ED Mathématiques et Informatique
Resource dimensioning for heterogeneous architectures
by Vincent ALBA (LaBRI - Laboratoire Bordelais de Recherche en Informatique)
The defense will take place at 10h00 - Amphi LaBRI Domaine universitaire, 351 Cr de la Libération, LaBRI (Laboratoire Bordelais de Recherche en Informatique), 33405 Talence
in front of the jury composed of
- Denis BARTHOU - Professeure des universités - Bordeaux INP - Directeur de these
- Cedric BASTOUL - Professeur des universités - Université de Strasbourg - Rapporteur
- Henri-Pierre CHARLES - Directeur de recherche - CEA Grenoble - Rapporteur
- Corinne ANCOURT - Professeure - MINES ParisTech - Examinateur
- Yves COUDIERE - Professeur des universités - Université de Bordeaux - Examinateur
Over the last decades, to match the increasing demands for computational power, high-performance computing systems have been equipped with increasingly more complex architectures. Recent architectures now integrate accelerators such as FPGA and GPUs, multi-GPUs, alongside complex interconnect topologies. However while this allows architectures to reach unprecedented peak performance, fully exploiting these architectures is becoming increasingly more specific. In particular, the growing gap between cores performance and the bandwidth of memory buses, and the introduction of Non-Uniform Memory Access (NUMA) can greatly limit the performance of memory-intensive applications, making them memory-bound. In this context, memory-intensive applications, or memory-intensive phases within an application, will often achieve better performance and energy efficiency on a subset of the available resources, therefore using less cores and accelerators thus reducing the amount of required data accesses and avoiding NUMA effects. However, finding the optimal set of resources to run these applications adds another optimization challenge to developers, especially when considering multiple architectures, as this optimal set will vary depending on the architecture topology. To relieve this burden, we will present in this thesis two dynamic resource tuning heuristics able to transparently select an efficient set of GPUs to run iterative applications. These heuristics exploit both online performance measurement and data access pattern observations as well as information about the target architecture topology, to efficiently explore and select the most efficient set of resources without incurring significant overhead, and regardless of the architecture. We validate our heuristics on two different sets of benchmarks and three architectures. The first set of benchmarks assesses the accuracy of our heuristics. We found that we are able to find the best or second best configuration 98.33% of the time, never selecting a configuration more than 9% slower than optimal. The second set of benchmarks compares our heuristics to naive implementations. Both heuristics outperform the naive heuristics on most scenarios. We also observe energy efficiency improvements proportional to the resulting speedup. Finally, our heuristics achieve at least 92.6% of the observed peak performance on all benchmarks, regardless of the target architectures, indicating good performance portability.
An Adaptive Recommender System Based on Incremental Classification in an E-Learning Environment
by Oussama LAAROUSSI (LaBRI - Laboratoire Bordelais de Recherche en Informatique)
The defense will take place at 9h30 - A LaBRI, Université de Bordeaux, Bâtiment A30, 351 cours de la Libération, 33400 Talence
in front of the jury composed of
- Henri NICOLAS - Professeur - Université de Bordeaux - Directeur de these
- Mounir ZRIGUI - Professeur - Université de Monastir - CoDirecteur de these
- Kais HADDAR - Professeur - Université De Sfax - Examinateur
- Akka ZEMMARI - Professeur - université de bordeaux - Examinateur
- Zied KECHAOU - Professeur - Université de Kairouan, Tunisie - Rapporteur
- Mohamed HAMROUN - Maître de conférences - Université de limoges - Rapporteur
This thesis addresses Arabic book recommendation from heterogeneous sources, jointly targeting personalization, explainability, and temporal adaptation. Using a Goodreads corpus, we build a traceable pipeline: normalization of reviews (MSA/dialects), de-duplication and cleaning, metadata harmonization (author, title, description), and lightweight semantic enrichment. We introduce D-MARS, which encodes each modality accordingly (reviews via a dialect-aware Arabic language model, ratings with an ordinal-aware perceptron, metadata with dedicated representations), then aggregates them through hierarchical attention, combining intra-view (metadata) and inter-view weighting (source calibration) prior to interaction modeling. D-MARS+ adds session-based incremental learning with controlled replay, mitigating forgetting and stabilizing quality over time. Evaluation (strict temporal split, ablations, sensitivity analyses) leverages interpretable attention weights, showing how information load shifts across reviews, metadata, and ratings depending on input richness. Contributions include (i) a cleaned corpus and reproducible pipeline tailored to Arabic specifics, (ii) an explainable fusion architecture leveraging cross-view complementarity without unnecessary complexity, and (iii) a simple, effective incremental strategy improving temporal consistency. Limitations involve dialectal noise, uneven metadata completeness, and textual encoding cost. Future work explores rank-aligned objectives, encoder distillation/quantization for inference, integration with a semantic graph (authors/themes), and in vivo evaluations covering diversity, fairness, and robustness.
