cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25387/g3.14978991
title: Supplemental Material for Clark et al., 2021

description: File S1 is a figure from FastQ Screen analysis. File S2 is a tarball containing the reference-guided assemblies for BA_411 and WI_6. Assembly files with "clean" appended to the name have been filtered for scaffolds without reference coverage. File S3 is a tarball containing Blobtools output. File S4 is a tarball containing BUSCO outputs. <br><b>Supplementary Figure 1: FastQC Screen Analysis Indicates the Expected Composition of Reads Based on Screened Genomes. </b>Read subsets from each <i>D. pulicaria </i>library were mapped against several common and selected sequencing contaminants using bowtie2. Plots indicate that majority of the reads are mapping uniquely to the bait genome PA42 (“<i>Daphnia</i>”), as expected. For other genomes in the search library, the reads did not map uniquely and likely represent low-complexity regions. There is a significant proportion of the read subset that does not map to any represented sequences represented with grey bars. <b></b> <b>Supplementary Figure 2: Sourmash Distance Estimates Indicate Higher Similarity Between <i>D. pulicaria</i> Strains (BA411 & WI6), Relative to the <i>D. pulex</i> (PA42) Reference. </b>Dendrograms on the top and left recapitulate the relationship between samples in the distance analysis that is also visualized by the matrix. The color gradient indicates the sourmash distance estimate, where darker colors indicate high similarity between samples and lighter colors indicate more divergent samples. The <i>D. pulicaria</i> assemblies only vary by 0.1 when compared to each other.<b></b><br>
DOI: 10.5517/ccdc.csd.cc27p7nv
title: CCDC 2075997: Experimental Crystal Structure Determination

description: Related Article: Vinod G. Landge, Aaron J. Grant, Yu Fu, Allison M. Rabon, John L. Payton, Michael C. Young|2021|J.Am.Chem.Soc.|143|10352|doi:10.1021/jacs.1c04261
DOI: 10.5517/ccdc.csd.cc27p7pw
title: CCDC 2075998: Experimental Crystal Structure Determination

description: Related Article: Vinod G. Landge, Aaron J. Grant, Yu Fu, Allison M. Rabon, John L. Payton, Michael C. Young|2021|J.Am.Chem.Soc.|143|10352|doi:10.1021/jacs.1c04261
DOI: 10.5517/ccdc.csd.cc27p7qx
title: CCDC 2075999: Experimental Crystal Structure Determination

description: Related Article: Vinod G. Landge, Aaron J. Grant, Yu Fu, Allison M. Rabon, John L. Payton, Michael C. Young|2021|J.Am.Chem.Soc.|143|10352|doi:10.1021/jacs.1c04261
DOI: 10.5517/ccdc.csd.cc27p7ry
title: CCDC 2076000: Experimental Crystal Structure Determination

description: Related Article: Vinod G. Landge, Aaron J. Grant, Yu Fu, Allison M. Rabon, John L. Payton, Michael C. Young|2021|J.Am.Chem.Soc.|143|10352|doi:10.1021/jacs.1c04261
DOI: 10.5517/ccdc.csd.cc27p7sz
title: CCDC 2076001: Experimental Crystal Structure Determination

description: Related Article: Vinod G. Landge, Aaron J. Grant, Yu Fu, Allison M. Rabon, John L. Payton, Michael C. Young|2021|J.Am.Chem.Soc.|143|10352|doi:10.1021/jacs.1c04261
DOI: 10.5517/ccdc.csd.cc27p7t0
title: CCDC 2076002: Experimental Crystal Structure Determination

description: Related Article: Vinod G. Landge, Aaron J. Grant, Yu Fu, Allison M. Rabon, John L. Payton, Michael C. Young|2021|J.Am.Chem.Soc.|143|10352|doi:10.1021/jacs.1c04261
DOI: 10.6084/m9.figshare.15052872
title: Brand Attachment

