global efforts to treat and eliminate this disease. Molecular markers that predict failure of artemisinin combination therapy are urgently needed to monitor the spread of partner drug resistance, and to recommend alternative treatments in southeast Asia and beyond. We did a genome-wide association study of 297 P falciparum isolates from Cambodia to investigate the relationship of 11 630 exonic single-nucleotide polymorphisms (SNPs) and 43 copy number variations (CNVs) with in-vitro piperaquine 50% inhibitory concentrations (IC50s), and tested whether these genetic variants are markers of treatment failure with dihydroartemisinin-piperaquine. We then did a survival analysis of 133 patients to determine whether candidate molecular markers predicted parasite recrudescence following dihydroartemisinin-piperaquine treatment. Piperaquine IC50s increased significantly from 2011 to 2013 in three Cambodian provinces (2011 vs 2013 median IC50s: 20·0 nmol/L [IQR 13·7-29·0] vs 39·2 nmol/L [32·8-48·1] for Ratanakiri, 19·3 nmol/L [15·1-26·2] vs 66·2 nmol/L [49·9-83·0] for Preah Vihear, and 19·6 nmol/L [11·9-33·9] vs 81·1 nmol/L [61·3-113·1] for Pursat; all p≤10(-3); Kruskal-Wallis test). Genome-wide analysis of SNPs identified a chromosome 13 region that associates with raised piperaquine IC50s. A non-synonymous SNP (encoding a Glu415Gly substitution) in this region, within a gene encoding an exonuclease, associates with parasite recrudescence following dihydroartemisinin-piperaquine treatment. Genome-wide analysis of CNVs revealed that a single copy of the mdr1 gene on chromosome 5 and a novel amplification of the plasmepsin 2 and plasmepsin 3 genes on chromosome 14 also associate with raised piperaquine IC50s. After adjusting for covariates, both

  1. Adaptive mutations enhance assembly and cell-to-cell transmission of a high-titer hepatitis C virus genotype 5a Core-NS2 JFH1-based recombinant

    DEFF Research Database (Denmark)

    Mathiesen, Christian K; Prentoe, Jannick; Meredith, Luke W

    2015-01-01

    UNLABELLED: Recombinant hepatitis C virus (HCV) clones propagated in human hepatoma cell cultures yield relatively low infectivity titers. Here, we adapted the JFH1-based Core-NS2 recombinant SA13/JFH1C3405G,A3696G (termed SA13/JFH1orig), of the poorly characterized genotype 5a, to Huh7.5 cells......81-deficient Huh7-derived cells demonstrated that these changes did not affect replication but increased HCV assembly and specific infectivity as early as 24 h posttransfection. Infectious coculture assays in Huh7.5 cells showed a significant increase in cell-to-cell transmission for SA13/JFH1Core...

  2. Optimizing choice of oral interferon-free treatment for genotype 1 hepatitis C virus using testing for NS5A resistance: a cost-utility analysis from the perspective of the Italian National Health Service

    Science.gov (United States)

    Westerhout, Kirsten Y; Bouwmeester, Walter; Duchesne, Inge; Pisini, Marta; Piena, Marjanne A; Damele, Francesco; Gueron, Beatrice; Treur, Maarten; Belsey, Jonathan

    2017-01-01

    Background Patients with genotype-1 hepatitis C virus infection who have failed to respond to standard therapy or who relapse following treatment may be considered for an interferon-free regimen incorporating a nonstructural protein 5A (NS5A) inhibitor. Sustained virologic response (SVR) with these regimens is typically >90%, but this is reduced in patients with NS5A resistance. European Association for Study of the Liver guidelines recommend simeprevir + sofosbuvir ± ribavirin (SMV+SOF±R) for re-treating patients failing an NS5A inhibitor-containing regimen. An alternative strategy would be to test for NS5A resistance prior to treatment, with therapy optimized based on the results. This study investigates the cost-effectiveness of this strategy. Materials and methods A Markov model was used to estimate disease progression for treatment-experienced genotype 1 patients with severe fibrosis or compensated cirrhosis. Targeted treatment with either SMV+SOF±R or sofosbuvir + ledipasvir ± ribavirin (SOF+LDV±R) based on pretreatment NS5A resistance testing was compared to routine SOF+LDV±R without testing. Treatment duration was 12 or 24 weeks for patients with severe fibrosis or compensated cirrhosis (Metavir F3/F4). SVR data for the treatment options were based on the results of published clinical trials. The analysis was carried out from the perspective of the Italian National Health Service. Results Optimized treatment using NS5A resistance testing yielded 0.163 additional QALYs and increased costs of €2,789 per patient versus no testing. The incremental cost-effectiveness ratio (ICER) was €17,078/QALY. Sensitivity analysis identified the SVR attributable to each of the treatment regimens as the most sensitive determinant of ICER (range: €10,055/QALY–€43,501/QALY across plausible range). Probabilistic sensitivity analysis demonstrated that, at a willingness-to-pay threshold of €30,000/QALY, the probability that NS5A-directed treatment will be cost

  3. Stratification by smoking status reveals an association of CHRNA5-A3-B4 genotype with body mass index in never smokers.

    Science.gov (United States)

    Taylor, Amy E; Morris, Richard W; Fluharty, Meg E; Bjorngaard, Johan H; Åsvold, Bjørn Olav; Gabrielsen, Maiken E; Campbell, Archie; Marioni, Riccardo; Kumari, Meena; Hällfors, Jenni; Männistö, Satu; Marques-Vidal, Pedro; Kaakinen, Marika; Cavadino, Alana; Postmus, Iris; Husemoen, Lise Lotte N; Skaaby, Tea; Ahluwalia, Tarunveer S; Treur, Jorien L; Willemsen, Gonneke; Dale, Caroline; Wannamethee, S Goya; Lahti, Jari; Palotie, Aarno; Räikkönen, Katri; Kisialiou, Aliaksei; McConnachie, Alex; Padmanabhan, Sandosh; Wong, Andrew; Dalgård, Christine; Paternoster, Lavinia; Ben-Shlomo, Yoav; Tyrrell, Jessica; Horwood, John; Fergusson, David M; Kennedy, Martin A; Frayling, Tim; Nohr, Ellen A; Christiansen, Lene; Ohm Kyvik, Kirsten; Kuh, Diana; Watt, Graham; Eriksson, Johan; Whincup, Peter H; Vink, Jacqueline M; Boomsma, Dorret I; Davey Smith, George; Lawlor, Debbie; Linneberg, Allan; Ford, Ian; Jukema, J Wouter; Power, Christine; Hyppönen, Elina; Jarvelin, Marjo-Riitta; Preisig, Martin; Borodulin, Katja; Kaprio, Jaakko; Kivimaki, Mika; Smith, Blair H; Hayward, Caroline; Romundstad, Pål R; Sørensen, Thorkild I A; Munafò, Marcus R; Sattar, Naveed

    2014-12-01

    We previously used a single nucleotide polymorphism (SNP) in the CHRNA5-A3-B4 gene cluster associated with heaviness of smoking within smokers to confirm the causal effect of smoking in reducing body mass index (BMI) in a Mendelian randomisation analysis. While seeking to extend these findings in a larger sample we found that this SNP is associated with 0.74% lower body mass index (BMI) per minor allele in current smokers (95% CI -0.97 to -0.51, P = 2.00 × 10(-10)), but also unexpectedly found that it was associated with 0.35% higher BMI in never smokers (95% CI +0.18 to +0.52, P = 6.38 × 10(-5)). An interaction test confirmed that these estimates differed from each other (P = 4.95 × 10(-13)). This difference in effects suggests the variant influences BMI both via pathways unrelated to smoking, and via the weight-reducing effects of smoking. It would therefore be essentially undetectable in an unstratified genome-wide association study of BMI, given the opposite association with BMI in never and current smokers. This demonstrates that novel associations may be obscured by hidden population sub-structure. Stratification on well-characterized environmental factors known to impact on health outcomes may therefore reveal novel genetic associations.

  4. NAT2 genotype guided regimen reduces isoniazid-induced liver injury and early treatment failure in the 6-month four-drug standard treatment of tuberculosis: a randomized controlled trial for pharmacogenetics-based therapy.

    Science.gov (United States)

    Azuma, Junichi; Ohno, Masako; Kubota, Ryuji; Yokota, Soichiro; Nagai, Takayuki; Tsuyuguchi, Kazunari; Okuda, Yasuhisa; Takashima, Tetsuya; Kamimura, Sayaka; Fujio, Yasushi; Kawase, Ichiro

    2013-05-01

    This study is a pharmacogenetic clinical trial designed to clarify whether the N-acetyltransferase 2 gene (NAT2) genotype-guided dosing of isoniazid improves the tolerability and efficacy of the 6-month four-drug standard regimen for newly diagnosed pulmonary tuberculosis. In a multicenter, parallel, randomized, and controlled trial with a PROBE design, patients were assigned to either conventional standard treatment (STD-treatment: approx. 5 mg/kg of isoniazid for all) or NAT2 genotype-guided treatment (PGx-treatment: approx. 7.5 mg/kg for patients homozygous for NAT2 4: rapid acetylators; 5 mg/kg, patients heterozygous for NAT2 4: intermediate acetylators; 2.5 mg/kg, patients without NAT2 4: slow acetylators). The primary outcome included incidences of 1) isoniazid-related liver injury (INH-DILI) during the first 8 weeks of therapy, and 2) early treatment failure as indicated by a persistent positive culture or no improvement in chest radiographs at the 8th week. One hundred and seventy-two Japanese patients (slow acetylators, 9.3 %; rapid acetylators, 53.5 %) were enrolled in this trial. In the intention-to-treat (ITT) analysis, INH-DILI occurred in 78 % of the slow acetylators in the STD-treatment, while none of the slow acetylators in the PGx-treatment experienced either INH-DILI or early treatment failure. Among the rapid acetylators, early treatment failure was observed with a significantly lower incidence rate in the PGx-treatment than in the STD-treatment (15.0 % vs. 38 %). Thus, the NAT2 genotype-guided regimen resulted in much lower incidences of unfavorable events, INH-DILI or early treatment failure, than the conventional standard regimen. Our results clearly indicate a great potential of the NAT2 genotype-guided dosing stratification of isoniazid in chemotherapy for tuberculosis.

  5. Optimizing choice of oral interferon-free treatment for genotype 1 hepatitis C virus using testing for NS5A resistance: a cost-utility analysis from the perspective of the Italian National Health Service

    Directory of Open Access Journals (Sweden)

    Westerhout KY

    2017-02-01

    Full Text Available Kirsten Y Westerhout,1 Walter Bouwmeester,1 Inge Duchesne,2 Marta Pisini,2 Marjanne A Piena,1 Francesco Damele,3 Beatrice Gueron,2 Maarten Treur,1 Jonathan Belsey4 1Pharmerit BV, Marten Meesweg, Rotterdam, the Netherlands; 2Janssen EMEA, Turnhoutseweg, Beerse, Belgium; 3Janssen-Cilag SpA, Via Michelangelo Buonarroti, Cologno Monzese, Italy; 4JB Medical Ltd, Old Brickworks, Little Cornard, United Kingdom Background: Patients with genotype-1 hepatitis C virus infection who have failed to respond to standard therapy or who relapse following treatment may be considered for an interferon-free regimen incorporating a nonstructural protein 5A (NS5A inhibitor. Sustained virologic response (SVR with these regimens is typically >90%, but this is reduced in patients with NS5A resistance. European Association for Study of the Liver guidelines recommend simeprevir + sofosbuvir ± ribavirin (SMV+SOF±R for re-treating patients failing an NS5A inhibitor-containing regimen. An alternative strategy would be to test for NS5A resistance prior to treatment, with therapy optimized based on the results. This study investigates the cost-effectiveness of this strategy.Materials and methods: A Markov model was used to estimate disease progression for treatment-experienced genotype 1 patients with severe fibrosis or compensated cirrhosis. Targeted treatment with either SMV+SOF±R or sofosbuvir + ledipasvir ± ribavirin (SOF+LDV±R based on pretreatment NS5A resistance testing was compared to routine SOF+LDV±R without testing. Treatment duration was 12 or 24 weeks for patients with severe fibrosis or compensated cirrhosis (Metavir F3/F4. SVR data for the treatment options were based on the results of published clinical trials. The analysis was carried out from the perspective of the Italian National Health Service.Results: Optimized treatment using NS5A resistance testing yielded 0.163 additional QALYs and increased costs of €2,789 per patient versus no testing. The

  6. Effect of specific ADRB1/ADRB2/AGT genotype combinations on the association between survival and carvedilol treatment in chronic heart failure

    DEFF Research Database (Denmark)

    Petersen, Morten; Andersen, Jon; Jimenez-Solem, Espen;

    2012-01-01

    the downregulated ADRB2 genotype (Gln27-carrier) was added to the ADRB1/AGT combination (Pinteraction=0.0005; hazard ratio 2.67, 95% confidence interval 1.51-4.72, P=0.0007). Two hundred and four patients were treated with metoprolol. There was no interaction between metoprolol treatment and the specific genotype...

  7. Frequency of Natural Resistance within NS5a Replication Complex Domain in Hepatitis C Genotypes 1a, 1b: Possible Implication of Subtype-Specific Resistance Selection in Multiple Direct Acting Antivirals Drugs Combination Treatment

    Directory of Open Access Journals (Sweden)

    Sabrina Bagaglio

    2016-03-01

    Full Text Available Different HCV subtypes may naturally harbor different resistance selection to anti-NS5a inhibitors. 2761 sequences retrieved from the Los Alamos HCV database were analyzed in the NS5a domain 1, the target of NS5a inhibitors. The NS5a resistance-associated polymorphisms (RAPs were more frequently detected in HCV G1b compared to G1a. The prevalence of polymorphisms associated with cross-resistance to compounds in clinical use (daclatasvir, DCV, ledipasvir, LDV, ombitasvir, and OMV or scheduled to come into clinical use in the near future (IDX719, elbasvir, and ELV was higher in G1b compared to G1a (37/1552 (2.4% in 1b sequences and 15/1209 (1.2% in 1a isolates, p = 0.040. Interestingly, on the basis of the genotype-specific resistance pattern, 95 (6.1% G1b sequences had L31M RAP to DCV/IDX719, while 6 sequences of G1a (0.5% harbored L31M RAP, conferring resistance to DCV/LDV/IDX719/ELV (p < 0.0001. Finally, 28 (2.3% G1a and none of G1b isolates harbored M28V RAP to OMV (p < 0.0001. In conclusion, the pattern of subtype-specific resistance selection in the naturally occurring strains may guide the treatment option in association with direct acting antivirals (DAAs targeting different regions, particularly in patients that are difficult to cure, such as those with advanced liver disease or individuals who have failed previous DAAs.

  8. Infectious genotype 1a, 1b, 2a, 2b, 3a, 5a, 6a and 7a hepatitis C virus lacking the hypervariable region 1 (HVR1)

    DEFF Research Database (Denmark)

    2014-01-01

    .sub.1389c,A1590G (6a/2a) constructs for the deletion of Hypervariable Region 1 (HVR1) to construct viable, JFH 1 (genotype 2a) based, genomes. The present inventors serially passaged the viruses in cell culture obtaining relatively high HCV RNA titers and infectivity titers. Sequence analysis...... of the viruses identified mutations adapting H77/JFH 1.sub.T27OOC,A4O8OT,.DELTA.HVR1 (1a/2a), J8/JFH .sub.1.DELTA.HVR1 (2b/2a), S52/JFH 1.sub.T2718G,T716OC,.DELTA.HVR1 (3a/2a) and J4/JFH 1.sub.T2996C,A4827T,.DELTA.HVR1 (1b/2a) to the HVR1 deletion.......The present inventors used the previously developed H77/JFH 1.sub.T27OOC,A4O8OT (1a/2a), J4/JFH .sub.1T2996C,A4827T,.DELTA.HVRI (1b/2a), J6/JFH .sub.1.DELTA.HVRI (2a/2a), J8/JFH 1.sub..DELTA.HVRI (2b/2a), S52/JFH 1.sub.T27i8G,.tau.7i6oc (3a/2a), SA13/JFH 1.sub.C34O5G,A3696G (5a/2a) and HK6a/JFH 1T...

  9. Evaluation of Resistance-Associated Substitutions in NS5A Using Direct Sequence and Cycleave Method and Treatment Outcome with Daclatasvir and Asunaprevir for Chronic Hepatitis C Genotype 1

    Science.gov (United States)

    Ishii, Kunihide; Morita, Masaru; Morita, Yasuyo; Sugiyama, Gen; Fukushima, Hirofumi; Yano, Yoichi; Noguchi, Kazunori; Nakamura, Hiroki; Hisatomi, Junjiro; Kumemura, Hiroto; Shirachi, Miki; Iwane, Shinji; Okada, Michiaki; Honma, Yuichi; Arinaga-Hino, Teruko; Miyajima, Ichiro; Ogata, Kei; Kuwahara, Reiichiro; Amano, Keisuke; Kawaguchi, Toshihiro; Kuromatsu, Ryoko; Torimura, Takuji

    2016-01-01

    Background The aim of this study was to evaluate the efficacy of daclatasvir plus asunaprevir therapy in patients infected with hepatitis C virus and determine its relevance to resistant variants. Methods A total of 629 consecutive patients infected with hepatitis C virus genotype 1 were assessed. Daclatasvir (60 mg/day) plus asunaprevir (200 mg/day) was given for 24 weeks. The virological responses and resistance-associated substitutions of hepatitis C virus mutants were examined by the direct sequence and cycleave methods were evaluated. Results Overall, 89.4% (555/621) of patients exhibited a sustained virological response (SVR). The SVR rates in the patients with wild type, mixed, and mutant type Y93 by direct sequencing were 92.5% (520/562), 70.3% (26/37), and 42.9% (9/21), respectively. The SVR rates in the patients with 100%, 90%, 80%-30%, and 20%-0% Y93 wild by the cycleave method were 93.4% (456/488), 88.2%(30/34), 56.0%(14/25), and 36.8%(7/19), respectively. In contrast, the SVR rates for the wild type and mixed/mutant type L31 by direct sequencing were 90.2% (534/592) and 72.4% (21/29), respectively. In the multivariate analyses, the wild type Y93, no history of simeprevir therapy, the wild type L31, and low HCV RNA level were independent factors of SVR. Conclusion NS5A resistance-associated substitutions, especially Y93H, were major factors predicting the SVR. Although direct sequencing can predict the SVR rate, the cycleave method is considered to be more useful for predicting the SVR when used in combination. PMID:27684567

  10. Counsel the genotype, treat the phenotype

    NARCIS (Netherlands)

    van der Zwaag, Paul A.; van Tintelen, J. Peter

    2011-01-01

    This editorial refers to 'Novel correlations between the genotype and the phenotype of hypertrophic and dilated cardiomyopathy: results from the German Competence Network Heart Failure' by S. Waldmuller et al., published in this issue on pages 1185-1192.

  11. Desmanthus GENOTYPES

    Directory of Open Access Journals (Sweden)

    JOSÉ HENRIQUE DE ALBUQUERQUE RANGEL

    2015-01-01

    Full Text Available Desmanthus is a genus of forage legumes with potential to improve pastures and livestock produc-tion on clay soils of dry tropical and subtropical regions such as the existing in Brazil and Australia. Despite this patterns of natural or enforced after-ripening of Desmanthus seeds have not been well established. Four year old seed banks of nine Desmanthus genotypes at James Cook University were accessed for their patterns of seed softe-ning in response to a range of temperatures. Persistent seed banks were found to exist under all of the studied ge-notypes. The largest seeds banks were found in the genotypes CPI 78373 and CPI 78382 and the smallest in the genotypes CPI’s 37143, 67643, and 83563. An increase in the percentage of softened seeds was correlated with higher temperatures, in two patterns of response: in some accessions seeds were not significantly affected by tempe-ratures below 80º C; and in others, seeds become soft when temperature rose to as little as 60 ºC. At 80 °C the heat started to depress germination. High seed production of Desmanthus associated with dependence of seeds on eleva-ted temperatures to softening can be a very important strategy for plants to survive in dry tropical regions.

  12. Premature ovarian failure : from phenotype to genotype

    NARCIS (Netherlands)

    Knauff, A.H.

    2009-01-01

    Postponement of childbearing has led to increased rates of age-related female subfertility. Age-related decreases in ovarian follicle numbers and decay in oocyte quality influence the natural loss of fecundity and ultimately the start of menopause. The rate of ovarian ageing is highly variable among

  13. Retreatment efficacy and predictors of ledipasvir plus sofosbuvir to HCV genotype 1 in Japan.

    Science.gov (United States)

    Akuta, Norio; Sezaki, Hitomi; Suzuki, Fumitaka; Fujiyama, Shunichiro; Kawamura, Yusuke; Hosaka, Tetsuya; Kobayashi, Masahiro; Kobayashi, Mariko; Saitoh, Satoshi; Suzuki, Yoshiyuki; Arase, Yasuji; Ikeda, Kenji; Kumada, Hiromitsu

    2017-02-01

    Predictors of treatment efficacy with ledipasvir plus sofosbuvir as direct-acting antiviral (DAA) regimen for HCV infection are still unclear. Retreatment efficacy of ledipasvir plus sofosbuvir for failures to prior DAA regimens, including NS5A inhibitors, are also unknown because resistance-associated variants (RAVs) in NS5A have been shown to persist up to the long-term of post-treatment. One hundred seventy-five patients with chronic HCV genotype 1 infection, without decompensated liver cirrhosis and hepatocellular carcinoma, were evaluated SVR12 by ledipasvir 90 mg plus sofosbuvir 400 mg once-daily for 12 weeks. Overall, SVR12 were 92%, based on intention to treat analysis. In failures to daclatasvir plus asunaprevir, SVR12 were 71%. The study using ultra-deep sequencing showed that ledipasvir plus sofosbuvir was effective to one case of failures to daclatasvir plus asunaprevir with multidrug RAVs (triple mutation in NS3-D168/NS5A-L31/NS5A-Y93). Multivariate analysis identified FIB4 index (plus sofosbuvir for HCV genotype 1 infection, including multidrug RAVs in Japan. Treatment efficacy could be predicted by the combination of viral and host factors. J. Med. Virol. 89:284-290, 2017. © 2016 Wiley Periodicals, Inc.

  14. Hepatitis C Virus Genotypes

    Directory of Open Access Journals (Sweden)

    Kayhan Azadmanesh

    2005-09-01

    , based on its phenotype according to its disease pattern or cytopathology, and serotype based on a panel of cross-neutralization antibodies, impossible(21. Phylogenetic analysis may aid in the separation of sequences into distinct types(22. So far six majorgenotypes (HCV-1 to HCV-6 have been described, each containing multiple subtypes (e.g., 1a, 1b, etc.. More than 50 subtypes have been reported todate and are normally identified on the bases of partial gene sequences from E1 and NS5B. The isolates formerly published as genotypes 7 to 11 are now considered subtypes within genotypes 3 (subtype 10 and 6 (subtypes 7, 8, 9, and 11(22.In general, sequence characteristics of a particular subtype are found throughout the HCV genome. Thus, the HCV genotype has been determined primarily based on analysis of partial genome sequences. The most extensive database exists for the 5'-UTR, core, E1, and NS5B (23-28. Whereas the 5'-UTR is highly conserved and therefore preferred for diagnosis, the core, the envelope, and the NS5B regions are less conserved and therefore highly discriminative and preferred for subtyping. Although the 5'-UTR contains characteristic sequence motifs of some genotypes, analysis of this region may not accurately predict all genotypes or subtypes. HCV Genotyping MethodsMolecular Genotyping Because differences in geographical distribution, disease outcome, and response to therapy among HCV genotypes have been suggested, reliable 1 573 1149 2187 3078 4971 5916 9033C E1 E2 P7 NS2 NS3 NS4A NS4B NS5A NS5B Figure 1. The HCV genome contains a single open reading frame (ORF. The genes for structural proteins (C, E1, E2, P7 are situated towards the N-terminus of the ORF. Genes coding for proteins necessary for viral replication are found towards the C-terminus of the ORF. methods for determining the HCV genotype may become an important clinical test. The HCV genotype can be determined by nucleotide sequencing of a specific PCR-amplified portion of the HCV genome

  15. Genotype adaptability and stability

    Directory of Open Access Journals (Sweden)

    Dimitrijević Miodrag

    2000-01-01

    Full Text Available One of the primary concerns in breeding programs is a small genotype reaction to environmental factor variation for better usage of yield genetic potential. Particularly if one takes in consideration that yield could van greatly because of more and more variable meteorological conditions. Studies conducted to observe genotype and environmental relations relay on numerous mathematical models, but genotype behavior in various ecological conditions is not, still, precisely defined Major sources of variation influencing genotype behavior in different environments are genotype/environment interaction, genetic background and environmental conditions. These factors could play an important role in establishing growth regions for maximal realization of genotype genetic potential, as well as in selection of genotypes having better response to complex requirements of particular growth region. Stability, the genotype ability to perform high, uniform yield no meter of different environmental conditions, and adaptability, genotype ability to give uniform yield in a different environmental conditions, are two common terms used to define genotype reaction in a consequence of environmental changes. Most of the models dealing with stability and adaptability are based on variation sources appearing under the influence of treatment, multivariate effects and residue. No meter which statistical model is used for GE interaction estimation, there is an opinion that no solid proof for the existence of stable genotypes obtained in breeding programs, which make some space for further investigations. There are still questions to answer dealing with definitions, sources of variation, usage value of existent models and interpretation of the results. .

  16. Heart Failure

    Science.gov (United States)

    ... heart failure due to systolic dysfunction. http://www.uptodate.com/home. Accessed Sept. 26, 2014. Colucci WS. ... patient with heart failure or cardiomyopathy. http://www.uptodate.com/home. Accessed Sept. 26, 2014. Colucci WS. ...

  17. HCV genotyping from NGS short reads and its application in genotype detection from HCV mixed infected plasma.

    Science.gov (United States)

    Qiu, Ping; Stevens, Richard; Wei, Bo; Lahser, Fred; Howe, Anita Y M; Klappenbach, Joel A; Marton, Matthew J

    2015-01-01

    Genotyping of hepatitis C virus (HCV) plays an important role in the treatment of HCV. As new genotype-specific treatment options become available, it has become increasingly important to have accurate HCV genotype and subtype information to ensure that the most appropriate treatment regimen is selected. Most current genotyping methods are unable to detect mixed genotypes from two or more HCV infections. Next generation sequencing (NGS) allows for rapid and low cost mass sequencing of viral genomes and provides an opportunity to probe the viral population from a single host. In this paper, the possibility of using short NGS reads for direct HCV genotyping without genome assembly was evaluated. We surveyed the publicly-available genetic content of three HCV drug target regions (NS3, NS5A, NS5B) in terms of whether these genes contained genotype-specific regions that could predict genotype. Six genotypes and 38 subtypes were included in this study. An automated phylogenetic analysis based HCV genotyping method was implemented and used to assess different HCV target gene regions. Candidate regions of 250-bp each were found for all three genes that have enough genetic information to predict HCV genotypes/subtypes. Validation using public datasets shows 100% genotyping accuracy. To test whether these 250-bp regions were sufficient to identify mixed genotypes, we developed a random primer-based method to sequence HCV plasma samples containing mixtures of two HCV genotypes in different ratios. We were able to determine the genotypes without ambiguity and to quantify the ratio of the abundances of the mixed genotypes in the samples. These data provide a proof-of-concept that this random primed, NGS-based short-read genotyping approach does not need prior information about the viral population and is capable of detecting mixed viral infection.

  18. HCV genotyping from NGS short reads and its application in genotype detection from HCV mixed infected plasma.

    Directory of Open Access Journals (Sweden)

    Ping Qiu

    Full Text Available Genotyping of hepatitis C virus (HCV plays an important role in the treatment of HCV. As new genotype-specific treatment options become available, it has become increasingly important to have accurate HCV genotype and subtype information to ensure that the most appropriate treatment regimen is selected. Most current genotyping methods are unable to detect mixed genotypes from two or more HCV infections. Next generation sequencing (NGS allows for rapid and low cost mass sequencing of viral genomes and provides an opportunity to probe the viral population from a single host. In this paper, the possibility of using short NGS reads for direct HCV genotyping without genome assembly was evaluated. We surveyed the publicly-available genetic content of three HCV drug target regions (NS3, NS5A, NS5B in terms of whether these genes contained genotype-specific regions that could predict genotype. Six genotypes and 38 subtypes were included in this study. An automated phylogenetic analysis based HCV genotyping method was implemented and used to assess different HCV target gene regions. Candidate regions of 250-bp each were found for all three genes that have enough genetic information to predict HCV genotypes/subtypes. Validation using public datasets shows 100% genotyping accuracy. To test whether these 250-bp regions were sufficient to identify mixed genotypes, we developed a random primer-based method to sequence HCV plasma samples containing mixtures of two HCV genotypes in different ratios. We were able to determine the genotypes without ambiguity and to quantify the ratio of the abundances of the mixed genotypes in the samples. These data provide a proof-of-concept that this random primed, NGS-based short-read genotyping approach does not need prior information about the viral population and is capable of detecting mixed viral infection.

  19. Systems failure.

    OpenAIRE

    Macleod, Anna

    1998-01-01

    Systems Failure A solo exhibition of new work by Anna Macleod developed in conversation with curator Liz Burns. The Dock, Carrick on Shannon, Co Leitrim. Ireland. 12th February – 17th April 2010. The works for the exhibition Systems Failure include drawings, prints and small constructions that examine the delicate balance that exists between need and aspects of failure rooted in the relationship between humanity and land use. The work seeks to question the relationship between scient...

  20. Relapse of HCV Genotype 1b Infection After Sofosbuvir/Ledipasvir Treatment Presenting as De Novo Cryoglobulinemic Vasculitis

    Science.gov (United States)

    Moreno, Alan D.; Joseph, Nora; Kim, George; Fimmel, Claus J.

    2017-01-01

    Relapse of hepatitis C virus (HCV) genotype 1 infection after combination therapy with sofosbuvir and ledipasvir is unusual. We report a treatment-naïve, non-cirrhotic patient in whom the relapse of genotype 1b HCV infection was accompanied by de novo cryoglobulinemic vasculitis and glomerulonephritis, requiring hemodialysis for acute renal failure. Sequence analysis revealed several resistance-associated variants in the HCV NS5a gene but not in NS3/4A. The patient’s vasculitis was successfully treated with immunosuppression and plasmapheresis, followed by retreatment of HCV with a combination of sofosbuvir, simeprevir, and ribavirin. The patient achieved sustained virological response, recovered his renal function, and remains in remission from cryoglobulinemia. PMID:28184378

  1. APOE Genotyping, Cardiovascular Disease

    Science.gov (United States)

    ... Home Visit Global Sites Search Help? APOE Genotyping, Cardiovascular Disease Share this page: Was this page helpful? Also ... of choice to decrease the risk of developing cardiovascular disease (CVD) . However, there is a wide variability in ...

  2. Heart failure

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    2008275 Relationship of calcineure in mRNA level in peripheral blood and cardiac muscle of patients with heart failure.WANG Mengmeng(王萌萌),et al.Dept Cardiol,Shandong Prov Hosp,Shandong Univ,Jinan 250021.Chin Cir J 2008;23(2):113-116.Objective To study the relationship of calcineurin mRNA level between peripheral lymphocytes and cardiac muscles of patients with chronic heart failure.Methods

  3. Heart failure

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    2008037 Factors associated with efficacy of cardiac resynchronization therapy for patients with congestive heart failure. SHI Haoying(史浩颖), et al. Dept Cardiol, Zhongshan Hosp Fudan Univ, Shanghai 200032. Chin J Cardiol 2007;35(12):1099-1163. Objective The efficacy of cardiac resynchronization therapy (CRT) in patients with congestive heart failure and the potential factors associated with responder or nonresponder were investigated. Methods Fifty

  4. School failure.

    Science.gov (United States)

    Dworkin, P H

    1989-04-01

    Numerous factors may contribute to a child's failure to learn. Certain causes of school failure, such as specific learning disabilities, mental retardation, sensory impairment, and chronic illness may be regarded as intrinsic characteristics of the child. Other causes, such as family dysfunction, social problems, and ineffective schooling, are characteristics of the child's environment. Still other influences on school performance, such as temperamental dysfunction, attention deficits, and emotional illness, may be viewed as the consequence of the interaction between the child and his or her environment. The reasons for a child's school failure must not be considered in isolation but rather within the context of social and environmental circumstances. Evaluation must consider the myriad of reasons for a child's school failure and attempt to identify "clusters" of adverse influences on school performance. Detailed information must be sought from the student, parents, and school system through the history and physical examination. Questionnaires are useful in data gathering. Ancillary methods of assessment that may be of value include neurodevelopmental screening and laboratory studies. Further investigations and referrals, particularly psychoeducational evaluation, are of major importance. Traditional roles of the pediatrician in school failure include the treatment of underlying medical conditions, counseling, the coordination of further investigations and referrals, and the facilitation of communication with community services and resources. Participation with other disciplines in the development of a child's educational plan is feasible and useful.

  5. Respiratory failure

    Institute of Scientific and Technical Information of China (English)

    1997-01-01

    970318 A study on evoked potentials in cor pul-monale patients with chronic respiratory failure.QIAO Hui(乔慧), et al. Beijing Neurosurg Instit,Beijing, 100050. Chin J Geriatr 1997; 16(1): 43-45. Objective: Evoked protential was used to detect thechange of brain function in cor pulmonale patients with

  6. Heart failure

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    2009170 Curcumin attenuates left ventricular dysfunction and remodeling in rabbits with chronic heart failure. TANG Yanhong(唐艳红),et al.Dept Cardiol,Renmin Hosp,Wuhan Univ,Wuhan 430060.Chin J Cardiol,2009;37(3):262-267.

  7. Heart failure

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    2008411 Expression of S100B during heart failure in rats. JIANG Zhenni(蒋珍妮), et al. Dept Cardiol, 2nd Affili Hosp, Zhejiang Univ, Coll Med Hangzhou 310009. Chin J Emerg Med 2008;17(5):475-478. Objective To evaluate the value of S100B gene on cardiovascular remodeling in rats with abdominal aorta coarctation.

  8. Heart failure

    Institute of Scientific and Technical Information of China (English)

    1997-01-01

    970284 Effects of enalapril on heart rate variabilityin patients with congestive heart failure. ZHANGYouhua(章友华), et a1. Dept Cardiol, Cardiovasc Instit& Fuwai Hosp, CAMS & PUMC, Beijing, 100037. ChinCir J 1996; 11(2): 729-732.

  9. Failure Modes

    DEFF Research Database (Denmark)

    Jakobsen, K. P.; Burcharth, H. F.; Ibsen, Lars Bo;

    1999-01-01

    The present appendix contains the derivation of ten different limit state equations divided on three different failure modes. Five of the limit state equations can be used independently of the characteristics of the subsoil, whereas the remaining five can be used for either drained or undrained...

  10. Axiom turkey genotyping array

    Science.gov (United States)

    The Axiom®Turkey Genotyping Array interrogates 643,845 probesets on the array, covering 643,845 SNPs. The array development was led by Dr. Julie Long of the USDA-ARS Beltsville Agricultural Research Center under a public-private partnership with Hendrix Genetics, Aviagen, and Affymetrix. The Turk...

  11. (Brassica napus L.) genotypes

    African Journals Online (AJOL)

    STORAGESEVER

    2009-10-05

    Oct 5, 2009 ... The genetic diversity and relationships among rapeseed genotypes were ... dent of environment and plant growth stage, unlimited ..... interactions that lead to the expression of particular traits .... thesis, Faculty of Agriculture, University of Novi Sad. ... in the U.S. hard red winter wheat cultivars as reveled by.

  12. Hepatitis C virus expressing reporter tagged NS5A protein

    DEFF Research Database (Denmark)

    2014-01-01

    Hepatitis C reporter viruses containing Core through NS2 of prototype isolates of all major HCV genotypes and the remaining genes of isolate JFH1, by insertion of reporter genes in domain III of HCV NS5A were developed. A deletion upstream of the inserted reporter gene sequence conferred favorable...

  13. Renal failure

    Institute of Scientific and Technical Information of China (English)

    1993-01-01

    930150 Epidermal growth factor and its recep-tor in the renal tissue of patients with acute re-nal failure and normal persons.LIU Zhihong(刘志红),et al.Jinling Hosp,Nanjing,210002.Natl Med J China 1992;72(10):593-595.Epidermal growth factor(EGF)and its receptor(EGF-R)were identified by immunohis-tochemical method(4 layer PAP)in the renaltissue specimens obtained from 11 normal kid-neys and 17 cases of acute renal failure(ARF).The quantitative EGF and EGF-R in the tissuewere expressed as positive tubules per mm~2.The amount of EGF and EGF-R in renal tissue

  14. Heart failure

    Institute of Scientific and Technical Information of China (English)

    1992-01-01

    920647 Comparative effects of commonvasodilators on experimental cardiac fai-lure. LI Zhijian (李志坚), et al. Dept Cardiol,2nd Hosp, Tianjin Med Coll. Tianjin Med J1992; 20(8): 456-458. A 9×9 latin square design was employed forcomparing the effects of (1) placebo, (2) nitr-oprusside, (3) phentolamine, (4) isosorbide dini-trate. (5) captopril, (6) captopril-isosorbide

  15. Heart failure

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    2005186 The diagnostic application of bedside measurement of plasma brain natriuretic in patients with heart failure. SHAO Le-wen (邵乐文) , Advanced Ward Dept, 1st Hosp, Med Sch, Zhejiang Univ, Hangzhou 310003. Chin J Intern Med, 2005;44(2): 99-101. Objective: To investigate differential diagnosis value of ultra-rapid bedside measurement of brain na-triuretic peptide (BNP) in patients with dyspnea.

  16. Heart failure

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    2010316 Tissue doppler imaging observation on effect of long-term use of gingko biloba tabtet on left ventricular function in patients with chronic heart failure. ZHANG Hui(张辉),et al. Dept Cardiovasc Med, 2nd Hosp, Hebei Med Univ,Shijiazhuang 050000. Chin J Integr Tradit & West Med 2010;30(5):478-481. Objective To quantitatively observe the effect of long-term

  17. Renal failure

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    2008463 Protective effect of recombination rat augmenter of liver regeneration on kidney in acute renal failure rats. TANG Xiaopeng(唐晓鹏), et al. Dept Nephrol, 2nd Affili Hosp Chongqing Med Univ, Chongqing 400010.Chin J Nephrol 2008;24(6):417-421. Objective To investigate the protective effects of recombination rat augmenter of liver regeneration (rrALR) on tubular cell injury and renal dysfunction

  18. Heart failure - tests

    Science.gov (United States)

    CHF - tests; Congestive heart failure - tests; Cardiomyopathy - tests; HF - tests ... the best test to: Identify which type of heart failure (systolic versus diastolic, valvular) Monitor your heart failure ...

  19. Heart failure - home monitoring

    Science.gov (United States)

    ... failure - discharge Heart failure - fluids and diuretics Heart failure - what to ask ... Medical Center, University of Washington Medical School, Seattle, WA. Also reviewed by David Zieve, MD, ...

  20. SNP genotyping technologies

    DEFF Research Database (Denmark)

    Studer, Bruno; Kölliker, Roland

    2013-01-01

    for this is the availability of high-throughput platforms for multiplexed SNP genotyping. Advancements in these technologies have enabled increased flexibility and throughput, allowing for the generation of adequate SNP marker data at very competitive cost per data point.......In the recent years, single nucleotide polymorphism (SNP) markers have emerged as the marker technology of choice for plant genetics and breeding applications. Besides the efficient technologies available for SNP discovery even in complex genomes, one of the main reasons...

  1. SNP genotyping technologies

    DEFF Research Database (Denmark)

    Studer, Bruno; Kölliker, Roland

    2013-01-01

    In the recent years, single nucleotide polymorphism (SNP) markers have emerged as the marker technology of choice for plant genetics and breeding applications. Besides the efficient technologies available for SNP discovery even in complex genomes, one of the main reasons...... for this is the availability of high-throughput platforms for multiplexed SNP genotyping. Advancements in these technologies have enabled increased flexibility and throughput, allowing for the generation of adequate SNP marker data at very competitive cost per data point....

  2. Susceptibility of biallelic haplotype and genotype frequencies to genotyping error.

    Science.gov (United States)

    Moskvina, Valentina; Schmidt, Karl Michael

    2006-12-01

    With the availability of fast genotyping methods and genomic databases, the search for statistical association of single nucleotide polymorphisms with a complex trait has become an important methodology in medical genetics. However, even fairly rare errors occurring during the genotyping process can lead to spurious association results and decrease in statistical power. We develop a systematic approach to study how genotyping errors change the genotype distribution in a sample. The general M-marker case is reduced to that of a single-marker locus by recognizing the underlying tensor-product structure of the error matrix. Both method and general conclusions apply to the general error model; we give detailed results for allele-based errors of size depending both on the marker locus and the allele present. Multiple errors are treated in terms of the associated diffusion process on the space of genotype distributions. We find that certain genotype and haplotype distributions remain unchanged under genotyping errors, and that genotyping errors generally render the distribution more similar to the stable one. In case-control association studies, this will lead to loss of statistical power for nondifferential genotyping errors and increase in type I error for differential genotyping errors. Moreover, we show that allele-based genotyping errors do not disturb Hardy-Weinberg equilibrium in the genotype distribution. In this setting we also identify maximally affected distributions. As they correspond to situations with rare alleles and marker loci in high linkage disequilibrium, careful checking for genotyping errors is advisable when significant association based on such alleles/haplotypes is observed in association studies.

  3. Genotyping panel for assessing response to cancer chemotherapy

    Directory of Open Access Journals (Sweden)

    Hampel Heather

    2008-06-01

    Full Text Available Abstract Background Variants in numerous genes are thought to affect the success or failure of cancer chemotherapy. Interindividual variability can result from genes involved in drug metabolism and transport, drug targets (receptors, enzymes, etc, and proteins relevant to cell survival (e.g., cell cycle, DNA repair, and apoptosis. The purpose of the current study is to establish a flexible, cost-effective, high-throughput genotyping platform for candidate genes involved in chemoresistance and -sensitivity, and treatment outcomes. Methods We have adopted SNPlex for genotyping 432 single nucleotide polymorphisms (SNPs in 160 candidate genes implicated in response to anticancer chemotherapy. Results The genotyping panels were applied to 39 patients with chronic lymphocytic leukemia undergoing flavopiridol chemotherapy, and 90 patients with colorectal cancer. 408 SNPs (94% produced successful genotyping results. Additional genotyping methods were established for polymorphisms undetectable by SNPlex, including multiplexed SNaPshot for CYP2D6 SNPs, and PCR amplification with fluorescently labeled primers for the UGT1A1 promoter (TAnTAA repeat polymorphism. Conclusion This genotyping panel is useful for supporting clinical anticancer drug trials to identify polymorphisms that contribute to interindividual variability in drug response. Availability of population genetic data across multiple studies has the potential to yield genetic biomarkers for optimizing anticancer therapy.

  4. Visible Genotype Sensor Array

    Directory of Open Access Journals (Sweden)

    Takashi Imai

    2008-04-01

    Full Text Available A visible sensor array system for simultaneous multiple SNP genotyping has been developed using a new plastic base with specific surface chemistry. Discrimination of SNP alleles is carried out by an allele-specific extension reaction using immobilized oligonucleotide primers. The 3’-ends of oligonucleotide primers are modified with a locked nucleic acid to enhance their efficiency in allelic discrimination. Biotin-dUTPs included in the reaction mixture are selectively incorporated into extending primer sequences and are utilized as tags for alkaline phosphatase-mediated precipitation of colored chemical substrates onto the surface of the plastic base. The visible precipitates allow immediate inspection of typing results by the naked eye and easy recording by a digital camera equipped on a commercial mobile phone. Up to four individuals can be analyzed on a single sensor array and multiple sensor arrays can be handled in a single operation. All of the reactions can be performed within one hour using conventional laboratory instruments. This visible genotype sensor array is suitable for “focused genomics” that follows “comprehensive genomics”.

  5. Respiratory failure

    Institute of Scientific and Technical Information of China (English)

    1993-01-01

    930118 Facial or nasal mask pressure supportventilation in managing acute exacerbation ofchronic respiratory failure in COPD patients.CHEN Rongchang(陈荣昌),et al.GuangzhouInstit Respir Dis,Guangzhou 510120.Chin Tu-berc & Respir Dis 1992;15(5)285-287.Eleven COPD patients(age:65±9 yrs)withacute exacerbation of chronic respiratory failure(PaCO2 11.3±1.1kPa)were treated with maskpressure support ventilation,another 10 similarpatients(age:68±12yrs)served as controls.Bi-PAP ventilator was used with the followingmodifications:(1)Non-rehreathing valve set-in proximal to mask;(2)5 LPM oxygen flow de-livered into mask to reduce the dead space ef-fect.Mask ventilation was given 2-3 hours ev-ery time and 1-2 times daily for 7 days.Syn-

  6. STR MARKERS. GENOTYPING APPLICATIONS

    Directory of Open Access Journals (Sweden)

    I. O. Sirbu

    2001-01-01

    Full Text Available STR (short tandem repeats loci consist of short, repetitive sequence elements of 2-8 bp in length. These abundant repeats are well distributed throughout the human genome and are rich source of highly polymorphic markers. There are literally hundreds of STR systems which have been mapped throughout the human genome. Several dozen have been investigated for application to human identity testing. These STR loci are found on almost every chromosome in the genome. They may be amplified using a variety of PCR primers. Tetranucleotide repeats have been most popular among forensic scientists due to their fidelity in PCR amplification although some tri- and pentanucleotide repeats are also in use. In this paper we intend (far from being exhaustive to present a synthesis of the characteristics of these genetic markers and their applications in genotyping, giving as an example the use of the STRs in a paternity testing case.

  7. HBV genotypic variability in Cuba.

    Science.gov (United States)

    Loureiro, Carmen L; Aguilar, Julio C; Aguiar, Jorge; Muzio, Verena; Pentón, Eduardo; Garcia, Daymir; Guillen, Gerardo; Pujol, Flor H

    2015-01-01

    The genetic diversity of HBV in human population is often a reflection of its genetic admixture. The aim of this study was to explore the genotypic diversity of HBV in Cuba. The S genomic region of Cuban HBV isolates was sequenced and for selected isolates the complete genome or precore-core sequence was analyzed. The most frequent genotype was A (167/250, 67%), mainly A2 (149, 60%) but also A1 and one A4. A total of 77 isolates were classified as genotype D (31%), with co-circulation of several subgenotypes (56 D4, 2 D1, 5 D2, 7 D3/6 and 7 D7). Three isolates belonged to genotype E, two to H and one to B3. Complete genome sequence analysis of selected isolates confirmed the phylogenetic analysis performed with the S region. Mutations or polymorphisms in precore region were more common among genotype D compared to genotype A isolates. The HBV genotypic distribution in this Caribbean island correlates with the Y lineage genetic background of the population, where a European and African origin prevails. HBV genotypes E, B3 and H isolates might represent more recent introductions.

  8. HBV Genotypic Variability in Cuba

    Science.gov (United States)

    Loureiro, Carmen L.; Aguilar, Julio C.; Aguiar, Jorge; Muzio, Verena; Pentón, Eduardo; Garcia, Daymir; Guillen, Gerardo; Pujol, Flor H.

    2015-01-01

    The genetic diversity of HBV in human population is often a reflection of its genetic admixture. The aim of this study was to explore the genotypic diversity of HBV in Cuba. The S genomic region of Cuban HBV isolates was sequenced and for selected isolates the complete genome or precore-core sequence was analyzed. The most frequent genotype was A (167/250, 67%), mainly A2 (149, 60%) but also A1 and one A4. A total of 77 isolates were classified as genotype D (31%), with co-circulation of several subgenotypes (56 D4, 2 D1, 5 D2, 7 D3/6 and 7 D7). Three isolates belonged to genotype E, two to H and one to B3. Complete genome sequence analysis of selected isolates confirmed the phylogenetic analysis performed with the S region. Mutations or polymorphisms in precore region were more common among genotype D compared to genotype A isolates. The HBV genotypic distribution in this Caribbean island correlates with the Y lineage genetic background of the population, where a European and African origin prevails. HBV genotypes E, B3 and H isolates might represent more recent introductions. PMID:25742179

  9. Kidney (Renal) Failure

    Science.gov (United States)

    ... How is kidney failure treated? What is kidney (renal) failure? The kidneys are designed to maintain proper fluid ... marrow and strengthen the bones. The term kidney (renal) failure describes a situation in which the kidneys have ...

  10. Acute kidney failure

    Science.gov (United States)

    Kidney failure; Renal failure; Renal failure - acute; ARF; Kidney injury - acute ... There are many possible causes of kidney damage. They include: ... cholesterol (cholesterol emboli) Decreased blood flow due to very ...

  11. Living with Heart Failure

    Science.gov (United States)

    ... page from the NHLBI on Twitter. Living With Heart Failure Currently, heart failure has no cure. You'll ... avoid harmful side effects. Take Steps To Prevent Heart Failure From Getting Worse Certain actions can worsen your ...

  12. Classes of Heart Failure

    Science.gov (United States)

    ... Disease Venous Thromboembolism Aortic Aneurysm More Classes of Heart Failure Updated:Sep 28,2016 Doctors usually classify patients' ... Blood Pressure Tracker Find additional helpful resources here Heart Failure • Home • About Heart Failure Introduction Types of Heart ...

  13. About Heart Failure

    Science.gov (United States)

    ... talk about your health and the medicines About Heart Failure Heart failure is a disease where the heart cannot do ... very important for your health. common causes of heart failure are diseases or conditions that damage the heart. ...

  14. What Is Heart Failure?

    Science.gov (United States)

    ... page from the NHLBI on Twitter. What Is Heart Failure? Heart failure is a condition in which the heart can' ... force. Some people have both problems. The term "heart failure" doesn't mean that your heart has stopped ...

  15. Acute Kidney Failure

    Science.gov (United States)

    ... out of balance. Acute kidney failure — also called acute renal failure or acute kidney injury — develops rapidly over ... 2015. Palevsky PM. Definition of acute kidney injury (acute renal failure). http://www.uptodate.com/home. Accessed April ...

  16. Complex Pattern of Resistance-Associated Substitutions of Hepatitis C Virus after Daclatasvir/Asunaprevir Treatment Failure

    Science.gov (United States)

    Hasebe, Chitomi; Osaki, Yukio; Joko, Kouji; Yagisawa, Hitoshi; Sakita, Shinya; Okushin, Hiroaki; Satou, Takashi; Hisai, Hiroyuki; Abe, Takehiko; Tsuji, Keiji; Tamada, Takashi; Kobashi, Haruhiko; Mitsuda, Akeri; Ide, Yasushi; Ogawa, Chikara; Tsuruta, Syotaro; Takaguchi, Kouichi; Murakawa, Miyako; Asahina, Yasuhiro; Enomoto, Nobuyuki; Izumi, Namiki

    2016-01-01

    Backgrounds & Aims We aimed to clarify the characteristics of resistance-associated substitutions (RASs) after treatment failure with NS5A inhibitor, daclatasvir (DCV) in combination with NS3/4A inhibitor, asunaprevir (ASV), in patients with chronic hepatitis C virus genotype 1b infection. Methods This is a nationwide multicenter study conducted by the Japanese Red Cross Liver Study Group. The sera were obtained from 68 patients with virological failure after 24 weeks of DCV/ASV treatment. RASs in NS5A and NS3 were determined by population sequencing. Results The frequency of signature RASs at position D168 of NS3 was 68%, and at positions L31 and Y93 of NS5A was 79 and 76%, respectively. The frequency of dual signature RASs in NS5A (L31-RAS and Y93-RAS) was 63%. RASs at L28, R30, P32, Q54, P58, and A92 in addition to dual signature RAS were detected in 5, 5, 1, 22, 2, and 0 patients, respectively. In total, triple, quadruple, and quintuple RASs in combination with dual signature RAS were detected in 35, 10, and 1.5% patients, respectively. These RASs were detected in patients without baseline RASs or who prematurely discontinued therapy. Co-existence of D168 RAS in NS3 and L31 and/or Y93 RAS in NS5A was observed in 62% of patients. Conclusion Treatment-emergent RASs after failure with DCV/ASV combination therapy are highly complex in more than 50% of the patients. The identification of complex RAS patterns, which may indicate high levels of resistance to NS5A inhibitors, highlights the need for RAS sequencing when considering re-treatment with regimens including NS5A inhibitors. PMID:27776192

  17. HCV Antibody Response and Genotype Distribution in Different Areas and Races of China

    OpenAIRE

    Leili Jia, Jiyun Yu, Hongbin Song, Xuelin Liu, Weina Ma, Yuanyong Xu, Chuanfu Zhang, Shicun Dong, Qiao Li

    2009-01-01

    Hepatitis C virus (HCV) heterogeneity accounts for the failure of effective vaccine development and the lack of successful anti-viral therapy in some patients. Little is known about the immune response to HCV peptides and the region or race specific genotypes in China. The objective of this study was to characterize HCV antibody immune response to HCV peptides and HCV genotypes in different regions and races of China. A total of 363 serum samples were collected from HCV carriers in 6 regions ...

  18. Genotype transposer: automated genotype manipulation for linkage disequilibrium analysis.

    Science.gov (United States)

    Cox, D G; Canzian, F

    2001-08-01

    The purpose of this work is to provide the modern molecular geneticist with tools to perform more efficient and more accurate analysis of the genotype data they produce. By using Microsoft Excel macros written in Visual Basic, we can translate genotype data into a form readable by the versatile software 'Arlequin', read the Arlequin output, calculate statistics of linkage disequilibrium, and put the results in a format for viewing with the software 'GOLD'. The software is available by FTP at: ftp://xcsg.iarc.fr/cox/Genotype_Transposer/. Detailed instruction and examples are available at: ftp://xcsg.iarc.fr/cox/Genotype&_Transposer/. Arlequin is available at: http://lgb.unige.ch/arlequin/. GOLD is available at: http://www.well.ox.ac.uk/asthma/GOLD/.

  19. Types of Heart Failure

    Science.gov (United States)

    ... Disease Venous Thromboembolism Aortic Aneurysm More Types of Heart Failure Updated:Feb 9,2017 Left-sided heart failure ... making. This content was last reviewed April 2015. Heart Failure • Home • About Heart Failure Introduction Types of Heart ...

  20. Understanding chronic heart failure

    OpenAIRE

    Fenton, Matthew; Burch, Michael

    2007-01-01

    The key principles of chronic heart failure and the development of clinical management strategies are described. The physiological changes in chronic heart failure and the clinical management of children with heart failure are considered, but the treatment of heart failure related to congenital heart disease or the intensive care management of heart failure are not mentioned as both topics require consideration in their own right. A greater understanding of the maladaptive responses to chroni...

  1. Immune mediated liver failure

    OpenAIRE

    Wang, Xiaojing; Ning, Qin

    2014-01-01

    Liver failure is a clinical syndrome of various etiologies, manifesting as jaundice, encephalopathy, coagulopathy and circulatory dysfunction, which result in subsequent multiorgan failure. Clinically, liver failure is classified into four categories: acute, subacute, acute-on-chronic and chronic liver failure. Massive hepatocyte death is considered to be the core event in the development of liver failure, which occurs when the extent of hepatocyte death is beyond the liver regenerative capac...

  2. Understanding contraceptive failure

    OpenAIRE

    Trussell, James

    2009-01-01

    Contraceptive failure is a major source of unintended pregnancy. This chapter will review sources of data and measurement of contraceptive failure, summarize results from the literature on the risks of contraceptive failure during typical and perfect use for available methods of contraception, provide a tool for communicating risks of contraceptive failure to clients, examine determinants of contraceptive failure, and identify methodological pitfalls in the published literature.

  3. Efficient cell culture system for hepatitis C virus genotype 5A

    DEFF Research Database (Denmark)

    2013-01-01

    of in vitro transcripts in Huh7.5 cells, production of infectious viruses was delayed. However, in subsequent viral passages efficient spread of infection and HCV RNA titers as high as for J6/JFH were obtained. Infectivity titers were at all time points analyzed comparable to J6/JFH control virus. Sequence...

  4. Successful Treatment of Mixed Hepatitis C Genotypes in a Cirrhotic Patient With an All-Oral, Interferon-Free Regimen

    Science.gov (United States)

    Ahmed Sakr, Ayman; Hanifi, Jasmine M.

    2017-01-01

    Mixed hepatitis C virus (HCV) genotype infection is emerging with improved methods of detection. It is commonly seen in hemodialysis patients and intravenous drug users due to repeated HCV exposure and absence of protective immunity, and can contribute to treatment failure. Direct-acting antiviral regimens have been extensively studied in patients with different individual HCV genotypes; however, there are no reported data on their use in patients with mixed HCV genotype. We present a case of mixed HCV genotype 1a and 2 infection in a decompensated cirrhotic patient treated successfully with sofosbuvir, ledipasvir, and ribavirin. PMID:28184373

  5. Transforming microbial genotyping: a robotic pipeline for genotyping bacterial strains.

    Directory of Open Access Journals (Sweden)

    Brian O'Farrell

    Full Text Available Microbial genotyping increasingly deals with large numbers of samples, and data are commonly evaluated by unstructured approaches, such as spread-sheets. The efficiency, reliability and throughput of genotyping would benefit from the automation of manual manipulations within the context of sophisticated data storage. We developed a medium- throughput genotyping pipeline for MultiLocus Sequence Typing (MLST of bacterial pathogens. This pipeline was implemented through a combination of four automated liquid handling systems, a Laboratory Information Management System (LIMS consisting of a variety of dedicated commercial operating systems and programs, including a Sample Management System, plus numerous Python scripts. All tubes and microwell racks were bar-coded and their locations and status were recorded in the LIMS. We also created a hierarchical set of items that could be used to represent bacterial species, their products and experiments. The LIMS allowed reliable, semi-automated, traceable bacterial genotyping from initial single colony isolation and sub-cultivation through DNA extraction and normalization to PCRs, sequencing and MLST sequence trace evaluation. We also describe robotic sequencing to facilitate cherrypicking of sequence dropouts. This pipeline is user-friendly, with a throughput of 96 strains within 10 working days at a total cost of 200,000 items were processed by two to three people. Our sophisticated automated pipeline can be implemented by a small microbiology group without extensive external support, and provides a general framework for semi-automated bacterial genotyping of large numbers of samples at low cost.

