Datasets:
dataesr
/
paragraph_classification_eval

Dataset card Data Studio Files
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dataset
10.1167_jov.23.6.7
doi10.1167_jov.23.6.7
The configurations and codes for this experiment are available in: Github github.com/Znasif/ColorCalibration, Google Colab colab.research.google.com/drive/1eHDXJPRn3HaeAqcdGbOKHVJSiNBXBCMv.
false
false
true
dataset
10.1371_journal.pmed.1003998
doi10.1371_journal.pmed.1003998
Data Availability Statement Data will be available to successful applications for clearly specified research projects following the MRC CTU at UCL standard data sharing processes: https://www.mrcctu.ucl.ac.uk/our-research/other-research-policy/data-sharing/ Discussion with the trial team is encouraged to determine whether the relevant data to support the application are available. Email to: mrcctu.datareleaserequest@ucl.ac.uk.
false
true
false
dataset
10.7554_elife.86784
doi10.7554_elife.86784
Data availabilityCryo-EM maps and atomic coordinates for the GC-C-Hsp90-Cdc37 complex have been deposited in the EMDB (EMD-29523) and PDB (8FX4). Material availability: The plasmids used in this study are uploaded in (Supplementary file 1).
false
true
true
dataset
10.1038_s41467-022-32646-w
doi10.1038_s41467-022-32646-w
Data availability The data that support the findings in this study are available from the corresponding authors upon reasonable request. Source data are provided with this paper. Code availability All code to reproduce the main simulation results can be found on GitHub (https://github.com/babaf/motor-adaptation-local-vs-input.git).
false
true
true
dataset
10.1371_journal.pone.0219089
doi10.1371_journal.pone.0219089
Data Availability Statement All relevant data are within the paper and its Supporting Information files.
false
true
false
dataset
10.1093_pnasnexus_pgad113
doi10.1093_pnasnexus_pgad113
Data availability The processed experimental files for all single-cell data sets used in this study are available on Zenodo at https://doi.org/10.5281/zenodo.7474099; Table 1 lists the Gene Expression Omnibus (GEO) accession numbers for each data set. The saved model weights for DELAY are available on Zenodo at https://doi.org/10.5281/zenodo.7474115. All experimental logs from this study are available at https://tensorboard.dev/experiment/RBVBetLMRDiEvO7sBl452A. We have provided an open-source implementation of DELAY in PyTorch with listed requirements and documentation at https://github.com/calebclayreagor/DELAY.
false
true
true
dataset
10.1371_journal.pone.0294847
doi10.1371_journal.pone.0294847
Data Availability Statement: All relevant data are within the paper and its Supporting information files.
false
true
false
dataset
10.1371_journal.pone.0243922
doi10.1371_journal.pone.0243922
Data Availability Statement All relevant data are within the paper and its Supporting Information files.
false
true
false
dataset
10.1017_jfm.2023.90
doi10.1017_jfm.2023.90
Data availability statement. The codes used in this study are openly available in GitHub at https://github. com/Maplenormandy/qg-edgeofchaos.
false
true
true
dataset
10.1371_journal.ppat.1011346
doi10.1371_journal.ppat.1011346
Data Availability Statement All relevant data are within the manuscript and its Supporting Information files.
false
true
true
dataset
10.1371_journal.pone.0269555
doi10.1371_journal.pone.0269555
Data Availability Statement All relevant data are within the paper and its Supporting Information files.
false
true
false
dataset
10
doi10
Data availability The microbial growth data generated in this study are provided in the Supplementary Table S2. Code availability The model code is deposited on GitHub (https://github.com/LevineLab/POMmodel) and citable using https://doi.org/10.5281/zenodo.6015020.
false
true
true
dataset
10.1073_pnas.1913292117
doi10.1073_pnas.1913292117
Data Availability Statement. All data discussed in the paper are available to readers through Harvard Dataverse, https://doi.org/10.7910/DVN/RFGT4S.
false
true
false
dataset
10.1371_journal.pntd.0010231
doi10.1371_journal.pntd.0010231
Data Availability Statement De-identified data is available online via the COR-NTD Research Dataverse: https://dataverse.unc.edu/dataset.xhtml?persistentId=doi:10.15139/S3/WOYRUW.
false
true
false
dataset
10.1371_journal.pmed.1002934
doi10.1371_journal.pmed.1002934
Data Availability Statement A minimal dataset and STATA DO file are included as Supporting information files to enable readers to replicate our analysis.
