cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.m63xsj41r
title: Marine derivatives prevent wMUS81 in silico studies

description: The winged-helix domain of the methyl methanesulfonate and ultraviolet
 sensitive 81 (wMUS81) is a potential cancer drug target. In this context,
 marine fungi compounds were indicated to be able to prevent wMUS81
 structure. The work was established via molecular docking, molecular
 dynamics (MD), and replica exchange molecular dynamics (REMD) simulations.
 The binding free energy of ligands to wMUS81 was revealed using
 perturbation simulations. Eight compounds such as D197 (Tryptoquivaline
 U), D220 (Epiremisporine B), D67 (Aspergiolide A), D153 (Preussomerin G),
 D547 (12,13-dihydroxyfumitremorgin C), D152 (Preussomerin K), D20
 (Marinopyrrole B), and D559 (Fumuquinazoline K) were indicated that they
 are able to prevent the conformation of wMUS81 via forming a strong
 binding affinity to the enzyme. The electrostatic interaction is the
 dominant factor in the binding process of ligands to wMUS81. The residues
 Trp55, Arg59, Leu62, His63, and Arg69 were found that they frequently form
 nonbonded contacts and hydrogen bonds to inhibitors. Moreover, the
 influence of the ligand D197, which formed the lowest binding free energy
 to wMUS81, on the structural change of enzyme was investigated using REMD
 simulations. The obtained results indicated that a ligand, which forms a
 strong binding affinity, can change the structure of wMUS81. Overall, the
 marine compounds probably inhibit wMUS81 due to forming a strong binding
 affinity to the enzyme as well as altering the enzymic conformation.
description: The molecular docking simulations were performed using AutoDock
 Vina The MD simulations were performed using GROMACS
 2019.4 The REMD simulations were performed using
 GROMACS 2019.4
DOI: 10.5061/dryad.dncjsxkzs
title: Incomplete reproductive isolation and strong transcriptomic signature of hybridization between sympatric sister species of salmon

description: Global change is altering ecosystems at an unprecedented rate. The
 resulting shifts in species ranges and reproductive timing are opening the
 potential for hybridization between closely-related species which could
 dramatically alter the genetic diversity, adaptive capacity, and
 evolutionary trajectory of interbreeding taxa. Here, we used
 behavioural breeding experiments, in vitro fertilization experiments, and
 whole-transcriptome gene expression data to assess the potential for and
 consequences of hybridization between Chinook and Coho salmon. We show
 that behavioural and gametic prezygotic barriers between socioeconomically
 valuable Chinook and Coho salmon are incomplete. Postzygotically, we
 demonstrate a clear transcriptomic response to hybridization among F1
 Chinook-Coho offspring. Genes transgressively expressed within hybrids
 were significantly enriched with genes encoded in the nucleus but
 localized to the mitochindrion, suggesting a potential role for
 mito-nuclear incompatibilities as a postzygotic mechanism of hybrid
 breakdown. Chinook and Coho salmon are expected to continue to respond to
 climate change with shifts in migration timing and habitat use,
 potentiating hybridization between these species. The downstream
 consequences of hybridization on the future of these threatened salmon,
 and the ecosystems they inhabit, is unknown.
DOI: 10.5061/dryad.f7m0cfxvr
title: Genotype-environment interaction reveals varied developmental responses to unpredictable host phenology in a tropical insect

