Modeling ion channel dynamics through reflected stochastic differential equations

Ion channels are membrane proteins that open and close at random and play a vital role in the electrical dynamics of excitable cells. The stochastic nature of the conformational changes these proteins undergo can be significant, however current stochastic modeling methodologies limit the ability to study such systems. Discrete-state Markov chain models are seen as the "gold standard," but are computationally intensive, restricting investigation of stochastic effects to the single-cell level. Continuous stochastic methods that use stochastic differential equations (SDEs) to model the system are more efficient but can lead to simulations that have no biological meaning. In this paper we show that modeling the behavior of ion channel dynamics by a reflected SDE ensures biologically realistic simulations, and we argue that this model follows from the continuous approximation of the discrete-state Markov chain model. Open channel and action potential statistics from simulations of ion channel dynamics using the reflected SDE are compared with those of a discrete-state Markov chain method. Results show that the reflected SDE simulations are in good agreement with the discrete-state approach. The reflected SDE model therefore provides a computationally efficient method to simulate ion channel dynamics while preserving the distributional properties of the discrete-state Markov chain model and also ensuring biologically realistic solutions. This framework could easily be extended to other biochemical reaction networks. © 2012 American Physical Society.

Microcosm study of ion mobilization and greenhouse gas evolution in soils of a plantation-forested subtropical coastal catchment

This study examined the potential for Fe mobilization and greenhouse gas (GHG, e.g. CO2, and CH4) evolution in SEQ soils associated with a range of plantation forestry practices and water-logged conditions. Intact, 30-cm-deep soil cores collected from representative sites were saturated and incubated for 35 days in the laboratory, with leachate and headspace gas samples periodically collected. Minimal Fe dissolution was observed in well-drained sand soils associated with mature, first-rotation Pinus and organic Fe complexation, whereas progressive Fe dissolution occurred over 14 days in clear-felled and replanted Pinus soils with low organic matter and non-crystalline Fe fractions. Both CO2 and CH4 effluxes were relatively lower in clear-felled and replanted soils compared with mature, first-rotation Pinus soils, despite the lack of statistically significant variations in total GHG effluxes associated with different forestry practices. Fe dissolution and GHG evolution in low-lying, water-logged soils adjacent to riparian and estuarine, native-vegetation buffer zones were impacted by mineral and physical soil properties. Highest levels of dissolved Fe and GHG effluxes resulted from saturation of riparian loam soils with high Fe and clay content, as well as abundant organic material and Fe-metabolizing bacteria. Results indicate Pinus forestry practices such as clear-felling and replanting may elevate Fe mobilization while decreasing CO2 and CH4 emissions from well-drained, SEQ plantation soils upon heavy flooding. Prolonged water-logging accelerates bacterially mediated Fe cycling in low-lying, clay-rich soils, leading to substantial Fe dissolution, organic matter mineralization, and CH4 production in riparian native-vegetation buffer zones.

Children physical activity correlates and parent physical activity do not have a strong association with physical activity amongst adolescents

