Assembly and annotation of a non-model gastropod (Nerita melanotragus) transcriptome: a comparison of De novo assemblers

Background The sequencing, de novo assembly and annotation of transcriptome datasets generated with next generation sequencing (NGS) has enabled biologists to answer genomic questions in non-model species with unprecedented ease. Reliable and accurate de novo assembly and annotation of transcriptomes, however, is a critically important step for transcriptome assemblies generated from short read sequences. Typical benchmarks for assembly and annotation reliability have been performed with model species. To address the reliability and accuracy of de novo transcriptome assembly in non-model species, we generated an RNAseq dataset for an intertidal gastropod mollusc species, Nerita melanotragus, and compared the assembly produced by four different de novo transcriptome assemblers; Velvet, Oases, Geneious and Trinity, for a number of quality metrics and redundancy. Results Transcriptome sequencing on the Ion Torrent PGM™ produced 1,883,624 raw reads with a mean length of 133 base pairs (bp). Both the Trinity and Oases de novo assemblers produced the best assemblies based on all quality metrics including fewer contigs, increased N50 and average contig length and contigs of greater length. Overall the BLAST and annotation success of our assemblies was not high with only 15-19% of contigs assigned a putative function. Conclusions We believe that any improvement in annotation success of gastropod species will require more gastropod genome sequences, but in particular an increase in mollusc protein sequences in public databases. Overall, this paper demonstrates that reliable and accurate de novo transcriptome assemblies can be generated from short read sequencers with the right assembly algorithms. Keywords: Nerita melanotragus; De novo assembly; Transcriptome; Heat shock protein; Ion torrent

Making the fun stop : youth justice reform in Queensland

In 2013 the newly elected conservative Liberal National Party government instigated amendments to the Youth Justice Act 1992 (Qld). Boot camps replaced court ordered youth justice conferencing. In 2014 there were more drastic changes, including opening the Children’s Court proceedings to the public, permitting publication of identifying information of repeat offenders, removing the principle of ‘detention as a last resort’, facilitating prompt transferral of 17 year olds to adult prisons and instigating new bail offences and mandatory boot camp orders for recidivist motor vehicle offenders in Townsville. This article compares these amendments to the legislative frameworks in other jurisdictions and current social research. It argues that these amendments are out of step with national and international best practice benchmarks for youth justice. Early indications are that Indigenous children are now experiencing increased rates of unsentenced remand. The article argues that the government’s policy initiatives are resulting in negative outcomes and that early and extensive evaluations of these changes are essential.

Medical semantic similarity with a neural language model

Advances in neural network language models have demonstrated that these models can effectively learn representations of words meaning. In this paper, we explore a variation of neural language models that can learn on concepts taken from structured ontologies and extracted from free-text, rather than directly from terms in free-text. This model is employed for the task of measuring semantic similarity between medical concepts, a task that is central to a number of techniques in medical informatics and information retrieval. The model is built with two medical corpora (journal abstracts and patient records) and empirically validated on two ground-truth datasets of human-judged concept pairs assessed by medical professionals. Empirically, our approach correlates closely with expert human assessors ($\approx$ 0.9) and outperforms a number of state-of-the-art benchmarks for medical semantic similarity. The demonstrated superiority of this model for providing an effective semantic similarity measure is promising in that this may translate into effectiveness gains for techniques in medical information retrieval and medical informatics (e.g., query expansion and literature-based discovery).

Practices to enhance peer program implementation integrity to safeguard peer leaders and learners

The powerful influence of peers on fellow students’ learning engagement and their ability to foster self-efficacy is well recognised. A positive learner mindset can be fostered through establishment of guided meaningful relationships formed between peers. Recognising the value of peer connections in shaping the student learning experience, peer programs have been widely adopted by universities as a mechanism to facilitate these connections. While potentially beneficial, a lack of knowledge and inexperience by program implementers can lead to program outcomes being compromised. To mitigate this risk, QUT has established university wide systems and benchmarks for enacting peer programs. These measures aim to promote program implementation integrity by supporting and developing the knowledge and capabilities of peer leaders and program coordinators. This paper describes a range of measures that have been instigated to optimise the quality of programs and ensure outcomes are mutually constructive and beneficial for all stakeholders.

