DataSeer/das-extraction-raw-labels · Datasets at Hugging Face

10.1038_s41467-023-38867-x.pdf

Data availabilityComplete genome sequences for the viral isolates cultured from nasal swabs (BA.1 and BA.1.23) are available in GenBank (accession numbers ON220548, ON220539, ON196014, ON193425, ON220529, ON220571, ON220533, ON934538, ON934577, ON934030, ON934607, ON854465, ON619382). RNA-seq data are available in the Sequence Read Archive (SRA), submission SUB12865927 under BioProject number PRJNA623586 (BioSample accession numbers SAMN33273632 - SAMN33273655). Datasets generated and/or analysed during the current study are appended as supplementary data. Source data are provided with this paper.Code availabilityThe vRAPID pipeline was developed for reference-based viral genome assembly of short-read sequencing data. The custom code is at vRAPID [https://zenodo.org/record/7829342].

Data availability Complete genome sequences for the viral isolates cultured from nasal swabs (BA.1 and BA.1.23) are available in GenBank (accession numbers ON220548, ON220539, ON196014, ON193425, ON220529, ON220571, ON220533, ON934538, ON934577, ON934030, ON934607, ON854465, ON619382 ). RNA-seq data are available in the Sequence Read Archive (SRA), submission SUB12865927 under BioProject number PRJNA623586 (BioSample accession numbers SAMN33273632 -SAMN33273655). Datasets generated and/or analysed during the current study are appended as supplementary data. Source data are provided with this paper. Code availability The vRAPID pipeline was developed for reference-based viral genome assembly of short-read sequencing data. The custom code is at vRAPID [ https://zenodo.org/record/7829342 ].

10.1126_sciadv.adi3088.pdf

Data and materials availability: All data needed to evaluate the conclusions in the paper are present in the paper and/or the Supplementary Materials. The data for this study have been deposited in the database: https://doi.org/10.5281/zenodo.8161407.

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10.3390_s22093318.pdf

Data Availability StatementNot applicable.

Data Availability Statement: Not applicable.

10.1371_journal.pone.0255090.pdf

Data Availability Statement All relevant data are within the paper and its Supporting Information files.

All relevant data are within the paper and its Supporting Information files.

10.1371_journal.pone.0261838.pdf

Data Availability Statement All relevant data are within the manuscript and its Supporting information files.

All relevant data are within the manuscript and its Supporting information files.

10.1103_physrevd.107.034506.pdf

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10.1016_j.celrep.2023.112621.pdf

Data and code availability Cryo-EM maps and atomic models have been deposited at the Electron Microscopy DataBank and the Protein DataBank under the following accession codes: EMD: EMD-26058 and PDB: 7TPK (SARS-CoV-2 E406W RBD) and EMD: EMD-26056 and PDB: 7TPI (SARS-CoV-2 E406W Ectodomain). 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.

Materials availability Plasmids generated in this study will be available upon request with a completed Materials Transfer Agreement. Data and code availability d Cryo-EM maps and atomic models have been deposited at the Electron Microscopy DataBank and the Protein DataBank under the following accession codes: EMD: EMD-26058 and PDB: 7TPK (SARS-CoV-2 E406W RBD) and EMD: EMD-26056 and PDB: 7TPI (SARS-CoV-2 E406W Ectodomain). d This paper does not report original code. d Any additional information required to reanalyze the data reported in this paper is available from the lead contact upon request.

10.1186_s13071-019-3601-x.pdf

Availability of data and materials All data generated or analysed during this study are included in this published article. The datasets used and/or analysed during the present study available from the corresponding author upon reasonable request.

10.31557_APJCP.2020.21.1.157.pdf

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10.1371_journal.pgph.0001413.pdf

Data Availability Statement The data supporting the results of this study are available within the article and the accompanying Supplementary material. The metadata described in this article are available in the Open Science Framework at http://osf.io/xec69.

The data supporting the results of this study are available within the article and the accompanying Supplementary material. The metadata described in this article are available in the Open Science Framework at http:// osf.io/xec69 .

10.1002_acn3.51270.pdf

Data availability statement Deidentified data related to this study will be made available from the corresponding author upon request.

10.1038_s41467-023-40788-8.pdf

Data availabilityThe NCBI non-redundant protein sequences (nr) database can be found at https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastp&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome. All other data supporting the findings of this study are available within the paper and its Supplementary Information. Source data are provided with this paper.

Data availability The NCBI non-redundant protein sequences (nr) database can be found at https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM= blastp&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome . All other data supporting the findings of this study are available within the paper and its Supplementary Information. Source data are provided with this paper.

10.1088_1402-4896_ad0f84.pdf

Data availability statementNo new data were created or analysed in this study.

Data availability statement No new data were created or analysed in this study.

10.1186_s12889-023-15729-1.pdf

Availability of data and materials The datasets used during the current study are available from the corresponding author on reasonable request.

