NEU-MODEL : a multi-level object-oriented dynamic emulation laboratory

Computational neuroscience aims to elucidate the mechanisms of neural information processing and population dynamics, through a methodology of incorporating biological data into complex mathematical models. Existing simulation environments model at a particular level of detail; none allow a multi-level approach to neural modelling. Moreover, most are not engineered to produce compute-efficient solutions, an important issue because sufficient processing power is a major impediment in the field. This project aims to apply modern software engineering techniques to create a flexible high performance neural modelling environment, which will allow rigorous exploration of model parameter effects, and modelling at multiple levels of abstraction.

Implicating animals: The symbolic power of scapegoating animals in marine pollution debates

Animals are often used as symbols in policy debates and media accounts of marine pollution. Images of miserable oil-soaked marine birds and mammals are prominent following high profile oil spills such as the Exxon Valdez, Prestige and Pacific Adventurer incidents. Portrayed as hapless victims, these animal actors are not only cast as powerful symbols of the effects of anthropogenic pollution but also represent an environment in crisis. Animals, like the broader environment, are seen as something which is acted upon. Less attention has been given to the ways in which animals have been cast as either the cause of marine pollution or as having the potential to actively mitigate the potential impacts of anthropogenic marine pollution. This article explores how animals are constructed with respect to vessel-sourced sewage pollution. Through a process of interpretive policy analysis, drawing on media reports and responses to an Australian regulatory review process this study found that, when defending the perceived right to pollute recreational boaters implicated animals such as dogs, fish, turtles, dolphins and seabirds in their pollution discourses. Scapegoating was an important rhetorical feature of claims-making strategies designed to avoid responsibility for changing sewage disposal practices.

Structural complexity in structural health monitoring: Design of laboratory model and test plan

Many researchers in the field of civil structural health monitoring (SHM) have developed and tested their methods on simple to moderately complex laboratory structures such as beams, plates, frames, and trusses. Fieldwork has also been conducted by many researchers and practitioners on more complex operating bridges. Most laboratory structures do not adequately replicate the complexity of truss bridges. Informed by a brief review of the literature, this paper documents the design and proposed test plan of a structurally complex laboratory bridge model that has been specifically designed for the purpose of SHM research. Preliminary results have been presented in the companion paper.

Limitations of a laboratory scale model in predicting optimal pilot scale conditions for dilute acid pretreatment of sugarcane bagasse

Pilot and industrial scale dilute acid pretreatment data can be difficult to obtain due to the significant infrastructure investment required. Consequently, models of dilute acid pretreatment by necessity use laboratory scale data to determine kinetic parameters and make predictions about optimal pretreatment conditions at larger scales. In order for these recommendations to be meaningful, the ability of laboratory scale models to predict pilot and industrial scale yields must be investigated. A mathematical model of the dilute acid pretreatment of sugarcane bagasse has previously been developed by the authors. This model was able to successfully reproduce the experimental yields of xylose and short chain xylooligomers obtained at the laboratory scale. In this paper, the ability of the model to reproduce pilot scale yield and composition data is examined. It was found that in general the model over predicted the pilot scale reactor yields by a significant margin. Models that appear very promising at the laboratory scale may have limitations when predicting yields on a pilot or industrial scale. It is difficult to comment whether there are any consistent trends in optimal operating conditions between reactor scale and laboratory scale hydrolysis due to the limited reactor datasets available. Further investigation is needed to determine whether the model has some efficacy when the kinetic parameters are re-evaluated by parameter fitting to reactor scale data, however, this requires the compilation of larger datasets. Alternatively, laboratory scale mathematical models may have enhanced utility for predicting larger scale reactor performance if bulk mass transport and fluid flow considerations are incorporated into the fibre scale equations. This work reinforces the need for appropriate attention to be paid to pilot scale experimental development when moving from laboratory to pilot and industrial scales for new technologies.

