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15,733 results for “article”
Dataset and code for article "Expanded detection and impact of BAP1 alterations in cancer"
<p>Dataset and code for article titled "Expanded detection and impact of <em>BAP1 </em>alterations in cancer". Includes Singularity image and Nextflow code for somatic variant calling pipeline. Also includes figure code (qmd, html, and pdf formats), analysis code (qmd), and public raw and processed data of reasonable file size. Controlled-access data and large file size data (e.g., combined dataset of pan-cancer individual RNA-seq files) must be downloaded separately from the TCGA Genomic Data Commons or PanCanAtlas Publication pages. R code written in R version 4.4.1 and provided with R environment (renv) information.</p>
Manually annotated RNA-focused scientific articles -- Experimental dataset
<p>In this repository, we store 100 <a href="../records/11393776/files/annotations.json?download=1">paragraphs sourced from RNA-focused scientific articles that have been manually annotated</a> (both for entities and relations) according to a <a href="../records/11393776/files/RNA-KG.yaml?download=1">LinkML template</a> that represent associations among genes, proteins, RNAs, chemicals, variants (SNPs), GO terms, and diseases. The template reflects a <a href="../records/11393776/files/meta-graph.pdf?download=1">subportion of RNA-KG's meta-graph</a>. <a href="https://doi.org/10.48550/arXiv.2312.00183">RNA-KG</a> data are available at: <a href="../records/10078876">https://zenodo.org/records/10078876</a>.</p>
The role of non-native plant species in modulating riverbank erosion: a systematic review - extracted coded articles dataset
<p>Data extraction sheet of code typologies for the review titled: The role of non-native plant species in modulating riverbank erosion: a systematic review. The uploaded csv file contains all the extracted values for each typology. </p>
Data and code of "Germline mutation rate predicts cancer mortality across 37 vertebrate species" article
<p>Data and code used in this article.</p> <p>The "Data.csv" file contains information about each species class, common name, average yearly mutation rate, trophic level, number of animals per species that died from cancer, records of mortality per species, the minimum confidence interval (CI) for the cancer mortality values, the maximum CI for the cancer mortality values, the standard error (SE) of the records of mortality per species, cancer mortality, average parental age (measured in months), maximum lifespan (measured in months), average parental age (measured in months), and whether a species is reported as domesticated/semidomesticated or not. The way the authors obtained these data, and the original sources of these data, are described in the methodology section of the article.</p> <p>The "Regression_analyses.R" file is the code we used in the regression analyses conducted in this article. The .phy file is the phylogenetic tree used in the regression analyses.</p> <p>The .txt, .nwk, .Rproj, and "germFit.R" files are the data and code we used for comparing the different models of phenotype evolution (comparison of 3 different models: Ornstein–Uhlenbeck, Brownian, and Early Burst).</p>
Raw Data to the article Mlynsky et al., J. Chem. Theory Comput. 2023
<p>Raw data to the article "Mlynsky, V., Kuhrova, P., Stadlbauer, P., Krepl, M., Otyepka, M., Banas, P., & Sponer, J. (2023). Simple adjustment of intranucleotide base-phosphate interaction in the ol3 amber force field improves RNA simulations. <em>Journal of Chemical Theory and Computation</em>, <em>19</em>(22), 8423-8433". See readme.txt file for additional info. The upload now contains the original JCTC article and its Supporting Information.</p>
Methodology data of "A qualitative and quantitative citation analysis toward retracted articles: a case of study"
<p>This document contains the datasets and visualizations generated after the application of the methodology defined in our work: <em>"A qualitative and quantitative citation analysis toward retracted articles: a case of study"</em>. The methodology defines a citation analysis of the Wakefield et al. [1] retracted article from a quantitative and qualitative point of view. The data contained in this repository are based on the first two steps of the methodology. The first step of the methodology (i.e. “Data gathering”) builds an annotated dataset of the citing entities, this step is largely discussed also in [2]. The second step (i.e. "Topic Modelling") runs a topic modeling analysis on the textual features contained in the dataset generated by the first step. </p> <p><strong>Note:</strong> the data are all contained inside the "<strong><em>method_data.zip"</em> </strong>file. You need to unzip the file to get access to all the files and directories listed below.