Datasets:
dataesr
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paragraph_classification_eval

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dataset
10.1038_s41598-019-57366-y
doi10.1038_s41598-019-57366-y
Data availability The datasets generated during and/or analysed during the current study are available from the corresponding author on reasonable request.
false
true
false
dataset
10.1371_journal.ppat.1008185
doi10.1371_journal.ppat.1008185
Data Availability Statement All relevant data are within the manuscript and its Supporting Information files.
false
true
true
dataset
10.1186_s40168-023-01556-4
doi10.1186_s40168-023-01556-4
Availability of data and materials The virome data were deposited in Science Data Bank (ScienceDB) Database under the DOI accession link http://www.doi.org/10.57760/sciencedb.06132.
false
true
false
dataset
10.1088_1361-6595_acfe94
doi10.1088_1361-6595_acfe94
Data availability statementThe data that support the findings of this study are openly available at the following URL/DOI: http://doi.org/10.5281/zenodo.7904634.
false
true
false
dataset
10.1136_bmjgh-2021-005690
doi10.1136_bmjgh-2021-005690
Data availability statement Data are available upon request. All data relevant to the study are included in the article or uploaded as supplemental information.
false
true
false
dataset
10.1038_s41467-020-20536-y
doi10.1038_s41467-020-20536-y
Data availabilityZebra finch PacBio long reads, Hi-C data, parental short-read data, triobinned parental Canu assemblies: [https://vgp.github.io/genomeark/Taeniopygia_guttata/]. FALCON-Unzip contigs: [https://www.ncbi.nlm.nih.gov/bioproject/PRJNA604785], [https://www.ncbi.nlm.nih.gov/bioproject/PRJNA604786]. FALCON-Phase contigs: [https://www.ncbi.nlm.nih.gov/bioproject/PRJNA604789], [https://www.ncbi.nlm.nih.gov/bioproject/PRJNA604788]. FALCON-Phase scaffolds: [https://www.ncbi.nlm.nih.gov/bioproject/PRJNA604793], [https://www.ncbi.nlm.nih.gov/bioproject/PRJNA604794]. Cow PacBio long reads, Hi-C data, parental short-read data, triobinned parental canu assemblies: [https://www.ncbi.nlm.nih.gov/bioproject/PRJNA432857]. FALCON-Unzip contigs: [https://www.ncbi.nlm.nih.gov/bioproject/PRJNA604814], [https://www.ncbi.nlm.nih.gov/bioproject/PRJNA604813]. FALCON-Phase contigs: [https://www.ncbi.nlm.nih.gov/bioproject/PRJNA604823], [https://www.ncbi.nlm.nih.gov/bioproject/PRJNA604824]. FALCON-Phase scaffolds: [https://www.ncbi.nlm.nih.gov/bioproject/PRJNA604826], [https://www.ncbi.nlm.nih.gov/bioproject/PRJNA604827]. HG00733 PacBio long reads: [https://www.ncbi.nlm.nih.gov/sra/SRR7615963]. Hi-C data: [https://www.ncbi.nlm.nih.gov/sra/ERR1225141], [https://www.ncbi.nlm.nih.gov/sra/ERR1225146]. Parental short-read data: [https://www.ncbi.nlm.nih.gov/bioproject/PRJNA42573]. Triobinned parental canu assemblies: [https://obj.umiacs.umd.edu/marbl_publications/triobinning/h_sapiens_HG00733_dad.fasta], [https://obj.umiacs.umd.edu/marbl_publications/triobinning/h_sapiens_HG00733_mom.fasta]. FALCON-Unzip contigs: [https://www.ncbi.nlm.nih.gov/bioproject/PRJNA604844], [https://www.ncbi.nlm.nih.gov/bioproject/PRJNA604843]. FALCON-Phase contigs: [https://www.ncbi.nlm.nih.gov/bioproject/PRJNA604845], [https://www.ncbi.nlm.nih.gov/bioproject/PRJNA604846]. FALCON-Phase scaffolds: [https://www.ncbi.nlm.nih.gov/assembly/GCA_003634875.1] mHomSap3 PacBio long reads, Hi-C data, parental short-read data: [https://vgp.github.io/genomeark/Homo_sapiens/]. Triobinned parental canu assemblies: [https://genomeark.s3.amazonaws.com/species/Homo_sapiens/mHomSap3/assembly_nhgri_trio_1.6/intermediates/mHomSap3_mat_t1.fasta.gz], [https://genomeark.s3.amazonaws.com/species/Homo_sapiens/mHomSap3/assembly_nhgri_trio_1.6/intermediates/mHomSap3_pat_t1.fasta.gz]. FALCON-Unzip contigs: [https://www.ncbi.nlm.nih.gov/bioproject/PRJNA604831], [https://www.ncbi.nlm.nih.gov/bioproject/PRJNA604832]. FALCON-Phase contigs: [https://www.ncbi.nlm.nih.gov/bioproject/PRJNA604836], [https://www.ncbi.nlm.nih.gov/bioproject/PRJNA604835]. FALCON-Phase scaffolds: [https://www.ncbi.nlm.nih.gov/bioproject/PRJNA604839], [https://www.ncbi.nlm.nih.gov/bioproject/PRJNA604838]. HG002 PacBio HiFi Reads: [https://www.ncbi.nlm.nih.gov/sra/SRR10382244], [https://www.ncbi.nlm.nih.gov/sra/SRR10382245], [https://www.ncbi.nlm.nih.gov/sra/SRR10382248], [https://www.ncbi.nlm.nih.gov/sra/SRR10382249]. Hi-C data: [https://github.com/human-pangenomics/HG002_Data_Freeze_v1.0]. Parental short-read data: [ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/AshkenazimTrio/HG004_NA24143_mother/NIST_Illumina_2x250bps/reads/], [ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/AshkenazimTrio/HG003_NA24149_father/NIST_Illumina_2x250bps/reads/]. IPA contigs:[https://www.ncbi.nlm.nih.gov/bioproject/PRJNA667512], [https://www.ncbi.nlm.nih.gov/bioproject/PRJNA667511]. FALCON-Phase contigs: [https://www.ncbi.nlm.nih.gov/bioproject/PRJNA667513], [https://www.ncbi.nlm.nih.gov/bioproject/PRJNA667514].
