cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.7294/nfsk-2m11
title: Conservation wildflower plantings do not enhance on-farm abundance of Amblyomma americanum

description: Planting wildflowers is a commonly suggested measure to conserve pollinators. While beneficial for pollinators, plots of wildflowers may be inadvertently performing an ecosystem disservice by providing suitable habitat for arthropod disease vectors like ticks. The lone star tick, Amblyomma americanum (L)., is a medically important tick species that might be able to utilize wildflower plantings as suitable habitat. In this two-year study, ticks were sampled using dry-ice baited traps from wildflower plots, weedy field margins, and forested areas to determine if wildflower plantings were increasing the on-farm abundance of A. americanum. Abiotic and biotic environmental variables were also measured to better understand which factors affect A. americanum abundance. We found no more A. americanum in wildflower plots than in weedy field margins. Forested areas harbored the greatest number of A. americanum sampled. The height of vegetation in the sampled habitats was a significant factor in determining A. americanum abundance. Depending on the sampled habitat and life stage, this relationship can be positive or negative. The relationship to vegetation height may be related to the behavior of the white-tailed deer and the questing success of A. americanum. Overall, wildflower plots do not pose an increased risk of exposure to A. americanum on farms.
DOI: 10.7294/w4m32szs
title: Nonlinear Optofluidic Processes in Microdroplets

description: High quality (Q) factor whispering gallery modes (WGMs) can induce nonlinear effects in liquid droplets through radiation pressure, light scattering, thermocapillarity, Kerr nonlinearity, and thermal effect. In our recent studies published in Physical Review E, we investigated such effects on a micron-sized liquid spherical resonator. In the first study, numerical analyses based on the boundary element method helped to quantify the deformation of the droplet under the radiation pressure. We showed that the nonlinear optofluidic effect induced by the radiation pressure is stronger than the Kerr effect and the thermal effects. We further confirmed the possibility that it may only take a few photons to produce measurable WGM resonance shift through radiation-pressure-induced droplet deformation. The effect of the scattering force on the interfacial dynamics of the droplet was quantified in the second study. The interface deformation produced by the thermocapillarity as a result of the WGM energy absorption and temperature increase was also explored. We developed a boundary element program to calculate the fluid motion and quantify the nonlinearity induced by the optical scattering force and thermocapillarity. Our work provides a numerical tool for the study of optofluidic phenomena in liquid microdroplets.
DOI: 10.7294/16543164.v1
title: Trees, alignments, and iTOL datasets for publication "Phylogenetic Signal, Congruence, and Uncertainty across Bacteria and Archaea"

description: <div>This folder contains the
treefile files (.nwk), raw alignments (.aln), and iTOL datasets to color
branches by phylum (.txt) used in Martinez-Gutierrez and Aylward, 2021<br></div><div><br></div>
DOI: 10.7294/58g1-9c77
title: ERS_calibration

description: A Matlab code for the manuscript 'Electronic Raman Scattering as an Internal Standard for Quantitative SERS and Improved Biostatistical Analysis', Proceedings of the National Academy of Sciences of the United States of America
DOI: 10.7294/14547273.v1
title: Non-migrating diurnal tides in effective neutral temperature and column O/N2 ratio from TIE-GCM

description: <p>Files containing the non-migrating diurnal tidal amplitudes and phases in effective neutral temperature and column O/N<sub>2</sub> ratio as a function of latitude (degrees) during October and January simulated by the TIE-GCM model.  O/N<sub>2 </sub>amplitudes are reported as percent relative to the zonal mean.  Temperature amplitudes are in units of Kelvin.  Phases are reported as the universal time of maximum at 0º longitude.  An additional file is provided reporting the contribution function as a function of altitude (km) for nadir viewing (emission angle equal to 0º) and solar zenith angle equal to 70º.  The contribution function, provided by Computational Physics, Inc., weights the neutral temperature profiles used to derive the tides.  The vertical column O/N2 ratio is computed relative to a standard reference N<sub>2</sub><sub> </sub>depth of 10<sup>17</sup> cm<sup>-2</sup> .</p>
DOI: 10.7294/w46q1v5d
title: The Effect of Binaural Beats on Visuospatial Working Memory and Cortical Connectivity