</p> <p> </p> <p><strong>Data gathering</strong></p> <p>The data generated by this step are stored in <strong>"<em>data/</em>"</strong>:</p> <ol> <li><em><strong>"cits_features.csv": </strong></em>a dataset containing all the entities (rows in the CSV) which have cited the Wakefield et al. retracted article, and a set of features characterizing each citing entity (columns in the CSV). The features included are: DOI ("doi"), year of publication ("year"), the title ("title"), the venue identifier ("source_id"), the title of the venue ("source_title"), yes/no value in case the entity is retracted as well ("retracted"), the subject area ("area"), the subject category ("category"), the sections of the in-text citations ("intext_citation.section"), the value of the reference pointer ("intext_citation.pointer"), the in-text citation function ("intext_citation.intent"), the in-text citation perceived sentiment ("intext_citation.sentiment"), and a yes/no value to denote whether the in-text citation context mentions the retraction of the cited entity ("intext_citation.section.ret_mention").<br> <strong>Note: </strong>this dataset is licensed under a <a href="https://creativecommons.org/publicdomain/zero/1.0/legalcode">Creative Commons public domain dedication (CC0)</a>.<br> </li> <li><em><strong>"cits_text.csv": </strong>this dataset stores the abstract ("abstract") and the in-text citations context ("intext_citation.context") </em>for each citing entity identified using the DOI value ("doi").<br> <strong>Note: </strong>the data keep their original license (the one provided by their publisher). This dataset is provided in order to favor the reproducibility of the results obtained in our work.</li> </ol> <p> </p> <p><strong>Topic modeling</strong><br> We run a topic modeling analysis on the textual features gathered (i.e. abstracts and citation contexts). The results are stored inside the <em><strong>"topic_modeling/"</strong></em> directory. The topic modeling has been done using MITAO, a tool for mashing up automatic text analysis tools, and creating a completely customizable visual workflow [3]. The topic modeling results for each textual feature are separated into two different folders, <em><strong>"abstracts/"</strong></em> for the abstracts, and <em><strong>"intext_cit/"</strong></em> for the in-text citation contexts. Both the directories contain the following directories/files: <strong> </strong></p> <ol> <li> <p><em><strong>"mitao_workflows/"</strong></em>: the workflows of MITAO. These are JSON files that could be reloaded in MITAO to reproduce the results following the same workflows.</p> </li> <li> <p><em><strong>"corpus_and_dictionary/": </strong></em>it contains the dictionary and the vectorized corpus given as inputs for the LDA topic modeling.</p> </li> <li> <p><em><strong>"coherence/coherence.csv":</strong></em> the coherence score of several topic models trained on a number of topics from 1 - 40.</p> </li> <li> <p><em><strong>"datasets_and_views/": </strong></em>the datasets and visualizations generated using MITAO. </p> </li> </ol> <p> </p> <p><strong>References</strong></p> <ol> <li>Wakefield, A., Murch, S., Anthony, A., Linnell, J., Casson, D., Malik, M., Berelowitz, M., Dhillon, A., Thomson, M., Harvey, P., Valentine, A., Davies, S., & Walker-Smith, J. (1998). RETRACTED: Ileal-lymphoid-nodular hyperplasia, non-specific colitis, and pervasive developmental disorder in children. <em>The Lancet</em>, <em>351</em>(9103), 637–641. <a href="https://doi.org/10.1016/S0140-6736(97)11096-0">https://doi.org/10.1016/S0140-6736(97)11096-0</a></li> <li> <p>Heibi, I., & Peroni, S. (2020). A methodology for gathering and annotating the raw-data/characteristics of the documents citing a retracted article v1 (protocols.io.bdc4i2yw) [Data set]. In protocols.io. ZappyLab, Inc. <a href="https://doi.org/10.17504/protocols.io.bdc4i2yw">https://doi.org/10.17504/protocols.io.bdc4i2yw</a></p> </li> <li> <p> </p> Ferri, P., Heibi, I., Pareschi, L., & Peroni, S. (2020). MITAO: A User Friendly and Modular Software for Topic Modelling [JD]. PuntOorg International Journal, 5(2), 135–149. <a href="https://doi.org/10.19245/25.05.pij.5.2.3">https://doi.org/10.19245/25.05.pij.5.2.3</a> <p> </p> </li> </ol>
Effect size data for the meta-analysis article ""Effects of vegetation management intensity on biodiversity and ecosystem services in vineyards: a meta-analysis"
<p>This Exel file includes the effect size dataset used for the statistical analysis for the paper "Effect of vegetation management intensity on biodiversity and ecosystem services in vineyards: a meta-analysis", which will be published in the Journal of Applied Ecology in 2018.</p> <p>This meta-analysis was conducted in the course of the project VineDivers (<a href="http://www.vinedivers.eu/">www.vinedivers.eu</a>) funded through the 2013-2014 BiodivERsA/FACCE-JPI joint call for research proposals, with the national funders: Austrian Science Fund (FWF), Spanish Ministry for Economy and Competitiveness (MINECO), French National Research Agency (ANR), Romanian Executive Agency for Higher Education, Research, Development and Innovation Funding (UEFISCDI) and Federal Ministry of Education and Research (BMBF/Germany). P. Batáry was supported by the German Research Foundation (DFG BA4438/2-1) and by the Economic Development and Innovation Operational Programme of Hungary (GINOP–2.3.2–15–2016–00019).</p> <p> </p>
Raw coordinates of 3D landmarks related to the article 'A new zooarchaeological application for geometric morphometric methods: Distinguishing Ovis aries morphotypes to address connectivity and mobility of prehistoric Central Asian pastoralists' by Haruda et al.
