Interview with Dr. Young-Ki Paik, President of the Human Proteome Organization (HUPO): Pharmacoproteomics and the approaching wave of “Proteomics Diagnostics”

Dr. Young-Ki Paik directs the Yonsei Proteome Research Center in Seoul, Korea and was elected as the President of the Human Proteome Organization (HUPO) in 2009. In the December 2009 issue of the Current Pharmacogenomics and Personalized Medicine (CPPM), Dr. Paik explains the new field of pharmacoproteomics and the approaching wave of “proteomics diagnostics” in relation to personalized medicine, HUPO’s role in advancing proteomics technology applications, the HUPO Proteomics Standards Initiative, and the future impact of proteomics on medicine, science, and society. Additionally, he comments that (1) there is a need for launching a Gene-Centric Human Proteome Project (GCHPP) through which all representative proteins encoded by the genes can be identified and quantified in a specific cell and tissue and, (2) that the innovation frameworks within the diagnostics industry hitherto borrowed from the genetics age may require reevaluation in the case of proteomics, in order to facilitate the uptake of pharmacoproteomics innovations. He stresses the importance of biological/clinical plausibility driving the evolution of biotechnologies such as proteomics,instead of an isolated singular focus on the technology per se. Dr. Paik earned his Ph.D. in biochemistry from the University of Missouri-Columbia and carried out postdoctoral work at the Gladstone Foundation Laboratories of Cardiovascular Disease, University of California at San Francisco. In 2005, his research team at Yonsei University first identified and characterized the chemical structure of C. elegans dauer pheromone (daumone) which controls the aging process of this nematode. He is interviewed by a multidisciplinary team specializing in knowledge translation, technology regulation, health systems governance, and innovation analysis.

Queensland Aborigines, multiple realities and the social sources of suffering: Psychiatry and moral regions of being (Part 1)

This two part paper considers the experience of a range of magico-religious experiences (such as visions and voices) and spirit beliefs in a rural Aboriginal town. The papers challenge the tendency of institutionalised psychiatry to medicalise the experiences and critiques the way in which its individualistic practice is intensified in the face of an incomprehensible Aboriginal „other‟ to become part of the power imbalance that characterises the relationship between Indigenous and white domains. The work reveals the internal differentiation and politics of the Aboriginal domain, as the meanings of these experiences and actions are contested and negotiated by the residents and in so doing they decentre the concerns of the white domain and attempt to control their relationship with it. Thus the plausibility structure that sustains these multiple realities reflects both accommodation and resistance to the material and historical conditions imposed and enacted by mainstream society on the residents, and to current socio- political realities. I conclude that the residents‟ narratives chart the grounds of moral adjudication as the experiences were rarely conceptualised by local people as signs of individual pathology but as reflections of social reality. Psychiatric drug therapy and the behaviourist assumptions underlying its practice posit atomised individuals as the appropriate site of intervention as against the multiple realities revealed by the phenomenology of the experiences. The papers thus call into question Australian mainstream „commonsense‟ that circulates about Aboriginal and Torres Strait Islander people which justifies representations of them as sickly outcasts in Australian society.

Information security management : a case study of an information security culture

This thesis argues that in order to establish a sound information security culture it is necessary to look at organisation's information security systems in a socio- technical context. The motivation for this research stems from the continuing concern of ineffective information security in organisations, leading to potentially significant monetary losses. It is important to address both technical and non- technical aspects when dealing with information security management. Culture has been identified as an underlying determinant of individuals' behaviour and this extends to information security culture, particularly in developing countries. This research investigates information security culture in the Saudi Arabia context. The theoretical foundation for the study is based on organisational and national culture theories. A conceptual framework for this study was constructed based on Peterson and Smith's (1997) model of national culture. This framework guides the study of national, organisational and technological values and their relationships to the development of information security culture. Further, the study seeks to better understand how these values might affect the development and deployment of an organisation's information security culture. Drawing on evidence from three exploratory case studies, an emergent conceptual framework was developed from the traditional human behaviour and the social environment perspectives used in social work, This framework contributes to in- formation security management by identifying behaviours related to four modes of information security practice. These modes provide a sound basis that can be used to evaluate individual organisational members' behaviour and the adequacy of ex- isting security measures. The results confirm the plausibility of the four modes of practice. Furthermore, a final framework was developed by integrating the four modes framework into the research framework. The outcomes of the three case stud- ies demonstrate that some of the national, organisational and technological values have clear impacts on the development and deployment of organisations' informa- tion security culture. This research, by providing an understanding the in uence of national, organi- sational and technological values on individuals' information security behaviour, contributes to building a theory of information security culture development within an organisational context. The research reports on the development of an inte- grated information security culture model that highlights recommendations for developing an information security culture. The research framework, introduced by this research, is put forward as a robust starting point for further related work in this area.

