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.

Perceiving and pursuing novelty : a grounded theory of adolescent creativity

Creativity plays an increasingly important role in our personal, social, educational, and community lives. For adolescents, creativity can enable self-expression, be a means of pushing boundaries, and assist learning, achievement, and completion of everyday tasks. Moreover, adolescents who demonstrate creativity can potentially enhance their capacity to face unknown future challenges, address mounting social and ecological issues in our global society, and improve their career opportunities and contribution to the economy. For these reasons, creativity is an essential capacity for young people in their present and future, and is highlighted as a priority in current educational policy nationally and internationally. Despite growing recognition of creativity’s importance and attention to creativity in research, the creative experience from the perspectives of the creators themselves and the creativity of adolescents are neglected fields of study. Hence, this research investigated adolescents’ self-reported experiences of creativity to improve understandings of their creative processes and manifestations, and how these can be supported or inhibited. Although some aspects of creativity have been extensively researched, there were no comprehensive, multidisciplinary theoretical frameworks of adolescent creativity to provide a foundation for this study. Therefore, a grounded theory methodology was adopted for the purpose of constructing a new theory to describe and explain adolescents’ creativity in a range of domains. The study’s constructivist-interpretivist perspective viewed the data and findings as interpretations of adolescents’ creative experiences, co-constructed by the participants and the researcher. The research was conducted in two academically selective high schools in Australia: one arts school, and one science, mathematics, and technology school. Twenty adolescent participants (10 from each school) were selected using theoretical sampling. Data were collected via focus groups, individual interviews, an online discussion forum, and email communications. Grounded theory methods informed a process of concurrent data collection and analysis; each iteration of analysis informed subsequent data collection. Findings portray creativity as it was perceived and experienced by participants, presented in a Grounded Theory of Adolescent Creativity. The Grounded Theory of Adolescent Creativity comprises a core category, Perceiving and Pursuing Novelty: Not the Norm, which linked all findings in the study. This core category explains how creativity involved adolescents perceiving stimuli and experiences differently, approaching tasks or life unconventionally, and pursuing novel ideas to create outcomes that are not the norm when compared with outcomes by peers. Elaboration of the core category is provided by the major categories of findings. That is, adolescent creativity entailed utilising a network of Sub-Processes of Creativity, using strategies for Managing Constraints and Challenges, and drawing on different Approaches to Creativity – adaptation, transfer, synthesis, and genesis – to apply the sub-processes and produce creative outcomes. Potentially, there were Effects of Creativity on Creators and Audiences, depending on the adolescent and the task. Three Types of Creativity were identified as the manifestations of the creative process: creative personal expression, creative boundary pushing, and creative task achievement. Interactions among adolescents’ dispositions and environments were influential in their creativity. Patterns and variations of these interactions revealed a framework of four Contexts for Creativity that offered different levels of support for creativity: high creative disposition–supportive environment; high creative disposition–inhibiting environment; low creative disposition–supportive environment; and low creative disposition–inhibiting environment. These contexts represent dimensional ranges of how dispositions and environments supported or inhibited creativity, and reveal that the optimal context for creativity differed depending on the adolescent, task, domain, and environment. This study makes four main contributions, which have methodological and theoretical implications for researchers, as well as practical implications for adolescents, parents, teachers, policy and curriculum developers, and other interested stakeholders who aim to foster the creativity of adolescents. First, this study contributes methodologically through its constructivist-interpretivist grounded theory methodology combining the grounded theory approaches of Corbin and Strauss (2008) and Charmaz (2006). Innovative data collection was also demonstrated through integration of data from online and face-to-face interactions with adolescents, within the grounded theory design. These methodological contributions have broad applicability to researchers examining complex constructs and processes, and with populations who integrate multimedia as a natural form of communication. Second, applicable to creativity in diverse domains, the Grounded Theory of Adolescent Creativity supports a hybrid view of creativity as both domain-general and domain-specific. A third major contribution was identification of a new form of creativity, educational creativity (ed-c), which categorises creativity for learning or achievement within the constraints of formal educational contexts. These theoretical contributions inform further research about creativity in different domains or multidisciplinary areas, and with populations engaged in formal education. However, the key contribution of this research is that it presents an original Theory and Model of Adolescent Creativity to explain the complex, multifaceted phenomenon of adolescents’ creative experiences.

