Moussab/ORKG-training-evaluation-set huggingface dataset:
Research field: Bioinformatics
Title: Efficacy and tolerability of short-term duloxetine treatment in adults with generalized anxiety disorder: A meta-analysis
Abstract: Objective To investigate the efficacy and tolerability of duloxetine during short-term treatment in adults with generalized anxiety disorder (GAD). Methods We conducted a comprehensive literature review of the PubMed, Embase, Cochrane Central Register of Controlled Trials, Web of Science, and ClinicalTrials databases for randomized controlled trials(RCTs) comparing duloxetine or duloxetine plus other antipsychotics with placebo for the treatment of GAD in adults. Outcome measures were (1) efficacy, assessed by the Hospital Anxiety and Depression Scale(HADS) anxiety subscale score, the Hamilton Rating Scale for Anxiety(HAM-A) psychic and somatic anxiety factor scores, and response and remission rates based on total scores of HAM-A; (2) tolerability, assessed by discontinuation rate due to adverse events, the incidence of treatment emergent adverse events(TEAEs) and serious adverse events(SAEs). Review Manager 5.3 and Stata Version 12.0 software were used for all statistical analyses. Results The meta-analysis included 8 RCTs. Mean changes in the HADS anxiety subscale score [mean difference(MD) = 2.32, 95% confidence interval(CI) 1.77–2.88, P<0.00001] and HAM-A psychic anxiety factor score were significantly greater in patients with GAD that received duloxetine compared to those that received placebo (MD = 2.15, 95%CI 1.61–2.68, P<0.00001). However, there was no difference in mean change in the HAM-A somatic anxiety factor score (MD = 1.13, 95%CI 0.67–1.58, P<0.00001). Discontinuation rate due to AEs in the duloxetine group was significantly higher than the placebo group [odds ratio(OR) = 2.62, 95%CI 1.35–5.06, P = 0.004]. The incidence of any TEAE was significantly increased in patients that received duloxetine (OR = 1.76, 95%CI 1.36–2.28, P<0.0001), but there was no significant difference in the incidence of SAEs (OR = 1.13, 95%CI 0.52–2.47, P = 0.75). Conclusion Duloxetine resulted in a greater improvement in symptoms of psychic anxiety and similar changes in symptoms of somatic anxiety compared to placebo during short-term treatment in adults with GAD and its tolerability was acceptable.
Extracted statement — uses: Stata
Research field: Bioinformatics
Title: Comparisons between different elements of reported burden and common mental disorder in caregivers of ethnically diverse people with dementia in Trinidad
Abstract: Objective Culture plays a significant role in determining family responsibilities and possibly influences the caregiver burden associated with providing care for a relative with dementia. This study was carried out to determine the elements of caregiver burden in Trinidadians regarding which interventions will provide the most benefit. Methods Seventy-five caregivers of patients diagnosed with dementia participated in this investigation. Demographic data were recorded for each caregiver and patient. Caregiver burden was assessed using the Zarit Burden Interview (ZBI), and the General Health Questionnaire (GHQ) was used as a measure of psychiatric morbidity. Statistical analyses were performed using Stata and SPSS software. Associations between individual ZBI items and GHQ-28 scores in caregivers were analyzed in logistic regression models; the above-median GHQ-28 scores were used a binary dependent variable, and individual ZBI item scores were entered as 5-point ordinal independent variables. Results The caregiver sample was composed of 61 females and 14 males. Caregiver burden was significantly associated with the participant being male; there was heterogeneity by ethnic group, and a higher burden on female caregivers was detected at borderline levels of significance. Upon examining the associations between different ZBI items and the above-median GHQ-28 scores in caregivers, the strongest associations were found with domains reflecting the caregiver’s health having suffered, the caregiver not having sufficient time for him/herself, the caregiver’s social life suffering, and the caregiver admitting to feeling stressed due to caregiving and meeting other responsibilities. Conclusions In this sample, with a majority of female caregivers, the factors of the person with dementia being male and belonging to a minority ethnic group were associated with a greater degree of caregiver burden. The information obtained through the association of individual ZBI items and above-median GHQ-28 scores is a helpful guide for profiling Trinidadian caregiver burden.
