Semantic oscillations : encoding context and structure in complex valued holographic vectors

In computational linguistics, information retrieval and applied cognition, words and concepts are often represented as vectors in high dimensional spaces computed from a corpus of text. These high dimensional spaces are often referred to as Semantic Spaces. We describe a novel and efficient approach to computing these semantic spaces via the use of complex valued vector representations. We report on the practical implementation of the proposed method and some associated experiments. We also briefly discuss how the proposed system relates to previous theoretical work in Information Retrieval and Quantum Mechanics and how the notions of probability, logic and geometry are integrated within a single Hilbert space representation. In this sense the proposed system has more general application and gives rise to a variety of opportunities for future research.

The application of a profluorescent nitroxide probe to detect reactive oxygen species derived from combustion-generated particulate matter

Particulate pollution has been widely recognised as an important risk factor to human health. In addition to increases in respiratory and cardiovascular morbidity associated with exposure to particulate matter (PM), WHO estimates that urban PM causes 0.8 million premature deaths globally and that 1.5 million people die prematurely from exposure to indoor smoke generated from the combustion of solid fuels. Despite the availability of a huge body of research, the underlying toxicological mechanisms by which particles induce adverse health effects are not yet entirely understood. Oxidative stress caused by generation of free radicals and related reactive oxygen species (ROS) at the sites of deposition has been proposed as a mechanism for many of the adverse health outcomes associated with exposure to PM. In addition to particle-induced generation of ROS in lung tissue cells, several recent studies have shown that particles may also contain ROS. As such, they present a direct cause of oxidative stress and related adverse health effects. Cellular responses to oxidative stress have been widely investigated using various cell exposure assays. However, for a rapid screening of the oxidative potential of PM, less time-consuming and less expensive, cell-free assays are needed. The main aim of this research project was to investigate the application of a novel profluorescent nitroxide probe, synthesised at QUT, as a rapid screening assay in assessing the oxidative potential of PM. Considering that this was the first time that a profluorescent nitroxide probe was applied in investigating the oxidative stress potential of PM, the proof of concept regarding the detection of PM–derived ROS by using such probes needed to be demonstrated and a sampling methodology needed to be developed. Sampling through an impinger containing profluorescent nitroxide solution was chosen as a means of particle collection as it allowed particles to react with the profluorescent nitroxide probe during sampling, avoiding in that way any possible chemical changes resulting from delays between the sampling and the analysis of the PM. Among several profluorescent nitroxide probes available at QUT, bis(phenylethynyl)anthracene-nitroxide (BPEAnit) was found to be the most suitable probe, mainly due to relatively long excitation and emission wavelengths (λex= 430 nm; λem= 485 and 513 nm). These wavelengths are long enough to avoid overlap with the background fluorescence coming from light absorbing compounds which may be present in PM (e.g. polycyclic aromatic hydrocarbons and their derivatives). Given that combustion, in general, is one of the major sources of ambient PM, this project aimed at getting an insight into the oxidative stress potential of combustion-generated PM, namely cigarette smoke, diesel exhaust and wood smoke PM. During the course of this research project, it was demonstrated that the BPEAnit probe based assay is sufficiently sensitive and robust enough to be applied as a rapid screening test for PM-derived ROS detection. Considering that for all three aerosol sources (i.e. cigarette smoke, diesel exhaust and wood smoke) the same assay was applied, the results presented in this thesis allow direct comparison of the oxidative potential measured for all three sources of PM. In summary, it was found that there was a substantial difference between the amounts of ROS per unit of PM mass (ROS concentration) for particles emitted by different combustion sources. For example, particles from cigarette smoke were found to have up to 80 times less ROS per unit of mass than particles produced during logwood combustion. For both diesel and wood combustion it has been demonstrated that the type of fuel significantly affects the oxidative potential of the particles emitted. Similarly, the operating conditions of the combustion source were also found to affect the oxidative potential of particulate emissions. Moreover, this project has demonstrated a strong link between semivolatile (i.e. organic) species and ROS and therefore, clearly highlights the importance of semivolatile species in particle-induced toxicity.

