Evolving noisy oscillatory dynamics in genetic regulatory networks

We introduce a genetic programming (GP) approach for evolving genetic networks that demonstrate desired dynamics when simulated as a discrete stochastic process. Our representation of genetic networks is based on a biochemical reaction model including key elements such as transcription, translation and post-translational modifications. The stochastic, reaction-based GP system is similar but not identical with algorithmic chemistries. We evolved genetic networks with noisy oscillatory dynamics. The results show the practicality of evolving particular dynamics in gene regulatory networks when modelled with intrinsic noise.

Tracking the Brisbane residential property market : Post GFC

Prior to the GFC, Brisbane and Perth were experiencing the highest increases in median residential house prices, compared to the other major Australian cities, due to strong demand for both owner occupied and investment residential property. In both these cities, a major driver of this demand and subsequent increases in residential property prices was the strong resources sector. With the onset of the GFC in 2008, the resources and construction sectors in Queensland contracted significantly and this had both direct and indirect impacts on the Brisbane residential property market. However, this impact was not consistent across Brisbane residential property sectors. The affect on houses and units differed, as did the impact based on geographic location and suburb value. This paper tracks Brisbane residential property sales listings, sales and returns over the period February 2009 to July 2010 and provides an analysis of the residential market for 24 Brisbane suburbs. These suburbs cover main residential areas of Brisbane and are based on an equal number of low, medium and high socioeconomic areas of Brisbane. This assessment of socio-economic status for the suburbs is based on both median household income and median house price. The analysis will cover both free standing residential property and residential units/townhouses/villas. The results will show how each of these residential property sub markets have performed following the GFC.

Novel numerical methods for time-space fractional reaction diffusion equations in two dimensions

We consider time-space fractional reaction diffusion equations in two dimensions. This equation is obtained from the standard reaction diffusion equation by replacing the first order time derivative with the Caputo fractional derivative, and the second order space derivatives with the fractional Laplacian. Using the matrix transfer technique proposed by Ilic, Liu, Turner and Anh [Fract. Calc. Appl. Anal., 9:333--349, 2006] and the numerical solution strategy used by Yang, Turner, Liu, and Ilic [SIAM J. Scientific Computing, 33:1159--1180, 2011], the solution of the time-space fractional reaction diffusion equations in two dimensions can be written in terms of a matrix function vector product $f(A)b$ at each time step, where $A$ is an approximate matrix representation of the standard Laplacian. We use the finite volume method over unstructured triangular meshes to generate the matrix $A$, which is therefore non-symmetric. However, the standard Lanczos method for approximating $f(A)b$ requires that $A$ is symmetric. We propose a simple and novel transformation in which the standard Lanczos method is still applicable to find $f(A)b$, despite the loss of symmetry. Numerical results are presented to verify the accuracy and efficiency of our newly proposed numerical solution strategy.

Globally networked public spheres? The Australian media reaction to WikiLeaks

The global release of 250,000 US Embassy diplomatic cables to selected media sites worldwide through the WikiLeaks website, was arguably the major global media event of 2010. As well as the implications of the content of the cables for international politics and diplomacy, the actions of WikiLeaks and its controversial editor-in-chief, the Australian Julian Assange, bring together a range of arguments about how the media, news and journalism are being transformed in the 21st century. This paper will focus on the reactions of Australian online news media sites to the release of the diplomatic cables by WikiLeaks, including both the online sites of established news outlets such as The Australian, Sydney Morning Herald and The Age, the ABC’s The Drum site, and online-only sites such as Crikey, New Matilda and On Line Opinion. The study focuses on opinion and commentary rather than straight news reportage, and analysis is framed around three issues: WikiLeaks and international diplomacy; implications of WikiLeaks for journalism; and WikiLeaks and democracy, including debates about the organisation and the ethics of its own practice. It also whether a “WikiLeaks Effect” has wider implications for how journalism is conducted in the future, particularly the method of ‘redaction’ of large amounts of computational data.

Investigation of phenol degradation : True reaction kinetics on fixed film titanium dioxide photocatalyst

This study of photocatalytic oxidation of phenol over titanium dioxide films presents a method for the evaluation of true reaction kinetics. A flat plate reactor was designed for the specific purpose of investigating the influence of various reaction parameters, specifically photocatalytic film thickness, solution flow rate (1–8 l min−1), phenol concentration (20, 40 and 80 ppm), and irradiation intensity (70.6, 57.9, 37.1and 20.4 W m−2), in order to further understand their impact on the reaction kinetics. Special attention was given to the mass transfer phenomena and the influence of film thickness. The kinetics of phenol degradation were investigated with different irradiation levels and initial pollutant concentration. Photocatalytic degradation experiments were performed to evaluate the influence of mass transfer on the reaction and, in addition, the benzoic acid method was applied for the evaluation of mass transfer coefficient. For this study the reactor was modelled as a batch-recycle reactor. A system of equations that accounts for irradiation, mass transfer and reaction rate was developed to describe the photocatalytic process, to fit the experimental data and to obtain kinetic parameters. The rate of phenol photocatalytic oxidation was described by a Langmuir–Hinshelwood type law that included competitive adsorption and degradation of phenol and its by-products. The by-products were modelled through their additive effect on the solution total organic carbon.

