Aerial image analysis using spiking neural networks with application to power line corridor monitoring

Trees, shrubs and other vegetation are of continued importance to the environment and our daily life. They provide shade around our roads and houses, offer a habitat for birds and wildlife, and absorb air pollutants. However, vegetation touching power lines is a risk to public safety and the environment, and one of the main causes of power supply problems. Vegetation management, which includes tree trimming and vegetation control, is a significant cost component of the maintenance of electrical infrastructure. For example, Ergon Energy, the Australia’s largest geographic footprint energy distributor, currently spends over $80 million a year inspecting and managing vegetation that encroach on power line assets. Currently, most vegetation management programs for distribution systems are calendar-based ground patrol. However, calendar-based inspection by linesman is labour-intensive, time consuming and expensive. It also results in some zones being trimmed more frequently than needed and others not cut often enough. Moreover, it’s seldom practicable to measure all the plants around power line corridors by field methods. Remote sensing data captured from airborne sensors has great potential in assisting vegetation management in power line corridors. This thesis presented a comprehensive study on using spiking neural networks in a specific image analysis application: power line corridor monitoring. Theoretically, the thesis focuses on a biologically inspired spiking cortical model: pulse coupled neural network (PCNN). The original PCNN model was simplified in order to better analyze the pulse dynamics and control the performance. Some new and effective algorithms were developed based on the proposed spiking cortical model for object detection, image segmentation and invariant feature extraction. The developed algorithms were evaluated in a number of experiments using real image data collected from our flight trails. The experimental results demonstrated the effectiveness and advantages of spiking neural networks in image processing tasks. Operationally, the knowledge gained from this research project offers a good reference to our industry partner (i.e. Ergon Energy) and other energy utilities who wants to improve their vegetation management activities. The novel approaches described in this thesis showed the potential of using the cutting edge sensor technologies and intelligent computing techniques in improve power line corridor monitoring. The lessons learnt from this project are also expected to increase the confidence of energy companies to move from traditional vegetation management strategy to a more automated, accurate and cost-effective solution using aerial remote sensing techniques.

The development of ground impact models for the analysis of the risks associated with Unmanned Aircraft Operations over inhabited areas

With the emergence of Unmanned Aircraft Systems (UAS) there is a growing need for safety standards and regulatory frameworks to manage the risks associated with their operations. The primary driver for airworthiness regulations (i.e., those governing the design, manufacture, maintenance and operation of UAS) are the risks presented to people in the regions overflown by the aircraft. Models characterising the nature of these risks are needed to inform the development of airworthiness regulations. The output from these models should include measures of the collective, individual and societal risk. A brief review of these measures is provided. Based on the review, it was determined that the model of the operation of an UAS over inhabited areas must be capable of describing the distribution of possible impact locations, given a failure at a particular point in the flight plan. Existing models either do not take the impact distribution into consideration, or propose complex and computationally expensive methods for its calculation. A computationally efficient approach for estimating the boundary (and in turn area) of the impact distribution for fixed wing unmanned aircraft is proposed. A series of geometric templates that approximate the impact distributions are derived using an empirical analysis of the results obtained from a 6-Degree of Freedom (6DoF) simulation. The impact distributions can be aggregated to provide impact footprint distributions for a range of generic phases of flight and missions. The maximum impact footprint areas obtained from the geometric template are shown to have a relative error of typically less than 1% compared to the areas calculated using the computationally more expensive 6DoF simulation. Computation times for the geometric models are on the order of one second or less, using a standard desktop computer. Future work includes characterising the distribution of impact locations within the footprint boundaries.

