Bridging experiments, models and simulations : an integrative approach to validation in computational cardiac electrophysiology

Computational models in physiology often integrate functional and structural information from a large range of spatio-temporal scales from the ionic to the whole organ level. Their sophistication raises both expectations and scepticism concerning how computational methods can improve our understanding of living organisms and also how they can reduce, replace and refine animal experiments. A fundamental requirement to fulfil these expectations and achieve the full potential of computational physiology is a clear understanding of what models represent and how they can be validated. The present study aims at informing strategies for validation by elucidating the complex interrelations between experiments, models and simulations in cardiac electrophysiology. We describe the processes, data and knowledge involved in the construction of whole ventricular multiscale models of cardiac electrophysiology. Our analysis reveals that models, simulations, and experiments are intertwined, in an assemblage that is a system itself, namely the model-simulation-experiment (MSE) system. Validation must therefore take into account the complex interplay between models, simulations and experiments. Key points for developing strategies for validation are: 1) understanding sources of bio-variability is crucial to the comparison between simulation and experimental results; 2) robustness of techniques and tools is a pre-requisite to conducting physiological investigations using the MSE system; 3) definition and adoption of standards facilitates interoperability of experiments, models and simulations; 4) physiological validation must be understood as an iterative process that defines the specific aspects of electrophysiology the MSE system targets, and is driven by advancements in experimental and computational methods and the combination of both.

Abandoning the Magic Circle

As a concept, the magic circle is in reality just 4 years old. Whilst often accredited to Johan Huizinga (1955), the modern usage of term in truth belongs to Katie Salen and Eric Zimmerman. It became in academia following the publication of “Rules of Play” in 2003. Because of the terminologyused, it carries with it unhelpful preconceptions that the game world, or play-space, excludes reality. In this paper, I argue that Salen and Zimmerman (2003) have taken a term used as an example, and applied a meaning to it that was never intended, based primarily upon definitions given by other authors, namely Apter (1991) and Sniderman (n.d.). I further argue that the definition itself contains a logical fallacy, which has prevented the full understanding of the definition in later work. Through a study of the literature in Game Theory, and examples of possible issues which could arise in contemporary games, I suggest that the emotions of the play experience continue beyond the play space, and that emotions from the “real world” enter it with the participants. I consider a reprise of the Stanley Milgram Obedience Experiment (2006), and what that tells us about human emotions and the effect that events taking place in a virtual environment can have upon them. I evaluate the opinion espoused by some authors of there being different magic circles for different players, and assert that this is not a useful approach to take when studying games, because it prevents the analysis of a game as a single entity. Furthermore I consider the reasons given by other authors for the existence of the Magic Circle, and I assert that the term “Magic Circle” should be discarded, that it has no relevance to contemporary games, and indeed it acts as a hindrance to the design and study of games. I conclude that the play space which it claims to protect from the courts and other governmental authorities would be better served by the existing concepts of intent, consent, and commonly accepted principles associated with international travel.

Heat strain evaluation of overt and covert body armour in a hot and humid environment

The aim of this study was to elucidate the thermophysiological effects of wearing lightweight non-military overt and covert personal body armour (PBA) in a hot and humid environment. Eight healthy males walked on a treadmill for 120 min at 22% of their heart rate reserve in a climate chamber simulating 31 °C (60%RH) wearing either no armour (control), overt or covert PBA in addition to a security guard uniform, in a randomised controlled crossover design. No significant difference between conditions at the end of each trial was observed in core temperature, heart rate or skin temperature (P > 0.05). Covert PBA produced a significantly greater amount of body mass change (−1.81 ± 0.44%) compared to control (−1.07 ± 0.38%, P = 0.009) and overt conditions (−1.27 ± 0.44%, P = 0.025). Although a greater change in body mass was observed after the covert PBA trial; based on the physiological outcome measures recorded, the heat strain encountered while wearing lightweight, non-military overt or covert PBA was negligible compared to no PBA. Practitioner summary The wearing of bullet proof vests or body armour is a requirement of personnel engaged in a wide range of occupations including police, security, customs and even journalists in theatres of war. This randomised controlled crossover study is the first to examine the thermophysiological effects of wearing lightweight non-military overt and covert personal body armour (PBA) in a hot and humid environment. We conclude that the heat strain encountered while wearing both overt and covert lightweight, non-military PBA was negligible compared to no PBA.

