cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.21213047.v1
title: Supplementary Material for: Efficacy and Safety of Vagus Nerve Stimulation in Stroke Rehabilitation: A Systematic Review and Meta-Analysis

description: <b><i>Introduction:</i></b> Recent randomized controlled trials (RCTs) have assessed the role of vagus nerve stimulation (VNS) when paired with standard rehabilitation in stroke patients. This review aimed to evaluate the efficacy and safety of VNS as a novel treatment option for post-stroke recovery. <b><i>Methods:</i></b> We searched PubMed, EMBASE, Cochrane Database of Systematic Reviews, Cochrane Central Register of Controlled Trials (CENTRAL), and CINAHL Plus for articles published from their date of inception to June 2021. RCTs investigating the efficacy or safety of VNS on post-stroke recovery were included. The outcomes were upper limb sensorimotor function, health-related quality of life, level of independence, cardiovascular effects, and adverse events. The risk of bias was assessed using the Cochrane risk-of-bias tool, while the certainty of the evidence was assessed using the Grading of Recommendations, Assessment, Development, and Evaluations (GRADE) criteria. Review Manager 5.4 was used to conduct the meta-analysis. <b><i>Results:</i></b> Seven RCTs (<i>n</i> = 236 subjects) met the eligibility criteria. Upper limb sensorimotor function, assessed by the Fugl-Meyer Assessment for Upper Extremity (FMA-UE), improved at day 1 (<i>n</i> = 4 RCTs; standardized mean difference [SMD] 1.01; 95% confidence interval [CI]: 0.35–1.66) and day 90 post-intervention (<i>n</i> = 3 RCTs; SMD 0.64; 95% CI: 0.31–0.98; moderate certainty of evidence) but not at day 30 follow-up (<i>n</i> = 2 RCTs; SMD 1.54; 95% CI: −0.39 to 3.46). Clinically significant upper limb sensorimotor function recovery, as defined by ≥6 points increase in FMA-UE, was significantly higher at day 1 (<i>n</i> = 2 RCTs; risk ratio [RR] 2.01; 95% CI: 1.02–3.94) and day 90 post-intervention (<i>n</i> = 2 RCTs; RR 2.14; 95% CI: 1.32–3.45; moderate certainty of the evidence). The between-group effect sizes for upper limb sensorimotor function recovery was medium to large (Hedges’ g 0.535–2.659). While the level of independence improved with VNS, its impact on health-related quality of life remains unclear as this was only studied in two trials with mixed results. Generally, adverse events reported were mild and self-limiting. <b><i>Conclusion:</i></b> VNS may be an effective and safe adjunct to standard rehabilitation for post-stroke recovery; however, its clinical significance and long-term efficacy and safety remain unclear.
DOI: 10.6084/m9.figshare.20347443
title: Supplementary Material for: Real-world effectiveness of lipid-lowering medications on outcomes after stroke: potential implications of the new-user design

description: Introduction: Observational studies are increasingly being used to provide evidence on the real-world effectiveness of medications for preventing vascular diseases, such as stroke. We investigated whether the real-world effectiveness of treatment with lipid-lowering medications after ischemic stroke is affected by prevalent user bias. Methods: An observational cohort study of 90-day survivors of ischemic stroke, using person-level data from the Australian Stroke Clinical Registry (2012-2016; 45 hospitals) linked to administrative (pharmaceutical, hospital, death) records. Use of, and adherence to (proportion of days covered &lt;80% [poor adherence] vs. ≥80% [good adherence]), lipid-lowering medications within 90 days post-discharge was determined from pharmaceutical records. Users were further classified as prevalent (continuing) or new-users, based dispensing within 90 days prior to stroke. Propensity score-adjusted Cox regression was used to evaluate the effectiveness of lipid-lowering medications on outcomes (all-cause mortality, all-cause and cardiovascular disease readmission) within the subsequent year. Analyses were undertaken using prevalent-user (all users vs. non-users) and new-user designs (new-users vs. non-users). Results: Of 11,217 eligible patients (median age 72 years, 42% female), 9,294 (83%) used lipid-lowering medications within 90 days post-discharge, including 5,479 new-users. In both prevalent-user and new-user designs, non-users (vs. users) had significantly greater rates of mortality (hazard ratio [HR] 2.35, 95% CI 1.89-2.92) or all-cause readmissions (HR 1.22, CI 1.05-1.40), but not cardiovascular disease readmission. In contrast, associations between having poor (vs. good) adherence on outcomes were stronger among new-users than all-users. Among new-users, having poor adherence was associated with greater rates of mortality (HR 1.48, CI 1.12-1.96), all-cause readmission (HR 1.14, CI 1.02-1.27), and cardiovascular disease readmission (HR 1.20, CI 1.01-1.42). Conclusions: The real-world effectiveness of treatment with lipid-lowering medications after stroke is attenuated when evaluated based on prevalent-user rather than new-user design. These findings may have implications for designing studies on the real-world effectiveness of secondary prevention medications.
DOI: 10.6084/m9.figshare.20347443.v1
title: Supplementary Material for: Real-world effectiveness of lipid-lowering medications on outcomes after stroke: potential implications of the new-user design

