cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.s3cc172
title: Data from: Evolution of heterophil/lymphocyte ratios in response to ecological and life-history traits: a comparative analysis across the avian tree of life

description: 1. Lymphocytes and heterophils are the two most abundant leukocyte types,
 which play a major role in adaptive and innate immune defence,
 respectively. The ratio of heterophils to lymphocytes (H/L ratio) may
 reflect a readiness to cope with infection through injury (via
 heterophils) rather than with a communicable disease (via lymphocytes).
 Since elevated H/L ratio constitutes a corticosterone-mediated response to
 external stressors, this trait is generally acknowledged as the robust
 measure of physiological stress in vertebrates. 2. Here, I hypothesized
 that baseline H/L ratios of birds (as measured under normal physiological
 function) could be an important evolutionary trait shaped by species’
 ecology and life-history. I predicted that H/L ratios should be determined
 by traits related to pathogen exposure (migratoriness, sociality, breeding
 latitude) and trade-offs between investment in reproduction (clutch size)
 and self-maintenance (longevity). 3. I compiled published data on
 leukocyte profiles for nearly 250 bird species representing over half of
 all extant avian orders and nearly 30% of all extant avian families.
 Phylogenetically-informed comparative methods were used to assess
 evolutionary associations of H/L ratios with ecological and life-history
 traits across the avian tree of life. 4. Relatively strong phylogenetic
 signal and phylogenetic autocorrelation in avian H/L ratios indicated that
 most diversification in this trait occurred relatively early in bird
 radiation. Fluctuating selection and drift were identified as the major
 forces responsible for the evolution of H/L ratios in birds, while low H/L
 ratios were identified as an ancestral state in birds. Finally,
 phylogenetically-informed Bayesian models showed that H/L ratios
 correlated negatively with longevity and positively with sociality and
 breeding latitude. 5. This study was the first to describe the patterns of
 avian H/L ratio evolution in a broad phylogenetic framework. The results
 indicate that H/L ratios should not be merely recognized as a proxy for
 the intra-specific variation in physiological stress, but also as an
 important evolutionary trait which probably have adaptive significance
 visible in a wider phylogenetic perspective.
description: Raw
 dataRaw data for
 heterophil/lymphocyte ratios and life-history traits of
 birds.Minias RAW
 DATA.xlsx
DOI: 10.5061/dryad.qc6tf
title: Data from: Micro-scale environmental variation amplifies physiological variation among individual mussels

description: The contributions of temporal and spatial environmental variation to
 physiological variation remain poorly resolved. Rocky intertidal zone
 populations are subjected to thermal variation over the tidal cycle,
 superimposed with micro-scale variation in individuals’ body temperatures.
 Using the sea mussel (Mytilus californianus), we assessed the consequences
 of this micro-scale environmental variation for physiological variation
 among individuals, first by examining the latter in field-acclimatized
 animals, second by abolishing micro-scale environmental variation via
 common garden acclimation, and third by restoring this variation using a
 reciprocal outplant approach. Common garden acclimation reduced the
 magnitude of variation in tissue-level antioxidant capacities by ~30%
 among mussels from a wave-protected (warm) site, but it had no effect on
 antioxidant variation among mussels from a wave-exposed (cool) site. The
 field-acclimatized level of antioxidant variation was restored only when
 protected-site mussels were outplanted to a high, thermally stressful
 site. Variation in organismal oxygen consumption rates reflected
 antioxidant patterns, decreasing dramatically among protected-site mussels
 after common gardening. These results suggest a highly plastic
 relationship between individuals’ genotypes and their physiological
 phenotypes that depends on recent environmental experience. Corresponding
 context-dependent changes in the physiological mean-variance relationships
 within populations complicate prediction of responses to shifts in
 environmental variability that are anticipated with global change.
description: Jimenez et al Proc B
 mussel varn DryadThis file contains
 treatment details, antioxidant values for 9 different assays, and
 corresponding repeated metabolic rate measurements from mussels under four
 different conditions (field-acclimatized; common-garden; outplant-high;
 outplant-low) and at three timepoints on an experimental thermal challenge
 (baseline; top of ramp; recovery 4h later).
DOI: 10.5061/dryad.gj21173
title: Data from: Circulating cortisol and cognitive and structural brain measures in a middle-aged cohort: the Framingham Heart Study

