cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.gn5c8
title: Data from: Observational study of hemostatic dysfunction and bleeding in neonates with hypoxic-ischemic encephalopathy

description: Objective: Evaluate the relationship between initial haemostatic
 parameters and the frequency and severity of bleeding in neonates with
 hypoxic–ischaemic encephalopathy (HIE). Design: Retrospective
 observational cohort study. Setting: 2 academically affiliated level III
 neonatal intensive care units in Atlanta, Georgia. Participants: 98
 neonates with moderate-to-severe HIE who underwent haemostatic testing
 within 12 hours of birth and were born from 1 January 2008 to 31 December
 2013. Primary and secondary outcome measures: Initial haemostatic
 dysfunction was defined as one or more of the following: prothrombin time
 (PT) ≥18 s, platelet count &lt;100×103/μL or fibrinogen
 &lt;150 mg/dL. Bleeding assessed using the Neonatal Bleeding
 Assessment Tool and graded according to the WHO bleeding scale. The robust
 Poisson regression was used to evaluate the independent association
 between components of initial haemostatic dysfunction and bleeding.
 Results: Among the 98 neonates evaluated, the prevalence of initial
 haemostatic dysfunction was 69% (95% CI 59% to 78%). 27 neonates (28%; 95%
 CI 19% to 38%) had abnormal bleeding events and 56 (57%) received at least
 1 blood product transfusion. 3 neonates died from bleeding complications.
 The most common products transfused were fresh-frozen plasma (71%),
 followed by packed red blood cells (24%) and platelets (21%). In
 multivariable analysis, fibrinogen &lt;150 mg/dL (adjusted relative
 risk 2.41, 95% CI 1.09 to 5.36) and platelet count &lt;100×103/μL
 (adjusted relative risk 2.59, 95% CI 1.30 to 5.16), but not initial PT,
 were associated with an increased risk of bleeding. The most severe
 bleeding occurred in neonates with a fibrinogen &lt;150 mg/dL.
 Conclusions: Among neonates with moderate-to-severe HIE, haemostatic
 dysfunction is prevalent and associated with an increased risk of bleeding
 and high transfusion burden. Further studies are needed to determine the
 appropriate transfusion approaches in this population to prevent bleeding.
description: DatasetThe dataset file contains the fully de-identified study dataset. The first tab contains important information regarding the dataset. The second tab contains the variable dictionary. The final two tabs contain de-identified study data with variables unlabeled (coded) and labelled.
DOI: 10.5061/dryad.t7kp7
title: Data from: Comparison of T2*-weighted and QSM contrasts in Parkinson's disease to visualize the STN with MRI

description: The subthalamic nucleus (STN) plays a crucial role in the surgical
 treatment of Parkinson's disease (PD). Studies investigating optimal
 protocols for STN visualization using state of the art magnetic resonance
 imaging (MRI) techniques have shown that susceptibility weighted images,
 which display the magnetic susceptibility distribution, yield better
 results than T1-weighted, T2-weighted, and T2*-weighted contrasts.
 However, these findings are based on young healthy individuals, and
 require validation in elderly individuals and persons suffering from PD.
 Using 7T MRI, the present study set out to investigate which MRI contrasts
 yielded the best results for STN visualization in 12 PD patients and
 age-matched healthy controls (HC). We found that STNs were more difficult
 to delineate in PD as reflected by a lower inter-rater agreement when
 compared to HCs. No STN size differences were observed between the groups.
 Analyses of quantitative susceptibility mapping (QSM) images showed a
 higher inter-rater agreement reflected by increased Dice-coefficients. The
 location of the center of mass of the STN was not affected by contrast.
 Overall, contrast-to-noise ratios (CNR) were higher in QSM than in
 T2*-weighted images. This can at least partially, explain the higher
 inter-rater agreement in QSM. The current results indicate that the
 calculation of QSM contrasts contributes to an improved visualization of
 the entire STN. We conclude that QSM contrast is the preferred choice for
 the visualization of the STN in persons with PD as well as in aging HC.
description: STN probability
 atlasThis atlas takes
 advantage of ultra-high resolution 7T MRI to provide unprecedented levels
 of detail on structures of the basal ganglia in-vivo. The atlas includes a
 disease-specific probability map of the subthalamic Nucleus based on
 Parkinson's Disease patients. The atlas is based either on QSM or
 T2*-weighted structural scans.STN_pd_plosone_atlas.zip
DOI: 10.5061/dryad.b0k20
title: Data from: Female MHC type affects male testosterone levels and sperm number in the horse (Equus caballus)

