Showing papers by "Mines ParisTech published in 2006"

An accurate and interpretable model for siRNA efficacy prediction

Abstract: The use of exogenous small interfering RNAs (siRNAs) for gene silencing has quickly become a widespread molecular tool providing a powerful means for gene functional study and new drug target identification. Although considerable progress has been made recently in understanding how the RNAi pathway mediates gene silencing, the design of potent siRNAs remains challenging. We propose a simple linear model combining basic features of siRNA sequences for siRNA efficacy prediction. Trained and tested on a large dataset of siRNA sequences made recently available, it performs as well as more complex state-of-the-art models in terms of potency prediction accuracy, with the advantage of being directly interpretable. The analysis of this linear model allows us to detect and quantify the effect of nucleotide preferences at particular positions, including previously known and new observations. We also detect and quantify a strong propensity of potent siRNAs to contain short asymmetric motifs in their sequence, and show that, surprisingly, these motifs alone contain at least as much relevant information for potency prediction as the nucleotide preferences for particular positions. The model proposed for prediction of siRNA potency is as accurate as a state-of-the-art nonlinear model and is easily interpretable in terms of biological features. It is freely available on the web at http://cbio.ensmp.fr/dsir

A review of the development of three generations of small diameter silicon carbide fibres

Abstract: Three generations of small diameter ceramic fibres based on polycrystalline silicon carbide have been developed over a period of thirty years. This has been possible due to studies into the relationships between the microstructures and properties of the fibres. A variety of techniques have been employed by research teams on three continents. The fibres are made by the conversion of polymer precursors to ceramic fibres and all three generations are presently produced commercially. The nature of the precursor and the techniques used for cross-linking have been varied in order to optimise both properties and cost of manufacture. It has been possible to improve the characteristics of the fibres as the processes involved in the cross-linking of the precursor fibres have been better understood and the mechanisms governing both room temperature and high temperature behaviour determined. The result is that, although first generation fibres were limited by a low Young's modulus at room temperature and by creep and instability of the structure at temperatures far lower than those limiting the behaviour of bulk silicon carbide, the third generation fibres shows many of the characteristics of stoichiometric silicon carbide. This remarkable improvement in characteristics has been due to a thorough understanding of the materials science governing the behaviour of these fibres which are reinforcements for ceramic matrix composite materials.

A Review of the Use of Chitosan for the Removal of Particulate and Dissolved Contaminants

Abstract: Chitosan has unique properties among biopolymers, especially due to the presence of primary amino groups. Chitosan has been used for the chelation of metal ions in near‐neutral solution, the complexation of anions in acidic solution (cationic properties due to amine protonation), the coagulation of negatively charged contaminants under acidic conditions, and for precipitative flocculation at pH above the pKa of chitosan. The coagulation and flocculation properties can be used to treat particulate suspensions (organic or inorganic) and also to treat dissolved organic materials (including dyes and humic acid). This paper will give an overview of the principal results obtained in the treatment of various suspensions and solutions: (a) bentonite suspensions; (b) organic suspensions; (c) anionic dye solutions; and (d) humic acid solutions. Stoichiometry and charge restabilization were determined for the coagulation of humic acid, kaolin, and organic dyes with chitosan, indicating charge neutralization...

Development of the local approach to fracture over the past 25 years: Theory and applications

