cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.kq868g
title: Occurrence Download

description: A dataset containing 161 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is one of (Croatia, North Macedonia, Bulgaria, Romania, Bosnia and Herzegovina, Serbia, Albania, Kosovo)",
 "TaxonKey is Centaurea salonitana"
 ]
}

 The dataset includes 161 records from 34 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003201-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.0k6djhb35
title: Data from: Effects of fixatives and storage duration on avian sperm morphology

description: Sperm cells are variable both within and among species. To be able to
 accurately measure sperm cells and understand their function, it is
 important that sperm cells are preserved in a manner that maintains their
 structural integrity. Formalin is a widely used fixative and storage
 medium for sperm cells, but few studies have examined the effect of
 fixation and long-term storage on their morphological integrity. Ethanol
 is also a common fixation and storage agent for tissue samples, and here
 we examine if fixation and storage in formalin or ethanol alters sperm
 cell size and structural integrity. We found no significant effects of the
 fixation process on fresh sperm cells fixed in formalin or ethanol.
 Further, there were no consistent length changes in sperm cells stored in
 formalin or ethanol over a period of 227 days, or in sperm cells stored in
 formalin for three years. A comparison across 13-14 years of storage time
 showed a small but significant reduction in sperm cell length of 0.93%.
 Furthermore, sperm cells initially fixed in formalin remained quite stable
 in dry storage on glass slides for a minimum of six months (we found a
 mean reduction in sperm cell length of 0.18% after six months). The
 proportion of sperm cells with head damage was, however, much higher for
 samples stored in ethanol than for those stored in formalin. Overall, 70%
 of sperm cells had acrosome damage in ethanol versus only 3% in formalin.
 Finding intact sperm cells for measuring length therefore required greater
 effort in ethanol samples than in formalin samples. Our findings indicate
 that use of sperm cells from long-term storage for the study of sperm
 morphometrics is justified for either fixative, although formalin clearly
 preserves the sperm cells better.
description: Microsoft Excel, can also be opened in Google Sheets.
DOI: 10.5061/dryad.zw3r228bb
title: Combining CRISPR/Cas9 and brain imaging to study the link from genes to molecules to networks

description: Receptors, transporters, and ion channels are important targets for
 therapy development in neurological diseases, but their mechanistic role
 in pathogenesis is often poorly understood. Gene-editing and in vivo
 imaging approaches will help to identify the molecular and functional role
 of these targets and the consequence of their regional dysfunction on the
 whole-brain level. We combine CRISPR/Cas9 gene-editing with in vivo
 positron emission tomography (PET) and functional magnetic resonance
 imaging (fMRI) to investigate the direct link between genes, molecules,
 and the brain connectome. The extensive knowledge of the Slc18a2 gene
 encoding the vesicular monoamine transporter (VMAT2), involved in the
 storage and release of dopamine, makes it an excellent target for studying
 the gene network relationships while structurally preserving neuronal
 integrity and function. We edited the Slc18a2 in the substantia nigra pars
 compacta of adult rats and used in vivo molecular imaging besides
 behavioral, histological, and biochemical assessments to characterize the
 CRISPR/Cas9-mediated VMAT2 knockdown. Simultaneous PET/fMRI was performed
 to investigate molecular and functional brain alterations. We found that
 stage-specific adaptations of brain functional connectivity follow the
 selective impairment of presynaptic dopamine storage and release. Our
 study reveals that recruiting different brain networks is an early
 response to the dopaminergic dysfunction preceding neuronal cell loss. Our
 combinatorial approach is a novel tool to investigate the impact of
 specific genes on brain molecular and functional dynamics, which will help
 to develop tailored therapies for normalizing brain function.
description: The collection of the data set and the processing of the data are
 described in detail in the supplementary information of the
 manuscript.
description: Matlab SPM, QModeling toolbox, Marseille Boîte À Région d'Intérêt (MarsBaR) Toolbox Analysis of Functional NeuroImages (AFNI, National Institute of Mental Health (NIMH), Bethesda, Maryland, USA) PMOD software
DOI: 10.5061/dryad.wm37pvmqt
title: Floral visitation to alien plants is non-linearly related to their phylogenetic and floral similarity to native plants

