Evidence for time dependency of molecular rate estimates

Long-term changes in the genetic composition of a population occur by the fixation of new mutations, a process known as substitution. The rate at which mutations arise in a population and the rate at which they are fixed are expected to be equal under neutral conditions (Kimura, 1968). Between the appearance of a new mutation and its eventual fate of fixation or loss, there will be a period in which it exists as a transient polymorphism in the population (Kimura and Ohta, 1971). If the majority of mutations are deleterious (and nonlethal), the fixation probabilities of these transient polymorphisms are reduced and the mutation rate will exceed the substitution rate (Kimura, 1983). Consequently, different apparent rates may be observed on different time scales of the molecular evolutionary process (Penny, 2005; Penny and Holmes, 2001). The substitution rate of the mitochondrial protein-coding genes of birds and mammals has been traditionally recognized to be about 0.01 substitutions/site/million years (Myr) (Brown et al., 1979; Ho, 2007; Irwin et al., 1991; Shields and Wilson, 1987), with the noncoding D-loop evolving several times more quickly (e.g., Pesole et al., 1992; Quinn, 1992). Over the past decade, there has been mounting evidence that instantaneous mutation rates substantially exceed substitution rates, in a range of organisms (e.g., Denver et al., 2000; Howell et al., 2003; Lambert et al., 2002; Mao et al., 2006; Mumm et al., 1997; Parsons et al., 1997; Santos et al., 2005). The immediate reaction to the first of these findings was that the polymorphisms generated by the elevated mutation rate are short-lived, perhaps extending back only a few hundred years (Gibbons, 1998; Macaulay et al., 1997). That is, purifying selection was thought to remove these polymorphisms very rapidly.

Use of Bayesian MUNE to show differing rate of loss of motor units in subgroups of ALS

Objectives To evaluate differences among patients with different clinical features of ALS, we used our Bayesian method of motor unit number estimation (MUNE). Methods We performed serial MUNE studies on 42 subjects who fulfilled the diagnostic criteria for ALS during the course of their illness. Subjects were classified into three subgroups according to whether they had typical ALS (with upper and lower motor neurone signs) or had predominantly upper motor neurone weakness with only minor LMN signs, or predominantly lower motor neurone weakness with only minor UMN signs. In all subjects we calculated the half life of MUs, defined as the expected time for the number of MUs to halve, in one or more of the abductor digiti minimi (ADM), abductor pollicis brevis (APB) and extensor digitorum brevis (EDB) muscles. Results The mean half life of MUs was less in subjects who had typical ALS with both upper and lower motor neurone signs than in those with predominantly upper motor neurone weakness or predominantly lower motor neurone weakness. In 18 subjects we analysed the estimated size of the MUs and demonstrated the appearance of large MUs in subjects with upper or lower motor neurone predominant weakness. We found that the appearance of large MUs was correlated with the half life of MUs. Conclusions Patients with different clinical features of ALS have different rates of loss and different sizes of MUs. Significance: These findings could indicate differences in disease pathogenesis.

An analysis of holding cost impact on housing affordability in relation to midsized Greenfield residential property developments in South East Queensland

The position of housing demand and supply is not consistent. The Australian situation counters the experience demonstrated in many other parts of the world in the aftermath of the Global Financial Crisis, with residential housing prices proving particularly resilient. A seemingly inexorable housing demand remains a critical issue affecting the socio-economic landscape. Underpinned by high levels of population growth fuelled by immigration, and further buoyed by sustained historically low interest rates, increasing income levels, and increased government assistance for first home buyers, this strong housing demand level ensures problems related to housing affordability continue almost unabated. A significant, but less visible factor impacting housing affordability relates to holding costs. Although only one contributor in the housing affordability matrix, the nature and extent of holding cost impact requires elucidation: for example, the computation and methodology behind the calculation of holding costs varies widely - and in some instances completely ignored. In addition, ambiguity exists in terms of the inclusion of various elements that comprise holding costs, thereby affecting the assessment of their relative contribution. Such anomalies may be explained by considering that assessment is conducted over time in an ever-changing environment. A strong relationship with opportunity cost - in turn dependant inter alia upon prevailing inflation and / or interest rates - adds further complexity. By extending research in the general area of housing affordability, this thesis seeks to provide a detailed investigation of those elements related to holding costs specifically in the context of midsized (i.e. between 15-200 lots) greenfield residential property developments in South East Queensland. With the dimensions of holding costs and their influence over housing affordability determined, the null hypothesis H0 that holding costs are not passed on can be addressed. Arriving at these conclusions involves the development of robust economic and econometric models which seek to clarify the componentry impacts of holding cost elements. An explanatory sequential design research methodology has been adopted, whereby the compilation and analysis of quantitative data and the development of an economic model is informed by the subsequent collection and analysis of primarily qualitative data derived from surveying development related organisations. Ultimately, there are significant policy implications in relation to the framework used in Australian jurisdictions that promote, retain, or otherwise maximise, the opportunities for affordable housing.

