bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dissecting the decline of hepatitis C in first‐time donors in England and Wales
Authors: Reynolds C. A. , Davison K. L. , Andrews N. , Patel P. , Kitchen A. , Brailsford S. R. 
Published: February 2018

Background and ObjectivesThe rate of confirmed hepatitis C virus (HCV) cases, in first‐time donors, is much lower in 2015 than 20 years ago. We investigate reasons for the decline.Materials and MethodsHCV rates were analysed by gender and birth cohort for 1996 to 2015 and ethnic group for 2006 to 2015. Variables for confirmed positive cases were compared for two ten‐year periods (1996 to 2005 and 2006 to 2015) including genotyping data for 2006 to 2015.ResultsThere were 2007 confirmed HCV cases identified between 1996 and 2015. The rate per 100 000 donations fell from 78·6 in 1996 to 26·9 by 2015. By birth cohort, HCV rates were highest in donors born in the 1950s and 1960s who contributed a decreasing proportion of first‐time donors. Between 2006 and 2015, there was no significant decline in HCV rate. The HCV‐positive donor profile has changed in the last 10 years with increased proportions of younger donors, donors born abroad and decreased reported injecting drug use. Genotype 1a remains predominate, but genotype 1b has increased associated with this change in birth cohort and ethnicity.ConclusionThe decline in number and rate of confirmed HCV‐positive first‐time donors is mainly due to a decrease in first‐time donors born before 1970, with the highest rate of HCV. However, the decline has slowed and the profile of HCV‐positive first‐time donors is changing. A better understanding of behaviour and sources of HCV in younger and ethnic minority donors are needed.
Precautions
at Fukushima That Would Have Suppressed the Accident
Severity
Authors: Iino Kenji , Yoshioka Ritsuo , Fuchigami Masao , Nakao Masayuki 
Published: February 2018

Abstract
The Great East Japan Earthquake on Mar. 11, 2011 triggered huge tsunami waves that attacked Fukushima Daiichi Nuclear Power Plant (Fukushima-1). Units 1, 3, and 4 had hydrogen explosions. Units 1–3 had core meltdowns and released a large amount of radioactive material. Published investigation reports did not explain how the severity of the accident could have been prevented. We formed a study group to find: (A) Was the earthquake-induced huge tsunami predictable at Fukushima-1? (B) If it was predictable, what preparations at Fukushima-1 could have avoided the severity of the accident? Our conclusions were: (a) The tsunami that hit Fukushima-1 was predictable, and (b) the severity could have been avoided if the plant had prepared a set of equipment, and most of all, had exercised actions to take against such tsunami. Necessary preparation included: (1) a number of direct current (DC) batteries, (2) portable underwater pumps, (3) portable alternating current (AC) generators with sufficient gasoline supply, (4) high voltage AC power trucks, and (5) drills against extended loss of all electric power and seawater pumps. This set applied only to this specific accident. A thorough preparation would have added (6) portable compressors, (7) watertight modification to reactor core isolation cooling system (RCIC) and high pressure coolant injection system (HPCI) control and instrumentation, and (8) fire engines for alternate low pressure water injection. Item (5), i.e., to study plans and carry out exercises against the tsunami would have identified all other necessary preparations.
Draft Genome Sequence of the Nitrogen-Fixing and Hormogonia-Inducing Cyanobacterium
Nostoc cycadae
Strain WK-1, Isolated from the Coralloid Roots of
Cycas revoluta
Authors: Kanesaki Yu , Hirose Masaki , Hirose Yuu , Fujisawa Takatomo , Nakamura Yasukazu , Watanabe Satoru , Matsunaga Shigeru , Uchida Hiroko , Murakami Akio 
Published: February 2018

ABSTRACT

We report here the whole-genome sequence of
Nostoc cycadae
strain WK-1, which was isolated from cyanobacterial colonies growing in the coralloid roots of the gymnosperm
Cycas revoluta
. It can provide valuable resources to study the mutualistic relationships and the syntrophic metabolisms between the cyanobacterial symbiont and the host plant,
C. revoluta
.
Draft Genome Sequences of
Escherichia coli
Isolates from India
Authors: Karunakaran Athira Cheruplackal , Milton Arockiasamy Arun Prince , Rajendrakumar Arunraj Mekhemadhom , Sahu Amit R. , Pandey A. , Ghatak Sandeep , Abhishek  , Nagaleekar Viswas Konasagara , Gandham Ravikumar , Agarwal Rajesh Kumar 
Published: February 2018

