Evolutionary biology of Gondwanan non-biting midges (Diptera: Chironomidae)

The potential restriction to effective dispersal and gene flow caused by habitat fragmentation can apply to multiple levels of evolutionary scale; from the fragmentation of ancient supercontinents driving diversification and speciation on disjunct landmasses, to the isolation of proximate populations as a result of their inability to cross intervening unsuitable habitat. Investigating the role of habitat fragmentation in driving diversity within and among taxa can thus include inferences of phylogenetic relationships among taxa, assessments of intraspecific phylogeographic structure and analyses of gene flow among neighbouring populations. The proposed Gondwanan clade within the chironomid (non-biting midge) subfamily Orthocladiinae (Diptera: Chironomidae) represents a model system for investigating the role that population fragmentation and isolation has played at different evolutionary scales. A pilot study by Krosch et al (2009) indentified several highly divergent lineages restricted to ancient rainforest refugia and limited gene flow among proximate sites within a refuge for one member of this clade, Echinocladius martini Cranston. This study provided a framework for investigating the evolutionary history of this taxon and its relatives more thoroughly. Populations of E. martini were sampled in the Paluma bioregion of northeast Queensland to investigate patterns of fine-scale within- and among-stream dispersal and gene flow within a refuge more rigorously. Data was incorporated from Krosch et al (2009) and additional sites were sampled up- and downstream of the original sites. Analyses of genetic structure revealed strong natal site fidelity and high genetic structure among geographically proximate streams. Little evidence was found for regular headwater exchange among upstream sites, but there was distinct evidence for rare adult flight among sites on separate stream reaches. Overall, however, the distribution of shared haplotypes implied that both larval and adult dispersal was largely limited to the natal stream channel. Patterns of regional phylogeographic structure were examined in two related austral orthoclad taxa – Naonella forsythi Boothroyd from New Zealand and Ferringtonia patagonica Sæther and Andersen from southern South America – to provide a comparison with patterns revealed in their close relative E. martini. Both taxa inhabit tectonically active areas of the southern hemisphere that have also experienced several glaciation events throughout the Plio-Pleistocene that are thought to have affected population structure dramatically in many taxa. Four highly divergent lineages estimated to have diverged since the late Miocene were revealed in each taxon, mirroring patterns in E. martini; however, there was no evidence for local geographical endemism, implying substantial range expansion post-diversification. The differences in pattern evident among the three related taxa were suggested to have been influenced by variation in the responses of closed forest habitat to climatic fluctuations during interglacial periods across the three landmasses. Phylogeographic structure in E. martini was resolved at a continental scale by expanding upon the sampling design of Krosch et al (2009) to encompass populations in southeast Queensland, New South Wales and Victoria. Patterns of phylogeographic structure were consistent with expectations and several previously unrecognised lineages were revealed from central- and southern Australia that were geographically endemic to closed forest refugia. Estimated divergence times were congruent with the timing of Plio-Pleistocene rainforest contractions across the east coast of Australia. This suggested that dispersal and gene flow of E. martini among isolated refugia was highly restricted and that this taxon was susceptible to the impacts of habitat change. Broader phylogenetic relationships among taxa considered to be members of this Gondwanan orthoclad group were resolved in order to test expected patterns of evolutionary affinities across the austral continents. The inferred phylogeny and estimated divergence times did not accord with expected patterns based on the geological sequence of break-up of the Gondwanan supercontinent and implied instead several transoceanic dispersal events post-vicariance. Difficulties in appropriate taxonomic sampling and accurate calibration of molecular phylogenies notwithstanding, the sampling regime implemented in the current study has been the most intensive yet performed for austral members of the Orthocladiinae and unsurprisingly has revealed both novel taxa and phylogenetic relationships within and among described genera. Several novel associations between life stages are made here for both described and previously unknown taxa. Investigating evolutionary relationships within and among members of this clade of proposed Gondwanan orthoclad taxa has demonstrated that a complex interaction between historical population fragmentation and dispersal at several levels of evolutionary scale has been important in driving diversification in this group. While interruptions to migration, colonisation and gene flow driven by population fragmentation have clearly contributed to the development and maintenance of much of the diversity present in this group, long-distance dispersal has also played a role in influencing diversification of continental biotas and facilitating gene flow among disjunct populations.

