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10.1073_pnas.2300360120.pdf
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Data, Materials, and Software Availability The EM maps and corresponding structures reported here have been deposited in EMDB (Electron Microscopy Data Bank) and PDB with the following accession IDs: HR1HR2 N969K: EMDB 28947 (35), PDB 8fa1 (36); and Omicron HR1—42Gv2: EMDB 28948 (37), PDB 8fa2 (38).
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10.1038_s41467-022-35532-7.pdf
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Data availability The P, T data generated in this study have been deposited in the Cor- nell University e-commons data repository database under accession code https://doi.org/10.7298/1sw8-f758.
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Data availability The P, T data generated in this study have been deposited in the Cornell University e-commons data repository database under accession code https://doi.org/10.7298/1sw8-f758 .
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10.1038/s41467-022-30572-5
|
Data availability
The velocity field and wave height products used to run TrackMPD model are available
on the E.U. Copernicus Marine Environment Service Information website (CMEMS,
http://marine.copernicus.eu/). The Mediterranean shore steepness is available on
Copernicus Land Monitoring Service (European Environment Agency, EEA) and on the
US Geological Survey website (https://earthexplorer.usgs.gov/). The crossroadness and
plastic crossroads maps, the detailed origin of the plastic debris intercepted by the plastic
crossroads, the plastic sources distribution, as well all the data necessary to produce the
figures of the Main Text and Supplementary Note are available at https://doi.org/10.
5281/zenodo.5931213. The in situ plastic concentrations are available at https://doi.org/
10.5281/zenodo.5538237.
Code availability
The TrackMPD code is available at https://github.com/IJalonRojas/TrackMPD.
|
Data availability The velocity field and wave height products used to run TrackMPD model are available on the E.U. Copernicus Marine Environment Service Information website (CMEMS, http://marine.copernicus.eu/ ). The Mediterranean shore steepness is available on Copernicus Land Monitoring Service (European Environment Agency, EEA) and on the US Geological Survey website ( https://earthexplorer.usgs.gov/ ). The crossroadness and plastic crossroads maps, the detailed origin of the plastic debris intercepted by the plastic crossroads, the plastic sources distribution, as well all the data necessary to produce the figures of the Main Text and Supplementary Note are available at https://doi.org/10. 5281/zenodo.5931213 . The in situ plastic concentrations are available at https://doi.org/ 10.5281/zenodo.5538237 . Code availability The TrackMPD code is available at https://github.com/IJalonRojas/TrackMPD .
|
10.1371_journal.pmed.1004337.pdf
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Data Availability Statement: The data are freely available upon request by contacting Esther López-GarcÃa at the Department of Preventive Medicine and Public Health, Faculty of Medicine, Universidad Autónoma de Madrid (UAM)-IdiPaz, CIBERESP (CIBER of Epidemiology and Public Health), 28029, Madrid, Spain. E-mail address: esther.lopez@uam.es. UAM website: https://www.uam.es/ss/Satellite/Medicina/es/1242658444664/subhome/Departamento_de_Medicina_Preventiva_y_Salud_Publica_y_Microbiologia.htm.
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The data are freely available upon request by contacting Esther Lo ´pez-Garcı ´a at the
|
10.26508_lsa.202000853.pdf
| null | null |
10.1038_s41467-023-40142-y.pdf
|
Data availabilityOriginal data is provided in Source Data file. All other data is available upon request. Source data are provided with this paper.Code availabilityThe customized python code for data analyzation can be found at https://github.com/sihaohuanguc/larva_trajectory_process or Zenodo (10.5281/zenodo.8011787).
|
Data availability Original data is provided in Source Data file. All other data is available upon request. Source data are provided with this paper. Code availability The customized python code for data analyzation can be found at https://github.com/sihaohuanguc/larva_trajectory_process or Zenodo ( https://doi.org/10.5281/zenodo.8011787 ).
|
10.1038_s41467-020-14862-4.pdf
|
Data availability Crystal structure coordinates and structure factors have been deposited to the Protein Data Bank under accession codes dsA2/GM (6TDO), dsA2/GL (6TDP), dsA2/GM2 (6TDQ), dsA2/peptide_free-1 (6TDR), and dsA2/peptide_free-2 (6TDS), respectively. The thermostability fluorescence data for wtA2 and dsA2 in the presence of different dipeptide concentrations are reported as the 350/330 ratio in the Source Data file for Fig. 1a, b. The outcome of the dihedral angle distribution from the MD simulations is also reported in the Source Data file for Fig. 6a, b. Other data are available from the corresponding authors upon reasonable request.
|
Data availability Crystal structure coordinates and structure factors have been deposited to the Protein Data Bank under accession codes dsA2/GM (6TDO), dsA2/GL (6TDP), dsA2/GM2 (6TDQ), dsA2/peptide_free-1 (6TDR), and dsA2/peptide_free-2 (6TDS), respectively. The thermostability fluorescence data for wtA2 and dsA2 in the presence of different dipeptide concentrations are reported as the 350/330 ratio in the Source Data file for Fig. 1a , b . The outcome of the dihedral angle distribution from the MD simulations is also reported in the Source Data file for Fig. 6a , b . Other data are available from the corresponding authors upon reasonable request.
