cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17632/3x6yp5jdjc.2
title: Critical Role of Sea Spray Aerosol Production Pathways in Particulate Transfer Across the Sea-Air Interface

description: Sea spray aerosols (SSA) play a crucial role in transferring particulates from oceanic water to the atmosphere. The production pathways of SSA from bubble bursting include jet drops from bubble cavity collapse, surface film drops from bubble cap disintegration and collision film drops from underwater bubble collision. While the physical formation of these drops has been extensively studied, the mechanisms governing particle enrichment and transfer within these individual drop types remain poorly understood. This study systematically investigates particle enrichment and transfer across the three types of drops. While previous studies suggested only hydrophobic particles could be enriched by SSA, our findings reveal that both hydrophilic and hydrophobic particles can be enriched in all drop types, with surface film drops exhibiting significantly greater enrichment than previously reported. We propose for the first time that particle enrichment occurs during bubble film drainage because particles tend to remain within the thinning film rather than being uniformly drained out, leading to additional concentration within the film. These findings enhance our understanding of mass transfer at water-air interface.
DOI: 10.22002/1vrfr-em163
title: Vesicle CF4Q 4111V

description: Sample Vesicle CF4Q 4111V
description: <strong>Tilt Series Date:</strong> 2014-12-10</p>
<strong>Data Taken By:</strong> Ariane Briegel</p>
<strong>Species / Specimen:</strong> Escherichia coli in vitro</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: -10.0 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> Lynmarie Thompson</p>
<strong>Sample Preparation:</strong> samples were frozen on 11/07/14</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/aba2014-12-10-9/rawdata/</p>Vesicle411VNEW0009.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/aba2014-12-10-9/rawdata/Vesicle411VNEW0009.mrc"
        > <i class="download icon"></i> Download </a></p>

        Vesicle411VNEW0009_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/aba2014-12-10-9/3dimage_48704/Vesicle411VNEW0009_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.15468/dl.fcp7ku
title: Occurrence Download

description: A dataset containing 10 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Agrostis coarctata hyperborea, Agrostis coarctata syreistschikowii, Agrostis coarctata syreitchekowii, Agrostis coarctata trinii, Agrostis coarctata nyaradyana, Agrostis coarctata subalpina, Agrostis decumbens coarctata, Agrostis ericetorum, Agrostis flaccida trinii, Agrostis flaccida trinii, Agrostis hyperborea, Agrostis hyperborea, Agrostis hyperborea, Agrostis kronokensis, Agrostis kudoi, Agrostis kudoi inermis, Agrostis kunmingensis, Agrostis macrostachya, Agrostis marschalliana, Agrostis nivalis, Agrostis palustris coarctata, Agrostis planifolia, Agrostis planifolia calamagrostoides, Agrostis pusilla, Agrostis rubra ericetorum, Agrostis rubra ericetorum, Agrostis rubra ericetorum, Agrostis rubra hyperborea, Agrostis rubra surculifera, Agrostis rubra surculifera, Agrostis rubra vinealis, Agrostis ruprechtii, Agrostis setifolia, Agrostis setifolia, Agrostis signata coarctata, Agrostis stolonifera coarctata, Agrostis stolonifera coarctata, Agrostis stolonifera coarctata, Agrostis stolonifera coarctata, Agrostis stolonifera coarctata, Agrostis stolonifera coarctata, Agrostis stricta, Agrostis stricta, Agrostis stricta syreistchikovii, Agrostis stricta syreistchikowii, Agrostis stricta syreistschikowii, Agrostis stricta syreitschikowii, Agrostis sublaevipes, Agrostis sublaevipes, Agrostis sublaevirens)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen, Machine Observation)"
 ]
 }
 },
 "Continent is Europe",
 "Year is greater than or equal to 1980",
 "Year is less than or equal to 2024"
 ]
}

