Accurately simulating the production of radiotherapy portal images using non-zero beam angles

In this study, the delivery and portal imaging of one square-field and one conformal radiotherapy treatment was simulated using the Monte Carlo codes BEAMnrc and DOSXYZnrc. The treatment fields were delivered to a humanoid phantom from different angles by a 6 MV photon beam linear accelerator, with an amorphous-silicon electronic portal imaging device (a-Si EPID) used to provide images of the phantom generated by each field. The virtual phantom preparation code CTCombine was used to combine a computed-tomography-derived model of the irradiated phantom with a simple, rectilinear model of the a-Si EPID, at each beam angle used in the treatment. Comparison of the resulting experimental and simulated a-Si EPID images showed good agreement, within \[gamma](3%, 3 mm), indicating that this method may be useful in providing accurate Monte Carlo predictions of clinical a-Si EPID images, for use in the verification of complex radiotherapy treatments.

Development of a high-level gene expression system for the production of bioplastics in sugarcane

Despite various approaches, the production of biodegradable plastics such as polyhydroxybutyrate (PHB) in transgenic plants has met with limited success due largely to low expression levels. Even in the few instances where high levels of protein expression have been reported, the transgenic plants have been stunted indicating PHB is phytotoxic (Poirier 2002). This PhD describes the application of a novel virus-based gene expression technology, termed InPAct („In Plant Activation.), for the production of PHB in tobacco and sugarcane. InPAct is based on the rolling circle replication mechanism by which circular ssDNA viruses replicate and provides a system for controlled, high-level gene expression. Based on these features, InPAct was thought to represent an ideal system to enable the controlled, high-level expression of the three phb genes (phbA, phbB and phbC) required for PHB production in sugarcane at a preferred stage of plant growth. A Tobacco yellow dwarf virus (TbYDV)-based InPAct-phbA vector, as well as linear vectors constitutively expressing phbB and phbC were constructed and different combinations were used to transform tobacco leaf discs. A total of four, eight, three and three phenotypically normal tobacco lines were generated from discs transformed with InPAct-phbA, InPAct-phbA + p1300-TaBV P-phbB/phbC- 35S T, p1300-35S P-phbA-NOS T + p1300-TaBV P-phbB/phbC-35S T and InPAct-GUS, respectively. To determine whether the InPAct cassette could be activated in the presence of the TbYDV Rep, leaf samples from the eight InPActphbA + p1300-TaBV P-phbB/phbC-35S T plants were agroinfiltrated with p1300- TbYDV-Rep/RepA. Three days later, successful activation was indicated by the detection of episomes using both PCR and Southern analysis. Leaf discs from the eight InPAct-phbA + p1300-TaBV P-phbB/phbC-35S T transgenic plant lines were agroinfiltrated with p1300-TbYDV-Rep/RepA and leaf tissue was collected ten days post-infiltration and examined for the presence of PHB granules. Confocal microscopy and TEM revealed the presence of typical PHB granules in five of the eight lines, thus demonstrating the functionality of InPActbased PHB production in tobacco. However, analysis of leaf extracts by HPLC failed to detect the presence of PHB suggesting only very low level expression levels. Subsequent molecular analysis of three lines revealed low levels of correctly processed mRNA from the catalase intron contained within the InPAct cassette and also the presence of cryptic splice sites within the intron. In an attempt to increase expression levels, new InPAct-phb cassettes were generated in which the castorbean catalase intron was replaced with a synthetic intron (syntron). Further, in an attempt to both increase and better control Rep/RepA-mediated activation of InPAct cassettes, Rep/RepA expression was placed under the control of a stably integrated alc switch. Leaf discs from a transgenic tobacco line (Alc ML) containing 35S P-AlcR-AlcA P-Rep/RepA were supertransformed with InPAct-phbAsyn or InPAct-GUSsyn using Agrobacterium and three plants (lines) were regenerated for each construct. Analysis of the RNA processing of the InPAct-phbAsyn cassette revealed highly efficient and correct splicing of the syntron, thus supporting its inclusion within the InPAct system. To determine the efficiency of the alc switch to activate InPAct, leaf material from the three Alc ML + InPAct-phbAsyn lines was either agroinfiltrated with 35S P-Rep/RepA or treated with ethanol. Unexpectedly, episomes were detected not only in the infiltrated and ethanol treated samples, but also in non-treated samples. Subsequent analysis of transgenic Alc ML + InPAct-GUS lines, confirmed that the alc switch was leaky in tissue culture. Although this was shown to be reversible once plants were removed from the tissue culture environment, it made the regeneration of Alc ML + InPAct-phbsyn plant lines extremely difficult, due to unintentional Rep expression and therefore high levels of phb expression and phytotoxic PHB production. Two Alc ML + InPAct-phbAsyn + p1300-TaBV P-phbB/phbC-35S T transgenic lines were able to be regenerated, and these were acclimatised, alcohol-treated and analysed. Although episome formation was detected as late as 21 days post activation, no PHB was detected in the leaves of any plants using either microscopy or HPLC, suggesting the presence of a corrupt InPAct-phbA cassette in both lines. The final component of this thesis involved the application of both the alc switch and the InPAct systems to sugarcane in an attempt to produce PHB. Initial experiments using transgenic Alc ML + InPAct-GUS lines indicated that the alc system was not functional in sugarcane under the conditions tested. The functionality of the InPAct system, independent of the alc gene switch, was subsequently examined by bombarding the 35S Rep/RepA cassette into leaf and immature leaf whorl cells derived from InPAct-GUS transgenic sugarcane plants. No GUS expression was observed in leaf tissue, whereas weak and irregular GUS expression was observed in immature leaf whorl tissue derived from two InPAct- GUS lines and two InPAct-GUS + 35S P-AlcR-AlcA P-GUS lines. The most plausible reason to explain the inconsistent and low levels of GUS expression in leaf whorls is a combination of low numbers of sugarcane cells in the DNA replication-conducive S-phase and the irregular and random nature of sugarcane cells bombarded with Rep/RepA. This study details the first report to develop a TbYDV-based InPAct system under control of the alc switch to produce PHB in tobacco and sugarcane. Despite the inability to detect quantifiable levels of PHB levels in either tobacco or sugarcane, the findings of this study should nevertheless assist in the further development of both the InPAct system and the alc system, particularly for sugarcane and ultimately lead to an ethanol-inducible InPAct gene expression system for the production of bioplastics and other proteins of commercial value in plants.

