21 Works

Dataset associated with 'Quantification of Ebola virus replication kinetics in vitro'

Laura Liao, Jonathan Carruthers, Sophie J. Smither, , Simon A. Weller, Diane Williamson, Thomas R. Laws, Isabel Garcia-Dorival, Julian Hiscox, Benjamin P. Holder, Catherine Beauchemin, Alan S. Perelson, MARTIN LOPEZ-GARCIA, Grant Lythe, John Barr & carmen molina-parís
This dataset is associated with ‘Quantification of Ebola virus replication kinetics in vitro’. In the paper, a mathematical model is developed to describe the replication of Ebola virus in Vero cells. The model is parametrised using measurements of total and infectious extracellular virus at three different multiplicities of infection. The results provide insights into the distribution of time an infected cell spends in the eclipse phase (the period between infection and the start of virus...

Rapid mineral precipitation during shear fracturing of carbonate-rich shale: Supporting xCT data

Anne Menefee, Bill Carey, Luke Frash, Wes Hicks & Brian Ellis
X-ray computed tomography data supporting the work presented in the manuscript "Rapid mineral precipitation during shear fracturing of carbonate-rich shales" (Journal of Geophysical Research-Solid Earth, 2020) by Anne H. Menefee, Nathan J. Welch, Luke P. Frash, Wes Hicks, J. William Carey, and Brian R. Ellis. Descriptions are provided with each sample and xCT data set but please refer to the manuscript for more detailed information on samples and scanning parameters.

Data from: Immunoglobulin detection in wild birds: effectiveness of three secondary anti-avian IgY antibodies in direct ELISAs in 41 avian species

Carol A. Fassbinder-Orth, Travis E. Wilcoxen, Tiffany Tran, Raoul K. Boughton, Jeanne M. Fair, Erik K. Hofmeister, Jennifer L. Grindstaff & Jen C. Owen
1.Immunological reagents for wild, non-model species are limited or often non-existent for many species. 2. In this study, we compare the reactivity of a new anti-passerine IgY secondary antibody with existing secondary antibodies developed for use with birds. Samples from 41 species from the following six avian orders were analysed: Anseriformes (1 family, 1 species), Columbiformes (1 family, 2 species), Galliformes (1 family, 1 species), Passeriformes (16 families, 34 species), Piciformes (1 family, 2 species)...

Data from: Avian demographic responses to drought and fire: a community-level perspective

James F. Saracco, Stephen M. Fettig, George L. San Miguel, David W. Mehlman, Brent E. Thompson & Steven K. Albert
Drought stress is an important consideration for wildlife in arid and semi-arid regions under climate change. Drought can impact plant and animal populations directly, through effects on their physiology, as well as indirectly through effects on vegetation productivity and resource availability, and by creating conditions conducive to secondary disturbance, such as wildfire. We implemented a novel approach to understanding community-level demographic responses of birds and their habitats to these stressors in the context of climate...

Data from: Convergence in resource use efficiency across trees with differing hydraulic strategies in response to ecosystem precipitation manipulation

Jean-Marc Limousin, Enrico A. Yepez, Nate G. McDowell & William T. Pockman
1. Plants are expected to respond to drought by maximizing the efficiency of the most limiting resource, the water use efficiency (WUE), at the expense of nitrogen and carbon use efficiencies (NUE and CUE). Therefore, plants resource use efficiencies are viewed as indicators of species drought tolerance. 2. We tested these predictions by measuring leaf-level intrinsic WUE (WUEi, the ratio of net assimilation to stomatal conductance), photosynthetic NUE (PNUE, the ratio of daily maximum net...

Data from: Spatiotemporal incidence of Zika and associated environmental drivers for the 2015-2016 epidemic in Colombia

Amir S. Siraj, I. Rodriguez-Barraquer, Christopher M. Barker, Natalia Tejedor-Garavito, Dennis Harding, Christopher Lorton, Dejan Lukacevic, Gene Oates, Guido Espana, Moritz U. G. Kraemer, Carrie Manore, Michael A. Johansson, Andrew J. Tatem, Robert C. Reiner & T. Alex Perkins
Despite a long history of mosquito-borne virus epidemics in the Americas, the impact of the Zika virus (ZIKV) epidemic of 2015-2016 was unexpected. The need for scientifically informed decision-making is driving research to understand the emergence and spread of ZIKV. To support that research, we assembled a data set of key covariates for modeling ZIKV transmission dynamics in Colombia, where ZIKV transmission was widespread and the government made incidence data publically available. On a weekly...

