cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.nv3846b
title: Data from: Hierarchy in adaptive radiation: a case study using the Carnivora (Mammalia)

description: Simpson’s “early burst” model of adaptive radiation was intended to
 explain the early proliferation of morphological and functional variation
 in diversifying clades. Yet, despite much empirical testing, questions
 remain regarding its frequency across the tree of life. Here, we evaluate
 the support for an early burst adaptive radiation in 14 ecomorphological
 traits plus body mass for the extant mammalian order Carnivora and its
 constituent families. We find strong support for an early burst of
 evolution in dental traits, suggesting a classic Simpsonian adaptive
 radiation along dietary resource axes. However, the signal of this early
 burst is not consistently recovered in analyses at the family level, where
 support for a variety of different models emerges. Furthermore, we find no
 evidence for early burst–like dynamics in size–related traits, and
 Bayesian analyses of evolutionary correlations corroborate a decoupling of
 size and dental evolution, driven in part by dietary specialization. Our
 results are consistent with the perspective that trait diversification
 unfolds hierarchically, with early bursts restricted to traits associated
 with higher level niches, such as macrohabitat use and dietary strategy,
 and thus with the origins of higher taxa. The lack of support for early
 burst adaptive radiation in previous phylogenetic studies may be a
 consequence of focusing on low-level niche traits (i.e., those associated
 with microhabitat use) in clades at shallow phylogenetic levels. A richer
 understanding of early burst adaptive radiation will require a renewed
 focus on functional traits and their evolution over higher-level clades.
description: Carnivora_MCC_treeMaximum Clade Credibility tree for CarnivoraCarnivora_MCC.trecarnivora_beast_xmlXML file for beastcarnivora_beastinput_edit.xmlcarnivora_phylo_dataR data object containing species means and standard errors for ecomorphological data, family level assignments, and phylogenybasic_trait_analysesR script to perform basic trait evolutionary model fitting analyseslasso output functionsutility functions to process the output of L1OUsummarize.lasso.output.Rl1OUcode to run L1OU on carnivore rlga dataRateMatrixFunctionsutility functions to process rate matrix outputRateMatrix_by_dietscript to run rate matrix on carnivore dataPMCuses phylogenetic Monte Carlo procedure of Boettiger et al. to assess support for EB or SSP in family level clades.
DOI: 10.5061/dryad.174667c
title: Data from: Intestinal Serum Amyloid A suppresses systemic neutrophil activation and bactericidal activity in response to microbiota colonization

description: The intestinal microbiota influences the development and function of
 myeloid lineages such as neutrophils, but the underlying molecular
 mechanisms are unresolved. Using gnotobiotic zebrafish, we identified the
 immune effector Serum amyloid A (Saa) as one of the most highly induced
 transcripts in digestive tissues following microbiota colonization. Saa is
 a conserved secreted protein produced in the intestine and liver with
 described effects on neutrophils in vitro, however its in vivo functions
 remain poorly defined. We engineered saa mutant zebrafish to test
 requirements for Saa on innate immunity in vivo. Zebrafish mutant for saa
 displayed impaired neutrophil responses to wounding but augmented
 clearance of pathogenic bacteria. At baseline, saa mutants exhibited
 moderate neutrophilia and altered neutrophil tissue distribution.
 Molecular and functional analyses of isolated neutrophils revealed that
 Saa suppresses expression of pro-inflammatory markers and bactericidal
 activity. Saa’s effects on neutrophils depend on microbiota colonization,
 suggesting this protein mediates the microbiota’s effects on host innate
 immunity. To test tissue-specific roles of Saa on neutrophil function, we
 over-expressed saa in the intestine or liver and found that sufficient to
 partially complement neutrophil phenotypes observed in saa mutants. These
 results indicate Saa produced by the intestine in response to microbiota
 serves as a systemic signal to neutrophils to restrict aberrant
 activation, decreasing inflammatory tone and bacterial killing potential
 while simultaneously enhancing their ability to migrate to wounds.
description: Fig1These file archives
 contain the raw data used in PPATHOGENS-D-18-01928R1. It includes excel
 files (.xlsx), image files (.lif, .tif, .czi), and text files (.txt). For
 complete details regarding generation of data presented in this paper
 please see the corresponding materials and methods
 sectionFig2Fig3Fig4Fig5S1 FigS2 FigS3 FigS4 FigS5 FigS6 FigS7 FigS8 Fig
DOI: 10.5281/zenodo.18389878
title: Data set - "From left to right? The effect of political orientation on attitudes towards labor-related regularization among rejected asylum seekers"

