A unified hardware/software runtime environment for FPGA-based reconfigurable computers using BORPH

Fulltext linkThis paper explores the design and implementation of BORPH, an operating system designed for FPGA-based reconfigurable computers. Hardware designs execute as normal UNIX processes under BORPH, having access to standard OS services, such as file system support. Hardware and software components of user designs may, therefore, run as communicating processes within BORPH's runtime environment. The familiar language independent UNIX kernel interface facilitates easy design reuse and rapid application development. To develop hardware designs, a Simulink-based design flow that integrates with BORPH is employed. Performances of BORPH on two on-chip systems implemented on a BEE2 platform are compared. © 2008 ACM.link_to_subscribed_fulltex

The 1.4-Å crystal structure of the S. pombe Pop2p deadenylase subunit unveils the configuration of an active enzyme

Deadenylation is the first and probably also rate-limiting step of controlled mRNA decay in eukaryotes and therefore central for the overall rate of gene expression. In yeast, the process is maintained by the mega-Dalton Ccr4-Not complex, of which both the Ccr4p and Pop2p subunits are 3′–5′ exonucleases potentially responsible for the deadenylation reaction. Here, we present the crystal structure of the Pop2p subunit from Schizosaccharomyces pombe determined to 1.4 Å resolution and show that the enzyme is a competent ribonuclease with a tunable specificity towards poly-A. In contrast to S. cerevisiae Pop2p, the S. pombe enzyme contains a fully conserved DEDDh active site, and the high resolution allows for a detailed analysis of its configuration, including divalent metal ion binding. Functional data further indicates that the identity of the ions in the active site can modulate both activity and specificity of the enzyme, and finally structural superposition of single nucleotides and poly-A oligonucleotides provide insight into the catalytic cycle of the protein

Haemorrhagic Colitis Associated with Enterohaemorrhagic \u3ci\u3eEscherichia coli\u3c/i\u3e O165:H25 Infection in a Yearling Feedlot Heifer

Introduction: Enterohaemorrhagic Escherichia coli (EHEC) cause haemorrhagic colitis and haemolytic uraemic syndrome in humans. Although EHEC infection typically results in haemorrhagic colitis in all ages of human patients, in cattle it is usually limited to 1- to 5-week-old nursing calves. Case Presentation: A 1-year-old feedlot beef heifer was moribund with neurological signs and bloody diarrhoea. At necropsy, the colonic mucosa contained multiple grossly visible haemorrhagic erosions, each measuring \u3c1 mm in diameter. Histologically, foci corresponding to the gross erosions had E. coli O165 antigen-positive bacterial rods adherent to the apical surfaces of degenerate and necrotic colonic mucosal epithelial cells in association with attaching and effacing lesions, and also within cytoplasmic vacuoles in some of these cells. An E. coli O165:H25 strain was isolated from the colonic mucosal tissue, and by microarray analysis was found to contain virulence genes corresponding to type III secretion system (T3SS) structure and regulation (cesD, cesT, escD, escF, escN/escV, escR, escT, ler, sepL, sepQ), T3SS effectors (espA, espB, espC, espD, espD, espF, espH, espJ, nleB, nleC, nleD, nleH, tir), serine proteases (eatA, espC, espP), Shiga toxin (stx2), EHEC-haemolysin (ehxA), and adhesins [intimin-ε (eae-ε), type 1 fimbria (fimA, fimB, fimH), type IV pili (pilA, pilB, pilC, pilM, pilP, pilQ) and non-fimbrial adhesin (efa1/lifA)]. Conclusion: To the best of our knowledge, this is the first report of disease in cattle associated with EHEC O165:H25 infection, the oldest bovine EHEC disease case with isolation of the pathogen and the first bovine case to demonstrate grossly evident, haemorrhagic, colonic mucosal erosions associated with EHEC infection

Haemorrhagic Colitis Associated with Enterohaemorrhagic \u3ci\u3eEscherichia coli\u3c/i\u3e O165:H25 Infection in a Yearling Feedlot Heifer

