bluuebunny/crossref_metadata_2025_split huggingface dataset:
Differential Control of BST2 Restriction and Plasmacytoid Dendritic Cell Antiviral Response by Antagonists Encoded by HIV-1 Group M and O Strains
Authors: Bego Mariana G. , Cong Lijun , Mack Katharina , Kirchhoff Frank , Cohen Éric A. 
Published: September 2016

ABSTRACT
BST2/tetherin is a type I interferon (IFN-I)-stimulated host factor that restricts the release of HIV-1 by entrapping budding virions at the cell surface. This membrane-associated protein can also engage and activate the plasmacytoid dendritic cell (pDC)-specific immunoglobulin-like transcript 7 (ILT7) inhibitory receptor to downregulate the IFN-I response by pDCs. Pandemic HIV-1 group M uses Vpu (M-Vpu) to counteract the two BST2 isoforms (long and short) that are expressed in human cells. M-Vpu efficiently downregulates surface long BST2, while it displaces short BST2 molecules away from viral assembly sites. We recently found that this attribute is used by M-Vpu to activate the BST2/ILT7-dependent negative-feedback pathway and to suppress pDC IFN-I responses during sensing of infected cells. However, whether this property is conserved in endemic HIV-1 group O, which has evolved Nef (O-Nef) to counteract specifically the long BST2 isoform, remains unknown. In the present study, we validated that O-Nefs have the capacity to downregulate surface BST2 and enhance HIV-1 particle release although less efficiently than M-Vpu. In contrast to M-Vpu, O-Nef did not efficiently enhance viral spread in T cell culture or displace short BST2 from viral assembly sites to prevent its occlusion by tethered HIV-1 particles. Consequently, O-Nef impairs the ability of BST2 to activate negative ILT7 signaling to suppress the IFN-I response by pDC-containing peripheral blood mononuclear cells (PBMCs) during sensing of infected cells. These distinctive features of BST2 counteraction by O-Nefs may in part explain the limited spread of HIV-1 group O in the human population.

IMPORTANCE
The geographical distributions and prevalences of different HIV-1 groups show large variations. Understanding drivers of distinctive viral spread may aid in the development of therapeutic strategies for controlling the spread of HIV-1 pandemic strains. The differential spread of HIV-1 groups appears to be linked to their capacities to antagonize the long and short isoforms of the BST2 restriction factor. We found that the endemic HIV-1 group O-encoded BST2 antagonist Nef is unable to counteract the restriction mediated by short BST2, a condition that impairs its ability to activate ILT7 and suppress pDC antiviral responses. This is in contrast to the pandemic HIV-1 group M-specified BST2 countermeasure Vpu, which displays a diverse array of mechanisms to counteract short and long BST2 isoforms, an attribute that allows the effective control of pDC antiviral responses. These findings may help explain the limited spread of HIV-1 group O as well as the continued predominance of HIV-1 group M throughout the world.
Efficiency in Complexity: Composition and Dynamic Nature of Mimivirus Replication Factories
Authors: Fridmann-Sirkis Yael , Milrot Elad , Mutsafi Yael , Ben-Dor Shifra , Levin Yishai , Savidor Alon , Kartvelishvily Elena , Minsky Abraham 
Published: September 2016

ABSTRACT
The recent discovery of multiple giant double-stranded DNA (dsDNA) viruses blurred the consensual distinction between viruses and cells due to their size, as well as to their structural and genetic complexity. A dramatic feature revealed by these viruses as well as by many positive-strand RNA viruses is their ability to rapidly form elaborate intracellular organelles, termed “viral factories,” where viral progeny are continuously generated. Here we report the first isolation of viral factories at progressive postinfection time points. The isolated factories were subjected to mass spectrometry-based proteomics, bioinformatics, and imaging analyses. These analyses revealed that numerous viral proteins are present in the factories but not in mature virions, thus implying that multiple and diverse proteins are required to promote the efficiency of viral factories as “production lines” of viral progeny. Moreover, our results highlight the dynamic and highly complex nature of viral factories, provide new and general insights into viral infection, and substantiate the intriguing notion that viral factories may represent the living state of viruses.