description: Understanding the genetic architecture of life history plasticity may
 inform resilience under environmental change, but relatively little is
 known for the inhabitants of unpredictable wet-dry tropical environments.
 Here I explore the quantitative genetics of juvenile growth and
 development relative to hostplant phenology in the butterfly Eurema
 hecabe. Wet season generations of this species breed explosively on
 leguminous annuals whereas dry season generations subsist at low density
 upon an alternative perennial host. The wet-to-dry season transition is
 temporally unpredictable and marked by widespread host defoliation,
 forcing a large cohort of stranded larvae to either pupate prematurely or
 prolong development in the hope of renewed foliage production. A
 split-brood experiment demonstrated greater performance on high quality
 annual as opposed to perennial host foliage and a marked decline under the
 stressed conditions faced by stranded wet season larvae. Genetic variances
 for rates of growth and development were equivalent among high quality
 treatments but strikingly elevated under resource stress, and the
 associated cross-environment genetic correlations were indistinguishable
 from zero. The results demonstrate genotype-environment interaction
 involving both rank order and variance scale, thereby revealing genetic
 variance for norms of reaction that may reflect variable risk aversion
 given an unpredictable tropical host phenology.
description: Missing values in the dataset are denoted "NA."
DOI: 10.5061/dryad.dv41ns1xp
title: Age-specific habitat preference, carrying capacity, and landscape structure determine the response of population spatial variability to fishing-driven age truncation

description: 1. Understanding the mechanisms underlying spatial variability of
 exploited fish is critical for the sustainable management of fish stocks.
 Empirical studies suggest that size-selective fishing can elevate fish
 population spatial variability (i.e., more heterogeneous distribution)
 through age truncation, making the population less resilient to changing
 environment. However, species differ in how their spatial variability
 respond to age truncation and the underlying mechanisms remain unclear. 2.
 We hypothesize that age-specific habitat preference, together with
 environmental carrying capacity and landscape structure, determines the
 response of population spatial variability to fishing-induced age
 truncation. To test these hypotheses, we design an individual-based model
 of an age-structured fish population on a two-dimensional landscape under
 size-selective fishing. Individual fish reproduces and survives, and moves
 between habitats according to age-specific habitat preference and
 density-dependent habitat selection. 3. Population spatial variability
 elevates with increasing age truncation and the response is stronger for
 populations with stronger age-specific habitat preference. On a gradient
 landscape, reducing carrying capacity elevates the relative importance of
 density-dependence in habitat selection, which weakens the response of
 spatial variability to age truncation for populations with strong
 age-specific habitat preference. On a fragmented landscape, both
 populations with strong and weak age-specific habitat preferences are
 restricted at local optimal habitats, and reducing carrying capacity
 weakens the responses of spatial variability to age truncation for both
 populations. 4. Synthesis and applications. We demonstrate that to track
 and predict the changes in population spatial variability under
 exploitation, it is essential to consider the interactive effects of
 age-specific habitat preference, carrying capacity, and landscape
 structure. To improve spatial management in fisheries, it is crucial to
 enhance empirical and theoretical developments in the methodology to
 quantify age-specific habitat preference of marine fish, and to understand
 how climatic change influences carrying capacity and landscape continuity.
DOI: 10.15468/dl.5mt47w
title: Occurrence Download

description: A dataset containing 223 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Saraca dives"
 ]
}

 The dataset includes 223 records from 26 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002827-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.np5hqbzsj
title: Dataset for estimation of the biotic and climatic niche breadths and geographic range size of beech (Fagus) species worldwide

description: This dataset could be used to test whether the commonly observed positive
 range size–niche breadth relationship, as posited by the “niche breadth
 hypothesis”, exists for Fagus, one of the most dominant and
 widespread broad‐leaved deciduous tree genera in temperate forests of the
 Northern Hemisphere. There are many ways to estimate niche breadth. Here,
 we estimated biotic and climatic niche breadths per species using
 plot‐based co‐occurrence data and climate data, respectively. The range
 sizes of the Fagus species were estimated with the raw data from the
 Chorology Database Halle. We examined the relationships of these
 estimates, and found that neither biotic niche breadth nor climatic niche
 breadth was correlated with range size, and the two niche breadths were
 incongruent as well. Our findings proved that the “niche breadth
 hypothesis” did not apply to the genus Fagus, and thus more attention
 should be paid to other factors (e.g., high among‐region variation in
 available niche space, landscape heterogeneity and Quaternary history)
 when explaining the geographic distribution patterns of Fagus. In
 addition, the climate data provided here could be used for climate-related
 studies on Fagus species worldwide.
description: The raw plot data for the estimation of biotic niche breadth can
 be applied from the sPlot vegetation database (Bruelheide et al., 2019),
 and the estimation method was described in Fridley et al. (2007) and
 Manthey & Fridley (2009). The climate data used for climatic niche
 breadth estimation were extracted from the CHELSA database
 (https://chelsa-climate.org/; Karger et al., 2017) based on the plot
 coordinates. The raw data for range size estimation were collected from
 sPlot as describe above and  Chorology Database Halle (CDH; <b style="cursor:pointer;text-align:start;">http://chorologie.biologie.uni</b><b style="cursor:pointer;text-align:start;">‐</b><b style="cursor:pointer;text-align:start;">halle.de//areale/</b>). For each <i style="text-align:start;">Fagus</i> species, the range size was calculated as the geographical area (km<sup>2</sup>) of the range polygons in an equal-area cartographic projection, and isolated point clusters were converted to minimum convex polygons.
description: See README file.
DOI: 10.15468/dl.qty7uz
title: Occurrence Download

