cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5066/p9twtr2f
title: Croton setiger predators, herbivores, and damage collected in California 2013-2014

description: A pollen addition experiment was conducted on the leaves of Croton setiger, a Californian forb. Pollen was added to leaves of randomly selected plants, and control plants had no pollen added. Over 2013 and 2014 the number of predatory and herbivorous insects were counted on each plant, and the number of damaged leaves and plant size were measured.
DOI: 10.5066/p9tyf93i
title: Co-occurrence and Occupancy Dynamics of Mourning Doves and Eurasian Collared-Doves

description: Data on mourning dove and Eurasian collared-dove occurrences, and associated covariates.
DOI: 10.5066/p9u2uzcp
title: Body condition scores and foaling outcomes in 2021 for 18 mares at Sulphur herd management area, Utah treated with gonadotropin releasing hormone

description: These data present outcomes for monitoring of 18 mares at Sulphur herd management area, Utah. Data include Henneke body condition scores (BCS) and foaling success, measured by visual observations of mares during the 2021 breeding season (April to September 2021) to determine if mares had a foal at foot. Mares were treated with gonadotropin releasing hormone vaccine on September 2, 2020 and boosters were administered on November 1, 2020.
DOI: 10.5066/p9u461pj
title: Data Release: Possibility for reverse zoonotic transmission of SARS-CoV-2 to free-ranging wildlife: a case study of bats

description: The table illustrates global patterns of betacoronavirus (&beta;-CoV) associations in bats. The table lists bat species in which betacoronaviruses (&beta;-CoVs) were detected, organized by viral subgenera and clade [for Sarbecorviruses], bat family, bat suborder, and general global region where the species of bat occurs. Reference to the published literature sources of information for each row are listed in the last column.
DOI: 10.5066/p9u7278u
title: Data on interannual seed set variation, weather, and reproductive traits for global plants

description: Data were collected on seed production dynamics of long-lived plants, reproductive plant traits of those plant species, and weather variability for sites where those species live. Data include the coefficient of variation in seed production over time, the variation (coefficient of variation or standard deviation) in weather over years, and reproductive traits such as pollination mode and seed dispersal mechanism. Data series were distributed globally and encompass 920 data series containing 311 plant species. Data series are all 6 or more years in length.
DOI: 10.5066/p9ukso98
title: Greenhouse observations of plant herbivore interactions on Lepidium draba to test effects of ontogenic variability

description: Data were collected from an experimental greenhouse study in which Lepidium draba plants were grown from root cuttings to create plants at different ontogenic stages. Plants were arranged in mixed-age and single-age stands and exposed to the Lepidopteran herbivore, diamondback moth caterpillars. The success (biomass gain and surivival) of herbivores, the amount of feeding, and the growth of plants were recorded as responses to ontogenic stage. In addition, glucosinolates (a group of secondary metabolites known to act as defenses against herbivores) were quantified on plants of differing ontogenic stage.
DOI: 10.5066/p9ur2k3e
title: Field measurements, laboratory, and field experimental data for Sky Pond, Rocky Mountain National Park Colorado, nutrient and warming study, 2015-2017

description: The data include measurements of chlorophyll a and algal stoichiometry from benthic algae collected from Sky Pond, Rocky Mountain National Park, Colorado, in 2015-2017; results of nutrient diffusion experiments in Sky Pond including chlorophyll a and other pigments to identify chlorophytes, bacillariophytes, and myxomycetes, and results of a laboratory incubation using benthic chlorophytes to identify ecosystem responses (nitrogen uptake, net primary productivity, ecosystem respiration, net ecosystem productivity, and dissolved organic carbon production) under nutrient and temperature treatments.
DOI: 10.5066/p9use8ch
title: Arizona Grasshopper Sparrow nest monitoring data 2011 to 2013

description: These data include nest-specific information about Arizona Grasshopper Sparrow nests monitored during 2011 to 2013. The data are formatted as we used them in Program MARK to evaluate factors affecting daily nest survival. Data includes information on when the nest was found, when it was last known to be active, nest fate, and nest age. In addition, we provide vegetation data from the nest site itself and the nest plot as well as summary seasonal precipitation data collected from other sources and used in these analyses.
DOI: 10.5066/p9v5h833
title: In Support of the U.S. Fish and Wildlife Service 3-Bat Species Status Assessment: Wind Energy Influence

