cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.ctrz7c
title: Occurrence Download

description: A dataset listing the 0 species recorded in GBIF matching the query:
{
 "and" : [
 "Continent is North America",
 "License is CC0 1.0",
 "TaxonKey is Fusarium oxysporum cubense"
 ]
}

 The dataset's 0 records were derived from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015660-260129131611470/datasets/export for details.
DOI: 10.15468/dl.jqqy2f
title: Occurrence Download

description: A dataset containing 554 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Librodor japonicus"
 ]
}

 The dataset includes 554 records from 32 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015670-260129131611470/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gycytk
title: Occurrence Download

description: A dataset containing 38659 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Impatiens noli-tangere, Impatiens noli-tangere, Impatiens noli-tangere)",
 "Year is greater than or equal to 1900",
 "Geometry POLYGON ((8.643 46.99, 14.1 46.92, 14.43 50.75, 8.534 50.83, 8.643 46.99))",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "BasisOfRecord is one of (Observation, Human Observation, Machine Observation, Material sample)"
 ]
}

 The dataset includes 38659 records from 63 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015668-260129131611470/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.dfys8w
title: Occurrence Download

description: A dataset containing 4 species occurrences available in GBIF matching the query:
{
 "and" : [
 "PublishingOrg is 8483a1f0-1032-11db-ae00-b8a03c50a862",
 "TaxonKey is Aristelliger reyesi"
 ]
}

 The dataset includes 4 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015671-260129131611470/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.syuyzv
title: Occurrence Download

description: A dataset containing 76402 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((97 21,109 21,109 30,97 30,97 21))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Month is one of (January, February, March, November, December)",
 "OccurrenceStatus is Present",
 "Year 2019-2020"
 ]
}

 The dataset includes 76402 records from 106 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015643-260129131611470/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xbk9vb
title: Occurrence Download

description: A dataset containing 12 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is CHN.2_1",
 "OccurrenceStatus is Present",
 "TaxonKey is Cinclus pallasii",
 "Year is 2022"
 ]
}

 The dataset includes 12 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015672-260129131611470/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.98jezv
title: Occurrence Download

description: A dataset containing 9148 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Inula conyzae, Inula conyzae, Inula conyzae, Inula conyzaea, Conyza squarrosa, Conyza squarrosa, Conyza squarrosa, Inula conyza)",
 "Year is greater than or equal to 1900",
 "Geometry POLYGON ((8.643 46.99, 14.1 46.92, 14.43 50.75, 8.534 50.83, 8.643 46.99))",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "BasisOfRecord is one of (Observation, Human Observation, Machine Observation, Material sample)"
 ]
}

 The dataset includes 9148 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015673-260129131611470/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.cprdw6
title: Occurrence Download

description: A dataset listing the 1481 species recorded in GBIF matching the query:
{
 "and" : [
 "Country is Nepal",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Fungi"
 ]
}

 The dataset's 1481 records were derived from 66 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015661-260129131611470/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.18501090
title: Geometric Curvature Susceptibility in Large-scale Structure dataset

description: This dataset accompanies the preprint Geometric Curvature Susceptibility in Large-scale Structure.

 

The archive contains all processed data products, structural proxies, masking variants, and statistical outputs used to evaluate the geometric activation conditions of the gravitational response kernel. The analysis tests whether gravitational coupling emerges as a function of collective curvature organization rather than solely local mass distribution.

 

Included data products support boundary sensitivity analyses, curvature-mode activation tests, null rotations, and structural coherence sweeps across multiple observational tracers. These materials enable independent replication of all figures, response surfaces, and statistical diagnostics presented in the associated paper.

 

The dataset is observationally grounded and constructed from publicly available cosmological survey sources, including Planck PR4 CMB lensing convergence maps and SDSS/BOSS CMASS large-scale structure tracers, along with derived structural conditioning fields.

 

All processing pipelines, intermediate products, and final statistical outputs required for reproduction are included or referenced within the archive documentation.
DOI: 10.5281/zenodo.18501091
title: Geometric Curvature Susceptibility in Large-scale Structure dataset

description: This dataset accompanies the preprint Geometric Curvature Susceptibility in Large-scale Structure.

 

The archive contains all processed data products, structural proxies, masking variants, and statistical outputs used to evaluate the geometric activation conditions of the gravitational response kernel. The analysis tests whether gravitational coupling emerges as a function of collective curvature organization rather than solely local mass distribution.

 

Included data products support boundary sensitivity analyses, curvature-mode activation tests, null rotations, and structural coherence sweeps across multiple observational tracers. These materials enable independent replication of all figures, response surfaces, and statistical diagnostics presented in the associated paper.

