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.

More is not necessarily better. A biomechanical study on distal screw numbers in volar locking distal radius plates

INTRODUCTION: Currently available volar locking plates for the treatment of distal radius fractures incorporate at least two distal screw rows for fixation of the metaphyseal fragment and have a variable-angle locking mechanism which allows placement of the screws in various directions There is, however no evidence that these plates translate into better outcomes or have superior biomechanical properties to first generation plates, which had a single distal screw row and fixed-angle locking. The aim of our biomechanical study was to compare fixed-angle single-row plates with variable-angle multi-row plates to clarify the optimal number of locking screws. MATERIALS AND METHODS: Five different plate-screw combinations of three different manufacturers were tested, each group consisting of five synthetic fourth generation distal radius bones. An AO type C2 fracture was created and the fractures were plated according to each manufacturer's recommendations. The specimens then underwent cyclic and load-to-failure testing. An optical motion analysis system was used to detect displacement of fragments. RESULTS: No significant differences were detected after cyclic loading as well as after load-to-failure testing, neither in regard to axial deformation, implant rigidity or maximum displacement. The fixed-angle single-row plate showed the highest pre-test rigidity, least increase in post-testing rigidity and highest load-to-failure rigidity and least radial shortening. The radial shortening of plates with two distal screw rows was 3.1 and 4.3 times higher, respectively, than that of the fixed-angle single-row plate. CONCLUSION: The results of our study indicate that two distal screw rows do not add to construct rigidity and resistance against loss of reduction. Well conducted clinical studies based on the findings of biomechanical studies are necessary to determine the optimal number of screws necessary to achieve reproducibly good results in the treatment of distal radius fractures.

Measurement constructs to explore innovation diffusion in construction

Although the drivers of innovation have been studied extensively in construction, greater attention is required on how innovation diffusion can be effectively assessed within this complex and interdependent project-based industry. The authors draw on a highly cited innovation diffusion model by Rogers (2006) and develop a tailored conceptual framework to guide future empirical work aimed at assessing innovation diffusion in construction. The conceptual framework developed and discussed in this paper supports a five-stage process model of innovation diffusion namely: 1) knowledge and idea generation, 2) persuasion and evaluation; 3) decision to adopt, 4) integration and implementation, and 5) confirmation. As its theoretical contribution, this paper proposes three critical measurements constructs which can be used to assess the effectiveness of the diffusion process. These measurement constructs comprise: 1) nature and introduction of an innovative idea, 2) organizational capacity to acquire, assimilate, transform and exploit an innovation, and 3) rates of innovation facilitation and adoption. The constructs are interpreted in the project-based context of the construction industry, extending the contribution of general management theorists. Research planned by the authors will test the validity and reliability of the constructs developed in this paper.

Empirical analysis of the effect of dimension reduction and word order on semantic vectors

The aim of this paper is to provide a comparison of various algorithms and parameters to build reduced semantic spaces. The effect of dimension reduction, the stability of the representation and the effect of word order are examined in the context of the five algorithms bearing on semantic vectors: Random projection (RP), singular value decom- position (SVD), non-negative matrix factorization (NMF), permutations and holographic reduced representations (HRR). The quality of semantic representation was tested by means of synonym finding task using the TOEFL test on the TASA corpus. Dimension reduction was found to improve the quality of semantic representation but it is hard to find the optimal parameter settings. Even though dimension reduction by RP was found to be more generally applicable than SVD, the semantic vectors produced by RP are somewhat unstable. The effect of encoding word order into the semantic vector representation via HRR did not lead to any increase in scores over vectors constructed from word co-occurrence in context information. In this regard, very small context windows resulted in better semantic vectors for the TOEFL test.

Does teaching sequence matter when teaching high school chemistry with scientific visualisations?

Five Canadian high school Chemistry classes in one school, taught by three different teachers, studied the concepts of dynamic chemical equilibria and Le Chatelier’s Principle. Some students received traditional teacher-led explanations of the concept first and used an interactive scientific visualisation second, while others worked with the visualisation first and received the teacher-led explanation second. Students completed a test of their conceptual understanding of the relevant concepts prior to instruction, after the first instructional session and at the end of instruction. Data on students’ academic achievement (highest, middle or lowest third of the class on the mid-term exam) and gender were also collected to explore the relationship between these factors, conceptual development and instructional sequencing. Results show, within this context at least, that teaching sequence is not important in terms of students’ conceptual learning gains.

