Development of rapid and highly resolving combinatorial genotyping schemes for Campylobacter jejuni and Campylobacter coli

Campylobacter jejuni followed by Campylobacter coli contribute substantially to the economic and public health burden attributed to food-borne infections in Australia. Genotypic characterisation of isolates has provided new insights into the epidemiology and pathogenesis of C. jejuni and C. coli. However, currently available methods are not conducive to large scale epidemiological investigations that are necessary to elucidate the global epidemiology of these common food-borne pathogens. This research aims to develop high resolution C. jejuni and C. coli genotyping schemes that are convenient for high throughput applications. Real-time PCR and High Resolution Melt (HRM) analysis are fundamental to the genotyping schemes developed in this study and enable rapid, cost effective, interrogation of a range of different polymorphic sites within the Campylobacter genome. While the sources and routes of transmission of campylobacters are unclear, handling and consumption of poultry meat is frequently associated with human campylobacteriosis in Australia. Therefore, chicken derived C. jejuni and C. coli isolates were used to develop and verify the methods described in this study. The first aim of this study describes the application of MLST-SNP (Multi Locus Sequence Typing Single Nucleotide Polymorphisms) + binary typing to 87 chicken C. jejuni isolates using real-time PCR analysis. These typing schemes were developed previously by our research group using isolates from campylobacteriosis patients. This present study showed that SNP + binary typing alone or in combination are effective at detecting epidemiological linkage between chicken derived Campylobacter isolates and enable data comparisons with other MLST based investigations. SNP + binary types obtained from chicken isolates in this study were compared with a previously SNP + binary and MLST typed set of human isolates. Common genotypes between the two collections of isolates were identified and ST-524 represented a clone that could be worth monitoring in the chicken meat industry. In contrast, ST-48, mainly associated with bovine hosts, was abundant in the human isolates. This genotype was, however, absent in the chicken isolates, indicating the role of non-poultry sources in causing human Campylobacter infections. This demonstrates the potential application of SNP + binary typing for epidemiological investigations and source tracing. While MLST SNPs and binary genes comprise the more stable backbone of the Campylobacter genome and are indicative of long term epidemiological linkage of the isolates, the development of a High Resolution Melt (HRM) based curve analysis method to interrogate the hypervariable Campylobacter flagellin encoding gene (flaA) is described in Aim 2 of this study. The flaA gene product appears to be an important pathogenicity determinant of campylobacters and is therefore a popular target for genotyping, especially for short term epidemiological studies such as outbreak investigations. HRM curve analysis based flaA interrogation is a single-step closed-tube method that provides portable data that can be easily shared and accessed. Critical to the development of flaA HRM was the use of flaA specific primers that did not amplify the flaB gene. HRM curve analysis flaA interrogation was successful at discriminating the 47 sequence variants identified within the 87 C. jejuni and 15 C. coli isolates and correlated to the epidemiological background of the isolates. In the combinatorial format, the resolving power of flaA was additive to that of SNP + binary typing and CRISPR (Clustered regularly spaced short Palindromic repeats) HRM and fits the PHRANA (Progressive hierarchical resolving assays using nucleic acids) approach for genotyping. The use of statistical methods to analyse the HRM data enhanced sophistication of the method. Therefore, flaA HRM is a rapid and cost effective alternative to gel- or sequence-based flaA typing schemes. Aim 3 of this study describes the development of a novel bioinformatics driven method to interrogate Campylobacter MLST gene fragments using HRM, and is called ‘SNP Nucleated Minim MLST’ or ‘Minim typing’. The method involves HRM interrogation of MLST fragments that encompass highly informative “Nucleating SNPS” to ensure high resolution. Selection of fragments potentially suited to HRM analysis was conducted in silico using i) “Minimum SNPs” and ii) the new ’HRMtype’ software packages. Species specific sets of six “Nucleating SNPs” and six HRM fragments were identified for both C. jejuni and C. coli to ensure high typeability and resolution relevant to the MLST database. ‘Minim typing’ was tested empirically by typing 15 C. jejuni and five C. coli isolates. The association of clonal complexes (CC) to each isolate by ‘Minim typing’ and SNP + binary typing were used to compare the two MLST interrogation schemes. The CCs linked with each C. jejuni isolate were consistent for both methods. Thus, ‘Minim typing’ is an efficient and cost effective method to interrogate MLST genes. However, it is not expected to be independent, or meet the resolution of, sequence based MLST gene interrogation. ‘Minim typing’ in combination with flaA HRM is envisaged to comprise a highly resolving combinatorial typing scheme developed around the HRM platform and is amenable to automation and multiplexing. The genotyping techniques described in this thesis involve the combinatorial interrogation of differentially evolving genetic markers on the unified real-time PCR and HRM platform. They provide high resolution and are simple, cost effective and ideally suited to rapid and high throughput genotyping for these common food-borne pathogens.