Relative entropy rate based model selection for linear hybrid system filters of uncertain nonlinear systems

Hybrid system representations have been exploited in a number of challenging modelling situations, including situations where the original nonlinear dynamics are too complex (or too imprecisely known) to be directly filtered. Unfortunately, the question of how to best design suitable hybrid system models has not yet been fully addressed, particularly in the situations involving model uncertainty. This paper proposes a novel joint state-measurement relative entropy rate based approach for design of hybrid system filters in the presence of (parameterised) model uncertainty. We also present a design approach suitable for suboptimal hybrid system filters. The benefits of our proposed approaches are illustrated through design examples and simulation studies.

Intrinsic kinetics of titania photocatalysis : simplified models for their investigation

Even though titanium dioxide photocatalysis has been promoted as a leading green technology for water purification, many issues have hindered its application on a large commercial scale. For the materials scientist the main issues have centred the synthesis of more efficient materials and the investigation of degradation mechanisms; whereas for the engineers the main issues have been the development of appropriate models and the evaluation of intrinsic kinetics parameters that allow the scale up or re-design of efficient large-scale photocatalytic reactors. In order to obtain intrinsic kinetics parameters the reaction must be analysed and modelled considering the influence of the radiation field, pollutant concentrations and fluid dynamics. In this way, the obtained kinetic parameters are independent of the reactor size and configuration and can be subsequently used for scale-up purposes or for the development of entirely new reactor designs. This work investigates the intrinsic kinetics of phenol degradation over titania film due to the practicality of a fixed film configuration over a slurry. A flat plate reactor was designed in order to be able to control reaction parameters that include the UV irradiance, flow rates, pollutant concentration and temperature. Particular attention was paid to the investigation of the radiation field over the reactive surface and to the issue of mass transfer limited reactions. The ability of different emission models to describe the radiation field was investigated and compared to actinometric measurements. The RAD-LSI model was found to give the best predictions over the conditions tested. Mass transfer issues often limit fixed film reactors. The influence of this phenomenon was investigated with specifically planned sets of benzoic acid experiments and with the adoption of the stagnant film model. The phenol mass transfer coefficient in the system was calculated to be km,phenol=8.5815x10-7Re0.65(ms-1). The data obtained from a wide range of experimental conditions, together with an appropriate model of the system, has enabled determination of intrinsic kinetic parameters. The experiments were performed in four different irradiation levels (70.7, 57.9, 37.1 and 20.4 W m-2) and combined with three different initial phenol concentrations (20, 40 and 80 ppm) to give a wide range of final pollutant conversions (from 22% to 85%). The simple model adopted was able to fit the wide range of conditions with only four kinetic parameters; two reaction rate constants (one for phenol and one for the family of intermediates) and their corresponding adsorption constants. The intrinsic kinetic parameters values were defined as kph = 0.5226 mmol m-1 s-1 W-1, kI = 0.120 mmol m-1 s-1 W-1, Kph = 8.5 x 10-4 m3 mmol-1 and KI = 2.2 x 10-3 m3 mmol-1. The flat plate reactor allowed the investigation of the reaction under two different light configurations; liquid and substrate side illumination. The latter of particular interest for real world applications where light absorption due to turbidity and pollutants contained in the water stream to be treated could represent a significant issue. The two light configurations allowed the investigation of the effects of film thickness and the determination of the catalyst optimal thickness. The experimental investigation confirmed the predictions of a porous medium model developed to investigate the influence of diffusion, advection and photocatalytic phenomena inside the porous titania film, with the optimal thickness value individuated at 5 ìm. The model used the intrinsic kinetic parameters obtained from the flat plate reactor to predict the influence of thickness and transport phenomena on the final observed phenol conversion without using any correction factor; the excellent match between predictions and experimental results provided further proof of the quality of the parameters obtained with the proposed method.

Impact of region-of-interest video coding on perceived quality in mobile video

Effective streaming of video can be achieved by providing more bits to the most important region in the frame at the cost of reduced bits in the less important regions. This strategy can be beneficial for delivering high quality videos in mobile devices, especially when the availability of bandwidth is usually low and limited. While the state-of-the-art video codecs such as H.264 may have been optimised for perceived quality, it is hypothesised that users will give more attention to interesting region/object when watching videos. Therefore, giving a higher quality to region of interest (ROI)while reducing quality of other areas may result in improving the overall perceived quality without necessarily increasing the bitrate. In this paper, the impact of ROI-based encoded video on perceived quality is investigated by conducting a user study for varous target bitrates. The results from the user study demonstrate that ROI-based video coding has superior perceived quality compared to normal encoded video at the same bitrate in the lower bitrate range.

