Optimisation of Banana streak virus (BSV) diagnostic assays

Bananas are one of the world�fs most important crops, serving as a staple food and an important source of income for millions of people in the subtropics. Pests and diseases are a major constraint to banana production. To prevent the spread of pests and disease, farmers are encouraged to use disease�] and insect�]free planting material obtained by micropropagation. This option, however, does not always exclude viruses and concern remains on the quality of planting material. Therefore, there is a demand for effective and reliable virus indexing procedures for tissue culture (TC) material. Reliable diagnostic tests are currently available for all of the economically important viruses of bananas with the exception of Banana streak viruses (BSV, Caulimoviridae, Badnavirus). Development of a reliable diagnostic test for BSV is complicated by the significant serological and genetic variation reported for BSV isolates, and the presence of endogenous BSV (eBSV). Current PCR�] and serological�]based diagnostic methods for BSV may not detect all species of BSV, and PCR�]based methods may give false positives because of the presence of eBSV. Rolling circle amplification (RCA) has been reported as a technique to detect BSV which can also discriminate between episomal and endogenous BSV sequences. However, the method is too expensive for large scale screening of samples in developing countries, and little information is available regarding its sensitivity. Therefore the development of reliable PCR�]based assays is still considered the most appropriate option for large scale screening of banana plants for BSV. This MSc project aimed to refine and optimise the protocols for BSV detection, with a particular focus on developing reliable PCR�]based diagnostics Initially, the appropriateness and reliability of PCR and RCA as diagnostic tests for BSV detection were assessed by testing 45 field samples of banana collected from nine districts in the Eastern region of Uganda in February 2010. This research was also aimed at investigating the diversity of BSV in eastern Uganda, identifying the BSV species present and characterising any new BSV species. Out of the 45 samples tested, 38 and 40 samples were considered positive by PCR and RCA, respectively. Six different species of BSV, namely Banana streak IM virus (BSIMV), Banana streak MY virus (BSMYV), Banana streak OL virus (BSOLV), Banana streak UA virus (BSUAV), Banana streak UL virus (BSULV), Banana streak UM virus (BSUMV), were detected by PCR and confirmed by RCA and sequencing. No new species were detected, but this was the first report of BSMYV in Uganda. Although RCA was demonstrated to be suitable for broad�]range detection of BSV, it proved time�]consuming and laborious for identification in field samples. Due to the disadvantages associated with RCA, attempts were made to develop a reliable PCR�]based assay for the specific detection of episomal BSOLV, Banana streak GF virus (BSGFV), BSMYV and BSIMV. For BSOLV and BSGFV, the integrated sequences exist in rearranged, repeated and partially inverted portions at their site of integration. Therefore, for these two viruses, primers sets were designed by mapping previously published sequences of their endogenous counterparts onto published sequences of the episomal genomes. For BSOLV, two primer sets were designed while, for BSGFV, a single primer set was designed. The episomalspecificity of these primer sets was assessed by testing 106 plant samples collected during surveys in Kenya and Uganda, and 33 leaf samples from a wide range of banana cultivars maintained in TC at the Maroochy Research Station of the Department of Employment, Economic Development and Innovation (DEEDI), Queensland. All of these samples had previously been tested for episomal BSV by RCA and for both BSOLV and BSGFV by PCR using published primer sets. The outcome from these analyses was that the newly designed primer sets for BSOLV and BSGFV were able to distinguish between episomal BSV and eBSV in most cultivars with some B�]genome component. In some samples, however, amplification was observed using the putative episomal�]specific primer sets where episomal BSV was not identified using RCA. This may reflect a difference in the sensitivity of PCR compared to RCA, or possibly the presence of an eBSV sequence of different conformation. Since the sequences of the respective eBSV for BSMYV and BSIMV in the M. balbisiana genome are not available, a series of random primer combinations were tested in an attempt to find potential episomal�]specific primer sets for BSMYV and BSIMV. Of an initial 20 primer combinations screened for BSMYV detection on a small number of control samples, 11 primers sets appeared to be episomal�]specific. However, subsequent testing of two of these primer combinations on a larger number of control samples resulted in some inconsistent results which will require further investigation. Testing of the 25 primer combinations for episomal�]specific detection of BSIMV on a number of control samples showed that none were able to discriminate between episomal and endogenous BSIMV. The final component of this research project was the development of an infectious clone of a BSV endemic in Australia, namely BSMYV. This was considered important to enable the generation of large amounts of diseased plant material needed for further research. A terminally redundant fragment (.1.3 �~ BSMYV genome) was cloned and transformed into Agrobacterium tumefaciens strain AGL1, and used to inoculate 12 healthy banana plants of the cultivars Cavendish (Williams) by three different methods. At 12 weeks post�]inoculation, (i) four of the five banana plants inoculated by corm injection showed characteristic BSV symptoms while the remaining plant was wilting/dying, (ii) three of the five banana plants inoculated by needle�]pricking of the stem showed BSV symptoms, one plant was symptomless while the remaining had died and (iii) both banana plants inoculated by leaf infiltration were symptomless. When banana leaf samples were tested for BSMYV by PCR and RCA, BSMYV was confirmed in all banana plants showing symptoms including those were wilting and/or dying. The results from this research have provided several avenues for further research. By completely sequencing all variants of eBSOLV and eBSGFV and fully sequencing the eBSIMV and eBSMYV regions, episomal BSV�]specific primer sets for all eBSVs could potentially be designed that could avoid all integrants of that particular BSV species. Furthermore, the development of an infectious BSV clone will enable large numbers of BSVinfected plants to be generated for the further testing of the sensitivity of RCA compared to other more established assays such as PCR. The development of infectious clones also opens the possibility for virus induced gene silencing studies in banana.