10.3390/antiox9030263

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10.1088_1748-9326_ad13b7.pdf

Data availability statementThe NSIDC ice age version 4.1 (V4.1) data is freely distributed at https://nsidc.org/data/nsidc-0611/versions/4. The NSIDC ice motion V4.1 and sea ice concentration V1.1 products are used for the sea ice budget analyses and can be downloaded at https://nsidc.org/data/nsidc-0116/versions/4 and https://nsidc.org/data/nsidc-0051/versions/1, respectively. Open access monthly oceanic and atmospheric reanalysis: ORAS5 (www.copernicus.eu/en/access-data/copernicus-services-catalogue/reanalysis-oras5), ERA5 (www.ecmwf.int/en/forecasts/datasets/browse-reanalysis-datasets), NCEP/DOE R2 (https://psl.noaa.gov/data/gridded/data.ncep.reanalysis2.html). All data were accessed 18 August 2023. All data that support the findings of this study are included within the article (and any supplementary files).

Data availability statements The NSIDC ice age version 4.1 (V4.1) data is freely distributed at https://nsidc.org/data/nsidc- 0611/versions/4 . The NSIDC ice motion V4.1 and sea ice concentration V1.1 products are used for the sea ice budget analyses and can be downloaded at https://nsidc.org/data/nsidc-0116/ versions/4 and https://nsidc.org/data/nsidc-0051/ versions/1 , respectively. Open access monthly oceanic and atmospheric reanalysis: ORAS5 ( www. copernicus.eu/en/access-data/copernicus-services- catalogue/reanalysis-oras5 ), ERA5 ( www.ecmwf.int/ en/forecasts/datasets/browse-reanalysis-datasets ), NCEP/DOE R2 ( https://psl.noaa.gov/data/gridded/ data.ncep.reanalysis2.html ). All data were accessed 18 August 2023. All data that support the findings of this study are included within the article (and any supplementary files).

10.1371_journal.pone.0247356.pdf

Data Availability Statement All relevant data are within the manuscript and its Supporting Information files.

All relevant data are within the manuscript and its Supporting Information files.

10.1038_s41467-020-14824-w.pdf

Data availability The data generated during the study are available in a public repository (https://osf.io/mktdb/).

Data availability The data generated during the study are available in a public repository ( https://osf.io/ mktdb/ ). Code availability The codes generated during the study are available in a public repository ( https://osf.io/ mktdb/ ).

10.1016_j.xcrm.2023.101003.pdf

Data and code availabilityThis paper does not report original code. NGS data have been deposited at NCBI sequence read archive (SRA) under accession numbers 32312762-32312784 and are publicly available as of the date of publication. The crystal structure reported in this manuscript has been deposited at the Protein Data Bank (PDB) under accession number 8E1P. Any additional information is available from the lead contacts upon request.

Materials availability The MAbs generated in this study will be available under an MTA with Amsterdam UMC. Data and code availability This paper does not report original code. NGS data have been deposited at NCBI sequence read archive (SRA) under accession numbers 32312762-32312784 and are publicly available as of the date of publication. The crystal structure reported in this manuscript has been deposited at the Protein Data Bank (PDB) under accession number 8E1P. Any additional information is available from the lead contacts upon request.

10.1371_journal.pone.0252389.pdf

Data Availability Statement All relevant data are within the manuscript and its S1 File.

All relevant data are within the manuscript and its S1 File.

10.3201_eid2605.191638.pdf

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10.1242/bio.058617

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10.1088_1361-6501_ad0939.pdf

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.

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10.18063_ijb.v9i2.668.pdf

Availability of data The datasets used and analyzed during the present study can be obtained from the corresponding author on request.

10.1016_j.neuroimage.2020.116835.pdf

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10.1371_journal.pgph.0003036.pdf

Data Availability Statement: Data are publicly available using the following Harvard Dataverse repository links: https://doi.org/10.7910/DVN/NTXO8M; https://doi.org/10.7910/DVN/RNLU3J; https://doi.org/10.7910/DVN/ETQZO2; https://doi.org/10.7910/DVN/ZF6SJE.

Data are publicly available using the following Harvard Dataverse repository links: https://doi.org/10.7910/DVN/ NTXO8M ; https://doi.org/10.7910/DVN/RNLU3J ; https://doi.org/10.7910/DVN/ETQZO2 ; https://doi. org/10.7910/DVN/ZF6SJE .

10.1103_physrevd.106.062002.pdf

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10.1088_1367-2630_ad06da.pdf

Data availability statementThe data that support the findings of this study are openly available at the following URL/DOI: https://github.com/fine-group-us/disordered-resetting.

Data availability statement The data that support the findings of this study are openly available at the following URL/DOI: https:// github.com/fine-group-us/disordered-resetting .