description: Objective: To assess the association of early morning serum cortisol with
 cognitive performance and brain structural integrity in community-dwelling
 young and middle-aged adults without dementia. Methods: We evaluated
 dementia-free Framingham Study (Generation 3) participants (mean age 48.5
 years; 46.8% men), who underwent cognitive testing for memory, abstract
 reasoning, visual perception, attention, and executive function (n= 2231),
 and brain MRI (n=2018) to assess total white matter, lobar gray matter,
 and white matter hyperintensity volumes and fractional anisotropy (FA)
 measures. We used linear and logistic regression to assess the relations
 of cortisol (categorized in tertiles, with the middle tertile as referent)
 to measures of cognition, MRI volumes, presence of covert brain infarcts
 (CBI) and cerebral microbleeds (CMB), and voxel-based microstructural
 white matter integrity and gray matter density, adjusting for age, sex,
 APOE and vascular risk factors. Results: Higher cortisol (highest tertile
 vs. middle tertile) was associated with worse memory and visual
 perception, as well as lower total cerebral brain, occipital and frontal
 lobar gray matter volumes. Higher cortisol was associated with multiple
 areas of microstructural changes (decreased regional FA), especially in
 the splenium of corpus callosum and the posterior corona radiata. The
 association of cortisol with total cerebral brain volume varied by sex (p
 interaction=0.048); higher cortisol was inversely associated with cerebral
 brain volume in women [p=0.001] but not in men [p=0.717]). There was no
 effect modification by the apoE4 genotype of the relations of cortisol and
 cognition or imaging traits. Conclusions: Higher serum cortisol was
 associated with lower brain volumes and impaired memory in asymptomatic
 younger to middle-aged adults, with the association being evident
 particularly in women.
description: Cortisol-Brain
 Outcomes-FHS-SupplementaryMaterialSupplementary material
 showing additional tables and figures, which include results pertaining to
 the manuscript.
DOI: 10.15468/dl.64d8zs
title: Occurrence Download

description: A dataset containing 383 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Specimen)",
 "Geometry POLYGON((105 20,170 20,170 70,105 70,105 20))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Sanguisorba stipulata"
 ]
}

 The dataset includes 383 records from 27 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000896-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.pf56m
title: Data from: Predictive value of apelin-12 in ST-elevation myocardial infarction patients with different renal function: a prospective observational study

description: Objectives: To investigate the factors predicting the onset of major
 adverse cardiovascular events (MACEs) after primary percutaneous coronary
 intervention (pPCI) for ST-segment elevation myocardial infarction (STEMI)
 patients. Background: apelin-12 has been regarded acting essential role in
 cardiovascular homeostasis. However, current knowledge of the optimal
 prognostic predictive value is limited. Methods: 464 STEMI patients
 (63.0±11.9 years, 355 men) who underwent successful pPCI were enrolled.
 Patients were followed-up for 2.5 years. Multivariate cox regression
 analyses and receiver operating characteristic curve analysis were
 performed to determine the factors predicting MACEs. Results: There were
 118 patients (25.4%) who experienced MACEs in the follow-up period.
 Multivariate cox regression analysis demonstrated that low apelin-12
 (HR=0.132, 95% CI=0.060-0.292, p＜0.001), low left ventricular ejection
 fraction (LVEF) (HR=0.965, 95% CI=0.941-0.991, p=0.007), low estimated
 glomerular filtration rate (eGFR) (HR=0.985, 95% CI=0.977-0.993, p＜0.001),
 Killip’s classification＞I (HR=0.610, 95% CI=0.408-0.912, p=0.016) and
 pathological Q-wave (HR=1.536, 95% CI=1.058-2.230, p=0.024) were
 independent predictors of 2.5 MACEs. Low apelin-12 could also predict
 worse in-hospital prognosis and showed advantage in predicting 2.5 year
 MACEs compared with Δapelin-12 (p=0.0115）and eGFR (p=0.0071) among
 patients with eGFR＞90 mL/min1.73m2. Further analysis prompt Δapelin-12＜20%
 was usually associated with MACEs in patients whose apelin-12 admission
 below 0.76 ng/ml (p=0.0075). Conclusions: STEMI patients receiving pPCI
 with lower apelin-12 are more likely to suffer MACEs in hospitalization
 and 2.5-year follow-up, especially for those with normal level of eGFR.
description: bmjopen-2017-018595study data of bmjopen-2017-018595.xlsx
DOI: 10.5061/dryad.541v5
title: Data from: Cryptic species, native populations and biological invasions by a eucalypt forest pathogen

