The use of external fixator in the management of gunshot related open limb fractures

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Encoding Synchronous Interactions Using Labelled Petri Nets

International audienceWe present an encoding of (bound) CSP processes with replication into Petri nets with labelled transitions. Through the encoding, the firing semantics of Petri nets models the standard operational semantics of CSP processes, which is both preserved and reflected. This correspondence allows for describing by net semantics the standard CSP observational equivalences. Since the encoding is modular with respect to process syntax, the paper puts on a firm ground the technology transfer between the two formalisms, e.g. recasting into the CSP framework well-established results like decidability of coverability for nets. This work complements previous results concerning the encoding of asynchronous interactions, thus witnessing the expressiveness of (open) labelled nets in modelling process calculi with alternative communication patterns

Dependencies and Simultaneity in Membrane Systems

Membrane system computations proceed in a synchronous fashion: at each step all the applicable rules are actually applied. Hence each step depends on the previous one. This coarse view can be refined by looking at the dependencies among rule occurrences, by recording, for an object, which was the a rule that produced it and subsequently (in a later step), which was the a rule that consumed it. In this paper we propose a way to look also at the other main ingredient in membrane system computations, namely the simultaneity in the rule applications. This is achieved using zero-safe nets that allows to synchronize transitions, i.e., rule occurrences. Zero-safe nets can be unfolded into occurrence nets in a classical way, and to this unfolding an event structure can be associated. The capability of capturing simultaneity of zero-safe nets is transferred on the level of event structure by adding a way to express which events occur simultaneously

A bird’s eye view on the use of whole exome sequencing in rare congenital ophthalmic diseases

Phenotypic and genotypic heterogeneity in congenital ocular diseases, especially in anterior segment dysgenesis (ASD), have created challenges for proper diagnosis and classification of diseases. Over the last decade, genomic research has indeed boosted our understanding in the molecular basis of ASD and genes associated with both autosomal dominant and recessive patterns of inheritance have been described with a wide range of expressivity. Here we describe the molecular characterization of a cohort of 162 patients displaying isolated or syndromic congenital ocular dysgenesis. Samples were analyzed with diverse techniques, such as direct sequencing, multiplex ligation-dependent probe amplification, and whole exome sequencing (WES), over 20 years. Our data reiterate the notion that PAX6 alterations are primarily associated with ASD, mostly aniridia, since the majority of the cohort (66.7%) has a pathogenic or likely pathogenic variant in the PAX6 locus. Unexpectedly, a high fraction of positive samples (20.3%) displayed deletions involving the 11p13 locus, either partially/totally involving PAX6 coding region or abolishing its critical regulatory region, underlying its significance. Most importantly, the use of WES has allowed us to both assess variants in known ASD genes (i.e., CYP1B1, ITPR1, MAB21L1, PXDN, and PITX2) and to identify rarer phenotypes (i.e., MIDAS, oculogastrointestinal-neurodevelopmental syndrome and Jacobsen syndrome). Our data clearly suggest that WES allows expanding the analytical portfolio of ocular dysgenesis, both isolated and syndromic, and that is pivotal for the differential diagnosis of those conditions in which there may be phenotypic overlaps and in general in ASD

A lattice gas model of II-VI(001) semiconductor surfaces

We introduce an anisotropic two-dimensional lattice gas model of metal terminated II-IV(001) seminconductor surfaces. Important properties of this class of materials are represented by effective NN and NNN interactions, which result in the competition of two vacancy structures on the surface. We demonstrate that the experimentally observed c(2x2)-(2x1) transition of the CdTe(001) surface can be understood as a phase transition in thermal equilbrium. The model is studied by means of transfer matrix and Monte Carlo techniques. The analysis shows that the small energy difference of the competing reconstructions determines to a large extent the nature of the different phases. Possible implications for further experimental research are discussed.Comment: 7 pages, 2 figure

Biocontrol traits of Bacillus licheniformis GL174, a culturable endophyte of Vitis vinifera cv. Glera

Background Bacillus licheniformis GL174 is a culturable endophytic strain isolated from Vitis vinifera cultivar Glera, the grapevine mainly cultivated for the Prosecco wine production. This strain was previously demonstrated to possess some specific plant growth promoting traits but its endophytic attitude and its role in biocontrol was only partially explored. In this study, the potential biocontrol action of the strain was investigated in vitro and in vivo and, by genome sequence analyses, putative functions involved in biocontrol and plant-bacteria interaction were assessed. Results Firstly, to confirm the endophytic behavior of the strain, its ability to colonize grapevine tissues was demonstrated and its biocontrol properties were analyzed. Antagonism test results showed that the strain could reduce and inhibit the mycelium growth of diverse plant pathogens in vitro and in vivo. The strain was demonstrated to produce different molecules of the lipopeptide class; moreover, its genome was sequenced, and analysis of the sequences revealed the presence of many protein-coding genes involved in the biocontrol process, such as transporters, plant-cell lytic enzymes, siderophores and other secondary metabolites. Conclusions This step-by-step analysis shows that Bacillus licheniformis GL174 may be a good biocontrol agent candidate, and describes some distinguished traits and possible key elements involved in this process. The use of this strain could potentially help grapevine plants to cope with pathogen attacks and reduce the amount of chemicals used in the vineyard

