cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.vx0k6djvz
title: Duck harvest and crippling in Illinois in 2018-19

description: Crippling loss (waterfowl downed, but not retrieved) is a recognized
 component of waterfowl harvest, but there are few contemporary estimates.
 We used a zero-inflated negative binomial model to account for false
 reporting of zeros and estimated true waterfowl crippling losses from
 harvest data reported in a 2018–19 survey of waterfowl hunters in
 Illinois, USA. We found that crippling rates declined rapidly with
 increasing harvest and moderately with increasing days afield. For the
 most active hunters (days afield), the probability of falsely reporting
 zero crippling loss increased with the number of ducks they reported
 harvesting, whereas for the least active hunters we found the reverse. We
 suggest that modest improvements in hunter skill could produce significant
 reductions in crippling loss.
description: We collected waterfowl harvest
 data for the 2018 – 2019 Illinois waterfowl season via a repeat-mail
 survey. We drew a sample of 5,000 randomly selected Illinois waterfowl
 hunters from purchasers of the Illinois State Waterfowl Permit during the
 2017–2018 waterfowl season (including both resident and non-resident
 hunters). In 2019, each participant was mailed an 8-page questionnaire
 with a prepaid return envelope and cover letter explaining the purpose of
 the survey (henceforth referred to as survey packet). Participants were
 mailed a reminder/thank you postcard 14 days after the initial survey
 packet with a second survey packet sent to non-respondents 14 days later.
 Participants were sent a second reminder postcard after 14 days, followed
 by a final survey packet to remaining non-respondents 14 days later. We
 extracted questions of relevance for our study from the full survey
 including data on the number of ducks harvested per hunter (excluding teal
 [e.g., Spatula discors] harvested during the September special teal
 season), how many ducks they downed
 but were unable
 to retrieve (crippled), days hunted, age, age first hunted waterfowl, and
 whether they used decoys. The percent crippled was calculated based on the
 total number of ducks hit (total duck harvested + total ducks downed but
 not retrieved). We treated age minus age respondents first hunted
 waterfowl as a measure of experience and assumed that hunters hunted most
 years from the age that they first started but recognize that there are
 limitations to this approach. We excluded respondents who reported not
 hunting waterfowl from analysis.
DOI: 10.5061/dryad.pg4f4qrt3
title: Input files for WRF simulations Across the the iCMV

description: The west-east terrain cross-section along ~150km of the northern part of
 Israel has a coastal-plain—mountain—valley structure; hereafter denoted
 iCMV. The boundary layer height (BLH) evolution mechanism across the iCMV
 has not yet been fully understood. We use Weather Research and Forecasting
 (WRF) simulations and ceilometer measurements to decipher the iCMV BLH
 evolution mechanism during the late summertime period of 5-14 September
 2017, where the daily maximum BLH at the mountainous city of Jerusalem
 (JrM; 800m above sea-level) varies by ~1000m. We first verify the BLH,
 simulated by 5 model configurations (with 4 different BL schemes). The
 RMSE for the 3 best configurations are around 160 and 200m for the coastal
 and JrM areas, respectively. An analysis of the simulated daily BL
 evolution reveals a general mechanism. In the early morning, the up-slope
 flows and synoptic forcing interact to induce a surface flow convergence
 (SFC) zone. During a westerly (easterly) synoptic flow, the SFC is induced
 east (west) of JrM. Assisted by the inland propagating sea breeze front,
 the SFC is advected eastwards during the afternoon, until it collapses at
 the valley bottom. The SFC zone is accompanied by a substantial
 positive vertical-wind column and a locally-elevated BLH. The more western
 the morning-time SFC is, the more likely the elevated BLH will pass during
 midday through JrM, with a higher daily maximum
 BLH.  The exact dependence of the BLH evolution and the
 associated temperature and humidity variations upon the synoptic regime
 require further study.
DOI: 10.13130/rd_unimi/sk4k2k/6tr9ln
title: SKYTEM_dune_area.xyz

description: SKYTEM survey data collected over a dune area. The dataset is published in the standard AEM XYZ format and includes the relative transmitter–receiver positions, flight altitude, gate-time, low-moment and high-moment measurements, and the corresponding data standard deviation (STD) information.
DOI: 10.13130/rd_unimi/sk4k2k/zw3ay1
title: SKYTEM_Cal_DualWaveform_XYZ_25hz.gex

