KNN-MDR: a learning approach for improving interactions mapping performances in genome wide association studies

Background Finding epistatic interactions in large association studies like genome-wide association studies (GWAS) with the nowadays-available large volume of genomic data is a challenging and largely unsolved issue. Few previous studies could handle genome-wide data due to the intractable difficulties met in searching a combinatorial explosive search space and statistically evaluating epistatic interactions given a limited number of samples. Our work is a contribution to this field. We propose a novel approach combining K-Nearest Neighbors (KNN) and Multi Dimensional Reduction (MDR) methods for detecting gene-gene interactions as a possible alternative to existing algorithms, e especially in situations where the number of involved determinants is high. After describing the approach, a comparison of our method (KNN-MDR) to a set of the other most performing methods (i.e., MDR, BOOST, BHIT, MegaSNPHunter and AntEpiSeeker) is carried on to detect interactions using simulated data as well as real genome-wide data. Results Experimental results on both simulated data and real genome-wide data show that KNN-MDR has interesting properties in terms of accuracy and power, and that, in many cases, it significantly outperforms its recent competitors. Conclusions The presented methodology (KNN-MDR) is valuable in the context of loci and interactions mapping and can be seen as an interesting addition to the arsenal used in complex traits analyses

Evaluation morphométrique des chevaux pur-sang Arabe en Algérie: mensurations corporelles et proposition d’équations barymétriques

Cette étude vise à la caractérisation morphobiométrique des chevaux de course pur-sang arabe et à l’estimation d’équations barymétriques adaptées à cette race. La caractérisation a concerné 98 chevaux, dont 44 femelles et 54 mâles, tous âgés de trois ans et plus, auprès de 77 propriétaires-éleveurs dans 3 hippodromes d’Algérie (Zemmouri, Tiaret et Caroubier). Dix-neuf mensurations étaient relevées ainsi que le poids vif (PV). Le poids moyen est de 456,2 +/- 43,0 kg, variant de 335 kg à 545 kg. La sélection des variables à inclure dans les équations barymétriques a été réalisée à l’aide de la procédure stepwise du SAS. Quatre mensurations parmi les 19 réalisées ont été retenues pour la proposition d’équations d’estimation du poids vif des chevaux : le périmètre thoracique (PT), la hauteur à la croupe (HC), la longueur de l’encolure (LE) et le tour de l’encolure (TE). Ainsi, les équations proposées pour les mâles et pour les femelles sont respectivement de : PV= 7,024*PT - 787,119 (R²=0,99); PV=6,207*PT + 0,633*HC + 0,668*TE - 0,878*LE - 746,370 (R²=0,96). Les résultats de cette étude devraient permettre aux propriétaires-éleveurs et entraineurs de suivre aisément le poids de leurs chevaux. Ce suivi est nécessaire pour adapter l’activité et l’alimentation des chevaux et favoriser leur performance en course

