bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome Sequence of Kocuria polaris Strain CD08_4, an Isolate from the Duodenal Mucosa of a Celiac Disease Patient
Authors: Chander Atul Munish , Kumari Munesh , Kochhar Rakesh , Dhawan Devinder Kumar , Bhadada Sanjay Kumar , Mayilraj Shanmugam 
Published: October 2017

ABSTRACT

We report here the 3.8-Mb genome sequence of
Kocuria polaris
strain CD08_4, an isolate from the duodenal mucosa of a celiac disease patient. The genome consists of specific virulence determinant genes, antibiotic resistance genes, genes for coping with oxidative stress, and genes responsible for iron acquisition and metabolism, suggestive of its pathogenic attributes.
Complete Genome Sequence of Eubacterium hallii Strain L2-7
Authors: Shetty Sudarshan A. , Ritari Jarmo , Paulin Lars , Smidt Hauke , De Vos Willem M. 
Published: October 2017

ABSTRACT

The complete genome sequence of
Eubacterium hallii
strain L2-7 is reported here. This intestinal strain produces butyrate from glucose as well as lactate when acetate is provided in the growth medium. In addition, strain L2-7 has been shown to improve insulin sensitivity in db/db mice, indicating its application potential.
Genomic Sequences of Epizootic Hemorrhagic Disease Viruses Isolated from Florida White-Tailed Deer
Authors: Subramaniam Kuttichantran , Lednicky John A. , Loeb Julia , Sayler Katherine A. , Wisely Samantha M. , Waltzek Thomas B. 
Published: October 2017

ABSTRACT

Epizootic hemorrhagic disease virus
(EHDV) serotypes 1 and 2 were isolated from Florida white-tailed deer in 2015 and 2016, respectively, and their genomes were completely sequenced. To our knowledge, these are the first full genome sequences for EHDV-1 and -2 from Florida.
Genome Sequence of the Lager-Brewing Yeast
Saccharomyces
sp. Strain M14, Used in the High-Gravity Brewing Industry in China
Authors: Liu Chunfeng , Li Qi , Niu Chengtuo , Zheng Feiyun , Li Yongxian , Zhao Yun , Yin Xiangsheng 
Published: October 2017

ABSTRACT

Lager-brewing yeasts are mainly used for the production of lager beers. Illumina and PacBio-based sequence analyses revealed an approximate genome size of 22.8 Mb, with a GC content of 38.98%, for the Chinese lager-brewing yeast
Saccharomyces
sp. strain M14. Based on
ab initio
prediction, 9,970 coding genes were annotated.
Complete Genome Sequence of Desulfovibrio desulfuricans Strain G11, a Model Sulfate-Reducing, Hydrogenotrophic, and Syntrophic Partner Organism
Authors: Sheik Cody S. , Sieber Jessica R. , Badalamenti Jonathan P. , Carden Kendall , Olson Adam 
Published: October 2017

ABSTRACT

Here, we report the draft genome of the Gram-negative, sulfate-reducing bacterium
Desulfovibrio desulfuricans
strain G11. Isolated from a rumen fluid enrichment, this culture has been a model syntrophic partner due to its metabolic flexibility. The assembly yielded a single circular chromosome of 3,414,943 bp and a 57% G+C content.
Complete Genome Sequence of the Hippuricase-Positive Campylobacter avium Type Strain LMG 24591
Authors: Miller William G. , Chapman Mary H. , Yee Emma , Revez Joana , Bono James L. , Rossi Mirko 
Published: October 2017

ABSTRACT

Campylobacter avium
is a thermotolerant
Campylobacter
species that has been isolated from poultry.
C. avium
was also the second hippuricase-positive species to be identified within
Campylobacter
. Here, we present the genome sequence of the
C. avium
type strain LMG 24591 (=CCUG 56292
T
), isolated in 2006 from a broiler chicken in Italy.
Mechanisms of liver disease in patients infected with HIV
Authors: Kaspar Matthew B , Sterling Richard K 
Published: October 2017

