cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.28436891
title: Data from: Changes in flexibility but not in compactness underlie the thermal adaptation of prokaryotic adenylate kinases

description: <b>CONTENTS OF THIS DATASET</b><br><br><b>1) ADK_characteristics.csv: </b>a dataset with the main characteristics (accession, superkingdom, species, monomeric vs trimeric, short vs long LID, native temperature group) of the 70 adenylate kinases (ADKs) included in our study.<br><br><b>2) ADK_gene_tree.nwk:</b> maximum-likelihood tree of the 70 ADKs.<br><br><b>3) </b><b>alignment_of_all_ADKs.fasta:</b> multiple sequence alignment of all 70 ADKs.<br><br><b>4) alignment_of_monomeric_ADKs.fasta:</b> multiple sequence alignment of the 58 monomeric ADKs.<br><br><b>5) alignment_of_trimeric_ADKs.fasta</b><b>:</b> multiple sequence alignment of the 12 trimeric ADKs.<br><br><b>6) amino_acid_contacts.zip:</b> a compressed directory of directories with information regarding contacts between amino acid pairs, observed during molecular dynamics simulations of the 70 ADKs.<br><br><b>7) amino_acid_contacts_dataset.csv</b><b>:</b> a dataset of counts of the four types of amino acid contacts observed during molecular dynamics simulations of each ADK.<br><br><b>8) kinetic_dataset.csv</b><b>:</b> a subset of the 193-species Muir et al., bioRxiv, 2024 dataset of kinetic parameter measurements of ADKs. This file includes measurements for only the 17 ADKs that are shared between the Muir et al. dataset and our study.<br><br><b>9) </b><b>phylogenetic_random_effect_ln_neg_pol.csv:</b> the estimated values of the phylogenetic random effect on the intercept for ln(neg-pol).<br><br><b>10) </b><b>phylogenetic_random_effect_ln_pol_pol.csv:</b> the estimated values of the phylogenetic random effect on the intercept for ln(pol-pol).<br><br><b>11) </b><b>phylogenetic_random_effect_rgyr.csv:</b> the estimated values of the phylogenetic random effect on the intercept for the radius of gyration (rgyr).<br><br><b>12) </b><b>phylogenetic_random_effect_RMSF.csv:</b> the estimated values of the phylogenetic random effect on the intercept for the root mean square fluctuation (RMSF).<br><br><b>13) </b><b>phylogenetic_random_effect_SASA.csv:</b> the estimated values of the phylogenetic random effect on the intercept for the solvent-accessible surface area (SASA).<br><br><b>14) </b><b>RMSF_SASA_rgyr_dataset.csv:</b> mean and standard error of RMSF, SASA, and rgyr for each ADK. For simulations that were performed at a 'non-native' temperature, this is reported in the "Offset_from_native_temperature" column. <br><br><b>15) </b><b>species_tree_with_node_IDs.pdf:</b> visualization of the time-calibrated species tree, with each node being annotated with an ID number.<br><br><b>16) </b><b>time_calibrated_species_tree.nwk:</b> the time-calibrated species tree used for the analyses of the present study.<br><br>Further information about the contents of these files can be found in our study.
DOI: 10.6084/m9.figshare.28436891.v1
title: Data from: Changes in flexibility but not in compactness underlie the thermal adaptation of prokaryotic adenylate kinases

