cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.t722h
title: Data from: Distinguishing migration events of different timing for wild boar in the Balkans

description: Aim: We compared the power of different nuclear markers to investigate
 genetic structure of southern Balkan wild boar. We distinguished between
 historic events, such as isolation in different refugia during glacial
 periods, from recent demographic processes, such as naturally occurring
 expansions. Location: Southern Balkans/Greece. Methods: We sampled 555
 wild boars from 20 different locations in southern Balkans/Greece. All
 individuals were analysed with 10 microsatellites and a subgroup of 91
 with 49,508 single nucleotide polymorphisms (SNPs). Patterns of genetic
 structure and demographic processes were assessed with Bayesian
 clustering, linkage disequilibrium and past effective population size
 estimation analysis. Results: Both microsatellite and SNP data analyses
 detected genetic structure caused by historic events and support the
 existence of three groups in the studied area. A hybrid zone between two
 of the groups was also detected. We also showed that genome-wide SNP data
 analysis can identify recent events in bottlenecked populations. Main
 conclusions: We inferred the three groups diverged ~50,000–10,000 yr bp
 when populations contracted to different refugia. Our findings
 strengthened the evidence that the southern Balkan area was a glacial
 refugium including further local smaller refugia. Genome-wide genotyping
 inferred a recent population expansion that can mimic a ‘refugium within
 refugium’ scenario. It seems that microsatellite data tend to overestimate
 genetic structure when genetic drift happens in bottlenecked populations
 over a short distance. Therefore, genome-wide SNPs are more powerful at
 inferring phylogeography in natural populations, resolving inconsistencies
 from mitochondrial and microsatellite data sets.
description: PA_Wild_boar_ped91 Southern Balkan wild boar genotypes in 49508 SNPs in .ped format for PLINKWB_SNPs.pedPA_Wild_boar_mapInformation on the 49508 autosomal SNPs in .map file format corresponding to the genotypes in the PA_Wild_boar.ped file for use in PLINK softwareWB_SNPs.mapPA_Wild_boar_SNP_structureSTRUCTURE file with 91 wild boar SNP genotypes from Southern BalkansWB_SNPs.strPA_Wild_boar_info_SNPsWild boar sample information corresponding to PA_Wild_boar_ped and PA_Wild_boar_SNP_structureWB_info_SNPs.txtPA_Wild_boar_micros555 Southern Balkan wild boar microsatellite genotypesWB_micros.xlsPA_Wild_boar_micros_structureSTRUCTURE file of 555 Southern Balkan wild boar microsatellite genotypesWB_micros.strPA_Wild_boar_info_microsWild boar sample information corresponding to PA_Wild_boar_micros and PA_Wild_boar_micros_structureWB_info_micros.txtREADMEShort explanation of file content
DOI: 10.5061/dryad.j47h4
title: Data from: Phylogeny and temporal diversification of the New World pond turtles (Emydidae)

description: We present a comprehensive multigene phylogeny and time tree for the
 turtle family Emydidae. Our phylogenetic analysis, based on 30 nuclear and
 four mitochondrial genes (23,330 total base pairs) sequenced for two
 individuals for each of the currently recognized species of the subfamily
 Emydinae and two species from each of the more species-rich Deirochelyinae
 genera, yielded a well-supported tree that provides an evolutionary
 framework for this well-studied clade and a basis for a stable taxonomy.
 We calibrated an emydid time tree using three well-vetted fossils, modeled
 uncertainty in fossil ages to reflect their accuracy in node dating, and
 extracted stem/crown ages of a number of key diversification events. We
 date the age of crown emydids at a relatively young 44 Ma, and the crown
 age of both contained subfamilies at roughly 30 Ma. One deirochelyine
 clade, which includes the genera Graptemys, Malaclemys, Pseudemys, and
 Trachemys and contains 11% of all turtle species, dates to 21 Ma just
 prior to the mid-Miocene climatic optimum, suggesting a potential causal
 link between warm, moist conditions and rapid species accumulation of
 these highly aquatic turtles. Both nuclear DNA data alone and in
 combination with mitochondrial DNA support the monophyly of an inclusive
 genus Emys containing the old world species orbicularis and trinacris and
 the new world blandingii, marmorata and pallida. Given that all members of
 this group were originally aligned in the genus Emys and that the age of
 the clade is roughly equal to other emydine genera, we strongly support a
 classification that places these five species in a single genus rather
 than the alternative three-genus scheme (Emys (orbicularis, trinacris),
 Actinemys (marmorata, pallida), Emydoidea (blandingii). The phylogeny and
 resulting time tree presented here provides a comprehensive foundation for
 future comparative analyses of the Emydidae that will shed light on the
 historical ecology and conservation prioritization of this diverse
 chelonian clade.
description: 42alldatayuleThis is the XML file used for the BEAST analyses. This file contains both mitochondrial and nuclear sequence data for all 34 loci analyzed here.42mtDNA.yule.xmlThis is the XML file used in the BEAST analyses. This file contains mtDNA sequences only.42nuDNAYuleThis is the XML file used in the BEAST analyses. This file contains sequence data from nuclear loci only.
DOI: 10.5061/dryad.2dh81
title: Data from: Concessions, lifetime fitness consequences and the evolution of coalitionary behavior