10.1016_j.isci.2022.105093.pdf

Data and code availability d All data reported in this paper will be shared by the lead contact upon request. d This paper does not report original code. d Any additional information required to reanalyze the data reported in this paper is available from the lead contact upon request.

Materials availability This study did not generate new unique reagents. Data and code availability d All data reported in this paper will be shared by the lead contact upon request. d This paper does not report original code. d Any additional information required to reanalyze the data reported in this paper is available from the lead contact upon request.

10.1371_journal.pntd.0007421.pdf

Data Availability Statement All relevant data are within the manuscript and its Supporting Information files.

All relevant data are within the manuscript and its Supporting Information files.

10.1186_s12877-021-02434-0.pdf

Availability of data and materials The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request.

10.1038_s41590-023-01527-9.pdf

Data availabilityThe data supporting this publication have been deposited at ImmPort (https://www.immport.org) under study accession SDY2213. An h5ad file for CELLXGENE interactive data viewer is also available for download. Source data are provided with this paper.Code availabilityThe customized code used in the present study is publicly available at: https://github.com/viannegao/RA_Fibroblast_Multiome_Analysis.git

Resource https://doi.org/10.1038/s41590-023-01527-9 medium and plated at 20,000 cells per well in a 96-well plate. After adhering for 30 min, they were stimulated for 24 h with TNF (20 ng ml -1 ), IFN-γ (100 U ml -1 ) and IL-1β (1 ng ml -1 ) or a medium-only control. Supernatant was collected, centrifuged and assayed via a custom Procarta-Plex assay (Thermo Fisher Scientific) on a Luminex 200 Instrument. The cells were collected in trizol for bulk RNA sequencing. Data availability The data supporting this publication have been deposited at ImmPort ( https://www.immport.org ) under study accession SDY2213 . An h5ad file for CELLXGENE interactive data viewer is also available for download. Source data are provided with this paper. Code availability The customized code used in the present study is publicly available at: https://github.com/viannegao/RA_Fibroblast_Multiome_Analysis.git Resource https://doi.org/10.1038/s41590-023-01527-9 Extended Data Fig. 4 | See next page for caption. Nature Immunology Resource https://doi.org/10.1038/s41590-023-01527-9

10.1038_s41467-019-12557-z.pdf

Data availability The data underlying all figures are provided as part of the Open Science Framework (OSF; https://osf.io/y325a; Digital Object Identifier (DOI): 10.17605/OSF.IO/Y325A). The OSF project contains a zip folder with all source Data files (.mat), a spreadsheet detailing the names of the source data files and all scripts relevant for producing the figures (make_figX.m). Unthresholded fMRI maps of all contrasts are available on Neurovault (https://identifiers.org/neurovault.collection:5765).

Data availability The data underlying all figures are provided as part of the Open Science Framework (OSF; https://osf.io/y325a ; Digital Object Identifier (DOI): https://doi.org/10.17605/OSF. IO/Y325A ). The OSF project contains a zip folder with all source Data files (.mat), a spreadsheet detailing the names of the source data files and all scripts relevant for producing the figures (make_figX.m). Unthresholded fMRI maps of all contrasts are available on Neurovault ( https://identifiers.org/neurovault.collection:5765 ).

10.3389_fonc.2022.895544.pdf

DATA AVAILABILITY STATEMENT The datasets studied for this study is collected from a clinical trial; due to PHI protection, the original image data cannot be published in the public domain. The studied deep learning design model will be available upon direct request to the corresponding author. Requests to access the datasets should be directed to chunhao.wang@duke.edu.

DATA AVAILABILITY STATEMENT The datasets studied for this study is collected from a clinical trial; due to PHI protection, the original image data cannot be published in the public domain. The studied deep learning design model will be available upon direct request to the corresponding author. Requests to access the datasets should be directed to chunhao.wang@duke.edu .

10.1093_mnras_stab3539.pdf

DATA AVAILABILITY All of the data presented in this paper are publicly available. The HST data can be found under the programme 15701 (PI S. Chap- man), the Spitzer-IRAC data can be found under the four pro- grammes 60194 (PI J. Vieira), 80032 (PI S. Stanford), 13224 (PI S. Chapman), and 14216 (PI S. Chapman), the Gemini-South data can be found under the programme GS-2017B-Q-7 (PI A. Chap- man), and the ALMA data can be found under the two programmes 2017.1.00273.S (PI S. Chapman) and 2018.1.00058.S (PI S. Chap- man).

DATA AVAILABILITY All of the data presented in this paper are publicly available. The HST data can be found under the programme 15701 (PI S. Chapman), the Spitzer-IRAC data can be found under the four programmes 60194 (PI J. Vieira), 80032 (PI S. Stanford), 13224 (PI S. Chapman), and 14216 (PI S. Chapman), the Gemini-South data can be found under the programme GS-2017B-Q-7 (PI A. Chapman), and the ALMA data can be found under the two programmes 2017.1.00273.S (PI S. Chapman) and 2018.1.00058.S (PI S. Chapman).

