Integrated Bayesian network frameworks for modelling complex ecological issues

Ecological problems are typically multi faceted and need to be addressed from a scientific and a management perspective. There is a wealth of modelling and simulation software available, each designed to address a particular aspect of the issue of concern. Choosing the appropriate tool, making sense of the disparate outputs, and taking decisions when little or no empirical data is available, are everyday challenges facing the ecologist and environmental manager. Bayesian Networks provide a statistical modelling framework that enables analysis and integration of information in its own right as well as integration of a variety of models addressing different aspects of a common overall problem. There has been increased interest in the use of BNs to model environmental systems and issues of concern. However, the development of more sophisticated BNs, utilising dynamic and object oriented (OO) features, is still at the frontier of ecological research. Such features are particularly appealing in an ecological context, since the underlying facts are often spatial and temporal in nature. This thesis focuses on an integrated BN approach which facilitates OO modelling. Our research devises a new heuristic method, the Iterative Bayesian Network Development Cycle (IBNDC), for the development of BN models within a multi-field and multi-expert context. Expert elicitation is a popular method used to quantify BNs when data is sparse, but expert knowledge is abundant. The resulting BNs need to be substantiated and validated taking this uncertainty into account. Our research demonstrates the application of the IBNDC approach to support these aspects of BN modelling. The complex nature of environmental issues makes them ideal case studies for the proposed integrated approach to modelling. Moreover, they lend themselves to a series of integrated sub-networks describing different scientific components, combining scientific and management perspectives, or pooling similar contributions developed in different locations by different research groups. In southern Africa the two largest free-ranging cheetah (Acinonyx jubatus) populations are in Namibia and Botswana, where the majority of cheetahs are located outside protected areas. Consequently, cheetah conservation in these two countries is focussed primarily on the free-ranging populations as well as the mitigation of conflict between humans and cheetahs. In contrast, in neighbouring South Africa, the majority of cheetahs are found in fenced reserves. Nonetheless, conflict between humans and cheetahs remains an issue here. Conservation effort in South Africa is also focussed on managing the geographically isolated cheetah populations as one large meta-population. Relocation is one option among a suite of tools used to resolve human-cheetah conflict in southern Africa. Successfully relocating captured problem cheetahs, and maintaining a viable free-ranging cheetah population, are two environmental issues in cheetah conservation forming the first case study in this thesis. The second case study involves the initiation of blooms of Lyngbya majuscula, a blue-green algae, in Deception Bay, Australia. L. majuscula is a toxic algal bloom which has severe health, ecological and economic impacts on the community located in the vicinity of this algal bloom. Deception Bay is an important tourist destination with its proximity to Brisbane, Australia’s third largest city. Lyngbya is one of several algae considered to be a Harmful Algal Bloom (HAB). This group of algae includes other widespread blooms such as red tides. The occurrence of Lyngbya blooms is not a local phenomenon, but blooms of this toxic weed occur in coastal waters worldwide. With the increase in frequency and extent of these HAB blooms, it is important to gain a better understanding of the underlying factors contributing to the initiation and sustenance of these blooms. This knowledge will contribute to better management practices and the identification of those management actions which could prevent or diminish the severity of these blooms.

Choosing "interesting" research methods and facing the challenges for publication

This paper discusses the choice to use two less conventional or “interesting” research methods, Q Methodology and Experience Sampling Method, rather than “status quo” research methods so common in the marketing discipline. It is argued that such methods have value for marketing academics because they widen the potential for discovery. The paper outlines these two research methods, providing examples of how they have been used in an experiential consumption perspective. Additionally the paper identifies some of the challenges to be faced when trying to publish research that use such less conventional methods, as well as offering suggestions to address them.

