Oskar Bordeaux
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Generation of metabolomic-informed models of metabolism for microbial communities
No full textLa génération de réseaux métaboliques à l'échelle du génome est devenue une analyse de routine pour des organismes individuels ou des communautés. Cependant, ces réseaux métaboliques générés automatiquement sont incomplets car ils sont construits sur la base de la combinaison de l'annotation des gènes et des réactions disponibles dans des bases de données génériques (Metacyc, BIGG, ModelSEED...). Ces bases de données sont orientées vers des organismes bien connus ou des organismes modèles et passent à côté de fonctions importantes du métabolisme secondaire. Nous proposons de combiner l'analyse de données métabolomiques, la modélisation métabolique et l'annotation métabolique et la modélisation métabolique et l'annotation minière pour construire des modèles de haute qualité du métabolisme microbien avec l'objectif à long terme d'une meilleure compréhension des communautés microbiennes. En termes d'application des méthodes aux communautés microbiennes végétales, nous espérons que les modèles nouvellement développés permettront de mieux comprendre le processus de recrutement microbien par la plante : fonctions métaboliques impliquées, micro-organismes associés à ces fonctions.The generation of genome-wide metabolic networks has become a routine analysis for individual organisms or communities communities. However, these automatically generated metabolic networks are incomplete because they are constructed by based on the combination of gene annotation and reactions available in generic available in generic databases (Metacyc, BIGG, ModelSEED...). These are oriented towards well-known organisms or organisms or model organisms and miss out on important functions secondary metabolism. We propose to combine metabolomic data analysis, metabolic modelling and annotation metabolic modelling and annotation mining to build high-quality models of high quality models of microbial metabolism with the long-term aim of better understanding of microbial communities. In terms of application of the methods to plant microbial communities, we hope that the plant microbial communities, we hope that the newly developed models will provide a better understanding of the process of microbial recruitment by the plant: metabolic functions involved, micro-organisms associated with these functions.Computationel models of crop plant microbial biodiversit
Linear Dimensionality Reduction
No full textThis book provides an overview of some classical linear methods in Multivariate Data Analysis. This is an old domain, well established since the 1960s, and refreshed timely as a key step in statistical learning. It can be presented as part of statistical learning, or as dimensionality reduction with a geometric flavor. Both approaches are tightly linked: it is easier to learn patterns from data in low-dimensional spaces than in high-dimensional ones. It is shown how a diversity of methods and tools boil down to a single core method, PCA with SVD, so that the efforts to optimize codes for analyzing massive data sets like distributed memory and task-based programming, or to improve the efficiency of algorithms like Randomized SVD, can focus on this shared core method, and benefit all methods.This book is aimed at graduate students and researchers working on massive data who have encountered the usefulness of linear dimensionality reduction and are looking for a recipe to implement it. It has been written according to the view that the best guarantee of a proper understanding and use of a method is to study in detail the calculations involved in implementing it. With an emphasis on the numerical processing of massive data, it covers the main methods of dimensionality reduction, from linear algebra foundations to implementing the calculations. The basic requisite elements of linear and multilinear algebra, statistics and random algorithms are presented in the appendix
High-risk human papillomavirus cervical infection prevalence: a nationwide retrospective study comparing opportunistic and organised screening, France, 2020 to 2023
No full textBACKGROUND In France, cervical cancer screening for females aged 30–65 years primarily tests for high-risk (HR) human papillomavirus (HPV) infections. AIM We aimed to map the prevalence of cervical infections caused by HPV16 and/or 18, or by any of 12 other carcinogenic HPV genotypes and compare prevalence estimates from tests from spontaneous medical visits (opportunistic screening) or the national screening programme (organised screening). METHODS We extracted data from a large network of biology laboratories, containing all available results from HR HPV tests performed between 1 January 2020 and 30 November 2023 in metropolitan France. A full hierarchical Bayesian model was used to compute spatially resolved expected prevalence maps at the postcode level. RESULTS The analytic sample contained results of 362,963 HR HPV tests. Among samples positive for HPV16 and/or 18, 2.9% and 3.8% were from organised and opportunistic screening, respectively. Samples positive for other genotypes were 6.9% and 9.4%, respectively. During the last week of the study (week 48 2023), among females aged 30 years, opportunistic screening was associated with a greater expected prevalence of HPV16 and/or 18 and other genotypes in 97.2% and 99.9% of postcodes, respectively. The probability this percentage was lower among females aged 66 years was below 95% for both genotype groups. For organised screening, a pronounced north-west/south-east gradient in infection prevalence was found across France for both genotype groups, with hotspots located at the border with Italy, Spain and Switzerland.CONCLUSION Opportunistic screening is associated with systematic inflation of HR HPV infection prevalence
DC and RF aging test of AlGaN/GaN HEMT technology on SiC substrate
No full textThis article focuses on the comprehensive evaluation of performance and robustness in microwave AlGaN/GaN HEMTs. The study investigates whether the degradation mechanisms observed during DC aging test align with those observed during RF aging test. A time-domain load-pull setup (1.8 GHz – 18 GHz) is utilized to measure key parameters during RF stresses and characterize the devices, highlighting key differences in degradation mechanisms between RF and DC aging tests. These findings shed light on the behavior of HEMTs when subjected to a RF signal, emphasizing the necessity of comprehensive analysis for ensuring device reliability in practical scenarios