QoC Elastic Scheduling for Real-Time Control Systems

The elastic task model, a significant development in scheduling of real-time control tasks, provides a mechanism for flexible workload management in uncertain environments. It tells how to adjust the control periods to fulfill the workload constraints. However, it is not directly linked to the quality-of-control (QoC) management, the ultimate goal of a control system. As a result, it does not tell how to make the best use of the system resources to maximize the QoC improvement. To fill in this gap, a new feedback scheduling framework, which we refer to as QoC elastic scheduling, is developed in this paper for real-time process control systems. It addresses the QoC directly through embedding both the QoC management and workload adaptation into a constrained optimization problem. The resulting solution for period adjustment is in a closed-form expressed in QoC measurements, enabling closed-loop feedback of the QoC to the task scheduler. Whenever the QoC elastic scheduler is activated, it improves the QoC the most while still meeting the system constraints. Examples are given to demonstrate the effectiveness of the QoC elastic scheduling.

Towards automated and in-situ, near-real time 3-D reconstruction of coral reef environments

Coral reefs are biologically complex ecosystems that support a wide variety of marine organisms. These are fragile communities under enormous threat from natural and human-based influences. Properly assessing and measuring the growth and health of reefs is essential to understanding impacts of ocean acidification, coastal urbanisation and global warming. In this paper, we present an innovative 3-D reconstruction technique based on visual imagery as a non-intrusive, repeatable, in situ method for estimating physical parameters, such as surface area and volume for efficient assessment of long-term variability. The reconstruction algorithms are presented, and benchmarked using an existing data set. We validate the technique underwater, utilising a commercial-off-the-shelf camera and a piece of staghorn coral, Acropora cervicornis. The resulting reconstruction is compared with a laser scan of the coral piece for assessment and validation. The comparison shows that 77% of the pixels in the reconstruction are within 0.3 mm of the ground truth laser scan. Reconstruction results from an unknown video camera are also presented as a segue to future applications of this research.

A transport protocol for real-time applications in wireless networked control systems

A Networked Control System (NCS) is a feedback-driven control system wherein the control loops are closed through a real-time network. Control and feedback signals in an NCS are exchanged among the system’s components in the form of information packets via the network. Nowadays, wireless technologies such as IEEE802.11 are being introduced to modern NCSs as they offer better scalability, larger bandwidth and lower costs. However, this type of network is not designed for NCSs because it introduces a large amount of dropped data, and unpredictable and long transmission latencies due to the characteristics of wireless channels, which are not acceptable for real-time control systems. Real-time control is a class of time-critical application which requires lossless data transmission, small and deterministic delays and jitter. For a real-time control system, network-introduced problems may degrade the system’s performance significantly or even cause system instability. It is therefore important to develop solutions to satisfy real-time requirements in terms of delays, jitter and data losses, and guarantee high levels of performance for time-critical communications in Wireless Networked Control Systems (WNCSs). To improve or even guarantee real-time performance in wireless control systems, this thesis presents several network layout strategies and a new transport layer protocol. Firstly, real-time performances in regard to data transmission delays and reliability of IEEE 802.11b-based UDP/IP NCSs are evaluated through simulations. After analysis of the simulation results, some network layout strategies are presented to achieve relatively small and deterministic network-introduced latencies and reduce data loss rates. These are effective in providing better network performance without performance degradation of other services. After the investigation into the layout strategies, the thesis presents a new transport protocol which is more effcient than UDP and TCP for guaranteeing reliable and time-critical communications in WNCSs. From the networking perspective, introducing appropriate communication schemes, modifying existing network protocols and devising new protocols, have been the most effective and popular ways to improve or even guarantee real-time performance to a certain extent. Most previously proposed schemes and protocols were designed for real-time multimedia communication and they are not suitable for real-time control systems. Therefore, devising a new network protocol that is able to satisfy real-time requirements in WNCSs is the main objective of this research project. The Conditional Retransmission Enabled Transport Protocol (CRETP) is a new network protocol presented in this thesis. Retransmitting unacknowledged data packets is effective in compensating for data losses. However, every data packet in realtime control systems has a deadline and data is assumed invalid or even harmful when its deadline expires. CRETP performs data retransmission only in the case that data is still valid, which guarantees data timeliness and saves memory and network resources. A trade-off between delivery reliability, transmission latency and network resources can be achieved by the conditional retransmission mechanism. Evaluation of protocol performance was conducted through extensive simulations. Comparative studies between CRETP, UDP and TCP were also performed. These results showed that CRETP significantly: 1). improved reliability of communication, 2). guaranteed validity of received data, 3). reduced transmission latency to an acceptable value, and 4). made delays relatively deterministic and predictable. Furthermore, CRETP achieved the best overall performance in comparative studies which makes it the most suitable transport protocol among the three for real-time communications in a WNCS.

