cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.27158950
title: Biology and genetic diversity of <i>Candida krusei</i> isolates from fermented vegetables and clinical samples in China

description: <i>Candida krusei</i>, also known as <i>Pichia kudriavzevii</i>, is an emerging non-<i>albicans Candida</i> (NAC) species causing both superficial and deep-seated infections in humans. This fungal pathogen is inherently resistant to the first-line antifungal drug, fluconazole, and is widely distributed in natural environments such as soil, foods, vegetables, and fruits. In this study, we collected 86 <i>C. krusei</i> strains from clinical settings and traditional fermented vegetables from different areas of China. Compared to <i>C. krusei</i> strains from fermented vegetables, clinical isolates exhibited a higher ability to undergo filamentation and biofilm development, which could facilitate its host colonization and infections. Isolates from fermented vegetables showed higher resistance to several antifungal drugs including fluconazole, voriconazole, itraconazole, amphotericin B, and caspofungin, than clinical strains, while they were more susceptible to posaconazole than clinical strains. Although <i>C. krusei</i> has been thought to be a diploid organism, we found that one-fourth of clinical strains and the majority of isolates from fermented vegetables (87.5%) are triploid. Whole-genome sequencing and population genetic analyses demonstrated that isolates from clinical settings and fermented food are genetically associated, and distributed across a wide range of genetic clusters. Additionally, we found that six nucleotide substitutions at the promoter region of the <i>ABC11</i> gene, encoding a multidrug efflux pump, could play a critical role in antifungal resistance in this species. Given the ubiquitous distribution of <i>C. krusei</i> strains in fermented vegetables and their genetic association with clinical strains, a One Health approach will be necessary to control the prevalence of this pathogen.
DOI: 10.6084/m9.figshare.27158950.v1
title: Biology and genetic diversity of <i>Candida krusei</i> isolates from fermented vegetables and clinical samples in China

description: <i>Candida krusei</i>, also known as <i>Pichia kudriavzevii</i>, is an emerging non-<i>albicans Candida</i> (NAC) species causing both superficial and deep-seated infections in humans. This fungal pathogen is inherently resistant to the first-line antifungal drug, fluconazole, and is widely distributed in natural environments such as soil, foods, vegetables, and fruits. In this study, we collected 86 <i>C. krusei</i> strains from clinical settings and traditional fermented vegetables from different areas of China. Compared to <i>C. krusei</i> strains from fermented vegetables, clinical isolates exhibited a higher ability to undergo filamentation and biofilm development, which could facilitate its host colonization and infections. Isolates from fermented vegetables showed higher resistance to several antifungal drugs including fluconazole, voriconazole, itraconazole, amphotericin B, and caspofungin, than clinical strains, while they were more susceptible to posaconazole than clinical strains. Although <i>C. krusei</i> has been thought to be a diploid organism, we found that one-fourth of clinical strains and the majority of isolates from fermented vegetables (87.5%) are triploid. Whole-genome sequencing and population genetic analyses demonstrated that isolates from clinical settings and fermented food are genetically associated, and distributed across a wide range of genetic clusters. Additionally, we found that six nucleotide substitutions at the promoter region of the <i>ABC11</i> gene, encoding a multidrug efflux pump, could play a critical role in antifungal resistance in this species. Given the ubiquitous distribution of <i>C. krusei</i> strains in fermented vegetables and their genetic association with clinical strains, a One Health approach will be necessary to control the prevalence of this pathogen.
DOI: 10.6084/m9.figshare.25921603
title: Integrative and conjugative elements of <i>Pasteurella multocida</i>: Prevalence and signatures in population evolution

