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10.1186_s12879-021-05907-0.pdf
Availability of data and materials All data is publically available through Google Trends and through The Behavioral Risk Factor Surveillance System (BRFSS).
Availability of data and materials All data is publically available through Google Trends and through The Behavioral Risk Factor Surveillance System (BRFSS). Ethics approval and consent to participate Our research was exempted from an ethics review by the University of California at San Diego Human Research Protections Program.
10.3390_genes14061211.pdf
Data Availability Statement The whole genome data used in this manuscript are available in the GenBank database under BioProject accession PRJNA416233, PRJEB10098, PRJEB10854, PRJNA168142, PRJNA205517, PRJNA230019, PRJNA233529, PRJNA288817 and PRJNA291776.
Data Availability Statement: The whole genome data used in this manuscript are available in the GenBank database under BioProject accession PRJNA416233, PRJEB10098, PRJEB10854, PRJNA168142, PRJNA205517, PRJNA230019, PRJNA233529, PRJNA288817 and PRJNA291776.
10.1038_s41598-021-03242-7.pdf
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10.1038_s41590-023-01504-2.pdf
Data availability Raw and processed bulk, scRNA-seq and Visium data from mouse are available from the Gene Expression Omnibus under super series accession GSE202159. Human tumor scRNA-seq data are available at the Human Tumor Atlas Network (HTAN) data coordinating center web platform (https://humantumoratlas.org/). Source data are provided with this paper.
Data availability Raw and processed bulk, scRNA-seq and Visium data from mouse are available from the Gene Expression Omnibus under super series accession GSE202159 . Human tumor scRNA-seq data are available at the Human Tumor Atlas Network (HTAN) data coordinating center web platform ( https://humantumoratlas.org/ ). Source data are provided with this paper. Code availability No new algorithms were developed for this paper. All analysis code is available at https://github.com/dpeerlab/Treg_ depletion_reproducibility /.
10.1103_physrevx.12.021038.pdf
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10.1155_2019_8132520.pdf
Data Availability The data used to support the findings of this study are available from the corresponding author upon request.
Data Availability The data used to support the findings of this study are available from the corresponding author upon request.
10.1186_s12884-019-2192-z.pdf
Availability of data and materialsQualified researchers may request access to patient-level data and related study documents including the clinical study report, study protocol with any amendments, blank case report form, statistical analysis plan, and dataset specifications. Patient level data will be anonymized and study documents will be redacted to protect the privacy of trial participants. Further details on Sanofi’s data sharing criteria, eligible studies, and process for requesting access can be found at: https://www.clinicalstudydatarequest.com.
Availability of data and materials Qualified researchers may request access to patient-level data and related study documents including the clinical study report, study protocol with any amendments, blank case report form, statistical analysis plan, and dataset specifications. Patient level data will be anonymized and study documents will be redacted to protect the privacy of trial participants. Further details on Sanofi's data sharing criteria, eligible studies, and process for requesting access can be found at: https://www.clinicalstudydatarequest.com .
10.1371_journal.pone.0244962.pdf
Data Availability Statement Data cannot be shared publicly because of this was not permitted by the consent form signed by participants. Data are available from the Keller-Lamar Health Foundation ([email protected]) for researchers who can provide evidence of IRB approval for access.
Data cannot be shared publicly because of this was not permitted by the consent form signed by participants. Data are available from the Keller-Lamar Health Foundation ( [email protected] ) for researchers who can provide evidence of IRB approval for access.
10.1186_s40168-023-01519-9.pdf
Availability of data and materials The raw data in this study is from reference [3]. All analyzed data in this study is available in Additional file 3. The source code is available at https://github.com/Neina-0830/WWTP_community_prediction.
Availability of data and materials The raw data in this study is from reference [3] . All analyzed data in this study is available in Additional file 3. The source code is available at https:// github. com/ Neina-0830/ WWTP_ commu nity_ predi ction .
10.1371_journal.pwat.0000137.pdf
Data Availability Statement Data have been uploaded to Zenodo 10.5281/zenodo.7447637.
Data have been uploaded to Zenodo 10.5281/zenodo.7447637 .
10.1038_s41467-021-24130-8.pdf
Data availabilitySingle-cell RNA-seq data files are available in “GSE151337”. 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. A reporting summary for this article is available as a Supplementary Information file. Source data are provided with this paper.Code availabilityCodes used in this analysis were deposited onto GitHub: 10.5281/zenodo.4743036.
Code availability Codes used in this analysis were deposited onto GitHub: https://doi.org/10.5281/ zenodo.4743036 . Data availability Single-cell RNA-seq data files are available in ' GSE151337' . 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. A reporting summary for this article is available as a Supplementary Information file. Source data are provided with this paper.
10.1371_journal.pone.0254310.pdf
Data Availability Statement All data are public and available on the Brazilian Institute of Geography and Statistics website (www.ibge.gov.br).
All data are public and available on the Brazilian Institute of Geography and Statistics website ( www.ibge.gov. br ).
