cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.4qrfj6qcx
title: Data for: On the identification of hypoxic regions in subject-specific cerebral vasculature by combined CFD/MRI

description: A long-time exposure to lack of oxygen (hypoxia) in some regions of the
 cerebrovascular system is believed to be one of the causes of cerebral
 neurological disease. Performing {\em in vivo} studies on the human brain
 is complicated and can be highly risky for patients. In the present study,
 we show how a combination of Magnetic Resonance Imaging (MRI) and
 Computational Fluid Dynamics (CFD) can provide a non-invasive alternative
 for studying blood flow and transport of oxygen within the cerebral
 vasculature. We perform computer simulations of oxygen mass transfer in
 the subject-specific geometry of the Circle of Willis. The computational
 domain and boundary conditions are based on 4D flow MRI measurements. Two
 different oxygen mass transfer models are considered: passive (where
 oxygen is treated as a dilute chemical species in plasma) and active
 (where oxygen is bonded to hemoglobin) models. We show that neglecting
 hemoglobin transport results in a significant underestimation of the
 arterial wall-mass transfer of oxygen. We identified the hypoxic regions
 along the arterial walls by introducing the critical thresholds that are
 obtained by comparison of the estimated range of Damk\"{o}hler number
 ($Da\subset\langle9;57\rangle$) with the local Sherwood number. Finally,
 we recommend additional validations of the combined MRI/CFD approach
 proposed here for larger groups of subject- or patient-specific brain
 vasculature systems.
description: The results obtained are performed by the computational fluid
 dynamics (CFD) of the blood flow in the subject-specific of the brain
 vascular system.  The data are saved in the Tecplot
 visualization software format (.plt).
description: The data are saved in the Tecplot visualization software format
 (.plt) (www.tecplot.com). The data can be opened directly from Tecplot or by using open-source visualization software ParaView.
DOI: 10.5061/dryad.dv41ns21s
title: Data for: Can pharmaceutical pollution alter the spread of infectious disease? A case study using fluoxetine.

description: Human activity is changing global environments at an unprecedented rate,
 imposing new ecological and evolutionary ramifications on wildlife
 dynamics, including host-parasite interactions. Here we investigate how an
 emerging concern of modern human activity, pharmaceutical pollution,
 influences the spread of disease in a population, using the water flea
 Daphnia magna and the bacterial pathogen Pasteuria ramosa as a model
 system. We found that exposure to different concentrations of fluoxetine—a
 widely prescribed psychoactive drug and widespread contaminant of aquatic
 ecosystems—affected the severity of disease experienced by an individual
 in a non-monotonic manner. The direction and magnitude of any effect,
 however, varied with both the infection outcome measured, as well as the
 genotype of the pathogen. In contrast, the characteristics of unexposed
 animals, and thus the growth and density of susceptible hosts, were robust
 to fluoxetine. Using our data to parameterise an epidemiology model, we
 show that fluoxetine is unlikely to lead to a net increase or decrease in
 the likelihood of an infectious disease outbreak, as measured by a
 pathogen’s transmission rate or basic reproductive number. Instead, any
 given pathogen genotype may experience a two-fold change in likely
 fitness, but often in opposing directions. Our study demonstrates that
 changes in pharmaceutical pollution give rise to complex
 genotype-by-environment interactions in its influence on disease dynamics,
 with repercussions on pathogen genetic diversity and evolution.
DOI: 10.5061/dryad.g4f4qrfsx
title: An underwater Serengeti: Seagrass-mediated effects on intake and cultivation grazing behavior of a marine megaherbivore

