bluuebunny/crossref_metadata_2025_split huggingface dataset:
Field Study of Dried Blood Spot Specimens for HIV-1 Drug Resistance Genotyping
Authors: Parry C. M. , Parkin N. , Diallo K. , Mwebaza S. , Batamwita R. , DeVos J. , Bbosa N. , Lyagoba F. , Magambo B. , Jordan M. R. , Downing R. , Zhang G. , Kaleebu P. , Yang C. , Bertagnolio S. 
Published: May 2014

ABSTRACTDried blood spots (DBS) are an alternative specimen type for HIV drug resistance genotyping in resource-limited settings. Data relating to the impact of DBS storage and shipment conditions on genotyping efficiency under field conditions are limited. We compared the genotyping efficiencies and resistance profiles of DBS stored and shipped at different temperatures to those of plasma specimens collected in parallel from patients receiving antiretroviral therapy in Uganda. Plasma and four DBS cards from anti-coagulated venous blood and a fifth card from finger-prick blood were prepared from 103 HIV patients with a median viral load (VL) of 57,062 copies/ml (range, 1,081 to 2,964,191). DBS were stored at ambient temperature for 2 or 4 weeks or frozen at −80°C and shipped from Uganda to the United States at ambient temperature or frozen on dry ice for genotyping using a broadly sensitive in-house method. Plasma (97.1%) and DBS (98.1%) stored and shipped frozen had similar genotyping efficiencies. DBS stored frozen (97.1%) or at ambient temperature for 2 weeks (93.2%) and shipped at ambient temperature also had similar genotyping efficiencies. Genotyping efficiency was reduced for DBS stored at ambient temperature for 4 weeks (89.3%,P= 0.03) or prepared from finger-prick blood and stored at ambient temperature for 2 weeks (77.7%,P< 0.001) compared to DBS prepared from venous blood and handled similarly. Resistance profiles were similar between plasma and DBS specimens. This report delineates the optimal DBS collection, storage, and shipping conditions and opens a new avenue for cost-saving ambient-temperature DBS specimen shipments for HIV drug resistance (HIVDR) surveillances in resource-limited settings.
Functional Annotation of Cotesia congregata Bracovirus: Identification of Viral Genes Expressed in Parasitized Host Immune Tissues
Authors: Chevignon Germain , Thézé Julien , Cambier Sébastien , Poulain Julie , Da Silva Corinne , Bézier Annie , Musset Karine , Moreau Sébastien J. M. , Drezen Jean-Michel , Huguet Elisabeth 
Published: May 2014

ABSTRACTBracoviruses (BVs) from thePolydnaviridaefamily are symbiotic viruses used as biological weapons by parasitoid wasps to manipulate lepidopteran host physiology and induce parasitism success. BV particles are produced by wasp ovaries and injected along with the eggs into the caterpillar host body, where viral gene expression is necessary for wasp development. Recent sequencing of the proviral genome ofCotesia congregataBV (CcBV) identified 222 predicted virulence genes present on 35 proviral segments integrated into the wasp genome. To date, the expressions of only a few selected candidate virulence genes have been studied in the caterpillar host, and we lacked a global vision of viral gene expression. In this study, a large-scale transcriptomic analysis by 454 sequencing of two immune tissues (fat body and hemocytes) of parasitizedManduca sextacaterpillar hosts allowed the detection of expression of 88 CcBV genes expressed 24 h after the onset of parasitism. We linked the expression profiles of these genes to several factors, showing that different regulatory mechanisms control viral gene expression in the host. These factors include the presence of signal peptides in encoded proteins, diversification of promoter regions, and, more surprisingly, gene position on the proviral genome. Indeed, most genes for which expression could be detected are localized in particular proviral regions globally producing higher numbers of circles. Moreover, this polydnavirus (PDV) transcriptomic analysis also reveals that a majority of CcBV genes possess at least one intron and an arthropod transcription start site, consistent with an insect origin of these virulence genes.IMPORTANCEBracoviruses (BVs) are symbiotic polydnaviruses used by parasitoid wasps to manipulate lepidopteran host physiology, ensuring wasp offspring survival. To date, the expressions of only a few selected candidate BV virulence genes have been studied in caterpillar hosts. We performed a large-scale analysis of BV gene expression in two immune tissues ofManduca sextacaterpillars parasitized byCotesia congregatawasps. Genes for which expression could be detected corresponded to genes localized in particular regions of the viral genome globally producing higher numbers of circles. Our study thus brings an original global vision of viral gene expression and paves the way to the determination of the regulatory mechanisms enabling the expression of BV genes in targeted organisms, such as major insect pests. In addition, we identify sequence features suggesting that most BV virulence genes were acquired from insect genomes.
Regulation of the Human Endogenous Retrovirus K (HML-2) Transcriptome by the HIV-1 Tat Protein
Authors: Gonzalez-Hernandez Marta J. , Cavalcoli James D. , Sartor Maureen A. , Contreras-Galindo Rafael , Meng Fan , Dai Manhong , Dube Derek , Saha Anjan K. , Gitlin Scott D. , Omenn Gilbert S. , Kaplan Mark H. , Markovitz David M. 
Published: May 2014

