cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.22002/zpzba-71c48
title: Hpylori_dFliF_FISE

description: These are H_pylori cells that are lacking FliP protein. In these cells, FliF protein was knocked out  .  to examine its relation to the hat-like complex.
description: <strong>Tilt Series Date:</strong> 2020-10-08</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: 120.0 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> The cells were prepared and sent by Carrie Schaffer from the university of Kentucky. The cells were grown at 37C with 5% CO2 on sheep blood agar plates for 2 days from a -80C. No growth was seen . on the plates after 24 hr therefore the plates were kept in the . incubator for another 24Hr.</p>
<strong>Purification / Growth Conditions / Treatment:</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/mka2020-10-08-448/rawdata/</p>Hpylori_DFliF_FISE_453.mrc,  Tilt Series (Pixel Size 0.452 nm), 1.9 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2020-10-08-448/rawdata/Hpylori_DFliF_FISE_453.mrc"
        > <i class="download icon"></i> Download </a></p>

        Hpylori_DFliF_FISE_453_full.rec,  Reconstruction (Pixel Size 1.808 nm), 737.3 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2020-10-08-448/3dimage_114344/Hpylori_DFliF_FISE_453_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.5281/zenodo.16986659
title: Code and Dataset for manuscript "AI-Enabled Conditional Nonlinear Optimal Perturbation Enhances Ensemble Prediction of Extreme ENSO Events"

description: The attachments include the raw data required for the study, CNOP solution code, ensemble prediction code, and model outputs. You are welcome to use them. If you have any questions, please contact me at: email: zhoulu327@foxmail.com.
DOI: 10.5281/zenodo.16986660
title: Code and Dataset for manuscript "AI-Enabled Conditional Nonlinear Optimal Perturbation Enhances Ensemble Prediction of Extreme ENSO Events"

description: The attachments include the raw data required for the study, CNOP solution code, ensemble prediction code, and model outputs. You are welcome to use them. If you have any questions, please contact me at: email: zhoulu327@foxmail.com.
DOI: 10.22002/f8ms7-emy33
title: JV9082_Janelia42k

description: DotF-sfGFP fusion
description: <strong>Tilt Series Date:</strong> 2018-08-29</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: (-54.0°, 54.0°), step: 3.0°, constant angular increment, dosage: 100.0 eV/Å²,  defocus: -7.0 μm,  magnification: 42000x. </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. Janelia Krios.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Cells were grown in AYE liquid culture with following supplements: ferric nitrate, cysteine hydrochloride and thymidine.</p>
<strong>Sample Preparation:</strong> 6 grids were frozen for the JV9082 strain (2x concentrated culture); Vitrobot (MK iv) settings: 100% humidity, 4µl sample, Blot force 6, blot time 4.5 sec. Wait time 0 sec. Drain time 1 sec. Ethane/propane mix. Grid: Quantifoil Cu 2/2 200.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2018-08-29-19/rawdata/</p>JV9082_201808290051.mrc,  Tilt Series (Pixel Size 0.26 nm), 1.1 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2018-08-29-19/rawdata/JV9082_201808290051.mrc"
        > <i class="download icon"></i> Download </a></p>

        JV9082_201808290051_full.rec,  Reconstruction (Pixel Size 1.04 nm), 445.4 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2018-08-29-19/3dimage_96346/JV9082_201808290051_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/x5fr5-09885
title: JV9082_K3_janelia