true
true
true
dataset
10.1038_s41467-022-31739-w
doi10.1038_s41467-022-31739-w
Data availability All data analyzed in this paper can be downloaded in raw form from the original publication. Specifically, the DLPFC data is available in the “spatialLIBD package [http:// spatial.libd.org/spatialLIBD]. The processed Stereo-seq data from mouse olfactory bulb tissue is accessible at “SEDR analyses [https://github.com/JinmiaoChenLab/SEDR_ analyses]”. The chicken heart ST data is retrieved from GEO database under accession code “GSE149457 [https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE149457]”. The human breast cancer ST data can be obtained from the Zenodo dataset “4751624”. The sample we used is the same as the one demonstrated in the original paper (patient G-sample 1). Both chicken heart ST data and breast cancer ST data were sequenced by 10x Visium platform. The Slide-seq V2 can be accessed in Squidpy package71 or downloaded from “Broad Institute database [https://singlecell.broadinstitute.org/single_ cell/study/SCP815/highly-sensitive-spatial-transcriptomics-at-near-cellular-resolution- with-slide-seqv2]”. The seqFISH data can be accessed at the “Spatial Mouse Atlas [https:// marionilab.cruk.cam.ac.uk/SpatialMouseAtlas/]”. The Gene Ontology Consortium database can be accessed via “Gene Ontology Consortium [http://geneontology.org/]”. All other relevant data supporting the key findings of this study are available within the article and its Supplementary Information files or from the corresponding author upon reasonable request. Code availability The SpaceFlow package is implemented in Python with a dependency of Pytorch and is available on the GitHub repository “SpaceFlow [https://github.com/hongleir/ SpaceFlow]”. It is also deposited at Zenodo dataset “6668286”.
false
true
true
dataset
10.1093_mnras_stab2591
doi10.1093_mnras_stab2591
DATA AVA IL AB IL IT Y The X-shooter and SINFONI data underlying paper article are available in the ESO archive at https://archive.eso.org/ under ESO programme IDs 0102.A-0704(A) and 075.B-0636(B), respectively The HST data underlying this paper are available in the MAST archive at 10.17909/T9-9KG5-HG27. The reduced data underlying this paper will be shared on reasonable request to the corresponding author.
true
true
false
dataset
10.7554_elife.79027
doi10.7554_elife.79027
Data availability Source data and analysis code are available at the following Open Science Framework repository: https://osf.io/cs8d6/. Pre-processed eye-tracker data can be found here: https://osf.io/mrhk9/. Raw fMRI data is available at the following G-Node Infrastructure repository: https://gin.g-node.org/ipolti/ TTC_HPCF.git. The following datasets were generated: Author(s) Year Dataset title Dataset URL Database and Identifier Polti I, Nau M, Kaplan R, Wassenhove van, Doeller CF 2022 Time-To-Contact https://gin.g-node. org/ipolti/TTC_HPCF. git G-Node Infrastructure, 10.12751/g-node.pwn4qz Frey M, Nau M, Doeller CF 2021 DeepMReye https://osf.io/mrhk9/ Open Science Framework, 10.17605/OSF.IO/MRHK9 Polti I, Nau M 2022 Rapid encoding of task regularities in the human hippocampus guides sensorimotor timing https://osf.io/cs8d6/ Open Science Framework, cs8d6
false
true
true
dataset
10.1371_journal.pdig.0000481
doi10.1371_journal.pdig.0000481
Data Availability Statement: Deidentified individual participant data has been deposited in the Open Science Framework (OSF) repository (DOI: 10.17605/OSF.IO/RUQ4G). The dataset does not include the full demographic data collected to avoid indirect identification of participants. Following the guidance in Hrynaszkiewicz et al. (2010), we have included only 3 indirect identifiers: age, gender, and ethnicity. Two participants did not consent for their data to be made available for future studies, so that data has been removed from the available dataset.
