cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.4ht07
title: Data from: Feeder use predicts both acquisition and transmission of a contagious pathogen in a North American songbird

description: Individual heterogeneity can influence the dynamics of infectious diseases
 in wildlife and humans alike. Thus, recent work has sought to identify
 behavioural characteristics that contribute disproportionately to
 individual variation in pathogen acquisition (super-receiving) or
 transmission (super-spreading). However, it remains unknown whether the
 same behaviours enhance both acquisition and transmission, a scenario
 likely to result in explosive epidemics. Here, we examined this
 possibility in an ecologically relevant host–pathogen system: house
 finches and their bacterial pathogen, Mycoplasma gallisepticum, which
 causes severe conjunctivitis. We examined behaviours likely to influence
 disease acquisition (feeder use, aggression, social network affiliations)
 in an observational field study, finding that the time an individual
 spends on bird feeders best predicted the risk of conjunctivitis. To test
 whether this behaviour also influences the likelihood of transmitting M.
 gallisepticum, we experimentally inoculated individuals based on feeding
 behaviour and tracked epidemics within captive flocks. As predicted,
 transmission was fastest when birds that spent the most time on feeders
 initiated the epidemic. Our results suggest that the same behaviour
 underlies both pathogen acquisition and transmission in this system and
 potentially others. Identifying individuals that exhibit such behaviours
 is critical for disease management.
description: Association Matrix for
 NetworksAssociation matrix used
 in social network analyses for wild PIT-tagged house
 finches.Adelman et al Association
 Matrix for Networks.csvFirst Transmission Event
 by Captive FlockTable of the first
 transmission event in each captive flock as defined by various pathology
 and pathogen load cutoffs.Adelman et al Captive First
 Transmission by Flock.csvCaptive Pathogen Load
 and Eye ScoresSampling data from
 captive transmission experiment, including eye scores (visible pathology)
 and pathogen load.Adelman et al Captive Pathogen
 Load Eye Scores.csvTime Spent on Feeder by
 Week - Captive ExperimentTime each individual
 house finch in our captive experiment spent on the feeder by
 week.Adelman et al Captive Time on
 Feeder by Week.csvDisease and RFID
 Behavior Data - Field StudyDisease status data and
 social behavior data gathered via radio-frequency identification for wild
 house finches included in the field study.Adelman et al Field Disease
 Data.csvEye Score vs. Pathogen
 Load - Field StudyEye scores (visible
 pathology) and pathogen loads for wild house finches included in the field
 study.Adelman et al Field Eye Score
 vs qPCR.csvGroup by Individual
 Matrix for Networks - Field StudyPresence/absence of each
 wild PIT-tagged house finch within foraging groups detected via
 radio-frequency identification.Adelman et al Group by
 Individual Matrix for Networks.csv
DOI: 10.5061/dryad.4km38
title: Data from: The effects of sexual selection on trait divergence in a peripheral population with gene flow

description: The unique aspects of speciation and divergence in peripheral populations
 have long sparked much research. Unidirectional migration, received by
 some peripheral populations, can hinder the evolution of distinct
 differences from their founding populations. Here we explore the effects
 that sexual selection, long hypothesized to drive the divergence of
 distinct traits used in mate choice, can play in the evolution of such
 traits in a partially isolated peripheral population. Using population
 genetic continent-island models, we show that with phenotype matching,
 sexual selection increases the frequency of an island-specific mating
 trait only when female preferences are of intermediate strength. We
 identify regions of preference strength for which sexual selection can
 instead cause an island-specific trait to be lost, even when it would have
 otherwise been maintained at migration-selection balance. When there are
 instead separate preference and trait loci, we find that sexual selection
 can lead to low trait frequencies or trait loss when female preferences
 are weak to intermediate, but that sexual selection can increase trait
 frequencies when preferences are strong. We also show that novel
 preference strengths almost universally cannot increase, under either
 mating mechanism, precluding the evolution of premating isolation in
 peripheral populations at the early stages of species divergence.
description: Supplementary
 Information File S1 - Trait divergence under the phenotype matching
 modelAnalyses of trait
 divergence under a continent-island phenotype matching model. Accompanies
 Appendices S1 and S2.Supplementary Information File
 S1.nbSupplementary
 Information File S2 - Trait divergence under the preference/trait
 modelAnalyses of trait
 divergence under a continent-island preference/trait model. Accompanies
 Appendix S4.Supplementary Information File
 S2.nbSupplementary
 Information File S3 - Trait divergence under the prefernece/trait model
 (continued)Analyses of trait
 divergence under a continent-island preference/trait model. Accompanies
 Appendix S3.Supplementary Information File
 S3.nbSupplementary
 Information File S4 - Evolution of preference strength under the phenotype
 matching modelAnalyses of the
 evolution of preference strength under a continent-island phenotype
 matching model. Accompanies Appendix S6.Supplementary Information File
 S4.nbSupplementary
 Information File S5 - Evolution of preference strength under the
 preference/trait modelAnalyses of the
 evolution of preference strength under a continent-island preference/trait
 model. Accompanies Appendix S7.Supplementary Information File
 S5.nb
DOI: 10.5061/dryad.n63m4
title: Data from: A database to enable discovery and design of piezoelectric materials

