cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.13077920
title: Sayaman et al., TCGA Germline-Immune GWAS Summary Statistics

description: TCGA Germline Immune Response GWAS Summary Statistics (plink) for the 33 Heritable Immune Traits<br>Please cite Sayaman, Saad et al., Immunity 2021 when using the TCGA germline immune GWAS summary statistics.<br>FULL CITATIONSayaman, Saad, et al., Germline genetic contribution to the immune landscape of cancer, Immunity (2021), https://doi.org/10.1016/j.immuni.2021.01.011<br><br>LEAD CONTACT Rosalyn W. Sayaman, rwsayaman@gmail.com<br>CORRESPONDING AUTHORSRosalyn W. Sayaman, rwsayaman@gmail.comElad Ziv, elad.ziv@ucsf.eduDavide Bedognetti, dbedognetti@sidra.org<br><br>RESOURCESThe code generated during this study has been deposited to github: https://github.com/rwsayaman/TCGA_PanCancer_Immune_Genetics<br>Interactive visualization is available at CRI iAtlas: https://www.cri-iatlas.org/<br>
DOI: 10.6084/m9.figshare.13819376
title: ants_statistics.csv

description: Measurements of ommatidia count and diameter were taken on microscope images of eye molds or replicas of five ant species taken previously: Notoncus ectatommoides and Camponotus aeneopilosus (from Palavalli-Nettimi and Narendra (2018)), Myrmecia nigrocincta, M. tarsata, and Rhytidoponera inornata (from Palavalli-Nettimi et al. (2019)).<br><br>References:<br><br>Palavalli-Nettimi, Ravindra, and Ajay Narendra. 2018. “Miniaturisation Decreases Visual Navigational Competence in Ants.” Journal of Experimental Biology 221(7):jeb177238.<br><br>Palavalli-Nettimi, Ravindra, Yuri Ogawa, Laura A. Ryan, Nathan S. Hart, and Ajay Narendra. 2019. “Miniaturisation Reduces Contrast Sensitivity and Spatial Resolving Power in Ants.” Journal of Experimental Biology 222(12). doi: 10.1242/jeb.203018.
DOI: 10.6084/m9.figshare.13102451
title: MAGs

description: Metagenome-assembled genomes (MAGs) were recovered from the co-assembly (contig &gt; 500 bp) using MaxBin2 (v2.2.1.). While this generated a total of 278 MAGs, only those meeting the quality threshold (completeness &gt;50% and contamination &lt;20%) were included in the downstream analysis. This encompassed 149 MAGs, here provided at NA (contigs) and AA (functional annotated proteins) level. In addition, the full list of functional annotations from Interproscan5 and the quality measurement table from CheckM (v.1.0.13) is provided. Note that e.g. "coM.001" in the contig header corresponds to MAG ID "MAG001". <br>
DOI: 10.6084/m9.figshare.13102451.v1
title: MAGs

description: Metagenome-assembled genomes (MAGs) were recovered from the co-assembly (contig &gt; 500 bp) using MaxBin2 (v2.2.1.). While this generated a total of 278 MAGs, only those meeting the quality threshold (completeness &gt;50% and contamination &lt;20%) were included in the downstream analysis. This encompassed 149 MAGs, here provided at NA (contigs) and AA (functional annotated proteins) level. In addition, the full list of functional annotations from Interproscan5 and the quality measurement table from CheckM (v.1.0.13) is provided. Note that e.g. "coM.001" in the contig header corresponds to MAG ID "MAG001". <br>
DOI: 10.6084/m9.figshare.13819376.v2
title: ants_statistics.csv

description: Measurements of ommatidia count and diameter were taken on microscope images of eye molds or replicas of five ant species taken previously: Notoncus ectatommoides and Camponotus aeneopilosus (from Palavalli-Nettimi and Narendra (2018)), Myrmecia nigrocincta, M. tarsata, and Rhytidoponera inornata (from Palavalli-Nettimi et al. (2019)).<br><br>References:<br><br>Palavalli-Nettimi, Ravindra, and Ajay Narendra. 2018. “Miniaturisation Decreases Visual Navigational Competence in Ants.” Journal of Experimental Biology 221(7):jeb177238.<br><br>Palavalli-Nettimi, Ravindra, Yuri Ogawa, Laura A. Ryan, Nathan S. Hart, and Ajay Narendra. 2019. “Miniaturisation Reduces Contrast Sensitivity and Spatial Resolving Power in Ants.” Journal of Experimental Biology 222(12). doi: 10.1242/jeb.203018.
DOI: 10.6084/m9.figshare.13819376.v1
title: ants_statistics.csv

