Showing papers by "Conservatoire national des arts et métiers published in 2013"

Improved whole-chromosome phasing for disease and population genetic studies.

Abstract: SHAPEIT2 uses multithreading so that multiple cores can be used to phase whole chromosomes, allowing users to make the best use of their computational resources. We tested SHAPEIT2 on several large-sample, whole-chromosome data sets from a range of SNP genotyping chips (Supplementary Note 1). SHAPEIT2 outperforms other methods (Fig. 1a–c) in terms of switch error rate (SER) and the mean distance between switch errors (Supplementary Figs. 1 and 2). As compared to SHAPEIT1, SHAPEIT2 reduced SER by as much as 45% on these data sets. For example, on 1,229 Vietnamese samples assayed on the Illumina 660K chip on chromosome 22, the SERs of SHAPEIT2 (K = 100, W = 2 Mb), SHAPEIT1 (K = 100) (ref. 2), HAPI-UR (v1.01) (ref. 4), Beagle (v3.3) (ref. 5), Impute2 v2.1.2 (K = 100) (ref. 3), MaCH v1.0.18 (K = 100) (ref. 6) and fastPHASE (v1.4) (ref. 7) were 2.87%, 4.64%, 4.75%, 5.14%, 5.57%, 6.05% and 6.34%, respectively. In general, SHAPEIT2 with low values of K outperformed SHAPEIT1 with high values of K (Fig. 1a–c). As the number of samples increased (up to ~9,000 samples in our tests), we found that SHAPEIT2 outperformed other methods and had the property that SER decreases as sample size increases (Fig. 1d). We assessed accuracy on sequence data by phasing 381 European samples from the 1000 Genomes Project (TGP) together with genotypes from two trio parents sequenced at high coverage. We found that SHAPEIT2 (K = 100, W = 0.3 Mb) reduced SER by 38% compared to Beagle (Supplementary Table 1 and Supplementary Note 2), illustrating that the SHAPEIT2 model can adapt to data sets with very high SNP density. The computational performance of SHAPEIT2 is competitive compared to other methods. Figure 1e shows the computational Improved whole-chromosome phasing for disease and population genetic studies

Haplotype Estimation Using Sequencing Reads

Abstract: High-throughput sequencing technologies produce short sequence reads that can contain phase information if they span two or more heterozygote genotypes. This information is not routinely used by current methods that infer haplotypes from genotype data. We have extended the SHAPEIT2 method to use phase-informative sequencing reads to improve phasing accuracy. Our model incorporates the read information in a probabilistic model through base quality scores within each read. The method is primarily designed for high-coverage sequence data or data sets that already have genotypes called. One important application is phasing of single samples sequenced at high coverage for use in medical sequencing and studies of rare diseases. Our method can also use existing panels of reference haplotypes. We tested the method by using a mother-father-child trio sequenced at high-coverage by Illumina together with the low-coverage sequence data from the 1000 Genomes Project (1000GP). We found that use of phase-informative reads increases the mean distance between switch errors by 22% from 274.4 kb to 328.6 kb. We also used male chromosome X haplotypes from the 1000GP samples to simulate sequencing reads with varying insert size, read length, and base error rate. When using short 100 bp paired-end reads, we found that using mixtures of insert sizes produced the best results. When using longer reads with high error rates (5–20 kb read with 4%–15% error per base), phasing performance was substantially improved.

Control of Nonlinear and LPV Systems: Interval Observer-Based Framework

Abstract: The problem of output stabilization of a class of nonlinear systems subject to parametric and signal uncertainties is studied. First, an interval observer is designed estimating the set of admissible values for the state. Next, it is proposed to design a control algorithm for the interval observer providing convergence of interval variables to zero, that implies a similar convergence of the state for the original nonlinear system. An application of the proposed technique shows that a robust stabilization can be performed for linear time-varying and linear-parameter-varying (LPV) systems without assumption that the vector of scheduling parameters is available for measurements. Efficiency of the proposed approach is demonstrated through two examples.

