Identification, expression, and DNA sequence of the GDP-mannose biosynthesis genes encoded by the O7 rfb gene cluster of strain VW187 (Escherichia coli O7:K1)

The O7-specific lipopolysaccharide (LPS) in strains of Escherichia coli consists of a repeating unit made of galactose, mannose, rhamnose, 4-acetamido-2,6-dideoxyglucose, and N-acetylglucosamine. We have recently cloned and characterized genetically the O7-specific LPS biosynthesis region (rfbEcO7) of the E. coli O7:K1 strain VW187 (C. L. Marolda, J. Welsh, L. Dafoe, and M. A. Valvano, J. Bacteriol. 172:3590-3599, 1990). In this study, we localized the gnd gene encoding gluconate-6-phosphate dehydrogenase at one end of the rfbEcO7 gene cluster and sequenced that end of the cluster. Three open reading frames (ORF) encoding polypeptides of 275, 464, and 453 amino acids were identified upstream of gndEcO7, all transcribed toward the gnd gene. ORF275 had 45% similarity at the protein level with ORF16.5, which occupies a similar position in the Salmonella enterica LT2 rfb region, and presumably encodes a nucleotide sugar transferase. The polypeptides encoded by ORFs 464 and 453 were expressed under the control of the ptac promoter and visualized in Coomassie blue-stained sodium dodecyl sulfate-polyacrylamide gels and by maxicell analysis. ORF464 expressed GDP-mannose pyrophosphorylase and ORF453 encoded a phosphomannomutase, the enzymes for the biosynthesis pathway of GDP-mannose, one of the nucleotide sugar precursors for the formation of the O7 repeating unit. They were designated rfbMEcO7 and rfbKEcO7, respectively. The RfbMEcO7 polypeptide was homologous to the corresponding protein in S. enterica LT2, XanB of Xanthomonas campestris, and AlgA of Pseudomonas aeruginosa, all GDP-mannose pyrophosphorylases. RfbKEcO7 was very similar to CpsG of S. enterica LT2, an enzyme presumably involved in the biosynthesis of the capsular polysaccharide colanic acid, but quite different from the corresponding RfbK protein of S. enterica LT2.

Core-based Methodology: An Automated Approach for Implementing a Complete System From Algorithms to a Heterogeneous Network Including FPGAs

In this paper, we present a methodology for implementing a complete Digital Signal Processing (DSP) system onto a heterogeneous network including Field Programmable Gate Arrays (FPGAs) automatically. The methodology aims to allow design refinement and real time verification at the system level. The DSP application is constructed in the form of a Data Flow Graph (DFG) which provides an entry point to the methodology. The netlist for parts that are mapped onto the FPGA(s) together with the corresponding software and hardware Application Protocol Interface (API) are also generated. Using a set of case studies, we demonstrate that the design and development time can be significantly reduced using the methodology developed.

Semiring induced valuation algebras: Exact and approximate local computation algorithms

Local computation in join trees or acyclic hypertrees has been shown to be linked to a particular algebraic structure, called valuation algebra.There are many models of this algebraic structure ranging from probability theory to numerical analysis, relational databases and various classical and non-classical logics. It turns out that many interesting models of valuation algebras may be derived from semiring valued mappings. In this paper we study how valuation algebras are induced by semirings and how the structure of the valuation algebra is related to the algebraic structure of the semiring. In particular, c-semirings with idempotent multiplication induce idempotent valuation algebras and therefore permit particularly efficient architectures for local computation. Also important are semirings whose multiplicative semigroup is embedded in a union of groups. They induce valuation algebras with a partially defined division. For these valuation algebras, the well-known architectures for Bayesian networks apply. We also extend the general computational framework to allow derivation of bounds and approximations, for when exact computation is not feasible.