description: Piezoelectric materials are used in numerous applications requiring a
 coupling between electrical fields and mechanical strain. Despite the
 technological importance of this class of materials, for only a small
 fraction of all inorganic compounds which display compatible
 crystallographic symmetry, has piezoelectricity been characterized
 experimentally or computationally. In this work we employ first-principles
 calculations based on density functional perturbation theory to compute
 the piezoelectric tensors for nearly a thousand compounds, thereby
 increasing the available data for this property by more than an order of
 magnitude. The results are compared to select experimental data to
 establish the accuracy of the calculated properties. The details of the
 calculations are also presented, along with a description of the format of
 the database developed to make these computational results publicly
 available. In addition, the ways in which the database can be accessed and
 applied in materials development efforts are described.
description: A database to enable
 discovery and design of piezoelectric materialsThis JSON-file contains
 metadata pertaining to the compounds studied in this work and the
 associated calculated piezoelectric properties.piezo.json
DOI: 10.5281/zenodo.16897608
title: Data for Epstein-Barr Virus Orchestrates Spatial Reorganization and Immunomodulation within the classical Hodgkin Lymphoma Tumor Microenvironment

description: Here is a brief description of each data:



MIBI_data contains the MIBI proteomics image, segmentation masks, and the annotated proteomics dataframe. 

GeoMx_data contains the GeoMx proteomics image, segmentation masks, annotated proteomics dataframe, and transcriptomics count table.

CosMx_data contains the Seurat object used for all CosMx related analysis.

CODEX_data contains the CODEX proteomics image, segmentation masks, and the annotated proteomics dataframe. It also contains geojson files that can be opened together with the proteomics image in QuPath to simultaneously visualize both the multiplex image and the annotation of each cell.
DOI: 10.5061/dryad.6970v
title: Data from: The diverse fossil chelonians from Milia (Late Pliocene, Grevena, Greece) with a new species of Testudo Linnaeus, 1758 (Testudines: Testudinidae)

description: The late Pliocene (early Villafranchian, MN 16a) locality of Milia
 (Grevena, Greece) has yielded numerous remains of mammals, such as
 zygodons, mastodons, rhinocerotids, hipparions, bovids, cervids, suids,
 carnivorans and tapirs. Several specimens of chelonians have also been
 discovered and comprise a small testudinid, a geoemydid and a giant
 tortoise. The presence of a giant tortoise and the presence of a geoemydid
 with large dimensions are further examples of the trend towards gigantism
 evidenced by the diverse fauna of Milia. In terms of taxonomic abundance
 of extinct turtles, this is the richest locality in Greece. The small
 testudinid is of particular importance because it preserves a posteriorly
 flared carapace, as in the extant Testudo marginata, but the posterior
 carapace is much taller and anteroposteriorly shorter. These characters
 allow us to erect a new species, Testudo brevitesta sp. nov., and to
 discuss the presence of the marginated tortoise and closely related forms
 in Greece. The new taxon is analysed in a phylogenetic context within
 other extant and extinct testudinids, providing new information on the
 clade Testudona.
description: Description of specimens
 and definition of charactersThis document contains
 detailed descriptions of the specimens presented here and additional
 information on the definition of characters used in the phylogenetic
 analysis1_ONLINE
 SUPPL_R1.docxThe character/taxon
 matrix in TNT formatThis file contains the
 character/taxon matrix in TNT format.Matrix.txtConsensus tree of the constrained analysisThis file contains the consensus tree (in txt format) of the constrained analysis with the list of common synapomorphies.consensus.txt4 most parsimonious trees of the constrained analysisThis file contains the 4 most parsimonious trees (in txt format) of the constrained analysis with the list of common synapomorphies.Trees.zipStrict consensus tree of the unconstrained (A) and the constrained (B) analysisStrict consensus tree of the unconstrained (A) and the constrained (B) analysis. Extinct taxa are marked with an asterisk. See text for further details.Fig_Suppl-R1.tif
DOI: 10.5061/dryad.rm5dr
title: Data from: From ratites to rats: the size of fleshy fruits shapes species' distributions and continental rainforest assembly