Extracted statement — uses: Stata
Research field: Bioinformatics
Title: The Use of a Chronic Disease and Risk Factor Surveillance System to Determine the Age, Period and Cohort Effects on the Prevalence of Obesity and Diabetes in South Australian Adults - 2003–2013
Abstract: Background Age, period and cohort (APC) analyses, using representative, population-based descriptive data, provide additional understanding behind increased prevalence rates. Methods Data on obesity and diabetes from the South Australian (SA) monthly chronic disease and risk factor surveillance system from July 2002 to December 2013 (n = 59,025) were used. Age was the self-reported age of the respondent at the time of the interview. Period was the year of the interview and cohort was age subtracted from the survey year. Cohort years were 1905 to 1995. All variables were treated as continuous. The age-sex standardised prevalence for obesity and diabetes was calculated using the Australia 2011 census. The APC models were constructed with ‘‘apcfit’’ in Stata. Results The age-sex standardised prevalence of obesity and diabetes increased in 2002-2013 from 18.6% to 24.1% and from 6.2% to 7.9%. The peak age for obesity was approximately 70 years with a steady increasing rate from 20 to 70 years of age. The peak age for diabetes was approximately 80 years. There were strong cohort effects and no period effects for both obesity and diabetes. The magnitude of the cohort effect is much more pronounced for obesity than for diabetes. Conclusion The APC analyses showed a higher than expected peak age for both obesity and diabetes, strong cohort effects with an acceleration of risk after 1960s for obesity and after 1940s for diabetes, and no period effects. By simultaneously considering the effects of age, period and cohort we have provided additional evidence for effective public health interventions.
Extracted statement — uses: Stata
Research field: Bioinformatics
Title: Predictive value of traction force measurement in vacuum extraction: Development of a multivariate prognostic model
Abstract: Objective To enable early prediction of strong traction force vacuum extraction. Design Observational cohort. Setting Karolinska University Hospital delivery ward, tertiary unit. Population and sample size Term mid and low metal cup vacuum extraction deliveries June 2012—February 2015, n = 277. Methods Traction forces during vacuum extraction were collected prospectively using an intelligent handle. Levels of traction force were analysed pairwise by subjective category strong versus non-strong extraction, in order to define an objective predictive value for strong extraction. Statistical analysis A logistic regression model based on the shrinkage and selection method lasso was used to identify the predictive capacity of the different traction force variables. Predictors Total (time force integral, Newton minutes) and peak traction (Newton) force in the first to third pull; difference in traction force between the second and first pull, as well as the third and first pull respectively. Accumulated traction force at the second and third pull. Outcome Subjectively categorized extraction as strong versus non-strong. Results The prevalence of strong extraction was 26%. Prediction including the first and second pull: AUC 0,85 (CI 0,80–0,90); specificity 0,76; sensitivity 0,87; PPV 0,56; NPV 0,94. Prediction including the first to third pull: AUC 0,86 (CI 0,80–0,91); specificity 0,87; sensitivity 0,70; PPV 0,65; NPV 0,89. Conclusion Traction force measurement during vacuum extraction can help exclude strong category extraction from the second pull. From the third pull, two-thirds of strong extractions can be predicted.
