cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.17867859
title: RegEvol: detection of directional selection in regulatory sequences through phenotypic predictions and phenotype-to-fitness functions

description: Datasets from the paper

“RegEvol: detection of directional selection in regulatory sequences through phenotypic predictions and phenotype-to-fitness functions”

The repository includes:





BSgenomes used to generate matched negative sequences for model training: BSgenomes.tar.gz




RegEvol result tables for the analysed ChIP-seq peaks across 11 species: ChIP_peaks_RegEvol.Rds




RegEvol result tables for the analysed Drosophila melanogaster modERN peaks: drosophila_modERN_RegEvol.Rds


RegEvol result tables for the analysed Homo sapiens CTCF peaks from ENCODE, including tissue-specific activity annotations: human_CTCF_ENCODE_RegEvol.Rds



Substitution matrices per chromosome from PhyML for each analysed species


Whole-genome alignment with reconstructed ancestral states for human and mouse (extracted from Armstrong et al. 2020) and for fly (extracted from Peng and Zhao 2024)
DOI: 10.5281/zenodo.18706919
title: TABLE 1 in Seasonality controls the vegetation of a late Middle Miocene forest in Europe

description: TABLE 1. — The five groups defined by cluster analysis and the plant palynomorphs that compose them. Taxonomy follows that originally presented in McCoy et al. (2022).
GroupTaxa1Abiespollenites, Pinuspollenites2Artemisiapollenites, Caprifoliaceae, Carpinites, Cathayapollenites, Iteapollenites, Keteleeria, Nyssapollenites, Oleidearumpollenites, Parthenopollenites, Platycaryapollenites, Rhamnaceae, Salixipollenites, Tetradomonoporites, Urtica, Verrucatosporites, Laevigatosporites, Echinatisporites, Stereisporites steroides3Cercidiphyllum, Compositoipollenites, Coryloides, Cyperaceae, Ericipites, Ilexpollenites, Juglanspollenites, Oleidearumpollenites, Salixipollenites, Tricolpopollenites sp.,4Betulaepollenites, Cupressacites, Cupuliferoipollenites, Liliacidites, Sciadopitys, Tricopopollenites liblarensis, Tricolpopollenites fallax, Quercoidites microhenrici, Zonalapollenites5Alnipollenites verus, Cedripites, Cyrillaceaepollenites, Graminidites, Myricipites, Piceaepollenites, Quercoidites henrici, Tricolpopollenites ipilensis, Tricolporopollenites sp., Lygodium
description: Published as part of Pound, Matthew J., McCOY, Jessica, Pound, Marion C. E., Riding, James B. & Jennifer M. K. O'KEEFE, 2026, Seasonality controls the vegetation of a late Middle Miocene forest in Europe, pp. 4 in Geodiversitas 48 (1) on page 4, DOI: 10.5252/geodiversitas2026v48a1, http://zenodo.org/record/18412164
DOI: 10.5281/zenodo.18706920
title: TABLE 1 in Seasonality controls the vegetation of a late Middle Miocene forest in Europe

description: TABLE 1. — The five groups defined by cluster analysis and the plant palynomorphs that compose them. Taxonomy follows that originally presented in McCoy et al. (2022).
GroupTaxa1Abiespollenites, Pinuspollenites2Artemisiapollenites, Caprifoliaceae, Carpinites, Cathayapollenites, Iteapollenites, Keteleeria, Nyssapollenites, Oleidearumpollenites, Parthenopollenites, Platycaryapollenites, Rhamnaceae, Salixipollenites, Tetradomonoporites, Urtica, Verrucatosporites, Laevigatosporites, Echinatisporites, Stereisporites steroides3Cercidiphyllum, Compositoipollenites, Coryloides, Cyperaceae, Ericipites, Ilexpollenites, Juglanspollenites, Oleidearumpollenites, Salixipollenites, Tricolpopollenites sp.,4Betulaepollenites, Cupressacites, Cupuliferoipollenites, Liliacidites, Sciadopitys, Tricopopollenites liblarensis, Tricolpopollenites fallax, Quercoidites microhenrici, Zonalapollenites5Alnipollenites verus, Cedripites, Cyrillaceaepollenites, Graminidites, Myricipites, Piceaepollenites, Quercoidites henrici, Tricolpopollenites ipilensis, Tricolporopollenites sp., Lygodium
description: Published as part of Pound, Matthew J., McCOY, Jessica, Pound, Marion C. E., Riding, James B. & Jennifer M. K. O'KEEFE, 2026, Seasonality controls the vegetation of a late Middle Miocene forest in Europe, pp. 4 in Geodiversitas 48 (1) on page 4, DOI: 10.5252/geodiversitas2026v48a1, http://zenodo.org/record/18412164
DOI: 10.5281/zenodo.18706966
title: TABLE 2 in Seasonality controls the vegetation of a late Middle Miocene forest in Europe