description: Brand Attachment is e safe way to obtain customers' continuance commitment and their advocacy intentions.
DOI: 10.5281/zenodo.5137717
title: PESO: Prostate Epithelium Segmentation on H&E-stained prostatectomy whole slide images

description: Large set of whole-slide-images (WSI) of prostatectomy specimens with various grades of prostate cancer (PCa). More information can be found in the corresponding paper: https://doi.org/10.1038/s41598-018-37257-4 The WSIs in this dataset can be viewed using the open-source software ASAP or Open Slide. Due to the large size of the complete dataset, the data has been split up in to multiple archives. The data from the training set: <strong>peso_training_masks.zip: </strong>Training masks (N=62) that have been used to train the main network of our paper. These masks are generated by a trained U-Net on the corresponding IHC slides. <strong>peso_training_masks_corrected.zip: </strong>A subset of the color deconvolution masks (N=25) on which manual annotations have been made. Within these regions, stain and other artifacts have been removed. <strong>peso_training_colordeconvolution.zip: </strong>Mask files (N=62) containing the P63&CK8/18 channel of the color deconvolution operation. These masks mark all regions that are stained by either P63 or CK8/18 in the IHC version of the slides. <strong>peso_training_wsi_{1-6}.zip: </strong>Zip files containing the whole slide images of the training set (N=62). Each archive contains 10 slides, excluding the last which contains 12. These images are exported at a pixel resolution of 0.48mu/pixels. The data from the test set: <strong>peso_testset_regions.zip: </strong>Collection of annotation XML files with outlines of the test regions. These can be used to view the test regions in more detail using ASAP. <strong>peso_testset_png.zip: </strong>Export of the test set regions in PNG format (2500x2500 pixels per region). <strong>peso_testset_png_padded.zip: </strong>Export of the test regions in PNG format padded with a 500 pixel wide border (3500x3500 pixels per region). Useful for segmenting pixels at the border of the regions. <strong>peso_testset_mapping.csv: </strong>A csv file mapping files from the test set (numbered 1-160) to regions in the xml files. The csv file also contains the label (benign or cancer) for each region. <strong>peso_testset_groundtruth_masks.zip: </strong>The ground truth (pixel) masks (N=40) of all regions in the test set. For each pixel in the test set regions, these masks contain the ground truth: 0 for unlabelled, 1 for background and 2 for epithelial tissue. <strong>peso_testset_wsi_{1-4}.zip: </strong>Zip files containing the whole slide images of the test set (N=40). Each archive contains 10 slides of the test set. These images are exported at a pixel resolution of 0.48mu/pixels. This study was financed by a grant from the Dutch Cancer Society (KWF), grant number KUN 2015-7970. <strong>If you make use of this dataset please cite both the dataset itself and the corresponding paper: </strong>https://doi.org/10.1038/s41598-018-37257-4 <strong>Update July 2021: </strong>We have added the ground truth masks for the test set.
description: {"references": ["https://doi.org/10.1038/s41598-018-37257-4"]}
DOI: 10.5281/zenodo.1485966
title: PESO: Prostate Epithelium Segmentation on H&E-stained prostatectomy whole slide images

