LLukas22/scidocs huggingface dataset:
Risk of bias in overviews of reviews: a scoping review of methodological guidance and four-item checklist.

OBJECTIVE
To assess the conditions under which employing an overview of systematic reviews is likely to lead to a high risk of bias.


STUDY DESIGN
To synthesise existing guidance concerning overview practice, a scoping review was conducted. Four electronic databases were searched with a pre-specified strategy (PROSPERO 2015:CRD42015027592) ending October 2015. Included studies needed to describe or develop overview methodology. Data were narratively synthesised to delineate areas highlighted as outstanding challenges or where methodological recommendations conflict.


RESULTS
Twenty-four papers met the inclusion criteria. There is emerging debate regarding overlapping systematic reviews; systematic review scope; quality of included research; updating; and synthesizing and reporting results. While three functions for overviews have been proposed-identify gaps, explore heterogeneity, summarize evidence-overviews cannot perform the first; are unlikely to achieve the second and third simultaneously; and can only perform the third under specific circumstances. Namely, when identified systematic reviews meet the following four conditions: (1) include primary trials that do not substantially overlap, (2) match overview scope, (3) are of high methodological quality, and (4) are up-to-date.


CONCLUSION
Considering the intended function of proposed overviews with the corresponding methodological conditions may improve the quality of this burgeoning publication type. Copyright © 2017 John Wiley & Sons, Ltd.
Complex software project development: agile methods adoption

The Agile Software Development paradigm has become increasingly popular in the last few years, since it claims lower costs, better productivity, better quality and better business satisfaction. Supply chain management (SCM) is a complex software development project. Owing to its scope and uncertain, complex and unstable requirements, it is not possible to develop it with predictable software development process models. Agile methodologies are targeted toward such kinds of problems that involve change and uncertainty, and are adaptive rather than predictive. How an agile process is introduced will significantly impact the implementation success of the process change. The objective of this paper is to analyze the agile development methodologies and management approach used in developing a complex software project. This further demonstrates how to overcome risks and barriers in each development phase of such complex inventive software projects. It also provides a set of guidelines regarding how the agile methodologies can be adopted, combined and used in these kinds of complex software projects. These findings have implications for software engineers and managers developing software by agile methods. Copyright q 2011 John Wiley & Sons, Ltd.
Impact of baseline tissue status (diffusion-weighted imaging lesion) versus perfusion status (severity of hypoperfusion) on hemorrhagic transformation.

BACKGROUND AND PURPOSE
The frequency of hemorrhagic transformation (HT) on gradient echo imaging and its impact on stroke outcomes continues to be debated. We investigated the factors associated with HTs and the influence of the HTs observed on gradient echo imaging on the early course after a stroke.


METHODS
We analyzed the data from a prospectively maintained registry of patients who were eligible for recanalization therapy. Serial diffusion-weighted imaging and perfusion-weighted imaging were performed, and HTs were assessed on follow-up gradient echo imaging. Tmax perfusion lesion maps were generated and hypoperfused regions were divided into severe (Tmax >or=8 seconds) delay and mild (Tmax >or=2 seconds but Tmax <8 seconds) delay. The factors associated with HTs, including the mode of recanalization therapy, pretreatment diffusion-weighted imaging and perfusion-weighted imaging lesion volumes, and reperfusion indices, were evaluated. The early clinical outcome was assessed during the first 7 days of admission.


RESULTS
A total of 184 patients were included in this study. HTs were noted in 73 (39.7%) patients. Multiple logistic regression analysis identified aggressive treatment (OR, 5.12; 95% CI, 1.73 to 15.18) and a large area of severe perfusion delay (OR for highest quartile of Tmax >8 seconds, 12.91; 95% CI, 3.69 to 45.17) as independent predictors of HTs. Neither risk factor profiles nor diffusion-weighted imaging lesion volumes were associated with HTs. There was a poor correlation between the radiological (HT types) and clinical (asymptomatic or symptomatic) categories of HTs. Even a parenchymal hematoma was not always associated with symptomatic worsening or affected the early clinical outcomes.