false
true
false
dataset
10.1088_1361-6552_ad001a
doi10.1088_1361-6552_ad001a
Data availability statementThe data cannot be made publicly available upon publication due to legal restrictions preventing unrestricted public distribution. The data that support the findings of this study are available upon reasonable request from the authors.
false
true
false
dataset
10.1371_journal.pone.0296688
doi10.1371_journal.pone.0296688
Data Availability Statement: All data files are available from the OpenBU database (https://hdl.handle.net/2144/45321).
false
true
false
dataset
10.1371_journal.pcbi.1007117
doi10.1371_journal.pcbi.1007117
Data Availability Statement All relevant data are within the manuscript and its Supporting Information files.
false
true
true
dataset
10.1088_1402-4896_ad16b7
doi10.1088_1402-4896_ad16b7
Data availability statementThe data that support the findings of this study are available upon reasonable request from the authors.
false
true
false
dataset
10.1016_j.isci.2021.102204
doi10.1016_j.isci.2021.102204
Data and code availability The data that support the findings of this study and sequences were submitted to the NCBI sequence read archive (SRA) under BioProject ID: PRJNA633714. Code for analysis is available on github repository: https://github.com/galud27.
false
true
true
dataset
10.1371_journal.pone.0253387
doi10.1371_journal.pone.0253387
Data Availability Statement Raw genome sequencing data for 23 strains are available from the NCBI with BioProject PRJNA683613.
false
true
false
dataset
10.1038_s41467-023-39652-6
doi10.1038_s41467-023-39652-6
Data availabilityAll demographic information and metadata used in this study for brain tissue analysis are available in the supplementary data files. The resulting data from all relevant limma, GSEA, and GSVA analyses for brain and blood are also included in the supplementary data files. Raw data generated from this study and gene expression values for brain RNA-seq data used in this study have been deposited in the GEO database under the accession code GSE205450 (link). Raw data and individual-level metadata used for blood transcriptome analysis in this study are available for downloading from PPMI (https://www.ppmi-info.org/access-data-specimens/download-data) through Laboratory of Neuro Imaging (LONI) Image Data Archive (IDA). For PDBP, data are available for downloading from AMP PD (https://www.amp-pd.org). To access individual-level data, users need to complete a data use agreement and submit an online application. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE80 partner repository with the dataset identifier PXD042154 (link). Source data are provided with this paper.Code availabilityCustom codes used in this study are available on GitHub and can be accessed at https://github.com/carynhale/PD_RNAseq.
false
true
true
dataset
10.1088_1402-4896_ad0a2d
doi10.1088_1402-4896_ad0a2d
Data availability statementAll data that support the findings of this study are included within the article (and any supplementary files).
false
true
false
dataset
10.1074_jbc.ra120.015632
doi10.1074_jbc.ra120.015632
Data availability All data discussed are presented in the article. Any analysis tools from the article will be shared upon request to the corre- sponding author: Christopher M. Yengo, cmy11@psu.edu.
false
true
false
dataset
10.1371_journal.ppat.1011456
doi10.1371_journal.ppat.1011456
Data Availability Statement All relevant data are within the paper and its Supporting Information files.
false
true
false
dataset
10.1007_s40993-022-00395-w
doi10.1007_s40993-022-00395-w
Data availability The datasets generated during and/or analysed during the current study are available in the GitHub repository, triangularModularCurves.
false
true
true
dataset
10.1111_disa.12560
doi10.1111_disa.12560
Data availability statement Research data are not shared.10
false
true
false
dataset
10.1186_s13015-023-00235-1
doi10.1186_s13015-023-00235-1
Availability of data and materialsAll data, scripts, and instructions for reproducing the results presented are available at https://github.com/matsengrp/gp-benchmark-1. Readers can independently reproduce the MrBayes posterior samples, branch length estimates on the DS datasets for both VBPI and GP, and rerun GP on the Makona dataset. We note that MrBayes posterior samples on each dataset required multiple days. The repository includes copies of the posterior samples for reproduction without requiring the full MrBayes runs. Additionally, the repository includes copies of the raw output after VBPI and GP estimation used for figures and results presented in this manuscript.
false
true
true
dataset
10.1371_journal.pone.0229102
doi10.1371_journal.pone.0229102
Data Availability Statement All relevant data are within the paper and its Supporting Information files.
false
true
false
dataset
10.3390_ijms241210379
doi10.3390_ijms241210379
Data Availability StatementData are available upon request.
false
true
false
dataset
10.3390_fluids7040122
doi10.3390_fluids7040122
Data Availability Statement: Not applicable.
