A Python package for Bayesian estimation using Markov Chain Monte Carlo

Markov chain Monte Carlo (MCMC) estimation provides a solution to the complex integration problems that are faced in the Bayesian analysis of statistical problems. The implementation of MCMC algorithms is, however, code intensive and time consuming. We have developed a Python package, which is called PyMCMC, that aids in the construction of MCMC samplers and helps to substantially reduce the likelihood of coding error, as well as aid in the minimisation of repetitive code. PyMCMC contains classes for Gibbs, Metropolis Hastings, independent Metropolis Hastings, random walk Metropolis Hastings, orientational bias Monte Carlo and slice samplers as well as specific modules for common models such as a module for Bayesian regression analysis. PyMCMC is straightforward to optimise, taking advantage of the Python libraries Numpy and Scipy, as well as being readily extensible with C or Fortran.

Developing a research method to test a new first-order decision making model for the procurement of public sector major infrastructure

Given global demand for new infrastructure, governments face substantial challenges in funding new infrastructure and simultaneously delivering Value for Money (VfM). The paper begins with an update on a key development in a new early/first-order procurement decision making model that deploys production cost/benefit theory and theories concerning transaction costs from the New Institutional Economics, in order to identify a procurement mode that is likely to deliver the best ratio of production costs and transaction costs to production benefits, and therefore deliver superior VfM relative to alternative procurement modes. In doing so, the new procurement model is also able to address the uncertainty concerning the relative merits of Public-Private Partnerships (PPP) and non-PPP procurement approaches. The main aim of the paper is to develop competition as a dependent variable/proxy for VfM and a hypothesis (overarching proposition), as well as developing a research method to test the new procurement model. Competition reflects both production costs and benefits (absolute level of competition) and transaction costs (level of realised competition) and is a key proxy for VfM. Using competition as a proxy for VfM, the overarching proposition is given as: When the actual procurement mode matches the predicted (theoretical) procurement mode (informed by the new procurement model), then actual competition is expected to match potential competition (based on actual capacity). To collect data to test this proposition, the research method that is developed in this paper combines a survey and case study approach. More specifically, data collection instruments for the surveys to collect data on actual procurement, actual competition and potential competition are outlined. Finally, plans for analysing this survey data are briefly mentioned, along with noting the planned use of analytical pattern matching in deploying the new procurement model and in order to develop the predicted (theoretical) procurement mode.

Shanghai : images of modernity

This chapter profiles China's biggest city and economic powerhouse, Shanghai. The authors examine the city’s use of culture to position itself as a global city and how a particular narrative of the city has informed western commentators and Shanghai policy makers. They also analyze the development of an arts and cultural infrastructure and the parallel separation of art and entertainment, with contemporary art as an unexpected challenge, but one the city successfully negotiated. They looks at the marketisation of culture and the context in which this takes place, tracing the connections between market reforms in culture and those in the wider economy. The authors are convinced that the half-formed or distorted use of western concepts like creative industries or creative clusters, rather than indicating a duplicity or an incomplete modernity actually highlight some of the complicities of canonical cultural policy.

Wide baseline correspondence extraction beyond local features

Robust, affine covariant, feature extractors provide a means to extract correspondences between images captured by widely separated cameras. Advances in wide baseline correspondence extraction require looking beyond the robust feature extraction and matching approach. This study examines new techniques of extracting correspondences that take advantage of information contained in affine feature matches. Methods of improving the accuracy of a set of putative matches, eliminating incorrect matches and extracting large numbers of additional correspondences are explored. It is assumed that knowledge of the camera geometry is not available and not immediately recoverable. The new techniques are evaluated by means of an epipolar geometry estimation task. It is shown that these methods enable the computation of camera geometry in many cases where existing feature extractors cannot produce sufficient numbers of accurate correspondences.

Shanghai: city of other people’s dreams

Shanghai as a place where other people's dreams inform the imaginary landscape. How does this relate to the new possibilities available to the current citizens of the city?

Identification of a cryptic Prokaryotic promoter within the cDNA encoding the 5′ End of Dengue Virus RNA Genome

Infectious cDNA clones of RNA viruses are important research tools, but flavivirus cDNA clones have proven difficult to assemble and propagate in bacteria. This has been attributed to genetic instability and/or host cell toxicity, however the mechanism leading to these difficulties has not been fully elucidated. Here we identify and characterize an efficient cryptic bacterial promoter in the cDNA encoding the dengue virus (DENV) 5′ UTR. Following cryptic transcription in E. coli, protein expression initiated at a conserved in-frame AUG that is downstream from the authentic DENV initiation codon, yielding a DENV polyprotein fragment that was truncated at the N-terminus. A more complete understanding of constitutive viral protein expression in E. coli might help explain the cloning and propagation difficulties generally observed with flavivirus cDNA.

