Variation in parental magmas of Mt Rouse, a complex polymagmatic monogenetic volcano in the basaltic intraplate Newer Volcanics Province, southeast Australia

Monogenetic volcanoes have long been regarded as simple in nature, involving single magma batches and uncomplicated evolutions; however, recent detailed research into individual centres is challenging that assumption. Mt Rouse (Kolor) is the volumetrically largest volcano in the monogenetic Newer Volcanics Province of southeast Australia. This study presents new major, trace and Sr–Nd–Pb isotope data for samples selected on the basis of a detailed stratigraphic framework analysis of the volcanic products from Mt Rouse. The volcano is the product of three magma batches geochemically similar to Ocean–Island basalts, featuring increasing LREE enrichment with each magma batch (batches A, B and C) but no evidence of crustal contamination; the Sr–Nd–Pb isotopes define two groupings. Modelling suggests that the magmas were sourced from a zone of partial melting crossing the lithosphere–asthenosphere boundary, with batch A forming a large volume partial melt in the deep lithosphere (1.7 GPa/55.5 km); and batches B and C from similar areas within the shallow asthenosphere (1.88 GPa/61 km and 1.94 GPa/63 km, respectively). The formation and extraction of these magmas may have been due to high deformation rates in the mantle caused by edge-driven convection and asthenospheric upwelling. The lithosphere– asthenosphere boundary is important with respect to NVP volcanism. An eruption chronology involves sequential eruption of magma batches A, C and B, followed by simultaneous eruption of batches A and B. Mt Rouse is a complex polymagmatic monogenetic volcano that illustrates the complexity of monogenetic volcanism and demonstrates the importance of combining detailed stratigraphic analysis alongside systematic geochemical sampling.

Trailing Touch

Trailing Touch (2014) is a twenty minute classically-based dance work set to music by composers Carter Burwell and Hildur Gudnadottir. It is an abstract work that explores images based on imperfect patterns and seeks to transmit the sensations felt when clusters form and disperse through the space or crisscross to create swirling wave-like reactions in the dancers’ tulle skirts. These simple references are inspired by the lyrical use of arms found in ballet, particular to the ballet aesthetic. Trailing Touch was created in collaboration with QUT’s third-year BFA (Dance Performance) students and performed as part of Dance14 at QUT’s Gardens Points Theatre from the 4th to 8th November 2014 and was performed in Singapore as part of Contact Contemporary Dance Festival on 30th November, 2014. Additionally, the creative process of Trailing Touch (2014) forms the initial project of Phase III of my PhD research, Writing the Dance Score in the Twenty-first Century: An approach for the Independent Choreographer. This PhD research will examine the potential of dance scores as a suite of choreographic strategies to map key aspects of the choreographic process. While a certain degree of ambiguity drives the creative process, the suite of choreographic strategies attempt to capture what is transmitted through the lived experience of dance. “[T]hese documents harbor a force of expression, a visual energy related to the body and the movement” (Louppe 1994, 7) that triggers movement responses, unforeseen intensities and enables personal interpretation. Consequently, Phase III will test and evaluate the relevance of Phase II research within the pressures of mainstream dance rehearsal and performance contexts. In Project One Trailing Touch this was demonstrated in the dance scores produced by the choreographer and interpreted by the dancers within the performance. By drawing from both the theoretical and practical, it is anticipated that this research will suggest a form of languaging movement that is not reliant on images or numbers, but generated in response to the intuitive and complex process underpinning choreographic practice. Rather than constructing a codified dance notation system, it will focus on strategies that reveal movement, its spatial patterns, qualities and intensities of expression and the procedures underlying key choreographic concepts. The outcome of this research project aims to support the independent choreographer in two major areas, by facilitating and enriching the choreographic process for both the performers and choreographer, and by strengthening artistic development and performance outcomes.

Reducing grant application numbers : the shame stick or prize carrot?

Researchers spend an average of 38 working days preparing an NHMRC Project Grant proposal, but with success rates of just 15% then over 500 years of researcher went into failed applications in 2014. This time would likely have been better spent on actual research. Many applications are non-competitive and could possibly be culled early, saving time for both researchers and funding agencies. Our analysis of the major health and medical scheme in Australia estimated that 61% of applications were never likely to be funded...

Bayesian networks for information synthesis in complex systems

This thesis introduces a method of applying Bayesian Networks to combine information from a range of data sources for effective decision support systems. It develops a set of techniques in development, validation, visualisation, and application of Complex Systems models, with a working demonstration in an Australian airport environment. The methods presented here have provided a modelling approach that produces highly flexible, informative and applicable interpretations of a system's behaviour under uncertain conditions. These end-to-end techniques are applied to the development of model based dashboards to support operators and decision makers in the multi-stakeholder airport environment. They provide highly flexible and informative interpretations and confidence in these interpretations of a system's behaviour under uncertain conditions.

