cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5068/d1208q
title: Data from: Specifying high-altitude electrons using low-altitude LEO systems: the SHELLS model

description: We describe an artificial neural network model of the near-Earth space
 radiation environment. The geomagnetic activity index  Kp and
 low-earth-orbit (LEO) electron flux measurements from the National Oceanic
 and Atmospheric Administration Polar-orbiting Operational Environmental
 Satellite (POES) operational spacecraft are used as model training inputs.
 Electron fluxes from National Aeronautics and Space Administration's
 Van Allen Probe spacecraft form the training outputs. We demonstrate that
 the model can accurately specify outer radiation belt (L ∼3-7)
 electron fluxes at two energies, 350 keV and 1 MeV. Various performance
 metrics are calculated using out-of-sample data, and we find high
 correlations and low errors between the model specification and the
 observed flux. We emphasize that once the model is trained, the Van Allen
 Probes data are no longer needed at model run time; only the POES fluxes
 and the Kp index are required to specify the outer electron belt using the
 model.
description: # Data from: Specifying high-altitude electrons using low-altitude LEO
 systems: the SHELLS model
 [https://doi.org/10.5068/D1208Q](https://doi.org/10.5068/D1208Q) ##
 Description of the data and file structure The dataset includes a tarball
 of all of the data shown in the figures in the manuscript, along with the
 neural network coefficients as described in the Appendix of the
 manuscript.
DOI: 10.15468/dl.sqd2tw
title: Occurrence Download

description: A dataset containing 233921 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is United States of America",
 "TaxonKey is Odocoileus virginianus"
 ]
}

 The dataset includes 233921 records from 142 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002006-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.0p2ngf1w0
title: Metabolomic Analysis of the Effects of Leptin Replacement Therapy in Patients with Lipodystrophy

description: Context and Objective Leptin treatment has dramatic clinical effects on
 glucose and lipid metabolism in leptin-deficient patients with
 lipodystrophy. Further elucidation of metabolic effects of exogenous
 leptin therapy will shed light on understanding leptin physiology in
 humans. Our objective was to utilize metabolomic profiling to examine the
 changes associated with administration of short-term metreleptin therapy
 in patients with lipodystrophy. Study Design We conducted a pre-post
 treatment study in 19 patients (75% female) with varying forms of
 lipodystrophy (congenital generalized lipodystrophy, n=10; acquired
 generalized lipodystrophy, n=1; familial partial lipodystrophy, n=8) who
 received daily subcutaneous metreleptin injections for a period of 16 - 23
 weeks. A 3-hour oral glucose tolerance test and body composition
 measurements were conducted before and after the treatment period, and
 fasting blood samples were used for metabolomic profiling. The study
 outcome aimed at measuring changes in physiologically relevant metabolites
 pre- and post- leptin therapy. Results Metabolomic analysis revealed
 changes in pathways involving branched-chain amino acid metabolism, fatty
 acid oxidation, protein degradation, urea cycle, tryptophan metabolism,
 nucleotide catabolism, vitamin E, and steroid metabolism. Fold-changes in
 pre- to post-treatment metabolite levels indicated increased breakdown of
 fatty acids, branched chain amino acids proteins, and nucleic acids.
 Conclusions Leptin replacement therapy has significant effects on
 important metabolic pathways implicated in patients with lipodystrophy.
 Continued metabolomic studies may provide further insight into the
 mechanisms of action of leptin replacement therapy and provide novel
 biomarkers of lipodystrophy.
DOI: 10.5061/dryad.sj3tx961j
title: Pre-closure fishing pressure predicts effects of marine protected areas

description: 1. Marine Protected Areas (MPAs) can be effective tools for marine
 resource management. However, despite evidence of the positive effects of
 MPAs, such as increases in body sizes of organisms targeted by fisheries,
 there is often heterogeneity in biological outcomes among them. 2. Because
 fishing can drastically impact fish populations, the goal of this study
 was to determine if the levels of exploitation prior to protection could
 predict variation in the magnitude of MPA effects. 3. Using a diver
 operated stereo-video camera system, we compared sizes of fishes targeted
 by anglers within seven MPAs spanning the Southern California Bight to
 nearby comparison areas (non-MPAs). We used fine-scale data on pre-closure
 fishing pressure to test responses of fishes to protection along a
 gradient of exploitation. 4. Fish size responded to protection in
 proportion to pre-closure fishing pressure, with MPAs in areas with high
 pre-closure fishing having greater responses in average lengths and size
 distributions than those in areas with low fishing pressure. 5. This
 response was evident in species heavily targeted by recreational fishing,
 but not in species that were not targeted in fisheries. 6. Synthesis and
 applications: Pre-closure fishing pressure of an area can impact the
 efficacy of MPAs, and, when available, should be considered when
 predicting and evaluating MPA performance. Prioritizing heavily exploited
 areas for protection when implementing spatial management tools could
 maximize ecological outcomes.
DOI: 10.5061/dryad.cc2fqz62r
title: Increased spatial-genetic structure in a population of the clonal aquatic plant Sagittaria latifolia (Alismataceae) following disturbance