10.21468_scipostphys.14.3.029.pdf
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10.1111_eva.13529.pdf
DATA AVAILABILITY STATEMENT Sequence data are hosted at the SRA under BIOPROJECT SUB10359598. Plasmids, ancestor, and mutator clones are avail- able on request. Evolved mutants can be shared subject to Material Transfer Agreements. Experimental data are available at Zenodo with a permanent doi: 10.5281/zenodo.7503995.
DATA AVA I L A B I L I T Y S TAT E M E N T Sequence data are hosted at the SRA under BIOPROJECT SUB10359598. Plasmids, ancestor, and mutator clones are available on request. Evolved mutants can be shared subject to Material Transfer Agreements. Experimental data are available at Zenodo with a permanent doi: 10.5281/zenodo.7503995 .
10.15252_embj.2022112118.pdf
Data availability The data that support the findings of this study are available from the corresponding author. RNA-sequencing data have been deposited in GEO under accession number (GSE215951; http:// www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE215951).
Data availability The data that support the findings of this study are available from the corresponding author. RNA-sequencing data have been deposited in GEO under accession number (GSE215951; http:// www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE215951 ). Expanded View for this article is available online .
10.1371_journal.pntd.0007072.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_1361-6501_ad095a.pdf
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 authors.
Data availability statements The 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 authors.
10.1016_j.enpol.2022.113313.pdf
Data availabilityThe data that has been used is confidential.
Data availability The data that has been used is confidential.
10.1038_s42255-023-00774-2.pdf
Data availability All data generated or analysed during this study are included in the article and its Supplementary Information. Results of the ORFeome, the CRISPR–Cas9 and the PRISM screens are available in Supplementary Table 1. Data from the Cancer Cell Line Encyclopedia are available at https://depmap.org/portal/. Source data are provided with this paper.
Statistics and reproducibility All data are expressed as the mean ± s.e.m., with the exception of oxygraphic data that are expressed as the mean ± s.d. All reported sample sizes (n) represent biological replicate plates or a different mouse. All attempts at replication were successful. All Student's t-tests were two sided. Statistical tests were performed using Microsoft Excel and GraphPad Prism 9. Data availability All data generated or analysed during this study are included in the article and its Supplementary Information. Results of the ORFeome, the CRISPR-Cas9 and the PRISM screens are available in Supplementary Table 1 . Data from the Cancer Cell Line Encyclopedia are available at https://depmap.org/portal /. Source data are provided with this paper.
10.1371_journal.pcbi.1010923.pdf
Data Availability Statement All relevant data are within the manuscript and its Supporting Information files. RNA-seq of samples of human left ventricle heart, left atrial appendage, aorta, tibial arteries, and coronary arteries were downloaded from the GTEx project [29] via dbGaP (phs000424.v8.p2). In addition, we downloaded RNA-seq datasets of dilated cardiomyopathy (DCM), ischemic cardiomyopathy (ICM), and controls (SRA database, accession code GSE116250) [40]. The ribosome profiling dataset of DCM patients was downloaded from the SRA database (GSE131111) [47]. finally, we downloaded additional RNA-seq datasets of ICM from the left and right ventricles of left-sided heart failure, biventricular heart failure, and controls (SRA database accession code GSE120852) [65]. Tables with raw data used for figure plotting can be found in S4 Table.
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10.1007_s43076-022-00253-9.pdf
Data Availability Data not available due to ethical restrictions.Due to the nature of this research, partici- pants of this study did not agree for their data (whole transcripts) to be shared publicly. However, some supporting material concerning the data analysis process will be available for both reviewers and readers.
Data Availability Data not available due to ethical restrictions.Due to the nature of this research, participants of this study did not agree for their data (whole transcripts) to be shared publicly. However, some supporting material concerning the data analysis process will be available for both reviewers and readers.
10.1112_topo.12275.pdf
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10.7554_elife.88204.pdf
Data availability The 3D cryo-EM density maps have been deposited in the Electron Microscopy Data Bank under the accession number EMD-29861. Atomic coordinates for the atomic model have been deposited in the Protein Data Bank under the accession number 8G94. All other data needed to evaluate the conclusions in the paper are present in the paper and/or the supplementary materials. The following datasets were generated: ChenHLiX2023Structure of CD69-bound S1PR1 coupled to heterotrimeric GiRCSB Protein Data Bank8G94 ChenHLiX2023Structure of CD69-bound S1PR1 coupled to heterotrimeric GiEMBDEMD-29861
Data availability The 3D cryo-EM density maps have been deposited in the Electron Microscopy Data Bank under the accession number EMD-29861. Atomic coordinates for the atomic model have been deposited in the Protein Data Bank under the accession number 8G94. All other data needed to evaluate the conclusions in the paper are present in the paper and/or the supplementary materials.
10.1007_s10796-023-10369-7.pdf
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10.1103_physrevd.107.035006.pdf
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10.1016_j.jbc.2023.105073.pdf
Data availabilityAll relevant data are contained within the main article or supplemental information. Please email [email protected] with requests for raw data or reagents.