description: Biological invasions are key to understanding ecological processes that
 determine the formation of novel interactions. Alien species can
 negatively impact floral visitation to native species, but native species
 may also facilitate early establishment of closely related alien species
 by providing a preadapted pollinator community. We tested whether floral
 visitation to alien species depended on phylogenetic relatedness and
 floral similarity to native species. In a field experiment, we simulated
 the early stages of an invasion by adding potted alien plants into
 co-flowering native communities. We paired each alien plant with a host
 native plant, and recorded floral visitation to them for 3,068 hours
 (totalling 84,814 visits). We used 34 alien and 20 native species in 151
 species combinations. We tested whether the number of floral visits to
 alien plants, the proportion of visits to alien plant relative to visits
 to both alien and native plants, and the similarity in flower visitor
 compositions of alien and native plants depended on phylogenetic and
 floral trait distances between alien and native species. Floral visitation
 to alien species was highest when they had intermediate floral trait
 distances to native species, and either low or high phylogenetic
 distances. Alien species received more similar flower-visitor groups to
 natives when they had low phylogenetic and either low or high floral trait
 distances to native species. Co-flowering native species may facilitate
 floral visitation to closely related alien species, and distantly related
 alien plants seem to avoid competition for flower visitors with native
 plants. Alien species with similar floral traits to natives compete with
 them for flower visitors, and alien species with dissimilar floral traits
 may not share flower visitors with native species. Alien species with
 intermediate floral trait distances to natives are most likely to receive
 flower visitors, as they are not too dissimilar and may still share flower
 visitors with native species, but not too similar to compete for flower
 visitors with them. The non-linear patterns between floral visitation and
 similarity of the alien and native species suggest that an interplay of
 facilitation and competition simultaneously drives the formation of novel
 plant-pollinator interactions.
DOI: 10.5061/dryad.q83bk3jm7
title: Data for: Leveraging spatio-temporal genomic breeding value estimates of dry matter yield and herbage quality in ryegrass via random regression models

description: Joint modeling of correlated multi-environment and multi-harvest data of
 perennial crop species may offer advantages in prediction schemes and a
 better understanding of the underlying dynamics in space and time. The
 goal of the present study was to investigate the relevance of
 incorporating the longitudinal dimension of within-season multiple
 measurements of forage perennial ryegrass traits in a reaction norm model
 setup that additionally accounts for genotype-environment interactions
 (G×E). Genetic parameters and accuracy of genomic breeding value (gEBV)
 predictions were investigated by fitting three random regression models
 (gRRM) using Legendre polynomial functions to the data. Genomic DNA
 sequencing of family pools of diploid perennial ryegrass was performed
 using DNA nanoball-based technology and yielded 56,645 single nucleotide
 polymorphisms which were used to calculate the allele frequency-based
 genomic relationship matrix. Biomass yield's estimated additive
 genetic variance and heritability values were higher in later harvests.
 The additive genetic correlations were moderate to low in early
 measurements and peaked at intermediates, with fairly stable values across
 the environmental gradient, except for the initial harvest data
 collection. This led to the conclusion that complex (G×E) arises from
 spatial and temporal dimensions in the early season, with lower re-ranking
 trends thereafter. In general, modeling the temporal dimension with a
 second-order orthogonal polynomial improved the accuracy of gEBV
 prediction for nutritive quality traits, but no gain in prediction
 accuracy was detected for dry matter yield. This study leverages the
 flexibility and usefulness of gRRM models for perennial ryegrass breeding
 and can be readily extended to other multi-harvest crops.
DOI: 10.5061/dryad.95x69p8nv
title: Bacterial community of the Lambro river (Italy)