10.1371_journal.pone.0230651.pdf

Data Availability Statement All relevant data are within the manuscript and its Supporting Information files.

All relevant data are within the manuscript and its Supporting Information files.

10.1371_journal.pone.0277927.pdf

Data Availability Statement All relevant data are within the paper and its Supporting information files. In Jordan, the engraved slab from Jibal al-Khashabiyeh is stored at the French Institute for the Near East (Ifpo, Amman) and is expected to be soon housed in the Hussein Bin Talal University exhibition room of the South-Eastern Badia Archaeological Project in Wadi Musa. In Saudi Arabia, the engraved boulder at Jebel az-Zilliyat has not been removed from its original location.

All relevant data are within the paper and its Supporting information files. In Jordan, the engraved slab from Jibal al-Khashabiyeh is stored at the French Institute for

10.1016_j.stemcr.2019.12.007.pdf

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10.1371_journal.pgph.0002801.pdf

Data Availability Statement: The datasets upon which our findings are based belong to the US Centers for Disease Control and Prevention. For confidentiality reasons, the datasets are not publicly available. However, the data sets can be availed upon reasonable request from the secretariat of the Uganda Public Health Fellowship program at jnamagulu@musph.ac.ug, and with permission from the US Centers for Disease Control and Prevention.

The datasets upon which our findings are based belong to the US Centers for Disease Control and Prevention. For confidentiality reasons, the datasets are not publicly available. However, the data sets can be availed upon reasonable request from the secretariat of the Uganda Public

10.1371_journal.ppat.1011448.pdf

Data AvailabilityAll relevant data are within the manuscript and its Supporting Information files.

All relevant data are within the manuscript and its Supporting Information files.

10.1186_s12879-021-06753-w.pdf

Availability of data and materialsThe datasets used and/or analyzed in the current study are available from the corresponding author upon reasonable request.

Availability of data and materials The datasets used and/or analyzed in the current study are available from the corresponding author upon reasonable request.

10.14814_phy2.15703.pdf

DATA AVAILABILITY STATEMENT The data that support the findings of this study are avail- able from the corresponding author upon reasonable request.

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10.1371_journal.pone.0239702.pdf

Data Availability Statement All SAXS data used in the analysis are available as supplementary data. The data averaged series with a 5.0 mg/ml protein concentration at pH 7.5 have been deposited in SASBDB (the Small Angle Scattering Biological Data Bank) as SASDHG6. The crystal structure has been deposited in the Protein Data Bank (PDB) as 6VE1.

All SAXS data used in the analysis are available as supplementary data. The data averaged series with a 5.0 mg/ml protein concentration at pH 7.5 have been deposited in SASBDB (the Small Angle Scattering Biological Data Bank) as SASDHG6. The crystal structure has been

10.1371_journal.pbio.3002555.pdf

Data Availability Statement: All relevant data are within the paper and its Supporting information files, and from OSF: https://osf.io/wzrdk/ and https://osf.io/sc7pr/. Raw sequencing reads available from the SRA database under accession PRJNA949791.

All relevant data are within the paper and its Supporting information files, and from OSF: https://osf.io/wzrdk/ and https://osf.io/sc7pr/ . Raw sequencing reads available from the SRA database under accession PRJNA949791.

10.1103_physrevresearch.4.013041.pdf

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10.1016_j.indmarman.2022.12.003.pdf

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10.1140_epjc_s10052-023-11191-w.pdf

Data Availability Statement This manuscript has no associated data or the data will not be deposited. [Authors’ comment: All the results in this paper can be reproduced using the HEPfit package, publicly available at https://github.com/silvest/HEPfit/. The configuration file adopted for this study can be provided upon request.]

Data Availability Statement This manuscript has no associated data or the data will not be deposited. [Authors' comment: All the results in this paper can be reproduced using the HEPfit package, publicly available at https://github.com/silvest/HEPfit/ . The configuration file adopted for this study can be provided upon request.] Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article

10.1038_s41467-020-15693-z.pdf

Data availability The data that support the findings of this study are available from the corresponding authors on request (total data size approximately 1 TB). The source data underlying Figs. 2, 3, and 4c–f are provided as a Source Data file. Code availability All computer code (in MATLAB) developed for this study is available from the corresponding authors on request.

Data availability The data that support the findings of this study are available from the corresponding authors on request (total data size approximately 1 TB). The source data underlying Figs. 2 , 3 , and 4c-f are provided as a Source Data file. Code availability All computer code (in MATLAB) developed for this study is available from the corresponding authors on request.

10.3847/1538-4357/acc250

Software: Athena (Stone et al. 2008), VisIt (Department Of Energy (DOE) Advanced Simulation & Computing Initiative (ASCI), 2011).

