cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.d7wm37px9
title: Spatial sampling bias and model complexity in stream-based species distribution models: a case study of Paddlefish (Polyodon spathula) in the Arkansas River basin, U.S.A.

description: Leveraging existing presence records and geospatial datasets, species
 distribution modeling has been widely applied to informing species
 conservation and restoration efforts. Maxent is one of the most popular
 modeling algorithms, yet recent research has demonstrated Maxent models
 are vulnerable to prediction errors related to spatial sampling bias and
 model complexity.  Despite elevated rates of biodiversity
 imperilment in stream systems, the application of Maxent models to stream
 networks has lagged, as has the availability of tools to address potential
 sources of error and calculate model evaluation metrics when modeling in
 non-raster environments (such as stream networks). Herein, we use Maxent
 and customized R code to estimate the potential distribution of paddlefish
 (Polyodon spathula) at a stream segment-level within the Arkansas River
 basin, U.S.A, while accounting for potential spatial sampling bias and
 model complexity. Filtering the presence data appeared to adequately
 remove an eastward, large-river sampling bias that was evident within the
 unfiltered presence dataset. In particular, our novel riverscape filter
 provided a repeatable means of obtaining a relatively even coverage of
 presence data among watersheds and streams of varying sizes. The greatest
 differences in estimated distributions were observed among models
 constructed with default versus AICC -selected parameterization. Although
 all models had similarly high performance and evaluation metrics, the AICC
 -selected models were more inclusive of westward-situated and smaller,
 headwater streams. Overall, our results solidified the importance of
 accounting for model complexity and spatial sampling bias in SDMs
 constructed within stream networks and provided a roadmap for future
 paddlefish restoration efforts in the study area.
DOI: 10.5061/dryad.pzgmsbcg3
title: Mosquito heat seeking is driven by an ancestral cooling receptor

description: Mosquitoes transmit pathogens that kill &gt;700,000 people annually.
 These insects use body heat to locate and feed on warm-blooded hosts, but
 the molecular basis of such behavior is unknown. Here, we identify
 ionotropic receptor IR21a, a receptor conserved throughout insects, as a
 key mediator of heat seeking in the malaria vector Anopheles gambiae.
 Although Ir21a mediates heat avoidance in Drosophila, we find it drives
 heat seeking and heat-stimulated blood feeding in Anopheles. At a cellular
 level, Ir21a is essential for the detection of cooling, suggesting that
 during evolution mosquito heat seeking relied on cooling-mediated
 repulsion. Our data indicate that the evolution of blood feeding in
 Anopheles involves repurposing an ancestral thermoreceptor from
 non–blood-feeding Diptera.
description: These data are collected and processed as described in:  Mosquito heat-seeking is driven by
 an ancestral cooling receptor; Chloe
 Greppi<sup>1†</sup>, Willem J.
 Laursen<sup>1†</sup>, Gonzalo Budelli<sup>1</sup>,
 Elaine C. Chang<sup>1</sup>, Abigail M.
 Daniels<sup>1</sup>, Lena van Giesen<sup>1</sup>,
 Andrea L. Smidler<sup>2,3</sup>, Flaminia
 Catteruccia<sup>2</sup>, and Paul A.
 Garrity<sup>1*</sup>
description: "ReadMe_Garrity" file contains list of data files
DOI: 10.5061/dryad.d7wm37pxb
title: A test of island biogeographic theory applied to estimates of gene flow in a Fijian bird is largely consistent with neutral expectations

