High order direct Arbitrary-Lagrangian-Eulerian schemes on moving Voronoi meshes with topology changes

We present a new family of very high order accurate direct Arbitrary-Lagrangian-Eulerian (ALE) Finite Volume (FV) and Discontinuous Galerkin (DG) schemes for the solution of nonlinear hyperbolic PDE systems on moving 2D Voronoi meshes that are regenerated at each time step and which explicitly allow topology changes in time. The Voronoi tessellations are obtained from a set of generator points that move with the local fluid velocity. We employ an AREPO-type approach, which rapidly rebuilds a new high quality mesh rearranging the element shapes and neighbors in order to guarantee a robust mesh evolution even for vortex flows and very long simulation times. The old and new Voronoi elements associated to the same generator are connected to construct closed space--time control volumes, whose bottom and top faces may be polygons with a different number of sides. We also incorporate degenerate space--time sliver elements, needed to fill the space--time holes that arise because of topology changes. The final ALE FV-DG scheme is obtained by a redesign of the fully discrete direct ALE schemes of Boscheri and Dumbser, extended here to moving Voronoi meshes and space--time sliver elements. Our new numerical scheme is based on the integration over arbitrary shaped closed space--time control volumes combined with a fully-discrete space--time conservation formulation of the governing PDE system. In this way the discrete solution is conservative and satisfies the GCL by construction. Numerical convergence studies as well as a large set of benchmarks for hydrodynamics and magnetohydrodynamics (MHD) demonstrate the accuracy and robustness of the proposed method. Our numerical results clearly show that the new combination of very high order schemes with regenerated meshes with topology changes lead to substantial improvements compared to direct ALE methods on conforming meshes

Paclitaxel-Loaded Nanosponges Inhibit Growth and Angiogenesis in Melanoma Cell Models

This study investigated the effects of free paclitaxel (PTX) and PTX-loaded in pyromellitic nanosponges (PTX-PNS) in reducing in vitro and in vivo melanoma cell growth and invasivity, and in inhibiting angiogenesis. To test the response of cells to the two PTX formulations, the cell viability was evaluated by MTT assay in seven continuous cell lines, in primary melanoma cells, both in 2D and 3D cultures, and in human umbilical vein endothelial cells (HUVECs) after exposure to different concentrations of PTX or PTX-PNS. Cell motility was assessed by a scratch assay or Boyden chamber assay, evaluating cell migration in presence or absence of diverse concentrations of PTX or PTX-PNS. The effect of PTX and PTX-PNS on angiogenesis was evaluated as endothelial tube formation assay, a test able to estimate the formation of three-dimensional vessels in vitro. To assess the anticancer effect of PTX and PTX-PNS in in vivo experiments, the two drug formulations were tested in a melanoma mouse model obtained by B16-BL6 cell implantation in C57/BL6 mice. Results obtained were as follows: 1) MTT analysis revealed that cell proliferation was more affected by PTX-PNS than by PTX in all tested cell lines, in both 2D and 3D cultures; 2) the analysis of the cell migration showed that PTX-PNS acted at very lower concentrations than PTX; 3) tube formation assay showed that PTX-PNS were more effective in inhibiting tube formation than free PTX; and 4) in vivo experiments demonstrated that tumor weights, volumes, and growth were significantly reduced by PTX-PNS treatment with respect to PTX; the angiogenesis and the cell proliferation, detected in the tumor samples with CD31 and Ki-67 antibodies, respectively, indicated that, in the PTX-PNS-treated tumors, the tube formation was inhibited, and a low amount of proliferating cells was present. Taken together, our data demonstrated that our new PTX nanoformulation can respond to some important issues related to PTX treatment, lowering the anti-tumor effective doses and increasing the effectiveness in inhibiting melanoma growth in vivo

Loss of the Chr16p11.2 ASD candidate gene QPRT leads to aberrant neuronal differentiation in the SH-SY5Y neuronal cell model

Background: Altered neuronal development is discussed as the underlying pathogenic mechanism of autism spectrum disorders (ASD). Copy number variations of 16p11.2 have recurrently been identified in individuals with ASD. Of the 29 genes within this region, quinolinate phosphoribosyltransferase (QPRT) showed the strongest regulation during neuronal differentiation of SH-SY5Y neuroblastoma cells. We hypothesized a causal relation between this tryptophan metabolism-related enzyme and neuronal differentiation. We thus analyzed the effect of QPRT on the differentiation of SH-SY5Y and specifically focused on neuronal morphology, metabolites of the tryptophan pathway, and the neurodevelopmental transcriptome. Methods: The gene dosage-dependent change of QPRT expression following Chr16p11.2 deletion was investigated in a lymphoblastoid cell line (LCL) of a deletion carrier and compared to his non-carrier parents. Expression of QPRT was tested for correlation with neuromorphology in SH-SY5Y cells. QPRT function was inhibited in SH-SY5Y neuroblastoma cells using (i) siRNA knockdown (KD), (ii) chemical mimicking of loss of QPRT, and (iii) complete CRISPR/Cas9-mediated knock out (KO). QPRT-KD cells underwent morphological analysis. Chemically inhibited and QPRT-KO cells were characterized using viability assays. Additionally, QPRT-KO cells underwent metabolite and whole transcriptome analyses. Genes differentially expressed upon KO of QPRT were tested for enrichment in biological processes and co-regulated gene-networks of the human brain. Results: QPRT expression was reduced in the LCL of the deletion carrier and significantly correlated with the neuritic complexity of SH-SY5Y. The reduction of QPRT altered neuronal morphology of differentiated SH-SY5Y cells. Chemical inhibition as well as complete KO of the gene were lethal upon induction of neuronal differentiation, but not proliferation. The QPRT-associated tryptophan pathway was not affected by KO. At the transcriptome level, genes linked to neurodevelopmental processes and synaptic structures were affected. Differentially regulated genes were enriched for ASD candidates, and co-regulated gene networks were implicated in the development of the dorsolateral prefrontal cortex, the hippocampus, and the amygdala. Conclusions: In this study, QPRT was causally related to in vitro neuronal differentiation of SH-SY5Y cells and affected the regulation of genes and gene networks previously implicated in ASD. Thus, our data suggest that QPRT may play an important role in the pathogenesis of ASD in Chr16p11.2 deletion carriers

High-order Arbitrary-Lagrangian-Eulerian schemes on crazy moving Voronoi meshes

International audienceHyperbolic partial differential equations (PDEs) cover a wide range of interesting phenomena, from human and hearth-sciences up to astrophysics: this unavoidably requires the treatment of many space and time scales in order to describe at the same time observer-size macrostructures, multi-scale turbulent features, and also zero-scale shocks. Moreover, numerical methods for solving hyperbolic PDEs must reliably handle different families of waves: smooth rarefactions, and discontinuities of shock and contact type. In order to achieve these goals, an effective approach consists in the combination of space-time-based high-order schemes, very accurate on smooth features even on coarse grids, with Lagrangian methods, which, by moving the mesh with the fluid flow, yield highly resolved and minimally dissipative results on both shocks and contacts. However, ensuring the high quality of moving meshes is a huge challenge that needs the development of innovative and unconventional techniques. The scheme proposed here falls into the family of Arbitrary-Lagrangian-Eulerian (ALE) methods, with the unique additional freedom of evolving the shape of the mesh elements through connectivity changes. We aim here at showing, by simple and very salient examples, the capabilities of high-order ALE schemes, and of our novel technique, based on the high-order space-time treatment of topology changes