cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.37pvmcvfj
title: Genome data for avian MHC

description: Long-read sequencing technology has the potential to greatly improve our
 understanding of the Major Histocompatibility Complex (MHC), which is a
 major component of the adaptive immune system, but it has been difficult
 to study because of highly repetitive regions. In this study we used
 genomes based on long-read sequencing to predict the number and location
 of MHC loci in a broad range of bird taxa. We also examined species that
 had not previously been studied at the MHC but had a published genome.
 Overall, in the long-read based genomes of 28 species, we found that there
 was extremely large variation in the number of MHC loci in passerines,
 particularly in manakins (up to 193 class II loci), which had previously
 not been studied at the MHC. Overall, there were greater numbers of both
 class I and II loci in passerines than non-passerines. Our results provide
 the first direct evidence from passerine genomes of this high level of
 duplication. We also found different duplication patterns; i.e., in some
 species both MHC class I and II genes were duplicated together, while in
 most species they were duplicated separately. Our study shows that
 long-read sequencing can provide dramatic increases in our knowledge of
 MHC structure, although further improvements in chromosome level assembly
 are needed to study the mechanisms producing these high levels of
 duplication.
DOI: 10.5061/dryad.tb2rbnzwp
title: Data from: Can patterns of habitat use by western Nearctic-Neotropical migratory landbirds in winter inform conservation priorities?

description: ABSTRACT—I use point-count survey data collected from 171 locations across
 11 vegetation conditions in western Mexico to illustrate common patterns
 of winter habitat use by 97 Nearctic-Neotropical migratory landbird
 species.  A number of bird species are relatively restricted in
 their habitat use, with some [e.g., Northern Waterthrush (Parkesia
 noveboracensis), American Redstart (Setophaga ruticilla)] occurring only
 in relatively undisturbed habitats, and others [e.g., Say’s Phoebe
 (Sayornis saya), Horned Lark (Eremophila alpestris)] occurring only in
 relatively disturbed lands associated with agriculture.  A large
 number of bird species [e.g., Cassin’s Vireo (Vireo cassinii),
 MacGillivray’s Warbler (Geothlypis tolmiei)] use every one of the
 vegetation types considered, from low-elevation tropical deciduous forests
 to high-elevation conifer forests.  Bird species showing patterns
 of restricted habitat use deserve conservation attention, but so might
 more broadly distributed species that become significantly less abundant
 in human-altered habitats.  Identifying the latter will require
 the inclusion of a wider spectrum of altered vegetation types/conditions
 than what I included here, or than what is typically considered in
 wildlife-habitat relationship programs.
description: data were collected using 10-minute point counts in locations
 outlined in manuscript.  Each line is the result of a count, with the
 occurrence of coded bird species indicated by a zero (absent) or a 1
 (present).  Bird variables are conventional 4-letter codes for English
 names; codes are translated in the separate metadata file.
 videos were recorded on a hi-8 camcorder
description: nothing else
DOI: 10.5061/dryad.z34tmpg8f
title: Mechanisms for color convergence in a mimetic radiation of poison frogs

description: In animals, bright colors often evolve to mimic other species when a
 resemblance is selectively favored. Understanding the proximate mechanisms
 underlying such color mimicry can give insights into how mimicry evolves,
 for example, whether color convergence evolves from a shared set of
 mechanisms or through the evolution of novel color production mechanisms.
 We studied color production mechanisms in poison frogs (Dendrobatidae),
 focusing on the mimicry complex of Ranitomeya imitator. Using reflectance
 spectrometry, skin pigment analysis, electron microscopy, and color
 modeling, we found that the bright colors of these frogs, both within and
 outside the mimicry complex, are largely structural and produced by
 iridophores, but that color production depends crucially on interactions
 with pigments. Color variation and mimicry is regulated predominantly by
 iridophore platelet thickness and, to a lesser extent, concentration of
 the red pteridine pigment drosopterin. Compared to each of the four morphs
 of model species which it resembles, R. imitator displays greater
 variation in both structural and pigmentary mechanisms, which may have
 facilitated phenotypic divergence in this species. Analyses of non-mimetic
 dendrobatids in other genera demonstrate that these mechanisms are
 widespread within the family, and that poison frogs share a complex
 physiological “color palette” that can produce diverse and highly
 reflective colors.
description: see manuscript
description: see README document A description of how to
 use these scripts is available in "top_level_text.R"
 In order to properly use these scripts, read all of the
 documentation until the heading "code" Note:
 The structural color production model presented here relies on methods
 (matrix transfer function "multilayer_adj" in
 "functions.R") previously developed by: Maia, R., Caetano, J. V.
 O., Bao, S. N., & Macedo, R. H. (2009). Iridescent structural
 colour production in male blue-black grassquit feather barbules: the role
 of keratin and melanin. Journal of the Royal Society Interface,
 6(suppl_2), S203-S211. See link to projects github
 repository below https://github.com/morgankain/Twomey_et_al_color_mimicry
DOI: 10.5061/dryad.ghx3ffbjn
title: High-resolution modelling of uplift landscapes can inform micro-siting of wind turbines for soaring raptors