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10.3390_s19071571.pdf

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10.3390_v14112464.pdf

Data Availability Statement: All nonsimulated data on COVID-19’s development used in this paper were pulled from the tool developed in [33]. The tool aggregates data from a variety of data sources including the WHO, each state’s individual department of health, and the CDC. The data used included reports on case counts, active cases, and deaths within each individual U.S. state. We also include a direct link to the github for the tool here: https://github.com/CSSEGISandData/COVID-19 (accessed on 29 August 2022).

Data Availability Statement: All nonsimulated data on COVID-19's development used in this paper were pulled from the tool developed in [33] . The tool aggregates data from a variety of data sources including the WHO, each state's individual department of health, and the CDC. The data used included reports on case counts, active cases, and deaths within each individual U.S. state. We also include a direct link to the github for the tool here: https://github.com/CSSEGISandData/COVID-19 (accessed on 29 August 2022).

10.3390_ijms20184562.pdf

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10.1371_journal.pone.0241981.pdf

Data Availability Statement The mobile phone data at the antenna- and commune-level aggregated to the year 2013 including noisy antenna locations as well as instructions for replicating the study results have been added as part of the Supporting information. In order to access record-level mobile phone data and exact antenna locations, one would need to contact Sonatel directly and present the research project that would require the data (contact: Mr El Hadji Birahim Gueye, Direction des Systèmes d’information Sonatel, ebgueye@orange-sonatel.com or post mail: Orange-Sonatel, 46 Boulevard de la République, BP 69 Dakar, Senegal). GUF data cannot be shared publicly because third-party access conditions apply (for scientific, non-commercial use). However, it is available for research purposes under a data user agreement. For data access, please contact the German Aerospace Agency under guf@dlr.de (https://www.dlr.de/eoc/en/PortalData/60/Resources/dokumente/guf/DLR-GUF_LicenseAgreement-and-OrderForm.pdf). Census data used in the study cannot be shared publicly because third-party access conditions apply. However, it is available for research purposes under a data user agreement. For data access, please visit the microdata catalogue of the statistical office in Senegal (http://anads.ansd.sn/index.php/catalog/51) or send the inquiry to statsenegal@ansd.sn. All code required for replicating the findings of this study is fully available in the Supporting information of this submission (S1 and S2 Files) and under https://github.com/tilluz/geomatching_open.

cannot be shared publicly because third-party access conditions apply (for scientific, noncommercial use). However, it is available for research purposes under a data user agreement. For data access, please contact the German Aerospace Agency under guf@dlr.de ( https://www. dlr.de/eoc/en/PortalData/60/Resources/ dokumente/guf/DLR-GUF_LicenseAgreement-and- OrderForm.pdf ). Census data used in the study cannot be shared publicly because third-party access conditions apply. However, it is available for research purposes under a data user agreement. For data access, please visit the microdata catalogue of the statistical office in Senegal ( http:// anads.ansd.sn/index.php/catalog/51 ) or send the inquiry to statsenegal@ansd.sn . All code required for replicating the findings of this study is fully available in the Supporting information of this submission (S1 and S2 Files) and under https:// github.com/tilluz/geomatching_open .

10.1371_journal.pone.0276413.pdf

Data AvailabilityThe PDB file and structure factors for the structure reported in this paper are available from the RCSB database (PDB ID 8E4T) doi 10.2210/pdb8e4t/pdb

The PDB file and structure factors for the structure reported in this paper are available from the RCSB database (PDB ID 8E4T) doi 10.2210/pdb8e4t/pdb

10.1088_1361-648x_ad1217.pdf

Data availability statementAll data that support the findings of this study are included within the article (and any supplementary files).

Data availability statement All data that support the findings of this study are included within the article (and any supplementary files).

10.5194_gmd-14-7155-2021.pdf

Code availability. The commented OMEN-SED-RCM source code (MATLAB) to this article is available for download in the two links provided below or see Pika and Hülse (2021). The specific version of the OMEN-SED model used in this pa- per is tagged as release v1.1, has been assigned a DOI of https://doi.org/10.5281/zenodo.4029488 (Hülse and Pika, 2021) and is hosted on GitHub. A version including the code to plot some of the presented results has the DOI of https://doi.org/10.5281/zenodo.4421777 (Pika and Hülse, 2021) and is hosted on GitHub. Data availability. Data sets used in this study are available from the studies cited in the text and figures.

Code availability. The commented OMEN-SED-RCM source code (MATLAB) to this article is available for download in the two links provided below or see Pika and Hülse (2021) . The specific version of the OMEN-SED model used in this paper is tagged as release v1.1, has been assigned a DOI of https://doi.org/10.5281/zenodo.4029488 (Hülse and Pika, 2021) and is hosted on GitHub. A version including the code to plot some of the presented results has the DOI of https://doi.org/10.5281/zenodo.4421777 (Pika and Hülse, 2021) and is hosted on GitHub . Data availability. Data sets used in this study are available from the studies cited in the text and figures.

