bluuebunny/crossref_metadata_2025_split huggingface dataset:
Chemical Cross-Linking Stabilizes Native-Like HIV-1 Envelope Glycoprotein Trimer Antigens
Authors: Schiffner Torben , de Val Natalia , Russell Rebecca A. , de Taeye Steven W. , de la Peña Alba Torrents , Ozorowski Gabriel , Kim Helen J. , Nieusma Travis , Brod Florian , Cupo Albert , Sanders Rogier W. , Moore John P. , Ward Andrew B. , Sattentau Quentin J. 
Published: October 2015

ABSTRACT
Major neutralizing antibody immune evasion strategies of the HIV-1 envelope glycoprotein (Env) trimer include conformational and structural instability. Stabilized soluble trimers such as BG505 SOSIP.664 mimic the structure of virion-associated Env but nevertheless sample different conformational states. Here we demonstrate that treating BG505 SOSIP.664 trimers with glutaraldehyde or a heterobifunctional cross-linker introduces additional stability with relatively modest effects on antigenicity. Thus, most broadly neutralizing antibody (bNAb) epitopes were preserved after cross-linking, whereas the binding of most weakly or nonneutralizing antibodies (non-NAb) was reduced. Cross-linking stabilized all Env conformers present within a mixed population, and individual conformers could be isolated by bNAb affinity chromatography. Both positive selection of cross-linked conformers using the quaternary epitope-specific bNAbs PGT145, PGT151, and 3BC315 and negative selection with non-NAbs against the V3 region enriched for trimer populations with improved antigenicity for bNAbs. Similar results were obtained using the clade B B41 SOSIP.664 trimer. The cross-linking method may, therefore, be useful for countering the natural conformational heterogeneity of some HIV-1 Env proteins and, by extrapolation, also vaccine immunogens from other pathogens.

IMPORTANCE
The development of a vaccine to induce protective antibodies against HIV-1 is of primary public health importance. Recent advances in immunogen design have provided soluble recombinant envelope glycoprotein trimers with near-native morphology and antigenicity. However, these trimers are conformationally flexible, potentially reducing B-cell recognition of neutralizing antibody epitopes. Here we show that chemical cross-linking increases trimer stability, reducing binding of nonneutralizing antibodies while largely maintaining neutralizing antibody binding. Cross-linking followed by positive or negative antibody affinity selection of individual stable conformational variants further improved the antigenic and morphological characteristics of the trimers. This approach may be generally applicable to HIV-1 Env and also to other conformationally flexible pathogen antigens.
Knockout of the Host Resistance Gene
Pkr
Fully Restores Replication of Murine Cytomegalovirus m142 and m143 Mutants
In Vivo
Authors: Ostermann Eleonore , Warnecke Gabriele , Waibler Zoe , Brune Wolfram 
Published: October 2015

ABSTRACT

Murine cytomegalovirus (MCMV) proteins m142 and m143 are essential for viral replication. They bind double-stranded RNA and prevent protein kinase R-induced protein synthesis shutoff. Whether the two viral proteins have additional functions such as their homologs in human cytomegalovirus do remained unknown. We show that MCMV m142 and m143 knockout mutants attain organ titers equivalent to those attained by wild-type MCMV in
Pkr
knockout mice, suggesting that these viral proteins do not encode additional PKR-independent functions relevant for pathogenesis
in vivo
.
Fluid Spatial Dynamics of West Nile Virus in the United States: Rapid Spread in a Permissive Host Environment
Authors: Di Giallonardo Francesca , Geoghegan Jemma L. , Docherty Douglas E. , McLean Robert G. , Zody Michael C. , Qu James , Yang Xiao , Birren Bruce W. , Malboeuf Christine M. , Newman Ruchi M. , Ip Hon S. , Holmes Edward C. 
Published: October 2015