  6. NS5A Resistance: Clinical Implications and Treatment Possibilities.

    Science.gov (United States)

    Calleja, José Luis; Llerena, Susana; Perelló, Christie; Crespo, Javier

    2016-01-01

    Treatments with interferon-free direct-acting antiviral agents have high efficacy, with sustained virological response rates of more than 90%. Nevertheless, they fail to eliminate the infection in 1-7% of patients. The majority of virological failures are due to relapse following treatment discontinuation, while virological rebound during therapy is rare. Although not the only factor, the presence of resistance-associated variants is one of the major causes for said failure. Resistance-associated variants affect the sequence involved in protein synthesis on which different direct-acting antiviral agents act (NS3/4A, NS5A, NS5B). Of all these variants, the ones with the greatest impact are resistance-associated variants that affect the NS5A region due to their long-term persistence. In this article we will describe the most significant NS5A resistance-associated variants, the clinical relevance of their detection both before and after treatment, their persistence over time, and lastly, we will devote particular attention to discussing what approach to adopt when dealing with treatment failure to an antiviral regimen that includes NS5A inhibitors.

  7. Haplotypes versus genotypes on pedigrees

    Directory of Open Access Journals (Sweden)

    Kirkpatrick Bonnie B

    2011-04-01

    Full Text Available Abstract Background Genome sequencing will soon produce haplotype data for individuals. For pedigrees of related individuals, sequencing appears to be an attractive alternative to genotyping. However, methods for pedigree analysis with haplotype data have not yet been developed, and the computational complexity of such problems has been an open question. Furthermore, it is not clear in which scenarios haplotype data would provide better estimates than genotype data for quantities such as recombination rates. Results To answer these questions, a reduction is given from genotype problem instances to haplotype problem instances, and it is shown that solving the haplotype problem yields the solution to the genotype problem, up to constant factors or coefficients. The pedigree analysis problems we will consider are the likelihood, maximum probability haplotype, and minimum recombination haplotype problems. Conclusions Two algorithms are introduced: an exponential-time hidden Markov model (HMM for haplotype data where some individuals are untyped, and a linear-time algorithm for pedigrees having haplotype data for all individuals. Recombination estimates from the general haplotype HMM algorithm are compared to recombination estimates produced by a genotype HMM. Having haplotype data on all individuals produces better estimates. However, having several untyped individuals can drastically reduce the utility of haplotype data.

  8. Differential expression of eIF5A-1 and eIF5A-2 in human cancer cells

    Science.gov (United States)

    Clement, Paul M. J.; Johansson, Hans E.; Wolff, Edith C.; Park, Myung H.

    2015-01-01

    Eukaryotic translation initiation factor 5A (eIF5A) is the only cellular protein that contains the unusual amino acid hypusine [Nε-(4-amino-2-hydroxybutyl)lysine]. Vertebrates carry two genes that encode two eIF5A isoforms, eIF5A-1 and eIF5A-2, which, in humans, are 84% identical. eIF5A-1 mRNA (1.3 kb) and protein (18 kDa) are constitutively expressed in human cells. In contrast, expression of eIF5A-2 mRNA (0.7–5.6 kb) and eIF5A-2 protein (20 kDa) varies widely. Whereas eIF5A-2 mRNA was demonstrable in most cells, eIF5A-2 protein was detectable only in the colorectal and ovarian cancer-derived cell lines SW-480 and UACC-1598, which showed high overexpression of eIF5A-2 mRNA. Multiple forms of eIF5A-2 mRNA (5.6, 3.8, 1.6 and 0.7 kb) were identified as the products of one gene with various lengths of 3′-UTR, resulting from the use of different polyadenylation (AAUAAA) signals. The eIF5A-1 and eIF5A-2 precursor proteins were modified comparably in UACC-1598 cells and both were similarly stable. When eIF5A-1 and eIF5A-2 coding sequences were expressed from mammalian vectors in 293T cells, eIF5A-2 precursor was synthesized at a level comparable to that of eIF5A-1 precursor, indicating that the elements causing inefficient translation of eIF5A-2 mRNA reside outside of the open reading frame. On sucrose gradient separation of cytoplasmic RNA, only a small portion of total eIF5A-2 mRNA was associated with the polysomal fraction, compared with a much larger portion of eIF5A-1 mRNA in the polysomes. These findings suggest that the failure to detect eIF5A-2 protein even in eIF5A-2 mRNA positive cells is, at least in part, due to inefficient translation. PMID:16519677

  9. [Understanding heart failure].

    Science.gov (United States)

    Boo, José Fernando Guadalajara

    2006-01-01

    Heart failure is a disease with several definitions. The term "heart failure" is used by has brougth about confusion in the terminology. For this reason, the value of the ejection fraction (< 0.40 or < 0.35) is used in most meganalyses on the treatment of heart failure, avoiding the term "heart failure" that is a confounding concept. In this paper we carefully analyze the meaning of contractility, ventricular function or performance, preload, afterload, heart failure, compensation mechanisms in heart failure, myocardial oxygen consumption, inadequate, adequate and inappropriate hypertrophy, systole, diastole, compliance, problems of relaxation, and diastolic dysfunction. Their definitions are supported by the original scientific descriptions in an attempt to clarify the concepts about ventricular function and heart failure and, in this way, use the same scientific language about the meaning of ventricular function, heart failure, and diastolic dysfunction.

  10. Real System Failures

    Data.gov (United States)

    National Aeronautics and Space Administration — This resource area contains descriptions of actual electronic systems failure scenarios with an emphasis on the diversity of failure modes and effects that can...

  11. Contraceptive failure in China.

    Science.gov (United States)

    Wang, Duolao

    2002-09-01

    This study examines patterns and differentials of contraceptive failure rates by method and characteristics of users, using the Chinese Two-per-Thousand Fertility Survey data. The results show that contraceptive failure rates for modern methods including sterilization are some of the highest in the world. The first year failure rates are 4.2% for male sterilization, 0.7% for female sterilization, 10.3% for IUD, 14.5% for pill, and 19.0% for condom. There are also some differentials in contraceptive failure rates by users' sociodemographic and fertility characteristics. Contraceptive failure rate declines with women's age for all reversible methods. Rural women have higher sterilization, IUD, and condom contraceptive failure rates than urban women. Women with two or more children have a higher failure rate for sterilization methods but have lower failure rates for other methods.

  12. Acute liver failure

    DEFF Research Database (Denmark)

    Larsen, Fin Stolze; Bjerring, Peter Nissen

    2011-01-01

    Acute liver failure (ALF) results in a multitude of serious complications that often lead to multi-organ failure. This brief review focuses on the pathophysiological processes in ALF and how to manage these.......Acute liver failure (ALF) results in a multitude of serious complications that often lead to multi-organ failure. This brief review focuses on the pathophysiological processes in ALF and how to manage these....

  13. In Support of Failure

    Science.gov (United States)

    Carr, Allison

    2013-01-01

    In this essay, I propose a concerted effort to begin devising a theory and pedagogy of failure. I review the discourse of failure in Western culture as well as in composition pedagogy, ultimately suggesting that failure is not simply a judgement or indication of rank but is a relational, affect-bearing concept with tremendous relevance to…

  14. Evaluation and management of early virological failure.

    Science.gov (United States)

    Sax, Paul E

    2006-09-01

    To describe the causes, evaluation, and management of early virological failure in patients treated with their first antiretroviral regimen. Combination antiretroviral therapy predictably induces a rapid virological response, with the majority of patients achieving an undetectable HIV-RNA load by week 24. In clinical trials and cohorts, rates of virological suppression have improved over time. Poor adherence to therapy remains the most common cause of virological failure, and genotype resistance testing is a critical step in evaluating the optimal subsequent approach. Most studies suggest that transient HIV-RNA elevations do not warrant changing treatment, and may be a consequence of laboratory variation. For those who experience virological failure, resistance to individual components of the antiretroviral regimen is dependent on the initial choice of treatment. Once virological failure is confirmed and adherence issues addressed, a prompt change in treatment is warranted to limit the selection of further drug resistance. Resistance that occurs with early virological failure follows typical patterns, with limited resistance to most antiretroviral agents in the nucleoside reverse transcriptase and protease inhibitor classes. The likelihood of achieving virological suppression with subsequent regimens should be high so long as adherence can be assured.

  15. Population samples and genotyping technology.

    Science.gov (United States)

    Mack, S J; Sanchez-Mazas, A; Single, R M; Meyer, D; Hill, J; Dron, H A; Jani, A J; Thomson, G; Erlich, H A

    2007-04-01

    The 14th International HLA (human leukocyte antigen) Immunogenetics Workshop (14th-IHIWS) Biostatistics and Anthropology/Human Genetic Diversity project continues the population sampling, genotype data generation, and biostatistic analyses of the 13th International Histocompatibility Workshop Anthropology/Human Genetic Diversity Component, with the overall goal of further characterizing global HLA allele and haplotype diversity and better describing the relationships between major histocompatibility complex diversity, geography, linguistics, and population history. Since the 13th Workshop, new investigators have and continue to be recruited to the project and new high-resolution class I and class II genotype data are being generated for 112 population samples from around the world.

  16. Is the COL5A1 rs12722 gene polymorphism associated with running economy?

    Directory of Open Access Journals (Sweden)

    Rômulo Bertuzzi

    Full Text Available The COL5A1 rs12722 polymorphism is considered to be a novel genetic marker for endurance running performance. It has been postulated that COL5A1 rs12722 may influence the elasticity of tendons and the energetic cost of running. To date, there are no experimental data in the literature supporting the relationship between range of motion, running economy, and the COL5A1 rs12722 gene polymorphism. Therefore, the main purpose of the current study was to analyze the influence of the COL5A1rs12722 polymorphism on running economy and range of motion. One hundred and fifty (n = 150 physically active young men performed the following tests: a a maximal incremental treadmill test, b two constant-speed running tests (10 km · h(-1 and 12 km · h(-1 to determine the running economy, and c a sit-and-reach test to determine the range of motion. All of the subjects were genotyped for the COL5A1 rs12722 single-nucleotide polymorphism. The genotype frequencies were TT = 27.9%, CT = 55.8%, and CC = 16.3%. There were no significant differences between COL5A1 genotypes for running economy measured at 10 km · h(-1 (p = 0.232 and 12 km · h(-1 (p = 0.259. Similarly, there were no significant differences between COL5A1 genotypes for range of motion (p = 0.337. These findings suggest that the previous relationship reported between COL5A1 rs12722 genotypes and running endurance performance might not be mediated by the energetic cost of running.

  17. Pooled DNA genotyping on Affymetrix SNP genotyping arrays

    Directory of Open Access Journals (Sweden)

    Owen Michael J

    2006-02-01

    Full Text Available Abstract Background Genotyping technology has advanced such that genome-wide association studies of complex diseases based upon dense marker maps are now technically feasible. However, the cost of such projects remains high. Pooled DNA genotyping offers the possibility of applying the same technologies at a fraction of the cost, and there is some evidence that certain ultra-high throughput platforms also perform with an acceptable accuracy. However, thus far, this conclusion is based upon published data concerning only a small number of SNPs. Results In the current study we prepared DNA pools from the parents and from the offspring of 30 parent-child trios that have been extensively genotyped by the HapMap project. We analysed the two pools with Affymetrix 10 K Xba 142 2.0 Arrays. The availability of the HapMap data allowed us to validate the performance of 6843 SNPs for which we had both complete individual and pooled genotyping data. Pooled analyses averaged over 5–6 microarrays resulted in highly reproducible results. Moreover, the accuracy of estimating differences in allele frequency between pools using this ultra-high throughput system was comparable with previous reports of pooling based upon lower throughput platforms, with an average error for the predicted allelic frequencies differences between the two pools of 1.37% and with 95% of SNPs showing an error of Conclusion Genotyping thousands of SNPs with DNA pooling using Affymetrix microarrays produces highly accurate results and can be used for genome-wide association studies.

  18. Bone Marrow Failure Secondary to Cytokinesis Failure

    Science.gov (United States)

    2015-12-01

    have assessed the role of FA pathway in mitosis and confirmed that murine FA-deficient hematopoietic stem cells exhibit p53- mediated growth defects...results suggest that bone marrow failure in FA may be caused, in part, by p53- mediated cellular defects and underscore the importance of... mediated apoptosis of HSCs due to cytokinesis failure. The major goal of the project was to assess whether the p53- mediated apoptosis due to

  19. FTO genotype and weight loss

    DEFF Research Database (Denmark)

    Livingstone, Katherine M; Celis-Morales, Carlos; Papandonatos, George D

    2016-01-01

    OBJECTIVE: To assess the effect of the FTO genotype on weight loss after dietary, physical activity, or drug based interventions in randomised controlled trials. DESIGN: Systematic review and random effects meta-analysis of individual participant data from randomised controlled trials. DATA SOURC...

  20. FTO genotype and weight loss

    DEFF Research Database (Denmark)

    Livingstone, Katherine M; Celis-Morales, Carlos; Papandonatos, George D;

    2016-01-01

    OBJECTIVE: To assess the effect of the FTO genotype on weight loss after dietary, physical activity, or drug based interventions in randomised controlled trials. DESIGN: Systematic review and random effects meta-analysis of individual participant data from randomised controlled trials. DATA SOURC...

  1. Microsatellite genotyping of carnation varieties

    NARCIS (Netherlands)

    Smulders, M.J.M.; Noordijk, Y.; Rus-Kortekaas, W.; Bredemeijer, G.M.M.; Vosman, B.

    2003-01-01

    A set of 11 sequence-tagged microsatellite markers for carnation (Dianthus caryophyllus) was developed using a DNA library enriched for microsatellites. Supplemented with three markers derived from sequence database entries, these were used to genotype carnation varieties using a semi-automated fluo

  2. Genotyping with TaqMAMA.

    Science.gov (United States)

    Li, Baohui; Kadura, Ibrahim; Fu, Dong-Jing; Watson, David E

    2004-02-01

    TaqMAMA combines the quantitative strengths of TaqMan with the allele-specific PCR of MAMA. In this article we develop TaqMAMA as a technique for screening human DNA samples for known genetic polymorphisms. In the first set of experiments, plasmids that model all types of genetic polymorphisms were used to understand the relationship between TaqMAMA primer/template mismatches and their strength of allelic discrimination. These data can be used to improve allelic discrimination of other primer extension genotyping methodologies through directed use of nucleotide mismatches. We used the data to derive a guide for TaqMAMA primer design and DNA strand selection for TaqMAMA genotyping assays. The guide was then used to develop assays for 11 known and novel human genetic polymorphisms. Genotypes were assigned quickly and accurately in all cases. TaqMAMA genotyping assays require minimal development time, have a high probability of success, produce reliable data that are straightforward to analyze, and are very cost-competitive.

  3. What factors determine the severity of hepatitis A-related acute liver failure?

    Science.gov (United States)

    Ajmera, V.; Xia, G.; Vaughan, G.; Forbi, J. C.; Ganova-Raeva, L. M.; Khudyakov, Y.; Opio, C. K.; Taylor, R.; Restrepo, R.; Munoz, S.; Fontana, R. J.; Lee, W. M.

    2016-01-01

    SUMMARY The reason(s) that hepatitis A virus (HAV) infection may progress infrequently to acute liver failure are poorly understood. We examined host and viral factors in 29 consecutive adult patients with HAV-associated acute liver failure enrolled at 10 sites participating in the US ALF Study Group. Eighteen of twenty-four acute liver failure sera were PCR positive while six had no detectable virus. HAV genotype was determined using phylogenetic analysis and the full-length genome sequences of the HAV from a cute liver failure sera were compared to those from self-limited acute HAV cases selected from the CDC database. We found that rates of nucleotide substitution did not vary significantly between the liver failure and non-liver failure cases and there was no significant variation in amino acid sequences between the two groups. Four of 18 HAV isolates were subgenotype IB, acquired from the same study site over a 3.5-year period. Sub-genotype IB was found more frequently among acute liver failure cases compared to the non-liver failure cases (chi-square test, P viral clearance and its association with poor outcomes in acute liver failure as well as the finding of familial cases imply a possible host genetic predisposition that contributes to a fulminant course. Recurrent cases of the rare subgenotype IB over several years at a single centre imply a community reservoir of infection and possible increased pathogenicity of certain infrequent viral genotypes. PMID:21143345

  4. Managing Feelings about Heart Failure

    Science.gov (United States)

    ... About Heart Failure Module 6: Managing Feelings About Heart Failure Download Module Order Hardcopy Heart failure can cause ... professional help for emotional problems. Common Feelings About Heart Failure It is common for people to feel depressed ...

  5. Genotype × genotype interactions between the toxic cyanobacterium Microcystis and its grazer, the waterflea Daphnia

    Science.gov (United States)

    Lemaire, Veerle; Brusciotti, Silvia; van Gremberghe, Ineke; Vyverman, Wim; Vanoverbeke, Joost; De Meester, Luc

    2012-01-01

    Toxic algal blooms are an important problem worldwide. The literature on toxic cyanobacteria blooms in inland waters reports widely divergent results on whether zooplankton can control cyanobacteria blooms or cyanobacteria suppress zooplankton by their toxins. Here we test whether this may be due to genotype × genotype interactions, in which interactions between the large-bodied and efficient grazer Daphnia and the widespread cyanobacterium Microcystis are not only dependent on Microcystis strain or Daphnia genotype but are specific to genotype × genotype combinations. We show that genotype × genotype interactions are important in explaining mortality in short-time exposures of Daphnia to Microcystis. These genotype × genotype interactions may result in local coadaptation and a geographic mosaic of coevolution. Genotype × genotype interactions can explain why the literature on zooplankton–cyanobacteria interactions is seemingly inconsistent, and provide hope that zooplankton can contribute to the suppression of cyanobacteria blooms in restoration projects. PMID:25568039

  6. HBV genotypes prevalence, precore and basal core mutants in Morocco.

    Science.gov (United States)

    Baha, Warda; Ennaji, My Mustapha; Lazar, Fatiha; Melloul, Marouane; El Fahime, Elmostafa; El Malki, Abdelouahad; Bennani, Abdelouaheb

    2012-08-01

    The study of hepatitis B virus (HBV) genomic heterogeneity has become a major issue in investigations aimed at understanding the relationship between HBV mutants and the wide spectrum of clinical and pathological conditions associated with HBV infection. The objective of the current study was to find out the pattern of HBV genotypes circulating in Morocco and to investigate the precore (PC) and basal core promoter (BCP) mutants' status in Moroccan chronic hepatitis B patients. Viral genotypes were determined in 221 chronic carriers using INNO-LiPA HBV assay and hemi-nested PCR. Phylogenetic analysis was performed in 70 samples, and multiplex PCR method was used to confirm some genotyping results. PC and CP mutants were determined using Inno-Lipa. All isolates were successfully genotyped. The genotype distribution was D in 90.45% of cases, A (5.9%), E (1 case), and mixed genotypes (5 A/D and 2 D/F) in 3.17% patients. HBV carried in the HBV/D samples could be assigned to D7 (63.3%), D1 (32.7%) and 2% of strains to each D4 and D5, all HBV/A belonged to A2 subgenotype and HBV/E strain could not be sub-genotyped. In 70 studied strains, HBV mutants were detected in 88.6% of cases; PC mutants were detected in (40%) of patients and 21.5% present a mixture of wild type and G1896A mutation. BCP mutants were observed in 65.7% of cases, 22.9% were found to have the T1762/1764A double mutation, 18.6% had A1762/1764T mutation and 22.9% of patients showed the A1762T/G1764A double mutation with either A1762T/G1764T mutation. Co-infection by PC and BCP mutants was detected in 52.9% of cases. Movement from place to place most likely shapes the observed genotype distribution and consequent prevalence of genotypes other than A2 or D7 in this population. High circulation of PC and BCP mutants is common in chronic hepatitis B infection in Morocco.

  7. The Genetic Variability of Prolactin and Signal Transducers and Activators of Transcription 5A (STAT5A Genes in Bali Cattle

    Directory of Open Access Journals (Sweden)

    K. A. Paramitasari

    2015-04-01

    Full Text Available The aim of this study was to identify the genetic variability of PRL and STAT5A genes in Bali cattle from Bali, West Nusa Tenggara (NTB, and South Sulawesi (SS using PCR-RFLP method. A total of 262 Bali cattle were identified using RsaI (PRL and AvaI (STAT5A restriction enzymes. PRL gene exon 3, PRL gene exon 4, and STAT5A gene exon 7 amplifications resulted fragments with the lengths of 156 bp, 294 bp, 215 bp, respectively. Genotyping of PRL gene both at exon 3 and 4 produced three genotypes in Bali population and two genotypes in NTB and SS population. For the PRL gene, frequencies of A allele (exon 3 and G allele (exon 4 were dominant to the B allele (exon 3 and A allele (exon 4 across all populations. The results showed that STAT5A|AvaI loci had monomorphic C allele. Heterozygosity values were found low at both exons 3 and 4 of PRL gene in all population. Sequence analysis results of PRL gene both for exons 3 and 4 showed that there was a mutation between adenine (A and guanine (G bases in the RsaI recognized site, whereas in STAT5A gene we can confirm the existence of AvaI restriction site (C|CCGAG.

  8. Resistance remains a problem in treatment failure

    Directory of Open Access Journals (Sweden)

    Martin Obermeier

    2014-11-01

    Full Text Available Introduction: Proven resistance against HIV drugs, either by phenotyping or genotyping is a rare event in clinical trials. The overall assumption of drug resistance disappearing is additionally driven by the recommendations to screen for transmitted drug resistance, leading to large numbers of examinations with relatively low rates of resistance. Goal of our analysis was to assess if drug resistance in treatment failure is also decreasing outside of clinical trials. Materials and Methods: The MIB database at timepoint of analysis consists of data from 2876 HIV infected patients. Besides various laboratory parameters, clinical data and treatment history is included. HIV-1 protease and reverse transcriptase sequences were analyzed using the HIV-GRADE drug resistance algorithm. As in only a small number of patients genotypic resistance testing for integrase inhibitors was performed, mainly due to reimbursement reasons, it was assumed that failing treatment on a previous integrase inhibitor containing regimen is equate to resistance. Results: Of the 2876 patients in the database, 220 had a treatment change due to treatment failure between 2009 and 2012, a genotypic resistance testing at an appropriate timepoint of maximum four weeks before treatment change and a treatment duration of at least six months before treatment failure. In 2009, 61% of patients showed no drug resistance while 39% showed resistance against one or more drug classes (two or more drug classes: 19.5%; three or more drug classes: 2.4%, four drug classes 2.4%. In 2012, no resistance was found in 52% of patients while resistance against three or more drug classes was found in nearly 14% of patients (one or more: 48%; two or more 23%; four classes: 4.5%. Conclusions: Treatment failure with viral load sufficiently high for drug resistance testing was not frequently observed in our database. Nevertheless, treatment failure was often associated with drug resistance against at least one

  9. Mouse models of SCN5A-related cardiac arrhythmias

    Directory of Open Access Journals (Sweden)

    Flavien eCharpentier

    2012-06-01

    Full Text Available Mutations of SCN5A gene, which encodes the α-subunit of the voltage-gated Na+ channel NaV1.5, underlie hereditary cardiac arrhythmic syndromes such as the type 3 long QT syndrome, cardiac conduction diseases, the Brugada syndrome, the sick sinus syndrome, atrial standstill and numerous overlap syndromes. Patch-clamp studies in heterologous expression systems have provided important information to understand the genotype-phenotype relationships of these diseases. However, they could not clarify how SCN5A mutations can be responsible for such a large spectrum of diseases, for the late age of onset or the progressiveness of some of these diseases and for the overlapping syndromes. Genetically modified mice rapidly appeared as promising tools for understanding the pathophysiological mechanisms of cardiac SCN5A-related arrhythmic syndromes and several mouse models have been established. This paper reviews some of the results obtained on these models that, for most of them, recapitulate the clinical phenotypes of the patients. It also points out that these models also have their own limitations. Overall, mouse models appear as powerful tools to elucidate the pathophysiological mechanisms of SCN5A-related diseases and offer the opportunity to investigate the secondary cellular consequences of SCN5A mutations such as the expression remodelling of other genes that might participate to the overall phenotype. Finally, they constitute useful tools for addressing the role of genetic and environmental modifiers on cardiac electrical activity.

  10. Bituminous Pavement Failures

    Directory of Open Access Journals (Sweden)

    Surajo Abubakar Wada

    2016-02-01

    Full Text Available Pavement deterioration is a serious problem for road and traffic sector in almost every country, the most affecting causes of bituminous pavement failures have been studied in this paper. The paper describes the lessons learnt from pavement failures and problems experienced. Failures of bituminous pavements are caused due to many reasons or combination of reasons. Application of correction in the existing surface will enhance the life of maintenance works as well as that of strengthening layer. Along with the maintenance techniques there are various methods for pavement preservation which will help in enhancing the life of pavement and delaying of its failure.This paper discusses the possible causes of pavement failures, and recommendbetter ways to minimize and hopefully eliminate the causes of failures in bituminous pavements.

  11. Failure Analysis Handbook

    Science.gov (United States)

    1989-08-18

    47) described a method they called the "failure-experience matrix." This matrix was a three-dimensional array of cells , with failure modes along one...Russo, DFat ý , compiled by McDonnell-Dcuglas Astrovautics Cmpany, Huntington Beach, California, published by Metals and Ceramics Information Center...matrix." This matrix was a three dimensional array of cells , with failure modes along one axis, ryont "mechardcal function along a second axis and

  12. Failure to thrive.

    Science.gov (United States)

    Krugman, Scott D; Dubowitz, Howard

    2003-09-01

    Failure to thrive is a condition commonly seen by primary care physicians. Prompt diagnosis and intervention are important for preventing malnutrition and developmental sequelae. Medical and social factors often contribute to failure to thrive. Either extreme of parental attention (neglect or hypervigilance) can lead to failure to thrive. About 25 percent of normal infants will shift to a lower growth percentile in the first two years of life and then follow that percentile; this should not be diagnosed as failure to thrive. Infants with Down syndrome, intrauterine growth retardation, or premature birth follow different growth patterns than normal infants. Many infants with failure to thrive are not identified unless careful attention is paid to plotting growth parameters at routine checkups. A thorough history is the best guide to establishing the etiology of the failure to thrive and directing further evaluation and management. All children with failure to thrive need additional calories for catch-up growth (typically 150 percent of the caloric requirement for their expected, not actual, weight). Few need laboratory evaluation. Hospitalization is rarely required and is indicated only for severe failure to thrive and for those whose safety is a concern. A multidisciplinary approach is recommended when failure to thrive persists despite intervention or when it is severe.

  13. FTO genotype and weight loss

    DEFF Research Database (Denmark)

    Livingstone, Katherine M; Celis-Morales, Carlos; Papandonatos, George D;

    2016-01-01

    OBJECTIVE: To assess the effect of the FTO genotype on weight loss after dietary, physical activity, or drug based interventions in randomised controlled trials. DESIGN: Systematic review and random effects meta-analysis of individual participant data from randomised controlled trials. DATA SOURCES...... well to dietary, physical activity, or drug based weight loss interventions and thus genetic predisposition to obesity associated with the FTO minor allele can be at least partly counteracted through such interventions. SYSTEMATIC REVIEW REGISTRATION: PROSPERO CRD42015015969.......: Ovid Medline, Scopus, Embase, and Cochrane from inception to November 2015. ELIGIBILITY CRITERIA FOR STUDY SELECTION: Randomised controlled trials in overweight or obese adults reporting reduction in body mass index, body weight, or waist circumference by FTO genotype (rs9939609 or a proxy) after...

  14. Two-mode clustering of genotype by trait and genotype by environment data

    NARCIS (Netherlands)

    Hageman, J.A.; Malosetti, M.; Eeuwijk, van F.A.

    2012-01-01

    In this paper, we demonstrate the use of two-mode clustering for genotype by trait and genotype by environment data. In contrast to two separate (one mode) clusterings on genotypes or traits/environments, two-mode clustering simultaneously produces homogeneous groups of genotypes and traits/environm

  15. Selection of common bean (Phaseolus vulgaris L.) genotypes using a genotype plus genotype x environment interaction biplot.

    Science.gov (United States)

    Corrêa, A M; Teodoro, P E; Gonçalves, M C; Santos, A; Torres, F E

    2016-08-05

    Recently, the genotype plus genotype x environment interaction (GGE) biplot methodology has been used to investigate genotype x environment interactions in several crop species, but has not been applied to the common bean (Phaseolus vulgaris L.) crop in Brazil. The aim of this study was to identify common bean genotypes that exhibit high grain yield and stability in the State of Mato Grosso do Sul, Brazil. We conducted 12 trials from 2000 to 2006 in the municipalities of Aquidauana and Dourados, and evaluated 13 genotypes in a randomized block design with three replications. Grain yield data were subjected to individual and joint analyses of variance. After analyzing the GE interaction, the adaptability and phenotypic stability of the common bean genotypes were analyzed using GGE biplot methodology. The genotypes EMGOPA-201, Xamego, and Aporé are recommended for growing in Mato Grosso do Sul, because they exhibited high grain yield and phenotypic stability.

  16. SCN5A mutation in patients with Brugada electrocardiographic pattern induced by fever

    Institute of Scientific and Technical Information of China (English)

    俞建华

    2014-01-01

    Objective To explore the relationship between SCN5A,SCN1b,SCN3b and GPD1L genotypes and the risk of malignant arrhythmia in patients with Brugada electrocardiographic pattern induced by fever.Methods The clinical data and peripheral blood of patients with Brugada electrocardiographic pattern induced by fever were

  17. HIV-1 genotypic resistance profile of patients failing antiretroviral therapy in Paraná, Brazil

    Directory of Open Access Journals (Sweden)

    Paula Virginia Michelon Toledo

    2010-08-01

    Full Text Available Antiretroviral therapy (ART has reduced morbidity and mortality related to human immunodeficiency virus (HIV infection, but in spite of this advance, HIV mutations decrease antiretroviral susceptibility, thus contributing to treatment failure in patients. Genotyping HIV-1 allows the selection of new drugs after initial drug failure. This study evaluated the genotypic profile of HIV-1 isolates from treated (drug-experienced patients in Paraná, Brazil. The prevalence of mutations in reverse transcriptase (RT and protease (PR genes were assessed. We analyzed 467 genotypes of patients with HIV-1 viral loads above 1,000 copies/mL. Mutations at HIV-1 RT and PR genes and previously used ART regimens were recorded. The most prevalent RT mutations were: 184V (68.31%, 215YF (51.6%, 103NS (46%, 41L (39.4%, 67N (38.54%, 210W (23.5%, 190ASE (23.2%, and 181C (17.4%. PR mutations were 90M (33.33%, 82ATFS (29%, 46I (26.8% and 54V (22.2%. The prevalence of mutations was in line with previous national and international reports, except to nonnucleoside analogue reverse transcriptase inhibitors related mutations, which were more prevalent in this study. Previous exposure to antiretroviral drugs was associated with genotypic resistance to specific drugs, leading to treatment failure in HIV patients.

  18. Chronic heart failure

    African Journals Online (AJOL)

    population, and up to 10% in people aged 75 years and older. It is also estimated that ... The first step in the development of heart failure is an injury to the myocardium ... treatment of heart failure by blocking the compensatory mechanisms with ... pulmonary disease, cognitive dysfunction, depression, chronic kidney disease ...

  19. Heart failure overview

    Science.gov (United States)

    ... symptoms) You feel a severe crushing chest pain Prevention Most cases of heart failure can be prevented by living a healthy lifestyle and taking steps aimed at reducing your risk for heart disease . . Alternative Names CHF; Congestive heart failure; Left-sided ...

  20. Progress in genotyping of Chlamydia trachomatis

    Institute of Scientific and Technical Information of China (English)

    Xia Yong; Xiong Likuan

    2014-01-01

    Objective To review the common genotyping techniques of Chlamydia trachomatis in terms of their principles,characteristics,applications and limitations.Data sources Data used in this review were mainly from English literatures of PubMed database.The search terms were "Chlamydia trachomatis" and "genotyping".Meanwhile,data from World Health Organization were also cited.Study selection Original articles and reviews relevant to present review's theme were selected.Results Different genotyping techniques were applied on different occasions according to their characteristics,especially in epidemiological studies worldwide,which pushed the study of Chlamydia trachomatis forward greatly.In addition,summaries of some epidemiological studies by genotyping were also included in this work for reference and comparison.Conclusions A clear understanding of common genotyping techniques could be helpful to genotype C.trachomatis more appropriately and effectively.Furthermore,more studies on the association of genotypes of Ch/amydia trachomatis with clinical manifestations should be performed.

  1. Dual daclatasvir and sofosbuvir for treatment of genotype 3 chronic hepatitis C virus infection.

    Science.gov (United States)

    Sundaram, Vinay; Kowdley, Kris V

    2016-01-01

    Chronic hepatitis C virus (HCV) infection is one of the most common etiologies of liver-related mortality throughout the world. Traditionally, therapy has been focused on pegylated interferon in combination with ribavirin, with clinical trials demonstrating that HCV genotype 1 had the lowest response rate (40-50%), while genotype 3 had an intermediate response rate (60-70%). Recently, significant advances have been made with all-oral direct-acting antiviral (DAA) therapy, which have significantly improved cure rates for HCV genotype 1. Accordingly, HCV genotype 3 is now potentially the most difficult to treat. One of the most potent DAA medications is sofosbuvir, a pan-genotypic nucleotide analogue that inhibits the NS5B polymerase of HCV. Daclatasvir, a pan-genotypic inhibitor of the HCV NS5A replication complex, was recently approved in the United States for treatment of HCV genotype 3 in conjunction with sofosbuvir. This combination may provide a powerful tool in the treatment of HCV genotype 3.

  2. Managing first-line failure.

    Science.gov (United States)

    Cooper, David A

    2014-01-01

    WHO standard of care for failure of a first regimen, usually 2N(t)RTI's and an NNRTI, consists of a ritonavir-boosted protease inhibitor with a change in N(t)RTI's. Until recently, there was no evidence to support these recommendations which were based on expert opinion. Two large randomized clinical trials, SECOND LINE and EARNEST both showed excellent response rates (>80%) for the WHO standard of care and indicated that a novel regimen of a boosted protease inhibitor with an integrase inhibitor had equal efficacy with no difference in toxicity. In EARNEST, a third arm consisting of induction with the combined protease and integrase inhibitor followed by protease inhibitor monotherapy maintenance was inferior and led to substantial (20%) protease inhibitor resistance. These studies confirm the validity of the current recommendations of WHO and point to a novel public health approach of using two new classes for second line when standard first-line therapy has failed, which avoids resistance genotyping. Notwithstanding, adherence must be stressed in those failing first-line treatments. Protease inhibitor monotherapy is not suitable for a public health approach in low- and middle-income countries.

  3. Managing first-line failure

    Directory of Open Access Journals (Sweden)

    David A Cooper

    2014-11-01

    Full Text Available WHO standard of care for failure of a first regimen, usually 2N(tRTI's and an NNRTI, consists of a ritonavir-boosted protease inhibitor with a change in N(tRTI's. Until recently, there was no evidence to support these recommendations which were based on expert opinion. Two large randomized clinical trials, SECOND LINE and EARNEST both showed excellent response rates (>80% for the WHO standard of care and indicated that a novel regimen of a boosted protease inhibitor with an integrase inhibitor had equal efficacy with no difference in toxicity. In EARNEST, a third arm consisting of induction with the combined protease and integrase inhibitor followed by protease inhibitor monotherapy maintenance was inferior and led to substantial (20% protease inhibitor resistance. These studies confirm the validity of the current recommendations of WHO and point to a novel public health approach of using two new classes for second line when standard first-line therapy has failed, which avoids resistance genotyping. Notwithstanding, adherence must be stressed in those failing first-line treatments. Protease inhibitor monotherapy is not suitable for a public health approach in low- and middle-income countries.

  4. HCV Antibody Response and Genotype Distribution in Different Areas and Races of China

    Directory of Open Access Journals (Sweden)

    Leili Jia, Jiyun Yu, Jinliang Yang, Hongbin Song, Xuelin Liu, Yong Wang, Yuanyong Xu, Chuanfu Zhang, Yanwei Zhong, Qiao Li

    2009-01-01

    Full Text Available Hepatitis C virus (HCV heterogeneity accounts for the failure of effective vaccine development and the lack of successful anti-viral therapy in some patients. Little is known about the immune response to HCV peptides and the region or race specific genotypes in China. The objective of this study was to characterize HCV antibody immune response to HCV peptides and HCV genotypes in different regions and races of China. A total of 363 serum samples were collected from HCV carriers in 6 regions in China. The immune response to HCV peptides was evaluated by ELISA. HCV genotypes were examined using nested RT-PCR. We found that the anti-HCV antibody neutralization rates were significantly different among the serum samples from different areas or from different races in the same area. For samples from Tibet and Sinkiang, the rates of neutralization by HCV peptides were only 3.2% and 30.8%, respectively. The genotypes of samples from Tibet and Sinkiang were apparently heterogeneic and included type I, II, III and multiple types (I/II/III, I/II, I/III, II/III. One specific sample with multiple-genotype (I/II/III HCV infection was found to consist of type I, II, III, II/III and an unclassified genotype. These studies indicate that the anti-HCV antibody immune response to HCV peptides varied across regions and among races. The distribution of HCV genotypes among Tibetans in Tibet and Uighurs in Sinkiang was different from that in the inner areas of China. In addition, a “master” genotype, type II, was found to exist in HCV infection with multiple HCV genotypes.

  5. HCV antibody response and genotype distribution in different areas and races of China.

    Science.gov (United States)

    Jia, Leili; Yu, Jiyun; Yang, Jinliang; Song, Hongbin; Liu, Xuelin; Wang, Yong; Xu, Yuanyong; Zhang, Chuanfu; Zhong, Yanwei; Li, Qiao

    2009-06-13

    Hepatitis C virus (HCV) heterogeneity accounts for the failure of effective vaccine development and the lack of successful anti-viral therapy in some patients. Little is known about the immune response to HCV peptides and the region or race specific genotypes in China. The objective of this study was to characterize HCV antibody immune response to HCV peptides and HCV genotypes in different regions and races of China. A total of 363 serum samples were collected from HCV carriers in 6 regions in China. The immune response to HCV peptides was evaluated by ELISA. HCV genotypes were examined using nested RT-PCR. We found that the anti-HCV antibody neutralization rates were significantly different among the serum samples from different areas or from different races in the same area. For samples from Tibet and Sinkiang, the rates of neutralization by HCV peptides were only 3.2% and 30.8%, respectively. The genotypes of samples from Tibet and Sinkiang were apparently heterogeneic and included type I, II, III and multiple types (I/II/III, I/II, I/III, II/III). One specific sample with multiple-genotype (I/II/III) HCV infection was found to consist of type I, II, III, II/III and an unclassified genotype. These studies indicate that the anti-HCV antibody immune response to HCV peptides varied across regions and among races. The distribution of HCV genotypes among Tibetans in Tibet and Uighurs in Sinkiang was different from that in the inner areas of China. In addition, a "master" genotype, type II, was found to exist in HCV infection with multiple HCV genotypes.

  6. Frequency distribution of hepatitis C virus genotypes in different geographical regions of Pakistan and their possible routes of transmission

    Directory of Open Access Journals (Sweden)

    Riazuddin Sheikh

    2008-05-01

    Full Text Available Abstract Background Information regarding hepatitis C virus genotypes and subtypes circulating in Pakistan and various risk factors for their transmission are not known well. The specific objective of this study was to find out the frequency of various HCV genotypes present in well-characterized Pakistani HCV isolates and their possible routes of transmission. Methods A total of 3351 serum samples were tested by type-specific genotyping assay. Out of 3351 HCV RNA positive patients, 2039 were males and 1312 were females. As regard as genotyped samples, 2165 belonged to Punjab region, 823 belonged to N.W.F.P., 239 to Sindh and 124 patients were from Balochistan. Results Out of the total 3351 tested serum samples, type-specific PCR fragments were observed in 3150 (94.00% serum samples. The distribution of genotypes of the typeable samples as determined by this assay, was as follows: 1664 (49.05% genotype 3a; 592 (17.66% genotype 3b; 280 (8.35% genotype 1a; 252 (7.52% genotype 2a; 101 (3.01% genotype 1b; 50 (1.49% with genotype 4; 25 (0.75% with 3c; 27 (0.80% genotype 2b; 6 (0.18% with subtype 5a; 5 (0.15% genotype 1c; 4 (0.12% with subtype 6a; 3 (0.09% genotype 2c; and 161 (4.80% patients were infected with mixed infection. Two hundred and one (5.99% serum samples were found untypeable by the present genotyping system. More than 86% and 72% patients with genotypes 3a and 3b respectively had received multiple injections in past. For genotypes 1a and 1b the route of transmission was major/minor surgery along with unknown reasons. Majority of the cases with type 2a, 2b and indeterminate genotypes were sporadic. Mixed infections were common in thalassaemic patients. Conclusion The most common HCV genotype in Pakistan is type 3a. Regional difference in genotypes was observed only in Balochistan province of Pakistan. More than 70% of the cases were acquired in hospitals through reuse of needles/syringes and major/minor surgery that is very common in this

  7. [Heart failure and comorbidities].

    Science.gov (United States)

    Boully, Clémence; Hanon, Olivier

    2015-03-01

    Heart failure is a frequent disease in the elderly. Its clinical presentation is less typical and the prognosis more severe than in younger subjects because heart failure occurs in patients with multiple comorbidities. A comprehensive geriatric assessment should therefore be performed to detect the vulnerabilities and manage the comorbidities. The main diseases associated with heart failure are dementia, depression, malnutrition, atrial fibrillation, coronary artery disease, orthostatic hypotension, renal failure, anemia and iron deficiency. Comorbidities worsen heart failure and makes its treatment more difficult. The identification and treatment of comorbidities improve the prognosis in terms of mortality but especially in terms of quality of life. Caution with drugs is necessary because of pharmacokinetic or pharmacodynamic changes related to aging and the comorbidities. In this context, clinical and laboratory monitoring should be increased, mostly during an acute event (acute heart failure, infection, dehydration, fall, new therapy…). Therefore, the follow-up of elderly patients with heart failure requires a multidisciplinary approach that involves close cooperation between cardiologists, geriatricians, general practitioners, nurses, and pharmacists.

  8. Damage mechanics - failure modes

    Energy Technology Data Exchange (ETDEWEB)

    Krajcinovic, D.; Vujosevic, M. [Arizona State Univ., Tempe, AZ (United States)

    1996-12-31

    The present study summarizes the results of the DOE sponsored research program focused on the brittle failure of solids with disordered microstructure. The failure is related to the stochastic processes on the microstructural scale; namely, the nucleation and growth of microcracks. The intrinsic failure modes, such as the percolation, localization and creep rupture, are studied by emphasizing the effect of the micro-structural disorder. A rich spectrum of physical phenomena and new concepts that emerges from this research demonstrates the reasons behind the limitations of traditional, deterministic, and local continuum models.

  9. Are Sema5a mutant mice a good model of autism? A behavioral analysis of sensory systems, emotionality and cognition.

    Science.gov (United States)

    Gunn, Rhian K; Huentelman, Matthew J; Brown, Richard E

    2011-11-20

    Semaphorin 5A (Sema5A) expression is reduced in the brain of individuals with autism, thus mice with reduced Sema5A levels may serve as a model of this neurodevelopmental disorder. We tested male and female Sema5a knockout mice (B6.129P2SEMA5A()/J) and C57BL/6J controls for emotionality, visual ability, prepulse inhibition, motor learning and cognition. Overall, there were only two genotype differences in emotionality: Sema5a mutant mice had more stretch-attend postures in the elevated plus-maze and more defecations in the open field. All mice could see, but Sema5a mice had better visual ability than C57BL/6J mice. There were no genotype differences in sensory-motor gating. Sema5a mice showed higher levels of activity in the elevated plus-maze and light/dark transition box, and there were sex by genotype differences in the Rotarod, suggesting a sex difference in balance and coordination differentially affected by Sema5a. There were no genotype effects on cognition: Sema5a mice did not differ from C57BL/6J in the Morris water maze, set-shifting or cued and contextual fear conditioning. In the social recognition test, all mice preferred social stimuli, but there was no preference for social novelty, thus the Sema5A mice do not have a deficit in social behavior. Overall, there were a number of sex differences, with females showing greater activity and males performing better in tests of spatial learning and memory, but no deficits in the behavior of Sema5A mice. We conclude that the Sema5a mice do not meet the behavioral criteria for a mouse model of autism. Copyright © 2011 Elsevier B.V. All rights reserved.

  10. Rotavirus genotypes in Belarus, 2008-2012.

    Science.gov (United States)

    Semeiko, Galina V; Yermalovich, Marina A; Poliakova, Nadezhda; Mijatovic-Rustempasic, Slavica; Kerin, Tara K; Wasley, Annemarie; Videbaek, Dovile; Gentsch, Jon R; Bowen, Michael D; Samoilovich, Elena O

    2014-12-01

    This study describes group A rotavirus (RVA) genotype prevalence in Belarus from 2008 to 2012. In 2008, data from 3 sites in Belarus (Brest, Mogilev, Minsk) indicated that G4P[8] was the predominant genotype. Data from Minsk (2008-2012) showed that G4P[8] was the predominant RVA genotype in all years except in 2011 when G3P[8] was most frequently detected. Other RVA genotypes common in Europe (G1P[8], G2P[4]) were detected each year of the study. This study reveals the dominance of genotype G4P[8] in Belarus and helps to establish the baseline genotype prevalence prior to RVA vaccine introduction in the country.

  11. Grain yield stability of early maize genotypes

    Directory of Open Access Journals (Sweden)

    Chitra Bahadur Kunwar

    2016-12-01

    Full Text Available The objective of this study was to estimate grain yield stability of early maize genotypes. Five early maize genotypes namely Pool-17, Arun1EV, Arun-4, Arun-2 and Farmer’s variety were evaluated using Randomized Complete Block Design along with three replications at four different locations namely Rampur, Rajahar, Pakhribas and Kabre districts of Nepal during summer seasons of three consecutive years from 2010 to 2012 under farmer’s fields. Genotype and genotype × environment (GGE biplot was used to identify superior genotype for grain yield and stability pattern. The genotypes Arun-1 EV and Arun-4 were better adapted for Kabre and Pakhribas where as pool-17 for Rajahar environments. The overall findings showed that Arun-1EV was more stable followed by Arun-2 therefore these two varieties can be recommended to farmers for cultivation in both environments.

  12. Advanced Heart Failure

    Science.gov (United States)

    ... patients and their doctors, making good decisions requires teamwork. Through shared decision making, doctors and patients consider ... Heart Failure and Knowing Your Options Planning Ahead Communicating With Your Healthcare Provider Overcoming Barriers to Shared ...

  13. Hyperkalemia in Heart Failure.

    Science.gov (United States)

    Sarwar, Chaudhry M S; Papadimitriou, Lampros; Pitt, Bertram; Piña, Ileana; Zannad, Faiez; Anker, Stefan D; Gheorghiade, Mihai; Butler, Javed

    2016-10-01

    Disorders of potassium homeostasis can potentiate the already elevated risk of arrhythmia in heart failure. Heart failure patients have a high prevalence of chronic kidney disease, which further heightens the risk of hyperkalemia, especially when renin-angiotensin-aldosterone system inhibitors are used. Acute treatment for hyperkalemia may not be tolerated in the long term. Recent data for patiromer and sodium zirconium cyclosilicate, used to treat and prevent high serum potassium levels on a more chronic basis, have sparked interest in the treatment of hyperkalemia, as well as the potential use of renin-angiotensin-aldosterone system inhibitors in patients who were previously unable to take these drugs or tolerated only low doses. This review discusses the epidemiology, pathophysiology, and outcomes of hyperkalemia in heart failure; provides an overview of traditional and novel ways to approach management of hyperkalemia; and discusses the need for further research to optimally treat heart failure.

  14. Heart failure - medicines

    Science.gov (United States)

    ... are working and to measure your potassium levels. Beta Blockers Beta blockers slow your heart rate and decrease the strength ... muscle contracts in the short term. Long term beta blockers help keep your heart failure from becoming worse. ...

  15. Central oxygen pipeline failure

    African Journals Online (AJOL)

    Anaesthetic and critical care staff play a governing role in the comprehension of a ... complete central oxygen pipeline failure occurred throughout. Tygerberg Hospital. ..... emergency stations and at plant room emergency supply manifolds.

  16. Acute heart failure syndrome

    African Journals Online (AJOL)

    tandfonline.com/ ... When heart failure develops gradually, there is time for the compensatory ... of this can be seen in acute brain injury, some forms of takotsubo syndrome or .... reduce blood pressure in cases presenting with elevated blood pressure.

  17. Pathophysiology of heart failure.

    Science.gov (United States)

    Chiariello, M; Perrone-Filardi, P

    1999-01-01

    Heart failure is a leading cause of mortality and morbidity in Western countries. Common etiology is mostly represented by ischemic and hypertensive heart disease. Clinically, heart failure can be defined as an impaired cardiac performance, unable to meet the energy requirements of the periphery. Pathophysiologically, the clinical onset of heart failure symptoms already represents an advanced stage of disease when compensatory mechanisms triggered by the underlying decrease in contractility are no longer capable of maintaining adequate cardiac performance during exercise and, subsequently, under resting conditions. Independent of its underlying etiology, cardiac failure is always characterized by an impairment in the intrinsic contractility of myocytes. As a consequence of reduced contractility, a number of central and peripheral compensatory mechanisms take place that are capable of effectively counteracting reduced intravascular intrinsic performance for a long period of time. Among them, recruitment of preload reserve, enhanced neurohormonal stimulation and cardiac hypertrophy are the most important. All of them, however, also carry unfavorable effects that contribute to further deterioration of cardiac function. In fact, increased end-diastolic volume determines increased wall stress that further reduces systolic performance; sympathetic and angiotensin stimulation increases peripheral resistance and contributes to increase volume expansion; hypertrophic myocytes demonstrate impaired intrinsic contractility and relaxation, and hypertrophy causes a clinically relevant deterioration of ventricular relaxation and compliance that substantially participates in increased end-diastolic pressure, and, therefore, to limited exercise performance. Diastolic dysfunction usually accompanies systolic dysfunction, although in some cases it may represent the prevalent mechanism of congestive heart failure in patients in whom systolic performance is preserved. Biological causes

  18. Renal failure (chronic)

    OpenAIRE

    Clase, Catherine

    2011-01-01

    Chronic renal failure is characterised by a gradual and sustained decline in renal clearance or glomerular filtration rate (GFR). Continued progression of renal failure will lead to renal function too low to sustain healthy life. In developed countries, such people will be offered renal replacement therapy in the form of dialysis or renal transplantation. Requirement for dialysis or transplantation is termed end-stage renal disease (ESRD).Diabetes, glomerulonephritis, hypertension, pyelone...

  19. Lungs in Heart Failure

    Directory of Open Access Journals (Sweden)

    Anna Apostolo

    2012-01-01

    Full Text Available Lung function abnormalities both at rest and during exercise are frequently observed in patients with chronic heart failure, also in the absence of respiratory disease. Alterations of respiratory mechanics and of gas exchange capacity are strictly related to heart failure. Severe heart failure patients often show a restrictive respiratory pattern, secondary to heart enlargement and increased lung fluids, and impairment of alveolar-capillary gas diffusion, mainly due to an increased resistance to molecular diffusion across the alveolar capillary membrane. Reduced gas diffusion contributes to exercise intolerance and to a worse prognosis. Cardiopulmonary exercise test is considered the “gold standard” when studying the cardiovascular, pulmonary, and metabolic adaptations to exercise in cardiac patients. During exercise, hyperventilation and consequent reduction of ventilation efficiency are often observed in heart failure patients, resulting in an increased slope of ventilation/carbon dioxide (VE/VCO2 relationship. Ventilatory efficiency is as strong prognostic and an important stratification marker. This paper describes the pulmonary abnormalities at rest and during exercise in the patients with heart failure, highlighting the principal diagnostic tools for evaluation of lungs function, the possible pharmacological interventions, and the parameters that could be useful in prognostic assessment of heart failure patients.

  20. Hepatitis C virus genotypes in Myanmar.

    Science.gov (United States)

    Win, Nan Nwe; Kanda, Tatsuo; Nakamoto, Shingo; Yokosuka, Osamu; Shirasawa, Hiroshi

    2016-07-21

    Myanmar is adjacent to India, Bangladesh, Thailand, Laos and China. In Myanmar, the prevalence of hepatitis C virus (HCV) infection is 2%, and HCV infection accounts for 25% of hepatocellular carcinoma. In this study, we reviewed the prevalence of HCV genotypes in Myanmar. HCV genotypes 1, 3 and 6 were observed in volunteer blood donors in and around the Myanmar city of Yangon. Although there are several reports of HCV genotype 6 and its variants in Myanmar, the distribution of the HCV genotypes has not been well documented in areas other than Yangon. Previous studies showed that treatment with peginterferon and a weight-based dose of ribavirin for 24 or 48 wk could lead to an 80%-100% sustained virological response (SVR) rates in Myanmar. Current interferon-free treatments could lead to higher SVR rates (90%-95%) in patients infected with almost all HCV genotypes other than HCV genotype 3. In an era of heavy reliance on direct-acting antivirals against HCV, there is an increasing need to measure HCV genotypes, and this need will also increase specifically in Myanmar. Current available information of HCV genotypes were mostly from Yangon and other countries than Myanmar. The prevalence of HCV genotypes in Myanmar should be determined.

  1. Direct-acting Antiviral Agents Resistance-associated Polymorphisms in Chinese Treatment-na(i)ve Patients Infected with Genotype 1b Hepatitis C Virus

    Institute of Scientific and Technical Information of China (English)

    Ye Wang; Hui-Ying Rao; Xing-Wang Xie; Lai Wei

    2015-01-01

    Background:It has been reported that several baseline polymorphisms of direct-acting antivirals (DAAs) agents resistance-associated variants (RAVs) would affect the treatment outcomes of patients chronically infected with hepatitis C virus (CHC).The aim of this study is to investigate the prevalence of DAAs RAVs in treatment-na(i)ve GT1b CHC patients.Methods:Direct sequencing and ultra-deep sequencing of the HCV NS3,NS5A,and NS5B gene were performed in baseline serum samples of treatment-ha(i)ve patients infected with genotype lb hepatitis C virus (HCVs).Results:One hundred and sixty CHC patients were studied.Complete sequence information was obtained for 145 patients (NS3),148 patients (NS5A),and 137 patients (NS5B).Treatment-failure associated variants of DAAs were detected:56.6% (82/145) of the patients presented S122G for simeprevir (NS3 protease inhibitor);10.1% (14/148) of the patients presented Y93H for daclatasvir and ledipasvir (NS5A protein inhibitors);94.2% (129/137) of the patients presented C316N for sofosbuvir (NS5B polymerase inhibitor).Nearly,all of the DAAs RAVs detected by ultra-deep sequencing could be detected by direct sequencing.Conclusions:The majority of genotype lb CHC patients in China present a virus population carrying HCV DAAs RAVs.Pretreatment sequencing of HCV genome might need to be performed when patients infected with GTlb HCV receiving DAAs-containing regimens in China.Population sequencing would be quite quantified for the work.

  2. Efficient hepatitis c virus genotype 1b core-NS5A recombinants permit efficacy testing of protease and NS5A inhibitors

    DEFF Research Database (Denmark)

    Pham, Long V.; Ramirez Almeida, Santseharay; Carlsen, Thomas H R

    2017-01-01

    cell culture adaptive substitutions A1226G, R1496L, and Q1773H. These viruses spread efficiently in Huh7.5 cells by acquiring additional adaptive substitutions, and final recombinants yielded peak supernatant infectivity titers of 4 to 5 log10 focus-forming units (FFU)/ml. We subsequently succeeded...

  3. Synergistic effect of stromelysin-1 (matrix metalloproteinase-3 promoter (-1171 5A->6A polymorphism in oral submucous fibrosis and head and neck lesions

    Directory of Open Access Journals (Sweden)

    Shukla Shirish

    2010-07-01

    Full Text Available Abstract Background Matrix metalloproteinases (MMPs are enzymes that degrade all the components of extra cellular matrix and collagen. Various types of MMPs are known to be expressed and activated in patients with oral submucous fibrosis (OSMF as well as head and neck squamous cell carcinoma (HNSCC. The purpose of this study was to asses the association of the single nucleotide polymorphism (SNP adenosine insertion/deletion polymorphism (-1171 5A->6A in the MMP-3 promoter region in these lesions. Methods MMP-3 SNP was genotyped by polymerase chain reaction-restriction fragment polymorphism (PCR-RFLP analysis in a case control study consisting of 362 participants; 101 cases of OSMF, 135 of HNSCC and 126 controls, compared for age, sex and habits. ROC distribution was plotted to assess the contributions of genetic variation in MMP-3 genotypes with relation to age. Results Analysis of MMP 3 (-1171 5A->6A polymorphism revealed the frequency of 5A allele in OSMF, HNSCC and controls to be 0.15, 0.13 and 0.07, respectively. A significant difference was found in 5A genotype frequency between OSMF (5A genotype frequency = 0.15, p = 0.01, OR = 2.26, 95% CI = 1.22-4.20 and in controls (5A genotype frequency 0.07 as well as HNSCC (5A genotype frequency 0.13, p = 0.03,95%CI = 1.06-3.51 and controls (5A genotype frequency = 0.07 In this study, 5A genotype had greater than two fold risk for developing OSMF (OR = 2.26 and nearly the same in case of HNSCC (OR = 1.94 as compared to controls. In patients with OSMF as well as HNSCC, the ROC analysis between the MMP-3 genotype and age, 6A/6A allele was found to be significant in patients both over and under 45 years of age; while the 5A/5A carrier alleles showed an association only in patients less than 45 years of age. Conclusions This study concluded that the expression of MMP-3 genotype associated with the 5A alleles, it may have an important role in the susceptibility of the patients to develop OSMF and HNSCC.

