cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.x3ffbg7ms
title: Artificial displacement alters movement behavior of a terrestrial amphibian

description: Homing abilities have been widely documented in amphibians, but it remains
 unclear whether individuals have homing tendencies in the absence of
 motivational cues related to breeding and site fidelity. We tested whether
 artificial displacement would affect the movement behavior of a
 nonphilopatric terrestrial amphibian, the Fowler’s Toad (Anaxyrus
 fowleri), within its home range and after its breeding season had ended.
 We translocated 65 male and female Fowler’s Toads from their initial
 points of capture a total of 104 times over one of three different
 distances (100 m, 250 m, and 500 m) and compared these toads’ subsequent
 24-h movements with those of a control group of 43 untranslocated toads.
 To shield the translocated toads from auditory, visual, and olfactory cues
 en route, we translocated them in opaque enclosed boxes and performed the
 experiment in the uniformly unobstructed landscape of the Lake Erie
 shoreline of Long Point, ON, Canada. We mainly investigated directionality
 bias as the orientation between control and translocated groups, homing
 tendency as the correlation between movements after translocation and
 translocation distance, and homing accuracy as the variation in distance
 between final and initial capture points. Our results provide clear
 evidence that translocation changes the movement behavior of these toads
 and that they possess homing tendencies outside of their breeding season.
 Toads had a strong directional bias to move in the opposite direction to
 the one in which they were artificially displaced, in contrast with the
 control group, which showed no directional bias among 61 recorded 24-h
 movements. This tendency for amphibians to home after artificial
 displacement might be a significant confounding factor in any procedure
 involving their relocation.
description: The dataset was collected through a capture-mark-recapture method
 extensively used on this population in previous studies. Individuals were
 translocated (n = 104) to three distances (100 m, 250 m, 500 m) as an
 extension of the survey method. Homing tendency was assessed as the
 distance between the release site post-translocation to the final capture
 site, 24 hours later, in comparison to the distance translocated from the
 initial capture point.
DOI: 10.5061/dryad.djh9w0w2h
title: Individual or group signatures in spotted hyena whoops

description: In animal societies, identity signals mediate interactions within groups,
 and allow individuals to discriminate group-mates from out-group
 competitors. However, individual recognition becomes increasingly
 challenging as group size increases and as signals must be transmitted
 over greater distances. Group vocal signatures appear to evolve when
 successful in-group/out-group distinctions are at the crux of
 fitness-relevant decisions, but individual-based recognition systems may
 be favored when differentiated within-group relationships are important
 for decision-making. Spotted hyenas are social carnivores that live in
 stable clans of &lt;125 individuals composed of multiple unrelated
 matrilines. Clan members cooperate to defend resources and communal
 territories from neighboring clans and other mega carnivores; this
 collective defense is mediated by long-range (up to 5 km range)
 recruitment vocalizations, called whoops. Here, we use machine learning to
 determine that spotted hyena whoops contain individual but not group
 signatures, and that fundamental frequency features that propagate well
 are critical for individual discrimination. For effective clan-level
 cooperation, hyenas face the cognitive challenge of remembering and
 recognizing individual voices at long range. We show that serial
 redundancy in whoop bouts increases individual classification accuracy and
 thus extended call bouts used by hyenas likely evolved to overcome the
 challenges of communicating individual identity at long distance.
DOI: 10.5281/zenodo.18353540
title: Data supporting article A Hybrid Finite-Volume Reconstruction Framework for Efficient High-Order Shock-Capturing on Unstructured Meshes

description: Data supporting article "A Hybrid Finite-Volume Reconstruction Framework for Efficient High-Order Shock-Capturing on Unstructured Meshes".

The compressed file contains the folders with all the data generated from the simulations that are included in this article. 

https://doi.org/10.1016/j.compfluid.2026.106988
DOI: 10.5281/zenodo.18353541
title: Data supporting article A Hybrid Finite-Volume Reconstruction Framework for Efficient High-Order Shock-Capturing on Unstructured Meshes

description: Data supporting article "A Hybrid Finite-Volume Reconstruction Framework for Efficient High-Order Shock-Capturing on Unstructured Meshes".

