cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.22002/s27bv-wse93
title: MP III4 27.5KX

description: Mycoplasma pneumonia III4 mutant, attachment organelle
description: <strong>Tilt Series Date:</strong> 2010-04-01</p>
<strong>Data Taken By:</strong> Jian Shi</p>
<strong>Species / Specimen:</strong> Mycoplasma pneumoniae</p>
<strong>Strain:</strong> None</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-65.0°, 65.0°), step: 1°, constant angular increment, dosage: 150.0 eV/Å²,  defocus: -10.0 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> data collected by Jian; processed by Jian</p>
<strong>Sample Preparation:</strong> QF grid, 10nm gold, 100% humidity...</p>
  jsa2010-04-01-7_slicer13256.jpg: 3 Attachment Organelle? jsa2010-04-01-7_slicer13257.jpg: Attachment Organelle jsa2010-04-01-7_slicer13258.jpg: Attachment Organelle jsa2010-04-01-7_slicer13259.jpg: Partial Attachment Organelle?
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/jsa2010-04-01-7/rawdata/</p>10apr01a_B718a_007.mrc,  Tilt Series (Pixel Size 0.774 nm), 1.1 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/jsa2010-04-01-7/rawdata/10apr01a_B718a_007.mrc"
        > <i class="download icon"></i> Download </a></p>

        10apr01a_B718a_007_full.rec,  Reconstruction (Pixel Size 1.548 nm), 314.6 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/jsa2010-04-01-7/3dimage_16623/10apr01a_B718a_007_full.rec"
        > <i class="download icon"></i> Download </a></p>

        10apr01a_B718a_007_SIRT.rec,  Reconstruction (Pixel Size 0.0 nm), 524.3 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/jsa2010-04-01-7/3dimage_56018/10apr01a_B718a_007_SIRT.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/2ybj0-v6231
title: liposomes + 1uL CdvA

description: tetraether liposomes from Sulfolobus cells + 1uL CdvA
description: <strong>Tilt Series Date:</strong> 2011-08-02</p>
<strong>Data Taken By:</strong> Megan Dobro</p>
<strong>Species / Specimen:</strong> tetraether liposomes + CdvA</p>
<strong>Strain:</strong> </p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-61.0°, 61.0°), step: 1°, constant angular increment, dosage: 8.0 eV/Å²,  defocus: -5.0 μm,  magnification: 22500x. </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> sent by Rachel Samson at Oxford University, purified by Parkson Lee-Gau Chong at Temple University</p>
<strong>Purification / Growth Conditions / Treatment:</strong> heavy vortexing for 10 mins at 80 C</p>
<strong>Sample Preparation:</strong> prepared by Parkson Lee-Gau Chong</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mdj2011-08-02-2/rawdata/</p>liposomes1uLcdvA_27500x0015.mrc,  Tilt Series (Pixel Size 7.74 nm), 1.0 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        liposomes1uLcdvA_27500x0015_full.rec,  Reconstruction (Pixel Size 1.5 nm), 386.1 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mdj2011-08-02-2/3dimage_19419/liposomes1uLcdvA_27500x0015_full.rec"
        > <i class="download icon"></i> Download </a></p>

        liposomes1uLcdvA_27500x0015.rec,  Reconstruction (Pixel Size 1.5 nm), 193.0 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mdj2011-08-02-2/3dimage_19420/liposomes1uLcdvA_27500x0015.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.15468/dl.bgrs6q
title: Occurrence Download

description: A dataset containing 8193 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Insecta",
 "OccurrenceStatus is Present",
 "DecimalLatitude is less than or equal to -3.019",
 "DecimalLongitude is less than or equal to -59.9217",
 "DecimalLatitude is greater than or equal to -3.2190000000000003",
 "DecimalLongitude is greater than or equal to -60.121700000000004"
 ]
}

