Parallel implementation of stochastic simulation for large scale cellular processes

Experimental and theoretical studies have shown the importance of stochastic processes in genetic regulatory networks and cellular processes. Cellular networks and genetic circuits often involve small numbers of key proteins such as transcriptional factors and signaling proteins. In recent years stochastic models have been used successfully for studying noise in biological pathways, and stochastic modelling of biological systems has become a very important research field in computational biology. One of the challenge problems in this field is the reduction of the huge computing time in stochastic simulations. Based on the system of the mitogen-activated protein kinase cascade that is activated by epidermal growth factor, this work give a parallel implementation by using OpenMP and parallelism across the simulation. Special attention is paid to the independence of the generated random numbers in parallel computing, that is a key criterion for the success of stochastic simulations. Numerical results indicate that parallel computers can be used as an efficient tool for simulating the dynamics of large-scale genetic regulatory networks and cellular processes

Entry into Valhalla : contextualising the learning of legal ethics through the use of Second Life machinima

An ability to recognise and resolve ethical dilemmas was identified by the Australian Law Reform Commission as one of the ten fundamental lawyering skills. While the ‘Priestley 11’ list of areas of law required to qualify for legal practice includes ethics and professional responsibility, the commitment to ethics learning in Australian law schools has been far from uniform. The obligation imposed by the Priestley 11 is frequently discharged by a traditional teaching and learning approach involving lectures and/or tutorials and focusing on the content of the formal rules of professional responsibility. However, the effectiveness of such an approach is open to question. Instead, a practical rather than a theoretical approach to the teaching of legal ethics is required. Effective final-year student learning of ethics may be achieved by an approach which engages students, enabling them to appreciate the relevance of what they are learning to the real world and facilitating their transition from study to their working lives. Entry into Valhalla comprises a suite of modules featuring ‘machinima’ (computer-generated imagery) created using the Second Life virtual environment to contextualise otherwise abstract concepts. It provides an engaging learning environment which enables students to obtain an appreciation of ethical responsibility in a real-world context and facilitates understanding and problem-solving ability.

Understanding the legal implications of data sharing, access and reuse in the Australian research landscape

Researchers are increasingly involved in data-intensive research projects that cut across geographic and disciplinary borders. Quality research now often involves virtual communities of researchers participating in large-scale web-based collaborations, opening their earlystage research to the research community in order to encourage broader participation and accelerate discoveries. The result of such large-scale collaborations has been the production of ever-increasing amounts of data. In short, we are in the midst of a data deluge. Accompanying these developments has been a growing recognition that if the benefits of enhanced access to research are to be realised, it will be necessary to develop the systems and services that enable data to be managed and secured. It has also become apparent that to achieve seamless access to data it is necessary not only to adopt appropriate technical standards, practices and architecture, but also to develop legal frameworks that facilitate access to and use of research data. This chapter provides an overview of the current research landscape in Australia as it relates to the collection, management and sharing of research data. The chapter then explains the Australian legal regimes relevant to data, including copyright, patent, privacy, confidentiality and contract law. Finally, this chapter proposes the infrastructure elements that are required for the proper management of legal interests, ownership rights and rights to access and use data collected or generated by research projects.

Perspectives on practical experiences in professional education : an editorial and introduction

How important are the practical experiences through which our neophyte professionals are prepared for the real world of work? P. E. P. E. (Practical Experiences in Professional Education) Inc has generated this book with, not only, the aim of disseminating knowledge through networks within the professional silos of distinctive disciplines but to generate a space and platform for generic concepts and practices that can be examined and incorporated across many disciplines. Mentoring, ethics and transitioning into the profession are explored in the book but each chapter illustrates how PEPE Inc has within its community a culture of engagement, experimentation and deep thinking that connects all aspects of learning in the field. Ken Zeichner’s research clearly shows that field experiences are important occasions for professional learning rather than merely times for pre-service candidates to demonstrate or apply things previously learned. Susan Groundwater-Smith acknowledges PEPE Inc on being a leader in supporting the evolution of a developmental practicum curriculum in the initial education of professionals, mainly in the field of education, but also with respect to the preparation of health and allied professionals, those preparing to become social workers and even in professional practices such as engineering and architecture.

