Sequence Changes in Six Variants of Rice Tungro Bacilliform Virus and Their Phylogenetic Relationships

The DNA of three biological variants, G1, Ic and G2, which originated from the same greenhouse isolate of rice tungro bacilliform virus (RTBV) at the International Rice Research Institute (IRRI), was cloned and sequenced. Comparison of the sequences revealed small differences in genome sizes. The variants were between 95 and 99% identical at the nucleotide and amino acid levels. Alignment of the three genome sequences with those of three published RTBV sequences (Phi-1, Phi-2 and Phi-3) revealed numerous nucleotide substitutions and some insertions and deletions. The published RTBV sequences originated from the same greenhouse isolate at IRRI 20, 11 and 9 years ago. All open reading frames (ORFs) and known functional domains were conserved across the six variants. The cysteine-rich region of ORF3 showed the greatest variation. When the six DNA sequences from IRRI were compared with that of an isolate from Malaysia (Serdang), similar changes were observed in the cysteine-rich region in addition to other nucleotide substitutions and deletions across the genome. The aligned nucleotide sequences of the IRRI variants and Serdang were used to analyse phylogenetic relationships by the bootstrapped parsimony, distance and maximum-likelihood methods. The isolates clustered in three groups: Serdang alone; Ic and G1; and Phi-1, Phi-2, Phi-3 and G2. The distribution of phylogenetically informative residues in the IRRI sequences shared with the Serdang sequence and the differing tree topologies for segments of the genome suggested that recombination, as well as substitutions and insertions or deletions, has played a role in the evolution of RTBV variants. The significance and implications of these evolutionary forces are discussed in comparison with badnaviruses and caulimoviruses.

Editorial : knowledge-based development of cities : a myth or reality?

Urban development in the first decade of the 21st century has faced many challenges ranging from rapid to shrinking urbanisation, from emerging knowledge economy to global division of labour and from globalisation to climate change. Along with these challenges new concepts, such as essentialism, environmentalism and dematerialism, are emerged and started to influence the way urban development plans are prepared and visions for the development of cities are made. Beyond this, scholars, practitioners and decision-makers have also started to discuss the need for an new urban planning and development approach in order to achieve a development that is sustainable and knowledge-based. Limited successful examples of alternative planning and development approaches showcased potentials of moving towards a new plan-making mindset in the era of knowledge economy. This paper presents a new urban planning and development approach that is taking application ground in many parts of the globe, namely knowledge-based urban development. After providing the theoretical foundation and conceptual framework of knowledge-based urban development the paper discusses whether knowledge-based development of cities is a myth or a reality.

Intake of isoflavone and lignan phytoestrogens and associated demographic and lifestyle factors in older Australian women

The purpose was to determine intake of phytoestrogens in a sample of older Australian women, and to investigate associated lifestyle factors. Subjects were an age-stratified sample of 511 women aged 40-80 y, randomly selected from the electoral roll and participating in the Longitudinal Assessment of Ageing in Women at the Royal Brisbane and Women’s Hospital. A cross-sectional study was conducted to assess isoflavone and lignan intake over the past month from food and supplements using a 112-item phytoestrogen frequency questionnaire. Data were also collected on nutrient intakes, physical activity, smoking, alcohol, non-prescription supplements, hormone therapy, education and occupation. Logistic regression was used to evaluate associations between demographic and lifestyle variables and soy/linseed consumption while controlling for age. Isoflavone intakes were significantly higher in the younger compared to older age groups (p<0.001); there were no age-related differences in lignan intake. Forty-five percent of women consumed at least one serve of a soy and/or linseed item and were defined as a soy/linseed consumer. Median (range) intakes by consumers for isoflavones and lignans (3.9 (0-172) mg/d and 2.4 (0.1-33) mg/d) were higher than intakes by non-consumers (0.004 (0-2.6) mg/d and 1.57 (0.44-4.7) mg/d), respectively (p<0.001). Consumers had higher intakes of dietary fibre (p=0.003), energy (p=0.04) and polyunsaturated fat (p=0.004), and higher levels of physical activity (p=0.006), socio-economic position (p<0.001), education (p<0.001) and supplement use (p<0.001). Women who consumed soy or linseed foods differed in lifestyle and demographic characteristics suggesting these factors should be considered when investigating associations with chronic disease outcomes.

