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Ms.FPOP: An Exact and Fast Segmentation Algorithm With a Multiscale Penalty
No full text38 pages, 17 figuresInternational audienceGiven a time series in with a piecewise constant mean and independent noises, we propose an exact dynamic programming algorithm to minimize a least square criterion with a multiscale penalty promoting well-spread changepoints. Such a penalty has been proposed in Verzelen et al. (2020), and it achieves optimal rates for changepoint detection and changepoint localization. Our proposed algorithm, named Ms.FPOP, extends functional pruning ideas of Rigaill (2015) and Maidstone et al. (2017) to multiscale penalties. For large signals, , with relatively few real changepoints, Ms.FPOP is typically quasi-linear and an order of magnitude faster than PELT. We propose an efficient C++ implementation interfaced with R of Ms.FPOP allowing to segment a profile of up to in a matter of seconds. Finally, we illustrate on simple simulations that for large enough profiles () Ms.FPOP using the multiscale penalty of Verzelen et al. (2020) is typically more powerfull than FPOP using the classical BIC penalty of Yao (1989)
SENSE: A Force-Sensor-Free, Model-Based Framework for Estimating External Interaction Forces on Humanoid Robots
No full textInternational audienceThis study introduces SENSE, an innovative sensorless external force estimation framework for humanoid robots, built on a model-driven approach. Unlike conventional methods that depend on the simplified Linear Inverted Pendulum (LIP) model and offline data processing, SENSE enables real-time and online estimation. By leveraging centroidal dynamics and integrating angular momentum, our approach accurately infers external forces without the need for Force/Torque (F/T) sensors. The proposed method is validated in simulation using the NAO humanoid robot model within the qBullet physics engine, under both static standing and realistic dynamic walking conditions. Robustness is evaluated using two external force profiles: constant and time-varying (e.g., sinusoidal). Results show that SENSE provides accurate and stable force estimation, even in challenging scenarios such as foot contact transitions where low-cost sensors like Force-Sensing Resistors (FSRs) typically become unreliable. With its low computational cost and reliance only on onboard sensors, SENSE offers a practical alternative to expensive F/T sensors for medium-sized humanoid platforms. To promote reproducibility and further research, the full implementation is publicly available
Sexual reproduction is controlled by successive transcriptomic waves in Podospora anserina
No full textDespite the inherent challenge of finding suitable mating partners, most eukaryotes use sexual reproduction to produce offspring endowed with increase genetic diversity and fitness. The persistence of this mode of reproduction is a key question in evolutionary biology. Fungi offer valuable insights into this question, due to their diversity and short lifecycle. This study focuses on Podospora anserina , a pseudohomothallic ascomycete fungus that bypasses self-sterility by maintaining two compatible nuclei in one mycelium. We performed genome-wide gene expression profiling during ten stages of P. anserina sexual reproduction and identified five major expression patterns. Our expert annotation approaches identified differentially expressed genes related to secondary metabolite production, fungal vegetative incompatibility, programmed cell death, and epigenetic regulation. In addition, master transcriptional regulators and their target networks were uncovered. This study provides a comprehensive database for future functional genomics experiments and novel pathway characterization during sexual reproduction
Role of RNase III enzymes and 3D chromatin structure in nitrogen-fixing symbiosis of Medicago truncatula
