cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.22002/zr2s3-6ak69
title: intact HIV VLP -- 8.2 vector

description: Raw data files of intact HIV VLP -- 8.2 vector
description: <strong>Tilt Series Date:</strong> 2008-04-17</p>
<strong>Data Taken By:</strong> Zhiheng Yu</p>
<strong>Species / Specimen:</strong> mature HIV-1</p>
<strong>Strain:</strong> </p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 66.0°), step: 2°, constant angular increment, dosage: 160.0 eV/Å²,  defocus: 8.0 μm,  magnification: 0x. </p>
<strong>Acquisition Software:</strong> UCSF Tomo</p>
<strong>Upload Method:</strong> webload</p>
<strong>Processing Software Used:</strong> </p>
description: Files available via S3 at ttps://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/zyh2008-04-17-6/rawdata/</p>080418_8d2viron_sam2_sq03_h05_41k.mrc,  Tilt Series (Pixel Size 0.52 nm), 545.4 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/zyh2008-04-17-6/rawdata/080418_8d2viron_sam2_sq03_h05_41k.mrc"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/tkppq-59w41
title: FtsZ

description: Raw data files of FtsZ
description: <strong>Tilt Series Date:</strong> 2007-09-25</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: (-63.0°, 63.0°), step: 1°, constant angular increment, dosage: 200.0 eV/Å²,  defocus: 12.0 μm,  magnification: 0x. </p>
<strong>Acquisition Software:</strong> UCSF Tomo</p>
<strong>Upload Method:</strong> webload</p>
<strong>Processing Software Used:</strong> </p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/zla2007-09-25-8/rawdata/</p>FtsZ926734k12u200e000.mrc,  Tilt Series (Pixel Size 0.644 nm), 1.1 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/zla2007-09-25-8/rawdata/FtsZ926734k12u200e000.mrc"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/nyz8t-p2d31
title: in vitro assembled CA-NC cone

description: Raw data files of in vitro assembled CA-NC cone
description: <strong>Tilt Series Date:</strong> 2008-06-30</p>
<strong>Data Taken By:</strong> Zhiheng Yu</p>
<strong>Species / Specimen:</strong> in vitro assembled HIV CA-NC cones</p>
<strong>Strain:</strong> None</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-64.0°, 66.0°), step: 2°, constant angular increment, dosage: 90.0 eV/Å²,  defocus: 18.0 μm,  magnification: 0x. </p>
<strong>Acquisition Software:</strong> UCSF Tomo</p>
<strong>Upload Method:</strong> webload</p>
<strong>Processing Software Used:</strong> </p>
description: Files available via S3 at ttps://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/zyh2008-06-30-8/rawdata/</p>cone080630sam1sq02h02_41k.mrc,  Tilt Series (Pixel Size 0.52 nm), 570.6 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/zyh2008-06-30-8/rawdata/cone080630sam1sq02h02_41k.mrc"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/gnwww-tf861
title: FzlC

description: Raw data files of FzlC
description: <strong>Tilt Series Date:</strong> 2008-11-21</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: (-63.0°, 63.0°), step: 1°, constant angular increment, dosage: 180.0 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</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/zla2008-11-21-22/rawdata/</p>08nov21a_box507_1_022.st,  Tilt Series (Pixel Size 0.644 nm), 1.1 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/zla2008-11-21-22/rawdata/08nov21a_box507_1_022.st"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.15468/dl.qt5mhv
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Hypsolebias hamadryades)",
 "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 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002702-250827131500795/datasets/export for details.
DOI: 10.22002/q9xqx-5my24
title: FtsZ-associated proteins

description: Raw data files of FtsZ-associated proteins
description: <strong>Tilt Series Date:</strong> 2008-10-29</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: (-62.0°, 62.0°), step: °, constant angular increment, dosage: 180.0 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> IMOD</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/zla2008-10-29-11/rawdata/</p>08oct29a_bx402_011.mrc,  Tilt Series (Pixel Size 0.644 nm), 1.1 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/zla2008-10-29-11/rawdata/08oct29a_bx402_011.mrc"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/gm71z-wv685
title: in vitro assembled CA-NC cone

