cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.22002/y4821-4xn76
title: Alongum

description: Alongum_periplasmiclayers
description: <strong>Tilt Series Date:</strong> 2012-05-20</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: (-30.0°, 30.0°), 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> WesleyChen helped remove layers</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/etl2012-05-20-81/rawdata/</p>AlnoOMa0009.mrc,  Tilt Series (Pixel Size 0.95 nm), 677.3 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2012-05-20-81/rawdata/AlnoOMa0009.mrc"
        > <i class="download icon"></i> Download </a></p>

        AlnoOMa0009_full.rec,  Reconstruction (Pixel Size 1.95 nm), 412.9 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2012-05-20-81/3dimage_56881/AlnoOMa0009_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.5281/zenodo.16871669
title: Acute supplementation of beta-hydroxybutyrate increases visual cortical excitability in humans: a combined Electro-EncephaloGraphy and – Magnetic Resonance Spectroscopy study

description: 1_Demographics_PlasmaLevels.csvparticipant-level demographic and physiological data:



Demographics: sex and age of each participant.

Metabolic measurements: plasma levels of βHB, glucose, insulin, c-peptide, glucagon and GLP1, measured at baseline and after 60, 120, and 180 minutes from the acute β-hydroxybutyrate (βHB) oral supplementation.


2_MRS.csvMagnetic Resonance Spectroscopy (MRS) results from the MEGA-PRESS sequence:



Alpha-corrected GABA+ and glutamate concentrations measured before (pre) and after (post) acute βHB supplementation.


3_EEG_SteadyStateVisualEvokedPotentials.csvSteady-State Visual Evoked Potential amplitudes (second harmonic of the EEG response measured by the OZ electrode):



Responses to an individual grating, before (pre) and after (post) acute βHB supplementation.

Responses to the same grating superimposed with an orthogonal mask, before (pre) and after (post) acute βHB supplementation.


4_EEG_RestingState.csvEEG resting-state with eyes open:



Amplitude of the resting-state EEG signal in the theta, alpha and beta ranges, each measured before (pre) and after (post) acute βHB supplementation, in three regions of interest: the individual OZ electrode, PO electrodes (PO8, PO3, PO4) and FC electrodes in frontal and central regions (Pz, Cz, Fz).
DOI: 10.5281/zenodo.16871670
title: Acute supplementation of beta-hydroxybutyrate increases visual cortical excitability in humans: a combined Electro-EncephaloGraphy and – Magnetic Resonance Spectroscopy study

description: 1_Demographics_PlasmaLevels.csvparticipant-level demographic and physiological data:



Demographics: sex and age of each participant.

Metabolic measurements: plasma levels of βHB, glucose, insulin, c-peptide, glucagon and GLP1, measured at baseline and after 60, 120, and 180 minutes from the acute β-hydroxybutyrate (βHB) oral supplementation.


2_MRS.csvMagnetic Resonance Spectroscopy (MRS) results from the MEGA-PRESS sequence:



Alpha-corrected GABA+ and glutamate concentrations measured before (pre) and after (post) acute βHB supplementation.


3_EEG_SteadyStateVisualEvokedPotentials.csvSteady-State Visual Evoked Potential amplitudes (second harmonic of the EEG response measured by the OZ electrode):



Responses to an individual grating, before (pre) and after (post) acute βHB supplementation.

Responses to the same grating superimposed with an orthogonal mask, before (pre) and after (post) acute βHB supplementation.


4_EEG_RestingState.csvEEG resting-state with eyes open:



Amplitude of the resting-state EEG signal in the theta, alpha and beta ranges, each measured before (pre) and after (post) acute βHB supplementation, in three regions of interest: the individual OZ electrode, PO electrodes (PO8, PO3, PO4) and FC electrodes in frontal and central regions (Pz, Cz, Fz).
DOI: 10.22002/by33d-xy279
title: UU 2804- A413T CheA deltaP2

