bluuebunny/crossref_metadata_2025_split huggingface dataset:
High conservation combined with high plasticity: genomics and evolution of Borrelia bavariensis
Authors: Becker Noémie S. , Rollins Robert E. , Nosenko Kateryna , Paulus Alexander , Martin Samantha , Krebs Stefan , Takano Ai , Sato Kozue , Kovalev Sergey Y. , Kawabata Hiroki , Fingerle Volker , Margos Gabriele 
Published: October 2020

Abstract
Background
Borrelia bavariensis is one of the agents of Lyme Borreliosis (or Lyme disease) in Eurasia. The genome of the Borrelia burgdorferi sensu lato species complex, that includes B. bavariensis, is known to be very complex and fragmented making the assembly of whole genomes with next-generation sequencing data a challenge.

Results
We present a genome reconstruction for 33 B. bavariensis isolates from Eurasia based on long-read (Pacific Bioscience, for three isolates) and short-read (Illumina) data. We show that the combination of both sequencing techniques allows proper genome reconstruction of all plasmids in most cases but use of a very close reference is necessary when only short-read sequencing data is available. B. bavariensis genomes combine a high degree of genetic conservation with high plasticity: all isolates share the main chromosome and five plasmids, but the repertoire of other plasmids is highly variable. In addition to plasmid losses and gains through horizontal transfer, we also observe several fusions between plasmids. Although European isolates of B. bavariensis have little diversity in genome content, there is some geographic structure to this variation. In contrast, each Asian isolate has a unique plasmid repertoire and we observe no geographically based differences between Japanese and Russian isolates. Comparing the genomes of Asian and European populations of B. bavariensis suggests that some genes which are markedly different between the two populations may be good candidates for adaptation to the tick vector, (Ixodes ricinus in Europe and I. persulcatus in Asia).

Conclusions
We present the characterization of genomes of a large sample of B. bavariensis isolates and show that their plasmid content is highly variable. This study opens the way for genomic studies seeking to understand host and vector adaptation as well as human pathogenicity in Eurasian Lyme Borreliosis agents.
Going web or staying paper? The use of web-surveys among older people
Authors: Kelfve Susanne , Kivi Marie , Johansson Boo , Lindwall Magnus 
Published: October 2020

Abstract
Background
Web-surveys are increasingly used in population studies. Yet, web-surveys targeting older individuals are still uncommon for various reasons. However, with younger cohorts approaching older age, the potentials for web-surveys among older people might be improved. In this study, we investigated response patterns in a web-survey targeting older adults and the potential importance of offering a paper-questionnaire as an alternative to the web-questionnaire.

Methods
We analyzed data from three waves of a retirement study, in which a web-push methodology was used and a paper questionnaire was offered as an alternative to the web questionnaire in the last reminder. We mapped the response patterns, compared web- and paper respondents and compared different key outcomes resulting from the sample with and without the paper respondents, both at baseline and after two follow-ups.

Results
Paper-respondents, that is, those that did not answer until they got a paper questionnaire with the last reminder, were more likely to be female, retired, single, and to report a lower level of education, higher levels of depression and lower self-reported health, compared to web-respondents. The association between retirement status and depression was only present among web-respondents. The differences between web and paper respondents were stronger in the longitudinal sample (after two follow-ups) than at baseline.

Conclusions
We conclude that a web-survey might be a feasible and good alternative in surveys targeting people in the retirement age range. However, without offering a paper-questionnaire, a small but important group will likely be missing with potential biased estimates as the result.
Case report: Candida krusei spondylitis in an immunocompromised patient
Authors: Overgaauw Audrey J. C. , de Leeuw David C. , Stoof Susanne P. , van Dijk Karin , Bot Joost C. J. , Hendriks Eef J. 
Published: October 2020

Abstract
Background
Invasive infections with Candida krusei are uncommon and rarely complicated by spondylitis. Previous described cases were solely treated with antimycotic therapy, despite guidelines recommending surgical interventions.