Identification of novel markers for uncomplicated lower genital tract infections and upper genital tract pathology due to Chlamydia trachomatis.

Background: Untreated Chlamydia trachomatis infections in women can result in disease sequelae such as salpingitis and pelvic inflammatory disease (PID), ultimately culminating in tubal occlusion and infertility. Whilst nucleic acid amplification tests can effectively diagnose uncomplicated lower genital tract (LGT) infections, they are not suitable for diagnosing upper genital tract (UGT) pathological sequelae. As a consequence, this study aimed to identify serological markers that can, with a high degree of sensitivity and specificity, discriminate between LGT infections and UGT pathology. Methods: Plasma was collected from 73 women with a history of LGT infection, UGT pathology due to C. trachomatis or no serological evidence of C. trachomatis infection. Western blotting was used to analyse antibody reactivity against extracted chlamydial proteins. Sensitivity and specificity of differential markers were also calculated. Results: Four antigens (CT157, CT423, CT727 and CT396) were identified and found to be capable of discriminating between the infection and disease sequelae state. Sensitivity and specificity calculations showed that our assay for diagnosing LGT infection had a sensitivity and specificity of 75% and 76% respectively, whilst the assay for identifying UGT pathology demonstrated 80% sensitivity and 86% specificity. Conclusions: The use of these assays could potentially facilitate earlier diagnoses in women suffering UGT pathology due to C. trachomatis.

Estimates of crowding in long-term care: Comparing two approaches

Objective: Because studies of crowding in long-term care settings are lacking, the authors sought to: (1) generate initial estimates of crowding in nursing homes and assisted living facilities; and (2) evaluate two operational approaches to its measurement. ----- ----- Background: Reactions to density and proximity are complex. Greater density intensifies people's reaction to a situation in the direction (positive or negative) that they would react if the situation were to occur under less dense conditions. People with dementia are especially reactive to the environment. ----- ----- Methods: Using a cross-sectional correlational design in nursing homes and assisted living facilities involving 185 participants, multiple observations (N = 6,455) of crowding and other environmental variables were made. Crowding, location, and sound were measured three times per observation; ambiance was measured once. Data analyses consisted of descriptive statistics, t-tests, and one-way analysis of variance. ----- ----- Results: Crowding estimates were higher for nursing homes and in dining and activity rooms. Crowding also varied across settings and locations by time of day. Overall, the interaction of location and time affected crowding significantly (N = 5,559, df [47, 511], F = 105.69, p < .0001); effects were greater within location-by-hour than between location-by-hour, but the effect explained slightly less variance in Long-Term Care Crowding Index (LTC-CI) estimates (47.41%) than location alone. Crowding had small, direct, and highly significant correlations with sound and with the engaging subscale for ambiance; a similar, though inverse, correlation was seen with the soothing subscale for ambiance. ----- ----- Conclusions: Crowding fluctuates consistent with routine activities such as meals in long-term care settings. Furthermore, a relationship between crowding and other physical characteristics of the environment was found. The LTC-CI is likely to be more sensitive than simple people counts when seeking to evaluate the effects of crowding on the behavior of elders-particularly those with dementia-in long-term care settings. aging in place.

Knowledge-based development of cities : a myth or reality?

Urban development in the 21st decade of the 21st century has faced many challenges ranging from rapid to shrinking urbanisation, from emerging knowledge economy to global division of labour and from globalisation to climate change. Along with with these challenges new concepts, such as essentialism, environmentalism and dematerialism, are emerged and started to influence the way urban development plans are prepared and visions for the development of cities are made. Beyond this, scholars, practitioners and decision-makers have also started to discuss the need for an new urban planning and development approach in order to achieve a development that is sustainable and knowledge-based. Limited successful examples of alternative planning and development approaches showcased potentials of moving towards a new plan-making mindset in the era of knowledge economy. This paper presents a new urban planning and development approach that is taking application ground in many parts of the globe, namely knowledge-based urban development. After providing the theoretical foundation and conceptual framework of knowledge-based urban development the paper discusses whether knowledge-based development of cities is a myth or a reality.