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10.1038_s41598-019-40420-0.pdf
Data Availability ESBL or carbapenemase gene sequence data that support the findings of this study have been deposited into GenBank with the accession numbers listed in Table 1. The data that support the descriptive statistical analyses of sample characteristics and resistance gene presence are available from the corresponding author upon reasonable request.
Data Availability ESBL or carbapenemase gene sequence data that support the findings of this study have been deposited into GenBank with the accession numbers listed in Table 1 . The data that support the descriptive statistical analyses of sample characteristics and resistance gene presence are available from the corresponding author upon reasonable request.
10.1088_1748-605x_acf90a.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).
10.1038_s41398-023-02450-1.pdf
Data availabilityThe source data can be available from the corresponding authors on reasonable request.
DATA AVAILABILITY The source data can be available from the corresponding authors on reasonable request.
10.1126_sciadv.adg1671.pdf
Data and materials availability: All data are available in the main text and/or the Supplementary Materials. The raw FASTQ files of the scRNA-seq and the processed files (output from CellRanger) are accessible through GEO (accession number: GSE224031). The code for data analyses is available on figshare (doi: 10.6084/m9.figshare.22490956) and via the link: https://figshare.com/s/ca568d8f44d020cb6389.
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10.1371_journal.ppat.1012032.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.
10.1111_jcmm.15814.pdf
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 or ethical restrictions.
DATA AVA I L A B I L I T Y S TAT E M E N T 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 or ethical restrictions.
10.1085/jgp.202213131
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10.1103_physrevresearch.4.l032021.pdf
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10.1371_journal.pone.0285473.pdf
Data Availability Statement All relevant data are available at: https://www.ebi.ac.uk/biostudies/studies/S-BSST1078.
All relevant data are available at: https://www.ebi.ac.uk/biostudies/ studies/S-BSST1078 .
10.1088_2752-5295_acc08a.pdf
Data availability statementThe data that support the findings of this study are available upon request from the authors.
Data availability statement The data that support the findings of this study are available upon request from the authors.
10.1038_s41586-023-06157-7.pdf
Data availabilityThe authors declare that the data supporting the findings of this study are available within the paper and its supplementary information files. Sequencing data are available from the Sequencing Read Archive under BioProject identifiers PRJNA602546 and PRJNA867730. The raw data and all other datasets generated in this study are available from the corresponding authors upon reasonable request. Source data are provided with this paper.Code availabilityScripts and pipelines used for all sequencing data analysis and for image analysis are available at the GitHub online repository (https://github.com/chengzhongzhangDFCI/nature2023)47.
Data availability The authors declare that the data supporting the findings of this study are available within the paper and its supplementary information files. Sequencing data are available from the Sequencing Read Archive under BioProject identifiers PRJNA602546 and PRJNA867730 . The raw data and all other datasets generated in this study are available from the corresponding authors upon reasonable request. Source data are provided with this paper. Code availability Scripts and pipelines used for all sequencing data analysis and for image analysis are available at the GitHub online repository ( https://github. com/chengzhongzhangDFCI/nature2023 ) 47 .
10.1038_s41467-022-29759-7.pdf
Data availability The data generated in this study have been deposited in the figshare database under the accession code: https://doi.org/10.6084/m9.figshare.17026607.v1. Code availability Code used to analyse data in this manuscript are available from the corresponding author upon reasonable request.
Data availability The data generated in this study have been deposited in the figshare database under the accession code: https://doi.org/10.6084/m9.figshare.17026607.v1 . Code availability Code used to analyse data in this manuscript are available from the corresponding author upon reasonable request.
10.1186_s12875-021-01601-x.pdf
Availability of data and materials All major data generated or analysed during this study are included in this published article. Additional information can be provided on request.
Availability of data and materials All major data generated or analysed during this study are included in this published article. Additional information can be provided on request.
10.1371_journal.pgen.1010804.pdf
Data AvailabilityAll the relevant data are within the manuscript and its Supporting Information files.
All the relevant data are within the manuscript and its Supporting Information files.
10.1126_science.adg7883.pdf
Data and materials availability: The cryo-EM map has been deposited in the Electron Microscopy Data Bank with accession code EMD-40033. The coordinates for the atomic model have been deposited in the Protein Data Bank with accession code 8GH6. The raw cryo-EM data have been deposited in EMPIAR with accession code EMPIAR-11458.
Data and materials availability: The cryo-EM map has been deposited in the Electron Microscopy Data Bank with accession code EMD-40033. The coordinates for the atomic model have been deposited in the Protein Data Bank with accession code 8GH6. The raw cryo-EM data have been deposited in EMPIAR with accession code EMPIAR-11458.
10.2196_39479.pdf
Data Availability Statement The data supporting the findings of this study are available from the corresponding author upon reasonable request.
Data Availability The data supporting the findings of this study are available from the corresponding author upon reasonable request.
10.1088_2050-6120_acf97b.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.0238646.pdf
Data Availability Statement All relevant data are within the paper.
All relevant data are within the paper.
