Detecting wheels

A \emph{wheel} is a graph made of a cycle of length at least~4 together with a vertex that has at least three neighbors in the cycle. We prove that the problem whose instance is a graph $G$ and whose question is "does $G$ contains a wheel as an induced subgraph" is NP-complete. We also settle the complexity of several similar problems

Relations structure/fonction de la dynamine mitochondriale Msp1 : étude de ses relations avec la membrane interne et de ses activités biochimiques

La dynamique mitochondriale est définie comme un équilibre entre des forces antagonistes de fusion et de fission des membranes qui modulent la morphologie des mitochondries et jouent un rôle majeur dans la régulation des fonctions de l'organelle. Notre équipe a identifié l'un des acteurs de cette dynamique, une GTPase de la famille des dynamines appelée Msp1 chez la levure S. pombe et OPA1 chez l'homme. Le dysfonctionnement d'OPA1 est responsable de l'atrophie optique dominante de type 1. Cette dynamine agit sur la fusion des mitochondries, la structure des crêtes et le maintien de l'ADN mitochondrial (ADNmt). Elle module aussi la respiration et la synthèse d'ATP, avec des conséquences sur la viabilité cellulaire et sur l'apoptose chez les eucaryotes supérieurs. Au vue de cette pléiotropie, notre hypothèse est que la dynamine OPA1/Msp1 intervient dans l'organisation de la membrane interne des mitochondries. Mon travail de thèse a été initié pour définir les activités biochimiques de Msp1 à l'origine de ses effets biologiques, et les bases structurales sous-jacentes. Le rôle de deux domaines hydrophobes (TM1 et TM2) dans l'association aux membranes et les fonctions de Msp1 a été analysé in vivo dans la levure S. pombe. Les propriétés biochimiques de Msp1 dans l'organisation des membranes ont été étudiées in vitro après purification et reconstitution dans des liposomes de composition phospholipidique similaire à celle de la membrane interne. Nos études in vivo ont montré que TM1 et TM2, et un troisième site d'interaction membranaire (SIM3), ont des rôles distincts dans l'association de Msp1 aux membranes, et dans la fusion des mitochondries et le maintien de l'ADNmt. Nous suggérons que l'organisation locale de la membrane interne est modulée par les proportions relatives des sites (TM1 + TM2) / SIM3, reflet du rapport entre une forme longue, l-Msp1, et une forme courte, s-Msp1, qui co-existent naturellement chez la levure et diffèrent par la présence de TM1 et TM2 dans l-Msp1 uniquement, SIM3 étant commun aux deux isoformes. Dans notre système in vitro, l'association de l-Msp1 et s-Msp1 aux liposomes et leur topologie reproduisent la situation observée dans les mitochondries. Nous avons montré que s-Msp1 a une activité GTPase caractéristique des dynamines avec une faible affinité apparente pour le GTP et une forte activité catalytique et qu'un motif coiled-coil C-terminal est nécessaire au développement de cette activité. Grâce à ce système, nous mettons en évidence pour la première fois que Msp1 favorise l'hémifusion des liposomes et a donc un rôle direct dans la fusion membranaire. L'hémifusion est induite par les deux isoformes l Msp1 et s-Msp1 et est indépendante de l'activité GTPase et de l'oligomérisation de la dynamine. SIM3, qui est commun à l-Msp1 et s-Msp1, pourrait donc contenir les éléments structuraux requis pour l'hémifusion. L'ensemble de ce travail nous permet de proposer un modèle dans lequel Msp1 agirait comme organisateur de la membrane et comme commutateur moléculaire. A chacun de ses sites d'action, la dynamine entrerait dans des complexes multi-protéiques distincts dont la composition dépendrait des proportions relatives de chacune des isoformes, donc du rapport (TM1+TM2) / SIM3. La modification de ce rapport par l'hydrolyse du GTP modulerait l'organisation locale de la membrane et donc la composition et l'activité de ces complexes.Mitochondrial dynamics is defined as an equilibrium between antagonistic fusion and fission forces that control mitochondrial morphology and play a major role in the regulation of mitochondrial functions. Our group identified one actor of mitochondrial dynamics, a GTPase of the dynamins' family called Msp1 in the S.pombe yeast and OPA1 in humans. OPA1 dysfunction leads to type 1 dominant optic atrophy. This dynamin acts in mitochondrial fusion and is involved in the maintenance of cristae structure and of mitochondrial DNA (mtDNA). It also controls respiration and ATP synthesis with impacts on cellular viability and apoptosis in higher eukaryotes. Given this large spectrum of action, our hypothesis is that Msp1/OPA1 acts on the organization of the mitochondrial inner membrane. My PhD thesis was initiated to define the biochemical activities of Msp1 responsible for its biological effects, and the underlying structural basis. The role of two hydrophobic domains (TM1 and TM2) in Msp1 membrane association and functions was analysed in vivo in S. pombe cells. The biochemical properties of Msp1 in membranes organization were studied in vitro after purification and reconstitution into liposomes of phospholipd composition similar to that of the mitochondrial inner membrane. Our in vivo studies showed that TM1 and TM2, and a third site of membrane interaction (SIM3), play distinct roles in Msp1 membrane association and in mitochondrial fusion and mtDNA maintenance. We suggest that the local organisation of the inner membrane varies with the relative proportions of the domains (TM1+TM2)/SIM3 reflecting the ratio between a long, l-Msp1, and a short, s-Msp1, isoform that naturally occur in S. pombe and differ by the presence of TM1 and TM2 in l-Msp1 only, SIM 3 being common to both. In our in vitro system, the association and topology of l-Msp1 and s-Msp1 onto liposomes are similar to that observed in mitochondria. We showed that s-Msp1 has a GTPase activity similar to that of dynamins, with a low affinity for GTP and a high catalytic activity, and that a C-terminal coiled-coil motif is essential for this activity. With this system we show for the first time that Msp1 induces hemifusion of liposomes, indicating a direct role in membrane fusion. Hemifusion was induced by both l-Msp1 and s-Msp1 isoforms and was independent from GTPase activity and from self-assembly. SIM3, which is common to l-Msp1 and s-Msp1, may thus contain the structural requirements for hemifusion. Altogether, this work allows us to propose a model in which Msp1 could act as a membrane organizer and as a molecular switch. At each of its sites of action, the dynamin could enter in distinct multi-protein complexes, the composition of which could depend on the relative proportions of each Msp1 isoforms, i.e. of the (TM1+TM2)/SIM3 ratio. Modification of this ratio by GTP hydrolysis would modulate local membrane organisation, and hence the composition and activity of these complexes

