cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.22002/pmfd3-f2d81
title: Ecoli_Cojugation

description: These are donor E coli cells (ANB35) and recipient Ecoli cells (ANB24). These are the same  .  cells described in the Science paper (Direct visualization of horizontal gene transfer). The .  cells were mixed on the grid and then plunge frozen and imaged with cryo-ET without CLEM. .  Targets were imaged with cryo-ET randomly.
description: <strong>Tilt Series Date:</strong> 2019-02-28</p>
<strong>Data Taken By:</strong> Mohammed Kaplan</p>
<strong>Species / Specimen:</strong> Escherichia coli</p>
<strong>Strain:</strong> </p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-50.0°, 50.0°), step: 1°, constant angular increment, dosage: 130.0 eV/Å²,  defocus: -10.0 μm,  magnification: 26000x. </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> The cells were sent to the Jensen lab from the lab of Ariel Lindner in Paris. These are the same . cells used in their Science paper (direct visualization of horizontal gene transfer).</p>
<strong>Purification / Growth Conditions / Treatment:</strong> ANB 35 were grown in LB while ANB24 (Recipient) in M9. I followed the same protocol . described in the Science paper described above.</p>
<strong>Sample Preparation:</strong> The donor and recipient cells were mixed on the EM grid, incubated in the vitrobot chamber with . 100% humidity and then blotted and plunge frozen.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2019-02-28-93/rawdata/</p>Ecoli_CONjugation53.mrc,  Tilt Series (Pixel Size 0.541 nm), 2.9 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2019-02-28-93/rawdata/Ecoli_CONjugation53.mrc"
        > <i class="download icon"></i> Download </a></p>

        Ecoli_CONjugation53_full.rec,  Reconstruction (Pixel Size 2.164 nm), 445.4 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2019-02-28-93/3dimage_107189/Ecoli_CONjugation53_full.rec"
        > <i class="download icon"></i> Download </a></p>

        Ecoli_CONjugation53.mrc.mdoc,  50.9 kB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/jdgrx-h7g71
title: Ecoli_Cojugation

description: These are donor E coli cells (ANB35) and recipient Ecoli cells (ANB24). These are the same  .  cells described in the Science paper (Direct visualization of horizontal gene transfer). The .  cells were mixed on the grid and then plunge frozen and imaged with cryo-ET without CLEM. .  Targets were imaged with cryo-ET randomly.
description: <strong>Tilt Series Date:</strong> 2019-02-28</p>
<strong>Data Taken By:</strong> Mohammed Kaplan</p>
<strong>Species / Specimen:</strong> Escherichia coli</p>
<strong>Strain:</strong> </p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-50.0°, 50.0°), step: 1°, constant angular increment, dosage: 130.0 eV/Å²,  defocus: -10.0 μm,  magnification: 26000x. </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> The cells were sent to the Jensen lab from the lab of Ariel Lindner in Paris. These are the same . cells used in their Science paper (direct visualization of horizontal gene transfer).</p>
<strong>Purification / Growth Conditions / Treatment:</strong> ANB 35 were grown in LB while ANB24 (Recipient) in M9. I followed the same protocol . described in the Science paper described above.</p>
<strong>Sample Preparation:</strong> The donor and recipient cells were mixed on the EM grid, incubated in the vitrobot chamber with . 100% humidity and then blotted and plunge frozen.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2019-02-28-58/rawdata/</p>Ecoli_CONjugation25.mrc,  Tilt Series (Pixel Size 0.541 nm), 2.9 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2019-02-28-58/rawdata/Ecoli_CONjugation25.mrc"
        > <i class="download icon"></i> Download </a></p>

        Ecoli_CONjugation25_full.rec,  Reconstruction (Pixel Size 2.164 nm), 445.4 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2019-02-28-58/3dimage_107123/Ecoli_CONjugation25_full.rec"
        > <i class="download icon"></i> Download </a></p>

        Ecoli_CONjugation25.mrc.mdoc,  51.0 kB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/4zwjz-ap379
title: Ecoli_Cojugation

