Topology Preserving Simplification of 2D Non-Manifold Meshes with Embedded Structures

International audienceMesh simplification has received tremendous attention over the past years. Most of the previous works deal with a proper choice of error measures to guide the simplification. Preserving the topological characteristics of the mesh and possibly of data attached to the mesh is a more recent topic, the present paper is about.We introduce a new topology preserving simplification algorithm for triangular meshes, possibly non-manifold, with embedded polylines. In this context embedded means that the edges of the polylines are also edges of the mesh. The paper introduces a robust test to detect if the collapse of an edge in the mesh modifies either the topology of the mesh or the topology of the embedded polylines. This validity test is derived using combinatorial topology results. More precisely we define a so-called extended complex from the input mesh and the embedded polylines. We show that if an edge collapse of the mesh preserves the topology of this extended complex, then it also preserves both the topology of the mesh and the embedded polylines. Our validity test can be used for any 2-complex mesh, including non-manifold triangular meshes. It can be combined with any previously introduced error measure. Implementation of this validity test is described. We demonstrate the power and versatility of our method with scientific data sets from neuroscience, geology and CAD/CAM models from mechanical engineering

Piecewise polynomial monotonic interpolation of 2D gridded data

International audienceA method for interpolating monotone increasing 2D scalar data with a monotone piecewise cubic C$^1$-continuous surface is presented. Monotonicity is a sufficient condition for a function to be free of critical points inside its domain. The standard axial monotonicity for tensor-product surfaces is however too restrictive. We therefore introduce a more relaxed monotonicity constraint. We derive sufficient conditions on the partial derivatives of the interpolating function to ensure its monotonicity. We then develop two algorithms to effectively construct a monotone C$^1$ surface composed of cubic triangular Bézier surfaces interpolating a monotone gridded data set. Our method enables to interpolate given topological data such as minima, maxima and saddle points at the corners of a rectangular domain without adding spurious extrema inside the function domain. Numerical examples are given to illustrate the performance of the algorithm

Human Lsg1 defines a family of essential GTPases that correlates with the evolution of compartmentalization

BACKGROUND: Compartmentalization is a key feature of eukaryotic cells, but its evolution remains poorly understood. GTPases are the oldest enzymes that use nucleotides as substrates and they participate in a wide range of cellular processes. Therefore, they are ideal tools for comparative genomic studies aimed at understanding how aspects of biological complexity such as cellular compartmentalization evolved. RESULTS: We describe the identification and characterization of a unique family of circularly permuted GTPases represented by the human orthologue of yeast Lsg1p. We placed the members of this family in the phylogenetic context of the YlqF Related GTPase (YRG) family, which are present in Eukarya, Bacteria and Archea and include the stem cell regulator Nucleostemin. To extend the computational analysis, we showed that hLsg1 is an essential GTPase predominantly located in the endoplasmic reticulum and, in some cells, in Cajal bodies in the nucleus. Comparison of localization and siRNA datasets suggests that all members of the family are essential GTPases that have increased in number as the compartmentalization of the eukaryotic cell and the ribosome biogenesis pathway have evolved. CONCLUSION: We propose a scenario, consistent with our data, for the evolution of this family: cytoplasmic components were first acquired, followed by nuclear components, and finally the mitochondrial and chloroplast elements were derived from different bacterial species, in parallel with the formation of the nucleolus and the specialization of nuclear components

A conserved structural element in the RNA helicase UPF1 regulates its catalytic activity in an isoform-specific manner

The RNA helicase UPF1 is a key component of the nonsense mediated mRNA decay (NMD) pathway. Previous X-ray crystal structures of UPF1 elucidated the molecular mechanisms of its catalytic activity and regulation. In this study, we examine features of the UPF1 core and identify a structural element that adopts different conformations in the various nucleotide- and RNA-bound states of UPF1. We demonstrate, using biochemical and single molecule assays, that this structural element modulates UPF1 catalytic activity and thereby refer to it as the regulatory loop. Interestingly, there are two alternatively spliced isoforms of UPF1 in mammals which differ only in the lengths of their regulatory loops. The loop in isoform 1 (UPF11) is 11 residues longer than that of isoform 2. We find that this small insertion in UPF11 leads to a two-fold increase in its translocation and ATPase activities. To determine the mechanistic basis of this differential catalytic activity, we have determined the X-ray crystal structure of the helicase core of UPF11 in its apo-state. Our results point toward a novel mechanism of regulation of RNA helicases, wherein alternative splicing leads to subtle structural rearrangements within the protein that are critical to modulate enzyme movements and catalytic activity