description: Human associated introduction of pathogens and consequent invasions are
 very evident in areas where no related organisms existed before. In areas
 where related but distinct populations or closely related cryptic species
 already exist, the invasion process is much harder to unravel. In this
 study, the population structure of the Eucalyptus leaf pathogen
 Teratosphaeria nubilosa was studied within its native range in Australia,
 including both commercial plantations and native forests. A collection of
 521 isolates from across its distribution was characterized using eight
 microsatellite loci, resulting in 112 multilocus haplotypes (MLH).
 Multivariate and Bayesian analyses of the population conducted in
 STRUCTURE revealed three genetically isolated groups (A, B and C), with no
 evidence for recombination or hybridization among groups, even when they
 co-occur in the same plantation. DNA sequence data of the ITS (n=32),
 β-tubulin (n=32) and 27 anonymous loci (n=16) were consistent with
 microsatellite data in suggesting that T. nubilosa should be considered as
 a species complex. Patterns of genetic diversity provided evidence of
 biological invasions by the pathogen within Australia in the states of
 Western Australia and New South Wales, and helped unravel the pattern of
 invasion beyond Australia into New Zealand, Brazil and Uruguay. No
 significant genetic differences in pathogen populations collected in
 native forests and commercial plantations were observed. This emphasizes
 the importance of sanitation in the acquisition of nursery stock for the
 establishment of commercial plantations.
description: individual_by_individual_sampling_location_and_genotypesThis file contains individual by individual information about sampling and microsatellite Multilocus Haplotypes. This includes Country, State, locality, site number sensu table 1, whether the isolate was collected on native forest or commercial plantation, host and GPS coordinates. Because 112 MLHs were observed on the populations the internal code for MLHs (#MLH) is provided. Three genetic groups were identified using Structure, this info is also presented individual by individual. The isolate name and the culture collection number (CMW) of the Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, South Africa is also presented individual by individual. Finally the allele for each of the eight microsatellite loci (MN-1, MN-2, MN-3, MN-7, MN-9, MN-10, MN-11 and MN-14) amplified using the fluorescently labelled T. nubilosa-specific primers developed by Hunter et al. (2006) are provided.clon_corrected_datasetThis file contains the 112 MLHs (clone corrected) used for population analyses
DOI: 10.15468/dl.8n3ucg
title: Occurrence Download

description: A dataset containing 549 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Specimen)",
 "Geometry POLYGON((105 20,170 20,170 70,105 70,105 20))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Sibbaldia procumbens"
 ]
}

