cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.57760/sciencedb.j00266.00009
title: Microbial (bacterial) communities of riverbed and riverbank sediments collected from a urban river
title: Microbial (bacterial) communities of riverbed and riverbank sediments collected from a urban river

description: This file contains ASV abundance and taxonomy information for seven riverbed and riverbank sediment samples collected from four sites along the Beiyun River—a typical urban river that receives effluent from urban and industrial wastewater treatment plants.Using these sediments, we conducted 28-day oxic incubation experiments with and without the addition of environmentally relevant levels of sulfonamides (10 µg/L each of sulfamethazine, sulfadiazine, and sulfamethoxazole). Our aim was to assess changes in the urban river microbial community following incubation and to determine whether these changes were related to the trace sulfonamide additions. This work ultimately contributes to the assessment of antibiotic risks in aquatic environments.For each sediment type (e.g., bed_H), there are six samples:Duplicate initial samples representing raw river sediments (bed_H1a and bed_H2a),Duplicate samples taken after incubation with trace antibiotics (bed_H1b and bed_H2b),One sample taken after incubation without antibiotics (bed_H0),One sample taken after storing raw river sediment at 4°C for one month (bed_H3).Overall, the file includes data for 42 samples across the seven sediment types.
description: This file contains ASV abundance and taxonomy information for seven riverbed and riverbank sediment samples collected from four sites along the Beiyun River—a typical urban river that receives effluent from urban and industrial wastewater treatment plants.Using these sediments, we conducted 28-day oxic incubation experiments with and without the addition of environmentally relevant levels of sulfonamides (10 µg/L each of sulfamethazine, sulfadiazine, and sulfamethoxazole). Our aim was to assess changes in the urban river microbial community following incubation and to determine whether these changes were related to the trace sulfonamide additions. This work ultimately contributes to the assessment of antibiotic risks in aquatic environments.For each sediment type (e.g., bed_H), there are six samples:Duplicate initial samples representing raw river sediments (bed_H1a and bed_H2a),Duplicate samples taken after incubation with trace antibiotics (bed_H1b and bed_H2b),One sample taken after incubation without antibiotics (bed_H0),One sample taken after storing raw river sediment at 4°C for one month (bed_H3).Overall, the file includes data for 42 samples across the seven sediment types.
DOI: 10.15468/dl.whuqfm
title: Occurrence Download

description: A dataset containing 189 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Adonis amurensis",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 189 records from 24 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012998-260129131611470/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.7910/dvn/hcbbpl
title: Multiplexed Expansion Revealing (multiExR) manuscript raw images

description: Raw (unregistered, unprocessed, Nikon format) images accompanying Kang*, Schroeder* et al. Multiplexed Expansion Revealing (multiExR) manuscript. Images are from proteins in mouse brain tissue. See https://doi.org/10.7910/DVN/JJBULY for additional metadata.
DOI: 10.15468/dl.ewwvu6
title: Occurrence Download

description: A dataset containing 32 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Anemonastrum polyanthes",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 32 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013000-260129131611470/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.u5drk5
title: Occurrence Download

description: A dataset containing 352060 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Tracheophyta",
 "HasCoordinate is true",
 "Year is greater than or equal to 1970",
 "Year is less than or equal to 1974",
 "Geometry POLYGON((-25.0 59.0, 45.0 59.0, 45.0 64.0, -25.0 64.0, -25.0 59.0))"
 ]
}

 The dataset includes 352060 records from 156 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012973-260129131611470/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bpv3g9
title: Occurrence Download

description: A dataset containing 3808 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Leucania loreyi",
 "BasisOfRecord is Human Observation",
 "Year is greater than or equal to 1990",
 "Year is less than or equal to 2026"
 ]
}

 The dataset includes 3808 records from 85 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013003-260129131611470/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7t2h98
title: Occurrence Download

description: A dataset containing 7 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Anemone anemonoides",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 7 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013005-260129131611470/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9rj8f5
title: Occurrence Download

description: A dataset containing 65594 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "PublishingCountry is Colombia",
 {
 "and" : [
 "Country is Colombia",
 {
 "not" : {
 "Issue" : [
 "is Country coordinate mismatch"
 ]
 }
 }
 ]
 }
 ]
 },
 {
 "and" : [
 {
 "or" : [
 "Geometry POLYGON((-75.26086 5.392,-75.26086 5.3332,-75.10886 5.3332,-75.10886 5.392,-75.26086 5.392))",
 "Geometry POLYGON((-75.17798 5.38073,-75.1855 5.38041,-75.19089 5.37672,-75.1892 5.36703,-75.18073 5.35565,-75.16306 5.35565,-75.1566 5.36671,-75.16179 5.38041,-75.17798 5.38073))"
 ]
 },
 "TaxonKey is one of (Aves [GBIF Backbone Taxonomy])"
 ]
 }
 ]
}