Lucky or Lagging? Anne Summers's On Luck [A Review]

Described as 'The Lucky Country' over forty-years ago, Australia continues to play on and onward with a fervent belief in luck, her people often described, usually by themselvess, as 'graced' or as living in 'God's Own'. With our comfortable lifestyle and isolated location, white sands and soft mangoes, it is easy to see why we embraced the term so eagerly. Where else could you win the lottery twice? While these national stereotypes are an essential part of the romance that drives and defines us, the idea that luck is the central motif of Australian culture has become a cliche, and a dangerous, almost disastrous one at that. In On Luck, Anne Summers observes, "You hear it everywhere: in all sorts of conversations, in Qantas ads, from the mouths of travellers returning from overseas trips full of complaints about the climate, the crowds, the uncivility of other places".

Assessment of commercial network RTK user positioning performance over long inter-station distances

The paper provides an assessment of the performance of commercial Real Time Kinematic (RTK) systems over longer than recommended inter-station distances. The experiments were set up to test and analyse solutions from the i-MAX, MAX and VRS systems being operated with three triangle shaped network cells, each having an average inter-station distance of 69km, 118km and 166km. The performance characteristics appraised included initialization success rate, initialization time, RTK position accuracy and availability, ambiguity resolution risk and RTK integrity risk in order to provide a wider perspective of the performance of the testing systems. ----- ----- The results showed that the performances of all network RTK solutions assessed were affected by the increase in the inter-station distances to similar degrees. The MAX solution achieved the highest initialization success rate of 96.6% on average, albeit with a longer initialisation time. Two VRS approaches achieved lower initialization success rate of 80% over the large triangle. In terms of RTK positioning accuracy after successful initialisation, the results indicated a good agreement between the actual error growth in both horizontal and vertical components and the accuracy specified in the RMS and part per million (ppm) values by the manufacturers. ----- ----- Additionally, the VRS approaches performed better than the MAX and i-MAX when being tested under the standard triangle network with a mean inter-station distance of 69km. However as the inter-station distance increases, the network RTK software may fail to generate VRS correction and then may turn to operate in the nearest single-base RTK (or RAW) mode. The position uncertainty reached beyond 2 meters occasionally, showing that the RTK rover software was using an incorrect ambiguity fixed solution to estimate the rover position rather than automatically dropping back to using an ambiguity float solution. Results identified that the risk of incorrectly resolving ambiguities reached 18%, 20%, 13% and 25% for i-MAX, MAX, Leica VRS and Trimble VRS respectively when operating over the large triangle network. Additionally, the Coordinate Quality indicator values given by the Leica GX1230 GG rover receiver tended to be over-optimistic and not functioning well with the identification of incorrectly fixed integer ambiguity solutions. In summary, this independent assessment has identified some problems and failures that can occur in all of the systems tested, especially when being pushed beyond the recommended limits. While such failures are expected, they can offer useful insights into where users should be wary and how manufacturers might improve their products. The results also demonstrate that integrity monitoring of RTK solutions is indeed necessary for precision applications, thus deserving serious attention from researchers and system providers.

Concomitant or sequential administration of live attenuated Japanese encephalitis chimeric virus vaccine and yellow fever 17D vaccine : randomized double-blind phase II evaluation of safety and immunogenicity

A randomized, double-blind, study was conducted to evaluate the safety, tolerability and immunogenicity of a live attenuated Japanese encephalitis chimeric virus vaccine (JE-CV) co-administered with live attenuated yellow fever (YF) vaccine (YF-17D strain; Stamaril(®), Sanofi Pasteur) or administered successively. Participants (n = 108) were randomized to receive: YF followed by JE-CV 30 days later, JE followed by YF 30 days later, or the co-administration of JE and YF followed or preceded by placebo 30 days later or earlier. Placebo was used in a double-dummy fashion to ensure masking. Neutralizing antibody titers against JE-CV, YF-17D and selected wild-type JE virus strains was determined using a 50% serum-dilution plaque reduction neutralization test. Seroconversion was defined as the appearance of a neutralizing antibody titer above the assay cut-off post-immunization when not present pre-injection at day 0, or a least a four-fold rise in neutralizing antibody titer measured before the pre-injection day 0 and later post vaccination samples. There were no serious adverse events. Most adverse events (AEs) after JE vaccination were mild to moderate in intensity, and similar to those reported following YF vaccination. Seroconversion to JE-CV was 100% and 91% in the JE/YF and YF/JE sequential vaccination groups, respectively, compared with 96% in the co-administration group. All participants seroconverted to YF vaccine and retained neutralizing titers above the assay cut-off at month six. Neutralizing antibodies against JE vaccine were detected in 82-100% of participants at month six. These results suggest that both vaccines may be successfully co-administered simultaneously or 30 days apart.

