Detecting epistasis via Markov bases

Rapid research progress in genotyping techniques have allowed large genome-wide association studies. Existing methods often focus on determining associations between single loci and a specific phenotype. However, a particular phenotype is usually the result of complex relationships between multiple loci and the environment. In this paper, we describe a two-stage method for detecting epistasis by combining the traditionally used single-locus search with a search for multiway interactions. Our method is based on an extended version of Fisher's exact test. To perform this test, a Markov chain is constructed on the space of multidimensional contingency tables using the elements of a Markov basis as moves. We test our method on simulated data and compare it to a two-stage logistic regression method and to a fully Bayesian method, showing that we are able to detect the interacting loci when other methods fail to do so. Finally, we apply our method to a genome-wide data set consisting of 685 dogs and identify epistasis associated with canine hair length for four pairs of SNPs

Detecting a stochastic background of gravitational waves by correlating n detectors

We discuss the optimal detection strategy for a stochastic background of gravitational waves in the case n detectors are available. In literature so far, only two cases have been considered: 2- and n-point correlators. We generalize these analysises to m-point correlators (with m<n) built out of the n detector signals, obtaining the result that the optimal choice is to combine 2-point correlators. Correlating n detectors in this optimal way will improve the (suitably defined) signal-to-noise ratio with respect to the n=2 case by a factor equal to the fourth root of n(n-1)/2. Finally we give an estimation of how this could improve the sensitivity for a network of multi-mode spherical antennas.Comment: 12 pages, version accepted by Class. & Quant. Gra

Hermite regularization of the Lattice Boltzmann Method for open source computational aeroacoustics

The lattice Boltzmann method (LBM) is emerging as a powerful engineering tool for aeroacoustic computations. However, the LBM has been shown to present accuracy and stability issues in the medium-low Mach number range, that is of interest for aeroacoustic applications. Several solutions have been proposed but often are too computationally expensive, do not retain the simplicity and the advantages typical of the LBM, or are not described well enough to be usable by the community due to proprietary software policies. We propose to use an original regularized collision operator, based on the expansion in Hermite polynomials, that greatly improves the accuracy and stability of the LBM without altering significantly its algorithm. The regularized LBM can be easily coupled with both non-reflective boundary conditions and a multi-level grid strategy, essential ingredients for aeroacoustic simulations. Excellent agreement was found between our approach and both experimental and numerical data on two different benchmarks: the laminar, unsteady flow past a 2D cylinder and the 3D turbulent jet. Finally, most of the aeroacoustic computations with LBM have been done with commercial softwares, while here the entire theoretical framework is implemented on top of an open source library (Palabos).Comment: 34 pages, 12 figures, The Journal of the Acoustical Society of America (in press

La cicatrisation du tendon et la récupération des amplitudes articulaires après chirurgie de la coiffe des rotateurs par arthroscopie: influence d'un protocole de rééducation précoce comparé à un protocole d'immobilisation : revue de la littérature : travail de Bachelor

Introduction : Dans le domaine des pathologies de l’épaule, la plus rencontrée est la rupture de/des tendons de la coiffe des rotateurs. Après chirurgie réparatrice par arthroscopie différents protocoles de rééducation sont appliqués. Récemment cités comme la cause des récidives, ces protocoles de rééducation sont au cœur d’une controverse sur les résultats cliniques post-opératoires. L’objectif de cette revue est d’identifier les répercussions d’un protocole de rééducation incluant de la mobilisation passive précoce (J1) comparé à un protocole d’immobilisation, après chirurgie réparatrice de la coiffe des rotateurs par arthroscopie, sur la cicatrisation tendineuse et les amplitudes articulaires, avec un recul d’une année. Problématique : «La mobilisation immédiate passive (J1) après chirurgie de la coiffe des rotateurs par arthroscopie, est-elle préjudiciable à la cicatrisation complète du/des tendon(s), augmente t-elle le risque de récidive et est-elle bénéfique à la récupération des amplitudes articulaires ?» Méthode : Nous avons effectué notre recherche sur les bases de données suivantes : Medline, Cochrane library, PEDro, et Kinédoc. Nous avons inclus 4 études de design RCT analysant des patients ayant bénéficié d’une chirurgie réparatrice effectuée par arthroscopie et comprenant la comparaison d’un protocole de rééducation précoce avec un protocole d’immobilisation. Résultats : Ces 4 publications ne reportent aucun avantage significatif dans l’application d’un protocole précoce comparé à un protocole d’immobilisation. Cependant, l’application d’un protocole d’immobilisation a tendance à induire une meilleure cicatrisation sans effets néfastes sur la récupération des amplitudes articulaires. Conclusion : Des résultats presque similaires sont obtenus avec les deux protocoles de rééducation après une année. Les auteurs se questionnent maintenant sur l’application de protocoles individualisés à chaque patient.Introduction : The most common pathologies encountered in the area of shoulder disorders are rotators cuff’s tendons tears. After reconstructive surgery by arthroscopy, several rehabilitation protocols can be applied. Those protocols have been identified by some in the literature as the cause of recurrence and are therefore at the heart of a controversy about the post-operation outcomes. The goal of this review is to identify the effects of two types of protocols. The two protocols differ in terms of the timing of the mobilization after reconstructive surgery of the cuff by arthroscopy. We will discuss the effects of an early mobilization versus immobilization on the healing of the tendon and the range of motion one year after the operation. Main questions : "Is the immediate passive mobilization (J1) detrimental to the complete healing of the tendon? Does an immediate mobilization increase the risk of recurrence and is it beneficial in terms of the amplitude of the shoulder motion?” Methods : We reviewed the literature by including publications found in the following databases: Cochrane library, PEDro and Kinedoc. We have concentrated in particular on four design RCT studies that analyze patients having benefited from a reconstructive surgery by arthroscopy. Those studies compare an early versus late mobilization protocol in the rehabilitation stage. Results : In all four studies there is no evidence of a significant improvement of an early mobilization versus immobilization protocol. Nevertheless, late protocols tend to result in a better healing with no negative impact on the range motion at one year. Conclusion : Based on those four studies, it is not possible to favor one rehabilitation protocol. The authors therefore discuss a future area of research, mainly the establishment of a protocol specific to each patient

