cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.22002/rkcx5-se710
title: JV9298

description: Legionella pneumophila JV9298 DotF-GFP DotB E191K
description: <strong>Tilt Series Date:</strong> 2020-04-23</p>
<strong>Data Taken By:</strong> Yuxi Liu</p>
<strong>Species / Specimen:</strong> Legionella pneumophila</p>
<strong>Strain:</strong> Philadelphia-1_Lp02</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-54.0°, 54.0°), step: 3°, constant angular increment, dosage: 100.0 eV/Å²,  defocus: -4.0 μm,  magnification: 33000x. </p>
<strong>Acquisition Software:</strong> Serial EM</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> imod, tomo3d</p>
<strong>Collaborators and Roles:</strong> Sample preparation & data collection: Yuxi Liu Data processing: Phyllis Wang & Yuxi Liu</p>
<strong>Purification / Growth Conditions / Treatment:</strong> O.D. 2.5-3.0 in AYE</p>
<strong>Sample Preparation:</strong> Quantifoil R2/2 copper grid, 10nm gold, 100% humidity, 25deg C, 4uL of 2X concentrated cells Blotting: force 6, blot 3sec, wait 1sec</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ylx2020-04-23-146/3dimage_123972/</p>JV9298_PD-1-3_531_SIRT_1k.mrc,  Reconstruction (Pixel Size 1.04 nm), 2.1 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ylx2020-04-23-146/3dimage_123972/JV9298_PD-1-3_531_SIRT_1k.mrc"
        > <i class="download icon"></i> Download </a></p>

        JV9298_PD-1-3_531.mrc,  Tilt Series (Pixel Size 0.26 nm), 1.7 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ylx2020-04-23-146/rawdata/JV9298_PD-1-3_531.mrc"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/62tzz-xf470
title: JV9298

description: DotF-sfGFP DotB E191K
description: <strong>Tilt Series Date:</strong> 2019-10-14</p>
<strong>Data Taken By:</strong> Yuxi Liu</p>
<strong>Species / Specimen:</strong> Legionella pneumophila</p>
<strong>Strain:</strong> Philadelphia-1_Lp02</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-54.0°, 54.0°), step: 3°, constant angular increment, dosage: 100.0 eV/Å²,  defocus: -5.0 μm,  magnification: 33000x. </p>
<strong>Microscope:</strong> PNCC Krios 3</p>
<strong>Acquisition Software:</strong> Serial EM</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> Strain from Joe Vogel</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Late exponential/Early stationary</p>
<strong>Sample Preparation:</strong> Quantifoil R2/2 copper. Vitrobot 22 deg C, 100% humidity, 4uL of 2X concentrated culture, blot force 6, blot time 3 sec, drain time 1 sec, wait time 0 sec.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ylx2019-10-14-210/rawdata/</p>JV9298_98_D4.mrc,  Tilt Series (Pixel Size 0.1323 nm), 14.0 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ylx2019-10-14-210/rawdata/JV9298_98_D4.mrc"
        > <i class="download icon"></i> Download </a></p>

        JV9298_98_D4_part37_3.rec,  Reconstruction (Pixel Size 1.0584 nm), 1.0 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ylx2019-10-14-210/3dimage_109872/JV9298_98_D4_part37_3.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/0fadc-pzx26
title: Shewanella oneidensis MR-1

description: Raw data files of Shewanella oneidensis MR-1
description: <strong>Tilt Series Date:</strong> 2018-05-22</p>
<strong>Data Taken By:</strong> Mohammed Kaplan</p>
<strong>Species / Specimen:</strong> Shewanella oneidensis</p>
<strong>Strain:</strong> MR-1</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 2.0°, constant angular increment, dosage: 150.0 eV/Å²,  defocus: -8.0 μm,  magnification: 27500x. </p>
<strong>Microscope:</strong> Caltech Polara</p>
<strong>Acquisition Software:</strong> Serial EM</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> Cells were prepared in chemostat (2 days) by Sahand from Moh's group in USC.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> These are fixed cells prepared in chemostat (2 days). Poorna has prepared these grids but they were not good (only few cells present per grid). I imaged them on the Polara to check if they have "iron cores" so that I send them to Sharon in Weizmann Institute.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2018-05-22-3/rawdata/</p>tilt3.mrc,  Tilt Series (Pixel Size 0.39 nm), 1.4 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2018-05-22-3/rawdata/tilt3.mrc"
        > <i class="download icon"></i> Download </a></p>