description: Odours of vertebrates often contain information about the major
 histocompatibility complex (MHC), and are used in kin recognition, mate
 choice or female investment in pregnancy. It is, however, still unclear
 whether MHC-linked signals can also affect male reproductive strategies.
 We used horses (Equus caballus) to study this question under experimental
 conditions. Twelve stallions were individually exposed either to an
 unfamiliar MHC-similar mare and then to an unfamiliar MHC-dissimilar mare,
 or vice versa. Each exposure lasted over a period of four weeks.
 Peripheral blood testosterone levels were determined weekly. Three
 ejaculates each were collected in the week after exposure to both mares
 (i.e. in the ninth week) to determine mean sperm number and sperm
 velocity. We found high testosterone levels when stallions were kept close
 to MHC-dissimilar mares and significantly lower ones when kept close to
 MHC-similar mares. Mean sperm number per ejaculate (but not sperm
 velocity) was positively correlated to mean testosterone levels and also
 affected by the order of presentation of mares: sperm numbers were higher
 if MHC-dissimilar mares were presented last than if MHC-similar mares were
 presented last. We conclude that MHC-linked signals influence testosterone
 secretion and semen characteristics, two indicators of male reproductive
 strategies.
description: Data Burger et al.
 ProcB"sim" = MHC
 similar; "dissim" = MHC dissimilar; "Testost" =
 peripheral testosterone blood level; "µ" = mean; "ELA"
 = MHC antigens of horses; "VSL", "VCL", and
 "VAP" = sperm velocity measures
DOI: 10.5061/dryad.c5v81v1
title: Data from: Marginal sinks or potential refuges? Costs and benefits for coral-obligate reef fishes at deep range margins

description: Escalating climate-related disturbances and asymmetric habitat losses will
 increasingly result in species living in more marginal habitats. Marginal
 habitats may represent important refuges if individuals can acquire
 adequate resources to survive and reproduce. However, resources at range
 margins are often distributed more sparsely; therefore increased effort to
 acquire resources can result in sub-optimal performance and lead to
 marginal populations becoming non-self-sustaining sink-populations.
 Shifting resource availability is likely to be particularly problematic
 for dietary specialists. Here, we use extensive in-situ behavioural
 observations and physiological condition measurements to examine the costs
 and benefits of resource-acquisition along a depth-gradient in two
 obligate corallivore reef fishes with contrasting levels of dietary
 specialisiation. As expected, the space utilised to secure coral-resources
 increased towards the lower depth margin. However, increased territory
 sizes resulted in equal or greater availability of resources within deeper
 territories. In addition, we observed decreased competition and no
 differences in foraging-distance, pairing-behaviour, body condition or
 fecundity at greater depths. Contrary to expectation, our results
 demonstrate that coral-obligate fishes can select high-quality coral
 patches on the deeper-reef to access equal or greater resources than their
 shallow-water counterparts, with no extra costs. This suggests depth
 offers a viable potential refuge for some at-risk coral-specialist fishes.
description: Chaetodon Territiorial
 Ecolology Data Along a Depth GradientDepth stratified data of
 the size, position and resource availability of territories, and
 territorial maintenance behaviours of two species of Chaetodon butterfly
 fishes.ChaetTerEcolDepthData.csvChaetodon Body Condition Along a Depth GradientBody Condition metrics for two Chaetodon species along a coral reef depth gradient.ChaetDepthBodCond.csv
DOI: 10.5061/dryad.k14f4
title: Data from: The peril of proportions: robust niche indices for categorical data

