cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.7294/w4tar0jd88
title: (V1, superseded by new version, doi:10.7294/284t-bf10) Viral Networks: Connecting Digital Humanities and Medical History

description: (V1, superseded by new version, doi:10.7294/284t-bf10) Viral Networks: Connecting Digital Humanities and Medical History is a collection of original essays examining networks as an object of study, a tool for analysis, a framework for collaboration, and a means of scholarly communication. The chapters began as papers for the Viral Networks Workshop, hosted by the History of Medicine Division of the National Library of Medicine (NIH), funded by the Office of Digital Humanities of the National Endowment for the Humanities, and organized by Virginia Tech. The scholars involved in this project examined networks in medical history even as they became participants in a network of scholars engaged in collaborative learning. Inspired by models of networked pedagogy, these chapters developed through a connected series of activities that began with reading proposals, included one face-to-face and two virtual conferences, and ended with final edits on revised chapters. The papers should therefore be understood and read as a fully networked project, not as chapters written individually and placed together. The chapters in this collection demonstrate what a network analysis can reveal, but also how a network analysis can help a humanities scholar approach a problem a different way, or understand what is missing in their sources or interpretations. The dataset contains data and data visualization related to the workshop and book.
DOI: 10.7294/w4gm85g8
title: Supplementary Material for Means and Marek, 2017 (V2)

description: This supplementary dataset includes the species distributions (latitude and longitude) and the morphology scoring matrix used in 'Is geography an accurate predictor of evolutionary history in the millipede family Xystodesmidae?' by Means and Marek, 2017. This dataset was updated on 20170621 with additional data points in the MeansandMarek2017_Species_Distribution_Perimiters_20170621_V2.csv file. The original dataset can be found at the following DOI, doi:10.7294/W4G15XSD.
DOI: 10.34740/kaggle/dsv/3468355
title: WallStreetBets 2022
DOI: 10.7294/14992041.v1
title: James Cave Epikarst Monitoring Drip Data: 2007-2018

description: <p></p><p>Cave
drip measurements were made at three drip monitoring stations within James Cave
(Pulaski County, Virginia) from fall 2007 to winter 2018. Measurements were
made in mm on a 10 minute interval using HOBO® tipping bucket rain gauges and
stored on HOBO® multi-station data loggers. Measurements in mm can be converted
to ml (3.7 ml to 0.2 mm). Data were downloaded bimonthly to quarterly and
compiled to form a continuous time series. 
Missing data reflect periods of instrumentation failure. The location of
cave drip monitoring sites can be found in Figure 4 of Groce-Wright (2021; <a href="http://hdl.handle.net/10919/104202">http://hdl.handle.net/10919/104202</a>).  The geologic map can be found as Figure 3 in
Groce-Wright (2021; <a href="http://hdl.handle.net/10919/104202">http://hdl.handle.net/10919/104202</a>).
Photos of the drip monitoring sites within the cave can be found as Figure 5 in
Groce-Wright (2021; <a href="http://hdl.handle.net/10919/104202">http://hdl.handle.net/10919/104202</a>).</p>

<p> </p>

<p>The
raw data were used in Groce-Wright (2021; <a href="http://hdl.handle.net/10919/104202">http://hdl.handle.net/10919/104202</a>) to
create drip hydrographs, which were analyzed using recession methods to
calculate alpha, the recession coefficient, which reflects the hydrogeologic
characteristics of the overlying epikarst (soil and weathered bedrock above the
cave), and the storage volume. </p><br><p></p>
DOI: 10.7294/17710973.v1
title: World's Coast Vertical Land Motion

description: Vertical Land Motion Along the world's coast as shown in Fig 3 of Shirzaei et al. (2021) Nature Reviews.<br>The estimated rate of land subsidence at coastal areas observed by using global navigation satellite system networks within the IGS14 reference frame. Note that these rates are likely a lower bound on the actual subsidence rate in several cases, owing to the absence of shallow signals.<br><br>
DOI: 10.7294/w4hq3x3w
title: Investigation of the Disposal and Recovery of Wood and Wood Packaging in the United States

