cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.5mhmcb
title: Occurrence Download

description: A dataset containing 8603 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Prunus caroliniana (Mill.) Aiton"
 ]
}

 The dataset includes 8603 records from 171 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0031101-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hah667
title: Occurrence Download

description: A dataset listing the 255 species recorded in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((134.67953 -24.04275,135.1091 -24.04452,135.11264 -23.62025,134.6866 -23.62025,134.67953 -24.04275))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Plantae"
 ]
}

 The dataset's 255 records were derived from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0031094-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xmgaum
title: Occurrence Download

description: A dataset containing 490 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "TaxonKey is Diclinanona Diels"
 ]
}

 The dataset includes 490 records from 45 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0031102-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.7939/r3-w2bj-5t66
title: Chad's Creek Sites Data
DOI: 10.5517/ccdc.csd.cc2mwzfy
title: CCDC 2439961: Experimental Crystal Structure Determination

description: Related Article: Benjamin Zheng, Mark S. Taylor|2025|J.Org.Chem.|90|6278|doi:10.1021/acs.joc.5c00380
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2mwzgz
title: CCDC 2439962: Experimental Crystal Structure Determination

description: Related Article: Benjamin Zheng, Mark S. Taylor|2025|J.Org.Chem.|90|6278|doi:10.1021/acs.joc.5c00380
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.15468/dl.25jfv6
title: Occurrence Download

description: A dataset containing 18901 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "TaxonKey is Dicliptera Juss."
 ]
}

 The dataset includes 18901 records from 476 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0031104-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wp6psy
title: Occurrence Download

description: A dataset containing 5225612 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Colombia",
 "DatasetKey is EOD – eBird Observation Dataset",
 "Geometry POLYGON((-180 -70,180 -70,180 4,-180 4,-180 -70))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 5225612 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0031090-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vg7ebw
title: Occurrence Download

description: A dataset containing 29 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Catasetum mattosianum Bicalho"
 ]
}

 The dataset includes 29 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0031111-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.e8rdrc
title: Occurrence Download

description: A dataset containing 48936 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-78.48078 -1.42806,-77.98231 -1.42746,-77.98289 -0.87772,-78.48126 -0.87809,-78.48078 -1.42806))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Aves"
 ]
}

 The dataset includes 48936 records from 25 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0031108-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22002/ksjm8-3cv09
title: Campylobacter jejuni

description: Session notes: High magnification tomograms of whole WT Campylobacter cells. Tilt series notes: WT Campylobacter Tomogram notes:
description: <strong>Tilt Series Date:</strong> 2011-02-16</p>
<strong>Data Taken By:</strong> Morgan Beeby</p>
<strong>Species / Specimen:</strong> Campylobacter jejuni</p>
<strong>Strain:</strong> subsp. jejuni 81116</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-65.0°, 65.0°), step: 1°, constant angular increment, dosage: 200.0 eV/Å²,  defocus: 5.0 μm,  magnification: 0x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> imod</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mba2011-02-16-116/rawdata/</p>11feb16a_WTCampy_155.mrc,  Tilt Series (Pixel Size 0.512 nm), 1.1 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        11feb16a_WTCampy_155_SIRT.rec,  Reconstruction (Pixel Size 0.512 nm), 216.0 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/5nyg2-rsy51
title: Campylobacter jejuni

description: Session notes: Campy motB mutant, filtered 0.28, 0.02 after binning 2x more (to ~5.5nm resolution) Tilt series notes:  Tomogram notes:
description: <strong>Tilt Series Date:</strong> 2012-01-13</p>
<strong>Data Taken By:</strong> Morgan Beeby</p>
<strong>Species / Specimen:</strong> Campylobacter jejuni</p>
<strong>Strain:</strong> subsp. jejuni 81116</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-66.0°, 66.0°), step: 1.5°, constant angular increment, dosage: 200.0 eV/Å²,  defocus: 15.0 μm,  magnification: 0x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> </p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mba2012-01-13-2/rawdata/</p>12jan13a_motB_0041.st,  Tilt Series (Pixel Size 0.774 nm), 743.2 MB  
        
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        > <i class="download icon"></i> Download </a></p>

        12jan13a_motB_0041.rec,  Reconstruction (Pixel Size 1.56 nm), 16.4 MB  
        
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DOI: 10.22002/2bfzg-tjn64
title: Project: storage_granules

description: Session notes: Tilt series of R. eutropha storage granules from cells grown for 9hrs in minimal media then mildly lysed. Tilt series notes: Sonicated cell - unclear how much it had collapsed. Looks smaller than otheres, granules take up a large proportion of cell, probably collapsed. Tomogram notes: Sonicated cell, five large granules, fiducials appearing and disappearing without splitting, borders of granules not very distinct, first slide of stack excluded from tomogram. Reconstructed by Wesley.
description: <strong>Tilt Series Date:</strong> 2009-03-27</p>
<strong>Data Taken By:</strong> Morgan Beeby</p>
<strong>Species / Specimen:</strong> Cupriavidus necator</p>
<strong>Strain:</strong> H16</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-61.0°, 61.0°), step: 1.5°, constant angular increment, dosage: 40.0 eV/Å²,  defocus: -8.0 μm,  magnification: 0x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> imod</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mba2009-03-27-2/rawdata/</p>09mar27b_b401_2b_004.mrc,  Tilt Series (Pixel Size 0.632 nm), 687.9 MB  
        
