RCytoscape: Tools for Exploratory Network Analysis

Background: Biomolecular pathways and networks are dynamic and complex, and the perturbations to them which cause disease are often multiple, heterogeneous and contingent. Pathway and network visualizations, rendered on a computer or published on paper, however, tend to be static, lacking in detail, and ill-equipped to explore the variety and quantities of data available today, and the complex causes we seek to understand. Results: RCytoscape integrates R (an open-ended programming environment rich in statistical power and datahandling facilities) and Cytoscape (powerful network visualization and analysis software). RCytoscape extends Cytoscape\u27s functionality beyond what is possible with the Cytoscape graphical user interface. To illustrate the power of RCytoscape, a portion of the Glioblastoma multiforme (GBM) data set from the Cancer Genome Atlas (TCGA) is examined. Network visualization reveals previously unreported patterns in the data suggesting heterogeneous signaling mechanisms active in GBM Proneural tumors, with possible clinical relevance. Conclusions: Progress in bioinformatics and computational biology depends upon exploratory and confirmatory data analysis, upon inference, and upon modeling. These activities will eventually permit the prediction and control of complex biological systems. Network visualizations -- molecular maps -- created from an open-ended programming environment rich in statistical power and data-handling facilities, such as RCytoscape, will play an essential role in this progression

From solid solution to cluster formation of Fe and Cr in α\alpha-Zr

To understand the mechanisms by which Fe and Cr additions increase the corrosion rate of irradiated Zr alloys, a combination of experimental (atom probe tomography, x-ray diffraction and thermoelectric power measurements) and modelling (density functional theory) techniques are employed to investigate the non-equilibrium solubility and clustering of Fe and Cr in binary Zr alloys. Cr occupies both interstitial and substitutional sites in the {\alpha}-Zr lattice, Fe favours interstitial sites, and a low-symmetry site that was not previously modelled is found to be the most favourable for Fe. Lattice expansion as a function of alloying concentration (in the dilute regime) is strongly anisotropic for Fe additions, expanding the $c$-axis while contracting the $a$-axis. Defect clusters are observed at higher solution concentrations, which induce a smaller amount of lattice strain compared to the dilute defects. In the presence of a Zr vacancy, all two-atom clusters are more soluble than individual point defects and as many as four Fe or three Cr atoms could be accommodated in a single Zr vacancy. The Zr vacancy is critical for the increased solubility of defect clusters, the implications for irradiation induced microstructure changes in Zr alloys are discussed.Comment: 15 pages including figure, 9 figures, 2 tables. Submitted for publication in Acta Mater, Journal of Nuclear Materials (2015

Daily oral grepafloxacin vs. twice daily oral doxycycline in the treatment of Chlamydia trachomatis endocervical infection.

OBJECTIVE: To compare the efficacy and safety of a 7-day course of treatment with oral grepafloxacin, 400 mg once daily, and oral doxycycline, 100 mg twice daily, in patients with chlamydial cervicitis. METHODS: Women aged 18 years or older attending 17 sexually transmitted disease clinics in the United States who had clinical signs of mucopurulent cervicitis or who had a recent positive culture or nonculture test for Chlamydia trachomatis or who had contact with a male partner with a positive culture for C. trachomatis were enrolled into this randomized, double-blind, active-controlled clinical study. The diagnosis of chlamydial cervicitis was based on culture for C. trachomatis. Patients were randomized to receive a 7-day course of treatment with either oral grepafloxacin, 400 mg once daily, or oral doxycycline, 100 mg twice daily. Response to therapy was assessed 3-8 days and 21-28 days after completion of treatment. The primary measure of efficacy was eradication of C. trachomatis at the 21-28 day follow-up visit. Clinical success, defined as improvement or complete resolution of the signs and symptoms of cervicitis, was a secondary measure of efficacy. RESULTS: Of the 451 female patients enrolled, 228 received grepafloxacin and 223 received doxycycline. In all, 154/451 (35%) patients were evaluable at the 21-28 day follow-up (81 who received grepafloxacin and 73 who received doxycycline). Microbiologic and clinical success rates demonstrated the equivalence of the two treatments. The C. trachomatis eradication rates were 96.3% (78/81) and 98.6% (72/73) for patients receiving grepafloxacin or doxycycline, respectively. The two study drugs were also equivalent in resolving clinical signs and symptoms, with clinical success rates of 88.9% (64/72) and 89.5% (51/57) for patients treated with grepafloxacin and doxycycline, respectively. Both drugs were well tolerated, with 47% of patients receiving grepafloxacin and 46% of patients receiving doxycycline experiencing drug-related adverse events, none of which was serious. CONCLUSIONS: Seven days of treatment with oral grepafloxacin, 400 mg once daily, was as effective as 7 days of treatment with oral doxycycline, 100 mg twice daily, in patients with cervicitis caused by C. trachomatis. Both agents were well tolerated and had comparable safety profiles. Grepafloxacin's once-daily dosing regimen may offer advantages in terms of patient compliance