description: For this study, over 200 Municipal Solid Waste (MSW) facilities responded to a survey regarding the wood pallets and packaging they received in 2016. These questions asked respondents to provide the total tonnage of total waste and wood waste landfilled and recovered with additional questions on facility operations and tipping fees.  Many respondents also provided additional commentary about how their facilities process wood and wood packaging waste, giving valuable insights to the current state of the market.   Over 200 facilities responded to the survey providing direct information on their tonnages and practices.  We found that each facility received an average 183,000 tons of MSW waste for a national estimate of 281 million tons of waste generated.  Additionally, on average each facility received approximately 17,911 tons of wood, of which 5863 tons were recovered in some way.  It was found that 58% of facilities operate a wood and pallet recovery area, which was a significant increase from previous studies.
DOI: 10.7294/14597751.v1
title: Redlining Virginia Preservation Dataset

description: <p>This dataset  includes all content and structural components for the project Redlining Virginia (http://redliningvirginia.org/). The purpose is to provide a description of the original project, a description of the preservation package, and any specialized software to open any component with the potential for reuse, reconstruction, or recreation. </p><p><br></p><p>Project Description: “Congress created the Home Owners' Loan Corporation (HOLC) in 1933 to rescue the real estate industry and restructure the home mortgage market. In the process, HOLC also strengthened residential racial segregation. HOLC promoted racial covenants on deeds to prevent mixed-race neighborhoods and created color-coded maps of American cities that made race a key element in assessing financial risk. This exhibit explores the actions of HOLC in Virginia and its impact on Virginia cities.”</p><p><br></p><p>Additional Redlining mappings that extend beyond Virginia and West Virginia regions can be found at https://doi.org/10.7294/cnha-n469. </p>
DOI: 10.7294/mpcg-qx45
title: Wire-tailed manakin telomere analysis (V1 SUPERSEDED)

description: (This version of the dataset has been superseded by the newer version at doi 10.7294/E6C2-7987) As aging is predicted to influence reproductive behaviors, biomarkers of aging (e.g., telomere lengths) should also be related to variation in reproductive behaviors. However, these relationships have not been well established in free-living animals. Wire-tailed manakins (Pipra filicauda) are a lekking songbird in which floater males ascend a social hierarchy and become territory-holders before they can reproduce. Males perform coordinated courtship displays and these displays form the basis of cooperative display coalitions. A floater’s cooperative behavior is predictive of his social ascension and more cooperative territory-holding males attain higher reproductive success. Here, we tested for status-specific patterns of aging by measuring telomere lengths of known-age male wire-tailed manakins. We also examined the relationship between cooperative reproductive behaviors and telomere lengths. Only among territory-holders were telomere lengths negatively correlated with age. Shorter telomeres were also associated with more frequent cooperative interactions and a more exclusive position within an individual’s social network. These results describe how socioecological variables influence patterns of biological aging and also suggest that short telomeres are associated with greater reproductive investments. Given that shorter telomeres are also associated with higher mortality risks, these results support the hypothesis that males with low future reproductive potential invest more in reproduction.
DOI: 10.7294/vc4t-xw67
title: Data for manuscript "An analytical approach to ascertain saturation-excess versus infiltration-excess overland flow in urban and reference landscapes"

