Supplementary material : large scale read classification for next generation sequencing

Next Generation Sequencing (NGS) has revolutionised molecular biology, resulting in an explosion of data sets and an increasing role in clinical practice. Such applications necessarily require rapid identification of the organism as a prelude to annotation and further analysis. NGS data consist of a substantial number of short sequence reads, given context through downstream assembly and annotation, a process requiring reads consistent with the assumed species or species group. Highly accurate results have been obtained for restricted sets using SVM classifiers, but such methods are difficult to parallelise and success depends on careful attention to feature selection. This work examines the problem at very large scale, using a mix of synthetic and real data with a view to determining the overall structure of the problem and the effectiveness of parallel ensembles of simpler classifiers (principally random forests) in addressing the challenges of large scale genomics.

Anthropogenic-based regional-scale factors most consistently explain plot-level exotic diversity in grasslands

Aim Evidence linking the accumulation of exotic species to the suppression of native diversity is equivocal, often relying on data from studies that have used different methods. Plot-level studies often attribute inverse relationships between native and exotic diversity to competition, but regional abiotic filters, including anthropogenic influences, can produce similar patterns.We seek to test these alternatives using identical scale-dependent sampling protocols in multiple grasslands on two continents. Location Thirty-two grassland sites in North America and Australia. Methods We use multiscale observational data, collected identically in grain and extent at each site, to test the association of local and regional factors with the plot-level richness and abundance of native and exotic plants. Sites captured environmental and anthropogenic gradients including land-use intensity, human population density, light and soil resources, climate and elevation. Site selection occurred independently of exotic diversity, meaning that the numbers of exotic species varied randomly thereby reducing potential biases if only highly invaded sites were chosen. Results Regional factors associated directly or indirectly with human activity had the strongest associations with plot-level diversity. These regional drivers had divergent effects: urban-based economic activity was associated with high exotic : native diversity ratios; climate- and landscape-based indicators of lower human population density were associated with low exotic : native ratios. Negative correlations between plot-level native and exotic diversity, a potential signature of competitive interactions, were not prevalent; this result did not change along gradients of productivity or heterogeneity. Main conclusion We show that plot-level diversity of native and exotic plants are more consistently associatedwith regional-scale factors relating to urbanization and climate suitability than measures indicative of competition. These findings clarify the long-standing difficulty in resolving drivers of exotic diversity using single-factor mechanisms, suggesting that multiple interacting anthropogenic-based processes best explain the accumulation of exotic diversity in modern landscapes.

Fostering rapid transitions to education for sustainable development through a whole-system approach to curriculum and organizational change

Despite decades of attempts to embed sustainability within higher education, literature clearly suggests that highly regulated disciplines such as engineering have been relatively slow to incorporate sustainability knowledge and skill areas, and are generally poorly prepared to do so. With current efforts, it is plausible that sustainability could take another two decades to be embedded within the curriculum. Within this context, this paper presents a whole system approach to implement systematic, intentional and timely curriculum renewal that is responsive to emerging challenges and opportunities, encompassing curriculum and organizational change. The paper begins by considering the evolution of curriculum renewal processes, documenting a number of whole system considerations that have been empirically distilled from literature, case studies, pilot trials, and a series of workshops with built environment educators from around the world over the last decade. The paper outlines a whole-of-institution curriculum renewal approach to embedding sustainability knowledge and skills within the DNA of the institutional offerings. The paper concludes with a discussion of research and practice implications for the field of education research, within and beyond higher education.

Soil moisture monitoring at the field scale using neutron probe

Measurement of the moisture variation in soils is required for geotechnical design and research because soil properties and behavior can vary as moisture content changes. The neutron probe, which was developed more than 40 years ago, is commonly used to monitor soil moisture variation in the field. This study reports a full-scale field monitoring of soil moisture using a neutron moisture probe for a period of more than 2 years in the Melbourne (Australia) region. On the basis of soil types available in the Melbourne region, 23 sites were chosen for moisture monitoring down to a depth of 1500 mm. The field calibration method was used to develop correlations relating the volumetric moisture content and neutron counts. Observed results showed that the deepest “wetting front” during the wet season was limited to the top 800 to 1000 mm of soil whilst the top soil layer down to about 550mmresponded almost immediately to the rainfall events. At greater depths (550 to 800mmand below 800 mm), the moisture variations were relatively low and displayed predominantly periodic fluctuations. This periodic nature was captured with Fourier analysis to develop a cyclic moisture model on the basis of an analytical solution of a one-dimensional moisture flow equation for homogeneous soils. It is argued that the model developed can be used to predict the soil moisture variations as applicable to buried structures such as pipes.

