An analytical tool that quantifies cellular morphology changes from three-dimensional fluorescence images

The most common software analysis tools available for measuring fluorescence images are for two-dimensional (2D) data that rely on manual settings for inclusion and exclusion of data points, and computer-aided pattern recognition to support the interpretation and findings of the analysis. It has become increasingly important to be able to measure fluorescence images constructed from three-dimensional (3D) datasets in order to be able to capture the complexity of cellular dynamics and understand the basis of cellular plasticity within biological systems. Sophisticated microscopy instruments have permitted the visualization of 3D fluorescence images through the acquisition of multispectral fluorescence images and powerful analytical software that reconstructs the images from confocal stacks that then provide a 3D representation of the collected 2D images. Advanced design-based stereology methods have progressed from the approximation and assumptions of the original model-based stereology(1) even in complex tissue sections(2). Despite these scientific advances in microscopy, a need remains for an automated analytic method that fully exploits the intrinsic 3D data to allow for the analysis and quantification of the complex changes in cell morphology, protein localization and receptor trafficking. Current techniques available to quantify fluorescence images include Meta-Morph (Molecular Devices, Sunnyvale, CA) and Image J (NIH) which provide manual analysis. Imaris (Andor Technology, Belfast, Northern Ireland) software provides the feature MeasurementPro, which allows the manual creation of measurement points that can be placed in a volume image or drawn on a series of 2D slices to create a 3D object. This method is useful for single-click point measurements to measure a line distance between two objects or to create a polygon that encloses a region of interest, but it is difficult to apply to complex cellular network structures. Filament Tracer (Andor) allows automatic detection of the 3D neuronal filament-like however, this module has been developed to measure defined structures such as neurons, which are comprised of dendrites, axons and spines (tree-like structure). This module has been ingeniously utilized to make morphological measurements to non-neuronal cells(3), however, the output data provide information of an extended cellular network by using a software that depends on a defined cell shape rather than being an amorphous-shaped cellular model. To overcome the issue of analyzing amorphous-shaped cells and making the software more suitable to a biological application, Imaris developed Imaris Cell. This was a scientific project with the Eidgenössische Technische Hochschule, which has been developed to calculate the relationship between cells and organelles. While the software enables the detection of biological constraints, by forcing one nucleus per cell and using cell membranes to segment cells, it cannot be utilized to analyze fluorescence data that are not continuous because ideally it builds cell surface without void spaces. To our knowledge, at present no user-modifiable automated approach that provides morphometric information from 3D fluorescence images has been developed that achieves cellular spatial information of an undefined shape (Figure 1). We have developed an analytical platform using the Imaris core software module and Imaris XT interfaced to MATLAB (Mat Works, Inc.). These tools allow the 3D measurement of cells without a pre-defined shape and with inconsistent fluorescence network components. Furthermore, this method will allow researchers who have extended expertise in biological systems, but not familiarity to computer applications, to perform quantification of morphological changes in cell dynamics.

Analyzing the factors influencing the successful design and uptake of interactive systems to support social networks in urban neighborhoods

In urban residential environments in Australia and other developed countries, Internet access is on the verge of becoming a ubiquitous utility like gas or electricity. From an urban sociology and community informatics perspective, this article discusses new emerging social formations of urban residents that are based on networked individualism and the potential of Internet-based systems to support them. It proposes that one of the main reasons for the disappearance or nonexistence of urban residential communities is a lack of appropriate opportunities and instruments to encourage and support local interaction in urban neighborhoods. The article challenges the view that a mere reappropriation of applications used to support dispersed virtual communities is adequate to meet the place and proximity-based design requirements that community networks in urban neighborhoods pose. It argues that the key factors influencing the successful design and uptake of interactive systems to support social networks in urban neighborhoods include the swarming social behavior of urban dwellers; the dynamics of their existing communicative ecology; and the serendipitous, voluntary, and place-based quality of interaction between residents on the basis of choice, like-mindedness, mutual interest and support needs. Drawing on an analysis of these factors, the conceptual design framework of a prototype system — the urban tribe incubator — is presented.

