cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.22002/apf2b-7g884
title: Agro VirB8-GFP

description: Raw data files of Agro VirB8-GFP
description: <strong>Tilt Series Date:</strong> 2013-10-03</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: 1.0°, constant angular increment, dosage: 200.0 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> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> Pat Zambryski</p>
<strong>Purification / Growth Conditions / Treatment:</strong> cells were grown in liquid at 19C and induced with 200uM AS for 24 hours</p>
<strong>Sample Preparation:</strong> Vitrobot</p>
description: Files available via S3 at ttps://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2013-10-03-24/rawdata/</p>virb8_24h_2750025.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/etl2013-10-03-24/rawdata/virb8_24h_2750025.mrc"
        > <i class="download icon"></i> Download </a></p>

        virb8_24h_2750025_part121_57.rec,  Reconstruction (Pixel Size 1.56 nm), 801.8 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2013-10-03-24/3dimage_31860/virb8_24h_2750025_part121_57.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.15468/dl.tf8g2c
title: Occurrence Download

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

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002306-250827131500795/datasets/export for details.
DOI: 10.22002/3hmg9-23t82
title: Eco 120208 012

description: Escherichia coli, 09feb08c_6_1_2_120208_012_066,
description: <strong>Tilt Series Date:</strong> 2009-02-08</p>
<strong>Data Taken By:</strong> Martin Pilhofer</p>
<strong>Species / Specimen:</strong> Escherichia coli</p>
<strong>Strain:</strong> 6.1.2 Martin</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>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mpa2009-02-08-17/rawdata/</p>09feb08c_6_1_2_120208_012_066.mrc,  Tilt Series (Pixel Size 0.95 nm), 1.0 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        09feb08c_6_1_2_120208_012_066_full.rec,  Reconstruction (Pixel Size 1.9 nm), 838.9 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/h874h-vcj25
title: wild type B. subtilis

description: sacculi of sporulating wtBsubtilis
description: <strong>Tilt Series Date:</strong> 2011-07-05</p>
<strong>Data Taken By:</strong> Elitza Tocheva</p>
<strong>Species / Specimen:</strong> Bacillus subtilis</p>
<strong>Strain:</strong> subsp. subtilis str. 168</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>
  etl2011-07-05-31_slicer4406.jpg: Nucleoid etl2011-07-05-31_slicer4415.jpg: unknown
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2011-07-05-31/3dimage_25126/</p>target20006_full.rec,  Reconstruction (Pixel Size 1.9 nm), 627.6 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2011-07-05-31/3dimage_25126/target20006_full.rec"
        > <i class="download icon"></i> Download </a></p>

        target20006.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/etl2011-07-05-31/rawdata/target20006.mrc"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.15468/dl.p2k7m9
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Malus sieboldii",
 "Country is Canada",
 "HasCoordinate is true"
 ]
}

 The dataset includes 3 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002304-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22002/rsmd9-k7760
title: Ote 090409 MP22

description: Opitutus terrae, 09sep10b_090409MP22_044,
description: <strong>Tilt Series Date:</strong> 2009-09-10</p>
<strong>Data Taken By:</strong> Martin Pilhofer</p>
<strong>Species / Specimen:</strong> Opitutus terrae</p>
<strong>Strain:</strong> DSM 11246</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>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mpa2009-09-10-75/rawdata/</p>09sep10b_090409MP22_044.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/mpa2009-09-10-75/rawdata/09sep10b_090409MP22_044.mrc"
        > <i class="download icon"></i> Download </a></p>

