Maximal outerplanar graphs as chordal graphs, path-neighborhood graphs, and triangle graphs

Maximal outerplanar graphs are characterized using three different classes of graphs. A path-neighborhood graph is a connected graph in which every neighborhood induces a path. The triangle graph $T(G)$ has the triangles of the graph $G$ as its vertices, two of these being adjacent whenever as triangles in $G$ they share an edge. A graph is edge-triangular if every edge is in at least one triangle. The main results can be summarized as follows: the class of maximal outerplanar graphs is precisely the intersection of any of the two following classes: the chordal graphs, the path-neighborhood graphs, the edge-triangular graphs having a tree as triangle graph.maximal outerplanar graph;path-neighborhood graph;triangle graph;chordal graph;elimination ordering

Comparative study of different scattering geometries for the proposed Indian X-ray polarization measurement experiment using Geant4

Polarization measurements in X-rays can provide unique opportunity to study the behavior of matter and radiation under extreme magnetic fields and extreme gravitational fields. Unfortunately, over past two decades, when X-ray astronomy witnessed multiple order of magnitude improvement in temporal, spatial and spectral sensitivities, there is no (or very little) progress in the field of polarization measurements of astrophysical X-rays. Recently, a proposal has been submitted to ISRO for a dedicated small satellite based experiment to carry out X-ray polarization measurement, which aims to provide the first X-ray polarization measurements since 1976. This experiment will be based on the well known principle of polarization measurement by Thomson scattering and employs the baseline design of a central low Z scatterer surrounded by X-ray detectors to measure the angular intensity distribution of the scattered X-rays. The sensitivity of such experiment is determined by the collecting area, scattering and detection efficiency, X-ray detector background, and the modulation factor. Therefore, it is necessary to carefully select the scattering geometry which can provide the highest modulation factor and thus highest sensitivity within the specified experimental constraints. The effective way to determine optimum scattering geometry is by studying various possible scattering geometries by means of Monte Carlo simulations. Here we present results of our detailed comparative study based on Geant4 simulations of five different scattering geometries which can be considered within the weight and size constraints of the proposed small satellite based X-ray polarization measurement experiment.Comment: 14 pages, 6 figures, accepted for publication in "Nuclear Inst. and Methods in Physics Research, A

Maximal outerplanar graphs as chordal graphs, path-neighborhood graphs, and triangle graphs

Maximal outerplanar graphs are characterized using three different classes of graphs. A path-neighborhood graph is a connected graph in which every neighborhood induces a path. The triangle graph $T(G)$ has the triangles of the graph $G$ as its vertices, two of these being adjacent whenever as triangles in $G$ they share an edge. A graph is edge-triangular if every edge is in at least one triangle. The main results can be summarized as follows: the class of maximal outerplanar graphs is precisely the intersection of any of the two following classes: the chordal graphs, the path-neighborhood graphs, the edge-triangular graphs having a tree as triangle graph

A simple axiomatization of the median procedure on median graphs

A profile = (x1, ..., xk), of length k, in a finite connected graph G is a sequence of vertices of G, with repetitions allowed. A median x of is a vertex for which the sum of the distances from x to the vertices in the profile is minimum. The median function finds the set of all medians of a profile. Medians are important in location theory and consensus theory. A median graph is a graph for which every profile of length 3 has a unique median. Median graphs are well studied. They arise in many arenas, and have many applications. We establish a succinct axiomatic characterization of the median procedure on median graphs. This is a simplification of the characterization given by McMorris, Mulder and Roberts [17] in 1998. We show that the median procedure can be characterized on the class of all median graphs with only three simple and intuitively appealing axioms: anonymity, betweenness and consistency. We also extend a key result of the same paper, characterizing the median function for profiles of even length on median graphs

Phage inducible islands in the gram-positive cocci

The SaPIs are a cohesive subfamily of extremely common phage-inducible chromosomal islands (PICIs) that reside quiescently at specific att sites in the staphylococcal chromosome and are induced by helper phages to excise and replicate. They are usually packaged in small capsids composed of phage virion proteins, giving rise to very high transfer frequencies, which they enhance by interfering with helper phage reproduction. As the SaPIs represent a highly successful biological strategy, with many natural Staphylococcus aureus strains containing two or more, we assumed that similar elements would be widespread in the Gram-positive cocci. On the basis of resemblance to the paradigmatic SaPI genome, we have readily identified large cohesive families of similar elements in the lactococci and pneumococci/streptococci plus a few such elements in Enterococcus faecalis. Based on extensive ortholog analyses, we found that the PICI elements in the four different genera all represent distinct but parallel lineages, suggesting that they represent convergent evolution towards a highly successful lifestyle. We have characterized in depth the enterococcal element, EfCIV583, and have shown that it very closely resembles the SaPIs in functionality as well as in genome organization, setting the stage for expansion of the study of elements of this type. In summary, our findings greatly broaden the PICI family to include elements from at least three genera of cocci