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        09mar27b_b401_2b_004.rec,  Reconstruction (Pixel Size 1.264 nm), 484.4 MB  
        
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DOI: 10.22002/zb154-x8m70
title: Salmonella typhimurium

description: Session notes: Salmonella fliL minicells with T3SS Tilt series notes:  Tomogram notes:
description: <strong>Tilt Series Date:</strong> 2012-09-26</p>
<strong>Data Taken By:</strong> Morgan Beeby</p>
<strong>Species / Specimen:</strong> Salmonella typhimurium</p>
<strong>Strain:</strong> serovar Typhimurium str. LT2</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-66.0°, 66.0°), step: -1.5°, constant angular increment, dosage: 200.0 eV/Å²,  defocus: 5.0 μm,  magnification: 0x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> </p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mba2012-09-26-4/rawdata/</p>12sep26a_fliL_0011.st,  Tilt Series (Pixel Size 0.512 nm), 636.0 MB  
        
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        12sep26a_fliL_0011.rec,  Reconstruction (Pixel Size 1.12 nm), 353.3 MB  
        
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DOI: 10.25345/c58g8fw78
title: MassIVE MSV000098917 - Multiomic Analysis Reveals Molecular Pathways Associated with Intestinal Aggregation of a-Synuclein
title: Aggregates of the protein a-synuclein may initially form in the gut before propagating to the brain in Parkinson disease. Indeed, our prior work supports that enteroendocrine cells (specialized intestinal epithelial cells) could play a key role in the development of this disease. Enteroendocrine cells natively express a-synuclein and synapse with enteric neurons as well as the vagus nerve. Severing the vagus nerve reduces the load of a-synuclein aggregates in the brain, suggesting that this nerve is a conduit for gut-to-brain spread. Enteroendocrine cells line the gut lumen, as such, they are in constant contact with metabolites of the gut microbiota. We previously found that when enteroendocrine cells are exposed to nitrite - a potent oxidant produced by gut bacterial Enterobacteriaceae - a biochemical pathway is initiated that results in a-synuclein aggregation. Here, we determined that dopamine production is critical to this mechanism of nitrite-induced a-synuclein aggregation. Using enteroendocrine cells, we modulated dopamine biosynthesis and profiled the cellular proteome and lipidome. Proteomic signatures in dopamine-free cells were distinctly different than in enteroendocrine cells, highlighting pathways relevant to intestinal development of Parkinson disease. Intriguingly, we observed that enteroendocrine cells maintain viability upon exposure to nitrite and in the presence of a-synuclein aggregates. This cellular robustness suggests that dopamine-producing enteroendocrine cells may be a reservoir of toxic a-synuclein aggregates, which can spread through a prion-like process. As a possible antidote, our findings show that benserazide - a chemical inhibitor of dopamine biosynthesis - limits formation of these aggregates in enteroendocrine cells. These studies lay a foundation for mechanistically informed therapeutic targets to prevent intestinal formation of a-synuclein aggregates before they spread to the brain.
DOI: 10.22002/k8s0p-52560
title: Project: skinny_bugs

description: Session notes: Data collection of skinny buy Sphingopyxis alaskensis Tilt series notes: Single, long Sphingopyxis alaskensis.  Tomogram notes: OK reconstruction. Granules and septa.
description: <strong>Tilt Series Date:</strong> 2009-05-15</p>
<strong>Data Taken By:</strong> Morgan Beeby</p>
<strong>Species / Specimen:</strong> Sphingopyxis alaskensis</p>
<strong>Strain:</strong> DSM No. 13593</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-65.0°, 65.0°), step: 1.5°, constant angular increment, dosage: 100.0 eV/Å²,  defocus: -12.0 μm,  magnification: 0x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> raptor3</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mba2009-05-15-24/rawdata/</p>09may15a_grid4_010.mrc,  Tilt Series (Pixel Size 0.95 nm), 738.2 MB  
        
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        09may15a_grid4_010_full.rec,  Reconstruction (Pixel Size 1.9 nm), 1.0 GB  
        