Practical stability of approximating discrete-time filters with respect to model mismatch using relative entropy concepts

This paper establishes practical stability results for an important range of approximate discrete-time filtering problems involving mismatch between the true system and the approximating filter model. Using local consistency assumption, the practical stability established is in the sense of an asymptotic bound on the amount of bias introduced by the model approximation. Significantly, these practical stability results do not require the approximating model to be of the same model type as the true system. Our analysis applies to a wide range of estimation problems and justifies the common practice of approximating intractable infinite dimensional nonlinear filters by simpler computationally tractable filters.

Ovarian steroid hormones: effects on immune responses and Chlamydia trachomatis infections of the female genital tract

Female sex hormones are known to regulate the adaptive and innate immune functions of the female reproductive tract. This review aims to update our current knowledge of the effects of the sex hormones estradiol and progesterone in the female reproductive tract on innate immunity, antigen presentation, specific immune responses, antibody secretion, genital tract infections caused by Chlamydia trachomatis, and vaccine-induced immunity.

Relative entropy rate based design for linear hybrid system models

Hybrid system representations have been applied to many challenging modeling situations. In these hybrid system representations, a mixture of continuous and discrete states is used to capture the dominating behavioural features of a nonlinear, possible uncertain, model under approximation. Unfortunately, the problem of how to best design a suitable hybrid system model has not yet been fully addressed. This paper proposes a new joint state measurement relative entropy rate based approach for this design purpose. Design examples and simulation studies are presented which highlight the benefits of our proposed design approaches.

The WIL (Work Integrated Learning) report : a national scoping study [Final Report]

This report provides an account of the first large-scale scoping study of work integrated learning (WIL) in contemporary Australian higher education. The explicit aim of the project was to identify issues and map a broad and growing picture of WIL across Australia and to identify ways of improving the student learning experience in relation to WIL. The project was undertaken in response to high levels of interest in WIL, which is seen by universities both as a valid pedagogy and as a means to respond to demands by employers for work-ready graduates, and demands by students for employable knowledge and skills. Over a period of eight months of rapid data collection, 35 universities and almost 600 participants contributed to the project. Participants consistently reported the positive benefits of WIL and provided evidence of commitment and innovative practice in relation to enhancing student learning experiences. Participants provided evidence of strong partnerships between stakeholders and highlighted the importance of these relationships in facilitating effective learning outcomes for students. They also identified a range of issues and challenges that face the sector in growing WIL opportunities; these issues and challenges will shape the quality of WIL experiences. While the majority of comments focused on issues involved in ensuring quality placements, it was recognised that placements are just one way to ensure the integration of work with learning. Also, the WIL experience is highly contextualised and impacted by the expectations of students, employers, the professions, the university and government policy.

Practical stability with respect to model mismatch of approximate discrete-time output feedback control

This paper establishes a practical stability result for discrete-time output feedback control involving mismatch between the exact system to be stabilised and the approximating system used to design the controller. The practical stability is in the sense of an asymptotic bound on the amount of error bias introduced by the model approximation, and is established using local consistency properties of the systems. Importantly, the practical stability established here does not require the approximating system to be of the same model type as the exact system. Examples are presented to illustrate the nature of our practical stability result.

Identification of area-level influences on regions of high cancer incidence in Queensland, Australia : a classification tree approach

Background: Strategies for cancer reduction and management are targeted at both individual and area levels. Area-level strategies require careful understanding of geographic differences in cancer incidence, in particular the association with factors such as socioeconomic status, ethnicity and accessibility. This study aimed to identify the complex interplay of area-level factors associated with high area-specific incidence of Australian priority cancers using a classification and regression tree (CART) approach. Methods: Area-specific smoothed standardised incidence ratios were estimated for priority-area cancers across 478 statistical local areas in Queensland, Australia (1998-2007, n=186,075). For those cancers with significant spatial variation, CART models were used to identify whether area-level accessibility, socioeconomic status and ethnicity were associated with high area-specific incidence. Results: The accessibility of a person’s residence had the most consistent association with the risk of cancer diagnosis across the specific cancers. Many cancers were likely to have high incidence in more urban areas, although male lung cancer and cervical cancer tended to have high incidence in more remote areas. The impact of socioeconomic status and ethnicity on these associations differed by type of cancer. Conclusions: These results highlight the complex interactions between accessibility, socioeconomic status and ethnicity in determining cancer incidence risk.