|
10.1371_journal.pwat.0000227.pdf
|
Data Availability Statement: Data are available from the University of Kentucky Center for Clinical and Translational Science RedCAP data repository (https://www.ccts.uky.edu/services-resources-researchers/redcap) for researchers who meet the criteria for access to human subjects data. To access the data, please contact the database administrator, Brent Seeders (brent.seeders@uky.edu) and request access to data from the Martin County Drinking Water Project.
|
Data Availability Statement: Data are available from the University of Kentucky Center for Clinical and Translational Science RedCAP data repository ( https://www.ccts.uky.edu/services-resources-researchers/ redcap ) for researchers who meet the criteria for access to human subjects data. To access the data, please contact the database administrator, Brent Seeders (brent.seeders@uky.edu) and request access to data from the Martin County Drinking Water Project.
|
10.3389_fcell.2023.1118766.pdf
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Data availability statement The original contributions presented in the study are publicly available. This data can be found here: The RNA-Seq data presented in the study are deposited in the Gene Expression Omnibus (GEO) database, accession no GSE221908. The TMT-prroteomics data are deposited to the ETH Research Collection, DOI: https://doi.org/10.3929/ethz-b-000602269.
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Data availability statement The original contributions presented in the study are publicly available. This data can be found here: The RNA-Seq data presented in the study are deposited in the Gene Expression Omnibus (GEO) database, accession no GSE221908. The TMT-prroteomics data are deposited to the ETH Research Collection, DOI: https://doi.org/10. 3929/ethz-b-000602269 .
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10.1038_s41598-022-08333-7.pdf
|
Data availability The datasets used and/or analyzed during the current study will be available from the corresponding author on reasonable request.
|
Data availability The datasets used and/or analyzed during the current study will be available from the corresponding author on reasonable request.
|
10.1080_17453674.2020.1853341.pdf
| null | null |
10.15252_embj.2023114534.pdf
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Data availabilityCustom software written in MATLAB (R2021a) was used for TIRF colocalization residence lifetime analysis and plot generation. The source code is publicly available at https://github.com/FredHutch/Automated‐Single‐Molecule‐Colocalization‐Analysis. All primary datasets and associated data used for analysis in all figures are available at Zenodo, https://zenodo.org/ and assigned the identifier (10.5281/zenodo.7939301). All primary data reported in this paper will be shared by the lead contact upon request.
|
Data availability Custom software written in MATLAB (R2021a) was used for TIRF colocalization residence lifetime analysis and plot generation. The source code is publicly available at https://github.com/FredHutch/ Automated-Single-Molecule-Colocalization-Analysis . All primary datasets and associated data used for analysis in all figures are available at Zenodo, https://zenodo.org/ and assigned the identifier ( 10.5281/zenodo.7939301 ). All primary data reported in this paper will be shared by the lead contact upon request. Expanded View for this article is available online .
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10.1007_s13348-023-00391-y.pdf
| null | null |
10.1371_journal.pone.0218311.pdf
|
Data Availability Statement The data underlying the results presented in the study are available from the Open Science Framework via https://osf.io/uatkn/.
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The data underlying the results presented in the study are available from the Open Science Framework via https://osf. io/uatkn/ .
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10.1371_journal.pmed.1003980.pdf
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Data Availability Statement All participating ethics committees were project partners and granted us access to confidential study protocols under the condition that only aggregated data will be made publicly available. All investigators signed a corresponding confidentiality agreement with ethics committees. All aggregated data that were used for this study are presented in Tables and Figures of the manuscript or the appendix. The appendix also includes the used statistical code (STATA; S5 Text).
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10.2196_13220.pdf
| null | null |
10.1371_journal.pone.0285197.pdf
|
Data Availability Statement All relevant data are within the paper and its Supporting Information files.
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All relevant data are within the paper and its Supporting Information files.
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10.1016_j.cell.2023.07.039.pdf
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Data and code availabilityAll sequencing data have been deposited at the NCBI Sequence Read Archive database and are publicly available as of the date of publication. Accession numbers are listed in the key resources table.All original code is available in Notes S1 and S2.Any additional information required to reanalyze the data reported in this paper is available from the lead contact upon request.
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10.1007_s43441-020-00159-7.pdf
| null | null |
10.1186_s12909-023-04421-y.pdf
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Availability of data and materials The datasets generated during and/or analysed during the current study are available from the corresponding author on reasonable request.
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Availability of data and materials The datasets generated during and/or analysed during the current study are available from the corresponding author on reasonable request.
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10.1371_journal.pstr.0000101.pdf
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Data Availability Statement: All interview questions and those answers that are anonymized are available in the manuscript and Supporting Information files. Some data cannot be shared publicly due to privacy of the interview participants.
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All interview questions and those answers that are anonymized are available in the manuscript and Supporting expectations. When pivoting to a new product or market, returning to a natural style is beneficial. Information files. Some data cannot be shared publicly due to privacy of the interview participants.
