cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.dn3f3j
title: Occurrence Download

description: A dataset containing 9630 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Geomys bursarius"
 ]
}

 The dataset includes 9630 records from 116 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009897-260108223611665/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.18249409
title: Blumenbachia Schrad. In: Marchesi E., Mailhos A. & Bonifacino J.M. (Eds.). Flora Uruguaya: Flora Vascular del Uruguay. ISSN 3121-2050, V. 1.0.

description: Citable snapshot. Includes PDF and CSV of collections. Date: January 13th, 2026 at 16:43
DOI: 10.5281/zenodo.18249410
title: Blumenbachia Schrad. In: Marchesi E., Mailhos A. & Bonifacino J.M. (Eds.). Flora Uruguaya: Flora Vascular del Uruguay. ISSN 3121-2050, V. 1.0.

description: Citable snapshot. Includes PDF and CSV of collections. Date: January 13th, 2026 at 16:43
DOI: 10.5281/zenodo.18249416
title: Blumenbachia insignis Schrad. In: Marchesi E., Mailhos A. & Bonifacino J.M. (Eds.). Flora Uruguaya: Flora Vascular del Uruguay. ISSN 3121-2050, V. 1.0.

description: Citable snapshot. Includes PDF and CSV of collections. Date: January 13th, 2026 at 16:43
DOI: 10.5281/zenodo.18249415
title: Blumenbachia insignis Schrad. In: Marchesi E., Mailhos A. & Bonifacino J.M. (Eds.). Flora Uruguaya: Flora Vascular del Uruguay. ISSN 3121-2050, V. 1.0.

description: Citable snapshot. Includes PDF and CSV of collections. Date: January 13th, 2026 at 16:43
DOI: 10.15468/dl.mrt9ns
title: Occurrence Download

description: A dataset containing 484263 records in GBIF matching the query:
SELECT
 kingdom,
 kingdomkey,
 phylum,
 phylumkey,
 class,
 classkey,
 "order",
 orderkey,
 family,
 familykey,
 genus,
 genuskey,
 species,
 specieskey,
 "year",
 IF(ISNULL(kingdomkey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY kingdomkey, "year")) kingdomcount,
 IF(ISNULL(phylumkey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY phylumkey, "year")) phylumcount,
 IF(ISNULL(classkey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY classkey, "year")) classcount,
 IF(ISNULL(orderkey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY orderkey, "year")) ordercount,
 IF(ISNULL(familykey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY familykey, "year")) familycount,
 IF(ISNULL(genuskey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY genuskey, "year")) genuscount,
 COUNT(*) occurrences,
 MIN(GBIF_TEMPORALUNCERTAINTY(eventdate, eventtime)) mintemporaluncertainty,
 MIN(COALESCE(coordinateuncertaintyinmeters, 1000)) mincoordinateuncertaintyinmeters
FROM
 occurrence
WHERE
 occurrence.countrycode = 'EC'
 AND occurrence.occurrencestatus = 'PRESENT'
 AND occurrence.hasgeospatialissues = FALSE
 AND NOT GBIF_STRINGARRAYCONTAINS(occurrence.issue, 'TAXON_MATCH_FUZZY', TRUE)
 AND (occurrence.distancefromcentroidinmeters &gt;= 2000.0 OR occurrence.distancefromcentroidinmeters IS NULL)
 AND NOT occurrence.basisofrecord IN ('FOSSIL_SPECIMEN', 'LIVING_SPECIMEN')
 AND (occurrence.specieskey IS NOT NULL AND occurrence."year" IS NOT NULL)
GROUP BY
 occurrence.kingdom,
 occurrence.kingdomkey,
 occurrence.phylum,
 occurrence.phylumkey,
 occurrence.class,
 occurrence.classkey,
 occurrence."order",
 occurrence.orderkey,
 occurrence.family,
 occurrence.familykey,
 occurrence.genus,
 occurrence.genuskey,
 occurrence.species,
 occurrence.specieskey,
 occurrence."year"