Spectrum sensing, detection and optimisation in cognitive radio for non-stationary primary user signals

Cognitive radio is an emerging technology proposing the concept of dynamic spec- trum access as a solution to the looming problem of spectrum scarcity caused by the growth in wireless communication systems. Under the proposed concept, non- licensed, secondary users (SU) can access spectrum owned by licensed, primary users (PU) so long as interference to PU are kept minimal. Spectrum sensing is a crucial task in cognitive radio whereby the SU senses the spectrum to detect the presence or absence of any PU signal. Conventional spectrum sensing assumes the PU signal as ‘stationary’ and remains in the same activity state during the sensing cycle, while an emerging trend models PU as ‘non-stationary’ and undergoes state changes. Existing studies have focused on non-stationary PU during the transmission period, however very little research considered the impact on spectrum sensing when the PU is non-stationary during the sensing period. The concept of PU duty cycle is developed as a tool to analyse the performance of spectrum sensing detectors when detecting non-stationary PU signals. New detectors are also proposed to optimise detection with respect to duty cycle ex- hibited by the PU. This research consists of two major investigations. The first stage investigates the impact of duty cycle on the performance of existing detec- tors and the extent of the problem in existing studies. The second stage develops new detection models and frameworks to ensure the integrity of spectrum sensing when detecting non-stationary PU signals. The first investigation demonstrates that conventional signal model formulated for stationary PU does not accurately reflect the behaviour of a non-stationary PU. Therefore the performance calculated and assumed to be achievable by the conventional detector does not reflect actual performance achieved. Through analysing the statistical properties of duty cycle, performance degradation is proved to be a problem that cannot be easily neglected in existing sensing studies when PU is modelled as non-stationary. The second investigation presents detectors that are aware of the duty cycle ex- hibited by a non-stationary PU. A two stage detection model is proposed to improve the detection performance and robustness to changes in duty cycle. This detector is most suitable for applications that require long sensing periods. A second detector, the duty cycle based energy detector is formulated by integrat- ing the distribution of duty cycle into the test statistic of the energy detector and suitable for short sensing periods. The decision threshold is optimised with respect to the traffic model of the PU, hence the proposed detector can calculate average detection performance that reflect realistic results. A detection framework for the application of spectrum sensing optimisation is proposed to provide clear guidance on the constraints on sensing and detection model. Following this framework will ensure the signal model accurately reflects practical behaviour while the detection model implemented is also suitable for the desired detection assumption. Based on this framework, a spectrum sensing optimisation algorithm is further developed to maximise the sensing efficiency for non-stationary PU. New optimisation constraints are derived to account for any PU state changes within the sensing cycle while implementing the proposed duty cycle based detector.

Maintenance optimisation of a multi-state series-parallel system considering economic dependence and state-dependent inspection intervals

This paper presents a maintenance optimisation method for a multi-state series-parallel system considering economic dependence and state-dependent inspection intervals. The objective function considered in the paper is the average revenue per unit time calculated based on the semi-regenerative theory and the universal generating function (UGF). A new algorithm using the stochastic ordering is also developed in this paper to reduce the search space of maintenance strategies and to enhance the efficiency of optimisation algorithms. A numerical simulation is presented in the study to evaluate the efficiency of the proposed maintenance strategy and optimisation algorithms. The simulation result reveals that maintenance strategies with opportunistic maintenance and state-dependent inspection intervals are more cost-effective when the influence of economic dependence and inspection cost is significant. The study further demonstrates that the optimisation algorithm proposed in this paper has higher computational efficiency than the commonly employed heuristic algorithms.

