cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.22002/wcvm6-dna76
title: H.hepaticus

description: Helicobacter hepaticus cell poles
description: <strong>Tilt Series Date:</strong> 2013-04-06</p>
<strong>Data Taken By:</strong> Ariane Briegel</p>
<strong>Species / Specimen:</strong> Helicobacter hepaticus</p>
<strong>Strain:</strong> ATCC 51449</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-66.0°, 66.0°), step: 1°, constant angular increment, dosage: 165.0 eV/Å²,  defocus: -10.0 μm,  magnification: 41000x. </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> grown in the Mazmanian lab</p>
<strong>Purification / Growth Conditions / Treatment:</strong> grown in the Mazmanian lab</p>
  aba2013-04-06-17_slicer5005.jpg: Chemoreceptors .  Flagellar motor .  Peptidoglycan
description: Files available via S3 at ://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/aba2013-04-06-17/rawdata/</p>hepaticus41mag0012.mrc,  Tilt Series (Pixel Size 0.28 nm), 3.8 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/aba2013-04-06-17/rawdata/hepaticus41mag0012.mrc"
        > <i class="download icon"></i> Download </a></p>

        hepaticus41mag0012_full.rec,  Reconstruction (Pixel Size 1.12 nm), 706.7 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.15468/dl.h9yehy
title: Occurrence Download

description: A dataset containing 36 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Zungaro jahu)",
 "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 36 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0044853-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22002/sxmx9-xjm89
title: Sacculi Parachlamydia acanthamobae

description: Sacculus preparation
description: <strong>Tilt Series Date:</strong> 2013-01-04</p>
<strong>Data Taken By:</strong> Martin Pilhofer</p>
<strong>Species / Specimen:</strong> Parachlamydia acanthamoebae</p>
<strong>Strain:</strong> UV-7</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (0.0°, 0.0°), step: °, constant angular increment, dosage: 180.0 eV/Å²,  defocus: -10.0 μm,  magnification: 34000x. </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> Matthias Horn</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Purified sacculi</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mpa2013-01-04-10/rawdata/</p>01042013_MP115__0008.st,  Tilt Series (Pixel Size 1.23 nm), 862.2 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mpa2013-01-04-10/rawdata/01042013_MP115__0008.st"
        > <i class="download icon"></i> Download </a></p>

        01042013_MP115__0008.rec,  Reconstruction (Pixel Size 2.47 nm), 132.5 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/qbex3-m5x50
title: M. xanthus (Dk1622)

description: Imaged for Lotte in search of T6SS. This is the WT strain that they work with.
description: <strong>Tilt Series Date:</strong> 2012-08-17</p>
<strong>Data Taken By:</strong> Matt Swulius</p>
<strong>Species / Specimen:</strong> Myxococcus xanthus</p>
<strong>Strain:</strong> </p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-64.0°, 64.0°), step: 1°, constant angular increment, dosage: 200.0 eV/Å²,  defocus: -10.0 μm,  magnification: 23000x. </p>
<strong>Microscope:</strong> UCLA 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> Lotte Soregard-Anderson</p>
  mst2012-08-17-35_slicer4757.jpg: Extracellular vesicles mst2012-08-17-35_slicer4758.jpg: Vesicles and granules mst2012-08-17-35_slicer4761.jpg: Unknown filaments
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mst2012-08-17-35/rawdata/</p>081712_2_DK1622_16.mrc,  Tilt Series (Pixel Size 1.11 nm), 1.1 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mst2012-08-17-35/rawdata/081712_2_DK1622_16.mrc"
        > <i class="download icon"></i> Download </a></p>