        tilt3_full.rec,  Reconstruction (Pixel Size 1.56 nm), 533.4 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2018-05-22-3/3dimage_92650/tilt3_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/2fnpg-jxf27
title: JV9298

description: Legionella pneumophila JV9298 DotF-GFP DotB E191K
description: <strong>Tilt Series Date:</strong> 2020-04-23</p>
<strong>Data Taken By:</strong> Yuxi Liu</p>
<strong>Species / Specimen:</strong> Legionella pneumophila</p>
<strong>Strain:</strong> Philadelphia-1_Lp02</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-54.0°, 54.0°), step: 3°, constant angular increment, dosage: 100.0 eV/Å²,  defocus: -4.0 μm,  magnification: 33000x. </p>
<strong>Acquisition Software:</strong> Serial EM</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> imod, tomo3d</p>
<strong>Collaborators and Roles:</strong> Sample preparation & data collection: Yuxi Liu Data processing: Phyllis Wang & Yuxi Liu</p>
<strong>Purification / Growth Conditions / Treatment:</strong> O.D. 2.5-3.0 in AYE</p>
<strong>Sample Preparation:</strong> Quantifoil R2/2 copper grid, 10nm gold, 100% humidity, 25deg C, 4uL of 2X concentrated cells Blotting: force 6, blot 3sec, wait 1sec</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ylx2020-04-23-280/3dimage_124222/</p>JV9298_PD-1-3_205_SIRT_1k.mrc,  Reconstruction (Pixel Size 1.04 nm), 2.1 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ylx2020-04-23-280/3dimage_124222/JV9298_PD-1-3_205_SIRT_1k.mrc"
        > <i class="download icon"></i> Download </a></p>

        JV9298_PD-1-3_205.mrc,  Tilt Series (Pixel Size 0.26 nm), 1.6 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ylx2020-04-23-280/rawdata/JV9298_PD-1-3_205.mrc"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/q062x-g6f83
title: U937 infection

description: Lp02 pCyaA::RalF-Ub V76 .  U937
description: <strong>Tilt Series Date:</strong> 2020-07-31</p>
<strong>Data Taken By:</strong> Yuxi Liu</p>
<strong>Species / Specimen:</strong> Legionella pneumophila</p>
<strong>Strain:</strong> Philadelphia-1_Lp02</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 2°, constant angular increment, dosage: 120.0 eV/Å²,  defocus: -6.0 μm,  magnification: 33000x. </p>
<strong>Microscope:</strong> Caltech Titan Krios</p>
<strong>Acquisition Software:</strong> Serial EM</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> Stephen Carter</p>
<strong>Purification / Growth Conditions / Treatment:</strong> 1h infection, 1-2 washes, fibronectin/vitronectin/no matrix. Legionella: 2.5 O.D, 3h after 200mM  IPTG induction, at O.D. 3</p>
<strong>Sample Preparation:</strong> 200mesh Gold quantifoil,  10nm gold, 37deg C, 80-90% humidity</p>
description: Files available via S3 at s://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ylx2020-07-31-36/rawdata/</p>tomography8_155.mrc,  Tilt Series (Pixel Size 0.265 nm), 2.9 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ylx2020-07-31-36/rawdata/tomography8_155.mrc"
        > <i class="download icon"></i> Download </a></p>

        tomography8_155_full.rec,  Reconstruction (Pixel Size 1.06 nm), 516.1 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ylx2020-07-31-36/3dimage_113207/tomography8_155_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.5281/zenodo.16906683
title: Spectral Functions of an Extended Antiferromagnetic S=1/2 Heisenberg Model on the Triangular Lattice

