Effect of family relatedness on characteristics of estimated IBD probabilities in relation to precision of QTL estimates

Background: A random QTL effects model uses a function of probabilities that two alleles in the same or in different animals at a particular genomic position are identical by descent (IBD). Estimates of such IBD probabilities and therefore, modeling and estimating QTL variances, depend on marker polymorphism, strength of linkage and linkage disequilibrium of markers and QTL, and the relatedness of animals in the pedigree. The effect of relatedness of animals in a pedigree on IBD probabilities and their characteristics was examined in a simulation study. Results: The study based on nine multi-generational family structures, similar to a pedigree structure of a real dairy population, distinguished by an increased level of inbreeding from zero to 28 % across the studied population. Highest inbreeding level in the pedigree, connected with highest relatedness, was accompanied by highest IBD probabilities of two alleles at the same locus, and by lower relative variation coefficients. Profiles of correlation coefficients of IBD probabilities along the marked chromosomal segment with those at the true QTL position were steepest when the inbreeding coefficient in the pedigree was highest. Precision of estimated QTL location increased with increasing inbreeding and pedigree relatedness. A method to assess the optimum level of inbreeding for QTL detection is proposed, depending on population parameters. Conclusions: An increased overall relationship in a QTL mapping design has positive effects on precision of QTL position estimates. But the relationship of inbreeding level and the capacity for QTL detection depending on the recombination rate of QTL and adjacent informative marker is not linear. © 2010 Freyer et al., licensee BioMed Central Ltd.

Immigrant wage differentials and the role of self-employment in Australia

Immigration has played an important role in the historical development of Australia. Thus, it is no surprise that a large body of empirical work has developed, which focuses upon how migrants fare in the land of opportunity. Much of the literature is comparatively recent, i.e. the last ten years or so, encouraged by the advent of public availability of Australian crosssection micro data. Several different aspects of migrant welfare have been addressed, with major emphasis being placed upon earnings and unemployment experience. For recent examples see Haig (1980), Stromback (1984), Chiswick and Miller (1985), Tran-Nam and Nevile (1988) and Beggs and Chapman (1988). The present paper contributes to the literature by providing additional empirical evidence on the native/migrant earnings differential. The data utilised are from the rather neglected Australian Bureau of Statistics, ABS Special Supplementary Survey No.4. 1982, otherwise known as the Family Survey. The paper also examines the importance of distinguishing between the wage and salary sector and the self-employment sector when discussing native/migrant differentials. Separate earnings equations for the two labour market groups are estimated and the native/migrant earnings differential is broken down by employment status. This is a novel application in the Australian context and provides some insight into the earnings of the selfemployed, a group that despite its size (around 20 per cent of the labour force) is frequently ignored by economic research. Most previous empirical research fails to examine the effect of employment status on earnings. Stromback (1984) includes a dummy variable representing self-employment status in an earnings equation estimated over a pooled sample of paid and self-employed workers. The variable is found to be highly significant, which leads Stromback to question the efficacy of including the self-employed in the estimation sample. The suggestion is that part of self-employed earnings represent a return to non-human capital investment, i.e. investments in machinery, buildings etc, the structural determinants of earnings differ significantly from those for paid employees. Tran-Nam and Nevile (1988) deal with differences between paid employees and the selfemployed by deleting the latter from their sample. However, deleting the self-employed from the estimation sample may lead to bias in the OLS estimation method (see Heckman 1979). The desirable properties of OLS are dependent upon estimation on a random sample. Thus, the 'Ran-Nam and Nevile results are likely to suffer from bias unless individuals are randomly allocated between self-employment and paid employment. The current analysis extends Tran-Nam and Nevile (1988) by explicitly treating the choice of paid employment versus self-employment as being endogenously determined. This allows an explicit test for the appropriateness of deleting self-employed workers from the sample. Earnings equations that are corrected for sample selection are estimated for both natives and migrants in the paid employee sector. The Heckman (1979) two-step estimator is employed. The paper is divided into five major sections. The next section presents the econometric model incorporating the specification of the earnings generating process together with an explicit model determining an individual's employment status. In Section 111 the data are described. Section IV draws together the main econometric results of the paper. First, the probit estimates of the labour market status equation are documented. This is followed by presentation and discussion of the Heckman two-stage estimates of the earnings specification for both native and migrant Australians. Separate earnings equations are estimated for paid employees and the self-employed. Section V documents estimates of the nativelmigrant earnings differential for both categories of employees. To aid comparison with earlier work, the Oaxaca decomposition of the earnings differential for paid-employees is carried out for both the simple OLS regression results as well as the parameter estimates corrected for sample selection effects. These differentials are interpreted and compared with previous Australian findings. A short section concludes the paper.