Understanding the phenomenon of IS success in China through the lens of the IS-Impact model

This study is conducted within the IS-Impact Research Track at Queensland University of Technology (QUT). The goal of the IS-Impact Track is, “to develop the most widely employed model for benchmarking information systems in organizations for the joint benefit of both research and practice” (Gable et al, 2006). IS-Impact is defined as “a measure at a point in time, of the stream of net benefits from the IS, to date and anticipated, as perceived by all key-user-groups” (Gable Sedera and Chan, 2008). Track efforts have yielded the bicameral IS-Impact measurement model; the “impact” half includes Organizational-Impact and Individual-Impact dimensions; the “quality” half includes System-Quality and Information-Quality dimensions. The IS-Impact model, by design, is intended to be robust, simple and generalizable, to yield results that are comparable across time, stakeholders, different systems and system contexts. The model and measurement approach employ perceptual measures and an instrument that is relevant to key stakeholder groups, thereby enabling the combination or comparison of stakeholder perspectives. Such a validated and widely accepted IS-Impact measurement model has both academic and practical value. It facilitates systematic operationalization of a main dependent variable in research (IS-Impact), which can also serve as an important independent variable. For IS management practice it provides a means to benchmark and track the performance of information systems in use. The objective of this study is to develop a Mandarin version IS-Impact model, encompassing a list of China-specific IS-Impact measures, aiding in a better understanding of the IS-Impact phenomenon in a Chinese organizational context. The IS-Impact model provides a much needed theoretical guidance for this investigation of ES and ES impacts in a Chinese context. The appropriateness and soundness of employing the IS-Impact model as a theoretical foundation are evident: the model originated from a sound theory of IS Success (1992), developed through rigorous validation, and also derived in the context of Enterprise Systems. Based on the IS-Impact model, this study investigates a number of research questions (RQs). Firstly, the research investigated what essential impacts have been derived from ES by Chinese users and organizations [RQ1]. Secondly, we investigate which salient quality features of ES are perceived by Chinese users [RQ2]. Thirdly, we seek to answer whether the quality and impacts measures are sufficient to assess ES-success in general [RQ3]. Lastly, the study attempts to address whether the IS-Impact measurement model is appropriate for Chinese organizations in terms of evaluating their ES [RQ4]. An open-ended, qualitative identification survey was employed in the study. A large body of short text data was gathered from 144 Chinese users and 633 valid IS-Impact statements were generated from the data set. A generally inductive approach was applied in the qualitative data analysis. Rigorous qualitative data coding resulted in 50 first-order categories with 6 second-order categories that were grounded from the context of Chinese organization. The six second-order categories are: 1) System Quality; 2) Information Quality; 3) Individual Impacts;4) Organizational Impacts; 5) User Quality and 6) IS Support Quality. The final research finding of the study is the contextualized Mandarin version IS-Impact measurement model that includes 38 measures organized into 4 dimensions: System Quality, information Quality, Individual Impacts and Organizational Impacts. The study also proposed two conceptual models to harmonize the IS-Impact model and the two emergent constructs – User Quality and IS Support Quality by drawing on previous IS effectiveness literatures and the Work System theory proposed by Alter (1999) respectively. The study is significant as it is the first effort that empirically and comprehensively investigates IS-Impact in China. Specifically, the research contributions can be classified into theoretical contributions and practical contributions. From the theoretical perspective, through qualitative evidence, the study test and consolidate IS-Impact measurement model in terms of the quality of robustness, completeness and generalizability. The unconventional research design exhibits creativity of the study. The theoretical model does not work as a top-down a priori seeking for evidence demonstrating its credibility; rather, the study allows a competitive model to emerge from the bottom-up and open-coding analysis. Besides, the study is an example extending and localizing pre-existing theory developed in Western context when the theory is introduced to a different context. On the other hand, from the practical perspective, It is first time to introduce prominent research findings in field of IS Success to Chinese academia and practitioner. This study provides a guideline for Chinese organizations to assess their Enterprise System, and leveraging IT investment in the future. As a research effort in ITPS track, this study contributes the research team with an alternative operationalization of the dependent variable. The future research can take on the contextualized Mandarin version IS-Impact framework as a theoretical a priori model, further quantitative and empirical testing its validity.

