Model choice problems using approximate Bayesian computation with applications to pathogen transmission data sets

Analytically or computationally intractable likelihood functions can arise in complex statistical inferential problems making them inaccessible to standard Bayesian inferential methods. Approximate Bayesian computation (ABC) methods address such inferential problems by replacing direct likelihood evaluations with repeated sampling from the model. ABC methods have been predominantly applied to parameter estimation problems and less to model choice problems due to the added difficulty of handling multiple model spaces. The ABC algorithm proposed here addresses model choice problems by extending Fearnhead and Prangle (2012, Journal of the Royal Statistical Society, Series B 74, 1–28) where the posterior mean of the model parameters estimated through regression formed the summary statistics used in the discrepancy measure. An additional stepwise multinomial logistic regression is performed on the model indicator variable in the regression step and the estimated model probabilities are incorporated into the set of summary statistics for model choice purposes. A reversible jump Markov chain Monte Carlo step is also included in the algorithm to increase model diversity for thorough exploration of the model space. This algorithm was applied to a validating example to demonstrate the robustness of the algorithm across a wide range of true model probabilities. Its subsequent use in three pathogen transmission examples of varying complexity illustrates the utility of the algorithm in inferring preference of particular transmission models for the pathogens.

Detoxification enzyme activities (CYP1A1 and GST) in the skin of humpback whales as a function of organochlorine burdens and migration status

The activities of glutathione-s-transferase (GST) and cytochrome P-450 1A1 (CYP1A1) enzymes were measured in freshly extracted epidermis of live-biopsied, migrating, southern hemisphere humpback whales (Megaptera novaeangliae). The two quantified enzyme activities did not correlate strongly with each other. Similarly, neither correlated strongly with any of the organochlorine compound groups previously measured in the superficial blubber of the sample biopsy core, likely reflecting the anticipated low levels of typical aryl-hydrocarbon receptor ligands. GST activity did not differ significantly between genders or between northward (early migration) or southward (late migration) migrating cohorts. Indeed, the inter-individual variability in GST measurements was relatively low. This observation raises the possibility that measured activities were basal activities and that GST function was inherently impacted by the fasting state of the sampled animals, as seen in other species. These results do not support the implementation of CYP1A1 or GST as effective biomarkers of organochlorine contaminant burdens in southern hemisphere populations of humpback whales as advocated for other cetacean species. Further investigation of GST activity in feeding versus fasting cohorts may, however, provide some insight into the fasting metabolism of these behaviourally adapted populations.

Preventing infections through cleaner hospitals project

While many Australian hospitals have good infection control practices, research about the role cleaning in the hospital environment plays in preventing infections is limited.

Pollen image classification using the classifynder system: Algorithm comparison and a case study on New Zealand honey

We describe an investigation into how Massey University’s Pollen Classifynder can accelerate the understanding of pollen and its role in nature. The Classifynder is an imaging microscopy system that can locate, image and classify slide based pollen samples. Given the laboriousness of purely manual image acquisition and identification it is vital to exploit assistive technologies like the Classifynder to enable acquisition and analysis of pollen samples. It is also vital that we understand the strengths and limitations of automated systems so that they can be used (and improved) to compliment the strengths and weaknesses of human analysts to the greatest extent possible. This article reviews some of our experiences with the Classifynder system and our exploration of alternative classifier models to enhance both accuracy and interpretability. Our experiments in the pollen analysis problem domain have been based on samples from the Australian National University’s pollen reference collection (2,890 grains, 15 species) and images bundled with the Classifynder system (400 grains, 4 species). These samples have been represented using the Classifynder image feature set.We additionally work through a real world case study where we assess the ability of the system to determine the pollen make-up of samples of New Zealand honey. In addition to the Classifynder’s native neural network classifier, we have evaluated linear discriminant, support vector machine, decision tree and random forest classifiers on these data with encouraging results. Our hope is that our findings will help enhance the performance of future releases of the Classifynder and other systems for accelerating the acquisition and analysis of pollen samples.