  4. [Heart failure and anemia].

    Science.gov (United States)

    Reda, S; Motloch, L J; Hoppe, U C

    2013-09-01

    Chronic heart failure has an age-dependent prevalence of 2% and is therefore one of the most frequent diseases in western societies. A reduced hemoglobin concentration according to the definition of the World Health Organization is a common comorbidity affecting more than half of all heart failure patients. Elderly patients, patients suffering from renal impairment and women are more likely to develop anemia but a definitive etiology of anemia is only identified in the minority of cases. Anemia is associated with a poor clinical status and a greater risk of hospitalization and is a predictive factor for increased mortality. The incidence of anemia appears to increase with a poorer functional class. Intravenous iron therapy improves the exercise capacity in patients with systolic heart failure and iron deficiency and is currently being recommended for patients with persistent symptoms despite optimal medical and device therapy. However, erythropoietin-stimulating agents as a treatment for anemia in chronic heart failure have failed to improve clinical outcome in a large randomized trial. In patients with heart failure but with maintained ejection fraction, anemia is also associated with a poor prognosis. Specific therapeutic recommendations for these patients are still not available.

  5. Ejection Fraction Heart Failure Measurement

    Science.gov (United States)

    ... Disease Venous Thromboembolism Aortic Aneurysm More Ejection Fraction Heart Failure Measurement Updated:Feb 15,2017 The ejection fraction ( ... failure This content was last reviewed April 2015. Heart Failure • Home • About Heart Failure • Causes and Risks for ...

  6. BIOASSAY VESSEL FAILURE ANALYSIS

    Energy Technology Data Exchange (ETDEWEB)

    Vormelker, P

    2008-09-22

    Two high-pressure bioassay vessels failed at the Savannah River Site during a microwave heating process for biosample testing. Improper installation of the thermal shield in the first failure caused the vessel to burst during microwave heating. The second vessel failure is attributed to overpressurization during a test run. Vessel failure appeared to initiate in the mold parting line, the thinnest cross-section of the octagonal vessel. No material flaws were found in the vessel that would impair its structural performance. Content weight should be minimized to reduce operating temperature and pressure. Outer vessel life is dependent on actual temperature exposure. Since thermal aging of the vessels can be detrimental to their performance, it was recommended that the vessels be used for a limited number of cycles to be determined by additional testing.

  7. Ductile failure modeling

    DEFF Research Database (Denmark)

    Benzerga, Ahmed Amine; Leblond, Jean Baptiste; Needleman, Alan

    2016-01-01

    anisotropy, or the influence of nonlocal effects that bring a material size scale into the models. Often the voids are not present in the material from the beginning, and realistic nucleation models are important. The final failure process by coalescence of neighboring voids is an issue that has been given......Ductile fracture of structural metals occurs mainly by the nucleation, growth and coalescence of voids. Here an overview of continuum models for this type of failure is given. The most widely used current framework is described and its limitations discussed. Much work has focused on extending void...... growth models to account for non-spherical initial void shapes and for shape changes during growth. This includes cases of very low stress triaxiality, where the voids can close up to micro-cracks during the failure process. The void growth models have also been extended to consider the effect of plastic...

  8. Hepatitis B virus genotypes:an overview

    Institute of Scientific and Technical Information of China (English)

    Mamun-Al Mahtab; Salimur Rahman; Mobin Khan; Fazal Karim

    2008-01-01

    BACKGROUND: Hepatitis B virus (HBV) infection is a major cause of mortality and morbidity globally. The quest continues to identify viral factors that inlfuence disease progression and severity as well as responses to treatment of HBV infection. Based on variations in HBV, the virus has been divided into a number of genotypes. DATA SOURCES: Review of published literature on HBV genotypes. RESULTS: HBV genotypes are likely to be important in determining the severity and progression of HBV-induced liver disease as well as responses to different anti-viral agents. CONCLUSION: Although HBV genotyping is not yet recommended for routine use in treating HBV infection, available data suggest that, as in hepatitis C virus infection, HBV genotyping is also likely to become a routine investigation for HBV treatment, perhaps in the not too distant future.

  9. Toward fully automated genotyping: Genotyping microsatellite markers by deconvolution

    Energy Technology Data Exchange (ETDEWEB)

    Perlin, M.W.; Lancia, G.; See-Kiong, Ng [Carnegie Mellon Univ., Pittsburgh, PA (United States)

    1995-11-01

    Dense genetic linkage maps have been constructed for the human and mouse genomes, with average densities of 2.9 cM and 0.35 cM, respectively. These genetic maps are crucial for mapping both Mendelian and complex traits and are useful in clinical genetic diagnosis. Current maps are largely comprised of abundant, easily assayed, and highly polymorphic PCR-based microsatellite markers, primarily dinucleotide (CA){sub n} repeats. One key limitation of these length polymorphisms is the PCR stutter (or slippage) artifact that introduces additional stutter bands. With two (or more) closely spaced alleles, the stutter bands overlap, and it is difficult to accurately determine the correct alleles; this stutter phenomenon has all but precluded full automation, since a human must visually inspect the allele data. We describe here novel deconvolution methods for accurate genotyping that mathematically remove PCR stutter artifact from microsatellite markers. These methods overcome the manual interpretation bottleneck and thereby enable full automation of genetic map construction and use. New functionalities, including the pooling of DNAs and the pooling of markers, are described that may greatly reduce the associated experimentation requirements. 32 refs., 5 figs., 3 tabs.

  10. Failure of granular assemblies

    OpenAIRE

    Welker, Philipp

    2011-01-01

    This work investigates granular assemblies subjected to increasing external forces in the quasi-static limit. In this limit, the system’s evolution depends on static properties of the system, but is independent of the particles’ inertia. At the failure, which occurs at a certain value of the external forces, the particles’ motions increase quickly. In this thesis, the properties of granular systems during the weakening process and at the failure are investigated with the Discrete Element Meth...

  11. Modeling Epidemic Network Failures

    DEFF Research Database (Denmark)

    Ruepp, Sarah Renée; Fagertun, Anna Manolova

    2013-01-01

    the SID model’s behavior and impact on the network performance, as well as the severity of the infection spreading. The simulations are carried out in OPNET Modeler. The model provides an important input to epidemic connection recovery mechanisms, and can due to its flexibility and versatility be used......This paper presents the implementation of a failure propagation model for transport networks when multiple failures occur resulting in an epidemic. We model the Susceptible Infected Disabled (SID) epidemic model and validate it by comparing it to analytical solutions. Furthermore, we evaluate...

  12. Modeling Epidemic Network Failures

    DEFF Research Database (Denmark)

    Ruepp, Sarah Renée; Fagertun, Anna Manolova

    2013-01-01

    This paper presents the implementation of a failure propagation model for transport networks when multiple failures occur resulting in an epidemic. We model the Susceptible Infected Disabled (SID) epidemic model and validate it by comparing it to analytical solutions. Furthermore, we evaluate...... the SID model’s behavior and impact on the network performance, as well as the severity of the infection spreading. The simulations are carried out in OPNET Modeler. The model provides an important input to epidemic connection recovery mechanisms, and can due to its flexibility and versatility be used...... to evaluate multiple epidemic scenarios in various network types....

  13. Automotive component failures

    CSIR Research Space (South Africa)

    Heyes, AM

    1998-06-01

    Full Text Available be expected[ 023 A[ M[ HEYES Fig[ 6[ Low magni_cation fractograph showing the seam defect "S#\\ fatigue area "F# and the brittle fracture area "B#[ Fig[ 7[ Fracture surface marked F in Fig[ 6\\ typical of a fatigue fracture surface in a high strength steel... Ltd[ All rights reserved[ Keywords] Accident investigation\\ automotive failures\\ decarburization\\ fatigue\\ weld fatigue[ 0[ INTRODUCTION Failure of automotive components is an occurrence which a}ects the life of almost every person at one stage...

  14. Lactulose and renal failure.

    Science.gov (United States)

    Vogt, B; Frey, F J

    1997-01-01

    The introduction of lactulose as a new therapeutic agent for treatment of hepatic encephalopathy was a major breakthrough in this field. It was hypothesized that lactulose might prevent postoperative renal impairment after biliary surgery in patients with obstructive jaundice. The presumable mechanism purported was the diminished endotoxinemia by lactulose. Unfortunately, such a reno-protective effect has not been shown conclusively until now in clinical studies. In chronic renal failure lactulose is known to promote fecal excretion of water, sodium, potassium, amonium, urea, creatinine and protons. Thus, lactulose could be useful for the treatment of chronic renal failure. However, compliance to the therapy represents a major problem.

  15. Identification of Mislabeled Samples and Sample Mix-ups in Genotype Data using Barcode Genotypes

    DEFF Research Database (Denmark)

    Have, Christian Theil; Appel, Emil Vincent Rosenbaum; Grarup, Niels

    2014-01-01

    barcode genotypes. To detect mislabeled samples we calculate the probability that the discordance between genotypes in the data and in the independent genotypes can be attributed to random (non-mislabeling) genotyping errors. To identify mix-ups we calculate the probability of identifying the set...... of identical genotypes between sample x and sample y by chance. Based on this we calculate a mix-up confidence score with penalization for introducing mismatches in the proposed new label and adjustment for independency among the genotypes. This confidence score is used to identify probable mix-ups.......Abstract—Undetected mislabeled samples may affect the results of genotype studies, particular when rare genetic variants are investigated. Mislabeled samples are often not detected during quality control and if they are detected, they are normally discarded due to a lack of a reliable method...

  16. Response of Plasmodium falciparum to cotrimoxazole therapy: relationship with plasma drug concentrations and dihydrofolate reductase and dihydropteroate synthase genotypes

    DEFF Research Database (Denmark)

    Khalil, Insaf F; Rønn, Anita M; Alifrangis, Michael;

    2005-01-01

    , MSP-1, MSP-2, and glutamate-rich protein before treatment and upon recrudescence showed that all recurring parasites were recrudescences. The plasma levels of TRM, AcSMX, and SMX indicated adequate drug absorption in all patients. This suggests parasite resistance as a cause of treatment failure...... treatment and at days 3, 7, and 14 or upon recrudescence to ascertain drug absorption. Forty patients (89%) had an adequate clinical response, one patient (2%) had an early treatment failure response, while four patients (8%) showed late treatment failure responses. Genotyping of merozoite surface protein 1....... The presence of dhfr Ile 51 and Asn 108 alone or coupled with dhps Ala-436 among parasites that were cleared after treatment indicates that these alleles alone are insufficient to cause in vivo resistance. However, the presence of the triple mutant dhfr (Ile-51/Arg-59/Asn-108) with the dhps Gly-437 genotype...

  17. Genomic evaluations with many more genotypes

    Directory of Open Access Journals (Sweden)

    Wiggans George R

    2011-03-01

    Full Text Available Abstract Background Genomic evaluations in Holstein dairy cattle have quickly become more reliable over the last two years in many countries as more animals have been genotyped for 50,000 markers. Evaluations can also include animals genotyped with more or fewer markers using new tools such as the 777,000 or 2,900 marker chips recently introduced for cattle. Gains from more markers can be predicted using simulation, whereas strategies to use fewer markers have been compared using subsets of actual genotypes. The overall cost of selection is reduced by genotyping most animals at less than the highest density and imputing their missing genotypes using haplotypes. Algorithms to combine different densities need to be efficient because numbers of genotyped animals and markers may continue to grow quickly. Methods Genotypes for 500,000 markers were simulated for the 33,414 Holsteins that had 50,000 marker genotypes in the North American database. Another 86,465 non-genotyped ancestors were included in the pedigree file, and linkage disequilibrium was generated directly in the base population. Mixed density datasets were created by keeping 50,000 (every tenth of the markers for most animals. Missing genotypes were imputed using a combination of population haplotyping and pedigree haplotyping. Reliabilities of genomic evaluations using linear and nonlinear methods were compared. Results Differing marker sets for a large population were combined with just a few hours of computation. About 95% of paternal alleles were determined correctly, and > 95% of missing genotypes were called correctly. Reliability of breeding values was already high (84.4% with 50,000 simulated markers. The gain in reliability from increasing the number of markers to 500,000 was only 1.6%, but more than half of that gain resulted from genotyping just 1,406 young bulls at higher density. Linear genomic evaluations had reliabilities 1.5% lower than the nonlinear evaluations with 50

  18. Poverty and Aspirations Failure

    NARCIS (Netherlands)

    Dalton, P.S.; Ghosal, S.; Mani, A.

    2011-01-01

    We develop a theoretical framework to study the psychology of poverty and 'aspirations failure'. In our framework, the rich and the poor share the same preferences - and also a behavioral bias in setting aspirations. Greater downside risks imposed by poverty exacerbates the effects of this behaviora

  19. Acute liver failure

    DEFF Research Database (Denmark)

    Bernal, William; Lee, William M; Wendon, Julia

    2015-01-01

    Over the last three decades acute liver failure (ALF) has been transformed from a rare and poorly understood condition with a near universally fatal outcome, to one with a well characterized phenotype and disease course. Complex critical care protocols are now applied and emergency liver...

  20. Heart failure in COPD

    NARCIS (Netherlands)

    Rutten, Frans Hendrik

    2005-01-01

    The main aim of the thesis was to assess the prevalence of heart failure in patients with a diagnosis of chronic obstructive pulmonary disease (COPD). Furthermore, to explore diagnostic strategies (including natriuretic peptides and cardiovascular magnetic resonance imaging (CMR)) to identify heart

  1. Copeptin in Heart Failure

    DEFF Research Database (Denmark)

    Balling, Louise; Gustafsson, Finn

    2016-01-01

    Heart failure (HF) is one of the most common causes of hospitalization and mortality in the modern Western world and an increasing proportion of the population will be affected by HF in the future. Although HF management has improved quality of life and prognosis, mortality remains very high...

  2. Perioperative acute renal failure.

    LENUS (Irish Health Repository)

    Mahon, Padraig

    2012-02-03

    PURPOSE OF REVIEW: Recent biochemical evidence increasingly implicates inflammatory mechanisms as precipitants of acute renal failure. In this review, we detail some of these pathways together with potential new therapeutic targets. RECENT FINDINGS: Neutrophil gelatinase-associated lipocalin appears to be a sensitive, specific and reliable biomarker of renal injury, which may be predictive of renal outcome in the perioperative setting. For estimation of glomerular filtration rate, cystatin C is superior to creatinine. No drug is definitively effective at preventing postoperative renal failure. Clinical trials of fenoldopam and atrial natriuretic peptide are, at best, equivocal. As with pharmacological preconditioning of the heart, volatile anaesthetic agents appear to offer a protective effect to the subsequently ischaemic kidney. SUMMARY: Although a greatly improved understanding of the pathophysiology of acute renal failure has offered even more therapeutic targets, the maintenance of intravascular euvolaemia and perfusion pressure is most effective at preventing new postoperative acute renal failure. In the future, strategies targeting renal regeneration after injury will use bone marrow-derived stem cells and growth factors such as insulin-like growth factor-1.

  3. Failure to thrive

    Science.gov (United States)

    ... caused by medical problems or factors in the child’s environment, such as abuse or neglect. There are many medical causes of failure to thrive. These include: Problems with genes, such as Down syndrome Organ problems Hormone problems Damage to the brain ...

  4. Equilibria with Coordination Failures

    NARCIS (Netherlands)

    Herings, P.J.J.; van der Laan, G.; Talman, A.J.J.

    2004-01-01

    This paper extends the recent literature on equilibria with coordination failures to arbitrary convex sets of admissible prices.We introduce a new equilibrium concept, called quantity constrained equilibrium (QCE), giving a uni.ed treatment to all cases considered in the literature so far.At a QCE

  5. Poverty and Aspirations Failure

    NARCIS (Netherlands)

    Dalton, P.S.; Ghosal, S.; Mani, A.

    2011-01-01

    We develop a theoretical framework to study the psychology of poverty and 'aspirations failure'. In our framework, the rich and the poor share the same preferences - and also a behavioral bias in setting aspirations. Greater downside risks imposed by poverty exacerbates the effects of this behaviora

  6. Flavonoid profile of green asparagus genotypes.

    Science.gov (United States)

    Fuentes-Alventosa, J M; Jaramillo, S; Rodríguez-Gutiérrez, G; Cermeño, P; Espejo, J A; Jiménez-Araujo, A; Guillén-Bejarano, R; Fernández-Bolaños, J; Rodríguez-Arcos, R

    2008-08-27

    The determination of flavonoid profiles from different genotypes of triguero asparagus and their comparison to those from green asparagus commercial hybrids was the main goal of this study. The samples consisted of 32 commercial hybrids and 65 genotypes from the Huetor-Tajar population variety (triguero). The analysis of individual flavonoids by HPLC-DAD-MS has allowed the determination of eight naturally occurring flavonol derivatives in several genotypes of triguero asparagus. Those compounds included mono-, di-, and triglycosides of three flavonols, that is, quercetin, isorhamnetin, and kaempferol. The detailed analysis of the flavonoid profiles revealed significant differences among the distinct genotypes. These have been classified in three distinct groups as the result of a k-means clustering analysis, two of them containing both commercial hybrids and triguero asparagus and another cluster constituted by 21 genotypes of triguero asparagus, which contain several key flavonol derivatives able to differentiate them. Hence, the triglycosides tentatively identified as quercetin-3-rhamnosyl-rutinoside, isorhamnetin-3-rhamnosyl-rutinoside, and isorhamnetin-3-O-glucoside have been detected only in the genotypes grouped in the above-mentioned cluster. On the other hand, the compound tentatively identified as isorhamnetin-3-glucosyl-rutinoside was present in most genotypes of triguero asparagus, whereas it has not been detected in any of the commercial hybrids.

  7. HPV Genotyping 9G Membrane Test

    Directory of Open Access Journals (Sweden)

    Danishmalik Rafiq Sayyed

    2013-11-01

    Full Text Available The results of the genital human papillomavirus (HPV detection in 439 cervical samples by cervical cytology were compared with sequencing analysis and a newly developed HPV genotyping 9G membrane test. The excellent sensitivity and specificity of the HPV genotyping 9G membrane test was assured by a signal to noise ratio of more than 300 and a target hybridization to non-target hybridization ratio of 300 ~ 400 at 25 °C. The final results can be obtained in 29 min by simple loading of the hybridization and washing solutions and scanning the membranes without any drying steps or special handling. The 100% identical results of the HPV genotyping 9G membrane test with sequencing results in 439 clinical samples demonstrate significant clinical application for this test. HPV genotyping 9G membrane tests can identify and discriminate five HR-HPV genotypes which are prevalent in almost 87% of cervical cancer cases. Its simple handling makes the HPV genotyping 9G membrane test a very convenient platform for accurate HPV genotyping.

  8. Angiotensin converting enzyme insertion/deletion polymorphism and the risk of heart failure in hypertensive subjects.

    NARCIS (Netherlands)

    Schut, A.; Bleumink, G.S.; Stricker, B.H.C.; Hofman, A.W.I.M.; Witteman, J.C.; Pols, H.; Deckers, J.W.; Deinum, J.; Duijn, C.M. van

    2004-01-01

    AIMS: Cardiac angiotensin-I converting enzyme (ACE) activity is influenced by the ACE I/D polymorphism. Evidence suggests that the DD-genotype may be a risk factor for cardiac hypertrophy and heart failure, especially in hypertensive subjects. We assessed the relation between the ACE I/D

  9. Molecular epidemiological analysis of Cryptosporidium spp. in the United Kingdom: results of genotyping Cryptosporidium spp. in 1,705 fecal samples from humans and 105 fecal samples from livestock animals.

    Science.gov (United States)

    McLauchlin, J; Amar, C; Pedraza-Díaz, S; Nichols, G L

    2000-11-01

    Cryptosporidium present in 1,705 fecal samples from humans and 105 from livestock animals were analyzed by PCR-restriction fragment length polymorphism of the Cryptosporidium oocyst wall protein. Overall, genotype 1 (human exclusive type) was detected in 37.8% of the samples from humans, genotype 2 (broad host range) was detected in 61.5%, a third genotype designated genotype 3 (Cryptosporidium meleagridis) was detected in 0.3%, and both genotypes 1 and 2 were recovered from 0.4%. All samples from livestock yielded genotype 2. Among 469 patients infected during eight drinking water-related outbreaks, five outbreaks were predominantly due to genotype 1, and three were due to genotype 2. Fifty-four samples were collected from patients involved with five swimming pool-associated outbreaks: two outbreaks were due to genotype 1, one was due to genotype 2, and the remaining two involved both genotypes 1 and 2. Among 26 family outbreaks and 1 children's nursery outbreak (2 to 3 members per group), the same genotype was recovered from the different members of each outbreak: 13 were due to genotype 1, and 14 were due to genotype 2. In eighteen patients reporting contact with animals and/or farms, genotype 1 was recovered from one patient and genotype 2 was recovered from the remaining 17. Among the sporadic cases, there were distinct geographical and temporal variations in the distribution of the genotypes. The spring peak in cases was due to genotype 2. Genotype 1 was significantly more common in patients infected during the late-summer-autumn peak and in those with a history of foreign travel.

  10. HCV genotype-specific correlation with serum markers: Higher predictability for genotype 4a

    Directory of Open Access Journals (Sweden)

    Asad Sultan

    2011-06-01

    Full Text Available Abstract Background Several factors have been proposed to assess the clinical outcome of HCV infection. The correlation of HCV genotypes to possible serum markers in clinical prediction is still controversial. The main objective of this study was to determine the existence of any correlation between HCV genotypes to viral load and different clinical serum markers. Methods We performed a prospective cross-sectional and observational study. About 3160 serum HCV RNA positive patients were chosen from 4020 randomly selected anti-HCV positive patients. Statistical analysis was performed using the SPSS 16 software package. ROC (receiver operating characteristics curves were used to compare diagnostic values of serum markers to predict genotypes. Results The most prevalent genotype was 3a (73.9% followed by 1a (10.7%, 4a (6.4% and 3b (6.1% in Pakistani population. No correlation was found between viral load and serum markers for genotype 3a in a large no. of sample (n = 2336. While significant correlation was observed between viral load and AST in genotype 3b, ALP with viral load and ALT for genotype 1a. Patients with genotype 4a showed a significant inverse correlation with viral load and Hb level and AST with ALP. For genotype 4a, AUC (area under the curve of ALT, ALP, AST, bilirubin, Hb level and viral load was 0.790, 0.763, 0.454, 0.664, 0.458 and 0.872 respectively. Conclusions In conclusion, there was a significant variable response of HCV genotypes with serum markers. Severity of disease is independent of serum marker level in genotype 3a, while the liver damage in genotype 4a may associate with viral cytopathic effect as well as the immune-mediated process. An index using six serum markers may correctly predict genotype 4a in patients with ≥75% accuracy.

  11. Time between failures model and failure analysis of CNC system

    Institute of Scientific and Technical Information of China (English)

    ZHANG Hai-bo; JIA Ya-zhou; ZHOU Guang-wen

    2007-01-01

    To provide basis for the reliability improvement design of CNC system, the failure data of a type of CNC system in one year are collected under field conditions in workshops. The distribution model parameters of time between failures are estimated by least square method and hypothesis testing is done by d-test method. It is proved that the time between failures of the CNC system follows Weibull distribution and the system has entered into the wear-out failure period. The failure positions and failure causes are analyzed further to indicate the weak subsystems of the CNC system. It can be found that servo unit, electrical system, detecting unit and power supply are principal failure positions and the main failure cause is breakage of components. The corresponding improvement measures are put forward. The paper provides a reference to reliability design and analysis of CNC system for the manufacturer and has great guidance to using and maintaining CNC system for the user.

  12. OBSTETRIC RENAL FAILURE

    Directory of Open Access Journals (Sweden)

    Rajeshwari

    2015-11-01

    Full Text Available Renal failure in obstetrics is rare but important complication, associated with significant mortality and long term morbidity.1,2 It includes acute renal failure due to obstetrical complications or due to deterioration of existing renal disease. AIMS AND OBJECTIVES: To evaluate the etiology and outcome of renal failure in obstetric patients. METHODS: We prospectively analyzed 30 pregnant and puerperal women with acute renal failure or pre-existing renal disease developing renal failure during pregnancy between November 2007 to sep-2009. Patients who presented/developed ARF during the hospital stay were included in this study. RESULTS: Among 30 patients, mean age was 23 years and 33 years age group. 12 cases (40% patients were primigravidae and 9(30% patients were multigravidae and 9 cases (30% presented in post-partum period. Eighteen cases (60% with ARF were seen in third trimester, followed by in postpartum period 9 cases (30%. Most common contributing factors to ARF were Pre-eclampsia, eclampsia and HELLP syndrome 60%, sepsis 56.6%, post abortal ARF 10%. DIC 40%. Haemorrhage as the aetiology for ARF was present 46%, APH in 20% and PPH in 26.6%. The type of ARF was renal in (63% and prerenal (36%; Oliguric seen in 10 patients (33% and high mortality (30%. Among the 20 pregnant patients with ARF, The average period of gestation was 33±2 weeks (30 -36 weeks, 5 cases (25% presented with intrauterine fetal demise and 18 cases (66% had preterm vaginal delivery and 2 cases (10% had induced abortion. And the average birth weight was 2±0.5 kg (1.5 kg. Eight cases (26% required dialysis. 80% of patients recovered completely of renal functions. 63% patients recovered without renal replacement therapy whereas 17% required dialysis. the maternal mortality was 20%, the main reason for mortality was septic shock and multi organ dysfunction (66%. CONCLUSION: ARF related pregnancy was seen commonly in the primigravidae and in the third trimester, the most

  13. Hepatitis C virus genotypes in Pakistan: a systemic review

    Directory of Open Access Journals (Sweden)

    Ali Ijaz

    2011-09-01

    Full Text Available Abstract Background and aim Phylogenetic analysis has led to the classification of hepatitis C virus (HCV into 1-6 major genotypes. HCV genotypes have different biological properties, clinical outcome and response to antiviral treatment and provide important clues for studying the epidemiology, transmission and pathogenesis. This article deepens the current molecular information about the geographical distribution of HCV genotypes and subgenotypes in population of four provinces of Pakistan. 34 published papers (1996-2011 related to prevalence of HCV genotypes/serotypes and subgenotypes in Pakistan were searched. Result HCV genotype/s distribution from all 34 studies was observed in 28,400 HCV infected individuals in the following pattern: 1,999 (7.03% cases of genotype 1; 1,085 (3.81% cases of genotype 2; 22,429 (78.96% cases of genotype 3; 453 (1.59% cases of genotype 4; 29 (0.10% cases of genotype 5; 37 (0.13% cases of genotype 6; 1,429 (5.03% cases of mixed genotypes, and 939 (3.30% cases of untypeable genotypes. Overall, genotype 3a was the predominant genotype with a rate of 55.10%, followed by genotype 1a, 3b and mixed genotype with a rate of 10.25%, 8.20%, and 5.08%, respectively; and genotypes 4, 5 and 6 were rare. Genotype 3 occurred predominately in all the provinces of Pakistan. Second more frequently genotype was genotype 1 in Punjab province and untypeable genotypes in Sindh, Khyber Pakhtunkhwa and Balochistan provinces.

  14. Hepatitis B virus genotypes circulating in Brazil: molecular characterization of genotype F isolates

    Directory of Open Access Journals (Sweden)

    Virgolino Helaine A

    2007-11-01

    Full Text Available Abstract Background Hepatitis B virus (HBV isolates have been classified in eight genotypes, A to H, which exhibit distinct geographical distributions. Genotypes A, D and F are predominant in Brazil, a country formed by a miscegenated population, where the proportion of individuals from Caucasian, Amerindian and African origins varies by region. Genotype F, which is the most divergent, is considered indigenous to the Americas. A systematic molecular characterization of HBV isolates from different parts of the world would be invaluable in establishing HBV evolutionary origins and dispersion patterns. A large-scale study is needed to map the region-by-region distribution of the HBV genotypes in Brazil. Results Genotyping by PCR-RFLP of 303 HBV isolates from HBsAg-positive blood donors showed that at least two of the three genotypes, A, D, and F, co-circulate in each of the five geographic regions of Brazil. No other genotypes were identified. Overall, genotype A was most prevalent (48.5%, and most of these isolates were classified as subgenotype A1 (138/153; 90.2%. Genotype D was the most common genotype in the South (84.2% and Central (47.6% regions. The prevalence of genotype F was low (13% countrywide. Nucleotide sequencing of the S gene and a phylogenetic analysis of 32 HBV genotype F isolates showed that a great majority (28/32; 87.5% belonged to subgenotype F2, cluster II. The deduced serotype of 31 of 32 F isolates was adw4. The remaining isolate showed a leucine-to-isoleucine substitution at position 127. Conclusion The presence of genotypes A, D and F, and the absence of other genotypes in a large cohort of HBV infected individuals may reflect the ethnic origins of the Brazilian population. The high prevalence of isolates from subgenotype A1 (of African origin indicates that the African influx during the colonial slavery period had a major impact on the circulation of HBV genotype A currently found in Brazil. Although most genotype F

  15. Ledipasvir/sofosbuvir fixed-dose combination for treatment of hepatitis C virus genotype 4 infection.

    Science.gov (United States)

    Nehra, V; Tan, E M; Rizza, S A; Temesgen, Z

    2016-02-01

    Hepatitis C virus (HCV) genotype 4 accounts for 8-13% of all chronic HCV infections worldwide. Patients with HCV genotype 4 have been reported to have poor treatment responses to PEGylated interferon and ribavirin regimens. Recently a single tablet, fixed-dose combination of sofosbuvir, an RNA-directed RNA polymerase (NS5B) inhibitor, and ledipasvir, a nonstructural protein 5A (NS5A) inhibitor, has been approved for treatment of chronic HCV infection. Two studies using the fixed-dose combination in chronic HCV genotype 4 for 12 weeks reported sustained virologic response rates at 12 weeks (SVR12) of 93-95%. Data also support the use of ledipasvir/sofosbuvir in chronic HCV genotype 4 and HIV co-infection. Administered as a single once-daily oral regimen, this ribavirin- and interferon-free regimen is well tolerated, with low potential for adverse effects and represents a significant advancement in the treatment of chronic HCV genotype 4 infection.

  16. Global distribution of novel rhinovirus genotype

    DEFF Research Database (Denmark)

    Briese, Thomas; Renwick, Neil; Venter, Marietjie

    2008-01-01

    Global surveillance for a novel rhinovirus genotype indicated its association with community outbreaks and pediatric respiratory disease in Africa, Asia, Australia, Europe, and North America. Molecular dating indicates that these viruses have been circulating for at least 250 years Udgivelsesdato...

  17. Global distribution of novel rhinovirus genotype

    DEFF Research Database (Denmark)

    Briese, Thomas; Renwick, Neil; Venter, Marietjie

    2008-01-01

    Global surveillance for a novel rhinovirus genotype indicated its association with community outbreaks and pediatric respiratory disease in Africa, Asia, Australia, Europe, and North America. Molecular dating indicates that these viruses have been circulating for at least 250 years....

  18. HPV genotypes concordance between sex partners.

    Science.gov (United States)

    Benevolo, M; Mottolese, M; Marandino, F; Carosi, M; Diodoro, M G; Sentinelli, S; Visca, P; Rollo, F; Mariani, L; Vocaturo, G; Sindico, R; Di Giannuario, D; Perrone Donnorso, R; Pellicciotta, M; Vocaturo, A

    2007-12-01

    The HPV genotype concordance in the sexual couples could support the sexual viral transmission of HPV infection. The present study contains a case-report of a stable Italian sex couple harbouring the same five HPV genotypes in their genital samples. The female partner, affected by vulvar condilomatosis, evidenced positivity in her cervicovaginal scraping with high risk HPV DNA Hybrid Capture 2 test and was negative at liquid-based performed Pap Test and at colposcopic examination. The male partner was clinically healthy regarding his external genitalia. In both male and female genital scrapings, the following HPV genotypes were detected by means of a PCR-based assay: 6, 16, 53, 73 and 84. This considerably high genotype concordance does not appear to be casual and supports, in our opinion, the hypothesis that genital HPV types are sexually transmitted agents

  19. ApoE (Apolipoprotein E) Genotyping

    Science.gov (United States)

    ... Home Visit Global Sites Search Help? APOE Genotyping, Alzheimer Disease Share this page: Was this page helpful? Formal ... help in the diagnosis of probable late onset Alzheimer disease (AD) in symptomatic adults. It is called susceptibility ...

  20. Forensic SNP genotyping with SNaPshot

    DEFF Research Database (Denmark)

    Fondevila, M; Børsting, C; Phillips, C

    2017-01-01

    This review explores the key factors that influence the optimization, routine use, and profile interpretation of the SNaPshot single-base extension (SBE) system applied to forensic single-nucleotide polymorphism (SNP) genotyping. Despite being a mainly complimentary DNA genotyping technique...... to routine STR profiling, use of SNaPshot is an important part of the development of SNP sets for a wide range of forensic applications with these markers, from genotyping highly degraded DNA with very short amplicons to the introduction of SNPs to ascertain the ancestry and physical characteristics...... of an unidentified contact trace donor. However, this technology, as resourceful as it is, displays several features that depart from the usual STR genotyping far enough to demand a certain degree of expertise from the forensic analyst before tackling the complex casework on which SNaPshot application provides...

  1. Can Clustering in Genotype Space Reveal "Niches"?

    Science.gov (United States)

    D'Andrea, Rafael; Ostling, Annette

    2016-01-01

    Community ecology lacks the success enjoyed by population genetics to quantify the relative roles played by deterministic and stochastic processes. It has been proposed that clustered patterns of abundance in genotype space provide evidence of selection in microbial communities, since no such clustering would arise in the absence of selection. We critique this test for its unrealistic null hypothesis. We show mathematically and with simulations that point mutations alone lead to clustering in genotype space by causing correlations between abundances of similar genotypes. We also show potential deviations from the mutation-only pattern caused by immigration from a source pool. Clustered patterns in genotype space may still be revealing of selection if analyzed quantitatively but only if neutral and selective regimes can be distinguished once mutation and immigration are included in the null model.

  2. AFLP analysis among Ethiopian arabica coffee genotypes

    African Journals Online (AJOL)

    STORAGESEVER

    2008-09-17

    Sep 17, 2008 ... sequence information, produces a large number of infor- mative polymorphic markers per primer, requires a small amount of ..... and 53 were monomorphic across all coffee genotypes collected from .... molecular markers.

  3. Early seedling development of Medicago truncatula genotypes ...

    African Journals Online (AJOL)

    adel

    2014-01-08

    Jan 8, 2014 ... germinated on filter papers imbibed in distilled water or in sodium .... Wards minimum variance method as a clustering algorithm. ... Mean values of plumule: radicle ratio of M. truncatula genotypes under different salt stress ...

  4. HMSRP Hawaiian Monk Seal Microsatellite Genotypes

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Currently ~2,400 Hawaiian monk seal specimens have been analyzed genetically, providing genotypes at 18 microsatellite loci. These data are organized by individual,...

  5. Generalized Block Failure

    DEFF Research Database (Denmark)

    Jönsson, Jeppe

    2015-01-01

    Block tearing is considered in several codes as a pure block tension or a pure block shear failure mechanism. However in many situations the load acts eccentrically and involves the transfer of a substantial moment in combination with the shear force and perhaps a normal force. A literature study...... yield lines around the block leads to simple interaction formulas similar to other interaction formulas in the codes.......Block tearing is considered in several codes as a pure block tension or a pure block shear failure mechanism. However in many situations the load acts eccentrically and involves the transfer of a substantial moment in combination with the shear force and perhaps a normal force. A literature study...

  6. [Nutrition and liver failure].

    Science.gov (United States)

    Plauth, M

    2013-06-01

    In the critically ill liver patient, nutrition support is not very different from that given for other illnesses. In hyperacute liver failure, nutrition support is of less importance than in the other subtypes of acute liver failure that take a more protracted course. Nasoenteral tube feeding using a polymeric standard formula should be the first-line approach, while parenteral nutrition giving glucose, fat, amino acids, vitamins, and trace elements is initiated when enteral nutrition is insufficient or impracticable. In chronic liver disease, notably cirrhosis, there is frequently protein malnutrition indicating a poor prognosis and requiring immediate initiation of nutrition support. Enteral nutrition ensuring an adequate provision of energy and protein should be preferred. Particular care should be taken to avoid refeeding syndrome and to treat vitamin and trace element deficiency.

  7. Predicting Small Bank Failure

    OpenAIRE

    Heyliger, Wilton E.; Don P. Holdren

    1991-01-01

    There are many studies of bank performance and bank failure in the literature. Most of these studies used banking ratios as variables in their models without giving consideration to their appropriateness, nor was much consideration given to the stability of those ratios through time and across asset size. Many studies also failed to recognize that bank structure may differ by asset size. This study evaluates a large number of banking variables in order to identify stable ratios. These ratios ...

  8. LHC Magnet test failure

    CERN Multimedia

    2007-01-01

    "On Tueday, March 22, a Fermilab-built quadrupole magnet, one of an "inner triplet" of three focusing magnets, failed a high-pressure test at Point 5 in the tunnel of the LHC accelerator at CERN. Since Tuesday, teams at CERN and Fermilab have worked closely together to address the problem and have identified the cause of the failure. Now they are at work on a solution.:" (1 page)

  9. Peat slope failure in Ireland

    OpenAIRE

    Boylan, Noel; Jennings, Paul; Long, Michael

    2008-01-01

    Recent peat failures in Ireland in the autumn of 2003 at Pollatomish, County Mayo and Derrybrien, County Galway have focused attention on such events. However, peat failures are not a recent phenomenon with possible evidence of peat failures in Ireland having been identified as far back as the Early Bronze Age. This paper summarises the issues surrounding peat failures in Ireland that would be of interest to an engineer\\engineering geologist assessing this geohazard. The distri...

  10. 5A/6A Polymorphism of the Stromelysin-1 Gene and Angiographic Restenosis After Coronary Artery Stenting

    Directory of Open Access Journals (Sweden)

    Kuan-Rau Chiou

    2005-11-01

    Conclusion: There is a low frequency of the stromelysin-1 promoter 5A allele in the Chinese population in Taiwan. How stromelysin-1 5A/6A polymorphism affects ISR appears to be linked to angina status. These results merit further study to identify patients carrying genotypes which put them at increased risk of ISR, and which matrix metalloproteinase inhibitors or drug-eluting stents are more effective for those at risk.

  11. Genotypic Variation for Salinity Tolerance in Sorghum (Sorghum bicolor (L. Moench Genotypes at Early Growth Stages

    Directory of Open Access Journals (Sweden)

    Tigabu, Endalew

    2013-04-01

    Full Text Available Sorghum (Sorghum bicolor L. Moench is the fifth most economically important crop among cereals in the world. Salinity is an abiotic factor which reduces productivity of sorghum. Exploiting genetic variability to identify salt tolerant genotype is one of the strategies used to overcome salinity. Pot experiment was carried out to evaluate the genetic variation of eleven sorghum genotypes for NaCl salinity response at germination and early seedling stages. The experimental treatments were five NaCl salinity levels (0, 2, 4, 8, and 16 dS m-1 and eleven sorghum genotypes (Gambella1107, Melkam, S-35, ESH-2, Gobye, 97MW6130, Meko, 76T1#23, ICSV-111, Abshir and Teshale. The experimental design was completely randomized design with three replicates.Data was analyzed using SAS (version 9.0 statistical software and means were separated by LSD. Germination rate, final germination percentage, seedling shoot length and seedling root length were measured. The ANOVA for treatments, genotypes and their interaction was found to be highly significant (p<0.001 with regard to all parameters. Genotypes Meko, Gambella1107, ICSV-111 and Melkam were found salt tolerant during germination and seedling growth stages. However, genotypes ESH-2 and Gobye were salt sensitive during both stages. The rest sorghum genotypes were intermediate in their salt tolerance. The study affirmed the presence of wide genotypic variation among the sorghum genotypes for NaCl salt tolerance.

  12. Molecular epidemiology of different hepatitis C genotypes in serum and peripheral blood mononuclear cells in jahrom city of iran.

    Science.gov (United States)

    Ashrafi Hafez, Asghar; Baharlou, Rasoul; Mousavi Nasab, Seyed Dawood; Ahmadi Vasmehjani, Abbas; Shayestehpour, Mohammad; Joharinia, Negar; Ahmadi, Nayeb Ali

    2014-05-01

    The Hepatitis C Virus (HCV) is considered essentially hepatotropic, yet the virus compartments have also been found in important extra hepatic sites. Detection of HCV RNA in extra hepatic reservoirs such as peripheral blood mononuclear cells (PBMCs) is important for determining disease progression and treatment effectiveness. The present study aimed to determine different HCV genotypes in patients' plasma and PBMC specimens, in Jahrom city of Iran. Blood samples of 137 patients with established HCV were collected at the Honari clinic. These patients were anti-HCV and plasma HCV RNA positive. After plasma RNA extraction and obtaining a pellet of approximately 3-5 × 10(6) PBMCs, Real-time PCR was performed, using specific-genotype primers. Finally, data analysis was done by the Statistical Package for Social Sciences (SPSS) software. Subtype 3 was the most common genotype in plasma (57.7%) and PBMCs (51.1%). Subtype 1a was detected in 36.5% and 30.7% of plasma samples and PBMCs, respectively whereas subtype 4 was not detected in any of the cases. There was a genotype difference between plasma and PBMCs of 12.4% of patients. In four patients no genotype was detected in their plasma but genotype 3 was detected in the PBMCs. It is suggested that determination of the target genotype by plasma subtyping for choosing the proper antiviral therapy is essential but may result in therapy failure. HCV genotyping in PBMC samples, along with plasma specimens, might be more beneficial. Therefore determining the HCV genotype in PBMCs, before beginning the therapy is useful due to the possibility of occult infection detection.

  13. CRITERIA FOR ROCK ENGINEERING FAILURE

    Institute of Scientific and Technical Information of China (English)

    ZHUDeren; ZHANGYuzhuo

    1995-01-01

    A great number of underground rock projects are maintained in the rock mass which is subject to rock damage and failure development. In many cases, the rock. engineering is still under normal working conditions even though rock is already fails to some extent. This paper introduces two different concepts: rock failure and rock engineering failure. Rock failure is defined as a mechanical state under which an applicable characteristic is changed or lost.However, the rock engineering failure is an engineering state under which an applicable function is changed or lost. The failure of surrounding rocks is the major reason of rock engineering failure. The criterion of rock engineering failure depends on the limit of applicable functions. The rock engineering failure state possesses a corresponding point in rock failure state. In this paper, a description of rock engineering failure criterion is given by simply using a mechanical equation or expression. It is expected that the study of rock engineering failure criterion will be an optimal approach that combines research of rock mechanics with rock engineering problems.

  14. Novel therapies in heart failure

    NARCIS (Netherlands)

    Liu, Licette Cécile Yang

    2016-01-01

    Heart failure is a clinical condition that is characterized by the inability of the heart to meet the oxygen requirements of peripheral tissues and organs, despite normal filling pressures. Despite recent developments in the treatment of heart failure, the prognosis of heart failure patients remains

  15. Novel therapies in heart failure

    NARCIS (Netherlands)

    Liu, Licette Cécile Yang

    2016-01-01

    Heart failure is a clinical condition that is characterized by the inability of the heart to meet the oxygen requirements of peripheral tissues and organs, despite normal filling pressures. Despite recent developments in the treatment of heart failure, the prognosis of heart failure patients remains

  16. Resistance Patterns Associated with HCV NS5A Inhibitors Provide Limited Insight into Drug Binding

    Directory of Open Access Journals (Sweden)

    Moheshwarnath Issur

    2014-11-01

    Full Text Available Direct-acting antivirals (DAAs have significantly improved the treatment of infection with the hepatitis C virus. A promising class of novel antiviral agents targets the HCV NS5A protein. The high potency and broad genotypic coverage are favorable properties. NS5A inhibitors are currently assessed in advanced clinical trials in combination with viral polymerase inhibitors and/or viral protease inhibitors. However, the clinical use of NS5A inhibitors is also associated with new challenges. HCV variants with decreased susceptibility to these drugs can emerge and compromise therapy. In this review, we discuss resistance patterns in NS5A with focus prevalence and implications for inhibitor binding.

  17. Blood Group ABO Genotyping in Paternity Testing.

    Science.gov (United States)

    Bugert, Peter; Rink, Gabriele; Kemp, Katharina; Klüter, Harald

    2012-06-01

    BACKGROUND: The ABO blood groups result from DNA sequence variations, predominantly single nucleotide and insertion/deletion polymorphisms (SNPs and indels), in the ABO gene encoding a glycosyltransferase. The ABO blood groups A(1), A(2), B and O predominantly result from the wild type allele A1 and the major gene variants that are characterized by four diallelic markers (261G>del, 802G>A, 803G>C, 1061C>del). Here, we were interested to evaluate the impact of ABO genotyping compared to ABO phenotyping in paternity testing. METHODS: The major ABO alleles were determined by PCR amplification with sequence-specific primers (PCR-SSP) in a representative sample of 1,335 blood donors. The genotypes were compared to the ABO blood groups registered in the blood donor files. Then, the ABO phenotypes and genotypes were determined in 95 paternity trio cases that have been investigated by 12 short tandem repeat (STR) markers before. We compared statistical parameters (PL, paternity likelihood; PE, power of exclusion) of both blood grouping approaches. RESULTS: The prevalence of the major ABO alleles and genotypes corresponded to the expected occurrence of ABO blood groups in a Caucasian population. The low resolution genotyping of 4 diallelic markers revealed a correct genotype-phenotype correlation in 1,331 of 1,335 samples (99.7%). In 60 paternity trios with confirmed paternity of the alleged father based on STR analysis both PL and PE of the ABO genotype was significantly higher than of the ABO phenotype. In 12 of 35 exclusion cases (34.3%) the ABO genotype also excluded the alleged father, whereas the ABO phenotype excluded the alleged father only in 7 cases (20%). CONCLUSION: In paternity testing ABO genotyping is superior to ABO phenotyping with regard to PL and PE, however, ABO genotyping is not sufficient for valid paternity testing. Due to the much lower mutation rate compared to STR markers, blood group SNPs in addition to anonymous SNPs could be considered for

  18. Blood Group ABO Genotyping in Paternity Testing

    Science.gov (United States)

    Bugert, Peter; Rink, Gabriele; Kemp, Katharina; Klüter, Harald

    2012-01-01

    Background The ABO blood groups result from DNA sequence variations, predominantly single nucleotide and insertion/deletion polymorphisms (SNPs and indels), in the ABO gene encoding a glycosyltransferase. The ABO blood groups A1, A2, B and O predominantly result from the wild type allele A1 and the major gene variants that are characterized by four diallelic markers (261G>del, 802G>A, 803G>C, 1061C>del). Here, we were interested to evaluate the impact of ABO genotyping compared to ABO phenotyping in paternity testing. Methods The major ABO alleles were determined by PCR amplification with sequence-specific primers (PCR-SSP) in a representative sample of 1,335 blood donors. The genotypes were compared to the ABO blood groups registered in the blood donor files. Then, the ABO phenotypes and genotypes were determined in 95 paternity trio cases that have been investigated by 12 short tandem repeat (STR) markers before. We compared statistical parameters (PL, paternity likelihood; PE, power of exclusion) of both blood grouping approaches. Results The prevalence of the major ABO alleles and genotypes corresponded to the expected occurrence of ABO blood groups in a Caucasian population. The low resolution genotyping of 4 diallelic markers revealed a correct genotype-phenotype correlation in 1,331 of 1,335 samples (99.7%). In 60 paternity trios with confirmed paternity of the alleged father based on STR analysis both PL and PE of the ABO genotype was significantly higher than of the ABO phenotype. In 12 of 35 exclusion cases (34.3%) the ABO genotype also excluded the alleged father, whereas the ABO phenotype excluded the alleged father only in 7 cases (20%). Conclusion In paternity testing ABO genotyping is superior to ABO phenotyping with regard to PL and PE, however, ABO genotyping is not sufficient for valid paternity testing. Due to the much lower mutation rate compared to STR markers, blood group SNPs in addition to anonymous SNPs could be considered for future

  19. Animation of boom failure processes

    Energy Technology Data Exchange (ETDEWEB)

    An, C. F.; Brown, H. M.; Goodman, R. H. [Imperial Oil Resources, Calgary, AB (Canada); Clavelle, E. J. [Calgary Univ., AB (Canada)

    1997-10-01

    Computer animations of oil boom failure mechanisms were discussed. The animations are useful in demonstrating the transient processes of boom failure. They consist of a series of images obtained from the graphical output of a computational fluid dynamics program, FLUENT, while the modeling is based on boom failure experiments carried out in flowing water channels. The animations can be viewed on a PC running under Windows `95. Three types of failures are presented, i. e. drainage failure, droplet entrainment and critical accumulation. 11 refs., 3 figs.

  20. Cotton genotypes selection through artificial neural networks.

    Science.gov (United States)

    Júnior, E G Silva; Cardoso, D B O; Reis, M C; Nascimento, A F O; Bortolin, D I; Martins, M R; Sousa, L B

    2017-09-27

    Breeding programs currently use statistical analysis to assist in the identification of superior genotypes at various stages of a cultivar's development. Differently from these analyses, the computational intelligence approach has been little explored in genetic improvement of cotton. Thus, this study was carried out with the objective of presenting the use of artificial neural networks as auxiliary tools in the improvement of the cotton to improve fiber quality. To demonstrate the applicability of this approach, this research was carried out using the evaluation data of 40 genotypes. In order to classify the genotypes for fiber quality, the artificial neural networks were trained with replicate data of 20 genotypes of cotton evaluated in the harvests of 2013/14 and 2014/15, regarding fiber length, uniformity of length, fiber strength, micronaire index, elongation, short fiber index, maturity index, reflectance degree, and fiber quality index. This quality index was estimated by means of a weighted average on the determined score (1 to 5) of each characteristic of the HVI evaluated, according to its industry standards. The artificial neural networks presented a high capacity of correct classification of the 20 selected genotypes based on the fiber quality index, so that when using fiber length associated with the short fiber index, fiber maturation, and micronaire index, the artificial neural networks presented better results than using only fiber length and previous associations. It was also observed that to submit data of means of new genotypes to the neural networks trained with data of repetition, provides better results of classification of the genotypes. When observing the results obtained in the present study, it was verified that the artificial neural networks present great potential to be used in the different stages of a genetic improvement program of the cotton, aiming at the improvement of the fiber quality of the future cultivars.

  1. Steam generator tube failures

    Energy Technology Data Exchange (ETDEWEB)

    MacDonald, P.E.; Shah, V.N.; Ward, L.W.; Ellison, P.G.

    1996-04-01

    A review and summary of the available information on steam generator tubing failures and the impact of these failures on plant safety is presented. The following topics are covered: pressurized water reactor (PWR), Canadian deuterium uranium (CANDU) reactor, and Russian water moderated, water cooled energy reactor (VVER) steam generator degradation, PWR steam generator tube ruptures, the thermal-hydraulic response of a PWR plant with a faulted steam generator, the risk significance of steam generator tube rupture accidents, tubing inspection requirements and fitness-for-service criteria in various countries, and defect detection reliability and sizing accuracy. A significant number of steam generator tubes are defective and are removed from service or repaired each year. This wide spread damage has been caused by many diverse degradation mechanisms, some of which are difficult to detect and predict. In addition, spontaneous tube ruptures have occurred at the rate of about one every 2 years over the last 20 years, and incipient tube ruptures (tube failures usually identified with leak detection monitors just before rupture) have been occurring at the rate of about one per year. These ruptures have caused complex plant transients which have not always been easy for the reactor operators to control. Our analysis shows that if more than 15 tubes rupture during a main steam line break, the system response could lead to core melting. Although spontaneous and induced steam generator tube ruptures are small contributors to the total core damage frequency calculated in probabilistic risk assessments, they are risk significant because the radionuclides are likely to bypass the reactor containment building. The frequency of steam generator tube ruptures can be significantly reduced through appropriate and timely inspections and repairs or removal from service.

  2. Renal Failure in Pregnancy.

    Science.gov (United States)

    Balofsky, Ari; Fedarau, Maksim

    2016-01-01

    Renal failure during pregnancy affects both mother and fetus, and may be related to preexisting disease or develop secondary to diseases of pregnancy. Causes include hypovolemia, sepsis, shock, preeclampsia, thrombotic microangiopathies, and renal obstruction. Treatment focuses on supportive measures, while pharmacologic treatment is viewed as second-line therapy, and is more useful in mitigating harmful effects than treating the underlying cause. When supportive measures and pharmacotherapy prove inadequate, dialysis may be required, with the goal being to prolong pregnancy until delivery is feasible. Outcomes and recommendations depend primarily on the underlying cause.

  3. Potential applications of pharmacogenomics to heart failure therapies.

    Science.gov (United States)

    Parikh, Kishan S; Ahmad, Tariq; Fiuzat, Mona

    2014-10-01

    Pharmacogenomics explores one drug's varying effects on different patient genotypes. A better understanding of genomic variation's contribution to drug response can impact 4 arenas in heart failure (HF): (1) identification of patients most likely to receive benefit from therapy, (2) risk stratify patients for risk of adverse events, (3) optimize dosing of drugs, and (4) steer future clinical trial design and drug development. In this review, the authors explore the potential applications of pharmacogenomics in patients with HF in the context of these categories.

  4. Phenotypic and genotypic variation in Iranian Pistachios

    Directory of Open Access Journals (Sweden)

    Somayeh Tayefeh Aliakbarkhani

    2015-12-01

    Full Text Available As Iran is one of the richest pistachio germplasms a few studies have been conducted on different sexes of pistachio trees, in areas where this crop emerged. To this end, 40 male and female Iranian pistachio genotypes from Feizabad region, Khorasan, Iran; were evaluated using morphological characters and randomly amplified polymorphic DNA (RAPD markers. For morphological assessments, 54 variables were considered to investigate similarities between and among the studied genotypes. Morphological data indicated relative superiority in some female genotypes (such as Sefid 1, Sefid Sabuni 2, Garmesiah, and Ghermezdorosht Z regarding characters such as halfcrackedness, the percentages of protein and fat content. 115 polymorphic bands were recorded with 92.83% average polymorphism among all primers. The total resolving power (Rp of the primers was 74.54. The range of genetic similarity varied from about 0.31 to about 0.70. Genotypes were segregated into eight groups at the similarity limit of 0.41. Results of present investigation could be helpful for strategic decisions for maintaining Iranian pistachio genotypes.

  5. Scaling of structural failure

    Energy Technology Data Exchange (ETDEWEB)

    Bazant, Z.P. [Northwestern Univ., Evanston, IL (United States); Chen, Er-Ping [Sandia National Lab., Albuquerque, NM (United States)

    1997-01-01

    This article attempts to review the progress achieved in the understanding of scaling and size effect in the failure of structures. Particular emphasis is placed on quasibrittle materials for which the size effect is complicated. Attention is focused on three main types of size effects, namely the statistical size effect due to randomness of strength, the energy release size effect, and the possible size effect due to fractality of fracture or microcracks. Definitive conclusions on the applicability of these theories are drawn. Subsequently, the article discusses the application of the known size effect law for the measurement of material fracture properties, and the modeling of the size effect by the cohesive crack model, nonlocal finite element models and discrete element models. Extensions to compression failure and to the rate-dependent material behavior are also outlined. The damage constitutive law needed for describing a microcracked material in the fracture process zone is discussed. Various applications to quasibrittle materials, including concrete, sea ice, fiber composites, rocks and ceramics are presented.

  6. Heart Failure Readmission Reduction.

    Science.gov (United States)

    Drozda, Joseph P; Smith, Donna A; Freiman, Paul C; Pursley, Janet; VanSlette, Jeffrey A; Smith, Timothy R

    Little is known regarding effectiveness of readmission reduction programs over time. The Heart Failure Management Program (HFMP) of St. John's Physician Group Practice (PGP) Demonstration provided an opportunity to assess outcomes over an extended period. Data from an electronic health record, an inpatient database, a disease registry, and the Social Security Death Master File were analyzed for patients admitted with heart failure (HF) for 5 years before (Period 1) and 5 years after (Period 2) inception of PGP. HF admissions decreased (Period 1, 58.3/month; Period 2, 52.4/month, P = .007). Thirty-day all-cause readmission rate dropped from Period 1 (annual average 18.8% [668/3545]) to year 1 of Period 2 (16.9% [136/804], P = .04) and remained stable thereafter (annual average 16.8% [589/3503]). Thirty-day mortality rate was flat throughout. HFMP was associated with decreased readmissions, primarily related to outpatient case management, while mortality remained stable.

