cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.14031452
title: AlphaFold2-Based Characterization of Apo and Holo Protein Structures and Conformational Ensembles Using Randomized Alanine Sequence Scanning Adaptation: Capturing Shared Signature Dynamics and Ligand-Induced Conformational Changes

description: Proteins often exist in multiple conformational states, influenced by the binding of ligands or substrates. The study of these states, particularly the apo (unbound) and holo (ligand-bound) forms, is crucial for understanding protein function, dynamics, and interactions. In the current study, we use AlphaFold2 that combines randomized  alanine  sequence masking  with shallow multiple sequence alignment  subsampling to expand the conformational diversity of the predicted structural  ensembles and   capture conformational changes between apo and holo protein forms. Using several well-established datasets of  structurally diverse apo-holo protein pairs, the proposed approach enables  robust predictions of apo and holo structures and conformational ensembles, while also displaying notably similar dynamics distributions. These observations are consistent with  the view  that the intrinsic dynamics of allosteric proteins is defined by the structural topology of the fold and favors conserved conformational motions driven by soft modes among orthologs. We also found  a significant correlation between conformational flexibility and  AlphaFold2 metric of statistical significance pLDDT for the apo-holo pairs in which ligand binding induced local moderate conformational changes. For apo-holo pairs exhibiting larger structural changes, this relationship  becomes nonlinear, reflecting inability of AlphaFold2 confidence metrics to identify high energy functional conformations. Our findings support the notion that AlphaFold2 approaches can yield reasonable accuracy in predicting minor conformational adjustments between apo and holo states, especially for proteins with  moderate localized changes upon ligand binding. However, for large, hinge-like domain movements, AF2 tends to predict the most stable domain orientation which is typically the apo form rather than the full range of functional conformations characteristic of the holo ensemble. These results indicate that modeling of multiple functional states of proteins may require more accurate detection of flexible region conformations and cannot solely rely on the pLDDT metric as the major determinant of the prediction accuracy in reproducing functional conformational ensembles.
DOI: 10.6084/m9.figshare.27569631
title: ALIGNN_BERT_TL train dataset

description: Train, validation and test dataset for ALIGNN_BERT_TL project
DOI: 10.6084/m9.figshare.27569631.v1
title: ALIGNN_BERT_TL train dataset

description: Train, validation and test dataset for ALIGNN_BERT_TL project
DOI: 10.15468/dl.5ehu8m
title: Occurrence Download

description: A dataset containing 120 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Spain",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Genista haenseleri Boiss."
 ]
}

 The dataset includes 120 records from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020216-241024112534372/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14031447
title: Behavioural underpinning of mito-nuclear discordances: insights from fire salamanders

description: Mito-nuclear discordances across secondary contact zones have been described in a wide range of organisms. They consist of a spatial mismatch between nuclear and mitochondrial genomes in terms of location and extension of the contact zone between distinct evolutionary lineages. Despite the evolutionary and biogeographic causes of mito-nuclear discordances have been extensively investigated, we still lack a clear understanding of their phenotypic underpinnings. Here, we test the hypothesis that mtDNA variation could be associated with behavioural variation, and that such association could contribute to asymmetric mitochondrial introgression across a secondary contact zone. We analysed behavioural variation across the mtDNA secondary contact zone of the fire salamander Salamandra salamandra in central Italy, which is displaced 600 km from the nuclear contact zone. We found distinct behavioural profiles in the two mitotypes co-occurring in the contact zone. The introgressed mitotype was associated with a ‘slow-thorough’ dispersal profile, characterized by a less active but more cautious and accurate exploration strategy. This pattern was consistent across life stages and contexts: aquatic larvae and terrestrial juveniles, spontaneous activity and response to novelty. These results support the intriguing hypothesis that personality traits associated with distinct mitotypes could contribute to differential mitochondrial introgression and the formation of biogeographic patterns of mito-nuclear discordance.
DOI: 10.5281/zenodo.6799067
title: Behavioural underpinning of mito-nuclear discordances: insights from fire salamanders

description: Mito-nuclear discordances across secondary contact zones have been described in a wide range of organisms. They consist of a spatial mismatch between nuclear and mitochondrial genomes in terms of location and extension of the contact zone between distinct evolutionary lineages. Despite the evolutionary and biogeographic causes of mito-nuclear discordances have been extensively investigated, we still lack a clear understanding of their phenotypic underpinnings. Here, we test the hypothesis that mtDNA variation could be associated with behavioural variation, and that such association could contribute to asymmetric mitochondrial introgression across a secondary contact zone. We analysed behavioural variation across the mtDNA secondary contact zone of the fire salamander Salamandra salamandra in central Italy, which is displaced 600 km from the nuclear contact zone. We found distinct behavioural profiles in the two mitotypes co-occurring in the contact zone. The introgressed mitotype was associated with a ‘slow-thorough’ dispersal profile, characterized by a less active but more cautious and accurate exploration strategy. This pattern was consistent across life stages and contexts: aquatic larvae and terrestrial juveniles, spontaneous activity and response to novelty. These results support the intriguing hypothesis that personality traits associated with distinct mitotypes could contribute to differential mitochondrial introgression and the formation of biogeographic patterns of mito-nuclear discordance.
DOI: 10.5281/zenodo.6799068
title: Behavioural foundation of a massive mitochondrial introgression in the fire salamander, Salamandra salamandra