Regularized characteristic boundary condition for the Lattice Boltzmann methods at high Reynolds number flows

This paper reports the investigations done to adapt the Characteristic Boundary Conditions (CBC) to the Lattice-Boltzmann formalism for high Reynolds number applications. Three CBC formalisms are implemented and tested in an open source LBM code: the baseline one-dimension inviscid (BL-LODI) approach, its extension including the effects of the transverse terms (CBC-2D) and a local streamline approach in which the problem is reformulated in the incident wave framework (LS-LODI). Then all implementations of the CBC methods are tested for a variety of test cases, ranging from canonical problems (such as 2D plane and spherical waves and 2D vortices) to a 2D NACA profile at high Reynolds number (Re = 100,000), representative of aeronautic applications. The LS-LODI approach provides the best results for pure acoustics waves (plane and spherical waves). However, it is not well suited to the outflow of a convected vortex for which the CBC-2D associated with a relaxation on density and transverse waves provides the best results. As regards numerical stability, a regularized adaptation is necessary to increase the Reynolds number. The so-called regularized FD adaptation, a modified regularized approach where the off-equilibrium part of the stress tensor is computed thanks to a finite difference scheme, is the only tested adaptation that can handle the high Reynolds computation

Automatic grid refinement criterion for lattice Boltzmann method

In all kinds of engineering problems, and in particular in methods for computational fluid dynamics based on regular grids, local grid refinement is of crucial importance. To save on computational expense, many applications require to resolve a wide range of scales present in a numerical simulation by locally adding more mesh points. In general, the need for a higher (or a lower) resolution is not known a priori, and it is therefore difficult to locate areas for which local grid refinement is required. In this paper, we propose a novel algorithm for the lattice Boltzmann method, based on physical concepts, to automatically construct a pattern of local refinement. We apply the idea to the two-dimensional lid-driven cavity and show that the automatically refined grid can lead to results of equal quality with less grid points, thus sparing computational resources and time. The proposed automatic grid refinement strategy has been implemented in the parallel open-source library Palabos

Human bony labyrinth is an indicator of population history and dispersal from Africa.

The dispersal of modern humans from Africa is now well documented with genetic data that track population history, as well as gene flow between populations. Phenetic skeletal data, such as cranial and pelvic morphologies, also exhibit a dispersal-from-Africa signal, which, however, tends to be blurred by the effects of local adaptation and in vivo phenotypic plasticity, and that is often deteriorated by postmortem damage to skeletal remains. These complexities raise the question of which skeletal structures most effectively track neutral population history. The cavity system of the inner ear (the so-called bony labyrinth) is a good candidate structure for such analyses. It is already fully formed by birth, which minimizes postnatal phenotypic plasticity, and it is generally well preserved in archaeological samples. Here we use morphometric data of the bony labyrinth to show that it is a surprisingly good marker of the global dispersal of modern humans from Africa. Labyrinthine morphology tracks genetic distances and geography in accordance with an isolation-by-distance model with dispersal from Africa. Our data further indicate that the neutral-like pattern of variation is compatible with stabilizing selection on labyrinth morphology. Given the increasingly important role of the petrous bone for ancient DNA recovery from archaeological specimens, we encourage researchers to acquire 3D morphological data of the inner ear structures before any invasive sampling. Such data will constitute an important archive of phenotypic variation in present and past populations, and will permit individual-based genotype-phenotype comparisons

Reducing memory requirements for large size LBM simulations on GPUs

The scientific community in its never-ending road of larger and more efficient computational resources is in need of more efficient implementations that can adapt efficiently on the current parallel platforms. Graphics processing units are an appropriate platform that cover some of these demands. This architecture presents a high performance with a reduced cost and an efficient power consumption. However, the memory capacity in these devices is reduced and so expensive memory transfers are necessary to deal with big problems. Today, the lattice-Boltzmann method (LBM) has positioned as an efficient approach for Computational Fluid Dynamics simulations. Despite this method is particularly amenable to be efficiently parallelized, it is in need of a considerable memory capacity, which is the consequence of a dramatic fall in performance when dealing with large simulations. In this work, we propose some initiatives to minimize such demand of memory, which allows us to execute bigger simulations on the same platform without additional memory transfers, keeping a high performance. In particular, we present 2 new implementations, LBM-Ghost and LBM-Swap, which are deeply analyzed, presenting the pros and cons of each of them.This project was funded by the Spanish Ministry of Economy and Competitiveness (MINECO): BCAM Severo Ochoa accreditation SEV-2013-0323, MTM2013-40824, Computación de Altas Prestaciones VII TIN2015-65316-P, by the Basque Excellence Research Center (BERC 2014-2017) pro- gram by the Basque Government, and by the Departament d' Innovació, Universitats i Empresa de la Generalitat de Catalunya, under project MPEXPAR: Models de Programació i Entorns d' Execució Paral·lels (2014-SGR-1051). We also thank the support of the computing facilities of Extremadura Research Centre for Advanced Technologies (CETA-CIEMAT) and NVIDIA GPU Research Center program for the provided resources, as well as the support of NVIDIA through the BSC/UPC NVIDIA GPU Center of Excellence.Peer ReviewedPostprint (author's final draft