Pulse-coupled neural network performance for real-time identification of vegetation during forced landing

Safety concerns in the operation of autonomous aerial systems require safe-landing protocols be followed during situations where the a mission should be aborted due to mechanical or other failure. On-board cameras provide information that can be used in the determination of potential landing sites, which are continually updated and ranked to prevent injury and minimize damage. Pulse Coupled Neural Networks have been used for the detection of features in images that assist in the classification of vegetation and can be used to minimize damage to the aerial vehicle. However, a significant drawback in the use of PCNNs is that they are computationally expensive and have been more suited to off-line applications on conventional computing architectures. As heterogeneous computing architectures are becoming more common, an OpenCL implementation of a PCNN feature generator is presented and its performance is compared across OpenCL kernels designed for CPU, GPU and FPGA platforms. This comparison examines the compute times required for network convergence under a variety of images obtained during unmanned aerial vehicle trials to determine the plausibility for real-time feature detection.

Pulse-coupled neural network performance for real-time identification of vegetation during forced landing

Safety concerns in the operation of autonomous aerial systems require safe-landing protocols be followed during situations where the mission should be aborted due to mechanical or other failure. This article presents a pulse-coupled neural network (PCNN) to assist in the vegetation classification in a vision-based landing site detection system for an unmanned aircraft. We propose a heterogeneous computing architecture and an OpenCL implementation of a PCNN feature generator. Its performance is compared across OpenCL kernels designed for CPU, GPU, and FPGA platforms. This comparison examines the compute times required for network convergence under a variety of images to determine the plausibility for real-time feature detection.

Teaching scenario analysis – An action learning pedagogy

In this paper we provide an introduction to our teaching of scenario analysis. Scenario analysis offers an excellent instructional vehicle for investigating ‘wicked problems’; issues that are complex and ambiguous and require trans-disciplinary inquiry. We outline the pedagogical underpinning based on action learning and provide a critical approach from the intuitive logics school of scenario analysis. We use this in our programme in which student groups engage in semi-structured, but divergent and inclusive analysis of a selected focal issue. They then develop a set of scenario storylines that outline the limits of possibility and plausibility for a selected time-horizon year. The scenarios are portrayed not as narratives, but as vehicles for exploration of the causes and outcomes of the interplay between forces in the contextual environment that drive the unfolding future in the context of the focal issue. In this way, we provide internally-generated challenges to both individual pre-conceptions and group-level thinking.

Visualization tools for high angular resolution diffusion imaging

There is a major effort in medical imaging to develop algorithms to extract information from DTI and HARDI, which provide detailed information on brain integrity and connectivity. As the images have recently advanced to provide extraordinarily high angular resolution and spatial detail, including an entire manifold of information at each point in the 3D images, there has been no readily available means to view the results. This impedes developments in HARDI research, which need some method to check the plausibility and validity of image processing operations on HARDI data or to appreciate data features or invariants that might serve as a basis for new directions in image segmentation, registration, and statistics. We present a set of tools to provide interactive display of HARDI data, including both a local rendering application and an off-screen renderer that works with a web-based viewer. Visualizations are presented after registration and averaging of HARDI data from 90 human subjects, revealing important details for which there would be no direct way to appreciate using conventional display of scalar images.

Evidence of genetic association between TNFRSF1A encoding the p55 tumour necrosis factor receptor, and ankylosing spondylitis in UK Caucasians

