Molecular characterisation of dicot-infecting mastreviruses from Australia

Monocotyledonous and dicotyledonous plant infecting mastreviruses threaten various agricultural systems throughout Africa, Eurasia and Australasia. In Australia three distinct mastrevirus species are known to infect dicotyledonous hosts such as chickpea, bean and tobacco. Amongst 34 new "dicot-infecting" mastrevirus full genome sequences obtained from these hosts we discovered one new species, four new strains, and various variants of previously described mastrevirus species. Besides providing additional support for the hypothesis that evolutionary processes operating during dicot-infecting mastrevirus evolution (such as patterns of pervasive homologous and non-homologous recombination, and strong purifying selection acting on all genes) have mostly mirrored those found in their monocot-infecting counterparts, we find that the Australian dicot-infecting viruses display patterns of phylogeographic clustering reminiscent of those displayed by monocot infecting mastrevirus species such as Panicum streak virus and Maize streak virus.

Sweetpotato consumer research: insights to increasing consumption

This report provides an evaluation of the behaviours and purchasing drivers of key sweetpotato consumers defined by Nielsen consumer research as Established Couples (two or more adults with no children 17 and under, and head of house 35-59), Senior Couples (two or more adults with no children 17 or under, and head of house 60 or over), and Independent Singles (one person household 35 or over, no children 17 or under). Research was qualitative in nature. Methods used included focus groups, depth interviews and shop-a-longs. The report found that preferences for sweetpotato amongst these groups were varied. In general a smaller torpedo shaped vegetable was valued for ease of preparation and the convenience of being of sufficient size for a meal for two. Satisfaction with sweetpotato was high with negative comments on quality exceedingly rare within discussions. However, shop-a-longs revealed that some quality issues were apparent at retail such as withered product, pitting and occasionally damage. A display with stock resting in any amount of water was a barrier to purchase for consumers and this was apparent on two out 15 occasions. A high quality sweetpotato was of a deep orange/red colour, had a smooth skin and was extremely dense and hard. An inferior sweetpotato was wrinkly, spongy, pitted and damaged. Awareness of sweetpotato was a relatively recent phenomenon amongst the respondents of this study with most recalling eating the vegetable in the last five to 10 years. Life-time eating patterns emerged as a consequence of childhood food experiences such as growing up with a ‘meat and three’ veg philosophy and traditional Australian meals. However, this was dependent on cultural background and those with ties to diverse cultures were more likely to have always known of the vegetable. Sweetpotato trial and consumption coincided with a breaking away from these traditional patterns, or was integrated into conventional meals such as a baked vegetable to accompany roasts. Increased health consciousness also led to awareness of the vegetable. A primary catalyst for consumption within the Established and Senior Couples groups was the health benefits associated with sweetpotato. Consumers had very little knowledge of the specific health properties of the vegetable and were surprised at the number of benefits consumption provided. Sweetpotato was important for diabetics for its low Glycemic Index status. Top-of-the-mind awareness of the vegetable resulted from the onset of the disease. Increasing fibre was a key motive for this demographic and this provided a significant link between consumption and preventing bowel cancer. For those on a weight loss regime, sweetpotato was perceived as a tasty, satisfying food that was low in carbohydrates. Swapping behaviours where white potato was replaced by sweetpotato was often a response to these health concerns. Other health properties mentioned by participants through the course of the research included the precursor β-carotene and Vitamins A & C. The sweetpotato was appreciated for its hedonic and timesaving qualities. For consumers with a high involvement in food, the vegetable was valued for its versatility in meals. These consumers took pride in cooking and the flavour and texture of sweetpotato lent itself to a variety of meals such as soups, salads, roasts, curries, tagines and so on. Participants who had little time or desire to prepare and cook meals valued sweetpotato because it was an easy way to add colour and variety to the plate and because including an orange vegetable to meals is a shortcut to ensuring vitamin intake. Several recommendations are made to the sweetpotato industry. • Vigorously promote the distinct nutritional and health properties of sweetpotatoes, particularly if they can be favourably compared to other vegetables or foods • Promote the salient properties to specific targets such as diabetics, those that are at risk to bowel cancer, and those embarking on a weight-loss regime. Utilise specialist channels of communication such as diabetic magazines and websites • Promote styles of cooking of sweetpotato that would appeal to traditionalists such as roasts and BBQs • Promote the vegetable as a low maintenance vegetable, easy to store, easy to cook and particularly focusing on it as a simple way to boost the appearance and nutritional value of meals. • Promote the vegetable to high food involvement consumers through exotic recipes and linking it to feelings of accomplishment with cooking • Promote the versatility of the vegetable • Devise promotions that link images and tone of communications with enjoying life to the fullest, having time to enjoy family and grandchildren, and of partaking in social activities • Educate retailers on consumer perceptions of quality and ensuring moisture and mould is not present at displays Qualitative information while providing a wealth of detail cannot be extrapolated to the overall target population and this may be considered a limitation to the research. However, within research theory, effective quantitative design is believed to stem from the insights developed from qualitative studies. • Develop and implement a quantitative study on sweetpotato attitudes and behaviours based on the results of this study.