description: <b>CONTENTS OF THIS DATASET</b><br><br><b>1) ADK_characteristics.csv: </b>a dataset with the main characteristics (accession, superkingdom, species, monomeric vs trimeric, short vs long LID, native temperature group) of the 70 adenylate kinases (ADKs) included in our study.<br><br><b>2) ADK_gene_tree.nwk:</b> maximum-likelihood tree of the 70 ADKs.<br><br><b>3) </b><b>alignment_of_all_ADKs.fasta:</b> multiple sequence alignment of all 70 ADKs.<br><br><b>4) alignment_of_monomeric_ADKs.fasta:</b> multiple sequence alignment of the 58 monomeric ADKs.<br><br><b>5) alignment_of_trimeric_ADKs.fasta</b><b>:</b> multiple sequence alignment of the 12 trimeric ADKs.<br><br><b>6) amino_acid_contacts.zip:</b> a compressed directory of directories with information regarding contacts between amino acid pairs, observed during molecular dynamics simulations of the 70 ADKs.<br><br><b>7) amino_acid_contacts_dataset.csv</b><b>:</b> a dataset of counts of the four types of amino acid contacts observed during molecular dynamics simulations of each ADK.<br><br><b>8) kinetic_dataset.csv</b><b>:</b> a subset of the 193-species Muir et al., bioRxiv, 2024 dataset of kinetic parameter measurements of ADKs. This file includes measurements for only the 17 ADKs that are shared between the Muir et al. dataset and our study.<br><br><b>9) </b><b>phylogenetic_random_effect_ln_neg_pol.csv:</b> the estimated values of the phylogenetic random effect on the intercept for ln(neg-pol).<br><br><b>10) </b><b>phylogenetic_random_effect_ln_pol_pol.csv:</b> the estimated values of the phylogenetic random effect on the intercept for ln(pol-pol).<br><br><b>11) </b><b>phylogenetic_random_effect_rgyr.csv:</b> the estimated values of the phylogenetic random effect on the intercept for the radius of gyration (rgyr).<br><br><b>12) </b><b>phylogenetic_random_effect_RMSF.csv:</b> the estimated values of the phylogenetic random effect on the intercept for the root mean square fluctuation (RMSF).<br><br><b>13) </b><b>phylogenetic_random_effect_SASA.csv:</b> the estimated values of the phylogenetic random effect on the intercept for the solvent-accessible surface area (SASA).<br><br><b>14) </b><b>RMSF_SASA_rgyr_dataset.csv:</b> mean and standard error of RMSF, SASA, and rgyr for each ADK. For simulations that were performed at a 'non-native' temperature, this is reported in the "Offset_from_native_temperature" column. <br><br><b>15) </b><b>species_tree_with_node_IDs.pdf:</b> visualization of the time-calibrated species tree, with each node being annotated with an ID number.<br><br><b>16) </b><b>time_calibrated_species_tree.nwk:</b> the time-calibrated species tree used for the analyses of the present study.<br><br>Further information about the contents of these files can be found in our study.
DOI: 10.15468/dl.2r24v7
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Garveia franciscana",
 "Country is Netherlands",
 "HasCoordinate is true"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029833-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7gcxsn
title: Occurrence Download

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

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029832-250811113504898/datasets/export for details.
DOI: 10.5281/zenodo.16907260
title: Optically accessible high-finesse millimeter-wave resonator for cavity quantum electrodynamics with atom arrays

description: Raw data in support of "Optically accessible high-finesse millimeter-wave resonator for cavity quantum electrodynamics with atom arrays" [arXiv:2506.05804].
DOI: 10.5281/zenodo.16922976
title: Optically accessible high-finesse millimeter-wave resonator for cavity quantum electrodynamics with atom arrays

description: Raw data in support of "Optically accessible high-finesse millimeter-wave resonator for cavity quantum electrodynamics with atom arrays" [arXiv:2506.05804].
DOI: 10.15468/dl.5ef95b
title: Occurrence Download

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

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029834-250811113504898/datasets/export for details.
DOI: 10.15468/dl.4r8btg
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Solanum mammosum",
 "Country is Brunei Darussalam",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029835-250811113504898/datasets/export for details.
DOI: 10.15468/dl.vtq7tt
title: Occurrence Download

description: A dataset containing 6 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Solanum mammosum",
 "Country is Cuba",
 "HasCoordinate is true"
 ]
}

 The dataset includes 6 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029836-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.16923097
title: Data for Persistence of Coffee-Ring Deposits in Concentrated Suspensions of Anisotropic Colloids

description: raw profilometry data and SEM images corresponding to paper figures
DOI: 10.5281/zenodo.16923098
title: Data for Persistence of Coffee-Ring Deposits in Concentrated Suspensions of Anisotropic Colloids

description: raw profilometry data and SEM images corresponding to paper figures
DOI: 10.15468/dl.j2hk8q
title: Occurrence Download

description: A dataset containing 5 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Garveia franciscana",
 "Country is Ukraine",
 "HasCoordinate is true"
 ]
}

 The dataset includes 5 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029837-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.q7qata
title: Occurrence Download

description: A dataset containing 49 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Garveia franciscana",
 "Country is United States of America",
 "HasCoordinate is true"
 ]
}

