MULTIPRED: A computational system for prediction of promiscuous HLA binding peptides

MULTIPRED is a web-based computational system for the prediction of peptide binding to multiple molecules ( proteins) belonging to human leukocyte antigens (HLA) class I A2, A3 and class II DR supertypes. It uses hidden Markov models and artificial neural network methods as predictive engines. A novel data representation method enables MULTIPRED to predict peptides that promiscuously bind multiple HLA alleles within one HLA supertype. Extensive testing was performed for validation of the prediction models. Testing results show that MULTIPRED is both sensitive and specific and it has good predictive ability ( area under the receiver operating characteristic curve A(ROC) > 0.80). MULTIPRED can be used for the mapping of promiscuous T-cell epitopes as well as the regions of high concentration of these targets termed T-cell epitope hotspots. MULTIPRED is available at http:// antigen.i2r.a-star.edu.sg/ multipred/.

Tuberculosis and health sector reform: experience of integrating tuberculosis services into the district health system in rural South Africa

SETTING: Hlabisa health district, South Africa. OBJECTIVE: To describe the integration of a vertical tuberculosis control programme into an emerging 'horizontal' district health system, within the context of health sector reform. DESIGN: Descriptive account of the process of integration of the programme into the health system. RESULTS: A highly 'vertical' system of delivering tuberculosis treatment (with poor programme outcomes) was converted into a (horizontal' team, integrated within the district health system, that used available resources such as village clinics and community health workers, with improved programme outcomes. CONCLUSIONS: In some settings at least, integration of tuberculosis 'programmes' into the district health system as tuberculosis 'teams' is feasible, and may produce highly cost-effective outcomes.

Challenge-induced plasma exudation and mucinous secretion in human airways

Secretion of mucins and exudation of plasma are distinct processes of importance to innate immunity and inflammatory disease. Yet, little is known about their relation in human airways. The objective of the present study was to use the human nasal airway to determine mucinous secretion and plasma exudation in response to common challenge agents and mediators. Ten healthy volunteers were subjected to nasal challenge-lavage procedures. Thus, the nasal mucosa was exposed to increasing doses of histamine (40 and 400 mu g ml(-1)), methacholine (12.5 and 25 mg) and capsaicin (30 and 300 ng ml(-1)). Fucose was selected as a global marker of mucinous secretion and alpha(2)-macroglobulin as an index of exudation of bulk plasma. All challenge agents increased the mucosal output of fucose to about the same level (P < 0.01-0.05). Once significant secretion had been induced the subsequently increased dose of the challenge agent, in the case of histamine and methacholine, failed to further increase the response. Only histamine increased the mucosal output of alpha(2)-macroglobulin (P < 0.01). We conclude that prompt but potentially rapidly depleted mucinous secretion is common to different kinds of airway challenges, whereas inflammatory histamine-type mediators are required to produce plasma exudation. Along with the acknowledged secretion of mucins, a practically non-depletable, pluripotent mucosal output of plasma emerges as an important component of the innate immunity of human airways.

Integrating attribute and space characteristics in choropleth display and spatial data mining

This paper develops an interactive approach for exploratory spatial data analysis. Measures of attribute similarity and spatial proximity are combined in a clustering model to support the identification of patterns in spatial information. Relationships between the developed clustering approach, spatial data mining and choropleth display are discussed. Analysis of property crime rates in Brisbane, Australia is presented. A surprising finding in this research is that there are substantial inconsistencies in standard choropleth display options found in two widely used commercial geographical information systems, both in terms of definition and performance. The comparative results demonstrate the usefulness and appeal of the developed approach in a geographical information system environment for exploratory spatial data analysis.

Commercial-in-confidence: An obituary to transparency?

This article addresses the issue of accountability and transparency in relation to the use of commercial-in-confidence clauses to withhold information. The issue is contentious. On the one hand some like the Senate Finance and Public Administration Reference Committee (SFPARC) argue that: 'Put simply there can be no accountability if there is no information' (SFPARC 2000). On the other hand, an alternative view is: 'I think that the sanctity of contract... [is] a fundamental pillar of our legal system, and if private businesses enter into contracts with governments that specify confidentiality, then that ought to be respected' (Paterson 1999). This paper is an abridged version of a keynote address to CPA Australia (Queensland Division) Audit Intensive Day 2000, Brisbane Hilton, 10 November 2000.

Australian empirical study into genetic discrimination

This paper outlines a major empirical study that is being undertaken by an interdisciplinary team into genetic discrimination in Australia. The 3-year study will examine the nature and extent of this newly emerging phenomenon across the perspectives of consumers, third parties, and the legal system and will analyze its social and legal dimensions. Although the project is confined to Australia, it is expected that the outcomes will have significance for the wider research community as this is the most substantial study of its kind to be undertaken to date into genetic discrimination.