In silico biology : making the most of parallel computing

Biological systems are typically complex and adaptive, involving large numbers of entities, or organisms, and many-layered interactions between these. System behaviour evolves over time, and typically benefits from previous experience by retaining memory of previous events. Given the dynamic nature of these phenomena, it is non-trivial to provide a comprehensive description of complex adaptive systems and, in particular, to define the importance and contribution of low-level unsupervised interactions to the overall evolution process. In this chapter, the authors focus on the application of the agent-based paradigm in the context of the immune response to HIV. Explicit implementation of lymph nodes and the associated lymph network, including lymphatic chain structure, is a key objective, and requires parallelisation of the model. Steps taken towards an optimal communication strategy are detailed.

Visualization of complex biological systems: An immune response model using OpenGL

In this paper we present an update on our novel visualization technologies based on cellular immune interaction from both large-scale spatial and temporal perspectives. We do so with a primary motive: to present a visually and behaviourally realistic environment to the community of experimental biologists and physicians such that their knowledge and expertise may be more readily integrated into the model creation and calibration process. Visualization aids understanding as we rely on visual perception to make crucial decisions. For example, with our initial model, we can visualize the dynamics of an idealized lymphatic compartment, with antigen presenting cells (APC) and cytotoxic T lymphocyte (CTL) cells. The visualization technology presented here offers the researcher the ability to start, pause, zoom-in, zoom-out and navigate in 3-dimensions through an idealised lymphatic compartment.

Incorporating complex train paths to an analysis of absolute capacity

Railways are an important mode of transportation. They are however large and complex and their construction, management and operation is time consuming and costly. Evidently planning the current and future activities is vital. Part of that planning process is an analysis of capacity. To determine what volume of traffic can be achieved over time, a variety of railway capacity analysis techniques have been created. A generic analytical approach that incorporates more complex train paths however has yet to be provided. This article provides such an approach. This article extends a mathematical model for determining the theoretical capacity of a railway network. The main contribution of this paper is the modelling of more complex train paths whereby each section can be visited many times in the course of a train’s journey. Three variant models are formulated and then demonstrated in a case study. This article’s numerical investigations have successively shown the applicability of the proposed models and how they may be used to gain insights into system performance.

Reduced intensity conditioning for allogeneic hematopoietic stem cell transplant determines the kinetics of acute Graft-Versus-Host Disease

Background Preparative myeloablative conditioning regimens for allogeneic hematopoietic stem-cell transplantation (HSCT) may control malignancy and facilitate engraftment but also contribute to transplant related mortality, cytokine release, and acute graft-versus-host disease (GVHD). Reduced intensity conditioning (RIC) regimens have decreased transplant related mortality but the incidence of acute GVHD, while delayed, remains unchanged. There are currently no in vivo allogeneic models of RIC HSCT, limiting studies into the mechanism behind RIC-associated GVHD. Methods We developed two RIC HSCT models that result in delayed onset GVHD (major histocompatibility complex mismatched (UBI-GFP/BL6 [H-2b]→BALB/c [H-2d]) and major histocompatibility complex matched, minor histocompatibility mismatched (UBI-GFP/BL6 [H-2b]→BALB.B [H-2b])) enabling the effect of RIC on chimerism, dendritic cell (DC) chimerism, and GVHD to be investigated. Results In contrast with myeloablative conditioning, we observed that RIC-associated delayed-onset GVHD is characterized by low production of tumor necrosis factor-α, maintenance of host DC, phenotypic DC activation, increased T-regulatory cell numbers, and a delayed emergence of activated donor DC. Furthermore, changes to the peritransplant milieu in the recipient after RIC lead to the altered activation of DC and the induction of T-regulatory responses. Reduced intensity conditioning recipients suffer less early damage to GVHD target organs. However, as donor cells engraft, activated donor DC and rising levels of tumor necrosis factor-α are associated with a later onset of severe GVHD. Conclusions Delineating the mechanisms underlying delayed onset GVHD in RIC HSCT recipients is vital to improve the prediction of disease onset and allow more targeted interventions for acute GVHD.