Case presentation
We describe a case of C. krusei spondylitis in a patient treated with chemotherapy for acute myeloid leukemia. After induction chemotherapy, the patient developed a candidemia, which was treated with micafungin. One month after the candidemia, the patient was admitted with severe lumbar pain. Spondylitis of the L4 and L5 vertebra was diagnosed on MR-imaging, with signs suggesting an atypical infection. The patient was treated with anidulafungin combined with voriconazole. Despite maximal conservative management symptoms gradually worsened eventually requiring surgical intervention.

Conclusions
In contrast to previous case reports, antimycotic treatment alone could be insufficient in treating C. krusei spondylitis.
Prevalence of and socioeconomic gradient in low birth weight in Ethiopia: further analysis of the 2016 demographic and health survey data
Authors: Shibre Gebretsadik , Tamire Mulugeta 
Published: October 2020

Abstract
Background
Evidence suggests appearance of socioeconomic gradient in the probability of low birth weight (LBW). Such evidence, however, is scanty in Ethiopia. The study aimed to examine the prevalence of and socioeconomic gradient in LBW in Ethiopia.

Method
Data for the study were drawn from the Ethiopia Demographic and Health Survey conducted in 2016. The 2016 EDHS is the fourth wave in the series of nationally representative household surveys carried out in the country to deliver up-to-date health and demographic indicators for the Ethiopian population. Women aged 15 to 49 years were the main focus of the survey, with data also gathered from men aged 15 to 59 years and under five children. The study pursued complex sampling strategy to draw samples representative at national as well as at urban and rural levels. The data are available to the public domain and were accessed from the MEASURE DHS following registration. Multivariable logistic regression model and marginal standardization were used to estimate socioeconomic gradient in the probability of LBW. We performed sensitivity analysis to evaluate variation of LBW according to different categories of socioeconomic position. Maternal education and household wealth were used as measures of the socioeconomic position in the study.

Results
13.2% (95% confidence interval = 10.73, 15.65) of births were complicated by LBW. The findings showed that socioeconomic gradient was evident between maternal education and LBW; as education increases from no education to secondary education, the probability of occurrence of LBW consistently declined. However, no gradient in LBW was detected for household wealth.

Conclusions
We have identified education gradient in LBW, with the highest burden of LBW occurring among the non-educated women. To redress the observed education disparity in LBW, targeted interventions need to be implemented with greater emphasis placed on illiterate women.
Improving infant sleep safety via electronic health record communication: a randomized controlled trial
Authors: Canty Ethan A. , Fogel Benjamin N. , Batra Erich K. , Schaefer Eric W. , Beiler Jessica S. , Paul Ian M. 
Published: October 2020

Abstract
Background
With increased use of telehealth, interventions to improve infant sleep environments have not been explored. This study sought to assess the feasibility and efficacy of using electronic health record patient portals to transmit photographs of infant sleep between mothers and healthcare professionals as part of an intervention to promote sleep environments consistent with AAP guidelines.

Methods
One hundred eighty-four mother-newborn dyads consented to participate in a randomized trial requiring patient portal registration within 1 month of delivery. We first assessed feasibility as measured by a) the proportion of consented mothers enrolling in the portal and b) maternal adherence to prompts to submit photographs of their infant sleeping to the research team through the patient portal. Intervention group mothers were prompted at 1 and 2 months; controls were prompted only at 2 months. Efficacy was determined via research assistant review of submitted photographs. These assistants were trained to detect sudden unexplained infant death risk factors utilizing AAP guidelines. Standardized feedback was returned to mothers through the patient portal. We used Fisher’s Exact test to assess group differences in guideline adherence at 2 months.

Results
One hundred nine mothers (59%) enrolled in the patient portal and were randomized to intervention (N = 55) and control (N = 54) groups. 21 (38, 95% CI 25–52%) intervention group participants sent photographs at 1 month and received personalized feedback. Across both groups at 2 months, 40 (37, 95% CI 28–46%) sent photographs; 56% of intervention group participants who submitted photographs met all safe sleep criteria compared with 46% of controls (difference 0.10, 95% CI − 0.26 to 0.46, p = .75). Common reasons for guideline non-adherence were sleeping in a room without a caregiver (43%), loose bedding (15%) and objects (8%) on the sleep surface.

