DNA methylation at the novel CpG sites in the promoter of MED15/PCQAP gene as a biomarker for head and neck cancers

Head and neck cancers (HNCs) represent a significant and ever-growing burden to the modern society, mainly due to the lack of early diagnostic methods. A significant number of HNCs is often associated with drinking, smoking, chewing beetle nut, and human papilloma virus (HPV) infections. We have analyzed DNA methylation patterns in tumor and normal tissue samples collected from head and neck squamous cell carcinoma (HNSCC) patients who were smokers. We have identified novel methylation sites in the promoter of the mediator complex subunit 15 (MED15/PCQAP) gene (encoing a co-factor important for regulation of transcription initiation for promoters of many genes), hypermethylated specifically in tumor cells. Two clusters of CpG dinucleotides methylated in tumors, but not in normal tissue from the same patients, were identified. These CpG methylation events in saliva samples were further validated in a separate cohort of HNSCC patients (who developed cancer due to smoking or HPV infections) and healthy controls using methylation-specific PCR (MSP). We used saliva as a biological medium because of its non-invasive nature, close proximity to the tumors, easiness and it is an economically viable option for large-scale screening studies. The methylation levels for the two identified CpG clusters were significantly different between the saliva samples collected from healthy controls and HNSCC individuals (Welch's t-test returning P, 0.05 and Mann-Whitney test P, 0.01 for both). The developed MSP assays also provided a good discriminative ability with AUC values of 0.70 (P, 0.01) and 0.63 (P, 0.05). The identified novel CpG methylation sites may serve as potential non-invasive biomarkers for detecting HNSCC. © the authors.

Epigenetics and migraine; complex mitochondrial interactions contributing to disease susceptibility

Migraine is a common neurological disorder classified by the World Health Organisation (WHO) as one of the top twenty most debilitating diseases in the developed world. Current therapies are only effective for a proportion of sufferers and new therapeutic targets are desperately needed to alleviate this burden. Recently the role of epigenetics in the development of many complex diseases including migraine has become an emerging topic. By understanding the importance of acetylation, methylation and other epigenetic modifications, it then follows that this modification process is a potential target to manipulate epigenetic status with the goal of treating disease. Bisulphite sequencing and methylated DNA immunoprecipitation have been used to demonstrate the presence of methylated cytosines in the human D-loop of mitochondrial DNA (mtDNA), proving that the mitochondrial genome is methylated. For the first time, it has been shown that there is a difference in mtDNA epigenetic status between healthy controls and those with disease, especially for neurodegenerative and age related conditions. Given co-morbidities with migraine and the suggestive link between mitochondrial dysfunction and the lowered threshold for triggering a migraine attack, mitochondrial methylation may be a new avenue to pursue. Creative thinking and new approaches are needed to solve complex problems and a systems biology approach, where multiple layers of information are integrated is becoming more important in complex disease modelling.

Computation of Mathematical Models for Complex Industrial Processes

Designed for undergraduate and postgraduate students, academic researchers and industrial practitioners, this book provides comprehensive case studies on numerical computing of industrial processes and step-by-step procedures for conducting industrial computing. It assumes minimal knowledge in numerical computing and computer programming, making it easy to read, understand and follow. Topics discussed include fundamentals of industrial computing, finite difference methods, the Wavelet-Collocation Method, the Wavelet-Galerkin Method, High Resolution Methods, and comparative studies of various methods. These are discussed using examples of carefully selected models from real processes of industrial significance. The step-by-step procedures in all these case studies can be easily applied to other industrial processes without a need for major changes and thus provide readers with useful frameworks for the applications of engineering computing in fundamental research problems and practical development scenarios.

Synonymization of key pest species within the Bactrocera dorsalis species complex (Diptera: Tephritidae): Taxonomic changes based on a review of 20 years of integrative morphological, molecular, cytogenetic, behavioural and chemoecological data

