Text mining with semantic annotation : using enriched text representation for entity-oriented retrieval, semantic relation identification and text clustering

This project is a step forward in the study of text mining where enhanced text representation with semantic information plays a significant role. It develops effective methods of entity-oriented retrieval, semantic relation identification and text clustering utilizing semantically annotated data. These methods are based on enriched text representation generated by introducing semantic information extracted from Wikipedia into the input text data. The proposed methods are evaluated against several start-of-art benchmarking methods on real-life data-sets. In particular, this thesis improves the performance of entity-oriented retrieval, identifies different lexical forms for an entity relation and handles clustering documents with multiple feature spaces.

The BAD project: data mining, database and prediction of protein adsorption on surfaces

Protein adsorption at solid-liquid interfaces is critical to many applications, including biomaterials, protein microarrays and lab-on-a-chip devices. Despite this general interest, and a large amount of research in the last half a century, protein adsorption cannot be predicted with an engineering level, design-orientated accuracy. Here we describe a Biomolecular Adsorption Database (BAD), freely available online, which archives the published protein adsorption data. Piecewise linear regression with breakpoint applied to the data in the BAD suggests that the input variables to protein adsorption, i.e., protein concentration in solution; protein descriptors derived from primary structure (number of residues, global protein hydrophobicity and range of amino acid hydrophobicity, isoelectric point); surface descriptors (contact angle); and fluid environment descriptors (pH, ionic strength), correlate well with the output variable-the protein concentration on the surface. Furthermore, neural network analysis revealed that the size of the BAD makes it sufficiently representative, with a neural network-based predictive error of 5% or less. Interestingly, a consistently better fit is obtained if the BAD is divided in two separate sub-sets representing protein adsorption on hydrophilic and hydrophobic surfaces, respectively. Based on these findings, selected entries from the BAD have been used to construct neural network-based estimation routines, which predict the amount of adsorbed protein, the thickness of the adsorbed layer and the surface tension of the protein-covered surface. While the BAD is of general interest, the prediction of the thickness and the surface tension of the protein-covered layers are of particular relevance to the design of microfluidics devices.

The effect of using different regions of interest on local and mean skin temperature

The dynamic nature of tissue temperature and the subcutaneous properties, such as blood flow, fatness, and metabolic rate, leads to variation in local skin temperature. Therefore, we investigated the effects of using multiple regions of interest when calculating weighted mean skin temperature from four local sites. Twenty-six healthy males completed a single trial in a thermonetural laboratory (mean ± SD): 24.0 (1.2) °C; 56 (8%) relative humidity; < 0.1 m/s air speed). Mean skin temperature was calculated from four local sites (neck, scapula, hand and shin) in accordance with International Standards using digital infrared thermography. A 50 x 50 mm square, defined by strips of aluminium tape, created six unique regions of interest, top left quadrant, top right quadrant, bottom left quadrant, bottom right quadrant, centre quadrant and the entire region of interest, at each of the local sites. The largest potential error in weighted mean skin temperature was calculated using a combination of a) the coolest and b) the warmest regions of interest at each of the local sites. Significant differences between the six regions interest were observed at the neck (P < 0.01), scapula (P < 0.001) and shin (P < 0.05); but not at the hand (P = 0.482). The largest difference (± SEM) at each site was as follows: neck 0.2 (0.1) °C; scapula 0.2 (0.0) °C; shin 0.1 (0.0) °C and hand 0.1 (0.1) °C. The largest potential error (mean ± SD) in weighted mean skin temperature was 0.4 (0.1) °C (P < 0.001) and the associated 95% limits of agreement for these differences was 0.2 to 0.5 °C. Although we observed differences in local and mean skin temperature based on the region of interest employed, these differences were minimal and are not considered physiologically meaningful.

A fast semi-implicit difference method for a nonlinear two-sided space-fractional diffusion equation with variable diffusivity coefficients

In this paper, we derive a new nonlinear two-sided space-fractional diffusion equation with variable coefficients from the fractional Fick’s law. A semi-implicit difference method (SIDM) for this equation is proposed. The stability and convergence of the SIDM are discussed. For the implementation, we develop a fast accurate iterative method for the SIDM by decomposing the dense coefficient matrix into a combination of Toeplitz-like matrices. This fast iterative method significantly reduces the storage requirement of O(n2)O(n2) and computational cost of O(n3)O(n3) down to n and O(nlogn)O(nlogn), where n is the number of grid points. The method retains the same accuracy as the underlying SIDM solved with Gaussian elimination. Finally, some numerical results are shown to verify the accuracy and efficiency of the new method.

