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Search Results: 1 - 10 of 3532 matches for " Julien Roux "
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Developmental Constraints on Vertebrate Genome Evolution
Julien Roux,Marc Robinson-Rechavi
PLOS Genetics , 2008, DOI: 10.1371/journal.pgen.1000311
Abstract: Constraints in embryonic development are thought to bias the direction of evolution by making some changes less likely, and others more likely, depending on their consequences on ontogeny. Here, we characterize the constraints acting on genome evolution in vertebrates. We used gene expression data from two vertebrates: zebrafish, using a microarray experiment spanning 14 stages of development, and mouse, using EST counts for 26 stages of development. We show that, in both species, genes expressed early in development (1) have a more dramatic effect of knock-out or mutation and (2) are more likely to revert to single copy after whole genome duplication, relative to genes expressed late. This supports high constraints on early stages of vertebrate development, making them less open to innovations (gene gain or gene loss). Results are robust to different sources of data—gene expression from microarrays, ESTs, or in situ hybridizations; and mutants from directed KO, transgenic insertions, point mutations, or morpholinos. We determine the pattern of these constraints, which differs from the model used to describe vertebrate morphological conservation (“hourglass” model). While morphological constraints reach a maximum at mid-development (the “phylotypic” stage), genomic constraints appear to decrease in a monotonous manner over developmental time.
Development of a Printed Coil for Wirelessly Charging a Tracking Elderly Patch  [PDF]
Bouchta Hajjine, Christophe Escriba, Samuel Charlot, Anne Hemeryck, Julien Roux, Sabeha Fettouma Zedek, Jean-Yves Fourniols
Wireless Engineering and Technology (WET) , 2016, DOI: 10.4236/wet.2016.72009
Abstract: Monitoring systems for elderly require a compromise between reduced size and operational autonomy. The latter to get a system as independent as possible and to fit with our application needs for daily use. Our patch is developed as a surveillance system for old people; we chose to equip it with a wireless charging system for greater ease of use, imperceptible in the everyday life and waterproofing. This paper presents the development of a printed receiver coil to be integrated in a wireless charger to be used in an elderly tracking patch. The proposed design is validated using simulation that presents a good agreement with measurement results: Simulation (@150 KHz: L = 10.74 μH; R = 3 Ω) and Measurement (@150 KHz: L = 10.8 μH; R = 3.16 Ω). The receiver coil is elaborated on a polyimide substrate in the cleanroom of our laboratory LAAS-CNRS (Laboratory for Analysis and Architecture of Systems-National Center for Scientific Research) and a PCB (Printed Circuit Board) charger prototype is fabricated to test its performances before the integration of the wireless charging property in the tracking patch. The proposed coil presents a good compromise between small size and efficiency. For a charging current of 7.5 mA, this coil can ensure the recharging of the patch up to a distance of 4.8 mm between the Qi transmitter and receiver which is more than enough for our application.
Advanced Thermopile IR Dual Line Sensor for Smart Home  [PDF]
Christophe Escriba, Julien Roux, Georges Soto-Romero, Pascal Acco, David Bourrier, Eric Campo, Jean-Yves Fourniols
Journal of Sensor Technology (JST) , 2018, DOI: 10.4236/jst.2018.84006
Abstract: This article presents all steps between the advanced design and the production of CMOS compatible thermoelectric effect infrared sensors dedicated to smart home applications. It will start by making a comparison between thermopile, bolometer and pyroelectric technologies. Although sensitivity performances available with bolometers appear to be better at first sight, it is found that thermopiles have non-negligible advantages that make them more suitable for this application field. Then the different steps necessary for the design will be described, starting from the thermoelectric model of the sensor (temperature gradient, electrical sensitivity, etc.) and considering all steps up to technological manufacturing in a clean room. The results obtained on the structures produced on a specific computer-controlled measurement bench (temperature regulation with an onboard preamplification card) will be presented. Finally, the results prove that the square structures have better performances (S = 82 V/W and NETD = 208 mK).