 The dataset's 484263 records were derived from 1924 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009878-260108223611665/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.15172463
title: Dataset for "Ephrin B1 and B2 mediate Cedar virus entry into Egyptian fruit bat cells"

description: Cedar virus (CedV), closely related to Hendra and Nipah virus, is a novel Henipavirus originally isolated from flying foxes in Australia in 2012. Although its glycoprotein G exhibits relatively low sequence similarity with its counterparts of Hendra and Nipah virus, CedV also uses ephrin receptors, i.e., ephrins B1, B2, A2 and A5 to enters human cells. Nevertheless, the entry mechanism of CedV into bat cells remains unexplored. Considering that Rousettus aegyptiacus (Egyptian Rousette bat, ERB) is postulated to be a reservoir host for henipaviruses, we aim to reveal the receptors utilized by CedV enabling its entry into ERB cells. To this end, we cloned class A and B ephrins of ERB and generated CHO-K1 cells stably expressing individual ephrins. We also developed a lentivirus-based pseudovirus system containing the firefly luciferase reporter. Assessment of luciferase activity in cells expressing single ephrins demonstrated that ERB ephrin B1 and B2 mediated CedV pseudovirus entry. Further, we generated a recombinant CedV expressing the fluorescent protein TurboFP635 (rCedV-nTurbo635). By performing high-content microscopy and flow cytometry, we unveiled that in addition to ephrin B1 and B2, ephrin A5 was also able to mediate rCedV-nTurbo635 entry, although to a much lesser extent. In contrast to human ephrin A2, ERB ephrin A2 failed to mediate rCedV-nTurbo635 entry. Finally, we generated ERB epithelial cells with ephrin B1 and/or ephrin B2 knockdown (KD). The entry of rCedV-nTurbo635 into ERB epithelial cells was drastically impaired by ephrin B1/B2 KD, validating the importance of ephrin B1 and B2 in its entry. Altogether, we conclude that CedV primarily employs ERB ephrin B1, B2 and possibly A5 for its entry into ERB cells.
DOI: 10.5281/zenodo.15172462
title: Dataset for "Ephrin B1 and B2 mediate Cedar virus entry into Egyptian fruit bat cells"

description: Cedar virus (CedV), closely related to Hendra and Nipah virus, is a novel Henipavirus originally isolated from flying foxes in Australia in 2012. Although its glycoprotein G exhibits relatively low sequence similarity with its counterparts of Hendra and Nipah virus, CedV also uses ephrin receptors, i.e., ephrins B1, B2, A2 and A5 to enters human cells. Nevertheless, the entry mechanism of CedV into bat cells remains unexplored. Considering that Rousettus aegyptiacus (Egyptian Rousette bat, ERB) is postulated to be a reservoir host for henipaviruses, we aim to reveal the receptors utilized by CedV enabling its entry into ERB cells. To this end, we cloned class A and B ephrins of ERB and generated CHO-K1 cells stably expressing individual ephrins. We also developed a lentivirus-based pseudovirus system containing the firefly luciferase reporter. Assessment of luciferase activity in cells expressing single ephrins demonstrated that ERB ephrin B1 and B2 mediated CedV pseudovirus entry. Further, we generated a recombinant CedV expressing the fluorescent protein TurboFP635 (rCedV-nTurbo635). By performing high-content microscopy and flow cytometry, we unveiled that in addition to ephrin B1 and B2, ephrin A5 was also able to mediate rCedV-nTurbo635 entry, although to a much lesser extent. In contrast to human ephrin A2, ERB ephrin A2 failed to mediate rCedV-nTurbo635 entry. Finally, we generated ERB epithelial cells with ephrin B1 and/or ephrin B2 knockdown (KD). The entry of rCedV-nTurbo635 into ERB epithelial cells was drastically impaired by ephrin B1/B2 KD, validating the importance of ephrin B1 and B2 in its entry. Altogether, we conclude that CedV primarily employs ERB ephrin B1, B2 and possibly A5 for its entry into ERB cells.
DOI: 10.5281/zenodo.15268291
title: Synthesizing Safety Data on Novel Intravaginal Formulations: A Comprehensive Scoping Review of In vivo and In vitro Research
DOI: 10.5281/zenodo.15268292
title: Synthesizing Safety Data on Novel Intravaginal Formulations: A Comprehensive Scoping Review of In vivo and In vitro Research
DOI: 10.5281/zenodo.15268260
title: Table 2 in A new Late Viséan ammonoid assemblage from the Anti-Atlas (Early Carboniferous, Morocco)

