Multiscale analysis of protein functions and stochastic modelling of gene transcriptional regulatory networks

Genomic and proteomic analyses have attracted a great deal of interests in biological research in recent years. Many methods have been applied to discover useful information contained in the enormous databases of genomic sequences and amino acid sequences. The results of these investigations inspire further research in biological fields in return. These biological sequences, which may be considered as multiscale sequences, have some specific features which need further efforts to characterise using more refined methods. This project aims to study some of these biological challenges with multiscale analysis methods and stochastic modelling approach. The first part of the thesis aims to cluster some unknown proteins, and classify their families as well as their structural classes. A development in proteomic analysis is concerned with the determination of protein functions. The first step in this development is to classify proteins and predict their families. This motives us to study some unknown proteins from specific families, and to cluster them into families and structural classes. We select a large number of proteins from the same families or superfamilies, and link them to simulate some unknown large proteins from these families. We use multifractal analysis and the wavelet method to capture the characteristics of these linked proteins. The simulation results show that the method is valid for the classification of large proteins. The second part of the thesis aims to explore the relationship of proteins based on a layered comparison with their components. Many methods are based on homology of proteins because the resemblance at the protein sequence level normally indicates the similarity of functions and structures. However, some proteins may have similar functions with low sequential identity. We consider protein sequences at detail level to investigate the problem of comparison of proteins. The comparison is based on the empirical mode decomposition (EMD), and protein sequences are detected with the intrinsic mode functions. A measure of similarity is introduced with a new cross-correlation formula. The similarity results show that the EMD is useful for detection of functional relationships of proteins. The third part of the thesis aims to investigate the transcriptional regulatory network of yeast cell cycle via stochastic differential equations. As the investigation of genome-wide gene expressions has become a focus in genomic analysis, researchers have tried to understand the mechanisms of the yeast genome for many years. How cells control gene expressions still needs further investigation. We use a stochastic differential equation to model the expression profile of a target gene. We modify the model with a Gaussian membership function. For each target gene, a transcriptional rate is obtained, and the estimated transcriptional rate is also calculated with the information from five possible transcriptional regulators. Some regulators of these target genes are verified with the related references. With these results, we construct a transcriptional regulatory network for the genes from the yeast Saccharomyces cerevisiae. The construction of transcriptional regulatory network is useful for detecting more mechanisms of the yeast cell cycle.

Encryption schemes and key exchange protocols in the certificateless setting

The contributions of this thesis fall into three areas of certificateless cryptography. The first area is encryption, where we propose new constructions for both identity-based and certificateless cryptography. We construct an n-out-of- n group encryption scheme for identity-based cryptography that does not require any special means to generate the keys of the trusted authorities that are participating. We also introduce a new security definition for chosen ciphertext secure multi-key encryption. We prove that our construction is secure as long as at least one authority is uncompromised, and show that the existing constructions for chosen ciphertext security from identity-based encryption also hold in the group encryption case. We then consider certificateless encryption as the special case of 2-out-of-2 group encryption and give constructions for highly efficient certificateless schemes in the standard model. Among these is the first construction of a lattice-based certificateless encryption scheme. Our next contribution is a highly efficient certificateless key encapsulation mechanism (KEM), that we prove secure in the standard model. We introduce a new way of proving the security of certificateless schemes based that are based on identity-based schemes. We leave the identity-based part of the proof intact, and just extend it to cover the part that is introduced by the certificateless scheme. We show that our construction is more efficient than any instanciation of generic constructions for certificateless key encapsulation in the standard model. The third area where the thesis contributes to the advancement of certificateless cryptography is key agreement. Swanson showed that many certificateless key agreement schemes are insecure if considered in a reasonable security model. We propose the first provably secure certificateless key agreement schemes in the strongest model for certificateless key agreement. We extend Swanson's definition for certificateless key agreement and give more power to the adversary. Our new schemes are secure as long as each party has at least one uncompromised secret. Our first construction is in the random oracle model and gives the adversary slightly more capabilities than our second construction in the standard model. Interestingly, our standard model construction is as efficient as the random oracle model construction.