description: Populations of green turtles (Chelonia mydas), a megaherbivore that
 consumes seagrasses via cultivation grazing, are recovering worldwide.
 Information on plant-mediated effects on herbivore foraging behavior is
 critical to understanding plant-herbivore interactions and sustainability
 of grazing as ecosystems continue to change. In a Caribbean seagrass
 ecosystem, we use stationary cameras and benthic surveys to evaluate
 effects of seagrass morphology and leaf nitrogen content on green turtle
 grazing behavior. Thalassia testudinum leaf morphology has significant
 effects on forage intake (mg dry mass [DM] min-1) for green turtles,
 whereas leaf nitrogen content has no effect. Intake increases in grazed
 areas with shorter leaves and higher leaf biomass concentration (mg DM
 cm-3), indicating more efficient foraging under these conditions. Bite
 rate (bites min-1) increases in grazed areas with short leaves, a result
 of reduced search time. Bite size (mg DM bite-1) increases in grazed areas
 with short but dense canopies, because a turtle crops more shoots with
 each bite. Increased foraging efficiency and reduced search time in grazed
 areas with high biomass concentrations collectively maximize intake.
 Ingested leaves are shorter than the mean height of all available leaves
 in grazed areas, indicating herbivore selection for shorter leaves. Our
 estimate for daily intake is 86.1 g DM d-1 per 33-kg turtle. Our study
 provides a novel contribution on the effects of plant-level cues on the
 grazing behavior of a marine megaherbivore, and how cultivation grazing
 behavior optimizes the green turtle foraging strategy by maximizing
 foraging efficiency and intake.
description: Please refer to the corresponding publication for detailed
 methodology.
description: Please refer to attached Readme.txt file
DOI: 10.5061/dryad.wstqjq2pv
title: Survival data of Martes Americana and landscape variables associated with mortality events

description: To test the effects of seasonal heterogeneity on a reintroduced carnivore,
 American martens (Martes americana), we compared metrics of local and
 season-specific heterogeneity to traditional forest metrics on the
 survival of 242 individuals across 8 years and predicted a survival
 landscape for 13 reintroduction sites. We identified a set of variables
 that characterized potentially important drivers of marten survival,
 allowing for a comparison between heterogeneity metrics (i.e., complexity
 of vegetation, land cover, and abiotic conditions) and landscape variables
 representing composition and configuration. We summarized environmental
 conditions encountered by individuals by extracting landscape variables
 and measures of heterogeneity within 95% kernel density estimate. To test
 the influence of landscape variables and heterogeneity on survival, we
 modeled mortality risk from time-to-event data using a Bayesian framework.
DOI: 10.15468/dl.5snycu
title: Occurrence Download

description: A dataset containing 519 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 Myosotis sylvatica"
 ]
}

 The dataset includes 519 records from 28 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003167-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.m63xsj44w
title: Ungulate herbivores as drivers of Aspen recruitment and understory composition throughout arid Montane landscapes

description: Herbivory by wild and domestic ungulates can influence tree recruitment
 and understory forest communities throughout the world. Herbivore-driven
 declines in tree recruitment have been observed for quaking aspen (Populus
 tremuloides), a foundation species whose health and management is
 recognized as a critical priority throughout much of its range. Livestock
 fencing is commonly used to promote aspen regeneration, but its
 effectiveness is rarely assessed, especially across large spatial scales.
 Using a livestock-reduction experiment, we evaluated the effects of
 ungulate herbivory on aspen in the Great Basin and southern Cascades, an
 expansive and environmentally heterogeneous region where aspen faces the
 interacting threats of climate change, conifer encroachment, and
 herbivory. We found that livestock fencing only reduced the intensity of
 herbivore browsing on aspen when wild ungulate abundance was low, and did
 not increase stem densities of aspen recruits. Contrary to expectations,
 wild ungulate abundance was a strong driver of browsing intensity on
 juvenile aspen within fenced, but not unfenced aspen stands, and when the
 abundance of these herbivores was high, browsing intensity in fenced
 stands exceeded that in unfenced stands. The density of aspen recruits
 decreased with browsing intensity on juvenile aspen and with the density
 of both adult aspen and conifers, suggesting that both herbivory and
 intra- and interspecific competition are important drivers of recruitment.
 Fire history was also an important driver of recruitment, with stands that
 burned 10-20 years ago having the greatest density of aspen recruits.
 Finally, in the stand understory, we found that livestock fencing
 decreased forb cover, increased shrub species richness, and increased the
 cover of exotic annual grasses, a group dominated by Bromus tectorum. This
 latter finding suggests that livestock fencing may not be appropriate in
 areas where controlling the spread of this invader is a priority. In sum,
 our findings indicate that aspen recruitment is limited by browsing by
 both wild and domestic ungulates, is mediated by competition with
 neighboring trees and fire history, and will require management actions
 beyond livestock fencing, as this approach does not control browsing by
 wild ungulates.
DOI: 10.5061/dryad.80gb5mktb
title: Paleohistological inferences of thermometabolic regimes in Notosuchia