The pet factor - Companion animals as a conduit for getting to know people, friendship formation and social support

BACKGROUND: While companion animals have been previously identified as a direct source of companionship and support to their owners, their role as a catalyst for friendship formation or social support networks among humans has received little attention. This study investigated the indirect role of pets as facilitators for three dimensions of social relatedness; getting to know people, friendship formation and social support networks. METHODS: A telephone survey of randomly selected residents in four cities, one in Australia (Perth; n = 704) and three in the U.S. (San Diego, n = 690; Portland, n = 634; Nashville, n = 664) was conducted. All participants were asked about getting to know people within their neighborhood. Pet owners were asked additional questions about the type/s of pet/s they owned, whether they had formed friendships as a result of their pet, and if they had received any of four different types of social support from the people they met through their pet. RESULTS: Pet owners were significantly more likely to get to know people in their neighborhood than non-pet owners (OR 1.61; 95%CI: 1.30, 1.99). When analyzed by site, this relationship was significant for Perth, San Diego and Nashville. Among pet owners, dog owners in the three U.S. cities (but not Perth) were significantly more likely than owners of other types of pets to regard people whom they met through their pet as a friend (OR 2.59; 95%CI: 1.94, 3.46). Around 40% of pet owners reported receiving one or more types of social support (i.e. emotional, informational, appraisal, instrumental) via people they met through their pet. CONCLUSION: This research suggests companion animals can be a catalyst for several dimensions of human social relationships in neighborhood settings, ranging from incidental social interaction and getting to know people, through to formation of new friendships. For many pet owners, their pets also facilitated relationships from which they derived tangible forms of social support, both of a practical and emotionally supportive nature. Given growing evidence for social isolation as a risk factor for mental health, and, conversely, friendships and social support as protective factors for individual and community well-being, pets may be an important factor in developing healthy neighborhoods.

A laboratory assessment of the choice of vessel size under individual transferable quota regimes

This paper examines the effect of individual transferable quota regimes on technology choice, such as choice of vessel size, by using the laboratory experiment method. We find that even if vessel sizes change over time, the quota price can converge to the fundamental value conditioned on the vessels chosen. We also find that subjects choose their vessel type to maximise their profits based on the quota trading prices in the previous period. This result implies that the efficiency of quota markets in the beginning period is important because any inefficiency in quota markets may affect vessel sizes in ensuing periods. Moreover, we find that the initial allocations may significantly influence vessel sizes through two channels: first, a higher initial allocation to a subject increases the likelihood that the subject invests in a large-sized vessel; second, the quota price may be higher and more unstable under unequal allocation than under equal allocation; thus, whether the allocation is equal influences subjects' choice of vessel type. © 2014 Australian Agricultural and Resource Economics Society Inc.

Inadvertent hypothermia after procedural sedation and analgesia in a cardiac catheterisation laboratory: A prospective observational study

Objective To identify the prevalence of and risk factors for inadvertent hypothermia after procedures performed with procedural sedation and analgesia in a cardiac catheterisation laboratory. Design Single-centre, prospective observational study. Setting Tertiary care private hospital in Australia. Participants A convenience sample of 399 patients undergoing elective procedures with procedural sedation and analgesia were included. Propofol infusions were used when an anaesthetist was present. Otherwise, bolus doses of either midazolam or fentanyl or a combination of these medications was used. Interventions None Measurements and main results Hypothermia was defined as a temperature <36.0° Celsius. Multivariate logistic regression was used to identify risk factors. Hypothermia was present after 23.3% (n=93; 95% confidence interval [CI] 19.2%-27.4%) of 399 procedures. Sedative regimens with the highest prevalence of hypothermia were any regimen that included propofol (n=35; 40.2%; 95% CI 29.9%-50.5%) and the use of fentanyl combined with midazolam (n=23; 20.3%; 95% CI 12.9%-27.7%). Difference in mean temperature from pre to post-procedure was -0.27°C (Standard deviation [SD] 0.45). Receiving propofol (odds ratio [OR] OR 4.6 95% CI 2.5-8.6), percutaneous coronary intervention (OR 3.2 95% CI 1.7-5.9), body mass index <25 (OR 2.5 95% CI 1.4-4.4) and being hypothermic prior to the procedure (OR 4.9; 95% CI 2.3-10.8) were independent predictors of post-procedural hypothermia. Conclusions A moderate prevalence of hypothermia was observed. The small absolute change in temperature observed may not be a clinically important amount. More research is needed to increase confidence in our estimates of hypothermia in sedated patients and its impact on clinical outcomes.