Intraurban rail access : Policy implications of five revealed perspectives from a Q-sorting exercise in three Australian cities

This project advances current understanding of intra-urban rail passengers and their travel experiences in order to help rail industry leaders tailor policy approaches to fit specific, relevant segments of their target population. Using a Q sorting technique and cluster analysis, our preliminary research identified five perspectives occurring in a small sample of rail passengers, who varied in their frequency and location of rail travel as well as certain socio-demographic characteristics. Revealed perspectives (named to capture the gist of their content) included: ‘Rail Travel is About the Destination, Not the Journey’; ‘Despite Challenges, Public Transport is Still the Best Option’; ‘Rail Travel is Fine’; ‘Rail Travel? So Far, So Good’; and ‘Bad Taste for Rail Travel’. This paper discusses each of the perspectives in detail, and considers them in terms of tailored policy implications. An overarching finding from this study is that improving railway travel ‘access’ requires attention to physical, psychological, financial, and social facets of accessibility. For example, designing waiting areas to be more socially functional and comfortable has the potential to increase ridership by addressing social forms of access, decreasing perceived wait times, and making time at the station feel like time well spent. Even at this preliminary stage, the Q sorting technique promises to provide a valuable, holistic albeit fine-grained analysis of passenger attitudes and experiences that will assist industry efforts to increase ridership.

A customisable dashboard display for environmental performance visualisations

We conducted an exploratory study of a mobile energy monitoring tool: The Dashboard. Our point of departure from prior work was the emphasis of end-user customisation and social sharing. Applying extensive feedback, we deployed the Dashboard in real-world conditions to socially linked research participants for a period of five weeks. Participants were encouraged to devise, construct, place, and view various data feeds. The aim of our study was to test the assumption that participants, having control over their Dashboard configuration, would engage, and remain engaged, with their energy feedback throughout the trial. Our research points to a set of design issues surrounding the adoption and continued use of such tools. A novel finding of our study is the impact of social links between participants and their continued engagement with the Dashboard. Our results also illustrate the emergence of energy-voyeurism, a form of social energy monitoring by peers.

Factors affecting two- and five-year re-offence rates in Queensland drink drivers

Risk factors for repeat drink driving, an important road safety issue, are well known, but estimates of Australian recidivism rates by risk factors, apart from a recent NSW study, are not. Driving records of a cohort of Queensland drink drivers matched by age, region, BAC level and prior offence to participants in a drink driving rehabilitation program were used to estimate sex-specific two- and five-year re-offence rates overall and by these factors. Estimates of the proportion of Queensland drink drivers with a prior DD offence in 2004 were used to standardise rates to the Queensland drink driving population. Rates were higher in remote areas, as were rates in males, young drivers, drivers with high BAC levels and in drivers with one and especially with at least two prior DD convictions. Five-year rates for Queensland were estimated as 21.8% in males and 16.4% in females, appreciably higher than in NSW.

Intratherapist reliability in the rating of scapula posture in multiple planes of reference

Background: Evaluation of scapular posture is a fundamental component in the clinical evaluation of the upper quadrant. This study examined the intrarater reliability of scapular posture ratings. Methods: A test-retest reliability investigation was undertaken with one week between assessment sessions. At each session physical therapists conducted visual assessments of scapula posture (relative to the thorax) in five different scapula postural planes (plane of scapula, sagittal plane, transverse plane, horizontal plane, and vertical plane). These five plane ratings were performed for four different scapular posture perturbating conditions (rest, isometric shoulder; flexion, abduction, and external rotation). Results. A total of 100 complete scapular posture ratings (50 left, 50 right) were undertaken at each assessment. The observed agreement between the test and retest postural plane ratings ranged from 59% to 87%; 16 of the 20 plane-condition combinations exceeded 75% observed agreement. Kappa (and prevalence adjusted bias adjusted kappa) values were inconsistent across the postural planes and perturbating conditions. Conclusions: This investigation generally revealed fair to moderate intrarater reliability in the rating of scapular posture by visual inspection. However, enough disagreement between assessments was present to warrant caution when interpreting perceived changes in scapula position between longitudinal assessments using visual inspection alone.

