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Cell Trajectory Inference based on Schrödinger Problem and a Mechanistic Model of Stochastic Gene Expression
No full textCellular differentiation is the biological process that leads a cell to opt for a particular cellular identity. Recently, single-cell RNA-sequencing has enabled the simultaneous measurement of gene expression levels at specific times for a large number of individual cells and a large number of genes. Repeating such measurements at different time points gives then access to the temporal variation, or transport, of a distribution on a gene expression space. The whole temporal trajectory of distributions thus characterizes the differentiation process at population level, but trajectories of individual cells are still out of reach since most measurement techniques are destructive.The optimal transport theory that has been used so far to infer cellular differentiation trajectories from time-stamped single-cell RNA-seq data involves solving the so-called Schrödinger problem in its most common version. This implies assuming that cells move, in the gene expression space, by diffusion. Yet, real gene dynamics are much more complex.In the present work, we assume that mRNA dynamics are characterized by brief and important production of RNA, with long periods of inactivity in between, and consider the so-called Bursty model of gene dynamics. We use this model to define a reference process for the Schrödinger problem. By comparing the solutions of the Schrödinger problems with a Diffusive and a Bursty reference process, under different conditions, we show that the Bursty model provides a better approximation of the underlying gene dynamics than the standard Diffusive process when inferring cell trajectories
Overcoming the Generalization Limits of SLM Finetuning for Shape-Based Extraction of Datatype and Object Properties
No full textAccepted at KCAP2025 - Preprint version not updated with reviewsInternational audienceSmall language models (SLMs) have shown promises for relation extraction (RE) when extracting RDF triples guided by SHACL shapes focused on common datatype properties. This paper investigates how SLMs handle both datatype and object properties for a complete RDF graph extraction. We show that the key bottleneck is related to long-tail distribution of rare properties. To solve this issue, we evaluate several strategies: stratified sampling, weighted loss, dataset scaling, and template-based synthetic data augmentation. We show that the best strategy to perform equally well over unbalanced target properties is to build a training set where the number of occurrences of each property exceeds a given threshold. To enable reproducibility, we publicly released our datasets, experimental results and code. Our findings offer practical guidance for training shape-aware SLMs and highlight promising directions for future work in semantic RE
Euclid Quick Data Release (Q1). The average far-infrared properties of Euclid-selected star-forming galaxies
No full textInternational audienceThe first Euclid Quick Data Release contains millions of galaxies with excellent optical and near-infrared (IR) coverage. To complement this dataset, we investigate the average far-IR properties of Euclid-selected main sequence (MS) galaxies using existing Herschel and SCUBA-2 data. We use 17.6deg (2.4deg) of overlapping Herschel (SCUBA-2) data, containing 2.6 million (240000) MS galaxies. We bin the Euclid catalogue by stellar mass and photometric redshift and perform a stacking analysis following SimStack, which takes into account galaxy clustering and bin-to-bin correlations. We detect stacked far-IR flux densities across a significant fraction of the bins. We fit modified blackbody spectral energy distributions in each bin and derive mean dust temperatures, dust masses, and star-formation rates (SFRs). We find similar mean SFRs compared to the Euclid catalogue, and we show that the average dust-to-stellar mass ratios decreased from z1 to the present day. Average dust temperatures are largely independent of stellar mass and are well-described by the function , where is the age of the Universe, K, K, and Gyr. We argue that since the dust temperatures are converging to a non-zero value below , the dust is now primarily heated by the existing cooler and older stellar population, as opposed to hot young stars in star-forming regions at higher redshift. We show that since the dust temperatures are independent of stellar mass, the correlation between dust temperature and SFR depends on stellar mass. Lastly, we estimate the contribution of the Euclid catalogue to the cosmic IR background (CIB), finding that it accounts for >60% of the CIB at 250, 350, and 500m. Forthcoming Euclid data will extend these results to higher redshifts, lower stellar masses, and recover more of the CIB
La place du psychologue en institution : l’habitat d’une singularité plurielle