        081712_2_DK1622_16_full.rec,  Reconstruction (Pixel Size 2.22 nm), 1.0 GB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/tsr39-j0w34
title: pNL_Huvecs_PI

description: Whole cells were grown on Au finder grids and infected with pNLGFP-VSVG. Sample frozen 24h post infection
description: <strong>Tilt Series Date:</strong> 2013-12-02</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: 1.0°, 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> UCSFTomo</p>
<strong>Collaborators and Roles:</strong> pNLGFP obtained from Irvin Chen UCLA</p>
<strong>Sample Preparation:</strong> manual blotting</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/cwl2013-12-02-7/rawdata/</p>13dec02_C177-2_pNL_Huvecs_PI_AT1BT1_0001.mrc,  Tilt Series (Pixel Size 0.49 nm), 3.4 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        13dec02_C177-2_pNL_Huvecs_PI_AT1BT1_0001_full.rec,  Reconstruction (Pixel Size 1.96 nm), 445.4 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/01xb6-0fq51
title: B subtilis bMD208

description: (Ω) cat::Pxyl-gfp-mreB  ΔponA::kan 30 mM xyloseNotes from Mike Dion:clump mildly in liquid LB.  This can be easily disrupted by very mild vortexing, or growing them in the presence of 10 mM MgCl2.  The clumping is the result of their ponA deletionbMD208 and 210 are Graumann's strains that I just recently knocked ponA out of.  These strains have the mut1 variant of GFP that, in addition to mut1, is also L236P.  I determined this by sequencing both of Gruamann's strains.  Both of these grow very slow on LB agar (bMD208 grows worse than bMD210, on LB agar)
description: <strong>Tilt Series Date:</strong> 2013-12-04</p>
<strong>Data Taken By:</strong> Matt Swulius</p>
<strong>Species / Specimen:</strong> Bacillus subtilis</p>
<strong>Strain:</strong> bMD208</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 2°, constant angular increment, dosage: 200.0 eV/Å²,  defocus: -10.0 μm,  magnification: 26000x. </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> Ethan Garner and Mike Dion</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mst2013-12-04-24/rawdata/</p>120413_bs208_40015.mrc,  Tilt Series (Pixel Size 0.42 nm), 1.7 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mst2013-12-04-24/rawdata/120413_bs208_40015.mrc"
        > <i class="download icon"></i> Download </a></p>

        120413_bs208_40015_part61_1.rec,  Reconstruction (Pixel Size 1.68 nm), 861.2 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.15468/dl.mg7xzx
title: Occurrence Download

description: A dataset containing 191019 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-101.389 19.582,-101.045 19.582,-101.045 19.77,-101.389 19.77,-101.389 19.582))",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 191019 records from 303 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0044804-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22002/djc9k-71k43
title: Agrobacterium tumefaciens C58

description: Agrobacterium_wild type C58
description: <strong>Tilt Series Date:</strong> 2013-06-27</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: 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 Pat Zambryski</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/etl2013-06-27-15/3dimage_32185/</p>c580001_part121_2.rec,  Reconstruction (Pixel Size 1.92 nm), 623.6 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2013-06-27-15/3dimage_32185/c580001_part121_2.rec"
        > <i class="download icon"></i> Download </a></p>

        c580001.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/etl2013-06-27-15/rawdata/c580001.mrc"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/qpmxf-ntn13
title: drp1

description: purified drp1
description: <strong>Tilt Series Date:</strong> 2013-09-10</p>
<strong>Data Taken By:</strong> Elitza Tocheva</p>
<strong>Species / Specimen:</strong> Drp1</p>
<strong>Strain:</strong> </p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 2.0°, constant angular increment, dosage: 100.0 eV/Å²,  defocus: -8.0 μm,  magnification: 27x. </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> David Chan</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2013-09-10-24/rawdata/</p>drp1_275_8defocus0024.mrc,  Tilt Series (Pixel Size 0.39 nm), 1.7 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        drp1_275_8defocus0024_full.rec,  Reconstruction (Pixel Size 1.56 nm), 267.3 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.5281/zenodo.16946154
title: Yangtze River Delta County-Level Sustainable Developmet Index