IMPORTANCE
Large dsDNA viruses such as vaccinia virus and the giant mimivirus, as well as many positive-strand RNA viruses, generate elaborate cytoplasmic organelles in which the multiple and diverse transactions required for viral replication and assembly occur. These organelles, which were termed “viral factories,” are attracting much interest due to the increasing realization that the rapid and continuous production of viral progeny is a direct outcome of the elaborate structure and composition of the factories, which act as efficient production lines. To get new insights into the nature and function of viral factories, we devised a method that allows, for the first time, the isolation of these organelles. Analyses of the isolated factories generated at different times postinfection by mass spectrometry-based proteomics provide new perceptions of their role and reveal the highly dynamic nature of these organelles.
Plasmodium Helical Interspersed Subtelomeric (PHIST) Proteins, at the Center of Host Cell Remodeling
Authors: Warncke Jan D. , Vakonakis Ioannis , Beck Hans-Peter 
Published: September 2016

SUMMARY

During the asexual cycle,
Plasmodium falciparum
extensively remodels the human erythrocyte to make it a suitable host cell. A large number of exported proteins facilitate this remodeling process, which causes erythrocytes to become more rigid, cytoadherent, and permeable for nutrients and metabolic products. Among the exported proteins, a family of 89 proteins, called the
Plasmodium
helical interspersed subtelomeric (PHIST) protein family, has been identified. While also found in other
Plasmodium
species, the PHIST family is greatly expanded in
P. falciparum
. Although a decade has passed since their first description, to date, most PHIST proteins remain uncharacterized and are of unknown function and localization within the host cell, and there are few data on their interactions with other host or parasite proteins. However, over the past few years, PHIST proteins have been mentioned in the literature at an increasing rate owing to their presence at various localizations within the infected erythrocyte. Expression of PHIST proteins has been implicated in molecular and cellular processes such as the surface display of PfEMP1, gametocytogenesis, changes in cell rigidity, and also cerebral and pregnancy-associated malaria. Thus, we conclude that PHIST proteins are central to host cell remodeling, but despite their obvious importance in pathology, PHIST proteins seem to be understudied. Here we review current knowledge, shed light on the definition of PHIST proteins, and discuss these proteins with respect to their localization and probable function. We take into consideration interaction studies, microarray analyses, or data from blood samples from naturally infected patients to combine all available information on this protein family.
The mechanism of partial rupture of a locked megathrust: The role of fault morphology
Authors: Qiu Qiang , Hill Emma M. , Barbot Sylvain , Hubbard Judith , Feng Wanpeng , Lindsey Eric O. , Feng Lujia , Dai Keren , Samsonov Sergey V. , Tapponnier Paul 
Published: September 2016

Abstract
Assessment of seismic hazard relies on estimates of how large an area of a tectonic fault could potentially rupture in a single earthquake. Vital information for these forecasts includes which areas of a fault are locked and how the fault is segmented. Much research has focused on exploring downdip limits to fault rupture from chemical and thermal boundaries, and along-strike barriers from subducted structural features, yet we regularly see only partial rupture of fully locked fault patches that could have ruptured as a whole in a larger earthquake. Here we draw insight into this conundrum from the 25 April 2015 Mw 7.8 Gorkha (Nepal) earthquake. We invert geodetic data with a structural model of the Main Himalayan thrust in the region of Kathmandu, Nepal, showing that this event was generated by rupture of a décollement bounded on all sides by more steeply dipping ramps. The morphological bounds explain why the event ruptured only a small piece of a large fully locked seismic gap. We then use dynamic earthquake cycle modeling on the same fault geometry to reveal that such events are predicted by the physics. Depending on the earthquake history and the details of rupture dynamics, however, great earthquakes that rupture the entire seismogenic zone are also possible. These insights from Nepal should be applicable to understanding bounds on earthquake size on megathrusts worldwide.
Detecting magma-poor orogens in the detrital record
Authors: O’Sullivan G.J. , Chew D.M. , Samson S.D. 
Published: September 2016