Pseudo-marginal algorithms with multiple CPUs

The emergence of pseudo-marginal algorithms has led to improved computational efficiency for dealing with complex Bayesian models with latent variables. Here an unbiased estimator of the likelihood replaces the true likelihood in order to produce a Bayesian algorithm that remains on the marginal space of the model parameter (with latent variables integrated out), with a target distribution that is still the correct posterior distribution. Very efficient proposal distributions can be developed on the marginal space relative to the joint space of model parameter and latent variables. Thus psuedo-marginal algorithms tend to have substantially better mixing properties. However, for pseudo-marginal approaches to perform well, the likelihood has to be estimated rather precisely. This can be difficult to achieve in complex applications. In this paper we propose to take advantage of multiple central processing units (CPUs), that are readily available on most standard desktop computers. Here the likelihood is estimated independently on the multiple CPUs, with the ultimate estimate of the likelihood being the average of the estimates obtained from the multiple CPUs. The estimate remains unbiased, but the variability is reduced. We compare and contrast two different technologies that allow the implementation of this idea, both of which require a negligible amount of extra programming effort. The superior performance of this idea over the standard approach is demonstrated on simulated data from a stochastic volatility model.

Urban transit quality of service : user perception and behaviour

Despite its potential multiple contributions to sustainable policy objectives, urban transit is generally not widely used by the public in terms of its market share compared to that of automobiles, particularly in affluent societies with low-density urban forms like Australia. Transit service providers need to attract more people to transit by improving transit quality of service. The key to cost-effective transit service improvements lies in accurate evaluation of policy proposals by taking into account their impacts on transit users. If transit providers knew what is more or less important to their customers, they could focus their efforts on optimising customer-oriented service. Policy interventions could also be specified to influence transit users’ travel decisions, with targets of customer satisfaction and broader community welfare. This significance motivates the research into the relationship between urban transit quality of service and its user perception as well as behaviour. This research focused on two dimensions of transit user’s travel behaviour: route choice and access arrival time choice. The study area chosen was a busy urban transit corridor linking Brisbane central business district (CBD) and the St. Lucia campus of The University of Queensland (UQ). This multi-system corridor provided a ‘natural experiment’ for transit users between the CBD and UQ, as they can choose between busway 109 (with grade-separate exclusive right-of-way), ordinary on-street bus 412, and linear fast ferry CityCat on the Brisbane River. The population of interest was set as the attendees to UQ, who travelled from the CBD or from a suburb via the CBD. Two waves of internet-based self-completion questionnaire surveys were conducted to collect data on sampled passengers’ perception of transit service quality and behaviour of using public transit in the study area. The first wave survey is to collect behaviour and attitude data on respondents’ daily transit usage and their direct rating of importance on factors of route-level transit quality of service. A series of statistical analyses is conducted to examine the relationships between transit users’ travel and personal characteristics and their transit usage characteristics. A factor-cluster segmentation procedure is applied to respodents’ importance ratings on service quality variables regarding transit route preference to explore users’ various perspectives to transit quality of service. Based on the perceptions of service quality collected from the second wave survey, a series of quality criteria of the transit routes under study was quantitatively measured, particularly, the travel time reliability in terms of schedule adherence. It was proved that mixed traffic conditions and peak-period effects can affect transit service reliability. Multinomial logit models of transit user’s route choice were estimated using route-level service quality perceptions collected in the second wave survey. Relative importance of service quality factors were derived from choice model’s significant parameter estimates, such as access and egress times, seat availability, and busway system. Interpretations of the parameter estimates were conducted, particularly the equivalent in-vehicle time of access and egress times, and busway in-vehicle time. Market segmentation by trip origin was applied to investigate the difference in magnitude between the parameter estimates of access and egress times. The significant costs of transfer in transit trips were highlighted. These importance ratios were applied back to quality perceptions collected as RP data to compare the satisfaction levels between the service attributes and to generate an action relevance matrix to prioritise attributes for quality improvement. An empirical study on the relationship between average passenger waiting time and transit service characteristics was performed using the service quality perceived. Passenger arrivals for services with long headways (over 15 minutes) were found to be obviously coordinated with scheduled departure times of transit vehicles in order to reduce waiting time. This drove further investigations and modelling innovations in passenger’ access arrival time choice and its relationships with transit service characteristics and average passenger waiting time. Specifically, original contributions were made in formulation of expected waiting time, analysis of the risk-aversion attitude to missing desired service run in the passengers’ access time arrivals’ choice, and extensions of the utility function specification for modelling passenger access arrival distribution, by using complicated expected utility forms and non-linear probability weighting to explicitly accommodate the risk of missing an intended service and passenger’s risk-aversion attitude. Discussions on this research’s contributions to knowledge, its limitations, and recommendations for future research are provided at the concluding section of this thesis.