Propagation of low power low divergence Gaussian fields in unbiased self-defocusing photorefractive media and their interactions

Many optical networks are limited in speed and processing capability due to the necessity for the optical signal to be converted to an electrical signal and back again. In addition, electronically manipulated interconnects in an otherwise optical network lead to overly complicated systems. Optical spatial solitons are optical beams that propagate without spatial divergence. They are capable of phase dependent interactions, and have therefore been extensively researched as suitable all optical interconnects for over 20 years. However, they require additional external components, initially high voltage power sources were required, several years later, high power background illumination had replaced the high voltage. However, these additional components have always remained as the greatest hurdle in realising the applications of the interactions of spatial optical solitons as all optical interconnects. Recently however, self-focusing was observed in an otherwise self-defocusing photorefractive crystal. This observation raises the possibility of the formation of soliton-like fields in unbiased self-defocusing media, without the need for an applied electrical field or background illumination. This thesis will present an examination of the possibility of the formation of soliton-like low divergence fields in unbiased self-defocusing photorefractive media. The optimal incident beam and photorefractive media parameters for the formation of these fields will be presented, together with an analytical and numerical study of the effect of these parameters. In addition, preliminary examination of the interactions of two of these fields will be presented. In order to complete an analytical examination of the field propagating through the photorefractive medium, the spatial profile of the beam after propagation through the medium was determined. For a low power solution, it was found that an incident Gaussian field maintains its Gaussian profile as it propagates. This allowed the beam at all times to be described by an individual complex beam parameter, while also allowing simple analytical solutions to the appropriate wave equation. An analytical model was developed to describe the effect of the photorefractive medium on the Gaussian beam. Using this model, expressions for the required intensity dependent change in both the real and imaginary components of the refractive index were found. Numerical investigation showed that under certain conditions, a low powered Gaussian field could propagate in self-defocusing photorefractive media with divergence of approximately 0.1 % per metre. An investigation into the parameters of a Ce:BaTiO3 crystal showed that the intensity dependent absorption is wavelength dependent, and can in fact transition to intensity dependent transparency. Thus, with careful wavelength selection, the required intensity dependent change in both the real and imaginary components of the refractive index for the formation of a low divergence Gaussian field are physically realisable. A theoretical model incorporating the dependence of the change in real and imaginary components of the refractive index on propagation distance was developed. Analytical and numerical results from this model are congruent with the results from the previous model, showing low divergence fields with divergence less than 0.003 % over the propagation length of the photorefractive medium. In addition, this approach also confirmed the previously mentioned self-focusing effect of the self-defocusing media, and provided an analogy to a negative index GRIN lens with an intensity dependent focal length. Experimental results supported the findings of the numerical analysis. Two low divergence fields were found to possess the ability to interact in a Ce:BaTiO3 crystal in a soliton-like fashion. The strength of these interactions was found to be dependent on the degree of divergence of the individual beams. This research found that low-divergence fields are possible in unbiased self-defocusing photorefractive media, and that soliton-like interactions between two of these fields are possible. However, in order for these types of fields to be used in future all optical interconnects, the manipulation of these interactions, together with the ability for these fields to guide a second beam at a different wavelength, must be investigated.

Accurately simulating the production of radiotherapy portal images using non-zero beam angles

In this study, the delivery and portal imaging of one square-field and one conformal radiotherapy treatment was simulated using the Monte Carlo codes BEAMnrc and DOSXYZnrc. The treatment fields were delivered to a humanoid phantom from different angles by a 6 MV photon beam linear accelerator, with an amorphous-silicon electronic portal imaging device (a-Si EPID) used to provide images of the phantom generated by each field. The virtual phantom preparation code CTCombine was used to combine a computed-tomography-derived model of the irradiated phantom with a simple, rectilinear model of the a-Si EPID, at each beam angle used in the treatment. Comparison of the resulting experimental and simulated a-Si EPID images showed good agreement, within \[gamma](3%, 3 mm), indicating that this method may be useful in providing accurate Monte Carlo predictions of clinical a-Si EPID images, for use in the verification of complex radiotherapy treatments.

