bluuebunny/crossref_metadata_2025_split huggingface dataset:
Combining abbreviated literature searches with single-reviewer screening: three case studies of rapid reviews
Authors: Affengruber Lisa , Wagner Gernot , Waffenschmidt Siw , Lhachimi Stefan K. , Nussbaumer-Streit Barbara , Thaler Kylie , Griebler Ursula , Klerings Irma , Gartlehner Gerald 
Published: February 2020

Abstract
Background Decision-makers increasingly request rapid answers to clinical or public health questions. To save time, personnel, and financial resources, rapid reviews streamline the methodological steps of the systematic review process. Methods Using three cases studies, we evaluated a rapid review approach that consisted of a substantially abbreviated literature search and single-reviewer screening of abstracts and full texts. We used a convenience sample of three ongoing Cochrane reviews as reference standards. Two reviews addressed oncological topics and one addressed a public health topic. For each of the three topics, three reviewers screened the literature independently. Our primary outcome was the change in conclusions between the rapid reviews and the respective Cochrane reviews. In case the rapid approach missed studies, we recalculated the meta-analyses for the main outcomes and asked Cochrane review authors if the new body of evidence would change their original conclusion compared with the reference standards. Additionally, we assessed the sensitivity of the rapid review approach compared with the results of the original Cochrane reviews. Results For the two oncological topics (case studies 1 and 2), the three rapid reviews each yielded the same conclusions as the Cochrane reviews. However, the authors would have had less certainty about their conclusion in case study 2. For case study 3, the public health topic, only one of the three rapid reviews led to the same conclusion as the Cochrane review. The other two rapid reviews provided insufficient information for the authors to draw conclusions. Using the rapid review approach, the sensitivity was 100% (3 of 3) for case study 1. For case study 2, the three rapid reviews identified 40% (4 of 10), 50% (5 of 10), and 60% (6 of 10) of the included studies, respectively; for case study 3, the respective numbers were 38% (8 of 21), 43% (9 of 21), and 48% (10 of 21). ConclusionsWithin the limitations of these case studies, a rapid review approach that combines abbreviated literature searches with single-reviewer screening may be feasible for focused clinical questions. For complex public health topics, sensitivity seems to be insufficient.
Lack of genetic differentiation between two sympatric species of Astyanax (Characidae:Teleostei) in Lake Catemaco, Mexico
Authors: Doadrio Ignacio , Ornelas Patricia , Gonzalez Elena G. , Tautz Diethard 
Published: February 2020

Abstract

Background Fish of the genus Astyanax are known to be able to adapt to a wide range of ecological conditions and are especially known for repeated colorizations of cave systems. In lakes they often occur in species pairs. In the case we study here, they show major morphological differences, such that they were originally classified in different genera. Previous studies have shown that these morphological differences correlate with occupation of different trophic niches. Hence, this could be an example of ecological speciation under sympatric conditions, which predicts that differential ecological adaptation becomes coupled to assortative mating and to the formation of genetically distinct groups that may be called species. We have tested this prediction by typing a set of microsatellites for the two morphs in the lake in comparison to an allopatric population.Results While we find the expected differentiation with respect to the allopatric population, there is a complete lack of genetic differentiation between the two morphs within the lake. Hence, the two morphs in the lake are either in an extremely early phase of speciation or represent two extreme morphotypes derived from a single gene pool.Conclusions Even when we failed to recover the two morphs as reproductively isolated, this model provides a unique opportunity to characterize those factors that would promote the ecological divergence, thus, our lacustrine morphs system gives a unique opportunity to understand the genetic basis of how morphological divergence in the presence of gene flow.
Colombian frogs: promising source of new antibiotics
Authors: Alzate Esteban , Mejía Laura , Nuñez Maria Clara , Benavides Julie , Galvis-Pareja David , Zapata Paola 
Published: February 2020