Consistent HMM parameter estimation using Kerridge inaccuracy rates

In this paper, we propose a novel online hidden Markov model (HMM) parameter estimator based on Kerridge inaccuracy rate (KIR) concepts. Under mild identifiability conditions, we prove that our online KIR-based estimator is strongly consistent. In simulation studies, we illustrate the convergence behaviour of our proposed online KIR-based estimator and provide a counter-example illustrating the local convergence properties of the well known recursive maximum likelihood estimator (arguably the best existing solution).

Identification and estimation of equivalent area parameters using synchronised phasor measurements

A new approach is proposed for obtaining a non-linear area-based equivalent model of power systems to express the inter-area oscillations using synchronised phasor measurements. The generators that remain coherent for inter-area disturbances over a wide range of operating conditions define the areas, and the reduced model is obtained by representing each area by an equivalent machine. The parameters of the reduced system are identified by processing the obtained measurements, and a non-linear Kalman estimator is then designed for the estimation of equivalent area angles and frequencies. The simulation of the approach on a two-area system shows substantial reduction of non-inter-area modes in the estimated angles. The proposed methods are also applied to a ten-machine system to illustrate the feasibility of the approach on larger and meshed networks.

Has portfolio theory got any principles?

Recently, Portfolio Theory (PT) has been proposed for Information Retrieval. However, under non-trivial conditions PT violates the original Probability Ranking Principle (PRP). In this poster, we shall explore whether PT upholds a different ranking principle based on Quantum Theory, i.e. the Quantum Probability Ranking Principle (QPRP), and examine the relationship between this new model and the new ranking principle. We make a significant contribution to the theoretical development of PT and show that under certain circumstances PT upholds the QPRP, and thus guarantees an optimal ranking according to the QPRP. A practical implication of this finding is that the parameters of PT can be automatically estimated via the QPRP, instead of resorting to extensive parameter tuning.

A simple model for the establishment of tick-borne pathogens of Ixodes scapularis : a global sensitivity analysis of R0

The basic reproduction number of a pathogen, R 0, determines whether a pathogen will spread (R0>1R 0>1), when introduced into a fully susceptible population or fade out (R0<1R 0<1), because infected hosts do not, on average, replace themselves. In this paper we develop a simple mechanistic model for the basic reproduction number for a group of tick-borne pathogens that wholly, or almost wholly, depend on horizontal transmission to and from vertebrate hosts. This group includes the causative agent of Lyme disease, Borrelia burgdorferi, and the causative agent of human babesiosis, Babesia microti, for which transmission between co-feeding ticks and vertical transmission from adult female ticks are both negligible. The model has only 19 parameters, all of which have a clear biological interpretation and can be estimated from laboratory or field data. The model takes into account the transmission efficiency from the vertebrate host as a function of the days since infection, in part because of the potential for this dynamic to interact with tick phenology, which is also included in the model. This sets the model apart from previous, similar models for R0 for tick-borne pathogens. We then define parameter ranges for the 19 parameters using estimates from the literature, as well as laboratory and field data, and perform a global sensitivity analysis of the model. This enables us to rank the importance of the parameters in terms of their contribution to the observed variation in R0. We conclude that the transmission efficiency from the vertebrate host to Ixodes scapularis ticks, the survival rate of Ixodes scapularis from fed larva to feeding nymph, and the fraction of nymphs finding a competent host, are the most influential factors for R0. This contrasts with other vector borne pathogens where it is usually the abundance of the vector or host, or the vector-to-host ratio, that determine conditions for emergence. These results are a step towards a better understanding of the geographical expansion of currently emerging horizontally transmitted tick-borne pathogens such as Babesia microti, as well as providing a firmer scientific basis for targeted use of acaricide or the application of wildlife vaccines that are currently in development.