description: E. coli strain A413T (locked in CheA off state) with deletion of P2 in CheA
description: <strong>Tilt Series Date:</strong> 2012-08-31</p>
<strong>Data Taken By:</strong> Ariane Briegel</p>
<strong>Species / Specimen:</strong> Escherichia coli</p>
<strong>Strain:</strong> RP 437</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-64.0°, 64.0°), step: 1°, constant angular increment, dosage: 180.0 eV/Å²,  defocus: -8.0 μm,  magnification: 34000x. </p>
<strong>Acquisition Software:</strong> UCSFTomo</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> UCSFtomo/IMOD/tomo3D</p>
<strong>Collaborators and Roles:</strong> John S. Parkinson</p>
<strong>Purification / Growth Conditions / Treatment:</strong> cells grown to log phase in TB media, lysed with penicillin for one hour</p>
<strong>Sample Preparation:</strong> plunge frozen on R2/2 Quantifoil grids in liquid ethane/propane</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/aba2012-08-31-18/rawdata/</p>2804atlas10018.mrc,  Tilt Series (Pixel Size 0.33 nm), 3.7 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/aba2012-08-31-18/rawdata/2804atlas10018.mrc"
        > <i class="download icon"></i> Download </a></p>

        2804atlas10018_full.rec,  Reconstruction (Pixel Size 0.66 nm), 2.8 GB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/1zhbt-azt98
title: Agro_C58_22C_liq

description: Raw data files of Agro_C58_22C_liq
description: <strong>Tilt Series Date:</strong> 2014-09-05</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: (-60.0°, 60.0°), step: 1.0°, 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> reupload_downloaded</p>
<strong>Processing Software Used:</strong> IMOD</p>
<strong>Collaborators and Roles:</strong> strain from Pat Zambryski</p>
<strong>Purification / Growth Conditions / Treatment:</strong> 22C liquid</p>
<strong>Sample Preparation:</strong> Vitrobot</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2014-09-05-34/rawdata/</p>c58_22_liq20007.mrc,  Tilt Series (Pixel Size 0.5 nm), 3.4 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2014-09-05-34/rawdata/c58_22_liq20007.mrc"
        > <i class="download icon"></i> Download </a></p>

        c58_22_liq20007_part121_12.rec,  Reconstruction (Pixel Size 0.0 nm), 534.5 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/sgqgz-rg580
title: HUVECs infx pNLGFP

description: Raw data files of HUVECs infx pNLGFP
description: <strong>Tilt Series Date:</strong> 2013-09-12</p>
<strong>Data Taken By:</strong> Cora Woodward</p>
<strong>Species / Specimen:</strong> Unspecified</p>
<strong>Strain:</strong> None</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1.0°, constant angular increment, dosage: 150.0 eV/Å²,  defocus: -6.0 μm,  magnification: 26000x. </p>
<strong>Acquisition Software:</strong> UCSFTomo</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> UCSFTomo</p>
<strong>Collaborators and Roles:</strong> pNLGFP obtained from Irvin Chen (UCLA)</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Whole cells were grown on Au finder grids and infected with pNLGFP- VSVG. Sample frozen 24h post infection</p>
<strong>Sample Preparation:</strong> manual blotting</p>
description: Files available via S3 at ttps://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/cwl2013-09-12-23/rawdata/</p>13sep12_HuvpNLgfp_24hPI_PI0008.mrc,  Tilt Series (Pixel Size 0.42 nm), 3.3 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        13sep12_HuvpNLgfp_24hPI_PI0008_full.rec,  Reconstruction (Pixel Size 1.68 nm), 430.6 MB  
        
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DOI: 10.22002/7z9v0-63p61
title: COS7 pNLGFP

description: Cos7 cells transfected with pNLGFP provirus construct. Sample #C112
description: <strong>Tilt Series Date:</strong> 2012-05-14</p>
<strong>Data Taken By:</strong> Cora Woodward</p>
<strong>Species / Specimen:</strong> Cercopithecus aethiops (monkey, African green)</p>
<strong>Strain:</strong> COS-7 ATCC CRL-1651</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1.5°, 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> pNLGFP construct provided by Irvin Chen, UCLA. Cells transfected, frozen and imaged at Caltech by Cora Woodward</p>
<strong>Purification / Growth Conditions / Treatment:</strong> whole cells grown on grids and transfected using lipofectamine</p>
<strong>Sample Preparation:</strong> manual blotting</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/cwl2012-05-14-24/3dimage_69356/</p>12may14_C112_2_pNLonly_AT3BT1d_0017_part82_6.rec,  Reconstruction (Pixel Size 2.0 nm), 619.4 MB  
        
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        > <i class="download icon"></i> Download </a></p>

        12may14_C112_2_pNLonly_AT3BT1d_0017.mrc,  Tilt Series (Pixel Size 0.5 nm), 677.3 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.5281/zenodo.16948106
title: Project 2 – Family Recipes Analysis

description: This dataset contains a **fictitious corpus of 12 family recipes**, created as part of the *MiniData Project 2025* for training in research data management and open science.

