bluuebunny/crossref_metadata_2025_split huggingface dataset:
Xpert MTB/RIF assay for diagnosis of extrapulmonary tuberculosis in children: A systematic review and meta-analysis
Authors: Seo Young Seok , Kang Ji-Man , Kim Dong Soo , Ahn Jong Gyun 
Published: September 2019

Abstract
Background: The Xpert® MTB/RIF assay (Xpert; Cepheid, Sunnyvale, CA, USA) is a cartridge-based nucleic acid amplification assay for rapid tuberculosis diagnosis and assessment of antibiotic sensitivity. Although previous evidence supports the use of Xpert for diagnosing extrapulmonary tuberculosis (EPTB) in adults, information regarding the accuracy of Xpert for EPTB only in children is lacking. This meta-analysis aimed to assess the accuracy of Xpert for detecting EPTB in children.

Methods: We searched the MEDLINE, EMBASE, and the Cochrane Infectious Diseases Group Specialized Register from January 1, 2010, to July 16, 2019, for studies on diagnostic performance wherein Xpert was analyzed against cultures or composite reference standards for <18-year-old children with EPTB.

Results: Exclusively on the basis of pediatric studies, 7 studies including 560 samples were selected. The pooled sensitivity and specificity of Xpert for all samples were 67% (95% CI 0.51-0.79) and 94% (95% CI 0.87-0.98), respectively. The area under the summary receiver operating characteristic (sROC) curve was 0.89. For lymph node tissues or aspirates, the pooled sensitivity and specificity of Xpert were 75% (95% CI 0.54-0.89) and 90% (95% CI 0.77-0.96), respectively; for cerebrospinal fluid (CSF), they were 40% (95% CI 0.23-0.60) and 96% (95% CI 0.85-0.99), respectively.

Conclusion: Overall, Xpert displayed high specificity but modest specificity across various samples in the diagnosis of pediatric EPTB in comparison with the composite reference standard. Xpert sensitivity varied with the sampling site, and was especially lower for CSF samples. Positive Xpert results may be considered to indicate a presumptive case of pediatric EPTB, whereas negative test results indicate that the possibility of pediatric EPTB should not be excluded.
Breast cancer risk factors that are identical and differential associated with menopause status of women in Northeast Brazil
Authors: Gomes Kedma Anne Lima , Jerônimo Aline Ferreira de Araújo , Ramos Raissa de Oliveira , Andrade Lorena Sofia dos Santos , Weller Mathias 
Published: September 2019

Abstract
Background: This case-control study was aimed at the identification of factors that modify breast cancer risk in a population from Northeastern Brazil. Breast cancer risk factors in this population are poorly understood. Methods: Data of 291 patients with invasive breast cancer and 291 healthy controls were obtained from medical records and personal interviews. Odds ratios (OR) and confidence intervals (CI) were determined using univariate and multiple regression analysis. Results: Oral contraceptive use increased the risk of breast cancer among pre- and post-menopause women 3.661 (95% CI: 1.81-7.39; p < 0.001) and 3.086 (95%CI: 1.85-5.79; p < 0.001) times. Family history increased the risk of breast cancer among pre- and post-menopause women 3.791 (95%CI: 1.85-7.77; p < 0.001) and 3.538 (95%CI: 2.16-5.79; p = 0.000) times. Risk of breast cancer among post-menopause women who regularly consumed alcohol was 4.21 (95%CI: 2.08-8.50; p < 0.001) times increased compared to women who did not consume alcohol. Obese and overweight post-menopause women had 2.117 (95%CI: 1.15-3.88) and 1.217 (95%CI: 0.74-2.19) times increased risk, compared to women with normal weight ( p = 0.044). Waist-to-hip ratio > 0.8 increased the risk of breast cancer among pre- menopause women 2.026 (0.94-4.38; p = 0.067) times in the univariate analysis. Nulliparous post-menopause women had 2.667 (95%CI: 1.30-5.50; p = 0.070) times increased risk. Univariate analysis of nulliparity among pre-menopause women indicated 2.59 (OR= 0.386; 95%CI: 0.15-0.98; p = 0.038) times decreased risk. Conclusions: Oral contraceptive use, family history and alcohol consumption increased the risk of breast cancer among pre- and post-menopause women. High body mass index increased the risk only among post-menopause women, whereas unadjusted high waist-to-hip ratio increased the risk of pre- menopause women. Nulliparous pre-menopause women tended to have decreased risk, whereas nulliparous post-menopause women tended to have increased risk of breast cancer.
Women’s empowerment is associated with maternal nutrition and low birth weight: Evidence from Bangladesh Demographic Health Survey
Authors: Kabir Alamgir , Rashid Md Mahbubur , Hossain Kamal , Khan Md Arifuzzaman , Shikder Shegufta Shefa , Gidding Heather F 
Published: September 2019

