cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.17480985
title: Ipseity Daily Data

description: At what rate do individuals say they are X?

Begining on 2025-07-08, I surveyed a small random sample of American adults on a daily cadence.  They responded to many items of the form: Does <signifier> describe you today?

The file ipseity-daily-aggregated.csv in this repository contains the aggregated results through 2025-07-28.  The columns are as follows:



signifier - a word, phrase or emoji

yes_count - the number of respondents who answered yes (aggregated all-time).

no_count - the number of respondents who answered no (aggregated all-time).

prevalence_per_10k - an estimate of the prevalence per 10,000.  If we were to survey 10,000 American adults, how many would we expect to respond yes to this signifier?  The number is calculated as yes_count / (yes_count + no_count) * 10,000.

earliest_obs_date - this date represents the first time this particular signifier was ever displayed to a respondent.  Signifiers are chosen with stochasticity from a long list; new signifiers are sometimes added, old signifiers are sometimes deleted, and a signifier may be moved higher or lower in priority for sampling.

latest_obs_date - the date closest to the present date on which signifier was most recently presented to a respondent.


Version created on 2025-10-30 — cumulative data.
DOI: 10.5281/zenodo.17480936
title: x-ray
DOI: 10.5281/zenodo.17480937
title: x-ray
DOI: 10.15468/dl.dqcynd
title: Occurrence Download

description: A dataset containing 3096 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((177.09959 -37.08785,175.00984 -34.06693,173.47404 -33.42587,171.79791 -34.59187,173.78376 -37.98058,175.76961 -38.08989,177.09959 -37.08785))",
 "OccurrenceStatus is Present",
 "TaxonKey is Agathis australis"
 ]
}

 The dataset includes 3096 records from 33 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007668-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17461593
title: Single-cell profiling identifies a pathogenic Msx2⁺ VSMC subpopulation underlying aortic arch-specific vascular calcification

description: This study investigates why the aortic arch is more prone to calcification than the descending aorta. Vascular calcification is a serious condition with no effective treatment, where blood vessel cells become similar to bone-forming cells. We used single-cell RNA sequencing on a mouse model of vitamin D-induced calcification to compare these two aortic regions. Our key discovery was a specific subpopulation of Msx2-positive vascular smooth muscle cells that is uniquely found in the aortic arch and appears to drive its increased calcification. This finding provides new insights into the cellular basis of regional calcification differences and could lead to new therapeutic targets.
description: Vascular calcification was induced in mice via subcutaneous injection of high-dose vitamin D3 (vD3). The treatment group received vD3 (5×10^5 IU/kg/day; Sigma-Aldrich, #PHR1237) dissolved in the vehicle, while the control group received the vehicle alone. Injections were administered for three consecutive days. Animals were euthanized, and aortic tissues were collected at two time points: day 4 and day 7 after the first injection.

Single-cell suspensions were prepared from pooled aortic arch (AA) or descending thoracic aorta (DTA) segments (n=6 pools per group). Briefly, aortas were dissected from mice at day 0, 4, and 7 post-vitamin D3 treatment, cleaned of adherent tissues in HBSS under a stereomicroscope, and segmented into AA and DTA. Tissues from the same type and time point were pooled, minced, and enzymatically digested at 37°C using a solution of collagenase type I and dispase. The dissociated cell suspension was then triturated, filtered through a 70-μm strainer, and centrifuged. The resulting cell pellet was resuspended, and cell viability was confirmed to be >80% prior to single-cell library preparation.
description: Raw sequencing reads were processed using the 10x Genomics Cell Ranger pipeline for demultiplexing, alignment to the reference genome (e.g., mm10), cell barcode assignment, and unique molecular identifier (UMI) counting to generate the final gene expression matrix.
DOI: 10.5281/zenodo.17461594
title: Single-cell profiling identifies a pathogenic Msx2⁺ VSMC subpopulation underlying aortic arch-specific vascular calcification

description: This study investigates why the aortic arch is more prone to calcification than the descending aorta. Vascular calcification is a serious condition with no effective treatment, where blood vessel cells become similar to bone-forming cells. We used single-cell RNA sequencing on a mouse model of vitamin D-induced calcification to compare these two aortic regions. Our key discovery was a specific subpopulation of Msx2-positive vascular smooth muscle cells that is uniquely found in the aortic arch and appears to drive its increased calcification. This finding provides new insights into the cellular basis of regional calcification differences and could lead to new therapeutic targets.
description: Vascular calcification was induced in mice via subcutaneous injection of high-dose vitamin D3 (vD3). The treatment group received vD3 (5×10^5 IU/kg/day; Sigma-Aldrich, #PHR1237) dissolved in the vehicle, while the control group received the vehicle alone. Injections were administered for three consecutive days. Animals were euthanized, and aortic tissues were collected at two time points: day 4 and day 7 after the first injection.