Difference in mosquito species (Diptera: Culicidae) and the transmission of Ross River Virus between coastline and inland areas in Brisbane, Australia

This study examined the distribution of major mosquito species and their roles in the transmission of Ross River virus (RRV) infection for coastline and inland areas in Brisbane, Australia (27°28′ S, 153°2′ E). We obtained data on the monthly counts of RRV cases in Brisbane between November 1998 and December 2001 by statistical local areas from the Queensland Department of Health and the monthly mosquito abundance from the Brisbane City Council. Correlation analysis was used to assess the pairwise relationships between mosquito density and the incidence of RRV disease. This study showed that the mosquito abundance of Aedes vigilax (Skuse), Culex annulirostris (Skuse), and Aedes vittiger (Skuse) were significantly associated with the monthly incidence of RRV in the coastline area, whereas Aedes vigilax, Culex annulirostris, and Aedes notoscriptus (Skuse) were significantly associated with the monthly incidence of RRV in the inland area. The results of the classification and regression tree (CART) analysis show that both occurrence and incidence of RRV were influenced by interactions between species in both coastal and inland regions. We found that there was an 89% chance for an occurrence of RRV if the abundance of Ae. vigifax was between 64 and 90 in the coastline region. There was an 80% chance for an occurrence of RRV if the density of Cx. annulirostris was between 53 and 74 in the inland area. The results of this study may have applications as a decision support tool in planning disease control of RRV and other mosquito-borne diseases.

Using Web 2.0 tools to facilitate knowledge transfer in complex organisational environments : a primer

An often neglected but well recognised aspect of successful engineering asset management is the achievement of co-operation and collaboration between various occupational, functional and hierarchical levels present within complex technical environments. Engineering and technical contexts have been well documented for the presence of highly cohesive groups based around around functional or role orientations. However while highly cohesive groups are potentially advantageous they are also often correlated with the emergence of knowledge and information silos based around those same functional or occupational clusters. Improved collaboration and co-operation between groups has been demonstrated to result in a number of positive outcomes at an individual, group and organisational level. Example outcomes include an increased capacity for problem solving, improved responsiveness and adaptation to organisational crises, higher morale and an increased ability to leverage workforce capability. However, an essential challenge for organisations wishing to overcome informational silos is to implement mechanisms that facilitate, encourage and sustain interactions between otherwise disconnected groups. This paper reviews the ability of Web 2.0 technologies and mobile computing devices to facilitate and encourage knowledge sharing between “silo’d” groups. Commonly available tools such as Facebook, Twitter, Blogs, Wiki’s and others will be reviewed in relation to their applicability, functionality and ease-of-use by engineering and technical personnel. The paper also documents three case examples of engineering organisations that have successfully employed Web 2.0 to achieve superior knowledge management. With a number of clear recommendations he paper is an essential starting point for any organization looking at the use of new generation technologies for achieving the significant outcomes associated with knowledge transfer.

The ecology of Bactrocera tryoni (Froggatt) (Diptera: Tephritdae) : what do we know to assist pest management?

The distribution, systematics and ecology of Bactrocera tryoni, the Queensland fruit fly are reviewed. Bactrocera tryoni is a member of the B. tryoni complex of species, which currently includes four named species, viz. B. tryoni s.s., B. neohumeralis, B. melas and B. aquilonis. The species status of B. melas and B. aquilonis are unclear (they may be junior synonyms of B. tryoni) and their validity, or otherwise, needs to be confirmed as a matter of urgency. While Queensland fruit fly is regarded as a tropical species, it cannot be assumed that its distribution will spread further south under climate change scenarios. Increasing aridity and hot dry summers, as well as more complex, indirect interactions resulting from elevated CO2, make predicting the future distribution and abundance of B. tryoni difficult. The ecology of B. tryoni is reviewed with respect to current control approaches (with the exception of Sterile Insect Technique which is covered in a companion paper). We conclude that there are major gaps in the knowledge required to implement most non-insecticide based management approaches. Priority areas for future research include host plant interactions, protein and cue-lure foraging and use, spatial dynamics, development of new monitoring tools, investigating the use of natural enemies and better integration of fruit flies into general horticultural IPM systems.