TUNEL analysis of DNA fragmentation in mouse unfertilized oocytes : the effect of microorganisms within human follicular fluid collected during IVF cycles

Recently we reported the presence of bacteria within follicular fluid. Previous studies have reported that DNA fragmentation in human spermatozoa after in vivo or in vitro incubation with bacteria results in early embryo demise and a reduced rate of ongoing pregnancy, but the effect of bacteria on oocytes is unknown. This study examined the DNA within mouse oocytes after 12 hours’ incubation within human follicular fluids (n = 5), which were collected from women undergoing in vitro fertilization (IVF) treatment. Each follicular fluid sample was cultured to detect the presence of bacteria. Terminal deoxynucleotidyl transferase mediated dUTP nick-end labeling (TUNEL) was used to label DNA fragmentation in ovulated, non-fertilized mouse oocytes following in vitro incubation in human follicular fluid. The bacteria Streptococcus anginosus and Peptoniphilus spp., Lactobacillus gasseri (low-dose), L. gasseri (high-dose), Enterococcus faecalis, or Propionibacterium acnes were detected within the follicular fluids. The most severe DNA fragmentation was observed in oocytes incubated in the follicular fluids containing P. acnes or L. gasseri (high-dose). No DNA fragmentation was observed in the mouse oocytes incubated in the follicular fluid containing low-dose L. gasseri or E. faecalis. Low human oocyte fertilization rates (<29%) were associated with extensive fragmentation in mouse oocytes (80–100%). Bacteria colonizing human follicular fluid in vivo may cause DNA fragmentation in mouse oocytes following 12 h of in vitro incubation. Follicular fluid bacteria may result in poor quality oocytes and/or embryos, leading to poor IVF outcomes.

A comparative analysis of Mitochondrial genomes in Coleoptera (Arthropoda: Insecta) and genome descriptions of six new beetles

Coleoptera is the most diverse group of insects with over 360,000 described species divided into four suborders: Adephaga, Archostemata, Myxophaga, and Polyphaga. In this study, we present six new complete mitochondrial genome (mtgenome) descriptions, including a representative of each suborder, and analyze the evolution of mtgenomes from a comparative framework using all available coleopteran mtgenomes. We propose a modification of atypical cox1 start codons based on sequence alignment to better reflect the conservation observed across species as well as findings of TTG start codons in other genes. We also analyze tRNA-Ser(AGN) anticodons, usually GCU in arthropods, and report a conserved UCU anticodon as a possible synapomorphy across Polyphaga. We further analyze the secondary structure of tRNA-Ser(AGN) and present a consensus structure and an updated covariance model that allows tRNAscan-SE (via the COVE software package) to locate and fold these atypical tRNAs with much greater consistency. We also report secondary structure predictions for both rRNA genes based on conserved stems. All six species of beetle have the same gene order as the ancestral insect. We report noncoding DNA regions, including a small gap region of about 20 bp between tRNA-Ser(UCN) and nad1 that is present in all six genomes, and present results of a base composition analysis.

Fungal spore fragmentation as a function of airflow rates and fungal generation methods

The aim of this study was to characterise and quantify the fungal fragment propagules derived and released from several fungal species (Penicillium, Aspergillus niger and Cladosporium cladosporioides) using different generation methods and different air velocities over the colonies. Real time fungal spore fragmentation was investigated using an Ultraviolet Aerodynamic Particle Sizer (UVASP) and a Scanning Mobility Particle Sizer (SMPS). The study showed that there were significant differences (p < 0.01) in the fragmentation percentage between different air velocities for the three generation methods, namely the direct, the fan and the fungal spore source strength tester (FSSST) methods. The percentage of fragmentation also proved to be dependant on fungal species. The study found that there was no fragmentation for any of the fungal species at an air velocity ≤ 0.4 m/s for any method of generation. Fluorescent signals, as well as mathematical determination also showed that the fungal fragments were derived from spores. Correlation analysis showed that the number of released fragments measured by the UVAPS under controlled conditions can be predicted on the basis of the number of spores, for Penicillium and Aspergillus niger, but not for Cladosporium cladosporioides. The fluorescence percentage of fragment samples was found to be significantly different to that of non-fragment samples (p < 0.0001) and the fragment sample fluorescence was always less than that of the non-fragment samples. Size distribution and concentration of fungal fragment particles were investigated qualitatively and quantitatively, by both UVAPS and SMPS, and it was found that the UVAPS was more sensitive than the SMPS for measuring small sample concentrations, and the results obtained from the UVAPS and SMAS were not identical for the same samples.