The expansion of amino-acid repeats is not associated to adaptive evolution in mammalian genes
Fernando Cruz, Julien Roux, Marc Robinson-Rechavi
BMC Genomics , 2009, DOI: 10.1186/1471-2164-10-619
Abstract: Mammalian positively selected genes have accumulated more recent amino acid repeats than other mammalian genes. However, we found little support for an accelerated evolutionary rate as the main driver for the expansion of amino acid repeats. The most significant predictors of amino acid repeats are gene function and GC content. There is no correlation with expression level.Our analyses show that amino acid repeat expansions are causally independent from protein adaptive evolution in mammalian genomes. Relaxed purifying selection or positive selection do not associate with more or more recent amino acid repeats. Their occurrence is slightly favoured by the sequence context but mainly determined by the molecular function of the gene.Microsatellites or simple sequence repeats (SSRs) are DNA tracts composed of 1-6 bp long motifs repeated in tandem. A balance between slippage events, that increase the purity of the repeat, and point mutations, that tend to eliminate perfect repeats, determines their length distribution. However, as the slippage rate is higher than the point mutation rate, the purity of the repeated tract will be an inverse measure of the age of the SSR [1-3].Triplet repeats are more common within coding regions [4], as they are less likely to alter the reading frame and can be translated into amino-acid repeats (AARs). AARs are frequently associated with disease [e.g. [5,6]]. Strong effects on morphology and phenotype have also been described in dog breeds [7]. Examples of AARs contributing to adaptive evolution [2,8] have been found in case studies in insects [9], plants [10,11] and mammals [12].Genomic comparisons have shown that highly variable AARs have a higher purity in their coding sequence [13,14]. AAR expansion has been found to correlate with the non-synonymous rate of substitution [13,15,16] supporting a role of selection in their expansion. The correlation is consistent with either relaxed purifying selection, or with positive selection; the
Advances in Deoxynivalenol Toxicity Mechanisms: The Brain as a Target
Marion S. Bonnet,Julien Roux,Lourdes Mounien,Michel Dallaporta,Jean-Denis Troadec
Toxins , 2012, DOI: 10.3390/toxins4111120
Abstract: Deoxynivalenol (DON), mainly produced by Fusarium fungi, and also commonly called vomitoxin, is a trichothecene mycotoxin. It is one of the most abundant trichothecenes which contaminate cereals consumed by farm animals and humans. The extent of cereal contamination is strongly associated with rainfall and moisture at the time of flowering and with grain storage conditions. DON consumption may result in intoxication, the severity of which is dose-dependent and may lead to different symptoms including anorexia, vomiting, reduced weight gain, neuroendocrine changes, immunological effects, diarrhea, leukocytosis, hemorrhage or circulatory shock. During the last two decades, many studies have described DON toxicity using diverse animal species as a model. While the action of the toxin on peripheral organs and tissues is well documented, data illustrating its effect on the brain are significantly less abundant. Yet, DON is known to affect the central nervous system. Recent studies have provided new evidence and detail regarding the action of the toxin on the brain. The purpose of the present review is to summarize critical studies illustrating this central action of the toxin and to suggest research perspectives in this field.
Non-medical use of opioids among HIV-infected opioid dependent individuals on opioid maintenance treatment: the need for a more comprehensive approach
Perrine Roux, Patrizia M Carrieri, Julien Cohen, Isabelle Ravaux, Bruno Spire, Michael Gossop, Sandra D Comer
Harm Reduction Journal , 2011, DOI: 10.1186/1477-7517-8-31
Abstract: The MANIF 2000 study is a longitudinal study that enrolled a cohort of 476 HIV-infected opioid-dependent individuals. Data were collected in outpatient hospital services delivering HIV care in France. The sample comprised all patients receiving OMT (either methadone or buprenorphine) who attended at least one follow-up visit with data on adherence to OMT (N = 235 patients, 1056 visits). Non-medical use of opioids during OMT was defined as having reported use of opioids in a non-medical context, and/or the misuse of the prescribed oral OMT by an inappropriate route of administration (injection or sniffing). After adjusting for the non-random assignment of OMT type, a model based on GEE was then used to identify predictors of non-medical use of opioids.Among the 235 patients, 144 (61.3%) and 91 (38.9%) patients were receiving buprenorphine and methadone, respectively, at baseline. Non-medical use of opioids was found in 41.6% of visits for 83% of individual patients. In the multivariate analysis, predictors of non-medical use of opioids were: cocaine, daily cannabis, and benzodiazepine use, experience of opioid withdrawal symptoms, and less time since OMT initiation.Non-medical use of opioids was found to be comparable in OMT patients receiving methadone or buprenorphine. The presence of opioid withdrawal symptoms was a determinant of non-medical use of opioids and may serve as a clinical indicator of inadequate dosage, medication, or type of follow-up. Sustainability and continuity of care with adequate monitoring of withdrawal symptoms and polydrug use may contribute to reduced harms from ongoing non-medical use of opioids.Among HIV-infected opioid dependent individuals, the clinical management of drug dependence is a matter of great concern. This issue is especially relevant in those countries where the HIV epidemic is driven by injecting drug users (IDUs) [1,2]. Even in industrialized countries, HIV-infected opioid-dependent persons seeking care for their drug dep
Comparative modular analysis of gene expression in vertebrate organs
Barbara Piasecka, Zoltán Kutalik, Julien Roux, Sven Bergmann, Marc Robinson-Rechavi
