An evaluation of contemporary hidden Markov model genefinders with a predicted exon taxonomy

We present an independent evaluation of six recent hidden Markov model (HMM) genefinders. Each was tested on the new dataset (FSH298), the results of which showed no dramatic improvement over the genefinders tested five years ago. In addition, we introduce a comprehensive taxonomy of predicted exons and classify each resulting exon accordingly. These results are useful in measuring (with finer granularity) the effects of changes in a genefinder. We present an analysis of these results and identify four patterns of inaccuracy common in all HMM-based results.

A morphological model for sexing nestling peregrine falcons (Falco Peregrinus Macropus) verified through genetic analysis

Adult peregrine falcons (Falco peregrinus macropus) have monotypic plumage and display strong reversed sexual dimorphism, with females significantly larger than males. Reversed sexual dimorphism is measurable among nestlings in the latter stages of their development and can therefore be used to differentiate between sexes. In the early stages of development, however, nestlings cannot be sexed with any degree of certainty because morphological differentiation between the sexes is not well developed. During this study we developed a model for sexing younger nestlings based on genetic analysis and morphometric data collected as part of a long-term banding study of this species. A discriminant function model based on morphological characteristics was developed for determining the sex of nestlings (n = 150) in the field and was shown to be 96.0% accurate. This predictive model was further tested against an independent morphometric dataset taken from a second group of nestlings (n = 131). The model correctly allocated sex to 96.2% of this second group of nestlings. Sex can reliably be determined (98.6% accurate) for nestlings that have a wing length of at least 9 cm using this model. Application of this model, therefore, allows the banding of younger nestlings and, as such, significantly increases the period of time over which banding can occur. Another important implication of this model is that by banding nestlings earlier, they are less likely to jump from the nest, therefore reducing the risk of injury to both the brood and the bander.

Development of the multi-scale analysis model to simulate strain localization occurring during material processing

Abstract A detailed description of possibilities given by the developed Cellular Automata—Finite Element (CAFE) multi scale model for prediction of the initiation and propagation of micro shear bands and shear bands in metallic materials subjected to plastic deformation is presented in the work. Particular emphasis in defining the criterion for initiation of micro shear and shear bands, as well as in defining the transition rules for the cellular automata, is put on accounting for the physical aspects of these phenomena occurring in two different scales in the material. The proposed approach led to the creation of the real multi scale model of strain localization phenomena. This model predicts material behavior in various thermo-mechanical processes. Selected examples of applications of the developed model to simulations of metal forming processes, which involve strain localization, are presented in the work. An approach based on the Smoothed Particle Hydrodynamic, which allows to overcome difficulties with remeshing in the traditional CAFE method, is a subject of this work as well. In the developed model remeshing becomes possible and difficulties limiting application of the CAFE method to simple deformation processes are solved. Obtained results of numerical simulaA detailed description of possibilities given by the developed Cellular Automata—Finite Element (CAFE) multi scale model for prediction of the initiation and propagation of micro shear bands and shear bands in metallic materials subjected to plastic deformation is presented in the work. Particular emphasis in defining the criterion for initiation of micro shear and shear bands, as well as in defining the transition rules for the cellular automata, is put on accounting for the physical aspects of these phenomena occurring in two different scales in the material. The proposed approach led to the creation of the real multi scale model of strain localization phenomena. This model predicts material behavior in various thermo-mechanical processes. Selected examples of applications of the developed model to simulations of metal forming processes, which involve strain localization, are presented in the work. An approach based on the Smoothed Particle Hydrodynamic, which allows to overcome difficulties with remeshing in the traditional CAFE method, is a subject of this work as well. In the developed model remeshing becomes possible and difficulties limiting application of the CAFE method to simple deformation processes are solved. Obtained results of numerical simulations are compared with the experimental results of cold rolling process to show good predicative capabilities of the developed model.tions are compared with the experimental results of cold rolling process to show good predicative capabilities of the developed model.

Optimization of mixing parameters through a water model for metal matrix composites synthesis

The influence of the mixing parameters on the synthesis of Al–SiCp reinforced metal matrix composites (MMCs) by the stir casting technique is investigated through a water model. The effects of some important mixing parameters such as impeller blade angle, rotating speed, direction of impeller rotation and effect of baffles are investigated and optimized. The results have shown that the axial concentration variation of natural graphite during stirring in the presence of four vertical baffles is 1.0 wt% against in the absence of baffles it is increased to 2.3 wt%. The variations observed in natural graphite concentration in water during mixing are in close agreement with the earlier modeling and limited experimental studies reported on the real molten aluminum–SiC system. Semi-empirical correlations arrived at between the dimensionless numbers for stirred water – natural graphite slurries are Po = Re−0.0545 Fr−1.099 and Po = Re−0.0219 Fr−1.0382 for clockwise and counter clockwise rotation respectively.