description: Indices of niche breadth and niche overlap for categorical data are
 typically expressed in terms of proportions of resources use. These are
 unit-sum constrained data; hence, direct application of standard general
 linear modelling methods to such indices can lead to spurious correlations
 and misleading inference. To overcome these limitations, we introduce a
 compositional data analysis (CoDA) approach and derive compositional
 expressions of niche breadth, niche overlap and specialization.
 Compositional data analysis is specifically devoted to the analysis of
 vectors of proportions (i.e. compositions) and represents the appropriate
 framework for the study of sets of data with unit-sum constraint as those
 typically used in the calculation of niche indices. We show that
 compositional indices exhibit suitable statistical properties that make
 them flexible and robust, allowing downstream application of the full
 toolbox of multivariate analysis techniques to these estimators, a
 possibility not available with classical indices. In addition, we find
 that when characterizing niche breadth, niche overlap and specialization
 in terms of vectors of proportions, these concepts are naturally
 integrated in a coherent unifying framework. When data are categorical, we
 recommend the use of compositional indices for the statistical analysis of
 specialization metrics, niche breadth and niche overlap. We believe that
 the unified framework emerging from our compositional approach to niche
 metrics will allow a more thorough understanding of specialization at
 multiple levels of biological organization and provide novel insights in
 complex phenomena such as invasions and niche shifts.
description: Gracilinanus_microtarsus_dietDiet data of the gracile mouse opossum Gracilinanus microtarsus from Araujo et al. (2010), Oikos 119: 81-88, kindly provided by Dr Mauricio Araujo to Pierotti, Martin-Fernandez & Barcelo-Vidal for the simulations performed in this paper.Gracilinanus_microtarsus.xlsx
DOI: 10.5061/dryad.77843
title: Data from: Persistence of antibiotic resistance plasmids in bacterial biofilms

description: The emergence and spread of antibiotic resistance is a crisis in health
 care today. Antibiotic resistance is often horizontally transferred to
 susceptible bacteria by means of multi-drug resistance plasmids that may
 or may not persist in the absence of antibiotics. Because bacterial
 pathogens often grow as biofilms, there is a need to better understand the
 evolution of plasmid persistence in these environments. Here we compared
 the evolution of plasmid persistence in the pathogen Acinetobacter
 baumannii when grown under antibiotic selection in biofilms versus
 well-mixed liquid cultures. After four weeks, clones in which the plasmid
 was more stably maintained in the absence of antibiotic selection were
 present in both populations. On average plasmid persistence increased more
 in liquid batch cultures, but variation in the degree of persistence was
 greater among biofilm-derived clones. The results of this study show for
 the first time that the persistence of MDR plasmids improves in biofilms
description: qPCR Estimates of trfA
 and 16S rRNA concentrationsThe data provided are
 the estimates that resulted from raw qPCR fluorescence data (available
 upon request). The data are those used in the analyses described in the
 associated manuscript. See the ReadMe file for column
 descriptions.evolAppData.csv
DOI: 10.5061/dryad.14mt6
title: Data from: Parasite infection induces size-dependent host dispersal: consequences for parasite persistence

description: Host dispersal is now recognized as a key predictor of the landscape-level
 persistence and expansion of parasites. However, current theories treat
 post-infection dispersal propensities as a fixed trait, and the plastic
 nature of host’s responses to parasite infection has long been
 underappreciated. Here, we present a mark-recapture experiment in a
 single-host parasite system (larval parasites of the freshwater mussel
 Margaritifera laevis and its salmonid fish host Oncorhynchus masou masou)
 and provide the first empirical evidence that parasite infection induces
 size-dependent host dispersal in the field. In response to parasite
 infection, large fish become more dispersive, whereas small fish tend to
 stay at the home patch. The observed plasticity in dispersal is
 interpretable from the viewpoint of host fitness: expected benefits
 (release from further infection) may exceed dispersal-associated costs for
 individuals with high dispersal ability (i.e., large fish) but are
 marginal for individuals with limited dispersal ability (i.e., small
 fish). Indeed, our growth analysis revealed that only small fish hosts
 incurred dispersal costs (reduced growth). Strikingly, our simulation
 study revealed that this plastic dispersal response of infected hosts
 substantially enhanced parasite persistence and occupancy in a spatially
 structured system. These results suggest that dispersal plasticity in host
 species is critical for understanding how parasites emerge, spatially
 spread, and persist in nature. Our findings provide a novel starting point
 for building a reliable, predictive model for parasite/disease management.
description: data_for_submit_finaldata_submission.zip
DOI: 10.5061/dryad.kb015
title: Data from: Balanced genetic diversity improves population fitness