Considering the economic value of natural design elements at city scale

With increasing signs of climate change and the influence of national and international carbon-related laws and agreements, governments all over the world are grappling with how to rapidly transition to low-carbon living. This includes adapting to the impacts of climate change that are very likely to be experienced due to current emission levels (including extreme weather and sea level changes), and mitigating against further growth in greenhouse gas emissions that are likely to result in further impacts. Internationally, the concept of ‘Biophilic Urbanism’, a term coined by Professors Tim Beatley and Peter Newman to refer to the use of natural elements as design features in urban landscapes, is emerging as a key component in addressing such climate change challenges in rapidly growing urban contexts. However, the economics of incorporating such options is not well understood and requires further attention to underpin a mainstreaming of biophilic urbanism. Indeed, there appears to be an ad hoc, reactionary approach to creating economic arguments for or against the design, installation or maintenance of natural elements such as green walls, green roofs, streetscapes, and parklands. With this issue in mind, this paper will overview research as part of an industry collaborative research project that considers the potential for using a number of environmental economic valuation techniques that have evolved over the last several decades in agricultural and resource economics, to systematically value the economic value of biophilic elements in the urban context. Considering existing literature on environmental economic valuation techniques, the paper highlights opportunities for creating a standardised language for valuing biophilic elements. The conclusions have implications for expanding the field of environmental economic value to support the economic evaluations and planning of the greater use of natural elements in cities. Insights are also noted for the more mature fields of agricultural and resource economics.

Two-scale computational modelling of unsaturated flow in soils exhibiting small scale heterogeneities

Unsaturated water flow in soil is commonly modelled using Richards’ equation, which requires the hydraulic properties of the soil (e.g., porosity, hydraulic conductivity, etc.) to be characterised. Naturally occurring soils, however, are heterogeneous in nature, that is, they are composed of a number of interwoven homogeneous soils each with their own set of hydraulic properties. When the length scale of these soil heterogeneities is small, numerical solution of Richards’ equation is computationally impractical due to the immense effort and refinement required to mesh the actual heterogeneous geometry. A classic way forward is to use a macroscopic model, where the heterogeneous medium is replaced with a fictitious homogeneous medium, which attempts to give the average flow behaviour at the macroscopic scale (i.e., at a scale much larger than the scale of the heterogeneities). Using the homogenisation theory, a macroscopic equation can be derived that takes the form of Richards’ equation with effective parameters. A disadvantage of the macroscopic approach, however, is that it fails in cases when the assumption of local equilibrium does not hold. This limitation has seen the introduction of two-scale models that include at each point in the macroscopic domain an additional flow equation at the scale of the heterogeneities (microscopic scale). This report outlines a well-known two-scale model and contributes to the literature a number of important advances in its numerical implementation. These include the use of an unstructured control volume finite element method and image-based meshing techniques, that allow for irregular micro-scale geometries to be treated, and the use of an exponential time integration scheme that permits both scales to be resolved simultaneously in a completely coupled manner. Numerical comparisons against a classical macroscopic model confirm that only the two-scale model correctly captures the important features of the flow for a range of parameter values.

Pilot plant studies of ion exchange for desalination of coal seam gas produced water

This paper reports a study of ion exchange (IX) as an alternative CSG water treatment to the widely used reverse osmosis (RO) desalination process. An IX pilot plant facility has been constructed and operated using both synthetic and real CSG water samples. Application of appropriate synthetic resin technology has proved the effectiveness of IX processes.

Informing engineering education for sustainable development using a deliberative dynamic model for curriculum renewal

Literature from around the world clearly suggests that engineering education has been relatively slow to incorporate significant knowledge and skill areas, including the rapidly emerging area of sustainable development. Within this context, this paper presents the findings of research that questioned how engineering educators could consistently implement systematic and intentional curriculum renewal that is responsive to emerging engineering challenges and opportunities. The paper presents a number of elements of systematic and intentional curriculum renewal that have been empirically distilled from a qualitative multiple-method iterative research approach including literature review, narrative enquiry, pilot trials and peer-review workshops undertaken by the authors with engineering educators from around the world. The paper also presents new knowledge arising from the research, in the form of a new model that demonstrates a dynamic and deliberative mechanism for strategically accelerating for curriculum renewal efforts. Specifically the paper discusses implications of this model to achieve education for sustainable development, across all disciplines of engineering. It concludes with broader research and practice implications for the field of education research.

