Identification of long intergenic region sequences involved in maize streak virus replication

The main cis-acting control regions for replication of the single-stranded DNA genome of maize streak virus (MSV) are believed to reside within an approximately 310 nt long intergenic region (LIR). However, neither the minimum LIR sequence required nor the sequence determinants of replication specificity have been determined experimentally. There are iterated sequences, or iterons, both within the conserved inverted-repeat sequences with the potential to form a stem-loop structure at the origin of virion-strand replication, and upstream of the rep gene TATA box (the rep-proximal iteron or RPI). Based on experimental analyses of similar iterons in viruses from other geminivirus genera and their proximity to known Rep-binding sites in the distantly related mastrevirus wheat dwarf virus, it has been hypothesized that the iterons may be Rep-binding and/or -recognition sequences. Here, a series of LIR deletion mutants was used to define the upper bounds of the LIR sequence required for replication. After identifying MSV strains and distinct mastreviruses with incompatible replication-specificity determinants (RSDs), LIR chimaeras were used to map the primary MSV RSD to a 67 nt sequence containing the RPI. Although the results generally support the prevailing hypothesis that MSV iterons are functional analogues of those found in other geminivirus genera, it is demonstrated that neither the inverted-repeat nor RPI sequences are absolute determinants of replication specificity. Moreover, widely divergent mastreviruses can trans-replicate one another. These results also suggest that sequences in the 67 nt region surrounding the RPI interact in a sequence-specific manner with those of the inverted repeat.

Volume-dependent response of precooling for intermittent-sprint exercise in the heat

Purpose: To assess the effects of pre-cooling volume on neuromuscular function and performance in free-paced intermittent-sprint exercise in the heat. Methods: Ten male, teamsport athletes completed four randomized trials involving an 85-min free-paced intermittentsprint exercise protocol in 33°C±33% relative humidity. Pre-cooling sessions included whole body (WB), head+hand (HH), head (H) and no cooling (CONT), applied for 20-min pre-exercise and 5-min mid exercise. Maximal voluntary contractions (MVC) were assessed pre- and postintervention and mid- and post-exercise. Exercise performance was assessed with sprint times, % decline and distances covered during free-paced bouts. Measures of core(Tc) and skin (Tsk) temperatures, heart rate, perceptual exertion and thermal stress were monitored throughout. Venous and capillary blood was analyzed for metabolite, muscle damage and inflammatory markers. Results: WB pre-cooling facilitated the maintenance of sprint times during the exercise protocol with reduced % decline (P=0.04). Mean and total hard running distances increased with pre cooling 12% compared to CONT (P<0.05), specifically, WB was 6-7% greater than HH (P=0.02) and H (P=0.001) respectively. No change was evident in mean voluntary or evoked force pre- to post-exercise with WB and HH cooling (P>0.05). WB and HH cooling reduced Tc by 0.1-0.3°C compared to other conditions (P<0.05). WB Tsk was suppressed for the entire session(P=0.001). HR responses following WB cooling were reduced(P=0.05; d=1.07) compared to CONT conditions during exercise. Conclusion: A relationship between pre-cooling volume and exercise performance seems apparent, as larger surface area coverage augmented subsequent free-paced exercise capacity, in conjunction with greater suppression of physiological load. Maintenance of MVC with pre-cooling, despite increased work output suggests the role of centrally-mediated mechanisms in exercise pacing regulation and subsequent performance.

Building intercultural competence one “Patch” at a time

This paper describes a program called Patches that was implemented to assist a group of Australian and Malaysian pre-service teachers to enhance their intercultural competence through their involvement in a series of reciprocal learning activities. Each learning experience was considered a “patch” that eventually created a “quilt of intercultural learning.” The purpose of this study was to enhance the intercultural competence of domestic and international students through organized intercultural activities, through a series of reflective writing sessions, and mutual engagement on a common project. The effectiveness of the Patches program was analysed in accordance with Deardorff’s elements of intercultural competence. The qualitative findings indicate that both cohorts of preservice teachers showed elements of intercultural competence through participation in the program, with both groups reporting a deeper appreciation and understanding of how to communicate more effectively in intercultural contexts.