ED Sciences Chimiques
Lipid-oligonucleotides (LONs): amphiphilic bioconjugates foranticancer application
by Faith KIVUNGA (Acides nucléiques : Régulations Naturelles et Artificielles)
The defense will take place at 9h30 - Amphitheatre BBS 2 rue Dr. Hoffmann Martinot Building BBS 33076 Bordeaux cedex
in front of the jury composed of
- Philippe BARTHELEMY - Professeur des universités - Université de Bordeaux - Directeur de these
- Eugen STULZ - Associate Professor - University of Southampton - Rapporteur
- Ling PENG - Directrice de recherche - Aix-Marseille University - Rapporteur
- Jean DESSOLIN - Chargé de recherche - Université de Bordeaux - Examinateur
Pancreatic ductal adenocarcinoma (PDAC) accounts for over 90% of pancreatic cancer cases and exhibits poor survival due to late diagnosis, aggressive biology, and resistance to current therapies. Proto oncogenes mutations drive most PDACs, making theses relevant genes key therapeutic targets; however, current inhibitors show limited efficacy and toxicity. This study explores oligonucleotide-based strategies for targeting relevant oncogenes. A novel multiconjugate antisense oligonucleotide (ASO) bearing modified biomolecules was designed to enhance delivery and gene silencing. In parallel, conjugated G-quadruplex (G4) decoys were developed to inhibit transcription factors binding to G-rich promoter regions of reported oncogenes. Oligonucleotides were synthesised, structurally characterised, and evaluated for biological activity in PDAC cell lines. The novel multiconjugate ASO achieved a four-fold reduction in KRAS expression compared to the unmodified ASO but showed limited impact on cell proliferation. Conjugated G-quadruplex demonstrated potent multi-gene silencing, downregulating multiple oncogenes, leading to reduced proliferation, migration, and spheroid growth. Combination with gemcitabine produced synergistic effects, with lipid G4restoring drug sensitivity. These findings highlight multi-conjugation and G4-based decoys as promising strategies for improving oligonucleotide delivery and achieving multi-targeted cancer therapy with reduced toxicity.
ED Droit
The proportionality of incrimination
by Apo ASSALE (INSTITUT DE SCIENCES CRIMINELLES ET DE LA JUSTICE)
The defense will take place at 9h00 - Salle RG Pôle juridique et judiciaire de Pey-Berland , 35, place Pey-Berland bordeaux, 33000 Bordeaux
in front of the jury composed of
- Maxime BRENAUT - Professeur des universités - Université de Bordeaux - Examinateur
- Marie BARDET - Professeure des universités - Université Bretagne Sud - Rapporteur
- Olivier CAHN - Professeur des universités - Université Paris Nanterre - Rapporteur
- Valerie MALABAT - Professeure des universités - Université de Bordeaux - Directeur de these
The gradual diffusion of proportionality review within criminal law has undeniably resulted in an expansion of its scope, extending from the realm of sentencing to that of the very norms of criminal incrimination. This development has been further reinforced by the considerable growth of fundamental rights and the consolidation of their protection at the international level, thereby transforming the criminal norm of incrimination into a legitimate subject of judicial challenge. Incrimination, indeed, constitutes the normative framework within which the general rules are defined through which the legislature seeks to ensure the preservation of social order. As a genuine instrument of criminal policy, it requires the constant pursuit of a balance between, on the one hand, infringements upon fundamental rights and freedoms and, on the other, the attainment of the objectives pursued by the normative authorities. From this perspective, the requirement of proportionality tends to establish itself within the sphere of criminal incrimination as a regulatory mechanism of normative power. The present thesis thus examines the binding force of this requirement in the exercise of the power to punish. More precisely, it seeks to highlight, in a critical manner, the strengths and weaknesses inherent in the implementation of the principle of proportionality during both the elaboration and the application of criminal incrimination norms, thereby encompassing all dimensions of the incrimination process. While proportionality appears as an omnipresent principle throughout the repressive system, it nonetheless remains a contingent requirement. On the one hand, at the stage of normative elaboration, a clear discrepancy persists between the theoretical ambitions associated with the requirement of proportionality and the realities of legislative practice: ultimately, proportionality proves to be too subtle and fragile to impose itself as a genuinely binding norm upon the normative authorities. On the other hand, at the stage of application, proportionality assumes a more assertive consistency: it emerges as the essential condition for the integration of the criminal norm of incrimination within the repressive system, and as the ultimate criterion of its legitimacy when translated into terms of reasonableness and justice.
Privacy in the Digital Age: A Challenge for Criminal Law. A Comparative Study of France and Romania
by Catalin BOACNA (INSTITUT DE SCIENCES CRIMINELLES ET DE LA JUSTICE)
The defense will take place at 14h00 - Amphithéâtre Ellul 35 place Pey Berland, Bordeaux
in front of the jury composed of
- Jean-Christophe SAINT-PAU - Professeur - Université de Bordeaux - Directeur de these
- Marie‑Christine SORDINO - Professeure - Université de Montpellier - Rapporteur
- Tudorel TOADER - Professeur - Université Al. I. Cuza de Iași - CoDirecteur de these
- Răducanu RUXANDRA - Professeure - Université de Craiova - Rapporteur
- Charlotte CLAVERIE-ROUSSET - Professeure - Université de Bordeaux - Examinateur
- Guillaume BEAUSSONIE - Professeur - Université Toulouse-Capitole - Examinateur
From a philosophical concept delineating the boundary between the intimate and the public spheres, private life has, in the modern era, become a fundamental right. In the age of technological change, its scope is being reconfigured by social networks, mass data collection, artificial intelligence, algorithms, and omnipresent surveillance, whether exercised by large platforms or by state actors. From a comparative perspective, this dissertation examines the mechanisms through which criminal law is called upon to recalibrate its preventive and repressive functions without abandoning the principles of legality, necessity, proportionality, and subsidiarity. It highlights imminent challenges—mass profiling, continuous monitoring, biometrics, behavioural prediction—indeed, the tendency to reduce human identity to a number. Private life thus tends to become a binary mechanism of identification: a number, threatened by other numbers and, at the same time, protected by other numbers. Today, criminal law is called to accompany the transformation of the concept of privacy not merely as a clerk recording the drafting of the synallagmatic contract concluded between human and algorithm, but as a notary vested with full authority. The diligence of criminal law in protecting privacy must be effective and tailored to situations in which only a balance between legal regulatory mechanisms and technological developments can ensure the best form of protection. In no case do I endorse normative hypertrophy; nor do I encourage the legislator's harmful passivity that allows mass profiling or unjustified intrusions by technology giants into private life to be reduced to mere sources of monetization. Nor do I reject the idea of a lis pendens between protection in the digital environment and in real life: both domains share privacy as their central concern and call upon the same criminal law to guarantee it. The lack of synchronization between criminal law and technological developments has, in many instances, produced abusive intrusions into private life—paradoxical situations in which, for example, the warrant for intercepting telephone conversations would be “patented” more than a century after the invention of the telephone. Even Samuel D. Warren, the visionary father of the right to privacy, could scarcely have foreseen in the 1890s that some of Alan Turing's boldest mathematical calculations would bear directly on privacy, or that vehicles once started by turning an external crank would become systems monitoring users' behavioural reactions to warn them they are too fatigued. It would have seemed downright extravagant at the time to imagine that mathematics could be so closely bound up with privacy. Overall, the approach adopted here views matters from the standpoint of criminal law—the last redoubt against an unprecedented assault on individual privacy and even on the autonomy of the will.
