A novel representation of bioacoustic events for content-based search in field audio data

Bioacoustic data can provide an important base for environmental monitoring. To explore a large amount of field recordings collected, an automated similarity search algorithm is presented in this paper. A region of an audio defined by frequency and time bounds is provided by a user; the content of the region is used to construct a query. In the retrieving process, our algorithm will automatically scan through recordings to search for similar regions. In detail, we present a feature extraction approach based on the visual content of vocalisations – in this case ridges, and develop a generic regional representation of vocalisations for indexing. Our feature extraction method works best for bird vocalisations showing ridge characteristics. The regional representation method allows the content of an arbitrary region of a continuous recording to be described in a compressed format.

The association of single nucleotide polymorphisms with endometrial cancer risk and prognosis

Endometrial cancer is one of the most common female diseases in developed nations and is the most commonly diagnosed gynaecological cancer in Australia. The disease is commonly classified by histology: endometrioid or non-endometrioid endometrial cancer. While non-endometrioid endometrial cancers are accepted to be high-grade, aggressive cancers, endometrioid cancers (comprising 80% of all endometrial cancers diagnosed) generally carry a favourable patient prognosis. However, endometrioid endometrial cancer patients endure significant morbidity due to surgery and radiotherapy used for disease treatment, and patients with recurrent disease have a 5-year survival rate of less than 50%. Genetic analysis of women with endometrial cancer could uncover novel markers associated with disease risk and/or prognosis, which could then be used to identify women at high risk and for the use of specialised treatments. Proteases are widely accepted to play an important role in the development and progression of cancer. This PhD project hypothesised that SNPs from two protease gene families, the matrix metalloproteases (MMPs, including their tissue inhibitors, TIMPs) and the tissue kallikrein-related peptidases (KLKs) would be associated with endometrial cancer susceptibility and/or prognosis. In the first part of this study, optimisation of the genotyping techniques was performed. Results from previously published endometrial cancer genetic association studies were attempted to be validated in a large, multicentre replication set (maximum cases n = 2,888, controls n = 4,483, 3 studies). The rs11224561 progesterone receptor SNP (PGR, A/G) was observed to be associated with increased endometrial cancer risk (per A allele OR 1.31, 95% CI 1.12-1.53; p-trend = 0.001), a result which was initially reported among a Chinese sample set. Previously reported associations for the remaining 8 SNPs investigated for this section of the PhD study were not confirmed, thereby reinforcing the importance of validation of genetic association studies. To examine the effect of SNPs from the MMP and KLK families on endometrial cancer risk, we selected the most significantly associated MMP and KLK SNPs from genome-wide association study analysis (GWAS) to be genotyped in the GWAS replication set (cases n = 4,725, controls n = 9,803, 13 studies). The significance of the MMP24 rs932562 SNP was unchanged after incorporation of the stage 2 samples (Stage 1 per allele OR 1.18, p = 0.002; Combined Stage 1 and 2 OR 1.09, p = 0.002). The rs10426 SNP, located 3' to KLK10 was predicted by bioinformatic analysis to effect miRNA binding. This SNP was observed in the GWAS stage 1 result to exhibit a recessive effect on endometrial cancer risk, a result which was not validated in the stage 2 sample set (Stage 1 OR 1.44, p = 0.007; Combined Stage 1 and 2 OR 1.14, p = 0.08). Investigation of the regions imputed surrounding the MMP, TIMP and KLK genes did not reveal any significant targets for further analysis. Analysis of the case data from the endometrial cancer GWAS to identify genetic variation associated with cancer grade did not reveal SNPs from the MMP, TIMP or KLK genes to be statistically significant. However, the representation of SNPs from the MMP, TIMP and KLK families by the GWAS genotyping platform