Inherent limitations of probabilistic models for protein-DNA binding specificity

The specificities of transcription factors are most commonly represented with probabilistic models. These models provide a probability for each base occurring at each position within the binding site and the positions are assumed to contribute independently. The model is simple and intuitive and is the basis for many motif discovery algorithms. However, the model also has inherent limitations that prevent it from accurately representing true binding probabilities, especially for the highest affinity sites under conditions of high protein concentration. The limitations are not due to the assumption of independence between positions but rather are caused by the non-linear relationship between binding affinity and binding probability and the fact that independent normalization at each position skews the site probabilities. Generally probabilistic models are reasonably good approximations, but new high-throughput methods allow for biophysical models with increased accuracy that should be used whenever possible

Cylindrical Invisibility Cloak with Simplified Material Parameters is Inherently Visible

It was proposed that perfect invisibility cloaks can be constructed for hiding objects from electromagnetic illumination (Pendry et al., Science 312, p. 1780). The cylindrical cloaks experimentally demonstrated (Schurig et al., Science 314, p. 997) and proposed (Cai et al., Nat. Photon. 1, p. 224) have however simplified material parameters in order to facilitate easier realization as well as to avoid infinities in optical constants. Here we show that the cylindrical cloaks with simplified material parameters inherently allow the zeroth-order cylindrical wave to pass through the cloak as if the cloak is made of a homogeneous isotropic medium, and thus visible. To all high-order cylindrical waves, our numerical simulation suggests that the simplified cloak inherits some properties of the ideal cloak, but finite scatterings exist.Comment: 10 pages, 3 figure

Identifying network communities with a high resolution

Community structure is an important property of complex networks. An automatic discovery of such structure is a fundamental task in many disciplines, including sociology, biology, engineering, and computer science. Recently, several community discovery algorithms have been proposed based on the optimization of a quantity called modularity (Q). However, the problem of modularity optimization is NP-hard, and the existing approaches often suffer from prohibitively long running time or poor quality. Furthermore, it has been recently pointed out that algorithms based on optimizing Q will have a resolution limit, i.e., communities below a certain scale may not be detected. In this research, we first propose an efficient heuristic algorithm, Qcut, which combines spectral graph partitioning and local search to optimize Q. Using both synthetic and real networks, we show that Qcut can find higher modularities and is more scalable than the existing algorithms. Furthermore, using Qcut as an essential component, we propose a recursive algorithm, HQcut, to solve the resolution limit problem. We show that HQcut can successfully detect communities at a much finer scale and with a higher accuracy than the existing algorithms. Finally, we apply Qcut and HQcut to study a protein-protein interaction network, and show that the combination of the two algorithms can reveal interesting biological results that may be otherwise undetectable.Comment: 14 pages, 5 figures. 1 supplemental file at http://cic.cs.wustl.edu/qcut/supplemental.pd

Prevention and control of Zika fever as a mosquito-borne and sexually transmitted disease

The ongoing Zika virus (ZIKV) epidemic poses a major global public health emergency. It is known that ZIKV is spread by \textit{Aedes} mosquitoes, recent studies show that ZIKV can also be transmitted via sexual contact and cases of sexually transmitted ZIKV have been confirmed in the U.S., France, and Italy. How sexual transmission affects the spread and control of ZIKV infection is not well-understood. We presented a mathematical model to investigate the impact of mosquito-borne and sexual transmission on spread and control of ZIKV and used the model to fit the ZIKV data in Brazil, Colombia, and El Salvador. Based on the estimated parameter values, we calculated the median and confidence interval of the basic reproduction number R0=2.055 (95% CI: 0.523-6.300), in which the distribution of the percentage of contribution by sexual transmission is 3.044 (95% CI: 0.123-45.73). Our study indicates that R0 is most sensitive to the biting rate and mortality rate of mosquitoes while sexual transmission increases the risk of infection and epidemic size and prolongs the outbreak. In order to prevent and control the transmission of ZIKV, it must be treated as not only a mosquito-borne disease but also a sexually transmitted disease

Dust-related interannual and intraseasonal variability of Martian climate using data assimilation

Data assimilation has been applied in several studies [Montabone et al., 2005; Lewis et al., 2005; Montabone et al., 2006a; Montabone et al., 2006b; Lewis et al., 2007; Wilson et al., 2008; Rogberg et al. 2010] as an effective tool with which to analyze spacecraft observations and phenomena (e.g., atmospheric tides, transient wave behavior, effects of clouds in the tropics, weather predictability, etc.) in the Martian atmosphere. A data assimilation scheme combined with a Martian Global Circulation Model (GCM) is able to provide a complete, balanced, four-dimensional solution consistent with observations. The GCM we use [Forget et al., 1999] combines a spectral dynamical solver and a tracer transport scheme developed in UK and Laboratoire de Météorologie Dynamique (LMD; Paris, France) physics package developed in collaboration with Oxford, The Open University and Instituto de Astrofisica de Andalucia (Granada, Spain). Here, we describe and discuss dust-related interannual and intraseasonal variability of the Martian climate. The results shown in this study come from a reanalysis using the Martian GCM with data assimilation scheme which assimilates Mars Global Surveyor/ Thermal Emission Spectrometer (MGS/TES) retrievals of temperature and column dust opacity. The detailed model setup was described by Montabone et al. [2006a], and the data assimilation scheme employed in this study was introduced in the work of Lewis et al. [2007]