Coexistence and conviviality in multi-faith, multi-ethnic Burgazadasi, the princes' islands of Istanbul

This thesis aims to provide an understanding of the existing cultural plurality and diversity in Burgazadası, within a post-Ottoman and homogenising context in Turkey. Most of the scholars working on conflict resolution and peace projects in the Balkans and the Middle East have attempted to analyse cultural plurality with the concept of “coexistence”. “Coexistence” as a concept presupposes the pre-existing categories of ethnicity, class and religion (i.e. coexistence between Israelis and Palestinians; Greek and Turkish Cypriots; Serbs, Croats and Bosnians). In this thesis, I demonstrate the inadequacy of the concept of “coexistence” and propose a “conviviality” approach to explore cultural pluralism. In the post-Ottoman, Turkish context in Burgaz, “coexistence” can be used when describing the homogenisation process, the construction and perception of categorisations of differences, the crystallisation of ethnic and religious identities and ruptures to cultural pluralism; but it is deficient in describing the continuity of cultural pluralism and what is shared between the members of the community in Burgaz. By contrast, “conviviality” provides an understanding of the continuity of cultural pluralism in Burgaz, the changes in sociality patterns, shared ways of living, the diversity and differentiations within “different groups”, the islanders' sense of belonging in Burgaz, their appreciation of diversity and acts of solidarity at the times of crisis. I argue that the homogenisation process in Turkey brought ruptures in cultural pluralism in Turkey, and changed the demographics in Burgaz; however the homogenisation process did not rupture the conviviality on the island and Burgazian identity which embraces all types of diversities of its inhabitants. At times of crisis, like in September 1955 riots, Burgaz islanders emphasised their shared Burgaz identity which overrode religious, class and ethnic differencesEThOS - Electronic Theses Online ServiceGBUnited Kingdo

MPath2PN - Translating Metabolic Pathways into Petri Nets

We propose MPath2PN, a tool which automatically translates metabolic pathways, as described in the major biological databases, into corresponding Petri net representations. The aim is to allow for a systematic reuse, in the setting of metabolic pathways, of the variety of tools existing for Petri net analysis and simulation. The current prototype implementation of MPath2PN inputs the KEGG description of a metabolic pathway and produces two Petri nets, mainly differing for the treatment of ubiquitous substances. Such Petri nets are represented using PNML, a standard format for many Petri net tools. We are extending the tool by considering further formats for metabolic pathways in input and for Petri nets in output. MPath2PN is part of a more general project aimed at developing an integrated framework which should offer the possibility of automatically querying databases for metabolic pathways, producing corresponding Petri net models and performing analysis and simulation on them by means of various tools

Characterization of Reachable Attractors Using Petri Net Unfoldings

International audienceAttractors of network dynamics represent the long-term behaviours of the modelled system. Their characterization is therefore crucial for understanding the response and differentiation capabilities of a dynamical system. In the scope of qualitative models of interaction networks, the computation of attractors reachable from a given state of the network faces combinatorial issues due to the state space explosion. In this paper, we present a new algorithm that exploits the concurrency between transitions of parallel acting components in order to reduce the search space. The algorithm relies on Petri net unfoldings that can be used to compute a compact representation of the dynamics. We illustrate the applicability of the algorithm with Petri net models of cell signalling and regulation networks, Boolean and multi-valued. The proposed approach aims at being complementary to existing methods for deriving the attractors of Boolean models, while being %so far more generic since it applies to any safe Petri net

A verified algorithm enumerating event structures

An event structure is a mathematical abstraction modeling concepts as causality, conflict and concurrency between events. While many other mathematical structures, including groups, topological spaces, rings, abound with algorithms and formulas to generate, enumerate and count particular sets of their members, no algorithm or formulas are known to generate or count all the possible event structures over af inite set of events. We present an algorithm to generate such a family, along with a functional implementation verified using Isabelle/HOL. As byproducts, we obtain a verified enumeration of all possible preorders and partial orders. While the integer sequences counting preorders and partial orders are already listed on OEIS (On-line Encyclopedia of Integer Sequences), the one counting event structures is not. We therefore used our algorithm to submit a formally verified addition, which has been successfully reviewed and is now part of the OEIS.Postprin