Abstract: This review paper is devoted to the local approach to fracture (LAF) for the prediction of the fracture toughness of structural steels. The LAF has been considerably developed over the past two decades, not only to provide a better understanding of the fracture behaviour of materials, in particular the failure micromechanisms, but also to deal with loading conditions which cannot easily be handled with the conventional linear elastic fracture mechanics and elastic-plastic fracture mechanics global approaches. The bases of this relatively newly developed methodology are first presented. Both ductile rupture and brittle cleavage fracture micromechanisms are considered. The ductile-to-brittle transition observed in ferritic steels is also briefly reviewed. Two types of LAF methods are presented: (i) those assuming that the material behaviour is not affected by damage (e.g. cleavage fracture), (ii) those using a coupling effect between damage and constitutive equations (e.g. ductile fracture). The micromechanisms of brittle and ductile fracture investigated in elementary volume elements are briefly presented. The emphasis is laid on cleavage fracture in ferritic steels. The role of second phase particles (carbides or inclusions) and grain boundaries is more thoroughly discussed. The distinction between nucleation and growth controlled fracture is made. Recent developments in the theory of cleavage fracture incorporating both the effect of stress state and that of plastic strain are presented. These theoretical results are applied to the crack tip situation to predict the fracture toughness. It is shown that the ductile-to-brittle transition curve can reasonably be well predicted using the LAF approach. Additional applications of the LAF approach methods are also shown, including: (i) the effect of loading rate and prestressing; (ii) the influence of residual stresses in welds; (iii) the mismatch effects in welds; (iv) the warm-prestressing effect. An attempt is also made to delineate research areas where large improvements should be made for a better understanding of the failure behaviour of structural materials.

A mutation of spastin is responsible for swellings and impairment of transport in a region of axon characterized by changes in microtubule composition

Abstract: Mutations of the spastin gene (Sp) are responsible for the most frequent autosomal dominant form of spastic paraplegia, a disease characterized by the degeneration of corticospinal tracts. We show that a deletion in the mouse Sp gene, generating a premature stop codon, is responsible for progressive axonal degeneration, restricted to the central nervous system, leading to a late and mild motor defect. The degenerative process is characterized by focal axonal swellings, associated with abnormal accumulation of organelles and cytoskeletal components. In culture, mutant cortical neurons showed normal viability and neurite density. However, they develop neurite swellings associated with focal impairment of retrograde transport. These defects occur near the growth cone, in a region characterized by the transition between stable microtubules rich in detyrosinated alpha-tubulin and dynamic microtubules composed almost exclusively of tyrosinated alpha-tubulin. Here, we show that the Sp mutation has a major impact on neurite maintenance and transport both in vivo and in vitro. These results highlight the link between spastin and microtubule dynamics in axons, but not in other neuronal compartments. In addition, it is the first description of a human neurodegenerative disease which involves this specialized region of the axon.

Consistency and Convergence Rates of One-Class SVMs and Related Algorithms

Abstract: We determine the asymptotic behaviour of the function computed by support vector machines (SVM) and related algorithms that minimize a regularized empirical convex loss function in the reproducing kernel Hilbert space of the Gaussian RBF kernel, in the situation where the number of examples tends to infinity, the bandwidth of the Gaussian kernel tends to 0, and the regularization parameter is held fixed. Non-asymptotic convergence bounds to this limit in the L2 sense are provided, together with upper bounds on the classification error that is shown to converge to the Bayes risk, therefore proving the Bayes-consistency of a variety of methods although the regularization term does not vanish. These results are particularly relevant to the one-class SVM, for which the regularization can not vanish by construction, and which is shown for the first time to be a consistent density level set estimator.

Metrology in a scanning electron microscope: theoretical developments and experimental validation

Abstract: A novel approach for correcting both spatial and drift distortions that are present in scanning electron microscope (SEM) images is described. Spatial distortion removal is performed using a methodology that employs a series of in-plane rigid body motions and a generated warping function. Drift distortion removal is performed using multiple, time-spaced images to extract the time-varying relative displacement field throughout the experiment. Results from numerical simulations clearly demonstrate that the correction procedures successfully remove both spatial and drift distortions. Specifically, in the absence of intensity noise the distortion removal methods consistently give excellent results with errors on the order of +/- 0.01 pixels. Results from the rigid body motion and tensile loading experiments at 200 x indicate that, after correction for distortions, (a) the displacements have nearly random variability with a standard deviation of 0.02 pixels; (b) the measured strain fields are unbiased and in excellent agreement with previous full-field experimental data obtained with optical illumination; (c) the strain field variability is on the order of 60 microstrain in all components with a spatial resolution on the order of 25 pixels. Taken together, the analytical, computational and experimental studies clearly show that the correction procedures successfully remove both spatial and drift distortions while retaining excellent spatial resolution, confirming that the SEM-based method can be used for both micromaterial and nanomaterial characterization in either the elastic or elastic-plastic deformation regimes.