Background: Physical activity is a key modifiable behavior impacting a number of important health outcomes. The path to developing chronic diseases commonly commences with lifestyle patterns developed during childhood and adolescence. This study examined whether parent physical activity and other factors correlated with physical activity amongst children are associated with self-reported physical activity in adolescents. Methods: A total of 115 adolescents (aged 12-14) and their parents completed questionnaire assessments. Self-reported physical activity was measured amongst adolescents and their parents using the International Physical Activity Questionnaire for Adolescents (IPAQ-A), and the International Physical Activity Questionnaire (IPAQ) respectively. Adolescents also completed the Children’s Physical Activity Correlates (CPAC), which measured factors that have previously demonstrated association with physical activity amongst children. To examine whether parent physical activity or items from the CPAC were associated with self-reported adolescent physical activity, backward step-wise regression was undertaken. One item was removed at each step in descending order of significance (until two tailed item alpha=0.05 was achieved). Results: A total of 93 (80.9%) adolescents and their parents had complete data sets and were included in the analysis. Independent variables were removed in the order: perceptions of parental role modeling; importance of exercise; perceptions of parental encouragement; peer acceptance; fun of physical exertion; perceived competence; parent physical activity; self-esteem; liking of exercise; and parental influence. The only variable remaining in the model was ‘liking of games and sport’ (p=0.003, adjusted r-squared=0.085). Discussion: These findings indicate that factors associated with self-reported physical activity in adolescents are not necessarily the same as younger children (aged 8-11). While ‘liking of games and sport’ was included in the final model, the r-squared value did not indicate a strong association. Interestingly, parent self-reported physical activity was not included in the final model. It is likely that adolescent physical activity may be influenced by a variety of direct and indirect forms of socialization. These findings do support the view that intrinsically motivated themes such as the liking of games and sport take precedence over outside influences, like those presented by parents, in determining youth physical activity behaviors. These findings do not suggest that parents have no influence on adolescent physical activity patterns, but rather, the influence is likely to be more complex than physical activity behavior modeling perceived by the adolescent. Further research in this field is warranted in order to better understand potential contributors to successful physical activity promotion interventions amongst young adolescents.

The experiences of learner drivers, provisional drivers and supervisors with graduated driver licensing in two Australian jurisdictions