description: Land use datasets from the ESA(European Space Agency) at 300-meter resolution in the WGS84 geographic coordinate system. The CCI global land characterization utilizes FAO's LCCS framework to establish 22 categorical divisions. To align with analytical requirements, the land cover classes were reclassified into a simplified framework. The CO2 emission data were obtained from CGER (Center for Global Environmental Research)as 1km×1km resolution raster data and aggregated to county-level annual CO₂ emissions (units, metric tons) for the YRD (2000–2022). Spatial resolution of PM2.5 concentration data was standardized through resampling to 1km×1km grid cells, and aggregated to county-level annual PM2.5 concentrations (2000–2022) using zonal statistics. Population data sourced from Landscan Global Population Grids (Oak Ridge National Laboratory, USA), which integrates census data, land cover, nighttime lights, and remote sensing imagery at 1km×1km resolution. Annual population data (2000–2022) for counties in the YRD were extracted via zonal statistics. Annual maximum NDVI values were from Google Earth Engine (GEE) and aggregated to county-level data (2000–2022) using zonal statistics (Yang, et al. 2019).

The National Geographic Information Public Service Platform of China provided county-level administrative boundary vectors covering the YRD region (Approval No. GS (2024) 0650). Key socioeconomic indicators (GDP, industrial output, employment rates) originated from China's official statistical repositories, specifically the Urban Statistical Yearbook and National Annual Database. Data deficiencies were supplemented via referencing regional statistical yearbooks, with residual gaps imputed through spatial kriging interpolation, ensuring comprehensive coverage for multivariate regression analysis.
DOI: 10.5281/zenodo.16946155
title: Yangtze River Delta County-Level Sustainable Developmet Index

description: Land use datasets from the ESA(European Space Agency) at 300-meter resolution in the WGS84 geographic coordinate system. The CCI global land characterization utilizes FAO's LCCS framework to establish 22 categorical divisions. To align with analytical requirements, the land cover classes were reclassified into a simplified framework. The CO2 emission data were obtained from CGER (Center for Global Environmental Research)as 1km×1km resolution raster data and aggregated to county-level annual CO₂ emissions (units, metric tons) for the YRD (2000–2022). Spatial resolution of PM2.5 concentration data was standardized through resampling to 1km×1km grid cells, and aggregated to county-level annual PM2.5 concentrations (2000–2022) using zonal statistics. Population data sourced from Landscan Global Population Grids (Oak Ridge National Laboratory, USA), which integrates census data, land cover, nighttime lights, and remote sensing imagery at 1km×1km resolution. Annual population data (2000–2022) for counties in the YRD were extracted via zonal statistics. Annual maximum NDVI values were from Google Earth Engine (GEE) and aggregated to county-level data (2000–2022) using zonal statistics (Yang, et al. 2019).

The National Geographic Information Public Service Platform of China provided county-level administrative boundary vectors covering the YRD region (Approval No. GS (2024) 0650). Key socioeconomic indicators (GDP, industrial output, employment rates) originated from China's official statistical repositories, specifically the Urban Statistical Yearbook and National Annual Database. Data deficiencies were supplemented via referencing regional statistical yearbooks, with residual gaps imputed through spatial kriging interpolation, ensuring comprehensive coverage for multivariate regression analysis.
DOI: 10.22002/176f2-xfn95
title: R9deltaEnv MOLT

description: fixed, wt, molt, R9
description: <strong>Tilt Series Date:</strong> 2014-08-25</p>
<strong>Data Taken By:</strong> Luiza Mendonca</p>
<strong>Species / Specimen:</strong> HIV and deltaNef</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: 100.0 eV/Å²,  defocus: -6.0 μm,  magnification: 26000x. </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>Purification / Growth Conditions / Treatment:</strong> fixed w/ 1% formaldehyde</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/lmm2014-08-25-14/rawdata/</p>L029_grid4_0010.mrc,  Tilt Series (Pixel Size 0.39 nm), 3.3 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/lmm2014-08-25-14/rawdata/L029_grid4_0010.mrc"
        > <i class="download icon"></i> Download </a></p>