description: Patterns of mito-nuclear discordance across secondary contact zones have been reported in a wide range of organisms. They consist of a spatial mismatch between nuclear and mitochondrial genomes, in terms of geographic location and/or extension of the contact zone between distinct evolutionary lineages. Several theoretical and empirical studies have identified massive mitochondrial introgression as putative source of these mismatches. Yet, we still lack a clear understanding of the phenotypic underpinnings of such massive introgression. We hypothesised that mtDNA variation across a contact zone could be associated with variation in phenotypic traits affecting dispersal propensity. We analysed patterns of behavioural and genetic variation across a mtDNA secondary contact zone of the fire salamander Salamandra salamandra in central Italy, which is over 600 km displaced from its nuclear counterpart. We found distinct behavioural profiles associated with the two co-occurring mitotypes. Counterintuitively, the introgressed mitotype was associated to a ‘slow-thorough’ dispersal profile, characterized by shy, less active and less exploratory personality traits. This pattern was consistent across life-stages and contexts, i.e., aquatic larvae and terrestrial juveniles. These results provide for the first time robust evidence that personality traits associated with distinct mitotypes could promote differential mitochondrial introgression within alternative nuclear backgrounds.
DOI: 10.15468/dl.xaqysd
title: Occurrence Download

description: A dataset containing 289 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Spain",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Genista sanabrensis Valdés Berm., Castrov. & Casaseca"
 ]
}

 The dataset includes 289 records from 32 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020218-241024112534372/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.t3hbbj
title: Occurrence Download

description: A dataset containing 79504 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is one of (United States of America, Mexico, Brazil)",
 "TaxonKey is Selaginella P.Beauv."
 ]
}

 The dataset includes 79504 records from 546 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020217-241024112534372/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.nnwvex
title: Occurrence Download

description: A dataset containing 56505 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Europe",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Lynx lynx (Linnaeus, 1758)"
 ]
}

 The dataset includes 56505 records from 172 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020219-241024112534372/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.b88kqj
title: Occurrence Download

description: A dataset containing 800 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Spain",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Genista falcata Brot."
 ]
}

 The dataset includes 800 records from 33 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020220-241024112534372/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.27600309
title: Data used to produce figures in "<b>Elevated mutation rates in multi-azole resistant</b> <b><i>Aspergillus fumigatus </i></b><b>drive rapid evolution of antifungal resistance"</b>

description: Data used to produce figures for "Elevated mutation rates in multi-azole resistant <i>Aspergillus fumigatus </i>drive rapid evolution of antifungal resistance". WGS data produced in the work are available at PRJEB81974, and genome sequences used to create the phylogeny presented in Figure 1 are available at PRJEB27135 and in the extended datasets accompanying the paper. Data for SI figures S4-S6 are available as extended datasets accompanying the paper.
DOI: 10.6084/m9.figshare.27600309.v1
title: Data used to produce figures in "<b>Elevated mutation rates in multi-azole resistant</b> <b><i>Aspergillus fumigatus </i></b><b>drive rapid evolution of antifungal resistance"</b>

description: Data used to produce figures for "Elevated mutation rates in multi-azole resistant <i>Aspergillus fumigatus </i>drive rapid evolution of antifungal resistance". WGS data produced in the work are available at PRJEB81974, and genome sequences used to create the phylogeny presented in Figure 1 are available at PRJEB27135 and in the extended datasets accompanying the paper. Data for SI figures S4-S6 are available as extended datasets accompanying the paper.
DOI: 10.15468/dl.bbt5ax
title: Occurrence Download

description: A dataset containing 163 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is one of (Culicoides paraensis (Goeldi, 1905), Culicoides sonorensis Wirth & Jones, 1957)"
 ]
}

 The dataset includes 163 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020222-241024112534372/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3wx6py
title: Occurrence Download

description: A dataset containing 889946 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Peru",
 "DatasetKey is one of (Tropicos MO Specimen Data, Tropicos Specimens Non-MO, iNaturalist Research-grade Observations, Royal Botanic Gardens, Kew - Herbarium Specimens)"
 ]
}