description: A dataset containing 11554 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Peltophorum pterocarpum"
 ]
}

 The dataset includes 11554 records from 192 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002826-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.x3ffbg7j6
title: Whole genome re-sequencing of mother and offspring D. magna genotypes

description: Inbreeding refers to the fusion of related individuals' gametes, with
 self-fertilization (selfing) being an extreme form of inbreeding—involving
 gametes produced by the same individual. Selfing is expected to reduce
 heterozygosity by an average of 50 % in one generation; however, little is
 known about the empirical variation on a genome level surrounding this
 figure, and the factors that affect variation. We selfed genotypes of the
 cyclic parthenogen Daphnia magna and analyzed whole genomes of mothers and
 selfed offspring, observing the predicted 50 % heterozygosity reduction on
 average. We also saw substantial variation around this value and
 significant differences among mother-offspring pairs. Crossover analysis
 confirmed the known trend of recombination occurring more often towards
 the telomeres. This effect was shown, through simulations, to increase the
 variance of heterozygosity reduction compared to when a uniform
 distribution of crossovers was used. Similarly, we simulated inbred line
 production after several generations of selfing and we observed higher
 variance in achieved homozygosity when we consider a higher recombination
 rate towards the telomeres. Our empirical and simulation study highlights
 that the expected mean values of heterozygosity reduction show remarkable
 variation, which can help understand, for example, differences among
 inbred individuals.
DOI: 10.5061/dryad.fbg79cntn
title: Longer telomeres during early life predict higher lifetime fitness in females but not males

description: The mechanisms that contribute to variation in lifetime reproductive
 success are not well understood. One possibility is that telomeres,
 conserved DNA sequences at chromosome ends that often shorten with age and
 stress exposures, may reflect differences in vital processes or themselves
 influence fitness. Telomere length often predicts longevity, but longevity
 is only one component of fitness and little is known about how longevity
 and lifetime reproductive success relate to telomere dynamics in wild
 populations. We examined the relationships between telomere length
 beginning in early life, telomere loss into adulthood, and lifetime
 reproductive success in free-living house sparrows (Passer domesticus). We
 found that females, but not males, with longer telomeres during early life
 had higher lifetime reproductive success, due to associations with
 longevity and not reproduction per year or attempt. Telomeres decreased
 with age in both sexes, but telomere loss was not associated with lifetime
 fitness. Sparrow telomeres may reflect differences in quality or condition
 rather than in pace of life, but only in females. Sexually discordant
 selection on telomeres is expected to influence the stability and
 maintenance of within population variation in telomere dynamics and
 suggests that any role telomeres play in mediating life-history trade-offs
 may be sex specific.
description: The samples we used came from a long-term study of a free-living
 population of house sparrows (<i>Passer domesticus</i>)
 breeding in artificial nest boxes located at the University of Kentucky’s
 Agricultural Experiment Station North Farm complex in Lexington, KY. Blood
 samples were collected from birds in the nest at 10 days of age and then
 at least once post-independence. To measure relative telomere length, DNA
 was extracted from whole blood samples and relative telomere length was
 measured using quantitative PCR (qPCR). Measures of longevity and
 reproductive success were collected by frequent census of breeding sites
 (nest-boxes) to identify color-marked individuals and to document clutch
 size and survival of offspring to 10 days of age. The data have been
 organized into 4 datsets, described in the MS and the
 Supplement. 
description: Please see Read Me file for desciptions of variables in each of 4
 datasets. To replicate the analyses in the associated MS, see Supplement,
 uploaded here and available from PRSB when paper is published.
DOI: 10.5061/dryad.6t1g1jwz4
title: New opabiniid diversifies the weirdest wonders of the euarthropod stem group