description: TABLE 2. — Pearson’s correlation coefficients matrix.
Group 1Group 2Group 3Group 4Group 5Mean Annual TemperatureSummer TemperatureWinter TemperatureMean Annual PrecipitationSummer PrecipitationWinter PrecipitationWetlandHerbaceousBroadleaved deciduous shrubsBroadleaved evergreen shrubsNeedleleaved evergreen treesBroadleaved deciduous treesBroadleaved evergreen treesLianas and ClimbersGroup 1–0.233771–0.547930–0.113635–0.276478–0.146316–0.207692–0.137656–0.403299–0.346783–0.288032–0.372488–0.3798970.2913450.3546360.4154460.4136630.144255–0.218639Group 20.203680–0.5691800.5419780.3412920.1559090.424343–0.0879800.139733–0.3691710.2111230.381642–0.238003–0.288086–0.178342–0.068708–0.420274–0.187193Group 3–0.2994940.2420640.1915530.2221760.1671780.2675110.3184980.1220840.2812200.1985420.015580–0.001812–0.345827–0.388746–0.2006890.258309Group 4–0.796860–0.377906–0.101515–0.5070280.341266–0.0247670.607783–0.189641–0.175526–0.0242650.1157390.037573–0.0135450.4329550.245368Group 50.0797910.0354920.204333–0.0116490.030707–0.0532230.1204540.099533–0.060582–0.099012–0.049649–0.079747–0.3258950.041996Mean Annual Temperature0.9065240.969246–0.0708220.244628–0.4453050.148392–0.1530540.1976960.141355–0.2139350.0583680.102158–0.150597Summer Temperature0.7864850.1688490.417308–0.1917840.148108–0.1992940.1986340.208615–0.275736–0.0219560.240117–0.033491Winter Temperature–0.2224460.108468–0.5377190.174834–0.1000230.1679140.057768–0.1693980.089282–0.008155–0.220950Mean Annual Precipitation0.8370660.6981700.0490810.193409–0.167128–0.091793–0.311880–0.3183540.1807840.313053Summer Precipitation0.2922870.0394240.218021–0.063124–0.033931–0.312360–0.2990680.0418570.247478Winter Precipitation–0.0402140.218020–0.171561–0.105102–0.218899–0.3075600.1975070.243191
description: Published as part of Pound, Matthew J., McCOY, Jessica, Pound, Marion C. E., Riding, James B. & Jennifer M. K. O'KEEFE, 2026, Seasonality controls the vegetation of a late Middle Miocene forest in Europe, pp. 9 in Geodiversitas 48 (1) on page 9, DOI: 10.5252/geodiversitas2026v48a1, http://zenodo.org/record/18412164
DOI: 10.5281/zenodo.18706965
title: TABLE 2 in Seasonality controls the vegetation of a late Middle Miocene forest in Europe

