cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.17698918
title: Data Related to:  Environmental Effects via Frozen Density Embedding in Real-Time Time-Dependent Dirac–Kohn–Sham Theory: Solvation of Lead Halides

description: 1) The "Data_for_Figure_5" folder contains all data and the Python script (gen_figure.py) necessary to generate the spectra shown in Figure 5.

2) The "Data_for_Figure_6" folder contains all data and the Python script (gen_figure.py) necessary to generate the spectra shown in Figure 6.

3) The "Geometry" folder contains all the geometrical structures used in the article, provided in XYZ format.

4) The folder "PbCl2_32GBL_calculation/Dyall2vdz" provides an example calculation for the PbCl2(32GBL) system using the dyall.2vdz basis set. The three subdirectories (Dir_X_weak_F_Gen2v1, Dir_Y_weak_F_Gen2v1 and Dir_Z_weak_F_Gen2v1) contain the submission scripts to run the calculation on the PbCl2(32GBL) system by applying the perturbation field along the three Cartesian axes, respectively.

These files are:-"script.pbs": The submission script. The final result is the induced dipole moment reported as a function of time (dipole.txt).-"extract_spectra.sh": This script performs the Fourier transform using the Padé method, saving the output to "ftoutput.txt."The total isotropic spectrum is obtained using the Python script "gen_total_spectra.py" and is stored in the file "total_DKS_spectrumPbCl2+32GBL.txt".~
DOI: 10.5281/zenodo.17698919
title: Data Related to:  Environmental Effects via Frozen Density Embedding in Real-Time Time-Dependent Dirac–Kohn–Sham Theory: Solvation of Lead Halides

description: 1) The "Data_for_Figure_5" folder contains all data and the Python script (gen_figure.py) necessary to generate the spectra shown in Figure 5.

2) The "Data_for_Figure_6" folder contains all data and the Python script (gen_figure.py) necessary to generate the spectra shown in Figure 6.

3) The "Geometry" folder contains all the geometrical structures used in the article, provided in XYZ format.

4) The folder "PbCl2_32GBL_calculation/Dyall2vdz" provides an example calculation for the PbCl2(32GBL) system using the dyall.2vdz basis set. The three subdirectories (Dir_X_weak_F_Gen2v1, Dir_Y_weak_F_Gen2v1 and Dir_Z_weak_F_Gen2v1) contain the submission scripts to run the calculation on the PbCl2(32GBL) system by applying the perturbation field along the three Cartesian axes, respectively.

These files are:-"script.pbs": The submission script. The final result is the induced dipole moment reported as a function of time (dipole.txt).-"extract_spectra.sh": This script performs the Fourier transform using the Padé method, saving the output to "ftoutput.txt."The total isotropic spectrum is obtained using the Python script "gen_total_spectra.py" and is stored in the file "total_DKS_spectrumPbCl2+32GBL.txt".~
DOI: 10.15468/dl.xcmapn
title: Occurrence Download

description: A dataset containing 19 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Indosasa patens"
 ]
}

 The dataset includes 19 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005451-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.44s9er
title: Occurrence Download

description: A dataset containing 4245 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Mitragyna inermis"
 ]
}

 The dataset includes 4245 records from 132 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005452-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.yndqux
title: Occurrence Download

description: A dataset containing 66 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Machine Observation, Human Observation, Living Specimen)",
 "TaxonKey is Gopherus flavomarginatus"
 ]
}

