Christophe Guyeux

Global emergence of the widespread Pseudomonas aeruginosa ST235 clone

OBJECTIVESnDespite the non-clonal epidemic population structure of Pseudomonas aeruginosa, several multi-locus sequence types are distributed worldwide and are frequently associated with epidemics where multidrug resistance confounds treatment. ST235 is the most prevalent of these widespread clones. In this study we aimed to understand the origin of ST235 and the molecular basis for its success.nnnMETHODSnThe genomes of 79 P.xa0aeruginosa ST235 isolates collected worldwide over a 27-year period were examined. A phylogenetic network was built, using a Bayesian approach to find the Most Recent Common Ancestor, and we identified antibiotic resistance determinants and ST235-specific genes.nnnRESULTSnOur data suggested that the ST235 sublineage emerged in Europe around 1984, coinciding with the introduction of fluoroquinolones as an antipseudomonal treatment. The ST235 sublineage seemingly spread from Europe via two independent clones. ST235 isolates then appeared to acquire resistance determinants to aminoglycosides, β-lactams and carbapenems locally. Additionally, we found that all the ST235 genomes contained the exoU-encoded exotoxin and identified 22 ST235-specific genes clustering in blocks and implicated in transmembrane efflux, DNA processing and bacterial transformation. These unique combinations of genes may have contributed to the poor outcome associated with P.xa0aeruginosa ST235 infections and increased the ability of this international clone to acquire mobile resistance elements.nnnCONCLUSIONnOur data suggest that P.xa0aeruginosa ST235 (a) has become prevalent across the globe potentially due to the selective pressure of fluoroquinolones and (b) readily became resistant to aminoglycosides, β-lactams and carbapenems through mutation and acquisition of resistance elements among local populations.

Dendrochemical assessment of mercury releases from a pond and dredged-sediment landfill impacted by a chlor-alkali plant

Although current Hg emissions from industrial activities may be accurately monitored, evidence of past releases to the atmosphere must rely on one or more environmental proxies. We used Hg concentrations in tree cores collected from poplars and willows to investigate the historical changes of Hg emissions from a dredged sediment landfill and compared them to a nearby control location. Our results demonstrated the potential value of using dendrochemistry to record historical Hg emissions from past industrial activities.

Discrete Dynamical Systems and Chaotic Machines: Theory and Applications

For computer scientists, especially those in the security field, the use of chaos has been limited to the computation of a small collection of famous but unsuitable maps that offer no explanation of why chaos is relevant in the considered contexts. Discrete Dynamical Systems and Chaotic Machines: Theory and Applications shows how to make finite machines, such as computers, neural networks, and wireless sensor networks, work chaotically as defined in a rigorous mathematical framework. Taking into account that these machines must interact in the real world, the authors share their research results on the behaviors of discrete dynamical systems and their use in computer science. Covering both theoretical and practical aspects, the book presents: Key mathematical and physical ideas in chaos theory Computer science fundamentals, clearly establishing that chaos properties can be satisfied by finite state machines Concrete applications of chaotic machines in computer security, including pseudorandom number generators, hash functions, digital watermarking, and steganography Concrete applications of chaotic machines in wireless sensor networks, including secure data aggregation and video surveillance Until the authors recent research, the practical implementation of the mathematical theory of chaos on finite machines raised several issues. This self-contained book illustrates how chaos theory enables the study of computer security problems, such as steganalysis, that otherwise could not be tackled. It also explains how the theory reinforces existing cryptographically secure tools and schemes.

CIPRNG: A VLSI Family of Chaotic Iterations Post-Processings for

Hardware pseudorandom number generators are continuously improved to satisfy both physical and ubiquitous computing security system challenges. The main contribution of this paper is to propose two post-processing modules in hardware, to improve the randomness of linear PRNGs while succeeding in passing the TestU01 statistical battery of tests. They are based on chaotic iterations and are denoted by CIPRNG-MC and CIPRNG-XOR. They have various interesting properties, encompassing the ability to improve the statistical profile of the generators on which they iterate. Such post-processing have been implemented on FPGA and ASIC without inferring any blocs (RAM or DSP). A comparison in terms of area, throughput, and statistical tests, is performed. The hardware pseudorandom number generation can reach a throughput/latency ratio equal to 8.5 Gbps for Zynq-FPGA and 10.9 Gbps for ASIC, being thus the fastest FPGA generators based on chaos that can pass TestU01. In particular, it is established that CIPRNG-XOR is 2.5 times faster and 5 times more efficient that almost all linear PRNGs who pass TestU01.

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The rapid development of medical sensors has increased the interest in Wireless Body Area Network (WBAN) applications where physiological data from the human body and its environment is gathered, monitored, and analyzed to take the proper measures. In WBANs, it is essential to design MAC protocols that ensure adequate Quality of Service (QoS) such as low delay and high scalability. This paper investigates Medium Access Control (MAC) protocols used in WBAN, and compares their performance in a high traffic environment. Such scenario can be induced in case of emergency for example, where physiological data collected from all sensors on human body should be sent simultaneously to take appropriate action. This study can also be extended to cover collaborative WBAN systems where information from different bodies is sent simultaneously leading to high traffic. OPNET simulations are performed to compare the delay and scalability performance of the different MAC protocols under the same experimental conditions and to draw conclusions about the best protocol to be used in a high traffic environment.

-Linear Pseudorandom Number Generation Based on Zynq MPSoC

BackgroundNon-Negative Matrix factorization has become an essential tool for feature extraction in a wide spectrum of applications. In the present work, our objective is to extend the applicability of the method to the case of missing and/or corrupted data due to outliers.ResultsAn essential property for missing data imputation and detection of outliers is that the uncorrupted data matrix is low rank, i.e. has only a small number of degrees of freedom. We devise a new version of the Bregman proximal idea which preserves nonnegativity and mix it with the Augmented Lagrangian approach for simultaneous reconstruction of the features of interest and detection of the outliers using a sparsity promoting ℓ1 penality.ConclusionsAn application to the analysis of gene expression data of patients with bladder cancer is finally proposed.

Investigating low level protocols for Wireless Body Sensor Networks

In this paper, we present a toolbox for a specific optimization problem that frequently arises in bioinformatics or genomics. In this specific optimisation problem, the state space is a set of words of specified length over a finite alphabet. To each word is associated a score. The overall objective is to find the words which have the lowest possible score. This type of general optimization problem is encountered in e.g 3D conformation optimisation for protein structure prediction, or largest core genes subset discovery based on best supported phylogenetic tree for a set of species. In order to solve this problem, we propose a toolbox that can be easily launched using MPI and embeds 3 well-known metaheuristics. The toolbox is fully parametrized and well documented. It has been specifically designed to be easy modified and possibly improved by the user depending on the application, and does not require to be a computer scientist. We show that the toolbox performs very well on two difficult practical problems.

A Bregman-proximal point algorithm for robust non-negative matrix factorization with possible missing values and outliers - application to gene expression analysis

Hardware security for an Internet of Things or cyber physical system drives the need for ubiquitous cryptography to different sensing infrastructures in these fields. In particular, generating strong cryptographic keys on such resource-constrained device depends on a lightweight and cryptographically secure random number generator. In this research work, we have introduced a new hardware chaos-based pseudorandom number generator, which is mainly based on the deletion of an Hamilton cycle within the <inline-formula><tex-math notation=LaTeX>

Finding optimal finite biological sequences over finite alphabets: The OptiFin toolbox

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A Hardware and Secure Pseudorandom Generator for Constrained Devices

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