Spatial analysis of biomineralization associated gene expression from the mantle organ of the pearl oyster Pinctada maxima

Background: Biomineralization is a process encompassing all mineral containing tissues produced within an organism. One of the most dynamic examples of this process is the formation of the mollusk shell, comprising a variety of crystal phases and microstructures. The organic component incorporated within the shell is said to dictate this architecture. However general understanding of how this process is achieved remains ambiguous. The mantle is a conserved organ involved in shell formation throughout molluscs. Specifically the mantle is thought to be responsible for secreting the protein component of the shell. This study employs molecular approaches to determine the spatial expression of genes within the mantle tissue to further the elucidation of the shell biomineralization. Results: A microarray platform was custom generated (PmaxArray 1.0) from the pearl oyster Pinctada maxima. PmaxArray 1.0 consists of 4992 expressed sequence tags (ESTs) originating from mantle tissue. This microarray was used to analyze the spatial expression of ESTs throughout the mantle organ. The mantle was dissected into five discrete regions and analyzed for differential gene expression with PmaxArray 1.0. Over 2000 ESTs were determined to be differentially expressed among the tissue sections, identifying five major expression regions. In situ hybridization validated and further localized the expression for a subset of these ESTs. Comparative sequence similarity analysis of these ESTs revealed a number of the transcripts were novel while others showed significant sequence similarities to previously characterized shell related genes.

Numerical analysis for a variable-order nonlinear cable equation

In this paper, a variable-order nonlinear cable equation is considered. A numerical method with first-order temporal accuracy and fourth-order spatial accuracy is proposed. The convergence and stability of the numerical method are analyzed by Fourier analysis. We also propose an improved numerical method with second-order temporal accuracy and fourth-order spatial accuracy. Finally, the results of a numerical example support the theoretical analysis.

Contribution of take-out food consumption to socioeconomic differences in fruit and vegetable intake : a mediation analysis

Lower fruit and vegetable intake among socioeconomically disadvantaged groups has been well documented, and may be a consequence of a higher consumption of take-out foods. This study examined whether, and to what extent, take-out food consumption mediated (explained) the association between socioeconomic position and fruit and vegetable intake. A cross-sectional postal survey was conducted among 1500 randomly selected adults aged 25–64 years in Brisbane, Australia in 2009 (response rate = 63.7%, N = 903). A food frequency questionnaire assessed usual daily servings of fruits and vegetables (0 to 6), overall take-out consumption (times/week) and the consumption of 22 specific take-out items (never to ≥once/day). These specific take-out items were grouped into “less healthy” and “healthy” choices and indices were created for each type of choice (0 to 100). Socioeconomic position was ascertained by education. The analyses were performed using linear regression, and a bootstrap re-sampling approach estimated the statistical significance of the mediated effects. Mean daily serves of fruits and vegetables was 1.89 (SD 1.05) and 2.47 (SD 1.12) respectively. The least educated group were more likely to consume fewer serves of fruit (B= –0.39, p<0.001) and vegetables (B= –0.43, p<0.001) compared with the highest educated. The consumption of “less healthy” take-out food partly explained (mediated) education differences in fruit and vegetable intake; however, no mediating effects were observed for overall and “healthy” take-out consumption. Regular consumption of “less healthy” take-out items may contribute to socioeconomic differences in fruit and vegetable intake, possibly by displacing these foods.

Why evolutionary realism underpins evolutionary economic analysis and theory

This paper offers a reply to Jochen Runde's critical appraisal of the ontological framework underpinning Dopfer and Potts's (2008) General Theory of Economic Evolution. We argue that Runde's comprehensive critique contains several of what we perceive to be misunderstandings in relation to the key concepts of ‘generic’ and ‘meso’ that we seek here to unpack and redress.

Vibrational spectroscopic analysis of the mineral crandallite CaAl3(PO4)2(OH)5•(H2O) from the Jenolan Caves, Australia

The mineral crandallite CaAl3(PO4)2(OH)5•(H2O) has been identified in deposits found in the Jenolan Caves, New South Wales, Australia by using a combination of X-ray diffraction and Raman spectroscopic techniques. A comparison is made between the vibrational spectra of crandallite found in the Jenolan Caves and a standard crandallite. Raman and infrared bands are assigned to PO43- and HPO42- stretching and bending modes. The predominant features are the internal vibrations of the PO43 and HPO42- groups. A mechanism for the formation of crandallite is presented and the conditions for the formation are elucidated.