 The dataset includes 549 records from 30 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000897-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.n2m8v
title: Data from: Reliable genotyping of the koala (Phascolarctos cinereus) using DNA isolated from a single faecal pellet

description: The koala, an Australian icon, has been added to the threatened species
 list. Rationale for the listing includes proposed declines in population
 size, threats to populations (e.g. disease) and loss and fragmentation of
 habitat. There is now an urgent need to obtain accurate data to assess the
 status of koala populations in Australia, to ensure the long-term
 viability of this species. Advances in genetic techniques have enabled DNA
 analysis to study and inform the management of wild populations; however,
 sampling of individual koalas is difficult in tall, often remote, eucalypt
 forest. The collection of faecal pellets (scats) from the forest floor
 presents an opportunistic sampling strategy, where DNA can be collected
 without capturing or even sighting an individual. Obtaining DNA via
 noninvasive sampling can be used to rapidly sample a large proportion of a
 population; however, DNA from noninvasively collected samples is often
 degraded. Factors influencing DNA quality and quantity include
 environmental exposure, diet and methods of sample collection, storage and
 DNA isolation. Reduced DNA quality and quantity can introduce genotyping
 errors and provide inaccurate DNA profiles, reducing confidence in the
 ability of such data to inform management/conservation strategies. Here,
 we present a protocol that produces a reliable individual koala genotype
 from a single faecal pellet and highlight the importance of optimizing DNA
 isolation and analysis for the species of interest. This method could
 readily be adapted for genetic studies of mammals other than koalas,
 particularly those whose diet contains high proportions of volatile
 materials that are likely to induce DNA damage.
description: Genotypic data and DNA
 concentrationsExcel spread sheet
 containing the following data: Genotypic and DNA concentration Data for
 the scat collection and storage experiment (41 samples). DNA concentration
 273 samples, genotypic and DNA conctration data for 21 samples for DNA
 yeild and optimization experiment.Gimlet and Gemini input
 filesGenotypic data for 41
 DNA samples grouped by treatment for the scat collection and storage and
 21 DNA samples grouped by DNA concentration DNA yield and error
 calculations.Gimlet & Gemini input
 files.zip
DOI: 10.5061/dryad.4f7qg
title: Data from: The ace-1 locus is amplified in all resistant Anopheles gambiae mosquitoes: fitness consequences of homogeneous and heterogeneous duplications.

description: Gene copy-number variations are widespread in natural populations, but
 investigating their phenotypic consequences requires contemporary
 duplications under selection. Such duplications have been found at the
 ace-1 locus (encoding the organophosphate and carbamate insecticides’
 target) in the mosquito Anopheles gambiae (the major malaria vector);
 recent studies have revealed their intriguing complexity, consistent with
 the involvement of various numbers and types (susceptible or resistant to
 insecticide) of copies. We used an integrative approach, from genome to
 phenotype level, to investigate the influence of duplication architecture
 and gene-dosage on mosquito fitness. We found that both heterogeneous
 (i.e., one susceptible and one resistant ace-1 copy) and homogeneous
 (i.e., identical resistant copies) duplications segregated in field
 populations. The number of copies in homogeneous duplications was variable
 and positively correlated with acetylcholinesterase activity and
 resistance level. Determining the genomic structure of the duplicated
 region revealed that, in both types of duplication, ace-1 and 11 other
 genes formed tandem 203kb amplicons. We developed a diagnostic test for
 duplications, which showed that ace-1 was amplified in all 173 resistant
 mosquitoes analyzed (field-collected in several African countries), in
 heterogeneous or homogeneous duplications. Each type was associated with
 different fitness trade-offs: heterogeneous duplications conferred an
 intermediate phenotype (lower resistance and fitness costs), whereas
 homogeneous duplications tended to increase both resistance and fitness
 cost, in a complex manner. The type of duplication selected seemed thus to
 depend on the intensity and distribution of selection pressures. This
 versatility of trade-offs available through gene duplication highlights
 the importance of large mutation events in adaptation to environmental
 variation. This impressive adaptability could have a major impact on
 vector control in Africa.
description: Full_DataThis file contains all the data underlying the results presented in our study (set apart genomic data which were deposited on NCBI), namely: Phenotyping data from field sampled mosquitoes, ace-1 CNV, AChE1 activity measures, Life history trait measures of various mosquito strains and experimental evolution data.Insert sizesInsert sizes distribution for Kisumu, Acerkis and AcerDuplikis strainsInsertSize.xlsx
DOI: 10.5061/dryad.31k1f
title: Data from: Diagnostic pathways and direct medical costs incurred by new adult pulmonary tuberculosis patients prior to anti-tuberculosis treatment – Tamil Nadu, India