description: Binaural beats utilize a phenomenon that occurs within the cortex when two different frequencies are presented separately to each ear. This procedure produces a third phantom binaural beat, whose frequency is equal to the difference of the two presented tones and which can be manipulated for non-invasive brain stimulation. The effects of binaural beats on working memory, the system in control of temporary retention and online organization of thoughts for successful goal directed behavior, have not been well studied. Furthermore, no studies have evaluated the effects of binaural beats on brain connectivity during working memory tasks. In this study, we determined the effects of different acoustic stimulation conditions on participant response accuracy and cortical network topology, as measured by EEG recordings, during a visuospatial working memory task. Three acoustic stimulation control conditions and three binaural beat stimulation conditions were used: None, Pure Tone, Classical Music, 5Hz binaural beats, 10Hz binaural beats, and 15Hz binaural beats. We found that listening to 15Hz
binaural beats during a visuospatial working memory task not only increased the response accuracy, but also modified the strengths of the cortical networks during the task. The three auditory control conditions and the 5Hz and 10Hz binaural beats all decreased accuracy. Based on graphical network analyses, the cortical activity during 15Hz binaural beats produced networks characteristic of high information transfer with consistent connection strengths throughout the visuospatial working memory task.
DOI: 10.7294/w4t43r7j
title: Forecast and parameter chain: A mid-century ecological forecast with partitioned uncertainty predicts increases in loblolly pine forest productivity

description: Ecological forecasting of forest productivity involves integrating observations into a process-based model and propagating the dominant components of uncertainty to generate probability distributions for future states and fluxes.  Here we develop a forecast for the biomass change in loblolly pine (Pinus taeda) forests of the Southeastern U.S and evaluate the relative contribution of different forms of uncertainty to the total forecast uncertainty. Specifically, we assimilated observations of carbon and flux stocks and fluxes from sites across the region, including global change experiments, into a forest ecosystem model to calibrate the parameter distributions and estimate the process uncertainty (i.e., model structure uncertainty revealed in the residuals of the calibration).  Using this calibration, we forecasted the change in biomass within each 12-digit Hydrologic (H12) unit across the native range of loblolly pine between 2010 and 2055 under the Representative Concentration Pathway 8.5 scenario. Averaged across the region, productivity is predicted to increase by a mean of 31% between 2010 and 2055 with an average forecast 95% quantile interval of ± 15 percentage units. The largest increases were predicted in cooler locations, corresponding to the largest projected changes in temperature.  The forecasted mean change varied considerably among the H12 units (3 - 80% productivity increase), but only units in the warmest and driest extents of the loblolly pine range had forecast distributions with probabilities of a decline in productivity that exceeded 5%.  By isolating the individual components of the forecast uncertainty, we found that ecosystem model process uncertainty made the largest individual contribution. Ecosystem model parameter and climate model uncertainty had similar contributions to the overall forecast uncertainty, but with differing spatial patterns across the study region.  The probabilistic framework developed here could be modified to include additional sources of uncertainty, including changes due to fire, insects, and pests - processes that would result in lower productivity changes than forecasted here.  Overall, this study presents an ecological forecast at the ecosystem management scale so that land managers can explicitly account for uncertainty in decision analysis. Furthermore, it highlights that future work should focus on quantifying, propagating, and reducing ecosystem model process uncertainty.
DOI: 10.7294/j1aw-sm37
title: Faculty Perceptions of Research Assessment at Virginia Tech