description: Islands were key to the development of allopatric speciation theory
 because they are a natural laboratory of repeated barriers to gene flow
 caused by open water gaps. Despite their proclivity for promoting
 divergence, little empirical work has quantified the extent of gene flow
 among island populations. Following classic island biogeographic theory,
 two metrics of interest are relative island size and distance. Fiji
 presents an ideal system for studying these dynamics, with four main
 islands that form two large-small pairs. We sequenced thousands of
 ultraconserved elements (UCEs) of the Fiji bush-warbler Horornis
 ruficapilla, a passerine distributed on these four Fijian islands, and
 performed a demographic analysis to test hypotheses of the effects of
 island size and distance on rates of gene flow. Our demographic analysis
 inferred low levels of gene flow from each large island to its small
 counterpart and little or none in the opposite direction. The difference
 in the distance between these two island pairs manifested itself in lower
 levels of gene flow between more distant islands. Both findings are
 generally concordant with classic island biogeography. The amount of
 reduction in gene flow based on distance was consistent with predictions
 from island biogeographic equations, while the reduction from small to
 large islands was possibly greater than expected. These findings offer a
 hypothesis and framework to guide future study of inter-island gene flow
 in archipelagos as the study of island biogeography progresses into the
 genomic era.
description: The dataset is based on ultraconserved elements (UCEs) and SNPs
 called from them. The input files for phylogenetic and population genetic
 analyses are included here. Scripts used to produce and use these files
 can be found at https://github.com/ethangyllenhaal/horornis_UCE.
description: These are descriptions of files in this Dryad upload for the
 paper: TableS3_FullFastsimcoalFull.xlsx: Supplemental
 table with full fastsimcoal output with all Kadavu individuals.<br>
 TableS4_FullFastsimcoalNoAdmix.xlsx: Supplemental table with full
 fastsimcoal output without the putative admixed Kadavu
 individual.<br> horo_100_rand.vcf: VCF file used for most pop gen
 analyses (not sNMF).<br> horo_100_rand_noSingle.vcf: VCF file used
 for sNMF analysis.<br> horornis_partition_finder.cfg: Configuration
 file used to run PartitionFinder2.<br> horornis_partitions.txt:
 Partitions output from PartitionFinder2.<br>
 horornis_min95_renamed.phy: Input phylip file used for RAxML
 analysis. Scripts used to generate this input and run
 analyses can be found
 at: https://github.com/ethangyllenhaal/horornis_UCE.
DOI: 10.5061/dryad.cnp5hqc1f
title: Numerical Simulations of Laboratory-Scale, Hypervelocity-Impact Experiments for Asteroid-Deflection Code Validation

description: Asteroids and comets have the potential to impact Earth and cause damage
 at the local to global scale. Deflection or disruption of a potentially
 hazardous object could prevent future Earth impacts, but due to our
 limited ability to perform experiments directly on asteroids, our
 understanding of the process relies upon large-scale hydrodynamic
 simulations. Related simulations must be vetted through code validation by
 benchmarking against relevant laboratory-scale hypervelocity-impact
 experiments. To this end, we compare simulation results from Spheral, an
 Adaptive Smoothed-Particle Hydrodynamics (ASPH) code, to the fragment-mass
 and velocity data from the 1991 two-stage light gas-gun impact experiment
 on a basalt sphere target, conducted at Kyoto University by Nakamura and
 Fujiwara. We find that the simulations are sensitive to the selected
 strain models, strength models and material parameters. We find that, by
 using appropriate choices for these models in conjunction with
 well-constrained material parameters, the simulations closely resemble
 with the experimental results. Numerical codes implementing these model
 and parameter selections may provide new insight into the formation of
 asteroid families (Michel et al., 2015) and predictions of deflection for
 the Double Asteroid Redirection (DART) mission (Stickle et al., 2017).
DOI: 10.5061/dryad.wpzgmsbh2
title: Data from: Primary dermal fibroblasts and pectoralis muscle show similar patterns of oxidative stress in tropical and temperate birds despite differing life-histories