Preference among four Bactrocera species (Diptera: Tephritidae) by Diachasmimorpha kraussii (Fullaway) (Hymenoptera: Braconidae)

Diachasmimorpha kraussii is an endoparasitoid of larval dacine fruit flies. To date the only host preference study done on D. kraussii has used fruit flies from outside its native range (Australia, Papua New Guinea, Solomon Islands). In contrast, this paper investigates host preference for four fly species (Bactrocera cacuminata, B. cucumis, B. jarvisi and B. tryoni) which occur sympatrically with the wasp in the Australian component of the native range. Diachasmimorpha kraussii oviposition preference, host suitability (parasitism rate, number of progeny, sex ratio), and offspring performance measures (body length, hind tibial length, developmental time) were investigated with respect to the four fly species in the laboratory in both no-choice and choice situations. The parasitoid accepted all four fruit fly species for oviposition in both no-choice and choice tests; however, adult wasps only emerged from B. jarvisi and B. tryoni. Through dissection, it was demonstrated that parasitoid eggs were encapsulated in both B. cacuminata and B. cucumis. Between the two suitable hosts, measurements of oviposition preference, host suitability and offspring performance measurements either did not vary significantly, or varied in an inconsistent manner. Based on our results, and a related study by other authors, we conclude that D. krausii, at the point of oviposition, cannot discriminate between physiologically suitable and unsuitable hosts.

Host use and crop impacts of Oribius Marshall species (Coleoptera: Curculionidae) in Eastern Highlands Province, Papua New Guinea

Oribius species are small flightless weevils endemic to the island of New Guinea and far northern Cape York, Australia. The adults feed externally on leaves, developing fruit and green bark, but their impact as pests and general host use patterns are poorly known. Working in Eastern Highlands Province, Papua New Guinea, we carried out structured host use surveys, farmer surveys, shade-house growth trials, and on-farm and on-station impact trials to: (i) estimate the host range of the local Oribius species; (ii) understand adult daily activity patterns; (iii) elucidate feeding habits of the soil dwelling larvae; and (iv) quantify the impacts of adult feeding damage. Oribius inimicus and O. destructor accounted for nearly all the Oribius species encountered locally: of these two O. inimicus was the most abundant. Weevils were collected from 31 of 33 plants surveyed in the Aiyura Valley and a combination of farmer interviews and literature records provided evidence for the beetles being pestiferous on 43 crops currently or previously grown in the Highlands. Adult weevils had a distinct diurnal pattern of being in the upper plant canopy early in the morning and, to a lesser extent, again late in the afternoon. For the remainder of the day beetles resided within the canopy, or possibly off the plant. Movement of adults between plants appeared frequent. Pot trials confirmed the larvae are root feeders. Quantified impact studies showed that the weevils are damaging to a range of vegetable and orchard crops (broccoli, capsicum, celery, French bean, Irish potato, lettuce, orange and strawberry), causing average yield losses of around 30-40%, but up to 100% on citrus. Oribius weevils pose a significant and apparently growing problem for Highland’s agriculture.

Using Web 2.0 tools to facilitate knowledge transfer in complex organisational environments : a primer

An often neglected but well recognised aspect of successful engineering asset management is the achievement of co-operation and collaboration between various occupational, functional and hierarchical levels present within complex technical environments. Engineering and technical contexts have been well documented for the presence of highly cohesive groups based around around functional or role orientations. However while highly cohesive groups are potentially advantageous they are also often correlated with the emergence of knowledge and information silos based around those same functional or occupational clusters. Improved collaboration and co-operation between groups has been demonstrated to result in a number of positive outcomes at an individual, group and organisational level. Example outcomes include an increased capacity for problem solving, improved responsiveness and adaptation to organisational crises, higher morale and an increased ability to leverage workforce capability. However, an essential challenge for organisations wishing to overcome informational silos is to implement mechanisms that facilitate, encourage and sustain interactions between otherwise disconnected groups. This paper reviews the ability of Web 2.0 technologies and mobile computing devices to facilitate and encourage knowledge sharing between “silo’d” groups. Commonly available tools such as Facebook, Twitter, Blogs, Wiki’s and others will be reviewed in relation to their applicability, functionality and ease-of-use by engineering and technical personnel. The paper also documents three case examples of engineering organisations that have successfully employed Web 2.0 to achieve superior knowledge management. With a number of clear recommendations the paper is an essential starting point for any organization looking at the use of new generation technologies for achieving the significant outcomes associated with knowledge transfer.

