cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.30073830
title: Anti-plasmid defense in hypervirulent <i>Klebsiella pneumoniae</i> involves Type I-like and Type IV restriction modification systems

description: Hypervirulent <i>Klebsiella pneumoniae</i> (hvKp) and classical multidrug-resistant (MDR) strains belong to distinct lineages and hvKp are typically characterized by hypermucoid capsules that have been shown to limit horizontal gene transfer (HGT), including plasmid acquisition. However, the convergence of hypervirulence and MDR is increasingly common worldwide. When we profiled 127 antibiotic-susceptible hvKp strains, we found that most (86%) are highly permissive to plasmid transfer despite their capsules. In the few strains that showed low permissiveness, we identified two restriction modification (RM) systems: the Type IV restriction system McrBC that targets bacteriophage, and a unique Type I RM system. Both systems effectively inhibit plasmid uptake in recipient strains. Further analysis reveals that L-arginine and spermidine metabolism regulates the Type I-like RM system through S-adenosyl methionine. Strains lacking these RM systems were highly receptive to plasmids, and clinical isolates worldwide often lack these systems, correlating with their antibiotic resistance. Collectively, our study provides the first report on the susceptibility of hvKp strains to plasmid transfer and evidence of unusual RM systems restricting plasmid acquisition. It reveals an arms race between plasmids evolving to bypass RM systems and host strains developing new defenses. This dynamic and the rarity of these RM systems help explain the emergence of MDR hvKp strains in clinical settings driven by antibiotic pressure.
DOI: 10.6084/m9.figshare.30073830.v2
title: Anti-plasmid defense in hypervirulent <i>Klebsiella pneumoniae</i> involves Type I-like and Type IV restriction modification systems

description: Hypervirulent <i>Klebsiella pneumoniae</i> (hvKp) and classical multidrug-resistant (MDR) strains belong to distinct lineages and hvKp are typically characterized by hypermucoid capsules that have been shown to limit horizontal gene transfer (HGT), including plasmid acquisition. However, the convergence of hypervirulence and MDR is increasingly common worldwide. When we profiled 127 antibiotic-susceptible hvKp strains, we found that most (86%) are highly permissive to plasmid transfer despite their capsules. In the few strains that showed low permissiveness, we identified two restriction modification (RM) systems: the Type IV restriction system McrBC that targets bacteriophage, and a unique Type I RM system. Both systems effectively inhibit plasmid uptake in recipient strains. Further analysis reveals that L-arginine and spermidine metabolism regulates the Type I-like RM system through S-adenosyl methionine. Strains lacking these RM systems were highly receptive to plasmids, and clinical isolates worldwide often lack these systems, correlating with their antibiotic resistance. Collectively, our study provides the first report on the susceptibility of hvKp strains to plasmid transfer and evidence of unusual RM systems restricting plasmid acquisition. It reveals an arms race between plasmids evolving to bypass RM systems and host strains developing new defenses. This dynamic and the rarity of these RM systems help explain the emergence of MDR hvKp strains in clinical settings driven by antibiotic pressure.
DOI: 10.6084/m9.figshare.30073830.v1
title: Anti-plasmid defense in hypervirulent <i>Klebsiella pneumoniae</i> involves Type I-like and Type IV restriction modification systems

description: Hypervirulent <i>Klebsiella pneumoniae</i> (hvKp) and classical multidrug-resistant (MDR) strains belong to distinct lineages and hvKp are typically characterized by hypermucoid capsules that have been shown to limit horizontal gene transfer (HGT), including plasmid acquisition. However, the convergence of hypervirulence and MDR is increasingly common worldwide. When we profiled 127 antibiotic-susceptible hvKp strains, we found that most (86%) are highly permissive to plasmid transfer despite their capsules. In the few strains that showed low permissiveness, we identified two restriction modification (RM) systems: the Type IV restriction system McrBC that targets bacteriophage, and a unique Type I RM system. Both systems effectively inhibit plasmid uptake in recipient strains. Further analysis reveals that L-arginine and spermidine metabolism regulates the Type I-like RM system through S-adenosyl methionine. Strains lacking these RM systems were highly receptive to plasmids, and clinical isolates worldwide often lack these systems, correlating with their antibiotic resistance. Collectively, our study provides the first report on the susceptibility of hvKp strains to plasmid transfer and evidence of unusual RM systems restricting plasmid acquisition. It reveals an arms race between plasmids evolving to bypass RM systems and host strains developing new defenses. This dynamic and the rarity of these RM systems help explain the emergence of MDR hvKp strains in clinical settings driven by antibiotic pressure.
DOI: 10.15468/dl.t3knnq
title: Occurrence Download