false
true
false
dataset
10.1371_journal.pone.0246344
doi10.1371_journal.pone.0246344
Data Availability Statement The data is restricted as it concerns sensitive and potentially identifying patient information in a limited population within a single institute. Ethical consent was obtained from the METC Utrecht (Medical Ethical Committee Utrecht) and the need for informed consent was waived for this retrospective observational part of the PEARL study (METC research file NL72115.041.19 version 2, METC-protocol number 19/783, Netherlands trial register number NL8192). Thus patients did not provide informed consent for data to be made public in this manner. However, data can be shared with interested researchers upon request via direct contact with the principle investigators, or via Harm van Tinteren (contact via H.vanTinteren@prinsesmaximacentrum.nl).
false
true
false
dataset
10
doi10
Data availability statement No data are available. The data are pseudonymised according to national (Swedish) and European Union legislation, and cannot be anonymised and published in an open repository. Participants in the trial have not consented for their data to be shared with other researchers for research purposes.
false
true
false
dataset
10.1371_journal.pone.0216465
doi10.1371_journal.pone.0216465
Data Availability Statement All relevant data are within the manuscript and its Supporting Information files.
false
true
true
dataset
10.1371_journal.pone.0285980
doi10.1371_journal.pone.0285980
Data Availability Statement All relevant data are within the paper and its Supporting information files.
false
true
false
dataset
10
doi10
Data availability Since the datasets used in this work contain patient data, these cannot be made generally available to the public due to privacy concerns. Code availability The code for the AngioNet architecture and examples of synthetic angiograms are available at https://github. com/kritiyer/AngioNet. This code is licensed under a Polyform Noncommercial license.
false
true
true
dataset
10.1038_s41422-023-00790-7
doi10.1038_s41422-023-00790-7
Data availability All the data required for the understanding and critical evaluation of this study are provided in the manuscript and supplementary materials. RNA-seq and 16S rDNA sequencing data are available from the SRA database using accession numbers PRJNA645758 and PRJNA645764, respectively.
false
true
true
dataset
10.1371_journal.pone.0251901
doi10.1371_journal.pone.0251901
Data Availability Statement All relevant data are within the paper and its Supporting Information files.
false
true
false
dataset
10.1038_s41564-023-01447-2
doi10.1038_s41564-023-01447-2
Data availabilityThe protein identification number in the NCBI database for each enzyme characterized is as follows: L. crispatus PulA (EEU28204.2), L. iners PulA (EFQ51965.1), G. vaginalis PulA (EPI56559.1), M. mulieris PulA (EEZ90738.1), P. bivia PulA (WP_061450340.1), P. bivia GH13 (WP_036862728.1). The L. crispatus C0176A1 (PulA−) genome can be found under accession number JAEDCG000000000. The metagenomic and metatranscriptomic datasets used in this study can be found under Bioproject PRJNA797778. The proteomics data from this study can be accessed in the PRIDE database using accession code PXD042917. Protein domain annotations were from the Pfam and CAZy databases. All data that support the findings of this study are available in a data repository at synapse.org and can be accessed at https://www.synapse.org/#!Synapse:syn51422003. Source data are provided with this paper.
false
true
true
dataset
10.1371_journal.pone.0227132
doi10.1371_journal.pone.0227132
Data Availability Statement All relevant data are within the paper and its Supporting Information files.
false
true
false
dataset
10.1371_journal.pone.0247289
doi10.1371_journal.pone.0247289
Data Availability Statement All relevant data are within the paper and its Supporting information files.
false
true
false
dataset
10.1186_s40168-023-01532-y
doi10.1186_s40168-023-01532-y
Availability of data and materials The sequencing data were deposited in the SRA database under the accession number PRJNA828340 and PRJNA906637.
false
true
false
dataset
10.1186_s12913-019-3983-7
doi10.1186_s12913-019-3983-7
Availability of data and materialsThe data that support the findings of this study are available from Centers for Medicare & Medicaid Services. Medicare Current Beneficiary Survey (MCBS). https://www.cms.gov/Research-Statistics-Data-and-Systems/Research/MCBS/.
false
true
false
dataset
10.1002_advs.202102414
doi10.1002_advs.202102414
Data Availability Statement The data that support the findings of this study are available from the corresponding author upon reasonable request.