Art and the anxious city: Public art, public interest and the public good

While public art is often considered a key hallmark of a creative city, artworks in the public realm also have the capacity to act as lightening rods for social anxiety at times of perceived crisis. This paper considers recent debates about government-sponsored public art projects in Queensland in light of three international case studies: Rodin’s Thinker in Paris, Tilted Arc in New York and Vault in Melbourne. It considers whether consensus positions on public art are possible or desirable in light of issues of spatial control, and proposes that well-negotiated anxieties about public art may be an indicator of creative vibrancy and dynamism that will assist in the future understanding of Queensland’s experiment with government-mandated public art.

Direct measurement as a tool for assessing the accuracy of inverse dynamics

The understanding of the loads generated within the prosthetic leg can aid engineers in the design of components and clinicians in the process of rehabilitation. Traditional methods to assess these loads have relied on inverse dynamics. This indirect method estimates the applied load using video recordings and force-plates located at a distance from the region of interest, such as the base of the residuum. The well-known limitations of this method are related to the accuracy of this recursive model and the experimental conditions required (Frossard et al., 2003). Recent developments in sensors (Frossard et al., 2003) and prosthetic fixation (Brånemark et al., 2000) permit the direct measurement of the loads applied on the residuum of transfemoral amputees. In principle, direct measurement should be an appropriate tool for assessing the accuracy of inverse dynamics. The purpose of this paper is to determine the validity of this assumption. The comparative variable used in this study is the velocity of the relative body center of mass (VCOM(t)). The relativity is used to align the static (w.r.t. position) force plate measurement with the dynamic load cell measurement.

Rejected! The harmful effects of workgroup mistreatment and the moderating role of organisational norms

This program of research investigated the harmful effects of mistreatment by the workgroup, and the role of perceived rejection as a critical mediator linking mistreatment and outcomes. This research program had three primary purposes. First, the research aimed to examine the important role of workgroup mistreatment as an independent predictor of negative outcomes, over and above the influence of supervisor mistreatment. Second, the research aimed to examine the effect of perceived rejection as an explanatory variable linking workgroup mistreatment and outcomes. Finally, the moderating effect of organizational norms on the relationship between workgroup mistreatment and perceived rejection was examined. The relationships of interest were examined over four studies, using multiple methods of data collection, across part-time and full-time working samples. In Study 1 (Chapter 2), the independent role of workgroup mistreatment and the mediating role of perceived rejection were examined. One hundred and forty two part-time working participants took part in the study. The participants completed a questionnaire on workplace behaviors in their organizations. The results of hierarchical regression analyses revealed a strong harmful effect of workgroup mistreatment, independent of mistreatment by the supervisor. In addition, the results showed that perceived rejection fully mediated the relationship between workgroup mistreatment and depression and organizational based self esteem. The study highlighted that perceived rejection acts as a key underlying psychological mechanism involved in the effect of workgroup mistreatment. This study has been published in the Journal of Occupational Health Psychology. Study 2 and Study 3 were presented as one paper in Chapter 3. The aims of these two studies was to explore the effects of workgroup mistreatment on a wider range of individual and organizational level outcomes, and to provide further evidence of the mediating role of perceived rejection as observed in Study 1. The results from both studies demonstrated that workgroup mistreatment had a significant and independent role in predicting negative individual and organizational level outcomes, providing support for the findings of Study 1. In the first study, 189 participants received scenarios manipulating workgroup mistreatment and supervisor mistreatment. The results of hierarchical regression analyses revealed that workgroup mistreatment harmfully affected participants, over and above that of the supervisor. The results also demonstrated that perceived rejection mediated the positive relationships between workgroup mistreatment and depression and organizational deviance, and also the negative relationships between workgroup mistreatment and organizational based self esteem and organizational citizenship behaviors. The second study included an additional aim, to examine the moderating role of supportive organizational norms. Two hundred and twenty nine participants read scenarios that manipulated workgroup mistreatment, supervisor mistreatment and organizational norms. The results of hierarchical regression analyses revealed the significant harmful effects of workgroup mistreatment, over and above the influence of supervisor mistreatment. The results also revealed the mediating role of perceived rejection. The direct effect of positive organizational norms also emerged, consistent with previous research. In addition, the result revealed that employees who experienced supportive organizational norms were more likely to reconcile with their workgroup members after experiencing mistreatment compared to employees who experienced hostile organizational norms. Finally, an unexpected pattern on the key affective variables of depression and organizational based self esteem emerged, such that mistreatment led to more negative outcomes in the supportive norms condition than in the hostile condition, where employees appeared to be desensitized. This paper is currently under review at the Journal of Applied Social Psychology. In Study 4 (Chapter 4), the overall model of workplace mistreatment was tested on a sample of full-time workers in an applied setting. One hundred and seventy two adults took part in the study. Participants were required to evaluate their workplace regarding mistreatment and organizational norms and to report their own psychological, behavioral and organizational outcomes. The results revealed that workgroup mistreatment was associated with increased depression, stress and avoidance, over and above supervisor mistreatment. In addition, the results revealed that perceived rejection acted as an explanatory variable linking workgroup mistreatment to a number of outcomes. Furthermore, the moderating role of hostile organizational norms emerged on depression, stress, reconciliation and avoidance. This paper is currently under review at the Journal of Occupational Health Psychology. Overall, the four studies provided empirical support for the majority of the hypotheses. The effects were demonstrated for a range of psychological, behavioral, and organizational level outcomes, using multiple methods of data collection, across part-time and full-time workers. At the conclusion of the thesis (Chapter 5), an overall summary is provided of the findings across all four studies, practical and theoretical implications and research directions.