Removal of toxic metals in a multi metal system using sorbents for potential application to urban stormwater treatment

In the context of increasing demand for potable water and the depletion of water resources, stormwater is a logical alternative. However, stormwater contains pollutants, among which metals are of particular interest due to their toxicity and persistence in the environment. Hence, it is imperative to remove toxic metals in stormwater to the levels prescribed by drinking water guidelines for potable use. Consequently, various techniques have been proposed, among which sorption using low cost sorbents is economically viable and environmentally benign in comparison to other techniques. However, sorbents show affinity towards certain toxic metals, which results in poor removal of other toxic metals. It was hypothesised in this study that a mixture of sorbents that have different metal affinity patterns can be used for the efficient removal of a range of toxic metals commonly found in stormwater. The performance of six sorbents in the sorption of Al, Cr, Cu, Pb, Ni, Zn and Cd, which are the toxic metals commonly found in urban stormwater, was investigated to select suitable sorbents for creating the mixtures. For this purpose, a multi criteria analytical protocol was developed using the decision making methods: PROMETHEE (Preference Ranking Organisation METHod for Enrichment Evaluations) and GAIA (Graphical Analysis for Interactive Assistance). Zeolite and seaweed were selected for the creation of trial mixtures based on their metal affinity pattern and the performance on predetermined selection criteria. The metal sorption mechanisms employed by seaweed and zeolite were defined using kinetics, isotherm and thermodynamics parameters, which were determined using the batch sorption experiments. Additionally, the kinetics rate-limiting steps were identified using an innovative approach using GAIA and Spearman correlation techniques developed as part of the study, to overcome the limitation in conventional graphical methods in predicting the degree of contribution of each kinetics step in limiting the overall metal removal rate. The sorption kinetics of zeolite was found to be primarily limited by intraparticle diffusion followed by the sorption reaction steps, which were governed mainly by the hydrated ionic diameter of metals. The isotherm study indicated that the metal sorption mechanism of zeolite was primarily of a physical nature. The thermodynamics study confirmed that the energetically favourable nature of sorption increased in the order of Zn < Cu < Cd < Ni < Pb < Cr < Al, which is in agreement with metal sorption affinity of zeolite. Hence, sorption thermodynamics has an influence on the metal sorption affinity of zeolite. On the other hand, the primary kinetics rate-limiting step of seaweed was the sorption reaction process followed by intraparticle diffusion. The boundary layer diffusion was also found to limit the metal sorption kinetics at low concentration. According to the sorption isotherm study, Cd, Pb, Cr and Al were sorbed by seaweed via ion exchange, whilst sorption of Ni occurred via physisorption. Furthermore, ionic bonding is responsible for the sorption of Zn. The thermodynamics study confirmed that sorption by seaweed was energetically favourable in the order of Zn < Cu < Cd < Cr . Al < Pb < Ni. However, this did not agree with the affinity series derived for seaweed suggesting a limited influence of sorption thermodynamics on metal affinity for seaweed. The investigation of zeolite-seaweed mixtures indicated that mixing sorbents have an effect on the kinetics rates and the sorption affinity. Additionally, the theoretical relationships were derived to predict the boundary layer diffusion rate, intraparticle diffusion rate, the sorption reaction rate and the enthalpy of mixtures based on that of individual sorbents. In general, low coefficient of determination (R2) for the relationships between theoretical and experimental data indicated that the relationships were not statistically significant. This was attributed to the heterogeneity of the properties of sorbents. Nevertheless, in relative terms, the intraparticle diffusion rate, sorption reaction rate and enthalpy of sorption had higher R2 values than the boundary layer diffusion rate suggesting that there was some relationship between the former set of parameters of mixtures and that of sorbents. The mixture, which contained 80% of zeolite and 20% of seaweed, showed similar affinity for the sorption of Cu, Ni, Cd, Cr and Al, which was attributed to approximately similar sorption enthalpy of the metal ions. Therefore, it was concluded that the seaweed-zeolite mixture can be used to obtain the same affinity for various metals present in a multi metal system provided the metal ions have similar enthalpy during sorption by the mixture.

Context-aware rate-adaptive beaconing for efficient and scalable vehicular safety communication

Vehicular safety applications, such as cooperative collision warning systems, rely on beaconing to provide situational awareness that is needed to predict and therefore to avoid possible collisions. Beaconing is the continual exchange of vehicle motion-state information, such as position, speed, and heading, which enables each vehicle to track its neighboring vehicles in real time. This work presents a context-aware adaptive beaconing scheme that dynamically adapts the beaconing repetition rate based on an estimated channel load and the danger severity of the interactions among vehicles. The safety, efficiency, and scalability of the new scheme is evaluated by simulating vehicle collisions caused by inattentive drivers under various road traffic densities. Simulation results show that the new scheme is more efficient and scalable, and is able to improve safety better than the existing non-adaptive and adaptive rate schemes.

