cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.3886/e237530v1
title: CULTIVATE

description: In the United States, racial biases have been tied to poor health outcomes and difficulties accessing healthcare. There is growing evidence that structural racism is linked to the uneven experience of illness and early death experienced by Black, Indigenous, and People of Color (BIPOC) communities. In healthcare settings, structural racism affects BIPOC patients’ experiences navigating and accessing healthcare, and it also impacts the quality of the care they receive. The quality of provider communication, whether the provider centers the patients’ perspective in decisions regarding their care, whether the provider recommends and makes referrals for specific tests and procedures; are factors that may be impacted by structural racism.The researchers conducting this study want to find out if virtual reality can be used in medical education to help dismantle structural racism. The project aims to develop virtual reality scenarios that put healthcare providers in the shoes of BIPOC patients navigating the healthcare system. Researchers want to determine if the changes in medical education enhanced by new technology, like virtual reality, will improve health access and health outcomes for BIPOC communities.CULTIVATE (Combating Unequal Treatment in Healthcare Through Virtual Awareness and Training in Empathy) will use VR to deliver diversity, equity, and inclusion (DEI) training to healthcare providers. CULTIVATE will put non-BIPOC healthcare providers in their Black and Latinx patients’ shoes using VR-based training scenarios simulating BIPOC patients’ experience accessing healthcare. This project aims to understand if changes in medical education enhanced by VR will improve health access and health outcomes of BIPOC people.
DOI: 10.22002/931p5-pt417
title: Lp02_2nd

description: 2nd time collection: Jan 2016. Defocus -6.Lp02 is thymidine auxotroph of the parental strain Lp01 originating from Philadelphia-1 strain. Cells were grown in AYE liquid culture with following supplements: ferric nitrate, cysteine hydrochloride and thymidine. Scrape cells off a plate, dissolve in the media, adjust the cell density to 0.6 and make a dilution series. Start O/N culture with all of them and freeze cells next day from the one in early stationary phase that is OD ~ 3.0
description: <strong>Tilt Series Date:</strong> 2016-01-15</p>
<strong>Data Taken By:</strong> Debnath Ghosal</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: 1.50°, constant angular increment, dosage: 100.0 eV/Å²,  defocus: -6.0 μm,  magnification: 26000x. </p>
<strong>Microscope:</strong> Janelia Titan</p>
<strong>Acquisition Software:</strong> UCSFTomo</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> Strain sent to us by Joseph P. Vogel, Washington University School of Medicine. Data collected and processed by Debnath Ghosal. This data was collected at the Janelia Krios.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Lp02 is thymidine auxotroph of the parental strain Lp01 originating from Philadelphia-1 strain. Cells were grown in AYE liquid culture with following supplements: ferric nitrate, cysteine hydrochloride and thymidine. Scrape cells off a plate, dissolve in the media, adjust the cell density to 0.6 and make a dilution series. Start O/N culture with all of them and freeze cells next day from the one in early stationary phase that is OD ~ 3.0. Added gold before freezing.</p>
<strong>Sample Preparation:</strong> Grids were stored in Janelia from previous imaging. See previous Lp02 sample prep. Vitrobot (MK iv) settings: 100% humidity, 4µl sample, Blot force 6, blot time 3 sec. Wait time 0 sec. Drain time 1 sec. Ethane/propane mix. Grid: Quantifoil Cu 2/2 200. Add gold to cells prior to freezing: 1ul of gold to 4 ul of cells, freeze.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2016-01-15-89/rawdata/</p>atlas_area_a0012.mrc,  Tilt Series (Pixel Size 0.42 nm), 2.2 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2016-01-15-89/rawdata/atlas_area_a0012.mrc"
        > <i class="download icon"></i> Download </a></p>

        atlas_area_a0012_full.rec,  Reconstruction (Pixel Size 1.68 nm), 430.6 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2016-01-15-89/3dimage_72958/atlas_area_a0012_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/gfzyb-kew16
title: JV3579_Polara_Mag27.5