Crowd Navigation in VR: exploring haptic rendering of collisions

International audienceVirtual reality (VR) is a valuable experimental tool for studying human movement, including the analysis of interactions during locomotion tasks for developing crowd simulation algorithms. However, these studies are generally limited to distant interactions in crowds, due to the difficulty of rendering realistic sensations of collisions in VR. In this work, we explore the use of wearable haptics to render contacts during virtual crowd navigation. We focus on the behavioural changes occurring with or without haptic rendering during a navigation task in a dense crowd, as well as on potential after-effects introduced by the use haptic rendering. Our objective is to provide recommendations for designing VR setup to study crowd navigation behaviour. To this end, we designed an experiment (N=23) where participants navigated in a crowded virtual train station without, then with, and then again without haptic feedback of their collisions with virtual characters. Results show that providing haptic feedback improved the overall realism of the interaction, as participants more actively avoided collisions. We also noticed a significant after-effect in the users' behaviour when haptic rendering was once again disabled in the third part of the experiment. Nonetheless, haptic feedback did not have any significant impact on the users' sense of presence and embodiment

Genome sequencing of Xanthomonas axonopodis pv. phaseoli CFBP4834-R reveals that flagellar motility is not a general feature of xanthomonads.

Xanthomonads are plant-associated bacteria that establish neutral, commensal or pathogenic relationships with plants. The list of common characteristics shared by all members of the genus Xanthomonas is now well established based on the entire genome sequences that are currently available and that represent various species, numerous pathovars of X. axonopodis (sensu Vauterin et al., 2000), X. oryzae and X. campestris, and many strains within some pathovars. These ?-proteobacteria are motile by a single polar flagellum. Motility is an important feature involved in biofilm formation, plant colonization and hence considered as a pathogenicity factor. X. axonopodis pv. phaseoli var. fuscans (Xapf) is one of the causal agents of common bacterial blight of bean and 4834-R is a highly aggressive strain of this pathogen that was isolated from a seed-borne epidemic in France in 1998. We obtained a high quality assembled sequence of the genome of this strain with 454-Solexa and 2X Sanger sequencing. Housekeeping functions are conserved in this genome that shares core characteristics with genomes of other xanthomonads: the six secretion systems which have been described so far in Gram negative bacteria are all present, as well as their ubiquitous substrates or effectors and a rather usual number of mobile elements. Elements devoted to the adaptation to the environment constitute an important part of the genome with a chemotaxis island and dispersed MCPs, numerous two-component systems, and numerous TonB dependent transporters. Furthermore, numerous multidrug efflux systems and functions dedicated to biofilm formation that confer resistance to stresses are also present. An intriguing feature revealed by genome analysis is a long deletion of 35 genes (33 kbp) involved in flagellar biosynthesis. This deletion is replaced by an insertion sequence called ISXapf2. Genes such as flgB to flgL and fliC to fleQ which are involved in the flagellar structure (rod, P- and L-ring, hook, cap and filament) are absent in the genome of strain 4834-R that is not motile. Primers were designed to detect this deletion by PCR in a collection of more than 300 strains representing different species and pathovars of Xanthomonas, and less than 5% of the tested xanthomonads strains were found nonmotile because of a deletion in the flagellum gene cluster. We observed that half of the Xapf strains isolated from the same epidemic than strain 4834-R was non-motile and that this ratio was conserved in the strains colonizing the next bean seed generation. Isolation of such variants in a natural epidemic reveals that either flagellar motility is not a key function for fitness or that some complementation occurs within the bacterial population. (Résumé d'auteur