Developing academic and intercultural competence : the impact of a Patches program

This symposium focuses on an innovative Patches program that addresses imperatives with respect to the development of intercultural competence. The term, Patches, in this project refers to writing tasks and intercultural activities wherein each task becomes a ‘patch’ that eventually creates a quilt of learning as experienced by 58 second year BEd students from Malaysia and 14 fourth year domestic (Australian) BEd students. We take intercultural competence to mean students “ability to communicate effectively and appropriately in intercultural situations based on [their] intercultural knowledge, skills and attitudes” (Deardorff, 2006). The papers in this symposium provide detailed information about the design of the program, its impact on students’ perceptions of themselves as students, writers, and emerging professionals, and students’ development of intercultural competence.

Editorial : infectious disease modelling

The aim of this Special Issue is to collect together a group of outstanding applied mathematics research articles that provide new insight into our understanding of infectious diseases and infectious disease modelling. The scope of the articles is broad, encompassing both specific applications of modelling to particular examples of infectious diseases, as well as articles that are devoted to the development of more general theoretical insight.

Distinguishing between mean-field, moment dynamics and stochastic descriptions of birth-death-movement processes

Mathematical descriptions of birth–death–movement processes are often calibrated to measurements from cell biology experiments to quantify tissue growth rates. Here we describe and analyze a discrete model of a birth–death-movement process applied to a typical two–dimensional cell biology experiment. We present three different descriptions of the system: (i) a standard mean–field description which neglects correlation effects and clustering; (ii) a moment dynamics description which approximately incorporates correlation and clustering effects, and; (iii) averaged data from repeated discrete simulations which directly incorporates correlation and clustering effects. Comparing these three descriptions indicates that the mean–field and moment dynamics approaches are valid only for certain parameter regimes, and that both these descriptions fail to make accurate predictions of the system for sufficiently fast birth and death rates where the effects of spatial correlations and clustering are sufficiently strong. Without any method to distinguish between the parameter regimes where these three descriptions are valid, it is possible that either the mean–field or moment dynamics model could be calibrated to experimental data under inappropriate conditions, leading to errors in parameter estimation. In this work we demonstrate that a simple measurement of agent clustering and correlation, based on coordination number data, provides an indirect measure of agent correlation and clustering effects, and can therefore be used to make a distinction between the validity of the different descriptions of the birth–death–movement process.

Dengue fever viral exposure rates among blood donors during outbreaks in North Queensland

Introduction: Dengue poses a problem for safe transfusion of blood components with confirmed reports of transfusion-transmission in Hong Kong and Singapore. The largest outbreak in 50 years occurred in North Queensland during 2008/2009 with more than 1,000 confirmed cases in Cairns and Townsville. During this outbreak, supplementary questioning for all donors was implemented, and fresh components were not manufactured from at risk donors. We aim to determine the seroprevalence of dengue exposure in this population during this epidemic. Methods: Samples were collected from blood donors during the 2008/2009 epidemic and 3 months after the last confirmed case. These samples were tested for anti-Dengue IgM, IgG and NS1 antigen with commercially available ELISA based assay kits from PanBio. Results: Initial analyses revealed 2.7% of samples from deferred donors were IgM repeat reactive. Of these, 16% were also positive for anti-dengue IgG, while none of these were positive for the NS1 viral antigen. However, two NS1 positives were found in samples collected from deferred donors. Conclusions: This initial analysis represents recent and cumulative past exposure in a presumed asymptomatic population, and will provide documentation of the rate of asymptomatic dengue infection during the epidemic. This data can also be used to assess the risk of dengue becoming endemic in North Queensland given that the mosquito vector is established in this region.

The Alcohol Intervention Training Program (AITP): a response to alcohol misuse in the farming community

Background Farm men and women in Australia have higher levels of problematic alcohol use than their urban counterparts and experience elevated health risks associated with excessive alcohol consumption. The Sustainable Farm Families (SFF) program has worked successfully with farm men and women to address health, well- being and safety and has identified that further research and training is required to understand and address alcohol misuse behaviours. This project will add an innovative component to the program by training health professionals working with farm men and women to discuss and respond to alcohol-related physical and mental health problems. Methods/Design A mixed method design with multi-level evaluation will be implemented following the development and delivery of a training program (The Alcohol Intervention Training Program {AITP}) for Sustainable Farm Families health professionals. Pre-, post- and follow-up surveys will be used to assess both the impact of the training on the knowledge, confidence and skills of the health professionals to work with alcohol misuse and associated problems, and the impact of the training on the attitudes, behaviour and mental health of farm men and women who participate in the SFF project. Evaluations will take a range of forms including self-rated outcome measures and interviews. Discussion The success of this project will enhance the health and well-being of a critical population, the farm men and women of Australia, by producing an evidence-based strategy to assist them to adopt more positive alcohol-related behaviours that will lead to better physical and mental health.

