bluuebunny/crossref_metadata_2025_split huggingface dataset:
Draft Genome Sequence of “
Candidatus
Bacteroides periocalifornicus,” a New Member of the
Bacteriodetes
Phylum Found within the Oral Microbiome of Periodontitis Patients
Authors: McLean Jeffrey S. , Liu Quanhui , Thompson John , Edlund Anna , Kelley Scott 
Published: December 2015

ABSTRACT

Here we present the draft genome of a distantly related member within the phylum
Bacteriodetes
, “
Candidatus
Bacteroides
periocalifornicus
.” The draft genome sequence was assembled with metagenomic data from a patient with periodontitis. The closest relative has less than 68% average nucleic identity, supporting a novel family within
Bacteriodetes
.
Comparison of Multilocus Sequence Typing and the Xpert C. difficile/Epi Assay for Identification of Clostridium difficile 027/NAP1/BI
Authors: McMillen Tracy , Kamboj Mini , Babady N. Esther 
Published: December 2015

ABSTRACT

Clostridium difficile
027/NAP1/BI is the most common
C. difficile
strain in the United States. The Xpert
C. difficile
/Epi assay allows rapid, presumptive identification of
C. difficile
NAP1. We compared Xpert
C. difficile
/Epi to multilocus sequence typing for identification of
C. difficile
NAP1 and found “very good” agreement at 97.9% (κ = 0.86; 95% confidence interval, 0.80 to 0.91).
Dual Role of Herpes Simplex Virus 1 pUS9 in Virus Anterograde Axonal Transport and Final Assembly in Growth Cones in Distal Axons
Authors: Miranda-Saksena Monica , Boadle Ross A. , Diefenbach Russell J. , Cunningham Anthony L. 
Published: December 2015

ABSTRACT

The herpes simplex virus type 1 (HSV-1) envelope protein pUS9 plays an important role in virus anterograde axonal transport and spread from neuronal axons. In this study, we used both confocal microscopy and transmission electron microscopy (TEM) to examine the role of pUS9 in the anterograde transport and assembly of HSV-1 in the distal axon of human and rat dorsal root ganglion (DRG) neurons using US9 deletion (US9
−
), repair (US9R), and wild-type (strain F, 17, and KOS) viruses. Using confocal microscopy and single and trichamber culture systems, we observed a reduction but not complete block in the anterograde axonal transport of capsids to distal axons as well as a marked (∼90%) reduction in virus spread from axons to Vero cells with the US9 deletion viruses. Axonal transport of glycoproteins (gC, gD, and gE) was unaffected. Using TEM, there was a marked reduction or absence of enveloped capsids, in varicosities and growth cones, in KOS strain and US9 deletion viruses, respectively. Capsids (40 to 75%) in varicosities and growth cones infected with strain 17, F, and US9 repair viruses were fully enveloped compared to less than 5% of capsids found in distal axons infected with the KOS strain virus (which also lacks pUS9) and still lower (<2%) with the US9 deletion viruses. Hence, there was a secondary defect in virus assembly in distal axons in the absence of pUS9 despite the presence of key envelope proteins. Overall, our study supports a dual role for pUS9, first in anterograde axonal transport and second in virus assembly in growth cones in distal axons.

IMPORTANCE
HSV-1 has evolved mechanisms for its efficient transport along sensory axons and subsequent spread from axons to epithelial cells after reactivation. In this study, we show that deletion of the envelope protein pUS9 leads to defects in virus transport along axons (partial defect) and in virus assembly and egress from growth cones (marked defect). Virus assembly and exit in the neuronal cell body are not impaired in the absence of pUS9. Thus, our findings indicate that pUS9 contributes to the overall HSV-1 anterograde axonal transport, including a major role in virus assembly at the axon terminus, which is not essential in the neuronal cell body. Overall, our data suggest that the process of virus assembly at the growth cones differs from that in the neuronal cell body and that HSV-1 has evolved different mechanisms for virus assembly and exit from different cellular compartments.
Structural Evolution of the Emerging 2014-2015 GII.17 Noroviruses
Authors: Singh Bishal Kumar , Koromyslova Anna , Hefele Lisa , Gürth Clara , Hansman Grant S. 
Published: December 2015