Façade maritime : Atlantique (Aquitaine), Rapport de sondages sur estran (2024), commune de Soulac-sur-Mer (Gironde) - OA 5326
No full textInitiating and Replicating the Observations of Interactional Properties by User Studies Optimizing Applicative Prototypes
Get PDFLa science des Interactions Humain-Machine (IHM) revêt beaucoup
de résultats empiriques isolés, souvent liés à des technologies, des
conceptions et des tâches spécifiques. Le présent article propose
un formalisme d’observation de l’interaction (plutôt que des
interfaces) adossé à une méthode de révélation (la diffraction
de boucles d’interaction). Les propriétés interactionnelles ainsi
étudiées sont propices à des réplications au travers de conditions
variées (prototypes, technologies, tâches et profils de personnes
utilisatrices). Surtout, elles peuvent émerger et être répliquées
lors du traitement de cas applicatifs, qui bénéficient en retour
d’une optimisation des prototypes. La publication de cas applicatifs
continue alors d’illustrer l’utilité des technologies, tout en
produisant des résultats qui conduiront de futures recherches à
consolider ou établir des théories, et à aboutir à un catalogue
et une science de propriétés interactionnelles pertinentes. Ces propriétés contribueront à de meilleures interactions en utilisation,
particulièrement pour la variété d’interfaces ubiquitaires.The science of Human–Computer Interaction (HCI) is populated
by isolated empirical findings, often tied to specific technologies,
designs, and tasks. This paper proposes a formalization of user
interaction observations (instead of user interfaces) and an
associated revealing method (interaction loop diffraction). The
resulting interactional properties that are studied in a calibrated
manner, are well suited to replication across various conditions
(prototypes, technologies, tasks, and user profiles). In particular,
interactional properties can emerge and be replicated within
the workflow of applicative cases, which in return benefit from
the optimization of applicative prototypes. Applicative cases’
publications will then contribute to demonstrating technology
utility, along with providing empirical results that will lead future
work to theory consolidation and theory building, and finally to
a catalog and a science of relevant interactional properties. These
properties will contribute to better user interactions, especially for
the variety of ubiquitous user interfaces
Genetic diversity of isoetid communities of Aquitaine shallow lakes
No full textLes lacs du littoral Aquitain constituent un refuge pour une diversité exceptionnelle de plantes aquatiques dont des isoétides rares, espèces jouant un rôle crucial dans le maintien des fonctions écosystémiques. Cependant, depuis les années 1970, l’extinction locale de ces espèces protégées en raison des changements globaux menace l’écosystème. Ce projet vise à étudier la structure génétique des populations d’isoétides et à mieux comprendre les communautés qu’elles occupent, afin de développer des plans de conservation améliorés pour ces écosystèmes.Afin d’explorer la diversité génétique des communautés de macrophytes et sa variation au sein et entre les cinq lacs Aquitains où persistent les isoétides protégées (Lobelia dortmanna et Littorella uniflora), nous avons analysé neuf espèces grâce au génotypage de microsatellites par séquençage, une méthode révélant une diversité génétique plus fine que les approches classiques basées sur la taille. L’étude vise trois objectifs principaux : (i) identifier les processus influençant la structure génétique des populations, (ii) déterminer les facteurs historiques et contemporains environnementaux affectant la diversité génétique de ces macrophytes, et (iii) comprendre la composition et l’organisation des communautés de macrophytes grâce à la comparaison de la diversité génétique et taxonomique.Ces résultats fourniront des informations sur la capacité d’adaptation, l’histoire démographique, les capacités de dispersion et la structure générale des populations de ces communautés de macrophytes, essentielles d’un point de vue écologique. Ce projet apportera des éléments clés pour les plans de conservation dans la région Aquitaine et contribuera à une meilleure compréhension de la structuration des communautés végétales d’eau douce et de leurs réponses face aux menaces anthropiques. En identifiant le potentiel adaptatif et les réponses des communautés aux pressions, ce travail permettra aux acteurs concernés de mieux protéger la biodiversité et les services écosystémiques vitaux associés.Mots-clés : Génétique de la conservation, génotypage par microsatellites, flux de gènes, diversité multi-échelle
Life-history trade-offs explain local adaptation in Arabidopsis thaliana
No full textLocal adaptation has been demonstrated in many organisms, but the traits involved, and the temporal and spatial scales at which selection acts are generally unknown. We carried out a multi-year study of 200 accessions (natural inbred lines) of Swedish Arabidopsis thaliana using local field sites and a combination of common-garden experiments that measured adult survival and fecundity, and selection experiments that measured fitness over the full life cycle. We found evidence of strong and variable selection, with particular genotypes favored more than five-fold in certain years and locations. Fecundity showed evidence of classical local adaptation, with accessions generally performing better close to their home. However, southern accessions usually had the highest fecundity—but were far more sensitive to harsh winters and slug herbivory, which strongly decreased both survival and fecundity. Accessions originally sampled on beaches had low fecundity in all environments, but massively outperformed all other accessions in the selection experiments, presumably due to an advantage during seedling establishment associated with their very large seeds. We conclude that local adaptation in A. thaliana reflects strong temporally and spatially varying selection on multiple traits, generally involving trade-offs and different life-history strategies, making fitness difficult to predict and measure