cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5517/ccdc.csd.cc2q0l0c
title: CCDC 2503002: Experimental Crystal Structure Determination

description: Related Article: Eleanor Dodd, Simon J. Coles, William Fraser|2026|Carbohydr.Res.|562||doi:10.1016/j.carres.2026.109831
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5061/dryad.qjq2bvqsk
title: Transcriptomic and metabolomic analysis identifies potential targets of HADHA lactylation in LPS-treated H9c2 cells

description: Serum lactate levels are used to evaluate tissue hypoxia and predict
 outcomes in cases of sepsis and septic shock. Lactate can participate in a
 posttranslational modification known as lactylation, but its role in
 sepsis-induced myocardial depression remains unclear. H9c2 cells were
 transfected with plasmids with flag-tagged trifunctional enzyme subunit
 alpha (HADHA, Flag-HADHA) or HADHA mutated at sites 166 and 728
 (Flag-HADHAK166R/K728R). After LPS treatment, the transcriptomic and
 metabolomic analyses were performed with the transfected H9c2 cells. The
 differentially expressed genes (DEGs) from transcriptomic analysis and
 differential metabolites from metabolomic analysis were obtained. These
 DEGs and differential metabolites may help reveal a role for HADHA in
 sepsis-induced myocardial depression.
description: # Transcriptomic and metabolomic analysis identifies potential targets of
 HADHA lactylation in LPS-treated H9c2 cells Dataset DOI:
 [10.5061/dryad.qjq2bvqsk](10.5061/dryad.qjq2bvqsk) ## Description of the
 data and file structure ### **Data description** The plasmids with
 flag-tagged trifunctional enzyme subunit alpha (HADHA, Flag-HADHA) or
 HADHA mutated at sites 166 and 728 (Flag-HADHAK166R/K728R) were
 constructed and transfected into H9c2 cells. The vector plasmid was a
 control. The H9c2 cells were transfected with indicated plasmids for 48 h
 and then treated with LPS for 24 h. Cells were harvested and total RNA or
 protein were extracted (N = 6 per group, N = 18 in total) according to the
 manufacturer’s protocol and for further transcriptome and metabolome
 analysis. ### **Files and variables** File 1 Differentially Expressed
 Genes File 1 is a excel file contains differentially expressed genes in
 six samples per group in comparing Flag-HADHA +LPS vs. Vector +LPS
 (Sheet1), Flag-HADHAK166R/K728R +LPS vs. Vector +LPS (Sheet2), and
 Flag-HADHAK166R/K728R +LPS vs. Flag-HADHA +LPS (Sheet3), respectively. The
 columns include the UniProt ID, Gene name, foldchange (FC), log2FC, P
 value, and Adjusted P value, respectively. The use of "n/a"
 represents "not applicable" in the gene column when the gene
 does not have an official gene name.   File 2 Differential Metabolites
 File 2 is a excel file contains differential metabolites in six samples
 per group in comparing Flag-HADHA +LPS vs. Vector +LPS (Sheet1),
 Flag-HADHAK166R/K728R +LPS vs. Vector +LPS (Sheet2), and
 Flag-HADHAK166R/K728R +LPS vs. Flag-HADHA +LPS (Sheet3), respectively. The
 columns include the ID, metabolite name, foldchange (FC), log2FC, P value,
 and False Discovery Rate (FDR), respectively. The term "n/a" in
 the ID column represents "not applicable."
DOI: 10.6084/m9.figshare.30150076.v2
title: Supplementary and dataset for:

description: Mesophotic coral ecosystems have gained attention for their potential role as refugia from climate-driven coral bleaching, yet their resilience to prolonged marine heatwaves remains uncertain. Here, we experimentally assessed the thermal tolerance of two Red Sea corals with contrasting depth distributions: the mesophotic specialist <i>Leptoseris glabra</i> and the depth-generalist <i>Acropora squarrosa</i>. Through controlled thermal stress experiments simulating strong to extreme marine heatwave events, we quantified photophysiological, optical, and biochemical responses. Under thermal stress, <i>L. glabra</i> exhibited severe declines in photosynthetic efficiency and energy reserves, coupled by a three-fold increase in tissue reflectance, indicative of extensive symbiont loss. In contrast, mesophotic <i>A. squarrosa</i> maintained stable photophysiology and energy reserves, whereas its shallow conspecific showed marked declines in photosynthetic efficiency, symbiont density, and lipid stores. Skeletal optical analysis revealed that shallow <i>A. squarrosa</i> exhibited higher scattering coefficient and reflectance than its mesophotic counterpart, while <i>L. glabra</i> shared similar optical properties with mesophotic <i>A. squarrosa</i>. These findings suggest that enhanced skeletal light scattering may have exacerbated bleaching in shallow <i>A. squarrosa</i>, whereas reduced light exposure and greater lipid content contributed to mesophotic <i>A. squarrosa’s</i> resilience. Critically, 20-year <i>in situ </i>temperature analysis revealed accelerated warming across intermediate to upper mesophotic depths compared to shallow reefs. This dual threat of species-specific vulnerability combined with accelerated warming at presumed refuge depths, suggests that refugia capacity in mesophotic ecosystems may not be universal across all taxa, but instead depend on species-specific traits.
DOI: 10.15468/dl.qnude5
title: Occurrence Download

description: A dataset containing 4190 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "TaxonKey is Lutzomyia cruciata"
 ]
}

 The dataset includes 4190 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004322-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.xd2547dtv
title: Data from: Multiple genomic ancestries in the broom hare mark the complex biogeographic history of hares in the Iberian Peninsula

description: Pleistocene climatic fluctuations have often driven range shifts and
 hybridization among related species, leaving present-day genomic
 footprints. In the Iberian Peninsula, repeated and transient post-glacial
 contacts among hare species has left extensive mitochondrial DNA traces,
 but the genomic correlates and underlying biogeographic scenarios are
 still incompletely understood. Here, we study genome admixture in the
 broom hare, Lepus castroviejoi, endemic to the Cantabrian region, using
 its non-Iberian sister species, L. corsicanus, for contrast. Coalescent
 analyses of 10 genomes estimate that these species remained isolated since
 their divergence around 50,000 years ago, consistent with their current
 allopatry. Further analyses with 25 additional genomes indicate that small
 fractions of the L. castroviejoi genome originate from L. granatensis, L.
 timidus, and L. europaeus (0.72%, 0.08%, and 0.04%, respectively).
 Introgression dating based on tract lengths suggests L. granatensis was
 already admixed with L. timidus when it hybridized with L. castroviejoi,
 which could explain granatensis-timidus ancestry tract junctions detected
 in L. castroviejoi. Genomic segments with such junctions contain genes
 enriched for cell signaling and olfactory receptor activity, suggesting
 functional drivers facilitating genetic exchange. This research
 demonstrates that genomic ancestry inferences can reveal complex multiway
 admixture histories, which can be used to illuminate complex past
 biogeographic events.
description: # Data from: Multiple genomic ancestries in the broom hare mark the
 complex biogeographic history of hares in the Iberian Peninsula Dataset
 DOI: [10.5061/dryad.xd2547dtv](10.5061/dryad.xd2547dtv) ## Description of
 the data and file structure Fasta file of a hare pseudo-reference genome,
 built based on the whole genome re-sequencing dataset from the original
 paper using an iterative mapping approach (Sarver et al., 2017) and using
 the European rabbit (*Oryctolagus cuniculus*) reference genome as template
 (OryCun2.0). ### Files and variables #### File:
 AncestralHare_3it.v2.gatk.iteration3.consensus.FINAL.fa.gz
 **Description:** Fasta file. ## Access information Data was derived from
 the following source: Next-generation sequencing data from Lepus
 castroviejoi, Lepus corsicanus, Lepus granatensis, Lepus europaeus, Lepus
 timidus, and Lepus americanus. Pseudo-reference built based on the
 European rabbit reference genome (OryCun2.0).
DOI: 10.5061/dryad.gmsbcc30h
title: Spontaneous ectopic head formation enables reversal of the body axis polarity in microscopic flatworms