description: Seed dispersal is a key process in plant spatial dynamics. However,
 consistently applicable generalisations about dispersal across scales are
 mostly absent because of the constraints on measuring propagule dispersal
 distances for many species. Here, we focus on fleshy-fruited taxa,
 specifically taxa with large fleshy fruits and their dispersers across an
 entire continental rainforest biome. We compare species-level results of
 whole-chloroplast DNA analyses in sister taxa with large and small fruits,
 to regional plot-based samples (310 plots), and whole of continent
 patterns for the distribution of woody species with either large
 (&gt;30mm) or smaller fleshy fruits (1093 taxa). The pairwise genomic
 comparison found higher genetic distances between populations and between
 regions in the large-fruited species (Endiandra globosa), but higher
 overall diversity within the small-fruited species (Endiandra discolor).
 Floristic comparisons among plots confirmed lower numbers of large-fruited
 species in areas where more extreme rainforest contraction occurred, and
 re-colonisation by small-fruited species readily dispersed by the
 available fauna. Species distribution patterns showed that larger-fruited
 species had smaller geographic ranges than smaller-fruited species and
 locations with stable refugia (and high endemism) aligned with
 concentrations of large fleshy-fruited taxa, making them a potentially
 valuable conservation-planning indicator.
description: Endiandra globosa and
 Endiandra discolour chloroplast genome and reads(1.) Folder contains
 chloroplast reads extracted from each population of Endiandra species
 studied. For example, “enddis BS” folder contains chloroplast reads for
 the E. discolour Big Scrub population. Abbreviations of the populations
 are explained in Figure 1 of the paper. (2.) The GenBank files contain
 partial chloroplast genomes of Endiandra globosa and E. discolour which
 were used in analysing within and among population genetic variation.
 Annotations are included.DryAd proceedings
 b.zip
DOI: 10.5061/dryad.c1jr3
title: Data from: Relationship between spectral characteristics of spontaneous postural sway and motion sickness susceptibility

description: Motion sickness (MS) usually occurs for a narrow band of frequencies of
 the imposed oscillation. It happens that this frequency band is close to
 that which are spontaneously produced by postural sway during natural
 stance. This study examined the relationship between reported
 susceptibility to motion sickness and postural control. The hypothesis is
 that the level of MS can be inferred from the shape of the Power Spectral
 Density (PSD) profile of spontaneous sway, as measured by the displacement
 of the center of mass during stationary, upright stance. In Experiment 1,
 postural fluctuations while standing quietly were related to MS history
 for inertial motion. In Experiment 2, postural stability measures
 registered before the onset of a visual roll movement were related to MS
 symptoms following the visual stimulation. Study of spectral
 characteristics in postural control showed differences in the distribution
 of energy along the power spectrum of the antero-posterior sway signal.
 Participants with MS history provoked by exposure to inertial motion
 showed a stronger contribution of the high frequency components of the
 sway signal. When MS was visually triggered, sick participants showed more
 postural sway in the low frequency range. The results suggest that
 subject-specific PSD details may be a predictor of the MS level.
 Furthermore, the analysis of the sway frequency spectrum provided insight
 into the intersubject differences in the use of postural control
 subsystems. The relationship observed between MS susceptibility and
 spontaneous posture is discussed in terms of postural sensory weighting
 and in relation to the nature of the provocative stimulus.
description: Raw posturographic and
 MS dataThis ZIP file contains
 the center of pressure (CoP) data and the MSSQ and SSQ scores for all
 subjects included in the study. For details, please see the file
 README.pdf contained in the ZIP file.posturography-ms-data.zip
DOI: 10.5061/dryad.sp698
title: Data from: Divergent effects of forest edges on host distribution and seed disperser activity influence mistletoe distribution and recruitment