false
true
false
dataset
10.1186_s12891-023-06345-6
doi10.1186_s12891-023-06345-6
Availability of data and materials We propose a literature review and a meta-analysis. All data are from the articles listed in the summary tables included in the manuscript.
false
true
false
dataset
10.1088_1361-665x_ad0394
doi10.1088_1361-665x_ad0394
Data availability statementNo new data were created or analysed in this study.
false
true
false
dataset
10.1371_journal.pone.0217459
doi10.1371_journal.pone.0217459
Data Availability Statement All relevant data are within the paper and its Supporting Information files.
false
true
false
dataset
10.2196_42978
doi10.2196_42978
Data Availability The data analyzed are not publicly available as they contain personal data but may be made available subject to an application and research proposal meeting the ethical and governance requirements of accessing the data.
false
true
false
dataset
10
doi10
Data Availability Statement: The data that support the findings of this study are available on request from the corresponding author. The data are not publicly available due to privacy restrictions. The code used to perform the 3-compartment model fits has been made publicly available at https: //github.com/pcorrado/Dynamic-Cardiac-FDG-Kinetic-Modeling (accessed on 21 March 2021).
false
true
true
dataset
10.1371_journal.pone.0240348
doi10.1371_journal.pone.0240348
Data Availability Statement All relevant data are available from GitHub (https://github.com/stccenter/COVID-19-Data/tree/master/US).
false
true
true
dataset
10.1073_pnas.2305556120
doi10.1073_pnas.2305556120
Data, Materials, and Software AvailabilitySource data for the single-molecule experiments are provided as Matlab “intervals” files that can be read and manipulated by the program imscroll (https://github.com/gellesbrandeis/CoSMoS_Analysis) (57). The source data are archived at doi: 10.5281/zenodo.7814499 (58).
false
true
true
dataset
10.1371_journal.pgen.1010931
doi10.1371_journal.pgen.1010931
Data AvailabilityAll the genetic data analyzed in the manuscripts were either simulated or published. The software used in this manuscript is publicly available at: https://uqrmaie1.github.io/admixtools/.
false
true
true
dataset
10.1186_s13058-023-01650-3
doi10.1186_s13058-023-01650-3
Availability of data and materials Data generated or analyzed during the study are available from the corresponding author by request.
false
true
false
dataset
10.1371_journal.pone.0255359
doi10.1371_journal.pone.0255359
Data Availability Statement All relevant data are within the manuscript and its Supporting Information files.
false
true
true
dataset
10.1371_journal.pone.0284699
doi10.1371_journal.pone.0284699
Data Availability Statement All relevant data are within the paper and its Supporting Information files.
false
true
false
dataset
10.1371_journal.pmed.1004362
doi10.1371_journal.pmed.1004362
Data Availability Statement: All relevant data are within the manuscript and its Supporting information files.
false
true
true
dataset
10.1371_journal.pmed.1004211
doi10.1371_journal.pmed.1004211
Data Availability Statement Data cannot be shared publicly because data privacy is subject to French, Cambodian, Senegalese and Malagasy regulations. Data are available from the Ethics Committee (contact via irb@pasteur.fr) for researchers who meet the criteria for access to confidential data.
false
true
false
dataset
10.1186_s40249-021-00834-3
doi10.1186_s40249-021-00834-3
Availability of data and materialsAll original (de-identified) data and materials are available upon request from the corresponding author.
false
true
false
dataset
10.1186_s12933-021-01314-6
doi10.1186_s12933-021-01314-6
Availability of data and materials Not applicable.
false
true
false
dataset
10.1088_1402-4896_ad1561
doi10.1088_1402-4896_ad1561
Data availability statementAll data that support the findings of this study are included within the article (and any supplementary files).
false
true
false
dataset
10.1038_s41598-023-36120-5
doi10.1038_s41598-023-36120-5
Data availabilityThe datasets generated and/or analysed during the current study belong to the Centre for Interdisciplinary Research in Animal Health (CIISA), Faculty of Veterinary Medicine, University of Lisbon. rDNA sequences obtained from all seven Mucor isolates were uploaded to the GenBank database, on 5 April 2022, with the accession numbers being provided in the Methods section. All data can be made available by requesting it from the Corresponding Author.
false
true
false
dataset
10.1371_journal.pstr.0000095
doi10.1371_journal.pstr.0000095
Data Availability Statement: The Fig 1 in the main text as well as in the supplementary information the Figure A in S1 Appendix and the Figures A to D in S2 Appendix are based on publicly available sources. The data is available through the references [144,151,154–158].
false
true
false
dataset
10.1371_journal.pone.0198463
doi10.1371_journal.pone.0198463
Data Availability Statement All FASTQ files containing the sequencing data for unsorted (control) and sorted cells from the screens analyzed in this study have been deposited in the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) with Study accession number SRP094861. All BAIMS pipeline software files are available through Github (https://github.com/RohatgiLab/BAIMS-Pipeline).
false
true
true
dataset
10.1080_13814788.2023.2223928
doi10.1080_13814788.2023.2223928
Data availability statementThe datasets generated and/or analysed during the current study are not publicly available beacause participants did not give permission for recordings or transcripts to be released to other researchers but are available from the corresponding author at reasonable request.