description: Through the North American Bat Monitoring Program, United States Geological Survey (USGS) provided technical and science support to assist in U.S. Fish and Wildlife Services' Species Status Assessment ("SSA") for the northern long-eared bat (Myotis septentrionalis), little brown bat (Myotis lucifugus), and tri-colored bat (Perimyotis subflavus). USGS facilitated the SSA data call, provided data archival for repeatable and transparent analyses, provided statistical support to assess the historical, current, and future population status for each of the three species, and developed a demographic projection tool to evaluate future viability of each species under multiple threat scenarios. These data represent the derived species-specific index of potential wind energy influence of each NABat grid cell ("grid cell") from 2007-2020 derived based on the U.S. Wind Turbine Database after joining turbine locations to the NABat grid and aggregating at the grid cell. This metric is summarized for each grid cell and year, and reflects both the proximity of each grid cell to all wind energy locations on the landscape (with respect to the mean dispersal distance of each species in kilometers) and also the intensity (rated capacity in megawatts) at each location. It was derived based on the total rated wind energy capacities of grid cells, and the distances from grid cells with wind energy to all other NABat grid cells, the mean migration distance of each species, and an exponential dispersal kernel as a weighting function.
DOI: 10.5066/p9vachx0
title: Capture-recapture, disease and covariate data for boreal toads from Blackrock Wyoming 2019

description: We investigated population dynamics in boreal toads relative to abiotic (fall temperatures and snowpack -the covariates provided here) and biotic (the abundance of another anuran host,data provide here) characteristics of the local environment at 6 sites in Wyoming, USA. We used capture-recapture data (i.e., 1 or 0, provided here) and a robust design multi-state model framework that incorporates disease state uncertainty to assess our a priori hypotheses about interactions among covariates (temperature, snowpack and presence of spotted frogs) and boreal toad survival. Files include: br_bd.csv, disease data; br_cmr.csv, capture-mark recapture data (1,0); br_cov.csv, soil and snow information detailed in this file; br_eggmass.csv, counts of spotted frog egg masses.
DOI: 10.5066/p9vjxjny
title: Spatial layers generated by the Prioritizing Restoration of Sagebrush Ecosystems Tool (PReSET) applied in Southern Wyoming

description: All data layers included in this data release were created using the Prioritizing Restoration of Sagebrush Ecosystems Tool (PReSET) tool, which relies on spatial inputs on species distributions and likelihood of restoration success to select parcels for sagebrush restoration. The PReSET is a workflow that relies on the prioritizr package in program R to identify parcels for effective and meaningful sagebrush restoration.Inputs into the tool included occupancy data layers for six focal species (Brewer&rsquo;s sparrow (Spizella breweri), sagebrush sparrow (Artemisiospiza nevadensis), sage thrasher (Oreoscoptes montanus), greater sage-grouse (Centrocercus urophasianus), pronghorn (Antilocapra americana) and greater short-horned lizard (Phrynosoma hernandesi) generated within the Sagebrush Ecosystem Conservation and Management: Ecoregional Assessment Tools and Models for the Wyoming Basins (Hanser et al. 2011). The layer to assess restoration suitability was predicted time to sagebrush recovery (Monroe et al. 2021; https://doi.org/10.5066/P9XV8GH7). This data release consists of 9 rasters and 1 polygon shapefile organized into three bundles associated with distinct problem sets addressing issues in sagebrush restoration. 1) Landscape weighting scenarios (Fig 3), 2) Protected lands connectivity (Fig. 4), and 3) Local-scale wellpad restoration (Fig. 5). Each of these bundles is described further in subsequent metadata files. Spatial data associated with these data sets include selected pixels or polygons under various scenarios prioritizing sagebrush restoration. Raster layers (90x90m cell size) associated with Figure 3 in the manuscript include selected pixels based on time-to recovery of sagebrush and habitat potential for target species, for all species and a stacked raster layer representing the number of times each pixel occurred in one or more scenarios. Raster layers (360x360m cell size) associated with figure 4 in the manuscript include a comparison of selected cells with no connectivity requirements, with a penalty for unconnected features, and with a penalty for unconnected features and including &ldquo;locked-in&rdquo; protected lands. Spatial polygons associated with Figure 5 in the manuscript include selection wellpads under projected oil and gas buildout, requiring protection of 10% of habitat for all species under no, low, moderate, and high connectivity requirements. PReSET tool is currently housed at USGS FORT.
DOI: 10.5066/p9vlb2yz
title: Fecal samples collected in May, August, and October 2014 from Little Book Cliffs Herd Management Area, Colorado, for determination of diet, persistence of DNA in the environment, individual identity, and seed germination.

