Physical Sciences and Mathematics Commons^™

Estimating Shared Copy Number Aberrations For Array Cgh Data: The Linear-Median Method, Yan-Xia Lin, Veera Baladandayuthapani, V Bonato, K.-A. Do

Associate Professor Yan-Xia Lin

Motivation: Existing methods for estimating copy number variations in array comparative genomic hybridization (aCGH) data are limited to estimations of the gain/loss of chromosome regions for single sample analysis. We propose the linear-median method for estimating shared copy numbers in DNA sequences across multiple samples, demonstrate its operating characteristics through simulations and applications to real cancer data, and compare it to two existing methods.

Results: Our proposed linear-median method has the power to estimate common changes that appear at isolated single probe positions or very short regions. Such changes are hard to detect by current methods. This new …

The Probability Distribution Of Distance Tss-Tls Is Organism Characteristic And Can Be Used For Promoter Prediction, Yun Dai, Ren Zhang, Yan-Xia Lin

Associate Professor Yan-Xia Lin

Transcription is a complicated process which involves the interactions of promoter cis-elements with multiple trans-protein factors. The specific interactions rely not only on the specific sequence recognition between the cis- and trans-factors but also on certain spatial arrangement of the factors in a complex. The relative positioning of involved cis-elements provides the framework for such a spatial arrangement. The distance distribution between gene transcription and translation start sites (TSS-TLS) is the subject of the present study to test an assumption that over evolution, the TSS-TLS distance becomes a distinct character for a given organism. Four representative organisms (Escherichia cloi, Saccharomyces …

Seasonal Adjustment Of An Aggregate Series Using Univariate And Multivariate Basic Structural Models, David Steel, Yan-Xia Lin, Carole Birrell

Associate Professor Yan-Xia Lin

Time series resulting from aggregation of several sub-series can be seasonally adjusted directlyor indirectly. With model-based seasonal adjustment, the sub-series may also be considered as amultivariate system of series and the analysis may be done jointly. This approach has considerableadvantage over the indirect method, as it utilises the covariance structure between the sub-series.This paper compares a model-based univariate and multivariate approach to seasonal adjustment.Firstly, the univariate basic structural model (BSM) is applied directly to the aggregate series. Secondly,the multivariate BSM is applied to a transformed system of sub-series. The prediction meansquared errors of the seasonally adjusted aggregate series resulting from …

A Dynamic Platform For Business Process Management (Bpm) Using Service-Oriented Enterprise (Soe), Nantika Prinyapol, Joshua Fan, Sim Lau

Dr Sim Kim Lau

No abstract provided.

A Dynamic Nursing Workflow Management System: A Thailand Hospital Scenario, Nantika Prinyapol, Joshua Fan, Sim Lau

Dr Sim Kim Lau

No abstract provided.

Ontology Matching Techniques: A 3-Tier Classification Framework, Nelson Leung, Seung Kang, S Lau, Joshua Fan

Dr Sim Kim Lau

No abstract provided.

Ontology-Driven Accounting Information System: Case Study Of The Stock Exchange Of Thailand, Jira Yammeesri, Seung Hwan Kang, S Lau

Dr Sim Kim Lau

Accounting information systems have improved conventional information control. Due to corporate meltdowns, corporate governance has come under greater scrutiny to improve practices of managing, retrieving and extracting accounting information within organizations. This paper introduces a framework for an ontology-driven accounting information system as a mean to share information in line of common agreement. The proposed approach contributes to weakening of asymmetric information and information transparency problems.

Ontology Information Retrieval For Academic Resources, Norasykin Mohd Zaid, Sim Lau

Dr Sim Kim Lau

No abstract provided.

Measuring The Maturity Level Of A Community Portal, Peter Hyland, Lejla Vrazalic

Associate Professor Peter Hyland

No abstract provided.

Benefits Of Online Patient Education (Ope) For Chronic Disease, Naffisah Hassan, Khin Than Win, Peter Hyland

Associate Professor Peter Hyland

No abstract provided.