Extracted statement — uses: Statistica
Research field: Bioinformatics
Title: Ecological Genetics of Chinese Rhesus Macaque in Response to Mountain Building: All Things Are Not Equal
Abstract: Background Pliocene uplifting of the Qinghai-Tibetan Plateau (QTP) and Quaternary glaciation may have impacted the Asian biota more than any other events. Little is documented with respect to how the geological and climatological events influenced speciation as well as spatial and genetic structuring, especially in vertebrate endotherms. Macaca mulatta is the most widely distributed non-human primate. It may be the most suitable model to test hypotheses regarding the genetic consequences of orogenesis on an endotherm. Methodology and Principal Findings Using a large dataset of maternally inherited mitochondrial DNA gene sequences and nuclear microsatellite DNA data, we discovered two maternal super-haplogroups exist, one in western China and the other in eastern China. M. mulatta formed around 2.31 Ma (1.51–3.15, 95%), and divergence of the two major matrilines was estimated at 1.15 Ma (0.78–1.55, 95%). The western super-haplogroup exhibits significant geographic structure. In contrast, the eastern super-haplogroup has far greater haplotypic variability with little structure based on analyses of six variable microsatellite loci using Structure and Geneland. Analysis using Migrate detected greater gene flow from WEST to EAST than vice versa. We did not detect signals of bottlenecking in most populations. Conclusions Analyses of the nuclear and mitochondrial datasets obtained large differences in genetic patterns for M. mulatta. The difference likely reflects inheritance mechanisms of the maternally inherited mtDNA genome versus nuclear biparentally inherited STRs and male-mediated gene flow. Dramatic environmental changes may be responsible for shaping the matrilineal history of macaques. The timing of events, the formation of M. mulatta, and the divergence of the super-haplogroups, corresponds to both the uplifting of the QTP and Quaternary climatic oscillations. Orogenesis likely drove divergence of western populations in China, and Pleistocene glaciations are likely responsible for genetic structuring in the eastern super-haplogroup via geographic isolation and secondary contact.
Extracted statement — uses: Structure
Research field: Bioinformatics
Title: Telescope: Characterization of the retrotranscriptome by accurate estimation of transposable element expression
Abstract: Characterization of Human Endogenous Retrovirus (HERV) expression within the transcriptomic landscape using RNA-seq is complicated by uncertainty in fragment assignment because of sequence similarity. We present Telescope, a computational software tool that provides accurate estimation of transposable element expression (retrotranscriptome) resolved to specific genomic locations. Telescope directly addresses uncertainty in fragment assignment by reassigning ambiguously mapped fragments to the most probable source transcript as determined within a Bayesian statistical model. We demonstrate the utility of our approach through single locus analysis of HERV expression in 13 ENCODE cell types. When examined at this resolution, we find that the magnitude and breadth of the retrotranscriptome can be vastly different among cell types. Furthermore, our approach is robust to differences in sequencing technology and demonstrates that the retrotranscriptome has potential to be used for cell type identification. We compared our tool with other approaches for quantifying transposable element (TE) expression, and found that Telescope has the greatest resolution, as it estimates expression at specific TE insertions rather than at the TE subfamily level. Telescope performs highly accurate quantification of the retrotranscriptomic landscape in RNA-seq experiments, revealing a differential complexity in the transposable element biology of complex systems not previously observed. Telescope is available at https://github.com/mlbendall/telescope.
Extracted statement — creates: Telescope
Research field: Bioinformatics
Title: Telescope: Characterization of the retrotranscriptome by accurate estimation of transposable element expression
Abstract: Characterization of Human Endogenous Retrovirus (HERV) expression within the transcriptomic landscape using RNA-seq is complicated by uncertainty in fragment assignment because of sequence similarity. We present Telescope, a computational software tool that provides accurate estimation of transposable element expression (retrotranscriptome) resolved to specific genomic locations. Telescope directly addresses uncertainty in fragment assignment by reassigning ambiguously mapped fragments to the most probable source transcript as determined within a Bayesian statistical model. We demonstrate the utility of our approach through single locus analysis of HERV expression in 13 ENCODE cell types. When examined at this resolution, we find that the magnitude and breadth of the retrotranscriptome can be vastly different among cell types. Furthermore, our approach is robust to differences in sequencing technology and demonstrates that the retrotranscriptome has potential to be used for cell type identification. We compared our tool with other approaches for quantifying transposable element (TE) expression, and found that Telescope has the greatest resolution, as it estimates expression at specific TE insertions rather than at the TE subfamily level. Telescope performs highly accurate quantification of the retrotranscriptomic landscape in RNA-seq experiments, revealing a differential complexity in the transposable element biology of complex systems not previously observed. Telescope is available at https://github.com/mlbendall/telescope.