description: Measurements of ommatidia count and diameter were taken on microscope images of eye molds or replicas of five ant species taken previously: Notoncus ectatommoides and Camponotus aeneopilosus (from Palavalli-Nettimi and Narendra (2018)), Myrmecia nigrocincta, M. tarsata, and Rhytidoponera inornata (from Palavalli-Nettimi et al. (2019)).<br><br>References:<br><br>Palavalli-Nettimi, Ravindra, and Ajay Narendra. 2018. “Miniaturisation Decreases Visual Navigational Competence in Ants.” Journal of Experimental Biology 221(7):jeb177238.<br><br>Palavalli-Nettimi, Ravindra, Yuri Ogawa, Laura A. Ryan, Nathan S. Hart, and Ajay Narendra. 2019. “Miniaturisation Reduces Contrast Sensitivity and Spatial Resolving Power in Ants.” Journal of Experimental Biology 222(12). doi: 10.1242/jeb.203018.
DOI: 10.6084/m9.figshare.13102493
title: Assembly

description: Samples were collected from three timepoints during the incubation of the digestate: before N2O was added, and after 115 and 325 hours with N2O inclusion. Additionally, samples from a pre-treated digestate (heat-treated at 55 °C for 2 hours before incubation with N2O) was included to increase the the differential coverage for improved binning. DNA was extracted (PowerLyzer® PowerSoil® DNA Isolation kit from QIAGEN, following the kit protocol) and and sequenced (TruSeq PCR-free library preparation, HiSeq4000 150PE sequencing).The generated raw reads were trimmed with Trimmomatic (v0.36) before co-assembly with metaSPAdes (v3.10.1). Short contigs (&lt;500 bp) are excluded before the generated contigs were subjected to downstream analysis (i.e. binning and functional annotation).
DOI: 10.6084/m9.figshare.13102493.v1
title: Assembly

description: Samples were collected from three timepoints during the incubation of the digestate: before N2O was added, and after 115 and 325 hours with N2O inclusion. Additionally, samples from a pre-treated digestate (heat-treated at 55 °C for 2 hours before incubation with N2O) was included to increase the the differential coverage for improved binning. DNA was extracted (PowerLyzer® PowerSoil® DNA Isolation kit from QIAGEN, following the kit protocol) and and sequenced (TruSeq PCR-free library preparation, HiSeq4000 150PE sequencing).The generated raw reads were trimmed with Trimmomatic (v0.36) before co-assembly with metaSPAdes (v3.10.1). Short contigs (&lt;500 bp) are excluded before the generated contigs were subjected to downstream analysis (i.e. binning and functional annotation).
DOI: 10.6084/m9.figshare.13826066
title: Purslane data (growth and bioassay).xlsx

description: Dataset for research addressing effect of kairomones from herbivores fed different diets on plant growth and defense<br>
DOI: 10.6084/m9.figshare.13826066.v1
title: Purslane data (growth and bioassay).xlsx

description: Dataset for research addressing effect of kairomones from herbivores fed different diets on plant growth and defense<br>
DOI: 10.6084/m9.figshare.12838187
title: Supporting data from: 'Adaptation to vector-based transmission in a honey bee virus'

description: Raw data includes qPCR results, calculated absolute and relative viral loads per bee, and colony data. R scripts used to conduct the analysis and generate figures have been included along with accompanying csv data files.
DOI: 10.6084/m9.figshare.12838187.v5
title: Supporting data from: 'Adaptation to vector-based transmission in a honey bee virus'