  7. Use of Sequenom sample ID Plus® SNP genotyping in identification of FFPE tumor samples.

    Directory of Open Access Journals (Sweden)

    Jessica K Miller

    Full Text Available Short tandem repeat (STR analysis, such as the AmpFlSTR® Identifiler® Plus kit, is a standard, PCR-based human genotyping method used in the field of forensics. Misidentification of cell line and tissue DNA can be costly if not detected early; therefore it is necessary to have quality control measures such as STR profiling in place. A major issue in large-scale research studies involving archival formalin-fixed paraffin embedded (FFPE tissues is that varying levels of DNA degradation can result in failure to correctly identify samples using STR genotyping. PCR amplification of STRs of several hundred base pairs is not always possible when DNA is degraded. The Sample ID Plus® panel from Sequenom allows for human DNA identification and authentication using SNP genotyping. In comparison to lengthy STR amplicons, this multiplexing PCR assay requires amplification of only 76-139 base pairs, and utilizes 47 SNPs to discriminate between individual samples. In this study, we evaluated both STR and SNP genotyping methods of sample identification, with a focus on paired FFPE tumor/normal DNA samples intended for next-generation sequencing (NGS. The ability to successfully validate the identity of FFPE samples can enable cost savings by reducing rework.

  8. Sofosbuvir/velpatasvir regimen promises an effective pan-genotypic hepatitis C virus cure

    Science.gov (United States)

    Mir, Fazia; Kahveci, Alp S; Ibdah, Jamal A; Tahan, Veysel

    2017-01-01

    Hepatitis C virus (HCV) is a global pandemic, with nearly 200 million infected patients worldwide. HCV is the most common blood-borne infection in the US with numerous health implications including liver fibrosis, cirrhosis, and hepatocellular cancer. Traditional genotype-based HCV therapies with interferon resulted in moderate success in the sustained elimination of viral genome. Recent clinical trials of the once-daily combination tablet of sofosbuvir, a nonstructural (NS) 5B polymerase inhibitor, and velpatasvir, an NS5A inhibitor, demonstrate sustained virologic response rates of about 95%, regardless of prior treatment experience or presence of cirrhosis across all HCV genotypes. Patients reported improvements in general health, fatigue, and emotional and mental well-being after completing combination therapy. The combination treatment is effective, but does need to be administered with caution in patients receiving certain medications or with certain diseases. Herein, we review the safety and efficacy of sofosbuvir/velpatasvir combination regimen for all HCV genotypes.

  9. Insomnia Self-Management in Heart Failure

    Science.gov (United States)

    2016-12-07

    Cardiac Failure; Heart Failure; Congestive Heart Failure; Heart Failure, Congestive; Sleep Initiation and Maintenance Disorders; Chronic Insomnia; Disorders of Initiating and Maintaining Sleep; Fatigue; Pain; Depressive Symptoms; Sleep Disorders; Anxiety

  10. Automated SNP Genotype Clustering Algorithm to Improve Data Completeness in High-Throughput SNP Genotyping Datasets from Custom Arrays

    Institute of Scientific and Technical Information of China (English)

    Edward; M.; Smith; Jack; Littrell; Michael; Olivier

    2007-01-01

    High-throughput SNP genotyping platforms use automated genotype calling algo- rithms to assign genotypes. While these algorithms work efficiently for individual platforms, they are not compatible with other platforms, and have individual biases that result in missed genotype calls. Here we present data on the use of a second complementary SNP genotype clustering algorithm. The algorithm was originally designed for individual fluorescent SNP genotyping assays, and has been opti- mized to permit the clustering of large datasets generated from custom-designed Affymetrix SNP panels. In an analysis of data from a 3K array genotyped on 1,560 samples, the additional analysis increased the overall number of genotypes by over 45,000, significantly improving the completeness of the experimental data. This analysis suggests that the use of multiple genotype calling algorithms may be ad- visable in high-throughput SNP genotyping experiments. The software is written in Perl and is available from the corresponding author.

  11. Identification of Some Walnut Genotypes in Lorestan Province of Iran and Selection of 54 Superior Genotypes

    Directory of Open Access Journals (Sweden)

    A. Mohammadi

    2015-06-01

    Full Text Available Identification and selection of superior genotypes is the first step in walnut breeding programs. For identifying superior genotypes in Lorestan province, Iran, 35000 seedling genotypes were evaluated during 2008-2009. 29 Phenological traits were evaluated using IPGIRI descriptors in 288 selected seedling genotypes. Finally 54 promising genotypes with 10 major phenological traits were evaluated and classified to five groups. Based on the results, The first group included B17 alone as a late leafing genotype. The second group included A11, J14, K20, H19, M13, J1, B14, E14, E6, G17, M7, O9, B7, L6, L10, F12, D6, J15, J16, N5 and N15 genotypes with high kernel percentage, very bright kernel colors, less shell thickness and medium basal fruit pore. M9 with the highest kernel percent among all of the genotypes and 80% of lateral bearing, closed basal fruit pore, less shell thickness and high fruit and kernel weight was classified in another groupe. A7, C5, N3, N18, A17, D1, N14, D4, I4, J6, K17, N4, N19, C10, E13, N13 and N16 genotypes with medium to high fruit diameter, less shell thickness, medium fruit and kernel weight and kernel percentage were classified in the next group. The fifth group included 10 promising genotypes consisting A1, A2, C12, D10, D11, D13, F3, D17, A3, N7, I13, J7, K9 and N11 with quite late leafing and lateral fruit bearing of more than 90% .

  12. Zeolite 5A Catalyzed Etherification of Diphenylmethanol

    Science.gov (United States)

    Cooke, Jason; Henderson, Eric J.; Lightbody, Owen C.

    2009-01-01

    An experiment for the synthetic undergraduate laboratory is described in which zeolite 5A catalyzes the room temperature dehydration of diphenylmethanol, (C[subscript 6]H[subscript 5])[subscript 2]CHOH, producing 1,1,1',1'-tetraphenyldimethyl ether, (C[subscript 6]H[subscript 5])[subscript 2]CHOCH(C[subscript 6]H[subscript 5])[subscript 2]. The…

  13. Saponin profile of green asparagus genotypes.

    Science.gov (United States)

    Vázquez-Castilla, Sara; Jaramillo-Carmona, Sara; Fuentes-Alventosa, Jose María; Jiménez-Araujo, Ana; Rodríguez-Arcos, Rocío; Cermeño-Sacristán, Pedro; Espejo-Calvo, Juan Antonio; Guillén-Bejarano, Rafael

    2013-11-20

    The main goal of this study was to determine the saponin profiles of different "triguero" asparagus genotypes and to compare them to green asparagus commercial hybrids. The samples consisted of 31 commercial hybrids and 58 genotypes from the Huétor-Tájar (HT) population variety ("triguero"). The saponin analysis by high-performance liquid chromatography-mass spectrometry allowed for the determination of 12 saponins derived from a furostan-type steroidal genin, 4 of which had never been described in the edible part of asparagus. The saponin profile of "triguero" asparagus was a combination of these new saponins and protodioscin. Although protodioscin was the major saponin found in commercial hybrids, some of these 12 saponins were detected as major components in some of the commercial hybrids. The total contents of saponins described in some of these HT genotypes reach values as high as 10-100 times higher than those found in commercial hybrids.

  14. ABO Genotyping of Complete Hydatidiform Moles

    Directory of Open Access Journals (Sweden)

    R. A. Fisher

    1993-01-01

    Full Text Available It has been suggested that the ABO blood group of a patient and her partner influence the clinical outcome for patients having a pregnancy with a complete hydatidiform mole (CHM. Since CHM lack red blood Cells, it has not previously been possible to type CHM serologically and investigate the relationship between the blood group of the CHM and that of the patient. In the present study we have demonstrated the feasibility of using molecular genotyping to determine the ABO genotype of CHM, the ABO genotype being consistent with the androgenetic origin of CHM in all cases. In the series of 48 cases of CHM, the requirement for chemotherapy was not significantly different in those patients with a CHM of like blood group compared with those with a CHM of unlike blood group.

  15. An Application of Molecular Genotyping in Mice

    Directory of Open Access Journals (Sweden)

    Underkoffler Lara A.

    2003-01-01

    Full Text Available Microsatellite markers are simple sequence repeats within the mammalian genome that can be used for identifying disease loci, mapping genes of interest as well as studying segregation patterns related to meiotic nondisjunction. Different strains of mice have variable CA repeat lengths and PCR based methods can be used to identify them, thus allowing for specific genotypes to be assigned. Molecular genotyping offers such identification at any developmental stage, which allows for a broad range of anomalies to be studied. We studied chromosomal segregation in relation to nondisjunction in early-gestation mouse embryos using molecular genotyping. Information on the parental origin as well as the number of chromosomes a given progeny carried was obtained in our analysis.

  16. Tree species, tree genotypes and tree genotypic diversity levels affect microbe-mediated soil ecosystem functions in a subtropical forest

    OpenAIRE

    Purahong, Witoon; Durka, Walter; Fischer, Markus; Dommert, Sven; Schöps, Ricardo; Buscot, François; Wubet, Tesfaye

    2016-01-01

    Tree species identity and tree genotypes contribute to the shaping of soil microbial communities. However, knowledge about how these two factors influence soil ecosystem functions is still lacking. Furthermore, in forest ecosystems tree genotypes co-occur and interact with each other, thus the effects of tree genotypic diversity on soil ecosystem functions merit attention. Here we investigated the effects of tree species, tree genotypes and genotypic diversity levels, alongside soil physicoch...

  17. Daclatasvir vs telaprevir plus peginterferon alfa/ribavirin for hepatitis C virus genotype 1

    Science.gov (United States)

    Jacobson, Ira; Zeuzem, Stefan; Flisiak, Robert; Knysz, Brygida; Lueth, Stefan; Zarebska-Michaluk, Dorota; Janczewska, Ewa; Ferenci, Peter; Diago, Moises; Zignego, Anna Linda; Safadi, Rifaat; Baruch, Yaacov; Abdurakhmanov, Dzhamal; Shafran, Stephen; Thabut, Dominique; Bruck, Rafael; Gadano, Adrian; Thompson, Alexander James; Kopit, Justin; McPhee, Fiona; Michener, Tracy; Hughes, Eric A; Yin, Philip D; Noviello, Stephanie

    2016-01-01

    AIM: To evaluate daclatasvir vs telaprevir, each combined with peginterferon alfa-2a/ribavirin (pegIFN/RBV), in treatment-naive hepatitis C virus (HCV) genotype (GT) 1-infected patients. METHODS: In this phase 3, randomized, open-label, noninferiority study, 602 patients were randomly assigned (2:1) to daclatasvir vs telaprevir, stratified by IL28B rs12979860 host genotype (CC vs non-CC), cirrhosis status (compensated cirrhosis vs no cirrhosis), and HCV GT1 subtype (GT1a vs GT1b). Patients were selected by study inclusion criteria from a total of 793 enrolled patients. Patients received daclatasvir 60 mg once daily or telaprevir 750 mg 3 times daily plus pegIFN/RBV. Daclatasvir recipients received 24 wk of daclatasvir plus pegIFN/RBV; those without an extended rapid virologic response (eRVR; undetectable HCV-RNA at weeks 4 and 12) received an additional 24 wk of pegIFN/RBV. Telaprevir-treated patients received 12 wk of telaprevir plus pegIFN/RBV followed by 12 (with eRVR) or 36 (no eRVR) wk of pegIFN/RBV. The primary objective was to compare for noninferiority of sustained virologic response rates at posttreatment week 12 (SVR12) in GT1b-infected patients. Key secondary objectives were to demonstrate that the rates of anemia (hemoglobin < 10 g/dL) and rash-related events, through week 12, were lower with daclatasvir + pegIFN/RBV than with telaprevir + pegIFN/RBV among GT1b-infected patients. Resistance testing was performed using population-based sequencing of the NS5A region for all patients at baseline, and for patients with virologic failure or relapse and HCV-RNA ≥ 1000 IU/mL, to investigate any link between NS5A polymorphisms associated with daclatasvir resistance and virologic outcome. RESULTS: Patient demographics and disease characteristics were generally balanced across treatment arms; however, there was a higher proportion of black/African Americans in the daclatasvir groups (6.0% and 8.2% in the GT1b and GT1a groups, respectively) than in the

  18. Genome-Wide Association Mapping of Yield and Grain Quality Traits in Winter Wheat Genotypes.

    Directory of Open Access Journals (Sweden)

    W Tadesse

    Full Text Available The main goal of this study was to investigate the genetic basis of yield and grain quality traits in winter wheat genotypes using association mapping approach, and identify linked molecular markers for marker assisted selection. A total of 120 elite facultative/winter wheat genotypes were evaluated for yield, quality and other agronomic traits under rain-fed and irrigated conditions for two years (2011-2012 at the Tel Hadya station of ICARDA, Syria. The same genotypes were genotyped using 3,051 Diversity Array Technologies (DArT markers, of which 1,586 were of known chromosome positions. The grain yield performance of the genotypes was highly significant both in rain-fed and irrigated sites. Average yield of the genotypes ranged from 2295 to 4038 kg/ha and 4268 to 7102 kg/ha under rain-fed and irrigated conditions, respectively. Protein content and alveograph strength (W ranged from 13.6-16.1% and 217.6-375 Jx10-4, respectively. DArT markers wPt731910 (3B, wPt4680 (4A, wPt3509 (5A, wPt8183 (6B, and wPt0298 (2D were significantly associated with yield under rain-fed conditions. Under irrigated condition, tPt4125 on chromosome 2B was significantly associated with yield explaining about 13% of the variation. Markers wPt2607 and wPt1482 on 5B were highly associated with protein content and alveograph strength explaining 16 and 14% of the variations, respectively. The elite genotypes have been distributed to many countries using ICARDA's International system for potential direct release and/or use as parents after local adaptation trials by the NARSs of respective countries. The QTLs identified in this study are recommended to be used for marker assisted selection after through validation using bi-parental populations.

  19. Pretreatment HIV Drug Resistance and HIV-1 Subtype C Are Independently Associated With Virologic Failure: Results From the Multinational PEARLS (ACTG A5175) Clinical Trial

    Science.gov (United States)

    Kantor, Rami; Smeaton, Laura; Vardhanabhuti, Saran; Hudelson, Sarah E.; Wallis, Carol L.; Tripathy, Srikanth; Morgado, Mariza G.; Saravanan, Shanmugham; Balakrishnan, Pachamuthu; Reitsma, Marissa; Hart, Stephen; Mellors, John W.; Halvas, Elias; Grinsztejn, Beatriz; Hosseinipour, Mina C.; Kumwenda, Johnstone; La Rosa, Alberto; Lalloo, Umesh G.; Lama, Javier R.; Rassool, Mohammed; Santos, Breno R.; Supparatpinyo, Khuanchai; Hakim, James; Flanigan, Timothy; Kumarasamy, Nagalingeswaran; Campbell, Thomas B.; Eshleman, Susan H.

    2015-01-01

    Background. Evaluation of pretreatment HIV genotyping is needed globally to guide treatment programs. We examined the association of pretreatment (baseline) drug resistance and subtype with virologic failure in a multinational, randomized clinical trial that evaluated 3 antiretroviral treatment (ART) regimens and included resource-limited setting sites. Methods. Pol genotyping was performed in a nested case-cohort study including 270 randomly sampled participants (subcohort), and 218 additional participants failing ART (case group). Failure was defined as confirmed viral load (VL) >1000 copies/mL. Cox proportional hazards models estimated resistance–failure association. Results. In the representative subcohort (261/270 participants with genotypes; 44% women; median age, 35 years; median CD4 cell count, 151 cells/µL; median VL, 5.0 log10 copies/mL; 58% non-B subtypes), baseline resistance occurred in 4.2%, evenly distributed among treatment arms and subtypes. In the subcohort and case groups combined (466/488 participants with genotypes), used to examine the association between resistance and treatment failure, baseline resistance occurred in 7.1% (9.4% with failure, 4.3% without). Baseline resistance was significantly associated with shorter time to virologic failure (hazard ratio [HR], 2.03; P = .035), and after adjusting for sex, treatment arm, sex–treatment arm interaction, pretreatment CD4 cell count, baseline VL, and subtype, was still independently associated (HR, 2.1; P = .05). Compared with subtype B, subtype C infection was associated with higher failure risk (HR, 1.57; 95% confidence interval [CI], 1.04–2.35), whereas non-B/C subtype infection was associated with longer time to failure (HR, 0.47; 95% CI, .22–.98). Conclusions. In this global clinical trial, pretreatment resistance and HIV-1 subtype were independently associated with virologic failure. Pretreatment genotyping should be considered whenever feasible. Clinical Trials

  20. New product failure

    DEFF Research Database (Denmark)

    Dijksterhuis, Garmt Bernard

    2016-01-01

    When new consumer products are developed and later launched, 50 to 75 percent of them are removed from the market far short of meeting their projected financial targets. In short: they fail. We conclude that this failure is due to institutionalized insufficiencies in the use of the sciences...... these factors: (1) 'pillars' (too many different functions addressing different aspects of the consumers and of product development), (2) 'higher management focus' (not geared towards understanding consumer behaviour), (3) 'popular science books' (out-dated research directives resulting from a hierarchical...... that are best geared to understand and predict consumer behaviour, viz. the behavioural sciences. These are not necessarily the same as the marketing science that is performed by marketing departments. A scientific approach to understanding consumer behaviour appears to be lacking in many corporate research...

  1. Premature ovarian failure.

    Science.gov (United States)

    Shelling, Andrew N

    2010-11-01

    Premature ovarian failure (POF) is a common cause of infertility in women, and is characterised by amenorrhoea, hypo-oestrogenism and elevated gonadotrophin levels in women under the age of 40. Known causes include iatrogenic agents that cause permanent damage to the ovaries, such as chemotherapy, radiation therapy and surgery, autoimmune conditions, X-chromosome abnormalities and autosomal genetic conditions. However, few genes have been identified that can explain a substantial proportion of cases of POF. Most women with POF are deeply upset by the diagnosis, partly due to the unexpected menopausal symptoms, but also due to infertility. Therefore, early detection would provide better opportunity for early intervention, and furthermore, the identification of specific gene defects will help to direct potential targets for future treatment.

  2. Iridium: failures & successes

    Science.gov (United States)

    Christensen, CarissaBryce; Beard, Suzette

    2001-03-01

    This paper will provide an overview of the Iridium business venture in terms of the challenges faced, the successes achieved, and the causes of the ultimate failure of the venture — bankruptcy and system de-orbit. The paper will address technical, business, and policy issues. The intent of the paper is to provide a balanced and accurate overview of the Iridium experience, to aid future decision-making by policy makers, the business community, and technical experts. Key topics will include the history of the program, the objectives and decision-making of Motorola, the market research and analysis conducted, partnering strategies and their impact, consumer equipment availability, and technical issues — target performance, performance achieved, technical accomplishments, and expected and unexpected technical challenges. The paper will use as sources trade media and business articles on the Iridium program, technical papers and conference presentations, Wall Street analyst's reports, and, where possible, interviews with participants and close observers.

  3. Promoter polymorphism MMP-1 (-1607 2G/1G) and MMP-3 (-1612 5A/6A) in development of HAND and modulation of pathogenesis of HAND

    Indian Academy of Sciences (India)

    HARI OM SINGH; SHRUTI D MARATHE; SUMITRA NAIN; DHARMESH SAMANI; VIJAY NEMA; MANISHAV GHATE; R R GANGAKHEDKAR

    2017-09-01

    The pathogenesis of HIV-associated neurocognitive disorder (HAND) is modulated by host genetic susceptibility factorssuch as Matrix metalloproteinases (MMPs). Promoter polymorphism of MMP-1 and MMP-3 may modify the expression ofthe gene. Hence, we evaluated the association of MMP-1-16072G/1G and MMP-3-1612 5A/6A polymorphisms withdevelopment of HAND and the modulation of pathogenesis of HAND. We enrolled a total of 180 individuals, 50 HIVinfectedindividuals with HAND, 130 without HAND, and 150 healthy controls. Polymorphism of MMP-1 and MMP-3were genotyped by PCR-RFLP. MMP-1-1607 2G1G, -16071G/2G-1G/1G genotypes and -1607 1G allele were associatedwith the development of HAND (OR = 1.64, P = 0.05; OR = 1.45, P = 0.04; OR = 1.69, P = 0.05). MMP-1-16071G1G, MMP-3-16125A5A genotypes increased the risk for the development of HAND (OR = 1.78, P = 0.25;OR = 2.39, P = 0.13). MMP-3-1612 5A5A, -1612 6A/5A-5A/5A genotypes and -1612 5A allele were associated with thereduced risk of HAND (OR = 0.40, P = 0.05; OR = 0.53, P = 0.04; OR = 0.40, P = 0.01). Haplotype 5A1G increasedthe risk of development of HAND (OR = 1.93, P = 0.05). As observed in advanced HIV disease stage, MMP-1-16071G1G genotype enhance the risk for advancement of HIV disease (OR = 1.69, P = 0.89). MMP-3-1612 6A5A genotypeshowed higher risk for development of HAND in alcohol users (0R = 1.65, P = 0.44). MMP-1 genotype may have aninfluence on development of HAND whereas MMP3-1612 5A5A genotype may reduce risk for pathogenesis of HAND.

  4. Premature ovarian failure

    Directory of Open Access Journals (Sweden)

    Vujović Svetlana

    2012-01-01

    Full Text Available Premature ovarian failure (POF is the occurrence of hypergonadotropic hypoestrogenic amenorrhea in women under the age of forty years. It is idiopathic in 74-90% patients. Known cases can be divided into primary and secondary POF. In primary POF genetic aberrations can involve the X chromosome (monosomy, trisomy, translocations, deletions or autosomes. Genetic mechanisms include reduced gene dosage and non-specific chromosome effects impairing meiosis, decreasing the pool of primordial follicles and increasing atresia due to apoptosis or failure of follicle maturation. Autoimmune ovarian damage is caused by alteration of T-cell subsets and T-cell mediated injury, increase of autoantibody producing B-cells, a low number of effector/cytotoxic lymphocyte, which decreases the number and activity of natural killer cells. Bilateral oophorectomy, chemotherapy, radiotherapy and infections cause the secondary POF. Symptoms of POF include irritability, nervousness, loss of libido, depression, lack of concentration, hot flushes, weight gaining, dry skin, vaginal dryness, frequent infections etc. The diagnosis is confirmed by the level of FSH of over 40 IU/L and estradiol below 50 pmol/L in women aged below 40 years. Biochemical and other hormonal analysis (free thyroxin, TSH, prolactin, testosterone, karyotype (<30 years of age, ultrasound of the breasts and pelvis are advisable. Optimal therapy is combined estrogen progestagen therapy given in a sequential rhythm, after excluding absolute contraindications. Testosterone can be added to adnexectomized women and those with a low libido. Sequential estrogen progestagen replacement therapy is the first line therapy for ovulation induction in those looking for pregnancy and after that oocyte donation will be advised. Appropriate estro-progestagen therapy improves the quality of life and prevents complications such as cardiovascular diseases, osteoporosis, stroke etc.

  5. CHRONIC RENAL FAILURE TODAY

    Directory of Open Access Journals (Sweden)

    Svetislav Kostić

    2004-07-01

    Full Text Available The syndrome of chronic renal failure (CRF is already known for more than 150 years. Current research in this domain changed our understanding in epidemiology, aetiology, prevention of disease progression, classifications, definition, and adequate treatment of comorbid conditions in predialytic period. With data collection and registration on CRF patients it is obvious an increase in prevalence and incidence of patients with CRF in the world. The diabetic nephropathy is the most common disease leading in 40% of cases to terminal CRF. In the follow up of these patients the most important goal is slowing down the disease progression with low protein diet (0,6-0,8 g/kg BW/day and vigorous blood pressure control (target values: 120-135/75-85 mmHg. The adequate therapy of anaemia and secondary hyperparathyroidism including predialytic use of erythopoietin and vitamin D significantly slow down the progression of CRF and postpones the beginning of dialytic treatment. Numerous comorbid conditions present in predialytic period fasten the progression of CRF. The most common are of cardiovascular origin (congestive heart failure and coronary artery disease. Those cardiovascular comorbid conditions have an impact on CRF progresion as well as on the outcome in dialytic therapy. The most common causes of cardiovascular comorbidity are hypertension, anemia and secondary hyperparathyroidism, all of which should be treated in predialytic period. Of special concern is use of nephrotoxic drugs, particularly nephrotoxic antibioticsaminoglycosides. The optimal timing of creation of permanent vascular access and vaccination against hepatitis B in predialytic period are cost-effective and have an impact on quality of dialysis.

  6. Multiple interactions between the alpha2C- and beta1-adrenergic receptors influence heart failure survival

    Directory of Open Access Journals (Sweden)

    Case Karen L

    2008-10-01

    Full Text Available Abstract Background Persistent stimulation of cardiac β1-adrenergic receptors by endogenous norepinephrine promotes heart failure progression. Polymorphisms of this gene are known to alter receptor function or expression, as are polymorphisms of the α2C-adrenergic receptor, which regulates norepinephrine release from cardiac presynaptic nerves. The purpose of this study was to investigate possible synergistic effects of polymorphisms of these two intronless genes (ADRB1 and ADRA2C, respectively on the risk of death/transplant in heart failure patients. Methods Sixteen sequence variations in ADRA2C and 17 sequence variations in ADRB1 were genotyped in a longitudinal study of 655 white heart failure patients. Eleven sequence variations in each gene were polymorphic in the heart failure cohort. Cox proportional hazards modeling was used to identify polymorphisms and potential intra- or intergenic interactions that influenced risk of death or cardiac transplant. A leave-one-out cross-validation method was utilized for internal validation. Results Three polymorphisms in ADRA2C and five polymorphisms in ADRB1 were involved in eight cross-validated epistatic interactions identifying several two-locus genotype classes with significant relative risks ranging from 3.02 to 9.23. There was no evidence of intragenic epistasis. Combining high risk genotype classes across epistatic pairs to take into account linkage disequilibrium, the relative risk of death or transplant was 3.35 (1.82, 6.18 relative to all other genotype classes. Conclusion Multiple polymorphisms act synergistically between the ADRA2C and ADRB1 genes to increase risk of death or cardiac transplant in heart failure patients.

  7. Genotype 1 hepatitis C virus envelope features that determine antiviral response assessed through optimal covariance networks.

    Directory of Open Access Journals (Sweden)

    John M Murray

    Full Text Available The poor response to the combined antiviral therapy of pegylated alfa-interferon and ribavarin for hepatitis C virus (HCV infection may be linked to mutations in the viral envelope gene E1E2 (env, which can result in escape from the immune response and higher efficacy of viral entry. Mutations that result in failure of therapy most likely require compensatory mutations to achieve sufficient change in envelope structure and function. Compensatory mutations were investigated by determining positions in the E1E2 gene where amino acids (aa covaried across groups of individuals. We assessed networks of covarying positions in E1E2 sequences that differentiated sustained virological response (SVR from non-response (NR in 43 genotype 1a (17 SVR, and 49 genotype 1b (25 SVR chronically HCV-infected individuals. Binary integer programming over covariance networks was used to extract aa combinations that differed between response groups. Genotype 1a E1E2 sequences exhibited higher degrees of covariance and clustered into 3 main groups while 1b sequences exhibited no clustering. Between 5 and 9 aa pairs were required to separate SVR from NR in each genotype. aa in hypervariable region 1 were 6 times more likely than chance to occur in the optimal networks. The pair 531-626 (EI appeared frequently in the optimal networks and was present in 6 of 9 NR in one of the 1a clusters. The most frequent pairs representing SVR were 431-481 (EE, 500-522 (QA in 1a, and 407-434 (AQ in 1b. Optimal networks based on covarying aa pairs in HCV envelope can indicate features that are associated with failure or success to antiviral therapy.

  8. LETTER TO THE EDITOR Performance of the ViroSeq® HIV-1 Genotyping System v2.0 in Central Africa.

    Science.gov (United States)

    Mouafo, Linda Chapdeleine Mekue; Péré, Hélène; Ndjoyi-Mbiguino, Angélique; Koyalta, Donato; Longo, Jean De Dieu; Mbopi-Kéou, François-Xavier; Kane, Coumba Toure; Bélec, Laurent

    2015-01-01

    Resistance genotypes in pol gene of HIV-1 were obtained by the ViroSeq(®) HIV-1 Genotyping System v2.0 (Celera Diagnostics, Alameda, CA, USA) in 138 of 145 (95%) antiretroviral treatment-experienced adults in virological failure living in Central Africa (Cameroon, Central African Republic, Chad, Gabon). HIV-1 group M exhibited broad genetic diversity. Performance of the 7 ViroSeq(®) sequencing primers showed high failure rate, from 3% to 76% (D: 76%; F: 17%; A and H: 15%; G and B: 4%; C: 3%). These findings emphasize the need of updating the ViroSeq(®) HIV-1 genotyping system for non-B subtypes HIV-1.

  9. A Failure Criterion for Concrete

    DEFF Research Database (Denmark)

    Ottosen, N. S.

    1977-01-01

    A four-parameter failure criterion containing all the three stress invariants explicitly is proposed for short-time loading of concrete. It corresponds to a smooth convex failure surface with curved meridians, which open in the negative direction of the hydrostatic axis, and the trace in the devi......A four-parameter failure criterion containing all the three stress invariants explicitly is proposed for short-time loading of concrete. It corresponds to a smooth convex failure surface with curved meridians, which open in the negative direction of the hydrostatic axis, and the trace...

  10. A Failure Criterion for Concrete

    DEFF Research Database (Denmark)

    Ottosen, N. S.

    1977-01-01

    A four-parameter failure criterion containing all the three stress invariants explicitly is proposed for short-time loading of concrete. It corresponds to a smooth convex failure surface with curved meridians, which open in the negative direction of the hydrostatic axis, and the trace in the devi......A four-parameter failure criterion containing all the three stress invariants explicitly is proposed for short-time loading of concrete. It corresponds to a smooth convex failure surface with curved meridians, which open in the negative direction of the hydrostatic axis, and the trace...

  11. Strategies of learning from failure.

    Science.gov (United States)

    Edmondson, Amy C

    2011-04-01

    Many executives believe that all failure is bad (although it usually provides Lessons) and that Learning from it is pretty straightforward. The author, a professor at Harvard Business School, thinks both beliefs are misguided. In organizational life, she says, some failures are inevitable and some are even good. And successful learning from failure is not simple: It requires context-specific strategies. But first leaders must understand how the blame game gets in the way and work to create an organizational culture in which employees feel safe admitting or reporting on failure. Failures fall into three categories: preventable ones in predictable operations, which usually involve deviations from spec; unavoidable ones in complex systems, which may arise from unique combinations of needs, people, and problems; and intelligent ones at the frontier, where "good" failures occur quickly and on a small scale, providing the most valuable information. Strong leadership can build a learning culture-one in which failures large and small are consistently reported and deeply analyzed, and opportunities to experiment are proactively sought. Executives commonly and understandably worry that taking a sympathetic stance toward failure will create an "anything goes" work environment. They should instead recognize that failure is inevitable in today's complex work organizations.

  12. Failure Mode/Mechanism Distributions

    Science.gov (United States)

    1991-09-01

    nsc. Modas /Mach Dist. Dist. Suurce(,%)/Detai19 Bolt, MahineSources :1 Brcikon 𔃺.1% 59.0% Broken Bolt(s) (25j01-(000,Qty:l) C25101-000,Qty:Ij., Part...Center (RAC) * 201 Mill St., Rome, NY 13440 * 315-337-0900 3-114 Failure Distribution Summaries FMD-91 ? art Failure Norm Fail Data Docm. Mode/Moch Dist... Deco . Mode/Mech Dist. Dist. Source(s)/Details Lamp,Bulb Sourcent 4 Lamp Failure 68.8% 53.8% Light Bulb Failure (23038-00l,Qty:3) (23038-004,Qty:l

  13. Robust and persistent replication of the genotype 6a hepatitis C virus replicon in cell culture.

    Science.gov (United States)

    Yu, Mei; Peng, Betty; Chan, Katie; Gong, Ruoyu; Yang, Huiling; Delaney, William; Cheng, Guofeng

    2014-05-01

    Genotype 6 (GT6) hepatitis C virus (HCV) is prevalent in Southeast Asia and southern China, where it can constitute up to 50% of HCV infections. Despite this, no direct-acting antivirals are approved to treat GT6 HCV infection, and no cell culture systems have been described. In this study, we aimed to develop a GT6 HCV subgenomic replicon to facilitate the identification and development of new HCV therapies with pan-genotype activity. A subgenomic replicon cDNA encoding a GT6a consensus sequence plus an NS5A amino acid substitution (S232I) was synthesized. Electroporation of RNA encoding the GT6a replicon into Huh-7-derived cells consistently yielded 20 to 100 stable replicon colonies. Genotypic analyses of individual replicon colonies revealed new adaptive mutations across multiple viral nonstructural proteins. The E30V and K272R mutations in NS3 and the K34R mutation in NS4A were observed most frequently and were confirmed to enhance GT6a replicon replication in the presence of the NS5A amino acid substitution S232I. These new adaptive mutations allowed establishment of robust luciferase-encoding GT6a replicons for reproducible quantification of HCV replication, and the luciferase-encoding replicons enabled efficient determinations of antiviral activity for HCV inhibitors in a 384-well assay format. While nucleoside/nucleotide NS5B inhibitors and cyclophilin A inhibitors had similar antiviral activities against both GT6a and GT1b replicons, some nonnucleoside NS5B inhibitors, NS3 protease inhibitors, and NS5A inhibitors had less antiviral activity against GT6a replicons. In conjunction with other genotype replicons, this robust GT6a replicon system will aid in the development of pan-genotypic HCV regimens.

  14. Therapie der chronischen Hepatitis C Genotyp 1 – Update 2015

    Directory of Open Access Journals (Sweden)

    Gschwantler M

    2015-01-01

    Full Text Available Die Therapie der chronischen Hepatitis C hat sich während der vergangenen zwei Jahre fundamental verändert. Durch eine Kombination von zwei oder drei neuen DAAs („direct acting antiviral agents“ kann bei fast allen Patienten eine Elimination des Virus praktisch ohne Nebenwirkungen erzielt werden. Auch bei den meisten Patienten mit dekompensierter Leberzirrhose konnte nach virologischer Heilung innerhalb weniger Wochen eine Verbesserung der Leberfunktion beobachtet werden. Derzeit stehen in Österreich folgende neue DAAs für die Therapie zur Verfügung: Die Proteasehemmer Simeprevir und Paritaprevir, die NS5A-Inhibitoren Daclatasvir, Ledipasvir und Ombitasvir, sowie die Polymerasehemmer Sofosbuvir und Dasabuvir. Die effektivsten Therapieregime beim Genotyp 1 sind die Kombinationen Sofosbuvir/Simeprevir, Sofosbuvir/Daclatasvir, Sofosbuvir/Ledipasvir und Paritaprevir/Ritonavir/Ombitasvir/Dasabuvir.

  15. Robust HCV Genotype 3a Infectious Cell Culture System Permits Identification of Escape Variants With Resistance to Sofosbuvir

    DEFF Research Database (Denmark)

    Ramirez Almeida, Santseharay; Mikkelsen, Lotte S.; Gottwein, Judith M.

    2016-01-01

    barrier to resistance for sofosbuvir, whereas resistance to this DAA can be induced in genotype 3a. We therefore isolated HCV genotype 3a variants with reduced sensitivity to sofosbuvir, with increased fitness and with cross-resistance to other NS5B inhibitors. These findings indicate that sofosbuvir......Background & Aims Direct-acting antivirals (DAAs) effectively eradicate chronic hepatitis C virus (HCV) infection, although HCV genotype 3a is less responsive to these drugs. We aimed to develop genotype 3a infectious cultures and study the effects of inhibitors of NS5A and NS5B and resistance...... with increasing concentrations of sofosbuvir was used to promote selection of HCV-resistant variants. Results We engineered a DBN3a variant with 17 substitutions (DBN3acc) that had replication and propagation kinetics in Huh7.5 cells comparable with prototype J6/JFH1. The adaptive mutations also produced culture...

  16. Gel versus capillary electrophoresis genotyping for categorizing treatment outcomes in two anti-malarial trials in Uganda

    Science.gov (United States)

    2010-01-01

    Background Molecular genotyping is performed in anti-malarial trials to determine whether recurrent parasitaemia after therapy represents a recrudescence (treatment failure) or new infection. The use of capillary instead of agarose gel electrophoresis for genotyping offers technical advantages, but it is unclear whether capillary electrophoresis will result in improved classification of anti-malarial treatment outcomes. Methods Samples were genotyped using both gel and capillary electrophoresis from randomized trials of artemether-lumefantrine (AL) vs. dihydroartemisinin-piperaquine (DP) performed in two areas of Uganda: Kanungu, where transmission is moderate, and Apac, where transmission is very high. Both gel and capillary methods evaluated polymorphic regions of the merozoite surface protein 1 and 2 and glutamine rich protein genes. Results Capillary electrophoresis detected more alleles and provided higher discriminatory power than agarose gel electrophoresis at both study sites. There was only moderate agreement between classification of outcomes with the two methods in Kanungu (kappa = 0.66) and poor agreement in Apac (kappa = 0.24). Overall efficacy results were similar when using gel vs. capillary methods in Kanungu (42-day risk of treatment failure for AL: 6.9% vs. 5.5%, p = 0.4; DP 2.4% vs. 2.9%, p = 0.5). However, the measured risk of recrudescence was significantly higher when using gel vs. capillary electrophoresis in Apac (risk of treatment failure for AL: 17.0% vs. 10.7%, p = 0.02; DP: 8.5% vs. 3.4%, p = 0.03). Risk differences between AL and DP were not significantly different whether gel or capillary methods were used. Conclusions Genotyping with gel electrophoresis overestimates the risk of recrudescence in anti-malarial trials performed in areas of high transmission intensity. Capillary electrophoresis provides more accurate outcomes for such trials and should be performed when possible. In areas of moderate transmission, gel electrophoresis

  17. Specificity of the Linear Array HPV Genotyping Test for detecting human papillomavirus genotype 52 (HPV-52)

    OpenAIRE

    Kocjan, Boštjan; Poljak, Mario; Oštrbenk, Anja

    2015-01-01

    Introduction: HPV-52 is one of the most frequent human papillomavirus (HPV) genotypes causing significant cervical pathology. The most widely used HPV genotyping assay, the Roche Linear Array HPV Genotyping Test (Linear Array), is unable to identify HPV- 52 status in samples containing HPV-33, HPV-35, and/or HPV-58. Methods: Linear Array HPV-52 analytical specificity was established by testing 100 specimens reactive with the Linear Array HPV- 33/35/52/58 cross-reactive probe, but not with the...

  18. Public Choice, Market Failure, and Government Failure in Principles Textbooks

    Science.gov (United States)

    Fike, Rosemarie; Gwartney, James

    2015-01-01

    Public choice uses the tools of economics to analyze how the political process allocates resources and impacts economic activity. In this study, the authors examine twenty-three principles texts regarding coverage of public choice, market failure, and government failure. Approximately half the texts provide coverage of public choice and recognize…

  19. Public Choice, Market Failure, and Government Failure in Principles Textbooks

    Science.gov (United States)

    Fike, Rosemarie; Gwartney, James

    2015-01-01

    Public choice uses the tools of economics to analyze how the political process allocates resources and impacts economic activity. In this study, the authors examine twenty-three principles texts regarding coverage of public choice, market failure, and government failure. Approximately half the texts provide coverage of public choice and recognize…

  20. Use of supplementary genotypes in AMMI analysis.

    Science.gov (United States)

    Pacheco, R M; Duarte, J B; Vencovsky, R; Pinheiro, J B; Oliveira, A B

    2005-03-01

    Improving stability of crop yield in a target production environment is an important breeding objective. It is well known that selection for better stability generally results in lower mean yields and, conversely, that selection for higher mean yields may lead to poorer stability. This paper explores the equivalence between the singular value decomposition used in AMMI analysis and the spectral decomposition used in principal components analysis. This equivalence enables scores of a "supplementary genotype" made up of the highest yield value within each environment to be obtained, and these may serve as the ideal check treatment for selection purposes. These scores are used to (1) display this check in a biplot graph, thereby providing a qualitative comparison with the real genotypes related to their interaction with environments; (2) obtain estimates of the squared distances from the projection of each real genotype to the projection of the "supplementary treatment", thereby allowing conclusions to be made on the yield stability of each real genotype. This procedure was effective in identifying the most stable soybean cultivars in an example shown for illustration.

  1. Polyembryony in non-apomictic citrus genotypes

    Science.gov (United States)

    Aleza, Pablo; Juárez, José; Ollitrault, Patrick; Navarro, Luis

    2010-01-01

    Background and Aims Adventitious embryony from nucellar cells is the mechanism leading to apomixis in Citrus sp. However, singular cases of polyembryony have been reported in non-apomictic genotypes as a consequence of 2x × 4x hybridizations and in vitro culture of isolated nucelli. The origin of the plants arising from the aforementioned processes remains unclear. Methods The genetic structure (ploidy and allelic constitution with microsatellite markers) of plants obtained from polyembryonic seeds arising from 2x × 4x sexual hybridizations and those regenerated from nucellus culture in vitro was systematically analysed in different non-apomictic citrus genotypes. Histological studies were also conducted to try to identify the initiation process underlying polyembryony. Key Results All plants obtained from the same undeveloped seed in 2x × 4x hybridizations resulted from cleavage of the original zygotic embryo. Also, the plants obtained from in vitro nucellus culture were recovered by somatic embryogenesis from cells that shared the same genotype as the zygotic embryos of the same seed. Conclusions It appears that in non-apomictic citrus genotypes, proembryos or embryogenic cells are formed by cleavage of the zygotic embryos and that the development of these adventitious embryos, normally hampered, can take place in vivo or in vitro as a result of two different mechanisms that prevent the dominance of the initial zygotic embryo. PMID:20675656

  2. Phenotyping peanut genotypes for drought tolerance

    Science.gov (United States)

    Drought and heat stress can result in aflatoxin contamination of peanuts especially when this occurs during the last three to six weeks of the growing season. Identifying drought-tolerant genotypes may aid in development of peanuts that are less susceptible to aflatoxin contamination. This study w...

  3. Investigation of Effect of STAT5A Gene on Milk Yield and Composition in Jersey Cows

    Directory of Open Access Journals (Sweden)

    Soner Çankaya

    2014-06-01

    Full Text Available In this study, the effect of STAT5A gene was investigated on milk yield and components (fat, protein in Jersey cows. Because, this gene is a member of the signal transducers and activators of transcription the factor (STAT family and thought to be the impact on milk yield and components. As a material in the research, 100 Jersey cows raised in Samsun Karakoy State Farm were used. Milk samples were collected 12 times with one month intervals after calving, and these samples were performed by ultrasonic milk analyzer for milk fat and protein content. In addition, test day milk yield (TDMY of each cow were also recorded in the control days. C/G polymorphism with PCR-RFLP method result in DNA isolation from blood samples taken from cows was determined at 8.exon at position 12195. Genotype distribution was detected as 69% CC, 28% CG and 3% GG. Allele frequencies were found as 0.83 for the C allele and 0.17 for G allele. As a result of the polymorphism identified in STAT5A gene, statistically no difference were detected among genotypes for TDMY, 305 day milk yield (305 DMY, milk fat and protein rates and milk fat and protein yield. As a result, no significant differences were found between the milk yield and compositions association with STAT5A

  4. 6 HCV genotyping 9G test and its comparison with VERSANT HCV genotype 2.0 assay (LiPA) for the hepatitis C virus genotyping.

    Science.gov (United States)

    Chantratita, Wasun; Song, Keum-Soo; GunHo, Choi; Pongthanapisith, Viroj; Thongbaiphet, Nipa; Wongtabtim, Garanyuta; Pasomsub, Ekawat; Angkanavin, Kanokwan; Nimse, Satish Balasaheb; Sonawane, Mukesh Digambar; Warkad, Shrikant Dasharath; Kim, Taisun

    2017-01-01

    In this article, we describe the 6 HCV Genotyping 9G test and its evaluation by using clinical samples and plasmid DNA standards. In tests with 981 plasmid DNA standards, the 6 HCV Genotyping 9G test showed higher than 92.5% sensitivity and 99.4% specificity. The 6 HCV Genotyping 9G test was compared with the VERSANT HCV Genotype 2.0 assay (LiPA 2.0) for detection and discrimination of HCV genotypes in clinical samples. The results of both tests were verified by genomic sequencing. The 6 HCV Genotyping 9G test demonstrated a 100% agreement with the sequencing results, which was higher than LiPA 2.0. These results indicate that the 6 HCV Genotyping 9G test can be a reliable, sensitive, and accurate diagnostic tool for the correct identification of HCV genotypes in clinical specimens. 6 HCV Genotyping 9G test can genotype six HCV types in 1 PCR in 30min after PCR amplification. The 6 HCV Genotyping 9G test, thus provide critical information to physicians and assist them to apply accurate drug regimen for the effective hepatitis C treatment.

  5. Parvovirus B19 genotype specific amino acid substitution in NS1 reduces the protein's cytotoxicity in culture.

    Science.gov (United States)

    Kivovich, Violetta; Gilbert, Leona; Vuento, Matti; Naides, Stanley J

    2010-05-25

    A clinical association between idiopathic liver disease and parvovirus B19 infection has been observed. Fulminant liver failure, not associated with other liver-tropic viruses, has been attributed to B19 in numerous reports, suggesting a possible role for B19 components in the extensive hepatocyte cytotoxicity observed in this condition. A recent report by Abe and colleagues (Int J Med Sci. 2007;4:105-9) demonstrated a link between persistent parvovirus B19 genotype I and III infection and fulminant liver failure. The genetic analysis of isolates obtained from these patients demonstrated a conservation of key amino acids in the nonstructural protein 1 (NS1) of the disease-associated genotypes. In this report we examine a conserved residue identified by Abe and colleagues and show that substitution of isoleucine 181 for methionine, as occurs in B19 genotype II, results in the reduction of B19 NS1-induced cytotoxicity of liver cells. Our results support the hypothesis that in the setting of persistent B19 infection, direct B19 NS1-induced cytotoxicity may play a role in idiopathic fulminant liver failure.

  6. Parvovirus B19 Genotype Specific Amino Acid Substitution in NS1 Reduces the Protein's Cytotoxicity in Culture

    Directory of Open Access Journals (Sweden)

    Violetta Kivovich, Leona Gilbert, Matti Vuento, Stanley J. Naides

    2010-01-01

    Full Text Available A clinical association between idiopathic liver disease and parvovirus B19 infection has been observed. Fulminant liver failure, not associated with other liver-tropic viruses, has been attributed to B19 in numerous reports, suggesting a possible role for B19 components in the extensive hepatocyte cytotoxicity observed in this condition. A recent report by Abe and colleagues (Int J Med Sci. 2007;4:105-9 demonstrated a link between persistent parvovirus B19 genotype I and III infection and fulminant liver failure. The genetic analysis of isolates obtained from these patients demonstrated a conservation of key amino acids in the nonstructural protein 1 (NS1 of the disease-associated genotypes. In this report we examine a conserved residue identified by Abe and colleagues and show that substitution of isoleucine 181 for methionine, as occurs in B19 genotype II, results in the reduction of B19 NS1-induced cytotoxicity of liver cells. Our results support the hypothesis that in the setting of persistent B19 infection, direct B19 NS1-induced cytotoxicity may play a role in idiopathic fulminant liver failure.

  7. Identification of zoonotic genotypes of Giardia duodenalis.

    Science.gov (United States)

    Sprong, Hein; Cacciò, Simone M; van der Giessen, Joke W B

    2009-12-01

    Giardia duodenalis, originally regarded as a commensal organism, is the etiologic agent of giardiasis, a gastrointestinal disease of humans and animals. Giardiasis causes major public and veterinary health concerns worldwide. Transmission is either direct, through the faecal-oral route, or indirect, through ingestion of contaminated water or food. Genetic characterization of G. duodenalis isolates has revealed the existence of seven groups (assemblages A to G) which differ in their host distribution. Assemblages A and B are found in humans and in many other mammals, but the role of animals in the epidemiology of human infection is still unclear, despite the fact that the zoonotic potential of Giardia was recognised by the WHO some 30 years ago. Here, we performed an extensive genetic characterization of 978 human and 1440 animal isolates, which together comprise 3886 sequences from 4 genetic loci. The data were assembled into a molecular epidemiological database developed by a European network of public and veterinary health Institutions. Genotyping was performed at different levels of resolution (single and multiple loci on the same dataset). The zoonotic potential of both assemblages A and B is evident when studied at the level of assemblages, sub-assemblages, and even at each single locus. However, when genotypes are defined using a multi-locus sequence typing scheme, only 2 multi-locus genotypes (MLG) of assemblage A and none of assemblage B appear to have a zoonotic potential. Surprisingly, mixtures of genotypes in individual isolates were repeatedly observed. Possible explanations are the uptake of genetically different Giardia cysts by a host, or subsequent infection of an already infected host, likely without overt symptoms, with a different Giardia species, which may cause disease. Other explanations for mixed genotypes, particularly for assemblage B, are substantial allelic sequence heterogeneity and/or genetic recombination. Although the zoonotic

  8. Multivariate Analysis of Genotype-Phenotype Association.

    Science.gov (United States)

    Mitteroecker, Philipp; Cheverud, James M; Pavlicev, Mihaela

    2016-04-01

    With the advent of modern imaging and measurement technology, complex phenotypes are increasingly represented by large numbers of measurements, which may not bear biological meaning one by one. For such multivariate phenotypes, studying the pairwise associations between all measurements and all alleles is highly inefficient and prevents insight into the genetic pattern underlying the observed phenotypes. We present a new method for identifying patterns of allelic variation (genetic latent variables) that are maximally associated-in terms of effect size-with patterns of phenotypic variation (phenotypic latent variables). This multivariate genotype-phenotype mapping (MGP) separates phenotypic features under strong genetic control from less genetically determined features and thus permits an analysis of the multivariate structure of genotype-phenotype association, including its dimensionality and the clustering of genetic and phenotypic variables within this association. Different variants of MGP maximize different measures of genotype-phenotype association: genetic effect, genetic variance, or heritability. In an application to a mouse sample, scored for 353 SNPs and 11 phenotypic traits, the first dimension of genetic and phenotypic latent variables accounted for >70% of genetic variation present in all 11 measurements; 43% of variation in this phenotypic pattern was explained by the corresponding genetic latent variable. The first three dimensions together sufficed to account for almost 90% of genetic variation in the measurements and for all the interpretable genotype-phenotype association. Each dimension can be tested as a whole against the hypothesis of no association, thereby reducing the number of statistical tests from 7766 to 3-the maximal number of meaningful independent tests. Important alleles can be selected based on their effect size (additive or nonadditive effect on the phenotypic latent variable). This low dimensionality of the genotype-phenotype map

  9. RAB5A — EDRN Public Portal

    Science.gov (United States)

    From UniProtKB/Swiss-Prot: The small GTPases Rab are key regulators of intracellular membrane trafficking, from the formation of transport vesicles to their fusion with membranes. Rabs cycle between an inactive GDP-bound form and an active GTP-bound form that is able to recruit to membranes different sets of downstream effectors directly responsible for vesicle formation, movement, tethering and fusion. RAB5A is required for the fusion of plasma membranes and early endosomes. Contributes to the regulation of filopodia extension.

  10. The potential of plant viruses to promote genotypic diversity via genotype x environment interactions

    DEFF Research Database (Denmark)

    van Mölken, Tamara; Stuefer, Josef F.

    2011-01-01

    † Background and Aims Genotype by environment (G × E) interactions are important for the long-term persistence of plant species in heterogeneous environments. It has often been suggested that disease is a key factor for the maintenance of genotypic diversity in plant populations. However, empirical...... evidence for this contention is scarce. Here virus infection is proposed as a possible candidate for maintaining genotypic diversity in their host plants. † Methods The effects of White clover mosaic virus (WClMV) on the performance and development of different Trifolium repens genotypes were analysed...... and the G × E interactions were examined with respect to genotypespecific plant responses to WClMV infection. Thus, the environment is defined as the presence or absence of the virus. † Key Results WClMV had a negative effect on plant performance as shown by a decrease in biomass and number of ramets...

  11. HIV-1 Drug Resistance Mutations: Potential Applications for Point-of-Care Genotypic Resistance Testing.

    Science.gov (United States)

    Rhee, Soo-Yon; Jordan, Michael R; Raizes, Elliot; Chua, Arlene; Parkin, Neil; Kantor, Rami; Van Zyl, Gert U; Mukui, Irene; Hosseinipour, Mina C; Frenkel, Lisa M; Ndembi, Nicaise; Hamers, Raph L; Rinke de Wit, Tobias F; Wallis, Carole L; Gupta, Ravindra K; Fokam, Joseph; Zeh, Clement; Schapiro, Jonathan M; Carmona, Sergio; Katzenstein, David; Tang, Michele; Aghokeng, Avelin F; De Oliveira, Tulio; Wensing, Annemarie M J; Gallant, Joel E; Wainberg, Mark A; Richman, Douglas D; Fitzgibbon, Joseph E; Schito, Marco; Bertagnolio, Silvia; Yang, Chunfu; Shafer, Robert W

    2015-01-01

    The increasing prevalence of acquired and transmitted HIV-1 drug resistance is an obstacle to successful antiretroviral therapy (ART) in the low- and middle-income countries (LMICs) hardest hit by the HIV-1 pandemic. Genotypic drug resistance testing could facilitate the choice of initial ART in areas with rising transmitted drug resistance (TDR) and enable care-providers to determine which individuals with virological failure (VF) on a first- or second-line ART regimen require a change in treatment. An inexpensive near point-of-care (POC) genotypic resistance test would be useful in settings where the resources, capacity, and infrastructure to perform standard genotypic drug resistance testing are limited. Such a test would be particularly useful in conjunction with the POC HIV-1 viral load tests that are currently being introduced in LMICs. A POC genotypic resistance test is likely to involve the use of allele-specific point mutation assays for detecting drug-resistance mutations (DRMs). This study proposes that two major nucleoside reverse transcriptase inhibitor (NRTI)-associated DRMs (M184V and K65R) and four major NNRTI-associated DRMs (K103N, Y181C, G190A, and V106M) would be the most useful for POC genotypic resistance testing in LMIC settings. One or more of these six DRMs was present in 61.2% of analyzed virus sequences from ART-naïve individuals with intermediate or high-level TDR and 98.8% of analyzed virus sequences from individuals on a first-line NRTI/NNRTI-containing regimen with intermediate or high-level acquired drug resistance. The detection of one or more of these DRMs in an ART-naïve individual or in a individual with VF on a first-line NRTI/NNRTI-containing regimen may be considered an indication for a protease inhibitor (PI)-containing regimen or closer virological monitoring based on cost-effectiveness or country policy.

  12. Molecular virology of hepatitis B virus, sub-genotype C4 in northern Australian Indigenous populations.

    Science.gov (United States)

    Littlejohn, M; Davies, J; Yuen, L; Edwards, R; Sozzi, T; Jackson, K; Cowie, B; Tong, S; Davis, J; Locarnini, S

    2014-04-01

    Indigenous Australians experience a significant health burden from chronic hepatitis B infection; however, the strain of hepatitis B virus (HBV) found among Indigenous Australians has not been well characterized. Blood samples were collected from 65 Indigenous Australians with chronic HBV infection from across the Top End of Australia's Northern Territory. Phylogenetic analysis of HBV from these samples revealed that 100% of the isolates were genotype C, sub-genotype C4, expressing the serotype ayw3. This strain is a divergent group within the HBV/C genotype, and has only been described in Indigenous Australians. Evidence of recombination was suggested by discordant phylogenetic clustering of the C4 sequences when comparing the full genome to the surface region and confirmed by recombination analysis which showed the surface gene region to be most closely related to genotype J, while the remaining regions of the genome were most similar to genotype C sequences. Mutational analysis revealed the presence of multiple mutations that have been linked with more rapid liver disease progression and an increased risk of hepatocellular carcinoma. These mutations were detected in the majority of sequences examined. Variants associated with vaccine failure were detected as the predominant viral quasi-species in 3/35 samples. In summary, the HBV C4 variant found in this population has a high potential to cause advanced liver disease and to escape vaccination programs. Further in vitro functional and natural history studies are warranted in order to determine the clinical and public health consequences of infection with the HBV C4 variant in these communities. © 2014 Wiley Periodicals, Inc.

  13. Transfusion-transmitted virus infection in hemodialysis patients in Arar, Saudi Arabia: Prevalence, predictors and genotyping

    Directory of Open Access Journals (Sweden)

    Sheref M El-taher

    2015-01-01

    Full Text Available Transfusion-transmitted virus (TTV is a single-stranded DNA virus that was identified in patients with post-transfusion hepatitis of non-A-to-G type. Patients with chronic renal failure on maintenance hemodialysis (HD have a higher risk of viral infections, and the prevalence of TTV infection is common. The aim of our study was to detect TTV-DNA and its genotype in HD patients. A case-control study compromising of 63 patients on maintenance HD therapy at the Nephrology Center of Central Arar Hospital and 100 healthy individuals who were tested for TTVDNA and its genotype by semi nested-polymerase chain reaction with primers derived from the conserved open reading frame 1 (ORF1 region followed by digestion with NdeI and PstI restriction enzyme. The results show that the prevalence of TTV in HD patients was high and statistically significant; 42.9% compared with 19% in the control group. History of blood transfusion was the only significant predictor, and we found that age of patients, duration of HD, hepatitis B and C infection, aspartate aminotransferase and alanine aminotransferase levels were not significant predictors of TT virus positivity in HD patients. TTV genotype 1 (G1 was found to be the most common genotype among both HD and healthy controls. The prevalence of TTV among HD patients was significantly higher than that in healthy individuals. History of blood transfusion was the only significant predictor of TTV positivity among them. Genotype 1 was the most predominant type among HD and healthy individuals. Further studies on TTV in peritoneal dialysis patients and transplant patients are needed.