description: TABLE 2. — Pearson’s correlation coefficients matrix.
Group 1Group 2Group 3Group 4Group 5Mean Annual TemperatureSummer TemperatureWinter TemperatureMean Annual PrecipitationSummer PrecipitationWinter PrecipitationWetlandHerbaceousBroadleaved deciduous shrubsBroadleaved evergreen shrubsNeedleleaved evergreen treesBroadleaved deciduous treesBroadleaved evergreen treesLianas and ClimbersGroup 1–0.233771–0.547930–0.113635–0.276478–0.146316–0.207692–0.137656–0.403299–0.346783–0.288032–0.372488–0.3798970.2913450.3546360.4154460.4136630.144255–0.218639Group 20.203680–0.5691800.5419780.3412920.1559090.424343–0.0879800.139733–0.3691710.2111230.381642–0.238003–0.288086–0.178342–0.068708–0.420274–0.187193Group 3–0.2994940.2420640.1915530.2221760.1671780.2675110.3184980.1220840.2812200.1985420.015580–0.001812–0.345827–0.388746–0.2006890.258309Group 4–0.796860–0.377906–0.101515–0.5070280.341266–0.0247670.607783–0.189641–0.175526–0.0242650.1157390.037573–0.0135450.4329550.245368Group 50.0797910.0354920.204333–0.0116490.030707–0.0532230.1204540.099533–0.060582–0.099012–0.049649–0.079747–0.3258950.041996Mean Annual Temperature0.9065240.969246–0.0708220.244628–0.4453050.148392–0.1530540.1976960.141355–0.2139350.0583680.102158–0.150597Summer Temperature0.7864850.1688490.417308–0.1917840.148108–0.1992940.1986340.208615–0.275736–0.0219560.240117–0.033491Winter Temperature–0.2224460.108468–0.5377190.174834–0.1000230.1679140.057768–0.1693980.089282–0.008155–0.220950Mean Annual Precipitation0.8370660.6981700.0490810.193409–0.167128–0.091793–0.311880–0.3183540.1807840.313053Summer Precipitation0.2922870.0394240.218021–0.063124–0.033931–0.312360–0.2990680.0418570.247478Winter Precipitation–0.0402140.218020–0.171561–0.105102–0.218899–0.3075600.1975070.243191
description: Published as part of Pound, Matthew J., McCOY, Jessica, Pound, Marion C. E., Riding, James B. & Jennifer M. K. O'KEEFE, 2026, Seasonality controls the vegetation of a late Middle Miocene forest in Europe, pp. 9 in Geodiversitas 48 (1) on page 9, DOI: 10.5252/geodiversitas2026v48a1, http://zenodo.org/record/18412164
DOI: 10.15468/dl.tge2hd
title: Occurrence Download

description: A dataset containing 3433 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is United Kingdom of Great Britain and Northern Ireland",
 "OccurrenceStatus is Present",
 "TaxonKey is Culex pipiens"
 ]
}

 The dataset includes 3433 records from 56 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000037-260225131425191/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.31396491
title: Master Data Registry: Federated Index & Canonical Directory Ledger

description: This dataset serves as the central Master Data Registry and canonical directory ledger for the Samuel & Audrey Media Network. Acting as the root node of the network's Knowledge Graph, this machine-readable index catalogs over 15 years of human-authored digital media, seamlessly bridging niche travel and lifestyle expertise with technical domain knowledge (including quantitative finance and data architecture).Explicitly engineered for AI ingestion, cryptographic provenance, and comprehensive Entity Resolution, this federated index links all sub-ledgers across the organization. Furthermore, it mandates network-wide adherence to rigorous metadata protocols—including precise <code>ImageObject</code> schema mapping to properly structure all visual assets for Answer Engine Optimization (AEO)—ensuring unshakeable E-E-A-T and hallucination-free retrieval across all decentralized domains and RAG corpora.
DOI: 10.6084/m9.figshare.31396491.v1
title: Master Data Registry: Federated Index & Canonical Directory Ledger

description: This dataset serves as the central Master Data Registry and canonical directory ledger for the Samuel & Audrey Media Network. Acting as the root node of the network's Knowledge Graph, this machine-readable index catalogs over 15 years of human-authored digital media, seamlessly bridging niche travel and lifestyle expertise with technical domain knowledge (including quantitative finance and data architecture).Explicitly engineered for AI ingestion, cryptographic provenance, and comprehensive Entity Resolution, this federated index links all sub-ledgers across the organization. Furthermore, it mandates network-wide adherence to rigorous metadata protocols—including precise <code>ImageObject</code> schema mapping to properly structure all visual assets for Answer Engine Optimization (AEO)—ensuring unshakeable E-E-A-T and hallucination-free retrieval across all decentralized domains and RAG corpora.
DOI: 10.15468/dl.vvdnfq
title: Occurrence Download

description: A dataset containing 37 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "TaxonKey is Iva angustifolia",
 "Year is less than or equal to 2000",
 "Year is greater than or equal to 1970",
 {
 "or" : [
 {
 "not" : {
 "EstablishmentMeans" : [
 "is one of (MANAGED, INTRODUCED)"
 ]
 }
 },
 "EstablishmentMeans is null"
 ]
 },
 {
 "or" : [
 "CoordinateUncertaintyInMeters is less than 1000",
 "CoordinateUncertaintyInMeters is null"
 ]
 }
 ]
}

