Survival analysis of DNA mutation motifs with penalized proportional hazards

Antibodies, an essential part of our immune system, develop through an intricate process to bind a wide array of pathogens. This process involves randomly mutating DNA sequences encoding these antibodies to find variants with improved binding, though mutations are not distributed uniformly across sequence sites. Immunologists observe this nonuniformity to be consistent with "mutation motifs", which are short DNA subsequences that affect how likely a given site is to experience a mutation. Quantifying the effect of motifs on mutation rates is challenging: a large number of possible motifs makes this statistical problem high dimensional, while the unobserved history of the mutation process leads to a nontrivial missing data problem. We introduce an $\ell_1$-penalized proportional hazards model to infer mutation motifs and their effects. In order to estimate model parameters, our method uses a Monte Carlo EM algorithm to marginalize over the unknown ordering of mutations. We show that our method performs better on simulated data compared to current methods and leads to more parsimonious models. The application of proportional hazards to mutation processes is, to our knowledge, novel and formalizes the current methods in a statistical framework that can be easily extended to analyze the effect of other biological features on mutation rates

Experimental investigation of wave propagation in three dimensions in unbounded particulate assemblies

Understanding wave propagation through soils is essential for site response analysis in earthquake engineering, interpretation of geophysical surveys and SASW (Spectral Analysis of Surface Waves), interpretation of laboratory bender element tests, etc. Analysis of wave propagation has largely been based on continuum descriptions and two dimensional analyses. This study presents recent developments in multiaxial testing that permit the combination of laboratory seismic testing with exploration of three-dimensional principal stress space. A Cubical Cell Apparatus with bender-extender piezoceramic elements fitted in all six faces are used so that wave propagation velocities of an analogue granular material can be determined. The results of a first series of wave propagation tests for a sample under isotropic confinement are presented

Cluster Agglomeration Induced by Dust-Density Waves in Complex Plasmas

International audienc

Análisis de la fecundidad de las mujeres haitianas por orden de nacimiento

The fertility of Haitian women is analyzed in order to reveal their reproductive behavior according to their sociodemographic and economic situation. We use data from the latest demographic and health survey conducted in Haiti. The present study only includes women at the end of their childbearing age between 45 and 49 years. The description of the baseline characteristics of the analytical sample was done using percentages. To analyze the data, we resorted to the probabilities of family enlargement (PAF) and multivariate survival models in discrete time (complementary log-log models) (LLC), which are two methodological approaches adaptable to the fertility situation. from the country. The analyzes cover various levels of study. First, a univariate descriptive statistical analysis was carried out with the objective of characterizing the profile of the population in question. Subsequently, a multivariate analysis was carried out to examine sociodemographic and economic factors, as well as spacing patterns in the reproduction of Haitian women. The results indicate that, from the birth of the fourth child, women demonstrate greater control over their fertility. Therefore, the probabilities remain high for the transition to high parity (more than 3 children). To control fertility, the longer the time between two successive births, the greater the tendency for reproduction to decline. Furthermore, the most vulnerable women, those who reside in rural contexts, with low economic resources and low educational levels, tend to have more children, begin having them at an earlier age and have shorter intervals between successive births.Se analiza la fecundidad de las mujeres haitianas a fin de revelar su comportamiento reproductivo según la situación sociodemográfica y económica. Usamos datos de la última encuesta demográfica y de salud realizada en Haití. El presente estudio sólo incluye a las mujeres al final de su edad fértil entre 45 y 49 años. La descripción de las características basales de la muestra analítica se realizó mediante porcentajes. Para el análisis de los datos, recurrimos a las probabilidades de agrandamiento de las familias (PAF) y modelos multivariantes de supervivencia en tiempo discreto (modelos log-log complementario) (LLC), que son dos aproximaciones metodológicas adaptables a la situación de la fecundidad del país. Los análisis abarcan diversos niveles de estudio. En primer lugar, se realizó un análisis estadístico descriptivo univariante con el objetivo de caracterizar el perfil de la población en cuestión. Posteriormente, se procedió a un análisis multivariante para examinar los factores sociodemográficos y económicos, así como los patrones de espaciamiento en la reproducción de las mujeres haitianas. Los resultados indican que, a partir del nacimiento del cuarto hijo, las mujeres demuestran un mayor control sobre su fecundidad. Por tanto, las probabilidades siguen siendo altas para la transición a una paridad alta (más de 3 hijos). Para controlar la fecundidad, cuanto mayor sea el tiempo entre dos nacimientos sucesivos, mayor será la tendencia a la disminución de la reproducción. Además, las mujeres más vulnerables, quienes residen en contextos rurales, con bajos recursos económicos y bajo nivel educativo, tienden a tener más hijos, comienzan a tenerlos a una edad más temprana y presentan intervalos más cortos entre los nacimientos sucesivos

Numerical MicroLocal Analysis Revisited

The report bundles a theoretical and a numerical papier presenting a stable version of the {\tt NMLA} algorithm as well a a new curvature estimation method and a linearization error correction method.Ce rapport rassemble un papier numérique et un papier théorique présentant une version stable de la méthode {\tt NMLA} ainsi qu'une nouvelle méthode d'estimation de la courbure et une méthode de correction des erreurs de linéarisation

Large-scale gene discovery in the pea aphid Acyrthosiphon pisum (Hemiptera)

Aphids are the leading pests in agricultural crops. A large-scale sequencing of 40,904 ESTs from the pea aphid Acyrthosiphon pisum was carried out to define a catalog of 12,082 unique transcripts. A strong AT bias was found, indicating a compositional shift between Drosophila melanogaster and A. pisum. An in silico profiling analysis characterized 135 transcripts specific to pea-aphid tissues (relating to bacteriocytes and parthenogenetic embryos). This project is the first to address the genetics of the Hemiptera and of a hemimetabolous insect.Beatriz Sabater-Muñoz... et al

The role of viscoelasticity on heterogeneous stress fields at frictional interfaces

We investigate the evolution of heterogeneous stress states along frictional in- terfaces. Using finite-element simulations, we model the occurrence of precur- sory slip sequences on a deformable-deformable as well as a deformable-rigid interface between two solids. Every interface rupture creates a stress concen- tration at its arrest position and erases the stress concentrations produced by previous slip events. While the interface is sticking perfectly between two slip events, erased stress concentrations reappear and survive several cycles of ruptures. Such reestablished stress concentrations are smaller than they were before the rupture. We show that the decrease rate of these stress concentrations is exponential with respect to the number of subsequent events and that the bulk viscoelasticity is at the origin of this history effect. During a slip event, the friction tractions at the interface change almost instantaneously, which leads, between two ruptures, to a relaxation-resembling viscous effect that restores the stress concentration. We describe the decrease rate analytically and highlight that it is proportional to the ratio of the viscous over the instantaneous Young’s moduli, and illustrate it by varying the material properties in our simulations