Application of Helix Cone Tree visualizations to dynamic call graph illustration

We describe a tool that enables users to record and visualise runtime behaviour of software applications developed in Java. The execution trace, stored in the form of an XML le is visualized using 3D call graphs that are an extension of the Cone Tree infor- mation visualisation technique. This tool gives the user the ability to create several call graph views from a program's execution trace, providing additional representations of the program execution to both novice and expert programmers for the purposes of program execution analysis

<i>S. cerevisiae</i> forms filamentous mats.

<p><b>A</b>) Wild-type cells (PC313) were spotted 2 cm apart onto 0.3% agar media that contained (YEPD; top panel) or lacked (YEP; bottom panel) glucose. The YEPD plate was incubated for 4 days and photographed; the YEP plate for 15 days. Bar = 1 cm. <b>B</b>) Microscopic examination of perimeters of mats in 1A. Bar = 100 microns. <b>C</b>) The origin of filamentous mats. Wild type (PC538) cells were examined on synthetic medium either containing 2% glucose (SCD) or lacking glucose (SC) in 0.3% agar medium for 24 h at 30°C. A compiled Z-stack rendering of typical microcolonies are shown. Bar = 20 microns. <b>D</b>) Same strains in 1C were examined on rich medium either containing 2% glucose (YEPD) or lacking glucose (YEP) in 0.3% agar. A representative microscopic image is shown. Bar = 10 microns. E) Vegetative mats mature into filamentous mats over time as nutrients become limiting. Two mats of wild type (PC313) strain were spotted bilaterally (1.5 cm apart) on YEPD and YEP media (+0.2% galactose) containing 0.3% agar media. The number of filaments occurring along the circumference of mats was scored on a scale of 1, 2, or 3 dots at 20× magnification corresponding to 3, 6, or 9 filaments or greater, respectively. Dots were plotted on a circle representing the outline of one of the mats with right hemispheres corresponding to the side of the mat facing a second mat. Asymmetric filamentation observed in the right hemisphere of 2d, Glu can possibly result from nutritional stress compounded by nutrient depletion from adjacent mats. Filamentation was monitored and plotted after growth for 1, 2, 3, and 4 days. Quantitation of pseudohyphae was complicated at longer time points when biofilms began to variegate <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0032294#pone.0032294-Halme1" target="_blank">[60]</a>. Bar = 1 cm.</p

The role of Flo11 overexpression on upward growth in the plane of the Z-axis.

<p><b>A</b>) Microcolonies of wild-type cells (PC538) and cells overexpressing <i>FLO11</i> (PC2712) were examined by microscopy at 10× after 24 h incubation at 30°C. Wild type and <i>ste12</i> mats on high agar concentrations is also shown Bar = 100 microns. <b>B</b>) Contour mapping of z-stack rendering of the indicated microcolonies in panel 7A are shown. Bar = 30 microns. See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0032294#pone.0032294.s006" target="_blank">Supplemental Movies S5</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0032294#pone.0032294.s007" target="_blank">S6</a>. <b>C</b>) Wild-type (PC538), <i>flo11</i>Δ (PC1029), and <i>GAL-FLO11</i> (PC2712) cells were spotted onto YEP-GAL medium (8%) agar atop nitrocellulose filters for 24 h at 30°C. Colonies were photographed in transmitted light. Bar = 1 cm. At right, separation of the <i>GAL-FLO11</i> mat from the surface using forceps. <b>D</b>) Microscopic examination of the mats in panel C. Bar = 200 microns.</p

The role of the MAPK pathway in regulating mat architecture when exposed to surfaces of different rigidities.

<p><b>A</b>) Contour maps in the Z-axis of wild type (PC538) mats incubated in media of different agar concentrations for 14d. Insets show mat morphology (left, photograph, bar, 1 cm; right, photomicrograph, bar, 200 microns) in 4% agar. The numbers in parentheses represent the average mat dry weight from two experiments with standard deviation shown. Scale bars for the X and Y-axes are in mm. <b>B</b>) Mats formed by a <i>ste12</i>Δ mutant (PC539) on different agar concentrations. Analysis is as described for panel A.</p

MAPK- and Flo11-dependent colony avoidance response.