10.3389_fnbeh.2023.1111908.pdf

Data availability statement The original contributions presented in the study are included in the article/Supplementary material, further inquiries can be directed to the corresponding authors.

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10.1186_s12882-021-02303-3.pdf

Availability of data and materials The data support the findings of this study are available on request, with permission of the study group, DAK Gesundheit and SBK.

10.1016_j.jbc.2022.102523.pdf

Data availability Coulomb potential maps were deposited in the Electron Microscopy Data Bank (EMDB) with accession numbers EMD-24964, EMD-26342, and EMD-26341, corresponding to retromer heterotrimer, dimers, and 3KE mutant particles. Substructure maps were deposited for C-VPS35 dimers as EMD-26343 and EMD-26345 and for the 3KE mutant as EMD-26340. The heterotrimer dataset was first reported very briefly (44), but its refinement and analysis are reported here. Coordinates for this updated retromer heterotrimer were deposited in the PDB as 7U6F.

Data availability Coulomb potential maps were deposited in the Electron Microscopy Data Bank (EMDB) with accession numbers EMD-24964, EMD-26342, and EMD-26341, corresponding to retromer heterotrimer, dimers, and 3KE mutant particles. Substructure maps were deposited for C-VPS35 dimers as EMD-26343 and EMD-26345 and for the 3KE mutant as EMD-26340. The heterotrimer dataset was first reported very briefly (44) , but its refinement and analysis are reported here. Coordinates for this updated retromer heterotrimer were deposited in the PDB as 7U6F.

10.1242_bio.059967.pdf

Data availability All data supporting this study have been made available in the Dryad Digital Repository (https://doi.org/10.5061/dryad.8sf7m0cth).

Data availability All data supporting this study have been made available in the Dryad Digital Repository ( https://doi.org/10.5061/dryad.8sf7m0cth ).

10.1103_physrevd.104.032009.pdf

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10.1371_journal.pone.0283318.pdf

Data Availability Statement Due to the limitations of the consent provided by the subjects in our study, we cannot disclose the data to the public. Only researchers who have formally applied to and been approved by the human research ethics committee of Kyushu University Hospital can access the data (ijkseimei@jimu.kyushu-u.ac.jp).

Due to the limitations of the consent provided by the subjects in our study, we cannot disclose the data to the public.

10.1371_journal.pmed.1004327.pdf

Data Availability Statement: The data underlying the results presented in the study are hosted by the Hong Kong Hospital Authority. Due to local regulation, the data are not available to the public. Request for data can be made via Hong Kong Hospital Authority: https://www3.ha.org.hk/data.

The data underlying the results presented in the study are hosted by the Hong Kong Hospital Authority. Due to local regulation, the data are not available to the public. Request for data can be made via https://www3.ha.org.hk/data .

10.1371_journal.pwat.0000210.pdf

Data Availability Statement: All data can be found in the manuscript and the supporting information file.

All data can be found in the manuscript and the supporting information file.

10.1088_1361-6501_ad0e3a.pdf

Data availability statementThe data cannot be made publicly available upon publication because no suitable repository exists for hosting data in this field of study. The data that support the findings of this study are available upon reasonable request from the authors.

Data availability statement The data cannot be made publicly available upon publication because no suitable repository exists for hosting data in this field of study. The data that support the findings of this study are available upon reasonable request from the authors.

10.1088_1751-8121_ad02ec.pdf

Data availability statementNo data were used to obtain the findings of this study/ Not applicable.

Data availability statement No data were used to obtain the findings of this study/ Not applicable.

10.1038_s41598-021-86143-z.pdf

Data availability The datasets generated during and/or analyzed during the current study are available from the corresponding author on reasonable request.

Data availability The datasets generated during and/or analyzed during the current study are available from the corresponding author on reasonable request. Received: 19 October 2020; Accepted: 11 March 2021

10.1088_1748-9326_ad114a.pdf

Data availability statementNo new data were created or analysed in this study.

Data availability statement No new data were created or analysed in this study.

10.1371_journal.pone.0239797.pdf

Data Availability Statement Replication codes and data for this study have been uploaded to the Harvard Dataverse and can be accessed at: https://doi.org/10.7910/DVN/7WX5UU.

Replication codes and data for this study have been uploaded to the Harvard Dataverse and can be accessed at: https:// doi.org/10.7910/DVN/7WX5UU .

10.1371_journal.pgph.0002467.pdf

Data Availability Statement: Our data came from four publicly available datasets: World Bankâ€™s World Development Indicators; U.S. governmentâ€™s foreignassistance.gov database; OECD Creditor Reporting System database; and the Institute of Health Metrics and Evaluation GBD Resultâ€™s Tool.