ABSTRACT
Recent reports suggest that human genogroup II genotype 17 (GII.17) noroviruses are increasing in prevalence. We analyzed the evolutionary changes of three GII.17 capsid protruding (P) domains. We found that the GII.17 P domains had little cross-reactivity with antisera raised against the dominant GII.4 strains. X-ray structural analysis of GII.17 P domains from 2002 to 2014 and 2015 suggested that surface-exposed substitutions on the uppermost part of the P domain might have generated a novel 2014-2015 GII.17 variant.
In children 18 years and under, what promotes recurrent shoulder instability after traumatic anterior shoulder dislocation? A systematic review and meta-analysis of risk factors
Authors: Olds M , Donaldson K , Ellis R , Kersten P 
Published: December 2015

BackgroundSkeletal maturity and age-related changes in the composition of the glenoid labrum and joint capsule may influence rates of recurrent instability in children. We systematically review risk factors which predispose children to recurrent shoulder instability.MethodsThe systematic review-concerned studies published before May 2015. Statistical analysis was undertaken to compare rates of recurrence for each extracted risk factor. Pooled ORs were analysed using random effects meta-analysis.Results6 retrospective cohort studies met the inclusion criteria. 8 risk factors were identified across the studies including age, sex, shoulder dominance and injury side, mechanism of injury, state of physis closure, and Hill-Sachs and Bankart lesions. The rate of recurrent instability was 73%. Children aged 14–18 years were 24 times more likely to experience recurrent instability than children aged 13 years and less (93% vs 40%; OR=24.14, 95% CI (3.71 to 156.99), Z=3.33, p=0.001, I2=6.83%). There was a non-significant trend indicating males were 3.4 times more likely to experience recurrent instability (OR=3.44, 95% CI (0.98 to 12.06), Z=1.93, p=0.053, I2=0%). Analysis of one study found that children with a closed physis are 14 times more likely to experience recurrent instability compared with those with an open physis (OR=14.0, 95% CI (1.46 to 134.25), Z=2.29, p=0.02, I2=0%) .ConclusionsMale children aged 14 years and over had the greatest risk of recurrent shoulder instability following a first-time traumatic anterior shoulder dislocation. This meta-analysis summarises a mix of 6 acceptable and poor quality level III retrospective cohort studies. Further examination of this population with blinded prospective cohort studies will assist clinicians in the appropriate management of first-time traumatic anterior shoulder dislocation.
Clinician-friendly physical performance tests in athletes part 3: a systematic review of measurement properties and correlations to injury for tests in the upper extremity
Authors: Tarara Daniel T , Fogaca Lucas K , Taylor Jeffrey B , Hegedus Eric J 
Published: December 2015

ObjectiveIn parts 1 and 2 of this systematic review, the methodological quality as well as the quality of the measurement properties of physical performance tests (PPTs) of the lower extremity in athletes was assessed. In this study, part 3, PPTs of the upper extremity in athletes are examined.MethodsDatabase and hand searches were conducted to identify primary literature addressing the use of upper extremity PPTs in athletes. The Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines were followed and the Consensus-based Standards for the selection of health Measurement Instruments (COSMIN) checklist was used to critique the methodological quality of each paper. The Terwee Scale was used to analyse the quality of the measurement properties of each test.Results11 articles that examined 6 PPTs were identified. The 6 PPTs were: closed kinetic chain upper extremity stability test (CKCUEST), seated shot put (2 hands), unilateral seated shot put, medicine ball throw, modified push-up test and 1-arm hop test. Best evidence synthesis provided moderate positive evidence for the CKCUEST and unilateral seated shot put. Limited positive evidence was available for the medicine ball throw and 1-arm hop test.ConclusionsThere are a limited number of upper extremity PPTs used as part of musculoskeletal screening examinations, or as outcome measures in athletic populations. The CKCUEST and unilateral seated shot put are 2 promising PPTs based on moderate evidence. However, the utility of the PPTs in injured populations is unsubstantiated in literature and warrants further investigation.
Prevalence and differentials of overweight and obesity in preschool children in Sub-Saharan Africa
Authors: Gebremedhin Samson 
Published: December 2015

