cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.14130494
title: Fast and accurate bootstrap confidence limits on genome-scale phylogenies using little bootstraps

description: Data Description<br>Simulated_Data: This directory contains a simulated DNA sequence alignment (Simulated_data.fasta) with 446 sequences and 134131 sites. This dataset was simulated under auto correlated evolutionary rates among lineages. A set of 100 genes were simulated using a wide range of realistic biological parameters. The Simulated_data is the concatenation of these simulated genes. The tree file (Sim_candiate_tree.nwk) is the candidate tree for this dataset. Fig 2(a) –(d) in the main text have been produced by analyzing this dataset. Small_datasets: This directory contains three single-gene DNA sequence datasets with 446 species and 4000 to 10000 sites. The tree file (Small_data_candidate_tree.nwk) is used as a candidate tree for the analysis. Fig 2(e)-(f) have been produced by analyzing these datasets. Empirical_Mammal_Dataset: The empirical DNA sequence dataset has been provided in this directory. The eutherian mammal dataset consists of 447 nuclear genes and 37 mammalian species sequences. The concatenated sequence alignment has 1,391,742 sites. The tree file (MAM2_candiate_tree.nwk) is the candidate tree for this empirical dataset. Large_Simulated_Datasets: There are five different simulated DNA sequence datasets, all with 446 species and a varying number of sites (pnas_test_50k: 50,000 sites, pnas_test_100k: 100,000 sites, pnas_test_200k: 200,000 sites, pnas_test_400k: 400,000 sites, pnas_test_all: 536,534 sites). The first four datasets were generated by a random sample of sites from the pnas_test_all dataset. The pnas_test_all.fasta sequence alignment was generated by concatenating four sets of randomly selected 100 genes which were simulated using different rate variation models. Fig 2(g) has been produced by analyzing these datasets. <br>
DOI: 10.6084/m9.figshare.14815140
title: Data from: Translating area-based conservation pledges into efficient biodiversity protection outcomes

description: Prioritisation rank and mask data used for the figures of the article titled "Translating area-based conservation pledges into efficient biodiversity protection outcomes".<br>Please see README file for usage notes.
DOI: 10.7302/z2js9nng
title: Data from "Genomic evidence of a widespread southern distribution during the Last Glacial Maximum for two eastern North American hickory species"

description: Raw SNP genotypes are provided in STRUCTURE format, with a maximum of one SNP reported per ddRAD locus. The files "caryco_SNP.str" and "caryov_SNP.str" are genotypes for Carya cordiformis and Carya ovata, respectively. The first column of each file is the individual name, the second column is the population (see original publication for information on population locations), and the remaining columns are genotypes of individual SNPs. Rows represent individuals, with the diploid genotypes contained on two lines per individual. Missing data are entered as "0" (zero). The first row is a header with a unique identifier for each SNP.;Occurrence records for each species are provided in the file "occs_carya.csv" and contain the latitude and longitude of each record.
description: Genotypes of bitternut hickory (Carya cordiformis) and shagbark hickory (Carya ovata) were generated from rangewide populations of each species. Individuals from each population were sequenced using double-digest Restriction-site Associated DNA (ddRAD) sequencing. Single nucleotide polymorphisms (SNPs) were identified and genotyped using the program Stacks (Catchen et al. 2011 G3: Genes, Genomes, Genetics
description: Catchen et al. 2013 Molecular Ecology). Occurrence records of each species used in species distribution modelling were obtained from the US Forest Service Forest Inventory Analysis Database (www.fia.fs.fed.us).
DOI: 10.25678/0004ya
title: Data for: Seasonaly modulates wind-driven mixing pathways in a large lake

