cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.547d7wmc5
title: Data from: Single cell transcriptomics shows dose-dependent disruption of hepatic zonation by TCDD in mice

description: 2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) dose-dependently induces the
 development of hepatic fat accumulation and inflammation with fibrosis in
 mice initially in the portal region. Conversely, differential gene and
 protein expression is first detected in the central region. To further
 investigate cell-specific and spatially resolved dose-dependent changes in
 gene expression elicited by TCDD, single-nuclei RNA sequencing and spatial
 transcriptomics were used for livers of male mice gavaged with TCDD every
 4 days for 28 days. The proportion of 11 cell (sub)types across 131,613
 nuclei dose-dependently changed with 68% of all portal and central
 hepatocyte nuclei in control mice being overtaken by macrophages following
 TCDD treatment. We identified 368 (portal fibroblasts) to 1,339
 (macrophages) differentially expressed genes. Spatial analyses revealed
 initial loss of portal identity that eventually spanned the entire liver
 lobule with increasing dose. Induction of R-spondin 3 (Rspo3) and
 pericentral Apc, suggested dysregulation of the Wnt/β-catenin signaling
 cascade in zonally resolved steatosis. Collectively, the integrated
 results suggest disruption of zonation contributes to the pattern of
 TCDD-elicited NAFLD pathologies.
description: <strong>Table S1. </strong>Molecular Cartography
 probe catalog numbers and target sequences.
 <strong>Table S2. </strong>Number of nuclei sequenced
 passing QC for each animal. <strong>Table
 S3.</strong> Number of nuclei sequenced passing QC for each animal
 and cell type. <strong>Table S4.</strong>
 Celltype marker genes of hepatic cell types.
 <strong>Table S5. </strong>Correlation of pseudobulk
 snRNAseq data and experimental bulk RNAseq data from the same liver
 samples. <strong>Table S6.
 </strong>Differential expression analysis of hepatic cell types
 using the scBT method. <strong>Table S7.
 </strong>Functional Enrichment analysis of cell-specific
 differentially expressed genes.
DOI: 10.17026/ar/62phwl
title: Gorssel-Zutphenseweg, gemeente Lochem. Inverntariserend veldonderzoek in de vorm van proefsleuven Gorssel-Zutphenseweg, gemeente Lochem

description: &lt;p&gt;ADC ArcheoProjecten heeft op 26 en 27 februari 2025 een Inventariserend Veldonderzoek (IVO) in de vorm van proefsleuven uitgevoerd op de locatie Zutphenseweg te Gorssel, gemeente Lochem. De aanleiding voor het onderzoek is de voorgenomen realisatie van flexwoningen aan de Zutphenseweg te Gorssel. Tijdens het IVO-P zijn acht proefsleuven aangelegd. De ligging van deze proefsleuven is conform het PvE (west-oost oriëntatie).&lt;br&gt;De hoge verwachting die op grond van het vooronderzoek zijn gesteld, kunnen op basis van het huidige onderzoek worden aangepast naar een lage verwachting. De hoge verwachting van het vooronderzoek was gebaseerd op de aanwezigheid van een intact plaggendek en inspoelingshorizont. Er bleek echter geen sprake te zijn van een intact plaggendek. Op sommige plekken was hoogstens nog een restant van een B-horizont aanwezig. Het proefsleuvenonderzoek heeft geen relevante sporen opgeleverd. Het onderzoeksgebied betreft een lager gelegen deel in het landschap en zal daarom in het verleden geen geschikte locatie voor bewoning geweest zijn.&lt;br&gt;Aangezien er geen relevante sporen zijn aangetroffen kan geconcludeerd worden dat er geen sprake is van een archeologische vindplaats. Daarom kan een waardering achterwege blijven en wordt geadviseerd om geen archeologisch vervolgonderzoek uit te voeren en het plangebied vrij te geven voor ontwikkeling.&lt;/p&gt;
DOI: 10.5061/dryad.pnvx0k6rc
title: Telomere length and rate of change, as they relate to body size and longevity

description: Telomeres, the terminal repetitive DNA sequences at the ends of linear
 chromosomes, have strong associations with longevity in some major taxa.
 Longevity has been linked to rate of decline in telomere length in birds
 and mammals, and absolute telomere length seems to be associated with body
 mass in mammals. Using a phylogenetic comparative method and 30 species of
 birds, we examined longevity (reflected by maximum lifespan), absolute
 telomere length, the rate of change in telomere length (TROC), and body
 mass (often strongly associated with longevity) to ascertain their degree
 of association. We divided lifespan into two life-history components, one
 reflected by body size (measured as body mass), and a component that was
 statistically independent of body mass. While both lifespan and body mass
 were strongly associated with a family tree of the species (viz., the
 phylogeny of the species), telomere measures were not. Telomere length was
 not significantly associated with longevity or body mass, or our measure
 of mass-independent lifespan. TROC, however, was strongly associated with
 mass-independent lifespan, but only to a much lesser degree at best with
 body mass-predicted lifespan. Our results supported an association of TROC
 and longevity, in particular longevity that was independent of body size
 and part of the pace-of-life syndrome of life histories.
description: Meta-analysis search of the literature
DOI: 10.15468/dl.e73244
title: Occurrence Download

description: A dataset containing 37 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Specimen)",
 "Geometry POLYGON((105 20,170 20,170 70,105 70,105 20))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Saxifraga merkii"
 ]
}

