cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.22002/cdahr-p2k33
title: HeLa cells

description: Raw data files of HeLa cells
description: <strong>Tilt Series Date:</strong> 2014-11-13</p>
<strong>Data Taken By:</strong> Rasika Ramdasi</p>
<strong>Species / Specimen:</strong> HeLa cells</p>
<strong>Strain:</strong> ATCC</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-55.0°, 55.0°), step: 1°, constant angular increment, dosage: 150.0 eV/Å²,  defocus: -10.0 μm,  magnification: 18000x. </p>
<strong>Microscope:</strong> Caltech Polara</p>
<strong>Acquisition Software:</strong> UCSFTomo</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> UCSF tomo</p>
<strong>Collaborators and Roles:</strong> cells and siRNA obtained from Doug Mackay/ Cathrine Ullman</p>
<strong>Sample Preparation:</strong> HeLa cells+ siRNA NUP153+ Thymidine 2mM, 14 h post thymidine release</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/rra2014-11-13-12/rawdata/</p>midbody60004.mrc,  Tilt Series (Pixel Size 0.6 nm), 3.2 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/rra2014-11-13-12/rawdata/midbody60004.mrc"
        > <i class="download icon"></i> Download </a></p>

        midbody60004_full.rec,  Reconstruction (Pixel Size 2.4 nm), 623.6 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/rra2014-11-13-12/3dimage_48024/midbody60004_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/eetmz-cwr14
title: HeLa cells

description: Raw data files of HeLa cells
description: <strong>Tilt Series Date:</strong> 2014-11-13</p>
<strong>Data Taken By:</strong> Rasika Ramdasi</p>
<strong>Species / Specimen:</strong> HeLa cells</p>
<strong>Strain:</strong> ATCC</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-55.0°, 55.0°), step: 1°, constant angular increment, dosage: 150.0 eV/Å²,  defocus: -10.0 μm,  magnification: 18000x. </p>
<strong>Microscope:</strong> Caltech Polara</p>
<strong>Acquisition Software:</strong> UCSFTomo</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> UCSF tomo</p>
<strong>Collaborators and Roles:</strong> cells and siRNA obtained from Doug Mackay/ Cathrine Ullman</p>
<strong>Sample Preparation:</strong> HeLa cells+ siRNA NUP153+ Thymidine 2mM, 14 h post thymidine release</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/rra2014-11-13-45/rawdata/</p>midbody50003.mrc,  Tilt Series (Pixel Size 0.6 nm), 3.2 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/rra2014-11-13-45/rawdata/midbody50003.mrc"
        > <i class="download icon"></i> Download </a></p>

        midbody50003_full.rec,  Reconstruction (Pixel Size 2.4 nm), 623.6 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/rra2014-11-13-45/3dimage_48084/midbody50003_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/r6dby-ra537
title: Agrobacterium tumefaciens

description: Agrobacterium_VirB8-GFP
description: <strong>Tilt Series Date:</strong> 2013-05-07</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°, constant angular increment, dosage: 200.0 eV/Å²,  defocus: -10.0 μm,  magnification: 26000x. </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 PatZambryski</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Titan_K2</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/etl2013-05-07-80/rawdata/</p>VirB80008.mrc,  Tilt Series (Pixel Size 0.42 nm), 3.4 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2013-05-07-80/rawdata/VirB80008.mrc"
        > <i class="download icon"></i> Download </a></p>

        VirB80008_full.rec,  Reconstruction (Pixel Size 1.68 nm), 430.6 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2013-05-07-80/3dimage_32500/VirB80008_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/01kf8-ez172
title: HIV capsid

description: Box C, 0.5 exposure, 152, 41000 mag 3 defocus, slit 20 eV, search track 13500
description: <strong>Tilt Series Date:</strong> 2013-12-05</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: 152.0 eV/Å²,  defocus: -3.0 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> 3dmod, need to reconstruct with SIRT</p>
<strong>Collaborators and Roles:</strong> Wes Sundquist</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Purified HIV cores</p>
<strong>Sample Preparation:</strong> Box C</p>
description: Files available via S3 at ttps://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/scd2013-12-05-49/rawdata/</p>hivcapsid00016.mrc,  Tilt Series (Pixel Size 0.26 nm), 3.4 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/scd2013-12-05-49/rawdata/hivcapsid00016.mrc"
        > <i class="download icon"></i> Download </a></p>