description: Airborne electromagnetic (AEM) system parameter information in standard GEX format, including the transmitter waveform, system model, transmitter coil geometry and dimensions, the number of transmitter coil turns, and filter informations.
DOI: 10.5061/dryad.d2547d859
title: Evidence that genomic incompatibilities and other multilocus processes impact hybrid fitness in a rattlesnake hybrid zone

description: Hybrid zones provide valuable opportunities to understand the genomic
 mechanisms that promote speciation by providing insight into factors
 involved in intermediate stages of speciation. Here we investigate
 introgression in a hybrid zone between two rattlesnake species (Crotalus
 viridis and C. oreganus concolor) that have undergone historical
 allopatric divergence and recent range expansion and secondary contact. We
 use Bayesian genomic cline models to characterize genomic patterns of
 introgression between these lineages and identify loci potentially subject
 to selection in hybrids. We find evidence for a large number of genomic
 regions with biased ancestry that deviate from the genomic background in
 hybrids (i.e., excess ancestry loci), which tend to be associated with
 genomic regions with higher recombination rates. We also identify suites
 of excess ancestry loci that show highly correlated allele frequencies
 (including conspecific and heterospecific combinations) across physically
 unlinked genomic regions in hybrids. Our findings provide evidence for
 multiple multilocus evolutionary processes impacting hybrid fitness in
 this system.
DOI: 10.5061/dryad.6q573n61w
title: Data from: Machine learning confirms new records of maniraptoran theropods in Middle Jurassic UK microvertebrate faunas

description: Current research suggests that the initial radiation of maniraptoran
 theropods occurred in the Middle Jurassic, although their fossil record is
 known almost exclusively from the Cretaceous. However, fossils of Jurassic
 maniraptorans are scarce, usually consisting solely of isolated teeth, and
 their identifications are often disputed. Here, we apply different machine
 learning models, in conjunction with morphological comparisons, to a suite
 of isolated theropod teeth from Bathonian microvertebrate sites in the UK
 in order to determine if any of these can be confidently assigned to
 Maniraptora. We generated three independent models developed on a training
 dataset with a wide range of theropod taxa and broad geographical and
 temporal coverage. Classifying the Middle Jurassic teeth in our sample
 against these models indicates the presence of at least three distinct
 dromaeosaur morphotypes, plus a therizinosaur and troodontid, in these
 assemblages, a conclusion supported by morphological comparison. These new
 referrals significantly extend the ranges of Therizinosauroidea and
 Troodontidae, by some 27 million years. These results indicate that not
 only were maniraptorans present in the Middle Jurassic, as predicted by
 previous phylogenetic analyses, but had already radiated into a diverse
 fauna that pre-dated the break-up of Pangaea. This study also demonstrates
 the power of machine learning to provide quantitative assessments of
 isolated teeth in providing a robust, testable framework for taxonomic
 identifications, and highlights the importance of assessing and including
 evidence from microvertebrate sites in faunal and evolutionary analyses.
description: Four CSV and XLSX files of morphometric measurements from
 isolated theropod teeth from various sources. References for each
 individual tooth are contained within the dataset.
 Training Data contains some 1,700 individual theropod tooth
 measurements to be used as input into the machine learning
 models. UK Bathonian Teeth contains 94 individual
 theropod tooth measurements from Hornsleasow, Kirtlington and Woodeaton
 Quarries and Watton Cliff in the UK. These are Bathonian microvertebrate
 sites. The dataset only contains those teeth where we have complete
 measurements for the morphometric variables. R-script
 to generate the machine learning models for classification.
 README.txt containing information on how to generate the
 models.
description: All machine learning models were generated using R version 3.6.0
 and above. The following packages are required: caret,
 MASS, mda, randomForest, C50 and the script will attempt to download them
 and install if they are not already on the system.
DOI: 10.5061/dryad.j0zpc86ht
title: Tim-3 regulates the immunosuppressive function of decidual MDSCs via the Fyn-STAT3-C/EBPβ pathway during Toxoplasma gondii infection

