Models of collective cell behaviour with crowding effects : comparing lattice-based and lattice-free approaches

Individual-based models describing the migration and proliferation of a population of cells frequently restrict the cells to a predefined lattice. An implicit assumption of this type of lattice based model is that a proliferative population will always eventually fill the lattice. Here we develop a new lattice-free individual-based model that incorporates cell-to-cell crowding effects. We also derive approximate mean-field descriptions for the lattice-free model in two special cases motivated by commonly used experimental setups. Lattice-free simulation results are compared to these mean-field descriptions and to a corresponding lattice-based model. Data from a proliferation experiment is used to estimate the parameters for the new model, including the cell proliferation rate, showing that the model fits the data well. An important aspect of the lattice-free model is that the confluent cell density is not predefined, as with lattice-based models, but an emergent model property. As a consequence of the more realistic, irregular configuration of cells in the lattice-free model, the population growth rate is much slower at high cell densities and the population cannot reach the same confluent density as an equivalent lattice-based model.

Robust performance analysis on YAWL process models with advanced constructs

The importance of actively managing and analyzing business processes is acknowledged more than ever in organizations nowadays. Business processes form an essential part of an organization and their ap-plication areas are manifold. Most organizations keep records of various activities that have been carried out for auditing purposes, but they are rarely used for analysis purposes. This paper describes the design and implementation of a process analysis tool that replays, analyzes and visualizes a variety of performance metrics using a process definition and its execution logs. Performing performance analysis on existing and planned process models offers a great way for organizations to detect bottlenecks within their processes and allow them to make more effective process improvement decisions. Our technique is applied to processes modeled in the YAWL language. Execution logs of process instances are compared against the corresponding YAWL process model and replayed in a robust manner, taking into account any noise in the logs. Finally, performance characteristics, obtained from replaying the log in the model, are projected onto the model.

OpenFABMAP : an open source toolbox for appearance-based loop closure detection

Appearance-based loop closure techniques, which leverage the high information content of visual images and can be used independently of pose, are now widely used in robotic applications. The current state-of-the-art in the field is Fast Appearance-Based Mapping (FAB-MAP) having been demonstrated in several seminal robotic mapping experiments. In this paper, we describe OpenFABMAP, a fully open source implementation of the original FAB-MAP algorithm. Beyond the benefits of full user access to the source code, OpenFABMAP provides a number of configurable options including rapid codebook training and interest point feature tuning. We demonstrate the performance of OpenFABMAP on a number of published datasets and demonstrate the advantages of quick algorithm customisation. We present results from OpenFABMAP’s application in a highly varied range of robotics research scenarios.

The unfinished landscape fractal geometry and the aesthetics of ecological design

During the late 20th century it was proposed that a design aesthetic reflecting current ecological concerns was required within the overall domain of the built environment and specifically within landscape design. To address this, some authors suggested various theoretical frameworks upon which such an aesthetic could be based. Within these frameworks there was an underlying theme that the patterns and processes of Nature may have the potential to form this aesthetic — an aesthetic based on fractal rather than Euclidean geometry. In order to understand how fractal geometry, described as the geometry of Nature, could become the referent for a design aesthetic, this research examines the mathematical concepts of fractal Geometry, and the underlying philosophical concepts behind the terms ‘Nature’ and ‘aesthetics’. The findings of this initial research meant that a new definition of Nature was required in order to overcome the barrier presented by the western philosophical Nature¯culture duality. This new definition of Nature is based on the type and use of energy. Similarly, it became clear that current usage of the term aesthetics has more in common with the term ‘style’ than with its correct philosophical meaning. The aesthetic philosophy of both art and the environment recognises different aesthetic criteria related to either the subject or the object, such as: aesthetic experience; aesthetic attitude; aesthetic value; aesthetic object; and aesthetic properties. Given these criteria, and the fact that the concept of aesthetics is still an active and ongoing philosophical discussion, this work focuses on the criteria of aesthetic properties and the aesthetic experience or response they engender. The examination of fractal geometry revealed that it is a geometry based on scale rather than on the location of a point within a three-dimensional space. This enables fractal geometry to describe the complex forms and patterns created through the processes of Wild Nature. Although fractal geometry has been used to analyse the patterns of built environments from a plan perspective, it became clear from the initial review of the literature that there was a total knowledge vacuum about the fractal properties of environments experienced every day by people as they move through them. To overcome this, 21 different landscapes that ranged from highly developed city centres to relatively untouched landscapes of Wild Nature have been analysed. Although this work shows that the fractal dimension can be used to differentiate between overall landscape forms, it also shows that by itself it cannot differentiate between all images analysed. To overcome this two further parameters based on the underlying structural geometry embedded within the landscape are discussed. These parameters are the Power Spectrum Median Amplitude and the Level of Isotropy within the Fourier Power Spectrum. Based on the detailed analysis of these parameters a greater understanding of the structural properties of landscapes has been gained. With this understanding, this research has moved the field of landscape design a step close to being able to articulate a new aesthetic for ecological design.

