Technical report : acoustic analysis of the natural environment

This technical report is concerned with one aspect of environmental monitoring—the detection and analysis of acoustic events in sound recordings of the environment. Sound recordings offer ecologists the advantage of cheaper and increased sampling but make available so much data that automated analysis becomes essential. The report describes a number of tools for automated analysis of recordings, including noise removal from spectrograms, acoustic event detection, event pattern recognition, spectral peak tracking, syntactic pattern recognition applied to call syllables, and oscillation detection. These algorithms are applied to a number of animal call recognition tasks, chosen because they illustrate quite different modes of analysis: (1) the detection of diffuse events caused by wind and rain, which are frequent contaminants of recordings of the terrestrial environment; (2) the detection of bird and calls; and (3) the preparation of acoustic maps for whole ecosystem analysis. This last task utilises the temporal distribution of events over a daily, monthly or yearly cycle.

Genome-wide identification and expression analysis of the NF-Y family of transcription factors in Triticum aestivum

Nuclear Factor Y (NF-Y) is a trimeric complex that binds to the CCAAT box, a ubiquitous eukaryotic promoter element. The three subunits NF-YA, NF-YB and NF-YC are represented by single genes in yeast and mammals. However, in model plant species (Arabidopsis and rice) multiple genes encode each subunit providing the impetus for the investigation of the NF-Y transcription factor family in wheat. A total of 37 NF-Y and Dr1 genes (10 NF-YA, 11 NF-YB, 14 NF-YC and 2 Dr1) in Triticum aestivum were identified in the global DNA databases by computational analysis in this study. Each of the wheat NF-Y subunit families could be further divided into 4-5 clades based on their conserved core region sequences. Several conserved motifs outside of the NF-Y core regions were also identified by comparison of NF-Y members from wheat, rice and Arabidopsis. Quantitative RT-PCR analysis revealed that some of the wheat NF-Y genes were expressed ubiquitously, while others were expressed in an organ-specific manner. In particular, each TaNF-Y subunit family had members that were expressed predominantly in the endosperm. The expression of nine NF-Y and two Dr1 genes in wheat leaves appeared to be responsive to drought stress. Three of these genes were up-regulated under drought conditions, indicating that these members of the NF-Y and Dr1 families are potentially involved in plant drought adaptation. The combined expression and phylogenetic analyses revealed that members within the same phylogenetic clade generally shared a similar expression profile. Organ-specific expression and differential response to drought indicate a plant-specific biological role for various members of this transcription factor family.

TaNF-YC11, one of the light-upregulated NF-YC members in Triticum aestivum, is co-regulated with photosynthesis-related genes

NF-Y is a heterotrimeric transcription factor complex. Each of the NF-Y subunits (NF-YA, NF-YB and NF-YC) in plants is encoded by multiple genes. Quantitative RT-PCR analysis revealed that five wheat NF-YC members (TaNF-YC5, 8, 9, 11 & 12) were upregulated by light in both the leaf and seedling shoot. Co-expression analysis of Affymetrix wheat genome array datasets revealed that transcript levels of a large number of genes were consistently correlated with those of the TaNF-YC11 and TaNF-YC8 genes in 3-4 separate Affymetrix array datasets. TaNF-YC11-correlated transcripts were significantly enriched with the Gene Ontology term photosynthesis. Sequence analysis in the promoters of TaNF-YC11-correlated genes revealed the presence of putative NF-Y complex binding sites (CCAAT motifs). Quantitative RT-PCR analysis of a subset of potential TaNF-YC11 target genes showed that ten out of the thirteen genes were also light-upregulated in both the leaf and seedling shoot and had significantly correlated expression profiles with TaNF-YC11. The potential target genes for TaNF-YC11 include subunit members from all four thylakoid membrane bound complexes required for the conversion of solar energy into chemical energy and rate limiting enzymes in the Calvin cycle. These data indicate that TaNF-YC11 is potentially involved in regulation of photosynthesis-related genes.

