Optimization of coarse-grained models: matching probability density in conformational space (2009)
Coarse-Graining (CG) models are low resolution approximation of high resolution models, such as all-atomic (AA) models. An effective CG model is expected to reproduce equilibrium values of sufficient...
Based on multiple short simulation trajectories started from dispersively selected initial conformations, the weighted ensemble dynamics (WED) method [Phys Rev. E,(in press) (2009) or...
Comparative genome analysis of lignin biosynthesis gene families across the plant kingdom (2009)
Xu, Zhanyou, Zhang, Dandan, Hu, Jun, Zhou, Xin, Ye, Xia, Reichel, Kristen L, ...
Abstract Background As a major component of plant cell wall, lignin plays important roles in mechanical support, water transport, and stress responses. As the main cause for the recalcitrance of...
Novel software package for cross-platform transcriptome analysis (CPTRA) (2009)
Zhou, Xin, Su, Zhen, Sammons, R Douglas, Peng, Yanhui, Tranel, Patrick J, Stewart, C Neal, ...
Abstract Background Next-generation sequencing techniques enable several novel transcriptome profiling approaches. Recent studies indicated that digital gene expression profiling based on short...
Structuring and sampling complex conformation space: Weighted ensemble dynamics simulations (2009)
Based on multiple simulation trajectories, which started from dispersively selected initial conformations, the weighted ensemble dynamics method is designed to robustly and systematically explore the...
In this paper attempts have been focused on using window-tracking technlque to analyse human body movement.According to the behavlor of human vision systen,an Idea of rough and precise search-space...
plantsUPS: a database of plants' Ubiquitin Proteasome System (2009)
Du, Zhou, Zhou, Xin, Li, Li, Su, Zhen
Abstract Background The ubiquitin 26S/proteasome system (UPS), a serial cascade process of protein ubiquitination and degradation, is the last step for most cellular proteins. There are many genes...
On the existence of min-max minimal torus (2009)
In this paper, we will study the existence problem of minmax minimal torus. We use classical conformal invariant geometric variational methods. We prove a theorem about the existence of minmax...
Imagawa, Kiwamu, Fang, Yue, Sugiura, Reiko, Zhou, Xin, Ma, Yan, Kuno, Takayoshi
We have previously demonstrated that calcineurin and the Pmk1 MAP kinasepathway play an antagonistic role in Cl– homeostasis. Using this relationship, wescreened for mutations that show vic...
Liu, Youning, Chen, Minjun, Zhao, Tiemei, Wang, Hui, Wang, Rui, Cai, Baiqiang, ...
Abstract Background Knowledge of predominant microbial patterns in community-acquired pneumonia (CAP) constitutes the basis for initial decisions about empirical antimicrobial treatment, so a...
Peng, Zhi-yu, Zhou, Xin, Li, Linchuan, Yu, Xiangchun, Li, Hongjiang, Jiang, Zhiqiang, ...
Plant hormones are small organic molecules that influence almost every aspect of plant growth and development. Genetic and molecular studies have revealed a large number of genes that are involved in...
University and Hospitals of Geneva at (2008)
Xin Zhou, Julien Gobeill, Patrick Ruch, Henning Müller
This article describes the participation of the University and Hospitals of Geneva at three tasks of the 2007 ImageCLEF image retrieval benchmark. Two of these tasks were medical tasks and one was a...
Construction and Refinement of Coarse-Grained Models (2008)
A general scheme, which includes constructions of coarse-grained (CG) models, weighted ensemble dynamics (WED) simulations and cluster analyses (CA) of stable states, is presented to detect dynamical...
We presented an efficient algorithm, fast adaptive flat-histogram ensemble (FAFE), to estimate the density of states (DOS) and to enhance sampling in large systems. FAFE calculates the means of an...
Discovery of molecular shells associated with supernova remnants. (II) Kesteven 75 (2008)
Su, Yang, Chen, Yang, Yang, Ji, Koo, Bon-Chul, Zhou, Xin, Jeong, Il-Gyo, ...
The young composite supernova remnant (SNR) Kesteven 75, with a pulsar wind nebula at its center, has an unusual morphology with a bright southern half-shell structure in multiwavelengths. The...
