Staphylococcus aureus genotyping using novel real-time PCR formats

One approach to microbial genotyping is to make use of sets of single-nucleotide polymorphisms (SNPs) in combination with binary markers. Here we report the modification and automation of a SNP-plus-binary-marker-based approach to the genotyping of Staphylococcus aureus and its application to 391 S. aureus isolates from southeast Queensland, Australia. The SNPs used were arcC210, tpi243, arcC162, gmk318, pta294, tpi36, tpi241, and pta383. These provide a Simpson's index of diversity (D) of 0.95 with respect to the S. aureus multilocus sequence typing database and define 61 genotypes and the major clonal complexes. The binary markers used were pvl, cna, sdrE, pT181, and pUB110. Two novel real-time PCR formats for interrogating these markers were compared. One of these makes use of light upon extension (LUX) primers and biplexed reactions, while the other is a streamlined modification of kinetic PCR using SYBR green. The latter format proved to be more robust. In addition, automated methods for DNA template preparation, reaction setup, and data analysis were developed. A single SNP-based method for ST-93 (Queensland clone) identification was also devised. The genotyping revealed the numerical importance of the South West Pacific and Queensland community-acquired methicillin-resistant S. aureus (MRSA) clones and the clonal complex 239 Aus-1/Aus-2 hospital-associated MRSA. There was a strong association between the community-acquired clones and pvl.

A reference architecture for instructional educational software

Our extensive research has indicated that high-school teachers are reluctant to make use of existing instructional educational software (Pollard, 2005). Even software developed in a partnership between a teacher and a software engineer is unlikely to be adopted by teachers outside the partnership (Pollard, 2005). In this paper we address these issues directly by adopting a reusable architectural design for instructional educational software which allows easy customisation of software to meet the specific needs of individual teachers. By doing this we will facilitate more teachers regularly using instructional technology within their classrooms. Our domain-specific software architecture, Interface-Activities-Model, was designed specifically to facilitate individual customisation by redefining and restructuring what constitutes an object so that they can be readily reused or extended as required. The key to this architecture is the way in which the software is broken into small generic encapsulated components with minimal domain specific behaviour. The domain specific behaviour is decoupled from the interface and encapsulated in objects which relate to the instructional material through tasks and activities. The domain model is also broken into two distinct models - Application State Model and Domainspecific Data Model. This decoupling and distribution of control gives the software designer enormous flexibility in modifying components without affecting other sections of the design. This paper sets the context of this architecture, describes it in detail, and applies it to an actual application developed to teach high-school mathematical concepts.

A synchronous multimedia annotation system for secure collaboratories

In this paper, we describe the Vannotea system - an application designed to enable collaborating groups to discuss and annotate collections of high quality images, video, audio or 3D objects. The system has been designed specifically to capture and share scholarly discourse and annotations about multimedia research data by teams of trusted colleagues within a research or academic environment. As such, it provides: authenticated access to a web browser search interface for discovering and retrieving media objects; a media replay window that can incorporate a variety of embedded plug-ins to render different scientific media formats; an annotation authoring, editing, searching and browsing tool; and session logging and replay capabilities. Annotations are personal remarks, interpretations, questions or references that can be attached to whole files, segments or regions. Vannotea enables annotations to be attached either synchronously (using jabber message passing and audio/video conferencing) or asynchronously and stand-alone. The annotations are stored on an Annotea server, extended for multimedia content. Their access, retrieval and re-use is controlled via Shibboleth identity management and XACML access policies.

Sausage: protein threading with flexible force fields

Sausage is a protein sequence threading program, but with remarkable run-time flexibility. Using different scripts, it can calculate protein sequence-structure alignments, search structure libraries, swap force fields, create models form alignments, convert file formats and analyse results. There are several different force fields which might be classed as knowledge-based, although they do not rely on Boltzmann statistics. Different force fields are used for alignment calculations and subsequent ranking of calculated models.