 The dataset includes 66 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005453-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.3886/e240565
title: HIFLD OPEN Overhead Pipeline Lines (USACE IENC)

description: The USACE IENCs coverage area consists of 7,260 miles across 21 rivers primarily located in the Central United States. IENCs apply to inland waterways that are maintained for navigation by USACE for shallow-draft vessels (e.g., maintained at a depth of 9-14 feet, dependent upon the waterway project authorization). Generally, IENCs are produced for those commercially navigable waterways which the National Oceanic and Atmospheric Administration (NOAA) does not produce Electronic Navigational Charts (ENCs). However, Special Purpose IENCs may be produced in agreement with NOAA.
description: Archived from the HIFLD Open GIS data repository, which was deactivated on August 26, 2025. (Downloaded 08/26)
DOI: 10.3886/e240565v1
title: HIFLD OPEN Overhead Pipeline Lines (USACE IENC)

description: The USACE IENCs coverage area consists of 7,260 miles across 21 rivers primarily located in the Central United States. IENCs apply to inland waterways that are maintained for navigation by USACE for shallow-draft vessels (e.g., maintained at a depth of 9-14 feet, dependent upon the waterway project authorization). Generally, IENCs are produced for those commercially navigable waterways which the National Oceanic and Atmospheric Administration (NOAA) does not produce Electronic Navigational Charts (ENCs). However, Special Purpose IENCs may be produced in agreement with NOAA.
description: Archived from the HIFLD Open GIS data repository, which was deactivated on August 26, 2025. (Downloaded 08/26)
DOI: 10.15468/dl.8tkv7w
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Sinobambusa rubroligula"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005454-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.se3jqn
title: Occurrence Download

description: A dataset containing 5971 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Agriades glandon",
 "Geometry POLYGON((-5 41, 9 41, 9 51, -5 51, -5 41))"
 ]
}

 The dataset includes 5971 records from 151 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005455-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17698963
title: Replication Package for the JEEA-FBBVA 2025 Lecture: Negative Rates andtheEffective LowerBound:TheoryandEvidence
DOI: 10.5281/zenodo.17698962
title: Replication Package for the JEEA-FBBVA 2025 Lecture: Negative Rates andtheEffective LowerBound:TheoryandEvidence
DOI: 10.34740/kaggle/dsv/13849854
title: Peer-to-Peer Boliviano (BOB) Exchange Data
DOI: 10.15468/dl.s234b7
title: Occurrence Download

description: A dataset containing 9140 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-0.2204 54.34512,32.19813 54.34512,32.19813 76.88504,-0.2204 76.88504,-0.2204 54.34512))",
 "OccurrenceStatus is Present",
 "TaxonKey is Phalangium opilio"
 ]
}

 The dataset includes 9140 records from 35 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005456-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.z5urn3
title: Occurrence Download

description: A dataset listing the 1134 species recorded in GBIF matching the query:
{
 "and" : [
 "Country is France",
 "OccurrenceStatus is Present",
 "TaxonKey is one of (Hesperiidae, Papilionidae, Pieridae, Nymphalidae, Lycaenidae, Riodinidae)",
 "Year 2010-2020"
 ]
}

 The dataset's 1134 records were derived from 4641 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005423-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2z55ns
title: Occurrence Download

description: A dataset containing 2047 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "TaxonKey is Sylvilagus bachmani (Waterhouse, 1839)"
 ]
}

 The dataset includes 2047 records from 63 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016036-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5uc45b
title: Occurrence Download

description: A dataset containing 9880 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Vulpes vulpes (Linnaeus, 1758)",
 "StateProvince is one of (Maine, New Hampshire, Vermont, Massachusetts, Rhode Island, Connecticut, New York, Pennsylvania, New Jersey, Delaware)"
 ]
}

 The dataset includes 9880 records from 34 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016037-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.15579410
title: Submitted Galaxy Scores to the Gravitational Wave Treasure Map for event MS250602t Preliminary

description: Attached in a .json file is the ranked galaxy information within the contour region of the EM counterpart search associated with the gravitational wave event MS250602t Preliminary. A reference to these calculations can be found here: https://ui.adsabs.harvard.edu/abs/2017ApJ...848L..33A/abstract
DOI: 10.5281/zenodo.15579411
title: Submitted Galaxy Scores to the Gravitational Wave Treasure Map for event MS250602t Preliminary

