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We describe a Bayesian method based on Markov chain simulation to study the phylogenetic relationship in a group of DNA sequences. Under simple models of mu-tational events, our method produces a Markov chain whose stationary distribution is the conditional distribution of the phylogeny given the observed sequences. Our algorithm strikes a reasonable(More)
BACKGROUND Although behavioral risk factors are strongly associated with urinary tract infection (UTI) risk, the role of genetics in acquiring this disease is poorly understood. METHODOLOGY/PRINCIPAL FINDINGS To test the hypothesis that polymorphisms in Toll-like receptor (TLR) pathway genes are associated with susceptibility to UTIs, we conducted a(More)
Microarrays are used increasingly to identify genes that are truly differentially expressed in tissues under different conditions. Planning such studies requires establishing a sample size that will ensure adequate statistical power. For microarray analyses, false discovery rate (FDR) is considered to be an appropriate error measure. Several FDR-controlling(More)
BACKGROUND The Thai Phase III Trial of ALVAC-HIV and AIDSVAX B/E showed an estimated vaccine efficacy (VE) of 31% to prevent acquisition of human immunodeficiency virus (HIV). Here we evaluated the effect of vaccination on disease progression after infection. METHODS CD4(+) T-cell counts and HIV viral load (VL) were measured serially. The primary analysis(More)
Acinetobacter calcoaceticus PHEA-2 utilizes phenol as its sole carbon and energy source and has a multi-component phenol hydroxylase-encoding gene operon (mphKLMNOP) for phenol degradation. Two additional genes, mphR and mphX, were found upstream and downstream of mphKLMNOP, respectively. The mphR gene encodes a XylR/DmpR-type regulator-like protein and is(More)
Although Toll-like receptors (TLRs) are critical mediators of the immune response to pathogens, the influence of polymorphisms in this gene family on human susceptibility to infection is poorly understood. We demonstrated recently that TLR5 recognizes flagellin, a potent inflammatory stimulus present in the flagellar structure of many bacteria. Here, we(More)
The innate antiviral factor TRIM5alpha restricts the replication of some retroviruses through its interaction with the viral capsid protein, leading to abortive infection. While overexpression of human TRIM5alpha results in modest restriction of human immunodeficiency virus type 1 (HIV-1), this inhibition is insufficient to block productive infection of(More)
Estimating haplotype frequencies becomes increasingly important in the mapping of complex disease genes, as millions of single nucleotide polymorphisms (SNPs) are being identified and genotyped. When genotypes at multiple SNP loci are gathered from unrelated individuals, haplotype frequencies can be accurately estimated using expectation-maximization (EM)(More)
Nested PCR is considered a sensitive and specific method for detecting malaria parasites and is especially useful in epidemiological surveys. However, the preparation of DNA templates for PCR is often time-consuming and costly. A simplified PCR method was developed to directly use a small blood filter paper square (2 × 2 mm) as the DNA template after(More)
In this letter, a mutated ant colony optimization (MACO) cognitive radio engine is proposed, and it is the first time to apply ACO algorithm to this problem. The cognitive radio is a promising technology nowadays to alleviate the apparent scarcity of available radio spectrum, and the cognitive radio engine determines the optimal radio transmission(More)