Asteroseismic study of solar-like pulsators along their evolution

Following the advent of space-borne missions (e.g. CoRoT, Kepler), came a wealth of data of unprecedented quality. This enabled asteroseismology to thrive and to probe the stellar structure of a wide variety of pulsating stars. Amongst these pulsating stars is the notable category of low-mass stars. These exhibit masses below 2.3 solar-mass , encompassing the case of our Sun. Throughout their evolution, these stars exhibit a few interesting peculiarities. First, during the main-sequence phase, they display a very regular pressure-mode oscillation spectrum. However, small perturbations to that regularity may occur. Such perturbations are the result of sharp and localised variations in the stellar structure. These create an oscillating feature, as a function of the frequency, in the oscillation spectrum, the so-called glitches. These glitches are of particular interest as they allow us to probe very localised regions of the stellar interior and provide diagnoses about specific stellar features, inaccessible by other means. In main-sequence low-mass stars, we distinguish two main causes of glitches: the helium second-ionisation zone, providing information about the surface helium abundance, and the base of the envelope convection zone, constraining the mixing processes in that region. The first part of my thesis was dedicated to the development of a seismic technique, WhoSGlAd, that consistently analyses the complete oscillation spectra of main-sequence low-mass stars and robustly retrieves the glitches signatures present in these spectra. Special care was put in the definition of stringent seismic indicators as we decorrelated them as much as possible. This is done thanks to a Gram-Schmidt orthonormalisation process. The defined indicators were then used to constrain stellar models and provide a characterisation of both the 16 Cygni system and the Kepler Legacy Sample, representing the best solar-like seismic data currently available. After the main-sequence phase, low-mass stars evolve on the subgiant and red-giant phases. Their core then contracts while their envelope expands, developing a large core-envelope density contrast. This produces the appearance of mixed-modes, presenting a twofold nature: a gravity- dominated nature in the inner radiative regions, and a pressure-dominated nature in the outer convective regions. These modes have the great advantage to propagate throughout most of the stellar interior and, therefore, to probe almost the complete stellar structure. To exploit the information these modes carry, we developed the EGGMiMoSA method. It relies on the asymptotic expression and allows us to precisely measure seismic indicators on both subgiant and red-giant stars. The method was applied to a grid of models extending from the subgiant phase to the luminosity bump. The results are excellent in regard to the asymptotic values of the seismic indicators and also qualitatively agree with observed and theoretical studies. These indicators also allow us to efficiently infer the stellar age, mass, and radius of subgiant stars and of red-giant stars with masses & 1.8 M . Below this threshold, we noted that the central electron degeneracy impaired our diagnosis of the stellar age, mass, and radius in red-giants. The combination of both methods should provide means to constrain the stellar structure of low-mass stars from the early main-sequence phase to the late red-giant one. This is a unique opportunity to study their structure through most of their evolution and, for example, pinpoint missing physical processes in their modelling

Semen quality of stress negative Piétrain and Duroc boars in the tropics: the case of Vietnam

This study was carried out in Dong Hiep pig farm, North of Vietnam in order to evaluate the semen quality of stress negative Piétrain and Duroc boars. A total of 722 ejaculates from 13 homozygous (CC), 7 heterozygous (CT) stress negative Piétrain and 10 Duroc CC boars was collected between 2008 and 2012. The sperm quality was assessed on each ejaculate using ejaculate volume (VOL), spermatozoa motility (MO), sperm concentration (CO) and total number of spermatozoids (NT). Genetic type of boars, season, year and (season x year) as well as (genetic type x year) interactions were included in the model as fixed factors. The results show that the semen quality was influenced by all studied effects (p<0.05) except VOL for season (p=0.45) and season x year (p=0.55), and CO for genetic type (p=0.93). VOL and NT (291.74ml and 103.37×109spz) of Piétrain CC were higher than those (241.40ml and 84.58×109spz) of Piétrain CT and (228.05ml and 77.15×109spz) of Duroc (p<0.001) although the values of the 3 genetic groups are in the range of normal semen. MO, CO and NT tend to be higher in cold than in hot season (p<0.001). These results suggest that semen from Piétrain and Duroc boars could be used in tropical climatic conditions (particularly Piétrain CC) and that the semen quality could be improved through reduction of heat stress

Study with WhoSGlAd of the acoustic depth of the helium glitch across the seismic HR diagram and its impact on the inferred helium abundance

The acoustic glitches' signature present in solar-like stars holds invaluable information. Indeed, it is caused by a sharp variation in the sound speed, therefore carrying localised information. One such glitch is the helium glitch caused by the hydrogen and first and second partial helium ionisation region, allowing us to constrain the surface helium abundance. However, the function adjusted to the glitch signature depends non-linearly on the acoustic depth at which it occurs, He. Retrieving the faint glitch signature and estimating $\tau_{\textrm{He}}$ are difficult but crucial tasks to accurately measure the glitch parameters and, ultimately, accurately infer the helium abundance. In the present paper, we aim at providing a way to estimate $\tau_{\textrm{He}}$ using precise seismic indicators, independent of stellar modelling. Consequently, we aim at improving the WhoSGlAd (Whole Spectrum and Glitches Adjustment) method by automatically providing a model independent measure of the glitch's parameters. We compute the evolution of $T_{\textrm{He}}$, a dimensionless form of the acoustic depth, along a grid of models and adjust an empirical linear relation between $T_{\textrm{He}}$ and the mean large separation and frequency ratio as defined in WhoSGlAd. We further optimise over the value of this estimate to ensure the stability and accuracy of the approach. The proposed approach provides an excellent estimate of the acoustic depth and allows us to swiftly retrieve the glitch signature of observed spectra. We demonstrate that the we can accurately model the helium abundance of four Kepler targets by comparing model (both versions of WhoSGlAd) and literature values.Comment: 9 pages, accepted for publication in MNRAS on the 14/03/202

