Which phylogenetic networks are merely trees with additional arcs?

A binary phylogenetic network may or may not be obtainable from a tree by the addition of directed edges (arcs) between tree arcs. Here, we establish a precise and easily tested criterion (based on `2-SAT') that efficiently determines whether or not any given network can be realized in this way. Moreover, the proof provides a polynomial-time algorithm for finding one or more trees (when they exist) on which the network can be based. A number of interesting consequences are presented as corollaries; these lead to some further relevant questions and observations, which we outline in the conclusion.Comment: The final version of this article will appear in Systematic Biology. 20 pages, 7 figure

"Building" exact confidence nets

Confidence nets, that is, collections of confidence intervals that fill out the parameter space and whose exact parameter coverage can be computed, are familiar in nonparametric statistics. Here, the distributional assumptions are based on invariance under the action of a finite reflection group. Exact confidence nets are exhibited for a single parameter, based on the root system of the group. The main result is a formula for the generating function of the coverage interval probabilities. The proof makes use of the theory of "buildings" and the Chevalley factorization theorem for the length distribution on Cayley graphs of finite reflection groups.Comment: 20 pages. To appear in Bernoull

Group-theoretic models of the inversion process in bacterial genomes

The variation in genome arrangements among bacterial taxa is largely due to the process of inversion. Recent studies indicate that not all inversions are equally probable, suggesting, for instance, that shorter inversions are more frequent than longer, and those that move the terminus of replication are less probable than those that do not. Current methods for establishing the inversion distance between two bacterial genomes are unable to incorporate such information. In this paper we suggest a group-theoretic framework that in principle can take these constraints into account. In particular, we show that by lifting the problem from circular permutations to the affine symmetric group, the inversion distance can be found in polynomial time for a model in which inversions are restricted to acting on two regions. This requires the proof of new results in group theory, and suggests a vein of new combinatorial problems concerning permutation groups on which group theorists will be needed to collaborate with biologists. We apply the new method to inferring distances and phylogenies for published Yersinia pestis data.Comment: 19 pages, 7 figures, in Press, Journal of Mathematical Biolog

Improving Brain–Machine Interface Performance by Decoding Intended Future Movements

Objective. A brain–machine interface (BMI) records neural signals in real time from a subject\u27s brain, interprets them as motor commands, and reroutes them to a device such as a robotic arm, so as to restore lost motor function. Our objective here is to improve BMI performance by minimizing the deleterious effects of delay in the BMI control loop. We mitigate the effects of delay by decoding the subject\u27s intended movements a short time lead in the future. Approach. We use the decoded, intended future movements of the subject as the control signal that drives the movement of our BMI. This should allow the user\u27s intended trajectory to be implemented more quickly by the BMI, reducing the amount of delay in the system. In our experiment, a monkey (Macaca mulatta) uses a future prediction BMI to control a simulated arm to hit targets on a screen. Main Results. Results from experiments with BMIs possessing different system delays (100, 200 and 300 ms) show that the monkey can make significantly straighter, faster and smoother movements when the decoder predicts the user\u27s future intent. We also characterize how BMI performance changes as a function of delay, and explore offline how the accuracy of future prediction decoders varies at different time leads. Significance. This study is the first to characterize the effects of control delays in a BMI and to show that decoding the user\u27s future intent can compensate for the negative effect of control delay on BMI performance

Changing patterns of religious affiliation, church attendance and marriage across five areas of Europe since the early 1980s: trends and associations

This study draws on three waves of the European Values Survey (conducted between 1981 and 1984, between 1989 and 1993, and between 1999 and 2004) across five countries for which full data are available (Great Britain, Italy, the Netherlands, Northern Ireland, Spain, and Sweden) in order to address five research questions. Question one examined changes in religious affiliation. Across all five countries, the proportions of the non-affiliated increased. Question two examined changes in church attendance. Across all five countries, the proportions of the non-attenders increased. Question three examined changes in marital status. Across all five countries the proportions of the population checking the category 'married' declined, although in Spain the decline was marginal. Question four examined the association between religious affiliation and being married. The religious affiliated were more likely to be married than the non-affiliated. Question five examined the association between church attendance and being married. Weekly attenders were more likely to be married than the non-attenders. Overall these data support the close association between religion and marriage across five European countries (where there are very different religious climates) and support the hypothesis that changing religious values and changing family values go hand-in-hand

Quest religious orientation among church leaders in Australia : a function of psychological predisposition or openness to mystical experience?

