Bayesian methodology for genetics of complex diseases

Genetic research of complex diseases is a challenging, but exciting, area of research. The early development of the research was limited, however, until the completion of the Human Genome and HapMap projects, along with the reduction in the cost of genotyping, which paves the way for understanding the genetic composition of complex diseases. In this thesis, we focus on the statistical methods for two aspects of genetic research: phenotype definition for diseases with complex etiology and methods for identifying potentially associated Single Nucleotide Polymorphisms (SNPs) and SNP-SNP interactions. With regard to phenotype definition for diseases with complex etiology, we firstly investigated the effects of different statistical phenotyping approaches on the subsequent analysis. In light of the findings, and the difficulties in validating the estimated phenotype, we proposed two different methods for reconciling phenotypes of different models using Bayesian model averaging as a coherent mechanism for accounting for model uncertainty. In the second part of the thesis, the focus is turned to the methods for identifying associated SNPs and SNP interactions. We review the use of Bayesian logistic regression with variable selection for SNP identification and extended the model for detecting the interaction effects for population based case-control studies. In this part of study, we also develop a machine learning algorithm to cope with the large scale data analysis, namely modified Logic Regression with Genetic Program (MLR-GEP), which is then compared with the Bayesian model, Random Forests and other variants of logic regression.

Gifted young adolescents : voices of self

Despite the challenges that giftedness can add to self-formation during early adolescence, gifted young adolescents seldom are asked about their lives outside of counselling and educational contexts. The study considers the complexities that face gifted young adolescents in the process of self-discovery and self-representation, thereby building a case for seeking their own viewpoints. A guiding assumption for the study was that gifted young adolescents may respond positively to the opportunity to share their own perspectives and their own versions of “who they are”. The theoretical underpinnings for this study drew from Dialogical Self Theory. The study resides within an interactive view of self as a dynamic construction rather than a static state, where “who we are” is formed in everyday exchanges with self and others. Self-making as a process among gifted young adolescents is presented as an interactive network of “I” voices interpreted to reflect internal and external dialogue. In this way, self is understood within dialogical concepts of voices as multiple expressions. The study invited twelve gifted young adolescents to write freely about themselves over a six month period in an email journal project. Participants were recruited online and by word-of-mouth and they were able to negotiate their own levels of involvement. Access to the lives of individual young adolescents was sought in an out-of-school setting using narrative methods of personal writing in the form of journals sent as emails to the researcher. The role of the researcher was to act as a supportive listener who responded to participant-led emails and thereby facilitated the process of authoring that occurred across the data-gathering phase. The listening process involved responses that were affirming and designed to build trust. Data in the form of email texts were analysed using a close listening method that uncovered patterns of voices that were explicitly or subtly expressed by participants. The interpretation of voices highlighted the tensions and contradictions involved in the process of participants forming a “self” that emerged as multiple “I” voices. There were three key findings of the study. First, the gifted young adolescent participants each constructed a self around four key voices of Author, Achiever, Resistor/Co-operator and Self-Innovator. These voices were dialogical selfconstructions that showed multiplicity as a normal way of being. Second, the selfmaking processes of the gifted young adolescent participants were guided by a hierarchy of voices that were directed through self-awareness. Third, authoring in association with a responsive adult listener emerged as a dialogic space for promoting self-awareness and a language of self-expression among gifted young adolescents. The findings of the study contribute to knowledge about gifted young adolescents by presenting their own versions of “who” they are, perspectives that might differ from mainstream perceptions. Participants were shown to have highly diverse, complex and individual expressions that have implications for how well they are understood and supported by others. The use of email journals helped to create a synergy for self-disclosure and a safe space for self-expression where participants’ abilities to be themselves were encouraged. Increased self-awareness and selfknowledge among gifted young adolescents is vital to their self-formation and their management of self and others’ expectations. This study makes an original contribution to the field of self-study by highlighting the processes and complexities of young adolescents’ self-constructions. Through the innovative use of narrative methods and an inter-disciplinary approach, the voices of gifted young adolescents were privileged. At a practical level, the study can inform educators, policy-makers, parents and all those who seek to contribute to the well-being of gifted young adolescents.

