Optimisation of Banana streak virus (BSV) diagnostic assays

Bananas are one of the world�fs most important crops, serving as a staple food and an important source of income for millions of people in the subtropics. Pests and diseases are a major constraint to banana production. To prevent the spread of pests and disease, farmers are encouraged to use disease�] and insect�]free planting material obtained by micropropagation. This option, however, does not always exclude viruses and concern remains on the quality of planting material. Therefore, there is a demand for effective and reliable virus indexing procedures for tissue culture (TC) material. Reliable diagnostic tests are currently available for all of the economically important viruses of bananas with the exception of Banana streak viruses (BSV, Caulimoviridae, Badnavirus). Development of a reliable diagnostic test for BSV is complicated by the significant serological and genetic variation reported for BSV isolates, and the presence of endogenous BSV (eBSV). Current PCR�] and serological�]based diagnostic methods for BSV may not detect all species of BSV, and PCR�]based methods may give false positives because of the presence of eBSV. Rolling circle amplification (RCA) has been reported as a technique to detect BSV which can also discriminate between episomal and endogenous BSV sequences. However, the method is too expensive for large scale screening of samples in developing countries, and little information is available regarding its sensitivity. Therefore the development of reliable PCR�]based assays is still considered the most appropriate option for large scale screening of banana plants for BSV. This MSc project aimed to refine and optimise the protocols for BSV detection, with a particular focus on developing reliable PCR�]based diagnostics Initially, the appropriateness and reliability of PCR and RCA as diagnostic tests for BSV detection were assessed by testing 45 field samples of banana collected from nine districts in the Eastern region of Uganda in February 2010. This research was also aimed at investigating the diversity of BSV in eastern Uganda, identifying the BSV species present and characterising any new BSV species. Out of the 45 samples tested, 38 and 40 samples were considered positive by PCR and RCA, respectively. Six different species of BSV, namely Banana streak IM virus (BSIMV), Banana streak MY virus (BSMYV), Banana streak OL virus (BSOLV), Banana streak UA virus (BSUAV), Banana streak UL virus (BSULV), Banana streak UM virus (BSUMV), were detected by PCR and confirmed by RCA and sequencing. No new species were detected, but this was the first report of BSMYV in Uganda. Although RCA was demonstrated to be suitable for broad�]range detection of BSV, it proved time�]consuming and laborious for identification in field samples. Due to the disadvantages associated with RCA, attempts were made to develop a reliable PCR�]based assay for the specific detection of episomal BSOLV, Banana streak GF virus (BSGFV), BSMYV and BSIMV. For BSOLV and BSGFV, the integrated sequences exist in rearranged, repeated and partially inverted portions at their site of integration. Therefore, for these two viruses, primers sets were designed by mapping previously published sequences of their endogenous counterparts onto published sequences of the episomal genomes. For BSOLV, two primer sets were designed while, for BSGFV, a single primer set was designed. The episomalspecificity of these primer sets was assessed by testing 106 plant samples collected during surveys in Kenya and Uganda, and 33 leaf samples from a wide range of banana cultivars maintained in TC at the Maroochy Research Station of the Department of Employment, Economic Development and Innovation (DEEDI), Queensland. All of these samples had previously been tested for episomal BSV by RCA and for both BSOLV and BSGFV by PCR using published primer sets. The outcome from these analyses was that the newly designed primer sets for BSOLV and BSGFV were able to distinguish between episomal BSV and eBSV in most cultivars with some B�]genome component. In some samples, however, amplification was observed using the putative episomal�]specific primer sets where episomal BSV was not identified using RCA. This may reflect a difference in the sensitivity of PCR compared to RCA, or possibly the presence of an eBSV sequence of different conformation. Since the sequences of the respective eBSV for BSMYV and BSIMV in the M. balbisiana genome are not available, a series of random primer combinations were tested in an attempt to find potential episomal�]specific primer sets for BSMYV and BSIMV. Of an initial 20 primer combinations screened for BSMYV detection on a small number of control samples, 11 primers sets appeared to be episomal�]specific. However, subsequent testing of two of these primer combinations on a larger number of control samples resulted in some inconsistent results which will require further investigation. Testing of the 25 primer combinations for episomal�]specific detection of BSIMV on a number of control samples showed that none were able to discriminate between episomal and endogenous BSIMV. The final component of this research project was the development of an infectious clone of a BSV endemic in Australia, namely BSMYV. This was considered important to enable the generation of large amounts of diseased plant material needed for further research. A terminally redundant fragment (.1.3 �~ BSMYV genome) was cloned and transformed into Agrobacterium tumefaciens strain AGL1, and used to inoculate 12 healthy banana plants of the cultivars Cavendish (Williams) by three different methods. At 12 weeks post�]inoculation, (i) four of the five banana plants inoculated by corm injection showed characteristic BSV symptoms while the remaining plant was wilting/dying, (ii) three of the five banana plants inoculated by needle�]pricking of the stem showed BSV symptoms, one plant was symptomless while the remaining had died and (iii) both banana plants inoculated by leaf infiltration were symptomless. When banana leaf samples were tested for BSMYV by PCR and RCA, BSMYV was confirmed in all banana plants showing symptoms including those were wilting and/or dying. The results from this research have provided several avenues for further research. By completely sequencing all variants of eBSOLV and eBSGFV and fully sequencing the eBSIMV and eBSMYV regions, episomal BSV�]specific primer sets for all eBSVs could potentially be designed that could avoid all integrants of that particular BSV species. Furthermore, the development of an infectious BSV clone will enable large numbers of BSVinfected plants to be generated for the further testing of the sensitivity of RCA compared to other more established assays such as PCR. The development of infectious clones also opens the possibility for virus induced gene silencing studies in banana.