Planning for sustainable urban futures: an ecological approach to sustainable urban development

In recent years, cities have shown increasing signs of environmental problems due to the negative impacts of urban activities. The degradation and depletion of natural resources, climate change, and development pressure on green areas have become major concerns for cities. In response to these problems, urban planning policies have shifted to a sustainable focus and authorities have begun to develop new strategies for improving the quality of urban ecosystems. An extremely important function of an urban ecosystem is to provide healthy and sustainable environments for both natural systems and communities. Therefore, ecological planning is a functional requirement in the establishment of sustainable built environment. With ecological planning, human needs are supplied while natural resources are used in the most effective and sustainable manner and ecological balance is sustained. Protecting human and environmental health, having healthy ecosystems, reducing environmental pollution and providing green spaces are just a few of the many benefits of ecological planning. In this context, this chapter briefly presents a short overview of the importance of the implementation of ecological planning into sustainable urban development. Furthermore, it presents a conceptual framework for a new methodology for developing sustainable urban ecosystems through ecological planning approach.

Communication and organizational social networks : a simulation model

Recent management research has evidenced the significance of organizational social networks, and communication is believed to impact the interpersonal relationships. However, we have little knowledge on how communication affects organizational social networks. This paper studies the dynamics between organizational communication patterns and the growth of organizational social networks. We propose an organizational social network growth model, and then collect empirical data to test model validity. The simulation results agree well with the empirical data. The results of simulation experiments enrich our knowledge on communication with the findings that organizational management practices that discourage employees from communicating within and across group boundaries have disparate and significant negative effect on the social network’s density, scalar assortativity and discrete assortativity, each of which correlates with the organization’s performance. These findings also suggest concrete measures for management to construct and develop the organizational social network.

Performance assessment of exponential Rosenbrock method for large systems of ODE

This paper studies time integration methods for large stiff systems of ordinary differential equations (ODEs) of the form u'(t) = g(u(t)). For such problems, implicit methods generally outperform explicit methods, since the time step is usually less restricted by stability constraints. Recently, however, explicit so-called exponential integrators have become popular for stiff problems due to their favourable stability properties. These methods use matrix-vector products involving exponential-like functions of the Jacobian matrix, which can be approximated using Krylov subspace methods that require only matrix-vector products with the Jacobian. In this paper, we implement exponential integrators of second, third and fourth order and demonstrate that they are competitive with well-established approaches based on the backward differentiation formulas and a preconditioned Newton-Krylov solution strategy.

An examination of keystroke dynamics for continuous user authentication

Most current computer systems authorise the user at the start of a session and do not detect whether the current user is still the initial authorised user, a substitute user, or an intruder pretending to be a valid user. Therefore, a system that continuously checks the identity of the user throughout the session is necessary without being intrusive to end-user and/or effectively doing this. Such a system is called a continuous authentication system (CAS). Researchers have applied several approaches for CAS and most of these techniques are based on biometrics. These continuous biometric authentication systems (CBAS) are supplied by user traits and characteristics. One of the main types of biometric is keystroke dynamics which has been widely tried and accepted for providing continuous user authentication. Keystroke dynamics is appealing for many reasons. First, it is less obtrusive, since users will be typing on the computer keyboard anyway. Second, it does not require extra hardware. Finally, keystroke dynamics will be available after the authentication step at the start of the computer session. Currently, there is insufficient research in the CBAS with keystroke dynamics field. To date, most of the existing schemes ignore the continuous authentication scenarios which might affect their practicality in different real world applications. Also, the contemporary CBAS with keystroke dynamics approaches use characters sequences as features that are representative of user typing behavior but their selected features criteria do not guarantee features with strong statistical significance which may cause less accurate statistical user-representation. Furthermore, their selected features do not inherently incorporate user typing behavior. Finally, the existing CBAS that are based on keystroke dynamics are typically dependent on pre-defined user-typing models for continuous authentication. This dependency restricts the systems to authenticate only known users whose typing samples are modelled. This research addresses the previous limitations associated with the existing CBAS schemes by developing a generic model to better identify and understand the characteristics and requirements of each type of CBAS and continuous authentication scenario. Also, the research proposes four statistical-based feature selection techniques that have highest statistical significance and encompasses different user typing behaviors which represent user typing patterns effectively. Finally, the research proposes the user-independent threshold approach that is able to authenticate a user accurately without needing any predefined user typing model a-priori. Also, we enhance the technique to detect the impostor or intruder who may take over during the entire computer session.

