Identifying Wetland Availability and Quality For Focal Species of the Illinois Wetlands Campaign W-184-R-1

The purpose of the study was to estimate functional quality of wetlands for focal species of the Illinois Wetlands Campaign, including the following objectives: 1) Estimate wetland habitat quality during spring, summer, and autumn for focal species of the Illinois Wetlands Campaign; 2) Develop a model to predict wetland quality for focal species of the Illinois Wetlands Campaign relative to wetland and landscape characteristics.Illinois Department of Natural Resources Contract Number: RC09-13FWUIUC Subagreement Number: SIU Carbondale 15-01unpublishednot peer reviewedOpe

Tree Establishment in Response to Hydrology at IDOT Wetland Mitigation Sites

The Illinois Department of Transportation (IDOT) has compensated for unavoidable impacts to wetlands in transportation project corridors by restoring and creating wetlands throughout Illinois. As part of the IDOT Wetlands Program, monitoring of performance measures is conducted by the Illinois Natural History Survey (INHS) and the Illinois State Geological Survey (ISGS). The goals of this research were to determine the effect of flood events on the establishment of planted and naturally recruiting trees in IDOT mitigation wetlands and to make specific recommendations for tree planting and the establishment of mitigation performance standards. We compiled and analyzed existing data from INHS and ISGS monitoring reports and conducted additional field surveys to determine long‐term planted tree survival and assess natural tree recruitment. Based on our compilation of data from INHS wetland monitoring reports, we determined that the number of planted trees alive at mitigation wetlands by the end of mitigation monitoring was, on average, 57% the number of trees planted originally. We revisited ten older mitigation wetlands in 2014 and recounted surviving planted trees, and found that survival rate continued to decline beyond site monitoring periods. Tree mortality was clearly related to site exposure to flood disturbance during individual years, through the end of site monitoring, and beyond site monitoring periods. Depth and duration of inundation were more important than flood frequency in determining tree survival. Natural colonization greatly exceeded planting in terms of both stem density and basal area. However, natural colonization was not clearly related to site flood exposure. In sites that are exposed to long‐duration or deep flooding, planted tree survival is likely to be low regardless of species planted or the degree of on‐site management of plantings. We recommend that realistically attainable mitigation performance standards be developed on a site‐specific basis, considering the likely hydrologic regime of the site. In some situations, faster‐growing species provide tangible environmental benefits. In addition, natural tree colonization can supplement planting, even in sites where planted hard‐ mast species are unlikely to persist.Illinois Department of Transportation, R27-143Ope

Sequential emergence and clinical implications of viral mutants with K70E and K65R mutation in reverse transcriptase during prolonged tenofovir monotherapy in rhesus macaques with chronic RT-SHIV infection.

BackgroundWe reported previously on the emergence and clinical implications of simian immunodeficiency virus (SIVmac251) mutants with a K65R mutation in reverse transcriptase (RT), and the role of CD8+ cell-mediated immune responses in suppressing viremia during tenofovir therapy. Because of significant sequence differences between SIV and HIV-1 RT that affect drug susceptibilities and mutational patterns, it is unclear to what extent findings with SIV can be extrapolated to HIV-1 RT. Accordingly, to model HIV-1 RT responses, 12 macaques were inoculated with RT-SHIV, a chimeric SIV containing HIV-1 RT, and started on prolonged tenofovir therapy 5 months later.ResultsThe early virologic response to tenofovir correlated with baseline viral RNA levels and expression of the MHC class I allele Mamu-A*01. For all animals, sensitive real-time PCR assays detected the transient emergence of K70E RT mutants within 4 weeks of therapy, which were then replaced by K65R mutants within 12 weeks of therapy. For most animals, the occurrence of these mutations preceded a partial rebound of plasma viremia to levels that remained on average 10-fold below baseline values. One animal eventually suppressed K65R viremia to undetectable levels for more than 4 years; sequential experiments using CD8+ cell depletion and tenofovir interruption demonstrated that both CD8+ cells and continued tenofovir therapy were required for sustained suppression of viremia.ConclusionThis is the first evidence that tenofovir therapy can select directly for K70E viral mutants in vivo. The observations on the clinical implications of the K65R RT-SHIV mutants were consistent with those of SIVmac251, and suggest that for persons infected with K65R HIV-1 both immune-mediated and drug-dependent antiviral activities play a role in controlling viremia. These findings suggest also that even in the presence of K65R virus, continuation of tenofovir treatment as part of HAART may be beneficial, particularly when assisted by antiviral immune responses