description: A dataset containing 968 species occurrences available 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 (Santander Department)",
 "GadmGid is one of (COL.28_2)"
 ]
 }
 ]
}

 The dataset includes 968 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005732-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.n8aqs2
title: Occurrence Download

description: A dataset containing 3450 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is South America",
 "Country is Colombia",
 "TaxonKey is Vultur gryphus"
 ]
}

 The dataset includes 3450 records from 25 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005734-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5258/soton/d3647
title: Dataset containing all data supporting PhD Thesis 'Community pharmacy alcohol-related liver disease risk identification and linkage to care through development of a complex intervention'

description: Dataset containing all data supporting PhD Thesis 'Community pharmacy alcohol-related liver disease risk identification and linkage to care through development of a complex intervention'. This includes the quantitative data used for the interrupted time series study (chapter three of thesis); the anonymised interview transcripts and demographic data used for the qualitative interview study (chapter five of thesis); blank consent form and participant information sheets used for the qualitative interview study.
DOI: 10.15468/dl.hxc224
title: Occurrence Download

description: A dataset containing 27381 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((3.69687 43.46986,3.76194 43.46414,3.80771 43.49667,3.82916 43.53314,3.80985 43.55388,3.77267 43.57319,3.72547 43.57426,3.70652 43.55316,3.68757 43.52563,3.69687 43.46986))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Plantae"
 ]
}

 The dataset includes 27381 records from 69 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005733-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.tbx6ay
title: Occurrence Download

description: A dataset containing 10 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Carex secalina",
 "Country is Belgium",
 "HasCoordinate is true"
 ]
}

 The dataset includes 10 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005737-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.97mwux
title: Occurrence Download

description: A dataset containing 4688 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cestrum nocturnum",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 4688 records from 262 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005736-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.uruwgy
title: Occurrence Download

description: A dataset containing 40572 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (function (name, pos = -1, envir = as.environment(pos), all.names = FALSE, pattern, sorted = TRUE) \n{\n if (!missing(name)) {\n pos &lt;- tryCatch(name, error = function(e) e)\n if (inherits(pos, \"error\")) {\n name &lt;- substitute(name)\n if (!is.character(name)) \n name &lt;- deparse(name)\n warning(gettextf(\"%s converted to character string\", sQuote(name)), domain = NA)\n pos &lt;- name\n }\n }\n all.names &lt;- .Internal(ls(envir, all.names, sorted))\n if (!missing(pattern)) {\n if ((ll &lt;- length(grep(\"[\", pattern, fixed = TRUE))) && ll != length(grep(\"]\", pattern, fixed = TRUE))) {\n if (pattern == \"[\") {\n pattern &lt;- \"\\\\[\"\n warning(\"replaced regular expression pattern '[' by '\\\\\\\\['\")\n }\n else if (length(grep(\"[^\\\\\\\\]\\\\[&lt;-\", pattern))) {\n pattern &lt;- sub(\"\\\\[&lt;-\", \"\\\\\\\\\\\\[&lt;-\", pattern)\n warning(\"replaced '[&lt;-' by '\\\\\\\\[&lt;-' in regular expression pattern\")\n }\n }\n grep(pattern, all.names, value = TRUE)\n }\n else all.names\n}, Bidens pilosa, Ageratina adenophora, Chromolaena odorata, Praxelis clematidea, Leucaena leucocephala, Mimosa diplotricha, Trifolium repens, Oenothera biennis, Malvastrum coromandelianum, Amaranthus blitum, Amaranthus viridis, Opuntia dillenii, Solanum erianthum, Synedrella nodiflora, Sphagneticola trilobata, Tridax procumbens, Calopogonium mucunoides, Euphorbia hypericifolia, Euphorbia peplus, Phyllanthus amarus, Waltheria indica, Sieruela rutidosperma, Mitracarpus hirtus, Coreopsis lanceolata)",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Living Specimen, Machine Observation, Literature Occurrence)",
 "Country is one of (China, Chinese Taipei)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 40572 records from 70 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005735-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25574/25536
title: Chandra X-ray Observatory ObsId 25536