CONCLUSIONS
The results of this study indicate that the perfusion status (severe perfusion delay) rather than the tissue status (diffusion-weighted imaging lesions) and aggressive treatment were independently associated with HTs. HT on gradient echo imaging was common but usually associated with severe hypoperfusion and not always associated with clinical deterioration.
Detecting emotional scenes using Semantic Analysis on Subtitles

In this project, our aim was to detect and clip emotional scenes from movies, using natural language processing techniques on their subtitles. Our approach involved the design of a naïve counting classifier, to which we gradually added semantic knowledge. With each increment, we analyzed the change in performance and made suitable modifications to our classifier. In our second approach, we trained a maximum entropy classifier on some handtagged subtitles and compared the performance of the MaxEnt classifier with different types of data and pre-learned emotional words. Using these classifiers, we then created an interactive tool for searching and watching 2-3 minute clips of movies. Subsequent sections of this paper describe our approaches in more detail.
The status of interprofessional education and interprofessional prevention education in academic health centers: a national baseline study.

PURPOSE
Given the emphasis on prevention in U.S. health care reform efforts, the importance of interprofessional education (IPE) that prepares health professions students to be part of effective health care teams is greater than ever. This study examined the prevalence and nature of IPE and interprofessional (IP) prevention education in U.S. academic health centers.


METHOD
The authors extracted a 10-item survey from the longer published IPE Assessment and Planning Instrument. In September 2010, they sent the survey to 346 health professions leaders in health sciences schools and colleges at 100 academic health centers. These institutions were identified via the online membership list of the Association of Academic Health Centers. The authors conducted descriptive statistical analysis and cross-tabulations.


RESULTS
Surveys were completed by 127 contacts at 68 universities in 31 states and the District of Columbia. IPE was more prevalent than IP prevention education in all categories of measurement. Respondents affirmed existence of IPE in courses (85.0%) and in clinical rotations/internships (80.3%). The majority reported personnel with responsibility for IPE (68.5%) or prevention education (59.8%) at their institutional unit, and 59.8% reported an IPE office or center.


CONCLUSIONS
This study provides evidence that IPE and IP prevention education exist in academic health centers, but additional attention should be paid to the development of IP prevention education. Sample syllabi, job descriptions, and policies may be available to support adoption of IPE and IP prevention education. Further effort is needed to increase the integration of IP and prevention education into practice.
Safety and efficacy of zinc supplementation for children with HIV-1 infection in South Africa: a randomised double-blind placebo-controlled trial

BACKGROUND
Zinc deficiency is associated with impaired immune function and an increased risk of infection. Supplementation can decrease the incidence of diarrhoea and pneumonia in children in resource-poor countries. However, in children with HIV-1 infection, the safety of zinc supplementation is uncertain. We aimed to assess the role of zinc in HIV-1 replication before mass zinc supplementation is recommended in regions of high HIV-1 prevalence.


METHODS
We did a randomised double-blind placebo-controlled equivalence trial of zinc supplementation at Grey's Hospital in Pietermaritzburg, South Africa. 96 children with HIV-1 infection were randomly assigned to receive 10 mg of elemental zinc as sulphate or placebo daily for 6 months. Baseline measurements of plasma HIV-1 viral load and the percentage of CD4+ T lymphocytes were established at two study visits before randomisation, and measurements were repeated 3, 6, and 9 months after the start of supplementation. The primary outcome measure was plasma HIV-1 viral load. Analysis was per protocol.


FINDINGS
The mean log(10) HIV-1 viral load was 5.4 (SD 0.61) for the placebo group and 5.4 (SD 0.66) for the zinc-supplemented group 6 months after supplementation began (difference 0.0002, 95% CI -0.27 to 0.27). 3 months after supplementation ended, the corresponding values were 5.5 (SD 0.77) and 5.4 (SD 0.61), a difference of 0.05 (-0.24 to 0.35). The mean percentage of CD4+ T lymphocytes and median haemoglobin concentrations were also similar between the two groups after zinc supplementation. Two deaths occurred in the zinc supplementation group and seven in the placebo group (p=0.1). Children given zinc supplementation were less likely to get watery diarrhoea than those given placebo. Watery diarrhoea was diagnosed at 30 (7.4%) of 407 clinic visits in the zinc-supplemented group versus 65 (14.5%) of 447 visits in the placebo group (p=0.001).