I/O Device Virtualization in the multi-core era, a QoS perspective

In this paper, we propose an extension to the I/O device architecture, as recommended in the PCI-SIG IOV specification, for virtualizing network I/O devices. The aim is to enable fine-grained controls to a virtual machine on the I/O path of a shared device. The architecture allows native access of I/O devices to virtual machines and provides device level QoS hooks for controlling VM specific device usage. For evaluating the architecture we use layered queuing network (LQN) models. We implement the architecture and evaluate it using simulation techniques, on the LQN model, to demonstrate the benefits. With the architecture, the benefit for network I/O is 60% more than what can be expected on the existing architecture. Also, the proposed architecture improves scalability in terms of the number of virtual machines intending to share the I/O device.

Stochastic growth of the Eastern King Prawn (melicertus plebejus (hess, 1865)) harvested off Eastern Australia

Stochastic growth models were fitted to length-increment data of eastern king prawns, Melicertus plebejus (Hess, 1865), tagged across eastern Australia. The estimated growth parameters and growth transition matrix are for each sex representative of the species' geographical distribution. Our study explicitly displays the stochastic nature of prawn growth. Capturing length-increment growth heterogeneity for short-lived exploited species such as prawns that cannot be readily aged is essential for length-based modelling and improved management.

A genomewide screen for autism susceptibility loci

We report the analysis of 335 microsatellite markers genotyped in 110 multiplex families with autism. All families include at least two "affected" siblings, at least one of whom has autism; the remaining affected sibs carry diagnoses of either Asperger syndrome or pervasive developmental disorder. Affected sib-pair analysis yielded multipoint maximum LOD scores (MLS) that reach the accepted threshold for suggestive linkage on chromosomes 5, X, and 19. Nominal evidence for linkage (point-wise P<.05) was obtained on chromosomes 2, 3, 4, 8, 10, 11, 12, 15, 16, 18, and 20, and secondary loci were found on chromosomes 5 and 19. Analysis of families sharing alleles at the putative X chromosomal linked locus and one or more other putative linked loci produced an MLS of 3.56 for the DXS470-D19S174 marker combination. In an effort to increase power to detect linkage, scan statistics were used to evaluate the significance of peak LOD scores based on statistical evidence at adjacent marker loci. This analysis yielded impressive evidence for linkage to autism and autism-spectrum disorders with significant genomewide P values <.05 for markers on chromosomes 5 and 8 and with suggestive linkage evidence for a marker on chromosome 19.

Development of a Multiplexed Bead-Based Suspension Array for the Detection and Discrimination of Pospiviroid Plant Pathogens

Efficient and reliable diagnostic tools for the routine indexing and certification of clean propagating material are essential for the management of pospiviroid diseases in horticultural crops. This study describes the development of a true multiplexed diagnostic method for the detection and identification of all nine currently recognized pospiviroid species in one assay using Luminex bead-based suspension array technology. In addition, a new data-driven, statistical method is presented for establishing thresholds for positivity for individual assays within multiplexed arrays. When applied to the multiplexed array data generated in this study, the new method was shown to have better control of false positives and false negative results than two other commonly used approaches for setting thresholds. The 11-plex Luminex MagPlex-TAG pospiviroid array described here has a unique hierarchical assay design, incorporating a near-universal assay in addition to nine species-specific assays, and a co-amplified plant internal control assay for quality assurance purposes. All assays of the multiplexed array were shown to be 100% specific, sensitive and reproducible. The multiplexed array described herein is robust, easy to use, displays unambiguous results and has strong potential for use in routine pospiviroid indexing to improve disease management strategies.