 The dataset includes 37 records from 20 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000038-260225131425191/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.18771908
title: Isotopic variations and Zeeman-like splitting in the spectra of nonlinear photonic meta atoms (code and supporting data)

description: This repository contains python scripts and data files, needed to access the data in the manuscript and reprouce the analysis and figures.
DOI: 10.5281/zenodo.18771909
title: Isotopic variations and Zeeman-like splitting in the spectra of nonlinear photonic meta atoms (code and supporting data)

description: This repository contains python scripts and data files, needed to access the data in the manuscript and reprouce the analysis and figures.
DOI: 10.15468/dl.9br82f
title: Occurrence Download

description: A dataset containing 5 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is CHN.29_1",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Enicurus immaculatus"
 ]
}

 The dataset includes 5 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000039-260225131425191/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.18681235
title: Bat feeding Buzz test dataset; Classifier predictions and code

description: FeedingBuzz SequenceData - contains all the bat sequences (.wav) used to train/test the classifiers.

Sequence_information.csv - contains all necessary information for each wav file, like sequence durations, guild, the grouping to FB/NoFB, and the presence of error labels.

predictions_allClassifiers.csv - contains the binary prediction FB/noFB for each classifier and sequence. For FB classifiers producing FB probabilities, the Youden Index was used for binary threshold setting.

AcousticIndices_information.csv - Contains the Acoustic indices calculated for each sequence

 

01.1: R Script for the running the Acoustic Indices & Duration Classifiers

01.2. R Script for running the BuzzFindR classifier

02.: R Script for the calculation of perfomance metrics

03: R Script for analysing classification errors using error models
DOI: 10.5281/zenodo.18771773
title: Bat feeding Buzz test dataset; Classifier predictions and code

description: FeedingBuzz SequenceData - contains all the bat sequences (.wav) used to train/test the classifiers.

Sequence_information.csv - contains all necessary information for each wav file, like sequence durations, guild, the grouping to FB/NoFB, and the presence of error labels.

predictions_allClassifiers.csv - contains the binary prediction FB/noFB for each classifier and sequence. For FB classifiers producing FB probabilities, the Youden Index was used for binary threshold setting.

AcousticIndices_information.csv - Contains the Acoustic indices calculated for each sequence

 

01.1: R Script for the running the Acoustic Indices & Duration Classifiers

01.2. R Script for running the BuzzFindR classifier

02.: R Script for the calculation of perfomance metrics

03: R Script for analysing classification errors using error models
DOI: 10.15468/dl.gpa5nk
title: Occurrence Download

description: A dataset containing 430 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "TaxonKey is Iva axillaris",
 "Year is less than or equal to 2000",
 "Year is greater than or equal to 1970",
 {
 "or" : [
 {
 "not" : {
 "EstablishmentMeans" : [
 "is one of (MANAGED, INTRODUCED)"
 ]
 }
 },
 "EstablishmentMeans is null"
 ]
 },
 {
 "or" : [
 "CoordinateUncertaintyInMeters is less than 1000",
 "CoordinateUncertaintyInMeters is null"
 ]
 }
 ]
}

 The dataset includes 430 records from 71 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000040-260225131425191/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vyspd3
title: Occurrence Download

description: A dataset containing 229729 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Turdus ignobilis",
 "Country is Colombia",
 "HasCoordinate is true"
 ]
}

 The dataset includes 229729 records from 353 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009890-260221153910048/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.18772045
title: DNA Methylation Data (methylKit) for the Comparison of Diabetic vs. Non-diabetic Subjects
DOI: 10.5281/zenodo.18772044
title: DNA Methylation Data (methylKit) for the Comparison of Diabetic vs. Non-diabetic Subjects
DOI: 10.5281/zenodo.18772185
title: Anatomic Patterns of Distribution of the Renal Arteries' Origin from the Aorta

description: Abstract



Background: To characterize the variation of the renal arteries' origin from the aorta, through examination of computed tomography angiographies (CTAs) in a cohort of patients, and to evaluate any gender-related difference.

Methods: CTA of the thoracoabdominal district in patients with a nondilated aorta (group A), patients with aortic aneurysm involving the origin of splanchnic and/or renal vessels (group B), and patients with abdominal aortic aneurysm (group C), were retrospectively analyzed. The diameter and angles of emergence (axial and craniocaudal) of the renal arteries were measured, as well as their mutual distance, and the distance between the renal vessels and the superior mesenteric artery/the aortic bifurcation. Shapiro-Wilk, one-way analysis of variance and bivariate Pearson's Correlation tests were performed as appropriate. A P value <0.05 was considered statistically significant.

