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First Case of Bacteraemia Due to Carbapenem-Resistant Bacteroides faecis

Charlotte Kaeuffer, Tiffany Ruge, Laure Diancourt, Benoît Romain, Yvon Ruch, Benoît Jaulhac, Pierre Boyer
2021 Antibiotics  
Multidrug resistant (MDR) bacteria are increasingly observed in nosocomial and community-acquired settings. Anaerobes are no exception to this rule, but there are fewer reports of MDR in the scientific literature on anaerobes than there are for other bacteria. In this short case report, we describe the first case of bacteraemia caused by a multidrug-resistant Bacteroides faecis, which produces a carbapenemase encoded by the blaCfiA gene. This bacteraemia followed a digestive surgery operation.
more » ... urprisingly, these findings did not lead to a change in antibiotic therapy, probably because the patient's clinical state had improved. Nevertheless this report calls for better knowledge of anaerobic bacteria and for a systematic antimicrobial stewardship procedure following bacteraemia.
doi:10.3390/antibiotics10030319 pmid:33808699 pmcid:PMC8003481 fatcat:yzzragupsjborltu5fmgblazny

A simulator for maxillo-facial surgery integrating cephalometry and orthodontia [article]

Georges Bettega, Benoit Mollard (TIMC - IMAG), Anthony Boyer, Stéphane Lavallee
2006 arXiv   pre-print
Objectives : This paper presents a new simulator for maxillo-facial surgery, that gathers the dental and the maxillo-facial analyses together into a single computer-assisted procedure. The idea is first to propose a repositioning of the maxilla, via the introduction of a 3D cephalometry, applied to a 3D virtual model of the patient's skull. Then, orthodontic data are integrated into this model, thanks to optical measurements of teeth plaster casts. Materials and Methods : The feasibility of the
more » ... maxillo-facial demonstrator was first evaluated on a dry skull. To simulate malformations (and thus to simulate a "real" patient), the skull was modified and manually cut by the surgeon, in order to generate a given maxillo-facial malformation (with asymmetries in the sagittal, frontal and axial planes). Results : The validation of our simulator consisted in evaluating its ability to propose a bone repositioning diagnosis that will put the skull as it was in its original configuration. A first qualitative validation is provided in this paper, with a 1.5-mm error in the repositioning diagnosis. Conclusions : These results mainly validate the concept of a maxillo-facial numerical simulator that integrates 3D cephalometry and guarantees a correct dental occlusion.
arXiv:physics/0606149v1 fatcat:nsrtaiyhpzaznouwie3uxm4qpe

A Formalism for Stochastic Adaptive Systems [chapter]

Benoît Boyer, Axel Legay, Louis-Marie Traonouez
2014 Lecture Notes in Computer Science  
Complex systems such as systems of systems result from the combination of several components that are organized in a hierarchical manner. One of the main characteristics of those systems is their ability to adapt to new situations by modifying their architecture. Those systems have recently been the subject of a series of works in the software engineering community. Most of those works do not consider quantitative features. The objective of this paper is to propose a modeling language for
more » ... ve systems whose behaviors depend on stochastic features. Our language relies on an extension of stochastic transition systems equipped with (1) an adaptive operator that allows to reason about the probability that a system has to adapt its architecture over time, and (2) dynamic interactions between processes. As a second contribution, we propose a contract-based extension of probabilistic linear temporal logic suited to reason about assumptions and guarantees of such systems. Our work has been implemented in the Plasma-Lab tool developed at Inria. This tool allows us to define stochastic adaptive systems with an extension of the Prism language, and properties with patterns. In addition, Plasma-Lab offers a simulation-based model checking procedure to reason about finite executions of the system. First experiments on a large case study coming from an industrial driven European project give encouraging results.
doi:10.1007/978-3-662-45231-8_12 fatcat:vffqq3lqwbejbllyo4uw6hktvm

On the Simulation of Time-Triggered Systems on a Chip with BIP [article]

