cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.z8w9ghx86
title: Data from: In vivo assessment of respiratory burst inhibition by xenobiotic exposure using larval zebrafish

description: Currently assessment of the potential immunotoxicity of a given agent
 involves a tiered approach for hazard identification and mechanistic
 studies, including observational studies, evaluation of immune function,
 and measurement of susceptibility to infectious and neoplastic diseases.
 These studies generally use costly low-throughput mammalian models.
 Zebrafish, however, offer an excellent alternative due to their rapid
 development, ease of maintenance, and homology to mammalian immune system
 function and development. Larval zebrafish also are a convenient model to
 study the innate immune system with no interference from the adaptive
 immune system. In this study, a respiratory burst assay (RBA) was utilized
 to measure reactive oxygen species (ROS) production after developmental
 xenobiotic exposure. Embryos were exposed to non-teratogenic doses of
 chemicals and at 96 hr post-fertilization, the ability to produce ROS was
 measured. Using the RBA, 12 compounds with varying immune-suppressive
 properties were screened. Seven compounds neither suppressed nor enhanced
 the respiratory burst. Five compounds reproducibly suppressed global ROS
 production with varying potencies: benzo[a]pyrene, 17b-estradiol, lead
 acetate, methoxychlor, and phenanthrene. These five compounds have all
 previously been reported as immunosressive in mammalian innate immunity
 assays. To evaluate whether the suppression of ROS by these compounds was
 a result of decreased immune cell numbers, flow cytometry with transgenic
 zebrafish larvae was used to count the numbers of neutrophils and
 macrophages after chemical exposure. With this assay, benzo[a]pyrene was
 found to be the only chemical that induced a change in the number of
 immune cells by increasing macrophage but not neutrophil numbers. Taken
 together, this work demonstrates the utility of zebrafish larvae as a
 vertebrate model for identifying compounds that impact innate immune
 function at non-teratogenic levels, and validates measuring ROS production
 and phagocyte numbers as metrics for monitoring how xenobiotic exposure
 alters the innate immune system.
description: Methods for collecting data are described in publication "In
 Vivo Assessment of Respiratory Burst Inhibition by Xenobiotic Exposure
 Using Larval Zebrafish."
description: Raw data from publication "In Vivo Assessment of Respiratory
 Burst Inhibition by Xenobiotic Exposure Using Larval Zebrafish" is
 provided in Excel spreadsheets (.xlsx).
DOI: 10.5061/dryad.8w9ghx3hs
title: Forest patch size predicts seed bank composition in urban areas

description: Questions: As urban areas expand around the world, understanding how to
 restore and maintain forests within the urban environment becomes
 increasingly important. Given that a comprehensive understanding of
 regeneration dynamics is critical to designating appropriate management
 interventions we ask the following: how does regeneration, vis-à-vis the
 buried seed bank, vary in heterogenous urban forests? And, can forest
 patch size be used to predict regeneration and consequent management
 interventions? Location: Vacant lots and public parks throughout New
 Haven, CT, USA. Methods: We sampled buried seed banks in 131 plots
 distributed across three forest patch sizes ranging from large intact
 parks (95-126 ha), to small parks (1-19 ha), and vacant lots (.05-.65 ha).
 We collected soil samples from the surface mineral soil and stratified
 them over sand in a greenhouse over a period of 5 months to record
 germination. Results: By examining seed bank floristics in a range of
 forest patch sizes we found that species composition and dominance of
 specific functional groups shifted with patch size representing a spectrum
 of urbanization within just one city. Seed bank floristics in large parks
 more closely resembled results from seed bank studies in rural forests
 with over 85% native germinants on average. In contrast, vacant lots were
 dominated by non-native germinants and more ruderal species indicative of
 earlier successional stages. Seed banks in small parks were variable and
 in some cases were more similar to large parks or vacant lots.
 Conclusions: Our findings suggest that large parks in urban areas may be
 largely self-sustaining whereas smaller parks may require more intensive
 management for site rehabilitation, especially in early states of
 succession. Furthermore, our results confirm the highly heterogeneous
 nature of urban forest patches and call for more systematic sampling of
 urban areas to capture this variation and improve management prescriptions
 and outcomes.
description: The data for this paper is comprised of three seperate CSV files.
 All of the data pertaining to the environmental characterisitics of the
 parks and plots can be found in the "EnvironmentalData" file.
 Species counts by plot are all located in "SpeciesData" file and
 traits (dispersal, nativity, lifeform) for all of the speices recorded in
 this study can be found in the "SpeciesTraits" file. The
 "Metadata" file offers an overview of all the variables
 measured.
DOI: 10.3886/e243214v1-198152
title: Death rates for suicide, by sex, race, Hispanic origin, and age: United States