Incorporating adverse event relatedness into dose-finding clinical trial designs

Dose-finding designs estimate the dose level of a drug based on observed adverse events. Relatedness of the adverse event to the drug has been generally ignored in all proposed design methodologies. These designs assume that the adverse events observed during a trial are definitely related to the drug, which can lead to flawed dose-level estimation. We incorporate adverse event relatedness into the so-called continual reassessment method. Adverse events that have ‘doubtful’ or ‘possible’ relationships to the drug are modelled using a two-parameter logistic model with an additive probability mass. Adverse events ‘probably’ or ‘definitely’ related to the drug are modelled using a cumulative logistic model. To search for the maximum tolerated dose, we use the maximum estimated toxicity probability of these two adverse event relatedness categories. We conduct a simulation study that illustrates the characteristics of the design under various scenarios. This article demonstrates that adverse event relatedness is important for improved dose estimation. It opens up further research pathways into continual reassessment design methodologies.

Parameter estimation of thrust models of uninhabited airborne systems

This paper presents a method for the estimation of thrust model parameters of uninhabited airborne systems using specific flight tests. Particular tests are proposed to simplify the estimation. The proposed estimation method is based on three steps. The first step uses a regression model in which the thrust is assumed constant. This allows us to obtain biased initial estimates of the aerodynamic coeficients of the surge model. In the second step, a robust nonlinear state estimator is implemented using the initial parameter estimates, and the model is augmented by considering the thrust as random walk. In the third step, the estimate of the thrust obtained by the observer is used to fit a polynomial model in terms of the propeller advanced ratio. We consider a numerical example based on Monte-Carlo simulations to quantify the sampling properties of the proposed estimator given realistic flight conditions.

A comprehensive analysis of parameter settings for novelty-biased cumulative gain

In the TREC Web Diversity track, novelty-biased cumulative gain (α-NDCG) is one of the official measures to assess retrieval performance of IR systems. The measure is characterised by a parameter, α, the effect of which has not been thoroughly investigated. We find that common settings of α, i.e. α=0.5, may prevent the measure from behaving as desired when evaluating result diversification. This is because it excessively penalises systems that cover many intents while it rewards those that redundantly cover only few intents. This issue is crucial since it highly influences systems at top ranks. We revisit our previously proposed threshold, suggesting α be set on a query-basis. The intuitiveness of the measure is then studied by examining actual rankings from TREC 09-10 Web track submissions. By varying α according to our query-based threshold, the discriminative power of α-NDCG is not harmed and in fact, our approach improves α-NDCG's robustness. Experimental results show that the threshold for α can turn the measure to be more intuitive than using its common settings.

Statistical analysis of reduction in tensile strength of cotton strips as a measure of soil microbial activity

The cotton strip assay (CSA) is an established technique for measuring soil microbial activity. The technique involves burying cotton strips and measuring their tensile strength after a certain time. This gives a measure of the rotting rate, R, of the cotton strips. R is then a measure of soil microbial activity. This paper examines properties of the technique and indicates how the assay can be optimised. Humidity conditioning of the cotton strips before measuring their tensile strength reduced the within and between day variance and enabled the distribution of the tensile strength measurements to approximate normality. The test data came from a three-way factorial experiment (two soils, two temperatures, three moisture levels). The cotton strips were buried in the soil for intervals of time ranging up to 6 weeks. This enabled the rate of loss of cotton tensile strength with time to be studied under a range of conditions. An inverse cubic model accounted for greater than 90% of the total variation within each treatment combination. This offers support for summarising the decomposition process by a single parameter R. The approximate variance of the decomposition rate was estimated from a function incorporating the variance of tensile strength and the differential of the function for the rate of decomposition, R, with respect to tensile strength. This variance function has a minimum when the measured strength is approximately 2/3 that of the original strength. The estimates of R are almost unbiased and relatively robust against the cotton strips being left in the soil for more or less than the optimal time. We conclude that the rotting rate X should be measured using the inverse cubic equation, and that the cotton strips should be left in the soil until their strength has been reduced to about 2/3.