 The dataset includes 8193 records from 93 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0044061-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22002/4qjz8-5vy69
title: Cryo-sectioned Jurkat VSVG-pNL4GFP

description: Jurkats infected by spinoculation with VSVG-pNL4GFP, collected 30 min after synchronous entry, HP frozen and cryo-sectioned by Mark Ladinsky
description: <strong>Tilt Series Date:</strong> 2011-12-12</p>
<strong>Data Taken By:</strong> Cora Woodward</p>
<strong>Species / Specimen:</strong> Jurkat Human T-cell</p>
<strong>Strain:</strong> Clone E6-1</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: -6.0 μm,  magnification: 22500x. </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> pNL4GFP provirus construct from Irvin Chen (UCLA). Vpr-gfp construct to label virus provided by Tom Hope. Virus made at Caltech by Cora Woodward</p>
<strong>Purification / Growth Conditions / Treatment:</strong> infected VSVG-pNL4GFP</p>
<strong>Sample Preparation:</strong> cryo-sectioned by Mark Ladinsky</p>
  11dec12_cryosec_pnlegfp_grid3_Batch5_0041_full.jpg: file associated to 3D Image #54397
description: Files available via S3 at ://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/cwl2011-12-12-24/rawdata/</p>11dec12_cryosec_pnlegfp_grid3_Batch5_0041.st,  Tilt Series (Pixel Size 0.5 nm), 1.0 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        11dec12_cryosec_pnlegfp_grid3_Batch5_0041_full.rec,  Reconstruction (Pixel Size 2.0 nm), 445.9 MB  
        
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        > <i class="download icon"></i> Download </a></p>

        11dec12_cryosec_pnlegfp_grid3_Batch5_0041_full.tiff,  file associated to 3D Image #54397, 1.2 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/gb2a2-9dz73
title: MamJ deletion (and might contain

description: Raw data files of MamJ deletion (and might contain
description: <strong>Tilt Series Date:</strong> 2010-02-18</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: 1.5°, constant angular increment, dosage: 110.0 eV/Å²,  defocus: -15.0 μm,  magnification: 18000x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> webload</p>
<strong>Processing Software Used:</strong> RAPTOR and Peach</p>
<strong>Collaborators and Roles:</strong> Cell culture were from Arash Komeili. Upon receiving, cells were frozen in 2 hours. Meanwhile they were kept in 30C. Data collected and processed by ZL.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Stationary phase. </p>
<strong>Sample Preparation:</strong> R2/2, 10nm gold, 100% humidity</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/zla2010-02-18-35/rawdata/</p>10feb18a_dJnofe5_035.mrc,  Tilt Series (Pixel Size 1.192 nm), 1.1 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/zla2010-02-18-35/rawdata/10feb18a_dJnofe5_035.mrc"
        > <i class="download icon"></i> Download </a></p>

        10feb18a_dJnofe5_035_full.rec,  Reconstruction (Pixel Size 2.384 nm), 524.3 MB  
        
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        > <i class="download icon"></i> Download </a></p>

        10feb18a_dJnofe5_035.tif,  2.4 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.57830/2305538
title: Southwestern Willow Flycatcher Inventory at Carlsbad Caverns National Park 2022-2023 - Open Format Dataset (sensitive version)

description: The Southwestern willow flycatcher (SWFL), Empidonax traillii extimus, is a federally listed species and has been detected at the Rattlesnake Springs unit of Carlsbad Caverns National Park (CAVE). Park staff need to know where SWFL territories are and how they need to change planned management and activities and inform an integrated planning document based on SWFL presence. There are timing restrictions for mowing activities in nesting and foraging habitat from April 1-Sept 1. There are also noise limits and time of day restrictions. Mitigations apply when mowing or similar activities are happening within a 1⁄4 mile of any nests or territories. In 2022, Southwestern Willow Flycatcher Surveys and Intensive 10-minute Point Count Surveys for all bird species were conducted on July 6, 2022 and July 12, 2022 in Rattlesnake Springs area within Carlsbad Caverns National Park and The Nature Conservancy’s Rattlesnake Springs Preserve. One hundred sixty-five Southwestern Willow Flycatcher call-back protocol point counts were conducted with zero detections. The Arizona Important Bird Areas Intensive Point Count Protocol for 10-minute surveys for all bird species detected a total of 31 species with 8 additional species detected by surveyors between point counts. In 2023, USFWS Southwestern Willow Flycatcher Surveys and Intensive 10-minute Point Count Surveys for all bird species were conducted on May 15, June 5, June 13, June 27, and July 10, 2023. Five hundred nineteen Southwestern Willow Flycatcher call-back protocol point counts were conducted with positive detections on June 5, 2023 (one bird), June 13, 2023 (two birds, likely pair) and June 27, 2023 (three birds, 1 pair and a single).
DOI: 10.22002/f0f48-2jh07
title: MP TopJ 27.5KX