ED Entreprise Economie Société
IMPACTS OF CLIMATE CHANGE ON AGRI-FOOD SYSTEMS: THE CASE OF THE FRENCH VITICULTURE AND WINEMAKING SECTOR
by Catherine LIS-CASTIBLANCO (BSE - Bordeaux sciences économiques)
The defense will take place at 17h00 - Salle de séminaire H2-116 BSE, Bâtiment H2 Avenue Léon Duguit 33600, Pessac
in front of the jury composed of
- Jean-Marie CARDEBAT - Professeur des universités - Université de Bordeaux - Directeur de these
- Magali DELMAS - Full professor - UCLA - Rapporteur
- Julian ALSTON - Professeur émérite - UC Davis - Rapporteur
- Karl STORCHMANN - Associate Professor - NYU - CoDirecteur de these
- Jean-Marc FIGUET - Professeur des universités - Université de Bordeaux - Examinateur
Climate change is reshaping the conditions under which agri-food systems operate, altering weather patterns, intensifying extremes, and raising uncertainty for producers and markets. These pressures are particularly consequential for high-value perennial sectors where long biological cycles, sunk capital, and institutional rules constrain rapid adjustment. This thesis studies the French wine and grape sector as a case of a quality-differentiated, geographically regulated industry in which adaptation is essential yet nontrivial. Chapter 1 applies an empirical strategy to measure temperature effects on grape yields while explicitly accounting for adaptation at two horizons. Historical long-run adaptation is captured by allowing the yield–weather relationship to vary across climate areas, recognizing that growers exposed to different regimes have already selected varieties, sites, and practices that shape marginal sensitivities. Future adaptation is incorporated by letting these sensitivities adjust with projected climates, constructing a forward-looking counterfactual. Three projection scenarios—no adaptation, historical adaptation only, and future adaptation—show that extreme heat reduces yields, but growers accustomed to hotter conditions are less sensitive at the margin. Nationally, average projected effects are positive in a warming climate, with larger gains in cooler regions. Crucially, projections that ignore adaptation misstate the sign and magnitude of effects in some areas, whereas allowing for future adaptation substantially attenuates losses that otherwise appear in warmer zones. Chapter 2 addresses a pervasive measurement problem: the use of fixed calendar windows to summarize growing-season weather. When phenology advances, fixed windows mismeasure exposure and bias projections. Focusing on Bordeaux red-wine appellations, the chapter estimates budburst and harvest dates with heat-accumulation models and computes weather indicators within these shifting, phenology-consistent windows. Tracking phenology can flip the sign of late-century impacts relative to fixed windows because sensitive stages occur earlier and on cooler days, reducing measured heat exposure. Chapter 3 turns to risk management and finance. Even if average yields change modestly, producers face heightened revenue risk as extremes become more common and quality shocks transmit directly to prices. The chapter evaluates whether bulk wine is sufficiently commodity-like to underwrite a standard futures market, emphasizing two conditions: cross-market product homogeneity and sufficient price volatility. Using a spatial market-integration framework and time-series models for France, Italy, and Spain, the evidence indicates weak cross-border homogeneity alongside substantial, time-varying volatility. A generic tri-national bulk-wine futures contract is therefore unlikely to be viable. This points to alternative instruments: more granular contracts tied to specific origins or quality tiers, weather derivatives indexed to phenology-relevant exposures, or revenue-style insurance that jointly reflects yield and price. Overall, the thesis links identification of adaptation, phenology-aware exposure, and the feasibility of price-risk instruments to provide an empirically grounded framework for anticipating climate risks and mobilizing adaptation in high-value perennial agriculture, where quality, reputation, and rules are central to performance.