false
true
false
dataset
10.1186_s12939-020-01197-1
doi10.1186_s12939-020-01197-1
Availability of data and materialsThe data used in this study are available at http://ghdx.healthdata.org/record/bolivia-health-and-nutrition-assessment-survey-2012
false
true
false
dataset
10.1371_journal.ppat.1011163
doi10.1371_journal.ppat.1011163
Data Availability All mass spectrometry data have been deposited on the Pride proteome exchange public repository. Project Name: KSHV ORF18 TurboID in human iSLK cell lines Project accession: PXD039694 Project DOI: 10.6019/PXD039694.
true
true
false
dataset
10.1186_s12889-023-15780-y
doi10.1186_s12889-023-15780-y
Data Availability Due to the nature of this research, participants of this study did not agree for their data to be shared publicly (as participants individual privacy could be compromised), so supporting data is not available. Please contact liz.saunders@research.uwa.edu.au for further details.
false
true
false
dataset
10.1371_journal.pclm.0000339
doi10.1371_journal.pclm.0000339
Data Availability Statement: Data are publicly available for download from the following refereed sources. 1. Data on GDP Percapita, LDC and Life Expectancy: World Bank. World Development Indicators 2023. The World Bank; 2023 March 01. https://databank.worldbank.org/source/world-development-indicators 2. Data on Temperature and Rainfall. World Bank. The Climate Change Knowledge Portal (CCKP) 2023. The World Bank; 2023 March 30. https://climateknowledgeportal.worldbank.org/.
false
true
false
dataset
10.1016_j.molcel.2023.02.026
doi10.1016_j.molcel.2023.02.026
Data and code availability Genomics data (CUT&Tag, ATAC-seq, and RNA-seq) have been deposited at GEO under accession number GSE212357 and are publicly available as of the date of publication. This paper also analyzes existing, publicly available data (GSE181062 and GSE181064 key resources table). Unprocessed blot images have been deposited in Mendeley (Mendeley data: https://doi.org/10.17632/7msw2d62r6.1). See Key Resources Table for details.
false
true
true
dataset
10.1017_s2633903x23000028
doi10.1017_s2633903x23000028
Data Availability Statement. Replication data and code can be found at https://github.com/yunpeng-shi/fast-cryoEM-PCA.
false
true
true
dataset
10.1021_acssynbio.2c00587
doi10.1021_acssynbio.2c00587
Data Availability Statement All data generated or analyzed during this study are included in the manuscript and supporting files.
false
true
true
dataset
10.1371_journal.pone.0215898
doi10.1371_journal.pone.0215898
Data Availability Statement The Boston University Medical Campus and Boston Medical Center Institutional Review Board concurs with the rationale for restricting the de-identified data due to ethical concerns. Although the data could be de-identified, the unique subject population that was enrolled in the study and the relatively small sample size indicate that there would be a potential large risk of deductive disclosure. The data itself includes responses to questions that ask about sensitive topics such as work and relationships (both family and romantic). Given the risk for deductive disclosure, data is available upon request by contacting (BU/BMC IRB’s email: medirb@bu.edu).
false
true
false
dataset
10.3390_ijms24119305
doi10.3390_ijms24119305
Data Availability Statement All data are available in the main manuscript or supplementary materials and additional data and reagents can be obtained by written request to rsh@uthscsa.edu.
false
true
true
dataset
10
doi10
Availability of data and materials The datasets supporting the conclusions of this article are available in the JGI Integrated Microbial Genomes & Microbiomes (IMG/M) database repository, https://img.jgi.doe.gov/cgi-bin/m/main.cgi. List of permalinks pointing to JGI- IMG webpages for each SAG generated for this study is included within addi- tional tables of this article (Supp. Table 2). In addition to provide assembled sequences, all metadata (samples location and depth of isolation, sequencing procedure and technology, bioinformatic processing and quality control, and genomic statistics) associated with SAGs are available there. Additional genomes used to build pangenome have been retrieved from NCBI, ftp://ftp. ncbi.nlm.nih.gov/genomes/genbank/bacteria/. Metagenome and metatran- scriptome data are available in the NCBI SRA projects PRJNA352737 and PRJNA358725. All other data products associated with this study are accessible online: population genomes, https://doi.org/10.6084/m9.figshare.14573751. v1, and Anvi’o databases, https://doi.org/10.6084/m9.figshare.14573046.v1.
false
true
true
dataset
10.1088_1361-6498_ad115a
doi10.1088_1361-6498_ad115a
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
10.3390_s21248442
doi10.3390_s21248442
Data Availability StatementThe datasets generated and analyzed during the current study are not publicly available due to the general data protection regulations but will be shared on reasonable request using a safe platform by the corresponding author.
