Some novel techniques of parameter estimation for the dynamical models in biological systems

Inverse problems based on using experimental data to estimate unknown parameters of a system often arise in biological and chaotic systems. In this paper, we consider parameter estimation in systems biology involving linear and non-linear complex dynamical models, including the Michaelis–Menten enzyme kinetic system, a dynamical model of competence induction in Bacillus subtilis bacteria and a model of feedback bypass in B. subtilis bacteria. We propose some novel techniques for inverse problems. Firstly, we establish an approximation of a non-linear differential algebraic equation that corresponds to the given biological systems. Secondly, we use the Picard contraction mapping, collage methods and numerical integration techniques to convert the parameter estimation into a minimization problem of the parameters. We propose two optimization techniques: a grid approximation method and a modified hybrid Nelder–Mead simplex search and particle swarm optimization (MH-NMSS-PSO) for non-linear parameter estimation. The two techniques are used for parameter estimation in a model of competence induction in B. subtilis bacteria with noisy data. The MH-NMSS-PSO scheme is applied to a dynamical model of competence induction in B. subtilis bacteria based on experimental data and the model for feedback bypass. Numerical results demonstrate the effectiveness of our approach.

Floods, earthquakes and insurance coverage : issues, problems and solutions

The recent floods in Queensland and elsewhere in Australia as well as the recent earthquakes in New Zealand have again given rise to very significant uninsured losses. This article looks at the issue of cover protection against catastrophes such as floods and earthquakes affecting home buildings and contents insurance and the standard cover provisions of the Insurance Contracts Act 1984 (Cth). It points also to the possibility of a national scheme to cover natural disasters including floods.

Development of a performance model for international construction joint venture : a system dynamics approach

The uncertain and dynamic nature of International Construction Joint Venture (ICJV) performance is evolved with many critical factors which lead to make partner relationships more complex in respect of making decisions to maintain a cohesive environment. Addressing to the fact, a generic system dynamics performance model for ICJV is developed by integrating a number variables as to get an overall impact on performance of ICJV and to make effective decisions based on that. In order to formulate and validate the model both structurally and behaviourally, both qualitative and quantitative data are gathered by conducting intensive interviews from two ICJVs in Thailand. After conducting intensive simulations of model, three major problems are identified related to negative value gap, low productivity in construction and high rate of ineffective information sharing of both ICJVs. Several policies are suggested and integrated application of these policies provides a maximum improvement to performance of the ICJV.

Year 7 students’ approaches to understanding and solving NAPLAN numeracy problems

This study investigated how the interpretation of mathematical problems by Year 7 students impacted on their ability to demonstrate what they can do in NAPLAN numeracy testing. In the study, mathematics is viewed as a culturally and socially determined system of signs and signifiers that establish the meaning, origins and importance of mathematics. The study hypothesises that students are unable to succeed in NAPLAN numeracy tests because they cannot interpret the questions, even though they may be able to perform the necessary calculations. To investigate this, the study applied contemporary theories of literacy to the context of mathematical problem solving. A case study design with multiple methods was used. The study used a correlation design to explore the connections between NAPLAN literacy and numeracy outcomes of 198 Year 7 students in a Queensland school. Additionally, qualitative methods provided a rich description of the effect of the various forms of NAPLAN numeracy questions on the success of ten Year 7 students in the same school. The study argues that there is a quantitative link between reading and numeracy. It illustrates that interpretation (literacy) errors are the most common error type in the selected NAPLAN questions, made by students of all abilities. In contrast, conceptual (mathematical) errors are less frequent amongst more capable students. This has important implications in preparing students for NAPLAN numeracy tests. The study concluded by recommending that increased focus on the literacies of mathematics would be effective in improving NAPLAN results.

BioPatML.NET – a bioinformatic pattern search engine

In the present paper, we introduce BioPatML.NET, an application library for the Microsoft Windows .NET framework [2] that implements the BioPatML pattern definition language and sequence search engine. BioPatML.NET is integrated with the Microsoft Biology Foundation (MBF) application library [3], unifying the parsers and annotation services supported or emerging through MBF with the language, search framework and pattern repository of BioPatML. End users who wish to exploit the BioPatML.NET engine and repository without engaging the services of a programmer may do so via the freely accessible web-based BioPatML Editor, which we describe below.

A node-based smoothed conforming point interpolation method (NS-CPIM) for elasticity problems

This paper formulates a node-based smoothed conforming point interpolation method (NS-CPIM) for solid mechanics. In the proposed NS-CPIM, the higher order conforming PIM shape functions (CPIM) have been constructed to produce a continuous and piecewise quadratic displacement field over the whole problem domain, whereby the smoothed strain field was obtained through smoothing operation over each smoothing domain associated with domain nodes. The smoothed Galerkin weak form was then developed to create the discretized system equations. Numerical studies have demonstrated the following good properties: NS-CPIM (1) can pass both standard and quadratic patch test; (2) provides an upper bound of strain energy; (3) avoid the volumetric locking; (4) provides the higher accuracy than those in the node-based smoothed schemes of the original PIMs.