ED Sciences de la Vie et de la Santé
Biochemical and biophysical aspects of G-quadruplex RNA in oncogenic KRAS mRNA regulation.
by Zahraa OTHMAN (Acides nucléiques : Régulations Naturelles et Artificielles)
The defense will take place at 9h30 - EDST Université Libanaise, École Doctorale en Sciences et Technologie, Campus Universitaire de Rafic Hariri
in front of the jury composed of
- Gilmar SALGADO - Associate Professor - Université de Bordeaux - Directeur de these
- Ahmad DAHER - Professeur - Professeur, Université Libanaise, Beyrouth - Directeur de these
- Mahmoud KHALIL - Professeur - Université Arabe, Beyrouth - Rapporteur
- Jose IBRAHIM - Maître de conférences - Université Libanaise Américaine (LAU), Beyrouth - Examinateur
- Patrizia ALBERTI - Maîtresse de conférences - Enseignante-chercheure, Laboratoire Structure et Instabilité des Génomes - Examinateur
- Jean-Baptiste BOULE - Directeur de recherche - Sorbonne Université - Rapporteur
The untranslated region (UTR) of messenger RNA (mRNA) in proto-oncogenes plays a crucial role in gene expression regulation. These UTRs, situated at the 5' and 3' ends of the mRNA, contain regulatory elements that influence translation and stability. In proto-oncogenes, the UTRs can harbor regulatory sequences that control the expression of the corresponding oncogenes. Dysregulation of UTR-mediated processes can reduce oncogenic transformation by affecting translation initiation, protein production levels, be the target of microRNAs, impacting mRNA stability and degradation. Understanding the complexities of UTR regulation in proto-oncogenes is vital for uncovering mechanisms behind cancer development and potential therapeutic interventions. In this proposal, we want to address this problem in KRAS 5'UTR region, where the partner-laboratory from Udine recently discovered the formation of unusual structures (G-quadruplexes) that are the target of regulatory proteins, confirmed here in Bordeaux as well by biophysical methods. Three regions (UTR-1, UTR-C and UTR-Z) from 5' region where independently target with RNA binding protein (RBP) hnRNPA1. Preliminary results using biochemical and biophysical tests evidence a regulatory and strong interaction particularly with UTR-Z.
Deep learning for the automatic segmentation and prediction of airway diseases, using innovative CT and MRI methods
by Amel HADJ BOUZID (Centre de recherche Cardio-Thoracique de Bordeaux)
The defense will take place at 10h00 - amphitheatre lyric Hôpital Xavier Arnozan Avenue du Haut Lévêque 33600 Pessac
in front of the jury composed of
- Salim SI-MOHAMED - Professeur des universités - praticien hospitalier - University Claude Bernard Lyon 1 - Rapporteur
- Olivier MEYRIGNAC - Professeur des universités - praticien hospitalier - AP-HP, Assistance Publique - Hôpitaux de Paris - Rapporteur
- Gael DOURNES - Professeur des universités - praticien hospitalier - Université de Bordeaux - CRCTB - Directeur de these
- Constance DE MARGERIE-MELLON - Maîtresse de conférences - praticienne hospitalière - AP-HP, Assistance Publique - Hôpitaux de Paris - Examinateur
This thesis lies at the intersection of medical imaging, artificial intelligence, and clinical pulmonology. Its objective is to develop tools for the detection and volumetric quantification of structural abnormalities of the airways. Cystic fibrosis has been chosen as the model pathology for this study, given the diversity and intensity of its pulmonary damage visible in imaging. Quantitative monitoring of such damage is a major clinical challenge, complicated by the limitations of current imaging modalities: computed tomography (CT), which is accurate but involves radiation exposure, and magnetic resonance imaging (MRI), which does not involve radiation exposure but lacks validated quantification tools. The objective is to develop robust imaging biomarkers for these two modalities. In the first part, we develop and validate a robust tool for CT, the reference modality. We propose a deep learning method based on a 3D network optimized for the semantic and holistic segmentation of structural airway abnormalities. The challenge is to evaluate the clinical validity of this quantitative approach, particularly its correlation with disease severity markers and its sensitivity to therapeutic response in cohorts of patients undergoing treatment. Finally, we evaluate the generalization of our CT approach to other chronic airway diseases with similar imaging symptoms, such as Alpha-1 Antitrypsin deficiency, to establish its potential as a cross-sectional phenotypic tool. In the second part of this thesis, we address the challenge of quantification on MRI, for which methods of segmenting airway lesions are non-existent. We introduce a reinforcement learning agent to dynamically adapt the network's learning strategy to the specificities of the MRI signal. The objective is to demonstrate the feasibility and clinical relevance of this approach as a non-irradiating alternative. Finally, the versatility of the developed framework is demonstrated through its successful application to the 3D segmentation of microscopic images in a murine asthma model, showcasing its potential beyond the initial clinical scope.