description: Table 2. Conch dimensions and ratios of selected specimens of Merocanites consequius sp. nov. from the Gara el Itima; reconstructed values in italics.
dmwwwhuwahww/dmww/whuw/dmWERIZRMB.C.32199.190.017.630.037.528.50.200.590.422.140.05MB.C.32199.2–36.570.6–––0.52–––
description: Published as part of Korn, Dieter, 2025, A new Late Viséan ammonoid assemblage from the Anti-Atlas (Early Carboniferous, Morocco), pp. 260 in European Journal of Taxonomy 987 on page 260, DOI: 10.5852/ejt.2025.987.2873, http://zenodo.org/record/15260621
DOI: 10.5281/zenodo.15258043
title: Datasets for ``Magnetorotational instability in a solar mean-field dynamo''

description: This directory contains an index.html file with links to the run
directories and idl plotting routines with secondary data for the
other figures for the paper "Magneto-rotational instability in a
solar mean-field dynamo" by Brandenburg, Larsson, Del Sordo, &
K&auml;pyl&auml; (2025).  In anything turns out to be incomplete, please
email brandenb@nordita.org.
DOI: 10.5281/zenodo.15258044
title: Datasets for ``Magnetorotational instability in a solar mean-field dynamo''

description: This directory contains an index.html file with links to the run
directories and idl plotting routines with secondary data for the
other figures for the paper "Magneto-rotational instability in a
solar mean-field dynamo" by Brandenburg, Larsson, Del Sordo, &
K&auml;pyl&auml; (2025).  In anything turns out to be incomplete, please
email brandenb@nordita.org.
DOI: 10.14288/1.0397756
title: Data from: Phylogenomics from whole genome sequences using aTRAM

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;Novel sequencing technologies are rapidly expanding the size of data sets that can be applied to phylogenetic studies. Currently the most commonly used phylogenomic approaches involve some form of genome reduction. While these approaches make assembling phylogenomic data sets more economical for organisms with large genomes, they reduce the genomic coverage and thereby the long-term utility of the data. Currently, for organisms with moderate to small genomes (&lt;1000 Mbp) it is feasible to sequence the entire genome at modest coverage (10−30×). Computational challenges for handling these large data sets can be alleviated by assembling targeted reads, rather than assembling the entire genome, to produce a phylogenomic data matrix. Here we demonstrate the use of automated Target Restricted Assembly Method (aTRAM) to assemble 1107 single-copy ortholog genes from whole genome sequencing of sucking lice (Anoplura) and out-groups. We developed a pipeline to extract exon sequences from the aTRAM assemblies by annotating them with respect to the original target protein. We aligned these protein sequences with the inferred amino acids and then performed phylogenetic analyses on both the concatenated matrix of genes and on each gene separately in a coalescent analysis. Finally, we tested the limits of successful assembly in aTRAM by assembling 100 genes from close- to distantly related taxa at high to low levels of coverage.
DOI: 10.14288/1.0397758
title: Data from: Genetic rediscovery of an ‘extinct’ Galápagos giant tortoise species

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;Genes from recently extinct species can live on in the genomes of extant individuals of mixed ancestry. Recently, Poulakakis et al. detected genetic signatures of the giant Galápagos tortoise once endemic to Floreana Island (Chelonoidis elephantopus) within eleven hybrid individuals of otherwise pure C. becki on Volcano Wolf, Isabela Island. Movement of tortoises among islands by pirate and whaling ships was not uncommon during the 1800’s, representing a likely mechanism by which individuals from Floreana were translocated to northern Isabela, despite being presumed extinct soon after Charles Darwin’s historic voyage to the Galápagos Islands in 1835. These eleven hybrid individuals with C. elephantopus ancestry were thought to be the last genetic vestiges of a unique evolutionary lineage in the wild. Here we report that reproductively mature purebred tortoises of the recently ‘extinct’ C. elephantopus from Floreana Island are very likely still alive today, as identified and tracked through the genetic footprints’ left in the genomes of very recent hybrid offspring on Volcano Wolf, Isabela Island. If found, these purebred C. elephantopus individuals could constitute core founders of a captive breeding program directed towards resurrecting this species.
DOI: 10.14288/1.0397760
title: Data from: Large‐scale molecular diet analysis in a generalist marine mammal reveals male preference for prey of conservation concern