10.3389_fphy.2022.1005333.pdf
Data availability statement Publicly available datasets were analyzed in this study. This data can be found here: https://inspirehep.net.
Data availability statement Publicly available datasets were analyzed in this study. This data can be found here: https://inspirehep.net .
10.1007_s00213-019-05336-7.pdf
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10.1371_journal.pcbi.1011928.pdf
Data Availability Statement: Code can be downloaded from https://git.exeter.ac.uk/mv286/hormonebayes.
Code can be downloaded from https://git.exeter.ac.uk/mv286/ hormonebayes .
10.1080_14756366.2019.1626375.pdf
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10.1088_1367-2630_ad121c.pdf
Data availability statementAll data that supports the findings of this study are included within the article.
Data availability statement All data that supports the findings of this study are included within the article.
10.1080/19420889.2020.1729601
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10.1088_1361-665x_acf970.pdf
Data availability statementThe data that support the findings of this study are available upon reasonable request from the authors.
Data availability statement The data that support the findings of this study are available upon reasonable request from the authors.
10.1186_s40478-022-01399-4.pdf
Availability of data and materials The datasets that were used and analyzed during the current study are avail‐ able from the corresponding author on reasonable request.
Availability of data and materials The datasets that were used and analyzed during the current study are available from the corresponding author on reasonable request.
10.1371_journal.pone.0267316.pdf
Data Availability Statement Data were submitted to European Bioinformatic Institute, EBI (https://www.ebi.ac.uk/). The accession was assigned as ArrayExpress accession E-MTAB-11136. Additionally, this information is available as a footnote in Tables 2 and 3 of the manuscript.
Data were submitted to European Bioinformatic Institute, EBI ( https:// www.ebi.ac.uk/ ). The accession was assigned as ArrayExpress accession E-MTAB-11136. Additionally, this information is available as a footnote in Tables 2 and 3 of the manuscript.
10.1371_journal.pone.0227835.pdf
Data Availability Statement: All serum biomarker values, imaging analysis results, and appropriate demographic data files are available via Open Science Framework: DOI 10.17605/OSF.IO/92ERQ.
All serum biomarker values, imaging analysis results, and appropriate demographic data files are available via Open Science Framework: DOI 10.17605/OSF.IO/92ERQ .
10.1371_journal.pone.0283603.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.
10.7554_elife.80854.pdf
Data availabilitySource files of all original gels and Western Blots were provided for the following figures: Figure 1—figure supplement 2B; Figure 4—figure supplement 1A, C, D, E; Figure 5—figure supplement 2B, F, G. RNA sequencing and ChIP sequencing data files that support the findings of this study have been deposited in the Gene Expression Omnibus under the accession code GSE85055, as well as in the Dryad digital repository (doi:10.5061/dryad.7pvmcvdwm; doi:10.5061/dryad.f1vhhmh0h). Sequences of sgRNAs, shRNAs, and primers used in this manuscript are included in the Supplementary File 1.
Data availability Source files of original gels and Western Blots were provided for the figures: Figure 1 The following datasets were generated: Author(s) Year Dataset title Dataset URL Database and Identifier Soto-Feliciano MY, Zhu C, Morris JP, Huang C-H, Koche RP, Y-J Ho, Banito A, Chen C-W, Shroff A, Tian S, Livshits G, Chen C-C, Fennell M, Armstrong SA, Allis CD, Tschaharganeh DF, Lowe SW 2022 Mll3 suppresses tumorigenesis by activating the Ink4a/Arf locus https:// doi. org/ 10. 5061/ dryad. 7pvmcvdwm Dryad Digital Repository, 10.5061/dryad.7pvmcvdwm Soto-Feliciano MY, Zhu C, Morris JP, Huang C-H, Roche RP, Y-J Ho, Banito A, Chen C-W, Shroff A, Tian S, Livshits G, Chen C-C, Fennell M, Armstrong SA, Allis CD, Tschaharganeh DF, Lowe SW 2022 MLL3 ChIP sequencing in murine and human HCC cells https:// doi. org/ 10. 5061/ dryad. f1vhhmh0h Dryad Digital Repository, 10.5061/dryad.f1vhhmh0h Lowe SW 2017 Mll3 suppresses tumorigenesis by activating the Ink4a/Arf locus https://www. ncbi. nlm. nih. gov/ geo/ query/ acc. cgi? acc= GSE85055 NCBI Gene Expression Omnibus, GSE85055
10.1371_journal.pstr.0000097.pdf
Data Availability Statement: We have no data to report.
We have no data to report.
10.1371_journal.pone.0287011.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.0286598.pdf
Data Availability Statement All relevant data are within the manuscript and its Supporting Information files.
All relevant data are within the
10.1093_cvr_cvab085.pdf
Data availability The data underlying this article will be shared on reasonable request to the corresponding author.
Data availability The data underlying this article will be shared on reasonable request to the corresponding author.
10.1103_physrevresearch.5.013169.pdf
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10.1007_s00220-023-04637-5.pdf
Data Availability Data sharing not applicable to this article as no datasets were generated or analysed during the current study.