No full textThe rhizobium-legume symbiosis (RLS) enables legumes to grow in nitrogen-poor soils through the formation of root nodules that harbor nitrogen-fixing rhizobia within a plant vesicle, the symbiosome.Nodulation involves, among others, the expression of genes encoding Nodule-Specific Cysteine-Rich (NCR) peptides as well as epigenetic modifications, including changes in ploidy levels, chromatin accessibility, histone modifications, and DNA methylation patterns. Additionally, the RNA-directed DNA methylation (RdDM) pathway, which depends on 24-nucleotide small interfering RNAs (24-nt siRNAs), plays a key role in nodule development.During my PhD, I focused on characterizing the 24-nt siRNA population involved in nodule development and their targets. Specifically, I studied DICER-LIKE 3 (DCL3), an enzyme involved in the biogenesis of 24-nt siRNAs. In order to obtain a KO stable mutant of DCL3, I developed a system to evaluate the efficiency of CRISPR/Cas9 guides in Medicago. Along the same lines, I also characterized RTL1b, an RNase III enzyme involved in nodule development, symbiosome maintenance, and the regulation of late nodulation genes and NCRs. Unlike its homolog in Arabidopsis thaliana, RTL1b does not appear to function as a silencing suppressor in Medicago, but rather as a regulator independent of siRNA pathways.Finally, by integrating Hi-C, ChIP-Seq, RNA-Seq, and ATAC-Seq data, we demonstrated that nodule differentiation is accompanied by chromatin rearrangements correlated with transcriptional regulation at both the A/B compartment level and chromatin loop formation. Some of these rearrangements depend on bacterial differentiation within the symbiotic cells. Notably, we identified an enhancer-promoter loop between a distal regulatory region of NIN and its proximal promoter, whose formation correlates with NIN expression levels in nodules. Our findings strongly suggest that this loop is positively regulated by cytokinins through the type-B response regulator 3 (RRB3) transcription factor, thereby promoting NIN induction in the root.Together, these findings highlight how epigenetic regulation, through RNase III enzymes and chromatin dynamics, shapes gene expression during rhizobium-legume symbiosis.La symbiose rhizobium-légumineuse (RLS) permet aux légumineuses de croître dans des sols pauvres en azote grâce à la formation de nodules racinaires abritant des rhizobia fixateurs d'azote. La nodulation implique, entre autres, l'expression des gènes qui codent pour des peptides NCR (« Nodule-Specific Cysteine-Rich Peptides ») ainsi que des modifications épigénétiques, incluant des variations de ploïdie, l'ouverture de la chromatine et des modifications des histones et des profils de méthylation de l'ADN. De plus, la voie de méthylation de l'ADN dépendante des petits ARN interférents de 24 nucléotides (siRNA 24-nt) joue un rôle clé dans le développement nodulaire.Au cours de mon doctorat, je me suis intéressé par caractériser la population des siRNA de 24-nt qui jouent un rôle dans le développement du nodule ainsi que ses cibles. Pour cela je me suis intéressé par DICER-LIKE 3, impliqué dans la biogenèse des siRNA 24-nt.Pour essayer d'obtenir un mutant KO de DCL3, j'ai développé un système pour évaluer l'efficacité des guides CRISPR/Cas9 chez Medicago. En poursuivant cette même ligne de recherche, j'ai également caractérisé RTL1b, une RNase III impliquée dans la régulation des gènes tardifs nodulaires et des NCRs. Contrairement à son homologue chez Arabidopsis, RTL1b ne semble pas agir comme un suppresseur du « silencing » chez Medicago, mais plutôt comme un régulateur indépendant des siRNA.Enfin, en intégrant des données Hi-C, ChIP-Seq, RNA-Seq et ATAC-Seq, nous avons montré que la différenciation nodulaire s'accompagne de réarrangements chromatinaux corrélés à la régulation transcriptionnelle, tant au niveau des compartiments AB que des boucles d'ADN. Une partie de ces réarrangements dépend de la différenciation bactérienne. Notamment, nous avons identifié une boucle enhancer-promoter entre une région distale de NIN et son promoteur proximal, dont la formation est corrélée avec son niveau d'expression dans le nodule. Tout porte à croire que cette boucle est également positivement régulée par les cytokinines via le facteur de transcription RRB3, favorisant ainsi l'induction de NIN dans la racine.Ensemble, ces travaux mettent en lumière comment la régulation épigénétique, via les enzymes RNase III et la dynamique chromatinienne, façonne l'expression génique au cours de la symbiose rhizobium-légumineuse
Making school: Women teachers in secular primary schools in Martinique from the 1920 to the 1960