Abstract
The clastic record is commonly interrogated by analysis of detrital heavy mineral assemblages, with the bulk of modern detrital geochronological studies employing U-Pb dating of detrital zircon. However, the bias of zircon toward felsic igneous sources, and the limited ability of the U-Pb system in zircon to record low- to medium-grade metamorphic events, means that the U-Pb detrital zircon record is largely insensitive to magma-poor orogens. In this study, U-Pb ages were obtained by laser ablation–inductively coupled plasma–mass spectrometry for apatite and rutile extracted from alluvium of the French Broad River (FBR) in the southern Appalachians (southeastern United States). In contrast to previously published FBR U-Pb zircon data sets, which yield essentially no record of the most recent Appalachian metamorphic events (ca. 320 Ma) associated with assembly of Pangea, the U-Pb detrital rutile and especially the U-Pb apatite systems together provide a complete record of complex polyphase Appalachian orogenesis. It is unexpected that the apatite and rutile U-Pb Appalachian age populations differ significantly, with probable low-temperature breakdown of rutile biasing the rutile data set toward the most recent (Alleghanian) metamorphic event. These data make the FBR one of the most intensely studied river systems globally for multiproxy single-grain U-Pb analysis, clearly demonstrate dependence of provenance information on mineral proxy choice, and emphasize the resolving power of multiproxy provenance studies.
Experimental evidence that clay inhibits bacterial decomposers: Implications for preservation of organic fossils
Authors: McMahon Sean , Anderson Ross P. , Saupe Erin E. , Briggs Derek E. G. 
Published: September 2016

Abstract
Exceptionally preserved organic fossils are commonly associated with clay-rich horizons or directly with clay minerals. It has been posited that interactions between clay minerals and organic tissues inhibit enzymatic reactions or protect carcasses in such a way that decay is impeded. However, interactions between clay minerals and the biological agents of decay, especially bacteria, may be at least as important to preservation potential. Here we show that clays of particle size &lt;2 μm in suspensions exceeding 10 mg/ml in concentration inhibit the growth of Pseudoalteromonas luteoviolacea, a marine heterotrophic bacterium involved in the decay of marine animals. Such clay-microbe interactions can contribute to exceptional preservation, and specific examples may play a role in shaping the distribution of Konservat-Lagerstätten through time.
Does physical activity moderate the association between alcohol drinking and all-cause, cancer and cardiovascular diseases mortality? A pooled analysis of eight British population cohorts
Authors: Perreault K , Bauman A , Johnson N , Britton A , Rangul V , Stamatakis E 
Published: September 2016

ObjectiveTo examine whether physical activity (PA) moderates the association between alcohol intake and all-cause mortality, cancer mortality and cardiovascular diseases (CVDs) mortality.DesignProspective study using 8 British population-based surveys, each linked to cause-specific mortality: Health Survey for England (1994, 1998, 1999, 2003, 2004 and 2006) and Scottish Health Survey (1998 and 2003).Participants36 370 men and women aged 40 years and over were included with a corresponding 5735 deaths and a mean of 353 049 person-years of follow-up.Exposures6 sex-specific categories of alcohol intake (UK units/week) were defined: (1) never drunk; (2) ex-drinkers; (3) occasional drinkers; (4) within guidelines (<14 (women); <21 (men)); (5) hazardous (14–35 (women); 21–49 (men)) and (6) harmful (>35 (women) >49 (men)). PA was categorised as inactive (≤7 MET-hour/week), active at the lower (>7.5 MET-hour/week) and upper (>15 MET-hour/week) of recommended levels.Main outcomes and measuresCox proportional-hazard models were used to examine associations between alcohol consumption and all-cause, cancer and CVD mortality risk after adjusting for several confounders. Stratified analyses were performed to evaluate mortality risks within each PA stratum.ResultsWe found a direct association between alcohol consumption and cancer mortality risk starting from drinking within guidelines (HR (95% CI) hazardous drinking: 1.40 (1.11 to 1.78)). Stratified analyses showed that the association between alcohol intake and mortality risk was attenuated (all-cause) or nearly nullified (cancer) among individuals who met the PA recommendations (HR (95% CI)).ConclusionsMeeting the current PA public health recommendations offsets some of the cancer and all-cause mortality risk associated with alcohol drinking.
Association of Mediterranean diet and cardiorespiratory fitness with the development of pre-diabetes and diabetes: the Coronary Artery Risk Development in Young Adults (CARDIA) study
Authors: Bantle Anne E , Chow Lisa S , Steffen Lyn M , Wang Qi , Hughes John , Durant Nefertiti H , Ingram Katherine H , Reis Jared P , Schreiner Pamela J 
Published: September 2016