Discovery of Molecular Shells Associated with Supernova Remnants. I. Kesteven 69 (2008)
Zhou, Xin, Chen, Yang, Su, Yang, Yang, Ji
Supernova remnant (SNR) Kes 69 is morphologically characterized by brightened radio, infrared, and X-ray emission on the southeastern rim, with the 1720 MHz OH masers detected in the northeastern and...
Gene Selection Using a New Error Bound for Support Vector Machines (2008)
The microarray technique has the power to simultaneously measure the expression levels of tens of thousands of genes in a single experiment [1, 2]. Selection of relevant genes for sample...
A Multicast Routing Algorithm for CSCW (2008)
Xiongfei Li, An Huan, Yuanfang Dong, Xin Zhou
Abstract. The CRMR, which is an algorithm for updating multicast tree dynamically, is presented. It constructs an initial multicast tree using KPP and builds a virtual trunk (VT) simultaneously. The...
Christopher Giblin, Alice Y. Liu, Samuel Müller, Birgit Pfitzmann, Xin Zhou, Christopher Giblin, ...
This report has been submitted for publication outside of IBM and will probably be copyrighted if accepted for publication. It has been issued as a Research Report for early dissemination of its...
Temporal Information Management using XML (2008)
Fusheng Wang, Xin Zhou, Carlo Zaniolo
A closer integration of XML and database systems is actively pursued by researchers and vendors because of the many practical benefits it offers. Additional special benefits can be achieved on...
Temporal Information Management using XML (2008)
Fusheng Wang, Xin Zhou, Carlo Zaniolo
A closer integration of XML and database systems is actively pursued by researchers and vendors because of the many practical benefits it offers. Additional special benefits can be achieved on...
Efficient Temporal Coalescing Query Support in Relational Database Systems (2008)
Xin Zhou, Fusheng Wang, Carlo Zaniolo
Abstract. The interest in and user demand for temporal databases have only increased with time; unfortunately, DBMS vendors and standard groups have not moved aggressively to extend their systems...
Osteoporosis is a common disorder which affects up to 30% women and 12% men at some point in life. This mostly age-associated disorder has becoming increasingly a major clinical and public health...
Inhibition of Wnt signaling by the osteoblast-specific transcription factor Osterix. (2008)
Zhang, Chi, Cho, Kyucheol, Huang, Yehong, Lyons, Jon P., Zhou, Xin, Sinha, Krishna, ...
The recent identification of the genes responsible for several human genetic diseases affecting bone homeostasis and the characterization of mouse models for these diseases indicated that canonical...
Janossy Densities for Unitary Ensembles at the Spectral Edge (2008)
For a broad class of unitary ensembles of random matrices, we demonstrate the universal nature of the Janossy densities of eigenvalues near the spectral edge, providing a different formulation of the...
tCal: transcriptional probability calculator using thermodynamic model (2008)
Summary: Thermodynamic model has been proposed as a realistic model of gene transcriptional regulation in bacteria, in which transcription probability calculation is based on physical interpretation...
Tovbis, Alexander, Venakides, Stephanos, Zhou, Xin
We consider the semiclassical limit for the focusing nonlinear (cubic) Schrödinger Equation (NLS) in the pure radiational case. We present a method of reconstructing the leading order terms of the...
Abstract Background It is always difficult to interpret microarray results. Recently, a handful of tools have been developed to meet this need, but almost none of them were designed to support...
Janossy densities for Unitary ensembles at the spectral edge (2007)
For a broad class of unitary ensembles of random matrices we demonstrate the universal nature of the Janossy densities of eigenvalues near the spectral edge, providing a different formulation of the...
MSVM-RFE: extensions of SVM-RFE for multiclass gene selection on DNA microarray data (2007)
Motivation: Given the thousands of genes and the small number of samples, gene selection has emerged as an important research problem in microarray data analysis. Support Vector Machine—Recursive...
Gene selection for DNA microarray data / (2007)
"Supervisor, Associate Professor Mao Kezhi."
Zhou, Xin, Jiang, Yi, Kremer, Kurt, Ziock, Hans, Rasmussen, Steen
We develop a generalized hyperdynamics method, which is able to simulate slow dynamics in atomistic general (both energy and entropy-dominated) systems. We show that a few functionals of the pair...
