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

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

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

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,

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

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

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

Monitoring the accumulation and dissipation of the photosensitizer protoporphyrin IX during standard dermatological methyl-aminolevulinate photodynamic therapy utilizing non-invasive fluorescence imaging and quantification

Author's post-print is subject to a Creative Commons Attribution Non-Commercial No Derivatives LicenseBACKGROUND: Dermatological methyl-aminolevulinate photodynamic therapy (MAL-PDT) is utilized to successfully treat dermatological conditions. This study monitored fluorescence changes attributed to the accumulation and destruction of the photosensitizer, protoporphyrin IX (PpIX), at several different stages during the first and second treatments of clinical dermatological MAL-PDT. METHODS: A commercially available, non-invasive, fluorescence imaging system (Dyaderm, Biocam, Germany) was utilized to monitor fluorescence changes during the first and second MAL-PDT treatments in seventy-five lesions. RESULTS: The clinical data indicated statistically significant increases in fluorescence within lesions following the application of MAL for both treatments (P<0.001 and P<0.01 respectively) and subsequent statistically significant decreases in fluorescence within the lesions following light irradiation for both treatments (P<0.001 and P<0.01 respectively) whilst normal skin fluorescence remained unaltered. Lesions receiving a second treatment accumulated and dissipated significantly less PpIX (P<0.05) than during the first treatment. No significant differences were noted in PpIX accumulation or dissipation during MAL-PDT when gender, age, lesion type and lesion surface area were considered. CONCLUSIONS: It can therefore be concluded that PpIX fluorescence imaging can be used in real-time to assess PpIX levels during dermatological PDT. Similar observations were recorded from the three currently licensed indications indicating that the standard 'one size fits all' protocol currently employed appears to allow adequate PpIX accumulation, which is subsequently fully utilized during light irradiation regardless of patient age, gender or lesion surface area

The relationship between protoporphyrin IX photobleaching during real-time dermatological methyl-aminolevulinate photodynamic therapy (MAL-PDT) and subsequent clinical outcome.

Journal Article"This is the peer reviewed version of the following article: Lasers in Surgery and Medicine 42:613–619 (2010), which has been published in final form at http://onlinelibrary.wiley.com/doi/10.1002/lsm.20943/pdf. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-Archiving."BACKGROUND AND OBJECTIVE: The relationship between protoporphyrin IX (PpIX) photobleaching and cellular damage during aminolevulinic (ALA) photodynamic therapy (PDT) has been studied at the cellular level. This study assessed the capability of a non-invasive fluorescence imaging system (Dyaderm, Biocam, Germany), to monitor changes in PpIX during real time methyl-aminolevulinate (MAL) PDT in dermatological lesions, and thus to act as a predictive tool in terms of observed clinical outcome post-treatment. MATERIALS AND METHODS: Patients attending Royal Cornwall Hospital (Truro, UK) for MAL-PDT to licensed lesions (actinic keratosis, Bowen's disease, and basal cell carcinoma) were monitored using the pre-validated non-invasive fluorescence imaging system. Patients were imaged at three distinct time points: prior to the application of MAL, after the 3 hours of MAL application and immediately following light irradiation. The fluorescence intensity of the images were analysed with image analysis software and the percentage change in fluorescence during light irradiation was related to the clinical outcome observed 3 months following treatment. In total 100 patients underwent at least one session of MAL-PDT. RESULTS: Significantly higher levels of change in PpIX fluorescence during light irradiation (P0.500) was observed in the total levels of PpIX recorded after MAL application in patients undergoing partial and complete clearance at 3 months. CONCLUSIONS: PpIX photobleaching is indicative of the level of cellular damage PDT treatment will induce and therefore the clinical outcome expected within patients. This study indicated the potential of the commercially available fluorescence imaging system investigated to predict treatment success at the time of light irradiation and in the future it may be possible to employ it to individualise treatment parameters to improve dermatological PDT efficacy/outcome