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10.1371_journal.pcbi.1009407.pdf
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Data Availability Statement All code written in support of this publication, processed data, simulation input files and simulation out put files are publicly available at https://gin.g-node.org/oportoles/SwitchingFCalongAtask. Raw data is available at https://www.jelmerborst.nl/models/.
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All code written in support of this publication, processed data, simulation input files and simulation out put files are publicly available at https://gin.g-node.org/ directed cognitive processing and the mechanisms needed to reach states of neural coordination. oportoles/SwitchingFCalongAtask . Raw data is available at https://www.jelmerborst.nl/models/ .
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10.1038_s41598-023-38605-9.pdf
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Data availabilityThe datasets generated and analysed during the current study are available from the corresponding authors on reasonable request. No sequencing was involved in this study.
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Data availability The datasets generated and analysed during the current study are available from the corresponding authors on reasonable request. No sequencing was involved in this study.
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10.14814_phy2.15750.pdf
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DATA AVAILABILITY STATEMENTThe datasets analyzed for this study are available upon request to the corresponding author.
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DATA AVAILABILITY STATEMENT The datasets analyzed for this study are available upon request to the corresponding author. ORCID Alicen A. Whitaker https://orcid. org/0000-0002-8701-9227 Eric D. Vidoni https://orcid.org/0000-0001-5181-7131 Robert N. Montgomery https://orcid. org/0000-0002-1423-0590 Sandra A. Billinger https://orcid. org/0000-0002-1618-7207
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10.1371_journal.pbio.3002069.pdf
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Data Availability Statement All relevant data are within the paper and its Supporting Information files.
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All relevant data are within the paper and its Supporting Information files.
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10.1038_s41467-023-39441-1.pdf
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Data availabilityThe 3D EM maps of the S. cerevisiae apo Pol α in states I at 3.7 Å and II at 3.8 Å, Pol α bound to template ssDNA (state III) at 5.6 Å, Pol α with T/P8 at 4.8 Å, Pol α with T/P10 at 4.5 Å, and Pol α with T/P15 at 3.5 Å resolution have been deposited in the EMDB under accession codes EMD-29345, EMD-29346, EMD-29347, EMD-29349, EMD-29351, and EMD-29352 respectively. The corresponding atomic models have been deposited in the Protein Data Bank under accession codes 8FOC, 8FOD, 8FOE, 8FOH, 8FOJ, and 8FOK, respectively. Source data are provided with this paper.
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Data availability The 3D EM maps of the S. cerevisiae apo Pol α in states I at 3.7 Å and II at 3.8 Å, Pol α bound to template ssDNA (state III) at 5.6 Å, Pol α with T/P8 at 4.8 Å, Pol α with T/P10 at 4.5 Å, and Pol α with T/P15 at 3.5 Å resolution have been deposited in the EMDB under accession codes EMD-29345, EMD-29346, EMD-29347, EMD-29349, EMD-29351, and EMD-29352 respectively. The corresponding atomic models have been deposited in the Protein Data Bank under accession codes 8FOC, 8FOD, 8FOE, 8FOH, 8FOJ, and 8FOK, respectively. Source data are provided with this paper.
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10.1371_journal.pgen.1011144.pdf
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Data Availability Statement: All code from bgspy and our Jupyter Lab (Kluyver et al. n.d.) notebooks for analysis are available on GitHub (https://github.com/vsbuffalo/bprime). The main model fits are available as Python Pickle objects on Data Dryad repository (https://doi.org/10.5061/dryad.qnk98sfnv).
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All code from bgspy and our Jupyter Lab (Kluyver et al. n.d.) notebooks for analysis are available on GitHub ( https://github. com/vsbuffalo/bprime ). The main model fits are available as Python
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10.1155_2019_3172647.pdf
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The original data of the current study are available in the following website: https://figshare.com/s/75bd66bf6fb68b4b0106.
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Data Availability The original data of the current study are available in the following website: https://figshare.com/s/ 75bd66bf6fb68b4b0106 .
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10.1103_physrevd.106.126017.pdf
| null | null |
10.1371_journal.pmed.1004313.pdf
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Data Availability Statement: The data underlying the results presented in the study are available from the Open Science Framework (https://osf.io/5ne6g).
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The data underlying the results presented in the study are available from the Open Science Framework ( https://osf.io/ 5ne6g ).
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10.1126_sciadv.adg3257.pdf
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Data and materials availability: All data needed to evaluate the conclusions in the paper are present in the paper and/or the Supplementary Materials. All primary sequencing data have been deposited in the NCBI’s Gene Expression Omnibus (GEO) under accession code GSE221252.
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10.3390_fractalfract7050351.pdf
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Data Availability Statement: Data sharing does not apply to this article, as no new data were created
or analyzed in this study.
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Data Availability Statement: Data sharing does not apply to this article, as no new data were created or analyzed in this study.
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10.1088_1361-6501_ad076c.pdf
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Data availability statementThe data that support the findings of this study are openly available at the following URL/DOI: http://phm09challenge.blogspot.com.