        hivcapsid00016_part121_13.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/scd2013-12-05-49/3dimage_35585/hivcapsid00016_part121_13.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/f26xj-5bt04
title: COS7 VPS4DN+pNLGFP

description: Cos7 cells transfected with VPS4DN (0.5 ug) and pNLGFP provirus construct (4 ug). Sample #C126
description: <strong>Tilt Series Date:</strong> 2012-05-05</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> VPS4DN construct provided by Wes Sundquist. 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 with lipofectamine</p>
<strong>Sample Preparation:</strong> manual blotting</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/cwl2012-05-05-26/3dimage_69309/</p>12may05_C126_4_pnlDN_Cos7_AT7BT1_0006_full.rec,  Reconstruction (Pixel Size 2.0 nm), 619.4 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/cwl2012-05-05-26/3dimage_69309/12may05_C126_4_pnlDN_Cos7_AT7BT1_0006_full.rec"
        > <i class="download icon"></i> Download </a></p>

        12may05_C126_4_pnlDN_Cos7_AT7BT1_0006.mrc,  Tilt Series (Pixel Size 0.5 nm), 677.3 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/cwl2012-05-05-26/rawdata/12may05_C126_4_pnlDN_Cos7_AT7BT1_0006.mrc"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/d1d3z-vsn42
title: Pva 121509 MP37

description: Prosthecobacter vanneervenii, 10jan13b_MP37_Pva-stat_006, putative btub structure, helical structures,
description: <strong>Tilt Series Date:</strong> 2010-01-13</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>
  mpa2010-01-13-4_slicer9824.jpg: Filament bundle .  Prosthecobacter vanneervenii mpa2010-01-13-4_slicer9826.jpg: REZ  .  Ribosome excluding zone .  Prosthecobacter vanneervenii
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mpa2010-01-13-4/rawdata/</p>10jan13b_MP37_Pva-stat_006.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/mpa2010-01-13-4/rawdata/10jan13b_MP37_Pva-stat_006.mrc"
        > <i class="download icon"></i> Download </a></p>

        10jan13b_MP37_Pva-stat_006_full.rec,  Reconstruction (Pixel Size 1.9 nm), 838.9 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mpa2010-01-13-4/3dimage_14403/10jan13b_MP37_Pva-stat_006_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/8n86m-3dc55
title: Rhodobacter 1558 cryosections

description: Cryosections by MArk Ladinsky
description: <strong>Tilt Series Date:</strong> 2010-09-27</p>
<strong>Data Taken By:</strong> Ariane Briegel</p>
<strong>Species / Specimen:</strong> Rhodobacter sphaeroides</p>
<strong>Strain:</strong> ATCC 17023</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-61.0°, 64.0°), step: °, constant angular increment, dosage: 120.0 eV/Å²,  defocus: -8.0 μm,  magnification: 34000x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> webload</p>
<strong>Processing Software Used:</strong> IMOD</p>
<strong>Collaborators and Roles:</strong> Judy Armitage</p>
<strong>Purification / Growth Conditions / Treatment:</strong> grown in SUX media</p>
<strong>Sample Preparation:</strong> prepared for cryosectioning (gold prep see JWIKI)</p>
description: Files available via S3 at ://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/aba2010-09-27-33/rawdata/</p>10sep27a_Rhsections_044.st,  Tilt Series (Pixel Size 0.0 nm), 528.5 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/aba2010-09-27-33/rawdata/10sep27a_Rhsections_044.st"
        > <i class="download icon"></i> Download </a></p>

        10sep27a_Rhsections_044.rec,  Reconstruction (Pixel Size 0.0 nm), 65.7 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/aba2010-09-27-33/3dimage_14909/10sep27a_Rhsections_044.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.15468/dl.cy9xz5
title: Occurrence Download

description: A dataset containing 33530 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "TaxonKey is Myosotis laxa caespitosa"
 ]
}

 The dataset includes 33530 records from 163 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0047625-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.15349455
title: Fjord bathymetry data in the vicinity of the Eqalorutsit Kangilliit Sermiat glacier calving front, Southern Greenland

description: Bathymetry data collected aboard the Adolf Jensen using single beam echosounder in the vicinity of the calving front of the Eqalorutsit Kangilliit Sermiat glacier, Southern Greenland. Additional data also included in the fjords of the following glaciers: Serminnguaq, Ilorliit, Qalerallit Sermiat

Data was collected over the course of three field campaigns in the 2022, 2023 and 2024 summer season. In the first two seasons, data were manually logged by visually checking the ship echosounder. In the 2024 season this was automated by recording the echosounder output, resulting in many more data points.

