Hierarchical models for 2D presence/absence data having ambiguous zeroes: With a biogeographical case study on dingo behaviour

This dissertation is primarily an applied statistical modelling investigation, motivated by a case study comprising real data and real questions. Theoretical questions on modelling and computation of normalization constants arose from pursuit of these data analytic questions. The essence of the thesis can be described as follows. Consider binary data observed on a two-dimensional lattice. A common problem with such data is the ambiguity of zeroes recorded. These may represent zero response given some threshold (presence) or that the threshold has not been triggered (absence). Suppose that the researcher wishes to estimate the effects of covariates on the binary responses, whilst taking into account underlying spatial variation, which is itself of some interest. This situation arises in many contexts and the dingo, cypress and toad case studies described in the motivation chapter are examples of this. Two main approaches to modelling and inference are investigated in this thesis. The first is frequentist and based on generalized linear models, with spatial variation modelled by using a block structure or by smoothing the residuals spatially. The EM algorithm can be used to obtain point estimates, coupled with bootstrapping or asymptotic MLE estimates for standard errors. The second approach is Bayesian and based on a three- or four-tier hierarchical model, comprising a logistic regression with covariates for the data layer, a binary Markov Random field (MRF) for the underlying spatial process, and suitable priors for parameters in these main models. The three-parameter autologistic model is a particular MRF of interest. Markov chain Monte Carlo (MCMC) methods comprising hybrid Metropolis/Gibbs samplers is suitable for computation in this situation. Model performance can be gauged by MCMC diagnostics. Model choice can be assessed by incorporating another tier in the modelling hierarchy. This requires evaluation of a normalization constant, a notoriously difficult problem. Difficulty with estimating the normalization constant for the MRF can be overcome by using a path integral approach, although this is a highly computationally intensive method. Different methods of estimating ratios of normalization constants (N Cs) are investigated, including importance sampling Monte Carlo (ISMC), dependent Monte Carlo based on MCMC simulations (MCMC), and reverse logistic regression (RLR). I develop an idea present though not fully developed in the literature, and propose the Integrated mean canonical statistic (IMCS) method for estimating log NC ratios for binary MRFs. The IMCS method falls within the framework of the newly identified path sampling methods of Gelman & Meng (1998) and outperforms ISMC, MCMC and RLR. It also does not rely on simplifying assumptions, such as ignoring spatio-temporal dependence in the process. A thorough investigation is made of the application of IMCS to the three-parameter Autologistic model. This work introduces background computations required for the full implementation of the four-tier model in Chapter 7. Two different extensions of the three-tier model to a four-tier version are investigated. The first extension incorporates temporal dependence in the underlying spatio-temporal process. The second extensions allows the successes and failures in the data layer to depend on time. The MCMC computational method is extended to incorporate the extra layer. A major contribution of the thesis is the development of a fully Bayesian approach to inference for these hierarchical models for the first time. Note: The author of this thesis has agreed to make it open access but invites people downloading the thesis to send her an email via the 'Contact Author' function.

The development of a serological-based diagnostic test for Dasheen mosaic potyvirus (DsMV)

Dasheen mosaic potyvirus (DsMV) is an important virus affecting taro. The virus has been found wherever taro is grown and infects both the edible and ornamental aroids, causing yield losses of up to 60%. The presence of DsMV, and other viruses,prevents the international movement of taro germplasm between countries. This has a significant negative impact on taro production in many countries due to the inability to access improved taro lines produced in breeding programs. To overcome this problem, sensitive and reliable virus diagnostic tests need to be developed to enable the indexing of taro germplasm. The aim of this study was to generate an antiserum against a recombinant DsMV coat protein (CP) and to develop a serological-based diagnostic test that would detect Pacific Island isolates of the virus. The CP-coding region of 16 DsMV isolates from Papua New Guinea, Samoa, Solomon Islands, French Polynesia, New Caledonia and Vietnam were amplified,cloned and sequenced. The size of the CP-coding region ranged from 939 to 1038 nucleotides and encoded putative proteins ranged from 313 to 346 amino acids, with the molecular mass ranging from 34 to 38 kDa. Analysis ofthe amino acid sequences revealed the presence of several amino acid motifs typically found in potyviruses,including DAG, WCIE/DN, RQ and AFDF. When the amino acid sequences were compared with each other and the DsMV sequences on the database, the maximum variability was21.9%. When the core region ofthe CP was analysed, the maximum variability dropped to 6% indicating most variability was present in the N terminus. Within seven PNG isolates ofDsMV, the maximum variability was 16.9% and 3.9% over the entire CP-coding region and core region, respectively. The sequence ofPNG isolate P1 was most similar to all other sequences. Phylogenetic analysis indicated that almost all isolates grouped according to their provenance. Further, the seven PNG isolates were grouped according to the region within PNG from which they were obtained. Due to the extensive variability over the entire CP-coding region, the core region ofthe CP ofPNG isolate Pl was cloned into a protein expression vector and expressed as a recombinant protein. The protein was purified by chromatography and SDS-PAGE and used as an antigen to generate antiserum in a rabbit. In western blots, the antiserum reacted with bands of approximately 45-47 kDa in extracts from purified DsMV and from known DsMV -infected plants from PNG; no bands were observed using healthy plant extracts. The antiserum was subsequently incorporated into an indirect ELISA. This procedure was found to be very sensitive and detected DsMV in sap diluted at least 1:1,000. Using both western blot and ELISA formats,the antiserum was able to detect a wide range ofDsMV isolates including those from Australia, New Zealand, Fiji, French Polynesia, New Caledonia, Papua New Guinea, Samoa, Solomon Islands and Vanuatu. These plants were verified to be infected with DsMV by RT-PCR. In specificity tests, the antiserum was also found to react with sap from plants infected with SCMV, PRSV-P, PRSV-W, but not with PVY or CMV -infected plants.