Chaos or complex systems? Identifying factors influencing the success of international and NESB graduate research students in Engineering and Information Technology Fields

The paper explores the results an on-going research project to identify factors influencing the success of international and non-English speaking background (NESB) gradúate students in the fields of Engineering and IT at three Australian universities: the Queensland University of Technology (QUT), the University of Western Australia (UWA), and Curtin University (CU). While the larger study explores the influence of factors from both sides of the supervision equation (e.g., students and supervisors), this paper focusses primarily on the results of an online survey involving 227 international and/or NESB graduate students in the areas of Engineering and IT at the three universities. The study reveals cross-cultural differences in perceptions of student and supervisor roles, as well as differences in the understanding of the requirements of graduate study within the Australian Higher Education context. We argue that in order to assist international and NESB research students to overcome such culturally embedded challenges, it is important to develop a model which recognizes the complex interactions of factors from both sides of the supervision relationship, in order to understand this cohort‟s unique pedagogical needs and develop intercultural sensitivity within postgraduate research supervision.

Numerical modelling of non-load bearing light gauge cold-formed steel frame walls under fire conditions

Recently an innovative composite panel system was developed, where a thin insulation layer was used externally between two plasterboards to improve the fire performance of light gauge cold-formed steel frame walls. In this research, finite-element thermal models of both the traditional light gauge cold-formed steel frame wall panels with cavity insulation and the new light gauge cold-formed steel frame composite wall panels were developed to simulate their thermal behaviour under standard and realistic fire conditions. Suitable apparent thermal properties of gypsum plasterboard, insulation materials and steel were proposed and used. The developed models were then validated by comparing their results with available fire test results. This article presents the details of the developed finite-element models of small-scale non-load-bearing light gauge cold-formed steel frame wall panels and the results of the thermal analysis. It has been shown that accurate finite-element models can be used to simulate the thermal behaviour of small-scale light gauge cold-formed steel frame walls with varying configurations of insulations and plasterboards. The numerical results show that the use of cavity insulation was detrimental to the fire rating of light gauge cold-formed steel frame walls, while the use of external insulation offered superior thermal protection to them. The effects of real fire conditions are also presented.

Deep Raman spectroscopy for the non-invasive standoff detection of concealed chemical threat agents

Deep Raman spectroscopy has been utilized for the standoff detection of concealed chemical threat agents from a distance of 15 meters under real life background illumination conditions. By using combined time and space resolved measurements, various explosive precursors hidden in opaque plastic containers were identified non-invasively. Our results confirm that combined time and space resolved Raman spectroscopy leads to higher selectivity towards the sub-layer over the surface layer as well as enhanced rejection of fluorescence from the container surface when compared to standoff spatially offset Raman spectroscopy. Raman spectra that have minimal interference from the packaging material and good signal-to-noise ratio were acquired within 5 seconds of measurement time. A new combined time and space resolved Raman spectrometer has been designed with nanosecond laser excitation and gated detection, making it of lower cost and complexity than picosecond-based laboratory systems.

Toward non-invasive detection of concealed energetic materials in-field under ambient-light conditions

Spatially offset Raman spectroscopy (SORS) is demonstrated for the non-contact detection of energetic materials concealed within non-transparent, diffusely scattering containers. A modified design of an inverse SORS probe has been developed and tested. The SORS probe has been successfully used for the detection of various energetic substances inside different types of plastic containers. The tests have been successfully conducted under incandescent and fluorescent background lights as well as under daylight conditions, using a non-contact working distance of 6 cm. The interrogation times for the detection of the substances were less than 1 minute in each case, highlighting the suitability of the device for near real-time detection of concealed hazards in the field. The device has potential applications in forensic analysis and homeland security investigations.

