Browsing by Author "Li, X."
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Item A Bayesian Latent Variable Approach to Aggregation of Partial and Top-Ranked Lists in Genomic Studies(Wiley) Li, X.; Choudhary, Pankaj K.; Biswas, Swati; Wang, X.; 0000 0001 2704 188X (Biswas, S); 0000-0002-0398-7459 (Choudary, PK); Choudhary, Pankaj K.; Biswas, SwatiIn genomic research, it is becoming increasingly popular to perform meta-analysis, the practice of combining results from multiple studies that target a common essential biological problem. Rank aggregation, a robust meta-analytic approach, consolidates such studies at the rank level. There exists extensive research on this topic, and various methods have been developed in the past. However, these methods have two major limitations when they are applied in the genomic context. First, they are mainly designed to work with full lists, whereas partial and/or top-ranked lists prevail in genomic studies. Second, the component studies are often clustered, and the existing methods fail to utilize such information. To address the above concerns, a Bayesian latent variable approach, called BiG, is proposed to formally deal with partial and top-ranked lists and incorporate the effect of clustering. Various reasonable prior specifications for variance parameters in hierarchical models are carefully studied and compared. Simulation results demonstrate the superior performance of BiG compared with other popular rank aggregation methods under various practical settings. A non–small-cell lung cancer data example is analyzed for illustration.Item Cofunctional Subpathways were Regulated by Transcription Factor with Common Motif, Common Family, or Common Tissue(Hindawi Publishing Corporation) Su, F.; Shang, D.; Xu, Y.; Feng, L.; Yang, H.; Liu, B.; Su, Shengyang; Chen, L.; Li, X.; Su, ShengyangDissecting the characteristics of the transcription factor (TF) regulatory subpathway is helpful for understanding the TF underlying regulatory function in complex biological systems. To gain insight into the influence of TFs on their regulatory subpathways, we constructed a global TF-subpathways network (TSN) to analyze systematically the regulatory effect of common-motif, common-family, or common-tissue TFs on subpathways. We performed cluster analysis to show that the common-motif, common-family, or common-tissue TFs that regulated the same pathway classes tended to cluster together and contribute to the same biological function that led to disease initiation and progression. We analyzed the Jaccard coefficient to show that the functional consistency of subpathways regulated by the TF pairs with common motif, common family, or common tissue was significantly greater than the random TF pairs at the subpathway level, pathway level, and pathway class level. For example, HNF4A (hepatocyte nuclear factor 4, alpha) and NR1I3 (nuclear receptor subfamily 1, group I, member 3) were a pair of TFs with common motif, common family, and common tissue. They were involved in drug metabolism pathways and were liver-specific factors required for physiological transcription. In short, we inferred that the cofunctional subpathways were regulated by common-motif, common-family, or common-tissue TFs.Item Decoupling the Influence of Surface Structure and Intrinsic Wettability on Boiling Heat Transfer(American Institute of Physics Inc.) Dai, Xianming (Simon); Wang, P.; Yang, F.; Li, X.; Li, C.; 0000-0001-5050-2867 (Dai, X); 308247739 (Dai, X; Dai, Xianming (Simon)Surface structure and intrinsic wettability are both important for boiling heat transfer. While superhydrophilic micro, nano, and hierarchical surfaces are widely used for boiling enhancement, in which the surface structure and intrinsic wettability usually couple together. This study aims to decouple their influences on boiling heat transfer. Copper meshes are utilized as the microporous structures, and conformal superhydrophilic films of TiO₂ are deposited by atomic layer deposition (ALD). Although ALD coatings for boiling have been done on flat surfaces, this study separates the influence of surface structure from that of intrinsic wettability on a three-dimensional microporous surface. By comparing two and four layer meshes, we show that the surface structure has no obvious influence on the critical heat flux (CHF), but can significantly enhance the heat transfer coefficient (HTC). The intrinsic superhydrophilicity dramatically increases the CHF due to the fast rewetting of dryout regions. Our conclusion is that fast rewetting is critical to increase the CHF, while large surface areas are vital to enhance the HTC. © 2018 Author(s).Item Mutations Associated with Reduced Surotomycin Susceptibility in Clostridium Difficile and Enterococcus Species(American Society for Microbiology, 2015-05-04) Adams, Hannah M.; Li, X.; Mascio, C.; Chesnel, Laurent; Palmer, Kelli L.; Adams, Hannah M.; Li, X. Chesnel, Laurent; Palmer, Kelli L.Clostridium difficile infection (CDI) is an urgent public health concern causing considerable clinical and economic burdens. CDI can be treated with antibiotics, but recurrence of the disease following successful treatment of the initial episode often occurs. Surotomycin is a rapidly bactericidal cyclic lipopeptide antibiotic that is in clinical trials for CDI treatment and that has demonstrated superiority over vancomycin in preventing CDI relapse. Surotomycin is a structural analogue of the membrane-active antibiotic daptomycin. Previously, we utilized in vitro serial passage experiments to derive C. difficile strains with reduced surotomycin susceptibilities. The parent strains used included ATCC 700057 and clinical isolates from the restriction endonu-clease analysis (REA) groups BI and K. Serial passage experiments were also performed with vancomycin-resistant and vancomycin-susceptible Enterococcus faecium and Enterococcus faecalis. The goal of this study is to identify mutations associated with reduced surotomycin susceptibility in C. difficile and enterococci. Illumina sequence data generated for the parent strains and serial passage isolates were compared. We identified nonsynonymous mutations in genes coding for cardiolipin synthase in C. difficile ATCC 700057, enoyl-(acyl carrier protein) reductase II (FabK) and cell division protein FtsH2 in C. difficile REA type BI, and a PadR family transcriptional regulator in C. difficile REA type K. Among the 4 enterococcal strain pairs, 20 mutations were identified, and those mutations overlap those associated with daptomycin resistance. These data give insight into the mechanism of action of surotomycin against C. difficile, possible mechanisms for resistance emergence during clinical use, and the potential impacts of surotomycin therapy on intestinal enterococci.Item SU(3) Quantum Hall Ferromagnetism in SnTe(American Physical Society, 2016-01-15) Li, X.; Zhang, Fan; MacDonald, A. H.; 0000-0003-4623-4200 (Zhang, F); Zhang, FanThe (111) surface of SnTe hosts one isotropic Γ-centered and three degenerate anisotropic M-centered Dirac surface states. We predict that a nematic phase with spontaneously broken C₃ symmetry will occur in the presence of a perpendicular magnetic field when the N=0 M Landau levels are 1/3 or 2/3 filled. The nematic state phase boundary is controlled by a competition between intravalley Coulomb interactions that favor a valley-polarized state and weaker intervalley scattering processes that increase in relative strength with magnetic field. An in-plane Zeeman field alters the phase diagram by lifting the threefold M Landau-level degeneracy, yielding a ground state energy with 2π/3 periodicity as a function of Zeeman-field orientation angle.