Online Sequential Monte Carlo smoother for partially observed stochastic differential equations

This paper introduces a new algorithm to approximate smoothed additive functionals for partially observed stochastic differential equations. This method relies on a recent procedure which allows to compute such approximations online, i.e. as the observations are received, and with a computational complexity growing linearly with the number of Monte Carlo samples. This online smoother cannot be used directly in the case of partially observed stochastic differential equations since the transition density of the latent data is usually unknown. We prove that a similar algorithm may still be defined for partially observed continuous processes by replacing this unknown quantity by an unbiased estimator obtained for instance using general Poisson estimators. We prove that this estimator is consistent and its performance are illustrated using data from two models

The Langevin diffusion as a continuous-time model of animal movement and habitat selection

TM was supported by the Centre for Advanced Biological Modelling at the University of Sheffield, funded by the Leverhulme Trust, award number DS-2014-081.1. The utilisation distribution of an animal describes the relative probability of space use. It is natural to think of it as the long-term consequence of the animal's short-term movement decisions: it is the accumulation of small displacements which, over time, gives rise to global patterns of space use. However, many estimation methods for the utilisation distribution either assume the independence of observed locations and ignore the underlying movement (e.g. kernel density estimation), or are based on simple Brownian motion movement rules (e.g. Brownian bridges). 2. We introduce a new continuous-time model of animal movement, based on the Langevin diffusion. This stochastic process has an explicit stationary distribution, conceptually analogous to the idea of the utilisation distribution, and thus provides an intuitive framework to integrate movement and space use. We model the stationary (utilisation) distribution with a resource selection function to link the movement to spatial covariates, and allow inference about habitat preferences of animals. 3. Standard approximation techniques can be used to derive the pseudo-likelihood of the Langevin diffusion movement model, and to estimate habitat preference and movement parameters from tracking data. We investigate the performance of the method on simulated data, and discuss its sensitivity to the time scale of the sampling. We present an example of its application to tracking data of Steller sea lions (Eumetopias jubatus). 4. Due to its continuous-time formulation, this method can be applied to irregular telemetry data. The movement model is specified using a habitat-dependent utilisation distribution, and it provides a rigorous framework to estimate long-term habitat selection from correlated movement data. The Langevin movement model can be approximated by linear model, which allows for very fast inference. Standard tools such as residuals can be used for model checking.PostprintPeer reviewe

Trypanosomiasis challenge estimation using the diminazene-aceturate (Berenil) index in Zebu in Gabon

A longitudinal study was conducted within a cattle ranch in Gabon to determine the diminazene aceturate (Berenil) index (DAI) in a group of Zebu, raised under low tsetse density; this measure providing an assessment of trypanosomiasis risk. The objective was to evaluate the trypanosomiasis pressure thus informing trypanosomiasis control methods and cattle management. Twenty female adult Zebu were monitored for 24 weeks during the dry season. Blood samples were collected on aweekly basis and subjected to parasitological and haematological analysis (n = 480), using the buffy-coat method and the packed cell volume value (PCV), respectively, infected animals were treated with a single intramuscular injection of diminazene aceturate (8 mg/kg). Twenty-nine single infectious events were recorded and a DAI of 1.45 was calculated. Two trypanosome species were identified: Trypanosoma congolense (96.2%) and Trypanosoma vivax (3.8%). The mean PCV value of the infected animals was lower (26.6) compared to non-infected animals (32.0). This study shows that DAI may be a useful tool to assess trypanosomiasis. However, this is a time-consumingmethod that may be improved by using randomly selected sentinel animals to adapt the chemoprophylactic schemes, hence decreasing the costs and the drug resistance risk

The Athena X-ray Integral Field Unit: a consolidated design for the system requirement review of the preliminary definition phase