description: Large set of whole-slide-images (WSI) of prostatectomy specimens with various grades of prostate cancer (PCa). More information can be found in the corresponding paper: https://doi.org/10.1038/s41598-018-37257-4 The WSIs in this dataset can be viewed using the open-source software ASAP or Open Slide. Due to the large size of the complete dataset, the data has been split up in to multiple archives. The data from the training set: <strong>peso_training_masks.zip: </strong>Training masks (N=62) that have been used to train the main network of our paper. These masks are generated by a trained U-Net on the corresponding IHC slides. <strong>peso_training_masks_corrected.zip: </strong>A subset of the color deconvolution masks (N=25) on which manual annotations have been made. Within these regions, stain and other artifacts have been removed. <strong>peso_training_colordeconvolution.zip: </strong>Mask files (N=62) containing the P63&CK8/18 channel of the color deconvolution operation. These masks mark all regions that are stained by either P63 or CK8/18 in the IHC version of the slides. <strong>peso_training_wsi_{1-6}.zip: </strong>Zip files containing the whole slide images of the training set (N=62). Each archive contains 10 slides, excluding the last which contains 12. These images are exported at a pixel resolution of 0.48mu/pixels. The data from the test set: <strong>peso_testset_regions.zip: </strong>Collection of annotation XML files with outlines of the test regions. These can be used to view the test regions in more detail using ASAP. <strong>peso_testset_png.zip: </strong>Export of the test set regions in PNG format (2500x2500 pixels per region). <strong>peso_testset_png_padded.zip: </strong>Export of the test regions in PNG format padded with a 500 pixel wide border (3500x3500 pixels per region). Useful for segmenting pixels at the border of the regions. <strong>peso_testset_mapping.csv: </strong>A csv file mapping files from the test set (numbered 1-160) to regions in the xml files. The csv file also contains the label (benign or cancer) for each region. <strong>peso_testset_groundtruth_masks.zip: </strong>The ground truth (pixel) masks (N=40) of all regions in the test set. For each pixel in the test set regions, these masks contain the ground truth: 0 for unlabelled, 1 for background and 2 for epithelial tissue. <strong>peso_testset_wsi_{1-4}.zip: </strong>Zip files containing the whole slide images of the test set (N=40). Each archive contains 10 slides of the test set. These images are exported at a pixel resolution of 0.48mu/pixels. This study was financed by a grant from the Dutch Cancer Society (KWF), grant number KUN 2015-7970. <strong>If you make use of this dataset please cite both the dataset itself and the corresponding paper: </strong>https://doi.org/10.1038/s41598-018-37257-4 <strong>Update July 2021: </strong>We have added the ground truth masks for the test set.
description: {"references": ["https://doi.org/10.1038/s41598-018-37257-4"]}
DOI: 10.5281/zenodo.5137843
title: BRG1 shRNA knockdown in ALCL cell lines

description: To determine the consequences of Brg1 expression in ALCL, cells were transfected with shRNA to Brg1 leading to a decrease in Brg1 transcript and protein levels. RNA was isolated 72 hours later from the shRNA5 (TRCN0000015551) expressing cells and sequencing conducted to examine changes to the transcriptome mediated by Brg1. Following differential gene expression analysis of the scrambled shRNA versus shRNA5, the transcriptome was identified as being dramatically altered showing both downregulation (2,527 mRNA transcripts: of a cumulative 26,833 genes, adj. <em>p</em> ≤ 0.05) and upregulation (2,900 mRNA transcripts, of a cumulative 26,833 genes, adj. <em>p</em> ≤ 0.05) of genes. When analysing the the 15,285 protein-coding genes alone, 1,934 (13%) were downregulated while 2,797 (18%) were upregulated (adj. <em>p</em> ≤ 0.05). To establish which physiological processes are most affected by the activity of BRG1, pathway enrichment analyses were undertaken. The input comprised of the significant (adj. <em>p</em> ≤ 0.05) protein-coding targets, where the absolute log2 fold change of expression was ± 1.5. Transcripts whose expression was either induced (n=33) or repressed (n=243) by BRG1 were investigated. Reactome analysis suggests that BRG1 plays roles in upregulating genes associated with the cell cycle, while suppressing genes associated with epigenetic regulation.
DOI: 10.5281/zenodo.5137842
title: BRG1 shRNA knockdown in ALCL cell lines

