Physical and linkage maps for Drosophila serrata, a model species for studies of clinal adaptation and sexual selection

Drosophila serrata is a member of the montium group, which contains more than 98 species and until recently was considered a subgroup within the melanogaster group. This Drosophila species is an emerging model system for evolutionary quantitative genetics and has been used in studies of species borders, clinal variation and sexual selection. Despite the importance of D. serrata as a model for evolutionary research, our poor understanding of its genome remains a significant limitation. Here, we provide a first-generation gene-based linkage map and a physical map for this species. Consistent with previous studies of other drosophilids we observed strong conservation of genes within chromosome arms homologous with D. melanogaster but major differences in within-arm synteny. These resources will be a useful complement to ongoing genome sequencing efforts and QTL mapping studies in this species

The wMel Wolbachia strain blocks dengue and invades caged Aedes aegypti populations

Dengue fever is the most important mosquito-borne viral disease of humans with more than 50 million cases estimated annually in more than 100 countries. Disturbingly, the geographic range of dengue is currently expanding and the severity of outbreaks is increasing. Control options for dengue are very limited and currently focus on reducing population abundance of the major mosquito vector, Aedes aegypti. These strategies are failing to reduce dengue incidence in tropical communities and there is an urgent need for effective alternatives. It has been proposed that endosymbiotic bacterial Wolbachia infections of insects might be used in novel strategies for dengue control. For example, the wMelPop-CLA Wolbachia strain reduces the lifespan of adult A. aegypti mosquitoes in stably transinfected lines. This life-shortening phenotype was predicted to reduce the potential for dengue transmission. The recent discovery that several Wolbachia infections, including wMelPop-CLA, can also directly influence the susceptibility of insects to infection with a range of insect and human pathogens has markedly changed the potential for Wolbachia infections to control human diseases. Here we describe the successful transinfection of A. aegypti with the avirulent wMel strain of Wolbachia, which induces the reproductive phenotype cytoplasmic incompatibility with minimal apparent fitness costs and high maternal transmission, providing optimal phenotypic effects for invasion. Under semi-field conditions, the wMel strain increased from an initial starting frequency of 0.65 to near fixation within a few generations, invading A. aegypti populations at an accelerated rate relative to trials with the wMelPop-CLA strain. We also show that wMel and wMelPop-CLA strains block transmission of dengue serotype 2 (DENV-2) in A. aegypti, forming the basis of a practical approach to dengue suppression.

An expressed sequence tag (EST) library for Drosophila serrata, a model system for sexual selection and climatic adaptation studies

The native Australian fly Drosophila serrata belongs to the highly speciose montium subgroup of the melanogaster species group. It has recently emerged as an excellent model system with which to address a number of important questions, including the evolution of traits under sexual selection and traits involved in climatic adaptation along latitudinal gradients. Understanding the molecular genetic basis of such traits has been limited by a lack of genomic resources for this species. Here, we present the first expressed sequence tag (EST) collection for D. serrata that will enable the identification of genes underlying sexually-selected phenotypes and physiological responses to environmental change and may help resolve controversial phylogenetic relationships within the montium subgroup.

The current workforce status of prehospital care in China

Abstract The Chinese Emergency Medicine System is primarily composed of three sectors; prehospital care, emergency department in a city hospital, and intensive care unit ward. While all sectors are integral to the system, the prehospital care system is less developed than the others. There are many possible contributors to the under-development of the prehospital care system, however, workforce issues may play a significant role. Firstly, there is no officially recognised paramedic profession in China. The staff members working in the prehospital care system are medical doctors, registered nurses, patient-carriers, and drivers. Secondly, these doctors and nurses are either over-qualified or under-qualified for practicing in the prehospital care system. Lastly, Chinese health professionals have taken actions to improve the current workforce status with initiatives such as short-term training workshops for doctors and nurses, implementation of a trial unit in a university, and development of a Major Degree of Emergency Medicine in a medical university. All of these actions are important steps toward improving the current workforce status in the prehospital care system. However, a long term workforce development plan is still essential for the Chinese system, and implementation of a professional paramedic education system in a medical university/college in China, may provide the solution. Keywords: China; emergency medicine system; health services; prehospital care system; workforce; service delivery