description: Raw data files of in vitro assembled CA-NC cone
description: <strong>Tilt Series Date:</strong> 2008-06-30</p>
<strong>Data Taken By:</strong> Zhiheng Yu</p>
<strong>Species / Specimen:</strong> in vitro assembled HIV CA-NC cones</p>
<strong>Strain:</strong> None</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-68.0°, 68.0°), step: 2°, constant angular increment, dosage: 90.0 eV/Å²,  defocus: 15.0 μm,  magnification: 0x. </p>
<strong>Acquisition Software:</strong> UCSF Tomo</p>
<strong>Upload Method:</strong> webload</p>
<strong>Processing Software Used:</strong> </p>
description: Files available via S3 at ttps://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/zyh2008-06-30-9/rawdata/</p>cone080630sam2sq06h01_41k.mrc,  Tilt Series (Pixel Size 0.52 nm), 587.3 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/zyh2008-06-30-9/rawdata/cone080630sam2sq06h01_41k.mrc"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/y9t35-s1f64
title: Caulobacter crescentus

description: Raw data files of Caulobacter crescentus
description: <strong>Tilt Series Date:</strong> 2005-11-11</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: (0.0°, 0.0°), step: °, constant angular increment, dosage: 0.0 eV/Å²,  defocus: 0.0 μm,  magnification: 0x. </p>
<strong>Acquisition Software:</strong> UCSF Tomo</p>
<strong>Upload Method:</strong> webload</p>
<strong>Processing Software Used:</strong> </p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/zla2005-11-11-2/3dimage_639/</p>cclcnov11_0min_01.rec.mrc,  Reconstruction (Pixel Size 0.0 nm), 129.5 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/zla2005-11-11-2/3dimage_639/cclcnov11_0min_01.rec.mrc"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/bm2gn-z3625
title: FtsZ-associated proteins

description: Raw data files of FtsZ-associated proteins
description: <strong>Tilt Series Date:</strong> 2008-10-27</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: (0.0°, 0.0°), step: °, constant angular increment, dosage: 0.0 eV/Å²,  defocus: 0.0 μm,  magnification: 0x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> webload</p>
<strong>Processing Software Used:</strong> IMOD</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/zla2008-10-27-3/rawdata/</p>08oct27a_bx799_1_003.mrc,  Tilt Series (Pixel Size 0.0 nm), 696.3 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/zla2008-10-27-3/rawdata/08oct27a_bx799_1_003.mrc"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/fpm6g-ea913
title: Caulobacter crescentus

description: Raw data files of Caulobacter crescentus
description: <strong>Tilt Series Date:</strong> 2008-01-20</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: 1.5°, constant angular increment, dosage: 200.0 eV/Å²,  defocus: -12.0 μm,  magnification: 0x. </p>
<strong>Acquisition Software:</strong> UCSF Tomo</p>
<strong>Upload Method:</strong> webload</p>
<strong>Processing Software Used:</strong> </p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/zla2008-01-20-11/rawdata/</p>mrebgfpbx290x6601dot57255cts12u007b.mrc,  Tilt Series (Pixel Size 1.259 nm), 688.0 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.15468/dl.778mj2
title: Occurrence Download

description: A dataset containing 149 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Lindera chienii"
 ]
}

 The dataset includes 149 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002703-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22002/dnacf-86140
title: Ty3 virus like particles

description: Protease mutant
description: <strong>Tilt Series Date:</strong> 2007-11-12</p>
<strong>Data Taken By:</strong> Zhiheng Yu</p>
<strong>Species / Specimen:</strong> Ty3</p>
<strong>Strain:</strong> None</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-66.0°, 66.0°), step: 2°, constant angular increment, dosage: 75.0 eV/Å²,  defocus: 8.0 μm,  magnification: 0x. </p>
<strong>Acquisition Software:</strong> UCSF Tomo</p>
<strong>Upload Method:</strong> webload</p>
<strong>Processing Software Used:</strong> </p>
description: Files available via S3 at ttps://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/zyh2007-11-12-5/rawdata/</p>Ty3_071112_sam2_sq04_h02_41k.mrc,  Tilt Series (Pixel Size 0.52 nm), 595.7 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.6084/m9.figshare.29954564.v2
title: Supplementary Data: On the mechanics of inhaled bronchial transmission of pathogenic microdroplets generated from the upper respiratory tract, with implications for downwind infection onset

