Computational investigations of folded self-avoiding walks related to protein folding

Various subsets of self-avoiding walks naturally appear when investigating existing methods designed to predict the 3D conformation of a protein of interest. Two such subsets, namely the folded and the unfoldable self-avoiding walks, are studied computationally in this article. We show that these two sets are equal and correspond to the whole $n$-step self-avoiding walks for $n\leqslant 14$, but that they are different for numerous $n \geqslant 108$, which are common protein lengths. Concrete counterexamples are provided and the computational methods used to discover them are completely detailed. A tool for studying these subsets of walks related to both pivot moves and proteins conformations is finally presented.Comment: Not yet submitte

Adaptation de modèles de Markov cachés - Application à la reconnaissance de caractères imprimés

International audienceWe present in this paper a new algorithm for the adaptation of hidden Markov models (HMM models). The principle of our iterative adaptive algorithm is to alternate an HMM structure adaptation stage with an HMM Gaussian MAP adaptation stage. This algorithm is applied to the recognition of printed characters to adapt the models learned by a polyfont character recognition engine to new forms of characters. Comparing the results with those of MAP and MLLR classic adaptations shows a slight increase in the performance of the recognition system

Détection automatique de la structure organisationnelle de documents à partir de marqueurs visuels et lexicaux

National audienceLa compréhension d'un texte s'opère à travers les niveaux d'information visuelle, logique et discursive, et leurs relations d'interdépendance. La majorité des travaux ayant étudié ces relations a été menée dans le cadre de la génération de textes, où les propriétés visuelles sont inférées à partir des éléments logiques et discursifs. Les travaux présentés ici adoptent une démarche inverse en proposant de générer automatiquement la structure organisationnelle du texte (structure logique) à partir de sa forme visuelle. Le principe consiste à (i) labelliser des blocs visuels par apprentissage afin d'obtenir des unités logiques et (ii) relier ces unités par des relations de coordination ou de subordination pour construire un arbre. Pour ces deux tâches, des Champs Aléatoires Conditionnels et un Maximum d'Entropie sont respectivement utilisés. Après apprentissage, les résultats aboutissent à une exactitude de 80,46% pour la labellisation et 97,23% pour la construction de l'arbre

Tomographic and Time-Resolved PIV measurement of an Impinging Jet on a Slotted Plate

In order to reveal the complete topology of unsteady coherent flow structures the instantaneous measurement of the 3D velocity field is being of the great interest in fluid mechanic. Several different methods were proposed to achieve a 3D version of the technique (scanning light sheet, holography, 3D PTV). We aimed in our study to develop a 3D technique than enables to obtain the 3D kinematic field of an impinging jet by using 2D measurements. In this study and in order to validate the proposed technique [1], the tomographic particle image velocimetry technique has been applied to time resolved PIV recordings. The first step before the validation was to study the vortex shedding phenomena between the jet exit and the slotted plate. The experiments were performed at a Re = 4458 with an initial velocity U0=7m/s using three cameras Phantom V711 and a Nd: YLF LDY 300 Litron laser. In the present study, we analyzed the coherent structures organization by a 3D-velocity visualization. Both mean and fluctuating part of velocity were analyzed for several positions in z. The results has shown that a couple of vortex rolls are created downstream the flow at y/H=2

Volumetric Proper Orthogonal Decomposition of an impinging jet using SPIV measurement

Impinging jets which interact with sharp edges like slotted plates can be found in ventilation and air conditioning systems. In some cases, these configurations can be a source of desirable sounds like in musical instruments. However, they can be a source of noise in other applications such as air conditioning systems. Thus in order to reduce the noise produced from such configurations a more profound study of the flow dynamics should be implemented. All previous studies of impinging jets on a slotted plate were done in 2D. Accordingly, the objective of the present study was to reconstruct the studied volume by combining stereoscopic PIV measurements and the POD method. Consequently, an experimental set up has been developed and implemented in order to generate a flow that hits a slotted plate. On the other side, the PIV technique was used in order to study the dynamics of such a flow. The kinematic fields of twenty two parallel planes are measured by means of stereoscopic PIV. Afterwards, the analysis of the most energetic modes was obtained by the application of the snapshot POD on the kinematic fields obtained by POD. The results showed that the reconstruction of each of the planes needed only three first three modes. The reconstructed volume is obtained by an interpolation of the reconstructed planes which were phased by a trigger signal. The analysis of the vortex structures were done by the application of several vortex detection criteria