description: JV9082:DotF-sfGFP fusion
description: <strong>Tilt Series Date:</strong> 2019-12-04</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: (-54.0°, 54.0°), step: 3.0°, constant angular increment, dosage: 90.0 eV/Å²,  defocus: -3.0 μm,  magnification: 26000x. </p>
<strong>Microscope:</strong> Janelia Titan</p>
<strong>Acquisition Software:</strong> SerialEM</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.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Cells were grown in AYE liquid culture with following supplements: ferric nitrate, cysteine hydrochloride and thymidine.</p>
<strong>Sample Preparation:</strong> Vitrobot (MK iv) settings: 100% humidity, 4µl sample, Blot force 6, blot time 4.5 sec. Wait time 0 sec. Drain time 1 sec. Ethane/propane mix. Grid: Quantifoil Cu 2/2 200. Data collected at Janelia Krios (K3 camera). Mag: 26000, pixel size: 2.61A. Defocus range -2 to -4 um.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2019-12-04-6/rawdata/</p>9082_Box1_No4_S74.mrc,  Tilt Series (Pixel Size 0.261 nm), 1.7 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2019-12-04-6/rawdata/9082_Box1_No4_S74.mrc"
        > <i class="download icon"></i> Download </a></p>

        9082_Box1_No4_S74_full.rec,  Reconstruction (Pixel Size 1.044 nm), 737.3 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2019-12-04-6/3dimage_112950/9082_Box1_No4_S74_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/mt5ga-t3756
title: JV9082_Janelia42k

description: DotF-sfGFP fusion
description: <strong>Tilt Series Date:</strong> 2018-08-29</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: (-54.0°, 54.0°), step: 3.0°, constant angular increment, dosage: 100.0 eV/Å²,  defocus: -7.0 μm,  magnification: 42000x. </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. Janelia Krios.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Cells were grown in AYE liquid culture with following supplements: ferric nitrate, cysteine hydrochloride and thymidine.</p>
<strong>Sample Preparation:</strong> 6 grids were frozen for the JV9082 strain (2x concentrated culture); Vitrobot (MK iv) settings: 100% humidity, 4µl sample, Blot force 6, blot time 4.5 sec. Wait time 0 sec. Drain time 1 sec. Ethane/propane mix. Grid: Quantifoil Cu 2/2 200.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2018-08-29-367/rawdata/</p>JV9082_20180901a0141.mrc,  Tilt Series (Pixel Size 0.26 nm), 1.1 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2018-08-29-367/rawdata/JV9082_20180901a0141.mrc"
        > <i class="download icon"></i> Download </a></p>

        JV9082_20180901a0141_full.rec,  Reconstruction (Pixel Size 1.04 nm), 445.4 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2018-08-29-367/3dimage_97073/JV9082_20180901a0141_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.5258/soton/d3228
title: Dataset in support of the thesis 'Traits, species and communities in planktic foraminifera during Plio-Pleistocene climate change'

description: This dataset contains:

Trait measurements data of planktic foraminifera species Menardella limbata and Menardella multicamerata (925_Menardellids_Traits.csv)
Trait measurements of planktic foraminifera species Menardella limbata and Menardella multicamerata (925_Menardellids_Traits_Images.zip)
Planktic foraminifera species last occurrence data at Site 925 (925_Species_Last_Occurrences.csv)
Planktic foraminifera species assemblage counts data at Site 925 (925_Assemblages.csv)
Planktic foraminifera species trait measurements data at Site 925 (925_Traits.csv)
Planktic foraminifera species trait measurements data at Site 925 (925_Traits_Images.zip)
DOI: 10.5281/zenodo.15601619
title: Idaho Annual Temperature Mean (1980-2022)

description: Annual mean of daily minimum and maximum temperature from the DAYMET dataset for Idaho. These data were prepared by the ISU GIS TREC to support the NSF EPSCoR I-CREWS study https://www.idahoepscor.org/i-crews.  Original source data provided in NetCDF format (*.NC).  These data were imported using Idrisi Terrset and converted into individual daily raster TIF layers to support all modern GIS software.  The entire dataset was then clipped to the I-CREWS study area, designated as all HUC08 watersheds intersecting the state of Idaho.  

This is a multidimensional dataset stored in cloud raster format (CRF)
DOI: 10.5281/zenodo.15601620
title: Idaho Annual Temperature Mean (1980-2022)

description: Annual mean of daily minimum and maximum temperature from the DAYMET dataset for Idaho. These data were prepared by the ISU GIS TREC to support the NSF EPSCoR I-CREWS study https://www.idahoepscor.org/i-crews.  Original source data provided in NetCDF format (*.NC).  These data were imported using Idrisi Terrset and converted into individual daily raster TIF layers to support all modern GIS software.  The entire dataset was then clipped to the I-CREWS study area, designated as all HUC08 watersheds intersecting the state of Idaho.  