Abstract
Background The burden of maternal malnutrition and low birth weight (LBW) incurs enormous economic costs due to their adverse consequences. Women’s empowerment is believed to be one of the key factors for attaining maternal and child health and nutritional goals. Our objective was to investigate the association of women’s empowerment with maternal malnutrition and LBW.Methods We used nationally representative data from the Bangladesh Demographic Health Survey for 2011 and 2014. We analysed 27,357 women and 9,234 mother-child pairs. A women’s empowerment index (WEI) was constructed using principal component analysis. We estimated odds ratios as the measure of association between the WEI and the outcome measures using generalized estimating equations to account for the cluster level correlation.Results The overall prevalence of maternal malnutrition was 20% and LBW was 18%. The WEI was significantly associated with both maternal malnutrition and LBW with a dose-response relationship. The adjusted odds of having a LBW baby was 32% [AOR (95% CI):0.68 (0.57, 0.82)] lower in the highest quartile of the WEI relative to the lowest quartile. Household wealth significantly modified the effect of the WEI on maternal nutrition.; in the highest wealth quintile, the odds of maternal malnutrition was 54% [AOR (95% CI): 0.46 (0.33, 0.64)] lower while in the lowest wealth quintile the odds of malnutrition was only 18% [AOR (95% CI): 0.82 (0.67, 1.00)] lower comparing the highest WEI quartile with the lowest WEI quartile. However, the absolute differences in prevalence of malnutrition between the highest and lowest WEI quartiles were similar across wealth quintiles (6-8%).Conclusions This study used a comprehensive measure of women’s empowerment and provides strong evidence that low levels of women’s empowerment is associated with maternal malnutrition as well as with delivering LBW babies in Bangladesh. Therefore, policies to increase empowerment of women would contribute to improved population health.
Predicting the microbial cause of community-acquired pneumonia: can physicians or a data-driven method differentiate viral from bacterial pneumonia at patient presentation?
Authors: LHOMMET Claire , GAROT Denis , GRAMMATICO-GUILLON Leslie , JOURDANNAUD Cassandra , ASFAR Pierre , FAISY Christophe , MULLER Grégoire , BARKER Kimberly A. , MERCIER Emmanuelle , ROBERT Sylvie , LANOTTE Philippe , GOUDEAU Alain , BLASCO Helene , Guillon Antoine 
Published: September 2019

Abstract
Background Severe community-acquired pneumonia (sCAP) requires urgent and specific antimicrobial therapy. However, the causal pathogen is typically unknown at the point when anti-infective therapeutics must be initiated. Physicians synthesize information from diverse data streams to make appropriate decisions. Artificial intelligence (AI) excels at finding complex relationships in large volumes of data. We aimed to evaluate the abilities of experienced physicians and AI to answer this question at patient admission: is it a viral or a bacterial pneumonia? Methods We included patients hospitalized for sCAP and recorded clinical/paraclinical data available in the first 3-hour period of care. We built a machine learning model prediction using all collected data. Finally, an independent validation set of samples was used to test the pathogen prediction performance of: ( i ) a panel of three experts and ( ii ) the AI algorithm. Both were blinded regarding the final microbial diagnosis. Positive likelihood ratio (LR) values >10 and negative LR values <0.1 were considered clinically relevant.Results We included 153 patients with sCAP (70.6% men; 62 [51-73] years old; mean SAPSII, 37 [27-47]). The discriminant abilities of the AI approach were low to moderate (LR+ = 2.12 for viral and 6.29 for bacterial pneumonia), and the discriminant abilities of the experts were very low to low (LR+ = 3.81 for viral and 1.89 for bacterial pneumonia).Conclusion Neither experts nor an AI algorithm can predict the microbial etiology of sCAP within the first hours of hospitalization when there is an urgent need to define the anti-infective therapeutic strategy.
Does the association between guardians’ sense of coherence and their children’s untreated caries differ according to socioeconomic status?
Authors: Mizuta Akiko , Aida Jun , Nakamura Mieko , Ojima Toshiyuki 
Published: September 2019