        L029_grid4_0010_part121_5.rec,  Reconstruction (Pixel Size 1.56 nm), 430.6 MB  
        
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DOI: 10.22002/b033w-8f559
title: 25ugchloramphenicol

description: Bacteriophage contamination may exist
description: <strong>Tilt Series Date:</strong> 2013-11-28</p>
<strong>Data Taken By:</strong> Poorna Subramanian</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: 160.0 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>
  psa2013-11-28-7_slicer4714.jpg: Extracellular vesicle psa2013-11-28-7_slicer4716.jpg: Vesicle psa2013-11-28-7_slicer4717.jpg: S layer and one layer peptidoglycan psa2013-11-28-7_slicer4721.jpg: Budding vesicle
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/psa2013-11-28-7/rawdata/</p>atlas10007.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/psa2013-11-28-7/rawdata/atlas10007.mrc"
        > <i class="download icon"></i> Download </a></p>

        atlas10007_full.rec,  Reconstruction (Pixel Size 1.92 nm), 445.4 MB  
        
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DOI: 10.6084/m9.figshare.29985133
title: Data for: Soil microplastics pollution can reduce viral abundance and have less consistent impacts on bacteria

description: Viruses represent the most abundant biological entities on Earth and may play crucial roles in structuring microbial communities and biogeochemical cycles. A number of environmental factors may affect viruses and their microbial hosts differentiate. Here we report two experiments that addressed the impacts of microplastics (MP) on viruses and bacteria in soils. In a pure culture experiment, soil microcosms in test tubes with only bacterium <i>Pseudomonas fluorescens</i> SBW25, or bacteriophage SBW25Φ2, were exposed polyethylene (PE) or polyvinyl chloride (PVC) pollution. In a microbial community experiment, soils with natural microbes in pots planted with maize were given PE or PVC contamination with a gradient of dosage. In both experiments, PE and PVC significantly reduced viral abundances. However, their effects on bacterial abundances were context-dependent. Bacterial growth in pure culture soil microcosms was unaffected by MP exposure. In the microbial community experiment, high-dose PE increased bacterial abundance and decreased the virus-to-bacteria ratio (VBR). High-dose PVC markedly reduced bacterial abundance without substantially altering VBR. This study reveals that MP contamination may induce viral inactivation in soil environments, potentially diminishing the top-down control of bacteria by viruses.
DOI: 10.6084/m9.figshare.29985133.v1
title: Data for: Soil microplastics pollution can reduce viral abundance and have less consistent impacts on bacteria

description: Viruses represent the most abundant biological entities on Earth and may play crucial roles in structuring microbial communities and biogeochemical cycles. A number of environmental factors may affect viruses and their microbial hosts differentiate. Here we report two experiments that addressed the impacts of microplastics (MP) on viruses and bacteria in soils. In a pure culture experiment, soil microcosms in test tubes with only bacterium <i>Pseudomonas fluorescens</i> SBW25, or bacteriophage SBW25Φ2, were exposed polyethylene (PE) or polyvinyl chloride (PVC) pollution. In a microbial community experiment, soils with natural microbes in pots planted with maize were given PE or PVC contamination with a gradient of dosage. In both experiments, PE and PVC significantly reduced viral abundances. However, their effects on bacterial abundances were context-dependent. Bacterial growth in pure culture soil microcosms was unaffected by MP exposure. In the microbial community experiment, high-dose PE increased bacterial abundance and decreased the virus-to-bacteria ratio (VBR). High-dose PVC markedly reduced bacterial abundance without substantially altering VBR. This study reveals that MP contamination may induce viral inactivation in soil environments, potentially diminishing the top-down control of bacteria by viruses.