Sensitivity of the lane change test as a measure of in-vehicle system demand

The Lane Change Test (LCT) is one of the growing number of methods developed to quantify driving performance degradation brought about by the use of in-vehicle devices. Beyond its validity and reliability, for such a test to be of practical use, it must also be sensitive to the varied demands of individual tasks. The current study evaluated the ability of several recent LCT lateral control and event detection parameters to discriminate between visual-manual and cognitive surrogate In-Vehicle Information System tasks with different levels of demand. Twenty-seven participants (mean age 24.4 years) completed a PC version of the LCT while performing visual search and math problem solving tasks. A number of the lateral control metrics were found to be sensitive to task differences, but the event detection metrics were less able to discriminate between tasks. The mean deviation and lane excursion measures were able to distinguish between the visual and cognitive tasks, but were less sensitive to the different levels of task demand. The other LCT metrics examined were less sensitive to task differences. A major factor influencing the sensitivity of at least some of the LCT metrics could be the type of lane change instructions given to participants. The provision of clear and explicit lane change instructions and further refinement of its metrics will be essential for increasing the utility of the LCT as an evaluation tool.

"Surviving" adolescence : apocalyptic and post-apocalyptic transformations in young adult fiction

This study, entitled "Surviving" Adolescence: Apocalyptic and post-apocalyptic transformations in young adult fiction‖, analyses how discourses surrounding the apocalyptic and post-apocalyptic are represented in selected young adult fiction published between 1997 and 2009. The term ―apocalypse‖ is used by current theorists to refer to an uncovering or disclosure (most often a truth), and ―post-apocalypse‖ means to be after a disclosure, after a revelation, or after catastrophe. This study offers a double reading of apocalyptic and post-apocalyptic discourses, and the dialectical tensions that are inherent in, and arise from, these discourses. Drawing on the current scholarship of children‘s and young adult literature this thesis uses post-structural theoretical perspectives to develop a framework and methodology for conducting a close textual analysis of exclusion, ‗un‘differentiation, prophecy, and simulacra of death. The combined theoretical perspectives and methodology offer new contributions to young adult fiction scholarship. This thesis finds that rather than conceiving adolescence as the endurance of a passing phase of a young person‘s life, there is a new trend emerging in young adult fiction that treats adolescence as a space of transformation essential to the survival of the young adult, and his/her community.

An empirical test of causal relationships of factors affecting ICT adoption for building project management : an Indian SME case study

Purpose - Building project management (BPM) requires effective coordination and collaboration between multiple project team organisations which can be achieved by real time information flow between all participants. In the present scenario, this can be achieved by the use of information communication technologies (ICT). The purpose of this paper is to present part of a research project conducted to study the causal relationships between factors affecting ICT adoption for BPM by small and medium enterprises. Design/methodology/approach - This paper discusses structural equation modelling (SEM) analysis conducted to test the causal relationships between quantitative factors. Data for quantitative analysis were gathered through a questionnaire survey conducted in the Indian construction industry. Findings - SEM analysis results help in demonstrating that an increased and matured use of ICT for general administration within the organisation would lead to: an improved ICT infrastructure within the organisation; development of electronic databases; and a staff that is confident of using information technology (IT) tools. In such a scenario, staff would use advanced software and IT technologies for project management (PM) processes and that would lead to an increased adoption of ICT for PM processes. But, for general administration also, ICT adoption would be enhanced if the organisation is interacting more with geographically separated agencies and senior management perceives that significant benefits would accrue by adoption of ICT. All the factors are inter-related and their effect cannot be maximized in isolation. Originality/value - The results provide direction to building project managements for strategically adopting the effective use of ICT within their organisations and for BPM general.