Abstract
Background Untreated caries is the most prevalent disease in the world. A sense of coherence (SOC) is believed to contribute to oral health. However, it is unclear whether the contribution of SOC is larger among children with lower socioeconomic status (SES). We aimed to clarify the association between guardians’ SOC and their children’s caries based on socioeconomic status (SES) in Japan.Methods This study’s subjects were Japanese public junior high schoolers, aged 12-15, and their guardians. We administered a questionnaire survey among guardians in 2016 to assess their SOC and family environment. With their students’ consent, public junior high schools shared the results of the dental examinations that were part of their school physicals. Multivariate logistic regression was conducted to clarify the association between guardians’ SOC and their children’s untreated decayed permanent teeth. We also conducted a stratified analysis according to a relative poverty line. Furthermore, the interaction between annual equivalent incomes, educational attainment with guardians’ SOC was evaluated by including the interaction term respectably.Results Proportion of untreated decayed permanent teeth of adolescents was 9.37% for 12 - 13 years, 9.02% for 14 years, and 11.78% for 15 years. Guardians’ SOC score was 15.1 (SD 3.2, range 3 - 21). We observed in the multivariate regression, a significant inverse association between children’s untreated decay and their guardians’ SOC (OR 0.93, 95%CI 0.87-1.00). Equivalent annual income had a significant marginal association with decayed teeth (OR 0.14, 95%CI 0.02-1.04). The association of SOC was stronger in the low economic group (OR 0.64, 95%CI 0.43-0.95). The interaction terms of educational attainment and guardians’ SOC was not significant. In the high economic group, educational attainment was significantly associated with decayed teeth (OR 0.50, 95%CI 0.27-0.91). The interaction terms of educational attainment and guardians’ SOC was not significant.Conclusions Guardians with higher SOC were associated with children having fewer caries. Guardians’ SOC is an important factor for the incidence of caries and access to dental care, especially among children with low economic status.
Educational roles as a continuum of mentoring’s role in medicine – A systematic review and thematic analysis of educational studies from 2000 to 2018
Authors: Krishna Lalit , Renganathan Yaazhini , Tay Kuang Teck , Tan Benjamin Jia Xing , Chong Jia Yan , Ching Ann Hui , Prakash Kishore , Quek Nicholas Wei Sheng , Peh Rachel Huidi , Chin Annelissa Mien Chew , Taylor David C M , Mason Stephen , Kanesvaran Ravindran , Toh Ying Pin 
Published: September 2019

Abstract
Introduction: Mentoring studies have gone through great lengths to differentiate mentoring from teaching, tutoring, role modelling, coaching and supervision in efforts to better understand mentoring processes. This review seeks to evaluate the notion that teaching, tutoring, role modelling, coaching and supervision may in fact be part of the mentoring process. To evaluate this theory, this review scrutinizes current literature on teaching, tutoring, role modelling, coaching and supervision to evaluate their commonalities with prevailing concepts of novice mentoring. Methods: A three staged approach is adopted to evaluate this premise. Stage one involves four systematic reviews into teaching, tutoring, role modelling, coaching and supervision published between 1st January 2000 and 31st December 2018. Braun and Clarke’s (2006) approach to thematic analysis was used to identify key elements within these approaches and facilitate comparisons between them. Stage two will provide an updated view of novice mentoring to contextualize the discussion. Stage three infuses mentoring into the findings delineated in stage one. Results: 17499 citations were reviewed, 235 full-text articles were reviewed, and 104 articles were thematically analysed. Four themes were identified – characteristics, processes, nature of relationship, and problems faced in each of the four educational roles. Discussion: Role modelling, teaching and tutoring, coaching and supervision lie within a mentoring spectrum of increasingly structured interactions assisted by assessments, feedback and personalised support that culminate with a mentoring approach. Still requiring validation these findings necessitate a reconceptualization of mentoring and changes to mentor training programs and how mentoring is assessed and supported.
A non-randomised trial of video and written educational adjuncts in undergraduate ophthalmology
Authors: Hogg Henry David Jeffry , Pereira Michael , Purdy Julian , Fre Richard J.R. , Lau Gordon B. 
Published: September 2019