Real-time detection of concealed chemical hazards under ambient light conditions using Raman spectroscopy

Current concerns regarding terrorism and international crime highlight the need for new techniques for detecting unknown and hazardous substances. A novel Raman spectroscopy-based technique, spatially offset Raman spectroscopy (SORS), was recently devised for non-invasively probing the contents of diffusely scattering and opaque containers. Here, we demonstrate a modified portable SORS sensor for detecting concealed substances in-field under different background lighting conditions. Samples including explosive precursors, drugs and an organophosphate insecticide (chemical warfare agent surrogate) were concealed inside diffusely scattering packaging including plastic, paper and cloth. Measurements were carried out under incandescent and fluorescent light as well as under daylight to assess the suitability of the probe for different real-life conditions. In each case, it was possible to identify the substances against their reference Raman spectra in less than one minute. The developed sensor has potential for rapid detection of concealed hazardous substances in airports, mail distribution centers and customs checkpoints.

Numerical simulation of a new two-dimensional variable-order fractional percolation equation in non-homogeneous porous media

Percolation flow problems are discussed in many research fields, such as seepage hydraulics, groundwater hydraulics, groundwater dynamics and fluid dynamics in porous media. Many physical processes appear to exhibit fractional-order behavior that may vary with time, or space, or space and time. The theory of pseudodifferential operators and equations has been used to deal with this situation. In this paper we use a fractional Darcys law with variable order Riemann-Liouville fractional derivatives, this leads to a new variable-order fractional percolation equation. In this paper, a new two-dimensional variable-order fractional percolation equation is considered. A new implicit numerical method and an alternating direct method for the two-dimensional variable-order fractional model is proposed. Consistency, stability and convergence of the implicit finite difference method are established. Finally, some numerical examples are given. The numerical results demonstrate the effectiveness of the methods. This technique can be used to simulate a three-dimensional variable-order fractional percolation equation.

Entrepreneurship education in non-business schools : best practice for Australian contexts of knowledge and innovation communities (Final Report)

In the current era of global economic instability, business and industry have already identified a widening gap between graduate skills and employability. An important element of this is the lack of entrepreneurial skills in graduates. This Teaching Fellowship investigated two sides of a story about entrepreneurial skills and their teaching. Senior players in the innovation commercialisation industry, a high profile entrepreneurial sector, were surveyed to gauge their needs and experiences of graduates they employ. International contexts of entrepreneurship education were investigated to explore how their teaching programs impart the skills of entrepreneurship. Such knowledge is an essential for the design of education programs that can deliver the entrepreneurial skills deemed important by industry for future sustainability. Two programs of entrepreneurship education are being implemented at QUT that draw on the best practice exemplars investigated during this Fellowship. The QUT Innovation Space (QIS) focuses on capturing the innovation and creativity of students, staff and others. The QIS is a physical and virtual meeting and networking space; a connected community enhancing the engagement of participants. The Q_Hatchery is still embryonic; but it is intended to be an innovation community that brings together nascent entrepreneurial businesses to collaborate, train and support each other. There is a niche between concept product and business incubator where an experiential learning environment for otherwise isolated ‘garage-at-home’ businesses could improve success rates. The QIS and the Q_Hatchery serve as living research laboratories to trial the concepts emerging from the skills survey. The survey of skills requirements of the innovation commercialisation industry has produced a large and high quality data set still being explored. Work experience as an employability factor has already emerged as an industry requirement that provides employee maturity. Exploratory factor analysis of the skills topics surveyed has led to a process-based conceptual model for teaching and learning higher-order entrepreneurial skills. Two foundational skills domains (Knowledge, Awareness) are proposed as prerequisites which allow individuals with a suite of early stage entrepreneurial and behavioural skills (Pre-leadership) to further leverage their careers into a leadership role in industry with development of skills around higher order elements of entrepreneurship, management in new business ventures and progressing winning technologies to market. The next stage of the analysis is to test the proposed model through structured equation modelling. Another factor that emerged quickly from the survey analysis broadens the generic concept of team skills currently voiced in Australian policy documents discussing the employability agenda. While there was recognition of the role of sharing, creating and using knowledge in a team-based interdisciplinary context, the adoption and adaptation of behaviours and attitudes of other team members of different disciplinary backgrounds (interprofessionalism) featured as an issue. Most undergraduates are taught and undertake teamwork in silos and, thus, seldom experience a true real-world interdisciplinary environment. Enhancing the entrepreneurial capacity of Australian industry is essential for the economic health of the country and can only be achieved by addressing the lack of entrepreneurial skills in graduates from the higher education system. This Fellowship has attempted to address this deficiency by identifying the skills requirements and providing frameworks for their teaching.

