cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.18432127
title: The dataset of "Large-scale multi-omics profiling reveals environmental and evolutionary drivers of fungal phylogeographic and metabolic diversity," published in Nature Communications

description: The article "Large-scale multi-omics profiling reveals environmental and evolutionary drivers of fungal phylogeographic and metabolic diversity" utilized 450 Aspergillus flavus strain genomes downloaded from public databases, along with a supplementary table.
DOI: 10.5281/zenodo.18388157
title: UKBOL gap analysis raw data

description: Input data files for the analysis of UK species (from UKSI database) against barcode marker genes:1. COI (BOLD) = result_output.tsv.gz (9th January 2026 public snapshot)2. RBCL (NCBI) = ncbi_rbcl_otu.tsv.gz (ncbi download 23rd January 2026)3. ITS (UNITE) = unite_tsv_output.tsv.gz (sh_general_release_s_all_19.02.2025 = https://doi.org/10.15156/BIO/3301232)4. 12S (MIDORI2) = midori_12S_otu.tsv.gz (MIDORI2_TOTAL_NUC_GB269)5. 16S (MIDORI2) = midori_16S_otu.tsv.gz (MIDORI2_TOTAL_NUC_GB269)

Analysed using these scripts: https://github.com/ukbol/mind-the-gapPresented using these scripts: https://github.com/ukbol/speciesPresented on this website: https://ukbol.github.io/species/index.html

The overarching mind-map for the gap analysis process is included as gaplist-pipeline.pdf
DOI: 10.15468/dl.sdfckb
title: Occurrence Download

description: A dataset containing 15977 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is Fourmis de France métropolitaine : données AntArea",
 "Geometry POLYGON((-33.89286 29.15890,43.92220 29.15890,43.92220 60.27160,-33.89286 60.27160,-33.89286 29.15890))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 15977 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002624-260129131611470/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.18436420
title: Clinical Utility of Salivary Biomarkers in Oral Squamous Cell Carcinoma
DOI: 10.5281/zenodo.18436421
title: Clinical Utility of Salivary Biomarkers in Oral Squamous Cell Carcinoma
DOI: 10.5281/zenodo.18249784
title: MESA inlists for the paper 'The collision and merger products of stars do not look alike: A magnetohydrodynamics comparison'

description: Relevant paper: 'The collision and merger products of stars do not look alike: A magnetohydrodynamics comparison' (arXiv:2510.13736, accepted by the Astrophysical Journal).

This repository contains initial inlists which were used to generate 1D models of stars using the code MESA (Paxton et al. 2011; doi: 10.1088/0067-0049/192/1/3). In our paper, we generate models of masses 5 Msun, 7 Msun, 8 Msun, 10 Msun and metallicities 0.02. The density, temperature, pressure and chemical composition profiles of each star at 10 Myr were then converted to 3D spherical data to input in the magnetohydrodynamics code AREPO (Springel et al. 2010; 10.1111/j.1365-2966.2009.15715.x).

To use our inlists, the MESA and MESA SDK versions are required to be 24.08.1 and 24.7.1, respectively. Please contact the first author (Pavan Vynatheya) for any additional clarifications or questions related to MESA data.
DOI: 10.5281/zenodo.18249783
title: MESA inlists for the paper 'The collision and merger products of stars do not look alike: A magnetohydrodynamics comparison'

description: Relevant paper: 'The collision and merger products of stars do not look alike: A magnetohydrodynamics comparison' (arXiv:2510.13736, accepted by the Astrophysical Journal).

This repository contains initial inlists which were used to generate 1D models of stars using the code MESA (Paxton et al. 2011; doi: 10.1088/0067-0049/192/1/3). In our paper, we generate models of masses 5 Msun, 7 Msun, 8 Msun, 10 Msun and metallicities 0.02. The density, temperature, pressure and chemical composition profiles of each star at 10 Myr were then converted to 3D spherical data to input in the magnetohydrodynamics code AREPO (Springel et al. 2010; 10.1111/j.1365-2966.2009.15715.x).

To use our inlists, the MESA and MESA SDK versions are required to be 24.08.1 and 24.7.1, respectively. Please contact the first author (Pavan Vynatheya) for any additional clarifications or questions related to MESA data.
DOI: 10.5683/sp3/eif6a7
title: Replication code for: Human papillomavirus intermittence, redetections, and associated risk of cytological abnormalities in the Ludwig-McGill cohort study of adult women

description: Replication code for: Human papillomavirus intermittence, redetections, and associated risk of cytological abnormalities in the Ludwig-McGill cohort study of adult women.

