cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.3535/td9-ye8-zhe
title: Saxifraga rosacea subsp. sponhemica (C. C. Gmel.) D. A. Webb

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/v4k-qg3-cpt
title: Sparganium emersum Rehmann

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/yj1-nts-bj3
title: Cudoniella acicularis (Bull.) J. Schröt.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/ztr-3ge-jng
title: Cudoniella acicularis (Bull.) J. Schröt.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.15468/dl.t9zpjq
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/0002202-160526112335914/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ye9mas
title: Occurrence Download

description: A dataset containing 407559274 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Tracheophyta"
 ]
}

 The dataset includes 407559274 records from 11606 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021281-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qtaduh
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Rhinella marina",
 "HasCoordinate is true",
 "Country is Canada"
 ]
}

 The dataset includes 3 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011945-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.18497525
title: HitFrequencyVectors

description: The datasets contain each 5 million query sequences (16-mers) with there according Hit Frequency Vectors.

Hit Frequency Vectors conain information on the number of occurances of approximated strings given a dissimilarity threshold.

Columns: site, bin[0-16] (one column per bin)



HDE contains exactly computed Hit Frequency Vectors based on Hamming distance

HDA contains approximated Hit Frequency Vectors based on Hamming distance

EDA contains approximated Hit Frequency Vectors based on edit distance


The zipped folders contain prediction results for each of the datasets for 2 predicitve models BUT and KD.
DOI: 10.5281/zenodo.18497524
title: HitFrequencyVectors

description: The datasets contain each 5 million query sequences (16-mers) with there according Hit Frequency Vectors.

Hit Frequency Vectors conain information on the number of occurances of approximated strings given a dissimilarity threshold.

Columns: site, bin[0-16] (one column per bin)



HDE contains exactly computed Hit Frequency Vectors based on Hamming distance

HDA contains approximated Hit Frequency Vectors based on Hamming distance

EDA contains approximated Hit Frequency Vectors based on edit distance


The zipped folders contain prediction results for each of the datasets for 2 predicitve models BUT and KD.
DOI: 10.15468/dl.2zz98c
title: Occurrence Download

description: A dataset containing 59 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Rhinella marina",
 "HasCoordinate is true",
 "Country is Barbados"
 ]
}

 The dataset includes 59 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011944-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.21954/ou.rd.31289674
title: Supplementary data: Cutler et al., "Dynamic Earth System response to interacting climate forcing factors through the Penultimate Deglaciation and Last Interglacial"

description: Model code and data associated with the accepted manuscript, Cutler et al., "Dynamic Earth System response to interacting climate forcing factors through the Penultimate Deglaciation and Last Interglacial" in the journal Paleoceanography and Paleoclimatology.PLASIM-GENIE model code and modifications.Model boundary conditions and configuration files.Processed model output for Global Mean Surface Temperature, Atlantic Meridional Overturning Circulation, Indian and Southeast Asian monsoon regions precipitation.
DOI: 10.21954/ou.rd.31289674.v1
title: Supplementary data: Cutler et al., "Dynamic Earth System response to interacting climate forcing factors through the Penultimate Deglaciation and Last Interglacial"

description: Model code and data associated with the accepted manuscript, Cutler et al., "Dynamic Earth System response to interacting climate forcing factors through the Penultimate Deglaciation and Last Interglacial" in the journal Paleoceanography and Paleoclimatology.PLASIM-GENIE model code and modifications.Model boundary conditions and configuration files.Processed model output for Global Mean Surface Temperature, Atlantic Meridional Overturning Circulation, Indian and Southeast Asian monsoon regions precipitation.
DOI: 10.15468/dl.szwmhy
title: Occurrence Download

description: A dataset containing 268 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Clitandra cymulosa",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 268 records from 21 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011947-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9ze4ck
title: Occurrence Download

description: A dataset containing 62 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Pilea cornutocucullata"
 ]
}

 The dataset includes 62 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011949-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.beat4v
title: Occurrence Download

description: A dataset containing 84538 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Oecetis",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 84538 records from 356 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011873-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.97ykt8
title: Occurrence Download

description: A dataset containing 228 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Rhinella marina",
 "HasCoordinate is true",
 "Country is Dominican Republic"
 ]
}

 The dataset includes 228 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011950-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ykgm2p
title: Occurrence Download

description: A dataset containing 74 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Rhinella marina",
 "HasCoordinate is true",
 "Country is Micronesia (Federated States of)"
 ]
}