Atomic Layer Deposition of Electroluminescent ZnS, SrS, and BaS Thin Films

The light emitted by flat panel displays (FPD) can be generated in many different ways, such as for example alternating current thin film electroluminescence (ACTFEL), liquid crystal display (LCD), light emitting diode (LED), or plasma display panel (PDP) technologies. In this work, the focus was on ACTFEL devices and the goal was to develop new thin film processes for light emitting materials in ACTFEL devices. The films were deposited with the atomic layer deposition (ALD) method, which has been utilized in the manufacturing of ACTFEL displays since the mid-1980s. The ALD method is based on surface-controlled self-terminated reactions and a maximum of one layer of the desired material can be prepared during one deposition cycle. Therefore, the film thickness can be controlled simply by adjusting the number of deposition cycles. In addition, both large areas and deep trench structures can be covered uniformly. During this work, new ALD processes were developed for the following thin film materials: BaS, CuxS, MnS, PbS, SrS, SrSe, SrTe, SrS1-xSex, ZnS, and ZnS1-xSex. In addition, several ACTFEL devices were prepared where the light emitting material was BaS, SrS, SrS1-xSex, ZnS, or ZnS1-xSex thin film that was doped with Ce, Cu, Eu, Mn, or Pb. The sulfoselenide films were made by substituting the elemental selenium for sulfur on the substrate surface during film deposition. In this way, it was possible to replace a maximum of 90% of the sulfur with selenium, and the XRD analyses indicated that the films were solid solutions. The polycrystalline BaS, SrS, and ZnS thin films were deposited at 180-400, 120-460, and 280-500 °C, respectively, and the processes had a wide temperature range where the growth rate of the films was independent of the deposition temperature. The electroluminescence studies showed that the doped sulfoselenide films resulted in low emission intensity. However, the emission intensities and emission colors of the doped SrS, BaS, and ZnS films were comparable with those found in earlier studies. It was also shown that the electro-optical properties of the different ZnS:Mn devices were different as a consequence of different ZnS:Mn processes. Finally, it was concluded that because the higher deposition temperature seemed to result in a higher emission intensity, the thermal stability of the reactants has a significant role when the light emitting materials of ACTFEL devices are deposited with the ALD method.

The need for speed: Timely prevention of the dispersal of noxious weeds in relief fodder using efficient sampling procedures

Invasive and noxious weeds are well known as a pervasive problem, imposing significant economic burdens on all areas of agriculture. Whilst there are multiple possible pathways of weed dispersal in this industry, of particular interest to this discussion is the unintended dispersal of weed seeds within fodder. During periods of drought or following natural disasters such as wild fire or flood, there arises the urgent need for 'relief' fodder to ensure survival and recovery of livestock. In emergency situations, relief fodder may be sourced from widely dispersed geographic regions, and some of these regions may be invaded by an extensive variety of weeds that are both exotic and detrimental to the intended destination for the fodder. Pasture hay is a common source of relief fodder and it typically consists of a mixture of grassy and broadleaf species that may include noxious weeds. When required urgently, pasture hay for relief fodder can be cut, baled, and transported over long distances in a short period of time, with little opportunity for prebaling inspection. It appears that, at the present time, there has been little effort towards rapid testing of bales, post-baling, for the presence of noxious weeds, as a measure to prevent dispersal of seeds. Published studies have relied on the analysis of relatively small numbers of bales, tested to destruction, in order to reveal seed species for identification and enumeration. The development of faster, more reliable, and non-destructive sampling methods is essential to increase the fodder industry's capacity to prevent the dispersal of noxious weeds to previously unaffected locales.