description: The relationship between the costs of coalitionary behavior and the
 evolution of such behavior has not been closely examined by theoretical
 studies. Here, we create a set of life-history models for species whose
 coalitionary behavior is genetically determined to investigate how
 different types of costs afflicted upon members of failed coalitions, in
 terms of survival, fecundity, and social rank, may influence the nature of
 coalitionary behavior that emerges at evolutionary equilibrium. We also
 extend previous theory by examining the coevolution between coalitionary
 behavior and concessions granted by dominant individuals to prevent
 dominants from being targeted by coalitions. We show that species that
 form coalitions to contest social rank evolve to regularly form bridging
 coalitions under a vast majority of social and ecological settings,
 whereas species that contest fecundity form all-up coalitions under most
 conditions. Further, dominant individuals concede resources to
 subordinates to prevent coalitionary attacks only in very few
 circumstances, and these concessions occur only to ensure another
 individual is a more attractive coalition target. We compare and contrast
 results to empirical data to provide an evolutionary context for commonly
 observed coalitionary behaviors in the animal kingdom.
description: Fecundity[Scramble]Fecundity[Sequential]Fecundity[Sequential+DifferenceinCost]Rank[Scramble]Rank[Sequential]Rank+Fecundity[Sequential]Survival[Scramble]Survival[Sequential]
DOI: 10.5281/zenodo.13986859
title: Histo-Miner: Use case CPI dataset

description: Use case dataset from an unpublished paper. The dataset files will be available only after publication of the paper in a journal. The list of feature is openly avaialble on the github repository.*

The datasets consists of 45 WSI images in .ndpi format from 45 Cutaneous Squamous Cell Carcinamo skin cancer (cSCC) patients. The images are scan of skin tissue stained with H&E. WSIs come from 6 medical centers. The metadata file, containing the binary class labels of the images, is available as a CSV. A classifier was trained for classification and the features extracted from the slides to train the classifier are listed in List_of_features_including_morphology_features.json and List_of_features_without_morphology_features.json and the ranking of features by mRMR method during cross-validation are available in Ranking_of_features.json. 

How to visualize the jsons files 

If you are unfamiliar with this format, one simple way to visualize a JSON file is to paste all the content of the JSON file (that you can open with any text editors) into jsongrid.com or jsontotable.org. There is no need to save the data on these websites (Save or Share buttons). 

 

The dataset size is 75.83 GB.

* The dataset was publicly available few days after publication of the preprint but was made private again after discussion and agreement with co-authors. The list of feature stays available (see github repository of the project).
DOI: 10.5281/zenodo.13986860
title: Histo-Miner: Use case CPI dataset

description: Use case dataset from an unpublished paper. The dataset files will be available only after publication of the paper in a journal. The list of feature is openly avaialble on the github repository.*

The datasets consists of 45 WSI images in .ndpi format from 45 Cutaneous Squamous Cell Carcinamo skin cancer (cSCC) patients. The images are scan of skin tissue stained with H&E. WSIs come from 6 medical centers. The metadata file, containing the binary class labels of the images, is available as a CSV. A classifier was trained for classification and the features extracted from the slides to train the classifier are listed in List_of_features_including_morphology_features.json and List_of_features_without_morphology_features.json and the ranking of features by mRMR method during cross-validation are available in Ranking_of_features.json. 