Large-scale interlaboratory study to develop, analytically validate and apply highly multiplexed, quantitative peptide assays to measure cancer-relevant proteins in plasma

There is an increasing need in biology and clinical medicine to robustly and reliably measure tens-to-hundreds of peptides and proteins in clinical and biological samples with high sensitivity, specificity, reproducibility and repeatability. Previously, we demonstrated that LC-MRM-MS with isotope dilution has suitable performance for quantitative measurements of small numbers of relatively abundant proteins in human plasma, and that the resulting assays can be transferred across laboratories while maintaining high reproducibility and quantitative precision. Here we significantly extend that earlier work, demonstrating that 11 laboratories using 14 LC-MS systems can develop, determine analytical figures of merit, and apply highly multiplexed MRM-MS assays targeting 125 peptides derived from 27 cancer-relevant proteins and 7 control proteins to precisely and reproducibly measure the analytes in human plasma. To ensure consistent generation of high quality data we incorporated a system suitability protocol (SSP) into our experimental design. The SSP enabled real-time monitoring of LC-MRM-MS performance during assay development and implementation, facilitating early detection and correction of chromatographic and instrumental problems. Low to sub-nanogram/mL sensitivity for proteins in plasma was achieved by one-step immunoaffinity depletion of 14 abundant plasma proteins prior to analysis. Median intra- and inter-laboratory reproducibility was <20%, sufficient for most biological studies and candidate protein biomarker verification. Digestion recovery of peptides was assessed and quantitative accuracy improved using heavy isotope labeled versions of the proteins as internal standards. Using the highly multiplexed assay, participating laboratories were able to precisely and reproducibly determine the levels of a series of analytes in blinded samples used to simulate an inter-laboratory clinical study of patient samples. Our study further establishes that LC-MRM-MS using stable isotope dilution, with appropriate attention to analytical validation and appropriate quality c`ontrol measures, enables sensitive, specific, reproducible and quantitative measurements of proteins and peptides in complex biological matrices such as plasma.

Improving wound management for residents in Residential Aged Care Facilities: National dissemination and implementation of the evidence based Champions for Skin Integrity Program

