cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.22002/8gxdf-kvy73
title: Vibrio cholerae PM16

description: delta vc1403
description: <strong>Tilt Series Date:</strong> 2015-07-15</p>
<strong>Data Taken By:</strong> Ariane Briegel</p>
<strong>Species / Specimen:</strong> Vibrio cholerae</p>
<strong>Strain:</strong> O1 biovar El Tor</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> Simon Ringgaard</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/aba2015-07-15-70/rawdata/</p>Vibriodelta1403doubleMCP0037.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/aba2015-07-15-70/rawdata/Vibriodelta1403doubleMCP0037.mrc"
        > <i class="download icon"></i> Download </a></p>

        Vibriodelta1403doubleMCP0037_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/aba2015-07-15-70/3dimage_59333/Vibriodelta1403doubleMCP0037_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/v6mgt-cq680
title: T9_wt

description: This was a wt sample prepared with Paul when he was visiting
description: <strong>Tilt Series Date:</strong> 2016-04-30</p>
<strong>Data Taken By:</strong> Poorna Subramanian</p>
<strong>Species / Specimen:</strong> Porphyromonas gingivalis</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: 140.0 eV/Å²,  defocus: -10.0 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> Paul Veith and Eric Reynolds</p>
<strong>Purification / Growth Conditions / Treatment:</strong> See pages 84-86</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/psa2016-04-30-12/rawdata/</p>atlas10009.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/psa2016-04-30-12/rawdata/atlas10009.mrc"
        > <i class="download icon"></i> Download </a></p>

        atlas10009_full.rec,  Reconstruction (Pixel Size 1.56 nm), 445.4 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/psa2016-04-30-12/3dimage_74531/atlas10009_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/gcf3j-vj746
title: M. xanthus PilY1.3-sfGFP

description: PilY1.3-sfGFP (SA7661+pMAT321)Grid box YWC262
description: <strong>Tilt Series Date:</strong> 2017-11-27</p>
<strong>Data Taken By:</strong> Yi-Wei Chang</p>
<strong>Species / Specimen:</strong> Myxococcus xanthus</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: -6.0 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> Strain form Lotte Sogaard-Andersen</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2017-11-27-66/rawdata/</p>20171127_YWC262_10068.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/ycw2017-11-27-66/rawdata/20171127_YWC262_10068.mrc"
        > <i class="download icon"></i> Download </a></p>

        20171127_YWC262_10068_full.rec,  Reconstruction (Pixel Size 1.56 nm), 534.5 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2017-11-27-66/3dimage_90667/20171127_YWC262_10068_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/qytse-8sd46
title: H. pylori 26695 WT

description: grid box YWC259
description: <strong>Tilt Series Date:</strong> 2017-07-06</p>
<strong>Data Taken By:</strong> Yi-Wei Chang</p>
<strong>Species / Specimen:</strong> Helicobacter pylori</p>
<strong>Strain:</strong> 26695</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: -6.0 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> Strain and sample prepared by Carrie Shaffer</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2017-07-06-86/rawdata/</p>20170706_YWC259_10087.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/ycw2017-07-06-86/rawdata/20170706_YWC259_10087.mrc"
        > <i class="download icon"></i> Download </a></p>

        20170706_YWC259_10087.rec,  Reconstruction (Pixel Size 1.56 nm), 1.1 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2017-07-06-86/3dimage_85821/20170706_YWC259_10087.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.57996/cran.ceres-2784
title: Data for Tracing the botanical origins of UK heather honey by relative quantification of plant DNA

