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

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

Gitelman syndrome associated with chondrocalcinosis: description of two cases

Gitelman syndrome is a rare inherited tubulopathy, characterized by hypomagnesemia, hypokalemia, metabolic alkalosis, hypocalciuria and hyperreninemic hyperaldosteronism. The clinical spectrum is wide and includes: cramps, myalgies, muscle weakness, until episodes of carpo-podalic spasm, tetania, rabdomyolisis and paralysis. Some cases have been described in literature underlining the association of this condition with chondrocalcinosis, as a typical example of hypomagnesemia-induced crystal deposition disease. The therapy of Gitelman syndrome consists on the administration of defective electrolytes, althought not always effective. We describe two cases of Gitelman syndrome associated with chondrocalcinosis showing the wide range of presentation of this clinical condition

Algorithms for Visualizing Phylogenetic Networks

We study the problem of visualizing phylogenetic networks, which are extensions of the Tree of Life in biology. We use a space filling visualization method, called DAGmaps, in order to obtain clear visualizations using limited space. In this paper, we restrict our attention to galled trees and galled networks and present linear time algorithms for visualizing them as DAGmaps.Comment: Appears in the Proceedings of the 24th International Symposium on Graph Drawing and Network Visualization (GD 2016

Advances on Testing C-Planarity of Embedded Flat Clustered Graphs

We show a polynomial-time algorithm for testing c-planarity of embedded flat clustered graphs with at most two vertices per cluster on each face.Comment: Accepted at GD '1

severe drug hypersensitivity syndrome due to sulphasalazine in patient with rheumatoid arthritis

Drug Hypersensitivity Syndrome, also known as Drug Rash with Eosinophilia and Systemic Symptoms is a severe adverse reaction characterized by clinical manifestations including fever, skin eruption, lymphoadenopathy, associated with eosinophilia, leukocytosis and multiple visceral involvement, with 10% of mortality due to development of multiple organ failure. This reaction usually occurs between two and six-eight weeks after the beginning of the treatment and may not resolve with interruption of the suspected drug. Sulfonamides, anticonvulsant, allopurinol are the most frequently involved molecules, but recently cases have been described also with gabapentin and strontium ranelate. In the present report we describe a case of a patient with rheumatoid arthritis who presented severe drug hypersensitivity syndrome, with liver and kidney involvement due to sulphasalazine

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 $\Gamma_H$

Upward Three-Dimensional Grid Drawings of Graphs

A \emph{three-dimensional grid drawing} of a graph is a placement of the vertices at distinct points with integer coordinates, such that the straight line segments representing the edges do not cross. Our aim is to produce three-dimensional grid drawings with small bounding box volume. We prove that every $n$-vertex graph with bounded degeneracy has a three-dimensional grid drawing with $O(n^{3/2})$ volume. This is the broadest class of graphs admiting such drawings. A three-dimensional grid drawing of a directed graph is \emph{upward} if every arc points up in the z-direction. We prove that every directed acyclic graph has an upward three-dimensional grid drawing with $(n^3)$ volume, which is tight for the complete dag. The previous best upper bound was $O(n^4)$. Our main result is that every $c$-colourable directed acyclic graph ($c$ constant) has an upward three-dimensional grid drawing with $O(n^2)$ volume. This result matches the bound in the undirected case, and improves the best known bound from $O(n^3)$ for many classes of directed acyclic graphs, including planar, series parallel, and outerplanar