ObjectiveTo better understand the association between a modified Mediterranean diet pattern in young adulthood, cardiorespiratory fitness in young adulthood, and the odds of developing pre-diabetes or diabetes by middle age.Research design and methodsParticipants from the Coronary Artery Risk Development in Young Adults (CARDIA) study who did not have pre-diabetes or diabetes at baseline (year 0 (Y0), ages 18–30) and who had data available at the Y0 and year 25 (Y25) visits were included in this analysis (n=3358). Polytomous logistic regression models were used to assess the association between baseline dietary intake and fitness data and odds of pre-diabetes or diabetes by middle age (Y25, ages 43–55).ResultsAt the Y25 visit, 1319 participants (39%) had pre-diabetes and 393 (12%) had diabetes. Higher baseline fitness was associated with lower odds of pre-diabetes and of diabetes at Y25. After adjustment for covariates, each SD increment in treadmill duration (181 s) was associated with lower odds for pre-diabetes (OR 0.85, 95% CI 0.75 to 0.95, p=0.005) and for diabetes (OR 0.71, 95% CI 0.60 to 0.85, p=0.0002) when compared to normal glycemia. A modified Mediterranean diet pattern was not associated with either pre-diabetes or diabetes. No interaction between cardiorespiratory fitness and dietary intake was observed, but baseline fitness remained independently associated with incident pre-diabetes and diabetes following adjustment for diet.ConclusionsHigher cardiorespiratory fitness in young adulthood, but not a modified Mediterranean diet pattern, is associated with lower odds of pre-diabetes and of diabetes in middle age.Trial registration numberNCT00005130.
Investigating the epidemiology of medication errors and error-related adverse drug events (ADEs) in primary care, ambulatory care and home settings: a systematic review protocol
Authors: Assiri Ghadah Asaad , Grant Liz , Aljadhey Hisham , Sheikh Aziz 
Published: September 2016

IntroductionThere is a need to better understand the epidemiology of medication errors and error-related adverse events in community care contexts.Methods and analysisWe will systematically search the following databases: Cumulative Index to Nursing and Allied Health Literature (CINAHL), EMBASE, Eastern Mediterranean Regional Office of the WHO (EMRO), MEDLINE, PsycINFO and Web of Science. In addition, we will search Google Scholar and contact an international panel of experts to search for unpublished and in progress work. The searches will cover the time period January 1990–December 2015 and will yield data on the incidence or prevalence of and risk factors for medication errors and error-related adverse drug events in adults living in community settings (ie, primary care, ambulatory and home). Study quality will be assessed using the Critical Appraisal Skills Program quality assessment tool for cohort and case–control studies, and cross-sectional studies will be assessed using the Joanna Briggs Institute Critical Appraisal Checklist for Descriptive Studies. Meta-analyses will be undertaken using random-effects modelling using STATA (V.14) statistical software.Ethics and disseminationThis protocol will be registered with PROSPERO, an international prospective register of systematic reviews, and the systematic review will be reported in the peer-reviewed literature using Preferred Reporting Items for Systematic Reviews and Meta-Analyses.
Social facilitation maintenance treatment for adults with obesity: study protocol for a randomised-controlled feasibility study (SFM study)
Authors: Hilbert Anja 
Published: September 2016