description: Once considered ‘weird wonders’ of the Cambrian, the emblematic Burgess
 Shale animals Anomalocaris and Opabinia are now recognized as lower stem
 group euarthropods and have provided crucial data for constraining the
 polarity of key morphological characters in the group. Anomalocaris and
 its relatives (radiodonts) had a worldwide distribution and survived until
 at least the Devonian. However, despite intense study, Opabinia remains
 the only formally described opabiniid to date. Here we
 reinterpret a fossil from the Wheeler Formation of Utah as a new
 opabiniid, Utaurora comosa nov. gen. et sp. By visualizing the
 sample of phylogenetic topologies in treespace, our results fortify
 support for the position of U. comosa beyond the nodal support
 traditionally applied. Our phylogenetic evidence expands opabiniids to
 multiple Cambrian Stages. Our results underscore the power of treespace
 visualization for resolving imperfectly preserved fossils and expanding
 the known diversity and spatiotemporal ranges within the euarthropod lower
 stem group.
description: Readme file: README.txt Nexus (.nex) is a
 common file type for phylogenetic data, and the required runfile to use
 MrBayes for phylogenetic analysis. .p are sampled
 parameter files from MrBayes analysis, output for each run
 specified. Newick (.tre) files are phylogenetic tree
 outputs, which can be visualized directly e.g. with Figtree.
 .tnt is a file type for phylogenetic data, specifically the
 required runfile to conduct maximum parsimony phylogenetic analysis in
 TNT.
DOI: 10.5061/dryad.ngf1vhht8
title: No short-term effect of sinking microplastics on heterotrophy or sediment clearing in the tropical coral Stylophora pistillata

description: Investigations of encounters between corals and microplastics have, to
 date, used particle concentrations that are several orders of magnitude
 above environmentally relevant levels. Here we investigate whether
 concentrations closer to values reported in tropical coral reefs affect
 sediment shedding and heterotrophy in reef-building corals. We show that
 single-pulse microplastic deposition elicits significantly more coral
 polyp retraction than comparable amounts of calcareous sediments. When
 deposited separately from sediments, microplastics remain longer on corals
 than sediments, through stronger adhesion and longer periods of
 examination by the coral polyps. Contamination of sediments with
 microplastics does not retard corals’ sediment clearing rates. Rather,
 sediments speed-up microplastic shedding, possibly affecting its
 electrostatic behaviour. Heterotrophy rates are three times higher than
 microplastic ingestion rates when corals encounter microzooplankton
 (Artemia salina cysts) and microplastics separately. Exposed to
 cysts-microplastic combinations, corals feed preferentially on cysts
 regardless of microplastic concentration. Chronic-exposure experiments
 should test whether our conclusions hold true under environmental
 conditions typical of inshore marginal coral reefs.
DOI: 10.5061/dryad.s1rn8pk76
title: Data from: Prevalence of disability associated with head injury with loss of consciousness: a population-based study