description: Myeloid-derived suppressor cells (MDSCs) play a key role in maintaining
 maternal-fetal tolerance for a successful pregnancy, but the role of MDSCs
 in abnormal pregnancy caused by Toxoplasma gondii infection is
 unknown. Herein, we revealed a distinct mechanism by which T-cell
 immunoglobulin domain- and mucin domain-containing protein-3 (Tim-3), an
 immune checkpoint receptor that balances maternal-fetal tolerance during
 pregnancy, contributes to the immunosuppressive function of MDSCs during
 T. gondii infection. The expression of Tim-3 in decidual MDSCs was
 signiﬁcantly downregulated following T. gondii infection. The proportion
 of monocytic MDSC population, the inhibitory effect of MDSCs on T-cell
 proliferation, the levels of STAT3 phosphorylation, and the expression of
 functional molecules (Arg-1 and IL-10) in MDSCs were all decreased in T.
 gondii-infected pregnant Tim-3 gene knockout (Tim-3KO) mice compared with
 infected pregnant WT mice. After treatment with Tim-3-neutralizing Ab in
 vitro, the expression levels of Arg-1, IL-10, C/EBPβ, and p-STAT3 were
 decreased, the interaction between Fyn and Tim-3 or between Fyn and STAT3
 was weakened, and the binding ability of C/EBPβ to the promoters of ARG1
 and IL10 was decreased in human decidual MDSCs with T. gondii infection,
 while opposite results were observed following treatment with galectin-9
 (a ligand for Tim-3). Inhibitors of Fyn and STAT3 also downregulated the
 expression of Arg-1 and IL-10 in decidual MDSCs and exacerbated adverse
 pregnancy outcomes caused by T. gondii infection in mice. Therefore, our
 studies discovered that the decrease of Tim-3 after T. gondii infection
 could downregulate the functional molecules of Arg-1 and IL-10 expression
 in decidual MDSCs through the Fyn-STAT3-C/EBPβ signaling pathway and
 weaken their immunosuppressive function, which eventually contributes to
 the development of adverse pregnancy outcomes.
DOI: 10.5061/dryad.ht76hdrk0
title: Relationships between egg size and maternal size, life-history forms, and habitats of Greenlandic Arctic charr (Salvelinus alpinus)

description: Arctic charr (Salvelinus alpinus [L.] complex) has been
 widely used as a model system for studies in
 evolutionary ecology because of its diversity in feeding ecology,
 habitat use, life-history forms, and associated
 morphologies observed in matured individuals.
 However, we still know relatively little about
 traits exhibited early in life of the species, although the trait
 diversity of matured individuals may largely be shaped during development.
 Egg size is a key determinant ofvarious traits exhibited
 early in life. Therefore, describing egg size variation within-
 and between-individuals as well as the link between egg
 size and adult traits will be a useful step in understanding the
 early life trait diversity of Arctic charr. Here, using Greenlandic Arctic
 charr, which includes alternative life-history forms
 (i.e., anadromous and resident) and spawning habitat use (i.e., lake- and
 river- spawner), we described egg size variation (i.e.,
 clutch-mean egg diameter and within-clutch variation)
 and explored the link between egg size variation and female
 body length, life-history form, and spawning habitats. As in many
 other fishes, clutch-mean egg diameter increased
 with female body length. No significant effect
 of other female traits on clutch
 mean-egg diameter was detected, suggesting that
 female body size variation could be a direct cause of early life history
 trait variation. On the other hand, we found that the degree of
 within-clutch variation of the anadromous life-history form was higher
 than that of the resident life-history form. The pattern could be
 interpreted in an adaptive context. For instance, given that the
 anadromous life-history form tends to be semelparous,
 anadromous females could decrease the likelihood of
 complete reproductive failure by producing variable-sized offspring within
 a clutch since at least some offspring are expected to be matched to the
 prevailing environment.
DOI: 10.5061/dryad.fqz612jvx
title: Data from: A short peptide exerts neuroprotective effects on cerebral ischemia-reperfusion injury by reducing inflammation via the miR-6328/IKKβ/NF-κB axis