description: This data set represents the data analyzed and discussed in a research article for the Journal of Altmetrics (JOA) of the same title/name. However, the original survey project was commissioned by Virginia Tech Faculty Senate to assess faculty perceptions of research assessment and salary considerations at Virginia Tech. The project was overseen by the Faculty Senate Research Assessment Committee and the resulting report was submitted to Faculty Senate and presented to the Virginia Tech Board of Visitors at their June 2019 meeting. That report can be found at https://bov.vt.edu/assets/Attachment II_Constituent Reports_June 2019.pdf, pages 12-118 (includes survey questions). The data that are available in this data set represent data that were analyzed and included in the JOA research article. Certain data, including responses to questions about salaries, are not included in this data set, because they were not a part of the analysis for the JOA publication.
This data set includes four files: the survey instrument (all questions, PDF format), select quantitative responses (.csv), select qualitative responses (.csv), and the codebook for the questions in the response files (.csv). All response data have been anonymized; please see each file for more details.  Racial data and departmental data are eliminated to ensure anonymity.  The survey was submitted to the Institutional Review Board of Virginia Tech and was determined to not be research involving human subjects as defined by HHS and FDA regulations, resulting in approval to broadly distribute the survey to Virginia Tech faculty with expectations that responses are kept anonymous and results do not claim to be generalizable knowledge (IRB reference number 19-234).
DOI: 10.7294/18306044.v1
title: Dataset for a kirigami composite metamaterial sheet

description: <p>This dataset contains the mechanical properties, stiffness, and
shape-fixing data for a kirigami composite metamaterial sheet.</p>
DOI: 10.7294/be34-zs61
title: Calculating most probable absolute population density and its 95% confidence bounds

description: Step by step
instructions to calculating most probable absolute population density and its
95% confidence bounds.
DOI: 10.7294/29kx-e267
title: Microsatellite genotypes obtained from Banded Mongoose in Chobe District Botswana

description: Disease
transmission can be strongly influenced by the manner in which conspecifics are
connected across a landscape and the effects of land use upon these dynamics.
In northern Botswana, the territorial and group-living banded mongoose (<i>Mungos
mungo</i>) lives across urban and natural landscapes and is infected with a
novel <i>Mycobacterium tuberculosis</i> complex pathogen, <i>M. mungi</i>.
Using microsatellite markers amplified from DNA derived from banded mongoose
fecal and tissue samples (<i>n </i>= 168), we evaluated population genetic
structure, individual dispersal, and gene flow for 12 troops. Genetic structure
was detectable and moderately strong across groups (<i>F</i><sub>ST </sub>=
0.086), with <i>K </i>= 7 being the best-supported number of genetic clusters.
Indications of admixture in certain troops suggest formation of new groups
through recent fusion events. Differentiation was higher for troops inhabiting
natural (<i>F</i><sub>ST </sub>= areas 0.102) than for troops in urban
landscapes (<i>F</i><sub>ST </sub>= 0.081). While this suggests increased
levels of gene flow between urban-dwelling troops, the inclusion of a smaller
number of study troops from natural land types may have influenced these
findings. Of those individuals confirmed infected with <i>M. mungi</i>, the
majority  (73%, <i>n </i>= 11) were
assigned to their natal group consistent with previous observations linking
lower levels of dispersal with infection. Twenty-one probable dispersing
individuals were identified, with the all suspected migrants originating from
troops within the urban landscape. Findings suggest that urbanized landscapes
may increase both gene flow and dispersal behavior with a concomitant increase
in the risk of pathogen spread.  As urban
landscapes expand, there is an increasing need to understand how land use and
pathogen infection may change wildlife behavior and disease transmission
potential.
DOI: 10.7294/w49s1p7v
title: Computational Study of HIV gp120 as a Target for Polyanionic Entry Inhibitors: Exploiting the V3 Loop Region