ObjectiveTo determine the prevalence and differentials of overweight/obesity (body mass index (BMI)-for-age z-score >2) in preschool children in Sub-Saharan Africa (SSA).DesignCross-sectional study.SettingThe study was conducted on the basis of the data of 26 Demographic and Health Surveys carried out in SSA since 2010.ParticipantsThe records of 155 726 children aged 0–59 months were included in the analysis.Primary outcomeOverweight/obesity.ResultsThe prevalence of overweight/obesity was 6.8% (95% CI 6.7% to 6.9%). Among the countries represented, higher figures were reported in Sierra Leone (16.9%), Comoros (15.9%) and Malawi (14.5%), whereas lower prevalence was found in Ethiopia (3.0%), Togo (2.6) and Senegal (2.0%). In 11 of the countries, overweight/obesity was more prevalent than wasting. It is estimated that in the whole subcontinent, 10.7 million children were affected by the problem. The prevalence of overweight/obesity was slightly higher in boys than in girls. Overweight/obesity was three times more frequent in stunted children than in normal children. The risk also significantly increased with increasing maternal BMI and birth weight and decreased with increasing maternal age, maternal education, child's age and number of siblings. On the other hand, no significant association was observed with national gross domestic product per capita, place of residence (urban–rural) and household wealth index.ConclusionChildhood overweight/obesity has become a sizeable problem in the subcontinent.
An algorithm to identify rheumatoid arthritis in primary care: a Clinical Practice Research Datalink study
Authors: Muller Sara , Hider Samantha L , Raza Karim , Stack Rebecca J , Hayward Richard A , Mallen Christian D 
Published: December 2015

ObjectiveRheumatoid arthritis (RA) is a multisystem, inflammatory disorder associated with increased levels of morbidity and mortality. While much research into the condition is conducted in the secondary care setting, routinely collected primary care databases provide an important source of research data. This study aimed to update an algorithm to define RA that was previously developed and validated in the General Practice Research Database (GPRD).MethodsThe original algorithm consisted of two criteria. Individuals meeting at least one were considered to have RA. Criterion 1: ≥1 RA Read code and a disease modifying antirheumatic drug (DMARD) without an alternative indication. Criterion 2: ≥2 RA Read codes, with at least one ‘strong’ code and no alternative diagnoses. Lists of codes for consultations and prescriptions were obtained from the authors of the original algorithm where these were available, or compiled based on the original description and clinical knowledge. 4161 people with a first Read code for RA between 1 January 2010 and 31 December 2012 were selected from the Clinical Practice Research Datalink (CPRD, successor to the GPRD), and the criteria applied.ResultsCode lists were updated for the introduction of new Read codes and biological DMARDs. 3577/4161 (86%) of people met the updated algorithm for RA, compared to 61% in the original development study. 62.8% of people fulfilled both Criterion 1 and Criterion 2.ConclusionsThose wishing to define RA in the CPRD, should consider using this updated algorithm, rather than a single RA code, if they wish to identify only those who are most likely to have RA.
Dermatological disease in the older age group: a cross-sectional study in aged care facilities
Authors: Deo Maneka S , Kerse Ngaire , Vandal Alain C , Jarrett Paul 
Published: December 2015

ObjectivesTo estimate the prevalence of dermatological disease in aged care facilities, and the relationship between cognitive or physical disability and significant disease.Setting2 large aged care facilities in Auckland, New Zealand, each providing low and high level care.ParticipantsAll 161 residents of the facilities were invited to participate. The only exclusion criterion was inability to obtain consent from the individual or designated guardian. 88 participants were recruited—66 females (75%), 22 males (25%) with average age 87.1 years (SD 5.5 years).Primary and secondary outcome measuresPrimary—presence of significant skin disease (defined as that which in the opinion of the investigators needed treatment or was identified as a patient concern) diagnosed clinically on full dermatological examination by a dermatologist or dermatology trainee.Secondary—functional and cognitive status (Rehabilitation Complexity Scale and Abbreviated Mental Test Score).Results81.8% were found to have at least one significant condition. The most common disorders were onychomycosis 42 (47.7%), basal cell carcinoma 13 (14.8%), asteototic eczema 11 (12.5%) and squamous cell carcinoma in situ 9 (10.2%). Other findings were invasive squamous cell carcinoma 7 (8%), bullous pemphigoid 2 (2.3%), melanoma 2 (2.3%), lichen sclerosus 2 (2.3%) and carcinoma of the breast 1 (1.1%). Inflammatory disease was more common in those with little physical disability compared with those with serious physical disability (OR 3.69; 95% CI 1.1 to 12.6, p=0.04). No significant association was found between skin disease and cognitive impairment.ConclusionsA high rate of dermatological disease was found. Findings ranged from frequent but not life-threatening conditions (eg, onychomycosis), to those associated with a significant morbidity (eg, eczema, lichen sclerosus and bullous pemphigoid), to potentially life-threatening (eg, squamous cell carcinoma, melanoma and breast cancer). Those with less significant physical impairment were found to be at greater risk of inflammatory dermatoses.
Awareness of the severity of liver disease re-examined using software-combined biomarkers of liver fibrosis and necroinflammatory activity
Authors: Poynard Thierry , Deckmyn Olivier , Munteanu Mona , Ngo Yen , Drane Fabienne , Castille Jean Marie , Housset Chantal , Ratziu Vlad 
Published: December 2015