Evaluating the transport impacts of transit oriented developments (TODS)

Sustainable transport has become a necessity instead of an option, to address the problems of congestion and urban sprawl, whose effects include increased trip lengths and travel time. A more sustainable form of development, known as Transit Oriented Development (TOD) is presumed to offer sustainable travel choices with reduced need to travel to access daily destinations, by providing a mixture of land uses together with good quality of public transport service, infrastructure for walking and cycling. However, performance assessment of these developments with respect to travel characteristics of their inhabitants is required. This research proposes a five step methodology for evaluating the transport impacts of TODs. The steps for TOD evaluation include pre–TOD assessment, traffic and travel data collection, determination of traffic impacts, determination of travel impacts, and drawing outcomes. Typically, TODs are comprised of various land uses; hence have various types of users. Assessment of characteristics of all user groups is essential for obtaining an accurate picture of transport impacts. A case study TOD, Kelvin Grove Urban Village (KGUV), located 2km of north west of the Brisbane central business district in Australia was selected for implementing the proposed methodology and to evaluate the transport impacts of a TOD from an Australian perspective. The outcomes of this analysis indicated that KGUV generated 27 to 48 percent less traffic compared to standard published rates specified for homogeneous uses. Further, all user groups of KGUV used more sustainable modes of transport compared to regional and similarly located suburban users, with higher trip length for shopping and education trips. Although the results from this case study development support the transport claims of reduced traffic generation and sustainable travel choices by way of TODs, further investigation is required, considering different styles, scales and locations of TODs. The proposed methodology may be further refined by using results from new TODs and a framework for TOD evaluation may be developed.

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.

YouTube

Originally launched in 2005 with a focus on user-generated content, YouTube has become the dominant platform for online video worldwide, and an important location for some of the most significant trends and controversies in the contemporary new-media environment. Throughout its very short history, it has also intersected with and been the focus of scholarly debates related to the politics, economics, and cultures of the new media—in particular, the “participatory turn” associated with “Web 2.0” business models’ partial reliance on amateur content and social networking. Given the slow pace of traditional scholarly publishing, the body of media and cultural studies literature substantively dedicated to describing and critically understanding YouTube’s texts, practices, and politics is still small, but it is growing steadily. At the same time, since its inception scholars from a wide range of disciplines and critical perspectives have found YouTube useful as a source of examples and case studies, some of which are included here; others have experimented directly with the scholarly and educational potential of the platform itself. For these reasons, although primarily based around the traditional publishing outlets for media, Internet, and cultural studies, this bibliography draws eclectically on a wide range of sources—including sources very closely associated with the web business literature and with the YouTube community itself.

Planning for SMEs’ Proactive Waste Management in Office Building Retrofit Projects

Office building retrofit projects face many challenges for on-site waste management. While the projects themselves have the potential for a significant level of reuse and recycling from decon-struction and demolition, their unique characteristics often prohibit direct application of existing waste management systems, which are typically based on managing waste generated through new material application in new build projects. Moreover, current waste management plans include no stimuli to involve Small and Medium Enterprises (SMEs) for on-site waste management. As SMEs carry out the majority of on-site work as subcontractors, their active involvements will result in more proactive approaches to waste management and enhance project delivery. This paper discusses the interim results of a continuing research aimed at engaging SMEs in the planning processes of waste management through the collaboration between subcontractors and main contractors of retrofitting projects. It introduces a conceptual model for SMEs to proactively plan and manage on-site waste generation for both deconstruction and construction stages, before traditional waste management plans by the main contractor come into place. The model also suggests a collaboration process between SMEs as subcontractors and large companies as the main contractor to improve the involvement and performance of SMEs in waste management of office building retrofit projects.

Beyond MOF constraints : multiple constraint set metamodelling for lifecycle management

The management of models over time in many domains requires different constraints to apply to some parts of the model as it evolves. Using EMF and its meta-language Ecore, the development of model management code and tools usually relies on the meta- model having some constraints, such as attribute and reference cardinalities and changeability, set in the least constrained way that any model user will require. Stronger versions of these constraints can then be enforced in code, or by attaching additional constraint expressions, and their evaluations engines, to the generated model code. We propose a mechanism that allows for variations to the constraining meta-attributes of metamodels, to allow enforcement of different constraints at different lifecycle stages of a model. We then discuss the implementation choices within EMF to support the validation of a state-specific metamodel on model graphs when changing states, as well as the enforcement of state-specific constraints when executing model change operations.