description: Background Despite considerable efforts, ischemic stroke (IS) remains a
 challenging clinical problem. Therefore, the discovery of effective
 therapeutic and targeted drugs based on the underlying molecular mechanism
 is crucial for effective IS treatment. Methods A cDNA-encoding peptide was
 extracted and identified from RNA extracted from Rana limnocharis skin,
 and its neuroprotective properties were evaluated using a middle cerebral
 artery occlusion/reperfusion (MCAO/R) model in rats and an oxygen-glucose
 deprivation/reperfusion (OGD/R) model in neuron-like PC12 cells. The
 underlying molecular mechanisms were explored using microRNA (miRNA)
 sequencing, quantitative real-time polymerase chain reaction,
 dual-luciferase reporter gene assay, and western blotting. Results A new
 peptide (NP1) with an amino acid sequence of ‘FLPAAICLVIKTC’ was
 identified. NP1 showed no obvious toxicities in vivo and in vitro.
 Intraperitoneal administration of NP1 (10 nmol/kg) effectively reduced the
 volume of cerebral infarction and relieved neurological dysfunction in
 MCAO/R model rats. Moreover, NP1 significantly alleviated the decrease in
 viability of PC12 cells induced by OGD/R. NP1 effectively suppressed
 inflammation by reducing interleukin-1β (IL-1β) and tumor necrosis
 factor-α (TNF-α) levels in vitro and in vivo. Furthermore, NP1
 up-regulated the expression of miRNA-6328, which targeted down-regulation
 of the inflammation-related factor inhibitor kappa B kinase β (IKKβ),
 thereby reducing nuclear factor-kappa B p65 (NF-κB p65) and inhibitor of
 NF-κB (I-κB) phosphorylation and inhibiting the NF-κB pathway. Conclusions
 NP1 exerted neuroprotective effects by reducing inflammation via the
 miRNA-6328/IKKβ/NF-κB axis. This study highlights the importance of
 peptides in the development of new drugs, elucidation of pathological
 mechanisms, and discovery of new drug targets.
DOI: 10.5061/dryad.2bvq83bt9
title: The diverse effects of phenotypic dominance on hybrid fitness

description: When divergent populations interbreed, their alleles are brought together
 in hybrids. In the initial F1 cross, most divergent loci are heterozygous.
 Therefore, F1 fitness can be influenced by dominance effects that could
 not have been selected to function well together. We present a systematic
 study of these F1 dominance effects by introducing variable phenotypic
 dominance into Fisher's geometric model. We show that dominance often
 reduces hybrid fitness, which can generate optimal outbreeding followed by
 a steady decline in F1 fitness, as is often observed. We also show that
 "lucky" beneficial effects sometimes arise by chance, which
 might be important when hybrids can access novel environments. We then
 show that dominance can lead to violations of Haldane’s Rule (reduced
 fitness of the heterogametic F1) but strengthens Darwin’s Corollary (F1
 fitness differences between cross directions). Taken together, results
 show that the effects of dominance on hybrid fitness can be surprisingly
 difficult to isolate because they often resemble the effects of
 uniparental inheritance or expression. Nevertheless, we identify a pattern
 of environment-dependent heterosis that only dominance can explain, and
 for which there is some suggestive evidence. Our results also show how
 existing data set upper bounds on the size of dominance effects. These
 bounds could explain why additive models often provide good predictions
 for later-generation recombinant hybrids, even when dominance
 qualitatively changes outcomes for the F1.
description: Individual based simulations using Fisher's geometric model
 were performed and all substitutions recorded. These evolved populations
 were randomly paired to compute their log fitness and that of their F1
 hybrid.
DOI: 10.5068/d11m43
title: Genetic and ecological drivers of molt in a migratory bird

