Fuzzy methods for analysis of microarrays and networks

Bioinformatics involves analyses of biological data such as DNA sequences, microarrays and protein-protein interaction (PPI) networks. Its two main objectives are the identification of genes or proteins and the prediction of their functions. Biological data often contain uncertain and imprecise information. Fuzzy theory provides useful tools to deal with this type of information, hence has played an important role in analyses of biological data. In this thesis, we aim to develop some new fuzzy techniques and apply them on DNA microarrays and PPI networks. We will focus on three problems: (1) clustering of microarrays; (2) identification of disease-associated genes in microarrays; and (3) identification of protein complexes in PPI networks. The first part of the thesis aims to detect, by the fuzzy C-means (FCM) method, clustering structures in DNA microarrays corrupted by noise. Because of the presence of noise, some clustering structures found in random data may not have any biological significance. In this part, we propose to combine the FCM with the empirical mode decomposition (EMD) for clustering microarray data. The purpose of EMD is to reduce, preferably to remove, the effect of noise, resulting in what is known as denoised data. We call this method the fuzzy C-means method with empirical mode decomposition (FCM-EMD). We applied this method on yeast and serum microarrays, and the silhouette values are used for assessment of the quality of clustering. The results indicate that the clustering structures of denoised data are more reasonable, implying that genes have tighter association with their clusters. Furthermore we found that the estimation of the fuzzy parameter m, which is a difficult step, can be avoided to some extent by analysing denoised microarray data. The second part aims to identify disease-associated genes from DNA microarray data which are generated under different conditions, e.g., patients and normal people. We developed a type-2 fuzzy membership (FM) function for identification of diseaseassociated genes. This approach is applied to diabetes and lung cancer data, and a comparison with the original FM test was carried out. Among the ten best-ranked genes of diabetes identified by the type-2 FM test, seven genes have been confirmed as diabetes-associated genes according to gene description information in Gene Bank and the published literature. An additional gene is further identified. Among the ten best-ranked genes identified in lung cancer data, seven are confirmed that they are associated with lung cancer or its treatment. The type-2 FM-d values are significantly different, which makes the identifications more convincing than the original FM test. The third part of the thesis aims to identify protein complexes in large interaction networks. Identification of protein complexes is crucial to understand the principles of cellular organisation and to predict protein functions. In this part, we proposed a novel method which combines the fuzzy clustering method and interaction probability to identify the overlapping and non-overlapping community structures in PPI networks, then to detect protein complexes in these sub-networks. Our method is based on both the fuzzy relation model and the graph model. We applied the method on several PPI networks and compared with a popular protein complex identification method, the clique percolation method. For the same data, we detected more protein complexes. We also applied our method on two social networks. The results showed our method works well for detecting sub-networks and give a reasonable understanding of these communities.

Vulnerable and invisible : depictions of trafficking victims in public awareness campaigns

Public concern about the crime of human trafficking has dramatically risen over the last two decades. . This concern and panic has both spawned and been fuelled by an array of public awareness campaigns that aim to educate the public about this crime. Campaigns such as the Blue Blindfold Campaign in the UK, the UN-driven Blue Heart Campaign, and the worldwide Body Shop campaign have contributed to the public’s awareness and, to an extent, understanding of the phenomenon of human trafficking. This research explores these and other government and non-government campaigns aimed at raising public awareness of human trafficking. It questions the rationale, call to action and impact of these efforts, and analyses the depiction of trafficking victims in these campaigns. In particular, this research argues that some of these campaigns perpetuate an understanding of a hierarchy of victimisation of trafficking. A public focus on sex trafficking often results in the conflation of prostitution and trafficking, and renders invisible the male and female victims of trafficking for other forms of labour.

Really really

In “Really Really”, a series of words float through animated star constellations. While apparently drifting aimlessly, the words can be rearranged in numerous ways to recount roughly the same sappy avowal of long-distance love. The many combinations of words, and their predictable associations, call attention to the thresholds of verbal expression. When some sincere words are needed most it seems as if they’ve all been said before. And so, this declaration of love is both enabled and haunted by the tension between sentiment and formula. “Really Really” continues my interests in how meaning is constructed and circulated, and in particular, how common models of communication continue to frame and yet fall short of our personal experiences.

