Digital scholarship and pedagogy, the next step : cultural science.

There are two aspects to the problem of digital scholarship and pedagogy. One is to do with scholarship; the other with pedagogy. In scholarship, the association of knowledge with its printed form remains dominant. In pedagogy, the desire to abandon print for ‘new’ media is urgent, at least in some parts of the academy. Film and media studies are thus at the intersection of opposing forces – pulling the field ‘back’ to print and ‘forward’ to digital media. These tensions may be especially painful in a field whose own object of study is another form of communication, neither print nor digital but broadcast. Although print has been overtaken in the popular marketplace by audio-visual forms, this was never achieved in the domain of scholarship. Even when it is digitally distributed, the output of research is still a ‘paper.’ But meanwhile, in the realm of teaching, production- and practice-based pedagogy has become firmly established. Nevertheless a disjunction remains, between high-end scholarship in research universities and vocational training in teaching institutions; but neither is well equipped to deal with the digital challenge.

The genesis of science education research in Australasia

Although the sciences were being taught in Australian schools well before the Second World War, the only evidence of research studies of this teaching is to be found in the report, published by ACER in 1932 of Roy Stanhope’s survey of the teaching of chemistry in New South Wales and a standardized test he had developed. Roy Stanhope was a science teacher with a research masters degree in chemistry. He had won a scholarship to go to Stanford University for doctoral studies, but returned after one year when his scholarship was not extended. He went on to be a founder in 1943 of the Australian Science Teachers Association (ASTA), which honours this remarkable pioneer through its annual Stanhope Oration. In his retirement Stanhope undertook a comparative study of science

neXus2. An investigation into the library and information services workforce in Australia: The institutional perspective. Final report prepared for the Australian Library and Information Association and National and State Libraries Australia

The neXus2 research project has sought to investigate the library and information services (LIS) workforce in Australia, from the institutional or employer perspective. The study builds on the neXus1 study, which collected data from individuals in the LIS workforce in order to present a snapshot of the profession in 2006, highlighting the demographics, educational background and career details of library and information professionals in Australia. To counterbalance this individual perspective, library institutions were invited to participate in a survey to contribute further data as employers. This final report on the neXus2 project compares the findings from the different library sectors, ie academic libraries, TAFE libraries, the National and State libraries, public libraries, special libraries and school libraries.

A Reliable Basis for Approximate Association Rules

For most of the work done in developing association rule mining, the primary focus has been on the efficiency of the approach and to a lesser extent the quality of the derived rules has been emphasized. Often for a dataset, a huge number of rules can be derived, but many of them can be redundant to other rules and thus are useless in practice. The extremely large number of rules makes it difficult for the end users to comprehend and therefore effectively use the discovered rules and thus significantly reduces the effectiveness of rule mining algorithms. If the extracted knowledge can’t be effectively used in solving real world problems, the effort of extracting the knowledge is worth little. This is a serious problem but not yet solved satisfactorily. In this paper, we propose a concise representation called Reliable Approximate basis for representing non-redundant approximate association rules. We prove that the redundancy elimination based on the proposed basis does not reduce the belief to the extracted rules. We also prove that all approximate association rules can be deduced from the Reliable Approximate basis. Therefore the basis is a lossless representation of approximate association rules.

Preliminary spatiotemporal analysis of the association between socio-environmental factors and suicide

Background: The seasonality of suicide has long been recognised. However, little is known about the relative importance of socio-environmental factors in the occurrence of suicide in different geographical areas. This study examined the association of climate, socioeconomic and demographic factors with suicide in Queensland, Australia, using a spatiotemporal approach. Methods: Seasonal data on suicide, demographic variables and socioeconomic indexes for areas in each Local Government Area (LGA) between 1999 and 2003 were acquired from the Australian Bureau of Statistics. Climate data were supplied by the Australian Bureau of Meteorology. A multivariable generalized estimating equation model was used to examine the impact of socio-environmental factors on suicide. Results: The preliminary data analyses show that far north Queensland had the highest suicide incidence (e.g., Cook and Mornington Shires), while the south-western areas had the lowest incidence (e.g., Barcoo and Bauhinia Shires) in all the seasons. Maximum temperature, unemployment rate, the proportion of Indigenous population and the proportion of population with low individual income were statistically significantly and positively associated with suicide. There were weaker but not significant associations for other variables. Conclusions: Maximum temperature, the proportion of Indigenous population and unemployment rate appeared to be major determinants of suicide at a LGA level in Queensland.