Bactrocera papayae Drew & Hancock, Bactrocera philippinensis Drew & Hancock, Bactrocera carambolae Drew & Hancock, and Bactrocera invadens Drew, Tsuruta & White are four horticultural pest tephritid fruit fly species that are highly similar, morphologically and genetically, to the destructive pest, the Oriental fruit fly, Bactrocera dorsalis (Hendel) (Diptera: Tephritidae). This similarity has rendered the discovery of reliable diagnostic characters problematic, which, in view of the economic importance of these taxa and the international trade implications, has resulted in ongoing difficulties for many areas of plant protection and food security. Consequently, a major international collaborative and integrated multidisciplinary research effort was initiated in 2009 to build upon existing literature with the specific aim of resolving biological species limits among B. papayae, B. philippinensis, B. carambolae, B. invadens and B. dorsalis to overcome constraints to pest management and international trade. Bactrocera philippinensis has recently been synonymized with B. papayae as a result of this initiative and this review corroborates that finding; however, the other names remain in use. While consistent characters have been found to reliably distinguish B. carambolae from B. dorsalis, B. invadens and B. papayae, no such characters have been found to differentiate the latter three putative species. We conclude that B. carambolae is a valid species and that the remaining taxa, B. dorsalis, B. invadens and B. papayae, represent the same species. Thus, we consider B. dorsalis (Hendel) as the senior synonym of B. papayae Drew and Hancock syn.n. and B. invadens Drew, Tsuruta & White syn.n. A redescription of B. dorsalis is provided. Given the agricultural importance of B. dorsalis, this taxonomic decision will have significant global plant biosecurity implications, affecting pest management, quarantine, international trade, postharvest treatment and basic research. Throughout the paper, we emphasize the value of independent and multidisciplinary tools in delimiting species, particularly in complicated cases involving morphologically cryptic taxa.

Investigating tween children's capacity to conceptualise the complex issue of wellbeing

Wellbeing is an area that has gained increased global focus, particularly when considering children’s lives. With the growing focus on children’s wellbeing, it is apparent that this is an important aspect that is being considered in the policy and provision designed for children. The decision-making surrounding wellbeing provision for children typically occurs without the direct input of the children that these services are designed to benefit. With the children’s capacities being variably considered in wider society, opportunities for children to participate in decision-making on matters that affect them are often limited. The absence of children’s perspectives on matters that affect their lives, such as wellbeing, reveal that adults may be missing a key perspective when seeking to understand and cater for children’s wellbeing needs. This article outlines the results of a study that investigated how children aged 8 to 12 years o age (tweens) defined and conceptualised wellbeing. This article proposes that children can be included in the conceptualisation and development of policy and provision designed to benefit them and argues for increased presence of the voice and participation of children in wider societal initiatives.

Clustering and labeling a web scale document collection using Wikipedia clusters

Clustering is an important technique in organising and categorising web scale documents. The main challenges faced in clustering the billions of documents available on the web are the processing power required and the sheer size of the datasets available. More importantly, it is nigh impossible to generate the labels for a general web document collection containing billions of documents and a vast taxonomy of topics. However, document clusters are most commonly evaluated by comparison to a ground truth set of labels for documents. This paper presents a clustering and labeling solution where the Wikipedia is clustered and hundreds of millions of web documents in ClueWeb12 are mapped on to those clusters. This solution is based on the assumption that the Wikipedia contains such a wide range of diverse topics that it represents a small scale web. We found that it was possible to perform the web scale document clustering and labeling process on one desktop computer under a couple of days for the Wikipedia clustering solution containing about 1000 clusters. It takes longer to execute a solution with finer granularity clusters such as 10,000 or 50,000. These results were evaluated using a set of external data.

Memory and Epileptogenesis in Complex Biological and Simulated Systems

Oscillations of neural activity may bind widespread cortical areas into a neural representation that encodes disparate aspects of an event. In order to test this theory we have turned to data collected from complex partial epilepsy (CPE) patients with chronically implanted depth electrodes. Data from regions critical to word and face information processing was analyzed using spectral coherence measurements. Similar analyses of intracranial EEG (iEEG) during seizure episodes display HippoCampal Formation (HCF)—NeoCortical (NC) spectral coherence patterns that are characteristic of specific seizure stages (Klopp et al. 1996). We are now building a computational memory model to examine whether spatio-temporal patterns of human iEEG spectral coherence emerge in a computer simulation of HCF cellular distribution, membrane physiology and synaptic connectivity. Once the model is reasonably scaled it will be used as a tool to explore neural parameters that are critical to memory formation and epileptogenesis.