Newly licensed drivers on a provisional or intermediate licence have the highest crash risk when compared with any other group of drivers. In comparison, learner drivers have the lowest crash risk. Graduated driver licensing is one countermeasure that has been demonstrated to effectively reduce the crashes of novice drivers. This thesis examined the graduated driver licensing systems in two Australian states in order to better understand the behaviour of learner drivers, provisional drivers and the supervisors of learner drivers. By doing this, the thesis investigated the personal, social and environmental influences on novice driver behaviour as well as providing effective baseline data against which to measure subsequent changes to the licensing systems. In the first study, conducted prior to the changes to the graduated driver licensing system introduced in mid-2007, drivers who had recently obtained their provisional licence in Queensland and New South Wales were interviewed by telephone regarding their experiences while driving on their learner licence. Of the 687 eligible people approached to participate at driver licensing centres, 392 completed the study representing a response rate of 57.1 per cent. At the time the data was collected, New South Wales represented a more extensive graduated driver licensing system when compared with Queensland. The results suggested that requiring learners to complete a mandated number of hours of supervised practice impacts on the amount of hours that learners report completing. While most learners from New South Wales reported meeting the requirement to complete 50 hours of practice, it appears that many stopped practising soon after this goal was achieved. In contrast, learners from Queensland, who were not required to complete a specific number of hours at the time of the survey, tended to fall into three groups. The first group appeared to complete the minimum number of hours required to pass the test (less than 26 hours), the second group completed 26 to 50 hours of supervised practice while the third group completed significantly more practice than the first two groups (over 100 hours of supervised practice). Learner drivers in both states reported generally complying with the road laws and were unlikely to report that they had been caught breaking the road rules. They also indicated that they planned to obey the road laws once they obtained their provisional licence. However, they were less likely to intend to comply with recommended actions to reduce crash risk such as limiting their driving at night. This study also identified that there were relatively low levels of unaccompanied driving (approximately 15 per cent of the sample), very few driving offences committed (five per cent of the sample) and that learner drivers tended to use a mix of private and professional supervisors (although the majority of practice is undertaken with private supervisors). Consistent with the international literature, this study identified that very few learner drivers had experienced a crash (six per cent) while on their learner licence. The second study was also conducted prior to changes to the graduated driver licensing system and involved follow up interviews with the participants of the first study after they had approximately 21 months driving experience on their provisional licence. Of the 392 participants that completed the first study, 233 participants completed the second interview (representing a response rate of 59.4 per cent). As with the first study, at the time the data was collected, New South Wales had a more extensive graduated driver licensing system than Queensland. For instance, novice drivers from New South Wales were required to progress through two provisional licence phases (P1 and P2) while there was only one provisional licence phase in Queensland. Among the participants in this second study, almost all provisional drivers (97.9 per cent) owned or had access to a vehicle for regular driving. They reported that they were unlikely to break road rules, such as driving after a couple of drinks, but were also unlikely to comply with recommended actions, such as limiting their driving at night. When their provisional driving behaviour was compared to the stated intentions from the first study, the results suggested that their intentions were not a strong predictor of their subsequent behaviour. Their perception of risk associated with driving declined from when they first obtained their learner licence to when they had acquired provisional driving experience. Just over 25 per cent of participants in study two reported that they had been caught committing driving offences while on their provisional licence. Nearly one-third of participants had crashed while driving on a provisional licence, although few of these crashes resulted in injuries or hospitalisations. To complement the first two studies, the third study examined the experiences of supervisors of learner drivers, as well as their perceptions of their learner’s experiences. This study was undertaken after the introduction of the new graduated driver licensing systems in Queensland and New South Wales in mid- 2007, providing insights into the impacts of these changes from the perspective of supervisors. The third study involved an internet survey of 552 supervisors of learner drivers. Within the sample, approximately 50 per cent of participants supervised their own child. Other supervisors of the learner drivers included other parents or stepparents, professional driving instructors and siblings. For two-thirds of the sample, this was the first learner driver that they had supervised. Participants had provided an average of 54.82 hours (sd = 67.19) of supervision. Seventy-three per cent of participants indicated that their learners’ logbooks were accurate or very accurate in most cases, although parents were more likely than non-parents to report that their learners’ logbook was accurate (F (1,546) = 7.74, p = .006). There was no difference between parents and non-parents regarding whether they believed the log book system was effective (F (1,546) = .01, p = .913). The majority of the sample reported that their learner driver had had some professional driving lessons. Notwithstanding this, a significant proportion (72.5 per cent) believed that parents should be either very involved or involved in teaching their child to drive, with parents being more likely than non-parents to hold this belief. In the post mid-2007 graduated driver licensing system, Queensland learner drivers are able to record three hours of supervised practice in their log book for every hour that is completed with a professional driving instructor, up to a total of ten hours. Despite this, there was no difference identified between Queensland and New South Wales participants regarding the amount of time that they reported their learners spent with professional driving instructors (X2(1) = 2.56, p = .110). Supervisors from New South Wales were more likely to ensure that their learner driver complied with the road laws. Additionally, with the exception of drug driving laws, New South Wales supervisors believed it was more important to teach safety-related behaviours such as remaining within the speed limit, car control and hazard perception than those from Queensland. This may be indicative of more intensive road safety educational efforts in New South Wales or the longer time that graduated driver licensing has operated in that jurisdiction. However, other factors may have contributed to these findings and further research is required to explore the issue. In addition, supervisors reported that their learner driver was involved in very few crashes (3.4 per cent) and offences (2.7 per cent). This relatively low reported crash rate is similar to that identified in the first study. Most of the graduated driver licensing research to date has been applied in nature and lacked a strong theoretical foundation. These studies used Akers’ social learning theory