The compressed file contains the folders with all the data generated from the simulations that are included in this article. 

https://doi.org/10.1016/j.compfluid.2026.106988
DOI: 10.5061/dryad.0k6djhb29
title: Decomposing cover crops modify root-associated microbiome composition and disease tolerance of cash crop seedlings

description: The assembly of root-associated microbes during the seedling stage has
 strong impact on subsequent performance of crops. Major factors
 influencing this assembly are crop species identity and composition of
 potential root-colonizing microbes in the bulk soil. The latter can be
 modified by soil management, such as organic amendments. The incorporation
 of residues of cover crops before the start of the growing season of cash
 crops presents an interesting option for steering of root-associated
 seedling microbiomes as there is a wide range of cover crops species with
 different properties available for farmers. In a greenhouse study, we
 examined the effect of soil amendments with milled shoot and root
 materials of seven cover crop species (niger seed, phacelia, rapeseed,
 radish, vetch, black oat and buckwheat) on the soil nitrogen and biomass
 of seedlings of four cash crop species (asparagus, carrot, onion and sugar
 beet) and their root-associated bacteria and fungi. Field-grown cover
 crops material used for the study was collected at two time points (before
 and after winter) which had strong impact on plant elemental composition.
 Since the soil used for the study was a mixture of sandy arable soils with
 a history of soil-borne fungal diseases (Fusarium and Rhizoctonia), we
 also examined whether decomposing cover crop residues had an influence on
 the severity of damping-off diseases. Within the context of a strong
 selection of root-associated microbes by cash crop species, we found
 significant modifying effects by cover crop materials. High-quality
 residues (with low C/N ratio) caused profound shifts within
 root-associated Proteobacteria and increases in relative abundance of
 certain microbial groups such as Bacillaceae and Mortierellomycetes. These
 changes coincided with differences in establishment and survival of cash
 crop seedlings. This indicates that fine-tuning of cover crops amendments
 for different cash crops is required to realize enhanced functioning of
 root microbiomes.
description: Sequencing data - ENA accession number PRJEB37146
DOI: 10.5061/dryad.bvq83bkbk
title: A novel trophic cascade between cougars and feral donkeys shapes desert wetlands

description: Introduced large herbivores have partly filled ecological gaps formed in
 the late Pleistocene, when many of the Earth’s megafauna were driven
 extinct. However, extant predators are generally considered incapable of
 exerting top-down influences on introduced megafauna, leading to unusually
 strong disturbance and herbivory relative to native herbivores. We report
 on the first documented predation of juvenile feral donkeys (Equus
 africanus asinus) by cougars (Puma concolor) in the Mojave and Sonoran
 Deserts of North America. We then investigated how cougar predation
 corresponds with differences in feral donkey behavior and associated
 effects on desert wetlands. Focusing on a feral donkey population in Death
 Valley National Park, we compared donkey activity patterns and impacts
 between wetlands with and without cougar predation. Donkeys were primarily
 diurnal at wetlands with cougar predation, thereby avoiding cougars.
 However, donkeys were active throughout the day and night at sites without
 predation. Donkeys were ~87% less active (measured as hours of activity a
 day) at wetlands with predation (p&lt;0.0001).  Sites with
 predation had reduced donkey disturbance and herbivory, including ~46%
 fewer access trails, 43% less trampled bare ground, and 192% more canopy
 cover (PERMANOVA, R2 = 0.22, p=0.0003). Our study is the first to reveal a
 trophic cascade involving cougars, feral equids, and vegetation. Cougar
 predation appears to rewire an ancient food web, with diverse implications
 for modern ecosystems. Our results suggest that protecting apex predators
 could have important implications for the ecological effects of introduced
 megafauna.
description: These data include camera trap detection and effort files,
 wetland vegetation data, and R scripts to analyze them. Camera trap data
 consists of raw detections, identified to species, with an ‘eventID’
 indicating whether detections of a species at a site were within 30
 minutes of each other. The effort file indicates whether a camera trap was
 operating on a given day and includes daily covariates (maximum daily
 temperature). 
description: All scripts required to run analyses are included in repository.
 All scripts were written in R.
DOI: 10.5061/dryad.dncjsxm24
title: Data from: Large herbivores trigger spatiotemporal changes in forest plant diversity