 The dataset includes 10 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0047151-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kpzms6
title: Occurrence Download

description: A dataset containing 139 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Serranochromis angusticeps)",
 "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 139 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0047152-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22002/vebv2-kds31
title: JT5_cellulosome

description: cellulosome
description: <strong>Tilt Series Date:</strong> 2013-06-17</p>
<strong>Data Taken By:</strong> Elitza Tocheva</p>
<strong>Species / Specimen:</strong> Bacteroidetes</p>
<strong>Strain:</strong> JT5-1</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> UCSF Tomo</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> ZAS-1</p>
  etl2013-06-17-5_slicer20247.jpg: Fuzzy density and protuberances - Nicholas
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2013-06-17-5/rawdata/</p>jt50005.mrc,  Tilt Series (Pixel Size 0.48 nm), 3.4 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2013-06-17-5/rawdata/jt50005.mrc"
        > <i class="download icon"></i> Download </a></p>

        jt50005_full.rec,  Reconstruction (Pixel Size 1.92 nm), 445.4 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2013-06-17-5/3dimage_27519/jt50005_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/6wy61-1va07
title: dK203 uninduced grown 2 days

description: dK203 is the dQ167 strain in which dK has also been deactivated. It is only inducible for dQ.
description: <strong>Tilt Series Date:</strong> 2014-12-21</p>
<strong>Data Taken By:</strong> Poorna Subramanian</p>
<strong>Species / Specimen:</strong> Magnetospirillum magneticum </p>
<strong>Strain:</strong> deltaQ 167</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1.0°, constant angular increment, dosage: 100.0 eV/Å²,  defocus: -15.0 μm,  magnification: 18000x. </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> Arash Komeili</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/psa2014-12-21-19/rawdata/</p>dkuninduced_atlas6_montage10004.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/psa2014-12-21-19/rawdata/dkuninduced_atlas6_montage10004.mrc"
        > <i class="download icon"></i> Download </a></p>

        dkuninduced_atlas6_montage10004_part121_19.rec,  Reconstruction (Pixel Size 2.4 nm), 623.6 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/psa2014-12-21-19/3dimage_49896/dkuninduced_atlas6_montage10004_part121_19.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.17632/d29csxjjtc
title: Supplementary Material for Stable isotope analysis reveals dietary and foraging ecology in Neotropical birds

description: This supplementary material provides additional analyses related to the article Stable isotope analysis reveals dietary and foraging ecology in Neotropical birds. It includes complementary information on species-level variation that helps to contextualize and expand upon the results presented in the main manuscript.
The file includes mean isotopic values for sampled species (δ¹³C and δ¹⁵N), Bayesian regression outputs, pairwise comparisons across dietary guilds and foraging strata, and maps of sampling sites.
DOI: 10.22002/9jkc7-sh385
title: Sulfolobus Solfactaricus P2

description: Looking for dividing cells
description: <strong>Tilt Series Date:</strong> 2014-03-13</p>
<strong>Data Taken By:</strong> Rasika Ramdasi</p>
<strong>Species / Specimen:</strong> Sulfolobus solfataricus </p>
<strong>Strain:</strong> P2</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-55.0°, 55.0°), step: 1.0°, constant angular increment, dosage: 180.0 eV/Å²,  defocus: -10.0 μm,  magnification: 18000x. </p>
<strong>Microscope:</strong> Caltech Polara</p>
<strong>Acquisition Software:</strong> UCSFTomo</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> UCSF tomo</p>
<strong>Sample Preparation:</strong> grown at home, synchronized using primary baby machine</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/rra2014-03-13-3/rawdata/</p>atlas20003.mrc,  Tilt Series (Pixel Size 0.63 nm), 3.2 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/rra2014-03-13-3/rawdata/atlas20003.mrc"
        > <i class="download icon"></i> Download </a></p>

        atlas20003_part111_23.rec,  Reconstruction (Pixel Size 2.52 nm), 623.6 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/rra2014-03-13-3/3dimage_40112/atlas20003_part111_23.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.17632/d29csxjjtc.1
title: Supplementary Material for Stable isotope analysis reveals dietary and foraging ecology in Neotropical birds

description: This supplementary material provides additional analyses related to the article Stable isotope analysis reveals dietary and foraging ecology in Neotropical birds. It includes complementary information on species-level variation that helps to contextualize and expand upon the results presented in the main manuscript.
The file includes mean isotopic values for sampled species (δ¹³C and δ¹⁵N), Bayesian regression outputs, pairwise comparisons across dietary guilds and foraging strata, and maps of sampling sites.
DOI: 10.17632/nfw4mcshkp
title: western blot original images