No full textInternational audienceMy doctoral thesis, titled “Making school: Women teachers in Secular Primary Schools in Martinique from the 1920s to the 1960s”, examines the role of women educators in shaping the educational institution in Martinique during the 20th century. The verb “to make” schooling underscores the pedagogical and social contributions of these women in building Martinican education. My research begins in the 1920s, a time when women represent 65,8% of teachers in primary schools (349 women and 181 men in post on January 1st, 1925), and when teachers began to form unions, with the Martinican section of the French National Union of Teachers created in 1924. The study ends in the early 1960s, when the professional landscape of teachers in Martinique became more diverse regarding formation and diplomas, due to evolving educational reforms in France (Prost, 2013).This research aims to examine the role of colonized women in the educational system of Martinique, one of the oldest French colonies, located in the Caribbean. Though granted citizenship in 1848, the population of Martinique remained under colonial rule until 1946 when the colony becomes a French overseas department. The thesis explores how these mostly black, colonized, civil servants, women participated in a field perceived as a "women's job” (Tilly & Scott, 2002) where women teachers are perceived as a continuation of mothers in the classroom, in charge of spreading French republican and secular values to future citizens (Gemie, 1995; Clark, 2023). I examine their political and social role in a post-slavery society and look at the way teaching allows them to advance socially (Barthelemy, 2010).The core research question for this presentation is: From the analysis of women teachers’ career files, how to study the political stakes and the gendered and racialized power dynamics existing in primary education in Martinique during colonial period? My primary sources are teacher career files—comprising inspectors’ reports, correspondence with the education administration, and personal data such as salary, marital status, ranking, posting across the Empire and health information. These files are kept in Martinique Territorial Archives. I analyzed 321 of the 530 teachers listed in 1925, including 211 women and 110 men. This data allowed me to build a database with quantitative details and to do a qualitative analysis of the teachers' experiences during their careers.The inspectors’ reports particularly provide insight into the relationship between the administration and teachers. They reflect the expectations placed on educators and how teachers, particularly women, navigated these demands. The inspectors have several missions, mainly to control morality of the personnel, to evaluate the practice of teachers and sometimes to advise them, and finally to manage their career as he can promote or demote them (Condette, 2017). In return, teachers can follow the rules, adapt the pedagogical instructions or transgress them. In this regard, the reports are windows to specific pedagogical, social and administrative encounters which take place in the classrooms. Since inspectors were all white, male, colonial administrators from metropolitan France until the late 1970s, these interactions reveal important moments of colonial power dynamics in the classroom. The reports contain two types of documents: the Individual Report Card, which includes personal and professional details such as the list of positions occupied and of leaved obtained to date; and the Inspection Report, which documents the inspector's observations during his visits. These reports shed light on the administration’s concerns—discipline, pedagogical quality, relationships with colleagues, and general comments on the teacher’s performance. Teachers must read and sign the document and express wishes that can be considered by the administration in managing promotions for civil servants.Despite their value, these sources have limitations. For example, the power dynamics between inspectors and teachers are difficult to fully understand, as racial and social tensions were often veiled in administrative categories, rather than being openly expressed in racial terms such as in French African colonies where teachers are divided between “white” and “indigenous” or “black” (Colonna, 1975; Jézéquel, 2024). Additionally, the records rarely capture teachers’ agency beyond the brief comments they could add to the reports, which undermines their active role in shaping their careers and their teaching practices (Labrune-Badiane & Smith, 2018; Rosnes et al., 2024).In conclusion, by examining these career files of women teachers, I aim to shed light on the experiences of women teachers in Martinique, emphasizing how they navigated colonial power structures and shaped education in the context of a post-slavery society and of a “colony of citizens” (Dubois, 2004; Larcher, 2014). The role of women teachers in Martinique, as both agents of the French Republic “civilized mission” (Conklin, 1997) and as civil servants with their own agency, is a crucial component of the history of education in the French colonies. Their contributions to the educational system, despite being shaped by colonial ideologies, demonstrate how women navigated complex racial, gendered, and political landscapes, in a society moving toward full assimilation to Franc