description: Introduction: Observational studies are increasingly being used to provide evidence on the real-world effectiveness of medications for preventing vascular diseases, such as stroke. We investigated whether the real-world effectiveness of treatment with lipid-lowering medications after ischemic stroke is affected by prevalent user bias. Methods: An observational cohort study of 90-day survivors of ischemic stroke, using person-level data from the Australian Stroke Clinical Registry (2012-2016; 45 hospitals) linked to administrative (pharmaceutical, hospital, death) records. Use of, and adherence to (proportion of days covered &lt;80% [poor adherence] vs. ≥80% [good adherence]), lipid-lowering medications within 90 days post-discharge was determined from pharmaceutical records. Users were further classified as prevalent (continuing) or new-users, based dispensing within 90 days prior to stroke. Propensity score-adjusted Cox regression was used to evaluate the effectiveness of lipid-lowering medications on outcomes (all-cause mortality, all-cause and cardiovascular disease readmission) within the subsequent year. Analyses were undertaken using prevalent-user (all users vs. non-users) and new-user designs (new-users vs. non-users). Results: Of 11,217 eligible patients (median age 72 years, 42% female), 9,294 (83%) used lipid-lowering medications within 90 days post-discharge, including 5,479 new-users. In both prevalent-user and new-user designs, non-users (vs. users) had significantly greater rates of mortality (hazard ratio [HR] 2.35, 95% CI 1.89-2.92) or all-cause readmissions (HR 1.22, CI 1.05-1.40), but not cardiovascular disease readmission. In contrast, associations between having poor (vs. good) adherence on outcomes were stronger among new-users than all-users. Among new-users, having poor adherence was associated with greater rates of mortality (HR 1.48, CI 1.12-1.96), all-cause readmission (HR 1.14, CI 1.02-1.27), and cardiovascular disease readmission (HR 1.20, CI 1.01-1.42). Conclusions: The real-world effectiveness of treatment with lipid-lowering medications after stroke is attenuated when evaluated based on prevalent-user rather than new-user design. These findings may have implications for designing studies on the real-world effectiveness of secondary prevention medications.
DOI: 10.5281/zenodo.7115723
title: Manually verified publication prediction dataset.

description: Includes the clinical trial identifiers with publication status decisions sourced from three studies: - Joseph S Ross, Tony Tse, Deborah A Zarin, Hui Xu, Lei Zhou, and Harlan M Krumholz. Publication of NIH funded trials registered in clinicaltrials. gov: cross sectional analysis. BMJ, 344, 2012. - Adam G Dunn, Enrico Coiera, and Florence T Bourgeois. Unreported links between trial registrations and published articles were identified using document similarity measures in a cross-sectional analysis of ClinicalTrials. gov. Journal of clinical epidemiology 95: 94-101, 2018. - Deborah A Zarin, Tony Tse, Rebecca J Williams, Robert M Califf, and Nicholas C Ide. The ClinicalTrials. gov results database—update and key issues. New England Journal of Medicine 364, no. 9: 852-860, 2011. The authors of the studies have agreed with the publication of this dataset.<br>
DOI: 10.24400/527896/a01-2022.006.220209
title: Mesoscale Eddy Trajectory Atlas META3.2 Delayed-Time two satellites
title: version META3.2 DT twosat

description: This dataset is composed of the trajectories and all associated parameters for the eddies detected with the py-eddy-tracker algorithm (Mason et al., 2014. DOI:10.1175/JTECH-D-14-00019.1) freely released under a GPL V3 license (https://github.com/AntSimi/py-eddy-tracker). The detection is made on maps of Absolute Dynamic Topography (ADT) computed with two altimeter satellites, the maps are distributed by the Copernicus Climate Change Service (https://climate.copernicus.eu/, cf user manual for details). The maps are high-pass filtered with a half-power cutoff wavelenght of 700 km. The amplitude must be over 0.4 cm, the minimum number of grid points within a contour is 5 and the shape error must be below 70% on the raw effective contour. Note that the contour storage resampling may slightly change the provided error. The tracking is made through the overlap of the eddies. In case of multiple candidates, the eddy with the higher ratio overlap area over union area is associated to the trajectory. Trajectories are considered reliable when they last at least 10 days.
DOI: 10.25416/ntr.21187165
title: Experimental Errors Lectures Questions