description: The spatial genetic structure (SGS) of plant populations is determined by
 the outcome of key ecological processes, including pollen and seed
 dispersal, the intensity of local resource competition among newly
 recruited plants, and patterns of mortality among established plants.
 Changes in the magnitude of SGS over time can provide insights into the
 operation of these processes. We measured SGS in a population of the
 clonal aquatic plant, Sagittaria latifolia that had been disturbed by
 flooding, both before and after the flood. . Over the four-year interval
 between measurements, we found substantial changes in the magnitude of
 SGS. In the first measurement (pre-flood), SGS was weak, even over short
 distances. By contrast, there was substantial SGS in the second
 measurement (post-flood), particularly over short distances. This change
 in SGS was accompanied by near complete turnover in the genotypic
 composition of the population. The genotypic richness of the population
 (the number of unique clones scaled by the sample size) was halved over
 the four-year interval. The clonal subrange – the distances between shoots
 within clones – also shrank considerably, with more than 5% of shoots
 having clone-mates at distances greater than 10 m before the flood, but
 fewer than 5% of shoots having clone-mates at distances beyond 2 m
 afterwards. Clonal turnover and the re-establishment of SGS in clonal
 populations are both expected following local extirpation and recruitment.
 These data reveal the genetic signatures of disturbance and a subsequent
 flush of seedling recruitment and subsequent clonal expansion.
DOI: 10.5061/dryad.5dv41ns2r
title: Data from: Substrate stoichiometry determines nitrogen fixation throughout succession in southern Chinese forests

description: The traditional view holds that biological nitrogen (N) fixation often
 peaks in early- or mid-successional ecosystems and declines throughout
 succession based on the hypothesis that soil N richness and/or phosphorus
 (P) depletion become disadvantageous to N fixers. This view, however,
 fails to support the observation that N fixers can remain active in many
 old-growth forests despite the presence of N-rich and/or P-limiting soils.
 Here, we found unexpected increases in N fixation rates in the soil,
 forest floor, and moss throughout three successional forests and along six
 age-gradient forests in southern China. We further found that the
 variation in N fixation was controlled by substrate carbon(C):N and
 C:(N:P) stoichiometry rather than by substrate N or P. Our findings
 highlight the utility of ecological stoichiometry in illuminating the
 mechanisms that couple forest succession and N cycling.
description: Data of substrate resources, stoichiometry, and N fixation rates
 from our studied sites.
DOI: 10.5061/dryad.34tmpg4g1
title: Data from: Phylogenomic data reveal reticulation and incongruence among mitochondrial candidate species in Dusky Salamanders (Desmognathus)

description: Gene flow between evolutionarily distinct lineages is increasingly
 recognized as a common occurrence. Such processes distort our ability to
 diagnose and delimit species, as well as confound attempts to estimate
 phylogenetic relationships. A conspicuous example is Dusky Salamanders
 (Desmognathus), a common model-system for ecology, evolution, and
 behavior. Only 22 species are described; 7 in the last 40 years. However,
 mitochondrial datasets indicate the presence of up to 45 “candidate
 species” presenting a complex history of reticulation. Some authors have
 even suggested that the search for species boundaries in the group may be
 in vain. Here, we analyze nuclear and mitochondrial data containing 161
 individuals from at least 49 distinct evolutionary lineages that we treat
 as candidate species. Concatenated and species-tree methods fail to
 provide satisfactory resolution for relationships among these taxa.
 Comparing topologies and applying methods for estimating phylogenetic
 networks, we find strong support for numerous instances of hybridization
 throughout the history of the group. We suggest that these processes may
 be more common than previously thought across the
 phylogeography-phylogenetics continuum, and that while the search for
 species boundaries in Desmognathus may not be in vain, it will be
 complicated by factors such as crypsis, parallelism, and gene-flow.
description: Sanger sequencing - Mitochondria Anchored
 Hybrid Enrichment - Phylogenomics See MS & SI
 for details.
description: desmo161_381loci_trim_names_astrid_mlbs.tre - ASTRID tree
 estimated from AHE loci with multi-locus bootstrapping
 desmo161_381loci_trim_names_astrid.tre - ASTRID tree estimated
 from AHE loci with quartet support
 desmo161_381loci_trim_names_concatenated.tre - ML tree estimated
 from concatenated AHE loci
 desmo161_381loci_trim_names.charSets - partitions for
 concatenated AHE loci desmo161_381loci_trim_names.phy -
 concatenated AHE loci desmo161_381loci_trim_names.trees
 - individual gene trees for AHE loci
 desmo161_mt.charSets - partitions for mitochondrial
 data desmo161_mt.phy - mitochondrial
 alignment desmo161_mt.tre - ML phylogeny of
 mitochondrial data JW_161_58_concat.part - partitions
 for ddRAD + AHE loci  JW_161_58_concat.phy -
 concatenated dataset for ddRAD + AHE loci
 JW_161_58_concat.tre - ML phylogeny for concatenated ddRAD + AHE
 loci
DOI: 10.5061/dryad.4b8gtht82
title: Spectral-ratio tomography for attenuation estimation