Accuracy of rate estimation using relaxed-clock models with a critical focus on the early metazoan radiation

In recent years, a number of phylogenetic methods have been developed for estimating molecular rates and divergence dates under models that relax the molecular clock constraint by allowing rate change throughout the tree. These methods are being used with increasing frequency, but there have been few studies into their accuracy. We tested the accuracy of several relaxed-clock methods (penalized likelihood and Bayesian inference using various models of rate change) using nucleotide sequences simulated on a nine-taxon tree. When the sequences evolved with a constant rate, the methods were able to infer rates accurately, but estimates were more precise when a molecular clock was assumed. When the sequences evolved under a model of autocorrelated rate change, rates were accurately estimated using penalized likelihood and by Bayesian inference using lognormal and exponential models of rate change, while other models did not perform as well. When the sequences evolved under a model of uncorrelated rate change, only Bayesian inference using an exponential rate model performed well. Collectively, the results provide a strong recommendation for using the exponential model of rate change if a conservative approach to divergence time estimation is required. A case study is presented in which we use a simulation-based approach to examine the hypothesis of elevated rates in the Cambrian period, and it is found that these high rate estimates might be an artifact of the rate estimation method. If this bias is present, then the ages of metazoan divergences would be systematically underestimated. The results of this study have implications for studies of molecular rates and divergence dates.

Concept combination and the origins of complex cognition

At the core of our uniquely human cognitive abilities is the capacity to see things from different perspectives, or to place them in a new context. We propose that this was made possible by two cognitive transitions. First, the large brain of Homo erectus facilitated the onset of recursive recall: the ability to string thoughts together into a stream of potentially abstract or imaginative thought. This hypothesis is sup-ported by a set of computational models where an artificial society of agents evolved to generate more diverse and valuable cultural outputs under conditions of recursive recall. We propose that the capacity to see things in context arose much later, following the appearance of anatomically modern humans. This second transition was brought on by the onset of contextual focus: the capacity to shift between a minimally contextual analytic mode of thought, and a highly contextual associative mode of thought, conducive to combining concepts in new ways and ‘breaking out of a rut’. When contextual focus is implemented in an art-generating computer program, the resulting artworks are seen as more creative and appealing. We summarize how both transitions can be modeled using a theory of concepts which high-lights the manner in which different contexts can lead to modern humans attributing very different meanings to the interpretation of one concept.

Stop and revive? : the effectiveness of nap and active rest breaks for reducing driver sleepiness

The incidence of sleep-related crashes has been estimated to account for approximately 20% of all fatal and severe crashes. The use of sleepiness countermeasures by drivers is an important component to reduce the incidence rates of sleep-related crashes. Taking a brief nap and stopping for a rest break are two highly publicised countermeasures for driver sleepiness and are also believed by drivers to be the most effective countermeasures. Despite this belief, there is scarce evidence to support the utility of these countermeasures for reducing driver sleepiness levels. Therefore, determining the effectiveness of these countermeasures is an important road safety concern. The current study utilised a young adult sample (N = 20) to investigate the effectiveness of a nap and an active rest break. The countermeasures effects were evaluated by physiological, behavioural (hazard perception skill), and subjective measures previously found sensitive to sleepiness. Participants initially completed two hours of a simulated driving task followed by a 15 minute nap opportunity or a 15 minute active rest break that included 10 minutes of brisk walking. After the break, participants completed one final hour of the simulated driving task. A within-subjects design was used so that each participant completed both the nap and the active rest break conditions on separate occasions. The analyses revealed that only the nap break provided any meaningful reduction in physiological sleepiness, reduced subjective sleepiness levels, and maintained hazard perception performance. In contrast, the active rest break had no effect for reducing physiological sleepiness and resulted in a decrement in hazard perception performance (i.e., an increase of reaction time latencies), with a transient reduction in subjective sleepiness levels. A number of theoretical, empirical and practical issues were identified by the current study.

A tan in a test tube -in vitro models for investigating ultraviolet radiation-induced damage in skin

Presently, global rates of skin cancers induced by ultraviolet radiation (UVR) exposure are on the rise. In view of this, current knowledge gaps in the biology of photocarcinogenesis and skin cancer progression urgently need to be addressed. One factor that has limited skin cancer research has been the need for a reproducible and physiologically-relevant model able to represent the complexity of human skin. This review outlines the main currently-used in vitro models of UVR-induced skin damage. This includes the use of conventional two-dimensional cell culture techniques and the major animal models that have been employed in photobiology and photocarcinogenesis research. Additionally, the progression towards the use of cultured skin explants and tissue-engineered skin constructs, and their utility as models of native skin's responses to UVR are described. The inherent advantages and disadvantages of these in vitro systems are also discussed.