description: Large herbivores can exert top-down control on terrestrial plant
 communities, but the magnitude, direction, and scale-dependency of their
 impacts remain equivocal, especially in temperate and boreal forests,
 where multiple disturbances often interact. Using a unique, long-term and
 replicated landscape experiment, we assessed the influence of a high
 density of white-tailed deer (Odocoileus virginianus) on the
 spatiotemporal dynamics of diversity, composition, and successional
 trajectories of understorey plant assemblages in recently logged boreal
 forests. This experiment provided a rare opportunity to test whether deer
 herbivory represents a direct filter on plant communities or if it mainly
 acts to suppress dominant plants which, in turn, release other plant
 species from strong negative plant-plant interactions. These two
 hypotheses make different predictions about changes in community
 composition, alpha and beta diversity in different vegetation
 layers and at different spatial scales. Our results showed that deer had
 strong effects on plant community composition and successional
 trajectories, but the resulting impacts on plant alpha and beta diversity
 patterns were markedly scale-dependent in both time and space. Responses
 of tree and non-tree vegetation layers were strongly asymmetric. Deer
 acted both as a direct filter and as a suppressor of dominant plant
 species during early forest succession, but the magnitude of both
 processes was specific to tree and non-tree vegetation layers. Although
 our data supported the ungulate-driven homogenization hypothesis,
 compositional shifts and changes of alpha diversity were poor predictors
 of beta diversity loss. Our findings underscore the importance of
 long-term studies in revealing non-linear temporal community trends, and
 they challenge managers to prioritize particular community properties and
 scales of interest, given contrasting trends of composition, alpha, and
 beta diversity across spatial scales.
DOI: 10.15468/dl.svmmpn
title: Occurrence Download

description: A dataset containing 133 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Dolichopsis monticola",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 133 records from 28 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003086-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.qjq2bvqj4
title: Data from: Legacy and emerging per- and polyfluoroalkyl substances suppress the neutrophil respiratory burst

description: Per- and polyfluoroalkyl substances (PFASs) are used in a multitude of
 processes and products, including nonstick coatings, food wrappers, and
 fire-fighting foams. These chemicals are environmentally persistent,
 ubiquitous, and can be detected in the serum of 98% of Americans. Despite
 evidence that PFASs alter adaptive immunity, few studies have investigated
 their effects on innate immunity. We investigated the impact of nine
 environmentally relevant PFASs [perfluorooctanoic acid (PFOA),
 perfluorooctane sulfonic acid potassium salt (PFOS-K), perfluorononanoic
 acid (PFNA), perfluorohexanoic acid (PFHxA), perfluorohexane sulfonic acid
 (PFHxS), perfluorobutane sulfonic acid (PFBS), ammonium
 perfluoro(2-methyl-3-oxahexanoate) (GenX),
 7H-perfluoro-4-methyl-3,6-dioxaoctane sulfonic acid (Nafion byproduct 2),
 and perfluoromethoxyacetic acid sodium salt (PFMOAA-Na)] on one component
 of the innate immune response, the neutrophil respiratory burst. The
 respiratory burst is a key innate immune process by which microbicidal
 reactive oxygen species (ROS) are rapidly induced by neutrophils in
 response to pathogens, and defects in the respiratory burst can increase
 susceptibility to infection. We utilized larval zebrafish, a human
 neutrophil-like cell line, and primary human neutrophils to ascertain
 whether PFAS exposure inhibits ROS production in the respiratory burst. We
 observed that exposure to PFHxA and GenX suppresses the respiratory burst
 in zebrafish larvae and a human neutrophil-like cell line. GenX also
 suppresses the respiratory burst in primary human neutrophils. This report
 is the first to demonstrate that these PFASs suppress neutrophil function
 and supports the utility of employing zebrafish larvae and a human cell
 line as screening tools to identify chemicals that may suppress human
 immune function. 
description: Datasets are raw results collected from biological experiments.
 Detailed methods are provided in the research article "Legacy and
 emerging per- and polyfluoroalkyl substances suppress the neutrophil
 respiratory burst" (https://doi.org/10.1080/1547691X.2023.2176953). A summary of methods is provided in the README file.
description: To view these data, Microsoft Excel is highly recommended to
 ensure proper formatting of the .xlsx files.
DOI: 10.5061/dryad.crjdfn368
title: Forest disturbances and climate constrain carbon allocation dynamics in trees

