cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.22002/vpshp-9wd23
title: Cryo-sectioned Jurkat VSVG-pNL4GFP

description: Jurkats infected by spinoculation with VSVG-pNL4GFP, collected 30 min after synchronous entry, HP frozen and cryo-sectioned by Mark Ladinsky-Grid4
description: <strong>Tilt Series Date:</strong> 2011-12-25</p>
<strong>Data Taken By:</strong> Cora Woodward</p>
<strong>Species / Specimen:</strong> Jurkat Human T-cell</p>
<strong>Strain:</strong> Clone E6-1</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1°, constant angular increment, dosage: 150.0 eV/Å²,  defocus: -6.0 μm,  magnification: 22500x. </p>
<strong>Acquisition Software:</strong> UCSF tomo</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> imod</p>
<strong>Collaborators and Roles:</strong> pNL4GFP provirus construct from Irvin Chen (UCLA). Vpr-gfp construct to label virus provided by Tom Hope. Virus made at Caltech by Cora Woodward. Cryo-sectioning by Mark Ladinsky.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> infected VSVG-pNL4GFP</p>
<strong>Sample Preparation:</strong> cryo-sectioned by Mark Ladinsky</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/cwl2011-12-25-11/rawdata/</p>11dec25_cryosec_JurkatpNLgfp_grid4_AT1BT2_0025.st,  Tilt Series (Pixel Size 0.5 nm), 512.1 MB  
        
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        > <i class="download icon"></i> Download </a></p>

        11dec25_cryosec_JurkatpNLgfp_grid4_AT1BT2_0025_full.rec,  Reconstruction (Pixel Size 2.0 nm), 386.1 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/9bxwv-bgr51
title: Pva 020409 007

description: Prosthecobacter vanneervenii, 09feb23a_Pva_plate__007_w2_008,
description: <strong>Tilt Series Date:</strong> 2009-02-23</p>
<strong>Data Taken By:</strong> Martin Pilhofer</p>
<strong>Species / Specimen:</strong> Prosthecobacter vanneervenii</p>
<strong>Strain:</strong> None</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1°, constant angular increment, dosage: 180.0 eV/Å²,  defocus: -10.0 μm,  magnification: 22500x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> raptor</p>
<strong>Collaborators and Roles:</strong> cultured by Martin Pilhofer; data collected by Martin Pilhofer; processed by Martin Pilhofer</p>
<strong>Sample Preparation:</strong> quantifoil grid, 10nm gold, 100% humidity, blotting 1/-2/2/0/1/4/200</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mpa2009-02-23-18/rawdata/</p>09feb23a_Pva_plate__007_w2_008.mrc,  Tilt Series (Pixel Size 0.95 nm), 1.0 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        09feb23a_Pva_plate__007_w2_008_full.rec,  Reconstruction (Pixel Size 1.9 nm), 838.9 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.57745/mr9qf5
title: chebis.csv.gz

description: 8 columns:
* smiles (String) SMILES of the ChEBI molecule
* chebi (List[String]) List of ChEBI identifiers sharing the same SMILES
* num_heavy_atoms (Integer) Number of heavy atoms retrieved in the molecule
* exact_mol_wt (Integer) Molecular weight of the molecule
* additional_substituents_smiles (List[String]) SMILES of the molecule retrieved from PubChem that match the core structure of the molecule, allowing for the possibility of atoms being present not only at the R-group locations.
* additional_substituents_pubchem_cid (List[List[Integer]]) PubChem identifiers of the molecules. A single molecule may correspond to one or several PubChem identifiers.
* only_match_rgroup_smiles (List[String]) SMILES of the molecule retrieved from PubChem that match the core structure of the molecule, only at the R-group locations.
* only_match_rgroup_pubchem_cid (List[List[Integer]]) PubChem identifiers of the molecules. A single molecule may correspond to one or several PubChem identifiers.
DOI: 10.57745/k53odt
title: chebis.csv.gz