Development of descriptor tools for the characterisation of Australian sugar mill evaporator scale

Cleaning of sugar mill evaporators is an expensive exercise. Identifying the scale components assists in determining which chemical cleaning agents would result in effective evaporator cleaning. The current methods (based on x-ray diffraction techniques, ion exchange/high performance liquid chromatography and thermogravimetry/differential thermal analysis) used for scale characterisation are difficult, time consuming and expensive, and cannot be performed in a conventional analytical laboratory or by mill staff. The present study has examined the use of simple descriptor tests for the characterisation of Australian sugar mill evaporator scales. Scale samples were obtained from seven Australian sugar mill evaporators by mechanical means. The appearance, texture and colour of the scale were noted before the samples were characterised using x-ray fluorescence and x-ray powder diffraction to determine the compounds present. A number of commercial analytical test kits were used to determine the phosphate and calcium contents of scale samples. Dissolution experiments were carried out on the scale samples with selected cleaning agents to provide relevant information about the effect the cleaning agents have on different evaporator scales. Results have shown that by simply identifying the colour and the appearance of the scale, the elemental composition and knowing from which effect the scale originates, a prediction of the scale composition can be made. These descriptors and dissolution experiments on scale samples can be used to provide factory staff with an on-site rapid process to predict the most effective chemicals for chemical cleaning of the evaporators.

On-line scale monitoring device

Developments in evaporator cleaning have accelerated in the past 10 years as a result of an extended period of research into scale formation and scale composition. Chemical cleaning still provides the most cost effective method of cleaning the evaporators. The paper describes a system that was designed to obtain on-line samples of evaporator scale negating the need to open up hot evaporator vessels for scale collection. This system was successfully implemented in a number of evaporators at a sugar mill. This paper also describes a recent experience in a sugar factory in which the cleaning procedure was slightly modified, resulting in effective removal of intractable scale.

On-line scale monitoring device

Developments in evaporator cleaning have accelerated in the past 10 years as a result of an extended period of research into scale formation and scale composition. Chemical cleaning still provides the most cost effective method of cleaning the evaporators. The paper describes a system that was designed to obtain on-line samples of evaporator scale negating the need to open up hot evaporator vessels for scale collection. This system was successfully implemented in a number of evaporators at a sugar mill. This paper also describes a recent experience in a sugar factory in which the cleaning procedure was slightly modified resulting in effective removal of intractable scale.

Registration of clinical trials: Challenges for global regulation

In 2004 the International Committee of Medical Journal Editors (ICMJE) issued a statement indicating that from 1 July 2005 registration in a publicly accessible trials registry would be a condition of publication in an ICMJE member journal. The World Health Organisation is coordinating the International Clinical Trials Registry Platform (ICTRP) as a means of providing a standardised framework for registration. This article considers the practical challenges and opportunities that arise from these developments and considers the relevance of trial registration for women and minorities and for developing countries.

Evaluating the use of a very large-scale presentation and collaboration framework

In this paper we describe the use and evaluation of CubIT, a multi-user, very large-scale presentation and collaboration framework. CubIT is installed at the Queensland University of Technology’s (QUT) Cube facility. The “Cube” is an interactive visualisation facility made up of five very large-scale interactive multi-panel wall displays, each consisting of up to twelve 55-inch multi-touch screens (48 screens in total) and massive projected display screens situated above the display panels. The paper outlines the unique design challenges, features, use and evaluation of CubIT. The system was built to make the Cube facility accessible to QUT’s academic and student population. CubIT enables users to easily upload and share their own media content, and allows multiple users to simultaneously interact with the Cube’s wall displays. The features of CubIT are implemented via three user interfaces, a multi-touch interface working on the wall displays, a mobile phone and tablet application and a web-based content management system. The evaluation reveals issues around the public use and functional scope of the system.

