Library Research Support in developing, testing and promoting an open cyberinfrastructure

QUT Library continues to rethink research support with eResearch as a primary driver. The support to the development of the Lens, an open global cyberinfrastructure, has been especially important in the light of technology transfer promotion, and partly in the response to researchers’ needs in following the innovation landscapes not only within the scientific but also patent literature. The Lens http://www.lens.org/lens/ project makes innovation more efficient, fair, transparent and inclusive. It is a joint effort between Cambia http://www.cambia.org.au and Queensland University of Technology (QUT). The Lens serves more than 84 million patent documents in the world as open, annotatable digital public goods that are integrated with scholarly and technical literature along with regulatory and business data. Users can link from search results to visualization and document clusters; from a patent document description to its full-text; from there, if applicable, the sequence data can also be found. Figure 1 shows a BLAST Alignment (DNA) using the Lens. A unique feature of the Lens is the ability to embed search and BLAST results into blogs and websites, and provide real-time updates to them. PatSeq Explorer http://www.lens.org/lens/bio/patseqexplorer allows users to navigate patent sequences that map onto the human genome and in the future, many other genomes. PatSeq Explorer offers three level views for the sequence information and links each group of sequences at the chromosomal level to their corresponding patent documents in the Lens. By integrating sequence and patent search and document clustering capabilities, users can now understand the big and small details on the true extent and scope of genetic sequence patents. QUT Library supported Cambia in developing, testing and promoting the Lens. This poster demonstrates QUT Library’s provision of best practice and holistic research support to a research group and how QUT Librarians have acquired new capabilities to meet the needs of the researchers beyond traditional research support practices.

Structural dynamics education in the new millennium

Structural Dynamics is the study of the response of structures to dynamic or time varying loads. This topic has emerged to be one of importance to all structural engineers due to three important issues with structural engineering in the new millennium. These are: (1) vibration and problems in slender structures that have emerged due to new material technology and aesthetic requirements, (ii) ageing structures such as bridges whoese health needs to be monitored and appropriate retrofitting carried out to prevent failure and (iii) increased vulnerability of structures to random loads such as seismic, impact and blast loads. Knowledge of structural dynamics is necessary to address these issues and their consequences. During the past two decades, research in structural dynamics has generated considerable amount of new information to address these issues. This new knowledge is not readily made available to practicing engineers and very little or none of it enters the classrooms. There is no universal emphasis on including structural dynamics and their recently generated new knowledge into the civil/structural curriculum. This paper argues for the need to include structural dynamics into the syllabus of all civil engineering courses especially those having a first or second major in structural engineering. This will enable our future structural engineers to design and maintain safe and efficient structures.

Design of a traumatic injury simulator for assessing lower limb response to high loading rates

Current military conflicts are characterized by the use of the improvised explosive device. Improvements in personal protection, medical care, and evacuation logistics have resulted in increasing numbers of casualties surviving with complex musculoskeletal injuries, often leading to lifelong disability. Thus, there exists an urgent requirement to investigate the mechanism of extremity injury caused by these devices in order to develop mitigation strategies. In addition, the wounds of war are no longer restricted to the battlefield; similar injuries can be witnessed in civilian centers following a terrorist attack. Key to understanding such mechanisms of injury is the ability to deconstruct the complexities of an explosive event into a controlled, laboratory-based environment. In this article, a traumatic injury simulator, designed to recreate in the laboratory the impulse that is transferred to the lower extremity from an anti-vehicle explosion, is presented and characterized experimentally and numerically. Tests with instrumented cadaveric limbs were then conducted to assess the simulator’s ability to interact with the human in two mounting conditions, simulating typical seated and standing vehicle passengers. This experimental device will now allow us to (a) gain comprehensive understanding of the load-transfer mechanisms through the lower limb, (b) characterize the dissipating capacity of mitigation technologies, and (c) assess the bio-fidelity of surrogates.

The comparative behaviour of two combat boots under impact

Background Improvised explosive devices have become the characteristic weapon of conflicts in Iraq and Afghanistan. While little can be done to mitigate against the effects of blast in free-field explosions, scaled blast simulations have shown that the combat boot can attenuate the effects on the vehicle occupants of anti-vehicular mine blasts. Although the combat boot offers some protection to the lower limb, its behaviour at the energies seen in anti-vehicular mine blast has not been documented previously. Methods The sole of eight same-size combat boots from two brands currently used by UK troops deployed to Iraq and Afghanistan were impacted at energies of up to 518 J, using a spring-assisted drop rig. Results The results showed that the Meindl Desert Fox combat boot consistently experienced a lower peak force at lower impact energies and a longer time-to-peak force at higher impact energies when compared with the Lowa Desert Fox combat boot. Discussion This reduction in the peak force and extended rise time, resulting in a lower energy transfer rate, is a potentially positive mitigating effect in terms of the trauma experienced by the lower limb. Conclusion Currently, combat boots are tested under impact at the energies seen during heel strike in running. Through the identification of significantly different behaviours at high loading, this study has shown that there is rationale in adding the performance of combat boots under impact at energies above those set out in international standards to the list of criteria for the selection of a combat boot.