Conclusions
Utilizing the patient portal to individualize safe infant sleep is possible, however, we encountered numerous barriers in this trial to assess its effects on promoting safe infant sleep. Photographs of infants sleeping showed substantial non-adherence to AAP guidelines, suggesting further needs for improvement to promote safe infant sleep practices.

Trial registration
Name: Improving Infant Sleep Safety With the Electronic Health Record; Clinicaltrials.gov: NCT03662048; Date of Registration: September 7, 2018;
Data Sharing Statement: None
Correlation of medical students' situational motivation and performance of non-technical skills during simulation-based emergency training
Authors: Schulte-Uentrop Leonie , Cronje Jonathan S. , Zöllner Christian , Kubitz Jens C. , Sehner Susanne , Moll-Khosrawi Parisa 
Published: October 2020

AbstractBackgroundNon-technical skills (NTS) are an indispensable element of emergency care and need to be prevalent alongside with good technical skills. Though, questions of how to teach (instructional design) and improve NTS effectively remain unresolved. One adjustment screw to enhance performance of NTS, which is detached from instructional designs and learning efforts might be motivation. Theoretical models and observational studies suggest that high levels of intrinsic (situational) motivation result in better performance and better learning. Therefore, this study analyzed the influence of motivation on performance of NTS, by exploring if high levels of intrinsic motivation lead to better performance of NTS in medical students.MethodsIn this prospective cross-sectional cohort study, the authors assessed the correlation of situational motivation and performance of NTS within a cohort of 449 undergraduates in their 1st to 4th year of medical studies, in a total of 101 emergency simulation trainings. Situational motivation was measured with the validated Situational Motivation Scale (SIMS), which was completed by every undergraduate directly before each simulation training. The NTS were evaluated with the Anesthesiology Students´ Non-Technical skills (AS-NTS) rating tool, a validated taxonomy, especially developed to rate NTS of undergraduates.ResultsStudent situational motivation was weakly correlated with their performance of NTS in simulation-based emergency trainings.ConclusionAlthough motivation has been emphasized as a determining factor, enhancing performance in different fields and in medicine in particular, in our study, student situational motivation was independent from their performance of NTS in simulation-based emergency trainings (SBET).
How to enhance and assess reflection in specialist training: a mixed method validation study of a new tool for global assessment of reflection ability
Authors: Lillevang Gunver , Ibsen Helle , Prins Søren Hast , Kjaer Niels Kristian 
Published: October 2020

Abstract
Background
In Danish GP training we had the ambition to enhance and assess global reflection ability, but since we found no appropriate validated method in the literature, we decided to develop a new assessment tool. This tool is based on individual trainee developed mind maps and structured trainer-trainee discussions related to specific complex competencies. We named the tool Global Assessment of Reflection ability (GAR) and conducted a mixed method validation study. Our goal was to investigate whether it is possible to enhance and assess reflection ability using the tool.

Methods
In order to investigate acceptability, feasibility, face validity, and construct validity of the tool we conducted a mixed method validation study that combined 1) qualitative data obtained from 750 GP trainers participating in train-the-trainer courses, 2) a questionnaire survey sent to 349 GP trainers and 214 GP trainees and 3) a thorough analysis of eight trainer-trainee discussions.

Results
Our study showed an immediate high acceptance of the GAR tool. Both trainers and trainees found the tool feasible, useful, and relevant with acceptable face validity. Rating of eight audio recordings showed that the tool can demonstrate reflection during assessment of complex competencies.

Conclusions
We have developed an assessment tool (GAR) to enhance and assess reflection. GAR was found to be acceptable, feasible, relevant and with good face- and construct validity. GAR seems to be able to enhance the trainees’ ability to reflect and provide a good basis for assessment in relation to complex competencies.
Integration of palliative care in services for children with life-limiting neurodevelopmental disabilities and their families: a Delphi study
Authors: Guerin Suzanne , Kiernan Gemma , Courtney Eileen , McQuillan Regina , Ryan Karen 
Published: October 2020

Abstract
Background
The aim of this study was to explore expert professionals’ opinions on service provision to children under six with life-limiting neurodevelopmental disabilities (LLNDD), including the goals of care and the integration and coordination of palliative care in general and specialist services.