VO2max in overweight and obese adults

Purpose: The purpose of this study was to determine whether adiposity affects the attainment of VO2max. Methods: Sixty-seven male and 68 female overweight (body mass index (BMI) = 25-29.9 kg·m-2) and obese (BMI >= 30 kg·m-2) participants undertook a graded treadmill test to volitional exhaustion (phase 1) followed by a verification test (phase 2) to determine the proportion who could achieve a plateau in VO2 and other "maximal" markers (RER, lactate, HR, RPE). Results: At the end of phase 1, 46% of the participants reached a plateau in VO2, 83% increased HR to within 11 beats of age-predicted maximum, 89% reached an RER of >=1.15, 70% reached a blood lactate concentration of >=8 mmol·L-1, and 74% reached an RPE of >=18. No significant differences between genders and between BMI groups were found with the exception of blood lactate concentration (males = 84% vs females = 56%, P < 0.05). Neither gender nor fatness predicted the number of other markers attained, and attainment of other markers did not differentiate whether a VO2 plateau was achieved. The verification test (phase 2) revealed that an additional 52 individuals (39%) who did not exhibit a plateau in V·O2 in phase 1 had no further increase in VO2 in phase 2 despite an increase in workload. Conclusions: These findings indicate that the absence of a plateau in VO2 alone is not indicative of a failure to reach a true maximal VO2 and that individuals with excessive body fat are no less likely than "normal-weight" individuals to exhibit a plateau in VO2 provided that the protocol is appropriate and encouragement to exercise to maximal exertion is provided.

Assessment of pile driving refusal using the standard test (SPT)

The design of driven pile foundations involves an iterative process requiring an initial estimate of the refusal level to determine the depth of boreholes for subsequent analyses. Current procedures for determining borehole depths incorporate parameters typically unknown at the investigation stage. Thus, a quantifiable procedure more applicable at this preliminary stage would provide greater confidence in estimating the founding level of driven piles. This paper examines the effectiveness of the Standard Penetration Test (SPT) in directly estimating driven pile refusal levels. A number of significant correlations were obtained between SPT information and pile penetration records demonstrating the potential application of the SPT. Results indicated pile penetration was generally best described as a function of both the pile toe and cumulative shaft SPT values. The influence of the toe SPT increased when piles penetrated rock. A refusal criteria was established from the results to guide both the estimation of borehole depths and likely pile lengths during the design stage.

Smart Grid Test Bed Design and Implementation

Given there is currently a migration trend from traditional electrical supervisory control and data acquisition (SCADA) systems towards a smart grid based approach to critical infrastructure management. This project provides an evaluation of existing and proposed implementations for both traditional electrical SCADA and smart grid based architectures, and proposals a set of reference requirements which test bed implementations should implement. A high-level design for smart grid test beds is proposed and initial implementation performed, based on the proposed design, using open source and freely available software tools. The project examines the move towards smart grid based critical infrastructure management and illustrates the increased security requirements. The implemented test bed provides a basic framework for testing network requirements in a smart grid environment, as well as a platform for further research and development. Particularly to develop, implement and test network security related disturbances such as intrusion detection and network forensics. The project undertaken proposes and develops an architecture of the emulation of some smart grid functionality. The Common Open Research Emulator (CORE) platform was used to emulate the communication network of the smart grid. Specifically CORE was used to virtualise and emulate the TCP/IP networking stack. This is intended to be used for further evaluation and analysis, for example the analysis of application protocol messages, etc. As a proof of concept, software libraries were designed, developed and documented to enable and support the design and development of further smart grid emulated components, such as reclosers, switches, smart meters, etc. As part of the testing and evaluation a Modbus based smart meter emulator was developed to provide basic functionality of a smart meter. Further code was developed to send Modbus request messages to the emulated smart meter and receive Modbus responses from it. Although the functionality of the emulated components were limited, it does provide a starting point for further research and development. The design is extensible to enable the design and implementation of additional SCADA protocols. The project also defines an evaluation criteria for the evaluation of the implemented test bed, and experiments are designed to evaluate the test bed according to the defined criteria. The results of the experiments are collated and presented, and conclusions drawn from the results to facilitate discussion on the test bed implementation. The discussion undertaken also present possible future work.