description: These are donor E coli cells (ANB35) and recipient Ecoli cells (ANB24). These are the same  .  cells described in the Science paper (Direct visualization of horizontal gene transfer). The .  cells were mixed on the grid and then plunge frozen and imaged with cryo-ET without CLEM. .  Targets were imaged with cryo-ET randomly.
description: <strong>Tilt Series Date:</strong> 2019-02-28</p>
<strong>Data Taken By:</strong> Mohammed Kaplan</p>
<strong>Species / Specimen:</strong> Escherichia coli</p>
<strong>Strain:</strong> </p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-50.0°, 50.0°), step: 1°, constant angular increment, dosage: 130.0 eV/Å²,  defocus: -10.0 μm,  magnification: 26000x. </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> The cells were sent to the Jensen lab from the lab of Ariel Lindner in Paris. These are the same . cells used in their Science paper (direct visualization of horizontal gene transfer).</p>
<strong>Purification / Growth Conditions / Treatment:</strong> ANB 35 were grown in LB while ANB24 (Recipient) in M9. I followed the same protocol . described in the Science paper described above.</p>
<strong>Sample Preparation:</strong> The donor and recipient cells were mixed on the EM grid, incubated in the vitrobot chamber with . 100% humidity and then blotted and plunge frozen.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2019-02-28-75/rawdata/</p>Ecoli_CONjugation37.mrc,  Tilt Series (Pixel Size 0.541 nm), 2.6 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2019-02-28-75/rawdata/Ecoli_CONjugation37.mrc"
        > <i class="download icon"></i> Download </a></p>

        Ecoli_CONjugation37_full.rec,  Reconstruction (Pixel Size 2.164 nm), 445.4 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2019-02-28-75/3dimage_107155/Ecoli_CONjugation37_full.rec"
        > <i class="download icon"></i> Download </a></p>

        Ecoli_CONjugation37.mrc.mdoc,  45.9 kB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/1r4pt-cbz59
title: Ecoli_Cojugation

description: These are donor E coli cells (ANB35) and recipient Ecoli cells (ANB24). These are the same  .  cells described in the Science paper (Direct visualization of horizontal gene transfer). The .  cells were mixed on the grid and then plunge frozen and imaged with cryo-ET without CLEM. .  Targets were imaged with cryo-ET randomly.
description: <strong>Tilt Series Date:</strong> 2019-02-28</p>
<strong>Data Taken By:</strong> Mohammed Kaplan</p>
<strong>Species / Specimen:</strong> Escherichia coli</p>
<strong>Strain:</strong> </p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-50.0°, 50.0°), step: 1°, constant angular increment, dosage: 130.0 eV/Å²,  defocus: -10.0 μm,  magnification: 26000x. </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> The cells were sent to the Jensen lab from the lab of Ariel Lindner in Paris. These are the same . cells used in their Science paper (direct visualization of horizontal gene transfer).</p>
<strong>Purification / Growth Conditions / Treatment:</strong> ANB 35 were grown in LB while ANB24 (Recipient) in M9. I followed the same protocol . described in the Science paper described above.</p>
<strong>Sample Preparation:</strong> The donor and recipient cells were mixed on the EM grid, incubated in the vitrobot chamber with . 100% humidity and then blotted and plunge frozen.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2019-02-28-34/rawdata/</p>Ecoli_Conjugation6.mrc,  Tilt Series (Pixel Size 0.541 nm), 2.9 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2019-02-28-34/rawdata/Ecoli_Conjugation6.mrc"
        > <i class="download icon"></i> Download </a></p>

        Ecoli_Conjugation6_part101_5.rec,  Reconstruction (Pixel Size 2.164 nm), 445.4 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2019-02-28-34/3dimage_107060/Ecoli_Conjugation6_part101_5.rec"
        > <i class="download icon"></i> Download </a></p>

        Ecoli_Conjugation6.mrc.mdoc,  50.7 kB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/7ttgc-99m60
title: Ecoli_EPEC_8612

description: These are E coli cells (EPEC 8612) obtained from Ritesh (Ilan Rosenshine lab at the Hebrew  .  university). The idea is to image bacterial nanotubes in these cells.
description: <strong>Tilt Series Date:</strong> 2020-02-08</p>
<strong>Data Taken By:</strong> Mohammed Kaplan</p>
<strong>Species / Specimen:</strong> Escherichia coli</p>
<strong>Strain:</strong> 8612, EPEC Δrof1-escLΔrof3-mpcΔescN-espFΔflhBAΔfliOPQRΔminCD</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-51.0°, 51.0°), step: 3°, constant angular increment, dosage: 80.0 eV/Å²,  defocus: -8.0 μm,  magnification: 19500x. </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> These cells were prepared with Ritesh in Ilan Rosenshine lab at the Hebrew University. </p>
<strong>Purification / Growth Conditions / Treatment:</strong> The cells were incubated on grids on agar plates (DMEM agar plates for three hours) and then . on starvation medium agar plate for 1 hour. Then washed with PBS and blotted and then plunge . frozen. Yuxi helped in sample preparation and data collection.</p>
<strong>Sample Preparation:</strong> The cells were incubated on grids on agar plates (DMEM agar plates for three hours) and then . on starvation medium agar plate for 1 hour. </p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2020-02-08-31/rawdata/</p>EPEC_8612_tilt5_positive.mrc,  Tilt Series (Pixel Size 0.449 nm), 672.9 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2020-02-08-31/rawdata/EPEC_8612_tilt5_positive.mrc"
        > <i class="download icon"></i> Download </a></p>