### Contents- Structured datasets (`family_recipes.csv`, `family_recipes.json`)- Python and R scripts for ingredient frequency analysis- Example plot of the top ingredients (`top_ingredients.png`)- Three fictitious recipe scans (`scan_recipe_*.jpg`)- Documentation: README, metadata (DataCite XML), sample Data Management Plan (PDF)- Methodological note (deposited separately on HAL)

### PurposeThe dataset is intended **exclusively for training purposes**.  It demonstrates best practices in:- dataset documentation with README and metadata- licensing adapted to different data types (MIT for scripts, CC BY for structured data, CC0 for metadata, CC BY-NC for scans)- open repository deposit (Zenodo for datasets, GitHub for software, HAL for publications)- linking research outputs in **OpenAIRE** under Horizon Europe open science requirements

### DisclaimerThis dataset is fictitious. The recipes and scans do not represent real personal or cultural data.
DOI: 10.5281/zenodo.16948107
title: Project 2 – Family Recipes Analysis

description: This dataset contains a **fictitious corpus of 12 family recipes**, created as part of the *MiniData Project 2025* for training in research data management and open science.

### Contents- Structured datasets (`family_recipes.csv`, `family_recipes.json`)- Python and R scripts for ingredient frequency analysis- Example plot of the top ingredients (`top_ingredients.png`)- Three fictitious recipe scans (`scan_recipe_*.jpg`)- Documentation: README, metadata (DataCite XML), sample Data Management Plan (PDF)- Methodological note (deposited separately on HAL)

### PurposeThe dataset is intended **exclusively for training purposes**.  It demonstrates best practices in:- dataset documentation with README and metadata- licensing adapted to different data types (MIT for scripts, CC BY for structured data, CC0 for metadata, CC BY-NC for scans)- open repository deposit (Zenodo for datasets, GitHub for software, HAL for publications)- linking research outputs in **OpenAIRE** under Horizon Europe open science requirements

### DisclaimerThis dataset is fictitious. The recipes and scans do not represent real personal or cultural data.
DOI: 10.22002/vyark-qfq34
title: HIV capsid purified trim5 alpha

description: 22500 df8, 26/A2 with no silt. Decorated HIV cores with TRIM5 alpha.
description: <strong>Tilt Series Date:</strong> 2013-12-13</p>
<strong>Data Taken By:</strong> Stephen Carter</p>
<strong>Species / Specimen:</strong> HIV cores</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: 26.0 eV/Å²,  defocus: -8.0 μm,  magnification: 22500x. </p>
<strong>Microscope:</strong> Caltech Polara</p>
<strong>Acquisition Software:</strong> Undefined</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> 3dmod and SIRT</p>
<strong>Collaborators and Roles:</strong> Wes Sundquist</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Recombinant TRIM5 alpha, decorated HIV cores</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/scd2013-12-13-18/rawdata/</p>Trimb20018.mrc,  Tilt Series (Pixel Size 0.48 nm), 3.4 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/scd2013-12-13-18/rawdata/Trimb20018.mrc"
        > <i class="download icon"></i> Download </a></p>