false
true
false
dataset
10.1088_1367-2630_ac836b
doi10.1088_1367-2630_ac836b
Data availability statement No new data were created or analysed in this study.
false
true
false
dataset
10.1007_s00127-021-02039-3
doi10.1007_s00127-021-02039-3
Availability of data and material The datasets generated and/or analyzed for the current study are not publicly available due to legal and ethical regulations, but may be made available upon request to data management of the Generation R Study (datamanagementgenr@erasmusmc.nl), in accordance with the local, national, and European Union regulations.
false
true
false
dataset
10.1038_s41598-020-78032-8
doi10.1038_s41598-020-78032-8
Data availability The data that support the findings of this study are available on request from the corresponding author.
false
true
false
dataset
10.1021_acssynbio.3c00148
doi10.1021_acssynbio.3c00148
Data Availability StatementAll data is included in the Supporting Information and data file.
false
true
false
dataset
10
doi10
Data Availability Statement: The data presented in this study are available on request from the corresponding author. The data are not publicly available due to privacy.
false
true
false
dataset
10.1371_journal.pwat.0000226
doi10.1371_journal.pwat.0000226
Data Availability Statement: The in-situ data used in this study was acquired from the following open-access publication: https://www.sciencedirect.com/science/article/pii/S2352340923002664?via%3Dihub This data can be downloaded directly from the following public repository: https://dataverse.ird.fr/dataset.xhtml?persistentId=doi:10.23708/NKQDNB.
false
true
false
dataset
10.1016_j.isci.2023.106601
doi10.1016_j.isci.2023.106601
Data and code availability Additional Supplemental Items are available from Mendeley Data at https://data.mendeley.com/datasets/h6rn55h86x/1. All data reported in this paper will be shared by the lead contact upon request. This paper does not report original code. Any additional information required to reanalyze the data reported in this paper is available from the lead contact upon request.
false
true
true
dataset
10
doi10
Data Availability Statement: The full reconstruction of Bombus thick filament as well as the segmented flightin density have been deposited in EMDB under accession code EMD-28208. The atomic model of Bombus flightin is deposited in the PDB under the entry 8EW5.
false
true
true
dataset
10.1038_s41598-020-74100-1
doi10.1038_s41598-020-74100-1
Data availability Te data that support the fndings of this study are available in the Gene Expression Omnibus (GEO) database at: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?token=epajoakqppkvbub&acc=GSE85307 reference number GSE85307. Additional data were derived from the following resources available in the public domain of GEO database: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE9984, https://www.ncbi.nlm.nih.gov/geo/ query/acc.cgi?acc=GSE75010, and https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE142974.
false
true
true
dataset
10.1088_2752-664x_ad04e3
doi10.1088_2752-664x_ad04e3
Data availability statementThe data that support the findings of this study are openly available at the following URL/DOI: https://gcrg.sdsu.edu/.
false
true
false
dataset
10
doi10
Data availability POM, hydrography, and metagenomes from Bio-GO-SHIP cruises used in this study are publicly available28,73. Nutrient stress data of phytoplankton can be accessed from the original publication cited in the main text31. GLODAP version2.2016b data is publicly available (https://doi.org/10.5194/essd-8-297-2016). The model output from the CEMS2 Large Ensemble Simulation is available here (https://doi.org/10.26024/kgmp-c556). Code availability All codes (data manipulation, analyses, figures, and tables) can be downloaded from the GitHub repository https://github.com/tanio003/CNPGlobal_paper_repo/tree/ CommsEarthEnv. When using the data or code from this project, please cite https://doi. org/10.5281/zenodo.7076407.
false
true
true
dataset
10
doi10
Availability of data and materials The single-cell raw and processed data generated in this study is publicly available on GEO, with accession number GSE180697 [66]. The codes generated during this study are publicly available at https://github.com/SDTCCPMed/DigiTwin_framework [67]. The datasets used for reference construction are publicly available in BioGPS (biogps.org/downloads/), Human U133A/ GNF1H Gene Atlas [34], and upon request from the authors of [20]. The bulk cell-profling datasets for meta-analysis can be found on GEO, GSE75214 [40], and GSE32924 [41]. The DEGs based on single-cell data for meta-analysis were downloaded from [46], and the processed single cell data for meta-analysis can be found on EMBL-EBI, E-MTAB-8901 [47].
false
true
true
dataset
10.1186_s13054-020-03210-z
doi10.1186_s13054-020-03210-z
Availability of data and materialsNot applicable.
false
true
false
dataset
10.1371_journal.pone.0246437
doi10.1371_journal.pone.0246437
Data Availability Statement All relevant data are within the manuscript and its Supporting information files.
