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Towards space-efficient data structures for large genome-distance matrices with quick retrieval
No full textInternational audienceThe explosion of genomic data presents a significant computational challenge for all downstream analyses. Particularly challenging are microbial collections, which already encompass several millions of genomes (e.g., AllTheBacteria [1]: 2.4M bacterial isolates; GISAID [2]: 15M SARS-CoV-2 sequences) and are further growing exponentially [3]. Many standard bioinformatics analyses lean on pairwise distances between genomes, including phylogeny inference [4, 5, 6] and genome clustering [7]. As a result, the scalability of multiple downstream analyses relies on the efficient computation and storage of pairwise distance matrices.However, while the efficient computation of distances have been addressed by modern sketching-based methods such as Mash [8] and successors (see [9] for a survey), the storage and indexing of the resulting matrices remain a significant challenge. In fact, due to their quadratic size in the number of genomes, these matrices already surpass most storage capacities (e.g., 24 TB required for AllTheBacteria) and are thus heavily truncated when stored (e.g., [10]). This calls for a dedicated data structure that would be space-efficient and support near-constant-time distance retrieval queries. However, despite all the recent advances in compression of restricted families of matrices, such as sparse or low-rank ones [11, 12, 13], to the best of our knowledge, no scalable method is currently available for large genome-distance matrices.In this presentation, we will discuss our ongoing work on subquadratic compression of distance matrices of large bacterial genome collections. Building upon insights from [14, 3], our approach takes advantage of the peculiar structure of those collections, that can extensively be explained by their underlying phylogeny. As a first step, we focus on phylogenetic trees as a candidate backbone for a compact data structure for pairwise distances. During this talk, we will show that collections of genomes following idealised evolutionary models can be stored in linear space supporting constant-time queries. We will then demonstrate our preliminary results on the tradeoffs that exist between (monitored) metric distortion and storing cost in various practical use cases. Overall, our work draws a path towards practical data structures that would be applicable to collections of millions of genomes with only negligible distance data distortion.</p
Mucin O-glycosylation and B-cell homing: a new bridge for the gut-kidney axis in IgA nephropathy?
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Les horizons du trail : entre dépassement de soi et connexion à la nature
No full textInternational audienceUltra-trail running is a distinctive sporting practice located at the intersection of self-transcendence, extreme embodied experience, and environmental immersion. This chapter explores the horizons of trail running through four complementary perspectives: the psychological profiles of runners, sensory awareness, discipline, and human warmth. Research in sport psychology shows that ultra-trail runners display specific traits such as high resilience, a strong capacity for self-transcendence, and emotional regulation skills that support perseverance in the face of pain and fatigue. From a phenomenological perspective, the sensory experience of trail running reveals an intensification of the relationship to the body, a transformation of time perception, and a strengthened connection to nature. Discipline, understood as a rigorous process of mental and physical preparation, emerges as a central condition for engagement in ultra-endurance events. Finally, the chapter highlights the collective dimension of ultra-trail running, characterized by mutual support, gratitude, and a strong sense of community belonging. Balancing individual challenge and solidarity, ultra-trail running thus appears as a privileged laboratory for understanding contemporary relationships between the body, the environment, and human capacities.L’ultra-trail constitue une pratique sportive singulière, située à l’intersection du dépassement de soi, de l’expérience corporelle extrême et de l’immersion environnementale. Ce chapitre analyse les horizons du trail running à partir de quatre axes complémentaires : les profils psychologiques des coureurs, la conscience sensorielle, la discipline et la chaleur humaine. Les recherches en psychologie du sport montrent que les pratiquants d’ultra-trail présentent des traits spécifiques, tels qu’une forte résilience, une capacité d’auto-transcendance et une régulation émotionnelle favorisant la persévérance face à la douleur et à la fatigue. L’expérience sensorielle, appréhendée dans une perspective phénoménologique, révèle une intensification du rapport au corps, une modification de la perception du temps et un renforcement de la connexion à la nature. La discipline, entendue comme un travail de préparation mentale et physique rigoureux, apparaît comme une condition centrale de l’engagement dans l’ultra-endurance. Enfin, le chapitre met en lumière la dimension collective de l’ultra-trail, marquée par l’entraide, la gratitude et un fort sentiment d’appartenance communautaire. Entre exigence individuelle et solidarité, l’ultra-trail se révèle ainsi comme un laboratoire privilégié pour comprendre les relations contemporaines entre corps, environnement et capacités humaines