ABSTRACTApproximately 8% of the human genome is made up of endogenous retroviral sequences. As the HIV-1 Tat protein activates the overall expression of the human endogenous retrovirus type K (HERV-K) (HML-2), we used next-generation sequencing to determine which of the 91 currently annotated HERV-K (HML-2) proviruses are regulated by Tat. Transcriptome sequencing of total RNA isolated from Tat- and vehicle-treated peripheral blood lymphocytes from a healthy donor showed that Tat significantly activates expression of 26 unique HERV-K (HML-2) proviruses, silences 12, and does not significantly alter the expression of the remaining proviruses. Quantitative reverse transcription-PCR validation of the sequencing data was performed on Tat-treated PBLs of seven donors using provirus-specific primers and corroborated the results with a substantial degree of quantitative similarity.IMPORTANCEThe expression of HERV-K (HML-2) is tightly regulated but becomes markedly increased following infection with HIV-1, in part due to the HIV-1 Tat protein. The findings reported here demonstrate the complexity of the genome-wide regulation of HERV-K (HML-2) expression by Tat. This work also demonstrates that although HERV-K (HML-2) proviruses in the human genome are highly similar in terms of DNA sequence, modulation of the expression of specific proviruses in a given biological situation can be ascertained using next-generation sequencing and bioinformatics analysis.
Influenza Virus PB1 and Neuraminidase Gene Segments Can Cosegregate during Vaccine Reassortment Driven by Interactions in the PB1 Coding Region
Authors: Cobbin Joanna C. A. , Ong Chi , Verity Erin , Gilbertson Brad P. , Rockman Steven P. , Brown Lorena E. 
Published: May 2014

ABSTRACT
Egg-grown influenza vaccine yields are maximized by infection with a seed virus produced by “classical reassortment” of a seasonal isolate with a highly egg-adapted strain. Seed viruses are selected based on a high-growth phenotype and the presence of the seasonal hemagglutinin (HA) and neuraminidase (NA) surface antigens. Retrospective analysis of H3N2 vaccine seed viruses indicated that, unlike other internal proteins that were predominantly derived from the high-growth parent A/Puerto Rico/8/34 (PR8), the polymerase subunit PB1 could be derived from either parent depending on the seasonal strain. We have recently shown that A/Udorn/307/72 (Udorn) models a seasonal isolate that yields reassortants bearing the seasonal PB1 gene. This is despite the fact that the reverse genetics-derived virus that includes Udorn PB1 with Udorn HA and NA on a PR8 background has inferior growth compared to the corresponding virus with PR8 PB1. Here we use competitive plasmid transfections to investigate the mechanisms driving selection of a less fit virus and show that the Udorn PB1 gene segment cosegregates with the Udorn NA gene segment. Analysis of chimeric PB1 genes revealed that the coselection of NA and PB1 segments was not directed through the previously identified packaging sequences but through interactions involving the internal coding region of the PB1 gene. This study identifies associations between viral genes that can direct selection in classical reassortment for vaccine production and which may also be of relevance to the gene constellations observed in past antigenic shift events where creation of a pandemic virus has involved reassortment.