Introduction: Enterohaemorrhagic Escherichia coli (EHEC) cause haemorrhagic colitis and haemolytic uraemic syndrome in humans. Although EHEC infection typically results in haemorrhagic colitis in all ages of human patients, in cattle it is usually limited to 1- to 5-week-old nursing calves. Case Presentation: A 1-year-old feedlot beef heifer was moribund with neurological signs and bloody diarrhoea. At necropsy, the colonic mucosa contained multiple grossly visible haemorrhagic erosions, each measuring \u3c1 mm in diameter. Histologically, foci corresponding to the gross erosions had E. coli O165 antigen-positive bacterial rods adherent to the apical surfaces of degenerate and necrotic colonic mucosal epithelial cells in association with attaching and effacing lesions, and also within cytoplasmic vacuoles in some of these cells. An E. coli O165:H25 strain was isolated from the colonic mucosal tissue, and by microarray analysis was found to contain virulence genes corresponding to type III secretion system (T3SS) structure and regulation (cesD, cesT, escD, escF, escN/escV, escR, escT, ler, sepL, sepQ), T3SS effectors (espA, espB, espC, espD, espD, espF, espH, espJ, nleB, nleC, nleD, nleH, tir), serine proteases (eatA, espC, espP), Shiga toxin (stx2), EHEC-haemolysin (ehxA), and adhesins [intimin-ε (eae-ε), type 1 fimbria (fimA, fimB, fimH), type IV pili (pilA, pilB, pilC, pilM, pilP, pilQ) and non-fimbrial adhesin (efa1/lifA)]. Conclusion: To the best of our knowledge, this is the first report of disease in cattle associated with EHEC O165:H25 infection, the oldest bovine EHEC disease case with isolation of the pathogen and the first bovine case to demonstrate grossly evident, haemorrhagic, colonic mucosal erosions associated with EHEC infection

Variational Bayesian mixed-effects inference for classification studies

Multivariate classification algorithms are powerful tools for predicting cognitive or pathophysiological states from neuroimaging data. Assessing the utility of a classifier in application domains such as cognitive neuroscience, brain-computer interfaces, or clinical diagnostics necessitates inference on classification performance at more than one level, i.e., both in individual subjects and in the population from which these subjects were sampled. Such inference requires models that explicitly account for both fixed-effects (within-subjects) and random-effects (between-subjects) variance components. While models of this sort are standard in mass-univariate analyses of fMRI data, they have not yet received much attention in multivariate classification studies of neuroimaging data, presumably because of the high computational costs they entail. This paper extends a recently developed hierarchical model for mixed-effects inference in multivariate classification studies and introduces an efficient variational Bayes approach to inference. Using both synthetic and empirical fMRI data, we show that this approach is equally simple to use as, yet more powerful than, a conventional t-test on subject-specific sample accuracies, and computationally much more efficient than previous sampling algorithms and permutation tests. Our approach is independent of the type of underlying classifier and thus widely applicable. The present framework may help establish mixed-effects inference as a future standard for classification group analyses

Bayesian mixed-effects inference on classification performance in hierarchical data sets

Classification algorithms are frequently used on data with a natural hierarchical structure. For instance, classifiers are often trained and tested on trial-wise measurements, separately for each subject within a group. One important question is how classification outcomes observed in individual subjects can be generalized to the population from which the group was sampled. To address this question, this paper introduces novel statistical models that are guided by three desiderata. First, all models explicitly respect the hierarchical nature of the data, that is, they are mixed-effects models that simultaneously account for within-subjects (fixed-effects) and across-subjects (random-effects) variance components. Second, maximum-likelihood estimation is replaced by full Bayesian inference in order to enable natural regularization of the estimation problem and to afford conclusions in terms of posterior probability statements. Third, inference on classification accuracy is complemented by inference on the balanced accuracy, which avoids inflated accuracy estimates for imbalanced data sets. We introduce hierarchical models that satisfy these criteria and demonstrate their advantages over conventional methods usingMCMC implementations for model inversion and model selection on both synthetic and empirical data. We envisage that our approach will improve the sensitivity and validity of statistical inference in future hierarchical classification studies. © 2012

Novel statistical approaches for non-normal censored immunological data: analysis of cytokine and gene expression data