A Two-step Statistical Approach for Inferring Network Traffic Demands (Revises Technical Report BUCS-2003-003)

Accurate knowledge of traffic demands in a communication network enables or enhances a variety of traffic engineering and network management tasks of paramount importance for operational networks. Directly measuring a complete set of these demands is prohibitively expensive because of the huge amounts of data that must be collected and the performance impact that such measurements would impose on the regular behavior of the network. As a consequence, we must rely on statistical techniques to produce estimates of actual traffic demands from partial information. The performance of such techniques is however limited due to their reliance on limited information and the high amount of computations they incur, which limits their convergence behavior. In this paper we study a two-step approach for inferring network traffic demands. First we elaborate and evaluate a modeling approach for generating good starting points to be fed to iterative statistical inference techniques. We call these starting points informed priors since they are obtained using actual network information such as packet traces and SNMP link counts. Second we provide a very fast variant of the EM algorithm which extends its computation range, increasing its accuracy and decreasing its dependence on the quality of the starting point. Finally, we evaluate and compare alternative mechanisms for generating starting points and the convergence characteristics of our EM algorithm against a recently proposed Weighted Least Squares approach.National Science Foundation (ANI-0095988, EIA-0202067, ITR ANI-0205294

Analysis of OD Flows (Raw Data)

In a recent paper, Structural Analysis of Network Traffic Flows, we analyzed the set of Origin Destination traffic flows from the Sprint-Europe and Abilene backbone networks. This report presents the complete set of results from analyzing data from both networks. The results in this report are specific to the Sprint-1 and Abilene datasets studied in the above paper. The following results are presented here: 1 Rows of Principal Matrix (V) 2 1.1 Sprint-1 Dataset ................................ 2 1.2 Abilene Dataset.................................. 9 2 Set of Eigenflows 14 2.1 Sprint-1 Dataset.................................. 14 2.2 Abilene Dataset................................... 21 3 Classifying Eigenflows 26 3.1 Sprint-1 Dataset.................................. 26 3.2 Abilene Datase.................................... 44Centre National de la Recherche Scientifique (CNRS) France; Sprint Labs; Office of Naval Research (N000140310043); National Science Foundation (ANI-9986397, CCR-0325701

