Microarray and proteomic analysis of the human alcoholic brain

The superior frontal cortex (SFC) is selectively damaged in chronic alcohol abuse, with localized neuronal loss and tissue atrophy. Regions such as motor cortex show little neuronal loss except in severe co-morbidity (liver cirrhosis or WKS). Altered gene expression was found in microarray comparisons of alcoholic and control SFC samples [1]. We used Western blots and proteomic analysis to identify the proteins that also show differential expression. Tissue was obtained at autopsy under informed, written consent from uncomplicated alcoholics and age- and sex-matched controls. Alcoholics had consumed 80 g ethanol/day chronically (often, 200 g/day for 20 y). Controls either abstained or were social drinkers ( 20 g/day). All subjects had pathological confirmation of liver and brain diagnosis; none had been polydrug abusers. Samples were homogenized in water and clarified by brief centrifugation (1000g, 3 min) before storage at –80°C. For proteomics the thawed suspensions were centrifuged (15000g, 50 min) to prepare soluble fractions. Aliquots were pooled from SFC samples from the 5 chronic alcoholics and 5 matched controls used in the previous microarray study [1]. 2-Dimensional electrophoresis was performed in triplicate using 18 cm format pH 4–7 and pH 6–11 immobilized pH gradients for firstdimension isoelectric focusing. Following second-dimension SDS-PAGE the proteins were fluorescently stained and the images collected by densitometry. 182 proteins differed by 2-fold between cases and controls. 141 showed lower expression in alcoholics, 33 higher, and 8 were new or had disappeared. To date 63 proteins have been identified using MALDI-MS and MS-MS. Western blots were performed on uncentrifuged individual samples from 76 subjects (controls, uncomplicated alcoholics and cirrhotic alcoholics). A common standard was run on every gel. After transfer, immunolabeling, and densitometry, the intensities of the unknown bands were compared to those of the standards. We focused on proteins from transcripts that showed clear differences in a series of microarray studies, classified into common sets including Regulators of G-protein Signaling and Myelin-associated proteins. The preponderantly lower level of differentially expressed proteins in alcoholics parallels the microarray mRNA analysis in the same samples. We found that mRNA and protein expression do not frequently correspond; this may help identify pathogenic processes acting at the level of transcription, translation, or post-translationally.

An inverse methodology for high frequency RF head coil design with pre-emphasized B1 field in MRI

An inverse methodology to assist in the design of radio-frequency (RF) head coils for high field MRI application is described in this work. Free space time-harmonic electromagnetic Green's functions and preemphasized B1 field are used to calculate the current density on the coil cylinder. With B1 field preemphasized and lowered in the middle of the RF transverse plane, the calculated current distribution can generate an internal magnetic field that can reduce the EM field/tissue interactions at high frequencies. The current distribution of a head coil operating at 4 T is calculated using inverse methodology with preemphasized B1 fields. FDTD is employed to calculate B1 field and signal intensity inside a homogenous cylindrical phantom and human head. A comparison with conventional RF birdcage coil is reported here and demonstrated that inverse-method designed coil with preemphasized B1 field can help in decreasing the notorious bright region caused by EM field/tissue interactions in the human head images at 4 T.

Transmitting focussed B1 field and SENSE reconstruction using an 8-element transceive torso phased array coil

In this work, a new design concept in chest imaging for MRI application is presented. A focused, 8-element transceive torso phased array coil is designed to investigate transmitting focused B1 field deep within the torso to enhance signal intensity and use in conjunction with SENSE reconstruction technique. Hybrid FDTD/MOM method is used to accurately predict the RF behavior inside the human torso. The simulation results reported herein demonstrate the feasibility of the design concept which shows that B1 field focusing with SENSE reconstruction is achievable, and the 8-element transceive torso phased array coil has the advantage to be used in transmit and receive mode for optimum and fast chest imaging.

Formalising behaviour trees with CSP

Behaviour Trees is a novel approach for requirements engineering. It advocates a graphical tree notation that is easy to use and to understand. Individual requirements axe modelled as single trees which later on are integrated into a model of the system as a whole. We develop a formal semantics for a subset of Behaviour Trees using CSP. This work, on one hand, provides tool support for Behaviour Trees. On the other hand, it builds a front-end to a subset of the CSP notation and gives CSP users a new modelling strategy which is well suited to the challenges of requirements engineering.

