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.

Elements pour adapter les systemes de recherche d'information aux dyslexiques [Elements to adapt information retrieval systems to dyslexic users]

RÉSUMÉ. La prise en compte des troubles de la communication dans l’utilisation des systèmes de recherche d’information tels qu’on peut en trouver sur le Web est généralement réalisée par des interfaces utilisant des modalités n’impliquant pas la lecture et l’écriture. Peu d’applications existent pour aider l’utilisateur en difficulté dans la modalité textuelle. Nous proposons la prise en compte de la conscience phonologique pour assister l’utilisateur en difficulté d’écriture de requêtes (dysorthographie) ou de lecture de documents (dyslexie). En premier lieu un système de réécriture et d’interprétation des requêtes entrées au clavier par l’utilisateur est proposé : en s’appuyant sur les causes de la dysorthographie et sur les exemples à notre disposition, il est apparu qu’un système combinant une approche éditoriale (type correcteur orthographique) et une approche orale (système de transcription automatique) était plus approprié. En second lieu une méthode d’apprentissage automatique utilise des critères spécifiques , tels que la cohésion grapho-phonémique, pour estimer la lisibilité d’une phrase, puis d’un texte. ABSTRACT. Most applications intend to help disabled users in the information retrieval process by proposing non-textual modalities. This paper introduces specific parameters linked to phonological awareness in the textual modality. This will enhance the ability of systems to deal with orthographic issues and with the adaptation of results to the reader when for example the reader is dyslexic. We propose a phonology based sentence level rewriting system that combines spelling correction, speech synthesis and automatic speech recognition. This has been evaluated on a corpus of questions we get from dyslexic children. We propose a specific sentence readability measure that involves phonetic parameters such as grapho-phonemic cohesion. This has been learned on a corpus of reading time of sentences read by dyslexic children.

Determining operational measures from multi-camera surveillance systems using soft biometrics

CCTV and surveillance networks are increasingly being used for operational as well as security tasks. One emerging area of technology that lends itself to operational analytics is soft biometrics. Soft biometrics can be used to describe a person and detect them throughout a sparse multi-camera network. This enables them to be used to perform tasks such as determining the time taken to get from point to point, and the paths taken through an environment by detecting and matching people across disjoint views. However, in a busy environment where there are 100's if not 1000's of people such as an airport, attempting to monitor everyone is highly unrealistic. In this paper we propose an average soft biometric, that can be used to identity people who look distinct, and are thus suitable for monitoring through a large, sparse camera network. We demonstrate how an average soft biometric can be used to identify unique people to calculate operational measures such as the time taken to travel from point to point.

Stochastic chemical kinetics and the quasi-steady-state assumption : application to the stochastic simulation algorithm and chemical master equation

Recently the application of the quasi-steady-state approximation (QSSA) to the stochastic simulation algorithm (SSA) was suggested for the purpose of speeding up stochastic simulations of chemical systems that involve both relatively fast and slow chemical reactions [Rao and Arkin, J. Chem. Phys. 118, 4999 (2003)] and further work has led to the nested and slow-scale SSA. Improved numerical efficiency is obtained by respecting the vastly different time scales characterizing the system and then by advancing only the slow reactions exactly, based on a suitable approximation to the fast reactions. We considerably extend these works by applying the QSSA to numerical methods for the direct solution of the chemical master equation (CME) and, in particular, to the finite state projection algorithm [Munsky and Khammash, J. Chem. Phys. 124, 044104 (2006)], in conjunction with Krylov methods. In addition, we point out some important connections to the literature on the (deterministic) total QSSA (tQSSA) and place the stochastic analogue of the QSSA within the more general framework of aggregation of Markov processes. We demonstrate the new methods on four examples: Michaelis–Menten enzyme kinetics, double phosphorylation, the Goldbeter–Koshland switch, and the mitogen activated protein kinase cascade. Overall, we report dramatic improvements by applying the tQSSA to the CME solver.

