Uncertainty quantification of medium-term heat storage from short-term geophysical experiments using Bayesian Evidential Learning

In theory, aquifer thermal energy storage (ATES) systems can recover in winter the heat stored in the aquifer during summer to increase the energy efficiency of the system. In practice, the energy efficiency is often lower than expected from simulations due to spatial heterogeneity of hydraulic properties or non-favorable hydrogeological conditions. A proper design of ATES systems should therefore consider the uncertainty of the prediction related to those parameters. We use a novel framework called Bayesian Evidential Learning (BEL) to estimate the heat storage capacity of an alluvial aquifer using a heat tracing experiment. BEL is based on two main stages: pre- and post-field data acquisition. Before data acquisition, Monte Carlo simulations and global sensitivity analysis are used to assess the information content of the data to reduce the uncertainty of the prediction. After data acquisition, prior falsification and machine learning based on the same Monte Carlo are used to directly assess uncertainty on key prediction variables from observations. The result is a full quantification of the posterior distribution of the prediction conditioned to observed data, without any explicit full model inversion. We demonstrate the methodology in field conditions and validate the framework using independent measurements. Plain Language Summary : Geothermal energy can be extracted or stored in shallow aquifers through systems called aquifer thermal energy storage (ATES). In practice, the energy efficiency of those systems is often lower than expected because of the uncertainty related to the subsurface. To assess the uncertainty, a common method in the scientific community is to generate multiple models of the subsurface fitting the available data, a process called stochastic inversion. However this process is time consuming and difficult to apply in practice for real systems. In this contribution, we develop a novel approach to avoid the inversion process called Bayesian Evidential Learning. We are still using many models of the subsurface, but we do not try to fit the available data. Instead, we use the model to learn a direct relationship between the data and the response of interest to the user. For ATES systems, this response corresponds to the energy extracted from the system. It allows to predict the amount of energy extracted with a quantification of the uncertainty. This framework makes uncertainty assessment easier and faster, a prerequisite for robust risk analysis and decision making. We demonstrate the method in a feasibility study of ATES design

Étude des microbiotes endogènes et exogènes de patients atteints de maladie respiratoire chronique