Potential of Lignins as Antioxidant Additive in Active Biodegradable Packaging Materials

Abstract: Due to their polyphenolic structure lignins bear a number of interesting functional properties, such as antioxidant activity. Natural antioxidants are very much looked for in the aim of protection of light or oxygen sensitive goods and are being used in active packaging. Poly(lactide) (PLA)-lignin films were prepared by twin screw extrusion followed by thermo-compression using two different commercial sources of alkali lignins obtained from gramineous plants. A good dispersion of lignin in the matrix was observed. Mechanical properties of the compounded material were merely diminished and oxygen barrier properties slightly enhanced. The chromatographic study of the lignins revealed that the low molecular weight fraction of both lignins increased during the polymer processing. The migration of low molecular weight compounds in an ethanol/water solution simulating fatty foodstuff was performed and the antioxidant activity of the extract was analysed. It was found that the activity increases with increasing severity of the heat treatment because of the generation of free phenolic monomers during processing. These results open an interesting way for application of lignins as an active compound in packaging materials. Lignins do not impair the mechanical and barrier performance of the polymer and the plastics processing even allows for the generation of active substances.

Interval Observers for Time-Varying Discrete-Time Systems

Abstract: This techical note deals with interval state observer design for time-varying discrete-time systems. The problem of a similarity transformation computation which connects a (time-varying) matrix and its nonnegative representation is studied. Three solutions are proposed: for a generic time-varying system, a system with positive state, and for a particular class of periodical systems. Numerical simulations are provided to demonstrate advantages of the developed techniques.

Association study of common genetic variants and HIV-1 acquisition in 6,300 infected cases and 7,200 controls

Abstract: Multiple genome-wide association studies (GWAS) have been performed in HIV-1 infected individuals, identifying common genetic influences on viral control and disease course. Similarly, common genetic correlates of acquisition of HIV-1 after exposure have been interrogated using GWAS, although in generally small samples. Under the auspices of the International Collaboration for the Genomics of HIV, we have combined the genome-wide single nucleotide polymorphism (SNP) data collected by 25 cohorts, studies, or institutions on HIV-1 infected individuals and compared them to carefully matched population-level data sets (a list of all collaborators appears in Note S1 in Text S1). After imputation using the 1,000 Genomes Project reference panel, we tested approximately 8 million common DNA variants (SNPs and indels) for association with HIV-1 acquisition in 6,334 infected patients and 7,247 population samples of European ancestry. Initial association testing identified the SNP rs4418214, the C allele of which is known to tag the HLA-B*57:01 and B*27:05 alleles, as genome-wide significant (p = 3.6×10−11). However, restricting analysis to individuals with a known date of seroconversion suggested that this association was due to the frailty bias in studies of lethal diseases. Further analyses including testing recessive genetic models, testing for bulk effects of non-genome-wide significant variants, stratifying by sexual or parenteral transmission risk and testing previously reported associations showed no evidence for genetic influence on HIV-1 acquisition (with the exception of CCR5Δ32 homozygosity). Thus, these data suggest that genetic influences on HIV acquisition are either rare or have smaller effects than can be detected by this sample size.

How much can air conditioning increase air temperatures for a city like Paris, France?

Abstract: A consequence of urban heat islands in summer is an increase in the use of air conditioning in urbanized areas, which while cooling the insides of buildings, releases waste heat to the atmosphere. A coupled model consisting of a meso-scale meteorological model (MESO-NH) and an urban energy balance model (TEB) has been used to simulate and quantify the potential impacts on street temperature of four air conditioning scenarios at the scale of Paris. The first case consists of simulating the current types of systems in the city and was based on inventories of dry and evaporative cooling towers and free cooling systems with the river Seine. The other three scenarios were chosen to test the impacts of likely trends in air conditioning equipment in the city: one for which all evaporative and free cooling systems were replaced by dry systems, and the other two designed on a future doubling of the overall air conditioning power but with different technologies. The comparison between the scenarios with heat releases in the street and the baseline case without air conditioning showed a systematic increase in the street air temperature, and this increase was greater at nighttime than day time. It is counter-intuitive because the heat releases are higher during the day. This is due to the shallower atmospheric boundary layer during the night. The increase in temperature was 0.5 °C in the situation with current heat releases, 1 °C with current releases converted to only sensible heat, and 2 °C for the future doubling of air conditioning waste heat released to air. These results demonstrated to what extent the use of air conditioning could enhance street air temperatures at the scale of a city like Paris, and the importance of a spatialized approach for a reasoned planning for future deployment of air conditioning in the city.