Participants of the Ludwig-McGill cohort study did not consent to have their data made publicly available, and confidentiality precludes the publishing of their data. To access the data for research purposes, please contact Eduardo Franco (eduardo.franco@mcgill.ca) or Luisa Villa (l.villa@hc.fm.usp.br). The files included here are SAS and R program code provided as documentation for reproducibility of results in the study titled: "Human papillomavirus intermittence, redetections, and associated risk of cytological abnormalities in the Ludwig-McGill cohort study of adult women" by Talía Malagón, Helen Trottier, Mariam El-Zein, Luisa L Villa, Eduardo Franco, for the Ludwig-McGill Cohort Study.

Text versions (.txt) of SAS and R program files are included for interoperability.
DOI: 10.15468/dl.q8xj6w
title: Occurrence Download

description: A dataset containing 34649 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 Galium mollugo L.",
 "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 34649 records from 225 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012243-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ajsdb7
title: Occurrence Download

description: A dataset containing 752 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Germany",
 "GadmGid is DEU.14_1",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Rubus idaeus L."
 ]
}

 The dataset includes 752 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012245-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.h85mxh
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Sagamichthys Parr, 1953",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((-1.9734 4.2478,-0.0352 5.0957,-0.0352 10.8496,-9.0352 10.8496,-9.0352 4.4397,-8.4168 4.1049,-7.389 3.8664,-5.7288 4.5489,-4.0108 4.7359,-1.9734 4.2478))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012246-250525065834625/datasets/export for details.
DOI: 10.15468/dl.pks9ks
title: Occurrence Download

description: A dataset containing 52 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 Galium richardianum (Gillies ex Hook. & Arn.) Endl. ex Walp.",
 "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 52 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012247-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3vfr8c
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Sagamichthys Parr, 1953",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((-8.8018 33.6743,-9.0352 33.4562,-9.0352 28.8496,-0.0352 28.8496,-0.0352 36.4794,-0.2209 36.3968,-1.3537 36.1876,-1.6551 35.769,-2.0234 35.5842,-2.5138 35.6803,-2.6212 36.2387,-2.9881 36.451,-3.4424 36.249,-3.506 35.7605,-4.4004 35.671,-4.7609 35.8337,-4.8512 36.1709,-5.2296 36.4083,-6.2415 36.1841,-7.168 34.4152,-8.8018 33.6743))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012248-250525065834625/datasets/export for details.
DOI: 10.15468/dl.cqznjv
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Sagamichthys Parr, 1953",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((-0.0352 28.8496,-9.0352 28.8496,-9.0352 19.8496,-0.0352 19.8496,-0.0352 28.8496))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012250-250525065834625/datasets/export for details.
DOI: 10.15468/dl.wm943y
title: Occurrence Download

description: A dataset containing 34435 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 Galium saxatile L.",
 "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 34435 records from 160 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012249-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.96up7k
title: Occurrence Download

description: A dataset containing 129362 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Lolium multiflorum Lam."
 ]
}

 The dataset includes 129362 records from 1766 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012229-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.bg79cnpdz
title: Accumulation of gene copy number variations during the early phase of free-spawning abalone speciation

description: The genetic basis of speciation in free-spawning marine invertebrates is
 poorly understood. Although gene copy number variations (GCNVs) as well as
 nucleotide variations possibly trigger the speciation of these organisms,
 empirical evidence for such a hypothesis is limited. In this study, we
 searched for genomic signatures of GCNVs that may contribute to the
 speciation of Western Pacific abalone species. Whole-genome sequencing
 data suggested the existence of significant amounts of GCNVs in closely
 related abalones, Haliotis discus and H. madaka, in the early phase of
 speciation. In addition, the degree of interspecies genetic
 differentiation in the genes where GCNVs were estimated was higher than
 that in other genes, suggesting that nucleotide divergence also
 accumulates in the genes with GCNVs. GCNVs in some genes were also
 detected in other related abalone species, suggesting that these GCNVs are
 derived from both ancestral and de novo mutations. Our findings suggest
 that GCNVs have been accumulated in the early phase of free-spawning
 abalone speciation.
description: # Title of Dataset: --- The perl scripts to detect 3 allele sequences from
 bam files and their results. These are custom scripts I created, so it
 might be difficult to understand. If you find it confusing, please feel
 free to contact me. Please see text for other analysis methods in this
 study. The WGS data used in this study are provided in
 Table [A1](https://onlinelibrary.wiley.com/doi/full/10.1002/ece3.9816#ece39816-tbl-0001 "Link to table") in Appendix [A](https://onlinelibrary.wiley.com/doi/full/10.1002/ece3.9816#ece39816-app-0001 "Link to appendix").  ### Description of the data and file structure **VCF_haplotype_detect_pipeline_american_abalone.pl** This perl script was used to detect 3 allele sequences from bam files of North American abalones **VCF_haplotype_detect_pipeline_Japanese_abalone.pl** This perl script was used to detect 3 allele sequences from bam files of Japanese abalones **haplotype_all_counts_american_species_dryad.xlsx** Numbers of 3 allele sequences detected from bam files of North American abalones by VCF_haplotype_detect_pipeline_american_abalone.pl. This table provides a representation of abalone individuals across its columns, with each row corresponding to a different gene ID. For example, the cell of STRG.10195 and red1 shows that "red1 have no 3 allele sequences in the STRG.10195". **haplotype_all_counts_three_species_dryad.xlsx** Numbers of 3 allele sequences detected from bam files of Japanese abalones by VCF_haplotype_detect_pipeline_Japanese_abalone.pl. This table provides a representation of abalone individuals across its columns, with each row corresponding to a different gene ID. For example, the cell of STRG.10195 and HD1 shows that "HD1 have no 3 allele sequences in the STRG.10195".
DOI: 10.5061/dryad.v41ns1s13
title: Dataset for Disordered dolomite as an unusual biomineralization product found in the center of a natural Cassis pearl