<p><b>A</b>) Wild-type cells were spotted in three spots and examined daily. The photograph showing the embossed appearance of colonies was taken at day 3. Left three panels, Bar = 1 cm. Far right panel, micrograph of cells at the perimeter of an asymmetrically forming biofilm. Bar, 200 microns. Mat borders facing (red arrows) or not facing (blue arrows) another mat are indicated. <b>B</b>) Wild type (PC538), <i>flo</i>11Δ (PC1029), and <i>ste</i>12Δ (PC2382) cells were grown on YEPD media for 18 h. Equal concentrations of cells were spotted, 1 cm apart, on to YEPD media containing 0.3% agar. Plates were incubated for 48 h at 30°C and photographed using transmitted light. Bar = 1 cm. <b>C</b>) Bar graph of height measurements (in mm) of the mat borders facing/not facing the adjacent mats on the right in B. Contour maps in the Z-axis of mats was generated. Seven readings after the first peak in the Z-axis were averaged to plot the graph. Standard deviation between measurements were used to generate the error bars.</p

Model for the different mat responses controlled by the MAPK pathway.

<p>Schematic of a mat expanding under nutrient-limiting conditions is shown. Different responses regulated by the MAPK pathway may include: 1) mat expansion in the plane of the XY-axis (surface growth, through Flo11 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0032294#pone.0032294-Reynolds1" target="_blank">[23]</a>), 2) cell differentiation that causes invasive growth in the Z-axis (downward growth, Flo11 and differentiation), and 3) upward growth in the plane of the Z-axis in response to surface rigidity and nutrient-limiting conditions (Flo11 and differentiation). This upward growth may represent a type of chemorepulsion. An extracellular matrix (ECM), which may contain shed Flo11 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0032294#pone.0032294-Karunanithi1" target="_blank">[48]</a> as well as other proteins is depicted.</p

Assessment of Genetic Variability and Structuring of Riverine Buffalo Population (<i>Bubalus bubalis</i>) of Indo-Gangetic Basin

<div><p>The buffalo population of Uttar Pradesh (UP) constitutes 26.1% of the total buffalo population of India, yet this population has not been classified into distinct breeds or subpopulations due to lack of systematic study. Genetic variation at 30 microsatellite loci was examined and statistical analysis was carried out to reveal genetic diversity, demographic parameters of these buffaloes and to investigate the existence of population substructures underlying geographical distribution. The mean number of alleles per locus was 13.26 and mean effective number of alleles was 3.74, whereas mean observed and expected heterozygosities were found to be 0.57 and 0.67 in UP buffaloes. Principal component analysis (PCA) based on allele frequency data revealed subclustering of UP buffalo population. Bayesian analysis result also revealed clear membership of individuals into five clusters indicating a genetic subdivision within the UP buffalo population. The buffaloes of Western and Central regions of UP were subtly separated while buffaloes of Tarai area and Bhadawari buffaloes revealed distinctive population structure. The buffaloes of Mau, Ballia and Ghazipur districts of Eastern region also had a distinctive genetic structure. The analysis of data on buffaloes of Indo-Gangetic plains revealed that population was in mutation drift equilibrium. The observed mean M ratio in the population was above the critical significance value (Mc) suggesting that it has not suffered any severe reduction in effective population size. The statistical tests revealed a historical constancy of size of buffalo in this geographical area. The high level of genetic variability indicates UP buffalo population is a vast reservoir of genetic diversity and this shall help in taking informed conservation decisions and sustainable utilization.</p> </div

SUPPLEMENTARY MATERIAL; Cytochrome B Haplotypes; D-loop Haplotypes from Phylogenetic evidence for the ancient Himalayan wolf: towards a clarification of their taxonomic status based on genetic sampling from western Nepal

The supplementary material contains details on the genetic analysis procedure, tables with details on genetic sequences used in the analyses, and additional phylogenies built with Neighbourhood-joining; This file contains the two unique Cytochrome b haplotypes for Himalayan wolf and the one unque haplotype for domestic dog found in Humla Nepal.; This file contains the three unique D-loop haplotypes for Himalayan wolf and the one unique haplotype for domestic dog found in Humla Nepal. It also contains two Grey wolf haplotypes found in scats from Mongolia that were in the authors collection