description: Although genetic diversity within a population is suggested to improve
 population-level fitness and productivity, the existence of these effects
 is controversial because empirical evidence for an ecological effect of
 genetic diversity and the underlying mechanisms is scarce and incomplete.
 Here, we show that the natural single-gene behavioural polymorphism (Rover
 and sitter) in Drosophila melanogaster has a positive effect on population
 fitness. Our simple numerical model predicted that the fitness of a
 polymorphic population would be higher than that expected with two
 monomorphic populations, but only under balancing selection. Moreover,
 this positive diversity effect of genetic polymorphism was attributable to
 complementarity effect, rather than to selection effect. Our empirical
 tests using the behavioural polymorphism in D. melanogaster clearly
 supported the model predictions. These results provide direct evidence for
 an ecological effect of genetic diversity on population fitness and its
 condition dependence.
description: DataSurvival rate, biomass
 and weight.data.txt
DOI: 10.5061/dryad.d4600
title: Data from: Dietary antioxidants and flight exercise in female birds affect allocation of nutrients to eggs: how carry-over effects work

description: Physiological challenges during one part of the annual cycle can carry
 over and affect performance at a subsequent phase, and antioxidants could
 be one mediator of trade-offs between phases. We performed a controlled
 experiment with zebra finches to examine how songbirds use nutrition to
 manage trade-offs in antioxidant allocation between endurance flight and
 subsequent reproduction. Our treatment groups included (1) a
 non-supplemented, non-exercised group (control group) fed a standard diet
 with no exercise beyond that experienced during normal activity in an
 aviary; (2) a supplemented non-exercised group fed a water- and
 lipid-soluble antioxidant-supplemented diet with no exercise; (3) a
 non-supplemented exercised group fed a standard diet and trained to
 perform daily endurance flight for 6 weeks; and (4) a supplemented
 exercised group fed an antioxidant-supplemented diet and trained to
 perform daily flight for 6 weeks. After flight training, birds were paired
 within treatment groups for breeding. We analyzed eggs for lutein and
 vitamin E concentrations and the plasma of parents throughout the
 experiment for non-enzymatic antioxidant capacity and oxidative damage.
 Exercised birds had higher oxidative damage levels than non-exercised
 birds after flight training, despite supplementation with dietary
 antioxidants. Supplementation with water-soluble antioxidants decreased
 the deposition of lipid-soluble antioxidants into eggs and decreased yolk
 size. Flight exercise also lowered deposition of lutein, but not vitamin
 E, to eggs. These findings have important implications for future studies
 of wild birds during migration and other oxidative challenges.
description: Skrip_et_al-JEB-zebra_finch_dataThis file contains data used to perform statistical analyses: circulating oxidative damage data from adult zebra finches for repeated measures ANOVA; circulating antioxidant capacity data from zebra finches for repeated measures ANOVA; liver antioxidant enzyme data from adult zebra finches for ANOVA; yolk antioxidant and egg size data from zebra finch eggs for mixed general linear models.Skrip_et_al-JEB-data_repository.xlsx
DOI: 10.15468/dl.a6pf8m
title: Occurrence Download

description: A dataset containing 279 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Caiophora chuquitensis",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 279 records from 26 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001067-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.8080c
title: Data from: Extracting DNA from ‘jaws’: high yield and quality from archived tiger shark (Galeocerdo cuvier) skeletal material