 The dataset includes 49 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029838-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.433xn3
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Garveia franciscana",
 "Country is Venezuela (Bolivarian Republic of)",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029840-250811113504898/datasets/export for details.
DOI: 10.15468/dl.ubgrf3
title: Occurrence Download

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

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029839-250811113504898/datasets/export for details.
DOI: 10.15468/dl.nqmexr
title: Occurrence Download

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

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029842-250811113504898/datasets/export for details.
DOI: 10.15468/dl.bwutde
title: Occurrence Download

description: A dataset containing 39 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Barentsia benedeni",
 "Country is United States of America",
 "HasCoordinate is true"
 ]
}

 The dataset includes 39 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029844-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.16922984
title: Genotypes and Coordinates for Atrina vexillum in French Polynesia

description: This dataset contains multilocus microsatellite genotype data, geographic coordinates, and sampling metadata for 2,420 individuals of Atrina vexillum, a large Indo-Pacific fan mussel. Samples were collected in 2022 across six islands of the Society Archipelago in French Polynesia: Bora-Bora, Raiatea, Taha'a, Huahine, Moorea, and Tahiti.

Field sampling was conducted using snorkeling, towed free diving, and SCUBA. Individuals were georeferenced and sampled non-lethally in shallow lagoon habitats (<20 m depth). DNA was extracted using QIAcube HT or Gentra Puregene kits (QIAGEN®), and genotyping was performed using 21 microsatellite markers (9 di-, 5 tri-, and 7 tetra-nucleotide loci), grouped into five multiplexes. Allele scoring was done with GENEMAPPER v5 (Applied Biosystems™) following capillary electrophoresis (ABI 3730xl, GenoScreen, France).

Each row corresponds to a unique individual and includes:

Sample ID

Sampling island code (BO = Bora-Bora, HU = Huahine, RA = Raiatea, TA = Taha'a, MO = Moorea, TH = Tahiti)

Latitude and Longitude in decimal degrees

Two alleles per locus (formatted as Locus-A1, Locus-A2 for 21 loci)

Missing allele calls are encoded as 0.

This dataset supports the following publication:Guttierez T., Boissin E., Planes S. (submitted). Unexpected sharp genetic breaks in a marine bivalve reveal limited connectivity and question a potential vulnerability. Proceedings of the Royal Society B.

Microsatellite marker sequences are available in GenBank under accession numbers PP586094–PP586143.
DOI: 10.5281/zenodo.16922985
title: Genotypes and Coordinates for Atrina vexillum in French Polynesia

description: This dataset contains multilocus microsatellite genotype data, geographic coordinates, and sampling metadata for 2,420 individuals of Atrina vexillum, a large Indo-Pacific fan mussel. Samples were collected in 2022 across six islands of the Society Archipelago in French Polynesia: Bora-Bora, Raiatea, Taha'a, Huahine, Moorea, and Tahiti.

Field sampling was conducted using snorkeling, towed free diving, and SCUBA. Individuals were georeferenced and sampled non-lethally in shallow lagoon habitats (<20 m depth). DNA was extracted using QIAcube HT or Gentra Puregene kits (QIAGEN®), and genotyping was performed using 21 microsatellite markers (9 di-, 5 tri-, and 7 tetra-nucleotide loci), grouped into five multiplexes. Allele scoring was done with GENEMAPPER v5 (Applied Biosystems™) following capillary electrophoresis (ABI 3730xl, GenoScreen, France).

Each row corresponds to a unique individual and includes:

Sample ID

Sampling island code (BO = Bora-Bora, HU = Huahine, RA = Raiatea, TA = Taha'a, MO = Moorea, TH = Tahiti)

Latitude and Longitude in decimal degrees

Two alleles per locus (formatted as Locus-A1, Locus-A2 for 21 loci)

Missing allele calls are encoded as 0.

This dataset supports the following publication:Guttierez T., Boissin E., Planes S. (submitted). Unexpected sharp genetic breaks in a marine bivalve reveal limited connectivity and question a potential vulnerability. Proceedings of the Royal Society B.