The development of the extended adolescent injury checklist (E-AIC) : a measure for injury prevention program evaluation

The Extended Adolescent Injury Checklist (E-AIC), a self-report measure of injury based on the model of the Adolescent Injury Checklist (AIC), was developed for use in the evaluation of school-based interventions. The three stages of this development involved focus groups with adolescents and consultations with medical staff, pilot testing of the revised AIC in a high school context, and use of the finalised checklist in pre- and post-questionnaires to examine its utility. Results revealed that responses to the final version of the E-AIC were meaningful and remained consistent over time. The E-AIC appears to be a promising measure of adolescent injury that is simple, time-efficient and appropriate for use in the evaluation of school-based injury prevention programs.

Systematics and biogeography of the Gondwanan Orthocladiinae (Diptera: Chironomidae)

Restrictions to effective dispersal and gene flow caused by the fragmentation of ancient supercontinents are considered to have driven diversification and speciation on disjunct landmasses globally. Investigating the role that these processes have played in the development of diversity within and among taxa is crucial to understanding the origins and evolution of regional biotas. Within the chironomid (non-biting midge) subfamily Orthocladiinae (Diptera: Chironomidae), a group of genera that are distributed across the austral continents (Australia, New Zealand, South America) have been proposed to represent a relict Gondwanan clade. We used a molecular approach to resolve relationships among taxa with the aim to determine the relative roles that vicariance and dispersal may have played in the evolution of this group. Continental biotas did not form monophyletic groups, in accordance with expectations given existing morphological evidence. Patterns of phylogenetic relationships among taxa did not accord with expected patterns based on the geological sequence of break-up of the Gondwanan supercontinent. Likewise, divergence time estimates, particularly for New Zealand taxa, largely post-dated continental fragmentation and implied instead that several transoceanic dispersal events may have occurred post-vicariance. Passive dispersal of gravid female chironomid adults is the most likely mechanism for transoceanic movement, potentially facilitated by West Wind Drift or anti-cyclone fronts. Estimated timings of divergence among Australian and South American Botryocladius, on the other hand, were congruent with the proposed ages of separation of the two continents from Antarctica. Taken together, these data suggest that a complex relationship between both vicariance and dispersal may explain the evolution of this group. The sampling regime we implemented here was the most intensive yet performed for austral members of the Orthocladiinae and unsurprisingly revealed several novel taxa that will require formal description.

Analysing the effect of digital technology on channel strategy, power and disintermediation in the home video market : the demise of the video store?

The antecedents of channel power (e.g. El-Ansary and Stern, 1972) and the impact of channel structure ( e.g. Anderson and Narus,1984) on channel dynamics have long been important topics within the channel literature. In addition to the theoretical and methodological contributions, research in these areas has helped channel managers to understand how power is generated and used in coordinating distribution strategies in different contexts. The study presented in this paper builds upon these previous literatures, which are first briefly reviewed below.

Sustaining the ecological, social and economic values of the forests of Southern Tasmania

This thesis articulates a methodology that can be applied to the analysis and design of underlying organisational structures and processes that will consistently and effectively address ‘wicked problems’ (the most difficult class of problems that we can conceptualise: problems which consist of ‘clusters’ of problems; problems within these clusters cannot be solved in isolation from one another, and include sociopolitical and moral-spiritual issues (Rittel and Webber 1973)) in forestry. This transdisciplinary methodology has been developed from the perspective of institutional economics synthesised with perspectives from ecological economics and system dynamics. The institutionalist policymaking framework provides an approach for the explicit development of holistic policy. An illustrative application of this framework has been applied to the wicked problem of forestry in southern Tasmania as an example of the applicability of the approach in the Australian context. To date all attempts to seek solutions to that prevailing wicked problem set have relied on non-reflexive, partial and highly reductionist thinking. A formal assessment of prevailing governance and process arrangements applying to that particular forestry industry has been undertaken using the social fabric matrix. This methodology lies at the heart of the institutionalist policymaking framework, and allows for the systematic exploration of elaborately complex causal links and relationships, such as are present in southern Tasmania. Some possible attributes of an alternative approach to forest management that sustains ecological, social and economic values of forests have been articulated as indicative of the alternative policy and management outcomes that real-world application of this transdisciplinary, discursive and reflexive framework may crystallise. Substantive and lasting solutions to wicked problems need to be formed endogenously, that is, from within the system. The institutionalist policymaking framework is a vehicle through which this endogenous creation of solutions to wicked problems may be realised.