Overview The incidence of skin tears, pressure injuries and chronic wounds increases with age [1-4] and therefore is a serious issue for staff and residents in Residential Aged Care Facilities (RACFs). A pilot project funded in Round 2 of the Encouraging Best Practice in Residential Aged Care (EBPRAC) program by the then Australian Government Department of Health and Ageing found that a substantial proportion of residents in aged care facilities experienced pressure injuries, skin tears or chronic wounds. It also found the implementation of the evidence based Champions for Skin Integrity (CSI) model of wound care was successful in significantly decreasing the prevalence and severity of wounds in residents, improving staff skills and knowledge of evidence based wound management, increasing staff confidence with wound management, increasing implementation of evidence based wound management and prevention strategies, and increasing staff awareness of their roles in evidence based wound care at all levels [5]. Importantly, during the project, the project team developed a resource kit on evidence based wound management. Two critical recommendations resulting from the project were that: - The CSI model or a similar strategic approach should be implemented in RACFs to facilitate the uptake of evidence based wound management and prevention - The resource kit on evidence based wound management should be made available to all Residential Aged Care Facilities and interested parties A proposal to disseminate or rollout the CSI model of wound care to all RACFs across Australia was submitted to the department in 2012. The department approved funding from the Aged Care Services Improvement Healthy Ageing Grant (ACSIHAG) at the same time as the Round 3 of the Encouraging Better Practice in Aged Care (EBPAC) program. The dissemination involved two crucial elements: 1. The updating, refining and distribution of a Champions for Skin Integrity Resource Kit, more commonly known as a CSI Resource Kit and 2. The presentation of intensive one day Promoting Healthy Skin “Train the Trainer” workshops in all capital cities and major regional towns across Australia Due to demand, the department agreed to fund a second round of workshops focussing on regional centres and the completion date was extended to accommodate the workshops. Later, the department also decided to host a departmental website for a number of clinical domains, including wound management, so that staff from the residential aged care sector had easy access to a central repository of helpful clinical resource material that could be used for improving the health and wellbeing of their older adults, consumers and carers. CSI Resource Kit Upgrade and Distribution: At the start of the project, a full evidence review was carried out on the material produced during the EBPRAC-CSI Stage 1 project and the relevant evidence based changes were made to the documentation. At the same time participants in the EBPRAC-CSI Stage 1 project were interviewed for advice on how to improve the resource material. Following this the documentation, included in the kit, was sent to independent experts for peer review. When this process was finalised, a learning designer and QUT’s Visual Communications Services were engaged to completely refine and update the design of the resources, and combined resource kit with the goal of keeping the overall size of the kit suitable for bookshelf mounting and the cost at reasonable levels. Both goals were achieved in that the kit is about the same size as a 25 mm A4 binder and costs between $19.00 and $28.00 per kit depending on the size of the print run. The dissemination of the updated CSI resource kit was an outstanding success. Demand for the kits was so great that a second print run of 2,000 kits was arranged on top of the initial print run of 4,000 kits. All RACFs across Australia were issued with a kit, some 2,740 in total. Since the initial distribution another 1,100 requests for kits has been fulfilled as well as 1,619 kits being distributed to participants at the Promoting Healthy Skin workshops. As the project was winding up a final request email was sent to all workshop participants asking if they required additional kits or resources to distribute the remaining kits and resources. This has resulted in requests for 200 additional kits and resources. Feedback from the residential aged care sector and other clinical providers who have interest in wound care has been very positive regarding the utility of the kit, (see Appendix 4). Promoting Healthy Skin Workshops The workshops also exceeded the project team’s initial objective. Our goal of providing workshop training for staff from one in four facilities and 450 participants was exceeded, with overwhelming demand for workshop places resulting in the need to provide a second round of workshops across Australia. At the completion of the second round, 37 workshops had been given, with 1286 participants, representing 835 facilities. A number of strategies were used to promote the workshops ranging from invitations included in the kit, to postcard mail-outs, broadcast emailing to all facilities and aged care networks and to articles and paid advertising in aged care journals. The most effective method, by far, was directly phoning the facilities. This enabled the caller to contact the relevant staff member and enlist their support for the workshop. As this is a labour intensive exercise, it was only used where numbers needed bolstering, with one venue rising from 3 registrants before the calls to 53 registrants after. The workshops were aimed at staff who had the interest and the capability of implementing evidence-based wound management within their facility or organisation. This targeting was successful in that a large proportion (68%) of participants were Registered Nurses, Nurse Managers, Educators or Consultants. Twenty percent were Endorsed Enrolled Nurses with the remaining 12% being made up of Personal Care Workers or Allied Health Professionals. To facilitate long term sustainability, the workshop employed train-the-trainer strategies. Feedback from the EBPRAC-CSI Stage 1 interviews was used in the development of workshop content. In addition, feedback from the workshop conducted at the end of the EBPRAC-CSI Stage 1 project suggested that change management and leadership training should be included in the workshops. The program was trialled in the first workshop conducted in Brisbane and then rolled out across Australia. Participants were asked to complete pre and post workshop surveys at the beginning and end of the workshop to determine how knowledge and confidence improved over the day. Results from the pre and post surveys showed significant improvements in the level of confidence in attendees’ ability to implement evidence based wound management. The results also indicated a significant increase in the level of confidence in ability to implement change within their facility or organisation. This is an important indication that the inclusion of change management/leadership training with clinical instruction can increase staff capacity and confidence in translating evidence into practice. To encourage the transfer of the evidence based content of the workshop into practice, participants were asked to prepare an Action Plan to be followed by a simple one page progress report three months after the workshop. These reports ranged from simple (e.g. skin moisturising to prevent skin tears), to complex implementation plans for introducing the CSI model across the whole organisation. Outcomes described in the project reports included decreased prevalence of skin tears, pressure injuries and chronic wounds, along with increased staff and resident knowledge and resident comfort. As stated above, some organisations prepared large, complex plans to roll out the CSI model across their organisation. These plans included a review of the organisation’s wound care system, policies and procedures, the creation of new processes, the education of staff and clients, uploading education and resource material onto internal electronic platforms and setting up formal review and evaluation processes. The CSI Resources have been enthusiastically sought and incorporated into multiple health care settings, including aged care, acute care, Medicare Local intranets (e.g. Map of Medicine e-pathways), primary health care, community and home care organisations, education providers and New Zealand aged and community health providers. Recommendations: Recommendations for RACFs, aged care and health service providers and government  Skin integrity and the evidence-practice gap in this area should be recognised as a major health issue for health service providers for older adults, with wounds experienced by up to 50% of residents in aged care settings (Edwards et al. 2010). Implementation of evidence based wound care through the Champions for Skin Integrity model in this and the pilot project has demonstrated the prevalence of wounds, wound healing times and wound infections can be halved.  A national program and Centre for Evidence Based Wound Management should be established to: - expand the reach of the model to other aged care facilities and health service providers for older adults - sustain the uptake of models such as the Champions for Skin Integrity (CSI) model - ensure current resources, expertise and training are available for consumers and health care professionals to promote skin integrity for all older adults  Evidence based resources for the CSI program and similar projects should be reviewed and updated every 3 – 4 years as per NH&MRC recommendations  Leadership and change management training is fundamental to increasing staff capacity, at all levels, to promote within-organisation dissemination of skills and knowledge gained from projects providing evidence based training Recommendations for future national dissemination projects  A formal program of opportunities for small groups of like projects to share information and resources, coordinate activities and synergise education programs interactively would benefit future national dissemination projects - Future workshop programs could explore an incentive program to optimise attendance and reduce ‘no shows’ - Future projects should build in the capacity and funding for increased follow-up with workshop attendees, to explore the reasons behind those who are unable to translate workshop learnings into the workplace and identify factors to address these barriers.

