Robust Parameter Selection for Parallel Tempering

This paper describes an algorithm for selecting parameter values (e.g. temperature values) at which to measure equilibrium properties with Parallel Tempering Monte Carlo simulation. Simple approaches to choosing parameter values can lead to poor equilibration of the simulation, especially for Ising spin systems that undergo $1^st$-order phase transitions. However, starting from an initial set of parameter values, the careful, iterative respacing of these values based on results with the previous set of values greatly improves equilibration. Example spin systems presented here appear in the context of Quantum Monte Carlo.Comment: Accepted in International Journal of Modern Physics C 2010, http://www.worldscinet.com/ijmp

Seeking Quantum Speedup Through Spin Glasses: The Good, the Bad, and the Ugly

There has been considerable progress in the design and construction of quantum annealing devices. However, a conclusive detection of quantum speedup over traditional silicon-based machines remains elusive, despite multiple careful studies. In this work we outline strategies to design hard tunable benchmark instances based on insights from the study of spin glasses - the archetypal random benchmark problem for novel algorithms and optimization devices. We propose to complement head-to-head scaling studies that compare quantum annealing machines to state-of-the-art classical codes with an approach that compares the performance of different algorithms and/or computing architectures on different classes of computationally hard tunable spin-glass instances. The advantage of such an approach lies in having to only compare the performance hit felt by a given algorithm and/or architecture when the instance complexity is increased. Furthermore, we propose a methodology that might not directly translate into the detection of quantum speedup, but might elucidate whether quantum annealing has a "`quantum advantage" over corresponding classical algorithms like simulated annealing. Our results on a 496 qubit D-Wave Two quantum annealing device are compared to recently-used state-of-the-art thermal simulated annealing codes.Comment: 14 pages, 8 figures, 3 tables, way too many reference

Evolutionary Approaches to Optimization Problems in Chimera Topologies

Chimera graphs define the topology of one of the first commercially available quantum computers. A variety of optimization problems have been mapped to this topology to evaluate the behavior of quantum enhanced optimization heuristics in relation to other optimizers, being able to efficiently solve problems classically to use them as benchmarks for quantum machines. In this paper we investigate for the first time the use of Evolutionary Algorithms (EAs) on Ising spin glass instances defined on the Chimera topology. Three genetic algorithms (GAs) and three estimation of distribution algorithms (EDAs) are evaluated over $1000$ hard instances of the Ising spin glass constructed from Sidon sets. We focus on determining whether the information about the topology of the graph can be used to improve the results of EAs and on identifying the characteristics of the Ising instances that influence the success rate of GAs and EDAs.Comment: 8 pages, 5 figures, 3 table

Topical curcumin nanocarriers are neuroprotective in eye disease

Curcumin (1,7-bis-(4-hydroxy-3-methoxyphenyl)-1,6-heptadiene-3,5dione) is a polyphenol extracted from turmeric that has long been advocated for the treatment of a variety of conditions including neurodegenerative and inflammatory disorders. Despite this promise, the clinical use of curcumin has been limited by the poor solubility and low bioavailability of this molecule. In this article, we describe a novel nanocarrier formulation comprising Pluronic-F127 stabilised D-α-Tocopherol polyethene glycol 1000 succinate nanoparticles, which were used to successfully solubilize high concentrations (4.3 mg/mL) of curcumin. Characterisation with x-ray diffraction and in vitro release assays localise curcumin to the nanocarrier interior, with each particle measuring <20 nm diameter. Curcumin-loaded nanocarriers (CN) were found to significantly protect against cobalt chloride induced hypoxia and glutamate induced toxicity in vitro, with CN treatment significantly increasing R28 cell viability. Using established glaucoma-related in vivo models of ocular hypertension (OHT) and partial optic nerve transection (pONT), topical application of CN twice-daily for three weeks significantly reduced retinal ganglion cell loss compared to controls. Collectively, these results suggest that our novel topical CN formulation has potential as an effective neuroprotective therapy in glaucoma and other eye diseases with neuronal pathology

Bayesian Parameter Estimation for Latent Markov Random Fields and Social Networks

Undirected graphical models are widely used in statistics, physics and machine vision. However Bayesian parameter estimation for undirected models is extremely challenging, since evaluation of the posterior typically involves the calculation of an intractable normalising constant. This problem has received much attention, but very little of this has focussed on the important practical case where the data consists of noisy or incomplete observations of the underlying hidden structure. This paper specifically addresses this problem, comparing two alternative methodologies. In the first of these approaches particle Markov chain Monte Carlo (Andrieu et al., 2010) is used to efficiently explore the parameter space, combined with the exchange algorithm (Murray et al., 2006) for avoiding the calculation of the intractable normalising constant (a proof showing that this combination targets the correct distribution in found in a supplementary appendix online). This approach is compared with approximate Bayesian computation (Pritchard et al., 1999). Applications to estimating the parameters of Ising models and exponential random graphs from noisy data are presented. Each algorithm used in the paper targets an approximation to the true posterior due to the use of MCMC to simulate from the latent graphical model, in lieu of being able to do this exactly in general. The supplementary appendix also describes the nature of the resulting approximation.Comment: 26 pages, 2 figures, accepted in Journal of Computational and Graphical Statistics (http://www.amstat.org/publications/jcgs.cfm

Extra-human epidemiology of Acinetobacter baumannii in Lebanon

Presence of Acinetobacter baumannii outside hospitals is still a controversial issue. The objective of our study was to explore the extra hospital epidemiology of A. baumannii in Lebanon. From February 2012 to October 2013, a total of 73 water samples, 51 soil samples, 37 raw cow milk samples, 50 cow meat samples, 7 raw cheese samples and 379 animal samples were analysed by cultural methods for the presence of A. baumannii. Species identification was performed by rpoB gene sequencing. Antibiotic susceptibility was investigated and A. baumannii population was studied by two genotyping approaches: Multilocus Sequence Typing (MLST) and blaOXA-51 Sequence-Based Typing (blaOXA-51 SBT). A. baumannii was detected in 6.9% of water samples, 2.7% of milk samples, 8.0% of meat samples, 14.3% of cheese samples and 7.7% of animal samples. All isolates showed a susceptible phenotype against most of the antibiotics tested and lacked carbapenemase encoding genes except one that harboured a blaOXA-143 gene. MLST analysis revealed the presence of 36 sequence types (ST), among them 24 were novel ST(s), reported for the first time in this study. blaOXA-51 SBT showed the presence of 34 variants, among them 21 were novel and all isolated from animal origin. Finally, 30 isolates had new partial rpoB sequences and were considered as putative new Acinetobacter species. In conclusion, animals can be a potential reservoir for A. baumannii and the dissemination of new emerging carbapenemases. The role of novel identified animal clones in community-acquired infections should be investigated

Current molecular methods in epidemiological typing of Acinetobacter baumannii

International audienc

Genomic history of the seventh pandemic of cholera in Africa.

The seventh cholera pandemic has heavily affected Africa, although the origin and continental spread of the disease remain undefined. We used genomic data from 1070 Vibrio cholerae O1 isolates, across 45 African countries and over a 49-year period, to show that past epidemics were attributable to a single expanded lineage. This lineage was introduced at least 11 times since 1970, into two main regions, West Africa and East/Southern Africa, causing epidemics that lasted up to 28 years. The last five introductions into Africa, all from Asia, involved multidrug-resistant sublineages that replaced antibiotic-susceptible sublineages after 2000. This phylogenetic framework describes the periodicity of lineage introduction and the stable routes of cholera spread, which should inform the rational design of control measures for cholera in Africa