ABSTRACT
The introduction of West Nile virus (WNV) into North America in 1999 is a classic example of viral emergence in a new environment, with its subsequent dispersion across the continent having a major impact on local bird populations. Despite the importance of this epizootic, the pattern, dynamics, and determinants of WNV spread in its natural hosts remain uncertain. In particular, it is unclear whether the virus encountered major barriers to transmission, or spread in an unconstrained manner, and if specific viral lineages were favored over others indicative of intrinsic differences in fitness. To address these key questions in WNV evolution and ecology, we sequenced the complete genomes of approximately 300 avian isolates sampled across the United States between 2001 and 2012. Phylogenetic analysis revealed a relatively star-like tree structure, indicative of explosive viral spread in the United States, although with some replacement of viral genotypes through time. These data are striking in that viral sequences exhibit relatively limited clustering according to geographic region, particularly for those viruses sampled from birds, and no strong phylogenetic association with well-sampled avian species. The genome sequence data analyzed here also contain relatively little evidence for adaptive evolution, particularly of structural proteins, suggesting that most viral lineages are of similar fitness and that WNV is well adapted to the ecology of mosquito vectors and diverse avian hosts in the United States. In sum, the molecular evolution of WNV in North America depicts a largely unfettered expansion within a permissive host and geographic population with little evidence of major adaptive barriers.

IMPORTANCE
How viruses spread in new host and geographic environments is central to understanding the emergence and evolution of novel infectious diseases and for predicting their likely impact. The emergence of the vector-borne West Nile virus (WNV) in North America in 1999 represents a classic example of this process. Using approximately 300 new viral genomes sampled from wild birds, we show that WNV experienced an explosive spread with little geographical or host constraints within birds and relatively low levels of adaptive evolution. From its introduction into the state of New York, WNV spread across the United States, reaching California and Florida within 4 years, a migration that is clearly reflected in our genomic sequence data, and with a general absence of distinct geographical clusters of bird viruses. However, some geographically distinct viral lineages were found to circulate in mosquitoes, likely reflecting their limited long-distance movement compared to avian species.
Structure and Function of the N-Terminal Domain of the Vesicular Stomatitis Virus RNA Polymerase
Authors: Qiu Shihong , Ogino Minako , Luo Ming , Ogino Tomoaki , Green Todd J. 
Published: October 2015

ABSTRACT

Viruses have various mechanisms to duplicate their genomes and produce virus-specific mRNAs. Negative-strand RNA viruses encode their own polymerases to perform each of these processes. For the nonsegmented negative-strand RNA viruses, the polymerase is comprised of the large polymerase subunit (L) and the phosphoprotein (P). L proteins from members of the
Rhabdoviridae
,
Paramyxoviridae
, and
Filoviridae
share sequence and predicted secondary structure homology. Here, we present the structure of the N-terminal domain (conserved region I) of the L protein from a rhabdovirus, vesicular stomatitis virus, at 1.8-Å resolution. The strictly and strongly conserved residues in this domain cluster in a single area of the protein. Serial mutation of these residues shows that many of the amino acids are essential for viral transcription but not for mRNA capping. Three-dimensional alignments show that this domain shares structural homology with polymerases from other viral families, including segmented negative-strand RNA and double-stranded RNA (dsRNA) viruses.

IMPORTANCE
Negative-strand RNA viruses include a diverse set of viral families that infect animals and plants, causing serious illness and economic impact. The members of this group of viruses share a set of functionally conserved proteins that are essential to their replication cycle. Among this set of proteins is the viral polymerase, which performs a unique set of reactions to produce genome- and subgenome-length RNA transcripts. In this article, we study the polymerase of vesicular stomatitis virus, a member of the rhabdoviruses, which has served in the past as a model to study negative-strand RNA virus replication. We have identified a site in the N-terminal domain of the polymerase that is essential to viral transcription and that shares sequence homology with members of the paramyxoviruses and the filoviruses. Newly identified sites such as that described here could prove to be useful targets in the design of new therapeutics against negative-strand RNA viruses.
Identification of Positively Charged Residues in Enterovirus 71 Capsid Protein VP1 Essential for Production of Infectious Particles
Authors: Yuan Shilin , Li Guiming , Wang Ying , Gao Qianqian , Wang Yizhuo , Cui Rui , Altmeyer Ralf , Zou Gang 
Published: October 2015

