cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.57830/2305156
title: Grassland Bird and Raptor Inventory at Harpers Ferry National Historical Park 2022 - Open Format Dataset

description: Harpers Ferry National Historical Park (NHP) includes grassland habitats that are maintained for the interpretation of historic Civil War battles. In 2022, as part of the National Park Service Inventory and Monitoring program, the University of Delaware conducted a grassland bird and raptor inventory in the park. The goals of this inventory were to determine the grassland bird use of Harpers Ferry grasslands during Spring and Fall migration, estimate the abundance and daily nest survival for focal breeding species, and determine the raptor use during migration. We established and used multiple avian sampling techniques to address these goals including distance sampling using line transects, mist-netting to capture passerine birds, point counts, hawk watching, and nest searching and monitoring. We conducted this inventory during the annual cycle starting in March 2022 and completed the sampling in October 2022. During the course of this effort, we detected 111 species using the Harpers Ferry grasslands at some time during the year. We found that the park is supporting migrating and breeding grassland birds and that the avian species composition changes over the course of the annual cycle. During migration, we detected focal grassland bird species including Bobolink, Savannah Sparrow, Grasshopper Sparrow, and Eastern Meadowlark. During the breeding season, we located and monitored Eastern Meadowlark and Grasshopper Sparrow nests with adequate sample sizes to estimate daily nest survival. We found that Eastern Meadowlark daily nest survival was relatively high (99%) and was influenced by the proximity of the nest to a forested edge.
DOI: 10.22002/n89bv-y6339
title: MamJ deletion w/o iron

description: No magnetosome vesicles, suspected as a mutant that has lost the magnetosome island
description: <strong>Tilt Series Date:</strong> 2010-01-22</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: (-60.0°, 60.0°), step: 1°, constant angular increment, dosage: 120.0 eV/Å²,  defocus: -16.0 μm,  magnification: 18000x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> webload</p>
<strong>Processing Software Used:</strong> Raptor and Peach, IMOD</p>
<strong>Collaborators and Roles:</strong> Mutant constructed by Arash Komeili, cells shipped to and imaged by Zhuo Li</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Stationary phase</p>
<strong>Sample Preparation:</strong> Quantifoid grid, 10-nm gold, 100% humidity</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/zla2010-01-22-4/3dimage_9175/</p>10jan22a_dJnofe2_0071K.rec,  Reconstruction (Pixel Size 0.0 nm), 124.3 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/zla2010-01-22-4/3dimage_9175/10jan22a_dJnofe2_0071K.rec"
        > <i class="download icon"></i> Download </a></p>

        10jan22a_dJnofe2_007.mrc,  Tilt Series (Pixel Size 0.0 nm), 1.0 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/zla2010-01-22-4/rawdata/10jan22a_dJnofe2_007.mrc"
        > <i class="download icon"></i> Download </a></p>

        10jan22a_dJnofe2_007_part.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/zla2010-01-22-4/3dimage_9177/10jan22a_dJnofe2_007_part.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.6084/m9.figshare.29983663.v1
title: All or nothing: highly variable species-level performance of BirdNET’s bird classifier and a new Australian frog classifier

description: Effective conservation relies on accurate data on species distributions and their change over time. Recent advances in low-cost acoustic recorders and artificial intelligence (AI) now offer powerful new ways to collect these data, revitalising the use of ecoacoustics for monitoring fauna at scale. While open-source, multi-species AI models like BirdNET are now available for most bird species, similar tools for amphibians remain limited. Here, we present the first open-source, multi-species frog classifier for 16 native species from Victoria, Australia, and evaluate its performance alongside the bird classifier BirdNET using real-world data from freshwater wetlands. Both classifiers exhibited a characteristic bimodal distribution in precision, with most species detected either with very high (&gt;90%) or very low (&lt;25%) accuracy, and relatively few species in between. For our frog classifier, misclassifications were often associated with simultaneous calls from acoustically similar frog species. For the default bird classifier, precision tended to be higher for species with short, simple, downward-sloping calls. Despite being trained on a relatively small, targeted dataset, our frog classifier achieved low false-positive rates, suggesting that modest datasets can yield robust results. These classifiers are currently most effective for rapidly screening long recordings, allowing users to focus on segments most likely to contain relevant calls while maintaining low false-positive rates. To support further development and collaboration, we release our frog classifier as an open-access tool. Broader efforts to expand multi-species classifiers across taxa and regions will be critical to realising the full potential of AI-powered ecoacoustics in biodiversity monitoring.
DOI: 10.6084/m9.figshare.29983663
title: All or nothing: highly variable species-level performance of BirdNET’s bird classifier and a new Australian frog classifier

