Circular Networks from Distorted Metrics

Trees have long been used as a graphical representation of species relationships. However complex evolutionary events, such as genetic reassortments or hybrid speciations which occur commonly in viruses, bacteria and plants, do not fit into this elementary framework. Alternatively, various network representations have been developed. Circular networks are a natural generalization of leaf-labeled trees interpreted as split systems, that is, collections of bipartitions over leaf labels corresponding to current species. Although such networks do not explicitly model specific evolutionary events of interest, their straightforward visualization and fast reconstruction have made them a popular exploratory tool to detect network-like evolution in genetic datasets. Standard reconstruction methods for circular networks, such as Neighbor-Net, rely on an associated metric on the species set. Such a metric is first estimated from DNA sequences, which leads to a key difficulty: distantly related sequences produce statistically unreliable estimates. This is problematic for Neighbor-Net as it is based on the popular tree reconstruction method Neighbor-Joining, whose sensitivity to distance estimation errors is well established theoretically. In the tree case, more robust reconstruction methods have been developed using the notion of a distorted metric, which captures the dependence of the error in the distance through a radius of accuracy. Here we design the first circular network reconstruction method based on distorted metrics. Our method is computationally efficient. Moreover, the analysis of its radius of accuracy highlights the important role played by the maximum incompatibility, a measure of the extent to which the network differs from a tree.Comment: Submitte

The Impact Of Ownership Structure On Corporate Debt Policy: Two Stage Least Square Simultaneous Model Approach For Post Crisis Period: Evidence From Kuala Lumpur Stock Exchange

Ownership concentration as a governance mechanism has received considerable attention among academician, practitioners as well as policy makers because large-block shareholders are increasingly active in their demands that corporations adopt effective governance mechanisms to control managerial decisions, which include corporate debt policy.  Earlier study on the agency model of the firm widely recognizes that the managerial ownership and external debt play an important role in mitigating agency conflicts and enhancing firm value. They also found that increase in the external monitors, for example the institutional investors, can actually play a useful role in limiting agency problems in the firm.  This paper, using 100 Composite Index companies from Brusa Malaysia between 1998 to 2002 explores the impact of institutional holdings on managerial ownership and debt policy in an integrated framework by using a simultaneous equations estimation procedure (2SLS). The findings show that there is a significant impact of institutional ownership which serves effective control mechanism on managerial ownership and corporate debt policy as hypothesized. Findings of such evidence suggest that institutional holding thus have played an important role in managers' strategic management decision and reduce agency conflict. In addition, corporate debt policy too is governed by managerial ownership and exhibited a negative relation

Les Pavages d'Anges et de Diables

On utilise la méthode des symboles de Delaney pour classifier à l’aide de I’ordinateur, à homéomorphisme équivariant près, tous les pavages périodiques du plan dont les pavés peuvent être colories de noir et de blanc de telle manière que les pavés se partageant une arête soient de couleurs différentes, que le groupe de symétrie agisse de faGon transitive sur les pavés noirs, que tout pavé possède au moins trois arêtes et que de chaque sommet soient issues au moins trois arêtes.The method of Delaney symbols is used to classify by a computer program all periodic tilings of the Euclidean plane up to equivariant homeomorphisms for which the tiles can be coloured by black and white such that tiles sharing an edge have different colours, the symmetry group acts transitively on the black tiles, every tile has at least three edges and from every vertex at least three edges originate.Peer Reviewe

Pengaruh Komitmen Kerja, Stres Kerja Dan Disiplin Kerja Terhadap Kinerja Karyawan Bagian Spinning III PT. Apac Inti Corpora

The need for human resources are not small and labor requirements vary with the complex challenges of the work is a problem for a company. PT. APAC INTI CORPORA engaged in textiles that need to maintain human resources work in order to meet the quantity and quality of the product. However, in 2013 the production and performance of any inconsistency unfavorable assessments on the performance of the employee.The purpose of research to determine the effect of work commitment, job stress, and work discipline on employee performance Spinning Part III PT. APAC INTI CORPORA. This research method is explanatory, data collection through interviews with questionnaires. Proportionate stratified random sampling technique is used with a sample of 87 people. The analysis technique used was qualitative and quantitative. Quantitative analysis using validity, reliability test, correlation coefficient, simple and multiple regression analysis, the coefficient of determination, cross tabulation, and tests of significance.Categorization work commitment is high, but there are some that in the low category. Employee stress is low, but there is still residing in the high category. Discipline employees in good condition, although there is still a lack of good condition. The level of employee performance is good, but there are still employees who have low performance. Results and discussion showed the higher commitment to work, the higher the performance of employees, reduced work stress, the higher the performance of employees, and the better labour discipline, the higher the performance of employees, simultaneously work commitment, work stress, and labour discipline affect employee performance.Companies must increase loyalty to employees, to put forward a conducive atmosphere in work activities, and socializing with good rules, provide counseling regarding the standards and efficiency of work, and the need for further research by the company or outside parties on other variables such motivation, job satisfaction, training work, which can affect employee performance improvement

