Compatibility of stormwater treatment performance data between different geographical areas

Using a case study approach, this paper presents a robust methodology for assessing the compatibility of stormwater treatment performance data between two geographical regions in relation to a treatment system. The desktop analysis compared data derived from a field study undertaken in Florida, USA, with South East Queensland (SEQ) rainfall and pollutant characteristics. The analysis was based on the hypothesis that when transposing treatment performance information from one geographical region to another, detailed assessment of specific rainfall and stormwater quality parameters is required. Accordingly, characteristics of measured rainfall events and stormwater quality in the Florida study were compared with typical characteristics for SEQ. Rainfall events monitored in the Florida study were found to be similar to events that occur in SEQ in terms of their primary characteristics of depth, duration and intensity. Similarities in total suspended solids (TSS) and total nitrogen (TN) concentration ranges for Florida and SEQ suggest that TSS and TN removal performances would not be very different if the treatment system is installed in SEQ. However, further investigations are needed to evaluate the treatment performance of total phosphorus (TP). The methodology presented also allows comparison of other water quality parameters.

miRPlant : an integrated tool for identification of plant miRNA from RNA sequencing data

Background Small RNA sequencing is commonly used to identify novel miRNAs and to determine their expression levels in plants. There are several miRNA identification tools for animals such as miRDeep, miRDeep2 and miRDeep*. miRDeep-P was developed to identify plant miRNA using miRDeep’s probabilistic model of miRNA biogenesis, but it depends on several third party tools and lacks a user-friendly interface. The objective of our miRPlant program is to predict novel plant miRNA, while providing a user-friendly interface with improved accuracy of prediction. Result We have developed a user-friendly plant miRNA prediction tool called miRPlant. We show using 16 plant miRNA datasets from four different plant species that miRPlant has at least a 10% improvement in accuracy compared to miRDeep-P, which is the most popular plant miRNA prediction tool. Furthermore, miRPlant uses a Graphical User Interface for data input and output, and identified miRNA are shown with all RNAseq reads in a hairpin diagram. Conclusions We have developed miRPlant which extends miRDeep* to various plant species by adopting suitable strategies to identify hairpin excision regions and hairpin structure filtering for plants. miRPlant does not require any third party tools such as mapping or RNA secondary structure prediction tools. miRPlant is also the first plant miRNA prediction tool that dynamically plots miRNA hairpin structure with small reads for identified novel miRNAs. This feature will enable biologists to visualize novel pre-miRNA structure and the location of small RNA reads relative to the hairpin. Moreover, miRPlant can be easily used by biologists with limited bioinformatics skills.

An experimental approach to air gap optimisation for a correction-less small field diode

Aim A recent Monte Carlo based study has shown that it is possible to design a diode that measures small field output factors equivalent to that in water. This is accomplished by placing an appropriate sized air gap above the silicon chip (1) with experimental results subsequently confirming that a particular Monte Carlo design was accurate (2). The aim of this work was to test if a new correction-less diode could be designed using an entirely experimental methodology. Method: All measurements were performed on a Varian iX at a depth of 5 cm, SSD of 95 cm and field sizes of 5, 6, 8, 10, 20 and 30 mm. Firstly, the experimental transfer of kq,clin,kq,msr from a commonly used diode detector (IBA, stereotactic field diode (SFD)) to another diode detector (Sun Nuclear, unshielded diode, (EDGEe)) was tested. These results were compared to Monte Carlo calculated values of the EDGEe. Secondly, the air gap above the EDGEe silicon chip was optimised empirically. Nine different air gap “tops” were placed above the EDGEe (air depth = 0.3, 0.6, 0.9 mm; air width = 3.06, 4.59, 6.13 mm). The sensitivity of the EDGEe was plotted as a function of air gap thickness for the field sizes measured. Results: The transfer of kq,clin,kq,msr from the SFD to the EDGEe was correct to within the simulation and measurement uncertainties. The EDGEe detector can be made “correction-less” for field sizes of 5 and 6 mm, but was ∼2% from being “correction-less” at field sizes of 8 and 10 mm. Conclusion Different materials will perturb small fields in different ways. A detector is only “correction-less” if all these perturbations happen to cancel out. Designing a “correction-less” diode is a complicated process, thus it is reasonable to expect that Monte Carlo simulations should play an important role.

Xenome--a tool for classifying reads from xenograft samples

Motivation Shotgun sequence read data derived from xenograft material contains a mixture of reads arising from the host and reads arising from the graft. Classifying the read mixture to separate the two allows for more precise analysis to be performed. Results We present a technique, with an associated tool Xenome, which performs fast, accurate and specific classification of xenograft-derived sequence read data. We have evaluated it on RNA-Seq data from human, mouse and human-in-mouse xenograft datasets.