Peptide-functionalized polymeric nanoparticles for active targeting of damaged tissue in animals with experimental autoimmune encephalomyelitis

Increased permeability of blood vessels is an indicator for various injuries and diseases, including multiple sclerosis (MS), of the central nervous system. Nanoparticles have the potential to deliver drugs locally to sites of tissue damage, reducing the drug administered and limiting associated side effects, but efficient accumulation still remains a challenge. We developed peptide-functionalized polymeric nanoparticles to target blood clots and the extracellular matrix molecule nidogen, which are associated with areas of tissue damage. Using the induction of experimental autoimmune encephalomyelitis in rats to provide a model of MS associated with tissue damage and blood vessel lesions, all targeted nanoparticles were delivered systemically. In vivo data demonstrates enhanced accumulation of peptide functionalized nanoparticles at the injury site compared to scrambled and naive controls, particularly for nanoparticles functionalized to target fibrin clots. This suggests that further investigations with drug laden, peptide functionalized nanoparticles might be of particular interest in the development of treatment strategies for MS.

Structural identification of a laboratory-based steel through truss cantilevered bridge with suspended span using a layered genetic algorithm with patternsearch step (GAPS)

Structural identification (St-Id) can be considered as the process of updating a finite element (FE) model of a structural system to match the measured response of the structure. This paper presents the St-Id of a laboratory-based steel through-truss cantilevered bridge with suspended span. There are a total of 600 degrees of freedom (DOFs) in the superstructure plus additional DOFs in the substructure. The St-Id of the bridge model used the modal parameters from a preliminary modal test in the objective function of a global optimisation technique using a layered genetic algorithm with patternsearch step (GAPS). Each layer of the St-Id process involved grouping of the structural parameters into a number of updating parameters and running parallel optimisations. The number of updating parameters was increased at each layer of the process. In order to accelerate the optimisation and ensure improved diversity within the population, a patternsearch step was applied to the fittest individuals at the end of each generation of the GA. The GAPS process was able to replicate the mode shapes for the first two lateral sway modes and the first vertical bending mode to a high degree of accuracy and, to a lesser degree, the mode shape of the first lateral bending mode. The mode shape and frequency of the torsional mode did not match very well. The frequencies of the first lateral bending mode, the first longitudinal mode and the first vertical mode matched very well. The frequency of the first sway mode was lower and that of the second sway mode was higher than the true values, indicating a possible problem with the FE model. Improvements to the model and the St-Id process will be presented at the upcoming conference and compared to the results presented in this paper. These improvements will include the use of multiple FE models in a multi-layered, multi-solution, GAPS St-Id approach.

A novel 15N tracer approach for the quantification of N2 and N2O emissions from soil incubations in a completely automated laboratory set up

