Un algorithme tabou stochastique pour le problème de recouvrement d'ensemble à coûts unitaires

RÉSUMÉ Le problème de recouvrement d’ensemble avec coûts unitaires (USCP) est un problème NP-difficile. Ce problème possède plusieurs applications importantes comme le problème d’affectation des équipages. Le but de notre travail est de résoudre de manière efficace le problème USCP. Pour atteindre cet objectif, nous avons commencé par développer un algorithme tabou qui s’inspire du meilleur algorithme conçu pour résoudre ce problème. L’un des points faibles de ce dernier algorithme est l’absence d’une technique permettant un réglage efficace des paramètres. Notre principal objectif était de trouver une manière efficace de régler les paramètres. Durant notre travail, nous avons exploré plusieurs approches. La première approche consistait à trouver des formules générales pour nos listes taboues. Nous n’avons pas réussi à trouver des formules simples, mais les résultats des tests réalisés avec nos deux formules compliquées sont meilleurs que ceux obtenus par le meilleur algorithme de la littérature. La deuxième approche consistait à adapter l’algorithme tabou réactif à notre problème USCP. Les tests réalisés avec cette approche ont montré que l’algorithme ne produit pas des cycles avec les jeux de grande taille, donc incapable de régler dynamiquement les longueurs des listes taboues. Notre troisième idée consistait à combiner le recuit simulé avec l’algorithme tabou. Nos tests ont révélé que l’algorithme obtient des résultats médiocres lorsque la température n’est pas suffisamment basse. Grâce aux résultats obtenus avec la troisième approche, nous avons développé notre algorithme tabou stochastique STS. Notre algorithme STS nous a permis de régler plus facilement les longueurs des listes taboues. Les résultats de STS sont meilleurs que ceux obtenus par RWLS -- le meilleur algorithme de la littérature publié récemment. Notre algorithme obtient 6 nouveaux records et atteint tous les meilleurs résultats sur le reste des jeux de données. Pour rendre nos algorithmes plus rapides, nous avons développé une implémentation efficace. Notre implémentation est fondée sur deux caractéristiques clés. La première est l’utilisation d’algorithmes de bas niveau incrémentaux. Le deuxième point fort de notre implémentation est l’utilisation des files de priorité qui rendent la sélection d’un mouvement plus rapide. Les tests effectués montrent l’efficacité de nos files de priorités sur la majorité des jeux de données traités dans notre travail.----------ABSTRACT The unicost set covering problem (USCP) is an NP-hard problem. This problem has many important real-life applications such as the crew scheduling problem. In this work, we aim to effectively solve the USCP. To achieve this goal, we first developed a tabu search algorithm inspired by the best algorithm designed to solve the USCP. One of the weaknesses of the latter algorithm is the absence of an effective technique for setting the parameters. Our main objective was to find an effective way to adjust the tabu lists parameters. During our work, we explored several approaches. The first approach was to find general formulas for our tabu lists. We have not managed to find simple formulas, but the results of the tests performed with our two complicated formulas are better than those obtained by the best performing algorithms in the literature. The second approach was to adapt the reactive tabu algorithm to our problem. Tests performed with this approach have shown that the algorithm does not produce cycles when applied to big instances, so it is unable to dynamically adjust the length of the tabu lists. Our third idea was to combine a simulated annealing algorithm with the tabu algorithm. Our tests revealed that the algorithm performs poorly when the temperature is not low enough. Thanks to the results obtained with the third approach, we have developed our stochastic tabu algorithm STS. Our STS algorithm allowed us to easily adjust the lengths of the tabu lists. STS results are better than those obtained by RWLS - the best algorithm in the literature which was recently published. Our algorithm obtains 6 new records and achieves the best results on all the remaining instances. To make our algorithm faster, we have developed an efficient implementation. Our implementation is based on two features. The first is the use of incremental low level algorithms. The second feature of our implementation is the use of priority queues that make the selection of the movements faster. The tests show the effectiveness of using the priority queues on the majority of the instances used in this work

