A University Support Model for eResearch

Queensland University of Technology (QUT) is faced with a rapidly growing research agenda built upon a strategic research capacity-building program. This presentation will outline the results of a project that has recently investigated QUT’s research support requirements and which has developed a model for the support of eResearch across the university. QUT’s research building strategy has produced growth at the faculty level and within its research institutes. This increased research activity is pushing the need for university-wide eResearch platforms capable of providing infrastructure and support in areas such as collaboration, data, networking, authentication and authorisation, workflows and the grid. One of the driving forces behind the investigation is data-centric nature of modern research. It is now critical that researchers have access to supported infrastructure that allows the collection, analysis, aggregation and sharing of large data volumes for exploration and mining in order to gain new insights and to generate new knowledge. However, recent surveys into current research data management practices by the Australian Partnership for Sustainable Repositories (APSR) and by QUT itself, has revealed serious shortcomings in areas such as research data management, especially its long term maintenance for reuse and authoritative evidence of research findings. While these internal university pressures are building, at the same time there are external pressures that are magnifying them. For example, recent compliance guidelines from bodies such as the ARC, and NHMRC and Universities Australia indicate that institutions need to provide facilities for the safe and secure storage of research data along with a surrounding set of policies, on its retention, ownership and accessibility. The newly formed Australian National Data Service (ANDS) is developing strategies and guidelines for research data management and research institutions are a central focus, responsible for managing and storing institutional data on platforms that can be federated nationally and internationally for wider use. For some time QUT has recognised the importance of eResearch and has been active in a number of related areas: ePrints to digitally publish research papers, grid computing portals and workflows, institutional-wide provisioning and authentication systems, and legal protocols for copyright management. QUT also has two widely recognised centres focused on fundamental research into eResearch itself: The OAK LAW project (Open Access to Knowledge) which focuses upon legal issues relating eResearch and the Microsoft QUT eResearch Centre whose goal is to accelerate scientific research discovery, through new smart software. In order to better harness all of these resources and improve research outcomes, the university recently established a project to investigate how it might better organise the support of eResearch. This presentation will outline the project outcomes, which include a flexible and sustainable eResearch support service model addressing short and longer term research needs, identification of resource requirements required to establish and sustain the service, and the development of research data management policies and implementation plans.

The distribution and spread of citrus canker in Emerald, Australia

Citrus canker is a disease of citrus and closely related species, caused by the bacterium Xanthomonas citri subsp. citri. This disease, previously exotic to Australia, was detected on a single farm [infested premise-1, (IP1). IP is the terminology used in official biosecurity protocols to describe a locality at which an exotic plant pest has been confirmed or is presumed to exist. IP are numbered sequentially as they are detected] in Emerald, Queensland in July 2004. During the following 10 months the disease was subsequently detected on two other farms (IP2 and IP3) within the same area and studies indicated the disease first occurred on IP1 and spread to IP2 and IP3. The oldest, naturally infected plant tissue observed on any of these farms indicated the disease was present on IP1 for several months before detection and established on IP2 and IP3 during the second quarter (i.e. autumn) 2004. Transect studies on some IP1 blocks showed disease incidences ranged between 52 and 100% (trees infected). This contrasted to very low disease incidence, less than 4% of trees within a block, on IP2 and IP3. The mechanisms proposed for disease spread within blocks include weather-assisted dispersal of the bacterium (e.g. wind-driven rain) and movement of contaminated farm equipment, in particular by pivot irrigator towers via mechanical damage in combination with abundant water. Spread between blocks on IP2 was attributed to movement of contaminated farm equipment and/or people. Epidemiology results suggest: (i) successive surveillance rounds increase the likelihood of disease detection; (ii) surveillance sensitivity is affected by tree size; and (iii) individual destruction zones (for the purpose of eradication) could be determined using disease incidence and severity data rather than a predefined set area.

