cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.sf2bt
title: Data from: Elucidating mechanisms for insect body size: partial support for the oxygen-dependent induction of moulting hypothesis

description: Body size is a key life history trait and knowledge of its mechanistic
 basis is crucial in life history biology. Such knowledge is accumulating
 in holometabolous insects, whose growth is characterised and body size
 affected by moulting. According to the oxygen-dependent induction of
 moulting (ODIM) hypothesis, moult is induced at a critical mass where
 oxygen demand of growing tissues overrides the supply that principally
 grows only at moults. Support for the ODIM hypothesis is controversial
 partly because of a lack of proper data to explicitly test the hypothesis.
 The ODIM hypothesis predicts that the critical mass is positively
 correlated with oxygen partial pressure (pO2) and negatively with
 temperature. To resolve the controversy that surrounds the ODIM
 hypothesis, we rigorously test these predictions by exposing
 penultimate-instar Orthosia gothica (Lepidoptera: Noctuidae) larvae to
 temperature and moderate pO2 manipulations in a factorial experiment. The
 relative mass increment in the focal instar increased along with
 increasing pO2, as predicted, but there was only weak suggestive evidence
 of the temperature effect. Probably due to a high measurement error in the
 trait, pO2 effect on the critical mass was sex-specific; high pO2 had a
 positive effect only in females, whereas low pO2 had a negative effect
 only in males. Critical mass was independent of temperature. Support for
 the ODIM hypothesis is partial because of only suggestive evidence of a
 temperature effect on moulting, but the role of oxygen in moult induction
 seems unambiguous. The ODIM mechanism, thus, seems worth considering in
 body size analyses.
description: O.gothica_DryadData from a laboratory experiment. All masses in the data file are in milligrams and growth duration is given in days. Growth rate has the unit of ln(mg/day).
DOI: 10.5061/dryad.ch4p5
title: Data from: Candidate risk factors and mechanisms for tolvaptan-induced liver injury are identified using a collaborative cross approach

description: Clinical trials of tolvaptan showed it to be a promising candidate for the
 treatment of Autosomal Dominant Polycystic Kidney Disease (ADPKD) but also
 revealed potential for idiosyncratic drug-induced liver injury (DILI) in
 this patient population. To identify risk factors and mechanisms
 underlying tolvaptan DILI, 8 mice in each of 45 strains of the genetically
 diverse Collaborative Cross (CC) mouse population were treated with a
 single oral dose of either tolvaptan or vehicle. Significant elevations in
 plasma alanine aminotransferase (ALT) were observed in tolvaptan-treated
 animals in 3 of the 45 strains. Genetic mapping coupled with
 transcriptomic analysis in the liver was used to identify several
 candidate susceptibility genes including epoxide hydrolase 2, interferon
 regulatory factor 3, and mitochondrial fission factor. Gene pathway
 analysis revealed that oxidative stress and immune response pathways were
 activated in response to tolvaptan treatment across all strains, but genes
 involved in regulation of bile acid homeostasis were most associated with
 tolvaptan-induced elevations in ALT. Secretory leukocyte peptidase
 inhibitor (Slpi) mRNA was also induced in the susceptible strains and was
 associated with increased plasma levels of Slpi protein, suggesting a
 potential serum marker for DILI susceptibility. In summary, tolvaptan
 induced signs of oxidative stress, mitochondrial dysfunction, and innate
 immune response in all strains, but variation in bile acid homeostasis was
 most associated with susceptibility to the liver response. This CC study
 has indicated potential mechanisms underlying tolvaptan DILI and
 biomarkers of susceptibility that may be useful in managing the risk of
 DILI in ADPKD patients.
description: Phenotype_data_FINALsee readme
DOI: 10.5061/dryad.8qk1v
title: Data from: Disentangling environmental drivers of metabolic flexibility in birds: the importance of temperature extremes versus temperature variability