used in this PhD project was examined and observed to be very low, with the genetic variation of four genes (MMP23A, MMP23B, MMP28 and TIMP1) not captured at all by this technique. This suggests that comprehensive candidate gene association studies will be required to assess the role of SNPs from these genes with endometrial cancer risk and prognosis. Meta-analysis of gene expression microarray datasets curated as part of this PhD study identified a number of MMP, TIMP and KLK genes to display differential expression by endometrial cancer status (MMP2, MMP10, MMP11, MMP13, MMP19, MMP25 and KLK1) and histology (MMP2, MMP11, MMP12, MMP26, MMP28, TIMP2, TIMP3, KLK6, KLK7, KLK11 and KLK12). In light of these findings these genes should be prioritised for future targeted genetic association studies. Two SNPs located 43.5 Mb apart on chromosome 15 were observed from the GWAS analysis to be associated with increased endometrial cancer grade, results that were validated in silico in two independent datasets. One of these SNPs, rs8035725 is located in the 5' untranslated region of a MYC promoter binding protein DENND4A (Stage 1 OR 1.15, p = 9.85 x 10P -5 P, combined Stage 1 and in silico validation OR 1.13, p = 5.24 x 10P -6 P). This SNP has previously been reported to alter the expression of PTPLAD1, a gene involved in the synthesis of very long fatty acid chains and in the Rac1 signaling pathway. Meta-analysis of gene expression microarray data found PTPLAD1 to display increased expression in the aggressive non-endometrioid histology compared with endometrioid endometrial cancer, suggesting that the causal SNP underlying the observed genetic association may influence expression of this gene. Neither rs8035725 nor significant SNPs identified by imputation were predicted bioinformatically to affect transcription factor binding sites, indicating that further studies are required to assess their potential effect on other regulatory elements. The other grade- associated SNP, rs6606792, is located upstream of an inferred pseudogene, ELMO2P1 (Stage 1 OR 1.12, p = 5 x 10P -5 P; combined Stage 1 and in silico validation OR 1.09, p = 3.56 x 10P -5 P). Imputation of the ±1 Mb region surrounding this SNP revealed a cluster of significantly associated variants which are predicted to abolish various transcription factor binding sites, and would be expected to decrease gene expression. ELMO2P1 was not included on the microarray platforms collected for this PhD, and so its expression could not be investigated. However, the high sequence homology of ELMO2P1 with ELMO2, a gene important to cell motility, indicates that ELMO2 could be the parent gene for ELMO2P1 and as such, ELMO2P1 could function to regulate the expression of ELMO2. Increased expression of ELMO2 was seen to be associated with increasing endometrial cancer grade, as well as with aggressive endometrial cancer histological subtypes by microarray meta-analysis. Thus, it is hypothesised that SNPs in linkage disequilibrium with rs6606792 decrease the transcription of ELMO2P1, reducing the regulatory effect of ELMO2P1 on ELMO2 expression. Consequently, ELMO2 expression is increased, cell motility is enhanced leading to an aggressive endometrial cancer phenotype. In summary, these findings have identified several areas of research for further study. The results presented in this thesis provide evidence that a SNP in PGR is associated with risk of developing endometrial cancer. This PhD study also reports two independent loci on chromosome 15 to be associated with increased endometrial cancer grade, and furthermore, genes associated with these SNPs to be differentially expressed according in aggressive subtypes and/or by grade. The studies reported in this thesis support the need for comprehensive SNP association studies on prioritised MMP, TIMP and KLK genes in large sample sets. Until these studies are performed, the role of MMP, TIMP and KLK genetic variation remains unclear. Overall, this PhD study has contributed to the understanding of genetic variation involvement in endometrial cancer susceptibility and prognosis. Importantly, the genetic regions highlighted in this study could lead to the identification of novel gene targets to better understand the biology of endometrial cancer and also aid in the development of therapeutics directed at treating this disease.