Abstract
Background: In middle Magdalena of the Antioquia region, Colombia frog secretions have been used as antibacterial agents, the purpose of this study is to assess the antibacterial activity of six frog species secretions. Methods: the Kirby-Bauer and the microdilution methods were used to evaluate antibacterial activity of the frogs secretions against S. aureus and E. coli, using two positive controls, ampicillin and ciprofloxacin. Results: secretions of all six families showed inhibition zones, the concentration at which this zone was bigger was assayed later by the microdilution method and compared to ampicillin and ciprofloxacin. Only the secretion from the Phyllomedusidae exhibited a comparable effect to that one of control antibiotics. Conclusions: in here we provide evidence that secretions from local frogs have an antibacterial effect against two strains of bacteria, further studies are needed to identify the peptides in the secretions and a wider range of safe concentrations for human use.
Noninvasive KRAS mutation estimation in colorectal cancer using a deep learning method based on routine CT imaging
Authors: He kan , Liu Xiaoming , Li Mingyang , Li Xueyan , Yang Hualin , zhang huimao 
Published: February 2020

Abstract
Background: The detection of KRAS gene mutations in colorectal cancer (CRC) is key to the optimal design of individualized therapeutic strategies. The noninvasive prediction of the KRAS status in CRC is challenging. Deep learning (DL) in medical imaging has shown its high performance in diagnosis, classification, and prediction in recent years. In this paper, we investigated predictive performance by using a DL method with a residual neural network ( ResNet ) to estimate the KRAS mutation status in CRC patients based on routine pre-treatment contrast-enhanced CT imaging. Methods: We have collected a dataset consisting of 157 patients with pathology-confirmed CRC who were randomly divided into a training cohort (n = 117) and a validation cohort (n = 40). We developed an ResNet model that used portal venous phase CT images to estimate KRAS mutations in the axial, coronal, and sagittal directions of the training cohort and validated the model in the validation cohort. Several groups of expended ROI patches were generated for the ResNet model, to explore whether tissues around the tumor can contribute to cancer assessment. We also explored a radiomics model with the random forest classifier (RFC) to predict KRAS mutations and compared it with the DL model. Results: The ResNet model in the axial direction achieved the higher area under the curve (AUC) value (0.90) in the validation cohort and peaked at 0.93 with an input of “ROI and 20-pixel” surrounding area. In the training cohort, the AUC was 0.945 (sensitivity: 0.75; specificity: 0.94), and in the validation cohort, the AUC was0.818 (sensitivity: 0.70; specificity: 0.85). In comparison, the ResNet model showed better predictive ability . Conclusions: Our experiments reveal that the computerized assessment of the pre-treatment CT images of CRC patients using a DL model has the potential to precisely predict KRAS mutations. This new model has the potential to assist in noninvasive KRAS mutation estimation. Keywords: Colorectal Neoplasm, Mutation, Deep Learning
Cost-effectiveness and budget impact of flucytosine as induction therapy in the treatment of cryptococcal meningitis in HIV-infected adults in South Africa
Authors: Miot Jacqui , Leong Trudy , Takuva Simbarashe , Parrish Andrew , Dawood Halima 
Published: February 2020