description: Date of data collection: 2021 - 2025 Geographic location of data collection: Cranfield University, College Road, Cranfield, MK43 0AL, UK. This repository contains the following data files: a) a.honey_Cq_RQ_DODD2025.csv :a dataset containing qPCR amplification (Cq value) for all honey samples , relative quantification calculation and the resulting class group. b) b.BLAST_ling_DODD2025.pdf :complete in silico analysis of the Calluna vulgaris marker using PrimerBLAST. c) c.BLAST_bell_DODD2025.pdf :complete in silico analysis of the Erica cinerea marker using PrimerBLAST. DATA-SPECIFIC INFORMATION FOR: [a.honey_Cq_RQ_DODD2025.csv] Number of variables: 15 Number of cases/rows: 271 Variable List: The Cq values from reaction 1-3 for trnL_P6 marker, The Cq values from reaction 1-3 for CV_trnL marker, The Cq values from reaction 1-3 for EC_trnL marker, The relative quantity (RQ) of ling, The relative quantity (RQ) of bell, The standard deviation (SD) of RQ of ling, The SD of RQ of bell, the final class of ling, the final class of bell. Missing data codes: na: not amplified, N/A: not applicable Specialized formats or other abbreviations used: ling: Calluna vulgaris plant, bell: Erica cinerea plant, final class calculated according to RQ value for ling or bell (dominant: &gt; 0.45, secondary: 0.16 – 0.45, important minor: 0.03 – 0.16, trace: 0.03 – 0.01, sporadic: 0.01 – 0.001 and none: &lt;0.001) Grant: BB/T008776/1
description: Heather honey is an important honey type produced in the UK, valued for its unique flavour, thixotropic texture and health promoting properties. Botanical authentication can be challenging due to the natural variability in honey composition and typical pollen analysis relies heavily on expert knowledge. As an alternative, real-time PCR (qPCR) can be a rapid and robust method to identify floral species in honey. Therefore, species-specific markers for Calluna vulgaris and Erica cinerea were developed and used to quantify 266 honey samples relative to the plant trnL P6 loop. The method classed 94% of 234 heather honeys as containing &gt; 3% heather DNA, with 68% classified as dominant (&gt; 45%) for ling heather origin. Moreover, high specificity was achieved with negligible amplification in the 32 non-heather honeys. Our qPCR method offered comparable results to melissopalynology, DNA metabarcoding and digital PCR, showing potential as an alternative and accessible method for botanical authentication of heather honeys.
DOI: 10.17632/vxtgv3k5vd
title: A frontal-temporal network for motoric synchronization to both auditory and visual rhythms

description: Data and MATLAB scripts for peer review.
DOI: 10.17632/vxtgv3k5vd.2
title: A frontal-temporal network for motoric synchronization to both auditory and visual rhythms

description: Data and MATLAB scripts for peer review.
DOI: 10.17632/x54scv9w28
title: RNA exosome component EXOSC10 variants identified in a patient with premature ovarian insufficiency SUPPLEMENTARY DATA

description: Premature ovarian insufficiency (POI) impacts ~1-3.7% of women under the age of 40 globally and is characterised by an absence or complete loss of ovarian function. POI is clinically heterogenous in nature and researchers have identified &gt;100 causative genes harbouring variants responsible for POI thus far. Genes identified to date include those associated with cell differentiation/development, mitochondrial maintenance, hormone receptors, transcription/translation factors, DNA repair/replication, and metabolic processes. Genes encoding cell components that facilitate these processes should therefore also be considered in POI gene candidature. The RNA exosome is a critical component in RNA processing, degradation, and biogenesis in eukaryotic cells. Catalytic activity of the RNA exosome is supplied by two subunits, DIS3 and EXOSC10. Dysregulation of RNA exosome function results in conditions known as exosomopathies that have a broad spectrum of phenotypic severity. RNA transcript regulation is essential in transcriptionally inactive maturing mammalian oocytes with its disruption negatively impacting meiosis and fertilization. Notably, oocyte depletion of Exosc10 significantly impacts the fertility of female mice. Herein we identified, via whole exome sequencing, the first instance of a human POI patient with an EXOSC10 homozygous missense variant. Using Drosophila melanogaster we modelled the impact of knockdown of the EXOSC10 ortholog, Rrp6, on both somatic and germline ovarian cells. We observed that Rrp6 is required in ovarian development in Drosophila. Due to the conserved role of EXOSC10 in fertility maintenance across species we contend that variants in EXOSC10 identified in POI patients may be causative.
DOI: 10.22002/6s5zg-zqm82
title: B/r H266 / R1-16 conjugation

description: Grid box YWC238
description: <strong>Tilt Series Date:</strong> 2017-01-19</p>
<strong>Data Taken By:</strong> Yi-Wei Chang</p>
<strong>Species / Specimen:</strong> Escherichia coli</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: 150.0 eV/Å²,  defocus: -6.0 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> Strain and sample prepared by Carrie Shaffer</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2017-01-19-5/rawdata/</p>20160119_YWC238_10005.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/ycw2017-01-19-5/rawdata/20160119_YWC238_10005.mrc"
        > <i class="download icon"></i> Download </a></p>