Role demands and work-family balance experience in Malaysia : the different moderating effects of collectivism and gender role identity among diverse ethnic groups

The purpose of this thesis is to examine the influence of ethnic cultural values on the relationship of role demands and the work-family balance (WFB) experience. Past studies have found that the demands from work and family roles have a different impact on the work-family experience in people of different ethnicity. Researchers attribute these results to the cultural differences across the groups. However, there has been no empirical support for these assumptions because most past studies did not explicitly measure the cultural dimension in their design. Therefore, although studies have found ethnic differences in work-family experience, as cultural variables were not measured, it cannot be determined whether these differences were due to the differing ethnic groups’ cultural styles. The present thesis is set up to address this limitation in the literature, employing the Malay and Chinese ethnic groups in Malaysia as the study samples. The investigation consisted of pilot interviews and two survey studies. The interviews were carried out to establish the perception of WFB by target participants of a non-western nation. The first survey served to identify whether the Malay and Chinese ethnic groups residing under the same economic and social systems vary in their perceptions of work and family roles. The second survey tests the research model empirically, that is, whether cultural values moderate the relationship between role demands and WFB and if these moderation effects vary across ethnic groups. From the interviews, the results indicated that work-family experience is not a universal experience, but is partly culture-specific. Specifically, in the case of Malaysia, WFB is very much observed from the role obligation perspective. In particular, balance is perceived when work duties and household affairs are both adequately fulfilled. On the other hand, the conceptualisation of WFB in terms of role satisfaction and role interference also emerged in the interviews, suggesting the universality of these constructs across cultures. The findings from Survey One indicated that participants of different ethnicities in this study do not differ greatly in their perceptions regarding their participation in work and family roles. Generally, these participants revealed the less traditional attitudes towards women’s participation in work and family roles. However, variations were observed between the two groups in terms of reasons for working, spouses’ preferences towards their employment, and the extent to which their work role is perceived to impede their normative role performance in the household. Despite these differences, the Malay and Chinese ethnic groups showed more similarities than differences in their perceptions of work and family. The findings from Survey Two, which tested the research model, produced mixed results. On the whole, the results showed that the cultural dimensions examined in this study (i.e. collectivism, work identity and family identity) did influence the relationship between role demands and WFB experience, thus providing empirical evidence for the assumption in the literature that the relationship between role demand and work-family experience is moderated by cultural values. Most importantly, support was found for the proposition that these moderation effects vary between the Malay and Chinese ethnic groups. Moreover, this study also found evidence that Malays and Chinese differ significantly on collectivism and work identity cultural dimensions where Malays are found to be more collectivist than the Chinese, while work identity is stronger in the Chinese than in the Malays. There is no difference in the levels of family identity between the two groups. Of all the three moderators, work identity was deemed the most important because many of the supported hypotheses pertained to the work identity moderating effects. In contrast, family identity does not seem to have much moderating influence on role demand-WFB relationships, while the results for the collectivism moderator are mixed. As such, although not conclusive, it can be deduced that variations in the effects of role demand on work-family experience across ethnicity are a result of the groups’ cultural differences, thereby supporting the assumption in the literature.

Do we have a legally binding contract?

Legal advisers are often called upon to advise whether informal correspondence between clients may give rise to a binding contract. The decision of Mullins J in Teviot Downs Estate Pty Ltd v MTAA Superannuation Fund (Flagstone Creek and Spring Mountain Park) Property Pty Ltd [2003] QSC 403 provides general guidance as to matters that may be relevant when faced with this thorny issue.

Online we are all able bodied : Online psychological sense of community and social support found through membership of disability-specific websites promotes well-being for people living with a physical disability

People with a physical disability are a population who for a number of reasons may be vulnerable to social isolation. Research into Internet-based support sites has found that social support and an online sense of community can be developed through computer mediated communication channels. This study aims to gain an understanding of the benefits that membership of disability-specific online communities may have for people with a physical disability. An online survey was administered to a sample of users of such sites (N = 160). Results indicated that users did receive moral support and personal advice through participating in such online communities. Further, results indicated that online social support and feeling a sense of community online were positively associated with participants' well-being in the areas of personal relations and personal growth.