An Application Of The 5-S Activity Theoretic Requirements Method, Robert Brown, Peter Hyland, Ian Piper

Associate Professor Peter Hyland

One of the most crucial aspects of highly interactive, multi-user, organisational systems is the interface. The Human Computer Interaction (HCI) community has not adopted rigorous Formal Methods with open arms (Paterno, 1996). However, the HCI community has widely adopted Usability Engineering approaches (Corporate Solutions 2006), such as Nielsen’s (1994), which offers considerable formality. There remains, however, scope for user interface (UI) design to adopt a theoretical framework to enhance consistency across the whole design and development lifecycle. A theoretically-consistent framework from initial conceptual elicitation to evaluation of the finished product may prove useful. Since the aim of UI design is …

A Study Of Information Security Awareness And Practices In Saudi Arabia, Abdulaziz Alarifi, Holly Tootell, Peter Hyland

Associate Professor Peter Hyland

Although the Web, cell phoneand cloud computing put a world of information at our fingertips, that information is under constant threat from cyber vandals and hackers. While awareness of information threats is growing in the Western world, in places like Saudi Arabia, information security is very poor. Unlike Western pluralistic democracies, Saudi Arabia is a highly-censored country, with a patriarchical and tribal culture, which may influence its poor information security rating. This paper examines the level of information security awareness (ISA) among the general public in Saudi Arabia, using an anonymous online survey, based on instruments produced by the Malaysian …

Loss Protection In Pairs Trading Through Minimum Profit Bounds: A Cointegration Approach, Chandra Gulati, Yan-Xia Lin, Michael Mccrae

Dr Chandra Gulati

No abstract provided.

Identify And Extract Delta Of Materialized View With Limited Collaborations, Z. Lu, Janusz Getta

Dr Janusz Getta

This work considers the materialized view maintenance in a distributed environment where the collaboration of the operational systems is limited to granting read only access on the selected relational tables. In addition, due to possibly large volumes of source relational tables involved in the view maintenance process and consequently enormous overhead associated with data extracting and transporting, the efficiency issues have been taken into the consideration and some optimization techniques are included in this paper.

Using Digital Tickets To Protect Personal Privacy, Yibing Kong, Jennifer Seberry, Janusz Getta, Ping Yu

Dr Janusz Getta

No abstract provided.

Model-Based Fuzzy Control For Buildings Installed With Magneto-Rheological Dampers, Haiping Du, Nong Zhang

Dr Haiping Du

No abstract provided.

Robust Vehicle Stability Control Based On Sideslip Angle Estimation, Haiping Du, Nong Zhang

Dr Haiping Du

No abstract provided.

Development And Simulation Evaluation Of A Magnetorheological Elastomer Isolator For Seat Vibration Control, Weihua Li, Xianzhou Zhang, Haiping Du

Dr Haiping Du

Driver fatigue is one of the leading factors contributing to road crashes. Environmental stress, such as unwanted seat vibration, is a key contributor to fatigue. This article presents the design and development of a magnetorheological elastomer isolator for a seat suspension system. By altering the magnetorheological elastomer isolator’s stiffness through a controllable magnetic field and selecting suitable control strategy, the system’s natural frequency can be changed to avoid resonance, which consequently reduce the vehicle’s vibration energy input to seat, and thus suppress the seat’s response. Experimental results show that the developed magnetorheological elastomer isolator is able to reduce vibration more …

A Comparative Study Of Vehicle Drive Performance And Energy Efficiency, S. Abdul Rahman, P. D. Walker, Nong Zhang, Jianguo Zhu, Haiping Du

Dr Haiping Du

In this paper, two types of increasingly more efficient and greener vehicles are analyzed and compared. These vehicles are: a proposed conceptual seriesparallel powertrain, the University of Technology, Sydney plug-in hybrid electric vehicle (UTS PREY); and, a conventional series-parallel hybrid electric vehicle with an internal combustion engine .. The UTS PREY requires only a single electric machine to function as an electric motor or generator in different time intervals controlled by a special energy management strategy. The UTS PREV uses two energy storage devices, the battery and the ultracapacitor, which can work together effectively to maintain the state of charge …