Shape-formed ceramic superconductors by slip-casting

In order to rigorously test emerging applications using prototypes and pilot designs, high temperature superconductor (HTS) materials must be fabricated into a variety of shapes in an economical manner. We have developed a simple, economical, ceramic slip-casting approach to form complex shaped monolithic HTS articles for which high bulk density has been achieved. The sintered articles exhibit good Meissner signal and consist of phase-pure HTSC phase. A low transport critical current density is observed and is explained on the basis of densification and grain growth. © 1995 The Metallurgical of Society of AIME.

Molecular dynamics investigation on edge stress and shape transition in graphene nanoribbons

Graphene nanoribbon (GNR) with free edges demonstrates unique pre-existing edge energy and edge stress, leading to non-flat morphologies. Using molecular dynamics (MD) methods, we evaluated edge energies as well as edge stresses for four different edge types, including regular edges (armchair and zigzag), armchair edge terminated with hydrogen and reconstructed armchair. The results showed that compressive stress exists in the regular and hydrogen-terminated edges along the edge direction. In contrast, the reconstructed armchair edge is generally subject to tension. Furthermore, we also investigated shape transition between flat and rippled configurations of GNRs with different free edges. It was found that the pre-existing stress at free edges can greatly influence the initial energy state and the shape transition.

Optimisation of bio-oil extraction process from Beauty Leaf (Calophyllum inophyllum) oil seed as a second generation biodiesel source

The Beauty Leaf tree (Calophyllum inophyllum) is a potential source of non-edible vegetable oil for producing future generation biodiesel because of its ability to grow in a wide range of climate conditions, easy cultivation, high fruit production rate, and the high oil content in the seed. This plant naturally occurs in the coastal areas of Queensland and the Northern Territory in Australia, and is also widespread in south-east Asia, India and Sri Lanka. Although Beauty Leaf is traditionally used as a source of timber and orientation plant, its potential as a source of second generation biodiesel is yet to be exploited. In this study, the extraction process from the Beauty Leaf oil seed has been optimised in terms of seed preparation, moisture content and oil extraction methods. The two methods that have been considered to extract oil from the seed kernel are mechanical oil extraction using an electric powered screw press, and chemical oil extraction using n-hexane as an oil solvent. The study found that seed preparation has a significant impact on oil yields, especially in the screw press extraction method. Kernels prepared to 15% moisture content provided the highest oil yields for both extraction methods. Mechanical extraction using the screw press can produce oil from correctly prepared product at a low cost, however overall this method is ineffective with relatively low oil yields. Chemical extraction was found to be a very effective method for oil extraction for its consistence performance and high oil yield, but cost of production was relatively higher due to the high cost of solvent. However, a solvent recycle system can be implemented to reduce the production cost of Beauty Leaf biodiesel. The findings of this study are expected to serve as the basis from which industrial scale biodiesel production from Beauty Leaf can be made.

Interpersonal coordination tendencies shape 1-vs-1 sub-phase performance outcomes in youth soccer

This study investigated the influence of interpersonal coordination tendencies on performance outcomes of 1-vs-1 subphases in youth soccer. Eight male developing soccer players (age: 11.8+0.4 years; training experience: 3.6+1.1 years) performed an in situ simulation of a 1-vs-1 sub-phase of soccer. Data from 82 trials were obtained with motion-analysis techniques, and relative phase used to measure the space-time coordination tendencies of attacker-defender dyads. Approximate entropy (ApEn) was then used to quantify the unpredictability of interpersonal interactions over trials. Results revealed how different modes of interpersonal coordination emerging from attacker-defender dyads influenced the 1-vs-1 performance outcomes. High levels of space-time synchronisation (47%) and unpredictability in interpersonal coordination processes (ApEn: 0.91+0.34) were identified as key features of an attacking player’s success. A lead-lag relation attributed to a defending player (34% around 7308 values) and a more predictable coordination mode (ApEn: 0.65+0.27, P50.001), demonstrated the coordination tendencies underlying the success of defending players in 1-vs-1 sub-phases. These findings revealed how the mutual influence of each player on the behaviour of dyadic systems shaped emergent performance outcomes. More specifically, the findings showed that attacking players should be constrained to exploit the space-time synchrony with defenders in an unpredictable and creative way, while defenders should be encouraged to adopt postures and behaviours that actively constrain the attacker’s actions.