Objectives: To replicate the possible genetic association between ankylosing spondylitis (AS) and TNFRSF1A. Methods: TNFRSF1A was re-sequenced in 48 individuals with AS to identify novel polymorphisms. Nine single nucleotide polymorphisms (SNPs) in TNFRSF1A and 5 SNPs in the neighbouring gene SCNN1A were genotyped in 1604 UK Caucasian individuals with AS and 1019 matched controls. An extended study was implemented using additional genotype data on 8 of these SNPs from 1400 historical controls from the 1958 British Birth Cohort. A meta-analysis of previously published results was also undertaken. Results: One novel variant in intron 6 was identified but no new coding variants. No definite associations were seen in the initial study but in the extended study there were weak associations with rs4149576 (p=0.04) and rs4149577 (p=0.007). In the metaanalysis consistent, somewhat stronger associations were seen with rs4149577 (p=0.002) and rs4149578 (p=0.006). Conclusions: These studies confirm the weak genetic associations between AS and TNFRSF1A. In view of the previously reported associations of TNFRSF1A with AS, in Caucasians and Chinese, and the biological plausibility of this candidate gene, replication of this finding in well powered studies is clearly indicated.

Development and validation of the Emergency Department Assessment of Chest pain Score and 2h accelerated diagnostic protocol

Objective Risk scores and accelerated diagnostic protocols can identify chest pain patients with low risk of major adverse cardiac event who could be discharged early from the ED, saving time and costs. We aimed to derive and validate a chest pain score and accelerated diagnostic protocol (ADP) that could safely increase the proportion of patients suitable for early discharge. Methods Logistic regression identified statistical predictors for major adverse cardiac events in a derivation cohort. Statistical coefficients were converted to whole numbers to create a score. Clinician feedback was used to improve the clinical plausibility and the usability of the final score (Emergency Department Assessment of Chest pain Score [EDACS]). EDACS was combined with electrocardiogram results and troponin results at 0 and 2 h to develop an ADP (EDACS-ADP). The score and EDACS-ADP were validated and tested for reproducibility in separate cohorts of patients. Results In the derivation (n = 1974) and validation (n = 608) cohorts, the EDACS-ADP classified 42.2% (sensitivity 99.0%, specificity 49.9%) and 51.3% (sensitivity 100.0%, specificity 59.0%) as low risk of major adverse cardiac events, respectively. The intra-class correlation coefficient for categorisation of patients as low risk was 0.87. Conclusion The EDACS-ADP identified approximately half of the patients presenting to the ED with possible cardiac chest pain as having low risk of short-term major adverse cardiac events, with high sensitivity. This is a significant improvement on similar, previously reported protocols. The EDACS-ADP is reproducible and has the potential to make considerable cost reductions to health systems.

Using global formulary apportionment for international profit allocation: The case of Indonesia's mining industry

My thesis examined an alternative approach, referred to as the unitary taxation approach to the allocation of profit, which arises from the notion that as a multinational group exists as a single economic entity, it should be taxed as one taxable unit. The plausibility of a unitary taxation regime achieving international acceptance and agreement is highly contestable due to its implementation issues, and economic and political feasibility. Using a case-study approach focusing on Freeport-McMoRan and Rio Tinto's mining operations in Indonesia, this thesis compares both tax regimes against the criteria for a good tax system - equity, efficiency, neutrality and simplicity. This thesis evaluates key issues that arise when implementing a unitary taxation approach with formulary apportionment based on the context of mining multinational firms in Indonesia.

Computation of confined swirling flow using RNG and k-epsilon turbulence models

In this work we numerically model isothermal turbulent swirling flow in a cylindrical burner. Three versions of the RNG k-epsilon model are assessed against performance of the standard k-epsilon model. Sensitivity of numerical predictions to grid refinement, differing convective differencing schemes and choice of (unknown) inlet dissipation rate, were closely scrutinised to ensure accuracy. Particular attention is paid to modelling the inlet conditions to within the range of uncertainty of the experimental data, as model predictions proved to be significantly sensitive to relatively small changes in upstream flow conditions. We also examine the characteristics of the swirl--induced recirculation zone predicted by the models over an extended range of inlet conditions. Our main findings are: - (i) the standard k-epsilon model performed best compared with experiment; - (ii) no one inlet specification can simultaneously optimize the performance of the models considered; - (iii) the RNG models predict both single-cell and double-cell IRZ characteristics, the latter both with and without additional internal stagnation points. The first finding indicates that the examined RNG modifications to the standard k-e model do not result in an improved eddy viscosity based model for the prediction of swirl flows. The second finding suggests that tuning established models for optimal performance in swirl flows a priori is not straightforward. The third finding indicates that the RNG based models exhibit a greater variety of structural behaviour, despite being of the same level of complexity as the standard k-e model. The plausibility of the predicted IRZ features are discussed in terms of known vortex breakdown phenomena.