A Systematic Approach to Identifying Protein-Ligand Binding Profiles on a Proteome Scale

Identification of protein-ligand interaction networks on a proteome scale is crucial to address a wide range of biological problems such as correlating molecular functions to physiological processes and designing safe and efficient therapeutics. We have developed a novel computational strategy to identify ligand binding profiles of proteins across gene families and applied it to predicting protein functions, elucidating molecular mechanisms of drug adverse effects, and repositioning safe pharmaceuticals to treat different diseases

A Tale of Three Galaxies: Anomalous Dust Properties in IRASF10398+1455, IRASF21013-0739 and SDSSJ0808+3948

On a galactic scale the 9.7um silicate emission is usually only seen in type 1 active galactic nuclei (AGNs). They usually also display a flat emission continuum at ~5--8um and the absence of polycyclic aromatic hydrocarbon (PAH) emission bands. In contrast, starburst galaxies, luminous infrared (IR) galaxies (LIRGs), and ultraluminous IR galaxies (ULIRGs) exhibit a red 5--8um emission continuum, strong 10um and 18um silicate absorption features, and strong PAH emission bands. Here we report the detection of anomalous dust properties by Spitzer/Infrared Spectrograph in three galaxies (IRASF10398+1455, IRASF21013-0739 and SDSSJ0808+3948) which are characterized by the simultaneous detection of a red 5--8um emission continuum, the 9.7 and 18um silicate emission features as well as strong PAH emission bands. These apparently contradictory dust IR emission properties are discussed in terms of iron-poor silicate composition, carbon dust deficit, small grain size and low dust temperature in the young AGN phase of these three galaxies.Comment: accepted for publication in ApJ

Environmental Activism, Social Networks and the Internet

Social networks and the internet both have a substantial individual effect on environmental activism in China. In this article, we speculate that social linking patterns between environmental actors, which often facilitate activism on the ground, may also exist in cyberspace in the form of an online network. The article addresses the following empirical questions. Does such an online network exist? If so, who are the constituent actors? Are these the same actors observed on the ground? In addressing these questions the article aims to contribute to the growing debate on the implications of the internet for the potential emergence of social movements in China

A Tale of Three Galaxies: Deciphering the Infrared Emission of the Spectroscopically Anomalous Galaxies IRAS F10398+1455, IRAS F21013-0739 and SDSS J0808+3948

The \textit{Spitzer}/Infrared Spectrograph spectra of three spectroscopically anomalous galaxies (IRAS~F10398+1455, IRAS~F21013-0739 and SDSS~J0808+3948) are modeled in terms of a mixture of warm and cold silicate dust, and warm and cold carbon dust. Their unique infrared (IR) emission spectra are characterized by a steep \simali5--8\mum emission continuum, strong emission bands from polycyclic aromatic hydrocarbon (PAH) molecules, and prominent silicate emission. The steep \simali5--8\mum emission continuum and strong PAH emission features suggest the dominance of starbursts, while the silicate emission is indicative of significant heating from active galactic nuclei (AGNs). With warm and cold silicate dust of various compositions ("astronomical silicate," amorphous olivine, or amorphous pyroxene) combined with warm and cold carbon dust (amorphous carbon, or graphite), we are able to closely reproduce the observed IR emission of these %spectroscopically anomalous galaxies. We find that the dust temperature is the primary cause in regulating the steep $\sim$5--8\mum continuum and silicate emission, insensitive to the exact silicate or carbon dust mineralogy and grain size $a$ as long as a\simlt1\mum. More specifically, the temperature of the \simali5--8\mum continuum emitter (which is essentially carbon dust) of these galaxies is $\sim$250--400\K, much lower than that of typical quasars which is $\sim$640\K. Moreover, it appears that larger dust grains are preferred in quasars. The lower dust temperature and smaller grain sizes inferred for these three galaxies compared with that of quasars could be due to the fact that they may harbor a young/weak AGN which is not maturely developed yet.Comment: 31 pages, 14 figures, accepted for publication in Ap

Two-stage hybrid feature selection algorithms for diagnosing erythemato-squamous diseases

This paper proposes two-stage hybrid feature selection algorithms to build the stable and efficient diagnostic models where a new accuracy measure is introduced to assess the models. The two-stage hybrid algorithms adopt Support Vector Machines (SVM) as a classification tool, and the extended Sequential Forward Search (SFS), Sequential Forward Floating Search (SFFS), and Sequential Backward Floating Search (SBFS), respectively, as search strategies, and the generalized F-score (GF) to evaluate the importance of each feature. The new accuracy measure is used as the criterion to evaluated the performance of a temporary SVM to direct the feature selection algorithms. These hybrid methods combine the advantages of filters and wrappers to select the optimal feature subset from the original feature set to build the stable and efficient classifiers. To get the stable, statistical and optimal classifiers, we conduct 10-fold cross validation experiments in the first stage; then we merge the 10 selected feature subsets of the 10-cross validation experiments, respectively, as the new full feature set to do feature selection in the second stage for each algorithm. We repeat the each hybrid feature selection algorithm in the second stage on the one fold that has got the best result in the first stage. Experimental results show that our proposed two-stage hybrid feature selection algorithms can construct efficient diagnostic models which have got better accuracy than that built by the corresponding hybrid feature selection algorithms without the second stage feature selection procedures. Furthermore our methods have got better classification accuracy when compared with the available algorithms for diagnosing erythemato-squamous diseases

Universal Boundary Entropies in Conformal Field Theory: A Quantum Monte Carlo Study

Recently, entropy corrections on nonorientable manifolds such as the Klein bottle are proposed as a universal characterization of critical systems with an emergent conformal field theory (CFT). We show that entropy correction on the Klein bottle can be interpreted as a boundary effect via transforming the Klein bottle into an orientable manifold with nonlocal boundary interactions. The interpretation reveals the conceptual connection of the Klein bottle entropy with the celebrated Affleck-Ludwig entropy in boundary CFT. We propose a generic scheme to extract these universal boundary entropies from quantum Monte Carlo calculation of partition function ratios in lattice models. Our numerical results on the Affleck-Ludwig entropy and Klein bottle entropy for the $q$-state quantum Potts chains with $q=2,3$ show excellent agreement with the CFT predictions. For the quantum Potts chain with $q=4$, the Klein bottle entropy slightly deviates from the CFT prediction, which is possibly due to marginally irrelevant terms in the low-energy effective theory.Comment: 10 pages, 4 figures. Published versio