A geographical analysis of the role of water supply and sanitation in the risk of helminth infections of children in West Africa

Background We investigated the geographical variation of water supply and sanitation indicators (WS&S) and their role to the risk of schistosomiasis and hookworm infection in school age children in West Africa. The aim was to predict large-scale geographical variation in WS&S, quantify the attributable risk of S. haematobium, S. mansoni and hookworm infections due to WS&S and identify communities where sustainable transmission control could be targeted across the region. Methods National cross-sectional household-based demographic health surveys were conducted in 24,542 households in Burkina Faso, Ghana and Mali, in 2003–2006. We generated spatially-explicit predictions of areas without piped water, toilet facilities and finished floors in West Africa, adjusting for household covariates. Using recently published helminth prevalence data we developed Bayesian geostatistical models (MGB) of S. haematobium, S. mansoni and hookworm infection in West Africa including environmental and the mapped outputs for WS&S. Using these models we estimated the effect of WS&S on parasite risk, quantified their attributable fraction of infection, and mapped the risk of infection in West Africa. Findings Our maps show that most areas in West Africa are very poorly served by water supply except in major urban centers. There is a better geographical coverage for toilet availability and improved household flooring. We estimated smaller attributable risks for water supply in S. mansoni (47%) compared to S. haematobium (71%), and 5% of hookworm cases could be averted by improving sanitation. Greater levels of inadequate sanitation increased the risk of schistosomiasis, and increased levels of unsafe water supply increased the risk of hookworm. The role of floor type for S. haematobium infection (21%) was comparable to that of S. mansoni (16%), but was significantly higher for hookworm infection (86%). S. haematobium and hookworm maps accounting for WS&S show small clusters of maximal prevalence areas in areas bordering Burkina Faso and Mali smaller. The map of S. mansoni shows that this parasite is much more wide spread across the north of the Niger River basin than previously predicted. Interpretation Our maps identify areas where the Millennium Development Goal for water and sanitation is lagging behind. Our results show that WS&S are important contributors to the burden of major helminth infections of children in West Africa. Including information about WS&S as well as the “traditional” environmental risk factors in spatial models of helminth risk yielded a substantial gain both in model fit and at explaining the proportion of spatial variance in helminth risk. Mapping the distribution of infection risk adjusted for WS&S allowed the identification of communities in West Africa where integrative preventive chemotherapy and engineering interventions will yield the greatest public health benefits.

The impact of taxes on optimal portfolio choice : an Australian study

Taxes are an important component of investing that is commonly overlooked in both the literature and in practice. For example, many understand that taxes will reduce an investment’s return, but less understood is the risk-sharing nature of taxes that also reduces the investment’s risk. This thesis examines how taxes affect the optimal asset allocation and asset location decision in an Australian environment. It advances the model of Horan & Al Zaman (2008), improving the method by which the present value of tax liabilities are calculated, by using an after-tax risk-free discount rate, and incorporating any new or reduced tax liabilities generated into its expected risk and return estimates. The asset allocation problem is examined for a range of different scenarios using Australian parameters, including different risk aversion levels, personal marginal tax rates, investment horizons, borrowing premiums, high or low inflation environments, and different starting cost bases. The findings support the Horan & Al Zaman (2008) conclusion that equities should be held in the taxable account. In fact, these findings are strengthened with most of the efficient frontier maximising equity holdings in the taxable account instead of only half. Furthermore, these findings transfer to the Australian case, where it is found that taxed Australian investors should always invest into equities first through the taxable account before investing in super. However, untaxed Australian investors should invest their equity first through superannuation. With borrowings allowed in the taxable account (no borrowing premium), Australian taxed investors should hold 100% of the superannuation account in the risk-free asset, while undertaking leverage in the taxable account to achieve the desired risk-return. Introducing a borrowing premium decreases the likelihood of holding 100% of super in the risk-free asset for taxable investors. The findings also suggest that the higher the marginal tax rate, the higher the borrowing premium in order to overcome this effect. Finally, as the investor’s marginal tax rate increases, the overall allocation to equities should increase due to the increased risk and return sharing caused by taxation, and in order to achieve the same risk/return level as the lower taxation level, the investor must take on more equity exposure. The investment horizon has a minimal impact on the optimal allocation decision in the absence of factors such as mean reversion and human capital.

Evaluation framework for focused link discovery

Information has no value unless it is accessible. Information must be connected together so a knowledge network can then be built. Such a knowledge base is a key resource for Internet users to interlink information from documents. Information retrieval, a key technology for knowledge management, guarantees access to large corpora of unstructured text. Collaborative knowledge management systems such as Wikipedia are becoming more popular than ever; however, their link creation function is not optimized for discovering possible links in the collection and the quality of automatically generated links has never been quantified. This research begins with an evaluation forum which is intended to cope with the experiments of focused link discovery in a collaborative way as well as with the investigation of the link discovery application. The research focus was on the evaluation strategy: the evaluation framework proposal, including rules, formats, pooling, validation, assessment and evaluation has proved to be efficient, reusable for further extension and efficient for conducting evaluation. The collection-split approach is used to re-construct the Wikipedia collection into a split collection comprising single passage files. This split collection is proved to be feasible for improving relevant passages discovery and is devoted to being a corpus for focused link discovery. Following these experiments, a mobile client-side prototype built on iPhone is developed to resolve the mobile Search issue by using focused link discovery technology. According to the interview survey, the proposed mobile interactive UI does improve the experience of mobile information seeking. Based on this evaluation framework, a novel cross-language link discovery proposal using multiple text collections is developed. A dynamic evaluation approach is proposed to enhance both the collaborative effort and the interacting experience between submission and evaluation. A realistic evaluation scheme has been implemented at NTCIR for cross-language link discovery tasks.