The impacts of power outages on the residents of contemporary multistorey apartment buildings in subtropical environments

With significant population growth experienced in South East Queensland over the past two decades and a high rate of growth expected to continue in coming decades, the Queensland Government is promoting urban consolidation planning policies to manage growth sustainably. Multi-residential buildings will play an important role in facilitating the increased densities which urban consolidation policies imply. However, a major flood event in January 2011 has brought to light the vulnerability of certain types of multi-residential typologies to power outages. The crisis conditions exposed how contemporary building design and construction practices, coupled with regulatory and planning issues, appear to have compromised the resilience and habitability of multi-storey residential buildings. In the greater urban area of Brisbane, Queensland, the debilitating dependence that certain types of apartment buildings have on mains electricity was highlighted by residents’ experiences of the Brisbane River flood disaster, before, during and after the event. This research examined high density residential buildings in West End, Brisbane, an inner city suburb which was severely affected by the flood and is earmarked for significant urban densification under the Brisbane City Plan. Medium-to-high-density residential buildings in the suburb were mapped in flooded and non-flooded locations and a database containing information about the buildings was created. Parameters included date of construction, number of storeys, systems of access and circulation, and potential for access to natural light and ventilation for habitable areas. A series of semi-structured interviews were conducted with residents involved in the owners’ management committees of several buildings to verify information the mapping could not provide. The interviews identified a number of critical systems failures due to power outage which had a significant impact on residents’ wellbeing, comfort and safety. Building services such as lifts, running water, fire alarms, security systems and air-conditioning ceased to operate when power was disconnected to neighbourhoods and buildings in anticipation of rising flood waters. Lack of access to buildings and dwellings, lack of safety, lack of building security, and lack of thermal comfort affected many residents whether or not their buildings were actually subjected to inundation, with some buildings rendered uninhabitable for a prolonged period. The extent of the impact on residents was dramatically influenced by the scale and type of building inhabited, with those dwelling in buildings under a 25m height limit, with a single lift, found to be most affected. The energy-dependency and strong trend of increasing power demands of high-rise buildings is well-documented. Extended electricity outages such as the one brought about by the 2011 flood in Queensland are likely to happen more frequently than the 50-year average of the flood event itself. Electricity blackouts can result from a number of man-made or natural causes, including shortages caused by demand exceeding supply. This paper highlights the vulnerability of energy-dependent buildings to power outages and investigates options for energy security for occupants of multi-storey buildings and makes recommendations to increase resilience and general liveability in multi-residential buildings in the subtropics through design modifications.

Enabling access to and re-use of publicly funded research data as Open Educational Resources : a strategy for overcoming the legal barriers to data access and re-use

Open Educational Resources (OER) are teaching, learning and research materials that have been released under an open licence that permits online access and re-use by others. The 2012 Paris OER Declaration encourages the open licensing of educational materials produced with public funds. Digital data and data sets produced as a result of scientific and non-scientific research are an increasingly important category of educational materials. This paper discusses the legal challenges presented when publicly funded research data is made available as OER, arising from intellectual property rights, confidentiality and information privacy laws, and the lack of a legal duty to ensure data quality. If these legal challenges are not understood, addressed and effectively managed, they may impede and restrict access to and re-use of research data. This paper identifies some of the legal challenges that need to be addressed and describes 10 proposed best practices which are recommended for adoption to so that publicly funded research data can be made available for access and re-use as OER.