Identity fraud and land registration systems : an Australian perspective

There is no doubt that fraud in relation to land transactions is a problem that resonates amongst land academics, practitioners, and stakeholders involved in conveyancing. As each land registration and conveyancing process increasingly moves towards a fully electronic environment, we need to make sure that we understand and guard against the frauds that can occur. What this paper does is examine the types of fraud that have occurred in paper-based conveyancing systems in Australia and considers how they might be undertaken in the National Electronic Conveyancing System (NECS) that is currently under development. Whilst no system can ever be infallible, it is suggested that by correctly imposing the responsibility for identity verification on the appropriate individual, the conveyancing system adopted can achieve the optimum level of fairness in terms of allocation of responsibility and loss. As we sit on the cusp of a new era of electronic conveyancing, the framework suggested here provides a model for minimising the risks of forged mortgages and appropriately allocating the loss. Importantly it also recognises that the electronic environment will see new opportunities for those with criminal intent to undermine the integrity of land transactions. An appreciation of this now, can see the appropriate measures put in place to minimise the risk.

Urban Informatics Research and Insights for Libraries, Cultural Industries and Innovation Systems

Over less than a decade, we have witnessed a seismic shift in the way knowledge is produced and exchanged. This is opening up new opportunities for civic and community engagement, entrepreneurial behaviour, sustainability initiatives and creative practices. It also has the potential to create fresh challenges in areas of privacy, cyber-security and misuse of data and personal information. The field of urban informatics focuses on the use and impacts of digital media technology in urban environments. Urban informatics is a dynamic and cross-disciplinary area of inquiry that encapsulates social media, ubiquitous computing, mobile applications and location-based services. Its insights suggest the emergence of a new economic force with the potential for driving innovation, wealth and prosperity through technological advances, digital media and online networks that affect patterns of both social and economic development. Urban informatics explores the intersections between people, place and technology, and their implications for creativity, innovation and engagement. This paper examines how the key learnings from this field can be used to position creative and cultural institutions such as galleries, libraries, archives and museums (GLAM) to take advantage of the opportunities presented by these changing social and technological developments. This paper introduces the underlying principles, concepts and research areas of urban informatics, against the backdrop of modern knowledge economies. Both theoretical ideas and empirical examples are covered in this paper. The first part discusses three challenges: a. People, and the challenge of creativity: The paper explores the opportunities and challenges of urban informatics that can lead to the design and development of new tools, methods and applications fostering participation, the democratisation of knowledge, and new creative practices. b. Technology, and the challenge of innovation: The paper examines how urban informatics can be applied to support user-led innovation with a view to promoting entrepreneurial ideas and creative industries. c. Place, and the challenge of engagement: The paper discusses the potential to establish place-based applications of urban informatics, using the example of library spaces designed to deliver community and civic engagement strategies. The discussion of these challenges is illustrated by a review of projects as examples drawn from diverse fields such as urban computing, locative media, community activism, and sustainability initiatives. The second part of the paper introduces an empirically grounded case study that responds to these three challenges: The Edge, the Queensland Government’s Digital Culture Centre which is an initiative of the State Library of Queensland to explore the nexus of technology and culture in an urban environment. The paper not only explores the new role of libraries in the knowledge economy, but also how the application of urban informatics in prototype engagement spaces such as The Edge can provide transferable insights that can inform the design and development of responsive and inclusive new library spaces elsewhere. To set the scene and background, the paper begins by drawing the bigger picture and outlining some key characteristics of the knowledge economy and the role that the creative and cultural industries play in it, grasping new opportunities that can contribute to the prosperity of Australia.

Identifying experts in information systems for system evaluations

This research-in-progress paper reports preliminary findings of a study that is designed to identify characteristics of an expert in the discipline of Information Systems (IS). The paper delivers a formative research model to depict characteristics of an expert with three additive constructs, using concepts derived from psychology, knowledge management and social-behaviour research. The paper then explores the formation and application ‘expertise’ using four investigative questions in the context of System Evaluations. Data have been gathered from 220 respondents representing three medium sized companies in India, using the SAP Enterprise Resource Planning system. The paper summarizes planned data analyses in construct validation, model testing and model application. A validated construct of expertise of IS will have a wide range of implications for research and practice.