Unifying the processing of xml streams and relational data streams (2006)
Xin Zhou, Hetal Thakkar, Carlo Zaniolo
Relational data streams and XML streams have previously provided two separate research foci, but their unified support by a single Data Stream Management System (DSMS) is very desirable from an...
Recursive shift indexing: a fast multi-pattern string matching Algorithm (2006)
Abstract. String matching algorithms are essential for network devices that filter packets and flows based on their payload. Applications like intrusion detection/prevention, web filtering,...
Motivation: Feature selection approaches, such as filter and wrapper, have been applied to address the gene selection problem in the literature of microarray data analysis. In wrapper methods, the...
Fusheng Wang, Xin Zhou, Carlo Zaniolo
Better support for temporal applications by database systems represents an important technical objective that is difficult to achieve since it requires integrated solutions for technical problems...
TIMECENTER Participants (2005)
Fusheng Wang, Xin Zhou, Carlo Zaniolo, Copyright Fusheng, Wang Xin, Zhou Carlo, ...
Any software made available via TIMECENTER is provided “as is ” and without any express or implied warranties, including, without limitation, the implied warranty of merchantability and fitness...
TIMECENTER Participants (2005)
Fusheng Wang, Xin Zhou, Carlo Zaniolo, Copyright Fusheng, Wang Xin, Zhou Carlo, ...
Any software made available via TIMECENTER is provided “as is ” and without any express or implied warranties, including, without limitation, the implied warranty of merchantability and fitness...
LS Bound based gene selection for DNA microarray data (2005)
Motivation: One problem with discriminant analysis of DNA microarray data is that each sample is represented by quite a large number of genes, and many of them are irrelevant, insignificant or...
Enhancement of solid-state proton NMR via SPINOE with laser-polarized xenon (2004)
Zhou, Xin, Luo, Jun, Sun, Xian-ping, Zeng, Xi-zhi, Ding, Shang-wu, Liu, Mai-li, ...
We have first successfully transferred the 129Xe polarization of natural isotopic composition to the proton of solid-state 1HCl via Spin Polarization-Induced Nuclear Overhauser Effect (SPINOE), by...
Motivation: One problem with discriminant analysis of DNA microarray data is that each sample is represented by quite a large number of genes, and many of them are irrelevant, insignificant or...
LS bound based gene selection for DNA microarray data (2004)
Motivation: One problem with discriminant analysis of DNA microarray data is that each sample is represented by a quite large number of genes, and many of them are irrelevant, insignificant or...
LS bound based gene selection for DNA microarray data (2004)
Motivation: One problem with discriminant analysis of DNA microarray data is that each sample is represented by a quite large number of genes, and many of them are irrelevant, insignificant or...
Zhou, Xin, Luo, Jun, Sun, Xian-ping, Zeng, Xi-zhi, Zhan, Ming-sheng, Ding, Shang-wu, ...
Radiation damping is generally observed when the sample with high spin concentration and high gyro-magnetic ratio is placed in a high magnetic field. However, we firstly observed liquid state 129Xe...
Orientational orders in binary mixtures of hard HGO molecules (2003)
Zhou, Xin, Chen, Hu, Iwamoto, Mitsumasa
studied liquid crystal phases of binary mixtures of non-spherical molecules. The components of the mixtures are two kinds of hard Gaussian overlap (HGO) molecules, one kind of molecules with a small...
Orientational orders of small anisotropic molecules confined in slit pores (2003)
Zhou, Xin, Chen, Hu, Iwamoto, Mitsumasa
We have studied phase behavior of hard gaussian overlap molecules with small anisotropic parameter confined in two plane parallel structureless hard walls. Our investigation based on standard...
Thesis (M.S.)--University of Cincinnati, 2003.
Direction-Of-Arrival (DOA) and Frequency-Of-Arrival (FOA) estimation has attracted great attention among researchers in recent years. The ML (Maximum Likelihood) approach and subspace-based...
Thesis (M.S.)--University of Cincinnati, 2003.
Zhou, Xin., OhioLINK Electronic Theses And Dissertations Center.
Direction-Of-Arrival (DOA) and Frequency-Of-Arrival (FOA) estimation has attracted great attention among researchers in recent years. The ML (Maximum Likelihood) approach and subspace-based...
iFlow: middleware-assisted rendezvous-based information access for mobile ad hoc applications (2003)
Zongpeng Li, Baochun Li, Dongyan Xu, Xin Zhou
Due to node mobility and limitations on bandwidth availability in wireless channels, there exist unique challenges towards achieving efficient and effective information access in wireless ad hoc...