description: Example questions taken from a course on measurements and their uncertainties, a lecture course designed to support year one physics laboratories. The questions were used via Poll everywhere during the lecture. <br> <br> The course/resource is based on the following book: <br> Hughes, I., & Hase, T. (2010). <em>Measurements and their uncertainties: a practical guide to modern error analysis</em>. OUP Oxford. <br>
DOI: 10.25416/ntr.21187165.v1
title: Experimental Errors Lectures Questions

description: Example questions taken from a course on measurements and their uncertainties, a lecture course designed to support year one physics laboratories. The questions were used via Poll everywhere during the lecture. <br> <br> The course/resource is based on the following book: <br> Hughes, I., & Hase, T. (2010). <em>Measurements and their uncertainties: a practical guide to modern error analysis</em>. OUP Oxford. <br>
DOI: 10.5255/ukda-sn-855967
title: Drugs and (Dis)order Forced Eradication Incidents in Colombia, 2016-2020

description: Collection of press reporting and videos on confrontations between state forces and rural populations that occurred during forced manual eradication of illicit crops in Colombia. It is based on a database created by the Observatory for the Restitution and Regulation of Agrarian Property Rights in Colombia, and continues to be updated as new events are registered. This version of the database contains 107 incidents registered between November 2016 and July 2020. The collection of videos contains 40 videos of forced eradication carried out by the Mobile Anti-Riot Squadron (ESMAD) and/or the Armed Forces. Most videos were recorded by peasants for use in formal complaints against the perpetrators, between February 2017 and July 2020.
DOI: 10.6084/m9.figshare.21214028
title: 06-Rodriguez-Cortes-ANEXOS.pdf

description: anexos
DOI: 10.6084/m9.figshare.21214028.v1
title: 06-Rodriguez-Cortes-ANEXOS.pdf

description: anexos
DOI: 10.6084/m9.figshare.20514912
title: Supporting Information

description: <strong>benign prostatic hyperplasia</strong>
DOI: 10.6084/m9.figshare.20514912.v2
title: Supporting Information

description: <strong>benign prostatic hyperplasia</strong>
DOI: 10.6084/m9.figshare.20514912.v1
title: Supporting Information of plos one

description: <strong>benign prostatic hyperplasia</strong>
DOI: 10.6084/m9.figshare.21213896
title: Data for: Estimating heritability of song considering within-individual variance in a wild songbird: the collared flycatcher

description: Data for: Heritability of song in the collared flycatcher <br> The table "songheritability_data.csv" contains all data used in the animal models investigating variance components five song traits: song length, mean frequency, frequency bandwidth, tempo and complexity. The other variables are date and year of the measurements, age and identity of the birds, order of the songs in the recording, recording ID and song ID. Continuous variables were z-transformed. <br> The table "geneticsimilaritymatrix.csv" contains the genetic similarity matrix of the individuals with song data, used in the animal models. <br> The R script file "songheritability_code.R" contains R code necessary for reproducing the results reported in the manuscript. <br> Song recording was collected from collared flycatchers (<em>Ficedula albicollis</em>) from 2008-18. We catched these birds and collected blood samples from them and recorded their age (one-year old or older). Five song traits, which were extracted from the song recordings with the help of Ficedula toolbox, were used in the analyses: song length, mean frequency, frequency bandwidth, tempo and complexity. All continuous variables included into the models were z-transformed. Genetic similarity matrix was calculated based on more than 50 000 single nucleotide polymorphism.
DOI: 10.5281/zenodo.7003730
title: Dataset for in silico and in vitro studies confirm Ondansetron as a novel AChE and BChE inhibitor.

description: Compressed data from IFD and MD simulations of Ondansetron, Tacrine and Rivastigmine binding to AChE and BChE. Structures of AChE and BChE after protein preparation.
DOI: 10.5281/zenodo.7003729
title: Dataset for in silico and in vitro studies confirm Ondansetron as a novel AChE and BChE inhibitor.