Jan Olaf Blech, Benoit Boyer, Thanh Hung Nguyen
2011 arXiv   pre-print
In this report, we present functional models for software and hardware components of Time-Triggered Systems on a Chip (TTSoC). These are modeled in the asynchronous component based language BIP. We demonstrate the usability of our components for simulation of software which is developed for the TTSoC. Our software comprises services and an application part. Our approach allows us to simulate and validate aspects of the software system at an early stage in the development process and without the need to have the TTSoC hardware at hand.
arXiv:1109.5505v1 fatcat:3c7mxz5oajdlndtz4p2rbv63le

Feasibility of individual patient data meta-analyses in orthopaedic surgery

Benoit Villain, Agnès Dechartres, Patrick Boyer, Philippe Ravaud
2015 BMC Medicine  
The number of individual patient data meta-analyses published is very low especially in surgical domains. Our aim was to assess the feasibility of individual patient data (IPD) meta-analyses in orthopaedic surgery by determining whether trialists agree to send IPD for eligible trials. Methods: We performed a literature search to identify relevant research questions in orthopaedic surgery. For each question, we developed a protocol synopsis for an IPD meta-analysis and identified all related
more » ... omized controlled trials (RCTs) with results published since 2000. Corresponding authors of these RCTs were sent personalized emails that presented a project for an IPD meta-analysis corresponding to one of the research questions, with a link to the protocol synopsis, and asking for IPD from their RCT. We guaranteed patient confidentiality and secure data storage, and offered co-authorship and coverage of costs related to extraction. Results: We identified 38 research questions and 273 RCTs related to these questions. We could contact 217 of the 273 corresponding authors (79 %; 56 had unavailable or non-functional email addresses) and received 68/273 responses (25 %): 21 authors refused to share IPD, 10 stated that our request was under consideration and 37 agreed to send IPD. Four corresponding authors required authorship and three others asked for financial support to send the IPD. Overall, we could obtain IPD for 5,110 of 33,602 eligible patients (15 %). Among the 38 research questions, only one IPD meta-analysis could be potentially initiated because we could receive IPD for more than 50 % of participants. Conclusion: The present study illustrates the difficulties in initiating IPD meta-analyses in orthopaedic surgery. Significant efforts must be made to improve data sharing.
doi:10.1186/s12916-015-0376-6 pmid:26040278 pmcid:PMC4464630 fatcat:g2wmpqchpra6tauuvjndbwie6a

Equational Abstraction Refinement for Certified Tree Regular Model Checking [chapter]