 The dataset includes 74 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011951-260208012135463/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.31240696
title: Rapid drug resistance prediction in positive <i>Mycobacterium tuberculosis</i> clinical samples using an extensive targeted next-generation sequencing panel

description: Tuberculosis (TB) remains a global health challenge, exacerbated by the emergence of drug-resistant <i>Mycobacterium tuberculosis</i> strains. Most methods for drug susceptibility testing (DST) are culture-dependent and time consuming, possibly delaying optimal TB-treatment. This study aimed to develop an extensive targeted next-generation sequencing (tNGS) approach for rapid genotypic DST directly from clinical samples. We designed a tNGS panel comprising 30 amplicons targeting 19 genomic regions associated with resistance to 20 antibiotics. This method was applied to 71 smear-positive (0–3+) pulmonary TB clinical samples collected at the Portuguese National Reference Laboratory. DNA was extracted and amplified using multiplex PCRs, followed by sequencing on Oxford Nanopore Technologies MinION platform. Sequencing data were using TB-Profiler and the tNGS results compared to phenotypic DST and whole genome sequencing (WGS) data from corresponding isolates. The tNGS demonstrated high concordance with both phenotypic and WGS-based DST across different sample types and smear positivity levels. For first-line drugs, tNGS showed 88% categorical agreement (CA) with pDST, increasing to 97% when excluding undetermined results. Compared to WGS across all analysed antibiotics, tNGS achieved 92% CA, increasing to &gt;99% when excluding undetermined results. Validation of the tNGS panel showed 90% (1,895/2,076) of amplicons reaching &gt;10x coverage at all analysed positions and 43 (61%) samples with all complete amplicons above this threshold. Non-specific amplification of contaminant bacterial DNA was minimal, with most mapped off-target reads being of human origin. This method enables comprehensive resistance prediction directly from clinical samples and signifies an important development in TB diagnostics and resistance monitoring.
DOI: 10.6084/m9.figshare.31240696.v1
title: Rapid drug resistance prediction in positive <i>Mycobacterium tuberculosis</i> clinical samples using an extensive targeted next-generation sequencing panel

description: Tuberculosis (TB) remains a global health challenge, exacerbated by the emergence of drug-resistant <i>Mycobacterium tuberculosis</i> strains. Most methods for drug susceptibility testing (DST) are culture-dependent and time consuming, possibly delaying optimal TB-treatment. This study aimed to develop an extensive targeted next-generation sequencing (tNGS) approach for rapid genotypic DST directly from clinical samples. We designed a tNGS panel comprising 30 amplicons targeting 19 genomic regions associated with resistance to 20 antibiotics. This method was applied to 71 smear-positive (0–3+) pulmonary TB clinical samples collected at the Portuguese National Reference Laboratory. DNA was extracted and amplified using multiplex PCRs, followed by sequencing on Oxford Nanopore Technologies MinION platform. Sequencing data were using TB-Profiler and the tNGS results compared to phenotypic DST and whole genome sequencing (WGS) data from corresponding isolates. The tNGS demonstrated high concordance with both phenotypic and WGS-based DST across different sample types and smear positivity levels. For first-line drugs, tNGS showed 88% categorical agreement (CA) with pDST, increasing to 97% when excluding undetermined results. Compared to WGS across all analysed antibiotics, tNGS achieved 92% CA, increasing to &gt;99% when excluding undetermined results. Validation of the tNGS panel showed 90% (1,895/2,076) of amplicons reaching &gt;10x coverage at all analysed positions and 43 (61%) samples with all complete amplicons above this threshold. Non-specific amplification of contaminant bacterial DNA was minimal, with most mapped off-target reads being of human origin. This method enables comprehensive resistance prediction directly from clinical samples and signifies an important development in TB diagnostics and resistance monitoring.
DOI: 10.26071/90af2587-227a-44d2
title: CTD Data for the 2023 C2023-01 Cruise in the Saint-Lawrence Estuary
title: Données CTD de la mission C2023-01 2023 dans l'estuaire du Saint-Laurent

description: The objective of mission C2023-01 (id: 2023_16) is to collect vibration and acoustic data in the St. Lawrence Estuary.
The mission aims to address two major issues: the loss of dissolved oxygen in the bottom waters of the Laurentian Channel, which affects ecosystems and has economic repercussions, and the noise generated by maritime traffic, which affects aquatic wildlife.
As part of this mission, vertical CTD (conductivity, temperature, depth) profiles were taken at three sites between Sainte-Luce and Saint-Ulric. The CTD was also equipped with sensors to measure dissolved oxygen, clarity, fluorescence, and pH in the water column. 
In addition, four hydrophone moorings comprising the MARS station were deployed. These hydrophones were designed to observe ambient noise and noise generated by maritime traffic in the St. Lawrence Estuary.
This dataset is part of the EDMS-ISMER-QO collection.
description: Le but de la mission C2023-01 (id : 2023_16) est la collecte de données vibratoires et acoustique dans l’estuaire du Saint-Laurent.
La mission doit permettre de répondre à 2 enjeux majeurs, soit la perte d’oxygène dissous dans les eaux de fond du chenal Laurentien qui affecte les écosystèmes avec des répercussion économiques et le bruit engendré par le trafic maritime qui affecte la faune aquatique.
Dans le cadre de cette mission, des profils verticaux CTD (conductivité, température, profondeur), répartis sur 3 sites comprenant 3 entre Sainte-Luce et Saint-Ulric, ont été réalisés. La CTD était également équipée de capteurs pour mesurer l'oxygène dissous, la clareté, la fluorescence et le pH dans la colonne d'eau. 
De plus, quatre mouillages d'hydrophones constituant la station MARS ont été déployés. Ces hydrophones étaient destinés à observer le bruit ambiant et généré par le trafic maritime dans l’estuaire du Saint-Laurent.
Ce jeu de données fait partie de la collection SGDE-ISMER-QO
DOI: 10.6084/m9.figshare.31239331
title: The emergence and biological characteristics of linezolid-resistant <i>Clostridioides difficile</i> isolates in the Asia-Pacific region