The Athena X-ray Integral Unit (X-IFU) is the high resolution X-ray spectrometer, studied since 2015 for flying in the mid-30s on the Athena space X-ray Observatory, a versatile observatory designed to address the Hot and Energetic Universe science theme, selected in November 2013 by the Survey Science Committee. Based on a large format array of Transition Edge Sensors (TES), it aims to provide spatially resolved X-ray spectroscopy, with a spectral resolution of 2.5 eV (up to 7 keV) over an hexagonal field of view of 5 arc minutes (equivalent diameter). The X-IFU entered its System Requirement Review (SRR) in June 2022, at about the same time when ESA called for an overall X-IFU redesign (including the X-IFU cryostat and the cooling chain), due to an unanticipated cost overrun of Athena. In this paper, after illustrating the breakthrough capabilities of the X-IFU, we describe the instrument as presented at its SRR, browsing through all the subsystems and associated requirements. We then show the instrument budgets, with a particular emphasis on the anticipated budgets of some of its key performance parameters. Finally we briefly discuss on the ongoing key technology demonstration activities, the calibration and the activities foreseen in the X-IFU Instrument Science Center, and touch on communication and outreach activities, the consortium organisation, and finally on the life cycle assessment of X-IFU aiming at minimising the environmental footprint, associated with the development of the instrument. Thanks to the studies conducted so far on X-IFU, it is expected that along the design-to-cost exercise requested by ESA, the X-IFU will maintain flagship capabilities in spatially resolved high resolution X-ray spectroscopy, enabling most of the original X-IFU related scientific objectives of the Athena mission to be retained. (abridged).Comment: 48 pages, 29 figures, Accepted for publication in Experimental Astronomy with minor editin

The Athena X-ray Integral Field Unit: a consolidated design for the system requirement review of the preliminary definition phase

The Athena X-ray Integral Unit (X-IFU) is the high resolution X-ray spectrometer studied since 2015 for flying in the mid-30s on the Athena space X-ray Observatory. Athena is a versatile observatory designed to address the Hot and Energetic Universe science theme, as selected in November 2013 by the Survey Science Committee. Based on a large format array of Transition Edge Sensors (TES), X-IFU aims to provide spatially resolved X-ray spectroscopy, with a spectral resolution of 2.5 eV (up to 7 keV) over a hexagonal field of view of 5 arc minutes (equivalent diameter). The X-IFU entered its System Requirement Review (SRR) in June 2022, at about the same time when ESA called for an overall X-IFU redesign (including the X-IFU cryostat and the cooling chain), due to an unanticipated cost overrun of Athena. In this paper, after illustrating the breakthrough capabilities of the X-IFU, we describe the instrument as presented at its SRR (i.e. in the course of its preliminary definition phase, so-called B1), browsing through all the subsystems and associated requirements. We then show the instrument budgets, with a particular emphasis on the anticipated budgets of some of its key performance parameters, such as the instrument efficiency, spectral resolution, energy scale knowledge, count rate capability, non X-ray background and target of opportunity efficiency. Finally, we briefly discuss the ongoing key technology demonstration activities, the calibration and the activities foreseen in the X-IFU Instrument Science Center, touch on communication and outreach activities, the consortium organisation and the life cycle assessment of X-IFU aiming at minimising the environmental footprint, associated with the development of the instrument. Thanks to the studies conducted so far on X-IFU, it is expected that along the design-to-cost exercise requested by ESA, the X-IFU will maintain flagship capabilities in spatially resolved high resolution X-ray spectroscopy, enabling most of the original X-IFU related scientific objectives of the Athena mission to be retained. The X-IFU will be provided by an international consortium led by France, The Netherlands and Italy, with ESA member state contributions from Belgium, Czech Republic, Finland, Germany, Poland, Spain, Switzerland, with additional contributions from the United States and Japan.The French contribution to X-IFU is funded by CNES, CNRS and CEA. This work has been also supported by ASI (Italian Space Agency) through the Contract 2019-27-HH.0, and by the ESA (European Space Agency) Core Technology Program (CTP) Contract No. 4000114932/15/NL/BW and the AREMBES - ESA CTP No.4000116655/16/NL/BW. This publication is part of grant RTI2018-096686-B-C21 funded by MCIN/AEI/10.13039/501100011033 and by “ERDF A way of making Europe”. This publication is part of grant RTI2018-096686-B-C21 and PID2020-115325GB-C31 funded by MCIN/AEI/10.13039/501100011033