ObjectiveTo describe the various mechanisms of liver disease in patients with HIV infection, and to link these mechanisms to disease states which may utilise them.BackgroundNon-AIDS causes of morbidity and mortality are becoming increasingly common in patients chronically infected with HIV. In particular, liver-related diseases have risen to become one of the leading causes of non-AIDS-related death. A thorough understanding of the mechanisms driving the development of liver disease in these patients is essential when evaluating and caring for these patients.MethodsThe literature regarding mechanisms of liver disease by which different disease entities may cause hepatic injury and fibrosis was reviewed and synthesised.ResultsA number of discrete mechanisms of injury were identified, to include: oxidative stress, mitochondrial injury, lipotoxicity, immune-mediated injury, cytotoxicity, toxic metabolite accumulation, gut microbial translocation, systemic inflammation, senescence and nodular regenerative hyperplasia. Disease states may use any number of these mechanisms to exert their effect on the liver.ConclusionsThe mechanisms by which liver injury may occur in patients with HIV infection are numerous. Most disease states use multiple mechanisms to cause hepatic injury and fibrosis.
Combination of obstructive sleep apnoea and insomnia treated by continuous positive airway pressure with the SensAwake pressure relief technology to assist sleep: a randomised cross-over trial protocol
Authors: Pepin Jean Louis , Gagnadoux Frédéric , Foote Alison , Vicars Rachel , Ogra Bhavi , Viot-Blanc Véronique , Benmerad Meriem , D’Ortho Marie-Pia , Tamisier Renaud 
Published: October 2017

IntroductionObstructive sleep apnoea (OSA) is a common sleep breathing disorder affecting up to 17% of the middle-aged population. Continuous positive airway pressure (CPAP) is the primary treatment for patients with OSA, but acceptance and adherence to therapy is suboptimal in specific subgroups particularly those with insomnia or poor sleep quality (40%–80% of patients with OSA). Pressure intolerance, particularly during periods of wakefulness, inhibiting sleep onset or return to sleep, is one reason for poor CPAP adherence. AutoCPAPs continually monitor airflow changes and only increase the pressure when the upper airway requires it. Reducing the pressure during wakefulness-sleep transition and wakefulness-after-sleep-onset (WASO) may improve therapy comfort and potentially adherence without compromising therapy efficacy. We hypothesise that SensAwake, a pressure relief function that reduces CPAP pressure on the transition from sleep to wakefulness and on WASO, may improve objective sleep quality.Methods and analysisThis is a multicentre, randomised double-blind crossover clinical trial on patients with both OSA and insomnia. Insomnia is defined as Insomnia Severity Index >15 at screening. Baseline data, including actigraphy, are collected for 1 week before randomisation (1:1) to either conventional AutoCPAP or AutoCPAP with SensAwake for 4 weeks. After an evaluation visit, patients are switched to the other treatment arm for a further 4 weeks. Allowing for 20% dropout, 48 patients are required. If applicable, repeated measures analysis of variance will be used to assess differences in WASO measured by actigraphy (primary outcome), other actigraphy measures, AutoCPAP compliance, subjective questionnaire scores (Epworth Sleepiness Scale, Pittsburgh Sleep Quality Index, Short-Form 12 Health Survey) and 24 hours blood pressure (secondary outcomes).Ethics and disseminationThe protocol was approved by the regional Ethics Committee (CPP Sud-Est–V, IRB N°6705) on 9 December 2015, is registered on ClincalTrials.gov (NCT02721329) and started in June 2016 with expected publication of primary outcome results in 2018.Trial registration numberNCT0272132; Pre-results.
Cohort profile: a nationwide cohort of Finnish military recruits born in 1958 to study the impact of lifestyle factors in early adulthood on disease outcomes
Authors: Sormunen Jorma , Arnold Melina , Soerjomataram Isabelle , Pukkala Eero 
Published: October 2017

PurposeThe cohort was set up to study the impact of lifestyle factors in early adulthood on disease outcomes, with a focus on assessing the influence of body composition and physical performance in early adulthood on subsequent cancer risk.ParticipantsMen born in 1958 who performed their military service between the ages of 17 and 30 years were included in this study (n=31 158). They were eligible for military service if they were healthy or had only minor health problems diagnosed at the beginning of their service. Men with chronic illnesses requiring regular medication or treatment were not eligible for service. Comprehensive health data including diagnosed illnesses, anthropometric measures and health behaviour were collected at the beginning and at the end of military service, including data from medical check-ups.Findings to dateDuring the follow-up, 1124 new cancer cases were diagnosed between baseline (ie, end of the military service for each individual) and end of the year 2014. In the end of the follow-up, 91% of the study participants were still alive. Overweight (body mass index (BMI) ≥25 kg/m2) and obesity (BMI ≥30 kg/m2) were associated with an overall increased risk of cancer. A good or excellent physical condition significantly reduced cancer risk.Future plansThe dataset offers the possibility of linkage with other databases, such as the Finnish Cancer Registry (eg, primary site of the tumour, morphology, time of detection, spreading and primary treatment), vital statistics (date of emigration or deaths), censuses (socioeconomic indicators), hospital discharge data (comorbidity) and population surveys (life habits).
Prevalence and time trends in overweight and obesity among urban women: an analysis of demographic and health surveys data from 24 African countries, 1991–2014
Authors: Amugsi Dickson Abanimi , Dimbuene Zacharie T , Mberu Blessing , Muthuri Stella , Ezeh Alex C 
Published: October 2017