Data Availability Data sharing not applicable to this article as no datasets were generated or analysed during the current study.
10.1038_s41467-023-37945-4.pdf
Data availability Whole genome bisulfite sequencing data are available at GenBank/NCBI under accession number GSE182212. RNA-sequencing data are available at GenBank / NCBI under accession number PRJNA780766. All other data are available as Source Data files as part of this publication. Source data are provided with this paper.
Data availability Whole genome bisulfite sequencing data are available at GenBank/ NCBI under accession number GSE182212 . RNA-sequencing data are available at GenBank / NCBI under accession number PRJNA780766 . All other data are available as Source Data files as part of this publication. Source data are provided with this paper. Code availability All custom code used for analyses is deposited in the following GitHub repository: https://github.com/schmitzlab/Methylome-of-clonal-ant_ Obir-v5.4.git .
10.1186_s12870-023-04147-5.pdf
Availability of data and materialsThe datasets generated and/or analyzed during the current study are available in the NCBI repository, [ https://www.ncbi.nlm.nih.gov/bioproject/906276] [Accession number: PRJNA906276].
Availability of data and materials The datasets generated and/or analyzed during the current study are available in the NCBI repository, [ https:// www. ncbi. nlm. nih. gov/ biopr oject/ 906276 ] [Accession number: PRJNA906276].
10.1073_pnas.2221415120.pdf
Data, Materials, and Software AvailabilityMatlab code and data have been deposited in Zenodo repositories (86, 87).
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10.1371_journal.pone.0251004.pdf
Data Availability Statement All data files are available from the Open Science Framework (OSF) database. URL: https://osf.io/2zty9/.
All data files are available from the Open Science Framework (OSF) database. URL: https://osf.io/2zty9/ .
10.1371_journal.pgph.0001789.pdf
Data Availability Statement The data presented here are from the Low Birthweight Infant Feeding Exploration (LIFE) study which is filed with Clinicaltrials.gov NCT04002908 and Clinical Trial Registry of India CTRI/2019/02/017475. De-identified individual participant data (including data dictionaries) will be made available, in addition to study protocols, and the informed consent form in a public, open access repository. The data will be made available upon publication through the Harvard Dataverse Platform under the BetterBirth Dataverse website. This can be found at: https://dataverse.harvard.edu/dataverse/BetterBirthData
The data presented here are from the Low Birthweight Infant Feeding Exploration
10.1371_journal.pone.0245201.pdf
Data Availability Statement All sequences are available from the GenBank database (accession number: MN816222, MN816223, MN816224, MN816225, MN816226, MN814829, MN814830, MN814831, MT012386 and MT012387). Other relevant data are within the paper and its Supporting Information files.
All sequences are available from the GenBank database (accession number: MN816222, MN816223, MN816224, MN816225, MN816226, MN814829, MN814830, MN814831, MT012386 and MT012387). Other relevant data are within the paper and its Supporting Information files.
10.1088_1361-6501_ad180f.pdf
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.
Data availability statement The 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.
10.1103_physrevresearch.5.013123.pdf
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10.1371_journal.pone.0260153.pdf
Data Availability Statement Data cannot be shared publicly because to do so could potentially identify our study participants and individual healthcare facilities, and assurances were given to respondents that any publication would not do so. Requests for access to the data underlying our findings will be considered by the National Ethical Committee of Public Health/CNES South Kivu province, and should be addressed to Prof Kitoka Moke at [email protected].
Data cannot be shared publicly because to do so could potentially identify our study participants and individual healthcare facilities, and assurances were given to respondents that any publication would not do so. Requests for access to the data underlying our findings will
10.1371_journal.pone.0270817.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.pntd.0011435.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_ad03bf.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.
Data availability statement The 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.
10.1093/geroni/igaa018
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10.1038_s41593-023-01332-5.pdf
Data availability Data from this study are available at https://github.com/axellaboratory/Cury_and_Axel_2023 and upon request. Trained pose estimation models and the supervised behavioral classifier can be accessed via Dropbox (https://www.dropbox.com/sh/jh4422f3ld95j1a/AAAHVb-pFsmcEk40BgSHm1TEa?dl=0).
Article https://doi.org/10.1038/s41593-023-01332-5 Data availability Data from this study are available at https://github.com/axellaboratory/ Cury_and_Axel_2023 and upon request. Trained pose estimation models and the supervised behavioral classifier can be accessed via Dropbox ( https://www.dropbox.com/sh/jh4422f3ld95j1a/AAAHVb-pFsmcEk40 BgSHm1TEa?dl=0 ). Code availability Code used for processing the data is available at https://github.com/ axellaboratory/Cury_and_Axel_2023 . Extended Data
10.1523/JNEUROSCI.1734-20.2020
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10.1038_s41598-019-41663-7.pdf
Data Availability The datasets generated during and/or analyzed during the current study cannot be publicly available because they are owned by Yamagata Municipalities Mutual Aid Association and Sports Medical Research Center, Keio University. Please ask Sports Center of Keio University about data availability (http://sports.hc.keio.ac.jp/ja/).