Are SC-FDE systems robust to CFO?

This paper investigates the impact of carrier frequency offset (CFO) on Single Carrier wireless communication systems with Frequency Domain Equalization (SC-FDE). We show that CFO in SC-FDE systems causes irrecoverable channel estimation error, which leads to inter-symbol-interference (ISI). The impact of CFO on SC-FDE and OFDM is compared in the presence of CFO and channel estimation errors. Closed form expressions of signal to interference and noise ratio (SINR) are derived for both systems, and verified by simulation results. We find that when channel estimation errors are considered, SC-FDE is similarly or even more sensitive to CFO, compared to OFDM. In particular, in SC-FDE systems, CFO mainly deteriorates the system performance via degrading the channel estimation. Both analytical and simulation results highlight the importance of accurate CFO estimation in SC-FDE systems.

A Novel Approach to Haptic Tele-operation of Aerial Robot Vehicles

We present a novel, simple and effective approach for tele-operation of aerial robotic vehicles with haptic feedback. Such feedback provides the remote pilot with an intuitive feel of the robot’s state and perceived local environment that will ensure simple and safe operation in cluttered 3D environments common in inspection and surveillance tasks. Our approach is based on energetic considerations and uses the concepts of network theory and port-Hamiltonian systems. We provide a general framework for addressing problems such as mapping the limited stroke of a ‘master’ joystick to the infinite stroke of a ‘slave’ vehicle, while preserving passivity of the closed-loop system in the face of potential time delays in communications links and limited sensor data

Transforming agriculture through pervasive wireless sensor networks

A large-scale, outdoor, pervasive computing system based on the Fleck hardware platform applies sensor network technology to farming. Comprising static and animal-borne mobile nodes, the system measures the state of a complex, dynamic system comprising climate, soil, pasture, and animals. This data supports prediction of the land's future state and improved management outcomes through closed-loop control. This article is part of a special issue, Building a Sensor-Rich World.

Dynamic Image-based visual servo control using centroid and optic flow features

This paper considers the question of designing a fully image-based visual servo control for a class of dynamic systems. The work is motivated by the ongoing development of image-based visual servo control of small aerial robotic vehicles. The kinematics and dynamics of a rigid-body dynamical system (such as a vehicle airframe) maneuvering over a flat target plane with observable features are expressed in terms of an unnormalized spherical centroid and an optic flow measurement. The image-plane dynamics with respect to force input are dependent on the height of the camera above the target plane. This dependence is compensated by introducing virtual height dynamics and adaptive estimation in the proposed control. A fully nonlinear adaptive control design is provided that ensures asymptotic stability of the closed-loop system for all feasible initial conditions. The choice of control gains is based on an analysis of the asymptotic dynamics of the system. Results from a realistic simulation are presented that demonstrate the performance of the closed-loop system. To the author's knowledge, this paper documents the first time that an image-based visual servo control has been proposed for a dynamic system using vision measurement for both position and velocity.

ElectricCOW : A simulator for mobile sensors and actuators mounted on herds of cattle

ElectricCOW is a network, animal behaviour and agent simulator designed to allow detailed simulation of an ad-hoc model network built from small mote-like devices called flecks. Detailed radio communications, cattle behaviour and sensor and actuator network modelling allows a closed-loop environment, where the network can influence the behaviour of its mobile platforms.

