bluuebunny/crossref_metadata_2025_split huggingface dataset:
GenTB: A user-friendly genome-based predictor for tuberculosis resistance powered by machine learning
Authors: Gröschel Matthias I. , Owens Martin , Freschi Luca , Vargas Roger , Marin Maximilian G. , Phelan Jody , Iqbal Zamin , Dixit Avika , Farhat Maha R. 
Published: August 2021

Abstract
Background
Multidrug-resistant Mycobacterium tuberculosis (Mtb) is a significant global public health threat. Genotypic resistance prediction from Mtb DNA sequences offers an alternative to laboratory-based drug-susceptibility testing. User-friendly and accurate resistance prediction tools are needed to enable public health and clinical practitioners to rapidly diagnose resistance and inform treatment regimens.

Results
We present Translational Genomics platform for Tuberculosis (GenTB), a free and open web-based application to predict antibiotic resistance from next-generation sequence data. The user can choose between two potential predictors, a Random Forest (RF) classifier and a Wide and Deep Neural Network (WDNN) to predict phenotypic resistance to 13 and 10 anti-tuberculosis drugs, respectively. We benchmark GenTB’s predictive performance along with leading TB resistance prediction tools (Mykrobe and TB-Profiler) using a ground truth dataset of 20,408 isolates with laboratory-based drug susceptibility data. All four tools reliably predicted resistance to first-line tuberculosis drugs but had varying performance for second-line drugs. The mean sensitivities for GenTB-RF and GenTB-WDNN across the nine shared drugs were 77.6% (95% CI 76.6–78.5%) and 75.4% (95% CI 74.5–76.4%), respectively, and marginally higher than the sensitivities of TB-Profiler at 74.4% (95% CI 73.4–75.3%) and Mykrobe at 71.9% (95% CI 70.9–72.9%). The higher sensitivities were at an expense of ≤ 1.5% lower specificity: Mykrobe 97.6% (95% CI 97.5–97.7%), TB-Profiler 96.9% (95% CI 96.7 to 97.0%), GenTB-WDNN 96.2% (95% CI 96.0 to 96.4%), and GenTB-RF 96.1% (95% CI 96.0 to 96.3%). Averaged across the four tools, genotypic resistance sensitivity was 11% and 9% lower for isoniazid and rifampicin respectively, on isolates sequenced at low depth (< 10× across 95% of the genome) emphasizing the need to quality control input sequence data before prediction. We discuss differences between tools in reporting results to the user including variants underlying the resistance calls and any novel or indeterminate variants

Conclusions
GenTB is an easy-to-use online tool to rapidly and accurately predict resistance to anti-tuberculosis drugs. GenTB can be accessed online at https://gentb.hms.harvard.edu, and the source code is available at https://github.com/farhat-lab/gentb-site.
Accelerated osteoarthritis in women with polycystic ovary syndrome: a prospective nationwide registry-based cohort study
Authors: Kluzek Stefan , Rubin Katrine Hass , Sanchez-Santos Maria , O’Hanlon Mary S. , Andersen Marianne , Glintborg Dorte , Abrahamsen Bo 
Published: August 2021

AbstractBackgroundOsteoarthritis (OA) is the most common form of arthritis with multiple risk factors implicated including female sex and obesity. Metabolic dysregulation associated with obesity leading to metabolic syndrome is a proposed component of that association. Polycystic ovary syndrome (PCOS) commonly affects women of reproductive age and these women are at higher risk of developing metabolic syndrome and thus likely to represent a high-risk group for early OA development. There are no published studies exploring the epidemiology of knee, hip and hand OA in women diagnosed with PCOS.Study aimTo assess the prevalence and incidence of knee, hip and hand osteoarthritis (OA) in women with polycystic ovary syndrome (PCOS) when compared with age-matched controls.MethodsProspective Danish national registry-based cohort study. The prevalence of OA in 2015 and incidence rates of OA over 11.1 years were calculated and compared in more than 75,000 Danish women with either a documented diagnosis of PCOS ± hirsutism (during the period of 1995 to 2012) or age-matched females without those diagnoses randomly drawn from the same population register.ResultsIn 2015, the prevalence of hospital treated knee, hip and hand OA was 5.2% in women with PCOS diagnosis. It was 73% higher than that seen in age-matched controls. Significantly higher incidence rates were observed in the PCOS cohort compared with the age-matched controls during the follow-up period (up to 20 years), with the following hazard ratios (HR): 1.9 (95% CI 1.7 to 2.1) for knee, 1.8 (95% CI 1.3–2.4) for hand and 1.3 (95% CI 1.1 to 1.6) for hip OA. After excluding women with obesity, similar associations were observed for knee and hand OA. However, risk of developing hip OA was no longer significant.ConclusionsIn this large prospective study, women with PCOS diagnosis had higher prevalence and accelerated onset of OA of both weight and non-weight bearing joints, when compared with age-matched controls. Further studies are needed to understand the relative effect of metabolic and hormonal changes linked with PCOS and their role in promoting development of OA.
Epidemiology and treatment of Behçet’s disease in the USA: insights from the Rheumatology Informatics System for Effectiveness (RISE) Registry with a comparison with other published cohorts from endemic regions
Authors: Hammam Nevin , Li Jing , Evans Michael , Kay Julia L. , Izadi Zara , Anastasiou Christine , Gianfrancesco Milena A. , Yazdany Jinoos , Schmajuk Gabriela 
Published: August 2021