description: Collision risk of soaring birds is partly associated with updrafts to
 which they are attracted. To identify risk-enhancing landscape features, a
 micro-siting tool was developed to model orographic and thermal updraft
 velocities from high-resolution remote sensing data. The tool was applied
 to the island of Hitra, and validated using GPS-tracked white-tailed
 eagles (Haliaeetus albicilla). Resource selection functions predicted that
 eagles preferred ridges with high orographic uplift, especially at flight
 altitudes within the rotor-swept zone (40-110 m). Flight activity was
 negatively associated with the widely distributed areas with high thermal
 uplift at lower flight altitudes (&lt;110 m). Both the existing
 wind-power plant and planned extension are placed at locations rendering
 maximum orographic updraft velocities around the minimum sink rate for
 white-tailed eagles (0.75 m/s) but slightly higher thermal updraft
 velocities. The tool can contribute to improved micro-siting of wind
 turbines to reduce environmental impacts, especially for soaring raptors.
DOI: 10.5061/dryad.fbg79cnr6
title: Data from: The association between morphological and ecological characters across a global passerine radiation

description: Strong relationships between morphological and ecological characters are
 commonly predicted to reflect the association between form and function,
 with this hypothesis being well supported in restricted taxonomic and
 geographic contexts. Conversely, among broader sets of species, ecological
 variables have been shown to have limited power to explain morphological
 variation.    To understand these apparent
 discrepancies, for a large and globally distributed passerine radiation we
 test (i) whether the character states of four ecological variables
 (foraging mode, diet, strata and habitat) have different morphological
 optima, (ii) whether ecological variables explain substantial variance in
 morphology, and (iii) whether ecological character states can be
 accurately predicted from morphology. We collected ten linear
 morphological measurements for 782 species of corvoid passerines, and
 assessed (i) the fit of models of continuous trait evolution with
 different morphological optima for each ecological character state, (ii)
 variation in morphological traits among ecological character states using
 phylogenetically corrected regressions, and (iii) the accuracy of
 morphological traits in predicting species-level membership of ecological
 character states using linear discriminant analysis (LDA). Models of
 morphological evolution with different ecological optima were well
 supported across numerous morphological axes, corresponding with
 significant differences in trait distributions among ecological character
 states. LDA also showed that membership of the ecological categories can
 be predicted with relatively high accuracy by morphology. In contrast to
 these findings, ecological variables explain limited amounts of variation
 in morphological traits. For a global radiation of passerine birds, we
 confirm that the generation of morphological variation is generally
 consistent with ecological selection pressures, but that ecological
 characters are of limited utility in explaining morphological differences
 among species. Although selection towards different optima means that
 membership of ecological character states tend to be well predicted by
 morphology, the overall morphospace of individual ecological character
 states tend to be broad, implying that morphology can evolve in multiple
 ways in response to similar selection pressures. Extensive variation in
 morphological adaptations among similar ecological strategies is likely to
 be a widespread phenomenon across the tree of life.
DOI: 10.5061/dryad.vmcvdncpf
title: Data from: Decoding and encoding models reveal the role of mental simulation in the brain representation of meaning

description: How the brain representation of conceptual knowledge vary as a function of
 processing goals, strategies and task-factors remains a key unresolved
 question in cognitive neuroscience. Here we asked how the brain
 representation of semantic categories is shaped by the depth of processing
 during mental simulation. Participants were presented with visual words
 during functional magnetic resonance imaging (fMRI). During shallow
 processing, participants had to read the items. During deep processing,
 they had to mentally simulate the features associated with the words.
 Multivariate classification, informational connectivity and encoding
 models were used to reveal how the depth of processing determines the
 brain representation of word meaning. Decoding accuracy in putative
 substrates of the semantic network was enhanced when the depth processing
 was high, and the brain representations were more generalizable in
 semantic space relative to shallow processing contexts. This pattern was
 observed even in association areas in inferior frontal and parietal
 cortex. Deep information processing during mental simulation also
 increased the informational connectivity within key substrates of the
 semantic network. To further examine the properties of the words encoded
 in brain activity, we compared computer vision models - associated with
 the image referents of the words - and word embedding. Computer vision
 models explained more variance of the brain responses across multiple
 areas of the semantic network. These results indicate that the brain
 representation of word meaning is highly malleable by the depth of
 processing imposed by the task, relies on access to visual representations
 and is highly distributed, including prefrontal areas previously
 implicated in semantic control.
DOI: 10.25574/30641
title: Chandra X-ray Observatory ObsId 30641

