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3,172 results for “Publications”
Tumor Compendium v11 Public PolyA (April 2020)
This compendium was released in April 2020. It includes a total of 12,747 samples from Treehouse clinical sites (identifiers start with "TH"), publicly available repositories, TCGA and TARGET projects. These data were generated by library preparation methods including polyA selection. The dataset in the CCDC includes only those patients under the age of 40 years old.
Tumor Compendium v9 Public Ribodeplete (March 2019)
This compendium was released in March 2019. It includes samples from Treehouse clinical sites (identifiers start with "TH"), publicly available repositories, and TARGET projects. These data were generated by library preparation methods including ribodepletion.
Tumor cohorts for Vaske et al. publication (October 2019)
"Comparative Tumor RNA Sequencing Analysis for Difficult-to-Treat Pediatric and Young Adult Patients With Cancer", published in JAMA Network Open October 25, 2019, presents a framework for comparative RNA-Seq analysis of pediatric tumors across multiple precision medicine studies. Links to the resources used in the publication, including a Background Cohort of 11,340 samples and a Participants Cohort of 144 samples, both with rich clinical fields, are available on the Resources for Vaske et al. (2019) data hub.
Public Dataset for Leif
<p>The public dataset for Leif's evaluation experiment, including raw experiment data and analytical results.</p>
Coded interviews - dataset - project: From dialog to deliberation. Non-public actors as (non)present participants in local decision-making
<p>Coded interviews - dataset. The interviews were conducted as part of the project <em>From dialog to deliberation. Non-public actors as (non)present participants in local decision-making, </em>financed within the framework of the Programme DIALOG by the Ministry of Science and Higher Education of the Republic of Poland, in the years 2018-2020 (project no. DIALOG 0163/2017). </p>
unarXive: A Large Scholarly Data Set with Publications' Full-Text, Annotated In-Text Citations, and Links to Metadata
<h2><strong>Description</strong></h2> <p><strong>unarXive</strong> is a scholarly data set containing <strong>publications' full-text</strong>, annotated <strong>in-text citations</strong>, and a <strong>citation network</strong>.</p> <p>The data is <strong>generated from all LaTeX sources on </strong><a href="https://arxiv.org/"><strong>arXiv</strong></a> and therefore of higher quality than data generated from PDF files.</p> <p>Typical <strong>use cases</strong> are</p> <ul> <li>Citation recommendation</li> <li>Citation context analysis</li> <li>Bibliographic analyses</li> <li>Reference string parsing</li> </ul> <p>This version (v3) of our data set is based on all arXiv publications until 2020-07-31 and on the Microsoft Academic Graph as of 2020-08-18. As additional contribution, we included a table with the publication date and the scientific discipline for each paper for easier filtering.</p> <p><strong>Note:</strong> This Zenodo record is an old version of unarXive. You can find the <strong>most recent version</strong> at <a href="../record/7752754">https://zenodo.org/record/7752754</a> and <a href="../record/7752615">https://zenodo.org/record/7752615</a></p> <h2><strong>Access</strong></h2> <p>┏━━━━━━━━━━━━━━━━━━━━━━━━━━┓<br>┃ <a href="https://github.com/IllDepence/unarXive/blob/legacy_2020/doc/unarXive_sample.tar.bz2"><strong>D O W N L O A D S A M P L E</strong></a>  ┃<br>┗━━━━━━━━━━━━━━━━━━━━━━━━━━┛</p> <p>To download the whole data set send an access request and note the following:</p> <blockquote> <p><strong>Note</strong>: this Zenodo record is a "full" version of unarXive, which was generated from all of arXiv.org <em>including non-permissively licensed papers</em>. Make sure that your use of the data is compliant with the paper's licensing terms.¹</p> <p>¹ For information on papers' licenses use <a href="https://info.arxiv.org/help/bulk_data/index.html">arXiv's bulk metadata access</a>.</p> </blockquote> <p>The <strong>code</strong> used for generating the data set is <a href="https://github.com/IllDepence/unarXive/tree/legacy_2020/">publicly available</a>.</p> <p><strong>Usage examples</strong> for our data set are provided at <a href="https://github.com/IllDepence/unarXive/tree/legacy_2020/#usage-examples">here on GitHub</a>.</p> <h2><strong>Citing</strong></h2> <p>This initial version of unarXive is described in the following journal article.</p> <p><em>Tarek Saier, Michael Färber: "</em><a href="http://dx.doi.org/10.1007/s11192-020-03382-z"><em>unarXive: A Large Scholarly Data Set with Publications' Full-Text, Annotated In-Text Citations, and Links to Metadata</em></a><em>", Scientometrics, 2020,</em><br>[<a href="https://www.aifb.kit.edu/images/f/f9/UnarXive_Scientometrics2020.pdf">link to an author copy]</a></p> <p>The <strong>updated version</strong> is described in the following conference paper.</p> <p><em>Tarek Saier, Michael Färber. "</em><a href="10.1109/JCDL57899.2023.00020"><em>unarXive 2022: All arXiv Publications Pre-Processed for NLP, Including Structured Full-Text and Citation Network</em></a><em>", JCDL 2023.</em><br>[<a href="https://doi.org/10.48550/arXiv.2303.14957">link to an author copy</a>]</p>