A collagen network phase improves cell seeding of open-pore structure scaffolds under perfusion

Scaffolds with open-pore morphologies offer several advantages in cell-based tissue engineering, but their use is limited by a low cell seeding efficiency. We hypothesized that inclusion of a collagen network as filling material within the open-pore architecture of polycaprolactone-tricalcium phosphate (PCL-TCP) scaffolds increases human bone marrow stromal cells (hBMSC) seeding efficiency under perfusion and in vivo osteogenic capacity of the resulting constructs. PCL-TCP scaffolds, rapid prototyped with a honeycomb-like architecture, were filled with a collagen gel and subsequently lyophilized, with or without final crosslinking. Collagen-free scaffolds were used as controls. The seeding efficiency was assessed after overnight perfusion of expanded hBMSC directly through the scaffold pores using a bioreactor system. By seeding and culturing freshly harvested hBMSC under perfusion for 3 weeks, the osteogenic capacity of generated constructs was tested by ectopic implantation in nude mice. The presence of the collagen network, independently of the crosslinking process, significantly increased the cell seeding efficiency (2.5-fold), and reduced the loss of clonogenic cells in the supernatant. Although no implant generated frank bone tissue, possibly due to the mineral distribution within the scaffold polymer phase, the presence of a non crosslinked collagen phase led to in vivo formation of scattered structures of dense osteoids. Our findings verify that the inclusion of a collagen network within open morphology porous scaffolds improves cell retention under perfusion seeding. In the context of cell-based therapies, collagen-filled porous scaffolds are expected to yield superior cell utilization, and could be combined with perfusion-based bioreactor devices to streamline graft manufacture.

The benefits of not managing change and not communicating : towards a complex systems view of communication in evolving organisations

The relationship between change in organisations and communication about change in organisations can be analysed as a particular case of a general debate in social theory about the extent to which reality is socially constructed. Social constructivists emphasise the role of language in the construction of social realities, enacted through controlling the message agenda; material determinists assert that economic and social structural factors are more constitutive of reality as seen in strategies emphasising structural and resource interventions. Here we define a third view of language and materiality - one that leads to the potential for a reflexive, experimental approach to change based on the view that organisations are complex evolving systems.

Social network and aesthetic reflexivity in the creative industries

This article reviews some key critical writing about the commodification or exploitation of networked social relations in the creative industries. Through a comparative case study of networks in fashion and new media industries in the city of Manchester, UK, the article draws attention to the social, cultural and aesthetic aspects of the networks among creative practitioners. It argues that within the increasing commercialisation in the creative industries there are networked spaces within which non-instrumental values are created. The building of social networks reflects on the issue of how creatives perceive their work in these industries both economically and socially/culturally.

Schooling and refugees : engaging with the complex trajectories of globalisation

This paper examines the complexities associated with educating a mobile and politically marginalised population, refugee students, in the state of Queensland, Australia. Historically, schools have been national institutions concerned with social reproduction and citizenship formation with a focus on spatially fixed populations. While education authorities in much of the developed world now acknowledge the need to prepare students for a more interconnected world of work and opportunity, they have largely failed to provide systemic support for one category of children on the move - refugees. We begin this paper with a discussion of forced migration and its links with ‘globalisation’. We then present our research findings about the educational challenges confronting individual refugee youth and schools in Queensland. This is followed with a summary of good practice in refugee education. The paper concludes with a discussion of how nation-states might play a more active role in facilitating transitions to citizenship for refugee youth.

The sample complexity of pattern classification with neural networks: the size of the weights is more important than the size of the network

Sample complexity results from computational learning theory, when applied to neural network learning for pattern classification problems, suggest that for good generalization performance the number of training examples should grow at least linearly with the number of adjustable parameters in the network. Results in this paper show that if a large neural network is used for a pattern classification problem and the learning algorithm finds a network with small weights that has small squared error on the training patterns, then the generalization performance depends on the size of the weights rather than the number of weights. For example, consider a two-layer feedforward network of sigmoid units, in which the sum of the magnitudes of the weights associated with each unit is bounded by A and the input dimension is n. We show that the misclassification probability is no more than a certain error estimate (that is related to squared error on the training set) plus A3 √((log n)/m) (ignoring log A and log m factors), where m is the number of training patterns. This may explain the generalization performance of neural networks, particularly when the number of training examples is considerably smaller than the number of weights. It also supports heuristics (such as weight decay and early stopping) that attempt to keep the weights small during training. The proof techniques appear to be useful for the analysis of other pattern classifiers: when the input domain is a totally bounded metric space, we use the same approach to give upper bounds on misclassification probability for classifiers with decision boundaries that are far from the training examples.