ObjectiveTo examine the prevalence and trends in overweight and obesity among non-pregnant urban women in Africa over the past two and a half decades.DesignCross-sectional surveys conducted between 1991 and 2014.SettingsDemographic and Health Surveys (DHS), repeated cross-sectional data collected in 24 African countries.ParticipantsAdult non-pregnant women aged 15–49 years. The earlier DHS collected anthropometric data on only those women who had children aged 0–5 years. The main analyses were limited to this subgroup. The participants were classified as overweight (25.0–29.9 kg/m2) and obese (≥30.0 kg/m2).ResultsThe prevalence of overweight and obesity among women increased in all the 24 countries. Trends were statistically significant in 17 of the 24 countries in the case of obesity and 13 of the 24 for overweight. In Ghana, overweight almost doubled (p=0.001) while obesity tripled (p=0.001) between 1993 and 2014. Egypt has the highest levels of overweight and obesity at 44% (95% CI 42%, 46.5%) and 39% (95% CI 36.6%, 41.8%), respectively, in 2014 and the trend showed significant increase (p=0.005) from 1995 levels. Also, obesity doubled in Kenya, Benin, Niger, Rwanda, Ivory Coast and Uganda, while tripled in Zambia, Burkina Faso, Mali, Malawi and Tanzania. Ethiopia and Madagascar had the lowest prevalence of both obesity and overweight, with overweight ranging from 7% to 12% and obesity from 1% to 4%.ConclusionsOverweight and obesity are increasing among women of reproductive age in urban Africa, with obesity among this age group having more than doubled or tripled in 12 of the 24 countries. There is an urgent need for deliberate policies and interventions to encourage active lifestyles and healthy eating behaviour to curb this trend in urban Africa.
Child maltreatment as a predictor of adult physical functioning in a prospective British birth cohort
Authors: Archer Gemma , Pinto Pereira Snehal , Power Christine 
Published: October 2017

ObjectiveChild maltreatment (abuse and neglect) has established associations with mental health; however, little is known about its relationship with physical functioning. Physical functioning (ie, the ability to perform the physical tasks of daily living) in adulthood is an important outcome to consider, as it is strongly associated with an individual’s ability to work, and future disability and dependency. We aimed to establish whether maltreatment was associated with physical functioning, independent of other early-life factors.Setting1958 British birth cohort.Participants8150 males and females with data on abuse and who participated at age 50 years.Outcome measuresThe primary outcome was poor physical functioning at 50 years (<65 on the Short-Form 36 survey physical functioning subscale). Secondary outcomes included mental health and self-reported health at 50 years.Results23% of participants reported at least one type of maltreatment; 12% were identified with poor physical functioning. Neglect (ORadj1.55, 95% CI 1.24 to 1.93), psychological abuse (ORadj1.49, 1.17–1.88) and sexual abuse (ORadj2.56, 1.66–3.96) were associated with poor physical functioning independent of other maltreatments and covariates, including childhood social class, birth weight and childhood illness. Odds of poor physical functioning increased with multiple types of maltreatment (ptrend<0.001); ORadjranged from 1.49 (1.23–1.82) for a single type to 2.09 (1.53–2.87) for those reporting>3 types of maltreatment, compared with those with none. Associations of similar magnitude were observed for mental and self-reported health outcomes.ConclusionsChild neglect, psychological and sexual abuse were associated with poor physical functioning at 50 years, with accumulating risk for those with multiple types of maltreatment. Associations were independent of numerous early-life factors and were comparable in magnitude to those observed for mental health and self-rated health. Prevention or alleviation of the ill effects of maltreatment could be an effective policy intervention to promote healthy ageing.
Reorganisation of stroke care and impact on mortality in patients admitted during weekends: a national descriptive study based on administrative data
Authors: Balinskaite Violeta , Bottle Alex , Shaw Louise Johanna , Majeed Azeem , Aylin Paul 
Published: October 2017