description: This data set includes relevant data for the manuscript "From left to right? The effect of political orientation on attitudes towards labor-related regularization among rejected asylum seekers".
DOI: 10.5281/zenodo.18389879
title: Data set - "From left to right? The effect of political orientation on attitudes towards labor-related regularization among rejected asylum seekers"

description: This data set includes relevant data for the manuscript "From left to right? The effect of political orientation on attitudes towards labor-related regularization among rejected asylum seekers".
DOI: 10.5061/dryad.85k53v8
title: Data from: Tropical tree height and crown allometries for the Barro Colorado Nature Monument, Panama: a comparison of alternative hierarchical models incorporating interspecific variation in relation to life history traits

description: Tree allometric relationships are widely employed for estimating forest
 biomass and production and are basic building blocks of dynamic vegetation
 models. In tropical forests, allometric relationships are often modeled by
 fitting scale-invariant power functions to pooled data from multiple
 species, an approach that fails to capture changes in scaling during
 ontogeny and physical limits to maximum tree size and that ignores
 interspecific differences in allometry. Here, we analyzed allometric
 relationships of tree height (9884 individuals) and crown area (2425) with
 trunk diameter for 162 species from the Barro Colorado Nature Monument,
 Panama. We fit nonlinear, hierarchical models informed by species traits –
 wood density, mean sapling growth, or sapling mortality – and assessed the
 performance of three alternative functional forms: the scale-invariant
 power function and the saturating Weibull and generalized Michaelis–Menten
 (gMM) functions. The relationship of tree height with trunk diameter was
 best fit by a saturating gMM model in which variation in allometric
 parameters was related to interspecific differences in sapling growth
 rates, a measure of regeneration light demand. Light-demanding species
 attained taller heights at comparatively smaller diameters as juveniles
 and had shorter asymptotic heights at larger diameters as adults. The
 relationship of crown area with trunk diameter was best fit by a power
 function model incorporating a weak positive relationship between crown
 area and species-specific wood density. The use of saturating functional
 forms and the incorporation of functional traits in tree allometric models
 is a promising approach for improving estimates of forest biomass and
 productivity. Our results provide an improved basis for parameterizing
 tropical plant functional types in vegetation models.
description: DiameterHeightCrown20190130`DiameterHeightCrown20190104.csv` includes 9885 tree height and 2425 crown area measurements at Barro Colorado National Monument.SpeciesTraits20190104`SpeciesTraits20190104.csv` includes species-specific traits that entered as covariates in our allometric models; these data were included only for completeness, please refer to the original sources and include a citation to the manuscripts detailed in the readme file in case you want to use these data.
DOI: 10.5061/dryad.2v7s52d
title: Data from: Coalescent models characterize sources and demographic history of recent round goby colonization of Great Lakes and inland waters