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Data availability statement The data that support the findings of this study are openly available at the following URL/DOI: http://phm09challenge. blogspot.com .
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10.1371_journal.pone.0290569.pdf
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Data Availability Statement: All Data files are available from the Figshare database: Links: S1_Measuring Facial Mimicry Affdex vs. EMG_Psychometric Data https://figshare.com/articles/dataset/Untitled_ItemMeasuring_Facial_Mimicry_Automated_Facial_Coding_vs_EMG_Psychometric_Data/21777281 S2_Measuring Facial Mimicry Affdex vs. EMG_EMG Data https://figshare.com/articles/dataset/Measuring_Facial_Mimicry_Automated_Facial_Coding_vs_EMG_EMG_Data/21777275 S3_Measuring Facial Mimicry Affdex vs. EMG_Affdex Data https://figshare.com/articles/dataset/Measuring_Facial_Mimicry_Automated_Facial_Coding_vs_EMG_Affdex_Data/21777200 S4_Measuring Facial Mimicry Affdex vs. EMG_Code for Statistics in R https://figshare.com/articles/software/S4_Measuring_Facial_Mimicry_Affdex_vs_EMG_Code_for_Statistics_in_R/22639150.
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All Data files are available from the Figshare database: Links: S1_Measuring Facial Mimicry Affdex vs. EMG_Psychometric Data https://figshare.com/ articles/dataset/Untitled_ItemMeasuring_Facial_ Mimicry_Automated_Facial_Coding_vs_EMG_ Psychometric_Data/21777281 S2_Measuring Facial Mimicry Affdex vs. EMG_EMG Data https:// figshare.com/articles/dataset/Measuring_Facial_ Mimicry_Automated_Facial_Coding_vs_EMG_ EMG_Data/21777275 S3_Measuring Facial Mimicry Affdex vs. EMG_Affdex Data https:// figshare.com/articles/dataset/Measuring_Facial_ Mimicry_Automated_Facial_Coding_vs_EMG_ Affdex_Data/21777200 S4_Measuring https://figshare.com/articles/software/S4_ Measuring_Facial_Mimicry_Affdex_vs_EMG_ Code_for_Statistics_in_R
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10.7554_elife.78558.pdf
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Data availability 16S rRNA gene sequencing data (Figure 3D) and RNA sequencing data (Figure 6A and B; Figure 1—figure supplement 1; Figure 6—figure supplement 1) are available from the Sequence Read Archive under BioProject ID PRJNA793870. All mouse strains used are available commercially. The following dataset was generated: PendseMRajPHooperLV2022Macrophages control gastrointestinal motility through complement component 1qNCBI BioProjectPRJNA793870 The following previously published dataset was used: GattuSBangYCharaAHarrisTKuangZRuhnKSockanathanSHooperLV2019Epithelial retinoic acid receptor beta regulates serum amyloid A expression and vitamin A-dependent intestinal immunityNCBI Gene Expression OmnibusGSE122471
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Data availability 16S rRNA gene sequencing data (Figure 3D ) and RNA sequencing data (Figure 6A and B ; Figure 1 figure supplement 1; Figure 6-figure supplement 1) are available from the Sequence Read Archive under BioProject ID PRJNA793870. All mouse strains used are available commercially. The following dataset was generated:
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10.2196_44330.pdf
| null | null |
10.1073_pnas.2221163120.pdf
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Data, Materials, and Software Availability Python scripts for analysis are available at https://github.com/d-ghose/laub (53). Datasets generated during this study have been deposited in the National Center for Biotechnology Information Sequence Read Archive (NCBI SRA). Raw reads can be found under BioProject ID PRJNA902002 (54). All other data are included in the manuscript and/or SI Appendix.
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10.1371_journal.ppat.1009495.pdf
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Data Availability Statement All relevant data are within the manuscript and its Supporting Information files.
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All relevant data are within the manuscript and its Supporting Information files.
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10.3390_md19090504.pdf
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Data Availability StatementThe data presented in this study are available on request from the corresponding author.
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Data Availability Statement: The data presented in this study are available on request from the corresponding author.
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10.1371_journal.pone.0285697.pdf
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Data Availability Statement All relevant data are within the paper and its Supporting Information files.
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All relevant data are within the paper and its Supporting Information files.
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10.1371_journal.pone.0269830.pdf
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Data Availability Statement All relevant data are within the article and its Supporting information files.
|
All relevant data are within the article and its Supporting information files.
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10.1186_s12870-020-02783-9.pdf
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Availability of data and materials The datasets used and/or analysed during the current study are available from the corresponding author on reasonable request.
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Availability of data and materials The datasets used and/or analysed during the current study are available from the corresponding author on reasonable request.