Integrating PV systems into distribution networks with battery energy storage systems

Integrating Photovoltaic (PV) systems with battery energy storage in the distribution network will be essential to allow for continued uptake of domestic PV system installations. With increasing concerns regarding environmental and climate change issues, incorporating sources of renewable energy into power networks across the world will be key for a sustainable future. Australia is well placed to utilise solar energy as a significant component of its future energy generation and within the last 5 years there has been a rapid growth in the penetration levels seen by the grid. This growth of PV systems is causing a number of issues including intermittency of supply, negative power flow and voltage rises. Using the simulator tool GridLAB-D with a model of a typical South-East Queensland (SEQ) 11 kV distribution feeder, the effect of various configurations of PV systems have been offset with Battery Energy Storage Systems (BESS). From this, combinations of PV and storage that are most effective at mitigating the issues were explored.

A transcriptome resource for the koala (Phascolarctos cinereus) : insights into koala retrovirus transcription and sequence diversity

Background The koala, Phascolarctos cinereus, is a biologically unique and evolutionarily distinct Australian arboreal marsupial. The goal of this study was to sequence the transcriptome from several tissues of two geographically separate koalas, and to create the first comprehensive catalog of annotated transcripts for this species, enabling detailed analysis of the unique attributes of this threatened native marsupial, including infection by the koala retrovirus. Results RNA-Seq data was generated from a range of tissues from one male and one female koala and assembled de novo into transcripts using Velvet-Oases. Transcript abundance in each tissue was estimated. Transcripts were searched for likely protein-coding regions and a non-redundant set of 117,563 putative protein sequences was produced. In similarity searches there were 84,907 (72%) sequences that aligned to at least one sequence in the NCBI nr protein database. The best alignments were to sequences from other marsupials. After applying a reciprocal best hit requirement of koala sequences to those from tammar wallaby, Tasmanian devil and the gray short-tailed opossum, we estimate that our transcriptome dataset represents approximately 15,000 koala genes. The marsupial alignment information was used to look for potential gene duplications and we report evidence for copy number expansion of the alpha amylase gene, and of an aldehyde reductase gene. Koala retrovirus (KoRV) transcripts were detected in the transcriptomes. These were analysed in detail and the structure of the spliced envelope gene transcript was determined. There was appreciable sequence diversity within KoRV, with 233 sites in the KoRV genome showing small insertions/deletions or single nucleotide polymorphisms. Both koalas had sequences from the KoRV-A subtype, but the male koala transcriptome has, in addition, sequences more closely related to the KoRV-B subtype. This is the first report of a KoRV-B-like sequence in a wild population. Conclusions This transcriptomic dataset is a useful resource for molecular genetic studies of the koala, for evolutionary genetic studies of marsupials, for validation and annotation of the koala genome sequence, and for investigation of koala retrovirus. Annotated transcripts can be browsed and queried at http://koalagenome.org

Sexual selection in true fruit flies (Diptera: Tephritidae) : transcriptome and experimental evidences for phytochemicals increasing male competitive ability

In male tephritid fruit flies of the genus Bactrocera, feeding on secondary plant compounds (sensu lato male lures = methyl eugenol, raspberry ketone and zingerone) increases male mating success. Ingested male lures alter the male pheromonal blend, normally making it more attractive to females and this is considered the primary mechanism for the enhanced mating success. However, the male lures raspberry ketone and zingerone are known, across a diverse range of other organisms, to be involved in increasing energy metabolism. If this also occurs in Bactrocera, then this may represent an additional benefit to males as courtship is metabolically expensive and lure feeding may increase a fly's short-term energy. We tested this hypothesis by performing comparative RNA-seq analysis between zingerone-fed and unfed males of Bactrocera tryoni. We also carried out behavioural assays with zingerone- and cuelure-fed males to test whether they became more active. RNA-seq analysis revealed, in zingerone-fed flies, up-regulation of 3183 genes with homologues transcripts to those known to regulate intermale aggression, pheromone synthesis, mating and accessory gland proteins, along with significant enrichment of several energy metabolic pathways and gene ontology terms. Behavioural assays show significant increases in locomotor activity, weight reduction and successful mating after mounting; all direct/indirect measures of increased activity. These results suggest that feeding on lures leads to complex physiological changes, which result in more competitive males. These results do not negate the pheromone effect, but do strongly suggest that the phytochemical-induced sexual selection is governed by both female preference and male competitive mechanisms.