Non-redundant sequential association rule mining based on closed sequential patterns

In many applications, e.g., bioinformatics, web access traces, system utilisation logs, etc., the data is naturally in the form of sequences. People have taken great interest in analysing the sequential data and finding the inherent characteristics or relationships within the data. Sequential association rule mining is one of the possible methods used to analyse this data. As conventional sequential association rule mining very often generates a huge number of association rules, of which many are redundant, it is desirable to find a solution to get rid of those unnecessary association rules. Because of the complexity and temporal ordered characteristics of sequential data, current research on sequential association rule mining is limited. Although several sequential association rule prediction models using either sequence constraints or temporal constraints have been proposed, none of them considered the redundancy problem in rule mining. The main contribution of this research is to propose a non-redundant association rule mining method based on closed frequent sequences and minimal sequential generators. We also give a definition for the non-redundant sequential rules, which are sequential rules with minimal antecedents but maximal consequents. A new algorithm called CSGM (closed sequential and generator mining) for generating closed sequences and minimal sequential generators is also introduced. A further experiment has been done to compare the performance of generating non-redundant sequential rules and full sequential rules, meanwhile, performance evaluation of our CSGM and other closed sequential pattern mining or generator mining algorithms has also been conducted. We also use generated non-redundant sequential rules for query expansion in order to improve recommendations for infrequently purchased products.