Personalized modeling for real-time pressure ulcer prevention in sitting posture

, Ischial pressure ulcer is an important risk for every paraplegic person and a major public health issue. Pressure ulcers appear following excessive compression of buttock's soft tissues by bony structures, and particularly in ischial and sacral bones. Current prevention techniques are mainly based on daily skin inspection to spot red patches or injuries. Nevertheless, most pressure ulcers occur internally and are difficult to detect early. Estimating internal strains within soft tissues could help to evaluate the risk of pressure ulcer. A subject-specific biomechanical model could be used to assess internal strains from measured skin surface pressures. However, a realistic 3D non-linear Finite Element buttock model, with different layers of tissue materials for skin, fat and muscles, requires somewhere between minutes and hours to compute, therefore forbidding its use in a real-time daily prevention context. In this article, we propose to optimize these computations by using a reduced order modeling technique (ROM) based on proper orthogonal decompositions of the pressure and strain fields coupled with a machine learning method. ROM allows strains to be evaluated inside the model interactively (i.e. in less than a second) for any pressure field measured below the buttocks. In our case, with only 19 modes of variation of pressure patterns, an error divergence of one percent is observed compared to the full scale simulation for evaluating the strain field. This reduced model could therefore be the first step towards interactive pressure ulcer prevention in a daily setup. Highlights-Buttocks biomechanical modelling,-Reduced order model,-Daily pressure ulcer prevention

A high-order finite volume method for hyperbolic systems: Multi-dimensional Optimal Order Detection (MOOD).

International audienceIn this paper, we investigate an original way to deal with the problems generated by the limitation process of high-order finite volume methods based on polynomial reconstructions. Multi-dimensional Optimal Order Detection (MOOD) breaks away from classical limitations employed in high-order methods. The proposed method consists of detecting problematic situations after each time update of the solution and of reducing the local polynomial degree before recomputing the solution. As multi-dimensional MUSCL methods, the concept is simple and independent of mesh structure. Moreover MOOD is able to take physical constraints such as density and pressure positivity into account through an “a posteriori” detection. Numer- ical results on classical and demanding test cases for advection and Euler system are presented on quadrangular meshes to support the promising potential of this approach

The MOOD method in the three-dimensional case: Very-High-Order Finite Volume Method for Hyperbolic Systems.

The Multi-dimensional Optimal Order Detection (MOOD) method for two-dimensional geometries has been introduced in "A high-order finite volume method for hyperbolic systems: Multi-dimensional Optimal Order Detection (MOOD)", J. Comput. Phys. 230 (2011), and enhanced in "Improved Detection Criteria for the Multi-dimensional Optimal Order Detection (MOOD) on unstructured meshes with very high-order polynomials", Comput. & Fluids 64 (2012). We present in this paper the extension to 3D mixed meshes composed of tetrahedra, hexahedra, pyramids and prisms. In addition, we simplify the u2 detection process previously developed and show on a relevant set of numerical tests for both the convection equation and the Euler system that the optimal high-order of accuracy is reached on smooth solutions while spurious oscillations near singularities are prevented. At last, the intrinsic positivity-preserving property of the MOOD method is confirmed in 3D and we provide simple optimizations to reduce the computational cost such that the MOOD method is very competitive compared to existing high-order Finite Volume methods

Three-dimensional preliminary results of the MOOD method: A Very High-Order Finite Volume method for Conservation Laws.

The Multi-dimensional Optimal Order Detection (MOOD) method has been designed by authors in [5] and extended in [7] to reach Very-High-Order of accuracy for systems of Conservation Laws in a Finite Volume (FV) framework on 2D unstructured meshes. In this paper we focus on the extension of this method to 3D unstructured meshes. We present preliminary results for the three-dimensional advection equation which confirm the good behaviour of the MOOD method. More precisely, we show that the scheme yields up to sixth-order accuracy on smooth solutions while preventing oscillations from appearing on discontinuous profiles

Multi-dimensional Optimal Order Detection (MOOD) — A very high-order Finite Volume Scheme for conservation laws on unstructured meshes.

Preprint for Finite Volume for Complex Applications 6 (FVCA6)The Multi-dimensional Optimal Order Detection (MOOD) method is an original Very High-Order Finite Volume (FV) method for conservation laws on unstructured meshes. The method is based on an a posteriori degree reduction of local polynomial reconstructions on cells where prescribed stability conditions are not fulfilled. Numerical experiments on advection and Euler equations problems are drawn to prove the efficiency and competitiveness of the MOOD method