bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prevalence and characterisation of Staphylococcus aureus causing community‐acquired skin and soft tissue infections on Java and Bali, Indonesia
Authors: Santosaningsih Dewi , Santoso Sanarto , Setijowati Nanik , Rasyid Harun A. , Budayanti Nyoman S. , Suata Ketut , Widhyatmoko Dicky B. , Purwono Priyo B. , Kuntaman Kuntaman , Damayanti Damayanti , Prakoeswa Cita R. S. , Laurens Mitchell , van Nierop Josephine W. I. , Nanninga Geraldine L. , Oudenes Neline , de Regt Michelle , Snijders Susan V. , Verbrugh Henri A. , Severin Juliëtte A. 
Published: November 2017

AbstractObjectivesTo define the role of Staphylococcus aureus in community settings among patients with skin and soft tissue infections (SSTI) in Indonesia.MethodsStaphylococcus aureus were cultured from anterior nares, throat and wounds of 567 ambulatory patients presenting with SSTI. The mecA gene and genes encoding Panton–Valentine leukocidin (PVL; lukF‐PV and lukS‐PV) and exfoliative toxin (ET; eta and etb) were determined by PCR. Clonal relatedness among methicillin‐resistant S. aureus (MRSA) and PVL‐positive S. aureus was analysed using multilocus variable‐number tandem‐repeat analysis (MLVA) typing, and multilocus sequence typing (MLST) for a subset of isolates. Staphylococcal cassette chromosome mec (SCCmec) was determined for all MRSA isolates. Moreover, determinants for S. aureus SSTI, and PVL/ET‐positive vs PVL/ET‐negative S. aureus were assessed.ResultsStaphylococcus aureus were isolated from SSTI wounds of 257 (45.3%) patients, eight (3.1%) of these were MRSA. Genes encoding PVL and ETs were detected in 21.8% and 17.5% of methicillin‐susceptible S. aureus (MSSA), respectively. PVL‐positive MRSA was not detected. Nasopharyngeal S. aureus carriage was an independent determinant for S. aureus SSTI (odds ratio [OR] 1.8). Primary skin infection (OR 5.4) and previous antibiotic therapy (OR 3.5) were associated with PVL‐positive MSSA. Primary skin infection (OR 2.2) was the only factor associated with ET‐positive MSSA. MLVA typing revealed two more prevalent MSSA clusters. One ST1‐MRSA‐SCCmec type IV isolate and a cluster of ST239‐MRSA‐SCCmec type III were found.ConclusionsCommunity‐acquired SSTI in Indonesia was frequently caused by PVL‐positive MSSA, and the hospital‐associated ST239‐MRSA may have spread from the hospital into the community.
The limited role of differential fractionation in genome content variation and function in maize (Zea mays L.) inbred lines
Authors: Brohammer Alex B. , Kono Thomas J. Y. , Springer Nathan M. , McGaugh Suzanne E. , Hirsch Candice N. 
Published: November 2017

SummaryMaize is a diverse paleotetraploid species with considerable presence/absence variation and copy number variation. One mechanism through which presence/absence variation can arise is differential fractionation. Fractionation refers to the loss of duplicate gene pairs from one of the maize subgenomes during diploidization. Differential fractionation refers to non‐shared gene loss events between individuals following a whole‐genome duplication event. We investigated the prevalence of presence/absence variation resulting from differential fractionation in the syntenic portion of the genome using two whole‐genome de novo assemblies of the inbred lines B73 and PH207. Between these two genomes, syntenic genes were highly conserved with less than 1% of syntenic genes being subject to differential fractionation. The few variably fractionated syntenic genes that were identified are unlikely to contribute to functional phenotypic variation, as there is a significant depletion of these genes in annotated gene sets. In further comparisons of 60 diverse inbred lines, non‐syntenic genes were six times more likely to be variable than syntenic genes, suggesting that comparisons among additional genome assemblies are not likely to result in the discovery of large‐scale presence/absence variation among syntenic genes.
A sociolinguistic profile of English in Lebanon
Authors: ESSEILI FATIMA 
Published: November 2017

