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Browsing by Author "Baker, Nathan"

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    LibX IE: An Internet Explorer Add-On for Direct Library Access
    Baker, Nathan (Virginia Tech, 2007-09-06)
    Increasingly, students choose to use general search engines for research rather than taking advantage of the resources provided by university libraries. As university libraries offer services such as the careful selection of material and subscriptions to peer-reviewed journals, it is important that the library become integrated into research workflows. Existing technologies on library servers do not provide the level of integration we believe is most helpful to users. LibX is a browser add-on designed to assist research by making library resources more accessible than they are through the library's own tools. It provides a client-side interface to these library services through the web browser. This integration enhances productivity and augments the user's existing information-seeking behavior. We extended the existing Firefox version of LibX into a browser-agnostic framework, allowing LibX services to be provided on multiple browser platforms. We created a toolbar and context menu system, written in C#, to extend the existing LibX features to the Internet Explorer web browser. The primary focus of this work is on the software engineering challenges presented in creating this version. We also designed a new framework for web localization, allowing pages viewed by the user to be modified on the client side by rules written by LibX developers, library staff, or individual users. The framework also provides a way for these rules to be distributed, updated, and composed, enhancing the browsing experience by augmenting it with additional information. The design and behavior of this framework is a secondary focus of this work.
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    Why double-stranded RNA resists condensation
    Tolokh, Igor S.; Pabit, Suzette A.; Katz, Andrea M.; Chen, Yujie; Drozdetski, Aleksander V.; Baker, Nathan; Pollack, Lois; Onufriev, Alexey V. (2014-09-15)
    The addition of small amounts of multivalent cations to solutions containing double-stranded DNA leads to inter-DNA attraction and eventual condensation. Surprisingly, the condensation is suppressed in double-stranded RNA, which carries the same negative charge as DNA, but assumes a different double helical form. Here, we combine experiment and atomistic simulations to propose a mechanism that explains the variations in condensation of short (25 base-pairs) nucleic acid (NA) duplexes, from B-like form of homopolymeric DNA, to mixed sequence DNA, to DNA: RNA hybrid, to A-like RNA. Circular dichroism measurements suggest that duplex helical geometry is not the fundamental property that ultimately determines the observed differences in condensation. Instead, these differences are governed by the spatial variation of cobalt hexammine (CoHex) binding to NA. There are two major NA-CoHex binding modes-internal and external-distinguished by the proximity of bound CoHex to the helical axis. We find a significant difference, up to 5-fold, in the fraction of ions bound to the external surfaces of the different NA constructs studied. NA condensation propensity is determined by the fraction of CoHex ions in the external binding mode.