description: JV3579 Legionella thyA ΔdotF(May10th, 2017)
description: <strong>Tilt Series Date:</strong> 2017-05-10</p>
<strong>Data Taken By:</strong> Debnath Ghosal</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: 110.0 eV/Å²,  defocus: -8.0 μm,  magnification: 27500x. </p>
<strong>Microscope:</strong> Caltech Polara</p>
<strong>Acquisition Software:</strong> UCSFTomo</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> Strain sent to us by Joseph P. Vogel, Washington University School of Medicine. Data collected and processed by Debnath Ghosal at F30, Caltech.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Cells were grown in AYE liquid culture with following supplements: ferric nitrate, cysteine hydrochloride and thymidine. Scrape cells off a plate, dissolve in the media, adjust the cell density to 0.6 and make a dilution series. Start O/N culture with all of them and freeze cells next day from the one in early stationary phase that is OD ~ 3.0. This time cell density was ~2.9</p>
<strong>Sample Preparation:</strong> 6 grids were frozen for the JV3579 strain at OD~ 2.9, cell density was increased to 2x. Vitrobot (MK iv) settings: 100% humidity, 4µl sample, Blot force 6, blot time 3 sec. Wait time 0 sec. Drain time 1 sec. Ethane/propane mix. Grid: Quantifoil Cu 2/2 200. Add gold to cells prior to freezing: 1ul of gold to 4 ul of cells, freeze.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2017-05-10-42/3dimage_84354/</p>JV3579_20170510c0038.rec,  Reconstruction (Pixel Size 1.56 nm), 890.9 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2017-05-10-42/3dimage_84354/JV3579_20170510c0038.rec"
        > <i class="download icon"></i> Download </a></p>

        JV3579_20170510c0038.mrc,  Tilt Series (Pixel Size 0.39 nm), 882.9 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2017-05-10-42/rawdata/JV3579_20170510c0038.mrc"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/5h494-sm642
title: JV7091_ΔdotEP

description: JV7091_ΔdotEP (Deletion of dotE and dotP)
description: <strong>Tilt Series Date:</strong> 2017-09-05</p>
<strong>Data Taken By:</strong> Debnath Ghosal</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: 100.0 eV/Å²,  defocus: -7.0 μm,  magnification: 27500x. </p>
<strong>Microscope:</strong> Caltech Polara</p>
<strong>Acquisition Software:</strong> UCSFTomo</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> Strain sent to us by Joseph P. Vogel, Washington University School of Medicine. Data collected and processed by Debnath Ghosal at F30, Caltech.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Cells were grown in AYE liquid culture with following supplements: ferric nitrate, cysteine hydrochloride and thymidine. Scrape cells off a plate, dissolve in the media, adjust the cell density to 0.6 and make a dilution series. Start O/N culture with all of them and freeze cells next day from the one in early stationary phase that is OD ~ 3.0. This time cell density was ~2.8</p>
<strong>Sample Preparation:</strong> 6 grids were frozen for this strain at OD~ 2.8, cell density was increased to 2x by centrifugation. Vitrobot (MK iv) settings: 100% humidity, 4µl sample, Blot force 6, blot time 4 sec. Wait time 0 sec. Drain time 1 sec. Ethane/propane mix. Grid: Quantifoil Cu 2/2 200. Add gold to cells prior to freezing: 1ul of gold to 4 ul of cells, freeze.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2017-09-05-72/rawdata/</p>JV7091_20170906n0023.mrc,  Tilt Series (Pixel Size 0.39 nm), 1.7 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2017-09-05-72/rawdata/JV7091_20170906n0023.mrc"
        > <i class="download icon"></i> Download </a></p>

        JV7091_20170906n0023.rec,  Reconstruction (Pixel Size 1.56 nm), 889.0 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2017-09-05-72/3dimage_88292/JV7091_20170906n0023.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/qq7rd-1k592
title: H-pylori_dFliM_GC