Robust Links Minified JavaScript File

Shawn Jones, Martin Klein, Herbert Van de Sompel & Michael Nelson
Are you an author of web pages and you don't want your links to die? Link rot occurs when following a link yields a "404 Not Found" error message. Content drift occurs when the content at the end of the link changes over time, possibly to the point where it loses all similarity with the originally linked content. Robust Links addresses both of these problems by providing multiple pathways to revisit a link's original content,...

Data from: Sex ratio of Western Bluebirds Sialia mexicana is mediated by phenology and clutch size

Andrew Bartlow, Mark Jankowski, Charles Hathcock, Randall Ryti, Steven Reneau & Jeanne Fair
Mothers may produce more of one sex to maximize their fitness if there are differences in the cost of producing each sex or there are differences in their relative reproductive value. We tested if breeding date, clutch size and drought conditions influenced offspring sex ratios in Western Bluebirds (Sialia mexicana) from 1997 to 2017. We found that hatch dates late in the breeding season were associated with the production of more females. When clutch size...

Data from: Population and genetic outcomes 20 years after reintroducing bobcats (Lynx rufus) to Cumberland Island, Georgia USA

Duane Diefenbach, Leslie Hansen, Justin Bohling & Cassandra Miller-Butterworth
In 1988–1989, 32 bobcats Lynx rufus were reintroduced to Cumberland Island (CUIS), Georgia, USA, from which they had previously been extirpated. They were monitored intensively for 3 years immediately post-reintroduction, but no estimation of the size or genetic diversity of the population had been conducted in over 20 years since reintroduction. We returned to CUIS in 2012 to estimate abundance and effective population size of the present-day population, as well as to quantify genetic diversity...

Data from: Sexual selection constrains the body mass of male but not female mice

James S. Ruff, Douglas H. Cornwall, Linda C. Morrison, Joseph W. Cauceglia, Adam C. Nelson, Shannon M. Gaukler, Shawn Meagher, Lara S. Carroll & Wayne K. Potts
Sexual size dimorphism results when female and male body size is influenced differently by natural and sexual selection. Typically, in polygynous species larger male body size is thought to be favored in competition for mates and constraints on maximal body size are due to countervailing natural selection on either sex; however, it has been postulated that sexual selection itself may result in stabilizing selection at an optimal mass. Here we test this hypothesis by retrospectively...

Data from: The plant microbiome and native plant restoration: the example of native mycorrhizal fungi

Liz Koziol, Peggy A. Schultz, Geoffrey L. House, Jonathan T. Bauer, Elizabeth L. Middleton & James D. Bever
Ecological restoration efforts can increase the diversity and function of degraded areas. However, current restoration practices cannot typically re-establish the full diversity and species composition of remnant plant communities. We present evidence that restoration quality can be improved by reintroducing key organisms from the native plant microbiome. In particular, root symbionts called arbuscular mycorrhizal fungi are critical in shaping grassland communities, but are sensitive to anthropogenic disturbance, which may pose a problem for grassland restoration....

Data for \"Quantum well states in fractured crystals of the heavy fermion material CeCoIn5\"

Nicolas Gauthier, Jonathan A. Sobota, Makoto Hashimoto, Heike Pfau, Dong-Hui Lu, Eric D. Bauer, Filip Ronning, Patrick S. Kirchmann & Zhi-Xun Shen
This HDF5 file contains the data that supports the findings of "Quantum well states in fractured crystals of the heavy fermion material CeCoIn5" authored by N. Gauthier, J. A. Sobota, M. Hashimoto, H. Pfau, D.-H. Lu, E. D. Bauer, F. Ronning, P. S. Kirchmann, and Z.-X. Shen. Preprint available at https://arxiv.org/abs/2006.16301.

Genetic diversity in two insular populations of bobcats (Lynx rufus)

Duane Diefenbach, Cassandra Miller-Butterworth, Jessie Edson, Leslie Hansen, James Jordan, Tess Gingery & Amy Russell
We documented changes in genetic diversity in an isolated, reintroduced population of bobcats on Cumberland Island (CUIS), Georgia, USA, compared to another bobcat population on Kiawah Island, South Carolina, USA, that was naturally established and experiences limited immigration from the mainland. We compared the predictions of a novel population viability analysis (PVA) to empirical estimates of abundance and genetic diversity on CUIS and used our PVA to identify management actions that are likely to support...