In-vehicle extremity injuries from improvised explosive devices : current and future foci

The conflicts in Iraq and Afghanistan have been epitomized by the insurgents’ use of the improvised explosive device against vehicle-borne security forces. These weapons, capable of causing multiple severely injured casualties in a single incident, pose the most prevalent single threat to Coalition troops operating in the region. Improvements in personal protection and medical care have resulted in increasing numbers of casualties surviving with complex lower limb injuries, often leading to long-term disability. Thus, there exists an urgent requirement to investigate and mitigate against the mechanism of extremity injury caused by these devices. This will necessitate an ontological approach, linking molecular, cellular and tissue interaction to physiological dysfunction. This can only be achieved via a collaborative approach between clinicians, natural scientists and engineers, combining physical and numerical modelling tools with clinical data from the battlefield. In this article, we compile existing knowledge on the effects of explosions on skeletal injury, review and critique relevant experimental and computational research related to lower limb injury and damage and propose research foci required to drive the development of future mitigation technologies.

A standing vehicle occupant is likely to sustain a more severe injury than one who has flexed knees in an under‐vehicle explosion : a cadaveric study

The lower limb of military vehicle occupants has been the most injured body part due to undervehicle explosions in recent conflicts. Understanding the injury mechanism and causality of injury severity could aid in developing better protection. Therefore, we tested 4 different occupant postures (seated, brace, standing, standing with knee locked in hyper‐extension) in a simulated under‐vehicle explosion (solid blast) using our traumatic injury simulator in the laboratory; we hypothesised that occupant posture would affect injury severity. No skeletal injury was observed in the specimens in seated and braced postures. Severe, impairing injuries were observed in the foot of standing and hyper‐extended specimens. These results demonstrate that a vehicle occupant whose posture at the time of the attack incorporates knee flexion is more likely to be protected against severe skeletal injury to the lower leg.

Use of cadavers and anthropometric test devices (ATDs) for assessing lower limb injury outcome from under‐vehicle explosions

Lower extremities are particularly susceptible to injury in an under‐vehicle explosion. Operational fitness of military vehicles is assessed through anthropometric test devices (ATDs) in full‐scale blast tests. The aim of this study was to compare the response between the Hybrid‐III ATD, the MiL‐Lx ATD and cadavers in our traumatic injury simulator, which is able to replicate the response of the vehicle floor in an under‐vehicle explosion. All specimens were fitted with a combat boot and tested on our traumatic injury simulator in a seated position. The load recorded in the ATDs was above the tolerance levels recommended by NATO in all tests; no injuries were observed in any of the 3 cadaveric specimens. The Hybrid‐III produced higher peak forces than the MiL‐Lx. The time to peak strain in the calcaneus of the cadavers was similar to the time to peak force in the ATDs. Maximum compression of the sole of the combat boot was similar for cadavers and MiL‐Lx, but significantly greater for the Hybrid‐III. These results suggest that the MiL‐Lx has a more biofidelic response to under‐vehicle explosive events compared to the Hybrid‐III. Therefore, it is recommended that mitigation strategies are assessed using the MiL‐Lx surrogate and not the Hybrid‐III.

Genomic resources notes accepted 1 December 2013 - 31 January 2014

This article documents the public availability of (i) transcriptome sequence data, assembled and annotated contigs and unigenes, and BLAST hits from the Queensland fruit fly, Bactrocera tryoni; (ii) 75 single-nucleotide variants (SNVs) from 454 sequencing of reduced representation libraries for Phalangiidae harvestmen, Megabunus armatus, Megabunus vignai, Megabunus lesserti, and Rilaena triangularis; and (iii) expressed sequence tags from 454 sequencing of the lepidopterans Lymantria dispar and Lymantria monacha.

Rho GTPases mediate the mechanosensitive lineage commitment of neural stem cells

Adult neural stem cells (NSCs) play important roles in learning and memory and are negatively impacted by neurological disease. It is known that biochemical and genetic factors regulate self-renewal and differentiation, and it has recently been suggested that mechanical and solid-state cues, such as extracellular matrix (ECM) stiffness, can also regulate the functions of NSCs and other stem cell types. However, relatively little is known of the molecular mechanisms through which stem cells transduce mechanical inputs into fate decisions, the extent to which mechanical inputs instruct fate decisions versus select for or against lineage-committed blast populations, or the in vivo relevance of mechanotransductive signaling molecules in native stem cell niches. Here we demonstrate that ECM-derived mechanical signals act through Rho GTPases to activate the cellular contractility machinery in a key early window during differentiation to regulate NSC lineage commitment. Furthermore, culturing NSCs on increasingly stiff ECMs enhances RhoA and Cdc42 activation, increases NSC stiffness, and suppresses neurogenesis. Likewise, inhibiting RhoA and Cdc42 or downstream regulators of cellular contractility rescues NSCs from stiff matrix- and Rho GTPase-induced neurosuppression. Importantly, Rho GTPase expression and ECM stiffness do not alter proliferation or apoptosis rates indicating that an instructive rather than selective mechanism modulates lineage distributions. Finally, in the adult brain, RhoA activation in hippocampal progenitors suppresses neurogenesis, analogous to its effect in vitro. These results establish Rho GTPase-based mechanotransduction and cellular stiffness as biophysical regulators of NSC fate in vitro and RhoA as an important regulatory protein in the hippocampal stem cell niche.