description: 8 columns:
* smiles (String) SMILES of the ChEBI molecule
* chebi (List[String]) List of ChEBI identifiers sharing the same SMILES
* num_heavy_atoms (Integer) Number of heavy atoms retrieved in the molecule
* exact_mol_wt (Float) Molecular weight of the molecule
* core_superstructure_smiles (List[String]) SMILES of the molecule retrieved from PubChem that match the core structure of the molecule, allowing for the possibility of atoms being present not only at the R-group locations.
* core_superstructure_pubchem_cid (List[List[Integer]]) PubChem identifiers of the molecules. A single molecule may correspond to one or several PubChem identifiers.
* rgroup_extended_smiles (List[String]) SMILES of the molecule retrieved from PubChem that match the core structure of the molecule, only at the R-group locations.
* rgroup_extended_pubchem_cid (List[List[Integer]]) PubChem identifiers of the molecules. A single molecule may correspond to one or several PubChem identifiers.
DOI: 10.22002/dr60c-0qz26
title: Pva 020209 377

description: Prosthecobacter vanneervenii, 09feb08c__Pva_grid_020209_377_w1_003, putative btub structure (several tubes)
description: <strong>Tilt Series Date:</strong> 2009-02-08</p>
<strong>Data Taken By:</strong> Martin Pilhofer</p>
<strong>Species / Specimen:</strong> Prosthecobacter vanneervenii</p>
<strong>Strain:</strong> None</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1°, constant angular increment, dosage: 180.0 eV/Å²,  defocus: -10.0 μm,  magnification: 22500x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> imod</p>
<strong>Collaborators and Roles:</strong> cultured by Martin Pilhofer; data collected by Martin Pilhofer; processed by Martin Pilhofer</p>
<strong>Sample Preparation:</strong> quantifoil grid, 10nm gold, 100% humidity, blotting 1/-2/2/0/1/4/200</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mpa2009-02-08-36/rawdata/</p>09feb08c__Pva_grid_020209_377_w1_003.mrc,  Tilt Series (Pixel Size 0.95 nm), 1.0 GB  
        
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        09feb08c__Pva_grid_020209_377_w1_003.rec,  Reconstruction (Pixel Size 1.9 nm), 103.5 MB  
        
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DOI: 10.15468/dl.taup6r
title: Occurrence Download

description: A dataset listing the 668 species recorded in GBIF matching the query:
{
 "and" : [
 "Country is Bulgaria",
 "Elevation 529.0-785.0m",
 "Geometry POLYGON((22.95866 42.37407,23.88289 42.37407,23.88289 43.03907,22.95866 43.03907,22.95866 42.37407))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Plantae"
 ]
}

 The dataset's 668 records were derived from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045725-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22002/mfg3v-8zq21
title: BsubtilisMJ007 spores

description: Bsubtilis MJ007 spores
description: <strong>Tilt Series Date:</strong> 2011-07-19</p>
<strong>Data Taken By:</strong> Elitza Tocheva</p>
<strong>Species / Specimen:</strong> Bacillus subtilis </p>
<strong>Strain:</strong> MJ007, ponA null</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1°, constant angular increment, dosage: 200.0 eV/Å²,  defocus: -10.0 μm,  magnification: 22500x. </p>
<strong>Acquisition Software:</strong> UCSF tomo</p>
<strong>Upload Method:</strong> uploadraptor</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> strain from Kit Pogliano at UCSD</p>
<strong>Purification / Growth Conditions / Treatment:</strong> sporulation media</p>
<strong>Sample Preparation:</strong> quantifoil grid R2/2, 20nm gold, 100% humidity</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2011-07-19-33/3dimage_25053/</p>spore0002_full.rec,  Reconstruction (Pixel Size 1.9 nm), 666.8 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2011-07-19-33/3dimage_25053/spore0002_full.rec"
        > <i class="download icon"></i> Download </a></p>

        spore0002.mrc,  Tilt Series (Pixel Size 0.95 nm), 1.0 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2011-07-19-33/rawdata/spore0002.mrc"
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DOI: 10.6084/m9.figshare.29986714.v2
title: Supplementary tables_CEAM