description: These data were collected in May, August, and October in west central Colorado from a Bureau of Land Management wild horse herd management area (HMA). Samples were already on the ground, not fresh from the horse. The Diet dataset includes proportion of plant species found in fecal samples using two different lab techniques -- plant DNA bar-coding,and microhistology. Results of both methods to determine diet are in the same spreadsheet. The dung aging dataset consists of samples of different known ages of feces and their amplification results; 8 markers were amplified and data shown in each column indicate whether that marker loci amplified or not. Germination data showed which plant species germinated from fecal samples that were tended in a lab, along with number of plants and dry weight of germinated plants. Repeated sampling dataset includes all samples that were collected, amplification results by loci, and provides the individual genotype for each sample.
DOI: 10.5066/p9vlm7z6
title: Standardized Precipitation Evaporation Index for the Upper Green River Basin (1896-2017)

description: The standardized precipitation evapotranspiration index (SPEI) was summarized for the Upper Green River Basin to quantify climate variability over the last century. The SPEI incorporates both precipitation and temperature data, therefore the index has the capacity to include the effects of temperature variability on drought. The SPEI considers the difference between precipitation and potential evapotranspiration to calculate a climatic water balance at a given time scale (Vicente-Serrano et al. 2010). The number of standard deviations the climatic water balance deviates from the long-term mean for a given time period represents the SPEI for the time period. Here, I calculated the SPEI for each water year (Oct-Sept) between 1896 and 2017. The SPEI score is shown on the y-axis and time on the x-axis. Years in red indicate a lower SPEI than the long-term mean, whereas years in blue indicate a higher SPEI than the long-term mean. Data (4km2 SPEI data) was obtained from the Western Regional Climate Center (http://www.wrcc.dri.edu; accessed 14 January 2017) and calculated the water year mean (12-month data) for the Upper Green River Basin. Literature Cited Vicente-Serrano, S. M., S. Begueria, and J. I. Lopez-Moreno. 2010. A multiscalar drought index sensitive to global warming: The standardized precipitation evapotranspiration index. Journal of Climate 23:1696-1718.
DOI: 10.5066/p9vp7bfu
title: Data on the impacts of garlic mustard from a weeding experiment in Pennsylvania 2006-2016

description: Data were collected on the abundance of plants in a 10-year weeding experiment of garlic mustard, located at Trillium Trails Park in Pennsylvania. Garlic mustard was weeded annually to suppress its abundance, and the impacts of garlic mustard were measured based on the response of the plant community to garlic mustard weeding. Because garlic mustard is known to suppress mycorrhizal fungi, the mycorrhizal status of each plant species was determined and recorded. The experiment was arranged in a blocked design, where plots had subareas with and without garlic mustard removal. Cover of each plant species was measured as the average percent cover recorded in 18 2x2 meter quadrats with garlic mustard removed per plot and 18 2x2 meter subplots with garlic mustard remaining per plot.
DOI: 10.6084/m9.figshare.21572346
title: RNAseq_data_rawcount.txt

description: The changes in macrophages induced by the addition of skeletal myotube-derived extracellular vesicles were analyzed by RNA-seq. The results of raw count for each gene.
DOI: 10.6084/m9.figshare.21572346.v1
title: RNAseq_data_rawcount.txt

description: The changes in macrophages induced by the addition of skeletal myotube-derived extracellular vesicles were analyzed by RNA-seq. The results of raw count for each gene.
DOI: 10.5066/p9vpekgv
title: Data on finite population change for 3 species of prairie dogs in Montana and Utah, USA, 2000-2005