National Institute for Clinical Studies Report for Phase 1, Evidence Uptake Network : Best Practice Community Care for Clients with Chronic Venous Leg Ulcers

Chronic leg ulcers cause significant pain, cost, decreased quality of life and morbidity for a considerable segment of the older population (Graham et al., 2003a). At any given time the prevalence of patients with open leg ulcers receiving treatment is between 0.11% - 0.18% (Briggs & Closs 2003). Chronic leg ulcers occur in approximately 1 - 2% of the over 60 population in the US, UK, Europe and Australia (Baker & Stacey 1994; Johnson 1995; Lees & Lambert 1992; Margolis et al. 2002). Considerable research has been undertaken to determine the best treatment practices that will aid in the management and the healing of these ulcers, and practical and effective strategies and techniques for healing venous leg ulcers have been trialled to demonstrate their beneficial effects (Nelson et al. 2004; Cullum et al. 2001)...

The digital transformation of 21st century news journalism

This presentation will deal with the transformations that have occurred in news journalism worldwide in the early 21st century. I will argue that they have been the most significant changes to the profession for 100 years, and the challenges facing the news media industry in responding to them are substantial, as are those facing journalism education. It will develop this argument in relation to the crisis of the newspaper business model, and why social media, blogging and citizen journalism have not filled the gap left by the withdrawal of resources from traditional journalism. It will also draw upon Wikileaks as a case study in debates about computational and data-driven journalism, and whether large-scale "leaks" of electronic documents may be the future of investigative journalism.

Short answer versus multiple choice examination questions for first year chemistry

Multiple choice (MC) examinations are frequently used for the summative assessment of large classes because of their ease of marking and their perceived objectivity. However, traditional MC formats usually lead to a surface approach to learning, and do not allow students to demonstrate the depth of their knowledge or understanding. For these reasons, we have trialled the incorporation of short answer (SA) questions into the final examination of two first year chemistry units, alongside MC questions. Students’ overall marks were expected to improve, because they were able to obtain partial marks for the SA questions. Although large differences in some individual students’ performance in the two sections of their examinations were observed, most students received a similar percentage mark for their MC as for their SA sections and the overall mean scores were unchanged. In-depth analysis of all responses to a specific question, which was used previously as a MC question and in a subsequent semester in SA format, indicates that the SA format can have weaknesses due to marking inconsistencies that are absent for MC questions. However, inclusion of SA questions improved student scores on the MC section in one examination, indicating that their inclusion may lead to different study habits and deeper learning. We conclude that questions asked in SA format must be carefully chosen in order to optimise the use of marking resources, both financial and human, and questions asked in MC format should be very carefully checked by people trained in writing MC questions. These results, in conjunction with an analysis of the different examination formats used in first year chemistry units, have shaped a recommendation on how to reliably and cost-effectively assess first year chemistry, while encouraging higher order learning outcomes.

Agronomic and economic evaluation of irrigation strategies on cotton lint yield in Australia

Cotton is one of the most important irrigated crops in subtropical Australia. In recent years, cotton production has been severely affected by the worst drought in recorded history, with the 2007–08 growing season recording the lowest average cotton yield in 30 years. The use of a crop simulation model to simulate the long-term temporal distribution of cotton yields under different levels of irrigation and the marginal value for each unit of water applied is important in determining the economic feasibility of current irrigation practices. The objectives of this study were to: (i) evaluate the CROPGRO-Cotton simulation model for studying crop growth under deficit irrigation scenarios across ten locations in New South Wales (NSW) and Queensland (Qld); (ii) evaluate agronomic and economic responses to water inputs across the ten locations; and (iii) determine the economically optimal irrigation level. The CROPGRO-Cotton simulation model was evaluated using 2 years of experimental data collected at Kingsthorpe, Qld. The model was further evaluated using data from nine locations between northern NSW and southern Qld. Long-term simulations were based on the prevalent furrowirrigation practice of refilling the soil profile when the plant -available soil water content is<50%. The model closely estimated lint yield for all locations evaluated. Our results showed that the amounts of water needed to maximise profit and maximise yield are different, which has economic and environmental implications. Irrigation needed to maximise profits varied with both agronomic and economic factors, which can be quite variable with season and location. Therefore, better tools and information that consider the agronomic and economic implications of irrigation decisions need to be developed and made available to growers.

