cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.xackm2
title: Occurrence Download

description: A dataset containing 29209 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Spizaetus ornatus (Daudin, 1800)"
 ]
}

 The dataset includes 29209 records from 99 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0037078-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9wa842
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Tomopterna marmorata (Peters, 1854)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((25.5395 -23.2724,25.1306 -24.0715,25.5395 -24.0715,25.5395 -23.2724))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0037079-250525065834625/datasets/export for details.
DOI: 10.34740/kaggle/dsv/12134806
title: Peer-to-Peer Boliviano (BOB) Exchange Data
DOI: 10.15468/dl.6b95kg
title: Occurrence Download

description: A dataset containing 860 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is Fish Specimens",
 "TaxonKey is Hybognathus placitus Girard, 1856"
 ]
}

 The dataset includes 860 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0037080-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xkpyrx
title: Occurrence Download

description: A dataset containing 9553 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is South America",
 "Country is one of (Brazil, Argentina, Paraguay)",
 "TaxonKey is Glyphorynchus spirurus (Vieillot, 1819)"
 ]
}

 The dataset includes 9553 records from 32 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0037082-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.29298224
title: Supplementary material for cardiac responses to environmental heat exposure in young and older adults.docx

description: Older individuals are at a greater risk for adverse cardiovascular events during extreme heat events. However, detailed characterisation of their cardiac responses to environmental heat exposure are lacking. In 20 young (18 to 39 years) and 20 older (&gt; 65 years) adults (50% male in both groups), we document the echocardiography assessed left-ventricular responses to a very hot and dry (DRY, 47°C and 15% RH) and hot humid (HUMID, 41°C and 40% RH) 3-hour heat exposure, with intermittent bouts of light physical activity throughout. In both climates and in both age groups, heat stress <i>a)</i> increased cardiac output by ~0.7 ± 0.8 L/min, <i>b)</i> decreased stroke volume by ~7 ± 10 mL and <i>c)</i> augmented diastolic function through increased atrial contribution to filling by 5 ± 5%. In the DRY climate, mitral annual systolic velocity (s’) increased to a greater extent in older subjects (Δ3.3 ± 2.1 vs Δ1.5 ± 1.5 cm/s, <i>p</i> = 0.002), with less difference in HUMID (Δ2.1 ± 1.3 cm/s vs 1.4 ± 1.3 cm/s, <i>p</i> = 0.096). Despite these adjustments, systolic blood pressure was only maintained in the younger group and fell consistently in older individuals (0 ± 8 mmHg) in DRY (Δ-11 ± 14 mmHg vs 1 ± 8 mmHg, <i>p</i> = 0.001) and HUMID (Δ-9 ± 15 mmHg vs -1 ± 8 mmHg, <i>p</i> = 0.030). In summary, older adults rely on a greater augmentation of systolic function during extreme heat exposure, but the magnitude of depends on the heat stress severity.
DOI: 10.6084/m9.figshare.29298224.v1
title: Supplementary material for cardiac responses to environmental heat exposure in young and older adults.docx