Equilibrium and Kinetics: Water Confined in Carbon Nanotube as 1D Lattice Gas (2002)
Zhou, Xin, Li, Cheng-Quan, Iwamoto, Mitsumasa
A simple 1D lattice gas model is presented, which very well describes the equilibrium and kinetic behaviors of water confined in a thin carbon nanotube found in an atomistic molecular dynamics(MD)...
Heat Conduction and Long-Range Spatial Correlation in 1D Models (2002)
Heat conduction in one-dimensional (1D) systems is studied based on an analytical S-matrix method, which is developed in the mesoscopic electronic transport theory and molecular dynamic (MD)...
A priori Lp-estimates for solutions of Riemann-Hilbert problems (2002)
We use steepest-descent ideas to obtain a priori Lp-estimates for solutions of Riemann-Hilbert problems. Such estimates play a crucial role, in particular, in analyzing the long-time behavior of...
Baik, Jinho, Deift, Percy, McLaughlin, Ken, Miller, Peter, Zhou, Xin
In this paper, we obtain optimal uniform lower tail estimates for the probability distribution of the properly scaled length of the longest up/right path of the last passage site percolation model...
Large deformation of spherical vesicle studied by perturbation theory and Surface evolver (2001)
Zhou, Jianjun, Zhang, Yong, Zhou, Xin, Zhong-can, Ou-Yang
With tangent angle perturbation approach the axial symmetry deformation of a spherical vesicle in large under the pressure changes is studied by the elasticity theory of Helfrich spontaneous...
The Polarizability and Electric Field-Induced Energy Gaps In Carbon Nanotubes (2001)
Zhou, Xin, Chen, Hu, Zhong-can, Ou-Yang
A simple method to calculate the static electric polarization of single-walled carbon nanotube (SWNT) is obtained within the second-order perturbation approximation. The results are in agreement with...
Preschool children's use of counting to compare two sets in cardinal situations / (2001)
Thesis (Ed. D.)--Boston University, 2001.
Jinho Baik, Percy Deift, Ken McLaughlin, Peter Miller, Xin Zhou
In this paper, we obtain optimal uniform lower tail estimates for the probability distribution of the properly scaled length of the longest up/right path of the last passage site percolation model...
Can Electric Field Induced Energy Gaps In Metallic Carbon Nanotubes? (2000)
Zhou, Xin, Chen, Hu, Zhong-can, Ou-Yang
The low-energy electronic structure of metallic single-walled carbon nanotube (SWNT) in an external electric field perpendicular to the tube axis is investigated. Based on tight-binding...
The structure relaxation of carbon nanotube (2000)
Zhou, Xin, Chen, Hu, Zhou, Jianjun, Zhong-can, Ou-Yang
A simple macroscopic continuum elasticity theory (CET) is used to calculate the structure relaxation of single-wall carbon nanotube (SWNT), an analytic formula is obtained. We also expand an atomic...
Thesis (Ph. D.)--Michigan Technological University, 2000.
A pulsed (10 Hz) optical parametric oscillator (OPO) laser system based on $\beta$-barium borate (BBO) was characterized for use in analytical atomic spectrometry. The laser was used as the...
Abstract (2 leaves) bound with copy.
Typescript.
Printout.
Thesis (M.S.)--University of Cincinnati, 1993.
Thesis (M.S.)--Ohio University, November, 1992.
A steepest descent method for oscillatory Riemann-Hilbert problems (1991)
In this announcement we present a general and new approach to analyzing the asymptotics of oscillatory Riemann-Hilbert problems. Such problems arise, in particular, in evaluating the long-time...
Appearance and reality in Katherine Anne Porter's selected short novels / (1990)
Thesis (M.A.)--Southern Connecticut State University, 1990.
Thesis (M.A.)--Southern Connecticut State University, 1990.
Data acquisition system for chemical kinetic studies (1989)
Yu-zhen Zhu, Xin Zhou, Xiang-sheng Zang
The computer-interfaced system for second-order chemical kinetic studies was applied to the determination of the rate constant of the saponification of ethyl acetate at 35°C. For this specific...