IMPORTANCE
Influenza vaccine must be produced and administered in a timely manner in order to provide protection during the winter season, and poor-growing vaccine seed viruses can compromise this process. To maximize vaccine yields, manufacturers create hybrid influenza viruses with gene segments encoding the surface antigens from a seasonal virus isolate, important for immunity, and others from a virus with high growth properties. This involves coinfection of cells with both parent viruses and selection of dominant progeny bearing the seasonal antigens. We show that this method of creating hybrid viruses does not necessarily select for the best yielding virus because preferential pairing of gene segments when progeny viruses are produced determines the genetic makeup of the hybrids. This not only has implications for how hybrid viruses are selected for vaccine production but also sheds light on what drives and limits hybrid gene combinations that arise in nature, leading to pandemics.
Cryo-Electron Microscopy Structure of Lactococcal Siphophage 1358 Virion
Authors: Spinelli Silvia , Bebeacua Cecilia , Orlov Igor , Tremblay Denise , Klaholz Bruno P. , Moineau Sylvain , Cambillau Christian 
Published: May 2014

ABSTRACT

Lactococcus lactis
, a Gram
+
lactic acid-producing bacterium used for the manufacture of several fermented dairy products, is subject to infection by diverse virulent tailed phages, leading to industrial fermentation failures. This constant viral risk has led to a sustained interest in the study of their biology, diversity, and evolution. Lactococcal phages now constitute a wide ensemble of at least 10 distinct genotypes within the
Caudovirales
order, many of them belonging to the
Siphoviridae
family. Lactococcal siphophage 1358, currently the only member of its group, displays a noticeably high genomic similarity to some
Listeria
phages as well as a host range limited to a few
L. lactis
strains. These genomic and functional characteristics stimulated our interest in this phage. Here, we report the cryo-electron microscopy structure of the complete 1358 virion. Phage 1358 exhibits noteworthy features, such as a capsid with
dextro
handedness and protruding decorations on its capsid and tail. Observations of the baseplate of virion particles revealed at least two conformations, a closed and an open, activated form. Functional assays uncovered that the adsorption of phage 1358 to its host is Ca
2+
independent, but this cation is necessary to complete its lytic cycle. Taken together, our results provide the complete structural picture of a unique lactococcal phage and expand our knowledge on the complex baseplate of phages of the
Siphoviridae
family.

IMPORTANCE
Phages of
Lactococcus lactis
are investigated mainly because they are sources of milk fermentation failures in the dairy industry. Despite the availability of several antiphage measures, new phages keep emerging in this ecosystem. In this study, we provide the cryo-electron microscopy reconstruction of a unique lactococcal phage that possesses genomic similarity to particular
Listeria
phages and has a host range restricted to only a minority of
L. lactis
strains. The capsid of phage 1358 displays the almost unique characteristic of being
dextro
handed. Its capsid and tail exhibit decorations that we assigned to nonspecific sugar binding modules. We observed the baseplate of 1358 in two conformations, a closed and an open form. We also found that the adsorption to its host, but not infection, is Ca
2+
independent. Overall, this study advances our understanding of the adhesion mechanisms of siphophages.
Evaluating and classifying the readiness of technology specifications for national standardization
Authors: Baker Dixie B , Perlin Jonathan B , Halamka John 
Published: May 2014

Abstract
The American Recovery and Reinvestment Act (ARRA) of 2009 clearly articulated the central role that health information technology (HIT) standards would play in improving healthcare quality, safety, and efficiency through the meaningful use of certified, standards based, electronic health record (EHR) technology. In 2012, the Office of the National Coordinator (ONC) asked the Nationwide Health Information Network (NwHIN) Power Team of the Health Information Technology Standards Committee (HITSC) to develop comprehensive, objective, and, to the extent practical, quantitative criteria for evaluating technical standards and implementation specifications and classifying their readiness for national adoption. The Power Team defined criteria, attributes, and metrics for evaluating and classifying technical standards and specifications as ‘emerging,’ ‘pilot,’ or ‘ready for national standardization’ based on their maturity and adoptability. The ONC and the HITSC are now using these metrics for assessing the readiness of technical standards for national adoption.
Identifying priority medicines policy issues for New Zealand: a general inductive study
Authors: Babar Zaheer-Ud-Din , Francis Susan 
Published: May 2014

