Automatic annotation of multigene families, the case of peroxidases

Une famille de gènes est un groupe de gènes homologues, partageant un ancêtre commun, et ayant des similarités au niveau de leurs séquences et de leurs fonctions. Mon équipe d'accueil, Evolution et Expression des Peroxydases, s'intéresse particulièrement à l'annotation de la superfamille des peroxydases. Les peroxydases sont des enzymes universelles du monde vivant qui catalysent des réactions d'oxydo-réduction impliquant la réduction d'un peroxyde d'hydrogène et l'oxydation d'un substrat, variable d'une classe de peroxydase à une autre. Avec la baisse du coût et du temps nécessaire au séquençage de nouveaux génomes, maintenir une annotation manuelle experte est devenu illusoire. Aussi, pour gérer ce flux croissant de données d'une manière fiable, la première étape était de mettre à jour notre base de données des peroxydases, la PeroxiBase. Dans cette optique, plusieurs outils et pipelines ont été mis en place pour faciliter et accélérer la procédure d'annotation des peroxydases tout en maintenant une haute qualité d'annotations. Tout d'abord, deux pipelines automatiques, " proteome_filter " et " EST_filter ", pour l'annotation des familles multigéniques ont été développés. Ils se basent sur une recherche par homologie à l'aide d'un BLAST dans le but d'identifier les séquences appartenant à la superfamille des peroxydases à partir du protéome ou des données d'ESTs. De plus, GECA, un logiciel pour comparer l'organisation en exon/intron et ainsi détecter les variations de structures de gènes a été développé. Par ailleurs, cette information sur les structures de gènes peut être utilisée aussi pour valider l'annotation des membres des familles multigéniques. Ces outils ont été testés dans le cadre des ligninases. Le choix de cette famille est justifié par l'annotation massive des génomes des champignons en raison de l'intérêt industriel accru pour les ligninases. Ces enzymes appartiennent à la famille des peroxydases de classe II qui se trouve essentiellement chez les champignons où ils sont responsables de la dégradation de la lignine (polymère présent dans la paroi des plantes terrestres). Bénéficiant d'une base de données experte sur les peroxydases, j'ai entrepris des études sur ces enzymes pour les classer et analyser leur évolution. En parallèle, je me suis impliqué dans des projets annexes comme la construction d'un pipeline pour avoir une analyse phylogénétique complète et une étude de l'évolution de huit familles de gènes chez l'Eucalyptus.Gene families are groups of homologous genes with a common ancestor that are likely to have highly similar sequences and functions. In our team, we are mainly interested in one of these families, the peroxidase superfamily. Peroxidases are universal enzymes present in all organisms where they typically catalyze the reduction of peroxides, such as hydrogen peroxide and the oxidation of a variety of organic and inorganic compounds. However, with the continually reducing cost and time of genome sequencing, expert manual annotation became a cumbersome task. Therefore, in order to handle the flood of data in an expert manner, the first step was to update the peroxidases database, the PeroxiBase. For this first aim, several tools and pipelines were set in place to facilitate and accelerate the annotation process of peroxidases all while maintaining a high quality of annotations. First of all, two new automatic pipelines, " proteome_filter " et " EST_filter ", for the annotation of multigene families were developed. They are based on a BLAST homology search in order to detect sequences that may be related to the families in question. Plus, a new tool named GECA, was developed for comparing exon/intron organization and therefore to help detecting gene structure variations. Furthermore, this gene structure information can be used as means to validate the annotation of multigene families. The new pipelines and GECA were implemented and tested with the family of ligninases. The choice for this family is supported by the massive annotation of fungi genomes due to the increased industrial interest in ligninases. These enzymes belong to the class II peroxidase, found essentially in fungi and responsible of degrading lignin (a high molecular compound found in the cell wall of land plants). Having a specialized databank on peroxidases, I started classifying, analyzing and studying the evolution of these ligninases. Finally, in addition to my work I was implicated in several side projects, such as designing a semi-automatic annotation workflows, constructing a pipeline for a complete phylogenic study and finally, studying of the evolution of eight gene families in Eucalyptus