description: The ability of animals to sync the timing and location of molting (the
 replacement of hair, skin, exoskeletons or feathers) with peaks in
 resource availability has important implications for their ecology and
 evolution. In migratory birds, the timing and location of pre-migratory
 feather molting, a period when feathers are shed and replaced with newer,
 more aerodynamic feathers, can vary within and between species. While
 hypotheses to explain the evolution of intraspecific variation in the
 timing and location of molt have been proposed, little is known about the
 genetic basis of this trait or the specific environmental drivers that may
 result in natural selection for distinct molting phenotypes. Here we take
 advantage of intraspecific variation in the timing and location of molt in
 the iconic songbird, the Painted Bunting (Passerina ciris) to investigate
 the genetic and ecological drivers of distinct molting phenotypes.
 Specifically, we use genome-wide genetic sequencing in combination with
 stable isotope analysis to determine population genetic structure and
 molting phenotype across thirteen breeding sites. We then use genome-wide
 association analysis (GWAS) to identify a suite of genes associated with
 molting and pair this with gene-environment association analysis (GEA) to
 investigate potential environmental drivers of genetic variation in this
 trait. Associations between genetic variation in molt-linked genes and the
 environment are further tested via targeted SNP genotyping in 25
 additional breeding populations across the range. Together, our
 integrative analysis suggests that molting is in part regulated by genes
 linked to feather development and structure
 (GLI2 and CSPG4) and that genetic variation in these
 genes is associated with seasonal variation in precipitation and aridity.
 Overall, this work provides important insights into the genetic basis and
 potential selective forces behind phenotypic variation in what is arguably
 one of the most important fitness-linked traits in a migratory bird.
description: The .bed file, a plink binary genotype requires
 <em>plink </em>software to open with the corresponding .bim
 and .fam files. Otherwise all data files can be opend with any text
 editor.
DOI: 10.5061/dryad.4tmpg4fd9
title: Data for: Investigating signal modalities of aposematism in a poison frog

description: Aposematic species combine a conspicuous signal with a secondary defense,
 the majority of which are studied in the context of a visual signal. While
 multimodality of the aposematic signal appears to be common in
 invertebrate species, we know very little about the presence or absence of
 multimodality in vertebrates. Here we examine the possibility of
 multimodality of aposematism in the green and black poison frog,
 Dendrobates auratus. Using a non-visual predator (the cat-eyed snake,
 Leptodeira annulata) and extractions of chemicals in frog skins, we test
 whether there is sufficient non-visual information for predators to avoid
 this aposematic species without using visual cues. We found that
 experienced predators avoid chemicals in this poison frog’s skin by
 olfactory cues alone in trials with live frogs and extracts from captive
 poison frogs, whereas extracts from wild poison frogs did not lead to
 avoidance behaviors in predators. Further, in our limited sampling, naïve
 predators demonstrate no avoidance. This not only indicates that predators
 can make informed decisions from the frog’s odor but also indicates that
 avoidance based on olfactory cue is a learned response.
DOI: 10.5061/dryad.ngf1vhhx8
title: Data from: Paternal hatching care regulates the timing, synchrony, and success of hatching in a coral reef fish

description: In oviparous species, the timing of hatching is a crucial decision, but
 for developing embryos, assessing cues that indicate the optimal time to
 hatch is challenging. In species with parental care, parents can assess
 environmental conditions and induce their offspring to hatch. We provide
 the first documentation of parental hatching regulation in a coral reef
 fish, demonstrating that male neon gobies (Elacatinus colini) directly
 regulate hatching by removing embryos from the clutch and spitting
 hatchlings into the water column. All male gobies synchronized hatching
 within 2h of sunrise, regardless of when eggs were laid.
 Paternally-incubated embryos hatched later in development, more
 synchronously, and had higher hatching success than artificially-incubated
 embryos that were shaken to simulate paternal hatching cues or not
 stimulated. Artificially-incubated embryos displayed substantial
 plasticity in hatching times (range: 88 – 244 hours post-fertilization),
 suggesting that males could respond to environmental heterogeneity by
 modifying the hatching time of their offspring. Finally,
 paternally-incubated embryos hatched with smaller yolk sacs and larger
 propulsive areas than artificially-incubated embryos, suggesting that
 paternal effects on hatchling phenotypes may influence larval dispersal
 and fitness. These findings highlight the complexity of fish parental care
 and may have important, and currently unstudied, consequences for fish
 population dynamics.
description: Paternal hatching care data was collected using infrared video
 cameras. Videos were then watched to describe paternal hatching care and
 determine hatching duration. Larvae that hatched from
 artificially-incubated stimulated and artificially-incubated
 not-stimulated treatments were collected every 8hrs, enumerated, and
 photographed. ImageJ was used to measure the total length, body depth,
 yolk sac area, and propulsive area of larvae from photographs. All
 statistical analyses were completed using R version 4.1.0.