Stress cellulaire et modulation de l'activité des cytidines désaminases APOBEC3

APOBEC3 proteins (A3A-A3H) catalyse the deamination of cytosine (C) to thymidine (T) on single stranded DNA. This activity, called cytidine deaminase, has initially been described as a mechanism involved in restriction against retroviruses and DNA viruses by massively inducing C->T mutations on viral genome : this phenomenon is called "hypermutations". Nevertheless, this activity is not virus-specific and some A3 can induce mutations on mitochondrial DNA (A3A, C, F, G, H) and nuclear DNA (A3A and A3B). Thus, the impact of those proteins on cancer formation is now established in cancers where mutations mostly show an APOBEC3 signature. In view of those considerations, we decided to study how those enzymes are regulated in the context of a viral cellular stress or an endogenous cellular stress. The first part of our work is focused on A3DE, the only APOBEC3 lacking a cytidine deaminase activity. Interestingly, A3DE is upregulated in cirrhotic livers infected by HBV, HCV or coinfected with HBV & HCV. We show that A3DE inhibits A3F & A3G activity by interacting with those HBV restriction involved A3. Then, we studied the attributes of the genotoxicity potential of A3B. This protein, by his strictly nuclear localization, constitutes the only double domain A3 which is not regulated by A3DE. Unlike A3A, A3B is weakly active on nuclear DNA and does not induce double strand breaks. We determine by directed mutagenesis the clusters of A3B involved in genotoxicity attenuation compared with A3A. We also show that this attenuation is conserved among primates. Finally, we investigated the role and regulation of A3A in the context of DNA catabolism. We proved that mitochondrial cytoplasmic DNA (mtcyDNA) triggers the RIG-I/DNA polymerase III pathway, which induces IFN production leading to A3A expression. So A3A will be involved in mtcyDNA catabolism and contribute to the clearance of this stress signal, but will also induce double strand breaks on nuclear DNA. A3 are major enzymes of the innate immune response and DNA catabolism. We show that A3DE modulates A3F and A3G activity while A3B is attenuated among primates and is less genotoxic than A3A. A3A participates to cytoplasmic DNA catabolism and limits inflammation. Nevertheless, A3A could be dangerous for the genomic integrity and contributes to cancer, especially in cases of chronic inflammation.Les protéines APOBEC3 (A3A-A3H) catalysent la désamination des cytidines (C) présentes sur l'ADN simple brin en thymidine (T). Cette activité cytidines désaminase a initialement été décrite comme impliquée dans la restriction des rétrovirus et de certains virus à ADN par leur capacité à induire de nombreuses mutations C->T, ou hypermutations, sur les génomes viraux. Il apparait néanmoins que leur activité n'est pas restreinte aux génomes viraux et que certaines A3 peuvent induire des mutations sur l'ADN mitochondrial (A3A, C, F, G et H) et nucléaire (A3A et A3B). Ainsi, l'impact somatique des A3 est désormais établi dans la formation de certains cancers, dont la majorité des mutations, portent signatures des APOBEC3. Aux vues de ces observations, nous nous sommes intéressés à la façon dont sont régulées ces enzymes dans le contexte du stress cellulaire viro-induit ou endogène. La première partie de nos travaux a porté sur la protéine A3DE, seul membre de la famille APOBEC3 ne possédant pas d'activité cytidine désaminase. De façon intéressante, il apparait qu'A3DE est surexprimée dans les cirrhoses infectées par le VHB, VHC ou co-infectées par le VHC et le VHB. Nous avons pu mettre en évidence qu'A3DE interagit et module l'activité d'A3F et d'A3G, deux cytidines désaminases exprimées dans le foie et impliquées dans la restriction du VHB. Dans un second temps, nous nous sommes intéressés à la caractérisation du potentiel génotoxique de la protéine A3B. Cette protéine, de par sa localisation strictement nucléaire, constitue la seule A3 à double domaine n'interagissant pas avec A3DE. Contrairement à A3A, A3B est faiblement active sur l’ADN nucléaire et n’induit pas de cassures de l’ADN double brin. Nous avons pu mettre en évidence par mutagénèse les régions de la protéine impliquées dans l’atténuation de la génotoxicité d’A3B par rapport à A3A et que cette atténuation est conservée chez les primates. Enfin, nous avons étudié le rôle et la régulation d’A3A dans le catabolisme. Nous avons mis en évidence que l’ADN mitochondrial cytoplasmique (ADNcymt) active la voie RIG-I/ARN polymérase III ce qui a pour effet d’induire la production d’IFN qui va activer l’expression d’A3A. A3A va ainsi jouer un rôle dans le catabolisme de l’ADNcymt et contribue à l'élimination de cette source de stress cellulaire, mais occasionnant par la même des dommages sur l’ADN nucléaire. Les A3 sont des enzymes fondamentales de la défense immunitaire innée et du catabolisme de l’ADN. Nous montrons qu’A3DE a pour fonction de moduler l’activité d’A3F et d’A3G tandis qu’A3B, possède un phénotype atténué chez tous les primates et s’avère moins génotoxique que’A3A. Cette dernière participe à la dégradation de l’ADN cytoplasmique, limitant ainsi l’inflammation. Néanmoins, A3A peut s’avérer dangereuse pour l’intégrité génomique et contribuer à l’émergence de cancers, notamment en cas d’inflammation chronique