Game Design Feedback Collection Methods in Pre-Release Game Development

The development of games is secretive in nature due to its creative constraints, and a project can run over the course of a few years. With the advent of agile methodologies, software projects have involved customers in the development process to iterate on received feedback. By exploring the different methods game developers employ to involve customers or tackle issues that interfere with the value of the final product, this study offers an insight into what practitioners actually do to collect the feedback they deem useful. We find that there are two main categories of feedback methods, those that are internal to the company and those that involve potential customers. Within these categories, different mechanisms are employed with differing goals and targets at different stages of the development process. While there are clear patterns on what constitutes useful feedback to practitioners, the implementation of those feedback collection mechanisms differs across the industry

The Representations of Islam and Muslims in popular media: Educational Strategies and to develop critical media literacy

ABSTRACT The way Islam is understood today, and for much of the Western world, is based on the perception that was established by Orientalist scholars of the 18th to 20th century. Many studies have demonstrated that the negative images of the Muslim world, in American Western mass media, particularly Hollywood movies, are inherited attitudes from the old ‘guild tradition’ school of Orientalism. As the matter of fact, these biased attitudes, which still in some ways dominate the Western way of thinking, are deeply rooted in the history of colonialism and orientalist scholarship. Today, American mass media and particularly Hollywood is taking these inherited misconceptions of the Muslim World and representing it to the world in a new format. This study examines the representations and portrayal of Islam and Muslims in American Popular Culture, especially Hollywood movie productions. The findings indicate that Islam and Muslims received negative coverage. A consistent stereotyped association with violence, terrorism, fundamentalism and extremism marks the representations of Islam and Muslims in Hollywood movies. These representations encapsulate the perception of Islam and Muslims by mass media to the point it becomes very difficult to perceive Islam and Muslims differently. The study also attempts to examine the role of education in demystifying the negative representations of Islam and Arab Muslims in Popular Culture. Moreover, it demonstrates that the critical study of these misrepresentations in the American popular culture may contribute towards establishing a more democratic, peaceful, and just world

Effects of the optimized resonator dimensions on the performance of the standing-wave thermoacoustic refrigerator

Thermoacoustic refrigerator is an alternative cooling system, which is environmentally safe due to the absence of any refrigerants. The resonator tube of the system is of great importance; its design and dimensions influence the design and performance of the entire refrigerator. The central component of the resonator is the stack. So this work describes the design of the stack and the resonator along with the influence of its dimensions on the performance of the standing-wave thermoacoustic refrigerator. The resonator consists of two tubes, one larger than the other, characterized by the diameter ratio of the small over the larger diameter. A Lagrange multiplier method is used as a technique to optimize the coefficient of performance (COP) of the system. The computational analyses show that the resonator small diameter tube dissipates minimum acoustic power at a diameter ratio of 0.46, which is about 17 percent (at least) less than the published values. Moreover, the results show that the resonator length increases gradually with the increase of the mean design temperature. The increase of the resonator length leads to increase of the total acoustic power dissipated by the resonator, which reduces the COP of the standing-wave thermoacoustic refrigerator

On uncoordinated wireless ad-hoc networks:data dissemination over WIFI and cross-layer optimization for ultra wide band impulse radio