description: Examining physiological traits across large spatial scales can shed light
 on the environmental factors driving physiological variation. For
 endotherms, flexibility in aerobic metabolism is especially important for
 coping with thermally challenging environments and recent research has
 shown that aerobic metabolic scope [the difference between maximum
 thermogenic capacity (Msum) and basal metabolic rate (BMR)] increases with
 latitude in mammals. One explanation for this pattern is the climatic
 variability hypothesis, which predicts that flexibility in aerobic
 metabolism should increase as a function of local temperature variability.
 An alternative explanation is the cold adaptation hypothesis, which
 predicts that cold temperature extremes may also be an important driver of
 variation in metabolic scope. To determine the thermal drivers of aerobic
 metabolic flexibility in birds, we combined data on metabolic scope from
 40 bird species sampled across a range of environments with several
 indices of local ambient temperature. Using phylogenetically-informed
 analyses, we found that minimum winter temperature was the best predictor
 of variation in avian metabolic scope, outperforming all other thermal
 variables. Additionally, Msum was a better predictor of latitudinal
 patterns of metabolic scope than BMR, with species inhabiting colder
 environments exhibiting increased Msum over their counterparts in warmer
 environments. Taken together, these results suggest that cold temperature
 extremes drive latitudinal patterns of metabolic scope via selection for
 enhanced thermogenic performance in cold environments, supporting the cold
 adaptation hypothesis. Temperature extremes may therefore be an important
 selective pressure driving macrophysiological trends of aerobic
 performance in endotherms.
description: Supplementary Table A1 -
 Metabolic and climatic dataTable includes metabolic
 scope data and associated climatic data of all bird species included in
 the analysis
DOI: 10.5061/dryad.n895b
title: Data from: Prevalence and outcomes of multimorbidity in South Asia: a systematic review

description: Objective: To systematically review the studies of prevalence, patterns
 and consequences of multimorbidity reported from South Asia. Design:
 Systematic review. Setting: South Asia. Data sources: Articles were
 retrieved from two electronic databases (PubMed and Embase) and from the
 relevant references lists. Methodical data extraction according to
 Preferred Reporting Items for Systematic reviews and Meta-Analyses
 (PRISMA) guidelines was followed. English-language studies published
 between 2000 and March 2015 were included. Eligibility criteria: Studies
 addressing prevalence, consequences and patterns of multimorbidity in
 South Asia. Articles documenting presence of two or more chronic
 conditions were included in the review. The quality and risk of bias were
 assessed using STROBE criteria. Data selection: Two reviewers
 independently assessed studies for eligibility, extracted data and
 assessed study quality. Due to heterogeneity in methodologies among
 reported studies, only narrative synthesis of the results was carried out.
 Results: Of 11 132, 61 abstracts were selected and 13 were included for
 final data synthesis. The number of health conditions analysed per study
 varied from 7 to 22, with prevalence of multimorbidity from 4.5% to 83%.
 The leading chronic conditions were hypertension, arthritis, diabetes,
 cardiac problems and skin diseases. The most frequently reported outcomes
 were increased healthcare utilisation, lowered physical functioning and
 quality of life, and psychological distress. Conclusions: Our study, a
 comprehensive mapping of multimorbidity research in South Asia, reveals
 the insufficient volume of work carried out in this domain. The published
 studies are inadequate to provide an indication of the magnitude of
 multimorbidity in these countries. Research into clinical and
 epidemiological aspects of multimorbidity is warranted to build up
 scientific evidence in this geographic region. The wide heterogeneity
 observed in the present review calls for greater methodological rigour
 while conducting these epidemiological studies. Trial registration number:
 CRD42013005456.
description: Data
 extractionExtracted data for the
 systematic review.
DOI: 10.5061/dryad.sg46n
title: Data from: Cuticular hydrocarbon cues of immune-challenged workers elicit immune activation in honeybee queens

