cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.16964977
title: Data_WP5_5 Cardiorespiratory function measures

description: This dataset encompasses quantifiable clinical outcomes related to the cardiorespiratory health of participants, collected both before and after the interventions (Phase IIa and Phase IIb). It aims to identify risk factors that may adversely affect the cardiorespiratory systems of individuals enrolled in the URBANOME study. The dataset includes the following examinations and tests:



Spirometry: A pulmonary function test that provides several key indicators of lung performance. Variables include:



Forced Expiratory Volume in 1 second (FEV1) (liters)

Forced Vital Capacity (FVC), including predicted values based on demographics (liters)

FEV1/FVC ratio (%), a standard index of airway obstruction

Forced Expiratory Flow at 25–75% of FVC (FEF25–75) (liters/second)

Percent change in spirometry values (e.g., post-bronchodilator)

Indicator or flag denoting whether the spirometry was performed and valid


Exhaled Nitric Oxide (FeNO): Measured using a portable NIOX device, FeNO quantifies the concentration of nitric oxide in exhaled air (ppb), serving as a non-invasive biomarker of airway inflammation. 

Oxygen Saturation (SpO₂): Assessed via pulse oximetry to determine blood oxygenation levels (%). 

Blood Pressure: Systolic Blood Pressure (SBP) and Diastolic Blood Pressure (DBP) are measured in mmHg.

Carboxyhemoglobin (COHb) Levels: the concentration of carbon monoxide (CO) in the body was assessed by measuring COHb, formed when CO binds with hemoglobin in the lungs. Elevated COHb levels indicate exposure to harmful pollutants and impaired respiratory function due to reduced oxygen transport.


Data are stored by Urban Living Lab, and each file is accompanied by a data dictionary to facilitate the identification and interpretation of variables, measurement units, and data structure.
DOI: 10.5281/zenodo.16964978
title: Data_WP5_5 Cardiorespiratory function measures

description: This dataset encompasses quantifiable clinical outcomes related to the cardiorespiratory health of participants, collected both before and after the interventions (Phase IIa and Phase IIb). It aims to identify risk factors that may adversely affect the cardiorespiratory systems of individuals enrolled in the URBANOME study. The dataset includes the following examinations and tests:



Spirometry: A pulmonary function test that provides several key indicators of lung performance. Variables include:



Forced Expiratory Volume in 1 second (FEV1) (liters)

Forced Vital Capacity (FVC), including predicted values based on demographics (liters)

FEV1/FVC ratio (%), a standard index of airway obstruction

Forced Expiratory Flow at 25–75% of FVC (FEF25–75) (liters/second)

Percent change in spirometry values (e.g., post-bronchodilator)

Indicator or flag denoting whether the spirometry was performed and valid


Exhaled Nitric Oxide (FeNO): Measured using a portable NIOX device, FeNO quantifies the concentration of nitric oxide in exhaled air (ppb), serving as a non-invasive biomarker of airway inflammation. 

Oxygen Saturation (SpO₂): Assessed via pulse oximetry to determine blood oxygenation levels (%). 

Blood Pressure: Systolic Blood Pressure (SBP) and Diastolic Blood Pressure (DBP) are measured in mmHg.

Carboxyhemoglobin (COHb) Levels: the concentration of carbon monoxide (CO) in the body was assessed by measuring COHb, formed when CO binds with hemoglobin in the lungs. Elevated COHb levels indicate exposure to harmful pollutants and impaired respiratory function due to reduced oxygen transport.


Data are stored by Urban Living Lab, and each file is accompanied by a data dictionary to facilitate the identification and interpretation of variables, measurement units, and data structure.
DOI: 10.15468/dl.g3py39
title: Occurrence Download

description: A dataset containing 62 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Styphnolobium japonicum",
 "Country is Netherlands",
 "HasCoordinate is true"
 ]
}

 The dataset includes 62 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0050168-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ysm4pq
title: Occurrence Download

description: A dataset containing 70 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Styphnolobium japonicum",
 "Country is Portugal",
 "HasCoordinate is true"
 ]
}

 The dataset includes 70 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0050169-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.tbeph9
title: Occurrence Download

description: A dataset containing 20 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Styphnolobium japonicum",
 "Country is Romania",
 "HasCoordinate is true"
 ]
}

 The dataset includes 20 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0050170-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bz43np
title: Occurrence Download

description: A dataset containing 7852 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Australia",
 "OccurrenceStatus is Present",
 "TaxonKey is Hakea sericea Schrad. & J.C.Wendl."
 ]
}

 The dataset includes 7852 records from 69 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022548-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.13839383
title: Probing Nuclear Structure of Heavy Ions at the Large Hadron Collider

description: The dataset contains event-by-event results for particle yields, their averaged transverse momentum, and anisotropic flow vectors for Pb+Pb and Xe+Xe collisions at LHC energies with different parameter settings.