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10.1084_jem.20230668.pdf
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Data availabilityData are provided in Tables S1, S2, and S3. The raw sequencing data and computer scripts associated with Fig. 2 have been deposited at Github (https://github.com/stratust/igpipeline/tree/igpipeline2_timepoint_v2), and single-cell sequencing data is deposited in GSE233230. This study also uses data from “A Public Database of Memory and Naive B-Cell Receptor Sequences” (https://doi.org/10.5061/dryad.35ks2), PDB (6VYB and 6NB6), cAb-Rep (https://cab-rep.c2b2.columbia.edu/), Sequence Read Archive (accession SRP010970), and from “High frequency of shared clonotypes in human B cell receptor repertoires” (Soto et al., 2019). Computer code to process the antibody sequences is available at GitHub (https://github.com/stratust/igpipeline/tree/igpipeline2_timepoint_v2).
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Data availability Data are provided in Tables S1 , S2 , and S3. The raw sequencing data and computer scripts associated with Fig. 2 have been deposited at Github ( https://github.com/stratust/igpipeline/tree/ igpipeline2_timepoint_v2 ), and single-cell sequencing data is deposited in GSE233230. This study also uses data from 'A Public Database of Memory and Naive B-Cell Receptor Sequences' ( https://doi.org/10.5061/dryad.35ks2 ), PDB (6VYB and 6NB6), cAb-Rep ( https://cab-rep.c2b2.columbia.edu/ ), Sequence Read Archive (accession SRP010970), and from 'High frequency of shared clonotypes in human B cell receptor repertoires' (Soto et al., 2019) . Computer code to process the antibody sequences is available at GitHub ( https://github.com/stratust/igpipeline/ tree/igpipeline2_timepoint_v2 ).
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10.1371_journal.pone.0284609.pdf
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Data Availability Statement The study’s minimal underlying dataset can be found as follows: 1. Annual counts of deaths and crude mortality rates among state prisoners and yearend prison custody populations for all 50 states for years 2001-2015 obtained from the Bureau of Justice Statistics are available as Supplementary Information files. 2. De-identified individual-level data for all deaths among California state prisoners obtained from the from the California Deaths in Custody (DIC) reporting program are available as a Supplementary Information file. 3. Individual-level state prison inmate term records for California and several other states for years 2000-2015 are available as a restricted use dataset from the Inter-university Consortium for Political and Social Research (ICPSR). See: United States Department Of Justice. Office Of Justice Programs. Bureau Of Justice Statistics. National Corrections Reporting Program, 2000-2015: Version 1. 2017. doi:10.3886/ICPSR36746.V1. This data source is available from ICPSR for researchers who meet the criteria for access via https://www.icpsr.umich.edu/web/pages/ (ICPSR 36746).
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This data source is available from ICPSR for researchers who meet the criteria for access via https://www.icpsr.umich.edu/web/ pages/ (ICPSR 36746).
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10.1155_2020_2389527.pdf
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Data Availability The yeast cell gene chip data used to support the findings of this study have been deposited by Spellman et al. in Stanford University.
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Data Availability e yeast cell gene chip data used to support the findings of this study have been deposited by Spellman et al. in Stanford University.
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10.1186_s12889-023-15713-9.pdf
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Data Availability The datasets used and analysed during the current study are available from the University of Bristol data archive, https://data.bris.ac.uk/data/.
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Data Availability The datasets used and analysed during the current study are available from the University of Bristol data archive, https://data.bris.ac.uk/data/ .
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10.1371_journal.pone.0285835.pdf
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Data Availability Statement All relevant data are within the paper.
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All relevant data are within the paper.
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10.1103_prxquantum.4.010306.pdf
| null | null |
10.3390_economies11010021.pdf
| null | null |
10.1186_s12916-023-02895-7.pdf
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Availability of data and materials The data that support the findings of this study are available from the corresponding author upon reasonable request.
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Availability of data and materials The data that support the findings of this study are available from the corresponding author upon reasonable request.
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10.1371_journal.pone.0255694.pdf
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Data Availability Statement All relevant data are within the manuscript.
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All relevant data are within the manuscript.
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10.1038_s41467-023-36996-x.pdf
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Data availability Data in Figs. 2 and 3, Supplementary Figures 3–6, 8, and 10, and DNA receptor sequences in Table 1 and Supplementary Table 1 are provided in the Source Data file. Chemicals catalogs are provided as Supplementary Data 1 and DNA staple sequences are provided as Supplementary Data 2. Source data are provided with this paper.
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Data availability Data in Figs. 2 and 3 , Supplementary Figures 3 4 5 6 , 8, and 10, and DNA receptor sequences in Table 1 and Supplementary Table 1 are provided in the Source Data file. Chemicals catalogs are provided as Supplementary Data 1 and DNA staple sequences are provided as Supplementary Data 2. Source data are provided with this paper. Code availability Files related to DNA origami design (see folder cadnano), CRN simulator (see folder crn), and PERL scripts (see folder perl_scripts) are provided as Supplementary Software files.
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10.1088_1748-3190_ad1336.pdf
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Data availability statementAll data that support the findings of this study are included within the article (and any supplementary files).
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Data availability statement All data that support the findings of this study are included within the article (and any supplementary files).