ObjectivesTo identify priority medicines policy issues for New Zealand.SettingStakeholders from a broad range of healthcare and policy institutions including primary, secondary and tertiary care.ParticipantsExploratory, semistructured interviews were conducted with 20 stakeholders throughout New Zealand.Primary and secondary outcome measuresThe interviews were digitally recorded, transcribed and coded into INVIVO 10, then compared and grouped for similarity of theme. Perceptions, experiences and opinions regarding New Zealand's medicines policy issues were recorded.ResultsA large proportion of stakeholders appeared to be unaware of New Zealand's (NZ) medicines policy. In general, the policy was considered to offer consistency to guide decision-making. In the context of Pharmaceutical Management Agency's (PHARMAC's) fixed budget for procuring and subsidising medicines, there was reasonable satisfaction with the range of medicines available—rare disorder medicines being the clear exception. Concerns raised were by whom and how decisions are made and whether desired health outcomes are being measured. Other concerns included inconsistencies in evidence and across health technologies. Despite attempts to improve the situation, lower socioeconomic groups (including rural residents) Māori and Pacific ethnicities and people with rare disorders face challenges with regards to accessing medicines. Other barriers include, convenience to and affordability of prescribers and the increase of prescription fees from NZ$3 to NZ$5. Concerns related to the PHARMAC of New Zealand included: a constraining budget; non-transparency of in-house analysis; lack of consistency in recommendations between the Pharmacology and Therapeutics Advisory Committee. Constraints and inefficiencies also exist in the submission process to access high-cost medicines.ConclusionsThe results suggest reasonable satisfaction with the availability of subsidised medicines. However, some of the major challenges include access to medicines in vulnerable groups, increasing costs and demand for new medicines, access to prescribers, budgetary constraints, cultural and health literacy, patient affordability and evidence requirement for gaining subsidy for medicines.
Care seeking in tuberculosis: results from a countrywide cluster randomised survey in Bangladesh
Authors: Hossain Shahed , Zaman K , Quaiyum Abdul , Banu Sayera , Husain Ashaque , Islam Akramul , Borgdorff Martien , van Leth Frank 
Published: May 2014

ObjectivesTo explore systematically the care seeking trajectories of tuberculosis (TB) cases up to four subsequent places of care and to assess the type of services provided at each place.MethodsTB cases detected actively during the 2007–2009 national TB prevalence survey and passively under the routine programme in the same period were interviewed by administering a standardised questionnaire. Care seeking and services provided up to four subsequent points were explored. Care seeking was further explored by categorising the providers into formal, informal and ‘self-care’ groups.ResultsA total of 273 TB cases were included in this study, of which 33 (12%) were detected during the survey and 240 (88%) from the TB registers. Out of the 118 passively detected cases who first sought care from an informal provider, 52 (44.1%) remained in the informal sector at the second point of care. Similarly, out of the 52, 17 (32.7%) and out of the 17, 5 (29.4%) remained in the informal sector at the third and fourth subsequent points of care, respectively. All the 33 actively detected cases had ‘self-care’ at the first point, and 27 (81.8%) remained with ’self-care’ up to the fourth point of care. Prescribing drugs (59–99%) was the major type of care provided by the formal and informal care providers at each point and was limited to the non-existent practice of investigation or referrals.ConclusionsFree TB services are still underutilised by TB cases and informal caregivers remained the major care providers for such cases in Bangladesh. In order to improve case detection, it is necessary that the National Tuberculosis Programme immediately takes effective initiatives to engage all types of care providers, particularly informal providers who are the first point of care for the majority of the TB suspects.
Material, psychosocial and sociodemographic determinants are associated with positive mental health in Europe: a cross-sectional study
Authors: Dreger Stefanie , Buck Christoph , Bolte Gabriele 
Published: May 2014