Improved Subject Identification in Surveillance Video using Super Resolution

The time consuming and labour intensive task of identifying individuals in surveillance video is often challenged by poor resolution and the sheer volume of stored video. Faces or identifying marks such as tattoos are often too coarse for direct matching by machine or human vision. Object tracking and super-resolution can then be combined to facilitate the automated detection and enhancement of areas of interest. The object tracking process enables the automatic detection of people of interest, greatly reducing the amount of data for super-resolution. Smaller regions such as faces can also be tracked. A number of instances of such regions can then be utilized to obtain a super-resolved version for matching. Performance improvement from super-resolution is demonstrated using a face verification task. It is shown that there is a consistent improvement of approximately 7% in verification accuracy, using both Eigenface and Elastic Bunch Graph Matching approaches for automatic face verification, starting from faces with an eye to eye distance of 14 pixels. Visual improvement in image fidelity from super-resolved images over low-resolution and interpolated images is demonstrated on a small database. Current research and future directions in this area are also summarized.

Eliciting metacognitive experiences and reflection in a year 11 chemistry classroom : an activity theory perspective

Concerns regarding students' learning and reasoning in chemistry classrooms are well documented. Students' reasoning in chemistry should be characterized by conscious consideration of chemical phenomenon from laboratory work at macroscopic, molecular/sub-micro and symbolic levels. Further, students should develop metacognition in relation to such ways of reasoning about chemistry phenomena. Classroom change eliciting metacognitive experiences and metacognitive reflection is necessary to shift entrenched views of teaching and learning in students. In this study, Activity Theory is used as the framework for intepreting changes to the rules/customs and tools of the activity systems of two different classes of students taught by the same teacher, Frances, who was teaching chemical equilibrium to those classes in consecutive years. An interpretive methodolgy involving multiple data sources was employed. Frances explicitly changed her pedagogy in the second year to direct students attention to increasingly consider chemical phenomena at the molecular/sub-micro level. Additonally, she asked students not to use the textbook until toward the end of the equilibrium unit and sought to engage them in using their prior knowledge of chemistry to understand their observations from experiments. Frances' changed pedagogy elicited metacognitive experiences and reflection in students and challenged them to reconsider their metacognitive beliefs about learning chemistry and how it might be achieved. While teacher change is essential for science education reform, students are not passive players in the change efforts and they need to be convinced of the viability of teacher pedagogical change in the context of their goals, intentions, and beliefs.

Tracheobronchial and alveolar dose of submicrometer particles for different population age groups in Italy

Exposure to ultrafine particles (diameter less than 100 nm) is an important topic in epidemiological and toxicological studies. This study used the average particle number size distribution data obtained from our measurement survey in major micro-environments, together with the people activity pattern data obtained from the Italian Human Activity Pattern Survey to estimate the tracheobronchial and alveolar dose of submicrometer particles for different population age groups in Italy. We developed a numerical methodology based on Monte Carlo method, in order to estimate the best combination from a probabilistic point of view. More than 106 different cases were analyzed according to a purpose built sub-routine and our results showed that the daily alveolar particle number and surface area deposited for all of the age groups considered was equal to 1.5 x 1011 particles and 2.5 x 1015 m2, respectively, varying slightly for males and females living in Northern or Southern Italy. In terms of tracheobronchial deposition, the corresponding values for daily particle number and surface area for all age groups was equal to 6.5 x 1010 particles and 9.9 x 1014 m2, respectively. Overall, the highest contributions were found to come from indoor cooking (female), working time (male) and transportation (i.e. traffic derived particles) (children).

Anatomy of a submarine pyroclastic flow and associated turbidity current : July 2003 dome collapse, Soufrière Hills volcano, Montserrat, West Indies

The 12 to 13 July 2003 andesite lava dome collapse at the Soufrière Hills volcano, Montserrat, provides the first opportunity to document comprehensively both the sub-aerial and submarine sequence of events for an eruption. Numerous pyroclastic flows entered the ocean during the collapse, depositing approximately 90% of the total material into the submarine environment. During peak collapse conditions, as the main flow penetrated the air–ocean interface, phreatic explosions were observed and a surge cloud decoupled from the main flow body to travel 2 to 3 km over the ocean surface before settling. The bulk of the flow was submerged and rapidly mixed with sea water forming a water-saturated mass flow. Efficient sorting and physical differentiation occurred within the flow before initial deposition at 500 m water depth. The coarsest components (∼60% of the total volume) were deposited proximally from a dense granular flow, while the finer components (∼40%) were efficiently elutriated into the overlying part of the flow, which evolved into a far-reaching turbidity current.

Some reflection of research 'Schools' and geographies

Reflecting on real and perceived differences between European and North American research cultures, I challenge views that ‘European’ research is under appreciated or discriminated against, and caution against isolationist European positions. Instead, I argue that although no distinctive and coherent European tradition or culture really exists, there may be elements of the prevalent research culture that can be turned into an advantage for Europe-based and/or European-trained researchers in helping to influence and improve one, global research conversation. Of course, a range of sub-communities and sub-conversations will and should exist, but there is no reason for these to be based on geography.