Emerging pervasive wireless networks, pocket switched networks, Internet of things, vehicular networks and even sensor networks present very challenging communication circumstances. They might involve up to several hundreds of wireless devices with mobility and intermittent connectivity. Centralized coordination in such networks is practically unfeasible. We deal with these challenge using two potential technologies: WIFI and Ultra Wide Band (UWB) Impulse Radio (IR) for medium and short communication range, respectively. Our main goal is to improve the communication performance and to make these networks sustainable in the absence of a centralized coordination. With WIFI, the goal is to design an environment-oblivious data dissemination protocol that holds in highly dynamic unpredictable wireless ad-hoc networks. To this end, we propose a complete design for a scope limited, multi-hop broadcast middleware, which is adapted to the variability of the ad-hoc environment and works in unlimited ad-hoc networks such as a crowd in a city, or car passengers in a busy highway system. We address practical problems posed by: the impossibility of setting the TTL correctly at all times, the poor performance of multiple access protocols in broadcast mode, flow control when there is no acknowledgment and scheduling of multiple concurrent broadcasts. Our design, called "Self Limiting Epidemic Forwarding" (SLEF), automatically adapts its behavior from single hop MAC layer broadcast to epidemic forwarding when the environment changes from being extremely dense to sparse, sporadically connected. A main feature of SLEF is a non-classical manipulation of the TTL field, which combines the usual decrement-when-sending to many very small decrements when receiving. Then, we identify vulnerabilities that are specific to epidemic forwarding. We address broadcast applications over wireless ad-hoc networks. Epidemic forwarding employs several mechanisms such as forwarding factor control and spread control, and each of them can be implemented using alternative methods. Thus, the existence of vulnerabilities is highly dependent on the methods used. We examine the links between them. We classify vulnerabilities into two categories: malicious and rational. We examine the effect of the attacks according to the number of attackers and the different network settings such as density, mobility and congestion. We show that malicious attacks are hard to achieve and their effects are scenario-dependent. In contrast, rational attackers always obtain a significant benefit. The evaluation is carried out using detailed realistic simulations over networks with up to 1000 nodes. We consider static scenarios, as well as vehicular networks. In order to validate our simulation results, we build a solid and widely adaptable experimental testbed for wireless networks. It is composed of 57 mobile wireless nodes equipped with WIFI interface. The adopted platform is OpenWrt, a Linux-like firmware, which makes the testbed robust and easily configurable. With UWB IR, the main problem we deal with is the presence of uncontrolled interference. Indeed, similarly to Code Division Multiple Access (CDMA) systems, signal acquisition with UWB IR signaling requires power control in the presence of interferers, which is very expensive in an uncoordinated system. We solve this problem through a cross-layer optimization: We propose a new signal acquisition method that is independent of the received signal power and we adapt the MAC layer accordingly. Our signal acquisition method is designed to solve the IUI (Inter-User Interference) that occurs in some ad-hoc networks where concurrent transmissions are allowed with heterogeneous power levels. In such scenarios, the conventional detection method, which is based on correlating the received IR signal with a Template Pulse Train (TPT), does not always perform well. The complexity of our proposal is similar to that of the conventional method. We evaluate its performance with the Line Of Sight (LOS) and the Non-LOS (NLOS) office indoor-channel models proposed by the IEEE P802.15.4a study group and find that the improvement is significant. We also investigate the particular case where the concurrent transmissions have the same time-hopping code, and we show that it does not result in collision, such scenarios appear in ad-hoc networks that employ a common code for control or broadcast purposes. At the MAC level, we focus only on one component of a MAC layer, which is the sleeping mode that could be added to any MAC layer proposal adequate to UWB IR. We are motivated by the low power consumption constraint required by the potential applications. We identify the design elements that should be taken into account for an optimal design for a sleeping protocol for UWB-IR such as the possibility of transmitting concurrently without collision and the power consumption model of the hardware behind which is completely different than with the narrow-band signaling. Then, we design two sleeping protocols for centralized and decentralized ad-hoc networks, respectively. We evaluate their performance analytically with the adopted metric being the average life-time of the wireless nodes

Morphometry and Identification of Brain Sulci on Three-Dimensional MR Images

International audiencePositron emission tomography (PET) is widely used for the study of human cerebral activity. As PET images do not reflect brain anatomy of pationts, functional areas identified in such examinations cannot be localized precisely. Thus, a matching between PET and anatomical data from other sources is necessary to make the most of PET images. An approach to this problem is the direct recognition of cortical sulci on 3D magnetic resonance images (MRI) in order to build an accurate parcellation of brain for the localization of functional areas found in PET examinations