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.

Reflections, successes and pitfalls of coordinating online discussion forums in a foreign language

The advent of e-learning has seen the adaptation and use of a plethora of educational techniques. Of these, online discussion forums have met with success and been used widely in both undergraduate and postgraduate education. The authors of this paper, having previously used online discussion forums in the postgraduate arena with success, adopted this approach for the design and subsequent delivery of a learning and teaching subject. This learning and teaching subject, however, was part of an international collaboration and designed for nurse academics in another country – Vietnam. With the nursing curriculum in Vietnam currently moving to adopt a competency based approach, two learning and teaching subjects were designed by an Australian university for Vietnamese nurse academics. Subject materials constituted a DVD which arrived by post and access to an online platform. Assessment for the subject included (but was not limited to) mandatory participation in online discussion with the other nurse academics enrolled in the subject. The purpose behind the online discussion was to generate discourse between the Vietnamese nurse academics located across Vietnam. Consequently the online discussions occurred in both Vietnamese and English; the Australian academic moderating the discussion did so in Australia with a Vietnamese translator. For the Australian University delivering this subject the difference between this and past online discussions were twofold: delivery was in a foreign language; and the teaching experience of the Vietnamese nurse teachers was mixed and frequently very limited. This paper will provide a discussion addressing the design of an online learning environment for foreign correspondents, the resources and translation required to maximise the success of the online discussion, the lessons learnt and consequent changes made, as well as the rationale of delivering complex content in a foreign language. While specifically addressing the first iteration of the first learning module designed, this paper will also address subsequent changes made for the second iteration of the first module and comment on their success. While a translator is clearly a key component of success, the elements of simplicity and clarity in hand with supportive online moderation must not be overlooked.

Engineering sustainable solutions program : critical literacies for engineers portfolio

Purpose While a number of universities in Australia have embraced concepts such as project/problem‐based learning and design of innovative learning environments for engineering education, there has been a lack of national guidance on including sustainability as a “critical literacy” into all engineering streams. This paper was presented at the 2004 International Conference on Engineering Education in Sustainable Development (EESD) in Barcelona, Spain, outlining a current initiative that is seeking to address the “critical literacy” dilemma. Design/methodology/approach The paper presents the positive steps taken by Australia's peak engineering body, the Institution of Engineers Australia (EA), in considering accreditation requirements for university engineering courses and its responsibility to ensure the inclusion of sustainability education material. It then describes a current initiative called the “Engineering Sustainable Solutions Program – Critical Literacies for Engineers Portfolio” (ESSP‐CL), which is being developed by The Natural Edge Project (TNEP) in partnership with EA and Unesco. Findings Content for the module was gathered from around the world, drawing on research from the publication The Natural Advantage of Nations: Business Opportunities, Innovation, and Governance in the Twenty‐first Century. Parts of the first draft of the ESSP‐CL have been trialled at Griffith University, Queensland, Australia with first year environmental engineering students, in May 2004. Further trials are now proceeding with a number of other universities and organisations nationally and internationally. Practical implications It is intended that ESSP‐CL will be a valuable resource to universities, professional development activities or other education facilities nationally and internationally. Originality/value This paper fulfils an identified information/resources need.

The design and development of an undergraduate signal processing laboratory

The School of Electrical and Electronic Systems Engineering of Queensland University of Technology (like many other universities around the world) has recognised the importance of complementing the teaching of signal processing with computer based experiments. A laboratory has been developed to provide a "hands-on" approach to the teaching of signal processing techniques. The motivation for the development of this laboratory was the cliche "What I hear I remember but what I do I understand." The laboratory has been named as the "Signal Computing and Real-time DSP Laboratory" and provides practical training to approximately 150 final year undergraduate students each year. The paper describes the novel features of the laboratory, techniques used in the laboratory based teaching, interesting aspects of the experiments that have been developed and student evaluation of the teaching techniques

Parameter estimation for a phenomenological model of the cardiac action potential

The action potential (ap) of a cardiac cell is made up of a complex balance of ionic currents which flow across the cell membrane in response to electrical excitation of the cell. Biophysically detailed mathematical models of the ap have grown larger in terms of the variables and parameters required to model new findings in subcellular ionic mechanisms. The fitting of parameters to such models has seen a large degree of parameter and module re-use from earlier models. An alternative method for modelling electrically exciteable cardiac tissue is a phenomenological model, which reconstructs tissue level ap wave behaviour without subcellular details. A new parameter estimation technique to fit the morphology of the ap in a four variable phenomenological model is presented. An approximation of a nonlinear ordinary differential equation model is established that corresponds to the given phenomenological model of the cardiac ap. The parameter estimation problem is converted into a minimisation problem for the unknown parameters. A modified hybrid Nelder–Mead simplex search and particle swarm optimization is then used to solve the minimisation problem for the unknown parameters. The successful fitting of data generated from a well known biophysically detailed model is demonstrated. A successful fit to an experimental ap recording that contains both noise and experimental artefacts is also produced. The parameter estimation method’s ability to fit a complex morphology to a model with substantially more parameters than previously used is established.