Microsatellite marker sequences are available in GenBank under accession numbers PP586094–PP586143.
DOI: 10.15468/dl.txdtdh
title: Occurrence Download

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

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029843-250811113504898/datasets/export for details.
DOI: 10.15468/dl.47h3p4
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Barentsia benedeni",
 "Country is Australia",
 "HasCoordinate is true"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029841-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.27z3xx
title: Occurrence Download

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

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029845-250811113504898/datasets/export for details.
DOI: 10.15468/dl.m4twg7
title: Occurrence Download

description: A dataset containing 165 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Corbula gibba",
 "Country is Australia",
 "HasCoordinate is true"
 ]
}

 The dataset includes 165 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029846-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.f8tbs5
title: Occurrence Download

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

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029847-250811113504898/datasets/export for details.
DOI: 10.15468/dl.7evq3t
title: Occurrence Download

description: A dataset containing 7 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Discosporangium mesarthrocarpum",
 "Country is Australia",
 "HasCoordinate is true"
 ]
}

 The dataset includes 7 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029849-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.nv6wr5
title: Occurrence Download

description: A dataset containing 343 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Ecuador",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Epipedobates tricolor",
 "Year 2015-2025"
 ]
}

 The dataset includes 343 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029850-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.u97ugm
title: Occurrence Download

description: A dataset containing 70 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Ficopomatus enigmaticus",
 "Country is Argentina",
 "HasCoordinate is true"
 ]
}

 The dataset includes 70 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029851-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rpccdx
title: Occurrence Download

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

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029852-250811113504898/datasets/export for details.
DOI: 10.5281/zenodo.16923117
title: Lower Fungom Mufu 500 Nouns Wordlist

description: Sound wise, among some speakers of Mufu (Mufu Ji, ISO 639-3: boe, mund1328), the sonority of the coda nasal is very strong for it to be considered syllabic. Hence we need to crosscheck the sonority strength through instrumental phonetics with the use of Praat. Another distinct characterists of Mufu is its sparing employment of glottal stops, vowel ablaut and consonant mutation as compared to Mundabli (Voll 2017). Structurally, had it been we elicited just three words “chief, father, mother” in Mufu, we would have had the impression that Mufu is rich in prefixes meanwhile these are the only words with prefixes among the 500 nouns recorded from both speakers. Thus, Mufu has lost all its affixes or it is about creating suffixes from determinants, that is, its determiners are being grammaticalized into suffixes. Mufu ~ Mumfu   language is a Yemne-Kimbi (Good et al 2011) speech variety spoken in Lower Fungom in Menchum Division in the North West Region of Cameroon.
DOI: 10.5281/zenodo.16923118
title: Lower Fungom Mufu 500 Nouns Wordlist

description: Sound wise, among some speakers of Mufu (Mufu Ji, ISO 639-3: boe, mund1328), the sonority of the coda nasal is very strong for it to be considered syllabic. Hence we need to crosscheck the sonority strength through instrumental phonetics with the use of Praat. Another distinct characterists of Mufu is its sparing employment of glottal stops, vowel ablaut and consonant mutation as compared to Mundabli (Voll 2017). Structurally, had it been we elicited just three words “chief, father, mother” in Mufu, we would have had the impression that Mufu is rich in prefixes meanwhile these are the only words with prefixes among the 500 nouns recorded from both speakers. Thus, Mufu has lost all its affixes or it is about creating suffixes from determinants, that is, its determiners are being grammaticalized into suffixes. Mufu ~ Mumfu   language is a Yemne-Kimbi (Good et al 2011) speech variety spoken in Lower Fungom in Menchum Division in the North West Region of Cameroon.
DOI: 10.15468/dl.c37m65
title: Occurrence Download

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

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029855-250811113504898/datasets/export for details.
DOI: 10.15468/dl.am3xz6
title: Occurrence Download

description: A dataset containing 7 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Caspiobdella fadejewi",
 "Country is France",
 "HasCoordinate is true"
 ]
}

 The dataset includes 7 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029856-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xgg8mt
title: Occurrence Download

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

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029854-250811113504898/datasets/export for details.
DOI: 10.15468/dl.mj6w63
title: Occurrence Download

description: A dataset containing 667 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Ecuador",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Amblyrhynchus cristatus",
 "Year 2025-2025"
 ]
}

 The dataset includes 667 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029857-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.85rn89
title: Occurrence Download

description: A dataset containing 74 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Ficopomatus enigmaticus",
 "Country is Belgium",
 "HasCoordinate is true"
 ]
}

 The dataset includes 74 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029858-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.