Extracted statement — deposits: Telescope
Research field: Bioinformatics
Title: Telescope: Characterization of the retrotranscriptome by accurate estimation of transposable element expression
Abstract: Characterization of Human Endogenous Retrovirus (HERV) expression within the transcriptomic landscape using RNA-seq is complicated by uncertainty in fragment assignment because of sequence similarity. We present Telescope, a computational software tool that provides accurate estimation of transposable element expression (retrotranscriptome) resolved to specific genomic locations. Telescope directly addresses uncertainty in fragment assignment by reassigning ambiguously mapped fragments to the most probable source transcript as determined within a Bayesian statistical model. We demonstrate the utility of our approach through single locus analysis of HERV expression in 13 ENCODE cell types. When examined at this resolution, we find that the magnitude and breadth of the retrotranscriptome can be vastly different among cell types. Furthermore, our approach is robust to differences in sequencing technology and demonstrates that the retrotranscriptome has potential to be used for cell type identification. We compared our tool with other approaches for quantifying transposable element (TE) expression, and found that Telescope has the greatest resolution, as it estimates expression at specific TE insertions rather than at the TE subfamily level. Telescope performs highly accurate quantification of the retrotranscriptomic landscape in RNA-seq experiments, revealing a differential complexity in the transposable element biology of complex systems not previously observed. Telescope is available at https://github.com/mlbendall/telescope.
Extracted statement — uses: Telescope
Research field: Bioinformatics
Title: QuIN: A Web Server for Querying and Visualizing Chromatin Interaction Networks
Abstract: Recent studies of the human genome have indicated that regulatory elements (e.g. promoters and enhancers) at distal genomic locations can interact with each other via chromatin folding and affect gene expression levels. Genomic technologies for mapping interactions between DNA regions, e.g., ChIA-PET and HiC, can generate genome-wide maps of interactions between regulatory elements. These interaction datasets are important resources to infer distal gene targets of non-coding regulatory elements and to facilitate prioritization of critical loci for important cellular functions. With the increasing diversity and complexity of genomic information and public ontologies, making sense of these datasets demands integrative and easy-to-use software tools. Moreover, network representation of chromatin interaction maps enables effective data visualization, integration, and mining. Currently, there is no software that can take full advantage of network theory approaches for the analysis of chromatin interaction datasets. To fill this gap, we developed a web-based application, QuIN, which enables: 1) building and visualizing chromatin interaction networks, 2) annotating networks with user-provided private and publicly available functional genomics and interaction datasets, 3) querying network components based on gene name or chromosome location, and 4) utilizing network based measures to identify and prioritize critical regulatory targets and their direct and indirect interactions. AVAILABILITY: QuIN’s web server is available at http://quin.jax.org QuIN is developed in Java and JavaScript, utilizing an Apache Tomcat web server and MySQL database and the source code is available under the GPLV3 license available on GitHub: https://github.com/UcarLab/QuIN/.
Extracted statement — uses: Tomcat
Research field: Bioinformatics
Title: Classifying semantic relations in bioscience texts
Abstract: A crucial step toward the goal of automatic extraction of propositional information from natural language text is the identification of semantic relations between constituents in sentences. We examine the problem of distinguishing among seven relation types that can occur between the entities "treatment" and "disease" in bioscience text, and the problem of identifying such entities. We compare five generative graphical models and a neural network, using lexical, syntactic, and semantic features, finding that the latter help achieve high classification accuracy.