description: In microscopic flatworms from the genus Stenostomum the new head and tail
 structures are inserted in the pre-existing body plan during the asexual
 process known as paratomy. Here, we report a spontaneously occurring
 developmental error that results in the formation of worms with double
 heads at opposite ends of their bodies, lacking posterior pole identity.
 The first part of the dataset includes confocal images of the normal and
 double head worms. The animals were stained with antibodies and phalloidin
 for morphology, as well as HCR in situ for visualization of the expression
 of head and tail molecular markers. We also demonstrate that the piece of
 the worm with ectopic head can survive, regenerate the tail on its
 previously anterior pole and resume asexual reproduction. The second part
 of the dataset includes microphotographs of two regeneration time series
 of fragments with an ectopic head - one that retained the ectopic head
 after amputation and one that resorbed it. 
description: # Spontaneous ectopic head formation enables reversal of the body axis
 polarity in microscopic flatworms Dataset DOI:
 [10.5061/dryad.gmsbcc30h](10.5061/dryad.gmsbcc30h) ## Description of the
 data and file structure This submission includes unprocessed microscopy
 images related with the manuscript "Spontaneous ectopic head
 formation enables reversal of the body axis polarity in microscopic
 flatworms". **Usage notes** Both .tif and .nd files can be opened,
 viewed, and edited through the open-access software Fiji (available at
 [https://fiji.sc/](https://fiji.sc/)). **Confocal images:** Morphology of
 the asexual *Stenostomum brevipharyngium* * file: LG097_asex_worm05.tif -
 staining (C stands for Channel): * C1: Hoechst * C2: Tyrosinated Tubulin
 (antibody staining) * C3: Phalloidin * C4: 5HT (antibody staining) * C5:
 transmitted light Morphology of the double head *Stenostomum
 brevipharyngium* * file: LG001_W2_Large_1x3.nd2 * stainings (C stands for
 Channel): * C1: Hoechst * C2: Tyrosinated Tubulin (antibody staining) *
 C3: Phalloidin * C4: 5HT (antibody staining) Gene expression in the
 asexual *Stenostomum brevipharyngium* * file: LG002_W2_60x_3D.nd2 *
 stainings (C stands for Channel): * C1: Hoechst * C2: SLC26A2 (HCR in situ
 staining) * C3: MEF2C (HCR in situ staining) Gene expression in the double
 head *Stenostomum brevipharyngium* * file: LG003_W1_60x_3D.nd2 * stainings
 (C stands for Channel): * C1: Hoechst * C2: SLC26A2 (HCR in situ staining)
 * C3: MEF2C (HCR in situ staining) **Light microscopy images:** Head
 retention time series (hpa stands for hours post amputation): * 19 hpa,
 file: retention_P_19hpa_02.tif * 43 hpa, file: retention_P_43hpa_03.tif *
 67 hpa, file: retention_P_67hpa_05.tif * 91 hpa file:
 retention_P_91hpa_05.tif Head regression time series (hpa stands for hours
 post amputation): * 19hpa, file: regression_P_19hpa_04.tif * 43 hpa, file:
 regression_P_43hpa_03.tif * 67 hpa file: regression_P_67hpa_04.tif * 91
 hpa, file: regression_P_91hpa_08.tif
DOI: 10.5061/dryad.k3j9kd5kp
title: Artificial selection on female preferences rapidly alters choosiness and acceptance of divergent male songs in Drosophila

description: Most models of speciation by sexual selection assume that reproductive
 isolation is driven by divergence in female mating preferences. 
 However, we still know little about the evolvability of preference
 functions, whether they exhibit constraint, and how their specific
 properties evolve.  Thus, I imposed artificial selection on
 Drosophila athabasca (WN), utilizing no-choice mating trials on females
 accepting divergent Inter-Pulse-Interval (IPI) male courtship songs, a key
 target of species recognition.  Response to selection resulted in
 increased female acceptance of low and high IPI songs by 30 and 26% in
 only 10 generations, respectively.  Females selected to mate in
 the presence of high IPI songs akin to its sibling D. mahican (EA)
 increased their matings to the same level as with their conspecific IPI
 songs.  In contrast, females selected to accept low IPI songs
 relaxed choosiness; increasing acceptance of both low and high IPI songs
 with no evidence of peak preference shift.  These divergent
 responses to selection suggest that choosiness and peak preference can
 both evolve.  Finally, selection was mostly driven by dominant
 alleles, supporting “Haldane’s sieve” and raising the question of their
 maintenance.  Overall, these results imply that sexual selection
 systems can be easily destabilized in nature.
description: # Artificial selection on female preferences rapidly alters choosiness and
 acceptance of divergent male songs in Drosophila Dataset DOI:
 [10.5061/dryad.k3j9kd5kp](10.5061/dryad.k3j9kd5kp) ## Description of the
 data and file structure This video is a 5 min. example of a 15 min.
 recording session with song playback with wingless males used in both
 selection experiments and in post-selection assays.  In this example, I
 played back the original (11 msec.) IPI courtship song recording.  Note
 several copulations occurring during the recording and their visibility,
 duration and placement in the vials. ## Code/software any video app such
 as media player
DOI: 10.6084/m9.figshare.30150076
title: Supplementary and dataset for: <b>Species-specific vulnerability of northern Red Sea mesophotic corals to accelerated warming</b>