description: Effective conservation relies on accurate data on species distributions and their change over time. Recent advances in low-cost acoustic recorders and artificial intelligence (AI) now offer powerful new ways to collect these data, revitalising the use of ecoacoustics for monitoring fauna at scale. While open-source, multi-species AI models like BirdNET are now available for most bird species, similar tools for amphibians remain limited. Here, we present the first open-source, multi-species frog classifier for 16 native species from Victoria, Australia, and evaluate its performance alongside the bird classifier BirdNET using real-world data from freshwater wetlands. Both classifiers exhibited a characteristic bimodal distribution in precision, with most species detected either with very high (&gt;90%) or very low (&lt;25%) accuracy, and relatively few species in between. For our frog classifier, misclassifications were often associated with simultaneous calls from acoustically similar frog species. For the default bird classifier, precision tended to be higher for species with short, simple, downward-sloping calls. Despite being trained on a relatively small, targeted dataset, our frog classifier achieved low false-positive rates, suggesting that modest datasets can yield robust results. These classifiers are currently most effective for rapidly screening long recordings, allowing users to focus on segments most likely to contain relevant calls while maintaining low false-positive rates. To support further development and collaboration, we release our frog classifier as an open-access tool. Broader efforts to expand multi-species classifiers across taxa and regions will be critical to realising the full potential of AI-powered ecoacoustics in biodiversity monitoring.
DOI: 10.22002/16jzw-5ea64
title: liposomes + 1uL CdvA

description: tetraether liposomes from Sulfolobus cells + 1uL CdvA
description: <strong>Tilt Series Date:</strong> 2011-07-29</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/mdj2011-07-29-4/rawdata/</p>liposomes1uLcdvA_27500x0001.mrc,  Tilt Series (Pixel Size 7.74 nm), 1.0 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mdj2011-07-29-4/rawdata/liposomes1uLcdvA_27500x0001.mrc"
        > <i class="download icon"></i> Download </a></p>

        liposomes1uLcdvA_27500x0001_full.rec,  Reconstruction (Pixel Size 1.5 nm), 303.5 MB  
        
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        > <i class="download icon"></i> Download </a></p>

        liposomes1uLcdvA_27500x0001.rec,  Reconstruction (Pixel Size 1.5 nm), 151.7 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/x3rrr-90k57
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/mdj2011-08-02-5/rawdata/</p>liposomes1uLcdvA_27500x0018.mrc,  Tilt Series (Pixel Size 7.74 nm), 1.0 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mdj2011-08-02-5/rawdata/liposomes1uLcdvA_27500x0018.mrc"
        > <i class="download icon"></i> Download </a></p>

        liposomes1uLcdvA_27500x0018_full.rec,  Reconstruction (Pixel Size 1.5 nm), 421.2 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mdj2011-08-02-5/3dimage_19428/liposomes1uLcdvA_27500x0018_full.rec"
        > <i class="download icon"></i> Download </a></p>

        liposomes1uLcdvA_27500x0018.rec,  Reconstruction (Pixel Size 1.5 nm), 210.6 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.7910/dvn/nikhl1
title: Latinobarometer 2002

description: The Latinobarometer is an annual survey conducted in 17 Latin American countries. The survey measures public opinions, attitudes and behaviors on topics covering:
Economics and International Trade;
 Integration and Trade Agreements;
 Democracy;
 Politics and Institutions;
 Civic Culture and Participation;
 Social Capital;
 Environment; 
 and Gender and Gender Discrimination
DOI: 10.22002/aqd65-kn087
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_0040_full.jpg: file associated to 3D Image #54395
description: Files available via S3 at ://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/cwl2011-12-12-23/rawdata/</p>11dec12_cryosec_pnlegfp_grid3_Batch5_0040.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/cwl2011-12-12-23/rawdata/11dec12_cryosec_pnlegfp_grid3_Batch5_0040.st"
        > <i class="download icon"></i> Download </a></p>

        11dec12_cryosec_pnlegfp_grid3_Batch5_0040_full.rec,  Reconstruction (Pixel Size 2.0 nm), 536.8 MB  
        
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        > <i class="download icon"></i> Download </a></p>

        11dec12_cryosec_pnlegfp_grid3_Batch5_0040_full.tiff,  file associated to 3D Image #54395, 1.3 MB  
        