AITPM Email Newsletter Volume 0904, April 2009: Presidents Message

President’s Report Hello fellow AITPM members, A few weeks ago we saw another example of all levels of Government pulling together in real time to try to deal with a major transport incident, this time it was container loads of ammonium nitrate falling off the Pacific Adventurer during Cyclone Hamish and the associated major oil spill due to piercing of its hull off Moreton Bay in southern Queensland. The oil spill was extensive, affecting beaches and estuaries from Moreton Island north to the Sunshine Coast; a coastal stretch of at least 60km. We saw the Queensland Government, Brisbane, Moreton Bay and Sunshine Coast Regional Council crews deployed quickly once the gravity of the situation was realised to clean up toxic oil on beaches and prevent extensive upstream contamination. Environmental agencies public and private were quick to respond to help affected wildlife. The Navy’s HMAS Yarra and another minesweeper were deployed to search for the containers in the coastal area in an effort to have them salvaged before all ammonium nitrate could leach into and harm marine habitat, which would have a substantial impact not only on that environment but also the fishing industry. all of this during the final fortnight before a State election.) While this could be branded as a maritime problem, the road transport and logistics system was crucial to the cleanup. The private vehicular ferries were enlisted to transport plant and equipment from Brisbane to Moreton Island. The plant themselves, such as graders, were drawn from road building and maintenance inventory. Hundreds of Councils’ staff were released from other activities to undertake the cleanup. While it will take some time for us to know the long term impacts of this incident, it seems difficult to fault “grassroots” government crews and their private counterparts, such as Island tourism staff, in the initial cleanup effort. From a traffic planning and management perspective, we should also remember that this sort of incident has happened on road and rail corridors in the past, albeit on lesser scales. It underlines that we do need to continue to protect communities, commercial interests, and the environment through rigorous heavy vehicle management, planning and management of dangerous goods routesincluding rail corridors through urban areas), and carefully considered incident and disaster recovery plans and protocols. I’d like to close in reminding everyone again that AITPM’s flagship event, the 2009 AITPM National Conference, Traffic Beyond Tomorrow, is being held in Adelaide from 5 to 7 August. SA Branch President Paul Morris informs me that we have had over 50 paper submissions to date, from which a very balanced and informative programme of sessions has been prepared. www.aitpm.com has all of the details about how to register, sponsor a booth, session, etc. Best regards all, Jon Bunker

Host searching behaviour of Diachasmimorpha kraussii (Fullaway) (Hymenoptera: Braconidae: Opiinae), a polyphagous parasitoid of Dacinae fruit flies (Diptera: Tephritidae)