Abstract
Background
Behçet’s disease (BD), a chronic systemic vasculitis, has distinct geographical and ethnic variation. Data regarding the epidemiology of patients with BD in the U.S. are limited; therefore, we sought to describe BD patient characteristics and medication use in the U.S., and compared them with data from patients from endemic regions.

Methods
We conducted a cross-sectional study using data from the RISE registry (2014–2018). Patients aged ≥ 18 years with BD were included. Sociodemographic and treatment information was extracted. We compared patients from the RISE registry to data from other published studies of patients with BD from endemic areas.

Results
One thousand three hundred twenty-three subjects with BD from the RISE registry were included. Mean age was 48.7 ± 16.3 years, female to male ratio was 3.8:1, and 66.7% were White. The most frequently used medications included glucocorticoids (67.6%) and colchicine (55.0%). Infliximab and adalimumab were the most used biologics (14.5% and 14.1%, respectively); 3.2% of patients used apremilast. The RISE registry had more women (79.3%), and patients were older compared to previously published BD studies from endemic areas. Methotrexate and TNFi were more commonly reported in RISE (21.8% and 29.4%) compared to studies from Egypt and Turkey. Colchicine, cyclosporine, and cyclophosphamide were more commonly used in cohorts from Egypt, Turkey, and Iran.

Conclusions
Findings from the largest BD dataset in the U.S. suggest that BD patients are predominantly female. Further research is needed to explore the reasons for the higher prevalence of BD among women in the U.S. and its possible impact on disease severity and management.
More than a meeting: identifying the needs of the community-based seniors’ services sector as providers of health promotion services
Authors: Tong Catherine E. , Sims-Gould Joanie , Lusina-Furst Sarah , McKay Heather 
Published: August 2021

AbstractObjectiveMany economically developed countries have seen a decline in publicly funded community programming. Within this context, community-based seniors’ service (CBSS) organizations have been increasingly tasked to deliver programs to support the health and wellbeing of older citizens (e.g., home support, physical activity programs, and chronic disease management education). The primary objective of this study was to capture of the current needs of CBSS leaders in British Columbia, Canada, who attended a seminal event in the CBSS sector’s development—the inaugural Summit on Aging.ResultsOur evaluation of the Summit included: pre/post Summit surveys (N = 79/76), ethnographic observations, and follow-up interviews (n = 22). Our detailed evaluation plan may inform others undertaking similar data collection; the most informative results were derived from the follow-up interviews and our findings suggest that interviews may be sufficient for similar evaluations. Summit delegates identified key opportunities to strengthen the CBSS as a sector, including enhanced collaboration; improved mechanisms that foster connecting and collaborating; and more resources, including training and qualified staff, to increase their capacity to deliver community-based health services. These findings echo work already completed in the community-based health promotion sector.
SonoGames: sounds of the right kind introducing gamification into radiology training
Authors: Ali Maria Fatima , Nadeem Naila , Khalid Farah , Anwar Naveed Muhammad , Nabie Ghulam , Docherty Charles 
Published: August 2021

Abstract
Background
Radiology as compared to other fields of medicine has lagged, in incorporating modern training modalities such as gamification and simulation into its teaching curriculum.