to explore the self-reported behaviour of novice drivers and their supervisors. This theory was selected as it has previously been found to provide a relatively comprehensive framework for explaining a range of driver behaviours including novice driver behaviour. Sensation seeking was also used in the first two studies to complement the non-social rewards component of Akers’ social learning theory. This program of research identified that both Akers’ social learning theory and sensation seeking were useful in predicting the behaviour of learner and provisional drivers over and above socio-demographic factors. Within the first study, Akers’ social learning theory accounted for an additional 22 per cent of the variance in learner driver compliance with the law, over and above a range of socio-demographic factors such as age, gender and income. The two constructs within Akers’ theory which were significant predictors of learner driver compliance were the behavioural dimension of differential association relating to friends, and anticipated rewards. Sensation seeking predicted an additional six per cent of the variance in learner driver compliance with the law. When considering a learner driver’s intention to comply with the law while driving on a provisional licence, Akers’ social learning theory accounted for an additional 10 per cent of the variance above socio-demographic factors with anticipated rewards being a significant predictor. Sensation seeking predicted an additional four per cent of the variance. The results suggest that the more rewards individuals anticipate for complying with the law, the more likely they are to obey the road rules. Further research is needed to identify which specific rewards are most likely to encourage novice drivers’ compliance with the law. In the second study, Akers’ social learning theory predicted an additional 40 per cent of the variance in self-reported compliance with road rules over and above socio-demographic factors while sensation seeking accounted for an additional five per cent of the variance. A number of Aker’s social learning theory constructs significantly predicted provisional driver compliance with the law, including the behavioural dimension of differential association for friends, the normative dimension of differential association, personal attitudes and anticipated punishments. The consistent prediction of additional variance by sensation seeking over and above the variables within Akers’ social learning theory in both studies one and two suggests that sensation seeking is not fully captured within the non social rewards dimension of Akers’ social learning theory, at least for novice drivers. It appears that novice drivers are strongly influenced by the desire to engage in new and intense experiences. While socio-demographic factors and the perception of risk associated with driving had an important role in predicting the behaviour of the supervisors of learner drivers, Akers’ social learning theory provided further levels of prediction over and above these factors. The Akers’ social learning theory variables predicted an additional 14 per cent of the variance in the extent to which supervisors ensured that their learners complied with the law and an additional eight per cent of the variance in the supervisors’ provision of a range of practice experiences. The normative dimension of differential association, personal attitudes towards the use of professional driving instructors and anticipated rewards were significant predictors for supervisors ensuring that their learner complied with the road laws, while the normative dimension was important for range of practice. This suggests that supervisors who engage with other supervisors who ensure their learner complies with the road laws and provide a range of practice to their own learners are more likely to also engage in these behaviours. Within this program of research, there were several limitations including the method of recruitment of participants within the first study, the lower participation rate in the second study, an inability to calculate a response rate for study three and the use of self-report data for all three studies. Within the first study, participants were only recruited from larger driver licensing centres to ensure that there was a sufficient throughput of drivers to approach. This may have biased the results due to the possible differences in learners that obtain their licences in locations with smaller licensing centres. Only 59.4 per cent of the sample in the first study completed the second study. This may be a limitation if there was a common reason why those not participating were unable to complete the interview leading to a systematic impact on the results. The third study used a combination of a convenience and snowball sampling which meant that it was not possible to calculate a response rate. All three studies used self-report data which, in many cases, is considered a limitation. However, self-report data may be the only method that can be used to obtain some information. This program of research has a number of implications for countermeasures in both the learner licence phase and the provisional licence phase. During the learner phase, licensing authorities need to carefully consider the number of hours that they mandate learner drivers must complete before they obtain their provisional driving licence. If they mandate an insufficient number of hours, there may be inadvertent negative effects as a result of setting too low a limit. This research suggests that logbooks may be a useful tool for learners and their supervisors in recording and structuring their supervised practice. However, it would appear that the usage rates for logbooks will remain low if they remain voluntary. One strategy for achieving larger amounts of supervised practice is for learner drivers and their supervisors to make supervised practice part of their everyday activities. As well as assisting the learner driver to accumulate the required number of hours of supervised practice, it would ensure that they gain experience in the types of environments that they will probably encounter when driving unaccompanied in the future, such as to and from education or work commitments. There is also a need for policy processes to ensure that parents and professional driving instructors communicate effectively regarding the learner driver’s progress. This is required as most learners spend at least some time with a professional instructor despite receiving significant amounts of practice with a private supervisor. However, many supervisors did not discuss their learner’s progress with the driving instructor. During the provisional phase, there is a need to strengthen countermeasures to address the high crash risk of these drivers. Although many of these crashes are minor, most involve at least one other vehicle. Therefore, there are social and economic benefits to reducing these crashes. If the new, post-2007 graduated driver licensing systems do not significantly reduce crash risk, there may be a need to introduce further provisional licence restrictions such as separate night driving and peer passenger restrictions (as opposed to the hybrid version of these two restrictions operating in both Queensland and New South Wales). Provisional drivers appear to be more likely to obey some provisional licence laws, such as lower blood alcohol content limits, than others such as speed limits. Therefore, there may be a need to introduce countermeasures to encourage provisional drivers to comply with specific restrictions. When combined, these studies provided significant information regarding graduated driver licensing programs. This program of research has investigated graduated driver licensing utilising a cross-sectional and longitudinal design in order to develop our understanding of the experiences of novice drivers that progress through the system in order to help reduce crash risk once novice drivers commence driving by themselves.