description: Data on death rates for suicide, by selected population characteristics. Please refer to the PDF or Excel version of this table in the HUS 2019 Data Finder (https://www.cdc.gov/nchs/hus/contents2019.htm) for critical information about measures, definitions, and changes over time.

SOURCE: NCHS, National Vital Statistics System (NVSS); Grove RD, Hetzel AM. Vital statistics rates in the United States, 1940–1960. National Center for Health Statistics. 1968; numerator data from NVSS annual public-use Mortality Files; denominator data from U.S. Census Bureau national population estimates; and Murphy SL, Xu JQ, Kochanek KD, Arias E, Tejada-Vera B. Deaths: Final data for 2018. National Vital Statistics Reports; vol 69 no 13. Hyattsville, MD: National Center for Health Statistics. 2021. Available from: https://www.cdc.gov/nchs/products/nvsr.htm. For more information on the National Vital Statistics System, see the corresponding Appendix entry at https://www.cdc.gov/nchs/data/hus/hus19-appendix-508.pdf.
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DOI: 10.5061/dryad.j0zpc86b2
title: Metal ions confinement defines the architecture of G-quartet, G-quadruplex fibrils and their assembly into nematic tactoids

description: G-quadruplex, assembled from a square of guanine (G) molecules, is an
 important structure with crucial biological roles in vivo but also a
 vesitile template for ordered functional material. Although the
 understanding of G-quadruplex structures is the focus of numerous studies,
 little is known regarding the control of G-quartet stacking modes and the
 spontaneous orientation of G-quadruplex fibrils. Here, the effects of
 different metal ions and their concentrations on stacking modes of
 G-quartets are elucidated. Monovalent cations (typically K+) facilitate
 the formation of G-quadruplex hydrogels with both heteropolar and
 homopolar stacking modes, showing weak mechanical strength. In contrast,
 divalent metal ions (Ca2+, Sr2+, and Ba2+) at given concentrations can
 control G-quartet stacking modes and increase the mechanical rigidity of
 the resulting hydrogels through ionic bridge effects between divalent ions
 and borate. We show that for Ca2+ and Ba2+ at suitable concentrations, the
 assembly of G-quadruplexes results in the establishment of a mesoscopic
 chirality of the fibrils with a regular left-handed twist. Finally, we
 report the discovery of nematic tactoids self-assembled from G-quadruplex
 fibrils characterized by homeotropic fibril alignment with respect to the
 interface. We use the Frank-Oseen elastic energy and the Rapini-Papoular
 anisotropic surface energy to rationalize two different configurations of
 the tactoids. These results deepen our understanding of G-quadruplex
 structures and G-quadruplex fibrils, paving the way for their use in
 self-assembly and biomaterials.
DOI: 10.5061/dryad.pk0p2ngjz
title: Data from: Evaluating the existence and benefit of major histocompatibility complex-based mate choice in an isolated owl population