Writing the oriental woman : an examination of the representation of Japanese women in contemporary Australian crime fiction

This study considers the challenges in representing women from other cultures in the crime fiction genre. The study is presented in two parts; an exegesis and a creative practice component consisting of a full length crime fiction novel, Batafurai. The exegesis examines the historical period of a section of the novel—post-war Japan—and how the area of research known as Occupation Studies provides an insight into the conditions of women during this period. The exegesis also examines selected postcolonial theory and its exposition of representations of the 'other' as a western construct designed to serve Eurocentric ends. The genre of crime fiction is reviewed, also, to determine how characters purportedly representing Oriental cultures are constricted by established stereotypes. Two case studies are examined to investigate whether these stereotypes are still apparent in contemporary Australian crime fiction. Finally, I discuss my own novel, Batafurai, to review how I represented people of Asian background, and whether my attempts to resist stereotype were successful. My conclusion illustrates how novels written in the crime fiction genre are reliant on strategies that are action-focused, rather than character-based, and thus often use easily recognizable types to quickly establish frameworks for their stories. As a sub-set of popular fiction, crime fiction has a tendency to replicate rather than challenge established stereotypes. Where it does challenge stereotypes, it reflects a territory that popular culture has already visited, such as the 'female', 'black' or 'gay' detective. Crime fiction also has, as one of its central concerns, an interest in examining and reinforcing the notion of societal order. It repeatedly demonstrates that crime either does not pay or should not pay. One of the ways it does this is to contrast what is 'good', known and understood with what is 'bad', unknown, foreign or beyond our normal comprehension. In western culture, the east has traditionally been employed as the site of difference, and has been constantly used as a setting of contrast, excitement or fear. Crime fiction conforms to this pattern, using the east to add a richness and depth to what otherwise might become a 'dry' tale. However, when used in such a way, what is variously eastern, 'other' or Oriental can never be paramount, always falling to secondary side of the binary opposites (good/evil, known/unknown, redeemed/doomed) at work. In an age of globalisation, the challenge for contemporary writers of popular fiction is to be responsive to an audience that demands respect for all cultures. Writers must demonstrate that they are sensitive to such concerns and can skillfully manage the tensions caused by the need to deliver work that operates within the parameters of the genre, and the desire to avoid offence to any cultural or ethnic group. In my work, my strategy to manage these tensions has been to create a back-story for my characters of Asian background, developing them above mere genre types, and to situate them with credibility in time and place through appropriate historical research.

Capturing the 'authentic voice' : challenges and opportunities for voice and self-representation in two ABC storytelling projects

In recent years there has been a noticeable move by various public institutions, such as public service broadcasters and community media organisations, to capture and disseminate the voices and viewpoints of ‘ordinary people’ through inviting them to share stories about their lives. One of the foremost objectives of many such projects is to provide under-represented individuals and groups with an opportunity to express and represent themselves; as such, the capture and broadcast of ‘authentic voices’ is a central value. This paper discusses the notion of ‘authentic voice’, and questions the framing role of public media organisations in storytelling projects that aim to provide individuals with space for self-expression and self-representation. It considers the ways in which tensions arise on multiple levels when individuals are asked to express and represent themselves within projects and spaces that are managed by institutions. This paper begins by discussing the challenges and opportunities that arise within storytelling projects that are facilitated by public institutions and community media arts organisations, and that aim to amplify the voices of “ordinary people” (Thumim, 2009). It examines ways in which ‘voice’ is facilitated, curated, broadcast and distributed within such projects, particularly questioning the ways in which project facilitation and the curation of stories for public broadcast can both help and hinder the amplification of ‘authentic voice’. Furthermore, we seek to discuss how ‘authentic voice’ is defined, and what is involved in the process of amplification. The paper moves on to discuss a case study in order to demonstrate some of the tensions that are evident within a storytelling project that is managed by a public institution – Australia’s national broadcaster – and the ways these tensions impact upon the capture and broadcast of an ‘authentic voice’ for project participants. The Australian Broadcasting Corporation’s (ABC) ‘Heywire’ project is a storytelling competition and website that aims to ‘give voice’ to 16-22 year olds who live in rural, regional and remote parts of Australia. Looking at tensions that exist on organisational, political and philosophical levels within the Heywire project reveals a number of conflicts of interest and objectives between the institution and project participants. This leads us to question whether institutionally-managed storytelling projects can effectively support individuals to have an ‘authentic voice’, and whether struggles of aims and objectives diminish the personal benefits that people may derive from expressing and representing themselves within such projects.