Interactive health communication in preventive medicine - Internet-based strategies in teaching and research

Interactive health communication using Internet technologies is expanding the range and flexibility of intervention and teaching options available in preventive medicine and the health sciences. Advantages of interactive health communication include the enhanced convenience, novelty, and appeal of computer-mediated communication; its flexibility and interactivity; and automated processing. We outline some of these fundamental aspects of computer-mediated communication as it applies to preventive medicine. Further, a number of key pathways of information technology evolution are creating new opportunities for the delivery of professional education in preventive medicine and other health domains, as well as for delivering automated, self-instructional health behavior-change programs through the Internet. We briefly describe several of these key evolutionary pathways, We describe some examples from work we have done in Australia. These demonstrate how we have creatively responded to the challenges of these new information environments, and how they may be pursued in the education of preventive medicine and other health care practitioners and in the development and delivery of health behavior change programs through the Internet. Innovative and thoughtful applications of this new technology can increase the consistency, reliability, and quality of information delivered.

CysView: protein classification based on cysteine pairing patterns

CysView is a web-based application tool that identifies and classifies proteins according to their disulfide connectivity patterns. It accepts a dataset of annotated protein sequences in various formats and returns a graphical representation of cysteine pairing patterns. CysView displays cysteine patterns for those records in the data with disulfide annotations. It allows the viewing of records grouped by connectivity patterns. CysView's utility as an analysis tool was demonstrated by the rapid and correct classification of scorpion toxin entries from GenPept on the basis of their disulfide pairing patterns. It has proved useful for rapid detection of irrelevant and partial records, or those with incomplete annotations. CysView can be used to support distant homology between proteins. CysView is publicly available at http://research.i2r.a-star.edu.sg/CysView/.

Critical cyber pedagogy: Doing multiliteracies in the Singapore classrooms

The Ministry of Education in Singapore has embarked on the ambitious project of introducing IT in schools. The IT Masterplan, budgeted at a cost of $2 billion, aims to wire up all schools by the year 2002. While the well-funded IT Masterplan is seeing the project in its final phase of implementation, this paper argues for a "critical cyber pedagogy" along with the acquisition of the functional and operational skills of technology. Drawing on theories of critical multiliteracies (Burbules & Callister, 2000; Luke, 2000b; New London Group, 1996), this paper explores and suggests how an instructional design of two classroom activities can be utilized as new forms of cyber and technoliteracies. Through the critical evaluation of websites and hypertext construction, students will be equipped with a new literacy that extends reading and writing by incorporating new blended forms of hybrid textualities. This technology-assisted pedagogy can achieve the desired outcome of self-directed learning, teamwork, critical thinking and problem solving strategies necessary for a knowledge-based society.

On-line analysis of froth surface in coal and mineral flotation using JKFrothCam

The personal computer revolution has resulted in the widespread availability of low-cost image analysis hardware. At the same time, new graphic file formats have made it possible to handle and display images at resolutions beyond the capability of the human eye. Consequently, there has been a significant research effort in recent years aimed at making use of these hardware and software technologies for flotation plant monitoring. Computer-based vision technology is now moving out of the research laboratory and into the plant to become a useful means of monitoring and controlling flotation performance at the cell level. This paper discusses the metallurgical parameters that influence surface froth appearance and examines the progress that has been made in image analysis of flotation froths. The texture spectrum and pixel tracing techniques developed at the Julius Kruttschnitt Mineral Research Centre are described in detail. The commercial implementation, JKFrothCam, is one of a number of froth image analysis systems now reaching maturity. In plants where it is installed, JKFrothCam has shown a number of performance benefits. Flotation runs more consistently, meeting product specifications while maintaining high recoveries. The system has also shown secondary benefits in that reagent costs have been significantly reduced as a result of improved flotation control. (C) 2002 Elsevier Science B.V. All rights reserved.

The effectiveness of parent management training to increase self-efficacy in parents of children with Asperger syndrome

This study was a trial of an intervention programme aimed to improve parental self-efficacy in the management of problem behaviours associated with Asperger syndrome. The intervention was compared across two formats, a I day workshop and six individual sessions, and also with a non-intervention control group. The results indicated that, compared with the control group, parents in both intervention groups reported fewer problem behaviours and increased self-efficacy following the interventions, at both 4 weeks and 3 months follow-up. The results also showed a difference in self-efficacy between mothers and fathers, with mothers reporting a significantly greater increase in self-efficacy following intervention than fathers. There was no significant difference between the workshop format and the individual sessions.