description: Mesophotic coral ecosystems have gained attention for their potential role as refugia from climate-driven coral bleaching, yet their resilience to prolonged marine heatwaves remains uncertain. Here, we experimentally assessed the thermal tolerance of two Red Sea corals with contrasting depth distributions: the mesophotic specialist <i>Leptoseris glabra</i> and the depth-generalist <i>Acropora squarrosa</i>. Through controlled thermal stress experiments simulating strong to extreme marine heatwave events, we quantified photophysiological, optical, and biochemical responses. Under thermal stress, <i>L. glabra</i> exhibited severe declines in photosynthetic efficiency and energy reserves, coupled by a three-fold increase in tissue reflectance, indicative of extensive symbiont loss. In contrast, mesophotic <i>A. squarrosa</i> maintained stable photophysiology and energy reserves, whereas its shallow conspecific showed marked declines in photosynthetic efficiency, symbiont density, and lipid stores. Skeletal optical analysis revealed that shallow <i>A. squarrosa</i> exhibited higher scattering coefficient and reflectance than its mesophotic counterpart, while <i>L. glabra</i> shared similar optical properties with mesophotic <i>A. squarrosa</i>. These findings suggest that enhanced skeletal light scattering may have exacerbated bleaching in shallow <i>A. squarrosa</i>, whereas reduced light exposure and greater lipid content contributed to mesophotic <i>A. squarrosa’s</i> resilience. Critically, 20-year <i>in situ </i>temperature analysis revealed accelerated warming across intermediate to upper mesophotic depths compared to shallow reefs. This dual threat of species-specific vulnerability combined with accelerated warming at presumed refuge depths, suggests that refugia capacity in mesophotic ecosystems may not be universal across all taxa, but instead depend on species-specific traits.
DOI: 10.6084/m9.figshare.30150076.v4
title: Supplementary and dataset for: <b>Species-specific vulnerability of northern Red Sea mesophotic corals to accelerated warming</b>

description: Mesophotic coral ecosystems have gained attention for their potential role as refugia from climate-driven coral bleaching, yet their resilience to prolonged marine heatwaves remains uncertain. Here, we experimentally assessed the thermal tolerance of two Red Sea corals with contrasting depth distributions: the mesophotic specialist <i>Leptoseris glabra</i> and the depth-generalist <i>Acropora squarrosa</i>. Through controlled thermal stress experiments simulating strong to extreme marine heatwave events, we quantified photophysiological, optical, and biochemical responses. Under thermal stress, <i>L. glabra</i> exhibited severe declines in photosynthetic efficiency and energy reserves, coupled by a three-fold increase in tissue reflectance, indicative of extensive symbiont loss. In contrast, mesophotic <i>A. squarrosa</i> maintained stable photophysiology and energy reserves, whereas its shallow conspecific showed marked declines in photosynthetic efficiency, symbiont density, and lipid stores. Skeletal optical analysis revealed that shallow <i>A. squarrosa</i> exhibited higher scattering coefficient and reflectance than its mesophotic counterpart, while <i>L. glabra</i> shared similar optical properties with mesophotic <i>A. squarrosa</i>. These findings suggest that enhanced skeletal light scattering may have exacerbated bleaching in shallow <i>A. squarrosa</i>, whereas reduced light exposure and greater lipid content contributed to mesophotic <i>A. squarrosa’s</i> resilience. Critically, 20-year <i>in situ </i>temperature analysis revealed accelerated warming across intermediate to upper mesophotic depths compared to shallow reefs. This dual threat of species-specific vulnerability combined with accelerated warming at presumed refuge depths, suggests that refugia capacity in mesophotic ecosystems may not be universal across all taxa, but instead depend on species-specific traits.
DOI: 10.6084/m9.figshare.30150076.v3
title: Supplementary and dataset for: <b>Species-specific vulnerability of northern Red Sea mesophotic corals to accelerated warming</b>