ABSTRACT

Escherichia coli
causes diarrhea and extraintestinal infections in humans and animals. Here, we report the draft genome sequences of
Escherichia coli
strains 360/16 and 646, isolated from neonatal calves.
Complete Genome Sequence of the
Bacillus pumilus
Phage Leo2
Authors: Badran Sondos , Morales Nathanael , Schick Phillip , Jacoby Brandon , Villella William , Lorenz Todd 
Published: February 2018

ABSTRACT

Bacillus
spp. are ubiquitous Gram-positive microbes with many ecological and symbiotic interactions and can be pathogens. Phage Leo2 was found to infect a
Bacillus pumilus
strain isolated from soil. The sequence of phage Leo2 revealed 74 genes; 31% of the genes have associated functions, and 67% of coding regions are unidentified open reading frames.
Draft Genome Sequence of a Pathogenic
Vibrio vulnificus
Strain Isolated in Brazil
Authors: Tiba-Casas Monique Ribeiro , Lemes-Marques Eneida Gonçalves , Almeida Elisabete Aparecida , Soares Flávia Barrosa , Camargo Carlos Henrique 
Published: February 2018

ABSTRACT

We describe the draft genome sequence of the clinical
Vibrio vulnificus
strain 03_7315, isolated in 2016 from the blood of a diabetic patient who died of septicemia after ingestion of seafood. The draft genome, with 4,755,588 bp covering two chromosomes, presented 4,434 genes, 4,213 coding sequences, and 117 pseudogenes.
Draft Genome Sequence of the Sordariomycete
Lecythophora
(
Coniochaeta
)
hoffmannii
CBS 245.38
Authors: Leonhardt Sabrina , Büttner Enrico , Gebauer Anna Maria , Hofrichter Martin , Kellner Harald 
Published: February 2018

ABSTRACT

Lecythophora
(
Coniochaeta
)
hoffmannii
, a soil- and lignocellulose-inhabiting sordariomycete (Ascomycota) that can also live as a facultative tree pathogen causing soft rot, belongs to the family Coniochaetaceae. The strain CBS 245.38 sequenced here was assembled into 869 contigs, has a size of 30.8 Mb, and comprises 10,596 predicted protein-coding genes.
High-Quality Draft Genome Sequences of Five
Xanthomonas arboricola
pv. fragariae Isolates
Authors: Gétaz Michael , Baeyen Steve , Blom Jochen , Maes Martine , Cottyn Bart , Pothier Joël F. 
Published: February 2018

ABSTRACT

Xanthomonas arboricola
pv. fragariae was described in 2001 as the causal agent of strawberry bacterial leaf blight. We report here the first draft whole-genome sequences of five
X. arboricola
pv. fragariae isolates from Italy and France.
The 38K-Mediated Specific Dephosphorylation of the Viral Core Protein P6.9 Plays an Important Role in the Nucleocapsid Assembly of Autographa californica Multiple Nucleopolyhedrovirus
Authors: Lai Qingying , Wu Wenbi , Li Ao , Wang Wei , Yuan Meijin , Yang Kai 
Published: February 2018

ABSTRACT

Encapsidation of the viral genomes, leading to the assembly of the nucleocapsids to form infectious progeny virions, is a key step in many virus life cycles. Baculovirus nucleocapsid assembly is a complex process that involves many proteins. Our previous studies showed that the deletion of the core gene
38K
(
ac98
) interrupted the nucleocapsid assembly by producing capsid sheaths devoid of viral genomes by an unknown mechanism. All homologs of 38K contain conserved motifs of the haloacid dehalogenase superfamily, which are involved in phosphoryl transfer. The requirements of these motifs for nucleocapsid assembly, confirmed in the present study, suggest that 38K may be a functioning haloacid dehalogenase. P6.9 is also encoded by a core gene (
ac100
) and is required for viral genome encapsidation. It has been reported that multiple phosphorylated species of P6.9 are present in virus-infected cells, while only an unphosphorylated species is detected in the budded virus. Therefore, whether 38K mediates the dephosphorylation of P6.9 was investigated. An additional phosphorylated species of P6.9 in
38K
-deleted or -mutated virus-transfected cells was detected, and the dephosphorylated sites mediated by 38K were determined by mass spectrometry. To assess the effects of dephosphorylation of P6.9 mediated by 38K on virus replication, these sites were mutated to glutamic acids (phosphorylation-mimic mutant) or to alanines (phosphorylation-deficient mutant). Studies showed that the nucleocapsid assembly was interrupted in phosphorylation-mimic mutant virus-transfected cells. Taken together, our findings demonstrate that 38K mediates the dephosphorylation of specific sites at the C terminus of P6.9, which is essential for viral genome encapsidation.