Cost-effectiveness of screening of coronary artery disease in patients with type 2 DIABetes at a very high cardiovascular risk (SCADIAB study) rational and design

Background: Screening for coronary artery disease (CAD) remains broadly performed in patients with type 2 diabetes (T2DM), although the lack of evidence. We conduct a real-world evidence (RWE) study to assess the risk of major clinical outcomes and economic impact of routine CAD screening in T2DM individuals at a very high cardiovascular risk. Methods: SCADIAB is a comparative nationwide cohort study using data from the French National Health Data System. The main inclusion criteria are: age ≥ 40 years, DT2 diagnosed for ≥ 7 years, with ≥ 2 additional cardiovascular risk factors plus a history of microvascular or macrovascular disease, except CAD. We estimated ≥ 90,000 eligible participants for our study. Data will be extracted from 01/01/2008 to 31/12/2019. Eligible participants will be identified during a first 7-year selection period (2008–2015). Each participant will be assigned either in experimental (CAD screening procedure during the selection period) or control group (no CAD screening) on 01/01/2015, and followed for 5 years. The primary endpoint is the incremental cost per life year saved over 5 years in CAD screening group versus no CAD screening. The main secondary endpoints are: total 5-year direct costs of each strategy; incidence of major cardiovascular (acute coronary syndrome, hospitalization for heart failure, coronary revascularization or all-cause death), cerebrovascular (hospitalization for transient ischemic attack, stroke, or carotid revascularization) and lower-limb events (peripheral artery disease, ischemic diabetic foot, lower-limb revascularization or amputation); and the budget impact for the French Insurance system to promote the cost-effective strategy. Analyses will be adjusted for a high-dimension propensity score taking into account known and unknown confounders. SCADIAB has been funded by the French Ministry of Health and the protocol has been approved by the French ethic authorities. Data management and analyses will start in the second half of 2021. Discussion: SCADIAB is a large and contemporary RWE study that will assess the economic and clinical impacts of routine CAD screening in T2DM people at a very high cardiovascular risk. It will also evaluate the clinical practice regarding CAD screening and help to make future recommendations and optimize the use of health care resources

Differences in proteome perturbations caused by the Wolbachia strain wAu suggest multiple mechanisms of Wolbachia-mediated antiviral activity.

All datasets used for the named publication. Including Prism files used to produce graphs, images and cellprofile files used to measure spots in cells

Differences in proteome perturbations caused by the Wolbachia strain wAu suggest multiple mechanisms of Wolbachia-mediated antiviral activity

Some strains of the inherited bacterium Wolbachia have been shown to be effective at reducing the transmission of dengue virus (DENV) and other RNA viruses by Aedes aegypti in both laboratory and field settings and are being deployed for DENV control. The degree of virus inhibition varies between Wolbachia strains. Density and tissue tropism can contribute to these differences but there are also indications that this is not the only factor involved: for example, strains wAu and wAlbA are maintained at similar intracellular densities but only wAu produces strong DENV inhibition. We previously reported perturbations in lipid transport dynamics, including sequestration of cholesterol in lipid droplets, with strains wMel/wMelPop in Ae. aegypti. To further investigate the cellular basis underlying these differences, proteomic analysis of midguts was carried out on Ae. aegypti lines carrying strains wAu and wAlbA: with the hypothesis that differences in perturbations may underline Wolbachia-mediated antiviral activity. Surprisingly, wAu-carrying midguts not only showed distinct proteome perturbations when compared to non-Wolbachia carrying and wAlbA-carrying midguts but also wMel-carrying midguts. There are changes in RNA processing pathways and upregulation of a specific set of RNA-binding proteins in the wAu-carrying line, including genes with known antiviral activity. Lipid transport and metabolism proteome changes also differ between strains, and we show that strain wAu does not produce the same cholesterol sequestration phenotype as wMel. Moreover, in contrast to wMel, wAu antiviral activity was not rescued by cyclodextrin treatment. Together these results suggest that wAu could show unique features in its inhibition of arboviruses compared to previously characterized Wolbachia strains