Computing a rectilinear shortest path amid splinegons in plane

We reduce the problem of computing a rectilinear shortest path between two given points s and t in the splinegonal domain \calS to the problem of computing a rectilinear shortest path between two points in the polygonal domain. As part of this, we define a polygonal domain \calP from \calS and transform a rectilinear shortest path computed in \calP to a path between s and t amid splinegon obstacles in \calS. When \calS comprises of h pairwise disjoint splinegons with a total of n vertices, excluding the time to compute a rectilinear shortest path amid polygons in \calP, our reduction algorithm takes O(n + h \lg{n}) time. For the special case of \calS comprising of concave-in splinegons, we have devised another algorithm in which the reduction procedure does not rely on the structures used in the algorithm to compute a rectilinear shortest path in polygonal domain. As part of these, we have characterized few of the properties of rectilinear shortest paths amid splinegons which could be of independent interest

Lower bounds on the dilation of plane spanners

(I) We exhibit a set of 23 points in the plane that has dilation at least $1.4308$, improving the previously best lower bound of $1.4161$ for the worst-case dilation of plane spanners. (II) For every integer $n\geq13$, there exists an $n$-element point set $S$ such that the degree 3 dilation of $S$ denoted by $\delta_0(S,3) \text{ equals } 1+\sqrt{3}=2.7321\ldots$ in the domain of plane geometric spanners. In the same domain, we show that for every integer $n\geq6$, there exists a an $n$-element point set $S$ such that the degree 4 dilation of $S$ denoted by $\delta_0(S,4) \text{ equals } 1 + \sqrt{(5-\sqrt{5})/2}=2.1755\ldots$ The previous best lower bound of $1.4161$ holds for any degree. (III) For every integer $n\geq6$, there exists an $n$-element point set $S$ such that the stretch factor of the greedy triangulation of $S$ is at least $2.0268$.Comment: Revised definitions in the introduction; 23 pages, 15 figures; 2 table

A generic algorithm for layout of biological networks

BackgroundBiological networks are widely used to represent processes in biological systems and to capture interactions and dependencies between biological entities. Their size and complexity is steadily increasing due to the ongoing growth of knowledge in the life sciences. To aid understanding of biological networks several algorithms for laying out and graphically representing networks and network analysis results have been developed. However, current algorithms are specialized to particular layout styles and therefore different algorithms are required for each kind of network and/or style of layout. This increases implementation effort and means that new algorithms must be developed for new layout styles. Furthermore, additional effort is necessary to compose different layout conventions in the same diagram. Also the user cannot usually customize the placement of nodes to tailor the layout to their particular need or task and there is little support for interactive network exploration.ResultsWe present a novel algorithm to visualize different biological networks and network analysis results in meaningful ways depending on network types and analysis outcome. Our method is based on constrained graph layout and we demonstrate how it can handle the drawing conventions used in biological networks.ConclusionThe presented algorithm offers the ability to produce many of the fundamental popular drawing styles while allowing the exibility of constraints to further tailor these layouts.publishe

Application of Approximate Pattern Matching in Two Dimensional Spaces to Grid Layout for Biochemical Network Maps

Background For visualizing large-scale biochemical network maps, it is important to calculate the coordinates of molecular nodes quickly and to enhance the understanding or traceability of them. The grid layout is effective in drawing compact, orderly, balanced network maps with node label spaces, but existing grid layout algorithms often require a high computational cost because they have to consider complicated positional constraints through the entire optimization process. Results We propose a hybrid grid layout algorithm that consists of a non-grid, fast layout (preprocessor) algorithm and an approximate pattern matching algorithm that distributes the resultant preprocessed nodes on square grid points. To demonstrate the feasibility of the hybrid layout algorithm, it is characterized in terms of the calculation time, numbers of edge-edge and node-edge crossings, relative edge lengths, and F-measures. The proposed algorithm achieves outstanding performances compared with other existing grid layouts. Conclusions Use of an approximate pattern matching algorithm quickly redistributes the laid-out nodes by fast, non-grid algorithms on the square grid points, while preserving the topological relationships among the nodes. The proposed algorithm is a novel use of the pattern matching, thereby providing a breakthrough for grid layout. This application program can be freely downloaded from http://www.cadlive.jp/hybridlayout/hybridlayout.html

Turner syndrome and sexual differentiation of the brain: implications for understanding male-biased neurodevelopmental disorders

Turner syndrome (TS) is one of the most common sex chromosome abnormalities. Affected individuals often show a unique pattern of cognitive strengths and weaknesses and are at increased risk for a number of other neurodevelopmental conditions, many of which are more common in typical males than typical females (e.g., autism and attention-deficit hyperactivity disorder). This phenotype may reflect gonadal steroid deficiency, haploinsufficiency of X chromosome genes, failure to express parentally imprinted genes, and the uncovering of X chromosome mutations. Understanding the contribution of these different mechanisms to outcome has the potential to improve clinical care for individuals with TS and to better our understanding of the differential vulnerability to and expression of neurodevelopmental disorders in males and females. In this paper, we review what is currently known about cognition and brain development in individuals with TS, discuss underlying mechanisms and their relevance to understanding male-biased neurodevelopmental conditions, and suggest directions for future research