In search of Nirvana : why Nirvana : the True Story could never be "true"

In my book Nirvana: The True Story (2006), I undertake an autoethnographical approach to biography, attempting to impart an understanding of my chosen subject - the rock band Nirvana - via discussion of my own experiences. On numerous occasions, I veer off into tangential asides, frequently using extensive footnotes to explain obscure musical references. Personal anecdotes are juxtaposed with "insider" information; at crucial points in the story (notable concerts, the first meeting of singer Kurt Cobain with his future wife Courtney Love, the news of Cobain's suicide), the linear thread of the narrative spills over into a multi-faceted approach, with several different (and sometimes opposing) voices given equal prominence. Despite my firsthand experience of the band, however, Nirvana: The True Story is not considered authoritative, even within its own field. This article considers the reasons why this may be the case.In my book Nirvana: The True Story (2006), I undertake an autoethnographical approach to biography, attempting to impart an understanding of my chosen subject - the rock band Nirvana - via discussion of my own experiences. On numerous occasions, I veer off into tangential asides, frequently using extensive footnotes to explain obscure musical references. Personal anecdotes are juxtaposed with "insider" information; at crucial points in the story (notable concerts, the first meeting of singer Kurt Cobain with his future wife Courtney Love, the news of Cobain's suicide), the linear thread of the narrative spills over into a multi-faceted approach, with several different (and sometimes opposing) voices given equal prominence. Despite my firsthand experience of the band, however, Nirvana: The True Story is not considered authoritative, even within its own field. This article considers the reasons why this may be the case.

A modified Density-Based Scanning Algorithm with Noise for spatial travel pattern analysis from Smart Card AFC data

Smart Card Automated Fare Collection (AFC) data has been extensively exploited to understand passenger behavior, passenger segment, trip purpose and improve transit planning through spatial travel pattern analysis. The literature has been evolving from simple to more sophisticated methods such as from aggregated to individual travel pattern analysis, and from stop-to-stop to flexible stop aggregation. However, the issue of high computing complexity has limited these methods in practical applications. This paper proposes a new algorithm named Weighted Stop Density Based Scanning Algorithm with Noise (WS-DBSCAN) based on the classical Density Based Scanning Algorithm with Noise (DBSCAN) algorithm to detect and update the daily changes in travel pattern. WS-DBSCAN converts the classical quadratic computation complexity DBSCAN to a problem of sub-quadratic complexity. The numerical experiment using the real AFC data in South East Queensland, Australia shows that the algorithm costs only 0.45% in computation time compared to the classical DBSCAN, but provides the same clustering results.

Developing knowledge and leadership in pre-service teacher education systems

Pre-service teacher education institutions are large and complex organizations, which are notoriously difficult to change. One factor is that many change efforts focus largely on individual pre-service teacher educators altering their practice. We report here on our experience using a model for effecting change, which views pre-service teacher education institutions and educators as a part of a much broader system. We identified numerous possibilities for, and constraints on, embedding change, but focus only on two in this paper: participants’ knowledge of change strategies and their leadership capacities. As a result of our study findings and researcher reflections, we argue that being a leader in an academic area within pre-service teacher education does not equate to leadership knowledge or skills to initiate and enact systems-wide change. Furthermore, such leadership capacities must be explicitly developed if education for sustainability is to become embedded in pre-service teacher education.

Reducing pressure injuries in critically ill patients by using a patient skin integrity care bundle (InSPiRE)

Purpose To test an interventional patient skin integrity bundle, InSPiRE protocol, on the impact of pressure injuries (PrIs) in critically ill patients in an Australian adult intensive care unit (ICU). Methods Before and after design was used where the group of patients receiving the intervention (InSPiRE protocol) was compared with a similar control group who received standard care. Data collected included demographic and clinical variables, skin assessment, PrI presence and stage, and a Sequential Organ Failure Assessment (SOFA) score. Results Overall, 207 patients were enrolled, 105 in the intervention group and 102 in the control group. Most patients were men, mean age 55. The groups were similar on major demographic variables (age, SOFA scores, ICU length of stay). Pressure injury cumulative incidence was significantly lower in the intervention group (18%) compared to the control group for skin injuries(30.4%) (χ2=4.271, df=1, p=0.039) and mucous injuries (t test =3.27, p=<0.001) . Significantly fewer PrIs developing over time in the intervention group (Logrank= 11.842, df=1, p=<0.001) and patients developed fewer skin injuries (>3 PrIs/patient = 1/105) compared with the control group (>3 injuries/patient = 10/102) (p=0.018). Conclusion The intervention group, recieving the InSPiRE protocol, had lower PrI cumulative incidence, and reduced number and severity of PrIs that developed over time. Systematic and ongoing assessment of the patient's skin and PrI risk as well as implementation of tailored prevention measures are central to preventing PrIs.