description: How mate preferences evolve in the first place has been a major conundrum
 for sexual selection. Some hypotheses explaining this assume fitness
 benefit derived from subsequent generations. Major Histocompatibility
 Complex (MHC)-based mate choice is a representative example of the mate
 choice that is associated with such trans-generational mechanisms. To
 provide evidences for fitness benefit of MHC-based mate choice, previous
 studies assessed the association between own MHC genotype and own fitness
 components. However, the association between MHC-based mate choice in the
 parental generation and fitness components in the resultant offspring
 generation has only rarely been measured in wild populations. Focusing on
 the isolated population of the monogamous Ryukyu Scops Owl (Otus elegans
 interpositus) on Minami-daito Island, Japan, we found evidence of
 MHC-based mate choice. However, we found no evidence of MHC-based mate
 choice increasing own reproductive success or offspring survival. This is
 a rare case study that directly examines the existence of the
 trans-generational indirect benefit of MHC-based mate choice for genetic
 compatibility from trans-generational data in a wild bird population. By
 investigating the fitness benefits of mate choice, this study serves to
 facilitate our understanding of the evolution of MHC-based mate choice.
DOI: 10.5061/dryad.tht76hdwf
title: Data from: Seafloor microplastic hotspots controlled by deep-sea circulation

description: While microplastics are known to pervade the global seafloor, the
 processes that control their dispersal and concentration in the deep sea
 remain largely unknown. Here we show that thermohaline-driven currents,
 which build extensive seafloor sediment accumulations, can control the
 distribution of microplastics and create hotspots of up to 1.9 million
 pieces m^2. This is the highest reported value for any seafloor setting,
 globally. Previous studies propose that microplastics are transported to
 the seafloor by vertical settling from surface accumulations; instead we
 demonstrate that the spatial distribution and ultimate fate of
 microplastics is strongly controlled by near-bed thermohaline currents
 (bottom currents). These currents are known to supply oxygen and nutrients
 to deep sea benthos suggesting that deep sea biodiversity hotspots are
 also likely to be microplastic hotspots.
description: EMODNET Bathymetry is
 available from this link: https://portal.emodnet-bathymetry.eu/ P90 bed shear stress, near bed velocity and velocity vectors used to create all graphs in the manuscript are named BSS (.tfw, .tif. and .xml), speed (.tfw, .tif, .xml) and velocity vectors (.dbf, .prj, .sbn, .sbx, .shp, .xml,.shx) respectively. FTIR data are here recorded in csv and sp files. Microplastic samples were randomly chosen from the confirmed plastics recorded in the samples; this is not intended as a complete data set or analysis, rather just a snapshot of plastic types in the samples. Grain Size data were established using laser diffraction analysis at the Univeristy of Manchester. Pdf files 1-8 Microplastic counts and colours are listed here: 'MP data' excel spreadsheet The artistic block diagram is included here and should be referred to appropriately, using the citation (Kane et al.) and doi.
description: See methods above. Any questions, please direct them to
 ian.kane@manchester.ac.uk
DOI: 10.5061/dryad.g4f4qrfmv
title: Data from: Novel reverse radioisotope labelling experiment reveals carbon assimilation of marine calcifiers under ocean acidification conditions

description: 1. Ocean acidification by anthropogenic carbon dioxide emissions is
 projected to depress metabolic and physiological activity in marine
 calcifiers. To evaluate the sensitivity of marine organisms against ocean
 acidification, the assimilation of nutrients into carbonate shells and
 soft tissues must be examined. 2. We designed a novel experimental
 protocol, reverse radioisotope labelling, to trace partitioning of
 nutrients within a single bivalve species under ocean acidification
 conditions. Injecting CO2 gas, free from radiocarbon, can provide a large
 contrast between carbon dissolved in the water and the one assimilated
 from atmosphere. By culturing modern aquifer organisms in acidified
 seawater, we were able to determine differences in the relative
 contributions of the end members, dissolved inorganic carbon (DIC) in
 seawater and metabolic CO2, to shell carbonate and soft tissues. 3. Under
 all pCO2 conditions (463, 653, 872, 1137, and 1337 μatm), radiocarbon
 (Δ14C) values of the bivalve (Scapharca broughtonii) shell were
 significantly correlated with seawater DIC values; therefore, shell
 carbonate was derived principally from seawater DIC. The Δ14C results
 together with stable carbon isotope (δ13C) data suggest that in S.
 broughtonii shell δ13C may reflect the kinetics of isotopic equilibration
 as well as end-member contributions; thus, care must be taken when
 analyzing end-member contributions by a previous method using δ13C. The
 insensitivity of S. broughtonii to perturbations in pCO2 up to at least
 1337 µatm indicates that this species can withstand ocean acidification.
 4. Usage of radioisotope to dope for tracer experiments requires strict
 rules to conduct any operations. Yet, reverse radioisotope labeling
 proposing in this study has a large advantage and is a powerful tool to
 understanding physiology of aquifer organisms that can be applicable to
 various organisms and culture experiments, such as temperature, salinity,
 and acidification experiments, to improve understanding of the proportions
 of nutrients taken in by marine organisms under changing environments.
DOI: 10.5061/dryad.7wm37pvq1
title: Data from: Effect of tower base painting on willow ptarmigan collision rates with wind turbines