Investigation of the effect of organics on the water uptake of marine aerosols

Water uptake refers to the ability of atmospheric particles to take up water vapour from the surrounding atmosphere. This is an important property that affects particle size and phase and therefore influences many characteristics of aerosols relevant to air quality and climate. However, the water uptake properties of many important atmospheric aerosol systems, including those related to the oceans, are still not fully understood. Therefore, the primary aim of this PhD research program was to investigate the water uptake properties of marine aerosols. In particular, the effect of organics on marine aerosol water uptake was investigated. Field campaigns were conducted at remote coastal sites on the east coast of Australia (Agnes Water; March-April 2007) and west coast of Ireland (Mace Head; June 2007), and laboratory measurements were performed on bubble-generated sea spray aerosols. A combined Volatility-Hygroscopicity-Tandem Differential Mobility Analyser (VH-TDMA) was employed in all experiments. This system probes the changes in the hygroscopic properties of nanoparticles as volatile organic components are progressively evaporated. It also allows particle composition to be inferred from combined volatility-hygroscopicity measurements. Frequent new particle formation and growth events were observed during the Agnes Water campaign. The VH-TDMA was used to investigate freshly nucleated particles (17-22.5 nm) and it was found that the condensation of sulphate and/or organic vapours was responsible for driving particle growth during the events. Aitken mode particles (~40 nm) were also measured with the VH-TDMA. In 3 out of 18 VH-TDMA scans evaporation of a volatile, organic component caused a very large increase in hygroscopicity that could only be explained by an increase in the absolute water uptake of the particle residuals, and not merely an increase in their relative hygroscopicity. This indicated the presence of organic components that were suppressing the hygroscopic growth of mixed particles on the timescale of humidification in the VH-TDMA (6.5 secs). It was suggested that the suppression of water uptake was caused by either a reduced rate of hygroscopic growth due to the presence of organic films, or organic-inorganic interactions in solution droplets that had a negative effect on hygroscopicity. Mixed organic-inorganic particles were rarely observed by the VH-TDMA during the summer campaign conducted at Mace Head. The majority of particles below 100 nm in clean, marine air appeared to be sulphates neutralised to varying degrees by ammonia. On one unique day, 26 June 2007, particularly large concentrations of sulphate aerosol were observed and identified as volcanic emissions from Iceland. The degree of neutralisation of the sulphate aerosol by ammonia was calculated by the VH-TDMA and found to compare well with the same quantity measured by an aerosol mass spectrometer. This was an important verification of the VH-TMDA‘s ability to identify ammoniated sulphate aerosols based on the simultaneous measurement of aerosol volatility and hygroscopicity. A series of measurements were also conducted on sea spray aerosols generated from Moreton Bay seawater samples in a laboratory-based bubble chamber. Accumulation mode sea spray particles (38-173 nm) were found to contain only a minor organic fraction (< 10%) that had little effect on particle hygroscopicity. These results are important because previous studies have observed that accumulation mode sea spray particles are predominantly organic (~80% organic mass fraction). The work presented here suggests that this is not always the case, and that there may be currently unknown factors that are controlling the transfer of organics to the aerosol phase during the bubble bursting process. Taken together, the results of this research program have significantly improved our understanding of organic-containing marine aerosols and the way they interact with water vapour in the atmosphere.

Locating 'Agency' Within Ubiquitous Computing Systems

The final shape of the "Internet of Things" ubiquitous computing promises relies on a cybernetic system of inputs (in the form of sensory information), computation or decision making (based on the prefiguration of rules, contexts, and user-generated or defined metadata), and outputs (associated action from ubiquitous computing devices). My interest in this paper lies in the computational intelligences that suture these positions together, and how positioning these intelligences as autonomous agents extends the dialogue between human-users and ubiquitous computing technology. Drawing specifically on the scenarios surrounding the employment of ubiquitous computing within aged care, I argue that agency is something that cannot be traded without serious consideration of the associated ethics.