Comparative analysis of FimB and FimE recombinase activity

FimB and FimE are site-specific recombinases, part of the λ integrase family, and invert a 314 bp DNA switch that controls the expression of type 1 fimbriae in Escherichia coli. FimB and FimE differ in their activity towards the fim switch, with FimB catalysing inversion in both directions in comparison to the higher-frequency but unidirectional on-to-off recombination catalysed by FimE. Previous work has demonstrated that FimB, but not FimE, recombination is completely inhibited in vitro and in vivo by a regulator, PapB, expressed from a distinct fimbrial locus. The aim of this work was to investigate differences between FimB and FimE activity by exploiting the differential inhibition demonstrated by PapB. The research focused on genetic changes to the fim switch that alter recombinase binding and its structural context. FimB and FimE still recombined a switch in which the majority of fimS DNA was replaced with a larger region of non-fim DNA. This demonstrated a minimal requirement for FimB and FimE recombination of the Fim binding sites and associated inverted repeats. With the original leucine-responsive regulatory protein (Lrp) and integration host factor (IHF)-dependent structure removed, PapB was now able to inhibit both recombinases. The relative affinities of FimB and FimE were determined for the four ‘half sites’. This analysis, along with the effect of extensive swaps and duplications of the half sites on recombination frequency, demonstrated that FimB recruitment and therefore subsequent activity was dependent on a single half site and its context, whereas FimE recombination was less stringent, being able to interact initially with two half sites with equally high affinity. While increasing FimB recombination frequencies failed to overcome PapB repression, mutations made in recombinase binding sites resulted in inhibition of FimE recombination by PapB. Overall, the data support a model in which the recombinases differ in loading order and co-operative interactions. PapB exploits this difference and FimE becomes susceptible when its normal loading is restricted or changed.

Addressing alcohol related harms within maxillofacial trauma practice

Background A brief intervention, conducted in the acute setting care setting after an alcohol-related injury, has been reported to be highly beneficial in reducing the risk of re-injury and in reducing subsequent level of alcohol consumption. This project aimed to understand Australasian Oral and Maxillofacial Surgeons' attitudes, knowledge and skills in terms of alcohol screening and brief intervention within acute settings for patients admitted with facial trauma. Materials and Methods A web-based survey was made available to all members (n=200-250) of the Australian and New Zealand Association of Oral and Maxillofacial Surgeons (ANZAOMS), promoted through a number of email bulletins sent by the Association to all members. Implied consent is assumed for participants who complete the online survey. The survey explored their current level of involvement in treating patients with alcohol-relatd facial trauma, as well as their knowledge of and attitudes towards alcohol screening and brief intervention. The survey also explored their willingness for further training and involvement in implementing a SBI program. Parts of the survey were based on a hypothetical case with facial injury and drinking history which was presented to the participants and the participants were asked to give their response to this scenario. Results A total of 58 surgeons completed the on-line survey. 91% of surgeons surveyed were males and 88% were consultant surgeons. 71% would take alcohol history; 29% would deliver a brief alcohol intervention and 14% would refer the patients to an alcohol treatment service or clinician. 40% agreed to have adequate training in managing patients with alcohol-related injuries, while 17% and 19% felt they had adequate time and resources. 76% of surgeons reported the need for more information on where to refer patients for appropriate alcohol treatment. Conclusion The study findings confirm the challenges and barriers to implementing brief alcohol intervention in current practice. There are service gaps that exist, as well as opportunities for training.

An economic case for providing free access to antiretroviral therapy for HIV-positive people in South Australia

Background As financial constraints can be a barrier to accessing HIV antiretroviral therapy (ART), we argue for the removal of copayment requirements from HIV medications in South Australia. Methods Using a simple mathematical model informed by available behavioural and biological data and reflecting the HIV epidemiology in South Australia, we calculated the expected number of new HIV transmissions caused by persons who are not currently on ART compared with transmissions for people on ART. The extra financial investment required to cover the copayments to prevent an HIV infection was compared with the treatment costs saved due to averting HIV infections. Results It was estimated that one HIV infection is prevented per year for every 31.4 persons (median, 24.0–42.7 interquartile range (IQR)) who receive treatment. By considering the incremental change in costs and outcomes of a change in program from the current status quo, it would cost the health sector $17 860 per infection averted (median, $13 651–24 287 IQR) if ART is provided as a three-dose, three-drug combination without requirements for user-pay copayments. Conclusions The costs of removing copayment fees for ART are less than the costs of treating extra HIV infections that would result under current conditions. Removing the copayment requirement for HIV medication would be cost-effective from a governmental perspective.