Effect of a multifaceted intervention on adherence to hand hygiene among healthcare workers:A cluster-randomized trial

OBJECTIVES. Adherence to hand hygiene among healthcare workers (HCWs) is widely believed to be a key factor in reducing the spread of healthcare-associated infection. The objective of this study was to evaluate the impact of a multifaceted intervention to increase rates of adherence to hand hygiene among HCWs and to assess the effect on the incidence of hospital-acquired methicillin-resistant Staphylococcus aureus (MRSA) colonization. DESIGN. Cluster-randomized controlled trial. SETTING. Thirty hospital units in 3 tertiary care hospitals in Hamilton, Ontario, Canada. INTERVENTION. After a 3-month baseline period of data collection, 15 units were randomly assigned to the intervention arm (with performance feedback, small-group teaching seminars, and posters) and 15 units to usual practice. Hand hygiene was observed during randomly selected 15-minute periods on each unit, and the incidence of MRSA colonization was measured using weekly surveillance specimens from June 2007 through May 2008. RESULTS. We found that 3,812 (48.2%) of 7,901 opportunities for hand hygiene in the intervention group resulted in adherence, compared with 3,205 (42.6%) of 7,526 opportunities in the control group (P <.001; independent t test). There was no reduction in the incidence of hospital-acquired MRSA colonization in the intervention group. CONCLUSION. Among HCWs in Ontario tertiary care hospitals, the rate of adherence to hand hygiene had a statistically significant increase of 6% with a multifaceted intervention, but the incidence of MRSA colonization was not reduced.

Do obesity and sleep problems cluster in the workplace?:A multivariate, multilevel study

OBJECTIVES: The aim of this study was to examine the co-occurrence of obesity and sleep problems among employees and workplaces. METHODS: We obtained data from 39 873 men and women working in 3040 workplaces in 2000-2002 (the Finnish Public Sector Study). Individual- and workplace-level characteristics were considered as correlates of obesity and sleep problems, which were modelled simultaneously using a multivariate, multilevel approach. RESULTS: Of the participants, 11% were obese and 23% reported sleep problems. We found a correlation between obesity and sleep problems at both the individual [correlation coefficient 0.048, covariance 0.047, standard error (SE) 0.005) and workplace (correlation coefficient 0.619, covariance 0.068, SE 0.011) level. The latter, but not the former, correlation remained after adjustment for individual- and workplace-level confounders, such as age, sex, socioeconomic status, shift work, alcohol consumption, job strain, and proportion of temporary employees and manual workers at the workplace. CONCLUSIONS: Obese employees and those with sleep problems tend to cluster in the same workplaces, suggesting that, in addition to targeting individuals at risk, interventions to reduce obesity and sleep problems might benefit from identifying "risky" workplaces.

Algorithms and architectures for high performance recursive filtering

Recently, a number of most significant digit (msd) first bit parallel multipliers for recursive filtering have been reported. However, the design approach which has been used has, in general, been heuristic and consequently, optimality has not always been assured. In this paper, msd first multiply accumulate algorithms are described and important relationships governing the dependencies between latency, number representations, etc are derived. A more systematic approach to designing recursive filters is illustrated by applying the algorithms and associated relationships to the design of cascadable modules for high sample rate IIR filtering and wave digital filtering.

Fast VLSI algorithms for division and square root

Real time digital signal processing demands high performance implementations of division and square root. This can only be achieved by the design of fast and efficient arithmetic algorithms which address practical VLSI architectural design issues. In this paper, new algorithms for division and square root are described. The new schemes are based on pre-scaling the operands and modifying the classical SRT method such that the result digits and the remainders are computed concurrently and the computations in adjacent rows are overlapped. Consequently, their performance exceeds that of the SRT methods. The hardware cost for higher radices is considerably more than that of the SRT methods but for many applications, this is not prohibitive. A system of equations is presented which enables both an analysis of the method for any radix and the parameters of implementations to be easily determined. This is illustrated for the case of radix 2 and radix 4. In addition, a highly regular array architecture combining the division and square root method is described. © 1994 Kluwer Academic Publishers.

Rapid silicon design of discrete orthonormal wavelet transforms based algorithms

A methodology has been developed which allows a non-specialist to rapidly design silicon wavelet transform cores for a variety of specifications. The cores include both forward and inverse orthonormal wavelet transforms. This methodology is based on efficient, modular and scaleable architectures utilising time-interleaved coefficients for the wavelet transform filters. The cores are parameterized in terms of wavelet type and data and coefficient word lengths. The designs have been captured in VHDL and are hence portable across a range of silicon foundries as well as FPGA and PLD implementations.