Morphologic and genomic characterisation of the koala Chlamydia pneumoniae strain

Chlamydia pneumoniae is a common human and animal pathogen associated with a wide range of upper and lower respiratory tract infections. In more recent years there has been increasing evidence to suggest a link between C. pneumoniae and chronic diseases in humans, including atherosclerosis, stroke and Alzheimer’s disease. C. pneumoniae human strains show little genetic variation, indicating that the human-derived strain originated from a common ancestor in the recent past. Despite extensive information on the genetics and morphology processes of the human strain, knowledge concerning many other hosts (including marsupials, amphibians, reptiles and equines) remains virtually unexplored. The koala (Phascolarctos cinereus) is a native Australian marsupial under threat due to habitat loss, predation and disease. Koalas are very susceptible to chlamydial infections, most commonly affecting the conjunctiva, urogenital tract and/or respiratory tract. To address this gap in the literature, the present study (i) provides a detailed description of the morphologic and genomic architecture of the C. pneumoniae koala (and human) strain, and shows that the koala strain is microscopically, developmentally and genetically distinct from the C. pneumoniae human strain, and (ii) examines the genetic relationship of geographically diverse C. pneumoniae isolates from human, marsupial, amphibian, reptilian and equine hosts, and identifies two distinct lineages that have arisen from animal-to-human cross species transmissions. Chapter One of this thesis explores the scientific problem and aims of this study, while Chapter Two provides a detailed literature review of the background in this field of work. Chapter Three, the first results chapter, describes the morphology and developmental stages of C. pneumoniae koala isolate LPCoLN, as revealed by fluorescence and transmission electron microscopy. The profile of this isolate, when cultured in HEp-2 human epithelial cells, was quite different to the human AR39 isolate. Koala LPCoLN inclusions were larger; the elementary bodies did not have the characteristic pear-shaped appearance, and the developmental cycle was completed within a shorter period of time (as confirmed by quantitative real-time PCR). These in vitro findings might reflect biological differences between koala LPCoLN and human AR39 in vivo. Chapter Four describes the complete genome sequence of the koala respiratory pathogen, C. pneumoniae LPCoLN. This is the first animal isolate of C. pneumoniae to be fully-sequenced. The genome sequence provides new insights into genomic ‘plasticity’ (organisation), evolution and biology of koala LPCoLN, relative to four complete C. pneumoniae human genomes (AR39, CWL029, J138 and TW183). Koala LPCoLN contains a plasmid that is not shared with any of the human isolates, there is evidence of gene loss in nucleotide salvage pathways, and there are 10 hot spot genomic regions of variation that were previously not identified in the C. pneumoniae human genomes. Sequence (partial-length) from a second, independent, wild koala isolate (EBB) at several gene loci confirmed that the koala LPCoLN isolate was representative of a koala C. pneumoniae strain. The combined sequence data provides evidence that the C. pneumoniae animal (koala LPCoLN) genome is ancestral to the C. pneumoniae human genomes and that human infections may have originated from zoonotic infections. Chapter Five examines key genome components of the five C. pneumoniae genomes in more detail. This analysis reveals genomic features that are shared by and/or contribute to the broad ecological adaptability and evolution of C. pneumoniae. This analysis resulted in the identification of 65 gene sequences for further analysis of intraspecific variation, and revealed some interesting differences, including fragmentation, truncation and gene decay (loss of redundant ancestral traits). This study provides valuable insights into metabolic diversity, adaptation and evolution of C. pneumoniae. Chapter Six utilises a subset of 23 target genes identified from the previous genomic comparisons and makes a significant contribution to our understanding of genetic variability among C. pneumoniae human (11) and animal (6 amphibian, 5 reptilian, 1 equine and 7 marsupial hosts) isolates. It has been shown that the animal isolates are genetically diverse, unlike the human isolates that are virtually clonal. More convincing evidence that C. pneumoniae originated in animals and recently (in the last few hundred thousand years) crossed host species to infect humans is provided in this study. It is proposed that two animal-to-human cross species events have occurred in the context of the results, one evident by the nearly clonal human genotype circulating in the world today, and the other by a more animal-like genotype apparent in Indigenous Australians. Taken together, these data indicate that the C. pneumoniae koala LPCoLN isolate has morphologic and genomic characteristics that are distinct from the human isolates. These differences may affect the survival and activity of the C. pneumoniae koala pathogen in its natural host, in vivo. This study, by utilising the genetic diversity of C. pneumoniae, identified new genetic markers for distinguishing human and animal isolates. However, not all C. pneumoniae isolates were genetically diverse; in fact, several isolates were highly conserved, if not identical in sequence (i.e. Australian marsupials) emphasising that at some stage in the evolution of this pathogen, there has been an adaptation/s to a particular host, providing some stability in the genome. The outcomes of this study by experimental and bioinformatic approaches have significantly enhanced our knowledge of the biology of this pathogen and will advance opportunities for the investigation of novel vaccine targets, antimicrobial therapy, or blocking of pathogenic pathways.