        EPEC_8612_tilt5_positive_full.rec,  Reconstruction (Pixel Size 1.796 nm), 501.1 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2020-02-08-31/3dimage_110692/EPEC_8612_tilt5_positive_full.rec"
        > <i class="download icon"></i> Download </a></p>

        EPEC_8612_tilt5_positive.mrc.mdoc,  12.0 kB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2020-02-08-31/rawdata/EPEC_8612_tilt5_positive.mrc.mdoc"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/yz63c-yd010
title: Ecoli_Cojugation

description: These are donor E coli cells (ANB35) and recipient Ecoli cells (ANB24). These are the same  .  cells described in the Science paper (Direct visualization of horizontal gene transfer). The .  cells were mixed on the grid and then plunge frozen and imaged with cryo-ET without CLEM. .  Targets were imaged with cryo-ET randomly.
description: <strong>Tilt Series Date:</strong> 2019-02-28</p>
<strong>Data Taken By:</strong> Mohammed Kaplan</p>
<strong>Species / Specimen:</strong> Escherichia coli</p>
<strong>Strain:</strong> </p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-50.0°, 50.0°), step: 1°, constant angular increment, dosage: 130.0 eV/Å²,  defocus: -10.0 μm,  magnification: 26000x. </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> The cells were sent to the Jensen lab from the lab of Ariel Lindner in Paris. These are the same . cells used in their Science paper (direct visualization of horizontal gene transfer).</p>
<strong>Purification / Growth Conditions / Treatment:</strong> ANB 35 were grown in LB while ANB24 (Recipient) in M9. I followed the same protocol . described in the Science paper described above.</p>
<strong>Sample Preparation:</strong> The donor and recipient cells were mixed on the EM grid, incubated in the vitrobot chamber with . 100% humidity and then blotted and plunge frozen.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2019-02-28-79/rawdata/</p>Ecoli_CONjugation40.mrc,  Tilt Series (Pixel Size 0.541 nm), 2.9 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2019-02-28-79/rawdata/Ecoli_CONjugation40.mrc"
        > <i class="download icon"></i> Download </a></p>

        Ecoli_CONjugation40_full.rec,  Reconstruction (Pixel Size 2.164 nm), 445.4 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2019-02-28-79/3dimage_107162/Ecoli_CONjugation40_full.rec"
        > <i class="download icon"></i> Download </a></p>

        Ecoli_CONjugation40.mrc.mdoc,  51.0 kB  
        
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DOI: 10.3886/e228141
title: ComPASS Coordinating Center Year 1 CHESI Capacity Needs Assessment Survey

description: The Capacity Needs Assessment Survey (CNAS) was completed as part of the larger "Advancing Health Equity Through Innovative Community Capacity Building, Data Science & Delivering Community-Centered Structural Interventions & Outcomes: Drexel's ComPASS Coordination Center (C3)" cooperative agreement. This funding tasked C3 with providing oversight for the planning, implementation, and evaluation of the Community Partnerships to Advance Science for Society (ComPASS) Program, a first-of-its-kind national effort to advance community-led health equity structural intervention research. Acting as its backbone, the C3 administered and coordinated multiple components of the ComPASS Program through its three interdependent cores (Administrative, Data, and Capacity-Building), and coordinating the work of 24 community-led health equity structural intervention (CHESI) teams located throughout the United States. The CHESI Capacity Needs Assessment Survey (CNAS) aimed to assess each CHESI's partnership experience and baseline capacity related to partnering, planning, implementing, evaluating, and sustaining a structural intervention. Its purpose was to understand CHESI team’s training priorities and needs based on their work so far under ComPASS, tailor C3 and regional hub supports, and evaluate how CHESIs' research capacity changes over time.​ ComPASS was terminated before the second annual survey.
description: N/A<br>
description: Response Rates: Of the 566 people contacted, 1 was a duplicate, 401 were eligible but did not respond, and 164 responded (159 complete, 5 partials). The response rate, using the RR2 definition from the American Association for Public Opinion Research, was 40.9%. We used contact directory information and snowball sampling in this baseline to build the sample roster for subsequent annual surveys.<br>American Association for Public Opinion Research. (2016). Standard Definitions: Final Dispositions of Case Codes and Outcome Rates for Surveys. https://aapor.org/wp-content/uploads/2022/11/Standard-Definitions20169theditionfinal.pdf<br><br>
description: All staff at the CHESIs and their local HERAs were contacted for this survey.<br>
description: All ComPASS Consortium core CHESI project team members and all local Health Equity Research Assembly (HERA) members. Smallest Geographic Unit: N/A
description: web-based survey;
DOI: 10.3886/e228141v1
title: ComPASS Coordinating Center Year 1 CHESI Capacity Needs Assessment Survey