ObjectiveTo evaluate mortality differences between weekend and weekday emergency stroke admissions in England over time, and in particular, whether a reconfiguration of stroke services in Greater London was associated with a change in this mortality difference.Design, setting and participantsRisk-adjusted difference-in-difference time trend analysis using hospital administrative data. All emergency patients with stroke admitted to English hospitals from 1 January 2008 to 31 December 2014 were included.Main outcomesMortality difference between weekend and weekday emergency stroke admissions.ResultsWe identified 507 169 emergency stroke admissions: 26% of these occurred during the weekend. The 7-day in-hospital mortality difference between weekend and weekday admissions declined across England throughout the study period. In Greater London, where the reorganisation of stroke services took place, an adjusted 28% (relative risk (RR)=1.28, 95% CI 1.09 to 1.47) higher weekend/weekday 7-day mortality ratio in 2008 declined to a non-significant 9% higher risk (RR=1.09, 95% CI 0.91 to 1.32) in 2014. For the rest of England, a 15% (RR=1.15, 95% CI 1.09 to 1.22) higher weekend/weekday 7-day mortality ratio in 2008 declined to a non-significant 3% higher risk (RR=1.03, 95% CI 0.97 to 1.10) in 2014. During the same period, in Greater London an adjusted 12% (RR=1.12, 95% CI 1.00 to 1.26) weekend/weekday 30-day mortality ratio in 2008 slightly increased to 14% (RR=1.14, 95% CI 1.00 to 1.30); however, it was not significant. In the rest of England, an 11% (RR=1.11, 95% CI 1.07 to 1.15) higher weekend/weekday 30-day mortality ratio declined to a non-significant 4% higher risk (RR=1.04, 95% CI 0.99 to 1.09) in 2014. We found no statistically significant association between decreases in the weekend/weekday admissions difference in mortality and the centralisation of stroke services in Greater London.ConclusionsThere was a steady reduction in weekend/weekday differences in mortality in stroke admissions across England. It appears statistically unrelated to the centralisation of stroke services in Greater London, and is consistent with an overall national focus on improving stroke services.
Pathways of undue influence in health policy-making: a main actor’s perspective
Authors: Hernández-Aguado Ildefonso , Chilet-Rosell Elisa 
Published: October 2017

BackgroundIt is crucial to know the extent to which influences lead to policy capture—by which the policy-making process is shifted away from the public interest towards narrow private interests. Using the case study of Spain, our aim was to identify interactions between public administration, civil society and private companies that could influence health policies.Methods54 semistructured interviews with key actors related to health policy. The interviews were used to gather information on main policy actors as well as on direct and subtle influences that could modify health policies. The analysis identified and described, from the interviewed persons’ experiences, both the inappropriate influences exerted on the actors and those that they exerted.ResultsInappropriate influences were identified at all levels of administration and policy. They included actions for personal benefits, pressure for blocking health policies and pressure from high levels of government in favour of private corporations. The private sector played a significant role in these strategies through bribery, personal gifts, revolving doors, negative campaigns and by blocking unfavourable political positions or determining the knowledge agenda. The interviewees reported subtle forms of influence (social events, offers of technical support, invitations, etc) that contributed to the intellectual and cultural capture of health officials.ConclusionThe health policy decision-making processes in Spain are subject to influences by stakeholders that determine a degree of policy capture, which is avoidable. The private sector uses different strategies, from subtle influences to outright corruption, taking advantage in many cases of flexible legislation.
Genome-wide association study identified copy number variants associated with sporadic colorectal cancer risk
Authors: Thean Lai Fun , Low Yee Syuen , Lo Michelle , Teo Yik-Ying , Koh Woon-Puay , Yuan Jian-Min , Chew Min Hoe , Tang Choong Leong , Cheah Peh Yean 
Published: October 2017