 The dataset includes 65594 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012950-260129131611470/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9ypb3f
title: Occurrence Download

description: A dataset containing 24 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is South Africa",
 "OccurrenceStatus is Present",
 "TaxonKey is Austropuccinia psidii",
 "Year is greater than or equal to 2013"
 ]
}

 The dataset includes 24 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013004-260129131611470/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qe25xv
title: Occurrence Download

description: A dataset containing 482 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Anemone patens",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 482 records from 61 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013007-260129131611470/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.34740/kaggle/dsv/14736439
title: ONCO-360 | DATASUS | INCA | CNES | SIOPS
DOI: 10.15468/dl.75ast5
title: Occurrence Download

description: A dataset containing 103 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-87.72166 33.8949,-86.88056 33.8949,-86.88056 34.36734,-87.72166 34.36734,-87.72166 33.8949))",
 "HasGeospatialIssue is false",
 "TaxonKey is Percina sipsi"
 ]
}

 The dataset includes 103 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013008-260129131611470/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vuj48w
title: Occurrence Download

description: A dataset containing 58 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "OccurrenceStatus is Present",
 "TaxonKey is Solanum rostratum"
 ]
}

 The dataset includes 58 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013009-260129131611470/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/vbpgex
title: Odonata Central

description: This citizen science web site is focused on expanding our understanding of the distribution, biogeography, biodiversity, and identification of Odonata (dragonflies and damselflies) in the Western Hemisphere. Citizen scientists are encouraged to contribute their Odonata observations to the database using a web-based interface for submission. These observations may be human observation only or may be vouchered by photographs or specimens. An expert team of vetters reviews records of the rarer species and either accepts or declines the record based on the documentation. Declined records are not uploaded to GBIF. Odonata Central was started in 2003 but older records are accepted into the database.
DOI: 10.15468/dl.u734m7
title: Occurrence Download

description: A dataset containing 81385 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is one of (Aedes aegypti)"
 ]
}

 The dataset includes 81385 records from 112 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012985-260129131611470/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.18464368
title: Increased vulnerability of alpine soil organic carbon is associated with glomalin decline under disturbances
DOI: 10.5281/zenodo.18464367
title: Increased vulnerability of alpine soil organic carbon is associated with glomalin decline under disturbances
DOI: 10.15468/dl.a9eybv
title: Occurrence Download

description: A dataset containing 700 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Anemonella thalictroides",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 700 records from 73 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013010-260129131611470/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.18394195
title: Data and Analysis Code for "Topography-Induced Stationary Waves and the Onset of Nightside Warming on Rocky Planets around M-dwarf Stars"

description: This repository contains the model output data and Python analysis scripts required to reproduce all figures in the manuscript Topography-Induced Stationary Waves and the Onset of Nightside Warming on Rocky Planets around M-dwarf Stars by Howard Chen et al. The archive includes (i) processed simulation outputs used in the paper’s analyses and (ii) Python workflows that regenerate every figure panel from the archived data.
DOI: 10.6084/m9.figshare.30184042
title: <b>Cross-host Transmission of </b><b><i>Riemerella anatipestifer</i></b><b> to Chickens: Genomic Evolution and Identification of the Novel </b><b><i>vapX</i></b><b>-like-</b><b><i>vapD</i></b><b> Toxin-Antitoxin System</b>