How to design extended finite state machine test models in Java

This chapter is a tutorial that teaches you how to design extended finite state machine (EFSM) test models for a system that you want to test. EFSM models are more powerful and expressive than simple finite state machine (FSM) models, and are one of the most commonly used styles of models for model-based testing, especially for embedded systems. There are many languages and notations in use for writing EFSM models, but in this tutorial we write our EFSM models in the familiar Java programming language. To generate tests from these EFSM models we use ModelJUnit, which is an open-source tool that supports several stochastic test generation algorithms, and we also show how to write your own model-based testing tool. We show how EFSM models can be used for unit testing and system testing of embedded systems, and for offline testing as well as online testing.

A Reliability test system for educational purposes-basic data

The IEEE Subcommittee on the Application of Probability Methods (APM) published the IEEE Reliability Test System (RTS) [1] in 1979. This system provides a consistent and generally acceptable set of data that can be used both in generation capacity and in composite system reliability evaluation [2,3]. The test system provides a basis for the comparison of results obtained by different people using different methods. Prior to its publication, there was no general agreement on either the system or the data that should be used to demonstrate or test various techniques developed to conduct reliability studies. Development of reliability assessment techniques and programs are very dependent on the intent behind the development as the experience of one power utility with their system may be quite different from that of another utility. The development and the utilization of a reliability program are, therefore, greatly influenced by the experience of a utlity and the intent of the system manager, planner and designer conducting the reliability studies. The IEEE-RTS has proved to be extremely valuable in highlighting and comparing the capabilities (or incapabilities) of programs used in reliability studies, the differences in the perception of various power utilities and the differences in the solution techniques. The IEEE-RTS contains a reasonably large power network which can be difficult to use for initial studies in an educational environment.

A Reliability test system for educational purposes-basic data

The IEEE Reliability Test System (RTS) developed by the Application of Probability Method Subcommittee has been used to compare and test a wide range of generating capacity and composite system evaluation techniques and subsequent digital computer programs. A basic reliability test system is presented which has evolved from the reliability education and research programs conducted by the Power System Research Group at the University of Saskatchewan. The basic system data necessary for adequacy evaluation at the generation and composite generation and transmission system levels are presented together with the fundamental data required to conduct reliability-cost/reliability-worth evaluation

A Reliability test system for educational purposes-basic results

A set of basic reliability indices at the generation and composite generation and transmission levels for a small reliability test system are presented. The test system and the results presented have evolved from reliability research and teaching programs. The indices presented are for fundamental reliability applications which should be covered in a power system reliability teaching program. The RBTS test system and the basic indices provide a valuable reference for faculty and students engaged in reliability teaching and research

Five minute call : where are you just before the curtain goes up

For any dancer, whether a student or professional, the five minute call is the final prompt to say ‘Get ready, you’re about to go on!’ It can be a time of cool confidence or a last minute rehearsal of steps; joking with colleagues to take your mind off the performance, or a period of overwhelming anxiety about everything that could possibly go wrong.

Preliminary reliability and validity testing of a self-efficacy questionnaire for Chinese family caregivers

Objectives: To develop and test preliminary reliability and validity of a Self-Efficacy Questionnaire for Chinese Family Caregivers (SEQCFC). Methods: A cross-sectional survey of 196 family caregivers (CGs) of people with dementia (CGs) was conducted to determine the factor structure of a SEQCFC of people with dementia. Following factor analyses, preliminary testing was performed, including internal consistency, 4-week test retest reliability, and construct and convergent validity. Results: Factor analyses with direct oblimin rotation were performed. Eight items were removed and five subscales(selfefficacy for gathering information about treatment, symptoms and health care; obtaining support; responding to behaviour disturbances; managing household, personal and medical care; and managing distress associated with caregiving) were identified. The Cronbach’s alpha coefficients for the whole scale and for each subscale were all over 0.80. The 4-week testretest reliabilities for the whole scale and for each subscale ranged from 0.64 to 0.85. The convergent validity was acceptable. Conclusions: Evidence for the preliminary testing of the SEQCFC was encouraging. A future follow-up study using confirmatory factor analysis with a new sample from different recruitment centres in Shanghai will be conducted. Future psychometric property testings of the questionnaire will be required for CGs from other regions of mainland China.