No full textInternational audienceThe aim of this article is to offer an analytical insight into the question of the place of the psychologist in institution. A semi-marginal place that leads him to build a dwelling that is as plural as it is singular. For this purpose, we think that a request is hidden in the discourse that the institution has on the function of the psychologist. In this sense, this article will propose to think of the place of psychologist through a clinical situation where the place of psychologist has been interrogated by the other professionals of the institution. What will interest us will be to understand that the substance of the discourse essentially revolves around the notion of the place thanks to the concept of the four discourses proposed by Lacan in 1969. This contribution will allow us to understand that the place can be only plural.Cet article propose un éclairage analytique sur la question de la place du psychologue en institution. Une place en demi-marge qui le pousse à construire un habitat aussi pluriel que singulier. Pour ce faire, nous pensons qu'une demande se cache dans le discours que l'institution porte sur la fonction du psychologue. En ce sens, le présent article proposera de penser la place du psychologue à travers une situation clinique où la place de ce dernier a été questionnée par les autres professionnels de l'institution. Ce qui nous intéressera sera de comprendre que le fond du discours tourne essentiellement autour de la notion de place grâce au concept des quatre discours proposé par Lacan en 1969. Cet apport nous permettra de saisir que la place ne peut être que plurielle.</div
La place du sujet dans un parcours de soins
No full textInternational audienceIn this article, we look at the place of the subject in a care pathway. What place is given to desire in our care institutions? In response to the growing body of research on patients' quality of life, which could be summed up in a research question such as "What is quality of life for patients with chronic illnesses", we propose the following hypothesis: quality of life for patients means being welcomed as speaking beings, in other words showing hospitality and making room for their otherness. This presupposes the possibility of encountering carers and systems that make room for welcoming the real. But making room for the unimaginable means not all of us being in the same place. Managerial discourse promotes these caregivers as interchangeable.We will use a clinical vignette to illustrate this problem.Dans cet article, nous aborderons la place du sujet dans un parcours de soins. En effet, quelle place est faite au désir dans nos institutions de soins ? En réponse à l'augmentation des recherches sur la qualité de vie des patients qui pourrait se résumer par une question de recherche telle que : « Qu'est-ce que la qualité de vie pour les patients atteints de maladie chronique ? » nous proposerons une hypothèse : la qualité de vie pour le patient c'est d'être accueilli en tant qu'être parlant, c'est-à-dire de faire hospitalité et place à l'altérité de celui-ci. Cela sous-tend la possibilité de faire la rencontre de soignants et de dispositifs qui fassent une place à l'accueil du réel. Or faire place à cet insymbolisable ce n'est pas être tous à la même place. Le discours gestionnaire promeut ces soignants qui pourraient être interchangeables. Pour ce faire, nous illustrerons cette problématique par une vignette clinique.</div
Neural network-driven domain decomposition for efficient solutions to the Helmholtz equation
No full textInternational audienceAccurately simulating wave propagation is crucial in fields such as acoustics, electromagnetism, and seismic analysis. Traditional numerical methods, like finite difference and finite element approaches, are widely used to solve governing partial differential equations (PDEs) such as the Helmholtz equation. However, these methods face significant computational challenges when applied to high-frequency wave problems in complex two-dimensional domains. This work investigates Finite Basis Physics-Informed Neural Networks (FBPINNs) and their multilevel extensions as a promising alternative. These methods leverage domain decomposition, partitioning the computational domain into overlapping sub-domains, each governed by a local neural network. We assess their accuracy and computational efficiency in solving the Helmholtz equation for the homogeneous case, demonstrating their potential to mitigate the limitations of traditional approaches
Circulating tumor DNA strongly predicts efficacy of chemotherapy plus immune checkpoint inhibitors in patients with advanced gastro-esophageal adenocarcinoma