description: Turbulent mixing controls the vertical transfer of heat, gases and nutrients in stratified water bodies, shaping their response to environmental forcing. Nevertheless, due to technical limitations, the redistribution of wind-derived energy fuelling turbulence within stratified lakes has only been mapped over short (sub-annual) timescales. Here we present a year-round observational record of energy fluxes in the large Lake Geneva. Contrary to the standing view, we show that the benthic layers are the main locus for turbulent mixing only during winter. Instead, most turbulent mixing occurs in the water-column interior during the stratified summer season, when the co-occurrence of thermal stability and lighter winds weakens near-sediment currents. Since stratified conditions are becoming more prevalent --possibly reducing turbulent fluxes in deep benthic environments--, these results contribute to the ongoing efforts to anticipate the effects of climate change on freshwater quality and ecosystem services in large lakes.
DOI: 10.3334/cdiac/00066
title: A Coastal Hazards Data Base for the U.S. Gulf Coast (1993)

description: This document describes the contents of a digital data base that may be used to identify coastlines along the U.S. Gulf Coast at risk to sea-level rise. The data base integrates point, line, and polygon data for the U.S. Gulf Coast into 0.25° latitude by 0.25° longitude grid cells and into 1:2,000,000 digitized line segments that can be used by raster or vector geographic information systems (GIS) as well as by non-GIS data base systems. Each coastal grid cell and line segment contains data on elevations, geology, geomorphology, sea-level trends, shoreline displacement (erosion/accretion), tidal ranges, and wave heights.
DOI: 10.5281/zenodo.3747336
title: Single cell and immune repertoire profiling of COVID-19 patients reveal novel therapeutic candidates

description: COVID-19, a novel pneumonia caused by SARS-CoV-2, has rapidly become the largest threat to public health. Recent studies reported lymphocytopenia but also expansions of antigen-specific T/B cells during early-recovery stage. Here we investigated 16 early-recovery patients using scRNA-seq, HLA-genotyping and deep immune repertoire profling. Our analysis revealed 916 COVID-19-specific TCR groups enriched for a novel cytotoxic CD8+ phenotype with both resident memory (ZNF683+) and tissue exit (SIRP5) markers, and identified 114 statistically-confident virus epitopes. Further, we uncovered 374 BCR groups with somatic hypermutations and/or class switch recombinations. Molecular dynamics simulations revealed 15% of the highly expanded groups may serve as neutralizing antibodies against the virus Spike protein. Finally, we discovered that bacterial infection in COVID-19 patients may elevate monocytic myeloidderived suppressor cells via TLR4/NF!B signaling and cause disease aggravation. Together, we expect our findings and immune-receptor datasets to provide immediate therapeutic options against the pandemic of COVID-19.
DOI: 10.5281/zenodo.4384569
title: Data Set for: Bloch point-mediated skyrmion annihilation in three dimensions

description: This DOI contains both the experimental data and the simulation scripts to reproduce the results of <em>Bloch point-mediated skyrmion annihilation in three dimensions</em> by M. T. Birch, D. Cortés-Ortuño, N. D. Khanh, S. Seki, A. Štefančič, G. Balakrishnan, Y. Tokura and P. D. Hatton. Eprint available at https://arxiv.org/abs/2012.14813 Updates to these data files can be found at the corresponding Github repository: https://github.com/davidcortesortuno/paper-2021_bloch_point_mediated_skyrmion_annihilation_in_three_dimensions To cite this data set, you can use the following Bibtex entry: <pre><code>@Misc{Birch2021, author = {M. T. Birch and D. Cort\'es-Ortu\~no}, title = {{Data set for: Bloch point-mediated skyrmion annihilation in three dimensions}}, howpublished = {Zenodo \url{doi:10.5281/zenodo.4384569}. Github: \url{https://github.com/davidcortesortuno/https://github.com/davidcortesortuno/paper-2021_bloch_point_mediated_skyrmion_annihilation_in_three_dimensions}}, year = {2021}, doi = {10.5281/zenodo.4384569}, url = {https://doi.org/10.5281/zenodo.4384569}, }</code></pre>
DOI: 10.5281/zenodo.4557463
title: High-entropy alloys data sets of evidence-based recommender system for combinatorial materials synthesis

