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Search Results: 1 - 10 of 51582 matches for " Joyce Xiuweu-Xu Gu "
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CGI: Java Software for Mapping and Visualizing Data from Array-based Comparative Genomic Hybridization and Expression Profiling
Joyce Xiuweu-Xu Gu,Michael Yang Wei,Pulivarthi H. Rao,Ching C. Lau
Gene Regulation and Systems Biology , 2007,
Abstract: With the increasing application of various genomic technologies in biomedical research, there is a need to integrate these data to correlate candidate genes/regions that are identified by different genomic platforms. Although there are tools that can analyze data from individual platforms, essential software for integration of genomic data is still lacking. Here, we present a novel Java-based program called CGI (Cytogenetics-Genomics Integrator) that matches the BAC clones from array-based comparative genomic hybridization (aCGH) to genes from RNA expression profiling datasets. The matching is computed via a fast, backend MySQL database containing UCSC Genome Browser annotations. This program also provides an easy-to-use graphical user interface for visualizing and summarizing the correlation of DNA copy number changes and RNA expression patterns from a set of experiments. In addition, CGI uses a Java applet to display the copy number values of a specifi c BAC clone in aCGH experiments side by side with the expression levels of genes that are mapped back to that BAC clone from the microarray experiments. The CGI program is built on top of extensible, reusable graphic components specifically designed for biologists. It is cross-platform compatible and the source code is freely available under the General Public License.
Second Harmonic Generation Using an All-Fiber Q-Switched Yb-Doped Fiber Laser and MgO:c-PPLN
Yi Gan,Xijia Gu,Joyce Y. C. Koo,Wanguo Liang,Chang-qing Xu
Advances in OptoElectronics , 2008, DOI: 10.1155/2008/956908
Abstract: We have experimentally demonstrated an efficient all-fiber passively Q-switched Yb-doped fiber laser with Samarium doped fiber as a saturable absorber. Average output power of 3.4 W at a repetition rate of 250 kHz and a pulse width of 1.1 microseconds was obtained at a pump power of 9.0 W. By using this fiber laser system and an MgO-doped congruent periodically poled lithium niobate (MgO:c-PPLN), second harmonic generation (SHG) output at 532 nm was achieved at room temperature. The conversion efficiency is around 4.2% which agrees well with the theoretical simulation.
The Symbolic OBDD Algorithm for Finding Optimal Semi-matching in Bipartite Graphs  [PDF]
Tianlong Gu, Liang Chang, Zhoubo Xu
Communications and Network (CN) , 2011, DOI: 10.4236/cn.2011.32009
Abstract: The optimal semi-matching problem is one relaxing form of the maximum cardinality matching problems in bipartite graphs, and finds its applications in load balancing. Ordered binary decision diagram (OBDD) is a canonical form to represent and manipulate Boolean functions efficiently. OBDD-based symbolic algorithms appear to give improved results for large-scale combinatorial optimization problems by searching nodes and edges implicitly. We present novel symbolic OBDD formulation and algorithm for the optimal semi-matching problem in bipartite graphs. The symbolic algorithm is initialized by heuristic searching initial matching and then iterates through generating residual network, building layered network, backward traversing node-disjoint augmenting paths, and updating semi-matching. It does not require explicit enumeration of the nodes and edges, and therefore can handle many complex executions in each step. Our simulations show that symbolic algorithm has better performance, especially on dense and large graphs.
A Novel Symbolic Algorithm for Maximum Weighted Matching in Bipartite Graphs  [PDF]
Tianlong Gu, Liang Chang, Zhoubo Xu
Int'l J. of Communications, Network and System Sciences (IJCNS) , 2011, DOI: 10.4236/ijcns.2011.42014
Abstract: The maximum weighted matching problem in bipartite graphs is one of the classic combinatorial optimization problems, and arises in many different applications. Ordered binary decision diagram (OBDD) or algebraic decision diagram (ADD) or variants thereof provides canonical forms to represent and manipulate Boolean functions and pseudo-Boolean functions efficiently. ADD and OBDD-based symbolic algorithms give improved results for large-scale combinatorial optimization problems by searching nodes and edges implicitly. We present novel symbolic ADD formulation and algorithm for maximum weighted matching in bipartite graphs. The symbolic algorithm implements the Hungarian algorithm in the context of ADD and OBDD formulation and manipulations. It begins by setting feasible labelings of nodes and then iterates through a sequence of phases. Each phase is divided into two stages. The first stage is building equality bipartite graphs, and the second one is finding maximum cardinality matching in equality bipartite graph. The second stage iterates through the following steps: greedily searching initial matching, building layered network, backward traversing node-disjoint augmenting paths, updating cardinality matching and building residual network. The symbolic algorithm does not require explicit enumeration of the nodes and edges, and therefore can handle many complex executions in each step. Simulation experiments indicate that symbolic algorithm is competitive with traditional algorithms.