Exercise, appetite, and energy balance: The interactions between energy expenditure and intake, and the implications for weight management

This book disseminates current information pertaining to the modulatory effects of foods and other food substances on behavior and neurological pathways and, importantly, vice versa. This ranges from the neuroendocrine control of eating to the effects of life-threatening disease on eating behavior. The importance of this contribution to the scientific literature lies in the fact that food and eating are an essential component of cultural heritage but the effects of perturbations in the food/cognitive axis can be profound. The complex interrelationship between neuropsychological processing, diet, and behavioral outcome is explored within the context of the most contemporary psychobiological research in the area. This comprehensive psychobiology- and pathology-themed text examines the broad spectrum of diet, behavioral, and neuropsychological interactions from normative function to occurrences of severe and enduring psychopathological processes

Merging fact with fiction : a study of year 9 students' developing scientific literacy through the writing of hybridised scientific narratives on a socioscientific issue

International assessments of student science achievement, and growing evidence of students' waning interest in school science, have ensured that the development of scientific literacy continues to remain an important educational priority. Furthermore, researchers have called for teaching and learning strategies to engage students in the learning of science, particularly in the middle years of schooling. This study extends previous national and international research that has established a link between writing and learning science. Specifically, it investigates the learning experiences of eight intact Year 9 science classes as they engage in the writing of short stories that merge scientific and narrative genres (i.e., hybridised scientific narratives) about the socioscientific issue of biosecurity. This study employed a triangulation mixed methods research design, generating both quantitative and qualitative data, in order to investigate three research questions that examined the extent to which the students' participation in the study enhanced their scientific literacy; the extent to which the students demonstrated conceptual understanding of related scientific concepts through their written artefacts and in interviews about the artefacts; and the extent to which the students' participation in the project influenced their attitudes toward science and science learning. Three aspects of scientific literacy were investigated in this study: conceptual science understandings (a derived sense of scientific literacy), the students' transformation of scientific information in written stories about biosecurity (simple and expanded fundamental senses of scientific literacy), and attitudes toward science and science learning. The stories written by students in a selected case study class (N=26) were analysed quantitatively using a series of specifically-designed matrices that produce numerical scores that reflect students' developing fundamental and derived senses of scientific literacy. All students (N=152) also completed a Likert-style instrument (i.e., BioQuiz), pretest and posttest, that examined their interest in learning science, science self-efficacy, their perceived personal and general value of science, their familiarity with biosecurity issues, and their attitudes toward biosecurity. Socioscientific issues (SSI) education served as a theoretical framework for this study. It sought to investigate an alternative discourse with which students can engage in the context of SSI education, and the role of positive attitudes in engaging students in the negotiation of socioscientific issues. Results of the study have revealed that writing BioStories enhanced selected aspects of the participants' attitudes toward science and science learning, and their awareness and conceptual understanding of issues relating to biosecurity. Furthermore, the students' written artefacts alone did not provide an accurate representation of the level of their conceptual science understandings. An examination of these artefacts in combination with interviews about the students' written work provided a more comprehensive assessment of their developing scientific literacy. These findings support extensive calls for the utilisation of diversified writing-to-learn strategies in the science classroom, and therefore make a significant contribution to the writing-to-learn science literature, particularly in relation to the use of hybridised scientific genres. At the same time, this study presents the argument that the writing of hybridised scientific narratives such as BioStories can be used to complement the types of written discourse with which students engage in the negotiation of socioscientific issues, namely, argumentation, as the development of positive attitudes toward science and science learning can encourage students' participation in the discourse of science. The implications of this study for curricular design and implementation, and for further research, are also discussed.