description: Forest disturbances such as drought, fire and logging affect the forest
 carbon dynamics and the terrestrial carbon sink. Forest mortality after
 disturbances creates uncertainties that need to be accounted for to
 understand forest dynamics and their associated C-sink. We combined data
 from permanent resampling plots and biomass oriented dendroecological
 plots to estimate time series of annual woody biomass growth (ABI) in
 several forests. ABI time series were used to benchmark a vegetation model
 to analyze dynamics in forest productivity and carbon allocation forced by
 environmental variability. The model implements source and sink
 limitations explicitly by dynamically constraining carbon allocation of
 assimilated photosynthates as a function of temperature and moisture. Bias
 in tree-ring reconstructed ABI increased back in time from data collection
 and with increasing disturbance intensity. ABI bias ranged from zero, in
 open stands without recorded mortality, to over 100% in stands with major
 disturbances such as thinning or snowstorms. Stand leaf area was still
 lower than in control plots decades after heavy thinning. Disturbances,
 species life-history strategy and climatic variability affected carbon
 partioning patterns in trees. Resprouting broadleaves reached maximum
 biomass growth at earlier ages than nonresprouting conifers. Environmental
 variability and leaf area explained much variability in woody biomass
 allocation. Effects of stand competition on C-allocation were mediated by
 changes in stand leaf area except after major disturbances. Divergence
 between tree-ring estimated and simulated ABI were caused by unaccounted
 changes in allocation or misrepresentation of some functional process
 independently of the model calibration approach. Higher disturbance
 intensity produced greater modifications of the C-allocation pattern,
 increasing error in reconstructed biomass dynamics. Legacy effects from
 disturbances decreased model performance and reduce the potential use of
 ABI as a proxy to net primary productivity. Trait-based dynamics of
 C-allocation in response to environmental variability need to be refined
 in vegetation models.
DOI: 10.5061/dryad.fj6q573x5
title: Alignments of chloroplast noncoding regions for context-dependency analysis

description: Substitutions between closely related noncoding chloroplast DNA sequences
 are studied with respect to the composition of the three bases on each
 side of the substitution, that is the hexanucleotide context. There is
 about 100-fold variation in rate, amongst the contexts, particularly on
 substitutions of A and T. Rate heterogeneity of transitions differs from
 that of transversions, resulting in a more than 200-fold variation in the
 transitions:transversion bias. The data are consistent with a CpG effect,
 and it is shown that both the A+T content and the arrangement of
 purines/pyrimidines along the same DNA strand are correlated with rate
 variation. Expected equilibrium A+T content ranges from 36.4% to 82.8%
 across contexts, while G-C skew ranges from -77.4 to 72.2 and A-T skew
 from -63.9 to 68.2. The predicted equilibria are associated with specific
 features of the content of the hexanucleotide context, and also show close
 agreement with the observed context-dependent compositions. Finally, by
 controlling for the content of nucleotides closer to the substitution site
 it is shown that both the third and fourth nucleotide removed on each side
 of the substitution directly influence substitution dynamics at that site.
 Overall, the results demonstrate that noncoding sites in different
 contexts are evolving along very different evolutionary trajectories and
 that substitution dynamics are far more complex than typically assumed.
 This has important implications for a number of types of sequence
 analysis, particularly analyses of natural selection, and the
 context-dependent substitution matrices developed here can be applied in
 future analyses.
DOI: 10.5061/dryad.ncjsxksx0
title: Raw data from microCT tomography of Ausichicrinites zelenskyyi