Positioning as a source of competitive advantage: Benchmarking Rotorua’s position as a domestic short break holiday destination

Travellers are spoilt by holiday choice, and yet will usually only seriously consider a few destinations during the decision process. With thousands of destination marketing organisations (DMOs) competing for attention, places are becoming increasingly substitutable. The study of destination competitiveness is an emerging field, and thesis contributes to an enhanced understanding by addressing three topics that have received relatively little attention in the tourism literature: destination positioning, the context of short break holidays, and domestic travel in New Zealand. A descriptive model of positioning as a source of competitive advantage is developed, and tested through 12 propositions. The destination of interest is Rotorua, which was arguably New Zealand’s first tourist destination. The market of interest is Auckland, which is Rotorua’s largest visitor market. Rotorua’s history is explored to identify factors that may have contributed to the destination’s current image in the Auckland market. A mix of qualitative and quantitative procedures is then utilised to determine Rotorua’s position, relative to a competing set of destinations. Based on an applied research problem, the thesis attempts to bridge the gap between academia and industry by providing useable results and benchmarks for five regional tourism organisations (RTOs). It is proposed that, in New Zealand, the domestic short break market represents a valuable opportunity not explicitly targeted by the competitive set of destinations. Conceptually, the thesis demonstrates the importance of analysing a destination’s competitive position, from the demand perspective, in a travel context; and then the value of comparing this ‘ideal’ position with that projected by the RTO. The thesis concludes Rotorua’s market position in the Auckland short break segment represents a source of comparative advantage, but is not congruent with the current promotional theme, which is being used in all markets. The findings also have implications for destinations beyond the context of the thesis. In particular, a new definition for ‘destination attractiveness’ is proposed, which warrants consideration in the design of future destination positioning analyses.

A review of benchmarking in carbon labelling schemes for building materials

As one of the largest sources of greenhouse gas (GHG) emissions, the building and construction sector is facing increasing pressure to reduce its life cycle GHG emissions. One central issue in striving towards reduced carbon emissions in the building and construction sector is to develop a practical and meaningful yardstick to assess and communicate GHG results through carbon labelling. The idea of carbon labelling schemes for building materials is to trigger a transition to a low carbon future by switching consumer-purchasing habits to low-carbon alternatives. As such, failing to change purchasing pattern and behaviour can be disastrous to carbon labelling schemes. One useful tool to assist customers to change their purchasing behaviour is benchmarking, which has been very commonly used in ecolabelling schemes. This paper analyses the definition and scope of benchmarking in the carbon labelling schemes for building materials. The benchmarking process has been examined within the context of carbon labelling. Four practical issues for the successful implementation of benchmarking, including the availability of benchmarks and databases, the usefulness of different types of benchmarks and the selection of labelling practices have also been clarified.

A CCG virtual system for big data application communication costs analysis

Network topology and routing are two important factors in determining the communication costs of big data applications at large scale. As for a given Cluster, Cloud, or Grid system, the network topology is fixed and static or dynamic routing protocols are preinstalled to direct the network traffic. Users cannot change them once the system is deployed. Hence, it is hard for application developers to identify the optimal network topology and routing algorithm for their applications with distinct communication patterns. In this study, we design a CCG virtual system (CCGVS), which first uses container-based virtualization to allow users to create a farm of lightweight virtual machines on a single host. Then, it uses software-defined networking (SDN) technique to control the network traffic among these virtual machines. Users can change the network topology and control the network traffic programmingly, thereby enabling application developers to evaluate their applications on the same system with different network topologies and routing algorithms. The preliminary experimental results through both synthetic big data programs and NPB benchmarks have shown that CCGVS can represent application performance variations caused by network topology and routing algorithm.

Respite & Recoery at Al Wakra

International Design Competition for Qatar Psychiatric Hospital. The scheme for the Al Wakra Respite and Recovery Centre delivers on an all-in attitude toward evidence-based design. It sets new benchmarks in so many ways: the way it allows excellent separation between patient cohorts without unnecessary or visible restrictions; the way it allows sharing of most of the clinical kit and spaces; the way services reticulation and facilities management takes place without compromising security and safety; the ways It abandons the institutional axioms that are still so ubiquitous elsewhere, so it can appear as the friendly, welcoming and wholesome; the way it allows incredible flexibility to allow changes or flexion on the fly; the way it has such ‘good bones’ for more structural changes as the future unfolds. But most importantly, the scheme will be exemplary in the way the building itself plays a role in promoting the recovery and mental well-being of its residents. Like no other, the Centre will rise to the challenges of supporting and inspiring an exemplary mental health service and promote the well-being of the patients. The 160 bed scheme allows for 43,000m2 of landscape, packed with wholesome things to do and experience. The Aspire zone even has stables and a falconry, both to celebrate the love that Qatari people have for horses and birds.

ACE research briefing paper 009: Global Entrepreneurship Monitor: GEM Australia - 2014 National Report

Most policymakers and academics agree that entrepreneurship is critical to the development and wellbeing of society. Entrepreneurs create jobs. They drive and shape innovation, thereby speeding up structural changes in the economy. By introducing new competition they contribute indirectly to increased productivity and overall economic activity. Entrepreneurship is thus a catalyst for economic growth and national competitiveness. In 2014, the Global Entrepreneurship Monitor (GEM)conducted its 15th annual survey of the rate and profile of entrepreneurial activity around the globe. GEM interviewed over 206,000 adults aged 18–64 in 70 economies, spanning diverse geographies and a range of development levels. The Australian Centre for Entrepreneurship Research (ACE) participated as the Australian GEM partner, surveying 2,177 Australian adults. This report provides a summary of entrepreneurship in Australia as measured by GEM, and benchmarks this against other countries. We compare the level of entrepreneurship in the population across different phases of the entrepreneurial process, and provide a profile of some key characteristics of entrepreneurs and the businesses they are starting. We also report on some of the institutional and framework conditions that support entrepreneurship.

