cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.ktqu3x
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Galaxias zebratus (Castelnau, 1861)",
 "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 ((15.6372 -28.0032,16.2782 -28.5786,20.509 -28.5786,20.509 -24.0715,15.4933 -24.0715,15.4945 -24.1257,16.0509 -25.6631,15.6372 -28.0032))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022529-250525065834625/datasets/export for details.
DOI: 10.15468/dl.rxadw3
title: Occurrence Download

description: A dataset containing 105 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Country is Brazil",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Erythrostemon calycinus (Benth.) L.P.Queiroz"
 ]
}

 The dataset includes 105 records from 24 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022530-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22002/xnhh5-7md23
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/mka2020-10-08-227/rawdata/</p>Hpylori_DFliF_FISE_221.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/mka2020-10-08-227/rawdata/Hpylori_DFliF_FISE_221.mrc"
        > <i class="download icon"></i> Download </a></p>

        Hpylori_DFliF_FISE_221_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/mka2020-10-08-227/3dimage_113939/Hpylori_DFliF_FISE_221_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/x9znn-dtw09
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/dga2018-08-29-115/rawdata/</p>JV9082_201808290104.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/dga2018-08-29-115/rawdata/JV9082_201808290104.mrc"
        > <i class="download icon"></i> Download </a></p>

        JV9082_201808290104_part37_2.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/dga2018-08-29-115/3dimage_96589/JV9082_201808290104_part37_2.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/1m5bz-gny03
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/mka2020-10-08-246/rawdata/</p>Hpylori_DFliF_FISE_240.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/mka2020-10-08-246/rawdata/Hpylori_DFliF_FISE_240.mrc"
        > <i class="download icon"></i> Download </a></p>

        Hpylori_DFliF_FISE_240_part41_1.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/mka2020-10-08-246/3dimage_113980/Hpylori_DFliF_FISE_240_part41_1.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/6xp6t-wjj04
title: Exp phase S. acidocaldarius

description: Grid box 85 - grid1. Located dividing cells using projection images in a previous TEM session.
description: <strong>Tilt Series Date:</strong> 2018-02-04</p>
<strong>Data Taken By:</strong> Shrawan kumar Mageswaran</p>
<strong>Species / Specimen:</strong> Sulfolobus acidocaldarius</p>
<strong>Strain:</strong> </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: -10.0 μm,  magnification: 26000x. </p>
<strong>Microscope:</strong> Caltech Titan Krios</p>
<strong>Acquisition Software:</strong> SerialEM</p>
<strong>Upload Method:</strong> reupload_downloaded</p>
<strong>Processing Software Used:</strong> IMOD for backprojection, tomo3d for SIRT</p>
<strong>Collaborators and Roles:</strong> Megan Dobro's stock of cells</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Cells were harvested at 0.1 OD and kept at 4 C for further steps until freezing. Spun cells at 6000 xg for 3 min to concentrated cells to ~1 OD.</p>
<strong>Sample Preparation:</strong> Cu finder grids - glow discharged. Coated with 4 µL of 10 nm Au beads resuspended in 0.01 % BSA (7 µL of 10 nm Au + 93 µL of 0.01 % BSA) and dried. Added 3.5 µL of suspension and blotted for 2-3 sec from behind manually.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/smk2018-02-04-10/rawdata/</p>TS10_754.mrc,  Tilt Series (Pixel Size 0.541 nm), 1.7 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/smk2018-02-04-10/rawdata/TS10_754.mrc"
        > <i class="download icon"></i> Download </a></p>

        TS10_4bin_SIRT_rotx.rec,  Reconstruction (Pixel Size 0.0 nm), 3.2 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/smk2018-02-04-10/3dimage_102325/TS10_4bin_SIRT_rotx.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/enqb8-mnc60
title: Exp phase S. acidocaldarius