Yohan Boichut, Benoit Boyer, Thomas Genet, Axel Legay
2012 Lecture Notes in Computer Science  
Tree Regular Model Checking (TRMC) is the name of a family of techniques for analyzing infinite-state systems in which states are represented by trees and sets of states by tree automata. The central problem is to decide whether a set of bad states belongs to the set of reachable states. An obstacle is that this set is in general neither regular nor computable in finite time. This paper proposes a new CounterExample Guided Abstraction Refinement (CEGAR) algorithm for TRMC. Our approach relies
more » ... a new equational-abstraction based completion algorithm to compute a regular overapproximation of the set of reachable states in finite time. This set is represented by R /E -automata, a new extended tree automaton formalism whose structure can be exploited to detect and remove false positives in an efficient manner. Our approach has been implemented in TimbukCEGAR, a new toolset that is capable of analyzing Java programs by exploiting an elegant translation from the Java byte code to term rewriting systems. Experiments show that TimbukCEGAR outperforms existing CEGAR-based completion algorithms. Contrary to existing TRMC toolsets, the answers provided by TimbukCEGAR are certified by Coq, which means that they are formally proved correct. In this paper, we design the first efficient and certified CEGAR framework for equational-abstraction based completion algorithm. Our approach relies on R /E -automaton, that is a new tree automaton formalism for representing sets of reachable states. In R /E -automata, equational abstraction does not merge states, but rather link them with rewriting rules labeled with equations. Such technique is made easy by exploiting the nature of the completion step. During completion steps, such equations are propagated, and the information can used to efficiently decide whether a set of terms is reachable from the set of initial states. If the procedure concludes positively, then the term is indeed reachable. Else, one has to refine the R /E -automaton and restart the process again. Our approach has been implemented in TimbukCEGAR. (T)RMC toolsets result from the combination of several libraries, each of them being implemented with thousands of lines of code. It is thus impossible to manually prove that those tool deliver correct answers. A particularity of TimbukCEGAR is that it is certified. In order to ensure that the whole set of reachable states has been explored, any TRMC technique needs to check whether a candidate overapproximation B is indeed a fixed point, that is if L(B ) ⊇ R * (L(A)). Such check has been implemented in various TRMC toolsets, but there is no guarantee that it behaves correct. In [20], a checker for tree automata completion was designed and proved correct using the Coq [10] proof assistant. Any automaton B that passes the checker can be claimed to formally satisfy the fixed point. TimbukCEGAR implements an extension of [20] for R /E -automata, which means that the tool delivers correct answers. Our TimbukCEGAR is capable, in part, of analyzing Java programs by exploiting a elegant translation from the javabyte code to term rewriting systems. Experiments show that TimbukCEGAR outperforms existing CEGAR-based completion algorithms by orders of magnitude. Related work. Regular Model Checking (RMC) was first applied to compute the set of reachable states of systems whose configurations are represented by words [18, 14, 22] . The approach was then extended to trees and applied to very simple case studies [5, 19] . Other regular model checking works can be found in [3, 4] , where an abstraction of the transition relation allows to exploit well-quasi ordering for finite termination. Such techniques may introduce false positives; a CEGAR approach exists for the case of finite word [2], but not for the one of trees. Learning techniques apply to RMC [37, 38] but trees have not yet been considered. We mention that our work extends equational abstractions [33, 36] with counter-example detection and refinement. We mention the existence of other automata-based works that can handle a specific class of system [34] . CEGAR principles have been implemented in various tools such as Arme [35] or SLAM [8] . Those specific tools are more efficient than our approach. On the other hand, RMC and rewriting rules offers a more general framework in where the abstraction and the refinements can be computed in a systematic manner. Structure of the paper. Section 2 introduces the basic definitions and concepts used in the paper. TRMC and Completion are introduced in Section 3. R /E -automata are introduced in Section 4. A new completion procedure is then defined in Section 5. Section 6 proposes a CEGAR approach for TRMC and Completion. Section 7 presents TimbukCEGAR. Section 8 concludes the paper and discusses future research. Due to space constraints proofs are reported to appendix.
doi:10.1007/978-3-642-34281-3_22 fatcat:apa7bjj2lrgotl6mkp3d6tt4gu

PLASMA-lab: A Flexible, Distributable Statistical Model Checking Library [chapter]

Benoît Boyer, Kevin Corre, Axel Legay, Sean Sedwards
2013 Lecture Notes in Computer Science  
We present PLASMA-lab, a statistical model checking (SMC) library that provides the functionality to create custom statistical model checkers based on arbitrary discrete event modelling languages. PLASMAlab is written in Java for maximum cross-platform compatibility and has already been incorporated in various performance-critical software and embedded hardware platforms. Users need only implement a few simple methods in a simulator class to take advantage of our efficient SMC algorithms.
more » ... -lab may be instantiated from the command line or from within other software. We have constructed a graphical user interface (GUI) that exposes the functionality of PLASMA-lab and facilitates its use as a standalone application with multiple 'drop-in' modelling languages. The GUI adds the notion of projects and experiments, and implements a simple, practical means of distributing simulations using remote clients. Background and motivation
doi:10.1007/978-3-642-40196-1_12 fatcat:zc7ybuwyr5hrfbrs6lqqko6cmi

A Mechanically Verified Theory of Contracts [chapter]

Stéphane Kastenbaum, Benoît Boyer, Jean-Pierre Talpin
2021 Lecture Notes in Computer Science  
Cyber-physical systems (CPS) are assemblies of networked, heterogeneous, hardware, and software components sensing, evaluating, and actuating a physical environment. This heterogeneity induces complexity that makes CPSs challenging to model correctly. Since CPSs often have critical functions, it is however of utmost importance to formally verify them in order to provide the highest guarantees of safety. Faced with CPS complexity, model abstraction becomes paramount to make verification
more » ... e. To this end, assume/guarantee contracts enable component model abstraction to support a sound, structured, and modular verification process. While abstractions of models by contracts are usually proved sound, none of the related contract frameworks themselves have, to the best of our knowledge, been formally proved correct so far. In this aim, we present the formalization of a generic assume/guarantee contract theory in the proof assistant Coq. We identify and prove theorems that ensure its correctness. Our theory is generic, or parametric, in that it can be instantiated and used with any given logic, in particular hybrid logics, in which highly complex cyber-physical systems can uniformly be described.
doi:10.1007/978-3-030-85315-0_9 fatcat:wgv2ktq7rnfgjktp2ycduaozyy