BMC Genomics , 2012, DOI: 10.1186/1471-2164-13-124
Abstract: Here, we use a modularization algorithm to overcome this limitation through the identification of inter-species co-modules of organs and genes. We identify such co-modules using mouse and human microarray expression data. They are functionally coherent both in terms of genes and of organs from both organisms. We show that a large proportion of genes belonging to the same co-module are orthologous between mouse and human. Moreover, their zebrafish orthologs also tend to be expressed in the corresponding homologous organs. Notable exceptions to the general pattern of conservation are the testis and the olfactory bulb. Interestingly, some co-modules consist of single organs, while others combine several functionally related organs. For instance, amygdala, cerebral cortex, hypothalamus and spinal cord form a clearly discernible unit of expression, both in mouse and human.Our study provides a new framework for comparative analysis which will be applicable also to other sets of large-scale phenotypic data collected across different species.Specific over-expression of a gene in an organ is often taken to imply a function of the gene in that organ. If so, and if orthologous genes have conserved function, we would expect a slow rate of organ-specific expression evolution. Some early comparisons of microarray data between species suggested the opposite. The most studied data set in this regard is the GNF gene atlas of human and mouse organs [1,2]. Yanai, Graur and Ophir [3] used an early version of these data [1], and reported that the expression profiles of orthologous genes differed remarkably between two mammalian species. Moreover, comparing the expression profiles of 16 tissues (for both species), they found that human tissues were more similar to each other than to their corresponding mouse tissues. In contrast, Liao and Zhang [4], based on a more recent version of the data [2], and correcting for systematic error, found that human-mouse orthologous gene pairs had signi
Graph edit distance : a new binary linear programming formulation
Julien Lerouge,Zeina Abu-Aisheh,Romain Raveaux,Pierre Héroux,Sébastien Adam
Computer Science , 2015,
Abstract: Graph edit distance (GED) is a powerful and flexible graph matching paradigm that can be used to address different tasks in structural pattern recognition, machine learning, and data mining. In this paper, some new binary linear programming formulations for computing the exact GED between two graphs are proposed. A major strength of the formulations lies in their genericity since the GED can be computed between directed or undirected fully attributed graphs (i.e. with attributes on both vertices and edges). Moreover, a relaxation of the domain constraints in the formulations provides efficient lower bound approximations of the GED. A complete experimental study comparing the proposed formulations with 4 state-of-the-art algorithms for exact and approximate graph edit distances is provided. By considering both the quality of the proposed solution and the efficiency of the algorithms as performance criteria, the results show that none of the compared methods dominates the others in the Pareto sense. As a consequence, faced to a given real-world problem, a trade-off between quality and efficiency has to be chosen w.r.t. the application constraints. In this context, this paper provides a guide that can be used to choose the appropriate method.
Patterns of positive selection in seven ant genomes
Julien Roux,Eyal Privman,Sebastien Moretti,Josephine T. Daub,Marc Robinson-Rechavi,Laurent Keller
Quantitative Biology , 2013,
Abstract: The evolution of ants is marked by remarkable adaptations that allowed the development of very complex social systems. To identify how ant-specific adaptations are associated with patterns of molecular evolution, we searched for signs of positive selection on amino-acid changes in proteins. We identified 24 functional categories of genes which were enriched for positively selected genes in the ant lineage. We also reanalyzed genome-wide datasets in bees and flies with the same methodology, to check whether positive selection was specific to ants or also present in other insects. Notably, genes implicated in immunity were enriched for positively selected genes in the three lineages, ruling out the hypothesis that the evolution of hygienic behaviors in social insects caused a major relaxation of selective pressure on immune genes. Our scan also indicated that genes implicated in neurogenesis and olfaction started to undergo increased positive selection before the evolution of sociality in Hymenoptera. Finally, the comparison between these three lineages allowed us to pinpoint molecular evolution patterns that were specific to the ant lineage. In particular, there was ant-specific recurrent positive selection on genes with mitochondrial functions, suggesting that mitochondrial activity was improved during the evolution of this lineage. This might have been an important step toward the evolution of extreme lifespan that is a hallmark of ants.
An Overview of Basics Speech Recognition and Autonomous Approach for Smart Home IOT Low Power Devices  [PDF]
Jean-Yves Fourniols, Nadim Nasreddine, Christophe Escriba, Pascal Acco, Julien Roux, Georges Soto Romero
Journal of Signal and Information Processing (JSIP) , 2018, DOI: 10.4236/jsip.2018.94015
Abstract: Automatic speech recognition, often incorrectly called voice recognition, is a computer based software technique that analyzes audio signals captured by a microphone and translates them into machine interpreted text. Speech processing is based on techniques that need local CPU or cloud computing with an Internet link. An activation word starts the uplink; “OK google”, “Alexa”, … and voice analysis is not usually suitable for autonomous limited CPU system (16 bits microcontroller) with low energy. To achieve this realization, this paper presents specific techniques and details an efficiency voice command method compatible with an embedded IOT low-power device.
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