Quantitative studies of lower motor neuron degeneration in amyotrophic lateral sclerosis : Evidence for exponential decay of motor unit numbers and greatest rate of loss at the site of onset

Objective: To use our Bayesian method of motor unit number estimation (MUNE) to evaluate lower motor neuron degeneration in ALS. Methods: In subjects with ALS we performed serial MUNE studies. We examined the repeatability of the test and then determined whether the loss of MUs was fitted by an exponential or Weibull distribution. Results: The decline in motor unit (MU) numbers was well-fitted by an exponential decay curve. We calculated the half life of MUs in the abductor digiti minimi (ADM), abductor pollicis brevis (APB) and/or extensor digitorum brevis (EDB) muscles. The mean half life of the MUs of ADM muscle was greater than those of the APB or EDB muscles. The half-life of MUs was less in the ADM muscle of subjects with upper limb than in those with lower limb onset. Conclusions: The rate of loss of lower motor neurons in ALS is exponential, the motor units of the APB decay more quickly than those of the ADM muscle and the rate of loss of motor units is greater at the site of onset of disease. Significance: This shows that the Bayesian MUNE method is useful in following the course and exploring the clinical features of ALS. 2012 International Federation of Clinical Neurophysiology.

Consecutive days of cold water immersion: effects on cycling performance and heart rate variability.

We investigated performance and heart rate (HR) variability (HRV) over consecutive days of cycling with post-exercise cold water immersion (CWI) or passive recovery (PAS). In a crossover design, 11 cyclists completed two separate 3-day training blocks (120 min cycling per day, 66 maximal sprints, 9 min time trialling [TT]), followed by 2 days of recovery-based training. The cyclists recovered from each training session by standing in cold water (10 °C) or at room temperature (27 °C) for 5 min. Mean power for sprints, total TT work and HR were assessed during each session. Resting vagal-HRV (natural logarithm of square-root of mean squared differences of successive R-R intervals; ln rMSSD) was assessed after exercise, after the recovery intervention, during sleep and upon waking. CWI allowed better maintenance of mean sprint power (between-trial difference [90 % confidence limits] +12.4 % [5.9; 18.9]), cadence (+2.0 % [0.6; 3.5]), and mean HR during exercise (+1.6 % [0.0; 3.2]) compared with PAS. ln rMSSD immediately following CWI was higher (+144 % [92; 211]) compared with PAS. There was no difference between the trials in TT performance (-0.2 % [-3.5; 3.0]) or waking ln rMSSD (-1.2 % [-5.9; 3.4]). CWI helps to maintain sprint performance during consecutive days of training, whereas its effects on vagal-HRV vary over time and depend on prior exercise intensity.

The effect of post-exercise hydrotherapy on subsequent exercise performance and heart rate variability

We investigated the effect of hydrotherapy on time-trial performance and cardiac parasympathetic reactivation during recovery from intense training. On three occasions, 18 well-trained cyclists completed 60 min high-intensity cycling, followed 20 min later by one of three 10-min recovery interventions: passive rest (PAS), cold water immersion (CWI), or contrast water immersion (CWT). The cyclists then rested quietly for 160 min with R-R intervals and perceptions of recovery recorded every 30 min. Cardiac parasympathetic activity was evaluated using the natural logarithm of the square root of mean squared differences of successive R-R intervals (ln rMSSD). Finally, the cyclists completed a work-based cycling time trial. Effects were examined using magnitude-based inferences. Differences in time-trial performance between the three trials were trivial. Compared with PAS, general fatigue was very likely lower for CWI (difference [90% confidence limits; -12% (-18; -5)]) and CWT [-11% (-19; -2)]. Leg soreness was almost certainly lower following CWI [-22% (-30; -14)] and CWT [-27% (-37; -15)]. The change in mean ln rMSSD following the recovery interventions (ln rMSSD(Post-interv)) was almost certainly higher following CWI [16.0% (10.4; 23.2)] and very likely higher following CWT [12.5% (5.5; 20.0)] compared with PAS, and possibly higher following CWI [3.7% (-0.9; 8.4)] compared with CWT. The correlations between performance, ln rMSSD(Post-interv) and perceptions of recovery were unclear. A moderate correlation was observed between ln rMSSD(Post-interv) and leg soreness [r = -0.50 (-0.66; -0.29)]. Although the effects of CWI and CWT on performance were trivial, the beneficial effects on perceptions of recovery support the use of these recovery strategies.