Diachasmimorpha kraussii (Hymenoptera: Braconidae: Opiinae) is a koinobiont larval parasitoid of dacine fruit flies of the genus Bactrocera (Diptera: Tephritidae) in its native range (Australia, Papua New Guinea, Solomon Islands). The wasp is a potentially important control agent for pest fruit flies, having been considered for both classical and inundative biological control releases. I investigated the host searching, selection and utilisation mechanisms of the wasp against native host flies within its native range (Australia). Such studies are rare in opiine research where the majority of studies, because of the applied nature of the research, have been carried out using host flies and environments which are novel to the wasps. Diachasmimorpha kraussii oviposited equally into maggots of four fruit fly species, all of which coexist with the wasp in its native range (Australia), when tested in a choice trial using a uniform artificial diet media. While eggs laid into Bactrocera tryoni and B. jarvisi developed successfully through to adult wasps, eggs laid into B. cucumis and B. cacuminata were encapsulated. These results suggest that direct larval cues are not an important element in host selection by D. kraussii. Further exploring how D. kraussii locates suitable host larvae, I investigated the role of plant cues in host searching and selection. This was examined in a laboratory choice trial using uninfested fruit or fruit infested with either B. tryoni or B. jarvisi maggots. The results showed a consistent preference ranking among infested fruits by the wasp, with guava and peach most preferred, but with no response to uninfested fruits. Thus, it appears the wasp uses chemical cues emitted in response to fruit fly larval infestation for host location, but does not use cues from uninfested fruits. To further tease apart the role of (i) suitable and non-suitable maggots, (ii) infested and uninfested fruits of different plant species, and (iii) adult flies, in wasp host location and selection, I carried out a series of behavioural tests where I manipulated these attributes in a field cage. These trials confirmed that D. kraussii did not respond to cues in uninfested fruits, that there were consistent preferences by the wasps for different maggot infested fruits, that fruit preference did not vary depending on whether the maggots were physiologically suitable or not suitable for wasp offspring development, and finally, that adult flies appear to play a secondary role as indicators of larval infestation. To investigate wasp behaviour in an unrestrained environment, I concurrently observed diurnal foraging behaviours of both the wasp and one of its host fly in a small nectarine orchard. Wasp behaviour, both spatially and temporally, was not correlated with adult fruit fly behaviour or abundance. This study reinforced the point that infested fruit seems to be the primary cue used by foraging wasps. Wasp and fly feeding and mating was not observed in the orchard, implying these activities are occurring elsewhere. It is highly unlikely that these behaviours were happening within the orchard during the night as both insects are diurnal. As the final component of investigating host location, I carried out a habitat preference study for the wasp at the landscape scale. Using infested sentinel fruits, I tested the parasitism rate of B. tryoni in eucalyptus sclerophyll forest, rainforest and suburbia in South East Queensland. Although, rainforest is the likely endemic habitat of both B. tryoni and D. kraussii, B. tryoni abundance is significantly greater in suburban environments followed by eucalyptus sclerophyll forest. Parasitism rate was found to be higher in suburbia than in the eucalyptus sclerophyll forest, while no parasitism was recorded in the rainforest. This result suggests that wasps orient within the landscape towards areas of high host density and are not restricted by habitat types. Results from the different experiments suggest that host searching, selection and utilisation behaviour of D. kraussii are strongly influenced by cues associated with fruit fly larval feeding. Cues from uninfested fruits, the host larvae themselves, and the adult host flies play minimal roles. The discussion focuses on the fit of D. kraussii to Vinson’s classical parasitoid host location model and the implications of results for biological control, including recommendations for host and plant preference screening protocols and release regimes.

End-of-life care pathways for improving outcomes in caring for the dying (Protocol)

We aim to assess the effects of end-of-life care pathways, compared with usual care or with care guided by another end-of-life care pathway across all healthcare settings (hospitals, residential aged care facilities, community). In particular, we aim to assess the effects on symptom severity and quality of life of people who are dying and/or those related to the care such as families, caregivers and health professionals.

Knowledge discovery for adaptive negotiation agents in e-marketplaces

Intelligent software agents are promising in improving the effectiveness of e-marketplaces for e-commerce. Although a large amount of research has been conducted to develop negotiation protocols and mechanisms for e-marketplaces, existing negotiation mechanisms are weak in dealing with complex and dynamic negotiation spaces often found in e-commerce. This paper illustrates a novel knowledge discovery method and a probabilistic negotiation decision making mechanism to improve the performance of negotiation agents. Our preliminary experiments show that the probabilistic negotiation agents empowered by knowledge discovery mechanisms are more effective and efficient than the Pareto optimal negotiation agents in simulated e-marketplaces.

Modeling web search : preliminary results

This paper reports preliminary results from a study modeling the interplay between multitasking, cognitive coordination, and cognitive shifts during Web search. Study participants conducted three Web searches on personal information problems. Data collection techniques included pre- and post-search questionnaires; think-aloud protocols, Web search logs, observation, and post-search interviews. Key findings include: (1) users Web searches included multitasking, cognitive shifting and cognitive coordination processes, (2) cognitive coordination is the hinge linking multitasking and cognitive shifting that enables Web search construction, (3) cognitive shift levels determine the process of cognitive coordination, and (4) cognitive coordination is interplay of task, mechanism and strategy levels that underpin multitasking and task switching. An initial model depicts the interplay between multitasking, cognitive coordination, and cognitive shifts during Web search. Implications of the findings and further research are also discussed.