description: This publication contains eights high-entropy data sets, which are used to evaluate evidence-based recommender system for high-entropy alloys. The eight data sets consisting of binary, ternary, quaternary, and quinary alloys comprising multiple equiatomically combined elements. The data sets consist of data from experiments and calculations. The alloys contained in the data sets comprise {Fe, Co, Ir, Cu, Ni, Pt, Pd, Rh, Au, Ag, Ru, Os, Si, As, Al, Tc, Re, Mn, Ta, Ti, W, Mo, Cr, V, Hf, Nb, and Zr}. Alloys in this publication are represented using the binary elemental descriptors. Thus, an alloy is described by a 27-dimensional binary vector with elements of one or zero. Label of each alloy in the data sets can be either "High" or "Low", which indicates whether the alloy is an HEA. Any alloy is predicted as an HEA if its order-disorder transition temperature is below its melting temperature. The temperatures are collected from the reseach of Yoav Lederer.
description: {"references": ["Yoav Lederer, Cormac Toher, Kenneth S. Vecchio, Stefano Curtarolo, The search for high entropy alloys: A high-throughput ab-initio approach, Acta Materialia, Volume 159, 2018, Pages 364-383, ISSN 1359-6454, https://doi.org/10.1016/j.actamat.2018.07.042."]}
DOI: 10.5281/zenodo.4629927
title: Mesh files for idealized and image-based periarterial and perivenous spaces

description: Data set for the idealized periarterial (artery.geo), idelized perivenous (vein.geo), image-based periarterial (artery2.geo) and image-based perivenous space. Geo-files were used to create meshes in the study <em>Brain solute transport is more rapid in periarterial than perivenous spaces.</em>
DOI: 10.5281/zenodo.4767298
title: yeastDrop-Seq_ProcessedData

description: Source data used as inputs to generate the figure panels, with each Excel tab containing the data shown in specific figure panel(s)
DOI: 10.5281/zenodo.4772516
title: Dynamic FRET-FLIM based screens of signal transduction pathways: a feasibility study

description: Dataset accompanying the paper <em>Dynamic FRET-FLIM based screens of signal transduction pathways: a feasibility study</em>.
description: v1.0.2: Including 2021 data, to recreate Figure 1
DOI: 10.5281/zenodo.5101910
title: Atmospheric turbulence distorted video sequence dataset

description: This contains the full version of the dataset utilized in our paper "Neutralizing the impact of atmospheric turbulence on complex scene imaging via deep learning". Three main types of data are covered, which include algorithm simulated data, physical simulated data and real-world data. Specifically, the algorithm/physical simulated sequences are given with reference without turbulence distortion.
DOI: 10.5281/zenodo.5115742
title: An increase in food production in Europe could dramatically affect farmland biodiversity

description: <strong>Supplementary Data. Detailed average yield per region, and organic and non-organic management systems per crop type in MJ/ha (</strong><strong>+/- standard error) </strong><strong>in ten European farmland regions</strong>. Details on regions and country abbreviations are given in Supplementary Table 1.
DOI: 10.5281/zenodo.5235706
title: Dataset and Code for Manuscript "Multi-angle pulse shape detection of scattered light in flow cytometry for label-free cell cycle classification"

description: Dataset of measurements for cell cycle analysis with description: ReadMe file with explanations on the data set and analysis exemplary Matlab script file for analysis binary data files conatining the pulse shapes in all channels FCS data files containing common flow cytometry parameters in each channel Data on unsorted HEK cells, HEK cells sorted for cell cycle phases, and unsorted Jurkat cell are included.
DOI: 10.5285/a7f28dea-64f7-43b5-bc39-a6cfcdeefbda
title: Summary of instrumentation installed in boreholes drilled into Khumbu Glacier, Nepal, in 2017 and 2018 as part of EverDrill research project

description: The dataset lists information about the instrumentation of boreholes drilled into Khumbu Glacier, Nepal. Boreholes were drilled in May 2017 and May 2018 to investigate the internal properties of Khumbu Glacier, specifically ice thickness, temperature, deformation and structure, as part of the NERC-funded 'EverDrill' research project. The information provided includes each borehole's ID, length, location, elevation and instrumentation, including the type and depth of each sensor.