Spatial and temporal analysis of Barmah Forest virus disease in Queensland, Australia

Barmah Forest virus (BFV) disease is one of the most widespread mosquito-borne diseases in Australia. The number of outbreaks and the incidence rate of BFV in Australia have attracted growing concerns about the spatio-temporal complexity and underlying risk factors of BFV disease. A large number of notifications has been recorded continuously in Queensland since 1992. Yet, little is known about the spatial and temporal characteristics of the disease. I aim to use notification data to better understand the effects of climatic, demographic, socio-economic and ecological risk factors on the spatial epidemiology of BFV disease transmission, develop predictive risk models and forecast future disease risks under climate change scenarios. Computerised data files of daily notifications of BFV disease and climatic variables in Queensland during 1992-2008 were obtained from Queensland Health and Australian Bureau of Meteorology, respectively. Projections on climate data for years 2025, 2050 and 2100 were obtained from Council of Scientific Industrial Research Organisation. Data on socio-economic, demographic and ecological factors were also obtained from relevant government departments as follows: 1) socio-economic and demographic data from Australian Bureau of Statistics; 2) wetlands data from Department of Environment and Resource Management and 3) tidal readings from Queensland Department of Transport and Main roads. Disease notifications were geocoded and spatial and temporal patterns of disease were investigated using geostatistics. Visualisation of BFV disease incidence rates through mapping reveals the presence of substantial spatio-temporal variation at statistical local areas (SLA) over time. Results reveal high incidence rates of BFV disease along coastal areas compared to the whole area of Queensland. A Mantel-Haenszel Chi-square analysis for trend reveals a statistically significant relationship between BFV disease incidence rates and age groups (ƒÓ2 = 7587, p<0.01). Semi-variogram analysis and smoothed maps created from interpolation techniques indicate that the pattern of spatial autocorrelation was not homogeneous across the state. A cluster analysis was used to detect the hot spots/clusters of BFV disease at a SLA level. Most likely spatial and space-time clusters are detected at the same locations across coastal Queensland (p<0.05). The study demonstrates heterogeneity of disease risk at a SLA level and reveals the spatial and temporal clustering of BFV disease in Queensland. Discriminant analysis was employed to establish a link between wetland classes, climate zones and BFV disease. This is because the importance of wetlands in the transmission of BFV disease remains unclear. The multivariable discriminant modelling analyses demonstrate that wetland types of saline 1, riverine and saline tidal influence were the most significant risk factors for BFV disease in all climate and buffer zones, while lacustrine, palustrine, estuarine and saline 2 and saline 3 wetlands were less important. The model accuracies were 76%, 98% and 100% for BFV risk in subtropical, tropical and temperate climate zones, respectively. This study demonstrates that BFV disease risk varied with wetland class and climate zone. The study suggests that wetlands may act as potential breeding habitats for BFV vectors. Multivariable spatial regression models were applied to assess the impact of spatial climatic, socio-economic and tidal factors on the BFV disease in Queensland. Spatial regression models were developed to account for spatial effects. Spatial regression models generated superior estimates over a traditional regression model. In the spatial regression models, BFV disease incidence shows an inverse relationship with minimum temperature, low tide and distance to coast, and positive relationship with rainfall in coastal areas whereas in whole Queensland the disease shows an inverse relationship with minimum temperature and high tide and positive relationship with rainfall. This study determines the most significant spatial risk factors for BFV disease across Queensland. Empirical models were developed to forecast the future risk of BFV disease outbreaks in coastal Queensland using existing climatic, socio-economic and tidal conditions under climate change scenarios. Logistic regression models were developed using BFV disease outbreak data for the existing period (2000-2008). The most parsimonious model had high sensitivity, specificity and accuracy and this model was used to estimate and forecast BFV disease outbreaks for years 2025, 2050 and 2100 under climate change scenarios for Australia. Important contributions arising from this research are that: (i) it is innovative to identify high-risk coastal areas by creating buffers based on grid-centroid and the use of fine-grained spatial units, i.e., mesh blocks; (ii) a spatial regression method was used to account for spatial dependence and heterogeneity of data in the study area; (iii) it determined a range of potential spatial risk factors for BFV disease; and (iv) it predicted the future risk of BFV disease outbreaks under climate change scenarios in Queensland, Australia. In conclusion, the thesis demonstrates that the distribution of BFV disease exhibits a distinct spatial and temporal variation. Such variation is influenced by a range of spatial risk factors including climatic, demographic, socio-economic, ecological and tidal variables. The thesis demonstrates that spatial regression method can be applied to better understand the transmission dynamics of BFV disease and its risk factors. The research findings show that disease notification data can be integrated with multi-factorial risk factor data to develop build-up models and forecast future potential disease risks under climate change scenarios. This thesis may have implications in BFV disease control and prevention programs in Queensland.