BackgroundMultiple single nucleotide polymorphisms (SNPs) have been associated with colorectal cancer (CRC) risk. The role of structural or copy number variants (CNV) in CRC, however, remained unclear. We investigated the role of CNVs in patients with sporadic CRC.MethodsA genome-wide association study (GWAS) was performed on 1000 Singapore Chinese patients aged 50 years or more with no family history of CRC and 1000 ethnicity-matched, age-matched and gender-matched healthy controls using the Affymetrix SNP 6 platform. After 16 principal component corrections, univariate and multivariate segmentations followed by association testing were performed on 1830 samples that passed quality assurance tests.ResultsA rare CNV region (CNVR) at chromosome 14q11 (OR=1.92 (95% CI 1.59 to 2.32), p=2.7e-12) encompassing CHD8, and common CNVR at chromosomes 3q13.12 (OR=1.54 (95% CI 1.33 to 1.77), p=2.9e-9) and 12p12.3 (OR=1.69 (95% CI 1.41 to 2.01), p=2.8e-9) encompassing CD47 and RERG/ARHGDIB, respectively, were significantly associated with CRC risk. CNV loci were validated in an independent replication panel using an optimised copy number assay. Whole-genome expression data in matched tumours of a subset of cases demonstrated that copy number loss at CHD8 was significantly associated with dysregulation of several genes that perturb the Wnt, TP53 and inflammatory pathways.ConclusionsA rare CNVR at 14q11 encompassing the chromatin modifier CHD8 was significantly associated with sporadic CRC risk. Copy number loss at CHD8 altered expressions of genes implicated in colorectal tumourigenesis.
Discordant patient–physician assessments of disease activity and its persistence adversely impact quality of life and work productivity in US Hispanics with rheumatoid arthritis
Authors: Karpouzas George A , Ramadan Sera N , Cost Chelsie E , Draper Taylor L , Hernandez Elizabeth , Strand Vibeke , Ormseth Sarah R 
Published: October 2017

ObjectiveThis study was designed to evaluate the determinants of patient and physician global assessments (PtGA and MDGA, respectively) of disease activity, their discordance and change over 2 years in Hispanics with rheumatoid arthritis (RA). We further examined the impact of discordance and its persistence on health-related quality of life (HRQOL) and work productivity on final visit.MethodsWe studied 536 Hispanics with established RA from a single centre. PtGA and MDGA were measured annually on 10 cm visual analogue scales and discordance was defined as absolute difference between them ≥3 cm. Associations between predictors and outcomes of interest were evaluated using multivariable regression and analysis of covariance for cross-sectional and longitudinal data, respectively.ResultsIndependent predictors of baseline PtGA were pain, fatigue, depression, general health perceptions and tender joint count. MDGA was predicted by swollen joint count, tender joint count, erythrocyte sedimentation rate, fatigue and depression. Both PtGA and MDGA improved over time (all p<0.001). Discordance was observed in 43% at baseline, with fair stability over 2 years. Higher (worse) patient ratings were most prevalent; their presence at any time and increasing persistence predicted lower physical and mental HRQOL, decreased work productivity and more activity impairment at 2-year follow-up (all p<0.001).ConclusionsDeterminants of PtGA, MDGA and changes over 2 years were disparate in Hispanics with RA yielding significant discordance. Higher patient ratings at any time contributed to worse HRQOL, work productivity and activity impairment on final visit.
Smoke-free legislation and paediatric hospitalisations for acute respiratory tract infections: national quasi-experimental study with unexpected findings and important methodological implications
Authors: Been Jasper V , Mackay Daniel F , Millett Christopher , Soyiri Ireneous , van Schayck Constant P , Pell Jill P , Sheikh Aziz 
Published: October 2017

ObjectivesWe investigated whether Scottish implementation of smoke-free legislation was associated with a reduction in unplanned hospitalisations or deaths (‘events’) due to respiratory tract infections (RTIs) among children.DesignInterrupted time series (ITS).Setting/participantsChildren aged 0–12 years living in Scotland during 1996–2012.InterventionNational comprehensive smoke-free legislation (March 2006).Main outcome measureAcute RTI events in the Scottish Morbidity Record-01 and/or National Records of Scotland Death Records.Results135 134 RTI events were observed over 155 million patient-months. In our prespecified negative binomial regression model accounting for underlying temporal trends, seasonality, sex, age group, region, urbanisation level, socioeconomic status and seven-valent pneumococcal vaccination status, smoke-free legislation was associated with an immediate rise in RTI events (incidence rate ratio (IRR)=1.24, 95% CI 1.20 to 1.28) and an additional gradual increase (IRR=1.05/year, 95% CI 1.05 to 1.06). Given this unanticipated finding, we conducted a number of post hoc exploratory analyses. Among these, automatic break point detection indicated that the rise in RTI events actually preceded the smoke-free law by 16 months. When accounting for this break point, smoke-free legislation was associated with a gradual decrease in acute RTI events: IRR=0.91/year, 95% CI 0.87 to 0.96.ConclusionsOur prespecified ITS approach suggested that implementation of smoke-free legislation in Scotland was associated with an increase in paediatric RTI events. We were concerned that this result, which contradicted published evidence, was spurious. The association was indeed reversed when accounting for an unanticipated antecedent break point in the temporal trend, suggesting that the legislation may in fact be protective. ITS analyses should be subjected to comprehensive robustness checks to assess consistency.