        Trimb20018_full.rec,  Reconstruction (Pixel Size 1.92 nm), 445.4 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/hmt9k-c6671
title: Hylemonella gracilis

description: flagellar motor
description: <strong>Tilt Series Date:</strong> 2012-09-23</p>
<strong>Data Taken By:</strong> Yi-Wei Chang</p>
<strong>Species / Specimen:</strong> Hylemonella gracilis</p>
<strong>Strain:</strong> ATCC 19624</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1.0°, constant angular increment, dosage: 75.0 eV/Å²,  defocus: -15.0 μm,  magnification: 22500x. </p>
<strong>Acquisition Software:</strong> UCSFTomo</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> RAPTOR</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Cell grown 48 hr in Broth 233 at 26°C without antibiotics, Final OD600 < 0.1, Spun down by 1000 rcf for 5 min and concentrated by ~10x for plunge freezing</p>
<strong>Sample Preparation:</strong> Vitrobot setting: 100% humidity, 4 ul sample, 10 nm BSA treated gold, -3 offset, 4 s blot time, no drain, ethane/propane mix</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2012-09-23-31/rawdata/</p>20120923_Hylemonella_20004.mrc,  Tilt Series (Pixel Size 0.49 nm), 3.4 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2012-09-23-31/rawdata/20120923_Hylemonella_20004.mrc"
        > <i class="download icon"></i> Download </a></p>

        20120923_Hylemonella_20004_full.rec,  Reconstruction (Pixel Size 1.96 nm), 441.7 MB  
        
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DOI: 10.22002/y0b98-xav50
title: Crosslinked HIV-1 cores TRIM5a

description: Hyperstable purified HIV-1 cores crosslinked with TRIM5alpha.
description: <strong>Tilt Series Date:</strong> 2013-05-24</p>
<strong>Data Taken By:</strong> Stephen Carter</p>
<strong>Species / Specimen:</strong> HIV cores</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: 99.0 eV/Å²,  defocus: -6.0 μm,  magnification: 41000x. </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 and SIRT reconstruction</p>
<strong>Collaborators and Roles:</strong> Wes Sundquist</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Grids frozen in Utah</p>
<strong>Sample Preparation:</strong> Non infectious HIV-1 cores</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/scd2013-05-24-2/3dimage_42865/</p>montage0002_full.rec,  Reconstruction (Pixel Size 1.04 nm), 445.4 MB  
        
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        > <i class="download icon"></i> Download </a></p>

        montage0002.mrc,  Tilt Series (Pixel Size 0.26 nm), 3.4 GB  
        
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DOI: 10.22002/npqe0-c5g04
title: Vibrio delta-CheA1

description: Vibrio cholerae strain deleted for CheA1
description: <strong>Tilt Series Date:</strong> 2014-03-04</p>
<strong>Data Taken By:</strong> Ariane Briegel</p>
<strong>Species / Specimen:</strong> Vibrio cholerae</p>
<strong>Strain:</strong> O1 biovar El Tor</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1°, constant angular increment, dosage: 160.0 eV/Å²,  defocus: -10.0 μm,  magnification: 33000x. </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> Ikuro Kawagishi</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Grew in LB 24 hours at 30C; diluted 150 µL into 2 mL Ca-HEPES buffer and grew 16 hours at 30C</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/aba2014-03-04-4/rawdata/</p>deltaA1VibrioC0004.mrc,  Tilt Series (Pixel Size 0.33 nm), 3.3 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        deltaA1VibrioC0004_full.rec,  Reconstruction (Pixel Size 1.32 nm), 688.9 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/d30y1-gd075
title: Agrobacterium tumefaciens

description: Agro VG3101
description: <strong>Tilt Series Date:</strong> 2013-10-31</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: (-60.0°, 60.0°), step: 1.0°, 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> reupload_downloaded</p>
<strong>Processing Software Used:</strong> IMOD</p>
<strong>Collaborators and Roles:</strong> Elliot Meyerwitz</p>
<strong>Purification / Growth Conditions / Treatment:</strong> liquid LB+antibiotics</p>
<strong>Sample Preparation:</strong> Vitrobot blotting</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2013-10-31-4/rawdata/</p>agro_VG31010004.mrc,  Tilt Series (Pixel Size 0.4 nm), 3.4 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        agro_VG31010004_part121_5.rec,  Reconstruction (Pixel Size 0.0 nm), 801.8 MB  
        
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DOI: 10.15468/dl.n2eb9u
title: Occurrence Download

description: A dataset containing 143019 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "Sex is one of (Male, Female, Mixed, Indeterminate)",
 "TaxonKey is Polyommatus icarus"
 ]
}

 The dataset includes 143019 records from 250 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045801-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.