description: Natural pearls are produced without human intervention, mainly due to
 various irritations from the surrounding environment to their mantle
 tissues. Pearls usually possess similar mineral compositions to the host
 shells, which means they are also dominated by aragonite and calcite. In
 this study, we report a natural pearl from
 a Cassis species mollusk containing granular central
 structures. Raman spectroscopy, laser ablation inductively coupled plasma
 mass spectrometry (LA-ICPMS), energy dispersive X-ray spectroscopy (EDS)
 coupled with scanning electron microscope (SEM), and X-ray
 diffraction (XRD) analyses were carried out in order to characterize the
 mineral composition in the center region of this pearl. Our results showed
 that this pearl’s center was made of mostly disordered dolomite
 (Ca0.53Mg0.47CO3) mixing with small amount of aragonite and high
 magnesium-calcite. To the best of our knowledge, this is the first time
 disordered dolomite was conclusively identified inside of a natural pearl
 and such information expanded our knowledge on internal growth structures
 and formation of natural pearls.
description: A small fragment (~20 μm) was separated from the center of the
 pearl and mounted on a micro loop for XRD data collection. The data were
 collected on a 3 circle single-crystal X-ray diffractometer, which is
 equipped with a Rigaku 007 Cu-Kα X-ray source and a Bruker PROTEUM-F135
 CCD detector. Three φ+ω-rotation frames were collected for 600s/frame with
 a detector distance of 150 mm and 2θ=30°, 50°, 70°. The data were reduced
 to 1D powder diffraction pattern using APEX3 software. The crystal
 structure is refined using the Rietveld method against the integrated data
 in the Jana2006 program. Chemical analyses were
 performed using a Thermo Fisher Scientific’s iCAP Qc ICP-MS, coupled with
 an Elemental Scientific Lasers NWR213 laser ablation system with a
 frequency quintupled Nd:YAG laser operated in Q-switched (pulsed) mode at
 a wavelength of 213nm and pulse duration of 4 ns. Detailed operation
 conditions for the laser and the ICP-MS instrument are the same as what
 was described in the previously published paper. The chemical composition
 was initially internally standardized with 43Ca at a preset value of
 400400 ppmw calculated and assumed from pure calcium carbonate. The data
 was then normalized and converted to 100 wt. % oxides based on 1 carbon
 and 3 oxygen atoms. A Renishaw inVia Reflex micro-Raman
 spectrometer system with a 50× magnification Leica objective lens and an
 830 nm diode laser excitation wavelength at room temperature was used to
 analyze structural characteristics on various locations of the sample in a
 scanning range from 100 to 1600 cm<sup>–1</sup>. It is a
 common technique used to distinguish
 CaCO<sub>3</sub> polymorphs (mainly between aragonite and
 calcite) with reference to different band positions of carbonate ion
 (CO<sub>3</sub><sup>2−</sup>) modes.
DOI: 10.5061/dryad.tb2rbp045
title: Face processing in the infant brain after pandemic lockdown