Impact of Anatomy, Diagnosis, and Fenestration on the Incidence of Cardiovascular Events in Patients With Univentricular Physiology After Fontan Circulation
by Nabil DIB (Centre de recherche Cardio-Thoracique de Bordeaux)
The defense will take place at 16h00 - Salle de réunion 2 eme étage Avenue Magellan 33600 Pessac
in front of the jury composed of
- Jean-Benoit THAMBO - Professeur des universités - praticien hospitalier - Université de Bordeaux - Directeur de these
- Chloé JAMES - Professeure des universités - praticienne hospitalière - CHU Bordeaux - Examinateur
- Francis BESSIERE - Professeur des universités - praticien hospitalier - Université Lyon 1 - CHU Lyon - Rapporteur
- Virginie FOUILLOUX - Professeure des universités - praticienne hospitalière - Université de Marseille - Rapporteur
Congenital heart disease (CHD) represents the most common major congenital malformation, affecting more than 1% of newborns. Advances in surgery, intensive care, and imaging have enabled most children undergoing corrective or palliative procedures to reach adulthood, creating a new and growing population with specific challenges. Among the most complex forms, univentricular heart defects require multistage palliation culminating in the Fontan circulation. First described in 1971, this procedure has dramatically transformed the prognosis of these patients, and its technical variants aim to optimize hemodynamics and reduce complications. Despite these advances, numerous late complications persist, including arrhythmias, thromboembolic events, protein-losing enteropathy, hepatic dysfunction, and end-stage heart failure. Outcomes differ according to ventricular morphology and underlying diagnosis—particularly in hypoplastic left heart syndrome (HLHS), which remains associated with poorer prognosis. Fenestration, designed to improve early hemodynamic tolerance, offers perioperative benefits but its long-term role remains controversial, especially regarding thromboembolic and rhythm-related risks. In this multicenter cohort study, we assessed the influence of ventricular morphology and initial diagnosis on the occurrence of major cardiovascular events (arrhythmias, thrombosis, transplantation, and death) and analyzed the long-term impact of fenestration. We also examined the influence of anatomical repair type (univentricular vs. biventricular) on post-transplant outcomes. Our findings highlight the crucial prognostic role of anatomy, the increased vulnerability of patients with right ventricular Fontan physiology and HLHS, and the overall complexity of post-Fontan management. Although fenestration does not appear to significantly affect overall mortality, it may be associated with a higher risk of arrhythmias or embolic events in specific contexts. Finally, heart transplantation remains the ultimate therapeutic option, with higher early mortality among univentricular patients but comparable conditional long-term survival thereafter. These results underscore the need for personalized follow-up strategies based on ventricular morphology and individual risk profiles in the Fontan population. They also call for large prospective studies to optimize therapeutic strategies, anticipate transplantation, and improve the long-term quality of life of this expanding patient population.
Communication between toxigenic Fusarium and their microbial partners: role of small RNAs
by Marine NAVARRO (MycSA - Mycologie et Sécurité des Aliments)
The defense will take place at 14h00 - Amphithéâtre C & J Bové Centre INRAE - Amphithéâtre C & J Bové 71 Avenue Edouard Bourlaux 33140 Villenave d'Ornon
in front of the jury composed of
- Nadia PONTS - Chargée de recherche - Université de Bordeaux - Directeur de these
- Thomas GRENTZINGER - Cadre scientifique - Vienna Biocenter Core Facility - Rapporteur
- Fabienne MALAGNAC - Professeure des universités - Université Paris Saclay - Rapporteur
- Thierry NOëL - Professeur des universités - Département sciences biologiques et médicales, Université de Bordeaux - Examinateur
- Isabelle FUDAL - Directrice de recherche - UR BIOGER - INRAE - Examinateur
- Jean Philippe COMBIER - Directeur de recherche - Laboratoire de Recherche en Sciences Végétales UMR 5546 CNRS-UPS - Examinateur
The Fusarium genus contains more than 80 phytopathogenic species causing Fusarium head blight (FHB), a devastating cereal disease worldwide. FHB causes significant economic losses and health risks linked to the production of mycotoxins, thermostable molecules that are toxic to humans and animals if ingested. FHB results from interaction between several Fusarium species, including up to 16 different species. Recent studies have shown that the stage of infection and mycotoxin production are influenced by intra-microbial interactions mediated by molecular dialogue involving microRNAs (miRNAs). miRNAs are small non-coding RNAs, 18 to 25 nucleotides in length, that induce post-transcriptional gene silencing, the abundance and nature of which are influenced by various factors such as the stage of development and microbial interactions. Considering the importance of miRNAs in the interaction between microorganisms, this thesis focuses on studying the molecular mechanisms involved in inter- and intra-species communication, with an exploratory section on the interactions between F. graminearum and bacteria in the phytopathosystem. The aims are to 1) describe the morphological and molecular changes that accompany interactions between Fusaria, 2) explore the role of fungal miRNAs, and 3) describe the transcriptional changes that accompany F. graminearum/bacteria interactions. In vitro confrontations were performed between F. graminearum and several Fusarium species. Macroscopic and confocal microscopy analyses showed limited changes during intra-species interactions. Conversely, inter-species interactions revealed growth inhibition in strains confronted with F. graminearum, increased sporulation, and pigment variations reflecting metabolomic changes, suggesting a competitive relationship between Fusarium species. A multi-omic approach combining mRNA-seq, smRNA-seq, and untargeted metabolomics identified 934 fungal miRNAs, 441 of which were validated in silico. Signature miRNAs specific to a particular interaction and differentially expressed during confrontation were identified. The integration of transcriptomic and metabolomic data suggests that certain miRNAs could modulate defense or attack during interspecies interactions, while oxylipins and other secondary metabolites appear to play the role of chemical communication mediators. Inter-species interactions induce nutritional and oxidative stress as well as increased mycotoxin production, in contrast to relatively neutral intra-species interactions. The study of miRNA biogenesis has identified, in silico, AGO and DCL proteins whose protein domain architecture suggests conserved functions but with protein sequence variations that may indicate specialization in miRNA loading. The expression of Ago and Dcl genes is dynamic over time and is stimulated during interactions, corroborating the role of miRNAs in gene regulation. Finally, confrontations with wheat bacteria required the development of a 3D device to standardize the interaction zone. During these interactions, F. graminearum presented growth inhibition, pigment variations, and modulation of mycotoxin production depending on the bacterial strain encountered, revealing a dynamic and specialized molecular dialogue. Thus, this research provides insights into the regulation of miRNAs in Fusarium and their role as gene regulators during interactions. The interactions between F. graminearum and other microbial partners are highly complex, specific to the strain encountered, and dynamic over time.