description: 1. Birds colliding with turbine rotor blades is a well-known negative
 consequence of wind-power plants. However, there has been far less
 attention to the risk of birds colliding with the turbine towers, and how
 to mitigate this risk. 2. Based on data from the Smøla wind-power plant in
 Central Norway, it seems highly likely that willow ptarmigan (the only
 gallinaceous species found on the island) is prone to collide with turbine
 towers. By employing a BACI-approach, we tested if painting the lower
 parts of turbine towers black would reduce the collision risk. 3. Overall,
 there was a 48% reduction in the number of recorded ptarmigan carcasses
 per search at painted turbines relative to neighbouring control
 (unpainted) ones, with significant variation both within and between
 years. 4. Using contrast painting to the turbine towers resulted in
 significantly reduced number of ptarmigan carcasses found, emphasizing the
 effectiveness of such a relatively simple mitigation measure.
description: This dataset was collected through carcass searches using a
 trained dog. Searches were performed in the period 2006-2017 with varying
 search intensities. More details on the search regime can be found in the
 main document. Each row indicates one search, with or without any birds
 found. Post-processing of the data, summarizing number of searches and
 carcasss found per year or season, are scripted in the R script.
description: The data file (Ptarmigan_carcasses_Smola.csv) contains all data
 required to run the R script (Effect_collisions_base SI.R) for the
 analyses in the main document.
DOI: 10.5061/dryad.1rn8pk0qp
title: Genotypes of 6 InDel markers for species identification from the Calanus culture at the EMBRC-ERIC laboratory for low-level trophic interactions, NTNU SeaLab

description: Late developmental stages of marine copepods in the
 genus Calanus can spend extended periods in a dormant
 stage (diapause). During the growth season, copepods must accumulate
 sufficient lipid stores to survive diapause. Predation risk is often
 overlooked as a potential diapause-inducing cue. We tested experimentally
 if predation risk in combination with high or low food availability leads
 to differences in lipid metabolism, and potentially diapause initiation.
 Expression of lipid metabolism genes showed that food availability
 influences the copepods’ ability to cope with predator stress. Predation
 caused upregulation of lipid catabolism with high food, and downregulation
 with low food. Stage development and molecular markers demonstrated that
 copepods did not enter diapause, instead, development occurred faster in
 copepods with predator stress. This study demonstrates that lipid
 metabolism may be a sensitive endpoint for changes in the environment. Our
 findings can contribute towards understanding the mechanisms
 behind diapause timing. 
description: In the study described above, DNA was extracted from each
 specimen's antennules and used in a PCR reaction of 6 InDels. The
 dataset presented here contains the resulting genotypes, with the
 corresponding species ID attributed to each genotype.
 All the invididuals genotyped are adult females.
description: Missing values in genotypes are indicated by the value:
 "0".
DOI: 10.5061/dryad.r7sqv9s88
title: The macroecology and evolution of avian competence for Borrelia burgdorferi