description: Notosuchia is a group of mostly terrestrial crocodyliforms. The presence
 of a prominent crest overhanging the acetabulum, slender straight-shafted
 long bones with muscular insertions close to the joints, and a stable knee
 joint, suggests that they had an erect posture. This stance has been
 proposed to be linked to endothermy because it is present in mammals and
 birds, and it contributes to the efficiency of their respiratory systems.
 However, a bone paleohistological study unexpectedly suggested that
 Notosuchia were ectothermic organisms. The thermophysiological status of
 Notosuchia deserves further analysis because the methodology of the quoted
 study can be improved. First, it was based on a relationship between red
 blood cell size and bone vascular canal diameter tested using 14 extant
 tetrapod species. Here we present evidence for this relationship using a
 more comprehensive sample of extant tetrapods (31 species). Moreover,
 contrary to previous results, bone cross-sectional area appears as a
 significant explanatory variable (in addition to bone vascular canal
 diameter). Second, red blood cell size estimations were performed using
 phylogenetic eigenvector maps, and this method excludes a fraction of
 phylogenetic information. This is because it generates a high number of
 eigenvectors requiring a selection procedure to compile a subset of them
 to avoid model overfitting. Here we inferred the thermophysiology of
 Notosuchia using phylogenetic logistic regressions, a method that
 overcomes this problem by including the whole phylogenetic information.
 These analyses suggest that Araripesuchus wegeneri, Armadillosuchus
 arrudai, Baurusuchus sp., Iberosuchus macrodon and Stratiotosuchus
 maxhechti were ectothermic organisms.
DOI: 10.5061/dryad.h44j0zpp2
title: Light and malaise traps tell different stories about the spatial variations in arthropod biomass and method-specific insect abundance

description: 1. Conclusions reached in meta-analyses of changes in insect communities
 may be influenced by method-specific sampling biases, which may lead to
 inappropriate conservation measures. 2. We argue that the
 contradictory conclusions regarding terrestrial insect biomass, abundance
 and richness patterns are, at least partly, due to methodological
 limitations that reflect taxon-specific responses to environmental
 changes. 3. In this study, light and Malaise traps were
 simultaneously deployed to sample insects at 52 plots in a temperate
 forest in Germany along gradients of elevation (&gt; 1000 m) and
 canopy openness (3 - 100 %). These gradients were used as predictors in
 models of total arthropod biomass according to the two trapping methods,
 and in models of abundance and richness of three commonly targeted groups:
 nocturnal moths, sampled using light traps, and hoverflies and bees,
 collected with Malaise traps. 4. A comparison of the total
 arthropod biomass obtained with the two methods revealed contrary results
 along the canopy openness gradient. Biomass in light traps showed a
 decreasing trend with increasing canopy openness while biomass in Malaise
 traps increased. The same opposing pattern was found for the abundance of
 selected taxa. 5. The different patterns describing spatial
 variation of arthropod communities obtained using light and Malaise traps
 can be explained by differences in the taxa predominantly collected.
 Regarding the ongoing debate on insect decline, our results demonstrate
 that comparing different taxa from different taxon-specific traps is
 inappropriate. Thus, we recommend that future meta-analyses take into
 account the sampling methods and taxon-specific responses to environmental
 changes.
description: Comparison of two insect trapping method with regard to biomass,
 abundance and species richness.
DOI: 10.5061/dryad.dv41ns21t
title: Files associated with: Migration-based simulations for Canadian trees show limited tracking of suitable climate under climate change