Comparison of koala LPCoLN and human strains of Chlamydia pneumoniae highlights extended genetic diversity in the species

Background Chlamydia pneumoniae is a widespread pathogen causing upper and lower respiratory tract infections in addition to a range of other diseases in humans and animals. Previous whole genome analyses have focused on four essentially clonal (> 99% identity) C. pneumoniae human genomes (AR39, CWL029, J138 and TW183), providing relatively little insight into strain diversity and evolution of this species. Results We performed individual gene-by-gene comparisons of the recently sequenced C. pneumoniae koala genome and four C. pneumoniae human genomes to identify species-specific genes, and more importantly, to gain an insight into the genetic diversity and evolution of the species. We selected genes dispersed throughout the chromosome, representing genes that were specific to C. pneumoniae, genes with a demonstrated role in chlamydial biology and/or pathogenicity (n = 49), genes encoding nucleotide salvage or amino acid biosynthesis proteins (n = 6), and extrachromosomal elements (9 plasmid and 2 bacteriophage genes). Conclusions We have identified strain-specific differences and targets for detection of C. pneumoniae isolates from both human and animal origin. Such characterisation is necessary for an improved understanding of disease transmission and intervention.

Developing ethical identities in young offenders through restorative justice practice in Australia

Restorative justice is firmly established in Australian juvenile justice. While the official language used to describe restorative initiatives varies across states and territories, the most common form is a meeting or conference between young offenders and their victims (most commonly known as a family group or youth justice conference). During the past decade, an impressive amount of empirical research has examined how the restorative justice process affects offenders, victims and other participants (such as supporters for young offenders and victims). Results from this line of research are remarkably consistent and show that participants generally regard restorative conferences as procedurally fair and that they are satisfied with the outcomes (eg what young offenders agree to do to make up for their offending behaviour, such as offer a sincere apology or perform work for the victim or the community). What is less common, however, is the perception among participants that restorative conferences achieve the key aim of restoration.By ‘restoration’ we refer to encounters where ‘offenders apologise, their apologies are accepted, victims offer forgiveness,and conferences conclude with a feeling of mutual good will’.