false
true
true
dataset
10.1093_molbev_msad085
doi10.1093_molbev_msad085
Data availability The computer code used for the analysis is available at https://github.com/jbloomlab/SARS2-mut-spectrum as a fully reproducible Snakemake pipeline (Mölder et al. 2021). Interactive versions of many of the plots rendered with Altair (VanderPlas et al. 2018) are at https://jbloomlab.github.io/SARS2-mut-spectrum/.
false
true
true
dataset
10.1038_s41467-023-39751-4
doi10.1038_s41467-023-39751-4
Data availabilityThe high-throughput sequencing data generated in this study have been deposited in the National Center for Biotechnology information Gene Expression Omnibus database under accession code GSE221679. The mass spectrometry proteomics data generated in this study have been deposited in the ProteomeXchange Consortium via the PRIDE71 partner repository under accession code PXD039991. The TAIR10 reference genome used in this study are available at The Arabidopsis Information Resource website [https://www.arabidopsis.org/download/index-auto.jsp%3Fdir%3D%252Fdownload_files%252FGenes%252FTAIR10_genome_release]. The Col-0 DNA methylation data used in this study for screenshots in Figs. 1b, 3c, 5e, 6e and Supplementary Fig. 6b are available in the National Center for Biotechnology information Gene Expression Omnibus database under accession code GSE124746. The DNA methylation data of the nrpe1 mutant and corresponding Col-0 control plants used in this study for Supplementary Fig. 8a–c and Supplementary Fig. 10b–d are available in the National Center for Biotechnology information Gene Expression Omnibus database under accession code GSE39901. The Col-0 DNA methylation data used in this study for Supplementary Fig. 12c are available in the National Center for Biotechnology information Gene Expression Omnibus database under accession code GSE54677. The Col-0 DNA methylation data used in this study for Supplementary Fig. 3a are available in the National Center for Biotechnology information Gene Expression Omnibus database under accession code GSE80302 . Source data are provided as a Source Data file. Source data are provided with this paper.Code availabilityThe customized code used in this study have been deposited in the GitHub repository [https://github.com/Zhenhuiz/MOM1_NC_2023].
false
true
true
dataset
10.1126_science.adf4197
doi10.1126_science.adf4197
Data and materials availability: For the core INO80 of the INO80-Hexasome complex (class 1, class 2 and class 3) and the core INO80 of the INO80-Nucleosome complex (class 1 and class 2), the coordinates are deposited in the Protein Data Bank with the accession codes 8ETS, 8ETU, 8ETW, 8EU9, and 8EUF; the cryo-EM density maps are deposited in the Electron Microscopy Data Bank (EMDB) with the accession codes EMD-28597, EMD-28599, EMD-28601, EMD-28609, and EMD-28613. For the hexasome of the INO80-Hexasome complex (class 1, class 2 and class 3) and the nucleosome of the INO80-Nucleosome complex (class 1 and class 2), the coordinates are deposited in the Protein Data Bank with the accession codes 8ETT, 8ETV, 8EU2, 8EUE, and 8EUJ; the cryo-EM density maps are deposited in the Electron Microscopy Data Bank (EMDB) with the accession codes EMD-28598, EMD-28600, EMD-28602, EMD-28612, and EMD-28614.
false
true
true
dataset
10.7554_elife.80923
doi10.7554_elife.80923
Data availabilityAll data have been uploaded to Dryad.The following dataset was generated:TurnerGC2023Flexible specificity of memory in Drosophila depends on a comparison between choicesDryad Digital Repository10.5061/dryad.8931zcrtc
false
true
false
dataset
10.1371_journal.pone.0283930
doi10.1371_journal.pone.0283930
Data Availability Statement All relevant data are within the paper and its Supporting Information files.
false
true
false
dataset
10.1371_journal.pone.0235872
doi10.1371_journal.pone.0235872
Data Availability Statement All relevant data are within the manuscript and its Supporting files.
false
true
true
dataset
10.1371_journal.pone.0283477
doi10.1371_journal.pone.0283477
Data Availability• The minimal data set used to formulate the conclusions of this study is fully available from a permanent archive (DOI: 10.5281/zenodo.7523470). • The full protocol for radioligand binding experiments is publicly archived at dx.doi.org/10.17504/protocols.io.ewov1oxe2lr2/v1. • The full protocol for receptor internalization measurement experiments is publicly archived at dx.doi.org/10.17504/protocols.io.x54v9dz91g3e/v1. • The full protocol for Calcium fluorimetry experiments is publicly archived at dx.doi.org/10.17504/protocols.io.3byl4jdmjlo5/v1.
false
true
false
dataset
10.1371_journal.pcbi.1009322
doi10.1371_journal.pcbi.1009322
Data Availability Statement Data Availability Statement. Data associated with all figures and tables presented in the manuscript is available online at: https://doi.org/10.6084/m9.figshare.8247860. Code availability. Code for reproducing the all figures and tables presented in the manuscript is available online at: https://doi.org/10.6084/m9.figshare.8247860.