SPATIO-TEMPORAL JOINT MUSIC ALGORITHM FOR NARROWBAND AND WIDEBAND DIRECTION OF ARRIVAL ESTIMATION
Direction-Of-Arrival (DOA) and Frequency-Of-Arrival (FOA) estimation has attracted great attention among researchers in recent years. The ML (Maximum Likelihood) approach and subspace-based...
Huang, Wendong, Zhou, Xin, Lefebvre, Véronique, De Crombrugghe, Benoit
Sox9 is a high-mobility-group domain-containing transcription factor required for chondrocyte differentiation and cartilage formation. We used a yeast two-hybrid method based on Son of Sevenless...
Flagellin of Enteropathogenic Escherichia coli Stimulates Interleukin-8 Production in T84 Cells
Zhou, Xin, Girón, Jorge A., Torres, Alfredo G., Crawford, J. Adam, Negrete, Erasmo, Vogel, Stefanie N., ...
The type III secretion system (TTSS) of enteropathogenic Escherichia coli (EPEC) has been associated with the ability of these bacteria to induce secretion of proinflammatory cytokines, including...
Death Pathways Activated in CaCo-2 Cells by Clostridium perfringens Enterotoxin
Chakrabarti, Ganes, Zhou, Xin, McClane, Bruce A.
Clostridium perfringens enterotoxin (CPE), a 35-kDa polypeptide, induces cytotoxic effects in the enterocyte-like CaCo-2 cell culture model. To identify the mammalian cell death pathway(s) mediating...
Induction of Interleukin-8 in T84 Cells by Vibrio cholerae
Zhou, Xin, Gao, Da Q., Michalski, Jane, Benitez, Jorge A., Kaper, James B.
The induction of interleukin-8 (IL-8) in vitro has been suggested to correlate with the reactogenicity of Vibrio cholerae vaccine candidates. V. cholerae vaccine candidate 638, a hemagglutinin...
Transcriptional Responses of Intestinal Epithelial Cells to Infection with Vibrio cholerae
Stokes, Neil R., Zhou, Xin, Meltzer, Stephen J., Kaper, James B.
Vibrio cholerae is a noninvasive enteric bacterium that causes the severe diarrheal disease cholera. Candidate cholera vaccines have been engineered by deleting genes encoding known virulence factors...
Ikeda, Tamako, Nishitsuji, Hironori, Zhou, Xin, Nara, Nobuo, Ohashi, Takashi, Kannagi, Mari, ...
Nuclear import of viral cDNA is a critical step for establishing the proviral state of human immunodeficiency virus type 1 (HIV-1). The contribution of HIV-1 integrase (IN) to the nuclear import of...
Huang, Wendong, Zhou, Xin, Lefebvre, Véronique, De Crombrugghe, Benoit
Sox9 is a high-mobility-group domain-containing transcription factor required for chondrocyte differentiation and cartilage formation. We used a yeast two-hybrid method based on Son of Sevenless...
Flagellin of Enteropathogenic Escherichia coli Stimulates Interleukin-8 Production in T84 Cells
Zhou, Xin, Girón, Jorge A., Torres, Alfredo G., Crawford, J. Adam, Negrete, Erasmo, Vogel, Stefanie N., ...
The type III secretion system (TTSS) of enteropathogenic Escherichia coli (EPEC) has been associated with the ability of these bacteria to induce secretion of proinflammatory cytokines, including...
Death Pathways Activated in CaCo-2 Cells by Clostridium perfringens Enterotoxin
Chakrabarti, Ganes, Zhou, Xin, McClane, Bruce A.
Clostridium perfringens enterotoxin (CPE), a 35-kDa polypeptide, induces cytotoxic effects in the enterocyte-like CaCo-2 cell culture model. To identify the mammalian cell death pathway(s) mediating...
Induction of Interleukin-8 in T84 Cells by Vibrio cholerae
Zhou, Xin, Gao, Da Q., Michalski, Jane, Benitez, Jorge A., Kaper, James B.
The induction of interleukin-8 (IL-8) in vitro has been suggested to correlate with the reactogenicity of Vibrio cholerae vaccine candidates. V. cholerae vaccine candidate 638, a hemagglutinin...
