Development of a novel rolling-circle amplification technique to detect Banana streak virus which also discriminates between integrated and episomal virus sequences

Bananas are hosts to a large number of banana streak virus (BSV) species. However, diagnostic methods for BSV are inadequate because of the considerable genetic and serological diversity amongst BSV isolates and the presence of integrated BSV sequences in some banana cultivars which leads to false positives. In this study, a sequence non-specific, rolling-circle amplification (RCA) technique was developed and shown to overcome these limitations for the detection and subsequent characterisation of BSV isolates infecting banana. This technique was shown to discriminate between integrated and episomal BSV DNA, specifically detecting the latter in several banana cultivars known to contain episomal and/or integrated sequences of Banana streak Mysore virus (BSMyV), Banana streak OL virus (BSOLV) and Banana streak GF virus (BSGFV). Using RCA, the presence of BSMyV and BSOLV was confirmed in Australia, while BSOLV, BSGFV, Banana streak Uganda I virus (BSUgIV), Banana streak Uganda L virus (BSUgLV) and Banana streak Uganda M virus (BSUgMV) were detected in Uganda. This is the first confirmed report of episomally-derived BSUglV, BSUgLV and BSUgMV in Uganda. As well as its ability to detect BSV, RCA was shown to detect two other pararetroviruses, Sugarcane bacilliform virus in sugarcane and Cauliflower mosaic virus in turnip.

The effects of muscle fatigue on knee function during landing

The human knee acts as a sophisticated shock absorber during landing movements. The ability of the knee to perform this function in the real world is remarkable given that the context of the landing movement may vary widely between performances. For this reason, humans must be capable of rapidly adjusting the mechanical properties of the knee under impact load in order to satisfy many competing demands. However, the processes involved in regulating these properties in response to changing constraints remain poorly understood. In particular, the effects of muscle fatigue on knee function during step landing are yet to be fully explored. Fatigue of the knee muscles is significant for 2 reasons. First, it is thought to have detrimental effects on the ability of the knee to act as a shock absorber and is considered a risk factor for knee injury. Second, fatigue of knee muscles provides a unique opportunity to examine the mechanisms by which healthy individuals alter knee function. A review of the literature revealed that the effect of fatigue on knee function during landing has been assessed by comparing pre and postfatigue measurements, with fatigue induced by a voluntary exercise protocol. The information is limited by inconsistent results with key measures, such as knee stiffness, showing varying results following fatigue, including increased stiffness, decreased stiffness or failure to detect any change in some experiments. Further consideration of the literature questions the validity of the models used to induce and measure fatigue, as well as the pre-post study design, which may explain the lack of consensus in the results. These limitations cast doubt on the usefulness of the available information and identify a need to investigate alternative approaches. Based on the results of this review, the aims of this thesis were to: • evaluate the methodological procedures used in validation of a fatigue model • investigate the adaptation and regulation of post-impact knee mechanics during repeated step landings • use this new information to test the effects of fatigue on knee function during a step-landing task. To address the aims of the thesis, 3 related experiments were conducted that collected kinetic, kinematic and electromyographic data from 3 separate samples of healthy male participants. The methodologies involved optoelectronic motion capture (VICON), isokinetic dynamometry (System3 Pro, BIODEX) and wireless surface electromyography (Zerowire, Aurion, Italy). Fatigue indicators and knee function measures used in each experiment were derived from the data. Study 1 compared the validity and reliability of repetitive stepping and isokinetic contractions with respect to fatigue of the quadriceps and hamstrings. Fifteen participants performed 50 repetitions of each exercise twice in randomised order, over 4 sessions. Sessions were separated by a minimum of 1 week’s rest, to ensure full recovery. Validity and reliability depended on a complex interaction between the exercise protocol, the fatigue indicator, the individual and the muscle of interest. Nevertheless, differences between exercise protocols indicated that stepping was less effective in eliciting valid and reliable changes in peak power and spectral compression, compared with isokinetic exercise. A key finding was that fatigue progressed in a biphasic pattern during both exercises. The point separating the 2 phases, known as the transition point, demonstrated superior between-test reliability during the isokinetic protocol, compared with stepping. However, a correction factor should be used to accurately apply this technique to the study of fatigue during landing. Study 2 examined alterations in knee function during repeated landings, with a different sample (N =12) performing 60 consecutive step landing trials. Each landing trial was separated by 1-minute rest periods. The results provided new information in relation to the pre-post study design in the context of detecting adjustments in knee function during landing. First, participants significantly increased or decreased pre-impact muscle activity or post-impact mechanics despite environmental and task constraints remaining unchanged. This is the 1st study to demonstrate this effect in healthy individuals without external feedback on performance. Second, single-subject analysis was more effective in detecting alterations in knee function compared to group-level analysis. Finally, repeated landing trials did not reduce inter-trial variability of knee function in some participants, contrary to assumptions underpinning previous studies. The results of studies 1 and 2 were used to modify the design of Study 3 relative to previous research. These alterations included a modified isokinetic fatigue protocol, multiple pre-fatigue measurements and singlesubject analysis to detect fatigue-related changes in knee function. The study design incorporated new analytical approaches to investigate fatiguerelated alterations in knee function during landing. Participants (N = 16) were measured during multiple pre-fatigue baseline trial blocks prior to the fatigue model. A final block of landing trials was recorded once the participant met the operational fatigue definition that was identified in Study 1. The analysis revealed that the effects of fatigue in this context are heavily dependent on the compensatory response of the individual. A continuum of responses was observed within the sample for each knee function measure. Overall, preimpact preparation and post-impact mechanics of the knee were altered with highly individualised patterns. Moreover, participants used a range of active or passive pre-impact strategies to adapt post-impact mechanics in response to quadriceps fatigue. The unique patterns identified in the data represented an optimisation of knee function based on priorities of the individual. The findings of these studies explain the lack of consensus within the literature regarding the effects of fatigue on knee function during landing. First, functional fatigue protocols lack validity in inducing fatigue-related changes in mechanical output and spectral compression of surface electromyography (sEMG) signals, compared with isokinetic exercise. Second, fatigue-related changes in knee function during landing are confounded by inter-individual variation, which limits the sensitivity of group-level analysis. By addressing these limitations, the 3rd study demonstrated the efficacies of new experimental and analytical approaches to observe fatigue-related alterations in knee function during landing. Consequently, this thesis provides new perspectives into the effects of fatigue in knee function during landing. In conclusion: • The effects of fatigue on knee function during landing depend on the response of the individual, with considerable variation present between study participants, despite similar physical characteristics. • In healthy males, adaptation of pre-impact muscle activity and postimpact knee mechanics is unique to the individual and reflects their own optimisation of demands such as energy expenditure, joint stability, sensory information and loading of knee structures. • The results of these studies should guide future exploration of adaptations in knee function to fatigue. However, research in this area should continue with reduced emphasis on the directional response of the population and a greater focus on individual adaptations of knee function.