Modelling web-server Flash Events

A Flash Event (FE) represents a period of time when a web-server experiences a dramatic increase in incoming traffic, either following a newsworthy event that has prompted users to locate and access it, or as a result of redirection from other popular web or social media sites. This usually leads to network congestion and Quality-of-Service (QoS) degradation. These events can be mistaken for Distributed Denial-of-Service (DDoS) attacks aimed at disrupting the server. Accurate detection of FEs and their distinction from DDoS attacks is important, since different actions need to be undertaken by network administrators in these two cases. However, lack of public domain FE datasets hinders research in this area. In this paper we present a detailed study of flash events and classify them into three broad categories. In addition, the paper describes FEs in terms of three key components: the volume of incoming traffic, the related source IP-addresses, and the resources being accessed. We present such a FE model with minimal parameters and use publicly available datasets to analyse and validate our proposed model. The model can be used to generate different types of FE traffic, closely approximating real-world scenarios, in order to facilitate research into distinguishing FEs from DDoS attacks.

Evaluation of the cost-effectiveness of strategies claiming to reduce the risk of surgical site infections following primary total hip arthroplasty

Background Total hip arthroplasty (THA) is a commonly performed procedure and numbers are increasing with ageing populations. One of the most serious complications in THA are surgical site infections (SSIs), caused by pathogens entering the wound during the procedure. SSIs are associated with a substantial burden for health services, increased mortality and reduced functional outcomes in patients. Numerous approaches to preventing these infections exist but there is no gold standard in practice and the cost-effectiveness of alternate strategies is largely unknown. Objectives The aim of this project was to evaluate the cost-effectiveness of strategies claiming to reduce deep surgical site infections following total hip arthroplasty in Australia. The objectives were: 1. Identification of competing strategies or combinations of strategies that are clinically relevant to the control of SSI related to hip arthroplasty 2. Evidence synthesis and pooling of results to assess the volume and quality of evidence claiming to reduce the risk of SSI following total hip arthroplasty 3. Construction of an economic decision model incorporating cost and health outcomes for each of the identified strategies 4. Quantification of the effect of uncertainty in the model 5. Assessment of the value of perfect information among model parameters to inform future data collection Methods The literature relating to SSI in THA was reviewed, in particular to establish definitions of these concepts, understand mechanisms of aetiology and microbiology, risk factors, diagnosis and consequences as well as to give an overview of existing infection prevention measures. Published economic evaluations on this topic were also reviewed and limitations for Australian decision-makers identified. A Markov state-transition model was developed for the Australian context and subsequently validated by clinicians. The model was designed to capture key events related to deep SSI occurring within the first 12 months following primary THA. Relevant infection prevention measures were selected by reviewing clinical guideline recommendations combined with expert elicitation. Strategies selected for evaluation were the routine use of pre-operative antibiotic prophylaxis (AP) versus no use of antibiotic prophylaxis (No AP) or in combination with antibiotic-impregnated cement (AP & ABC) or laminar air operating rooms (AP & LOR). The best available evidence for clinical effect size and utility parameters was harvested from the medical literature using reproducible methods. Queensland hospital data were extracted to inform patients’ transitions between model health states and related costs captured in assigned treatment codes. Costs related to infection prevention were derived from reliable hospital records and expert opinion. Uncertainty of model input parameters was explored in probabilistic sensitivity analyses and scenario analyses and the value of perfect information was estimated. Results The cost-effectiveness analysis was performed from a health services perspective using a hypothetical cohort of 30,000 THA patients aged 65 years. The baseline rate of deep SSI was 0.96% within one year of a primary THA. The routine use of antibiotic prophylaxis (AP) was highly cost-effective and resulted in cost savings of over $1.6m whilst generating an extra 163 QALYs (without consideration of uncertainty). Deterministic and probabilistic analysis (considering uncertainty) identified antibiotic prophylaxis combined with antibiotic-impregnated cement (AP & ABC) to be the most cost-effective strategy. Using AP & ABC generated the highest net monetary benefit (NMB) and an incremental $3.1m NMB compared to only using antibiotic prophylaxis. There was a very low error probability that this strategy might not have the largest NMB (<5%). Not using antibiotic prophylaxis (No AP) or using both antibiotic prophylaxis combined with laminar air operating rooms (AP & LOR) resulted in worse health outcomes and higher costs. Sensitivity analyses showed that the model was sensitive to the initial cohort starting age and the additional costs of ABC but the best strategy did not change, even for extreme values. The cost-effectiveness improved for a higher proportion of cemented primary THAs and higher baseline rates of deep SSI. The value of perfect information indicated that no additional research is required to support the model conclusions. Conclusions Preventing deep SSI with antibiotic prophylaxis and antibiotic-impregnated cement has shown to improve health outcomes among hospitalised patients, save lives and enhance resource allocation. By implementing a more beneficial infection control strategy, scarce health care resources can be used more efficiently to the benefit of all members of society. The results of this project provide Australian policy makers with key information about how to efficiently manage risks of infection in THA.