  14. Sex differences in heart failure

    NARCIS (Netherlands)

    Meyer, Sven

    2016-01-01

    This thesis examined differences between men and women with heart failure. First, it was shown that biological sex is a strong modulator in the clinical expression of various cardiomyopathies. In the general population it was shown that men are more likely to develop heart failure with reduced eject

  15. Failure Rates in Introductory Programming

    DEFF Research Database (Denmark)

    Bennedsen, Jens; Caspersen, Michael Edelgaard

    2007-01-01

    It is a common conception that CS1 is a very difficult course and that failure rates are high. However, until now there has only been anecdotal evidence for this claim. This article reports on a survey among institutions around the world regarding failure rates in introductory programming courses...

  16. Failure Engineered Heavy Metal Penetrators

    Science.gov (United States)

    1992-12-01

    ARMY RESEARCH LABORATORY Failure Engineered Heavy Metal Penetrators, Phase I, SBIR ARL-CR-5· R. Cavalieri, W. Tiarn, and D. Nicholson prepared...REPORT DATE S. REPORT TYPE AND DATES COVERED December 1992 Final Report-1/1/92 - 7/31/92 4. TITLE AND SUBTITLE FAILURE ENGINEERED HEAVY METAL PENETRATORS

  17. Corrosion Failures in Marine Environment

    Directory of Open Access Journals (Sweden)

    R. Krishnan

    1985-04-01

    Full Text Available This paper gives a brief description of typical marine environments and the most common form of corrosion of materials used in this environment. Some typical case histories of failures pertaining to pitting, bimetallic corrosion, dealloying, cavitation and stress corrosion cracking are illustrated as typical examples of corrosion failures.

  18. Test of Poisson Failure Assumption.

    Science.gov (United States)

    1982-09-01

    o. ....... 37 00/ D itlr.: DVI r TEST OF POISSON FAILURE ASSUMPTION Chapter 1. INTRODUCTION 1.1 Background. In stockage models... precipitates a regular failure pattern; it is also possible that the coding of scheduled vs unscheduled does not reflect what we would expect. Data

  19. Aging, telomeres and heart failure

    NARCIS (Netherlands)

    Wong, Liza S. M.; van der Harst, Pim; de Boer, Rudolf A.; Huzen, Jardi; van Gilst, Wiek H.; van Veldhuisen, Dirk J.

    2010-01-01

    During normal aging, the heart undergoes functional, morphological and cellular changes. Although aging per se does not lead to the expression of heart failure, it is likely that age-associated changes lower the threshold for the manifestation of signs and symptoms of heart failure. In patients, the

  20. Intestinal failure in obstructive jaundice

    Institute of Scientific and Technical Information of China (English)

    Stelios F. Assimakopoulos; Constantine E. Vagianos; Aristides Charonis; Vassiliki N. Nikolopoulou; Chrisoula D. Scopa

    2005-01-01

    @@ TO THE EDITOR We read with great interest the article by Ding LA and LiJS, which aimed to review the current knowledge on the physiology of normal intestinal barrier function and highlight the role of intestinal failure after various injurious insults in the development of septic complications or multiple organ failure with subsequent rapid clinical deterioration or even death.

  1. Biomarkers in acute heart failure.

    Science.gov (United States)

    Mallick, Aditi; Januzzi, James L

    2015-06-01

    The care of patients with acutely decompensated heart failure is being reshaped by the availability and understanding of several novel and emerging heart failure biomarkers. The gold standard biomarkers in heart failure are B-type natriuretic peptide and N-terminal pro-B-type natriuretic peptide, which play an important role in the diagnosis, prognosis, and management of acute decompensated heart failure. Novel biomarkers that are increasingly involved in the processes of myocardial injury, neurohormonal activation, and ventricular remodeling are showing promise in improving diagnosis and prognosis among patients with acute decompensated heart failure. These include midregional proatrial natriuretic peptide, soluble ST2, galectin-3, highly-sensitive troponin, and midregional proadrenomedullin. There has also been an emergence of biomarkers for evaluation of acute decompensated heart failure that assist in the differential diagnosis of dyspnea, such as procalcitonin (for identification of acute pneumonia), as well as markers that predict complications of acute decompensated heart failure, such as renal injury markers. In this article, we will review the pathophysiology and usefulness of established and emerging biomarkers for the clinical diagnosis, prognosis, and management of acute decompensated heart failure. Copyright © 2015 Sociedad Española de Cardiología. Published by Elsevier España, S.L.U. All rights reserved.

  2. Heart failure - fluids and diuretics

    Science.gov (United States)

    ... this page: //medlineplus.gov/ency/patientinstructions/000112.htm Heart failure - fluids and diuretics To use the sharing features on ... at Home When you have heart failure, your heart does not pump out enough blood. This causes fluids to build up in your body. If you ...

  3. Highly efficient full-length hepatitis C virus genotype 1 (strain TN) infectious culture system

    DEFF Research Database (Denmark)

    Li, Yi-Ping; Ramirez, Santseharay; Jensen, Sanne B

    2012-01-01

    Chronic infection with hepatitis C virus (HCV) is an important cause of end stage liver disease worldwide. In the United States, most HCV-related disease is associated with genotype 1 infection, which remains difficult to treat. Drug and vaccine development was hampered by inability to culture......) culture systems in Huh7.5 cells. Here, we developed a highly efficient genotype 1a (strain TN) full-length culture system. We initially found that the LSG substitutions conferred viability to an intergenotypic recombinant composed of TN 5' untranslated region (5'UTR)-NS5A and JFH1 NS5B-3'UTR; recovered...... with 8 changes (designated TN cell-culture derived, TNcc) replicated efficiently and released infectious particles of ∼5 log(10) focus-forming units per mL; passaged TNcc did not require additional changes. IFN-α and directly acting antivirals targeting the HCV protease, NS5A, and NS5B, each inhibited...

  4. Adult intestinal failure

    Energy Technology Data Exchange (ETDEWEB)

    Davidson, J., E-mail: Jdavidson@doctors.org.u [Salford Royal Hospital, Salford (United Kingdom); Plumb, A.; Burnett, H. [Salford Royal Hospital, Salford (United Kingdom)

    2010-05-15

    Intestinal failure (IF) is the inability of the alimentary tract to digest and absorb sufficient nutrition to maintain normal fluid balance, growth, and health. It commonly arises from disease affecting the mesenteric root. Although severe IF is usually managed in specialized units, it lies at the end of a spectrum with degrees of nutritional compromise being widely encountered, but commonly under-recognized. Furthermore, in the majority of cases, the initial enteric insult occurs in non-specialist IF centres. The aim of this article is to review the common causes of IF, general principles of its management, some commoner complications, and the role of radiology in the approach to a patient with severe IF. The radiologist has a crucial role in helping provide access for feeding solutions (both enteral and parenteral) and controlling sepsis (via drainage of collections) in an initial restorative phase of treatment, whilst simultaneously mapping bowel anatomy and quality, and searching for disease complications to assist the clinicians in planning a later, restorative phase of therapy.

  5. Failure to recall.

    Science.gov (United States)

    Laming, Donald

    2009-01-01

    Mathematical analysis shows that if the pattern of rehearsal in free-recall experiments (of necessity, the pattern observed when participants rehearse aloud) be continued without any further interruption by stimuli (as happens during recall), it terminates with the retrieval of the same 1 word over and over again. Such a terminal state is commonly reached before some of the words in the list have been retrieved even once; those words are not recalled. The 1 minute frequently allowed for recall in free-recall experiments is ample time for retrieval to seize up in this way. The author proposes a model that represents the essential features of the pattern of rehearsal; validates that model by reference to the overt rehearsal data from B. B. Murdock, Jr., and J. Metcalfe (1978) and the recall data from B. B. Murdock, Jr., and R. Okada (1970); demonstrates the long-term properties of continued sequences of retrievals and, also, a fundamental relation linking recall to the total time of presentation; and, finally, compares failure to recall in free-recall experiments with forgetting in general.

  6. Failure Criteria for Reinforced Materials

    DEFF Research Database (Denmark)

    Rathkjen, Arne

    Failure of materials is often characterized as ductile yielding, brittle fracture, creep rupture, etc., and different criteria given in terms of different parameters have been used to describe different types of failure. Only criteria expressing failure in terms of stress are considered in what...... place until the matrix, the continuous component of the composite, fails. When an isotropic matrix is reinforced as described above, the result is an anisotropic composite material. Even if the material is anisotropic, it usually exhibits a rather high degree of symmetry and such symmetries place...... certain restrictions on the form of the failure criteria for anisotropic materials. In section 2, some failure criteria for homogenous materials are reviewed. Both isotropic and anisotropic materials are described, and in particular the constraints imposed on the criteria from the symmetries orthotropy...

  7. Bisoprolol for congestive heart failure

    DEFF Research Database (Denmark)

    Rosenberg, J.; Gustafsson, F.

    2008-01-01

    Background: beta-Blockers are a cornerstone in the treatment of systolic heart failure treatment, but not all beta-blockers are effective or in this setting. Objective: To define the role of bisoprolol, a highly selective beta(1)-antagonist in congestive heart failure due to systolic dysfunction....... Methods: Using the keywords 'bisoprolol' and 'heart failure' PubMed and BIOSIS databases were searched for information regarding pharmacology and relevant randomised clinical trials. Supplementary publications were acquired by scrutinising reference lists of relevant papers. Additional information...... was obtained from the FDA website. Conclusion: Bisoprolol is an effective and well-tolerated first-line beta-blocker for patients with systolic heart failure. The knowledge is primarily based on study patients with moderate-to-severe heart failure from the three CIBIS trials Udgivelsesdato: 2008/2...

  8. Nuclear cardiology and heart failure

    Energy Technology Data Exchange (ETDEWEB)

    Giubbini, Raffaele; Bertagna, Francesco [University of Brescia, Department of Nuclear Medicine, Brescia (Italy); Milan, Elisa [Ospedale Di Castelfranco Veneto, Nuclear Medicine Unit, Castelfranco Veneto (Italy); Mut, Fernando; Dondi, Maurizio [International Atomic Energy Agency, Nuclear Medicine Section, Division of Human Health, Vienna (Austria); Metra, Marco [University of Brescia, Department of Cardiology, Brescia (Italy); Rodella, Carlo [Health Physics Department, Spedali Civili di Brescia, Brescia (Italy)

    2009-12-15

    The prevalence of heart failure in the adult population is increasing. It varies between 1% and 2%, although it mainly affects elderly people (6-10% of people over the age of 65 years will develop heart failure). The syndrome of heart failure arises as a consequence of an abnormality in cardiac structure, function, rhythm, or conduction. Coronary artery disease is the leading cause of heart failure and it accounts for this disorder in 60-70% of all patients affected. Nuclear techniques provide unique information on left ventricular function and perfusion by gated-single photon emission tomography (SPECT). Myocardial viability can be assessed by both SPECT and PET imaging. Finally, autonomic dysfunction has been shown to increase the risk of death in patients with heart disease and this may be applicable to all patients with cardiac disease regardless of aetiology. MIBG scanning has a very promising prognostic value in patients with heart failure. (orig.)

  9. Proifle, spectrum and signiifcance of hepatitis B virus genotypes in chronic HBV-infected patients in Yunnan, China

    Institute of Scientific and Technical Information of China (English)

    Jing You; Bao-Zhang Tang; Hutcha Sriplung; Virasakdi Chongsuvivatwong; Alan Geater; Lin Zhuang; Jun-Hua Huang; Hong-Ying Chen; Lan Yu

    2008-01-01

    BACKGROUND:There are signiifcant variations in the geographical distribution of hepatitis B virus (HBV) genotypes throughout the world, and some genotypes are associated with different clinical outcomes. Eight genotypes of human HBV (designated A-H) have been reported. The present study was designed to examine the distribution of HBV genotypes among patients at various stages of chronic type B liver disease in Yunnan Province, China, and to explore its signiifcance and the relationship of HBV genotype with gender and age, clinical spectrum of chronic HBV infection, and viral replicative activity. METHODS:Serum samples from 126 patients with chronic HBV infection from Yunnan Province, including 26 chronic asymptomatic HBV carriers (ASC), 61 patients with chronic hepatitis B (CHB) (21 mild, 30 moderate and 10 severe), 20 patients with chronic fulminant hepatic failure (CFHF), 12 patients with HBV-related liver cirrhosis (LC) and 7 patients with HBV-related hepatocellular carcinoma (HCC) were analyzed using reverse dot blot (RDB) methodology, which is based on the reverse hybridization principle for HBV genotyping. The relations of HBV genotype with gender and age, clinical patterns, and serological data of the patients were analyzed. RESULTS: In this series, genotypes A, B, C, and D were found. 38.1%patients (48/126) belonged to B, 54.8%(69/126) to C, 0.8%(1/126) to D, 1.6%(2/126) to a mixture of B and C, and 1.6%(2/126) to a mixture of A and C. 3.2%patients (4/126) had unknown genotypes. No other genotypes (E, F, G, and H) were found. Genotypes B and C were predominant. There was a statistically signiifcant difference in the distributions of genotypes C and B (χ2=7.04, P=0.008), and C was the dominant genotype in all patient categories. The rate of genotype B in the mild CHB group was signiifcantly higher than that in the moderate and severe groups (χ2=12.16, P=0.0001; χ2=11.98, P=0.001, respectively), the ASC group (χ2=5.46, P=0.02), the CFHF group (χ2

  10. Polyandry in dragon lizards: inbred paternal genotypes sire fewer offspring.

    Science.gov (United States)

    Frère, Celine H; Chandrasoma, Dani; Whiting, Martin J

    2015-04-01

    Multiple mating in female animals is something of a paradox because it can either be risky (e.g., higher probability of disease transmission, social costs) or provide substantial fitness benefits (e.g., genetic bet hedging whereby the likelihood of reproductive failure is lowered). The genetic relatedness of parental units, particularly in lizards, has rarely been studied in the wild. Here, we examined levels of multiple paternity in Australia's largest agamid lizard, the eastern water dragon (Intellagama lesueurii), and determined whether male reproductive success is best explained by its heterozygosity coefficient or the extent to which it is related to the mother. Female polyandry was the norm: 2/22 clutches (9.2%) were sired by three or more fathers, 17/22 (77.2%) were sired by two fathers, and only 3/22 (13.6%) clutches were sired by one father. Moreover, we reconstructed the paternal genotypes for 18 known mother-offspring clutches and found no evidence that females were favoring less related males or that less related males had higher fitness. However, males with greater heterozygosity sired more offspring. While the postcopulatory mechanisms underlying this pattern are not understood, female water dragons likely represent another example of reproduction through cryptic means (sperm selection/sperm competition) in a lizard, and through which they may ameliorate the effects of male-driven precopulatory sexual selection.

  11. Role of ERalpha in the differential response of Stat5a loss in susceptibility to mammary preneoplasia and DMBA-induced carcinogenesis.

    Science.gov (United States)

    Miermont, Anne M; Parrish, Angela R; Furth, Priscilla A

    2010-06-01

    Deregulated estrogen signaling is evidently linked to breast cancer pathophysiology, although the role of signal transducer and activator of transcription (Stat)5a, integral to normal mammary gland development, is less clear. A mouse model of mammary epithelial cell-targeted deregulated estrogen receptor alpha (ERalpha) expression [conditional ERalpha in mammary epithelium (CERM)] was crossed with mice carrying a germ line deletion of Stat5a [Stat5a-/-] to investigate interactions between ERalpha and Stat5a in mammary tissue. CERM, CERM/Stat5a+/-, CERM/Stat5a-/-, Stat5a+/-, Stat5a-/- and wild-type (WT) mice were generated to test the roles of ERalpha and Stat5a on pubertal differentiation and cancer progression with and without exposure to the chemical carcinogen 7,12-dimethylbenz[a]anthracene (DMBA). Only CERM/Stat5a-/- mice demonstrated delayed pubertal terminal end bud differentiation. Without DMBA exposure, Stat5a loss abrogated ERalpha-initiated hyperplastic alveolar nodule (HAN) development and, similarly, Stat5a-/- mice did not develop HANs. However, although Stat5a loss still reduced ERalpha-initiated HAN prevalence following DMBA exposure, Stat5a loss without deregulated ERalpha was associated with an increased HAN prevalence compared with WT. Progression to ERalpha(+) and ERalpha(-) adenocarcinoma was found in all CERM-containing genotypes (CERM, CERM/Stat5a+/-, CERM/Stat5a-/-) and ERalpha(+) adenocarcinoma in the Stat5a-/- genotype. The mammary epithelial cell proliferative index was increased only in CERM mice independent of Stat5a loss. No differences in apoptotic indices were found. In summary, Stat5a cooperated with deregulated ERalpha in retarding pubertal mammary differentiation and contributed to ERalpha-initiated preneoplasia, but its loss did not prevent development of invasive cancer. Moreover, in the absence of deregulated ERalpha, Stat5a loss was associated with development of both HANs and invasive cancer following DMBA exposure.

  12. HPV genotypes in invasive cervical cancer in Danish women

    DEFF Research Database (Denmark)

    Kirschner, Benny; Junge, Jette; Holl, Katsiaryna

    2013-01-01

    Human papillomavirus (HPV) genotype distribution in invasive cervical cancers may differ by geographic region. The primary objective of this study was to estimate HPV-genotype distribution in Danish women with a diagnosis of invasive cervical cancer....

  13. Agronomical and phytochemical evaluation of Stevia rebaudiana genotypes

    National Research Council Canada - National Science Library

    Vouillamoz, José F; Wolfram-Schilling, Evelyn; Carron, Claude-Alain; Baroffio, Catherine A

    2016-01-01

    The agronomical potential and the phytochemical variability of 18 genotypes of the Paraguayan plant Stevia rebaudiana have been investigated in Switzerland in order identify the best genotype for local cultivation...

  14. Resistance of corn genotypes to fall armyworm Spodoptera ...

    African Journals Online (AJOL)

    Tuoyo Aghomotsegin

    2016-08-31

    Aug 31, 2016 ... The objective of this study was to evaluate resistance mechanisms in 12 corn genotypes (transgenic hybrids: ..... FAW that fed on GM corn genotypes exhibited lower ... preference for other food types, particularly given the.

  15. Comparison and suitability of genotype by environment analysis ...

    African Journals Online (AJOL)

    ACSS

    showed that genotype by environment interactions were significant at p<0.05 for grain .... Genotype by environment analysis methods for yield-related traits of pearl millet ...... PhD Thesis, Louisiana State ... set of sweet potato clones evaluated.

  16. Genotype W environment interaction effects on some physiological ...

    African Journals Online (AJOL)

    Genotype W environment interaction effects on some physiological yield ... Ghana Journal of Agricultural Science ... study the yield basis and environmental effects on 31cowpea genotypes of early, medium and late maturities. ... Article Metrics.

  17. Genotype 3 is the predominant hepatitis C genotype in a multi-ethnic Asian population in Malaysia.

    Science.gov (United States)

    Ho, Shiaw-Hooi; Ng, Kee-Peng; Kaur, Harvinder; Goh, Khean-Lee

    2015-06-01

    Genotypes of hepatitis C virus (HCV) are distributed differently across the world. There is a paucity of such data in a multi-ethnic Asian population like Malaysia. The objectives of this study were to determine the distribution of HCV genotypes between major ethnic groups and to ascertain their association with basic demographic variables like age and gender. This was a cross-sectional prospective study conducted from September 2007 to September 2013. Consecutive patients who were detected to have anti-HCV antibodies in the University of Malaya Medical Centre were included and tested for the presence of HCV RNA using Roche Cobas Amplicor Analyzer and HCV genotype using Roche single Linear Array HCV Genotyping strip. Five hundred and ninety-six subjects were found to have positive anti-HCV antibodies during this period of time. However, only 396 (66.4%) were HCV RNA positive and included in the final analysis. Our results showed that HCV genotype 3 was the predominant genotype with overall frequency of 61.9% followed by genotypes 1 (35.9%), 2 (1.8%) and 6 (0.5%). There was a slightly higher prevalence of HCV genotype 3 among the Malays when compared to the Chinese (P=0.043). No other statistical significant differences were observed in the distribution of HCV genotypes among the major ethnic groups. There was also no association between the predominant genotypes and basic demographic variables. In a multi-ethnic Asian society in Malaysia, genotype 3 is the predominant genotype among all the major ethnic groups with genotype 1 as the second commonest genotype. Both genotypes 2 and 6 are uncommon. Neither genotype 4 nor 5 was detected. There is no identification of HCV genotype according to ethnic origin, age and gender.

  18. Angiotensin converting enzyme genotype in cardiovascular disease

    Energy Technology Data Exchange (ETDEWEB)

    Summers, K.M.; Huggard, P.R.; West, M.J. [Univ. of Queensland, Brisbane (Australia)] [and others

    1994-09-01

    Angiotensin converting enzyme (ACE) catalyses formation of angiotensin II and degradation of bradykinin, vasoactive peptides with opposing properties. The result of ACE action is to promote vasoconstriction and cell growth. PCR is used to detect a common polymorphism due to the insertion of an Alu repeat element of 287 bp into intron 16. ACE genotype has been implicated in risk for myocardial infarction (MI) and hypertension in humans. We have studied a group of 640 patients (61% male aged 64 {plus_minus} 11 years) with myocardial ischaemic syndromes, followed for 12 months after initial hospital admission. In this group, the frequency of the insertion (I) allele was 0.47 (N=1170 chromosomes), not significantly higher than the frequency of 0.46 in 112 local blood donors (50% male aged 59 {plus_minus}5 years). In the 300 patients with diagnosed MI, I allele frequency was 0.48. This is significantly higher ({chi}{sup 2}=5.78, P=0.015) than the frequency of 0.42 reported in a multi-centre study of ACE genotype in 600 male European patients with MI . There was a non-significant increase in the frequency of a cardiac event within 6 months of hospital admission in those of II genotype (N=464, 47 events to date). These results suggest that in our population, the I allele and/or II genotype may be associated with risk of MI. This contrasts with the study cited above, where the D (deletion) allele and DD genotype frequency were raised in patients compared with controls. Hypertension is associated with the ACE D allele, and does not explain the heart disease risk, which may be associated with the I allele, in this group of survivors of myocardial ischaemic disease. The difference between our results and the previous study may be due to ascertainment or ethnic differences or to problems amplifying the I allele in some heterozygotes. Clearly, the role of ACE genotype in these diseases is complex.

  19. [Hepatitis B virus genotypes and the response to lamivudine therapy].

    Science.gov (United States)

    Zalewska, Małgorzata; Domagała, Małgorzata; Simon, Krzysztof; Gładysz, Andrzej

    2005-12-01

    Hepatitis B virus (HBV) can be classified into eight major genotypes (A-H) that have mainly a geographic distribution. The HBV genotype may influence disease progression, HBeAg seroconversion rates, response to antiviral treatment. The aim of study was to analyze the distribution and frequency of genotypes in patients with chronic hepatitis B. Response to lamivudine 100 mg daily therapy was examined in respect to genotype. Sixty six patients (45 (68,2%) male, 21 (31,8%) female) with chronic hepatits B were enrolled. HBV genotypes were assigned before treatment with INNO-LiPA HBV Genotyping, Innogenetics, N. V., Ghent assay, which is a line probe test based on the reverse hybridization principle. In baseline and after 12 months of treatment serological markers of HBV infection, alanine aminotransferase (ALT) activities and HBV DNA serum levels were tested. Patients with chronic hepatitis B were infected predominantly with genotype A. HBV genotype distribution was: 78,8% for genotype A, 13,6% for genotype D, 1,5% for mixed infection with genotypes A and D. Distribution of genotypes A and D was asymmetrically regardless of sex, HBeAg status, ALT and HBV DNA levels. Four (6,1%) specimens had indeterminate A results by LiPA. There were no significant differences between patients with genotypes A and D regarding age and sex. There were also no significant differences between these two groups regarding rates of HBeAg and anti-HBe positivity, ALT activity and viral load. Twenty months of lamivudine (100 mg daily) therapy resulted in significant decreases in serum HBV DNA and ALT activities in patients with genotype A as well as with genotype D. After 12 months of treatment there were no statistical differences in HBeAg seroconversion rates, ALT activities, viral loads, frequency of HBeAg and anti-HBe between genotypes A and D.

  20. A suitable duplex PCR for ovine embryo sex and genotype of PrnP gene determination for MOET-based selection programmes.

    Science.gov (United States)

    Dervishi, E; Sánchez, P; Alabart, J L; Cocero, M J; Folch, J; Calvo, J H

    2011-12-01

    The objective of this study was to test the suitability of a duplex PCR assay for sex and scrapie resistance genotype determination in fresh embryos. Duplex PCR amplified a repetitive and specific fragment of Y chromosome, used for sex diagnosis, and a PrnP fragment. PrnP codons 134 and 156, and codon 171 were genotyped by restriction fragment length polymorphisms and allele-specific PCR, respectively, after re-amplification of PrnP fragment. The specificity of the method was first assessed by testing 359 blood samples from Rasa Aragonesa sheep breed (161 males and 198 females). No amplification failures and total agreement between genotypic and phenotypic sex were found. In the same way, PrnP genotype determination by duplex PCR assay was in agreement with the PrnP animal's genotype established by sequencing. Finally, 73 samples of 1-10 cells from compact morulae were aspirated through the zona pellucida and genotyped for sex and PrnP. The efficiency was 96% when three or more cells were sampled. These results confirm that the duplex PCR assay reported in this work can be used for rapid sex determination in ovine embryos, with a high efficiency and accuracy (96%) when three or more cells are sampled, allowing sexed fresh embryos of known PrnP genotype to be transferred in multiple ovulation and embryo transfer programmes.

  1. Discovery of novel variants in genotyping arrays improves genotype retention and reduces ascertainment bias

    Directory of Open Access Journals (Sweden)

    Didion John P

    2012-01-01

    Full Text Available Abstract Background High-density genotyping arrays that measure hybridization of genomic DNA fragments to allele-specific oligonucleotide probes are widely used to genotype single nucleotide polymorphisms (SNPs in genetic studies, including human genome-wide association studies. Hybridization intensities are converted to genotype calls by clustering algorithms that assign each sample to a genotype class at each SNP. Data for SNP probes that do not conform to the expected pattern of clustering are often discarded, contributing to ascertainment bias and resulting in lost information - as much as 50% in a recent genome-wide association study in dogs. Results We identified atypical patterns of hybridization intensities that were highly reproducible and demonstrated that these patterns represent genetic variants that were not accounted for in the design of the array platform. We characterized variable intensity oligonucleotide (VINO probes that display such patterns and are found in all hybridization-based genotyping platforms, including those developed for human, dog, cattle, and mouse. When recognized and properly interpreted, VINOs recovered a substantial fraction of discarded probes and counteracted SNP ascertainment bias. We developed software (MouseDivGeno that identifies VINOs and improves the accuracy of genotype calling. MouseDivGeno produced highly concordant genotype calls when compared with other methods but it uniquely identified more than 786000 VINOs in 351 mouse samples. We used whole-genome sequence from 14 mouse strains to confirm the presence of novel variants explaining 28000 VINOs in those strains. We also identified VINOs in human HapMap 3 samples, many of which were specific to an African population. Incorporating VINOs in phylogenetic analyses substantially improved the accuracy of a Mus species tree and local haplotype assignment in laboratory mouse strains. Conclusion The problems of ascertainment bias and missing

  2. Discovery of novel variants in genotyping arrays improves genotype retention and reduces ascertainment bias.

    Science.gov (United States)

    Didion, John P; Yang, Hyuna; Sheppard, Keith; Fu, Chen-Ping; McMillan, Leonard; de Villena, Fernando Pardo-Manuel; Churchill, Gary A

    2012-01-19

    High-density genotyping arrays that measure hybridization of genomic DNA fragments to allele-specific oligonucleotide probes are widely used to genotype single nucleotide polymorphisms (SNPs) in genetic studies, including human genome-wide association studies. Hybridization intensities are converted to genotype calls by clustering algorithms that assign each sample to a genotype class at each SNP. Data for SNP probes that do not conform to the expected pattern of clustering are often discarded, contributing to ascertainment bias and resulting in lost information - as much as 50% in a recent genome-wide association study in dogs. We identified atypical patterns of hybridization intensities that were highly reproducible and demonstrated that these patterns represent genetic variants that were not accounted for in the design of the array platform. We characterized variable intensity oligonucleotide (VINO) probes that display such patterns and are found in all hybridization-based genotyping platforms, including those developed for human, dog, cattle, and mouse. When recognized and properly interpreted, VINOs recovered a substantial fraction of discarded probes and counteracted SNP ascertainment bias. We developed software (MouseDivGeno) that identifies VINOs and improves the accuracy of genotype calling. MouseDivGeno produced highly concordant genotype calls when compared with other methods but it uniquely identified more than 786000 VINOs in 351 mouse samples. We used whole-genome sequence from 14 mouse strains to confirm the presence of novel variants explaining 28000 VINOs in those strains. We also identified VINOs in human HapMap 3 samples, many of which were specific to an African population. Incorporating VINOs in phylogenetic analyses substantially improved the accuracy of a Mus species tree and local haplotype assignment in laboratory mouse strains. The problems of ascertainment bias and missing information due to genotyping errors are widely recognized as

  3. megasat: automated inference of microsatellite genotypes from sequence data.

    Science.gov (United States)

    Zhan, Luyao; Paterson, Ian G; Fraser, Bonnie A; Watson, Beth; Bradbury, Ian R; Nadukkalam Ravindran, Praveen; Reznick, David; Beiko, Robert G; Bentzen, Paul

    2017-03-01

    megasat is software that enables genotyping of microsatellite loci using next-generation sequencing data. Microsatellites are amplified in large multiplexes, and then sequenced in pooled amplicons. megasat reads sequence files and automatically scores microsatellite genotypes. It uses fuzzy matches to allow for sequencing errors and applies decision rules to account for amplification artefacts, including nontarget amplification products, replication slippage during PCR (amplification stutter) and differential amplification of alleles. An important feature of megasat is the generation of histograms of the length-frequency distributions of amplification products for each locus and each individual. These histograms, analogous to electropherograms traditionally used to score microsatellite genotypes, enable rapid evaluation and editing of automatically scored genotypes. megasat is written in Perl, runs on Windows, Mac OS X and Linux systems, and includes a simple graphical user interface. We demonstrate megasat using data from guppy, Poecilia reticulata. We genotype 1024 guppies at 43 microsatellites per run on an Illumina MiSeq sequencer. We evaluated the accuracy of automatically called genotypes using two methods, based on pedigree and repeat genotyping data, and obtained estimates of mean genotyping error rates of 0.021 and 0.012. In both estimates, three loci accounted for a disproportionate fraction of genotyping errors; conversely, 26 loci were scored with 0-1 detected error (error rate ≤0.007). Our results show that with appropriate selection of loci, automated genotyping of microsatellite loci can be achieved with very high throughput, low genotyping error and very low genotyping costs.

  4. A genotype probability index for multiple alleles and haplotypes.

    Science.gov (United States)

    Percy, A; Kinghorn, B P

    2005-12-01

    We use linear algebra to calculate an index of information content in genotype probabilities which has previously been calculated using trigonometry. The new method can be generalized allowing the index to be calculated for loci with more than two alleles. Applications of this index include its use in genotyping strategies, strategies to manage genetic disorders and in estimation of genotype effects.

  5. 21 CFR 862.3360 - Drug metabolizing enzyme genotyping system.

    Science.gov (United States)

    2010-04-01

    ... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Drug metabolizing enzyme genotyping system. 862... Test Systems § 862.3360 Drug metabolizing enzyme genotyping system. (a) Identification. A drug metabolizing enzyme genotyping system is a device intended for use in testing deoxyribonucleic acid...

  6. Periodontitis in Chronic Heart Failure.

    Science.gov (United States)

    Fröhlich, Hanna; Herrmann, Kristina; Franke, Jennifer; Karimi, Alamara; Täger, Tobias; Cebola, Rita; Katus, Hugo A; Zugck, Christian; Frankenstein, Lutz

    2016-08-01

    Periodontal disease has been associated with an increased risk of cardiovascular events. The purpose of our study was to investigate whether a correlation between periodontitis and chronic heart failure exists, as well as the nature of the underlying cause. We enrolled 71 patients (mean age, 54 ± 13 yr; 56 men) who had stable chronic heart failure; all underwent complete cardiologic and dental evaluations. The periodontal screening index was used to quantify the degree of periodontal disease. We compared the findings to those in the general population with use of data from the 4th German Dental Health Survey. Gingivitis, moderate periodontitis, and severe periodontitis were present in 17 (24%), 17 (24%), and 37 (52%) patients, respectively. Severe periodontitis was more prevalent among chronic heart failure patients than in the general population. In contrast, moderate periodontitis was more prevalent in the general population (P <0.00001). The severity of periodontal disease was not associated with the cause of chronic heart failure or the severity of heart failure symptoms. Six-minute walking distance was the only independent predictor of severe periodontitis. Periodontal disease is highly prevalent in chronic heart failure patients regardless of the cause of heart failure. Prospective trials are warranted to clarify the causal relationship between both diseases.

  7. New medications for heart failure.

    Science.gov (United States)

    Gordin, Jonathan S; Fonarow, Gregg C

    2016-08-01

    Heart failure is common and results in substantial morbidity and mortality. Current guideline-based therapies for heart failure with reduced ejection fraction, including beta blockers, angiotensin converting enzyme (ACE) inhibitors, and aldosterone antagonists aim to interrupt deleterious neurohormonal pathways and have shown significant success in reducing morbidity and mortality associated with heart failure. Continued efforts to further improve outcomes in patients with heart failure with reduced ejection fraction have led to the first new-in-class medications approved for heart failure since 2005, ivabradine and sacubitril/valsartan. Ivabradine targets the If channels in the sinoatrial node of the heart, decreasing heart rate. Sacubitril/valsartan combines a neprilysin inhibitor that increases levels of beneficial vasodilatory peptides with an angiotensin receptor antagonist. On a background of previously approved, guideline-directed medical therapies for heart failure, these medications have shown improved clinical outcomes ranging from decreased hospitalizations in a select group of patients to a reduction in all-cause mortality across all pre-specified subgroups. In this review, we will discuss the previously established guideline-directed medical therapies for heart failure with reduced ejection fraction, the translational research that led to the development of these new therapies, and the results from the major clinical trials of ivabradine and sacubitril/valsartan. Copyright © 2016 Elsevier Inc. All rights reserved.

  8. Strongyloides stercoralis genotypes in humans in Cambodia.

    Science.gov (United States)

    Schär, Fabian; Guo, Li; Streit, Adrian; Khieu, Virak; Muth, Sinuon; Marti, Hanspeter; Odermatt, Peter

    2014-06-01

    Little is known about the genetic variability of the soil-transmitted nematode, Strongyloides stercoralis, in humans. We sequenced portions of the small subunit rDNA (SSU), including the hyper variable regions (HVR) I and IV from S. stercoralis larvae derived from individuals living in a rural setting in Cambodia. We identified three polymorphic positions, including a previously reported one within the HVR I. HVR IV was invariable. Six different SSU alleles existed in our sample. Although different genotypes of S. stercoralis were found in the same individuals, no heterozygous larvae were found. This indicates that there is no or very little interbreeding between the different genotypes. Further studies are needed to examine if this is because sexual reproduction, which is facultative, is rare in our study area's S. stercoralis population or because what is considered to be S. stercoralis today is actually a complex of closely related species or subspecies.

  9. COMT genotype, gambling activity, and cognition

    DEFF Research Database (Denmark)

    Grant, Jon E; Leppink, Eric W; Redden, Sarah A

    2015-01-01

    gambling. This study examined adults with varying levels of gambling behavior to determine whether COMT genotype was associated with differences in gambling symptoms and cognitive functioning. 260 non-treatment-seeking adults aged 18-29 years with varying degrees of gambling behavior provided saliva...... significantly different from the Val/Met (13.2%) group (p = 0.001). The Val/Val COMT group was also associated with significantly more gambling disorder diagnostic criteria being met, greater frequency of gambling behavior, and significantly worse cognitive performance on the Cambridge Gamble Task (risk...... adjustment and delay aversion) and the Spatial Working Memory task (total errors). This study adds to the growing literature on the role of COMT in impulsive behaviors by showing that the Val/Val genotype was associated with specific clinical and cognitive elements among young adults who gamble...

  10. Huntington's Disease: Relationship Between Phenotype and Genotype.

    Science.gov (United States)

    Sun, Yi-Min; Zhang, Yan-Bin; Wu, Zhi-Ying

    2017-01-01

    Huntington's disease (HD) is an autosomal dominant inherited neurodegenerative disease with the typical manifestations of involuntary movements, psychiatric and behavior disorders, and cognitive impairment. It is caused by the dynamic mutation in CAG triplet repeat number in exon 1 of huntingtin (HTT) gene. The symptoms of HD especially the age at onset are related to the genetic characteristics, both the CAG triplet repeat and the modified factors. Here, we reviewed the recent advancement on the genotype-phenotype relationship of HD, mainly focus on the characteristics of different expanded CAG repeat number, genetic modifiers, and CCG repeat number in the 3' end of CAG triplet repeat and their effects on the phenotype. We also reviewed the special forms of HD (juvenile HD, atypical onset HD, and homozygous HD) and their phenotype-genotype correlations. The review will aid clinicians to predict the onset age and disease course of HD, give the genetic counseling, and accelerate research into the HD mechanism.

  11. Indexing Finite Language Representation of Population Genotypes

    CERN Document Server

    Sirén, Jouni; Mäkinen, Veli

    2010-01-01

    We propose a way to index population genotype information together with the complete genome sequence so that one can use the index to efficiently align a given sequence to the genome with all plausible genotype recombinations taken into account. This is achieved through converting the multiple alignment of individual genomes into a finite automaton recognizing the language of all substrings read from the alignment by switching the row at any time. The finite automaton is then indexed with an extension of Burrows-Wheeler transform to allow pattern search inside the plausible recombinant sequences generated in this way. The size of the finite automaton and the index created from it stay limited because of the high similarity of the individual genomes in the multiple alignment. In our experiments, the index took even less space than previous ones designed for indexing just the individual genomes. On a short-read alignment experiment, we found about 1% of matches to novel recombinants.

  12. BCL2 genotypes and prostate cancer survival

    Energy Technology Data Exchange (ETDEWEB)

    Renner, Wilfried [Medical University of Graz, Clinical Institute of Medical and Chemical Laboratory Diagnostics, Graz (Austria); Langsenlehner, Uwe [GKK Outpatient Department, Division of Internal Medicine, Graz (Austria); Krenn-Pilko, Sabine; Langsenlehner, Tanja [Medical University of Graz, Department of Therapeutic Radiology and Oncology, Graz (Austria); Eder, Petra [University Hospital Wuerzburg, Department of Internal Medicine I, Wuerzburg (Germany)

    2017-06-15

    The antiapoptotic B-cell lymphoma 2 (BCL2) gene is a key player in cancer development and progression. A functional single-nucleotide polymorphism (c.-938C>A, rs2279115) in the inhibitory P2 BCL2 gene promoter has been associated with clinical outcomes in various types of cancer. Aim of the present study was to analyze the role of BCL2-938C>A genotypes in prostate cancer mortality. The association between BCL2-938C>A (rs2279115) genotypes and prostate cancer outcome was studied within the prospective PROCAGENE study comprising 702 prostate cancer patients. During a median follow-up time of 92 months, 120 (17.1%) patients died. A univariate Cox regression model showed a significant association of the CC genotype with reduced cancer-specific survival (CSS; hazard ratio, HR, 2.13, 95% confidence interval, CI, 1.10-4.12; p = 0.024) and overall survival (OS; HR 2.34, 95% CI 1.58-3.47; p < 0.001). In a multivariate Cox regression model including age at diagnosis, risk group, and androgen deprivation therapy, the CC genotype remained a significant predictor of poor CSS (HR 2.05, 95% CI 1.05-3.99; p = 0.034) and OS (HR 2.25, 95% CI 1.51-3.36; p < 0.001). This study provides evidence that the homozygous BCL2-938 CC genotype is associated with OS and C in prostate cancer patients. (orig.) [German] Das antiapoptotische Gen B cell lymphoma 2 (BCL2) spielt eine Schluesselrolle in der Entstehung und Progression von Krebserkrankungen. Ein funktioneller Einzelnukleotid-Polymorphismus (c.-938C>A, rs2279115) im inhibitorischen P2-BCL2-Promotor wurde mit dem klinischen Outcome verschiedener Krebserkrankungen verknuepft. Ziel der vorliegenden Studie war die Untersuchung der Rolle von BCL2-938C>A-Genotypen fuer die Mortalitaet bei Patienten mit Prostatakarzinom. Der Zusammenhang zwischen BCL2-938C>A-Genotypen (rs2279115) und dem Outcome bei Prostatakrebs wurde in der prospektiven PROCAGENE-Studie, die 702 Patienten mit Prostatakarzinom umfasste, untersucht. Waehrend der medianen

  13. Identification of Zoonotic Genotypes of Giardia duodenalis

    DEFF Research Database (Denmark)

    Sprong, H.; Cacciò, S.M.; van der Giessen, J.W.B

    2009-01-01

    Giardia duodenalis, originally regarded as a commensal organism, is the etiologic agent of giardiasis, a gastrointestinal disease of humans and animals. Giardiasis causes major public and veterinary health concerns worldwide. Transmission is either direct, through the faecal-oral route, or indirect....... The data were assembled into a molecular epidemiological database developed by a European network of public and veterinary health Institutions. Genotyping was performed at different levels of resolution (single and multiple loci on the same dataset). The zoonotic potential of both assemblages A and B......, mixtures of genotypes in individual isolates were repeatedly observed. Possible explanations are the uptake of genetically different Giardia cysts by a host, or subsequent infection of an already infected host, likely without overt symptoms, with a different Giardia species, which may cause disease. Other...

  14. Daclatasvir plus peginterferon alfa and ribavirin for treatment-naive chronic hepatitis C genotype 1 or 4 infection

    DEFF Research Database (Denmark)

    Hézode, Christophe; Hirschfield, Gideon M; Ghesquiere, Wayne

    2015-01-01

    OBJECTIVE: To evaluate the safety and efficacy of daclatasvir, an HCV NS5A inhibitor with pangenotypic activity, administered with peginterferon-alfa-2a/ribavirin. DESIGN: In this Phase 2b double-blind, placebo-controlled study, treatment-naive adults with HCV genotype 1 (N=365) or 4 (N=30) infec...

  15. Failure probability under parameter uncertainty.

    Science.gov (United States)

    Gerrard, R; Tsanakas, A

    2011-05-01

    In many problems of risk analysis, failure is equivalent to the event of a random risk factor exceeding a given threshold. Failure probabilities can be controlled if a decisionmaker is able to set the threshold at an appropriate level. This abstract situation applies, for example, to environmental risks with infrastructure controls; to supply chain risks with inventory controls; and to insurance solvency risks with capital controls. However, uncertainty around the distribution of the risk factor implies that parameter error will be present and the measures taken to control failure probabilities may not be effective. We show that parameter uncertainty increases the probability (understood as expected frequency) of failures. For a large class of loss distributions, arising from increasing transformations of location-scale families (including the log-normal, Weibull, and Pareto distributions), the article shows that failure probabilities can be exactly calculated, as they are independent of the true (but unknown) parameters. Hence it is possible to obtain an explicit measure of the effect of parameter uncertainty on failure probability. Failure probability can be controlled in two different ways: (1) by reducing the nominal required failure probability, depending on the size of the available data set, and (2) by modifying of the distribution itself that is used to calculate the risk control. Approach (1) corresponds to a frequentist/regulatory view of probability, while approach (2) is consistent with a Bayesian/personalistic view. We furthermore show that the two approaches are consistent in achieving the required failure probability. Finally, we briefly discuss the effects of data pooling and its systemic risk implications. © 2010 Society for Risk Analysis.

  16. Human papillomaviruses genotyping in plantar warts.

    Science.gov (United States)

    de Planell-Mas, Elena; Martínez-Garriga, Blanca; Zalacain, Antonio Jesús; Vinuesa, Teresa; Viñas, Miguel

    2017-05-01

    Plantar warts are caused by human papillomaviruses (HPVs) and have been associated with several HPV genotypes. However, there are few studies focused exclusively on plantar warts. In this work, we aim to identify the HPV genotypes of plantar warts and explore their relation to demographic and clinical characteristics of patients. A total of 72 patients diagnosed with plantar warts were recruited at the Laser unit at Podiatric Hospital, University of Barcelona, Spain. Inner hyperkeratosis laminar sections of warts were collected and DNA of samples were extracted. Amplification of a conserved region of the HPV L1 gene was performed with the SK-Polymerase chain reaction method. DNA amplicons were sequenced and HPV types identified. The most prevalent genotypes detected among the 105 analyzed plantar warts were HPV-57 (37.1%), HPV-27 (23.8%), HPV-1a (20.9%), HPV-2 (15.2%), and HPV-65 (2.8%). The majority of patients (78%) presented one single plantar wart, whereas multiple warts were detected in 22.2% of patients. One patient with multiple warts presented HPV types from two different genera, suggesting the spread of warts by self-inoculation as well as by de novo infection. No significant differences between the number of warts in toes, midfoot and heel were found. The most prevalent HPV types detected in all areas belonged to the alpha genus. This work provides new insight on plantar warts and their associated HPV genotypes, and evidences the usefulness and reliability of both the sample collection procedure and the PCR method used for HPV detection and typing. J. Med. Virol. 89:902-907, 2017. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  17. [Baroreflex failure after chemodectoma resection].

    Science.gov (United States)

    Gómez Esteban, J C; Boyero, S; Fernández, C; Sagasta, A; Pérez, T; Velasco, F; Allue, I; Lezcano, E; Zarranz, J J

    2004-10-01

    Baroreflex failure after chemodectoma resection We present a case of baroreflex failure secondary to a unilateral injury of the glossopharyngeal nerve. The patient was operated for a left-sided chemodectoma in the carotid body. Some months after surgery she started to report presyncopal episodes exacerbated by mental stress and when standing up. During these episodes, the patient presented hypertensive crises and tachycardia. However, blood pressure was below normal ranges at rest. The diagnosis was baroreflex failure secondary to unilateral injury of the glossopharyngeal nerve. The case reported herein illustrates the fact that the presence of a bilateral injury is not essential for the occurrence of this disorder.

  18. Cardiomyocytic apoptosis and heart failure

    Institute of Scientific and Technical Information of China (English)

    Quanzhou Feng

    2008-01-01

    Heart failure is a major disease seriously threatening human health.Once left ventricular dysfunction develops,cardiac function usually deteriorates and progresses to congestive heart failure in several months or years even if no factors which accelerate the deterioration repeatedly exist.Mechanism through which cardiac function continually deteriorates is still unclear.Cardiomyocytic apoptosis can occur in acute stage of ischemic heart diseases and the compensated stage of cardiac dysfunction.In this review,we summarize recent advances in understanding the role of cardiomyocytic apoptosis in heart failure.

  19. Screening cotton genotypes for seedling drought tolerance

    Directory of Open Access Journals (Sweden)

    Penna Julio C. Viglioni

    1998-01-01

    Full Text Available The objectives of this study were to adapt a screening method previously used to assess seedling drought tolerance in cereals for use in cotton (Gossypium hirsutum L. and to identify tolerant accessions among a wide range of genotypes. Ninety genotypes were screened in seven growth chamber experiments. Fifteen-day-old seedlings were subjected to four 4-day drought cycles, and plant survival was evaluated after each cycle. Three cycles are probably the minimum required in cotton work. Significant differences (at the 0.05 level or lower among entries were obtained in four of the seven experiments. A "confirmation test" with entries previously evaluated as "tolerant" (high survival and "susceptible" (low survival was run. A number of entries duplicated their earlier performance, but others did not, which indicates the need to reevaluate selections. Germplasms considered tolerant included: `IAC-13-1', `IAC-RM4-SM5', `Minas Sertaneja', `Acala 1517E-1' and `4521'. In general, the technique is simple, though time-consuming, with practical value for screening a large number of genotypes. Results from the screening tests generally agreed with field information. The screening procedure is suitable to select tolerant accessions from among a large number of entries in germplasm collections as a preliminary step in breeding for drought tolerance. This research also demonstrated the need to characterize the internal lack of uniformity in growth chambers to allow for adequate designs of experiments.

  20. Wind Turbine Failures - Tackling current Problems in Failure Data Analysis

    Science.gov (United States)

    Reder, M. D.; Gonzalez, E.; Melero, J. J.

    2016-09-01

    The wind industry has been growing significantly over the past decades, resulting in a remarkable increase in installed wind power capacity. Turbine technologies are rapidly evolving in terms of complexity and size, and there is an urgent need for cost effective operation and maintenance (O&M) strategies. Especially unplanned downtime represents one of the main cost drivers of a modern wind farm. Here, reliability and failure prediction models can enable operators to apply preventive O&M strategies rather than corrective actions. In order to develop these models, the failure rates and downtimes of wind turbine (WT) components have to be understood profoundly. This paper is focused on tackling three of the main issues related to WT failure analyses. These are, the non-uniform data treatment, the scarcity of available failure analyses, and the lack of investigation on alternative data sources. For this, a modernised form of an existing WT taxonomy is introduced. Additionally, an extensive analysis of historical failure and downtime data of more than 4300 turbines is presented. Finally, the possibilities to encounter the lack of available failure data by complementing historical databases with Supervisory Control and Data Acquisition (SCADA) alarms are evaluated.

  1. Hepatitis B virus genotypes and hepatocellular carcinoma in Thailand

    Institute of Scientific and Technical Information of China (English)

    Pisit Tangkijvanich; Varocha Mahachai; Piyawat Komolmit; Juthatip Fongsaru; Apiradee Theamboonlers; Yong Poovorawan

    2005-01-01

    AIM: The role of hepatitis B virus (HBV) genotypes on the clinical features and prognosis of patients with hepatocellular carcinoma (HCC) is currently unknown. The aim of the present study was to evaluate the distribution of HBV genotypes and their clinical relevance in Thai patients.METHODS: HBV genotypes were determined by PCR-RFLP in stored sera of 93 asymptomatic carriers, 103 patients with chronic hepatitis, 60 patients with cirrhosis and 76patients with HCC. The clinical data were analyzed in relation to the HBV genotype.RESULTS: HBV genotypes C and B were predominant in Thailand, accounting for 73% and 21%, respectively. The distributions of genotypes B and C were similar in HCC patients compared to the other groups. Genotype C was significantly more common in HCC patients who were under 40 years old than genotype B (18% vs 0%, P= 0.03), but was significantly less common in patients older than 60 years (26% vs 56.5%, P= 0.01). The positive rate of hepatitis B e antigen (HBeAg) in patients with genotype C was significantly higher than that in patients with genotype B (71.6% vs 44.4%, P = 0.03 in chronic hepatitis; 56.8% vs 11.1%,P = 0.01 in cirrhosis). There were no differences between HCC patients with genotypes B and C regarding tumor staging by CLIP criteria and the overall median survival. Multivariate analyses showed that HBV genotype was not an independent prognostic factor of survival in HCC patients.CONCLUSION: Patients with genotype C had a higher positive rate of HBeAg and exhibited earlier progression of cirrhosis and HCC than those with genotype B. However,there were no differences in the risk of developing HCC and its prognosis between patients with these genotypes.

  2. Genetic diversity in soybean genotypes with resistance to Heterodera glycines

    Directory of Open Access Journals (Sweden)

    Ana Paula Oliveira Nogueira

    2011-01-01

    Full Text Available The purpose of this study was to analyze the genetic diversity among soybean genotypes inoculated with Heteroderaglycines race 3. The experiments were conducted in a greenhouse. In two performance tests of morphological characteristics andresistance to the pathogen, 27 soybean genotypes were assessed. The coefficient of genotypic determination was estimated by themethod of analysis of variance and the genetic diversity analyzed based on dendrograms and optimization method. The estimatedcoefficients of determination indicated a predominantly genetic origin of the genotypic differences in the traits. The genetic variabilitywas maintained in the superior genotypes, which can be used in breeding programs for resistance to soybean cyst nematode

  3. Hepatitis B virus taxonomy and hepatitis B virus genotypes

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Hepatitis B virus (HBV) is a member of the hepadnavirus family. Hepadnaviruses can be found in both mammals (orthohepadnaviruses) and birds (avihepadnaviruses).The genetic variability of HBV is very high. There are eight genotypes of HBV and three clades of HBV isolates from apes that appear to be additional genotypes of HBV. Most genotypes are now divided into subgenotypes with distinct virological and epidemiological properties. In addition, recombination among HBV genotypes increases the variability of HBV. This review summarises current knowledge of the epidemiology of genetic variability in hepadnaviruses and, due to rapid progress in the field,updates several recent reviews on HBV genotypes and subgenotypes.

  4. Identification of polymorphic inversions from genotypes

    Directory of Open Access Journals (Sweden)

    Cáceres Alejandro

    2012-02-01

    Full Text Available Abstract Background Polymorphic inversions are a source of genetic variability with a direct impact on recombination frequencies. Given the difficulty of their experimental study, computational methods have been developed to infer their existence in a large number of individuals using genome-wide data of nucleotide variation. Methods based on haplotype tagging of known inversions attempt to classify individuals as having a normal or inverted allele. Other methods that measure differences between linkage disequilibrium attempt to identify regions with inversions but unable to classify subjects accurately, an essential requirement for association studies. Results We present a novel method to both identify polymorphic inversions from genome-wide genotype data and classify individuals as containing a normal or inverted allele. Our method, a generalization of a published method for haplotype data 1, utilizes linkage between groups of SNPs to partition a set of individuals into normal and inverted subpopulations. We employ a sliding window scan to identify regions likely to have an inversion, and accumulation of evidence from neighboring SNPs is used to accurately determine the inversion status of each subject. Further, our approach detects inversions directly from genotype data, thus increasing its usability to current genome-wide association studies (GWAS. Conclusions We demonstrate the accuracy of our method to detect inversions and classify individuals on principled-simulated genotypes, produced by the evolution of an inversion event within a coalescent model 2. We applied our method to real genotype data from HapMap Phase III to characterize the inversion status of two known inversions within the regions 17q21 and 8p23 across 1184 individuals. Finally, we scan the full genomes of the European Origin (CEU and Yoruba (YRI HapMap samples. We find population-based evidence for 9 out of 15 well-established autosomic inversions, and for 52 regions

  5. Identification of zoonotic genotypes of Giardia duodenalis.

    Directory of Open Access Journals (Sweden)

    Hein Sprong

    Full Text Available Giardia duodenalis, originally regarded as a commensal organism, is the etiologic agent of giardiasis, a gastrointestinal disease of humans and animals. Giardiasis causes major public and veterinary health concerns worldwide. Transmission is either direct, through the faecal-oral route, or indirect, through ingestion of contaminated water or food. Genetic characterization of G. duodenalis isolates has revealed the existence of seven groups (assemblages A to G which differ in their host distribution. Assemblages A and B are found in humans and in many other mammals, but the role of animals in the epidemiology of human infection is still unclear, despite the fact that the zoonotic potential of Giardia was recognised by the WHO some 30 years ago. Here, we performed an extensive genetic characterization of 978 human and 1440 animal isolates, which together comprise 3886 sequences from 4 genetic loci. The data were assembled into a molecular epidemiological database developed by a European network of public and veterinary health Institutions. Genotyping was performed at different levels of resolution (single and multiple loci on the same dataset. The zoonotic potential of both assemblages A and B is evident when studied at the level of assemblages, sub-assemblages, and even at each single locus. However, when genotypes are defined using a multi-locus sequence typing scheme, only 2 multi-locus genotypes (MLG of assemblage A and none of assemblage B appear to have a zoonotic potential. Surprisingly, mixtures of genotypes in individual isolates were repeatedly observed. Possible explanations are the uptake of genetically different Giardia cysts by a host, or subsequent infection of an already infected host, likely without overt symptoms, with a different Giardia species, which may cause disease. Other explanations for mixed genotypes, particularly for assemblage B, are substantial allelic sequence heterogeneity and/or genetic recombination. Although the

  6. Creep-Fatigue Failure Diagnosis

    Directory of Open Access Journals (Sweden)

    Stuart Holdsworth

    2015-11-01

    Full Text Available Failure diagnosis invariably involves consideration of both associated material condition and the results of a mechanical analysis of prior operating history. This Review focuses on these aspects with particular reference to creep-fatigue failure diagnosis. Creep-fatigue cracking can be due to a spectrum of loading conditions ranging from pure cyclic to mainly steady loading with infrequent off-load transients. These require a range of mechanical analysis approaches, a number of which are reviewed. The microstructural information revealing material condition can vary with alloy class. In practice, the detail of the consequent cracking mechanism(s can be camouflaged by oxidation at high temperatures, although the presence of oxide on fracture surfaces can be used to date events leading to failure. Routine laboratory specimen post-test examination is strongly recommended to characterise the detail of deformation and damage accumulation under known and well-controlled loading conditions to improve the effectiveness and efficiency of failure diagnosis.

  7. Your Heart Failure Healthcare Team

    Science.gov (United States)

    ... them know how you're doing. With good teamwork and communication, you can improve the quality of ... Failure Recognition and Knowing Your Options Planning Ahead Communicating with Your Healthcare Provider Overcoming Barriers to Shared ...

  8. Severe Obesity and Heart Failure

    Science.gov (United States)

    ... https://medlineplus.gov/news/fullstory_161011.html Severe Obesity and Heart Failure Study sees link even without ... 2016 FRIDAY, Sept. 16, 2016 (HealthDay News) -- Severe obesity appears to be an independent risk factor for ...

  9. Warning Signs of Heart Failure

    Science.gov (United States)

    ... of heart failure may not be cause for alarm. But if you have more than one of ... also causing fluid retention in the tissues. Tiredness, fatigue ...a tired feeling all the time and difficulty ...