Novel educational training program for community pharmacists

There is little evidence that workshops alone have a lasting impact on the day-to-day practice of participants. The current paper examined a strategy to increase generalization and maintenance of skills in the natural environment using pseudo-patients and immediate performance feedback to reinforce skills acquisition. A random half of pharmacies (N=30) took part in workshop training aimed at optimizing consumers' use of nonprescription analgesic products. Pharmacies in the training group also received performance feedback on their adherence to the recommended protocol. Feedback occurred immediately after a pseudo-patient visit in which confederates posed as purchasers of analgesics, and combined positive and corrective elements. Trained pharmacists were significantly more accurate at identifying people who misused the medication (P<0.001). The trained pharmacists were more likely than controls to use open-ended questions (P<0.001), assess readiness to change problematic use (P <0.001), and to deliver a brief intervention that was tailored to the person's commitment to alter his/her usage (P <0.001). Participants responded to the feedback positively. Results were consistent with the hypothesis that when workshop is combined with on-site performance feedback, it enhances practitioners' adherence to protocols in the natural setting.

Comparison of methods for processing drinking water samples for the isolation of Myocbacterium avium and intracellulare

Several protocols for isolation of mycobacteria from water exist, but there is no established standard method. This study compared methods of processing potable water samples for the isolation of Mycobacterium avium and Mycobacterium intracellulare using spiked sterilized water and tap water decontaminated using 0.005% cetylpyridinium chloride (CPC). Samples were concentrated by centrifugation or filtration and inoculated onto Middlebrook 7H10 and 7H11 plates and Lowenstein-Jensen slants and into mycobacterial growth indicator tubes with or without polymyxin, azlocillin, nalidixic acid, trimethoprim, and amphotericin B. The solid media were incubated at 32°C, at 35°C, and at 35°C with CO2 and read weekly. The results suggest that filtration of water for the isolation of mycobacteria is a more sensitive method for concentration than centrifugation. The addition of sodium thiosulfate may not be necessary and may reduce the yield. Middlebrook M7H10 and 7H11 were equally sensitive culture media. CPC decontamination, while effective for reducing growth of contaminants, also significantly reduces mycobacterial numbers. There was no difference at 3 weeks between the different incubation temperatures.

The manipulation of apoptosis-related genes to generate resistance to Fusarium wilt and water stress in banana

