cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.22002/bwn8r-0rx68
title: BsubtilisMJ007

description: Bsubtilis MJ007, skinny Bacillus
description: <strong>Tilt Series Date:</strong> 2009-09-26</p>
<strong>Data Taken By:</strong> Elitza Tocheva</p>
<strong>Species / Specimen:</strong> Bacillus subtilis </p>
<strong>Strain:</strong> MJ007, ponA null</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/etl2009-09-26-16/3dimage_24624/</p>09sep26a_et-pos4_023_full.rec,  Reconstruction (Pixel Size 1.9 nm), 838.9 MB  
        
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        > <i class="download icon"></i> Download </a></p>

        09sep26a_et-pos4_023.mrc,  Tilt Series (Pixel Size 0.95 nm), 1.0 GB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/pckpp-2c715
title: pLE7_1mM_IPTG

description: These cells are highly overexpressing YFP-MreB from the pLE7 plasmid. These cells were a gift from Larry Rothfield.
description: <strong>Tilt Series Date:</strong> 2011-11-18</p>
<strong>Data Taken By:</strong> Matt Swulius</p>
<strong>Species / Specimen:</strong> Escherichia coli</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: 22500x. </p>
<strong>Acquisition Software:</strong> UCSFTomo</p>
<strong>Upload Method:</strong> uploadraptor</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Purification / Growth Conditions / Treatment:</strong> LB 37 Degrees</p>
<strong>Sample Preparation:</strong> Induced at an OD of .2 and grew for 2 hours (~OD of .8)</p>
  mst2011-11-18-1_slicer9709.jpg: Escherichia coli .  filament bundle .  contains MreB mst2011-11-18-1_slicer9710.jpg: Escherichia coli .  vesicle mst2011-11-18-1_slicer9711.jpg: Escherichia coli .  vesicle
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mst2011-11-18-1/rawdata/</p>20111118_ple7_1mMiptg0002.mrc,  Tilt Series (Pixel Size 0.95 nm), 1.1 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        20111118_ple7_1mMiptg0002_full.rec,  Reconstruction (Pixel Size 1.9 nm), 1.0 GB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.6084/m9.figshare.29998405
title: Silver Nanoparticle Systematic Review Data Extract

description: This systematic review synthesized evidence from 35 <i>in vivo</i> and 4 <i>in vitro </i>studies investigating AgNP-induced cardiovascular toxicity in animal models. Database searches across PubMed, ScienceDirect, ProQuest, SpringerLink, Wiley, and Taylor & Francis were conducted following PRISMA guidelines, with risk of bias assessed using the SYRCLE tool.
DOI: 10.6084/m9.figshare.29998405.v1
title: Silver Nanoparticle Systematic Review Data Extract

description: This systematic review synthesized evidence from 35 <i>in vivo</i> and 4 <i>in vitro </i>studies investigating AgNP-induced cardiovascular toxicity in animal models. Database searches across PubMed, ScienceDirect, ProQuest, SpringerLink, Wiley, and Taylor & Francis were conducted following PRISMA guidelines, with risk of bias assessed using the SYRCLE tool.
DOI: 10.15468/dl.yzgjdx
title: Occurrence Download

description: A dataset containing 9 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cotoneaster melanocarpus",
 "Country is Armenia",
 "HasCoordinate is true"
 ]
}

 The dataset includes 9 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002232-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zc93nq
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Chiloglanis reticulatus)",
 "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 3 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002235-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22002/1gy1m-58151
title: Hyphomonas session11 34KX

description: high-order DNA, H-NS, nucleoid, asymmetric cell division
description: <strong>Tilt Series Date:</strong> 2009-03-29</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: (-64.0°, 64.0°), step: 2°, constant angular increment, dosage: 130.0 eV/Å²,  defocus: -8.0 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...</p>
<strong>Sample Preparation:</strong> C-flat grid, 10nm gold, 100% humidity...</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/jsa2009-03-29-18/rawdata/</p>09mar29a_bx608a_018.mrc,  Tilt Series (Pixel Size 0.632 nm), 553.7 MB  
        
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        > <i class="download icon"></i> Download </a></p>

        09mar29a_bx608a_018_part.rec,  Reconstruction (Pixel Size 1.264 nm), 419.4 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/g6kj5-kn333
title: Skinny E. coli DS664

description: Raw data files of Skinny E. coli DS664
description: <strong>Tilt Series Date:</strong> 2009-11-23</p>
<strong>Data Taken By:</strong> Zhuo Li</p>
<strong>Species / Specimen:</strong> Escherichia coli</p>
<strong>Strain:</strong> </p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-63.0°, 63.0°), step: 1°, constant angular increment, dosage: 190.0 eV/Å²,  defocus: -12.0 μm,  magnification: 18000x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> webload</p>
<strong>Processing Software Used:</strong> IMOD, RAPTOR, Peach</p>
<strong>Collaborators and Roles:</strong> Cells provided by Daisuke Shiomi (BW25113 yhdE_deletion mreB-A125V). Data colleted by ZL.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Exponential phase in L Broth</p>
<strong>Sample Preparation:</strong> Quantifoil R2/1 or R2/2, 10 nm gold, 100% humidity</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/zla2009-11-23-60/rawdata/</p>09nov23a_DS664_060.mrc,  Tilt Series (Pixel Size 1.192 nm), 1.1 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        09nov23a_DS664_060_part.rec,  Reconstruction (Pixel Size 2.384 nm), 471.9 MB  
        