Vibration Control Of Seat Considering Vehicle Suspension And Human-Body Models, Haiping Du, Weihua Li, Nong Zhang

Dr Haiping Du

Vehicle seat suspension is one of very important components to provide ride comfort, in particular, commercial vehicles, to reduce driver fatigue due to long hours driving. This paper presents a study on active control of seat suspension to reduce vertical vibration transmitted from uneven road profile to driver body. The control problem will be firstly studied by proposing an integrated seat suspension model which includes vehicle chassis suspension, seat suspension, and driver body model. This is a new concept in the field of study because most of the current active and semi-active seat suspension studies only consider seat suspension or …

Ship Classification By Superstructure Moment Invariants, Prashan Premaratne, Farzad Safaei

Dr Prashan Premaratne

Direct observation using satellites and long range video surveillance is not possible for ship classification in adverse weather and during night. Radar and more specifically radar imaging offers a solution for the above adverse conditions. Ship Classification using radar is of utmost important to defense of any country to manage vast naval resources and to tell the friend from foe. Automatic ship classification based on radar images has been very successful in determining the ship class as well as other details to reliably recognize a ship type using machine vision. Inverse Synthetic Aperture Radar (ISAR) Imaging which relies on a …

Automated Change Impact Analysis For Agent Systems, Aditya Ghose, Hoa Dam

Dr Hoa Dam

Intelligent agent technology has evolved rapidly over the past few years along with the growing number of agent systems in various domains. Although a substantial amount of work in agent-oriented software engineering has provided methodologies for analysing, designing and implementing agent-based systems, recent studies have highlighted that there has been very little work on maintenance and evolution of agent-based systems. A critical issue in software maintenance and evolution is change impact analysis: determining the potential consequences of a proposed change. There has been a proliferation of techniques proposed to support change impact analysis of procedural or object-oriented systems, but to …

A Sparse Implementation Of The Average Information Algorithm For Factor Analytic And Reduced Rank Variance Models, R Thompson, Brian Cullis, A Smith, Arthur Gilmour

Professor Brian Cullis

Factor analytic variance models have been widely considered for the analysis of multivariate data particularly in the psychometrics area. Recently Smith, Cullis & Thompson (2001) have considered their use in the analysis of multi-environment data arising from plant improvement programs. For these data, the size of the problem and the complexity of the variance models chosen to account for spatial heterogeneity within trials implies that standard algorithms for fitting factor analytic models can be computationally expensive. This paper presents a sparse implementation of the average information algorithm (Gilmour, Thompson & Cullis, 1995) for fitting factor analytic and reduced rank variance …

Joint Modeling Of Additive And Non-Additive Genetic Line Effects In Single Field Trials, H Oakey, A Verbyla, Brian Cullis, W. Pitchford, H. Kuchel

Professor Brian Cullis

A statistical approach is presented for selection of best performing lines for commercial release and best parents for future breeding programs from standard agronomic trials. The method involves the partitioning of the genetic effect of a line into additive and non-additive effects using pedigree based inter-line relationships, in a similar manner to that used in animal breeding. A difference is the ability to estimate non-additive effects. Line performance can be assessed by an overall genetic line effect with greater accuracy than when ignoring pedigree information and the additive effects are predicted breeding values. A generalized definition of heritability is developed …

Assessing Barotrauma Among Angled Snapper (Pagrus Auratus) And The Utility Of Release Methods, Paul Butcher, Matt Broadhurst, Karina Hall, Brian Cullis, Shane Raidal

Professor Brian Cullis

Australian recreational and commercial fishers catch snapper (Pagrus auratus) from down to 120 m, often evoking barotrauma. Owing to minimum legal sizes and quotas or non-consumptive fishing practices, some afflicted fish are released, raising concerns over the potential for unaccounted fishing mortality. Two experiments were completed to quantify the (1) clinical signs of barotrauma among fish angled from 6 to 120 m (experiment 1) and (2) mortality (over 3 d) of fish with barotrauma that were released following either no treatment, venting (e.g. needle) or recompression (e.g. release weight) (experiment 2). In experiment 1, barotrauma was evident in some fish …