description: In the measurement of surface seismic data, an accurate
 attenuation-estimation method is necessary to compensate for the energy
 loss and phase distortion of seismic waves, and also beneficial for
 further quantitative amplitude analyses and reservoir parameters
 prediction. We design a more accurate Q tomography method to estimate Q
 values. This method inverts for the Q values in the overburden and target
 layer simultaneously without assumptions on the overburden, which allows
 us to separate the overburden effect during the inversion. As Q tomography
 methods estimate Q value by assuming the source wavelet is known, the
 results of Q value are often affected by the errors of the calculated
 source wavelet. Thus, from the same source, we take the spectral ratio of
 two reflections from the top and bottom of a target layer as an
 alternative for tomography input. For the log spectral ratio (LSR) method
 and attenuated traveltime tomography (t* tomography), picking two
 reflections at different traveltimes may be affected in different ways by
 lateral changes in the overburden (we call it the overburden effect).
 Thus, the accuracy of the conventional methods may be affected by
 differences between the ray paths in the overburden of the two picked
 reflections. In our method, we address this problem using an inversion
 method, which allows us to separate attenuation effects from the
 overburden by using traveltime difference in the tomography grid cells. Q
 values of the target layer and that of the overburden can be inverted
 simultaneously. We test the method in synthetic data and prove its
 feasibility and effectiveness by applying it to field data.
DOI: 10.5061/dryad.fn2z34tpz
title: Intelligent classification of platelet aggregates by agonist type

description: Platelets are anucleate cells in blood whose principal function is to stop
 bleeding by forming aggregates for hemostatic reactions. In addition to
 their participation in physiological hemostasis, platelet aggregates are
 also involved in pathological thrombosis and play an important role in
 inflammation, atherosclerosis, and cancer metastasis. The aggregation of
 platelets is elicited by various agonists, but these platelet aggregates
 have long been considered indistinguishable and impossible to classify.
 Here we present an intelligent method for classifying them by agonist
 type. It is based on a convolutional neural network trained by
 high-throughput imaging flow cytometry of blood cells to identify and
 differentiate subtle yet appreciable morphological features of platelet
 aggregates activated by different types of agonists. The method is a
 powerful tool for studying the underlying mechanism of platelet
 aggregation and is expected to open a window on an entirely new class of
 clinical diagnostics, pharmacometrics, and therapeutics.
description: The images were acquired using the OTS microscope and recovered
 using the program written in Matlab.
DOI: 10.5061/dryad.mw6m905t3
title: Phylogenetic signals in pest abundance and distribution range of spider mites

description: Attributes of pest species like host range are frequently reported as
 being evolutionarily constrained and showing phylogenetic signal. Because
 these attributes in turn could influence the abundance and impact of
 species, phylogenetic information could be useful in predicting the likely
 status of pests. In this study, we used regional (China) and global
 datasets to investigate phylogenetic patterns in occurrence patterns and
 host ranges of spider mites, which constitute a pest group of many
 cropping systems worldwide. We found significant phylogenetic signals in
 relative abundance and distribution range both at the regional and global
 scales. Relative abundance and range size of spider mite were positively
 correlated with host range, although these correlations became weaker
 after controlling for phylogeny. The results suggest that pest impacts are
 evolutionarily constrained. Information that is readily easily obtainable
 – including the number of known hosts and phylogenetic position of the
 mites – could therefore be useful in predicting future pest risk of
 species.
DOI: 10.5061/dryad.59zw3r23h
title: Detection of spatiotemporal variation in Ranavirus distribution using eDNA