        09sep10b_090409MP22_044_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/mpa2009-09-10-75/3dimage_14151/09sep10b_090409MP22_044_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/5r81q-1ta60
title: 1003_deletion

description: Raw data files of 1003_deletion
description: <strong>Tilt Series Date:</strong> 2009-10-06</p>
<strong>Data Taken By:</strong> Zhuo Li</p>
<strong>Species / Specimen:</strong> Magnetospirillum magneticum</p>
<strong>Strain:</strong> AMB-1</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-63.0°, 63.0°), step: 1°, constant angular increment, dosage: 110.0 eV/Å²,  defocus: -16.0 μm,  magnification: 18000x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> RAPTOR, Peach, IMOD</p>
<strong>Collaborators and Roles:</strong> Cells provided by Arash Komeili, data collected by ZL</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Probably stationary phase</p>
<strong>Sample Preparation:</strong> quantifoil grid R2/1 or R2/2, 10nm gold, 100% humidity</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/zla2009-10-06-16/rawdata/</p>09oct06a_A1003c_015.mrc,  Tilt Series (Pixel Size 1.192 nm), 1.1 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        09oct06a_A1003c_015_part.rec,  Reconstruction (Pixel Size 2.384 nm), 471.9 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/he15q-v9p74
title: HUVECs CHMP4A+VPS4DN

description: HUVECs transfected with CHMP4A+VPS4DN constructs using Nucleofector Kit. Sample# C58-2
description: <strong>Tilt Series Date:</strong> 2010-12-13</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°, constant angular increment, dosage: 150.0 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> imod</p>
<strong>Collaborators and Roles:</strong> CHMP4A and VPS4DN construct provided by Wes Sundquist. Cells transfected, frozen and imaged at Caltech by Cora Woodward</p>
<strong>Purification / Growth Conditions / Treatment:</strong> whole cells grown on grids and transfected</p>
<strong>Sample Preparation:</strong> manual blotting</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/cwl2010-12-13-1/rawdata/</p>10dec13a_C45_1_003.st,  Tilt Series (Pixel Size 0.5 nm), 1.0 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/cwl2010-12-13-1/rawdata/10dec13a_C45_1_003.st"
        > <i class="download icon"></i> Download </a></p>

        10dec13a_C45_1_003_full.rec,  Reconstruction (Pixel Size 2.0 nm), 4.1 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/cwl2010-12-13-1/3dimage_68164/10dec13a_C45_1_003_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/gqs3v-z2e79
title: MT-MreB treated w/ aurothiogluco

description: Raw data files of MT-MreB treated w/ aurothiogluco
description: <strong>Tilt Series Date:</strong> 2009-07-21</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: (-60.0°, 60.0°), step: 1°, constant angular increment, dosage: 190.0 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 Peach</p>
<strong>Collaborators and Roles:</strong> Cell culture and treatment by Zhuo Li. Data collected by Zhuo Li. Processed by Zhuo Li. </p>
<strong>Purification / Growth Conditions / Treatment:</strong> Exponentially growing MT310 cells were treated with 50 uM aurothioglucose for 20 hours before freezing. </p>
<strong>Sample Preparation:</strong> 10 nm gold. </p>
description: Files available via S3 at ps://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/zla2009-07-21-39/rawdata/</p>09jul21a_mtmrebaurothio_003.mrc,  Tilt Series (Pixel Size 1.2 nm), 1.0 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        09jul21a_mtmrebaurothio_003_full.rec,  Reconstruction (Pixel Size 2.4 nm), 367.0 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/g4j0p-t0321
title: Hyphomonas session9 34KX

description: high-order DNA, H-NS, nucleoid, asymmetric cell division
description: <strong>Tilt Series Date:</strong> 2009-03-07</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: 140.0 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/jsa2009-03-07-17/rawdata/</p>09mar07a_36c_017.mrc,  Tilt Series (Pixel Size 0.632 nm), 553.7 MB  
        
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        > <i class="download icon"></i> Download </a></p>

        09mar07a_36c_017_full.rec,  Reconstruction (Pixel Size 1.264 nm), 419.4 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/jsa2009-03-07-17/3dimage_6903/09mar07a_36c_017_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.5281/zenodo.16974352
title: Agroforestry Buffers Drought Stress by Enhancing Hydrological Redistribution in Dryland Apple Orchards
DOI: 10.5281/zenodo.16974353
title: Agroforestry Buffers Drought Stress by Enhancing Hydrological Redistribution in Dryland Apple Orchards
DOI: 10.22002/7vx7a-d1989
title: Pdj 030509 397