description: Linezolid-resistant <i>Clostridioides difficile,</i> conferred by the acquisition of <i>cfr</i>-like genes, has been reported in Europe and America. However, the emergence of linezolid resistance in <i>C. difficile</i> in the Asia-Pacific region and its impacts on <i>C. difficile</i> pathogenicity remain unclear. In this study, 881 <i>C. difficile</i> isolates from the Asia-Pacific region were screened for <i>cfr</i>-like genes. Whole genome sequencing was performed on 16 <i>cfr</i>-like gene-positive isolates from four countries. Thirteen isolates possessed <i>cfr</i>(B), which was located within Tn<i>6218</i>, while three isolates possessed <i>cfr</i>(C), which was located within the integrative and conjugative elements (ICE) F548 and DA275. Fourteen (87.5%, 14/16) of the <i>cfr</i>-like gene-positive isolates were resistant to linezolid. In comparison to the two isolates susceptible to linezolid, these 14 isolates exhibited significantly higher mRNA expression levels of <i>cfr</i>(B) and <i>cfr</i>(C), along with significantly higher bacterial density at 12 h. Conversely, they demonstrated reduced abilities for sporulation and biofilm formation. After the <i>cfr</i>(B) gene was knocked down by the CRISPR interference, the <i>C. difficile</i> strain presented lower bacterial density at 12 h, higher toxin production and stronger sporulation and biofilm formation abilities. Our findings reveal the emergence of <i>cfr</i>-like genes <i>C. difficile</i> isolates in the Asia-Pacific region, highlighting that <i>cfr</i>-like genes not only mediate linezolid resistance but also contribute to regulating pathogenic potential. Linezolid resistance in CDI should be closely monitored in specific patients.
DOI: 10.6084/m9.figshare.31239331.v1
title: The emergence and biological characteristics of linezolid-resistant <i>Clostridioides difficile</i> isolates in the Asia-Pacific Region

description: Linezolid-resistant <i>Clostridioides difficile,</i> conferred by the acquisition of <i>cfr</i>-like genes, has been reported in Europe and America. However, the emergence of linezolid resistance in <i>C. difficile</i> in the Asia-Pacific region and its impacts on <i>C. difficile</i> pathogenicity remain unclear. In this study, 881 <i>C. difficile</i> isolates from the Asia-Pacific region were screened for <i>cfr</i>-like genes. Whole genome sequencing was performed on 16 <i>cfr</i>-like gene-positive isolates from four countries. Thirteen isolates possessed <i>cfr</i>(B), which was located within Tn<i>6218</i>, while three isolates possessed <i>cfr</i>(C), which was located within the integrative and conjugative elements (ICE) F548 and DA275. Fourteen (87.5%, 14/16) of the <i>cfr</i>-like gene-positive isolates were resistant to linezolid. In comparison to the two isolates susceptible to linezolid, these 14 isolates exhibited significantly higher mRNA expression levels of <i>cfr</i>(B) and <i>cfr</i>(C), along with significantly higher bacterial density at 12 h. Conversely, they demonstrated reduced abilities for sporulation and biofilm formation. After the <i>cfr</i>(B) gene was knocked down by the CRISPR interference, the <i>C. difficile</i> strain presented lower bacterial density at 12 h, higher toxin production and stronger sporulation and biofilm formation abilities. Our findings reveal the emergence of <i>cfr</i>-like genes <i>C. difficile</i> isolates in the Asia-Pacific region, highlighting that <i>cfr</i>-like genes not only mediate linezolid resistance but also contribute to regulating pathogenic potential. Linezolid resistance in CDI should be closely monitored in specific patients.
DOI: 10.6084/m9.figshare.31239331.v2
title: The emergence and biological characteristics of linezolid-resistant <i>Clostridioides difficile</i> isolates in the Asia-Pacific region