How to visualize the jsons files 

If you are unfamiliar with this format, one simple way to visualize a JSON file is to paste all the content of the JSON file (that you can open with any text editors) into jsongrid.com or jsontotable.org. There is no need to save the data on these websites (Save or Share buttons). 

 

The dataset size is 75.83 GB.

* The dataset was publicly available few days after publication of the preprint but was made private again after discussion and agreement with co-authors. The list of feature stays available (see github repository of the project).
DOI: 10.5061/dryad.mt6m0
title: Data from: Microbiome changes through ontogeny of a tick pathogen vector

description: Blacklegged ticks (Ixodes scapularis) are one of the most important
 pathogen vectors in the United States, responsible for transmitting Lyme
 disease and other tick-borne diseases. The structure of a host's
 microbial community has the potential to affect the ecology and evolution
 of the host. We employed high-throughput sequencing of the 16S rRNA gene
 V3-V4 hypervariable regions in the first study to investigate the tick
 microbiome across all developmental stages (larvae, nymphs, adults). In
 addition to field-collected life stages, newly hatched laboratory-reared
 larvae were studied to determine the baseline microbial community
 structure and to assess transovarial transmission. We also targeted
 midguts and salivary glands due to their importance in pathogen
 maintenance and transmission. Over 100 000 sequences were produced per
 life stage replicate. Rickettsia was the most abundant bacterial genus
 across all sample types matching mostly the Ixodes rickettsial
 endosymbionts, and its proportion decreased as developmental stage
 progressed, with the exception of adult females that harboured a mean
 relative abundance of 97.9%. Laboratory-reared larvae displayed the lowest
 bacterial diversity, containing almost exclusively Rickettsia. Many of the
 remaining bacteria included genera associated with soil, water and plants,
 suggesting environmental acquisition while off-host. Female organs
 exhibited significantly different β-diversity than the whole tick from
 which they were derived. Our results demonstrate clear differences in both
 α- and β-diversity among tick developmental stages and between tick organs
 and the tick as a whole. Furthermore, field-acquired bacteria appear to be
 very important to the overall internal bacterial community of this tick
 species, with influence from the host bloodmeal appearing limited.
description: BIOM OTU table – All
 life stagesOTU table in BIOM format
 of all life stages of the blacklegged tick (Ixodes
 scapularis)otu_table_all_life_stages.biomBIOM OTU table – Female organsOTU table in BIOM format of female organs (salivary glands and midgut) of the blacklegged tick (Ixodes scapularis)otu_table_female_organs.biomJPLACE tree file of Rickettsia EPAAnnotated tree in JPLACE format of Rickettsia short sequences and reference longer sequences.RAxML_portableTree.rick_EPA.jplace
DOI: 10.5061/dryad.t8j15
title: Data from: Evidence for water-mediated mechanisms in coral–algal interactions

description: Although many coral reefs have shifted from coral-to-algal dominance, the
 consequence of such a transition for coral–algal interactions and their
 underlying mechanisms remain poorly understood. At the microscale, it is
 unclear how diffusive boundary layers (DBLs) and surface oxygen
 concentrations at the coral–algal interface vary with algal competitors
 and competitiveness. Using field observations and microsensor measurements
 in a flow chamber, we show that coral (massive Porites) interfaces with
 thick turf algae, macroalgae, and cyanobacteria, which are successful
 competitors against coral in the field, are characterized by a thick DBL
 and hypoxia at night. In contrast, coral interfaces with crustose
 coralline algae, conspecifics, and thin turf algae, which are poorer
 competitors, have a thin DBL and low hypoxia at night. Furthermore, DBL
 thickness and hypoxia at the interface with turf decreased with increasing
 flow speed, but not when thick turf was upstream. Our results support the
 importance of water-mediated transport mechanisms in coral–algal
 interactions. Shifts towards algal dominance, particularly dense
 assemblages, may lead to thicker DBLs, higher hypoxia, and higher
 concentrations of harmful metabolites and pathogens along coral borders,
 which in turn may facilitate algal overgrowth of live corals. These
 effects may be mediated by flow speed and orientation.
description: Jorissen et al 2016 RAW
 data
DOI: 10.5061/dryad.b1rr1
title: Data from: Risk factors for admission at three urban emergency departments in England: a cross-sectional analysis of attendances over 1 month