description: western blot to compare differnces in key protein expression before and after hypoxia
DOI: 10.22002/ym36e-4wy34
title: CA tubes

description: Received sample frozen on grids (1/1)
description: <strong>Tilt Series Date:</strong> 2012-11-25</p>
<strong>Data Taken By:</strong> Cora Woodward</p>
<strong>Species / Specimen:</strong> Unspecified</p>
<strong>Strain:</strong> None</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1.0°, constant angular increment, dosage: 150.0 eV/Å²,  defocus: None 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> Sundquist lab (Univ. Utah): Yen-Li Li, Vish Chandrasekaran</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/cwl2012-11-25-25/rawdata/</p>12nov25_CAtube_grid2_1_AT1bBT10018.mrc,  Tilt Series (Pixel Size 0.33 nm), 3.4 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/cwl2012-11-25-25/rawdata/12nov25_CAtube_grid2_1_AT1bBT10018.mrc"
        > <i class="download icon"></i> Download </a></p>

        12nov25_CAtube_grid2_1_AT1bBT10018_full.rec,  Reconstruction (Pixel Size 1.32 nm), 353.3 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/cwl2012-11-25-25/3dimage_23961/12nov25_CAtube_grid2_1_AT1bBT10018_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.17632/nfw4mcshkp.1
title: western blot original images

description: western blot to compare differnces in key protein expression before and after hypoxia
DOI: 10.22002/7wnzt-k7890
title: Falke C+O3

description: Crosslinking sample C+O3
description: <strong>Tilt Series Date:</strong> 2014-08-07</p>
<strong>Data Taken By:</strong> Ariane Briegel</p>
<strong>Species / Specimen:</strong> Escherichia coli in vitro</p>
<strong>Strain:</strong> </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: 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> Joe Falke</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/aba2014-08-07-4/rawdata/</p>FalkeCplusO3tomo0002.mrc,  Tilt Series (Pixel Size 0.64 nm), 1.7 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/aba2014-08-07-4/rawdata/FalkeCplusO3tomo0002.mrc"
        > <i class="download icon"></i> Download </a></p>

        FalkeCplusO3tomo0002_full.rec,  Reconstruction (Pixel Size 2.56 nm), 712.7 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/aba2014-08-07-4/3dimage_45303/FalkeCplusO3tomo0002_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.17632/wp9fht9k3k
title: Retinol Binding Protein 4 reactivates latent HIV-1 by triggering canonical NF-κB, JAK/STAT5 and JNK signalling

description: Reactivation of the latent viral reservoirs is crucial for a cure of HIV/AIDS. However, current latency reversing agents are inefficient and the endogenous factors that have the potential to reactivate HIV in vivo remain poorly understood. To identify natural activators of latent HIV-1, we screened a comprehensive peptide/protein library derived from human hemofiltrate, representing the entire blood peptidome, using J-Lat cell lines harboring transcriptionally silent HIV-1 GFP reporter viruses. Fractions potently reactivating HIV-1 from latency contained human Retinol Binding Protein 4 (RBP4), the carrier of retinol (vitamin A). We found that retinol-bound holo-RBP4 but not retinol-free apo-RBP4 strongly reactivates HIV-1 in a variety of latently infected T cell lines. Functional analyses indicate that this reactivation involves activation of the canonical NF-B pathway and is complemented by JAK/STAT5 and JNK signalling but does not require retinoic acid production. High levels of RBP4 were detected in plasma from both healthy individuals and people living with HIV-1. Physiological concentrations of RBP4 induced significant viral reactivation in latently infected cells from individuals on long-term antiretroviral therapy with undetectable viral loads. As a potent natural HIV-1 latency-reversing agent, RBP4 offers a novel approach to activating the latent reservoirs and bringing us closer to a cure.
DOI: 10.17632/wp9fht9k3k.2
title: Retinol Binding Protein 4 reactivates latent HIV-1 by triggering canonical NF-κB, JAK/STAT5 and JNK signalling