Humanitarianism or self-serving hypocrisy? : the provision of aid to South Africa under the Hawke-Keating and Howard governments

General perceptions of foreign aid commonly engender images of humanitarianism and altruism, whereby the humanitarian needs of the recipient of development assistance are of the utmost priority of the aid donor. However, the Australian governments led by Hawke, Keating and Howard often gave humanitarianism a low emphasis, frequently placing Australia’s own foreign policy and economic concerns at the forefront of aid allocation – often unashamedly. This self-interest met through aid meant that most was provided to Australia’s regional neighbourhood, neglecting some of the poorest, most struggling states, including South Africa. Other issues and events, including the Cold War, apartheid, terrorism and HIV/AIDS also affected Australia’s aid policy; mostly, they were used as excuses to limit aid to states like South Africa.

Use of acoustic emission technique for structural health monitoring of bridges

Bridges are valuable assets of every nation. They deteriorate with age and often are subjected to additional loads or different load patterns than originally designed for. These changes in loads can cause localized distress and may result in bridge failure if not corrected in time. Early detection of damage and appropriate retrofitting will aid in preventing bridge failures. Large amounts of money are spent in bridge maintenance all around the world. A need exists for a reliable technology capable of monitoring the structural health of bridges, thereby ensuring they operate safely and efficiently during the whole intended lives. Monitoring of bridges has been traditionally done by means of visual inspection. Visual inspection alone is not capable of locating and identifying all signs of damage, hence a variety of structural health monitoring (SHM) techniques is used regularly nowadays to monitor performance and to assess condition of bridges for early damage detection. Acoustic emission (AE) is one technique that is finding an increasing use in SHM applications of bridges all around the world. The chapter starts with a brief introduction to structural health monitoring and techniques commonly used for monitoring purposes. Acoustic emission technique, wave nature of AE phenomenon, previous applications and limitations and challenges in the use as a SHM technique are also discussed. Scope of the project and work carried out will be explained, followed by some recommendations of work planned in future.

Teaching sustainability : vehicle or endpoint?

In 2006, the Faculty of Built Environment and Engineering introduced the first faculty wide unit dedicated to sustainability at any Australian University. BEB200 Introducing Sustainability has semester enrolments of up to 1500 students. Instruments such as lectures, readings, field visits, group projects and structured tutorial activities are used and have evolved over the last five years in response to student and staff feedback and attempts to better engage students. More than seventy staff have taught in the unit, which is in its final offering in this form in 2010. This paper reflects on the experiences of five academics who have played key roles in the development and teaching of this unit over the last five years. They argue that sustainability is a paradigm that allows students to explore other ways of knowing as they engage with issues in a complex world, not an end in itself. From the students’ perspective, grappling with such issues enables them to move towards a context in which they can understand their own discipline and its role in the contradictory and rapidly changing professional world. Insights are offered into how sustainability units may be developed in the future.

Ureaplasma parvum and ureaplasma urealyticum detected in semen after washing prior to assisted reproductive technology procedures