        20160119_YWC238_10005.rec,  Reconstruction (Pixel Size 1.56 nm), 1.1 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2017-01-19-5/3dimage_81177/20160119_YWC238_10005.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.17632/x54scv9w28.1
title: RNA exosome component EXOSC10 variants identified in a patient with premature ovarian insufficiency SUPPLEMENTARY DATA

description: Premature ovarian insufficiency (POI) impacts ~1-3.7% of women under the age of 40 globally and is characterised by an absence or complete loss of ovarian function. POI is clinically heterogenous in nature and researchers have identified &gt;100 causative genes harbouring variants responsible for POI thus far. Genes identified to date include those associated with cell differentiation/development, mitochondrial maintenance, hormone receptors, transcription/translation factors, DNA repair/replication, and metabolic processes. Genes encoding cell components that facilitate these processes should therefore also be considered in POI gene candidature. The RNA exosome is a critical component in RNA processing, degradation, and biogenesis in eukaryotic cells. Catalytic activity of the RNA exosome is supplied by two subunits, DIS3 and EXOSC10. Dysregulation of RNA exosome function results in conditions known as exosomopathies that have a broad spectrum of phenotypic severity. RNA transcript regulation is essential in transcriptionally inactive maturing mammalian oocytes with its disruption negatively impacting meiosis and fertilization. Notably, oocyte depletion of Exosc10 significantly impacts the fertility of female mice. Herein we identified, via whole exome sequencing, the first instance of a human POI patient with an EXOSC10 homozygous missense variant. Using Drosophila melanogaster we modelled the impact of knockdown of the EXOSC10 ortholog, Rrp6, on both somatic and germline ovarian cells. We observed that Rrp6 is required in ovarian development in Drosophila. Due to the conserved role of EXOSC10 in fertility maintenance across species we contend that variants in EXOSC10 identified in POI patients may be causative.
DOI: 10.17632/6z6jyvpt2b
title: Unveiling Consumption Patterns during COVID-19: Insights from Credit Cards

description: Replication material for the paper "Unveiling Consumption Patterns during COVID-19: Insights from Credit Cards" submitted to Economic Modelling
DOI: 10.17632/6z6jyvpt2b.1
title: Unveiling Consumption Patterns during COVID-19: Insights from Credit Cards

description: Replication material for the paper "Unveiling Consumption Patterns during COVID-19: Insights from Credit Cards" submitted to Economic Modelling
DOI: 10.17632/3fy2pj3cr6
title: Planas-Paz et al - 2025 - Targeting ATR signaling in sarcoma with homologous recombination deficiency

description: Supporting data values for CELL REPORTS MEDICINE submission:

Homologous recombination deficiency (HRD) has emerged as a key vulnerability in selected cancer types and is associated with response to platinum and PARPi-based treatment strategies. However, additional biomarkers and targeted therapy options are needed to broaden the range of patients that could benefit from this therapeutic niche. Here, we show that the SARC-HRD signature, composed of ten genes of the homologous recombination repair pathway, stratifies a cohort of sarcoma patients, and associates with genomic biomarkers of HRD, with disease progression and with the CINSARC prognostic signature. Equivalently to CINSARC, high levels of SARC-HRD are associated with poor metastasis-free survival, underscoring the potential of SARC-HRD to predict disease outcome. By pharmacotyping patient-derived cell models, we identified promising drug targets within the DNA damage response for sarcoma with HRD traits. Inhibition of ATR, CHK1 and WEE1 elicited synthetic lethality in sarcoma cells with HRD, which concomitantly showed an upregulation of ATR signaling. Combinatorial drug testing further revealed synergistic drug combinations between ATRi, WEE1i, PARP1/2i and chemotherapeutic agents with potential clinical impact. Mechanistically, targeting ATR signaling at multiple levels induced a replication defect and apoptotic cell death. Taken together, our results demonstrate the therapeutic benefit of targeting DDR mechanisms in sarcoma with HRDness traits and their potential clinical utility for treating a broader spectrum of tumor types.
DOI: 10.22002/zg7zs-ep453
title: Cos7 cells

description: Looking for midbodies or Tunelling nanotubes
description: <strong>Tilt Series Date:</strong> 2015-03-05</p>
<strong>Data Taken By:</strong> Rasika Ramdasi</p>
<strong>Species / Specimen:</strong> Cos7</p>
<strong>Strain:</strong> Cos7 cells</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1.5°, constant angular increment, dosage: 100.0 eV/Å²,  defocus: -6.0 μm,  magnification: 22500x. </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> Synchronized cells with Thymidine 2mM. Frozen after 14 hours of washing.</p>
  rra2015-03-05-4_slicer12855.jpg: 2 nm filaments
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/rra2015-03-05-4/3dimage_52601/</p>atlas10004.rec,  Reconstruction (Pixel Size 2.0 nm), 1.2 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/rra2015-03-05-4/3dimage_52601/atlas10004.rec"
        > <i class="download icon"></i> Download </a></p>

        atlas10004.mrc,  Tilt Series (Pixel Size 0.5 nm), 2.3 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/rra2015-03-05-4/rawdata/atlas10004.mrc"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.17632/3fy2pj3cr6.1
title: Planas-Paz et al - 2025 - Targeting ATR signaling in sarcoma with homologous recombination deficiency

description: Supporting data values for CELL REPORTS MEDICINE submission:

Homologous recombination deficiency (HRD) has emerged as a key vulnerability in selected cancer types and is associated with response to platinum and PARPi-based treatment strategies. However, additional biomarkers and targeted therapy options are needed to broaden the range of patients that could benefit from this therapeutic niche. Here, we show that the SARC-HRD signature, composed of ten genes of the homologous recombination repair pathway, stratifies a cohort of sarcoma patients, and associates with genomic biomarkers of HRD, with disease progression and with the CINSARC prognostic signature. Equivalently to CINSARC, high levels of SARC-HRD are associated with poor metastasis-free survival, underscoring the potential of SARC-HRD to predict disease outcome. By pharmacotyping patient-derived cell models, we identified promising drug targets within the DNA damage response for sarcoma with HRD traits. Inhibition of ATR, CHK1 and WEE1 elicited synthetic lethality in sarcoma cells with HRD, which concomitantly showed an upregulation of ATR signaling. Combinatorial drug testing further revealed synergistic drug combinations between ATRi, WEE1i, PARP1/2i and chemotherapeutic agents with potential clinical impact. Mechanistically, targeting ATR signaling at multiple levels induced a replication defect and apoptotic cell death. Taken together, our results demonstrate the therapeutic benefit of targeting DDR mechanisms in sarcoma with HRDness traits and their potential clinical utility for treating a broader spectrum of tumor types.
DOI: 10.15468/dl.c3gj9e
title: Occurrence Download

description: A dataset containing 242 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cairina moschata",
 "Country is Japan",
 "HasCoordinate is true"
 ]
}

 The dataset includes 242 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005747-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17632/595dvg845z
title: Intraspecific variation in rapid cold hardening and acclimation of the adventive parrot’s feather weevil, Phytobius (=Parenthis) vestitus, in the southern USA

description: Plasticity in thermal tolerance, expressed through acclimation or rapid cold hardening, for example, provides organisms with a mechanism to deal with unexpected and often rapid changes in the thermal environment. Spatial variation in response to high or low temperatures may occur due to evolutionary adaptation, particularly if a fitness increase coincides with the ability to respond quickly to environmental change. Thermal tolerances of beneficial insects used for biological control dictate where and under what thermal conditions the insects will provide value to management programs. We investigated two aspects of thermal phenotypic plasticity in response to thermal conditions using four populations of the adventive parrot’s feather weevil, Phytobius vestitus, from the southern USA. At low temperatures, we determined the presence and variation in rapid cold hardening in two of the four populations using two temperature ramping rates. At high temperatures, all P. vestitus populations displayed a significant heat acclimation response, documented as elevated maximum critical and lethal temperatures after acclimation. The relationship between population mean thermal tolerance or plasticity and climate of the source population was not consistent. These results demonstrate the presence of geographic variation in phenotypic plasticity in response to thermal environments and provides an additional consideration for biological control programs for which understanding thermal limits of agents is a priority.
DOI: 10.17632/595dvg845z.1
title: Intraspecific variation in rapid cold hardening and acclimation of the adventive parrot’s feather weevil, Phytobius (=Parenthis) vestitus, in the southern USA

description: Plasticity in thermal tolerance, expressed through acclimation or rapid cold hardening, for example, provides organisms with a mechanism to deal with unexpected and often rapid changes in the thermal environment. Spatial variation in response to high or low temperatures may occur due to evolutionary adaptation, particularly if a fitness increase coincides with the ability to respond quickly to environmental change. Thermal tolerances of beneficial insects used for biological control dictate where and under what thermal conditions the insects will provide value to management programs. We investigated two aspects of thermal phenotypic plasticity in response to thermal conditions using four populations of the adventive parrot’s feather weevil, Phytobius vestitus, from the southern USA. At low temperatures, we determined the presence and variation in rapid cold hardening in two of the four populations using two temperature ramping rates. At high temperatures, all P. vestitus populations displayed a significant heat acclimation response, documented as elevated maximum critical and lethal temperatures after acclimation. The relationship between population mean thermal tolerance or plasticity and climate of the source population was not consistent. These results demonstrate the presence of geographic variation in phenotypic plasticity in response to thermal environments and provides an additional consideration for biological control programs for which understanding thermal limits of agents is a priority.