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Search Results: 1 - 10 of 14755 matches for " Yuyang Tang "
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Construction and immunogenicity prediction of Plasmodiumfalciparum CTL epitope minigene vaccine
Yuyang Tang,Heng Wang
Science China Life Sciences , 2001, DOI: 10.1007/BF02879327
Abstract: The minigenes encoding Plasmodiumfalciparum CTL epitopes restricted to human MHC class I molecular HLA-A2 and HLA-B51, which were both at high frequency among Chinese population, were constructed as mono-epitope CTL vaccines named pcDNA3.1/tr and pcDNA3.1/sh. The minigenes of the two epitopes were then tandem linked to form a dimeric CTL epitope minigene recombinant vaccine. After DNA transfection, the epitope minigenes were expressed respectively in two human cell lines, each bearing one MHC class I molecule named CIR/HLA-A2.1 and K562/HLA-B51. The intracellular expression of the CTL epitope minigenes not only enhanced the stability of HLA-A2.1 and HLA-B51 molecules but also increased the assemblage of MHC class I molecules on cell surfaces, which testified the specific process and presentation of those endogenous expressed epitopes. For the cells transfected with the dimeric minigene encoding two tandem linked epitopes, the expression and presentation of each epitope were also detected on cell membranes that bore different MHC class I molecules. It meant that the adjacency of the two CTL epitopes did not interfere with the specific process and presentation of each epitope. Compared with the ordinary CTL studies that inoculated synthesized epitope peptides with peripheral blood cells, this work aimed to process the epitopes directly inside HLA class I allele specific human cells, and thus theoretically imitated the same procedurein vivo. It was also an economical way to predict the immunogenicity of CTL epitopes at an early stage especially in laboratories with limited financial resource.
Cholesterol Depletion Inactivates XMRV and Leads to Viral Envelope Protein Release from Virions: Evidence for Role of Cholesterol in XMRV Infection
Yuyang Tang, Alvin George, Thyneice Taylor, James E. K. Hildreth
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0048013
Abstract: Membrane cholesterol plays an important role in replication of HIV-1 and other retroviruses. Here, we report that the gammaretrovirus XMRV requires cholesterol and lipid rafts for infection and replication. We demonstrate that treatment of XMRV with a low concentration (10 mM) of 2-hydroxypropyl-β-cyclodextrin (2OHpβCD) partially depleted virion-associated cholesterol resulting in complete inactivation of the virus. This effect could not be reversed by adding cholesterol back to treated virions. Further analysis revealed that following cholesterol depletion, virus-associated Env protein was significantly reduced while the virions remained intact and retained core proteins. Increasing concentrations of 2OHpβCD (≥20 mM) resulted in loss of the majority of virion-associated cholesterol, causing disruption of membrane integrity and loss of internal Gag proteins and viral RNA. Depletion of cholesterol from XMRV-infected cells significantly reduced virus release, suggesting that cholesterol and intact lipid rafts are required for the budding process of XMRV. These results suggest that unlike glycoproteins of other retroviruses, the association of XMRV glycoprotein with virions is highly dependent on cholesterol and lipid rafts.