description: Older individuals are at a greater risk for adverse cardiovascular events during extreme heat events. However, detailed characterisation of their cardiac responses to environmental heat exposure are lacking. In 20 young (18 to 39 years) and 20 older (&gt; 65 years) adults (50% male in both groups), we document the echocardiography assessed left-ventricular responses to a very hot and dry (DRY, 47°C and 15% RH) and hot humid (HUMID, 41°C and 40% RH) 3-hour heat exposure, with intermittent bouts of light physical activity throughout. In both climates and in both age groups, heat stress <i>a)</i> increased cardiac output by ~0.7 ± 0.8 L/min, <i>b)</i> decreased stroke volume by ~7 ± 10 mL and <i>c)</i> augmented diastolic function through increased atrial contribution to filling by 5 ± 5%. In the DRY climate, mitral annual systolic velocity (s’) increased to a greater extent in older subjects (Δ3.3 ± 2.1 vs Δ1.5 ± 1.5 cm/s, <i>p</i> = 0.002), with less difference in HUMID (Δ2.1 ± 1.3 cm/s vs 1.4 ± 1.3 cm/s, <i>p</i> = 0.096). Despite these adjustments, systolic blood pressure was only maintained in the younger group and fell consistently in older individuals (0 ± 8 mmHg) in DRY (Δ-11 ± 14 mmHg vs 1 ± 8 mmHg, <i>p</i> = 0.001) and HUMID (Δ-9 ± 15 mmHg vs -1 ± 8 mmHg, <i>p</i> = 0.030). In summary, older adults rely on a greater augmentation of systolic function during extreme heat exposure, but the magnitude of depends on the heat stress severity.
DOI: 10.15468/dl.m6r4fc
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Tomopterna marmorata (Peters, 1854)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((20.2855 -34.7533,20.509 -34.5676,20.509 -32.9007,17.7723 -32.9007,17.8156 -33.0786,18.3471 -33.7176,18.3748 -33.8287,18.2181 -34.0492,18.3197 -34.3408,18.4452 -34.429,18.5435 -34.4213,18.5872 -34.3667,18.5363 -34.167,18.7345 -34.1508,18.7216 -34.3637,18.7808 -34.4521,19.0289 -34.4206,19.0831 -34.4835,19.2655 -34.5017,19.2032 -34.6157,19.2394 -34.6926,19.375 -34.6963,19.6091 -34.8524,19.8251 -34.8396,19.9798 -34.9064,20.1081 -34.8731,20.1517 -34.7847,20.2855 -34.7533))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0037083-250525065834625/datasets/export for details.
DOI: 10.15468/dl.qfjc6w
title: Occurrence Download

description: A dataset containing 1947471340 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "Year 2013-2023"
 ]
}

 The dataset includes 1947471340 records from 44764 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0037014-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.7483/opendata.cms.9ctb.zi5b
title: /TprimeBToTH_TLep_Hbb_LH_MT2500_MH100_TuneCP5_13TeV-madgraph-pythia8/RunIISummer20UL16NanoAODv9-106X_mcRun2_asymptotic_v17-v1/NANOAODSIM
DOI: 10.17632/kvyyg4mc3g.1
title: SPORT-Good

description: sport-good dataset
DOI: 10.7483/opendata.cms.3h4k.mwxo
title: /TprimeBToTH_TLep_Hbb_LH_MT2500_MH125_TuneCP5_13TeV-madgraph-pythia8/RunIISummer20UL16MiniAODv2-106X_mcRun2_asymptotic_v17-v2/MINIAODSIM
DOI: 10.17044/scilifelab.14270159
title: Data from paper: Palmdelphin Regulates Nuclear Resilience to Mechanical Stress in the Endothelium

description: Raw data from bulk RNA-Seq on endothelial cell cultures grown under static or laminar flow conditions after silencing Palmdelphin or not.<br>Paper abstract: <b>Background:</b> Palmdelphin (PALMD), a protein of unknown function, belongs to the family of Paralemmin proteins implicated in cytoskeletal regulation. Single nucleotide polymorphisms (SNPs) in the <i>PALMD</i> locus, which reduce its expression, are strong risk factors for development of calcific aortic valve stenosis (CAVS) and for severity of the disease.<b>Methods:</b> Public database screening and immunodetection of PALMD showed dominant expression in endothelial cells (ECs). Mass spectrometry allowed identification of PALMD partners. The consequence of loss of PALMD expression was assessed in siRNA silenced EC cultures, in knockout mice and in human valve samples and EC cultures from patients. RNA sequencing on siRNA silenced cells and transcript arrays on valve samples from a Swedish SNP rs7543130 patient cohort informed about gene regulatory changes.<b>Results:</b> ECs express the cytoplasmic <i>PALMD-KKVI</i> splice variant, which was shown to exist in complex with RAN GTPase activating protein1 (RANGAP1). RANGAP1 regulates the activity of the GTPase RAN and thereby, nucleocytoplasmic shuttling via Exportin1 (XPO1). Reduced PALMD expression resulted in subcellular relocalization of RANGAP1 and XPO1, providing a mechanism for the gene regulatory changes established in PALMD-deficiency. Gene ontology analysis showed enrichment of actin and RHO GTPAse related terms in <i>PALMD</i>-silenced ECs. In accordance, <i>PALMD</i>-silenced ECs showed multiple changes in adhesive and migratory properties and cells were softer. In particular, <i>PALMD</i>-deficient ECs failed to form a perinuclear actin cap when exposed to flow. The perinuclear actin cap is known to provide protection against mechanical stress. Lack of the actin cap correlated with tilting of the nuclear long axis relative to the cell body, which was established in <i>PALMD</i>-deficient ECs, mice and patient valve samples. The loss of the actin cap may contribute to further dysregulated gene transcription eventually promoting calcific precipitations and inflammation in CAVS.<b>Conclusions:</b> We identify RANGAP1 as a PALMD partner in ECs. Disrupting the PALMD/RANGAP1 complex changes the subcellular localization of essential nucleocytoplasmic shuttling components, thereby instigating the loss of actin-dependent nuclear resilience, which in turn promotes further deterioration of gene expression patterns predisposing to the establishment of CAVS.
DOI: 10.17044/scilifelab.14270159.v1
title: Data from paper: Palmdelphin Regulates Nuclear Resilience to Mechanical Stress in the Endothelium