description: Multiple approaches are being utilized to develop therapeutics to treat HIV infection. One approach is designed to inhibit entry of HIV into host cells, with a target being the viral envelope glycoprotein, gp120. Polyanionic compounds have been shown to be effective in inhibiting HIV entry, with a mechanism involving electrostatic interactions with the V3 loop of gp120 being proposed. In this study, we applied computational methods to elucidate molecular interactions between the repeat unit of the precisely alternating polyanion, Poly(4,4′-stilbenedicarboxylate-alt–maleic acid) (DCSti-alt-MA) and the V3 loop of gp120 from strains of HIV against which these polyanions were previously tested (IIIb, BaL, 92UG037, JR-CSF) as well as two strains for which gp120 crystal structures are available (YU2, 2B4C). Homology modeling was used to create models of the gp120 proteins. Using monomers of the gp120 protein, we applied extensive molecular dynamics simulations to obtain dominant morphologies that represent a variety of open-closed states of the V3 loop to examine the interaction of 112 ligands of the repeating units of DCSti-alt-MA docked to the V3 loop and surrounding residues. Using the distance between the V1/V2 and V3 loops of gp120 as a metric, we revealed through MD simulations that gp120 from the lab-adapted strains (BaL and IIIb), which are more susceptible to inhibition by DCSti-alt-MA, clearly transitioned to the closed state in one replicate of each simulation set, whereas none of the replicates from the Tier II strains (92UG037 and JR-CSF) did so. Docking repeat unit microspecies to the gp120 protein before and after MD simulation enabled identification of residues that were key for binding. Notably, only a few residues were found to be important for docking both before and after MD simulation as a result of the conformational heterogeneity provided by the simulations. Consideration of the residues that were consistently involved in interactions with the ligand revealed the importance of both hydrophilic and hydrophobic moieties of the ligand for effective binding. The results also suggest that polymers of DCSti-alt-MA with repeating units of different configurations may have advantages for therapeutic efficacy.
DOI: 10.7294/15834846.v3
title: Data to accompany the paper ‘Redundancy analysis reveals complex den use patterns by eastern spotted skunks, a conditional specialist’, Ecosphere

description: <div><p>Wildlife
managers tasked with understanding habitat and resource selection at the
population level attempt to characterize patterns in nature that aid and inform
conservation. Resource selection functions (RSF), such as discrete choice
analyses, are the standard convention to characterize the effects of habitat
attributes on resource selection patterns. RSF are invaluable tools for in
wildlife management and conservation and have proven successful in numerous
studies. However, the analysis of small datasets using RSF becomes problematic
when attempting to account for for complex sources of variation and inclusion
of factors such as weather or intrinsic variation on target species’ response
may produce models with poor predictive ability. We compared the application of
generalized linear mixed modeling (GLMM) and redundancy analysis (RDA) on
Appalachian spotted skunk (Spilogale putorius putorius) den selection data at
four study sites within national forest and surrounding private lands in the
Appalachian Mountains of western Virginia and northeastern West Virginia. We
assessed the need for the inclusion of alternative sources of variation, (i.e.,
weather conditions and individual intrinsic variation) in addition to standard
habitat attributes to better identify sources of variation in den selection.
The RDA elucidated complex and opposing relationships whereby den type use was
based on reproductive status or weather condition, that were not evident in the
GLMM model that relied solely on habitat measures. Our results demonstrate the
importance of examining resource selection data using multivariate techniques
in addition to conventional discrete choice analyses to better understand
intricate habitat–species relationships, especially for small data sets.
Further, from our analyses, we propose that spotted skunks are neither a true
generalist nor specialist species. We introduce and define the term
‘conditional specialist’ to represent a species that is conditionally selective
of a given resource in response to one or more current environmental or
intrinsic conditions. </p><br></div>
DOI: 10.7294/15125586.v1
title: ERA5 Derived Integrated Water Vapor Transport for Eastern and Central U.S.

description: <p>integrated
water vapor transport (IVT) calculated using u-wind, v-wind, and specific
humidity from the European Centre for Medium-Range Weather Forecasts ERA5
Reanalysis Dataset on pressure levels from 1000 to 300 hPa. IVT is calculated
as follows:</p>