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DOI: 10.15468/dl.k6gf2z
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cotoneaster melanocarpus",
 "Country is Lithuania",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002234-250827131500795/datasets/export for details.
DOI: 10.15468/dl.jyvwb3
title: Occurrence Download

description: A dataset containing 140447 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Senegal",
 "OccurrenceStatus is Present",
 "Year 2000-2015"
 ]
}

 The dataset includes 140447 records from 161 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003707-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.uk4yce
title: Occurrence Download

description: A dataset containing 355 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Larix decidua",
 "Country is United States of America",
 "HasCoordinate is true"
 ]
}

 The dataset includes 355 records from 59 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003776-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kwn3k6
title: Occurrence Download

description: A dataset containing 19821 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Equisetum arvense, Equisetum pratense, Equisetum pallens, Equisetum fluviatile, Equisetum palustre, Equisetum lacustre, Equisetum diffusum, Equisetum hyemale, Equisetum scirpoides, Equisetum variegatum, Equisetum variegatum, Equisetum ramosissimum, Equisetum ramosissimum, Equisetum ramosissimum, Equisetum ramosissimum, Hypolepis punctata, Hypolepis punctata, Hypolepis punctata, Hypolepis punctata, Sitobolium zeylanicum, Microlepia hancei, Microlepia mannii, Microlepia mannii, Microlepia marginata, Microlepia marginalis, Micromeria marginata, Athyrium deltoidofrons, Athyrium devolii, Anisocampium niponicum, Deparia japonica, Deparia petersenii, Deparia petersonii, Diplazium esculentum, Diplazium succulentum, Diplazium donianum, Diplazium lobbianum, Diplazium toriianum, Diplazium boryanum, Diplazium montanum, Cornopteris christenseniana, Cornopteris decurrentialata, Macrothelypteris oligophlebia, Macrothelypteris torresiana, Macrothelypteris terresiana, Cyclosorus dentatus, Cyclosorus peltatus, Cyclosorus pennatus, Cyclosorus interruptus, Cyclosorus interruptus, Cyclosorus jaculosus, Cyclosorus truncatus, Cyclosorus truncatus, Cyclosorus parasiticus, Cyclosorus parasiticus, Cyclosorus acuminatus, Cyclosorus acuminatus, Cyclosorus acuminatus, Thelypteris palustris, Thelypteris fairbankii, Ampelopteris prolifera, Pronephrium penangianum, Pronephrium penangianum, Pseudocyclosorus subochthodes, Matteuccia struthiopteris, Pentarhizidium orientale, Pentarhizidium orientalis, Dryopteris tokyoensis, Dryopteris nokoensis, Dryopteris tonkinensis, Dryopteris peninsulae, Dryopteris paleolata, Dryopteris paleolata, Dryopteris paleata, Polystichum makinoi, Polystichum longiaristatum, Leptochilus hemionitideus, Marsilea quadrifolia, Marsilea quadrifolia, Marsilea quadrifolia, Marsilea quadrifoliata, Marsilea aegyptiaca, Marsilea aegyptiaca, Marsilea aegyptica, Marsea aegyptiaca, Marsilea minuta, Marsilea minuta)",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Living Specimen, Machine Observation, Literature Occurrence)",
 "Country is one of (China, Chinese Taipei, Hong Kong, Macao)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1949"
 ]
}

 The dataset includes 19821 records from 62 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003777-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3thpcp
title: Occurrence Download

description: A dataset containing 9 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Leiopotherapon plumbeus)",
 "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 9 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003779-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kt2ts5
title: Occurrence Download

description: A dataset containing 391138 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "TaxonKey is Teucrium scorodonia"
 ]
}

 The dataset includes 391138 records from 1831 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003621-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22002/gcjtx-cs568
title: JV9298

description: Legionella pneumophila JV9298 DotF-GFP DotB E191K
description: <strong>Tilt Series Date:</strong> 2020-04-23</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: (-54.0°, 54.0°), step: 3°, constant angular increment, dosage: 100.0 eV/Å²,  defocus: -4.0 μm,  magnification: 33000x. </p>
<strong>Acquisition Software:</strong> Serial EM</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> imod, tomo3d</p>
<strong>Collaborators and Roles:</strong> Sample preparation & data collection: Yuxi Liu Data processing: Phyllis Wang & Yuxi Liu</p>
<strong>Purification / Growth Conditions / Treatment:</strong> O.D. 2.5-3.0 in AYE</p>
<strong>Sample Preparation:</strong> Quantifoil R2/2 copper grid, 10nm gold, 100% humidity, 25deg C, 4uL of 2X concentrated cells Blotting: force 6, blot 3sec, wait 1sec</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ylx2020-04-23-239/3dimage_124149/</p>JV9298_PD-1-3_163_SIRT_1k.mrc,  Reconstruction (Pixel Size 1.04 nm), 2.1 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        JV9298_PD-1-3_163.mrc,  Tilt Series (Pixel Size 0.26 nm), 1.7 GB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/9qvjv-zty51
title: JV9082

