Drawing Binary Tanglegrams: An Experimental Evaluation

A binary tanglegram is a pair of binary trees whose leaf sets are in one-to-one correspondence; matching leaves are connected by inter-tree edges. For applications, for example in phylogenetics or software engineering, it is required that the individual trees are drawn crossing-free. A natural optimization problem, denoted tanglegram layout problem, is thus to minimize the number of crossings between inter-tree edges. The tanglegram layout problem is NP-hard and is currently considered both in application domains and theory. In this paper we present an experimental comparison of a recursive algorithm of Buchin et al., our variant of their algorithm, the algorithm hierarchy sort of Holten and van Wijk, and an integer quadratic program that yields optimal solutions.Comment: see http://www.siam.org/proceedings/alenex/2009/alx09_011_nollenburgm.pd

The Schr\"odinger Functional - a Renormalizable Probe for Non-Abelian Gauge Theories

Following Symanzik we argue that the Schr\"odinger functional in lattice gauge theories without matter fields has a well-defined continuum limit. Due to gauge invariance no extra counter terms are required. The Schr\"odinger functional is, moreover, accessible to numerical simulations. It may hence be used to study the scaling properties of the theory and in particular the evolution of the renormalized gauge coupling from low to high energies. A concrete proposition along this line is made and the necessary perturbative analysis of the Schr\"odinger functional is carried through to 1-loop order.Comment: 68 page

Comparative Benchmarks of full QCD Algorithms

We report performance benchmarks for several algorithms that we have used to simulate the Schr"odinger functional with two flavors of dynamical quarks. They include hybrid and polynomial hybrid Monte Carlo with preconditioning. An appendix describes a method to deal with autocorrelations for nonlinear functions of primary observables as they are met here due to reweighting.Comment: 24 pages, 3 figures, some added discussion, version submitted to Comput. Phys. Commu

ABC for people with HIV: responses to sexual behaviour recommendations among people receiving antiretroviral therapy in Jinja, Uganda.

People living with HIV who are taking antiretroviral therapy (ART) are increasingly involved in 'positive prevention' initiatives. These are generally oriented to promoting abstinence, 'being faithful' (partner reduction) and condom use (ABC). We conducted a longitudinal qualitative study with people living with HIV using ART, who were provided with adherence education and counselling support by a Ugandan non-governmental organisation, The AIDS Support Organisation (TASO). Forty people were selected sequentially as they started ART, stratified by sex, ART delivery mode (clinic- or home-based) and HIV progression stage (early or advanced) and interviewed at enrollment and at 3, 6, 18 and 30 months. At initiation of ART, participants agreed to follow TASO's positive-living recommendations. Initially poor health prevented sexual activity. As health improved, participants prioritised resuming economic production and support for their children. With further improvements, sexual desire resurfaced and people in relationships cemented these via sex. The findings highlight the limitations of HIV prevention based on medical care/personal counselling. As ART leads to health improvements, social norms, economic needs and sexual desires increasingly influence sexual behaviour. Positive prevention interventions need to seek to modify normative and economic influences on sexual behaviour, as well as to provide alternatives to condoms

Non-perturbative renormalization of lattice QCD at all scales

A general strategy to solve the non-perturbative renormalization problem in lattice QCD, using finite-size techniques and numerical simulations, is described. As an illustration we discuss the computation of the axial current normalization constant, the running coupling at zero quark masses and the scale evolution of the renormalized axial density. The non-perturbative calculation of O(a) correction terms (as they appear in Symanzik's improvement programme) is another important field of application.Comment: 14 pages, uuencoded gzipped postscript fil