Coopération entre Optimisation Combinatoire et Statistiques pour la Sélection animale

National audienceL'objectif de cette étude est d'élaborer des modèles prédictifs permettant, à partir de données génomiques, de déterminer les individus les plus performants selon certains critères quantitatifs. L'approche proposée allie les forces des méthodes statistiques et des méthodes d'optimisation combinatoire

Feature selection for high dimensional regression using local search and statistical criteria

International audienceGenomic selection is a genetic evaluation of animals from their DNA, based on a huge number of markers covering the whole genome. It requires advanced approaches and in particular feature selection methods. Feature selection is a combinatorial problem that may be addressed by combinatorial optimization methods. We propose to combine an iterated local search (ILS) with a statistical evaluation of a multivariate regression and we compared three criteria in order to analyse their impact on the performance of the local search

Feature selection in high dimensional regression problems for genomic

International audienceIn the context of genomic selection in animal breeding, an important objective consists in looking for explicative markers for a phe- notype under study. In order to deal with a high number of markers, we propose to use combinatorial optimization to perform variable selection. Results show that our approach outperforms some classical and widely used methods on simulated and "closed to real" datasets

Combining combinatorial optimization and statistics to mine high-throughput genotyping data

National audienceDepuis quelques années, la génomique a grandement évolué avec le développement de nouvelles technologies telles que le séquençage et le génotypage haut-débit. En ce qui concerne le domaine animal, nous sommes aujourd'hui capables de lire les informations génomiques sur près de 800 000 marqueurs sur des ensembles d'individus de plus en plus larges (de 3 000 à 10 000). Ces données peuvent donner lieu à des études d'association entre les marqueurs (GWAS : Genome-Wide Association Studies). Outre les contraintes biologiques (stockage des échantillons, manipulations longues et coûteuses...), la partie analyse de données (étude et extraction de connaissances) doit aussi être adaptée en terme de méthodologie et d'architecture matérielle et logicielle. L'objectif est d'élaborer des modéles prédictifs permettant, à partir des données génomiques, de déterminer les individus les plus performants selon certains critères quantitatifs de sélection animale. Pour cela, l'objectif théorique est à terme de définir de nouvelles méthodes permettant la coopération entre statistique et optimisation combinatoire spécifiquement dédiées aux données issues de génotypage haut débit en vue d'une implémentation

Effects of reflux laryngitis on laryngeal chemoreflexes in newborn lambs

It has been suggested that reflux laryngitis (RL) is involved in apneas-bradycardias of the newborn. The aim of the present study was to develop a unique RL model in newborn lambs to test the hypothesis that RL enhances the cardiorespiratory components of the laryngeal chemoreflexes (LCR) in the neonatal period. Gastric juice surrogate (2 ml of normal saline solution with HCl pH 2 + pepsin 300 U/ml) (RL group, n = 6) or normal saline (control group, n = 6) was repeatedly injected onto the posterior aspect of the larynx, 3 times a day for 6 consecutive days, via a retrograde catheter introduced into the cervical esophagus. Lambs instilled with gastric juice surrogate presented clinical signs of RL, as well as moderate laryngitis on histological observation. Laryngeal chemoreflexes were thereafter induced during sleep by injection of 0.5 ml of HCl (pH 2), ewe's milk, distilled water or saline into the laryngeal vestibule via a chronic, transcutaneous supraglottal catheter. Overall, RL led to a significantly greater respiratory inhibition compared with the control group during LCR, including longer apnea duration (P = 0.01), lower minimal respiratory rate (P = 0.002), and a more prominent decrease in arterial hemoglobin saturation (SpO(2)) (P = 0.03). No effects were observed on cardiac variables. In conclusion, 1) our unique neonatal ovine model presents clinical and histological characteristics of RL; and 2) the presence of RL in newborn lambs increases the respiratory inhibition observed with LCR, at times leading to severe apneas and desaturations

5-Hydroxytryptamine receptors (version 2019.4) in the IUPHAR/BPS Guide to Pharmacology Database

oai:ojs.pkp.sfu.ca:article/31555-HT receptors (nomenclature as agreed by the NC-IUPHAR Subcommittee on 5-HT receptors [194] and subsequently revised [176]) are, with the exception of the ionotropic 5-HT3 class, GPCRs where the endogenous agonist is 5-hydroxytryptamine. The diversity of metabotropic 5-HT receptors is increased by alternative splicing that produces isoforms of the 5-HT2A (non-functional), 5-HT2C (non-functional), 5-HT4, 5-HT6 (non-functional) and 5-HT7 receptors. Unique amongst the GPCRs, RNA editing produces 5-HT2C receptor isoforms that differ in function, such as efficiency and specificity of coupling to Gq/11 and also pharmacology [40, 482]. Most 5-HT receptors (except 5-ht1e and 5-ht5b) play specific roles mediating functional responses in different tissues (reviewed by [463, 382])

5-Hydroxytryptamine receptors in GtoPdb v.2023.1

5-HT receptors (nomenclature as agreed by the NC-IUPHAR Subcommittee on 5-HT receptors [198] and subsequently revised [180]) are, with the exception of the ionotropic 5-HT3 class, GPCRs where the endogenous agonist is 5-hydroxytryptamine. The diversity of metabotropic 5-HT receptors is increased by alternative splicing that produces isoforms of the 5-HT2A (non-functional), 5-HT2C (non-functional), 5-HT4, 5-HT6 (non-functional) and 5-HT7 receptors. Unique amongst the GPCRs, RNA editing produces 5-HT2C receptor isoforms that differ in function, such as efficiency and specificity of coupling to Gq/11 and also pharmacology [40, 491]. Most 5-HT receptors (except 5-ht1e and 5-ht5b) play specific roles mediating functional responses in different tissues (reviewed by [471, 387])

Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition

A unique collection of oceanic samples was gathered by the Tara Oceans expeditions (2009-2013), targeting plankton organisms ranging from viruses to metazoans, and providing rich environmental context measurements. Thanks to recent advances in the field of genomics, extensive sequencing has been performed for a deep genomic analysis of this huge collection of samples. A strategy based on different approaches, such as metabarcoding, metagenomics, single-cell genomics and metatranscriptomics, has been chosen for analysis of size-fractionated plankton communities. Here, we provide detailed procedures applied for genomic data generation, from nucleic acids extraction to sequence production, and we describe registries of genomics datasets available at the European Nucleotide Archive (ENA, www.ebi.ac.uk/ena). The association of these metadata to the experimental procedures applied for their generation will help the scientific community to access these data and facilitate their analysis. This paper complements other efforts to provide a full description of experiments and open science resources generated from the Tara Oceans project, further extending their value for the study of the world's planktonic ecosystems