Variable phenotype in 16p duplication within a family

Background More individuals are now being identified with very rare genetic syndromes. We present a family with an inherited duplication of 16p11.2 to 16q12.1 in ring formation. Three of the four children, (aged 15 months to 10 years), mother, uncle, and grandmother are affected. Our aim was to provide preliminary evidence of possible phenotypic patterns of learning and behaviour associated with this chromosome anomaly. Method Psychometric assessments were undertaken with all four children. The mother and uncle also agreed to participate in the study. Measures of development (Bayley or Mullen), intellectual ability (WISC-IV or WAIS-III), academic achievement (WIAT-II), adaptive behaviour (Vinelands), and other relevant aspects of functioning (e.g., Children’s Memory Scale) were administered. Results. The first-born child is the only one who is unaffected. Her intellectual ability was assessed as being within the superior range. The second child experienced early difficulties with speech and motor skills. Although his intelligence is average, he has learning difficulties and significant auditory memory problems. The third child’s speech and motor milestones were markedly delayed. He has a complex medical history that includes a vitamin B12 deficiency. On the Mullen Scales at age 4 his scores ranged from average to very low. The development of the youngest child (aged 15 months), who also had a B12 deficiency but was treated early, was assessed as being within typical limits. Conclusions There is considerable developmental variability among the three children with this inherited 16p duplication. We discuss the intriguing similarities and differences, considering common features that may reflect phenotypic patterns and speculating about possible explanations for the variable presentations.

Copula-based spatial modelling of geometallurgical variables

The most important aspect of modelling a geological variable, such as metal grade, is the spatial correlation. Spatial correlation describes the relationship between realisations of a geological variable sampled at different locations. Any method for spatially modelling such a variable should be capable of accurately estimating the true spatial correlation. Conventional kriged models are the most commonly used in mining for estimating grade or other variables at unsampled locations, and these models use the variogram or covariance function to model the spatial correlations in the process of estimation. However, this usage assumes the relationships of the observations of the variable of interest at nearby locations are only influenced by the vector distance between the locations. This means that these models assume linear spatial correlation of grade. In reality, the relationship with an observation of grade at a nearby location may be influenced by both distance between the locations and the value of the observations (ie non-linear spatial correlation, such as may exist for variables of interest in geometallurgy). Hence this may lead to inaccurate estimation of the ore reserve if a kriged model is used for estimating grade of unsampled locations when nonlinear spatial correlation is present. Copula-based methods, which are widely used in financial and actuarial modelling to quantify the non-linear dependence structures, may offer a solution. This method was introduced by Bárdossy and Li (2008) to geostatistical modelling to quantify the non-linear spatial dependence structure in a groundwater quality measurement network. Their copula-based spatial modelling is applied in this research paper to estimate the grade of 3D blocks. Furthermore, real-world mining data is used to validate this model. These copula-based grade estimates are compared with the results of conventional ordinary and lognormal kriging to present the reliability of this method.