description: A Systematic Survey of Extreme X-ray Variability of Weak-Line Quasars
DOI: 10.25574/27024
title: Chandra X-ray Observatory ObsId 27024

description: AO-24 Calibration Observations of A1795
DOI: 10.15468/dl.fqqpp7
title: Occurrence Download

description: A dataset containing 213 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Carex secalina",
 "Country is Russian Federation",
 "HasCoordinate is true"
 ]
}

 The dataset includes 213 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005738-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kd9yxx
title: Occurrence Download

description: A dataset containing 23 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Carex secalina",
 "Country is United States of America",
 "HasCoordinate is true"
 ]
}

 The dataset includes 23 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005739-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25574/27831
title: Chandra X-ray Observatory ObsId 27831

description: The Massive Relic Galaxy NGC 5872
DOI: 10.25574/27832
title: Chandra X-ray Observatory ObsId 27832

description: eROSITA NORMAL GALAXIES IN THE FINAL EQUATORIAL DEPTH SURVEY FIELD (EFEDS)
DOI: 10.15468/dl.evwqyp
title: Occurrence Download

description: A dataset containing 178 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Specimen)",
 "Geometry POLYGON((136.3475 -2.78569,136.94972 -2.78569,136.94972 -2.23444,136.3475 -2.23444,136.3475 -2.78569))",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Animalia"
 ]
}

 The dataset includes 178 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005740-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.swgruk
title: Occurrence Download

description: A dataset containing 1503 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Bauhinia monandra",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 1503 records from 131 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005741-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.sh9zx8
title: Occurrence Download

description: A dataset containing 17218 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cestrum parqui",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 17218 records from 145 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005745-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.sqhbah
title: Occurrence Download

description: A dataset containing 4112 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((3.7336 43.51701,3.73743 43.50503,3.74757 43.50187,3.77302 43.50636,3.78433 43.51518,3.78782 43.52632,3.78383 43.53464,3.76886 43.54129,3.75672 43.53979,3.74292 43.53497,3.73626 43.52981,3.7336 43.51701))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Plantae"
 ]
}

 The dataset includes 4112 records from 30 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005747-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.u2rka4
title: Occurrence Download

description: A dataset containing 503394 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is ESP.6.2_1",
 "OccurrenceStatus is Present",
 "Year 2022-2025"
 ]
}

 The dataset includes 503394 records from 53 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005704-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fs3wwq
title: Occurrence Download

description: A dataset containing 198847 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Observation, Machine Observation, Human Observation, Material sample, Material citation, Specimen, Living Specimen, Occurrence evidence)",
 "Continent is Asia",
 "Country is Pakistan",
 "GadmGid is PAK.7_1"
 ]
}

 The dataset includes 198847 records from 246 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005709-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.czrza7
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cyperus conglomeratus",
 "Country is Belgium",
 "HasCoordinate is true"
 ]
}

 The dataset includes 2 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005748-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hak2q4
title: Occurrence Download

description: A dataset containing 41 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Bauhinia multinervia",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 41 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005749-250920141307145/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.30178516
title: README file

description: Dataset Overview: This dataset includes genotypic and infection status data for amphibian individuals sampled in Picos de Europa and Zamora locations. It integrates immune gene markers (MHC.Pere, Alpe, HPLEU), location, and quantitative infection load data for Batrachochytrium dendrobatidis (Bd) and Ranavirus (Rv). The table allows analysis of associations between host genotypes, infection prevalence, and pathogen load. Fasta file Overview: This document include the fasta file where all the MHC class II exon 2 sequences are included.<br>
DOI: 10.6084/m9.figshare.30178516.v1
title: README file