description: Data on annual population change for prairie dogs in Montana and Utah, USA, 2000-2005. Prairie dog species included black-tailed prairie dogs (PDs) (BTPD, Cynomys ludovicianus) in north-central Montana, white-tailed PDs (WTPD, Cynomys leucurus) in eastern Utah, and Utah PDs (UPD, Cynomys parvidens) in southwestern Utah. Field research was completed by the U.S. Geological Survey, Fort Collins Science Center, and colleagues. Data were collected on paired plots. Each pair included a plot treated annually with deltamethrin dust for flea control and plague mitigation and a plot left untreated as baselines. Paired plots had similar ecological features on the same (split) or nearby (separate) colonies. One plot within each pair was randomly selected for deltamethrin dust treatment. We used summertime visual counts as an index to PD population size.We conducted visual counts annually during June-August, after young PDs were aboveground. We used binoculars and spotting scopes to systematically and repeatedly scan the plots (each plot was 3-9 hectares in area), beginning just after sunrise and continuing until warming temperatures caused a decline in counts. We repeated the procedure for three days, using for analysis the highest count obtained. We counted from the same locations each year, simultaneously counting treated and non-treated plots of each pair. Visual counts were transformed into values of finite population change by dividing the PD count at the end of an annual interval by the count at the beginning of the interval. For example, if year is 2001, then population change was for the interval 2000 to 2001. Primary funding was provided by the U.S. Fish and Wildlife Service, U.S. Geological Survey, and Bureau of Land Management, supplemented by the Utah Division of Wildlife Resources and the Utah Department of Natural Resources Endangered Species Mitigation Fund. In-kind support was provided by the Bryce Canyon National Park, Dixie National Forest and BLM offices in Utah (Vernal, Cedar City, Richfield, and Torrey), Colorado (Meeker), and Montana (Malta). R. Reading and B. Miller of the Denver Zoological Foundation provided logistical support for parts of the study.
DOI: 10.5066/p9vsg54z
title: Genetic variation in hoary bats (Lasiurus cinereus) assessed from archived samples

description: Hoary bats are among the bat species most commonly killed by turbine strikes in the midwestern United States. The impact of this mortality on species census size is not understood, due in part to the difficulty of estimating population size for this highly migratory and elusive species. Genetic effective population size (Ne) could provide an index of census population size if other factors affecting Ne are stable. In support of this and other population-genetic studies, we analyzed two temporally spaced cohorts: 96 hoary bats collected in 2009-2010 and an additional 96 collected in 2017-2018. Samples consisted of wing clips removed from archived carcasses and were obtained by agreement from the U.S. Fish and Wildlife Service, the sponsor of this research. All carcasses were originally collected post mortem at wind-turbine facilities in the state of Indiana and subsequently frozen, although for our research purposes the collection location or cause of death is not material. We sequenced restriction-site associated polymorphisms and generated a de novo genome assembly to guide the removal of sex-linked and multi-copy loci, as well as identify physically linked markers. This data release includes the computationally inferred genotypes at 12,915 single-nucleotide polymorphisms (SNPs) for 186 individuals, after excluding six individuals with insufficient data. It also includes the reference genome sequence used to identify physically linked loci and remove sex chromosomes from analysis.
DOI: 10.5066/p9w0vf4f
title: Data for cheatgrass mapping in Squirrel Creek Wildfire and Arapaho Wildfire, WY in 2014

description: This data bundle contains some of the inputs, all of the processing instructions and all outputs from a single VisTrails/SAHM workflow. This model specifically includes field data of locations with &gt;40% cover of cheatgrass (presence) and &lt;40% cover of cheatgrass (absence) from two wildfire locations in Wyoming. Predictors included rasters derived from Landsat 8 imagery and from a digital elevation model. Details about both inputs are included in the associated manuscript described in the larger work citation of the '_archive_bundle_metadata.xml' metadata record. We developed models for each location and tested the transferability of the models to the other location. We built on previous work developing models for the Squirrel Creek wildfire area only, but reran these models for consistency of predictors with those of Arapaho wildfire area. The contents of this data bundle include the following, each of which is documented in an individual metadata record. 1) '_archive_bundle_metadata.xml' which contains FGDC metadata describing the archive bundle. 2) 'arapaho_2014_with40_as_pres_for_sahm.csv' containing cheatgrass location data for Arapaho wildfire area. 3) 'squirrel_all_with40_as_presence_for_sahm.csv' containing cheatgrass location data for Squirrel Creek wildfire area. 4) 'predictorlist.csv' includes the list of rasters for Squirrel Creek wildfire area used to create the models. 5) 'predictorlistarapaho.csv' includes the list of rasters for Arapaho wildfire area used to create the models. 6)The remaining subfolders are individual model runs containing 2 or 3 subfolders, one of the fitted random forest model output and one apply model random forest of that model applied to the other area. The name of the folder specifies which (e.g., either Squirrel_34_31_and_topo (Squirrel creek RF model fit with Landsat Path 34, row 31 and topo data) or Squirrel_34_31_and_topo_to_Arapaho_34_31_and_topo (the former applied to Arapaho Landsat path 34 row 31).
DOI: 10.5281/zenodo.7254202
title: Structure-imposed electronic topology in cove-edged graphene nanoribbons

