A Reverse Hex Solver

We present Solrex,an automated solver for the game of Reverse Hex.Reverse Hex, also known as Rex, or Misere Hex, is the variant of the game of Hex in which the player who joins her two sides loses the game. Solrex performs a mini-max search of the state space using Scalable Parallel Depth First Proof Number Search, enhanced by the pruning of inferior moves and the early detection of certain winning strategies. Solrex is implemented on the same code base as the Hex program Solver, and can solve arbitrary positions on board sizes up to 6x6, with the hardest position taking less than four hours on four threads.Comment: Presented at Computers and Games 2016 Leiden, International Conference on Computers and Games. Springer International Publishing, 201

Modeling of residual stresses in structural stainless steel sections

The influence of residual stresses on structural members is to cause premature yielding and loss of stiffness, often leading to deterioration of load carrying capacity. Knowledge of their magnitude and distribution is therefore important for both structural design and finite-element simulations, and hence extensive studies have been performed on structural carbon steel components. With greater emphasis now being placed on durability and reducing consumption of resources, the use of stainless steel in construction is growing, heralding the need for a more precise understanding of its structural response. Stainless steel exhibits differing physical and thermal properties from carbon steel, both of which influence the formation of residual stresses, and it cannot simply be assumed that residual stress models for carbon steel are also appropriate for stainless steel. This paper examines all existing data on residual stresses in stainless steel sections, including data generated from a recent experimental program carried out at Imperial College, London and summarized herein. The collated residual stress data have been used to develop models for predicting the magnitude and distribution of residual stresses in press braked, cold rolled, hot rolled, and fabricated stainless steel structural sections

Life-cycle costing of metallic structures

Structural material selection has traditionally been based on Initial material cost. However, growing pressure on the construction industry to consider the longer-term financial and environmental implications of projects is encouraging a more holistic view. Thus, materials with higher initial costs, but which offer cost savings over the life cycle of a structure, are gaining increasing recognition. The life-cycle costs of structures of two such metallic materials, namely aluminium alloy and stainless steel, are compared with those of ordinary structural carbon steel in the present study. Two structural applications - a typical office building and a bridge - are analysed, while offshore applications are briefly discussed. The ratio of initial material cost per tonne was assumed to be 1.0:2.5:4.0 (carbon steel:aluminium alloy:stainless steel). Following a preliminary structural design to current European design standards taking due account of the material densities and structural properties (principally strength and stiffness), it was found that on an initial cost basis, carbon steel offers the most competitive solution for both the building and the bridge. However, considering the additional life-cycle costs including maintenance costs, end-of-life costs and the residual value of the structure (appropriately discounted to present values), the results indicate that carbon steel offers the most competitive life-cycle solution for the office building but delivers the most expensive life-cycle solution for the bridge. Overall, it is concluded that on a whole-life basis aluminium alloy and stainless steel may offer more competitive solutions than carbon steel for bridges and exposed areas of building structures

Anyons in a weakly interacting system

We describe a theoretical proposal for a system whose excitations are anyons with the exchange phase pi/4 and charge -e/2, but, remarkably, can be built by filling a set of single-particle states of essentially noninteracting electrons. The system consists of an artificially structured type-II superconducting film adjacent to a 2D electron gas in the integer quantum Hall regime with unit filling fraction. The proposal rests on the observation that a vacancy in an otherwise periodic vortex lattice in the superconductor creates a bound state in the 2DEG with total charge -e/2. A composite of this fractionally charged hole and the missing flux due to the vacancy behaves as an anyon. The proposed setup allows for manipulation of these anyons and could prove useful in various schemes for fault-tolerant topological quantum computation.Comment: 7 pages with 3 figures. For related work and info visit http://www.physics.ubc.ca/~fran

Who Watches the Watchmen? An Appraisal of Benchmarks for Multiple Sequence Alignment

Multiple sequence alignment (MSA) is a fundamental and ubiquitous technique in bioinformatics used to infer related residues among biological sequences. Thus alignment accuracy is crucial to a vast range of analyses, often in ways difficult to assess in those analyses. To compare the performance of different aligners and help detect systematic errors in alignments, a number of benchmarking strategies have been pursued. Here we present an overview of the main strategies--based on simulation, consistency, protein structure, and phylogeny--and discuss their different advantages and associated risks. We outline a set of desirable characteristics for effective benchmarking, and evaluate each strategy in light of them. We conclude that there is currently no universally applicable means of benchmarking MSA, and that developers and users of alignment tools should base their choice of benchmark depending on the context of application--with a keen awareness of the assumptions underlying each benchmarking strategy.Comment: Revie

Fine-grained parallel RNAalifold algorithm for RNA secondary structure prediction on FPGA