Objective
This study aims to evaluate effectiveness of simulation-based teaching in collaboration with gamification. Bandura’s conception of self-efficacy was used to provide qualitative assessment of participants’ learning process through training event. Modified competitive game-based teaching methodology was utilized in an experimental study conducted for radiology residents. Workshop was divided into two sessions, first being three interactive didactic lectures followed by three competitive rounds. All participants were required to fill pre and post-self-efficacy questionnaire along with an activity evaluation form.

Results
Significant self-efficacy scores were calculated for simulation-based stations of knowledge assessment and hands-on stations. Whereas significant association was also found between gender and knowledge assessment in communication skill (0.054), Professionalism (0.004), and general knowledge (0.018). Similarly, noteworthy correlation was found between gender and all hands-on skills. In conclusion, study reported an overall increase in knowledge of post-test scores compared to pre-test scores due to use of gamification in combination with simulation-based teaching which shows a positive role in clinical training. However, further consideration is needed to improve process of integrating simulation in clinical training of participants.
Dynamics of epigenetic regulator gene BCOR mutation and response predictive value for hypomethylating agents in patients with myelodysplastic syndrome
Authors: Li Xiao , Xu Feng , Zhang Zheng , Guo Juan , He Qi , Song Lu-Xi , Wu Dong , Zhou Li-Yu , Su Ji-Ying , Xiao Chao , Chang Chun-Kang , Wu Ling-Yun 
Published: August 2021

Abstract
Background
BCOR (BCL6 corepressor) is an epigenetic regulator gene involved in the specification of cell differentiation and body structure development. Recurrent somatic BCOR mutations have been identified in myelodysplastic syndrome (MDS). However, the clinical impact of BCOR mutations on MDS prognosis is controversial and the response of hypomethylating agents in MDS with BCOR mutations (BCORMUT) remains unknown.

Results
Among 676 MDS patients, 43 patients (6.4%) harbored BCOR mutations. A higher frequency of BCOR mutations (8.7%) was investigated in patients with normal chromosome, compared to 4.2% in patients with abnormal karyotype (p = 0.040). Compared to the BCORWT patients, the BCORMUT patients showed a higher ratio of refractory anemia with excess blasts subset (p = 0.008). The most common comutations with BCOR genes were ASXL1 (p = 0.002), DNMT3A (p = 0.114) and TET2 (p = 0.148). When the hierarchy of somatic mutations was analyzed, BCOR mutations were below the known initial mutations (ASXL1 or TET2) but were above U2AF1 mutations. Transformation-free survival was significantly shorter in BCORMUT patients than that in BCORWT patients (16 vs. 35 months; p = 0.035). RNA-sequencing was performed in bone marrow mononuclear cells from BCORMUT and BCORWT patients and revealed 2030 upregulated and 772 downregulated genes. Importantly, HOXA6, HOXB7, and HOXB9 were significantly over-expressed in BCORMUT patients, compared to BCORWT patients. Eight of 14 BCORMUT patients (57.1%) achieved complete remission (CR) with decitabine treatment, which was much higher than that in BCORWT patients (28.7%, p = 0.036). Paired sequencing results (before and after decitabine) showed three of 6 CR patients lost the mutated BCOR. The median survival of CR patients with a BCORMUT was 40 months, which was significantly longer than that in patients with BCORWT (20 months, p = 0.036). Notably, prolonged survival was observed in three BCORMUT CR patients even without any subsequent therapies.

Conclusions
BCOR mutations occur more frequently in CN MDS patients, predicting higher risk of leukemia transformation. BCORMUT patients showed a better response to decitabine and achieved longer post-CR survival.
The inferior vena cava: anatomical variants and acquired pathologies
Authors: Li Simon J. , Lee Jean , Hall Jonathan , Sutherland Tom R. 
Published: August 2021

AbstractThe inferior vena cava (IVC) is the largest vein in the body, draining blood from the abdomen, pelvis and lower extremities. This pictorial review summarises normal anatomy and embryological development of the IVC. In addition, we highlight a wide range of anatomical variants, acquired pathologies and a common pitfall in imaging of the IVC. This information is essential for clinical decision making and to reduce misdiagnosis.
Predictors and moderators of outcome of psychotherapeutic interventions for mental disorders in adolescents and young adults: protocol for systematic reviews
Authors: Vousoura Eleni , Gergov Vera , Tulbure Bogdan Tudor , Camilleri Nigel , Saliba Andrea , Garcia-Lopez LuisJoaquin , Podina Ioana R. , Prevendar Tamara , Löffler-Stastka Henriette , Chiarenza Giuseppe Augusto , Debbané Martin , Markovska-Simoska Silvana , Milic Branka , Torres Sandra , Ulberg Randi , Poulsen Stig 
Published: August 2021

Abstract
Background
Adolescence and young adulthood is a risk period for the emergence of mental disorders. There is strong evidence that psychotherapeutic interventions are effective for most mental disorders. However, very little is known about which of the different psychotherapeutic treatment modalities are effective for whom. This large systematic review aims to address this critical gap within the literature on non-specific predictors and moderators of the outcomes of psychotherapeutic interventions among adolescents and young adults with mental disorders.