description: Characterization of the microbial community of a river can provide various
 indications, such as its general state of health or the presence of
 contamination. Furthermore, the study of Bacteroidetes, which have a high
 degree of host specificity, can provide information on the species
 involved in any fecal contamination. We report the characterization of the
 bacterial community of the Lambro river (Italy) through the analysis of
 the 16S rRNA gene from 15 sampling points.
description: <strong>1.</strong> 400 ml water
 samples were taken from 15 different sampling
 points <strong>2a.</strong>
 samples were filtered through a paper filter to eliminate
 soil and/or plant contaminants, and subsequently, the bacteria were
 collected on a 0.22 µm membrane. The bacteria were then resuspended by
 stirring the filters in 3 ml of sterile H2O for 1 hour, and a subsequent
 centrifugation at 12,000 rpm for 30 minutes collected a bacterial pellet.
 Bacterial DNA was extracted using the NucleoSpin Tissue kit (Qiagen)
 following the supplier’s directions. The DNA was resuspended in a final
 volume of 40 µl of sterile H20.
 <strong>2b.</strong> The bacterial DNA from fecal
 samples, samples of human, dog, cat, and pig was obtained using the
 NucleoSpin Soil kit (Macherey-Nagel) starting from 25 mg of
 material. <strong>3. </strong>16S gene was
 amplified using 5 µL of the extracted DNA in a final reaction volume of 25
 µl using Platinum Taq DNA Polymerase High Fidelity (Thermofisher) in
 accordance with the manufacturer’s instructions. The amplifications were
 performed for 26 cycles using 55 °C as the annealing temperature. The
 following primers were used: Pro341F: 5′-CCTACGGGNBGCASCAG-3′ and Pro805R:
 Rev 5′-GACTACNVGGGTATCTAATCC-3′. <strong>4.
 </strong>The overhang adapter was added and followed by library
 construction. The libraries were purified with Beads Amplure XP 0.8X,
 amplified with Indexes Nextera XT Illumina, and then normalized, mixed,
 and loaded on Miseq with 2 × 300 bp (paired-end).
description: Any software that can read fastq files.
DOI: 10.60686/t-fsd4056
title: FSD4056 Public Procurement Notices 2025
DOI: 10.5061/dryad.41ns1rnhp
title: Fire severity as a key determinant of aboveground and belowground biological community recovery in managed even-aged boreal forests

description: Changes in fire regime of boreal forests in response to climate warming
 are expected to impact post-fire recovery. However, quantitative data on
 how managed forests sustain and recover from recent fire disturbance are
 limited.   Two years after a large wildfire in managed even-aged
 boreal forests in Sweden, we investigated how recovery of aboveground and
 belowground communities, i.e., understory vegetation and soil microbial
 and faunal communities, responded to variation in the severity of soil
 (i.e., consumption of soil organic matter) and canopy fires (i.e., tree
 mortality). While fire overall enhanced diversity of understory vegetation
 through colonization of fire adapted plant species, it reduced the
 abundance and diversity of soil biota. We observed contrasting effects of
 tree- and soil-related fire severity on survival and recovery of
 understory vegetation and soil biological communities. Severe
 fires that killed overstory Pinus sylvestris promoted a successional stage
 dominated by the mosses Ceratodon purpureus and Polytrichum juniperum, but
 reduced regeneration of tree seedlings and disfavoured the ericaceous
 dwarf-shrub Vaccinium vitis-idaea and the grass Deschampsia flexuosa.
 Moreover, high tree mortality from fire reduced fungal biomass and changed
 fungal community composition, in particular that of ectomycorrhizal fungi,
 and reduced the fungivorous soil Oribatida. In contrast, soil-related fire
 severity had little impact on vegetation composition, fungal communities
 and soil animals. Bacterial communities responded to both tree- and
 soil-related fire severity. Synthesis: Our results two years post-fire
 suggest that a change in fire regime from a historically low-severity
 ground-fire regime, with fires that mainly burns into the soil organic
 layer, to a stand-replacing fire regime with a high degree of tree
 mortality, as may be expected with climate change, is likely to impact the
 short-term recovery of stand structure and above- and belowground species
 composition of even-aged P. sylvestris boreal forests.
DOI: 10.15468/dl.kgpg3r
title: Occurrence Download