Polices et révolutionnaires en Europe occidentale. Des années 1780 à la fin du XXe siècle
No full textInternational audience« Art de gouverner les hommes » sous l’Ancien Régime, les polices européennes deviennent à la fin du XVIIIe siècle des institutions sécuritaires, aux domaines d’interventions resserrés relatifs à la préservation de l’ordre public, dotés du monopole de l’exercice de la violence légitime. Les épisodes révolutionnaires soulèvent nombre de questions lorsque s’enflamme le corps social, mais aussi au plan institutionnel et politique, quand sont remis en cause la légitimité des pouvoirs et, partant, celle des forces censées les défendre. Les polices ont alors à faire face à la concurrence des projets politiques dans des situations de double pouvoir et, parfois, à s’adapter et se révolutionner au sein de l’ordre nouveau qui devient à son tour à protéger et policer. Cette recherche collective, située au carrefour de deux chantiers historiographiques profondément renouvelés – l’histoire des révolutions, l’histoire des polices – , explore de manière comparatiste par-delà les frontières la multiplicité des relations entre polices et mouvements révolutionnaires, des révolutions atlantiques dans les années 1780 aux « années de plomb » et à l’effondrement du bloc de l’Est à la fin des années 1980
Spatio-temporal deep networks with feature disentangling for advancing earthquake monitoring
No full textInternational audienceEarthquake monitoring is essential for assessing seismic hazards and involves interconnected tasks such as phase picking and location estimation. Existing single-parameter estimation methods suffer from error accumulation caused by task interdependencies and typically rely on empirical values. Multi-parameter estimation methods often depend on data from multiple stations, posing challenges in modeling and revealing the inter-station relationships. To address these challenges, this study proposes a novel neural network, SINE, designed to simultaneously estimate key parameters in earthquake monitoring, including P-phase arrival time, location, and magnitude. SINE develops a multi-task framework that incorporates Graph Neural Networks (GNNs) and Bidirectional Long Short-Term Memory networks (BI-LSTM) to extract spatio-temporal features, effectively mitigating error accumulation across the tasks. Unlike previous GNN-based models, SINE incorporates a feature disentanglement structure to automatically identify multiple potential relationships between seismic stations. Additionally, the CNN-based parsing unit is employed to regress multiple seismic parameters simultaneously. Evaluation on datasets from Southern California and Italy shows that SINE outperforms existing DL models and traditional seismological methods. Furthermore, SINE effectively reduces inter-task dependencies, enhancing robustness in earthquake monitoring
Distribution des structures de domaines protéiques dans les génomes et les communautés planctoniques marines.
No full textMarine plankton plays a central role in biogeochemical cycles and food webs. It is made up of a wide variety of eukaryotic species as well as prokaryotes and viruses. As it is advected by currents, it is subject to variations in environmental conditions over vast geographical scales. The organisational dynamics of this microbiome are still poorly understood, even though they represent a central issue in the context of climate change.My research aimed at gaining a better understanding of the organisation of marine plankton communities at the level of protein domain structures (folds). Previous results describe certain consequences of abiotic selection pressure on protein structures but not on those of protein domains, which are the basic evolutionary and functional unit of proteins. Their structures, at the interface between phenotype and genotype, represent an interesting scale for studying this organisation.The structural annotation of proteomes was carried out using CATH[1,2] on the proteomes of 4,500 environmental genomes (MAGs)[3,4] including 