description: The establishment and spread of aquatic invasive species is ecologically
 and economically harmful and a source of conservation concern
 internationally. Processes of species invasion have traditionally been
 inferred from observational data of species presence/absence and relative
 abundance. However, genetic-based approaches can provide valuable sources
 of inference. Restriction-site associated DNA sequencing was used to
 identify and genotype single nucleotide polymorphism (SNP) loci for Round
 Gobies (Neogobius melanostomus) (N=440) from 18 sampling locations in the
 Great Lakes and in three Michigan, USA drainages (Flint, Au Sable, and
 Cheboygan River basins). Sampled rivers differed in size, accessibility,
 and physical characteristics including man-made dispersal barriers.
 Population levels of genetic diversity and inter-population variance in
 SNP allele frequency were used in coalescence-based Approximate Bayesian
 Computation (ABC) to statistically compare models representing competing
 hypotheses regarding source population, post-colonization dispersal, and
 demographic history in the Great Lakes and inland waters. Results indicate
 different patterns of colonization across the three drainages. In the
 Flint River, models indicate a strong population bottleneck (&lt; 3%
 of contemporary effective population size) and a single founding event
 from Saginaw Bay led to the colonization of inland river segments. In the
 Au Sable River, analyses could not distinguish potential source
 populations, but supported models indicated multiple introductions from
 one source population. In the Cheboygan River, supported models indicated
 that colonization likely proceeded from east (Lake Huron source) to west
 among inland locales sampled in the system. Despite the recent occupancy
 of Great Lakes and inland habitats, large numbers of loci analyzed in an
 ABC framework enable statistically supported identification of source
 populations and reconstruction of the direction of inland spread and
 demographic history following establishment. Information from analyses can
 direct management actions to limit the spread of invasive species from
 identified sources and most probable vectors into additional inland
 aquatic habitats.
description: Round Goby Genotypes in
 VCF (Variant Calling Format)SNP data based on
 sequencing data processed with STACKS V1.44. See methods for
 details.batch_3.vcf
DOI: 10.5061/dryad.7bm444s
title: Data from: Dynamic relocalization of replication origins by Fkh1 requires execution of DDK function and Cdc45 loading at origins

description: Chromosomal DNA elements are organized into spatial domains within the
 eukaryotic nucleus. For example, sites actively undergoing DNA
 replication, high-level transcription, and repair of double-strand breaks
 coalesce into foci, although the significance and mechanisms giving rise
 to these dynamic structures are poorly understood. In S. cerevisiae,
 replication origins exhibit characteristic subnuclear localizations prior
 to S phase that anticipate their initiation timing and/or efficiency
 during S phase: origins found within the nuclear interior in G1 phase
 initiate early and efficiently in S phase while origins found associated
 with the nuclear periphery in G1 phase initiate later and less
 efficiently. In this study, we link interior localization of replication
 origins in G1 phase with Fkh1 activity, which is required for their early
 replication timing. Using a Fkh1-dependent origin relocalization assay, we
 determine that execution of Dbf4-dependent kinase function, including
 Cdc45 loading, results in dynamic relocalization of a replication origin
 from the nuclear periphery to the interior in G1 phase. Origin mobility
 increases substantially with Fkh1-driven relocalization. These findings
 provide novel molecular insight into the mechanisms that govern dynamics
 and spatial organization of DNA replication origins and possibly other
 functional DNA elements.
description: Imaging quantification
 & sequencing data & ScriptThere are 3 subfolders
 in "Data Revision", Imaging quantification, Sequencing data and
 Script. The raw imaging quantification (.xlsx) and statistical analysis
 results (.csv) are provided in "Imaging quantification" folder
 with corresponding names. Movies for Fig6 are also available in this
 folder. Folders "Sequencing data" and "Script"
 includes all the sequencing data files and Matlab scripts for the paper
 (Figure2C; FigureS2 and FigureS4). In folder “Raw”, four fastq files used
 for both BrdU-IP-Seq (QBU) and ChIP-seq (ChIP) data analysis are provided.
 In folder “Processed”, processed sequencing data directly used for figure
 plotting were provided as bed files. Please see Excel file
 "README" for detailed description about each
 file.Data
 Revision.zip
DOI: 10.5061/dryad.v9637h8
title: Data from: Personality and social foraging tactic use in free-living Eurasian tree sparrows (Passer montanus)

description: Group-foraging individuals often use alternative behavioral tactics to
 acquire food: some individuals, the producers, actively search for food,
 while others, the scroungers, look for opportunities to exploit the
 finders’ discoveries. Although the use of social foraging tactics is
 partly flexible, yet some individuals tend mainly to produce, while others
 largely prefer to scrounge. This between-individual variation in tactic
 use closely resembles the phenomenon of animal personality, however the
 connection between personality and social foraging tactic use has rarely
 been investigated in wild animals. Here, we studied this relationship in
 free-living Eurasian tree sparrows (Passer montanus) during two winters.
 We found that in females, but not in males, social foraging tactic use was
 predicted by personality: more exploratory (i.e. more active in a novel
 environment) females scrounged more. Regardless of sex, the probability of
 scrounging increased with the density of individuals foraging on feeders
 and the time of feeding within a foraging bout, that is, the later the
 individual foraged within a foraging bout the higher the probability of
 scrounging was. Our results demonstrate that consistent individual
 behavioral differences are linked, in a sex-dependent manner, to
 group-level processes in the context of social foraging in free-living
 tree sparrows, suggesting that individual behavioral traits have
 implications for social evolution.
description: Exploration
 dataRaw data used to
 calculate exploration scores of individuals.Fulop_et_al_BEHAVECOL_exploration_DATA.csvIndividual dataSex and phenotypic data of individuals recorded during social foraging.Fulop_et_al_BEHAVECOL_individual_DATA.csvSocial foraging dataSocial foraging data of individuals.Fulop_et_al_BEHAVECOL_social_foraging_DATA.csv
DOI: 10.5061/dryad.4809qj4
title: Data from: Surface color and predictability determine contextual modulation of V1 firing and gamma oscillations