description: Compressed data from IFD and MD simulations of Ondansetron, Tacrine and Rivastigmine binding to AChE and BChE. Structures of AChE and BChE after protein preparation.
DOI: 10.6084/m9.figshare.20983588
title: Determinants of fluconazole resistance and echinocandin tolerance in <i>C. parapsilosis</i> isolates causing a large clonal candidemia outbreak among COVID-19 patients in a Brazilian ICU

description: Patients presenting with severe COVID-19 are predisposed to acquire secondary fungal infections such as COVID-19-associated candidemia (CAC), which are associated with poor clinical outcomes despite antifungal treatment. The extreme burden imposed on clinical facilities during the COVID-19 pandemic has provided a permissive environment for the emergence of clonal outbreaks of multiple <i>Candida</i> species, including <i>C. auris</i> and <i>C. parapsilosis</i>. Here we report the largest clonal CAC outbreak to date caused by fluconazole resistant (FLZR) and echinocandin tolerant (ECT) <i>C. parapsilosis</i>. Sixty <i>C. parapsilosis</i> strains were obtained from 57 patients at a tertiary care hospital in Brazil, 90% of them were FLZR and ECT. Although only 35.8% of FLZR isolates contained an <i>ERG11</i> mutation, all of them contained the <i>TAC1<sup>L518F</sup></i> mutation and significantly overexpressed <i>CDR1</i>. Introduction of <i>TAC1<sup>L518F</sup></i> into a susceptible background increased the MIC of fluconazole and voriconazole 8-fold and resulted in significant basal overexpression of <i>CDR1</i>. Additionally, FLZR isolates exclusively harboured E1939G outside of Fks1 hotspot-2, which did not confer echinocandin resistance, but significantly increased ECT. Multilocus microsatellite typing showed that 51/60 (85%) of the FLZR isolates belonged to the same cluster, while the susceptible isolates each represented a distinct lineage. Finally, biofilm production in FLZR isolates was significantly lower than in susceptible counterparts Suggesting that it may not be an outbreak determinant. In summary, we show that <i>TAC1<sup>L518F</sup></i> and <i>FKS1<sup>E1393G</sup></i> confer FLZR and ECT, respectively, in CAC-associated <i>C. parapsilosis</i>. Our study underscores the importance of antifungal stewardship and effective infection control strategies to mitigate clonal <i>C. parapsilosis</i> outbreaks.
DOI: 10.6084/m9.figshare.20983588.v2
title: Determinants of fluconazole resistance and echinocandin tolerance in <i>C. parapsilosis</i> isolates causing a large clonal candidemia outbreak among COVID-19 patients in a Brazilian ICU

description: Patients presenting with severe COVID-19 are predisposed to acquire secondary fungal infections such as COVID-19-associated candidemia (CAC), which are associated with poor clinical outcomes despite antifungal treatment. The extreme burden imposed on clinical facilities during the COVID-19 pandemic has provided a permissive environment for the emergence of clonal outbreaks of multiple <i>Candida</i> species, including <i>C. auris</i> and <i>C. parapsilosis</i>. Here we report the largest clonal CAC outbreak to date caused by fluconazole resistant (FLZR) and echinocandin tolerant (ECT) <i>C. parapsilosis</i>. Sixty <i>C. parapsilosis</i> strains were obtained from 57 patients at a tertiary care hospital in Brazil, 90% of them were FLZR and ECT. Although only 35.8% of FLZR isolates contained an <i>ERG11</i> mutation, all of them contained the <i>TAC1<sup>L518F</sup></i> mutation and significantly overexpressed <i>CDR1</i>. Introduction of <i>TAC1<sup>L518F</sup></i> into a susceptible background increased the MIC of fluconazole and voriconazole 8-fold and resulted in significant basal overexpression of <i>CDR1</i>. Additionally, FLZR isolates exclusively harboured E1939G outside of Fks1 hotspot-2, which did not confer echinocandin resistance, but significantly increased ECT. Multilocus microsatellite typing showed that 51/60 (85%) of the FLZR isolates belonged to the same cluster, while the susceptible isolates each represented a distinct lineage. Finally, biofilm production in FLZR isolates was significantly lower than in susceptible counterparts Suggesting that it may not be an outbreak determinant. In summary, we show that <i>TAC1<sup>L518F</sup></i> and <i>FKS1<sup>E1393G</sup></i> confer FLZR and ECT, respectively, in CAC-associated <i>C. parapsilosis</i>. Our study underscores the importance of antifungal stewardship and effective infection control strategies to mitigate clonal <i>C. parapsilosis</i> outbreaks.
DOI: 10.6084/m9.figshare.21213995
title: After the Uprising: the Intifada-Oslo Generation and Attitudes Toward the Palestinian Police