Comparison between electrically-evoked and voluntary wrist movements on sensorimotor and prefrontal cortical activation : A multi-channel time domain fNIRS study

Neuromuscular electrical stimulation (NMES) has been consistently demonstrated to improve skeletal muscle function in neurological populations with movement disorders, such as poststroke and incomplete spinal cord injury (Vanderthommen and Duchateau, 2007). Recent research has documented that rapid, supraspinal central nervous system reorganisation/neuroplastic mechanisms are also implicated during NMES (Chipchase et al., 2011). Functional neuroimaging studies have shown NMES to activate a network of sub-cortical and cortical brain regions, including the sensorimotor (SMC) and prefrontal (PFC) cortex (Blickenstorfer et al., 2009; Han et al., 2003; Muthalib et al., 2012). A relationship between increase in SMC activation with increasing NMES current intensity up to motor threshold has been previously reported using functional MRI (Smith et al., 2003). However, since clinical neurorehabilitation programmes commonly utilise NMES current intensities above the motor threshold and up to the maximum tolerated current intensity (MTI), limited research has determined the cortical correlates of increasing NMES current intensity at or above MTI (Muthalib et al., 2012). In our previous study (Muthalib et al., 2012), we assessed contralateral PFC activation using 1-channel functional near infrared spectroscopy (fNIRS) during NMES of the elbow flexors by increasing current intensity from motor threshold to greater than MTI and showed a linear relationship between NMES current intensity and the level of PFC activation. However, the relationship between NMES current intensity and activation of the motor cortical network, including SMC and PFC, has not been clarified. Moreover, it is of scientific and clinical relevance to know how NMES affects the central nervous system, especially in comparison to voluntary (VOL) muscle activation. Therefore, the aim of this study was to utilise multi-channel time domain fNIRS to compare SMC and PFC activation between VOL and NMESevoked wrist extension movements.

Carbon nanotube-based super nanotubes: Tunable thermal conductivity in three dimensions

Advances in nanomaterials/nanostructures offer the possibility of fabricating multifunctional materials for use in engineering applications. Carbon nanotube (CNT)-based nanostructures are a representative building block for these multifunctional materials. Based on a series of in silico studies, we investigated the possibility of tuning the thermal conductivity of a three-dimensional CNT-based nanostructure: a single-walled CNT-based super-nanotube. The thermal conductivity of the super-nanotubes was shown to vary with different connecting carbon rings and super-nanotubes with longer constituent single-walled CNTs and larger diameters had a smaller thermal conductivity. The inverse of the thermal conductivity of the super-nanotubes showed a good linear relationship with the inverse of the length. The thermal conductivity was approximately proportional to the inverse of the temperature, but was insensitive to the axial strain as a result of the Poisson ratio. These results provide a fundamental understanding of the thermal conductivity of the super-nanotubes and will guide their future design/fabrication and engineering applications.

A multiscale study on the structural and mechanical properties of the luffa sponge from Luffa cylindrica plant

Cellular materials that are often observed in biological systems exhibit excellent mechanical properties at remarkably low densities. Luffa sponge is one of such materials with a complex interconnecting porous structure. In this paper, we studied the relationship between its structural and mechanical properties at different levels of its hierarchical organization from a single fiber to a segment of whole sponge. The tensile mechanical behaviors of three single fibers were examined by an Instron testing machine and the ultrastructure of a fractured single fiber was observed in a scanning electronic microscope. Moreover, the compressive mechanical behaviors of the foam-like blocks from different locations of the sponge were examined. The difference of the compressive stress-strain responses of four sets of segmental samples were also compared. The result shows that the single fiber is a porous composite material mainly consisting of cellulose fibrils and lignin/hemicellulose matrix, and its Young's modulus and strength are comparable to wood. The mechanical behavior of the block samples from the hoop wall is superior to that from the core part. Furthermore, it shows that the influence of the inner surface on the mechanical property of the segmental sample is stronger than that of the core part; in particular, the former's Young's modulus, strength and strain energy absorbed are about 1.6 times higher. The present work can improve our understanding of the structure-function relationship of the natural material, which may inspire fabrication of new biomimetic foams with desirable mechanical efficiency for further applications in anti-crushing devices and super-light sandwich panels.

Design and Simulation of a Solar Powered UAV for Remote Sensing Tasks Technical Report

This research deals with the development of a Solar-Powered UAV designed for remote sensing, in particular to the development of the autopilot sub-system and path planning. The design of the Solar-Powered UAS followed a systems engineering methodology, by first defining system architecture, and selecting each subsystem. Validation tests and integration of autopilot is performed, in order to evaluate the performances of each subsystem and to obtain a global operational system for data collection missions. The flight tests planning and simulation results are also explored in order to verify the mission capabilities using an autopilot on a UAS. The important aspect of this research is to develop a Solar-Powered UAS for the purpose of data collection and video monitoring, especially data and images from the ground; transmit to the GS (Ground Station), segment the collected data, and afterwards analyze it with a Matlab code.