A psychosocial model of young adult passengers’ intervening in unsafe driving of their friends

Young adults are over-represented in motor vehicle crashes and the carrying of same passengers puts them at greater risk of crashing. The current study examined characteristics of the passengers who might play a positive role in reducing friends’ crashes by actively engaging in strategies to protect such friends. A psychosocial theoretical model of prosocial behavior including self-process and contextual cues explained intervening behavior among primarily novice driver college students (n=242) with the exception of the self-process, perspective taking. The results of this study provide support for countermeasure development that accounts for the positive role of peers to increase road safety, and reduce the incidence of crashes, among young adults.

Are academics messy? Testing the broken windows theory with a field experiment in the work environment

We test the broken windows theory using a field experiment in a shared area of an academic workplace(the department common room). More specifically, we explore academics’ and postgraduate students’ behavior under an order condition (a clean environment) and a disorder condition (a messy environment). We find strong evidence that signs of disorderly behavior trigger littering: In 59% of the cases, subjects litter in the disorder treatment as compared to 18% in the order condition. These results remain robust in a multivariate analysis even when controlling for a large set of factors not directly examined by previous studies. Overall, when academic staff and postgraduate students observe that others have violated the social norm of keeping the common room clean, all else being equal, the probability of littering increases by around 40%.

Screening and managing cannabis use: comparing GP's and nurses' knowledge, beliefs, and behavior

Background: General practitioners (GPs) and nurses are ideally placed to address the significant unmet demand for the treatment of cannabis-related problems given the numbers of people who regularly seek their care. The aim of this study was to evaluate differences between GPs and nurses’ perceived knowledge, beliefs, and behaviors toward cannabis use and its screening and management. Methods: This study involved 161 nurses and 503 GPs who completed a survey distributed via conference satchels to delegates of Healthed seminars focused on topics relevant to women and children’s health. Differences between GPs and nurses were analyzed using χ2- tests and two-sample t-tests, while logistic regression examined predictors of service provision. Results: GPs were more likely than nurses to have engaged in cannabis-related service provision, but also more frequently reported barriers related to time, interest, and having more important issues to address. Nurses reported less knowledge, skills, and role legitimacy. Perceived screening skills predicted screening and referral to alcohol and other drug (AOD) services, while knowing a regular user increased the likelihood of referrals only. Conclusions: Approaches to increase cannabis-related screening and intervention may be improved by involving nurses, and by leveraging the relationship between nurses and doctors, in primary care.