Ariel - Volume 8 Number 3

Executive Editor James W. Lockard, Jr. Business Manager Neeraj K. Kanwal University News Richard J . Perry World News Doug Hiller Opinions Elizabeth A. McGuire Features Patrick P. Sokas Sports Desk Shahab S. Minassian Managing Editor Edward H. Jasper Managing Associate Brenda Peterson Photography Editor Robert D. Lehman. Jr. Graphics Christine M. Kuhnl

Diffusion Quantum Monte Carlo Calculations of Excited States of Silicon

The band structure of silicon is calculated at the Gamma, X, and L wave vectors using diffusion quantum Monte Carlo methods. Excited states are formed by promoting an electron from the valence band into the conduction band. We obtain good agreement with experiment for states around the gap region and demonstrate that the method works equally well for direct and indirect excitations, and that one can calculate many excited states at each wave vector. This work establishes the fixed-node DMC approach as an accurate method for calculating the energies of low lying excitations in solids.Comment: 5 pages, 1 figur

Structure of the X-ray Emission from the Jet of 3C 273

We present images from five observations of the quasar 3C 273 with the Chandra X-ray Observatory. The jet has at least four distinct features which are not resolved in previous observations. The first knot in the jet (A1) is very bright in X-rays. Its X-ray spectrum is well fitted with a power law with alpha = 0.60 +/- 0.05. Combining this measurement with lower frequency data shows that a pure synchrotron model can fit the spectrum of this knot from 1.647 GHz to 5 keV (over nine decades in energy) with alpha = 0.76 +/- 0.02, similar to the X-ray spectral slope. Thus, we place a lower limit on the total power radiated by this knot of 1.5e43 erg/s; substantially more power may be emitted in the hard X-ray and gamma-ray bands. Knot A2 is also detected and is somewhat blended with knot B1. Synchrotron emission may also explain the X-ray emission but a spectral bend is required near the optical band. For knots A1 and B1, the X-ray flux dominates the emitted energy. For the remaining optical knots (C through H), localized X-ray enhancements that might correspond to the optical features are not clearly resolved. The position angle of the jet ridge line follows the optical shape with distinct, aperiodic excursions of +/-1 deg from a median value of -138.0deg. Finally, we find X-ray emission from the ``inner jet'' between 5 and 10" from the core.Comment: 10 pages, 5 figures; accepted for publication in the Astrophysical Journal Letters. For the color image, see fig1.ps or http://space.mit.edu/~hermanm/papers/3c273/fig1.jp

Parent-child interaction in Nigerian families: conversation analysis, context and culture

This paper uses a conversation analysis (CA) approach to explore parent child interaction (PCI) within Nigerian families. We illustrate how speech and language therapists (SLTs), by using CA, can tailor recommendations according to the interactional style of each individual family that are consonant with the family’s cultural beliefs. Three parent-child dyads were videoed playing and talking together in their home environments. The analysis uncovered a preference for instructional talk similar to that used in the classroom. Closer examination revealed that this was not inappropriate when considering the context of the activities and their perceived discourse role. Furthermore, this was not necessarily at the expense of responsivity or semantic contingency. The preference for instructional talk appeared to reflect deeply held cultural beliefs about the role of adults and children within the family and it is argued that the cultural paradigm is vitally important to consider when evaluating PCI. Given a potential risk that such young children may be vulnerable in terms of language difficulties, we offer an example of how PCI can be enhanced to encourage language development without disrupting the naturally occurring talk or the underlying purpose of the interaction