false
true
true
dataset
10.1088_1361-6668_acff24
doi10.1088_1361-6668_acff24
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_s41598-023-33920-7
doi10.1038_s41598-023-33920-7
Data availabilityThe datasets used in this study were obtained from two public datasets: the Autism Brain Imaging Data Exchange II (ABIDE-II) and Attention Deficit Hyperactivity Disorder (ADHD-200); and from two datasets that required authorization: Adolescent Brain Cognitive Development (ABCD) and Brazilian High-Risk Cohort Study (BHRCS). ADHD-200 and ABIDE-II can be downloaded from the NeuroImaging Tools & Resource Collaboratory Image Repository, after free registering and login, from the following download links, respectively: https://www.nitrc.org/ir/app/template/XDATScreen_report_xnat_projectData.vm/search_element/xnat:projectData/search_field/xnat:projectData.ID/search_value/adhd_200, and https://www.nitrc.org/ir/app/template/XDATScreen_report_xnat_projectData.vm/search_element/xnat:projectData/search_field/xnat:projectData.ID/search_value/ABIDE_II. For ABCD and BHRCS datasets, application and consortium approval of an NDA form are required. The data were collected and made publicly available according to the guidelines, and approval was provided by the local ethics committee for each project. Detailed information on these datasets and their acquisition parameters can be retrieved from ABIDE-II (http://fcon_1000.projects.nitrc.org/indi/abide/abide_II.html), ADHD-200 (http://fcon_1000.projects.nitrc.org/indi/adhd200/), ABCD (https://nda.nih.gov/abcd), and BHRCS (https://osf.io/ktz5h/wiki/home/).
true
true
true
dataset
10.1073_pnas.2221103120
doi10.1073_pnas.2221103120
Data, Materials, and Software Availability 3D structure data have been deposited in [Protein Data Bank (PDB)] (8FBY and 8FCF) for PLVAP CC1 crystal forms I and II, respectively (92, 93).
false
true
true
dataset
10.1371_journal.pdig.0000467
doi10.1371_journal.pdig.0000467
Data Availability Statement: The dataset of unimpaired gait is available from http://bytom.pja.edu.pl/projekty/hm-gpjatk. The stroke and PD datasets contain videos with identifiable information and are therefore not available. Code for our workflow is available at https://github.com/janstenum/GaitAnalysis-PoseEstimation/tree/Multiple-Perspectives.
false
true
true
dataset
10.1371_journal.pone.0281837
doi10.1371_journal.pone.0281837
Data Availability Statement The data underlying the results presented in the study are available from http://opendata.camara.cl https://github.com/dimoralesb/rollcall_votes_chile
false
true
true
dataset
10.7554_elife.85492
doi10.7554_elife.85492
Data availabilityThe new software presented in this manuscript (the ADMIXTOOLS 2 R package) is freely available at https://github.com/uqrmaie1/admixtools (copy archived at Maier et al., 2022), along with a detailed manual at https://uqrmaie1.github.io/admixtools/. The ancient human genome newly reported in this manuscript (Supplementary file 2) is freely available at the European Nucleotide Archive in the form of an alignment of reads to the hg19 human reference genome (project accession number PRJEB58199). Published software packages re-used in this manuscript are available at: https://bitbucket.org/nygcresearch/treemix/src/master/ (TreeMix, Pickrell and Pritchard, 2012) and at https://github.com/DReichLab/AdmixTools (David Reich Lab, 2023, ADMIXTOOLS, Patterson et al., 2012). Published archaeogenetic datasets re-analyzed in this manuscript were kindly shared by the corresponding authors of the following publications upon our requests: Bergström et al., 2020; Lazaridis et al., 2014; Librado et al., 2021; Lipson et al., 2020b; Shinde et al., 2019; Sikora et al., 2019; Wang et al., 2021; Hajdinjak et al., 2021. Various statistics for these re-used datasets are summarized in Supplementary file 1.
false
true
true
dataset
10.1186_s12917-019-1890-0
doi10.1186_s12917-019-1890-0
Availability of data and materialsThe datasets analyzed during the current study are not publicly available due to sharing agreements. These were necessary for the transfer of sequences and data from the diagnostic laboratories to the LEMP, to analyze data and report results.
false
true
false
dataset
10.3390_molecules28020474
doi10.3390_molecules28020474
Data Availability Statement: Not applicable.
false
true
false
dataset
10.1371_journal.pone.0238693
doi10.1371_journal.pone.0238693
Data Availability Statement All relevant data are within the manuscript and its Supporting Information files.