description: Mycoplasma pneumonia TopJ mutant, attachment organelle
description: <strong>Tilt Series Date:</strong> 2010-03-31</p>
<strong>Data Taken By:</strong> Jian Shi</p>
<strong>Species / Specimen:</strong> Mycoplasma pneumoniae</p>
<strong>Strain:</strong> None</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-65.0°, 65.0°), step: 1°, constant angular increment, dosage: 150.0 eV/Å²,  defocus: -10.0 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> data collected by Jian; processed by Jian</p>
<strong>Sample Preparation:</strong> QF grid, 10nm gold, 100% humidity...</p>
  jsa2010-03-31-13_slicer5669.jpg: unknown jsa2010-03-31-13_slicer5670.jpg: unknown jsa2010-03-31-13_slicer5672.jpg: unknown jsa2010-03-31-13_slicer5678.jpg: attatchment organelle jsa2010-03-31-13_slicer5685.jpg: filament jsa2010-03-31-13_slicer5692.jpg: filament
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/jsa2010-03-31-13/rawdata/</p>10mar31a_B572c_019.mrc,  Tilt Series (Pixel Size 0.774 nm), 1.1 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/jsa2010-03-31-13/rawdata/10mar31a_B572c_019.mrc"
        > <i class="download icon"></i> Download </a></p>

        10mar31a_B572c_019_full.rec,  Reconstruction (Pixel Size 1.548 nm), 314.6 MB  
        
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        > <i class="download icon"></i> Download </a></p>

        10mar31a_B572c_019_SIRT.rec,  Reconstruction (Pixel Size 0.0 nm), 524.3 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.57830/2305680
title: Desert Tortoise Inventory at Lake Mead National Recreation Area 2022 - Open Format Dataset (sensitive version)

description: The Lake Mead National Recreation Area (NRA) spans the Colorado River corridor in Arizona and Nevada and sits at an ecologically important intersection of the listed and unlisted Mojave tortoise populations. A large portion of the Lake Mead NRA contains suitable desert tortoise habitat, but no contemporary estimates of population densities exist for different areas of the recreation area. Three new Lake Mead NRA monitoring strata consisting of eight substrata were identified based on potential tortoise habitat and geography: 1) Detrital - Detrital 1 and Detrital 2, 2) Overton - Gold-Butte-Pakoon, Overton East, and Western Overton Arm, and 3) Eldorado Valley - Eldorado Mountain, Eldorado Valley, and Piute Valley. In 2022 at Lake Mead NRA, 25 teams surveyed a total of 170 12-km transects between 5 April and 2 May. Basing density estimates only on the tortoises that are visible will result in density estimates that are consistently underestimated. To account for this, we used telemetry to estimate the proportion of tortoises available for sampling. For the Lake Mead NRA surveys field technicians used high frequency receivers and directional antennas to locate 9-16 radio-equipped tortoises in two focal sites: Gold-Butte and Piute-Mid. Surveyors at Lake Mead NRA in 2022 reported five adult tortoises on transects and one additional adult, which was encountered opportunistically. Overall, the encounter rate was low, and the number of tortoises detected on transects was not sufficient to develop a detection function nor derive meaningful density estimates for any of the Lake Mead stratum.
DOI: 10.57830/2305848
title: Rare Plant Inventory at Assateague Island National Seashore 2023 - Open Format Dataset

description: The unique environmental conditions found on Assateague Island National Seashore (ASIS) are reflected in the dynamic continuum of habitats stretching from ocean to bay, including beaches, dunes, grass and shrublands, freshwater wetlands, maritime forests, and salt marshes. The diverse barrier island landscape provides habitat for a multitude of specialized plant species, at least 46 of which have been classified as rare, threatened, or endangered (RTE). To identify the current locations of RTE species in these areas, surveys were conducted during spring and fall 2023. Timed meander surveys were conducted along roadways and parking lots, and along access roads and around dwellings where demolition is proposed. Recommendations include fencing to protect the most vulnerable species from disturbance during construction and demolition activities, and flagging populations of more abundant species to increase visibility and minimize disturbance during construction. Future monitoring is recommended.
DOI: 10.22002/wm2ec-e7x12
title: pNLGFP Vpr-Gfp particles