Accelerated leap methods for simulating discrete stochastic chemical kinetics

Biologists are increasingly conscious of the critical role that noise plays in cellular functions such as genetic regulation, often in connection with fluctuations in small numbers of key regulatory molecules. This has inspired the development of models that capture this fundamentally discrete and stochastic nature of cellular biology - most notably the Gillespie stochastic simulation algorithm (SSA). The SSA simulates a temporally homogeneous, discrete-state, continuous-time Markov process, and of course the corresponding probabilities and numbers of each molecular species must all remain positive. While accurately serving this purpose, the SSA can be computationally inefficient due to very small time stepping so faster approximations such as the Poisson and Binomial τ-leap methods have been suggested. This work places these leap methods in the context of numerical methods for the solution of stochastic differential equations (SDEs) driven by Poisson noise. This allows analogues of Euler-Maruyuma, Milstein and even higher order methods to be developed through the Itô-Taylor expansions as well as similar derivative-free Runge-Kutta approaches. Numerical results demonstrate that these novel methods compare favourably with existing techniques for simulating biochemical reactions by more accurately capturing crucial properties such as the mean and variance than existing methods.

Knowledge management for enterprise systems: observations from small, medium and large organizations

Anecdotal evidence suggests that the lifecycle-wide management of Enterprise System (ES) related knowledge is critical for ES health and longevity. At a time where many ES-vendors now offering solutions to Small and Medium size organizations, this paper investigates the ability of Small and Medium size organizations to maintain a lifecycle-wide knowledge management strategy. The paper explores the alleged differences in the knowledge management practices across 27 small, medium and large organizations that had implemented a market-leading ES. Results suggest that: (1) despite similar knowledge creation efforts in all three organizational sizes, small organizations struggle with retaining, transferring and applying the knowledge. The study also reveals that, (2) the overall goodness of the knowledge management process in larger organizations remains higher than their small and medium counterparts.

Introducing a small and medium enterprises syllabi design: an enterprise systems hands-on approach

There is increasing attention to the importance of Enterprise Systems (ES) and Information Systems (IS) for Small and Medium Enterprises (SMEs). The same attention must be addressed in IS graduate curriculum. Studies reveal that despite healthy demand from the industry for IS management expertise, most IS graduates are ill-equipped to meet the challenges of modern organizations. The majority of contemporary firms, represented by SMEs, seek employees with a balance of business process knowledge and ES software skills. This article describes a curriculum that teaches Information Technology (IT) and IS managementconcepts in a SMEs context. The curriculum conceptualises a ‘learn-by-doing’ approach, to provide business process and ES software specific knowledge for its students. The approach recommends coverage of traditional content related to SMEs’’ operations, strategies, IT investment and management issues while providing an increased focus on strategic use of enterprise IT. The study addresses to an extent, the perennial challenge of updating IS curriculum, given the rapid pace of technological change.

Observing the relevance of an information systems success model

This paper contributes to the rigor vs. relevance debate in the Information Systems (IS) discipline. Using the Action Research methodology, this study evaluates the relevance of a rigorously validated IS evaluation model in practice. The study captures observations of operational end-users employing a market leading Enterprise System application for procurement and order fulfillment in an organization. The analysis of the observations demonstrates the broad relevance of the measurement instrument. More importantly, the study identifies several improvements and possible confusions in applying the instrument in the practice.

Coupling hybrid-game strategies with particle swarm optimisation for multi-objective high lift systems design optimisation

This paper investigates the High Lift System (HLS) application of complex aerodynamic design problem using Particle Swarm Optimisation (PSO) coupled to Game strategies. Two types of optimization methods are used; the first method is a standard PSO based on Pareto dominance and the second method hybridises PSO with a well-known Nash Game strategies named Hybrid-PSO. These optimization techniques are coupled to a pre/post processor GiD providing unstructured meshes during the optimisation procedure and a transonic analysis software PUMI. The computational efficiency and quality design obtained by PSO and Hybrid-PSO are compared. The numerical results for the multi-objective HLS design optimisation clearly shows the benefits of hybridising a PSO with the Nash game and makes promising the above methodology for solving other more complex multi-physics optimisation problems in Aeronautics.