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;Sex‐specific diet information is important in the determination of predator impacts on prey populations. Unfortunately, the diet of males and females can be difficult to describe, particularly when they are marine predators. We combined two molecular techniques to describe haul‐out use and prey preferences of male and female harbor seals (Phoca vitulina) from Comox and Cowichan Bay (Canada) during 2012–2013. DNA metabarcoding quantified the diet proportions comprised of prey species in harbor seal scat, and qPCR determined the sex of the individual that deposited each scat. Using 287 female and 260 male samples, we compared the monthly sex ratio with GLMs and analyzed prey consumption relative to sex, season, site, and year with PERMANOVA. The sex ratio between monthly samples differed widely in both years (range = 12%–79% males) and showed different patterns at each haul‐out site. Male and female diet differed across both years and sites: Females consumed a high proportion of demersal fish species while males consumed more salmonid species. Diet composition was related to both sex and season (PERMANOVA: R2 = 27%, p &lt; 0.001; R2 = 24%, p &lt; 0.001, respectively) and their interaction (PERMANOVA: R2 = 11%, p &lt; 0.001). Diet differences between males and females were consistent across site and year, suggesting fundamental foraging differences, including that males may have a larger impact on salmonids than females. Our novel combination of techniques allowed for both prey taxonomic and spatiotemporal resolution unprecedented in marine predators.
DOI: 10.14288/1.0397761
title: Data from: Multi-speed genome diploidization and diversification after an ancient allopolyploidization

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;Hybridization and genome doubling (allopolyploidy) have led to evolutionary novelties as well as to the origin of new clades and species. Despite the importance of allopolyploidization, the dynamics of post-polyploid diploidization (PPD) at the genome level has been only sparsely studied. The Microlepidieae (MICR) is a crucifer tribe of 17 genera and c. 56 species endemic to Australia and New Zealand. Our phylogenetic and cytogenomic analyses revealed that MICR originated via an inter-tribal hybridization between ancestors of Crucihimalayeae (n = 8; maternal genome) and Smelowskieae (n = 7; paternal genome), both native to the Northern Hemisphere. The reconstructed ancestral allopolyploid genome (n = 15) originated probably in north-eastern Asia or western North America during the Late Miocene (c. 10.6 - 7 million years ago) and reached the Australian mainland via long-distance dispersal. In Australia, the allotetraploid genome diverged into at least three main subclades exhibiting different levels of PPD and diversity: 1.25-fold descending dysploidy (DD) of n = 15 → n = 12 (autopolyploidy → 24) in perennial Arabidella (3 species), 1.5-fold DD of n = 15 → n = 10 in the perennial Pachycladon (11 spp.), and 2.1 to 3.75-fold DD of n = 15 → n = 7 - 4 in the largely annual crown group genera (42 spp. in 15 genera). These results are among the first to demonstrate multi-speed genome evolution in taxa descending from a common allopolyploid ancestor. It is suggested that clade-specific PPD can operate at different rates and efficacies, and can be tentatively linked to life histories and the extent of taxonomic diversity.
DOI: 10.14288/1.0397763
title: Data from: Adaptation with gene flow across the landscape in a dune sunflower

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;Isolation by adaptation increases divergence at neutral loci when natural selection against immigrants reduces the rate of gene flow between different habitats. This can occur early in the process of adaptive divergence and is a key feature of ecological speciation. Despite the ability of isolation by distance and other forms of landscape resistance to produce similar patterns of neutral divergence within species, few studies have used landscape genetics to control for these other forces. We have studied the divergence of Helianthus petiolaris ecotypes living in active sand dunes and adjacent non-dune habitat, using landscape genetics approaches, such as circuit theory and multiple regression of distance matrices, in addition to coalescent modelling. Divergence between habitats was significant, but not strong, and was shaped by isolation by distance. We expected that increased resistance due to patchy and unfavourable habitat in the dunes would contribute to divergence. Instead, we found that landscape resistance models with lower resistance in the dunes performed well as predictors of genetic distances among subpopulations. Nevertheless, habitat class remained a strong predictor of genetic distance when controlling for isolation by resistance and isolation by distance. We also measured environmental variables at each site and confirmed that specific variables, especially soil nitrogen and vegetation cover, explained a greater proportion of variance in genetic distance than did landscape or the habitat classification alone. Asymmetry in effective population sizes and numbers of migrants per generation was detected using coalescent modelling with Bayesian inference, which is consistent with incipient ecological speciation being driven by the dune habitat.
DOI: 10.14288/1.0397765
title: Data from: Measuring engagement in advance care planning: a cross-sectional multicentre feasibility study.