Abstract
Background Cryptococcal meningitis in HIV-infected patients in sub-Saharan Africa accounts for three-quarters of the global cases and 135 000 deaths per annum. Current treatment includes the use of fluconazole and amphotericin B. Recent evidence has shown that the synergistic use of flucytosine improves efficacy and reduces toxicity, however affordability and availability has hampered access to flucytosine in many countries. This study investigated the evidence and cost implications of introducing flucytosine as induction therapy for cryptococcal meningitis in HIV-infected adults in South Africa. Methods A decision analytic cost-effectiveness and budget impact model was developed based on survival estimates from the ACTA trial and local costs for flucytosine as induction therapy in HIV-infected adults with cryptococcal meningitis in a public sector setting in South Africa. The model considered four treatment arms: (a) standard of care; 2-week course of amphotericin B/fluconazole (2wk AmBd/Flu), (b) 2-week course of amphotericin B/flucytosine (2wk AmBd/5FC), (c) short course; 1-week course amphotericin B/flucytosine (1wk AmBd/5FC) and (d) oral course; 2-week oral fluconazole/flucytosine (oral). A sensitivity analysis was conducted on key variables. Results The highest total treatment costs were in the 2-week AmBd/5FC arm followed by the 2-week oral regimen, then the 1-week AmBd/5FC with the lowest cost in the standard of care arm. Compared to standard of care the 1-week flucytosine course is most cost-effective at USD31/QALY, followed by the oral 2-week course at USD155/QALY and the 2-week flucytosine course at USD568/QALY. The budget impact analysis shows that the 1-week course has the lowest incremental cost, followed by the oral course and then the 2-week flucytosine course compared to what is currently spent on standard of care. Sensitivity analyses suggest that the model is most sensitive to the price of flucytosine and hospital costs, particularly length of stay. Conclusions The addition of flucytosine as induction therapy for the treatment of cryptococcal meningitis in patients infected with HIV is cost-effective regardless of whether it is used as a 1-week, 2-week or oral regimen. Savings could be achieved with early discharge of patients as well as a reduction in the price of flucytosine.
The Establishment of National Standards for Health Checks in China and a comparison with American EHE Standards
Authors: Zhu YANhui , Lei Jianbo 
Published: February 2020

Abstract
Objective Different institutes utilize different test standards for routine health checks in China. It is necessary and urgent to establish unified standards for health checks to conserve medical resources and reduce the social burden in China. The purpose of this study is to determine standards of health items and evaluate the advantage and disadvantage by comparing with the American executive health exam (EHE) standards. Methods We collected health check items used in 60 top hospitals within mainland China. We excluded items that occurred in less than 80%. We compared the selected items with those used in the American EHE standards. Results China’s health check included physical examination, non-infectious disease screening, malignancy screening, laboratory screening, and imaging examinations. China’s health checks included more items than those used in the American EHE standards. Conclusion Our findings showed that China’s health check protocols could be simplified, except for the items currently used in the basic physical examination and malignancy screening.
The status of serum vitamin A/E and its effect on Recurrent Respiratory Tract Infections in children aged 2 to 17 years in Beijing, China, based on cross-sectional study
Authors: Wang Xiaoyan , Jin Chunhua , Wang Jiaxin , Wang Jianhong , Zhang Lili , Li Na , Song Wenhong , Li Xingming 
Published: February 2020

Abstract
Objective To test the association between serum vitamin A and vitamin E and the prevalence of recurrent respiratory tract infections (RRTIs) of children and adolescents. Method A total amount of 5780 children and adolescents aged 2 to 17 were involved, who were classified into:A) Control group ;B) Diagnosed as RRTI with RTI symptoms; C) With RRTI but currently no RTI symptoms being noticed, and D) Not RRTI but showing respiratory disease symptoms. The correlation between serum vitamin A/E level and the presence of RRTIs were analyzed. Results Comparing with the prevalence of RRTI in children with normal vitamin A level, the Odds Ratio(OR) of vitamin A deficiency for RRTIs with symptoms was 8.32 (95%CI: 6.15 ～ 11.27), while the OR of marginal vitamin A deficiency was 1.30 (95%CI: 1.10 ～ 1.55). The OR of vitamin A deficiency or marginal vitamin A deficiency for asymptomatic RRTIs were 1.52 (95%CI: 1.00 ～ 2.32) and 1.30 (95%CI: 1.10 ～ 1.55) respectively, while the OR of vitamin A deficiency or marginal vitamin A deficiency for other respiratory diseases were 7.09 (95%CI: 5.37 ～ 9.37) and 1.60 (95%CI: 1.38 ～ 1.86). Whereas, the OR of vitamin E deficiency or marginal vitamin E deficiency for RRTIs or normal respiratory infections were showed without statistical significance. Conclusion The low level of vitamin A in serum is a risk factor for children and adolescents getting RRTIs or RTIs, indicating a possibly regulatory role of vitamin A in the respiratory diseases. In comparison, the vitamin E deficiency seems to have a weaker but still positive effect on the RRTIs or RTI
Randomized trial: corticoids versus placebo in severe bronchiolitis. COTHEB study.
Authors: Felipe Aida , Balaguer Mònica , Alejandre Carme , Esteban Elisabeth , Alsina Laia , Muñoz-Almagro Carmen , Esteban Maria Esther , Cambra Francisco José , Jordan Lolanda 
Published: February 2020