Single-cell suspensions were prepared from pooled aortic arch (AA) or descending thoracic aorta (DTA) segments (n=6 pools per group). Briefly, aortas were dissected from mice at day 0, 4, and 7 post-vitamin D3 treatment, cleaned of adherent tissues in HBSS under a stereomicroscope, and segmented into AA and DTA. Tissues from the same type and time point were pooled, minced, and enzymatically digested at 37°C using a solution of collagenase type I and dispase. The dissociated cell suspension was then triturated, filtered through a 70-μm strainer, and centrifuged. The resulting cell pellet was resuspended, and cell viability was confirmed to be >80% prior to single-cell library preparation.
description: Raw sequencing reads were processed using the 10x Genomics Cell Ranger pipeline for demultiplexing, alignment to the reference genome (e.g., mm10), cell barcode assignment, and unique molecular identifier (UMI) counting to generate the final gene expression matrix.
DOI: 10.15468/dl.z6hkvy
title: Occurrence Download

description: A dataset containing 24554962 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Asia",
 "Country is Chinese Taipei",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 24554962 records from 725 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007647-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6c3vgs
title: Occurrence Download

description: A dataset containing 102 species occurrences available in GBIF matching the query:
{
 "and" : [
 "IucnRedListCategory is one of (VU, EN, CR, EW, NT)",
 "OccurrenceStatus is Present",
 "TaxonKey is Centropus nigrorufus",
 "Year 2000-2025"
 ]
}

 The dataset includes 102 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007670-251025141854904/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.30486860
title: dibai enema liquid improves ulcerative colitis by Inhibiting the Activation of Enteric Glial Cells through the S100β/RAGE/NF-κB Signaling Pathway

description: Emerging evidence implicates enteric glial cell (EGC) activation in ulcerative colitis (UC) pathogenesis. This study investigated how Dibai Enema Liquid (DBE) modulates EGC-mediated inflammation. LC–MS/MS qualitatively profiled DBE, and five neuroprotective constituents were docked to S100β. DBE enema efficacy was evaluated in dextran sulfate sodium–induced murine colitis by body weight, colon length, histopathology, and cytokines (ELISA); EGC activation markers were assessed by IHC, immunofluorescence co-localization, qPCR, and immunoblotting. An in vitro model used CRL-2690 enteric glia activated with lipopolysaccharide plus interferon-γ. LC–MS/MS revealed five bioactive components with strong S100βbinding. DSS increased TNF-α/IL-1β, disrupted tight junctions, and elevated S100β/GFAP at mRNA and protein levels, consistent with EGC hyperactivation; DBE significantly reversed these changes. In vitro, 15% DBE-containing drug serum reduced S100β, RAGE, iNOS (NOS2), and phosphorylated NF-κB p65. Collectively, DBE appears to alleviate UC by inhibiting EGC activation via the S100β/RAGE/NF-κB/iNOS cascade.
DOI: 10.6084/m9.figshare.30486860.v1
title: dibai enema liquid improves ulcerative colitis by Inhibiting the Activation of Enteric Glial Cells through the S100β/RAGE/NF-κB Signaling Pathway

description: Emerging evidence implicates enteric glial cell (EGC) activation in ulcerative colitis (UC) pathogenesis. This study investigated how Dibai Enema Liquid (DBE) modulates EGC-mediated inflammation. LC–MS/MS qualitatively profiled DBE, and five neuroprotective constituents were docked to S100β. DBE enema efficacy was evaluated in dextran sulfate sodium–induced murine colitis by body weight, colon length, histopathology, and cytokines (ELISA); EGC activation markers were assessed by IHC, immunofluorescence co-localization, qPCR, and immunoblotting. An in vitro model used CRL-2690 enteric glia activated with lipopolysaccharide plus interferon-γ. LC–MS/MS revealed five bioactive components with strong S100βbinding. DSS increased TNF-α/IL-1β, disrupted tight junctions, and elevated S100β/GFAP at mRNA and protein levels, consistent with EGC hyperactivation; DBE significantly reversed these changes. In vitro, 15% DBE-containing drug serum reduced S100β, RAGE, iNOS (NOS2), and phosphorylated NF-κB p65. Collectively, DBE appears to alleviate UC by inhibiting EGC activation via the S100β/RAGE/NF-κB/iNOS cascade.
DOI: 10.15468/dl.cgdzrw
title: Occurrence Download

description: A dataset containing 18 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Salix angustifolia",
 "HasCoordinate is true"
 ]
}