New algorithms and VLSI architectures for SRT division and square root

In real time digital signal processing, high performance modules for division and square root are essential if many powerful algorithms are to be implemented. In this paper, a new radix 2 algorithms for SRT division and square root are developed. For these new schemes, the result digits and the residuals are computed concurrently and the computations in adjacent rows are overlapped. Consequently, their performance should exceed that of the radix 2 SRT methods. VLSI array architectures to implement the new division and square root schemes are also presented.

Predicting low-velocity impact damage on a stiffened composite panel

An intralaminar damage model, based on a continuum damage mechanics approach, is presented to model the damage mechanisms occurring in carbon fibre composite structures incorporating fibre tensile and compressive breakage, matrix tensile and compressive fracture, and shear failure. The damage model, together with interface elements for capturing interlaminar failure, is implemented in a finite element package and used in a detailed finite element model to simulate the response of a stiffened composite panel to low-velocity impact. Contact algorithms and friction between delaminated plies were included, to better simulate the impact event. Analyses were executed on a high performance computer (HPC) cluster to reduce the actual time required for this detailed numerical analysis. Numerical results relating to the various observed interlaminar damage mechanisms, delamination initiation and propagation, as well as the model’s ability to capture post-impact permanent indentation in the panel are discussed. Very good agreement was achieved with experimentally obtained data of energy absorbed and impactor force versus time. The extent of damage predicted around the impact site also corresponded well with the damage detected by non destructive evaluation of the tested panel.

On the application of genetic algorithms for optimising composites against impact loading

A genetic algorithm (GA) was adopted to optimise the response of a composite laminate subject to impact. Two different impact scenarios are presented: low-velocity impact of a slender laminated strip and high-velocity impact of a rectangular plate by a spherical impactor. In these cases, the GA's objective was to, respectively, minimise the peak deflection and minimise penetration by varying the ply angles.

The GA was coupled to a commercial finite-element (FE) package LS DYNA to perform the impact analyses. A comparison with a commercial optimisation package, LS OPT, was also made. The results showed that the GA was a robust, capable optimisation tool that produced near optimal designs, and performed well with respect to LS OPT for the more complex high-velocity impact scenario tested.

Implementation and testing of Lanczos-based algorithms for Random-Phase Approximation eigenproblems

The treatment of the Random-Phase Approximation Hamiltonians, encountered in different frameworks, like time-dependent density functional theory or Bethe-Salpeter equation, is complicated by their non-Hermicity. Compared to their Hermitian Hamiltonian counterparts, computational methods for the treatment of non-Hermitian Hamiltonians are often less efficient and less stable, sometimes leading to the breakdown of the method. Recently [Gruning et al. Nano Lett. 8 (2009) 28201, we have identified that such Hamiltonians are usually pseudo-Hermitian. Exploiting this property, we have implemented an algorithm of the Lanczos type for Random-Phase Approximation Hamiltonians that benefits from the same stability and computational load as its Hermitian counterpart, and applied it to the study of the optical response of carbon nanotubes. We present here the related theoretical grounds and technical details, and study the performance of the algorithm for the calculation of the optical absorption of a molecule within the Bethe-Salpeter equation framework. (C) 2011 Elsevier B.V. All rights reserved.

Characterization and biological role of the O-polysaccharide gene cluster of Yersinia enterocolitica serotype O:9

Yersinia enterocolitica serotype O:9 is a gram-negative enteropathogen that infects animals and humans. The role of lipopolysaccharide (LPS) in Y. enterocolitica O:9 pathogenesis, however, remains unclear. The O:9 LPS consists of lipid A to which is linked the inner core oligosaccharide, serving as an attachment site for both the outer core (OC) hexasaccharide and the O-polysaccharide (OPS; a homopolymer of N-formylperosamine). In this work, we cloned the OPS gene cluster of O:9 and identified 12 genes organized into four operons upstream of the gnd gene. Ten genes were predicted to encode glycosyltransferases, the ATP-binding cassette polysaccharide translocators, or enzymes required for the biosynthesis of GDP-N-formylperosamine. The two remaining genes within the OPS gene cluster, galF and galU, were not ascribed a clear function in OPS biosynthesis; however, the latter gene appeared to be essential for O:9. The biological functions of O:9 OPS and OC were studied using isogenic mutants lacking one or both of these LPS parts. We showed that OPS and OC confer resistance to human complement and polymyxin B; the OPS effect on polymyxin B resistance could be observed only in the absence of OC.