false
true
true
dataset
10.1186_s12913-021-06331-5
doi10.1186_s12913-021-06331-5
Availability of data and materialsThe manuscript has data included as electronic supplementary material. More complete data is available from the authors upon request (contact: Marwân-al-Qays Bousmah. CEPED (UMR 196), Université de Paris, Campus Saint-Germain, 45 Rue des Saints-Pères, 75006 Paris, France. Tel.: + 33643521166. E-mail: marwan-al-qays.bousmah@ird.fr).
true
true
false
dataset
10.1088_1361-6501_ad1311
doi10.1088_1361-6501_ad1311
Data availability statementAll data that support the findings of this study are included within the article (and any supplementary files).
false
true
false
dataset
10.1088_1361-6420_ad0b26
doi10.1088_1361-6420_ad0b26
Data availability statementAll data that support the findings of this study are included within the article (and any supplementary files).
false
true
false
dataset
10.1371_journal.pone.0239340
doi10.1371_journal.pone.0239340
Data Availability Statement All relevant data are within the manuscript.
false
true
false
dataset
10.1186_s13054-023-04505-7
doi10.1186_s13054-023-04505-7
Availability of data and materials The datasets used and/or analyzed as well as R code used in the current study are available from the corresponding author upon reasonable request.
false
true
true
dataset
10.1371_journal.pone.0286055
doi10.1371_journal.pone.0286055
Data Availability Statement The data for this study is available and can be accessed by registering and logging into mics.unicef.org/surveys and downloading the dataset Ghana MICS6 SPSS Datasets.zip. The data for this study is contained in the child dataset labelled ch.sav and the following variables were used; HH1, HH2, BD2, BD3, BD4, BD5, BD6, BD7A, BD7A1, BD7B, BD7C, BD7C, BD7D1, BD7E, BD7E1, BD7X, BD8A, BD8A1, BD8B, BD8B1, BD8C, BD8D, BD8E, BD8F, BD8G, BD8H, BD8I, BD8J, BD8J1, BD8K, BD8L, BD8M, BD8N, BD8O, BD8P, BD8X, BD9, AN1, AN2, AN4, HH6, HH7, HL4, CAGE, CAGE_6, CAGE_11, CAGED, Stratum, melevel, caretakerdis, ethnicity, chweight, windex5 and PSU. The authors of this study had no special privileges in accessing these datasets which other interested researchers would not have.
false
true
true
dataset
10.1001_jamaneurol.2023.2363
doi10.1001_jamaneurol.2023.2363
Data Sharing Statement: See Supplement 4.
false
true
false
dataset
10.1016_j.str.2023.03.011
doi10.1016_j.str.2023.03.011
Data and code availability The unprocessed tilt series used for the data analysis are available upon request. Representative tomograms for Ana, Mega, and Halo GVs have been deposited in the Electron Microscopy Data Bank under accession codes EMDB: EMD-29922, EMD-29925, EMD-29924, EMD-29923. Subtomogram averages for native Ana and AnaS GV shell have been deposited in EMDB under accession codes EMD-29921 and EMD-29916, respectively. The integrative model of Ana GvpA/GvpC has been deposited in the Protein Data Bank (PDB): 8GBS. The XLMS data have been deposited to the ProteomeXchange Consortium with the dataset identifier PXD038631. The code for ultrasound data collection and processing is available upon request.
false
true
true
dataset
10.3390_ijms21144955
doi10.3390_ijms21144955
Availability of Data The raw sequences are available at [102] with the study accession number ERP122672.
false
true
false
dataset
10.1371_journal.pcbi.1011043
doi10.1371_journal.pcbi.1011043
Data Availability Statement All data and code are open access and are available in a public repository.(https://github.com/TK-21st/AntennalLobeLLY22).
false
true
true
dataset
10.1073_pnas.2304319120
doi10.1073_pnas.2304319120
Data, Materials, and Software AvailabilityAll data supporting the findings of this study are available within the Article, the SI Appendix Data and the NCBI Sequence Read Archive (SRA) repository (PRJNA902911) (83). All study data are included in the article and/or SI Appendix. Previously published data were used for this work (72).
true
true
true
dataset
10.1371_journal.pone.0231405
doi10.1371_journal.pone.0231405
Data Availability Statement All relevant data are within the manuscript and its Supporting Information files.
false
true
true
dataset
10.1088_1402-4896_ad081b
doi10.1088_1402-4896_ad081b
Data availability statementAll data that support the findings of this study are included within the article (and any supplementary files).
false
true
false
dataset
10.1039_d2sc04160j
doi10.1039_d2sc04160j
Data availability The data supporting this article are available in the ESI.†
false
true
false
dataset
10.1088_2053-1591_ad019a
doi10.1088_2053-1591_ad019a
Data availability statementThe data cannot be made publicly available upon publication because they are not available in a format that is sufficiently accessible or reusable by other researchers. The data that support the findings of this study are available upon reasonable request from the authors.