700 eukaryotes, 1,900 prokaryotes, 31,000 viruses, and reference proteomes from 990 eukaryotes[5]. In total, 14.5 million genes (9 million for the reference proteomes and 5.5 million for the MAGs) were annotated. In the first chapter, I validated the use of MAGs to study the distribution of folds in a wide range of species. In the second part, I used the relative abundances of MAGs in the metagenomes to study the distribution of folds in planktonic communities. This distribution is characterised by a particular power law, the Pareto type II law. The transition between power low in the genomes and Pareto type II law in the communities could be linked to the fact that molecular evolution and ecology combined shape the composition of communities at different organisational levels, by bringing into play both genomic and emergent processes resulting from ecological interactions. Finally, I was able to identify three fold abundance classes using the properties of the Pareto type II law and observe that the distribution of those in certain abundance classes in certain phyla is structured by geography, temperature and iron concentration.Overall, this thesis has shown that folds represent an informative biological scale for better understanding the organisation of marine plankton communities and its determinants.1 : Ian Sillitoe, Nicola Bordin, Natalie Dawson, Vaishali P Waman, Paul Ashford, Harry M Scholes, Camilla S M Pang, Laurel Woodridge, Clemens Rauer, Neeladri Sen, Mahnaz Abbasian, Sean Le Cornu, Su Datt Lam, Karel Berka, Ivana Hutařová Varekova, Radka Svobodova, Jon Lees, Christine A Orengo, CATH: increased structural coverage of functional space, Nucleic Acids Research, Volume 49, Issue D1, 8 January 2021, Pages D266-D273, https://doi.org/10.1093/nar/gkaa10792: CA Orengo, AD Michie, S Jones, DT Jones, MB Swindells, JM Thornton. CATH - a hierarchic classification of protein domain structures, Structure, Volume 5, Issue 8, 1997, Pages 1093-1109, ISSN 0969-2126, https://doi.org/10.1016/S0969-2126(97)00260-8.3: Delmont, Tom O.Sunagawa, Shinichi et al. Functional repertoire convergence of distantly related eukaryotic plankton lineages abundant in the sunlit ocean, Cell Genomics, Volume 2, Issue 5, 100123, https://doi.org/10.1016/j.xgen.2022.100123.4: M. Gaïa et al., “Mirusviruses link herpesviruses to giant viruses,” Nature, vol. 616, no. 7958, pp. 783-789, Apr. 2023, doi: 10.1038/s41586-023-05962-4.5: D. J. Richter et al., “EukProt: A database of genome-scale predicted proteins across the diversity of eukaryotes,” Peer Community J., vol. 2, 2022, doi: 10.24072/pcjournal.173.Le plancton marin a un rôle central dans les cycles biogéochimiques globaux et les réseaux trophiques. Il est composé d'une grande diversité d'espèces Eucaryotes ainsi que des Procaryotes et des Virus. Étant advecté par les courants, il est confronté à des variations de conditions environnementales sur de vastes échelles géographiques. Les dynamiques organisationnelles de ce microbiome sont encore mal comprises, alors qu'elles représentent un enjeu central dans un contexte de changement climatique.Les travaux de recherche que j'ai menés ici visent à mieux comprendre l'organisation des communautés planctoniques marines à l'échelle des structures de domaines protéiques (folds). Des résultats précédents décrivent certaines conséquences de la pression de sélection abiotique sur les structures de protéines mais pas sur celles des domaines protéiques, qui sont pourtant l'unité évolutive et fonctionnelle de base des protéines. Leurs structures, à l'interface entre phénotype et génotype représentent une échelle intéressante pour étudier cette organisation.L'annotation structurale des protéomes a été réalisée avec CATH[1,2] sur les protéomes de 4500 génomes environnementaux (MAGs)[3,4] comprenant 700 Eucaryotes, 1900 Procaryotes, 31000 Virus, et des protéomes de référence de 990 Eucaryotes[5]. Au total, 14.5 millions de gènes (9 millions pour les protéomes de références et 5.5 millions pour les MAGs) ont été annotés. Dans le premier chapitre, j'ai validé l'utilisation des MAGs pour étudier la distribution des folds dans une grande diversité d'espèces. Dans une deuxième partie, j'ai exploité les abondances relatives des MAGs dans les métagénomes pour étudier la distribution des folds dans les communautés planctoniques. Celle-ci est caractérisée par une loi puissance particulière, la loi de Pareto type II. La transition entre ces deux lois pourrait être liée au fait qu'évolution moléculaire