ABSTRACT
Enterovirus 71 (EV71), a positive-stranded RNA virus, is the major cause of hand, foot, and mouth disease (HFMD) in children, which can cause severe central nervous system disease and death. The capsids of EV71 consist of 60 copies of each of four viral structural proteins (VP1 to VP4), with VP1, VP2, and VP3 exposed on the surface and VP4 arranged internally. VP1 plays a central role in particle assembly and cell entry. To gain insight into the role of positively charged residues in VP1 function in these processes, a charged-to-alanine scanning analysis was performed using an infectious cDNA clone of EV71. Twenty-seven mutants containing single charged-to-alanine changes were tested. Sixteen of them were not viable, seven mutants were replication defective, and the remaining four mutants were replication competent. By selecting revertants, second-site mutations which could at least partially restore viral infectivity were identified within VP1 for four defective mutations and two lethal mutations. The resulting residue pairs represent a network of intra- and intermolecular interactions of the VP1 protein which could serve as a potential novel drug target. Interestingly, mutation K215A in the VP1 GH loop led to a significant increase in thermal stability, demonstrating that conditional thermostable mutants can be generated by altering the charge characteristics of VP1. Moreover, all mutants were sensitive to the EV71 entry inhibitor suramin, which binds to the virus particle via the negatively charged naphthalenetrisulfonic acid group, suggesting that single charged-to-alanine mutation is not sufficient for suramin resistance. Taken together, these data highlight the importance of positively charged residues in VP1 for production of infectious particles.

IMPORTANCE
Infection with EV71 is more often associated with neurological complications in children and is responsible for the majority of fatalities. No licensed vaccines or antiviral therapies are currently available for the prevention or treatment of EV71 infection. Understanding the determinants of virion assembly and entry will facilitate vaccine development and drug discovery. Here, we identified 23 out of 27 positively charged residues in VP1 which impaired or blocked the production of infectious particles. The defect could be rescued by second-site mutations within the VP1 protein. Our findings highlight the importance of positively charged residues in VP1 during infectious particle production and reveal a potential strategy for blocking EV71 infections by inhibiting intra- or intermolecular interactions of the VP1 protein.
The
Bacillus anthracis
Exosporium: What’s the Big “Hairy” Deal?
Authors: Bozue Joel A. , Welkos Susan , Cote Christopher K. 
Published: October 2015

ABSTRACT

In some
Bacillus
species, including
Bacillus subtilis
, the coat is the outermost layer of the spore. In others, such as the
Bacillus cereus
family, there is an additional layer that envelops the coat, called the exosporium. In the case of
Bacillus anthracis
, a series of fine hair-like projections, also referred to as a “hairy” nap, extends from the exosporium basal layer. The exact role of the exosporium in
B. anthracis
, or for any of the
Bacillus
species possessing this structure, remains unclear. However, it has been assumed that the exosporium would play some role in infection for
B. anthracis
, because it is the outermost structure of the spore and would make initial contact with host and immune cells during infection. Therefore, the exosporium has been a topic of great interest, and over the past decade much progress has been made to understand its composition, biosynthesis, and potential roles. Several key aspects of this spore structure, however, are still debated and remain undetermined. Although insights have been gained on the interaction of exosporium with the host during infection, the exact role and significance of this complex structure remain to be determined. Furthermore, because the exosporium is a highly antigenic structure, future strategies for the next-generation anthrax vaccine should pursue its inclusion as a component to provide protection against the spore itself during the initial stages of anthrax.
Determinants of childhood morbidity in Bangladesh: evidence from the Demographic and Health Survey 2011
Authors: Kamal Md Moustafa , Hasan Md Masud , Davey Rachel 
Published: October 2015