A boundary preserving numerical algorithm for the Wright-Fisher model with mutation

The Wright-Fisher model is an Itô stochastic differential equation that was originally introduced to model genetic drift within finite populations and has recently been used as an approximation to ion channel dynamics within cardiac and neuronal cells. While analytic solutions to this equation remain within the interval [0,1], current numerical methods are unable to preserve such boundaries in the approximation. We present a new numerical method that guarantees approximations to a form of Wright-Fisher model, which includes mutation, remain within [0,1] for all time with probability one. Strong convergence of the method is proved and numerical experiments suggest that this new scheme converges with strong order 1/2. Extending this method to a multidimensional case, numerical tests suggest that the algorithm still converges strongly with order 1/2. Finally, numerical solutions obtained using this new method are compared to those obtained using the Euler-Maruyama method where the Wiener increment is resampled to ensure solutions remain within [0,1].

Comparison of the binding stoichiometries of positively charged DNA-binding drugs using positive and negative ion electrospray ionization mass spectrometry

Positive and negative ion electrospray ionization (ESI) mass spectra of complexes of positively charged small molecules (distamycin, Hoechst 33258, [Ru(phen)2dpq]Cl2 and [Ru(phen)2dpqC]Cl2) have been compared. [Ru(phen)2dpq]Cl2 and [Ru(phen)2dpqC]Cl2 bind to DNA by intercalation. Negative ion ESI mass spectra of mixtures of [Ru(phen)2dpq]Cl2 or [Ru(phen)2dpqC]Cl2 with DNA showed ions from DNA-ligand complexes consistent with solution studies. In contrast, only ions from freeDNAwere present in positive ion ESI mass spectra of mixtures of [Ru(phen)2dpq]Cl2 or [Ru(phen)2dpqC]Cl2 with DNA, highlighting the need for obtaining ESI mass spectra of non-covalent complexes under a range of experimental conditions. Negative ion spectra of mixtures of the minor groove binder Hoechst 33258 with DNA containing a known minor groove binding sequence were dominated by ions from a 1:1 complex. In contrast, in positive ion spectra there were also ions present from a 2:1 (Hoechst 33258: DNA) complex, suggesting an alternative binding mode was possible either in solution or in the gas phase. When Hoechst 33258 was mixed with a DNA sequence lacking a high affinity minor groove binding site, the negative ion ESI mass spectra showed that 1:1 and 2:1 complexes were formed, consistent with existence of binding modes other than minor groove binding. The data presented suggest that comparison of positive and negative ion ESI-MS spectra might provide an insight into various binding modes in both solution and the gas phase.