<p>IVT =1/g  ∫(1000 hPa)^(300 hPa)qV  dp<br></p>
DOI: 10.7294/17711000.v2
title: Vertical Land Motion along California coast

description: <div>Vertical Land Motion along California Coast as a combination of InSAR and GNSS observations.</div><div>The SAR datasets spanning 2007–2018 include acquisitions from Sentinel-1A/B C-band satellite in descending and ascending orbit geometry and ALOS L-band satellite in ascending orbit geometry. The data set is processed using WabInSAR algorithm. See citations below for details.</div><div><br></div>
DOI: 10.7294/16587179.v1
title: Simulation data for replicating the results and figures of the study, "A general metric for the similarity of both stochastic and deterministic system dynamics"

description: <p>
This
dataset allows for the replication of all results and figures
appearing in the paper "A
general metric for the similarity of both stochastic and
deterministic system dynamics"
forthcoming in the journal <i>Entropy</i>.
The scripts for running all experiments and for generating figures
can be found at <a href="https://github.com/jantzen/distance_metric">https://github.com/jantzen/distance_metric</a>,
and code for the methods tested in these experiments is attainable
through the PyPI package "eugene" (e.g., via "pip
install eugene") or at <a href="https://github.com/jantzen/eugene">https://github.com/jantzen/eugene</a>.
However, by themselves these scripts will not exactly reproduce the
data we reported. This is because most of our numerical experiments
involve a stochastic component such that one cannot generate exactly
the same data twice. We have therefore preserved in this dataset the
specific results of the experimental runs reported in the published
study.</p>
<p>
<br>

</p>
<p>
To
replicate a figure from the paper, extract the  files in the relevant
zip archive  into the same directory as the figure generation script,
and rename the extracted data file folder "data". So, for
example, to run the generate_figures.py script, download the
generate_data.zip file and extract in the same directory as the
figure script. Change the name of the resulting "generate_data"
folder to "data", and then run "python3
generate_figures.py".</p>
DOI: 10.7294/16712872.v1
title: Hybrid dataset of historical cool-season lake effects from the eastern Great Lakes of North America

description: These are merged lake-effect data stemming from TSI (Suriano and Leathers, 2017) and SSC (Ellis et al., 2021) approaches as outlined in the manuscript under review in the journal "Frontiers in Water" (Ellis and Suriano, 2021).There are two FILES containing dates of lake-effect days for the eastern Great Lakes region (effects from Lakes Erie and Ontario), November 1964 through April 2015.
DOI: 10.7294/15143949.v1
title: field-dependent XFMR fitting

description: Co-edge XFMR amplitude-vs-field and phase-vs-field data sets; MATLAB code for fitting (example: fit results shown in Fig. 4 in 10.1021/acs.nanolett.0c01868)<div><br></div><div>Abstract of the associated publication (10.1021/acs.nanolett.0c01868)  - Spin currents can exert spin-transfer torques on magnetic systems even in the limit of vanishingly small net magnetization, as recently shown for antiferromagnets. Here, we experimentally show that a spin-transfer torque is operative in a macroscopic ensemble of weakly interacting, randomly magnetized Co nanomagnets. We employ element- and time-resolved X-ray ferromagnetic resonance (XFMR) spectroscopy to directly detect subnanosecond dynamics of the Co nanomagnets, excited into precession with cone angle ≳0.003° by an oscillating spin current. XFMR measurements reveal that as the net moment of the ensemble decreases, the strength of the spin-transfer torque increases relative to those of magnetic field torques. Our findings point to spin-transfer torque as an effective way to manipulate the state of nanomagnet ensembles at subnanosecond time scales.</div>
DOI: 10.7294/8ch0-7d40
title: Code for Sensometrics Presentation on Sorting Backbone Analysis

description: For the paper entitled, “Continued preference for suboptimal habitat reduces bat survival with white-nose syndrome,” published in Nature Communications, we counted and sampled Myotis lucigufus bats from 2013-2020 in Michigan and Wisconsin. These years encompassed periods before, during, and after Pseudogymnoascus destructans, the causative agent of white-nose syndrome, invaded the region. We determined whether fungal growth rates on bats and bat recapture rates from November to March were affected by bats’ early hibernation roosting temperatures. We also determined whether bats’ distributions across roosting temperatures had changed from pre- to post-invasion to evaluate whether bats were continuing to select warm habitats, which appear to be ecological traps. This repository contains all of the individual data from sampled bats and the count data from 12 sites that were sampled during all three invasion periods. This repository also contains all of the R script files needed to replicate the analyses in our paper.