An intelligent data mining technique for product quality improvement

Advances in data mining have provided techniques for automatically discovering underlying knowledge and extracting useful information from large volumes of data. Data mining offers tools for quick discovery of relationships, patterns and knowledge in large complex databases. Application of data mining to manufacturing is relatively limited mainly because of complexity of manufacturing data. Growing self organizing map (GSOM) algorithm has been proven to be an efficient algorithm to analyze unsupervised DNA data. However, it produced unsatisfactory clustering when used on some large manufacturing data. In this paper a data mining methodology has been proposed using a GSOM tool which was developed using a modified GSOM algorithm. The proposed method is used to generate clusters for good and faulty products from a manufacturing dataset. The clustering quality (CQ) measure proposed in the paper is used to evaluate the performance of the cluster maps. The paper also proposed an automatic identification of variables to find the most probable causative factor(s) that discriminate between good and faulty product by quickly examining the historical manufacturing data. The proposed method offers the manufacturers to smoothen the production flow and improve the quality of the products. Simulation results on small and large manufacturing data show the effectiveness of the proposed method.

A coupled meshless technique/molecular dynamics approach for deformation characterization of monocrystalline metal

This paper presents a multiscale study using the coupled Meshless technique/Molecular Dynamics (M2) for exploring the deformation mechanism of mono-crystalline metal (focus on copper) under uniaxial tension. In M2, an advanced transition algorithm using transition particles is employed to ensure the compatibility of both displacements and their gradients, and an effective local quasi-continuum approach is also applied to obtain the equivalent continuum strain energy density based on the atomistic poentials and Cauchy-Born rule. The key parameters used in M2 are firstly investigated using a benchmark problem. Then M2 is applied to the multiscale simulation for a mono-crystalline copper bar. It has found that the mono-crystalline copper has very good elongation property, and the ultimate strength and Young's modulus are much higher than those obtained in macro-scale.

