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

Centres of Hecke algebras: the Dipper-James conjecture

In this paper we prove the Dipper-James conjecture that the centre of the Iwahori-Hecke algebra of type A is the set of symmetric polynomials in the Jucys-Murphy operators.Comment: 27 pages. To appear J. Algebr

"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