INTERPRETATION
Zinc supplementation of HIV-1-infected children does not result in an increase in plasma HIV-1 viral load and could reduce morbidity caused by diarrhoea.


RELEVANCE TO PRACTICE
Programmes to enhance zinc intake in deficient populations with a high prevalence of HIV-1 infection can be implemented without concern for adverse effects on HIV-1 replication. In view of the reductions in diarrhoea and pneumonia morbidity, zinc supplementation should be used as adjunct therapy for children with HIV-1 infection.
Computational Argumentation Quality Assessment in Natural Language

Research on computational argumentation faces the problem of how to automatically assess the quality of an argument or argumentation. While different quality dimensions have been approached in natural language processing, a common understanding of argumentation quality is still missing. This paper presents the first holistic work on computational argumentation quality in natural language. We comprehensively survey the diverse existing theories and approaches to assess logical, rhetorical, and dialectical quality dimensions, and we derive a systematic taxonomy from these. In addition, we provide a corpus with 320 arguments, annotated for all 15 dimensions in the taxonomy. Our results establish a common ground for research on computational argumentation quality assessment.
Serum Metabolomic Profiling in Acute Alcoholic Hepatitis Identifies Multiple Dysregulated Pathways

BACKGROUND AND OBJECTIVES
While animal studies have implicated derangements of global energy homeostasis in the pathogenesis of acute alcoholic hepatitis (AAH), the relevance of these findings to the development of human AAH remains unclear. Using global, unbiased serum metabolomics analysis, we sought to characterize alterations in metabolic pathways associated with severe AAH and identify potential biomarkers for disease prognosis.


METHODS
This prospective, case-control study design included 25 patients with severe AAH and 25 ambulatory patients with alcoholic cirrhosis. Serum samples were collected within 24 hours of the index clinical encounter. Global, unbiased metabolomics profiling was performed. Patients were followed for 180 days after enrollment to determine survival.


RESULTS
Levels of 234 biochemicals were altered in subjects with severe AAH. Random-forest analysis, principal component analysis, and integrated hierarchical clustering methods demonstrated that metabolomics profiles separated the two cohorts with 100% accuracy. Severe AAH was associated with enhanced triglyceride lipolysis, impaired mitochondrial fatty acid beta oxidation, and upregulated omega oxidation. Low levels of multiple lysolipids and related metabolites suggested decreased plasma membrane remodeling in severe AAH. While most measured bile acids were increased in severe AAH, low deoxycholate and glycodeoxycholate levels indicated intestinal dysbiosis. Several changes in substrate utilization for energy homeostasis were identified in severe AAH, including increased glucose consumption by the pentose phosphate pathway, altered tricarboxylic acid (TCA) cycle activity, and enhanced peptide catabolism. Finally, altered levels of small molecules related to glutathione metabolism and antioxidant vitamin depletion were observed in patients with severe AAH. Univariable logistic regression revealed 15 metabolites associated with 180-day survival in severe AAH.


CONCLUSION
Severe AAH is characterized by a distinct metabolic phenotype spanning multiple pathways. Metabolomics profiling revealed a panel of biomarkers for disease prognosis, and future studies are planned to validate these findings in larger cohorts of patients with severe AAH.
Prediction of stage, grade, and survival in bladder cancer using genome-wide expression data: a validation study.

PURPOSE
To evaluate performances of published gene signatures for the assessment of urothelial carcinoma.


EXPERIMENTAL DESIGN
We evaluated 28 published gene signatures designed for diagnostic and prognostic purposes of urothelial cancer. The investigated signatures include eight signatures for stage, five for grade, four for progression, and six for survival. We used two algorithms for classification, nearest centroid classification and support vector machine, and Cox regression to evaluate signature performance in four independent data sets.