Mathematical modelling of chronic wound healing

Chronicwounds fail to proceed through an orderly process to produce anatomic and functional integrity and are a significant socioeconomic problem. There is much debate about the best way to treat these wounds. In this thesis we review earlier mathematical models of angiogenesis and wound healing. Many of these models assume a chemotactic response of endothelial cells, the primary cell type involved in angiogenesis. Modelling this chemotactic response leads to a system of advection-dominated partial differential equations and we review numerical methods to solve these equations and argue that the finite volume method with flux limiting is best-suited to these problems. One treatment of chronic wounds that is shrouded with controversy is hyperbaric oxygen therapy (HBOT). There is currently no conclusive data showing that HBOT can assist chronic wound healing, but there has been some clinical success. In this thesis we use several mathematical models of wound healing to investigate the use of hyperbaric oxygen therapy to assist the healing process - a novel threespecies model and a more complex six-species model. The second model accounts formore of the biological phenomena but does not lend itself tomathematical analysis. Bothmodels are then used tomake predictions about the efficacy of hyperbaric oxygen therapy and the optimal treatment protocol. Based on our modelling, we are able to make several predictions including that intermittent HBOT will assist chronic wound healing while normobaric oxygen is ineffective in treating such wounds, treatment should continue until healing is complete and finding the right protocol for an individual patient is crucial if HBOT is to be effective. Analysis of the models allows us to derive constraints for the range of HBOT protocols that will stimulate healing, which enables us to predict which patients are more likely to have a positive response to HBOT and thus has the potential to assist in improving both the success rate and thus the cost-effectiveness of this therapy.

Environmental management and wildlife in Queensland : a review of Queensland mammal species designated as scarce

From 19 authoritative lists with 164 entries of ‘endangered’ Australian mammal species, 39 species have been reported as extinct. When examined in the light of field conditions, the 18 of these species thought to be from Queensland consist of (a) species described from fragmentary museum material collected in the earliest days of exploration, (b) populations inferred to exist in Queensland by extrapolation from distribution records in neighbouring States or countries, (c) inhabitants of remote and harsh locations where search effort is extraordinarily difficult (especially in circumstances of drought or flooding). and/or (d) individuals that are clearly transitory or peripheral in distribution. ‘Rediscovery’ of such scarce species - a not infrequent occurrence - is nowadays attracting increasing attention. Management in respect of any scarce wildlife in Queensland presently derives from such official lists. The analyses here indicate that this method of prioritizing action needs review. This is especially so because action then tends to be centred on species chosen out of the lists for populist reasons and that mostly addresses Crown lands. There is reason to believe that the preferred management may lie private lands where casual observation has provided for rediscovery and where management is most desirable and practicable.

Insulin-like growth factor-i : vitronectin complex-induced changes in gene expression effect breast cell survival and migration

Recent studies have demonstrated that IGF-I associates with VN through IGF-binding proteins (IGFBP) which in turn modulate IGF-stimulated biological functions such as cell proliferation, attachment and migration. Since IGFs play important roles in transformation and progression of breast tumours, we aimed to describe the effects of IGF-I:IGFBP:VN complexes on breast cell function and to dissect mechanisms underlying these responses. In this study we demonstrate that substrate-bound IGF-I:IGFBP:VN complexes are potent stimulators of MCF-7 breast cell survival, which is mediated by a transient activation of ERK/MAPK and sustained activation of PI3-K/AKT pathways. Furthermore, use of pharmacological inhibitors of the MAPK and PI3-K pathways confirms that both pathways are involved in IGF-I:IGFBP:VN complex-mediated increased cell survival. Microarray analysis of cells stimulated to migrate in response to IGF-I:IGFBP:VN complexes identified differential expression of genes with previously reported roles in migration, invasion and survival (Ephrin-B2, Sharp-2, Tissue-factor, Stratifin, PAI-1, IRS-1). These changes were not detected when the IGF-I analogue (\[L24]\[A31]-IGF-I), which fails to bind to the IGF-I receptor, was substituted; confirming the IGF-I-dependent differential expression of genes associated with enhanced cell migration. Taken together, these studies have established that IGF-I:IGFBP:VN complexes enhance breast cell migration and survival, processes central to facilitating metastasis. This study highlights the interdependence of ECM and growth factor interactions in biological functions critical for metastasis and identifies potential novel therapeutic targets directed at preventing breast cancer progression.