description: We provide the data, i.e., the dynamical correlations and corresponding spectral function for various phases on the triangular lattice Heisenberg antiferromagnet with a scalar chiral interaction, and the plotting scripts for our publication. Code that transforms the correlation data into dynamical spin structure factors is also included.
DOI: 10.5281/zenodo.16906684
title: Spectral Functions of an Extended Antiferromagnetic S=1/2 Heisenberg Model on the Triangular Lattice

description: We provide the data, i.e., the dynamical correlations and corresponding spectral function for various phases on the triangular lattice Heisenberg antiferromagnet with a scalar chiral interaction, and the plotting scripts for our publication. Code that transforms the correlation data into dynamical spin structure factors is also included.
DOI: 10.15468/dl.gfy9ba
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Pternistis squamatus",
 "Country is China",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0048033-250811113504898/datasets/export for details.
DOI: 10.15468/dl.tyktgm
title: Occurrence Download

description: A dataset containing 39652 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "TaxonKey is Lythrum hyssopifolia"
 ]
}

 The dataset includes 39652 records from 861 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0048028-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jjp55g
title: Occurrence Download

description: A dataset containing 569 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "TaxonKey is Agonum errans (Say, 1823)",
 "Year is greater than or equal to 1950",
 {
 "or" : [
 "GadmGid is USA",
 "GadmGid is CAN",
 "GadmGid is MEX"
 ]
 }
 ]
}

 The dataset includes 569 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008823-250515123054153/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.7910/dvn/izj99d
title: Replication Data for: Blame Avoidance and Diversion of public criticism in China

description: This dataset contains all the downloaded Weibo texts and the code to run the results of the four figures in the paper. The texts are in .pkl format. The code is in .ipynb format, and can be accessed through Jupiter Notebook.
DOI: 10.6084/m9.figshare.29196785
title: Cell-Matrix Mechanical Modelling

description: The dataset shared was used to simulate the mechanical environment perceived by cells seeded inside 3D microporous biomaterials. Specifically porous collagen-based scaffolds utilized for skin regenerations and 3D printed scaffolds fabricated by two-photon photopolymerization.Here we include example models that were used in the study, guides on how the models can be used as well as custom code used to generate cell positions within the materials
DOI: 10.6084/m9.figshare.29196785.v1
title: Cell-Matrix Mechanical Modelling

description: The dataset shared was used to simulate the mechanical environment perceived by cells seeded inside 3D microporous biomaterials. Specifically porous collagen-based scaffolds utilized for skin regenerations and 3D printed scaffolds fabricated by two-photon photopolymerization.Here we include example models that were used in the study, guides on how the models can be used as well as custom code used to generate cell positions within the materials
DOI: 10.6084/m9.figshare.28846013
title: Spectra data for manuscript "Very low-yield nuclear test verification with post-experiment gamma spectrometry".

description: This file contains the data that is used to produce results and plots in this research. They contain arrays of numbers that represent gamma spectra computed with simulations of subcritical and supercritical tests and collected by a simulated HPGe gamma spectrometer placed outside of the test vessel, one month to one year after a test. These arrays are divided into two files: spectra obtained where the pre-test configuration is a thin shell (spectra_data_shell.txt) and those obtained for a solid sphere (spectra_data_sphere.txt). Within each file, each spectral data set is headed by input parameters (test parameters): alpha (the criticality level of the test), no (the initial number of fissions per kg of plutonium-239), and the time between the test and the measurement. The numbers in these arrays represent the counts of gamma photons detected in energy bins of 1 keV from 0 to 3000 keV.
DOI: 10.15468/dl.5hy5kk
title: Occurrence Download

description: A dataset containing 709671 species occurrences available in GBIF matching the query:
{
 "Geometry" : [
 "POLYGON((-96.19986 15.91187,-93.56558 15.91187,-93.56558 17.71556,-96.19986 17.71556,-96.19986 15.91187))"
 ]
}