BackgroundEffective antiviral treatment (direct-acting antiviral agents (DAAs)), the requirement for a fibrosis score to support DDA reimbursement and a screening strategy, such as the USA baby boomer campaign, should lead to an increased awareness of liver disease severity.ObjectiveTo compare the awareness of liver disease severity between the USA and France, two countries with similar access to hepatitis C virus (HCV) and hepatitis B virus (HBV) treatments, similar rules for treatment reimbursement and similar availability of validated fibrosis tests, but with different policies, as France has no screening.MethodThe global database of the FibroTest–ActiTest, including 1 085 657 subjects between 2002 and 2014, was retrospectively analysed. Awareness was defined as the test prescription rate and was compared between the USA and France, according to year of birth, gender and dates of DAA availability and screening campaign (2013–2014).ResultsIn the USA 252 688 subjects were investigated for HCV, with a dramatic increase (138%) in the test rate in 2013–2014 (119 271) compared with 2011–2012 (50 031). In France 470 762 subjects were investigated (subjects with HCV and other disease) and the rates were stable. In USA 82.4% of subjects and in France 84.6% were classified as either the highest or lowest priority. The most striking difference was the higher test rate in women born between 1935 and 1944 in France 30 384/200 672 (15.1%) compared with the USA 8035/97 079 (8.3%) (OR=1.98 (95% CI 1.93 to 2.03) p<0.0001). This resulted in twice as many cases of cirrhosis being detected, 2.6% (5191/200 672 women) and 1.3% (1303/97 079), respectively, despite the same prevalence of cirrhosis in this age group (17.1% vs 16.2%) and without any clear explanation as to why they had not been included in the USA screening.ConclusionsThis study highlighted in the USA the association between awareness of liver disease and both the HCV campaign and DAA availability. In comparison with France, there was a dramatically lower awareness of cirrhosis in the USA for women born between 1935 and 1944.
Harms from other people's drinking: an international survey of their occurrence, impacts on feeling safe and legislation relating to their control
Authors: Bellis Mark A , Quigg Zara , Hughes Karen , Ashton Kathryn , Ferris Jason , Winstock Adam 
Published: December 2015

ObjectiveTo examine factors associated with suffering harm from another person's alcohol consumption and explore how suffering such harms relate to feelings of safety in nightlife.DesignCross-sectional opportunistic survey (Global Drug Survey) using an online anonymous questionnaire in 11 languages promoted through newspapers, magazines and social media.SubjectsIndividuals (participating November 2014–January 2015) aged 18–34 years, reporting alcohol consumption in the past 12 months and resident in a country providing ≥250 respondents (n=21 countries; 63 725 respondents).Main outcome measuresHarms suffered due to others’ drinking in the past 12 months, feelings of safety on nights out (on the way out, in bars/pubs, in nightclubs and when travelling home) and knowledge of over-serving laws and their implementation.ResultsIn the past 12 months, >40% of respondents suffered at least one aggressive (physical, verbal or sexual assault) harm and 59.5% any harm caused by someone drunk. Suffering each category of harm was higher in younger respondents and those with more harmful alcohol consumption patterns. Men were more likely than women to have suffered physical assault (9.2% vs 4.7; p<0.001), with women much more likely to suffer sexual assault or harassment (15.3% vs 2.5%; p<0.001). Women were more likely to feel unsafe in all nightlife settings, with 40.8% typically feeling unsafe on the way home. In all settings, feeling unsafe increased with experiencing more categories of aggressive harm by a drunk person. Only 25.7% of respondents resident in countries with restrictions on selling alcohol to drunks knew about such laws and 75.8% believed that drunks usually get served alcohol.ConclusionsHarms from others’ drinking are a threat to people's health and well-being. Public health bodies must ensure that such harms are reflected in measures of the societal costs of alcohol, and must advocate for the enforcement of legislation designed to reduce such harms.
Road traffic injuries to children during the school commute in Hyderabad, India: cross-sectional survey
Authors: Tetali Shailaja , Edwards P , Murthy G V S , Roberts I 
Published: December 2015

