Efficient Non-Binary Gene Tree Resolution with Weighted Reconciliation Cost

Polytomies in gene trees are multifurcated nodes corresponding to unresolved parts of the tree, usually due to insufficient differentiation between sequences of homologous gene copies. Apart from gene sequences, other information such as that contained in the species tree can be used to resolve such intricate parts of a gene tree. The problem of resolving a multifurcated tree has been considered by many authors, the objective function often being the number of duplications and losses reflected by the reconciliation of the resolved gene tree with the species tree. Here, we present PolytomySolver, an algorithm accounting for a more general model allowing different costs for duplications and losses per species. The time complexity of this algorithm is linear for the unit cost and is quadratic for the general cost, which outperforms the best known solutions so far by a linear factor. We show on simulated trees that the gain in theoretical complexity has a real practical impact on running times

Non Destructive Determination Of Elastic Moduli By Two Dimensional Fourier Transformation And Laser Ultrasonic Technique

Broadband laser ultrasonics and two dimensional Fourier transformation are used to characterize the properties of varieties of foils and plates. Laser ultrasonics generation is achieved by use of a pulsed laser which deposits pulsed laser energy on the surface of the specimen. The displacement amplitude of the resulting broadband ultrasonic modes are monitored using a two wave mixing photo-refractive interferometer. By applying a two dimensional Fourier transformation to the detected spatial and temporal displacement waveforms, the images of density of state (DOS) for the excited ultrasounds are obtained. Results are presented for a 150 um thick paper sample, a 52.8 um stainless steel foil and a 1.27 mm thick aluminum plate. The DOS image demonstrates the ability to measure the properties of each generated ultrasonic modes and provides a direct, non destructive, measure of elastic moduli of the tested specimensComment: Laser ultrasonics, Fourier transformation, NDT&E, Lamb waves, plate mode

Reconstructing the History of Syntenies Through Super-Reconciliation

Classical gene and species tree reconciliation, used to infer the history of gene gain and loss explaining the evolution of gene families, assumes an independent evolution for each family. While this assumption is reasonable for genes that are far apart in the genome, it is clearly not suited for genes grouped in syntenic blocks, which are more plausibly the result of a concerted evolution. Here, we introduce the Super-Reconciliation model, that extends the traditional Duplication-Loss model to the reconciliation of a set of trees, accounting for segmental duplications and losses. From a complexity point of view, we show that the associated decision problem is NP-hard. We then give an exact exponential-time algorithm for this problem, assess its time efficiency on simulated datasets, and give a proof of concept on the opioid receptor genes

Contactless real-time monitoring of paper mechanical behavior during papermaking

Issued as final reportUnited States. Dept. of Energ

Evidence of surface acoustic wave band gaps in the phononic crystals created on thin plates

International audiencePhononic structures and acoustic band gaps based on bulk materials have been researched in length in the past decades. However, few investigations have been performed on phononic structures in thin plates to form surface acoustic wave (SAW) band gaps. In this letter, we report a new type of phononic crystals manufactured by patterning periodical air-filled holes in thin plates. We confirmed the existence of SAW band gaps in the created phononic crystals through laser ultrasonics measurements. Wide multiple SAW band gaps and special structures, such as narrow pass bands within a band gap were observed experimentally

A two-dimensional model for sensitivity studies on laser-generated ultrasound

International audienceA two-dimensional simulation model is presented that, within certain limitative assumptions, calculates the displacements generated by the absorption of a laser pulse in the thermoelastic regime. This model solves the Christoffel equations in an axisymmetrical configuration (the laser excitation is supposed to have a gaussian surface profile) over an infinite plate of finite thickness presenting a cylindrical orthotropy. The resolution of these Christoffel equations is made in the Laplace and Hankel spaces. After the validation of this model by the confrontation of its predictions to experimental data, we present two applications of it concerning the related temporal convolutions occurring to produce the longitudinal precursor

Photoacoustics and laser-ultrasonics applied to the characterization of a ZnO ceramic sample

International audienceWe present results of photoacoustics and laser-ultrasonics experiments that were performed on a ZnO ceramic sample and that led to optical, thermal and thermo-mechanical characterizations of this material

Laser ultrasonics for non-contact measurement of lamb waves in static and moving paper

"January 2000.""Submitted to Journal of Pulp and Paper Science.