        Funding was provided by the NERC grant NE/P00265X/1 and NE/P002021/1.
description: Borehole information was collected while boreholes were drilled using a hot-water drill in 2017 and 2018 on Khumbu Glacier, Nepal. Location and elevation were measured with a handheld GPS unit. Borehole depth was measured from the length of drilling hose in the borehole at the time when drilling progress ceased, and confirmed from the length of sensor cable lowered into the borehole. The type, and depth at which each sensor was installed is detailed, as well as each sensor ID.
DOI: 10.6084/m9.figshare.13312313
title: Metadata record for the manuscript: Mapping resource effectiveness across urban systems

description: <b>Summary</b> This metadata record provides details of the data supporting the claims of the related manuscript: “Mapping resource effectiveness across urban systems”. The related study identified the hotspots of imports in cities to redirect resources to where they are most needed, based on the system overall resource effectiveness to maximise the use of all resources available. It also developed a novel taxonomy of resource-use behaviour based on the clustering patterns of resource utilisation and conversion across inter-connected urban systems. <b>Data access</b> Seven datasets were generated and are shared openly as part of this figshare record. All datasets are named according to the terminology used in the related article. The datasets are as follows:<br> - Comtrade_data_UK (supporting a method in the Supplementary Information) - Effectiveness_results.txt (supporting Figs 3, 5, 6) - Efficiency_fua.txt (supporting Fig 7) - Exergy_conversion.xlsx (supporting a method in the Supplementary Information) - Export by sector.csv (supporting Fig 4) - Import by sector.csv (supporting Fig 4, 5, 6) - ONS_data_UK.xlsx (supporting Fig 4, 5, 6) <b>Corresponding author</b> Ling Min Tan, Department of Civil & Structural Engineering, University of Sheffield, Sir Frederick Mappin Building, Sheffield, S1 3JD, United Kingdom. Email: lingmin.tan@sheffield.ac.uk
DOI: 10.6084/m9.figshare.13352669
title: Gravitational wave detectors with broadband high frequency sensitivity - data

description: Data sets used in Supplementary Information of the publication "Gravitational Wave Detectors with Broadband High Frequency Sensitivity", accepted for publication in Communications Physics.<br>figS1data.txt is a set of data points describing the scaling of mechanical loss versus temperature for a single crystal bulk acoustic wave resonator. The mechanical mode is the m=65 204 MHz longitudinal mode of a 1mm thick, 15mm radius quartz plano-convex lens.<br>figS2 sets are theoretical and experimental data points which relate to the measurement of optical absorption heating of a silicon nitride membrane resonator acoustically shielded by a phononic crystal.
DOI: 10.6084/m9.figshare.14959809
title: Metadata record for the article: Acquired JAK2 mutations confer resistance to JAK inhibitors in cell models of acute lymphoblastic leukemia