description: Attached in a .json file is the ranked galaxy information within the contour region of the EM counterpart search associated with the gravitational wave event MS250602t Preliminary. A reference to these calculations can be found here: https://ui.adsabs.harvard.edu/abs/2017ApJ...848L..33A/abstract
DOI: 10.5061/dryad.d47h94c9
title: Data from: A new global palaeobiogeographical model for the late Mesozoic and early Tertiary

description: Late Mesozoic palaeobiogeography has been characterized by a distinction
 between the northern territories of Laurasia and the southern landmasses
 of Gondwana. The repeated discovery of Gondwanan lineages in Laurasia has
 led to the proposal of alternative scenarios to explain these anomalous
 occurrences. A new biogeographical model for late Mesozoic terrestrial
 ecosystems is here proposed, in which Europe and ‘Gondwanan’ territories
 possessed a common Eurogondwanan fauna during the earliest Cretaceous.
 Subsequently, following the Hauterivian, Europe severed from Africa and
 connected to Asiamerica resulting in a faunal interchange. This model
 explains the presence of ‘Gondwanan’ taxa in Laurasia and the absence of
 Laurasian forms in the southern territories during the Cretaceous. In
 order to test this new palaeobiogeographical model, tree reconciliation
 analyses (TRAs) were performed based on biogeographical signals provided
 by a supertree of late Mesozoic archosaurs. The TRAs found significant
 evidence for the presence of an earliest Cretaceous Eurogondwanan fauna,
 followed by a relatively short-term Gondwana-Laurasia dichotomy. The
 analysis recovered evidence for a biogeographical re-connection of the
 European territories with Africa and South America-Antarctica during the
 Campanian to Maastrichtian time-slice. This biogeographical scenario
 appears to continue through the early Tertiary and sheds light on the
 trans-Atlantic disjunct distributions of several extant plant and animal
 groups.
description: Ezcurra and Agnolin
 Appendix 1 R2Archosaur Semi-strict
 Supertree construction, Time Slicing Pruning criteria, Archosaur
 Geographic and Temporal Distribution, and TNT Semi-strict Supertree
 File.Ezcurra and Agnolin
 Appendix 2 R1Late Jurassic-Cretaceous
 Archosaur Semi-strict Supertree.Ezcurra and Agnolin
 Appendix 3 R2Treatment of the
 Widespread Taxa Problem, Optimal Area Cladograms Search Parameters,
 Randomisation Test Analyses, Test of Biogeographical Hypotheses on the
 Phylogeny of Archosaur Tetrapods, and Linkage between Sea Level and
 Biogeographical Models.Ezcurra and Agnolin
 Appendix 4 R2Dispersal-Vicariance
 Analyses, Results of S-DIVA, and Geographic Distribution of the Taxa used
 in the Dispersal-Vicariance Analyses.Ezcurra and Agnolin
 Appendix 5 R2Additional References
 Cited in the Appendices
DOI: 10.5281/zenodo.18391793
title: Electron density and molecular electrostatic potential of CO molecule
DOI: 10.15468/mwta62
title: Breaking ground below: first troglobitic Circoniscus (Isopoda: Scleropactidae) from Southeastern Brazil

description: This dataset contains the digitized treatments in Plazi based on the original journal article Galo, Júlia Barbosa, Cardoso, Giovanna Monticelli, Ferreira, Rodrigo Lopes (2025): Breaking ground below: first troglobitic Circoniscus (Isopoda: Scleropactidae) from Southeastern Brazil. Zootaxa 5723 (1): 117-126, DOI: 10.11646/zootaxa.5723.1.6, URL: https://doi.org/10.11646/zootaxa.5723.1.6AbstractA new troglobitic species of the genus Circoniscus is described from Brazil. Circoniscus boitata sp. nov. is the first troglobitic species of the genus reported from Southeastern Brazil and is found in two caves within the Cavernas do Peruaçu National Park, in Minas Gerais state. Additionally, we provide the first identification key for the troglobitic species of Circoniscus, along with electron micrographs and ecological notes on the species and the conservation status of its habitat.
DOI: 10.5061/dryad.sk318rd3
title: Data from: Proteomic divergence in Arabidopsis autopolyploids and allopolyploids and their progenitors