ObjectivesTo investigate the association between psychosocial, sociodemographic and material determinants of positive mental health in Europe.DesignCross-sectional analysis of survey data.Setting34 European countries.ParticipantsRepresentative Europe-wide sample consisting of 21 066 men and 22 569 women aged 18 years and over, from 34 European countries participating in the third wave of the European Quality of Life Survey (2011–2012).OutcomePositive mental health as measured by the WHO-5—Mental Well-being Index, while the lowest 25% centile indicated poor positive mental health.ResultsThe prevalence of poor positive mental health was 30% in women and 24% in men. Material, as well as psychosocial, and sociodemographic factors were independently associated with poor positive mental health in a Europe-wide sample from 34 European countries. When studying all factors together, the highest OR for poor positive mental health was reported for social exclusion (men: OR=1.73, 95% CI 1.59 to 1.90; women: OR=1.69, 95% CI 1.57 to 1.81) among the psychosocial factors. Among the material factors, material deprivation had the highest impact (men: OR=1.96, 95% CI 1.78 to 2.15; women: OR=1.93, 95% CI 1.79 to 2.08).ConclusionsThis study gives the first overview on determinants of positive mental health at a European level and could be used as the basis for preventive policies in the field of positive mental health in Europe.
Everyone gets involved: fostering a high quality teaching and learning culture in the NHS
Authors: McElnay Philip , Bakhbakhi Danya , Sansom Jane 
Published: May 2014

AbstractThe aim was to create an environment where doctors at all levels felt like an important part of the education team.Two teaching fellows were appointed to deliver teaching, encourage participation, and quality-assure teaching. An innovative electronic logbook named Teaching Log (T-Log) was developed to reliably “record and reward” teaching occurring at all career levels. A mentor scheme for medical students was established. Mentor training was provided for junior doctors. A near-peer teaching programme was developed for final year medical students on important skills required to be a safe junior doctor.Between September 2013 and January 2014, 83 doctors at our institution logged 657 teaching episodes using the electronic T-Log. 23% were F1s, 14% were F2s, 24% CT1-2s. 36% of sessions were delivered to 3rd year medical students and 36% were delivered to 5th year students. 24% were small group seminars, 26% were bedside teaching sessions, 12% were lectures, 5% were simulation sessions and 9% were clinical skills. 20% of sessions were delivered to a single student. 100% of respondents (15) agreed that T-Log was easy to use. 100% agreed that T-Log was useful. 100% agreed that they would continue to use T-Log.A survey found the mean score for usefulness of the mentor scheme to be 9.1 (1=not useful, 10=very useful). Students saw their mentors on average 6.5 times during a 10 week period. Confidence scores for all key areas of the curriculum were increased following implementation of the scheme. 100% of students would recommend this scheme to next year’s final year students and 100% of mentor respondents (n=8) would participate in the scheme again.Rewarding those who contribute to teaching provides incentive to further increase the quality of education provided to students. T-Log rewards teaching activity. It also provides useful data at an individual level or at institutional level.
Inequalities in unintentional injuries between indigenous and non-indigenous children: a systematic review
Authors: Möller Holger , Falster Kathleen , Ivers Rebecca , Jorm Louisa 
Published: May 2014

BackgroundIndigenous children suffer a disproportionally high burden of unintentional injuries. A more detailed understanding of the underlying causes, risk factors and gaps in research is required to inform prevention efforts and direct future research. The aim of this review was to systematically assess the evidence regarding differences in rates of unintentional injuries between indigenous and non-indigenous children and to identify leading causes and underlying risk factors contributing to these differences.MethodWe systematically searched the literature including 10 electronic databases, institutional websites and reference lists of relevant studies. Due to the substantial heterogeneity between studies, results were summarised in a narrative synthesis and no meta-analysis was carried out.ResultsA total of 39 studies were included in this review. Most studies were descriptive and only five adjusted for potential confounding in the analysis. Indigenous to non-indigenous rate ratios for morbidity and mortality for unintentional injury ranged from 1.2 to 2.3 and 1.8 to 8.2, respectively. The difference varied greatly by cause of injury and between studies, ranging from a reduced risk of hospitalisation due to fall injuries to a 17-fold increased risk of mortality due to pedestrian injuries. Burns, poisoning and transport injuries were the major contributors to the increased injury burden in indigenous children. The studies offered only limited insight into the underlying causes of these differences, but socioeconomic status and parents’ educational attainment were contributing factors.ConclusionsIndigenous children experience a significantly higher burden of morbidity and mortality from unintentional injuries across different indigenous communities worldwide. Most of these injuries are highly preventable, presenting substantial potential to improve indigenous child health. However, there is limited evidence to illuminate the underlying risk factors for unintentional injuries in indigenous children, and this is a priority for further research.