Taken for granted: Material relations between disability and codes/guidelines

This paper provides a critical examination of the taken for granted nature of the codes/guidelines used towards the creation of designed spaces, their social relations with designers, and their agency in designing for people with disabilities. We conducted case studies at three national museums in Canada where we began by questioning societal representations of disability within and through material culture through the potential of actor-network theory where non-human actors have considerable agency. Specifically, our exploration looks into how representations of disability for designing, are interpreted through mediums such as codes, standards and guidelines. We accomplish this through: deep analyses of the museums’ built environments (outdoors and indoors); interviewed curators, architects and designers involved in the creation of the spaces/displays; completed dialoguing while in motion interviews with people who have disabilities within the spaces; and analyzed available documents relating to the creation of the museums. Through analyses of our rich data set involving the mapping of codes/guidelines in their ‘representation’ of disability and their contributions in ‘fixing’ disability, this paper takes an alternative approach to designing for/with disability by aiming to question societal representations of disability within and through material culture.

Characterization of Mycobacterium leprae RecA intein, a LAGLIDADG homing endonuclease, reveals a unique mode of DNA-binding, helical distortion and cleavage, compared to a canonical LAGLIDADG homing endonuclease

Mycobacterium leprae, which has undergone reductive evolution leaving behind a minimal set of essential genes, has retained intervening sequences in four of its genes implicating a vital role for them in the survival of the leprosy bacillus. A single in-frame intervening sequence has been found embedded within its recA gene. Comparison of M. leprae recA intervening sequence with the known intervening sequences indicated that it has the consensus amino acid sequence necessary for being a LAGLIDADG-type homing endonuclease. In light of massive gene decay and function loss in the leprosy bacillus, we sought to investigate whether its recA intervening sequence encodes a catalytically active homing endonuclease. Here we show that the purified M. leprae RecA intein (PI-MleI) binds to cognate DNA and displays endonuclease activity in the presence of alternative divalent cations, Mg2+ or Mn2+. A combination of approaches including four complementary footprinting assays such as DNase I, Cu/phenanthroline, methylation protection and KMnO4, enhancement of 2-aminopurine fluorescence and mapping of the cleavage site revealed that PI-MleI binds to cognate DNA flanking its insertion site, induces helical distortion at the cleavage site and generates two staggered double-strand breaks. Taken together, these results implicate that PI-MleI possess a modular structure with separate domains for DNA target recognition and cleavage, each with distinct sequence preferences. From a biological standpoint, it is tempting to speculate that our findings have implications for understanding the evolution of LAGLIDADG family of homing endonucleases

Middleware for Mobile Sensing Applications in Urban Environments

Sensor networks represent an attractive tool to observe the physical world. Networks of tiny sensors can be used to detect a fire in a forest, to monitor the level of pollution in a river, or to check on the structural integrity of a bridge. Application-specific deployments of static-sensor networks have been widely investigated. Commonly, these networks involve a centralized data-collection point and no sharing of data outside the organization that owns it. Although this approach can accommodate many application scenarios, it significantly deviates from the pervasive computing vision of ubiquitous sensing where user applications seamlessly access anytime, anywhere data produced by sensors embedded in the surroundings. With the ubiquity and ever-increasing capabilities of mobile devices, urban environments can help give substance to the ubiquitous sensing vision through Urbanets, spontaneously created urban networks. Urbanets consist of mobile multi-sensor devices, such as smart phones and vehicular systems, public sensor networks deployed by municipalities, and individual sensors incorporated in buildings, roads, or daily artifacts. My thesis is that "multi-sensor mobile devices can be successfully programmed to become the underpinning elements of an open, infrastructure-less, distributed sensing platform that can bring sensor data out of their traditional close-loop networks into everyday urban applications". Urbanets can support a variety of services ranging from emergency and surveillance to tourist guidance and entertainment. For instance, cars can be used to provide traffic information services to alert drivers to upcoming traffic jams, and phones to provide shopping recommender services to inform users of special offers at the mall. Urbanets cannot be programmed using traditional distributed computing models, which assume underlying networks with functionally homogeneous nodes, stable configurations, and known delays. Conversely, Urbanets have functionally heterogeneous nodes, volatile configurations, and unknown delays. Instead, solutions developed for sensor networks and mobile ad hoc networks can be leveraged to provide novel architectures that address Urbanet-specific requirements, while providing useful abstractions that hide the network complexity from the programmer. This dissertation presents two middleware architectures that can support mobile sensing applications in Urbanets. Contory offers a declarative programming model that views Urbanets as a distributed sensor database and exposes an SQL-like interface to developers. Context-aware Migratory Services provides a client-server paradigm, where services are capable of migrating to different nodes in the network in order to maintain a continuous and semantically correct interaction with clients. Compared to previous approaches to supporting mobile sensing urban applications, our architectures are entirely distributed and do not assume constant availability of Internet connectivity. In addition, they allow on-demand collection of sensor data with the accuracy and at the frequency required by every application. These architectures have been implemented in Java and tested on smart phones. They have proved successful in supporting several prototype applications and experimental results obtained in ad hoc networks of phones have demonstrated their feasibility with reasonable performance in terms of latency, memory, and energy consumption.