Results: Six-hundred CTA of patients (452 males) were examined, being 286 in group A, 119 in group B, and 195 in group C. When examining the whole population and also the subgroup of female patients, the clock position of the right renal artery (RRA) was the only parameter that followed a Gaussian distribution, and its ostium raised from the aorta with a mean axial angle of -61.5° ± 16.6°. There was a negative correlation between left renal artery (LRA) and RRA's coronal angle and aortic diameter at the same level, as well as between the LRA's clock position and the aortic diameter at the same level. The longitudinal distances between established landmarks and both renal arteries positively correlated to the aortic diameter.

Conclusions: The LRA showed a high anatomic variability, both in males and in females. With the increase of the aortic diameters in the juxtarenal/infrarenal portion of the aorta, the renal vessels tended to have a more horizontal course in the coronal view, a more acute "clock-position" and longer longitudinal distances between their ostia and the aortic bifurcation.
DOI: 10.5281/zenodo.18772184
title: Anatomic Patterns of Distribution of the Renal Arteries' Origin from the Aorta

description: Abstract



Background: To characterize the variation of the renal arteries' origin from the aorta, through examination of computed tomography angiographies (CTAs) in a cohort of patients, and to evaluate any gender-related difference.

Methods: CTA of the thoracoabdominal district in patients with a nondilated aorta (group A), patients with aortic aneurysm involving the origin of splanchnic and/or renal vessels (group B), and patients with abdominal aortic aneurysm (group C), were retrospectively analyzed. The diameter and angles of emergence (axial and craniocaudal) of the renal arteries were measured, as well as their mutual distance, and the distance between the renal vessels and the superior mesenteric artery/the aortic bifurcation. Shapiro-Wilk, one-way analysis of variance and bivariate Pearson's Correlation tests were performed as appropriate. A P value <0.05 was considered statistically significant.

Results: Six-hundred CTA of patients (452 males) were examined, being 286 in group A, 119 in group B, and 195 in group C. When examining the whole population and also the subgroup of female patients, the clock position of the right renal artery (RRA) was the only parameter that followed a Gaussian distribution, and its ostium raised from the aorta with a mean axial angle of -61.5° ± 16.6°. There was a negative correlation between left renal artery (LRA) and RRA's coronal angle and aortic diameter at the same level, as well as between the LRA's clock position and the aortic diameter at the same level. The longitudinal distances between established landmarks and both renal arteries positively correlated to the aortic diameter.

Conclusions: The LRA showed a high anatomic variability, both in males and in females. With the increase of the aortic diameters in the juxtarenal/infrarenal portion of the aorta, the renal vessels tended to have a more horizontal course in the coronal view, a more acute "clock-position" and longer longitudinal distances between their ostia and the aortic bifurcation.
DOI: 10.15468/dl.tysx9w
title: Occurrence Download

description: A dataset containing 120 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "TaxonKey is Ixeris polycephala",
 "Year is less than or equal to 2000",
 "Year is greater than or equal to 1970",
 {
 "or" : [
 {
 "not" : {
 "EstablishmentMeans" : [
 "is one of (MANAGED, INTRODUCED)"
 ]
 }
 },
 "EstablishmentMeans is null"
 ]
 },
 {
 "or" : [
 "CoordinateUncertaintyInMeters is less than 1000",
 "CoordinateUncertaintyInMeters is null"
 ]
 }
 ]
}

 The dataset includes 120 records from 30 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000041-260225131425191/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6sg7ux
title: Occurrence Download

description: A dataset containing 87 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is CHN.29_1",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Enicurus schistaceus"
 ]
}

 The dataset includes 87 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000042-260225131425191/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.y2e43y
title: Occurrence Download

description: A dataset containing 19 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Typha domingensis",
 "Country is Colombia",
 "HasCoordinate is true"
 ]
}

 The dataset includes 19 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000044-260225131425191/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.11588/duerer.online.699efad51153d
title: Livländische Frau, https://d-nb.info/gnd/1199019925
DOI: 10.15468/dl.rzydn8
title: Occurrence Download

description: A dataset containing 39745 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Europe",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Geophilomorpha"
 ]
}

 The dataset includes 39745 records from 370 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000043-260225131425191/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.