Numerical simulation of weakly compressible Bingham flows: The restart of pipeline flows of waxy crude oils

Abstract: In this paper we examine the numerical simulation of isothermal transient flows for a weakly compressible viscoplastic fluid in an axisymmetric pipe geometry. We use the Bingham model to describe the viscoplastic feature of the fluid and the compressibility is introduced in the continuity equation using the isothermal compressibility coefficient. Particular attention is devoted to the velocity-pressure problem in which the "true" (without regularization procedure) viscoplastic model is accounted for by using Lagrange multipliers techniques and augmented Lagrangian/Uzawa methods. The mass, momentum and constitutive equations are discretized using a finite volume method on a staggered grid with a TVD (Total Variation Diminishing) scheme for the convective terms. The resulting numerical method highlights strong and robust convergence properties. Obtained results regarding the transient solution underline the influence of compressibility on the flow pattern, especially in terms of yielded/unyielded regions, pressure and time to restart the flow.

A 'small-world-like' model for comparing interventions aimed at preventing and controlling influenza pandemics

Abstract: Background With an influenza pandemic seemingly imminent, we constructed a model simulating the spread of influenza within the community, in order to test the impact of various interventions.

Effect of processing conditions on the formation of polypropylene/organoclay nanocomposites in a twin screw extruder

Abstract: Polypropylene (PP)/organoclay (Cloisite©20A) nanocomposites are prepared via direct melt intercalation in a co-rotating twin screw extruder. Maleic anhydride (MA)-grafted PP (PP-g-MA) is used as a compatibilizer to improve the dispersion of the clay. The formulation used to prepare the nanocomposites is fixed and is equal to 80/15/5 (PP/PP-g-MA/Cloisite©20A), expressed in mass fraction. The objective of the present study is to investigate the effects of processing conditions as well as screw profile upon the formation of PP nanocomposites. The parameters studied are the feed rate and the screw speed, which are varied independently, from 4.5 to 29.0 kg/h and from 100 to 300 rpm, respectively. The state of dispersion is quantified by wide angle X-ray diffraction (WAXD), transmission electron microscopy, and rheological measurements. WAXD results show that the nanocomposites obtained in different conditions have an intercalated structure, with an increase in interlayer spacing. However, this interlayer spacing is globally unaffected by processing parameters. On the opposite, the proportion of exfoliation, estimated by rheological measurements, is depending on operating conditions (screw speed and feed rate). It increases when the feed rate decreases and the screw speed increases. Investigations on the state of dispersion along the screw profile are also presented. They show that no evolution of intercalated structure is observed along the screws and that screw geometry is only efficient in particular extrusion conditions to delaminate clay platelets. Numerical simulations of the twin screw extrusion process, using the software Ludovic©, put in evidence that the total strain is a key factor for characterizing the level of exfoliation in the nanocomposites. POLYM. ENG. SCI. 46:314–323, 2006. © 2006 Society of Plastics Engineers