Re-thinking how we plan to address technically complex problems : drawing on planning theory to guide practice in revision of land use plans in coastal high hazard zones

Queensland's new State Planning Policy for Coastal Protection, released in March and approved in April 2011 as part of the Queensland Coastal Plan, stipulates that local governments prepare and implement adaptation strategies for built up areas projected to be subject to coastal hazards between present day and 2100. Urban localities within the delineated coastal high hazard zone (as determined by models incorporating a 0.8 meter rise in sea level and a 10% increase in the maximum cyclone activity) will be required to re-evaluate their plans to accommodate growth, revising land use plans to minimise impacts of anticipated erosion and flooding on developed areas and infrastructure. While implementation of such strategies would aid in avoidance or minimisation of risk exposure, communities are likely to face significant challenges in such implementation, especially as development in Queensland is so intensely focussed upon its coasts with these new policies directing development away from highly desirable waterfront land. This paper examines models of planning theory to understand how we plan when faced with technically complex problems towards formulation of a framework for evaluating and improving practice.

Problems with a great idea : referral by prehospital emergency services to a community-based falls-prevention service

Background and aim Falls are the leading cause of injury in older adults. Identifying people at risk before they experience a serious fall requiring hospitalisation allows an opportunity to intervene earlier and potentially reduce further falls and subsequent healthcare costs. The purpose of this project was to develop a referral pathway to a community falls-prevention team for older people who had experienced a fall attended by a paramedic service and who were not transported to hospital. It was also hypothesised that providing intervention to this group of clients would reduce future falls-related ambulance call-outs, emergency department presentations and hospital admissions. Methods An education package, referral pathway and follow-up procedures were developed. Both services had regular meetings, and work shadowing with the paramedics was also trialled to encourage more referrals. A range of demographic and other outcome measures were collected to compare people referred through the paramedic pathway and through traditional pathways. Results Internal data from the Queensland Ambulance Service indicated that there were approximately six falls per week by community-dwelling older persons in the eligible service catchment area (south west Brisbane metropolitan area) who were attended to by Queensland Ambulance Service paramedics, but not transported to hospital during the 2-year study period (2008–2009). Of the potential 638 eligible patients, only 17 (2.6%) were referred for a falls assessment. Conclusion Although this pilot programme had support from all levels of management as well as from the service providers, it did not translate into actual referrals. Several explanations are provided for these preliminary findings.

Wound problems following hip arthroplasty before and after the introduction of a direct thrombin inhibitor for thromboprophylaxis

NICE guidelines have stated that patients undergoing elective hip surgery are at increased risk for venous thromboembolic events (VTE) following surgery and have recommended thromboprophylaxis for 28-35 days1, 2. However the studies looking at the new direct thrombin inhibitors have only looked at major bleeding. We prospectively looked at wound discharge in patients who underwent hip arthroplasty and were given dabigatran postoperatively between March 2010 and April 2010 (n=56). We retrospectively compared these results to a matched group of patients who underwent similar operations six months earlier when all patients were given dalteparin routinely postoperatively until discharge, and discharged home on 150mg aspirin daily for 6 weeks (n=67). Wound discharge after 5 days was significantly higher in the patients taking dabigatran (32% dabigatran n=18, 10% dalteparin n=17, p=0.003) and our rate of delayed discharges due to wound discharge significantly increased from 7% in the dalteparin group (n=5) to 27% for dabigatran (n=15, p=0.004). Patients who received dabigatran were more than five times as likely to return to theatre with a wound complication as those who received dalteparin (7% dabigatran n=4, vs. 1% dalteparin n=1), however, this was not statistically significant (p=0.18). The significantly higher wound discharge and return to theatre rates demonstrated in this study have meant that we have changed our practice to administering dalteparin until the wound is dry and then starting dabigatran. Our study demonstrates the need for further clinical studies regarding wound discharge and dabigatran.

Improving web database search incorporating users query information

The growing importance and need of data processing for information extraction is vital for Web databases. Due to the sheer size and volume of databases, retrieval of relevant information as needed by users has become a cumbersome process. Information seekers are faced by information overloading - too many result sets are returned for their queries. Moreover, too few or no results are returned if a specific query is asked. This paper proposes a ranking algorithm that gives higher preference to a user’s current search and also utilizes profile information in order to obtain the relevant results for a user’s query.