description: Does experiencing a mass uprising during one’s formative years shape attitudes toward post-uprising institutions? Existing research on cohorts has not examined settings of ongoing statelessness. We focus on Palestinians who witnessed the First Intifada and subsequent Israeli-Palestinian negotiations during their youth-to- adulthood transition. Analyzing a pooled sample of surveys conducted between 1996 and 2000, we observe that men from this cohort – using a youth-based definition of one’s formative years – evaluated the Palestinian police more negatively than did other men, ceteris paribus. We test two, potential explanations. We find support for the proposition that men from this cohort held distinctive views about coercion and resistance that shaped their evaluations. We conclude that experiencing mass mobilization and transition during one’s formative years can influence attitudes, but additional work is needed to test for their long-term endurance. Further, a younger operationalization of one’s impressionable years may be salient in settings of insecurity.
DOI: 10.6084/m9.figshare.21213995.v1
title: After the Uprising: the Intifada-Oslo Generation and Attitudes Toward the Palestinian Police

description: Does experiencing a mass uprising during one’s formative years shape attitudes toward post-uprising institutions? Existing research on cohorts has not examined settings of ongoing statelessness. We focus on Palestinians who witnessed the First Intifada and subsequent Israeli-Palestinian negotiations during their youth-to- adulthood transition. Analyzing a pooled sample of surveys conducted between 1996 and 2000, we observe that men from this cohort – using a youth-based definition of one’s formative years – evaluated the Palestinian police more negatively than did other men, ceteris paribus. We test two, potential explanations. We find support for the proposition that men from this cohort held distinctive views about coercion and resistance that shaped their evaluations. We conclude that experiencing mass mobilization and transition during one’s formative years can influence attitudes, but additional work is needed to test for their long-term endurance. Further, a younger operationalization of one’s impressionable years may be salient in settings of insecurity.
DOI: 10.15129/a45be5c3-4f8b-4d43-9b29-c4f4222a7716
title: Data for: "Deep Learning approaches for the prediction of powder flow of pharmaceutical materials"

description: Deep learning models have been trained on a dataset formed by Morphologi G3 images.
DOI: 10.5281/zenodo.7104288
title: [Data] Earliest meteorological readings in San Fernando (Cádiz, Spain)

description: Daily, monthly and weekly meteorological observations recorded at the Royal Observatory of the Spanish Navy (located in San Fernando, Cádiz) during the period 1799-1813.
DOI: 10.5255/ukda-sn-855965
title: Drugs and (Dis)order Key Informant Interviews in Kachin State Myanmar, 2018

description: Collection of 261 face-to-face semi-structured interviews with interviewees in Kachin State, northern Myanmar, carried out as part of the GCRF Drugs and (dis)order project. Interviews were carried out in the first year of the project and explore narratives around illicit drugs across and within communities, and focus on the wider political and economic context of the area, issues around conflict and violence, and drug issues specifically. Evidence was generated on (1) how people interact with drugs and the drug economy, (2) the relationships between people, places and drugs, (3) organisations that shape people’s lives across Kachin State, including those that are related to drugs, (4) cultural engagement with drugs, and (5) economic dynamics of the Kachin borderland region and how they operate around drugs. The upland areas of Kachin are perfectly suited to the cultivation of opium poppy, which has provided livelihood security in impoverished rural areas but also became a financial pillar to sustain armed conflict. In recent decades, the relationship between drugs and conflict has become more complex. The issue has extended beyond opium cultivation to the manufacture and supply of other drugs, such as methamphetamines. Local communities are some of those must vulnerable to the harms related to changing patterns of drug use, including increasing levels of heroin-injecting and methamphetamine use.
DOI: 10.5281/zenodo.5931589
title: Collection of Extracted Data as part of the Publication "(Why) Do Taint Analyzers Fail in Practice? A Critical Literature Review"

description: This document provides an extensive list of the data extraction process for the systematic literature review. This anonymous version is review-friendly for double-blinded peer reviews.
DOI: 10.5281/zenodo.5931590
title: Collection of Extracted Data as part of the Publication "Let's $_GET Serious: A Systematic Literature Review on Taint Analyzers for Web Applications"

description: This document provides an extensive list of the data extraction process for the systematic literature review. This anonymous version is review-friendly for double-blinded peer reviews.