description: To determine the consequences of Brg1 expression in ALCL, cells were transfected with shRNA to Brg1 leading to a decrease in Brg1 transcript and protein levels. RNA was isolated 72 hours later from the shRNA5 (TRCN0000015551) expressing cells and sequencing conducted to examine changes to the transcriptome mediated by Brg1. Following differential gene expression analysis of the scrambled shRNA versus shRNA5, the transcriptome was identified as being dramatically altered showing both downregulation (2,527 mRNA transcripts: of a cumulative 26,833 genes, adj. <em>p</em> ≤ 0.05) and upregulation (2,900 mRNA transcripts, of a cumulative 26,833 genes, adj. <em>p</em> ≤ 0.05) of genes. When analysing the the 15,285 protein-coding genes alone, 1,934 (13%) were downregulated while 2,797 (18%) were upregulated (adj. <em>p</em> ≤ 0.05). To establish which physiological processes are most affected by the activity of BRG1, pathway enrichment analyses were undertaken. The input comprised of the significant (adj. <em>p</em> ≤ 0.05) protein-coding targets, where the absolute log2 fold change of expression was ± 1.5. Transcripts whose expression was either induced (n=33) or repressed (n=243) by BRG1 were investigated. Reactome analysis suggests that BRG1 plays roles in upregulating genes associated with the cell cycle, while suppressing genes associated with epigenetic regulation.
DOI: 10.5281/zenodo.5137709
title: Input files for simulation of potassium channels using the AMOEBA polarizable force field

description: This dataset contains input Tinker xyz and key files for the simulation of KcsA potassium channels in DOPC bilayer, a simple script for converting CHARMM pdb file to Tinker xyz file, and modified Tinker source code to support one-dimensional position restraints.<br> "params.tar.gz" contains a description of the force field modifications.<br> <br> To use "mod2", add the following lines to the key file. <pre><code>#compatible with amoebabio18.prm polarize 5 1.4500 0.3900 3 polarize 11 1.4500 0.3900 9 polarize 3 1.7500 0.3900 1 5 7 50 225 227 polarize 9 1.7500 0.3900 1 7 11 50 225 227</code></pre>
description: {"references": ["Jing et al. Chemical Science, 2021. DOI: 10.1039/d1sc01887f"]}
DOI: 10.5281/zenodo.4898328
title: Input files for simulation of potassium channels using the AMOEBA polarizable force field

description: This dataset contains input Tinker xyz and key files for the simulation of KcsA potassium channels in DOPC bilayer, a simple script for converting CHARMM pdb file to Tinker xyz file, and modified Tinker source code to support one-dimensional position restraints.<br> "params.tar.gz" contains a description of the force field modifications.<br> <br> To use "mod2", add the following lines to the key file. <pre><code>#compatible with amoebabio18.prm polarize 5 1.4500 0.3900 3 polarize 11 1.4500 0.3900 9 polarize 3 1.7500 0.3900 1 5 7 50 225 227 polarize 9 1.7500 0.3900 1 7 11 50 225 227</code></pre>
description: {"references": ["Jing et al. Chemical Science, 2021. DOI: 10.1039/d1sc01887f"]}
DOI: 10.25934/00006740
title: in-silico DMD: Developing computational predictive models for the progression of Duchenne Muscular Dystrophy

description: Vivli is an independent, non-profit organization that has developed a global data-sharing and analytics platform to serve all elements of the international research community. Our mission is to promote, coordinate, and facilitate scientific sharing and reuse of clinical research data through the creation and implementation of a sustainable global data-sharing enterprise. The Vivli platform includes an independent data repository, in-depth search engine and a cloud-based, secure analytics platform.
DOI: 10.5281/zenodo.5121510
title: Source-Agnostic Gravitational-Wave Detection with Recurrent Autoencoders: L1 detector

description: Gravitational Wave signals and random noise datasets, generated with the PyCBC library (https://pycbc.org). Data consists of 8 sec time sequences for a single detector (the L1 detector, mimicking LIGO Livingston), sampled at 2048 Hz and represented as a one-dimensional array with 16,384 entries. Signal samples are provided, corresponding to Binary Black Hole and Binary Neutron Star mergers overlapped to noise.
DOI: 10.5281/zenodo.5121509
title: Source-Agnostic Gravitational-Wave Detection with Recurrent Autoencoders: L1 detector