The effect of nano-particle TiO2 fillers on structure and transport in polymer electrolytes

Nano-particle oxide fillers including TiO₂, SiO₂ and Al₂O₃ have previously been shown to have a significant affect on the properties of polymer electrolytes, especially those based on polyether–lithium salt systems. In some cases, conductivity increases of more than one order of magnitude have been reported in crystalline PEO-based complexes. In this work, we report on the effects of TiO₂ on a completely amorphous polyether-based system to remove the complication of multiple phases presented by the semi-crystalline nature of PEO. Multinuclear magnetic resonance spectroscopy has shown that the lithium ion environment is changed by the addition of filler. Vibrational spectroscopy shows that the filler influences the disordered-longitudinal acoustic modes (DLAM) in the case of an amorphous polyether and suggests an interaction between the filler surface and the polymer. Positron annihilation lifetime spectroscopy indicates an increase in free volume upon addition of filler to an amorphous polyether–salt complex, coinciding with an apparent increase in polymer mobility as determined from ¹H T₂ NMR measurements. Impedance spectroscopy has shown clear evidence of an inter-phase region that may be more or less conductive than the bulk polymer electrolyte itself. The data support a model which includes conduction through an interfacial region in addition to the bulk polymer

Dialysis residential care : a future dialysis service model

People with chronic kidney disease are ageing and have increasing co-morbidities. The current delivery of renal replacement therapy, dialysis and transplantation, needs to adjust to changing patient needs. This paper proposes a potential future service delivery model featuring a dialysis residential care facility and a care coordination focus. The residential care facility would be composed of four levels of care; high, hostel, independent and outpatient. The paper argues that this model may result in decreased morbidity, improved patient quality of life and may prove cost effective. Patients' nutritional status, medication adherence and transport efficiency may be improved. We propose this model to stimulate further debate in order to meet the needs of current and future chronic kidney disease patients.

Mathematical modelling of downflow floating medium filter (DFF) with in-line flocculation arrangement

A laboratory-scale set-up consisting of rapid mixing device and floating medium filter was used to study the use of a downflow floating medium filter (DFF) with an in-line flocculation arrangement as a static flocculator and a prefilter. The semi-empirical mathematical model formulated incorporates flocculation within the filter, particle/floc attachment onto the filter and the detachment of flocs from the medium. The mathematical model for filtration takes into account the expansion of the filter bed. The removal efficiency of DFF and headless development were successfully simulated for different conditions of filtration velocity, filter depth and influent suspended solids (SS). The values of attachment coefficient a(p)β and headless coefficient β1 were found to be independent of filtration velocity, filter depth and influent SS concentration.

A predictive model of avian natal dispersal distance provides prior information for investigating response to landscape change

1. Informative Bayesian priors can improve the precision of estimates in ecological studies or estimate parameters for which little or no information is available. While Bayesian analyses are becoming more popular in ecology, the use of strongly informative priors remains rare, perhaps because examples of informative priors are not readily available in the published literature.
2. Dispersal distance is an important ecological parameter, but is difficult to measure and estimates are scarce. General models that provide informative prior estimates of dispersal distances will therefore be valuable.
3. Using a world-wide data set on birds, we develop a predictive model of median natal dispersal distance that includes body mass, wingspan, sex and feeding guild. This model predicts median dispersal distance well when using the fitted data and an independent test data set, explaining up to 53% of the variation.
4. Using this model, we predict a priori estimates of median dispersal distance for 57 woodland-dependent bird species in northern Victoria, Australia. These estimates are then used to investigate the relationship between dispersal ability and vulnerability to landscape-scale changes in habitat cover and fragmentation.
5. We find evidence that woodland bird species with poor predicted dispersal ability are more vulnerable to habitat fragmentation than those species with longer predicted dispersal distances, thus improving the understanding of this important phenomenon.
6. The value of constructing informative priors from existing information is also demonstrated. When used as informative priors for four example species, predicted dispersal distances reduced the 95% credible intervals of posterior estimates of dispersal distance by 8-19%. Further, should we have wished to collect information on avian dispersal distances and relate it to species' responses to habitat loss and fragmentation, data from 221 individuals across 57 species would have been required to obtain estimates with the same precision as those provided by the general model.