Looking for Root Hairs to Overcome Poor Soils

Thanyakorn Rongsawat, Jean-Benoît Peltier, Jean-Christophe Boyer, Anne-Aliénor Véry, Hervé Sentenac
2020 Trends in Plant Science  
U N C O R R E C T E D P R O O F 2Q2 Review Looking for Root Hairs to Overcome Poor Soils 4Q3 Q4 Thanyakorn Rongsawat, 1,2 Jean-Benoît Peltier, 1 Jean-Christophe Boyer, 1 Anne-Aliénor Véry, 1 and Hervé  ... 
doi:10.1016/j.tplants.2020.09.001 pmid:32980260 fatcat:vwrjg5bwybat7fc3yotlca3v2i

From Autonomic to Self-Self Behaviors

Sara Bouchenak, Fabienne Boyer, Benoit Claudel, Noel De Palma, Olivier Gruber, Sylvain Sicard
2011 ACM Transactions on Autonomous and Adaptive Systems  
Autonomic computing enables computing infrastructures to perform administration tasks with minimal human intervention. This wrap-up paper describes the experience we gained with the design and use of JADE-an architecture-based autonomic system. The contributions of this article are, (1) to explain how JADE provides autonomic management of a distributed system through an architecture-based approach, (2) to explain how we extended autonomic management from traditional self behaviors such as
more » ... ing or protecting a managed system to self-self behaviors where JADE also fully manages itself as it manages any other distributed system, (3) to report on our experience reaching self-self behaviors for two crucial autonomic properties, repair and protection.
doi:10.1145/2019591.2019597 fatcat:oavzed7ez5ao5osbvwioqssapa

Chronic pneumonia with Pseudomonas aeruginosa and impaired alveolar fluid clearance

Sophie Boyer, Karine Faure, Florence Ader, Odile Marie Husson, Eric Kipnis, Thierry Prangere, Xavier Leroy, Benoit P Guery
2005 Respiratory Research  
While the functional consequences of acute pulmonary infections are widely documented, few studies focused on chronic pneumonia. We evaluated the consequences of chronic Pseudomonas lung infection on alveolar function. Methods: P. aeruginosa, included in agar beads, was instilled intratracheally in Sprague Dawley rats. Analysis was performed from day 2 to 21, a control group received only sterile agar beads. Alveolar-capillary barrier permeability, lung liquid clearance (LLC) and distal
more » ... fluid clearance (DAFC) were measured using a vascular ( 131 I-Albumin) and an alveolar tracer ( 125 I-Albumin). Results: The increase in permeability and LLC peaked on the second day, to return to baseline on the fifth. DAFC increased independently of TNF-α or endogenous catecholamine production. Despite the persistence of the pathogen within the alveoli, DAFC returned to baseline on the 5 th day. Stimulation with terbutaline failed to increase DAFC. Eradication of the pathogen with ceftazidime did not restore DAFC response. Conclusions: From these results, we observe an adequate initial alveolar response to increased permeability with an increase of DAFC. However, DAFC increase does not persist after the 5 th day and remains unresponsive to stimulation. This impairment of DAFC may partly explain the higher susceptibility of chronically infected patients to subsequent lung injury.
doi:10.1186/1465-9921-6-17 pmid:15707485 pmcid:PMC551591 fatcat:alvsobslpjhh5amd7wztzzkoza