Testamentary capacity and aphasia: A descriptive case report with implications for clinical practice

Background: Testamentary capacity (the capacity to make a will) is recognised in the literature as an important issue for speech-language pathologists' assessment of people with aphasia, but current guidelines for clinical practice lack an empirical base. Aims: The research aimed to suggest some guidelines for clinical practice based on information considered relevant for the court in determining testamentary capacity. Methods & Procedures: A recent legal case involving a challenge to the will of a woman with severe aphasia was critically examined with reference to current guidelines in the literature regarding assessment of testamentary capacity. Outcomes & Results: Examination of the information available on the case indicated that the judge gave priority to accounts of the everyday communication of the person with aphasia (including reported discourse samples) over the information provided by expert medical witnesses. The extent to which communication effectiveness could be maximised was found to be a matter of key significance to the determination of capacity. Conclusions: This study has implications for speech-language pathologists' assessment practices and reports, as well as for scope of practice with regard to legal decision making of people with aphasia. These issues are discussed in relation to the World Health Organisation's ICF framework of functioning for social participation.

Investigating genetic discrimination in Australia: Opportunities and challenges in the early stages

Genetic discrimination, defined as the differential treatment of individuals or their relatives on the basis of actual or presumed genetic differences, is an emerging issue of interest in academic, clinical, social and legal contexts. While its potential significance has been discussed widely, verified empirical data are scarce. Genetic discrimination is a complex phenomenon to describe and investigate, as evidenced by the recent Australian Law Reform Commission inquiry in Australia. The authors research project, which commenced in 2002, aims to document the multiple perspectives and experiences regarding genetic discrimination in Australia and inform future policy development and law reform. Data are being collected from consumers, employers, insurers and the legal system. Attempted verification of alleged accounts of genetic discrimination will be a novel feature of the research. This paper overviews the early stages of the research, including conceptual challenges and their methodological implications.

Entanglement sharing and decoherence in the spin-bath

The monogamous nature of entanglement has been illustrated by the derivation of entanglement-sharing inequalities-bounds on the amount of entanglement that can be shared among the various parts of a multipartite system. Motivated by recent studies of decoherence, we demonstrate an interesting manifestation of this phenomena that arises in system-environment models where there exists interactions between the modes or subsystems of the environment. We investigate this phenomenon in the spin-bath environment, constructing an entanglement-sharing inequality bounding the entanglement between a central spin and the environment in terms of the pairwise entanglement between individual bath spins. The relation of this result to decoherence will be illustrated using simplified system-bath models of decoherence.

Reflective web interface agent

Web interface agent is used with web browsers to assist users in searching and interactions with the WWW. It is used for a variety of purposes, such as web-enabled remote control, web interactive visualization, and e-commerce activities. User may be aware or unaware of its existence. The intelligence of interface agent consists in its capability of learning and decision-making in performing interactive functions on behalf of a user. However, since web is an open system environment, the reasoning mechanism in an agent should be able to adapt changes and make decisions on exceptional situations, and therefore use meta knowledge. This paper proposes a framework of Reflective Web Interface Agent (RWIA) that is to provide causal connections between the application interfaces and the knowledge model of the interface agent. A prototype is also implemented for the purpose of demonstration.

Resilience and male identity for at-risk males in alternative programs

This paper deals with the discourses of power and gender that influence the way in which at-risk adolescent boys think and solve problems within a specific educational context. The focus is on how some adolescent boys perceive their masculinities, identity, and support networks after they have completed an alternative education program. The position being presented in this paper is that for recovery from adversity, at-risk boys must be provided with protective processes that address masculinities and the impact of power relations within masculinities. In doing so, the research connects gender and protective processes and the role that gender construction plays in successful educational outcomes. It is also argued that for successful reintegration of at-risk adolescent males into an educational setting requires opportunity to be provided within the environment to challenge the legitimacy of traditional masculine performances.

MHCWeb: Converting a WWW database into a knowledge-based collaborative environment

The World Wide Web (WWW) is useful for distributing scientific data. Most existing web data resources organize their information either in structured flat files or relational databases with basic retrieval capabilities. For databases with one or a few simple relations, these approaches are successful, but they can be cumbersome when there is a data model involving multiple relations between complex data. We believe that knowledge-based resources offer a solution in these cases. Knowledge bases have explicit declarations of the concepts in the domain, along with the relations between them. They are usually organized hierarchically, and provide a global data model with a controlled vocabulary, We have created the OWEB architecture for building online scientific data resources using knowledge bases. OWEB provides a shell for structuring data, providing secure and shared access, and creating computational modules for processing and displaying data. In this paper, we describe the translation of the online immunological database MHCPEP into an OWEB system called MHCWeb. This effort involved building a conceptual model for the data, creating a controlled terminology for the legal values for different types of data, and then translating the original data into the new structure. The 0 WEB environment allows for flexible access to the data by both users and computer programs.