Bananas are susceptible to a diverse range of biotic and abiotic stresses, many of which cause serious production constraints worldwide. One of the most destructive banana diseases is Fusarium wilt caused by the soil-borne fungus, Fusarium oxysporum f. sp. cubense (Foc). No effective control strategy currently exists for this disease which threatens global banana production. Although disease resistance exists in some wild bananas, attempts to introduce resistance into commercially acceptable bananas by conventional breeding have been hampered by low fertility, long generation times and association of poor agronomical traits with resistance genes. With the advent of reliable banana transformation protocols, molecular breeding is now regarded as a viable alternative strategy to generate disease-resistant banana plants. Recently, a novel strategy involving the expression of anti-apoptosis genes in plants was shown to result in resistance against several necrotrophic fungi. Further, the transgenic plants showed increased resistance to a range of abiotic stresses. In this thesis, the use of anti-apoptosis genes to generate transgenic banana plants with resistance to Fusarium wilt was investigated. Since water stress is an important abiotic constraint to banana production, the resistance of the transgenic plants to water stress was also examined. Embryogenic cell suspensions (ECS) of two commercially important banana cultivars, Grand Naine (GN) and Lady Finger (LF), were transformed using Agrobacterium with the anti-apoptosis genes, Bcl-xL, Bcl-xL G138A, Ced-9 and Bcl- 2 3’ UTR. An interesting, and potentially important, outcome was that the use of anti-apoptosis genes resulted in up to a 50-fold increase in Agrobacterium-mediated transformation efficiency of both LF and GN cells over vector controls. Regenerated plants were subjected to a complete molecular characterisation in order to detect the presence of the transgene (PCR), transcript (RT-PCR) and gene product (Western blot) and to determine the gene copy number (Southern blot). A total of 36 independently-transformed GN lines (8 x Bcl-xL, 5 x Bcl-xL G138A, 15 x Ced-9 and 8 x Bcl-2 3’ UTR) and 41 independently-transformed LF lines (8 x Bcl-xL, 7 x BclxL G138A, 13 x Ced-9 and 13 x Bcl-2 3’ UTR) were identified. The 41 transgenic LF lines were multiplied and clones from each line were acclimatised and grown under glasshouse conditions for 8 weeks to allow monitoring for phenotypic abnormalities. Plants derived from 3 x Bcl-xL, 2 x Ced-9 and 5 x Bcl-2 3’ UTR lines displayed a variety of aberrant phenotypes. However, all but one of these abnormalities were off-types commonly observed in tissue-cultured, non-transgenic banana plants and were therefore unlikely to be transgene-related. Prior to determining the resistance of the transgenic plants to Foc race 1, the apoptotic effects of the fungus on both wild-type and Bcl-2 3’ UTR-transgenic LF banana cells were investigated using rapid in vitro root assays. The results from these assays showed that apoptotic-like cell death was elicited in wild-type banana root cells as early as 6 hours post-exposure to fungal spores. In contrast, these effects were attenuated in the root cells of Bcl-2 3’ UTR-transgenic lines that were exposed to fungal spores. Thirty eight of the 41 transgenic LF lines were subsequently assessed for resistance to Foc race 1 in small-plant glasshouse bioassays. To overcome inconsistencies in rating the internal (vascular discolouration) disease symptoms, a MatLab-based computer program was developed to accurately and reliably assess the level of vascular discolouration in banana corms. Of the transgenic LF banana lines challenged with Foc race 1, 2 x Bcl-xL, 3 x Ced-9, 2 x Bcl-2 3’ UTR and 1 x Bcl-xL G138A-transgenic line were found to show significantly less external and internal symptoms than wild-type LF banana plants used as susceptible controls at 12 weeks post-inoculation. Of these lines, Bcl-2 3’ UTR-transgenic line #6 appeared most resistant, displaying very mild symptoms similar to the wild-type Cavendish banana plants that were included as resistant controls. This line remained resistant for up to 23 weeks post-inoculation. Since anti-apoptosis genes have been shown to confer resistance to various abiotic stresses in other crops, the ability of these genes to confer resistance against water stress in banana was also investigated. Clonal plants derived from each of the 38 transgenic LF banana plants were subjected to water stress for a total of 32 days. Several different lines of transgenic plants transformed with either Bcl-xL, Bcl-xL G138A, Ced-9 or Bcl-2 3’ UTR showed a delay in visual water stress symptoms compared with the wild-type control plants. These plants all began producing new growth from the pseudostem following daily rewatering for one month. In an attempt to determine whether the protective effect of anti-apoptosis genes in transgenic banana plants was linked with reactive oxygen species (ROS)-associated programmed cell death (PCD), the effect of the chloroplast-targeting, ROS-inducing herbicide, Paraquat, on wild-type and transgenic LF was investigated. When leaf discs from wild-type LF banana plants were exposed to 10 ìM Paraquat, complete decolourisation occurred after 48 hours which was confirmed to be associated with cell death and ROS production by trypan blue and 3,3-diaminobenzidine (DAB) staining, respectively. When leaf discs from the transgenic lines were exposed to Paraquat, those derived from some lines showed a delay in decolourisation, suggesting only a weak protective effect from the transgenes. Finally, the protective effect of anti-apoptosis genes against juglone, a ROS-inducing phytotoxin produced by the causal agent of black Sigatoka, Mycosphaerella fijiensis, was investigated. When leaf discs from wild-type LF banana plants were exposed to 25 ppm juglone, complete decolourisation occurred after 48 hours which was again confirmed to be associated with cell death and ROS production by trypan blue and DAB staining, respectively. Further, TdT-mediated dUTP nick-end labelling (TUNEL) assays on these discs suggested that the cell death was apoptotic. When leaf discs from the transgenic lines were exposed to juglone, discs from some lines showed a clear delay in decolourisation, suggesting a protective effect. Whether these plants are resistant to black Sigatoka is unknown and will require future glasshouse and field trials. The work presented in this thesis provides the first report of the use of anti-apoptosis genes as a strategy to confer resistance to Fusarium wilt and water stress in a nongraminaceous monocot, banana. Such a strategy may be exploited to generate resistance to necrotrophic pathogens and abiotic stresses in other economically important crop plants.