Pasture And Sheep Responses To Lime Application In A Grazing Experiment In A High-Rainfall Area, South-Eastern Australia. Ii. Liveweight Gain And Wool Production, G. Li, K. Helyar, M. Conyers, L. Castleman, R. Fisher, G Poile, C Lisle, Brian Cullis, P. Cregan

Professor Brian Cullis

‘Managing Acid Soils Through Efficient Rotations (MASTER)’ is a long-term pasture–crop rotation experiment commenced in 1992. One of the objectives was to demonstrate the extent of crop, pasture, and animal responses to lime application on a typical acidic soil in the 500–800 mm rainfall zone of south-eastern Australia. Two types of pastures (perennial v. annual pastures) with or without lime application were established in 1992. Fifteen- to eighteen-month-old Merino hoggets were used as test animals and were changed annually. This paper reports the results of sheep responses to liming from the 4 continuous pasture treatments over 6 years from 1992 …

Comparison Of Small-Scale And Large-Scale Mixing Characteristics: Correlations Between Small-Scale And Large-Scale Mixing And Extensional Characteristics Of Wheat Flour Dough, Helen Allen, Simon Diffey, Allen H, Zena Pumpa, Simon Nath, Jennifer Morell, Gulay Cullis, Alison Smith

Professor Brian Cullis

measurements provide valuable information about dough strength and stability (STAB) traits. These measurements are important in milling and baking operations, and for varietal selection in wheat breeding programmes. There are several techniques with different sample sizes used for measuring these traits so there is interest in examining the agreement between methods in terms of genotypic (varietal) rankings. This issue has been investigated by using two different mixing methods, a small-scale Mixograph (2 g) and large-scale Farinograph (50 g) using data from a doubled haploid population (190 lines) from a Chara (excellent dough strength)×WW2449 (poor dough strength) cross. The cross was …

The Analysis Of Longitudinal Data Using Mixed Model L-Splines, S. Welham, Brian Cullis, M. Kenward, R Thompson

Professor Brian Cullis

L-splines are a large family of smoothing splines defined in terms of a linear differential operator. This article develops L-splines within the context of linear mixed models and uses the resulting mixed model L-spline to analyze longitudinal data from a grassland experiment. In the spirit of time-series analysis, a periodic mixed model L-spline is developed, which partitions data into a smooth periodic component plus smooth long-term trend.

Effects Of Otter Boards On Catches Of An Australian Penaeid Trawl, Matt Broadhurst, David Sterling, Brian Cullis

Professor Brian Cullis

The effects of otter boards on the catches of Metapenaeus macleayi were quantified within the broad aim of promoting more hydrodynamic and environmentally benign trawl-spreading mechanisms. Two identical trawls (7.26 m footropes) were attached to 2.89-m sweeps and simultaneously fished in a double-rig; each alternately attached to either two otter boards or a rigid 6.0-m beam with parallel sleds (configured not to impact on the behaviour of M. macleayi). Both trawl configurations had the same total weight (143 kg) and initial wing-end spreads (predicted means of 4.33 and 4.45 m), although the otter boards caused significantly more variable wing-end spread …

On Spatial Prediction Of Soil Properties In The Presence Of A Spatial Trend: The Empirical Best Linear Unbiased Predictor (E-Blup) With Reml, R Lark, B Cullis, S Welham

Professor Brian Cullis

Geostatistical estimates of a soil property by kriging are equivalent to the best linear unbiased predictions (BLUPs). Universal kriging is BLUP with a fixed-effect model that is some linear function of spatial coordinates, or more generally a linear function of some other secondary predictor variable when it is called kriging with external drift. A problem in universal kriging is to find a spatial variance model for the random variation, since empirical variograms estimated from the data by method-of-moments will be affected by both the random variation and that variation represented by the fixed effects. The geostatistical model of spatial variation …