 

The dataset is observationally grounded and constructed from publicly available cosmological survey sources, including Planck PR4 CMB lensing convergence maps and SDSS/BOSS CMASS large-scale structure tracers, along with derived structural conditioning fields.

 

All processing pipelines, intermediate products, and final statistical outputs required for reproduction are included or referenced within the archive documentation.
DOI: 10.5281/zenodo.7679421
title: Kinbank: A global database of kinship terminology

description: The data repository for the Kinbank dataset
DOI: 10.15468/dl.pgwhsy
title: Occurrence Download

description: A dataset containing 0 records in GBIF matching the query:
SELECT
 kingdom,
 kingdomkey,
 phylum,
 phylumkey,
 class,
 classkey,
 "order",
 orderkey,
 family,
 familykey,
 genus,
 genuskey,
 species,
 specieskey,
 "year",
 IF(ISNULL(kingdomkey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY kingdomkey, "year")) kingdomcount,
 IF(ISNULL(phylumkey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY phylumkey, "year")) phylumcount,
 IF(ISNULL(classkey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY classkey, "year")) classcount,
 IF(ISNULL(orderkey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY orderkey, "year")) ordercount,
 IF(ISNULL(familykey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY familykey, "year")) familycount,
 IF(ISNULL(genuskey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY genuskey, "year")) genuscount,
 COUNT(*) occurrences,
 MIN(GBIF_TEMPORALUNCERTAINTY(eventdate, eventtime)) mintemporaluncertainty,
 MIN(COALESCE(coordinateuncertaintyinmeters, 1000)) mincoordinateuncertaintyinmeters
FROM
 occurrence
WHERE
 occurrence.continent = 'NORTH_AMERICA'
 AND occurrence.license = 'CC0_1_0'
 AND GBIF_STRINGARRAYCONTAINS(occurrence.classifications['d7dddbf4-2cf0-4f39-9b2a-bb099caae36c'], '5251977', TRUE)
 AND occurrence.hasgeospatialissues = FALSE
 AND NOT GBIF_STRINGARRAYCONTAINS(occurrence.issue, 'TAXON_MATCH_FUZZY', TRUE)
 AND (occurrence.distancefromcentroidinmeters &gt;= 2000.0 OR occurrence.distancefromcentroidinmeters IS NULL)
 AND NOT occurrence.basisofrecord IN ('FOSSIL_SPECIMEN', 'LIVING_SPECIMEN')
 AND occurrence.occurrencestatus = 'PRESENT'
 AND (occurrence.classificationdetails['d7dddbf4-2cf0-4f39-9b2a-bb099caae36c']['specieskey'] &lt;&gt; '' AND occurrence."year" IS NOT NULL)
GROUP BY
 occurrence.kingdom,
 occurrence.kingdomkey,
 occurrence.phylum,
 occurrence.phylumkey,
 occurrence.class,
 occurrence.classkey,
 occurrence."order",
 occurrence.orderkey,
 occurrence.family,
 occurrence.familykey,
 occurrence.genus,
 occurrence.genuskey,
 occurrence.species,
 occurrence.specieskey,
 occurrence."year"

 The dataset's 0 records were derived from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015663-260129131611470/datasets/export for details.
DOI: 10.15468/dl.d77hw7
title: Occurrence Download

description: A dataset containing 1348 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Inula hirta, Inula hirta)",
 "Year is greater than or equal to 1900",
 "Geometry POLYGON ((8.643 46.99, 14.1 46.92, 14.43 50.75, 8.534 50.83, 8.643 46.99))",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "BasisOfRecord is one of (Observation, Human Observation, Machine Observation, Material sample)"
 ]
}

 The dataset includes 1348 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015674-260129131611470/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.31272853
title: <b>Global multi-omics reveals that virus–host arms race drives antimicrobial resistance genes attenuation and thermophilic persistence in livestock manure composting</b>