description: The integration of direct bottom-up inputs with contextual information is
 a core feature of neocortical circuits. In area V1, neurons may reduce
 their firing rates when their receptive field input can be predicted by
 spatial context. Gamma-synchronized (30–80 Hz) firing may provide a
 complementary signal to rates, reflecting stronger synchronization between
 neuronal populations receiving mutually predictable inputs. We show that
 large uniform surfaces, which have high spatial predictability, strongly
 suppressed firing yet induced prominent gamma synchronization in macaque
 V1, particularly when they were colored. Yet, chromatic mismatches between
 center and surround, breaking predictability, strongly reduced gamma
 synchronization while increasing firing rates. Differences between
 responses to different colors, including strong gamma-responses to red,
 arose from stimulus adaptation to a full-screen background, suggesting
 prominent differences in adaptation between M- and L-cone signaling
 pathways. Thus, synchrony signaled whether RF inputs were predicted from
 spatial context, while firing rates increased when stimuli were
 unpredicted from context.
description: Dataset
 1Please see readme and
 description of dataset 1 in publication.Dataset1.zipDataset 2Please see readme and description of dataset 2 in publication.Dataset2.zipDataset 3Please see readme and description of dataset 3 in publication.Dataset3.zipDataset 4Please see readme and description of dataset 4 in publication.Dataset4.zipDataset 5Please see readme and description of dataset 5 in publication.Dataset5.zip
DOI: 10.15468/2u8gud
title: Inventory of marine amphipod species from Italian waters: an update

description: This dataset provides an updated inventory of amphipod species occurring in Italian marine waters, resulting from unpublished data by public and private institutions, in a period comprised between the early 1980s to 2025. A total of 4344 records were listed, representing 302 species, 127 genera, and 51 families. The highest species richness was registered in the Tyrrhenian Sea. The dataset also documents eleven non-indigenous species (NIS) for Mediterranean Sea.Habitat characterization of sampling sites revealed amphipod species across fifteen substrate types, underscoring their broad habitat plasticity. The spatial and temporal resolution of the compiled data offers valuable insights into patterns of amphipod distribution and community composition, and provides a robust baseline for biodiversity assessments, environmental monitoring, and the management of emerging NIS in Italian marine ecosystems. The present dataset integrates the Italian amphipod checklist.
DOI: 10.5061/dryad.325pp2h
title: Data from: Patients’ experiences with a behaviour change intervention to enhance physical activity in primary care: a mixed methods study

description: Objective: To explore the experiences of patients at risk for
 cardiovascular disease in primary care with the Activate intervention in
 relation to their success in increasing their physical activity. Methods:
 A convergent mixed-methods design, parallel to a cluster-randomised
 controlled trial in primary care, using a questionnaire and
 semi-structured interviews was conducted. Questionnaires from 67 patients
 were analysed, and semi-structured interviews of 22 patients were
 thematically analysed. Experiences of patients who had objectively
 increased their physical activity (responders) were compared to those who
 had not (non-responders). Objective success was analysed in relation to
 self-perceived success. Results: The questionnaire and interview data
 corresponded, and no substantial differences among responders and
 non-responders emerged. Participating in the intervention increased their
 awareness of their physical activity and their physical activity level.
 Key components of the intervention were nurses' subsequent
 consultations and trustful support and the use of self-monitoring tools.
 Patients highly valued jointly setting goals, planning actions, receiving
 feedback and review on their goal attainment and jointly solving problems.
 Nurses' support, using self-monitoring tools, and involving others
 incentivised patients. Internal circumstances and external circumstances
 challenged patients' engagement in increasing and maintaining their
 physical activity. Conclusion: Patients experienced the Activate
 intervention as valuable to increase and maintain their physical activity,
 irrespective of their objective change in physical activity. The findings
 enable the understanding of the effectiveness of the intervention and
 implementation in primary care. Trial registration: ClinicalTrials.gov
 NCT02725203
description: PONE-D-18-04427R1
DOI: 10.5061/dryad.hj4pb70
title: Data from: High-order thalamic inputs to primary somatosensory cortex are stronger and longer lasting than cortical inputs