description: pNLGFP particles labeled with Vpr-Gfp.  Particles only- same particles were used for CLEM experiments with sample#s C96 and C97
description: <strong>Tilt Series Date:</strong> 2011-10-07</p>
<strong>Data Taken By:</strong> Cora Woodward</p>
<strong>Species / Specimen:</strong> mature HIV-1</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: -6.0 μm,  magnification: 22500x. </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> pNLGFP proviral construct provided by Irvin Chen UCLA.  Vpr-GFP construct provided by Tom Hope. Virus prepared, frozen and imaged at Caltech by Cora Woodward.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Virus imaged by cryo-LM- correlative LM/EM not done due to thick ice.  </p>
<strong>Sample Preparation:</strong> manual blotting</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/cwl2011-10-07-1/3dimage_68495/</p>11oct07_C80_CLEM1_particles_1tgt_full.rec,  Reconstruction (Pixel Size 2.0 nm), 536.8 MB  
        
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        > <i class="download icon"></i> Download </a></p>

        11oct07_C80_CLEM1_particles_1tgt.st,  Tilt Series (Pixel Size 0.5 nm), 1.0 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        11oct07_C80_CLEM1_particles_1tgt_full.tiff,  file associated to 3D Image #68495, 826.7 kB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.15468/dl.k3uy8w
title: Occurrence Download

description: A dataset containing 72 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Hypostomus gymnorhynchus)",
 "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 72 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0044063-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22002/zt4v4-jd442
title: Agro C58 22C liq

description: Agrobacterium tumefaciens
description: <strong>Tilt Series Date:</strong> 2014-05-28</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: -10.0 μm,  magnification: 22500x. </p>
<strong>Acquisition Software:</strong> UCSFTomo</p>
<strong>Upload Method:</strong> reupload_downloaded</p>
<strong>Processing Software Used:</strong> IMOD</p>
<strong>Collaborators and Roles:</strong> From Pat Zambryski</p>
<strong>Purification / Growth Conditions / Treatment:</strong> cells were grown at 22C and induced with AS for one day in liquid</p>
<strong>Sample Preparation:</strong> Cells were not concentrated prior to freezing</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2014-05-28-1/rawdata/</p>cd8_22C_liq0001.mrc,  Tilt Series (Pixel Size 0.48 nm), 3.4 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        et2014-05-28-1_full.rec,  Reconstruction (Pixel Size 0.0 nm), 641.4 MB  
        
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        > <i class="download icon"></i> Download </a></p>

        et2014-05-28-1.tif,  2.1 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2014-05-28-1/file_11709/et2014-05-28-1.tif"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/aq9xv-jzj82
title: Treponema primitia

description: Treponema primitia.  The rest of the files are in ~/Images/050811
description: <strong>Tilt Series Date:</strong> 2005-08-11</p>
<strong>Data Taken By:</strong> Gavin Murphy</p>
<strong>Species / Specimen:</strong> Treponema primitia</p>
<strong>Strain:</strong> ZAS-2</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-65.0°, 65.0°), step: 1°, constant angular increment, dosage: 30.0 eV/Å²,  defocus: -12.0 μm,  magnification: 0x. </p>
<strong>Acquisition Software:</strong> UCSF tomo</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> imod, bsoft</p>
<strong>Collaborators and Roles:</strong> Cells provided by Eric Matson, Jared Leadbetter; Data collected and processed by Gavin Murphy</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Cells grown in standard media around exponential growth.  Removed from anaerobic tube with syringe.  Directly applied to grids, no centrifugation</p>
<strong>Sample Preparation:</strong> quantifoil grid, 10nm gold, 100% humidity...</p>
  T5_050811_tilt.jpg: * associated to rawdata T5_050811_rec.jpg: file associated to 3D Image #15
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/gme2005-08-11-5/rawdata/</p>T5_S488G3_22k10d110e.mrc,  Tilt Series (Pixel Size 0.98 nm), 1.2 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        T5B2s.mrc,  Reconstruction (Pixel Size 0.0 nm), 197.8 MB  
        
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        > <i class="download icon"></i> Download </a></p>

        T5B2sBB_28_partTrn.pif,  Reconstruction (Pixel Size 0.0 nm), 352.3 kB  
        
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