An assessment of development funding for new housing post GFC in Queensland, Australia

Purpose: The purpose of this paper is to identify changes in bank lending criteria due to the GFC and to explore the associated impacts on new housing supply in Queensland, Australia. Design/methodology/approach: This research involves a survey of each of Australia’s big four banks, as well as two prominent arrangers of development finance. Data on key lending criteria was collected: Pre GFC, during the GFC, and GFC recovery stage. Findings: The GFC has resulted in a retraction of funds available for residential development. The few institutions lending are filtering out only the best credit risks by way of constrictive loan covenants including: low loan to value ratios, high cash equity requirements, regional “no go” zones, and demonstrated borrower track record. The ability of developers to proceed with new housing developments is being constrained by their inability to obtain sufficient finance. Research limitations/implications: This research uses survey data, together with an understanding of the project finance process to extrapolate impacts on the residential development industry across Queensland. No regional or sub-market analysis is included. Future research will include subsequent surveys to track any loosening of credit policies over time and sub-market sector analysis. Practical implications: The inability to obtain project finance is identified as a key constraint to new housing supply. This research will inform policy makers and provide important quantitative evidence of the importance of availability of development finance in the housing supply chain. Social implications: Queensland is facing a supply shortfall, which if not corrected, may lead to upward pressure on house prices and falling housing affordability. Originality/value: There is very little academic research on development funding. This research is unique in linking bank lending criteria to new housing supply and demonstrating the impact on the development industry.

Post-operative CT assessment of interbody fusion two years after thoracoscopic scoliosis surgery

The relationship between radiologic union and clinical outcome in thoracoscopic scoliosis surgery is not clear, as apparent non-union of a spinal fusion does not always correspond to a poor clinical result. The aim of this study was to evaluate CT fusion rates 24 months after thoracoscopic anterior scoliosis surgery, and to explore the relationship between fusion scores and; (i) rod diameter, (ii) graft type, (iii) fusion level, (iv) occurrence of post-operative implant failure, and (v) lateral position of the fusion mass in the intervertebral disc space. We propose that moderate fusion scores on the Sucato scale secure successful clinical outcomes in thoracoscopic scoliosis surgery.

Detection of bacteriophage and respiratory viruses in droplets

Influenza is a widespread disease occurring in seasonal epidemics, and each year is responsible for up to 500,000 deaths worldwide. Influenza can develop into strains which cause severe symptoms and high mortality rates, and could potentially reach pandemic status if the virus’ properties allow easy transmission. Influenza is transmissible via contact with the virus, either directly (infected people) or indirectly (contaminated objects); via reception of large droplets over short distances (one metre or less); or through inhalation of aerosols containing the virus expelled by infected individuals during respiratory activities, that can remain suspended in the air and travel distances of more than one metre (the aerosol route). Aerosol transmission of viruses involves three stages: production of the droplets containing viruses; transport of the droplets and ability of a virus to remain intact and infectious; and reception of the droplets (via inhalation). Our understanding of the transmission of influenza viruses via the aerosol route is poor, and thus our ability to prevent a widespread outbreak is limited. This study explored the fate of viruses in droplets by investigating the effects of some physical factors on the recovery of both a bacteriophage model and influenza virus. Experiments simulating respiratory droplets were carried out using different types of droplets, generated from a commonly used water-like matrix, and also from an ‘artificial mucous’ matrix which was used to more closely resemble respiratory fluids. To detect viruses in droplets, we used the traditional plaque assay techniques, and also a sensitive, quantitative PCR assay specifically developed for this study. Our results showed that the artificial mucous suspension enhanced the recovery of infectious bacteriophage. We were able to report detection limits of infectious bacteriophage (no bacteriophage was detected by the plaque assay when aerosolised from a suspension of 103 PFU/mL, for three of the four droplet types tested), and that bacteriophage could remain infectious in suspended droplets for up to 20 minutes. We also showed that the nested real-time PCR assay was able to detect the presence of bacteriophage RNA where the plaque assay could not detect any intact particles. Finally, when applying knowledge from the bacteriophage experiments, we reported the quantitative recoveries of influenza viruses in droplets, which were more consistent and stable than we had anticipated. Influenza viruses can be detected up to 20 minutes (after aerosolisation) in suspended aerosols and possibly beyond. It also was detectable from nebulising suspensions with relatively low concentrations of viruses.

