cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.80mb4
title: Data from: Age and sex affect quantitative genetic parameters for dominance rank and aggression in free-living greylag geese

description: Knowledge of the genetic and environmental influences on a character is
 pivotal for understanding evolutionary changes in quantitative traits in
 natural populations. Dominance and aggression are ubiquitous traits that
 are selectively advantageous in many animal societies and have the
 potential to impact the evolutionary trajectory of animal populations.
 Here we provide age- and sex-specific estimates of additive genetic and
 environmental components of variance for dominance rank and aggression
 rate in a free-living, human-habituated bird population subject to natural
 selection. We use a long-term data set on individually marked greylag
 geese (Anser anser) and show that phenotypic variation in
 dominance-related behaviours contains significant additive genetic
 variance, parental effects and permanent environment effects. The relative
 importance of these variance components varied between age and sex
 classes, whereby the most pronounced differences concerned non-genetic
 components. In particular, parental effects were larger in juveniles of
 both sexes than in adults. In paired adults, the partner's identity
 had a larger influence on male dominance rank and aggression rate than in
 females. In sex- and age-specific estimates, heritabilities did not differ
 significantly between age and sex classes. Adult dominance rank was only
 weakly genetically correlated between the sexes, leading to considerably
 higher heritabilities in sex-specific estimates than across sexes. We
 discuss these patterns in relation to selection acting on dominance rank
 and aggression in different life history stages and sexes and suggest that
 different adaptive optima could be a mechanism for maintaining genetic
 variation in dominance-related traits in free-living animal populations.
description: pedigreecontains pedigree informationdominance_allcontains data on dominance rank and aggression rates in greylag geese of all ages and all relevant fixed and random effects (see read_me.txt)dominance_juvenilescontains data on dominance rank and aggression rates in juvenile greylag geese and all relevant fixed and random effects (see read_me.txt)dominance_pairscontains data on dominance rank and aggression rates in adult, paired greylag geese and all relevant fixed and random effects (see read_me.txt)dominance_4traitcontains data on dominance rank and aggression rates in juvenile and paired adult male and female greylag geese and all relevant fixed and random effects (see read_me.txt)
DOI: 10.5061/dryad.jt48n1c
title: Data from: Miniaturisation of biologgers is not alleviating the 5% rule

description: 1. The use of biologging technology has increased exponentially over the
 last decade, allowing us to study animal behaviour at a level of detail
 not previously possible. 2. It is clear from recent meta-analyses that the
 attachment of such devices can have negative effects on individual
 animals, particularly their behaviour and physiology. In recognition of
 this, a commonly applied rule is to ensure that devices borne by flying
 animals weigh less than 5% of their body mass. Over time, the continuing
 miniaturization of devices should facilitate the deployment of devices
 that are an ever-decreasing fraction of animal mass. 3. Despite these
 considerations regarding device mass, here we show that there has been no
 apparent reduction in the relationship between body mass and the mass of
 logging devices over the last 44 years. 4. Using a meta-analytical
 approach, we demonstrate that the ongoing miniaturization of animal-borne
 devices has resulted not in a decrease in the relative device mass borne
 by animals, but instead has prompted researchers to measure smaller and
 smaller species. 5. We recommend that researchers better exploit the
 ongoing miniaturization of devices to reduce the relative mass of the
 devices borne by animals.
description: Portugal and White MEE
 Table S1The full species, body
 masses, year of logger deployment and body mass of all data used in the
 study, with all associated references.
DOI: 10.5061/dryad.nh53j
title: Data from: Genotype-by-environment interactions for cuticular hydrocarbon expression in Drosophila simulans