 The dataset includes 889946 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020221-241024112534372/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.t5mvue
title: Occurrence Download

description: A dataset containing 29481 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is one of (Brazil, Colombia, Costa Rica, Ecuador, Peru, Bolivia (Plurinational State of), Mexico, Venezuela (Bolivarian Republic of), Panama)",
 "OccurrenceStatus is Present",
 "TaxonKey is Serpocaulon A.R.Sm."
 ]
}

 The dataset includes 29481 records from 399 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020223-241024112534372/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gkkwrv
title: Occurrence Download

description: A dataset containing 122 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "TaxonKey is Phrynomantis microps Peters, 1875"
 ]
}

 The dataset includes 122 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0040561-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5boayr
title: Occurrence Download

description: A dataset containing 546 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Pristimantis uranobates (Lynch, 1991)",
 "HasGeospatialIssue is false",
 "Geometry POLYGON((-89.71 -3.13,-89.71 14.26,-62.16 14.26,-62.16 -3.13,-89.71 -3.13))"
 ]
}

 The dataset includes 546 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008846-160311141623029/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.s22ex7
title: Occurrence Download

description: A dataset containing 417 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Dicranolepis laciniata Gilg"
 ]
}

 The dataset includes 417 records from 32 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023770-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ovnn6e
title: Occurrence Download

description: A dataset containing 499 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Caryodaphnopsis Airy Shaw"
 ]
}

 The dataset includes 499 records from 48 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008846-160526112335914/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.dzyzdy
title: Occurrence Download

description: A dataset containing 25521 species occurrences available in GBIF matching the query:
{
 "Geometry" : [
 "POLYGON ((-72 62.70324, -66 62.70324, -66 64.01077, -72 64.01077, -72 62.70324))"
 ]
}

 The dataset includes 25521 records from 152 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0040566-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.t5egjp
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Deschampsia sichotensis Prob., Tzvelev & Chiapella"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023797-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8xsoyn
title: Occurrence Download

description: A dataset containing 91744 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Carabus Linnaeus, 1758"
 ]
}

 The dataset includes 91744 records from 327 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008846-160822134323880/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4ahc59
title: Occurrence Download

description: A dataset containing 2662 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Ecuador",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is one of (Falco peregrinus Tunstall, 1771, Furnarius rufus (Gmelin, 1788))"
 ]
}

 The dataset includes 2662 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0040568-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.tbnmzm
title: Occurrence Download

description: A dataset containing 2280 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "TaxonKey is Dicrurus atripennis Swainson, 1837"
 ]
}

 The dataset includes 2280 records from 31 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023752-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.77gd8q
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "TaxonKey is Nyctalus montanus (Barrett-Hamilton, 1906)"
 ]
}

 The dataset includes 3 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0072543-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rao6iv
title: Occurrence Download

description: A dataset containing 566 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Neohygrocybe nitrata (Pers.) Herink"
 ]
}

 The dataset includes 566 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008846-170826194755519/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.sv46mt
title: Occurrence Download

description: A dataset containing 44 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Continent is Oceania",
 "Country is one of (Solomon Islands, Papua New Guinea)",
 "DatasetKey is one of (Museum of Comparative Zoology, Harvard University, Bernice P. Bishop Museum, CAS Herpetology (HERP), Brigham Young University (BYU) Herpetology Collection (Arctos), University of Michigan Museum of Zoology, Division of Reptiles & Amphibians, RBINS Reptile collection)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Alpinoscincus Slavenko, Tamar, Tallowin, Kraus, Allison, Carranza & Meiri, 2021"
 ]
}

 The dataset includes 44 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023715-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.b8xkmj
title: Occurrence Download

description: A dataset containing 27214666 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "HasCoordinate is true"
 ]
}

 The dataset includes 27214666 records from 2873 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015090-240216155721649/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.n874vv
title: Occurrence Download

description: A dataset containing 100 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Physaria brassicoides Rydb."
 ]
}

 The dataset includes 100 records from 26 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0064332-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wh6nds
title: Occurrence Download

description: A dataset containing 19 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Halodule emarginata Hartog"
 ]
}

 The dataset includes 19 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0237171-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fw7kds
title: Occurrence Download

description: A dataset containing 31701 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is one of (United Kingdom of Great Britain and Northern Ireland, Belgium, Ireland, Norway, France, Germany, Luxembourg, Austria, Finland, Switzerland)",
 "Geometry POLYGON((-16.26576 34.22154,47.13394 34.22154,47.13394 72.03866,-16.26576 72.03866,-16.26576 34.22154))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Lewinskya affinis (Brid.) F.Lara, Garilleti & Goffinet"
 ]
}

 The dataset includes 31701 records from 99 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0260814-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vcj74m
title: Occurrence Download

description: A dataset containing 319 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Colombia",
 "TaxonKey is Hyophila involuta (Hook.) A.Jaeger"
 ]
}

 The dataset includes 319 records from 26 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0184865-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.