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Théories et pratiques du gouvernement impérial, Empire byzantin, monde islamique, Occident latin (717-1025)
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Dynamics of the Bose-Hubbard Model Induced by On-Site or Long-Range Two-Body Losses
No full textWe present a theoretical study of the dissipative dynamics of the Bose-Hubbard model induced by on-site or long-range two-body losses. We first consider the one-dimensional chain and the two-dimensional square lattice, and study the dynamics induced by the sudden switch-on of two-body losses on a weakly-interacting superfluid state. The time-dependent density is obtained in the spirit of the Bogolyubov approach by calculating theoretically the equations of motion associated to the relevant quadratic bosonic correlators. In the one-dimensional case, our results compare very well with quasi-exact numerical calculations based on the quantum jump method implemented using tensor networks. We find that the intermediate-time dynamics of the density displays an algebraic decay characterized by an interaction-dependent power-law exponent. The latter property still holds for long-range two-body loss processes but it is absent in the two-dimensional square lattice with on-site losses.</div
The genetic architecture of HIV-1 virulence
No full textInternational audienceThe virulence of Human Immunodeficiency Virus-1 (HIV-1) is partly determined by viral genetic variation. Finding individual genetic variants affecting virulence is important for our understanding of HIV pathogenesis and evolution of virulence; however, very few have been identified. To this end, within the “Bridging the Evolution and Epidemiology of HIV in Europe” (BEEHIVE) collaboration, we produced whole-genome HIV sequence data for 2294 seroconverters from European countries for a genome-wide association study (GWAS). We considered two phenotypes: (i) set-point viral load (SPVL), the approximately stable viral load from 6 to 24 months after infection, and (ii) the rate of CD4 cell count decline. We developed a GWAS method that corrects for population structure with random effects, accounts for two or more alleles at each locus, and tests for the effect of multiple genetic variants including single-nucleotide polymorphisms (SNPs), k-mers, insertions and deletions, within-host variant frequency, the number of rare point mutations, and drug resistance. We confirmed with this new approach that viral genomes explained 26% [95% CI 17%–35%] of the variance in SPVL, while they explained only 0.9% [0.0%–2.1%] of the variance in the rate of CD4 cell count decline. After correction for multiple testing, among all tested variants, only two significantly explained SPVL: an epitope mutation allowing escape from the host HLA-B*57 allele and lowering SPVL by −0.26 copies/ml and an epitope mutation allowing escape from the host HLA-B*35 allele and increasing SPVL by +0.22 copies/ml. We attempted to replicate these two large effects in two additional independent datasets together encompassing 2445 seroconverters, with mixed results. Overall, the inferred effects of all SNPs and amino-acid variants weakly correlated (R2 ranging from 0.08 to 0.87%, P-values from 0.001 to 0.32) between our main dataset and these two additional datasets. Lastly, a lasso regression of phenotypes on genetic variants confirmed the heritability of SPVL and explained up to 6% of variance in SPVL in cross-validation datasets. These findings suggest that HIV SPVL is determined by viral genomes through HLA escape variants with potentially large, host-dependent effects that may not always be detected at the population level and many other variants with effects too weak to reach genome-wide significance in our GWAS
Inverse 3D Microscopy Rendering for Cell Shape Inference with Active Mesh
No full textInternational audienceTraditional methods for biological shape inference, such as deep learning (DL) and active contour models, face important limitations in 3D. DL approaches require large annotated datasets, which are often impractical to obtain, while active contour methods depend on carefully tuned heuristics for intensity attraction and shape regularization. We introduce deltaMic, a novel differentiable 3D renderer for fluorescence microscopy that formulates shape inference as an inverse problem. By leveraging differentiable convolutions, deltaMic simulates the image formation process, integrating a parameterized point spread function (PSF) with a triangle mesh-based representation of biological structures. Unlike DL-or contour-based segmentation, deltaMic directly optimizes both shape and optical parameters to align synthetic and real microscopy images, removing the need for large datasets or sample-specific fine-tuning. To ensure scalability, we implement a GPU-accelerated Fourier transform for triangle meshes along with narrow-band spectral filtering. We show that deltaMic accurately reconstructs cell geometries from both synthetic and diverse experimental 3D microscopy data, while remaining robust to noise and initialization. This establishes a new physics-informed framework for biophysical image analysis and inverse modeling
‘C’est de mon mal que doit être tiré mon remède’ : De la thériaque à la maladie d’amour dans la littérature gréco-arabe
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A novel RNP compartment boosts translation in growing mouse oocytes to avoid cytoplasm dilution
No full textPosted March 04, 2025 on bioRxiv.International audienceMammalian oocytes undergo a long growth phase in the ovary, during which transcriptional levels gradually decrease. Growing oocytes must therefore accumulate maternal stores and regulate their translation to achieve successful divisions and early embryo development. Using immunofluorescence, mass spectrometry and electron microscopy, we identified a novel and transient compartment, the Zollo Body, in late growing mouse oocytes, constituted of RNPs and organelles. Morphologically, this structure resembles the Balbiani body found in most vertebrate species but it stains positively for nascent translation and active phospho-mTOR. RNAseq analysis and dry mass measurements of growing oocytes with or without this compartment further support its key role in boosting translation, allowing growing oocytes to avoid cytoplasmic dilution despite their rapid size increase, ultimately ensuring their developmental potential
Comment habiter notre planète. Une lecture d'Avatar
No full textInternational audiencePar-delà l’admiration suscitée par les prouesses technologiques, le succès mondial de la saga Avatar, réalisée par James Cameron, s’explique par sa capacité à faire écho aux grandes interrogations du monde contemporain concernant la protection de l’environnement, la multiplication des guerres, le pouvoir des biotechnologies et le respect de la diversité culturelle. Même si les événements relatés se déroulent sur une lointaine planète, Pandora, ces films conduisent les spectateurs à s’interroger sur la manière de vivre sur Terre au début du troisième millénaire. En regardant ces images, nous sommes amenés à réfléchir à notre place dans l’univers et à notre rapport au vivant. Pour appréhender cette expérience, ce livre mobilise le regard de l’anthropologie de la vie, afin de montrer ce que la comparaison avec les peuples rencontrés dans Avatar révèle de notre humanité et de notre manière d’habiter notre planète