<p>Raw coordinates from 3D landmarks of <em>Ovis aries </em>astragali. These bones originate from Final Bronze Age archaeological contexts from central and southeastern Kazakhstan. These relate to the article 'A new zooarchaeological application for geometric morphometric methods: Distinguishing <em>Ovis aries</em> morphotypes to address connectivity and mobility of prehistoric Central Asian pastoralists' by Haruda et al. </p>
Data and code for article "Excitonic Emission of Monolayer Semiconductors Near-Field Coupled to High-Q Microresonators"
<p>Data, code and sample fabrication details for article "Excitonic Emission of Monolayer Semiconductors Near-Field Coupled to High-Q Microresonators".</p> <p>The code was tested with Matlab R2015b.</p>
International Relations Articles Clustering Case - Data File
<p>Data file in CSV format of "Perceptions Journal" articles (2010-2012)</p>
Data supplementing the article "Boosting DNA metabarcoding for biomonitoring with phylogenetic estimation of OTUs' ecological profiles" F. Keck, V. Vasselon, F. Rimet, A. Bouchez, and M. Kahlert submitted to Molecular Ecology Resources journal
<p>These data supplement the article "Enhancing DNA metabarcoding for biomonitoring with phylogenetic estimation of OTUs' ecological profiles" F. Keck, V. Vasselon, F. Rimet, A. Bouchez, and M. Kahlert submitted to Molecular Ecology Resources journal</p> <p>The directory contains the following files:</p> <p><strong>278 (139 x 2 replicates) samples fastq files.rar </strong>- contains the 278 fastq files provided by the sequencing platform with demultiplexed and contig DNA reads corresponding to the 139 samples with 2 sequencing replicates (A and B).</p> <p><strong>Counts_diatoms.xlsx </strong>- contains the morphological inventories with species list (Omnidia code) and valve abundances for the 139 samples.</p> <p><strong>Sites_list.xlsx </strong>- contains information regarding the 139 samples, including: River name, GPS coordinates, code used for molecular analysis and corresponding to sequencing fastq names.</p>
Aligned DNA sequence matrix for phylogenetic analyses of Scinax in the article "Advertisement calls and DNA sequences reveal a new species of Scinax (Anura: Hylidae) on the Pacific Lowlands of Ecuador"
<p>Aligned DNA sequence matrix for phylogenetic analyses of Scinax in the article "Advertisement calls and DNA sequences reveal a new species of Scinax (Anura: Hylidae) on the Pacific Lowlands of Ecuador". The matrix is in NEXUS format.</p> <p>Gene partition as arranged as follows (tRNAs are included as part of larger adjacent genes):</p> <p>12S RNA: 1-1033</p> <p>16S RNA: 1034-2832</p> <p>NADH dehydrogenase subunit 1: 2833-3793</p> <p>Cytochrome Oxidase sub-unit I: 3965-4654</p> <p>Cytochrome B: 4655-5447</p> <p> </p>
Data for the article "The Apparent Absence of Kilometer-sized Pyroclastic Volcanoes on Mercury: Are We Looking Right? "
<p>This file contains numerical data which has been used for generation of Figure 1, 2 and 3 in the paper "The Apparent Absence of Kilometer-sized Pyroclastic Volcanoes on Mercury: Are We Looking Right?"</p> <p>The profiles in files associated with Figure 3 are provided for the volume of 4.2 km<sup>3</sup>.</p>
Aligned DNA sequence matrix for phylogenetic analyses of the article "A bizarre new species of Lynchius (Amphibia, Anura, Strabomantidae) from the Andes of Ecuador and first report of Lynchius parkeri in Ecuador"
<p>Aligned DNA sequence matrix for phylogenetic analyses of the article "A bizarre new species of <em>Lynchius</em> (Amphibia, Anura, Strabomantidae) from the Andes of Ecuador and first report of <em>Lynchius parkeri</em> in Ecuador"</p> <p>The matrix is in NEXUS format. Genes are arranged as follows:</p> <p>RAG1: 1-652<br> Tyrosinase: 653-1195<br> 12S RNA: 1196-2242<br> tRNA Val: 2243-2313<br> 16S RNA: 2314-3994<br> tRNA Leu = 3995-4065<br> ND1: 4066-5026<br> tRNA Ile: 5027-5144;</p>