LR characterization of chirotopes of finite planar families of pairwise disjoint convex bodies

We extend the classical LR characterization of chirotopes of finite planar families of points to chirotopes of finite planar families of pairwise disjoint convex bodies: a map \c{hi} on the set of 3-subsets of a finite set I is a chirotope of finite planar families of pairwise disjoint convex bodies if and only if for every 3-, 4-, and 5-subset J of I the restriction of \c{hi} to the set of 3-subsets of J is a chirotope of finite planar families of pairwise disjoint convex bodies. Our main tool is the polarity map, i.e., the map that assigns to a convex body the set of lines missing its interior, from which we derive the key notion of arrangements of double pseudolines, introduced for the first time in this paper.Comment: 100 pages, 73 figures; accepted manuscript versio

Depicting the tree of life in museums: guiding principles from psychological research

The Tree of Life is revolutionizing our understanding of life on Earth, and, accordingly, evolutionary trees are increasingly important parts of exhibits on biodiversity and evolution. The authors argue that in using these trees to effectively communicate evolutionary principles, museums need to take into account research results from cognitive, developmental, and educational psychology while maintaining a focus on visitor engagement and enjoyment. Six guiding principles for depicting evolutionary trees in museum exhibits distilled from this research literature were used to evaluate five current or recent museum trees. One of the trees was then redesigned in light of the research while preserving the exhibit’s original learning goals. By attending both to traditional factors that influence museum exhibit design and to psychological research on how people understand diagrams in general and Tree of Life graphics in particular, museums can play a key role in fostering 21st century scientific literacy

Applying a User-centred Approach to Interactive Visualization Design

Analysing users in their context of work and finding out how and why they use different information resources is essential to provide interactive visualisation systems that match their goals and needs. Designers should actively involve the intended users throughout the whole process. This chapter presents a user-centered approach for the design of interactive visualisation systems. We describe three phases of the iterative visualisation design process: the early envisioning phase, the global specification hase, and the detailed specification phase. The whole design cycle is repeated until some criterion of success is reached. We discuss different techniques for the analysis of users, their tasks and domain. Subsequently, the design of prototypes and evaluation methods in visualisation practice are presented. Finally, we discuss the practical challenges in design and evaluation of collaborative visualisation environments. Our own case studies and those of others are used throughout the whole chapter to illustrate various approaches

Visual Similarity Perception of Directed Acyclic Graphs: A Study on Influencing Factors

While visual comparison of directed acyclic graphs (DAGs) is commonly encountered in various disciplines (e.g., finance, biology), knowledge about humans' perception of graph similarity is currently quite limited. By graph similarity perception we mean how humans perceive commonalities and differences in graphs and herewith come to a similarity judgment. As a step toward filling this gap the study reported in this paper strives to identify factors which influence the similarity perception of DAGs. In particular, we conducted a card-sorting study employing a qualitative and quantitative analysis approach to identify 1) groups of DAGs that are perceived as similar by the participants and 2) the reasons behind their choice of groups. Our results suggest that similarity is mainly influenced by the number of levels, the number of nodes on a level, and the overall shape of the graph.Comment: Graph Drawing 2017 - arXiv Version; Keywords: Graphs, Perception, Similarity, Comparison, Visualizatio

Sociobiological Control of Plasmid copy number

Background:
All known mechanisms and genes responsible for the regulation of plasmid replication lie with the plasmid rather than the chromosome. It is possible therefore that there can be copy-up mutants. Copy-up mutants will have within host selective advantage. This would eventually result into instability of bacteria-plasmid association. In spite of this possibility low copy number plasmids appear to exist stably in host populations. We examined this paradox using a computer simulation model.

Model:
Our multilevel selection model assumes a wild type with tightly regulated replication to ensure low copy number. A mutant with slightly relaxed replication regulation can act as a “cheater” or “selfish” plasmid and can enjoy a greater within-host-fitness. However the host of a cheater plasmid has to pay a greater cost. As a result, in host level competition, host cell with low copy number plasmid has a greater fitness. Furthermore, another mutant that has lost the genes required for conjugation was introduced in the model. The non-conjugal mutant was assumed to undergo conjugal transfer in the presence of another conjugal plasmid in the host cell.

Results:
The simulatons showed that if the cost of carrying a plasmid was low, the copy-up mutant could drive the wild type to extinction or very low frequencies. Consequently, another mutant with a higher copy number could invade the first invader. This process could result into an increasing copy number. However above a certain copy number within-host selection was overcompensated by host level selection leading to a rock-paper-scissor (RPS) like situation. The RPS situation allowed the coexistence of high and low copy number plasmids. The non-conjugal “hypercheaters” could further arrest the copy numbers to a substantially lower level.

Conclusions:
These sociobiological interactions might explain the stability of copy numbers better than molecular mechanisms of replication regulation alone