School-based programs for increasing connectedness and reducing risk behavior : a systematic review

School connectedness has a significant impact on adolescent outcomes, including reducing risk taking behavior. This paper critically examines the literature on school-based programs targeting increased connectedness for reductions in risk taking. Fourteen articles describing seven different school-based programs were reviewed. Programs drew on a range of theories to increase school connectedness, and evaluations conducted for the majority of programs demonstrated positive changes in school connectedness, risk behavior, or a combination of the two. Many of the reviewed programs involved widespread school system change, however, which is frequently a complex and time consuming task. Future research is needed to examine the extent of intervention complexity required to result in change. This review also showed a lack of consistency in definitions and measurement of connectedness as well as few mediation analyses testing assumptions of impact on risk taking behavior through increases in school connectedness. Additionally, this review revealed very limited evaluation of the elements of multi-component programs that are most effective in increasing school connectedness and reducing adolescent risk taking.

Design of open source framework for traffic and travel simulation

For the evaluation, design, and planning of traffic facilities and measures, traffic simulation packages are the de facto tools for consultants, policy makers, and researchers. However, the available commercial simulation packages do not always offer the desired work flow and flexibility for academic research. In many cases, researchers resort to designing and building their own dedicated models, without an intrinsic incentive (or the practical means) to make the results available in the public domain. To make matters worse, a substantial part of these efforts pertains to rebuilding basic functionality and, in many respects, reinventing the wheel. This problem not only affects the research community but adversely affects the entire traffic simulation community and frustrates the development of traffic simulation in general. For this problem to be addressed, this paper describes an open source approach, OpenTraffic, which is being developed as a collaborative effort between the Queensland University of Technology, Australia; the National Institute of Informatics, Tokyo; and the Technical University of Delft, the Netherlands. The OpenTraffic simulation framework enables academies from geographic areas and disciplines within the traffic domain to work together and contribute to a specific topic of interest, ranging from travel choice behavior to car following, and from response to intelligent transportation systems to activity planning. The modular approach enables users of the software to focus on their area of interest, whereas other functional modules can be regarded as black boxes. Specific attention is paid to a standardization of data inputs and outputs for traffic simulations. Such standardization will allow the sharing of data with many existing commercial simulation packages.

Internet and e-commerce law, business and policy

Over the last two decades, the internet and e-commerce have reshaped the way we communicate, interact and transact. In the converged environment enabled by high speed broadband, web 2.0, social media, virtual worlds, user-generated content, cloud computing, VoIP, open source software and open content have rapidly become established features of our online experience. Business and government alike are increasingly using the internet as the preferred platform for delivery of their goods and services and for effective engagement with their clients. New ways of doing things online and challenges to existing business, government and social activities have tested current laws and often demand new policies and laws, adapted to the new realities. The focus of this book is the regulation of social, cultural and commercial activity on the World Wide Web. It considers developments in the law that have been, and continue to be, brought about by the emergence of the internet and e-commerce. It analyses how the law is applied to define rights and obligations in relation to online infrastructure, content and practices.