description: Raw data includes qPCR results, calculated absolute and relative viral loads per bee, and colony data. R scripts used to conduct the analysis and generate figures have been included along with accompanying csv data files.
DOI: 10.6084/m9.figshare.12838187.v4
title: Supporting data from: 'Adaptation to vector-based transmission in a honey bee virus'

description: Raw data includes qPCR results, calculated absolute and relative viral loads per bee, and colony data. R scripts used to conduct the analysis and generate figures have been included along with accompanying csv data files.
DOI: 10.15482/usda.adc/1520771
title: Genetic fingerprinting of 184 Aspergillus from Ethiopia isolated in 2015 from peanut seeds, raw data
DOI: 10.24431/rw1k57p
title: Jakolof Bay and Bear Cove, Alaska, USA: pH, oxygen, salinity, and temperature measurements, October 2017-2018

description: Year-long high-frequency time series of pH, oxygen, salinity, and temperature in two enclosed bays (Jakolof Bay and Bear Cove) in Kachemak Bay, Alaska, USA. Measurements were recorded every 3 hours from 8 October 2017 – 8 October 2018 using SeaFET autonomous sensor, onset HOBO conductivity sensor, and an autonomous PME miniDOT. pH values were derived from potentiometric mV measurements using the Nernst equation, and salinity derived from conductivity was post-processed using the HOBOware Pro software.The data is available as a single comma-seperated values (CSV) file.
DOI: 10.25345/c5zv3z
title: MassIVE MSV000086829 - The B Cell Repertoire in Multiple Sclerosis Reveals Molecular Mimicry between EBNA1 and GlialCAM
title: In multiple sclerosis (MS) intrathecal B lymphocytes are directly involved in inflammation and secrete oligoclonal immunoglobulin. However, our understanding of their phenotype, function, and antigen-specificity in MS is incomplete. Molecular mimicry to viruses and self-antigens could be a trigger of autoimmunity. Here we describe phenotypic differences of B cells in blood and cerebro-spinal fluid (CSF) and predominantly implicate plasmablasts in MS pathogenesis. Single-cell paired-chain antibody repertoire sequencing in blood and CSF suggests ongoing intrathecal somatic hypermutation and antigen-specific clonal expansion of intrathecal plasmablasts. The presence of these antibodies was verified using mass spectrometry sequencing of the IgGs isolated from CSF. Selected CSF-derived antibodies were tested against a spectrum of viruses implicated in MS pathogenesis. Antibody MS39p2w174 binds Epstein-Barr Virus (EBV) transcription factor EBNA1 and cross-reacts to the glial cellular adhesion molecule GlialCAM, which is facilitated by serine-phosphorylation. EBNA1 peptide immunization aggravates the mouse model of MS. EBNA1-GlialCAM cross-reactive antibodies are more prevalent in MS patients than in healthy controls. Together, our results suggest that anti-EBNA1- antibodies cross-react with GlialCAM and contribute to MS pathology. This dataset contains the RAW files for the CSF isolated IgGs.
DOI: 10.7298/0mjr-6c90
title: Data from: Alternative Sigma factors regulate overlapping as well as distinct stress response and metabolic functions in Listeria monocytogenes stationary phase cells
DOI: 10.5281/zenodo.4527614
title: Data and code for manuscript: Validating a high-throughput tracking system: ATLAS as a regional-scale alternative to GPS

description: This repository contains the data and source code to complete the analysis and figures for the manuscript, <strong><em>Validating a high-throughput tracking system: ATLAS as a regional-scale alternative to GPS</em></strong> For any questions about the code please contact Christine at c.e.beardsworth@gmail.com To use any data contained in this repository contact Allert at allert.bijleveld@nioz.nl for permission. The data for the following code/ sections are found in data/ - `summaries.R`: produces the tables and results that are present in the manuscript<br> - `figures.R`: produces all the figures that are within the manuscript and supplementary material, these are then stored in figs/
DOI: 10.5281/zenodo.3934663
title: Monthly reference evapotranspiration for Brazil