The potentials of student initiated netspeak in a middle primary science-inspired mutliliteracies project

There is no denying that the information technology revolution of the late twentieth century has arrived. Whilst not equitably accessible for many, others hold high expectations for the contributions online activity will make to student learning outcomes. Concurrently, and not necessarily consequentially, the number of science and technology secondary school and university graduates throughout the world has declined substantially, as has their motivation and engagement with school science (OECD, 2006). The aim of this research paper is to explore one aspect of online activity, that of forum-based netspeak (Crystal, 2006), in relation to the possibilities and challenges it provides for forms of scientific learning. This paper reports findings from a study investigating student initiated netspeak in a science inspired multiliteracies (New London Group, 2000) project in one middle primary (aged 7-10 years) multi-age Australian classroom. Drawing on the theoretical description of the Five phases of enquiry proposed by Bybee (1997), an analytic framework is proffered that allows identification of student engagement, exploration, explanation, elaboration and evaluation of scientific enquiry. The findings provide insight into online forums for advancing learning in and motivation for science in the middle primary years.

A multi-disciplinary approach for the design and management of airport terminals

Multi-disciplinary approaches to complex problems are becoming more common – they enable criteria manifested in distinct (and potentially conflicting) domains to be jointly balanced and satisfied. In this paper we present airport terminals as a case study which requires multi-disciplinary knowledge in order to balance conflicting security, economic and passenger-driven needs and correspondingly enhance the design, management and operation of airport terminals. The need for a truly multi-disciplinary scientific approach which integrates information, process, people, technology and space domains is highlighted through a brief discussion of two challenges currently faced by airport operators. The paper outlines the approach taken by this project, detailing the aims and objectives of each of seven diverse research programs.

Thinking Collaboratively about the Peer-Review Process for Journal- Article Publication

In this conversation, Kevin K. Kumashiro shares his reflections on challenges to publishing anti-oppressive research in educational journals. He then invites eight current and former editors of leading educational research journals--William F. Pinar, Elizabeth Graue, Carl A. Grant, Maenette K. P. Benham, Ronald H. Heck, James Joseph Scheurich, Allan Luke, and Carmen Luke--to critique and expand on his analysis. Kumashiro begins the conversation by describing his own experiences submitting manuscripts to educational research journals and receiving comments by anonymous reviewers and journal editors. He suggests three ways to rethink the collaborative potential of the peer-review process: as constructive, as multilensed, and as situated. The eight current and former editors of leading educational research journals then critique and expand Kumashiro's analysis. Kumashiro concludes the conversation with additional reflections on barriers and contradictions involved in advancing anti-oppressive educational research in educational journals. (Contains 3 notes.)

Writing stories to enhance scientific literacy

In response to international concerns about scientific literacy and students’ waning interest in school science, this study investigated the effects of a science-writing project about the socioscientific issue of biosecurity on the development of students’ scientific literacy. Students generated two BioStories each that merged scientific information with the narrative storylines in the project. The study was conducted in two phases. In the exploratory phase, a qualitative case study of a 6th grade class involving classroom observations and interviews informed the design of the second, confirmatory phase of the study, which was conducted at a different school. This phase involved a mixed methods approach featuring a quasi-experimental design with two classes of Australian middle school students (i.e., 6th grade, 11 years of age, n=55). The results support the argument that writing the sequence of stories helped the students become more familiar with biosecurity issues, develop a deeper understanding of related biological concepts, and improve their interest in science. On the basis of these findings, teachers should be encouraged to engage their students in the practice of writing about socioscientific issues (SSI) in a way that integrates scientific information into narrative storylines. Extending the practice to older students, and exploring additional issues related to writing about SSI are recommended for further research.