The data was generated using the iEBE-MUSIC framework.

The event-by-event are saved as dictionaries in the Python Pickle format.

We also included the analysis scripts which read the event-by-event results and performed event averages for various experimental observables.
DOI: 10.5281/zenodo.13839384
title: Probing Nuclear Structure of Heavy Ions at the Large Hadron Collider

description: The dataset contains event-by-event results for particle yields, their averaged transverse momentum, and anisotropic flow vectors for Pb+Pb and Xe+Xe collisions at LHC energies with different parameter settings.

The data was generated using the iEBE-MUSIC framework.

The event-by-event are saved as dictionaries in the Python Pickle format.

We also included the analysis scripts which read the event-by-event results and performed event averages for various experimental observables.
DOI: 10.15468/dl.72cwfk
title: Occurrence Download

description: A dataset containing 2299 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Aphelandra longiflora (Lindl.) Profice"
 ]
}

 The dataset includes 2299 records from 148 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022549-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.cwxjcd
title: Occurrence Download

description: A dataset containing 144 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Portulaca mauritiensis Poelln."
 ]
}

 The dataset includes 144 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022550-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22002/ps79w-0re14
title: 1003_deletion

description: Raw data files of 1003_deletion
description: <strong>Tilt Series Date:</strong> 2009-10-21</p>
<strong>Data Taken By:</strong> Zhuo Li</p>
<strong>Species / Specimen:</strong> Magnetospirillum magneticum</p>
<strong>Strain:</strong> AMB-1</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-63.0°, 63.0°), step: 1°, constant angular increment, dosage: 110.0 eV/Å²,  defocus: -15.0 μm,  magnification: 18000x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> webload</p>
<strong>Processing Software Used:</strong> RAPTOR, Peach, IMOD</p>
<strong>Collaborators and Roles:</strong> Cells sent from Arash Komeili, data collected by ZL.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> (Could be) Stationary phase</p>
<strong>Sample Preparation:</strong> Quantifoil R2/1 or R2/2, 10nm gold, 100% humidity</p>
  zla2009-10-21-51_slicer7141.jpg: filament
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/zla2009-10-21-51/rawdata/</p>09oct21a_m1003_051.mrc,  Tilt Series (Pixel Size 1.192 nm), 1.1 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/zla2009-10-21-51/rawdata/09oct21a_m1003_051.mrc"
        > <i class="download icon"></i> Download </a></p>

        09oct21a_m1003_051_part.rec,  Reconstruction (Pixel Size 2.384 nm), 471.9 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/zla2009-10-21-51/3dimage_9994/09oct21a_m1003_051_part.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/nte1h-zqy29
title: Hyphomonas chq session19 34KX

description: high-order DNA, H-NS, nucleoid, asymmetric cell division
description: <strong>Tilt Series Date:</strong> 2009-06-25</p>
<strong>Data Taken By:</strong> Jian Shi</p>
<strong>Species / Specimen:</strong> Hyphomonas neptunium</p>
<strong>Strain:</strong> ATCC 15444</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-61.0°, 61.0°), step: 2°, constant angular increment, dosage: 75.0 eV/Å²,  defocus: -7.0 μm,  magnification: 0x. </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 Jian; data collected by Jian; processed by Jian</p>
<strong>Purification / Growth Conditions / Treatment:</strong> exponential phase in PYE media, chloroquine 1.0mg/ml, 4degree...</p>
<strong>Sample Preparation:</strong> QF grid, 10nm gold, 100% humidity...</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/jsa2009-06-25-25/rawdata/</p>09jun25a_bx217d_056.mrc,  Tilt Series (Pixel Size 0.632 nm), 536.9 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/jsa2009-06-25-25/rawdata/09jun25a_bx217d_056.mrc"
        > <i class="download icon"></i> Download </a></p>

        09jun25a_bx217d_056_full.rec,  Reconstruction (Pixel Size 1.264 nm), 419.4 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/jsa2009-06-25-25/3dimage_8120/09jun25a_bx217d_056_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/fgd9k-y1136
title: HUVECs CHMP4A+VPS4DN

description: HUVECs transfected with CHMP4A+VPS4DN constructs using Nucleofector Kit. Sample# C58-2
description: <strong>Tilt Series Date:</strong> 2010-12-13</p>
<strong>Data Taken By:</strong> Cora Woodward</p>
<strong>Species / Specimen:</strong> HUVECs</p>
<strong>Strain:</strong> </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: -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> CHMP4A and VPS4DN construct provided by Wes Sundquist. Cells transfected, frozen and imaged at Caltech by Cora Woodward</p>
<strong>Purification / Growth Conditions / Treatment:</strong> whole cells grown on grids and transfected</p>
<strong>Sample Preparation:</strong> manual blotting</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/cwl2010-12-13-15/rawdata/</p>10dec13a_C45_4_023.st,  Tilt Series (Pixel Size 0.5 nm), 1.0 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/cwl2010-12-13-15/rawdata/10dec13a_C45_4_023.st"
        > <i class="download icon"></i> Download </a></p>