false
true
false
dataset
10
doi10
Data availability The data supporting the findings of this study are available from the corresponding author upon reasonable request. Structure factor amplitudes and coordinates for the crystal structures of MB-60 bound PreP and Aβ-bound PreP are deposited in the Protein Data Bank under accession number 4RPU and 4NGE, respectively. The 3D cryoEM density maps generated in this study is deposited in the Electron Microscopy Data Bank under accession codes EMD-22278 (Apo-PreP pC1 state), EMD-22279 (Apo-PreP pC2 state), EMD-22280 (Apo-PreP open state), EMD-22281 (Aβ-bound PreP), and EMD-22282 (CS27-bound PreP). The corresponding atomic coordinates are deposited in the Protein Data Bank under accession numbers 6XOS (Apo-PreP pC1 state), 6XOT (Apo-PreP pC2 state), 6XOU (Apo-PreP open state), 6XOV (Aβ-bound PreP), and 6XOW (CS27-bound PreP). EM data in the form of unprocessed micrographs is deposited in the Electron Microscopy Public Image Archive (EMPIAR) under accession number EMPIAR-10937. The tomogram shown in the figures is deposited to the EMD with the accession number EMD-25921. Raw tomography data is deposited to EMPIAR with the accession number EMPIAR-10929. The HDX-MS data are deposited in ProteomeXchange under the accession number PXD029542. SAXS data is deposited in the Small Angle Scattering Biological Data Bank (SASBDB) under accession codes SASDKK3 (Apo-PreP), SASDKL3 (MB60-PreP), SASDKM3 (CS27-PreP), and SASDKN3 (Aβ-PreP). Source data are provided with this paper.
false
true
true
dataset
10.1002_hbm.25192
doi10.1002_hbm.25192
DATA AVAILABILITY STATEMENT The MRE templates are made openly available (github.com/mechneurolab/mre134) to foster collaboration across research institutions and to support robust cross‐center comparisons.
false
true
true
dataset
10.1088_2631-8695_ad0928
doi10.1088_2631-8695_ad0928
Data availability statementThe data that support the findings of this study are openly available at the following URL/DOI: https://doi.org/https://vlsicad.ucsd.edu/GSRC/bookshelf/Slots/Partitioning/TESTCASES/netD20-29.tar.gz.
false
true
false
dataset
10.1371_journal.pntd.0011397
doi10.1371_journal.pntd.0011397
Data Availability Statement The authors confirm that all data underlying the findings are fully available without restriction. All relevant data are within the paper and its Supporting Information files.
false
true
false
dataset
10.1038_s41586-023-06376-y
doi10.1038_s41586-023-06376-y
Data availabilityUnprocessed gels and micrographs are provided in Supplementary Fig. 1. All materials associated with this study are also deposited on Zenodo (10.5281/zenodo.7083051). The accession codes for proteins presented in Extended Data Fig. 5b are provided in the corresponding legend and can be publicly accessed at Protein Data Bank with the following identifiers: 1Y7Y, 2B5A, 3G5G and 5WOQ. Other experimental data that support the findings of this study are available without restriction by request from the corresponding author. Source data are provided with this paper.Code availabilityCustom code used to search, extract and analyse phage genome databases based on user-defined features and custom code for smFISH analysis are deposited on Zenodo (10.5281/zenodo.7083051).
false
true
true
dataset
10.1371_journal.pbio.3001024
doi10.1371_journal.pbio.3001024
Data Availability Statement All relevant data are within the paper and its Supporting information files.
false
true
false
dataset
10.1371_journal.pgen.1011134
doi10.1371_journal.pgen.1011134
Data Availability Statement: All relevant data are within the manuscript and its Supporting Information files.
false
true
true
dataset
10
doi10
Availability of data and materials The data for this research study were collected under informed consent of the volunteers. Thus, access to the data will be subject to approval by the Vanderbilt University Medical Center Institutional Review Board.
true
true
false
dataset
10.1038_s41598-020-76091-5
doi10.1038_s41598-020-76091-5
Data availability The datasets generated during and/or analysed during the current study are available from the corresponding author on reasonable request.
false
true
false
dataset
10.1371_journal.pone.0233658
doi10.1371_journal.pone.0233658
Data Availability Statement All relevant data are within the paper and its Supporting Information files.
false
true
false
dataset
10.1371_journal.pbio.3002098
doi10.1371_journal.pbio.3002098
Data AvailabilityAll relevant data are within the paper and its Supporting Information files. In addition, the ChIC-seq data have been deposited. GEO accession number for the ChIC-seq data is GSE212936.
false
true
false
dataset
10.1186_s13018-021-02887-4
doi10.1186_s13018-021-02887-4
Availability of data and materialsThe datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request.
false
true
false
dataset
10.1038_s41598-020-64158-2
doi10.1038_s41598-020-64158-2
Data availabilityThe authors declare that all other data supporting the findings of this study are available within the article and its Supplementary Information Files.
true
true
false
dataset
10.1088_2515-7639_acd723
doi10.1088_2515-7639_acd723
Data availability statementAll data that support the findings of this study are included within the article (and any supplementary files).