description: Objective: To provide nationally representative prevalence estimates of
 disability associated with prior head injury with loss of consciousness in
 the U.S. and to examine associations between prior head injury and
 disability. Methods: Cross-sectional analysis of 7,390 participants
 aged ³40 years in the 2011-2014 National Health and Nutrition
 Examination Surveys (NHANES). Head injury with loss of
 consciousness was assessed by self-report. Domains of disability were
 assessed using a standardized structured questionnaire and measured grip
 strength. Logistic regression models adjusted for demographic,
 socioeconomic/behavioral, and medical comorbidity variables were used.
 Multiple imputation was used to account for missing covariate data.
 Results: Mean age of participants was 58 years, 53% were female, 71% were
 non-Hispanic white, and 16% had a history of head injury. Overall,
 participants with a history of head injury had higher prevalence of
 disability in at least one domain of functioning compared to individuals
 without a history of head injury (47.4% versus 38.6%, p&lt;0.001),
 with the highest prevalence of disability in the domains of mobility and
 work productivity. In fully adjusted models, head injury was
 significantly positively associated with disability in all domains
 assessed on the standardized questionnaire (all
 p&lt;0.05), but not with upper extremity grip strength (all
 p&gt;0.05). Conclusions: 47.4% of individuals aged ≥40 years
 in the U.S with a history of head injury are living with disability in at
 least one domain of functioning, corresponding to approximately 11.4
 million affected individuals. This significant burden of disability
 suggests that efforts are needed to improve functioning among individuals
 with head injury.
DOI: 10.5061/dryad.6q573n5z8
title: Substrate induced currents through the monoamine transporters and single cell uptake of the fluorescent substrate APP+

description: The concentrative power of the transporters for dopamine (DAT),
 norepinephrine (NET) and serotonin (SERT) is thought to be fueled by the
 transmembrane Na+ gradient, but it is conceivable that they can also tap
 other energy sources, e.g. membrane voltage and/or the transmembrane K+
 gradient. We address this by recording uptake of endogenous substrates or
 the fluorescent substrate APP+
 ((4-(4-dimethylamino)phenyl-1-methylpyridinium) under voltage control in
 cells expressing DAT, NET or SERT. We show that DAT and NET differ from
 SERT in intracellular handling of K+. In DAT and NET, substrate uptake was
 voltage-dependent due to the transient nature of intracellular K+ binding,
 which precluded K+ antiport. SERT, however, antiports K+ and achieves
 voltage-independent transport. Thus, there is a trade-off between
 maintaining constant uptake and harvesting membrane potential for
 concentrative power, which we conclude to occur due to subtle differences
 in the kinetics of co-substrate ion binding in closely related
 transporters.
description: Collected via Clampex (Axon-Instruments) . It has not been
 processed. The data sets are raw files.
description: Can be visualized and analyzed with Clampfit
 (Axon-Instruments).
DOI: 10.5061/dryad.fj6q573tm
title: A Bayesian optimal escape model reveals bird species differ in their capacity to habituate to humans

description: The capacity to habituate to, or tolerate, the close proximity of humans
 varies among wildlife species and may mediate population and species
 viability. Some species readily habituate to human proximity while others
 remain sensitive. These differences are important for predicting human
 impact on wildlife, but can be difficult to quantify given wildlife
 responses are highly idiosyncratic and are often context-dependent. A
 general method for assimilating multiple sources of information and
 variation in individual responses is needed to extract meaningful
 descriptors of population- and species-level behavior. We apply a
 previously verified Bayesian optimal escape model to quantify differences
 in the perceived risk of seven species of waterbird, and generate a metric
 for species-specific sensitivity by estimating the relative change in risk
 perception of each species across an environmental gradient from low to
 high prevailing human activity level. We found that, in general, birds are
 the least habituated (evidently perceived the highest level of risk from
 humans) in sites with low human activity and the most habituated
 (evidently perceived lower levels of risk from humans) in sites with high
 human activity. Species varied in the degree of these differences, with
 some insensitive to human activity level, while others were highly
 sensitive. Aside from improving our ability to study the habituation of
 wild populations, this method for quantifying risk perception at
 population and species scales has broad applications in the management and
 monitoring of wildlife, and may aid in environmental impact assessments
 and identifying populations/species susceptible to disturbance.
description: Please see the associated README file for steps to run the
 included code and analyses using this data.