cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.22002/s78zj-2ee49
title: nanowire+doublepili mutant+Chemo

description: This sample is batch 2 collection. This is from double pili mutant run on a chemostat.Batch 1 collection was from WT grown in serum bottle
description: <strong>Tilt Series Date:</strong> 2015-04-12</p>
<strong>Data Taken By:</strong> Poorna Subramanian</p>
<strong>Species / Specimen:</strong> Shewanella oneidensis</p>
<strong>Strain:</strong> MR-1</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1.0°, constant angular increment, dosage: 100.0 eV/Å²,  defocus: -8.0 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> Moh, USC</p>
<strong>Sample Preparation:</strong> Went to USC and froze using manual vitrobot. Only 1 grid was good among 6 and cells were isolated so couldn't detect any nanowires so far</p>
  psa2015-04-12-16_slicer17063.jpg: F6 chemostat
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/psa2015-04-12-16/rawdata/</p>3_atlas_nanowires0015.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/psa2015-04-12-16/rawdata/3_atlas_nanowires0015.mrc"
        > <i class="download icon"></i> Download </a></p>

        3_atlas_nanowires0015_part121_33.rec,  Reconstruction (Pixel Size 1.92 nm), 534.5 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.15468/dl.ed9h2w
title: Occurrence Download

description: A dataset containing 1678693 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is USA.5.38_1",
 "OccurrenceStatus is Present",
 "TaxonKey is Aves",
 "Year 2020-2025"
 ]
}

 The dataset includes 1678693 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045117-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.4121/b02ace68-8e95-4355-bcea-f073c52e8a14
title: Supplementary data for the paper 'Loneliness, personality, and attention to AI-generated images depicting social threat: An eye-tracking study'

description: Attention bias towards social threat has been linked to loneliness and anxiety, though findings are mixed and concerns about measurement reliability persist. This study examined whether state and trait loneliness, along with personality, self-esteem, social anxiety, and life satisfaction, are associated with attention bias towards social threat images (indicating rejection or exclusion) in young adults (N = 241). AI-generated images were used to enhance control over stimulus content and category distinction. Participants completed an eye-tracking free-viewing task comprising 40 image matrices (four images per matrix, displayed for 6000 ms) and attention bias (dwell time percentage, total fixation duration percentage, and fixation count percentage) and initial orientation of attention (first fixation percentage) were computed. The attention bias measures showed adequate to good internal consistency (α = 0.61–0.86). No significant associations emerged between loneliness and attention to socially threatening stimuli, suggesting that heightened vigilance to social threat may not be a feature of loneliness in non-clinical young adults. However, it was found that females exhibited greater attention to social positive images, and baseline pupil diameter was associated with social anxiety. Future research should assess whether loneliness-specific attention bias is a replicable phenomenon, ideally by using an extreme-sampling approach with very lonely individuals.
DOI: 10.22002/ptdfd-ztj15
title: pED208_6um

description: t4ss in E.colli with F pilus
description: <strong>Tilt Series Date:</strong> 2015-02-11</p>
<strong>Data Taken By:</strong> Elitza Tocheva</p>
<strong>Species / Specimen:</strong> Escherichia coli</p>
<strong>Strain:</strong> </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: -6.0 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>Purification / Growth Conditions / Treatment:</strong> LB o/n 37C</p>
<strong>Sample Preparation:</strong> Vitrobot</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2015-02-11-54/rawdata/</p>pED-6um-20020.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/etl2015-02-11-54/rawdata/pED-6um-20020.mrc"
        > <i class="download icon"></i> Download </a></p>

        pED-6um-20020_full.rec,  Reconstruction (Pixel Size 2.0 nm), 445.4 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.4121/b02ace68-8e95-4355-bcea-f073c52e8a14.v1
title: Supplementary data for the paper 'Loneliness, personality, and attention to AI-generated images depicting social threat: An eye-tracking study'