Genome sequence of Xanthomonas fuscans subsp. fuscans strain 4834-R reveals that flagellar motility is not a general feature of xanthomonads

Abstract\ud \ud \ud \ud Background\ud Xanthomonads are plant-associated bacteria responsible for diseases on economically important crops. Xanthomonas fuscans subsp. fuscans (Xff) is one of the causal agents of common bacterial blight of bean. In this study, the complete genome sequence of strain Xff 4834-R was determined and compared to other Xanthomonas genome sequences.\ud \ud \ud \ud Results\ud Comparative genomics analyses revealed core characteristics shared between Xff 4834-R and other xanthomonads including chemotaxis elements, two-component systems, TonB-dependent transporters, secretion systems (from T1SS to T6SS) and multiple effectors. For instance a repertoire of 29 Type 3 Effectors (T3Es) with two Transcription Activator-Like Effectors was predicted. Mobile elements were associated with major modifications in the genome structure and gene content in comparison to other Xanthomonas genomes. Notably, a deletion of 33 kbp affects flagellum biosynthesis in Xff 4834-R. The presence of a complete flagellar cluster was assessed in a collection of more than 300 strains representing different species and pathovars of Xanthomonas. Five percent of the tested strains presented a deletion in the flagellar cluster and were non-motile. Moreover, half of the Xff strains isolated from the same epidemic than 4834-R was non-motile and this ratio was conserved in the strains colonizing the next bean seed generations.\ud \ud \ud \ud Conclusions\ud This work describes the first genome of a Xanthomonas strain pathogenic on bean and reports the existence of non-motile xanthomonads belonging to different species and pathovars. Isolation of such Xff variants from a natural epidemic may suggest that flagellar motility is not a key function for in planta fitness.AI is funded by a PhD grant from INRA-SPE and region Pays de la Loire, France. EG was funded by a PhD grant from the French Ministry of National Education and Research and French Guyana. SC, EG, MA, EL and LDN are funded by the LABEX TULIP (ANR-10-LABX-41), LSG is funded by ANR-2010-GENM-013 Xanthomix

Hiérarchisation et visualisation multirésolution de résultats issus de codes de simulation

Les simulations numériques génèrent une quantité de résultats disproportionnée par rapport aux moyens d'exploitation, sans espoir d'atténuation à terme. Les maillages supportant ces simulations, sont composés de plusieurs dizaines de millions de cellules volumiques avec, plus spécifiquement, des sous-structures imbriquées de différentes dimensions (surfaciques et linéiques) et des couches minces de matériaux. En phase de post-traitement, un utilisateur devrait être capable de visualiser et de manipuler ces données, à temps interactif, sur sa propre machine d'exploitation. Cependant, les outils existants en visualisation scientifique ne permettent pas ou que partiellement d'atteindre les objectifs souhaités avec ce type de données (grand nombre de mailles, sous-structures, couches minces, . . .). Dans cette thèse, une approche par hiérarchisation des données est proposée afin de construire une représentation multirésolution autorisant la visualisation interactive d'une grande quantité d'information. L'étape de hiérarchisation est basée sur un algorithme de simplification de maillages, par contractions itératives d'arêtes, préservant à la fois la topologie du maillage et celle de toutes les sous-structures imbriquées. Les critères topologiques robustes introduits dans ces travaux, s'appuient sur des notions théoriques en topologie algébrique. L'étape de visualisation utilise la représentation multirésolution pour accélérer l'affichage des résultats. De façon progressive, inversible et locale, l'utilisateur modifie dynamiquement la résolution selon ses besoins et les ressources matérielles dont il dispose. Cette thèse illustre la mise en oeuvre de ces techniques de hiérarchisation et de visualisation dans de nombreux domaines d'applications notamment dans le cadre d'exploitation de résultats issus de simulations en électromagnétisme du CEA/CESTA.GRENOBLE1-BU Sciences (384212103) / SudocSudocFranceF

Ultra Low Power Ambient Artificial Intelligence

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