description: Fossil comatulids, referred to as feather stars, are mostly known from
 highly disarticulated specimens. A single isolated element (centrodorsal)
 has been the basis for taxonomic description of a vast majority of fossil
 comatulids. Here, we report a nearly complete, and thus extremely rare,
 comatulid from the Upper Jurassic (Tithonian) of the Blue Nile Basin in
 central western Ethiopia that provides a unique insight into the
 morphology of comatulid arms and cirri. It is assigned to Ausichicrinites
 messingi gen. et sp. nov. and is the first Jurassic comatulid from the
 African continent. The new taxon shows close resemblance with the modern
 family Zygometridae, exclusively known from the Holocene of the western
 Pacific and eastern Indian Oceans.
description: The slab with the comatulid
 crinoid was transported from Ethiopia to the Palaeontological Laboratory
 of the Faculty of Natural Sciences of the University of Silesia in
 Katowice, Poland, in September 2021. It was cleaned there and photographed
 using a Canon Eos 350D
 digital camera. This specimen was also scanned with the X-ray
 computed tomography (CT-scanning) using a GE PHOENIX v|tome|s at the
 Institute of Biomedical Engineering, Faculty of Science and Technology,
 University of Silesia in Katowice, Poland (see Supplementary movies 1, 2).
 It was investigated using different settings (voltage: 140 kV, amperage:
 90 A, exposure time: 333 ms, projections: 2000, voxel resolution: 5 µm).
 Raw 2D X-ray data were then processed using phoenix datos|x. The movies
 were prepared using the following application VGStudio Max 2.0. The next
 step was to
 professionally prepare the
 specimen using a chemical method (it was treated with potassium hydroxide
 - caustic potassium, KOH) by Frank Siegel, Berlin, Germany,
 from HAUFWERK.COM (https://www.haufwerk.com/). Finally, the specimen was photographed using a Canon Eos 350D digital camera (Fig. 4A-C).
DOI: 10.5061/dryad.9kd51c5kg
title: Single-molecule tracking of Nodal and Lefty in live zebrafish embryos supports hindered diffusion model

description: The hindered diffusion model postulates that the movement of a signaling
 molecule through an embryo is affected by tissue geometry and
 binding-mediated hindrance, but these effects have not been directly
 demonstrated in vivo. Here, we visualize extracellular movement and
 binding of individual molecules of the activator-inhibitor signaling pair
 Nodal and Lefty in live developing zebrafish embryos using reflected
 light-sheet microscopy. We observe that diffusion coefficients of
 molecules are high in extracellular cavities, whereas mobility is reduced
 and bound fractions are high within cell-cell interfaces.
 Counterintuitively, molecules nevertheless accumulate in cavities, which
 we attribute to the geometry of the extracellular space by agent-based
 simulations. We further find that Nodal has a larger bound fraction than
 Lefty and shows a binding time of tens of seconds. Together, our
 measurements and simulations provide direct support for the hindered
 diffusion model and yield insights into the nanometer-to-micrometer-scale
 mechanisms that lead to macroscopic signal dispersal.
DOI: 10.6078/d1mx4p
title: Dissociable use-dependent processes for volitional goal-directed reaching

description: Repetition of a specific movement biases subsequent actions towards the
 practiced movement, a phenomenon known as use-dependent learning (UDL).
 Recent experiments that impose strict constraints on planning time have
 revealed two sources of use-dependent biases, one arising from dynamic
 changes occurring during motor planning and another reflecting a stable
 shift in motor execution. Here, we used a distributional analysis to
 examine the contribution of these biases in reaching. To create the
 conditions for UDL, the target appeared at a designated “frequent”
 location on most trials, and at one of six “rare” locations on other
 trials. Strikingly, the heading angles were bimodally distributed, with
 peaks at both frequent and rare target locations. Despite having no
 constraints on planning time, participants exhibited a robust bias towards
 the frequent target when movements were self-initiated quickly, the
 signature of a planning bias; notably, the peak near the rare target was
 shifted in the frequently practiced direction, the signature of an
 execution bias. Furthermore, these execution biases were not only
 replicated in a delayed response task but were also insensitive to reward.
 Taken together, these results extend our understanding of how volitional
 movements are influenced by recent experience.