false
true
true
dataset
10.1371_journal.pone.0237815
doi10.1371_journal.pone.0237815
Data Availability Statement All relevant data are within the manuscript and its Supporting Information file.
false
true
true
dataset
10.1371_journal.pntd.0008605
doi10.1371_journal.pntd.0008605
Data Availability Statement All relevant data are within the manuscript and its Supporting Information files.
false
true
true
dataset
10.1016_j.celrep.2023.112412
doi10.1016_j.celrep.2023.112412
Data and code availability This paper analyzes existing, publicly available data. The accession numbers for the datasets are listed in the key resources table. All original code has been deposited at https://github.com/nitzanlab/pareto_interactions_py and https://github.com/miriadler/pareto_interactions and is publicly available as of the date of publication. DOIs are listed in the key resources table. All data files used in this paper are deposited at https://zenodo.org/record/7569404#.ZBwyr-xByWB. Any additional information required to reanalyze the data reported in this paper is available from the lead contact upon request.
false
true
true
dataset
10.1155_2020_3938640
doi10.1155_2020_3938640
Data AvailabilityThe clinical data used to support the findings of this study are included within the article.
false
true
false
dataset
10.7554_elife.86852
doi10.7554_elife.86852
Data availability All data and code are available in the GitHub repository at https://github.com/jbloomlab/barcoded_flu_ pdmH1N1, copy archived at Bloom, 2023. The analysis can be reproduced by running the Snakemake pipeline and final analysis notebook according to the instructions at https://github.com/jbloomlab/ barcoded_flu_pdmH1N1/blob/main/README.md. Key output files are hosted at the following loca- tions. All raw sequencing files are available on GEO under the accession number GSE214938. The single-cell RNA sequencing cell-gene matrix is also available on GEO under the accession number GSE214938. An integrated CSV produced by the Snakemake pipeline with cell barcodes, viral gene expression, viral genome sequence, and viral barcode frequencies is available at https://github.com/ jbloomlab/barcoded_flu_pdmH1N1/blob/main/results/viral_fastq10x/all_samples.csv. The final CSV file with progeny contribution measurements, viral gene expression, and viral mutations (when avail- able) for the infected cells with complete measurements is available at https://github.com/jbloomlab/ barcoded_flu_pdmH1N1/blob/main/results/viral_fastq10x/all_samples_complete_measurements_ cells_data.csv. The following dataset was generated: Author(s) Year Dataset title Dataset URL Database and Identifier Bacsik DJ, Dadonaite B, Butler A, Greaney AJ, Heaton NS, Bloom JD 2022 Influenza virus transcription and progeny production are poorly correlated in single cells https://www.ncbi. nlm.nih.gov/geo/ query/acc.cgi?acc= GSE214938 NCBI Gene Expression Omnibus, GSE214938
false
true
true
dataset
10.1038_s41467-023-37169-6
doi10.1038_s41467-023-37169-6
Data availability The data that support this study are available from the corresponding authors upon request. Cryo-EM maps have been deposited in the Electron Microscopy Data Bank 9EMDB under accession codes EMD-27432 (LepRD1–D7 receptor complex), EMD-27433 (LepRD3–D7 receptor complex), and EMD-27434 (LepR focused interaction). Atomic coordinates have been deposited in the Protein Data Bank (PDB) under accession codes 8DH8 (LepRD1–D7 receptor complex), 8DH9 (LepRD3–D7 receptor complex), and 8DHA (LepR focused interaction). Source data underling Fig. 4b, d, f, g, i, and Supplementary Fig. 8b–e are provided in the Source Data File. Source data are provided with this paper.
false
true
true
dataset
10.1371_journal.pone.0297957
doi10.1371_journal.pone.0297957
Data Availability Statement: All relevant data are within the manuscript.
false
true
false
dataset
10.1073_pnas.2304730120
doi10.1073_pnas.2304730120
Data, Materials, and Software AvailabilityAll study data are included in the article and/or SI Appendix.
true
true
true
dataset
10.1186_s12859-023-05306-z
doi10.1186_s12859-023-05306-z
Availability of data and materials All data analyzed during this study are included in these published articles [10, 11, 18] and their supplementary information files. The BBUM fitting and significance-calling algorithm is available as an R package at https://github.com/wyppeter/bbum. Other code used for this work, including data analyses, simulations, and data visualization, is available at https://github.com/wyppeter/BBUM-TDMD_2022.