description: Background: Tuberculosis (TB) patients face substantial delays prior to
 treatment initiation, and out of pocket (OOP) expenditures often surpass
 the economic productivity of the household. We evaluated the
 pre-diagnostic cost and health seeking behaviour of new adult pulmonary TB
 patients registered at Primary Health Centres (PHCs) in Vellore district,
 Tamil Nadu, India. Methods: This descriptive study, part of a randomised
 controlled trial conducted in three rural Tuberculosis Units from Dec 2012
 to Dec 2015, collected data on number of health facilities, dates of
 visits prior to the initiation of anti-tuberculosis treatment, and direct
 OOP medical costs associated with TB diagnosis. Logistic regression
 analysis examined the factors associated with delays in treatment
 initiation and OOP expenditures. Results: Of 880 TB patients interviewed,
 34.7% presented to public health facilities and 65% patients sought
 private health facilities as their first point of care. The average
 monthly individual income was $77.79 (SD 57.14). About 69% incurred some
 pre-treatment costs at an average of $39.74. Overall, patients experienced
 a median of 6 days (3-11 IQR) of time to treatment initiation and 21 days
 (10-30 IQR) of health systems delay. Age ≤ 40 years (aOR: 1.73; CI: 1.22 -
 2.44), diabetes (aOR: 1.63; CI: 1.08 - 2.44) and first visit to a private
 health facility (aOR: 17.2; CI: 11.1 - 26.4) were associated with higher
 direct OOP medical costs, while age ≤ 40 years (aOR: 0.64; CI: 0.48 -
 0.85) and first visit to private health facility (aOR: 1.79, CI: 1.34 -
 2.39) were associated with health systems delay. Conclusion: The majority
 of rural TB patients registering at PHCs visited private health facilities
 first and incurred substantial direct OOP medical costs and delays prior
 to diagnosis and anti-tuberculosis treatment initiation. This study
 highlights the need for PHCs to be made as the preferred choice for first
 point of contact, to combat TB more efficiently.
description: Pathways and costs
 incurred by new adult pulmonary tuberculosis patients prior to
 anti-tuberculosis treatmentThis study used the
 pre-treatment pathways and costing data collected for the larger study-
 "Community Volunteers, Solidarity and Case management of
 Tuberculosis" conducted in rural south India.Pathways and costs
 data.csv
DOI: 10.5061/dryad.pd7vt
title: Data from: The use of clamping grips and friction pads by tree frogs for climbing curved surfaces

description: Most studies on the adhesive mechanisms of climbing animals have addressed
 attachment against flat surfaces, yet many animals can climb highly curved
 surfaces, like twigs and small branches. Here we investigated whether tree
 frogs use a clamping grip by recording the ground reaction forces on a
 cylindrical object with either a smooth or anti-adhesive, rough surface.
 Furthermore, we measured the contact area of fore and hindlimbs against
 differently sized transparent cylinders and the forces of individual pads
 and subarticular tubercles in restrained animals. Our study revealed that
 frogs use friction and normal forces of roughly a similar magnitude for
 holding on to cylindrical objects. When challenged with climbing a
 non-adhesive surface, the compressive forces between opposite legs nearly
 doubled, indicating a stronger clamping grip. In contrast to climbing flat
 surfaces, frogs increased the contact area on all limbs by engaging not
 just adhesive pads but also subarticular tubercles on curved surfaces. Our
 force measurements showed that tubercles can withstand larger shear
 stresses than pads. SEM images of tubercles revealed a similar structure
 to that of toe pads including the presence of nanopillars, though channels
 surrounding epithelial cells were less pronounced. The tubercles'
 smaller size, proximal location on the toes and shallow cells make them
 probably less prone to buckling and thus ideal for gripping curved
 surfaces.
description: Endlein_etal_2016_dataData for figures 2-4.