Virtual haptic cell model for operator training

Microrobotic cell injection is an area of growing research interest. Typically, operators rely on visual feedback to perceive the microscale environment and are subject to lengthy training times and low success rates. Haptic interaction offers the ability to utilise the operator’s haptic modality and to enhance operator performance. Our earlier work presented a haptically enabled system for assisting the operator with certain aspects of the cell injection task. The system aimed to enhance the operator’s controllability of the micropipette through a logical mapping between the haptic device and microrobot, as well as introducing virtual fixtures for haptic guidance. The system was also designed in such a way that given the availability of appropriate force sensors, haptic display of the cell penetration force is straightforward. This work presents our progress towards a virtual replication of the system, aimed at facilitating offline operator training. It is suggested that operators can use the virtual system to train offline and later transfer their skills to the physical system. In order to achieve the necessary representation of the cell within the virtual system, methods based on a particle-based cell model are utilised. In addition to providing the necessary visual representation, the cell model provides the ability to estimate cell penetration forces and haptically display them to the operator. Two different approaches to achieving the virtual system are discussed.

Policy recognition in the Abstract Hidden Markov Model

In this paper, we present a method for recognising an agent's behaviour in dynamic, noisy, uncertain domains, and across multiple levels of abstraction. We term this problem on-line plan recognition under uncertainty and view it generally as probabilistic inference on the stochastic process representing the execution of the agent's plan. Our contributions in this paper are twofold. In terms of probabilistic inference, we introduce the Abstract Hidden Markov Model (AHMM), a novel type of stochastic processes, provide its dynamic Bayesian network (DBN) structure and analyse the properties of this network. We then describe an application of the Rao-Blackwellised Particle Filter to the AHMM which allows us to construct an efficient, hybrid inference method for this model. In terms of plan recognition, we propose a novel plan recognition framework based on the AHMM as the plan execution model. The Rao-Blackwellised hybrid inference for AHMM can take advantage of the independence properties inherent in a model of plan execution, leading to an algorithm for online probabilistic plan recognition that scales well with the number of levels in the plan hierarchy. This illustrates that while stochastic models for plan execution can be complex, they exhibit special structures which, if exploited, can lead to efficient plan recognition algorithms. We demonstrate the usefulness of the AHMM framework via a behaviour recognition system in a complex spatial environment using distributed video surveillance data.

Learning and detecting activities from movement trajectories using the hierarchical hidden Markov model

Directly modeling the inherent hierarchy and shared structures of human behaviors, we present an application of the hierarchical hidden Markov model (HHMM) for the problem of activity recognition. We argue that to robustly model and recognize complex human activities, it is crucial to exploit both the natural hierarchical decomposition and shared semantics embedded in the movement trajectories. To this end, we propose the use of the HHMM, a rich stochastic model that has been recently extended to handle shared structures, for representing and recognizing a set of complex indoor activities. Furthermore, in the need of real-time recognition, we propose a Rao-Blackwellised particle filter (RBPF) that efficiently computes the filtering distribution at a constant time complexity for each new observation arrival. The main contributions of this paper lie in the application of the shared-structure HHMM, the estimation of the model's parameters at all levels simultaneously, and a construction of an RBPF approximate inference scheme. The experimental results in a real-world environment have confirmed our belief that directly modeling shared structures not only reduces computational cost, but also improves recognition accuracy when compared with the tree HHMM and the flat HMM.

Recognising behaviours of multiple people with hierarchical probabilistic model and statistical data association

Recognising behaviours of multiple people, especially high-level behaviours, is an important task in surveillance systems. When the reliable assignment of people to the set of observations is unavailable, this task becomes complicated. To solve this task, we present an approach, in which the hierarchical hidden Markov model (HHMM) is used for modeling the behaviour of each person and the joint probabilistic data association filters (JPDAF) is applied for data association. The main contributions of this paper lie in the integration of multiple HHMMs for recognising high-level behaviours of multiple people and the construction of the Rao-Blackwellised particle filters (RBPF) for approximate inference. Preliminary experimental results in a real environment show the robustness of our integrated method in behaviour recognition and its advantage over the use of Kalman filter in tracking people.

Using clinical trial data and linked administrative health data to reduce the risk of adverse events associated with the uptake of newly released drugs by older Australians : a model process

Background
The study was undertaken to evaluate the contribution of a process which uses clinical trial data plus linked de-identified administrative health data to forecast potential risk of adverse events associated with the use of newly released drugs by older Australian patients.