description: Tropical birds have a “slower pace of life,” with lower rates of
 whole-animal metabolism, smaller metabolically active organs, and lower
 cellular metabolic rates than their temperate counterparts. Oxidative
 stress is a physiological mechanism that may dictate differing
 life-histories such as those found between tropical and temperate birds.
 Oxygen is required to make ATP, resulting in the production of reactive
 oxygen species (ROS). If left unchecked, ROS can structurally alter
 proteins, induce mutations in DNA, and damage structural lipids. To combat
 accumulating oxidative damage, organisms have evolved an elaborate and
 costly antioxidant system that serves to sequester ROS before they wreak
 cellular havoc. We examined whether oxidative stress would differ between
 tropical and temperate birds. We used isolated primary dermal fibroblasts
 and pectoralis muscle tissue for measurements. We measured four aspects of
 oxidative stress in primary fibroblasts – reduced glutathione (GSH)
 concentration, ROS production, mitochondrial content, and lipid
 peroxidation (LPO) damage. We found no significant differences in the four
 variables between temperate and tropical birds.. In muscle tissue, we
 measured catalase (CAT), superoxide dismutase (SOD) glutathione peroxidase
 (GPx) activity, peroxyl and hydroxyl scavenging capacity, and LPO damage.
 We found that peroxyl scavenging capacity was significantly higher in
 tropical birds compared with temperate birds.
DOI: 10.15468/dl.srxgmw
title: Occurrence Download

description: A dataset containing 1544328 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Zonotrichia capensis"
 ]
}

 The dataset includes 1544328 records from 517 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001960-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.5tb2rbp0r
title: Macrophage coordination of the interferon lambda immune response

description: Lambda interferons (IFN-λs) are a major component of the innate immune
 defense to viruses, bacteria and fungi. In human liver, IFN-λ not only
 drives antiviral responses, but also promotes inflammation and fibrosis in
 viral and non-viral diseases. Here we demonstrate that macrophages are
 primary responders to IFN-λ, uniquely positioned to bridge the gap between
 IFN-λ producing cells and lymphocyte populations that are not
 intrinsically responsive to IFN-λ. While CD14+ monocytes do not express
 the IFN-λ receptor, IFNLR1, sensitivity is quickly gained upon
 differentiation to macrophages in vitro. IFN-λ stimulates macrophage
 cytotoxicity and phagocytosis as well as the secretion of pro-inflammatory
 cytokines and interferon stimulated genes that mediate immune cell
 chemotaxis and effector functions. In particular, IFN-λ induced CCR5 and
 CXCR3 chemokines, stimulating T and NK cell migration, as well as
 subsequent NK cell cytotoxicity. Using immunofluorescence and cell sorting
 techniques, we confirmed that human liver macrophages expressing CD14 and
 CD68 are highly responsive to IFN-λ ex vivo. Together, these data
 highlight a novel role for macrophages in shaping IFN-λ dependent immune
 responses both directly through pro-inflammatory activity and indirectly
 by recruiting and activating IFN-λ unresponsive lymphocytes.
DOI: 10.5061/dryad.g79cnp5kq
title: Fire regimes and pollinator behavior explain the genetic structure of Puya hamata (Bromeliaceae) rosette plants

description: The demography of the Andean Puya hamata has been linked to fire regimes
 and hummingbird behaviour, which might modify the plant’s population
 genetic diversity. Naturally poor dispersal results in patches of
 genetically related plants, a pattern intensified further by burning which
 promotes seedling germination around parent plants. Later, when these
 plants flower, large patches are attractive to territorial hummingbirds
 which prevent visits by traplining hummingbird species, carrying pollen
 from likely unrelated plants. To explore this hypothesis, a genetic study
 of P. hamata using microsatellite markers was conducted with (i) isolated
 and grouped adults in two size categories of patches, and (ii) seeds
 collected from the same patches and isolated individuals. Isolated
 individual plants were most genetically diverse with close to zero
 endogamy. Adult plants from large patches showed, lower diversity and
 higher endogamy than plants from other spatial contexts. Seed genetic
 structure displayed a gradient of diversity: lower at patch centres but
 higher at patch edges, in small patches and for isolated infructescences.
 The spatial context of these plants, especially the contrast between large
 patch centres and other situations, determines the genetic diversity of
 their seeds via hummingbird foraging behaviour. Territorial hummingbirds
 restrict gene flow in and out of large patches, but traplining
 hummingbirds maintain genetic diversity among isolated plants, small
 patches and plants at the edges of large patches. Our study illustrates
 the need to consider interactions between land use, plants and their
 pollinators when considering genetic diversity at the landscape scale.
DOI: 10.5061/dryad.b2rbnzs95
title: Data from: Glucose-6-phosphate dehydrogenase deficiency and stroke outcomes