Quest-religious orientation among church leaders signifies a style of leadership committed to religious explorations more than to religious certainties. For this study, we set out to explore the extent to which quest orientation among a sample of 1,265 religious church leaders who participated in the 2011 Australian National Church Life Survey was a function of psychological predisposition, conceptualized in terms of psychological type theory, or a function of distinctive forms of religious experience, conceptualized in terms of Happold’s (1963) model of mysticism. The data demonstrated that higher levels of mystical orientation were associated with psychological predisposition, involving extraversion, intuition, feeling, and perceiving. After controlling for sex, age, education, denominational groups, and psychological type, higher levels of mystical orientation were also associated with higher levels of quest-religious orientation. Mystical orientation partly mediated the effect of intuition on question orientation, but psychological preferences (for intuition and perceiving) and mystical orientation seemed independently to promote quest orientation. Thus, church leaders committed to religious explorations rather than to religious certainties seemed to have been shaped both by psychological predisposition and by distinctive forms of religious experience. (PsycINFO Database Record (c) 2017 APA, all rights reserved

Maximum likelihood estimates of pairwise rearrangement distances

Accurate estimation of evolutionary distances between taxa is important for many phylogenetic reconstruction methods. In the case of bacteria, distances can be estimated using a range of different evolutionary models, from single nucleotide polymorphisms to large-scale genome rearrangements. In the case of sequence evolution models (such as the Jukes-Cantor model and associated metric) have been used to correct pairwise distances. Similar correction methods for genome rearrangement processes are required to improve inference. Current attempts at correction fall into 3 categories: Empirical computational studies, Bayesian/MCMC approaches, and combinatorial approaches. Here we introduce a maximum likelihood estimator for the inversion distance between a pair of genomes, using the group-theoretic approach to modelling inversions introduced recently. This MLE functions as a corrected distance: in particular, we show that because of the way sequences of inversions interact with each other, it is quite possible for minimal distance and MLE distance to differently order the distances of two genomes from a third. This has obvious implications for the use of minimal distance in phylogeny reconstruction. The work also tackles the above problem allowing free rotation of the genome. Generally a frame of reference is locked, and all computation made accordingly. This work incorporates the action of the dihedral group so that distance estimates are free from any a priori frame of reference.Comment: 21 pages, 7 figures. To appear in the Journal of Theoretical Biolog

Models of deletion for visualizing bacterial variation: an application to tuberculosis spoligotypes

<p>Abstract</p> <p>Background</p> <p>Molecular typing methods are commonly used to study genetic relationships among bacterial isolates. Many of these methods have become standardized and produce portable data. A popular approach for analyzing such data is to construct graphs, including phylogenies. Inferences from graph representations of data assist in understanding the patterns of transmission of bacterial pathogens, and basing these graph constructs on biological models of evolution of the molecular marker helps make these inferences. Spoligotyping is a widely used method for genotyping isolates of <it>Mycobacterium tuberculosis </it>that exploits polymorphism in the direct repeat region. Our goal was to examine a range of models describing the evolution of spoligotypes in order to develop a visualization method to represent likely relationships among <it>M. tuberculosis </it>isolates.</p> <p>Results</p> <p>We found that inferred mutations of spoligotypes frequently involve the loss of a single or very few adjacent spacers. Using a second-order variant of Akaike's Information Criterion, we selected the Zipf model as the basis for resolving ambiguities in the ancestry of spoligotypes. We developed a method to construct graphs of spoligotypes (which we call spoligoforests). To demonstrate this method, we applied it to a tuberculosis data set from Cuba and compared the method to some existing methods.</p> <p>Conclusion</p> <p>We propose a new approach in analyzing relationships of <it>M. tuberculosis </it>isolates using spoligotypes. The spoligoforest recovers a plausible history of transmission and mutation events based on the selected deletion model. The method may be suitable to study markers based on loci of similar structure from other bacteria. The groupings and relationships in the spoligoforest can be analyzed along with the clinical features of strains to provide an understanding of the evolution of spoligotypes.</p

NorthStar, a support tool for the design and evaluation of quality improvement interventions in healthcare

Background: The Research-Based Education and Quality Improvement (ReBEQI) European partnership aims to establish a framework and provide practical tools for the selection, implementation, and evaluation of quality improvement (QI) interventions. We describe the development and preliminary evaluation of the software tool NorthStar, a major product of the ReBEQI project. Methods: We focused the content of NorthStar on the design and evaluation of QI interventions. A lead individual from the ReBEQI group drafted each section, and at least two other group members reviewed it. The content is based on published literature, as well as material developed by the ReBEQI group. We developed the software in both a Microsoft Windows HTML help system version and a web-based version. In a preliminary evaluation, we surveyed 33 potential users about the acceptability and perceived utility of NorthStar. Results: NorthStar consists of 18 sections covering the design and evaluation of QI interventions. The major focus of the intervention design sections is on how to identify determinants of practice (factors affecting practice patterns), while the major focus of the intervention evaluation sections is on how to design a cluster randomised trial. The two versions of the software can be transferred by email or CD, and are available for download from the internet. The software offers easy navigation and various functions to access the content. Potential users (55% response rate) reported above-moderate levels of confidence in carrying out QI research related tasks if using NorthStar, particularly when developing a protocol for a cluster randomised trial Conclusion: NorthStar is an integrated, accessible, practical, and acceptable tool to assist developers and evaluators of QI interventions