description: Reactivation of the latent viral reservoirs is crucial for a cure of HIV/AIDS. However, current latency reversing agents are inefficient and the endogenous factors that have the potential to reactivate HIV in vivo remain poorly understood. To identify natural activators of latent HIV-1, we screened a comprehensive peptide/protein library derived from human hemofiltrate, representing the entire blood peptidome, using J-Lat cell lines harboring transcriptionally silent HIV-1 GFP reporter viruses. Fractions potently reactivating HIV-1 from latency contained human Retinol Binding Protein 4 (RBP4), the carrier of retinol (vitamin A). We found that retinol-bound holo-RBP4 but not retinol-free apo-RBP4 strongly reactivates HIV-1 in a variety of latently infected T cell lines. Functional analyses indicate that this reactivation involves activation of the canonical NF-B pathway and is complemented by JAK/STAT5 and JNK signalling but does not require retinoic acid production. High levels of RBP4 were detected in plasma from both healthy individuals and people living with HIV-1. Physiological concentrations of RBP4 induced significant viral reactivation in latently infected cells from individuals on long-term antiretroviral therapy with undetectable viral loads. As a potent natural HIV-1 latency-reversing agent, RBP4 offers a novel approach to activating the latent reservoirs and bringing us closer to a cure.
DOI: 10.22002/m3e55-smp24
title: NLRP3

description: Lysate from macrophages expressing ASC / Caspase-1-CARD / NLRP3-PYD-NBD
description: <strong>Tilt Series Date:</strong> 2014-03-17</p>
<strong>Data Taken By:</strong> Ariane Briegel</p>
<strong>Species / Specimen:</strong> Macrophage lysate</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: -10.0 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> Hao Wu</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/aba2014-03-17-10/rawdata/</p>NLRP3_34k0010.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/aba2014-03-17-10/rawdata/NLRP3_34k0010.mrc"
        > <i class="download icon"></i> Download </a></p>

        NLRP3_34k0010_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/aba2014-03-17-10/3dimage_40187/NLRP3_34k0010_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.17632/yscvt9yw85
title: Iron Oxide-based SERS Bioprobe for Detecting Tumor Cells in Serous Effusion

description: We developed an iron oxide-based surface-enhanced Raman spectroscopy (SERS) bioprobe for detecting tumor cells in serous effusions. First, we characterized the bioprobe. Second, we validated its targeting ability and specificity. We first incubated the bioprobe with its target tumor cells for varying durations to determine the optimal incubation time. Then, we incubated it with different tumor cells to observe its specific targeting capability. Next, we evaluated its performance in detecting lung cancer cells in simulated pleural effusion and ovarian cancer cells in ascites. We incubated the IGR bioprobe with pleural effusion containing lung cancer cells and with pleural effusion without lung cancer cells, respectively; additionally, we incubated the IGR bioprobe (without antibodies) with pleural effusion containing lung cancer cells. We then compared the SERS signals among the three groups. We prepared simulated samples with tumor cells at varying concentrations and measured their average Raman signals. Subsequently, we established a classification model to differentiate tumor cells based on their concentrations. Finally, we validated the model using 105 clinical samples and employed machine learning to enhance the accuracy of the SERS bioprobe in classifying tumor cells according to their concentration.
DOI: 10.22002/gm9pw-cvj76
title: JT5_cellulosome

description: cellulosome
description: <strong>Tilt Series Date:</strong> 2013-06-17</p>
<strong>Data Taken By:</strong> Elitza Tocheva</p>
<strong>Species / Specimen:</strong> Bacteroidetes</p>
<strong>Strain:</strong> JT5-1</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> UCSF Tomo</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> ZAS-1</p>
  etl2013-06-17-7_slicer20248.jpg: What are these particles? - Nicholas
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2013-06-17-7/rawdata/</p>jt50007.mrc,  Tilt Series (Pixel Size 0.48 nm), 3.4 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2013-06-17-7/rawdata/jt50007.mrc"
        > <i class="download icon"></i> Download </a></p>

        jt50007_full.rec,  Reconstruction (Pixel Size 1.92 nm), 445.4 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2013-06-17-7/3dimage_27523/jt50007_full.rec"
        > <i class="download icon"></i> Download </a></p>