The microorganisms, some of which preceded us billions of years ago, have been identified from the North Pole to the bottom of the ocean until in the atmosphere. The advent of High Throughput Sequencing (HTS) technologies has facilitated the discovery and study of these microbial communities, including the human body. Thus, the human body appears to be composed of ten times more microorganisms than its own cells. Notably, the intestinal microbiota is one of the most investigated; it is composed of a significant biomass. In contrast, studies on the pulmonary microbiota are only in their early stages, particularly in the context of chronic respiratory diseases (CRD). While until recently lungs were considered as sterile organs, they are now found to be composed of a poly-microbial community of bacteria, viruses, phages and fungi. In the case of CRD, such as asthma and cystic fibrosis studied in this PhD work, the composition of the pulmonary microbiota determined by NGS appears to correlate with the clinical course of the patients.In cystic fibrosis (the most common genetic disease in the Caucasian population) and asthma (a multifactorial disease attributed to environmental factors associated with a genetic predisposition which knows a constantly increasing prevalence), changes in abundance and diversity (known as dysbiosis) of bacterial communities (endogenous microbiota) are well documented. However, the study of endogenous mycobiota (fungal community that resides into the lungs) remains much less investigated. Indeed, it presents methodological challenges inherent to its very low biomass, but also to the structure of fungi wall.In addition, very few information exits on the relationship between the endogenous pulmonary microbiota of patients and the corresponding indoor environment (or exogenous microbiota), whereas this specific fungal exposure represents a known risk factor for the development of a CRD. The study of such microbial exposome also presents methodological challenges, in terms of sampling and characterization of the microbial communities that are also of low biomass.The main objective of this work was initially to optimize mycobiota analysis, using an artificial fungal community from the extraction steps to the selection of the most efficient fungal targets to perform targeted metagenomics in cystic fibrosis and asthma context. Concerning the study of the microbial exposome, the evaluation of a device for the collection of microorganisms present in the patient's indoor environment was developed during this work in order to provide an optimized, standardized, and scientifically relevant tool.Secondly, the NGS characterization of endogenous microbiota and mycobiota of cystic fibrosis patients was investigated by taking into account their clinical state, in particular the existence of a pulmonary exacerbation. Correlations involving fungal genera known to be medically relevant such as Aspergillus, Scedosporium and Candida have been identified by focusing on the inter-kingdom network between bacteria and fungi identified in patients. It allowed us to confirm (from our experimental data) the role of the endogenous mycobiota in the ecological model “Climax / Attack" adapted to cystic fibrosis. [...]Du pôle nord au fin fond des océans jusque dans l’atmosphère, des microorganismes, qui nous ont précédé pour certain il y a des milliards d’années, ont été identifiés. L’avènement des technologies de séquençage haut débit (NGS) a facilité la découverte et l’étude de ces communautés microbiennes issues de divers milieux, dont le corps humain. Ainsi, le corps humain apparait composé de dix fois plus de microorganismes que de ses propres cellules. Le microbiote intestinal, de biomasse importante, est l’un des plus étudiés. En revanche, les études portant sur le microbiote pulmonaire n’en sont qu’à leurs prémisses, en particuliers dans le cadre de maladies respiratoires chroniques (MRC). Alors que les poumons étaient jusque très récemment considérés comme stériles, ils s’avèrent être composés d’une communauté poly-microbienne constituée de bactéries, de virus, de phages et de micromycètes. Dans le cas des MRC, comme l'asthme et la mucoviscidose étudiés dans ce travail, la composition du microbiote pulmonaire déterminée par NGS semble corrélée à l’évolution clinique des patients.Dans la mucoviscidose (maladie génétique la plus fréquente dans la population caucasienne) comme dans l’asthme (une pathologie multifactorielle attribuée à des facteurs environnementaux associés à une prédisposition génétique qui connait une prévalence en constante augmentation), les modifications en abondance et diversité (ou dysbiose) des communautés bactériennes (microbiote endogène) sont bien documentées. Cependant, l’étude du mycobiote endogène (des communautés de micromycètes au niveau pulmonaire) reste beaucoup moins réalisée. En effet, cette étude du mycobiote présente des défis méthodologiques inhérents à sa très faible biomasse, mais aussi à la structure même de la paroi des champignons.De plus, peu d’informations existent sur les relations entre ce microbiote pulmonaire endogène et celui de l’environnement immédiat des patients (microbiote exogène ou exposome), alors que cet exposome microbien en particulier fongique représente un facteur de risque connu de développement d’une MRC. L’étude de l’exposome microbien présente un challenge méthodologique, en termes d’échantillonnage et de caractérisation des communautés microbiennes qui sont aussi de faible biomasse.L’objectif de ce travail était dans un premier temps d’optimiser l’analyse du mycobiote, à partir de communautés artificielles de micromycètes depuis l’étape d’extraction jusqu’à la sélection des cibles les plus efficientes pour une approche de métagénomique ciblée appliquée à l’étude du mycobiote dans la mucoviscidose et l’asthme. Concernant l’étude de l’exposome microbien, l’évaluation d’un dispositif de recueil des microorganismes présents dans l’environnement intérieur des patients a fait l’objet d’un développement durant ce travail de thèse ; ceci afin de mettre à disposition de la communauté scientifique un outil optimisé et standardisé.Dans un second temps, les microbiotes et mycobiotes endogènes de patients atteints de mucoviscidose, caractérisés par NGS ont été analysés en prenant en compte l’état clinique des patients, notamment l’existence d’une exacerbation pulmonaire. En s’intéressant aux interactions interrègnes entre les bactéries et les micromycètes identifiés chez ces patients, des corrélations impliquant des genres fongiques connus comme pathogènes et pouvant être responsable de colonisation et/ou infections tel qu’Aspergillus, Scedosporium et Candida ont été mises en évidences. Ceci a permis pour la première fois de confirmer (à partir de nos données expérimentales) la place du mycobiome endogène dans le modèle écologique « Climax/Attack » adapté à la mucoviscidose. [...