description: Recently, evidence has shown that variations in the cuticular hydrocarbons
 (CHCs) profile allow healthy honeybees to identify diseased nestmates,
 eliciting agonistic responses in the former. Here, we determined whether
 these ‘immunologic cues’ emitted by diseased nestmates were only detected
 by workers, who consequently took hygienic measures and excluded these
 individuals from the colony, or whether queens were also able to detect
 these cues and respond accordingly. Healthy honeybee queens were exposed
 to (i) healthy, (ii) Ringer-injected and (iii) lipopolysaccharide
 (LPS)-injected nestmates by allowing direct body contact. Quantitative
 differences in the CHC profiles of these three groups were measured using
 GC-MS. The transcript levels of the products of four genes that encode for
 antimicrobial peptides (AMPs), which are part of the queen's immune
 response, were measured in bees exposed to direct contact using qPCR. A
 significant increase in the transcript levels of these AMP genes over
 baseline levels in queens was observed when body contact was allowed
 between the queens and the Ringer- and LPS-injected nestmates. These
 results provide the first evidence that the detection of CHCs contributes
 to the initiation of an immune response in insects. In an additional
 experiment, CHCs were extracted from diseased workers and directly
 presented to queens, which also evoked a similar immune response. A
 potential mechanism that relied on volatile compounds could be ruled out
 by conducting a distance experiment. The study helps to expand our
 knowledge of chemical communication in insects and sheds light on a likely
 new mechanism of social immunity.
description: Raw qPCR data for queens
 and workersct values
 queens+workers.xlsx
DOI: 10.5061/dryad.j1344c7
title: Data from: Bee movement across heterogeneous tropical forests: multi-paternal genetic analyses reveal the importance of neighborhood composition for pollen-mediated gene flow

description: Animal pollination is critical for maintaining the reproduction and
 genetic diversity of many plant species, especially those in tropical
 ecosystems. Despite the threat to pollination posed by tropical
 deforestation, it remains an understudied process. In particular, little
 is known about these dynamics in multi-paternal, successional plant
 species whose fruits can contain substantial genetic diversity. Given the
 importance of successional plants in reforestation, quantifying the
 factors that impact their reproduction is essential for understanding
 plant gene flow in the context of global change. In this study, we
 investigated pollen-mediated gene flow at the multi-paternal fruit level
 to quantify how tropical pollinators navigate and mediate gene flow in
 altered forests. Utilizing microsatellite genotyping and paternity
 analyses, we revealed that distinct plant neighborhood and individual
 factors drive pollen dispersal at the intra-fruit scale. Variance in
 pollen dispersal distances was greater for neighborhoods with higher
 conspecific density, indicating that density-dependent reproductive
 patterns play a role at this scale. Additionally, both the diversity of
 sires mediated by a single pollinator was affected by the size of the
 mother tree, i.e. larger mothers received pollen from a less diverse, less
 even pool of sires per fruit. Pollinator body size was not found to be a
 significant driver of pollen dispersal, indicating that both small and
 large-bodied pollinators were equally important pollen dispersers at this
 scale. By exploring patterns of variation at the intra-fruit level, we
 show that conspecific density and tree size significantly impact
 multi-paternal pollen-mediated gene flow, reinforcing the importance of
 investigating intraspecific, intra-individual variance in plant
 reproduction.
description: PollenDispersal_SeedLevelFile lists identities of sires (as per Cervus paternity analyses) of several Miconia affinis seeds within individual fruits and the dispersal distance traveled by specific pollinator species between the sires and the mother trees where they deposited pollen.PollenDispersal_MotherLevelFile includes data on study system independent variables per mother tree (1 fruit per mother tree), our calculations of the standard deviation, mean and maximum pollen dispersal distances, as well as our calculations of sire diversity and evenness per multi-paternal fruit.
DOI: 10.5061/dryad.0p78hg7g
title: Data from: Integrative taxonomy at work: DNA barcoding of taeniids harbored by wild and domestic cats