false
true
false
dataset
10.1371_journal.pwat.0000184
doi10.1371_journal.pwat.0000184
Data Availability Statement: The gridMET datasets are cataloged at https://thredds.northwestknowledge.net/thredds/reacch_climate_MET_catalog.html. Land use data are available online through the California Natural Resources Agency available at https://data.cnra.ca.gov/dataset/statewide-crop-mapping. Crop coefficients are available online California Natural Resources Agency available at https://data.cnra.ca.gov/dataset/cal-simetaw-unit-values. Code for calculations used in this manuscript is available on Github (https://github.com/kdrechsler2/Ag-Tax) and can be run in Octave (open access) or MATLAB. Spatial analyses were restricted to California Department of Water Resources sub-basin boundaries denominated as Planning Areas 606, 607, 608, 609, 702, 703, 704, 705, 706, 708, 709, and 710 described here https://data.cnra.ca.gov/dataset/ca-gw-basin-boundary-descriptions. These largely comport with the 15 groundwater basins used by Escriva-Bou et al. 2023. Map data sources for Fig 1 are cropping from CNRA as above; California State Outline from TIGER 2016 United State Census Bureau; and Global base map from Esri, HERE, Garmin, FAO, NOAA, USGS, © OpenStreetMap contributors, and the GIS User Community.
true
true
true
dataset
10.1038_s41556-023-01178-w
doi10.1038_s41556-023-01178-w
Data availabilityLipidomics data generated in this study are included in Supplementary Tables 3 and 4. Source data are provided with this paper. All other data supporting the findings of this study are available from the corresponding authors on reasonable request. Requests will be handled according to the Harvard T. H. Chan School of Public Health policies regarding MTA and related matters.
false
true
false
dataset
10.1371_journal.pone.0223386
doi10.1371_journal.pone.0223386
Data Availability Statement All software files are available through gitHub. (https://github.com/ukalwa/nematode_egg_counting).
false
true
true
dataset
10.1038_s44172-022-00044-1
doi10.1038_s44172-022-00044-1
Data availability All imaging data (MRI and digital pathology) analyzed in this study is available upon request. Please contact Kaitlin Stouffer (kstouff4@jhmi.edu) for requests. Code availability Code used for training and applying UNET in tau tangle detection can be found here: https://github.com/twardlab/ADproject. Code for solving Projective LDDMM, building measure theoretic data representations, and resampling across scales can be found here: https://github.com/kstouff4/projective-lddmm.
false
true
true
dataset
10.1186_s12883-023-03144-3
doi10.1186_s12883-023-03144-3
Data Availability The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request.
false
true
false
dataset
10.1088_1361-6501_ad080a
doi10.1088_1361-6501_ad080a
Data availability statementThe data cannot be made publicly available upon publication because they are owned by a third party and the terms of use prevent public distribution. The data that support the findings of this study are available upon reasonable request from the corresponding author.
false
true
false
dataset
10.1038_s41467-023-38411-x
doi10.1038_s41467-023-38411-x
Data availabilityThe atomic coordinates and the electron microscopy maps have been deposited in the Protein Data Bank (PDB) under accession numbers 8IUK, 8IUL, and 8IUM and Electron Microscopy Data Bank (EMDB) accession number EMD-35724, EMD-35725, and EMD-35726 for the PGF2α–FP–Gq and the LTPA–FP–Gq and the TFPA–FP–Gq complex, respectively. Previously published structures can be accessed via accession codes: 7CX2; 7D7M; 6IIU; 6WHY; 7MBY; 6WHA; 7WKD. Source data are provided in this paper.
false
true
true
dataset
10.1371_journal.pone.0284104
doi10.1371_journal.pone.0284104
Data Availability Statement There are legal restrictions on sharing the data set used for this study, as the data are owned by Koa Health, the funder organisation, and was used under licence for the current study, and so are not publicly available. These restrictions are imposed by Koa Health. Data are however available from the authors upon reasonable request (with non-commercial intent) and with permission of Koa Health. A non-author contact information to which data requests may be sent is: Daniel Clarke, SVP of CyberSecurity at Koa Health, email: d.clarke@koahealth.com.
false
true
false
dataset
10.7554_elife.86556
doi10.7554_elife.86556
Data availability All data generated or analyzed during this study are included in the manuscript and supporting source data files. Source Data files have been provided for Figure 2, Figure 2 - Figure supplement 1, Figure 3, Figure 4, and Figure 4 - Figure supplement 1. Video Files have been provided for Figure 6 - Videos 1- 6.
false
true
true
dataset
10.1371_journal.pone.0228134
doi10.1371_journal.pone.0228134
Data Availability Statement All relevant data are within the paper and its Supporting Information files.
false
true
false
dataset
10.1371_journal.pgen.1010766
doi10.1371_journal.pgen.1010766
Data Availability Statement All relevant data are within the manuscript and its Supporting Information files.
false
true
true
dataset
10.1371_journal.pcbi.1009023
doi10.1371_journal.pcbi.1009023
Data Availability Statement All relevant data are within the manuscript and its supporting information. The code is now available on GitHub: https://github.com/noelenorris/ABC_proteome_allocation.
false
true
true
dataset
10.1371_journal.ppat.1008708
doi10.1371_journal.ppat.1008708
Data Availability Statement The sequencing data are posted in the NCBI Sequence Read Archive Database, accession number PRJNA630461.