description: <strong>Abstract</strong> In cove-edged zigzag graphene nanoribbons (ZGNR-C), one terminal group per length unit is removed on each zigzag edge, forming a regular pattern of coves which controls their electronic structure. Based on three structural parameters that unambiguously characterize the atomistic structure of ZGNR-C, we present a scheme that classifies their electronic state, i.e., if they are metallic, topological insulators or trivial semiconductors, for all possible widths <em>N</em>, unit lengths <em>a</em> and cove position offsets at both edges <em>b</em>, thus showing the direct structure-electronic structure relation. We further present an empirical formula to estimate the band gap of the semiconducting ribbons from <em>N</em>,<em>a</em>, and <em>b</em>. Finally, we identify all geometrically possible ribbon terminations and provide rules to construct ZGNR-C with well-defined electronic structure. DOI: 10.1103/PhysRevLett.129.216401 <strong>Content of repository</strong> The repository contains the inputs and outputs of tight-binding (TB) calculations of ZGNR-C based on PythTB. For each analysed structure one subdirectory is created, labelled as "N-ZGNR-C_a_b_inv_cell\(\alpha\)_termination". This corresponds to a <em>N</em>-ZGNR-C(<em>a</em>,<em>b</em>) with inversion center at the unit cell boundary <em><strong>S</strong></em> or <em><strong>L</strong></em> ("inv"), unit cell angle \(\alpha\) ("cell\(\alpha\)": 60°, 90°, or 120°) and a given unit cell termination (armchair, zigzag or bearded). Each directory contains the atomic structure in xsf and cif format, the PythTB input file, the output as a json file, and the calculated band structure as image file. The json file contains the band structure information (path and eigenvalues), the raw Zak phase in units of \(\pi\) without modulo 2, and the final \(\mathbb{Z}_2\) invariant.
DOI: 10.5281/zenodo.7254203
title: Structure-imposed electronic topology in cove-edged graphene nanoribbons

description: <strong>Abstract</strong> In cove-edged zigzag graphene nanoribbons (ZGNR-C), one terminal group per length unit is removed on each zigzag edge, forming a regular pattern of coves which controls their electronic structure. Based on three structural parameters that unambiguously characterize the atomistic structure of ZGNR-C, we present a scheme that classifies their electronic state, i.e., if they are metallic, topological insulators or trivial semiconductors, for all possible widths <em>N</em>, unit lengths <em>a</em> and cove position offsets at both edges <em>b</em>, thus showing the direct structure-electronic structure relation. We further present an empirical formula to estimate the band gap of the semiconducting ribbons from <em>N</em>,<em>a</em>, and <em>b</em>. Finally, we identify all geometrically possible ribbon terminations and provide rules to construct ZGNR-C with well-defined electronic structure. DOI: 10.1103/PhysRevLett.129.216401 <strong>Content of repository</strong> The repository contains the inputs and outputs of tight-binding (TB) calculations of ZGNR-C based on PythTB. For each analysed structure one subdirectory is created, labelled as "N-ZGNR-C_a_b_inv_cell\(\alpha\)_termination". This corresponds to a <em>N</em>-ZGNR-C(<em>a</em>,<em>b</em>) with inversion center at the unit cell boundary <em><strong>S</strong></em> or <em><strong>L</strong></em> ("inv"), unit cell angle \(\alpha\) ("cell\(\alpha\)": 60°, 90°, or 120°) and a given unit cell termination (armchair, zigzag or bearded). Each directory contains the atomic structure in xsf and cif format, the PythTB input file, the output as a json file, and the calculated band structure as image file. The json file contains the band structure information (path and eigenvalues), the raw Zak phase in units of \(\pi\) without modulo 2, and the final \(\mathbb{Z}_2\) invariant.