Compositional Proofs in Differential Dynamic Logic dL

Simon Lunel, Benoit Boyer, Jean-Pierre Talpin
2017 2017 17th International Conference on Application of Concurrency to System Design (ACSD)  
Modularity and composability are essential properties to facilitate and scale the design of cyber-physical systems from the specification of hybrid, discrete and continuous, components. Modularity is essential to break down a system model into comprehensible and manageable component specifications. Composability is essential to design a system from component models while preserving their verified properties, expressed as assume-guarantee contracts. In this paper, we address the specification of
more » ... hybrid system using Platzer's differential dynamic logic (dL). Our contribution is threefold: (1) We define a new composition operator in dL and prove that it is associative and commutative (AC). Prior notions of composition in dL were not associative. (2) We provide a theorem which characterizes necessary conditions to automate the proof that composed components satisfy the composition of their individual contracts, enabling modular and compositional verification. (3) We case-study our AC composition operator by considering the modular and detailed specification of a cruise controller in KeYmaera X, the latest implementation of dL, to demonstrate the proof automation capability of our contribution and exemplify a compositional design methodology.
doi:10.1109/acsd.2017.16 dblp:conf/acsd/LunelBT17 fatcat:nvkzk7b74vgmxgfbo6zfqlr4ty

Human Co-Infections between Borrelia burgdorferi s.l. and Other Ixodes-Borne Microorganisms: A Systematic Review

Pierre H. Boyer, Cédric Lenormand, Benoît Jaulhac, Emilie Talagrand-Reboul
2022 Pathogens  
When it comes to tick-borne diseases, co-infections are often mentioned. This concept includes several entities. On the one hand, tick vectors or vertebrate reservoir host can harbor several microorganisms that can be pathogenic for humans. On the other hand, human co-infections can also be understood in different ways, ranging from seropositivity without clinical symptoms to co-disease, i.e., the simultaneous clinical expression of infections by two tick-borne microorganisms. The latter,
more » ... gh regularly speculated, is not often reported. Hence, we conducted a systematic review on co-infections between B. burgdorferi s.l., the etiological agent of Lyme borreliosis, and other microorganisms potentially transmitted to humans by Ixodes spp. ticks. A total of 68 relevant articles were included, presenting 655 cases of possible co-infections. Most cases of co-infections corresponded to patients with one tick-borne disease and presenting antibody against another tick-borne microorganism. Co-disease was particularly frequent in two situations: patients with clinical symptoms of high fever and erythema migrans (EM), and patients with neurological symptoms linked to the TBEv or a neuroborreliosis. No impact on severity was evidenced. Further studies are needed to better appreciate the frequency and the impact of co-infections between several tick-borne microorganisms.
doi:10.3390/pathogens11030282 pmid:35335606 pmcid:PMC8948674 fatcat:skl7hxph4ragje6itjywhfxzgy

A second polymorphic form of N,N′-diphenyl-1,4-phenylenediamine

Isabelle Boyer, Sophie Quillard, Benoit Corraze, Philippe Deniard, Michel Evain
2000 Acta Crystallographica Section C: Crystal Structure Communications  
C56, e159 [doi:10.1107/S0108270100003498] A second polymorphic form of N,N′-diphenyl-1,4-phenylenediamine Isabelle Boyer, Sophie Quillard, Benoit Corraze, Philippe Deniard and Michel Evain Computing details  ... 
doi:10.1107/s0108768100003499 fatcat:d2jlowgjqvdztgsyg5slkruaza

A 3d data intensive tele-immersive grid

Benjamin Petit, Thomas Dupeux, Benoit Bossavit, Joeffrey Legaux, Bruno Raffin, Emmanuel Melin, Jean-Sébastien Franco, Ingo Assenmacher, Edmond Boyer
2010 Proceedings of the international conference on Multimedia - MM '10  
Networked virtual environments like Second Life enable distant people to meet for leisure as well as work. But users are represented through avatars controlled by keyboards and mouses, leading to a low sense of presence especially regarding body language. Multi-camera real-time 3D modeling offers a way to ensure a significantly higher sense of presence. But producing quality geometries, well textured, and to enable distant user tele-presence in non trivial virtual environments is still a
more » ... ge today. In this paper we present a tele-immersive system based on multi-camera 3D modeling. Users from distant sites are immersed in a rich virtual environment served by a parallel terrain rendering engine. Distant users, present through their 3D model, can perform some local interactions while having a strong visual presence. We experimented our system between three large cities a few hundreds kilometers apart from each other. This work demonstrate the feasibility of a rich 3D multimedia environment ensuring users a strong sense of presence.
doi:10.1145/1873951.1874210 dblp:conf/mm/PetitDBLRMFAB10 fatcat:4rr3kyxaivaqjhit5fcrvrjyeu
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