ObjectivesThe present study aims to estimate the incidence of preventable infectious diseases or associated symptoms among young children in Bangladesh and also determine the factors affecting these conditions. The study hypothesised that various background characteristics of children as well as their parents influence the incidence of morbidity of children aged below 5 years.SettingThe study used data from the most recent nationally representative cross-sectional Bangladesh Demographic and Health Survey (BDHS) conducted in 2011.ParticipantsA total of 7550 children aged below 5 years during the survey from mothers aged between 12 and 49 years are the participants of the study.ResultsIn general, younger children were more likely to suffer from multiple health conditions than their older counterparts. Children belonging to households classified as poor (OR=1.425, 95% CI (1.130 to 1.796)) or middle (OR=1.349, 95% CI (1.113 to 1.636)) faced greater risk of illness than those from well-off households. A combination of source and treatment practices of drinking water showed a significant impact on incidence of childhood morbidity. Children from households using untreated non-piped water were 85.8% (OR=1.860, 95% CI (1.269 to 2.728)) more likely to suffer from comorbidity than those who treat their piped drinking water. However, we observed that water treatment alone has no impact unless the water itself was sourced from a pipe.ConclusionsAccelerated programmes promoting access to safe drinking water along with water treatment practices, and better household environment may prove effective in reducing the incidence of childhood morbidity in Bangladesh.
Identifying low-value clinical practices in critical care medicine: protocol for a scoping review
Authors: Niven Daniel J , McCormick T Jared , Straus Sharon E , Hemmelgarn Brenda R , Jeffs Lianne P , Stelfox Henry T 
Published: October 2015

IntroductionReducing unnecessary, low-value clinical practice (ie, de-adoption) is key to improving value for money in healthcare, especially among patients admitted to intensive care units (ICUs) where resource consumption exceeds other medical and surgical populations. Research suggests that low-value clinical practices are common in medicine, however systematically and objectively identifying them is a widely cited barrier to de-adoption. We will conduct a scoping review to identify low-value clinical practices in adult critical care medicine that are candidates for de-adoption.Methods and analysisWe will systematically search the literature to identify all randomised controlled trials or systematic reviews that focus on diagnostic or therapeutic interventions in adult patients admitted to medical, surgical or specialty ICUs, and are published in 3 general medical journals with the highest impact factor (New England Journal of Medicine,The Lancet,Journal of the American Medical Association). 2 investigators will independently screen abstracts and full-text articles against inclusion criteria, and extract data from included citations. Included citations will be classified according to whether or not they represent a repeat examination of the given research question (ie, replication research), and whether the results are similar or contradictory to the original study. Studies with contradictory results will determine clinical practices that are candidates for de-adoption.Ethics and disseminationOur scoping review will use robust methodology to systematically identify a list of clinical practices in adult critical care medicine with evidence supporting their de-adoption. In addition to adding to advancing the study of de-adoption, this review may also serve as the launching point for clinicians and researchers in critical care to begin reducing the number of low-value clinical practices. Dissemination of these results to relevant stakeholders will include tailored presentations at local, national and international meetings, and publication of a manuscript. Ethical approval is not required for this study.
Chronic fatigue syndrome (CFS) or myalgic encephalomyelitis (ME) is different in children compared to in adults: a study of UK and Dutch clinical cohorts
Authors: Collin Simon M , Nuevo Roberto , van de Putte Elise M , Nijhof Sanne L , Crawley Esther 
Published: October 2015

ObjectiveTo investigate differences between young children, adolescents and adults with chronic fatigue syndrome/myalgic encephalomyelitis (CFS/ME).Study designComparison of clinical cohorts from 8 paediatric and 27 adult CFS/ME services in the UK and a paediatric randomised controlled trial from the Netherlands. Outcome measures include: fatigue (the UK—Chalder Fatigue Scale); Disability (the UK—SF-36 physical function subscale; the Netherlands—CHQ-CF87); school attendance, pain, anxiety and depression (the UK—Hospital Anxiety & Depression Scale, Spence Children's Anxiety Scale; the Netherlands—Spielberger State-Trait Anxiety Inventory for Children, Children's Depression Inventory); symptoms; time-to-assessment; and body mass index. We used multinomial regression to compare younger (aged <12 years) and older (aged 12–18 years) children with adults, and logistic regression to compare UK and Dutch adolescents.ResultsYounger children had a more equal gender balance compared to adolescents and adults. Adults had more disability and fatigue, and had been ill for longer. Younger children were less likely to have cognitive symptoms (OR 0.18 (95% CI 0.13 to 0.25)) and more likely to present with a sore throat (OR 1.42 (1.07 to 1.90). Adolescents were more likely to have headaches (81.1%, OR 1.56 (1.36% to 1.80%)) and less likely to have tender lymph nodes, palpitations, dizziness, general malaise and pain, compared to adults. Adolescents were more likely to have comorbid depression (OR 1.51 (1.33 to 1.72)) and less likely to have anxiety (OR 0.46 (0.41 to 0.53)) compared to adults.ConclusionsPaediatricians need to recognise that children with CFS/ME present differently from adults. Whether these differences reflect an underlying aetiopathology requires further investigation.Trial registration numbersFITNET trial registration numbers areISRCTN59878666andNCT00893438. This paper includes secondary (post-results) analysis of data from this trial, but are unrelated to trial outcomes.
The incremental value of stress testing in patients with acute chest pain beyond serial cardiac troponin testing
Authors: Aldous Sally , Richards A Mark , Cullen Louise , Pickering John W , Than Martin 
Published: October 2015