description: Uncontrolled overland flow drives flooding, erosion, and contaminant transport, with the severity of these outcomes often amplified in urban areas. In pervious media such as urban soils, overland flow is initiated via either infiltration‐excess (where precipitation rate exceeds infiltration capacity) or saturation‐excess (when precipitation volume exceeds soil profile storage) mechanisms. These processes call for different management strategies, making it important for municipalities to discern between them. In this study, we derived a generalized one‐dimensional model that distinguishes between infiltration‐excess overland flow (IEOF) and saturation‐excess overland flow (SEOF) using Green–Ampt infiltration concepts. Next, we applied this model to estimate overland flow generation from pervious areas in 11 U.S. cities. We used rainfall forcing that represented low‐ and high‐intensity events and compared responses among measured urban versus predevelopment reference soil hydraulic properties. The derivation showed that the propensity for IEOF versus SEOF is related to the equivalence between two nondimensional ratios: (a) precipitation rate to depth‐weighted hydraulic conductivity and (b) depth of soil profile restrictive layer to soil capillary potential. Across all cities, reference soil profiles were associated with greater IEOF for the high‐intensity set of storms, and urbanized soil profiles tended towards production of SEOF during the lower intensity set of storms. Urban soils produced more cumulative overland flow as a fraction of cumulative precipitation than did reference soils, particularly under conditions associated with SEOF. These results will assist cities in identifying the type and extent of interventions needed to manage storm water produced from pervious areas.
DOI: 10.7294/w4jw8bsr
title: Wolf Creek Bridge - Point Clouds - 2017

description: This dataset consists of low-resolution point clouds generated during the Wolf Creek Bridge studies.
DOI: 10.7294/14531382.v1
title: Diverse landscapes but not wildflower plantings increase marketable crop yield

description: <p>These data were collected
as part of project assessing the drivers of ecosystem services in vegetable
crop production in eastern Virginia and Maryland. These are the data associated
with the path analysis that links together many of different response variables
measured. For further information on the data collection can be read in the
metadata file.</p>

<p>These are the data files and R script for Diverse landscapes but not
wildflower plantings increase marketable crop yield. This project contains six
files. There are four csv files that contain the data, one for each crop used.
The other two files are the R script used for the path analysis and the
metadata file. For more information on the descriptors of the project, the
data, and data collection, please read the metadata file.</p>
DOI: 10.7294/73hy-9s55
title: Genome_files_Draft assembly of Phytopthora capsici from long-read sequencing uncovers complexity

description: (V1, superseded by new version, doi:10.7294/83VW-6Z31) Resolving complex plant pathogen genomes is important for identifying the genomic shifts associated with rapid adaptation to selective agents such as host and fungicide, yet assembling these genomes remains challenging and expensive.  Phytophthora capsici is an important, globally distributed plant pathogen that exhibits wide-spread fungicide resistance and a broad host range.  As with other pathogenic oomycetes, P. capsici has a complex life history and a complex genome.  Here we leverage Oxford Nanopore Technology (ONT) and existing short read resources, to rapidly generate a low-cost, improved assembly.  We generated 10Gbp from a single MinIon flow cell resulting in > 1.25 million reads with an N50 of 13kb.  The resulting assembly is 124Mbp in 906 scaffolds with an N50 length of 232kb.  This assembly is 92% bigger than the current draft genome of 64Mbp. We confirmed this larger genome size using flow cytometry, with an estimated size of 110Mbp.  BUSCO analysis identified 96.5% complete orthologs (39.7% duplicated). Evolutionary analysis supports a recent whole genome duplication in this group. Our work provides a blueprint for rapidly integrating benchtop long-read sequencing with existing short-read data, to dramatically improve assembly quality and integrity of complex genomes and offer novel insights into pathogen genome function and evolution.
DOI: 10.7294/5en8-ak55
title: Systematic review of modeling assumptions and empirical evidence: does parasite transmission increase nonlinearly with host density?

description: For the paper entitled, “Systematic review of modeling assumptions and empirical evidence: does parasite transmission increase nonlinearly with host density?”, currently in review in Methods in Ecology and Evolution, we systematically reviewed seven representative ecology journals for host–parasite models that contain transmission functions, yielding 262 relevant papers. We analyzed each paper to determine whether each study used a single transmission function – the DD transmission function, the FD transmission function, or a single nonlinear transmission function – or whether the paper qualitatively or quantitatively evaluated multiple transmission functions. We also recorded whether authors worked with host numbers, densities, or frequencies, whether and how area was explicitly included within models, and whether area and/or host density were constants. All of these data are included in a single dataset in this repository. Additionally, we performed an extensive literature review to find experimental or observational studies that compared transmission functions in animal systems. For each of the 42 resulting papers, we determined which transmission functions were evaluated and which function the authors determined to be the most parsimonious description (best fit balanced against number of parameters) of the given host-parasite system. These data are included in a single dataset within this repository. The paper in review also includes a substantial model simulation component, which can be found in a different GitHub repository and as the R package ‘contactr’.
DOI: 10.7294/1hqp-sj66
title: Correlations Between the Thermosphere's Semi-Annual Density Variations and Infrared Emissions Measured with the SABER Instrument