Abstract
Background: Corticosteroids as modulation the inflammatory response is a controversial issue in the treatment of bronchiolitis. This study aimed to assess whether corticoid therapy influenced the inflammatory and clinical response of critically ill infants.
Methods: Prospective, randomized, double blind placebo-controlled trial of glucocorticoids (GCT) in infants of less than 12 months with severe or moderate bronchiolitis. Patients were randomized to receive corticoid therapy or placebo. The main outcomes were: a) levels of lymphocyte; b) levels of IL-2, IL-12, and IFNγ as pro-inflammatory factors, and c) levels of IL-4 and IL-10 as anti-inflammatory response. Secondary outcomes related with the clinical response were also analyzed.
Results: 97 patients were randomized. Evolution of lymphocyte subsets was similar in both groups. Pro-inflammatory interleukins and interferon decreased, but without differences. Antiinflammatory interleukins showed a significant decrease from baseline to the end of the study, and IL-10 values were significantly lower in the GCT group. GCT group showed a lower time of mechanical ventilation and of hospitalization, but without statistically significant differences No cases of severe adverse reaction to steroids were detected.
Conclusions: administration of systemic GCT did not modify the inflammatory not the clinical response of patients with severe bronchiolitis, except for IL-10 levels that were significantly lower in the GCT group.
Trial registration: Glucocorticoid Therapy Impact on the Inflammatory Response and Clinical Evolution in Patients With Severe Bronchiolitis, NCT02571517. ClinicalTrials.gov registration number: 2011-000337-36. Date of registration: 30 june 2012 (retrospectively registered).
Difference of microbiome and antibiotic resistome between earthworm gut and soil deciphered by a continental-scale survey
Authors: Zhu Yong-Guan , Zhu Dong , Delgado-Baquerizo Manuel , Su Jian-Qiang , Ding Jing , Li Hu , Gillings Michael R. , Penuelas Josep 
Published: February 2020

Abstract
Background Earthworms are globally distributed and quite capable of redistributing compounds, as well as bacteria and antibiotic resistance genes (ARGs) throughout the soil profile. The spread of medically relevant ARGs in soils has become an emerging environmental and health issue globally. However, our understanding on earthworm gut microbiome and antibiotic resistome is still lacking, especially at the large scale, and little is known about the role of earthworm in the dispersal of ARGs. Methods We conducted a continental-scale survey, including samples (earthworm gut and soil) from 28 provinces across China, from both natural and agricultural ecosystems (arable land: 35 sites and forested land: 16 sites). The 16S rRNA amplicon sequencing and high throughput quantitative PCR were used to characterize the microbiome and antibiotic resistome, respectively. We further explored potential mechanisms behind changes in the abundance and diversity of ARGs in the earthworm gut. Then, the microcosm experiments and long-term field experiments with or without earthworms were employed to test the potential for earthworms to reduce the abundance of ARGs in soils. Results The diversity and structure of bacterial community were observably different between the earthworm gut and soil. Firmicutes (35.7%) and Proteobacteria (34.8%) were the dominant phyla in all earthworm gut samples. A significant correlation between bacterial community dissimilarity and spatial distance was identified in the earthworm gut. The earthworm gut consistently had a lower diversity and abundance of ARGs than in the surrounding soil. We further revealed that the change of ARGs in the earthworm gut was likely a consequence of the reduction in the abundance of mobile genetic elements and dominant bacterial phylotypes that are the likely hosts of ARGs. The microcosm study and long-term field experiments provided the experimental evidence that the presence of earthworms reduced the abundance and diversity of ARGs in soils. Conclusions Our findings highlight that earthworm gut and soil present the distinct microbiome and resistome at the continental scale, and earthworms may play an important role in the continental-scale mitigation of antibiotic resistance.
Body Mass Index- and Waist Circumference-Defined Obesity with the risk of Total Knee Arthroplasty for Osteoarthritis: A prospective cohort study
Authors: Lim Yuan Z , Wang Yuanyuan , Cicuttini Flavia M , Giles Graham G , Graves Stephen , Wluka Anita E , Hussain Sultana Monira 
Published: February 2020