description: Attention bias towards social threat has been linked to loneliness and anxiety, though findings are mixed and concerns about measurement reliability persist. This study examined whether state and trait loneliness, along with personality, self-esteem, social anxiety, and life satisfaction, are associated with attention bias towards social threat images (indicating rejection or exclusion) in young adults (N = 241). AI-generated images were used to enhance control over stimulus content and category distinction. Participants completed an eye-tracking free-viewing task comprising 40 image matrices (four images per matrix, displayed for 6000 ms) and attention bias (dwell time percentage, total fixation duration percentage, and fixation count percentage) and initial orientation of attention (first fixation percentage) were computed. The attention bias measures showed adequate to good internal consistency (α = 0.61–0.86). No significant associations emerged between loneliness and attention to socially threatening stimuli, suggesting that heightened vigilance to social threat may not be a feature of loneliness in non-clinical young adults. However, it was found that females exhibited greater attention to social positive images, and baseline pupil diameter was associated with social anxiety. Future research should assess whether loneliness-specific attention bias is a replicable phenomenon, ideally by using an extreme-sampling approach with very lonely individuals.
DOI: 10.17172/nomad/2025.08.26-1
title: NOMAD dataset: peritetracene/Ag(110)
DOI: 10.22002/8dtcz-9c989
title: WT LP01 from Liu lab, Yale

description: Type four secretion system, T4SS
description: <strong>Tilt Series Date:</strong> 2016-11-28</p>
<strong>Data Taken By:</strong> Yuxi Liu</p>
<strong>Species / Specimen:</strong> Legionella pneumophila</p>
<strong>Strain:</strong> Philadelphia-1_Lp02</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-51.0°, 51.0°), step: 3°, constant angular increment, dosage: 50.0 eV/Å²,  defocus: -5.0 μm,  magnification: 15500x. </p>
<strong>Microscope:</strong> Caltech Polara</p>
<strong>Acquisition Software:</strong> Serial EM</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Batchruntomo</p>
<strong>Collaborators and Roles:</strong> Data collected by Bo Hu in Jun Liu lab at Yale from their Polara. Partial WT strain data set. Primary literature:  doi: 10.1038/s41564-018-0165-z</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ylx2016-11-28-199/rawdata/</p>T4SSWTDec12A044_driftcorr.mrc,  Tilt Series (Pixel Size 0.25 nm), 2.0 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        T4SSWTDec12A044_driftcorr.rec,  Reconstruction (Pixel Size 1.0 nm), 2.3 GB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/1ahs8-1zd25
title: Vibrio cholerae delta TcpB

description: Raw data files of Vibrio cholerae delta TcpB
description: <strong>Tilt Series Date:</strong> 2015-10-16</p>
<strong>Data Taken By:</strong> Andreas Kjaer</p>
<strong>Species / Specimen:</strong> Vibrio cholerae</p>
<strong>Strain:</strong> O395-N1</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: -8.0 μm,  magnification: 27500x. </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> SIRT</p>
<strong>Collaborators and Roles:</strong> Ronald K. Taylor</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Grown ON in LB with ampicillin and IPTG, refreshed in LB shortly prior to freezing.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/aka2015-10-16-57/3dimage_73372/</p>10162015_TcpB_10058_SIRT_2K.rec,  Reconstruction (Pixel Size 0.0 nm), 7.1 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        10162015_TcpB_10058.mrc,  Tilt Series (Pixel Size 0.39 nm), 3.4 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/aka2015-10-16-57/rawdata/10162015_TcpB_10058.mrc"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.15468/dl.gf2jxf
title: Occurrence Download

description: A dataset containing 6 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Moenkhausia orteguasae)",
 "BasisOfRecord is one of (Specimen, Literature Occurrence, Human Observation, Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1991",
 "Year is less than or equal to 2025"
 ]
}

 The dataset includes 6 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045159-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22002/356zr-y9n24
title: immunogoldMtrc_wt