description: <i>Pasteurella multocida</i> (<i>P. multocida</i>) is a bacterial pathogen responsible for a range of infections in humans and various animal hosts, causing significant economic losses in farming. Integrative and conjugative elements (ICEs) are important horizontal gene transfer elements, potentially enabling host bacteria to enhance adaptability by acquiring multiple functional genes. However, the understanding of ICEs in <i>P. multocida</i> and their impact on the transmission of this pathogen remains limited. In this study, 42 poultry-sourced <i>P. multocida</i> genomes obtained by high-throughput sequencing together with 393 publicly available <i>P. multocida</i> genomes were used to analyse the horizontal transfer of ICEs. Eighty-two ICEs were identified in <i>P. multocida</i>, including SXT/R391 and Tn916 subtypes, as well as three subtypes of ICE<i>Hin</i>1056 family, with the latter being widely prevalent in <i>P. multocida</i> and carrying multiple resistance genes. The correlations between insertion sequences and resistant genes in ICEs were also identified, and some ICEs introduced the carbapenem gene <i>bla</i><sub>OXA-2</sub> and the bleomycin gene <i>bleO</i> to <i>P. multocida</i>. Phylogenetic and collinearity analyses of these bioinformatics found that ICEs in <i>P. multocida</i> were transmitted vertically and horizontally and have evolved with host specialization. These findings provide insight into the transmission and evolution mode of ICEs in <i>P. multocida</i> and highlight the importance of understanding these elements for controlling the spread of antibiotic resistance.
DOI: 10.6084/m9.figshare.25921603.v1
title: Integrative and conjugative elements of <i>Pasteurella multocida</i>: Prevalence and signatures in population evolution

description: <i>Pasteurella multocida</i> (<i>P. multocida</i>) is a bacterial pathogen responsible for a range of infections in humans and various animal hosts, causing significant economic losses in farming. Integrative and conjugative elements (ICEs) are important horizontal gene transfer elements, potentially enabling host bacteria to enhance adaptability by acquiring multiple functional genes. However, the understanding of ICEs in <i>P. multocida</i> and their impact on the transmission of this pathogen remains limited. In this study, 42 poultry-sourced <i>P. multocida</i> genomes obtained by high-throughput sequencing together with 393 publicly available <i>P. multocida</i> genomes were used to analyse the horizontal transfer of ICEs. Eighty-two ICEs were identified in <i>P. multocida</i>, including SXT/R391 and Tn916 subtypes, as well as three subtypes of ICE<i>Hin</i>1056 family, with the latter being widely prevalent in <i>P. multocida</i> and carrying multiple resistance genes. The correlations between insertion sequences and resistant genes in ICEs were also identified, and some ICEs introduced the carbapenem gene <i>bla</i><sub>OXA-2</sub> and the bleomycin gene <i>bleO</i> to <i>P. multocida</i>. Phylogenetic and collinearity analyses of these bioinformatics found that ICEs in <i>P. multocida</i> were transmitted vertically and horizontally and have evolved with host specialization. These findings provide insight into the transmission and evolution mode of ICEs in <i>P. multocida</i> and highlight the importance of understanding these elements for controlling the spread of antibiotic resistance.
DOI: 10.6084/m9.figshare.27210025
title: Bactericidal and anti-quorum sensing activity of repurposing drug Visomitin against <i>Staphylococcus aureus</i>

description: With the growing antibiotic resistance in <i>Staphylococcus aureus</i>, it is imperative to develop innovative therapeutic strategies against new targets to reduce selective survival pressures and incidence of resistance. In <i>S. aureus</i>, interbacterial communication relies on a quorum sensing system that regulates gene expression and physiological activities. Here, we identified that Visomitin, an antioxidant small molecule, exhibited bactericidal efficacy against methicillin-resistant <i>S. aureus</i> and its high tolerance phenotypes like intracellular bacteria and persister cells without inducing resistance. Critically, sub-minimal inhibitory concentrations (sub-MICs) of Visomitin could serve as a potent quorum-quencher reducing virulence production (such as haemolysin and staphyloxanthin), along with inhibiting biofilm formation, self-aggregation, and colony spreading of <i>S. aureus</i>. These effects were probably mediated by interfering with the <i>S. aureus</i> accessory gene regulator quorum sensing system. In summary, our findings suggest that Visomitin shows dual antimicrobial effects, including bactericidal effects at the concentrations above MIC and quorum sensing inhibition effects at sub-MICs, which holds promise for treating MRSA-related refractory infections.
DOI: 10.6084/m9.figshare.27210025.v2
title: Bactericidal and anti-quorum sensing activity of repurposing drug Visomitin against <i>Staphylococcus aureus</i>