description: Gravitational Wave signals and random noise datasets, generated with the PyCBC library (https://pycbc.org). Data consists of 8 sec time sequences for a single detector (the L1 detector, mimicking LIGO Livingston), sampled at 2048 Hz and represented as a one-dimensional array with 16,384 entries. Signal samples are provided, corresponding to Binary Black Hole and Binary Neutron Star mergers overlapped to noise.
DOI: 10.6084/m9.figshare.14938755
title: Pre-activated anti-viral innate immunity in the upper airways controls early SARS-CoV-2 infection in children

description: <pre>This dataset comprises single-cell RNA-Seq data of nasopharyngeal samples of of adults and children with COVID-19 (n=24 and n=21, respectively) and SARS-CoV-2-negative controls in each age group (n=23 and 18, respectively).<br>An in-depth description is presented in the manuscript "Pre-activated anti-viral innate immunity in the upper airways controls early SARS-CoV-2 infection in children" (https://www.medrxiv.org/content/10.1101/2021.06.24.21259087v1).</pre>
DOI: 10.6084/m9.figshare.15026803.v1
title: Variable response of arsenic contaminated groundwater microbial community to electron acceptor regime revealed by microcosm based high-throughput sequencing approach

description: Arsenic (As) mobilization in alluvial aquifers is facilitated by microbially catalyzed redox transformations that depend on the availability of electron acceptors (EAs). In this study, the response of an As-contaminated groundwater microbial community from West Bengal, India towards varied EAs was elucidated through microcosm based 16S rRNA gene amplicon sequencing. <i>Acinetobacter, Deinococcus, Nocardioides,</i> etc., and several unclassified bacteria (<i>Ignavibacteria</i>) and archaea (<i>Bathyarchaeia, Micrarchaeia</i>) previously not reported from As-contaminated groundwater of West Bengal, characterized the groundwater community. Distinct shifts in community composition were observed in response to various EAs. Enrichment of operational taxonomic units (OTUs) affiliated to <i>Denitratisoma</i> (NO<sub>3</sub>ˉ)<i>, Spirochaetaceae</i> (Mn<sup>4+</sup>), <i>Deinococcus</i> (As<sup>5+</sup>), <i>Ruminiclostridium</i> (Fe<sup>3+</sup>), <i>Macellibacteroides</i> (SO<sub>4</sub><sup>2</sup>ˉ), <i>Holophagae</i>-<i>Subgroup 7</i> (HCO<sub>3</sub>ˉ), <i>Dechloromonas</i> and <i>Geobacter</i> (EA mixture) was noted. Alternatively, As<sup>3+</sup> amendment as electron donor allowed predominance of <i>Rhizobium</i>. Taxonomy based functional profiling highlighted the role of chemoorganoheterotrophs capable of concurrent reduction of NO<sub>3</sub>ˉ, Fe<sup>3+</sup>, SO<sub>4</sub><sup>2</sup>ˉ, and As biotransformation in As-contaminated groundwater of West Bengal. Our analysis revealed two major aspects of the community, (a) taxa selective toward responding to the EAs, and (b) multifaceted nature of taxa appearing in abundance in response to multiple substrates. Thus, the results emphasized the potential of microbial community members to influence the biogeochemical cycling of As and other dominant anions/cations.
DOI: 10.6084/m9.figshare.15026803
title: Variable response of arsenic contaminated groundwater microbial community to electron acceptor regime revealed by microcosm based high-throughput sequencing approach