description: Grid box 85 - grid1. Located dividing cells using projection images in a previous TEM session.
description: <strong>Tilt Series Date:</strong> 2018-02-04</p>
<strong>Data Taken By:</strong> Shrawan kumar Mageswaran</p>
<strong>Species / Specimen:</strong> Sulfolobus acidocaldarius</p>
<strong>Strain:</strong> </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: -10.0 μm,  magnification: 26000x. </p>
<strong>Microscope:</strong> Caltech Titan Krios</p>
<strong>Acquisition Software:</strong> SerialEM</p>
<strong>Upload Method:</strong> reupload_downloaded</p>
<strong>Processing Software Used:</strong> IMOD for backprojection, tomo3d for SIRT</p>
<strong>Collaborators and Roles:</strong> Megan Dobro's stock of cells</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Cells were harvested at 0.1 OD and kept at 4 C for further steps until freezing. Spun cells at 6000 xg for 3 min to concentrated cells to ~1 OD.</p>
<strong>Sample Preparation:</strong> Cu finder grids - glow discharged. Coated with 4 µL of 10 nm Au beads resuspended in 0.01 % BSA (7 µL of 10 nm Au + 93 µL of 0.01 % BSA) and dried. Added 3.5 µL of suspension and blotted for 2-3 sec from behind manually.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/smk2018-02-04-4/rawdata/</p>TS4_865.mrc,  Tilt Series (Pixel Size 0.541 nm), 1.7 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/smk2018-02-04-4/rawdata/TS4_865.mrc"
        > <i class="download icon"></i> Download </a></p>

        TS4_4bin_SIRT_rotx.rec,  Reconstruction (Pixel Size 0.0 nm), 2.1 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/smk2018-02-04-4/3dimage_102298/TS4_4bin_SIRT_rotx.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/21ed9-fs809
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/mka2020-10-08-303/rawdata/</p>Hpylori_DFliF_FISE_298.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/mka2020-10-08-303/rawdata/Hpylori_DFliF_FISE_298.mrc"
        > <i class="download icon"></i> Download </a></p>

        Hpylori_DFliF_FISE_298_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/mka2020-10-08-303/3dimage_114086/Hpylori_DFliF_FISE_298_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/6zk3s-mqz80
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/dga2018-08-29-284/rawdata/</p>JV9082_20180901a0058.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/dga2018-08-29-284/rawdata/JV9082_20180901a0058.mrc"
        > <i class="download icon"></i> Download </a></p>

        JV9082_20180901a0058_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/dga2018-08-29-284/3dimage_96991/JV9082_20180901a0058_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.15468/dl.vs3hbj
title: Occurrence Download

description: A dataset containing 104 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Caulerpa taxifolia",
 "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 104 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000667-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.n3cfn2
title: Occurrence Download

description: A dataset containing 6 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Melanotaenia mairasi)",
 "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 6 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000670-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ps2d46
title: Occurrence Download

description: A dataset containing 77 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Chile",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is one of (Matricaria discoidea, Matricaria matricarioides)"
 ]
}

 The dataset includes 77 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000672-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.j9jf4p
title: Occurrence Download

description: A dataset containing 15728 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Perilla frutescens",
 "Country is United States of America",
 "HasCoordinate is true"
 ]
}

 The dataset includes 15728 records from 92 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000673-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.16968027
title: Local adaptation experiment in Hyphantria cunea

description: CSV file containing experimental information and fitness measurements from reciprocal common garden experiment using Hyphantria cunea testing local adaptation.
DOI: 10.5281/zenodo.16968028
title: Local adaptation experiment in Hyphantria cunea

description: CSV file containing experimental information and fitness measurements from reciprocal common garden experiment using Hyphantria cunea testing local adaptation.
DOI: 10.15468/dl.47gtsa
title: Occurrence Download

description: A dataset containing 3042 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Doricha enicura"
 ]
}

 The dataset includes 3042 records from 54 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000675-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6nng68
title: Occurrence Download

description: A dataset containing 92 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "TaxonKey is Hancockia"
 ]
}

 The dataset includes 92 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000674-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5967/1kfr-3k25
title: Data for "Influence of chromium intercalation in self-intercalated van der Waals magnet Cr_{1+\delta}Te_{2}"

description: Input files for first-principles and spin dynamics simulations of Cr_(1+\delta)Te_2 using VASP, Wannier90, TB2J, and VAMPIRE
description: First-principles calculations were performed using density functional theory (DFT) as implemented in VASP. The relaxed structures and wavefunctions were used as input for Wannier90 to construct tight-binding Hamiltonians. Exchange interactions were computed using the TB2J package, which extracts Heisenberg exchange parameters from Wannier-based Hamiltonians. These parameters were then used in atomistic spin dynamics simulations using the VAMPIRE code to analyze their Curie temperature.
description: This dataset includes input files and representative configurations used for the DFT, tight-binding, exchange interaction, and atomistic spin dynamics calculations in the study of Cr_(1+\delta)Te2. The VASP input files (INCAR, POSCAR, KPOINTS) were used for structural and electronic relaxations. Wannier90 projections were employed to extract localized orbitals for TB2J, which provided Heisenberg exchange parameters. These were used in VAMPIRE simulations to analyze their Curie temperature. All scripts and initial spin configurations required to reproduce the simulations are provided.