A broad-scale analysis of links between coastal fisheries production and mangrove extent : a case-study for northeastern Australia

The paradigm that mangroves are critical for sustaining production in coastal fisheries is widely accepted, but empirical evidence has been tenuous. This study showed that links between mangrove extent and coastal fisheries production could be detected for some species at a broad regional scale (1000s of kilometres) on the east coast of Queensland, Australia. The relationships between catch-per-unit-effort for different commercially caught species in four fisheries (trawl, line, net and pot fisheries) and mangrove characteristics, estimated from Landsat images were examined using multiple regression analyses. The species were categorised into three groups based on information on their life history characteristics, namely mangrove-related species (banana prawns Penaeus merguiensis, mud crabs Scylla serrata and barramundi Lates calcarifer), estuarine species (tiger prawns Penaeus esculentus and Penaeus semisulcatus, blue swimmer crabs Portunus pelagicus and blue threadfin Eleutheronema tetradactylum) and offshore species (coral trout Plectropomus spp.). For the mangrove-related species, mangrove characteristics such as area and perimeter accounted for most of the variation in the model; for the non-mangrove estuarine species, latitude was the dominant parameter but some mangrove characteristics (e.g. mangrove perimeter) also made significant contributions to the models. In contrast, for the offshore species, latitude was the dominant variable, with no contribution from mangrove characteristics. This study also identified that finer scale spatial data for the fisheries, to enable catch information to be attributed to a particular catchment, would help to improve our understanding of relationships between mangroves and fisheries production.

Bioeconomic modelling and risk assessment of tiger prawn (Penaeus esculentus) stock enhancement in Exmouth Gulf, Australia

A bioeconomic model was developed to evaluate the potential performance of brown tiger prawn stock enhancement in Exmouth Gulf, Australia. This paper presents the framework for the bioeconomic model and risk assessment for all components of a stock enhancement operation, i.e. hatchery, grow-out, releasing, population dynamics, fishery, and monitoring, for a commercial scale enhancement of about 100 metric tonnes, a 25% increase in average annual catch in Exmouth Gulf. The model incorporates uncertainty in estimates of parameters by using a distribution for the parameter over a certain range, based on experiments, published data, or similar studies. Monte Carlo simulation was then used to quantify the effects of these uncertainties on the model-output and on the economic potential of a particular production target. The model incorporates density-dependent effects in the nursery grounds of brown tiger prawns. The results predict that a release of 21 million 1 g prawns would produce an estimated enhanced prawn catch of about 100 t. This scale of enhancement has a 66.5% chance of making a profit. The largest contributor to the overall uncertainty of the enhanced prawn catch was the post-release mortality, followed by the density-dependent mortality caused by released prawns. These two mortality rates are most difficult to estimate in practice and are much under-researched in stock enhancement.

Impact of temperature on childhood pneumonia estimated from satellite remote sensing

The effect of temperature on childhood pneumonia in subtropical regions is largely unknown so far. This study examined the impact of temperature on childhood pneumonia in Brisbane, Australia. A quasi-Poisson generalized linear model combined with a distributed lag non linear model was used to quantify the main effect of temperature on emergency department visits (EDVs) for childhood pneumonia in Brisbane from 2001 to 2010. The model residuals were checked to identify added effects due to heat waves or cold spells. Both high and low temperatures were associated with an increase in EDVs for childhood pneumonia. Children aged 2–5 years, and female children were particularly vulnerable to the impacts of heat and cold, and Indigenous children were sensitive to heat. Heat waves and cold spells had significant added effects on childhood pneumonia, and the magnitude of these effects increased with intensity and duration. There were changes over time in both the main and added effects of temperature on childhood pneumonia. Children, especially those female and Indigenous, should be particularly protected from extreme temperatures. Future development of early warning systems should take the change over time in the impact of temperature on children’s health into account.