false
true
true
dataset
10.1371_journal.pone.0247551
doi10.1371_journal.pone.0247551
Data Availability Statement All relevant data are within the manuscript and its Supporting Information files.
false
true
true
dataset
10.3390_biom13060949
doi10.3390_biom13060949
Data Availability Statement This study did not report any data not shown in the manuscript.
false
true
false
dataset
10
doi10
Data availability The sequencing data have been uploaded to SRA (Sequence Read Archive) under BioProject accession PRJNA63980
false
true
false
dataset
10.1186_s12872-020-01654-3
doi10.1186_s12872-020-01654-3
Availability of data and materials Due to restrictions related to Danish law and protecting patient privacy, the combined set of data used in this study can only be made available through a trusted third party, Statistics Denmark. This state organisation holds the data used for this study. University-based Danish scientific organisations can be authorized to work with data within Statistics Denmark and such organisation can provide access to individual scientists inside and outside of Denmark. Data are available upon request to authorized scientists by contacting Statistics Denmark: http://www.dst.dk/en/OmDS/organisation/TelefonbogOrg.aspx?kontor=13&tlfbogsort=sektion or the Danish Data Protection Agency: https://www.datatilsynet.dk/english/the-danish-data-protection-agency/contact/. More information regarding data access is available at https://www.dst.dk/en/TilSalg/Forskningsservice.
false
true
false
dataset
10.1371_journal.pone.0285166
doi10.1371_journal.pone.0285166
Data Availability Statement All data are included in this article, with the exception of raw RNAseq data, which can be accessed in the NCBI Genome Expression Omnibus public database through GEO Series accession no. GSE150805.
false
true
false
dataset
10.1038_s41598-021-87992-4
doi10.1038_s41598-021-87992-4
Data availability The datasets generated during and/or analyzed during the current study are not publicly available due to funding agency agreement and intellectual properties but are available from the corresponding author on reasonable request with permission of funding agency.
true
true
false
dataset
10.1371_journal.pgen.1011178
doi10.1371_journal.pgen.1011178
Data Availability Statement: Bacterial small RNA sequencing data are available at NCBI Bioproject PRJNA1062118. The numerical data for all the plots in all the figures have been included in S1 Data.
false
true
false
dataset
10.1038_s41467-023-38934-3
doi10.1038_s41467-023-38934-3
Data availability The 3D cryo-EM density maps generated in this study have been deposited in the Electron Microscopy Data Bank (EMDB) under accession numbers EMD-28577 (DGAT1-T863 complex) and EMD-28594 (DGAT1-DGAT1IN1 complex). The coordinates have been deposited into the Protein Data Bank (PDB) with accession numbers 8ESM (T863 bound) and 8ETM (DGAT1IN1 bound). This study also cited the published structure of human DGAT1 6VYI and EMD-21461, the oleoyl CoA bound state 6VZ1 and EMD-21481, and the human ACAT1 structure 6VUM and EMD-21390. Source data are provided in this paper.
false
true
true
dataset
10.1038_s41598-020-69969-x
doi10.1038_s41598-020-69969-x
Data availability The datasets generated and analysed during the current study are available from the corresponding author on reasonable request.
false
true
false
dataset
10.1088_1361-6382_acfd00
doi10.1088_1361-6382_acfd00
Data availability statementThe data that support the findings of this study are available upon reasonable request from the authors.
false
true
false
dataset
10.1038_s41467-023-37702-7
doi10.1038_s41467-023-37702-7
Data availability The data that support this study are available from the corresponding authors upon request. Cryo-EM maps have been deposited in the Electron Microscopy Data Base (EMDB) under accession codes EMD-27148 (Merged Lysolipid1A,2B,3C), EMD-27149 (Ligand-free), EMD-27150 (Lysolipid1A), EMD-27151 (Lysolipid1B), EMD-27152 (Lysolipid2B), and EMD-27153 (Lysolipid3C). The atomic coordinates have been deposited in the Protein Data Bank (PDB) under accession codes 8D2S (Merged Lysolipid1A,2B,3C), 8D2T (Ligand-free), 8D2U (Lysolipid1A), 8D2V (Lysolipid1B), 8D2W (Lysolipid2B), and 8D2X (Lysolipid3C).
false
true
true
dataset
10.1371_journal.pone.0263296
doi10.1371_journal.pone.0263296
Data Availability Statement All relevant data are within the paper and its Supporting information files. The whole trajectory files generated in the MD simulation have been deposited in the Zenodo server under digital object identifier: 10.5281/zenodo.5533040.
false
true
true