Extracted statement — Concept types: Treatment
Research field: Bioinformatics
Title: Quantifying Regional Differences in the Length of Twitter Messages
Abstract: The increasing usage of social media for conversations, together with the availability of its data to researchers, provides an opportunity to study human conversations on a large scale. Twitter, which allows its users to post messages of up to a limit of 140 characters, is one such social media. Previous studies of utterances in books, movies and Twitter have shown that most of these utterances, when transcribed, are much shorter than 140 characters. Furthermore, the median length of Twitter messages was found to vary across US states. Here, we investigate whether the length of Twitter messages varies across different regions in the UK. We find that the median message length, depending on grouping, can differ by up to 2 characters.
Extracted statement — uses: Twitter
Research field: Bioinformatics
Title: SNPdetector: A Software Tool for Sensitive and Accurate SNP Detection
Abstract: Identification of single nucleotide polymorphisms (SNPs) and mutations is important for the discovery of genetic predisposition to complex diseases. PCR resequencing is the method of choice for de novo SNP discovery. However, manual curation of putative SNPs has been a major bottleneck in the application of this method to high-throughput screening. Therefore it is critical to develop a more sensitive and accurate computational method for automated SNP detection. We developed a software tool, SNPdetector, for automated identification of SNPs and mutations in fluorescence-based resequencing reads. SNPdetector was designed to model the process of human visual inspection and has a very low false positive and false negative rate. We demonstrate the superior performance of SNPdetector in SNP and mutation analysis by comparing its results with those derived by human inspection, PolyPhred (a popular SNP detection tool), and independent genotype assays in three large-scale investigations. The first study identified and validated inter- and intra-subspecies variations in 4,650 traces of 25 inbred mouse strains that belong to either the Mus musculus species or the M. spretus species. Unexpected heterozgyosity in CAST/Ei strain was observed in two out of 1,167 mouse SNPs. The second study identified 11,241 candidate SNPs in five ENCODE regions of the human genome covering 2.5 Mb of genomic sequence. Approximately 50% of the candidate SNPs were selected for experimental genotyping; the validation rate exceeded 95%. The third study detected ENU-induced mutations (at 0.04% allele frequency) in 64,896 traces of 1,236 zebra fish. Our analysis of three large and diverse test datasets demonstrated that SNPdetector is an effective tool for genome-scale research and for large-sample clinical studies. SNPdetector runs on Unix/Linux platform and is available publicly (http://lpg.nci.nih.gov).
Extracted statement — uses: Unix
Research field: Bioinformatics
Title: Multi task sequence learning for depression scale prediction from video
Abstract: Depression is a typical mood disorder, which affects people in mental and even physical problems. People who suffer depression always behave abnormal in visual behavior and the voice. In this paper, an audio visual based multimodal depression scale prediction system is proposed. Firstly, features are extracted from video and audio are fused in feature level to represent the audio visual behavior. Secondly, long short memory recurrent neural network (LSTM-RNN) is utilized to encode the dynamic temporal information of the abnormal audio visual behavior. Thirdly, emotion information is utilized by multi-task learning to boost the performance further. The proposed approach is evaluated on the Audio-Visual Emotion Challenge (AVEC2014) dataset. Experiments results show the dimensional emotion recognition helps to depression scale prediction.
Extracted statement — Data: Voice
Research field: Bioinformatics
Title: Wham: Identifying Structural Variants of Biological Consequence
Abstract: Existing methods for identifying structural variants (SVs) from short read datasets are inaccurate. This complicates disease-gene identification and efforts to understand the consequences of genetic variation. In response, we have created Wham (Whole-genome Alignment Metrics) to provide a single, integrated framework for both structural variant calling and association testing, thereby bypassing many of the difficulties that currently frustrate attempts to employ SVs in association testing. Here we describe Wham, benchmark it against three other widely used SV identification tools–Lumpy, Delly and SoftSearch–and demonstrate Wham’s ability to identify and associate SVs with phenotypes using data from humans, domestic pigeons, and vaccinia virus. Wham and all associated software are covered under the MIT License and can be freely downloaded from github (https://github.com/zeeev/wham), with documentation on a wiki (http://zeeev.github.io/wham/). For community support please post questions to https://www.biostars.org/.
Extracted statement — creates: Wham