Validation and automation of the DYNJAWS component module of the BEAMnrc Monte Carlo code

The purpose of this work is to validate and automate the use of DYNJAWS; a new component module (CM) in the BEAMnrc Monte Carlo (MC) user code. The DYNJAWS CM simulates dynamic wedges and can be used in three modes; dynamic, step-and-shoot and static. The step-and-shoot and dynamic modes require an additional input file defining the positions of the jaw that constitutes the dynamic wedge, at regular intervals during its motion. A method for automating the generation of the input file is presented which will allow for the more efficient use of the DYNJAWS CM. Wedged profiles have been measured and simulated for 6 and 10 MV photons at three field sizes (5 cm x 5 cm , 10 cm x10 cm and 20 cm x 20 cm), four wedge angles (15, 30, 45 and 60 degrees), at dmax and at 10 cm depth. Results of this study show agreement between the measured and the MC profiles to within 3% of absolute dose or 3 mm distance to agreement for all wedge angles at both energies and depths. The gamma analysis suggests that dynamic mode is more accurate than the step-and-shoot mode. The DYNJAWS CM is an important addition to the BEAMnrc code and will enable the MC verification of patient treatments involving dynamic wedges.

Overview of the INEX 2010 XML mining track : clustering and classification of XML documents

The XML Document Mining track was launched for exploring two main ideas: (1) identifying key problems and new challenges of the emerging field of mining semi-structured documents, and (2) studying and assessing the potential of Machine Learning (ML) techniques for dealing with generic ML tasks in the structured domain, i.e., classification and clustering of semi-structured documents. This track has run for six editions during INEX 2005, 2006, 2007, 2008, 2009 and 2010. The first five editions have been summarized in previous editions and we focus here on the 2010 edition. INEX 2010 included two tasks in the XML Mining track: (1) unsupervised clustering task and (2) semi-supervised classification task where documents are organized in a graph. The clustering task requires the participants to group the documents into clusters without any knowledge of category labels using an unsupervised learning algorithm. On the other hand, the classification task requires the participants to label the documents in the dataset into known categories using a supervised learning algorithm and a training set. This report gives the details of clustering and classification tasks.

The mechanical heterogeneity of the hard callus influences local tissue strains during bone healing : a finite element study based on sheep experiments

During secondary fracture healing, various tissue types including new bone are formed. The local mechanical strains play an important role in tissue proliferation and differentiation. To further our mechanobiological understanding of fracture healing, a precise assessment of local strains is mandatory. Until now, static analyses using Finite Elements (FE) have assumed homogenous material properties. With the recent quantification of both the spatial tissue patterns (Vetter et al., 2010) and the development of elastic modulus of newly formed bone during healing (Manjubala et al., 2009), it is now possible to incorporate this heterogeneity. Therefore, the aim of this study is to investigate the effect of this heterogeneity on the strain patterns at six successive healing stages. The input data of the present work stemmed from a comprehensive cross-sectional study of sheep with a tibial osteotomy (Epari et al., 2006). In our FE model, each element containing bone was described by a bulk elastic modulus, which depended on both the local area fraction and the local elastic modulus of the bone material. The obtained strains were compared with the results of hypothetical FE models assuming homogeneous material properties. The differences in the spatial distributions of the strains between the heterogeneous and homogeneous FE models were interpreted using a current mechanobiological theory (Isakson et al., 2006). This interpretation showed that considering the heterogeneity of the hard callus is most important at the intermediate stages of healing, when cartilage transforms to bone via endochondral ossification.

Spatial and temporal variations of mechanical properties and mineral content of the external callus during bone healing

After bone fracture, various cellular activities lead to the formation of different tissue types, which form the basis for the process of secondary bone healing. Although these tissues have been quantified by histology, their material properties are not well understood. Thus, the aim of this study is to correlate the spatial and temporal variations in the mineral content and the nanoindentation modulus of the callus formed via intramembranous ossification over the course of bone healing. Midshaft tibial samples from a sheep osteotomy model at time points of 2, 3, 6 and 9 weeks were employed. PMMA embedded blocks were used for quantitative back scattered electron imaging and nanoindentation of the newly formed periosteal callus near the cortex. The resulting indentation modulus maps show the heterogeneity in the modulus in the selected regions of the callus. The indentation modulus of the embedded callus is about 6 GPa at the early stage. At later stages of mineralization, the average indentation modulus reaches 14 GPa. There is a slight decrease in average indentation modulus in regions distant to the cortex, probably due to remodelling of the peripheral callus. The spatial and temporal distribution of mineral content in the callus tissue also illustrates the ongoing remodelling process observed from histological analysis. Most interestingly the average indentation modulus, even at 9 weeks, remains as low as 13 GPa, which is roughly 60% of that for cortical sheep bone. The decreased indentation modulus in the callus compared to cortex is due to the lower average mineral content and may be perhaps also due to the properties of the organic matrix which might be different from normal bone.