description: Raw data from bulk RNA-Seq on endothelial cell cultures grown under static or laminar flow conditions after silencing Palmdelphin or not.<br>Paper abstract: <b>Background:</b> Palmdelphin (PALMD), a protein of unknown function, belongs to the family of Paralemmin proteins implicated in cytoskeletal regulation. Single nucleotide polymorphisms (SNPs) in the <i>PALMD</i> locus, which reduce its expression, are strong risk factors for development of calcific aortic valve stenosis (CAVS) and for severity of the disease.<b>Methods:</b> Public database screening and immunodetection of PALMD showed dominant expression in endothelial cells (ECs). Mass spectrometry allowed identification of PALMD partners. The consequence of loss of PALMD expression was assessed in siRNA silenced EC cultures, in knockout mice and in human valve samples and EC cultures from patients. RNA sequencing on siRNA silenced cells and transcript arrays on valve samples from a Swedish SNP rs7543130 patient cohort informed about gene regulatory changes.<b>Results:</b> ECs express the cytoplasmic <i>PALMD-KKVI</i> splice variant, which was shown to exist in complex with RAN GTPase activating protein1 (RANGAP1). RANGAP1 regulates the activity of the GTPase RAN and thereby, nucleocytoplasmic shuttling via Exportin1 (XPO1). Reduced PALMD expression resulted in subcellular relocalization of RANGAP1 and XPO1, providing a mechanism for the gene regulatory changes established in PALMD-deficiency. Gene ontology analysis showed enrichment of actin and RHO GTPAse related terms in <i>PALMD</i>-silenced ECs. In accordance, <i>PALMD</i>-silenced ECs showed multiple changes in adhesive and migratory properties and cells were softer. In particular, <i>PALMD</i>-deficient ECs failed to form a perinuclear actin cap when exposed to flow. The perinuclear actin cap is known to provide protection against mechanical stress. Lack of the actin cap correlated with tilting of the nuclear long axis relative to the cell body, which was established in <i>PALMD</i>-deficient ECs, mice and patient valve samples. The loss of the actin cap may contribute to further dysregulated gene transcription eventually promoting calcific precipitations and inflammation in CAVS.<b>Conclusions:</b> We identify RANGAP1 as a PALMD partner in ECs. Disrupting the PALMD/RANGAP1 complex changes the subcellular localization of essential nucleocytoplasmic shuttling components, thereby instigating the loss of actin-dependent nuclear resilience, which in turn promotes further deterioration of gene expression patterns predisposing to the establishment of CAVS.
DOI: 10.17044/scilifelab.14301317
title: Data used in exercises in course Introduction to Data Management Practices

description: This record contains the data files used in exercises in the NBIS course "Introduction to Data Management Practices".
DOI: 10.7483/opendata.cms.ywsd.zfwb
title: /TprimeBToTH_TLep_Hbb_LH_MT2500_MH125_TuneCP5_13TeV-madgraph-pythia8/RunIISummer20UL16NanoAODv9-106X_mcRun2_asymptotic_v17-v1/NANOAODSIM
DOI: 10.17044/scilifelab.14301317.v1
title: Data used in exercises in course Introduction to Data Management Practices