description: Genotype-by-environment interactions (G x Es) describe genetic variation
 for phenotypic plasticity. Recent interest in the role of these
 interactions in sexual selection has identified G x Es across a diverse
 range of species and sexual traits. Additionally, theoretical work
 predicts that G x Es in sexual traits could help to maintain genetic
 variation, but could also disrupt the reliability of these traits as
 signals of mate quality. However, empirical tests of these theoretical
 predictions are scarce. We reared iso-female lines of Drosophila simulans
 across two axes of environmental variation (diet and temperature) in a
 fully factorial design and tested for G x Es in the expression of
 cuticular hydrocarbons (CHCs), a multivariate sexual trait in this
 species. We find sex-specific environmental, genetic and G x E effects on
 CHC expression, with G x Es for diet in both male and female CHC profile
 and a G x E for temperature in females. We also find some evidence for
 ecological crossover in these G x Es, and by quantifying variance
 components, genetic correlations and heritabilities, we show the potential
 for these G x Es to help maintain genetic variation and cause sexual
 signal unreliability in D. simulans CHC profiles.
description: dryad
DOI: 10.5061/dryad.06ds7
title: Data from: Automatic recognition of self-acknowledged limitations in clinical research literature

description: Objective: To automatically recognize self-acknowledged limitations in
 clinical research publications to support efforts in improving research
 transparency. Materials and Methods: To develop our recognition methods,
 we used a set of 8,431 sentences from 1,197 PubMed Central articles. A
 subset of these sentences was manually annotated for training/testing and
 inter-annotator agreement was calculated. We cast the recognition problem
 as a binary classification task, in which we determine whether a given
 sentence from a publication discusses self-acknowledged limitations or
 not. We experimented with three methods: a rule-based approach based on
 document structure, supervised machine learning, and a semi-supervised
 method that uses self-training to expand the training set in order to
 improve classification performance. The machine learning algorithms used
 were logistic regression (LR) and support vector machines (SVM). Results:
 Annotators had good agreement in labeling limitation sentences
 (Krippendorff’s α=0.781). Of the three methods used, the rule-based method
 yielded the best performance with 91.5% accuracy (95% CI [90.1-92.9]),
 while self-training with SVM led to a small improvement over fully
 supervised learning (89.9%, 95% CI [88.4-91.4] vs. 89.6%, 95% CI
 [88.1-91.1]). Discussion: We attribute the effectiveness of the rule-based
 method to the highly localized and formulaic language used in reporting of
 limitations in clinical research publications. Experiments with training
 size and composition show that more data does not necessarily lead to
 higher accuracy in the machine learning-based approaches. Conclusion: The
 approach presented can be incorporated into the workflows of stakeholders
 focusing on research transparency to improve reporting of limitations in
 clinical studies.
description: Limitation Dataset
 version 2A dataset of sentences
 from clinical studies annotated for whether the sentence reports a
 self-acknowledged limitation or not.Limitation_Dataset_v2.xlsx
DOI: 10.5061/dryad.9540r
title: Data from: The timing of molecular and morphological changes underlying reproductive transitions in wild tomatoes (Solanum sect. Lycopersicon)

description: Molecular mechanisms underlying the transition from genetic
 self-incompatibility to self-compatibility are well documented, but the
 evolution of other reproductive trait changes that accompany shifts in
 reproductive strategy (mating system) remain comparatively poorly
 understood. A notable exception is the transition from exserted styles to
 styles with recessed positions relative to the anthers in wild tomatoes
 (Solanum Section Lycopersicon). This phenotypic change has been previously
 attributed to specific mutation in the promoter of a gene that influences
 style length (style2.1); however, whether this specific regulatory
 mutation arose concurrently with the transition from long- to
 short-styles, and whether it is causally responsible for this phenotypic
 transition, has been poorly investigated across this group. To address
 this gap, we assessed 74 accessions (populations) from 13 species for
 quantitative genetic variation in floral and reproductive traits as well
 as the presence/absence of deletions at two different locations (StyleD1,
 StyleD2) within the regulatory region upstream of style2.1. We confirmed
 that the putatively causal deletion variant (a 450bp deletion at StyleD1)
 arose within self-compatible lineages. However the variation and history
 of both StyleD1 and StyleD2 was more complex than previously inferred. In
 particular, although StyleD1 was statistically associated with differences
 in style length and stigma exsertion across all species, we found no
 evidence for this association within two species polymorphic for the
 StyleD1 mutation. We conclude that the previous association detected
 between phenotypic and molecular differences is most likely due to a
 phylogenetic association rather than a causal mechanistic relationship.
 Phenotypic variation in style length must therefore be due to other
 unexamined linked variants in the style2.1 regulatory region.
description: AllPlantDataStyle2_1Trait values and genotypes for individual experimental plantsAlignedContig_StyleD1&D2withBACsText file with StyleD1 and StyleD2 sequences aligned to S. lycopersicum and S. pennellii BACs, and coding sequences for S. lycopersicum loci L02 and L04AlignedContig_StyleD1&D2withBAC
DOI: 10.25345/c5n58d05j
title: MassIVE MSV000100595 - Endosidin2 Treatment on Differentiated SHSY5Y cells
title: Quantitative analysis of changes in biotinylated cell surface protein expression in SH-SY5Y cells in response to Endosidin-2 treatment. There are 2 experimental conditions (control (UN), treated (ES)) with 4 replicates of each (Samples 01-08). Surface proteins were biotinylated and isolated with Pierce purification kit, precipitated from elution buffer and then resuspended in RIPA.
DOI: 10.5061/dryad.bn249
title: Data from: Relationship between effective population size, inbreeding, and adult fitness-related traits in a steelhead (Oncorhynchus mykiss) population released in the wild