Nonlinear pedagogy underpins intrinsic motivation in sports coaching

A key challenge for sports coaches is to provide performers with learning environments that result in sustainable motivation. In this paper, we will demonstrate that programmes based around the principles of Nonlinear Pedagogy can support the three basic psychological needs that underpin self-determined motivation. Coaches can therefore ensure that practice sessions provide for intrinsic motivation with its associated motivational and emotional benefits.

Collective dynamics and control of a 3-D small-world network with time delays

The paper presents a detailed analysis on the collective dynamics and delayed state feedback control of a three-dimensional delayed small-world network. The trivial equilibrium of the model is first investigated, showing that the uncontrolled model exhibits complicated unbounded behavior. Then three control strategies, namely a position feedback control, a velocity feedback control, and a hybrid control combined velocity with acceleration feedback, are then introduced to stabilize this unstable system. It is shown in these three control schemes that only the hybrid control can easily stabilize the 3-D network system. And with properly chosen delay and gain in the delayed feedback path, the hybrid controlled model may have stable equilibrium, or periodic solutions resulting from the Hopf bifurcation, or complex stranger attractor from the period-doubling bifurcation. Moreover, the direction of Hopf bifurcation and stability of the bifurcation periodic solutions are analyzed. The results are further extended to any "d" dimensional network. It shows that to stabilize a "d" dimensional delayed small-world network, at least a "d – 1" order completed differential feedback is needed. This work provides a constructive suggestion for the high dimensional delayed systems.

An evolutionary computation approach to three-dimensional path planning for unmanned aerial vehicles with tactical and kinematic constraints

This paper presents a novel evolutionary computation approach to three-dimensional path planning for unmanned aerial vehicles (UAVs) with tactical and kinematic constraints. A genetic algorithm (GA) is modified and extended for path planning. Two GAs are seeded at the initial and final positions with a common objective to minimise their distance apart under given UAV constraints. This is accomplished by the synchronous optimisation of subsequent control vectors. The proposed evolutionary computation approach is called synchronous genetic algorithm (SGA). The sequence of control vectors generated by the SGA constitutes to a near-optimal path plan. The resulting path plan exhibits no discontinuity when transitioning from curve to straight trajectories. Experiments and results show that the paths generated by the SGA are within 2% of the optimal solution. Such a path planner when implemented on a hardware accelerator, such as field programmable gate array chips, can be used in the UAV as on-board replanner, as well as in ground station systems for assisting in high precision planning and modelling of mission scenarios.