Abstract
Background Provision of relevant pre-learning materials has been shown to increase student engagement and improve outcomes in medical education. This non-randomised study attempts to quantify the educational gains, and relative efficacy of video and written pre-learning materials, in ophthalmology undergraduate teaching.Methods 98 final year medical students were contacted prior to their three-day ophthalmology placements at a British tertiary ophthalmology unit. All participants were sent welcome packs prior to arrival requesting they undertake 90 minutes of work focusing on a list of specified ophthalmic conditions. In addition one cohort ( N =33) were sent written materials and another ( N =32) were provided with video materials. The teaching remained otherwise unchanged. On arrival participants completed a simple knowledge test, a questionnaire estimating the time they spent preparing for the placement and a self-reported knowledge score. At the conclusion of each placement participants completed a challenging knowledge test, a clinical skills test and repeated self-reported knowledge scores.Results 86.7% of students receiving specified materials claimed to complete pre-placement work compared to 69.7% of those receiving learning outcomes alone ( p =0.05). Students receiving learning materials scored higher in tests of knowledge ( p <0.001), 74.8% (72.4-77.2%) vs 63.6% (95%CI 59.3-67.9%) and skills ( p =0.04), 86.9% (83.9-89.9%) vs 81.3% (77.2-85.4%). Students using video resources outperformed students using written materials in their visual acuity assessment test ( p =0.03), 90.4% (86.6-94.2%) vs 83.6% (80.1-87.1%) whilst those receiving written rather than video material performed better in the end of placement knowledge test ( p =0.03), 72.0% (68.9%-75.1%) vs 77.7% (74.3-81.1%).Conclusion This study showed that providing pre-placement learning materials improves undergraduates’ commitment and achievement. Written materials better facilitate knowledge acquisition while video materials preferentially promote skill acquisition. This is a novel demonstration within ophthalmology and can help address the imbalance between the expectations placed on graduates and the resources committed to ensuring they are met.
Enhanced genome assembly and a new official gene set for Tribolium castaneum - from a draft to a reference genome
Authors: Herndon Nicolae , Shelton Jennifer , Gerischer Lizzy , Ioannidis Panos , Ninova Maria , Dönitz Jürgen , Waterhouse Robert M. , Liang Chun , Damm Carsten , Siemanowski Janna , Kitzmann Peter , Ulrich Julia , Dippel Stefan , Oberhofer Georg , Hu Yonggang , Schwirz Jonas , Schacht Magdalena , Lehmann Sabrina , Montino Alice , Posnien Nico , Gurska Daniela , Horn Thorsten , Seibert Jan , Jentzsch Iris M. Vargas , Panfilio Kristen A. , Li Jianwei , Wimmer Ernst A. , Stappert Dominik , Roth Siegfried , Schröder Reinhard , Park Yoonseong , Schoppmeier Michael , Klingler Martin , Chung Ho-Ryun , Kittelmann Sebastian , Friedrich Markus , Chen Rui , Altincicek Boran , Vilcinskas Andreas , Zdobnov Evgeny , Griffiths-Jones Sam , Ronshaugen Matthew , Stanke Mario , Brown Sue J. , Bucher Gregor 
Published: September 2019

Abstract
Background: The red flour beetle Tribolium castaneum has emerged as an important model organism for the study of gene function in development and physiology, for ecological and evolutionary genomics, for pest control and a plethora of other topics. RNA interference (RNAi), transgenesis and genome editing are well established and the resources for genome-wide RNAi screening have become available in this model. All these techniques depend on a high quality genome assembly and precise gene models. However, the first version of the genome assembly was generated before the advent of next generation sequencing and with a small set of RNA sequence data limiting annotation quality. Results: Here, we present a new genome assembly (Tcas5.2) and an enhanced genome annotation resulting in a new official gene set (OGS3) for Tribolium castaneum , which significantly increase the quality of the genomic resources. By adding large-distance jumping library DNA sequencing and using an improved assembly pipeline, the gaps in the genome assembly were reduced and the N50 increased to 4,753kbp. The precision of the gene models was enhanced by the use of a large body of RNA-Seq reads of different life history stages and tissue types, leading to the discovery of 1,452 novel gene sequences. We also added new features such as alternative splicing, well defined UTRs and miRNA target predictions. For quality control, 399 gene models were evaluated by manual inspection. The current gene set was submitted to Genbank and accepted as a RefSeq genome by NCBI. Conclusions: The new genome assembly (Tcas5.2) and the official gene set (OGS3) provide enhanced genomic resources for genetic work in Tribolium castaneum . The much improved information on transcription start sites supports transgenic and gene editing approaches. Further, novel types of information such as splice variants and microRNA target genes open additional possibilities for analysis.
Pearl extract protects HaCaT cells from UV radiation-induced apoptosis through mitochondrial pathway regulation
Authors: Chen Zhixiong , Wang Jing , Yang Anquan , Zhang Lihua , Lu Yaojia , Mo Jiahuan , Xie Min , Shen Xinzhong 
Published: September 2019