description: These are fast tilt series taken by Georges Chreifi on the Krios for dFliM mutant of Helicobacter  .  pylori.
description: <strong>Tilt Series Date:</strong> 2019-10-28</p>
<strong>Data Taken By:</strong> Mohammed Kaplan</p>
<strong>Species / Specimen:</strong> Helicobacter pylori</p>
<strong>Strain:</strong> 26695</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 3°, constant angular increment, dosage: 130.0 eV/Å²,  defocus: -6.0 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> None</p>
<strong>Collaborators and Roles:</strong> I received these cells from Carrie Schaffer from the university of Kentucky. These are wild type cells but they . don't express complete FliP protein. Therefore, they don't assemble full flagella. We knocked out FliM protein . of the flagellar motor to study the early assembly states of flagellar motor.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> I grew the cells on blood agar plates from -80 stock at 37C with 5% CO2. the cells were grown . for 48 hours and then spread on a new plate with a cotton swab and left to grow for 24 hours. . The grids were prepared from both batches (48 hours, and 24 hours, separately).</p>
<strong>Sample Preparation:</strong> The samples were prepared with Vitrobot IV. Blotting conditions were either: blot force 6, blot . time 3, drain time 1 OR blot force -3, blot time 4, drain time 1, 100% humidity. Cu grids. 10 nm . gold.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2019-10-28-81/rawdata/</p>Hpylori_FliM_083_af.mrc,  Tilt Series (Pixel Size 0.449 nm), 3.8 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2019-10-28-81/rawdata/Hpylori_FliM_083_af.mrc"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.15468/dl.76e2vm
title: Occurrence Download

description: A dataset containing 7057 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Verbena canadensis"
 ]
}

 The dataset includes 7057 records from 191 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014253-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17014054
title: Question-itemized Table of 96 Curated SEDOH Data Collection Instruments

description: After retrieval and review of social and environmental determinants of health (SEDOH) data collection instruments from the literature and other online resources, these surveys/questionnaires were filtered for select inclusion criteria prior to the manual extraction of individual question-items with their corresponding answer options. All typos inherent to the original devices were likely to have been maintained. For organizational purposes, each row item begins with a formula-derived underscore separated identifier that provides a unique reference for each question-item (and sub-item) per each instrument; e.g., for row 2:

=TEXTJOIN("_",TRUE,B2,E2,TEXTBEFORE(J2,""),IF(IFNA(L2,Q2)=Q2,Q2,L2),IF(IFNA(L2,Q2)=Q2,"",M2))

While instruments were selected for their accessibility, user discretion is advised.
DOI: 10.5281/zenodo.17014055
title: Question-itemized Table of 96 Curated SEDOH Data Collection Instruments

description: After retrieval and review of social and environmental determinants of health (SEDOH) data collection instruments from the literature and other online resources, these surveys/questionnaires were filtered for select inclusion criteria prior to the manual extraction of individual question-items with their corresponding answer options. All typos inherent to the original devices were likely to have been maintained. For organizational purposes, each row item begins with a formula-derived underscore separated identifier that provides a unique reference for each question-item (and sub-item) per each instrument; e.g., for row 2:

=TEXTJOIN("_",TRUE,B2,E2,TEXTBEFORE(J2,""),IF(IFNA(L2,Q2)=Q2,Q2,L2),IF(IFNA(L2,Q2)=Q2,"",M2))

While instruments were selected for their accessibility, user discretion is advised.
DOI: 10.15468/dl.bzq2xj
title: Occurrence Download

description: A dataset containing 9 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Taeniatherum caput-medusae",
 "Country is Belgium",
 "HasCoordinate is true"
 ]
}

 The dataset includes 9 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014255-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.f6hkkp
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Taeniatherum caput-medusae",
 "Country is Australia",
 "HasCoordinate is true"
 ]
}

 The dataset includes 3 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014254-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.a3ad46
title: Occurrence Download

description: A dataset containing 4 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Taeniatherum caput-medusae",
 "Country is Chile",
 "HasCoordinate is true"
 ]
}

 The dataset includes 4 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014256-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.439m5a
title: Occurrence Download

description: A dataset containing 78 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Lathyrus boissieri"
 ]
}

 The dataset includes 78 records from 21 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014257-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.55fpex
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Labeobarbus ruasae)",
 "BasisOfRecord is one of (Specimen, Literature Occurrence, Human Observation, Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1991",
 "Year is less than or equal to 2025"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014258-250827131500795/datasets/export for details.
DOI: 10.15468/dl.mk6xtw
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Taeniatherum caput-medusae",
 "Country is Denmark",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014260-250827131500795/datasets/export for details.
DOI: 10.15468/dl.8up7g8
title: Occurrence Download

description: A dataset containing 446 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cuphea racemosa racemosa"
 ]
}