description: <i>Riemerella anatipestifer </i>(<i>R. anatipestifer</i>)<i>, </i>a well-known waterfowl pathogen, increasingly threatens Chinese poultry by spreading to chickens. The genetic differentiation and host adaptation following cross-host transmission remain unclear. Here, we isolated and characterized a highly virulent, multidrug-resistant (MDR) <i>R. anatipestifer</i> strain (SDAU-RA1) in chickens and performed comparative genomics with global <i>R. anatipestifer</i> strains to elucidate population structure and evolutionary dynamics. SNP phylogeny revealed significant geographic clustering and dominant clonal groups. Strains from different hosts showed a pattern of “overall mixing with local clustering,” confirming cross-host transmission rather than strict host-specific evolution. In terms of virulence, certain virulence genes are enriched specifically in chicken-source strains. Notably, the study is the first to identify and confirm <i>vapX</i>-like-<i>vapD</i> as a functional type II toxin-antitoxin system in chicken- source <i>R. anatipestifer</i>, demonstrating that it enhances biofilm formation, intracellular survival, and the maintenance of antibiotic persisters. Analysis of the geographical distribution and temporal dynamics of antibiotic resistance genes (ARGs) reveals high heterogeneity among <i>R. anatipestifer</i> strains from different hosts. Pangenome analysis revealed that <i>R. anatipestifer</i> possesses an open pangenome, conferring high genetic plasticity. In conclusion, our study shows <i>R. anatipestifer</i> transmits to chickens without strict host-specific adaptation, though incipient genetic differentiation has emerged. The discovery of plasmid pRASD and its carried <i>vapX</i>-like-<i>vapD</i> system suggests key mechanisms for the adaptive evolution and enhanced pathogenicity of <i>R. anatipestifer</i>. These findings enhance our understanding of cross-host transmission and underscore the importance of continuous surveillance of chicken-source <i>R. anatipestifer</i> and its novel mobile genetic elements.
DOI: 10.6084/m9.figshare.30184042.v4
title: <b>Cross-host Transmission of </b><b><i>Riemerella anatipestifer</i></b><b> to Chickens: Genomic Evolution and Identification of the Novel </b><b><i>vapX</i></b><b>-like-</b><b><i>vapD</i></b><b> Toxin-Antitoxin System</b>

description: <i>Riemerella anatipestifer </i>(<i>R. anatipestifer</i>)<i>, </i>a well-known waterfowl pathogen, increasingly threatens Chinese poultry by spreading to chickens. The genetic differentiation and host adaptation following cross-host transmission remain unclear. Here, we isolated and characterized a highly virulent, multidrug-resistant (MDR) <i>R. anatipestifer</i> strain (SDAU-RA1) in chickens and performed comparative genomics with global <i>R. anatipestifer</i> strains to elucidate population structure and evolutionary dynamics. SNP phylogeny revealed significant geographic clustering and dominant clonal groups. Strains from different hosts showed a pattern of “overall mixing with local clustering,” confirming cross-host transmission rather than strict host-specific evolution. In terms of virulence, certain virulence genes are enriched specifically in chicken-source strains. Notably, the study is the first to identify and confirm <i>vapX</i>-like-<i>vapD</i> as a functional type II toxin-antitoxin system in chicken- source <i>R. anatipestifer</i>, demonstrating that it enhances biofilm formation, intracellular survival, and the maintenance of antibiotic persisters. Analysis of the geographical distribution and temporal dynamics of antibiotic resistance genes (ARGs) reveals high heterogeneity among <i>R. anatipestifer</i> strains from different hosts. Pangenome analysis revealed that <i>R. anatipestifer</i> possesses an open pangenome, conferring high genetic plasticity. In conclusion, our study shows <i>R. anatipestifer</i> transmits to chickens without strict host-specific adaptation, though incipient genetic differentiation has emerged. The discovery of plasmid pRASD and its carried <i>vapX</i>-like-<i>vapD</i> system suggests key mechanisms for the adaptive evolution and enhanced pathogenicity of <i>R. anatipestifer</i>. These findings enhance our understanding of cross-host transmission and underscore the importance of continuous surveillance of chicken-source <i>R. anatipestifer</i> and its novel mobile genetic elements.
DOI: 10.6084/m9.figshare.30184042.v5
title: <b>Cross-host Transmission of </b><b><i>Riemerella anatipestifer</i></b><b> to Chickens: Genomic Evolution and Identification of the Novel </b><b><i>vapX</i></b><b>-like-</b><b><i>vapD</i></b><b> Toxin-Antitoxin System</b>