Meta-level terrorism futures : constructing and deconstructing using causal layered analysis

Focused on the alternative futures of terrorism, this study engages with the different levels of terrorism knowledge to identify and challenge the restrictive narratives that define terrorism: that "society must be defended" from the "constant and evolving terrorist threat". Using Causal Layered Analysis to deconstruct and reconstruct strategies, alternative scenarios emerge. These alternative futures are depicted collectively as a maze, highlighting the prospect of navigating towards preferred and even shared terrorism futures, once these are supported by new and inclusive metaphors and stakeholder engagement.

Semi-binary based video features for activity representation

Efficient and effective feature detection and representation is an important consideration when processing videos, and a large number of applications such as motion analysis, 3D scene understanding, tracking etc. depend on this. Amongst several feature description methods, local features are becoming increasingly popular for representing videos because of their simplicity and efficiency. While they achieve state-of-the-art performance with low computational complexity, their performance is still too limited for real world applications. Furthermore, rapid increases in the uptake of mobile devices has increased the demand for algorithms that can run with reduced memory and computational requirements. In this paper we propose a semi binary based feature detectordescriptor based on the BRISK detector, which can detect and represent videos with significantly reduced computational requirements, while achieving comparable performance to the state of the art spatio-temporal feature descriptors. First, the BRISK feature detector is applied on a frame by frame basis to detect interest points, then the detected key points are compared against consecutive frames for significant motion. Key points with significant motion are encoded with the BRISK descriptor in the spatial domain and Motion Boundary Histogram in the temporal domain. This descriptor is not only lightweight but also has lower memory requirements because of the binary nature of the BRISK descriptor, allowing the possibility of applications using hand held devices.We evaluate the combination of detectordescriptor performance in the context of action classification with a standard, popular bag-of-features with SVM framework. Experiments are carried out on two popular datasets with varying complexity and we demonstrate comparable performance with other descriptors with reduced computational complexity.

Constructing a clinical decision-making framework for image-guided radiotherapy using a Bayesian Network

A decision-making framework for image-guided radiotherapy (IGRT) is being developed using a Bayesian Network (BN) to graphically describe, and probabilistically quantify, the many interacting factors that are involved in this complex clinical process. Outputs of the BN will provide decision-support for radiation therapists to assist them to make correct inferences relating to the likelihood of treatment delivery accuracy for a given image-guided set-up correction. The framework is being developed as a dynamic object-oriented BN, allowing for complex modelling with specific sub-regions, as well as representation of the sequential decision-making and belief updating associated with IGRT. A prototype graphic structure for the BN was developed by analysing IGRT practices at a local radiotherapy department and incorporating results obtained from a literature review. Clinical stakeholders reviewed the BN to validate its structure. The BN consists of a sub-network for evaluating the accuracy of IGRT practices and technology. The directed acyclic graph (DAG) contains nodes and directional arcs representing the causal relationship between the many interacting factors such as tumour site and its associated critical organs, technology and technique, and inter-user variability. The BN was extended to support on-line and off-line decision-making with respect to treatment plan compliance. Following conceptualisation of the framework, the BN will be quantified. It is anticipated that the finalised decision-making framework will provide a foundation to develop better decision-support strategies and automated correction algorithms for IGRT.

Capturing the ‘authentic voice’ : challenges and opportunities for voice and self-representation in two ABC storytelling projects

This paper discusses the opportunities and challenges that arise within storytelling projects that are facilitated by public service broadcasters and that aim to amplify the voices of ‘ordinary people’. In particular, it focuses on two of the Australian Broadcasting Corporation’s current life storytelling projects: ABC Open and Heywire.