Data Availability The datasets generated during and/or analyzed during the current study cannot be publicly available because they are owned by Yamagata Municipalities Mutual Aid Association and Sports Medical Research Center, Keio University. Please ask Sports Center of Keio University about data availability ( http://sports.hc.keio.ac.jp/ja/ ).
10.1186_s13071-020-3970-1.pdf
Availability of data and materialsThe RNA-seq data obtained in this study were deposited in the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) database (https://www.ncbi.nlm.nih.gov/sra) under accession number SUB6209220.
Availability of data and materials The RNA-seq data obtained in this study were deposited in the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) database ( https ://www.ncbi.nlm.nih.gov/sra ) under accession number SUB6209220.
10.1038_s41467-023-38328-5.pdf
Data availability The raw data from the prospective study, the raw scores of the retrospective analysis, the input structures and benchmarking scores for the efficiency study, and the raw data from the biolayer interferometry measurements are available at the following repository hosted by the Institute for Protein Design: The main supplement (136 MB) Contains these files: design_models_final_combo_optimized/ design_models_sequence/ design_models_ssm_natives/ design_stats/ dna_production_scripts/ figure_data/ ngs_analysis_scripts/ files.ipd.uw.edu/pub/improving_dl_binders_2023/supplemental_files/scripts_and_main_pdbs.tar.gz Experimental data and data derived from that data (155 MB) Contains these files: ngs_data/ ngs_data_analysis/ files.ipd.uw.edu/pub/improving_dl_binders_2023/supplemental_files/experimental_data_and_analysis.tar.gz All ordered proteins in.pdb.gz format: (~100 K files; 15 GB) Contains these files: design_models_pdbs/ files.ipd.uw.edu/pub/improving_dl_binders_2023/supplemental_files/design_models_pdb.tar.gz All ordered proteins in Rosetta binary silent format (6.1 GB) Contains these files: design_models_silent/ files.ipd.uw.edu/pub/improving_dl_binders_2023/supplemental_files/design_models_silent.tar.gz The docks we used for the efficiency benchmark (6.1 GB) Contains these files: efficiency_benchmark_docks/ files.ipd.uw.edu/pub/improving_dl_binders_2023/supplemental_files/efficiency_benchmark_docks.tar.gz. Source data are provided with this paper.
Data availability The raw data from the prospective study, the raw scores of the retrospective analysis, the input structures and benchmarking scores for the efficiency study, and the raw data from the biolayer interferometry measurements are available at the following repository hosted by the Institute for Protein Design: The main supplement (136 MB) Contains these files: design_models_final_combo_optimized/ design_models_sequence/ design_models_ssm_natives/ design_stats/ dna_production_scripts/ figure_data/ ngs_analysis_scripts/ files.ipd.uw.edu/pub/improving_dl_binders_2023/supplemental_ files/scripts_and_main_pdbs.tar.gz Experimental data and data derived from that data (155 MB) Contains these files: ngs_data/ ngs_data_analysis/ files.ipd.uw.edu/pub/improving_dl_binders_2023/supplemental_ files/experimental_data_and_analysis.tar.gz All ordered proteins in.pdb.gz format: (~100 K files; 15 GB) Contains these files: design_models_pdbs/ files.ipd.uw.edu/pub/improving_dl_binders_2023/supplemental_ files/design_models_pdb.tar.gz All ordered proteins in Rosetta binary silent format (6.1 GB) Contains these files: design_models_silent/ files.ipd.uw.edu/pub/improving_dl_binders_2023/supplemental_ files/design_models_silent.tar.gz The docks we used for the efficiency benchmark (6.1 GB) Contains these files: efficiency_benchmark_docks/ files.ipd.uw.edu/pub/improving_dl_binders_2023/supplemental_ files/efficiency_benchmark_docks.tar.gz . Source data are provided with this paper. Code availability The Rosetta macromolecular modeling suite ( https://www. rosettacommons.org ) is freely available to academic and noncommercial users. Commercial licenses for the suite are available via the University of Washington Technology Transfer Office. Scripts for running ProteinMPNN-FastRelax and AF2 with templating and initial guess are available at https://github.com/nrbennet/dl_binder_design 33 .
10.1021_acschembio.3c00092.pdf
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10.1523_eneuro.0144-22.2022.pdf
Code accessibility The code is included as Extended Data 1 and is available at https://github.com/tsmanning/bayesIdealObserverMoG.
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10.3389_fimmu.2021.689397.pdf
DATA AVAILABILITY STATEMENT The raw data supporting the conclusions of this article will be made available by the authors, without undue reservation.
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10.1038_s41467-023-36872-8.pdf
Data availability Source data are provided within this paper. Raw data that support the findings of this study are available from the corresponding author upon request. Source data are provided with this paper.
Data availability Source data are provided within this paper. Raw data that support the findings of this study are available from the corresponding author upon request. Source data are provided with this paper.