Chinese online literature : creative consumers and evolving business models

Purpose – The internet is transforming possibilities for creative interaction, experimentation and cultural consumption in China and raising important questions about the role that “publishers” might play in an open and networked digital world. The purpose of this paper is to consider the role that copyright is playing in the growth of a publishing industry that is being “born digital”. Design/methodology/approach – The paper approaches online literature as an example of a creative industry that is generating value for a wider creative economy through its social network market functions. It builds on the social network market definition of the creative industries proposed by Potts et al. and uses this definition to interrogate the role that copyright plays in a rapidly-evolving creative economy. Findings – The rapid growth of a market for crowd-sourced content is combining with growing commercial freedom in cultural space to produce a dynamic landscape of business model experimentation. Using the social web to engage audiences, generate content, establish popularity and build reputation and then converting those assets into profit through less networked channels appears to be a driving strategy in the expansion of wider creative industries markets in China. Originality/value – At a moment when publishing industries all over the world are struggling to come to terms with digital technology, the emergence of a rapidly-growing area of publishing that is being born digital offers important clues about the future of publishing and what social network markets might mean for the role of copyright in a digital age.

A hierarchical evolutionary algorithmic design (HEAD) system for generating and evolving building design models

This thesis develops a detailed conceptual design method and a system software architecture defined with a parametric and generative evolutionary design system to support an integrated interdisciplinary building design approach. The research recognises the need to shift design efforts toward the earliest phases of the design process to support crucial design decisions that have a substantial cost implication on the overall project budget. The overall motivation of the research is to improve the quality of designs produced at the author's employer, the General Directorate of Major Works (GDMW) of the Saudi Arabian Armed Forces. GDMW produces many buildings that have standard requirements, across a wide range of environmental and social circumstances. A rapid means of customising designs for local circumstances would have significant benefits. The research considers the use of evolutionary genetic algorithms in the design process and the ability to generate and assess a wider range of potential design solutions than a human could manage. This wider ranging assessment, during the early stages of the design process, means that the generated solutions will be more appropriate for the defined design problem. The research work proposes a design method and system that promotes a collaborative relationship between human creativity and the computer capability. The tectonic design approach is adopted as a process oriented design that values the process of design as much as the product. The aim is to connect the evolutionary systems to performance assessment applications, which are used as prioritised fitness functions. This will produce design solutions that respond to their environmental and function requirements. This integrated, interdisciplinary approach to design will produce solutions through a design process that considers and balances the requirements of all aspects of the design. Since this thesis covers a wide area of research material, 'methodological pluralism' approach was used, incorporating both prescriptive and descriptive research methods. Multiple models of research were combined and the overall research was undertaken following three main stages, conceptualisation, developmental and evaluation. The first two stages lay the foundations for the specification of the proposed system where key aspects of the system that have not previously been proven in the literature, were implemented to test the feasibility of the system. As a result of combining the existing knowledge in the area with the newlyverified key aspects of the proposed system, this research can form the base for a future software development project. The evaluation stage, which includes building the prototype system to test and evaluate the system performance based on the criteria defined in the earlier stage, is not within the scope this thesis. The research results in a conceptual design method and a proposed system software architecture. The proposed system is called the 'Hierarchical Evolutionary Algorithmic Design (HEAD) System'. The HEAD system has shown to be feasible through the initial illustrative paper-based simulation. The HEAD system consists of the two main components - 'Design Schema' and the 'Synthesis Algorithms'. The HEAD system reflects the major research contribution in the way it is conceptualised, while secondary contributions are achieved within the system components. The design schema provides constraints on the generation of designs, thus enabling the designer to create a wide range of potential designs that can then be analysed for desirable characteristics. The design schema supports the digital representation of the human creativity of designers into a dynamic design framework that can be encoded and then executed through the use of evolutionary genetic algorithms. The design schema incorporates 2D and 3D geometry and graph theory for space layout planning and building formation using the Lowest Common Design Denominator (LCDD) of a parameterised 2D module and a 3D structural module. This provides a bridge between the standard adjacency requirements and the evolutionary system. The use of graphs as an input to the evolutionary algorithm supports the introduction of constraints in a way that is not supported by standard evolutionary techniques. The process of design synthesis is guided as a higher level description of the building that supports geometrical constraints. The Synthesis Algorithms component analyses designs at four levels, 'Room', 'Layout', 'Building' and 'Optimisation'. At each level multiple fitness functions are embedded into the genetic algorithm to target the specific requirements of the relevant decomposed part of the design problem. Decomposing the design problem to allow for the design requirements of each level to be dealt with separately and then reassembling them in a bottom up approach reduces the generation of non-viable solutions through constraining the options available at the next higher level. The iterative approach, in exploring the range of design solutions through modification of the design schema as the understanding of the design problem improves, assists in identifying conflicts in the design requirements. Additionally, the hierarchical set-up allows the embedding of multiple fitness functions into the genetic algorithm, each relevant to a specific level. This supports an integrated multi-level, multi-disciplinary approach. The HEAD system promotes a collaborative relationship between human creativity and the computer capability. The design schema component, as the input to the procedural algorithms, enables the encoding of certain aspects of the designer's subjective creativity. By focusing on finding solutions for the relevant sub-problems at the appropriate levels of detail, the hierarchical nature of the system assist in the design decision-making process.