Interestingness Measures for Multi-Level Association Rules

Association rule mining is one technique that is widely used when querying databases, especially those that are transactional, in order to obtain useful associations or correlations among sets of items. Much work has been done focusing on efficiency, effectiveness and redundancy. There has also been a focusing on the quality of rules from single level datasets with many interestingness measures proposed. However, with multi-level datasets now being common there is a lack of interestingness measures developed for multi-level and cross-level rules. Single level measures do not take into account the hierarchy found in a multi-level dataset. This leaves the Support-Confidence approach,which does not consider the hierarchy anyway and has other drawbacks, as one of the few measures available. In this paper we propose two approaches which measure multi-level association rules to help evaluate their interestingness. These measures of diversity and peculiarity can be used to help identify those rules from multi-level datasets that are potentially useful.

Concise representations for association rules in multi-level datasets

Association rule mining has made many advances in the area of knowledge discovery. However, the quality of the discovered association rules is a big concern and has drawn more and more attention recently. One problem with the quality of the discovered association rules is the huge size of the extracted rule set. Often for a dataset, a huge number of rules can be extracted, but many of them can be redundant to other rules and thus useless in practice. Mining non-redundant rules is a promising approach to solve this problem. In this paper, we firstly propose a definition for redundancy; then we propose a concise representation called Reliable basis for representing non-redundant association rules for both exact rules and approximate rules. An important contribution of this paper is that we propose to use the certainty factor as the criteria to measure the strength of the discovered association rules. With the criteria, we can determine the boundary between redundancy and non-redundancy to ensure eliminating as many redundant rules as possible without reducing the inference capacity of and the belief to the remaining extracted non-redundant rules. We prove that the redundancy elimination based on the proposed Reliable basis does not reduce the belief to the extracted rules. We also prove that all association rules can be deduced from the Reliable basis. Therefore the Reliable basis is a lossless representation of association rules. Experimental results show that the proposed Reliable basis can significantly reduce the number of extracted rules.

Investigating the use of association rules in improving recommender systems

Recommender systems are widely used online to help users find other products, items etc that they may be interested in based on what is known about that user in their profile. Often however user profiles may be short on information and thus when there is not sufficient knowledge on a user it is difficult for a recommender system to make quality recommendations. This problem is often referred to as the cold-start problem. Here we investigate whether association rules can be used as a source of information to expand a user profile and thus avoid this problem, leading to improved recommendations to users. Our pilot study shows that indeed it is possible to use association rules to improve the performance of a recommender system. This we believe can lead to further work in utilising appropriate association rules to lessen the impact of the cold-start problem.

Kallikrein-related peptidase 4 activation of protease-activated receptor family members and association with prostate cancer