Multi-criteria ranking and receptor modelling of airborne fine particles at three sites in the Pearl River Delta region of China

The multi-criteria decision making methods, Preference METHods for Enrichment Evaluation (PROMETHEE) and Graphical Analysis for Interactive Assistance (GAIA), and the two-way Positive Matrix Factorization (PMF) receptor model were applied to airborne fine particle compositional data collected at three sites in Hong Kong during two monitoring campaigns held from November 2000 to October 2001 and November 2004 to October 2005. PROMETHEE/GAIA indicated that the three sites were worse during the later monitoring campaign, and that the order of the air quality at the sites during each campaign was: rural site > urban site > roadside site. The PMF analysis on the other hand, identified 6 common sources at all of the sites (diesel vehicle, fresh sea salt, secondary sulphate, soil, aged sea salt and oil combustion) which accounted for approximately 68.8 ± 8.7% of the fine particle mass at the sites. In addition, road dust, gasoline vehicle, biomass burning, secondary nitrate, and metal processing were identified at some of the sites. Secondary sulphate was found to be the highest contributor to the fine particle mass at the rural and urban sites with vehicle emission as a high contributor to the roadside site. The PMF results are broadly similar to those obtained in a previous analysis by PCA/APCS. However, the PMF analysis resolved more factors at each site than the PCA/APCS. In addition, the study demonstrated that combined results from multi-criteria decision making analysis and receptor modelling can provide more detailed information that can be used to formulate the scientific basis for mitigating air pollution in the region.

Cross-talk of subchondral bone osteoblasts and articular cartilage chondrocytes : a new insight in understanding osteoarthritis pathogenesis

Osteoarthritis (OA) is the most common musculoskeletal disorder and represents a major health burden to society. In the course of the pathological development of OA, articular cartilage chondrocytes (ACCs) undergo atypical phenotype changes characterized by the expression of hypertrophic differentiation markers. Also, the adjacent subchondral bone shows signs of abnormal mineral density and enhanced production of bone turnover markers, indicative of osteoblast dysfunction. Collectively these findings indicate that the pathological changes typical of OA, involve alterations of the phenotypic properties of cells in both the subchondral bone and articular cartilage. However, the mechanism(s) by which these changes occur during OA development are not completely understood. The purpose of this project was to address the question of how subchondral bone osteoblasts (SBOs) and ACCs interact with each other with respect to regulation of respective cells’ phenotypic properties and in particular the involvement of mitogen activated protein kinase (MAPK) signalling pathways under normal and OA joint condition. We also endeavoured to test the influence of cross-talk between SBOs and ACCs isolated from normal and OA joint on matrix metalloproteinase (MMP) expression. For this purpose tissues from the knees of OA patients and normal controls were collected to isolate SBOs and ACCs. The cellular cross-talk of SBOs and ACCs were studied by means of both direct and indirect co-culture systems, which made it possible to identify the role of both membrane bound and soluble factors. Histology, immunohistochemistry, qRT-PCR, zymography, ELISA and western blotting were some of the techniques applied to distinguish the changes in the co-cultured vs. non co-cultured cells. The MAPK signalling pathways were probed by using targeted MAPK inhibitors, and their activity monitored by western blot analysis using phospho MAPK specific antibodies. Our co-culture studies demonstrated that OA ACCs enhanced the SBOs differentiation compared to normal ACCs. We demonstrated that OA ACCs induced these phenotypic changes in the SBOs via activating an ERK1/2 signalling pathway. The findings from this study thus provided clear evidence that OA ACCs play an integral role in altering the SBO phenotype. In the second study, we tested the influence of normal SBOs and OA SBOs on ACCs phenotype changes. The results showed that OA SBOs increased the hypertrophic gene expression in co-cultured ACCs compared to normal SBOs, a phenotype which is considered as pathological to the health and integrity of articular cartilage. It was demonstrated that these phenotype changes occurred via de-activation of p38 and activation of ERK1/2 signaling pathways. These findings suggest that the pathological interaction of OA SBOs with ACCs is mediated by cross-talking between ERK1/2 and p38 pathways, resulting in ACCs undergoing hypertrophic differentiation. Subsequent experiments to determine the effect on MMP regulation, of SBOs and ACCs cross-talk, revealed that co-culturing OA SBOs with ACCs significantly enhanced the proteolytic activity and expression of MMP-2 and MMP-9. In turn, co-culture of OA ACCs with SBOs led to abundant MMP-2 expression in SBOs. Furthermore, we showed that the addition of ERK1/2 and JNK inhibitors reversed the elevated MMP-2 and MMP-9 production which otherwise resulted from the interactions of OA SBOs-ACCs. Thus, this study has demonstrated that the altered interactions between OA SBOs-ACCs are capable of triggering the pathological pathways leading to degenerative changes seen in the osteoarthritic joint. In conclusion, the body of work presented in this dissertation has given clear in vitro evidence that the altered bi-directional communication of SBOs and ACCs may play a role in OA development and that this process was mediated by MAPK signalling pathways. Targeting these altered interactions by the use of MAPK inhibitors may provide the scientific rationale for the development of novel therapeutic strategies in the treatment and management of OA.