description: The set of monthly ETo data referred to as monthly reference evapotranspiration for Brazil. It has a <strong>spatial resolution</strong> of <strong>30 seconds (~ 1 km²)</strong> and a <strong>temporal resolution of 1 month</strong>. The data set grid is in <strong>GeoTIFF format</strong>, and corresponds perfectly to WorldClim. It uses the <strong>geographic coordinate</strong> reference system, with <strong>WGS84 projection</strong> <strong>(EPSG: 4326)</strong>. The files are named as YEAR MONTH. Reference evapotranspiration (ETo) is a fundamental parameter for hydrological studies and irrigation management. The Penman-Monteith method is the standard for estimating ETo and requires several meteorological elements. Free remote sensing products with evapotranspiration information are rare. The objective of this study was to estimate the monthly ETo from the potential evapotranspiration (PET) made available by the MOD16 product. The monthly ETo estimated by the Penman-Monteith method was considered the standard. For this, data were acquired from the 265 meteorological station of the National Institute of Meteorology (INMET), throughout Brazil, in the period from 2000 to 2014 (15 years). Using machine learning algorithms, MOD16 images and WorldClim information as covariates, the ETo. All machine learning models were effective in improving the performance of the metrics evaluated. Cubist was the model that presented the best metrics for r² (0.91), NSE (0.90) and nRMSE (8.54%) and should be the preferred one for ETo prediction. The use of monthly ETo is recommended, which opens up possibilities for its use in numerous other studies. The article: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0245834
description: We are grateful for the financial support (master's scholarship) granted by the National Council for Scientific and Technological Development - Brazil (CNPq) under the contract number: 131565 / 2016-8 and Coordination for the Improvement of Higher Education Personnel - Brazil (CAPES) Financial Code 001. We also thank the Department of Agricultural Engineering (DEA), the Study and Solutions Group for Irrigated Agriculture (GESAI) at the Federal University of Viçosa (UFV).
description: {"references": ["R Core Team, 2020. R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria.", "Fick SE, Hijmans RJ. WorldClim 2: New 1-km spatial resolution climate surfaces for global land areas: New climate surfaces for global land areas. Int. J. Climatol. 2017; 37(12): 4302-4315. doi: 10.1002/joc.5086", "Mu Q, Zhao M, Running SW. Improvements to a MODIS global terrestrial evapotranspiration algorithm. Remote Sens. Environ. 2011(8); 115: 1781-1800. doi: 10.1016/j.rse.2011.02.019", "QGIS Development Team. QGIS Geographic Information System. Open Source Geospatial Foundation, World. 2017."]}
DOI: 10.5281/zenodo.3934662
title: Monthly reference evapotranspiration for Brazil

description: The set of monthly ETo data referred to as monthly reference evapotranspiration for Brazil. It has a <strong>spatial resolution</strong> of <strong>30 seconds (~ 1 km²)</strong> and a <strong>temporal resolution of 1 month</strong>. The data set grid is in <strong>GeoTIFF format</strong>, and corresponds perfectly to WorldClim. It uses the <strong>geographic coordinate</strong> reference system, with <strong>WGS84 projection</strong> <strong>(EPSG: 4326)</strong>. The files are named as YEAR MONTH. Reference evapotranspiration (ETo) is a fundamental parameter for hydrological studies and irrigation management. The Penman-Monteith method is the standard for estimating ETo and requires several meteorological elements. Free remote sensing products with evapotranspiration information are rare. The objective of this study was to estimate the monthly ETo from the potential evapotranspiration (PET) made available by the MOD16 product. The monthly ETo estimated by the Penman-Monteith method was considered the standard. For this, data were acquired from the 265 meteorological station of the National Institute of Meteorology (INMET), throughout Brazil, in the period from 2000 to 2014 (15 years). Using machine learning algorithms, MOD16 images and WorldClim information as covariates, the ETo. All machine learning models were effective in improving the performance of the metrics evaluated. Cubist was the model that presented the best metrics for r² (0.91), NSE (0.90) and nRMSE (8.54%) and should be the preferred one for ETo prediction. The use of monthly ETo is recommended, which opens up possibilities for its use in numerous other studies. The article: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0245834
description: We are grateful for the financial support (master's scholarship) granted by the National Council for Scientific and Technological Development - Brazil (CNPq) under the contract number: 131565 / 2016-8 and Coordination for the Improvement of Higher Education Personnel - Brazil (CAPES) Financial Code 001. We also thank the Department of Agricultural Engineering (DEA), the Study and Solutions Group for Irrigated Agriculture (GESAI) at the Federal University of Viçosa (UFV).
description: {"references": ["R Core Team, 2020. R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria.", "Fick SE, Hijmans RJ. WorldClim 2: New 1-km spatial resolution climate surfaces for global land areas: New climate surfaces for global land areas. Int. J. Climatol. 2017; 37(12): 4302-4315. doi: 10.1002/joc.5086", "Mu Q, Zhao M, Running SW. Improvements to a MODIS global terrestrial evapotranspiration algorithm. Remote Sens. Environ. 2011(8); 115: 1781-1800. doi: 10.1016/j.rse.2011.02.019", "QGIS Development Team. QGIS Geographic Information System. Open Source Geospatial Foundation, World. 2017."]}
DOI: 10.6084/m9.figshare.13661315.v8
title: Acoustic diversity dataset