The microbial mediated production of nitrous oxide (N2O) and its reduction to dinitrogen (N2) via denitrification represents a loss of nitrogen (N) from fertilised agro-ecosystems to the atmosphere. Although denitrification has received great interest by biogeochemists in the last decades, the magnitude of N2lossesand related N2:N2O ratios from soils still are largely unknown due to methodical constraints. We present a novel 15N tracer approach, based on a previous developed tracer method to study denitrification in pure bacterial cultures which was modified for the use on soil incubations in a completely automated laboratory set up. The method uses a background air in the incubation vessels that is replaced with a helium-oxygen gas mixture with a 50-fold reduced N2 background (2 % v/v). This method allows for a direct and sensitive quantification of the N2 and N2O emissions from the soil with isotope-ratio mass spectrometry after 15N labelling of denitrification N substrates and minimises the sensitivity to the intrusion of atmospheric N2 at the same time. The incubation set up was used to determine the influence of different soil moisture levels on N2 and N2O emissions from a sub-tropical pasture soil in Queensland/Australia. The soil was labelled with an equivalent of 50 μg-N per gram dry soil by broadcast application of KNO3solution (4 at.% 15N) and incubated for 3 days at 80% and 100% water filled pore space (WFPS), respectively. The headspace of the incubation vessel was sampled automatically over 12hrs each day and 3 samples (0, 6, and 12 hrs after incubation start) of headspace gas analysed for N2 and N2O with an isotope-ratio mass spectrometer (DELTA V Plus, Thermo Fisher Scientific, Bremen, Germany(. In addition, the soil was analysed for 15N NO3- and NH4+ using the 15N diffusion method, which enabled us to obtain a complete N balance. The method proved to be highly sensitive for N2 and N2O emissions detecting N2O emissions ranging from 20 to 627 μN kg-1soil-1hr-1and N2 emissions ranging from 4.2 to 43 μN kg-1soil-1hr-1for the different treatments. The main end-product of denitrification was N2O for both water contents with N2 accounting for 9% and 13% of the total denitrification losses at 80% and 100%WFPS, respectively. Between 95-100% of the added 15N fertiliser could be recovered. Gross nitrification over the 3 days amounted to 8.6 μN g-1 soil-1 and 4.7 μN g-1 soil-1, denitrification to 4.1 μN g-1 soil-1 and 11.8 μN g-1 soil-1at 80% and 100%WFPS, respectively. The results confirm that the tested method allows for a direct and highly sensitive detection of N2 and N2O fluxes from soils and hence offers a sensitive tool to study denitrification and N turnover in terrestrial agro-ecosystems.

Priority threat management of invasive animals to protect biodiversity under climate change

Climate change is a major threat to global biodiversity, and its impacts can act synergistically to heighten the severity of other threats. Most research on projecting species range shifts under climate change has not been translated to informing priority management strategies on the ground. We develop a prioritization framework to assess strategies for managing threats to biodiversity under climate change and apply it to the management of invasive animal species across one-sixth of the Australian continent, the Lake Eyre Basin. We collected information from key stakeholders and experts on the impacts of invasive animals on 148 of the region's most threatened species and 11 potential strategies. Assisted by models of current distributions of threatened species and their projected distributions, experts estimated the cost, feasibility, and potential benefits of each strategy for improving the persistence of threatened species with and without climate change. We discover that the relative cost-effectiveness of invasive animal control strategies is robust to climate change, with the management of feral pigs being the highest priority for conserving threatened species overall. Complementary sets of strategies to protect as many threatened species as possible under limited budgets change when climate change is considered, with additional strategies required to avoid impending extinctions from the region. Overall, we find that the ranking of strategies by cost-effectiveness was relatively unaffected by including climate change into decision-making, even though the benefits of the strategies were lower. Future climate conditions and impacts on range shifts become most important to consider when designing comprehensive management plans for the control of invasive animals under limited budgets to maximize the number of threatened species that can be protected.

Investigating sea level rise due to global warming in the teaching laboratory using Archimedes’ principle

A teaching laboratory experiment is described that uses Archimedes’ principle to precisely investigate the effect of global warming on the oceans. A large component of sea level rise is due to the increase in the volume of water due to the decrease in water density with increasing temperature. Water close to 0 °C is placed in a beaker and a glass marble hung from an electronic balance immersed in the water. As the water warms, the weight of the marble increases as the water is less buoyant due to the decrease in density. In the experiment performed in this paper a balance with a precision of 0.1 mg was used with a marble 40.0 cm3 and mass of 99.3 g, yielding water density measurements with an average error of -0.008 ± 0.011%.

A rapid and efficient two-step gel electrophoresis method for the purification of major rye grass pollen allergens

Purified proteins are mandatory for molecular, immunological and cellular studies. However, purification of proteins from complex mixtures requires specialised chromatography methods (i.e., gel filtration, ion exchange, etc.) using fast protein liquid chromatography (FPLC) or high-performance liquid chromatography (HPLC) systems. Such systems are expensive and certain proteins require two or more different steps for sufficient purity and generally result in low recovery. The aim of this study was to develop a rapid, inexpensive and efficient gel-electrophoresis-based protein purification method using basic and readily available laboratory equipment. We have used crude rye grass pollen extract to purify the major allergens Lol p 1 and Lol p 5 as the model protein candidates. Total proteins were resolved on large primary gel and Coomassie Brilliant Blue (CBB)-stained Lol p 1/5 allergens were excised and purified on a secondary "mini"-gel. Purified proteins were extracted from unstained separating gels and subjected to sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and immunoblot analyses. Silver-stained SDS-PAGE gels resolved pure proteins (i.e., 875 μg of Lol p 1 recovered from a 8 mg crude starting material) while immunoblot analysis confirmed immunological reactivity of the purified proteins. Such a purification method is rapid, inexpensive, and efficient in generating proteins of sufficient purity for use in monoclonal antibody (mAb) production, protein sequencing and general molecular, immunological, and cellular studies.