Methods
A Delphi design was used with three questionnaire rounds, one open-ended and two closed response rounds. Primary data collected over a six-month period from expert professionals with five years’ (or more) experience in pediatric, intellectual disability and/or palliative care settings. Ratings of agreement and prioritization were provided with agreement expressed as a median (threshold = 80%) and consensus reported as interquartile ranges. Stability was measured using non-parametric tests.

Results
Primary goals of care were achievement of best possible quality of life, effective communication and symptom management. Service integration and coordination were considered inadequate, and respondents agreed that areas of deficiency included palliative care. Improvement strategies included a single care plan, improved communication and key worker appointments.

Conclusions
The findings suggest that services do not serve this group well with deficiencies in care compounded by a lack of information on available services and sub-optimal communication between settings. Further research is needed to develop an expert-based consensus regarding the care of children with LLNDD.
Development, implementation and evaluation of an online course on evidence-based healthcare for consumers
Authors: Han Genie , Mayer Musa , Canner Joseph , Lindsley Kristina , Datar Reva , Le Jimmy , Bar-Cohen Annette , Bowie Janice , Dickersin Kay 
Published: October 2020

Abstract
Background
Evidence-based healthcare (EBHC) principles are essential knowledge for patient and consumer (“consumer”) engagement as research and research implementation stakeholders. The aim of this study was to assess whether participation in a free, self-paced online course affects confidence in explaining EBHC topics. The course comprises six modules and evaluations which together take about 6 h to complete.

Methods
Consumers United for Evidence-based Healthcare (CUE) designed, tested and implemented a free, online course for consumers, Understanding Evidence-based Healthcare: A Foundation for Action (“Understanding EBHC”). The course is offered through the Johns Hopkins Bloomberg School of Public Health. Participants rated their confidence in explaining EBHC topics on a scale of 1 (lowest) to 5 (highest), using an online evaluation provided before accessing the course (“Before”) and after (“After”) completing all six course modules. We analyzed data from those who registered for the course from May 31, 2007 to December 31, 2018 (n = 15,606), and among those persons, the 11,522 who completed the “Before” evaluation and 4899 who completed the “After” evaluation. Our primary outcome was the overall mean of within-person change (“overall mean change”) in self-reported confidence levels on EBHC-related topics between “Before” and “After” evaluations among course completers. Our secondary outcomes were the mean within-person change for each of the 11 topics (mean change by topic).

Results
From May 31, 2007 to December 31, 2018, 15,606 individuals registered for the course: 11,522 completed the “Before” evaluation, and 4899 of these completed the “After” evaluation (i.e., completed the course). The overall mean change in self-reported confidence levels (ranging from 1 to 5) from the “Before” to “After” evaluation was 1.27 (95% CI, 1.24–1.30). The mean change by topic ranged from 1.00 (95% CI, 0.96–1.03) to 1.90 (95% CI, 1.87–1.94).

Conclusion
Those who seek to involve consumer stakeholders can offer Understanding EBHC as a step toward meaningful consumer engagement. Future research should focus on long-term impact assessment of online course such as ours to understand whether confidence is retained post-course and applied appropriately.
Identification of African swine fever virus-like elements in the soft tick genome provides insights into the virus’ evolution
Authors: Forth Jan H. , Forth Leonie F. , Lycett Samantha , Bell-Sakyi Lesley , Keil Günther M. , Blome Sandra , Calvignac-Spencer Sébastien , Wissgott Antje , Krause Johannes , Höper Dirk , Kampen Helge , Beer Martin 
Published: October 2020

Abstract
Background
African swine fever virus (ASFV) is a most devastating pathogen affecting swine. In 2007, ASFV was introduced into Eastern Europe where it continuously circulates and recently reached Western Europe and Asia, leading to a socio-economic crisis of global proportion. In Africa, where ASFV was first described in 1921, it is transmitted between warthogs and soft ticks of the genus Ornithodoros in a so-called sylvatic cycle. However, analyses into this virus’ evolution are aggravated by the absence of any closely related viruses. Even ancient endogenous viral elements, viral sequences integrated into a host’s genome many thousand years ago that have proven extremely valuable to analyse virus evolution, remain to be identified. Therefore, the evolution of ASFV, the only known DNA virus transmitted by arthropods, remains a mystery.