Involvement of brainstem inhibitory networks in the organization of vestibulospinal reflexes
by Léandre LAVENU (Institut de neurosciences cognitives et intégratives d'Aquitaine)
The defense will take place at 14h00 - Amphi Centre Broca Nouvelle-Aquitaine 146 Rue Léo Saignat, 33076 Bordeaux Cedex
in front of the jury composed of
- Didier LE RAY - Chargé de recherche - Université de Bordeaux - Directeur de these
- Alexandra SéVERAC-CAUQUIL - Professeure - Centre de Recherche Cerveau & Cognition-UMR 5549 - Rapporteur
- Frédéric BROCARD - Directeur de recherche - Institut de Neurosciences de la Timone - Rapporteur
- Claire WYART - Directrice de recherche - Institut du Cerveau - Examinateur
- Mathieu BERANECK - Directeur de recherche - Integrative Neuroscience & Cognition Center - Examinateur
- Lora SWEENEY - Assistant professor - Institute of Science and Technology Austria - Examinateur
- Karine MASSé - Professeure - Institut des Maladies Neurodégénératives - Examinateur
- Pascal FOSSAT - Professeur - Institut des Maladies Neurodégénératives - CoDirecteur de these
In vertebrates, control of body posture largely involves vestibular reflexes. The excitatory vestibulospinal pathways underlying these reflexes have been described in many species and show significant similarities between species. Their anatomical organization is bilateral: they originate from secondary vestibular neurons located on either side of the brainstem in two bilateral central vestibular nuclei that project onto the spinal motor networks, one on the ipsilateral side of the spinal cord and the other in the contralateral hemispinal cord. Thus, a unilateral vestibular signal should result in the simultaneous expression of bilateral spinal motor responses, which would not correspond to the functional reflex actually produced. This implies the existence of a control mechanism for excitatory vestibulospinal pathways. We hypothesized that secondary inhibitory vestibular neural networks play a predominant role in orchestrating the vestibulospinal reflex, regardless of the complexity of the postural reflexes observed. To demonstrate this role, we focused on two distinct species with increasingly complex postural biomechanics: the larval and juvenile forms of an amphibian (Xenopus laevis) and an adult mammal (Mus musculus). Using various anatomical techniques, we demonstrate (or confirm) the existence of local and commissural secondary vestibular neurons of a GABAergic and glycinergic nature within the vestibulospinal nuclei, with distinct proportions depending on the stage of development and the species considered. Using an electrophysiological approach on a semi-isolated Xenopus larva preparation, we studied the function of these local and commissural inhibitory networks in modulating the expression of fictive spinal reflexes in response to vestibular afferents and direct electrical stimulation of the vestibulospinal nuclei. We describe in detail the effects of each of the two neurotransmitter systems and their interaction on the form of the spinal response. Using a behavioral approach in mice, based on optogenetic inactivation of GABAergic neurons in the medial vestibular nucleus, we investigated the impact of GABAergic activity suppression on the actual postural adjustments of freely behaving animals. Our analyses during locomotion show no major alteration in the mouse's speed of movement. Lateral neck movements during locomotion are also unaffected.
Crown procyanidins in wine: from the influence of winemaking practices to their structural and physicochemical characterization
by Manon FERREIRA (Oenologie)
The defense will take place at 9h30 - Amphithéâtre ISVV 210 Chemin de Leysotte, Institu des Sciences de la Vigne et du Vin, 33140, Villenave d'Ornon
in front of the jury composed of
- Michaël JOURDES - Professeur - Université de Bordeaux - Institut des Sciences de la Vigne et du Vin - Directeur de these
- Victor DE FREITAS - Full professor - Université de Porto - Rapporteur
- Sylvain GUYOT - Directeur de recherche - INRAE - Examinateur
- Maria del Carmen GARCIA PARRILLA - Professeure - Université de Seville - Rapporteur
- Liming ZENG - Professeure - Université de Changin, Haute école de viticulture et œnologie - Examinateur
Condensed tannins are present in many beverages and foods such as grapes, wine, tea, apples, and chocolate. In wine, they contribute to various organoleptic properties, notably astringency and bitterness, and play an important role in the evolution and stability of red wine color. Recently, a new subfamily of condensed tannins, possessing a macrocyclic skeleton with a cavity, was discovered and named crown procyanidins. This PhD project aimed to deepen the understanding of this new family of condensed tannins. The first line of research focused on the influence of different oenological matrices (rosé, clairet, orange wine, Ruby Port, and Tawny Port) on their concentration and their evolution over time. The second line of research involved an in-depth characterization of their structure by mass spectrometry and nuclear magnetic resonance (NMR), as well as of their physicochemical properties. Copigmentation phenomena and interactions with a model salivary peptide were also studied under different conditions.