Post-operative CT assessment of interbody fusion two years after thoracoscopic scoliosis surgery

The relationship between radiologic union and clinical outcome in thoracoscopic scoliosis surgery is not clear, as apparent non-union of a spinal fusion does not always correspond to a poor clinical result. The aim of this study was to evaluate CT fusion rates 2yrs after thoracoscopic surgery, and to explore the relationship between fusion scores and rod diameter, graft type, fusion level, implant failure, and lateral position in the disc space. This study suggests that moderate fusion scores secure successful clinical outcomes in thoracoscopic scoliosis surgery.

Identification of early-stage colorectal cancer patients at risk of relapse post-resection by immunobead reverse transcription-PCR analysis of peritoneal lavage fluid for malignant cells

Purpose: Colorectal cancer patients diagnosed with stage I or II disease are not routinely offered adjuvant chemotherapy following resection of the primary tumor. However, up to 10% of stage I and 30% of stage II patients relapse within 5 years of surgery from recurrent or metastatic disease. The aim of this study was to determine if tumor-associated markers could detect disseminated malignant cells and so identify a subgroup of patients with early-stage colorectal cancer that were at risk of relapse. Experimental Design: We recruited consecutive patients undergoing curative resection for early-stage colorectal cancer. Immunobead reverse transcription-PCR of five tumor-associated markers (carcinoembryonic antigen, laminin γ2, ephrin B4, matrilysin, and cytokeratin 20) was used to detect the presence of colon tumor cells in peripheral blood and within the peritoneal cavity of colon cancer patients perioperatively. Clinicopathologic variables were tested for their effect on survival outcomes in univariate analyses using the Kaplan-Meier method. A multivariate Cox proportional hazards regression analysis was done to determine whether detection of tumor cells was an independent prognostic marker for disease relapse. Results: Overall, 41 of 125 (32.8%) early-stage patients were positive for disseminated tumor cells. Patients who were marker positive for disseminated cells in post-resection lavage samples showed a significantly poorer prognosis (hazard ratio, 6.2; 95% confidence interval, 1.9-19.6; P = 0.002), and this was independent of other risk factors. Conclusion: The markers used in this study identified a subgroup of early-stage patients at increased risk of relapse post-resection for primary colorectal cancer. This method may be considered as a new diagnostic tool to improve the staging and management of colorectal cancer. © 2006 American Association for Cancer Research.

The effect of housing characteristics and occupant activities on the respiratory health of women and children in Lao PDR

The paper presents the results of a study conducted into the relationship between dwelling characteristics and occupant activities with the respiratory health of resident women and children in Lao People’s Democratic Republic (PDR). Lao is one of the least developed countries in south-east Asia with poor life expectancies and mortality rates. The study, commissioned by the World Health Organisation, included questionnaires delivered to residents of 356 dwellings in nine districts in Lao PDR over a five month period (December 2005-April 2006), with the aim of identifying the association between respiratory health and indoor air pollution, in particular exposures related to indoor biomass burning. Adjusted odds ratios were calculated for each health outcome separately using binary logistic regression. After adjusting for age, a wide range of symptoms of respiratory illness in women and children aged 1-4 years were positively associated with a range of indoor exposures related to indoor cooking, including exposure to a fire and location of the cooking place. Among women, “dust always inside the house” and smoking were also identified as strong risk factors for respiratory illness. Other strong risk factors for children, after adjusting for age and gender, included dust and drying clothes inside. This analysis confirms the role of indoor air pollution in the burden of disease among women and children in Lao PDR.

Governing a copyright culture in post-WTO China : copyright in the film and music industries, 2001 - 2005

In 2001 China amended its copyright law in accordance with the requirements of the Agreement on Trade Related Aspects of Intellectual Property (TRIPS). This thesis explores the impact of copyright reform on China’s domestic film and music industries. Through extensive interviews with film and music industry workers – directors, producers, executives, judges, lawyers and musicians – it investigates the role of copyright in film and music’s shift from state driven to commercially focussed. The construction and negotiation of a new ‘copyright culture’ in China is examined through the lens of Yurchak’s (1999) concept of ‘entrepreneurial governmentality.’ Administrative structures put in place prior to China’s economic reform are no longer capable of controlling film and music production and consumption and new approaches to managing it are becoming more important. High levels of unauthorised distribution are forcing these industries to adapt their business models so that they can function in a system with weak copyright protection. Legal, economic and political changes have resulted in the emergence of an ‘entrepreneurial governmentality’ among film and music industry professionals. This commercially focussed group is, in turn, increasing pressure on the state to expand the space in which it can function and support efforts to strengthen the copyright system that allows it to exist. It is suggested that the construction and negotiation of a new ‘copyright culture’ is now taking place. This thesis describes the current situation in the film and music industries. It examines the tension between the theoretical possibilities created by copyright law, and the practical challenges of operating in China. It observes innovative business models being applied by film and music businesses in China. It discusses the impact of traditional attitudes to copying and also examines the role that open licensing models might play in helping limit the negative effects of copyright protection on public access to content and in raising levels of education about copyright among key groups within the community.