Folding and unfolding phylogenetic trees and networks

Phylogenetic networks are rooted, labelled directed acyclic graphs which are commonly used to represent reticulate evolution. There is a close relationship between phylogenetic networks and multi-labelled trees (MUL-trees). Indeed, any phylogenetic network $N$ can be "unfolded" to obtain a MUL-tree $U(N)$ and, conversely, a MUL-tree $T$ can in certain circumstances be "folded" to obtain a phylogenetic network $F(T)$ that exhibits $T$. In this paper, we study properties of the operations $U$ and $F$ in more detail. In particular, we introduce the class of stable networks, phylogenetic networks $N$ for which $F(U(N))$ is isomorphic to $N$, characterise such networks, and show that they are related to the well-known class of tree-sibling networks.We also explore how the concept of displaying a tree in a network $N$ can be related to displaying the tree in the MUL-tree $U(N)$. To do this, we develop a phylogenetic analogue of graph fibrations. This allows us to view $U(N)$ as the analogue of the universal cover of a digraph, and to establish a close connection between displaying trees in $U(N)$ and reconcilingphylogenetic trees with networks

Auditor switch decision of Malaysian listed firms: tests of determinants and wealth effect

This article examines the economic rationale for auditor change by Malaysian listed firms by examining audit switch effect on share prices. The auditor change decision by management to retain or to change involves a switch across audit firms with different quality. Audit quality is defined by classifying the audit firms into Tier 1 (Big-5) firms and Tier 2 (non-Big 5) firms. The distinguishing attribute between the two groups of audit products is believed to be the credibility that each group brings to the audit engagement. Factors associated with the choice of audit firm and changes for firm characteristics associated with auditor choice were investigated using the logistic regression model. The findings show that the auditor switch of Malaysian listed firms is partly explained by changes in management and turnover growth. Changes in firms' characteristics such as asset growth, purchase of fixed asset to total asset, leverage and changes in financing activities explain auditor switches. There appears to be no evidence of significant wealth effect from auditor switch announcements

TopiaryExplorer: visualizing large phylogenetic trees with environmental metadata

Motivation: Microbial community profiling is a highly active area of research, but tools that facilitate visualization of phylogenetic trees and associated environmental data have not kept up with the increasing quantity of data generated in these studies

Functional significance may underlie the taxonomic utility of single amino acid substitutions in conserved proteins

We hypothesized that some amino acid substitutions in conserved proteins that are strongly fixed by critical functional roles would show lineage-specific distributions. As an example of an archetypal conserved eukaryotic protein we considered the active site of ß-tubulin. Our analysis identified one amino acid substitution—ß-tubulin F224—which was highly lineage specific. Investigation of ß-tubulin for other phylogenetically restricted amino acids identified several with apparent specificity for well-defined phylogenetic groups. Intriguingly, none showed specificity for “supergroups” other than the unikonts. To understand why, we analysed the ß-tubulin Neighbor-Net and demonstrated a fundamental division between core ß-tubulins (plant-like) and divergent ß-tubulins (animal and fungal). F224 was almost completely restricted to the core ß-tubulins, while divergent ß-tubulins possessed Y224. Thus, our specific example offers insight into the restrictions associated with the co-evolution of ß-tubulin during the radiation of eukaryotes, underlining a fundamental dichotomy between F-type, core ß-tubulins and Y-type, divergent ß-tubulins. More broadly our study provides proof of principle for the taxonomic utility of critical amino acids in the active sites of conserved proteins

The bacterial pedome associated with foot pathologies in sheep::a case study

Hoof lameness is considered to be a major health issue in sheep, and can impact on both animal welfare and production of livestock. However the causes, although generally assumed to have a microbiological basis, are poorly understood. The work presented here investigated the pedome (the bacterial community of the foot) of sheep which were seen to have one of the following conditions: foot rot; a toe granuloma; Ovine Interdigital Dermatitis (OID) / scald. These were compared relative to samples collected from the healthy feet of the same animals. Samples were collected from commercial lambs from two flocks of sheep (one Beulahs, one Suffolks) at times of routine husbandry work. All animals in the flocks and those which showed signs of lameness (7 per flock) were used for sample collection. Interdigital scrapes were collected from lame feet, together with controls (i.e. non-lame feet) from the same animals. Of the lame feet, 3 were classified as having foot rot, 10 had OID / scald and 1 had a toe granuloma. DNA was isolated from the interdigital scrapes and analysed by next generation sequencing following amplification of DNA by PCR. All foot rot samples showed unusual microbial communities: one having an elevated abundance of Fusobacterium spp.; another with an elevated level of a Corynebacterium sp.; and the third an increased level of a number of unidentified sequences. One of the OID samples also had a high abundance of Fusobacterium spp., and another had a similar pattern of unknown organisms to that seen in the example of the foot rot case. The toe granuloma case showed an elevated level of a Mycoplasma sp. Therefore the organisms described here are different from those previously identified in a similar investigation into this topic. However the other eight OID samples had patterns similar to those in controls. This suggests microbial communities associated with ovine foot rot are complex, and that there are bacteria associated with the condition which remain unknown