description: Autopolyploidy and allopolyploidy are common in many plants and some
 animals. Rapid changes in genomic composition and gene expression have
 been observed in both auto- and allopolyploids, but the effects of
 polyploidy on proteomic divergence are poorly understood. Here we report
 quantitative analysis of protein changes in leaves of Arabidopsis auto-
 and allotetraploids and their progenitors using isobaric tags for relative
 and absolute quantitation (iTRAQ) coupled with mass spectrometry. Over 1
 000 proteins analyzed, the levels of protein divergence were relatively
 high (~18%) between Arabidopsis thaliana and Arabidopsis arenosa,
 relatively low (~6.8%) between an A. thaliana diploid and autotetraploid,
 and intermediate (~8.3% and 8.2%) in F1 and F8 resynthesized
 allotetraploids relative to the mid-parent values, respectively. This
 pattern of proteomic divergence was consistent with the previously
 reported gene expression data. In particular, many nonadditively
 accumulated proteins (61-62%) in the F1 and F8 allotetraploids were also
 differentially expressed between the parents. The differentially
 accumulated proteins in functional categories of abiotic and biotic
 stresses were overrepresented between an A. thaliana autotetraploid and
 diploid and between two Arabidopsis species, but not significantly
 different between the allotetraploids and their progenitors. Although the
 trend of changes is similar, the percentage of differentially accumulated
 proteins that matched previously reported differentially expressed genes
 was relatively low. Western blot analysis confirmed several selected
 proteins with isoforms whose cumulative levels were differentially
 expressed. These data suggest high protein divergence between species as
 well as rapid changes in post-transcriptional regulation and translational
 modifications of proteins during polyploidization.
description: 11-Supp-Dataset
 1iTRAQ proteome
 comparison between related Arabidopsis species and their allotetraploids.
 Data are provided in Excel sheet formatMS
 SpectraRAW iTRAQ-MS/MS spectra
 files from 4 different MS runs described in the paper entitled
 "Proteomic divergence in Arabidopsis auto- and allopolyploids and
 their progenitors": (1) At2-At4; (2) At2-At4; (3) At4-Aa-F1-F8; 4
 At4-Aa-F1-F8. Data are available for download from the ProteomeCommons.org
 Tranche network using the provided hash.MS_spectra.txt
DOI: 10.5061/dryad.665vv1c7
title: Data from: The evolution of defense mechanisms correlate with the explosive diversification of autodigesting Coprinellus mushrooms (Agaricales, Fungi)

description: Bursts of diversification are known to have contributed significantly to
 the extant morphological and species diversity, but evidence for many of
 the theoretical predictions about adaptive radiations have remained
 contentious. Despite their tremendous diversity, patterns of evolutionary
 diversification and the contribution of explosive episodes in fungi are
 largely unknown. Here, using the genus Coprinellus (Psathyrellaceae,
 Agaricales) as a model, we report the first explosive fungal radiation,
 and infer that the onset of the radiation follows a change from a
 multi-layered to a much simpler defense structure on the fruiting bodies.
 We suggest that this change constitutes a key innovation, relaxing
 constraints on diversification imposed by nutritional investment into the
 development of protective tissues of fruiting bodies. Evidence for the
 impact of protective structures on diversification places our current
 understanding of fruiting body evolution in a new context. Fossil
 calibration suggests that Coprinellus mushrooms radiated during the
 Miocene coinciding with global radiation of large grazing mammals
 following expansion of dry open grasslands. In addition to
 diversification-rate based methods, we test the hard polytomy hypothesis,
 by analyzing the resolvability of internal nodes of the backbone of the
 putative radiation using Reversible-Jump MCMC. We discuss potential
 applications and pitfalls as well as how biologically meaningful
 polytomies can be distinguished from alignment shortcomings. Our data
 provide insights into the nature of adaptive radiations in general by
 revealing a deceleration of morphological diversification through time.
 The "rate" of morphological diversification was approximated by
 obtaining the temporal distribution of state changes in discrete traits
 along the trees and comparing it with the tempo of lineage accumulation.
 By using speciational trees, we found that the number of state changes
 correlate with the number of lineages, even in parts of the tree with
 short internal branches, and peaks around the onset of the explosive
 radiation followed by a slowdown, most likely because of the decrease in
 available niches.
description: Supplementary
 InformationThis file contains:
 Supplementary Methods, and Supplementary Figures 1-6.histogramAndBranchNumbersA perl script to perform the analyses on Fig 3.simmap_cladewisePerl script to extract mapping information from the output of SIMMAP.newickModified BioPerl module, necessary for the installation of the simmap_cladewise.pl script.nexusModified BioPerl module, required for the installation of the simmap_cladewise.pl script
DOI: 10.5061/dryad.mb4mv6pm
title: Data from: Geographic variation in the structure of oak hybrid zones provides insights into the dynamics of speciation