Improving combustion stability in sugar factory boilers

Reliable operation of a sugar factory boiler station is essential for efficient and timely processing of the cane supply. Sugar factory boilers have to contend with changes in fuel quality caused by variations in performance of the extraction station, different cane varieties and associated agronomic factors along with fluctuations in factory steam demand. These variations can affect the stability of combustion in boiler furnaces leading to reductions in boiler steam output and large furnace pressure fluctuations that can cause serious damage. This paper investigates the causes of unstable combustion, discusses aspects of boiler design that make a boiler more susceptible to unstable combustion and uses modelling to evaluate different options for improving combustion stability.

Effect of soil properties on the response of pile to underground explosion

This paper develops and presents a fully coupled non-linear finite element procedure to treat the response of piles to ground shocks induced by underground explosions. The Arbitrary Lagrange Euler coupling formulation with proper state material parameters and equations are used in the study. Pile responses in four different soil types, viz, saturated soil, partially saturated soil and loose and dense dry soils are investigated and the results compared. Numerical results are validated by comparing with those from a standard design manual. Blast wave propagation in soils, horizontal pile deformations and damages in the pile are presented. The pile damage presented through plastic strain diagrams will enable the vulnerability assessment of the piles under the blast scenarios considered. The numerical results indicate that the blast performance of the piles embedded in saturated soil and loose dry soil are more severe than those in piles embedded in partially saturated soil and dense dry soil. Present findings should serve as a benchmark reference for future analysis and design.

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

Robotic explosive charging in mining and construction applications

Describes the development and testing of a robotic system for charging blast holes in underground mining. The automation system supports four main tactical functions: detection of blast holes; teleoperated arm pose control; automatic arm pose control; and human-in-the-loop visual servoing. We present the system architecture, and analyse the major components, Hole detection is crucial for automating the process, and we discuss theoretical and practical aspects in detail. The sensors used are laser range finders and cameras installed in the end effector. For automatic insertion, we consider image processing techniques to support visual servoing the tool to the hole. We also discuss issues surrounding the control of heavy-duty mining manipulators, in particular, friction, stiction, and actuator saturation.

Locality-sensitive hashing for protein classification

Determination of sequence similarity is a central issue in computational biology, a problem addressed primarily through BLAST, an alignment based heuristic which has underpinned much of the analysis and annotation of the genomic era. Despite their success, alignment-based approaches scale poorly with increasing data set size, and are not robust under structural sequence rearrangements. Successive waves of innovation in sequencing technologies – so-called Next Generation Sequencing (NGS) approaches – have led to an explosion in data availability, challenging existing methods and motivating novel approaches to sequence representation and similarity scoring, including adaptation of existing methods from other domains such as information retrieval. In this work, we investigate locality-sensitive hashing of sequences through binary document signatures, applying the method to a bacterial protein classification task. Here, the goal is to predict the gene family to which a given query protein belongs. Experiments carried out on a pair of small but biologically realistic datasets (the full protein repertoires of families of Chlamydia and Staphylococcus aureus genomes respectively) show that a measure of similarity obtained by locality sensitive hashing gives highly accurate results while offering a number of avenues which will lead to substantial performance improvements over BLAST..

Dynamic simulation of CFRP strengthened steel column under impact loading

Carbon fibre reinforced polymer (CFRP) strengthening of metallic structures under static loading has shown great potential in the recent years. However, steel structures are often experienced natural (e.g. earthquake, wind) as well as man-made (e.g. vehicular impact, blast) dynamic loading. Therefore, there is a growing interest among the researchers to investigate the capability of CFRP strengthened members under such dynamic conditions. This study focuses on the finite element (FE) numerical modelling and simulation of CFRP strengthened steel column under transverse impact loading to predict the behaviour and failure modes. Impact simulation process and the CFRP strengthened steel column are validated with the existing experimental results in literature. The validated FE model of CFRP strengthened steel column is then further used to investigate the effects of transverse impact loading on its structural performance. The results are presented in terms of transvers e impact force, lateral and axial displacement, and deformed shape to evaluate the effectiveness of CFRP strengthening technique. Comparisons between the bare steel and CFRP strengthened steel columns clearly indicate the performance enhancement of strengthened column under transverse impact loading.