This is a multidimensional dataset stored in cloud raster format (CRF)
DOI: 10.5281/zenodo.15602022
title: Dataset used in the review "Socio-ecological modeling of water resources under uncertainty".

description: This Excel file contains the database developed for a systematic review of socio-ecological modeling of water resources under uncertainty literature. Each row corresponds to one reviewed publication. Column headers include full explanations of the variables analyzed, including binary codes (e.g., 1 = Yes, 0 = No, "-" = Not applicable), as specified in the header row. This dataset supports the article submitted to Water Resources Research under the TRANSCEND project (EU Horizon Europe, GA No. 101084110).
DOI: 10.5281/zenodo.15602023
title: Dataset used in the review "Socio-ecological modeling of water resources under uncertainty".

description: This Excel file contains the database developed for a systematic review of socio-ecological modeling of water resources under uncertainty literature. Each row corresponds to one reviewed publication. Column headers include full explanations of the variables analyzed, including binary codes (e.g., 1 = Yes, 0 = No, "-" = Not applicable), as specified in the header row. This dataset supports the article submitted to Water Resources Research under the TRANSCEND project (EU Horizon Europe, GA No. 101084110).
DOI: 10.15468/dl.uyddvj
title: Occurrence Download

description: A dataset containing 273 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Tricellaria inopinata",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Geometry POLYGON ((-6.6 29.26705, -6.6 50.94, 40.81373 50.94, 40.81373 29.26705, -6.6 29.26705))",
 "BasisOfRecord is one of (Human Observation, Machine Observation, Observation, Material sample)"
 ]
}

 The dataset includes 273 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000684-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5066/p1dc4xfg
title: Geospatial database for the cooperative national geologic maps
DOI: 10.15468/dl.x9hpx5
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Salvia splendens",
 "Country is Armenia",
 "HasCoordinate is true"
 ]
}

 The dataset includes 2 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000685-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mwkmna
title: Occurrence Download

description: A dataset containing 12 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Salvia splendens",
 "Country is Australia",
 "HasCoordinate is true"
 ]
}

 The dataset includes 12 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000686-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.myb34g
title: Occurrence Download

description: A dataset containing 26 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Salvia splendens",
 "Country is Czechia",
 "HasCoordinate is true"
 ]
}

 The dataset includes 26 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000687-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.agq9tr
title: Occurrence Download

description: A dataset containing 11 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Ethiopia",
 "OccurrenceStatus is Present",
 "TaxonKey is Aloe ankoberensis"
 ]
}

 The dataset includes 11 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000688-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.htx7hn
title: Occurrence Download

description: A dataset containing 161 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is South Africa",
 "TaxonKey is Encephalartos ghellinckii"
 ]
}

 The dataset includes 161 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000690-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zua78u
title: Occurrence Download

description: A dataset containing 4 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Callogorgia verticillata",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Geometry POLYGON ((-6.6 29.26705, -6.6 50.94, 40.81373 50.94, 40.81373 29.26705, -6.6 29.26705))",
 "BasisOfRecord is one of (Human Observation, Machine Observation, Observation, Material sample)"
 ]
}

 The dataset includes 4 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000689-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.29983594
title: Supporting data from the study: Gender Equity in Scientific Production in Peru and Colombia Project

description: This dataset corresponds to the study on gender equity in scientific production at public universities in Peru and Colombia. It includes the complete transcripts of the interviews and the database related to scientific production in both countries. The information collected constitutes the empirical corpus that supports the qualitative and quantitative analysis presented in the article. The data has been anonymized and organized to ensure the confidentiality of participants and facilitate its academic use.
DOI: 10.6084/m9.figshare.29983594.v1
title: Supporting data from the study: Gender Equity in Scientific Production in Peru and Colombia Project