Mechanistic and stochastique modelling of trajectories for fisheries science

Driven by ecological questions about determinism of individuals, movement ecology has known large developments in recent years. This enthusiasm was largely possible thanks to the emergence of GPS technologies for the last 20 years, and, therefore, the establishment of numerous databases of individual trajectories. These observations at fine spatial and temporal scales of individuals give the opportunity to identify specific behaviors of individuals and their perception of the environment in which they operate. To process this data, and identify the mechanisms of interest to ecologists, many recent movement models describing the movement mecanisms have been developed. In fisheries Science, with the development of GPS systems, the study of movement and behavior of fishing vessels has also experienced strong growth over the past ten years. Indeed many European fishing vessels are now mandatory equipped with onboard monitoring system (Vessel Monitoring System, VMS) creating a large monitored database. Primarly used for monitoring, these data are now used to address a variety of questions, such as analysis of the fishing effort at fine spatial and temporal scale of the fishing effort, or the analysis of the relationship between spatial-temporal dynamics of fishing activity and resource allocation. These data are mostly studied descriptively, without explicitation of the mechanisms underlying the movement. This thesis aims to explore the relevance of mechanistic models, widely used in ecology to address fisheries issues. Two stochastic and mechanistic modeling frameworks for analysis of trajectory data developed and applied to samples of the VMS database. Throughout the thesis, a special effort is being made to the development of statistical inference method to estimate the parameters controlling the movement. These inference is performed using discrete observations of positions along individual paths. The first model is binding behavior and trajectory and is based on hidden Markov models. Assuming that a transformation of the speed process of an individual follows an autoregressive process, the model is used to estimate fishing activity from trajectory data. The approach therefore achieves a fine description of the fishing effort. The relevance of this model compared to existing descriptive and mechanistic approaches is discussed. Analyzing the performance of the model lead us to investigate the relevance of using speed relative to the water instead of speed relative to the water mass when studying fishing vessel trajectories. This study highlighted the importance of the surface currents in the study of fishing vessel trajectories in Eastern Channel. The second approach develops a space and time continuous model that provides explicit mechanisms of drivers for trajectories. Individuals are supposed to follow the gradient of a cognitive map, representing their perception of the surrounding environment. The model is based on stochastic differential equations in which the deterministic component (the drift) of the motion reflects subjective attractive areas for fishermen. An estimation algorithm of these areas from positions of observations is developed and applied to french fishing vessels in the English Channel. The model, and the resulting estimates are used to test an important hypothesis in fisheries science. Do areas used by fishermen overlap with areas of high abundance estimated by scientific surveys ? The models developed here offer a promising basis for new models in fisheries and movement ecology. Moreover, associated inference algorithms detailled in the manuscript are robust to many extensions leading to a more realistic model.Impulsée par des questionnements sur les déterminismes du déplacement des individus, l’étude du mouvement en écologie s’est fortement développée ces dernières années. Cet engouement pour l’écologie du mouvement a été largement alimenté par l’émergence depuis 20 ans, de technologies GPS et par la constitution de nombreuses bases de données de trajectoires d’individus. Ces observations à des échelles spatiales et temporelles fines sont l’occasion de déceler les comportements des individus en lien avec l’environnement dans lequel ils évoluent. Pour reconstruire ces comportements et en comprendre les déterminismes sous-jacents, de nombreux modèles décrivant les trajectoires ont été développés et appliqués en écologie. En parallèle à ce courant de recherche en écologie du mouvement, l’étude du mouvement et du comportement des navires de pêche a aussi connu un fort développement.. En effet, sous l’effet d’une réglementation européenne en vigueur depuis 2005, de nombreux navires de pêches européens sont équipés de système embarqués de surveillance (le Vessel Monitoring System, VMS), alimentant ainsi une importante banque de données de trajectoires. Ces données permettent d’aborder des questionnements variés, comme l’analyse de la dynamique spatio-temporelle de l’effort de pêche à fine échelle ou l’analyse du lien entre dynamique spatio-temporelle de l’activité de pêche et de la ressource. Ces données ont pour l’instant surtout été étudiées de manière descriptive, sans explicitation des mécanismes sous-jacents au déplacement. Ce travail de thèse vise à explorer la pertinence des modèles mécanistes, largement utilisés en écologie, pour répondre aux questions halieutiques. Deux cadres de modélisation mécaniste et stochastique pour l’analyse des trajectoires sont développés et appliqués à l’analyse des trajectoires de navires de pêche. Tout au long de la thèse, un effort particulier est déployé pour le développement de méthodes d’inférence statistique basées sur la théorie du maximum de vraisemblance pour estimer les paramètres contrôlant le mouvement à partir d’observations discrètes des positions le long des trajectoires individuelles. Le premier modèle vise à reconstruire le comportement de l’individu le long de sa trajectoire observée à pas de temps réguliers et repose sur des modèles de Markov cachés. Il est utilisé pour analyser les trajectoires de navires de pêche en Manche Est. Plus particulièrement, l’approche permet de déterminer les séquences d’activités de pêche différentes au cours d’une marée, et ainsi d’atteindre une description spatiale et temporelle de l’effort de pêche à fine échelle. La pertinence de ce modèle par rapport aux approches descriptives et mécanistes existantes est discutée. Cette approche a permis de mettre en évidence l’importance de prendre en compte les courants de marées dans l’étude des trajectoires de navires en Manche Est. Le second cadre de modélisation propose une modélisation continue en temps et en espace et propose d’introduire un mécanisme explicite de dépendance de la trajectoire par rapport à l’environnement. Il repose sur les modèles d’équations différentielles stochastiques dans lequel la part de déterminisme dans le mouvement (dérive) retranscrit l’idée de l’existence d’un champ spatial sous-jacent à la trajectoire qui représenterait des zones fortement attractives pour la pêche. Un algorithme d’estimation de ces zones à partir d’observations de positions (type VMS) est développé et appliqué aux navires de la Manche Est. Cet algorithme se base sur les avancées récentes pour la simulation exacte des processus de diffusion. Enfin, le modèle est utilisé pour tester une hypothèse d’importance en halieutique : les zones exploitées par les pêcheurs recoupent-t-elles les zones de forte abondance estimées par campagne scientifique ? Au-delà des applications particulières sur lesquelles s’appuient ce travail de thèse, les modèles développés ont permis de construire des bases fondamentales prometteuses pour de nouveaux modèles en halieutique et en écologie du mouvement en général. De plus, les algorithmes d’inférence associés et explicités dans le manuscrit sont innovants et robustes à de nombreux ajouts pour un modèle plus réaliste.