Grouping people in social networks using a weighted multi-constraints clustering method

Grouping users in social networks is an important process that improves matching and recommendation activities in social networks. The data mining methods of clustering can be used in grouping the users in social networks. However, the existing general purpose clustering algorithms perform poorly on the social network data due to the special nature of users' data in social networks. One main reason is the constraints that need to be considered in grouping users in social networks. Another reason is the need of capturing large amount of information about users which imposes computational complexity to an algorithm. In this paper, we propose a scalable and effective constraint-based clustering algorithm based on a global similarity measure that takes into consideration the users' constraints and their importance in social networks. Each constraint's importance is calculated based on the occurrence of this constraint in the dataset. Performance of the algorithm is demonstrated on a dataset obtained from an online dating website using internal and external evaluation measures. Results show that the proposed algorithm is able to increases the accuracy of matching users in social networks by 10% in comparison to other algorithms.

Analytical model for fault section estimation and state identification of unobserved protective relays in power systems [电力系统故障诊断与不可观测保护状态识别的解析模型]

In recent years, some models have been proposed for the fault section estimation and state identification of unobserved protective relays (FSE-SIUPR) under the condition of incomplete state information of protective relays. In these models, the temporal alarm information from a faulted power system is not well explored although it is very helpful in compensating the incomplete state information of protective relays, quickly achieving definite fault diagnosis results and evaluating the operating status of protective relays and circuit breakers in complicated fault scenarios. In order to solve this problem, an integrated optimization mathematical model for the FSE-SIUPR, which takes full advantage of the temporal characteristics of alarm messages, is developed in the framework of the well-established temporal constraint network. With this model, the fault evolution procedure can be explained and some states of unobserved protective relays identified. The model is then solved by means of the Tabu search (TS) and finally verified by test results of fault scenarios in a practical power system.

A multi-scaled approach for simulating chemical reaction systems

In this paper we give an overview of some very recent work, as well as presenting a new approach, on the stochastic simulation of multi-scaled systems involving chemical reactions. In many biological systems (such as genetic regulation and cellular dynamics) there is a mix between small numbers of key regulatory proteins, and medium and large numbers of molecules. In addition, it is important to be able to follow the trajectories of individual molecules by taking proper account of the randomness inherent in such a system. We describe different types of simulation techniques (including the stochastic simulation algorithm, Poisson Runge-Kutta methods and the balanced Euler method) for treating simulations in the three different reaction regimes: slow, medium and fast. We then review some recent techniques on the treatment of coupled slow and fast reactions for stochastic chemical kinetics and present a new approach which couples the three regimes mentioned above. We then apply this approach to a biologically inspired problem involving the expression and activity of LacZ and LacY proteins in E coli, and conclude with a discussion on the significance of this work. (C) 2004 Elsevier Ltd. All rights reserved.

Analysis of productive performance of crop production systems: an integrated analytical framework

Recent literature has argued that environmental efficiency (EE), which is built on the materials balance (MB) principle, is more suitable than other EE measures in situations where the law of mass conversation regulates production processes. In addition, the MB-based EE method is particularly useful in analysing possible trade-offs between cost and environmental performance. Identifying determinants of MB-based EE can provide useful information to decision makers but there are very few empirical investigations into this issue. This article proposes the use of data envelopment analysis and stochastic frontier analysis techniques to analyse variation in MB-based EE. Specifically, the article develops a stochastic nutrient frontier and nutrient inefficiency model to analyse determinants of MB-based EE. The empirical study applies both techniques to investigate MB-based EE of 96 rice farms in South Korea. The size of land, fertiliser consumption intensity, cost allocative efficiency, and the share of owned land out of total land are found to be correlated with MB-based EE. The results confirm the presence of a trade-off between MB-based EE and cost allocative efficiency and this finding, favouring policy interventions to help farms simultaneously achieve cost efficiency and MP-based EE.