description: 1. Species interactions define functional diversity and community
 stability across ecosystems, and depend on the spatial distribution, the
 habitat requirements, and the sensitivity to disturbances of all
 interacting partners. Hence, assessing the effects of such anthropogenic
 disturbances on multi-species interactions may be essential to improve
 adaptation and mitigation measures for biodiversity conservation. 2. We
 determined the importance of edge effects on the interaction and
 distribution of three keystone species in South American temperate
 rainforests: the hemiparasitic mistletoe Tristerix corymbosus, its main
 host (the liana Campsidium valdivianum) and its only seed disperser (the
 marsupial Dromiciops gliroides). 3. The discordant impacts of forest edges
 on host (positive) and seed disperser (negative) affected mistletoe
 distribution at large spatial scales, owing to the combined effects of
 increased dispersal limitation and decreased host availability. More
 importantly, marsupial abundance had contrasting effects on mistletoe
 abundance at small and large spatial scales – suggesting a potential
 trade-off between local and long-distance dispersal. 4. We found the
 number of adult mistletoes per host increased with host size, which likely
 indicates that mistletoe colonization accumulated over the host's
 life-span. However, the number of juveniles found per host peaked at
 medium-sized hosts, increased with marsupial abundance and host
 availability and showed a negligible response to edges. 5. Synthesis: The
 lack of spatial congruence between host and seed disperser probably
 explains the scarcity of mistletoes in the study area, although the
 discordant drivers of juvenile and adult distributions suggest that there
 is a trade-off between recruitment patterns but also potential dispersal
 limitation at small scales. In essence, the interdependence among species
 linked by (mutualistic and antagonistic) interactions makes them more
 sensitive to anthropogenic disturbance, exacerbating its impact on the
 diversity and functioning of forest ecosystems.
description: Magrach et al 2015
 Dataset
DOI: 10.5061/dryad.5st3t
title: Data from: Transcriptome dynamics of the stomatal lineage: birth, amplification, and termination of a self-renewing population

description: Developmental transitions can be described in terms of morphology and the
 roles of individual genes, but also in terms of global transcriptional and
 epigenetic changes. Temporal dissections of transcriptome changes,
 however, are rare for intact, developing tissues. We used RNA sequencing
 and microarray platforms to quantify gene expression from labeled cells
 isolated by fluorescence-activated cell sorting to generate
 cell-type-specific transcriptomes during development of an adult stem-cell
 lineage in the Arabidopsis leaf. We show that regulatory modules in this
 early lineage link cell types that had previously been considered to be
 under separate control and provide evidence for recruitment of individual
 members of gene families for different developmental decisions. Because
 stomata are physiologically important and because stomatal lineage cells
 exhibit exemplary division, cell fate, and cell signaling behaviors, this
 dataset serves as a valuable resource for further investigations of
 fundamental developmental processes.
description: Table S1. Expression
 Dataset and Clustering Results of FACS-Isolated Stomatal Lineage Cells
 using RNA-seqExcel file (multiple
 tabs) containing information about gene expression of multiple stomatal
 lineage cell types. Files columns have notes explaining data
 within.mmc2.xlsxTable S3. Expression Dataset and Clustering Results of FACS-Isolated Stomatal Lineage Cells using ATH1 MicroarraysExcel file similar to Table S1, but using Ath1 microarraysmmc4.xlsx
DOI: 10.5061/dryad.n85m5
title: Data from: Plastid genome sequences of legumes reveal parallel inversions and multiple losses of rps16 in papilionoids