Two areas of particular importance in prostate cancer progression are primary tumour development and metastasis. These processes involve a number of physiological events, the mediators of which are still being discovered and characterised. Serine proteases have been shown to play a major role in cancer invasion and metastasis. The recently discovered phenomenon of their activation of a receptor family known as the protease activated receptors (PARs) has extended their physiological role to that of signaling molecule. Several serine proteases are expressed by malignant prostate cancer cells, including members of the kallikreinrelated peptidase (KLK) serine protease family, and increasingly these are being shown to be associated with prostate cancer progression. KLK4 is highly expressed in the prostate and expression levels increase during prostate cancer progression. Critically, recent studies have implicated KLK4 in processes associated with cancer. For example, the ectopic over-expression of KLK4 in prostate cancer cell lines results in an increased ability of these cells to form colonies, proliferate and migrate. In addition, it has been demonstrated that KLK4 is a potential mediator of cellular interactions between prostate cancer cells and osteoblasts (bone forming cells). The ability of KLK4 to influence cellular behaviour is believed to be through the selective cleavage of specific substrates. Identification of relevant in vivo substrates of KLK4 is critical to understanding the pathophysiological roles of this enzyme. Significantly, recent reports have demonstrated that several members of the KLK family are able to activate PARs. The PARs are relatively new members of the seven transmembrane domain containing G protein coupled receptor (GPCR) family. PARs are activated through proteolytic cleavage of their N-terminus by serine proteases, the resulting nascent N-terminal binds intramolecularly to initiate receptor activation. PARs are involved in a number of patho-physiological processes, including vascular repair and inflammation, and a growing body of evidence suggests roles in cancer. While expression of PAR family members has been documented in several types of cancers, including prostate, the role of these GPCRs in prostate cancer development and progression is yet to be examined. Interestingly, several studies have suggested potential roles in cellular invasion through the induction of cytoskeletal reorganisation and expression of basement membrane-degrading enzymes. Accordingly, this program of research focussed on the activation of the PARs by the prostate cancer associated enzyme KLK4, cellular processing of activated PARs and the expression pattern of receptor and agonist in prostate cancer. For these studies KLK4 was purified from the conditioned media of stably transfected Sf9 insect cells expressing a construct containing the complete human KLK4 coding sequence in frame with a V5 epitope and poly-histidine encoding sequences. The first aspect of this study was the further characterisation of this recombinant zymogen form of KLK4. The recombinant KLK4 zymogen was demonstrated to be activatable by the metalloendopeptidase thermolysin and amino terminal sequencing indicated that thermolysin activated KLK4 had the predicted N-terminus of mature active KLK4 (31IINED). Critically, removal of the pro-region successfully generated a catalytically active enzyme, with comparable activity to a previously published recombinant KLK4 produced from S2 insect cells. The second aspect of this study was the activation of the PARs by KLK4 and the initiation of signal transduction. This study demonstrated that KLK4 can activate PAR-1 and PAR-2 to mobilise intracellular Ca2+, but failed to activate PAR-4. Further, KLK4 activated PAR-1 and PAR-2 over distinct concentration ranges, with KLK4 activation and mobilisation of Ca2+ demonstrating higher efficacy through PAR-2. Thus, the remainder of this study focussed on PAR-2. KLK4 was demonstrated to directly cleave a synthetic peptide that mimicked the PAR-2 Nterminal activation sequence. Further, KLK4 mediated Ca2+ mobilisation through PAR-2 was accompanied by the initiation of the extra-cellular regulated kinase (ERK) cascade. The specificity of intracellular signaling mediated through PAR-2 by KLK4 activation was demonstrated by siRNA mediated protein depletion, with a reduction in PAR-2 protein levels correlating to a reduction in KLK4 mediated Ca2+mobilisation and ERK phosphorylation. The third aspect of this study examined cellular processing of KLK4 activated PAR- 2 in a prostate cancer cell line. PAR-2 was demonstrated to be expressed by five prostate derived cell lines including the prostate cancer cell line PC-3. It was also demonstrated by flow cytometry and confocal microscopy analyses that activation of PC-3 cell surface PAR-2 by KLK4 leads to internalisation of this receptor in a time dependent manner. Critically, in vivo relevance of the interaction between KLK4 and PAR-2 was established by the observation of the co-expression of receptor and agonist in primary prostate cancer and prostate cancer bone lesion samples by immunohistochemical analysis. Based on the results of this study a number of exciting future studies have been proposed, including, delineating differences in KLK4 cellular signaling via PAR-1 and PAR-2 and the role of PAR-1 and PAR-2 activation by KLK4 in prostate cancer cells and bone cells in prostate cancer progression.