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10.2196_45777.pdf
| null | null |
10.1103_physrevd.107.075029.pdf
| null | null |
10.1186_s13229-022-00503-8.pdf
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Availability of data and materials
The dataset generated during and analyzed during the current study is not
publicly available due the parameters of parent/participant consent, but is
available from the corresponding author on reasonable request.
|
Availability of data and materials The dataset generated during and analyzed during the current study is not publicly available due the parameters of parent/participant consent, but is available from the corresponding author on reasonable request.
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10.1371_journal.pone.0300509.pdf
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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.
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The authors confirm that all data underlying the findings are fully available without restriction. All relevant data are employed
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10.1088_2631-8695_ad1084.pdf
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Data availability statementAll data that support the findings of this study are included within the article (and any supplementary files).
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Data availability statement All data that support the findings of this study are included within the article (and any supplementary files).
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10.1371_journal.pone.0250260.pdf
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Data Availability Statement All relevant data are within the manuscript and its Supporting information files.
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All relevant data are within the manuscript and its Supporting information files.
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10.1103_physrevb.105.155136.pdf
| null | null |
10.1371_journal.pntd.0011798.pdf
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Data Availability Statement: Data cannot be shared publicly because of confidentiality. Data are available from the Centre for Bilharzia and Tropical Health Research for researchers who meet the criteria for access to confidential data. Email address for request: brightresearch.cbthr@gmail.com.
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Data cannot be shared publicly because of confidentiality. Data are available from the Centre for Bilharzia and Tropical Health Research for researchers who meet the criteria for access to confidential data. Email address for request: brightresearch.cbthr@gmail. com .
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10.3390_nu11061240.pdf
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Availability of Data and Materials The datasets used and/or analyzed in the present study are available from the corresponding author on reasonable request.
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Availability of Data and Materials: The datasets used and/or analyzed in the present study are available from the corresponding author on reasonable request.
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10.1088_1402-4896_ad130d.pdf
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Data availability statementAll data that support the findings of this study are included within the article.
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Data availability statement All data that support the findings of this study are included within the article.
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10.1002_advs.202101333.pdf
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Data Availability Statement The data that support the findings of this study are available from the corresponding author upon reasonable request.
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Data Availability Statement The data that support the findings of this study are available from the corresponding author upon reasonable request.
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10.1371_journal.pone.0266237.pdf
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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.
|
10.1007_s10661-023-11378-4.pdf
|
Data availabilityThe raw data analyzed during the current study are available from Miljödata-MVM. The generated data are included in this published article (and its supplementary information files). The full datasets generated or analyzed during this study are available from the corresponding author on reasonable request.
|
Data availability The raw data analyzed during the current study are available from Miljödata-MVM. The generated data are included in this published article (and its supplementary information files). The full datasets generated or analyzed during this study are available from the corresponding author on reasonable request.
|
10.1088_1361-6420_ad01d4.pdf
|
Data availability statementThe manuscript contains no data from true experiments. The only data used was synthetically generated via numerical simulation. Those simulations are described in the manuscript with sufficient detail that they are reproducible. If requested, we would be happy to share the data or the Matlab codes used, however, they are not sufficiently documented etc to be made available online at this time. The data that support the findings of this study are available upon reasonable request from the authors.
|
Data availability statement The manuscript contains no data from true experiments. The only data used was synthetically generated via numerical simulation. Those simulations are described in the manuscript with sufficient detail that they are reproducible. If requested, we would be happy to share the data or the Matlab codes used, however, they are not sufficiently documented etc to be made available online at this time. The data that support the findings of this study are available upon reasonable request from the authors.
|
10.1088_1361-6528_ace97b.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).
|
10.1088_1402-4896_ad1634.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).
|
10.1088_2632-2153_ad1200.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. https://github.com/hagabbar/cnn_matchfiltering.
|
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. https://github.com/hagabbar/ cnn_matchfiltering .
|
10.3389_fphy.2021.775465.pdf
|
DATA AVAILABILITY STATEMENT
The raw data supporting the conclusions of this article will be
made available by the author, without undue reservation.
|
DATA AVAILABILITY STATEMENT The raw data supporting the conclusions of this article will be made available by the author, without undue reservation.
|
10.1107_s2052252522010624.pdf
|
6. Software availability
Smart Leginon is freely and publicly available as two
components: (1) Leginon and Autoscreen are in myami-3.6
release and above (http://leginon.org) and licensed under the
Apache License, Version 2.0; and (2) Ptolemy is publicly
available for academic use only (https://github.com/SMLC-
NYSBC/ptolemy) and licensed under CC BY-NC 4.0. A
tutorial for how to set up and use Smart Leginon and Auto-
screen is available at https://emg.nysbc.org/redmine/projects/
leginon/wiki/Multi-grid_autoscreening
| null |
10.1371_journal.pgph.0001314.pdf
|
Data Availability Statement SEER data is publicly available on request from the National Cancer Institute (NCI), and can be downloaded through this link - https://seer.cancer.gov/data-software/.
|
SEER data is publicly available on request from the National Cancer Institute (NCI), and can be downloaded through this link - https://seer.cancer.gov/data-software/ .