description: Linezolid-resistant <i>Clostridioides difficile,</i> conferred by the acquisition of <i>cfr</i>-like genes, has been reported in Europe and America. However, the emergence of linezolid resistance in <i>C. difficile</i> in the Asia-Pacific region and its impacts on <i>C. difficile</i> pathogenicity remain unclear. In this study, 881 <i>C. difficile</i> isolates from the Asia-Pacific region were screened for <i>cfr</i>-like genes. Whole genome sequencing was performed on 16 <i>cfr</i>-like gene-positive isolates from four countries. Thirteen isolates possessed <i>cfr</i>(B), which was located within Tn<i>6218</i>, while three isolates possessed <i>cfr</i>(C), which was located within the integrative and conjugative elements (ICE) F548 and DA275. Fourteen (87.5%, 14/16) of the <i>cfr</i>-like gene-positive isolates were resistant to linezolid. In comparison to the two isolates susceptible to linezolid, these 14 isolates exhibited significantly higher mRNA expression levels of <i>cfr</i>(B) and <i>cfr</i>(C), along with significantly higher bacterial density at 12 h. Conversely, they demonstrated reduced abilities for sporulation and biofilm formation. After the <i>cfr</i>(B) gene was knocked down by the CRISPR interference, the <i>C. difficile</i> strain presented lower bacterial density at 12 h, higher toxin production and stronger sporulation and biofilm formation abilities. Our findings reveal the emergence of <i>cfr</i>-like genes <i>C. difficile</i> isolates in the Asia-Pacific region, highlighting that <i>cfr</i>-like genes not only mediate linezolid resistance but also contribute to regulating pathogenic potential. Linezolid resistance in CDI should be closely monitored in specific patients.
DOI: 10.6084/m9.figshare.31325417
title: Involvement of the African swine fever virus protein pH108R in virion morphogenesis

description: African swine fever virus (ASFV) is the causative agent of the highly contagious and devastating haemorrhagic swine disease for which there are no effective vaccines or treatments available. The ASFV infectious cycle initiates with the viral absorption and entry into the host cell, then ASFV undergoes the uncoating process, viral inner envelope and endosome membrane fusion, DNA replication and gene transcription as well as translation, subsequently ASFV morphogenesis takes place within viral factories. ASFV morphogenesis is highly complex, and the mechanisms involved in ASFV morphogenesis are not well understood at present. Here, we reported that the inner envelope protein pH108R is involved in the ASFV morphogenesis. Interestingly, the absence of pH108R results in the formation of large numbers of tubular structures and bilobulate structures, providing evidence that pH108R plays a role in ASFV morphogenesis. Furthermore, the absence of pH108R inhibits the proteolytic processing of core-shell polyproteins pp220 and pp62. pH108R is identified as associated with capsid proteins p49 and p72, displaying the function of pH108R in the assembly of the capsid. Besides, the absence of pH108R reduces the protein levels of pA104R. Additionally, the pathogenicity of the pH108R-deleted ASFV strain is attenuated in pigs compared with the parental virus. These findings elucidate the regulatory role of pH108R in ASFV morphogenesis and provide an attractive target for vaccine development.
DOI: 10.6084/m9.figshare.31325417.v1
title: Involvement of the African swine fever virus protein pH108R in virion morphogenesis

description: African swine fever virus (ASFV) is the causative agent of the highly contagious and devastating haemorrhagic swine disease for which there are no effective vaccines or treatments available. The ASFV infectious cycle initiates with the viral absorption and entry into the host cell, then ASFV undergoes the uncoating process, viral inner envelope and endosome membrane fusion, DNA replication and gene transcription as well as translation, subsequently ASFV morphogenesis takes place within viral factories. ASFV morphogenesis is highly complex, and the mechanisms involved in ASFV morphogenesis are not well understood at present. Here, we reported that the inner envelope protein pH108R is involved in the ASFV morphogenesis. Interestingly, the absence of pH108R results in the formation of large numbers of tubular structures and bilobulate structures, providing evidence that pH108R plays a role in ASFV morphogenesis. Furthermore, the absence of pH108R inhibits the proteolytic processing of core-shell polyproteins pp220 and pp62. pH108R is identified as associated with capsid proteins p49 and p72, displaying the function of pH108R in the assembly of the capsid. Besides, the absence of pH108R reduces the protein levels of pA104R. Additionally, the pathogenicity of the pH108R-deleted ASFV strain is attenuated in pigs compared with the parental virus. These findings elucidate the regulatory role of pH108R in ASFV morphogenesis and provide an attractive target for vaccine development.
DOI: 10.15468/dl.ep3cwc
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Conomitra linearis",
 "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/0011952-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.18623613
title: AI Transformation, Resource Reallocation, and Corporate Capacity Utilization
DOI: 10.5281/zenodo.18623614
title: AI Transformation, Resource Reallocation, and Corporate Capacity Utilization