Unlocking black box models of leadership effectiveness: Exploring alternative research and policy metaphors

There is an intimate interconnectivity between policy guidelines defining reform and the delineation of what research methods would be subsequently applied to determine reform success. Research is guided as much by the metaphors describing it as by the ensuing empirical definition of actions of results obtained from it. In a call for different reform policy metaphors Lumby and English (2010) note, “The primary responsibility for the parlous state of education... lies with the policy makers that have racked our schools with reductive and dehumanizing processes, following the metaphors of market efficiency, and leadership models based on accounting and the characteristics of machine bureaucracy” (p. 127)

Reframing the design of context-aware computing

From location-aware computing to mining the social web, representations of context have promised to make better software applications. The opportunities and challenges of context-aware computing from representational, situated and interactional perspectives have been well documented, but arguments from the perspective of design are somewhat disparate. This paper draws on both theoretical perspectives and a design framing, using the problem of designing a social mobile agile ridesharing system, in order to reflect upon and call for broader design approaches for context-aware computing and human-computer Interaction research in general.

Privacy compliance verification in cryptographic protocols

To provide privacy protection, cryptographic primitives are frequently applied to communication protocols in an open environment (e.g. the Internet). We call these protocols privacy enhancing protocols (PEPs) which constitute a class of cryptographic protocols. Proof of the security properties, in terms of the privacy compliance, of PEPs is desirable before they can be deployed. However, the traditional provable security approach, though well-established for proving the security of cryptographic primitives, is not applicable to PEPs. We apply the formal language of Coloured Petri Nets (CPNs) to construct an executable specification of a representative PEP, namely the Private Information Escrow Bound to Multiple Conditions Protocol (PIEMCP). Formal semantics of the CPN specification allow us to reason about various privacy properties of PIEMCP using state space analysis techniques. This investigation provides insights into the modelling and analysis of PEPs in general, and demonstrates the benefit of applying a CPN-based formal approach to the privacy compliance verification of PEPs.

Individuals in a mass market environment: Australian bequest donors seek better communication from charities

Swelling social need and competing calls on government funds have heightened the philanthropic dollar’s value. Yet, Australia is not regarded as having a robust giving culture: while 86% of adults give, a mere 16% plan their giving with those who do donating four times as much as spontaneous givers (Giving Australia, 2005). Traditionally, the prime planned giving example is a charitable bequest, a revenue stream not prevalent here (Baker, 2007). In fact, Baker’s Victorian probate data shows under 5% of estates provide a charitable bequest and just over 1% of estate assets is bequeathed. The UK, in contrast, sources 30% and the US 10% of charitable income through bequests (NCVO, 2004; Sargeant, Wymer and Hilton,2006). Australian charities could boost bequest giving. Understanding the donor market, which has or may remember them in their will is critical. This paper reports donor perceptions of Australian charities’ bequest communication/ marketing. The data forms part of a wider study of Australian donors’ bequest attitudes and behaviour. Charities spend heavily on bequest promotion, from advertising to personal selling to public relations and promotion. Infrastructure funds are scarce so guidance on what works for donors is important. Guy and Patton (1988) made their classic call for a nonprofit marketing perspective and identify the need for charities to better understand the motivations and behaviour of their supporters. In similar vein, this study aims to improve the way nonprofits and givers interact; and ultimately, enhance the giving experience and thus multiply planned giving participation. Academically, it offers insights to Australian bequest motivations and attitudes not studied empirically before.