description: Layer (L) 2/3 pyramidal neurons in the primary somatosensory cortex (S1)
 are sparsely active, spontaneously and during sensory stimulation.
 Long-range inputs from higher areas may gate L2/3 activity. We
 investigated their in vivo impact by expressing channelrhodopsin in three
 main sources of feedback to rat S1: primary motor cortex, secondary
 somatosensory cortex, and secondary somatosensory thalamic nucleus (the
 posterior medial nucleus, POm). Inputs from cortical areas were relatively
 weak. POm, however, more robustly depolarized L2/3 cells and, when paired
 with peripheral stimulation, evoked action potentials. POm triggered not
 only a stronger fast-onset depolarization but also a delayed all-or-none
 persistent depolarization, lasting up to 1 s and exhibiting
 alpha/beta-range oscillations. Inactivating POm somata abolished
 persistent but not initial depolarization, indicating a recurrent circuit
 mechanism. We conclude that secondary thalamus can enhance L2/3
 responsiveness over long periods. Such timescales could provide a
 potential modality-specific substrate for attention, working memory, and
 plasticity.
description: L23 barrel cortex
 responses to optogenetic and whisker stimuliZhang &
 Bruno.xlsx
DOI: 10.5061/dryad.h85261k
title: Data from: Depth-to-water mediates bryophyte response to harvesting in boreal forests

description: 1. Site moisture is an important component of the forest landscape for
 maintaining biodiversity, including forest-floor bryophytes, but little is
 known about its role in shaping understory responses to harvesting. 2. We
 investigated the influence of site wetness, determined using a
 remotely-sensed, topographic depth-to-water (DTW) index, on responses of
 bryophyte cover, richness, diversity, and composition to variable
 retention harvesting (comparing: 2% [clear-cut], 20%, and 50% dispersed
 green tree retention and uncut controls [100% retention]) in three boreal
 forest cover-types (broadleaf, mixed, and conifer forests) in western
 Canada. The DTW index provides an approximation of depth to water at or
 below the soil surface, and was derived from wet-areas mapping based on
 discrete Airborne Laser Scanning data acquired over an experimentally
 harvested landscape located in northwestern Alberta, Canada. 3. The
 effectiveness of leaving retention (versus clear-cutting) for conserving
 bryophyte communities depended on site wetness, as indicated by DTW, with
 the specifics varying among forest types. In broadleaf forests, bryophyte
 cover and richness were generally low and not much affected by harvesting
 but drier sites had higher richness and a few more unique species. In
 mixed and conifer forests, leaving retention (versus clear-cutting) on
 wetter (versus drier) sites was more effective for conserving bryophyte
 cover, wetter sites had higher total species richness, and more species
 were exclusive to wetter sites. 4. Synthesis and applications. Site
 wetness, as indicated using the remotely-sensed topographic site wetness
 index "depth-to-water," mediates bryophyte responses to
 variable-retention harvests. Specifically, our results suggested that in
 conifer and mixed forests it would be more beneficial to target wetter
 sites for retention patches or dispersed retention whereas in broadleaf
 sites there might be a slight advantage to targeting drier sites. Our
 study demonstrates that this tool could be used to inform management
 decisions around leaving dispersed or patch retention.28-Jan-2019
description: Bryophyte species and
 depth-to-water index valuesBryophyte (mosses and
 liverworts) species cover data and estimation of depth-to-water index
 values for retention harvest sites sampled in northwestern Alberta,
 Canada.Bartels-et-al-2019-deposited
 data-Dryad.xlsx