Appropriation des projets de reconversion en irrigation localisée dans les oasis du Tafilalet : cas de la commune territoriale de Fezna

Dans les oasis du Maroc, l'agriculture irriguée est confrontée à une pénurie en eau croissante due à des sécheresses fréquentes et à une forte pression sur la ressource hydrique. Pour pallier à cette situation, les agriculteurs ont de plus en plus recours à l'irrigation localisée. Afin de comprendre les modes d'appropriation de cette nouvelle technique au sein des systèmes oasiens, nous avons analysé 7 projets de reconversion individuelle et collective à la technique du goutte-à-goutte dans l'oasis de Fezna dans le Tafilalet. Trois modes d'appropriation de cette nouvelle technique ont été distingués : i) une appropriation ouverte caractérisée par une logique de prise de risque ; ii) une appropriation plutôt conservatrice dominée par une logique sécuritaire et enfin iii) une appropriation par bricolage expliquée par le manque de moyens matériels. L'innovation du goutte-à-goutte contribue à une dynamique d'intensification agricole, mais qui, de façon paradoxale, se traduit aussi par un accroissement notoire du recours aux ressources en eau souterraines, et de ce fait peut contribuer à accentuer les problèmes de durabilité du fonctionnement de cette oasis

Expressed Sequence Tags from the oomycete Plasmopara halstedii, an obligate parasite of the sunflower

<p>Abstract</p> <p>Background</p> <p>Sunflower downy mildew is a major disease caused by the obligatory biotrophic oomycete <it>Plasmopara halstedii</it>. Little is known about the molecular mechanisms underlying its pathogenicity. In this study we used a genomics approach to gain a first insight into the transcriptome of <it>P. halstedii</it>.</p> <p>Results</p> <p>To identify genes from the obligatory biotrophic oomycete <it>Plasmopara halstedii </it>that are expressed during infection in sunflower (<it>Helianthus annuus </it>L.) we employed the suppression subtraction hybridization (SSH) method from sunflower seedlings infected by <it>P. halstedii</it>. Using this method and random sequencing of clones, a total of 602 expressed sequence tags (ESTs) corresponding to 230 unique sequence sets were identified. To determine the origin of the unisequences, PCR primers were designed to amplify these gene fragments from genomic DNA isolated either from <it>P. halstedii </it>sporangia or from <it>Helianthus annuus</it>. Only 145 nonredundant ESTs which correspond to a total of 373 ESTs (67.7%) proved to be derived from <it>P. halstedii </it>genes and that are expressed during infection in sunflower. A set of 87 nonredundant sequences were identified as showing matches to sequences deposited in public databases. Nevertheless, about 7% of the ESTs seem to be unique to <it>P. halstedii </it>without any homolog in any public database.</p> <p>Conclusion</p> <p>A summary of the assignment of nonredundant ESTs to functional categories as well as their relative abundance is listed and discussed. Annotation of the ESTs revealed a number of genes that could function in virulence. We provide a first glimpse into the gene content of <it>P. halstedii</it>. These resources should accelerate research on this important pathogen.</p

Harmonic-NAS: Hardware-Aware Multimodal Neural Architecture Search on Resource-constrained Devices

