Parameter Synthesis for Parametric Interval Markov Chains

AELOS_HCERES2020, STR_HCERES2020Interval Markov Chains (IMCs) are the base of a classic probabilistic specification theory introduced by Larsen and Jonsson in 1991. They are also a popular abstraction for probabilistic systems. In this paper we study parameter synthesis for a parametric extension of Interval Markov Chains in which the endpoints of intervals may be replaced with parameters. In particular, we propose constructions for the synthesis of all parameter values ensuring several properties such as consistency and consistent reachability in both the existential and universal settings with respect to implementations. We also discuss how our constructions can be modified in order to synthesise all parameter values ensuring other typical properties

Methodological optimization and standardization of the metabarcoding of insects gut microbiome

Metabarcoding analysis of microbiota could help understand how Orthopteran species cope with challenges associated with environmental changes. Since microbial symbionts have a mutually beneficial relationship with its host and play important roles in the immune and physiological systems, they likely impact its ecology and evolution (i.e. plant range, life history, behaviour). In addition, the analysis of the complex pathogenic communities associated with locusts could be useful to discover unexplored pathogens and develop future research on biological control innovation. Yet, current knowledge of Orthopteran-associated microbial communities is limited. This is partly because recognizing cryptic, diverse, and numerous microorganisms hosted by insects is a difficult task. Despite the design of standard genes for their identification and the latest advances in high throughput sequencing, difficulties persist when we look at the microbiota of insects, including Orthopterans. (1) DNA purification is an essential step in all cultivationindependent approaches to characterize microbial diversity. Indeed, the microbial composition is mainly biased by the efficiency of cell lysis. (2) Another critical step for unbiased representation analysis and high taxonomic resolution is the choice of amplicon and primers. In particular, we showed that Enterobacteriacea, common in insects, were poorly resolved with some of currently used amplicons. (3) Moreover, in the case of phytophagous insects, it is necessary to avoid the amplification of plant remains contained in the digestive tract. In this study, we use (1) three mock community standards that contained equal and logarithmic numbers of eight species (ZymoBIOMICS), and equal numbers of twenty other species (ATCC), and (2) six samplesrepresenting the six main orders of insects (Orthoptera, Diptera, Hemiptera, Coleoptera, Hymenoptera and Lepidoptera). On these dedicated samples, we first statistically evaluate the most commonly used DNA purification kit (Qiagen DNeasy Blood and Tissue), two microorganisms-specific DNA purification kits (ZymoBIOMICS-96 bashing beads and DNeasy UltraClean 96 Microbial Kit) and two homemade procedures (bashing beads and enzymatic cocktails added to Qiagen DNeasy Blood and Tissue). These methods are compared on the basis of DNA yield, DNA shearing, reproducibility, and most importantly representation of microbial diversityin 16S rRNA gene sequences. . Secondly, we are currently evaluating the taxonomic representativity and resolution of different 16S gene primers to avoid plant chloroplast genes amplifications. Second, we evaluate, using in silico analyses, (1) the PCR efficiency (representativity), (2) the taxonomic resolution and (3) the risk to amplify plant chloroplasts of already published primers on various variable regions of the 16S gene (V3, V4, V6, V9) and of the rpoB gene. We then test and validate in vitro the best primer candidates on the dedicated samples

Fate of Pesticides in Soils: Toward an Integrated Approach of Influential Factors

Chapitre 29absen

Formally Tracing Executions From an Analysis Tool Back to a Domain Specific Modeling Language's Operational Semantics

The increasing complexity of software development requires rigorously defined domain specific modelling languages (DSML). Model-driven engineering (MDE) allows users to define their language's syntax in terms of metamodels. Several approaches for defining operational semantics of DSML have also been proposed. These approaches allow, in principle, for model execution and for formal analyses of the DSML. However, most of the time, the executions/analyses are performed via transformations to other languages: code generation, resp. translation to the input language of a model checker. The consequence is that the results (e.g., a program crash log, or a counterexample returned by a model checker) may not be straightforward to interpret by the users of a DSML. In this research report, we propose a formal and operational framework for tracing such results back to the original DSML's syntax and operational semantics.Le besoin en définitions rigoureuses de langages de modélisation métiers (LMM) croît avec la complexité du développement logiciel. L'ingénierie dirigée par les modèles (IDM), permet à des utilisateurs de définir la syntaxe de nouveaux langages à l'aide de metamodèles. Quelques approches proposent également des façons de définir la sémantique opérationnelle de ces langages. Ces approches permettent, en principe, l'exécution des programmes (modèles) et leur analyse formelle. Cependant, la plupart du temps, les analyses sont réalisées à l'aide de transformations de ces modèles vers d'autres langages, pour être exécutés (langages généralistes, type C par exemple) ou vérifiés (langages d'entrées de model checkers, de simulateurs, ...). En conséquence, ces résultats (un log de crash de programme, une exécution contre exemple provenant de la vérification d'une propriété par un model-checker, par exemple) peuvent ne pas être directement compréhensibles par les utilisateurs d'un LMM. Dans ce rapport, nous proposons une méthode formelle et opérationnelle pour exprimer ces exécutions en terme de syntaxe et sémantique du LMM initial

Categorizing chlordecone potential degradation products to explore their environmental fate

EA BIOmE SUPDAT INRAInternational audienceChlordecone (C10Cl10O; CAS number 143-50-0) has been used extensively as an organochlorine insecticide but is nowadays banned and listed on annex A in The Stockholm Convention on Persistent Organic Pollutants (POPs). Although experimental evidences of biodegradation of this compound are scarce, several dechlorination products have been proposed by Dolfing et al. (2012) using Gibbs free energy calculations to explore different potential transformation routes. We here present the results of an in silico classification (TyPol - Typology of Pollutants) of chlordecone transformation products (TPs) based on statistical analyses combining several environmental endpoints and structural molecular descriptors. Starting from the list of putative chlordecone TPs and considering available data on degradation routes of other organochlorine compounds, we used different clustering strategies to explore the potential environmental behaviour of putative chlordecone TPs from the knowledge on their molecular descriptors. The method offers the possibility to focus on TPs present in different classes and to infer their environmental fate. Thus, we have deduced some hypothetical trends for the environmental behaviour of TPs of chlordecone assuming that TPs, which were clustered away from chlordecone, would have different environmental fate and ecotoxicological impact compared to chlordecone. Our findings suggest that mono- and di-hydrochlordecone, which are TPs of chlordecone often found in contaminated soils, may have similar environmental behaviour in terms of persistence