 The dataset includes 37 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003283-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.905qfttpg
title: Data from: Plant species richness and sunlight exposure increase pollinator attraction to pollinator gardens

description: Evidence documenting the decline of insect populations is accumulating.
 Efforts have increased to mitigate pollinator losses by establishing
 gardens to support pollinator diversity. However, knowledge of the
 specific garden characteristics, landscape features and environmental
 factors that affect pollinator diversity and abundance is limited,
 particularly in biodiverse regions in North America. In order to better
 understand how garden characteristics affect pollinator attraction, we
 compared pollinator composition across 16 pollinator gardens in the
 Appalachian ecoregion in North America. We evaluated the effects of garden
 characteristics (e.g., plant richness, flower abundance, garden size,
 proportion of native species), landscape features (land-use type, distance
 to forest) and environmental factors (sunlight exposure) on pollinator
 richness, overall visitation rate and visitation rate by defined
 pollinator groups (i.e., solitary native bees, bumblebees, honeybees,
 lepidopterans and other insects). Solitary bees (i.e., native bees besides
 Bombus) were the most frequent visitors (61%). We found differences in
 pollinator species composition between urban and rural gardens. Moreover,
 plant richness had a positive effect on pollinator richness and an
 increase in flower abundance increased pollinator visitation rate. Flower
 abundance, plant richness and high sunlight exposure increased visitation
 rate of solitary bees. Visitation rate of solitary bees however, decreased
 with increasing proportion of native plants. Overall, our results indicate
 that garden characteristics, landscape and environmental factors all are
 important mediators of pollinator diversity and abundance. Solitary bees
 were most affected by garden (i.e., plant richness, number of flowers,
 proportion of native plants) and environmental factors (i.e., sunlight
 exposure). However, we also identified differential effects of garden and
 environmental factors across pollinator groups. We suggest that an
 integrated management approach that considers multiple garden and
 environmental characteristics could help improve the effectiveness of
 pollinator garden as a conservation tool and help preserve this key
 ecosystem service.
DOI: 10.5061/dryad.dfn2z355b
title: The AWRI wine microorganism yeast and bacterial screening collection

description: The AWRI Wine Microbial Culture Collection (AWMCC) contains an extensive
 collection of yeast and bacteria largely associated with winemaking. The
 AWMCC has been created from research collections, yeast deletion
 libraries, and commercial or environmental isolates. Between 2017 and
 today, the AWMCC has nearly doubled in size. Microbial strains within the
 collection are available to winemakers and researchers, enabling product
 experimentation and differentiation. New custom collections have been
 developed to facilitate high throughput screening of specific microbial
 genera. The strains available in these high-throughput collections are
 listed in this data repository.
DOI: 10.5061/dryad.3j9kd51nc
title: Molecular exploration of fossil eggshell uncovers hidden lineage of giant extinct bird

description: Madagascar’s extinct elephant birds are the least studied of the ratites,
 yet in recent years have proven to be critical for understanding the
 evolution of all birds. With large spatio-temporal gaps in the fossil
 record and poor biomolecular preservation of skeletal specimens, the
 systematics of these flightless giants remains controversial. Here, we
 overcome these limitations using a comprehensive molecular analysis of
 1000-year-old fossil eggshells to provide the first description of
 elephant bird phylogeography and reveal new insights into the ecology of
 the world’s largest birds. High-throughput sequencing of 21 mitochondrial
 genomes from across Madagascar reveals genetic variation that is
 correlated with eggshell morphology, stable isotope composition, and
 geographic distribution. The elephant bird crown is dated to ca. 30 Mya
 during the Eocene-Oligocene, a period of marked global cooling when
 Madagascar’s local palaeoclimate is estimated to have become less arid as
 the island moved northward. High levels of between-clade genetic variation
 argue for the reclassification of Mullerornis into a new family.
 Low levels of within-clade genetic variation are unexpected and suggest
 that there were only two elephant bird genera, with one species per genus
 existing in southern Madagascar during the Holocene. However, we reveal a
 newly discovered eggshell collection from Madagascar’s far north that is
 phylogenetically, morphologically, and ecologically distinct, representing
 a unique lineage of Aepyornis. Furthermore, molecular dating
 estimates that divergence within Aepyornis coincides
 with the aridification of Madagascar during the early Pleistocene ca. 1.5
 Ma, and is consistent with the fragmentation of populations in the
 highlands driving diversification, as well as the evolution of extreme
 gigantism over short timescales. Molecular analysis thus provides the
 first insight into elephant bird speciation, and we advocate for a
 revision of their taxonomy that integrates palaeogenomic and
 palaeoecological perspectives.
DOI: 10.5061/dryad.3bk3j9kns
title: Covariations and tradeoffs of phosphorus (P) acquisition strategies in dioecious Populus euphratica as affected by soil water availability