What vs how : comparing students' testing and coding skills

The well-known difficulties students exhibit when learning to program are often characterised as either difficulties in understanding the problem to be solved or difficulties in devising and coding a computational solution. It would therefore be helpful to understand which of these gives students the greatest trouble. Unit testing is a mainstay of large-scale software development and maintenance. A unit test suite serves not only for acceptance testing, but is also a form of requirements specification, as exemplified by agile programming methodologies in which the tests are developed before the corresponding program code. In order to better understand students’ conceptual difficulties with programming, we conducted a series of experiments in which students were required to write both unit tests and program code for non-trivial problems. Their code and tests were then assessed separately for correctness and ‘coverage’, respectively. The results allowed us to directly compare students’ abilities to characterise a computational problem, as a unit test suite, and develop a corresponding solution, as executable code. Since understanding a problem is a pre-requisite to solving it, we expected students’ unit testing skills to be a strong predictor of their ability to successfully implement the corresponding program. Instead, however, we found that students’testing abilities lag well behind their coding skills.

Multidisciplinary design and flight testing of a remote gas/particle airborne sensor system

The main objective of this paper is to describe the development of a remote sensing airborne air sampling system for Unmanned Aerial Systems (UAS) and provide the capability for the detection of particle and gas concentrations in real time over remote locations. The design of the air sampling methodology started by defining system architecture, and then by selecting and integrating each subsystem. A multifunctional air sampling instrument, with capability for simultaneous measurement of particle and gas concentrations was modified and integrated with ARCAA’s Flamingo UAS platform and communications protocols. As result of the integration process, a system capable of both real time geo-location monitoring and indexed-link sampling was obtained. Wind tunnel tests were conducted in order to evaluate the performance of the air sampling instrument in controlled nonstationary conditions at the typical operational velocities of the UAS platform. Once the remote fully operative air sampling system was obtained, the problem of mission design was analyzed through the simulation of different scenarios. Furthermore, flight tests of the complete air sampling system were then conducted to check the dynamic characteristics of the UAS with the air sampling system and to prove its capability to perform an air sampling mission following a specific flight path.

Testing the accuracy of luminance maps acquired by smart phone cameras

This paper looks at the accuracy of using the built-in camera of smart phones and free software as an economical way to quantify and analyse light exposure by producing luminance maps from High Dynamic Range (HDR) images. HDR images were captured with an Apple iPhone 4S to capture a wide variation of luminance within an indoor and outdoor scene. The HDR images were then processed using Photosphere software (Ward, 2010.) to produce luminance maps, where individual pixel values were compared with calibrated luminance meter readings. This comparison has shown an average luminance error of ~8% between the HDR image pixel values and luminance meter readings, when the range of luminances in the image is limited to approximately 1,500cd/m2.

Legal regulation of corporate social responsibility : evidence from Bangladesh

The business corporations' internal strategies in weak economies merely respond to the public policy goals for social development. The role of corporate self-regulation in Bangladesh is not an exception. The extent to which legal regulations related to the corporate social responsibility (CSR) of Bangladesh could contribute to including CSR notions at the core of self-regulated corporate responsibility is the focus of this paper. It explains that the major Bangladeshi laws related to corporate regulation and responsibility do not possess recurrent features to compel corporate self-regulators to contribute to developing a socially responsible corporate culture in Bangladesh. It suggests that, instead of relying on the prescriptive mode of regulation, Bangladesh could develop more business-friendly but strategic legal regulations.

Usability extensions for the worklet service

The YAWL Worklet Service is an effective approach to facilitating dynamic flexibility and exception handling in workflow processes. Recent additions to the Service extend its capabilities through a programming interface that provides easier access to rules storage and evaluation, and an event server that notifies listening servers and applications when exceptions are detected, which together serve enhance the functionality and accessibility of the Service's features and expand its usability to new potential domains.

Random Breath Testing in Australia: Is there an Optimum Level of Intensity?