Partial least squares algorithms and methods

Abstract: Partial least squares (PLS) refers to a set of iterative algorithms based on least squares that implement a broad spectrum of both explanatory and exploratory multivariate techniques, from regression to path modeling, and from principal component to multi-block data analysis. This article focuses on PLS regression and PLS path modeling, which are PLS approaches to regularized regression and to predictive path modeling. The computational flows and the optimization criteria of these methods are reviewed in detail, as well as the tools for the assessment and interpretation of PLS models. The most recent developments and some of the most promising on going researches are enhanced. WIREs Comput Stat 2013, 5:1–19. doi: 10.1002/wics.1239

Dual inhibition of HIV-1 replication by integrase-LEDGF allosteric inhibitors is predominant at the post-integration stage.

Abstract: LEDGF/p75 (LEDGF) is the main cellular cofactor of HIV-1 integrase (IN). It acts as a tethering factor for IN, and targets the integration of HIV in actively transcribed gene regions of chromatin. A recently developed class of IN allosteric inhibitors can inhibit the LEDGF-IN interaction. We describe a new series of IN-LEDGF allosteric inhibitors, the most active of which is Mut101. We determined the crystal structure of Mut101 in complex with IN and showed that the compound binds to the LEDGF-binding pocket, promoting conformational changes of IN which explain at the atomic level the allosteric effect of the IN/LEDGF interaction inhibitor on IN functions. In vitro, Mut101 inhibited both IN-LEDGF interaction and IN strand transfer activity while enhancing IN-IN interaction. Time of addition experiments indicated that Mut101 behaved as an integration inhibitor. Mut101 was fully active on HIV-1 mutants resistant to INSTIs and other classes of anti-HIV drugs, indicative that this compound has a new mode of action. However, we found that Mut101 also displayed a more potent antiretroviral activity at a post-integration step. Infectivity of viral particles produced in presence of Mut101 was severely decreased. This latter effect also required the binding of the compound to the LEDGF-binding pocket. Mut101 has dual anti-HIV-1 activity, at integration and post-integration steps of the viral replication cycle, by binding to a unique target on IN (the LEDGF-binding pocket). The post-integration block of HIV-1 replication in virus-producer cells is the mechanism by which Mut101 is most active as an antiretroviral. To explain this difference between Mut101 antiretroviral activity at integration and post-integration stages, we propose the following model: LEDGF is a nuclear, chromatin-bound protein that is absent in the cytoplasm. Therefore, LEDGF can outcompete compound binding to IN in the nucleus of target cells lowering its antiretroviral activity at integration, but not in the cytoplasm where post-integration production of infectious viral particles takes place.

On interval observer design for time-invariant discrete-time systems

Abstract: The problem of interval state observer design is addressed for time-invariant discrete-time systems. Two solutions are proposed: the first one is based on a similarity transformation synthesis, which connects a constant matrix with its nonnegative representation ensuring the observation error positivity. The second contribution shows that in the discrete-time case the estimation error dynamics always can be represented in a cooperative form without a transformation of coordinates. The corresponding observer gain can be found as a solution of the formulated LMIs. The performances of the proposed observers are demonstrated through computer simulations.

Plastids of marine phytoplankton produce bioactive pigments and lipids.

Abstract: Phytoplankton is acknowledged to be a very diverse source of bioactive molecules. These compounds play physiological roles that allow cells to deal with changes of the environmental constrains. For example, the diversity of light harvesting pigments allows efficient photosynthesis at different depths in the seawater column. Identically, lipid composition of cell membranes can vary according to environmental factors. This, together with the heterogenous evolutionary origin of taxa, makes the chemical diversity of phytoplankton compounds much larger than in terrestrial plants. This contribution is dedicated to pigments and lipids synthesized within or from plastids/photosynthetic membranes. It starts with a short review of cyanobacteria and microalgae phylogeny. Then the bioactivity of pigments and lipids (anti-oxidant, anti-inflammatory, anti-mutagenic, anti-cancer, anti-obesity, anti-allergic activities, and cardio- neuro-, hepato- and photoprotective effects), alone or in combination, is detailed. To increase the cellular production of bioactive compounds, specific culture conditions may be applied (e.g., high light intensity, nitrogen starvation). Regardless of the progress made in blue biotechnologies, the production of bioactive compounds is still limited. However, some examples of large scale production are given, and perspectives are suggested in the final section.