(Invited) Challenges of digital world based on ULSI and TFT technologies involving new neuromorphic approaches, Invited paper,
No full textScientific Advisory Committee MemberInternational audienceThe worldwide development of communication and data exchange systems, as well as research into environmental protection, have strongly encouraged the development of digital tools. The current trend is for this growth to accelerate, thanks to the emergence of numerous new applications, crypto-currencies such as blockchains (Bitcoin, Litecoin or Ethereum), and artificial intelligence (AI). The latter approach opens up a wide spectrum of applications in science and technology, but also in writing capabilities such as chatgpt or data processing for commercial or political purposes. The transparency of the operation of these tools and application on the user's side makes us forget that the associated energy consumption is growing exponentially and that we could reach a global dead end in less than 10 years, with the electrical consumption of digital technology exceeding the current world electrical production.These digital tools are physically dependent on electronics and microelectronics, the latter constituting the associated hardware. The solution is to reduce the energy consumption of all electronics, whether analog or digital, power, high-frequency, highly integrated or large-area, but also by modifying the calculation principle in a new algorithm based on neuromorphic similarity. Previous studies [1-2] have highlighted the technological approach of devices that can combine new semiconductor materials and a 3D architecture involving the stacking of ULSI and TFT circuits. These devices are expected to significantly reduce electrical power consumption and improve sustainability in terms of natural resource limitation. The proposed article focuses more on electronic circuits and their architecture, which should curb the considerable increase in power consumption expected as a result of the massive increase in processed data, particularly in artificial intelligence applications.To this end, a good expected solution is to develop a nano-inspired computing task associated with a neuromorphically inspired physical architecture, comprising equivalent neurons, axons or electronic synapses.Early studies were based on the dynamics of neural models that were encoded in software and computed on general-purpose digital hardware. Unfortunately, this technique turned out to require highly complex circuitry, a time-consuming computation process and, consequently, a huge consumption of electrical power. The second technique involves developing an analog hardware approach involving ULSI artificial neurons and synapses. This technique considerably reduces power consumption, but the amount of data processed remains very high.Another approach involves silicon artificial neurons (SAN) based on biophysical model. The most well-known model is the Morris-Leca model that electronically simulates the transport of potassium and sodium elements in the real biological neuron, generating a spike-shaped signal as in a brain. As a result, the energy consumption per spike can be as low as a femtojoule that is promising for future AI systems thanks to an adapted combination of ULSI and TFT technologies for analog circuits and of 3D memories.All these improvements will only be possible if we develop a pool of skills and know-how in the field of microelectronics and nanotechnologies, capable of driving innovation. Challenges that are just as important and complementary to those of a technical nature must therefore be met. As already mentioned, there is a growing skills deficit in the industry, with jobs in high shortage [3]. It is urgent to increase the pool of specialists in the field by innovating on the content of knowledge, and on the pedagogical approach focused on knowledge and know-how. Awareness and attractiveness actions must be carried out at the high school and student levels in order to attract good candidates who will become future actors of the field. One of the challenges of this action is to convince the youth to study in engineering and more especially in microelectronic field. The last part of the paper is dedicated to this challenge and to the actions underway at the French and European levels
Santé environnementale