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DOI: 10.22002/pm2jd-mc953
title: Campylobacter jejuni

description: Session notes: High magnification tomograms of whole WT Campylobacter cells. Tilt series notes: WT Campylobacter Tomogram notes:
description: <strong>Tilt Series Date:</strong> 2011-02-16</p>
<strong>Data Taken By:</strong> Morgan Beeby</p>
<strong>Species / Specimen:</strong> Campylobacter jejuni</p>
<strong>Strain:</strong> subsp. jejuni 81116</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-65.0°, 65.0°), step: 1°, constant angular increment, dosage: 200.0 eV/Å²,  defocus: 5.0 μm,  magnification: 0x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> imod</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mba2011-02-16-157/rawdata/</p>11feb16a_WTCampy_171.mrc,  Tilt Series (Pixel Size 0.512 nm), 1.1 GB  
        
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        11feb16a_WTCampy_171_bin1x_SIRT.rec,  Reconstruction (Pixel Size 0.512 nm), 209.9 MB  
        
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DOI: 10.22002/8gg00-pjk24
title: Campylobacter jejuni

description: Session notes: Campy cjj0413, filtered 0.28,0.02 after binning to pixel size 1.56 nm (so, ~5.5nm cutoff) Tilt series notes:  Tomogram notes:
description: <strong>Tilt Series Date:</strong> 2012-01-12</p>
<strong>Data Taken By:</strong> Morgan Beeby</p>
<strong>Species / Specimen:</strong> Campylobacter jejuni</p>
<strong>Strain:</strong> subsp. jejuni 81116</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-66.0°, 66.0°), step: 1.5°, constant angular increment, dosage: 200.0 eV/Å²,  defocus: 15.0 μm,  magnification: 0x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> </p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mba2012-01-12-6/rawdata/</p>12jan12a_cjj0413_0002.st,  Tilt Series (Pixel Size 0.774 nm), 743.2 MB  
        
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        12jan12a_cjj0413_0002.rec,  Reconstruction (Pixel Size 0.78 nm), 62.9 MB  
        
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DOI: 10.22002/ngant-hft95
title: Campylobacter jejuni

description: Session notes: High magnification tomograms of whole FlgP mutant Campylobacter cells. Tilt series notes: Cell pole on carbon Tomogram notes:
description: <strong>Tilt Series Date:</strong> 2010-08-26</p>
<strong>Data Taken By:</strong> Morgan Beeby</p>
<strong>Species / Specimen:</strong> Campylobacter jejuni</p>
<strong>Strain:</strong> subsp. jejuni 81116</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-61.0°, 61.0°), step: 1.5°, constant angular increment, dosage: 200.0 eV/Å²,  defocus: 5.0 μm,  magnification: 0x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> </p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mba2010-08-26-1/rawdata/</p>10aug26a_flgP_Campy_001.st,  Tilt Series (Pixel Size 0.512 nm), 645.9 MB  
        
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        10aug26a_flgP_Campy_001_bin2x_SIRT.rec,  Reconstruction (Pixel Size 1.024 nm), 24.8 MB  
        
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DOI: 10.22002/h1fea-jym29
title: Project: peptidoglycan

description: Session notes: Dosage and defocus trials Tilt series notes: notes Tomogram notes:
description: <strong>Tilt Series Date:</strong> 2008-12-24</p>
<strong>Data Taken By:</strong> Morgan Beeby</p>
<strong>Species / Specimen:</strong> Bacillus subtilis</p>
<strong>Strain:</strong> subsp. subtilis str. 168</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-64.5°, 64.5°), step: 1.5°, constant angular increment, dosage: 200.0 eV/Å²,  defocus: 4.0 μm,  magnification: 0x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> raptor2</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mba2008-12-24-5/rawdata/</p>08dec24a_grid1b_004.mrc,  Tilt Series (Pixel Size 0.782 nm), 738.2 MB  
        
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        08dec24a_grid1b_004_full.rec,  Reconstruction (Pixel Size 1.564 nm), 524.3 MB  
        
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DOI: 10.22002/a3pja-vvm49
title: Salmonella typhimurium

description: Session notes: Test run of Salmonella rabbit ears  Tilt series notes: Side wall of cell with multiple flagellar filaments visible. Large block of ice may hinder reconstruction? Tomogram notes: Large chunk of ice gets in the way a little. Many filaments; some pili visible (ice is good)
description: <strong>Tilt Series Date:</strong> 2010-02-26</p>
<strong>Data Taken By:</strong> Morgan Beeby</p>
<strong>Species / Specimen:</strong> Salmonella typhimurium</p>
<strong>Strain:</strong> serovar Typhimurium str. LT2</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-61.0°, 61.0°), step: 1.5°, constant angular increment, dosage: 200.0 eV/Å²,  defocus: 8.0 μm,  magnification: 0x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> raptor3</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mba2010-02-26-11/rawdata/</p>10feb26b_salmonella_005.mrc,  Tilt Series (Pixel Size 0.632 nm), 494.9 MB  
        
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        > <i class="download icon"></i> Download </a></p>

        10feb26b_salmonella_005_full.rec,  Reconstruction (Pixel Size 1.264 nm), 524.3 MB  
        
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