Equity in the twenty-first century

Issues of equity and inequity have always been part of employment relations and are a fundamental part of the industrial landscape. For example, in most countries in the nineteenth century and a large part of the twentieth century women and members of ethnic groups (often a minority in the workforce) were barred from certain occupations, industries or work locations, and received less pay than the dominant male ethnic group for the same work. In recent decades attention has been focused on issues of equity between groups, predominantly women and different ethnic groups in the workforce. This has been embodied in industrial legislation, for example in equal pay for women and men, and frequently in specific equity legislation. In this way a whole new area of law and associated workplace practice has developed in many countries. Historically, employment relations and industrial relations research has not examined employment issues disaggregated by gender or ethnic group. Born out of concern with conflict and regulation at the workplace, studies tended to concentrate on white, male, unionized workers in manufacturing and heavy industry (Ackers, 2002, p. 4). The influential systems model crafted by Dunlop (1958) gave rise to The discipline’s preoccupation with the ‘problem of order’ [which] ensures the invisibility of women, not only because women have generally been less successful in mobilizing around their own needs and discontents, but more profoundly because this approach identifies the employment relationship as the ultimate source of power and conflict at work (Forrest, 1993, p. 410). While ‘the system approach does not deliberately exclude gender . . . by reproducing a very narrow research approach and understanding of issues of relevance for the research, gender is in general excluded or looked on as something of peripheral interest’ (Hansen, 2002, p. 198). However, long-lived patterns of gender segregation in occupations and industries, together with discriminatory access to work and social views about women and ethnic groups in the paid workforce, mean that the employment experience of women and ethnic groups is frequently quite different to that of men in the dominant ethnic group. Since the 1980s, research into women and employment has figured in the employment relations literature, but it is often relegated to a separate category in specific articles or book chapters, with women implicitly or explicitly seen as the atypical or exceptional worker (Hansen, 2002; Wajcman, 2000). The same conclusion can be reached for other groups with different labour force patterns and employment outcomes. This chapter proposes that awareness of equity issues is central to employment relations. Like industrial relations legislation and approaches, each country will have a unique set of equity policies and legislation, reflecting their history and culture. Yet while most books on employment and industrial relations deal with issues of equity in a separate chapter (most commonly on equity for women or more recently on ‘diversity’), the reality in the workplace is that all types of legislation and policies which impact on the wages and working conditions interact, and their impact cannot be disentangled one from another. When discussing equity in workplaces in the twenty-first century we are now faced with a plethora of different terms in English. Terms used include discrimination, equity, equal opportunity, affirmative action and diversity with all its variants (workplace diversity, managing diversity, and so on). There is a lack of agreed definitions, particularly when the terms are used outside of a legislative context. This ‘shifting linguistic terrain’ (Kennedy-Dubourdieu, 2006b, p. 3) varies from country to country and changes over time even within the one country. There is frequently a division made between equity and its related concepts and the range of expressions using the term ‘diversity’ (Wilson and Iles, 1999; Thomas and Ely, 1996). These present dilemmas for practitioners and researchers due to the amount and range of ideas prevalent – and the breadth of issues that are covered when we say ‘equity and diversity in employment’. To add to these dilemmas, the literature on equity and diversity has become bifurcated: the literature on workplace diversity/management diversity appears largely in the business literature while that on equity in employment appears frequently in legal and industrial relations journals. Workplaces of the twenty-first century differ from those of the nineteenth and twentieth century not only in the way they deal with individual and group differences but also in the way they interpret what are fair and equitable outcomes for different individuals and groups. These variations are the result of a range of social conditions, legislation and workplace constraints that have influenced the development of employment equity and the management of diversity. Attempts to achieve employment equity have primarily been dealt with through legislative means, and in the last fifty years this legislation has included elements of anti-discrimination, affirmative action, and equal employment opportunity in virtually all OECD countries (Mor Barak, 2005, pp. 17–52). Established on human rights and social justice principles, this legislation is based on the premise that systemic discrimination has and/or continues to exist in the labour force and particular groups of citizens have less advantageous employment outcomes. It is based on group identity, and employment equity programmes in general apply across all workplaces and are mandatory. The more recent notions of diversity in the workplace are based on ideas coming principally from the USA in the 1980s which have spread widely in the Western world since the 1990s. Broadly speaking, diversity ideas focus on individual differences either on their own or in concert with the idea of group differences. The diversity literature is based on a business case: that is diversity is profitable in a variety of ways for business, and generally lacks a social justice or human rights justification (Burgess et al., 2009, pp. 81–2). Managing diversity is represented at the organizational level as a voluntary and local programme. This chapter discusses some major models and theories for equity and diversity. It begins by charting the history of ideas about equity in employment and then briefly discusses what is meant by equality and equity. The chapter then analyses the major debates about the ways in which equity can be achieved. The more recent ideas about diversity are then discussed, including the history of these ideas and the principles which guide this concept. The following section discusses both major frameworks of equity and diversity. The chapter then raises some ways in which insights from the equity and diversity literature can inform employment relations. Finally, the future of equity and diversity ideas is discussed.

A qualitative study of older adults’ responses to sitting-time questions : do we get the information we want?

Background: In the last decade, there has been increasing interest in the health effects of sedentary behavior, which is often assessed using self-report sitting-time questions. The aim of this qualitative study was to document older adults’ understanding of sitting-time questions from the International Physical Activity (PA) Questionnaire (IPAQ) and the PA Scale for the Elderly (PASE). Methods: Australian community-dwelling adults aged 65+ years answered the IPAQ and PASE sitting questions in face-to-face semi-structured interviews. IPAQ uses one open-ended question to assess sitting on a weekday in the last 7 days 'at work, at home, while doing coursework and during leisure time'; PASE uses a three-part closed question about daily leisure-time sitting in the last 7 days. Participants expressed their thoughts out loud while answering each question. They were then probed about their responses. Interviews were recorded, transcribed and coded into themes. Results: Mean age of the 28 male and 27 female participants was 73 years (range 65-89). The most frequently reported activity was watching TV. For both questionnaires, many participants had difficulties understanding what activities to report. Some had difficulty understanding what activities should be classified as ‘leisure-time sitting’. Some assumed they were being asked to only report activities provided as examples. Most reported activities they normally do, rather than those performed on a day in the previous week. Participants used a variety of strategies to select ‘a day’ for which they reported their sitting activities and to calculate sitting time on that day. Therefore, many different ways of estimating sitting time were used. Participants had particular difficulty reporting their daily sitting-time when their schedules were not consistent across days. Some participants declared the IPAQ sitting question too difficult to answer. Conclusion: The accuracy of older adults’ self-reported sitting time is questionable given the challenges they have in answering sitting-time questions. Their responses to sitting-time questions may be more accurate if our recommendations for clarifying the sitting domains, providing examples relevant to older adults and suggesting strategies for formulating responses are incorporated. Future quantitative studies should include objective criterion measures to assess validity and reliability of these questions.