Towards the pathogenesis of autoimmune liver disease

There have been recent improvements in the clinical understanding and definition of the major types of autoimmune liver disease. However, still lacking is knowledge of their prevalence and pathogenesis. Three areas of study are in progress in our laboratory. First, in type 1 autoimmune hepatitis, the search continues to identify a liver/disease-specific autoantigenic reactant. Using hepatocyte membrane preparations, immunoblotting has underlined the problem of distinguishing, among multiple reactants, those that may be causally rather than consequentially related to hepatocellular damage. Second, in primary biliary cirrhosis (PBC), the need for population screening to ascertain prevalence and detect preclinical cases can be met by a rapid automated procedure for detection, by specific enzyme inhibition in microtitre wells, of antibody (anti-M2) to the pyruvate dehydrogenase complex E2 subunit (PDC-E2). Third, the structure of the conformational epitope within the inner lipoyl domain of PDC-E2 is being investigated by screening random phage-displayed peptide libraries using PBC sera. This has yielded phage clones in which the sequence of the peptide insert portrays the structure of this epitope, as judged by clustering of PBC-derived sequences to particular branches of a guide-tree that shows relatedness of peptides, and by reactivity of selected phage clones with anti-PDC-E2. Thus phage display identifies a peptide 'mimotope' of the antibody epitope in the inner lipoyl domain of PDC-E2.

Mimicry of 21. 5 KDa myelin basic protein peptide by a Maedi Visna virus polymerase peptide does not contribute to the pathogenesis of encephalitis in sheep

Epitope mimicry is the theory that an infectious agent such as a virus causes pathological effects via mimicry of host proteins and thus elicits a cross-reactive immune response to host tissues. Weise and Carnegie (1988) found a region of sequence similarity between the pol gene of the Maedi Visna virus (MVV), which induces demyelinating encephalitis in sheep, and myelin basic protein (MBP), which is known to induce experimental allergic encephalitis (EAE) in laboratory animals. In this study, cross-reactions between sera raised in sheep against synthetic peptides of MVV (TGKIPWILLPGR) and 21.5 kDa MBP (SGKVPWLKRPGR) were demonstrated using enzyme-linked immunosorbant assay (ELISA) and thin layer chromatography (TLC) immunoprobing. The antibody responses of MVV-infected sheep were investigated using ELISA against the peptides, and MBP protein, immunoprobing of the peptides on TPC plates and Western blotting against MBP. Slight significant reactions to the 21.5 kDa MBP peptide (P < 0.001) and to a lesser extent sheep MBP (P < 0.004) were detected in ELISA. The MBP peptide evoked stronger responses from more sera than the MVV peptide on immunoprobed TLC plates. On the Western blots, eight of the 23 sheep with Visna had serum reactivity to MBP. This slight reaction to MBP in MVV-infected sheep is of interest because of the immune responses to MBP evident in multiple sclerosis and EAE, but its relevance in Visna is limited since no correlation with disease severity was observed. The cell-mediated immune responses of MVV-infected sheep against similar peptides was assessed. The peptides did not stimulate proliferation of peripheral blood lymphocytes of MVV-infected sheep. Since the MVV peptide was not recognised by antibodies or T lymphocytes from MVV-infected and encephalic sheep, it was concluded that epitope mimicry of this 21.5 kDa MBP peptide by the similar MVV pol peptide was not contributing to the immunopathogenesis of Visna. The slight antibody response to MBP and the MBP peptide can be attributed to by-stander effects of the immunopathology of MVV-induced encephalitis.