description: Could the microdroplets formed by viscoelastic fragmentation of mucosal liquids within the upper respiratory tract (URT) explain the brisk onset of deep lung infection following initial URT infections? Generally, particulates, inhaled through the nostrils and therefore navigating the intricate topography of the anterior nasal cavity, can efficiently reach the lower airway only if they are small enough, typically &lt; 5 microns. However, the fate of larger particulates, many exceeding 5-micron in diameter, that are sheared from the initial infection sites along the intra-URT mucosa during inhalation remains unresolved. These particulates originate primarily from the nasopharynx, oropharynx, and the laryngeal chamber containing the vocal folds. To investigate, this study employs a computed tomography-based three-dimensional anatomical airway reconstruction, isolating the tract from the larynx and mapping the tracheal cavity through to the third generation of the tracheobronchial tree; constituent transport across the distal bronchial outlets is also recorded to assess deep lung penetration. Within the defined geometry, airflow simulations are conducted with the Large Eddy Simulation scheme to replicate relaxed inhalation at 15 L/min flow rate. Against the ambient air flux, numerical experiments are performed to monitor the transport of particulates (aerosols/droplets) with diameters 1-30 microns, bearing physical properties akin to aerosolized mucus with embedded virions. The full-scale numerical transmission trends are consistent with findings from our reduced-order mathematical model that conceptualizes the influence of intra-airway vortex instabilities on local particle transport through point vortex idealization in an anatomy-guided two-dimensional potential flow domain. The results collectively demonstrate a markedly elevated lower airway penetration by URT-derived particulates, even by those as large as 10 and 15 microns. The high viral load, often exceeding the pathogen-specific infectious dose, carried by such droplets into the bronchial spaces of the sample airway, provides a plausible mechanistic explanation for the accelerated seeding of secondary lung infection.Uploaded by: Dr. Saikat Basu (Contact: Saikat.Basu@sdstate.edu)<br>Dated: August 21, 2025
DOI: 10.22002/sprks-1de94
title: Pseudomonas_aeruginosa_DfliP

description: This sample was imaged to check for the presence of the tentative flagellar inner-membrane- .  embedded structures in FliP knockout
description: <strong>Tilt Series Date:</strong> 2019-05-25</p>
<strong>Data Taken By:</strong> Mohammed Kaplan</p>
<strong>Species / Specimen:</strong> Pseudomonas aeruginosa</p>
<strong>Strain:</strong> </p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 2°, constant angular increment, dosage: 120.0 eV/Å²,  defocus: -8.0 μm,  magnification: 19500x. </p>
<strong>Microscope:</strong> Caltech Titan Krios</p>
<strong>Acquisition Software:</strong> Serial EM</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> I obtained these cells from Dianne Newman lab from the transposon library (mutant 10239 from . the full library excel file). Shannon Park helped me to get the cells.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Cells were first grown on LB plate with 100 ug/ml gentamicin over night (from -80 C stock). . Next dat, one colony was inoculated in 2 ml of LB (with 100 ug/ml gentamicin) and incubated . for 16 hours at 37 C with 175 rpm. After cells were mixed with gold beads (coated with BSA), . 4 ul were added to the grids, blotted and plunge frozen.</p>
<strong>Sample Preparation:</strong> Different plunge-freezing parameters: 1) blot force 6, blot time 3s, drain time 1s. 2) blot force 3, . blot time 2s, drain time 1s. 3) blot force -5, blot time 4s, drain time 1s. 4) blot force -3, blot time . 2s, drain time 1s. All conditions were at room temperature with 100 % humidity.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2019-05-25-19/rawdata/</p>P_aeruginosa_DfliP14.mrc,  Tilt Series (Pixel Size 0.449 nm), 2.9 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        P_aeruginosa_DfliP14_full.rec,  Reconstruction (Pixel Size 1.796 nm), 737.3 MB  
        
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        > <i class="download icon"></i> Download </a></p>

