Generalized binomial Tau-leap method for biochemical kinetics incorporating both delay and intrinsic noise

The delay stochastic simulation algorithm (DSSA) by Barrio et al. [Plos Comput. Biol.2, 117–E (2006)] was developed to simulate delayed processes in cell biology in the presence of intrinsic noise, that is, when there are small-to-moderate numbers of certain key molecules present in a chemical reaction system. These delayed processes can faithfully represent complex interactions and mechanisms that imply a number of spatiotemporal processes often not explicitly modeled such as transcription and translation, basic in the modeling of cell signaling pathways. However, for systems with widely varying reaction rate constants or large numbers of molecules, the simulation time steps of both the stochastic simulation algorithm (SSA) and the DSSA can become very small causing considerable computational overheads. In order to overcome the limit of small step sizes, various τ-leap strategies have been suggested for improving computational performance of the SSA. In this paper, we present a binomial τ- DSSA method that extends the τ-leap idea to the delay setting and avoids drawing insufficient numbers of reactions, a common shortcoming of existing binomial τ-leap methods that becomes evident when dealing with complex chemical interactions. The resulting inaccuracies are most evident in the delayed case, even when considering reaction products as potential reactants within the same time step in which they are produced. Moreover, we extend the framework to account for multicellular systems with different degrees of intercellular communication. We apply these ideas to two important genetic regulatory models, namely, the hes1 gene, implicated as a molecular clock, and a Her1/Her 7 model for coupled oscillating cells.

Mean and variance of estimates of the bispectrum of a harmonic random process-an analysis including leakage effects

Analytical expressions are derived for the mean and variance, of estimates of the bispectrum of a real-time series assuming a cosinusoidal model. The effects of spectral leakage, inherent in discrete Fourier transform operation when the modes present in the signal have a nonintegral number of wavelengths in the record, are included in the analysis. A single phase-coupled triad of modes can cause the bispectrum to have a nonzero mean value over the entire region of computation owing to leakage. The variance of bispectral estimates in the presence of leakage has contributions from individual modes and from triads of phase-coupled modes. Time-domain windowing reduces the leakage. The theoretical expressions for the mean and variance of bispectral estimates are derived in terms of a function dependent on an arbitrary symmetric time-domain window applied to the record. the number of data, and the statistics of the phase coupling among triads of modes. The theoretical results are verified by numerical simulations for simple test cases and applied to laboratory data to examine phase coupling in a hypothesis testing framework

Sit versus stand : can sitting be accurately identified using MTI accelerometer data?

High levels of sitting have been linked with poor health outcomes. Previously a pragmatic MTI accelerometer data cut-point (100 count/min-1) has been used to estimate sitting. Data on the accuracy of this cut-point is unavailable. PURPOSE: To ascertain whether the 100 count/min-1 cut-point accurately isolates sitting from standing activities. METHODS: Participants fitted with an MTI accelerometer were observed performing a range of sitting, standing, light & moderate activities. 1-min epoch MTI data were matched to observed activities, then re-categorized as either sitting or not using the 100 count/min-1 cut-point. Self-report demographics and current physical activity were collected. Generalized estimating equation for repeated measures with a binary logistic model analyses (GEE), corrected for age, gender and BMI, were conducted to ascertain the odds of the MTI data being misclassified. RESULTS: Data were from 26 healthy subjects (8 men; 50% aged <25 years; mean BMI (SD) 22.7(3.8)m/kg2). MTI sitting and standing data mode was 0 count/min-1, with 46% of sitting activities and 21% of standing activities recording 0 count/min-1. The GEE was unable to accurately isolate sitting from standing activities using the 100 count/min-1 cut-point, since all sitting activities were incorrectly predicted as standing (p=0.05). To further explore the sensitivity of MTI data to delineate sitting from standing, the upper 95% confidence interval of the mean for the sitting activities (46 count/min-1) was used to re-categorise the data; this resulted in the GEE correctly classifying 49% of sitting, and 69% of standing activities. Using the 100 count/min-1 cut-point the data were re-categorised into a combined ‘sit/stand’ category and tested against other light activities: 88% of sit/stand and 87% of light activities were accurately predicted. Using Freedson’s moderate cut-point of 1952 count/min-1 the GEE accurately predicted 97% of light vs. 90% of moderate activities. CONCLUSION: The distributions of MTI recorded sitting and standing data overlap considerably, as such the 100 count/min -1 cut-point did not accurately isolate sitting from other static standing activities. The 100 count/min -1 cut-point more accurately predicted sit/stand vs. other movement orientated activities.

Recovery-based practice: do we know what we mean or mean what we know?