description: <i>Riemerella anatipestifer </i>(<i>R. anatipestifer</i>)<i>, </i>a well-known waterfowl pathogen, increasingly threatens Chinese poultry by spreading to chickens. The genetic differentiation and host adaptation following cross-host transmission remain unclear. Here, we isolated and characterized a highly virulent, multidrug-resistant (MDR) <i>R. anatipestifer</i> strain (SDAU-RA1) in chickens and performed comparative genomics with global <i>R. anatipestifer</i> strains to elucidate population structure and evolutionary dynamics. SNP phylogeny revealed significant geographic clustering and dominant clonal groups. Strains from different hosts showed a pattern of “overall mixing with local clustering,” confirming cross-host transmission rather than strict host-specific evolution. In terms of virulence, certain virulence genes are enriched specifically in chicken-source strains. Notably, the study is the first to identify and confirm <i>vapX</i>-like-<i>vapD</i> as a functional type II toxin-antitoxin system in chicken- source <i>R. anatipestifer</i>, demonstrating that it enhances biofilm formation, intracellular survival, and the maintenance of antibiotic persisters. Analysis of the geographical distribution and temporal dynamics of antibiotic resistance genes (ARGs) reveals high heterogeneity among <i>R. anatipestifer</i> strains from different hosts. Pangenome analysis revealed that <i>R. anatipestifer</i> possesses an open pangenome, conferring high genetic plasticity. In conclusion, our study shows <i>R. anatipestifer</i> transmits to chickens without strict host-specific adaptation, though incipient genetic differentiation has emerged. The discovery of plasmid pRASD and its carried <i>vapX</i>-like-<i>vapD</i> system suggests key mechanisms for the adaptive evolution and enhanced pathogenicity of <i>R. anatipestifer</i>. These findings enhance our understanding of cross-host transmission and underscore the importance of continuous surveillance of chicken-source <i>R. anatipestifer</i> and its novel mobile genetic elements.
DOI: 10.15468/dl.ukrs2h
title: Occurrence Download

description: A dataset containing 1407 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Aquilegia coerulea",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 1407 records from 87 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013011-260129131611470/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.71862/7mx5-ep96
title: Data Deficiency

description: Data and R code used in the paper on Data Deficiency hotspots by Hayward et al. Map the location of data deficient species around the world, and determine the drivers of those features.

Project Background
Data deficiency is the bane of conservation status extinction risk assessments because incomplete data means we cannot accurately identify priority areas to conserve in protected area estate. Here, we use the IUCN distributions of amphibians, sharks and rays, fish, mammals, birds and reptiles to identify hotspots of Data Deficient species. We found that areas with high numbers of Data Deficient species are not randomly distributed and do not necessarily overlap with hotspots of biodiversity, particularly in the Amazon and West Africa. Data deficiency hotspots are concentrated around tropical South America, Africa, and South-east Asia, however this varies between taxa. Hotspots of data deficient amphibians are concentrated around the tropical Andean forests of Colombia, Peru and Ecuador, throughout Brazil, and in the New Guinea Highlands. The tropical forests of the Congo River basin, Papua New Guinea and The Philippines are hotspots for avian data deficiency. Data deficient Chondrichthyans are concentrated in the tropical seas, particularly around the west coast of Africa, East Asia, and the tropical Americas. Indochina is the primary hotspot for data deficient freshwater fish, while the Indo-Pacific is the primary hotspot for data deficient marine fish. Data deficient marine mammals are broadly distributed around the southern oceans, South America, South-east Asia, and North-west Africa. Data deficient herpetofauna are concentrated around tropical Asia, while tropical South America, Indonesia and central Africa are the hotspots for data deficient terrestrial mammals. While data deficiency reflects drivers of biodiversity more broadly (e.g., latitude), other factors are also influential, including the amount of conservation funding a country invests and population density. Increasing evidence suggests that data deficient species are disproportionately likely to be threatened with extinction. Scientists urgently need to focus their research efforts on these data deficiency hotspots and ensure protected area networks are suitably representative and include data deficient species. Furthermore, the accuracy of status assessments needs to be ascertained and Data Deficient species need to be prioritised for study to ensure they are not lost before we get to know them.
DOI: 10.15468/dl.zabpx4
title: Occurrence Download

description: A dataset containing 19296234 records in GBIF matching the query:
SELECT 
 "gbifid", "taxonkey", "phylum", "class", "order", "eventdate", "datasetkey", "countrycode", "stateprovince", "decimallongitude", "decimallatitude" 
FROM occurrence 
WHERE 
 ("hasgeospatialissues" = 'false') AND 
 ("hascoordinate" = 'true') AND 
 ("occurrencestatus" = 'PRESENT') AND 
 NOT("basisofrecord" IN ('FOSSIL_SPECIMEN', 'LIVING_SPECIMEN')) AND 
 ("decimallatitude" &gt;= -90) AND 
 ("decimallatitude" &lt; 91) AND 
 ("decimallongitude" &gt;= -58) AND 
 ("decimallongitude" &lt; -51) AND 
 ("year" &lt;= 2025)

 The dataset's 19296234 records were derived from 3234 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012997-260129131611470/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.