  10. Planning Ahead: Advanced Heart Failure

    Science.gov (United States)

    ... Peripheral Artery Disease Venous Thromboembolism Aortic Aneurysm More Planning Ahead: Advanced Heart Failure Updated:Sep 30,2016 ... making your preferences known is called advance care planning. It allows you to speak for yourself, even ...

  11. Decongestion in acute heart failure

    NARCIS (Netherlands)

    Mentz, Robert J.; Kjeldsen, Keld; Rossi, Gian Paolo; Voors, Adriaan A.; Cleland, John G. F.; Anker, Stefan D.; Gheorghiade, Mihai; Fiuzat, Mona; Rossignol, Patrick; Zannad, Faiez; Pitt, Bertram; O'Connor, Christopher; Felker, G. Michael

    2014-01-01

    Congestion is a major reason for hospitalization in acute heart failure (HF). Therapeutic strategies to manage congestion include diuretics, vasodilators, ultrafiltration, vasopressin antagonists, mineralocorticoid receptor antagonists, and potentially also novel therapies such as gut sequesterants

  12. Predicting Failures in Power Grids

    CERN Document Server

    Chertkov, Michael; Stepanov, Mikhail G

    2010-01-01

    Here we develop an approach to predict power grid weak points, and specifically to efficiently identify the most probable failure modes in load distribution for a given power network. This approach is applied to two examples: Guam's power system and also the IEEE RTS-96 system, both modeled within the static Direct Current power flow model. Our algorithm is a power network adaption of the worst configuration heuristics, originally developed to study low probability events in physics and failures in error-correction. One finding is that, if the normal operational mode of the grid is sufficiently healthy, the failure modes, also called instantons, are sufficiently sparse, i.e. the failures are caused by load fluctuations at only a few buses. The technique is useful for discovering weak links which are saturated at the instantons. It can also identify overutilized and underutilized generators, thus providing predictive capability for improving the reliability of any power network.

  13. Antibiotic managment in renal failure.

    Science.gov (United States)

    Winter, R E

    1976-06-01

    This is a brief compilation of the work of many investigators. It includes facts about toxicity and recommendations about antibiotic management in patients with renal failure. As new data are accrued, changes in these recommendations will be necessary.

  14. Avian nephritis virus (ANV) on Brazilian chickens farms: circulating genotypes and intra-genotypic diversity.

    Science.gov (United States)

    Espinoza, Luis Luna; Beserra, Laila A R; Soares, Rodrigo M; Gregori, Fabio

    2016-12-01

    Avian nephritis virus (ANV), which belongs to the family Astroviridae, is associated with different clinical manifestations (including enteric disorders). Despite being frequently found in the avian industry worldwide, information regarding genetic features of these viruses in Brazil is scarce. Therefore, sixty fecal sample pools (5-6 birds of the same flock), representing 60 poultry farms from six Brazilian States, were screened using an astrovirus-specific hemi-nested-PCR assay targeting the conserved ORF1b gene, followed by nucleotide sequencing of amplified products. PCR and phylogenetic analysis confirmed the detection of 21 positive samples to ANV (35 %). In order to investigate the genetic diversity represented by these viruses, amplification, cloning and phylogenetic analysis of the deduced amino acid sequence of ORF2 gene were attempted. Eight samples were successfully cloned (generating 32 clones in total) and sequenced. Based on phylogenetic analysis of ORF2, sequences defined in this study were classified into three genotypes: genotype 5, which has already been described in birds, and two other novel genotypes, tentatively named genotype 8 and 9, all of which occurred in single or mixed infections. Moreover, high intra-genotypic diversity and co-circulation of distinct strains in a same host population were observed. This study revealed the presence of new strains of ANV in Brazilian poultry and their circulation in commercial chicken flocks.

  15. Entire genome sequence analysis of genotype IX Newcastle disease viruses reveals their early-genotype phylogenetic position and recent-genotype genome size

    Directory of Open Access Journals (Sweden)

    Hu Shunling

    2011-03-01

    Full Text Available Abstract Background Six nucleotide (nt insertion in the 5'-noncoding region (NCR of the nucleoprotein (NP gene of Newcaslte disease virus (NDV is considered to be a genetic marker for recent genotypes of NDV, which emerged after 1960. However, F48-like NDVs from China, identified a 6-nt insert in the NP gene, have been previously classified into genotype III or genotype IX. Results In order to clarify their phylogenetic position and explore the origin of NDVs with the 6-nt insert and its significance in NDV evolution, we determined the entire genome sequences of five F48-like viruses isolated in China between 1946 and 2002 by RT-PCR amplification of overlapping fragments of full-length genome and rapid amplification of cDNA ends. All the five NDV isolates shared the same genome size of 15,192-nt with the recent genotype V-VIII viruses whereas they had the highest homology with early genotype III and IV isolates. Conclusions The unique characteristic of the genome size and phylogenetic position of F48-like viruses warrants placing them in a separate geno-group, genotype IX. Results in this study also suggest that genotype IX viruses most likely originate from a genotype III virus by insertion of a 6-nt motif in the 5'-NCR of the NP gene which had occurred as early as in 1940 s, and might be the common origin of genotype V-VIII viruses.

  16. Citrus tristeza virus: Evolution of Complex and Varied Genotypic Groups

    Science.gov (United States)

    Harper, S. J.

    2013-01-01

    Amongst the Closteroviridae, Citrus tristeza virus (CTV) is almost unique in possessing a number of distinct and characterized strains, isolates of which produce a wide range of phenotype combinations among its different hosts. There is little understanding to connect genotypes to phenotypes, and to complicate matters more, these genotypes are found throughout the world as members of mixed populations within a single host plant. There is essentially no understanding of how combinations of genotypes affect symptom expression and disease severity. We know little about the evolution of the genotypes that have been characterized to date, little about the biological role of their diversity and particularly, about the effects of recombination. Additionally, genotype grouping has not been standardized. In this study we utilized an extensive array of CTV genomic information to classify the major genotypes, and to determine the major evolutionary processes that led to their formation and subsequent retention. Our analyses suggest that three major processes act on these genotypes: (1) ancestral diversification of the major CTV lineages, followed by (2) conservation and co-evolution of the major functional domains within, though not between CTV genotypes, and (3) extensive recombination between lineages that have given rise to new genotypes that have subsequently been retained within the global population. The effects of genotype diversity and host-interaction are discussed, as is a proposal for standardizing the classification of existing and novel CTV genotypes. PMID:23630519

  17. Genotypic diversity of root and shoot characteristics of

    Directory of Open Access Journals (Sweden)

    ali ganjali

    2009-06-01

    Full Text Available Root and shoot characteristics of chickpea (Cicer arietinum L. genotypes are believed to be important in drought tolerance. There is a little information about the response of genotypes root growth in hydroponics and greenhouse culture, also the relationships between root size and drought tolerance. This study was conducted to observe whether genotypes differ in root size, and to see that root size is associated with drought tolerance during early vegetative growth. We found significant differences (p0.01 in root dry weight, total root length, tap root length, root area, leaf dry weight, leaf area and shoot biomass per plant among 30 genotypes of chickpea grown in hydroponics culture for three weeks. Each of these parameters correlated with all others, positively. Among 30 genotypes, 10 genotypes with different root sizes were selected and were grown in a greenhouse in sand culture experiment under drought stress (FC %30 for three weeks. There were not linear or non-linear significant correlations between root characters in hydroponics and greenhouse environments. It seems that environmental factors are dominant on genetic factors in seedling stage and so, the expression of genotypics potential for root growth characteristics of genotypes are different in hydroponic and greenhouse conditions. In this study, the selection of genotypes with vigorous roots system in hydroponic condition did not lead to genotypes with the same root characters in greenhouse environment. The genotype×drought interactions for root characters of chickpea seedlings in 30 days were not significant (p

  18. Epidemiology and Treatment of Hepatitis C Genotypes 5 and 6

    Directory of Open Access Journals (Sweden)

    Khalid Al Naamani

    2013-01-01

    Full Text Available Chronic hepatitis C infection is a major global health problem. The WHO estimates the number of infected people worldwide to be approximately 170 million. The estimated number of hepatitis C virus (HCV-infected people in Canada is approximately 250,000, with approximately 5000 Canadians newly infected each year. Based on the identification of genomic differences, HCV has been classified into six genotypes; genotype may influence the outcome of antiviral therapy. HCV genotypes 1, 2 and 3 are widely distributed throughout the world and have been the focus of the majority of epidemiological, natural course and treatment studies. Although HCV genotypes 5 and 6 are prevalent in certain geographical areas, they are studied less extensively. HCV genotypes 5 and 6 are uncommon in Canada and account for less than 5% of HCV-infected Canadians. However, immigration and travel can alter the epidemiology of these uncommon genotypes. The present article reviews and summarizes the available data regarding the epidemiology and treatment of HCV genotypes 5 and 6. Genotype 5 is endemic in the northern part of South Africa while genotype 6 is reported primarily in Asia. Available data show that 48 weeks of treatment with a combination of pegylated interferon and ribavirin lead to a higher sustained virological response compared with HCV genotypes 1 and 4. None of the approved direct-acting antiviral agents is currently recommended for the treatment of HCV genotypes 5 or 6.

  19. 17 CFR 259.5a - Form U5A, for notification of registration filed under section 5(a) of the Act.

    Science.gov (United States)

    2010-04-01

    ...: For Federal Register citations affecting Form U5A, see the List of CFR Sections Affected, which... 17 Commodity and Securities Exchanges 3 2010-04-01 2010-04-01 false Form U5A, for notification of... OF 1935 Forms for Registration and Annual Supplements § 259.5a Form U5A, for notification...

  20. [Does diastolic heart failure exist?].

    Science.gov (United States)

    Guadalajara Boo, José Fernando

    2003-01-01

    This paper reviews the concepts of systolic function, diastolic function, heart failure, diastolic dysfunction, and diastolic heart failure. We refer to the historic evolution of the concept of heart failure and the origin of the term diastolic heart failure. Based on the current concepts of the physiology of the heart and its pathophysiology, we discuss the inappropriateness of the term and to the confusion it has generated in clinical practice, treatment, and prognosis, as well as in numerous research papers (of which some examples are given) when terming as "heart failure" the diastolic dysfunction and using both terms indistinctively. We conclude that an increasing need has arisen, ever more imperative, to identify clearly the concepts of heart failure and diastolic dysfunction, emphasizing on their differences to recognize them as distinct clinical entities with their own personality and, hence, having different prognosis and treatment. This would be of great help to achieve more accuracy in the clinical guidelines, standards, and consensus, especially regarding treatment. Besides it would be useful to avoid, inconsistencies in the design of research, which appear in some of the publications just by the lack of a clear meaning of the terms. Finally, at present we have the necessary elements to conclude that the terms "diastolic heart failure" and "cardiac failure with preserved systolic function" are inexact, poorly gauged, and far away from the actual problem they try to define. Therefore, they should be substituted by the concept of Diastolic Dysfunction, which defines clearly the pathophysiology of the functional alteration, without having to state that "the heart is failing".

  1. Edge effects and delamination failures

    Science.gov (United States)

    Herakovich, C. T.

    1989-01-01

    The fundamental relationship between the morphology of a composite laminate and the resulting free edge effects is explored and related to delamination failures. Cross-ply, angle-ply, and quasi-isotropic laminates are discussed in detail. It is shown that the local mismatch in elastic properties of adjacent layers and the global stacking sequence of a laminate both have a significant influence on the interlaminar stresses and delamination failures.

  2. The failure-tolerant leader.

    Science.gov (United States)

    Farson, Richard; Keyes, Ralph

    2002-08-01

    "The fastest way to succeed," IBM's Thomas Watson, Sr., once said, "is to double your failure rate." In recent years, more and more executives have embraced Watson's point of view, coming to understand what innovators have always known: Failure is a prerequisite to invention. But while companies may grasp the value of making mistakes at the level of corporate practices, they have a harder time accepting the idea at the personal level. People are afraid to fail, and corporate culture reinforces that fear. In this article, psychologist and former Harvard Business School professor Richard Farson and coauthor Ralph Keyes discuss how companies can reduce the fear of miscues. What's crucial is the presence of failure-tolerant leaders--executives who, through their words and actions, help employees overcome their anxieties about making mistakes and, in the process, create a culture of intelligent risk-taking that leads to sustained innovation. Such leaders don't just accept productive failure, they promote it. Drawing from their research in business, politics, sports, and science, the authors identify common practices among failure-tolerant leaders. These leaders break down the social and bureaucratic barriers that separate them from their followers. They engage at a personal level with the people they lead. They avoid giving either praise or criticism, preferring to take a nonjudgmental, analytical posture as they interact with staff. They openly admit their own mistakes rather than trying to cover them up or shifting the blame. And they try to root out the destructive competitiveness built into most organizations. Above all else, failure-tolerant leaders push people to see beyond traditional definitions of success and failure. They know that as long as a person views failure as the opposite of success, rather than its complement, he or she will never be able to take the risks necessary for innovation.

  3. Compound heterozygous SCN5A gene mutations in asymptomatic Brugada syndrome child

    Directory of Open Access Journals (Sweden)

    Elena Sommariva

    2012-09-01

    Full Text Available Loss-of-function mutations in the SCN5A gene, encoding the cardiac Nav1.5 sodium channel, have been previously associated with Brugada syndrome (BrS. Despite the low prevalence of the disease, we identified a patient carrying two SCN5A mutations. We aimed at establishing a correlation between genotype, clinical phenotype and in vitro sodium current. A 3-year-old boy presented with right bundle branch block and ST-segment elevation. Genetic analysis and electrophysiology studies in transfected HEK293 cells were performed to identify possibly disease-causing variants and assess their effect on sodium channel function. Two SCN5A variants were identified: a new frameshift deletion causing premature truncation of the putative protein (c.3258_3261del4 and a missense substitution (p.F1293S. In vitro studies revealed that the truncated mutant did not produce functional channels and decreased total sodium current when co-expressed with p.F1293S channels compared to p.F1293S alone. In addition, p.F1293S channels presented with a steep slope of steady-state activation voltagedependency, which was shifted towards more positive potentials by the co-expression with the truncated channel. p.F1293S channels also showed shift towards more positive potentials of the steady-state inactivation both alone and co-expressed with the deletion mutant. Our data identified a severe reduction of sodium channel current associated with two distinct SCN5A changes. However, all mutation carriers were asymptomatic and BrS electrocardiogram was observed only transiently in the compound heterozygous subject. These observations underline the difficulty of genotype/ phenotype correlations in BrS patients and support the idea of a polygenic disorder, where different mutations and variants can contribute to the clinical phenotype.

  4. Circular RNAs in heart failure.

    Science.gov (United States)

    Devaux, Yvan; Creemers, Esther E; Boon, Reinier A; Werfel, Stanislas; Thum, Thomas; Engelhardt, Stefan; Dimmeler, Stefanie; Squire, Iain

    2017-06-01

    Cardiovascular disease, and particularly heart failure, is still a serious health care issue for which novel treatments and biomarkers are needed. The RNA family comprises different subgroups, among which the small-sized microRNAs and the larger long non-coding RNAs have shown some potential to aid in moving personalized health care of heart failure patients a step forward. Here, members of the Cardiolinc network review the recent findings suggesting that the less well-known circular RNAs may constitute a novel reservoir of therapeutic targets and biomarkers of heart failure. The knowledge of the mode of biogenesis of circular RNAs will first be reported, followed by a description of different features that make these RNA molecules of interest for the heart failure community. The functions of circular RNAs in the heart will be described, with some emphasis given to their regulation in the failing heart. Circulating in the bloodstream, circular RNAs have appeared as potential biomarkers and recent findings associated with the use of circular RNAs as heart failure biomarkers will be discussed. Finally, some directions for future research will be provided. © 2017 The Authors. European Journal of Heart Failure © 2017 European Society of Cardiology.

  5. Reassessing guidelines for heart failure

    Directory of Open Access Journals (Sweden)

    Helmut Drexler

    2004-03-01

    Full Text Available Significant progress has been made in the last few years in the management of heart failure. In particular several trials have given significant results. It has become apparent that heart failure may be prevented in some patients by treatment of risk factors such as coronary artery disease. Experience with angiotensin-converting enzyme (ACE inhibitors has shown that the survival and symptomatic benefits do last in the long term, and confirm that they are the first-line treatment in heart failure. The results of a number of trials using the angiotensin receptor blockers (ARBs candesartan, valsartan and losartan are presented and discussed. There is also some experience now in the use of candesartan for patients with heart failure and preserved left ventricular systolic function. The COMET trial compared the β-blockers carvedilol and metoprolol tartrate, and suggests that there may be differences in clinical effect between β-blockers. The selective aldosterone receptor blocker eplerenone was evaluated in the EPHESUS trial in post-MI patients with signs of heart failure. Based on these clinical trials, heart failure guidelines are now being updated.

  6. Experimental methods for identifying failure mechanisms

    Science.gov (United States)

    Daniel, I. M.

    1983-01-01

    Experimental methods for identifying failure mechanisms in fibrous composites are studied. Methods to identify failure in composite materials includes interferometry, holography, fractography and ultrasonics.

  7. Common Cause Failures and Ultra Reliability

    Science.gov (United States)

    Jones, Harry W.

    2012-01-01

    A common cause failure occurs when several failures have the same origin. Common cause failures are either common event failures, where the cause is a single external event, or common mode failures, where two systems fail in the same way for the same reason. Common mode failures can occur at different times because of a design defect or a repeated external event. Common event failures reduce the reliability of on-line redundant systems but not of systems using off-line spare parts. Common mode failures reduce the dependability of systems using off-line spare parts and on-line redundancy.

  8. Body mass index and obesity- and diabetes-associated genotypes and risk for pancreatic cancer.

    Science.gov (United States)

    Tang, Hongwei; Dong, Xiaoqun; Hassan, Manal; Abbruzzese, James L; Li, Donghui

    2011-05-01

    The genetic factors predisposing individuals with obesity or diabetes to pancreatic cancer have not been identified. To investigate the hypothesis that obesity- and diabetes-related genes modify the risk of pancreatic cancer. We genotyped 15 single nucleotide polymorphisms of fat mass and obesity-associated (FTO), peroxisome proliferators-activated receptor gamma (PPARγ), nuclear receptor family 5 member 2 (NR5A2), AMPK, and ADIPOQ genes in 1,070 patients with pancreatic cancer and 1,175 cancer-free controls. Information on risk factors was collected by personal interview. Adjusted ORs (AOR) and 95% CIs were calculated using unconditional logistic regression. The PPARγ P12A GG genotype was inversely associated with risk of pancreatic cancer (AOR, 0.21; 95% CI, 0.07-0.62). Three NR5A2 variants that were previously identified in a genome-wide association study were significantly associated with reduced risk of pancreatic cancer, AORs ranging from 0.57 to 0.79. Two FTO gene variants and one ADIPOQ variant were differentially associated with pancreatic cancer according to levels of body mass index (BMI; P(interaction) = 0.0001, 0.0015, and 0.03). For example, the AOR (95% CI) for FTO IVS1-2777AC/AA genotype was 0.72 (0.55-0.96) and 1.54 (1.14-2.09) in participants with a BMI of less than 25 or 25 kg/m(2) or more, respectively. We observed no significant association between AMPK genotype and pancreatic cancer and no genotype interactions with diabetes or smoking. Our findings suggest the PPARγ P12A GG genotype and NR5A2 variants may reduce the risk for pancreatic cancer. A positive association of FTO and ADIPOQ gene variants with pancreatic cancer may be limited to persons who are overweight. The discovery of genetic factors modifying the risk of pancreatic cancer may help to identify high-risk individuals for prevention efforts. ©2011 AACR.

  9. Laboratory Information Management Software for genotyping workflows: applications in high throughput crop genotyping

    Directory of Open Access Journals (Sweden)

    Prasanth VP

    2006-08-01

    Full Text Available Abstract Background With the advances in DNA sequencer-based technologies, it has become possible to automate several steps of the genotyping process leading to increased throughput. To efficiently handle the large amounts of genotypic data generated and help with quality control, there is a strong need for a software system that can help with the tracking of samples and capture and management of data at different steps of the process. Such systems, while serving to manage the workflow precisely, also encourage good laboratory practice by standardizing protocols, recording and annotating data from every step of the workflow. Results A laboratory information management system (LIMS has been designed and implemented at the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT that meets the requirements of a moderately high throughput molecular genotyping facility. The application is designed as modules and is simple to learn and use. The application leads the user through each step of the process from starting an experiment to the storing of output data from the genotype detection step with auto-binning of alleles; thus ensuring that every DNA sample is handled in an identical manner and all the necessary data are captured. The application keeps track of DNA samples and generated data. Data entry into the system is through the use of forms for file uploads. The LIMS provides functions to trace back to the electrophoresis gel files or sample source for any genotypic data and for repeating experiments. The LIMS is being presently used for the capture of high throughput SSR (simple-sequence repeat genotyping data from the legume (chickpea, groundnut and pigeonpea and cereal (sorghum and millets crops of importance in the semi-arid tropics. Conclusion A laboratory information management system is available that has been found useful in the management of microsatellite genotype data in a moderately high throughput genotyping

  10. Phylogenetic Analysis of Human Parvovirus B19 Sequences from Eleven Different Countries Confirms the Predominance of Genotype 1 and Suggests the Spread of Genotype 3b▿

    Science.gov (United States)

    Hübschen, Judith M.; Mihneva, Zefira; Mentis, Andreas F.; Schneider, François; Aboudy, Yair; Grossman, Zehava; Rudich, Hagit; Kasymbekova, Kalia; Sarv, Inna; Nedeljkovic, Jasminka; Tahita, Marc C.; Tarnagda, Zekiba; Ouedraogo, Jean-Bosco; Gerasimova, A. G.; Moskaleva, T. N.; Tikhonova, Nina T.; Chitadze, Nazibrola; Forbi, J. C.; Faneye, Adedayo O.; Otegbayo, Jesse A.; Charpentier, Emilie; Muller, Claude P.

    2009-01-01

    Phylogenetic analysis of 166 human parvovirus B19 sequences from 11 different countries attributed 91.57% to genotype 1, 5.42% to genotype 3b, and 3.01% to genotype 3a. Very similar viruses of genotype 1 circulated widely in Europe and Israel. Genotype 3b seems to show an increasing spread outside of Africa. PMID:19741071

  11. Genetic variants of CHRNA5-A3 and CHRNB3-A6 predict survival of patients with advanced non-small cell lung cancer.

    Science.gov (United States)

    Wang, Yang; Peng, Xiaonu; Zhu, Lijun; Hu, Likuan; Song, Yipeng

    2016-05-03

    Nicotinic acetylcholine receptors (nAChRs) play a key role in carcinogenesis and progression of lung cancer; and polymorphisms in CHRNA5-A3 and CHRNB3-A6, two gene clusters encoding nAChR subunits, have been associated with lung cancer risk. In this study, we investigated whether variants in the two gene clusters were associated with prognosis of advanced non-small cell lung cancer (NSCLC). A total of 165 stage IIIB-IV NSCLC patients were enrolled in this study. Three polymorphisms (rs667282 and rs3743073 in CHRNA5-A3 and rs13280604 in CHRNB3-A6) were genotyped using the TaqMan method. Overall survival (OS) was estimated using the log-rank test and the Cox models. Our results showed that patients with CHRNA5-A3 rs667282 TT or TC genotypes had a significantly shorter OS than those carrying the CC genotype (Log-rank, P = 0.043). Furthermore, multivariate Cox regression analysis showed that rs667282 TT/TC genotypes are significantly associated with increased risk of overall deaths (adjusted hazard ratio, 1.7; 95% CI, 1.1-2.7). However, the similar results were not observed for other two polymorphisms. Furthermore, no evident association was found between these variants and clinicopathologic features of advanced NSCLC. Our present study suggested that rs667282 in CHRNA5-A3 may modify the prognosis of patients with advanced NSCLC.

  12. Fulminant hepatitis failure in adults and children from a Public Hospital in Rio de Janeiro, Brazil

    Directory of Open Access Journals (Sweden)

    Damião Carlos Moraes dos Santos

    2009-10-01

    Full Text Available Fulminant hepatic failure (FHF is characterized by massive hepatocellular injury, whose physiopathology is still unclear. Hepatitis B (HBV is probably the most common viral cause of FHF, while hepatitis A (HAV virus seem occurs less frequently. However, the host and viral factors that determine the outcome of these infections are poorly understood. In the present study, viral load and genotyping determining regions of HAV and HBV genomes were sequenced. Eight FHF patients and one patient with severe acute hepatitis (SAH were included. Liver and blood samples were collected during liver transplantation or necropsy procedures. HAV-RNA and HBV-DNA were extracted from serum, biopsy and paraffin liver. Nucleotide sequencing of HAV-RNA was performed from VP1/2A and HBV-DNA from PreS/S region. The amplified samples were quantified by Real-Time PCR. The cases of HAV infection were due to subgenotype IA. The cases of HBV infection were due to genotype A2 and D4. The case of HAV/HBV coinfection was infected by genotype IA and D3. Hepatitis A and B infection were associated with genotypes most prevalent in Brazil. In hepatitis A infection the mean of period evolution was 13 days. In hepatitis B, FHF patients infected by genotype D have a shorter period of evolution than FHF patients infected by genotype A (mean 15 v. 53 days. There was no association with genotype-determining region with the severity of hepatitis, however nucleotide differences and high viral load could be observed among FHF.

  13. Organ failure associated with severe acute pancreatitis

    Institute of Scientific and Technical Information of China (English)

    Ai-Jun Zhu; Jing-Sen Shi; Xue-Jun Sun

    2003-01-01

    AIM: To investigate the relationship between severe acute pancreatitis (SAP) and organ failure.METHODS: Clinical data of 74 cases of SAP from Jan. 1993 to Dec. 2002 were retrospectively reviewed, and the relationship between organ failure and age, gender, etiology,extent of necrosis, infection of necrosis and mortality was analyzed.RESULTS: A total of 47 patients (63.5 %) showed organ failure, 20 patients (27.0 %) multiple organ failure, whereas 27 patients (36.5 %) with dysfunction of a single organ system. Pulmonary failure was the most common organ dysfunction (23.0 %) among single organ failures. There were no significant differences in age, gender and gallstone pancreatitis among patients with or without organ failure (P>0.05). The incidence of organ failure in infected necrosis was not higher compared with sterile necrosis, and patients with increased amount of necrosis did not have an increased prevalence of organ failure (P>0.05). Patients with organ failure had a higher mortality rate compared with those without organ failure (P<0.05). The death of SAP was associated with multiple organ failure (P<0.005), pulmonary failure (P<0.005), cardiovascular dysfunction (P<0.05) and gastrointestinal dysfunction (P<0.05).CONCLUSION: Organ failure is common in patients with SAP, and patients with multiple organ failure and pulmonary failure have a higher mortality rate. Prevention and active treatment of organ failure can improve the outcome of patients with SAP.

  14. RECOVERY STRATEGIES FOR SERVICE FAILURES

    Directory of Open Access Journals (Sweden)

    Budeanu Andreea

    2015-07-01

    Full Text Available Internationally, services represent the most important sector of the economy both in terms of economic performance and labor utilization. Becoming essential part of today society, they are considered the basis of a healthy economy, fact that has increased the importance of services and the research in the field.T hrough this work we intend to address a number of issues that require clarification and are relevant to this sector. Increased competition and customers higher demands lead to difficulties in service delivery, so managers of service organizations must work hard towards developing appropiate strategies that can lead to improved customers satisfaction and to increased efficiency. Because it is inevitably for service providers to face situations in which service failure occurs and their customers are not satisfied, understanding the nature of service failures and the ways in which an organization can recover after a failure are considered key factors for achieving customer satisfaction. Since the data suggests that over 50% of customers who are facing problems are not satisfied with the way they were resolved, we consider appropriate to approach this topic. We intend to draw attention to service providers to the importance of proper management of service failure. They can find ways to recover from these failures and even to turn them into some very pleasant situations that can contribute to customer loyalty. This paper begins by highlighting the various features specific to services which contribute to the increased chances of failure, it continues by presenting the concepts of service failure and service recovery and then it presents some links that exist between service recovery and other aspects of providing services that are demonstrated in the literature. We hope that this paper will significantly contribute to the knowledge and development of the sector under analysis and will highlight some practices that will lead to improved

  15. SBE primer : multiplexing minisequencing-based genotyping

    Energy Technology Data Exchange (ETDEWEB)

    Kaderali, L. (Lars); Deshpande, A. (Alina); Uribe-Romeo, F. J. (Francisco J.); Schliep, A.; Torney, D. C. (David C.)

    2002-01-01

    Single-nucleotide polymorphism (SNP) analysis is a powerful tool for mapping and diagnosing disease-related alleles. Most of the known genetic diseases are caused by point mutations, and a growing number of SNPs will be routinely analyzed to diagnose genetic disorders. Mutation analysis by polymerase mediated single-base primer extension (minisequencing) can be massively parallelized using for example DNA microchips or flow cytometry with microspheres as solid support. By adding a unique oligonucleotide tag to the 5-inch end of the minisequencing primer and attaching the complementary anti-tag to the array or bead surface, the assay can be 'demultiplexed'. However, such high-throughput scoring of SNPs requires a high level of primer multiplexing in order to analyze multiple loci in one assay, thus enabling inexpensive and fast polymorphism scoring. Primers can be chosen from either the plus or the minus strand, and primers used in the same experiment must not bind to one another. To genotype a given number of polymorphic sites, the question is which primer to use for each SNP, and which primers to group into the same experiment. Furthermore, a crosshybridization-free tag/anti-tag code is required in order to sort the extended primers to the corresponding microspheres or chip spots. These problems pose challenging algorithmic questions. We present a computer program lo automate the design process for the assay. Oligonucleotide primers for the reaction are automatically selected by the software, a unique DNA tag/anti-tag system is generated, and the pairing of primers and DNA-Tags is automatically done in a way to avoid any crossreactivity. We report first results on a 45-plex genotyping assay, indicating that minisequencing can be adapted to be a powerful tool for high-throughput, massively parallel genotyping.

  16. Association of CYP17 and SRD5A2 gene polymorphisms with Prostate cancer risk among Iranian and Indian populations

    Directory of Open Access Journals (Sweden)

    kh onsory

    2016-02-01

    Full Text Available Aims and objectives: Prostate cancer is a complicated disease that genetics and environmental factors may be playing a promoting role in its progression. Polymorphism of genes such as steroid hormone receptors are having very important role in developing this disease. One such gene, CYP17 is playing role in hydroxylation and SRD5A2 gene, the predominant 5&alpha-reductase isozyme in prostate, catalyzes the conversion of testosterone into the more potent androgen, dihydrotestosterone (DHT, which is required for the normal growth and development of the prostate gland. The purpose of this study was to investigate association of CYP17 and SRD5A2 genes polymorphisms with prostate cancer risk. Materials and methods: PCR-RFLP analysis of CYP17 and SRD5A2 genes were performed on 100 prostate cancer patients admitted to the Department of Urology, Postgraduate Institute of Medical Science and Research (PGIMER, Chandigarh, India, and 150 patients from Imam Khomeini Hospital, Tehran, Iran, compared with equal number of matching controls for each group visiting same centers for other reason. The data was analyzed using the computer software SPSS for windows (version 19, using logistic regression. Results: In this case-control study, there was a significant increase with risk of prostate cancer association for individuals carrying one copy of CYP17 A2 allele in Iranian (OR= 2.10 95% CI, 1.03-4.27 P=0.041 and Indian populations (OR= 2.16 95% CI, 1.08-4.33 P=0.029. While the risk was decreased in individuals having two A2 alleles in both groups. Compared with men having the VV genotype of SRD5A2 gene, there was no significant association between the VL genotype and the risk of prostate cancer among Iranian (OR, 0.87 95% CI, 0.49 -1.56 P=0.661 and Indian (OR, 0.99 95% CI, 0.54 -1.81 P=0.989 patients. Also there was no difference in the occurrence of the genotype LL between prostate cancer patients and control groups in both studied populations therefore, there

  17. Genotyping of Coxiella burnetii from domestic ruminants in northern Spain

    Directory of Open Access Journals (Sweden)

    Astobiza Ianire

    2012-12-01

    Full Text Available Abstract Background Information on the genotypic diversity of Coxiella burnetii isolates from infected domestic ruminants in Spain is limited. The aim of this study was to identify the C. burnetii genotypes infecting livestock in Northern Spain and compare them to other European genotypes. A commercial real-time PCR targeting the IS1111a insertion element was used to detect the presence of C. burnetii DNA in domestic ruminants from Spain. Genotypes were determined by a 6-loci Multiple Locus Variable number tandem repeat analysis (MLVA panel and Multispacer Sequence Typing (MST. Results A total of 45 samples from 4 goat herds (placentas, N = 4, 12 dairy cattle herds (vaginal mucus, individual milk, bulk tank milk, aerosols, N = 20 and 5 sheep flocks (placenta, vaginal swabs, faeces, air samples, dust, N = 21 were included in the study. Samples from goats and sheep were obtained from herds which had suffered abortions suspected to be caused by C. burnetii, whereas cattle samples were obtained from animals with reproductive problems compatible with C. burnetii infection, or consisted of bulk tank milk (BTM samples from a Q fever surveillance programme. C. burnetii genotypes identified in ruminants from Spain were compared to those detected in other countries. Three MLVA genotypes were found in 4 goat farms, 7 MLVA genotypes were identified in 12 cattle herds and 4 MLVA genotypes were identified in 5 sheep flocks. Clustering of the MLVA genotypes using the minimum spanning tree method showed a high degree of genetic similarity between most MLVA genotypes. Overall 11 different MLVA genotypes were obtained corresponding to 4 different MST genotypes: MST genotype 13, identified in goat, sheep and cattle from Spain; MST genotype 18, only identified in goats; and, MST genotypes 8 and 20, identified in small ruminants and cattle, respectively. All these genotypes had been previously identified in animal and human clinical samples from several

  18. Development and application of genotyping technologies

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    With the completion of Human Genome Project,International HapMap Project and the publication of copy number variation in human genome,a great number of accurate,rapid,and cost-effective technologies for SNP analysis have been developed,promoting the research of the complex diseases.This article presents a review of widely used genotyping techniques,and the progress and prospect in the study of complex diseases in terms of the projects and achievements of Chinese National Human Genome Center at Shanghai(CHGCs).

  19. Development and application of genotyping technologies

    Institute of Scientific and Technical Information of China (English)

    SHI JinXiu; WANG Ying; HUANG Wei

    2009-01-01

    With the completion of Human Genome Project, International HapMap Project and the publication of copy number variation in human genome, a great number of accurate, rapid, and cost-effective tech-nologies for SNP analysis have been developed, promoting the research of the complex diseases. This article presents a review of widely used genotyping techniques, and the progress and prospect in the study of complex diseases in terms of the projects and achievements of Chinese National Human Genome Center at Shanghai (CHGCs).

  20. Celer: an Efficient Program for Genotype Elimination

    Directory of Open Access Journals (Sweden)

    Nicoletta De Francesco

    2010-08-01

    Full Text Available This paper presents an efficient program for checking Mendelian consistency in a pedigree. Since pedigrees may contain incomplete and/or erroneous information, geneticists need to pre-process them before performing linkage analysis. Removing superfluous genotypes that do not respect the Mendelian inheritance laws can speed up the linkage analysis. We have described in a formal way the Mendelian consistency problem and algorithms known in literature. The formalization helped to polish the algorithms and to find efficient data structures. The performance of the tool has been tested on a wide range of benchmarks. The results are promising if compared to other programs that treat Mendelian consistency.

  1. Celer: an Efficient Program for Genotype Elimination

    CERN Document Server

    De Francesco, Nicoletta; Martini, Luca; 10.4204/EPTCS.33.4

    2010-01-01

    This paper presents an efficient program for checking Mendelian consistency in a pedigree. Since pedigrees may contain incomplete and/or erroneous information, geneticists need to pre-process them before performing linkage analysis. Removing superfluous genotypes that do not respect the Mendelian inheritance laws can speed up the linkage analysis. We have described in a formal way the Mendelian consistency problem and algorithms known in literature. The formalization helped to polish the algorithms and to find efficient data structures. The performance of the tool has been tested on a wide range of benchmarks. The results are promising if compared to other programs that treat Mendelian consistency.

  2. Prevalence of hepatitis C virus (HCV) genotypes in Balochistan.

    Science.gov (United States)

    Afridi, Sarwat; Naeem, Muhammad; Hussain, Abid; Kakar, Naseebullah; Babar, Masroor Ellahi; Ahmad, Jamil

    2009-07-01

    A molecular study was conducted to investigate the prevalence of Hepatitis C virus genotypes in HCV infected population of Balochistan. Forty HCV seropositive samples belonging to seven different locations of Balochistan were collected from different health care centres. Qualitative analysis of these samples using PCR resulted in 28 positive samples. The PCR positive samples were subjected to genotyping using the method described by Ohno et al (J Clin Microbiol 35:201-202, 1997) with minor modifications. Genotyping of 28 samples revealed three different genotypes including 3a, 3b and 1a. The most prevalent genotype was 3a with rate of 50% followed by genotype 3b and 1a, respectively. Nine samples remained untyped, suggesting the need of further investigation of genotypes in this region. It has been proposed that sequencing of these samples may be helpful to unreveal these genotypes and further epidemiology of HCV genotypes. Further more, extensive and large scale studies are needed to understand the epidemiology of HCV genotypes, as no such study has been carried in this province.

  3. The distribution of hepatitis B virus genotypes in Thailand.

    Science.gov (United States)

    Louisirirotchanakul, Suda; Olinger, Christophe M; Arunkaewchaemsri, Panida; Poovorawan, Yong; Kanoksinsombat, Chinda; Thongme, Chittima; Sa-Nguanmoo, Pattaratida; Krasae, Sasithorn; Theamboonlert, Apiradee; Oota, Sineenart; Fongsatitkul, Ladda; Puapairoj, Chintana; Promwong, Charuporn; Weber, Bernard

    2012-10-01

    Phylogenetic analysis was performed on hepatitis B virus (HBV) strains obtained from 86 hepatitis B surface antigen (HBsAg) positive donors from Thailand originating throughout the country. Based on the S gene, 87.5% of strains were of genotype C while 10.5% were of genotype B, with all genotype B strains obtained from patients originating from the central or the south Thailand. No genotype B strains were found in the north of Thailand. Surprisingly, one patient was infected with a genotype H strain while another patient was infected with a genotype G strain. Complete genome sequencing and recombination analysis identified the latter as being a genotype G and C2 recombinant with the breakpoint around nucleotide position 700. The origin of the genotype G fragment was not identifiable while the genotype C2 fragment most likely came from strains circulating in Laos or Malaysia. The performance of different HBsAg diagnostic kits and HBV nucleic acid amplification technology (NAT) was evaluated. The genotype H and G/C2 recombination did not interfere with HBV detection.

  4. Geographic distribution of hepatitis C virus genotypes in Brazil

    Directory of Open Access Journals (Sweden)

    Campiotto S.

    2005-01-01

    Full Text Available Brazil is a country of continental dimension with a population of different ethnic backgrounds. Thus, a wide variation in the frequencies of hepatitis C virus (HCV genotypes is expected to occur. To address this point, 1,688 sequential samples from chronic HCV patients were analyzed. HCV-RNA was amplified by the RT-PCR from blood samples collected from 1995 to 2000 at different laboratories located in different cities from all Brazilian States. Samples were collected in tubes containing a gel separator, centrifuged in the site of collection and sent by express mail in a refrigerated container to Laboratório Bioquímico Jardim Paulista, São Paulo, SP, Brazil. HCV- RNA was extracted from serum and submitted to RT and nested PCR using standard procedures. Nested PCR products were submitted to cycle sequencing reactions without prior purification. Sequences were analyzed for genotype determination and the following frequencies were found: 64.9% (1,095 for genotype 1, 4.6% (78 for genotype 2, 30.2% (510 for genotype 3, 0.2% (3 for genotype 4, and 0.1% (2 for genotype 5. The frequencies of HCV genotypes were statistically different among Brazilian regions (P = 0.00017. In all regions, genotype 1 was the most frequent (51.7 to 74.1%, reaching the highest value in the North; genotype 2 was more prevalent in the Center-West region (11.4%, especially in Mato Grosso State (25.8%, while genotype 3 was more common in the South (43.2%. Genotypes 4 and 5 were rarely found and only in the Southeast, in São Paulo State. The present data indicate the need for careful epidemiological surveys throughout Brazil since knowing the frequency and distribution of the genotypes would provide key information for understanding the spread of HCV.

  5. Is the CCR5-59029-G/G genotype a protective factor for cardiomyopathy in Chagas disease?

    Science.gov (United States)

    Fernández-Mestre, M T; Montagnani, S; Layrisse, Z

    2004-07-01

    Investigated were two CCR5 gene polymorphisms, the CCR5 Delta 32 deletion and the pCCR5 59029 A-->G promoter point mutation, in 107 ethnically mixed Venezuelan patients serologically positive for Trypanosoma cruzi (34 asymptomatic, 38 arrhythmic, 35 cardiomyopathic). No difference in the distribution of CCR5 Delta 32 among asymptomatic and symptomatic patients was found. We have observed an increase of the 59029-G phenotype among asymptomatic compared with symptomatic chagasic patients (68% vs. 58%), in agreement with previously reported data (57% vs. 31%). This frequency difference, although not statistically significant, is more marked when the 59029-G allele is present in homozygous form. However, a similar distribution of the G/G genotype is present among asymptomatic patients and patients with heart failure. Because it has been reported that the 59029G/G genotype associates with lower CCR5 expression, 37% of our T. cruzi-infected patients with heart failure are genetically predisposed to express low levels of CCR5 on the surface of CD8(+) T cells, contrary to what would be expected if an inflammatory response is required for severe cardiac damage. If confirmed, the possible protection that might be conferred by the G/G genotype may be due to the existence of other genes in linkage disequilibria.

  6. Genotyping of human Brucella melitensis biovar 3 isolated from Shanxi Province in China by MLVA16 and HOOF.

    Directory of Open Access Journals (Sweden)

    Pei Xiao

    Full Text Available BACKGROUND: Brucellosis presents a significant economic burden for China because it causes reproductive failure in host species and chronic health problems in humans. These problems can involve multiple organs. Brucellosis is highly endemic in Shanxi Province China. Molecular typing would be very useful to epidemiological surveillance. The purpose of this study was to assess the diversity of Brucella melitensis strains for epidemiological surveillance. Historical monitoring data suggest that Brucella melitensis biovar 3 is the predominant strain associated with the epidemic of brucellosis in Shanxi Province. METHODS/PRINCIPAL FINDINGS: Multiple-locus variable-number repeat analysis (MLVA-16 and hypervariable octameric oligonucleotide fingerprinting (HOOF-print were used to type a human-hosted Brucella melitensis population (81 strains. Sixty-two MLVA genotypes (discriminatory index: 0.99 were detected, and they had a genetic similarity coefficient ranging from 84.9% to 100%. Eighty strains of the population belonged to the eastern Mediterranean group with panel 1 genotypes 42 (79 strains and 43 (1 strain. A new panel 1 genotype was found in this study. It was named 114 MLVAorsay genotype and it showed similarity to the two isolates from Guangdong in a previous study. Brucella melitensis is distributed throughout Shanxi Province, and like samples from Inner Mongolia, the eastern Mediterranean genotype 42 was the main epidemic strain (97%. The HOOF-printing showed a higher diversity than MLVA-16 with a genetic similarity coefficient ranging from 56.8% to 100%. CONCLUSIONS: According to the MLVA-16 and HOOF-printing results, both methods could be used for the epidemiological surveillance of brucellosis. A new genotype was found in both Shanxi and Guangdong Provinces. In areas with brucellosis, the MLVA-16 scheme is very important for tracing cases back to their origins during outbreak investigations. It may facilitate the expansion and eradication

  7. Low Protective Efficacy of the Current Japanese Encephalitis Vaccine against the Emerging Genotype 5 Japanese Encephalitis Virus.

    Science.gov (United States)

    Cao, Lei; Fu, Shihong; Gao, Xiaoyan; Li, Minghua; Cui, Shiheng; Li, Xiaolong; Cao, Yuxi; Lei, Wenwen; Lu, Zhi; He, Ying; Wang, Huanyu; Yan, Jinghua; Gao, George Fu; Liang, Guodong

    2016-05-01

    The current Japanese encephalitis (JE) vaccine derived from G3 JE virus (JEV) can induce protective immunity against G1-G4 JEV genotypes. However, protective efficacy against the emerging G5 genotype has not been reported. Using in vitro and in vivo tests, biological phenotype and cross-immunoreactions were compared between G3 JEV and G5 JEV (wild strains). The PRNT90 method was used to detect neutralizing antibodies against different genotypes of JEV in JE vaccine-immunized subjects and JE patients. In JE vaccine-immunized mice, the lethal challenge protection rates against G3 and G5 JEV wild strains were 100% and 50%, respectively. The seroconversion rates (SCRs) of virus antibodies against G3 and G5 JEV among vaccinated healthy subjects were 100% and 35%, respectively. All clinically identified JE patients showed high levels of G3 JEV neutralizing antibodies (≥1:10-1280) with positive serum geometric mean titers (GMTs) of 43.2, while for G5 JEV, neutralizing antibody conversion rates were only 64% with positive serum GMTs of 11.14. Moreover, the positive rate of JEV neutralizing antibodies against G5 JEV in pediatric patients was lower than in adults. Low levels of neutralizing/protective antibodies induced by the current JE vaccine, based on the G3 genotype, were observed against the emerging G5 JEV genotype. Our results demonstrate the need for more detailed studies to reevaluate whether or not the apparent emergence of G5 JEV can be attributed to failure of the current vaccine to induce appropriate immune protectivity against this genotype of JEV.

  8. Gene therapy for heart failure.

    Science.gov (United States)

    Greenberg, Barry

    2017-04-01

    Novel strategies are needed to treat the growing population of heart failure patients. While new drug and device based therapies have improved outcomes over the past several decades, heart failure patients continue to experience amongst the lowest quality of life of any chronic disease, high likelihood of being hospitalized and marked reduction in survival. Better understanding of many of the basic mechanisms involved in the development of heart failure has helped identify abnormalities that could potentially be targeted by gene transfer. Despite success in experimental animal models, translating gene transfer strategies from the laboratory to the clinic remains at an early stage. This review provides an introduction to gene transfer as a therapy for treating heart failure, describes some of the many factors that need to be addressed in order for it to be successful and discusses some of the recent studies that have been carried out in heart failure patients. Insights from these studies highlight both the enormous promise of gene transfer and the obstacles that still need to be overcome for this treatment approach to be successful. Copyright © 2017 Elsevier Inc. All rights reserved.

  9. Failure to thrive: an update.

    Science.gov (United States)

    Cole, Sarah Z; Lanham, Jason S

    2011-04-01

    Failure to thrive in childhood is a state of undernutrition due to inadequate caloric intake, inadequate caloric absorption, or excessive caloric expenditure. In the United States, it is seen in 5 to 10 percent of children in primary care settings. Although failure to thrive is often defined as a weight for age that falls below the 5th percentile on multiple occasions or weight deceleration that crosses two major percentile lines on a growth chart, use of any single indicator has a low positive predictive value. Most cases of failure to thrive involve inadequate caloric intake caused by behavioral or psychosocial issues. The most important part of the outpatient evaluation is obtaining an accurate account of a child's eating habits and caloric intake. Routine laboratory testing rarely identifies a cause and is not generally recommended. Reasons to hospitalize a child for further evaluation include failure of outpatient management, suspicion of abuse or neglect, or severe psychosocial impairment of the caregiver. A multidisciplinary approach to treatment, including home nursing visits and nutritional counseling, has been shown to improve weight gain, parent-child relationships, and cognitive development. The long-term effects of failure to thrive on cognitive development and future academic performance are unclear.

  10. IL28B SNP rs8099917 is strongly associated with pegylated interferon-α and ribavirin therapy treatment failure in HCV/HIV-1 coinfected patients.

    Directory of Open Access Journals (Sweden)

    Ester Aparicio

    Full Text Available Recent genome-wide association studies report that the SNP rs8099917, located 8.9 kb upstream of the start codon of IL28B, is associated with both disease chronicity and therapeutic response to pegIFN-α and RBV in patients infected with genotype 1 HCV. To determine the effect of rs8099917 variation on the response of HCV to therapy, we genotyped this variant in a cohort of 160 HCV/HIV-1 coinfected patients in our clinic unit who received combined peg-IFN-α/RBV therapy. The rs8099917 T/G or G/G genotypes were observed in 56 patients (35%. Treatment failure occurred in 80% of G-allele carriers versus 48% of non-carriers (P<0.0001. This result reveals that the G allele was strongly associated with treatment failure in this patient cohort. Importantly, a highly significant association was found between the G-allele and response to therapy in HCV genotype 1-infected patients (P<0.0001 but not in HCV genotype 3-infected patients. Multivariate analysis (odds ratio; 95% confidence interval; P value indicated that the rs8099917 TT genotype was a strong predictor of treatment success (5.83; 1.26-26.92; P = 0.021, independent of baseline plasma HCV-RNA load less than 500 000 IU/ml (4.85; 1.18-19.95; P = 0.025 and absence of advanced liver fibrosis (5.24; 1.20-22.91; P = 0.025. These results reveal the high prevalence of the rs8099917 G allele in HCV/HIV-1 coinfected patients as well as its strong association with treatment failure in HCV genotype 1-infected patients. rs8099917 SNP genotyping may be a valid pre-treatment predictor of which patients are likely to respond to treatment in this group of difficult-to-treat HCV/HIV-infected patients.

  11. Everyday Attention Failures: An Individual Differences Investigation

    Science.gov (United States)

    Unsworth, Nash; McMillan, Brittany D.; Brewer, Gene A.; Spillers, Gregory J.

    2012-01-01

    The present study examined individual differences in everyday attention failures. Undergraduate students completed various cognitive ability measures in the laboratory and recorded everyday attention failures in a diary over the course of a week. The majority of attention failures were failures of distraction or mind wandering in educational…

  12. Epidemic Network Failures in Optical Transport Networks

    DEFF Research Database (Denmark)

    Ruepp, Sarah Renée; Katsikas, Dimitrios; Fagertun, Anna Manolova

    2013-01-01

    This paper presents a failure propagation model for transport networks which are affected by epidemic failures. The network is controlled using the GMPLS protocol suite. The Susceptible Infected Disabled (SID) epidemic model is investigated and new signaling functionality of GMPLS to support epid...... epidemic failure resolution is proposed. The results provide important input to service recovery mechanisms under epidemic failures....

  13. Everyday Attention Failures: An Individual Differences Investigation

    Science.gov (United States)

    Unsworth, Nash; McMillan, Brittany D.; Brewer, Gene A.; Spillers, Gregory J.

    2012-01-01

    The present study examined individual differences in everyday attention failures. Undergraduate students completed various cognitive ability measures in the laboratory and recorded everyday attention failures in a diary over the course of a week. The majority of attention failures were failures of distraction or mind wandering in educational…

  14. Understand Your Risk for Heart Failure

    Science.gov (United States)

    ... Thromboembolism Aortic Aneurysm More Causes and Risks for Heart Failure Updated:Feb 1,2017 Who Develops Heart Failure ( ... HF. This content was last reviewed April 2015. Heart Failure • Home • About Heart Failure • Causes and Risks for ...

  15. Effect of reference population size and available ancestor genotypes on imputation of Mexican Holstein genotypes

    Science.gov (United States)

    The effects of reference population size and the availability of information from genotyped ancestors on the accuracy of imputation of single nucleotide polymorphisms (SNPs) were investigated for Mexican Holstein cattle. Three scenarios for reference population size were examined: (1) a local popula...

  16. The potential of plant viruses to promote genotypic diversity via genotype x environment interactions

    DEFF Research Database (Denmark)

    van Mölken, Tamara; Stuefer, Josef F.

    2011-01-01

    for WClMV to provoke differential selection on T. repens genotypes, which may lead to negative frequency-dependent selection in host populations. †Conclusions The apparent G × E interaction and evident repercussions for relative fitness reported in this study stress the importance of viruses...

  17. Novel drugs in the management of difficult-to-treat hepatitis C genotypes

    Directory of Open Access Journals (Sweden)

    Cartwright EJ

    2013-08-01

    Full Text Available Emily J Cartwright, Lesley MillerDepartment of Medicine, Emory University School of Medicine, Atlanta, GA, USABackground: Hepatitis C virus (HCV infection is the most common chronic bloodborne infection in the United States, with approximately 3.2 million Americans being chronically infected. Rates of HCV-related end-stage liver disease and its associated morbidity and mortality have yet to peak, so there is a pressing need for more effective and tolerable HCV treatment. HCV genotypes 1, 4, 5, and 6 are considered difficult to treat, and the need for improved therapies is especially great for persons infected with these genotypes.Current strategies for HCV treatment: Current therapy for genotype 1 HCV infection includes triple therapy with pegylated interferon, ribavirin, and a NS3/4A protease inhibitor. Sustained virologic response (SVR rates with triple therapy range from 42% to 75%, a vast improvement over pegylated interferon and ribavirin therapy alone. However, response rates remain suboptimal, and triple therapy is associated with significant adverse effects and is only indicated for genotype 1 HCV infection.Novel drugs for HCV treatment: HCV drug development is proceeding at a rapid pace to meet this need. Novel direct acting antiviral agents in several classes, including new NS3/4A serine protease inhibitors, NS5A replication complex inhibitors, NS5B polymerase inhibitors, interferon lambda, and microRNAs, are in varying stages of development. These new therapeutic agents promise SVR rates of up to 100% with durations as short as 12 weeks and, often, fewer adverse effects.Conclusion: New drug development in HCV is proceeding at an unprecedented pace. Novel agents promise higher SVR rates, shorter duration of therapy, and fewer adverse effects than have been possible with HCV therapy to date.Keywords: hepatitis C, direct acting antivirals, genotype

  18. Tree species, tree genotypes and tree genotypic diversity levels affect microbe-mediated soil ecosystem functions in a subtropical forest

    Science.gov (United States)

    Purahong, Witoon; Durka, Walter; Fischer, Markus; Dommert, Sven; Schöps, Ricardo; Buscot, François; Wubet, Tesfaye

    2016-11-01

    Tree species identity and tree genotypes contribute to the shaping of soil microbial communities. However, knowledge about how these two factors influence soil ecosystem functions is still lacking. Furthermore, in forest ecosystems tree genotypes co-occur and interact with each other, thus the effects of tree genotypic diversity on soil ecosystem functions merit attention. Here we investigated the effects of tree species, tree genotypes and genotypic diversity levels, alongside soil physicochemical properties, on the overall and specific soil enzyme activity patterns. Our results indicate that tree species identity, tree genotypes and genotypic diversity level have significant influences on overall and specific soil enzyme activity patterns. These three factors influence soil enzyme patterns partly through effects on soil physicochemical properties and substrate quality. Variance partitioning showed that tree species identity, genotypic diversity level, pH and water content all together explained ~30% variations in the overall patterns of soil enzymes. However, we also found that the responses of soil ecosystem functions to tree genotypes and genotypic diversity are complex, being dependent on tree species identity and controlled by multiple factors. Our study highlights the important of inter- and intra-specific variations in tree species in shaping soil ecosystem functions in a subtropical forest.

  19. Tree species, tree genotypes and tree genotypic diversity levels affect microbe-mediated soil ecosystem functions in a subtropical forest

    Science.gov (United States)

    Purahong, Witoon; Durka, Walter; Fischer, Markus; Dommert, Sven; Schöps, Ricardo; Buscot, François; Wubet, Tesfaye

    2016-01-01

    Tree species identity and tree genotypes contribute to the shaping of soil microbial communities. However, knowledge about how these two factors influence soil ecosystem functions is still lacking. Furthermore, in forest ecosystems tree genotypes co-occur and interact with each other, thus the effects of tree genotypic diversity on soil ecosystem functions merit attention. Here we investigated the effects of tree species, tree genotypes and genotypic diversity levels, alongside soil physicochemical properties, on the overall and specific soil enzyme activity patterns. Our results indicate that tree species identity, tree genotypes and genotypic diversity level have significant influences on overall and specific soil enzyme activity patterns. These three factors influence soil enzyme patterns partly through effects on soil physicochemical properties and substrate quality. Variance partitioning showed that tree species identity, genotypic diversity level, pH and water content all together explained ~30% variations in the overall patterns of soil enzymes. However, we also found that the responses of soil ecosystem functions to tree genotypes and genotypic diversity are complex, being dependent on tree species identity and controlled by multiple factors. Our study highlights the important of inter- and intra-specific variations in tree species in shaping soil ecosystem functions in a subtropical forest. PMID:27857198

  20. Learning from Failures in Operations

    DEFF Research Database (Denmark)

    Koch, Christian

    2005-01-01

    product. The analysis showed that, among others, design review, project review, commencing and finalizing operations turned out to be critical junctions in the control of failures. Practical implications and improvements are discussed. The focus on critical junctions, points to supply chain management......This paper discusses failures and quality in operations in design and production of buildings. The importance of human action, interpretations and interactions in tackling complexity, fragmentation and disturbances in the building industry is underlined. Building processes encompass requisite...... parallelism and fragmentation due to their predominantly quantitative complexity. It is suggested that a number of critical junctions occur in these processes and that obtaining quality and avoiding failures quite often requires a series of competent and situational operation management actions. An empirical...