description: Objective: To ascertain whether G6PD deficiency affects outcomes at 3
 months after stroke, we recruited 1251 patients with acute ischemic stroke
 and detected erythrocyte-G6PD activity. Methods: The prospective study
 participants consisted of 1,251 patients with ischemic stroke within 2
 weeks of onset from four clinical centers in South China. Patients were
 individually categorized into the G6PD-deficiency group and
 non-G6PD-deficiency group according to erythrocyte-G6PD activity upon
 admission. Baseline characteristics and clinical outcomes (modified Rankin
 Scale score [mRS], poor functional outcome [mRS ≥ 2] at 3 months, and
 death) were compared between the two groups. The associations of G6PD
 deficiency with outcomes were evaluated using Cox proportional hazards and
 logistic regression analyses. Results: Among 1251 patients, 150 (12.0 %)
 were G6PD deficient; patients with G6PD deficiency had higher proportions
 of large-artery atherosclerosis (56.7% vs. 46.0% in non-G6PD-deficiency;
 odds ratio [OR] 1.53, 95% confidence interval [CI] 1.09-2.17) and stroke
 history (23.3% vs. 13.6% in non-G6PD-deficiency; OR 1.93, 95% CI
 1.26-2.90). Multivariable logistic regression analysis showed the
 G6PD-deficiency and non-G6PD-deficiency group differed significantly in
 their overall distribution of mRS scores (adjusted common OR 1.57, 95% CI
 1.14-2.17). Patients with G6PD deficiency had higher rates of poor
 functional outcome at 3 months (61.9% vs. 50.0% in non-G6PD-deficiency;
 adjusted OR 1.73, 95% CI 1.08-2.76). The hazard ratio of in-hospital death
 for patients with G6PD-deficiency was 1.46 (95% CI 1.37-1.84).
 Conclusions: G6PD deficiency is associated with the risk of poor
 functional outcome at 3 months after ischemic stroke, and may increase the
 risk of in-hospital death.
DOI: 10.15468/dl.zcgaqu
title: Occurrence Download

description: A dataset containing 208 species occurrences available in GBIF matching the query:
{
 "and" : [
 "CoordinateUncertaintyInMeters 0.0-51.0",
 "Country is Italy",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is one of (Saxifraga squarrosa, Saxifraga hostii)",
 "Year 2015-2026"
 ]
}

 The dataset includes 208 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002036-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.zw3r2284j
title: Herding mechanisms to maintain the cohesion of a harem group: two interaction phases during herding

description: In animal groups, individual interactions achieve coordinated movements to
 maintain cohesion. In horse harem groups, herding is a behavior in which
 males chase females from behind; it is considered to assist with group
 cohesiveness. However, the mechanisms by which the individuals move to
 maintain group cohesion are unknown. We applied novel non-invasive methods
 of drone filming and video tracking to observe horse movements in the
 field with high temporal and spatial resolution. We tracked all group
 members and drew trajectories. We analyzed the movements of females and
 found two phases of interactions based on their timing of movement
 initiation. The females that moved first were those nearest to the herding
 male, while the movement initiation of the later females was determined by
 the distance from the nearest moving female, not by the distance from the
 herding male. These interactions are unique among animal group movements
 and might represent a herding mechanism responsible for maintaining group
 cohesion. This might be due to long-term stable relationships within a
 harem group and strong social bonds between females. This study showed
 that the combination of drone filming and video tracking is a useful
 method for analyzing the movements of animals simultaneously in high
 resolution.
DOI: 10.15468/dl.8rkdep
title: Occurrence Download

description: A dataset containing 5215 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Country is Brazil",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is one of (Leptomicrurus, Micrurus, Bothrocophias, Bothrops, Bothrops, Crotalus, Crotalus, Lachesis)"
 ]
}