Variation in parental magmas of Mt Rouse, a complex polymagmatic monogenetic volcano in the basaltic intraplate Newer Volcanics Province, southeast Australia

Monogenetic volcanoes have long been regarded as simple in nature, involving single magma batches and uncomplicated evolutions; however, recent detailed research into individual centres is challenging that assumption. Mt Rouse (Kolor) is the volumetrically largest volcano in the monogenetic Newer Volcanics Province of southeast Australia. This study presents new major, trace and Sr–Nd–Pb isotope data for samples selected on the basis of a detailed stratigraphic framework analysis of the volcanic products from Mt Rouse. The volcano is the product of three magma batches geochemically similar to Ocean–Island basalts, featuring increasing LREE enrichment with each magma batch (batches A, B and C) but no evidence of crustal contamination; the Sr–Nd–Pb isotopes define two groupings. Modelling suggests that the magmas were sourced from a zone of partial melting crossing the lithosphere–asthenosphere boundary, with batch A forming a large volume partial melt in the deep lithosphere (1.7 GPa/55.5 km); and batches B and C from similar areas within the shallow asthenosphere (1.88 GPa/61 km and 1.94 GPa/63 km, respectively). The formation and extraction of these magmas may have been due to high deformation rates in the mantle caused by edge-driven convection and asthenospheric upwelling. The lithosphere– asthenosphere boundary is important with respect to NVP volcanism. An eruption chronology involves sequential eruption of magma batches A, C and B, followed by simultaneous eruption of batches A and B. Mt Rouse is a complex polymagmatic monogenetic volcano that illustrates the complexity of monogenetic volcanism and demonstrates the importance of combining detailed stratigraphic analysis alongside systematic geochemical sampling.

Trailing Touch

Trailing Touch (2014) is a twenty minute classically-based dance work set to music by composers Carter Burwell and Hildur Gudnadottir. It is an abstract work that explores images based on imperfect patterns and seeks to transmit the sensations felt when clusters form and disperse through the space or crisscross to create swirling wave-like reactions in the dancers’ tulle skirts. These simple references are inspired by the lyrical use of arms found in ballet, particular to the ballet aesthetic. Trailing Touch was created in collaboration with QUT’s third-year BFA (Dance Performance) students and performed as part of Dance14 at QUT’s Gardens Points Theatre from the 4th to 8th November 2014 and was performed in Singapore as part of Contact Contemporary Dance Festival on 30th November, 2014. Additionally, the creative process of Trailing Touch (2014) forms the initial project of Phase III of my PhD research, Writing the Dance Score in the Twenty-first Century: An approach for the Independent Choreographer. This PhD research will examine the potential of dance scores as a suite of choreographic strategies to map key aspects of the choreographic process. While a certain degree of ambiguity drives the creative process, the suite of choreographic strategies attempt to capture what is transmitted through the lived experience of dance. “[T]hese documents harbor a force of expression, a visual energy related to the body and the movement” (Louppe 1994, 7) that triggers movement responses, unforeseen intensities and enables personal interpretation. Consequently, Phase III will test and evaluate the relevance of Phase II research within the pressures of mainstream dance rehearsal and performance contexts. In Project One Trailing Touch this was demonstrated in the dance scores produced by the choreographer and interpreted by the dancers within the performance. By drawing from both the theoretical and practical, it is anticipated that this research will suggest a form of languaging movement that is not reliant on images or numbers, but generated in response to the intuitive and complex process underpinning choreographic practice. Rather than constructing a codified dance notation system, it will focus on strategies that reveal movement, its spatial patterns, qualities and intensities of expression and the procedures underlying key choreographic concepts. The outcome of this research project aims to support the independent choreographer in two major areas, by facilitating and enriching the choreographic process for both the performers and choreographer, and by strengthening artistic development and performance outcomes.

Bayesian networks for information synthesis in complex systems

This thesis introduces a method of applying Bayesian Networks to combine information from a range of data sources for effective decision support systems. It develops a set of techniques in development, validation, visualisation, and application of Complex Systems models, with a working demonstration in an Australian airport environment. The methods presented here have provided a modelling approach that produces highly flexible, informative and applicable interpretations of a system's behaviour under uncertain conditions. These end-to-end techniques are applied to the development of model based dashboards to support operators and decision makers in the multi-stakeholder airport environment. They provide highly flexible and informative interpretations and confidence in these interpretations of a system's behaviour under uncertain conditions.

Visualization of complex biological systems: An immune response model using OpenGL

In this paper we present an update on our novel visualization technologies based on cellular immune interaction from both large-scale spatial and temporal perspectives. We do so with a primary motive: to present a visually and behaviourally realistic environment to the community of experimental biologists and physicians such that their knowledge and expertise may be more readily integrated into the model creation and calibration process. Visualization aids understanding as we rely on visual perception to make crucial decisions. For example, with our initial model, we can visualize the dynamics of an idealized lymphatic compartment, with antigen presenting cells (APC) and cytotoxic T lymphocyte (CTL) cells. The visualization technology presented here offers the researcher the ability to start, pause, zoom-in, zoom-out and navigate in 3-dimensions through an idealised lymphatic compartment.