No full textInternational audienceBackground Efficacy of 2nd line treatment in advanced gastric or gastro-esophageal junction (GEJ) adenocarcinoma remains limited with no identified strong predictor of treatment efficacy. We evaluated the prognostic value of circulating tumor DNA (ctDNA) in predicting the efficacy of immune checkpoint inhibitors (ICI) plus chemotherapy in the randomized PRODIGE 59-FFCD 1707-DURIGAST trial. Methods ctDNA was evaluated before treatment (baseline) and at 4 weeks (before the third cycle of treatment, C3) using droplet-digital PCR assays based on the detection of CpG methylation.Results Progression-free survival (PFS) and overall survival (OS) were shorter in patients with a high (>1.1 ng/mL) versus low (<1.1 ng/mL) ctDNA concentration at baseline (2.3 vs. 5.8 months; HR = 2.19; 95% CI, 1.09-4.41; p = 0.03 and 4.5 vs. 12.9 months; HR = 2.73; 95% CI, 1.29-5.75; p < 0.01), respectively, after adjustment for identified prognostic variables. Patients with a ctDNA decrease ≤75% between baseline and C3 versus a ctDNA decrease >75% had a worse objective response rate (p = 0.007), shorter PFS (2.2 vs. 7.4 months, HR = 1.90; 95% CI, 1.03-3.51; p = 0.04) and OS (6.6 vs 16.0 months; HR = 2.18; 95% CI, 1.09-4.37; p = 0.03). Conclusions An early decrease in ctDNA concentration is a strong predictor of the therapeutic efficacy of ICI plus chemotherapy in advanced gastric/GEJ adenocarcinoma. Clinical Trial Information NCT03959293 (DURIGAST).The prognosis of advanced gastric and gastro-esophageal junction (GEJ) adenocarcinoma remains poor, with overall survival (OS) ranging from 10% to 15% at 5 years 1 . In Human Epidermal Growth Factor Receptor-2 (HER2) negative unresectable advanced/metastatic tumors, the most frequently used first-line palliative chemotherapy is a doublet of fluoropyrimidine (5fluorouracil (5FU) or capecitabine) plus a platinum salt (cisplatin or oxaliplatin) 2,3 . Recently, the addition of docetaxel (TFOX regimen), immune checkpoint inhibitors (ICI, in PD-L1 positive tumors) and anti-claudin 18.</div
Retrospective metabolomics via dual-dimensional deconvolution using ZT Scan DIA 2.0
No full textAbstract Herein, we present a scanning data-independent acquisition (DIA) approach (ZT Scan DIA 2.0) combined with dual-dimensional tandem mass spectrometry spectral filtering and deconvolution along both the quadrupole and retention time axes to reconstruct compound-specific MS2 spectra from complex mixtures. This approach outperformed conventional data-dependent acquisition (DDA) and window-based DIA methods in terms of annotation rates for hydrophilic metabolomics (114–160%) and lipidomics (105– 136%). Moreover, this approach achieved dot product score distributions comparable with those obtained with a 1-Da precursor isolation window. Furthermore, the platform enables lipid isomer separation through the retrospective analysis of complete DIA datasets covering 1,017 and 2,353 molecules for human plasma and mouse liver tissues, respectively. In addition, the platform yields compound-specific ground truth MS2 spectra that surpass DDA in terms of spectral purity. This establishes a transformative foundation for repository-scale metabolomics in line with the findable, accessible, interoperable, and reusable data principles
Sensibiliser par le jeu les citoyen·ne·s aux risques sur leur territoire et à leur gestion : Retour d'expériences sur les jeux développés par l'INRAE
No full textInternational audienc
Dynamical Evolution of Planetary Systems
No full textThis is a preprint of the following work: Dynamical Evolution of Planetary Systems by A. C. Petit et al. (updating the chapter originally written by A. Morbidelli) in Deeg and Belmonte, Handbook of Exoplanets, 2nd edition, 2025, Springer Nature Switzerland AG, reproduced with permission of Springer Nature Switzerland AGInternational audiencePlanetary systems can evolve dynamically even after the planets themselves have fully formed, and there is circumstantial evidence that most planetary systems become unstable after the disappearance of the gaseous protoplanetary disk. Theories of planet formation predict that chains of mean-motion resonances are the natural outcome of disk-driven planet migration, leading to the pile up of super-Earth resonant chains close to the inner edge of the disk and the formation of fragile chains for distant giant planets. Observations of young systems suggest that they are more often locked in these chains than older ones, which are instead mostly nonresonant. The instabilities thought responsible for this trend can arise intrinsically if the original systems are too closely packed or be due to external perturbations such as tides, planetesimal scattering, or torques from distant stellar companions. The solar system was not exceptional in this sense, as the outer giants saw the disruption of a resonant chain; meanwhile, the inner system was likely built through a series of giant impacts between closely packed planetary embryos. Thus, the orbital distributions of planetary systems that is observed today, both solar and extrasolar, can be different from those emerging from formation and assembly processes within the disk, and it is important to consider possible long-term dynamics to connect the two