RESULTS
The overlap of genes among the signatures was low, ranging from 11% among stage signatures to 0.6% among survival signatures. The published signatures predicted muscle-invasive and high-grade tumors with accuracies in the range of 70% to 90%. The performance for a given signature varied considerably with the validation data set used, and interestingly, some of the best performing signatures were not designed for the tested classification problem. In addition, several nonbladder-derived gene signatures performed equally well. Large randomly selected gene signatures performed better than the published signatures, and by systematically increasing signature size, we show that signatures with >150 genes are needed to obtain robust performance in independent validation data sets. None of the published survival signatures performed better than random assignments when applied to independent validation data.


CONCLUSION
We conclude that gene expression signatures with >150 genes predict muscle-invasive growth and high-grade tumors with robust accuracies. Special considerations have to be taken when designing gene signatures for outcome in bladder cancer.
The REMEDEE-OCT Study: An Evaluation of the Bioengineered COMBO Dual-Therapy CD34 Antibody-Covered Sirolimus-Eluting Coronary Stent Compared With a Cobalt-Chromium Everolimus-Eluting Stent in Patients With Acute Coronary Syndromes: Insights From Optical Coherence Tomography Imaging Analysis.

OBJECTIVES
The aim of the present study was to evaluate vascular healing of the bioengineered COMBO Dual Therapy Stent compared with a cobalt-chromium (CoCr) everolimus-eluting stent (EES) as assessed by optical coherence tomography in patients with acute coronary syndromes.


BACKGROUND
CD34+ cells promote endothelial repair after vascular injury. The bioengineered COMBO Dual Therapy Stent combines CD34+ cell-capturing technology with abluminal sirolimus release, but more data from clinical studies evaluating the vascular response are needed.


METHODS
In a prospective randomized multicenter clinical trial, 60 patients with acute coronary syndromes were randomized 1:1 to COMBO or CoCr EES implantation. The primary endpoint was the percentage of uncovered stent struts per stent. Stent assessment by optical coherence tomography was performed at baseline and at 60 days, followed by independent core laboratory analysis.


RESULTS
The percentage of uncovered struts per stent was higher with the COMBO than the CoCr EES at 60 days (median 14.7% vs. 7.7%; p = 0.04). However, no significant difference in uncovered stent struts was observed in the strut level-based analysis at 60 days, which also accounted for clustering (COMBO vs. CoCr EES; 13.6% vs. 6.9%; p = 0.09; generalized linear mixed models-adjusted analysis). Neointimal thickness at 60 days was lower with the COMBO compared with the CoCr EES (median 30.17 vs. 50.26 μm; p = 0.02; stent-level analysis). There were no significant differences in the frequency of major adverse cardiac events and each component of major adverse cardiac events within the study population between the 2 groups at 30, 60, 180, 360, and 540 days post-procedure. No target vessel stent thrombosis has been documented within 540 days.


CONCLUSIONS
The present multicenter, prospective clinical study for the first time compared the vascular response of the bioengineered COMBO Dual Therapy Stent with a CoCr EES in patients early after acute coronary syndrome by using intracoronary optical coherence tomographic analysis. The percentage of uncovered stent struts per stent was somewhat higher after COMBO versus CoCr EES implantation as detected by optical coherence tomography, associated with reduced neointimal thickness.
Pearl Formation: Persistence of the Graft During the Entire Process of Biomineralization

Most bivalves species of the genus Pinctada are well known throughout the world for production of white or black pearls of high commercial value. For cultured pearl production, a mantle allograft from a donor is implanted into the gonad of a recipient oyster, together with a small inorganic bead. Because of the dedifferentiation of cells during the first steps of the host oyster’s immunological reaction, so far the fate of the graft and its exact role in the process of pearl formation could not be determined via classical histological methods. Here we report the first molecular evidence of the resilience of the graft in the recipient organism by showing that cells containing genome from the donor are still present at the end of pearl formation. These results suggest the existence of a unique biological cooperation leading to the successful biomineralization process of nacreous secretion in pearl formation.
A meta-analysis of the relationship of academic performance and Social Network Site use among adolescents and young adults