Abstract
Background: Previous studies demonstrated that pearl extract (PE) promotes wound healing and skin whitening. However, whether PE can inhibit ultraviolet (UV) photodamage in HaCaT cells remains unclear. In this study, an in vitro photoaging cell model was established to observe the effect of PE on UV-induced damage and apoptosis of HaCaT cells. The aim was to provide a reference for future development of natural sunscreen agents. Results: PE concentrations of 0.1 and 1 μg/mL were considered as the most effective and safe concentrations. Compared to the control group, superoxide dismutase and glutathione peroxidase activities in the photoaging group were significantly reduced, while malondialdehyde and reactive oxygen species content, along with tumor necrosis factor-alpha (TNF-a) and interleukin (IL)-10 mRNA and protein levels were markedly increased. In contrast, Bcl-2 protein expression was significantly decreased, while caspase-3, caspase-9, and Bax protein expression levels were significantly increased. Compared to the photoaging group, HaCaT cell proliferation was significantly increased in the PE group. Both PE concentrations significantly increased superoxide dismutase and glutathione peroxidase activities in cells, reduced malondialdehyde and reactive oxygen species content, decreased TNF-a and IL-10 mRNA expression in cells, and reduced TNF-a and IL-10 protein levels in the supernatant. Additionally, Bcl-2 protein expression levels were significantly increased, while caspase-3, caspase-9, and Bax protein expression levels were significantly reduced by PE treatment. Conclusions: PE can inhibit UV-induced apoptosis by inhibiting mitochondria-mediated apoptosis and regulating TNF-a and IL-10 expression.
Age is a powerful predictor of survival in pT2N0M0 clear cell renal cell cancer patients: A SEER-based study
Authors: Huang Lanting , Cheng Wenfang , Chen Juhui , Teng Kaiyuan 
Published: September 2019

Abstract
Background: To elucidate whether age is a prognostic factor in clear cell renal cell cancer (ccRCC) with stage II (pT2N0M0,the American Joint Committee on Cancer 6 th or 7 th staging system) , we analyzed data from the SEER (Surveillance, Epidemiology and End Results) database to evaluate the impact of age on clinicopathological features and survival in pT2N0M0 ccRCC patients. Methods: A total of 2806 patients with stage II (pT2N0M0) were collected. Patients were categorized into three groups according to age at diagnosis as follows: young age (< 40 years, n = 129), middle-age (40-69 years, n = 2,075), and old age (≥ 70 years, n = 602) groups. Clinicopathological variables and survival rates were compared between the three groups. Results: 5-year overall survival (OS) rates were 93.0%, 83.9%, 69.3% respectively and 10-year OS rates were 87.6%, 74.5%, 47.0% respectively in the young, middle, and old age groups (P<0.001). 5-year cancer-specific survival (CSS) rates were 94.6%, 88.4%, 84.4% respectively and 10-year CSS rates were 90.7%, 82.1%, 74.6% respectively in the young, middle, and old age groups (P<0.001). Age at diagnosis was the only predictor for both overall survival and cancer-specific survival in multivariate analysis (each P<0.001). Age together with marital status, tumor size and grade were independent prognostic factors for CSS in multivariate analysis (P<0.001,P=0.017, P=0.001, P=0.02 respectively). Conclusions: Age at diagnosis is a powerful predictor for survival in pT2N0M0 clear cell renal cell cancer patients. Compared to their young counterparts, elder patients have a significantly worse outcome with regard to overall survival and cancer-specific survival.