Focused Prefetching: Performance Oriented Prefetching Based On Commit Stalls

Loads that miss in L1 or L2 caches and waiting for their data at the head of the ROB cause significant slow down in the form of commit stalls. We identify that most of these commit stalls are caused by a small set of loads, referred to as LIMCOS (Loads Incurring Majority of COmmit Stalls). We propose simple history-based classifiers that track commit stalls suffered by loads to help us identify this small set of loads. We study an application of these classifiers to prefetching. The classifiers are used to train the prefetcher to focus on the misses suffered by LIMCOS. This, referred to as focused prefetching, results in a 9.8% gain in IPC over naive GHB based delta correlation prefetcher along with a 20.3% reduction in memory traffic for a set of 17 memory-intensive SPEC2000 benchmarks. Another important impact of focused prefetching is a 61% improvement in the accuracy of prefetches. We demonstrate that the proposed classification criterion performs better than other existing criteria like criticality and delinquent loads. Also we show that the criterion of focusing on commit stalls is robust enough across cache levels and can be applied to any prefetcher without any modifications to the prefetcher.

Repeatable Condition-Invariant Visual Odometry for Sequence-Based Place Recognition

This paper describes a vision-only system for place recognition in environments that are tra- versed at different times of day, when chang- ing conditions drastically affect visual appear- ance, and at different speeds, where places aren’t visited at a consistent linear rate. The ma- jor contribution is the removal of wheel-based odometry from the previously presented algo- rithm (SMART), allowing the technique to op- erate on any camera-based device; in our case a mobile phone. While we show that the di- rect application of visual odometry to our night- time datasets does not achieve a level of perfor- mance typically needed, the VO requirements of SMART are orthogonal to typical usage: firstly only the magnitude of the velocity is required, and secondly the calculated velocity signal only needs to be repeatable in any one part of the environment over day and night cycles, but not necessarily globally consistent. Our results show that the smoothing effect of motion constraints is highly beneficial for achieving a locally consis- tent, lighting-independent velocity estimate. We also show that the advantage of our patch-based technique used previously for frame recogni- tion, surprisingly, does not transfer to VO, where SIFT demonstrates equally good performance. Nevertheless, we present the SMART system us- ing only vision, which performs sequence-base place recognition in extreme low-light condi- tions where standard 6-DOF VO fails and that improves place recognition performance over odometry-less benchmarks, approaching that of wheel odometry.

Sampling and management of Bemisia tabaci (Genn.) biotype B in Australian cotton

Data on seasonal population abundance of Bemisia tabaci biotype B (silverleaf whitefly (SLW)) in Australian cotton fields collected over four consecutive growing seasons (2002/2003-2005/2006) were used to develop and validate a multiple-threshold-based management and sampling plan. Non-linear growth trajectories estimated from the field sampling data were used as benchmarks to classify adult SLW field populations into six density-based management zones with associated control recommendations in the context of peak flowering and open boll crop growth stages. Control options based on application of insect growth regulators (IGRs) are recommended for high-density populations (>2 adults/leaf) whereas conventional (non-IGR) products are recommended for the control of low to moderate population densities. A computerised re-sampling program was used to develop and test a binomial sampling plan. Binomial models with thresholds of T=1, 2 and 3 adults/leaf were tested using the field abundance data. A binomial plan based on a tally threshold of T=2 adults/leaf and a minimum sample of 20 leaves at nodes 3, 4 or 5 below the terminal is recommended as the most parsimonious and practical sampling protocol for Australian cotton fields. A decision support guide with management zone boundaries expressed as binomial counts and control options appropriate for various SLW density situations is presented. Appropriate use of chemical insecticides and tactics for successful field control of whiteflies are discussed.