Outcomes following operative and non-operative management of humeral midshaft fractures: a prospective, observational cohort study of 47 patients

Background Although the non-operative management of closed humeral midshaft fractures has been advocated for years, the increasing popularity of operative intervention has left the optimal treatment choice unclear. Objective To compare the outcomes of operative and non-operative treatment of traumatic closed humeral midshaft fractures in adult patients. Methods A multicentre prospective comparative cohort study across 20 centres was conducted. Patients with AO type 12 A2, A3 and B2 fractures were treated with a functional brace or a retrograde-inserted unreamed humeral nail. Follow-up measurements were taken at 6, 12 and 52 weeks after the injury. The primary outcome was fracture healing after 1 year. Secondary outcomes included sub-items of the Constant score, general patient satisfaction, complications and cost-effectiveness parameters. Functions of the uninjured extremity were used as reference parameters. Intention-to-treat analysis was applied with the use of t-tests, Fisher’s exact tests, Mann–Whitney U-tests and adjusted analysis of variance (ANOVA). Results Forty-seven patients were included. The patient sample consisted of 23 women and 24 men, with a mean age of 52.7 years (range 17–86 years). Of the 47 cases, 14 were treated non-operatively and 33 operatively. The follow-up rate at 1 year was 81%. After 1 year, 11 fractures (100%) healed in the non-operative group and at least 24 fractures (≥89%) healed in the operative group [1 non-union patient (4%) and no data for 2 patients (7%)]. There were no significant differences in pain, range of motion (ROM) of the shoulder and elbow, and return to work after 6 weeks, 12 weeks and 1 year. Although operatively treated patients showed significantly greater shoulder abduction strength (p = 0.036), elbow flexion strength (p = 0.021), functional hand positioning (p = 0.008) and return to recreational activities (p = 0.043) after 6 weeks, no statistically significant differences existed in any outcome measure at the 1-year follow-up. Conclusions Our findings indicate that the non-operative management of humeral midshaft fractures can be expected to have similar functional outcomes and patient satisfaction at 1 year, despite an early benefit to operative treatment. If no radiological evidence of fracture healing exists in non-operatively treated patients during early follow-up, a switch to surgical treatment results in good functional outcomes and patient satisfaction. Keywords: Humeral shaft fracture, Non-operative treatment, Functional brace, Operative treatment, Unreamed humeral nail (UHN), Prospective, Cohort study

Phylogeography of Echinocladius martini Cranston (Diptera: Chironomidae) in closed forest streams of eastern Australia

The eastern Australian rainforests have experienced several cycles of range contraction and expansion since the late Miocene that are closely correlated with global glaciation events. Together with ongoing aridification of the continent, this has resulted in current distributions of native closed forest that are highly fragmented along the east coast. Several closed forest endemic taxa exhibit patterns of population genetic structure that are congruent with historical isolation of populations in discrete refugia and reflect evolutionary histories dramatically affected by vicariance. Currently, limited data are available regarding the impact of these past climatic fluctuations on freshwater invertebrate taxa. The non-biting midge species Echinocladius martini Cranston is distributed along the east coast and inhabits predominantly montane streams in closed forest habitat. Phylogeographic structure in E. martini was resolved here at a continental scale by incorporating data from a previous pilot study and expanding the sampling design to encompass populations in the Wet Tropics of north-eastern Queensland, south-east Queensland, New South Wales and Victoria. Patterns of phylogeographic structure revealed several deeply divergent mitochondrial lineages from central and south-eastern Australia that were previously unrecognised and were geographically endemic to closed forest refugia. Estimated divergence times were congruent with late Miocene onset of rainforest contractions across the east coast of Australia. This suggested that dispersal and gene flow among E. martini populations isolated in refugia has been highly restricted historically. Moreover, these data imply, in contrast to existing preconceptions about freshwater invertebrates, that this taxon may be acutely susceptible to habitat fragmentation.