ABSTRACTThis article provides an overview of the historical presence of foreign languages in Lebanon, focusing on language contact from the eighteenth century to date. Through sociolinguistic profiling, the paper describes the users and uses of English, as well as Lebanese attitudes towards English. The article begins by offering a general overview of the country, its languages and cultures, and its ethnic and religious groups. It presents a description of users of English along with a characterization of how the interpersonal, instrumental, regulative, and innovative functions of the language are manifested, while the final section of the article discusses attitudes to English in Lebanese society.
Raccoon roundworm (Baylisascaris procyonis) as an occupational hazard: 1. Knowledge of B. procyonis and attitudes towards it and other zoonoses among wildlife rehabilitators
Authors: Sapp S. G. H. , Murray B. A. , Hoover E. R. , Green G. T. , Yabsley M. J. 
Published: November 2017

SummaryWildlife rehabilitators are at risk of zoonotic diseases because they often have prolonged contact with many species of wildlife and their bodily fluids. Raccoon roundworm (Baylisascaris procyonis) is a common zoonotic parasite of raccoons that has the potential to cause severe or fatal neurologic disease in a broad variety of hosts if the eggs within raccoon faeces are ingested. We administered an online survey to wildlife rehabilitators to assess their knowledge regarding aspects of transmission, biology and disease caused by B. procyonis, and also to evaluate attitudes towards wildlife diseases and B. procyonis as an occupational hazard. Knowledge was assessed using multiple choice and true–false questions; attitudes were measured using Likert‐type items. A total of 659 complete or near‐complete responses (missing fewer than three knowledge or attitudes items and/or non‐response to some demographic fields) were collected. The median knowledge score was 7/14 questions correct (range: 0–14 correct). Generally, individuals with higher levels of education and rehabilitation experience, veterinary professionals and those who are members of professional wildlife rehabilitation groups scored above the median significantly more often (p < .01). Significantly more rehabilitators who were located in the south‐east and those with part‐time or infrequent commitments scored below the median overall knowledge score. There was general agreement that B. procyonis is a health risk of rehabilitators and that measures should be taken to control transmission to people and animals. Some factors explaining differences in attitudes include setting of rehabilitation (home versus animal care facility), veterinary profession, region, membership in a wildlife rehabilitation group and rehabilitation of raccoons. Findings emphasize the importance of awareness and mentorship to inform rehabilitators on the potential risks of B. procyonis and other potential zoonoses within captive wildlife settings, and the important role of professional wildlife rehabilitator groups in disseminating educational materials.
Social workers’ experiences with whistleblowing: To speak or not to speak?
Authors: Raymond Sally , Beddoe Liz , Staniforth Barbara 
Published: November 2017

INTRODUCTION: Reporting perceived inadequate and/or harmful practice has become known internationally as whistleblowing. Social workers have a responsibility to uphold ethical standards and may blow the whistle when faced with what they perceive as unethical conduct.METHOD: A small-scale, qualitative study explored the experiences of 10 social workers in Aotearoa New Zealand who, having observed what they believed to be poor or unsafe practice, attempted to have their concerns addressed by reporting to a third party or blowing the whistle.FINDINGS: The research reveals common experiences of limited support for, and retaliation from colleagues and organisations towards, those who spoke out. Participants experienced both personal and professional consequences.CONCLUSIONS: The research identifies the need for appropriate processes and support for whistleblowing social workers and their employing agencies. Social workers need to be better informed about their rights and responsibilities under the Protected Disclosures Act (2000).
Young people empathising with other animals: reflections on an Australian RSPCA Humane Education Program
Authors: Fraser Heather , Taylor Nik , Signal Tania 
Published: November 2017

INTRODUCTION: Empathy is associated with engagement, compassion, social support and emotional sensitivity, and it is a hallmark of good social work practice. Empathy rightfully receives much attention in social work practice, however, interspecies empathy has yet to be included. This article has been written to address this gap.METHODS: Two main research questions guide our conceptual discussion of young people, interspecies empathy and social work: (1) Why is empathy important to social work with young people? (2) What can an Australian RSPCA Humane Education Programme (HEP) teach social workers about the benefits of interspecies empathy for young people? After our literature review, we examine our illustrative example, which is an HEP offered mostly to newly arrived refugee and migrant young people living in the outer suburbs of Melbourne, whose prior experiences of and/or attitudes towards animals may not have been positive. FINDINGS: Social workers are wise to prioritise empathy because extensive research has shown that, across a diverse range of fields, modes of practice in and beyond social work, empathic practitioners are more effective, achieving better outcomes with their clients. From the letters the young people sent to the RSPCA Victoria after completing an HEP, we note their self-reported increases in empathy for animals, including those they had previously feared or shunned.CONCLUSION: There are many potential benefits of recognising, fostering and valuing interspecies empathy through humane education programmes. However, for these to be ethical, care and empathy must be shown towards the wellbeing of the animals involved, not just the human participants.
Complete Genome Sequence of Klebsiella pneumoniae Phages SopranoGao, MezzoGao, and AltoGao
Authors: Gao Sarah , Linden Sara B. , Nelson Daniel C. 
Published: November 2017