Assessment of endogenous and exogenous microbiotas of patients with chronic respiratory disease

Du pôle nord au fin fond des océans jusque dans l’atmosphère, des microorganismes, qui nous ont précédé pour certain il y a des milliards d’années, ont été identifiés. L’avènement des technologies de séquençage haut débit (NGS) a facilité la découverte et l’étude de ces communautés microbiennes issues de divers milieux, dont le corps humain. Ainsi, le corps humain apparait composé de dix fois plus de microorganismes que de ses propres cellules. Le microbiote intestinal, de biomasse importante, est l’un des plus étudiés. En revanche, les études portant sur le microbiote pulmonaire n’en sont qu’à leurs prémisses, en particuliers dans le cadre de maladies respiratoires chroniques (MRC). Alors que les poumons étaient jusque très récemment considérés comme stériles, ils s’avèrent être composés d’une communauté poly-microbienne constituée de bactéries, de virus, de phages et de micromycètes. Dans le cas des MRC, comme l'asthme et la mucoviscidose étudiés dans ce travail, la composition du microbiote pulmonaire déterminée par NGS semble corrélée à l’évolution clinique des patients.Dans la mucoviscidose (maladie génétique la plus fréquente dans la population caucasienne) comme dans l’asthme (une pathologie multifactorielle attribuée à des facteurs environnementaux associés à une prédisposition génétique qui connait une prévalence en constante augmentation), les modifications en abondance et diversité (ou dysbiose) des communautés bactériennes (microbiote endogène) sont bien documentées. Cependant, l’étude du mycobiote endogène (des communautés de micromycètes au niveau pulmonaire) reste beaucoup moins réalisée. En effet, cette étude du mycobiote présente des défis méthodologiques inhérents à sa très faible biomasse, mais aussi à la structure même de la paroi des champignons.De plus, peu d’informations existent sur les relations entre ce microbiote pulmonaire endogène et celui de l’environnement immédiat des patients (microbiote exogène ou exposome), alors que cet exposome microbien en particulier fongique représente un facteur de risque connu de développement d’une MRC. L’étude de l’exposome microbien présente un challenge méthodologique, en termes d’échantillonnage et de caractérisation des communautés microbiennes qui sont aussi de faible biomasse.L’objectif de ce travail était dans un premier temps d’optimiser l’analyse du mycobiote, à partir de communautés artificielles de micromycètes depuis l’étape d’extraction jusqu’à la sélection des cibles les plus efficientes pour une approche de métagénomique ciblée appliquée à l’étude du mycobiote dans la mucoviscidose et l’asthme. Concernant l’étude de l’exposome microbien, l’évaluation d’un dispositif de recueil des microorganismes présents dans l’environnement intérieur des patients a fait l’objet d’un développement durant ce travail de thèse ; ceci afin de mettre à disposition de la communauté scientifique un outil optimisé et standardisé.Dans un second temps, les microbiotes et mycobiotes endogènes de patients atteints de mucoviscidose, caractérisés par NGS ont été analysés en prenant en compte l’état clinique des patients, notamment l’existence d’une exacerbation pulmonaire. En s’intéressant aux interactions interrègnes entre les bactéries et les micromycètes identifiés chez ces patients, des corrélations impliquant des genres fongiques connus comme pathogènes et pouvant être responsable de colonisation et/ou infections tel qu’Aspergillus, Scedosporium et Candida ont été mises en évidences. Ceci a permis pour la première fois de confirmer (à partir de nos données expérimentales) la place du mycobiome endogène dans le modèle écologique « Climax/Attack » adapté à la mucoviscidose. [...]The microorganisms, some of which preceded us billions of years ago, have been identified from the North Pole to the bottom of the ocean until in the atmosphere. The advent of High Throughput Sequencing (HTS) technologies has facilitated the discovery and study of these microbial communities, including the human body. Thus, the human body appears to be composed of ten times more microorganisms than its own cells. Notably, the intestinal microbiota is one of the most investigated; it is composed of a significant biomass. In contrast, studies on the pulmonary microbiota are only in their early stages, particularly in the context of chronic respiratory diseases (CRD). While until recently lungs were considered as sterile organs, they are now found to be composed of a poly-microbial community of bacteria, viruses, phages and fungi. In the case of CRD, such as asthma and cystic fibrosis studied in this PhD work, the composition of the pulmonary microbiota determined by NGS appears to correlate with the clinical course of the patients.In cystic fibrosis (the most common genetic disease in the Caucasian population) and asthma (a multifactorial disease attributed to environmental factors associated with a genetic predisposition which knows a constantly increasing prevalence), changes in abundance and diversity (known as dysbiosis) of bacterial communities (endogenous microbiota) are well documented. However, the study of endogenous mycobiota (fungal community that resides into the lungs) remains much less investigated. Indeed, it presents methodological challenges inherent to its very low biomass, but also to the structure of fungi wall.In addition, very few information exits on the relationship between the endogenous pulmonary microbiota of patients and the corresponding indoor environment (or exogenous microbiota), whereas this specific fungal exposure represents a known risk factor for the development of a CRD. The study of such microbial exposome also presents methodological challenges, in terms of sampling and characterization of the microbial communities that are also of low biomass.The main objective of this work was initially to optimize mycobiota analysis, using an artificial fungal community from the extraction steps to the selection of the most efficient fungal targets to perform targeted metagenomics in cystic fibrosis and asthma context. Concerning the study of the microbial exposome, the evaluation of a device for the collection of microorganisms present in the patient's indoor environment was developed during this work in order to provide an optimized, standardized, and scientifically relevant tool.Secondly, the NGS characterization of endogenous microbiota and mycobiota of cystic fibrosis patients was investigated by taking into account their clinical state, in particular the existence of a pulmonary exacerbation. Correlations involving fungal genera known to be medically relevant such as Aspergillus, Scedosporium and Candida have been identified by focusing on the inter-kingdom network between bacteria and fungi identified in patients. It allowed us to confirm (from our experimental data) the role of the endogenous mycobiota in the ecological model “Climax / Attack" adapted to cystic fibrosis. [...