description: Aim: Predicting novel reservoirs of zoonotic pathogens would be improved
 by identifying inter-specific drivers of host competence, the ability to
 transmit pathogens to new hosts or vectors. Tick-borne pathogens can
 provide a useful model system, as larvae become infected only when feeding
 on a competent host during their first bloodmeal. For tick-borne diseases,
 competence has been best studied for Borrelia burgdorferi sensu lato
 (Bbsl), which causes Lyme borreliosis. Major reservoirs include several
 small mammal species, but birds may play an underrecognized role in human
 risk given their ability to disperse infected ticks across large spatial
 scales. Here, we provide a global synthesis of the ecological and
 evolutionary factors that determine the ability of bird species to infect
 larval ticks with Bbsl. Location: Global Time period: 1983 to 2019 Major
 taxa studied: Birds Methods: We compiled a dataset of Bbsl competence
 across 183 bird species and applied meta-analysis, phylogenetic
 factorization, and boosted regression trees to describe spatial and
 temporal patterns in competence, characterize its phylogenetic
 distribution across birds, reconstruct its evolution, and evaluate the
 trait profiles associated with competent avian species. Results: Half of
 sampled bird species show evidence of competence for Bbsl. Competence
 displays moderate phylogenetic signal, has evolved multiple times across
 bird species, and is pronounced in the genus Turdus. Trait-based analyses
 distinguished competent birds with 80% accuracy and show that such species
 have low baseline corticosterone, exist on both ends of the pace-of-life
 continuum, breed and winter at high latitudes, and have broad migratory
 movements into their breeding range. We use these trait profiles to
 predict various likely but unsampled competent species, including novel
 concentrations of avian reservoirs within the Neotropics. Main conclusion:
 Our results can generate new hypotheses for how birds contribute to the
 dynamics of tick-borne pathogens and help prioritize surveillance of
 likely but unsampled competent birds. Our findings further emphasize that
 birds display underrecognized variation in their contributions to enzootic
 cycles of Bbsl and the broader need to better consider competence in
 ecological and predictive studies of multi-host pathogens.
DOI: 10.5061/dryad.x69p8czfb
title: Nucleotide alignments of eight meiosis genes under extreme selection following whole genome duplication in Arabidopsis lyrata/A.arenosa.

description: In this study we performed a genotype-phenotype association analysis of
 meiotic stability in 10 autotetraploid Arabidopsis
 lyrata and A. lyrata/A. arenosa hybrid populations collected from the Wachau region and East Austrian Forealps. The aim was to determine the effect of eight meiosis genes under extreme selection upon adaptation to whole genome duplication. Individual plants were genotyped by high-throughput sequencing of the eight meiosis genes (ASY1, ASY3, PDS5b, PRD3, REC8, SMC3, ZYP1a/b) implicated in synaptonemal complex formation and phenotyped by assessing meiotic metaphase I chromosome configurations. Our results reveal that meiotic stability varied greatly (20–100%) between individual tetraploid plants and associated with segregation of a novel ASYNAPSIS3 (ASY3) allele derived from A. lyrata. The ASY3 allele that associates with meiotic stability possesses a putative in-frame tandem duplication (TD) of a serine-rich region upstream of the coiled-coil domain that appears to have arisen at sites of DNA microhomology. The frequency of multivalents observed in plants homozygous for the ASY3 TD haplotype was significantly lower than in plants heterozygous for ASY3 TD/ND (non-duplicated) haplotypes. The chiasma distribution was significantly altered in the stable plants compared to the unstable plants with a shift from proximal and interstitial to predominantly distal locations. The number of HEI10 foci at pachytene that mark class I crossovers was significantly reduced in a plant homozygous for ASY3 TD compared to a plant heterozygous for ASY3 ND/TD. Fifty-eight alleles of the 8 meiosis genes were identified from the 10 populations analysed, demonstrating dynamic population variability at these loci. Widespread chimerism between alleles originating from A. lyrata/A. arenosa and diploid/tetraploids indicates that this group of rapidly evolving genes may provide precise adaptive control over meiotic recombination in the tetraploids, the very process that gave rise to them.