Our data came from four publicly available datasets: World Bank's World Development Indicators; U.S. government's foreignassistance.gov database; OECD Creditor Reporting System database; and the Institute of Health Metrics and Evaluation GBD Result's Tool.

10.1016_j.pmedr.2019.101035.pdf

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10.1371_journal.pone.0250576.pdf

Data Availability Statement All relevant data are within the paper and its Supporting information files.

All relevant data are within the paper and its Supporting information files.

10.1088_1367-2630_ad1418.pdf

Data availability statementAll data that support the findings of this study are included within the article (and any supplementary files).

Data availability statement All data that support the findings of this study are included within the article (and any supplementary files).

10.1371_journal.pone.0270562.pdf

Data Availability Statement Data will be made available on request. The request can be sent to Ms. KV. Sripriya, administrative officer, Samarth. She can be contacted at admin@samarthngo.org.

Data will be made available on request. The request can be sent to Ms. KV. Sripriya, administrative officer, Samarth. She can be contacted at admin@samarthngo.org .

10.1088_1361-6463_ad10d4.pdf

Data availability statementThe data that support the findings of this study are available from the corresponding author upon reasonable request.

Data availability statement The data that support the findings of this study are available from the corresponding author upon reasonable request.

10.1038_s41598-020-66444-5.pdf

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10.1371_journal.pgen.1010754.pdf

Data Availability Statement All DNA sequence files used for MFA analysis are available from NCBI (SRA accession number: PRJNA738450). Numerical data for qPCR are provided in Supplementary data.

All DNA sequence files used for MFA analysis are available from NCBI (SRA accession number: PRJNA738450). Numerical data for qPCR are provided in Supplementary data.

10.1371_journal.pbio.3002472.pdf

Data Availability Statement: The raw sequencing reads for the metagenomic samples used in this study were downloaded from public repositories listed in the following publications: 10.1038/nature11209, 10.1038/nature11450, 10.1016/j.cels.2016.10.004, and 10.1101/gr.233940.117. Data underlying all figures, such as the numerical values of bar plots, can be found in 10.5281/zenodo.10304481. All other metadata, as well as the source code for the sequencing pipeline, downstream analyses, and figure generation are available at Zenodo (10.5281/zenodo.10368227) or GitHub (https://github.com/zhiru-liu/microbiome_evolution).

The raw sequencing reads for the metagenomic samples used in this study were downloaded from public repositories listed in the following publications: 5281/zenodo.10368227 ) or GitHub ( https://github.com/zhiru

10.1371_journal.pone.0284899.pdf

Data Availability Statement All relevant data are within the paper and its Supporting Information file.

All relevant data are within the paper and its Supporting Information file.

10.1371_journal.pone.0217829.pdf

Data Availability Statement All relevant data are within the manuscript and its Supporting Information files.

All relevant data are within the manuscript and its Supporting Information files.

10.1371_journal.pone.0256297.pdf

Data Availability Statement The data was derived from the second and third wave of the China Health and Retirement Longitudinal Study (CHARLS) (data and documentation are available at http://charls.pku.edu.cn/).

The data was derived from the second and third wave of the China Health and Retirement Longitudinal Study (CHARLS) (data and documentation are available at http:// charls.pku.edu.cn/ ).

10.1371_journal.pcbi.1010680.pdf

Data AvailabilityAll data are available in the main text or as supplementary materials. Scripts, computational methods, and design models are available on GitHub at https://github.com/willsheffler/rpxdock. For O43-rpxdock-EK1, coordinates are deposited in the Protein Data Bank with the accession code 8FWD; the cryo-EM density map is deposited in the Electron Microscopy Data Bank (EMDB) with the accession code EMD-29502.

All data are available in the main text or as supplementary materials. Scripts, computational methods, and design models are available on GitHub at https://github. com/willsheffler/rpxdock . For O43-rpxdock-EK1, coordinates are deposited in the Protein Data Bank with the accession code 8FWD; the cryo-EM density map is deposited in the Electron Microscopy Data Bank (EMDB) with the accession code EMD-29502. Availability and Future Directions Setup and installation At the time of publication, RPXDock has been verified to compile and function correctly on Linux-based operating systems. To set it up, a user must first clone the public repository of the full source code, which can be found at https://github.com/willsheffler/rpxdock , and set up a proper conda environment using the environment.yml file. Note that a user must obtain a pyrosetta license (free for non-profit users) and update the username and password fields for their pyrosetta license in the environment.yml file before creating the environment. Users may need to also install additional packages in their conda environment such as pyyaml to properly build the application. To build and compile the codebase with the newly created conda environment, a user may simply run the pytest command using a gcc>9-compatible compiler. To verify that the code compiled properly, execute rpxdock/app/dock.py --help in the new conda environment. The output should provide a list of options that are relevant for docking ( S1 Table). Note that several options are still experimental in nature and therefore are not described fully in this publication. For a template of how to set up a simple RPXDock run, please refer to the available example provided in tools/dock.sh in the GitHub repository.