description: DNA methylation signatures are highly cell type-specific, yet most epigenome-wide association studies (EWAS) are performed on bulk tissue, potentially obscuring critical cell type-specific patterns. Existing computational tools for detecting cell type-specific DNAm changes are often limited by the accuracy of cell type deconvolution algorithms. Here, we introduce CEAM (Cell-type Enrichment Analysis for Methylation), a robust and interpretable framework for cell type enrichment analysis in DNA methylation data. CEAM applies over-representation analysis with cell type-specific CpG panels from Illumina EPIC arrays derived from nuclei-sorted cortical post-mortem brains from neurologically healthy aged individuals. The constructed CpG panels were systematically evaluated using both simulated datasets and published EWAS results from Alzheimer’s disease, Lewy body disease, and multiple sclerosis. CEAM demonstrated resilience to shifts in cell type composition, a common confounder in EWAS, and remained accurate across a wide range of differentially methylated positions, underscoring its flexibility. Application to existing EWAS findings generated in neurodegenerative diseases revealed enrichment patterns concordant with established disease biology, confirming CEAM’s biological relevance. The workflow is publicly available as an interactive Shiny app (https://um-dementia-systems-biology.shinyapps.io/CEAM/) enabling rapid, interpretable analysis of cell type-specific DNAm changes from bulk EWAS.
DOI: 10.22002/mwhnt-7fn66
title: Wild type control

description: Raw data files of Wild type control
description: <strong>Tilt Series Date:</strong> 2009-08-01</p>
<strong>Data Taken By:</strong> Zhuo Li</p>
<strong>Species / Specimen:</strong> Caulobacter crescentus</p>
<strong>Strain:</strong> NA1000</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1°, constant angular increment, dosage: 200.0 eV/Å²,  defocus: -12.0 μm,  magnification: 0x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> webload</p>
<strong>Processing Software Used:</strong> RAPTOR, PEACH</p>
<strong>Collaborators and Roles:</strong> Experiments were done by Zhuo Li.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Exponential phase NA1000 cells.</p>
<strong>Sample Preparation:</strong> 10 nm gold </p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/zla2009-08-01-21/rawdata/</p>09aug01a_noaddctl1_021.mrc,  Tilt Series (Pixel Size 1.2 nm), 1.0 GB  
        
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        09aug01a_noaddctl1_021_part.rec,  Reconstruction (Pixel Size 2.4 nm), 367.0 MB  
        
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DOI: 10.22002/fk7cf-xs592
title: Agrobacterium tumefaciens C58

description: Agro C58
description: <strong>Tilt Series Date:</strong> 2013-10-23</p>
<strong>Data Taken By:</strong> Elitza Tocheva</p>
<strong>Species / Specimen:</strong> Agrobacterium tumefaciens</p>
<strong>Strain:</strong> </p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-55.0°, 55.0°), step: 1.0°, constant angular increment, dosage: 200.0 eV/Å²,  defocus: -10.0 μm,  magnification: 19500x. </p>
<strong>Microscope:</strong> Janelia Titan</p>
<strong>Acquisition Software:</strong> UCSFTomo</p>
<strong>Upload Method:</strong> reupload_downloaded</p>
<strong>Processing Software Used:</strong> IMOD</p>
<strong>Collaborators and Roles:</strong> Pat Zambryski</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Induction for T-pilus with 200uM AS</p>
<strong>Sample Preparation:</strong> Manual blotting</p>
description: Files available via S3 at ttps://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2013-10-23-40/rawdata/</p>c58_2_berk_home_195k0011.mrc,  Tilt Series (Pixel Size 0.56 nm), 3.1 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        c58_2_berk_home_195k0011.rec,  Reconstruction (Pixel Size 0.0 nm), 1.6 GB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/1dc5e-rr665
title: MJ sacculi

description: Skinny B. subtilis MJ007 sacculi of sporulating cells
description: <strong>Tilt Series Date:</strong> 2012-03-01</p>
<strong>Data Taken By:</strong> Elitza Tocheva</p>
<strong>Species / Specimen:</strong> Bacillus subtilis </p>
<strong>Strain:</strong> MJ007, ponA null</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-63.0°, 63.0°), step: 1°, constant angular increment, dosage: 200.0 eV/Å²,  defocus: -10.0 μm,  magnification: 22500x. </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> Kit Pogliano</p>
<strong>Purification / Growth Conditions / Treatment:</strong> see Mol Micro Tocheva et al reference</p>
<strong>Sample Preparation:</strong> Vitrobot</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2012-03-01-10/rawdata/</p>mjsac0010.mrc,  Tilt Series (Pixel Size 1.9 nm), 1.1 GB  
        