Transcriptional Responses of Intestinal Epithelial Cells to Infection with Vibrio cholerae
Stokes, Neil R., Zhou, Xin, Meltzer, Stephen J., Kaper, James B.
Vibrio cholerae is a noninvasive enteric bacterium that causes the severe diarrheal disease cholera. Candidate cholera vaccines have been engineered by deleting genes encoding known virulence factors...
Ikeda, Tamako, Nishitsuji, Hironori, Zhou, Xin, Nara, Nobuo, Ohashi, Takashi, Kannagi, Mari, ...
Nuclear import of viral cDNA is a critical step for establishing the proviral state of human immunodeficiency virus type 1 (HIV-1). The contribution of HIV-1 integrase (IN) to the nuclear import of...
Life Cycle Assessment (LCA) of Chinese energy chains for Shandong electricity scenarios
Roberto Dones, Xin Zhou, Chunxiu Tian
The Life Cycle Assessment (LCA) performed for the China Energy Technology Program (CETP) has established streamlined environmental inventories of coal, nuclear, natural gas, and wind energy systems...
Life Cycle Assessment (LCA) of Chinese energy chains for Shandong electricity scenarios
Roberto Dones, Xin Zhou, Chunxiu Tian
The Life Cycle Assessment (LCA) performed for the China Energy Technology Program (CETP) has established streamlined environmental inventories of coal, nuclear, natural gas, and wind energy systems...
RTE1 Is a Golgi-Associated and ETR1-Dependent Negative Regulator of Ethylene Responses1[C][W]
Zhou, Xin, Liu, Qian, Xie, Fang, Wen, Chi-Kuang
Arabidopsis (Arabidopsis thaliana) RTE1 encodes a membrane protein and negatively regulates ethylene responses. Genetic and transformation studies suggest that the function of the wild-type RTE1 is...
Two novel myocilin mutations in a Chinese family with primary open-angle glaucoma
Xie, Xiaobing, Zhou, Xin, Qu, Xiying, Wen, Jing, Tian, Yanli, Zheng, Fang
Data acquisition system for chemical kinetic studies
Zhu, Yu-zhen, Zhou, Xin, Zang, Xiang-sheng
A microcomputer-interfaced data acquisition system for chemical kinetics (interfacing with laboratory analogue instruments) has been developed. Analogue signals from instruments used in kinetics...
Inhibition of Wnt signaling by the osteoblast-specific transcription factor Osterix
Zhang, Chi, Cho, Kyucheol, Huang, Yehong, Lyons, Jon P., Zhou, Xin, Sinha, Krishna, ...
The recent identification of the genes responsible for several human genetic diseases affecting bone homeostasis and the characterization of mouse models for these diseases indicated that canonical...
Li, He, Ma, Xiao-qing, Ye, Fan, Zhang, Jing, Zhou, Xin, Wang, Zhi-hong, ...
Evidence suggests that the deterioration of communication between the sympathetic nervous system and cardiovascular system always accompanies the aging of human and animals. Cardiac sympathetic...
Peng, Zhi-yu, Zhou, Xin, Li, Linchuan, Yu, Xiangchun, Li, Hongjiang, Jiang, Zhiqiang, ...
Plant hormones are small organic molecules that influence almost every aspect of plant growth and development. Genetic and molecular studies have revealed a large number of genes that are involved in...
Harrison, Lisa M., Rallabhandi, Prasad, Michalski, Jane, Zhou, Xin, Steyert, Susan R., Vogel, Stefanie N., ...
Vaccine reactogenicity has complicated the development of safe and effective live, oral cholera vaccines. Δctx Vibrio cholerae mutants have been shown to induce inflammatory diarrhea in volunteers...
Zhou, Xin, Yuan, Youxi, Yang, Yong, Rutzke, Michael, Thannhauser, Theodore W., Kochian, Leon V., ...
Selenium (Se) is an essential micronutrient for animals and humans but becomes toxic at high dosage. Biologically based Se volatilization, which converts Se into volatile compounds, provides an...
Hyperpolarized xenon NMR and MRI signal amplification by gas extraction
Zhou, Xin, Graziani, Dominic, Pines, Alexander
A method is reported for enhancing the sensitivity of NMR of dissolved xenon by detecting the signal after extraction to the gas phase. We demonstrate hyperpolarized xenon signal amplification by gas...