Regulatory motif discovery using a population clustering evolutionary algorithm

This paper describes a novel evolutionary algorithm for regulatory motif discovery in DNA promoter sequences. The algorithm uses data clustering to logically distribute the evolving population across the search space. Mating then takes place within local regions of the population, promoting overall solution diversity and encouraging discovery of multiple solutions. Experiments using synthetic data sets have demonstrated the algorithm's capacity to find position frequency matrix models of known regulatory motifs in relatively long promoter sequences. These experiments have also shown the algorithm's ability to maintain diversity during search and discover multiple motifs within a single population. The utility of the algorithm for discovering motifs in real biological data is demonstrated by its ability to find meaningful motifs within muscle-specific regulatory sequences

The use of field-programmable gate arrays for the hardware acceleration of design automation tasks

This paper investigates the possibility of using Field-Programmable Gate Arrays (Fr’GAS) as reconfigurable co-processors for workstations to produce moderate speedups for most tasks in the design process, resulting in a worthwhile overall design process speedup at low cost and allowing algorithm upgrades with no hardware modification. The use of FPGAS as hardware accelerators is reviewed and then achievable speedups are predicted for logic simulation and VLSI design rule checking tasks for various FPGA co-processor arrangements

Estimating the Benefits of Water Quality Improvements in the Upper Narragansett Bay

An EPA-sponsored study of the benefits to Rhode Island residents of the water quality improvement in the Upper Narragansett Bay showed that the estimated annual costs ($2.9 million) exceeded the expected annual benefits ($2.0 million). That analysis evaluated only user benefits which were measured via expenditures; nonuser (intrinsic) benefits were not included. This study estimated the benefits to Rhode Island residents using the "Contingent Valuation" approach and responses from 435 residents to a 1985 survey about swimming and shellfishing. Aggregate annual benefits were estimated to be in the range of $30-60 million for "swimmable" and$30-70 million for "shellfishable" water quality, depending on the type of measure (mean or median) and survey format. Secondary objectives of the study were to test different versions of "willingness to pay" questions and compare mean and median values for measurement. Aside from payment vehicle bias, we found no evidence of serious bias.contingent valuation, pollution, water quality benefits, Environmental Economics and Policy, Resource /Energy Economics and Policy,

Image processing applications using a novel parallel computing machine based on reconfigurable logic

Zelig is a 32 physical node fine-grained computer employing field-programmable gate arrays. Its application to the high speed implementation of various image pre-processing operations (in particular binary morphology) is described together with typical speed-up result

Representation and use of chemistry in the global electronic age.

We present an overview of the current state of public semantic chemistry and propose new approaches at a strategic and a detailed level. We show by example how a model for a Chemical Semantic Web can be constructed using machine-processed data and information from journal articles.This manuscript addresses questions of robotic access to data and its automatic re-use, including the role of Open Access archival of data. This is a pre-refereed preprint allowed by the publisher's (Royal Soc. Chemistry) Green policy. The author's preferred manuscript is an HTML hyperdocument with ca. 20 links to images, some of which are JPEgs and some of which are SVG (scalable vector graphics) including animations. There are also links to molecules in CML, for which the Jmol viewer is recommended. We susgeest that readers who wish to see the full glory of the manuscript, download the Zipped version and unpack on their machine. We also supply a PDF and DOC (Word) version which obviously cannot show the animations, but which may be the best palce to start, particularly for those more interested in the text

Two \u3ci\u3eEntomophthora\u3c/i\u3e Species Associated with Disease Epizootics of the Alfalfa Weevil, \u3ci\u3eHypera Postica\u3c/i\u3e (Coleoptera: Curculionidae), in Ontario

Recent studies have shown that disease epizootics in Ontario populations of the alfalfa weevil, Hypera postica (Gyllenhal), are caused by a complex of two fungi

Evaluating tourism community preferences

A short online survey of Kingman Arizona residents included two approaches for determining the relative importance of social, cultural, environmental, and economic attributes to community quality of life. A simple multiattribute choice approach gave noticeably different results from a standard independent attribute ranking approach and lead researchers to recommend socially oriented tourism development projects over economically oriented ones

Hierarchical strategies for efficient fault recovery on the reconfigurable PAnDA device

A novel hierarchical fault-tolerance methodology for reconfigurable devices is presented. A bespoke multi-reconfigurable FPGA architecture, the programmable analogue and digital array (PAnDA), is introduced allowing fine-grained reconfiguration beyond any other FPGA architecture currently in existence. Fault blind circuit repair strategies, which require no specific information of the nature or location of faults, are developed, exploiting architectural features of PAnDA. Two fault recovery techniques, stochastic and deterministic strategies, are proposed and results of each, as well as a comparison of the two, are presented. Both approaches are based on creating algorithms performing fine-grained hierarchical partial reconfiguration on faulty circuits in order to repair them. While the stochastic approach provides insights into feasibility of the method, the deterministic approach aims to generate optimal repair strategies for generic faults induced into a specific circuit. It is shown that both techniques successfully repair the benchmark circuits used after random faults are induced in random circuit locations, and the deterministic strategies are shown to operate efficiently and effectively after optimisation for a specific use case. The methods are shown to be generally applicable to any circuit on PAnDA, and to be straightforwardly customisable for any FPGA fabric providing some regularity and symmetry in its structure

Tuning biexciton binding and anti-binding in core/shell quantum dots

We use a path integral quantum Monte Carlo method to simulate excitons and biexcitons in core shell nanocrystals with Type-I, II and quasi-Type II band alignments. Quantum Monte Carlo techniques allow for all quantum correlations to be included when determining the thermal ground state, thus producing accurate predictions of biexciton binding. These subtle quantum correlations are found to cause the biexciton to be binding with Type-I carrier localization and strongly anti-binding with Type-II carrier localization, in agreement with experiment for both core shell nanocrystals and dot in rod nanocrystal structures. Simple treatments based on perturbative approaches are shown to miss this important transition in the biexciton binding. Understanding these correlations offers prospects to engineer strong biexciton anti-binding which is crucial to the design of nanocrystals for single exciton lasing applications.Comment: 10 pages, 11 figure

Loss of strumpellin in the melanocytic lineage impairs the WASH Complex but does not affect coat colour

The five-subunit WASH complex generates actin networks that participate in endocytic trafficking, migration and invasion in various cell types. Loss of one of the two subunits WASH or strumpellin in mice is lethal, but little is known about their role in mammals in vivo. We explored the role of strumpellin, which has previously been linked to hereditary spastic paraplegia, in the mouse melanocytic lineage. Strumpellin knockout in melanocytes revealed abnormal endocytic vesicle morphology but no impairment of migration in vitro or in vivo and no change in coat colour. Unexpectedly, WASH and filamentous actin could still localize to vesicles in the absence of strumpellin, although the shape and size of vesicles was altered. Blue native PAGE revealed the presence of two distinct WASH complexes, even in strumpellin knockout cells, revealing that the WASH complex can assemble and localize to endocytic compartments in cells in the absence of strumpellin