description: In modern taxonomy, DNA barcoding is particularly useful where biometric
 parameters are difficult to determine or useless due to the poor quality
 of samples. These situations are frequent in parasitology. Here we present
 an integrated study, based on both DNA barcoding and morphological
 analysis, on cestodes belonging to the genus Taenia, for which
 biodiversity is still largely underestimated. In particular, we
 characterized cestodes from Italian wildcats (Felis silvestris
 silvestris), free-ranging domestic cats (F. s. catus) and their hybrids
 populations. Adult taeniids were collected by post-mortem examinations of
 the hosts, and morphologically identified as Taenia taeniaeformis. We
 produced the cox1 barcode sequences for all the analyzed specimens and we
 compared them with reference sequences of individuals belonging to the
 genus Taenia retrieved from GenBank. In order to evaluate the performance
 of a DNA barcoding approach to discriminate these parasites, the strength
 of correlation between species identification based on classical
 morphology-based approaches and the molecular divergence of cox1 sequences
 was measured. Our study provides clear evidence that DNA barcoding is
 highly efficient to reveal the presence of cryptic lineages within already
 described taeniid species. Indeed, we detected three well-defined
 molecular lineages within the whole panel of specimens morphologically
 identified as T. taeniaeformis. Two of these molecular groups were already
 identified by other authors and should be ranked at species level. The
 third molecular group encompasses only samples collected in Italy during
 this study, and it represents a third candidate species, still
 morphologically undescribed.
description: sampling details and
 Genbank accessionsThe file (.xls format),
 includes the list of taeniid samples examined in this study using a DNA
 barcoding approach with reference to: specimen voucher, host species
 (except for unrecognized individuals), GenBank accession numbers of newly
 identified sequences, sampling localities and assigned molecular lineage
 of each parasite sample based on the optimum threshold of molecular
 divergence inferred by our analyses.
DOI: 10.5061/dryad.7dn526gq
title: Data from: SSR-marker analysis of the intracultivar phenotypic variation discovered within 3 soybean cultivars

description: Genetic variation within homogeneous gene pools in various crops is
 assumed to be very limited. One objective of this study was to use 144
 simple sequence repeat (SSR) markers to determine if the single-plant
 lines selected at ultra-low plant density in honeycomb designs within the
 soybean cultivars Benning, Haskell, and Cook had unique SSR genetic
 fingerprints. Another objective was to investigate if the variation found
 was the result of residual genetic heterozygosity that could be detected
 in the original gene pool where selection initiated. Our results showed
 that the phenotypic variation for seed protein content and seed weight has
 a genotypic component identified by the SSR band variation. The seven
 lines from Haskell had a total of 63 variant alleles, the five lines from
 Benning had 34 variant alleles, and the seven lines from Cook had 34
 variant alleles, therefore, possessing unique genetic fingerprints. Most
 of the intra-cultivar SSR band variation discovered was the result of
 residual heterozygosity in the initial plant selected to become the
 cultivar. More specifically, 82% of the SSR variant alleles were traced in
 the Benning Foundation seed source, 93% in the Haskell seed source, and
 82% in the Cook seed source. The remaining variant bands (18% for Benning,
 7% for Haskell, and 18% for Cook) could not be detected in the Foundation
 seed source and were likely the result of mutation or some other mechanism
 generating de novo variation. These results provide evidence that genetic
 variation among individual plants is present even in homogeneous gene
 pools and can be further utilized in breeding programs.
description: TABLE - SSR marker
 dataThis Table provides a
 complete list of the 144 SSR markers used to screen the single-plant
 progeny lines selected from the soybean cultivars Benning, Cook, and
 Haskell and information about the markers, being polymorphic or
 not.
DOI: 10.5061/dryad.pd28pm7n
title: Data from: Ergosterol biosynthesis: a fungal pathway for life on land?