Background: Random Breath Testing (RBT) is the main drink driving law enforcement tool used throughout Australia. International comparative research considers Australia to have the most successful RBT program compared to other countries in terms of crash reductions (Erke, Goldenbeld, & Vaa, 2009). This success is attributed to the programs high intensity (Erke et al., 2009). Our review of the extant literature suggests that there is no research evidence that indicates an optimal level of alcohol breath testing. That is, we suggest that no research exists to guide policy regarding whether or not there is a point at which alcohol related crashes reach a point of diminishing returns as a result of either saturated or targeted RBT testing. Aims: In this paper we first provide an examination of RBTs and alcohol related crashes across Australian jurisdictions. We then address the question of whether or not an optimal level of random breath testing exists by examining the relationship between the number of RBTs conducted and the occurrence of alcohol-related crashes over time, across all Australian states. Method: To examine the association between RBT rates and alcohol related crashes and to assess whether an optimal ratio of RBT tests per licenced drivers can be determined we draw on three administrative data sources form each jurisdiction. Where possible data collected spans January 1st 2000 to September 30th 2012. The RBT administrative dataset includes the number of Random Breath Tests (RBTs) conducted per month. The traffic crash administrative dataset contains aggregated monthly count of the number of traffic crashes where an individual’s recorded BAC reaches or exceeds 0.05g/ml of alcohol in blood. The licenced driver data were the monthly number of registered licenced drivers spanning January 2000 to December 2011. Results: The data highlights that the Australian story does not reflective of all States and territories. The stable RBT to licenced driver ratio in Queensland (of 1:1) suggests a stable rate of alcohol related crash data of 5.5 per 100,000 licenced drivers. Yet, in South Australia were a relative stable rate of RBT to licenced driver ratio of 1:2 is maintained the rate of alcohol related traffic crashes is substantially less at 3.7 per 100,000. We use joinpoint regression techniques and varying regression models to fit the data and compare the different patterns between jurisdictions. Discussion: The results of this study provide an updated review and evaluation of RBTs conducted in Australia and examines the association between RBTs and alcohol related traffic crashes. We also present an evidence base to guide policy decisions for RBT operations.

Laboratory measurement of hydraulic conductivity functions of two unsaturated sandy soils during drying and wetting processes

The importance of applying unsaturated soil mechanics to geotechnical engineering design has been well understood. However, the consumption of time and the necessity for a specific laboratory testing apparatus when measuring unsaturated soil properties have limited the application of unsaturated soil mechanics theories in practice. Although methods for predicting unsaturated soil properties have been developed, the verification of these methods for a wide range of soil types is required in order to increase the confidence of practicing engineers in using these methods. In this study, a new permeameter was developed to measure the hydraulic conductivity of unsaturated soils using the steady-state method and directly measured suction (negative pore-water pressure) values. The apparatus is instrumented with two tensiometers for the direct measurement of suction during the tests. The apparatus can be used to obtain the hydraulic conductivity function of sandy soil over a low suction range (0-10 kPa). Firstly, the repeatability of the unsaturated hydraulic conductivity measurement, using the new permeameter, was verified by conducting tests on two identical sandy soil specimens and obtaining similar results. The hydraulic conductivity functions of the two sandy soils were then measured during the drying and wetting processes of the soils. A significant hysteresis was observed when the hydraulic conductivity was plotted against the suction. However, the hysteresis effects were not apparent when the conductivity was plotted against the volumetric water content. Furthermore, the measured unsaturated hydraulic conductivity functions were compared with predictions using three different predictive methods that are widely incorporated into numerical software. The results suggest that these predictive methods are capable of capturing the measured behavior with reasonable agreement.

Copyrights and copyfights : copyright law and the digital economy

This paper will consider questions around the reform of copyright law, and how they are increasingly being framed by the challenges of the digital economy. It discusses the review of copyright and the digital economy being undertaken by the Australian Law Reform Commission, with particular reference to the costs and benefits of copyright law to consumers and creative producers. We argue that there is a pressing need to develop fair copyright rules that encourage investment in the digital economy, allow widespread dissemination of knowledge through society, and support the innovative reuse of copyright works. To better align copyright law with these goals, we recommend that Australia introduce an open ended ‘fair use’ style copyright exception, and encourage the development of a digital copyright exchange of the sort discussed in the UK by the Hargreaves and Hooper Reports.