description: Inbreeding is of concern in supportive breeding programmes in Pacific
 salmonids, Oncorhynchus spp, where the number of breeding adults is
 limited by rearing space or poor survival to adulthood, and large numbers
 are released to supplement wild stocks and fisheries. We reconstructed the
 pedigree of 6602 migratory hatchery steelhead (Oncorhynchus mykiss) over
 four generations, to determine the incidence and fitness consequences of
 inbreeding in a northwest USA programme. The hatchery maintained an
 effective population size, = 107.9 from F0 to F2, despite an increasing
 census size (N), which resulted in a decreasing Ne/N ratio (0.35 in F0 to
 0.08 in F2). The reduced ratio was attributed to a small broodstock size,
 nonrandom transfers and high variance in reproductive success
 (particularly in males). We observed accumulation of inbreeding from the
 founder generation (in F4, percentage individuals with inbreeding
 coefficients Δf &gt; 0 = 15.7%). Generalized linear mixed models
 showed that body length and weight decreased significantly with increasing
 Δf, and inbred fish returned later to spawn in a model that included
 father identity. However, there was no significant correlation between Δf
 and age at return, female fecundity or gonad weight. Similarly, there was
 no relationship between Δf and reproductive success of F2 and F3
 individuals, which might be explained by the fact that reproductive
 success is partially controlled by hatchery mating protocols. This study
 is one of the first to show that small changes in inbreeding coefficient
 can affect some fitness-related traits in a monitored population
 propagated and released to the wild.
description: MEC-12-0879_DRYAD_dataGenotypes at 8 microsatellite loci for adult hatchery steelhead from Forks Creek Hatchery, Washington State, USA. Visualized on a MegaBACE 1000 and scored using their proprietary software.MEC-12-0879_DRYAD_phenotype_dataPhenotypic data and non-genetic data used for parentage analysis.
DOI: 10.5061/dryad.n8bm9
title: Data from: Mutualism persistence and abandonment during the evolution of the mycorrhizal symbiosis