description: The rise in flux of zeta Puppis
DOI: 10.5061/dryad.w3r2280m1
title: Assessing intrastate cattle shipments from interstate data and expert opinion

description: Live animal shipments are a potential route for transmitting animal
 diseases between holdings and are crucial when modeling spread of
 infectious diseases. Yet, complete contact networks are not available in
 all countries, including the United States. Here, we considered a 10%
 sample of Interstate Certificate of Veterinary Inspections from one year
 (2009). We focused on distance dependence in contacts and investigated how
 different functional forms affect estimates of unobserved intrastate
 shipments. To further enhance our predictions, we included responses from
 an expert elicitation survey about the proportion of shipments moving
 intrastate. We used hierarchical Bayesian modeling to estimate parameters
 describing the kernel and effects of expert data. We considered three
 functional forms of spatial kernels and the inclusion or exclusion of
 expert data. The resulting six models were ranked by WAIC and DIC and
 evaluated through within- and out-of-sample validation. We showed that
 predictions of intrastate shipments were mildly influenced by the
 functional form of the spatial kernel but kernel shapes that permitted a
 fat tail at large distances while maintaining a plateau shaped behavior at
 short distances better were preferred. Further, our study showed that
 expert data may not guarantee enhanced predictions when expert estimate
 are disparate.
DOI: 10.15468/dl.97evnb
title: Occurrence Download

description: A dataset containing 670 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-116.40813 49.44101,-116.45034 44.46247,-100.8779 44.37205,-100.32928 49.46844,-116.40813 49.44101))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Grindelia squarrosa",
 "Year 2015-2026"
 ]
}

 The dataset includes 670 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002068-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25574/30683
title: Chandra X-ray Observatory ObsId 30683

description: AO-26 Big Dither Observation of Mkn421
DOI: 10.5061/dryad.cjsxksn27
title: Data from: Morphological and physiological consequences of a dietary restriction during early life in bats

description: Early life adverse conditions can have major consequences on an
 individual’s life history traits. Oxidative stress has been hypothesized
 to be one main mechanism underlying the negative consequences of early
 life adverse conditions. To test this hypothesis, we restricted the food
 availability of Seba’s short-tailed bat (Carollia perspicillata) mothers
 of unweaned pups for 10 days, followed by ad libitum provisioning. We also
 had a control, unrestricted group. We explored the morphological
 consequences of dietary restriction during early life by measuring growth
 rate. We also measured four markers of blood oxidative balance during
 growth. We assessed the level of cortisol, and its inactive form
 cortisone, in the hair of the pups at the end of growth. Finally, we
 monitored survival during the first year. Food restriction triggered a
 slowdown in growth followed by catch-up growth when ad libitum feeding was
 restored which did not lead to full compensation in size or mass compared
 to control individuals. We found that higher growth rate was associated
 with elevated oxidative damage, suggesting an oxidative cost to
 growth.However, we found no clear evidence for physiological costs
 specific to the catch-up growth. Survival after a year was not impacted by
 the treatment, the oxidative balance or the level of glucocorticoids at
 the end of growth. In conclusion, our results show that individuals were
 able to efficiently mitigate the short-term consequences of adverse early
 life conditions. However, consequences might arise on the long-term, and
 could impact reproductive success or lifespan.
DOI: 10.5061/dryad.h18931zg6
title: Contrasting impacts of a novel specialist vector on multi-host viral pathogen epidemiology in wild and managed bees

description: Typically pathogens infect multiple host species. Such multi-host
 pathogens can show considerable variation in their degree of infection and
 transmission specificity, which has important implications for potential
 disease emergence. Transmission of multi-host pathogens can be driven by
 key host species and changes in such transmission networks can lead to
 disease emergence. We study two viruses that show contrasting patterns of
 prevalence and specificity in managed honeybees and wild bumblebees, black
 queen cell virus (BQCV) and slow bee paralysis virus (SBPV), in the
 context of the novel transmission route provided by the virus-vectoring
 Varroa destructor. Our key result is that viral communities and RNA virus
 genetic variation are structured by location, not host species or V.
 destructor presence. Interspecific transmission is pervasive with the same
 viral variants circulating between pollinator hosts in each location; yet,
 we find virus-specific host differences in prevalence and viral load.
 Importantly, V. destructor presence increases the prevalence in honeybees
 and, indirectly, in wild bumblebees, but in contrast to its impact on
 deformed wing virus (DWV), BQCV and SBPV viral loads are not increased by
 Varroa presence, and do not show genetic evidence of recent emergence.
 Effective control of Varroa in managed honeybee colonies is necessary to
 mitigate further disease emergence, and alleviate disease pressure on our
 vital wild bee populations. More generally, our results highlight the
 over-riding importance of geographical location to the epidemiological
 outcome despite the complexity of multi-host-parasite interactions.
description: We collected foraging bees (355 <i>A. mellifera</i>,
 281 <i>B. pascuorum</i>, 640 <i>B. terrestris</i>
 and 38 <i>B. lucorum </i>individuals) within a 1x1 km area,
 from four <i>Varroa</i>-free islands; three
 <i>Varroa</i>-positive islands; and five
 <i>Varroa</i>-positive mainland sites. We extracted RNA from
 individual bees, and converted it to cDNA and carried out PCRs and qPCR
 assays for individual viruses (black queen cell virus and slow bee
 paralysis virus) to collect prevalence data and viral load data. We also
 carried out Sanger and Pacbio sequencing, these data are uploaded to
 Genbank and accession numbers are detailed in the paper.
DOI: 10.15468/dl.a22muz
title: Occurrence Download