description: 1. Dioecious species may be particularly vulnerable to climate change
 because they often exhibit skewed sex ratios that are reinforced by the
 physiological and biological specialization of each sex to specific
 microhabitats. Yet, it is unclear how differences in functional traits
 between female and male plants lead to sex-specific responses to drought
 and whether these responses are associated with phosphorus (P) acquisition
 diverge or converge. 2. Here, we measured the morphological and
 physiological traits of roots, and the functional microorganisms related
 to P acquisition in Populus euphratica females and males
 in the rhizosphere under different water availability. 3. The specific
 root length of females was greater than that of males, regardless of soil
 water availability. Therefore, the P concentration of females was
 significantly higher than that of males under well-watered conditions. In
 contrast, the physiological adjustment to drought showed distinct sexual
 patterns: males significantly increased the foliar manganese concentration
 and maintained higher acid phosphatase activities in the rhizosphere.
 Moreover, the arbuscular mycorrhizal hyphal biomass was reduced less in
 males than in females under water deficiency. Soil water shortage also
 decreased the α diversity of phosphate solubilizing bacteria (PSB) and
 changed the co-occurrence network in the rhizosphere of females, but it
 had little effect on males. Therefore, the favorable physiological
 processes and effective maintenance of functional microbial homeostasis in
 the rhizosphere were the reasons that enabled males to reduce P loss in
 leaves under water deficiency. 4. Our study indicated that,
 within P. euphratica populations, covariations
 and tradeoffs simultaneously occurred among the three groups (root
 morphology, physiology, and functional microorganisms) of functional
 traits evaluated. More generally, the assessment of variations in
 sex-specific P acquisition strategies may help to understand the causes of
 sex ratio bias and how P. euphratica males and females
 mitigate resource shortage.
DOI: 10.5061/dryad.jdfn2z3dw
title: Visual processing and collective motion-related decision-making in desert locusts

description: Collectively moving groups of animals rely on decision-making of locally
 interacting individuals in order to maintain swarm cohesion. However, the
 complex and noisy visual environment poses a major challenge to the
 extraction and processing of relevant information. We addressed this
 challenge by studying swarming-related decision-making in desert locust
 nymphs. Controlled visual stimuli, in the form of random dot
 kinematograms, were presented to tethered locust nymphs in a trackball
 setup, while monitoring movement trajectory and walking parameters. In a
 complementary set of experiments, the neurophysiological basis of the
 observed behavioral responses was explored. Our results suggest that
 locusts utilize filtering and discrimination upon encountering multiple
 stimuli simultaneously. Specifically, we show that locusts are sensitive
 to differences in speed at the individual conspecific level, and to
 movement coherence at the group level, and may use these to filter out
 non-relevant stimuli. The locusts also discriminate and assign different
 weights to different stimuli, with an observed interactive effect of
 stimulus size, relative abundance, and motion direction. Our findings
 provide insights into the cognitive abilities of locusts in the domain of
 decision-making and visual-based collective motion and support locusts as
 a model for investigating sensory-motor integration and motion-related
 decision-making in the intricate swarm environment.
DOI: 10.5061/dryad.63xsj3v5f
title: Spore traits mediate disturbance effects on AM fungal community composition and mutualisms

description: Trait-based approaches in ecology are powerful tools for understanding how
 organisms interact with their environment.  These approaches show
 particular promise in disturbance and community ecology contexts for
 understanding how disturbances like prescribed fire and bison grazing
 influence interactions between mutualists like AM fungi and their plant
 hosts.  In this work, we examined how disturbance effects on AM
 fungal spore community composition and mutualisms were mediated by
 selection for specific functional spore traits at both the species and
 community level.  We tested these questions by analyzing AM
 fungal spore communities and traits from a frequently burned and grazed
 (bison) tallgrass prairie system and using these spores to inoculate a
 plant growth response experiment.  Selection for darker,
 pigmented AM fungal spores, changes in the abundance and volume of
 individual AM fungal taxa, and altered sporulation, were indicators of
 fire and grazing effects on AM fungal community composition. 
 Disturbance-associated changes in AM fungal community composition were
 then correlated with altered growth responses of Schizachyrium scoparium
 grass.  Our work shows that utilization of trait-based approaches
 in ecology can clarify the mechanisms that underly belowground responses
 to disturbance, and provide a useful framework for understanding
 interactions between organisms and their environment.
DOI: 10.5061/dryad.m63xsj45g
title: Plant litter chemistry controls coarse-textured soil carbon dynamics