description: To date, publicly available plastid genomes of legumes have for the most
 part been limited to the subfamily Papilionoideae. Here we report 13 new
 plastid genomes of legumes spanning all three subfamilies. The genomes
 representing Caesalpinioideae and Mimosoideae are highly conserved in gene
 content and gene order, similar to the ancestral angiosperm genome
 organization. Genomes within the Papilionoideae, however, have reduced
 sizes due to deletions in nine intergenic spacers primarily in the large
 single copy region. Our study also indicates that rps16 has been
 independently lost at least five times in legumes, with additional gene
 and intron losses scattered among the papilionoids. Additionally, genera
 from two distinct lineages within the papilionoids, Lupinus and Robinia,
 have a parallel inversion of 36 kb and 39 kb, respectively. This parallel
 inversion is novel as it appears to be caused by a 29 bp repeat within two
 trnS genes. This repeat is present in all available legume plastid genomes
 indicating that there is the potential for this inversion to be present in
 more species. This case of a homoplasious inversion is also evidence that
 some inversion events may not be reliable phylogenetic markers.
description: Legume plastid gene
 alignmentA 71 plastid gene
 alignment including 36 species of legumes. Phylip
 format.Fabaceae_36spp.phy
DOI: 10.5061/dryad.22f52
title: Data from: The kinetochore prevents centromere-proximal crossover recombination during meiosis

description: During meiosis, crossover recombination is essential to link homologous
 chromosomes and drive 22 faithful chromosome segregation. Crossover
 recombination is non-random across the genome, 23 and centromere-proximal
 crossovers are associated with an increased risk of aneuploidy, 24
 including Trisomy 21 in humans. Here, we identify the conserved Ctf19/CCAN
 kinetochore sub- 25 complex as a major factor that minimizes potentially
 deleterious centromere-proximal crossovers 26 in budding yeast. We uncover
 multi-layered suppression of pericentromeric recombination by the 27 Ctf19
 complex, operating across distinct chromosomal distances. The Ctf19
 complex prevents 28 meiotic DNA break formation, the initiating event of
 recombination, proximal to the centromere. 29 The Ctf19 complex
 independently drives the enrichment of cohesin throughout the broader 30
 pericentromere to suppress crossovers, but not DNA breaks. This
 non-canonical role of the 31 kinetochore in defining a chromosome domain
 that is refractory to crossovers adds a new layer 32 of functionality by
 which the kinetochore prevents the incidence of chromosome segregation 33
 errors that generate aneuploid gametes.
description: eLife_Dryad_Recombine_dataanalysis files from the Recombine software for clb2-iml3 tetrads
DOI: 10.5061/dryad.4c0s0
title: Data from: Concurrent effects of cold and hyperkalaemia cause insect chilling injury

description: Chilling injury and death are the ultimate consequence of low temperature
 exposure for chill susceptible insects, and low temperature tolerance is
 considered one of the most important factors determining insect
 distribution patterns. The physiological mechanisms that cause chilling
 injury are unknown, but chronic cold exposure that causes injury is
 consistently associated with elevated extracellular [K+], and cold
 tolerant insects possess a greater capacity to maintain ion balance at low
 temperatures. Here, we use the muscle tissue of the migratory locust
 (Locusta migratoria) to examine whether chill injury occurs during cold
 exposure or following return to benign temperature and we specifically
 examine if elevated extracellular [K+], low temperature, or a combination
 thereof causes cell death. We find that in vivo chill injury occurs during
 the cold exposure (when extracellular [K+] is high) and that there is
 limited capacity for repair immediately following the cold stress.
 Further, we demonstrate that that high extracellular [K+] causes cell
 death in situ, but only when experienced at low temperatures. These
 findings strongly suggest that that the ability to maintain ion
 (particularly K+) balance is critical to insect low temperature survival,
 and highlight novel routes of study in the mechanisms regulating cell
 death in insects in the cold.
description: locust.hemolymph.ionsLocust hemolymph K+ concentration dataChill coma recovery time datalocust.ccrt.csvlocust.surv.scoresLocust survival score datamuscle.damage.insitu.finalLocust in situ muscle damage datamuscle.damage.invivo.finalLocust in vivo muscle damage datain.situ.imagesMuscle tissue damage images from in situ experimentin.vivo.muscle.imagesImages from in vivo muscle damage experiment