false
true
false
dataset
10
doi10
DATA AVAILABILITY The datasets generated in the current study are available upon request from the corresponding authors.
false
true
false
dataset
10.3390_genes14061253
doi10.3390_genes14061253
Data Availability Statement The data presented are available on request from the corresponding author. The data are not publicly available due to ethical privacy.
false
true
false
dataset
10.1371_journal.pone.0285894
doi10.1371_journal.pone.0285894
Data Availability Statement All relevant data are within the manuscript and its Supporting Information files.
false
true
true
dataset
10.1371_journal.pone.0286321
doi10.1371_journal.pone.0286321
Data Availability Statement The data that support the findings are within the paper. In order to protect subjects' confidentiality and privacy, additional detailed data are only available on request. Interested researchers may contact the Academic Ethics Committee of Wuhan Sports University (2013028@whsu.edu.cn) directly.
false
true
false
dataset
10.1371_journal.pcbi.1011739
doi10.1371_journal.pcbi.1011739
Data Availability Statement: All data and computational code are available on OSF at https://osf.io/dw8ez/.
false
true
true
dataset
10.1021_jacs.3c02742
doi10.1021_jacs.3c02742
Accession CodesPDB id 8C3W contains the coordinates and associated structure factors of dnHEM1 that have been deposited in the Protein Data Bank (PDB) database.
true
true
false
dataset
10.3390_ijerph18052223
doi10.3390_ijerph18052223
Data Availability StatementThe data presented in this study are available on request from the corresponding author. The data are not publicly available due to privacy of participants.
false
true
false
dataset
10.3390_nu13103343
doi10.3390_nu13103343
Data Availability Statement The UK Biobank data are available through the UK Biobank Access Management System https://www.ukbiobank.ac.uk/ (accessed on 20 December 2020). We will return the derived data fields following UK Biobank policy; in due course, they will be available through the UK Biobank Access Management System.
true
true
false
dataset
10.1371_journal.pone.0224148
doi10.1371_journal.pone.0224148
Data Availability Statement The mass spectrometry proteomics data, including search, are available at the ProteomeXchange Consortium (www.proteomexchange.org) via the PRIDE partner repository with datasets identifiers PXD004970 and PXD004992.
false
true
false
dataset
10.3390_ijms241210237
doi10.3390_ijms241210237
Data Availability StatementAll data supporting our results is present in the paper.
false
true
false
dataset
10.1186_s12977-021-00568-y
doi10.1186_s12977-021-00568-y
Availability of data and materials Not applicable.
false
true
false
dataset
10.1371_journal.pcbi.1011149
doi10.1371_journal.pcbi.1011149
Data Availability Statement Code for replicating the analysis with synthetic data are available at https://github.com/sjfox/austin-disparities. Raw hospital admission and COVID-19 testing data are private due to their sensitive nature and will be made available upon reasonable request to Austin Public Health here; https://www.austintexas.gov/email/health.
false
true
true
dataset
10.1088_1361-6420_ad0fac
doi10.1088_1361-6420_ad0fac
Data availability statementAll data that support the findings of this study are included within the article (and any supplementary files).
false
true
false
dataset
10.1371_journal.pone.0241407
doi10.1371_journal.pone.0241407
Data Availability Statement All relevant data are within the paper and its Supporting Information files.
false
true
false
dataset
10.1371_journal.pgph.0001199
doi10.1371_journal.pgph.0001199
Data Availability Statement All data relevant to the paper has been presented within the paper itself (in the form of participant quotations). The datasets generated and/or analysed during the current study are not publicly available to protect participant confidentiality but are available in an anonymised form from the corresponding author on reasonable request. In the interest of maintaining long-term data accessibility, the University of the Western Cape Research Office can also be contacted for data requests at: research-office@uwc.ac.za.
false
true
false
dataset
10.1088_1361-6501_ad1289
doi10.1088_1361-6501_ad1289
Data availability statementThe data cannot be made publicly available upon publication because they contain commercially sensitive information. The data that support the findings of this study are available upon reasonable request from the authors.
false
true
false
dataset
10.1088_1361-6668_acf904
doi10.1088_1361-6668_acf904
Data availability statementAll data that support the findings of this study are included within the article (and any supplementary files).
false
true
false
dataset
10.1038_s41598-023-39102-9
doi10.1038_s41598-023-39102-9
Data availabilityThe RNAseq and ChIPseq datasets generated and analyzed in this study are available in the Gene Expression Omnibus (GEO) repository, accession numbers: GSE233301, GSE233302 and GSE233303.
false
true
true
dataset
10.1371_journal.ppat.1009980
doi10.1371_journal.ppat.1009980
Data Availability Statement All crystal structures are available from the RCSB protein structure database (accession numbers 7O9O, 7O9P, 7O9Q).
false
true
false
dataset
10.1016_j.neuroimage.2020.117112
doi10.1016_j.neuroimage.2020.117112
Data and code availability statement Data are freely available via nitrc.org. Code will be made available upon request.
false
true
true