ED Sciences Physiques et de l'Ingénieur
Gamma-ray source generation with ultra-high intensity lasers
by Florent BRUN (Centre Lasers Intenses et Applications)
The defense will take place at 14h00 - Amphithéatre C 351 Cr. de la Libération, Campus Peixotto Bâtiment A29, 33400, Talence
in front of the jury composed of
- Emmanuel D'HUMIERES - Professeur des universités - Université de Bordeaux - Directeur de these
- Cédric THAURY - Directeur de recherche - Centre National de la Rechercher Scientifique - Rapporteur
- Henri VINCENTI - Directeur de recherche - Institut Iramis - Rapporteur
- Philippe BALCOU - Directeur de recherche - Centre National de la Rechercher Scientifique - Examinateur
- Mickael GRECH - Chargé de recherche - Centre National de la Rechercher Scientifique - Examinateur
- Xavier RIBEYRE - Directeur de recherche - CEA CESTA - CoDirecteur de these
High energy photons (gamma) sources are omnipresent in the Universe and fundamental to fields of physics such as astrophysics and quantum electrodynamics (QED). Gamma photons in particular allow the study of various phenomena related to QED such as matter-antimatter generation, photon-photon scattering etc. The generation of bright photon beams has been made possible by the use of ultra-intense lasers, thanks to the invention Chirped Pulse Amplification techniques. The highest intensity achieved by lasers is on the order of (I∼10^23 W/cm²). At such intensities, electrons are accelerated to relativistic energies. Relativistic electrons will radiate high energy photons through the Bremsstrahlung process when they cross a thick target made of a high atomic number material. Electrons also radiate photons via the nonlinear inverse Compton scattering (NLCS) process when interacting with the intense laser field. These processes produce high energy photons from keV to hundreds of MeV for Bremsstrahlung and from MeV to tens of GeV for NLCS. These high energy photons can in turn trigger secondary mechanisms such as pair production. The objective of this thesis is to study gamma photons generation during the laser-plasma interaction. Two interactions regimes are considered. The first one involves the interaction between an intense and high energy laser with a solid target. We modeled the interaction between the PETAL laser and a solid tungsten target, aiming to explain and reproduce experimental results for the photons generated during the interaction. To model and characterize photon beams produced we used a chain of simulation codes (Hydrodynamics, Particle In Cell (PIC), Monte Carlo). This simulation chain allowed us to estimate the properties of photon beams from keV to tens of MeV. We showed that the measurement of energetic photons made by the CRACC-X detector were significantly affected, on the first imaging plates, by the electrons that escape the target. An estimate of the number of electron/positron pairs generated by the Bethe-Heitler and Breit-Wheeler processes was also performed. The second interaction regime concerns ultra-intense attosecond pulses interacting with a multilayer target. These attosecond pulses can be produced with High-order Harmonics Generation, i.e. during the interaction between an intense laser with a relativistic plasma mirror. These techniques are studied for producing laser pulses with higher intensities. Our multilayer target is made of a sub-critical plasma juxtaposed with a sur-critical plasma. High energy photons are produced by the NLCS process in a configuration involving only one laser pulse. The aim of this work is also to study the influence of the pulse duration on the interaction, for the same intensity. We performed PIC simulations for several number of cycles within the laser pulse, down to the limit of a quasi single-cycle pulse. Differences in electron dynamics and acceleration, as well as field reflection by the super-critical plasma, are described and explained. A description and analysis of the photon radiation regimes are provided, together with the properties of photon beams resulting from the interaction. We analyzed pairs produced by these photons. We also considered the influence of the carrier envelope phase on the radiated photons. The results of this study will help design future experiments on this interaction regime.
Sources of energetic alpha-particles, produced by means of intense lasers (SNAIL)
by Thomas CARRIERE (Centre Lasers Intenses et Applications)
The defense will take place at 10h00 - Amphithéâtre B Campus Peixotto Bâtiment A29 RDC, 33400, Talence
in front of the jury composed of
- Philippe NICOLAI - Directeur de recherche - Université de Bordeaux - Directeur de these
- Arnaud BECK - Ingénieur de recherche - ECOLE POLYTECHNIQUE - Examinateur
- Dimitri BATANI - Professeur - Université de Bordeaux - Examinateur
- Emmanuel D'HUMIèRES - Professeur - Université de Bordeaux - Examinateur
- Francesco MASSIMO - Chargé de recherche - Université Paris-Saclay - Rapporteur
- Alessio MORACE - Associate Professor - Université d'Osaka - Rapporteur
Intense lasers can be used to produce secondary sources of X rays, gamma rays or particles such as protons, neutrons or alpha particles. The interest in these latter is linked to the current quasi absence of accessible bright alpha-sources. The alpha particles are generally produced by decay of radioactive materials or by using large and rare cyclotrons, like the Arronax installation [Haddad et al, Eur. J. Nucl. Med. Mol. Imaging 35, 182 (2008)]. The use of lasers should allow to obtain bright, ultra-brief and spatially limited alpha particle sources. Various applications of these sources are of particular interest for industry and medicine [Szkliniarz et al, App. Rad. Isotopes 118, 182 (2016)] but also for fundamental physics, such as the study of the slowing down of alpha particles in dense and warm matter. It is possible to produce alpha particle sources, by means of intense lasers, by different ways: - through the interaction of a laser beam with a helium gas jet. By different processes of acceleration (radiation pressure, collisionless shock), it is possible to produce energetic alpha particles using a dense gas jet. However, the shape of the helium jet as well as the laser pulse must be tailored to optimize the energy and angle distribution of the particles. Specifically, the gas density profile needs to be tailored by laser pulses before interacting with the main laser pulse. - by non-thermal nuclear reactions, induced by laser-driven particles. In particular, proton-boron nuclear reactions have been investigated, in the recent years, because they have the advantage of producing very few neutrons, but a large number of alpha particles. However, this source, like the previous one, needs to be perfectly tuned to be usable for other applications. The general concept of these nuclear reactions is based on the acceleration of a proton population by means of a laser, followed by the interaction of these protons with a target containing boron. Protons can be accelerated using a specific target and then sent to a boron target or directly produced within the boron target. However, all the mechanisms are not, to date, perfectly understood and controlled. Several experimental campaigns have been proposed and accepted on different laser facilities to measure the production of alpha particles.