description: A dataset containing 7730 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((105.76143 18.58658,105.56143 18.56658,105.38143 18.50658,105.26143 18.40658,105.21143 18.27658,105.21143 18.13658,105.21143 17.99658,105.26143 17.86658,105.38143 17.76658,105.56143 17.70658,105.76143 17.68658,105.96143 17.70658,106.14143 17.76658,106.26143 17.86658,106.31143 17.99658,106.31143 18.13658,106.31143 18.27658,106.26143 18.40658,106.14143 18.50658,105.96143 18.56658,105.76143 18.58658))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 7730 records from 131 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003202-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.f4qrfj6zs
title: Give and take: Effects of genetic admixture on mutation load in endangered Florida panthers

description: Genetic admixture is a biological event inherent to genetic rescue
 programs aimed at the long-term conservation of endangered
 wildlife.  Although the success of such programs can be measured
 by the increase in genetic diversity and fitness of subsequent admixed
 individuals, predictions supporting admixture costs to fitness due to the
 introduction of novel deleterious alleles are necessary. Here, we analyzed
 nonsynonymous variation from conserved genes to quantify and compare
 levels of mutation load (i.e., proportion of deleterious alleles and
 genotypes carrying these alleles) among endangered Florida panthers and
 non-endangered Texas pumas. Specifically, we used canonical (i.e.,
 non-admixed) Florida panthers, Texas pumas, and F1 (canonical Florida x
 Texas) panthers dating from a genetic rescue program and Everglades
 National Park panthers with Central American ancestry resulting from an
 earlier admixture event. We found neither genetic drift nor selection
 significantly reduced overall proportions of deleterious alleles in the
 severely bottlenecked canonical Florida panthers. Nevertheless, the
 deleterious alleles identified were distributed into a disproportionately
 high number of homozygous genotypes due to close inbreeding in this group.
 Conversely, admixed Florida panthers (either with Texas or Central
 American ancestry) presented reduced levels of homozygous genotypes
 carrying deleterious alleles but increased levels of heterozygous
 genotypes carrying these variants relative to canonical Florida panthers.
 Although admixture is likely to alleviate the load of standing deleterious
 variation present in homozygous genotypes, our results suggest introduced
 novel deleterious alleles (temporarily present in heterozygous state) in
 genetically rescued populations could potentially be expressed in
 subsequent generations if their effective sizes remain small.
DOI: 10.5281/zenodo.18401425
title: Cosmological Application of Geometric Unification: Galactic Rotation Curves and Accelerated Expansion from Torsion-Gauge Field Coupling

description: We present a cosmological application of the geometric unification framework developed in (1),where spacetime torsion is dynamically coupled to Standard Model gauge fields through a funda-mental algebraic constraint. This application provides a unified geometric explanation for three keyastrophysical phenomena: (1) flat galactic rotation curves without additional dark matter particles,(2) the accelerated expansion of the Universe without cosmological constant, and (3) the origin anddiversity of galactic structures including spiral arms and thin disks. The mechanism involves theformation of chiral condensates in curved spacetime with torsion, leading to effective potentials thatmodify gravitational dynamics on galactic scales while naturally generating observed morphologies.All parameters are determined from first principles of the fundamental theory. We derive the modi-fied Friedmann equations from the geometric constraint, solve for galactic rotation profiles, explainspiral structure formation and galactic planarity, and demonstrate consistency with observationaldata from SPARC galaxies and Planck satellite. The model predicts testable signatures in CMBpolarization, gravitational lensing statistics, and detailed galactic structure properties, providingcomprehensive observational tests of the geometric unification framework.The model shows promising agreement with cosmological observations while making distinctive predictions for large-scale structure. Although a complete perturbation theory requires further development, parameterized predictions naturally address key tensions: suppressed growth resolves the S8 discrepancy, scale-independent weak lensing enhancement aligns with KiDS-1000, and modified background expansion fits Planck distance priors. The framework provides specific, falsifiable predictions for upcoming surveys including Euclid, DESI, and CMB-S4.
DOI: 10.15468/dl.seaw8t
title: Occurrence Download