BackgroundIndia is motorising rapidly. With increasing motorisation, road traffic injuries are predicted to increase. A third of a billion children travel to school every day in India, but little is known about children's safety during the school commute. We investigated road traffic injury to children during school journeys.MethodsWe conducted a cross-sectional survey in Hyderabad using a two-stage stratified cluster sampling design. We used school travel questionnaires to record any road injury in the past 12 months that resulted in at least 1 day of school missed or required treatment by a doctor or nurse. We estimated the prevalence of road injury by usual mode of travel and distance to school.ResultsThe total sample was 5842 children, of whom 5789 (99.1%) children answered the question on road injury. The overall prevalence of self-reported road injury in the last 12 months during school journeys was 17% (95% CI 12.9% to 21.7%). A higher proportion of boys (25%) reported a road injury than girls (11%). There was a strong association between road injury, travel mode and distance to school. Children who cycled to school were more likely to be injured compared with children who walked (OR 1.5; 95% CI 1.2 to 2.0). Travel by school bus was safer than walking (OR 0.5; 95% CI 0.3 to 0.9).ConclusionsA sixth of the children reported a road traffic injury in the past 12 months during school journeys in Hyderabad. Injury prevention interventions should focus on making walking and cycling safer for children.
CD4 count at antiretroviral therapy initiation and the risk of loss to follow-up: results from a multicentre cohort study
Authors: Grimsrud Anna , Cornell Morna , Schomaker Michael , Fox Matthew P , Orrell Catherine , Prozesky Hans , Stinson Kathryn , Tanser Frank , Egger Matthias , Myer Landon 
Published: December 2015

BackgroundAntiretroviral therapy (ART) initiation is now recommended irrespective of CD4 count. However data on the relationship between CD4 count at ART initiation and loss to follow-up (LTFU) are limited and conflicting.MethodsWe conducted a cohort analysis including all adults initiating ART (2008–2012) at three public sector sites in South Africa. LTFU was defined as no visit in the 6 months before database closure. The Kaplan-Meier estimator and Cox's proportional hazards models examined the relationship between CD4 count at ART initiation and 24-month LTFU. Final models were adjusted for demographics, year of ART initiation, programme expansion and corrected for unascertained mortality.ResultsAmong 17 038 patients, the median CD4 at initiation increased from 119 (IQR 54–180) in 2008 to 257 (IQR 175–318) in 2012. In unadjusted models, observed LTFU was associated with both CD4 counts <100 cells/μL and CD4 counts ≥300 cells/μL. After adjustment, patients with CD4 counts ≥300 cells/μL were 1.35 (95% CI 1.12 to 1.63) times as likely to be LTFU after 24 months compared to those with a CD4 150–199 cells/μL. This increased risk for patients with CD4 counts ≥300 cells/μL was largest in the first 3 months on treatment. Correction for unascertained deaths attenuated the association between CD4 counts <100 cells/μL and LTFU while the association between CD4 counts ≥300 cells/μL and LTFU persisted.ConclusionsPatients initiating ART at higher CD4 counts may be at increased risk for LTFU. With programmes initiating patients at higher CD4 counts, models of ART delivery need to be reoriented to support long-term retention.
The neurophysiology of failed visual perceptions: some implications for medical teaching
Authors: Welsby Philip D 
Published: December 2015

Abstract
Failed perceptions of clinical abnormalities may have a neurophysiological explanation including three major covert eye problems and seven major brain-processing problems. Seven suggestions are made in an attempt to minimise their effect. We see in detail much less than we think and there is no substitute for seeing real-life clinical abnormalities.