Virtual models of the HLA class I antigen processing pathway

Antigen recognition by cytotoxic CD8 T cells is dependent upon a number of critical steps in MHC class I antigen processing including proteosomal cleavage, TAP transport into the endoplasmic reticulum, and MHC class 1 binding. Based on extensive experimental data relating to each of these steps there is now the capacity to model individual antigen processing steps with a high degree of accuracy. This paper demonstrates the potential to bring together models of individual antigen processing steps, for example proteosome cleavage, TAP transport, and MHC binding, to build highly informative models of functional pathways. In particular, we demonstrate how an artificial neural network model of TAP transport was used to mine a HLA-binding database so as to identify H LA-binding peptides transported by TAP. This integrated model of antigen processing provided the unique insight that HLA class I alleles apparently constitute two separate classes: those that are TAP-efficient for peptide loading (HLA-B27, -A3, and -A24) and those that are TAP-inefficient (HLA-A2, -B7, and -B8). Hence, using this integrated model we were able to generate novel hypotheses regarding antigen processing, and these hypotheses are now capable of being tested experimentally. This model confirms the feasibility of constructing a virtual immune system, whereby each additional step in antigen processing is incorporated into a single modular model. Accurate models of antigen processing have implications for the study of basic immunology as well as for the design of peptide-based vaccines and other immunotherapies. (C) 2004 Elsevier Inc. All rights reserved.

Trends in five-year survival and risk of recurrent stroke after first-ever stroke in the Perth community stroke study

Background: Few studies provide information on trends in the long-term outcome of stroke. We aimed to determine trends in survival and recurrent stroke, over 5 years after first-ever stroke, for 2 cohorts of patients enrolled in the Perth Community Stroke Study in 1989 90 and 1995-96. Methods: For 12-month periods beginning February 1989 and February 1995, all individuals with an acute stroke who were resident in a geographically-defined and representative region of Perth, Western Australia, were registered and followed-up prospectively 5 years after the index event. Results: The 5-year cumulative risk of death was 59% (95% confidence interval (CI) 53%, 65%) and 58% (95% CI 52%, 65%) for the 1989-90 and 1995-96 cohorts, respectively (p = 0.94). The 5-year cumulative risk of first recurrent stroke was 32% (95% CI 25%, 40%) and 23% (95% CI 16%, 30%) for the 1989-90 and 1995-96 cohorts, respectively (p = 0.07). Conclusions: Although no statistically significant improvement occurred in 5-year survival after first-ever stroke in Perth between 1989-90 and 1995-96, there was a statistically nonsignificant trend towards a smaller cumulative risk of recurrent stroke over 5 years after a first-ever stroke. Serial community-based studies of the incidence and outcome of stroke are an important means of monitoring the translation of proven preventive interventions to improvements in population health. Copyright (C) 2005 S. Karger AG, Basel.

'Lots of little kindnesses': valuing the role of older Australians as informal volunteers in the community

This paper describes the ways in which older people contribute to their communities and families as informal volunteers. It challenges current ways of thinking that assign an economic value to the productive activities undertaken by older people. Using qualitative data from a study of older people resident in Queensland, Australia, the paper explores the ways that older people contribute to their families and to the community and the outcomes associated with these activities. Two specific themes emerged from the data: first, the ways' in which older people contribute to strong inter-generational relations, and second, how they provide essential mutual support that permits many older people to remain living in the community. These contributions, while often small in themselves, are in aggregate critical both to family functioning and to the maintenance of sustainable and healthy communities. Many are reciprocal interactions that add value to the lives of individuals and offer positive social roles in later life, and they may be particularly important for those from minority cultural backgrounds or at risk of social isolation. The findings suggest that older people are integral to community and civil society and, therefore, that social policy should respond to the ageing of Australia's population and recognise the positive contributions of older people, rather than emphasising the costs of demographic change.

The assessment of oral cytology utilizing ploidy analysis and virtual microscopy for the early detection of epithelial dysplasia and neoplasia in oral mucosal lesions

Oral squamous cell carcinoma (OSCC) is associated with high morbidity and mortality which is due, at least in part, to late detection. Precancerous and cancerous oral lesions may mimic any number of benign oral lesions, and as such may be left without investigation and treatment until they are well advanced. Over the past several years there has been renewed interest in oral cytology as an adjuvant clinical tool in the investigation of oral mucosal lesions. The purpose of the present study was to compare the usefulness of ploidy analysis after Feulgen stained cytological thin-prep specimens with traditional incisional biopsy and routine histopathological examination for the assessment of the pre-malignant potential of oral mucosal lesions. An analysis of the cytological specimens was undertaken with virtual microscopy which allowed for rapid and thorough analysis of the complete cytological specimen. 100 healthy individuals between 30 and 70 years of age, who were non-smokers, non-drinkers and not taking any medication, had cytological specimens collected from both the buccal mucosa and lateral margin of tongue to establish normal cytology parameters within a control population. Patients with a presumptive clinical diagnosis of lichen planus, leukoplakia or OSCC had lesional cytological samples taken prior to their diagnostic biopsy. Standardised thin preparations were prepared and each specimen stained by both Feuglen and Papanicolau methods. High speed scanning of the complete slide at 40X magnification was undertaken using the Aperio Scanscope TM and the green channel of the resultant image was analysed after threshold segmentation to isolate only nuclei and the integrated optical density of each nucleus taken as a gross measure of the DNA content (ploidy). Preliminary results reveal that ploidy assessment of oral cytology holds great promise as an adjunctive prognostic factor in the analysis of the malignant potential of oral mucosal lesions.

Virtual plants - integrating architectural and physiological models

Recent advances in computer technology have made it possible to create virtual plants by simulating the details of structural development of individual plants. Software has been developed that processes plant models expressed in a special purpose mini-language based on the Lindenmayer system formalism. These models can be extended from their architectural basis to capture plant physiology by integrating them with crop models, which estimate biomass production as a consequence of environmental inputs. Through this process, virtual plants will gain the ability to react to broad environmental conditions, while crop models will gain a visualisation component. This integration requires the resolution of the fundamentally different time scales underlying the approaches. Architectural models are usually based on physiological time; each time step encompasses the same amount of development in the plant, without regard to the passage of real time. In contrast, physiological models are based in real time; the amount of development in a time step is dependent on environmental conditions during the period. This paper provides a background on the plant modelling language, then describes how widely-used concepts of thermal time can be implemented to resolve these time scale differences. The process is illustrated using a case study. (C) 1997 Elsevier Science Ltd.