Responsible reconstruction : The architect's role

This paper investigates the role of the architect in post-disaster reconstruction and questions their ability to facilitate per- manent building solutions. There is an ever-increasing population of refugees and internally displaced persons due to disasters and conflicts who have a basic need for shelter. To date, housing solutions for such people has tended to focus on short-term, temporary shelter solutions that have been largely unsuccessful. This increasing demand for shelter has led to an emerging group of architects skilled in post-disaster reconstruction. These architects acknowledge that shelter is critical to survival, but believe architects should focus on rebuilding in a manner that is quick, durable but permanent. They believe that an architect skilled in post-disaster reconstruction can produce solutions that meet the requirement of the emergency phase, through to semi-permanent and even permanent homes, without wasting time and money on interim shelters. Case Study Research was used to examine and evaluate the assistance provided by Emergency Architects Australia (EAA) to the Kei Gold community in the Solomon Islands after the 2007 earthquake and tsunami. The results indicate that an architect’s response to a disaster must go beyond providing temporary shelter; they must create permanent building solutions that respond to the site and the culture while servicing the needs of the communi- ty. The vernacular reconstruction methods implemented by EAA in Kei Gold Village have been successful in develop- ing permanent housing solutions. Further research and development is required to gain a broader understanding of the role of the architect in disasters of varying scales and typologies.

Component modeling for SCADA network mapping

Supervisory Control and Data Acquisition systems (SCADA) are widely used to control critical infrastructure automatically. Capturing and analyzing packet-level traffic flowing through such a network is an essential requirement for problems such as legacy network mapping and fault detection. Within the framework of captured network traffic, we present a simple modeling technique, which supports the mapping of the SCADA network topology via traffic monitoring. By characterizing atomic network components in terms of their input-output topology and the relationship between their data traffic logs, we show that these modeling primitives have good compositional behaviour, which allows complex networks to be modeled. Finally, the predictions generated by our model are found to be in good agreement with experimentally obtained traffic.

Ethical values in emergency medical services: A pilot study

Background Ambulance professionals often address conflicts between ethical values. As individuals’ values represent basic convictions of what is right or good and motivate behaviour, research is needed to understand their value profiles. Objectives To translate and adapt the Managerial Values Profile to Spanish and Swedish, and measure the presence of utilitarianism, moral rights and/or social justice in ambulance professionals’ value profiles in Spain and Sweden. Methods The instrument was translated and culturally adapted. A content validity index was calculated. Pilot tests were carried out with 46 participants. Ethical considerations This study conforms to the ethical principles for research involving human subjects and adheres to national laws and regulations concerning informed consent and confidentiality. Findings Spanish professionals favoured justice and Swedish professionals’ rights in their ambulance organizations. Both countries favoured utilitarianism least. Gender differences across countries showed that males favoured rights. Spanish female professionals favoured justice most strongly of all. Discussion Swedes favour rights while Spaniards favour justice. Both contexts scored low on utilitarianism focusing on total population effect, preferring the opposite, individualized approach of the rights and justice perspectives. Organizational investment in a utilitarian perspective might jeopardize ambulance professionals’ moral right to make individual assessments based on the needs of the patient at hand. Utilitarianism and a caring ethos appear as stark opposites. However, a caring ethos in its turn might well involve unreasonable demands on the individual carer’s professional role. Since both the justice and rights perspectives portrayed in the survey mainly concern relationship to the organization and peers within the organization, this relationship might at worst be given priority over the equal treatment and moral rights of the patient. Conclusion A balanced view on ethical perspectives is needed to make professionals observant and ready to act optimally – especially if these perspectives are used in patient care. Research is needed to clarify how justice and rights are prioritized by ambulance services and whether or not these organization-related values are also implemented in patient care.