Classification of Airborne LIDAR Intensity Data Using Statistical Analysis and Hough Transform with Application to Power Line Corridors

Light Detection and Ranging (LIDAR) has great potential to assist vegetation management in power line corridors by providing more accurate geometric information of the power line assets and vegetation along the corridors. However, the development of algorithms for the automatic processing of LIDAR point cloud data, in particular for feature extraction and classification of raw point cloud data, is in still in its infancy. In this paper, we take advantage of LIDAR intensity and try to classify ground and non-ground points by statistically analyzing the skewness and kurtosis of the intensity data. Moreover, the Hough transform is employed to detected power lines from the filtered object points. The experimental results show the effectiveness of our methods and indicate that better results were obtained by using LIDAR intensity data than elevation data.

Investigation into submicrometer particle and gaseous emissions from airport ground running procedures

Emissions from airport operations are of significant concern because of their potential impact on local air quality and human health. The currently limited scientific knowledge of aircraft emissions is an important issue worldwide, when considering air pollution associated with airport operation, and this is especially so for ultrafine particles. This limited knowledge is due to scientific complexities associated with measuring aircraft emissions during normal operations on the ground. In particular this type of research has required the development of novel sampling techniques which must take into account aircraft plume dispersion and dilution as well as the various particle dynamics that can affect the measurements of the aircraft engine plume from an operational aircraft. In order to address this scientific problem, a novel mobile emission measurement method called the Plume Capture and Analysis System (PCAS), was developed and tested. The PCAS permits the capture and analysis of aircraft exhaust during ground level operations including landing, taxiing, takeoff and idle. The PCAS uses a sampling bag to temporarily store a sample, providing sufficient time to utilize sensitive but slow instrumental techniques to be employed to measure gas and particle emissions simultaneously and to record detailed particle size distributions. The challenges in relation to the development of the technique include complexities associated with the assessment of the various particle loss and deposition mechanisms which are active during storage in the PCAS. Laboratory based assessment of the method showed that the bag sampling technique can be used to accurately measure particle emissions (e.g. particle number, mass and size distribution) from a moving aircraft or vehicle. Further assessment of the sensitivity of PCAS results to distance from the source and plume concentration was conducted in the airfield with taxiing aircraft. The results showed that the PCAS is a robust method capable of capturing the plume in only 10 seconds. The PCAS is able to account for aircraft plume dispersion and dilution at distances of 60 to 180 meters downwind of moving a aircraft along with particle deposition loss mechanisms during the measurements. Characterization of the plume in terms of particle number, mass (PM2.5), gaseous emissions and particle size distribution takes only 5 minutes allowing large numbers of tests to be completed in a short time. The results were broadly consistent and compared well with the available data. Comprehensive measurements and analyses of the aircraft plumes during various modes of the landing and takeoff (LTO) cycle (e.g. idle, taxi, landing and takeoff) were conducted at Brisbane Airport (BNE). Gaseous (NOx, CO2) emission factors, particle number and mass (PM2.5) emission factors and size distributions were determined for a range of Boeing and Airbus aircraft, as a function of aircraft type and engine thrust level. The scientific complexities including the analysis of the often multimodal particle size distributions to describe the contributions of different particle source processes during the various stages of aircraft operation were addressed through comprehensive data analysis and interpretation. The measurement results were used to develop an inventory of aircraft emissions at BNE, including all modes of the aircraft LTO cycle and ground running procedures (GRP). Measurements of the actual duration of aircraft activity in each mode of operation (time-in-mode) and compiling a comprehensive matrix of gas and particle emission rates as a function of aircraft type and engine thrust level for real world situations was crucial for developing the inventory. The significance of the resulting matrix of emission rates in this study lies in the estimate it provides of the annual particle emissions due to aircraft operations, especially in terms of particle number. In summary, this PhD thesis presents for the first time a comprehensive study of the particle and NOx emission factors and rates along with the particle size distributions from aircraft operations and provides a basis for estimating such emissions at other airports. This is a significant addition to the scientific knowledge in terms of particle emissions from aircraft operations, since the standard particle number emissions rates are not currently available for aircraft activities.

