Double-diffusive sedimentation at high Schmidt numbers: Semi-Lagrangian simulations

International audienceWhen particle-laden freshwater is placed above clear saltwater, double-diffusive sedimentation can arise. Navier-Stokes direct numerical simulations by Burns and Meiburg showed that this process can be dominated by either Rayleigh-Taylor or double-diffusive fingering instabilities. Based on two-dimensional simulations, those authors identify a single dimensionless parameter that can be employed to distinguish between these regimes. Here we develop a high-performance semi-Lagrangian computational approach that enables us to extend these high Schmidt number simulations to three dimensions, and to confirm the validity of their proposed scaling law for three-dimensional flows

Surgical and Oncological Outcomes After Preoperative FOLFIRINOX Chemotherapy in Resected Pancreatic Cancer : An International Multicenter Cohort Study

Background. Preoperative FOLFIRINOX chemotherapy is increasingly administered to patients with borderline resectable (BRPC) and locally advanced pancreatic cancer (LAPC) to improve overall survival (OS). Multicenter studies reporting on the impact from the number of preoperative cycles and the use of adjuvant chemotherapy in relation to outcomes in this setting are lacking. This study aimed to assess the outcome of pancreatectomy after preoperative FOLFIRINOX, including predictors of OS.Methods. This international multicenter retrospective cohort study included patients from 31 centers in 19 European countries and the United States undergoing pancreatectomy after preoperative FOLFIRINOX chemotherapy (2012-2016). The primary end point was OS from diagnosis. Survival was assessed using Kaplan-Meier analysis and Cox regression.Results. The study included 423 patients who underwent pancreatectomy after a median of six (IQR 5-8) preoperative cycles of FOLFIRINOX. Postoperative major morbidity occurred for 88 (20.8%) patients and 90-day mortality for 12 (2.8%) patients. An R0 resection was achieved for 243 (57.4%) patients, and 259 (61.2%) patients received adjuvant chemotherapy. The median OS was 38 months (95% confidence interval [CI] 34-42 months) for BRPC and 33 months (95% CI 27-45 months) for LAPC. Overall survival was significantly associated with R0 resection (hazard ratio [HR] 1.63; 95% CI 1.20-2.20) and tumor differentiation (HR 1.43; 95% CI 1.08-1.91). Neither the number of preoperative chemotherapy cycles nor the use adjuvant chemotherapy was associated with OS.Conclusions. This international multicenter study found that pancreatectomy after FOLFIRINOX chemotherapy is associated with favorable outcomes for patients with BRPC and those with LAPC. Future studies should confirm that the number of neoadjuvant cycles and the use adjuvant chemotherapy have no relation to OS after resection.Peer reviewe

Modélisation numérique et calcul haute performance de transport de sédiments

The dynamic of sediment flows is a subject that covers many applications in geophysics, ranging from estuary silting issues to the comprehension of sedimentary basins. This PhD thesis deals with high resolution numerical modeling of sediment flows and implementation of the corresponding algorithms on hybrid calculators. Sedimentary flows involve multiple interacting phases, giving rise to several types of instabilities such as Rayleigh-Taylor instabilities and double diffusivity. The difficulties for the numerical simulation of these flows arise from the complex fluid/sediment interactions involving different physical scales. Indeed, these interactions are difficult to treat because of the great variability of the diffusion parameters in the two phases. When the ratio of the diffusivities, given by the Schmidt number, is too high, conventional methods show some limitations. This thesis extends the recent results obtained on the direct resolution of the transport of a passive scalar at high Schmidt number on hybrid CPU-GPU architectures and validates this approach on instabilities that occur in sediment flows. This work first reviews the numerical methods which are adapted to high Schmidt flows in order to apply effective accelerator implementation strategies and proposes an open source reference implementation named HySoP. The proposed implementation makes it possible, among other things, to simulate flows governed by the incompressible Navier-Stokes equations entirely on accelerator or coprocessor thanks to the OpenCL standard and tends towards optimal performances independently of the hardware. The numerical method and its implementation are first validated on several classical test cases and then applied to the dynamics of sediment flows which involve a two-way coupling between the transported scalars and the Navier-Stokes equations. We show that the joint use of adapted numerical methods and their implementation on accelerator makes it possible to describe accurately, at a very reasonable cost, sediment transport for Schmidt numbers difficult to reach with other methods.La dynamique des écoulements sédimentaires est un sujet qui concerne de nombreuses applications en géophysiques, qui vont des questions d'ensablement des estuaires à la compréhension des bassins sédimentaires. Le sujet de cette thèse porte sur la modélisation numérique à haute résolution de ces écoulements et l'implémentation des algorithmes associés sur accélérateurs. Les écoulements sédimentaires font intervenir plusieurs phases qui interagissent, donnant lieu à plusieurs types d'instabilités comme les instabilités de Rayleigh-Taylor et de double diffusivité. Les difficultés pour la simulation numérique de ces écoulements tiennent à la complexité des interactions fluides/sédiments qui font intervenir des échelles physiques différentes. En effet, ces interactions sont difficiles à traiter du fait de la grande variabilité des paramètres de diffusion dans les deux phases et les méthodes classiques présentent certaines limites pour traiter les cas où le rapport des diffusivités, donné par le nombre de Schmidt, est trop élevé. Cette thèse étend les récents résultats obtenus sur la résolution directe de la dynamique du transport d'un scalaire passif à haut Schmidt sur architecture hybride CPU-GPU et valide cette approche sur les instabilités qui interviennent dans des écoulements sédimentaires. Ce travail revisite tout d'abord les méthodes numériques adaptées aux écoulements à haut Schmidt afin de pouvoir appliquer des stratégies d'implémentations efficaces sur accélérateurs et propose une implémentation de référence open source nommée HySoP. L'implémentation proposée permet, entre autres, de simuler des écoulements régis par les équations de Navier-Stokes incompressibles entièrement sur accélérateur ou coprocesseur grâce au standard OpenCL et tend vers des performances optimales indépendamment du matériel utilisé. La méthode numérique et son implémentation sont tout d'abord validées sur plusieurs cas tests classiques avant d'être appliquées à la dynamique des écoulements sédimentaires qui font intervenir un couplage bidirectionnel entre les scalaires transportés et les équations de Navier-Stokes. Nous montrons que l'utilisation conjointe de méthodes numériques adaptées et de leur implémentation sur accélérateur permet de décrire précisément, à coût très raisonnable, le transport sédimentaire pour des nombres de Schmidt difficilement accessibles par d'autres méthodes