Methods
The protocol is being reported in accordance with the Preferred Reporting Items for Systematic Review and Meta-Analysis Protocols (PRISMA-P) Statement. PubMed and PsycINFO databases will be searched for randomized controlled and quasi-experimental/naturalistic clinical trials. Risk of bias of all included studies will be assessed by the Mixed Methods Appraisal Tool. The quality of predictor and moderator variables will be also assessed. A narrative synthesis will be conducted for all included studies.

Discussion
This systematic review will strengthen the evidence base on effective mental health interventions for young people, being the first to explore predictors and moderators of outcome of psychotherapeutic interventions for a wide range of mental disorders in young people.

Systematic review registration
PROSPERO CRD42020166756.
Strong convergence for monotone bilevel equilibria with constraints of variational inequalities and fixed points using subgradient extragradient implicit rule
Authors: He Long , Cui Yun-Ling , Ceng Lu-Chuan , Zhao Tu-Yan , Wang Dan-Qiong , Hu Hui-Ying 
Published: August 2021

AbstractIn a real Hilbert space, let GSVI and CFPP represent a general system of variational inequalities and a common fixed point problem of a countable family of nonexpansive mappings and an asymptotically nonexpansive mapping, respectively. In this paper, via a new subgradient extragradient implicit rule, we introduce and analyze two iterative algorithms for solving the monotone bilevel equilibrium problem (MBEP) with the GSVI and CFPP constraints, i.e., a strongly monotone equilibrium problem over the common solution set of another monotone equilibrium problem, the GSVI and the CFPP. Some strong convergence results for the proposed algorithms are established under the mild assumptions, and they are also applied for finding a common solution of the GSVI, VIP, and FPP, where the VIP and FPP stand for a variational inequality problem and a fixed point problem, respectively.
A pooled prevalence of fetal alcohol spectrum disorders in South Africa: a systematic review and meta-analysis protocol
Authors: Adebiyi Babatope O. , Mukumbang Ferdinand C. 
Published: August 2021

Abstract
Background
Fetal Alcohol Spectrum Disorder (FASD) remains a global public health problem. South Africa is estimated to have the highest recorded prevalence of FASD. However, no study has systematically evaluated the available prevalence studies to provide estimates that may facilitate effective planning and delivery of prevention and management services. Therefore, we propose to conduct a systematic review and meta-analysis to report a pooled estimate of the FASD prevalence among children, youth and adults in South Africa.

Methods
We will include quantitative (cohort and cross-sectional) studies that reported on the prevalence of FASD in South Africa. We will search databases such as Academic Search Complete, Education Resource Information Center (ERIC), SocINDEX, Health Source: Nursing/Academic Edition, Cumulative Index of Nursing and Allied Health and PsycARTICLES), Scopus, Science Direct, Springer Link, JSTOR, SAGE journals, PubMed, Web of Science and Sabinet. The references of included studies will be searched for additional studies on the prevalence of FASD. The search will be from inception to October 2021. Screening of (titles, abstracts and full text of the potentially relevant articles) will be done by two independent authors using software. All disagreements will be resolved by discussion. A standardised data extraction form will be designed for the extraction. Two authors will independently extract the data from the selected articles and all disagreements will be resolved by discussion. We will use a tool developed by Munn and colleagues to critically appraise all the included studies. The primary outcome will be the proportion of individuals with FASD in South Africa. We will use the Freeman–Tukey double arcsine transformation to transform the raw prevalence estimates so that the data can follow an approximately normal distribution. We will use random-effects models to calculate 95% confidence intervals and prediction intervals based on multiple meta-analyses with transformed proportions. We will test heterogeneity using Cochran’s Q and describe using the I2 statistic.

Discussion
The pooled prevalence estimate will assist the government and other stakeholders (such as non-profit organisations and researchers) to plan and prioritise prevention and management interventions.