description: Composting is a widely adopted strategy to mitigate the global burden of antimicrobial resistance (AMR) in livestock manure, yet the biological mechanisms driving resistome dynamics, particularly the role of the viral biosphere, remain a black box. Here, we leverage a massive global dataset of 420 metagenomes (9.1Tb) and 42 (840Gb) viromes (GVD_LMC), coupled with paired meta-transcriptomics, to decipher the phage–host evolutionary arms race in the ecological succession composting systems. We demonstrate that while composting effectively acts as an ecological filter, reducing total antimicrobial resistance genes (ARGs) and horizontal gene transfer risks, the process is bottlenecked by the selective enrichment of thermophilic antimicrobial-resistant bacteria (ARB). These recalcitrant hosts dominate (~60%) the residual resistome in the maturation phase, challenging the traditional reliance on thermal inactivation alone. Crucially, we reveal that bacteriophages function as the primary sanitizing agents in this succession, where lytic interactions (accounting for 39.5% of the virus-host network) quantitatively override transduction events (&lt;0.5%) in driving ARB decline. However, this viral predation exerts immense selective pressure, driving surviving ARB to evolve enriched antiviral defense systems (ADS), specifically CRISPR-Cas and Restriction-Modification systems, acting as a shield against lysis. Intriguingly, this immune shield simultaneously functions as a genetic firewall, actively blocking the horizontal acquisition of mobile ARGs. Our findings redefine composting as an intense evolutionary arena and suggest that precision strategies targeting the thermophilic reservoir are essential for maximizing ARGs mitigation and ensuring safer livestock manure recycling.
DOI: 10.6084/m9.figshare.31272853.v1
title: <b>Global multi-omics reveals that virus–host arms race drives antimicrobial resistance genes attenuation and thermophilic persistence in livestock manure composting</b>

description: Composting is a widely adopted strategy to mitigate the global burden of antimicrobial resistance (AMR) in livestock manure, yet the biological mechanisms driving resistome dynamics, particularly the role of the viral biosphere, remain a black box. Here, we leverage a massive global dataset of 420 metagenomes (9.1Tb) and 42 (840Gb) viromes (GVD_LMC), coupled with paired meta-transcriptomics, to decipher the phage–host evolutionary arms race in the ecological succession composting systems. We demonstrate that while composting effectively acts as an ecological filter, reducing total antimicrobial resistance genes (ARGs) and horizontal gene transfer risks, the process is bottlenecked by the selective enrichment of thermophilic antimicrobial-resistant bacteria (ARB). These recalcitrant hosts dominate (~60%) the residual resistome in the maturation phase, challenging the traditional reliance on thermal inactivation alone. Crucially, we reveal that bacteriophages function as the primary sanitizing agents in this succession, where lytic interactions (accounting for 39.5% of the virus-host network) quantitatively override transduction events (&lt;0.5%) in driving ARB decline. However, this viral predation exerts immense selective pressure, driving surviving ARB to evolve enriched antiviral defense systems (ADS), specifically CRISPR-Cas and Restriction-Modification systems, acting as a shield against lysis. Intriguingly, this immune shield simultaneously functions as a genetic firewall, actively blocking the horizontal acquisition of mobile ARGs. Our findings redefine composting as an intense evolutionary arena and suggest that precision strategies targeting the thermophilic reservoir are essential for maximizing ARGs mitigation and ensuring safer livestock manure recycling.
DOI: 10.15468/dl.p592xk
title: Occurrence Download

description: A dataset containing 1837 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Limonius poneli"
 ]
}

 The dataset includes 1837 records from 97 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015675-260129131611470/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pwmpfy
title: Occurrence Download

description: A dataset containing 6724 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Inula salicina, Inula salicina, Inula salicina, Inula salicina)",
 "Year is greater than or equal to 1900",
 "Geometry POLYGON ((8.643 46.99, 14.1 46.92, 14.43 50.75, 8.534 50.83, 8.643 46.99))",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "BasisOfRecord is one of (Observation, Human Observation, Machine Observation, Material sample)"
 ]
}

 The dataset includes 6724 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015676-260129131611470/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ecqsxm
title: Occurrence Download

description: A dataset containing 2262 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is CHN.2_1",
 "OccurrenceStatus is Present",
 "TaxonKey is Poecile palustris",
 "Year is 2022"
 ]
}

 The dataset includes 2262 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015677-260129131611470/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.x99ycy
title: Occurrence Download

description: A dataset containing 34610 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Iris pseudacorus)",
 "Year is greater than or equal to 1900",
 "Geometry POLYGON ((8.643 46.99, 14.1 46.92, 14.43 50.75, 8.534 50.83, 8.643 46.99))",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "BasisOfRecord is one of (Observation, Human Observation, Machine Observation, Material sample)"
 ]
}

 The dataset includes 34610 records from 73 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015679-260129131611470/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ymxn6u
title: Occurrence Download

description: A dataset containing 9 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Liometoxenus newtonarum"
 ]
}