|
10.1038_s41467-023-40595-1.pdf
|
Data availabilityThe data generated in this research is available in the Source Data file provided with this work. Reagents are available from the Lead Contact. The RNA-seq and snRNA-seq datasets generated in this work have been deposited in the Gene Expression Omnibus (GEO) databases under the following accession codes:GSE189214, RNA-seq dataset of thoraces of wildtype flies or flies with gut yki-tumors at different time points after tumor induction.GSE189218, RNA-seq dataset of thoraces upon overexpression of REPTOR[ACT] in muscle with dMef2-GAL4.GSE228034, RNA-seq dataset of C2C12 myofibers overexpressing Crebrf.GSE227038, snRNA-seq dataset of thoraces upon REPTOR[ACT] or FoxO[ACT] overexpression in muscle with dMef2-GAL4.The snRNA-seq dataset has also been made publicly available at DRSC/TRiP Functional Genomics Resources data portal [https://www.flyrnai.org/scRNA/thorax/] to allow users to query the expression of any gene of interest in thoraces. Source data are provided with this paper.
|
Data availability The data generated in this research is available in the Source Data file provided with this work. Reagents are available from the Lead Contact. The RNA-seq and snRNA-seq datasets generated in this work have been deposited in the Gene Expression Omnibus (GEO) databases under the following accession codes: GSE189214, RNA-seq dataset of thoraces of wildtype flies or flies with gut yki-tumors at different time points after tumor induction. GSE189218, RNA-seq dataset of thoraces upon overexpression of REPTOR [ACT] in muscle with dMef2-GAL4. GSE228034, RNA-seq dataset of C2C12 myofibers overexpressing Crebrf. GSE227038, snRNA-seq dataset of thoraces upon REPTOR [ACT] or FoxO [ACT] overexpression in muscle with dMef2-GAL4. The snRNA-seq dataset has also been made publicly available at DRSC/TRiP Functional Genomics Resources data portal [ https://www. flyrnai.org/scRNA/thorax/ ] to allow users to query the expression of any gene of interest in thoraces. Source data are provided with this paper.
|
10.1186_s12913-023-09326-6.pdf
|
Availability of data and materials The datasets used and/or analysed during the study are available from the corresponding author on request.
|
Availability of data and materials The datasets used and/or analysed during the study are available from the corresponding author on request.
|
10.1073_pnas.2306965120.pdf
|
Data, Materials, and Software AvailabilityRaw scRNA sequencing data generated in this study were deposited to the NCBI Gene Expression Omnibus under the accession number GSE240009 (81).
| null |
10.1186_s12885-020-6609-x.pdf
|
Availability of data and materialsThe dataset used and analysed during the present study is available from the corresponding author upon reasonable request.
|
Availability of data and materials The dataset used and analysed during the present study is available from the corresponding author upon reasonable request.
|
10.1073_pnas.2300052120.pdf
|
Data, Materials, and Software Availability Data have been deposited in the controlled access section of DbGaP consistent with informed consent of tissue donors and can be accessed through the direct link https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000639.v2.p1 (92).
| null |
10.1016_j.neo.2023.100910.pdf
| null | null |
10.1371_journal.pone.0295362.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.
|
10.1038/s41523-020-00191-8
|
DATA AVAILABILITY
The processed RNA-sequencing data generated during this study are publicly
available in Gene Expression Omnibus under the accession https://identifiers.org/geo:
GSE14182857. The raw fastq files are publicly available in Sequence Read Archive
under the accession https://identifiers.org/ncbi/insdc.sra:SRP23660556. Immunohistochemical quantification staining data and Supplementary Tables 1–14 are publicly
available in the figshare repository: https://doi.org/10.6084/m9.figshare.1279370055.
Data supporting Table 1, and Supplementary Tables 7–12, will be made available on
reasonable request from the corresponding author. Ingenuity pathways analysis (IPA)
datasets, supporting Supplementary Tables 7–12 are only available on the PI’s
personal account on IPA. UALCAN and cBioPortal data analyzed during the study are
publicly available on the cBioPortal and UALCAN databases as described in the
figshare data record above.
|
DATA AVAILABILITY The processed RNA-sequencing data generated during this study are publicly available in Gene Expression Omnibus under the accession https://identifiers.org/geo: GSE141828 57 . The raw fastq files are publicly available in Sequence Read Archive under the accession https://identifiers.org/ncbi/insdc.sra:SRP236605 56 . Immunohistochemical quantification staining data and Supplementary Tables 1-14 are publicly available in the figshare repository: https://doi.org/10.6084/m9.figshare.12793700 55 . Data supporting Table 1 , and Supplementary Tables 7 8 9 10 11 12 , will be made available on reasonable request from the corresponding author. Ingenuity pathways analysis (IPA) datasets, supporting Supplementary Tables 7-12 are only available on the PI's personal account on IPA. UALCAN and cBioPortal data analyzed during the study are publicly available on the cBioPortal and UALCAN databases as described in the figshare data record above.