Infection of Female Primary Lower Genital Tract Epithelial Cells after Natural Pseudotyping of HIV-1: Possible Implications for Sexual Transmission of HIV-1
Yuyang Tang, Alvin George, Franklin Nouvet, Stephanie Sweet, Nkiruka Emeagwali, Harry E. Taylor, Glenn Simmons, James E. K. Hildreth
PLOS ONE , 2014, DOI: 10.1371/journal.pone.0101367
Abstract: The global AIDS pandemic continues to expand and in some regions of the world, such as southern Africa, the prevalence of HIV-1 infection exceeds 20%. The devastating spread of the virus in young women in these countries appears disproportional to overall risk of infection. Regions with high prevalence of HIV-1 are often also highly endemic for other pathogenic viruses including HSV, CMV and HTLV. We propose that acquisition by HIV-1 of the envelope glycoproteins of other viruses, in a process we call “natural pseudotyping,” expands the cellular tropism of HIV-1, enabling it to infect female genital epithelial cells directly and thereby dramatically increasing risk of infection during sexual intercourse. In this proof-of-concept study, we demonstrate that when HIV-1 co-infects T cells along with the gammaretrovirus xenotropic murine leukemia virus-related virus (XMRV), progeny HIV-1 particles are produced capable of infecting primary vaginal, ectocervical and endocervical epithelial cells. These cell types are normally resistant to HIV-1 infection. Infection of primary genital cells was neutralized by antisera against the XMRV glycoprotein, confirming that infection was mediated by the XMRV glycoprotein acquired through pseudotyping of HIV. Inhibition by AZT showed that active replication of HIV-1 occurred in these cells and ruled out non-specific endocytic uptake of the virus. These results demonstrate that natural pseudotyping can expand the tropism of HIV-1 to include genital epithelial cells and have potential implications for sexual transmission of the virus.
The Best Approximation of the Sinc Function by a Polynomial of Degree with the Square Norm
Qiu Yuyang,Zhu Ling
Journal of Inequalities and Applications , 2010,
Abstract: The polynomial of degree n which is the best approximation of the sinc function on the interval (0, ] with the square norm is considered. By using Lagrange's method of multipliers, we construct the polynomial explicitly. This method is also generalized to the continuous function on the closed interval [a, b]. Numerical examples are given to show the effectiveness.
The Best Approximation of the Sinc Function by a Polynomial of Degree n with the Square Norm
Yuyang Qiu,Ling Zhu
Journal of Inequalities and Applications , 2010, DOI: 10.1155/2010/307892
Nonparametric Bayesian Mixed-effect Model: a Sparse Gaussian Process Approach
Yuyang Wang,Roni Khardon
Computer Science , 2012, DOI: 10.1007/978-3-642-33460-3_51
Abstract: Multi-task learning models using Gaussian processes (GP) have been developed and successfully applied in various applications. The main difficulty with this approach is the computational cost of inference using the union of examples from all tasks. Therefore sparse solutions, that avoid using the entire data directly and instead use a set of informative "representatives" are desirable. The paper investigates this problem for the grouped mixed-effect GP model where each individual response is given by a fixed-effect, taken from one of a set of unknown groups, plus a random individual effect function that captures variations among individuals. Such models have been widely used in previous work but no sparse solutions have been developed. The paper presents the first sparse solution for such problems, showing how the sparse approximation can be obtained by maximizing a variational lower bound on the marginal likelihood, generalizing ideas from single-task Gaussian processes to handle the mixed-effect model as well as grouping. Experiments using artificial and real data validate the approach showing that it can recover the performance of inference with the full sample, that it outperforms baseline methods, and that it outperforms state of the art sparse solutions for other multi-task GP formulations.
Research on the Drunk Driving Traffic Accidents Based on Logistic Regression Model  [PDF]
Shaohua Wang, Yanyan Chen, Jianling Huang, Yuyang Zhou, Yao Lu
Open Journal of Applied Sciences (OJAppS) , 2018, DOI: 10.4236/ojapps.2018.811039
Abstract: Most of the current studies on drunk driving accidents focus on law making and public education. However, especially in China, there is less statistical analysis on the severity of drunk driving accidents between driving under the influence of alcohol (DUI) and driving while intoxicated (DWI). 3368 drunk driving related crashes were collected from the blood-alcohol test report in a city of China at 2012 and 2013. After data pre-processing, Chi-square tests were used to analyze the association between different variables and the type of drunk driving. The logistic regression model is conducted to estimate the effect of the variables under DUI and DWI. The results show that Hour of the day, Driver’s age, Driver’s casualties and Accident area have significant correlation with drunk driving. There was a slightly decrease by 0.995 per year with age and a slightly increase by 1.014 with time in the possibility of DWI. DWI is more likely to cause death in traffic accidents (OR = 1.316) than DUI. Driver’s deaths (OR = 2.346) is more likely to happen than the injuries (OR = 1.910) under DWI cases. These findings show that more attention should be paid to strengthen controls on the DWI. It also can provide important basis for accident prevent, traffic law enforcement and traffic management.