Methods to estimate the size and shape of the unaccommodated crystalline lens in vivo

Purpose. The purpose of this article was to present methods capable of estimating the size and shape of the human eye lens without resorting to phakometry or magnetic resonance imaging (MRI). Methods. Previously published biometry and phakometry data of 66 emmetropic eyes of 66 subjects (age range [18, 63] years, spherical equivalent range [−0.75, +0.75] D) were used to define multiple linear regressions for the radii of curvature and thickness of the lens, from which the lens refractive index could be derived. MRI biometry was also available for a subset of 30 subjects, from which regressions could be determined for the vertex radii of curvature, conic constants, equatorial diameter, volume, and surface area. All regressions were compared with the phakometry and MRI data; the radii of curvature regressions were also compared with a method proposed by Bennett and Royston et al. Results. The regressions were in good agreement with the original measurements. This was especially the case for the regressions of lens thickness, volume, and surface area, which each had an R2 > 0.6. The regression for the posterior radius of curvature had an R2 < 0.2, making this regression unreliable. For all other regressions we found 0.25 < R2 < 0.6. The Bennett-Royston method also produced a good estimation of the radii of curvature, provided its parameters were adjusted appropriately. Conclusions. The regressions presented in this article offer a valuable alternative in case no measured lens biometry values are available; however care must be taken for possible outliers.

Numerical analysis of shape transition in graphene nanoribbons

Graphene nanoribbon (GNR) with free edges can exhibit non-flat morphologies due to pre-existing edge stress. Using molecular dynamics (MD) simulations, we investigate the free-edge effect on the shape transition in GNRs with different edge types, including regular (armchair and zigzag), armchair terminated with hydrogen and reconstructed armchair. The results show that initial edge stress and energy are dependent on the edge configurations. It is confirmed that pre-strain on the free edges is a possible way to limit the random shape transition of GNRs. In addition, the influence of surface attachment on the shape transition is also investigated in this work. It is found that surface attachment can lead to periodic ripples in GNRs, dependent on the initial edge configurations.

Condition-based maintenance optimisation without a predetermined strategy structure for a two-component series system

Most existing research on maintenance optimisation for multi-component systems only considers the lifetime distribution of the components. When the condition-based maintenance (CBM) strategy is adopted for multi-component systems, the strategy structure becomes complex due to the large number of component states and their combinations. Consequently, some predetermined maintenance strategy structures are often assumed before the maintenance optimisation of a multi-component system in a CBM context. Developing these predetermined strategy structure needs expert experience and the optimality of these strategies is often not proofed. This paper proposed a maintenance optimisation method that does not require any predetermined strategy structure for a two-component series system. The proposed method is developed based on the semi-Markov decision process (SMDP). A simulation study shows that the proposed method can identify the optimal maintenance strategy adaptively for different maintenance costs and parameters of degradation processes. The optimal maintenance strategy structure is also investigated in the simulation study, which provides reference for further research in maintenance optimisation of multi-component systems.

User-driven quality of experience modelling for mobile video optimisation

The increasing demand for mobile video has attracted much attention from both industry and researchers. To satisfy users and to facilitate the usage of mobile video, providing optimal quality to the users is necessary. As a result, quality of experience (QoE) becomes an important focus in measuring the overall quality perceived by the end-users, from the aspects of both objective system performance and subjective experience. However, due to the complexity of user experience and diversity of resources (such as videos, networks and mobile devices), it is still challenging to develop QoE models for mobile video that can represent how user-perceived value varies with changing conditions. Previous QoE modelling research has two main limitations: aspects influencing QoE are insufficiently considered; and acceptability as the user value is seldom studied. Focusing on the QoE modelling issues, two aims are defined in this thesis: (i) investigating the key influencing factors of mobile video QoE; and (ii) establishing QoE prediction models based on the relationships between user acceptability and the influencing factors, in order to help provide optimal mobile video quality. To achieve the first goal, a comprehensive user study was conducted. It investigated the main impacts on user acceptance: video encoding parameters such as quantization parameter, spatial resolution, frame rate, and encoding bitrate; video content type; mobile device display resolution; and user profiles including gender, preference for video content, and prior viewing experience. Results from both quantitative and qualitative analysis revealed the significance of these factors, as well as how and why they influenced user acceptance of mobile video quality. Based on the results of the user study, statistical techniques were used to generate a set of QoE models that predict the subjective acceptability of mobile video quality by using a group of the measurable influencing factors, including encoding parameters and bitrate, content type, and mobile device display resolution. Applying the proposed QoE models into a mobile video delivery system, optimal decisions can be made for determining proper video coding parameters and for delivering most suitable quality to users. This would lead to consistent user experience on different mobile video content and efficient resource allocation. The findings in this research enhance the understanding of user experience in the field of mobile video, which will benefit mobile video design and research. This thesis presents a way of modelling QoE by emphasising user acceptability of mobile video quality, which provides a strong connection between technical parameters and user-desired quality. Managing QoE based on acceptability promises the potential for adapting to the resource limitations and achieving an optimal QoE in the provision of mobile video content.