Exploiting medical hierarchies for concept-based information retrieval

Search technologies are critical to enable clinical sta to rapidly and e ectively access patient information contained in free-text medical records. Medical search is challenging as terms in the query are often general but those in rel- evant documents are very speci c, leading to granularity mismatch. In this paper we propose to tackle granularity mismatch by exploiting subsumption relationships de ned in formal medical domain knowledge resources. In symbolic reasoning, a subsumption (or `is-a') relationship is a parent-child rela- tionship where one concept is a subset of another concept. Subsumed concepts are included in the retrieval function. In addition, we investigate a number of initial methods for combining weights of query concepts and those of subsumed concepts. Subsumption relationships were found to provide strong indication of relevant information; their inclusion in retrieval functions yields performance improvements. This result motivates the development of formal models of rela- tionships between medical concepts for retrieval purposes.

Chemical variability of groundwater samples collected from a Coal Seam Gas exploration well, Maramarua, New Zealand

A pilot study has produced 31 groundwater samples from a coal seam gas (CSG) exploration well located in Maramarua, New Zealand. This paper describes sources of CSG water chemistry variations, and makes sampling and analytical recommendations to minimize these variations. The hydrochemical character of these samples is studied using factor analysis, geochemical modelling, and a sparging experiment. Factor analysis unveils carbon dioxide (CO2) degassing as the principal cause of sample variation (about 33%). Geochemical modelling corroborates these results and identifies minor precipitation of carbonate minerals with degassing. The sparging experiment confirms the effect of CO2 degassing by showing a steady rise in pH while maintaining constant alkalinity. Factor analysis correlates variations in the major ion composition (about 17%) to changes in the pumping regime and to aquifer chemistry variations due to cation exchange reactions with argillaceous minerals. An effective CSG water sampling program can be put into practice by measuring pH at the well head and alkalinity at the laboratory; these data can later be used to calculate the carbonate speciation at the time the sample was collected. In addition, TDS variations can be reduced considerably if a correct drying temperature of 180°C is consistently implemented.

Radiotherapy Monte Carlo simulation using cloud computing technology

Cloud computing allows for vast computational resources to be leveraged quickly and easily in bursts as and when required. Here we describe a technique that allows for Monte Carlo radiotherapy dose calculations to be performed using GEANT4 and executed in the cloud, with relative simulation cost and completion time evaluated as a function of machine count. As expected, simulation completion time decreases as 1=n for n parallel machines, and relative simulation cost is found to be optimal where n is a factor of the total simulation time in hours. Using the technique, we demonstrate the potential usefulness of cloud computing as a solution for rapid Monte Carlo simulation for radiotherapy dose calculation without the need for dedicated local computer hardware as a proof of principal. Funding source Cancer Australia (Department of Health and Ageing) Research Grant 614217