description: These data  files provide the processed data shown in Figures 2 through 11 in the publication'Correlations Between the Thermosphere's Semi-Annual Density Variations and Infrared Emissions Measured with the SABER Instrument' in the Journal of Geophysical Research Space Physics. These files are in NetCDF format.  The abstract from the publication follows:
This paper presents measurements of the amplitudes and timings of the combined, annual and semi-annual variations of thermospheric neutral density, and a comparison of these density variations with measurements of the infrared emissions from carbon dioxide and nitric oxide in the thermosphere.  The density values were obtained from measurements of the atmospheric drag experienced by the CHAMP, GRACE A, GOCE, and three Swarm satellites, while the optical emissions were measured with the SABER instrument on the TIMED satellite.  These data span a time period of 16 years.  A database containing global average densities that were derived from the orbits of about 5000 objects [Emmert, 2009, 2015b] was employed for calibrating these density data. A comparison with the NRLMSISE-00 model was used to derive measurements of how much the density changes over time due to these seasonal variations.  It is found that the seasonal density oscillations have significant variations in amplitude and timing.  In order to test the practicality of using optical emissions as a monitoring tool, the SABER data were fit to the measured variations. Even the most simple fit that used only filtered carbon dioxide emissions had good correlations with the measured oscillations. However, the density oscillations were also well-predicted by a simple Fourier series, contrary to original expectations. Nevertheless, measurements of the optical emissions from the thermosphere are expected to have a role in future understanding and prediction of the semi-annual variations.
DOI: 10.7294/14736411.v1
title: Data: Horsenettle (Solanum carolinense) fruit bacterial communities are not variable across fine spatial scales

description: <div>Associated mapping file for S. carolinense fruit microbiome data.<br></div><div><br></div><div>biogeosamplesscaro06092021.tar.gz : Raw data needed to complete the analysis of data associated with the manuscript</div><div><br></div><div>AH_BioGeo_Mapping_file_NAupper_neworder_newpop_site.xlsx :  Mapping file that contains information about samples and site-specific details including sampling distances. This file can be used to process raw reads and reproduce analyses in the manuscript.</div><div><br></div><div>Heminger_solanum_code.Rmd:  This file is an R markdown file for the generation that contains all of the analysis steps. Combined with the mapping file and raw reads, this script can reproduce all of the analyses presented in the manuscript.</div>
DOI: 10.7294/17192963.v2
title: Inversion Results associated with JGR Solid Earth Publication: Joint Inversion of GNSS and GRACE for Terrestrial Water Storage Change in California by Carlson et al.

description: This dataset contains results from an inversion of deformation data and GRACE data for terrestrial water storage change over California from January 2003 - December 2016.<div><br></div><div>This dataset is for plotting or using terrestrial water storage change
calculated across California and western Nevada from January 2003 – December
2016 using GNSS vertical deformation and GRACE JPL mascon products. The
inversion results are given for an inversion using only GNSS data as well as a
joint inversion of GNSS and GRACE. Each set of inversion results corresponds to
the same dates given in DT.csv and grid cell locations given by
GridCenters.csv. All inversion results are given in meter equivalent water
height.<br></div>
DOI: 10.7294/16958797.v1
title: Photo observations of flowers potentially available to and observed with Chauliognathus marginatus and Chauliognathus pensylvanicus from iNaturalist.org