Conceptual and statistical framework for a water quality component of the integrated report card for the Great Barrier Reef catchments

This report presents the final deliverable from the project titled Conceptual and statistical framework for a water quality component of an integrated report card’ funded by the Marine and Tropical Sciences Research Facility (MTSRF; Project 3.7.7). The key management driver of this, and a number of other MTSRF projects concerned with indicator development, is the requirement for state and federal government authorities and other stakeholders to provide robust assessments of the present ‘state’ or ‘health’ of regional ecosystems in the Great Barrier Reef (GBR) catchments and adjacent marine waters. An integrated report card format, that encompasses both biophysical and socioeconomic factors, is an appropriate framework through which to deliver these assessments and meet a variety of reporting requirements. It is now well recognised that a ‘report card’ format for environmental reporting is very effective for community and stakeholder communication and engagement, and can be a key driver in galvanising community and political commitment and action. Although a report card it needs to be understandable by all levels of the community, it also needs to be underpinned by sound, quality-assured science. In this regard this project was to develop approaches to address the statistical issues that arise from amalgamation or integration of sets of discrete indicators into a final score or assessment of the state of the system. In brief, the two main issues are (1) selecting, measuring and interpreting specific indicators that vary both in space and time, and (2) integrating a range of indicators in such a way as to provide a succinct but robust overview of the state of the system. Although there is considerable research and knowledge of the use of indicators to inform the management of ecological, social and economic systems, methods on how to best to integrate multiple disparate indicators remain poorly developed. Therefore the objective of this project was to (i) focus on statistical approaches aimed at ensuring that estimates of individual indicators are as robust as possible, and (ii) present methods that can be used to report on the overall state of the system by integrating estimates of individual indicators. It was agreed at the outset, that this project was to focus on developing methods for a water quality report card. This was driven largely by the requirements of Reef Water Quality Protection Plan (RWQPP) and led to strong partner engagement with the Reef Water Quality Partnership.

Profiling : an application assignment approach for green data centers

In the past few years, there has been a steady increase in the attention, importance and focus of green initiatives related to data centers. While various energy aware measures have been developed for data centers, the requirement of improving the performance efficiency of application assignment at the same time has yet to be fulfilled. For instance, many energy aware measures applied to data centers maintain a trade-off between energy consumption and Quality of Service (QoS). To address this problem, this paper presents a novel concept of profiling to facilitate offline optimization for a deterministic application assignment to virtual machines. Then, a profile-based model is established for obtaining near-optimal allocations of applications to virtual machines with consideration of three major objectives: energy cost, CPU utilization efficiency and application completion time. From this model, a profile-based and scalable matching algorithm is developed to solve the profile-based model. The assignment efficiency of our algorithm is then compared with that of the Hungarian algorithm, which does not scale well though giving the optimal solution.

A transcriptome resource for the koala (Phascolarctos cinereus) : insights into koala retrovirus transcription and sequence diversity

Background The koala, Phascolarctos cinereus, is a biologically unique and evolutionarily distinct Australian arboreal marsupial. The goal of this study was to sequence the transcriptome from several tissues of two geographically separate koalas, and to create the first comprehensive catalog of annotated transcripts for this species, enabling detailed analysis of the unique attributes of this threatened native marsupial, including infection by the koala retrovirus. Results RNA-Seq data was generated from a range of tissues from one male and one female koala and assembled de novo into transcripts using Velvet-Oases. Transcript abundance in each tissue was estimated. Transcripts were searched for likely protein-coding regions and a non-redundant set of 117,563 putative protein sequences was produced. In similarity searches there were 84,907 (72%) sequences that aligned to at least one sequence in the NCBI nr protein database. The best alignments were to sequences from other marsupials. After applying a reciprocal best hit requirement of koala sequences to those from tammar wallaby, Tasmanian devil and the gray short-tailed opossum, we estimate that our transcriptome dataset represents approximately 15,000 koala genes. The marsupial alignment information was used to look for potential gene duplications and we report evidence for copy number expansion of the alpha amylase gene, and of an aldehyde reductase gene. Koala retrovirus (KoRV) transcripts were detected in the transcriptomes. These were analysed in detail and the structure of the spliced envelope gene transcript was determined. There was appreciable sequence diversity within KoRV, with 233 sites in the KoRV genome showing small insertions/deletions or single nucleotide polymorphisms. Both koalas had sequences from the KoRV-A subtype, but the male koala transcriptome has, in addition, sequences more closely related to the KoRV-B subtype. This is the first report of a KoRV-B-like sequence in a wild population. Conclusions This transcriptomic dataset is a useful resource for molecular genetic studies of the koala, for evolutionary genetic studies of marsupials, for validation and annotation of the koala genome sequence, and for investigation of koala retrovirus. Annotated transcripts can be browsed and queried at http://koalagenome.org