ObjectiveIn patients with acute chest pain and normal range cardiac troponin (cTn), accurate risk stratification for acute coronary syndrome is challenging. This study assesses the incremental value of stress testing to identify patients for angiography with a view to revascularisation.MethodsA single-centre observational study recruited patients with acute chest pain in whom serial cTn tests were negative and stress testing (exercise tolerance testing/dobutamine stress echocardiography) was performed. Stress tests were reported as negative, non-diagnostic or positive. The primary outcomes were revascularisation on index admission, or cardiac death and myocardial infarction over 1 year follow-up.ResultsOf 749 patients recruited, 709 underwent exercise tolerance testing and 40 dobutamine stress echo of which 548 (73.2%) were negative, 169 (22.6%) were non-diagnostic and 32 (4.3%) were positive. Patients with positive tests (n=19 (59.4%)) were more likely to undergo index admission revascularisation than patients with non-diagnostic (n=15 (8.9%)) (p<0.001) tests who in turn were more likely undergo index admission revascularisation than those with negative tests (n=2 (0.4%)) (p<0.001). The risks of adverse events including cardiovascular death/acute myocardial infarction were low and were similar across stress test outcomes.ConclusionsThe incremental value of stress testing was the identification of an additional 34 (4.5% (95% CI 3.0% to 6.0%)) patients who underwent index admission revascularisation with a view to preventing future adverse events. Uncertainty in whether revascularisation prevents adverse events in patients with negative cTn means the choice to undertake stress testing depends on whether clinicians perceive value in identifying 4.5% of these patients for revascularisation.Clinical trial registrationsACTRN1260900028327, ACTRN12611001069943.
Wealth and mortality at older ages: a prospective cohort study
Authors: Demakakos Panayotes , Biddulph Jane P , Bobak Martin , Marmot Michael G 
Published: October 2015

BackgroundDespite the importance of socioeconomic position for survival, total wealth, which is a measure of accumulation of assets over the life course, has been underinvestigated as a predictor of mortality. We investigated the association between total wealth and mortality at older ages.MethodsWe estimated Cox proportional hazards models using a sample of 10 305 community-dwelling individuals aged ≥50 years from the English Longitudinal Study of Ageing.Results2401 deaths were observed over a mean follow-up of 9.4 years. Among participants aged 50–64 years, the fully adjusted HRs for mortality were 1.21 (95% CI 0.92 to 1.59) and 1.77 (1.35 to 2.33) for those in the intermediate and lowest wealth tertiles, respectively, compared with those in the highest wealth tertile. The respective HRs were 2.54 (1.27 to 5.09) and 3.73 (1.86 to 7.45) for cardiovascular mortality and 1.36 (0.76 to 2.42) and 2.53 (1.45 to 4.41) for other non-cancer mortality. Wealth was not associated with cancer mortality in the fully adjusted model. Similar but less strong associations were observed among participants aged ≥65 years. The use of repeated measurements of wealth and covariates brought about only minor changes, except for the association between wealth and cardiovascular mortality, which became less strong in the younger participants. Wealth explained the associations between paternal occupation at age 14 years, education, occupational class, and income and mortality.ConclusionsThere are persisting wealth inequalities in mortality at older ages, which only partially are explained by established risk factors. Wealth appears to be more strongly associated with mortality than other socioeconomic position measures.