cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.1594/pangaea.853810
title: Environmental context of all samples from the Tara Oceans Expedition (2009-2013), about depth specific features

description: The Tara Oceans Expedition (2009-2013) sampled the world oceans on board a 36 m long schooner, collecting environmental data and organisms from viruses to planktonic metazoans for later analyses using modern sequencing and state-of-the-art imaging technologies. Tara Oceans Data are particularly suited to study the genetic, morphological and functional diversity of plankton. The present data set provides environmental context to all samples from the Tara Oceans Expedition (2009-2013), including calculated averages of mesaurements made concurrently at the sampling location and depth, and calculated averages from climatologies (AMODIS, VGPM) and satellite products.
DOI: 10.22002/5z71a-sqr61
title: left handed DNA origami helixes

description: DNA origami- 10 nm gold particles on left-handed helix for handedness test
description: <strong>Tilt Series Date:</strong> 2012-04-17</p>
<strong>Data Taken By:</strong> Ariane Briegel</p>
<strong>Species / Specimen:</strong> DNAorigami</p>
<strong>Strain:</strong> </p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-63.0°, 63.0°), step: 1°, constant angular increment, dosage: 160.0 eV/Å²,  defocus: -10.0 μm,  magnification: 34000x. </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> Tim Leidl, Robert Schreiber</p>
<strong>Sample Preparation:</strong> negative stain</p>
description: Files available via S3 at ps://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/aba2012-04-17-1/rawdata/</p>DNAlefthandhelixnegstain1.mrc,  Tilt Series (Pixel Size 0.644 nm), 1.1 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/aba2012-04-17-1/rawdata/DNAlefthandhelixnegstain1.mrc"
        > <i class="download icon"></i> Download </a></p>

        DNAlefthandhelixnegstain1_full.rec,  Reconstruction (Pixel Size 1.288 nm), 516.1 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/aba2012-04-17-1/3dimage_18231/DNAlefthandhelixnegstain1_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.1594/pangaea.218135
title: (Appendix 4) Sedimentology of core LV28-42-4
DOI: 10.1594/pangaea.218145
title: (Table 2) AMS 14C dating in sediment core LV28-42-4

description: Dated material is planktonic foraminiferal tests (1000-2000 specimens of N. pachyderma sin.). Raw AMS 14C ages were converted into calendary years according to the work of Stuiver and Reimer (1993).
DOI: 10.1594/pangaea.208133
title: Mg/Ca ratio and sea-surface temperature (SST) of sediment core MD97-2120
DOI: 10.1594/pangaea.57808
title: (Table 1a) Age determinations of sediment core SO82_5-2
DOI: 10.22002/9h3ht-xa087
title: Rhodobacter sphaeroides cryosect

description: Rhodobacter sphaeroides JPA 543 with components of the cytoplmasmic array overexpressed
description: <strong>Tilt Series Date:</strong> 2013-09-13</p>
<strong>Data Taken By:</strong> Ariane Briegel</p>
<strong>Species / Specimen:</strong> Rhodobacter sphaeroides</p>
<strong>Strain:</strong> ATCC 17023</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 2°, constant angular increment, dosage: 160.0 eV/Å²,  defocus: -10.0 μm,  magnification: 41000x. </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 from Judy Armitage, sectioned by Mark Ladinsky</p>
description: Files available via S3 at ://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/aba2013-09-13-38/rawdata/</p>Rhodobactercryosectionssept0019.mrc,  Tilt Series (Pixel Size 0.26 nm), 1.7 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/aba2013-09-13-38/rawdata/Rhodobactercryosectionssept0019.mrc"
        > <i class="download icon"></i> Download </a></p>

        Rhodobactercryosectionssept0019_part61_15.rec,  Reconstruction (Pixel Size 0.52 nm), 2.8 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/aba2013-09-13-38/3dimage_31135/Rhodobactercryosectionssept0019_part61_15.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.1594/pangaea.875579
title: Environmental context of all samples from the Tara Oceans Expedition (2009-2013), about the water column features at the sampling location
DOI: 10.15468/dl.9vz2f8
title: Occurrence Download

description: A dataset containing 27 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Chaenomeles japonica",
 "Country is Lithuania",
 "HasCoordinate is true"
 ]
}