Axel Robotic Platform for Crater and Extreme Terrain Exploration

To be able to conduct science investigations on highly sloped and challenging terrains, it is necessary to deploy science payloads to such locations and collect and process in situ samples. A tethered robotic platform has been developed that is capable of exploring very challenging terrain. The Axel rover is a symmetrical rover that is minimally actuated, can traverse arbitrary paths, and operate upside-down or right-side up. It can be deployed from a larger platform (rover, lander, or aerobot) or from a dual Axel configuration. Axel carries and manages its own tether, reducing damage to the tether during operations. Fundamentally, Axel is a two-wheeled rover with a symmetric body and a trailing link. Because the primary goal is minimal complexity, this version of the Axel rover uses only four primary actuators to control its wheels, tether, and a trailing link. A fifth actuator is used for level winding of tether onto Axel s spool

Wetland management strategies lead to tradeoffs in ecological structure and function

Copyright © 2018 The Author(s). This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International License CC-BY 4.0, (http://creativecommons.org/licenses/by/4.0/)Anthropogenic legacy effects often occur as a consequence of land use change or land management and can leave behind long-lasting changes to ecosystem structure and function. This legacy is described as a memory in the form of ecological structure or ecological interactions that remains at a location from a previous condition. We examined how forested floodplain restoration strategy, based on planting intensity, influenced wetland community structure and soil chemical and physical factors after 15 years. The site was divided into 15 strips, and strips were assigned to one of five restoration treatments: plantings of acorns, 2-year-old seedlings, 5-ft bareroot trees, balled and burlapped trees, and natural seed bank regeneration. Our community composition survey revealed that plots planted with bareroot or balled and burlapped trees developed closed tree canopies with little herbaceous understory, while acorn plantings and natural colonization plots developed into dense stands of the invasive species reed canary grass (RCG; Phalaris arundinacea). Restoration strategy influenced bacterial community composition but to a lesser degree compared to the plant community response, and riverine hydrology and restoration strategy influenced wetland soil conditions. Soil ammonium concentrations and pH were similar across all wetland restoration treatments, while total organic carbon was highest in forest and RCG-dominated plots compared to mixed patches of trees and open areas. The differences in restoration strategy and associated economic investment resulted in ecological tradeoffs. The upfront investment in larger, more mature trees (i.e., bareroot, balled and burlapped) led to floodplain forested communities, while cheaper, more passive planting strategies (i.e., seedlings, seedbank, or acorns) resulted in dense stands of invasive RCG, despite the similar floodplain hydrology across all sites. Therefore, recovery of multiple ecosystem services that encompass plant and microbial-derived functions will need to include additional strategies for the recovery of plants, microbes, environment, and functions.ECU Open Access Publishing Support Fun

Frame-Dragging Vortexes and Tidal Tendexes Attached to Colliding Black Holes: Visualizing the Curvature of Spacetime

When one splits spacetime into space plus time, the spacetime curvature (Weyl tensor) gets split into an "electric" part E_{jk} that describes tidal gravity and a "magnetic" part B_{jk} that describes differential dragging of inertial frames. We introduce tools for visualizing B_{jk} (frame-drag vortex lines, their vorticity, and vortexes) and E_{jk} (tidal tendex lines, their tendicity, and tendexes), and also visualizations of a black-hole horizon's (scalar) vorticity and tendicity. We use these tools to elucidate the nonlinear dynamics of curved spacetime in merging black-hole binaries.Comment: 4 pages, 5 figure

Momentum flow in black-hole binaries: II. Numerical simulations of equal-mass, head-on mergers with antiparallel spins