Aligned DNA sequence matrix for phylogenetic analyses in the article "Systematics of Huicundomantis, a new subgenus of Pristimantis (Anura, Strabomantidae) with extraordinary cryptic diversity and eleven new species"
<p>Aligned DNA sequence matrix for phylogenetic analyses of the article "Systematics of Huicundomantis, a new subgenus of Pristimantis (Anura, Strabomantidae) with extraordinary cryptic diversity and eleven new species"</p> <p>The matrix is in NEXUS format. Genes are arranged as follows:</p> <p>16S RNA, tRNA-Leu = 1–1408<br> ND1 codon position 1 = 1409–2369\3;<br> ND1 codon position 2 = 1410–2367\3;<br> ND1 codon position 3 = 1411–2368\3;<br> tRNA-Ile, tRNA-Gln, rRNA-Met = 2370–2544; <br> RAG1 codon position 3 = 2545–3199\3;<br> RAG1 codon position 1 = 2546–3197\3<br> RAG1 codon position 2 = 2547–3198\3;</p>
Bayesian consensus phylogram from the article "Systematics of Huicundomantis, a new subgenus of Pristimantis (Anura, Strabomantidae) with extraordinary cryptic diversity and eleven new species"
<p>Bayesian consensus phylogram depicting relationships within <em>Pristimantis</em> (<em>Huicundomantis</em>). Museum catalog numbers are shown before the species name. Posterior probabilities resulting from Bayesian Markov chain Monte Carlo searches appear next to the branches.</p>
Dataset for the article "MiMiC: A Novel Framework for Multiscale Modeling in Computational Chemistry"
<p>This dataset contains additional material related to the article: "MiMiC: A Novel Framework for Multiscale Modeling in Computational Chemistry". The preprint is available at <a href="https://doi.org/10.26434/chemrxiv.7635986">https://doi.org/10.26434/chemrxiv.7635986</a>. Final article is available at <a href="https://doi.org/10.1021/acs.jctc.9b00093">https://doi.org/10.1021/acs.jctc.9b00093</a>.</p>
Experimental data of an article on the impact of coarse-grain protrusion on near-bed hydrodynamics
<p>This deposit contains experimental data related to the article entitled " impact of coarse-grain protrusion on near-bed hydrodynamics" that will be publised in Journal of Geophysical Research - Earth surface. It consists in post-processed data (turbulence statistics) for flows around hemispheres protruding from a bed of fine sediments. Calculated statistics (time-averaged and double-averaged) are provided along other inferred quantities (friction velocity, etc...) and experimental parameters (protrusion level, discharge, etc..) in matlab metadata format. Matlab functions are given to plot all the figures of the article.</p>
Analysis files for MSC Marc finite element software, Article: The analysis of shrink-fit connection – the methods of heating and the factors influencing the distribution of residual stresses
<p>This archive contains model files for Finite Element Analysis of the shrink-fit connection in crankshaft and the files for charts in GNUPlot.</p>
Data supplementing the article "Benthic diatom communities in an Alpine river impacted by waste water treatment effluents as revealed using DNA metabarcoding" , submitted to Frontiers in Microbiology
<p>These data supplement the article"Benthic diatom communities in an Alpine river impacted by waste water treatment effluents as revealed using DNA metabarcoding" submitted to Frontiers in Microbiology: </p> <p>The directory contains the following files:</p> <p><strong>64 PGM sequencing files (raw data, fastq files) </strong>- one file is provided for each sample by the sequencing platform with demultiplexed DNA reads (raw data prior any bioinformatics treatments).</p> <p><strong>Sample_Names.xlsx</strong> - contains the information relative to the 64 samples including: the ID used in Mothur analyses (corresponding to the name of the fastq files), the sample name and the raw reads number for each sample.</p>
ScienceDex guides
Understand access before you commit
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.