Growth performance and sperm quality of stress negative Piétrain boars and their hybrids with Duroc

peer reviewedThis study was conducted to evaluate the effects of genetic background and season on growth performance and semen quality of boars. Five genetic groups were evaluated, including stress-negative Piétrain boars with CC (PiCC) or CT (PiCT) halothane genotypes, and Piétrain x Duroc hybrid boars with various compositions (25% (PiDu25), 50% (PiDu50) or 75% (PiDu75) of Piétrain origin). The results showed that genetic group has a significant effect on growth performance and semen quality. The hybrid boars PiDu25, PiDu50 and PiDu75 had better growth rate, but lower lean meat in comparison with pure stress-negative Piétrain, except PiDu75 boars. PiDu25, PiDu50 and PiCC boars demonstrated high semen quality. A season effect was observed on most of semen quality traits of pure stress-negative Piétrain as well as hybrid boars with different genetic constitution. Sperm concentration was lower in Summer and Autumn, higher in Winter and Spring. The Piétrain x Duroc hybrid boars, especially PiDu75 seem to be promising as terminal boars

Exploring the risk factors for Salmonella in the ten biggest Belgian pig slaughterhouses

The goal of this work is to identify the risk factors related to Salmonella in the porcine die at the stage of the slaughterhouse. Thanks to investigations carried out into the ten biggest Belgian slaughterhouses, data concerning the manufacturing process and the working methods were gathered. Moreover, an access to the microbiological results carried out on these companies within the framework of the official plans of monitoring was asked to the Belgian Food Agency. A data base allowing to test the influence of risk factors on the presence of Salmonella was established. To quantify a relation between a risk factor and the presence of Salmonella, statistical methods such as the logistic regressions were used

Les ressources génétiques ovines en Algérie

Avec un cheptel avoisinant les 19 millions de têtes, l'élevage ovin occupe une place importante en Algérie. Outre sa contribution de plus de 50 % dans la production nationale de viandes rouges et de 10 à 15% dans le produit intérieur brut agricole, l’élevage ovin joue un rôle socioculturel important. Il se pratique dans toutes les zones climatiques, depuis la côte méditerranéenne jusqu'aux oasis du grand Sahara. Cette diversité pédoclimatique du plus grand pays africain offre à l’Algérie une extraordinaire diversité de races ovines, avec huit races caractérisées par une rusticité remarquable, adaptées à leurs milieux respectifs. Avec 63% du cheptel ovin total, la race Ouled Djellal, aussi appelée la race Blanche, est la plus importante race ovine algérienne. Elle est exploitée principalement pour la production de viande. La race Berbère représentant un quart du cheptel ovin national, est considérée comme la plus ancienne race algérienne. Elle est menacée par les croisements non-contrôlés avec d’autres races pour l’amélioration de son potentiel productif. La troisième race ovine très importante est la Rmbi avec 11,1% du cheptel national, considérée comme la plus lourde race ovine en Algérie avec des poids avoisinants les 90 kg chez le bélier et 60kg chez la brebis. Les races Hamra, Barbarine, D'man, Sidahou et Tazegzawt représentent ensemble moins de 1% du cheptel ovin algérien. Le déclin de ces populations illustre l’érosion dramatique que subit cette richesse exceptionnelle, appelant à la mise en place d’un plan national de gestion et de conservation des ressources génétiques