EUTOPIA 75+ : exploratory futures scenarios for baby boomers’ preferred living spaces

Australia is experiencing the global phenomenon of an ageing population with the baby boomer generation starting to reach retirement age in large numbers. As a result, there is a growing need for appropriate accommodation and this will continue to grow for the foreseeable future. However, the needs of the fit, mobile and techno savvy baby boomers are likely to be far different from those of previous generations of older people, but are as yet unknown and unanticipated. This paper reports on the findings of a Futuring research project to explore the preferred housing futures for the baby boomer generation in the city of Brisbane, an aspiring creative city in South East Queensland (SEQ), Australia. Their future home design and service needs are predicted by firstly employing a global environmental scan of related and associated ageing futures issues. This was followed by a micro-Futuring workshop, based on Inayatullah’s Futures Triangle Analysis, to identify a range of scenarios. The key aspects of the workshop culminated in the development of a Transformational Scenario – EUTOPIA 75+. From this, a suite of six design recommendations for seniors’ housing design and smart services provision are synthesised to give a sense of direction of preferred living styles, especially in terms of physical housing spaces, with a view to identifying new house design opportunities for the allied industries and research organisations. The issues identified are also of concern for aged care service providers, retirement living developers, and for academics involved in the social and physical design of living spaces for older people.

A communication model and partitioning algorithm for streaming applications for an embedded MPSoC

Energy efficient embedded computing enables new application scenarios in mobile devices like software-defined radio and video processing. The hierarchical multiprocessor considered in this work may contain dozens or hundreds of resource efficient VLIW CPUs. Programming this number of CPU cores is a complex task requiring compiler support. The stream programming paradigm provides beneficial properties that help to support automatic partitioning. This work describes a compiler for streaming applications targeting the self-build hierarchical CoreVA-MPSoC multiprocessor platform. The compiler is supported by a programming model that is tailored to fit the streaming programming paradigm. We present a novel simulated-annealing (SA) based partitioning algorithm, called Smart SA. The overall speedup of Smart SA is 12.84 for an MPSoC with 16 CPU cores compared to a single CPU implementation. Comparison with a state of the art partitioning algorithm shows an average performance improvement of 34.07%.

The BAD project: data mining, database and prediction of protein adsorption on surfaces

Protein adsorption at solid-liquid interfaces is critical to many applications, including biomaterials, protein microarrays and lab-on-a-chip devices. Despite this general interest, and a large amount of research in the last half a century, protein adsorption cannot be predicted with an engineering level, design-orientated accuracy. Here we describe a Biomolecular Adsorption Database (BAD), freely available online, which archives the published protein adsorption data. Piecewise linear regression with breakpoint applied to the data in the BAD suggests that the input variables to protein adsorption, i.e., protein concentration in solution; protein descriptors derived from primary structure (number of residues, global protein hydrophobicity and range of amino acid hydrophobicity, isoelectric point); surface descriptors (contact angle); and fluid environment descriptors (pH, ionic strength), correlate well with the output variable-the protein concentration on the surface. Furthermore, neural network analysis revealed that the size of the BAD makes it sufficiently representative, with a neural network-based predictive error of 5% or less. Interestingly, a consistently better fit is obtained if the BAD is divided in two separate sub-sets representing protein adsorption on hydrophilic and hydrophobic surfaces, respectively. Based on these findings, selected entries from the BAD have been used to construct neural network-based estimation routines, which predict the amount of adsorbed protein, the thickness of the adsorbed layer and the surface tension of the protein-covered surface. While the BAD is of general interest, the prediction of the thickness and the surface tension of the protein-covered layers are of particular relevance to the design of microfluidics devices.

Subtropical values and principles of subtropical design for the South East Queensland region : a report for the Office of Urban Management Queensland Government

The Office of Urban Management recognises that the values which characterise the SEQ region as 'subtropical' are important determinants of form in urban and regional planning. Subtropical values are those qualities on which our regional identity depends. A built environment which responds positively to these values is a critical ingredient for achieving a desirable future for the region. The Centre for Subtropical Design has undertaken this study to identify the particular set of values which characterises SEQ, and to translate theses values into design principals that will maintain and reinforce the value set. The principles not only apply to the overall balance between the natural environment and the built environment, but can be applied by local government authorities to guide local planning schemes and help shape specific built for outcomes.

The ways of things: Objects in the studio

Conventions of the studio presuppose the artist as the active agent, imposing his/her will upon and through objects that remain essentially inert. However, this characterisation of practice overlooks the complex object dynamics that underpin the art-making process. Far from passive entities, objects are resistant, ‘speaking back’ to the artist, impressing their will upon their surroundings. Objects stick to one another, fall over, drip, spill, spatter and chip one another. Objects support, dismantle, cover and transform one another. Objects are both the apparatus of the studio and its products. It can be argued that the work of art is as much shaped by objects as it is by human impulse. Within this alternate ontology, the artist becomes but one element in a constellation of objects. Drawing upon Graham Harman’s Object-Oriented Ontology and a selection of photographs of my studio processes, this practice-led paper will explore the notion of agentive objects and the ways in which the contemporary art studio can be reconsidered as a primary site for the production of new object relationships.

