Upper Extremity Biomechanical Model for Evaluation of Pediatric Joint Demands during Wheelchair Mobility

Current methods for evaluating upper extremity (UE) dynamics during pediatric wheelchair use are limited. We propose a new model to characterize UE joint kinematics and kinetics during pediatric wheelchair mobility. The bilateral model is comprised of the thorax, clavicle, scapula, upper arm, forearm, and hand segments. The modeled joints include: sternoclavicular, acromioclavicular, glenohumeral, elbow and wrist. The model is complete and is currently undergoing pilot studies for clinical application. Results may provide considerable quantitative insight into pediatric UE joint dynamics to improve wheelchair prescription, training and long term care of children with orthopaedic disabilities

Structural and Mutational Analysis of Escherichia coli AlkB Provides Insight into Substrate Specificity and DNA Damage Searching

Background: In Escherichia coli, cytotoxic DNA methyl lesions on the N1 position of purines and N3 position of pyrimidines are primarily repaired by the 2-oxoglutarate (2-OG) iron(II) dependent dioxygenase, AlkB. AlkB repairs 1-methyladenine (1meA) and 3-methylcytosine (3-meC) lesions, but it also repairs 1-methylguanine (1-meG) and 3-methylthymine (3-meT) at a much less efficient rate. How the AlkB enzyme is able to locate and identify methylated bases in ssDNA has remained an open question. Methodology/Principal Findings: We determined the crystal structures of the E. coli AlkB protein holoenzyme and the AlkBssDNA complex containing a 1-meG lesion. We coupled this to site-directed mutagenesis of amino acids in and around the active site, and tested the effects of these mutations on the ability of the protein to bind both damaged and undamaged DNA, as well as catalyze repair of a methylated substrate. Conclusions/Significance: A comparison of our substrate-bound AlkB-ssDNA complex with our unliganded holoenzyme reveals conformational changes of residues within the active site that are important for binding damaged bases. Sitedirected mutagenesis of these residues reveals novel insight into their roles in DNA damage recognition and repair. Our data support a model that the AlkB protein utilizes at least two distinct conformations in searching and binding methylated bases within DNA: a ‘‘searching’ ’ mode and ‘‘repair’ ’ mode. Moreover, we are able to functionally separate these mode

Assessing the Extent of Carbonate Deposition in Early Rift Settings

Select lacustrine and marine depositional settings show a spectrum of styles of carbonate deposition and illustrate the types of carbonates, with an emphasis on microbialites and tufa, to be expected in early rift settings. Early rift lake examples examined in this review article are all from East Africa: Lakes Turkana, Bogoria, Natron and Magadi, Manyara, and Tanganyika. Other lake examples include four from the western United States (Great Salt Lake and high lake level Lake Bonneville, Mono Lake and high lake level Russell Lake, Pyramid Lake and high lake level Lake Lahontan, and Searles Lake) and two from Australia (Lakes Clifton and Thetis). Marine basin examples are the Hamelin Pool part of Shark Bay from Australia (marginal marine) and the Red Sea (marine rift). Landsat images and digital elevation models for each example are used to delineate present and past lake-basin margins based on published lake-level elevations, and for some examples, the shorelines representing different lake levels can be compared to evaluate how changes in size, shape, and lake configuration might have impacted carbonate development. The early rift lakes show a range of characteristics to be expected in lacustrine settings during the earliest stages of continental extension and rifting, whereas the Red Sea shows well advanced rifting with marine incursion and reef–skeletal sand development. Collectively, the lacustrine examples show a wide range of sizes, with several of them being large enough that they could produce carbonate deposits of potential economic interest. Three of the areas—Great Salt Lake and high lake level Lake Bonneville, Pyramid Lake and high lake level Lake Lahontan, and the Red Sea—are exceedingly complex in that they illustrate a large degree of potential depositional facies heterogeneity because of their size, irregular pattern, and connectivity of subbasins within the overall basin outline

Pro-inflammatory flagellin proteins of prevalent motile commensal bacteria are variably abundant in the intestinal microbiome of elderly humans

Peer reviewedPublisher PD

Representation of Bed Stresses within a Model of Chesapeake Bay

This project focused on numerical modeling of the Estuarine Turbidity Maximum (ETM) with the goal of improving the representation of the bottom boundary layer and turbulent mixing within the Chesapeake Bay Program’s model [see Cerco and Noel, 2004]. The effort has been part of the EPA’s sediment modeling initiative for the Chesapeake Bay, in coordination with the U.S. Army Corps of Engineers (USACE), Engineering Research and Development Center (ERDC). Research activities focused on the Upper Chesapeake Bay and major tributaries in Maryland (such as the Potomac River); and assisted management of the U.S. EPA TMDL (Total Maximum Daily Load) project under the provision of the 1972 Clean Water Act. This document reports progress made during the study. Many of the analysis were extended beyond the Upper Chesapeake Bay so that the results included the entire Chesapeake Bay and major tributaries, to assist in ERDC baywide modeling efforts. Figure 1 shows the bathymetry of Chesapeake Bay, and a representative grid used by the ERDC hydrodynamic and water quality model. This effort was divided into three tasks: (1) estimation of bed shear stress, (2) data analysis, and (3) technology transfer. The following lists progress made within each task throughout the three year program

We Shall: Photographs by Paul D\u27Amato

https://via.library.depaul.edu/museum-publications/1014/thumbnail.jp

A Framework for Establishing Restoration Goals for Contaminated Ecosystems

This article represents 1 of 6 articles in the special series “Restoration of Impaired Ecosystems: An Ounce of Prevention or a Pound of Cure?” The articles result from a Technical Workshop organized by SETAC and the Society for Ecological Restoration, held June 2014 in Jackson, Wyoming, that focused on advancing the practice of restoring ecosystems that have been contaminated or impaired from industrial activities.As natural resources become increasingly limited, the value of restoring contaminated sites, both terrestrial and aquatic, becomes increasingly apparent. Traditionally, goals for remediation have been set before any consideration of goals for ecological restoration. The goals for remediation have focused on removing or limiting contamination whereas restoration goals have targeted the ultimate end use. Here, we present a framework for developing a comprehensive set of achievable goals for ecological restoration of contaminated sites to be used in concert with determining goals for remediation. This framework was developed during a Society of Environmental Toxicology and Chemistry (SETAC) and Society of Ecological Restoration (SER) cosponsored workshop that brought together experts from multiple countries. Although most members were from North America, this framework is designed for use internationally. We discuss the integration of establishing goals for both contaminant remediation and overall restoration, and the need to include both the restoration of ecological and socio-cultural-economic value in the context of contaminated sites. Although recognizing that in some countries there may be regulatory issues associated with contaminants and clean up, landscape setting and social drivers can inform the restoration goals. We provide a decision tree support tool to guide the establishment of restoration goals for contaminated ecosystems. The overall intent of this decision tree is to provide a framework for goal setting and to identify outcomes achievable given the contamination present at a site. Integr Environ Assess Manag 2016;12:264–272. 2015 The Authors. Integrated Environmental Assessment and Management published by Wiley Periodicals, Inc. on behalf of Society of Environmental Toxicology & Chemistry (SETAC