The colour of ochres explained by their composition

Abstract: The first purpose of this paper is to underline a relevant colorimetric co-ordinate characterizing the colour of ochres within their extremely wide range, from pale yellow to dark red. The second purpose is to link together quantitatively the variations of this colorimetric co-ordinate and the various chemical compositions of the samples, mainly hematite, goethite and white pigments. A group of 30 modern ochres and a group of 20 ancient ochres have been investigated. All these natural pigments have been commercialized. Diffuse reflectance spectrometry allows to calculate the colorimetric co-ordinates in the CIE-L*a*b* space and the position of the absorption band of each sample. Physico-chemical analysis has been obtained by quantitative X-ray diffraction, scanning and transmitting electronic microscopy and particle-size analysis by laser diffraction. The positive a* co-ordinate (redness) has been underlined, for the first time, to be the only relevant colorimetric parameter to characterize the colour of the ochres. Its variations are quantitatively connected to the shift of the absorption band due to the charge transfer between the ligand (OH− or O2−) and the Fe3+ ion contained in goethite and/or hematite. For ochres containing both hematite and goethite, the a* co-ordinate linearly increases with the relative amount of hematite while the absorption band progressively shifts towards the high wavelengths. Such a linear shift of the absorption band has never been underlined before. For ochres containing only one iron oxide, a* linearly decreases with the amount of white pigments, whatever the nature of the white charges. Moreover, this study gives the opportunity to show that only the nature, the amount and the size distribution of the white charges allow to discriminate the ochres according to their geographic origin.

Association of hydrogeological factors in temporal variations of fluoride concentration in a crystalline aquifer in India

Abstract: The major part of groundwater in India is found in granitic aquifers. Fluoride in groundwater from a crystalline aquifer in a semi-arid region of granitic rocks in India, known as Maheshwaram watershed, was analyzed for spatial and temporal variability during 1999-2002 to assess the effect of hydrogeological factors on fluoride concentration. Samples were collected from 32 representative wells in the area for the pre- and post-monsoon seasons and analyzed for F content. The CHESS computer program was used to calculate ionic activities of aqueous species and the mineral saturation index (SI) for calcite and fluorite. The GARDENIA computer program was used to calculate the recharge values in the study area. The influences of dissolution kinetics of fluoride minerals and recharge from rainfall on fluoride concentration were of interest and results clearly indicate that fluoride content in groundwater depends on the interaction period of groundwater with host rock. Results could also be utilized for designing remedial measures particularly with dilution method in an optimal way.

Analysis of air pollution mortality in terms of life expectancy changes: relation between time series, intervention, and cohort studies.

Abstract: Information on life expectancy change is of great concern for policy makers, as evidenced by the discussions of the so-called "harvesting" issue (i.e. the question being, how large a loss each death corresponds to in the mortality results of time series studies). Whereas most epidemiological studies of air pollution mortality have been formulated in terms of mortality risk, this paper shows that a formulation in terms of life expectancy change is mathematically equivalent, but offers several advantages: it automatically takes into account the constraint that everybody dies exactly once, regardless of pollution; it provides a unified framework for time series, intervention studies and cohort studies; and in time series and intervention studies, it yields the life expectancy change directly as a time integral of the observed mortality rate. Results are presented for life expectancy change in time series studies. Determination of the corresponding total number of attributable deaths (as opposed to the number of observed deaths) is shown to be problematic. The time variation of mortality after a change in exposure is shown to depend on the processes by which the body can repair air pollution damage, in particular on their time constants. Hypothetical results are presented for repair models that are plausible in view of the available intervention studies of air pollution and of smoking cessation. If these repair models can also be assumed for acute effects, the results of cohort studies are compatible with those of time series. The proposed life expectancy framework provides information on the life expectancy change in time series studies, and it clarifies the relation between the results of time series, intervention, and cohort studies.

Micromorphic continuum modelling of the deformation and fracture behaviour of nickel foams

Abstract: An anisotropic compressible plasticity model is incorporated into the framework of the micromorphic continuum theory in order to describe some size effects observed in ductile nickel foams. This continuum model reproduces the fact that the presence of a machined hole in a foam plate does not affect its mechanical response when the hole size becomes comparable to the cell size of the material. Finite element simulations are compared to strain field measurements in nickel foam plates with a machined hole for different hole sizes, in order to identify the characteristic length of the model. Based on a simple ductile damage law, the model is then shown to be able to account for the strong anisotropy of the initiation of crack propagation in central crack panels made of nickel foams under mode I loading conditions.