Large scale participatory acoustic sensor data analysis : tools and reputation models to enhance effectiveness

Acoustic sensors play an important role in augmenting the traditional biodiversity monitoring activities carried out by ecologists and conservation biologists. With this ability however comes the burden of analysing large volumes of complex acoustic data. Given the complexity of acoustic sensor data, fully automated analysis for a wide range of species is still a significant challenge. This research investigates the use of citizen scientists to analyse large volumes of environmental acoustic data in order to identify bird species. Specifically, it investigates ways in which the efficiency of a user can be improved through the use of species identification tools and the use of reputation models to predict the accuracy of users with unidentified skill levels. Initial experimental results are reported.

Stochastic analysis of the VEGF receptor response curve

Recently, an analysis of the response curve of the vascular endothelial growth factor (VEGF) receptor and its application to cancer therapy was described in [T. Alarcón, and K. Page, J. R. Soc. Lond. Interface 4, 283–304 (2007)]. The analysis is significantly extended here by demonstrating that an alternative computational strategy, namely the Krylov FSP algorithm for the direct solution of the chemical master equation, is feasible for the study of the receptor model. The new method allows us to further investigate the hypothesis of symmetry in the stochastic fluctuations of the response. Also, by augmenting the original model with a single reversible reaction we formulate a plausible mechanism capable of realizing a bimodal response, which is reported experimentally but which is not exhibited by the original model. The significance of these findings for mechanisms of tumour resistance to antiangiogenic therapy is discussed.

Assessing students in senior science: an analysis of questions in contextualised chemistry exams

This study explores the development of a coding system for analysing test questions in two context-based chemistry exams. We describe our unique analytical procedures before contrasting the data from both tests. Our findings indicate that when a new curriculum is developed such as a context-based curriculum, teachers are required to combine the previously separate domains of context and concept to develop contextualised assessment. We argue that constructing contextualised assessment items requires teachers to view concepts and context as interconnected rather than as separate entities that may polarise scientific endeavour. Implications for practice, curriculum and assessment-development in context-based courses are proposed.

Health Librarianship Workforce and Education : Research to plan the future. Final Report.

In late 2009, Health Libraries Australia (HLA) received a small grant to undertake a national research project to determine the future requirements for health librarians in the workforce in Australia and develop a structured, modular education framework (post-graduate qualification and continuing professional development structure) to meet these requirements. The main objective was to consider the education and professional development framework that would ensure that health librarians have a clearly defined scope of practice and the specific competency based knowledge and skills that enable them to contribute to the design and delivery of high quality health services in this country. The final report presents a detailed discussion of the changing Australian healthcare environment and the resulting impact on the health library sector, as well as an overview of international trends in health libraries and the implications for Australian health librarianship education. The research methodology is outlined, followed by an analysis of the findings from the two surveys with health librarians and health library managers and the semi-structured interviews conducted with employers. The Medical Library Association (MLA) in the United States had developed a policy document detailing the competencies required by health librarians. It was found that the MLA competencies represented an accepted professional framework of skills which could be used objectively in the survey instrument to measure the areas of professional knowledge and responsibilities that were relevant in the current workplace, and to identify how these requirements might change in the next three to five years. The research results underscore the imperative for health librarians to engage in regular, relevant professional development activities that will enable them to stay abreast with the rapid contextual changes impacting on their practice. In order to be accepted as key members of the multi-disciplinary health professional team, it is strongly believed that health librarians should commit to establishing the mechanisms for specialist certification maintained through compulsory CPD in an ongoing three-year cycle of revalidation. This development would align ALIA and health librarians with other health sector professional associations which are responsible for the self regulation of entry to and continuation in their profession.