Methods
The study uses publicly available data from the clinical trials of a newly released drug to ascertain which patient age groups, gender, comorbidities and co-medications were excluded in the trials. It then uses linked de-identified hospital morbidity and medications dispensing data to investigate the comorbidities and co-medications of patients who suffer from the target morbidity of the new drug and who are the likely target population for the drug. The clinical trial information and the linked morbidity and medication data are compared to assess which patient groups could potentially be at risk of an adverse event associated with use of the new drug.

Results
Applying the model in a retrospective real-world scenario identified that the majority of the sample group of Australian patients aged 65 years and over with the target morbidity of the newly released COX-2-selective NSAID rofecoxib also suffered from a major morbidity excluded in the trials of that drug, indicating a substantial potential risk of adverse events amongst those patients. This risk was borne out in post-release morbidity and mortality associated with use of that drug.

Conclusions
Clinical trial data and linked administrative health data can together support a prospective assessment of patient groups who could be at risk of an adverse event if they are prescribed a newly released drug in the context of their age, gender, comorbidities and/or co-medications. Communication of this independent risk information to prescribers has the potential to reduce adverse events in the period after the release of the new drug, which is when the risk is greatest.

Note: The terms 'adverse drug reaction' and 'adverse drug event' have come to be used interchangeably in the current literature. For consistency, the authors have chosen to use the wider term 'adverse drug event' (ADE).

Age at quitting smoking as a predictor of risk of cardiovascular disease incidence independent of smoking status, time since quitting and pack-years

Background: Risk prediction for CVD events has been shown to vary according to current smoking status, pack-years smoked over a lifetime, time since quitting and age at quitting. The latter two are closely and inversely related. It is not known whether the age at which one quits smoking is an additional important predictor of CVD events. The aim of this study was to determine whether the risk of CVD events varied according to age at quitting after taking into account current smoking status, lifetime pack-years smoked and time since quitting.
Findings. We used the Cox proportional hazards model to evaluate the risk of developing a first CVD event for a cohort of participants in the Framingham Offspring Heart Study who attended the fourth examination between ages 30 and 74 years and were free of CVD. Those who quit before the median age of 37 years had a risk of CVD incidence similar to those who were never smokers. The incorporation of age at quitting in the smoking variable resulted in better prediction than the model which had a simple current smoker/non-smoker measure and the one that incorporated both time since quitting and pack-years. These models demonstrated good discrimination, calibration and global fit. The risk among those quitting more than 5 years prior to the baseline exam and those whose age at quitting was prior to 44 years was similar to the risk among never smokers. However, the risk among those quitting less than 5 years prior to the baseline exam and those who continued to smoke until 44 years of age (or beyond) was two and a half times higher than that of never smokers.
Conclusions: Age at quitting improves the prediction of risk of CVD incidence even after other smoking measures are taken into account. The clinical benefit of adding age at quitting to the model with other smoking measures may be greater than the associated costs. Thus, age at quitting should be considered in addition to smoking status, time since quitting and pack-years when counselling individuals about their cardiovascular risk.

A predictive model of avian natal dispersal distance provides prior information for investigating response to landscape change

1. Informative Bayesian priors can improve the precision of estimates in ecological studies or estimate parameters for which little or no information is available. While Bayesian analyses are becoming more popular in ecology, the use of strongly informative priors remains rare, perhaps because examples of informative priors are not readily available in the published literature.

2. Dispersal distance is an important ecological parameter, but is difficult to measure and estimates are scarce. General models that provide informative prior estimates of dispersal distances will therefore be valuable.

3. Using a world-wide data set on birds, we develop a predictive model of median natal dispersal distance that includes body mass, wingspan, sex and feeding guild. This model predicts median dispersal distance well when using the fitted data and an independent test data set, explaining up to 53% of the variation.

4. Using this model, we predict a priori estimates of median dispersal distance for 57 woodland-dependent bird species in northern Victoria, Australia. These estimates are then used to investigate the relationship between dispersal ability and vulnerability to landscape-scale changes in habitat cover and fragmentation.

5. We find evidence that woodland bird species with poor predicted dispersal ability are more vulnerable to habitat fragmentation than those species with longer predicted dispersal distances, thus improving the understanding of this important phenomenon.

6. The value of constructing informative priors from existing information is also demonstrated. When used as informative priors for four example species, predicted dispersal distances reduced the 95% credible intervals of posterior estimates of dispersal distance by 8-19%. Further, should we have wished to collect information on avian dispersal distances and relate it to species' responses to habitat loss and fragmentation, data from 221 individuals across 57 species would have been required to obtain estimates with the same precision as those provided by the general model.