description: This is wt made in perfusion chamber and fixed with 2.5% glutaraldehyde and immune-gold labeled for Mtr complex. The grid # is PS123-#3
description: <strong>Tilt Series Date:</strong> 2015-12-29</p>
<strong>Data Taken By:</strong> Poorna Subramanian</p>
<strong>Species / Specimen:</strong> Shewanella oneidensis</p>
<strong>Strain:</strong> MR-1</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1.0°, constant angular increment, dosage: 143.0 eV/Å²,  defocus: -6.0 μm,  magnification: 34000x. </p>
<strong>Microscope:</strong> Caltech Polara</p>
<strong>Acquisition Software:</strong> UCSFTomo</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Batchruntomo</p>
<strong>Collaborators and Roles:</strong> Sahand and Moh, USC</p>
<strong>Sample Preparation:</strong> The sample was pulled out of Dh2O, was loaded on vitrobot with C side on left. Before blotting added 4ul of water. Blotting conditions: blot force -6, blot time -3.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/psa2015-12-29-5/3dimage_71953/</p>atlas2_sq150005.rec,  Reconstruction (Pixel Size 1.28 nm), 889.0 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/psa2015-12-29-5/3dimage_71953/atlas2_sq150005.rec"
        > <i class="download icon"></i> Download </a></p>

        atlas2_sq150005.mrc,  Tilt Series (Pixel Size 0.32 nm), 3.4 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/psa2015-12-29-5/rawdata/atlas2_sq150005.mrc"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/h7bzz-g3e69
title: TRIM5α decorated capsid tubes

description: 1mM Sulfo-EGS coassembled tubes
description: <strong>Tilt Series Date:</strong> 2016-01-10</p>
<strong>Data Taken By:</strong> Stephen Carter</p>
<strong>Species / Specimen:</strong> TRIM5α decorated HIV-1 tubes</p>
<strong>Strain:</strong> </p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1°, constant angular increment, dosage: 80.0 eV/Å²,  defocus: -5.0 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</p>
<strong>Collaborators and Roles:</strong> Wes Sundquist</p>
<strong>Sample Preparation:</strong> Quantafoil 300 mesh R2/2 grids</p>
description: Files available via S3 at s://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/scd2016-01-10-14/3dimage_72396/</p>tomography0015_part121_5.rec,  Reconstruction (Pixel Size 10.4 nm), 712.7 MB  
        
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        > <i class="download icon"></i> Download </a></p>

        tomography0015.mrc,  Tilt Series (Pixel Size 2.6 nm), 3.4 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/scd2016-01-10-14/rawdata/tomography0015.mrc"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.15468/dl.xdmsuc
title: Occurrence Download

description: A dataset containing 21901 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is KRILLBASE_antarctickrillssalpsdensity_1926_2016"
 ]
}

 The dataset includes 21901 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045160-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22002/ay9rr-hfg51
title: T5_1693Cys_Aumalemaide_5nm

description: This is a sample in which N terminus residue 1693 has been mutated to Cys residue. Minicells have been isolated by high-speed centrifugation and cells are Au maleimide labeled. No fiducials added.
description: <strong>Tilt Series Date:</strong> 2017-04-02</p>
<strong>Data Taken By:</strong> Poorna Subramanian</p>
<strong>Species / Specimen:</strong> Escherichia coli</p>
<strong>Strain:</strong> EC93 stick, UPEC536</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-65.0°, 65.0°), step: 1.0°, constant angular increment, dosage: 140.0 eV/Å²,  defocus: -10.0 μm,  magnification: 27500x. </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> Zach Ruhe and Chris Hayes</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Freezing in vitrobot.</p>
<strong>Sample Preparation:</strong> Sample prepared by Taylor Steven</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/psa2017-04-02-58/rawdata/</p>cys1693_sq48_4sqs0039.mrc,  Tilt Series (Pixel Size 0.39 nm), 3.7 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        cys1693_sq48_4sqs0039.rec,  Reconstruction (Pixel Size 1.56 nm), 889.0 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/qw8a1-8yk79
title: WT LP01 from Liu lab, Yale

description: Type four secretion system, T4SS
description: <strong>Tilt Series Date:</strong> 2016-11-28</p>
<strong>Data Taken By:</strong> Yuxi Liu</p>
<strong>Species / Specimen:</strong> Legionella pneumophila</p>
<strong>Strain:</strong> Philadelphia-1_Lp02</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-51.0°, 51.0°), step: 3°, constant angular increment, dosage: 50.0 eV/Å²,  defocus: -5.0 μm,  magnification: 15500x. </p>
<strong>Microscope:</strong> Caltech Polara</p>
<strong>Acquisition Software:</strong> Serial EM</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Batchruntomo</p>
<strong>Collaborators and Roles:</strong> Data collected by Bo Hu in Jun Liu lab at Yale from their Polara. Partial WT strain data set. Primary literature:  doi: 10.1038/s41564-018-0165-z</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ylx2016-11-28-249/rawdata/</p>T4SSWTDec12A094_driftcorr.mrc,  Tilt Series (Pixel Size 0.25 nm), 2.0 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        T4SSWTDec12A094_driftcorr.rec,  Reconstruction (Pixel Size 1.0 nm), 2.3 GB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/wxv06-35872
title: COS7 CHMP4B+VPS4DN