10.1371_journal.pone.0283491.pdf
Data Availability Statement Data cannot be shared publicly because we have used third-party data from National Health Insurance Service, and are not entitled to share the data. Data are available from the Review Board of National Health Insurance Service (contact via NHIS) for researchers who meet the criteria for access to confidential data. Anyone who conducts a joint study with a Korean researcher can access NHIS for customized health information data. Applications for data are available through National Health Insurance Data Sharing website (https://nhiss.nhis.or.kr/bd/ab/bdaba000eng.do), and additional information can be found at a customized health information data webpage (https://nhiss.nhis.or.kr/bd/ab/bdaba032eng.do).
Data cannot be shared publicly because we have used third-party data from National Health Insurance Service, and are not entitled to share the data. Data are available from the Review Board of National Health Insurance Service (contact via NHIS) for researchers who meet the criteria for access to confidential data. Anyone who conducts a joint study with a Korean researcher can access NHIS for customized health information data. Applications for data are available through National
10.1371_journal.pone.0222639.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.0240995.pdf
Data Availability Statement The medical ethical technical committee of Erasmus MC did not grant permission to publish these data due to ethical considerations and the sensitivity of the data. Data are however available from the Erasmus MC upon reasonable request. Contact person: Dr. Juliëtte Severin, Infection prevention and control (IPC) and antimicrobial resistance (AMR) (Data Access) E-mail: [email protected].
The medical ethical technical committee of Erasmus MC did not grant permission to publish these data due to ethical studies should investigate if data-driven cut-offs can add value to explain the outcome being modelled and not solely rely on standard medical cut-off values to identify risk factors. considerations and the sensitivity of the data. Data are however available from the Erasmus MC upon reasonable request. Contact person: Dr. Julie ¨tte
10.1126_scitranslmed.adh9917.pdf
Data and Materials Availability:All data associated with this study are in the paper or supplementary materials. All reasonable requests for materials to the corresponding author will be fulfilled. The VirScan library is available from S.J.E. under a material transfer agreement with the Brigham and Women’s Hospital.
Data and Materials Availability: All data associated with this study are in the paper or supplementary materials. All reasonable requests for materials to the corresponding author will be fulfilled. The VirScan library is available from S.J.E. under a material transfer agreement with the Brigham and Women's Hospital.
10.1088_1748-3190_ad0dae.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.
10.1038_s41598-021-96064-6.pdf
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10.1371_journal.pdig.0000457.pdf
Data Availability Statement: Data from this study has been made available as supplementary information.
Data from this study has been made available as supplementary information.
10.1371_journal.pone.0221212.pdf
Data Availability Statement All relevant data for reproducing indicators are within the paper and the Supporting Information files. All these data have been downloaded from https://www.scival.com/ under provision of the institutional standard contract held by University of Siena. Authors did not have any special access privileges to SCIVAL. Interested researchers may access Scival in the same way the authors did.
All relevant data for reproducing indicators are within the paper and the Supporting Information files. All these data have been downloaded from https://www.scival.com/ under provision of the institutional standard contract held by University of Siena. Authors did not have any special access privileges to SCIVAL. Interested researchers may access Scival in the same way the authors did.
10.1371_journal.pntd.0011960.pdf
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.
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.
10.1088_1361-6463_ad005f.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). ORCID iD Quanliang Cao  https://orcid.org/0000-0003-3691-2311
10.1093/g3journal/jkab168
Data availability The datasets, code for generating all figures, and Supplementary figures can be found at https://github.com/AndersenLab/swept_ broods. Supplementary File S1 contains the haplotype data of 403 C. elegans isotypes from CeNDR release 20200815. Supplementary File S2 contains genetic relatedness of 403 C. elegans isotypes. Supplementary File S3 contains lifetime fecundity of 121 C. ele- gans strains, their classification of swept strains and divergent strains, and the assay blocks of these strains. Supplementary File S4 contains daily fecundity and daily intrinsic growth rate of 121 C. elegans strains. Supplementary File S5 contains GWA results on lifetime fecundity of 121 C. elegans strains. Supplementary File S6 contains genotype and phenotype data of 121 C. elegans strains at the peak markers of GWA mapping. Supplementary File S7 con- tains the sampling locations of 121 C. elegans strains. Supplementary File S8 contains the GPS coordinates of sampling locations of 121 C. elegans strains. Supplementary File S9 contains lifetime fecundity and swept and divergent classifications of each of the four swept chromosomes for each of the 121 C. elegans strains. Supplementary File S10 contains LD results among the three QTL of GWA using 121 C. elegans strains. Supplementary File S11 contains the shared haplotypes of the 121 strains within the QTL of GWA mapping. Supplementary File S12 contains GWA results on fecundity data of 236 strains from a previous study (Hahnel et al. 2018). Supplementary File S13 contains genotype G. Zhang, J. D. Mostad, and E. C. Andersen | 3 and phenotype data of 236 strains at the peak marker of GWA mapping. Supplementary File S14 contains the shared haplotypes of the 236 strains within the QTL of GWA mapping. Supplementary File S15 contains the linkage mapping results for the 402 RIAILs in 1% water condition. Supplementary File S16 contains genotype and phenotype data of the 402 RIAILs at the peak markers and phenotype data of the parents in linkage map- ping results. Supplementary File S17 contains the linkage map- ping results for the 417 RIAILs in 1% DMSO condition. Supplementary File S18 contains genotype and phenotype data of the 417 RIAILs at the peak markers and phenotype data of the parents in linkage mapping results. Supplementary File S19 con- tains the linkage mapping results for the 432 RIAILs in 0.5% DMSO condition. Supplementary File S20 contains genotype and phenotype data of the 432 RIAILs at the peak markers and pheno- type data of the parents in linkage mapping results.