No full textNational audienceCe chapitre vise à donner au lecteur les clefs d'appropriation de la santé environnementale en tant que champ de production de connaissances des dangers et des risques sanitaires liés à l'environnement, de caractérisation et d'évaluation des impacts sanitaires associés, ainsi que de gestion de ces impacts pour protéger la santé publique. Au regard des précédentes éditions, il faut souligner l'accroissement spectaculaire des connaissances, particulièrement des mécanismes étiologiques par lesquels l'environnement agit sur la santé, et des interactions entre les facteurs environnementaux, le climat et la biodiversité et de leurs effets conjugués sur les impacts sanitaires. Cette évolution est liée aux innovations conceptuelles qui ont conduit au développement d'une recherche interdisciplinaire ouvrant la voie à des approches systémiques de caractérisation des risques, et aux innovations technologiques permettant leur mise en oeuvre. Elle a ainsi conduit à un élargissement et un approfondissement du champ de la santé environnementale mais aussi à sa complexification dont la prise en compte opérationnelle dans l'évaluation des risques et sa traduction dans l'élaboration des politiques publiques de prévention et de contrôle reste en grande partie à construire, alors même que la santé environnementale est aujourd'hui menacée, notamment par les intérêts des grands secteurs d'activité des groupes mondialisés
Work Exposome and Related Disorders of Firefighters: An Overview of Systematized Reviews
No full textInternational audienceIntroduction: Firefighters experience many exposures associated with negative health outcomes. Because of this, there are many studies on the subject. Our objective here was to conduct an umbrella review of systematized reviews to identify firefighting activities and related exposures associated with negative health outcomes. Methods: A comprehensive search of the PubMed, Web of Science, and Scopus (Health) was conducted using all firefighter systematized reviews. We extracted the country and date of the review, type of firefighter, types of exposure, and related health outcomes. Risk of bias was based on AMSTAR-2 checklist. Results: In 1130 studies, 47 systematized reviews were included, mostly in the last 5 years and from North America and Australia. The topics were diverse, ranging from general aspects to specific exposures, such as polycyclic aromatic hydrocarbons, wildland fires, organizational, traumatic, or psychological stress exposure, and from prevention or surveillance to specific health effects (e.g., cancer, mental health, musculoskeletal disorders, cardiovascular, and pulmonary health, etc.). The risk of bias assessment using the selection grid shows a significant heterogeneity, though some studies were of very high quality. Discussion: This umbrella review provides a comprehensive description of systematized reviews describing populations of firefighters, including information on exposure, health outcomes, and illness/ injury prevention. (c) 2025 Occupational Safety and Health Research Institute. Published by Elsevier B.V. on behalf of Institute, Occupational Safety and Health Research Institute, Korea Occupational Safety and Health Agency. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/ licenses/by-nc-nd/4.0/)
Les effets de la responsabilité subjective des sujets privés de liberté en Argentine : approches théorique et psychopathologique
No full textWhat link can be observed between the law and the statements made by the inmate during this meeting with the clinical psychologist in the prison environment? The behaviour of inmates raises questions when they break the codes that establish order in a given society. Our society in the 21st century is particularly virulent and lacks clear boundaries. This society, filled with objects and new technologies, creates more distant social ties. The effects: subjects without a compass, without boundaries, expressing themselves with words that are both empty and dense, and with complete literalness. To understand these effects, we will briefly discuss the history of the Penal Code in our country, Argentina, and then we will enter a high-security prison. We will listen to the words of the subjects through clinical excerpts, develop concepts and conduct an in-depth analysis from a psychoanalytical perspective. Our conceptual compass, that of subjective responsibility in relation to subjective truth, will enable us to stay on course throughout this study. The subject of our research invites us to focus on the grey areas of this encounter between the individual and collective spheres. The response we receive is that of subjects deprived of freedom who have cut themselves off from the chains of subjective imprisonment, suffering according to their family history but in close relationship with the current world that tends to dehumanise them.Quel lien peut-on observer entre la loi juridique et la prise de parole du sujet incarcéré lors de cette rencontre entre le