description: Objective: to investigate factors associated with unscheduled admission
 following presentation to Emergency Departments (EDs) at three hospitals
 in England. Design and setting: cross-sectional analysis of attendance
 data for patients from three urban EDs in England: a large teaching
 hospital and major trauma centre (Site 1), and two district general
 hospitals (Sites 2 and 3). Variables included: patient age, gender,
 ethnicity, deprivation score, arrival date and time, arrival by ambulance
 or otherwise, a variety of ED workload measures, inpatient bed occupancy
 rates and admission outcome. Coding inconsistencies in routine ED data
 used for this study meant that diagnosis could not be included. Outcome
 measure: The primary outcome for the study was unscheduled admission.
 Participants: all adults aged 16 and over attending the three inner London
 EDs in December 2013. Data on 19,734 unique patient attendances were
 gathered. Results: outcome data were available for 19,721 attendances
 (&gt;99%), of whom 6,263 (32%) were admitted to hospital. Site 1 was
 set as the baseline site for analysis of admission risk. Risk of admission
 was significantly greater at Sites 2 and 3 (AOR relative to Site 1 for
 Site 2 was 1.89, 95% CI 1.74-2.05, p&lt;0.001), and for patients of
 black or black British ethnicity (1.29, 1.16-1.44, p&lt;0.001).
 Deprivation was strongly associated with admission. Analysis of
 departmental and hospital-wide workload pressures gave conflicting
 results, but proximity to the “four-hour target” (a rule that limits
 patient stays in EDs to four hours in the NHS in England) emerged as a
 strong driver for admission in this analysis (3.61, 3.30-3.95,
 p&lt;0.001). Conclusion: this study found statistically significant
 variations in odds of admission between hospital sites when adjusting for
 various patient demographic and presentation factors, suggesting important
 variations in ED- and clinician-level behaviour relating to admission
 decisions. The four-hour target is a strong driver for emergency
 admission.
description: All admx for BMJ
 Open_v0.02Dataset for analysis of
 all emergency department presentations in relation to the above paper,
 along with a key.
DOI: 10.5061/dryad.2br2b
title: Data from: Quantifying species contributions to ecosystem processes: a global assessment of functional trait and phylogenetic metrics across avian seed-dispersal networks

description: Quantifying the role of biodiversity in ecosystems not only requires
 understanding the links between species and the ecological functions and
 services they provide, but also how these factors relate to measurable
 indices, such as functional traits and phylogenetic diversity. However,
 these relationships remain poorly understood, especially for heterotrophic
 organisms within complex ecological networks. Here, we assemble data on
 avian traits across a global sample of mutualistic plant–frugivore
 networks to critically assess how the functional roles of frugivores are
 associated with their intrinsic traits, as well as their evolutionary and
 functional distinctiveness. We find strong evidence for niche
 complementarity, with phenotypically and phylogenetically distinct birds
 interacting with more unique sets of plants. However, interaction
 strengths—the number of plant species dependent on a frugivore—were
 unrelated to evolutionary or functional distinctiveness, largely because
 distinct frugivores tend to be locally rare, and thus have fewer
 connections across the network. Instead, interaction strengths were better
 predicted by intrinsic traits, including body size, gape width and dietary
 specialization. Our analysis provides general support for the use of
 traits in quantifying species ecological functions, but also highlights
 the need to go beyond simple metrics of functional or phylogenetic
 diversity to consider the multiple pathways through which traits may
 determine ecological processes.
description: databaseS1Seed-dispersal networks, species traits and avian functional/ phylogenetic distance matricesDatabase S1.xlsx
DOI: 10.5061/dryad.md045
title: Data from: A cross-continental comparison of plant and beetle responses to retention of forest patches during timber harvest