The recent surge of interest surrounding Multimodal Neural Networks (MM-NN) is attributed to their ability to effectively process and integrate multiscale information from diverse data sources. MM-NNs extract and fuse features from multiple modalities using adequate unimodal backbones and specific fusion networks. Although this helps strengthen the multimodal information representation, designing such networks is labor-intensive. It requires tuning the architectural parameters of the unimodal backbones, choosing the fusing point, and selecting the operations for fusion. Furthermore, multimodality AI is emerging as a cutting-edge option in Internet of Things (IoT) systems where inference latency and energy consumption are critical metrics in addition to accuracy. In this paper, we propose Harmonic-NAS, a framework for the joint optimization of unimodal backbones and multimodal fusion networks with hardware awareness on resource-constrained devices. Harmonic-NAS involves a two-tier optimization approach for the unimodal backbone architectures and fusion strategy and operators. By incorporating the hardware dimension into the optimization, evaluation results on various devices and multimodal datasets have demonstrated the superiority of Harmonic-NAS over state-of-the-art approaches achieving up to 10.9% accuracy improvement, 1.91x latency reduction, and 2.14x energy efficiency gain.Comment: Accepted to the 15th Asian Conference on Machine Learning (ACML 2023

Positional cloning of a candidate gene for resistance to the sunflower downy mildew, Plasmopara halstedii race 300.

International audienceThe resistance of sunflower to Plasmopara halstedii is conferred by major resistance genes denoted Pl. Previous genetic studies indicated that the majority of these genes are clustered on linkage groups 8 and 13. The Pl6 locus is one of the main clusters to have been identified, and confers resistance to several P. halstedii races. In this study, a map-based cloning strategy was implemented using a large segregating F2 population to establish a fine physical map of this cluster. A marker derived from a bacterial artificial chromosome (BAC) clone was found to be very tightly linked to the gene conferring resistance to race 300, and the corresponding BAC clone was sequenced and annotated. It contains several putative genes including three toll-interleukin receptor-nucleotide binding site-leucine rich repeats (TIR-NBS-LRR) genes. However, only one TIR-NBS-LRR appeared to be expressed, and thus constitutes a candidate gene for resistance to P. halstedii race 300

Plasma Levels of Pentosidine, Carboxymethyl-Lysine, Soluble Receptor for Advanced Glycation End Products, and Metabolic Syndrome: The Metformin Effect

Metabolic syndrome (MetS) is considered one of the most important public health problems. Several and controversial studies showed that the role of advanced glycation end products (AGEs) and their receptor in the development of metabolic syndrome and therapeutic pathways is still unsolved. We have investigated whether plasma pentosidine, carboxymethyl-lysine (CML), and soluble receptor for advanced glycation end products (sRAGE) levels were increased in patients with MetS and the effect of metformin in plasma levels of pentosidine, CML, and sRAGE. 80 control subjects and 86 patients were included in this study. Pentosidine, CML, and sRAGE were measured in plasma by enzyme-linked immunosorbent assay (ELISA). Plasma pentosidine, CML, and sRAGE levels were significantly increased in patients compared to control subjects ( &lt; 0.001, &lt; 0.001, and = 0.014, resp.). Plasma levels of pentosidine were significantly decreased in patients who received metformin compared to untreated patients ( = 0.01). However, there was no significant difference between patients treated with metformin and untreated patients in plasma CML levels. Plasma levels of sRAGE were significantly increased in patients who received metformin and ACE inhibitors ( &lt; 0.001 and = 0.002, resp.). However, in a multiple stepwise regression analysis, pentosidine, sRAGE, and drugs treatments were not independently associated. Patients with metabolic syndrome showed increased levels of AGEs such as pentosidine and CML. Metformin treatment showed a decreased level of pentosidine but not of CML. Therapeutic pathways of AGEs development should be taken into account and further experimental and in vitro studies merit for advanced research

Sterols from the brown alga Cystoseira foeniculacea: Degradation of fucosterol into saringosterol epimers

AbstractThe present study was carried out in order to determine the phytochemical composition of the marine brown alga Cystoseira foeniculacea collected off the coasts of Algeria. After a preliminary fractionation of its organic crude extracts by column chromatography, the resulting fractions were further analysed by 1H NMR. Even though algal species of the genus Cystoseira are commonly known to produce a wide variety of meroditerpenoids, in the case of C. foeniculacea none of the fractions were found to contain such compounds: most of the fractions showed typical 1H NMR signals of fatty acids and derivatives (mainly glycerolipids and glycolipids). Nevertheless, the thorough analysis of a sterol-enriched fraction by RP-C8 HPLC led to the isolation, for the first time from this species, of fucosterol (1) and a mixture of saringosterols (2 and 3). The NMR data of compounds 1–3 were fully determined with the help of 1D and 2D experiments which allowed the reassignment of some attributions in comparison with those reported in the literature. This work also confirms evidence of the oxidative degradation of fucosterol into a C-24 epimeric mixture of saringosterols