description: Aim Species distribution models typically project climatically suitable
 habitat for trees in eastern North America to shift hundreds of kilometers
 this century. We simulated potential migration considering species’ life
 history and traits for 10 tree species and their ability to track
 climatically suitable habitat. Location Eastern Canada, covering ~3.7
 million km2 Methods We simulated migration-constrained range shifts
 through 2100 using a hybrid approach combining projections of climatically
 suitable habitat based on two Representative Concentration Pathways
 (RCP4.5, RCP8.5) for three time periods and two species distribution
 modelling approaches with process-based models parameterized using data
 related to dispersal ability and generation time. We developed a unique
 ‘migration kernel’ that uses seed dispersal traits and observed migration
 velocities to obtain kernel shape and dispersal probabilities. We then
 calculated lags between the migration-constrained range limits obtained
 through simulations and limits of climatically suitable habitat. Results
 All species demonstrated northward range shifts at the leading edge of
 their simulated distribution through 2100, but the magnitude and rate of
 that shift varied by species and time period. Climatically suitable
 habitat limits were found to be north of simulated distribution limits
 across both RCPs, with lags increasing through time. On average, the
 simulated distribution that remained within climatically suitable habitat
 showed higher decreases under RCP8.5 than RCP4.5, with large areas of the
 rear edge of the simulated distribution becoming partially or completely
 climatically unsuitable for many species. Main conclusions Climatically
 suitable habitat limits projected for 2100 far exceeded
 migration-constrained range limits for all 10 species, particularly for
 temperate species. This study underlines the limited extent to which
 species will track climate change via natural migration. Integrating
 observed migration velocities, seed dispersal and generation time with SDM
 outputs allows for more realistic evaluations of tree migration ability
 under climate change and may help orient forest conservation and
 restoration efforts.
description: Raster files of outputs from simulations of tree species
 migration in Eastern Canada at a resolution of 25m. Simulations were
 conducted over 90 years, corresponding to the time period 2011 to 2100.
 Climatically suitable habitat was projected for 3 time periods (2011–2040;
 2041–2070, 2071–2100) using 2 SDM approaches. Species
 and species codes: ABIBAL = Abies
 balsamea ACERUB = Acer rubrum
 ACESAC = Acer saccharum BETALL = Betula
 alleghaniensis BETPAP = Betula papyrifera
 PICMAR = Picea mariana PINSTR = Pinus
 strobus POPTRE = Populus tremuloides
 QUERUB = Quercus rubra THUOCC = Thuja
 occidentalis Species distribution models
 used: ANUCLIM or Maxent RCPs used: RCP 4.5, RCP
 8.5 GCM: Canadian Earth System Model
 (CanESM2)
DOI: 10.5061/dryad.1vhhmgqwd
title: VIIRS Sea ice leads detections using a U-Net