Mutation-based exploration of a method for verifying concurrent Java components

Summary form only given. The Java programming language supports concurrency. Concurrent programs are harder to verify than their sequential counterparts due to their inherent nondeterminism and a number of specific concurrency problems such as interference and deadlock. In previous work, we proposed a method for verifying concurrent Java components based on a mix of code inspection, static analysis tools, and the ConAn testing tool. The method was derived from an analysis of concurrency failures in Java components, but was not applied in practice. In this paper, we explore the method by applying it to an implementation of the well-known readers-writers problem and a number of mutants of that implementation. We only apply it to a single, well-known example, and so we do not attempt to draw any general conclusions about the applicability or effectiveness of the method. However, the exploration does point out several strengths and weaknesses in the method, which enable us to fine-tune the method before we carry out a more formal evaluation on other, more realistic components.

A case study in specification and implementation testing

Achieving consistency between a specification and its implementation is an important part of software development In previous work, we have presented a method and tool support for testing a formal specification using animation and then verifying an implementation of that specification. The method is based on a testgraph, which provides a partial model of the application under test. The testgraph is used in combination with an animator to generate test sequences for testing the formal specification. The same testgraph is used during testing to execute those same sequences on the implementation and to ensure that the implementation conforms to the specification. So far, the method and its tool support have been applied to software components that can be accessed through an application programmer interface (API). In this paper, we use an industrially-based case study to discuss the problems associated with applying the method to a software system with a graphical user interface (GUI). In particular, the lack of a standardised interface, as well as controllability and observability problems, make it difficult to automate the testing of the implementation. The method can still be applied, but the amount of testing that can be carried on the implementation is limited by the manual effort involved.

Testing java interrupts and timed waits

Testing concurrent software is difficult due to problems with inherent nondeterminism. In previous work, we have presented a method and tool support for the testing of concurrent Java components. In this paper, we extend that work by presenting and discussing techniques for testing Java thread interrupts and timed waits. Testing thread interrupts is important because every Java component that calls wait must have code dealing with these interrupts. For a component that uses interrupts and timed waits to provide its basic functionality, the ability to test these features is clearly even more important. We discuss the application of the techniques and tool support to one such component, which is a nontrivial implementation of the readers-writers problem.

A lightweight encryption algorithm for mobile online multimedia devices

Online multimedia data needs to be encrypted for access control. To be capable of working on mobile devices such as pocket PC and mobile phones, lightweight video encryption algorithms should be proposed. The two major problems in these algorithms are that they are either not fast enough or unable to work on highly compressed data stream. In this paper, we proposed a new lightweight encryption algorithm based on Huffman error diffusion. It is a selective algorithm working on compressed data. By carefully choosing the most significant parts (MSP), high performance is achieved with proper security. Experimental results has proved the algorithm to be fast. secure: and compression-compatible.

Bridging technical and HCI research: Creating usable ubiquitous computing

This paper describes methods used to support collaboration and communication between practitioners, designers and engineers when designing ubiquitous computing systems. We tested methods such as “Wizard of Oz” and design games in a real domain, the dental surgery, in an attempt to create a system that is: affordable; minimally disruptive of the natural flow of work; and improves human-computer interaction. In doing so we found that such activities allowed the practitioners to be on a ‘level playing ground’ with designers and engineers. The findings we present suggest that dentists are willing to engage in detailed exploration and constructive critique of technical design possibilities if the design ideas and prototypes are presented in the context of their work practice and are of a resolution and relevance that allow them to jointly explore and question with the design time. This paper is an extension of a short paper submitted to the Participatory Design Conference, 2004.

Engaging game characters: Informing design with player perspectives

The behavior of characters in current computer games is generally scripted and predictable. This paper discusses some issues related to creating game characters that enhance player engagement and identifies the need for a more player-centered approach to game character design. This paper reports the results of a focus group that was carried out with experienced game players to determine what game character behaviors would enhance their engagement in a game. The four general areas of concern that came out of this discussion were consistency with context, player expectations, social interactions and consistency with the environment. This paper discusses these issues and their implication for game character design with a view to creating engaging game characters. © Springer

A software engineering framework for context-aware pervasive computing

There is growing interest in the use of context-awareness as a technique for developing pervasive computing applications that are flexible, adaptable, and capable of acting autonomously on behalf of users. However, context-awareness introduces various software engineering challenges, as well as privacy and usability concerns. In this paper, we present a conceptual framework and software infrastructure that together address known software engineering challenges, and enable further practical exploration of social and usability issues by facilitating the prototyping and fine-tuning of context-aware applications.