Results
For the identification of ASFV-like sequences, we sequenced DNA from different recent Ornithodoros tick species, e.g. O. moubata and O. porcinus, O. moubata tick cells and also 100-year-old O. moubata and O. porcinus ticks using high-throughput sequencing. We used BLAST analyses for the identification of ASFV-like sequences and further analysed the data through phylogenetic reconstruction and molecular clock analyses. In addition, we performed tick infection experiments as well as additional small RNA sequencing of O. moubata and O. porcinus soft ticks.

Conclusion
Here, we show that soft ticks of the Ornithodoros moubata group, the natural arthropod vector of ASFV, harbour African swine fever virus-like integrated (ASFLI) elements corresponding to up to 10% (over 20 kb) of the ASFV genome. Through orthologous dating and molecular clock analyses, we provide data suggesting that integration could have occurred over 1.47 million years ago. Furthermore, we provide data showing ASFLI-element specific siRNA and piRNA in ticks and tick cells allowing for speculations on a possible role of ASFLI-elements in RNA interference-based protection against ASFV in ticks. We suggest that these elements, shaped through many years of co-evolution, could be part of an evolutionary virus-vector ‘arms race’, a finding that has not only high impact on our understanding of the co-evolution of viruses with their hosts but also provides a glimpse into the evolution of ASFV.
LDL-C: lower is better for longer—even at low risk
Authors: Penson Peter E. , Pirro Matteo , Banach Maciej 
Published: October 2020

Abstract
Background
Low-density lipoprotein cholesterol (LDL-C) causes atherosclerotic disease, as demonstrated in experimental and epidemiological cohorts, randomised controlled trials, and Mendelian randomisation studies.

Main text
There is considerable inconsistency between existing guidelines as to how to effectively manage patients at low overall risk of cardiovascular disease (CVD) who have persistently elevated levels of LDL-C.
We propose a step-by-step practical approach for the management of cardiovascular risks in individuals with low (< 1%) 10-year risk of CVD, and elevated (> 140 mg/dL, 3.6 mmol/L) LDL-C. The strategy proposed is based on the level of adherence to lifestyle interventions (LSI), and in case of non-adherence, stepwise practical management, including lipid-lowering therapy, is recommended to achieve a target LDL-C levels (< 115 mg/dL, 3.0 mmol/L).

Conclusions
Further studies are necessary to answer the questions on the long-term efficacy, safety, and cost-effectiveness of the suggested approach. This is critical, considering the ever-increasing numbers of such low-risk patients seen in clinical practice.
RETRACTED ARTICLE: Aging-related tumor associated fibroblasts changes could worsen the prognosis of GBM patients
Authors: Song Hongwang , Fu Xiaojun , Wu Chenxing , Li Shouwei 
Published: October 2020

Abstract
Background
Glioblastoma multiforme (GBM) is the most malignant tumor in human brain, with highly heterogeneity among different patients. Age could function as an incidence and prognosis risk factor for many tumors.

Method
A series of bioinformatic experiments were conducted to evaluate the differences of incidence, differential expressed genes, enriched pathways with the data from Surveillance, Epidemiology, and End Results (SEER) program, the cancer genome atlas (TCGA) and Chinese glioma genome atlas (CGGA) project.

Results
We discovered in our present study that distinct difference of incidence and prognosis of different aged GBM patients. By a series of bioinformatic method, we found that the tumor associated fibroblasts (TAFs) was the most crucial tumor microenvironment (TME) component that led to this phenomenon. Epithelial-mesenchymal transition (EMT) could be the mechanism by which TAFs regulate the progression of GBM.

Conclusion
We have proposed a close correlation between age and GBM incidence and prognosis, and propose the underlying mechanism behind this correlation by mining different databases, which laid the foundation for future research.