description: A dataset containing 636 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-115.27973 49.53,-115.56099 44.72315,-100.89498 44.66602,-101.85932 49.29472,-115.27973 49.53))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Heterotheca villosa",
 "Year 2015-2026"
 ]
}

 The dataset includes 636 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002071-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.g1jwstqmt
title: Homeless persons use of unscheduled care in St James's Hospital August 2015-July 2017

description: The data contains all ED presentations and unscheduled admissions to St
 James's Hospital, Dublin, from August 2015 to July 2017. Data has
 been anonymised. Individuals are coded as homeless (1) or non-homeless (2)
 based on the address recorded on their patient record.
DOI: 10.5061/dryad.vq83bk3p2
title: Natural variation for carotenoids in fresh kernels is controlled by uncommon variants in sweet corn

description: Sweet corn (Zea mays L.) is highly consumed in the United States,
 but does not make major contributions to the daily intake of carotenoids
 (provitamin A carotenoids, lutein and zeaxanthin) that would help in the
 prevention of health complications. A genome-wide association study of
 seven kernel carotenoids and twelve derivative traits was conducted in a
 sweet corn inbred line association panel ranging from light to dark yellow
 in endosperm color to elucidate the genetic basis of carotenoid levels in
 fresh kernels. In agreement with earlier studies of maize kernels
 at maturity, we detected an association of ß-carotene
 hydroxylase (crtRB1) with ß-carotene concentration
 and lycopene epsilon cyclase (lcyE) with the
 ratio of flux between the α- and ß-carotene branches in
 the carotenoid biosynthetic pathway. Additionally, we found that 5% or
 less of the evaluated inbred lines possessing
 the shrunken2 (sh2) endosperm mutation had the most
 favorable lycE allele
 or crtRB1 haplotype for elevating ß-branch
 carotenoids (ß-carotene and zeaxanthin) or ß-carotene,
 respectively. Genomic prediction models with genome-wide markers obtained
 moderately high predictive abilities for the carotenoid traits, especially
 lutein, and outperformed models with less markers that targeted candidate
 genes implicated in the synthesis, retention, and/or genetic control
 of kernel carotenoids. Taken together, our results constitute an
 important step toward increasing carotenoids in fresh sweet corn kernels.
description: FILLIN partially imputed genotypes from 308 sweet corn inbred
 lines using genotyping-by-sequencing (GBS) with 172,486 high confidence
 single-nucleotide polymorphism markers (SNPs) that were called using
 default parameters in the TASSEL 5 GBSv1 production pipeline with the
 ZeaGBSv2.7 Production TagsOnPhysicalMapfile in B73 RefGen_v2 coordinates.
 File in Hapmap format.
DOI: 10.25338/b8kg77
title: Bicycling comfort video experiment

description: This tabular data can be used to evaluate perceived bicycling
 comfort on distinct state highways in California. The highway settings are
 primarily urban, but vary in traffic conditions, lane configurations,
 speeds, and bicycling infrastructure. The data include survey responses to
 video clips of these state highways along with a series of additional
 survey data that co-varies with the video survey responses.
description: Data was gathered for this project
 from the Fall 2017 UC Davis Campus Travel Survey (CTS). The data includes
 participant ratings of bicycling comfort in a block designed video
 experiment. Other variables related to socio-demographics, travel
 characteristics, travel attitudes, travel perceptions, and travel
 experiences were collected in the survey. Most survey questions are
 measured on ratio and nominal scales. The CTS was an online web-survey
 using Qualtrics. The video clips and attributes of the video clips were
 obtained from UC Berkeley SafeTREC.
description: A description for each variable is provided in an associated
 metadata file. Missing values are present in many variables when survey
 participants chose not to answer a question (indicated by NA or
 blanks).