description: 1. As soils store more carbon (C) than the Earth’s atmosphere and
 terrestrial biomass together, the balance between soil C uptake in the
 form of soil organic matter and release as CO2 upon its decomposition is a
 critical determinant in the global C cycle regulating our planet’s
 climate. Although plant litter is the predominant source of C fueling both
 soil C build-up and losses, the issue of how litter chemistry influences
 this balance remains unresolved. 2. As a contribution to solving that
 issue, we traced the fate of C during near-complete decomposition of
 13C-labelled leaf and root litters from 12 plant species in a
 coarse-textured soil. We separated the soil organic carbon (SOC) into
 mineral-associated organic matter (MAOM) and particulate organic matter
 (POM) pools, and investigated how 14 litter chemical traits affected novel
 SOC formation and native SOC mineralization (i.e., the priming effect) in
 these soil fractions. 3. We observed an overall net increase in SOC due to
 the addition of litter, which was stronger for root than for leaf litters.
 The presumed stable MAOM-C pool underwent both substantial stabilization
 and mineralization, whereas the presumably less stable POM-C pool showed
 substantial stabilization and reduced mineralization. Overall, the initial
 increase in soil C mineralization was fully counterbalanced by a later
 decrease in native soil C mineralization. POM-C formation as well as
 MAOM-C formation and mineralization were positively related to the initial
 litter lignin concentration and negatively to that of the nitrogen
 leachates, whereas the opposite was observed for POM-C mineralization. 4.
 Synthesis. Our results highlight the importance of litter chemical traits
 for SOC formation, and stabilization, destabilization, and mineralization.
 In our coarse-textured soil, the amount of MAOM-C did not change despite
 large C fluxes through this pool. The litter chemical traits that drove
 these processes differed from those frequently reported for fine-textured
 soils far from mineral-associated C saturation. To account for these
 discrepancies, we propose an integrative perspective in which litter
 quality and soil texture interactively control soil C fluxes by modulating
 several SOC stabilization and destabilization mechanisms. Irrespective,
 our results open new critical perspectives for managing soil C pools
 globally.
description: Data collection is described in the corresponding article; the
 archieved data (except for the litter chemical traits) represent means
 across 3 repetitions. The archived data have the same units as reported in
 the corresponding article.
description: The data are archieved as a .csv text file.
DOI: 10.5061/dryad.h44j0zpp9
title: Data from: Interspecific variation in the response of fish to anthropogenic noise

description: Experiments concerned the responses of bluegill sunfish (Lepomis
 macrochirus) and spottail shiner (Notropus hudsonius) to elevated levels
 of underwater boat noise. Experiments were either controls ("c")
 or noise ("n") exposure with three separate sound files
 presented in randomized order to avoid pseudoreplication. Responses were
 quantified as exploring, resting, hiding, schooling (all as time spent),
 and the number of startles, C-starts, and foraging strikes. Fish were
 tested in groups of 2 over a total of 11 trials/treatment types.
description: Data collection was by individual scoring of video responses of
 fish to noise or control conditions.
description: # Data from: Interspecific variation in the response of fish to
 anthropogenic noise Dataset DOI:
 [10.5061/dryad.h44j0zpp9](https://doi.org/10.5061/dryad.h44j0zpp9) ##
 Description of the data and file structure ### Jacob_all_fish_data.xlsx
 Columns: * Species - either Bluegill (Lepomis macrochirus) or spottail
 shiner (Notropis hudsonius) * Fish – there were two fish per trial so
 identifies individuals * Trial – the trial number (1-11) * Soundfile – one
 of three sound files of recorded boat noise were randomly presented *
 Order – trials were run either control -&gt; experimental (1) or the
 opposite (2) * Treat - Treatments were either control (“c”), boat noise
 (“n”), or a recovery period ("r") * Exploring – time spent
 swimming around tank, in seconds * Resting - time spent resting on the
 bottom of the tank, in seconds * Hiding -time spent hiding in a structure,
 in seconds * Schooling – time spent schooling with other fish, in seconds
 * Startled - number of startle events that were not C-starts * Forages –
 number of foraging events * C-Start – number of startle events that were
 true C-starts. ## Code/software MS Excel