IntroductionThe long-term success of non-surgical weight loss treatment in adults with obesity is limited by substantial relapse, and only a few evidence-based weight loss maintenance treatments exist. This clinical trial investigates the feasibility and efficacy of a social facilitation maintenance programme for weight loss maintenance, tailored to meet the needs of obese adults who have undergone a lifestyle weight loss intervention.Methods and analysisIn a single-centre, open feasibility trial, 72 adults currently or previously obese or overweight who have undergone a lifestyle weight loss intervention are centrally randomised to 4 months of social facilitation maintenance treatment or treatment as a usual control condition. In 16 outpatient group sessions, the social facilitation maintenance treatment, based on a socioecological model and on evidence supporting social facilitation as a key process in maintaining weight loss, focuses on promoting interpersonal relationships to build up a healthy lifestyle for long-term weight loss maintenance. Primary outcome is the amount of weight regain at 6-month follow-up, compared with pre-treatment weight, derived from measured body weight. Secondary outcomes address feasibility, including recruitment, attrition, assessment non-completion, compliance and patients' programme evaluation; and in comparison with pre-weight loss maintenance, social and interpersonal functioning, eating behaviour and physical activity, psychological and physical symptoms, body composition and risk of comorbidity, and quality of life at post-treatment and follow-up assessments.Ethics and disseminationThe study was approved by the Ethical Committee at the University of Leipzig (165-13-15072013). The study results will be disseminated through peer-reviewed publications.Trial registration numberDRKS00005182.
Psychological impact and recovery after involvement in a patient safety incident: a repeated measures analysis
Authors: Van Gerven Eva , Bruyneel Luk , Panella Massimiliano , Euwema Martin , Sermeus Walter , Vanhaecht Kris 
Published: September 2016

ObjectiveTo examine individual, situational and organisational aspects that influence psychological impact and recovery of a patient safety incident on physicians, nurses and midwives.DesignCross-sectional, retrospective surveys of physicians, midwives and nurses.Setting33 Belgian hospitals.Participants913 clinicians (186 physicians, 682 nurses, 45 midwives) involved in a patient safety incident.Main outcome measuresThe Impact of Event Scale was used to retrospectively measure psychological impact of the safety incident at the time of the event and compare it with psychological impact at the time of the survey.ResultsIndividual, situational as well as organisational aspects influenced psychological impact and recovery of a patient safety incident. Psychological impact is higher when the degree of harm for the patient is more severe, when healthcare professionals feel responsible for the incident and among female healthcare professionals. Impact of degree of harm differed across clinicians. Psychological impact is lower among more optimistic professionals. Overall, impact decreased significantly over time. This effect was more pronounced for women and for those who feel responsible for the incident. The longer ago the incident took place, the stronger impact had decreased. Also, higher psychological impact is related with the use of a more active coping and planning coping strategy, and is unrelated to support seeking coping strategies. Rendered support and a support culture reduce psychological impact, whereas a blame culture increases psychological impact. No associations were found with job experience and resilience of the health professional, the presence of a second victim support team or guideline and working in a learning culture.ConclusionsHealthcare organisations should anticipate on providing their staff appropriate and timely support structures that are tailored to the healthcare professional involved in the incident and to the specific situation of the incident.
Can an ethics officer role reduce delays in research ethics approval? A mixed-method evaluation of an improvement project
Authors: Dixon-Woods Mary , Foy Chris , Hayden Charlotte , Al-Shahi Salman Rustam , Tebbutt Stephen , Schroter Sara 
Published: September 2016

ObjectiveFrustration continues to be directed at delays in gaining approvals for undertaking health research in the UK. We aimed to evaluate the impact of an ethics officer intervention on rates of favourable opinions (approval) and provisional opinions (requiring revision and resubmission) and on the time taken to reach a final opinion by research ethics committees (RECs), to characterise how the role operated in practice, and to investigate applicants' views.DesignMixed-method study involving (i) a 2-group, non-randomised before-and-after intervention study of RECs assigned an ethics officer and a matched comparator group; (ii) a process evaluation involving a survey of applicants and documentary analysis.Participants6 RECs and 3 associated ethics officers; 18 comparator RECs; REC applicants.ResultsRates of provisional and favourable opinions between ethics officer and comparator RECs did not show a statistically significant effect of the intervention (logistic regression, p=0.26 for favourable opinions and p=0.31 for provisional opinions). Mean time to reach a decision showed a non-significant reduction (ANOVA, p=0.22) from 33.3 to 32.0 days in the ethics officer RECs compared with the comparator RECs (32.6 to 32.9 days). The survey (30% response rate) indicated applicant satisfaction and also suggested that ethics officer support might be more useful before submission. Ethics officers were successful in identifying many issues with applications, but the intervention did not function exactly as designed: in 31% of applicants, no contact between the applicants and the ethics officer took place before REC review.LimitationsThis study was a non-randomised comparison cohort study. Some data were missing.ConclusionsAn ethics officer intervention, as designed and implemented in this study, did not increase the proportion of applications to RECs that were approved on first review and did not reduce the time to a committee decision.