sujet et le.la psychologue clinicien.ne dans le milieu carcéral ? Les effets des sujets incarcérés nous interrogent dès lors qu'ils transgressent les codes permettant d’établir un ordre dans une société donnée. La nôtre, dans ce XXIe siècle, est particulièrement virulente et sans limites claires. Cette société comblée d’objets et de nouvelles technologies crée des liens sociaux plus distants. Les effets : des sujets sans boussole, sans limite contenante, s’exprimant avec une parole à la fois vide et dense, et dans une littéralité pleine et entière. Pour comprendre ces effets, nous aborderons succinctement l’histoire du Code pénal dans notre pays, l’Argentine, puis nous entrerons dans une prison de haute sécurité. Nous écouterons la parole des sujets à travers des extraits cliniques, nous déploierons des concepts et nous mènerons une analyse approfondie depuis la psychanalyse. Notre boussole conceptuelle, celle de la responsabilité subjective en lien avec la vérité subjective, nous permettra de garder le cap tout au long de cette étude. Le sujet de notre recherche nous invite à mettre l’accent sur les zones d’ombre de cette rencontre entre les champs individuel et collectif. La réponse que nous accueillons est celle de sujets privés de liberté qui se sont coupés des chaînes d’un emprisonnement subjectif, souffrant selon leur roman familial mais en étroite relation avec ce monde actuel qui tend à les déshumaniser
Concert-enquête de Fourches « Silence dans les champs »
No full textBord de scène pour le Concert-enquête de Fourches « Silence dans les champs », avec Antoine Pasqualini (Monolithe Noir – batterie, synthé, chant), Arnaud Kermarrec-Tortorici (Mnemotechnic – basse, chant), François Joncour (Poing – guitare, synthé, chant) et Paul Le Galle (Collectif de vidéastes La Rocade – son, vidéo), en écho à l’ouvrage éponyme de Nicolas Legendre, ciné-concert donné au Tambour, Université Rennes 2, Rennes, le 11 décembre 2025Suite au ciné-concert, l’échange avec la salle souligne la grande force et sensibilité du spectacle proposé, qui n’est pas une mise en scène directe de l’ouvrage de Nicolas Legendre mais qui transmet, par la combinaison d’images d’archives, de vidéos contemporaines, de dialogues enregistrés, de poésie et de musique rock, de rendre sensible la complexité des sentiments qui traversent les paysans et les paysannes d’aujourd’hui. Les artistes expliquent leur enquête auprès de fermes et dans les paysages modernisés du Finistère et la manière dont ils ont construit leur proposition artistique. La question de l’anonymat relatif des sources est discutée. Yvon Le Caro pointe l’intérêt des archives de l’INA pour percevoir que le modèle agricole breton s’est construit entre 1952 et 1962 sous la forme d’une Révolution (dite silencieuse), l’arasement des talus comme la mort du cheval venant acter le meurtre symbolique du père paysan patriarcal et de sa civilisation paysanne par le jeune agriculteur professionnel ; ce qui explique en partie la violence des réactions ultérieures contre toute tentative post-moderne, interprétée comme contre-révolutionnaire dans le contexte agro-alimentaire breton. Il confirme la difficulté, pour les jeunes agriculteurs des années 80-2010, à opérer sur la ferme de leurs parents la réorientation agro-écologique nécessaire, tout en rapportant leur intérêt marqué pour les expériences menées à la ferme par les précurseurs, lorsque le lycée agricole ou le développement agricole leur permet de les rencontrer. Il suggère que ce spectacle, qui interroge mais respecte les doutes et les fractures intérieures des agriculteurs engagés dans la modernité agricole, puisse être proposé dans des enceintes agricoles comme opportunité de libérer une parole trop souvent autocensurée
AdaLite: A Distilled AdaBins Model for Depth Estimation on Resource-Limited Devices
No full textInternational audienceThis paper presents AdaLite, a knowledge distillation framework for monocular depth estimation designed for efficient deployment on resource-limited devices, without relying on quantization or pruning. While large-scale depth estimation networks achieve high accuracy, their computational and memory demands hinder real-time use. To address this problem, a large model is adopted as a teacher, and a compact encoder–decoder student with few trainable parameters is trained under a dual-supervision scheme that aligns its predictions with both teacher feature maps and ground-truth depths. AdaLite is evaluated on the NYUv2, SUN-RGBD and KITTI benchmarks using standard depth metrics and deployment-oriented measures, including inference latency. The distilled model achieves a 94% reduction in size and reaches 1.02 FPS on a Raspberry Pi 2 (2 GB CPU), while preserving 96.8% of the teacher’s accuracy (δ1) and providing over 11× faster inference. These results demonstrate the effectiveness of distillation-driven compression for real-time depth estimation in resource-limited environments. The code is publically available