 The dataset includes 9 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015680-260129131611470/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.18501495
title: Alongshore sediment transport in the central Jiangsu coast

description: Dataset for alongshore sediment transport in the central Jiangsu coast
DOI: 10.5281/zenodo.18501494
title: Alongshore sediment transport in the central Jiangsu coast

description: Dataset for alongshore sediment transport in the central Jiangsu coast
DOI: 10.15468/dl.buemt4
title: Occurrence Download

description: A dataset containing 7658 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Iris sibirica)",
 "Year is greater than or equal to 1900",
 "Geometry POLYGON ((8.643 46.99, 14.1 46.92, 14.43 50.75, 8.534 50.83, 8.643 46.99))",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "BasisOfRecord is one of (Observation, Human Observation, Machine Observation, Material sample)"
 ]
}

 The dataset includes 7658 records from 22 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015681-260129131611470/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17538008
title: De novo transcriptome assemblies for various RNAseq technologies

description: We performed de novo transcriptome assembly using isONform, RATTLE, RNA-Bloom2, rnaSPAdes, RNA-Bloom2-hybrid, and Trinity on 5 different datasets. Bambu was also used to generate reference-guided assembled transcriptome.

(1) Simulated Nanopore PCR-cDNA data and match Illumina short read RNAseq, 

(2) Nanopore PCR-cDNA sequencing of two human lung cancer cell lines with sequin spike-in transcripts and matched Illumina short read RNAseq,

(3) Nanopore direct RNA sequencing of breast and lung cancer cell lines and matched Illumina short read RNAseq,

(4) Nanopre PCR-cDNA sequencing of 4 pea cultivars and matched Illumina short read RNAseq,

(5) PacBio Kinnex single-cell RNAseq of PBMC data.
DOI: 10.5281/zenodo.17538009
title: De novo transcriptome assemblies for various RNAseq technologies

description: We performed de novo transcriptome assembly using isONform, RATTLE, RNA-Bloom2, rnaSPAdes, RNA-Bloom2-hybrid, and Trinity on 5 different datasets. Bambu was also used to generate reference-guided assembled transcriptome.

(1) Simulated Nanopore PCR-cDNA data and match Illumina short read RNAseq, 

(2) Nanopore PCR-cDNA sequencing of two human lung cancer cell lines with sequin spike-in transcripts and matched Illumina short read RNAseq,

(3) Nanopore direct RNA sequencing of breast and lung cancer cell lines and matched Illumina short read RNAseq,

(4) Nanopre PCR-cDNA sequencing of 4 pea cultivars and matched Illumina short read RNAseq,

(5) PacBio Kinnex single-cell RNAseq of PBMC data.
DOI: 10.15468/dl.quav3c
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Mosannona vasquezii",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 8 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015682-260129131611470/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.18501491
title: Injected and Leaked: Actively Inducing Side-channel Leakage Using Electromagnetic Injection And Hardware Non-Linearity
DOI: 10.5281/zenodo.18501490
title: Injected and Leaked: Actively Inducing Side-channel Leakage Using Electromagnetic Injection And Hardware Non-Linearity
DOI: 10.5281/zenodo.14263456
title: Simulation data for benchmarking de novo long read transcriptome assembly software

description: Method of simulation of differentially expressed biological replicates

We first obtained a subset of transcripts that are widely expressed in the GTEx v9 dataset (92 samples) using Gencode comprehensive annotation (v44). We kept transcripts with more than 5 reads in at least 15 samples after Salmon quantification (18145 genes, 40509 transcripts), and stored their mean count per million (CPM) values as the control group’s baseline expression. We then generated a perturbed set of CPM values where transcript expression was changed by: (1) randomly selecting 1000 genes and changing all transcripts belonging to that gene concordantly (500 genes 2 fold up and 500 genes 2 fold down), (2) selected another 1000 genes randomly, and then select 2 random transcripts from the gene and swap their expression, (3) selected another 1000 genes randomly, and then select 1 random transcript to change its expression (500 transcripts 2 fold up and 500 transcripts 2 fold down). The updated CPM were stored as the perturbed group baseline expression. We then generated a count matrix and CPM matrix for 3 control replicates and 3 perturbed replicates with gamma distribution, followed by a Poisson distribution (Baldoni et al., 2024). Both long-read and short-read FASTQ files were simulated using SQANTI-SIM with default settings and ONT R9.4 cDNA error profile (v 0.2.1) (Mestre-Tomás et al., 2023). The long read data contained 6 million reads in total, and an average read length of 1085 bp, and short read data was 100 bp paired-end. We then subsampled the short-read data to match the total number of base pairs in the long read data (6.5 billion bases). The simulated data was non-stranded, and contains 2000 DE genes, 2000 genes with DTU, 5927 transcripts with DTU and 6933 DE transcripts.

The scripts to generate the simulation data are available on GitHub.