 The dataset includes 18 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007671-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17481018
title: COVID-19-Todesfälle in Deutschland

description: Im Datensatz "COVID-19-Todesfälle in Deutschland" des Robert Koch-Instituts werden täglich aktualisierte Informationen zu COVID-19-bedingten Todesfällen in Deutschland bereitgestellt. Die Datenerhebung erfolgt im Rahmen des Infektionsschutzgesetzes (IfSG). Der Datensatz umfasst aggregierte Todesfallzahlen nach Berichtsdatum, Altersgruppen und Bundesländern und wird ergänzt durch den Fall-Verstorbenen-Anteil. Der Datensatz ermöglicht fundierte Analysen zur Bewertung der Krankheitsschwere und Verbreitung von COVID-19 in Deutschland.
DOI: 10.5281/zenodo.17481017
title: 7-Tage-Inzidenz der COVID-19-Fälle in Deutschland

description: Im Datensatz "7-Tage-Inzidenz der COVID-19-Fälle in Deutschland" des Robert Koch-Instituts werden die täglich aktualisierten COVID-19-Inzidenzen auf Bundes-, Landes- und Landkreisebene basierend auf den Meldungen nach dem Infektionsschutzgesetz (IfSG) bereitgestellt. Die 7-Tage-Inzidenz wird definiert als Anzahl gemeldeter Fälle der letzten sieben Tage pro 100.000 Einwohner:innen und differenziert nach Altersgruppen und Regionen. Die Datenverarbeitung erfolgt vollständig elektronisch über das Deutsche Elektronische Melde- und Informationssystem (DEMIS).
DOI: 10.15468/dl.brmtkw
title: Occurrence Download

description: A dataset containing 56841 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Asia",
 "TaxonKey is Anser indicus"
 ]
}

 The dataset includes 56841 records from 52 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007652-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14633468
title: Benchmarking deep learning methods for biologically conserved single-cell integration.

description: scIB-E is a comprehensive deep learning-based benchmarking framework for evaluating single-cell RNA sequencing (scRNA-seq) data integration methods.





Unified Benchmarking Framework:



Evaluates 16 deep-learning single-cell integration methods using a unified variational autoencoder (VAE) framework.

Incorporates batch information, cell-type labels, and combined strategies across three integration levels.





Refined Metrics for Intra-cell-type Variation:



Extends the single-cell integration benchmarking (scIB) metrics by adding new metrics to better capture intra-cell-type biological conservation.





Novel Loss Function:



Introduces Corr-MSE Loss, a correlation-based loss function designed to preserve global cellular relationships and enhance intra-cell-type biological variation.




 

The preprocessed datasets are available at src/data.
DOI: 10.15468/dl.yznzdk
title: Occurrence Download

description: A dataset containing 33512 species occurrences available in GBIF matching the query:
{
 "and" : [
 "MediaType is Image",
 "TaxonKey is Raphanus raphanistrum"
 ]
}

 The dataset includes 33512 records from 260 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007675-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rm3swh
title: Occurrence Download

description: A dataset containing 702 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Inventaires naturalistes conduits par l'association Entomo Fauna-Inventaire naturaliste de la commune de Grand-Santi (Guyane) : mission 2017 Entomo Fauna"
 ]
}