description: This record contains the data files used in exercises in the NBIS course "Introduction to Data Management Practices".
DOI: 10.7483/opendata.cms.3tu5.htug
title: /TprimeBToTH_TLep_Hbb_LH_MT2500_MH150_TuneCP5_13TeV-madgraph-pythia8/RunIISummer20UL16MiniAODv2-106X_mcRun2_asymptotic_v17-v2/MINIAODSIM
DOI: 10.17044/scilifelab.14301317.v2
title: Data used in exercises in course Introduction to Data Management Practices

description: This record contains the data files used in exercises in the NBIS course "Introduction to Data Management Practices".
DOI: 10.17044/scilifelab.14301317.v3
title: Data used in exercises in course Introduction to Data Management Practices

description: This record contains the data files used in exercises in the NBIS course "Introduction to Data Management Practices".
DOI: 10.17044/scilifelab.14315483
title: SARS-CoV-2 Wastewater Data from Stockholm, Sweden

description: The dataset is part of a research study lead by associate professor Zeynep Cetecioglu Gurol and colleagues (KTH Royal Institute of Technology), is a collaboration between the SciLifeLab COVID-19 National Research Program and Chemical Engineering and Protein Science departments at KTH, in close collaboration with Stockholm Vatten och Avfall and the Käppala Association.<br>The sampling of wastewater, started in mid-April 2020, from Bromma, Henriksdal, and Käppala wastewater treatment plants (WWTP). These treatment plants receive wastewater from a population of approximately 360,000; 860,000 and 500,000, respectively.After concentration, filtering, and preparation, the samples are analyzed using RT-qPCR technique for SARS CoV-2 RNA. Primers of the nucleocapsid (N) gene were used to detect the SARS-COV-2 gene (previously used and verified by Medema and colleagues (2020). In some cases, the raw wastewater has been frozen at –20 degrees, and concentrated wastewater or purified RNA have been stored at -80 C before the next analysis step was carried out. The concentration method used by prof. Zeynep Cetecioglu Gurol and her colleagues is based on their published study (Jafferali and colleagues, 2021). The gene copy nr / week is presented standardized for Bovine coronavirus (BCoV) and Pepper Mild Mottle Virus (PPMoV)For more information see https://www.covid19dataportal.se/data_types/environment/wastewater/ The dataset started week 16 2020 and updates weekly. The dataset is available as part of the Environmental Virus Profiling data section "The amount of SARS-CoV-2 virus in wastewater across Sweden" https://www.covid19dataportal.se/data_types/environment/wastewater/#stockholmon the Swedish COVID-19 Data Portal (https://covid19dataportal.se ).
DOI: 10.17044/scilifelab.14315777
title: Immunofluorescence data of 700 host cell proteins in Sars-CoV2 infected vs non-infected VeroE6 cells

description: The data set contains ≈ 75,000 confocal images of mixed Vero E6 cell populations (SARS-CoV2 infected vs non-infected). Cells had been infected with the virus for 1 h and fixed 24 hour post infection in 96 well plates. Using immunofluorescence (4 colours) cells were stained for the SARS-CoV2 virus (red), the endoplasmic reticulum (yellow) and nucleus (blue) – same for all images in the data set and used as reference markers. On top of this, 700 different target proteins were stained – one per well (green). Images were acquired with an Opera Phoenix microscope at 63X, using 9 FoV and 3 z-planes per protein target. IN the original study, intensity differences and spatial re-distribution of the target proteins were evaluated in infected vs the non-infected cells. The image resource was generated and described in detail in this research article: (to be added).
DOI: 10.7483/opendata.cms.mmji.xz44
title: /TprimeBToTH_TLep_Hbb_LH_MT2500_MH150_TuneCP5_13TeV-madgraph-pythia8/RunIISummer20UL16NanoAODv9-106X_mcRun2_asymptotic_v17-v1/NANOAODSIM
DOI: 10.17044/scilifelab.14315777.v1
title: Immunofluorescence data of 700 host cell proteins in Sars-CoV2 infected vs non-infected VeroE6 cells