Supplement : Efficient weak second-order stochastic Runge-Kutta methods for non-commutative Stratonvich stochastic differential equations

This paper gives a modification of a class of stochastic Runge–Kutta methods proposed in a paper by Komori (2007). The slight modification can reduce the computational costs of the methods significantly.

Comparison of intraocular pressure measurement between rebound, non-contact and Goldmann applanation tonometry in treated glaucoma patients

Background: To compare the intraocular pressure readings obtained with the iCare rebound tonometer and the 7CR non-contact tonometer with those measured by Goldmann applanation tonometry in treated glaucoma patients. Design: A prospective, cross sectional study was conducted in a private tertiary glaucoma clinic. Participants: 109 (54M:55F) patients including only eyes under medical treatment for glaucoma. Methods: Measurement by Goldmann applanation tonometry, iCare rebound tonometry and 7CR non-contact tonometry. Main Outcome Measures: Intraocular pressure. Results: There were strong correlations between the intraocular pressure measurements obtained with Goldmann and both the rebound and non-contact tonometers (Spearman r values ≥ 0.79, p < 0.001). However, there were small, statistically significant differences between the average readings for each tonometer. For the rebound tonometer, the mean intraocular pressure was slightly higher compared to the Goldmann applanation tonometer in the right eyes (p = 0.02), and similar in the left eyes (p = 0.93) however these differences did not reach statistical significance. The Goldmann correlated measurements from the noncontact tonometer were lower than the average Goldmann reading for both right (p < 0.001) and left (p > 0.01) eyes. The corneal compensated measurements from the non-contact tonometer were significantly higher compared to the other tonometers (p ≤ 0.001). Conclusions: The iCare rebound tonometer and the 7CR non-contact tonometer measure IOP in fundamentally different ways to the Goldmann applanation tonometer. The resulting IOP values vary between the instruments and will need to be considered when comparing clinical versus home acquired measurements.

Understanding the diversity of non-specialised units within Australian property degrees

Building on the recommendations of the Bradley Review (2008), the Australian Federal government intends to promote a higher level of penetration of tertiary qualification across the broader Australian community which is anticipated to result in increased levels of standardisation across university degrees. In the field of property, tertiary academic programs are very closely aligned to the needs of a range of built environment professions and there are well developed synergies between the relevant professional bodies and the educational institutions. The strong nexus between the academic and the professional content is characterised by ongoing industry accreditation which nominates a range of outcomes which the academic programs must maintain across a range of specified metrics. Commonly, the accrediting bodies focus on standard of minimum requirements especially in the area of specialised subject areas where they require property graduates to demonstrate appropriate learning and attitudes. In addition to nominated content fields, in every undergraduate degree program there are also many other subjects which provide a richer experience for the students beyond the merely professional. This study focuses on the nonspecialised knowledge field which varies across the universities offering property degree courses as every university has the freedom to pursue its own policy for these non-specialised units. With universities being sensitive to their role of in the appropriate socialisation of new entrants, first year units have been used as a vehicle to support students’ transition into university education and the final year units seek to support students’ integration into the professional world. Consequentially, many property programs have to squeeze their property-specific units to accommodate more generic units for both first year and final year units and the resulting diversity is a feature of the current range of property degrees across Australia which this research will investigate. The matrix of knowledge fields nominated by the Australian Property Institute for accreditation of degrees accepted for Certified Practising Valuer (CPV) educational requirement and the complementary requirements of the other major accrediting body (RICS) are used to classify and compare similarities and differences across property degrees in the light of the streamlining anticipated from the Bradley Review.