Research on extracting science from binary-black-hole (BBH) simulations has often adopted a "scattering matrix" perspective: given the binary's initial parameters, what are the final hole's parameters and the emitted gravitational waveform? In contrast, we are using BBH simulations to explore the nonlinear dynamics of curved spacetime. Focusing on the head-on plunge, merger, and ringdown of a BBH with transverse, antiparallel spins, we explore numerically the momentum flow between the holes and the surrounding spacetime. We use the Landau-Lifshitz field-theory-in-flat-spacetime formulation of general relativity to define and compute the density of field energy and field momentum outside horizons and the energy and momentum contained within horizons, and we define the effective velocity of each apparent and event horizon as the ratio of its enclosed momentum to its enclosed mass-energy. We find surprisingly good agreement between the horizons' effective and coordinate velocities. To investigate the gauge dependence of our results, we compare pseudospectral and moving-puncture evolutions of physically similar initial data; although spectral and puncture simulations use different gauge conditions, we find remarkably good agreement for our results in these two cases. We also compare our simulations with the post-Newtonian trajectories and near-field energy-momentum. [Abstract abbreviated; full abstract also mentions additional results.]Comment: Submitted to Phys. Rev.

Visualizing Spacetime Curvature via Frame-Drag Vortexes and Tidal Tendexes I. General Theory and Weak-Gravity Applications

When one splits spacetime into space plus time, the Weyl curvature tensor (vacuum Riemann tensor) gets split into two spatial, symmetric, and trace-free (STF) tensors: (i) the Weyl tensor's so-called "electric" part or tidal field, and (ii) the Weyl tensor's so-called "magnetic" part or frame-drag field. Being STF, the tidal field and frame-drag field each have three orthogonal eigenvector fields which can be depicted by their integral curves. We call the integral curves of the tidal field's eigenvectors tendex lines, we call each tendex line's eigenvalue its tendicity, and we give the name tendex to a collection of tendex lines with large tendicity. The analogous quantities for the frame-drag field are vortex lines, their vorticities, and vortexes. We build up physical intuition into these concepts by applying them to a variety of weak-gravity phenomena: a spinning, gravitating point particle, two such particles side by side, a plane gravitational wave, a point particle with a dynamical current-quadrupole moment or dynamical mass-quadrupole moment, and a slow-motion binary system made of nonspinning point particles. [Abstract is abbreviated; full abstract also mentions additional results.]Comment: 25 pages, 20 figures, matches the published versio

From Nonspecific DNA–Protein Encounter Complexes to the Prediction of DNA–Protein Interactions

©2009 Gao, Skolnick. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.doi:10.1371/journal.pcbi.1000341DNA–protein interactions are involved in many essential biological activities. Because there is no simple mapping code between DNA base pairs and protein amino acids, the prediction of DNA–protein interactions is a challenging problem. Here, we present a novel computational approach for predicting DNA-binding protein residues and DNA–protein interaction modes without knowing its specific DNA target sequence. Given the structure of a DNA-binding protein, the method first generates an ensemble of complex structures obtained by rigid-body docking with a nonspecific canonical B-DNA. Representative models are subsequently selected through clustering and ranking by their DNA–protein interfacial energy. Analysis of these encounter complex models suggests that the recognition sites for specific DNA binding are usually favorable interaction sites for the nonspecific DNA probe and that nonspecific DNA–protein interaction modes exhibit some similarity to specific DNA–protein binding modes. Although the method requires as input the knowledge that the protein binds DNA, in benchmark tests, it achieves better performance in identifying DNA-binding sites than three previously established methods, which are based on sophisticated machine-learning techniques. We further apply our method to protein structures predicted through modeling and demonstrate that our method performs satisfactorily on protein models whose root-mean-square Ca deviation from native is up to 5 Å from their native structures. This study provides valuable structural insights into how a specific DNA-binding protein interacts with a nonspecific DNA sequence. The similarity between the specific DNA–protein interaction mode and nonspecific interaction modes may reflect an important sampling step in search of its specific DNA targets by a DNA-binding protein