Granule-based knowledge representation for intra and inter transaction association mining

Abstract With the phenomenal growth of electronic data and information, there are many demands for the development of efficient and effective systems (tools) to perform the issue of data mining tasks on multidimensional databases. Association rules describe associations between items in the same transactions (intra) or in different transactions (inter). Association mining attempts to find interesting or useful association rules in databases: this is the crucial issue for the application of data mining in the real world. Association mining can be used in many application areas, such as the discovery of associations between customers’ locations and shopping behaviours in market basket analysis. Association mining includes two phases. The first phase, called pattern mining, is the discovery of frequent patterns. The second phase, called rule generation, is the discovery of interesting and useful association rules in the discovered patterns. The first phase, however, often takes a long time to find all frequent patterns; these also include much noise. The second phase is also a time consuming activity that can generate many redundant rules. To improve the quality of association mining in databases, this thesis provides an alternative technique, granule-based association mining, for knowledge discovery in databases, where a granule refers to a predicate that describes common features of a group of transactions. The new technique first transfers transaction databases into basic decision tables, then uses multi-tier structures to integrate pattern mining and rule generation in one phase for both intra and inter transaction association rule mining. To evaluate the proposed new technique, this research defines the concept of meaningless rules by considering the co-relations between data-dimensions for intratransaction-association rule mining. It also uses precision to evaluate the effectiveness of intertransaction association rules. The experimental results show that the proposed technique is promising.

Development of rapid and highly resolving combinatorial genotyping schemes for Campylobacter jejuni and Campylobacter coli

Campylobacter jejuni followed by Campylobacter coli contribute substantially to the economic and public health burden attributed to food-borne infections in Australia. Genotypic characterisation of isolates has provided new insights into the epidemiology and pathogenesis of C. jejuni and C. coli. However, currently available methods are not conducive to large scale epidemiological investigations that are necessary to elucidate the global epidemiology of these common food-borne pathogens. This research aims to develop high resolution C. jejuni and C. coli genotyping schemes that are convenient for high throughput applications. Real-time PCR and High Resolution Melt (HRM) analysis are fundamental to the genotyping schemes developed in this study and enable rapid, cost effective, interrogation of a range of different polymorphic sites within the Campylobacter genome. While the sources and routes of transmission of campylobacters are unclear, handling and consumption of poultry meat is frequently associated with human campylobacteriosis in Australia. Therefore, chicken derived C. jejuni and C. coli isolates were used to develop and verify the methods described in this study. The first aim of this study describes the application of MLST-SNP (Multi Locus Sequence Typing Single Nucleotide Polymorphisms) + binary typing to 87 chicken C. jejuni isolates using real-time PCR analysis. These typing schemes were developed previously by our research group using isolates from campylobacteriosis patients. This present study showed that SNP + binary typing alone or in combination are effective at detecting epidemiological linkage between chicken derived Campylobacter isolates and enable data comparisons with other MLST based investigations. SNP + binary types obtained from chicken isolates in this study were compared with a previously SNP + binary and MLST typed set of human isolates. Common genotypes between the two collections of isolates were identified and ST-524 represented a clone that could be worth monitoring in the chicken meat industry. In contrast, ST-48, mainly associated with bovine hosts, was abundant in the human isolates. This genotype was, however, absent in the chicken isolates, indicating the role of non-poultry sources in causing human Campylobacter infections. This demonstrates the potential application of SNP + binary typing for epidemiological investigations and source tracing. While MLST SNPs and binary genes comprise the more stable backbone of the Campylobacter genome and are indicative of long term epidemiological linkage of the isolates, the development of a High Resolution Melt (HRM) based curve analysis method to interrogate the hypervariable Campylobacter flagellin encoding gene (flaA) is described in Aim 2 of this study. The flaA gene product appears to be an important pathogenicity determinant of campylobacters and is therefore a popular target for genotyping, especially for short term epidemiological studies such as outbreak investigations. HRM curve analysis based flaA interrogation is a single-step closed-tube method that provides portable data that can be easily shared and accessed. Critical to the development of flaA HRM was the use of flaA specific primers that did not amplify the flaB gene. HRM curve analysis flaA interrogation was successful at discriminating the 47 sequence variants identified within the 87 C. jejuni and 15 C. coli isolates and correlated to the epidemiological background of the isolates. In the combinatorial format, the resolving power of flaA was additive to that of SNP + binary typing and CRISPR (Clustered regularly spaced short Palindromic repeats) HRM and fits the PHRANA (Progressive hierarchical resolving assays using nucleic acids) approach for genotyping. The use of statistical methods to analyse the HRM data enhanced sophistication of the method. Therefore, flaA HRM is a rapid and cost effective alternative to gel- or sequence-based flaA typing schemes. Aim 3 of this study describes the development of a novel bioinformatics driven method to interrogate Campylobacter MLST gene fragments using HRM, and is called ‘SNP Nucleated Minim MLST’ or ‘Minim typing’. The method involves HRM interrogation of MLST fragments that encompass highly informative “Nucleating SNPS” to ensure high resolution. Selection of fragments potentially suited to HRM analysis was conducted in silico using i) “Minimum SNPs” and ii) the new ’HRMtype’ software packages. Species specific sets of six “Nucleating SNPs” and six HRM fragments were identified for both C. jejuni and C. coli to ensure high typeability and resolution relevant to the MLST database. ‘Minim typing’ was tested empirically by typing 15 C. jejuni and five C. coli isolates. The association of clonal complexes (CC) to each isolate by ‘Minim typing’ and SNP + binary typing were used to compare the two MLST interrogation schemes. The CCs linked with each C. jejuni isolate were consistent for both methods. Thus, ‘Minim typing’ is an efficient and cost effective method to interrogate MLST genes. However, it is not expected to be independent, or meet the resolution of, sequence based MLST gene interrogation. ‘Minim typing’ in combination with flaA HRM is envisaged to comprise a highly resolving combinatorial typing scheme developed around the HRM platform and is amenable to automation and multiplexing. The genotyping techniques described in this thesis involve the combinatorial interrogation of differentially evolving genetic markers on the unified real-time PCR and HRM platform. They provide high resolution and are simple, cost effective and ideally suited to rapid and high throughput genotyping for these common food-borne pathogens.