description: The Capacity Needs Assessment Survey (CNAS) was completed as part of the larger "Advancing Health Equity Through Innovative Community Capacity Building, Data Science & Delivering Community-Centered Structural Interventions & Outcomes: Drexel's ComPASS Coordination Center (C3)" cooperative agreement. This funding tasked C3 with providing oversight for the planning, implementation, and evaluation of the Community Partnerships to Advance Science for Society (ComPASS) Program, a first-of-its-kind national effort to advance community-led health equity structural intervention research. Acting as its backbone, the C3 administered and coordinated multiple components of the ComPASS Program through its three interdependent cores (Administrative, Data, and Capacity-Building), and coordinating the work of 24 community-led health equity structural intervention (CHESI) teams located throughout the United States. The CHESI Capacity Needs Assessment Survey (CNAS) aimed to assess each CHESI's partnership experience and baseline capacity related to partnering, planning, implementing, evaluating, and sustaining a structural intervention. Its purpose was to understand CHESI team’s training priorities and needs based on their work so far under ComPASS, tailor C3 and regional hub supports, and evaluate how CHESIs' research capacity changes over time.​ ComPASS was terminated before the second annual survey.
description: N/A<br>
description: Response Rates: Of the 566 people contacted, 1 was a duplicate, 401 were eligible but did not respond, and 164 responded (159 complete, 5 partials). The response rate, using the RR2 definition from the American Association for Public Opinion Research, was 40.9%. We used contact directory information and snowball sampling in this baseline to build the sample roster for subsequent annual surveys.<br>American Association for Public Opinion Research. (2016). Standard Definitions: Final Dispositions of Case Codes and Outcome Rates for Surveys. https://aapor.org/wp-content/uploads/2022/11/Standard-Definitions20169theditionfinal.pdf<br><br>
description: All staff at the CHESIs and their local HERAs were contacted for this survey.<br>
description: All ComPASS Consortium core CHESI project team members and all local Health Equity Research Assembly (HERA) members. Smallest Geographic Unit: N/A
description: web-based survey;
DOI: 10.15468/dl.ed9ubm
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Dolichopteroides binocularis (Beebe, 1932)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((-10.6036 29.6447,-11.635 28.8496,-9.0352 28.8496,-9.0352 33.4562,-9.6631 32.8696,-9.7766 32.3158,-10.3241 31.5424,-10.3942 30.6542,-10.1716 30.2225,-10.6036 29.6447))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008807-250525065834625/datasets/export for details.
DOI: 10.15468/dl.neec88
title: Occurrence Download

description: A dataset containing 344 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Observation, Machine Observation, Human Observation, Fossil, Living Specimen, Occurrence evidence, Material citation, Specimen, Material sample)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Dixonius siamensis (Boulenger, 1899)"
 ]
}

 The dataset includes 344 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012372-250415084134356/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.60732/441f40b7
title: alkali-metal_intercalation_in_disordered_carbon_anode_materials_JMCA2019

description: A dataset created as part of a combination DFT-ML approach to study three alkali metals (K, Li, Na) in model carbon systems at a range of densities and degrees of disorder. The purpose of the study was to investigate the properties of alkali metals in hard (non-graphitising) and nanoporous carbons as potential anode materials for battery technology.
DOI: 10.60732/76208b62
title: CrCoNi_Cao_2022

description: Training dataset that captures chemical short-range order in equiatomic CrCoNi medium-entropy alloy published with our work Quantifying chemical short-range order in metallic alloys (description provided by authors)
DOI: 10.60732/a4e0fea6
title: 23-Single-Element-DNPs_all_trajectories

description: The full trajectories from the VASP runs used to generate the 23-Single-Element-DNPs training sets. Configuration sets are available for each element.
DOI: 10.60732/76701b84
title: aleatoric_epistemic_error_AIC2023

description: Dataset for H2CO, with and without added noise for testing the effects of noise on quality of fit. Configurations sets are included for clean energy values with different levels of gaussian noise added to atomic forces (including a set with no noise added), and energies perturbed at different levels (including a set with no perturbation). Configuration sets correspond to individual files found at the data link.