The role of the research system in 'Learning Economies'

This paper provides a framework for analysing the role of Australia’s research system in promoting national economic development. The paper is in two parts. Part One focuses on knowledge diffusion and technological development and emphasises the systemic nature of innovation processes within the emerging context of ‘learning economies’. The key understandings relevant to a nation’s research system are drawn out from contemporary developments in the international literature on ‘learning economies’. Some of the implications for Australia are discussed. The aim is to provide readers with some indications of what to look for in considering options for the future of Australia’s research system. More detailed information on relevant aspects of Australia’s industrial and trade structure, the extent of the R&D effort in industry and on issues such as management capability can be obtained from (Marceau et al 1997). In the second part, broad elements of the Australian research system are reviewed in the light of findings from the literature. The central role of universities in the innovation and research systems is described. Actions that can be taken by both universities and governments are suggested, particularly regarding the need to build and maintain efficient information flows at local, national and international levels. The paper briefly points to the nature of a research system capable of contributing effectively to the wealth of the nation and indicates some possible directions for enabling Australia to meet the demands of, and profit from, a knowledge-based economy.

Development of a workplace wellness promotion pilot framework : a case study of the Blue Care Staff Wellness Program

Workplace wellness initiatives are currently unreflective of the multidimensional and holistic nature of the wellness construct. There exists an opportunity for promoters of health to move toward models of workplace wellness promotion that more fully appreciate the interconnected nature of health dimensions and promote them even-handedly. The Blue Care Staff Wellness Program framework was developed in response to a recognised need for consistent and wellness-focused constructs for workplace wellness promotion and dissemination. The framework promotes and supports the individual and organisational wellness of the Blue Care employee population by providing a comprehensive and sustainable employee wellness program. This has been achieved by the adoption of consistent wellness principles to guide the framework conception and theory based development. The use of the framework in a pilot program will provide insight into the frameworks effectiveness in promoting a comprehensive workplace wellness program, and go further to establish the relationship between wellness and productivity in the workplace.

The dynamics and performance of the building and construction product system

During 1999 the Department of Industry, Science and Resources (ISR) published 4 research reports it had commissioned from the Australian Expert Group in Industry Studies (AEGIS), a research centre of the University of Western Sydney, Macarthur. ISR will shortly publish the fifth and final report in this series. The five reports were commissioned by the Department, as part of the Building and Construction Action Agenda process, to investigate the dynamics and performance of the sector, particularly in relation its innovative capacity. Professor Jane Marceau, PVCR at the University of Western Sydney and Director of AEGIS, led the research team. Dr Karen Manley was the researcher and joint author on three of the five reports. This paper outlines the approach and key findings of each of the five reports. The reports examined 5 key elements of the ‘building and construction product system’. The term ‘product system’ reflects the very broad range of industries and players we consider to contribute to the performance of the building and construction industries. The term ‘product system’ also highlights our focus on the systemic qualities of the building and construction industries. We were most interested in the inter-relationships between key segments and players and how these impacted on the innovation potential of the product system. The ‘building and construction product system’ is hereafter referred to as ‘the industry’ for ease of presentation. All the reports are based, at least in part, on an interviewing or survey research phase which involved gathering data from public and private sector players nationally. The first report ‘maps’ the industry to identify and describe its key elements and the inter-relationships between them. The second report focuses specifically on the linkages between public-sector research organisations and firms in the industry. The third report examines the conditions surrounding the emergence of new businesses in the industry. The fourth report examines how manufacturing businesses are responding to customer demands for ‘total solutions’ to their building and construction needs, by providing various services to clients. The fifth report investigates the capacity of the industry to encourage and undertake energy efficient building design and construction.