IMPORTANCE
Genome packaging is a fundamental process in the virus life cycle, and viruses have different strategies to perform this step. For several double-stranded DNA (dsDNA) viruses, the procapsid is formed before genome encapsidation, which may require basic proteins that help to neutralize the nucleic acid charge repulsion to facilitate the compaction of the genome within the confined capsid space. Baculovirus encodes a small basic protein, P6.9, which is required for a variety of processes in the virus infection cycle. The phosphorylation of P6.9 is thought to result in nucleocapsid uncoating, while the dephosphorylation of P6.9 is involved in viral DNA encapsidation during nucleocapsid assembly. Here, we demonstrate that a haloacid dehalogenase homolog encoded by baculovirus core gene
38K
is involved in nucleocapsid assembly by mediating the dephosphorylation of 5 specific sites at the C terminus of P6.9. This finding contributes to the understanding of the mechanisms of virus nucleocapsid assembly.
Estimates of prevalence, demographic characteristics and social factors among people with disabilities in the USA: a cross-survey comparison
Authors: Lauer Eric Andrew , Houtenville Andrew J 
Published: February 2018

ObjectiveA national priority for disability research in the USA is the standardised identification of people with disabilities in surveillance efforts. Mandated by federal statute, six dichotomous difficulty-focused questions were implemented in national surveys to identify people with disabilities. The aim of this study was to assess the prevalence, demographic characteristics and social factors among people with disabilities based on these six questions using multiple national surveys in the USA.SettingAmerican Community Survey (ACS), Current Population Survey Annual Social and Economic Supplement (CPS-ASEC), National Health Interview Survey (NHIS) and the Survey of Income and Program Participation (SIPP).ParticipantsCivilian, non-institutionalised US residents aged 18 and over from the 2009 to 2014 ACS, 2009 to 2014 CPS-ASEC, 2009 to 2014 NHIS and 2008 SIPP waves 3, 7 and 10.Primary and secondary outcome measuresDisability was assessed using six standardised questions asking people about hearing, vision, cognition, ambulatory, self-care and independent living disabilities. Social factors were assessed with questions asking people to report their education, employment status, family size, health and marital status, health insurance and income.ResultsRisk ratios and demographic distributions for people with disabilities were consistent across survey. People with disabilities were at decreased risk of having college education, employment, families with three or more people, excellent or very good self-reported health and a spouse. People with disabilities were also consistently at greater risk of having health insurance and living below the poverty line. Estimates of disability prevalence varied between surveys from 2009 to 2014 (range 11.76%–17.08%).ConclusionReplicating the existing literature, we found the estimation of disparities and inequity people with disabilities experience to be consistent across survey. Although there was a range of prevalence estimates, demographic factors for people with disabilities were consistent across surveys. Variations in prevalence estimates can be explained by survey context effects.
Estimating the met need for emergency obstetric care (EmOC) services in three payams of Torit County, South Sudan: a facility-based, retrospective cross-sectional study
Authors: Bayo Pontius , Itua Imose , Francis Suzie Paul , Boateng Kofi , Tahir Elijo Omoro , Usman Abdulmumini 
Published: February 2018