Dataset of 3D fluid phase distribution from drainage simulations (in micromodel and real rock geometry) examining inertial effects

Yu Chen, Qinjun Kang, Albert Valocchi & Hari Viswanathan
The dataset contains fluid phase distribution obtained from high-resolution drainage simulations in both a heterogenous micromodel and Bentheimer sandstone. The purpose is to investigate the influence of inertial effects on scCO2-brine displacement in complex geometries, where scCO2 is much less viscous than brine or oil meaning that the inertial effects may not be negligible. The direct numerical simulations in this work employ the continuum-surface-force based color-gradient multiple-relaxation-time lattice Boltzmann model combined with a geometrical wetting...

Fractures with variable roughness and wettability

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Single-Molecule Image Sequences of Trichoderma reesei Cel7A and Variants on Cellulose Fibrils

Tina Jeoh, Peter Goodwin & Akshata Mudinoor
Purified and Cy5-labeled Trichoderma reesei Cel7A and its variants (Cel7A catalytic domain, catalytically deficient E212Q mutant and the catalytic domain of E212Q) interacting at the surface of crystalline cellulose fibrils were imaged by Total Internal Reflectance Fluorescence Microscopy (TIRFM).

Robust Links CSS File

Shawn Jones, Martin Klein, Herbert Van de Sompel & Michael Nelson
Are you an author of web pages and you don't want your links to die? Link rot occurs when following a link yields a "404 Not Found" error message. Content drift occurs when the content at the end of the link changes over time, possibly to the point where it loses all similarity with the originally linked content. Robust Links addresses both of these problems by providing multiple pathways to revisit a link's original content,...

Principles Governing Establishment versus Collapse of HIV-1 Cellular Spread

Jason Hataye, Joseph Casazza, Katharine Best, C. Jason Liang, Taina Immonen, David Ambrozak, Samuel Darko, Amy Henry, Farida Laboune, Frank Maldarelli, Daniel Douek, Nicolas Hengartner, Takuya Yamamoto, Brandon Keele, Alan Perelson & Richard Koup
A population at low census might go extinct, or instead transition into exponential growth to become firmly established. Whether this pivotal event occurs for a within-host pathogen can be the difference between health and illness. Here we define the principles governing whether HIV-1 spread among cells fails or becomes established, by coupling stochastic modeling with laboratory experiments. Following ex vivo activation of latently-infected CD4 T cells without de novo infection, stochastic cell division and death...

Data from: Disentangling the effect of competition, CO2 and climate on intrinsic water-use efficiency and tree growth

Laura Fernández De Uña, Nate G. McDowell, Isabel Cañellas & Guillermo Gea-Izquierdo
1. Climate change scenarios forecast rising temperatures for the Mediterranean region, which could enhance vulnerability to drought stress in forest ecosystems. The long-term effects of climate forcing on tree performance can be, however, modulated by other environmental factors, such as competition and rising atmospheric CO2 concentrations. 2. We assessed the concomitant effect of competition, climate and CO2 concentrations on the tree-ring δ13C-derived intrinsic water-use efficiency (iWUE) and basal area increments (BAI) of species with different...

Data from: A polymer dataset for accelerated property prediction and design

Huan D. Tran, Arun Mannodi-Kanakkithodi, Chiho Kim, Vinit Sharma, Ghanshyam Pilania & Rampi Ramprasad
Emerging computation- and data-driven approaches are particularly useful for rationally designing materials with targeted properties. Generally, these approaches rely on identifying structure-property relationships by learning from a dataset of sufficiently large number of relevant materials. The learned information can then be used to predict the properties of materials not already in the dataset, thus accelerating the materials design. Herein, we develop a dataset of 1,073 polymers and related materials and make it available at http://khazana.uconn.edu/....

Data from: Larger trees suffer most during drought in forests worldwide

Amy C. Bennett, Nathan G. McDowell, Craig D. Allen & Kristina J. Anderson-Teixeira
The frequency of severe droughts is increasing in many regions around the world as a result of climate change. Droughts alter the structure and function of forests. Site- and region-specific studies suggest that large trees, which play keystone roles in forests and can be disproportionately important to ecosystem carbon storage and hydrology, exhibit greater sensitivity to drought than small trees. Here, we synthesize data on tree growth and mortality collected during 40 drought events in...

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