Lineage replacement accompanying duplication and rapid fixation of an RNA element in the nsP3 gene in a species of alphavirus

A sequence of thirty-six nucleotides in the nsP3 gene of Ross River virus (RRV), coding for the amino acid sequence HADTVSLDSTVS, was duplicated some time between 1969 and 1979 coinciding with the appearance of a new lineage of this virus and with a major outbreak of Epidemic Polyarthritis among residents of the Pacific Islands. This lineage of RRV continues to circulate throughout Australia and both earlier lineages, which lacked the duplicated element, now are extinct. Multiple copies of several other elements also were observed in this region of the nsP3 gene in all lineages of RRV. Multiple copies of one of these, coding for the amino acid sequence P*P*PR, were detected in the C-terminal region of the nsP3 protein of all alphaviruses except those of African origin. The fixation of duplications and insertions in 3' region of nsP3 genes from all lineages of alphaviruses, suggests they provide some fitness advantage

hSSB1 interacts directly with the MRN complex stimulating its recruitment to DNA double-strand breaks and its endo-nuclease activity

hSSB1 is a recently discovered single-stranded DNA binding protein that is essential for efficient repair of DNA double-strand breaks (DSBs) by the homologous recombination pathway. hSSB1 is required for the efficient recruitment of the MRN complex to sites of DSBs and for the efficient initiation of ATM dependent signalling. Here we explore the interplay between hSSB1 and MRN. We demonstrate that hSSB1 binds directly to NBS1, a component of the MRN complex, in a DNA damage independent manner. Consistent with the direct interaction, we observe that hSSB1 greatly stimulates the endo-nuclease activity of the MRN complex, a process that requires the C-terminal tail of hSSB1. Interestingly, analysis of two point mutations in NBS1, associated with Nijmegen breakage syndrome, revealed weaker binding to hSSB1, suggesting a possible disease mechanism.

hSSB1 rapidly binds at the sites of DNA double-strand breaks and is required for the efficient recruitment of the MRN complex

hSSB1 is a newly discovered single-stranded DNA (ssDNA)-binding protein that is essential for efficient DNA double-strand break signalling through ATM. However, the mechanism by which hSSB1 functions to allow efficient signalling is unknown. Here, we show that hSSB1 is recruited rapidly to sites of double-strand DNA breaks (DSBs) in all interphase cells (G1, S and G2) independently of, CtIP, MDC1 and the MRN complex (Rad50, Mre11, NBS1). However expansion of hSSB1 from the DSB site requires the function of MRN. Strikingly, silencing of hSSB1 prevents foci formation as well as recruitment of MRN to sites of DSBs and leads to a subsequent defect in resection of DSBs as evident by defective RPA and ssDNA generation. Our data suggests that hSSB1 functions upstream of MRN to promote its recruitment at DSBs and is required for efficient resection of DSBs. These findings, together with previous work establish essential roles of hSSB1 in controlling ATM activation and activity, and subsequent DSB resection and homologous recombination (HR).

The role of mother-centered factors influencing the complex social behaviour of breastfeeding : social support and self-efficacy

This research investigated the role of mother-centred issues that influence breastfeeding behaviours. The need for social marketing research for breastfeeding is indicated by the fact that despite evidence of the health benefits to both the infant and mother of longer breastfeeding duration, rates in developed countries have failed to increase in recent decades. Breastfeeding is a complex behaviour that for many women involves barriers that influence their commitment to continue breastfeeding. Structural equation modelling was used on a sample of 405 respondents to an online survey. The analysis revealed that personal social support had a significant impact on breastfeeding self-efficacy, which in turn had a significant impact on breastfeeding behaviour. The findings and implications for both social marketing theory and practice are discussed.