ObjectiveTo determine the met need for emergency obstetric care (EmOC) services in three Payams of Torit County, South Sudan in 2015 and to determine the frequency of each major obstetric complication.DesignThis was a retrospective cross-sectional study.SettingFour primary healthcare centres (PHCCs) and one state hospital in three payams (administrative areas that form a county) in Torit County, South Sudan.ParticipantsAll admissions in the obstetrics and gynaecology wards (a total of 2466 patient admission files) in 2015 in all the facilities designated to conduct deliveries in the study area were reviewed to identify obstetric complications.Primary and secondary outcome measuresThe primary outcome was met need for EmOC, which was defined as the proportion of all women with direct major obstetric complications in 2015 treated in health facilities providing EmOC services. The frequency of each complication and the interventions for treatment were the secondary outcomes.ResultsTwo hundred and fifty four major obstetric complications were admitted in 2015 out of 390 expected from 2602 pregnancies, representing 65.13% met need. The met need was highest (88%) for Nyong Payam, an urban area, compared with the other two rural payams, and 98.8% of the complications were treated from the hospital, while no complications were treated from three PHCCs. The most common obstetric complications were abortions (45.7%), prolonged obstructed labour (23.2%) and haemorrhage (16.5%). Evacuation of the uterus for retained products (42.5%), caesarean sections (32.7%) and administration of oxytocin for treatment of postpartum haemorrhage (13.3%) were the most common interventions.ConclusionThe met need for EmOC in Torit County is low, with 35% of women with major obstetric complications not accessing care, and there is disparity with Nyong Payam having a higher met need. We suggest more support supervision to the PHCCs to increase access for the rural population.
Do quality improvement initiatives for diabetes care address social inequities? Secondary analysis of a systematic review
Authors: Lu Jacquie Boyang , Danko Kristin J , Elfassy Michael D , Welch Vivian , Grimshaw Jeremy M , Ivers Noah M 
Published: February 2018

BackgroundSocially disadvantaged populations carry a disproportionate burden of diabetes-related morbidity and mortality. There is an emerging interest in quality improvement (QI) strategies in the care of patients with diabetes, however, the effect of these interventions on disadvantaged groups remains unclear.ObjectiveThis is a secondary analysis of a systematic review that seeks to examine the extent of equity considerations in diabetes QI studies, specifically quantifying the proportion of studies that target interventions toward disadvantaged populations and conduct analyses on the impact of interventions on disadvantaged groups.Research design and methodsStudies were identified using Medline, HealthStar and the Cochrane Effective Practice and Organisation of Care database. Randomised controlled trials assessing 12 QI strategies targeting health systems, healthcare professionals and/or patients for the management of adult outpatients with diabetes were eligible. The place of residence, race/ethnicity/culture/language, occupational status, gender/sexual identity, religious affiliations, education level, socioeconomic status, social capital, plus age, disability, sexual preferences and relationships (PROGRESS-Plus) framework was used to identify trials that focused on disadvantaged patient populations, to examine the types of equity-relevant factors that are being considered and to explore temporal trends in equity-relevant diabetes QI trials.ResultsOf the 278 trials that met the inclusion criteria, 95 trials had equity-relevant considerations. These include 64 targeted trials that focused on a disadvantaged population with the aim to improve the health status of that population and 31 general trials that undertook subgroup analyses to assess the extent to which their interventions may have had differential impacts on disadvantaged subgroups. Trials predominantly focused on race/ethnicity, socioeconomic status and place of residence as potential factors for disadvantage in patients receiving diabetes care.ConclusionsLess than one-third of diabetes QI trials included equity-relevant considerations, limiting the relevance and applicability of their data to disadvantaged populations. There is a need for better data collection, reporting, analysis and interventions on the social determinants of health that may influence the health outcomes of patients with diabetes.PROSPERO registration numberCRD42013005165.
Mortality and quality of death certification in a cohort of patients with Parkinson’s disease and matched controls in North Wales, UK at 18 years: a community-based cohort study
Authors: Hobson Peter , Meara Jolyon 
Published: February 2018