In search of the antecendents for risky driving at railway level crossings

This paper discusses human factors issues of low cost railway level crossings in Australia. Several issues are discussed in this paper including safety at passive level railway crossings, human factors considerations associated with unavailability of a warning device, and a conceptual model for how safety could be compromised at railway level crossings following prolonged or frequent unavailability. The research plans to quantify safety risk to motorists at level crossings using a Human Reliability Assessment (HRA) method, supported by data collected using an advanced driving simulator. This method aims to identify human error within tasks and task units identified as part of the task analysis process. It is anticipated that by modelling driver behaviour the current study will be able to quantify meaningful task variability including temporal parameters, between participants and within participants. The process of complex tasks such as driving through a level crossing is fundamentally context-bound. Therefore this study also aims to quantify those performance-shaping factors that contribute to vehicle train collisions by highlighting changes in the task units and driver physiology. Finally we will also consider a number of variables germane to ensuring external validity of our results. Without this inclusion, such an analysis could seriously underestimate the probabilistic risk assessment.

Multimedia search capabilities of Chinese language search engines

This paper reports results from a study exploring the multimedia search functionality of Chinese language search engines. Web searching in Chinese (Mandarin) is a growing research area and a technical challenge for popular commercial Web search engines. Few studies have been conducted on Chinese language search engines. We investigate two research questions: which Chinese language search engines provide multimedia searching, and what multimedia search functionalities are available in Chinese language Web search engines. Specifically, we examine each Web search engine's (1) features permitting Chinese language multimedia searches, (2) extent of search personalization and user control of multimedia search variables, and (3) the relationships between Web search engines and their features in the Chinese context. Key findings show that Chinese language Web search engines offer limited multimedia search functionality, and general search engines provide a wider range of features than specialized multimedia search engines. Study results have implications for Chinese Web users, Website designers and Web search engine developers. © 2009 Elsevier Ltd. All rights reserved.

A task-oriented approach to search engine usability studies

Usability is a multi-dimensional characteristic of a computer system. This paper focuses on usability as a measurement of interaction between the user and the system. The research employs a task-oriented approach to evaluate the usability of a meta search engine. This engine encourages and accepts queries of unlimited size expressed in natural language. A variety of conventional metrics developed by academic and industrial research, including ISO standards,, are applied to the information retrieval process consisting of sequential tasks. Tasks range from formulating (long) queries to interpreting and retaining search results. Results of the evaluation and analysis of the operation log indicate that obtaining advanced search engine results can be accomplished simultaneously with enhancing the usability of the interactive process. In conclusion, we discuss implications for interactive information retrieval system design and directions for future usability research. © 2008 Academy Publisher.

Using Web Search Logs to Identify Query Classification Terms

Purpose – The work presented in this paper aims to provide an approach to classifying web logs by personal properties of users. Design/methodology/approach – The authors describe an iterative system that begins with a small set of manually labeled terms, which are used to label queries from the log. A set of background knowledge related to these labeled queries is acquired by combining web search results on these queries. This background set is used to obtain many terms that are related to the classification task. The system then ranks each of the related terms, choosing those that most fit the personal properties of the users. These terms are then used to begin the next iteration. Findings – The authors identify the difficulties of classifying web logs, by approaching this problem from a machine learning perspective. By applying the approach developed, the authors are able to show that many queries in a large query log can be classified. Research limitations/implications – Testing results in this type of classification work is difficult, as the true personal properties of web users are unknown. Evaluation of the classification results in terms of the comparison of classified queries to well known age-related sites is a direction that is currently being exploring. Practical implications – This research is background work that can be incorporated in search engines or other web-based applications, to help marketing companies and advertisers. Originality/value – This research enhances the current state of knowledge in short-text classification and query log learning. Classification schemes, Computer networks, Information retrieval, Man-machine systems, User interfaces

Defining a session on Web search engines

Detecting query reformulations within a session by a Web searcher is an important area of research for designing more helpful searching systems and targeting content to particular users. Methods explored by other researchers include both qualitative (i.e., the use of human judges to manually analyze query patterns on usually small samples) and nondeterministic algorithms, typically using large amounts of training data to predict query modification during sessions. In this article, we explore three alternative methods for detection of session boundaries. All three methods are computationally straightforward and therefore easily implemented for detection of session changes. We examine 2,465,145 interactions from 534,507 users of Dogpile.com on May 6, 2005. We compare session analysis using (a) Internet Protocol address and cookie; (b) Internet Protocol address, cookie, and a temporal limit on intrasession interactions; and (c) Internet Protocol address, cookie, and query reformulation patterns. Overall, our analysis shows that defining sessions by query reformulation along with Internet Protocol address and cookie provides the best measure, resulting in an 82% increase in the count of sessions. Regardless of the method used, the mean session length was fewer than three queries, and the mean session duration was less than 30 min. Searchers most often modified their query by changing query terms (nearly 23% of all query modifications) rather than adding or deleting terms. Implications are that for measuring searching traffic, unique sessions may be a better indicator than the common metric of unique visitors. This research also sheds light on the more complex aspects of Web searching involving query modifications and may lead to advances in searching tools.