LSSVM Combined with SPA Applied to Near-Infrared Quantitative Determination of the Octane in Fuel Petrol Samples  [PDF]
Lili Xu, Jie Gu, Huazhou Chen, Jiangbei Wen, Gaili Xu
Open Journal of Applied Sciences (OJAppS) , 2018, DOI: 10.4236/ojapps.2018.89032
Abstract: Least square support vector machine (LSSVM) combined with successive projection algorithm (SPA) method was applied for?near-infrared (NIR)quantitative determination of the octane number in fuel petrol. The NIR spectra of 87 fuel petrol samples were?scanned?for model establishment and optimization. First order derivative Savitzky-Golay smoother?(1st-d’SG) wasutilized to improve theNIR predictive ability. Its pretreatment effect was compared with the raw data.?SPA was?applied for the extraction of informative wavelengths. Considering the linear and non-linear?training mechanism,?LSSVM?regression was employed to establish calibration
Effect of Oxidative Damage Due to Excessive Protein Ingestion on Pancreas Function in Mice
Chunmei Gu,Huiyong Xu
International Journal of Molecular Sciences , 2010, DOI: 10.3390/ijms11114591
Abstract: The present study was undertaken to evaluate the effect of oxidative damage due to excessive protein diet on pancreas function in mice. For this purpose, thirty male (C57BL/6J) mice were randomly divided into three groups and fed on different diets as follows: group 1 was fed on a normal diet, group 2 was fed on an excessive protein diet and group 3 was fed on an excessive protein diet supplemented with 0.06 g/kg cysteamine. Each group was fed for 2 weeks, and then pancreas samples were collected to examine oxidative and antioxidant parameters and pancreas function. The results showed that ingestion of an excessive protein diet markedly increased contents of malondialdehyde (MDA) and decreased T-AOC and activities of antioxidants SOD and GSH-Px, compared with a normal diet (P < 0.05). Pancreas weight and concentration of protein, DNA and RNA were significantly higher (P < 0.05), digestive enzyme activities were significantly lower and levels of somatostatin and insulin were higher in mice fed with an excessive protein diet than those fed with a normal protein diet. In the group fed with excessive protein diet supplemented with cysteamine, oxidative stress was mitigated and pancreas function was improved. These data demonstrate that excessive protein ingestion could increase oxidative damage of free radicals on pancreas function through destroying the balance of oxidants and antioxidants.
Extensive Design for Attack's Recognition and Resistance of Survivable Network
Hui Xu,Xiang Gu
Journal of Networks , 2012, DOI: 10.4304/jnw.7.2.222-228
Abstract: Extentics is a new discipline that studies the methods for dealing with contradictory problems. This paper gives a solution of attack defense of survivable network based on this theory. The basic knowledge of extension theory is introduced and the inspiration from it to our problem is illustrated. The contradictory characteristic of survivability of borderless network is explained. The extension model and algorithms of recognition and resistance of attacks is presented. The definitions of element, including message matter-element, defense affair-element, node relation-element and inform mixture-element, are given. The dependent function based on lateral distance with the most advantage point occurs in the left common endpoint, is constructed to solve the problem and its properties are discussed. Finally, an application of worm’s warning by this method is illustrated.
Superconductivity in a two-dimensional superconductor with Rashba and Dresselhaus spin-orbit couplings
Xu Yan,Qiang Gu
Physics , 2014, DOI: 10.1016/j.ssc.2014.02.013
Abstract: We present a general model with both Rashba and Dresselhaus spin-orbit couplings to describe a two-dimensional noncentrosymmetric superconductor. The combined effects of the two spin-orbit couplings on superconductivity are investigated in the framework of mean-field theory. We find that the Rashba and Dresselhaus spin-orbit couplings result in similar effects on superconductivity if they are present solely in the system. Mixing of spin-singlet and triplet pairings in electron band is induced under the assumption that each quasiparticle band is p-wave paired. If the two types of spin-orbit couplings appear jointly, both the singlet and triplet pairings are weakened and decreased down to their minimum values in the equal-Rashba-Dresselhaus case.
Spontaneous separation of two-component Fermi gases in a double-well trap
Junjun Xu,Qiang Gu
Physics , 2011, DOI: 10.1209/0295-5075/94/60001
Abstract: The two-component Fermi gas in a double-well trap is studied using the density functional theory and the density profile of each component is calculated within the Thomas-Fermi approximation. We show that the two components are spatially separate in the two wells once the repulsive interaction exceeds the Stoner point, signaling the occurrence of the ferromagnetic transition. Therefore, the double-well trap helps to explore itinerant ferromagnetism in atomic Fermi gases, since the spontaneous separation can be examined by measuring component populations in one well.
Berezinskii-Kosterlitz-Thouless transition of two-dimensional Bose gases in a synthetic magnetic field
Junjun Xu,Qiang Gu
Physics , 2011, DOI: 10.1103/PhysRevA.85.043608
Abstract: We study the Berezinskii-Kosterlitz-Thouless transition of two-dimensional Bose gases in a synthetic magnetic field using the standard Metropolis Monte Carlo method. The system is described by the frustrated XY model and the critical temperature is calculated though the absence of central peak of the wave function in momentum space, which can be directly measured by the time-of-flight absorbing imaging in cold atoms experiments. The results of our work show agreement with former studies on superconducting Josephson arrays.
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