et écologie combinées façonnent la composition des communautés à différents niveaux organisationnels, en mettant en jeu des processus à la fois génomiques et émergents résultant d'interactions écologiques. Enfin, j'ai pu identifier trois classes d'abondance de folds grâce aux propriétés de la loi de Pareto type II et observer que la distribution de ceux de certaines classes d'abondance dans certains phyla est structurée par la géographie, la température et la concentration en fer.Dans l'ensemble, cette thèse a montré que les folds représentent une échelle biologique informative pour mieux comprendre l'organisation des communautés planctoniques marines et ses déterminants.1 : Ian Sillitoe, Nicola Bordin, Natalie Dawson, Vaishali P Waman, Paul Ashford, Harry M Scholes, Camilla S M Pang, Laurel Woodridge, Clemens Rauer, Neeladri Sen, Mahnaz Abbasian, Sean Le Cornu, Su Datt Lam, Karel Berka, Ivana Hutařová Varekova, Radka Svobodova, Jon Lees, Christine A Orengo, CATH: increased structural coverage of functional space, Nucleic Acids Research, Volume 49, Issue D1, 8 January 2021, Pages D266-D273, https://doi.org/10.1093/nar/gkaa10792: CA Orengo, AD Michie, S Jones, DT Jones, MB Swindells, JM Thornton. CATH - a hierarchic classification of protein domain structures, Structure, Volume 5, Issue 8, 1997, Pages 1093-1109, ISSN 0969-2126, https://doi.org/10.1016/S0969-2126(97)00260-8.3: Delmont, Tom O.Sunagawa, Shinichi et al. Functional repertoire convergence of distantly related eukaryotic plankton lineages abundant in the sunlit ocean, Cell Genomics, Volume 2, Issue 5, 100123, https://doi.org/10.1016/j.xgen.2022.100123.4: M. Gaïa et al., “Mirusviruses link herpesviruses to giant viruses,” Nature, vol. 616, no. 7958, pp. 783-789, Apr. 2023, doi: 10.1038/s41586-023-05962-4.5: D. J. Richter et al., “EukProt: A database of genome-scale predicted proteins across the diversity of eukaryotes,” Peer Community J., vol. 2, 2022, doi: 10.24072/pcjournal.173
Le travail des algorithmes
No full textFor some years now, algorithms have been the subject of studies questioning the ways in which they are changing our lifestyles and modes of production. However, the question of what they do directly at work remains little studied and apprehended under the prism of technical delegation, which nevertheless continues to grow. The aim of this issue is to compensate for this lack, through contributions that examine what algorithms do at work, the consequences of technical delegation for the organization of salaried activities, and the political modalities of algorithms at work. The research in this issue is based on fieldwork and analyses of sectors and environments as diverse as medicine, the music industry, software, the state, journalism and the on-demand economy.Les algorithmes font depuis quelques années l’objet d’études qui interrogent les manières dont ils changent nos modes de vie et de production. Toutefois, la question de ce qu’ils font directement au travail reste peu étudiée et appréhendée sous le prisme de la délégation technique qui ne cesse pourtant de croître. L'objectif de ce numéro est de compenser ce manque, à travers des contributions rendant compte ce que les algorithmes font au travail, des conséquences de la délégation technique dans l’organisation des activités salariées, ou encore des modalités politiques des algorithmes dans le travail. Les recherches composant ce numéro s’appuient sur des terrains et analyses étudiant des secteurs et milieux aussi divers que ceux de la médecine, de l’industrie musicale, du logiciel, de l’État, du journalisme ou de l’économie à la demande
LAMN property for recurrent Random Walk in Random Environment
No full textWe consider a one-dimensional, nearest-neighbour, recurrent random walk in a random environment (RWRE). Assuming that the environment has a finite support, which is treated as a parameter, we establish the Local Asymptotic Mixed Normality (LAMN) property for this parameter. The asymptotic random Fisher information is expressed in terms of the invariant measure in the infinite valley, as introduced in Gantert et al. (2010).We further show that the Maximum Likelihood Estimator (MLE) of the support parameter converges to a mixture of normal distributions and is asymptotically efficient. The proofs rely on a recent result by Comets et al. (2024), which extends to recurrent RWRE the method of the "environment viewed from the particle", originally introduced in Kozlov and Molchanov (1984) for the transient ballistic RWRE