  1. DEALING WITH DENTAL IMPLANT FAILURES

    Science.gov (United States)

    Levin, Liran

    2008-01-01

    An implant-supported restoration offers a predictable treatment for tooth replacement. Reported success rates for dental implants are high. Nevertheless, failures that mandate immediate implant removal do occur. The consequences of implant removal jeopardize the clinician's efforts to accomplish satisfactory function and esthetics. For the patient, this usually involves further cost and additional procedures. The aim of this paper is to describe different methods and treatment modalities to deal with dental implant failure. The main topics for discussion include identifying the failing implant, implants replacing failed implants at the exact site, and the use of other restorative options. When an implant fails, a tailor made treatment plan should be provided to each patient according to all relevant variables. Patients should be informed regarding all possible treatment modalities following implant failure and give their consent to the most appropriate treatment option for them. PMID:19089213

  2. Dealing with dental implant failures

    Directory of Open Access Journals (Sweden)

    Liran Levin

    2008-06-01

    Full Text Available An implant-supported restoration offers a predictable treatment for tooth replacement. Reported success rates for dental implants are high. Nevertheless, failures that mandate immediate implant removal do occur. The consequences of implant removal jeopardize the clinician's efforts to accomplish satisfactory function and esthetics. For the patient, this usually involves further cost and additional procedures. The aim of this paper is to describe different methods and treatment modalities to deal with dental implant failure. The main topics for discussion include identifying the failing implant, implants replacing failed implants at the exact site, and the use of other restorative options.When an implant fails, a tailor made treatment plan should be provided to each patient according to all relevant variables. Patients should be informed regarding all possible treatment modalities following implant failure and give their consent to the most appropriate treatment option for them.

  3. Ciprofloxacin-Induced Renal Failure

    Directory of Open Access Journals (Sweden)

    Audra Fuller

    2015-10-01

    Full Text Available Acute renal failure (ARF is a common diagnosis in hospitalized patients, particularly in intensive care units (ICU. Determining the cause and contributing factors associated with ARF is crucial during treatment. The etiology is complex, and several factors often contribute to its development. Medications can cause acute tubular necrosis, acute interstitial nephritis, and crystal-induced or post-obstructive nephropathy. There have been several case reports of ARF secondary to fluoroquinolones. Here we report the development of acute renal failure within a few days of initiating oral ciprofloxacin therapy and briefly describe the different types of renal failure secondary to fluoroquinolone administration. Clinical studies demonstrate that using fluoroquinolones with other potentially nephrotoxic medications requires monitoring of renal function to limit the renal toxicity with these medications. Also, the risk-benefit profile of patients requiring fluoroquinolones should be considered.

  4. Respiratory failure in diabetic ketoacidosis

    Institute of Scientific and Technical Information of China (English)

    2015-01-01

    Respiratory failure complicating the course of diabeticketoacidosis (DKA) is a source of increased morbidityand mortality. Detection of respiratory failure in DKA requiresfocused clinical monitoring, careful interpretationof arterial blood gases, and investigation for conditionsthat can affect adversely the respiration. Conditions thatcompromise respiratory function caused by DKA can bedetected at presentation but are usually more prevalentduring treatment. These conditions include deficits ofpotassium, magnesium and phosphate and hydrostatic ornon-hydrostatic pulmonary edema. Conditions not causedby DKA that can worsen respiratory function under theadded stress of DKA include infections of the respiratorysystem, pre-existing respiratory or neuromuscular diseaseand miscellaneous other conditions. Prompt recognitionand management of the conditions that can lead torespiratory failure in DKA may prevent respiratory failureand improve mortality from DKA.

  5. Pseudoporphyria secondary to renal failure

    Directory of Open Access Journals (Sweden)

    Lilianna Kulczycka-Siennicka

    2017-04-01

    Full Text Available Introduction . Pseudoporphyria is a rare disease associated with chronic renal failure. Symptoms of pseudoporphyria may develop in response to UV exposure and medications. The literature reports cases of pseudoporphyria in patients infected with hepatis C virus, HIV and undergoing dialysis therapy. Objective . Presentation of the case of a patient with pseudoporphyria and uraemic pruritus, and overview of therapeutic management. Case report . A 64-year-old male patient, who had been on dialysis for chronic renal failure secondary to type 2 diabetes for the past 11 years, presented with tense bullae located on sun-exposed skin which had persisted for the previous 5 months. The patient was diagnosed with pseudoporphyria, and treatment was prescribed including N-acetylcysteine, chloroquine, paroxetine and mianserin. An improvement in the patient’s clinical condition and a regression of pruritus were achieved. Conclusions . Patients with renal failure may develop symptoms of pseudoporphyria requiring differentiation from porphyria cutanea tarda.

  6. Make Failure a Stepping Stone to Success

    Institute of Scientific and Technical Information of China (English)

    徐燕青

    2004-01-01

    People have different opinions on failure, and they think of failure in different ways. Some of them may connect failure with their pursuit of fame, others may connect failure with wealth and still others may connect failure with achievements. For most students,failure means failing to pass exams. Without good grades, a student may consider himself to be useless and he may even think he is doomed to failure. Whenever he is given a test, he focuses all his attention on the marks. High marks bring him hope and happiness. So every day, all he does is stay inside and study.

  7. Heart failure etiology impacts survival of patients with heart failure

    DEFF Research Database (Denmark)

    Pecini, Redi; Møller, Daniel Vega; Torp-Pedersen, Christian

    2010-01-01

    BACKGROUND: The impact of heart failure (HF) etiology on prognosis of HF is not well known. METHODS: 3078 patients (median age 75years, 61% male) hospitalized with HF were studied. Patients were classified into six etiology groups: hypertension (HTN, 13.9%), ischemic heart disease (IHD, 42...

  8. Weak factor automata: the failure of failure factor oracles?

    Directory of Open Access Journals (Sweden)

    Loek Cleophas

    2014-08-01

    Full Text Available In indexing of, and pattern matching on, DNA and text sequences, it is often important to represent all factors of a sequence. One efficient, compact representation is the factor oracle (FO. At the same time, any classical deterministic finite automata (DFA can be transformed to a so-called failure one (FDFA, which may use failure transitions to replace multiple symbol transitions, potentially yielding a more compact representation. We combine the two ideas and directly construct a failure factor oracle (FFO from a given sequence, in contrast to ex post facto transformation to an FDFA. The algorithm is suitable for both short and long sequences. We empirically compared the resulting FFOs and FOs on number of transitions for many DNA sequences of lengths 4 − 512, showing gains of up to 10% in total number of transitions, with failure transitions also taking up less space than symbol transitions. The resulting FFOs can be used for indexing, as well as in a variant of the FO-using backward oracle matching algorithm. We discuss and classify this pattern matching algorithm in terms of the keyword pattern matching taxonomies of Watson, Cleophas and Zwaan. We also empirically compared the use of FOs and FFOs in such backward reading pattern matching algorithms, using both DNA and natural language (English data sets. The results indicate that the decrease in pattern matching performance of an algorithm using an FFO instead of an FO may outweigh the gain in representation space by using an FFO instead of an FO.

  9. The Danish Heart Failure Registry

    DEFF Research Database (Denmark)

    Schjødt, Inge; Nakano, Anne; Egstrup, Kenneth

    2016-01-01

    AIM OF DATABASE: The aim of the Danish Heart Failure Registry (DHFR) is to monitor and improve the care of patients with incident heart failure (HF) in Denmark. STUDY POPULATION: The DHFR includes inpatients and outpatients (≥18 years) with incident HF. Reporting to the DHFR is mandatory...... in an annual report. All standards for the quality indicators have been met at a national level since 2014. Indicators for treatment status 1 year after diagnosis are under consideration (now prevalent HF). CONCLUSION: The DHFR is a valuable tool for continuous improvement of quality of care in patients...

  10. Management of advanced heart failure.

    Science.gov (United States)

    Van Bakel, Adrian B; Chidsey, Geoffrey

    2002-01-01

    Congestive heart failure (CHF) due to progressive systolic dysfunction has become a modern-day epidemic. Despite the increased incidence and prevalence, significant progress has been made in the past 10 to 15 years in the treatment of CHF at all stages. The current outlook for patients with newly diagnosed, mild heart failure is encouraging. It should be noted, however, that most of the morbidity and health care expenditure is incurred by a minority of patients diagnosed with CHF who are in the advanced stages of their disease. The thrust of this article will be to provide practical advice beyond current guidelines on the management of advanced CHF.

  11. A simple approach to modeling ductile failure.

    Energy Technology Data Exchange (ETDEWEB)

    Wellman, Gerald William

    2012-06-01

    Sandia National Laboratories has the need to predict the behavior of structures after the occurrence of an initial failure. In some cases determining the extent of failure, beyond initiation, is required, while in a few cases the initial failure is a design feature used to tailor the subsequent load paths. In either case, the ability to numerically simulate the initiation and propagation of failures is a highly desired capability. This document describes one approach to the simulation of failure initiation and propagation.

  12. Focus on renal congestion in heart failure

    OpenAIRE

    Afsar, Baris; Ortiz, Alberto; Covic, Adrian; Solak, Yalcin; Goldsmith, David; Kanbay, Mehmet

    2015-01-01

    Hospitalizations due to heart failure are increasing steadily despite advances in medicine. Patients hospitalized for worsening heart failure have high mortality in hospital and within the months following discharge. Kidney dysfunction is associated with adverse outcomes in heart failure patients. Recent evidence suggests that both deterioration in kidney function and renal congestion are important prognostic factors in heart failure. Kidney congestion in heart failure results from low cardia...

  13. Molecular genotyping of HCV infection in seropositive blood donor

    Science.gov (United States)

    Zarin, Siti Noraziah Abu; Ibrahim, Nazlina

    2013-11-01

    This study is to investigate the prevalence of hepatitis C virus infection in seropositive blood donor. RNA was extracted from 32 positive samples in National Blood Centre and Melaka Hospital. The core and NS5B sequences were obtained from 23 samples. Genotype 3a is most prevalent in this study followed by genotype 1a. Evidence of mixed-genotypes (3a and 1b) infections was found in 5 subjects.

  14. Deep sequencing analysis of HBV genotype shift and correlation with antiviral efficiency during adefovir dipivoxil therapy.

    Directory of Open Access Journals (Sweden)

    Yuwei Wang

    Full Text Available Viral genotype shift in chronic hepatitis B (CHB patients during antiviral therapy has been reported, but the underlying mechanism remains elusive.38 CHB patients treated with ADV for one year were selected for studying genotype shift by both deep sequencing and Sanger sequencing method.Sanger sequencing method found that 7.9% patients showed mixed genotype before ADV therapy. In contrast, all 38 patients showed mixed genotype before ADV treatment by deep sequencing. 95.5% mixed genotype rate was also obtained from additional 200 treatment-naïve CHB patients. Of the 13 patients with genotype shift, the fraction of the minor genotype in 5 patients (38% increased gradually during the course of ADV treatment. Furthermore, responses to ADV and HBeAg seroconversion were associated with the high rate of genotype shift, suggesting drug and immune pressure may be key factors to induce genotype shift. Interestingly, patients with genotype C had a significantly higher rate of genotype shift than genotype B. In genotype shift group, ADV treatment induced a marked enhancement of genotype B ratio accompanied by a reduction of genotype C ratio, suggesting genotype C may be more sensitive to ADV than genotype B. Moreover, patients with dominant genotype C may have a better therapeutic effect. Finally, genotype shifts was correlated with clinical improvement in terms of ALT.Our findings provided a rational explanation for genotype shift among ADV-treated CHB patients. The genotype and genotype shift might be associated with antiviral efficiency.

  15. Genomic Variants Revealed by Invariably Missing Genotypes in Nelore Cattle.

    Directory of Open Access Journals (Sweden)

    Joaquim Manoel da Silva

    Full Text Available High density genotyping panels have been used in a wide range of applications. From population genetics to genome-wide association studies, this technology still offers the lowest cost and the most consistent solution for generating SNP data. However, in spite of the application, part of the generated data is always discarded from final datasets based on quality control criteria used to remove unreliable markers. Some discarded data consists of markers that failed to generate genotypes, labeled as missing genotypes. A subset of missing genotypes that occur in the whole population under study may be caused by technical issues but can also be explained by the presence of genomic variations that are in the vicinity of the assayed SNP and that prevent genotyping probes from annealing. The latter case may contain relevant information because these missing genotypes might be used to identify population-specific genomic variants. In order to assess which case is more prevalent, we used Illumina HD Bovine chip genotypes from 1,709 Nelore (Bos indicus samples. We found 3,200 missing genotypes among the whole population. NGS re-sequencing data from 8 sires were used to verify the presence of genomic variations within their flanking regions in 81.56% of these missing genotypes. Furthermore, we discovered 3,300 novel SNPs/Indels, 31% of which are located in genes that may affect traits of importance for the genetic improvement of cattle production.

  16. Genotype X environment interactions. II. Some genetical considerations.

    Science.gov (United States)

    Mather, K

    1975-08-01

    An algebraic formulation, alternative to that of Mather and Jones (1958) and hierarchial rather than factorial in nauture, is presented for describing the differences among the phenotypes produced by a number of genotypes each grown in each of a number of environments. This formuationdoes not include terms representing statistical interactions between genotypes and environments: it depends instead on comparisons between the different genotypes in their variation over the relevant ranges of environemnts. The two-line case is considered ant eht condition established for linearity of the regress ion of genotype X enviroment interaction (g in Mather and Jones' formulation) on overall effect of the envirronment (e in Mather and Jones' formulation)...

  17. Trichothecene genotypes of Fusarium graminearum from wheat in Uruguay.

    Science.gov (United States)

    Pan, Dinorah; Calero, Natalia; Mionetto, Ana; Bettucci, Lina

    2013-03-01

    Gibberella zeae (Schwein.) Petch (anamorph F. graminearum Schwabe) is the primary causal agent of FHB of wheat in Uruguay. In the last decade, F. graminearum has produced destructive epidemics on wheat in Uruguay, causing yield losses and price discounts due to reduced seed quality. Strains of F. graminearum clade usually express one of three strain-specific profiles of trichothecene metabolites: nivalenol and its acetylated derivatives (NIV chemotype), deoxynivalenol and 3-acetyldeoxynivalenol (3-AcDON chemotype), or deoxynivalenol and 15-acetyldeoxynivalenol (15-AcDON chemotype). A multiplex PCR assay of Tri3, Tri5, and Tri7 was used to determine the trichothecene genotype of 111 strains of F. graminearum collected during 2003 and 2009 growing seasons from fields located in the major wheat production area of Uruguay. The result showed that all except one of the isolates were of DON genotype, with the remainder of NIV genotype in years 2003 and 2009. All strains with the DON genotype were also of the 15-AcDON genotype in 2003 and nearly all (45/50) in 2009. No DON/3-AcDON genotypes were found in either growing season. No potential shifts in the populations were found in the trichothecene genotypes between 2003 and the 2009 epidemic FHB harvest seasons. This study provides the first data on trichothecene genotypes of F. graminearum strains isolated from wheat in Uruguay and add to the current regional knowledge of trichothecene genotypes.

  18. Variability of acorn anatomical characteristics in Quercus robur L. genotypes

    Directory of Open Access Journals (Sweden)

    Nikolić Nataša P.

    2010-01-01

    Full Text Available The aim of this study was to examine variability of acorn anatomical characteristics in seventeen Quercus robur L. genotypes. Acorns were collected in clonal seed orchard Banov Brod (Srem, Vojvodina, Serbia. Microscopic measurements were done for pericarp (total thickness, thickness of exocarp and mesocarp, seed coat (total thickness, thickness of outer epidermis, parenchyma, and inner epidermis, and embryo axis (diameter, thickness of cortical region, and diameter of stellar zone. Obtained results revealed certain divergence between genotypes. The thickness of pericarp varied from 418 to 559 mm (genotypes 20 and 22, respectively. On average, the participation of exocarp in the total thickness of pericarp was 36.3%, of mesocarp 61.0%, while of endocarp 2.6%. The thickness of seed coat for individual genotypes ranged from 71 mm (genotype 28 to 157 mm (genotype 38. In addition, anatomic parameters of embryo axis varied among studied genotypes. The lowest cortical zone thickness and stellar zone diameter were measured in genotype 40, while the highest values in genotype 33.

  19. Interaction between thyroglobulin and ADAMTS16 in premature ovarian failure.

    Science.gov (United States)

    Pyun, Jung-A; Kim, Sunshin; Kwack, KyuBum

    2014-09-01

    The aim of the present study was to examine whether interactions between polymorphisms in the thyroglobulin and ADAM metallopeptidase with thrombospondin type 1 motif, 16 (ADAMTS16) genes are associated with the development of premature ovarian failure (POF). A total of 75 patients with POF and 196 controls were involved in this study. We used a GoldenGate assay to genotype single nucleotide polymorphisms (SNPs). Logistic regression analysis was performed to identify POF-associated polymorphisms and synergistic interactions between polymorphisms in the thyroglobulin and ADAMTS16 genes. Single gene analyses using logistic regression analysis showed no significant association between polymorphisms in the two genes and POF. In the results from interaction analyses, we found seven synergistic interactions between the polymorphisms in thyroglobulin and ADAMTS16, although there was no combination showing p-values lower than the significant threshold using the Bonferroni correction. When the AG genotype was present at the rs853326 missense SNP, the A and G alleles at the tagging SNPs rs16875268 and rs13168665 showed significant interactions (odds ratios=5.318 and 16.2 respectively; 95% confidence intervals, 1.64-17.28 and 2.08-126.4; p=0.0054 and 0.0079). Synergistic interactions between polymorphisms in the thyroglobulin and ADAMTS16 genes were associated with an increased risk of POF development in Korean women.

  20. Distribution of genotypes and subtypes of hepatitis B virus in the population of southern of Anhui Province%皖南地区乙型肝炎病毒基因型和亚型的分布特征

    Institute of Scientific and Technical Information of China (English)

    宋骏; 夏长胜

    2011-01-01

    目的:研究皖南地区人群乙型肝炎病毒(hepatitis B virus,HBV) 基因型和亚型流行及分布情况.方法:采用HBV基因型和亚型特异性引物PCR法,对皖南地区319例HBV DNA阳性患者进行基因型和亚型的检测.结果:皖南地区319例HBV感染者中,可检出基因型285例,检出率为89%,其中B型162例(57%),全部为Ba亚型;C型49例(17%),其中C1亚型38例,C2亚型9例,未分型2例;B+C 混合型74例(26%).B型感染者与C型感染者血清HBV DNA 水平差异无统计学意义(P>0.05),但均高于B 和C 基因型混合感染患者(P<0.01).结论:皖南地区人群HBV感染的基因型主要为B 型、B+C混合型及C 型;亚型则以Ba和C1亚型为主.%Objective:To investigate the distribution of genotypes and subtypes of hepatitis B virus (HBV) in the population living in southern area of Anhui Province. Methods: The genotypes were detected in 319 subjects infected with HBV by genotype/subtype-specific primer PCR.Results: HBV genotypes and subtypes were identified in 285 of the 319 serum samples(89% ), and genotype B, which totally fell into sub-genotype Ba, was seen in 162(57 % ) and genotype C in 49( 17% ) which included 38 genotypes of C1, 9 of C2 and failure of genotyping in 2.Mixed genotypes( B + C ) accounted for 26 % (74/285). There was no significant difference between patients infected with genotype B and those with genotype C in terms of serum HBV DNA loads(P>0.05), and yet the loads were greater than that of mixed genotypes of B and C.Conclusion: Genotype B, mixed genotypes ( B + C) and genotype C are prevalent in the population living in southern of Anhui province, and subtypes of Ba and C1 are predominant.

  1. Consequences of noncompliance for therapy efficacy and emergence of resistance in murine tuberculosis caused by the Beijing genotype of Mycobacterium tuberculosis.

    Science.gov (United States)

    de Steenwinkel, Jurriaan E M; ten Kate, Marian T; de Knegt, Gerjo J; Verbrugh, Henri A; Aarnoutse, Rob E; Boeree, Martin J; den Bakker, Michael A; van Soolingen, Dick; Bakker-Woudenberg, Irma A J M

    2012-09-01

    Despite great effort by health organizations worldwide in fighting tuberculosis (TB), morbidity and mortality are not declining as expected. One of the reasons is related to the evolutionary development of Mycobacterium tuberculosis, in particular the Beijing genotype strains. In a previous study, we showed the association between the Beijing genotype and an increased mutation frequency for rifampin resistance. In this study, we use a Beijing genotype strain and an East-African/Indian genotype strain to investigate with our mouse TB model whether the higher mutation frequency observed in a Beijing genotype strain is associated with treatment failure particularly during noncompliance therapy. Both genotype strains showed high virulence in comparison to that of M. tuberculosis strain H37Rv, resulting in a highly progressive infection with a rapid lethal outcome in untreated mice. Compliance treatment was effective without relapse of TB irrespective of the infecting strain, showing similar decreases in the mycobacterial load in infected organs and similar histopathological changes. Noncompliance treatment, simulated by a reduced duration and dosing frequency, resulted in a relapse of infection. Relapse rates were correlated with the level of noncompliance and were identical for Beijing infection and East African/Indian infection. However, only in Beijing-infected mice, isoniazid-resistant mutants were selected at the highest level of noncompliance. This is in line with the substantial selection of isoniazid-resistant mutants in vitro in a wide isoniazid concentration window observed for the Beijing strain and not for the EAI strain. These results suggest that genotype diversity of M. tuberculosis may be involved in emergence of resistance and indicates that genotype-tailor-made treatment should be investigated.

  2. Virological efficacy with first-line antiretroviral treatment in India: predictors of viral failure and evidence of viral resuppression.

    Science.gov (United States)

    Shet, Anita; Neogi, Ujjwal; Kumarasamy, N; DeCosta, Ayesha; Shastri, Suresh; Rewari, Bharat Bhushan

    2015-11-01

    Combination antiretroviral therapy (ART) has improved in efficacy, durability and tolerability. Virological efficacy studies in India are limited. We determined incidence and predictors of virological failure among patients initiating first-line ART and described virological resuppression after confirmed failure, with the goal of informing national policy. Therapy-naïve patients initiated on first-line ART as per national guidelines were monitored every 3 months for adherence and virological response over 2 years. Genotyping on baseline samples was performed to assess primary drug resistance. Multivariate Cox regression analysis was used to assess predictors of virological failure. Virological failure rate among 599 eligible patients was 10.7 failures per 100 person-years. Cumulative failure incidence was 13.2% in the first year and 16.5% over 2 years. Patients initiated on tenofovir had a significantly lower rate of virological failure than those on stavudine or zidovudine (6.7 vs. 11.9 failures per 100 person-years, P = 0.013). Virological failure was independently associated with age <40 years, mean adherence <95%, non-tenofovir-containing regimens and presence of primary drug resistance. In a subset of 311 patients who were reassessed after treatment failure, 19% (11/58) patients resuppressed their viral load to <400 copies/ml after confirmed virological failure. Our results support the inclusion of tenofovir as first-line ART in resource-limited settings and a role for regular adherence counselling and virological monitoring for enhanced treatment success. Detection of early virological failure should provide an opportunity to augment adherence counselling and repeat viral load testing before therapy switch is considered. © 2015 John Wiley & Sons Ltd.

  3. Children's Coping with Academic Failure

    Science.gov (United States)

    Raftery-Helmer, Jacquelyn N.; Grolnick, Wendy S.

    2016-01-01

    There is little consensus on how to conceptualize coping after perceived failure and less is known about the contextual resources that may support or undermine the use of specific coping strategies. This study examined parenting in relation to coping using the framework of self-determination theory and examined the motivational processes through…

  4. Failure rate analysis using GLIMMIX

    Energy Technology Data Exchange (ETDEWEB)

    Moore, L.M.; Hemphill, G.M.; Martz, H.F.

    1998-12-01

    This paper illustrates use of a recently developed SAS macro, GLIMMIX, for implementing an analysis suggested by Wolfinger and O`Connell (1993) in modeling failure count data with random as well as fixed factor effects. Interest in this software tool arose from consideration of modernizing the Failure Rate Analysis Code (FRAC), developed at Los Alamos National Laboratory in the early 1980`s by Martz, Beckman and McInteer (1982). FRAC is a FORTRAN program developed to analyze Poisson distributed failure count data as a log-linear model, possibly with random as well as fixed effects. These statistical modeling assumptions are a special case of generalized linear mixed models, identified as GLMM in the current statistics literature. In the nearly 15 years since FRAC was developed, there have been considerable advances in computing capability, statistical methodology and available statistical software tools allowing worthwhile consideration of the tasks of modernizing FRAC. In this paper, the approaches to GLMM estimation implemented in GLIMMIX and in FRAC are described and a comparison of results for the two approaches is made with data on catastrophic time-dependent pump failures from a report by Martz and Whiteman (1984). Additionally, statistical and graphical model diagnostics are suggested and illustrated with the GLIMMIX analysis results.

  5. Leveraging Failure in Design Research

    Science.gov (United States)

    Lobato, Joanne; Walters, C. David; Hohensee, Charles; Gruver, John; Diamond, Jaime Marie

    2015-01-01

    Even in the resource-rich, more ideal conditions of many design-based classroom interventions, unexpected events can lead to disappointing results in student learning. However, if later iterations in a design research study are more successful, the previous failures can provide opportunities for comparisons to reveal subtle differences in…

  6. Failure in imperfect anisotropic materials

    DEFF Research Database (Denmark)

    Legarth, Brian Nyvang

    2005-01-01

    The fundamental cause of crack growth, namely nucleation and growth of voids, is investigated numerically for a two phase imperfect anisotropic material. A unit cell approach is adopted from which the overall stress strain is evaluated. Failure is observed as a sudden stress drop and depending...

  7. Exercise Intolerance in Heart Failure

    DEFF Research Database (Denmark)

    Brassard, Patrice; Gustafsson, Finn

    2016-01-01

    Exercise tolerance is affected in patients with heart failure (HF). Although the inability of the heart to pump blood to the working muscle has been the conventional mechanism proposed to explain the lowered capacity of patients with HF to exercise, evidence suggests that the pathophysiological m...

  8. Insulin Signaling and Heart Failure.

    Science.gov (United States)

    Riehle, Christian; Abel, E Dale

    2016-04-01

    Heart failure is associated with generalized insulin resistance. Moreover, insulin-resistant states such as type 2 diabetes mellitus and obesity increases the risk of heart failure even after adjusting for traditional risk factors. Insulin resistance or type 2 diabetes mellitus alters the systemic and neurohumoral milieu, leading to changes in metabolism and signaling pathways in the heart that may contribute to myocardial dysfunction. In addition, changes in insulin signaling within cardiomyocytes develop in the failing heart. The changes range from activation of proximal insulin signaling pathways that may contribute to adverse left ventricular remodeling and mitochondrial dysfunction to repression of distal elements of insulin signaling pathways such as forkhead box O transcriptional signaling or glucose transport, which may also impair cardiac metabolism, structure, and function. This article will review the complexities of insulin signaling within the myocardium and ways in which these pathways are altered in heart failure or in conditions associated with generalized insulin resistance. The implications of these changes for therapeutic approaches to treating or preventing heart failure will be discussed.

  9. Political Failures and Intergovernmental Competition

    Directory of Open Access Journals (Sweden)

    Jean Hindriks

    2012-01-01

    Full Text Available In normative public economics, intergovernmental competition is usually viewed as harmful. Although empirical support for this position does not abound, market integration has intensified competition among developed countries. In this paper we argue that when assessing welfare effects of intergovernmental competition for various forms of political failures (the public choice critique, the outcome is ambiguous and competition can be welfare improving.

  10. [Acute cardiac failure in pheochromocytoma.

    DEFF Research Database (Denmark)

    Jønler, Morten; Munk, Kim

    2008-01-01

    Pheochromocytoma (P) is an endocrine catecholamine-secreting tumor. Classical symptoms like hypertension, attacks of sweating, palpitations, headache and palor are related to catecholamine discharge. We provide a case of P in a 71 year-old man presenting with acute cardiac failure, severe reduction...

  11. Leveraging Failure in Design Research

    Science.gov (United States)

    Lobato, Joanne; Walters, C. David; Hohensee, Charles; Gruver, John; Diamond, Jaime Marie

    2015-01-01

    Even in the resource-rich, more ideal conditions of many design-based classroom interventions, unexpected events can lead to disappointing results in student learning. However, if later iterations in a design research study are more successful, the previous failures can provide opportunities for comparisons to reveal subtle differences in…

  12. Nonresident Fathering and School Failure

    Science.gov (United States)

    Menning, Chadwick L.

    2006-01-01

    Does involvement by nonresident fathers affect adolescents' propensity to remain in school? If so, is some involvement necessarily better than none, and are changes in involvement with time associated with changes in the odds of school failure? What aspects of involvement matter the most? This study uses data from the National Longitudinal Study…

  13. Childhood heart failure in Ibadan

    African Journals Online (AJOL)

    respiratory tract infections (36%), intrinsic heart disease. (31%) and severe ... la maladie de coeur intrinsèque 31%, et l'anémie grave 28%. D'autres causes qui ..... Colucci N, Braunwald E. Pathophysiology of heart failure. In: Braunwald E ed.

  14. 10.3.Heart failure

    Institute of Scientific and Technical Information of China (English)

    1992-01-01

    920271 The relationship between plasmacatecholamines and cardiac function in pa-tients with congestive heart failure.ZHAOShuyuan (赵树元),et al.Dept Intern Med,HebeiProv Hosp.Chin Cir J 1991;6(6):484-486.

  15. Plant genotype, microbial recruitment and nutritional security.

    Science.gov (United States)

    Patel, Jai S; Singh, Akanksha; Singh, Harikesh B; Sarma, Birinchi K

    2015-01-01

    Agricultural food products with high nutritional value should always be preferred over food products with low nutritional value. Efforts are being made to increase nutritional value of food by incorporating dietary supplements to the food products. The same is more desirous if the nutritional value of food is increased under natural environmental conditions especially in agricultural farms. Fragmented researches have demonstrated possibilities in achieving the same. The rhizosphere is vital in this regard for not only health and nutritional status of plants but also for the microorganisms colonizing the rhizosphere. Remarkably robust composition of plant microbiome with respect to other soil environments clearly suggests the role of a plant host in discriminating its colonizers (Zancarini et al., 2012). A large number of biotic and abiotic factors are believed to manipulate the microbial communities in the rhizosphere. However, plant genotype has proven to be the key in giving the final shape of the rhizosphere microbiome (Berendsen et al., 2012; Marques et al., 2014).

  16. Apolipoprotein-E genotypes and myasthenia gravis.

    Science.gov (United States)

    Suhail, Hamid; Soundararajan, Christhunesa C; Vivekanandhan, Subbiah; Singh, Sumit; Behari, Madhuri

    2010-01-01

    Autoimmune myasthenia gravis (MG) is a disorder of neuromuscular junction. Possible role of multiple genes in the development of the MG has been documented. This case-control study, studied the association of apolipoprotein E (Apo-E) alleles with MG. Anti-AChR antibody was measured using radio receptor immunoassay. Apo-E genotypes were analyzed in 120 MG patients and 120 healthy subjects. Comparison between patients with MG and controls showed no significant association with Apo-E allelic variants. However, a significant association of Apo-E4 allele with AChR-antibody positive patients was observed (P = 0.007). Also, among seropositive patients, a significant association was seen between female gender and Apo-E4 allele (P = 0.023). Our results suggest that the presence of Apo-E4 allele might influence seropositive status in patients with MG and seems an associated susceptible factor in female patients.

  17. Probabilistic Transcriptome Assembly and Variant Graph Genotyping

    DEFF Research Database (Denmark)

    Sibbesen, Jonas Andreas

    the resulting sequencing data should be interpreted. This has over the years spurred the development of many probabilistic methods that are capable of modelling dierent aspects of the sequencing process. Here, I present two of such methods that were developed to each tackle a dierent problem in bioinformatics......, together with an application of the latter method to a large Danish sequencing project. The rst is a probabilistic method for transcriptome assembly that is based on a novel generative model of the RNA sequencing process and provides condence estimates on the assembled transcripts. We show...... that this approach outperforms existing state-of-the-art methods measured using sensitivity and precision on both simulated and real data. The second is a novel probabilistic method that uses exact alignment of k-mers to a set of variants graphs to provide unbiased estimates of genotypes in a population...

  18. Case report: successful retreatment of hepatitis C genotype 1b infection with sofosbuvir + simeprevir in a patient with cirrhosis who had prior virologic relapse after treatment with daclatasvir and asunaprevir

    OpenAIRE

    Safadi, Rifaat; Noviello, Stephanie; Boparai, Navdeep; McPhee, Fiona

    2016-01-01

    Key Clinical Message There is currently minimal clinical experience regarding retreatment options for patients failing direct‐acting antiviral combination regimens. Here, we report the outcomes of a HCV genotype 1b‐infected patient with virologic failure following treatment with daclatasvir and asunaprevir, who was successfully retreated with sofosbuvir plus simeprevir.

  19. Case report: successful retreatment of hepatitis C genotype 1b infection with sofosbuvir + simeprevir in a patient with cirrhosis who had prior virologic relapse after treatment with daclatasvir and asunaprevir.

    Science.gov (United States)

    Safadi, Rifaat; Noviello, Stephanie; Boparai, Navdeep; McPhee, Fiona

    2016-07-01

    There is currently minimal clinical experience regarding retreatment options for patients failing direct-acting antiviral combination regimens. Here, we report the outcomes of a HCV genotype 1b-infected patient with virologic failure following treatment with daclatasvir and asunaprevir, who was successfully retreated with sofosbuvir plus simeprevir.

  20. Automated genotyping of dinucleotide repeat markers

    Energy Technology Data Exchange (ETDEWEB)

    Perlin, M.W.; Hoffman, E.P. [Carnegie Mellon Univ., Pittsburgh, PA (United States)]|[Univ. of Pittsburgh, PA (United States)

    1994-09-01

    The dinucleotide repeats (i.e., microsatellites) such as CA-repeats are a highly polymorphic, highly abundant class of PCR-amplifiable markers that have greatly streamlined genetic mapping experimentation. It is expected that over 30,000 such markers (including tri- and tetranucleotide repeats) will be characterized for routine use in the next few years. Since only size determination, and not sequencing, is required to determine alleles, in principle, dinucleotide repeat genotyping is easily performed on electrophoretic gels, and can be automated using DNA sequencers. Unfortunately, PCR stuttering with these markers generates not one band for each allele, but a pattern of bands. Since closely spaced alleles must be disambiguated by human scoring, this poses a key obstacle to full automation. We have developed methods that overcome this obstacle. Our model is that the observed data is generated by arithmetic superposition (i.e., convolution) of multiple allele patterns. By quantitatively measuring the size of each component band, and exploiting the unique stutter pattern associated with each marker, closely spaced alleles can be deconvolved; this unambiguously reconstructs the {open_quotes}true{close_quotes} allele bands, with stutter artifact removed. We used this approach in a system for automated diagnosis of (X-linked) Duchenne muscular dystrophy; four multiplexed CA-repeats within the dystrophin gene were assayed on a DNA sequencer. Our method accurately detected small variations in gel migration that shifted the allele size estimate. In 167 nonmutated alleles, 89% (149/167) showed no size variation, 9% (15/167) showed 1 bp variation, and 2% (3/167) showed 2 bp variation. We are currently developing a library of dinucleotide repeat patterns; together with our deconvolution methods, this library will enable fully automated genotyping of dinucleotide repeats from sizing data.

  1. Association between DRD2/ANKK1 Taq1A genotypes, depression and smoking cessation with nicotine replacement therapy.

    Science.gov (United States)

    Stapleton, John Andrew; Sutherland, Gay; O'Gara, Colin; Spirling, Lucy I; Ball, David

    2011-08-01

    Tobacco dependence and depression are believed to have a common familial component, most probably genetic, and mood disorders have been reliably associated with failure to stop smoking. Variant genotypes of the Taq1A (DRD2/ANKK1, 32806T, rs1800497) polymorphism have been associated with failure to stop smoking in some studies, but not others. We investigated the association between Taq1A genotypes and smoking cessation, while also considering mental health. This was a prospective study in 419 smokers who attended a smoking cessation clinic and used standard doses of nicotine replacement therapy. DNA samples and baseline measures including demographics, severity of tobacco dependence, mental health history and history of drug misuse were taken. Smoking cessation at the end of treatment was biochemically verified using expired-air carbon monoxide. We found no simple relation between Taq1A genotype and smoking cessation, although the association between cessation and lifetime depression was significantly modified by genotype. The relationship was such that for those having only common alleles there was no association between depression and stopping smoking, whereas for those with at least one variant allele (A1A2/A1A1) depression was associated with a two-fold reduction in the likelihood of stopping. Those having a Taq1A variant allele and a history of depression are likely to experience particular difficulty when trying to stop smoking and may require treatment other than standard doses of nicotine replacement. This finding might explain previous conflicting results for Taq1A and smoking cessation in studies where depression history was not measured, and may help to explain the underlying link between depression and smoking.

  2. Mechanisms of heart failure in obesity.

    Science.gov (United States)

    Ebong, Imo A; Goff, David C; Rodriguez, Carlos J; Chen, Haiying; Bertoni, Alain G

    2014-01-01

    Heart failure is a leading cause of morbidity and mortality and its prevalence continues to rise. Because obesity has been linked with heart failure, the increasing prevalence of obesity may presage further rise in heart failure in the future. Obesity-related factors are estimated to cause 11% of heart failure cases in men and 14% in women. Obesity may result in heart failure by inducing haemodynamic and myocardial changes that lead to cardiac dysfunction, or due to an increased predisposition to other heart failure risk factors. Direct cardiac lipotoxicity has been described where lipid accumulation in the heart results in cardiac dysfunction inexplicable of other heart failure risk factors. In this overview, we discussed various pathophysiological mechanisms that could lead to heart failure in obesity, including the molecular mechanisms underlying cardiac lipotoxicity. We defined the obesity paradox and enumerated various premises for the paradoxical associations observed in the relationship between obesity and heart failure.

  3. Common cause failure prediction using data mapping

    Energy Technology Data Exchange (ETDEWEB)

    Kvam, Paul H.; Miller, J. Glenn

    2002-06-01

    To estimate power plant reliability, a probabilistic safety assessment might combine failure data from various sites. Because dependent failures are a critical concern in the nuclear industry, combining failure data from component groups of different sizes is a challenging problem. One procedure, called data mapping, translates failure data across component group sizes. This includes common cause failures, which are simultaneous failure events of two or more components in a group. In this paper, we present a framework for predicting future plant reliability using mapped common cause failure data. The prediction technique is motivated by discrete failure data from emergency diesel generators at US plants. The underlying failure distributions are based on homogeneous Poisson processes. Both Bayesian and frequentist prediction methods are presented, and if non-informative prior distributions are applied, the upper prediction bounds for the generators are the same.

  4. Phase Field Theory and Analysis of Pressure-Shear Induced Amorphization and Failure in Boron Carbide Ceramic

    Science.gov (United States)

    2014-08-01

    Phase Field Theory and Analysis of Pressure-Shear Induced Amorphization and Failure in Boron Carbide Ceramic by John D Clayton ARL-RP...Pressure-Shear Induced Amorphization and Failure in Boron Carbide Ceramic John D Clayton Weapons and Materials Research Directorate, ARL...and Analysis of Pressure-Shear Induced Amorphization and Failure in Boron Carbide Ceramic 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM

  5. In Vitro Antiviral Activity and Resistance Profile Characterization of the Hepatitis C Virus NS5A Inhibitor Ledipasvir

    Science.gov (United States)

    Tian, Yang; Doehle, Brian; Peng, Betty; Corsa, Amoreena; Lee, Yu-Jen; Gong, Ruoyu; Yu, Mei; Han, Bin; Xu, Simin; Dvory-Sobol, Hadas; Perron, Michel; Xu, Yili; Mo, Hongmei; Pagratis, Nikos; Link, John O.; Delaney, William

    2016-01-01

    Ledipasvir (LDV; GS-5885), a component of Harvoni (a fixed-dose combination of LDV with sofosbuvir [SOF]), is approved to treat chronic hepatitis C virus (HCV) infection. Here, we report key preclinical antiviral properties of LDV, including in vitro potency, in vitro resistance profile, and activity in combination with other anti-HCV agents. LDV has picomolar antiviral activity against genotype 1a and genotype 1b replicons with 50% effective concentration (EC50) values of 0.031 nM and 0.004 nM, respectively. LDV is also active against HCV genotypes 4a, 4d, 5a, and 6a with EC50 values of 0.11 to 1.1 nM. LDV has relatively less in vitro antiviral activity against genotypes 2a, 2b, 3a, and 6e, with EC50 values of 16 to 530 nM. In vitro resistance selection with LDV identified the single Y93H and Q30E resistance-associated variants (RAVs) in the NS5A gene; these RAVs were also observed in patients after a 3-day monotherapy treatment. In vitro antiviral combination studies indicate that LDV has additive to moderately synergistic antiviral activity when combined with other classes of HCV direct-acting antiviral (DAA) agents, including NS3/4A protease inhibitors and the nucleotide NS5B polymerase inhibitor SOF. Furthermore, LDV is active against known NS3 protease and NS5B polymerase inhibitor RAVs with EC50 values equivalent to those for the wild type. PMID:26824950

  6. Pharm GKB: Kidney Failure, Acute [PharmGKB

    Lifescience Database Archive (English)

    Full Text Available iew Alternate Names: Synonym ARF - Acute renal failure; Acute Kidney Failure; Acute Kidney Failures; Acute K...idney Insufficiencies; Acute Kidney Insufficiency; Acute Renal Failure; Acute Renal Failures; Acute... Renal Insufficiencies; Acute Renal Insufficiency; Acute renal failure syndrome, NOS; Failure, Acute... Kidney; Failure, Acute Renal; Failures, Acute Kidney; Failures, Acute Renal; Insufficiencies, Acute... Kidney; Insufficiencies, Acute Renal; Insufficiency, Acute Kidney; Insufficiency, Acute

  7. Hepatitis C virus genotypes in Cordoba, Argentina unexpected high prevalence of genotype 2

    Directory of Open Access Journals (Sweden)

    V. Re

    2003-06-01

    Full Text Available To determine hepatitis C virus (HCV genotypes circulating in the central region of Argentina, 96 consecutive anti-HCV positive subjects were studied. The presence of HCV RNA was detected in 60 samples by RT-nested PCR of the 5' noncoding region (5' NCR. Genotyping was performed by restriction fragment length polymorphism analysis of 5' NCR region combined with PCR using type-specific primers of the core region. The groups of individuals in this study included hemophilia and hemodialysis patients, injecting drug users, screened blood donors, and patients with acute or chronic liver disease, all from Córdoba, Argentina. Overall, genotype 2 was the most prevalent (55.0%, followed by genotypes 1 (38.3 %, and 3 (5.0%. Within genotype 1, subtype 1b was the most prevalent. An unexpected high prevalence of genotype 2 (61.9% was found among patients with acute or chronic HCV infection (without known risk factors. These figures differ from other cohorts from East-Argentina where genotype 1 has been found as the most prevalent. This indicates that regional differences of genotype distribution might exist between Central and East Argentina.A fin de determinar los genotipos del virus de la hepatitis C (HCV circulantes en la región central de Argentina, se estudiaron 96 individuos anti-HCV positivos. La presencia del ARN de HCV se detectó en 60 muestras mediante RT-nested PCR de la región 5' no codificante (5' NCR. La genotipificación se realizó mediante restricción enzimática y el análisis del polimorfismo de los fragmentos largos de la región 5' NCR combinada con PCR usando primers tipo específico de la región del core. El grupo de individuos estudiados incluyó pacientes hemofílicos y hemodializados, drogadictos intravenosos, donantes de sangre y pacientes con enfermedad hepática aguda y crónica, todos provenientes de Córdoba, Argentina. El genotipo 2 fue el más prevalente (55.0%, seguido por los genotipos 1 (38.3 %, con mayor prevalencia

  8. Failure modes of composite sandwich beams

    Directory of Open Access Journals (Sweden)

    Gdoutos E.

    2008-01-01

    Full Text Available A thorough investigation of failure behavior of composite sandwich beams under three-and four-point bending was undertaken. The beams were made of unidirectional carbon/epoxy facings and a PVC closed-cell foam core. The constituent materials were fully characterized and in the case of the foam core, failure envelopes were developed for general two-dimensional states of stress. Various failure modes including facing wrinkling, indentation failure and core failure were observed and compared with analytical predictions. The initiation, propagation and interaction of failure modes depend on the type of loading, constituent material properties and geometrical dimensions.

  9. Genotypic and phenotypic characterization of Chikungunya virus of different genotypes from Malaysia.

    Directory of Open Access Journals (Sweden)

    I-Ching Sam

    Full Text Available BACKGROUND: Mosquito-borne Chikungunya virus (CHIKV has recently re-emerged globally. The epidemic East/Central/South African (ECSA strains have spread for the first time to Asia, which previously only had endemic Asian strains. In Malaysia, the ECSA strain caused an extensive nationwide outbreak in 2008, while the Asian strains only caused limited outbreaks prior to this. To gain insight into these observed epidemiological differences, we compared genotypic and phenotypic characteristics of CHIKV of Asian and ECSA genotypes isolated in Malaysia. METHODS AND FINDINGS: CHIKV of Asian and ECSA genotypes were isolated from patients during outbreaks in Bagan Panchor in 2006, and Johor in 2008. Sequencing of the CHIKV strains revealed 96.8% amino acid similarity, including an unusual 7 residue deletion in the nsP3 protein of the Asian strain. CHIKV replication in cells and Aedes mosquitoes was measured by virus titration. There were no differences in mammalian cell lines. The ECSA strain reached significantly higher titres in Ae. albopictus cells (C6/36. Both CHIKV strains infected Ae. albopictus mosquitoes at a higher rate than Ae. aegypti, but when compared to each other, the ECSA strain had much higher midgut infection and replication, and salivary gland dissemination, while the Asian strain infected Ae. aegypti at higher rates. CONCLUSIONS: The greater ability of the ECSA strain to replicate in Ae. albopictus may explain why it spread far more quickly and extensively in humans in Malaysia than the Asian strain ever did, particularly in rural areas where Ae. albopictus predominates. Intergenotypic genetic differences were found at E1, E2, and nsP3 sites previously reported to be determinants of host adaptability in alphaviruses. Transmission of CHIKV in humans is influenced by virus strain and vector species, which has implications for regions with more than one circulating CHIKV genotype and Aedes species.

  10. HIV-1 Drug Resistance Mutations: Potential Applications for Point-of-Care Genotypic Resistance Testing.

    Directory of Open Access Journals (Sweden)

    Soo-Yon Rhee

    Full Text Available The increasing prevalence of acquired and transmitted HIV-1 drug resistance is an obstacle to successful antiretroviral therapy (ART in the low- and middle-income countries (LMICs hardest hit by the HIV-1 pandemic. Genotypic drug resistance testing could facilitate the choice of initial ART in areas with rising transmitted drug resistance (TDR and enable care-providers to determine which individuals with virological failure (VF on a first- or second-line ART regimen require a change in treatment. An inexpensive near point-of-care (POC genotypic resistance test would be useful in settings where the resources, capacity, and infrastructure to perform standard genotypic drug resistance testing are limited. Such a test would be particularly useful in conjunction with the POC HIV-1 viral load tests that are currently being introduced in LMICs. A POC genotypic resistance test is likely to involve the use of allele-specific point mutation assays for detecting drug-resistance mutations (DRMs. This study proposes that two major nucleoside reverse transcriptase inhibitor (NRTI-associated DRMs (M184V and K65R and four major NNRTI-associated DRMs (K103N, Y181C, G190A, and V106M would be the most useful for POC genotypic resistance testing in LMIC settings. One or more of these six DRMs was present in 61.2% of analyzed virus sequences from ART-naïve individuals with intermediate or high-level TDR and 98.8% of analyzed virus sequences from individuals on a first-line NRTI/NNRTI-containing regimen with intermediate or high-level acquired drug resistance. The detection of one or more of these DRMs in an ART-naïve individual or in a individual with VF on a first-line NRTI/NNRTI-containing regimen may be considered an indication for a protease inhibitor (PI-containing regimen or closer virological monitoring based on cost-effectiveness or country policy.

  11. Genotypic character relationship and phenotypic path coefficient analysis in chili pepper genotypes grown under tropical condition.

    Science.gov (United States)

    Usman, Magaji G; Rafii, Mohd Y; Martini, Mohammad Y; Oladosu, Yusuff; Kashiani, Pedram

    2017-03-01

    Studies on genotypic and phenotypic correlations among characters of crop plants are useful in planning, evaluating and setting selection criteria for the desired characters in a breeding program. The present study aimed to estimate the phenotypic correlation coefficients among yield and yield attributed characters and to work out the direct and indirect effects of yield-related characters on yield per plant using path coefficient analysis. Twenty-six genotypes of chili pepper were laid out in a randomized complete block design with three replications. Yield per plant showed positive and highly significant (P ≤ 0.01) correlations with most of the characters studied at both the phenotypic and genotypic levels. By contrast, disease incidence and days to flowering showed a significant negative association with yield. Fruit weight and number of fruits exerted positive direct effect on yield and also had a positive and significant (P ≤ 0.01) correlation with yield per plant. However, fruit length showed a low negative direct effect with a strong and positive indirect effect through fruit weight on yield and had a positive and significant association with yield. Longer fruits, heavy fruits and a high number of fruits are variables that are related to higher yields of chili pepper under tropical conditions and hence could be used as a reliable indicator in indirect selection for yield. © 2016 Society of Chemical Industry. © 2016 Society of Chemical Industry.

  12. Distribution of HCV genotypes in the metropolitan area of Naples

    Directory of Open Access Journals (Sweden)

    Giuseppe Sodano

    2013-08-01

    Full Text Available The Hepatitis C virus is characterized by high genomic variability that leads to the identification of six different genotypes and many subtypes. In this work, we show the prevalence of genotypes in patients living in the metropolitan area of Naples collected in one year, analyzing differences in the distribution depending on sex and age groups.

  13. The influence of temperature on photosynthesis of different tomato genotypes

    NARCIS (Netherlands)

    Gosiewski, W.; Nilwik, H.J.M.; Bierhuizen, J.F.

    1982-01-01

    Net photosynthesis and dark respiration from whole plants of various tomato genotypes were measured in a closed system. At low irradiance (27 W m−2) and low external CO2 concentration (550 mg m−3), net photosynthesis of 10 genotypes was found to vary between 0.122 and 0.209 mg CO2 m−2 s−1. Correlati

  14. Breeding of a Tomato Genotype Readily Accessible to Genetic Manipulation

    NARCIS (Netherlands)

    Koornneef, Maarten; Hanhart, Corrie; Jongsma, Maarten; Toma, Ingrid; Weide, Rob; Zabel, Pim; Hille, Jacques

    1986-01-01

    A tomato genotype, superior in regenerating plants from cell cultures, was obtained by transferring regeneration capacity from Lycopersicon peruvianum into L. esculentum by classical breeding. This genotype, MsK93, greatly facilitates genetic manipulation of tomato, as was demonstrated by successful

  15. Reaction of Drought Tolerant Soybean Genotypes to Macrophomina phaseolina

    Science.gov (United States)

    Charcoal rot caused by Macrophomina phaseolina is a common disease of soybean, and resistant genotypes are not available. Level of soybean genotype resistance and susceptibility to M. phaseolina is most frequently measured by determining colony forming units of M. phaseolina/g root, but using this ...

  16. Paternity testing and delivering trait-predictive genotypic data

    Science.gov (United States)

    In the RosBREED project, the Genotyping Team (Team Leader: Nahla Bassil) leads the effort to obtain DNA data needed to enable marker-assisted breeding for critical fruit quality traits. These data are obtained from reference genotypes of apple, peach, cherry and strawberry carefully chosen to repres...

  17. Genotyping of FCN and MBL2 polymorphisms using pyrosequencing

    DEFF Research Database (Denmark)

    Munthe-Fog, Lea; Madsen, Hans O.; Garred, Peter

    2014-01-01

    Pyrosequencing represents one of the most thorough methods used to analyze polymorphisms. One advantage of using pyrosequencing for genotyping is the ability to identify not only single-nucleotide polymorphisms (SNPs) but also tri-allelic variations, insertions and deletions (InDels). In contrast...... to most other genotyping assays the sequence surrounding the polymorphism provides an internal control making this method highly reliable....

  18. Clusters of incompatible genotypes evolve with limited dispersal

    Science.gov (United States)

    Erin L. Landguth; Norman A. Johnson; Samuel A. Cushman

    2015-01-01

    Theoretical and empirical studies have shown heterogeneous selection to be the primary driver for the evolution of reproductively isolated genotypes in the absence of geographic barriers. Here, we ask whether limited dispersal alone can lead to the evolution of reproductively isolated genotypes despite the absence of any geographic barriers or heterogeneous...

  19. Protein profiles and immunoreactivities of Acanthamoeba morphological groups and genotypes.

    Science.gov (United States)

    Pumidonming, Wilawan; Koehsler, Martina; Leitsch, David; Walochnik, Julia

    2014-11-01

    Acanthamoeba is a free-living protozoan found in a wide variety of habitats. A classification of Acanthamoeba into currently eighteen genotypes (T1-T18) has been established, however, data on differences between genotypes on the protein level are scarce. The aim of this study was to compare protein and immunoreactivity profiles of Acanthamoeba genotypes. Thirteen strains, both clinical and non-clinical, from genotypes T4, T5, T6, T7, T9, T11 and T12, representing three morphological groups, were investigated for their protein profiles and IgG, IgM and IgA immunoreactivities. It was shown that protein and immunoreactivity profiles of Acanthamoeba genotypes T4, T5, T6, T7, T9, T11 and T12 are clearly distinct from each other, but the banding patterns correlate to the morphological groups. Normal human sera revealed anti-Acanthamoeba antibodies against isolates of all investigated genotypes, interestingly, however only very weak IgM and virtually no IgA immunoreactivity with T7 and T9, both representing morphological group I. The strongest IgG, IgM and IgA immunoreactivities were observed for genotypes T4, T5 and T6. Differences of both, protein and immunological patterns, between cytopathic and non-cytopathic strains, particularly within genotype T4, were not at the level of banding patterns, but rather in expression levels.

  20. compensatory and susceptive responses of cowpea genotypes to ...

    African Journals Online (AJOL)

    User

    ABSTRACT. The aim of the study was to estimate yield loss to10 selected genotypes of cowpea as a result of ... Aphid's infestation period for studies in susceptive response in medium to .... The dry grain and biomass loss/gain due to ... Mean Grain weight (±SE) and Dry biomass (±SE) of cowpea genotypes on no infesta-.

  1. Characterization of cassava starch attributes of different genotypes

    NARCIS (Netherlands)

    Anggraini, V.; Sudarmonowati, E.; Hartati, N.Sri.; Suurs, L.C.J.M.; Visser, R.G.F.

    2009-01-01

    The genetic variation of starch of Indonesian cassava genotypes with various morphological characteristics of roots and eco-geographical origin was characterized and compared. The morphological characteristics of the roots of 71 collected cassava genotypes were classified into yellow and white for

  2. Breeding of a Tomato Genotype Readily Accessible to Genetic Manipulation

    NARCIS (Netherlands)

    Koornneef, Maarten; Hanhart, Corrie; Jongsma, Maarten; Toma, Ingrid; Weide, Rob; Zabel, Pim; Hille, Jacques

    1986-01-01

    A tomato genotype, superior in regenerating plants from cell cultures, was obtained by transferring regeneration capacity from Lycopersicon peruvianum into L. esculentum by classical breeding. This genotype, MsK93, greatly facilitates genetic manipulation of tomato, as was demonstrated by successful

  3. Caffeoylquinic Acids in Storage Roots of Sixteen Sweetpotato Genotypes

    Science.gov (United States)

    The contents of chlorogenic acid and the 3,4-, 3,5- and 4,5- isomers of dicaffeoylquinic acid (DCQA) in the storage root tissues of sixteen sweetpotato genotypes were determined. Averaged over genotypes, the contents of the four compounds were highest in the cortex, intermediate in the stele and lo...

  4. MLVA genotyping of human Brucella isolates from Peru

    NARCIS (Netherlands)

    H.L. Smits; B. Espinosa; R. Castillo; E. Hall; A. Guillen; M. Zevaleta; R.H. Gilman; P. Melendez; C. Guerra; A. Draeger; A. Broglia; K. Nöckler

    2009-01-01

    Recent human Brucella melitensis isolates from Peru were genotyped by multiple locus variable number repeat analysis. All 24 isolates originated from hospitalized patients living in the central part of Peru and consisted of six genomic groups comprising two to four isolates and nine unique genotypes

  5. Regional selection of hybrid Nacional cacao genotypes in Coastal Ecuador

    Science.gov (United States)

    Recent international demand for “nacional” flavour cacao has increased the need for local cacao producers in Ecuador to use high-yielding “nacional” hybrid genotypes. The relative potential of cacao genotypes over various environments needs to be assessed prior to final selection of potential candid...

  6. Apolipoprotein E genotype, cardiovascular biomarkers and risk of stroke

    DEFF Research Database (Denmark)

    Khan, Tauseef A; Shah, Tina; Prieto, David;

    2013-01-01

    At the APOE gene, encoding apolipoprotein E, genotypes of the ε2/ε3/ε4 alleles associated with higher LDL-cholesterol (LDL-C) levels are also associated with higher coronary risk. However, the association of APOE genotype with other cardiovascular biomarkers and risk of ischaemic stroke is less...

