Improved estimation of density of states for Monte Carlo sampling via MBAR

We present a new method to calculate the density of states using the multistate Bennett acceptance ratio (MBAR) estimator. We use a combination of parallel tempering (PT) and multicanonical simulation to demonstrate the efficiency of our method in a statistical model of sampling from a two-dimensional normal mixture and also in a physical model of aggregation of lattice polymers. While MBAR has been commonly used for final estimation of thermodynamic properties, our numerical results show that the efficiency of estimation with our new approach, which uses MBAR as an intermediate step, often improves upon conventional use of MBAR. We also demonstrate that it can be beneficial in our method to use full PT samples for MBAR calculations in cases where simulation data exhibit long correlation

Final Technical Report - Open Architectures, Standards and Information Systems (OASIS II) – Developing Capacity, Sharing Knowledge and Good Principles across eHealth in Africa

The OASIS II project aimed to build on aspects of the Open Architectures, Standards and Information Systems for Healthcare in Africa (OASIS) project, previously funded by IDRC through the South African Medical Research Council. The objectives of the project included over-arching, network-wide objectives and individual project objectives. In addition, OASIS II aimed to investigate a shared research purpose and combine existing methods between one existing and four new projects and partners to: 1) elaborate a network-wide OASIS II research methodology, 2) establish an open enterprise architectural framework for eHealth in developing countries and 3) create a collaborative framework for sharing new evidence regarding the impact of eHealth solutions in resource-poor settings

Labels direct infants’ attention to commonalities during novel category learning

Recent studies have provided evidence that labeling can influence the outcome of infants’ visual categorization. However, what exactly happens during learning remains unclear. Using eye-tracking, we examined infants’ attention to object parts during learning. Our analysis of looking behaviors during learning provide insights going beyond merely observing the learning outcome. Both labeling and non-labeling phrases facilitated category formation in 12-month-olds but not 8-month-olds (Experiment 1). Non-linguistic sounds did not produce this effect (Experiment 2). Detailed analyses of infants’ looking patterns during learning revealed that only infants who heard labels exhibited a rapid focus on the object part successive exemplars had in common. Although other linguistic stimuli may also be beneficial for learning, it is therefore concluded that labels have a unique impact on categorization

The relationship of myocardial contraction and electrical excitation—the correlation between scintigraphic phase image analysis and electrophysiologic mapping

Phase imaging derived from equilibrium radionuclide angiography presents the ventricular contraction sequence. It has been widely but only indirectly correlated with the sequence of electrical myocardial activation. We sought to determine the specific relationship between the sequence of phase progression and the sequence of myocardial activation, contraction and conduction, in order to document a noninvasive method that could monitor both. In 7 normal and 9 infarcted dogs, the sequence of phase angle was correlated with the epicardial activation map in 126 episodes of sinus rhythm and pacing from three ventricular sites. In each episode, the site of earliest phase angle was identical to the focus of initial epicardial activation. Similarly, the serial contraction pattern by phase image analysis matched the electrical epicardial activation sequence completely or demonstrated good agreement in approximately 85% of pacing episodes, without differences between normal or infarct groups. A noninvasive method to accurately determine the sequence of contraction may serve as a surrogate for the associated electrical activation sequence or be applied to identify their differences

Catalog of Galactic Beta Cephei Stars

We present an extensive and up-to-date catalog of Galactic Beta Cephei stars. This catalog is intended to give a comprehensive overview of observational characteristics of all known Beta Cephei stars. 93 stars could be confirmed to be Beta Cephei stars. For some stars we re-analyzed published data or conducted our own analyses. 61 stars were rejected from the final Beta Cephei list, and 77 stars are suspected to be Beta Cephei stars. A list of critically selected pulsation frequencies for confirmed Beta Cephei stars is also presented. We analyze the Beta Cephei stars as a group, such as the distributions of their spectral types, projected rotational velocities, radial velocities, pulsation periods, and Galactic coordinates. We confirm that the majority of these stars are multiperiodic pulsators. We show that, besides two exceptions, the Beta Cephei stars with high pulsation amplitudes are slow rotators. We construct a theoretical HR diagram that suggests that almost all 93 Beta Cephei stars are MS objects. We discuss the observational boundaries of Beta Cephei pulsation and their physical parameters. We corroborate that the excited pulsation modes are near to the radial fundamental mode in frequency and we show that the mass distribution of the stars peaks at 12 solar masses. We point out that the theoretical instability strip of the Beta Cephei stars is filled neither at the cool nor at the hot end and attempt to explain this observation

A hybrid approach to protein folding problem integrating constraint programming with local search

<p>Abstract</p> <p>Background</p> <p>The protein folding problem remains one of the most challenging open problems in computational biology. Simplified models in terms of lattice structure and energy function have been proposed to ease the computational hardness of this optimization problem. Heuristic search algorithms and constraint programming are two common techniques to approach this problem. The present study introduces a novel hybrid approach to simulate the protein folding problem using constraint programming technique integrated within local search.</p> <p>Results</p> <p>Using the face-centered-cubic lattice model and 20 amino acid pairwise interactions energy function for the protein folding problem, a constraint programming technique has been applied to generate the neighbourhood conformations that are to be used in generic local search procedure. Experiments have been conducted for a few small and medium sized proteins. Results have been compared with both pure constraint programming approach and local search using well-established local move set. Substantial improvements have been observed in terms of final energy values within acceptable runtime using the hybrid approach.</p> <p>Conclusion</p> <p>Constraint programming approaches usually provide optimal results but become slow as the problem size grows. Local search approaches are usually faster but do not guarantee optimal solutions and tend to stuck in local minima. The encouraging results obtained on the small proteins show that these two approaches can be combined efficiently to obtain better quality solutions within acceptable time. It also encourages future researchers on adopting hybrid techniques to solve other hard optimization problems.</p

Zeta Oph and the weak-wind problem

Mass-loss rate, $\dot{M}$, is one of the key parameters affecting evolution and observational manifestations of massive stars, and their impact on the ambient medium. Despite its importance, there is a factor of ~100 discrepancy between empirical and theoretical $\dot{M}$ of late-type O dwarfs, the so-called weak-wind problem. In this Letter, we propose a simple novel method to constrain $\dot{M}$ of runaway massive stars through observation of their bow shocks and Stromgren spheres, which might be of decisive importance for resolving the weak-wind problem. Using this method, we found that $\dot{M}$ of the well-known runaway O9.5 V star zeta Oph is more than an order of magnitude higher than that derived from ultraviolet (UV) line-fitting (Marcolino et al. 2009) and is by a factor of 6 to 7 lower than those based on the theoretical recipe by Vink et al. (2000) and the Halpha line (Mokiem et al. 2005). The discrepancy between $\dot{M}$ derived by our method and that based on UV lines would be even more severe if the stellar wind is clumpy. At the same time, our estimate of $\dot{M}$ agrees with that predicted by the moving reversing layer theory by Lucy (2010).Comment: 5 pages, 1 figure, 2 tables. Accepted for publication in MNRAS Letter