ABSTRACT

The
Klebsiella pneumoniae
phages SopranoGao, MezzoGao, and AltoGao were isolated from the Seneca Wastewater Treatment Plant in Germantown, MD. The following reports the complete genome sequence of these bacteriophages and describes their major features.
Complete Genome Sequences of Mycobacteriophages Clautastrophe, Kingsolomon, Krypton555, and Nicholas
Authors: Chung Hui-Min , D’Elia Tom , Ross Joseph F. , Alvarado Samuel M. , Brantley Molly-Catherine , Bricker Lydia P. , Butler Courtney R. , Crist Carson , Dane Julia M. , Farran Brett W. , Hobbs Sierra , Lapak Michelle , Lovell Conner , Ludergnani Nicholas , McMullen Allison , Mirza Sohail A. , Thrift Noah , Vaughan Donald P. , Worley Grace , Ejikemeuwa Amara , Zaw May , Albritton Claude F. , Bertrand Sarah C. , Chaudhry Shanzay S. , Cheema Vzair A. , Do Camilla , Do Michael L. , Duong Huyen M. , El-Desoky Dalia H. , Green Kelsey M. , Lee Rhea N. , Thornton Lauren A. , Vu James M. , Zahra Mah Noor , Cresawn Steven G. , Stoner Ty H. , Garlena Rebecca A. , Jacobs-Sera Deborah , Pope Welkin H. , Russell Daniel A. , Hatfull Graham F. 
Published: November 2017

ABSTRACT

We report here the complete genome sequences of four subcluster L3 mycobacteriophages newly isolated from soil samples, using
Mycobacterium smegmatis
mc
2
155 as the host. Comparative genomic analyses with four previously described subcluster L3 phages reveal strong nucleotide similarity and gene conservation, with several large insertions/deletions near their right genome ends.
Draft Genome Sequences of Three Terrestrial Isoprene-Degrading
Rhodococcus
Strains
Authors: Crombie Andrew T. , Emery Helen , McGenity Terry J. , Murrell J. Colin 
Published: November 2017

ABSTRACT

Isoprene is produced in abundance by plants and constitutes a carbon source for microbes. The genomes of three isoprene degraders isolated from tree leaves or soil from the campus of the University of East Anglia were sequenced. These high-GC-content isolates are actinobacteria belonging to the genus
Rhodococcus
.
Draft Genome Sequence of Novosphingobium panipatense Strain P5:ABC, Isolated from Hydrocarbon-Contaminated Soil from Noonmati Refinery, Assam, India
Authors: Singh Arvind Kumar , Chettri Bobby , Ghosh Arpita , Chikara Surendra K. , Tripathi Timir 
Published: November 2017

ABSTRACT

Novosphingobium panipatense
P5:ABC is a hydrocarbon-degrading bacterium isolated from petroleum-contaminated soil. Here, we present the 5.74-Mb draft genome sequence with 5,206 genes and an average G+C content of 64.7%. The genomic information will improve our understanding of the diversity of
N. panipatense
and the mechanisms of microbe-based hydrocarbon degradation.
Injuries in female and male elite taekwondo athletes: a 10-year prospective, epidemiological study of 1466 injuries sustained during 250 000 training hours
Authors: Park Ki Jun , Song Brian Byung 
Published: November 2017

