Leprosy in French Polynesia

International audienc

Pattern Matching for Arc-Annotated Sequences

A study of pattern matching for arc-annotated sequences is started. An O(nm) time algorithm is given to determine whether a length m sequence with nested arc annotations is an arc-preserving subsequence of a length n sequence with nested arc annotations, called APS(nested,nested). Arc-annotated sequences and, in particular, those with nested arc structure are motivated by applications in RNA structure comparison. Our algorithm can be used to accelerate a recent fixedparameter algorithm for LAPCS(nested,nested) and generalizes results for ordered tree inclusion problems. In particular, the presented dynamic programming methodology implies a quadratic time algorithm for an open problem posed by Vialette

Development and validation of experimental protocols for use of cardinal models for the prediction of microorganisms growth in food products

An experimental protocol to validate secondary-model application to foods was suggested. Escherichia coli, Listeria monocytogenes, Bacillus cereus, Clostridium perfringens, and Salmonella were observed in various food categories, such as meat, dairy, egg, or seafood products. The secondary model validated in this study was based on the gamma concept, in which the environmental factors temperature, pH, and water activity (aw) were introduced as individual terms with microbe-dependent parameters, and the effect of foodstuffs on the growth rates of these species was described with a food- and microbe-dependent parameter. This food-oriented approach was carried out by challenge testing, generally at 15 and 10°C for L. monocytogenes, E. coli, B. cereus, and Salmonella and at 25 and 20°C for C. perfringens. About 222 kinetics in foods were generated. The results were compared to simulations generated by existing software, such as PMP. The bias factor was also calculated. The methodology to obtain a food-dependent parameter (fitting step) and therefore to compare results given by models with new independent data (validation step) is discussed in regard to its food safety application. The proposed methods were used within the French national program of predictive microbiology, Sym′Previus, to include challenge test results in the database and to obtain predictive models designed for microbial growth in food products

What makes the arc-preserving subsequence problem hard ? Trans

Abstract. In molecular biology, RNA structure comparison and motif search are of great interest for solving major problems such as phylogeny reconstruction, prediction of molecule folding and identification of common functions. RNA structures can be represented by arc-annotated sequences (primary sequence along with arc annotations), and this paper mainly focuses on the so-called arc-preserving subsequence (APS) problem where, given two arc-annotated sequences (S, P) and (T, Q), we are asking whether (T, Q) can be obtained from (S, P) by deleting some of its bases (together with their incident arcs, if any). In previous studies, this problem has been naturally divided into subproblems reflecting the intrinsic complexity of the arc structures. We show that APS(Crossing, Plain) is NP-complete, thereby answering an open problem posed in [11]. Furthermore, to get more insight into where the actual border between the polynomial and the NP-complete cases lies, we refine the classical subproblems of the APS problem in much the same way as in [19] and prove that both APS({⊏, ≬}, ∅) and APS({<, ≬}, ∅) are NPcomplete. We end this paper by giving some new positive results, namely showing that APS({≬}, ∅) and APS({≬},{≬}) are polynomial time solvable

Approximation of RNA Multiple Structural Alignment

International audienc

Observatoire Régional du Pneumocoque en région Centre : Évolution de la résistance aux antibiotiques en 2013

National audienc