Corneal confocal microscopy : a novel noninvasive test to diagnose and stratify the severity of human diabetic neuropathy

OBJECTIVE: The accurate quantification of human diabetic neuropathy is important to define at-risk patients, anticipate deterioration, and assess new therapies. ---------- RESEARCH DESIGN AND METHODS: A total of 101 diabetic patients and 17 age-matched control subjects underwent neurological evaluation, neurophysiology tests, quantitative sensory testing, and evaluation of corneal sensation and corneal nerve morphology using corneal confocal microscopy (CCM). ---------- RESULTS: Corneal sensation decreased significantly (P = 0.0001) with increasing neuropathic severity and correlated with the neuropathy disability score (NDS) (r = 0.441, P < 0.0001). Corneal nerve fiber density (NFD) (P < 0.0001), nerve fiber length (NFL), (P < 0.0001), and nerve branch density (NBD) (P < 0.0001) decreased significantly with increasing neuropathic severity and correlated with NDS (NFD r = −0.475, P < 0.0001; NBD r = −0.511, P < 0.0001; and NFL r = −0.581, P < 0.0001). NBD and NFL demonstrated a significant and progressive reduction with worsening heat pain thresholds (P = 0.01). Receiver operating characteristic curve analysis for the diagnosis of neuropathy (NDS >3) defined an NFD of <27.8/mm2 with a sensitivity of 0.82 (95% CI 0.68–0.92) and specificity of 0.52 (0.40–0.64) and for detecting patients at risk of foot ulceration (NDS >6) defined a NFD cutoff of <20.8/mm2 with a sensitivity of 0.71 (0.42–0.92) and specificity of 0.64 (0.54–0.74). ---------- CONCLUSIONS: CCM is a noninvasive clinical technique that may be used to detect early nerve damage and stratify diabetic patients with increasing neuropathic severity. Established diabetic neuropathy leads to pain and foot ulceration. Detecting neuropathy early may allow intervention with treatments to slow or reverse this condition (1). Recent studies suggested that small unmyelinated C-fibers are damaged early in diabetic neuropathy (2–4) but can only be detected using invasive procedures such as sural nerve biopsy (4,5) or skin-punch biopsy (6–8). Our studies have shown that corneal confocal microscopy (CCM) can identify early small nerve fiber damage and accurately quantify the severity of diabetic neuropathy (9–11). We have also shown that CCM relates to intraepidermal nerve fiber loss (12) and a reduction in corneal sensitivity (13) and detects early nerve fiber regeneration after pancreas transplantation (14). Recently we have also shown that CCM detects nerve fiber damage in patients with Fabry disease (15) and idiopathic small fiber neuropathy (16) when results of electrophysiology tests and quantitative sensory testing (QST) are normal. In this study we assessed corneal sensitivity and corneal nerve morphology using CCM in diabetic patients stratified for the severity of diabetic neuropathy using neurological evaluation, electrophysiology tests, and QST. This enabled us to compare CCM and corneal esthesiometry with established tests of diabetic neuropathy and define their sensitivity and specificity to detect diabetic patients with early neuropathy and those at risk of foot ulceration.

Destination positioning opportunities elicited through the repertory test with laddering analysis

While in many travel situations consumers have an almost limitless range of destinations to choose from, their actual decision set will usually only comprise between two and six destinations. One of the greatest challenges facing destination marketers is positioning their destination, against the myriad of competing places that offer similar features, into consumer decision sets. Since positioning requires a narrow focus, marketing communications must present a succinct and meaningful proposition, the selection of which is often problematic for destination marketing organisations (DMO), which deal with a diverse and often eclectic range of attributes in addition to numerous self-interested and demanding stakeholders. This paper reports the application of two qualitative techniques used to explore the range of cognitive attributes, consequences and personal values that represent potential positioning opportunities in the context of short break holidays. The Repertory Test is an effective technique for understanding the salient attributes used by a traveller to differentiate destinations, while Laddering Analysis enables the researcher to explore the smaller set of personal values guiding such decision making. A key finding of the research was that while individuals might vary in their repertoire of salient attributes, there was a commonality of shared consequences and values.

Lost children and imaginary mothers in Sonya Hartnett's Of A Boy

In Powers of Horror, Julia Kristeva writes about lost children. These are what she calls “dejects,” who, in the psychodrama of subject formation, fail to fully absent the body of the mother, to accept the Law of the Father and the Symbolic, and subsequently to establish “clear boundaries which constitute the object-world for normal subjects.” Dejects are “strays” looking for a place to belong, a place that is bound up with the Imaginary mother of the pre-Oedipal period. Kristeva’s sketch of the deject as one who is unable to negotiate a proper path to the Symbolicis useful to a reading of Hartnett’s Of A Boy (2002),a novel that also deals with lost children and imaginary mothers. However, in its portrayal of children who are doomed to never achieve adulthood, Of A Boy enacts a haunting retrieval of the pre-Oedipal from the dark side of phallocentric representation, privileging the semiotic (Kristeva’s concept) and the maternal as necessary disruptive checks on a patriarchal Symbolic Order.