Illusions of Difference: Comparative Youth Justice in the Devolved UK

Surprisingly, there has been little or no systematic research to date that has explored the significance of UK devolution for youth justice policy and practice. This article explores the extent of differential justice in the United Kingdom, particularly as it is expressed in the myriad action plans, criminal justice reviews, frameworks for action, delivery plans and offending strategies that have surfaced since 1998. In particular, the article considers how far policy convergence and divergence are reflected through the discourses of risk, welfare, restoration and children's rights in the four administrations of England, Scotland, Wales and Northern Ireland. For comparative criminology, the United Kingdom offers a unique opportunity to explore how international and national pressures towards convergence and/or divergence can be challenged, rebranded, versioned, adapted or resisted at sub-national and local levels.

Strategies to engage academics in assuring graduate attributes

Assurance of learning (AoL) is a predominant feature in both quality assurance and quality enhancement in higher education. The process may be used for program development, and to inform external accreditation and evaluation bodies. However, there is an obvious challenge in trying to get academic staff to buy into the benefits of the AoL process. This project conducted an audit across 25 Australian Business Schools. The majority of those interviewed stated that academic staff considered AoL to be extra work and viewed the process as a box ticking exercise for external bodies rather than sound educational practice. A change management process is required to promote the necessary cultural change to embed AoL into practice. This paper showcases some of the educational leadership strategies that have been successfully implemented across Australia to foster staff engagement in the AoL process. These include: strong senior management commitment and leadership demonstrating a constant and high level drive for staff engagement until AoL becomes an institutional norm; developing leadership and champions among unit and program level staff, to share practices and promote the benefits that come from engaging in the process; providing professional development opportunities to discuss and resolve difficulties and tensions around AoL; demonstrating success and effectiveness by selling staff on the evidence that AoL makes a difference; and making the process inclusive with academics collaborating in the development and implementation of the process.

A two-metal ion mechanism operates in the hammerhead ribozyme-mediated cleavage of an RNA substrate

Evidence for a two-metal ion mechanism for cleavage of the HH16 hammerhead ribozyme is provided by monitoring the rate of cleavage of the RNA substrate as a function of La3+ concentration in the presence of a constant concentration of Mg2+. We show that a bell-shaped curve of cleavage activation is obtained as La3+ is added in micromolar concentrations in the presence of 8 mM Mg2+, with a maximal rate of cleavage being attained in the presence of 3 microM La3+. These results show that two-metal ion binding sites on the ribozyme regulate the rate of the cleavage reaction and, on the basis of earlier estimates of the Kd values for Mg2+ of 3.5 mM and > 50 mM, that these sites bind La3+ with estimated Kd values of 0.9 and > 37.5 microM, respectively. Furthermore, given the very different effects of these metal ions at the two binding sites, with displacement of Mg2+ by La3+ at the stronger (relative to Mg2+) binding site activating catalysis and displacement of Mg2+ by La3+ at the weaker (relative to Mg2+) (relative to Mg2+) binding site inhibiting catalysis, we show that the metal ions at these two sites play very different roles. We argue that the metal ion at binding site 1 coordinates the attacking 2'-oxygen species in the reaction and lowers the pKa of the attached proton, thereby increasing the concentration of the attacking alkoxide nucleophile in an equilibrium process. In contrast, the role of the metal ion at binding site 2 is to catalyze the reaction by absorbing the negative charge that accumulates at the leaving 5'-oxygen in the transition state. We suggest structural reasons why the Mg(2+)-La3+ ion combination is particularly suited to demonstrating these different roles of the two-metal ions in the ribozyme cleavage reaction.

Observations on catalysis by hammerhead ribozymes are consistent with a two-divalent-metal-ion mechanism

Significant cleavage by hammerhead ribozymes requires activation by divalent metal ions. Several models have been proposed to account for the influence of metal ions on hammerhead activity. A number of recent papers have presented data that have been interpreted as supporting a one-metal-hydroxide-ion mechanism. In addition, a solvent deuterium isotope effect has been taken as evidence against a proton transfer in the rate-limiting step of the cleavage reaction. We propose that these data are more easily explained by a two-metal-ion mechanism that does not involve a metal hydroxide, but does involve a proton transfer in the rate-limiting step.