Application de la méthodologie Pegase au bassin Rhin-Meuse

Le modèle Pegase (Planification Et Gestion de l’ASsainissement des Eaux) est un modèle intégré bassins hydrographiques/rivières qui permet de calculer de façon déterministe et prévisionnelle la qualité des eaux des rivières en fonction des rejets et apports de pollution (relation pression-impact). Développé depuis la fin des années 1980 à l’université de Liège, il permet d'orienter les choix des opérateurs publics et privés en matière de gestion des eaux de surface à l'échelle des petits et grands bassins versants. L'Agence de l’eau Rhin-Meuse a engagé en 1993 une collaboration avec trois équipes universitaires wallonnes (l'Université de Liège, les Facultés de Notre Dame de la Paix de Namur, et l'Université Libre de Bruxelles pour adapter aux rivières du bassin Rhin-Meuse le modèle PEGASE, initialement mis au point pour la région Wallonne. Les travaux réalisés lors de cette collaboration ont permis de montrer la faisabilité pour l'Agence d'utiliser cet outil comme instrument de programmation et de planification. Ce rapport de synthèse présente les éléments principaux de l'étude : des détails supplémentaires sont repris dans des rapports d'avancemen

Prevention de la dysbiose d'un microbiote intestinal immature avec une solution nutritionnelle innovante

International audienceThe postnatal period is critical to avoid permanent gut dysbiosis. It is largely dependent of the individual diet and may be improved. The present study was aimed at evaluating the synergetic effect of Caburyrate, Nutriose® and tannins on the prevention of gut microbiota dysbiosis. Material & Methods: Freshly weaned piglets were used as a model of gut dysbiosis. They were distributed in 7 groups to compare the different combinations of ingredients. Weight, mortality rate and antibiotic treatment were recorded throughout the study. Fecal swabs were taken at arrival, day 14 and at the end for targeted metagenomic analysis. Intestinal tissue and content were collected to evaluate the development and maturation of the gut and the absence of inflammation. Results: Control piglets showed the highest mortality rate (~15%). Only those that received butyrate presented no mortality. The group supplemented with the combination of the 3 were the biggest and had high mortality rate (~12%). The analysis of the microbiota composition will help to understand these results and will be correlated to the tissue analysis. Conclusion: We hope to recommend some of the combinations tested to targeted population at risk of gut dysbiosis to promote intestinal microbiota diversification and gut health

A European ECMM-ESCMID survey on goals and practices for mycobiota characterization using Next Generation Sequencing