Numerical treatment of a two-dimensional variable-order fractional nonlinear reaction-diffusion model

A two-dimensional variable-order fractional nonlinear reaction-diffusion model is considered. A second-order spatial accurate semi-implicit alternating direction method for a two-dimensional variable-order fractional nonlinear reaction-diffusion model is proposed. Stability and convergence of the semi-implicit alternating direct method are established. Finally, some numerical examples are given to support our theoretical analysis. These numerical techniques can be used to simulate a two-dimensional variable order fractional FitzHugh-Nagumo model in a rectangular domain. This type of model can be used to describe how electrical currents flow through the heart, controlling its contractions, and are used to ascertain the effects of certain drugs designed to treat arrhythmia.

Save the Reef! Civic crowdfunding and public interest environmental litigation

This article examines the emerging area of civic crowdfunding, a subset of crowdfunding, as a means of financing public interest environmental litigation. The literature surrounding civic crowdfunding and third party litigation funding is currently underdeveloped. The link between those areas and public interest environmental litigation takes a further step into the unknown. As a case study, the Sea Dumping Case presents exciting opportunities for civil society and access to justice, but further research is needed before any firm conclusions can be drawn.

The differential impact of monetary policy announcements and explanatory minutes releases on the Australian interest rate futures market

Unlike US and Continental European jurisdictions, Australian monetary policy announcements are not followed promptly by projections materials or comprehensive summaries that explain the decision process. This information is disclosed 2 weeks later when the explanatory minutes of the Reserve Bank board meeting are released. This paper is the first study to exploit the features of the Australian monetary policy environment in order to examine the differential impact of monetary policy announcements and explanatory statements on the Australian interest rate futures market. We find that both monetary policy announcements and explanatory minutes releases have a significant impact on the implied yield and volatility of Australian interest rate futures contracts. When the differential impact of these announcements is examined using the full sample, no statistically significant difference is found. However, when the sample is partitioned based on stable periods and the Global Financial Crisis, a differential impact is evident. Further, contrary to the findings of Kim and Nguyen (2008), Lu et al. (2009), and Smales (2012a), the response along the yield curve, is found to be indifferent between the short and medium terms.

Investigating the population structure of Queensland invasive Streptococcus pneumoniae isolates in children: Using a modified multi-locus variable number of tandem repeat analysis and a novel minimum SNPs capsular typing method

This research investigated the use of DNA fingerprinting to characterise the bacteria Streptococcus pneumoniae or pneumococcus, and hence gain insight into the development of new vaccines or antibiotics. Different bacterial DNA fingerprinting methods were studied, and a novel method was developed and validated, which characterises different cell coatings that pneumococci produce. This method was used to study the epidemiology of pneumococci in Queensland before and after the introduction of the current pneumococcal vaccine. This study demonstrated that pneumococcal disease is highly prevalent in children under four years, that the bacteria can `switch' its cell coating to evade the vaccine, and that some DNA fingerprinting methods are more discriminatory than others. This has an impact on understanding which strains are more prone to cause invasive disease. Evidence of the excellent research findings have been published in high impact internationally refereed journals.

Axial spondyloarthritis: A new disease entity, not necessarily early ankylosing spondylitis

New classification criteria for axial spondyloarthritis have been developed with the goal of increasing sensitivity of criteria for early inflammatory spondyloarthritis. However these criteria substantially increase heterogeneity of the resulting disease group, reducing their value in both research and clinical settings. Further research to establish criteria based on better knowledge of the natural history of non-radiographic axial spondyloarthritis, its aetiopathogenesis and response to treatment is required. In the meantime the modified New York criteria for ankylosing spondylitis remain a very useful classification criteria set, defining a relatively homogenous group of cases for clinical use and research studies.