description: <b>Summary</b>This metadata record provides details of the data supporting the claims of the related article: “Acquired JAK2 mutations confer resistance to JAK inhibitors in cell models of acute lymphoblastic leukemia”.The related study aimed to generate a murine pro-B cell model of ATF7IP-JAK2 with acquired resistance to multiple type-I JAK inhibitors. Type of data: exome sequencing data; flow cytometry; computational modelling Subject of data: <i>Homo sapiens; </i>antibodies; eukaryotic cell lines (parental Ba/F3 cell line)Recruitment: Cryopreserved bone marrow mononuclear cell samples from Ph-like B-ALL patients were obtained from the Children’s Cancer Institute Australia (CCIA), SA Pathology/Royal Adelaide Hospital, Australasian Leukaemia & Lymphoma Group (ALLG) tissue bank, or Queensland Children’s Tumour Bank. <b>Data access</b>The exome sequencing data are openly available in the <i>NCBI Sequence Read Archive</i> via the following accession: https://identifiers.org/ncbi/bioproject:PRJNA741841. All additional data files underlying the Figures and Supplementary Figures of the related article are shared openly as part of this <i>figshare </i>data record. Files underlying Figures:ATF7IP-JAK2_BaF3_pSTAT5Timecourse_Histograms.pdfATF7IP-JAK2_RuxR_TypeIJAKInhib_CellViabilities.xlsxG993A_JAK2r_BaF3_GFP.pdfNonMutG993A_BaF3_RUX_CellViabilities.xlsxNotMutG993A_TypeIJAKInhib_pSTAT5.xlsxATF7IP-JAK2_RuxR_CHZ868_CellViabilities.xlsxNonMutG993ABaF3_pSTAT5_CHZ868.pdf Files underlying Supplementary Figures:ATF7IP-JAK2_BaF3_GFP-Layout.pdfUnprocessed_WBImages.pdfATF7IP-JAK2_RuxR_TrypanCounts.xlsxEmptyVector_BaF3_JAKInhib_CellViabilities.xlsxJAK2r_BaF3_GFP.pdfNonMut_JAK2_BaF3_HAExp.pdfCellProliferation_Luminescence.xlsxNonMutG993A_pSTAT135Phosphoflow.pdfJAK2NonMutG993A_CellProliferation_Luminescence.xlsxNonMutG993A_pAKTpERK_MFI.xlsx <b>Corresponding author(s) for this study</b>Professor Deborah White, Director: Cancer Program. Deputy Theme Leader: Precision Medicine. South Australian Health and Medical Research Institute, North Terrace, Adelaide, SA 5000; deborah.white@sahmri.com<br> <b>Study approval </b>The use of samples was approved by Central Adelaide Local Health Network and the Royal Adelaide Hospital Human Research Ethics Committee. Samples were obtained with informed consent for prospective unspecified medical research, and to perform laboratory-based assays on existing specimens. All the participants were required to provide informed consent for their samples to be used in accordance with the Declaration of Helsinki.
DOI: 10.6084/m9.figshare.15181038
title: Datasets supporting Pant et al. Communications Biology

description: Fig1e.txt and Fig1f.txt: Corresponds to the dataset in Figure 1e and 1f of the paper. First column is the simulation time in ns, and rest of the column corresponds to the different instances (distances in Å). <br>Fig3a.txt: Corresponds to the PIP2 dissociation for 3 respective R214Q systems<br>Fig3d.txt: Corresponds to the PIP2 dissociation for 3 respective K219N systems<br><br><br>Fig3g.txt: Corresponds to the PIP2 dissociation for 3 respective R325Q systems<br><br>Fig3j.txt: Corresponds to the PIP2 dissociation for 3 respective R353Q systems<br><br>Fig7c-wPIP.txt: Corresponds the orientational changes captured in the presence of PIP2 lipids, as shown in Fig7c. <br>Fig7c-woPIP.txt: Corresponds the orientational changes captured in the absence of PIP2 lipids, as shown in Fig7c. <br><br>Fig7c-R353Q.txt: Corresponds the orientational changes captured in the mutant protein, as shown in Fig7c. <br><br>All the experimental raw data files are named as : CommsBio-20-2352T_FigXX_data.xlsx; where XX corresponds to figure number and panel.
DOI: 10.15151/esrf-es-925345008
title: Italian CryoEM Bag (ICB)