description: DotF-GFP, defocus range -3 to 6
description: <strong>Tilt Series Date:</strong> 2019-12-05</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: (-54.0°, 54.0°), step: 3°, constant angular increment, dosage: 100.0 eV/Å²,  defocus: -5.0 μm,  magnification: 33000x. </p>
<strong>Microscope:</strong> Janelia Titan</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> Strain from Joe Vogel lab</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Late exponential phase, early stationary phase</p>
<strong>Sample Preparation:</strong> 10nm gold, Quantifoil R2/2 copper mesh 200 Finder grid, Vitrobot 22 deg C, 100% humidity, blot . time 3 sec, blot force 6, drain 1 sec, wait 0 sec.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ylx2019-12-05-6/rawdata/</p>9082_box1_No1_123.mrc,  Tilt Series (Pixel Size 0.2612 nm), 1.7 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        9082_box1_No1_123_full.rec,  Reconstruction (Pixel Size 1.0448 nm), 516.1 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/bhxk7-e9415
title: Legionella_delta-lspGHIJK

description: Legionella pneumophila Philadelphia-1_Lp02. Lacks all the T2SS major and minor pseudopilins.
description: <strong>Tilt Series Date:</strong> 2019-05-18</p>
<strong>Data Taken By:</strong> Debnath Ghosal</p>
<strong>Species / Specimen:</strong> Legionella pneumophila</p>
<strong>Strain:</strong> Philadelphia-1_Lp02</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-45.0°, 45.0°), step: 3.0°, constant angular increment, dosage: 100.0 eV/Å²,  defocus: -7.0 μm,  magnification: 42000x. </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>Collaborators and Roles:</strong> Strain sent by Nicholas Cianciotto, Northwestern University. Data collected and processed by Debnath Ghosal.</p>
<strong>Sample Preparation:</strong> 6 grids were frozen for this strain (2x concentrated culture, OD~4.8); Vitrobot (MK iv) settings: 100% humidity, 4µl sample, Blot force 6, blot time 4.5 sec. Wait time 0 sec. Drain time 1 sec. Ethane/propane mix. Grid: Quantifoil Cu 2/2 200.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2019-05-18-53/rawdata/</p>DG8_201905180026.mrc,  Tilt Series (Pixel Size 0.26 nm), 882.8 MB  
        
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        > <i class="download icon"></i> Download </a></p>

        DG8_201905180026_full.rec,  Reconstruction (Pixel Size 1.04 nm), 445.4 MB  
        
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DOI: 10.22002/xp06d-4ev17
title: JV9298

description: DotF-sfGFP DotB E191K
description: <strong>Tilt Series Date:</strong> 2019-10-14</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: (-54.0°, 54.0°), step: 3°, constant angular increment, dosage: 100.0 eV/Å²,  defocus: -5.0 μm,  magnification: 33000x. </p>
<strong>Microscope:</strong> PNCC Krios 3</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> Strain from Joe Vogel</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Late exponential/Early stationary</p>
<strong>Sample Preparation:</strong> Quantifoil R2/2 copper. Vitrobot 22 deg C, 100% humidity, 4uL of 2X concentrated culture, blot force 6, blot time 3 sec, drain time 1 sec, wait time 0 sec.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ylx2019-10-14-91/rawdata/</p>JV9298_126_A4.mrc,  Tilt Series (Pixel Size 0.1323 nm), 13.6 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        JV9298_126_A4_part36_4.rec,  Reconstruction (Pixel Size 1.0584 nm), 737.3 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/veexx-mbm61
title: U937 infection

description: Lp02 pCyaA::RalF-Ub V76 .  U937
description: <strong>Tilt Series Date:</strong> 2020-07-31</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: (-60.0°, 60.0°), step: 2°, constant angular increment, dosage: 120.0 eV/Å²,  defocus: -6.0 μm,  magnification: 33000x. </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> Batchruntomo</p>
<strong>Collaborators and Roles:</strong> Stephen Carter</p>
<strong>Purification / Growth Conditions / Treatment:</strong> 1h infection, 1-2 washes, fibronectin/vitronectin/no matrix. Legionella: 2.5 O.D, 3h after 200mM  IPTG induction, at O.D. 3</p>
<strong>Sample Preparation:</strong> 200mesh Gold quantifoil,  10nm gold, 37deg C, 80-90% humidity</p>
description: Files available via S3 at s://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ylx2020-07-31-37/rawdata/</p>tomography9_156.mrc,  Tilt Series (Pixel Size 0.265 nm), 282.8 MB  
        
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        tomography9_156.rec,  Reconstruction (Pixel Size 1.06 nm), 1.0 GB  
        
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