Data for publication "Transcriptional and functional profiling of Endothelial Colony Forming Cells identifies inflammation and endothelial to mesenchymal transition as drivers for phenotypic heterogeneity"
<p>Here, the data is stored for the article "Transcriptional and functional profiling of Endothelial Colony Forming Cells identifies inflammation and endothelial to mesenchymal transition as drivers for phenotypic heterogeneity" which is currently submitted but not accepted.</p><p>it was not possible to include all data in this repository. the confocal tilescan images used for WPB and Cell morphology quantification and images used for the migration assay were too many and too large in size to include. However, this data is available upon request.</p>
data for the publication PSO paper
<p>This file had a problem with the structure, making it difficult to import the data.</p> <p>The same data may be found: https://zenodo.org/records/10796260</p> <p>All the details of the signal processing and data for recreating the results may be found in the paper</p>
haplotype results for publication
Open the record for dataset details and reuse information.
Dataset related to the publication "Prognostic role of transferrin saturation in heart failure patients"
<p><strong>Aims: </strong>In heart failure (HF) iron deficiency (ID) is frequently observed and represents a major mortality risk factor. Purpose of this study was to evaluate the correlation between mortality and ID in a cohort of 661 consecutive patients hospitalized for HF worsening.</p> <p><strong>Methods and results: </strong>Patients were grouped: (i)according to presence(+)/absence(-) of anaemia (A) and ID defined following World Health Organization (WHO) and European Society of Cardiology (ESC)-American College of Cardiology/American Heart Association/HF society of America (ACC/AHA/HFSA) definitions, respectively: Group A-ID- (n = 123), Group A+ID- (n = 80), Group A+ID+ (n = 247), and Group A-ID+ (n = 211); (ii) according to presence of absolute (serum ferritin < 100μg/L) and functional ID [ferritin between 100 and 300μg/L and transferrin saturation (TSAT) < 20%]; and (iii) according to TSAT <20% and ≥20%. Groups were not different for several clinical features but age, gender, kidney function, and chronic obstructive pulmonary disease. Average follow-up was 1.94 year (±420 days). Overall 5 years mortality rate was 29.5%. Only anaemia and functional ID but not ID as defined by guidelines showed an impact on prognosis. Transferrin saturation <20% (n = 360) patients showed worst prognosis compared to TSAT ≥20% (n = 301) patients. In addition, functional ID patients showed worse prognosis compared patients with ferritin <100μg/L and TSAT <20% or ≥20% likely due to more severe chronic inflammatory status [C-reactive protein, 7.4 (interquartile range 2.7-22.6) and 3.2 (1.4-8.7) mg/L, P < 0.0001 respectively].</p> <p><strong>Conclusion: </strong>We confirmed that in HF anaemia is associated to a poor prognosis. Moreover, we showed that patients with TSAT <20% had worse prognosis compared to those with TSAT ≥20% but the composite of ferritin between 100 and 300 μg/L and TSAT <20% identifies HF patients with the poorest survival rate.</p>
Locating and Costing Congestion for School Buses and Public Transportation
<p>Two geospatial polyline datasets, one for Durham County, NC and the other for Pinellas County, FL. The attributes show the minutes of delay per vehicle and the cumulative minutes of delay for school buses, public transit buses and total buses. These data can be displayed in a GIS software for further visualization and analysis. An online web-mapping application has been created to display this information for each location by hour of the day and can be accessed here: <a href="http://transitportal.org/cost_of_congestion.html">Cost of congestion (transitportal.org</a></p>
L'évaluation scientifique par les pairs : défaillances et régulations post publication
<p>Extrait du colloque SMS régulations et incertitudes qui s'est déroulé les 17 et 18 mai 2022 à la maison de la recherche de l'université Toulouse Jean-Jaurès.</p> <p>Présentation de Guillaume Cabanac : <em>"L'évaluation scientifique par les pairs : défaillances et régulations post publication"</em></p>
Women's Rights in Public Discourse in China Social Media
Open the record for dataset details and reuse information.