The concept of recovery is now widely promoted as the guiding principle for the provision of mental health services in Australia and overseas. While there is increasing pressure on service providers to ensure that services are recovery oriented, the way in which recovery-based practice is operationalized at the coalface presents a number of challenges. These are discussed in the context of five key questions that address (i) the appropriateness of recovery as a focus for service delivery, (ii) the distinction between recovery as a process and an outcome, (iii) the assessment of recovery initiatives, (iv) the alignment of recovery with current service delivery models, and (v) the risks associated with recovery-based practice. It is argued that these questions provide a framework for a debate that must extend beyond patients and providers of mental health services to the broader public, whose attitudes will ultimately determine the possibilities and limits of recovery-oriented practice.

Place and Space: Community in the Internet Economy and What This Will Mean for Property

By 2020 Australia‟s National Digital Economy Strategy aims to increase household online participation and engage 12 per cent of all employees in teleworking arrangements. Achieving these goals is generally perceived as positive due to the reduced impact on the natural environment from less use of transport. However, this also will enable greater flexibility as to where people live and thus will impact upon the maintenance and formation of communities and on property use. This paper commences by clarifying what is Australia‟s internet economy before highlighting the impact of the internet on community formation and maintenance. The paper concludes by identifying what the achievement of these goals will mean for property use in the future.

Do you see what I mean? charting changing representations and receptions of the disabled body in contemporary and pop cultural performance

The meaning of the body emerges through acts of seeing, looking and staring in daily and dramatic performances. Acts that are, as Maike Bleeker argues1, bound up with the scopic rules, regimes and narratives that apply in specific cultures at specific times. In Western culture, the disabled body has been seen as a sign of defect, deficiency, fear, shame or stigma. Disabled artists – Mat Fraser, Bill Shannon, Aaron Williamson, Katherine Araniello, Liz Crow and Ju Gosling – have attempted, via performances that co-opt conventional images of the disabled body, to challenge dominant ways of representing and responding such bodies from within. In this paper, I consider what happens when non-disabled artists co-opt images of the disabled body to draw attention to, affirm, and even exoticise, eroticise or beautify, other modalities of or desires for difference. As Carrie Sandahl has noted2, the signs, symbols and somatic idiosyncrasies of the disabled body are, today, transported or translated into theatre, film and television as a metaphor or "master trope" for every body’s experience of difference. This happens in performance art (Guillermo Gomez-Pena’s use of a wheelchair in Chamber of Confessions), performance (Marie Chouinard's use of crutches, canes and walkers to represent dancers’ experience of becoming different or mutant during training in bODY rEMIX /gOLDBERG vARIATIONS), and pop culture (characters in wheelchairs in Glee or Oz). In this paper, I chart changing representations and receptions of the disabled body in such contexts. I use analysis of this cultural shift as a starting point for a re-consideration of questions about whether a face-toface encounter with a disabled body is in fact a privileged site for the emergence of a politics, and whether co-opting disability as a metaphor for a range of difference differences reduces its currency as a category around which a specific group might mobilise a politics.

Mean-field descriptions of collective migration with strong adhesion

Random walk models based on an exclusion process with contact effects are often used to represent collective migration where individual agents are affected by agent-to-agent adhesion. Traditional mean field representations of these processes take the form of a nonlinear diffusion equation which, for strong adhesion, does not predict the averaged discrete behavior. We propose an alternative suite of mean-field representations, showing that collective migration with strong adhesion can be accurately represented using a moment closure approach.

iiNet’s Hollywood ending : what does its court victory mean for copyright law?

In what is being billed as iiNet versus Hollywood, the Australian internet service provider has come out an apparent winner after the High Court dismissed a copyright infringement case brought by industry movie studios. The case was a final appeal by the industry in its attempts to crack down on internet users infringing copyright by using BitTorrent to download movies.

Estimating the effects of environmental exposures using a weighted mean of monitoring stations

The health effects of environmental hazards are often examined using time series of the association between a daily response variable (e.g., death) and a daily level of exposure (e.g., temperature). Exposures are usually the average from a network of stations. This gives each station equal importance, and negates the opportunity for some stations to be better measures of exposure. We used a Bayesian hierarchical model that weighted stations using random variables between zero and one. We compared the weighted estimates to the standard model using data on health outcomes (deaths and hospital admissions) and exposures (air pollution and temperature) in Brisbane, Australia. The improvements in model fit were relatively small, and the estimated health effects of pollution were similar using either the standard or weighted estimates. Spatial weighted exposures would be probably more worthwhile when there is either greater spatial detail in the health outcome, or a greater spatial variation in exposure.