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The Single Amino Acid Polymorphism database (SAAPdb) is a new resource for the analysis and visualization of the structural effects of mutations. Our analytical approach is to map single nucleotide polymorphisms (SNPs) and pathogenic deviations (PDs) to protein structural data held within the Protein Data Bank. By mapping mutations onto protein structures,(More)
In HIV-1 infection, a population of latently infected cells facilitates viral persistence despite antiretroviral therapy (ART). With the aim of identifying individuals in whom ART might induce a period of viraemic control on stopping therapy, we hypothesised that quantification of the pool of latently infected cells in primary HIV-1 infection (PHI) would(More)
Learning classifier systems traditionally use genetic algorithms to facilitate rule discovery, where rule fitness is payoff based. Current research has shifted to the use of accuracy-based fitness. This paper re-examines the use of a particular payoff-based learning classifier system--ZCS. By using simple difference equation models of ZCS, we show that this(More)
Seminomas and dysgerminomas are epizootic in softshell clams, Mya arenaria, from three Maine estuaries contaminated with herbicides. The first epizootic was discovered in 22% of clams collected as Searsport near Long Cove Brook and three culverts that conveyed heating oil and jet fuel spilled from a tank farm in 1971. Data from subsequent epizootiological(More)
HLA class I polymorphism has a major influence on adult HIV disease progression. An important mechanism mediating this effect is the impact on viral replicative capacity (VRC) of the escape mutations selected in response to HLA-restricted CD8+ T-cell responses. Factors that contribute to slow progression in pediatric HIV infection are less well understood.(More)
Pseudomonas aeruginosa is a genetically complex bacterium which can adopt and switch between a free-living or biofilm lifestyle, a versatility that enables it to thrive in many different environments and contributes to its success as a human pathogen. Transcriptomes derived from growth states relevant to the lifestyle of P. aeruginosa were clustered using(More)
Droplet Digital PCR (ddPCR) represents a new and alternative platform to conventional quantitative-PCR (qPCR) for the quantitation of DNA templates. However, the proposed improvement in sensitivity and reproducibility offered by ddPCR is not yet fully proven, partly because the delineation between positive and negative responses is not always clear. Data(More)
The use and benefits of self-adaptive mutation operators are well known within evolutionary computing. In this paper, we begin by examining the use of self-adaptive mutation in learning classifier systems with the aim of improving their performance as controllers for autonomous mobile robots. We implement the operator in a zeroth level classifier system,(More)
Disease-free infection in HIV-infected adults is associated with human leukocyte antigen-mediated suppression of viremia, whereas in the sooty mangabey and other healthy natural hosts of simian immunodeficiency virus (SIV), viral replication continues unabated. To better understand factors preventing HIV disease, we investigated pediatric infection, where(More)