Efficient one-round key exchange in the standard model

We consider one-round key exchange protocols secure in the standard model. The security analysis uses the powerful security model of Canetti and Krawczyk and a natural extension of it to the ID-based setting. It is shown how KEMs can be used in a generic way to obtain two different protocol designs with progressively stronger security guarantees. A detailed analysis of the performance of the protocols is included; surprisingly, when instantiated with specific KEM constructions, the resulting protocols are competitive with the best previous schemes that have proofs only in the random oracle model.

Efficient one-round key exchange in the efficient one-round key exchange in the standard model

We consider one-round key exchange protocols secure in the standard model. The security analysis uses the powerful security model of Canetti and Krawczyk and a natural extension of it to the ID-based setting. It is shown how KEMs can be used in a generic way to obtain two different protocol designs with progressively stronger security guarantees. A detailed analysis of the performance of the protocols is included; surprisingly, when instantiated with specific KEM constructions, the resulting protocols are competitive with the best previous schemes that have proofs only in the random oracle model.

Efficient one-round key exchange in the standard model

We consider one-round key exchange protocols secure in the standard model. The security analysis uses the powerful security model of Canetti and Krawczyk and a natural extension of it to the ID-based setting. It is shown how KEMs can be used in a generic way to obtain two different protocol designs with progressively stronger security guarantees. A detailed analysis of the performance of the protocols is included; surprisingly, when instantiated with specific KEM constructions, the resulting protocols are competitive with the best previous schemes that have proofs only in the random oracle model.

The role of intermediaries in the implementation and development of asynchronous rural access

In Orissa state, India, the DakNet system supports asynchronous Internet communication between an urban hub and rural nodes. DakNet is noteworthy in many respects, not least in how the system leverages existing transport infrastructure. Wi-Fi transceivers mounted on local buses send and receive user data from roadside kiosks, for later transfer to/from the Internet via wireless protocols. This store-and-forward system allows DakNet to offer asynchronous communication capacity to rural users at low cost. The original ambition of the DakNet system was to provide email and SMS facilities to rural communities. Our 2008 study of the communicative ecology surrounding the DakNet system revealed that this ambition has now evolved – in response to market demand – to the extent that e-shopping (rather than email) has become the primary driver behind the DakNet offer.

Scheduling trains as a blocking parallel-machine job shop scheduling problem

In this paper, the train scheduling problem is modelled as a blocking parallel-machine job shop scheduling (BPMJSS) problem. In the model, trains, single-track sections and multiple-track sections, respectively, are synonymous with jobs, single machines and parallel machines, and an operation is regarded as the movement/traversal of a train across a section. Due to the lack of buffer space, the real-life case should consider blocking or hold-while-wait constraints, which means that a track section cannot release and must hold the train until next section on the routing becomes available. Based on literature review and our analysis, it is very hard to find a feasible complete schedule directly for BPMJSS problems. Firstly, a parallel-machine job-shop-scheduling (PMJSS) problem is solved by an improved shifting bottleneck procedure (SBP) algorithm without considering blocking conditions. Inspired by the proposed SBP algorithm, feasibility satisfaction procedure (FSP) algorithm is developed to solve and analyse the BPMJSS problem, by an alternative graph model that is an extension of the classical disjunctive graph models. The proposed algorithms have been implemented and validated using real-world data from Queensland Rail. Sensitivity analysis has been applied by considering train length, upgrading track sections, increasing train speed and changing bottleneck sections. The outcomes show that the proposed methodology would be a very useful tool for the real-life train scheduling problems