Two data formats are provided: comma delimited and MATLAB table. Bathymetry data is given as depth below sea level, corrected for the ship draft but not for ocean tides.

Datasets contain the following fields:x: x-coordinate of data point  (metres)y: y-coordinate of data point (metres)depth: (metres below sea level)year: year of data collectionlat: latitude of data point (decimal degrees)lon: longitude of data point (decimal degrees)method: either manual or automated

Note: x and y coordinates are given in north pole stereographic projection (EPSG:3413), using default parameters as given by the arctic mapping toolbox (https://ch.mathworks.com/matlabcentral/fileexchange/63324-arctic-mapping-tools).
DOI: 10.5281/zenodo.15349456
title: Fjord bathymetry data in the vicinity of the Eqalorutsit Kangilliit Sermiat glacier calving front, Southern Greenland

description: Bathymetry data collected aboard the Adolf Jensen using single beam echosounder in the vicinity of the calving front of the Eqalorutsit Kangilliit Sermiat glacier, Southern Greenland. 

Data was collected over the course of three field campaigns in the 2022, 2023 and 2024 summer season. In the first two seasons, data were manually logged by visually checking the ship echosounder. In the 2024 season this was automated by recording the echosounder output, resulting in many more data points.

Two data formats are provided: comma delimited and MATLAB table. Bathymetry data is given as depth below sea level, corrected for the ship draft but not for ocean tides.

Datasets contain the following fields:x: x-coordinate of data point  (metres)y: y-coordinate of data point (metres)depth: (metres below sea level)year: year of data collectionlat: latitude of data point (decimal degrees)lon: longitude of data point (decimal degrees)method: either manual or automated

Note: x and y coordinates are given in north pole stereographic projection, using default parameters as given by the arctic mapping toolbox (https://ch.mathworks.com/matlabcentral/fileexchange/63324-arctic-mapping-tools).
DOI: 10.5281/zenodo.15432859
title: Fjord bathymetry data in the vicinity of the Eqalorutsit Kangilliit Sermiat glacier calving front, Southern Greenland

description: Bathymetry data collected aboard the Adolf Jensen using single beam echosounder in the vicinity of the calving front of the Eqalorutsit Kangilliit Sermiat glacier, Southern Greenland. Additional data also included in the fjords of the following glaciers: Serminnguaq, Ilorliit, Qalerallit Sermiat

Data was collected over the course of three field campaigns in the 2022, 2023 and 2024 summer season. In the first two seasons, data were manually logged by visually checking the ship echosounder. In the 2024 season this was automated by recording the echosounder output, resulting in many more data points.

Two data formats are provided: comma delimited and MATLAB table. Bathymetry data is given as depth below sea level, corrected for the ship draft but not for ocean tides.

Datasets contain the following fields:x: x-coordinate of data point  (metres)y: y-coordinate of data point (metres)depth: (metres below sea level)year: year of data collectionlat: latitude of data point (decimal degrees)lon: longitude of data point (decimal degrees)method: either manual or automated

Note: x and y coordinates are given in north pole stereographic projection (EPSG:3413), using default parameters as given by the arctic mapping toolbox (https://ch.mathworks.com/matlabcentral/fileexchange/63324-arctic-mapping-tools).
DOI: 10.15468/dl.fjkk59
title: Occurrence Download

description: A dataset containing 214 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Stipa thurberiana",
 "HasCoordinate is true"
 ]
}

 The dataset includes 214 records from 33 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0044576-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.sghj5n
title: Occurrence Download

description: A dataset containing 13586 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is one of (iNaturalist Research-grade Observations, Pl@ntNet automatically identified occurrences)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Cynodon dactylon",
 "Year 2010-2025"
 ]
}