Application of a Bayesian Network complex system model to a successful community electricity demand reduction program

Utilities worldwide are focused on supplying peak electricity demand reliably and cost effectively, requiring a thorough understanding of all the factors influencing residential electricity use at peak times. An electricity demand reduction project based on comprehensive residential consumer engagement was established within an Australian community in 2008, and by 2011, peak demand had decreased to below pre-intervention levels. This paper applied field data discovered through qualitative in-depth interviews of 22 residential households at the community to a Bayesian Network complex system model to examine whether the system model could explain successful peak demand reduction in the case study location. The knowledge and understanding acquired through insights into the major influential factors and the potential impact of changes to these factors on peak demand would underpin demand reduction intervention strategies for a wider target group.

Variation in the complex carbohydrate biosynthesis loci of Acinetobacter baumannii genomes

Extracellular polysaccharides are major immunogenic components of the bacterial cell envelope. However, little is known about their biosynthesis in the genus Acinetobacter, which includes A. baumannii, an important nosocomial pathogen. Whether Acinetobacter sp. produce a capsule or a lipopolysaccharide carrying an O antigen or both is not resolved. To explore these issues, genes involved in the synthesis of complex polysaccharides were located in 10 complete A. baumannii genome sequences, and the function of each of their products was predicted via comparison to enzymes with a known function. The absence of a gene encoding a WaaL ligase, required to link the carbohydrate polymer to the lipid A-core oligosaccharide (lipooligosaccharide) forming lipopolysaccharide, suggests that only a capsule is produced. Nine distinct arrangements of a large capsule biosynthesis locus, designated KL1 to KL9, were found in the genomes. Three forms of a second, smaller variable locus, likely to be required for synthesis of the outer core of the lipid A-core moiety, were designated OCL1 to OCL3 and also annotated. Each K locus includes genes for capsule export as well as genes for synthesis of activated sugar precursors, and for glycosyltransfer, glycan modification and oligosaccharide repeat-unit processing. The K loci all include the export genes at one end and genes for synthesis of common sugar precursors at the other, with a highly variable region that includes the remaining genes in between. Five different capsule loci, KL2, KL6, KL7, KL8 and KL9 were detected in multiply antibiotic resistant isolates belonging to global clone 2, and two other loci, KL1 and KL4, in global clone 1. This indicates that this region is being substituted repeatedly in multiply antibiotic resistant isolates from these clones.

The O-specific polysaccharide structure and gene cluster of serotype O:12 of the Yersinia pseudotuberculosis complex, and the identification of a novel L-quinovose biosynthesis gene

A major virulence factor for Yersinia pseudotuberculosis is lipopolysaccharide, including O-polysaccharide (OPS). Currently, the OPS based serotyping scheme for Y. pseudotuberculosis includes 21 known O-serotypes, with genetic and structural data available for 17 of them. The completion of the OPS structures and genetics of this species will enable the visualization of relationships between O-serotypes and allow for analysis of the evolutionary processes within the species that give rise to new serotypes. Here we present the OPS structure and gene cluster of serotype O:12, thus adding one more to the set of completed serotypes, and show that this serotype is present in both Y. pseudotuberculosis and the newly identified Y. similis species. The O:12 structure is shown to include two rare sugars: 4-C[(R)-1-hydroxyethyl]-3,6-dideoxy-d-xylo-hexose (d-yersiniose) and 6-deoxy-l-glucopyranose (l-quinovose). We have identified a novel putative guanine diphosphate (GDP)-l-fucose 4-epimerase gene and propose a pathway for the synthesis of GDP-l-quinovose, which extends the known GDP-l-fucose pathway.

Use of parametric modelling and climate-based metrics for the efficient design of daylight strategies in buildings with complex geometries

The purpose of this research is to assess daylight performance of buildings with climatic responsive envelopes with complex geometry that integrates shading devices in the façade. To this end two case studies are chosen due to their complex geometries and integrated daylight devices. The effect of different parameters of the daylight devices is analysed through Climate base daylight metrics.