Aerial image analysis using spiking neural networks with application to power line corridor monitoring

Trees, shrubs and other vegetation are of continued importance to the environment and our daily life. They provide shade around our roads and houses, offer a habitat for birds and wildlife, and absorb air pollutants. However, vegetation touching power lines is a risk to public safety and the environment, and one of the main causes of power supply problems. Vegetation management, which includes tree trimming and vegetation control, is a significant cost component of the maintenance of electrical infrastructure. For example, Ergon Energy, the Australia’s largest geographic footprint energy distributor, currently spends over $80 million a year inspecting and managing vegetation that encroach on power line assets. Currently, most vegetation management programs for distribution systems are calendar-based ground patrol. However, calendar-based inspection by linesman is labour-intensive, time consuming and expensive. It also results in some zones being trimmed more frequently than needed and others not cut often enough. Moreover, it’s seldom practicable to measure all the plants around power line corridors by field methods. Remote sensing data captured from airborne sensors has great potential in assisting vegetation management in power line corridors. This thesis presented a comprehensive study on using spiking neural networks in a specific image analysis application: power line corridor monitoring. Theoretically, the thesis focuses on a biologically inspired spiking cortical model: pulse coupled neural network (PCNN). The original PCNN model was simplified in order to better analyze the pulse dynamics and control the performance. Some new and effective algorithms were developed based on the proposed spiking cortical model for object detection, image segmentation and invariant feature extraction. The developed algorithms were evaluated in a number of experiments using real image data collected from our flight trails. The experimental results demonstrated the effectiveness and advantages of spiking neural networks in image processing tasks. Operationally, the knowledge gained from this research project offers a good reference to our industry partner (i.e. Ergon Energy) and other energy utilities who wants to improve their vegetation management activities. The novel approaches described in this thesis showed the potential of using the cutting edge sensor technologies and intelligent computing techniques in improve power line corridor monitoring. The lessons learnt from this project are also expected to increase the confidence of energy companies to move from traditional vegetation management strategy to a more automated, accurate and cost-effective solution using aerial remote sensing techniques.

Arterial traffic congestion analysis using Bluetooth duration data

The aim of this study is to assess the potential use of Bluetooth data for traffic monitoring of arterial road networks. Bluetooth data provides the direct measurement of travel time between pairs of scanners, and intensive research has been reported on this topic. Bluetooth data includes “Duration” data, which represents the time spent by Bluetooth devices to pass through the detection range of Bluetooth scanners. If the scanners are located at signalised intersections, this Duration can be related to intersection performance, and hence represents valuable information for traffic monitoring. However the use of Duration has been ignored in previous analyses. In this study, the Duration data as well as travel time data is analysed to capture the traffic condition of a main arterial route in Brisbane. The data consists of one week of Bluetooth data provided by Brisbane City Council. As well, micro simulation analysis is conducted to further investigate the properties of Duration. The results reveal characteristics of Duration, and address future research needs to utilise this valuable data source.

Analysis of rural activity spaces and transport disadvantage using a multi-method approach

Current knowledge about the relationship between transport disadvantage and activity space size is limited to urban areas, and as a result, very little is known about this link in a rural context. In addition, although research has identified transport disadvantaged groups based on their size of activity space, these studies have, however, not empirically explained such differences and the result is often a poor identification of the problems facing disadvantaged groups. Research has shown that transport disadvantage varies over time. The static nature of analysis using the activity space concept in previous research studies has lacked the ability to identify transport disadvantage in time. Activity space is a dynamic concept; and therefore possesses a great potential in capturing temporal variations in behaviour and access opportunities. This research derives measures of the size and fullness of activity spaces for 157 individuals for weekdays, weekends, and for a week using weekly activity-travel diary data from three case study areas located in rural Northern Ireland. Four focus groups were also conducted in order to triangulate quantitative findings and to explain the differences between different socio-spatial groups. The findings of this research show that despite having a smaller sized activity space, individuals were not disadvantaged because they were able to access their required activities locally. Car-ownership was found to be an important life line in rural areas. Temporal disaggregation of the data reveals that this is true only on weekends due to a lack of public transport services. In addition, despite activity spaces being at a similar size, the fullness of activity spaces of low-income individuals was found to be significantly lower compared to their high-income counterparts. Focus group data shows that financial constraint, poor connections both between public transport services and between transport routes and opportunities forced individuals to participate in activities located along the main transport corridors.