HABITAT : a longitudinal multilevel study of physical acitvity change in mid-aged adults

Purpose. To explore the role of the neighborhood environment in supporting walking Design. Cross sectional study of 10,286 residents of 200 neighborhoods. Participants were selected using a stratified two-stage cluster design. Data were collected by mail survey (68.5% response rate). Setting. The Brisbane City Local Government Area, Australia, 2007. Subjects. Brisbane residents aged 40 to 65 years. Measures. Environmental: street connectivity, residential density, hilliness, tree coverage, bikeways, and street lights within a one kilometer circular buffer from each resident’s home; and network distance to nearest river or coast, public transport, shop, and park. Walking: minutes in the previous week categorized as < 30 minutes, ≥ 30 < 90 minutes, ≥ 90 < 150 minutes, ≥ 150 < 300 minutes, and ≥ 300 minutes. Analysis. The association between each neighborhood characteristic and walking was examined using multilevel multinomial logistic regression and the model parameters were estimated using Markov chain Monte Carlo simulation. Results. After adjustment for individual factors, the likelihood of walking for more than 300 minutes (relative to <30 minutes) was highest in areas with the most connectivity (OR=1.93, 99% CI 1.32-2.80), the greatest residential density (OR=1.47, 99% CI 1.02-2.12), the least tree coverage (OR=1.69, 99% CI 1.13-2.51), the most bikeways (OR=1.60, 99% CI 1.16-2.21), and the most street lights (OR=1.50, 99% CI 1.07-2.11). The likelihood of walking for more than 300 minutes was also higher among those who lived closest to a river or the coast (OR=2.06, 99% CI 1.41-3.02). Conclusion. The likelihood of meeting (and exceeding) physical activity recommendations on the basis of walking was higher in neighborhoods with greater street connectivity and residential density, more street lights and bikeways, closer proximity to waterways, and less tree coverage. Interventions targeting these neighborhood characteristics may lead to improved environmental quality as well as lower rates of overweight and obesity and associated chromic disease.

Dynamics of transformation and fragmentation of composite liquid nano-particles

Recent research on particle size distributions and particle concentrations near a busy road cannot be explained by the conventional mechanisms for particle evolution of combustion aerosols. Specifically they appear to be inadequate to explain the experimental observations of particle transformation and the evolution of the total number concentration. This resulted in the development of a new mechanism based on their thermal fragmentation, for the evolution of combustion aerosol nano-particles. A complex and comprehensive pattern of evolution of combustion aerosols, involving particle fragmentation, was then proposed and justified. In that model it was suggested that thermal fragmentation occurs in aggregates of primary particles each of which contains a solid graphite/carbon core surrounded by volatile molecules bonded to the core by strong covalent bonds. Due to the presence of strong covalent bonds between the core and the volatile (frill) molecules, such primary composite particles can be regarded as solid, despite the presence of significant (possibly, dominant) volatile component. Fragmentation occurs when weak van der Waals forces between such primary particles are overcome by their thermal (Brownian) motion. In this work, the accepted concept of thermal fragmentation is advanced to determine whether fragmentation is likely in liquid composite nano-particles. It has been demonstrated that at least at some stages of evolution, combustion aerosols contain a large number of composite liquid particles containing presumably several components such as water, oil, volatile compounds, and minerals. It is possible that such composite liquid particles may also experience thermal fragmentation and thus contribute to, for example, the evolution of the total number concentration as a function of distance from the source. Therefore, the aim of this project is to examine theoretically the possibility of thermal fragmentation of composite liquid nano-particles consisting of immiscible liquid v components. The specific focus is on ternary systems which include two immiscible liquid droplets surrounded by another medium (e.g., air). The analysis shows that three different structures are possible, the complete encapsulation of one liquid by the other, partial encapsulation of the two liquids in a composite particle, and the two droplets separated from each other. The probability of thermal fragmentation of two coagulated liquid droplets is discussed and examined for different volumes of the immiscible fluids in a composite liquid particle and their surface and interfacial tensions through the determination of the Gibbs free energy difference between the coagulated and fragmented states, and comparison of this energy difference with the typical thermal energy kT. The analysis reveals that fragmentation was found to be much more likely for a partially encapsulated particle than a completely encapsulated particle. In particular, it was found that thermal fragmentation was much more likely when the volume ratio of the two liquid droplets that constitute the composite particle are very different. Conversely, when the two liquid droplets are of similar volumes, the probability of thermal fragmentation is small. It is also demonstrated that the Gibbs free energy difference between the coagulated and fragmented states is not the only important factor determining the probability of thermal fragmentation of composite liquid particles. The second essential factor is the actual structure of the composite particle. It is shown that the probability of thermal fragmentation is also strongly dependent on the distance that each of the liquid droplets should travel to reach the fragmented state. In particular, if this distance is larger than the mean free path for the considered droplets in the air, the probability of thermal fragmentation should be negligible. In particular, it follows form here that fragmentation of the composite particle in the state with complete encapsulation is highly unlikely because of the larger distance that the two droplets must travel in order to separate. The analysis of composite liquid particles with the interfacial parameters that are expected in combustion aerosols demonstrates that thermal fragmentation of these vi particles may occur, and this mechanism may play a role in the evolution of combustion aerosols. Conditions for thermal fragmentation to play a significant role (for aerosol particles other than those from motor vehicle exhaust) are determined and examined theoretically. Conditions for spontaneous transformation between the states of composite particles with complete and partial encapsulation are also examined, demonstrating the possibility of such transformation in combustion aerosols. Indeed it was shown that for some typical components found in aerosols that transformation could take place on time scales less than 20 s. The analysis showed that factors that influenced surface and interfacial tension played an important role in this transformation process. It is suggested that such transformation may, for example, result in a delayed evaporation of composite particles with significant water component, leading to observable effects in evolution of combustion aerosols (including possible local humidity maximums near a source, such as a busy road). The obtained results will be important for further development and understanding of aerosol physics and technologies, including combustion aerosols and their evolution near a source.