Mobility and security: the perceived benefits of citizenship for resettled young people from refugee backgrounds

In recent decades, the meaning and value of formal state citizenship has shifted dramatically. In the same period, scholarship on citizenship has drawn attention to the proliferation of alternative forms of sub-, supra- and transnational citizenship, at times obscuring the ongoing importance of formal state citizenship. For refugees, however, formal state citizenship remains a critical and widely shared goal. Drawing on interviews with 51 young people from refugee backgrounds in Melbourne, Australia, this article explores the intersecting themes of mobility and security that were identified by participants as the most important benefits of acquiring formal state citizenship in the country of resettlement. In contrast to the insecurity of forced migration, formal state citizenship provides a privileged mobility that enables refugee-background youth to maintain and create transnational identities and attachments and to be protected while doing so, while also granting a secure status within the nation state and insurance against further displacement in an uncertain future. In offering these forms of mobility and security, formal state citizenship contributes to a sense of ontological security among refugee-background youth, providing an important foundation for building national and transnational futures.

Development and evaluation of a spatial decision support system for malaria elimination in Bhutan

Background: Bhutan has reduced its malaria incidence significantly in the last 5 years, and is aiming for malaria elimination by 2016. To assist with the management of the Bhutanese malaria elimination programme a spatial decision support system (SDSS) was developed. The current study aims to describe SDSS development and evaluate SDSS utility and acceptability through informant interviews. Methods: The SDSS was developed based on the open-source Quantum geographical information system (QGIS) and piloted to support the distribution of long-lasting insecticidal nets (LLINs) and indoor residual spraying (IRS) in the two sub-districts of Samdrup Jongkhar District. It was subsequently used to support reactive case detection (RACD) in the two sub-districts of Samdrup Jongkhar and two additional sub-districts in Sarpang District. Interviews were conducted to ascertain perceptions on utility and acceptability of 11 informants using the SDSS, including programme and district managers, and field workers. Results: A total of 1502 households with a population of 7165 were enumerated in the four sub-districts, and a total of 3491 LLINs were distributed with one LLIN per 1.7 persons. A total of 279 households representing 728 residents were involved with RACD. Informants considered that the SDSS was an improvement on previous methods for organizing LLIN distribution, IRS and RACD, and could be easily integrated into routine malaria and other vector-borne disease surveillance systems. Informants identified some challenges at the programme and field level, including the need for more skilled personnel to manage the SDSS, and more training to improve the effectiveness of SDSS implementation and use of hardware. Conclusions: The SDSS was well accepted and informants expected its use to be extended to other malaria reporting districts and other vector-borne diseases. Challenges associated with efficient SDSS use included adequate skills and knowledge, access to training and support, and availability of hardware including computers and global positioning system receivers.

Energy efficient multi storey residential developments

Worldwide, the current pattern of urban development is unsustainable and metropolitan planning and development strategies deliver poor environmental outcomes in relation to energy production. As a result, an increasing number of governments and private sector development companies are initiating projects that aim to deliver enhanced environmental outcomes rather than a ‘business as usual’ approach. This paper will summarise the findings from a study that explored the link between building orientation and energy efficiencies in sub-tropical and tropical climates. The study used a new thermal modelling software tool developed by CSIRO that responds more accurately to residential heating and cooling energy performance in those climate zones. This software tool responds to industry criticisms regarding cold climate modelling systems that do not make sufficient allowance for natural ventilation. The study examined a range of low, medium and high-density dwelling types and investigated the impact of orientation, insulation, ventilation and shading devices on energy efficiencies. This paper will examine the findings from the medium and high-density case study developments as these are relevant to residential developments in many South East Asian countries, such as Singapore, Hong Kong and Malaysia. Finally, the paper will explore the potential benefits that medium and high-density residential developments have in the development of ‘solar cities’ and ‘solar suburbs’.

Cases from the technology disciplines

This document is a collection of ‘cases’ adapted from interviews with supervisors of higher degree research students from the technology disciplines. The supervisors come from a wide range of sub disciplines and represent many levels of experience. We follow in this document Hammond and Ryland’s (2009)2 suggested ranking of supervision experience:  No completions – No experience or new supervisors, with no doctoral completions as principal supervisor  Experienced – 1 to 5 doctoral completions as principal supervisor  Very experienced – over 6 doctoral completions as principal supervisor The cases focus attention on thinking about supervision as a teaching and learning practice; a dimension of higher degree research supervision that is increasingly being recognized as important. They are offered as prompts for individuals and groups of supervisors in thinking about their supervision as a teaching and learning practice.