Pattern-Based Evaluation of Scientific Workflow Management Systems

In recent years several scientific Workflow Management Systems (WfMSs) have been developed with the aim to automate large scale scientific experiments. As yet, many offerings have been developed, but none of them has been promoted as an accepted standard. In this paper we propose a pattern-based evaluation of three among the most widely used scientific WfMSs: Kepler, Taverna and Triana. The aim is to compare them with traditional business WfMSs, emphasizing the strengths and deficiencies of both systems. Moreover, a set of new patterns is defined from the analysis of the three considered systems.

Model and prototype for querying multiple linked scientific datasets

Scientists need to transfer semantically similar queries across multiple heterogeneous linked datasets. These queries may require data from different locations and the results are not simple to combine due to differences between datasets. A query model was developed to make it simple to distribute queries across different datasets using RDF as the result format. The query model, based on the concept of publicly recognised namespaces for parts of each scientific dataset, was implemented with a configuration that includes a large number of current biological and chemical datasets. The configuration is flexible, providing the ability to transparently use both private and public datasets in any query. A prototype implementation of the model was used to resolve queries for the Bio2RDF website, including both Bio2RDF datasets and other datasets that do not follow the Bio2RDF URI conventions.

Crown copyright

Copyright protects much of the creative, cultural, educational, scientific and informational material generated by federal, State/Territory and local governments and their constituent departments and agencies. Governments at all levels develop, manage and distribute a vast array of materials in the form of documents, reports, websites, datasets and databases on CD or DVD and files that can be downloaded from a website. Under the Copyright Act 1968 (Cth), with few exceptions government copyright is treated the same as copyright owned by non-government parties insofar as the range of protected materials and the exclusive proprietary rights attaching to them are concerned. However, the rationale for recognizing copyright in public sector materials and vesting ownership of copyright in governments is fundamentally different to the main rationales underpinning copyright generally. The central justification for recognizing Crown copyright is to ensure that government documents and materials created for public administrative purposes are disseminated in an accurate and reliable form. Consequently, the exclusive rights held by governments as copyright owners must be exercised in a manner consistent with the rationale for conferring copyright ownership on them. Since Crown copyright exists primarily to ensure that documents and materials produced for use in the conduct of government are circulated in an accurate and reliable form, governments should exercise their exclusive rights to ensure that their copyright materials are made available for access and reuse, in accordance with any laws and policies relating to access to public sector materials. While copyright law vests copyright owners with extensive bundles of exclusive rights which can be exercised to prevent others making use of the copyright material, in the case of Crown copyright materials these rights should rarely be asserted by government to deviate from the general rule that Crown copyright materials will be available for “full and free reproduction” by the community at large.

Natural and engineered kallikrein inhibitors: an emerging pharmacopoeia

The kallikreins and kallikrein-related peptidases are serine proteases that control a plethora of developmental and homeostatic phenomena, ranging from semen liquefaction to skin desquamation and blood pressure. The diversity of roles played by kallikreins has stimulated considerable interest in these enzymes from the perspective of diagnostics and drug design. Kallikreins already have well-established credentials as targets for therapeutic intervention and there is increasing appreciation of their potential both as biomarkers and as targets for inhibitor design. Here, we explore the current status of naturally occurring kallikrein protease-inhibitor complexes and illustrate how this knowledge can interface with strategies for rational re-engineering of bioscaffolds and design of small-molecule inhibitors.