description: Digital
specimens collected by community members are a largely untapped source of
entomological data. By mining data from photo observations uploaded to online
community data repositories, researchers can utilize this wealth of information
to address questions about predator-prey interactions, phenotypic variation
within species, plant-pollinator interactions, and a host of other topics. We
mined data from photo observations on the community science website iNaturalist
to investigate patterns in host plant availability and affiliation by two
species of soldier beetles, <i>Chauliognathus marginatus</i> (Fabricius, 1775)
and <i>Chauliognathus pensylvanicus</i> (De Geer, 1774). This dataset contains
photo observations of these two species of beetles on flowering plants throughout
the eastern United States from 2000-2019. It also contains photo observations
of flowering plants potentially available to these two species, or blooming
across their range during their seasonal periods of activity, in 2018.
DOI: 10.7294/284t-bf10
title: Viral Networks: Connecting Digital Humanities and Medical History (V2)

description: Viral Networks: Connecting Digital Humanities and Medical History is a collection of original essays examining networks as an object of study, a tool for analysis, a framework for collaboration, and a means of scholarly communication. The chapters began as papers for the Viral Networks Workshop, hosted by the History of Medicine Division of the National Library of Medicine (NIH), funded by the Office of Digital Humanities of the National Endowment for the Humanities, and organized by Virginia Tech. The scholars involved in this project examined networks in medical history even as they became participants in a network of scholars engaged in collaborative learning. Inspired by models of networked pedagogy, these chapters developed through a connected series of activities that began with reading proposals, included one face-to-face and two virtual conferences, and ended with final edits on revised chapters. The papers should therefore be understood and read as a fully networked project, not as chapters written individually and placed together. The chapters in this collection demonstrate what a network analysis can reveal, but also how a network analysis can help a humanities scholar approach a problem a different way, or understand what is missing in their sources or interpretations. The dataset contains data and data visualization related to the workshop and book. The original dataset can be found at the following DOI, doi:10.7294/w4tar0jd88.
DOI: 10.7294/w4fb513g
title: Disturbance Detection and Diagnostics (D3) Algorithm

description: This study examines the effectiveness of using the Normalized Difference Vegetation Index (NDVI) derived from 1326 different Landsat Thematic Mapper and Enhanced Thematic Mapper images in finding low density development within the Commonwealth of Virginia’s forests. Individual NDVI images were stacked by year for the years 1995–2011 and the yearly maximum for each pixel was extracted, resulting in a 17-year image stack of all yearly maxima (a 98.7% data reduction). Using location data from housing starts and well permits, known previously forested housing starts were isolated from all other forest disturbance types. Samples from development disturbances and other forest disturbances, as well as from undisturbed forest, were used to derive vegetation index thresholds enabling separation of disturbed forest from undisturbed forest. Disturbances, once identified, could be separated into Development Disturbances and Non-Development Disturbances using a classification tree and only two variables from the Disturbance Detection and Diagnostics (D3) algorithm: the maximum NDVI in the available recovery period and the slope between the NDVI value at the time of the disturbance and the maximum NDVI in the available recovery period. Low density development disturbances of previous forest land cover had an F-measure, combining precision and recall into a single class-specific accuracy (β = 1), of 0.663. We compared our results to the NLCD 2001–2011 land cover changes from any forest (classes 41, 42, 43, and 90) to any developed (classes 21, 22, 23, and 24), resulting in an F-measure of 0.00 for the same validation points. Landsat time series stacks thus show promise for identifying even the small changes associated with low density development that have been historically overlooked/underestimated by prior mapping efforts. However, further research is needed to ensure that (1) the approach will work in other forest biomes and (2) enabling detection of these important, but spatially and spectrally subtle, disturbances still ensures accurate detection of other forest disturbances.
DOI: 10.7294/w4td9v7t
title: Gas Composition Data from a Carbon Dioxide Injection Test in Buchanan County, Virginia

description: Gas Composition Data from a Carbon Dioxide Injection Test in Buchanan County, Virginia