description: The data set contains ≈ 75,000 confocal images of mixed Vero E6 cell populations (SARS-CoV2 infected vs non-infected). Cells had been infected with the virus for 1 h and fixed 24 hour post infection in 96 well plates. Using immunofluorescence (4 colours) cells were stained for the SARS-CoV2 virus (red), the endoplasmic reticulum (yellow) and nucleus (blue) – same for all images in the data set and used as reference markers. On top of this, 700 different target proteins were stained – one per well (green). Images were acquired with an Opera Phoenix microscope at 63X, using 9 FoV and 3 z-planes per protein target. IN the original study, intensity differences and spatial re-distribution of the target proteins were evaluated in infected vs the non-infected cells. The image resource was generated and described in detail in this research article: (to be added).
DOI: 10.17044/scilifelab.14339153
title: Genomic characterization of the barnacle Balanus improvisus reveals extreme nucleotide diversity in coding regions

description: Pilot short-read genome assembly of one single adult barnacle, Balanus improvisus (=Amphibalanus imrpovisus), used to estimate genome size and heterocygosity. Bi01.clean.fa.gz is the final assembly with contaminations etc removed.<br> Alm Rosenblad et al., Marine Biotechnology 2021<br><b><br></b><b>Abstract </b>Barnacles are key marine crustaceans in several habitats and they constitute a common practical problem by causing biofouling on man-made marine constructions and ships. Despite causing considerable ecological and economic impacts, there is a surprising void of basic genomic knowledge, and a barnacle reference genome is lacking. We here set out to characterize the genome of the bay barnacle <i>Balanus improvisus</i> (= <i>Amphibalanus improvisus</i>) based on short-read whole genome sequencing and experimental genome size estimation.<br>We show both experimentally (DNA staining and flow cytometry) and computationally (<i>k</i>-mer analysis) that <i>B. improvisus</i> has a haploid genome size of ~ 740 Mbp. A pilot genome assembly rendered a total assembly size of ~600 Mbp and was highly fragmented with an N50 of only 2.2 kbp. Further assembly-based and assembly-free analyses revealed that the very limited assembly contiguity is due to the <i>B. improvisus</i> genome having an extremely high nucleotide diversity (π) in coding regions (average π ≈ 5% and average π in 4-fold degenerate sites ≈ 20%), and an overall high repeat content (at least 40%). We also report on high variation in the α-octopamine receptor OctA (average π = 3.6%), %), which might increase the risk that barnacle populations evolve resistance towards antifouling agents. The genomic features described here can help in planning for a future high-quality reference genome, which is urgently needed to properly explore and understand proteins of interest in barnacle biology and marine biotechnology and for developing better antifouling strategies.
DOI: 10.17044/scilifelab.14376104
title: Human T cell scRNAseq

description: This dataset contains genomic TCR beta sequences from single cell DNA samples amplified by multiple displacement amplification (MDA) and subjected to nested PCR targeting the genomic TCR beta locus. The individual files contain raw data representing nucleotide sequences including both productive and non-productive rearrangements of the TCR beta sequence (with dropout in some cases). <br>FASTQ files corresponding to single cell RNAseq data from single CD8+ T cells prepared by the smart-seq2 method.<br><br>FASTQ files for 25-cell ‘mini-bulk’ RNAseq for CD8+ T cells prepared according to the smart-seq2 protocol.
<br>
DOI: 10.17044/scilifelab.14376104.v1
title: Human T cell scRNAseq

description: This dataset contains genomic TCR beta sequences from single cell DNA samples amplified by multiple displacement amplification (MDA) and subjected to nested PCR targeting the genomic TCR beta locus. The individual files contain raw data representing nucleotide sequences including both productive and non-productive rearrangements of the TCR beta sequence (with dropout in some cases). <br>FASTQ files corresponding to single cell RNAseq data from single CD8+ T cells prepared by the smart-seq2 method.<br><br>FASTQ files for 25-cell ‘mini-bulk’ RNAseq for CD8+ T cells prepared according to the smart-seq2 protocol.
<br>
DOI: 10.7483/opendata.cms.ng83.l2vr
title: /TprimeBToTH_TLep_Hbb_LH_MT2500_MH175_TuneCP5_13TeV-madgraph-pythia8/RunIISummer20UL16MiniAODv2-106X_mcRun2_asymptotic_v17-v2/MINIAODSIM