Negative affect-induced food intake in non-dieting women is reward driven and associated with restrained-disinhibited eating subtype

In humans the presence of negative affect is thought to promote food intake, but there is widespread variability. Susceptibility to negative affect-induced eating may depend on trait eating behaviours, notably ‘emotional eating’, ‘restrained eating’ and ‘disinhibited eating’, but the evidence is not consistent. In the present study, 30 non-obese, non-dieting women were given access to palatable food whilst in a state of negative or neutral affect, induced by a validated autobiographical recall technique. As predicted, food intake was higher in the presence of negative affect; however, this effect was moderated by the pattern of eating behaviour traits and enhanced wanting for the test food. Specifically, the High Restraint-High Disinhibition subtype in combination with higher scores on emotional eating and food wanting was able to predict negative-affect intake (adjusted R2 = .61). In the absence of stress, individuals who are both restrained and vulnerable to disinhibited eating are particularly susceptible to negative affect food intake via stimulation of food wanting. Identification of traits that predispose individuals to overconsume and a more detailed understanding of the specific behaviours driving such overconsumption may help to optimise strategies to prevent weight gain.

Bilski v Kappos : The United States Supreme Court delivers mixed views on patenting non-physical inventions and business methods

The United States Supreme Court has handed down a once in a generation patent law decision that will have important ramifications for the patentability of non-physical methods, both internationally and in Australia. In Bilski v Kappos, the Supreme Court considered whether an invention must either be tied to a machine or apparatus, or transform an article into a different state or thing to be patentable. It also considered for the first time whether business methods are patentable subject matter. The decision will be of particular interest to practitioners who followed the litigation in Grant v Commissioner of Patents, a Federal Court decision in which a Brisbane-based inventor was denied a patent over a method of protecting an asset from the claims of creditors.

Transfer of Title by a Non-Owner : Personal Property Securities Act 2009 (Cth) exceptions to the nemo dat quod non habet rule

The fundamental personal property rule – no one can transfer a better title to property than they had – is subject to exceptions in the Sale of Goods legislation, which aim to protect innocent buyers who are deceived by a seller’s apparent physical possession of property. These exceptions cover a limited range of transactions and are restrictive in their operation. Australia now has national legislation - the Personal Property Securities Act 2009 (Cth) - which will apply to many transactions outside the scope of the Sale of Goods Act and which includes rules for sales by non-owners which will provide exceptions to the nemo dat quod non habet rule for many common commercial transactions. This article explores the effect of the Personal Property Securities Act 2009 (Cth) on the Sale of Goods exceptions, explains that the new provisions are so wide that there is little continuing relevance for the Sale of Goods Act exceptions, and indicates where they may still apply.

Non-pharmacological interventions for breathlessness management in patients with lung cancer : A systematic review

The aim is to review the published scientific literature for studies evaluating nonpharmacological interventions for breathlessness management in patients with lung cancer. The following selection criteria were used to systematically search the literature: studies were to be published research or systematic reviews; they were to be published in English and from 1990 to 2007; the targeted populations were adult patients with dyspnoea/breathlessness associated with lung cancer; and the study reported on the outcomes from use of non-pharmacological strategies for breathlessness. This review retrieved five studies that met all inclusion criteria. All the studies reported the benefits of non-pharmacological interventions in improving breathlessness regardless of differences in clinical contexts, components of programmes and methods for delivery. Analysis of the available evidence suggests that tailored instructions delivered by nurses with sufficient training and supervision may have some benefits over other delivery approaches. Based on the results, non-pharmacological interventions are recommended as effective adjunctive strategies in managing breathlessness for patients with lung cancer. In order to refine such interventions, future research should seek to explore the core components of such approaches that are critical to achieving optimal outcomes, the contexts in which the interventions are most effective, and to evaluate the relative benefits of different methods for delivering such interventions.