ObjectivesWe aimed to determine the injury patterns associated with training activities in elite South Korean taekwondo athletes training for the Olympic Games.MethodsWe collected data prospectively from 2007 to 2016 at the Korea National Training Center in Seoul, South Korea. A sports injury was defined as acute or chronic musculoskeletal signs and symptoms due to taekwondo activities during training sessions. Athletes were assessed by an on-site sports medicine specialist. The elite taekwondo athletes were stratified according to sex, weight class (flyweight, featherweight, welterweight and heavyweight), injury location (body region and site) and injury severity (mild or level I, requiring treatment for 1–3 days; moderate or level II, requiring treatment for 4–7 days; or severe or level III, requiring treatment for ≥8 days).ResultsAthlete exposure was 56 160 training sessions that took 249 600 hours. 1466 injuries were recorded in 283 athletes, with an average of 4.6 injuries per athlete annually. Of these, more than half (56%) were mild injuries, with most injuries occurring in the lower extremities (65.5%), followed by injuries to the trunk (16%), upper extremities (14%) and head and neck area (4%). Among these athletes, women had higher injury rates in the featherweight and welterweight categories (P≤0.0001), but there were no sex differences in other weight categories. In general, female athletes and male athletes experienced a comparable risk of injury (relative ratio: 1.55; 95% CI 0.89 to 2.68).ConclusionIn elite South Korean taekwondo athletes, most injuries occur in the lower extremities and were graded as minor. Injury severity depended on weight class.
Mortality and health-related habits in 900 Finnish former elite athletes and their brothers
Authors: Kontro Titta Katariina , Sarna Seppo , Kaprio Jaakko , Kujala Urho M 
Published: November 2017

BackgroundThere is conflicting evidence on the associations between participation in vigorous sports, health habits, familial factors and subsequent mortality. We investigated all-cause mortality and health-related behaviour among former elite athletes and their brothers.MethodsThe mortality of Finnish male former elite athletes, who had represented Finland between 1920 and 1965 (n=900) and their age-matched brothers (n=900), was followed from the time when athlete started an elite athlete career until 31 December 2015. The age-adjusted HRs were calculated by a paired Cox proportional hazards model. In 2001, surviving participants (n=199 athletes and n=199 age-matched brothers) reported their self-rated health (SRH), physical activity, alcohol consumption and smoking habits in the questionnaire.ResultsDuring the total follow-up period, 1296 deaths (72% of the cohort) occurred. The age-adjusted HRs for all-cause mortality in former athletes was 0.75 (95% CI 0.65 to 0.87, P<0.001) compared with their age-matched brothers. Median age at death was 79.9 years for endurance, 75.9 years for mixed sports and 72.2 years for power sports athletes, and 77.5, 73.7 and 72.2 years for their age-matched brothers, respectively. In 2001, compared with their brothers, former athletes smoked less (P<0.001), were more physically active (P<0.05) and rated their health more often as very good (P<0.05).ConclusionsFormer elite athletes are more physically active, smoke less, have better self-rated health and live longer than their brothers. Genetic differences between athletes and brothers, aerobic training for endurance elite sports and a healthier lifestyle may all contribute to reduced mortality.
Relationship between hormone replacement therapy and spinal osteoarthritis: a nationwide health survey analysis of the elderly Korean population
Authors: Park Jung-Ho , Hong Jae-Young , Han Kyungdo , Han Seung-Woo , Chun Eun Mi 
Published: November 2017

ObjectivesTo identify the effects of hormone replacement therapy (HRT) on spinal osteoarthritis (OA).Methods and designA cross-sectional study of a nationwide survey was performed.SettingThis study collected data from the fifth Korean National Health and Nutrition Examination Survey (2010–2012).ParticipantsAfter excluding ineligible respondents, the total number of participants in this study was 4265 females. Participants were asked to report symptoms and disabilities related to spinal OA. In addition, plain radiographs of the spine were taken of all patients.Primary and secondary outcome measuresDemographic and lifestyle variables were compared between the HRT and non-HRT groups. In addition, radiographic examination and symptom assessment were performed to determine the existence of spinal OA.ResultsMarital status, education, income and HRT were correlated with spinal OA. A risk analysis of related factors showed that HRT and age had effects on spinal OA (ORs 0.717 and 1.257). Nevertheless, in the HRT group, smokers had a increased risk of spinal OA. In addition, the HRT group demonstrated a lower prevalence of spinal OA. The calculated risk for compromised morbidity with HRT compared with the prevalence of spinal OA was 0.717 (OR). The duration of HRT was also related to the risk for spinal OA. The group that had been taking HRT for more than 1 year showed decreased risk (OR 0.686) compared with patients with <1 year of HRT (OR 0.744; P<0.05).ConclusionWomen receiving HRT showed a lower prevalence of spinal OA. HRT also correlated with a decrease in spinal OA morbidity.
Evaluation of psychometric properties of the German Hospital Survey on Patient Safety Culture and its potential for cross-cultural comparisons: a cross-sectional study
Authors: Gambashidze Nikoloz , Hammer Antje , Brösterhaus Mareen , Manser Tanja 
Published: November 2017