description: This dataset corresponds to the study on gender equity in scientific production at public universities in Peru and Colombia. It includes the complete transcripts of the interviews and the database related to scientific production in both countries. The information collected constitutes the empirical corpus that supports the qualitative and quantitative analysis presented in the article. The data has been anonymized and organized to ensure the confidentiality of participants and facilitate its academic use.
DOI: 10.60707/cpzd-pr68
title: X-ray CT data for Bennu particle OREX-800170-0
DOI: 10.17632/7f2rzyv2zh
title: Unravelling Plasma Extracellular Vesicle Diversity With Optimised Spectral Flow Cytometry

description: Extracellular vesicles (EVs) are crucial for intercellular communication and are found in various biological fluids. The identification and immunophenotyping of such small particles continue to pose significant challenges. Here, we have developed a workflow for the optimisation of a next-generation panel for in-depth immunophenotyping of circulating plasma EVs using spectral flow cytometry. Our data collection followed a multistep optimisation phase for both instrument setup and 21-colour panel design, thus maximising fluorescent signal recovery. This spectral approach enabled the identification of novel EV subpopulations. Indeed, besides common EVs released by erythrocytes, platelets, leukocytes and endothelial cells, we observed rare and poorly known EV subsets carrying antigens related to cell activation or exhaustion. Notably, the unsupervised data analysis of major EV subsets revealed subpopulations expressing up to five surface antigens simultaneously. However, the majority of EVs expressed only a single surface antigen, suggesting they may not fully represent the phenotype of their parent cells. This is likely due to the small surface area or the biogenesis of EVs rather than antibody steric hindrance. Finally, we tested our workflow by analysing the plasma EV landscape in a cohort of systemic lupus erythematosus (SLE) patients. Interestingly, we observed a significant increase in CD54+ EVs, supporting the notion of elevated circulating ICAM under SLE conditions. To our knowledge, these are the first data highlighting the importance of a spectral flow cytometry approach in deciphering the heterogeneity of plasma EVs paving the way for the routine use of a high-dimensional immunophenotyping in EV research.
DOI: 10.17632/7f2rzyv2zh.1
title: Unravelling Plasma Extracellular Vesicle Diversity With Optimised Spectral Flow Cytometry

description: Extracellular vesicles (EVs) are crucial for intercellular communication and are found in various biological fluids. The identification and immunophenotyping of such small particles continue to pose significant challenges. Here, we have developed a workflow for the optimisation of a next-generation panel for in-depth immunophenotyping of circulating plasma EVs using spectral flow cytometry. Our data collection followed a multistep optimisation phase for both instrument setup and 21-colour panel design, thus maximising fluorescent signal recovery. This spectral approach enabled the identification of novel EV subpopulations. Indeed, besides common EVs released by erythrocytes, platelets, leukocytes and endothelial cells, we observed rare and poorly known EV subsets carrying antigens related to cell activation or exhaustion. Notably, the unsupervised data analysis of major EV subsets revealed subpopulations expressing up to five surface antigens simultaneously. However, the majority of EVs expressed only a single surface antigen, suggesting they may not fully represent the phenotype of their parent cells. This is likely due to the small surface area or the biogenesis of EVs rather than antibody steric hindrance. Finally, we tested our workflow by analysing the plasma EV landscape in a cohort of systemic lupus erythematosus (SLE) patients. Interestingly, we observed a significant increase in CD54+ EVs, supporting the notion of elevated circulating ICAM under SLE conditions. To our knowledge, these are the first data highlighting the importance of a spectral flow cytometry approach in deciphering the heterogeneity of plasma EVs paving the way for the routine use of a high-dimensional immunophenotyping in EV research.
DOI: 10.15468/dl.zpxfja
title: Occurrence Download

description: A dataset containing 71 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Salvia splendens",
 "Country is India",
 "HasCoordinate is true"
 ]
}

 The dataset includes 71 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000694-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.g3wq8c
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Haplochromis worthingtoni)",
 "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/0000692-250827131500795/datasets/export for details.