  7. Hepatitis B virus genotypes and resistance mutations in patients under long term lamivudine therapy: characterization of genotype G in Brazil

    Directory of Open Access Journals (Sweden)

    Brandão Carlos E

    2008-01-01

    Full Text Available Abstract Background Lamivudine is an oral nucleoside analogue widely used for the treatment of chronic hepatitis B. The main limitation of lamivudine use is the selection of resistant mutations that increases with time of utilization. Hepatitis B virus (HBV isolates have been classified into eight genotypes (A to H with distinct geographical distributions. HBV genotypes may also influence pathogenic properties and therapeutic features. Here, we analyzed the HBV genotype distribution and the nature and frequency of lamivudine resistant mutations among 36 patients submitted to lamivudine treatment for 12 to 84 months. Results Half of the patients were homosexual men. Only 4/36 (11% patients were HBV DNA negative. As expected for a Brazilian group, genotypes A (24/32 positive individuals, 75%, D (3/32, 9.3% and F (1/32, 3% were present. One sample was from genotype C, which is a genotype rarely found in Brazil. Three samples were from genotype G, which had not been previously detected in Brazil. Lamivudine resistance mutations were identified in 20/32 (62% HBV DNA positive samples. Mean HBV loads of patients with and without lamivudine resistance mutations were not very different (2.7 × 107 and 6.9 × 107 copies/mL, respectively. Fifteen patients showed the L180M/M204V lamivudine resistant double mutation. The triple mutant rt173V/180M/204V, which acts as a vaccine escape mutant, was found in two individuals. The three isolates of genotype G were entirely sequenced. All three showed the double mutation L180M/M204V and displayed a large genetic divergence when compared with other full-length genotype G isolates. Conclusion A high (55% proportion of patients submitted to long term lamivudine therapy displayed resistant mutations, with elevated viral load. The potential of transmission of such HBV mutants should be monitored. The identification of genotypes C and G, rarely detected in South America, seems to indicate a genotype distribution different

  8. The Association of Il28b Genotype with the Histological Features of Chronic Hepatitis C Is HCV Genotype Dependent

    Directory of Open Access Journals (Sweden)

    Roberta D'Ambrosio

    2014-04-01

    Full Text Available The interleukin 28B (IL28B rs12979860 polymorphism is associated with treatment outcome in hepatitis C virus (HCV genotype 1 and 4 patients. Its association with the histological features of chronic hepatitis C and disease severity needs further clarifications. To assess the correlation between IL28B genotype, HCV genotype and liver biopsy findings in untreated patients. Materials and Methods: Pre-treatment liver biopsies from 335 HCV Caucasian patients (59% males, age 50 years enrolled in the MIST study were staged for fibrosis and inflammation according to the METAVIR and the Ishak scoring systems; steatosis was dichotomized as <5% or ≥5%. IL28B was typed by Taqman Single Nucleotide Polymorphism (SNP genotyping assay. HCV genotype was 1 in 151 (45%, 2 in 99 (30%, 3 in 50 (15% and 4 in 35 (10% patients. IL28B genotype was CC in 117 (34%, CT in 166 (49% and TT in 52 (15%. At univariate analysis, the IL28B CC genotype was associated with severe portal inflammation in HCV-1 patients (CC vs. CT/TT: 86% vs. 63%, p = 0.005, severe lobular inflammation in HCV-2 patients (CC vs. CT/TT: 44% vs. 23%, p = 0.03, and less fatty infiltration in HCV-1 patients (CC vs. CT/TT: 72% vs. 51%, p = 0.02. Despite the lack of any association between IL28B and fibrosis stage, in HCV-3 patients IL28B CC correlated with METAVIR F3-F4 (CC vs. CT/TT: 74% vs. 26%, p = 0.05. At multivariate analysis, the genotype CC remained associated with severe portal inflammation in HCV-1, only (Odds Ratio (OR: 95% Confidence Interval (CI: 3.24 (1.23–8.51. IL28B genotype is associated with the histological features of chronic hepatitis C in a HCV genotype dependent manner, with CC genotype being independently associated with severe portal inflammation.

  9. Distribution study of Chlamydia trachomatis genotypes in symptomatic patients in Buenos Aires, Argentina: association between genotype E and neonatal conjunctivitis

    Directory of Open Access Journals (Sweden)

    Corominas Ana I

    2010-02-01

    Full Text Available Abstract Background Chlamydia trachomatis infections are the most prevalent sexually transmitted bacterial infections in the world. There is scarce data available referring to the distribution of C. trachomatis genotypes in Argentina. The aim of this study was to identify the genotypes of C. trachomatis circulating in the metropolitan area of Buenos Aires (Argentina associated with ophthalmia neonatorum and genital infections. Findings From 2001 to 2006, 199 positive samples for C. trachomatis infection from symptomatic adult patients and neonates with ophthalmia neonatorum from two public hospitals were studied. C. trachomatis genotypes were determined by PCR-RFLP of an ompA fragment. Genotype E was the most prevalent regardless of the sample origin (46.3% 57/123 in adults and 72.4% 55/76 in neonates, followed by genotype D (19.5% 24/123 and F (14.6% 18/123 in adults, and G (9.2% 7/76 and D (7.9% 6/76 in neonates. We detected a significantly higher frequency of genotype E (p ophthalmia neonatorum than in genital specimens. Genotype D was associated with genital localization (p Conclusion We found a particularly increased frequency of C. trachomatis genotype E in neonatal conjunctivitis, which may indicate an epidemiological association between this genotype and the newborn population. The present study also contributed to increase the knowledge on genotype distribution of Chlamydia trachomatis in symptomatic adult patients in Buenos Aires, Argentina, in which genotypes E, D and F were the predominant ones.

  10. Understanding of failure and failure of understanding: Aspects of failure in the Old Testament

    Directory of Open Access Journals (Sweden)

    James Alfred Loader

    2014-08-01

    Full Text Available Taking its cue from Rudolf Bultmann’s famous verdict that the Old Testament is a ‘failure’ (‘Scheitern’, the article reviews three influential negative readings of Israel’s history as told in the Former Prophets. It is then argued that awareness of the theological problem posed by Israel’s history enabled the redactors of both the former and the latter prophetic collections to deal with the element of human failure in a way that facilitated Israel’s retaining of her faith. Next, the sapiential insight in failing human discernment is drawn into the equation. Failure of human action is here interrelated with failure to comprehend God’s order. By virtue of its incorporation into the totality of the Tanak, this insight became a constructive part of Israel’s faith. Therefore the concept of failure comprises more than coming to terms with Israel’s catastrophic history. Since it is encoded in Israel’s Holy Scripture, ‘failure’ is a major concept within the Old Testament internally and is therefore not suitable as a verdict over the Old Testament by an external value judgement. ‘Failure’ thus becomes a key hermeneutical category, not merely so that the Old Testament could become a ‘promise’ for the New Testament to fulfil, but as a manifestation of limits in human religion and thought. Far from undermining self-esteem, constructive use of the concept of her own failure sustained Israel in her catastrophe and should be adopted by Christianity – not least in South Africa, where the biblical message was often misappropriated to bolster apartheid.

  11. Understanding of failure and failure of understanding: Aspects of failure in the Old Testament

    Directory of Open Access Journals (Sweden)

    James Alfred Loader

    2014-02-01

    Full Text Available Taking its cue from Rudolf Bultmann’s famous verdict that the Old Testament is a ‘failure’ (‘Scheitern’, the article reviews three influential negative readings of Israel’s history as told in the Former Prophets. It is then argued that awareness of the theological problem posed by Israel’s history enabled the redactors of both the former and the latter prophetic collections to deal with the element of human failure in a way that facilitated Israel’s retaining of her faith. Next, the sapiential insight in failing human discernment is drawn into the equation. Failure of human action is here interrelated with failure to comprehend God’s order. By virtue of its incorporation into the totality of the Tanak, this insight became a constructive part of Israel’s faith. Therefore the concept of failure comprises more than coming to terms with Israel’s catastrophic history. Since it is encoded in Israel’s Holy Scripture, ‘failure’ is a major concept within the Old Testament internally and is therefore not suitable as a verdict over the Old Testament by an external value judgement. ‘Failure’ thus becomes a key hermeneutical category, not merely so that the Old Testament could become a ‘promise’ for the New Testament to fulfil, but as a manifestation of limits in human religion and thought. Far from undermining self-esteem, constructive use of the concept of her own failure sustained Israel in her catastrophe and should be adopted by Christianity – not least in South Africa, where the biblical message was often misappropriated to bolster apartheid.

  12. Moderator effect of CYP2B6 genotype in HIV-1 patients with tuberculosis treated with rifampicin and efavirenz

    Directory of Open Access Journals (Sweden)

    C De la Calle

    2012-11-01

    Full Text Available Efavirenz (EFV is the preferred non-nucleoside reverse transcriptase inhibitor component of the ARV regimen in HIV-TB patients. Concomitant use of EFV with rifampicin (RIF, an important component of first-line tuberculosis treatment, induces various hepatic cytochrome P450 enzymes and is known to decrease EFV plasma concentrations in healthy volunteers and HIV-1 patients and EFV plasma concentrations below 1,000 µg/mL have been associated with an increased risk of virological failure [1]. Moreover, previous studies have shown that inter-individual variability in EFV plasma concentrations are associated with the presence of allelic variants in CYP2B6 gene. Carriers of the T allele of polymorphism 516 G>T are reported to be associated with slower EFV oral clearance. The aim of our study was to determine the influence of CYP2B6 genotype in EFV levels in HIV patients with TB treated with RIF. Four HIV patients who started ARV treatment concomitantly with TB treatment were analyzed. These patients started a regimen based on EFV at doses higher than standard due to RIF interaction. Viral load, CD4+ cell count and plasma levels of EFV in plasma were measured at each visit, and genotyping for CYP2B6 (516G>T polymorphism were performed. The self-reported rates of adherence to HAART were very high. One patient, who had TT genotype, required progressive dose reduction by toxic levels (Cmin: 20 µg/mL and effects on the central nervous system. Dose was adjusted to 600 mg qd despite treatment with RIF, and he required even lower doses after completion of TB treatment, 400 mg qd. Two other patients with non-mutated genotype (GG required dose escalation up to 1000 mg qd to achieve minimum recommended EFV concentrations between 1 and 4 µg/mL. All of them achieved virological suppression at six months. The fourth patient, who had non-mutated genotype, required dose increases for several months until dose adjustment. He needed 1600 mg qd during treatment with

  13. Silhouette scores for assessment of SNP genotype clusters

    Directory of Open Access Journals (Sweden)

    Jonsson Mats

    2005-03-01

    Full Text Available Abstract Background High-throughput genotyping of single nucleotide polymorphisms (SNPs generates large amounts of data. In many SNP genotyping assays, the genotype assignment is based on scatter plots of signals corresponding to the two SNP alleles. In a robust assay the three clusters that define the genotypes are well separated and the distances between the data points within a cluster are short. "Silhouettes" is a graphical aid for interpretation and validation of data clusters that provides a measure of how well a data point was classified when it was assigned to a cluster. Thus "Silhouettes" can potentially be used as a quality measure for SNP genotyping results and for objective comparison of the performance of SNP assays at different circumstances. Results We created a program (ClusterA for calculating "Silhouette scores", and applied it to assess the quality of SNP genotype clusters obtained by single nucleotide primer extension ("minisequencing" in the Tag-microarray format. A Silhouette score condenses the quality of the genotype assignment for each SNP assay into a single numeric value, which ranges from 1.0, when the genotype assignment is unequivocal, down to -1.0, when the genotype assignment has been arbitrary. In the present study we applied Silhouette scores to compare the performance of four DNA polymerases in our minisequencing system by analyzing 26 SNPs in both DNA polarities in 16 DNA samples. We found Silhouettes to provide a relevant measure for the quality of SNP assays at different reaction conditions, illustrated by the four DNA polymerases here. According to our result, the genotypes can be unequivocally assigned without manual inspection when the Silhouette score for a SNP assay is > 0.65. All four DNA polymerases performed satisfactorily in our Tag-array minisequencing system. Conclusion "Silhouette scores" for assessing the quality of SNP genotyping clusters is convenient for evaluating the quality of SNP genotype

  14. SNPMClust: Bivariate Gaussian Genotype Clustering and Calling for Illumina Microarrays

    Directory of Open Access Journals (Sweden)

    Stephen W. Erickson

    2016-07-01

    Full Text Available SNPMClust is an R package for genotype clustering and calling with Illumina microarrays. It was originally developed for studies using the GoldenGate custom genotyping platform but can be used with other Illumina platforms, including Infinium BeadChip. The algorithm first rescales the fluorescent signal intensity data, adds empirically derived pseudo-data to minor allele genotype clusters, then uses the package mclust for bivariate Gaussian model fitting. We compared the accuracy and sensitivity of SNPMClust to that of GenCall, Illumina's proprietary algorithm, on a data set of 94 whole-genome amplified buccal (cheek swab DNA samples. These samples were genotyped on a custom panel which included 1064 SNPs for which the true genotype was known with high confidence. SNPMClust produced uniformly lower false call rates over a wide range of overall call rates.

  15. Effect of genotype on sugar beet yield and quality

    Directory of Open Access Journals (Sweden)

    Nenadić N.

    2003-01-01

    Full Text Available The effect of a considerable number of both domestic and foreign sugar beet genotypes on root yield and quality was investigated. The data demonstrated the most favorable results of some genotypes for root yield and sugar content. Trials were conducted on rhizomania infested soil, thus tolerant genotypes were used. Susceptible cultivars represented the control. In the trial root yield was high and sugar content low. On average, in the genotypes tested, root yield varied from 73.98 to 93.30 t/ha and sugar content from 11.90 to 13.36%, depending on weather conditions. Root yield of the genotypes investigated varied from 30.61 to 112.64 t/ha and sugar content from 10.60 to 14.20%. The Swedish cultivar Dorotea (tolerant to both rhizomania and cercospora was the most yielding. The least yielding (susceptible to both rhizomania and cercospora was the domestic cultivar Dana.

  16. Genetic relationships among some hawthorn (Crataegus spp.) species and genotypes.

    Science.gov (United States)

    Yilmaz, Kadir Ugurtan; Yanar, Makbule; Ercisli, Sezai; Sahiner, Hatice; Taskin, Tuncer; Zengin, Yasar

    2010-10-01

    The genus Crataegus is well distributed in Turkey as a wild plant, with numerous, inherently variable species and genotypes. RAPD markers were used to study 17 hawthorn genotypes belonging to Crataegus monogyna ssp. monogyna Jacq (2 genotypes), C. monogyna ssp. azarella Jacq (1), Crataegus pontica K.Koch (3), Crataegus orientalis var. orientalis Pallas Ex Bieb (3), Crataegus pseudoheterophylla Pojark (1), Crataegus aronia var. dentata Browicz (1), C. aronia var. aronia Browicz (4), and Crateagus x bornmuelleri Zabel (2). The 10 RAPD primers produced 72 polymorphic bands (88% polymorphism). A dendrogram based on Jaccard's index included four major groups and one outgroup according to taxa. The lowest genetic variability was observed within C. aronia var. aronia genotypes. The study demonstrated that RAPD analysis is efficient for genotyping wild-grown hawthorns.

  17. HCV prevalence and predominant genotype in IV drug users

    Directory of Open Access Journals (Sweden)

    Asad Andalibalshohada

    2014-07-01

    Full Text Available Hepatitis C virus (HCV causes 308000 deaths due to liver cancer and 758000 deaths due to cirrhosis every year. Almost 170 million people have HCV infection around the world. Information regarding this virus helps us to determine the prevalence of other hepatitis C genotypes in population, especially in intravenous drug users. It is assumed that some genotypes are more common in certain areas or groups of people. A recent study strongly confirms the central role of injecting network traits, not only as a transmission factor but also as a predictor of HCV genotype and phylogenetic determination in different communities. Hepatitis C genotypes and subtypes have different prevalence considering the country. Risk factors such as transfusion, hemodialysis, root of acquisition and etc, are detected in intravenous drug users. Several conducted studies have investigated the prevalence, risk factors, and predominance of HCV genotypes infection in different parts of Iran.

  18. Micropropagation of six Paulownia genotypes through tissue culture

    Directory of Open Access Journals (Sweden)

    Lydia Shtereva

    2014-12-01

    Full Text Available We investigated the effect of genotype and culture medium on the in vitro germination and development of plantlets from seeds of 6 different Paulownia genotypes (P. tomentosa, hybrid lines P. tomentosa P. fortunei (Mega, Ganter and Caroline, P. elongata and hybrid line P. elongata P. fortunei. Nodal and shoot tip explants were used for micropropagation of Paulownia genotypes by manipulating plant growth regulators. The highest germination percentage for all genotypes was obtained for seeds inoculated on medium supplemented with 50 mg*L GA3 (MSG2. On Thidiazuron containing media, the explants of hybrid line P. elongata P. fortunei exhibited the highest frequency of axillary shoot proliferation following by P. tomentosa P. fortunei. The results are discussed with the perspective of applying an improved protocol for in vitro seed germination and plantlet formation in several economically valuable Paulownia genotypes.

  19. Drug resistance in HIV patients with virological failure or slow virological response to antiretroviral therapy in Ethiopia

    DEFF Research Database (Denmark)

    Abdissa, Alemseged; Yilma, Daniel; Fonager, Jannik;

    2014-01-01

    BACKGROUND: The ongoing scale-up of antiretroviral therapy (ART) in sub-Saharan Africa has prompted the interest in surveillance of transmitted and acquired HIV drug resistance. Resistance data on virological failure and mutations in HIV infected populations initiating treatment in sub......-Saharan Africa is sparse. METHODS: HIV viral load (VL) and resistance mutations pre-ART and after 6 months were determined in a prospective cohort study of ART-naïve HIV patients initiating first-line therapy in Jimma, Ethiopia. VL measurements were done at baseline and after 3 and 6 months. Genotypic HIV drug...... was observed among 14 (5.3%) participants out of 265 patients. Twelve samples were genotyped and six had HIV drug resistance (HIVDR) mutations at baseline. Among virological failures, 9/11 (81.8%) harbored one or more HIVDR mutations at 6 months. The most frequent mutations were K103N and M184VI. CONCLUSIONS...

  20. Resistance profiles and adherence at primary virological failure in three different highly active antiretroviral therapy regimens: analysis of failure rates in a randomized study

    DEFF Research Database (Denmark)

    Roge, BT; Barfod, TS; Kirk, O

    2004-01-01

    copies/mL) among 293 patients randomized to two nucleoside reverse transcriptase inhibitors (NRTIs)+ritonavir+saquinavir (RS-arm) (n=115), two NRTIs+nevirapine+nelfinavir (NN-arm) (n=118), or abacavir+stavudine+didanosine (ASD-arm) (n=60) followed up for a median of 90 weeks. Data on adherence were...... collected from patient files, and genotyping was performed on plasma samples collected at time of failure. RESULTS: Treatment interruption or poor adherence was mainly caused by side effects and accounted for 74% of failures, and was associated with absence of resistance mutations. In the 30 failing...... patients not switched from randomized treatment, we found resistance in two of 12 patients in the RS-arm (M184 V only), four of six patients in the NN-arm [all four had non-nucleoside reverse transcriptase inhibitor (NNRTI) mutations], and seven of 12 patients in the ASD-arm (NRTI mutations only). Two...

  1. Gc protein (vitamin D-binding protein): Gc genotyping and GcMAF precursor activity.

    Science.gov (United States)

    Nagasawa, Hideko; Uto, Yoshihiro; Sasaki, Hideyuki; Okamura, Natsuko; Murakami, Aya; Kubo, Shinichi; Kirk, Kenneth L; Hori, Hitoshi

    2005-01-01

    The Gc protein (human group-specific component (Gc), a vitamin D-binding protein or Gc globulin), has important physiological functions that include involvement in vitamin D transport and storage, scavenging of extracellular G-actin, enhancement of the chemotactic activity of C5a for neutrophils in inflammation and macrophage activation (mediated by a GalNAc-modified Gc protein (GcMAF)). In this review, the structure and function of the Gc protein is focused on especially with regard to Gc genotyping and GcMAF precursor activity. A discussion of the research strategy "GcMAF as a target for drug discovery" is included, based on our own research.

  2. Shear failure of granular materials

    Science.gov (United States)

    Degiuli, Eric; Balmforth, Neil; McElwaine, Jim; Schoof, Christian; Hewitt, Ian

    2012-02-01

    Connecting the macroscopic behavior of granular materials with the microstructure remains a great challenge. Recent work connects these scales with a discrete calculus [1]. In this work we generalize this formalism from monodisperse packings of disks to 2D assemblies of arbitrarily shaped grains. In particular, we derive Airy's expression for a symmetric, divergence-free stress tensor. Using these tools, we derive, from first-principles and in a mean-field approximation, the entropy of frictional force configurations in the Force Network Ensemble. As a macroscopic consequence of the Coulomb friction condition at contacts, we predict shear failure at a critical shear stress, in accordance with the Mohr-Coulomb failure condition well known in engineering. Results are compared with numerical simulations, and the dependence on the microscopic geometric configuration is discussed. [4pt] [1] E. DeGiuli & J. McElwaine, PRE 2011. doi: 10.1103/PhysRevE.84.041310

  3. Coordination failure caused by sunspots

    DEFF Research Database (Denmark)

    Beugnot, Julie; Gürgüç, Zeynep; Øvlisen, Frederik Roose

    2012-01-01

    In a coordination game with Pareto-ranked equilibria, we study whether a sunspot can lead to either coordination on an inferior equilibrium (mis-coordination) or to out-of equilibrium behavior (dis-coordination). While much of the literature searches for mechanisms to attain coordination...... on the efficient equilibrium, we consider sunspots as a potential reason for coordination failure. We conduct an experiment with a three player 2x2x2 game in which coordination on the efficient equilibrium is easy and should normally occur. In the control session, we find almost perfect coordination on the payoff......-dominant equilibrium, but in the sunspot treatment, dis-coordination is frequent. Sunspots lead to significant inefficiency, and we conclude that sunspots can indeed cause coordination failure....

  4. CONGESTIVE HEART FAILURE: EXPERIMENTAL MODEL

    Directory of Open Access Journals (Sweden)

    Antonio Francesco Corno

    2013-10-01

    Full Text Available INTRODUCTION.Surgically induced, combined volume and pressure overload has been used in rabbits to create a simplified and reproducible model of acute left ventricular (LV failure.MATERIALS AND METHODS.New Zealand white male rabbits (n=24, mean weight 3.1±0.2kg were randomly assigned to either the Control group (n=10 or to the Heart Failure group (HF, n=14. Animals in the Control group underwent sham procedures. Animals in the HF group underwent procedures to induce LV volume overload by inducing severe aortic valve regurgitation with aortic cusp disruption and pressure overload using an occlusive silver clip positioned around the pre-renal abdominal aorta.RESULTS.Following Procedure-1 (volume overload echocardiography confirmed severe aortic regurgitation in all animals in the HF group, with increased mean pulse pressure difference from 18±3mmHg to 38±3mmHg (P

  5. Causes of aircraft electrical failures

    Science.gov (United States)

    Galler, Donald; Slenski, George

    1991-08-01

    The results of a survey of data on failures of aircraft electronic and electrical components that was conducted to identify problematic components are reported. The motivation for the work was to determine priorities for future work on the development of accident investigation techniques for aircraft electrical components. The primary source of data was the Airforce Mishap Database, which is maintained by the Directorate of Aerospace Safety at Norton Air Force Base. Published data from the Air Force Avionics Integrity Program (AVIP) and Hughes Aircraft were also reviewed. Statistical data from these three sources are presented. Two major conclusions are that problems with interconnections are major contributors to aircraft electrical equipment failures, and that environmental factors, especially corrosion, are significant contributors to connector problems.

  6. Comparison of methods for analysis of selective genotyping survival data

    Directory of Open Access Journals (Sweden)

    Dekkers Jack CM

    2006-11-01

    Full Text Available Abstract Survival traits and selective genotyping datasets are typically not normally distributed, thus common models used to identify QTL may not be statistically appropriate for their analysis. The objective of the present study was to compare models for identification of QTL associated with survival traits, in particular when combined with selective genotyping. Data were simulated to model the survival distribution of a population of chickens challenged with Marek disease virus. Cox proportional hazards (CPH, linear regression (LR, and Weibull models were compared for their appropriateness to analyze the data, ability to identify associations of marker alleles with survival, and estimation of effects when all individuals were genotyped (full genotyping and when selective genotyping was used. Little difference in power was found between the CPH and the LR model for low censoring cases for both full and selective genotyping. The simulated data were not transformed to follow a Weibull distribution and, as a result, the Weibull model generally resulted in less power than the other two models and overestimated effects. Effect estimates from LR and CPH were unbiased when all individuals were genotyped, but overestimated when selective genotyping was used. Thus, LR is preferred for analyzing survival data when the amount of censoring is low because of ease of implementation and interpretation. Including phenotypic data of non-genotyped individuals in selective genotyping analysis increased power, but resulted in LR having an inflated false positive rate, and therefore the CPH model is preferred for this scenario, although transformation of the data may also make the Weibull model appropriate for this case. The results from the research presented herein are directly applicable to interval mapping analyses.

  7. Correlation between pre-treatment quasispecies complexity and treatment outcome in chronic HCV genotype 3a.

    LENUS (Irish Health Repository)

    Moreau, Isabelle

    2012-02-03

    Pre-treatment HCV quasispecies complexity and diversity may predict response to interferon based anti-viral therapy. The objective of this study was to retrospectively (1) examine temporal changes in quasispecies prior to the start of therapy and (2) investigate extensively quasispecies evolution in a group of 10 chronically infected patients with genotype 3a, treated with pegylated alpha2a-Interferon and ribavirin. The degree of sequence heterogeneity within the hypervariable region 1 was assessed by analyzing 20-30 individual clones in serial serum samples. Genetic parameters, including amino acid Shannon entropy, Hamming distance and genetic distance were calculated for each sample. Treatment outcome was divided into (1) sustained virological responders (SVR) and (2) treatment failure (TF). Our results indicate, (1) quasispecies complexity and diversity are lower in the SVR group, (2) quasispecies vary temporally and (3) genetic heterogeneity at baseline can be use to predict treatment outcome. We discuss the results from the perspective of replicative homeostasis.

  8. Familial Mediterranean fever (FMF) and renal AA amyloidosis--phenotype-genotype correlation, treatment and prognosis.

    Science.gov (United States)

    Ben-Chetrit, Eldad

    2003-01-01

    Familial Mediterranean fever (FMF) is an autosomal recessive disease, which primarily affects the population surrounding the Mediterranean basin. It is characterized by recurrent attacks of fever and peritonitis, pleuritis, arthritis or erysipelas-like erythema. Amyloidosis, causing renal failure, is one of the most severe complications of the disease. The gene associated with FMF (MEFV) has been recently isolated. Phenotype-genotype correlation studies revealed that amyloidosis was more common in FMF patients originating from North-Africa who were homozygous for the M694V mutation. Such a correlation was not found in Turkish patients. The risk of amyloidosis is increased in male FMF patients and in patients bearing polymorphism a/a in the SAA1 gene. Colchicine is the chosen drug for the treatment of FMF and can prevent amyloidosis.

  9. Laminin alpha2 deficiency and muscular dystrophy; genotype-phenotype correlation in mutant mice

    DEFF Research Database (Denmark)

    Guo, L T; Zhang, X U; Kuang, W

    2003-01-01

    Deficiency of laminin alpha2 is the cause of one of the most severe muscular dystrophies in humans and other species. It is not yet clear how particular mutations in the laminin alpha2 chain gene affect protein expression, and how abnormal levels or structure of the protein affect disease. Animal...... models may be valuable for such genotype-phenotype analysis and for determining mechanism of disease as well as function of laminin. Here, we have analyzed protein expression in three lines of mice with mutations in the laminin alpha2 chain gene and in two lines of transgenic mice overexpressing...... substantially prevented the muscular dystrophy in these mice. However, dy(W)/dy(W) mice, expressing the human laminin alpha2 under the control of the striated muscle-specific portion of the desmin promoter, still developed muscular dystrophy. This failure to rescue is apparently because of insufficient...

  10. Real-World Effectiveness and Safety of Oral Combination Antiviral Therapy for Hepatitis C Virus Genotype 4 Infection.

    Science.gov (United States)

    Crespo, Javier; Calleja, Jose Luis; Fernández, Inmaculada; Sacristan, Begoña; Ruiz-Antorán, Belén; Ampuero, Javier; Hernández-Conde, Marta; García-Samaniego, Javier; Gea, Francisco; Buti, Maria; Cabezas, Joaquin; Lens, Sabela; Morillas, Rosa Maria; Salcines, Jose Ramon; Pascasio, Juan Manuel; Turnes, Juan; Sáez-Royuela, Federico; Arenas, Juan; Rincón, Diego; Prieto, Martin; Jorquera, Francisco; Sanchez Ruano, Juan Jose; Navascués, Carmen A; Molina, Esther; Moya, Adolfo Gallego; Moreno-Planas, José Maria

    2017-06-01

    Patients with hepatitis C virus (HCV) genotype 4 infection are poorly represented in clinical trials of second-generation direct-acting antiviral agents (DAAs). More data are needed to help guide treatment decisions. We investigated the effectiveness and safety of DAAs in patients with genotype 4 infection in routine practice. In this cohort study, HCV genotype 4-infected patients treated with ombitasvir/paritaprevir/ritonavir (OMV/PTVr) + ribavirin (RBV) (n=122) or ledipasvir/sofosbuvir (LDV/SOF) ± RBV (n=130) included in a national database were identified and prospectively followed up. Demographic, clinical and virologic data and serious adverse events (SAEs) were analyzed. Differences between treatment groups mean that data cannot be compared directly. Overall sustained virologic response at Week 12 post treatment (SVR12) was 96.2% with OMV/PTVr+RBV and 95.4% with LDV/SOF±RBV. In cirrhotic patients, SVR12 was 91.2% with OMV/PTVr+RBV and 93.2% with LDV/SOF±RBV. There was no significant difference in SVR12 according to degree of fibrosis in either treatment group (P = .243 and P = .244, respectively). On multivariate analysis, baseline albumin OMV/PTVr) and bilirubin >2 mg/dL (both cohorts) were significantly associated with failure to achieve SVR (P OMV/PTVr subcohort and 4.6% and 0.8%, respectively, in the LDV/SOF subcohort. DAA-based regimens returned high rates of SVR12, comparable to limited data from clinical trials, in cirrhotic and non-cirrhotic HCV genotype 4 patients managed in a realworld setting. Safety profiles of both regimens were good and comparable to those reported for other HCV genotypes. Copyright © 2017 AGA Institute. Published by Elsevier Inc. All rights reserved.

  11. Congenital hypopituitarism and renal failure

    Directory of Open Access Journals (Sweden)

    Gaurav Atreja

    2011-01-01

    Full Text Available Congenital hypopituitarism is potentially fatal in the newborn period but treatable if the diagnosis is made early. We report a neonate who presented with hypothermia and severe hypoglycemia. He also had undescended testis and micropenis. Initial screening revealed panhypopituitarism, which was corrected promptly. He developed renal failure due to initial cardiovascular compromise related to hypotension but recovered quickly with standard management. Magnetic resonance imaging revealed absent stalk of anterior pituitary.

  12. Heart Failure and Pulmonary Hypertension

    OpenAIRE

    Shin, Jordan T.; Semigran, Marc J.

    2010-01-01

    When PH and RV dysfunction accompany HF, the impact on functional capacity and prognosis are ominous. Newer clinical strategies to preferentially lower pulmonary pressures and pulmonary vascular tone improve functional performance and symptoms of heart failure by targeting the NO signal transduction pathways as with PDE5 inhibition. Additional studies are needed to delineate if these therapies will impact long-term patient outcomes and to elucidate the specific mechanisms whereby these treatm...

  13. SYNTHETIC SLING FAILURE - EVALUATIONS & RECOMMENDATIONS

    Energy Technology Data Exchange (ETDEWEB)

    MACKEY TC; HENDERSON CS

    2009-10-26

    The information and evaluations provided in this report were compiled to address the recurring problem of synthetic sling failure. As safety is the number one priority in all work aspects, a solution must be devised to prevent accidents from occurring. A total of thirteen cases regarding synthetic sling failure were evaluated in order to determine their causes, effects, and preventative measures. From the collected data, it was found that all cases in which the synthetic sling contacted the edge of its load resulted in sling failure. It is required that adequate synthetic sling protection devices be used to protect slings in any lift where the sling comes in direct contact with the edge or corner of its load. However, there are no consensus codes or standards stating the type, material, or purpose of the type of protective device used to protect the sling from being cut. Numerous industry standards and codes provide vague descriptions on how to protect synthetic slings. Without a clear, concise statement of how to protect synthetic slings, it is common for inadequate materials and sling protection devices to be used in an attempt to meet the intent of these requirements. The use of an inadequate sling protection device is the main cause of synthetic sling failure in all researched cases. Commercial sling protection devices come in many shapes and sizes, and have a variety of names, as well as advertised uses. 'Abrasion pads' and 'wear protectors' are two different names for products with the same intended purpose. There is no distinguishable way to determine the extent of sling protection which these devices will provide, or what specific scenarios they are made for. This creates room for error in a field where error is unacceptable. This report provides a recommended action for hoisting and rigging activities which require synthetic slings to contact a load, as well as recommended changes to industry standards which will benefit overall

  14. Rubble Mound Breakwater Failure Modes

    DEFF Research Database (Denmark)

    Burcharth, H. F.; Z., Liu

    1995-01-01

    The RMBFM-Project (Rubble Mound Breakwater Failure Modes) is sponsored by the Directorate General XII of the Commission of the European Communities under the Contract MAS-CT92- 0042, with the objective of contributing to the development of rational methods for the design of rubble mound breakwaters...... modes, plus development of related partial coefficients which make it possible to design according to preselected reliability levels. Due to limited space only the major activities are described....

  15. Accountability for network backup failures

    Energy Technology Data Exchange (ETDEWEB)

    Benson, W.H.

    1994-02-01

    Regular hard disk backups for workstations are widely recommended. The necessity of backups -- akin to one`s own mortality -- is something most people would rather not think about. This attitude has two consequences. When people do subscribe to automated network backups, they expect the system to perform at a high level of reliability and that their files will be there for them when they need them. Second, they usually fail to appreciate that reliability is a shared responsibility. Although ostensibly their only responsibility is to keep the computer powered on overnight, there are actually many more opportunities for failure within the user`s jurisdiction than in other parts of the infrastructure. High reliability is almost a sine qua non for backups. We describe a strategy for enhancing reliability based on the principle of accountability. This strategy involves monitoring the system, gathering statistics, detecting problems, anticipating problems, troubleshooting, and finally determining where failure occurred within the infrastructure and who should be accountable. We describe a specific backup system in a specific network environment to illustrate the value of accountability. This system, macdumps, backs up Macintosh disks over an AppleTalk network. The original software was written by Dan Tappan of BBN in the early years of the Mac and is available by ftp for noncommercial use. It has proven reliable and robust. Despite the high quality of the fundamental software, there are still many opportunities for failure within the infrastructure. We first discuss accountability in the context of network backups, then briefly describe how the backup system operates, the components of the infrastructure, types of failures experienced, and then summarize our experience.

  16. Genetic diversity of the genotype VII Newcastle disease virus: identification of a novel VIIj sub-genotype.

    Science.gov (United States)

    Xue, Cong; Cong, Yanlong; Yin, Renfu; Sun, Yixue; Ding, Chan; Yu, Shengqing; Liu, Xiufan; Hu, Shunlin; Qian, Jing; Yuan, Qianliang; Yang, Mingxi; Wang, Chunfeng; Ding, Zhuang

    2017-02-01

    Newcastle disease (ND) is a highly contagious disease of poultry caused by Newcastle disease virus (NDV). Multiple genotypes of NDV have been circulating worldwide and NDV is continuously evolving, resulting into more diversity. Of multiple viral genotypes, VII is particularly important given that it had been associated with most recent ND outbreaks worldwide. In this study, an epidemiological investigation performed in northeastern China during 2014-2015 showed that 11 genotype VII isolates amounted to 55 percent in a total number of NDV isolates. Therefore, to evaluate the genetic diversity worldwide and epidemiological distribution in China of genotype VII NDV, a phylogenetic analysis based on the 1255 complete F gene sequences showed that VII is the most predominant genotype worldwide. A further detailed characterization on genotype VII was conducted based on the 477 complete F gene sequences from 11 isolates and 466 reference viruses available in GenBank. The results demonstrated that VII can be further divided into 8 sub-genotypes (VIIb, VIId-VIIj), indicating its complex genetic diversity. It is worthy of note that the isolation rate of VIIj is increasing recently. It emphasizes the necessity to pay close attention to the epidemiological dynamic of genotype VII NDV and highlights the importance of vaccination program.

  17. Pepino mosaic virus genotype shift in North America and rapid genotype identification using loop-mediated isothermal amplification

    Science.gov (United States)

    Pepino mosaic, once an emerging disease a decade ago, has become endemic on greenhouse tomatoes worldwide in recent years. Three distinct genotypes of Pepino mosaic virus (PepMV), including EU, US1 and CH2 have been recognized. Our earlier study in 2006-2007 demonstrated a predominant EU genotype ...

  18. Changing genotypes of cholera toxin (CT) of Vibrio cholerae O139 in Bangladesh and description of three new CT genotypes.

    Science.gov (United States)

    Bhuiyan, Nurul A; Nusrin, Suraia; Alam, Munirul; Morita, Masatomo; Watanabe, Haruo; Ramamurthy, Thandavarayan; Cravioto, Alejandro; Nair, Gopinath Balakrish

    2009-11-01

    We determined the genotype of cholera toxin by amplifying and sequencing the B-subunit in a sequential collection of 90 strains of Vibrio cholerae O139 isolated over the past 13 years since its first description in 1992. Representative strains isolated during 1993-1997 harboured ctxB of El Tor type (genotype 3). Twenty-six strains isolated during 1999, 2001, 2005 and three strains isolated in 1998, 2000 and 2002 were identified to belong to new ctxB genotypes 4 and 5, respectively. Genotype 5 was similar to genotype 1 except at position 28 (D-->A). The genotype 6 was similar to genotype 4 except at position 34 (H-->P). The implication of switch in terms of function of the toxin and its impact on human disease is unclear. How this change has influenced their prevalence relative to that of V. cholerae O1 in human infection is also not clear. The other common virulence gene clusters including the Vibrio pathogenicity island-1, Vibrio seventh pandemic island (VSP)-I and VSP-II of V. cholerae O139 did not show any remarkable difference from that of the O1 El Tor strains. Overall, the majority of the O139 strains tested in this study were similar to the El Tor strains but had altered ctxB genotype. This change and the impact that it causes to the epidemiology of cholera caused by O139 should be closely monitored.

  19. TARDEC FMEA TRAINING: Understanding and Evaluating Failure Mode and Effects Analyses (FMEA)

    Science.gov (United States)

    2012-06-07

    Unclassified TARDEC FMEA TRAINING: Understanding and Evaluating Failure Mode and Effects Analyses ( FMEA ) TARDEC Systems Engineering Risk...JUN 2012 2. REPORT TYPE Briefing Charts 3. DATES COVERED 01-05-2012 to 31-05-2012 4. TITLE AND SUBTITLE TARDEC FMEA TRAINING: Understanding...and Evaluating Failure Mode and Effects Analyses ( FMEA ) 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) Kadry Rizk

  20. Predicting Electronic Failure from Smoke

    Energy Technology Data Exchange (ETDEWEB)

    Tanaka, T.J.

    1999-01-15

    Smoke can cause electronic equipment to fail through increased leakage currents and shorts. Sandia National Laboratories is studying the increased leakage currents caused by smoke with varying characteristics. The objective is to develop models to predict the failure of electronic equipment exposed to smoke. This requires the collection of data on the conductivity of smoke and knowledge of critical electrical systems that control high-consequence operations. We have found that conductivity is a function of the type of fuel, how it is burned, and smoke density. Video recordings of highly biased dc circuits exposed in a test chamber show that during a fire, smoke is attracted to high voltages and can build fragile carbon bridges that conduct leakage currents. The movement of air breaks the bridges, so the conductivity decreases after the fire is extinguished and the test chamber is vented. During the fire, however, electronic equipment may not operate correctly, leading to problems for critical operations dependent on electronic control. The potential for electronic failure is highly dependent on the type of electrical circuit, and Sandia National Laboratories plans to include electrical circuit modeling in the failure models.

  1. Failure During Sheared Edge Stretching

    Science.gov (United States)

    Levy, B. S.; van Tyne, C. J.

    2008-12-01

    Failure during sheared edge stretching of sheet steels is a serious concern, especially in advanced high-strength steel (AHSS) grades. The shearing process produces a shear face and a zone of deformation behind the shear face, which is the shear-affected zone (SAZ). A failure during sheared edge stretching depends on prior deformation in the sheet, the shearing process, and the subsequent strain path in the SAZ during stretching. Data from laboratory hole expansion tests and hole extrusion tests for multiple lots of fourteen grades of steel were analyzed. The forming limit curve (FLC), regression equations, measurement uncertainty calculations, and difference calculations were used in the analyses. From these analyses, an assessment of the primary factors that contribute to the fracture during sheared edge stretching was made. It was found that the forming limit strain with consideration of strain path in the SAZ is a major factor that contributes to the failure of a sheared edge during stretching. Although metallurgical factors are important, they appear to play a somewhat lesser role.

  2. Detecting failure of climate predictions

    Science.gov (United States)

    Runge, Michael C.; Stroeve, Julienne C.; Barrett, Andrew P.; McDonald-Madden, Eve

    2016-09-01

    The practical consequences of climate change challenge society to formulate responses that are more suited to achieving long-term objectives, even if those responses have to be made in the face of uncertainty. Such a decision-analytic focus uses the products of climate science as probabilistic predictions about the effects of management policies. Here we present methods to detect when climate predictions are failing to capture the system dynamics. For a single model, we measure goodness of fit based on the empirical distribution function, and define failure when the distribution of observed values significantly diverges from the modelled distribution. For a set of models, the same statistic can be used to provide relative weights for the individual models, and we define failure when there is no linear weighting of the ensemble models that produces a satisfactory match to the observations. Early detection of failure of a set of predictions is important for improving model predictions and the decisions based on them. We show that these methods would have detected a range shift in northern pintail 20 years before it was actually discovered, and are increasingly giving more weight to those climate models that forecast a September ice-free Arctic by 2055.

  3. Detecting failure of climate predictions

    Science.gov (United States)

    Runge, Michael C.; Stroeve, Julienne C.; Barrett, Andrew P.; McDonald-Madden, Eve

    2016-01-01

    The practical consequences of climate change challenge society to formulate responses that are more suited to achieving long-term objectives, even if those responses have to be made in the face of uncertainty1, 2. Such a decision-analytic focus uses the products of climate science as probabilistic predictions about the effects of management policies3. Here we present methods to detect when climate predictions are failing to capture the system dynamics. For a single model, we measure goodness of fit based on the empirical distribution function, and define failure when the distribution of observed values significantly diverges from the modelled distribution. For a set of models, the same statistic can be used to provide relative weights for the individual models, and we define failure when there is no linear weighting of the ensemble models that produces a satisfactory match to the observations. Early detection of failure of a set of predictions is important for improving model predictions and the decisions based on them. We show that these methods would have detected a range shift in northern pintail 20 years before it was actually discovered, and are increasingly giving more weight to those climate models that forecast a September ice-free Arctic by 2055.

  4. Model for heart failure education.

    Science.gov (United States)

    Baldonado, Analiza; Dutra, Danette; Abriam-Yago, Katherine

    2014-01-01

    Heart failure (HF) is the heart's inability to meet the body's need for blood and oxygen. According to the American Heart Association 2013 update, approximately 5.1 million people are diagnosed with HF in the United States in 2006. Heart failure is the most common diagnosis for hospitalization. In the United States, the HF direct and indirect costs are estimated to be US $39.2 billion in 2010. To address this issue, nursing educators designed innovative teaching frameworks on HF management both in academia and in clinical settings. The model was based on 2 resources: the American Association of Heart Failure Nurses (2012) national nursing certification and the award-winning Pierce County Responsive Care Coordination Program. The HF educational program is divided into 4 modules. The initial modules offer foundational levels of Bloom's Taxonomy then progress to incorporate higher-levels of learning when modules 3 and 4 are reached. The applicability of the key components within each module allows formatting to enhance learning in all areas of nursing, from the emergency department to intensive care units to the medical-surgical step-down units. Also applicable would be to provide specific aspects of the modules to nurses who care for HF patients in skilled nursing facility, rehabilitation centers, and in the home-health care setting.

  5. Can Stem Cell 'Patch' Help Heart Failure?

    Science.gov (United States)

    ... https://medlineplus.gov/news/fullstory_164475.html Can Stem Cell 'Patch' Help Heart Failure? Small improvement seen over ... Scientists report another step in the use of stem cells to help treat people with debilitating heart failure. ...

  6. Heart failure in patients treated with bisphosphonates

    DEFF Research Database (Denmark)

    Grove, Erik; Abrahamsen, B; Vestergaard, P

    2013-01-01

    The aim of this study was to investigate the occurrence of heart failure in patients treated with bisphosphonates.......The aim of this study was to investigate the occurrence of heart failure in patients treated with bisphosphonates....

  7. Dissociating Prediction Failure: Considerations from Music Perception

    DEFF Research Database (Denmark)

    Ross, Suzi; Hansen, Niels Christian

    2016-01-01

    Dissociating Prediction Failure: Considerations from Music Perception The Journal of Neuroscience, 16 March 2016, 36(11): 3103-3105;......Dissociating Prediction Failure: Considerations from Music Perception The Journal of Neuroscience, 16 March 2016, 36(11): 3103-3105;...

  8. CSM RCS Design Considerations and Failure Modes

    Science.gov (United States)

    Interbartolo, Michael

    2009-01-01

    Objectives include: a) Define major Command and Service Module (CSM) design considerations; b) List Command Module (CM) RCS failures and lessons learned; and c) List Service Module (SM) RCS failures and lessons learned.

  9. Structural and failure mechanics of sandwich composites

    CERN Document Server

    Carlsson, LA; Carlsson, Leif A

    2011-01-01

    Focusing on important deformation and failure modes of sandwich structures, this volume describes the mechanics behind fracture processes. The text also reviews test methods developed for the cr, structural integrity, and failure mechanisms of sandwich structures.

  10. Prognostic indices in childhood heart failure

    African Journals Online (AJOL)

    hood heart failure and highlight the factors that affect out- come among cases of heart failure ... month period were studied prospectively. Diagnosis of heart ... a case-fatality rate of 24% among the study population. Poor prognostic indices ...

  11. Single Endemic Genotype of Measles Virus Continuously Circulating in China for at Least 16 Years

    Science.gov (United States)

    Wang, Huiling; Zhu, Zhen; Ji, Yixin; Liu, Chunyu; Zhang, Xiaojie; Sun, Liwei; Zhou, Jianhui; Lu, Peishan; Hu, Ying; Feng, Daxing; Zhang, Zhenying; Wang, Changyin; Fang, Xueqiang; Zheng, Huanying; Liu, Leng; Sun, Xiaodong; Tang, Wei; Wang, Yan; Liu, Yan; Gao, Hui; Tian, Hong; Ma, Jiangtao; Gu, Suyi; Wang, Shuang; Feng, Yan; Bo, Fang; Liu, Jianfeng; Si, Yuan; Zhou, Shujie; Ma, Yuyan; Wu, Shengwei; Zhou, Shunde; Li, Fangcai; Ding, Zhengrong; Yang, Zhaohui; Rota, Paul A.; Featherstone, David; Jee, Youngmee; Bellini, William J.; Xu, Wenbo

    2012-01-01

    The incidence of measles in China from 1991 to 2008 was reviewed, and the nucleotide sequences from 1507 measles viruses (MeV) isolated during 1993 to 2008 were phylogenetically analyzed. The results showed that measles epidemics peaked approximately every 3 to 5 years with the range of measles cases detected between 56,850 and 140,048 per year. The Chinese MeV strains represented three genotypes; 1501 H1, 1 H2 and 5 A. Genotype H1 was the predominant genotype throughout China continuously circulating for at least 16 years. Genotype H1 sequences could be divided into two distinct clusters, H1a and H1b. A 4.2% average nucleotide divergence was found between the H1a and H1b clusters, and the nucleotide sequence and predicted amino acid homologies of H1a viruses were 92.3%–100% and 84.7%–100%, H1b were 97.1%–100% and 95.3%–100%, respectively. Viruses from both clusters were distributed throughout China with no apparent geographic restriction and multiple co-circulating lineages were present in many provinces. Cluster H1a and H1b viruses were co-circulating during 1993 to 2005, while no H1b viruses were detected after 2005 and the transmission of that cluster has presumably been interrupted. Analysis of the nucleotide and predicted amino acid changes in the N proteins of H1a and H1b viruses showed no evidence of selective pressure. This study investigated the genotype and cluster distribution of MeV in China over a 16-year period to establish a genetic baseline before MeV elimination in Western Pacific Region (WPR). Continuous and extensive MeV surveillance and the ability to quickly identify imported cases of measles will become more critical as measles elimination goals are achieved in China in the near future. This is the first report that a single endemic genotype of measles virus has been found to be continuously circulating in one country for at least 16 years. PMID:22532829

  12. Single endemic genotype of measles virus continuously circulating in China for at least 16 years.

    Directory of Open Access Journals (Sweden)

    Yan Zhang

    Full Text Available The incidence of measles in China from 1991 to 2008 was reviewed, and the nucleotide sequences from 1507 measles viruses (MeV isolated during 1993 to 2008 were phylogenetically analyzed. The results showed that measles epidemics peaked approximately every 3 to 5 years with the range of measles cases detected between 56,850 and 140,048 per year. The Chinese MeV strains represented three genotypes; 1501 H1, 1 H2 and 5 A. Genotype H1 was the predominant genotype throughout China continuously circulating for at least 16 years. Genotype H1 sequences could be divided into two distinct clusters, H1a and H1b. A 4.2% average nucleotide divergence was found between the H1a and H1b clusters, and the nucleotide sequence and predicted amino acid homologies of H1a viruses were 92.3%-100% and 84.7%-100%, H1b were 97.1%-100% and 95.3%-100%, respectively. Viruses from both clusters were distributed throughout China with no apparent geographic restriction and multiple co-circulating lineages were present in many provinces. Cluster H1a and H1b viruses were co-circulating during 1993 to 2005, while no H1b viruses were detected after 2005 and the transmission of that cluster has presumably been interrupted. Analysis of the nucleotide and predicted amino acid changes in the N proteins of H1a and H1b viruses showed no evidence of selective pressure. This study investigated the genotype and cluster distribution of MeV in China over a 16-year period to establish a genetic baseline before MeV elimination in Western Pacific Region (WPR. Continuous and extensive MeV surveillance and the ability to quickly identify imported cases of measles will become more critical as measles elimination goals are achieved in China in the near future. This is the first report that a single endemic genotype of measles virus has been found to be continuously circulating in one country for at least 16 years.

  13. Inferring haplotypes and parental genotypes in larger full sib-ships and other pedigrees with missing or erroneous genotype data

    Directory of Open Access Journals (Sweden)

    Nettelblad Carl

    2012-10-01

    Full Text Available Abstract Background In many contexts, pedigrees for individuals are known even though not all individuals have been fully genotyped. In one extreme case, the genotypes for a set of full siblings are known, with no knowledge of parental genotypes. We propose a method for inferring phased haplotypes and genotypes for all individuals, even those with missing data, in such pedigrees, allowing a multitude of classic and recent methods for linkage and genome analysis to be used more efficiently. Results By artificially removing the founder generation genotype data from a well-studied simulated dataset, the quality of reconstructed genotypes in that generation can be verified. For the full structure of repeated matings with 15 offspring per mating, 10 dams per sire, 99.89%of all founder markers were phased correctly, given only the unphased genotypes for offspring. The accuracy was reduced only slightly, to 99.51%, when introducing a 2% error rate in offspring genotypes. When reduced to only 5 full-sib offspring in a single sire-dam mating, the corresponding percentage is 92.62%, which compares favorably with 89.28%from the leading Merlin package. Furthermore, Merlin is unable to handle more than approximately 10 sibs, as the number of states tracked rises exponentially with family size, while our approach has no such limit and handles 150 half-sibs with ease in our experiments. Conclusions Our method is able to reconstruct genotypes for parents when genotype data is only available for offspring individuals, as well as haplotypes for all individuals. Compared to the Merlin package, we can handle larger pedigrees and produce superior results, mainly due to the fact that Merlin uses the Viterbi algorithm on the state space to infer the genotype sequence. Tracking of haplotype and allele origin can be used in any application where the marker set does not directly influence genotype variation influencing traits. Inference of genotypes can also reduce the

  14. Phenomenological Studies of Macroscale Failure in Metals

    Energy Technology Data Exchange (ETDEWEB)

    Kashiwa, Bryan Andrew [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Hull, Lawrence Mark [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2016-12-06

    Highlights of recent phenomenological studies of metal failure are given. Failure leading to spallation and fragmentation are typically of interest. The current ‘best model’ includes the following; a full history stress in tension; nucleation initiating dynamic relaxation; toward a tensile yield function; failure dependent on strain, strain rate, and temperature; a mean-preserving ‘macrodefect’ is introduced when failure occurs in tension; and multifield theoretical refinements

  15. Hypogonadism and renal failure: An update

    OpenAIRE

    Nannan Thirumavalavan; Wilken, Nathan A.; Ranjith Ramasamy

    2015-01-01

    The prevalence of both hypogonadism and renal failure is increasing. Hypogonadism in men with renal failure carries with it significant morbidity, including anemia and premature cardiovascular disease. It remains unclear whether testosterone therapy can affect the morbidity and mortality associated with renal failure. As such, in this review, we sought to evaluate the current literature addressing hypogonadism and testosterone replacement, specifically in men with renal failure. The articles ...

  16. Experimental investigations of hexagonal crimping die failure

    Directory of Open Access Journals (Sweden)

    Veera kumar M

    2016-06-01

    Full Text Available This paper deals with the hexagonal crimping die failure of high carbon high chromium steel material. The failure modes were initially revealed and identified by the visual examination. Then the chemical analysis and metallographic examination havebeen carried at different positions of the failure die surface using scanning electron microscope (SEM. The microstructure evaluation reveals that failure occurs due to undissolved austenitic structure resulting in improper transition duringheat treatment.

  17. Hypogonadism and renal failure: An update

    OpenAIRE

    Nannan Thirumavalavan; Nathan A Wilken; Ranjith Ramasamy

    2015-01-01

    The prevalence of both hypogonadism and renal failure is increasing. Hypogonadism in men with renal failure carries with it significant morbidity, including anemia and premature cardiovascular disease. It remains unclear whether testosterone therapy can affect the morbidity and mortality associated with renal failure. As such, in this review, we sought to evaluate the current literature addressing hypogonadism and testosterone replacement, specifically in men with renal failure. The articles ...

  18. Anemia and iron deficiency in heart failure.

    Science.gov (United States)

    Gil, Victor M; Ferreira, Jorge S

    2014-01-01

    Heart failure is a common problem and a major cause of mortality, morbidity and impaired quality of life. Anemia is a frequent comorbidity in heart failure and further worsens prognosis and disability. Regardless of anemia status, iron deficiency is a common and usually unidentified problem in patients with heart failure. This article reviews the mechanisms, impact on outcomes and treatment of anemia and iron deficiency in patients with heart failure.

  19. High quality copy number and genotype data from FFPE samples using Molecular Inversion Probe (MIP) microarrays

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Yuker; Carlton, Victoria E.H.; Karlin-Neumann, George; Sapolsky, Ronald; Zhang, Li; Moorhead, Martin; Wang, Zhigang C.; Richardson, Andrea L.; Warren, Robert; Walther, Axel; Bondy, Melissa; Sahin, Aysegul; Krahe, Ralf; Tuna, Musaffe; Thompson, Patricia A.; Spellman, Paul T.; Gray, Joe W.; Mills, Gordon B.; Faham, Malek

    2009-02-24

    A major challenge facing DNA copy number (CN) studies of tumors is that most banked samples with extensive clinical follow-up information are Formalin-Fixed Paraffin Embedded (FFPE). DNA from FFPE samples generally underperforms or suffers high failure rates compared to fresh frozen samples because of DNA degradation and cross-linking during FFPE fixation and processing. As FFPE protocols may vary widely between labs and samples may be stored for decades at room temperature, an ideal FFPE CN technology should work on diverse sample sets. Molecular Inversion Probe (MIP) technology has been applied successfully to obtain high quality CN and genotype data from cell line and frozen tumor DNA. Since the MIP probes require only a small ({approx}40 bp) target binding site, we reasoned they may be well suited to assess degraded FFPE DNA. We assessed CN with a MIP panel of 50,000 markers in 93 FFPE tumor samples from 7 diverse collections. For 38 FFPE samples from three collections we were also able to asses CN in matched fresh frozen tumor tissue. Using an input of 37 ng genomic DNA, we generated high quality CN data with MIP technology in 88% of FFPE samples from seven diverse collections. When matched fresh frozen tissue was available, the performance of FFPE DNA was comparable to that of DNA obtained from matched frozen tumor (genotype concordance averaged 99.9%), with only a modest loss in performance in FFPE. MIP technology can be used to generate high quality CN and genotype data in FFPE as well as fresh frozen samples.

  20. Combined use of phenotypic and genotypic information in sampling animalsfor genotyping in detection of quantitative trait loci

    DEFF Research Database (Denmark)

    Ansari-Mahyari, S; Berg, P

    2008-01-01

    Conventional selective genotyping which is using the extreme phenotypes (EP) was compared with alternative criteria to find the most informative animals for genotyping with respects to mapping quantitative trait loci (QTL). Alternative sampling strategies were based on minimizing the sampling error...... of the estimated QTL effect (MinERR) and maximizing likelihood ratio test (MaxLRT) using both phenotypic and genotypic information. In comparison, animals were randomly genotyped either within or across families. One hundred data sets were simulated each with 30 half-sib families and 120 daughters per family....... The strategies were compared in these datasets with respect to estimated effect and position of a QTL within a previously defined genomic region at genotyping 10, 20 or 30% of the animals. Combined linkage disequilibrium linkage analysis (LDLA) was applied in a variance component approach. Power to detect QTL...