ObjectiveTo study the psychometric characteristics of German version of the Hospital Survey on Patient Safety Culture and to compare its dimensionality to other language versions in order to understand the instrument’s potential for cross-national studies.DesignCross-sectional multicentre study to establish psychometric properties of German version of the survey instrument.Setting73 units from 37 departments of two German university hospitals.ParticipantsClinical personnel (n=995 responses, response rate 39.6%).Primary and secondary outcome measuresPsychometric properties (eg, model fit, internal consistency, construct validity) of the instrument and comparison of dimensionality across different language translations.ResultsThe instrument demonstrated acceptable to good internal consistency (Cronbach’s alpha 0.64–0.88). Confirmatory factor analysis of the original 12-factor model resulted in marginally satisfactory model fit (root mean square error of approximation (RMSEA)=0.05; standardised root mean residual (SRMR)=0.05; comparative fit index (CFI)=0.90; goodness of fit index (GFI)=0.88; Tucker-Lewis Index (TLI)=0.88). Exploratory factor analysis resulted in an alternative eight-factor model with good model fit (RMSEA=0.05; SRMR=0.05; CFI=0.95; GFI=0.91; TLI=0.94) and good internal consistency (Cronbach’s alpha 0.73–0.87) and construct validity. Analysis of the dimensionality compared with models from 10 other language versions revealed eight dimensions with relatively stable composition and appearance across different versions and four dimensions requiring further improvement.ConclusionsThe German version of Hospital Survey on Patient Safety Culture demonstrated satisfactory psychometric properties for use in German hospitals. However, our comparison of instrument dimensionality across different language versions indicates limitations concerning cross-national studies. Results of this study can be considered in interpreting findings across national contexts, in further refinement of the instrument for cross-national studies and in better understanding the various facets and dimensions of patient safety culture.
Cancer genes mutation profiling in calcifying epithelial odontogenic tumour
Authors: de Sousa Sílvia Ferreira , Diniz Marina Gonçalves , França Josiane Alves , Fontes Pereira Thaís dos Santos , Moreira Rennan Garcias , Santos Jean Nunes dos , Gomez Ricardo Santiago , Gomes Carolina Cavalieri 
Published: November 2017

AimsTo identify calcifying epithelial odontogenic tumour (CEOT) mutations in oncogenes and tumour suppressor genes.MethodsA panel of 50 genes commonly mutated in cancer was sequenced in CEOT by next-generation sequencing. Sanger sequencing was used to cover the region of the frameshift deletion identified in one sample.ResultsMissense single nucleotide variants (SNVs) with minor allele frequency (MAF) <1% were detected inPTEN,METandJAK3. A frameshift deletion inCDKN2Aoccurred in association with a missense mutation in the same gene region, suggesting a second hit in the inactivation of this gene.APC, KDR, KIT, PIK3CAandTP53missense SNVs were identified; however, these are common SNVs, showing MAF >1%.ConclusionCEOT harbours mutations in the tumour suppressorPTENandCDKN2Aand in the oncogenesJAK3andMET. As these mutations occurred in only one case each, they are probably not driver mutations for these tumours.
History of the development of Permian–Cretaceous rifts in East Africa: a series of interpreted maps through time
Authors: Macgregor Duncan 
Published: November 2017

East Africa represents the most rifted portion of crust on the planet, having been subjected to numerous phases of extension from Permian to Recent times. The first rifting phase commences in the Permian as the ‘Karoo’ set of narrow half-graben, many formed by lateral shear. Peak rifting appears to be of Middle Permian age for rifts south of Tanzania. In Kenya, Ethiopia and Somalia, this rift population merges into a set of rifts with peak rifting of earliest Triassic age.
A further phase of rifting is seen in the Toarcian–Aalenian. Many of these overlie Permo-Triassic rifts but others are displaced towards what will become the continental margin. Three unrelated populations of Late Jurassic–Early Cretaceous rifts are observed, including those in Somalia, a series of pull-apart basins on the Davie Ridge and a poorly documented set in southern Mozambique. The Anza Rift, with peak rifting in the Late Cretaceous associated with the building of rift shoulders kilometres in height, is proposed here to be an isolated plume-derived rift.
Evaluation of the petroleum potential associated with these rifts relies on an accurate assessment of each in terms of their age and affinity to well-documented systems.

Supplementary material:
A table of East Africa Permian–Mesozoic rift basins and references is available at
https://doi.org/10.6084/m9.figshare.c.3902653