 The dataset includes 27 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002128-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.1594/pangaea.786278
title: Bulk components of sediment core SO201-2-85
DOI: 10.1594/pangaea.858201
title: Environmental context of all samples from the Tara Oceans Expedition (2009-2013), about mesoscale features

description: The Tara Oceans Expedition (2009-2013) sampled the world oceans on board a 36 m long schooner, collecting environmental data and organisms from viruses to planktonic metazoans for later analyses using modern sequencing and state-of-the-art imaging technologies. Tara Oceans Data are particularly suited to study the genetic, morphological and functional diversity of plankton. The present data set provides environmental context to all samples from the Tara Oceans Expedition (2009-2013), about mesoscale features related to the sampling date, time and location. Includes calculated averages of mesaurements made concurrently at the sampling location and depth, and calculated averages from climatologies (AMODIS, VGPM) and satellite products.
DOI: 10.22002/dcs0f-re014
title: VSVGpNL4GFP entry HUVECs

description: HUVECs 30 min post spinoculation with VSVGpNL4GFP
description: <strong>Tilt Series Date:</strong> 2011-08-12</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: -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> Proviral construct from Irvin Chen UCLA</p>
<strong>Purification / Growth Conditions / Treatment:</strong> infected VSVG pNL4GFP by spinoculation</p>
<strong>Sample Preparation:</strong> manual blot</p>
description: Files available via S3 at ps://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/cwl2011-08-12-5/rawdata/</p>11aug12_batch_0003_ns.st,  Tilt Series (Pixel Size 0.5 nm), 982.7 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/cwl2011-08-12-5/rawdata/11aug12_batch_0003_ns.st"
        > <i class="download icon"></i> Download </a></p>

        11aug12_batch_0003_ns_full.rec,  Reconstruction (Pixel Size 2.0 nm), 536.8 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/cwl2011-08-12-5/3dimage_54206/11aug12_batch_0003_ns_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.1594/pangaea.858207
title: Environmental context of all samples from the Tara Oceans Expedition (2009-2013), about water column features

description: The Tara Oceans Expedition (2009-2013) sampled the world oceans on board a 36 m long schooner, collecting environmental data and organisms from viruses to planktonic metazoans for later analyses using modern sequencing and state-of-the-art imaging technologies. Tara Oceans Data are particularly suited to study the genetic, morphological and functional diversity of plankton. The present data set provides environmental context to all samples from the Tara Oceans Expedition (2009-2013), about water column features at the sampling location. Based on in situ measurements of... at the...
DOI: 10.1594/pangaea.786134
title: Sea surface temperature calculated from alkenones of sediment core SO201-2-85
DOI: 10.1594/pangaea.786194
title: Calcium carbonate of sediment core LV29-114-3
DOI: 10.15468/dl.wpztrj
title: Occurrence Download

description: A dataset containing 1068 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Chaenomeles japonica",
 "Country is Netherlands",
 "HasCoordinate is true"
 ]
}

 The dataset includes 1068 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002130-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.1594/pangaea.786108
title: Sea surface temperature calculated from alkenones of sediment core LV29-114-3
DOI: 10.22002/7w655-f0a66
title: Ruminococcus albus

description: cellulosome
description: <strong>Tilt Series Date:</strong> 2013-07-30</p>
<strong>Data Taken By:</strong> Elitza Tocheva</p>
<strong>Species / Specimen:</strong> Ruminococcus albus</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: 180.0 eV/Å²,  defocus: -10.0 μm,  magnification: 18000x. </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> Eric Matson</p>
<strong>Purification / Growth Conditions / Treatment:</strong> cells grown on cellulose, anaerobic</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2013-07-30-11/3dimage_29417/</p>Ralbus0011_part121_5.rec,  Reconstruction (Pixel Size 2.4 nm), 712.7 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2013-07-30-11/3dimage_29417/Ralbus0011_part121_5.rec"
        > <i class="download icon"></i> Download </a></p>