Inhibiting Eph kinase activity may not be “Eph”ective for cancer treatment

Several Eph receptor tyrosine kinases (RTKs) are commonly over-expressed in epithelial and mesenchymal cancers and are recognized as promising therapeutic targets. Although normal interaction between Eph receptors and their ephrin ligands stimulates kinase activity and is generally tumor suppressive, significant Eph over-expression allows activation of ligand- and/or kinase-independent signaling pathways that promote oncogenesis. Single-agent kinase inhibitors are widely used to target RTK-driven tumors but acquired and de novo resistance to such agents is a major limitation to effective clinical use. Accumulating evidence suggests that Ephs can be inhibited by “leaky” or low-specificity kinase inhibitors targeted at other RTKs. Such off-target effects may therefore inadvertently promote ligand- and/or kinase-independent oncogenic Eph signaling, thereby providing a new mechanism by which resistance to the RTK inhibitors can emerge. We propose that combining specific, non-leaky kinase inhibitors with tumor-suppressive stimulators of Eph signaling may provide more effective treatment options for overcoming treatment-induced resistance and clinical failure.

Virtual community, purchasing behaviour, and emotional well-being

The benefits of virtual communities in increasing firms' profits, instilling knowledge in consumers, and enhancing consumers' social experience and enjoyment are widely recognised. However, relatively little is known about how the use of a virtual community could influence consumers' emotional well-being. This study examines the relationships among virtual community features (structural and experiential routes) as antecedents of virtual community engagement, including quality of use of virtual communities (time spent online and level of information exchange), electronic word-of-mouth (eWOM) purchasing behaviour, and consumers' emotional experience. Furthermore, by extending the cultural perspective to virtual community engagement, this study examines the role of collectivistic values on the aforementioned relationships. The proposed hypotheses are tested on the basis of data collected from 286 members of different virtual communities in Taiwan. The results partially support the theory that features of virtual communities influenced the quality of use, which then has a subsequent effect on consumer eWOM purchasing and emotional well-being. The results of the empirical analysis add credence to the proposed relationships. The role of collectivistic values is also partially supported. A detailed discussion of the findings and limitations of this study is provided.

Connecting soundscape to landscape: Which acoustic index best describes landscape configuration?

Soundscape assessment has been proposed as a remote ecological monitoring tool for measuring biodiversity, but few studies have examined how soundscape patterns vary with landscape configuration and condition. The goal of our study was to examine a suite of published acoustic indices to determine whether they provide comparable results relative to varying levels of landscape fragmentation and ecological condition in nineteen forest sites in eastern Australia. Our comparison of six acoustic indices according to time of day revealed that two indices, the acoustic complexity and the bioacoustic index, presented a similar pattern that was linked to avian song intensity, but was not related to landscape and biodiversity attributes. The diversity indices, acoustic entropy and acoustic diversity, and the normalized difference soundscape index revealed high nighttime sound, as well as a dawn and dusk chorus. These indices appear to be sensitive to nocturnal biodiversity which is abundant at night in warm, subtropical environments. We argue that there is need to better understand temporal partitioning of the soundscape by specific taxonomic groups, and this should involve integrated research on amphibians, insects and birds during a 24 h cycle. The three indices that best connected the soundscape with landscape characteristics, ecological condition and bird species richness were acoustic entropy, acoustic evenness and the normalized difference soundscape index. This study has demonstrated that remote soundscape assessment can be implemented as an ecological monitoring tool in fragmented Australian forest landscapes. However, further investigation should be dedicated to refining and/or combining existing acoustic indices and also to determine if these indices are appropriate in other landscapes and for other survey purposes.

Policies and Procedures to Address Bullying at Australian Universities

While bullying is often researched in children and adolescents and in the workplace, there is limited research in the emerging adult population, especially in students at university. This is perhaps due to the fact that bullying generally declines as children and young people become older (e.g., Nansel et al., 2001; Wang, Iannotti, & Nansel, 2009). Although this may indeed be the case, it is apparent that bullying does not completely abate when students graduate from high school. The plethora of literature evidencing workplace bullying, clearly shows that bullying continues beyond the school years (e.g., Hoel, Cooper, & Faragher, 2001; Privitera & Campbell, 2009). With the advent of cyberbullying in the last decade it has been shown that this particular form of bullying may not decrease with age as does traditional bullying (Kowalski & Limber, 2007; Raskauskas & Stoltz, 2007). In addition, we know there is a spike in prevalence rates during the transition from primary to high school Pellegrini et al., 2010), so it is possible that new university students are at an increased risk of victimisation due to this being a transition period. This has led to some interest in examining the prevalence of bullying in the emerging adult population at universities (Chapell, Casey, & de la Cruz, 2004; Pontzer, 2010; Wensley & Campbell, 2009).