A Decentralized Session Management Framework for Heterogeneous Ad-Hoc and Fixed Networks

Wireless technologies are continuously evolving. Second generation cellular networks have gained worldwide acceptance. Wireless LANs are commonly deployed in corporations or university campuses, and their diffusion in public hotspots is growing. Third generation cellular systems are yet to affirm everywhere; still, there is an impressive amount of research ongoing for deploying beyond 3G systems. These new wireless technologies combine the characteristics of WLAN based and cellular networks to provide increased bandwidth. The common direction where all the efforts in wireless technologies are headed is towards an IP-based communication. Telephony services have been the killer application for cellular systems; their evolution to packet-switched networks is a natural path. Effective IP telephony signaling protocols, such as the Session Initiation Protocol (SIP) and the H 323 protocol are needed to establish IP-based telephony sessions. However, IP telephony is just one service example of IP-based communication. IP-based multimedia sessions are expected to become popular and offer a wider range of communication capabilities than pure telephony. In order to conjoin the advances of the future wireless technologies with the potential of IP-based multimedia communication, the next step would be to obtain ubiquitous communication capabilities. According to this vision, people must be able to communicate also when no support from an infrastructured network is available, needed or desired. In order to achieve ubiquitous communication, end devices must integrate all the capabilities necessary for IP-based distributed and decentralized communication. Such capabilities are currently missing. For example, it is not possible to utilize native IP telephony signaling protocols in a totally decentralized way. This dissertation presents a solution for deploying the SIP protocol in a decentralized fashion without support of infrastructure servers. The proposed solution is mainly designed to fit the needs of decentralized mobile environments, and can be applied to small scale ad-hoc networks or also bigger networks with hundreds of nodes. A framework allowing discovery of SIP users in ad-hoc networks and the establishment of SIP sessions among them, in a fully distributed and secure way, is described and evaluated. Security support allows ad-hoc users to authenticate the sender of a message, and to verify the integrity of a received message. The distributed session management framework has been extended in order to achieve interoperability with the Internet, and the native Internet applications. With limited extensions to the SIP protocol, we have designed and experimentally validated a SIP gateway allowing SIP signaling between ad-hoc networks with private addressing space and native SIP applications in the Internet. The design is completed by an application level relay that permits instant messaging sessions to be established in heterogeneous environments. The resulting framework constitutes a flexible and effective approach for the pervasive deployment of real time applications.

Exploring privacy for ubiquitous computing: Tools, methods and experiments

Ubiquitous computing is about making computers and computerized artefacts a pervasive part of our everyday lifes, bringing more and more activities into the realm of information. The computationalization, informationalization of everyday activities increases not only our reach, efficiency and capabilities but also the amount and kinds of data gathered about us and our activities. In this thesis, I explore how information systems can be constructed so that they handle this personal data in a reasonable manner. The thesis provides two kinds of results: on one hand, tools and methods for both the construction as well as the evaluation of ubiquitous and mobile systems---on the other hand an evaluation of the privacy aspects of a ubiquitous social awareness system. The work emphasises real-world experiments as the most important way to study privacy. Additionally, the state of current information systems as regards data protection is studied. The tools and methods in this thesis consist of three distinct contributions. An algorithm for locationing in cellular networks is proposed that does not require the location information to be revealed beyond the user's terminal. A prototyping platform for the creation of context-aware ubiquitous applications called ContextPhone is described and released as open source. Finally, a set of methodological findings for the use of smartphones in social scientific field research is reported. A central contribution of this thesis are the pragmatic tools that allow other researchers to carry out experiments. The evaluation of the ubiquitous social awareness application ContextContacts covers both the usage of the system in general as well as an analysis of privacy implications. The usage of the system is analyzed in the light of how users make inferences of others based on real-time contextual cues mediated by the system, based on several long-term field studies. The analysis of privacy implications draws together the social psychological theory of self-presentation and research in privacy for ubiquitous computing, deriving a set of design guidelines for such systems. The main findings from these studies can be summarized as follows: The fact that ubiquitous computing systems gather more data about users can be used to not only study the use of such systems in an effort to create better systems but in general to study phenomena previously unstudied, such as the dynamic change of social networks. Systems that let people create new ways of presenting themselves to others can be fun for the users---but the self-presentation requires several thoughtful design decisions that allow the manipulation of the image mediated by the system. Finally, the growing amount of computational resources available to the users can be used to allow them to use the data themselves, rather than just being passive subjects of data gathering.