 The dataset includes 702 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007676-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.15833632
title: PMIP and iTRACE model data for GSAT-MSST scaling relationship
DOI: 10.5281/zenodo.17481032
title: PMIP and iTRACE model data for GSAT-MSST scaling relationship
DOI: 10.21227/shkg-t342
title: "Auditory Listening and Imagery dataset"

description: "Listening to 5 Japanese vowels and imagine the sound they have heard.With white noise as control condition. Each participant was recorded at same time of two days. "
DOI: 10.5281/zenodo.17480119
title: Simulated Monthly Earthquake Catalogs (2000–2023) for the China Seismic Experimental Site (CSES)

description: This dataset contains simulated monthly earthquake catalogs for the China Seismic Experimental Site (CSES) covering the period from 2000 to 2023. For each forecast window, 100,000 synthetic catalogs were generated to ensure robust statistical sampling. Two models were used to produce the simulations: (1) the ETAS model with a constant background rate (ETASμ) and (2) the ETAS model with a spatially variable background rate (ETASμ(x, y)). The datasets provide the foundation for comparative analyses of spatially homogeneous versus heterogeneous earthquake triggering behavior within the CSES region.
DOI: 10.5281/zenodo.17480120
title: Simulated Monthly Earthquake Catalogs (2000–2023) for the China Seismic Experimental Site (CSES)

description: This dataset contains simulated monthly earthquake catalogs for the China Seismic Experimental Site (CSES) covering the period from 2000 to 2023. For each forecast window, 100,000 synthetic catalogs were generated to ensure robust statistical sampling. Two models were used to produce the simulations: (1) the ETAS model with a constant background rate (ETASμ) and (2) the ETAS model with a spatially variable background rate (ETASμ(x, y)). The datasets provide the foundation for comparative analyses of spatially homogeneous versus heterogeneous earthquake triggering behavior within the CSES region.
DOI: 10.15468/dl.mvfnaw
title: Occurrence Download

description: A dataset containing 145 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "OccurrenceStatus is Present",
 "TaxonKey is Amaranthus blitum"
 ]
}

 The dataset includes 145 records from 22 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007681-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2f65uz
title: Occurrence Download

description: A dataset containing 5173 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Rosa laevigata"
 ]
}

 The dataset includes 5173 records from 175 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007682-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.amp0b3
title: Occurrence Download

description: A dataset containing 32 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is (Table 1) Proportion of Toxoplasma gondii seropositive arctic foxes (Alopex lagopus) by age group and geographic area"
 ]
}

 The dataset includes 32 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009098-190621201848488/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.uhw6er
title: Occurrence Download

description: A dataset containing 4 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Kazakhstan",
 "Geometry POLYGON((47.95397 38.67419,58.16497 38.67419,58.16497 50.48065,47.95397 50.48065,47.95397 38.67419))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Caracal caracal (Schreber, 1776)"
 ]
}

 The dataset includes 4 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0071471-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.da4758
title: Occurrence Download

description: A dataset containing 7 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Nerisyrenia hypercorax P.J.Alexander & M.J.Moore"
 ]
}

 The dataset includes 7 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0041088-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5bpddw
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is (Table 1) Proportion of Toxoplasma gondii seropositive arctic foxes (Alopex lagopus) by age group and geographic area"
 ]
}

 The dataset includes 8 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007795-171219132708484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.od27xo
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is (Table 1) Proportion of Toxoplasma gondii seropositive arctic foxes (Alopex lagopus) by age group and geographic area"
 ]
}

 The dataset includes 8 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0046186-160910150852091/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.v8bila
title: Occurrence Download

description: A dataset containing 32 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is (Table 1) Proportion of Toxoplasma gondii seropositive arctic foxes (Alopex lagopus) by age group and geographic area"
 ]
}

 The dataset includes 32 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009125-190621201848488/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.edn6xw
title: Occurrence Download

description: A dataset containing 11 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Mathewsia peruviana O.E.Schulz"
 ]
}

 The dataset includes 11 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0041123-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.se2kpv
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is (Table 1) Proportion of Toxoplasma gondii seropositive arctic foxes (Alopex lagopus) by age group and geographic area"
 ]
}

 The dataset includes 8 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007815-171219132708484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.905ehu
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is (Table 1) Proportion of Toxoplasma gondii seropositive arctic foxes (Alopex lagopus) by age group and geographic area"
 ]
}

 The dataset includes 8 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015183-160311141623029/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.la4kqa
title: Occurrence Download

description: A dataset containing 32 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is (Table 1) Proportion of Toxoplasma gondii seropositive arctic foxes (Alopex lagopus) by age group and geographic area"
 ]
}

 The dataset includes 32 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009107-190621201848488/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pjuyrz
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is (Table 1) Proportion of Toxoplasma gondii seropositive arctic foxes (Alopex lagopus) by age group and geographic area"
 ]
}

 The dataset includes 8 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007880-171219132708484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.