description: Archived specimens are highly valuable sources of DNA for retrospective
 genetic/genomic analysis. However, often limited effort has been made to
 evaluate and optimize extraction methods, which may be crucial for
 downstream applications. Here, we assessed and optimized the usefulness of
 abundant archived skeletal material from sharks as a source of DNA for
 temporal genomic studies. Six different methods for DNA extraction,
 encompassing two different commercial kits and three different protocols,
 were applied to material, so-called bio-swarf, from contemporary and
 archived jaws and vertebrae of tiger sharks (Galeocerdo cuvier). Protocols
 were compared for DNA yield and quality using a qPCR approach. For jaw
 swarf, all methods provided relatively high DNA yield and quality, while
 large differences in yield between protocols were observed for vertebrae.
 Similar results were obtained from samples of white shark (Carcharodon
 carcharias). Application of the optimized methods to 38 museum and private
 angler trophy specimens dating back to 1912 yielded sufficient DNA for
 downstream genomic analysis for 68% of the samples. No clear relationships
 between age of samples, DNA quality and quantity were observed, likely
 reflecting different preparation and storage methods for the trophies.
 Trial sequencing of DNA capture genomic libraries using 20 000 baits
 revealed that a significant proportion of captured sequences were derived
 from tiger sharks. This study demonstrates that archived shark jaws and
 vertebrae are potential high-yield sources of DNA for genomic-scale
 analysis. It also highlights that even for similar tissue types, a careful
 evaluation of extraction protocols can vastly improve DNA yield.
description: Tiger shark primers and
 probesQPCR primers, probes and
 products for tiger shark assaysTiger QPCR raw data and
 ratiosReal time PCR raw CT
 scores for 100 and 200 bp QPCR assays with calculated ratios to determine
 DNA quality
DOI: 10.5061/dryad.984h0
title: Data from: Joint care can outweigh costs of nonkin competition in communal breeders

description: Competition between offspring can greatly influence offspring fitness and
 parental investment decisions, especially in communal breeders where
 unrelated competitors have less incentive to concede resources. Given the
 potential for escalated conflict, it remains unclear what mechanisms
 facilitate the evolution of communal breeding among unrelated females.
 Resolving this question requires simultaneous consideration of offspring
 in noncommunal and communal nurseries, but such comparisons are missing.
 In the Seychelles warbler Acrocephalus sechellensis, we compare nestling
 pairs from communal nests (2 mothers) and noncommunal nests (1 mother)
 with singleton nestlings. Our results indicate that increased provisioning
 rate can act as a mechanism to mitigate the costs of offspring rivalry
 among nonkin. Increased provisioning in communal broods, as a consequence
 of having 2 female parents, mitigates any elevated costs of offspring
 rivalry among nonkin: per-capita provisioning and survival was equal in
 communal broods and singletons, but lower in noncommunal broods.
 Individual offspring costs were also more divergent in noncommunal broods,
 likely because resource limitation exacerbates differences in competitive
 ability between nestlings. It is typically assumed that offspring rivalry
 among nonkin will be more costly because offspring are not driven by kin
 selection to concede resources to their competitors. Our findings are
 correlational and require further corroboration, but may help explain the
 evolutionary maintenance of communal breeding by providing a mechanism by
 which communal breeders can avoid these costs.
description: Complete data file - all
 analysesData for all analyses
 described in the manuscript. Each row represents one sampled
 individual.File for
 DRYAD.csv
DOI: 10.5061/dryad.1f43v
title: Data from: Effects of dispersal mode on the environmental and spatial correlates of nestedness and species turnover in pond communities

description: Advances in metacommunity theory have made a significant contribution to
 understanding the drivers of variation in biological communities. However,
 there has been limited empirical research exploring the expression of
 metacommunity theory for two fundamental components of beta diversity:
 nestedness and species turnover. In this paper, we examine the influence
 of local environmental and a range of spatial variables (hydrological
 connectivity, proximity and overall spatial structure) on total beta
 diversity and the nestedness and turnover components of beta diversity for
 the entire macroinvertebrate community and active and passively dispersing
 taxa within pond habitats. High beta diversity almost entirely reflects
 patterns of species turnover (replacement) rather than nestedness
 (differences in species richness) in our dataset. Local environmental
 variables were the main drivers of total beta diversity, nestedness and
 turnover when the entire community was considered and for both active and
 passively dispersing taxa. The influence of spatial processes on passively
 dispersing composition, total beta diversity and nestedness was
 significantly greater than for actively dispersing taxa. Our results
 suggest that species sorting (local environmental variables) operating
 through niche processes was the primary mechanism driving total beta
 diversity, nestedness and turnover for the entire community and active and
 passively dispersing taxa. In contrast, spatial factors (hydrological
 connectivity, proximity and spatial eigenvectors) only exerted a secondary
 influence on the nestedness and turnover components of beta diversity.
description: Hill et al.
 OikosPresence-absence
 macroinvertebrate species list