 The dataset includes 5215 records from 29 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002034-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.akpn94
title: Occurrence Download

description: A dataset containing 2250 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Tracking Red-necked stints (Calidris ruficollis) and Curlew sandpipers (Calidris ferruginea) along the East Asian-Australasian Flyway (EAAF)"
 ]
}

 The dataset includes 2250 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002035-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.0vt4b8gv1
title: Local adaptation to biotic interactions: a meta-analysis across latitudes

description: Adaptation to local conditions can increase species’ geographic
 distributions and rates of diversification, but which components of the
 environment commonly drive local adaptation—particularly the importance of
 biotic interactions—is unclear. Biotic interactions should drive local
 adaptation when they impose consistent divergent selection; if this is
 common we expect transplant experiments to detect more frequent and
 stronger local adaptation when biotic interactions are left intact. We
 tested this hypothesis using a meta-analysis of transplant experiments
 from &gt;125 studies (mostly on plants). Overall, local adaptation was
 common and biotic interactions affected fitness. Nevertheless, local
 adaptation was neither more common nor stronger when biotic interactions
 were left intact, either between experimental treatments within studies
 (control vs. biotic interactions experimentally manipulated) or between
 studies that used natural vs. biotically-altered transplant environments.
 However, the effect of ameliorating negative interactions varied with
 latitude, suggesting that interactions may promote local adaptation more
 often in tropical vs. temperate ecosystems, though few tropical studies
 were available to test this. Our results suggest that biotic interactions
 often fail to drive local adaptation even though they strongly affect
 fitness, perhaps because temperate biotic environments are unpredictable
 at the spatiotemporal scales required for local adaptation.
description: Data were extracted from primary literature as per description in
 published article. A large part of the data were originally collected for
 an article currently in preparation by Bontrager et al.
 Locations have been converted into decimal degrees.
 Composite fitness measures have been calculated.
 All other calculations are done in the associated R
 script.
description: Descriptions of each variable/column are given in the associated
 R script. The authors have additional studies in
 progress using the literature search results – other researchers are
 welcome to use the database but we would appreciate being notified if so
 (anna.hargreaves@mcgill.ca, mgbontrager@gmail.com,
 angert@mail.ubc.ca) For R code for the full
 phylogenetic analyses email rgermain@zoology.ubc.ca.
DOI: 10.15468/dl.pwjf2r
title: Occurrence Download

description: A dataset containing 1750 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "TaxonKey is Gentianopsis thermalis"
 ]
}

 The dataset includes 1750 records from 55 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002037-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.pg4f4qrjc
title: Estimating leaf nitrogen concentration based on the combination with fluorescence spectrum and first-derivative

description: Leaf nitrogen concentration (LNC) is a major indicator in the estimation
 of the crop growth status which has been diffusely applied in remote
 sensing. Thus, it is important to accurately obtain LNC by using passive
 or active technology. Laser-induced fluorescence (LIF) can be applied to
 monitor LNC in crops through analyzing the changing of fluorescence
 spectral information. Thus, the performance of fluorescence spectrum (FS)
 and first-derivative fluorescence spectrum (FDFS) for paddy rice
 (Yangliangyou 6 and Manly Indica) LNC estimation was discussed, and then
 the proposed FS+FDFS was used to monitor LNC by multivariate analysis. The
 results showed that the difference between FS (R2=0.781, SD=0.078) and
 FDFS R2=0.779, SD=0.097) for LNC estimation by using the artificial neural
 network (ANN) is not obvious. The proposed FS+FDFS can improved the
 accuracy of LNC estimation to some extent (R2=0.813, SD=0.051). Then,
 principal component analysis was used in FS and FDFS, and extracted the
 main fluorescence characteristics. The results indicated that the proposed
 FS+FDFS exhibited higher robustness and stability for LNC estimation
 (R2=0.851, SD=0.032) than that only using FS (R2=0.815, SD=0.059) or FDFS
 (R2=0.801, SD=0.065).