 The dataset includes 13586 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0044577-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.trwhyv
title: Occurrence Download

description: A dataset containing 2680 species occurrences available in GBIF matching the query:
{
 "Geometry" : [
 "POLYGON ((-111.5688 27.14913, -111.4188 27.14913, -111.4188 27.29913, -111.5688 27.29913, -111.5688 27.14913))"
 ]
}

 The dataset includes 2680 records from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0044578-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.c8yjsg
title: Occurrence Download

description: A dataset containing 9890 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Sawadaea",
 "HasCoordinate is true"
 ]
}

 The dataset includes 9890 records from 160 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0044579-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.30655598
title: Supplementary Material for: Probiotic, prebiotic or symbiotic supplementation in Parkinson´s Disease: A systematic review and meta-analysis with trial sequential analysis

description: Background: Alterations in gut microbiota have been linked to various neurological diseases, including Parkinson's disease (PD). Modifying the microbiota through probiotics, prebiotics, or synbiotics may help improve symptoms in PD patients. This study aimed to evaluate the efficacy and safety of these supplements in treating PD. Summary: A systematic search was conducted in several databases, including PubMed, EMBASE, Scopus, Cochrane Library, Web of Science, and Google Scholar, until September 2023. No restrictions were placed on language or publication date. Study quality was assessed, and data were analyzed using meta-analysis techniques and narrative synthesis tables. The certainty of evidence was evaluated using GRADE, and trial sequential analysis was performed for primary outcomes. Out of 3,608 studies identified, 69 were selected for review, with 16 analyzed qualitatively. Among these, 12 were randomized controlled trials, and 9 were included in the meta-analysis. Compared with the placebo group, the intervention group would improve non-motor symptoms related to constipation (weekly stools [MD]: 1.04; 95% CI: 0.83, 1.25; Bristol scale [MD]: 0.54; 95% CI: 0.38, 0.70, frequency of laxative use [MD]: -0.63, 95% CI: -0.94, -0.33), and could improve motor symptoms (UPDRS-III [MD]: -2.23; 95% CI: -5.00; 0.53), with very low certainty both due to indirectness and significant risk of bias. Key Messages: With very low to moderate certainty, probiotics, prebiotics, and synbiotics may improve constipation and motor symptoms in PD compared to placebo. These findings suggest a potential benefit, but more high-quality research is needed to confirm these effects and establish stronger evidence.
DOI: 10.6084/m9.figshare.30655598.v1
title: Supplementary Material for: Probiotic, prebiotic or symbiotic supplementation in Parkinson´s Disease: A systematic review and meta-analysis with trial sequential analysis

description: Background: Alterations in gut microbiota have been linked to various neurological diseases, including Parkinson's disease (PD). Modifying the microbiota through probiotics, prebiotics, or synbiotics may help improve symptoms in PD patients. This study aimed to evaluate the efficacy and safety of these supplements in treating PD. Summary: A systematic search was conducted in several databases, including PubMed, EMBASE, Scopus, Cochrane Library, Web of Science, and Google Scholar, until September 2023. No restrictions were placed on language or publication date. Study quality was assessed, and data were analyzed using meta-analysis techniques and narrative synthesis tables. The certainty of evidence was evaluated using GRADE, and trial sequential analysis was performed for primary outcomes. Out of 3,608 studies identified, 69 were selected for review, with 16 analyzed qualitatively. Among these, 12 were randomized controlled trials, and 9 were included in the meta-analysis. Compared with the placebo group, the intervention group would improve non-motor symptoms related to constipation (weekly stools [MD]: 1.04; 95% CI: 0.83, 1.25; Bristol scale [MD]: 0.54; 95% CI: 0.38, 0.70, frequency of laxative use [MD]: -0.63, 95% CI: -0.94, -0.33), and could improve motor symptoms (UPDRS-III [MD]: -2.23; 95% CI: -5.00; 0.53), with very low certainty both due to indirectness and significant risk of bias. Key Messages: With very low to moderate certainty, probiotics, prebiotics, and synbiotics may improve constipation and motor symptoms in PD compared to placebo. These findings suggest a potential benefit, but more high-quality research is needed to confirm these effects and establish stronger evidence.