Neighborhood disadvantage and physical activity : baseline results from the HABITAT multilevel longitudinal study

PURPOSE: To examine the association between neighborhood disadvantage and physical activity (PA). ---------- METHODS: We use data from the HABITAT multilevel longitudinal study of PA among mid-aged (40-65 years) men and women (n=11, 037, 68.5% response rate) living in 200 neighborhoods in Brisbane, Australia. PA was measured using three questions from the Active Australia Survey (general walking, moderate, and vigorous activity), one indicator of total activity, and two questions about walking and cycling for transport. The PA measures were operationalized using multiple categories based on time and estimated energy expenditure that were interpretable with reference to the latest PA recommendations. The association between neighborhood disadvantage and PA was examined using multilevel multinomial logistic regression and Markov Chain Monte Carlo simulation. The contribution of neighborhood disadvantage to between-neighborhood variation in PA was assessed using the 80% interval odds ratio. ---------- RESULTS: After adjustment for sex, age, living arrangement, education, occupation, and household income, reported participation in all measures and levels of PA varied significantly across Brisbane’s neighborhoods, and neighborhood disadvantage accounted for some of this variation. Residents of advantaged neighborhoods reported significantly higher levels of total activity, general walking, moderate, and vigorous activity; however, they were less likely to walk for transport. There was no statistically significant association between neighborhood disadvantage and cycling for transport. In terms of total PA, residents of advantaged neighborhoods were more likely to exceed PA recommendations. ---------- CONCLUSIONS: Neighborhoods may exert a contextual effect on residents’ likelihood of participating in PA. The greater propensity of residents in advantaged neighborhoods to do high levels of total PA may contribute to lower rates of cardiovascular disease and obesity in these areas

Morphologic and genomic characterisation of the koala Chlamydia pneumoniae strain

