Finding Optimal Pairs of Patterns

We consider the problem of finding the optimal pair of string patterns for discriminating between two sets of strings, i.e. finding the pair of patterns that is best with respect to some appropriate scoring function that gives higher scores to pattern pairs which occur more in the strings of one set, but less in the other. We present an O(N²) time algorithm for finding the optimal pair of substring patterns, where N is the total length of the strings. The algorithm looks for all possible Boolean combination of the patterns, e.g. patterns of the form p ∧ ¬q, which indicates that the pattern pair is considered to match a given string s, if p occurs in s, AND q does NOT occur in s. The same algorithm can be applied to a variant of the problem where we are given a single set of sequences along with a numeric attribute assigned to each sequence, and the problem is to find the optimal pattern pair whose occurrence in the sequences is correlated with this numeric attribute. An e#cient implementation based on suffix arrays is presented, and the algorithm is applied to several nucleotide sequence datasets of moderate size, combined with microarray gene expression data, aiming to find regulatory elements that cooperate, complement, or compete with each other in enhancing and/or silencing certain genomic functions

Human immunodeficiency virus continuum of care in 11 european union countries at the end of 2016 overall and by key population: Have we made progress?

Background. High uptake of antiretroviral treatment (ART) is essential to reduce human immunodeficiency virus (HIV) transmission and related mortality; however, gaps in care exist. We aimed to construct the continuum of HIV care (CoC) in 2016 in 11 European Union (EU) countries, overall and by key population and sex. To estimate progress toward the Joint United Nations Programme on HIV/AIDS (UNAIDS) 90-90-90 target, we compared 2016 to 2013 estimates for the same countries, representing 73% of the population in the region. Methods. A CoC with the following 4 stages was constructed: number of people living with HIV (PLHIV); proportion of PLHIV diagnosed; proportion of those diagnosed who ever initiated ART; and proportion of those ever treated who achieved viral suppression at their last visit. Results. We estimated that 87% of PLHIV were diagnosed; 92% of those diagnosed had ever initiated ART; and 91% of those ever on ART, or 73% of all PLHIV, were virally suppressed. Corresponding figures for men having sex with men were: 86%, 93%, 93%, 74%; for people who inject drugs: 94%, 88%, 85%, 70%; and for heterosexuals: 86%, 92%, 91%, 72%. The proportion suppressed of all PLHIV ranged from 59% to 86% across countries. Conclusions. The EU is close to the 90-90-90 target and achieved the UNAIDS target of 73% of all PLHIV virally suppressed, significant progress since 2013 when 60% of all PLHIV were virally suppressed. Strengthening of testing programs and treatment support, along with prevention interventions, are needed to achieve HIV epidemic control