description: This BAG application builds on the development of single particle cryo-EM in the Italian Structural Biology community, as in Italy there is no top-end instrument available. The groups in this application have acquired know-how in cryo.EM through international collaborations or by acquiring medium-level in-house equipment. Access to the CM01 beamline at the ESRF has been instrumental for the achievement of high-profile scientific results and publications in top journals. Presently three screening microscopes are available in Italy, these instruments will boost sample production and the number of applications to CM01. Given these premises a BAG from Italian institutions could ensure timely data collection, nurturing the expansion of the field in Italy and a high-level scientific production.
DOI: 10.17632/m2wg7xcrth.1
title: CBOE Volatility Index (VIX)

description: The monthly data of the VIX index, S&P500 index, and Nasdaq Composite index
DOI: 10.17632/hpyjdp33fx.1
title: hCPEB3_NMR_Spectra

description: NMR Spectra of human CPEB3's intrinsically disordered domain (residues 1-426 of isoform 2) obtained at pH 4.0 in 1 mM acetic acid (d4) and 25ºC.  The spectra were obtained on a Bruker 800 MHz (1H) Avance spectrometer equipped with a 3 channel cyroprobe and Z-gradients.  The disordered domain was studied as eight segments which are 100 residues long and overlap, i.e. segment 1 is residues 1-100, segment 2 is 51-150, segment 3 is 101 to 200, etc. 
Data is presented for 7 segments (1, 3, 4, 5, 6, 7 & 8);  segment 2 was insoluble.  For each segment, the spectral data for the 2D HSQC and 2D HCO; and/or hncacoNcaNCO, HNCO or hncaCOncaNCO are provided.
DOI: 10.5281/zenodo.7395559
title: Credit Card Fraud Detection

description: The dataset from https://www.kaggle.com/datasets/mlg-ulb/creditcardfraud The dataset contains transactions made by credit cards in September 2013 by European cardholders.<br> This dataset presents transactions that occurred in two days, where we have 492 frauds out of 284,807 transactions. The dataset is highly unbalanced, the positive class (frauds) account for 0.172% of all transactions.
DOI: 10.5281/zenodo.7395558
title: Credit Card Fraud Detection

description: The dataset from https://www.kaggle.com/datasets/mlg-ulb/creditcardfraud The dataset contains transactions made by credit cards in September 2013 by European cardholders.<br> This dataset presents transactions that occurred in two days, where we have 492 frauds out of 284,807 transactions. The dataset is highly unbalanced, the positive class (frauds) account for 0.172% of all transactions.
DOI: 10.5281/zenodo.7395604
title: Climate and geology overwrite land use effects on soil organic nitrogen cycling on a continental scale

description: <strong>Abstract.</strong> Soil fertility and plant productivity are globally constrained by N availability. Proteins are the largest N reservoir in soils and the cleavage of proteins into small peptides and amino acids has been shown to be the rate limiting step in the terrestrial N cycle. However, we are still lacking a profound understanding of the environmental controls of this process. Here we show that integrated effects of climate and soil geochemistry drive protein cleavage across large scales. We measured gross protein depolymerization rates in mineral and organic soils sampled across a 4000-km-long European transect covering a wide range of climates, geologies and land uses. Based on structural equation models we identified that soil organic N cycling was strongly controlled by substrate availability, e.g. by soil protein content. Soil geochemistry was a secondary predictor, by controlling protein stabilization mechanisms and protein availability. Precipitation was identified as the main climatic control on protein depolymerization, by affecting soil weathering and soil organic matter accumulation. In contrast, land use was a poor predictor of protein depolymerization. Our results highlight the need to consider geology and precipitation effects on soil geochemistry when estimating and predicting soil N cycling at large scales.
DOI: 10.5281/zenodo.7395634
title: Underlying data for In vivo assessment of the relationship between oral lichen planus and antioxidant status of vitamins A, C, and E in diabetic and hypertensive patients: An observational study

description: Underlying data for In vivo assessment of the relationship between oral lichen planus and antioxidant status of vitamins A, C, and E in diabetic and hypertensive patients: An observational study