Drug accumulation into single drug-sensitive and drug-resistant prostate cancer cells conducted on the single cell bioanalyzer

Multidrug resistance (MDR) occurs in prostate cancer, and this happens when the cancer cells resist chemotherapeutic drugs by pumping them out of the cells. MDR inhibitors such as cyclosporin A (CsA) can stop the pumping and enhance the drugs accumulated in the cells. The cellular drug accumulation is monitored using a microfluidic chip mounted on a single cell bioanalyzer. This equipment has been developed to measure accumulation of drugs such as doxorubicin (DOX) and fluorescently labeled paclitaxel (PTX) in single prostate cancer cells. The inhibition of drug efflux on the same prostate cell was examined in drug-sensitive and drug-resistant cells. Accumulation of these drug molecules was not found in the MDR cells, PC-3 RX-DT2R cells. Enhanced drug accumulation was observed only after treating the MDR cell in the presence of 5 μM of CsA as the MDR inhibitor. We envision this monitoring of the accumulation of fluorescent molecules (drug or fluorescent molecules), if conducted on single patient cancer cells, can provide information for clinical monitoring of patients undergoing chemotherapy in the future.

Evaluation of Interconnect Fabrics for an Embedded MPSoC in 28 nm FD-SOI

Embedded many-core architectures contain dozens to hundreds of CPU cores that are connected via a highly scalable NoC interconnect. Our Multiprocessor-System-on-Chip CoreVAMPSoC combines the advantages of tightly coupled bus-based communication with the scalability of NoC approaches by adding a CPU cluster as an additional level of hierarchy. In this work, we analyze different cluster interconnect implementations with 8 to 32 CPUs and compare them in terms of resource requirements and performance to hierarchical NoCs approaches. Using 28nm FD-SOI technology the area requirement for 32 CPUs and AXI crossbar is 5.59mm2 including 23.61% for the interconnect at a clock frequency of 830 MHz. In comparison, a hierarchical MPSoC with 4 CPU cluster and 8 CPUs in each cluster requires only 4.83mm2 including 11.61% for the interconnect. To evaluate the performance, we use a compiler for streaming applications to map programs to the different MPSoC configurations. We use this approach for a design-space exploration to find the most efficient architecture and partitioning for an application.

From Kafka to KAFTA: Intellectual property, and the Korea-Australia free trade agreement

This paper provides a critical examination of the intellectual property sections of the Korea-Australia Free Trade Agreement 2014. Chapter 13 of the Korea-Australia Free Trade Agreement 2014 deals with the subject of intellectual property law. The Chapter covers such topics as the purposes and objectives of intellectual property law; copyright law; trade mark law; patent law; and intellectual property enforcement. The Joint Standing Committee on Treaties in the Australian Parliament highlighted the controversy surrounding this chapter of the agreement: The intellectual property rights chapter of KAFTA has drawn considerable attention from academics and stakeholders regarding the proposed need for changes to Australian intellectual property law and the inclusion of intellectual property in the definition of investment with regard to the investor-state dispute mechanism. Other concerns raised with the Committee include the prescriptive nature of the chapter, the lack of recognition of the broader public interests of intellectual property rights, and possible changes to fair use provisions. Article 13.1.1 of the Korea-Australia Free Trade Agreement 2014 provides that: ‘Each Party recognises the importance of adequate and effective protection of intellectual property rights, while ensuring that measures to enforce those rights do not themselves become barriers to legitimate trade.’ This is an unsatisfactory description of the objectives and purposes of intellectual property law in both Australia and Korea. There is a failure to properly consider the range of public purposes served by intellectual property law – such as providing for access to knowledge, promoting competition and innovation, protecting consumer rights, and allowing for the protection of public health, food security, and the environment. Such a statement of principles and objectives detracts from the declaration in the TRIPS Agreement 1994 of the public interest objectives to be served by intellectual property. Chapter 11 of the Korea-Australia Free Trade Agreement 2014 is an investment chapter, with an investor-state dispute settlement regime. This chapter is highly controversial – given the international debate over investor-state dispute settlement; the Australian context for the debate; and the text of the Korea-Australia Free Trade Agreement 2014. In April 2014, the United Nations Conference on Trade and Development (UNCTAD) released a report on Recent Developments in Investor-State Dispute Settlement. The overall figures are staggering. UNCTAD reports a significant growth in investment-state dispute settlement, across a wide array of different fields of public regulation. Given the broad definition of investment, intellectual property owners will be able to use the investor-state dispute settlement regime in the Korea-Australia Free Trade Agreement 2014. This will have significant implications for all the various disciplines of intellectual property – including copyright law, trade mark law, and patent law.