Systematic review registration
The protocol has been registered with PROSPERO (registration number: CRD42020197979).
Admission screening and cohort care decrease carbapenem resistant enterobacteriaceae in Vietnamese pediatric ICU’s
Authors: Garpvall K. , Duong V. , Linnros S. , Quốc T. N. , Mucchiano D. , Modeen S. , Lagercrantz L. , Edman A. , Le N. K. , Huong T. , Hoang N. T. B. , Le H. T. , Khu D. TK. , Tran D. M. , Phuc P. H. , Hanberger H. , Olson L. , Larsson M. 
Published: August 2021

Abstract
Objectives
To assess if admission screening for Carbapenem Resistant Enterobacteriaceae (CRE) and cohort care can reduce CRE acquisition (CRE colonization during hospital stay), Hospital Acquired Infections (HAI), hospital-stay, mortality, and costs in three Intensive Care Units (ICU’s) at the Vietnamese National Children’s Hospital.

Method
CRE screening using rectal swabs and ChromIDCarbas elective culture at admission and if CRE negative, once weekly. Patients were treated in cohorts based on CRE colonization status.

Results
CRE colonization at baseline point-prevalence screening was 76.9% (103/134). Of 941 CRE screened at admission, 337 (35.8%) were CREpos. 694 patients met inclusion criteria. The 244 patients CRE negative at admission and screened > 2 times were stratified in 8 similar size groups (periods), based on time of admission. CRE acquisition decreased significant (OR − 3.2, p < 0.005) from 90% in period 2 (highest) to 48% in period 8 (last period). Patients with CRE acquisition compared to no CRE acquisition had a significantly higher rate of culture confirmed HAI, n = 20 (14%) vs. n = 2 (2%), longer hospital stays, 3.26 vs. 2.37 weeks, and higher total treatment costs, 2852 vs. 2295 USD.

Conclusion
Admission CRE screening and cohort care in pediatric ICU’s significantly decreased CRE acquisition, cases of HAI and duration of hospital-stay.
Pain and health-related quality of life in adolescents and the mediating role of self-esteem and self-efficacy: a cross-sectional study including adolescents and parents
Authors: Mikkelsen Hilde Timenes , Haraldstad Kristin , Helseth Sølvi , Skarstein Siv , Småstuen Milada Cvancarova , Rohde Gudrun 
Published: August 2021

Abstract
Background
To promote health-related quality of life (HRQOL) in adolescents with pain, it is important to study factors associated with pain. This study aimed to describe selected factors and pain in 14–15-year-old adolescents and their parents, to assess how these factors are associated with adolescent pain groups, and to explore whether the relationship between pain intensity and HRQOL in adolescents with persistent pain is mediated by self-esteem and self-efficacy.

Methods
A cross-sectional study was performed among 508 dyads of adolescents (14–15 years) and parents in a school-based setting. Among these, 148 adolescents had persistent pain. We explored the following variables: HRQOL, pain, self-efficacy, self-esteem, sleep, loneliness, stress and sociodemographic variables. All variables were assessed with well-validated instruments. HRQOL was measured with KIDSCREEN-27. Analyses included Chi-square, ANOVA, Mann–Whitney U tests, Kruskal–Wallis and the PROCESS macro method for mediation analyses.

Results
Adolescents with pain reported significantly higher levels of stress, loneliness and lack of sleep and lower levels of self-efficacy, self-esteem and HRQOL compared to adolescents without pain. More girls than boys reported pain. Adolescents with persistent pain scored significantly worse on self-esteem, stress, loneliness, lack of sleep, school absence, pain and HRQOL compared to adolescents with shorter pain duration. Adolescent pain groups did not differ significantly considering parental factors. However, more adolescents with persistent pain reported that someone in their family had pain. The associations between pain intensity and the HRQOL subscales in adolescents with persistent pain were completely mediated by self-esteem, but not by self-efficacy. The highest degree of mediation was estimated for the HRQOL subscale school environment (indirect effect = 73.5%).

Conclusions
Our findings highlight the complexity within adolescent pain, demonstrating that adolescents with pain differ from adolescents without pain when it comes to gender, school absence, factors within-person and between-persons. Longer pain duration makes adolescents more vulnerable. We confirm the importance of resilience factors for HRQOL but indicate that self-esteem is more important than self-efficacy. To promote HRQOL in adolescents with persistent pain, a strengthening of both their self-esteem and self-efficacy is recommended. We highlight the need for an individual, holistic approach to adolescent pain.