Developing the atlas of cancer in Queensland : methodological issues

Background: Achieving health equity has been identified as a major challenge, both internationally and within Australia. Inequalities in cancer outcomes are well documented, and must be quantified before they can be addressed. One method of portraying geographical variation in data uses maps. Recently we have produced thematic maps showing the geographical variation in cancer incidence and survival across Queensland, Australia. This article documents the decisions and rationale used in producing these maps, with the aim to assist others in producing chronic disease atlases. Methods: Bayesian hierarchical models were used to produce the estimates. Justification for the cancers chosen, geographical areas used, modelling method, outcome measures mapped, production of the adjacency matrix, assessment of convergence, sensitivity analyses performed and determination of significant geographical variation is provided. Conclusions: Although careful consideration of many issues is required, chronic disease atlases are a useful tool for assessing and quantifying geographical inequalities. In addition they help focus research efforts to investigate why the observed inequalities exist, which in turn inform advocacy, policy, support and education programs designed to reduce these inequalities.

A Multifaceted Strategy for Implementation of the Ottawa Ankle Rules in Two Emergency Departments

Problem Despite widespread acceptance of the Ottawa ankle rules for assessment of acute ankle injuries, their application varies considerably. Design Before and after study. Background and setting Emergency departments of a tertiary teaching hospital and a community hospital in Australia. Key measures for improvement Documentation of the Ottawa ankle rules, proportion of patients referred for radiography, proportion of radiographs showing a fracture. Strategies for change Education, a problem specific radiography request form, reminders, audit and feedback, and using radiographers as “gatekeepers.” Effects of change Documentation of the Ottawa ankle rules improved from 57.5% to 94.7% at the tertiary hospital, and 51.6% to 80.8% at the community hospital (P<0.001 for both). The proportion of patients undergoing radiography fell from 95.8% to 87.2% at the tertiary hospital, and from 91.4% to 78.9% at the community hospital (P<0.001 for both). The proportion of radiographs showing a fracture increased from 20.4% to 27.1% at the tertiary hospital (P=0.069), and 15.2% to 27.2% (P=0.002) at the community hospital. The missed fracture rate increased from 0% to 2.9% at the tertiary hospital and from 0% to 1.6% at the community hospital compared with baseline (P=0.783 and P=0.747). Lessons learnt Assessment of case note documentation has limitations. Clinician groups seem to differ in their capacity and willingness to change their practice. A multifaceted change strategy including a problem specific radiography request form can improve the selection of patients for radiography.

What We Have Here is a Failure to Communicate! Improving Communication between Tertiary to Primary Care for Chronic Heart Failure Patients

Background:  The aims of this study were to determine the documentation of pharmacotherapy optimization goals in the discharge letters of patients with the principal diagnosis of chronic heart failure. Methods:  A retrospective practice audit of 212 patients discharged to the care of their local general practitioner from general medical units of a large tertiary hospital. Details of recommendations regarding ongoing pharmacological and non-pharmacological management were reviewed. The doses of medications on discharge were noted and whether they met current guidelines recommending titration of angiotensin-converting enzyme inhibitors and beta-blockers. Ongoing arrangements for specialist follow up were also reviewed. Results:  The mean age of patients whose letters were reviewed was 78.4 years (standard deviation ± 8.6); 50% were men. Patients had an overall median of six comorbidities and eight regular medications on discharge. Mean length of stay for each admission was 6 days. Discharge letters were posted a median of 4 days after discharge, with 25% not posted at 10 days. No discharge letter was sent in 9.4% (20) of the cases. Only six (2.8%) letters had any recommendations regarding future titration of angiotensin-converting enzyme inhibitors and 6.6% (14) for beta-blockers. Recommendations for future non-pharmacological management, for example, diuretic action plans, regular weight monitoring and exercise plans were not found in the letters in this audit. Conclusion:  Hospital discharge is an opportunity to communicate management plans for treatment optimization effectively, and while this opportunity is spurned, implementation gaps in the management of cardiac failure will probably remain.