10.1093_nar_gkad329.pdf

DATA AVAILABILITY Raw sequencing data has been submitted to the NCBI SRA under accession numbers SRR19744356-SRR19744369. The corresponding BioSample accession numbers are SAMN29198687-SAMN29198700. Processed RNA-seq data are provided in the supplementary materials.

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10.1371_journal.pone.0260553.pdf

Data Availability Statement All relevant data are within the paper and its Supporting information files.

All relevant data are within the paper and its Supporting information files.

10.1016_j.celrep.2023.112657.pdf

Data and code availabilityStructures and coordinates have been deposited in the Protein DataBank with identification number PDB: 8ENT. X-ray diffraction images have been deposited in the SBGrid DataBank with accession 974. Cryo-EM maps have been deposited to the Electron Microscopy DataBank (EMDB) under accession ID EMDB: EMD-28278.This paper does not report original code.

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10.1038/s41467-021-24929-5

Data availability The coordinates and structure factors in this study have been deposited in the Protein Data Bank under accession codes 7KIH, 7KIL, and 7KIQ. The mass spectrometry proteomics data in this study have been deposited in the ProteomeXchange Consortium via the PRIDE partner repository45 with the dataset identifier PXD022172. Source data are provided with this paper.

Data availability The coordinates and structure factors in this study have been deposited in the Protein Data Bank under accession codes 7KIH, 7KIL, and 7KIQ . The mass spectrometry proteomics data in this study have been deposited in the ProteomeXchange Consortium via the PRIDE partner repository 45 with the dataset identifier PXD022172 . Source data are provided with this paper.

10.3390_ijms24129783.pdf

Data Availability StatementNot applicable.

Data Availability Statement: Not applicable.

10.1186_s12867-019-0122-2.pdf

Availability of data and materials All data generated or analysed during this study are included in this article.

10.1371_journal.pone.0244789.pdf

Data Availability Statement All relevant data are within the manuscript.

All relevant data are within the manuscript.

10.1371_journal.pbio.3000622.pdf

Data Availability Statement All relevant data are within the paper and its Supporting Information files.

All relevant data are within the paper and its Supporting Information files.

10.1371_journal.pgen.1008228.pdf

Data Availability Statement All relevant data are within the manuscript and its Supporting Information files.

All relevant data are within the manuscript and its Supporting Information files.

10.1103_physrevx.13.011039.pdf

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10.1021_acssynbio.3c00078.pdf

NotesPlasmids and their maps available for requests at Addgene (addgene.org/browse/article/28233817/). The key cell lines are available upon request. EM-Seq raw and processed data is deposited at Gene Expression Omnibus (GSE224403). Data and codes for analysis and generating figures are available at data.caltech (doi: 10.22002/ct5kt-cv878).

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10.1371_journal.pone.0284380.pdf

Data Availability Statement All relevant data are within the manuscript and its Supporting information files.

All relevant data are within the manuscript and its Supporting information files.

10.1088_1402-4896_ad0c14.pdf

Data availability statementThe data cannot be made publicly available upon publication because no suitable repository exists for hosting data in this field of study. The data that support the findings of this study are available upon reasonable request from the authors.

Data availability statement The data cannot be made publicly available upon publication because no suitable repository exists for hosting data in this field of study. The data that support the findings of this study are available upon reasonable request from the authors.

10.1371_journal.pclm.0000173.pdf

Data Availability Statement The data that support the findings of this study are openly available in Zenodo at http://doi.org/10.5281/zenodo.3524917. The codes can be retrieved from: https://git.idiv.de/fm58hufi/discounting-the-future.git.

The data that support the findings of this study are openly available in Zenodo at http://doi.org/10.5281/zenodo.3524917 . The codes can be retrieved from: https://git.idiv.de/ fm58hufi/discounting-the-future.git .

10.1371_journal.pone.0237574.pdf

Data Availability Statement All relevant data are within the manuscript and its Supporting Information files.

All relevant data are within the manuscript and its Supporting Information files.

10.1007_s00430-019-00655-0.pdf

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10.1088_1402-4896_ad0695.pdf

Data availability statementAll data that support the findings of this study are included within the article (and any supplementary files).

Data availability statement All data that support the findings of this study are included within the article (and any supplementary files).

10.1371_journal.pgen.1011003.pdf

Data Availability Statement: All relevant data are within the paper and its Supporting Information files. The whole genome sequencing data are available at the Sequencing Read Archive (PRJNA1044129). Raw and processed mRNA-Seq data have been deposited in GEO (GSE236037).

All relevant data are within the paper and its Supporting Information files.