Multilevel converter structure and control

In recent years, multilevel converters are becoming more popular and attractive than traditional converters in high voltage and high power applications. Multilevel converters are particularly suitable for harmonic reduction in high power applications where semiconductor devices are not able to operate at high switching frequencies or in high voltage applications where multilevel converters reduce the need to connect devices in series to achieve high switch voltage ratings. This thesis investigated two aspects of multilevel converters: structure and control. The first part of this thesis focuses on inductance between a DC supply and inverter components in order to minimise loop inductance, which causes overvoltages and stored energy losses during switching. Three dimensional finite element simulations and experimental tests have been carried out for all sections to verify theoretical developments. The major contributions of this section of the thesis are as follows: The use of a large area thin conductor sheet with a rectangular cross section separated by dielectric sheets (planar busbar) instead of circular cross section wires, contributes to a reduction of the stray inductance. A number of approximate equations exist for calculating the inductance of a rectangular conductor but an assumption was made that the current density was uniform throughout the conductors. This assumption is not valid for an inverter with a point injection of current. A mathematical analysis of a planar bus bar has been performed at low and high frequencies and the inductance and the resistance values between the two points of the planar busbar have been determined. A new physical structure for a voltage source inverter with symmetrical planar bus bar structure called Reduced Layer Planar Bus bar, is proposed in this thesis based on the current point injection theory. This new type of planar busbar minimises the variation in stray inductance for different switching states. The reduced layer planar busbar is a new innovation in planar busbars for high power inverters with minimum separation between busbars, optimum stray inductance and improved thermal performances. This type of the planar busbar is suitable for high power inverters, where the voltage source is supported by several capacitors in parallel in order to provide a low ripple DC voltage during operation. A two layer planar busbar with different materials has been analysed theoretically in order to determine the resistance of bus bars during switching. Increasing the resistance of the planar busbar can gain a damping ratio between stray inductance and capacitance and affects the performance of current loop during switching. The aim of this section is to increase the resistance of the planar bus bar at high frequencies (during switching) and without significantly increasing the planar busbar resistance at low frequency (50 Hz) using the skin effect. This contribution shows a novel structure of busbar suitable for high power applications where high resistance is required at switching times. In multilevel converters there are different loop inductances between busbars and power switches associated with different switching states. The aim of this research is to consider all combinations of the switching states for each multilevel converter topology and identify the loop inductance for each switching state. Results show that the physical layout of the busbars is very important for minimisation of the loop inductance at each switch state. Novel symmetrical busbar structures are proposed for multilevel converters with diode-clamp and flying-capacitor topologies which minimise the worst case in stray inductance for different switching states. Overshoot voltages and thermal problems are considered for each topology to optimise the planar busbar structure. In the second part of the thesis, closed loop current techniques have been investigated for single and three phase multilevel converters. The aims of this section are to investigate and propose suitable current controllers such as hysteresis and predictive techniques for multilevel converters with low harmonic distortion and switching losses. This section of the thesis can be classified into three parts as follows: An optimum space vector modulation technique for a three-phase voltage source inverter based on a minimum-loss strategy is proposed. One of the degrees of freedom for optimisation of the space vector modulation is the selection of the zero vectors in the switching sequence. This new method improves switching transitions per cycle for a given level of distortion as the zero vector does not alternate between each sector. The harmonic spectrum and weighted total harmonic distortion for these strategies are compared and results show up to 7% weighted total harmonic distortion improvement over the previous minimum-loss strategy. The concept of SVM technique is a very convenient representation of a set of three-phase voltages or currents used for current control techniques. A new hysteresis current control technique for a single-phase multilevel converter with flying-capacitor topology is developed. This technique is based on magnitude and time errors to optimise the level change of converter output voltage. This method also considers how to improve unbalanced voltages of capacitors using voltage vectors in order to minimise switching losses. Logic controls require handling a large number of switches and a Programmable Logic Device (PLD) is a natural implementation for state transition description. The simulation and experimental results describe and verify the current control technique for the converter. A novel predictive current control technique is proposed for a three-phase multilevel converter, which controls the capacitors' voltage and load current with minimum current ripple and switching losses. The advantage of this contribution is that the technique can be applied to more voltage levels without significantly changing the control circuit. The three-phase five-level inverter with a pure inductive load has been implemented to track three-phase reference currents using analogue circuits and a programmable logic device.