How do you ‘teach’ sustainability to engineers? introducing the engineering sustainable solutions program

Environmental engineers are increasingly being required to have knowledge about sustainability in their professional careers. Accreditation mechanisms for including sustainability in degree program requirements exist and are gradually being implemented by Engineers Australia. However, true integration of sustainability material into higher and vocational education curricula is still low, particularly outside the environmental engineering degree programs. In addition to environmental engineering, it is crucial for engineering across the specialisations, to be exposed to sustainability concepts and theories. This paper will demonstrate how sustainability as a ‘critical literacy’ can be designed for teaching within mainstream engineering education, using a current Australian project as a case study. The project demonstrates that sustainability education for all engineers is not only possible, but that there is international interest in collaborating in such an educational initiative. A pilot trial of the Introductory Module was undertaken in Semester 1 2004 and Version 2 trials are now proceeding with a number of universities and organisations nationally and internationally. Further modules are currently being developed in collaboration with Engineers Australia and UNESCO. The program is a finalist in the 2005 Banksia Awards (Category 11, Environmental Leadership Education and Training).

An assessment of the geographical scale of recurrent gene flow in wild populations of two species of Mekong River carps (Henicorhynchus spp.)

The Mekong is the most productive river fishery in the world, and such as, the Mekong River Basin (MRB) is very important to very large human populations across the region as a source of revenue (through fishing and marketing of aquatic resources products) and as the major source for local animal protein. Threats to biodiversity in the MRB, either to the fishery sector itself or to other sectors are a major concern, even though currently, fisheries across this region are still very productive. If not managed properly however, fish population declines will cause significant economic impact and affect livelihoods of local people and will have a major impact on food security and nutrition. Biodiversity declines will undoubtedly affect food security, income and socio-economic status of people in the MRB that depend on aquatic resources. This is an indicator of unsustainable development and hence should be avoided. Genetic diversity (biodiversity) that can be measured using techniques based on DNA markers; refers to variation within and among populations within the same species or reproductive units. In a population, new genetic variation is generated by sexual recombination contributed by individuals with mutations in genes and chromosomes. Over time, populations of a species that are not reproducing together will diverge as differential impacts of selection and genetic drift change their genetic attributes. For mud carp (Henicorhynchus spp.), understanding the status of breeding units in the MRB will be important for their long term persistence, sustainability and for implementing effective management strategies. Earlier analysis of stock structure in two economically important mud carp species (Henicorhynchus siamensis and H. lobatus) in the MRB completed with mtDNA markers identified a number of populations of both species where gene flow had apparently been interrupted or reduced but applying these data directly to management unit identification is potentially compromised because information was only available about female dispersal patterns. The current study aimed to address this problem and to fully assess the extent of current gene flow (nDNA) and reproductive exchange among selected wild populations of two species of carp (Henicorhynchus spp.) of high economic importance in the MRB using combined mtDNA and nDNA markers. In combination, the data can be used to define effective management units for each species. In general, nDNA diversity for H. lobatus (with average allelic richness (A) 7.56 and average heterozygosity (Ho) 0.61) was very similar to that identified for H. siamensis (A = 6.81 and Ho = 0.75). Both mud carp species show significant but low FST estimates among populations as a result of lower genetic diversity among sampled populations compared with genetic diversity within populations that may potentially mask any 'real' population structure. Overall, population genetic structure patterns from mtDNA and nDNA in both Henicorhynchus species were largely congruent. Different population structures however, were identified for the two Henicorhynchus species across the same geographical area. Apparent co-similarity in morphology and co-distribution of these two relatively closely related species does not apparently imply parallel evolutionary histories. Differences in each species population structure likely reflect historical drainage rearrangement of the Mekong River. The data indicate that H. siamensis is likely to have occupied the Mekong system for much longer than has H. lobatus in the past. Two divergent stocks were identified for H. lobatus in the MRB below the Khone Falls while a single stock had been evident in the earlier mtDNA study. This suggests that the two Henicorhynchus species may possess different life history traits and that different patterns of gene flow has likely influenced modern genetic structure in these close congeners. In combination, results of the earlier mtDNA and the current study have implications for effective management of both Henicorhynchus species across the MRB. Currently, both species are essentially treated as a single management unit in this region. This strategy may be appropriate for H. lobatus as a single stock was evident in the main stream of the MRB, but may not be appropriate for H. siamensis as more than a single stock was identified across the same range for this species. Management strategies should consider this difference to conserve overall biodiversity (local discrete populations) and this will include maintaining natural habitat and migration pathways, provision of fish sanctuaries (refuges) and may also require close monitoring of any stock declines, a signal that may require effective recovery strategies.