description: Dataset Overview: This dataset includes genotypic and infection status data for amphibian individuals sampled in Picos de Europa and Zamora locations. It integrates immune gene markers (MHC.Pere, Alpe, HPLEU), location, and quantitative infection load data for Batrachochytrium dendrobatidis (Bd) and Ranavirus (Rv). The table allows analysis of associations between host genotypes, infection prevalence, and pathogen load. Fasta file Overview: This document include the fasta file where all the MHC class II exon 2 sequences are included.<br>
DOI: 10.5281/zenodo.17068857
title: Using overlap of sky localization probability maps for filtering potentially lensed pairs of gravitational-wave signals

description: Data used in the paper: "Using overlap of sky localization probability maps for filtering potentially lensed pairs of gravitational-wave signals" (arXiv:2112.05932)



Plots of the ROC curves

Skymap overlap statistic of different event pairs

Parameter estimation results of events

Scripts to re-generate the data
DOI: 10.5281/zenodo.17177201
title: Using overlap of sky localization probability maps for filtering potentially lensed pairs of gravitational-wave signals

description: Data used in the paper: "Using overlap of sky localization probability maps for filtering potentially lensed pairs of gravitational-wave signals" (arXiv:2112.05932)



Plots of the ROC curves

Skymap overlap statistic of different event pairs

Parameter estimation results of events

Scripts to re-generate the data
DOI: 10.5281/zenodo.15092240
title: Underlying data for the article  "Nonequilibrium Critical Scaling of a Squeezing Phase Transition"

description: This repository contains the data and code for reproducing the figures contained in "Nonequilibrium Universality of a Squeezing Phase Transition"

We investigate phase transitions in the nonequilibrium dynamics of power-law interacting spin-1/2 bilayer XXZ models, which have recently been shown to allow generation of entanglement in the form of two-mode squeezing. We find a transition between a collective phase characterized by Heisenberg limited squeezing and a partially collective phase with scalable squeezing. We identify universal scaling of the squeezing dynamics in terms of system parameters and a divergent time-scale, establishing these as distinct dynamical phases within the framework of non-equilibrium critical phenomena. Our work demonstrates a novel dynamical phase transition with potential applications in quantum sensing and quantum simulation in cold-atomic, molecular or Rydberg platforms.
DOI: 10.5281/zenodo.17177617
title: Underlying data for the article  "Nonequilibrium Critical Scaling of a Squeezing Phase Transition"

description: This repository contains the data and code for reproducing the figures contained in "Nonequilibrium Universality of a Squeezing Phase Transition"

We investigate phase transitions in the nonequilibrium dynamics of power-law interacting spin-1/2 bilayer XXZ models, which have recently been shown to allow generation of entanglement in the form of two-mode squeezing. We find a transition between a collective phase characterized by Heisenberg limited squeezing and a partially collective phase with scalable squeezing. We identify universal scaling of the squeezing dynamics in terms of system parameters and a divergent time-scale, establishing these as distinct dynamical phases within the framework of non-equilibrium critical phenomena. Our work demonstrates a novel dynamical phase transition with potential applications in quantum sensing and quantum simulation in cold-atomic, molecular or Rydberg platforms.
DOI: 10.15468/dl.5ptq2c
title: Occurrence Download

description: A dataset containing 2825 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Chamaecytisus palmensis",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 2825 records from 37 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005753-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.w36ye2
title: Occurrence Download

description: A dataset containing 3808 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is South America",
 "Country is Colombia",
 "StateProvince is one of (Huila, Huila Department, Huila Dept, Huila Dept., Huila Depto.)",
 "TaxonKey is Cyanocorax yncas"
 ]
}

 The dataset includes 3808 records from 22 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005752-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5258/soton/d3670
title: Dataset supporting thesis titled: 'Data-driven modelling of nonlinear aerodynamics in high-speed aircraft using machine learning'

description: This ZIP archive contains multiple subfolders, each corresponding to a separate test case implemented as part of the doctoral thesis. Each folder includes the scripts used for running and analyzing the respective case.