        P_aeruginosa_DfliP14.mrc.mdoc,  32.2 kB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/4rnys-kw978
title: Pseudomonas_aeruginosa_DfliP

description: This sample was imaged to check for the presence of the tentative flagellar inner-membrane- .  embedded structures in FliP knockout
description: <strong>Tilt Series Date:</strong> 2019-05-25</p>
<strong>Data Taken By:</strong> Mohammed Kaplan</p>
<strong>Species / Specimen:</strong> Pseudomonas aeruginosa</p>
<strong>Strain:</strong> </p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 2°, constant angular increment, dosage: 120.0 eV/Å²,  defocus: -8.0 μm,  magnification: 19500x. </p>
<strong>Microscope:</strong> Caltech Titan Krios</p>
<strong>Acquisition Software:</strong> Serial EM</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> I obtained these cells from Dianne Newman lab from the transposon library (mutant 10239 from . the full library excel file). Shannon Park helped me to get the cells.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Cells were first grown on LB plate with 100 ug/ml gentamicin over night (from -80 C stock). . Next dat, one colony was inoculated in 2 ml of LB (with 100 ug/ml gentamicin) and incubated . for 16 hours at 37 C with 175 rpm. After cells were mixed with gold beads (coated with BSA), . 4 ul were added to the grids, blotted and plunge frozen.</p>
<strong>Sample Preparation:</strong> Different plunge-freezing parameters: 1) blot force 6, blot time 3s, drain time 1s. 2) blot force 3, . blot time 2s, drain time 1s. 3) blot force -5, blot time 4s, drain time 1s. 4) blot force -3, blot time . 2s, drain time 1s. All conditions were at room temperature with 100 % humidity.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2019-05-25-5/3dimage_103300/</p>P_aeruginosa_DfliP17_full.rec,  Reconstruction (Pixel Size 1.796 nm), 737.3 MB  
        
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        > <i class="download icon"></i> Download </a></p>

        P_aeruginosa_DfliP17.mrc,  Tilt Series (Pixel Size 0.449 nm), 2.9 GB  
        
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        P_aeruginosa_DfliP17.mrc.mdoc,  32.2 kB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/hrvpb-3cq40
title: IRE1α mNeon-Green MEF

description: Cryo-CLEM
description: <strong>Tilt Series Date:</strong> 2018-07-15</p>
<strong>Data Taken By:</strong> Stephen Carter</p>
<strong>Species / Specimen:</strong> Mouse Embryonic Fibroblasts</p>
<strong>Strain:</strong> IRE1α-mNeonGreen stable expression</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1°, constant angular increment, dosage: 120.0 eV/Å²,  defocus: -10.0 μm,  magnification: 27500x. </p>
<strong>Microscope:</strong> Caltech Polara</p>
<strong>Acquisition Software:</strong> Undefined</p>
<strong>Upload Method:</strong> reupload_downloaded</p>
<strong>Processing Software Used:</strong> IMOD and EMAN2</p>
<strong>Collaborators and Roles:</strong> Peter Walter</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Prior to cell plating, gold Quantifoil London finder grids (EMS R2/2 LF-Au-NH2) were UV treated to sterilize and coated with cell adhesion matrix. For MEFs-IRE1-mNG cell line, grids were coated in droplets of 500 ug/mL Fibronectins (Sigma-Aldrich S5171-.5MG) for 5 minutes on each side, washed in PBS, blotted and air-dried. For U2OS-IRE1-mNG cell line, grids were coated with ~4 mg/mL undiluted Collagen type I (Corning 354236) droplets for 20 minutes, washed in PBS, blotted and air-dried. Cells were seeded at 15% confluence and allowed to adhere for 8 hours and induced with Doxycycline (500 nM) for 6 or 18 hours for MEFs and U-2 OS cell lines, respectively. ER stress was then induced by treatment with 1.5 ug/mL of Tunicamycin for 2 hours.</p>
<strong>Sample Preparation:</strong> Manual Blotting</p>
description: Files available via S3 at s://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/scd2018-07-15-29/rawdata/</p>tomography18.mrc,  Tilt Series (Pixel Size 3.7126 nm), 3.2 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        tomography18_full.rec,  Reconstruction (Pixel Size 0.0 nm), 5.0 GB  
        
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        tomography18sirt.rec,  Reconstruction (Pixel Size 0.0 nm), 3.3 GB  
        
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        > <i class="download icon"></i> Download </a></p>