        Ralbus0011.mrc,  Tilt Series (Pixel Size 0.6 nm), 3.4 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2013-07-30-11/rawdata/Ralbus0011.mrc"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.1594/pangaea.984060
title: Basic measurements of radiation at station Lampedusa (2025-05)

description: On 13 May from 17:30 UT to 18:36 UT works to uninstall the radiometers on the sun tracker. On 14 May morning until 11:01 UT works on the sun tracker to install the radiometers and to optimize levelling and pointing.
DOI: 10.22002/0xkke-jr974
title: MP P200 27.5KX

description: Mycoplasma pneumonia P200 mutant, no feature
description: <strong>Tilt Series Date:</strong> 2009-12-29</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: (-60.0°, 60.0°), step: 1°, constant angular increment, dosage: 150.0 eV/Å²,  defocus: -12.0 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>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/jsa2009-12-29-19/rawdata/</p>09dec29a_b613a_019.mrc,  Tilt Series (Pixel Size 0.774 nm), 1.0 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/jsa2009-12-29-19/rawdata/09dec29a_b613a_019.mrc"
        > <i class="download icon"></i> Download </a></p>

        09dec29a_b613a_019_full.rec,  Reconstruction (Pixel Size 1.548 nm), 419.4 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/jsa2009-12-29-19/3dimage_16806/09dec29a_b613a_019_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.1594/pangaea.984061
title: Basic measurements of radiation at station Lampedusa (2025-06)
DOI: 10.5281/zenodo.12540417
title: Environmental context modulates sociability in ube3a zebrafish mutants via alterations in sensory pathways

description: Individuals with autism spectrum disorder (ASD) have a greater prevalence of deficits in social interactions and repetitive behaviours, which are influenced by hereditary and environmental factors. How environmental factors influence genetically predisposed individuals remains unknown. Here, we provide new evidence of the interplay between social behaviour and environmental influences, by manipulating perceived safety and threat levels in ube3a mutant zebrafish, a mutation that is linked to Angelman syndrome and ASD. Mutant fish demonstrated abnormal social behaviour in an aversive custom-made Styrofoam container, whereas these abnormalities ameliorated in a preferred Plexiglass setting. Our findings were further supported by elevated anxiety levels in the mutants when they performed conventional anxiety-related tests, such as the light‒dark test (LDT) and the novel tank diving test (NTT). Additionally, neural activity mapping using c-Fos in situ hybridization revealed differences in activation patterns in the brains of the mutants. Importantly, we performed an overrepresentation analysis (ORA) using RNA sequencing data from ube3a mutants and integrating datasets from human diseases. We identified the upregulation of vision- and comorbidity-related genes in ube3a mutants and alterations in sensory pathways, highlighting that abnormal processing of visual information is the cause of increased anxiety levels, resulting in decreased social interaction in a stressful Styrofoam environment. Our findings underscore the crucial impact of environmental factors on social behaviour and indicate that therapeutic options for ASD that focus on adjusting environmental contexts to modify perceived stimuli may ameliorate ASD-like behaviours.
DOI: 10.5281/zenodo.12540418
title: Environmental context modulates sociability in ube3a zebrafish mutants via alterations in sensory pathways