Comparing the cost-effectiveness of MRSA control strategies between ICU and non-ICU settings

Introduction / objectives Many strategies are used to control MRSA in hospitals. Only a few have been assessed in clinical trials and it is not obvious how findings should be generalised between settings. Uncertainty remains about which strategies represent the most appropriate use of scarce resources. We assess the cost-effectiveness of alternative MRSA screening and infection control strategies in England and Wales and discuss international relevance. Methods Models of MRSA transmission in ICUs and general medical (GM) wards were developed and used to evaluate different screening methods combined with decolonisation or isolation. Strategies were compared in terms of costs and health benefits (quality adjusted life years, QALYs). Different prevalences, proportions of high risk patients and ward sizes were investigated, and probabilistic sensitivity analyses (PSA) conducted. Results Decolonisation strategies were cost-saving in ICUs at a 5% admission prevalence, with admission and weekly PCR screening the most cost-effective (£3,929/QALY). In ICUs, screening and isolation reduced infection rates by ~10%. With admission prevalence ≤5%, targeting screening and isolation to high risk patients was optimal. In GM wards decolonisation and isolation strategies, though able to reduce MRSA infection rates up to ~50%, were not cost-effective. Conclusion The largest reductions in MRSA infection were achieved by screening and decolonisation strategies, and were cost-effective in ICU settings. In comparison, there is limited potential for screening and control strategies to be cost-effective in GM wards due to lower infection and mortality rates.

Natural convection in a triangular enclosure due to non-uniform cooling on top

Natural convection in a triangular enclosure subject to non-uniformly cooling at the inclined surfaces and uniformly heating at the base is investigated numerically. The numerical simulations of the unsteady flows over a range of Rayleigh numbers and aspect ratios are carried out using Finite Volume Method. Since the upper surface is cooled and the bottom surface is heated, the air flow in the enclosure is potentially unstable to Rayleigh Benard instability. It is revealed that the transient flow development in the enclosure can be classified into three distinct stages; an early stage, a transitional stage and a steady stage. It is also found that the flow inside the enclosure strongly depends on the governing parameters, Rayleigh number and aspect ratio. The asymmetric behaviour of the flow about the geometric centre line is discussed in detailed. The heat transfer through the roof and the ceiling as a form of Nusselt number is also reported in this study.