Reflections on a year of engineering leadership

Doug Hargreaves has completed a year as President of Engineers Australia, a 90,000 strong membership based organisation representing the engineering profession. In preparing for the year Doug decided that the core of his own leadership is his values and that the legacy he wanted to be remembered for at the end of his year, was how his values underpinned everything he did. The framework for this values approach was a book he co-authored entitled 'Values Driven Leadership'. The essence of Doug's philosophy is that a leader who bases their leadership on a strong sense of values will create an environment where people have a strong sense of Belonging, Identity and Purpose. This paper reflects on Doug's year of leadership of Engineers Australia and offers insights and examples of where his values driven leadership approach played out and contributed to various scenarios he encountered over the year. The paper will share Doug's approach to leadership and offer an understanding of how an effective leader actually does what he does. Too often leadership is seen as a nebulous capacity that people either have or do not have. In this paper, we will identify the specific skills and abilities within a values framework that will allow any leader to be more effective in their role.

Heidegger's hippies : a dissenting voice on "the problem of the subject"

This is a deliberately contentious paper about the future of the socio-political sphere in the West based on what we know about its past. I argue that the predominant public discourse in Western countries is best characterised as one of selective forgetfulness; a semi-blissful, amnesiacal state of collective dementia that manifests itself in symbolic idealism: informationalism. Informationalism is merely the latest form of idealism. It is a lot like religion insofar as it causally relates abstract concepts with reality and, consequently, becomes confused between the two. Historically, this has proven to be a dangerous state of affairs, especially when elites becomes confused between ideas about how a society should work, and the way it actually does work. Central to the idealism of the information age, at least in intellectual spheres, is the so called "problem of the subject". I argue that the "problem of the subject" is a largely synthetic, destabilising, and ultimately fruitless theoretical abstraction which turns on a synthetically derived, generalised intradiscursive space; existentialist nihilism; and the theoretical baubles of ontological metaphysics. These philosophical aberrations are, in turn, historically concomitant with especially destructive political and social configurations. This paper sketches a theoretical framework for identity formation which rejects the problem of the subject, and proposes potential resources, sources, and strategies with which to engage the idealism that underpins this obfuscating problematic in an age of turbulent social uncertainty. Quite simply, I turn to history as the source of human identity. While informationalism, like religion, is mostly focused on utopian futures, I assert that history, not the future, holds the solutions for substantive problematics concerning individual and social identities. I argue here that history, language, thought, and identity are indissolubly entangled and so should be understood as such: they are the fundamental parts of 'identities in action'. From this perspective, the ‘problem of the subject’ becomes less a substantive intellectual problematic and more a theoretical red herring.

A systematic review of environmental factors and obesogenic dietary intakes among adults : are we getting closer to understanding obesogenic environments?

This study examined whether physical, social, cultural and economical environmental factors are associated with obesogenic dietary behaviours and overweight/obesity among adults. Literature searches of databases (i.e. PubMed, CSA Illumina, Web of Science, PsychInfo) identified studies examining environmental factors and the consumption of energy, fat, fibre, fruit, vegetables, sugar-sweetened drinks, meal patterns and weight status. Twenty-eight studies were in-scope, the majority (n= 16) were conducted in the USA. Weight status was consistently associated with the food environment; greater accessibility to supermarkets or less access to takeaway outlets were associated with a lower BMI or prevalence of overweight/obesity. However, obesogenic dietary behaviours did not mirror these associations; mixed associations were found between the environment and obesogenic dietary behaviours. Living in a socioeconomically-deprived area was the only environmental factor consistently associated with a number of obesogenic dietary behaviours. Associations between the environment and weight status are more consistent than that seen between the environment and dietary behaviours. The environment may play an important role in the development of overweight/obesity, however the dietary mechanisms that contribute to this remain unclear and the physical activity environment may also play an important role in weight gain, overweight and obesity.