Shear behaviour and design of LiteSteel beams

OneSteel Australian Tube Mills has recently developed a new hollow flange channel cold-formed section, known as the LiteSteel Beam (LSB). The innovative LSB sections have the beneficial characteristics of torsionally rigid closed rectangular flanges combined with economical fabrication processes from a single strip of high strength steel. They combine the stability of hot-rolled steel sections with the high strength to weight ratio of conventional cold-formed steel sections. The LSB sections are commonly used as flexural members in residential, industrial and commercial buildings. In order to ensure safe and efficient designs of LSBs, many research studies have been undertaken on the flexural behaviour of LSBs. However, no research has been undertaken on the shear behaviour of LSBs. Therefore this thesis investigated the ultimate shear strength behaviour of LSBs with and without web openings including their elastic buckling and post-buckling characteristics using both experimental and finite element analyses, and developed accurate shear design rules. Currently the elastic shear buckling coefficients of web panels are determined by assuming conservatively that the web panels are simply supported at the junction between the web and flange elements. Therefore finite element analyses were conducted first to investigate the elastic shear buckling behaviour of LSBs to determine the true support condition at the junction between their web and flange elements. An equation for the higher elastic shear buckling coefficient of LSBs was developed and included in the shear capacity equations in the cold-formed steel structures code, AS/NZS 4600. Predicted shear capacities from the modified equations and the available experimental results demonstrated the improvements to the shear capacities of LSBs due to the presence of higher level of fixity at the LSB flange to web juncture. A detailed study into the shear flow distribution of LSB was also undertaken prior to the elastic buckling analysis study. The experimental study of ten LSB sections included 42 shear tests of LSBs with aspect ratios of 1.0 and 1.5 that were loaded at midspan until failure. Both single and back to back LSB arrangements were used. Test specimens were chosen such that all three types of shear failure (shear yielding, inelastic and elastic shear buckling) occurred in the tests. Experimental results showed that the current cold-formed steel design rules are very conservative for the shear design of LSBs. Significant improvements to web shear buckling occurred due to the presence of rectangular hollow flanges while considerable post-buckling strength was also observed. Experimental results were presented and compared with corresponding predictions from the current design rules. Appropriate improvements have been proposed for the shear strength of LSBs based on AISI (2007) design equations and test results. Suitable design rules were also developed under the direct strength method (DSM) format. This thesis also includes the shear test results of cold-formed lipped channel beams from LaBoube and Yu (1978a), and the new design rules developed based on them using the same approach used with LSBs. Finite element models of LSBs in shear were also developed to investigate the ultimate shear strength behaviour of LSBs including their elastic and post-buckling characteristics. They were validated by comparing their results with experimental test results. Details of the finite element models of LSBs, the nonlinear analysis results and their comparisons with experimental results are presented in this thesis. Finite element analysis results showed that the current cold-formed steel design rules are very conservative for the shear design of LSBs. They also confirmed other experimental findings relating to elastic and post-buckling shear strength of LSBs. A detailed parametric study based on validated experimental finite element model was undertaken to develop an extensive shear strength data base and was then used to confirm the accuracy of the new shear strength equations proposed in this thesis. Experimental and numerical studies were also undertaken to investigate the shear behaviour of LSBs with web openings. Twenty six shear tests were first undertaken using a three point loading arrangement. It was found that AS/NZS 4600 and Shan et al.'s (1997) design equations are conservative for the shear design of LSBs with web openings while McMahon et al.'s (2008) design equation are unconservative. Experimental finite element models of LSBs with web openings were then developed and validated by comparing their results with experimental test results. The developed nonlinear finite element model was found to predict the shear capacity of LSBs with web opening with very good accuracy. Improved design equations have been proposed for the shear capacity of LSBs with web openings based on both experimental and FEA parametric study results. This thesis presents the details of experimental and numerical studies of the shear behaviour and strength of LSBs with and without web openings and the results including the developed accurate design rules.

Study of industrially relevant boundary layer and axisymmetric flows, including swirl and turbulence

Micropolar and RNG-based modelling of industrially relevant boundary layer and recirculating swirling flows is described. Both models contain a number of adjustable parameters and auxiliary conditions that must be either modelled or experimentally determined, and the effects of varying these on the resulting flow solutions is quantified. To these ends, the behaviour of the micropolar model for self-similar flow over a surface that is both stretching and transpiring is explored in depth. The simplified governing equations permit both analytic and numerical approaches to be adopted, and a number of closed form solutions (both exact and approximate) are obtained using perturbation and order of magnitude analyses. Results are compared with the corresponding Newtonian flow solution in order to highlight the differences between the micropolar and classical models, and significant new insights into the behaviour of the micropolar model are revealed for this flow. The behaviour of the RNG-bas based models for swirling flow with vortex breakdown zones is explored in depth via computational modelling of two experimental data sets and an idealised breakdown flow configuration. Meticulous modeling of upstream auxillary conditions is required to correctly assess the behavior of the models studied in this work. The novel concept of using the results to infer the role of turbulence in the onset and topology of the breakdown zone is employed.