Characterisation of the TaNF-Y family of transcription factors in wheat

Light plays a unique role for plants as it is both a source of energy for growth and a signal for development. Light captured by the pigments in the light harvesting complexes is used to drive the synthesis of the chemical energy required for carbon assimilation. The light perceived by photoreceptors activates effectors, such as transcription factors (TFs), which modulate the expression of light-responsive genes. Recently, it has been speculated that increasing the photosynthetic rate could further improve the yield potential of three carbon (C3) crops such as wheat. However, little is currently known about the transcriptional regulation of photosynthesis genes, particularly in crop species. Nuclear factor Y (NF-Y) TF is a functionally diverse regulator of growth and development in the model plant species, with demonstrated roles in embryo development, stress response, flowering time and chloroplast biogenesis. Furthermore, a light-responsive NF-Y binding site (CCAAT-box) is present in the promoter of a spinach photosynthesis gene. As photosynthesis genes are co-regulated by light and co-regulated genes typically have similar regulatory elements in their promoters, it seems likely that other photosynthesis genes would also have light-responsive CCAAT-boxes. This provided the impetus to investigate the NF-Y TF in bread wheat. This thesis is focussed on wheat NF-Y members that have roles in light-mediated gene regulation with an emphasis on their involvement in the regulation of photosynthesis genes. NF-Y is a heterotrimeric complex, comprised of the three subunits NF-YA, NF-YB and NF-YC. Unlike the mammalian and yeast counterparts, each of the three subunits is encoded by multiple genes in Arabidopsis. The initial step taken in this study was the identification of the wheat NF-Y family (Chapter 3). A search of the current wheat nucleotide sequence databases identified 37 NF-Y genes (10 NF-YA, 11 NF-YB, 14 NF-YC & 2 Dr1). Phylogenetic analysis revealed that each of the three wheat NF-Y (TaNF-Y) subunit families could be divided into 4-5 clades based on their conserved core regions. Outside of the core regions, eleven motifs were identified to be conserved between Arabidopsis, rice and wheat NF-Y subunit members. The expression profiles of TaNF-Y genes were constructed using quantitative real-time polymerase chain reaction (RT-PCR). Some TaNF-Y subunit members had little variation in their transcript levels among the organs, while others displayed organ-predominant expression profiles, including those expressed mainly in the photosynthetic organs. To investigate their potential role in light-mediated gene regulation, the light responsiveness of the TaNF-Y genes were examined (Chapters 4 and 5). Two TaNF-YB and five TaNF-YC members were markedly upregulated by light in both the wheat leaves and seedling shoots. To identify the potential target genes of the light-upregulated NF-Y subunit members, a gene expression correlation analysis was conducted using publically available Affymetrix Wheat Genome Array datasets. This analysis revealed that the transcript expression levels of TaNF-YB3 and TaNF-YC11 were significantly correlated with those of photosynthesis genes. These correlated express profiles were also observed in the quantitative RT-PCR dataset from wheat plants grown under light and dark conditions. Sequence analysis of the promoters of these wheat photosynthesis genes revealed that they were enriched with potential NF-Y binding sites (CCAAT-box). The potential role of TaNF-YB3 in the regulation of photosynthetic genes was further investigated using a transgenic approach (Chapter 5). Transgenic wheat lines constitutively expressing TaNF-YB3 were found to have significantly increased expression levels of photosynthesis genes, including those encoding light harvesting chlorophyll a/b-binding proteins, photosystem I reaction centre subunits, a chloroplast ATP synthase subunit and glutamyl-tRNA reductase (GluTR). GluTR is a rate-limiting enzyme in the chlorophyll biosynthesis pathway. In association with the increased expression of the photosynthesis genes, the transgenic lines had a higher leaf chlorophyll content, increased photosynthetic rate and had a more rapid early growth rate compared to the wild-type wheat. In addition to its role in the regulation of photosynthesis genes, TaNF-YB3 overexpression lines flower on average 2-days earlier than the wild-type (Chapter 6). Quantitative RT-PCR analysis showed that there was a 13-fold increase in the expression level of the floral integrator, TaFT. The transcript levels of other downstream genes (TaFT2 and TaVRN1) were also increased in the transgenic lines. Furthermore, the transcript levels of TaNF-YB3 were significantly correlated with those of constans (CO), constans-like (COL) and timing of chlorophyll a/b-binding (CAB) expression 1 [TOC1; (CCT)] domain-containing proteins known to be involved in the regulation of flowering time. To summarise the key findings of this study, 37 NF-Y genes were identified in the crop species wheat. An in depth analysis of TaNF-Y gene expression profiles revealed that the potential role of some light-upregulated members was in the regulation of photosynthetic genes. The involvement of TaNF-YB3 in the regulation of photosynthesis genes was supported by data obtained from transgenic wheat lines with increased constitutive expression of TaNF-YB3. The overexpression of TaNF-YB3 in the transgenic lines revealed this NF-YB member is also involved in the fine-tuning of flowering time. These data suggest that the NF-Y TF plays an important role in light-mediated gene regulation in wheat.

Management characteristics and the decision to internationalize : Exploration of exporters vs. non-exporters within the Chilean wine industry

The objective of this exploratory study was to identify the key factors that enhance and inhibit the export activities of wineries and identify differences between exporters and non-exporters. Based on data collected from Chilean wineries, the findings of this study suggest that the major constraints for non-exporters are the lack of financial resources, limited quantities of stocks for market expansion, management’s lack of knowledge and experience, and the high cost of travelling and participating in trade shows. In addition, the main international markets for Chilean wineries were not psychically close markets as has been found for Australian or other wine industries. For domestic market oriented wineries cellar door sales were an important source of revenue. Finally, the results show that managers have educational levels and international experience exceeding those of other comparable New World wineries.