ObjectiveThis investigation reports the cause and the quality of death certification in a community cohort of patients with Parkinson’s disease (PD) and controls at 18 years.SettingDenbighshire North Wales, UK.ParticipantsThe community-based cohorts consisted of 166 patients with PD and 102 matched controls.Primary outcomesAll-cause mortality was ascertained at 18 years by review of hospitals’ primary care records and examination of death certificates obtained from the UK General Register Office. Mortality HRs were estimated using Cox proportional regression, controlling for covariates including age at study entry, age at death, gender, motor function, mood, health-related quality of life (HRQoL) and cognitive function.ResultsAfter 18 years, 158 (95%) of patients in the PD cohort and 34 (33%) in the control cohort had died. Compared with the general UK population, the PD cohort had a higher risk of mortality (standard mortality rate, 1.82, 95% CI 1.55 to 2.13). As the primary or underlying cause of death, PD was not reported in 75/158 (47%) of the death certificates. In addition, although 144/158 (91%) of the PD cohort had a diagnosis of dementia, this was reported in less than 10% of death certificates. The main cause of death reported in the PD cohort was pneumonia (53%), followed by cardiac-related deaths (21%). Compared with controls, patients with PD had a greater risk of pneumonia (2.03, 95% CI 1.34 to 3.6), poorer HRQoL and more likely to reside in institutional care at death (P<0.01).ConclusionThis investigation found that PD was associated with an excess risk of mortality compared with the general population. However, PD as a primary or underlying cause of death recorded on certificates was found to be suboptimal. This suggests that the quality of mortality statistics drawn from death certificates alone is not a valid or reliable source of data.
Longitudinal changes in intraocular pressure and association with systemic factors and refractive error: Lingtou Eye Cohort Study
Authors: Han Xiaotong , Yang Tangjian , Zhang Jian , Yu Sha , Guo Xinxing , Yan William , Hu Yin , He Mingguang 
Published: February 2018

ObjectivesTo investigate the longitudinal changes in intraocular pressure (IOP) and its associations with refractive error and systemic determinants in a Chinese geriatric population.DesignProspective cohort study.SettingGuangzhou Government Servant Physical Check-up Center, Guangzhou, China.Participants4413 government employees aged no less than 40 years (41.9% female) attending annual physical and eye examinations were included in this study. The inclusion criterion was having attended the 2010 follow-up examination. The exclusion criteria include glaucoma or intraocular surgery history, IOP >21 mm Hg at any visit or without available IOP data at all visits from 2010 to 2014.Primary and secondary outcome measuresThe outcome measure was IOP at each follow-up visit from 2010 to 2014. Mixed-effect model was used to assess the relationship between longitudinal changes in IOP and potential risk factors.ResultsFor the 2653 participants who had available IOP data at both the 2010 and 2014 follow-up visits, the average change in IOP was an increase of 0.43 (95% CI 0.36 to 0.50) mm Hg. For the whole study population and in the optimised mixed model, there was a non-linear increase of IOP with age (P<0.001), with greater changes in younger subjects and in women (P<0.001 and P=0.002, respectively). Elevations in systolic blood pressure, diastolic blood pressure, body mass index (BMI) and fasting plasma glucose (FPG), as well as a myopic shift (all with P<0.001), during the follow-up were associated with an increasing trend of IOP, while serum lipids were found to be not significantly associated.ConclusionsIn this cohort of elderly Chinese adults, IOP increases non-linearly with ageing. People with increasing blood pressure, BMI, FPG and myopic progression are more likely to have IOP elevation over time.
Task sharing to improve the prevention, diagnosis and management of rheumatic heart disease: a systematic review protocol
Authors: Abdullahi Leila Hussein , Smit Inge , Engel Mark E , Watkins David A , Zühlke Liesl Joanna 
Published: February 2018

IntroductionRheumatic heart disease (RHD) remains an important cause of cardiovascular morbidity and mortality globally due to weak health systems in many countries. RHD can be effectively prevented and managed; however, RHD-related interventions have not been widely adopted in countries with severe human resource constraints. Task sharing is a recognised approach to personnel shortages that could prove effective for RHD and has, anecdotally, been attempted in a few settings. We propose a systematic review and meta-analysis protocol to assess models that use non-physician workers to expand access to, and quality of, RHD-related healthcare.MethodsWe will include randomised controlled trials (RCT), cluster RCTs, quasi-experimental and controlled before and after studies providing information on the effectiveness of non-physician workers in providing care for streptoccocal pharyngitis, rheumatic fever and RHD. We will search relevant electronic databases and grey literature using medical subject headings. Standardised data extraction forms will be used to collect effect sizes that will be pooled in random-effects models. We will also conduct subgroup analyses and note other important quantitative findings, such as cost reduction, and qualitative findings, such as patient satisfaction. We will also assess study quality and risk of bias and metabias.Ethics and disseminationEthics approval is not required for this systematic review of previously published literature. The results of the systematic review will be broadly disseminated via conference presentations, multidisciplinary workshops and peer-reviewed publications.PROSPERO registration numberCRD42017072989.