 The dataset includes 446 records from 53 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014261-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.t2c6cf
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Taeniatherum caput-medusae",
 "Country is Estonia",
 "HasCoordinate is true"
 ]
}

 The dataset includes 2 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014262-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.p8t8fg
title: Occurrence Download

description: A dataset containing 42 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Taeniatherum caput-medusae",
 "Country is Russian Federation",
 "HasCoordinate is true"
 ]
}

 The dataset includes 42 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014263-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25403/upresearchdata.28554017
title: Immune cell subsets and cytokine levels in peripheral blood between healthy donors and triple-negative breast cancer (TNBC) patients and in patients before and after the first phase of chemotherapy

description: The study aimed to compare immune cell subsets and cytokine levels in peripheral blood between healthy donors and TNBC patients and in patients before and after the first phase (at least 3 cycles) of chemotherapy. Twenty-three patients recently diagnosed with TNBC and ten healthy donors consented to participate in this study. Patients were recruited from a private clinic in Johannesburg, Gauteng, with their consent. Blood was collected prior to treatment and after first-phase chemotherapy. Full blood counts, patient demographics, and treatment response were recorded. The percentage of circulating CD4<sup>+</sup> and CD8<sup>+</sup> T-cells, B-cells, natural killer (NK) cells, monocytes, and regulatory T-cells (Tregs), as well as the expression of various cell markers, was evaluated by flow cytometry and compared between participant groups. The concentrations of vascular endothelial growth factor (VEGF), granulocyte-macrophage colony stimulating factor (GM-CSF), growth and differentiation factor 15 (GDF-15), interleukins-6, -8, and -10 (IL-6, -8, -10) and interferon gamma-induced protein (IP-10) were evaluated in participant plasma by enzyme-linked immunosorbent assays (ELISAs), and the results were compared between participant groups. These were also compared to treatment outcomes. This study showed an increase in the percentage of CD14<sup>+</sup> monocytes and CD56<sup>high</sup> NK cells and a decrease in CD19<sup>+</sup> B-cells after first-phase chemotherapy, while no significant differences in cell percentages were seen between healthy donors and treatment-naïve patient groups.
DOI: 10.25403/upresearchdata.28554017.v1
title: Immune cell subsets and cytokine levels in peripheral blood between healthy donors and triple-negative breast cancer (TNBC) patients and in patients before and after the first phase of chemotherapy

description: The study aimed to compare immune cell subsets and cytokine levels in peripheral blood between healthy donors and TNBC patients and in patients before and after the first phase (at least 3 cycles) of chemotherapy. Twenty-three patients recently diagnosed with TNBC and ten healthy donors consented to participate in this study. Patients were recruited from a private clinic in Johannesburg, Gauteng, with their consent. Blood was collected prior to treatment and after first-phase chemotherapy. Full blood counts, patient demographics, and treatment response were recorded. The percentage of circulating CD4<sup>+</sup> and CD8<sup>+</sup> T-cells, B-cells, natural killer (NK) cells, monocytes, and regulatory T-cells (Tregs), as well as the expression of various cell markers, was evaluated by flow cytometry and compared between participant groups. The concentrations of vascular endothelial growth factor (VEGF), granulocyte-macrophage colony stimulating factor (GM-CSF), growth and differentiation factor 15 (GDF-15), interleukins-6, -8, and -10 (IL-6, -8, -10) and interferon gamma-induced protein (IP-10) were evaluated in participant plasma by enzyme-linked immunosorbent assays (ELISAs), and the results were compared between participant groups. These were also compared to treatment outcomes. This study showed an increase in the percentage of CD14<sup>+</sup> monocytes and CD56<sup>high</sup> NK cells and a decrease in CD19<sup>+</sup> B-cells after first-phase chemotherapy, while no significant differences in cell percentages were seen between healthy donors and treatment-naïve patient groups.
DOI: 10.15468/dl.e6c693
title: Occurrence Download

description: A dataset containing 115 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Notropis candidus)",
 "BasisOfRecord is one of (Specimen, Literature Occurrence, Human Observation, Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1991",
 "Year is less than or equal to 2025"
 ]
}

 The dataset includes 115 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014264-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3upxf2
title: Occurrence Download

description: A dataset containing 462 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Turnera sidoides pinnatifida"
 ]
}

 The dataset includes 462 records from 48 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014265-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.