description: Cos7 cells transfected with CHMP4B & VPS4DN constructs
description: <strong>Tilt Series Date:</strong> 2015-03-08</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: 1.0°, constant angular increment, dosage: 150.0 eV/Å²,  defocus: -6.0 μm,  magnification: 22500x. </p>
<strong>Acquisition Software:</strong> UCSFTomo</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> Constructs provided by Wes Sundquist. Cells transfected, frozen and imaged at Caltech by Cora Woodward</p>
<strong>Purification / Growth Conditions / Treatment:</strong> whole cells were grown on grids and transfected with Lipofectamine</p>
<strong>Sample Preparation:</strong> blotting</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/cwl2015-03-08-4/rawdata/</p>15mar08_C301-2_AT1BT1_0001.mrc,  Tilt Series (Pixel Size 0.5 nm), 3.4 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        15mar08_C301-2_AT1BT1_0001_part121_3.rec,  Reconstruction (Pixel Size 2.0 nm), 623.6 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/t7dpf-0gy02
title: WT LP01 from Liu lab, Yale

description: Type four secretion system, T4SS
description: <strong>Tilt Series Date:</strong> 2016-11-28</p>
<strong>Data Taken By:</strong> Yuxi Liu</p>
<strong>Species / Specimen:</strong> Legionella pneumophila</p>
<strong>Strain:</strong> Philadelphia-1_Lp02</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-51.0°, 51.0°), step: 3°, constant angular increment, dosage: 50.0 eV/Å²,  defocus: -5.0 μm,  magnification: 15500x. </p>
<strong>Microscope:</strong> Caltech Polara</p>
<strong>Acquisition Software:</strong> Serial EM</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Batchruntomo</p>
<strong>Collaborators and Roles:</strong> Data collected by Bo Hu in Jun Liu lab at Yale from their Polara. Partial WT strain data set. Primary literature:  doi: 10.1038/s41564-018-0165-z</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ylx2016-11-28-113/rawdata/</p>LP02Jan30A036_driftcorr.mrc,  Tilt Series (Pixel Size 0.25 nm), 2.0 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ylx2016-11-28-113/rawdata/LP02Jan30A036_driftcorr.mrc"
        > <i class="download icon"></i> Download </a></p>

        LP02Jan30A036_driftcorr.rec,  Reconstruction (Pixel Size 1.0 nm), 2.3 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ylx2016-11-28-113/3dimage_104900/LP02Jan30A036_driftcorr.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/m04qw-9jw65
title: WT LP01 from Liu lab, Yale

description: Type four secretion system, T4SS
description: <strong>Tilt Series Date:</strong> 2016-11-28</p>
<strong>Data Taken By:</strong> Yuxi Liu</p>
<strong>Species / Specimen:</strong> Legionella pneumophila</p>
<strong>Strain:</strong> Philadelphia-1_Lp02</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-51.0°, 51.0°), step: 3°, constant angular increment, dosage: 50.0 eV/Å²,  defocus: -5.0 μm,  magnification: 15500x. </p>
<strong>Microscope:</strong> Caltech Polara</p>
<strong>Acquisition Software:</strong> Serial EM</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Batchruntomo</p>
<strong>Collaborators and Roles:</strong> Data collected by Bo Hu in Jun Liu lab at Yale from their Polara. Partial WT strain data set. Primary literature:  doi: 10.1038/s41564-018-0165-z</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ylx2016-11-28-105/rawdata/</p>LP02Jan30A032_driftcorr.mrc,  Tilt Series (Pixel Size 0.25 nm), 2.0 GB  
        
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        LP02Jan30A032_driftcorr.rec,  Reconstruction (Pixel Size 1.0 nm), 2.3 GB  
        
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