description: Dataset and code for "<i>A machine learning approach for classifying and quantifying acoustic diversity</i>"<br><b></b>
DOI: 10.7277/6e4j-r892
title: Unreinforced Concrete Strut Database

description: &lt;p&gt;&lt;img alt="" src="https://datacenterhub.org/resources/136/download/strut-resource.png" style="height: 347px; width: 400px" /&gt;&lt;/p&gt; &lt;p&gt;&lt;span style="-webkit-text-stroke-width: 0px; display: inline !important; float: none; font-stretch: normal; text-align: left; white-space: normal; widows: 1"&gt;This dataset contains the results from tests of unreinforced concrete elements loaded in uniaxial compression. The data are organized to facilitate comparison of the strengths of prismatic and nonprismatic (bottle) struts. Data were obtained solely from published papers. These papers are not attached as reports due to copyrights of the respective publishers.&lt;/span&gt;&lt;/p&gt; &lt;p&gt;&lt;span style="-webkit-text-stroke-width: 0px; display: inline !important; float: none; font-stretch: normal; text-align: left; white-space: normal; widows: 1"&gt;This dataset has been added to since its creation. See below for a summary of additions.&lt;/span&gt;&lt;/p&gt; &lt;table border="1" cellpadding="1" cellspacing="1" style="width: 711px"&gt; &lt;tbody&gt; &lt;tr&gt; &lt;td style="width: 51px"&gt;&lt;strong&gt;Version&lt;/strong&gt;&lt;/td&gt; &lt;td style="width: 108px; text-align: center"&gt;&lt;strong&gt;Date&lt;/strong&gt;&lt;/td&gt; &lt;td style="width: 89px; text-align: center"&gt;&lt;strong&gt;Nr. Entries&lt;/strong&gt;&lt;/td&gt; &lt;td style="width: 137px; text-align: center"&gt;&lt;strong&gt;ID Range&lt;/strong&gt;&lt;/td&gt; &lt;td style="width: 300px"&gt;&lt;strong&gt;Version Notes&lt;/strong&gt;&lt;/td&gt; &lt;/tr&gt; &lt;tr&gt; &lt;td style="width: 51px; text-align: center"&gt;1&lt;/td&gt; &lt;td style="width: 108px; text-align: center"&gt;24-Mar-2015&lt;/td&gt; &lt;td style="width: 89px; text-align: center"&gt;183&lt;/td&gt; &lt;td style="width: 137px; text-align: center"&gt;7354 - 7536&lt;/td&gt; &lt;td style="width: 300px"&gt;Adapted from NEES.org published on 21-May-2014 (formerly at nees.org/resources/7915 but now no longer present)&lt;/td&gt; &lt;/tr&gt; &lt;tr&gt; &lt;td style="width: 51px; text-align: center"&gt;2&lt;/td&gt; &lt;td style="width: 108px; text-align: center"&gt;03-Apr-2016&lt;/td&gt; &lt;td style="width: 89px; text-align: center"&gt;207&lt;/td&gt; &lt;td style="width: 137px; text-align: center"&gt; &lt;p&gt;add 94567 - 94590&lt;/p&gt; &lt;/td&gt; &lt;td style="width: 300px"&gt;Added tests conducted fall 2014 by Puranam.&lt;/td&gt; &lt;/tr&gt; &lt;/tbody&gt; &lt;/table&gt; &lt;p&gt;The data from version 1 of this dataset support the following publication:&lt;br /&gt; Laughery, L., and Pujol, S. (2015), &quot;Compressive Strength of Unreinforced Struts,&quot; &lt;em&gt;ACI Structural Journal&lt;/em&gt;, V. 112, No. 5, Sept.-Oct., pp.617-624. doi: &lt;a href="http://dx.doi.org/10.14359/51687711"&gt;10.14359/51687711&lt;/a&gt;.&lt;/p&gt; &lt;nb:citations&gt;&lt;/nb:citations&gt;
DOI: 10.6084/m9.figshare.13404719
title: Single-molecule force spectroscopy measurements of pentosan polysulfate interacting with hamster prion protein