description: Individuals with autism spectrum disorder (ASD) have a greater prevalence of deficits in social interactions and repetitive behaviours, which are influenced by hereditary and environmental factors. How environmental factors influence genetically predisposed individuals remains unknown. Here, we provide new evidence of the interplay between social behaviour and environmental influences, by manipulating perceived safety and threat levels in ube3a mutant zebrafish, a mutation that is linked to Angelman syndrome and ASD. Mutant fish demonstrated abnormal social behaviour in an aversive custom-made Styrofoam container, whereas these abnormalities ameliorated in a preferred Plexiglass setting. Our findings were further supported by elevated anxiety levels in the mutants when they performed conventional anxiety-related tests, such as the light‒dark test (LDT) and the novel tank diving test (NTT). Additionally, neural activity mapping using c-Fos in situ hybridization revealed differences in activation patterns in the brains of the mutants. Importantly, we performed an overrepresentation analysis (ORA) using RNA sequencing data from ube3a mutants and integrating datasets from human diseases. We identified the upregulation of vision- and comorbidity-related genes in ube3a mutants and alterations in sensory pathways, highlighting that abnormal processing of visual information is the cause of increased anxiety levels, resulting in decreased social interaction in a stressful Styrofoam environment. Our findings underscore the crucial impact of environmental factors on social behaviour and indicate that therapeutic options for ASD that focus on adjusting environmental contexts to modify perceived stimuli may ameliorate ASD-like behaviours.
DOI: 10.15468/dl.qkrt6t
title: Occurrence Download

description: A dataset containing 27 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Country is Mexico",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Azadirachta indica"
 ]
}

 The dataset includes 27 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002126-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22002/0rpst-vjq09
title: sporulating Alongum purified sacculi

description: Alongum purified sacculi
description: <strong>Tilt Series Date:</strong> 2010-12-17</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: -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>Purification / Growth Conditions / Treatment:</strong> sporulation medium</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/etl2010-12-17-9/rawdata/</p>10dec17a_pos3_2_029.mrc,  Tilt Series (Pixel Size 0.95 nm), 729.8 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2010-12-17-9/rawdata/10dec17a_pos3_2_029.mrc"
        > <i class="download icon"></i> Download </a></p>

        29_full.rec,  Reconstruction (Pixel Size 1.9 nm), 786.4 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2010-12-17-9/3dimage_25927/29_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/tnwvp-7ys23
title: B. subtilis minicell lysate

description: B subtilis strain DK 720 minicell lysate
description: <strong>Tilt Series Date:</strong> 2013-09-05</p>
<strong>Data Taken By:</strong> Ariane Briegel</p>
<strong>Species / Specimen:</strong> Bacillus subtilis</p>
<strong>Strain:</strong> </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: -8.0 μm,  magnification: 34000x. </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> Dan Kearns</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Minicell isolation and Lysozyme lysis</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/aba2013-09-05-18/rawdata/</p>Bacilluslysemini0020.mrc,  Tilt Series (Pixel Size 0.32 nm), 3.4 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/aba2013-09-05-18/rawdata/Bacilluslysemini0020.mrc"
        > <i class="download icon"></i> Download </a></p>

        Bacilluslysemini0020_full.rec,  Reconstruction (Pixel Size 1.28 nm), 712.7 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/aba2013-09-05-18/3dimage_30435/Bacilluslysemini0020_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.15468/dl.fv9eua
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Pterorhinus albogularis",
 "Country is Chinese Taipei",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002129-250827131500795/datasets/export for details.
DOI: 10.22002/q40ha-md960
title: MP C1 27.5KX

description: Mycoplasma pneumonia C1 mutant
description: <strong>Tilt Series Date:</strong> 2010-01-01</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: (-60.0°, 60.0°), step: 1°, constant angular increment, dosage: 150.0 eV/Å²,  defocus: -12.0 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>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/jsa2010-01-01-10/rawdata/</p>10jan01b_B945b_008.mrc,  Tilt Series (Pixel Size 0.774 nm), 1.0 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/jsa2010-01-01-10/rawdata/10jan01b_B945b_008.mrc"
        > <i class="download icon"></i> Download </a></p>

        10jan01b_B945b_008_full.rec,  Reconstruction (Pixel Size 1.548 nm), 419.4 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/jsa2010-01-01-10/3dimage_16425/10jan01b_B945b_008_full.rec"
        > <i class="download icon"></i> Download </a></p>