description: Studying geographic variation in the rate of hybridization between closely
 related species could provide a useful window to understand the evolution
 of reproductive isolation. Reinforcement theory predicts greater
 prezygotic isolation in areas of prolonged contact between recently
 diverged species than in areas of recent contact, which implies that old
 contact zones would be dominated by parental phenotypes with few hybrids
 (bimodal hybrid zones) whereas recent contact zones would be characterized
 by hybrid swarms (unimodal hybrid zones). Here we investigate how the
 hybrid zones of two closely related Chinese oaks, Quercus mongolica and Q.
 liaotungensis, are structured geographically using both nuclear and
 chloroplast markers. We found that populations of Q. liaotungensis located
 around the Changbai Mountains in Northeast China, an inferred glacial
 refugium, are introgressed by genes from Q. mongolica, suggesting former
 contact between the two species in this region. Yet, these introgressed
 populations form sharp bimodal hybrid zones with Q. mongolica. In
 contrast, populations of Q. liaotungensis located in North China, which
 show no sign of ancient introgression with Q. mongolica, form unimodal
 hybrid zones with Q. mongolica. These results are consistent with the
 hypothesis that selection against hybrids has had sufficient time to
 reinforce the reproductive barriers between Q. liaotungensis and Q.
 mongolica in Northeast China but not in North China.
description: sample
 locationsnrSSR
 dataAFLP
 datacpSSR
 dataREADME
DOI: 10.5061/dryad.hk25q4d6
title: Data from: Deep phylogeographic structure and environmental differentiation in the carnivorous plant Sarracenia alata

description: We collected ~29kb of sequence data using Roche 454 pyrosequencing in
 order to estimate the timing and pattern of diversification in the
 carnivorous pitcher plant Sarracenia alata. Utilizing modified protocols
 for reduced representation library construction, we generated sequence
 data from 86 individuals across 10 populations from throughout the range
 of the species. We identified 76 high quality and high coverage loci
 (containing over 500 SNPs) using the bioinformatics pipeline PRGmatic.
 Results from a Bayesian clustering analysis indicate that populations are
 highly structured, and are similar in pattern to the topology of a
 population tree estimated using *BEAST. The pattern of diversification
 within S. alata implies that riverine barriers are the primary factor
 promoting population diversification, with divergence across the
 Mississippi River occurring more than 60,000 generations before present.
 Further, significant patterns of niche divergence and the identification
 of several outlier loci suggest that selection may contribute to
 population divergence. Our results demonstrate the feasibility of using
 next-generation sequencing to investigate intraspecific genetic variation
 in non-model species.
description: datazip file of aligned
 fasta lociSupplementaryTables_R1Excel file that contains five supplemental tables.SupplementaryFigure_1_R1Coverage per locus. Black bars correspond to number individuals used for analysis per locus and the black numbers on the x-axis. Gray bars represent the cumulative number of sequencing reads used to call a given locus and correspond to the gray values on the x-axis.SupplementaryFigure_2_R1Shown are results from STRUCTURE runs across 10 partitioning levels (k =2 to k = 11).