This meta-analysis explores the relationship between SNS-use and academic performance. Examination of the literature containing quantitative measurements of both SNS-use and academic performance produced a sample of 28 effects sizes (N 1⁄4 101,441) for review. Results indicated a significant negative relationship between SNS-use and academic performance. Further moderation analysis points to test type as an important source of variability in the relationship. We found a negative correlation between SNS-use and GPA, while a positive one for SNS-use and language test. Moreover, we found that the relationship of SNS-use and GPA was more strongly negative in females and college students. © 2017 Elsevier Ltd. All rights reserved.
The Institutionalisation of Ecotourism: Certification, Cultural Equity and Praxis

This paper offers a critical reading of the purpose, practice and institutionalisation of ecotourism. Tracing the evolving relationship between ecotourism and conservation, ecotourism and sustainable tourism, and ecotourism and certification/monitoring schemes as we do in this paper reveals conflicting values and possibly incompatible objectives. Sustainable tourism and ecotourism are rooted in notions of individual/ societal and environmental well-being. Yet, our study indicates significant inequities in ecotourism practice, particularly with respect to cultural aspects such as human ecological relationships. It is argued here that various actions and programmes associated with ecotourism’s inception and evolution have institutionalised a modernistic, commodified paradigm: the environment and its inhabitants (human and non-human) are dominated by scientific, industry and other interests that treat these primarily as means to an end, that is, instrumentally. The analysis suggests that ecotourism (and, by extension, ecotourism certification) needs to be re-oriented towards well-being, in other words, a social-cultural paradigm based on participatory democracy and equitable, meaningful relationships with the biophysical world. Suggestions are forwarded for re-envisioning ecotourism, particularly with respect to the notions of cultural equity, participatory practice and researcher praxis.
Deep Refinement Convolutional Networks for Human Pose Estimation

This work introduces a novel Convolutional Networkarchitecture (ConvNet) for the task of human poseestimation, that is the localization of body joints in a singlestatic image. The proposed coarse to fine architecture addressesshortcomings of the baseline architecture that stem from thefact that large inaccuracies of its coarse ConvNet cannot becorrected by the refinement ConvNet that refines the estimationwithin small windows of the coarse prediction. This is achievedby a) changes in architectural parameters that both increase theaccuracy of the coarse model and make the refinement modelmore capable of correcting the errors of the coarse model,b) the introduction of a Markov Random Field (MRF)-basedspatial model network between the coarse and the refinementmodel that introduces geometric constraints and c) a trainingscheme that adapts the data augmentation and the learning rateaccording to the difficulty of the data examples. The proposedarchitecture is trained in an end-to-end fashion. Experimentalresults show that the proposed method improves the baselinemodel and provides state of the art results on the FashionPose[8] and MPII benchmarks [1].
Mortality caused by influenza and respiratory syncytial virus by age group in England and Wales 1999–2010

BACKGROUND
The mortality burden caused by influenza cannot be quantified directly from death certificates because of under-recording; therefore, the estimated number of influenza deaths has to be obtained through statistical modelling.


OBJECTIVE
To estimate the number of deaths caused by influenza and respiratory syncytial virus (RSV) in England and Wales between 1999 and 2010 using a multivariable regression model.


METHODS
Generalised linear models were used to estimate weekly deaths by age group (<15, 15-44, 45-74 and 75+ years) as a function of positive influenza and RSV isolates. Adjustment was made for temperature variation (using weekly means of daily Central England temperature time series), underlying seasonal variation and temporal trends. The parameters from the model were used to predict the number of deaths caused by influenza and RSV across winter seasons.


RESULTS
Between 7000 and 25 000 deaths across all ages were associated with influenza in the winter periods 1999-2009. The mortality burden was the highest among the over 75 age group, among whom 2·5-8·1% of deaths were caused by influenza. The lowest number of influenza deaths was estimated for the winter 2009/2010 when pandemic influenza A/H1N1 (2009) was the predominant circulating strain. RSV accounted for 5000-7500 deaths each winter season.


CONCLUSIONS
The model presented provides a robust and reasonable approach to estimating the number of deaths caused by influenza and RSV by age group at the end of each winter.