Rethinking the effects paradigm in porn studies

It has been an assumption of most anti-pornography discourse that porn damages women (and children) in a variety of ways. In Porno? Chic!, the author interrogated this assumption by examining the correlation between the incidence of sexual violence and other indicators of misogyny, and the availability and accessibility of pornography within a number of societies. This article develops that work with a specific focus on the regulatory environment as it relates to pornography and sexual representation. Does a liberal regulatory regime in sexual culture correlate with a relatively advanced state of sexual politics in a given country? Conversely, does an illiberal regime, where pornography and other forms of sexual culture are banned or severely restricted, correlate with relatively strong patriarchal structures? A comparative cross-country analysis seeks to explain the correlations identified, and to assess the extent to which the availability of porn can be viewed as a causal or a consequential characteristic of those societies where feminism has achieved significant advances.

Reflexive Dwelling: The body as representation of wall

In a play-within-a-play, the Mechanicals' production within William Shakespeare's A Midsummer Night's Dream, the character Snout announces his transformation to play the character of Wall. Snout's portrayal of Wall is both comical and menacing as he represents the forces that separate the lovers Pyramus and Thisbe. Wall becomes a subject in a manner no different from the lovers that he separates; his influence on their situation is brought to life. The unbecoming nature of walls to demarcate, separate, intimidate, influence and control is a relationship most can relate to in their experiences with architecture. It is in these moments that architecture leaps from the sphere of object into the realm of subject; where we might be involved in some intense struggle with the placement of a wall, the wall that might separate us from a lover, justice, freedom, power or privacy. This study investigates how this struggle is portrayed through the human body as representation of walls in performance.

Causal behavioural profiles : efficient computation, applications, and evaluation

Analysis of behavioural consistency is an important aspect of software engineering. In process and service management, consistency verification of behavioural models has manifold applications. For instance, a business process model used as system specification and a corresponding workflow model used as implementation have to be consistent. Another example would be the analysis to what degree a process log of executed business operations is consistent with the corresponding normative process model. Typically, existing notions of behaviour equivalence, such as bisimulation and trace equivalence, are applied as consistency notions. Still, these notions are exponential in computation and yield a Boolean result. In many cases, however, a quantification of behavioural deviation is needed along with concepts to isolate the source of deviation. In this article, we propose causal behavioural profiles as the basis for a consistency notion. These profiles capture essential behavioural information, such as order, exclusiveness, and causality between pairs of activities of a process model. Consistency based on these profiles is weaker than trace equivalence, but can be computed efficiently for a broad class of models. In this article, we introduce techniques for the computation of causal behavioural profiles using structural decomposition techniques for sound free-choice workflow systems if unstructured net fragments are acyclic or can be traced back to S- or T-nets. We also elaborate on the findings of applying our technique to three industry model collections.

Efficient computation of causal behavioural profiles using structural decomposition

Identification of behavioural contradictions is an important aspect of software engineering, in particular for checking the consistency between a business process model used as system specification and a corresponding workflow model used as implementation. In this paper, we propose causal behavioural profiles as the basis for a consistency notion, which capture essential behavioural information, such as order, exclusiveness, and causality between pairs of activities. Existing notions of behavioural equivalence, such as bisimulation and trace equivalence, might also be applied as consistency notions. Still, they are exponential in computation. Our novel concept of causal behavioural profiles provides a weaker behavioural consistency notion that can be computed efficiently using structural decomposition techniques for sound free-choice workflow systems if unstructured net fragments are acyclic or can be traced back to S- or T-nets.

Developing Co-operating Legal Knowledge Based Systems

In attempting to build intelligent litigation support tools, we have moved beyond first generation, production rule legal expert systems. Our work supplements rule-based reasoning with case based reasoning and intelligent information retrieval. This research, specifies an approach to the case based retrieval problem which relies heavily on an extended object-oriented / rule-based system architecture that is supplemented with causal background information. Machine learning techniques and a distributed agent architecture are used to help simulate the reasoning process of lawyers. In this paper, we outline our implementation of the hybrid IKBALS II Rule Based Reasoning / Case Based Reasoning system. It makes extensive use of an automated case representation editor and background information.