description: A dataset containing 4985 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((94.54239 51.42724,97.33633 51.42724,97.33633 52.54338,94.54239 52.54338,94.54239 51.42724))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "PublishingCountry is Russian Federation"
 ]
}

 The dataset includes 4985 records from 41 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003203-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.wpzgmsbqn
title: Marine demosponge rheology / dissection microscopy

description: Sponges are animals that inhabit many aquatic environments while filtering
 small particles and ejecting metabolic wastes. They are composed of cells
 in a bulk extracellular matrix, often with an embedded scaffolding of
 stiff, siliceous spicules. We hypothesize that the mechanical response of
 this heterogeneous tissue to hydrodynamic flow influences cell
 proliferation in a manner that generates the body of a sponge. Toward a
 more complete picture of the emergence of sponge morphology, we dissected
 a set of species and subjected disks of living tissue to physiological
 shear and uniaxial deformations on a rheometer. Various species exhibited
 rheological properties such as anisotropic elasticity, shear softening and
 compression stiffening, negative normal stress, and non-monotonic
 dissipation as a function of both shear strain and frequency. Erect
 sponges possessed aligned, spicule-reinforced fibers which endowed three
 times greater stiffness axially compared with orthogonally. By contrast,
 tissue taken from shorter sponges was more isotropic but time-dependent,
 suggesting higher flow sensitivity in these compared with erect forms. We
 explore ecological and physiological implications of our results and
 speculate about flow-induced mechanical signaling in sponge cells.
description: This dataset was collected on Anton Paar MCR 502 WESP and Malvern
 Kinexus lab+ rheometers as well as optical, dissection, and USB
 microscopes. Images and raw data tables are included. See the paper for
 more details.
description: Microsoft Excel<br>Open-source alternative: Google
 Sheets
DOI: 10.5281/zenodo.18246901
title: The Climate Opportunities of Risks of Contrail Avoidance - Output Climate Data Cases 01-09

description: This repository contains climate data that is outputted to the Aviation Climate and Air Quality Impacts model to generate the climate outputs for the journal publication titled The Climate Opportunities and Risks of Contrail Avoidance. The output files in this repository are files 01 to 09 of 36, denoted by the two-digit number at the start of the file.

The climate data that has been deposited relates to the effective radiative forcing and global surface temperature rise due to carbon dioxide emissions from aviation and contrails, produced using Monte Carlo simulations of uncertain parameters, under various contrail avoidance and modified fuel composition scenarios. The data is separated and labelled with respect to these scenarios. Levels of contrail avoidance effectiveness of 0%, 25%, 50% and 75% are labelled as “no_action”, “eff=25%”, “eff=50%”, “eff=75%” respectively. The scenario with a of contrail avoidance effectiveness of 100% is unlabelled. The aviation growth projections (AGPs) of AGP 0.36, AGP 0.29, AGP 0.21 and AGP 0.14 are labelled as “exp_no_sat”, “exp_sat”, “lin” and “no_growth”, respectively. Scenarios that assume a modified fuel composition have the label “SAF”. Fuel burn penalties of 0.35%, 5% and 10% have the labels “0035”, “0500” and “1000”, respectively. Please see The Climate Opportunities and Risks of Contrail Avoidance for more information.