An analysis of regression models for predicting the speed of a wave glider autonomous surface vehicle

An important aspect of robotic path planning for is ensuring that the vehicle is in the best location to collect the data necessary for the problem at hand. Given that features of interest are dynamic and move with oceanic currents, vehicle speed is an important factor in any planning exercises to ensure vehicles are at the right place at the right time. Here, we examine different Gaussian process models to find a suitable predictive kinematic model that enable the speed of an underactuated, autonomous surface vehicle to be accurately predicted given a set of input environmental parameters.

Direct iodination of isoindolines and isoindoline nitroxides as precursors to functionalized nitroxides

A new method for the direct aryl iodination of isoindolines and isoindoline nitroxides which utilizes periodic acid and potassium iodide in sulfuric acid is presented. Di-iodo functionalized tetramethyl and tetraethyl isoindolines and a di-iodo tetramethyl isoindoline nitroxide were prepared in high yield (70-82%). The analogous mono-iodo species were afforded in modest yield (34-48%). Iodinated nitrones were also obtained from a tetraethyl isoindoline nitroxide.

Rural people and the land

There is a long and fundamental connection between rural place and the land. Whereas land is simply the foundation for the construction of towns and cities, whose urban culture and economy thrives on human ingenuity and industry that may have little direct attachment to the physical ground over which it occurs, historical discourses of rurality place the land at the heart of the rural economy and society. Rural people, such discourses hold, live on the land, work the land, tend the land and know the land. The land formed not only the base of the rural economy (as ‘a physical, tangible resource which can be ploughed, sown, grazed, built upon’ (Macnaghten and Urry 1998, 200)), but also shaped rural culture and the rural calendar, and contributed to the constitution of the rural character (see Bell 1994). As such, the land is central to rural sense of place.

Mid-Holocene sea-level and coral reef demise : U-Th dating of subfossil corals in Moreton Bay, Australia

It is increasingly apparent that sea-level data (e.g. microfossil transfer functions, dated coral microatolls and direct observations from satellite and tidal gauges) vary temporally and spatially at regional to local scales, thus limiting our ability to model future sea-level rise for many regions. Understanding sealevel response at ‘far-field’ locations at regional scales is fundamental for formulating more relevant sea-level rise susceptibility models within these regions under future global change projections. Fossil corals and reefs in particular are valuable tools for reconstructing past sea levels and possible environmental phase shifts beyond the temporal constraints of instrumental records. This study used abundant surface geochronological data based on in situ subfossil corals and precise elevation surveys to determine previous sea level in Moreton Bay, eastern Australia, a far-field site. A total of 64 U-Th dates show that relative sea level was at least 1.1 m above modern lowest astronomical tide (LAT) from at least ˜6600 cal. yr BP. Furthermore, a rapid synchronous demise in coral reef growth occurred in Moreton Bay ˜5800 cal. yr BP, coinciding with reported reef hiatus periods in other areas around the Indo-Pacific region. Evaluating past reef growth patterns and phases allows for a better interpretation of anthropogenic forcing versus natural environmental/climatic cycles that effect reef formation and demise at all scales and may allow better prediction of reef response to future global change.

Baidu’s perfect paradox : free speech and the right to censor

China’s biggest search engine has a constitutional right to filter its search results, a US court found last month. But that’s just the start of the story. Eight New York-based pro-democracy activists sued Baidu Inc in 2011, seeking damages because Baidu prevents their work from showing up in search results. Baidu follows Chinese law that requires it to censor politically sensitive results. But in what the plaintiffs’ lawyer has dubbed a “perfect paradox”, US District Judge Jesse Furman has dismissed the challenge, explaining that to hold Baidu liable for its decisions to censor pro-democracy content would itself infringe the right to free speech.

The unfinished revolution : what is missing from the E&P industry’s move to “big data”

One cannot help but be impressed by the inroads that digital oilfield technologies have made into the exploration and production (E&P) industry in the past decade. Today’s production systems can be monitored by “smart” sensors that allow engineers to observe almost any aspect of performance in real time. Our understanding of how reservoirs are behaving has improved considerably since the dawn of this revolution, and the industry has been able to move away from point answers to more holistic “big picture” integrated solutions. Indeed, the industry has already reaped the rewards of many of these kinds of investments. Many billions of dollars of value have been delivered by this heightened awareness of what is going on within our assets and the world around them (Van Den Berg et al. 2010).