Objective: This study investigated: (i) the prevalence of ureaplasmas in semen and washed semen and (ii) the effect of ureaplasmas on semen andrology parameters. Design: Prospective study. Setting: IVF unit -private hospital, Brisbane, Australia. Patient(s): Three hundred and forty three men participating in an assisted reproductive technology (ART) treatment cycle. Intervention(s): Semen and washed semen tested by culture, PCR assays and indirect immunofluorescent antibody assays. Statistical differences were determined by a t-test, Wilcoxon or Pearson’s Chi- square test where appropriate. Main Outcome Measure(s): The prevalence of ureaplasmas in semen and washed semen and the effect of these microorganisms on semen andrology parameters. Result(s): Ureaplasmas were detected in 73/343 (22%) semen samples and 29/343 (8.5%) washed semen samples. Ureaplasmas adherent to the surface of spermatozoa were demonstrated by indirect immunofluorescent antibody testing. U. parvum serovar 6 (36.6%) and U. urealyticum (30%) were the most prevalent isolates in washed semen. A comparison of the semen andrology parameters of washed semen ureaplasma positive and negative groups demonstrated a lower proportion of non-motile sperm in the washed semen ureaplasma positive group. Conclusion(s): Ureaplasmas are not always removed from semen by a standard ART washing procedure and can remain adherent to the surface of spermatozoa.

Risky driving or risky drivers? Exploring driving and crash histories of illegal street racing offenders

Illegal street racing has received increased attention in recent years from road safety professionals and the media as jurisdictions in Australia, Canada, and the United States have implemented laws to address the problem, which primarily involves young male drivers. Although some evidence suggests that the prevalence of illegal street racing is increasing, obtaining accurate estimates of the crash risk of this behavior is difficult because of limitations in official data sources. Although crash risk can be explored by examining the proportion of incidents of street racing that result in crashes, or the proportion of all crashes that involve street racing, this paper reports on the findings of a study that explored the riskiness of involved drivers. The driving histories of 183 male drivers with an illegal street racing conviction in Queensland, Australia, were compared with a random sample of 183 male Queensland drivers with the same age distribution. The offender group was found to have significantly more traffic infringements, license sanctions, and crashes than the comparison group. Drivers in the offender group were more likely than the comparison group to have committed infringements related to street racing, such as speeding, "hooning," and offenses related to vehicle defects or illegal modifications. Insufficient statistical capacity prevented full exploration of group differences in the type and nature of earlier crashes. It was concluded, however, that street racing offenders generally can be considered risky drivers who warrant attention and whose risky behavior cannot be explained by their youth alone.

Exposure of pipe insulation to high temperatures from domestic pumped storage (split) solar water heating systems in Australia and New Zealand

Pipe insulation between the collector and storage tank on pumped storage (commonly called split), solar water heaters can be subject to high temperatures, with a maximum equal to the collector stagnation temperature. The frequency of occurrence of these temperatures is dependent on many factors including climate, hot water demand, system size and efficiency. This paper outlines the findings of a computer modelling study to quantify the frequency of occurrence of pipe temperatures of 80 degrees Celsius or greater at the outlet of the collectors for these systems. This study will help insulation suppliers determine the suitability of their materials for this application. The TRNSYS program was used to model the performance of a common size of domestic split solar system, using both flat plate and evacuated tube, selective surface collectors. Each system was modelled at a representative city in each of the 6 climate zones for Australia and New Zealand, according to AS/NZS4234 - Heat Water Systems - Calculation of energy consumption, and the ORER RECs calculation method. TRNSYS was used to predict the frequency of occurrence of the temperatures that the pipe insulation would be exposed to over an average year, for hot water consumption patterns specified in AS/NZS4234, and for worst case conditions in each of the climate zones. The results show; * For selectively surfaced, flat plate collectors in the hottest location (Alice Sprints) with a medium size hot water demand according to AS/NZS2434, the annual frequency of occurrence of temperatures at and above 80 degrees Celsius was 33 hours. The frequency of temperatures at and above 140 degrees Celsius was insignificant. * For evacuated tube collectors in the hottest location (Alice Springs), the annual frequency of temperatures at and above 80 degrees Celsius was 50 hours. Temperatures at and above 140 degrees Celsius were significant and were estimated to occur for more than 21 hours per year in this climate zone. Even in Melbourne, temperatures at and above 80 degrees can occur for 12 hours per year and at and above 140 degrees for 5 hours per year. * The worst case identified was for evacuated tube collectors in Alice Springs, with mostly afternoon loads in January. Under these conditions, the frequency of temperatures at and above 80 degrees Celsius was 10 hours for this month only. Temperatures at and above 140 degrees Celsius were predicted to occur for 5 hours in January.