DNAGear: a free software for spa type identification in Staphylococcus aureus

Staphylococcus aureus is both human commensal and an important human pathogen, responsible for community-acquired and nosocomial infections ranging from superficial wound infections to invasive infections, such as osteomyelitis, bacteremia and endocarditis, pneumonia or toxin shock syndrome with a mortality rate up to 40%. S. aureus reveals a high genetic polymorphism and detecting the genotypes is extremely useful to manage and prevent possible outbreaks and to understand the route of infection. One of current and expanded typing method is based on the X region of the spa gene composed of a succession of repeats of 21 to 27 bp. More than 10000 types are known. Extracting the repeats is impossible by hand and needs a dedicated software. Unfortunately the only software on the market is a commercial program from Ridom. Findings This article presents DNAGear, a free and open source software with a user friendly interface written all in Java on top of NetBeans Platform to perform spa typing, detecting new repeats and new spa types and synchronizing automatically the files with the open access database. The installation is easy and the application is platform independent. In fact, the SPA identification is a formal regular expression matching problem and the results are 100% exact. As the program is using Java embedded modules written over string manipulation of well established algorithms, the exactitude of the solution is perfectly established. Conclusions DNAGear is able to identify the types of the S. aureus sequences and detect both new types and repeats. Comparing to manual processing, which is time consuming and error prone, this application saves a lot of time and effort and gives very reliable results. Additionally, the users do not need to prepare the forward-reverse sequences manually, or even by using additional tools. They can simply create them in DNAGear and perform the typing task. In short, researchers who do not have commercial software will benefit a lot from this application.Peer Reviewe

Structural bias in population-based algorithms

Challenging optimisation problems are abundant in all areas of science and industry. Since the 1950s, scientists have responded to this by developing ever-diversifying families of 'black box' optimisation algorithms. The latter are designed to be able to address any optimisation problem, requiring only that the quality of any candidate solution can be calculated via a 'fitness function' specific to the problem. For such algorithms to be successful, at least three properties are required: (i) an effective informed sampling strategy, that guides the generation of new candidates on the basis of the fitnesses and locations of previously visited candidates; (ii) mechanisms to ensure efficiency, so that (for example) the same candidates are not repeatedly visited; and (iii) the absence of structural bias, which, if present, would predispose the algorithm towards limiting its search to specific regions of the solution space. The first two of these properties have been extensively investigated, however the third is little understood and rarely explored. In this article we provide theoretical and empirical analyses that contribute to the understanding of structural bias. In particular, we state and prove a theorem concerning the dynamics of population variance in the case of real-valued search spaces and a 'flat' fitness landscape. This reveals how structural bias can arise and manifest as non-uniform clustering of the population over time. Critically, theory predicts that structural bias is exacerbated with (independently) increasing population size, and increasing problem difficulty. These predictions, supported by our empirical analyses, reveal two previously unrecognised aspects of structural bias that would seem vital for algorithm designers and practitioners. Respectively, (i) increasing the population size, though ostensibly promoting diversity, will magnify any inherent structural bias, and (ii) the effects of structural bias are more apparent when faced with (many classes of) 'difficult' problems. Our theoretical result also contributes to the 'exploitation/exploration' conundrum in optimisation algorithm design, by suggesting that two commonly used approaches to enhancing exploration - increasing the population size, and increasing the disruptiveness of search operators - have quite distinct implications in terms of structural bias

Les pleuro-pneumopathies graves à streptocoque b hémolytique du groupe A en réanimation (à propos de 3 cas)

MONTPELLIER-BU Médecine UPM (341722108) / SudocPARIS-BIUM (751062103) / SudocMONTPELLIER-BU Médecine (341722104) / SudocSudocFranceF

Staphylococcus aureus dans un service de réanimation (étude génétique, phénotypique et épidémiologique)

MONTPELLIER-BU Médecine UPM (341722108) / SudocPARIS-BIUP (751062107) / SudocMONTPELLIER-BU Médecine (341722104) / SudocSudocFranceF

Devenir et facteurs pronostiques des vascularites systémiques en réanimation (à propos de 31 cas)

MONTPELLIER-BU Médecine UPM (341722108) / SudocMONTPELLIER-BU Médecine (341722104) / SudocPARIS-BIUM (751062103) / SudocSudocFranceF

Légionellose avec syndrome de détresse respiratoire aiguë (à propos de huit cas)

MONTPELLIER-BU Médecine UPM (341722108) / SudocPARIS-BIUM (751062103) / SudocMONTPELLIER-BU Médecine (341722104) / SudocSudocFranceF

Épidémiologie et facteurs pronostiques des patients séropositifs pour le VIH hospitalisés en réanimation à l'ère des trithérapies incluant les antiprotéases (étude rétrospective de 103 cas)

MONTPELLIER-BU Médecine UPM (341722108) / SudocMONTPELLIER-BU Médecine (341722104) / SudocPARIS-BIUM (751062103) / SudocSudocFranceF

Ventilation non-invasive initiale ou exclusive au cours des pneumopathies aiguës (une étude rétrospective sur 3 ans en réanimation médicale)

MONTPELLIER-BU Médecine UPM (341722108) / SudocPARIS-BIUM (751062103) / SudocMONTPELLIER-BU Médecine (341722104) / SudocSudocFranceF

Abcès cérébral à rhodococcus equi en l'absence d'immunodépression (à propos d'un cas)

MONTPELLIER-BU Médecine (341722104) / SudocMONTPELLIER-BU Médecine UPM (341722108) / SudocPARIS-BIUM (751062103) / SudocSudocFranceF