 The dataset includes 709671 records from 826 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000794-250424135625364/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.60933/prdr/rd5mqs
title: Shaking table datasets

description: Shaking table datasets for "Simultaneous monitoring of displacement and rotation of a long-span bridge based on innovative integration of GNSS and accelerometer measurements"
DOI: 10.15468/dl.6f3mzt
title: Occurrence Download

description: A dataset containing 55260 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Observation, Human Observation, Living Specimen, Occurrence evidence)",
 "Geometry POLYGON((-73.945 10.045,-73.263 10.045,-73.263 10.468,-73.945 10.468,-73.945 10.045))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is one of (Magnoliopsida, Pinopsida)",
 "Year 1990-2025"
 ]
}

 The dataset includes 55260 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000793-250424135625364/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.15469651
title: c150_7.2Gb

description: Synthetic Metagenomic Dataset

Number of samples: 10  - Total size: 64 GB  - Complexity: 150  - Depth: 7.2 Gb per sample  

Contents:- `processed_read/sample?.?.fastq.gz`: Anonymous processed reads (paired)- `contig/sample?.contigs.fasta`: Gold standard contigs- `gsa_mapping/sample?_gsa_mapping.tsv`: GSA mapping files

Split parts:- Part 1: https://doi.org/10.5281/zenodo.15380694- Part 2: https://doi.org/10.5281/zenodo.15380874- Part 3: https://doi.org/10.5281/zenodo.15312613

To reconstruct:cat c150_7_2Gb_part_* > c150_7.2Gb.tar.gztar -xzf c150_7.2Gb.tar.gz
DOI: 10.5281/zenodo.15469652
title: c150_7.2Gb

description: Synthetic Metagenomic Dataset

Number of samples: 10  - Total size: 64 GB  - Complexity: 150  - Depth: 7.2 Gb per sample  

Contents:- `processed_read/sample?.?.fastq.gz`: Anonymous processed reads (paired)- `contig/sample?.contigs.fasta`: Gold standard contigs- `gsa_mapping/sample?_gsa_mapping.tsv`: GSA mapping files

Split parts:- Part 1: https://doi.org/10.5281/zenodo.15380694- Part 2: https://doi.org/10.5281/zenodo.15380874- Part 3: https://doi.org/10.5281/zenodo.15312613

To reconstruct:cat c150_7_2Gb_part_* > c150_7.2Gb.tar.gztar -xzf c150_7.2Gb.tar.gz
DOI: 10.22033/esgf/cmip6.2817
title: AWI AWI-CM1.1MR model output prepared for CMIP6 ScenarioMIP ssp585

description: Coupled Model Intercomparison Project Phase 6 (CMIP6) datasets: These data include all datasets published for 'CMIP6.ScenarioMIP.AWI.AWI-CM-1-1-MR.ssp585' with the full Data Reference Syntax following the template 'mip_era.activity_id.institution_id.source_id.experiment_id.member_id.table_id.variable_id.grid_label.version'.
 
 The AWI-CM 1.1 MR climate model, released in 2018, includes the following components:
 atmos: ECHAM6.3.04p1 (T127L95 native atmosphere T127 gaussian grid; 384 x 192 longitude/latitude; 95 levels; top level 80 km), land: JSBACH 3.20, ocean: FESOM 1.4 (unstructured grid in the horizontal with 830305 wet nodes; 46 levels; top grid cell 0-5 m), seaIce: FESOM 1.4. 
The model was run by the Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany (AWI) in native nominal resolutions: atmos: 100 km, land: 100 km, ocean: 25 km, seaIce: 25 km. 

Project: These data have been generated as part of the internationally-coordinated Coupled Model Intercomparison Project Phase 6 (CMIP6; see also GMD Special Issue: http://www.geosci-model-dev.net/special_issue590.html). The simulation data provides a basis for climate research designed to answer fundamental science questions and serves as resource for authors of the Sixth Assessment Report of the Intergovernmental Panel on Climate Change (IPCC-AR6).