Religion Explained? : A Philosophical Appraisal of the Cognitive Science of Religion

This study examines philosophically the main theories and methodological assumptions of the field known as the cognitive science of religion (CSR). The study makes a philosophically informed reconstruction of the methodological principles of the CSR, indicates problems with them, and examines possible solutions to these problems. The study focuses on several different CSR writers, namely, Scott Atran, Justin Barrett, Pascal Boyer and Dan Sperber. CSR theorising is done in the intersection between cognitive sciences, anthropology and evolutionary psychology. This multidisciplinary nature makes CSR a fertile ground for philosophical considerations coming from philosophy of psychology, philosophy of mind and philosophy of science. The study begins by spelling out the methodological assumptions and auxiliary theories of CSR writers by situating these theories and assumptions in the nexus of existing approaches to religion. The distinctive feature of CSR is its emphasis on information processing: CSR writers claim that contemporary cognitive sciences can inform anthropological theorising about the human mind and offer tools for producing causal explanations. Further, they claim to explain the prevalence and persistence of religion by cognitive systems that undergird religious thinking. I also examine the core theoretical contributions of the field focusing mainly on the (1) “minimally counter-intuitiveness hypothesis” and (2) the different ways in which supernatural agent representations activate our cognitive systems. Generally speaking, CSR writers argue for the naturalness of religion: religious ideas and practices are widespread and pervasive because human cognition operates in such a way that religious ideas are easy to acquire and transmit. The study raises two philosophical problems, namely, the “problem of scope” and the “problem of religious relevance”. The problem of scope is created by the insistence of several critics of the CSR that CSR explanations are mostly irrelevant for explaining religion. Most CSR writers themselves hold that cognitive explanations can answer most of our questions about religion. I argue that the problem of scope is created by differences in explanation-begging questions: the former group is interested in explaining different things than the latter group. I propose that we should not stick too rigidly to one set of methodological assumptions, but rather acknowledge that different assumptions might help us to answer different questions about religion. Instead of adhering to some robust metaphysics as some strongly naturalistic writers argue, we should adopt a pragmatic and explanatory pluralist approach which would allow different kinds of methodological presuppositions in the study of religion provided that they attempt to answer different kinds of why-questions, since religion appears to be a multi-faceted phenomenon that spans over a variety of fields of special sciences. The problem of religious relevance is created by the insistence of some writers that CSR theories show religious beliefs to be false or irrational, whereas others invoke CSR theories to defend certain religious ideas. The problem is interesting because it reveals the more general philosophical assumptions of those who make such interpretations. CSR theories can (and have been) interpreted in terms of three different philosophical frameworks: strict naturalism, broad naturalism and theism. I argue that CSR theories can be interpreted inside all three frameworks without doing violence to the theories and that these frameworks give different kinds of results regarding the religious relevance of CSR theories.

A noticeboard in "both worlds" unsurprising interfaces supporting easy bi-cultural content publication

We describe the design of a digital noticeboard to support communication within a remote Aboriginal community whose aspiration is to live in "both worlds", nurturing and extending their Aboriginal culture and actively participating in Western society and economy. Three bi-cultural aspects have emerged and are presented here: the need for a bi-lingual noticeboard to span both oral and written language traditions, the tension between perfunctory information exchange and social, embodied protocols of telling in person and the different ways in which time is represented in both cultures. The design approach, developed iteratively through consultation, demonstration and testing led to an "unsurprising interface", aimed at maximizing use and appropriation across cultures by unifying visual, text and spoken contents in both passive and interactive displays in a modeless manner.