description: Prosthecobacter dejongeii, 09mar19a_Pdjgrid_030509_397_w4_039, filaments,
description: <strong>Tilt Series Date:</strong> 2009-03-19</p>
<strong>Data Taken By:</strong> Martin Pilhofer</p>
<strong>Species / Specimen:</strong> Prosthecobacter dejongeii</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> imod</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>
  mpa2009-03-19-33_slicer9690.jpg: Filaments .  Prosthecobacter dejongeii
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mpa2009-03-19-33/rawdata/</p>09mar19a_Pdjgrid_030509_397_w4_039_orig.mrc,  Tilt Series (Pixel Size 0.95 nm), 1.0 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        09mar19a_Pdjgrid_030509_397_w4_039.rec,  Reconstruction (Pixel Size 1.9 nm), 338.7 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/m91wm-x8v43
title: A.longum on H2CO2+Propanediol

description: Raw data files of A.longum on H2CO2+Propanediol
description: <strong>Tilt Series Date:</strong> 2009-03-11</p>
<strong>Data Taken By:</strong> Elitza Tocheva</p>
<strong>Species / Specimen:</strong> Acetonema longum</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: 200.0 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>
<strong>Collaborators and Roles:</strong> Eric Matson grew the cells</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Exponential phase in standard media+Propanediol (induces pdu formation) </p>
<strong>Sample Preparation:</strong>  quantifoil grid, 10nm gold, 100% humidity</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2009-03-11-13/rawdata/</p>09mar12a_pos3Alongum_003.mrc,  Tilt Series (Pixel Size 0.961 nm), 1.0 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        3_full.rec,  Reconstruction (Pixel Size 1.922 nm), 415.2 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2009-03-11-13/3dimage_6421/3_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/3qhkq-8kj16
title: BsubtilisMJ007 germinating spores

description: Bsubtilis MJ007 germinating spores
description: <strong>Tilt Series Date:</strong> 2011-08-24</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> UCSF tomo</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/etl2011-08-24-25/3dimage_24981/</p>MJgermspore0005_full.rec,  Reconstruction (Pixel Size 1.9 nm), 825.8 MB  
        
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        > <i class="download icon"></i> Download </a></p>

        MJgermspore0005.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/etl2011-08-24-25/rawdata/MJgermspore0005.mrc"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.15468/dl.b7kg5v
title: Occurrence Download

description: A dataset containing 1710876 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Triticum aestivum, Triumfetta bogotensis, Triumfetta rhomboidea, Triumfetta semitriloba, Trollius europaeus, Tropaeolum majus, Tropaeolum pentaphyllum, Tropaeolum speciosum, Tsuga heterophylla, Turbina corymbosa, Turnera subulata, Turnera ulmifolia, Tussilago farfara, Typha angustifolia, Typha capensis, Typha domingensis, Typha latifolia, Ugni molinae, Ulex europaeus, Ulmus glabra)",
 "BasisOfRecord is one of (Machine Observation, Human Observation, Observation)",
 "HasCoordinate is true",
 "Year is greater than or equal to 1990"
 ]
}

 The dataset includes 1710876 records from 3085 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002274-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.48t33f
title: Occurrence Download

description: A dataset containing 2035872 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Pterygoplichthys pardalis, Ptilinus pectinicornis, Ptilohyale littoralis, Ptinus bicinctus, Pulvinaria floccifera, Pulvinaria hydrangeae, Pulvinaria regalis, Puntigrus tetrazona, Puntius titteya, Pycnonotus cafer, Pycnonotus jocosus, Pycnonotus leucotis, Pyemotes tritici, Pygocentrus cariba, Pygocentrus nattereri, Pygopristis denticulata, Pylodictis olivaris, Pyromaia tuberculata, Python bivittatus, Python brongersmai)",
 "BasisOfRecord is one of (Machine Observation, Human Observation, Observation)",
 "HasCoordinate is true",
 "Year is greater than or equal to 1990"
 ]
}

 The dataset includes 2035872 records from 482 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000093-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.18434/mds2-3929
title: Trojan Detection Software Challenge - llm-instruct-oct2024-test