description: Amphibian population declines have been associated with emerging diseases
 including ranaviruses, which can cause mass die-offs across entire
 amphibian communities. Understanding and mitigating disease spread
 requires knowledge of spatial and temporal patterns of pathogen
 distribution, but also how environmental factors influence pathogen
 occurrence. We applied environmental DNA (eDNA) detection tools to survey
 spatial and temporal distributions of ranaviruses by sampling 103
 waterbodies in southeastern Ontario, Canada, and assessed the role of
 abiotic factors as predictors of pathogen occurrence. Ten waterbodies
 sampled during June-August (&gt;30 km between sites) revealed that
 ranavirus was marginally more prevalent (p = 0.055) during the latter part
 of the summer. Ninety-three sites sampled at a finer scale (&lt;10km
 between sites) exhibited seasonal variability in ranavirus detection (site
 prevalence: 56% May; 66% July). Occupancy modeling revealed that wetland
 size and elevation influenced ranavirus occurrence while sampling date and
 water temperature influenced probability of detection. These findings
 indicate that biotic factors, such as host density and alternative hosts,
 should be investigated further as likely determinants of ranavirus
 prevalence across the landscape. Further, these results highlight the
 sensitivity of eDNA for detecting widespread presence of ranavirus, and
 that abiotic factors may have a limited role in determining its prevalence
 and infectivity.
description: Data shown represent values per capsule (n=5) per month. Values
 are given in pfu/mL. Water volume per capsule data are given in mL. qPCRs
 for each capsule were run in triplicate (REP 1, 2 and 3).
DOI: 10.5061/dryad.rbnzs7h77
title: Data from: Resource heterogeneity and the evolution of public-goods cooperation

description: Heterogeneity in resources is a ubiquitous feature of natural landscapes
 affecting many aspects of biology. However, the effect of environmental
 heterogeneity on the evolution of cooperation has been less well studied.
 Here, using a mixture of theory and experiments measuring siderophore
 production by the bacterium Pseudomonas aeruginosa as a
 model for public-goods based cooperation, we show that cooperation in
 metapopulations that were spatially heterogeneous in terms of resources
 can be maintained at a higher level than in homogeneous metapopulations of
 the same average resource value. The results can be explained by a
 positive covariance between fitness of cooperators, population size and
 resource availability, which allowed cooperators to have a
 disproportionate advantage within the heterogeneous metapopulations. These
 results suggest that natural environmental variation may help to maintain
 cooperation.
description: Three types of assay were used in the collection of these data:
 Growth assays, fitness assays, and per capita siderophore measures. Growth
 assays measure colony forming units after a period of growth, fitness
 assays compete a focal strain against a competitor, calculating the ratio
 of malthusian growth of the focal strain vs that of the competitior, and
 per capita sierophore assays measure the iron binding ability of the
 supernatent after a period of growth, scaled by the number of colony
 forming units that produced that same supernatent.
description: There are no missing values in this dataset. Where data is
 provided in wide format, users may wish to reshape these data to long
 format for analysis or for plotting.
DOI: 10.25574/28428
title: Chandra X-ray Observatory ObsId 28428

description: AO-25 LETG/HRC-S Calibration Observations of HZ43
DOI: 10.5061/dryad.gf1vhhmjv
title: How much do rare and crop-pollinating bees overlap in identity and flower preferences?

description: 1. The biodiversity-centered approach to conservation prioritizes rare
 species, whereas the ecosystem services approach prioritizes species that
 provide services to people. The two approaches align when rare species
 provide ecosystem services, or when both groups of species benefit from
 the same management action. We use data on bee pollinators and the plant
 species they forage on to determine if there are rare species among the
 most important crop pollinators, and the extent to which plant species
 selected to support crop pollinators would support rare species as well.
 2. To assess the plant preferences of these two groups of bee species, we
 collected two datasets on plant-pollinator interactions, one experimental
 and one observational. The experiment consisted of monospecific plots of
 17 plant species from which we collected bees over three years. The
 observational data consisted of bees collected from 66 species of plants
 growing in semi-natural meadows, also over three years. 3. Nineteen
 percent of the dominant crop pollinating species were regionally rare.
 Both rare species and crop-pollinating species had strong preferences for
 certain plants, and the preferences of rare and crop-pollinating bees were
 significantly but not strongly (r ≤ 0.54) correlated. Ten plant species
 were significantly preferred by both rare and crop-pollinating bees. 4.
 Synthesis and applications. We found several dominant crop pollinators
 that are rare at a regional scale, supporting the idea that rare species
 can be important providers of ecosystem services. The flower preferences
 of rare and crop-pollinating bees are significantly positively associated,
 suggesting that plants chosen to support crop pollinators will benefit
 rare species as well. We identify plant species that are preferred by
 regionally rare bees and by crop pollinators, including 10 plant species
 preferred by both types of bees, and recommend these for use in pollinator
 habitat plantings.28-Oct-2019
DOI: 10.15468/dl.2xgqsx
title: Occurrence Download

description: A dataset containing 37828 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Mosquito Alert Dataset"
 ]
}

 The dataset includes 37828 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002039-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pg2hw2
title: Occurrence Download

description: A dataset containing 10265 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is North America",
 "Country is Mexico",
 "OccurrenceStatus is Present",
 "StateProvince is one of (Baja California, Baja California Sur)",
 "TaxonKey is one of (Furcraea, Agave, Hesperoyucca, Nolina, Yucca)"
 ]
}

 The dataset includes 10265 records from 46 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002041-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.