In-cell quantitative structural imaging of phytoplankton using 3D electron microscopy

Phytoplankton is a minor fraction of the global biomass playing a major role in primary production and climate. Despite improved understanding of phytoplankton diversity and genomics, we lack nanoscale subcellular imaging approaches to understand their physiology and cell biology. Here, we present a complete Focused Ion Beam - Scanning Electron Microscopy (FIB-SEM) workflow (from sample preparation to image processing) to generate nanometric 3D phytoplankton models. Tomograms of entire cells, representatives of six ecologically-successful phytoplankton unicellular eukaryotes, were used for quantitative morphometric analysis. Besides lineage-specific cellular architectures, we observed common features related to cellular energy management: i) conserved cell-volume fractions occupied by the different organelles; ii) consistent plastid-mitochondria interactions, iii) constant volumetric ratios in these energy-producing organelles. We revealed detailed subcellular features related to chromatin organization and to biomineralization. Overall, this approach opens new perspectives to study phytoplankton acclimation responses to abiotic and biotic factors at a relevant biological scale

Morphological bases of phytoplankton energy management and physiological responses unveiled by 3D subcellular imaging

International audienceEukaryotic phytoplankton have a small global biomass but play major roles in primary production and climate. Despite improved understanding of phytoplankton diversity and evolution, we largely ignore the cellular bases of their environmental plasticity. By comparative 3D morphometric analysis across seven distant phytoplankton taxa, we observe constant volume occupancy by the main organelles and preserved volumetric ratios between plastids and mitochondria. We hypothesise that phytoplankton subcellular topology is modulated by energy-management constraints. Consistent with this, shifting the diatom Phaeodactylum from low to high light enhances photosynthesis and respiration, increases cell-volume occupancy by mitochondria and the plastid CO2-fixing pyrenoid, and boosts plastid-mitochondria contacts. Changes in organelle architectures and interactions also accompany Nannochloropsis acclimation to different trophic lifestyles, along with respiratory and photosynthetic responses. By revealing evolutionarily-conserved topologies of energy-managing organelles, and their role in phytoplankton acclimation, this work deciphers phytoplankton responses at subcellular scales

Livres sorciers

Ce volume examine les usages magiques du livre et de l’écriture développés par plusieurs sociétés dans le monde, en Europe, en Amérique du Sud, en MésoAmérique, en Afrique. Posant un regard critique sur le « grand partage » opposant la raison graphique à la pensée sauvage, anthropologues et historiens mènent leur enquête en s’interrogeant sur la sémiotique hybride de ces textes et l’étrange pouvoir prêté au langage de transformer la matière, d’ouvrir les portes du Paradis ou de sceller un pacte avec les morts. Par-delà les variations dans l’espace et dans le temps, c’est à un parcours à travers l’univers secret des signes magiques qu’il invite le lecteur