description: Sea ice leads are long and narrow sea ice fractures.
 Despite accounting for a small fraction of the Arctic surface
 area, leads play a critical role in the energy flux between the ocean and
 atmosphere. As the volume of sea ice in the Arctic has declined
 over recent decades, it is increasingly important to monitor the
 corresponding changes in sea ice leads. An approach described in
 Hoffman et al. 2021 uses artificial intelligence (AI) to detect sea ice
 leads using satellite thermal infrared window data from the Visible
 Infrared Imaging Radiometer Suite
 (VIIRS). The AI used to detect sea ice leads in
 satellite imagery is a particular kind of convolutional neural
 network, a U-Net. The originally published dataset
 included only a small case study of results. Here, the dataset is expanded
 to include the daily detection of leads since 2011 for the season between
 November through April.
description: AI is used to identify sea ice leads in thermal imagery from the
 11 µm from VIIRS (band I-5, SNPP and NOAA-20 imagery). A U-Net detection
 model is run for each satellite overpass and reported as daily aggregated
 results. The lead detection results are projected into a standard 1 km
 resolution EASE-Grid 2.0 projection. The included data arrays are the
 daily number satellite overpasses, number of overpasses a lead is
 identified, the maximum lead detection score from the U-Net, and a lead
 mask for each EASE-Grid 2.0 pixel.  Daily files are compressed inside
 November through April seasonal tar files.
description: The daily results are recorded as hdf5 format files. For each
 season, the daily results from November through April for each season are
 combined into a new tar file with gzip compression.
description: {"title":"VIIRS Sea ice leads detections using a
 U-Net","doi":"https://doi.org/10.5061/dryad.1vhhmgqwd","step":1}
DOI: 10.25338/b8gs8s
title: Data and code used in: The strength of reproductive isolating barriers in seed plants: insights from studies quantifying premating and postmating reproductive barriers over the past 15 years

description: Reproductive isolation data for 89 plant taxa pairs from 70 publications
 used in this analysis.   
description: Meta-analysis approach.  See manuscript and Supporting
 Information for detailed methods descriptions.
DOI: 10.6078/d15m69
title: Online appendix for: Hybridization and transgressive evolution as drivers of adaptive radiations: Reticulate evolution generates diversity in the Puerto Rican Anolis lizards

description: Interspecific hybridization may act as a major force contributing to the
 evolution of biodiversity. Although generally thought to reduce or
 constrain divergence between two species, hybridization can,
 paradoxically, promote divergence by increasing genetic variation or
 providing novel combinations of alleles that selection can act upon to
 move lineages toward new adaptive peaks. Hybridization may, then, play a
 key role in adaptive radiation by allowing lineages to diversify into new
 ecological space. Here, we test for signatures of historical hybridization
 in the Anolis lizards of Puerto Rico and evaluate two hypotheses for the
 role of hybridization in facilitating adaptive radiation – the hybrid
 swarm origins hypothesis and the syngameon hypothesis. Using whole genome
 sequences from all ten species of Puerto Rican anoles, we calculated D and
 f-statistics (from ABBA-BABA tests) to test for introgression across the
 radiation and employed multispecies network coalescent methods to
 reconstruct phylogenetic networks that allow for hybridization. We then
 analyzed morphological data for these species to test for patterns
 consistent with transgressive evolution, a phenomenon in which the trait
 of a hybrid lineage is found outside of the range of its two parents. Our
 analyses uncovered strong evidence for introgression at multiple stages of
 the radiation, including support for an ancient hybrid origin of a clade
 comprising half of the extant Puerto Rican anole species. Moreover, we
 detected significant signals of transgressive evolution for two
 ecologically-important traits, head length and toepad width, the latter of
 which has been described as a key innovation in Anolis. 
description: We collected whole genome sequences from species of Puerto Rican
 <em>Anolis</em> lizards. From the resulting data, we inferred
 gene trees using RAxML and a species tree using ASTRAL.  We then
 calculated D and f-statistics (from ABBA-BABA tests) to test for
 introgression across the Puerto Rican <em>Anolis</em>
 radiation and employed multispecies network coalescent methods (SNaQ,
 PhyloNet, and NANUQ) to reconstruct phylogenetic networks that allow for
 hybridization. We examined modes of speciation using likelihood ratio
 tests of speciation with gene flow. Finally, we reconstructed ancestral
 states for ecologically-important traits under a Brownian motion model on
 phylogenetic networks implemented in PhyloNetworks and then tested for
 transgressive evolution in these traits.