description: Mutualistic symbioses with mycorrhizal fungi are widespread in plants. The
 majority of plant species associate with arbuscular mycorrhizal (AM)
 fungi. By contrast, the minority associate with ectomycorrhizal (EM)
 fungi, have abandoned the symbiosis and are nonmycorrhizal (NM), or engage
 in an intermediate, weakly AM symbiosis (AMNM). To understand the
 processes that maintain the mycorrhizal symbiosis or cause its loss, we
 reconstructed its evolution using a ∼3,000-species seed plant phylogeny
 integrated with mycorrhizal state information. Reconstruction indicated
 that the common ancestor of seed plants most likely associated with AM
 fungi and that the EM, NM, and AMNM states descended from the AM state.
 Direct transitions from the AM state to the EM and NM states were
 infrequent and generally irreversible, implying that natural selection or
 genetic constraint could promote stasis once a particular state evolved.
 However, the evolution of the NM state was more frequent via an indirect
 pathway through the AMNM state, suggesting that weakening of the AM
 symbiosis is a necessary precursor to mutualism abandonment. Nevertheless,
 reversions from the AMNM state back to the AM state were an order of
 magnitude more likely than transitions to the NM state, suggesting that
 natural selection favors the AM symbiosis over mutualism abandonment.
description: Mycorrhizal state
 information for reconstruction of the mycorrhizal symbiosis in seed
 plants.The data file consists
 for 4 spreadsheet tabs: Table A1: A list of species records for
 mycorrhizal state from literature sources. Scrubbed names represent
 records from the taxonomic name resolution service (TNRS). Citations for
 each source are provided in the main manuscript. Published records that
 contained mutiple observations are indicated by multiple state identifiers
 (i.e., AM AM EM). Table A2: Species level list of mycorrhizal states
 derived from Table A1. Table A3: For those species that matched the Zanne
 et al. (2013) phylogeny, the number of literature observations for the
 state of each species is indicated, along with the consensus state used in
 the analysis. Table A4: The final list of species matched with the
 phylogeny, along with the consensus mycorrhizal state.Maherali.etal.AmNat.Data.xlsx
DOI: 10.5061/dryad.v01gs40
title: Data from: Conserved but flexible modularity in the zebrafish skull: implications for craniofacial evolvability

description: Morphological variation is the outward manifestation of development and
 provides fodder for adaptive evolution. Because of this contingency,
 evolution is often thought to be biased by developmental processes and
 functional interactions among structures, which are statistically
 detectable through forms of covariance among traits. This can take the
 form of substructures of integrated traits, termed modules, which together
 comprise patterns of variational modularity. While modularity is essential
 to an understanding of evolutionary potential, biologists currently have
 little understanding of its genetic basis, nor its temporal dynamics over
 generations. To address these open questions we compared patterns of
 craniofacial modularity among laboratory strains, defined mutant lines and
 a wild population of zebrafish (Danio rerio). Our findings suggest that
 relatively simple genetic changes can have profound effects on covariance,
 without greatly affecting craniofacial shape. Moreover, we show that
 instead of completely deconstructing the covariance structure among sets
 of traits, mutations cause shifts among seemingly latent patterns of
 modularity suggesting that the skull may be predisposed toward a limited
 number of phenotypes. This new insight may serve to greatly increase the
 evolvability of a population by providing a range of 'preset'
 patterns of modularity that can appear readily and allow for rapid
 evolution.
description: AB
 linexy coordinate
 dataABxy.txtALFxyALF coordinate dataLA022xyLA022 or btm mutant xy coordinate dataTL xyTL coordinate dataTUWTxytuebigen wild type coordinate datawild_zebrasxy coordinates for wild zebrafish
DOI: 10.5061/dryad.fg32t
title: Data from: Androgenesis is a maternal trait in the invasive ant Wasmannia auropunctata

description: Androgenesis is the production of an offspring containing exclusively the
 nuclear genome of the fathering male, via the maternal eggs. This unusual
 mating system is generally considered as a male trait, giving to
 androgenetic males a substantial fitness advantage over their sexually
 reproducing relatives. We here provide the first empirical study of the
 evolutionary outcomes of androgenesis in a haplo-diploid organism: the
 invasive ant Wasmannia auropunctata. Some of the populations of this
 species have a classical haplo-diploid sexual mating system. In other
 populations, females and males are produced through parthenogenesis and
 androgenesis, respectively, whereas workers are produced sexually. We
 conducted laboratory reciprocal-cross experiments with reproductive
 individuals from both types of populations and analyzed their progenies
 with genetic markers, to determine the respective contribution of males
 and females on the production of androgenetic males. We found that
 androgenesis was a parthenogenetic female trait. A population genetic
 study conducted in natura confirmed the parthenogenetic female origin of
 androgenesis, with the identification of introgression events of sexual
 male genotypes into androgenetic/parthenogenetic lineages. We argue that
 by producing males via androgenesis, parthenogenetic queen lineages may
 increase and/or maintain their adaptive potential, whilst maintaining the
 integrity of their own genome, by occasionally acquiring new male genetic
 material and avoiding inbreeding depression within the sexually produced
 worker cast.
description: microsatellite dataset
 from laboratory reciprocal-cross experimentsMsat-Data_crosses.xls
DOI: 10.15468/dl.dqgxa9
title: Occurrence Download