CMIP6 is a project coordinated by the Working Group on Coupled Modelling (WGCM) as part of the World Climate Research Programme (WCRP). Phase 6 builds on previous phases executed under the leadership of the Program for Climate Model Diagnosis and Intercomparison (PCMDI) and relies on the Earth System Grid Federation (ESGF) and the Centre for Environmental Data Analysis (CEDA) along with numerous related activities for implementation. The original data is hosted and partially replicated on a federated collection of data nodes, and most of the data relied on by the IPCC is being archived for long-term preservation at the IPCC Data Distribution Centre (IPCC DDC) hosted by the German Climate Computing Center (DKRZ).

The project includes simulations from about 120 global climate models and around 45 institutions and organizations worldwide. - Project website: https://pcmdi.llnl.gov/CMIP6.
DOI: 10.6084/m9.figshare.27968943
title: Transcriptome analysis of testes gene expression to explore genetic diversity of Mangalica and Camborough boars

description: Testis, Development, Mangalica boar, RNA-seq
DOI: 10.6084/m9.figshare.27968943.v1
title: Transcriptome analysis of testes gene expression to explore genetic diversity of Mangalica and Camborough boars

description: Testis, Development, Mangalica boar, RNA-seq
DOI: 10.22033/esgf/cmip6.625
title: MRI MRI-ESM2.0 model output prepared for CMIP6 CFMIP

description: Coupled Model Intercomparison Project Phase 6 (CMIP6) datasets: These data include all datasets published for 'CMIP6.CFMIP.MRI.MRI-ESM2-0' with the full Data Reference Syntax following the template 'mip_era.activity_id.institution_id.source_id.experiment_id.member_id.table_id.variable_id.grid_label.version'.
 
 The MRI-ESM2.0 climate model, released in 2017, includes the following components:
 aerosol: MASINGAR mk2r4 (TL95; 192 x 96 longitude/latitude; 80 levels; top level 0.01 hPa), atmos: MRI-AGCM3.5 (TL159; 320 x 160 longitude/latitude; 80 levels; top level 0.01 hPa), atmosChem: MRI-CCM2.1 (T42; 128 x 64 longitude/latitude; 80 levels; top level 0.01 hPa), land: HAL 1.0, ocean: MRI.COM4.4 (tripolar primarily 0.5 deg latitude/1 deg longitude with meridional refinement down to 0.3 deg within 10 degrees north and south of the equator; 360 x 364 longitude/latitude; 61 levels; top grid cell 0-2 m), ocnBgchem: MRI.COM4.4, seaIce: MRI.COM4.4. 
The model was run by the Meteorological Research Institute, Tsukuba, Ibaraki 305-0052, Japan (MRI) in native nominal resolutions: aerosol: 250 km, atmos: 100 km, atmosChem: 250 km, land: 100 km, ocean: 100 km, ocnBgchem: 100 km, seaIce: 100 km. 

Project: These data have been generated as part of the internationally-coordinated Coupled Model Intercomparison Project Phase 6 (CMIP6; see also GMD Special Issue: http://www.geosci-model-dev.net/special_issue590.html). The simulation data provides a basis for climate research designed to answer fundamental science questions and serves as resource for authors of the Sixth Assessment Report of the Intergovernmental Panel on Climate Change (IPCC-AR6).

CMIP6 is a project coordinated by the Working Group on Coupled Modelling (WGCM) as part of the World Climate Research Programme (WCRP). Phase 6 builds on previous phases executed under the leadership of the Program for Climate Model Diagnosis and Intercomparison (PCMDI) and relies on the Earth System Grid Federation (ESGF) and the Centre for Environmental Data Analysis (CEDA) along with numerous related activities for implementation. The original data is hosted and partially replicated on a federated collection of data nodes, and most of the data relied on by the IPCC is being archived for long-term preservation at the IPCC Data Distribution Centre (IPCC DDC) hosted by the German Climate Computing Center (DKRZ).

The project includes simulations from about 120 global climate models and around 45 institutions and organizations worldwide. - Project website: https://pcmdi.llnl.gov/CMIP6.