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DOI: 10.22002/6gek3-91y76
title: COS7 VPS4DN+pNLGFP

description: Cos7 cells transfected with VPS4DN (0.5 ug) and pNLGFP provirus construct (4 ug). Sample #C107
description: <strong>Tilt Series Date:</strong> 2012-01-16</p>
<strong>Data Taken By:</strong> Cora Woodward</p>
<strong>Species / Specimen:</strong> Cercopithecus aethiops (monkey, African green)</p>
<strong>Strain:</strong> COS-7 ATCC CRL-1651</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1.5°, 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> VPS4DN construct provided by Wes Sundquist. pNLGFP construct provided by Irvin Chen, UCLA. Cells transfected, frozen and imaged at Caltech by Cora Woodward</p>
<strong>Purification / Growth Conditions / Treatment:</strong> whole cells grown on grids and transfected with lipofectamine</p>
<strong>Sample Preparation:</strong> manual blotting</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/cwl2012-01-16-1/3dimage_68971/</p>12jan16_pNLDN_AT1BT10002_full.rec,  Reconstruction (Pixel Size 2.0 nm), 722.6 MB  
        
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        > <i class="download icon"></i> Download </a></p>

        12jan16_pNLDN_AT1BT10002.mrc,  Tilt Series (Pixel Size 0.5 nm), 1.0 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        12jan16_pNLDN_AT1BT10002_full.tiff,  file associated to 3D Image #68971, 960.5 kB  
        
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DOI: 10.22002/6prpj-b7167
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/zla2010-02-18-32/rawdata/</p>10feb18a_dJnofe5_032.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/zla2010-02-18-32/rawdata/10feb18a_dJnofe5_032.mrc"
        > <i class="download icon"></i> Download </a></p>

        10feb18a_dJnofe5_032_part.rec,  Reconstruction (Pixel Size 2.384 nm), 524.3 MB  
        
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        > <i class="download icon"></i> Download </a></p>

        10feb18a_dJnofe5_032.tif,  2.0 MB  
        
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DOI: 10.22002/a7ggj-5f302
title: Sulfolobus cells synchronized for division

description: search for ESCRT in dividing cells
description: <strong>Tilt Series Date:</strong> 2011-01-14</p>
<strong>Data Taken By:</strong> Megan Dobro</p>
<strong>Species / Specimen:</strong> Sulfolobus acidocaldarius</p>
<strong>Strain:</strong> </p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-65.0°, 65.0°), step: 1°, constant angular increment, dosage: 1.5 eV/Å²,  defocus: -15.0 μm,  magnification: 18000x. </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> grown and synchronized by Rachel Samson in Stephen Bell's lab, Oxford University</p>
<strong>Purification / Growth Conditions / Treatment:</strong> grown in Brock's Medium at 80C, synchronize with Baby Machine</p>
<strong>Sample Preparation:</strong> frozen at Kay Grunewald's lab. Harrick plasma cleaner. Blotted on both sides, 5 sec, sponge for humidity</p>
  mdj2011-01-14-7_slicer3739.jpg: archaellum with basal body mdj2011-01-14-7_slicer8305.jpg: Sulfolobus acidocaldarius .  pili
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mdj2011-01-14-7/rawdata/</p>11jan14a_Bx8g3_009.mrc,  Tilt Series (Pixel Size 1.192 nm), 1.1 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        11jan14a_Bx8g3_009_full.rec,  Reconstruction (Pixel Size 2.5 nm), 734.0 MB  
        
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        > <i class="download icon"></i> Download </a></p>

        11jan14a_Bx8g3_009.rec,  Reconstruction (Pixel Size 2.5 nm), 367.0 MB  
        
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DOI: 10.22002/tmz4s-95054
title: HUVECs CHMP4A+VPS4DN

description: HUVECs cells transfected with CHMP4A+VPS4DN constructs using Nucleofector Kit. Sample# C58-2
description: <strong>Tilt Series Date:</strong> 2011-03-31</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: -7.0 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> 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/cwl2011-03-31-16/3dimage_68431/</p>11mar31a_C_58-2_020_full.rec,  Reconstruction (Pixel Size 2.0 nm), 524.3 MB  
        
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        > <i class="download icon"></i> Download </a></p>

        11mar31a_C_58-2_020.st,  Tilt Series (Pixel Size 0.5 nm), 255.9 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/cwl2011-03-31-16/rawdata/11mar31a_C_58-2_020.st"
        > <i class="download icon"></i> Download </a></p>

        11mar31a_C_58-2_020_vault.tiff,  file associated to 3D Image #68431, 730.6 kB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.15468/dl.ketmp9
title: Occurrence Download

description: A dataset containing 19817 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Linaria vulgaris",
 "Country is Russian Federation",
 "HasCoordinate is true"
 ]
}

 The dataset includes 19817 records from 79 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0044039-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.