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        mjsac0010_full.rec,  Reconstruction (Pixel Size 3.8 nm), 619.4 MB  
        
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DOI: 10.15468/dl.zx666y
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Pterorhinus galbanus",
 "Country is China",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045748-250811113504898/datasets/export for details.
DOI: 10.22002/647at-p1h74
title: E. Coli A20S

description: Mutant MreB with sfGFP sandwich fusion.
description: <strong>Tilt Series Date:</strong> 2014-04-06</p>
<strong>Data Taken By:</strong> Matt Swulius</p>
<strong>Species / Specimen:</strong> Escherichia coli</p>
<strong>Strain:</strong> A20S</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-64.0°, 64.0°), step: 1°, constant angular increment, dosage: 200.0 eV/Å²,  defocus: -10.0 μm,  magnification: 22500x. </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> Josh Schaevitz</p>
<strong>Purification / Growth Conditions / Treatment:</strong> 37 degrees celsius to OD 600 ~ 0.3</p>
<strong>Sample Preparation:</strong> Plunge frozen in vitrobot with 100% humidity using manual blotting from rear.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mst2014-04-06-18/3dimage_41497/</p>040614_a20s_2_0006_full.rec,  Reconstruction (Pixel Size 1.92 nm), 890.9 MB  
        
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        > <i class="download icon"></i> Download </a></p>

        040614_a20s_2_0006.mrc,  Tilt Series (Pixel Size 0.48 nm), 3.7 GB  
        
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DOI: 10.22002/sh32x-4bm91
title: A. longum ProteinaseK digest

description: A. longum's cell wall was digested with proteinase K to determine the periplasmic layer composition
description: <strong>Tilt Series Date:</strong> 2012-04-26</p>
<strong>Data Taken By:</strong> Elitza Tocheva</p>
<strong>Species / Specimen:</strong> Acetonema longum</p>
<strong>Strain:</strong> None</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-50.0°, 50.0°), step: 1°, constant angular increment, dosage: 200.0 eV/Å²,  defocus: -10.0 μm,  magnification: 22500x. </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> Wesley Chen</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Cells were grown anaerobically and digested with 5mg/ml proteinase K enzyme</p>
<strong>Sample Preparation:</strong> Vitrobot</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2012-04-26-16/rawdata/</p>alongprotk0016.mrc,  Tilt Series (Pixel Size 1.9 nm), 842.5 MB  
        
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        alongprotk0016_full.rec,  Reconstruction (Pixel Size 3.8 nm), 619.4 MB  
        
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DOI: 10.22002/rgfnn-0mp09
title: Eco 082609 MP11

description: Escherichia coli, 09sep24a_MP11_082609_7_1_2_son_008,
description: <strong>Tilt Series Date:</strong> 2009-09-24</p>
<strong>Data Taken By:</strong> Martin Pilhofer</p>
<strong>Species / Specimen:</strong> Escherichia coli</p>
<strong>Strain:</strong> 7.1.2 Martin</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1°, constant angular increment, dosage: 180.0 eV/Å²,  defocus: -10.0 μm,  magnification: 22500x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> raptor</p>
<strong>Collaborators and Roles:</strong> cultured by Martin Pilhofer; data collected by Martin Pilhofer; processed by Martin Pilhofer</p>
<strong>Sample Preparation:</strong> quantifoil grid, 10nm gold, 100% humidity, blotting 1/-2/2/0/1/4/200</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mpa2009-09-24-8/rawdata/</p>09sep24a_MP11_082609_7_1_2_son_008.mrc,  Tilt Series (Pixel Size 0.95 nm), 1.0 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        09sep24a_MP11_082609_7_1_2_son_008_full.rec,  Reconstruction (Pixel Size 1.9 nm), 943.7 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.5281/zenodo.16947516
title: Nigerian Computer-Mediated Fraudulent Text Messages

description: This dataset comprises Nigerian digital fraudulent text messages collected between January 2022 and September 2024 through purposive sampling. The messages were sourced from the personal inboxes of researchers, colleagues, and students. The content primarily includes phishing and scam messages impersonating credible institutions (e.g., CBN, commercial banks), using themes such as BVN system upgrades, ATM card deactivation, incomplete bank registration, and cashless policy enforcement. Some messages also promote fraudulent investment schemes, crypto scams, and Ponzi schemes.