<p>Abstract</p> <p>Background</p> <p>In the field of RNA secondary structure prediction, the RNAalifold algorithm is one of the most popular methods using free energy minimization. However, general-purpose computers including parallel computers or multi-core computers exhibit parallel efficiency of no more than 50%. Field Programmable Gate-Array (FPGA) chips provide a new approach to accelerate RNAalifold by exploiting fine-grained custom design.</p> <p>Results</p> <p>RNAalifold shows complicated data dependences, in which the dependence distance is variable, and the dependence direction is also across two dimensions. We propose a systolic array structure including one master Processing Element (PE) and multiple slave PEs for fine grain hardware implementation on FPGA. We exploit data reuse schemes to reduce the need to load energy matrices from external memory. We also propose several methods to reduce energy table parameter size by 80%.</p> <p>Conclusion</p> <p>To our knowledge, our implementation with 16 PEs is the only FPGA accelerator implementing the complete RNAalifold algorithm. The experimental results show a factor of 12.2 speedup over the RNAalifold (<it>ViennaPackage </it>– 1.6.5) software for a group of aligned RNA sequences with 2981-residue running on a Personal Computer (PC) platform with Pentium 4 2.6 GHz CPU.</p

Quantitative model for inferring dynamic regulation of the tumour suppressor gene p53

Background: The availability of various "omics" datasets creates a prospect of performing the study of genome-wide genetic regulatory networks. However, one of the major challenges of using mathematical models to infer genetic regulation from microarray datasets is the lack of information for protein concentrations and activities. Most of the previous researches were based on an assumption that the mRNA levels of a gene are consistent with its protein activities, though it is not always the case. Therefore, a more sophisticated modelling framework together with the corresponding inference methods is needed to accurately estimate genetic regulation from "omics" datasets. Results: This work developed a novel approach, which is based on a nonlinear mathematical model, to infer genetic regulation from microarray gene expression data. By using the p53 network as a test system, we used the nonlinear model to estimate the activities of transcription factor (TF) p53 from the expression levels of its target genes, and to identify the activation/inhibition status of p53 to its target genes. The predicted top 317 putative p53 target genes were supported by DNA sequence analysis. A comparison between our prediction and the other published predictions of p53 targets suggests that most of putative p53 targets may share a common depleted or enriched sequence signal on their upstream non-coding region. Conclusions: The proposed quantitative model can not only be used to infer the regulatory relationship between TF and its down-stream genes, but also be applied to estimate the protein activities of TF from the expression levels of its target genes

Applied Interventions in the Prevention and Treatment of Obesity Through the Research of Professor Jane Wardle

Purpose of Review Obesity presents a challenge for practitioners, policy makers, researchers and for those with obesity themselves. This review focuses on psychological approaches to its management and prevention in children and adults. Recent Findings Through exploring the work of the late Professor Jane Wardle, we look at the earliest behavioural treatment approaches and how psychological theory has been used to develop more contemporary approaches, for example incorporating genetic feedback and habit formation theory into interventions. We also explore how Jane has challenged thinking about the causal pathways of obesity in relation to eating behaviour. Beyond academic work, Jane was an advocate of developing interventions which had real-world applications. Summary Therefore, we discuss how she not only developed new interventions but also made these widely available and the charity that she established

Cone Photoreceptor Structure in Patients With X-Linked Cone Dysfunction and Red-Green Color Vision Deficiency

Purpose: Mutations in the coding sequence of the L and M opsin genes are often associated with X-linked cone dysfunction (such as Bornholm Eye Disease, BED), though the exact color vision phenotype associated with these disorders is variable. We examined individuals with L/M opsin gene mutations to clarify the link between color vision deficiency and cone dysfunction. Methods: We recruited 17 males for imaging. The thickness and integrity of the photoreceptor layers were evaluated using spectral-domain optical coherence tomography. Cone density was measured using high-resolution images of the cone mosaic obtained with adaptive optics scanning light ophthalmoscopy. The L/M opsin gene array was characterized in 16 subjects, including at least one subject from each family. Results: There were six subjects with the LVAVA haplotype encoded by exon 3, seven with LIAVA, two with the Cys203Arg mutation encoded by exon 4, and two with a novel insertion in exon 2. Foveal cone structure and retinal thickness was disrupted to a variable degree, even among related individuals with the same L/M array. Conclusions: Our findings provide a direct link between disruption of the cone mosaic and L/M opsin variants. We hypothesize that, in addition to large phenotypic differences between different L/M opsin variants, the ratio of expression of first versus downstream genes in the L/M array contributes to phenotypic diversity. While the L/M opsin mutations underlie the cone dysfunction in all of the subjects tested, the color vision defect can be caused either by the same mutation or a gene rearrangement at the same locus