Best management practices for sustainable and safe playing surface of Australian Football League sports fields

In 2002, AFL Queensland and the Brisbane Lions Football Club approached the Department of Primary Industries and Fisheries (Queensland) for advice on improving their Premier League sports fields. They were concerned about player safety and dissatisfaction with playing surfaces, particularly uneven turf cover and variable under-foot conditions. They wanted to get the best from new investments in ground maintenance equipment and irrigation infrastructure. Their sports fields were representative of community-standard, multi-use venues throughout Australia; generally ‘natural’ soil fields, with low maintenance budgets, managed by volunteers. Improvements such as reconstruction, drainage, or regular re-turfing are generally not affordable. Our project aimed to: (a) Review current world practice and performance benchmarks; (b) Demonstrate best-practice management for community-standard fields; (c) Adapt relevant methods for surface performance testing; (d) Assess current soils, and investigate useful amendments; (e) Improve irrigation system performance; and (e) Build industry capacity and encourage patterns for ongoing learning. Most global sports field research focuses on elite, sand-based fields. We adjusted elite standards for surface performance (hardness, traction, soil moisture, evenness, sward cover/height) and maintenance programs, to suit community-standard fields with lesser input resources. In regularly auditing ground conditions across 12 AFLQ fields in SE QLD, we discovered surface hardness (measured by Clegg Hammer) was the No. 1 factor affecting player safety and surface performance. Other important indices were turf coverage and surface compaction (measured by penetrometer). AFLQ now runs regularly audits affiliated fields, and closes grounds with hardness readings greater than 190 Gmax. Aerating every two months was the primary mechanical practice improving surface condition and reducing hardness levels to < 110 Gmax on the renovated project fields. With irrigation installation, these fields now record surface conditions comparable to elite fields. These improvements encouraged many other sporting organisations to seek advice / assistance from the project team. AFLQ have since substantially invested in an expanded ground improvement program, to cater for this substantially increased demand. In auditing irrigation systems across project fields, we identified low maintenance (with < 65% of sprinklers operating optimally) as a major problem. Retrofitting better nozzles and adjusting sprinklers improved irrigation distribution uniformity to 75-80%. Research showed that reducing irrigation frequency to weekly, and preparedness to withhold irrigation longer after rain, reduced irrigation requirement by 30-50%, compared to industry benchmarks of 5-6 ML/ha/annum. Project team consultation with regulatory authorities enhanced irrigation efficiency under imposed regional water restrictions. Laboratory studies showed incorporated biosolids / composts, or topdressed crumb rubber, improved compaction resistance of soils. Field evaluations confirmed compost incorporation significantly reduced surface hardness of high wear areas in dry conditions, whilst crumb rubber assisted turf persistence into early winter. Neither amendment was a panacea for poor agronomic practices. Under the auspices of the project Trade Mark Sureplay®, we published > 80 articles, and held > 100 extension activities involving > 2,000 participants. Sureplay® has developed a multi-level curator training structure and resource materials, subject to commercial implementation. The partnerships with industry bodies (particularly AFLQ), frequent extension activities, and engagement with government/regulatory sectors have been very successful, and are encouraged for any future work. Specific aspects of sports field management for further research include: (a) Understanding of factors affecting turf wear resistance and recovery, to improve turf persistence under wear; (b) Simple tests for pinpointing areas of fields with high hardness risk; and (c) Evaluation of new irrigation infrastructure, ‘water-saving’ devices, and irrigation protocols, in improving water use and turf cover outcomes.

Synergistic Execution of Stream Programs on Multicores with Accelerators

The StreamIt programming model has been proposed to exploit parallelism in streaming applications oil general purpose multicore architectures. The StreamIt graphs describe task, data and pipeline parallelism which can be exploited on accelerators such as Graphics Processing Units (GPUs) or CellBE which support abundant parallelism in hardware. In this paper, we describe a novel method to orchestrate the execution of if StreamIt program oil a multicore platform equipped with an accelerator. The proposed approach identifies, using profiling, the relative benefits of executing a task oil the superscalar CPU cores and the accelerator. We formulate the problem of partitioning the work between the CPU cores and the GPU, taking into account the latencies for data transfers and the required buffer layout transformations associated with the partitioning, as all integrated Integer Linear Program (ILP) which can then be solved by an ILP solver. We also propose an efficient heuristic algorithm for the work-partitioning between the CPU and the GPU, which provides solutions which are within 9.05% of the optimal solution on an average across the benchmark Suite. The partitioned tasks are then software pipelined to execute oil the multiple CPU cores and the Streaming Multiprocessors (SMs) of the GPU. The software pipelining algorithm orchestrates the execution between CPU cores and the GPU by emitting the code for the CPU and the GPU, and the code for the required data transfers. Our experiments on a platform with 8 CPU cores and a GeForce 8800 GTS 512 GPU show a geometric mean speedup of 6.94X with it maximum of 51.96X over it single threaded CPU execution across the StreamIt benchmarks. This is a 18.9% improvement over it partitioning strategy that maps only the filters that cannot be executed oil the GPU - the filters with state that is persistent across firings - onto the CPU.

Remote Sensing - based precision agriculture tool for the sugar industry

The project will produce practical and relevant benchmarks, protocols and recommendations for the adoption of remote sensing technologies for improved in season management and therefore production within the Australian sugar cane industry.