Extreme ultraviolet (EUV) degradation of poly(olefin sulfone)s : towards applications as EUV photoresists

Poly(olefin sulfone)s, formed by the reaction of sulfur dioxide (SO2) and an olefin, are known to be highly susceptible to degradation by radiation and thus have been identified as candidate materials for chain scission-based extreme ultraviolet lithography (EUVL) resist materials. In order to investigate this further, the synthesis and characterisation of two poly(olefin sulfone)s namely poly(1-pentene sulfone) (PPS) and poly(2-methyl-1-pentene sulfone) (PMPS), was achieved and the two materials were evaluated for possible chain scission EUVL resist applications. It was found that both materials possess high sensitivities to EUV photons; however; the rates of outgassing were extremely high. The only observed degradation products were found to be SO2 and the respective olefin suggesting that depolymerisation takes place under irradiation in a vacuum environment. In addition to depolymerisation, a concurrent conversion of SO2 moieties to a sulfide phase was observed using XPS.

Chain scission resists for extreme ultraviolet lithography based on high performance polysulfone-containing polymers

A series of polymers with a comb architecture were prepared where the poly(olefin sulfone) backbone was designed to be highly sensitive to extreme ultraviolet (EUV) radiation, while the well-defined poly(methyl methacrylate) (PMMA) arms were incorporated with the aim of increasing structural stability. It is hypothesized that upon EUV radiation rapid degradation of the polysulfone backbone will occur leaving behind the well-defined PMMA arms. The synthesized polymers were characterised and have had their performance as chain-scission EUV photoresists evaluated. It was found that all materials possess high sensitivity towards degradation by EUV radiation (E0 in the range 4–6 mJ cm−2). Selective degradation of the poly(1-pentene sulfone) backbone relative to the PMMA arms was demonstrated by mass spectrometry headspace analysis during EUV irradiation and by grazing-angle ATR-FTIR. EUV interference patterning has shown that materials are capable of resolving 30 nm 1:1 line:space features. The incorporation of PMMA was found to increase the structural integrity of the patterned features. Thus, it has been shown that terpolymer materials possessing a highly sensitive poly(olefin sulfone) backbone and PMMA arms are able to provide a tuneable materials platform for chain scission EUV resists. These materials have the potential to benefit applications that require nanopattering, such as computer chip manufacture and nano-MEMS.

Patterning of tailored polycarbonate based non-chemically amplified resists using extreme ultraviolet lithography

A series of high-performance polycarbonates have been prepared with glass-transition temperatures and decomposition temperatures that are tunable by varying the repeat-unit chemical structure. Patterning of the polymers with extreme UV lithography has been achieved by taking advantage of direct photoinduced chain scission of the polymer chains, which results in a molecular-weight based solubility switch. After selective development of the irradiated regions of the polymers, feature sizes as small as 28.6 nm have been printed and the importance of resist-developer interactions for maximizing image quality has been demonstrated.

Polycarbonate based nonchemically amplified photoresists for extreme ultraviolet lithography

Some initial EUVL patterning results for polycarbonate based non-chemically amplified resists are presented. Without full optimization the developer a resolution of 60 nm line spaces could be obtained. With slight overexposure (1.4 × E0) 43.5 nm lines at a half pitch of 50 nm could be printed. At 2x E0 a 28.6 nm lines at a half pitch of 50 nm could be obtained with a LER that was just above expected for mask roughness. Upon being irradiated with EUV photons, these polymers undergo chain scission with the loss of carbon dioxide and carbon monoxide. The remaining photoproducts appear to be non-volatile under standard EUV irradiation conditions, but do exhibit increased solubility in developer compared to the unirradiated polymer. The sensitivity of the polymers to EUV light is related to their oxygen content and ways to increase the sensitivity of the polymers to 10 mJ cm-2 is discussed.

An accessible method for teaching doctors about death certification

The World Health Organization recommends that data on mortality in its member countries are collected utilising the Medical Certificate of Cause of Death published in the instruction volume of the ICD-10. However, investment in health information processes necessary to promote the use of this certificate and improve mortality information is lacking in many countries. An appeal for support to make improvements has been launched through the Health Metrics Network’s MOVE-IT strategy (Monitoring of Vital Events – Information Technology) [World Health Organization, 2011]. Despite this international spotlight on the need for capture of mortality data and in the use of the ICD-10 to code the data reported on such certificates, there is little cohesion in the way that certifiers of deaths receive instruction in how to complete the death certificate, which is the main source document for mortality statistics. Complete and accurate documentation of the immediate, underlying and contributory causes of death of the decedent on the death certificate is a requirement to produce standardised statistical information and to the ability to produce cause-specific mortality statistics that can be compared between populations and across time. This paper reports on a research project conducted to determine the efficacy and accessibility of the certification module of the WHO’s newly-developed web based training tool for coders and certifiers of deaths. Involving a population of medical students from the Fiji School of Medicine and a pre and post research design, the study entailed completion of death certificates based on vignettes before and after access to the training tool. The ability of the participants to complete the death certificates and analysis of the completeness and specificity of the ICD-10 coding of the reported causes of death were used to measure the effect of the students’ learning from the training tool. The quality of death certificate completion was assessed using a Quality Index before and after the participants accessed the training tool. In addition, the views of the participants about accessibility and use of the training tool were elicited using a supplementary questionnaire. The results of the study demonstrated improvement in the ability of the participants to complete death certificates completely and accurately according to best practice. The training tool was viewed very positively and its implementation in the curriculum for medical students was encouraged. Participants also recommended that interactive discussions to examine the certification exercises would be an advantage.