Abstract
Background There is a discordance in classification of obesity when defined by body mass index (BMI) or waist circumference (WC). We aimed to examine whether categories of BMI- and WC-defined obesity are differentially associated with the risk of total knee arthroplasty for osteoarthritis. Methods 38,924 participants from the Melbourne Collaborative Cohort Study with BMI and WC measured at baseline (1990-1994) were included. Obesity status was defined as: not obese (non-obese BMI and non-obese WC); WC-defined obesity only (non-obese BMI and obese WC); BMI-defined obesity only (non-obese WC and obese BMI); and BMI- and WC-defined obesity. The incidence of total knee arthroplasty for osteoarthritis between January 2001 and December 2013 was determined by linking participant records to the National Joint Replacement Registry. Results Over 11.5±3.1 years follow-up, 1,875 participants underwent total knee arthroplasty for osteoarthritis. Participants with WC-defined obesity only (HR=1.79, 95%CI 1.51-2.53), BMI-defined obesity only (HR=2.39, 95%CI 2.02-2.84), and BMI- and WC-defined obesity (HR=3.14, 95%CI 2.82-3.49) had an increased risk of total knee arthroplasty compared with those who were not obese. Conclusions Individuals with either BMI- or WC-defined obesity should be targeted for prevention of knee osteoarthritis as both are significant predictors for severe osteoarthritis requiring a total knee arthroplasty.
Prevalence, antimicrobial susceptibility patterns, and associated risk factors of Salmonella and Shigella among food handlers in Adigrat University student’s cafeteria, Northern Ethiopia, 2018
Authors: Legese Haftom , Kahsay Tsega , Gebrewahd Aderajew , Berhe Birhane , Fiseha Berhane , Tadesse Senait , Gebremariam Guesh , Negash Hadush , Mardu Titsum , Tesfay Kebede , Adhanom Gebre 
Published: February 2020

Abstract
Background : Food handlers play a significant role in the transmission of foodborne infection. Salmonella and Shigella are the most common foodborne pathogens and their infections are a major public health problem of the globe. Thus, this study was aimed to determine the prevalence, antimicrobial susceptibility patterns, and associated risk factors of Salmonella and Shigella among food handlers. Methodology: A cross-sectional study was conducted from March to August 2018 at Adigrat University student cafeteria, Northern Ethiopia. Data on socio-demographic and associated risk factors were collected using a structured questionnaire. Fresh stool samples were collected from 301 food handlers and transported to Adigrat University Microbiology Laboratory. Bacterial isolation and antimicrobial susceptibility test were performed using standard bacteriological methods. Data analysis was performed using SPSS version 22 and P < 0.05 with a corresponding 95% confidence interval was considered statistically significant. Results: A total of 301 food handlers were included in this study. The majority of study participants were females 265 (88.0 %). About 22 (7.3%) and 11 (3.7%) of food handlers were found to be positive for Salmonella and Shigella respectively. Hand washing after using a bathroom with water only, hand washing after using the bathroom, hand washing after touching dirty materials, hand washing before food handling and fingernails status were significant associated risk factors identified. None of the Salmonella and Shigella isolates were sensitive to ampicillin. On the other hand, low resistance was found for chloramphenicol , ceftriaxone, and ciprofloxacin. Conclusion: The present study revealed that the prevalence of Salmonella and Shigella among food handlers found to be 22 (7.3%) and 11 (3.7%) respectively. Such infected food handlers can contaminate food, drinks and could serve as a source of infection to consumers via the food chain. This indicates that the need for strengthened infection control measures to prevent Salmonella and Shigella transmission in the students’ cafeteria.