A unified treatment of boundary conditions in least-square based finite-volume methods

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High-Order IMEX-RK Finite Volume Methods for Multidimensional Hyperbolic Systems.

In this paper we present a high-order accurate cell-centered finite volume method for the semi-implicit discretization of multidimensional hyperbolic systems in conservative form on unstructured grids. This method is based on a special splitting of the physical flux function into a convective and a non-convective part. The convective contribution to the global flux is treated implicitly by mimicking the upwinding of a scalar linear flux function while the rest of the flux is discretized in an explicit way. The spatial accuracy is ensured by allowing non-oscillatory polynomial reconstruction procedures, while the time accuracy is attained by adopting a Runge-Kutta stepping scheme. The method can be naturally considered in the framework of the textbf{IM}plicit-textbf{EX}plicit (IMEX) schemes and the properties of the resulting operators are analysed using the properties of M-matrices

Knuthian Drawings of Series-Parallel Flowcharts

Inspired by a classic paper by Knuth, we revisit the problem of drawing flowcharts of loop-free algorithms, that is, degree-three series-parallel digraphs. Our drawing algorithms show that it is possible to produce Knuthian drawings of degree-three series-parallel digraphs with good aspect ratios and small numbers of edge bends.Comment: Full versio

Continuous global optimization for protein structure analysis

Optimization methods are a powerful tool in protein structure analysis. In this paper we show that they can be profitably used to solve relevant problems in drug design such as the comparison and recognition of protein binding sites and the protein-peptide docking. Binding sites recognition is generally based on geometry often combined with physico-chemical properties of the site whereas the search for correct protein-peptide docking is often based on the minimization of an interaction energy model. We show that continuous global optimization methods can be used to solve the above problems and show some computational results

Pseudotemporal ordering of spatial lymphoid tissue microenvironment profiles trails Unclassified DLBCL at the periphery of the follicle

: We have established a pseudotemporal ordering for the transcriptional signatures of distinct microregions within reactive lymphoid tissues, namely germinal center dark zones (DZ), germinal center light zones (LZ), and peri-follicular areas (Peri). By utilizing this pseudotime trajectory derived from the functional microenvironments of DZ, LZ, and Peri, we have ordered the transcriptomes of Diffuse Large B-cell Lymphoma cases. The apex of the resulting pseudotemporal trajectory, which is characterized by enrichment of molecular programs fronted by TNFR signaling and inhibitory immune checkpoint overexpression, intercepts a discrete peri-follicular biology. This observation is associated with DLBCL cases that are enriched in the Unclassified/type-3 COO category, raising questions about the potential extra-GC microenvironment imprint of this peculiar group of cases. This report offers a thought-provoking perspective on the relationship between transcriptional profiling of functional lymphoid tissue microenvironments and the evolving concept of the cell of origin in Diffuse Large B-cell Lymphomas

Upward Planar Morphs

We prove that, given two topologically-equivalent upward planar straight-line drawings of an $n$-vertex directed graph $G$, there always exists a morph between them such that all the intermediate drawings of the morph are upward planar and straight-line. Such a morph consists of $O(1)$ morphing steps if $G$ is a reduced planar $st$-graph, $O(n)$ morphing steps if $G$ is a planar $st$-graph, $O(n)$ morphing steps if $G$ is a reduced upward planar graph, and $O(n^2)$ morphing steps if $G$ is a general upward planar graph. Further, we show that $\Omega(n)$ morphing steps might be necessary for an upward planar morph between two topologically-equivalent upward planar straight-line drawings of an $n$-vertex path.Comment: Appears in the Proceedings of the 26th International Symposium on Graph Drawing and Network Visualization (GD 2018) The current version is the extended on

Comparison of mandibular arch expansion by the schwartz appliance using two activation protocols: A preliminary retrospective clinical study

Background and objectives: Dental crowding is more pronounced in the mandible than in the maxilla. When exceeding a significant amount, the creation of new space is required. The mandibular expansion devices prove to be useful even if the increase in the lower arch perimeter seems to be just ascribed to the vestibular inclination of teeth. The aim of the study was to compare two activation protocols of the Schwartz appliance in terms of effectiveness, particularly with regard to how quickly crowding is solved and how smaller is the increasing of vestibular inclination of the mandibular molars. Materials and methods: We compared two groups of patients treated with different activation's protocols of the lower Schwartz appliance (Group 1 protocol consisted in turning the expansion screw half a turn twice every two weeks and replacing the device every four months; Group 2 was treated by using the classic activation protocol-1/4 turn every week, never replacing the device). The measurements of parameters such as intercanine distance (IC), interpremolar distance (IPM), intermolar distance (IM), arch perimeter(AP), curve of Wilson (COW), and crowding (CR) were made on dental casts at the beginning and at the end of the treatment. Results: A significant difference between protocol groups was observed in the variation of COWL between time 0 and time 1 with protocol 1 with protocol 1 subjects showing a smaller increase in the parameter than protocol 2 subjects. The same trend was observed also for COWR, but the difference between protocol groups was slightly smaller and the interaction protocol-by-time did not reach the statistical significance. Finally, treatment duration in protocol 1 was significantly lower than in protocol 2. Conclusion: The results of our study suggest that the new activation protocol would seem more effective as it allows to achieve the objective of the therapy more quickly, and likely leading to greater bodily expansion

Finite volume scheme based on cell-vertex reconstructions for anisotropic diffusion problems with discontinuous coefficients

We propose a new second-order finite volume scheme for non-homogeneous and anisotropic diffusion problems based on cell to vertex reconstructions involving minimization of functionals to provide the coefficients of the cell to vertex mapping. The method handles complex situations such as large preconditioning number diffusion matrices and very distorted meshes. Numerical examples are provided to show the effectiveness of the method

Extending Upward Planar Graph Drawings

In this paper we study the computational complexity of the Upward Planarity Extension problem, which takes in input an upward planar drawing $\Gamma_H$ of a subgraph $H$ of a directed graph $G$ and asks whether $\Gamma_H$ can be extended to an upward planar drawing of $G$. Our study fits into the line of research on the extensibility of partial representations, which has recently become a mainstream in Graph Drawing. We show the following results. First, we prove that the Upward Planarity Extension problem is NP-complete, even if $G$ has a prescribed upward embedding, the vertex set of $H$ coincides with the one of $G$, and $H$ contains no edge. Second, we show that the Upward Planarity Extension problem can be solved in $O(n \log n)$ time if $G$ is an $n$-vertex upward planar $st$-graph. This result improves upon a known $O(n^2)$-time algorithm, which however applies to all $n$-vertex single-source upward planar graphs. Finally, we show how to solve in polynomial time a surprisingly difficult version of the Upward Planarity Extension problem, in which $G$ is a directed path or cycle with a prescribed upward embedding, $H$ contains no edges, and no two vertices share the same $y$-coordinate in $\Gamma_H$