Data for publication: Weighted manifold alignment using wave kernel signatures for aligning medical image datasets
<p>2D dynamic sagittal MR images, corresponding to volunteers E-H in the publication "Weighted manifold alignment using wave kernel signatures for aligning medical image datasets".</p>
Data used for Web of Science World Conservation Publication Index 1993 - 2016 | Biodiversity Publication Bias Compromises Setting Conservation Priorities
<p>Data used for Web of Science World Conservation Publication Index 1993 - 2016, see https://github.com/raffael-hickisch/rwosconsindex</p>
Timeline for cases associated with Letter to the Editors sent for publication in different biomedical journals
<p>These cases are concerned with the handling of the manuscript by journal editors and the experience gained by the eauthors.</p>
Research Incentive Programs for Closures of Public and Private Grade Crossings
<p>Corresponding data set for Tran-SET Project No. 17PPLSU13. Abstract of the final report is stated below for reference:</p> <p>"Vehicle-train crashes that occur at highway-rail crossings result in injuries, fatalities, and damage to equipment. In order to reduce the number of vehicle-train crashes, Federal Railroad Administration requires states which have challenges with crossing safety, including Louisiana, to develop a State Action Plan to improve grade crossing safety. Consequently, identification of specific solutions for improving safety at crossings was included in the 2015 Louisiana Transportation Plan as one of its objectives. This study seeks to identify and evaluate current and new incentive programs that encourage closure of at-grade railroad crossings to reduce the number of potential vehicle-train collision points, and hence improve safety. To accomplish this, a survey was designed and was distributed to personnel of state and railroad agencies. Survey responses from the DOTs revealed that currently, 16 states had no incentive programs for consolidation or closure of highway-rail crossings. Analysis of the survey data revealed that states without any incentive program had the least proportion of highway-rail crossing closures. The study revealed that cash incentives, while popular are not effective because although the Federal Government contributes to a state’s effort in offering cash incentives for closure of public grade crossings, the amount is not substantial enough to be considered a significant incentive by most local governments. Also, track relocation, while effective is mostly impractical due to the high costs involved. A literature review revealed that having a mathematical model to guide on the selection of crossings for consolidation or closure provides sound scientific basis and are usually welcomed by the community. The research team identified three potential new incentives that could work well for Louisiana namely crime rate reduction incentives, greenness improvement programs, and the development of a grade crossing consolidation model that considers safety, among a plethora of other factors, to be used to prioritize crossings to be closed. However, additional work is required to validate these programs for statewide deployment."</p>
genetic_linkage results for publication
<p>See https://github.com/gael-millot/genetic_linkage</p>
fisher_for_vcf results for publication
<p>See <a href="https://github.com/gael-millot/fisher_for_vcf">https://github.com/gael-millot/fisher_fi</a></p>
Dataset (II) related to publication: A cancer-associated K-RAS mutant protein that preferentially binds GDP displays gain-of-function and atypical signaling
<p>Dataset (II) related to publication:</p> <blockquote> <p>A cancer-associated K-RAS mutant protein that preferentially binds GDP displays gain-of-function and atypical signaling</p> </blockquote> <p>Includes raw trajectories of MD-simulations: K-RAS(M67L)+GDP replicas 11–20 (each replica 10 micros.)</p> <ul> <li>Individual .zip files contain raw-desmond trajectories (-out.cms files and trj-files)</li> </ul> <p>Other datasets related to this publication: 10.5281/zenodo.5506845 and 10.5281/zenodo.5507131</p>
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.