description: Mesophotic coral ecosystems have gained attention for their potential role as refugia from climate-driven coral bleaching, yet their resilience to prolonged marine heatwaves remains uncertain. Here, we experimentally assessed the thermal tolerance of two Red Sea corals with contrasting depth distributions: the mesophotic specialist <i>Leptoseris glabra</i> and the depth-generalist <i>Acropora squarrosa</i>. Through controlled thermal stress experiments simulating strong to extreme marine heatwave events, we quantified photophysiological, optical, and biochemical responses. Under thermal stress, <i>L. glabra</i> exhibited severe declines in photosynthetic efficiency and energy reserves, coupled by a three-fold increase in tissue reflectance, indicative of extensive symbiont loss. In contrast, mesophotic <i>A. squarrosa</i> maintained stable photophysiology and energy reserves, whereas its shallow conspecific showed marked declines in photosynthetic efficiency, symbiont density, and lipid stores. Skeletal optical analysis revealed that shallow <i>A. squarrosa</i> exhibited higher scattering coefficient and reflectance than its mesophotic counterpart, while <i>L. glabra</i> shared similar optical properties with mesophotic <i>A. squarrosa</i>. These findings suggest that enhanced skeletal light scattering may have exacerbated bleaching in shallow <i>A. squarrosa</i>, whereas reduced light exposure and greater lipid content contributed to mesophotic <i>A. squarrosa’s</i> resilience. Critically, 20-year <i>in situ </i>temperature analysis revealed accelerated warming across intermediate to upper mesophotic depths compared to shallow reefs. This dual threat of species-specific vulnerability combined with accelerated warming at presumed refuge depths, suggests that refugia capacity in mesophotic ecosystems may not be universal across all taxa, but instead depend on species-specific traits.
DOI: 10.15468/dl.e52kz6
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Neorhadinorhynchus atlanticus",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004326-260126135527185/datasets/export for details.
DOI: 10.15468/dl.cum2jk
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Ramnogaster arcuata",
 "HasCoordinate is true",
 "DecimalLatitude is greater than -90",
 "DecimalLatitude is less than 90",
 "DecimalLongitude is greater than -180",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 2015"
 ]
}

 The dataset includes 3 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004327-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17245769
title: Conjugated metabolome across public metabolomics repositories
DOI: 10.5281/zenodo.17245768
title: Conjugated metabolome across public metabolomics repositories
DOI: 10.5061/dryad.6t1g1jx9p
title: Data from: Evolutionary rescue of niche constructors from habitat exploitation

description: Organisms can improve their fitness by modifying their environments—a
 process known as (positive) niche construction. Since niche construction
 is inherently costly, requiring time and energy to perform, niche
 constructors are vulnerable to displacement by non-niche-constructing
 invaders that exploit the constructed habitats. One way constructors could
 avoid such displacement is by adapting to withstand the invaders and thus
 undergoing evolutionary rescue. Here we first analytically approximate the
 probability that a niche-constructing population—one building reproductive
 habitats—undergoes evolutionary rescue from habitat exploitation by an
 invading species. Then we evaluate the approximation under two different
 fitness costs of construction: a fecundity cost and a mortality cost. We
 find that fecundity costs are not only less harmful than mortality costs
 but can even promote rescue compared to no costs by reducing the rate at
 which constructors attempt reproduction and thus construction. The
 resulting lower habitat density slows invasion, which then buys
 constructors more time to mutate. This invasion-slowing benefit can be
 stronger if the fecundity cost, instead of deriving from construction,
 stems from niche destruction, where organisms destroy their own habitats.
 Our results suggest that the same fitness costs rendering constructors
 vulnerable to habitat exploitation can help rescue constructors from such
 exploitation.
description: # Usage notes This dataset contains four Mathematica notebooks created
 using Mathematica version 13.2.0.0. A summary of each notebook's
 contents is provided below. **Figure_1.nb** contains the code and
 simulation data used to create Figure 1, which shows the stochastic and
 expected dynamics of our evolutionary rescue model. **Figures_2–6.nb**
 contains the code and simulation data used to create Figures 2–6, which
 show how the probability of evolutionary rescue varies as a function of
 each of our model's constituent parameters.
 **Simulation_Code_Figure_1.nb** includes the code used to generate the
 simulation data in Figure 1. **Simulation_Code_Figures_2–6.nb** includes
 the code used to generate the simulation data in Figures 2–6.