Design of a static thruster for microair vehicle rotorcraft

This paper presents a case study of a design for a complete microair vehicle thruster. Fixed-pitch small-scale rotors, brushless motors, lithium-polymer cells, and embedded control are combined to produce a mechanically simple, high-performance thruster with potentially high reliability. The custom rotor design requires a balance between manufacturing simplicity and rigidity of a blade versus its aerodynamic performance. An iterative steady-state aeroelastic simulator is used for holistic blade design. The aerodynamic load disturbances of the rotor-motor system in normal conditions are experimentally characterized. The motors require fast dynamic response for authoritative vehicle flight control. We detail a dynamic compensator that achieves satisfactory closed-loop response time. The experimental rotor-motor plant displayed satisfactory thrust performance and dynamic response.

Greenhouse Gas Fluxes in Tropical and Temperae Agriculture: The Need for a Full-Cost Accounting of Global Warming Potentials

Agriculture's contribution to radiative forcing is principally through its historical release of carbon in soil and vegetation to the atmosphere and through its contemporary release of nitrous oxide (N2O) and methane (CHM4). The sequestration of soil carbon in soils now depleted in soil organic matter is a well-known strategy for mitigating the buildup of CO2 in the atmosphere. Less well-recognized are other mitigation potentials. A full-cost accounting of the effects of agriculture on greenhouse gas emissions is necessary to quantify the relative importance of all mitigation options. Such an analysis shows nitrogen fertilizer, agricultural liming, fuel use, N2O emissions, and CH4 fluxes to have additional significant potential for mitigation. By evaluating all sources in terms of their global warming potential it becomes possible to directly evaluate greenhouse policy options for agriculture. A comparison of temperate and tropical systems illustrates some of these options.

Nitrogen pools and fluxes in grassland soils sequestering carbon

Carbon sequestration in agricultural, forest, and grassland soils has been promoted as a means by which substantial amounts of CO2 may be removed from the atmosphere, but few studies have evaluated the associated impacts on changes in soil N or net global warming potential (GWP). The purpose of this research was to ( 1) review the literature to examine how changes in grassland management that affect soil C also impact soil N, ( 2) assess the impact of different types of grassland management on changes in soil N and rates of change, and (3) evaluate changes in N2O fluxes from differently managed grassland ecosystems to assess net impacts on GWP. Soil C and N stocks either both increased or both decreased for most studies. Soil C and N sequestration were tightly linked, resulting in little change in C: N ratios with changes in management. Within grazing treatments N2O made a minor contribution to GWP (0.1-4%), but increases in N2O fluxes offset significant portions of C sequestration gains due to fertilization (10-125%) and conversion (average = 27%). Results from this work demonstrate that even when improved management practices result in considerable rates of C and N sequestration, changes in N2O fluxes can offset a substantial portion of gains by C sequestration. Even for cases in which C sequestration rates are not entirely offset by increases in N2O fluxes, small increases in N2O fluxes can substantially reduce C sequestration benefits. Conversely, reduction of N2O fluxes in grassland soils brought about by changes in management represents an opportunity to reduce the contribution of grasslands to net greenhouse gas forcing.

The urban water cycle : towards integrated resource management and more sustainable water management systems

The increasing scarcity of water in the world, along with rapid population increase in urban areas, gives reason for concern and highlights the need for integrating water and wastewater management practices. The uncontrolled growth in urban areas has made planning, management and expansion of water and wastewater infrastructure systems very difficult and expensive. In order to achieve sustainable wastewater treatment and promote the conservation of water and nutrient resources, this chapter advocates the need for a closed-loop treatment system approach, and the transformation of the traditional linear treatment systems into integrated cyclical treatment systems. The recent increased understanding of integrated resource management and a shift towards sustainable management and planning of water and wastewater infrastructure are also discussed.