Foresight practice in Australia: a meta-scan of practitioners and organisations

This critical review of foresight professionals seeks to analyse their social interests, methodology, epistemological focal domains, capacitating focus, geography and organisational type. The call for a deeper understanding of the practice in the Australian context is made in order for the foundations for a National Foresight Strategy to be laid.

eBILITY : from tool use to partnerships

In this article we identify how computational automation achieved through programming has enabled a new class of music technologies with generative music capabilities. These generative systems can have a degree of music making autonomy that impacts on our relationships with them; we suggest that this coincides with a shift in the music-equipment relationship from tool use to a partnership. This partnership relationship can occur when we use technologies that display qualities of agency. It raises questions about the kinds of skills and knowledge that are necessary to interact musically in such a partnership. These are qualities of musicianship we call eBility. In this paper we seek to define what eBility might consist of and how consideration of it might effect music education practice. The 'e' in eBility refers not only to the electronic nature of computing systems but also to the ethical, enabling, experiential and educational dimensions of the creative relationship with technologies with agency. We hope to initiate a discussion around differentiating what we term representational technologies from those with agency and begin to uncover the implications of these ideas for music educators in schools and communities. We hope also to elucidate the emergent theory and practice that has enabled the development of strategies for optimising this kind of eBility where the tool becomes partner. The identification of musical technologies with agency adds to the authors’ list of metaphors for technology use in music education that previously included tool, medium and instrument. We illustrate these ideas with examples and with data from our work with the jam2jam interactive music system. In this discussion we will outline our experiences with jam2jam as an example of a technology with agency and describe the aspects of eBility that interaction with it promotes.

Move it, use it : university-school collaboration for learning to teach physical education in primary schools

Reports of increasing numbers of obese Australian children and adolescents have raised the alarm to be proactive in reducing this so called epidemic. It has evoked a call for greater emphasis on teaching physical education in schools, as a measure for attaining fitness not only with obese students but for all students. This paper emphasises how preservice teachers need to be a key target for implementing physical education (PE) reform in schools, as many primary teachers will be generalists and may not be confident enough to implement PE effectively. Through a review of existing literature, teaching practices essential for the effective promotion and implementation of PE were identified under six broad categories: personal-professional skills development, addressing system requirements, pedagogical practices, managing student behaviour, providing feedback to students, and reflecting on practice. Subsequently, the development of these practices in preservice teachers is considered in the context of a university-school collaboration where preservice teachers taught physical education to primary school students for one day per week over a four week period. These authentic teaching experiences provided the preservice teachers with vital opportunities to put theory into practice and interact with “real-world” students. Self-evaluative data from 38 of these preservice teachers, in the form of a five-part Likert scale survey and extended response survey, demonstrated that they were able to develop the majority of the essential teaching practices identified by literature. In particular, the preservice teachers developed self efficacy, enthusiasm, and motivation for teaching PE, facets which are often found to be lacking in generalist primary teachers and yet are essential if children’s perceptions and habits regarding physical activity are to be changed.

Application of Geographic Modeling Techniques to Quantify Spatial Access to Health Services Before and After an Acute Cardiac Event: The Cardiac ARIA Project

Background: Access to cardiac services is essential for appropriate implementation of evidence-based therapies to improve outcomes. The Cardiac Accessibility and Remoteness Index for Australia (Cardiac ARIA) aimed to derive an objective, geographic measure reflecting access to cardiac services. Methods: An expert panel defined an evidence-based clinical pathway. Using Geographic Information Systems (GIS), a numeric/alpha index was developed at two points along the continuum of care. The acute category (numeric) measured the time from the emergency call to arrival at an appropriate medical facility via road ambulance. The aftercare category (alpha) measured access to four basic services (family doctor, pharmacy, cardiac rehabilitation, and pathology services) when a patient returned to their community. Results: The numeric index ranged from 1 (access to principle referral center with cardiac catheterization service ≤ 1 hour) to 8 (no ambulance service, > 3 hours to medical facility, air transport required). The alphabetic index ranged from A (all 4 services available within 1 hour drive-time) to E (no services available within 1 hour). 13.9 million (71%) Australians resided within Cardiac ARIA 1A locations (hospital with cardiac catheterization laboratory and all aftercare within 1 hour). Those outside Cardiac 1A were over-represented by people aged over 65 years (32%) and Indigenous people (60%). Conclusion: The Cardiac ARIA index demonstrated substantial inequity in access to cardiac services in Australia. This methodology can be used to inform cardiology health service planning and the methodology could be applied to other common disease states within other regions of the world.