|
10.1371_journal.pmed.1004339.pdf
|
Data Availability Statement: As we are not the owners of the data we are not legally entitled to grant access to the data of the German Pharmacoepidemiological Research Database. In accordance with German data protection regulations, access to the data is granted only to employees of the Leibniz Institute for Prevention Research and Epidemiology – BIPS on the premises of the institute and in the context of approved research projects. Third parties may only access the data in cooperation with the Leibniz Institute for Prevention Research and Epidemiology – BIPS and after signing an agreement for guest researchers. Please contact gepard@leibniz-bips.de for help with this process.
|
As we are not the owners of the data we are not legally entitled to grant access to the data of the German Pharmacoepidemiological Research Database.
|
10.1371_journal.pone.0241200.pdf
|
Data Availability Statement Data is available from Figshare (doi: 10.6084/m9.figshare.13100225).
|
Data is available from Figshare (doi: 10.6084/m9.figshare.13100225 ).
|
10.1088_1361-6501_ad060e.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.
|
10.1186_s12909-021-02802-9.pdf
|
Availability of data and materials All data generated or analysed during this study are included in this submitted article as Appendix I and II.
|
Availability of data and materials All data generated or analysed during this study are included in this submitted article as Appendix I and II.
|
10.1186_s13567-019-0627-1.pdf
| null | null |
10.1172_jci152373.pdf
| null | null |
10.1088_1361-6528_acfa05.pdf
|
Data availability statementAll data that support the findings of this study are included within the article (and any supplementary files). Data will be available from 25 May 2023.
|
Data availability statement All data that support the findings of this study are included within the article (and any supplementary files). Data will be available from 25 May 2023.
|
10.7554_elife.85542.pdf
|
Data availability All data generated or analysed during this study are included in the manuscript and source data files. The pMK33-SAM vector, pLib8 vector, and libraries used in this study are available through DRSC/TRiP Functional Genomics Resources. The following dataset was generated: XiaBViswanathaRHuYMohrSEPerrimonN2023Data from: Pooled genome-wide CRISPR activation screening for rapamycin resistance genes in Drosophila cellsDryad Digital Repository10.5061/dryad.2547d7ww8
|
Data availability All data generated or analysed during this study are included in the manuscript and source data files. The pMK33-SAM vector, pLib8 vector, and libraries used in this study are available through DRSC/TRiP Functional Genomics Resources.
|
10.1073_pnas.2306564120.pdf
|
Data, Materials, and Software Availability3C-HTGTS and HTGTS-V(D)J-seq data were processed through published pipelines (http://robinmeyers.github.io/transloc_pipeline/) as described (18). D usage in VHDJH joins was processed via a custom pipeline (https://github.com/Yyx2626/VDJ_annotation/) (19). Productive and non-productive junctions were processed via another pipeline (https://github.com/Yyx2626/VDJ_annotation/) (19). HTGTS-V(D)J-seq, 3C-HTGTS and GRO-seq sequencing data reported in this study are available through GEO (GSE230605) (58). All study data are included in the article and/or SI Appendix. Previously published data were used for this work [GSE151910 (22) and GSE821126 (53)].
| null |
10.1371_journal.pone.0283609.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_2515-7620_ad1063.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 statement 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.
|
10.1186_s12889-021-11008-z.pdf
|
Availability of data and materials All data generated or analysed during this study are included in this published article and the Additional files.
|
Availability of data and materials All data generated or analysed during this study are included in this published article and the Additional files.
|
10.1371_journal.pone.0253540.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.
|
10.21468_scipostphys.12.2.078.pdf
| null | null |
10.1371_journal.pclm.0000122.pdf
|
Data Availability Statement Data is provided in the supporting information file.
|
Data is provided in the supporting information file.
|
10.1038_s41598-019-45336-3.pdf
| null | null |
10.1093_hmg_ddad091.pdf
|
Data AvailabilityThe data generated for this paper will be available from the corresponding author on reasonable request.
|
Data Availability The data generated for this paper will be available from the corresponding author on reasonable request.
|
10.1093_nar_gkad439.pdf
|
Data Availability The data underlying this article are available in the article and in its online supplementary material.
|
DA T A A V AILABILITY The data underlying this article are available in the article and in its online supplementary material.
|
10.1371_journal.pdig.0000349.pdf
|
Data Availability Statement: The questions of this exam cannot be made publicly because they will be used again in future exams. Consequently, the authors cannot share all the AI responses. Access to the study data can be requested by contacting fampop@uantwerpen.be and will be granted as long as the requestor can guarantee that they will not be made publicly and no students will have access to them. As supplementary material, we do provide a datasheet with our raw data excluding the answers and the questions (S1 Data and S2 Data). Individual student results, even anonymised will never be shared as it is impossible to ask permission to all students.
|
The questions of this exam cannot be made publicly because they will be used again in future exams. Consequently, the authors cannot share all the AI responses. Access be and will be granted as long as the requestor can guarantee that they will not be made publicly and no students will have access to them. As supplementary material, we do provide a datasheet with our raw data excluding the answers and the questions (S1 Data and S2 Data). Individual student results, even anonymised will never be shared as it is impossible to ask permission to all students.
|
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