description: A dataset containing 270624 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Observation, Human Observation, Specimen)",
 "Geometry POLYGON((-143.09 59.19,-95.32 59.19,-95.32 71.49,-143.09 71.49,-143.09 59.19))",
 "HasCoordinate is true",
 "License is one of (CC-BY-NC 4.0, CC-BY 4.0, CC0 1.0)",
 "OccurrenceStatus is Present",
 "TaxonKey is Plantae"
 ]
}

 The dataset includes 270624 records from 275 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000415-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.22h7c
title: Data from: Primary Sjogren’s syndrome and the risk of acute pancreatitis: a nationwide cohort study

description: Objective Studies on the risk of acute pancreatitis in patients with
 primary Sjogren’s syndrome (pSS) are limited. We evaluated the effects of
 pSS on the risk of acute pancreatitis in a nationwide, population-based
 cohort in Taiwan. Study design Population-based retrospective cohort
 study. Setting We studied the claims data of the &gt;97% Taiwan
 population from 2002 to 2012. Participants We identified 9468 patients
 with pSS by using the catastrophic illness registry of the National Health
 Insurance Database in Taiwan. We also selected 37 872 controls that were
 randomly frequency matched by age (in 5 year bands), sex and index year
 from the general population. Primary outcome measure We analysed the risk
 of acute pancreatitis by using Cox proportional hazards regression models
 including sex, age and comorbidities. Results From 23.74 million people in
 the cohort, 9468 patients with pSS (87% women, mean age=55.6 years) and
 37 872 controls were followed-up for 4.64 and 4.74 years, respectively. A
 total of 44 cases of acute pancreatitis were identified in the pSS cohort
 versus 105 cases in the non-pSS cohort. Multivariate Cox regression
 analysis indicated that the incidence rate of acute pancreatitis was
 significantly higher in the pSS cohort than in the non-pSS cohort
 (adjusted HR (aHR) 1.48, 95% CI 1.03 to 2.12). Cyclophosphamide use
 increased the risk of acute pancreatitis (aHR 5.27, 95% CI 1.16 to 23.86).
 By contrast, hydroxychloroquine reduced the risk of acute pancreatitis
 (aHR 0.23, 95% CI 0.09 to 0.55). Conclusion This nationwide, retrospective
 cohort study demonstrated that the risk of acute pancreatitis was
 significantly higher in patients with pSS than in the general population.
description: 2017 -pSS and acute
 pancreatitis2017
 -Hydrad.pdf
DOI: 10.7910/dvn/qcvosf
title: FireGate Biotech FG-001: In Silico Systems Analysis Supporting Triplet Mechanistic Complementarity

description: We performed an in silico systems-level functional association and enrichment analysis using the STRING database to assess whether a curated FG-001 Triplet axis gene/protein set forms a coherent non-random antiviral immune network. The analysis demonstrates highly signifi-cant protein–protein interaction enrichment and strong overrepresentation of antiviral response, interferon-associated innate immunity, and chemokine-mediated trafficking programs.



Non-clinical / non-human-subjects: This dataset contains only in silico analyses and database-derived outputs. No clinical trial data, patient-level data, or PHI are included.
Related record: Associated figure/report archived on Zenodo 
https://doi.org/10.5281/zenodo.18355853
description: Dataset includes STRING exports (interaction network tables, annotations, and enrichment outputs) used to generate figures for FG-001 Triplet axis systems analysis. Files are provided for transparency and reproducibility.