Life in the 'real world': a profile of Queensland University of Technology Library and Information Science graduates.

A graduate destination survey can provide a snap shot in time of a graduate’s career progression and outcome. This paper will present the results of a Queensland University of Technology study exploring the employment outcomes of students who had completed a library and information science course from the Faculty of Information Technology between 2000 and 2008. Seventy-four graduates completed an online questionnaire administered in July 2009. The study found that 90% of the graduates surveyed were working and living in Queensland, with over three quarters living and working in Brisbane. Nearly 70% were working full-time, while only 1.4% indicating that they were unemployed and looking for work. Over 80% of the graduates identified themselves as working in “librarianship”. This study is the first step in understanding the progression and destination of QUT’s library and information science graduates. It is recommended that this survey becomes an ongoing initiative so that the results can be analysed and compared over time.

After the marketplace: evidence, social science and educational research

This paper is an essay on the state of Australian education that frames new directions for educational research. It outlines three challenges faced by Australian educators: highly spatialised poverty with particularly strong mediating effects on primary school education; the need for intellectual and critical depth in pedagogy, with a focus in the upper primary and middle years; and the need to reinvent senior schooling to address emergent pathways from school to work and civic life. It offers a narrative description of the dynamics of policy making in Australia and North America and argues for an evidence-based approach to social and educational policy – but one quite unlike current test and market-based approaches. Instead, it argues for a multidisciplinary approach to a broad range of empirical and case-based evidence that subjects these to critical, hermeneutic social sciences. Such an approach would join educational policy with educational research, and broader social, community and governmental action with the aim of reorganising and redistributing material, cultural and social resources.

Don't sell social science short

The News of the Week article that reports on Senator Kay Bailey Hutchison (R-TX) questioning the need to fund social science research at the National Science Foundation is alarming and shortsighted ("Senate panel chair asks why NSF funds social sciences," 12 May, p. 829). Social science research is at the fundamental core of basic research and has much to contribute to the economic viability of the United States. Twenty years of direct and jointly funded social and ecosystem science research at Colorado State University's Natural Resource Ecology Laboratory has produced deep insights into environmental and societal impacts of political upheaval, land use, and climate change in parts of Africa, Asia, and the Americas. Beyond greatly advancing our understanding of the coupled human-environmental system, the partnership of social and ecosystem science has brought scientists and decision-makers together to begin to develop solutions to difficult problems.