Neural network learning:theoretical foundations

This important work describes recent theoretical advances in the study of artificial neural networks. It explores probabilistic models of supervised learning problems, and addresses the key statistical and computational questions. Chapters survey research on pattern classification with binary-output networks, including a discussion of the relevance of the Vapnik Chervonenkis dimension, and of estimates of the dimension for several neural network models. In addition, Anthony and Bartlett develop a model of classification by real-output networks, and demonstrate the usefulness of classification with a "large margin." The authors explain the role of scale-sensitive versions of the Vapnik Chervonenkis dimension in large margin classification, and in real prediction. Key chapters also discuss the computational complexity of neural network learning, describing a variety of hardness results, and outlining two efficient, constructive learning algorithms. The book is self-contained and accessible to researchers and graduate students in computer science, engineering, and mathematics

Artful inquiry : an arts-based facilitation approach for individual and organisational learning and development

The research undertaken in these two major doctoral studies investigates the field of artsbased learning, a pedagogical approach to individual and organisational learning and development, my professional creative facilitation practice and development as a researcher. While the studies are stand-alone projects they are intended to build on each other in order to tell the evolving story of my research and professional practice. The first study combines The Role of Arts-based Learning in a Creative Economy; The Need for Artistry in Professional Education the art of knowing what to do when you don’t know what to do and Lines of Inquiry: Making Sense of Research and Professional Practice. The Role of Arts-based Learning in a Creative Economy provides an overview of the field of arts-based learning in business. The study focuses on the relevant literature and interviews with people working in the field. The paper argues that arts-based learning is a valuable addition to organisations for building a culture of creativity and innovation. The Need for Artistry in Professional Education continues that investigation. It explores the way artists approach their work and considers what skills and capabilities from artistic practice can be applied to other professions’ practices. From this research the Sphere of Professional Artistry model is developed and depicts the process of moving toward professional artistry. Lines of Inquiry: making sense of research and professional practice through artful inquiry is a self-reflective study. It explores my method of inquiry as a researcher and as a creative facilitation practitioner using arts-based learning processes to facilitate groups of people for learning, development and change. It discusses how my research and professional practice influence and inspire the other and draws on cased studies. The second major research study Artful Inquiry: Arts-based Learning for Inquiry, Reflection and Action in Professional Practice is a one year practice-led inquiry. It continues the research into arts-based and aesthetic learning experiences and my arts-based facilitation practice. The research is conducted with members of a Women’s Network in a large government service agency. It develops the concept of ‘Artful Inquiry’’ a creative, holistic, and embodied approach for facilitation, inquiry, learning, reflection, and action. Storytelling as Inquiry is used as a methodology for understanding participants’ experiences of being involved in arts-based learning experiences. The study reveals the complex and emergent nature of practice and research. It demonstrates what it can mean to do practice-led research with others, within an organisational context, and to what effect.

Overcoming the complexity of diagnostic problems due to sensor network architecture

In fault detection and diagnostics, limitations coming from the sensor network architecture are one of the main challenges in evaluating a system’s health status. Usually the design of the sensor network architecture is not solely based on diagnostic purposes, other factors like controls, financial constraints, and practical limitations are also involved. As a result, it quite common to have one sensor (or one set of sensors) monitoring the behaviour of two or more components. This can significantly extend the complexity of diagnostic problems. In this paper a systematic approach is presented to deal with such complexities. It is shown how the problem can be formulated as a Bayesian network based diagnostic mechanism with latent variables. The developed approach is also applied to the problem of fault diagnosis in HVAC systems, an application area with considerable modeling and measurement constraints.

Group maintenance scheduling : a case study for a pipeline network

This paper presents a group maintenance scheduling case study for a water distributed network. This water pipeline network presents the challenge of maintaining aging pipelines with the associated increases in annual maintenance costs. The case study focuses on developing an effective maintenance plan for the water utility. Current replacement planning is difficult as it needs to balance the replacement needs under limited budgets. A Maintenance Grouping Optimization (MGO) model based on a modified genetic algorithm was utilized to develop an optimum group maintenance schedule over a 20-year cycle. The adjacent geographical distribution of pipelines was used as a grouping criterion to control the searching space of the MGO model through a Judgment Matrix. Based on the optimum group maintenance schedule, the total cost was effectively reduced compared with the schedules without grouping maintenance jobs. This optimum result can be used as a guidance to optimize the current maintenance plan for the water utility.

Stochastic simulation of chemical reactions in spatially complex media

Discrete stochastic simulations, via techniques such as the Stochastic Simulation Algorithm (SSA) are a powerful tool for understanding the dynamics of chemical kinetics when there are low numbers of certain molecular species. However, an important constraint is the assumption of well-mixedness and homogeneity. In this paper, we show how to use Monte Carlo simulations to estimate an anomalous diffusion parameter that encapsulates the crowdedness of the spatial environment. We then use this parameter to replace the rate constants of bimolecular reactions by a time-dependent power law to produce an SSA valid in cases where anomalous diffusion occurs or the system is not well-mixed (ASSA). Simulations then show that ASSA can successfully predict the temporal dynamics of chemical kinetics in a spatially constrained environment.