Chlamydia pneumoniae is a common human and animal pathogen associated with a wide range of upper and lower respiratory tract infections. In more recent years there has been increasing evidence to suggest a link between C. pneumoniae and chronic diseases in humans, including atherosclerosis, stroke and Alzheimer’s disease. C. pneumoniae human strains show little genetic variation, indicating that the human-derived strain originated from a common ancestor in the recent past. Despite extensive information on the genetics and morphology processes of the human strain, knowledge concerning many other hosts (including marsupials, amphibians, reptiles and equines) remains virtually unexplored. The koala (Phascolarctos cinereus) is a native Australian marsupial under threat due to habitat loss, predation and disease. Koalas are very susceptible to chlamydial infections, most commonly affecting the conjunctiva, urogenital tract and/or respiratory tract. To address this gap in the literature, the present study (i) provides a detailed description of the morphologic and genomic architecture of the C. pneumoniae koala (and human) strain, and shows that the koala strain is microscopically, developmentally and genetically distinct from the C. pneumoniae human strain, and (ii) examines the genetic relationship of geographically diverse C. pneumoniae isolates from human, marsupial, amphibian, reptilian and equine hosts, and identifies two distinct lineages that have arisen from animal-to-human cross species transmissions. Chapter One of this thesis explores the scientific problem and aims of this study, while Chapter Two provides a detailed literature review of the background in this field of work. Chapter Three, the first results chapter, describes the morphology and developmental stages of C. pneumoniae koala isolate LPCoLN, as revealed by fluorescence and transmission electron microscopy. The profile of this isolate, when cultured in HEp-2 human epithelial cells, was quite different to the human AR39 isolate. Koala LPCoLN inclusions were larger; the elementary bodies did not have the characteristic pear-shaped appearance, and the developmental cycle was completed within a shorter period of time (as confirmed by quantitative real-time PCR). These in vitro findings might reflect biological differences between koala LPCoLN and human AR39 in vivo. Chapter Four describes the complete genome sequence of the koala respiratory pathogen, C. pneumoniae LPCoLN. This is the first animal isolate of C. pneumoniae to be fully-sequenced. The genome sequence provides new insights into genomic ‘plasticity’ (organisation), evolution and biology of koala LPCoLN, relative to four complete C. pneumoniae human genomes (AR39, CWL029, J138 and TW183). Koala LPCoLN contains a plasmid that is not shared with any of the human isolates, there is evidence of gene loss in nucleotide salvage pathways, and there are 10 hot spot genomic regions of variation that were previously not identified in the C. pneumoniae human genomes. Sequence (partial-length) from a second, independent, wild koala isolate (EBB) at several gene loci confirmed that the koala LPCoLN isolate was representative of a koala C. pneumoniae strain. The combined sequence data provides evidence that the C. pneumoniae animal (koala LPCoLN) genome is ancestral to the C. pneumoniae human genomes and that human infections may have originated from zoonotic infections. Chapter Five examines key genome components of the five C. pneumoniae genomes in more detail. This analysis reveals genomic features that are shared by and/or contribute to the broad ecological adaptability and evolution of C. pneumoniae. This analysis resulted in the identification of 65 gene sequences for further analysis of intraspecific variation, and revealed some interesting differences, including fragmentation, truncation and gene decay (loss of redundant ancestral traits). This study provides valuable insights into metabolic diversity, adaptation and evolution of C. pneumoniae. Chapter Six utilises a subset of 23 target genes identified from the previous genomic comparisons and makes a significant contribution to our understanding of genetic variability among C. pneumoniae human (11) and animal (6 amphibian, 5 reptilian, 1 equine and 7 marsupial hosts) isolates. It has been shown that the animal isolates are genetically diverse, unlike the human isolates that are virtually clonal. More convincing evidence that C. pneumoniae originated in animals and recently (in the last few hundred thousand years) crossed host species to infect humans is provided in this study. It is proposed that two animal-to-human cross species events have occurred in the context of the results, one evident by the nearly clonal human genotype circulating in the world today, and the other by a more animal-like genotype apparent in Indigenous Australians. Taken together, these data indicate that the C. pneumoniae koala LPCoLN isolate has morphologic and genomic characteristics that are distinct from the human isolates. These differences may affect the survival and activity of the C. pneumoniae koala pathogen in its natural host, in vivo. This study, by utilising the genetic diversity of C. pneumoniae, identified new genetic markers for distinguishing human and animal isolates. However, not all C. pneumoniae isolates were genetically diverse; in fact, several isolates were highly conserved, if not identical in sequence (i.e. Australian marsupials) emphasising that at some stage in the evolution of this pathogen, there has been an adaptation/s to a particular host, providing some stability in the genome. The outcomes of this study by experimental and bioinformatic approaches have significantly enhanced our knowledge of the biology of this pathogen and will advance opportunities for the investigation of novel vaccine targets, antimicrobial therapy, or blocking of pathogenic pathways.