The internetalisation of information, knowledge and interaction components of the firm’s internationalisation process

Transcending traditional national borders, the Internet is an evolving technology that has opened up many new international market opportunities. However, ambiguity remains, with limited research and understanding of how the Internet influences the firm’s internationalisation process components. As a consequence, there has been a call for further investigation of the phenomenon. Thus, the purpose of this study was to investigate the Internet’s impact on the internationalisation process components, specifically, information availability, information usage, interactive communication and international market growth. Analysis was undertaken using structural equation modelling. Findings highlight the mediating impact of the Internet on information and knowledge transference in the internationalisation process. Contributions of the study test conceptualisations and give statistical validation of interrelationships, while illuminating the Internet’s impact on firm internationalisation.

Understanding the very nature of Project Management : a praxiological approach

Foreword: In this paper I call upon a praxiological approach. Praxeology (early alteration of praxiology) is the study of human action and conduct. The name praxeology/praxiologyakes is root in praxis, Medieval Latin, from Greek, doing, action, from prassein to do, practice (Merriam-Webster Dictionary). Having been involved in project management education, research and practice for the last twenty years, I have constantly tried to improve and to provide a better understanding/knowledge of the field and related practice, and as a consequence widen and deepen the competencies of the people I was working with (and my own competencies as well!), assuming that better project management lead to more efficient and effective use of resources, development of people and at the end to a better world. For some time I have perceived a need to clarify the foundations of the discipline of project management, or at least elucidate what these foundations could be. An immodest task, one might say! But not a neutral one! I am constantly surprised by the way the world (i.e., organizations, universities, students and professional bodies) sees project management: as a set of methods, techniques, tools, interacting with others fields – general management, engineering, construction, information systems, etc. – bringing some effective ways of dealing with various sets of problems – from launching a new satellite to product development through to organizational change.

Book Review: "Mark Considine, Jenny Lewis and Damon Alexander Networks, Innovation and Public Policy : Politicians, Bureaucrats and the Pathways to Change inside Government Houndsmills, UK: Palgrave Macmillan, 2009"

Having wrung the most from workforce and workplace productivity initiaitves, innovation has come to the fore as a key goal and directive for public sector organisations to become more efficient. This clarion call for innovation can be heard all around the world, with public services everywhere taking up the message to develop better, smarter, novel, more innovative processes, programs and policies. In the current push for innovation, networks are considered to be a superior vehicle through which collective knowledge can be shared and leveraged; replacing or at least supplementing the role function previously provided by inventive leaders...

"The greatest harbour in the world" : Sydney Harbour as a contested space in Australian culture

It is a matter of public record that the former Prime Minister of Australia, the Honourable Paul Keating, upset certain Australian architects with his intervention into the redevelopment of the 22-hectare “Barangaroo” site on Sydney Harbour. While Keating’s intervention continues to provide engaging theatre for Sydney residents the debate is also an interesting expression of the narrative of contestation that has been played out historically about the waters of Sydney Harbour. From a cultural studies perspective, the Harbour, and the Sydney Harbour Bridge, has been for many years a political and imaginative space that captures a diversity of local and national preoccupations. Keating’s announcement that planners have a “once-in-200-year opportunity to call a halt to the kind of encroachments we have seen in the past” is in fact another moment in the long history of disputation over the impact of the man-made environment on the natural landform in this area. This paper addresses the spaces of Sydney Harbour as represented in recent debates and in writing and film from previous decades. The argument suggests that the Harbour is a complex site of public and private enactment that is played out in a diverse range of cultural representations. In particular, the paper notes the work of Michel de Certeau on the mythic qualities of certain spaces in relation to the space of the Harbour. ‘The Greatest Harbour in the World’ argues that the Harbour, and the Bridge, fulfils a particular historical and cultural function that gives this space a set of meanings that are well beyond the typical parameters of urban development.