Online geographic information systems for improving health planning practice : lessons learned from the case study of Logan-Beaudesert, Australia

This study examines the impact of utilising a Decision Support System (DSS) in a practical health planning study. Specifically, it presents a real-world case of a community-based initiative aiming to improve overall public health outcomes. Previous studies have emphasised that because of a lack of effective information, systems and an absence of frameworks for making informed decisions in health planning, it has become imperative to develop innovative approaches and methods in health planning practice. Online Geographical Information Systems (GIS) has been suggested as one of the innovative methods that will inform decision-makers and improve the overall health planning process. However, a number of gaps in knowledge have been identified within health planning practice: lack of methods to develop these tools in a collaborative manner; lack of capacity to use the GIS application among health decision-makers perspectives, and lack of understanding about the potential impact of such systems on users. This study addresses the abovementioned gaps and introduces an online GIS-based Health Decision Support System (HDSS), which has been developed to improve collaborative health planning in the Logan-Beaudesert region of Queensland, Australia. The study demonstrates a participatory and iterative approach undertaken to design and develop the HDSS. It then explores the perceived user satisfaction and impact of the tool on a selected group of health decision makers. Finally, it illustrates how decision-making processes have changed since its implementation. The overall findings suggest that the online GIS-based HDSS is an effective tool, which has the potential to play an important role in the future in terms of improving local community health planning practice. However, the findings also indicate that decision-making processes are not merely informed by using the HDSS tool. Instead, they seem to enhance the overall sense of collaboration in health planning practice. Thus, to support the Healthy Cities approach, communities will need to encourage decision-making based on the use of evidence, participation and consensus, which subsequently transfers into informed actions.

Bayesian models for the determination of resonant frequencies in a DI diesel engine

A time series method for the determination of combustion chamber resonant frequencies is outlined. This technique employs the use of Markov-chain Monte Carlo (MCMC) to infer parameters in a chosen model of the data. The development of the model is included and the resonant frequency is characterised as a function of time. Potential applications for cycle-by-cycle analysis are discussed and the bulk temperature of the gas and the trapped mass in the combustion chamber are evaluated as a function of time from resonant frequency information.

An integrated framework to assess financial reward systems in construction projects

Motivation is a major driver of project performance. Despite team member ability to deliver successful project outcomes if they are not positively motivated to pursue joint project goals, then performance will be constrained. One approach to improving the motivation of project organizations is by offering a financial reward for the achievement of set performance standards above a minimum required level. However, little investigation has been undertaken into the features of successful incentive systems as a part of an overall delivery strategy. With input from organizational management literature, and drawing on the literature covering psychological and economic theories of motivation, this paper presents an integrated framework that can be used by project organizations to assess the impact of financial reward systems on motivation in construction projects. The integrated framework offers four motivation indicators which reflect key theoretical concepts across both psychological and economic disciplines. The indicators are: (1) Goal Commitment, (2) Distributive Justice, (3) Procedural Justice, and (4) Reciprocity. The paper also interprets the integrated framework against the results of a successful Australian social infrastructure project case study and identifies key learning’s for project organizations to consider when designing financial reward systems. Case study results suggest that motivation directed towards the achievement of incentive goals is influenced not only by the value placed on the financial reward for commercial benefit, but also driven by the strength of the project initiatives that encourage just and fair dealings, supporting the establishment of trust and positive reciprocal behavior across a project team. The strength of the project relationships was found to be influenced by how attractive the achievement of the goal is to the incentive recipient and how likely they were to push for the achievement of the goal. Interestingly, findings also suggested that contractor motivation is also influenced by the fairness of the performance measurement process and their perception of the trustworthiness and transparency of their client. These findings provide the basis for future research on the impact of financial reward systems on motivation in construction projects. It is anticipated that such research will shed new light on this complex topic and further define how reward systems should be designed to promote project team motivation. Due to the unique nature of construction projects with high levels of task complexity and interdependence, results are expected to vary in comparison to previous studies based on individuals or single-entity organizations.