Going the distance for protein function prediction: a new distance metric for protein interaction networks

Due to an error introduced in the production process, the x-axes in the first panels of Figure 1 and Figure 7 are not formatted correctly. The correct Figure 1 can be viewed here: http://dx.doi.org/10.1371/annotation/343bf260-f6ff-48a2-93b2-3cc79af518a9In protein-protein interaction (PPI) networks, functional similarity is often inferred based on the function of directly interacting proteins, or more generally, some notion of interaction network proximity among proteins in a local neighborhood. Prior methods typically measure proximity as the shortest-path distance in the network, but this has only a limited ability to capture fine-grained neighborhood distinctions, because most proteins are close to each other, and there are many ties in proximity. We introduce diffusion state distance (DSD), a new metric based on a graph diffusion property, designed to capture finer-grained distinctions in proximity for transfer of functional annotation in PPI networks. We present a tool that, when input a PPI network, will output the DSD distances between every pair of proteins. We show that replacing the shortest-path metric by DSD improves the performance of classical function prediction methods across the board.MC, HZ, NMD and LJC were supported in part by National Institutes of Health (NIH) R01 grant GM080330. JP was supported in part by NIH grant R01 HD058880. This material is based upon work supported by the National Science Foundation under grant numbers CNS-0905565, CNS-1018266, CNS-1012910, and CNS-1117039, and supported by the Army Research Office under grant W911NF-11-1-0227 (to MEC). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

Efficacy of gold weight implants in facial nerve palsy: quantitative alterations in blinking

AbstractDeficient eyelid closure is a major visual threat to patients with unresolved facial nerve palsy. Gold weight implants assisted eyelid closure in patients with paresis of the orbicularis oculi, ameliorating patient complaints of dry eye, excessive tearing, and corneal epithelial breakdown. We used dynamic measures to assess the efficacy of upper eyelid gold weight implantation surgery for facial nerve palsy. The search coil technique was used to record spontaneous blinks bilaterally in six patients, before and after unilateral gold weight implantations into the upper eyelid in severe facial nerve palsy. In uncomplicated facial nerve palsy, the amplitude of blink down-phases for the paretic eyelid was 28.6±5.7% of the amplitude of the contralateral, normal eyelid. Following corrective surgery, closure of the paretic eyelid improved to 42.6±7.5% (P<0.05). There was not a commensurate increase in the peak velocity of blink down-phases, suggesting that gold weight effects are mediated by a passive improvement in blink dynamics

Hsp90 governs dispersion and drug resistance of fungal biofilms

Fungal biofilms are a major cause of human mortality and are recalcitrant to most treatments due to intrinsic drug resistance. These complex communities of multiple cell types form on indwelling medical devices and their eradication often requires surgical removal of infected devices. Here we implicate the molecular chaperone Hsp90 as a key regulator of biofilm dispersion and drug resistance. We previously established that in the leading human fungal pathogen, Candida albicans, Hsp90 enables the emergence and maintenance of drug resistance in planktonic conditions by stabilizing the protein phosphatase calcineurin and MAPK Mkc1. Hsp90 also regulates temperature-dependent C. albicans morphogenesis through repression of cAMP-PKA signalling. Here we demonstrate that genetic depletion of Hsp90 reduced C. albicans biofilm growth and maturation in vitro and impaired dispersal of biofilm cells. Further, compromising Hsp90 function in vitro abrogated resistance of C. albicans biofilms to the most widely deployed class of antifungal drugs, the azoles. Depletion of Hsp90 led to reduction of calcineurin and Mkc1 in planktonic but not biofilm conditions, suggesting that Hsp90 regulates drug resistance through different mechanisms in these distinct cellular states. Reduction of Hsp90 levels led to a marked decrease in matrix glucan levels, providing a compelling mechanism through which Hsp90 might regulate biofilm azole resistance. Impairment of Hsp90 function genetically or pharmacologically transformed fluconazole from ineffectual to highly effective in eradicating biofilms in a rat venous catheter infection model. Finally, inhibition of Hsp90 reduced resistance of biofilms of the most lethal mould, Aspergillus fumigatus, to the newest class of antifungals to reach the clinic, the echinocandins. Thus, we establish a novel mechanism regulating biofilm drug resistance and dispersion and that targeting Hsp90 provides a much-needed strategy for improving clinical outcome in the treatment of biofilm infections

Interprofessional Integrative Medicine Training for Preventive Medicine Residents

Integrative medicine training was incorporated into the Rutgers New Jersey Medical School Preventive Medicine residency at the Rutgers Biomedical and Health Sciences Newark Campus as a collaboration between the Rutgers New Jersey Medical School and the School of Health Related Professions. Beginning in 2012, an interdisciplinary faculty team organized an Integrative Medicine program in a Preventive Medicine residency that leveraged existing resources across Rutgers Biomedical and Health Sciences. The overarching aim of the programs was to introduce residents and faculty to the scope and practice of integrative medicine in the surrounding Newark community and explore evidence-based research on integrative medicine. The faculty team tapped into an interprofessional network of healthcare providers to organize rotations for the preventive medicine residents that reflected the unique nature of integrative medicine in the greater Newark area. Residents provided direct care as part of interdisciplinary teams at clinical affiliates and shadowed health professionals from diverse disciplines as they filled different roles in providing patient care. The residents also participated in research projects. A combination of formal and informal programs on integrative medicine topics was offered to residents and faculty. The Integrative Medicine program, which ran from 2013 through 2014, was successful in exposing residents and faculty to the unique nature of integrative medicine across professions in the community served by Rutgers Biomedical and Health Sciences

The Schr\"oder functional equation and its relation to the invariant measures of chaotic maps

The aim of this paper is to show that the invariant measure for a class of one dimensional chaotic maps, $T(x)$, is an extended solution of the Schr\"oder functional equation, $q(T(x))=\lambda q(x)$, induced by them. Hence, we give an unified treatment of a collection of exactly solved examples worked out in the current literature. In particular, we show that these examples belongs to a class of functions introduced by Mira, (see text). Moreover, as a new example, we compute the invariant densities for a class of rational maps having the Weierstrass $\wp$ functions as an invariant one. Also, we study the relation between that equation and the well known Frobenius-Perron and Koopman's operators.Comment: 9 page

Planning the Future of U.S. Particle Physics (Snowmass 2013): Chapter 4: Cosmic Frontier

These reports present the results of the 2013 Community Summer Study of the APS Division of Particles and Fields ("Snowmass 2013") on the future program of particle physics in the U.S. Chapter 4, on the Cosmic Frontier, discusses the program of research relevant to cosmology and the early universe. This area includes the study of dark matter and the search for its particle nature, the study of dark energy and inflation, and cosmic probes of fundamental symmetries.Comment: 61 page

Abstract basins of attraction

Abstract basins appear naturally in different areas of several complex variables. In this survey we want to describe three different topics in which they play an important role, leading to interesting open problems