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;Objectives: To assess feasibility, acceptability, and clinical sensibility of a novel survey, the Advance Care Planning (ACP) Engagement Survey in various health care settings. Setting: A target sample of 50 patients from each of primary care, hospital, cancer care, and dialysis care settings. Participants: A convenience sample of patients without cognitive impairment who could speak and read English was recruited. Patients 50 years and older were eligible in primary care; patients 80 and older or 55 years and older with clinical markers of advanced chronic disease were recruited in hospital; patients aged 19 and older were recruited in cancer and renal dialysis centres. Outcomes: We assessed feasibility, acceptability and clinical sensibility of the ACP Engagement Survey using a 6-point scale. The ACP Engagement Survey measures ACP processes (knowledge, contemplation, self-efficacy, readiness) on 5-point Likert scales and actions (yes/no). Results: 196 patients (38 to 96 years old, 50.5% women) participated. Mean (±standard deviation) time to administer was 48.8 ±19.6 minutes. Mean acceptability scores ranged from 3.2±1.3 in hospital to 4.7±0.9 in primary care and mean relevance ranged from 3.5±1.0 in hospital to 4.9±0.9 in dialysis centres (p values &lt;0.001 for both). The mean process score was 3.1±0.6 and the mean action score was 11.2±5.6 (of a possible 25). Conclusions: The ACP Engagement Survey demonstrated feasibility and acceptability in out-patient settings, but was less feasible and acceptable among hospitalized patients due to length. A shorter version may improve feasibility. Engagement in ACP was low to moderate.
DOI: 10.14288/1.0397766
title: Data from: Quantifying sequence proportions in a DNA-based diet study using Ion Torrent amplicon sequencing: which counts count?

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;A goal of many environmental DNA barcoding studies is to infer quantitative information about relative abundances of different taxa based on sequence read proportions generated by high-throughput sequencing. However, potential biases associated with this approach are only beginning to be examined. We sequenced DNA amplified from faeces (scats) of captive harbour seals (Phoca vitulina) to investigate whether sequence counts could be used to quantify the seals’ diet. Seals were fed fish in fixed proportions, a chordate-specific mitochondrial 16S marker was amplified from scat DNA and amplicons sequenced using an Ion Torrent PGM™. For a given set of bioinformatic parameters, there was generally low variability between scat samples in proportions of prey species sequences recovered. However, proportions varied substantially depending on sequencing direction, level of quality filtering (due to differences in sequence quality between species) and minimum read length considered. Short primer tags used to identify individual samples also influenced species proportions. In addition, there were complex interactions between factors; for example, the effect of quality filtering was influenced by the primer tag and sequencing direction. Resequencing of a subset of samples revealed some, but not all, biases were consistent between runs. Less stringent data filtering (based on quality scores or read length) generally produced more consistent proportional data, but overall proportions of sequences were very different than dietary mass proportions, indicating additional technical or biological biases are present. Our findings highlight that quantitative interpretations of sequence proportions generated via high-throughput sequencing will require careful experimental design and thoughtful data analysis.
DOI: 10.15468/dl.khyy25
title: Occurrence Download

description: A dataset listing the 76 species recorded in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-29.54691 -0.71986,-26.65759 -7.94346,-17.68215 -2.92886,-20.58404 2.97962,-29.54691 -0.71986))",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Perciformes"
 ]
}

 The dataset's 76 records were derived from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000458-250424135625364/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.14288/1.0397767
title: Data from: Genetic coupling of female mate choice with polygenic ecological divergence facilitates stickleback speciation

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;Ecological speciation with gene flow is widespread in nature, but it presents a conundrum: how are associations between traits under divergent natural selection and traits that contribute to assortative mating maintained? Theoretical models suggest that genetic mechanisms inhibiting free recombination between loci underlying these two types of traits (hereafter, “genetic coupling”) can facilitate speciation. Here, we perform a direct test for genetic coupling by mapping both divergent traits and female mate choice in a classic model of ecological speciation: sympatric benthic and limnetic threespine stickleback (Gasterosteus aculeatus). By measuring mate choice in F2 hybrid females, we allowed for recombination between loci underlying assortative mating and those under divergent ecological selection. In semi-natural mating arenas in which females had access to both benthic and limnetic males, we found that F2 females mated with males similar to themselves in body size and shape. In addition, we found two quantitative trait loci (QTLs) associated with female mate choice that also predicted female morphology along the benthic-limnetic trait axis. Furthermore, a polygenic genetic model that explains adaptation to contrasting benthic and limnetic feeding niches also predicted F2 female mate choice. Together, these results provide empirical evidence that genetic coupling of assortative mating with traits under divergent ecological selection helps maintain species in the face of gene flow, despite a polygenic basis for adaptation to divergent environments.