Nonparametric Bayesian Estimation of Periodic Functions
Yuyang Wang,Roni Khardon,Pavlos Protopapas
Physics , 2011, DOI: 10.1088/0004-637X/756/1/67
Abstract: Many real world problems exhibit patterns that have periodic behavior. For example, in astrophysics, periodic variable stars play a pivotal role in understanding our universe. An important step when analyzing data from such processes is the problem of identifying the period: estimating the period of a periodic function based on noisy observations made at irregularly spaced time points. This problem is still a difficult challenge despite extensive study in different disciplines. The paper makes several contributions toward solving this problem. First, we present a nonparametric Bayesian model for period finding, based on Gaussian Processes (GP), that does not make strong assumptions on the shape of the periodic function. As our experiments demonstrate, the new model leads to significantly better results in period estimation when the target function is non-sinusoidal. Second, we develop a new algorithm for parameter optimization for GP which is useful when the likelihood function is very sensitive to the setting of the hyper-parameters with numerous local minima, as in the case of period estimation. The algorithm combines gradient optimization with grid search and incorporates several mechanisms to overcome the high complexity of inference with GP. Third, we develop a novel approach for using domain knowledge, in the form of a probabilistic generative model, and incorporate it into the period estimation algorithm. Experimental results on astrophysics data validate our approach showing significant improvement over the state of the art in this domain.
Infinite Shift-invariant Grouped Multi-task Learning for Gaussian Processes
Yuyang Wang,Roni Khardon,Pavlos Protopapas
Physics , 2012,
Abstract: Multi-task learning leverages shared information among data sets to improve the learning performance of individual tasks. The paper applies this framework for data where each task is a phase-shifted periodic time series. In particular, we develop a novel Bayesian nonparametric model capturing a mixture of Gaussian processes where each task is a sum of a group-specific function and a component capturing individual variation, in addition to each task being phase shifted. We develop an efficient \textsc{em} algorithm to learn the parameters of the model. As a special case we obtain the Gaussian mixture model and \textsc{em} algorithm for phased-shifted periodic time series. Furthermore, we extend the proposed model by using a Dirichlet Process prior and thereby leading to an infinite mixture model that is capable of doing automatic model selection. A Variational Bayesian approach is developed for inference in this model. Experiments in regression, classification and class discovery demonstrate the performance of the proposed models using both synthetic data and real-world time series data from astrophysics. Our methods are particularly useful when the time series are sparsely and non-synchronously sampled.
HIV-1 Populations in Semen Arise through Multiple Mechanisms
Jeffrey A. Anderson equal contributor,Li-Hua Ping equal contributor,Oliver Dibben,Cassandra B. Jabara,Leslie Arney,Laura Kincer,Yuyang Tang,Marcia Hobbs,Irving Hoffman,Peter Kazembe,Corbin D. Jones,Persephone Borrow,Susan Fiscus,Myron S. Cohen,Ronald Swanstrom ,and the Center for HIV/AIDS Vaccine Immunology
PLOS Pathogens , 2010, DOI: 10.1371/journal.ppat.1001053
Abstract: HIV-1 is present in anatomical compartments and bodily fluids. Most transmissions occur through sexual acts, making virus in semen the proximal source in male donors. We find three distinct relationships in comparing viral RNA populations between blood and semen in men with chronic HIV-1 infection, and we propose that the viral populations in semen arise by multiple mechanisms including: direct import of virus, oligoclonal amplification within the seminal tract, or compartmentalization. In addition, we find significant enrichment of six out of nineteen cytokines and chemokines in semen of both HIV-infected and uninfected men, and another seven further enriched in infected individuals. The enrichment of cytokines involved in innate immunity in the seminal tract, complemented with chemokines in infected men, creates an environment conducive to T cell activation and viral replication. These studies define different relationships between virus in blood and semen that can significantly alter the composition of the viral population at the source that is most proximal to the transmitted virus.
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