Lighting invariant urban street classification

In this paper we propose the hybrid use of illuminant invariant and RGB images to perform image classification of urban scenes despite challenging variation in lighting conditions. Coping with lighting change (and the shadows thereby invoked) is a non-negotiable requirement for long term autonomy using vision. One aspect of this is the ability to reliably classify scene components in the presence of marked and often sudden changes in lighting. This is the focus of this paper. Posed with the task of classifying all parts in a scene from a full colour image, we propose that lighting invariant transforms can reduce the variability of the scene, resulting in a more reliable classification. We leverage the ideas of “data transfer” for classification, beginning with full colour images for obtaining candidate scene-level matches using global image descriptors. This is commonly followed by superpixellevel matching with local features. However, we show that if the RGB images are subjected to an illuminant invariant transform before computing the superpixel-level features, classification is significantly more robust to scene illumination effects. The approach is evaluated using three datasets. The first being our own dataset and the second being the KITTI dataset using manually generated ground truth for quantitative analysis. We qualitatively evaluate the method on a third custom dataset over a 750m trajectory.

Submission to the Attorney-General's Department consultation on "Marrakesh Treaty options for implementation" discussion paper

It is extremely important to ensure that people with disabilities can access information and cultural works on an equal basis with others. Access is fundamentally important to enable people with disabilities to fully participate in economic, social, and political life. This is both a pressing moral imperative and a legal requirement in international law. Australia should take clear steps to affirmatively redress the fundamental inequalities of access that people with disabilities face. This requires a fundamental shift in the way that we think about copyright and disability rights: the mechanisms for enabling access should not be a limited exception to normal distribution, but should instead be strong positive rights that are able to be routinely and practically exercised.

FluMum : a prospective cohort study of mother-infant pairs assessing the effectiveness of maternal influenza vaccination in prevention of influenza in early infancy

INTRODUCTION Influenza vaccination in pregnancy is recommended for all women in Australia, particularly those who will be in their second or third trimester during the influenza season. However, there has been no systematic monitoring of influenza vaccine uptake among pregnant women in Australia. Evidence is emerging of benefit to the infant with respect to preventing influenza infection in the first 6 months of life. The FluMum study aims to systematically monitor influenza vaccine uptake during pregnancy in Australia and determine the effectiveness of maternal vaccination in preventing laboratory-confirmed influenza in their offspring up to 6 months of age. METHODS AND ANALYSIS A prospective cohort study of 10 106 mother-infant pairs recruited between 38 weeks gestation and 55 days postdelivery in six Australian capital cities. Detailed maternal and infant information is collected at enrolment, including influenza illness and vaccination history with a follow-up data collection time point at infant age 6 months. The primary outcome is laboratory-confirmed influenza in the infant. Case ascertainment occurs through searches of Australian notifiable diseases data sets once the infant turns 6 months of age (with parental consent). The primary analysis involves calculating vaccine effectiveness against laboratory-confirmed influenza by comparing the incidence of influenza in infants of vaccinated mothers to the incidence in infants of unvaccinated mothers. Secondary analyses include annual and pooled estimates of the proportion of mothers vaccinated during pregnancy, the effectiveness of maternal vaccination in preventing hospitalisation for acute respiratory illness and modelling to assess the determinants of vaccination. ETHICS AND DISSEMINATION The study was approved by all institutional Human Research Ethics Committees responsible for participating sites. Study findings will be published in peer review journals and presented at national and international conferences. TRIAL REGISTRATION NUMBER The study is registered with the Australia and New Zealand Clinical Trials Registry (ANZCTR) number: 12612000175875.