description: Arsenic (As) mobilization in alluvial aquifers is facilitated by microbially catalyzed redox transformations that depend on the availability of electron acceptors (EAs). In this study, the response of an As-contaminated groundwater microbial community from West Bengal, India towards varied EAs was elucidated through microcosm based 16S rRNA gene amplicon sequencing. <i>Acinetobacter, Deinococcus, Nocardioides,</i> etc., and several unclassified bacteria (<i>Ignavibacteria</i>) and archaea (<i>Bathyarchaeia, Micrarchaeia</i>) previously not reported from As-contaminated groundwater of West Bengal, characterized the groundwater community. Distinct shifts in community composition were observed in response to various EAs. Enrichment of operational taxonomic units (OTUs) affiliated to <i>Denitratisoma</i> (NO<sub>3</sub>ˉ)<i>, Spirochaetaceae</i> (Mn<sup>4+</sup>), <i>Deinococcus</i> (As<sup>5+</sup>), <i>Ruminiclostridium</i> (Fe<sup>3+</sup>), <i>Macellibacteroides</i> (SO<sub>4</sub><sup>2</sup>ˉ), <i>Holophagae</i>-<i>Subgroup 7</i> (HCO<sub>3</sub>ˉ), <i>Dechloromonas</i> and <i>Geobacter</i> (EA mixture) was noted. Alternatively, As<sup>3+</sup> amendment as electron donor allowed predominance of <i>Rhizobium</i>. Taxonomy based functional profiling highlighted the role of chemoorganoheterotrophs capable of concurrent reduction of NO<sub>3</sub>ˉ, Fe<sup>3+</sup>, SO<sub>4</sub><sup>2</sup>ˉ, and As biotransformation in As-contaminated groundwater of West Bengal. Our analysis revealed two major aspects of the community, (a) taxa selective toward responding to the EAs, and (b) multifaceted nature of taxa appearing in abundance in response to multiple substrates. Thus, the results emphasized the potential of microbial community members to influence the biogeochemical cycling of As and other dominant anions/cations.
DOI: 10.25386/genetics.14569044
title: Supplementary Material for Wolfe et al., 2021

description: Supplementary Material including Appendix, Figures and Tables for Wolfe et al. (in review) - Genomic mating in outbred species: predicting cross usefulness with additive and total genetic covariance matrices
DOI: 10.25386/genetics.14569044.v1
title: Supplementary Material for Wolfe et al., 2021

description: Supplementary Material including Appendix, Figures and Tables for Wolfe et al. (in review) - Genomic mating in outbred species: predicting cross usefulness with additive and total genetic covariance matrices
DOI: 10.5281/zenodo.5137872
title: Ultrafine particles and size distributions from airborne experiments

description: Dataset of ultrafine particles measured during aircraft campaigns with microloght D-MIFU and Dimona VH-OBS and VH-EOS for particle budget studies.
DOI: 10.5281/zenodo.5137871
title: Ultrafine particles and size distributions from airborne experiments

description: Dataset of ultrafine particles measured during aircraft campaigns with microloght D-MIFU and Dimona VH-OBS and VH-EOS for particle budget studies.
DOI: 10.5281/zenodo.5137866
title: Tissue Cytokine Data from Virotherapy Trial and concomitant Explant Model testing

description: Cytokine Data from serial biopsies from a virotherapy trial and Cytokine Data from systematic Explant Model testing with the similar treatment regimen.
DOI: 10.5281/zenodo.5137865
title: Tissue Cytokine Data from Virotherapy Trial and concomitant Explant Model testing

description: Cytokine Data from serial biopsies from a virotherapy trial and Cytokine Data from systematic Explant Model testing with the similar treatment regimen.
DOI: 10.5281/zenodo.5092291
title: A Pragmatic Trial of Interactive Online Statistical Webtools for Teaching Biostatistics to First Year Medical Students: A Constructivism-Informed Approach

description: Underlying quantitative and anonymised qualitative data for the study, "A Pragmatic Trial of Interactive Online Statistical Tools for Teaching Biostatistics to First Year Medical Students: A Constructivism-Informed Approach"
DOI: 10.5281/zenodo.5092290
title: A Pragmatic Trial of Interactive Online Statistical Webtools for Teaching Biostatistics to First Year Medical Students: A Constructivism-Informed Approach

description: Underlying quantitative and anonymised qualitative data for the study, "A Pragmatic Trial of Interactive Online Statistical Tools for Teaching Biostatistics to First Year Medical Students: A Constructivism-Informed Approach"