Use of acoustic emission technique for structural health monitoring of bridges

Bridges are valuable assets of every nation. They deteriorate with age and often are subjected to additional loads or different load patterns than originally designed for. These changes in loads can cause localized distress and may result in bridge failure if not corrected in time. Early detection of damage and appropriate retrofitting will aid in preventing bridge failures. Large amounts of money are spent in bridge maintenance all around the world. A need exists for a reliable technology capable of monitoring the structural health of bridges, thereby ensuring they operate safely and efficiently during the whole intended lives. Monitoring of bridges has been traditionally done by means of visual inspection. Visual inspection alone is not capable of locating and identifying all signs of damage, hence a variety of structural health monitoring (SHM) techniques is used regularly nowadays to monitor performance and to assess condition of bridges for early damage detection. Acoustic emission (AE) is one technique that is finding an increasing use in SHM applications of bridges all around the world. The chapter starts with a brief introduction to structural health monitoring and techniques commonly used for monitoring purposes. Acoustic emission technique, wave nature of AE phenomenon, previous applications and limitations and challenges in the use as a SHM technique are also discussed. Scope of the project and work carried out will be explained, followed by some recommendations of work planned in future.

Review: acoustic emission technique - opportunities, challenges and current work at QUT

Acoustic emission (AE) is the phenomenon where high frequency stress waves are generated by rapid release of energy within a material by sources such as crack initiation or growth. AE technique involves recording these stress waves by means of sensors placed on the surface and subsequent analysis of the recorded signals to gather information such as the nature and location of the source. AE is one of the several non-destructive testing (NDT) techniques currently used for structural health monitoring (SHM) of civil, mechanical and aerospace structures. Some of its advantages include ability to provide continuous in-situ monitoring and high sensitivity to crack activity. Despite these advantages, several challenges still exist in successful application of AE monitoring. Accurate localization of AE sources, discrimination between genuine AE sources and spurious noise sources and damage quantification for severity assessment are some of the important issues in AE testing and will be discussed in this paper. Various data analysis and processing approaches will be applied to manage those issues.

Stiffness and damping coefficients of 3-axial groove water lubricated bearing using perturbation technique

A Computational fluid dynamics (CFD) approach is used to model fluid flow in a journal bearing with three equi-spaced axial grooves and supplied with water from one end. Water is subjected to both velocity (Couette) & pressure induced (Poiseuille) flow. The working fluid passing through the bearing clearance generates driving force components that may increase the unstable vibration of the rotor. It is important to know the accurate rotor dynamic force component for predicting the instability of rotor bearing systems. In this paper a study has been made to obtain the stiffness and damping coefficients of 3 axial groove bearing using Perturbation technique.

Quantifying variability within technique and performance in elite fast bowlers : is technical variability dysfunctional or functional?

In fast bowling, cricketers are expected to produce a range of delivery lines and lengths while maximising ball speed. From a coaching perspective, technique consistency has been typically associated with superior performance in these areas. However, although bowlers are required to bowl consistently, at the elite level they must also be able to vary line, length and speed to adapt to opposition batters’ strengths and weaknesses. The relationship between technique and performance variability (and consistency) has not been investigated in previous fast bowling research. Consequently, the aim of this study was to quantify both technique (bowling action and coordination) and performance variability in elite fast bowlers from Australian Junior and National Pace Squads. Technique variability was analysed to investigate whether it could be classified as functional or dysfunctional in relation to speed and accuracy.

Challenging the distal-to-proximal cannulation technique for administration of anti-cancer therapies : a prospective cohort study

Background: Distal-to-proximal technique has been recommended for anti-cancer therapy administration. There is no evidence to suggest that a 24-hour delay of treatment is necessary for patients with a previous uncomplicated venous puncture proximal to the administration site. Objectives: This study aims to identify if the practice of 24-hour delay between a venous puncture and subsequent cannulation for anti-cancer therapies at a distal site is necessary for preventing extravasation. Methods: A prospective cohort study was conducted with 72 outpatients receiving anti-cancer therapy via an administration site distal to at least one previous uncomplicated venous puncture on the same arm in a tertiary cancer centre in Australia. Participants were interviewed and assessed at baseline data before treatment and on day 7 for incidence of extravasation/phlebitis. Results: Of 72 participants with 99 occasions of treatment, there was one incident of infiltration (possible extravasation) at the venous puncture site proximal to the administration site and two incidents of phlebitis at the administration site. Conclusions: A 24 hour delay is unnecessary if an alternative vein can be accessed for anti-cancer therapy after a proximal venous puncture. Implications for practice: Extravasation can occur at a venous puncture site proximal to an administration site in the same vein. However, the nurse can administer anti-cancer therapy at a distal site if the nurse can confidently determine the vein of choice is not in any way connected to the previous puncture site through visual inspection and palpation.