International audienceAlthough substantial efforts have been made to investigate about the composition of the microbiota, fungi that constitute the mycobiota play a pivotal role in maintaining microbial communities and physiological processes in the body. Here, we conducted an international survey focusing on laboratory's current procedures regarding their goals and practices of mycobiota characterisation using NGS. A questionnaire was proposed to laboratories affiliated to working groups from ECMM (NGS study group) and ESCMID (ESGHAMI and EFISG study groups). Twenty-six questionnaires from 18 countries were received. The use of NGS to characterise the mycobiota was not in routine for most of the laboratories (N = 23, 82%), and the main reason of using NGS was primary to understand the pathophysiology of a dysbiosis (N = 20), to contribute to a diagnosis (N = 16) or to implement a therapeutic strategy (N = 12). Other reported reasons were to evaluate the exposome (environmental studies) (N = 10) or to investigate epidemics (N = 8). Sputum is the main sample studied, and cystic fibrosis represents a major disease studied via the analysis of pulmonary microbiota. No consensus has emerged for the choice of the targets with 18S, ITS1 and ITS2 used alternatively among the laboratories. Other answers are detailed in the manuscript. We report a photography of mycobiota analysis that may become a major tool in the near future. We can draw some conclusions on the diversity of approaches within the answers of the 27 laboratories and underline the need for standardisation

le microbiote intestinal d'animaux monogastriques élevés avec une solution nutritionnelle innovante

International audienceWeaning is a critical transition phase for health of farm monogastric animals and often requires antibiotic treatments. To limit the spreading of antimicrobial-resistant microbes and improve the digestive comfort of rent animals during weaning, different nutritional solutions were tested. This study aims to investigate the effect of Ca-butyrate, chestnut tannins, and Nutriose® and their combinations on weaned piglets' growth and gut health by intestinal microbiota analysis. Two consecutive test rounds each involving 192 weaned piglets (6 piglets per pen) were conducted. Piglets were divided into six groups receiving the different combinations of the nutritional solutions tested and one control group. Piglets' weight and mortality rate were recorded all along the study as well as the individual antibiotic treatments, if any. By excluding piglets treated with antibiotics, a total of 694 fecal swabs was collected by sampling 2 pigs per pen at arrival, on day 14 and day 31 for subsequent targeted metagenomic analysis. At the end of the study, piglets of the control group showed the highest mortality rate (~15%) compared to groups with nutritional solutions. Among supplemented piglets, only those receiving Cabutyrate presented no mortality. Surprisingly, the group supplemented with the combination of Cabutyrate, tannins, and Nutriose® had the highest weight but also one of the highest mortality rates (~12%). Combined microbiota data with zootechnical results will give insights into the impact of the nutritional solution in improving weaned piglets' health and gut bacterial composition balance

le microbiote intestinal d'animaux monogastriques élevés avec une solution nutritionnelle innovante

International audienceWeaning is a critical transition phase for health of farm monogastric animals and often requires antibiotic treatments. To limit the spreading of antimicrobial-resistant microbes and improve the digestive comfort of rent animals during weaning, different nutritional solutions were tested. This study aims to investigate the effect of Ca-butyrate, chestnut tannins, and Nutriose® and their combinations on weaned piglets' growth and gut health by intestinal microbiota analysis. Two consecutive test rounds each involving 192 weaned piglets (6 piglets per pen) were conducted. Piglets were divided into six groups receiving the different combinations of the nutritional solutions tested and one control group. Piglets' weight and mortality rate were recorded all along the study as well as the individual antibiotic treatments, if any. By excluding piglets treated with antibiotics, a total of 694 fecal swabs was collected by sampling 2 pigs per pen at arrival, on day 14 and day 31 for subsequent targeted metagenomic analysis. At the end of the study, piglets of the control group showed the highest mortality rate (~15%) compared to groups with nutritional solutions. Among supplemented piglets, only those receiving Cabutyrate presented no mortality. Surprisingly, the group supplemented with the combination of Cabutyrate, tannins, and Nutriose® had the highest weight but also one of the highest mortality rates (~12%). Combined microbiota data with zootechnical results will give insights into the impact of the nutritional solution in improving weaned piglets' health and gut bacterial composition balance

The cuff leak test to predict failure of tracheal extubation for laryngeal edema

Laryngeal edema secondary to endotracheal intubation may require early re-intubation. Prior to extubation the absence of leak around an endotracheal tube may predict laryngeal edema after extubation. We evaluated the usefulness of a quantitative assessment of such a leak to identify the patients who will require early re-intubation for laryngeal edema.SCOPUS: ar.jinfo:eu-repo/semantics/publishe