description: With the growing antibiotic resistance in <i>Staphylococcus aureus</i>, it is imperative to develop innovative therapeutic strategies against new targets to reduce selective survival pressures and incidence of resistance. In <i>S. aureus</i>, interbacterial communication relies on a quorum sensing system that regulates gene expression and physiological activities. Here, we identified that Visomitin, an antioxidant small molecule, exhibited bactericidal efficacy against methicillin-resistant <i>S. aureus</i> and its high tolerance phenotypes like intracellular bacteria and persister cells without inducing resistance. Critically, sub-minimal inhibitory concentrations (sub-MICs) of Visomitin could serve as a potent quorum-quencher reducing virulence production (such as haemolysin and staphyloxanthin), along with inhibiting biofilm formation, self-aggregation, and colony spreading of <i>S. aureus</i>. These effects were probably mediated by interfering with the <i>S. aureus</i> accessory gene regulator quorum sensing system. In summary, our findings suggest that Visomitin shows dual antimicrobial effects, including bactericidal effects at the concentrations above MIC and quorum sensing inhibition effects at sub-MICs, which holds promise for treating MRSA-related refractory infections.
DOI: 10.6084/m9.figshare.27210025.v1
title: Bactericidal and anti-quorum sensing activity of repurposing drug visomitin against <i>staphylococcus aureus</i>

description: With the growing antibiotic resistance in <i>Staphylococcus aureus</i>, it is imperative to develop innovative therapeutic strategies against new targets to reduce selective survival pressures and incidence of resistance. In <i>S. aureus</i>, interbacterial communication relies on a quorum sensing system that regulates gene expression and physiological activities. Here, we identified that Visomitin, an antioxidant small molecule, exhibited bactericidal efficacy against methicillin-resistant <i>S. aureus</i> and its high tolerance phenotypes like intracellular bacteria and persister cells without inducing resistance. Critically, sub-minimal inhibitory concentrations (sub-MICs) of Visomitin could serve as a potent quorum-quencher reducing virulence production (such as haemolysin and staphyloxanthin), along with inhibiting biofilm formation, self-aggregation, and colony spreading of <i>S. aureus</i>. These effects were probably mediated by interfering with the <i>S. aureus</i> accessory gene regulator quorum sensing system. In summary, our findings suggest that Visomitin shows dual antimicrobial effects, including bactericidal effects at the concentrations above MIC and quorum sensing inhibition effects at sub-MICs, which holds promise for treating MRSA-related refractory infections.
DOI: 10.15468/dl.fds2a9
title: Occurrence Download

description: A dataset containing 8540 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is one of (Rana boylii)"
 ]
}

 The dataset includes 8540 records from 59 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008456-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8nt8qf
title: Occurrence Download

description: A dataset containing 1746 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-74.23759 4.99504,-74.24155 4.99074,-74.23971 4.98234,-74.2309 4.97476,-74.22734 4.97544,-74.21976 4.98241,-74.21874 4.98801,-74.21901 4.99238,-74.23274 4.99641,-74.23759 4.99504))",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 1746 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008457-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.j2ak7u
title: Occurrence Download

description: A dataset containing 45 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Phleum paniculatum",
 "Country is Estonia",
 "HasCoordinate is true"
 ]
}

 The dataset includes 45 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008460-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gybc48
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Phleum paniculatum",
 "Country is Denmark",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008458-250914085247600/datasets/export for details.
DOI: 10.15468/dl.2pmkf2
title: Occurrence Download

description: A dataset listing the 148 species recorded in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "PublishingCountry is Colombia",
 {
 "and" : [
 "Country is Colombia",
 {
 "not" : {
 "Issue" : [
 "is Country coordinate mismatch"
 ]
 }
 }
 ]
 }
 ]
 },
 {
 "and" : [
 "StateProvince is one of (Magdalena)",
 "Elevation 10-400m",
 "TaxonKey is one of (Mammalia [GBIF Backbone Taxonomy])",
 "Year 2015-2025"
 ]
 }
 ]
}

 The dataset's 148 records were derived from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008446-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hszgpt
title: Occurrence Download

description: A dataset containing 384 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Pseudochama exogyra",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Observation, Machine Observation, Human Observation, Occurrence evidence)",
 {
 "not" : {
 "OccurrenceStatus" : [
 "is one of (Absent)"
 ]
 }
 }
 ]
}

 The dataset includes 384 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008462-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7xjz56
title: Occurrence Download

description: A dataset containing 21 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Phleum paniculatum",
 "Country is Latvia",
 "HasCoordinate is true"
 ]
}