description: Timber harvest can adversely affect forest biota. Recent research and
 application suggest that retention of mature forest elements (‘retention
 forestry’), including unharvested patches (or ‘aggregates’) within larger
 harvested units, can benefit biodiversity compared to clearcutting.
 However, it is unclear whether these benefits can be generalized among the
 diverse taxa and biomes in which retention forestry is practiced. Lack of
 comparability in methods for sampling and analysing responses to timber
 harvest and edge creation presents a challenge to synthesis. We used a
 consistent methodology (similarly spaced plots or traps along transects)
 to investigate responses of vascular plants and ground-active beetles to
 aggregated retention at replicate sites in each of four temperate and
 boreal forest types on three continents: Douglas-fir forests in
 Washington, USA; aspen forests in Minnesota, USA; spruce forests in
 Sweden; and wet eucalypt forests in Tasmania, Australia. We assessed (i)
 differences in local (plot-scale) species richness and composition between
 mature (intact) and regenerating (previously harvested) forest; (ii) the
 lifeboating function of aggregates (capacity to retain species of
 unharvested forest); and whether intact forests and aggregates (iii) are
 susceptible to edge effects and (iv) influence the adjacent regenerating
 forest. Intact and harvested forests differed in composition but not
 richness of plants and beetles. The magnitude of this difference was
 generally similar among regions, but there was considerable heterogeneity
 of composition within and among replicate sites. Aggregates within harvest
 units were effective at lifeboating for both plant and beetle communities.
 Edge effects were uncommon even within the aggregates. In contrast,
 effects of forest influence on adjacent harvested areas were common and as
 strong for aggregates as for larger blocks of intact forest. Our results
 provide strong support for the widespread application of aggregated
 retention in boreal and temperate forests. The consistency of pattern in
 four very different regions of the world suggests that, for forest plants
 and beetles, responses to aggregated retention are likely to apply more
 widely. Our results suggest that through strategic placement of
 aggregates, it is possible to maintain the natural heterogeneity and
 biodiversity of mature forests managed for multiple objectives.
description: Retention
 forestry_plants_beetlesThis dataset includes
 vascular plants recorded during field surveys (% projected foliage cover
 of each species, averaged from two sub-plots) and ground-active beetles
 collected with pitfall traps (number of specimens per
 species).Full data for online
 depository.xlsx
DOI: 10.5061/dryad.1d28m
title: Data from: A collection of European sweet cherry phenology data for assessing climate change

description: Professional and scientific networks built around the production of sweet
 cherry (Prunus avium L.) led to the collection of phenology data for a
 wide range of cultivars grown in experimental sites characterized by
 highly contrasted climatic conditions. We present a dataset of flowering
 and maturity dates, recorded each year for one tree when available, or the
 average of several trees for each cultivar, over a period of 37 years
 (1978 - 2015). Such dataset is extremely valuable for characterizing the
 phenology response to climate change, but also the plasticity of the
 different cultivars’ behaviour under various environmental conditions. In
 addition, these records can support the development of predictive models
 exploitable at the continental scale to be used by growers and breeders,
 but also to anticipate breeding strategies in order to maintain and
 improve sweet cherry production in Europe.
description: Sweet cherry phenology
 data 1978-2015Sweet cherry
 phenological data were collected from two networks: flowering and maturity
 dates for up to 191 reference cultivars, and from 10 sites, were extracted
 from the French database, coordinated by a French national network of
 experimentation Centre technique interprofessionnel des fruits et legumes
 - CTIFL). At the European scale, in the context of the COST Action 1104
 (2012-2016; https://www.bordeaux.inra.fr/cherry/), flowering and maturity
 dates were collected from 14 sites. Recorded years span is 1978 - 2015.
 Metadata are included in the dataset as a separate
 spreadsheet.Sweet_cherry_phenology_data_1978-2015.xlsx
DOI: 10.5281/zenodo.18385569
title: Application of Cerium Oxide Nanoparticle for Root Canal Disinfection
DOI: 10.5281/zenodo.18385570
title: Application of Cerium Oxide Nanoparticle for Root Canal Disinfection