Trajectory Reconstruction and Behavior Identification Using Geolocation Data (chapter 1)

International audienc

Propriétés inflammatoires du polysaccharide capsulaire produit par la cyanobactérie thermophile mastigocladus laminosus.

Les cyanobactéries constituent un groupe important de micro organismes producteurs de molécules biologiquement actives qui présentent un intérêt thérapeutique. Elles forment des tapis qui sont utilisés empiriquement pour leurs propriétés pharmacodynamiques par les médecins des stations thermales. C'est le cas à Néris-les-Bains (chaîne thermale d'Auvergne, France) où Mastigocladus laminosus, une cyanobactérie thermophile, est utilisée mélangée à de l'argile afin de soigner la polyarthrite rhumatoïde et les douleurs rhumatismales traumatiques. Ces tapis de cyanobactéries produisent un polysaccharide exocellulaire dont la structure a été caractérisée chimiquement. Un effet anti-inflammatoire important et dépendant des doses administrées a été observé suite à l'application locale de ce polysaccharide sur l'oreille de souris présentant un œdème provoqué par de l'huile de croton. L'application d'un hydrolysat partiel du polymère, composé uniquement d'oligosaccharides, a réduit l'œdème de façon similaire au polymère, indiquant que l'activité anti-inflammatoire est associée à la fraction polysaccharidique