 The dataset includes 21 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008461-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6muzav
title: Occurrence Download

description: A dataset containing 288325 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Teiidae",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 288325 records from 621 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008403-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.r577hu
title: Occurrence Download

description: A dataset containing 14 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Europe",
 "Month is one of (May, June, July, August, September, October, November, December, January, February, March, April)",
 "TaxonKey is Exobasidium ledi",
 "Year 2023-2025"
 ]
}

 The dataset includes 14 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008463-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.99w77d
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Potamocorbula fasciata",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Observation, Machine Observation, Human Observation, Occurrence evidence)",
 {
 "not" : {
 "OccurrenceStatus" : [
 "is one of (Absent)"
 ]
 }
 }
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008467-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zzk2ba
title: Occurrence Download

description: A dataset containing 24 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Phleum paniculatum",
 "Country is Netherlands",
 "HasCoordinate is true"
 ]
}

 The dataset includes 24 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008466-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.asjs5q
title: Occurrence Download

description: A dataset containing 71 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Phleum paniculatum",
 "Country is Russian Federation",
 "HasCoordinate is true"
 ]
}

 The dataset includes 71 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008468-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14501223
title: MSM116 Heat flow measurements from 3.5m heat flow lance and MTL loggers

description: MSM116 Heat flow measurements from 3.5m heat flow lance and MTL loggers. Is supplement to https://dx.doi.org/10.48433/cr_msm116.
DOI: 10.5281/zenodo.14501224
title: MSM116 Heat flow measurements from 3.5m heat flow lance and MTL loggers

description: MSM116 Heat flow measurements from 3.5m heat flow lance and MTL loggers. Is supplement to https://dx.doi.org/10.48433/cr_msm116.
DOI: 10.15468/dl.dmhgtb
title: Occurrence Download

description: A dataset containing 5077 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Sporobolus fertilis (Steud.) Clayton",
 "Year 1970-2025"
 ]
}

 The dataset includes 5077 records from 106 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005666-250117142028555/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.m6zcnz
title: Occurrence Download

description: A dataset containing 18 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "TaxonKey is Rafflesia lagascae Blanco"
 ]
}

 The dataset includes 18 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005667-250117142028555/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.q4qs7z
title: Occurrence Download

description: A dataset containing 88271 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Netherlands",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "PublishingOrg is one of (642dd0e8-2661-4e9a-93b3-340976a8565e, e2e717bf-551a-4917-bdc9-4fa0f342c530, 815809f1-e6e6-44df-b3fd-b17a9d87eada, 28eb1a3f-1c15-4a95-931a-4af90ecb574d, bb646dff-a905-4403-a49b-6d378c2cf0d9, 0c6d40e3-5d96-4a2d-9342-b02833aaa766, 1f00d75c-f6fc-4224-a595-975e82d7689c, 396d5f30-dea9-11db-8ab4-b8a03c50a862, 04fd2e13-6881-4e5c-9dd1-8fdd9ab993c1)",
 "TaxonKey is Passer domesticus (Linnaeus, 1758)",
 "Year is greater than or equal to 2015"
 ]
}

 The dataset includes 88271 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005665-250117142028555/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14501100
title: Expedition MSM116 MeBo core Color Linescan Data

description: Expedition MSM116 MeBo core color linescan data. Is supplement to https://dx.doi.org/10.48433/cr_msm116.
DOI: 10.5281/zenodo.14501101
title: Expedition MSM116 MeBo core Color Linescan Data

description: Expedition MSM116 MeBo core color linescan data. Is supplement to https://dx.doi.org/10.48433/cr_msm116.
DOI: 10.57745/6ro2mv
title: normales.zip

description: normales (période 1990 − 2020) des indicateurs agroclimatiques calculés dans l'application AgroMetInfo à l'échelle de la maille SAFRAN
DOI: 10.15468/dl.7rj86m
title: Occurrence Download

description: A dataset containing 148 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Rubus lobatidens H.E.Weber & Stohr",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 148 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0084296-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ub8cdq
title: Occurrence Download

description: A dataset containing 9781 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Nehalennia Selys, 1850"
 ]
}

 The dataset includes 9781 records from 90 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0219439-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wi2npd
title: Occurrence Download

description: A dataset containing 7076556 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Great Backyard Bird Count"
 ]
}

 The dataset includes 7076556 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005176-190813142620410/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kdvn3v
title: Occurrence Download

description: A dataset containing 55 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Eubalaena japonica (Lacépède, 1818)"
 ]
}

 The dataset includes 55 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0238506-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.