        10dec13a_C45_4_023_full.rec,  Reconstruction (Pixel Size 2.0 nm), 471.9 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/cwl2010-12-13-15/3dimage_68201/10dec13a_C45_4_023_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/772pq-sn442
title: A22-treated wild type

description: Raw data files of A22-treated wild type
description: <strong>Tilt Series Date:</strong> 2009-07-21</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: 190.0 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> Cell culture and treatment by Zhuo Li. Data collected by Zhuo Li. Processed by Zhuo Li. </p>
<strong>Purification / Growth Conditions / Treatment:</strong> Exponentially growing NA1000 cells were treated with 10 ug/ml A22 for 2 hours before freezing. </p>
<strong>Sample Preparation:</strong> 10 nm gold. </p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/zla2009-07-21-52/rawdata/</p>09jul21a_A22wt_052.mrc,  Tilt Series (Pixel Size 1.2 nm), 1.0 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/zla2009-07-21-52/rawdata/09jul21a_A22wt_052.mrc"
        > <i class="download icon"></i> Download </a></p>

        09jul21a_A22wt_052_part.rec,  Reconstruction (Pixel Size 2.4 nm), 367.0 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/zla2009-07-21-52/3dimage_5928/09jul21a_A22wt_052_part.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/8pft9-ca044
title: Bsubtilis349

description: Bsubtilis JFG349 (MJ007, SpoIIIE78-11-GFP)
description: <strong>Tilt Series Date:</strong> 2011-11-01</p>
<strong>Data Taken By:</strong> Elitza Tocheva</p>
<strong>Species / Specimen:</strong> Bacillus subtilis </p>
<strong>Strain:</strong> JFG349, ponA null, SpoIIIE73-11-GFP</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/etl2011-11-01-4/3dimage_25264/</p>3490003_full.rec,  Reconstruction (Pixel Size 1.9 nm), 929.0 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2011-11-01-4/3dimage_25264/3490003_full.rec"
        > <i class="download icon"></i> Download </a></p>

        3490003.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/etl2011-11-01-4/rawdata/3490003.mrc"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.15468/dl.hj7cny
title: Occurrence Download

description: A dataset containing 22204 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "TaxonKey is Sison amomum"
 ]
}

 The dataset includes 22204 records from 389 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005827-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22002/f70cn-xwn62
title: B. subtilis 3267

description: Raw data files of B. subtilis 3267
description: <strong>Tilt Series Date:</strong> 2011-12-17</p>
<strong>Data Taken By:</strong> Elitza Tocheva</p>
<strong>Species / Specimen:</strong> Bacillus subtilis </p>
<strong>Strain:</strong> AD3267, ponA null, Alp7A-GFP</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>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> Joe Pogliano</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Grow in LB</p>
<strong>Sample Preparation:</strong> Polara</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2011-12-17-22/rawdata/</p>3267a0007.mrc,  Tilt Series (Pixel Size 1.9 nm), 1.0 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2011-12-17-22/rawdata/3267a0007.mrc"
        > <i class="download icon"></i> Download </a></p>

        3267a0007_full.rec,  Reconstruction (Pixel Size 3.8 nm), 929.0 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2011-12-17-22/3dimage_16251/3267a0007_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/sk2ma-4w263
title: wild type B. subtilis

description: sacculi of sporulating wtBsubtilis
description: <strong>Tilt Series Date:</strong> 2011-07-05</p>
<strong>Data Taken By:</strong> Elitza Tocheva</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: (-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> Leginon</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/etl2011-07-05-17/3dimage_25097/</p>target20008_full.rec,  Reconstruction (Pixel Size 1.9 nm), 825.8 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2011-07-05-17/3dimage_25097/target20008_full.rec"
        > <i class="download icon"></i> Download </a></p>

        target20008.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/etl2011-07-05-17/rawdata/target20008.mrc"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/7wtcy-em264
title: Eco 082609 MP11

description: Escherichia coli, 09sep24a_MP11_082609_7_1_2_son_019,
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/mpa2009-09-24-19/rawdata/</p>09sep24a_MP11_082609_7_1_2_son_019.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_019_full.rec,  Reconstruction (Pixel Size 1.9 nm), 943.7 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.15468/dl.sk428j
title: Occurrence Download

description: A dataset containing 1196 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Stenorrhina degenhardtii"
 ]
}

 The dataset includes 1196 records from 100 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005829-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.