Background: For several immune-mediated diseases, immunological analysis will become more complex in the future with datasets in which cytokine and gene expression data play a major role. These data have certain characteristics that require sophisticated statistical analysis such as strategies for non-normal distribution and censoring. Additionally, complex and multiple immunological relationships need to be adjusted for potential confounding and interaction effects. Objective: We aimed to introduce and apply different methods for statistical analysis of non-normal censored cytokine and gene expression data. Furthermore, we assessed the performance and accuracy of a novel regression approach in order to allow adjusting for covariates and potential confounding. Methods: For non-normally distributed censored data traditional means such as the Kaplan-Meier method or the generalized Wilcoxon test are described. In order to adjust for covariates the novel approach named Tobit regression on ranks was introduced. Its performance and accuracy for analysis of non-normal censored cytokine/gene expression data was evaluated by a simulation study and a statistical experiment applying permutation and bootstrapping. Results: If adjustment for covariates is not necessary traditional statistical methods are adequate for non-normal censored data. Comparable with these and appropriate if additional adjustment is required, Tobit regression on ranks is a valid method. Its power, type-I error rate and accuracy were comparable to the classical Tobit regression. Conclusion: Non-normally distributed censored immunological data require appropriate statistical methods. Tobit regression on ranks meets these requirements and can be used for adjustment for covariates and potential confounding in large and complex immunological datasets

Mercury in waste in the European Union : sources, disposal methods and risks

http://www.elsevier.com/locate/issn/09213449Over the recent decades, there has been widespread concern regarding the toxic impact of mercury (Hg) in the ecosystem due to its mobility, volatility and potential for bioaccumulation. Hg in fish and the aquatic environment is also a great problem in the Nordic region of the EU1 (European Union). Hg is classified as a dangerous chemical in the countries of the EU. Hg in the regulation of waste is regarded as a dangerous substance which, when contained in waste, is one of the properties, leading to a classification of waste as hazardous. Estimation of the quantity of Hg in waste within the EU countries is an important task although still incomplete. In this present study, Hg in waste in the EU has been estimated at around 990 metric tonnes (t) (including coal combustion products, landfills, chlor-alkali waste and incinerator slag) for the year 1995, and it is suggested that if complete information was available for the 15 member states, the amount would be 2–4 times larger. During the 1990s there were 45 Hg cell chlorine facilities in the EU and the amount of Hg in chlorine (Cl2) was calculated at 95.2 t based on 14–17 gHg t−1 of Cl2 capacity. The waste from coal-fired power plants in the EU member states contained about 16.5 t of Hg, which was transferred to products for road construction, and other industrial uses or stored in landfills. This Hg can then be exchanged between the atmospheric, aquatic and terrestrial compartments. Hg is occasionally recovered from waste, but this is often discouraged for economic reasons. Recovery units are found, for example, in Germany, France, Austria, and Sweden. The total amount of secondary Hg recovered from waste is not known. Metallic Hg and Hg-bearing waste are exported and imported from the EU member states, except for export from Sweden, which is banned by national legislation. The use of Hg in lamps and batteries is declining, and the Nordic countries, Germany and Austria have stringent regulations on the use of amalgam and Hg thermometers. It is found that 18% of municipal solid waste generated in the EU is burnt in incinerators, in order to decrease the volume. 88 t of Hg enter into the landfills of the EU through waste and residues from waste incineration. Prevention of the generation of hazardous waste containing Hg is one of the most challenging tasks for the EU, with regard to sustainable waste management

Enzymatic and Electron Transfer Activities in Crystalline Protein Complexes

Enzymatic and electron transfer activities have been studied by polarized absorption spectroscopy in single crystals of both binary and ternary complexes of methylamine dehydrogenase (MADH) with its redox partners. Within the crystals, MADH oxidizes methylamine, and the electrons are passed from the reduced tryptophan tryptophylquinone (TTQ) cofactor to the copper of amicyanin and to the heme of cytochrome c551i via amicyanin. The equilibrium distribution of electrons among the cofactors, and the rate of heme reduction after reaction with substrate, are both dependent on pH. The presence of copper in the ternary complex is not absolutely required for electron transfer from TTQ to heme, but its presence greatly enhances the rate of electron flow to the heme