Data availability The datasets, code for generating all figures, and Supplementary figures can be found at https://github.com/AndersenLab/swept_ broods . Supplementary File S1 contains the haplotype data of 403 C. elegans isotypes from CeNDR release 20200815. Supplementary File S2 contains genetic relatedness of 403 C. elegans isotypes. Supplementary File S3 contains lifetime fecundity of 121 C. elegans strains, their classification of swept strains and divergent strains, and the assay blocks of these strains. Supplementary File S4 contains daily fecundity and daily intrinsic growth rate of 121 C. elegans strains. Supplementary File S5 contains GWA results on lifetime fecundity of 121 C. elegans strains. Supplementary File S6 contains genotype and phenotype data of 121 C. elegans strains at the peak markers of GWA mapping. Supplementary File S7 contains the sampling locations of 121 C. elegans strains. Supplementary File S8 contains the GPS coordinates of sampling locations of 121 C. elegans strains. Supplementary File S9 contains lifetime fecundity and swept and divergent classifications of each of the four swept chromosomes for each of the 121 C. elegans strains. Supplementary File S10 contains LD results among the three QTL of GWA using 121 C. elegans strains. Supplementary File S11 contains the shared haplotypes of the 121 strains within the QTL of GWA mapping. Supplementary File S12 contains GWA results on fecundity data of 236 strains from a previous study (Hahnel et al. 2018) . Supplementary File S13 contains genotype and phenotype data of 236 strains at the peak marker of GWA mapping. Supplementary File S14 contains the shared haplotypes of the 236 strains within the QTL of GWA mapping. Supplementary File S15 contains the linkage mapping results for the 402 RIAILs in 1% water condition. Supplementary File S16 contains genotype and phenotype data of the 402 RIAILs at the peak markers and phenotype data of the parents in linkage mapping results. Supplementary File S17 contains the linkage mapping results for the 417 RIAILs in 1% DMSO condition. Supplementary File S18 contains genotype and phenotype data of the 417 RIAILs at the peak markers and phenotype data of the parents in linkage mapping results. Supplementary File S19 contains the linkage mapping results for the 432 RIAILs in 0.5% DMSO condition. Supplementary File S20 contains genotype and phenotype data of the 432 RIAILs at the peak markers and phenotype data of the parents in linkage mapping results. .
10.1038_s41477-023-01439-4.pdf
Data availabilityImage data are available at http://neomorph.salk.edu/downloads/phytomap/. Sequences of all the DNA probes used in this study are provided in Supplementary Table 2. Processed and annotated scRNA-seq data is available at the Gene Expression Omnibus (GSE152766).Code availabilityThe code to analyse PHYTOMap data is available at https://github.com/tnobori/PHYTOMap.
Data availability Image data are available at http://neomorph.salk.edu/downloads/phy- tomap/ . Sequences of all the DNA probes used in this study are provided in Supplementary Table 2 . Processed and annotated scRNA-seq data is available at the Gene Expression Omnibus ( GSE152766 ). Code availability The code to analyse PHYTOMap data is available at https://github.com/ tnobori/PHYTOMap . Extended Data
10.1088_1478-3975_acf5bd.pdf
Data availability statementThe data cannot be made publicly available upon publication because the cost of preparing, depositing and hosting the data would be prohibitive within the terms of this research project. 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 the cost of preparing, depositing and hosting the data would be prohibitive within the terms of this research project. The data that support the findings of this study are available upon reasonable request from the authors.
10.1126_sciadv.adh0411.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.
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10.3390_molecules25040938.pdf
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10.1038_s41586-023-06271-6.pdf
Data availabilityAll calcium imaging and fly behaviour time-course datasets analysed in the main figures are available on DANDI archive (calcium imaging data, 000247; fly choice tracking data, 000212; fly behavioural sequence tracking data, 000250). Technical documents (for example, CAD files and plasmid maps) and source data for all scatter plots and histograms are available on Figshare (10.6084/m9.figshare.c.6505732).Code availabilityScripts for data processing and plotting are available on request.
Data availability All calcium imaging and fly behaviour time-course datasets analysed in the main figures are available on DANDI archive (calcium imaging data, 000247; fly choice tracking data, 000212; fly behavioural sequence tracking data, 000250 ). Technical documents (for example, CAD files and plasmid maps) and source data for all scatter plots and histograms are available on Figshare ( https://doi.org/10.6084/ m9.figshare.c.6505732 ). Code availability Scripts for data processing and plotting are available on request.