description: File contains force extension curves showing unfolding/refolding transitions measured for hamster PrP in the presence of PPS. Data are presented as columns of extension (nm) and force (pN) values from successive individual unfolding and refolding trajectories. Each separate sheet in the .xls file corresponds to a set of pulling/relaxation curves measured on the same molecule.<br>
DOI: 10.6084/m9.figshare.13404719.v1
title: Single-molecule force spectroscopy measurements of pentosan polysulfate interacting with hamster prion protein

description: File contains force extension curves showing unfolding/refolding transitions measured for hamster PrP in the presence of PPS. Data are presented as columns of extension (nm) and force (pN) values from successive individual unfolding and refolding trajectories. Each separate sheet in the .xls file corresponds to a set of pulling/relaxation curves measured on the same molecule.<br>
DOI: 10.6084/m9.figshare.13831469
title: Relationships between climate, Muslim culture, and democracy

description: Data set with information on 145 countries<br>
DOI: 10.6084/m9.figshare.13831469.v1
title: Relationships between climate, Muslim culture, and democracy

description: Data set with information on 145 countries<br>
DOI: 10.6073/pasta/e189ff52024a464dabb31861f397de3a
title: Fine-scale meteorological observations from walking traverses in two Phoenix Area Social Survey (PASS) 2017 neighborhoods (2019)

description: This dataset includes human-biometeorological observations from 2.5 km walking traverses with a mobile weather station. The traverses occurred in two 2017 Phoenix Area Social Survey neighborhoods (U18: South Phoenix/Salt River (Audubon) and W15: Camelback Mountain) on one day in June and October, at 12pm and 4pm on each day. Specifically, air temperature, humidity, wind speed, and radiant energy (infrared and solar radiation) in 3-dimensions were measured at 2-second intervals. Additionally, mean radiant temperature was calculated from the radiation measurements. The meteorological observations are spatially referenced with latitude and longitude coordinates. The paths through the neighborhoods were chosen to maximize proximity to PASS 2017 participants’ homes.
DOI: 10.5281/zenodo.4480455
title: data for grl - lekima_vrw - wz bureau radar data

description: radar data provided by Wenzhou Bureau
DOI: 10.5281/zenodo.4480454
title: data for grl - lekima_vrw - wz bureau radar data

description: radar data provided by Wenzhou Bureau
DOI: 10.25345/c5v500
title: MassIVE MSV000086830 - GNPS - Burger ingredients common human diet
title: Samples from burger ingredients extracted with MeOH:Water 1:1 and prepared for LC-MS/MS. Data was acquired in positive ion mode.
DOI: 10.5281/zenodo.4527616
title: Orthrus Protocol Data, Code and Expected Output

description: Input data, scoring scripts and expected output for the Orthrus scoring protocol. The stable version of the Orthrus R package can be found at the following Github link: https://github.com/csbio/orthrus
DOI: 10.5281/zenodo.3998247
title: Orthrus Protocol Data, Code and Expected Output

description: Input data, scoring scripts and expected output for the Orthrus scoring protocol. The stable version of the Orthrus R package can be found at the following Github link: https://github.com/csbio/orthrus