Human pathogenic streptococcal proteomics and vaccine development

Gram-positive streptococci are non-motile, chain-forming bacteria commonly found in the normal oral and bowel flora of warm-blooded animals. Over the past decade, a proteomic approach combining 2-DE and MS has been used to systematically map the cellular, surface-associated and secreted proteins of human pathogenic streptococcal species. The public availability of complete streptococcal genomic sequences and the amalgamation of proteomic, genomic and bioinformatic technologies have recently facilitated the identification of novel streptococcal vaccine candidate antigens and therapeutic agents. The objective of this review is to examine the constituents of the streptococcal cell wall and secreted proteome, the mechanisms of transport of surface and secreted proteins, and describe the current methodologies employed for the identification of novel surface-displayed proteins and potential vaccine antigens.     

Experimental technique using FTIR to estimate IR optical properties at variable temperatures: application to PMDA-ODA polyimide thin films from 100 to 380 degrees C

An experimental technique is presented to measure reflectance at high sample temperature with respect to room temperature in the infrared using Fourier transform infrared fitted with a reflectometer. Sample temperature artifacts are accounted for by sequential measurements taken with the lamp source on and with the lamp source off. The sequential measurements are shown mathematically to correct for the modulation of sample and detector thermal emissions. Further, the technique is applied to a polyimide (PMDA-ODA) film on a layer of gold deposited on a thermally oxidized Si wafer. It is shown that the optical properties (index of refraction and extinction coefficient) remain relatively constant with temperature (from room temperature to 380 degrees C) in the 4000-6000 cm(-1) spectral region. The significant changes that occur with temperature are the change in thickness of the film and also the spectral properties in the 2000-4000 cm(-1) region. Also, by using a Lorentz oscillator model, it is shown that this method is able to discern that spectral features corresponding to the OH stretching bands at 3630 and 3470 cm(-1) show significant variation with increasing temperature.     

Solving surface structures from normal incidence X-ray standing wave data

A program is provided to determine structural parameters of atoms in or adsorbed on surfaces by refinement of atomistic models towards experimentally determined data generated by the normal incidence X-ray standing wave (NIXSW) technique. The method employs a combination of Differential Evolution Genetic Algorithms and Steepest Descent Line Minimisations to provide a fast, reliable and user friendly tool for experimentalists to interpret complex multidimensional NIXSW data sets.

Program summary

Program title: NIXSW Planewave SolverCatalogue identifier: ADZE_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADZE_v1_0.htmlProgram obtainable from: CPC Program Library, Queen's University, Belfast, N. IrelandLicensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.htmlNo. of lines in distributed program, including test data, etc.: 16 874No. of bytes in distributed program, including test data, etc.: 1 631 874Distribution format: tar.gzProgramming language: Borland C++ Builder 5Computer: Any Windows CompatibleOperating system: Windows 2000 and XPRAM: <10 MBClassification: 7.4Nature of problem: Using NIXSW experimental data to calculate atomic positions of adsorbates.Restrictions: Data from substrates must have cubic, tetragonal or orthorhombic crystal structures i.e. with 90° between conventional cell axes.Running time: Seconds-minutes dependant on the number of plane waves and the number of atomic sites.     

Context learning in the rodent hippocampus

We present a Bayesian statistical theory of context learning in the rodent hippocampus. While context is often defined in an experimental setting in relation to specific background cues or task demands, we advance a single, more general notion of context that suffices for a variety of learning phenomena. Specifically, a context is defined as a statistically stationary distribution of experiences, and context learning is defined as the problem of how to form contexts out of groups of experiences that cluster together in time. The challenge of context learning is solving the model selection problem: How many contexts make up the rodent's world? Solving this problem requires balancing two opposing goals: minimize the variability of the distribution of experiences within a context and minimize the likelihood of transitioning between contexts. The theory provides an understanding of why hippocampal place cell remapping sometimes develops gradually over many days of experience and why even consistent landmark differences may need to be relearned after other environmental changes. The theory provides an explanation for progressive performance improvements in serial reversal learning, based on a clear dissociation between the incremental process of context learning and the relatively abrupt context selection process. The impact of partial reinforcement on reversal learning is also addressed. Finally, the theory explains why alternating sequence learning does not consistently result in unique context-dependent sequence representations in hippocampus.     

On codes defined by bio-operations

We consider the classes of ⊕$\oplus$-codes and ⊗$\otimes$-codes, which are superclasses of outfix and hyper-codes, respectively. These restrictions are based on the synchronized insertion operation, which serves as a model for the gene rearrangement function in certain unicellular organisms. We investigate the classes of ⊕$\oplus$-codes and ⊗$\otimes$-codes from a theoretical perspective, examine their relationships with traditional code classes and consider related decidability problems.     

On the removal of shadows from images

This paper is concerned with the derivation of a progression of shadow-free image representations. First, we show that adopting certain assumptions about lights and cameras leads to a 1D, gray-scale image representation which is illuminant invariant at each image pixel. We show that as a consequence, images represented in this form are shadow-free. We then extend this 1D representation to an equivalent 2D, chromaticity representation. We show that in this 2D representation, it is possible to relight all the image pixels in the same way, effectively deriving a 2D image representation which is additionally shadow-free. Finally, we show how to recover a 3D, full color shadow-free image representation by first (with the help of the 2D representation) identifying shadow edges. We then remove shadow edges from the edge-map of the original image by edge in-painting and we propose a method to reintegrate this thresholded edge map, thus deriving the sought-after 3D shadow-free image.     

Organized knowledge sharing with book-centered Web sites: An architecture, implementation and analysis

For educators, the World Wide Web offers a valuable technology for knowledge sharing. It can complement more traditional approaches to knowledge sharing such as books and lectures. Here, we identify and differentiate three major approaches for Web-based knowledge sharing: course-centered sites, subject-centered sites, and book-centered sites. A rationale for book-centered sites, those developed to facilitate students’ and instructors’ efforts in courses that use the book, is advanced. We introduce an architecture of features that can guide developers of such sites. This is illustrated by a book-centered site implemented according to the architecture. Several sites for introductory business computing books are compared and contrasted in terms of the architecture, suggesting ways in which each can be extended. This revised version was published online in July 2006 with corrections to the Cover Date.     

Sequential architecture models for Prolog: A performance comparison

In this paper we investigate the relation between architectural support for Prolog and performance. We will show that partial support for tags does perform as well as full support, but it only reduces the execution time by approximately 10%. With respect to special addressing modes, auto address modification (post/pre increment, decrement on loads and stores) only yields a cycle reduction of approximately 6% and the introduction of a single shadow register set yields around 8%. Combining these optimizations, a performance gain of 20 to 25% can be achieved, depending on the memory system. Usingvliw techniques, which exploit instruction-level parallelism, the performance can be doubled, using three processing elements. Two processing elements already provide a significant speedup, but the use of four processing elements is not justified if we compare the gain in performance with the cost of the extra hardware. In general we observe only a small performance improvement (around 20%) when moving fromrisc to special-purposerisc architectures, an improvement which can also be achieved by applying advanced compiler technology, such as compiler optimization, optimizations forwam, and optimal scheduling techniques forvliw architectures. Unfortunately these hardware and software effects do not add up, as a better compiler reduces the effect of hardware support. Finally, the cycle time is essential for comparing the performance of different (micro)-architectures, but it is not always clear what the effects of the different tradeoffs are on the maximum achievable cycle time.