Becker and foucault on crime and punishment

Abstract: In his 1979 lectures at the College de France, The Birth of Biopolitics, Michel Foucault discussed and analyzed Gary Becker’s economic theory of crime and punishment, originally published in The Journal of Political Economy in 1968 under the title “Crime and Punishment: An Economic Approach.” In this historic, second encounter at the University of Chicago, Gary Becker responds to Foucault’s lectures and possible critical readings of his writings on crime and punishment, in conversation with Professors Francois Ewald (who was, at the time in 1979, Foucault’s assistant at the College and one of Foucault’s closest interlocutors) and Bernard Harcourt (a punishment theorist and an editor of Foucault’s lectures). The rich encounter explores potential overlaps, complementarities, and conflicts between Foucault’s theoretical work on punishment (both in Birth of Biopolitics and Discipline and Punish) and Becker’s economic theory of crime, builds on the previous confrontation over American neoliberalism, and provides a bridge between contemporary French philosophy and American economic theory.

Weakly Coupled Systems in Quantum Control

Abstract: Weakly coupled systems are a class of infinite dimensional conservative bilinear control systems with discrete spectrum. An important feature of these systems is that they can be precisely approached by finite dimensional Galerkin approximations. This property is of particular interest for the approximation of quantum system dynamics and the control of the bilinear Schrodinger equation. The present study provides rigorous definitions and analysis of the dynamics of weakly coupled systems and gives sufficient conditions for an infinite dimensional quantum control system to be weakly coupled. As an illustration we provide examples chosen among common physical systems.

Towards realistic estimates of HCV incidence in Egypt.

Abstract: Accurate incidence estimates are essential for quantifying hepatitis C virus (HCV) epidemic dynamics and monitoring the effectiveness of public health programmes, as well as for predicting future burden of disease and planning patient care. In Egypt, the country with the largest HCV epidemic worldwide, two modelling studies have estimated age-specific incidence rates that, applied to the age pyramid, would correspond to more than 500 000 Egyptians getting infected annually. This is in contrast to figures of the Egyptian Ministry of Health and Population that estimates new infections to be approximately 100 000 per year. We performed new analyses of nationwide data to examine the modelling assumptions that led to these estimates. Thus, we found that the key assumption of these models of a stationary epidemic is invalid. We propose an alternate approach to estimating incidence based on analysing cohort data; we find that the number of annual new infections is <150 000.

Short‐term effects of dietary soybean meal and lactic acid bacteria on the intestinal morphology and microbiota of Atlantic salmon (Salmo salar)

Abstract: The aim of this study was to evaluate the role of the intestinal microbiota in soybean meal enteritis. Three groups of Atlantic salmon (Salmo salar) were fed for 35 days with different diets: a control diet (CD) containing 510 g kg �1 fishmeal, diet 1 (D1) containing 378 g kg �1 of soybean meal and diet 2 (D2) containing D1 supplemented with two viable lactic acid bacteria (LAB). As expected, the fish fed with D1 showed clear signs of distal intestinal inflammation during the study compared with the fish fed CD. For the fish fed with D2, the addition of LAB diminished the inflammation at day 28, but did not abolish it. Microbiological analysis demonstrated that specific bacterial groups were not correlated with the development of enteritis, but were correlated with the three diets. Microbacterium, Pseudomonas, Lactococcus lactis sp. cremoris and Aeromonas VIa were correlated with the CD, Aeromonas VIb and Sporosarcina aquimarina were correlated with D1, and Alcaligenes, Acinetobacter, L. lactis sp. lactis and Carnobacterium maltaromaticum were correlated with D2. Shewanella was not affected by the diet and was present in all fish intestines. Our study suggests that LAB may modulate intestinal inflammation; however, the role of the microbiota in the aetiology of enteritis in fish still requires further study.

The First Official REPERE Evaluation.

Abstract: The REPERE Challenge aims to support research on people recognition in multimodal conditions. Following a 2012 dryrun [1], the first official evaluation of systems has been conducted at the beginning of 2013. To both help system development and assess the technology progress a specific corpus is developed. It current totals at 30 hours of video with multimodal annotations. The systems have to answer the following questions: Who is speaking? Who is present in the video? What names are cited? What names are displayed? The challenge is to combine the various informations coming from the speech and the images.