Spectrum sensing optimisation for dynamic primary user signal

We propose a multi-layer spectrum sensing optimisation algorithm to maximise sensing efficiency by computing the optimal sensing and transmission durations for a fast changing, dynamic primary user. Dynamic primary user traffic is modelled as a random process, where the primary user changes states during both the sensing period and transmission period to reflect a more realistic scenario. Furthermore, we formulate joint constraints to correctly reflect interference to the primary user and lost opportunity of the secondary user during the transmission period. Finally, we implement a novel duty cycle based detector that is optimised with respect to PU traffic to accurately detect primary user activity during the sensing period. Simulation results show that unlike currently used detection models, the proposed algorithm can jointly optimise the sensing and transmission durations to simultaneously satisfy the optimisation constraints for the considered primary user traffic.

Multi-objective design optimisation of GFRP sandwich beams

A novel Glass Fibre Reinforced Polymer (GFRP) sandwich panel was developed by an Australian manufacturer for civil engineering applications. This research is motivated by the new applications of GFRP sandwich structures in civil engineering such as slab, beam, girder and sleeper. An optimisation methodology is developed in this work to enhance the design of GFRP sandwich beams. The design of single and glue laminated GFRP sandwich beam were conducted by using numerical optimisation. The numerical multi-objective optimisation considered a design two objectives simultaneously. These objectives are cost and mass. The numerical optimisation uses the Adaptive Range Multi-objective Genetic Algorithm (ARMOGA) and Finite Element (FE) method. Trade-offs between objectives was found during the optimisation process. Multi-objective optimisation shows a core to skin mass ratio equal to 3.68 for the single sandwich beam cross section optimisation and it showed that the optimum core to skin thickness ratio is 11.0.

Analysis and optimisation of the preferences of decision-makers in black-start group decision-making

As the first stage of power system restoration after a blackout, an optimal black-start scheme is very important for speeding up the whole restoration procedure. Up to now, much research work has been done on generating or selecting an optimal black-start scheme by a single round of decision-making. However, less attention has been paid for improving the final decision-making results through a multiple-round decision-making procedure. In the group decision-making environment, decision-making results evaluated by different black-start experts may differ significantly with each other. Thus, the consistency of black-start decision-making results could be deemed as an important indicator in assessing the black-start group decision-making results. Given this background, an intuitionistic fuzzy distance-based method is presented to analyse the consistency of black-start group decision-making results. Moreover, the weights of black-start indices as well as the weights of decision-making experts are modified in order to optimise the consistency of black-start group decision-making results. Finally, an actual example is served for demonstrating the proposed method.

Blocking layer optimisation of poly(3-hexylthiopene)based solid state dye sensitized solar cells

The optimisation study of the fabrication of a compact TiO2 blocking layer (via Spray Pyrolysis Deposition) for poly (3-hexylthiopene) (P3HT) for Solid State Dye Sensitized Solar Cells (SDSCs) is reported. We used a novel spray TiO2 precursor solution composition obtained by adding acetylacetone to a conventional formulation (Diisopropoxytitanium bis (acetylacetonate) in ethanol). By Scanning Electron Microscopy a TiO2 layer with compact morphology and thickness of around 100 nmis shown. Through a Tafel plot analysis an enhancement of the device diode-like behaviour induced by the acetylacetone blocking layer respect to the conventional one is observed. Significantly, the device fabricatedwith the acetylacetone blocking layer shows an overall increment of the cell performance with respect to the cellwith the conventional one (DJsc/Jsc = +13.8%, DFF/FF = +39.7%, DPCE/PCE = +55.6%). A conversion efficiency optimumis found for 15 successive spray cycles where the diode-like behaviour of the acetylacetone blocking layer is more effective. Over three batches of cells (fabricated with P3HT and dye D35) an average conversion efficiency value of 3.9% (under a class A sun simulator with 1 sun A.M. 1.5 illumination conditions) was measured. From the best cell we fabricated a conversion efficiency value of 4.5% was extracted. This represents a significant increment with respect to previously reported values for P3HT/dye D35 based SDSCs.