Response of the bioclimatic architecture to the problem of buildings in extreme warm climates: development and experimentation of active and passive strategies
by Abraham SAMUEL (I2M - Institut de Mécanique et d'Ingénierie de Bordeaux)
The defense will take place at 10h30 - amphi 3 740 Cr de la Libération, 33400 Talence
in front of the jury composed of
- Denis BRUNEAU - Professeur des universités - Ecole Nationale Supérieure d'Architecture et de Paysage de Bordeaux - Directeur de these
- Martin HENDEL - Maître de conférences - Université Paris Cité - UMR 8236 CNRS LIED (Laboratoire interdisciplinaire des énergiesdedemain) - Examinateur
- Saed RAJI - Docteur - NOBATEK - Examinateur
- Marie DUQUESNE - Professeure des universités - Université de La Rochelle - Rapporteur
- Jean-Philippe COSTES - Professeur des universités - Ecole Nationale Supérieure d'Architecture de Clermont-Ferrand - Rapporteur
- Philippe LAGIERE - Maître de conférences émérite - Université de Bordeaux - Examinateur
This research aims to tackle the challenges buildings face in extremely hot climates by testing the BaityKool prototype, designed using bioclimatic architecture principles. The 105.5 m² prototype, created for the Solar Decathlon Middle East 2018, was built to withstand harsh conditions. An eco-responsive design and construction process was developed through a collaborative approach involving students, professors, and industry experts from various fields. Drawing inspiration from traditional medina houses, BaityKool features a C-shaped design with inward-facing layouts that maximize openings to the courtyard while minimizing them on the outside. The architecture and orientation of the house optimize the benefits of sunlight, and it includes a compact envelope system made with Ultra High Performance Concrete walls and sun control features. During the 14-day testing period at SDME 2018, BaityKool delivered positive results, earning 3rd place overall and performing strongly in six contests. The Jury praised the house's bioclimatic efficiency, noting innovative methods for storing cool nighttime energy and using it during the day through thermal storage, as well as the courtyard design, advanced engineering, PV-integrated systems, and the use of sustainable materials. After the competition, the prototype was relocated to The Sustainable City Dubai as a ‘BaityKool living lab,' serving as a platform for research and development of solar and eco-friendly building solutions for hot climates. The study aims to assess the effectiveness of bioclimatic strategies in the BaityKool prototype, designed for extremely hot climates. Experimental testing is planned throughout the year to examine the design, performance, impacts, and benefits of dynamic actions such as Solar Shading, Natural Ventilation, Night Ventilation with Solar Shading, and Patio Shading. These actions are evaluated for their influence on thermal comfort and the potential to reduce energy demand for cooling under various scenarios.
ED Sciences et environnements
The Late Middle Paleolithic Technical Variability in Iran: a New Variant with Bifacial Elements from Qaleh Bozi
by Fereidoun BIGLARI (De la Préhistoire à l'Actuel : Culture, Environnement, Anthropologie)
The defense will take place at 14h00 - Amphi PABA, Bâtiment B5 UMR PACEA 5199 UNIVERSITÉ DE BORDEAUX Allée Geoffroy Saint-Hilaire CS 50023 33615 PESSAC Cedex
in front of the jury composed of
- Jacques JAUBERT - Professeur des universités - Université de Bordeaux - Directeur de these
- Anne DELAGNES - Directrice de recherche - Université de Bordeaux - CoDirecteur de these
- Enza SPINAPOLICE - Assistant professor - Université de Rome - Examinateur
- Marjan MASHKOUR - Directrice de recherche - Muséum national d'Histoire naturelle - Examinateur
- Marco PERESANI - Professeur des universités - Università degli Studi di Ferrara - Rapporteur
- Rémy CRASSARD - Directeur de recherche - Université Lumière Lyon 2 - Rapporteur
Qaleh Bozi site complex located at south-southwest of Isfahan, close to the inner foothills of the Zagros range, on the south-western margin of the Central Iran. A large sample of animal bones and lithics were recovered from these sites 2005-2008. The lithic artifacts were made from small river worn pebbles. Chain operation took place entirely at the site as shown by the high percentages of cortical flakes, some intact and tested pebbles and cobbles and cores and small debris. Façonnage technology and core reduction are present in the industry. There are very few Levallois elements. Tools and flakes are predominant and making up three quarters of the assemblage. The remaining artifact types consist of cores, waste and debris. The tool group is dominated by various types of scrapers, followed by the retouched pieces, notch-denticulates, borers and bifacial tools. The diversity and the significant number of large and medium species such as equids, rhino, aurochs, caprini, and gazelles, the relative absence of carnivores, the presence of thick ash lenses, and the presence of almost the entire chain operation in Qaleh Bozi 2, indicate a possible base camp function for QB 2, probably for a number of months on a yearly basis, during the Middle Paleolithic. But the evidence from Qaleh Bozi 3 indicates short-term stays probably related to hunting activities at the Qaleh Bozi Mountain and Zayandeh Rud plain. This is indicated by the dominance of bifacial and uinfacial points in the tool-kit and also the abundance of caprids and gazelles in identifiable faunal remains. Analysis of the archaeological assemblage recovered from the Qaleh Bozi sites offers significant contributions to our understanding of hominin adaptation in a geographically strategic zone between the central Iranian deserts and the Zagros Mountains during the early MIS 3 (60-40 ka). A key differentiating factor between the Qaleh Bozi lithic industry and both Zagros Mousterian and Central Iranian Levallois industries is the application of bifacial reduction techniques. The occurrence of bifacially-worked tools at Qaleh Bozi warrants its classification as a distinct variant within the Zagros Mousterian complex. While exhibiting similarities to other Zagros assemblages through a diverse range of scrapers and points, Qaleh Bozi is further distinguished by a significant bifacial component, a high frequency of notches and denticulates, and the virtual absence of burins, truncated-faceted pieces, and few Levallois technological elements.