description: The role of visual experience in the development of face processing has
 long been debated. We present a new angle on this question through a
 serendipitous study that cannot easily be repeated. Infants viewed short
 blocks of faces during fMRI in a repetition suppression task. The same
 identity was presented multiple times in half of the blocks (Repeat
 condition) and diﬀerent identities were presented once each in the other
 half (Novel condition). In adults, the fusiform face area (FFA) tends to
 show greater neural activity for Novel vs. Repeat blocks in such designs,
 suggesting that it can distinguish same vs. diﬀerent face identities. As
 part of an ongoing study, we collected data before the COVID-19 pandemic
 and after an initial local lockdown was lifted. The resulting sample of 12
 infants (9–24 months) was divided equally into pre-and post-lockdown
 groups with matching ages and data quantity/quality. The groups had
 strikingly diﬀerent FFA responses: pre-lockdown infants showed repetition
 suppression (Novel &gt; Repeat), whereas post-lockdown infants showed
 the opposite (Repeat &gt; Novel), often referred to as repetition
 enhancement. These findings provide speculative evidence that altered
 visual experience during the lockdown, or other correlated environmental
 changes, may have affected face processing in the infant brain.
description: Please refer to the manuscript for details.
   Citation: Yates, T. S., Ellis, C. T.,
 & Turk-Browne, N. B. (2022). Face processing in the infant brain
 after pandemic lockdown. Developmental Psychobiology.
description: Please refer to the README for guidance on how to use this
 data.
DOI: 10.5061/dryad.stqjq2c6r
title: Data from: Dispersal-induced social stress prolongs gestation in wild meerkats

description: In the majority of mammals, gestation length is relatively consistent and
 seldom varies by more than 3%. In a few species, females can adjust
 gestation length by delaying the development of the embryo after
 implantation. Delays in embryonic development allow females to defer the
 rising energetic costs of gestation when conditions are unfavourable,
 reducing the risk of embryo loss. Dispersal in mammals that breed
 cooperatively is a period when food intake is likely to be suppressed and
 stress levels are likely to be high. Here we show that pregnant dispersing
 meerkats (Suricata suricatta), which have been aggressively evicted from
 their natal group and experience weight loss and extended periods of
 social stress, prolong their gestation by means of delayed embryonic
 development. Repeated ultrasound scans of wild, unanaesthetised females
 throughout their pregnancies showed that pregnancies of dispersers were on
 average 6.3% longer and more variable in length (52-65 days) than those of
 residents (54-56 days). The variation in dispersers shows that, unlike
 most mammals, meerkats can adapt to stress by adjusting their pregnancy
 length by up to 25%. By doing so, they potentially rearrange the costs of
 gestation during adverse conditions of dispersal and enhance offspring
 survival.
DOI: 10.5061/dryad.6hdr7sr4m
title: Study of the medical service efficiency of county-level public general hospitals based on medical quality constraints: A cross-sectional study

description: Objectives: Since the new medical reform in 2009, county-level hospitals
 in China have achieved rapid development, but health
 resource waste and shortage issues still exist. Design:
 We applied the Meta-frontier and
 SBM-undesirable（Slacks-based Measurement-undesirable) DEA(Data Envelopment
 Analysis) model to measure the medical service
 efficiency with or without medical quality constraints of the
 county-level public general hospitals (CPGHs). The assessment
 includes four inputs, three desirable outputs, and one undesirable output.
 We conducted the assessment via Max-DEA V.8.19 software. Moreover, we
 analyze the factors affecting CPGHs’ medical service
 efficiency based on the FRM model.  Setting: A total of 77 sample
 CPGHs were selected from Shanxi province in China from 2013 to
 2018. Results: The results of this study showed that the efficiency level
 of county-level public hospitals in Shanxi Province is relatively low
 overall (the mean value of efficiency is 0.61 without quality constraints
 and 0.63 under quality constraints). This showed that ignoring medical
 quality constraints will result in lower efficiency and lower health
 resource utilization for high-medical-quality hospitals. The medical
 service efficiency of CPGHs differs greatly among different regions. Under
 the meta-frontier, the hospitals in the central region had the highest
 efficiency (efficiency score 0.70), followed by those in the south
 (efficiency score 0.63), and the hospitals in the north had the lowest
 efficiency (efficiency score 0.54). Factors that have larger
 impacts on the service efficiency of county public hospitals are the
 average length of hospital stay, per capita disposable income and
 financial subsidy income. Conclusions: To improve
 CPGHs’ medical service efficiency, the government should
 increase investment in the northern region, and hospitals should improve
 the management level and allocate human resources rationally.
description: The data are mainly from the 2013–2018 Shanxi (a province with a
 population of 37 million in China) Statistical Yearbook and China Health
 Statistics Yearbook. Overall, 77 CPGHs in Shanxi Province were
 selected. The data excluded other types of hospitals, such as traditional
 Chinese medical hospitals, maternal and child health care hospitals and
 other medical institutions, so they met the homogeneity requirement
 of the DEA(Data Envelopment Analysis) method.