description: Sterols, essential lipids of most eukaryotic cells, ensure important
 structural and signaling functions. The selection pressure which has led
 to different dominant sterols in the three eukaryotic kingdoms remains
 unknown. Here we investigated the influence of the progression in the
 different steps of the ergosterol biosynthetic pathway (EBP) on the yeast
 resistance to transitions from aqueous to aerial media, typical
 perturbations of the higher fungi habitats. Five mutants of the EBP
 (ergΔ), accumulating different sterol intermediates in the EBP, and the WT
 strain were exposed to drying under atmospheric air or nitrogen and
 wetting. Results show that the progression in the EBP parallels an
 increase in the yeast resistance to air-drying with a maximal survival
 rate for the WT strain. When drying/wetting was performed under nitrogen,
 yeast survival was higher, particularly for the earlier mutants of the
 EBP. Thus, ergosterol, through its protective role against mechanical and
 oxidative stress, might have been selected by the pressure induced by
 drying/wetting cycles occurring in the fungi habitats. These results
 support the Bloch hypothesis, which postulates that the properties of
 sterols are gradually optimized for function along the biosynthetic
 pathway and provide a response to the enduring question “why ergosterol in
 fungi?”.
description: DataData concerning the
 survival of the different yeast strains after drying treatments and yeast
 sterol analysis
DOI: 10.5061/dryad.8c134
title: Data from: Improving PCR detection of prey in molecular diet studies: importance of group-specific primer set selection and extraction protocol performances

description: While morphological identification of prey remains in feces of predators
 is the method most commonly used to study trophic interactions, many
 studies indicate that this method does not detect all consumed prey.
 Polymerase Chain Reaction based methods are increasingly used to detect
 prey DNA in the predator food bolus and have proved themselves efficient,
 with high accuracy. When studying complex diet samples, the extraction of
 total DNA is a critical step, as PCR inhibitors may be co-extracted.
 Another critical step consist in carefully select suitable group-specific
 primer sets that should only amplify prey DNA from the targeted taxon. In
 this study, the food boluses of five Rattus rattus and seven Rattus
 exulans were analyzed using both morphological and molecular methods. We
 tested a panel of 30 PCR specific primer sets targeting Bird, Invertebrate
 and Plant sequences and four were finally selected to be use as
 group-specific primer pairs in PCR protocols. The performances of four DNA
 extraction protocols (QIAamp DNA stool mini kit, DNeasy mericon food kit
 and two CTAB-based methods) were compared using four variables: DNA
 concentration, A260/A280 absorbance ratio, food compartment analyzed
 (stomach or fecal contents), total number of prey specific PCR
 amplification per sample. Our results clearly indicate that the A260/A280
 absorbance ratio, which varies between extraction protocols, is positively
 correlated to the number of PCR amplifications of each prey taxon. We
 recommend using the DNeasy mericon food kit (Qiagen), which yielded
 results very similar to those achieved with the morphological approach.
description: Alignment of
 group-specific primer set regionsSequence alignment of
 DNA regions targeted by the four group-specific primer pairs amplifying
 Bird, Invertebrate and Plant (mitochondrial and chloroplastic) DNA. Target
 and non target species were aligned for each group-specific primer pair.
 Target species were chosen to be as much as possible divergent in order to
 highlight the potentiality of each primer pair to amplify a wide prey
 diversity. "N" represents unavailable nucleotide in the existing
 Genbank sequence, "-" indicates gap and nucleotides between
 brackets indicate insertions. Note that because Animals do not have
 chloraplastic DNA, only sequences from target species were aligned for the
 Plant chloroplastic primer pair.
DOI: 10.5061/dryad.587
title: Data from: Divergence and reticulation among montane populations of a jumping spider (Habronattus pugillis Griswold)

description: Populations of the jumping spider Habronattus pugillis Griswold isolated
 on nearby mountain ranges in southern Arizona are differentiated in many
 features of the males (color, shape and orientation of setae on face,
 shape of carapace, markings of palpi and legs, motions during courtship
 behavior). These features are (mostly) consistent within a range and
 different between ranges. The concentration of differences to male
 courtship behavior and body parts exposed to the female during courtship
 and correlations between form and courtship behavior suggest sexual
 selection was involved in the differentiation. A phylogenetic analysis of
 the populations yields a tree that for the most part groups geographic
 neighbors, but the history of H. pugillis populations may not be
 adequately described by a tree. Geographic proximity of apparent
 convergences suggests that populations from at least some of the mountain
 ranges acquired characteristics through introgression. Lowering of the
 woodland habitat during the last glacial period probably brought some
 populations into contact, but it is not clear if the interrange woodlands
 would have provided corridors for extensive mixing.
description: Maddison and McMahon
 Data Setmaddison.wd