Breaking organizational barriers for greening Australian

Sustainability is an issue for everyone. For instance, the higher education sector is being asked to take an active part in creating a sustainable future, due to their moral responsibility, social obligation, and their own need to adapt to the changing higher education environment. By either signing declarations or making public statements, many universities are expressing their desire to become role models for enhancing sustainability. However, too often they have not delivered as much as they had intended. This is particularly evident in the lack of physical implementation of sustainable practices in the campus environment. Real projects such as green technologies on campus have the potential to rectify the problem in addition to improving building performance. Despite being relatively recent innovations, Green Roof and Living Wall have been widely recognized because of their substantial benefits, such as runoff water reduction, noise insulation, and the promotion of biodiversity. While they can be found in commercial and residential buildings, they only appear infrequently on campuses as universities have been very slow to implement sustainability innovations. There has been very little research examining the fundamental problems from the organizational perspective. To address this deficiency, the researchers designed and carried out 24 semi-structured interviews to investigate the general organizational environment of Australian universities with the intention to identify organizational obstacles to the delivery of Green Roof and Living Wall projects. This research revealed that the organizational environment of Australian universities still has a lot of room to be improved in order to accommodate sustainability practices. Some of the main organizational barriers to the adoption of sustainable innovations were identified including lack of awareness and knowledge, the absence of strong supportive leadership, a weak sustainability-rooted culture and several management challenges. This led to the development of a set of strategies to help optimize the organizational environment for the purpose of better decision making for Green Roof and Living Wall implementation.

Extending persistent monitoring by combining ocean models and Markov decision processes

Ocean processes are complex and have high variability in both time and space. Thus, ocean scientists must collect data over long time periods to obtain a synoptic view of ocean processes and resolve their spatiotemporal variability. One way to perform these persistent observations is to utilise an autonomous vehicle that can remain on deployment for long time periods. However, such vehicles are generally underactuated and slow moving. A challenge for persistent monitoring with these vehicles is dealing with currents while executing a prescribed path or mission. Here we present a path planning method for persistent monitoring that exploits ocean currents to increase navigational accuracy and reduce energy consumption.

Applying Bayesian hierarchical models to examine motorcycle crashes at signalized intersections

Motorcycles are overrepresented in road traffic crashes and particularly vulnerable at signalized intersections. The objective of this study is to identify causal factors affecting the motorcycle crashes at both four-legged and T signalized intersections. Treating the data in time-series cross-section panels, this study explores different Hierarchical Poisson models and found that the model allowing autoregressive lag 1 dependent specification in the error term is the most suitable. Results show that the number of lanes at the four-legged signalized intersections significantly increases motorcycle crashes largely because of the higher exposure resulting from higher motorcycle accumulation at the stop line. Furthermore, the presence of a wide median and an uncontrolled left-turn lane at major roadways of four-legged intersections exacerbate this potential hazard. For T signalized intersections, the presence of exclusive right-turn lane at both major and minor roadways and an uncontrolled left-turn lane at major roadways of T intersections increases motorcycle crashes. Motorcycle crashes increase on high-speed roadways because they are more vulnerable and less likely to react in time during conflicts. The presence of red light cameras reduces motorcycle crashes significantly for both four-legged and T intersections. With the red-light camera, motorcycles are less exposed to conflicts because it is observed that they are more disciplined in queuing at the stop line and less likely to jump start at the start of green.

An investigation on multi-vehicle motorcycle crashes using log-linear models

Motorcyclists are the most crash-prone road-user group in many Asian countries including Singapore; however, factors influencing motorcycle crashes are still not well understood. This study examines the effects of various roadway characteristics, traffic control measures and environmental factors on motorcycle crashes at different location types including expressways and intersections. Using techniques of categorical data analysis, this study has developed a set of log-linear models to investigate multi-vehicle motorcycle crashes in Singapore. Motorcycle crash risks in different circumstances have been calculated after controlling for the exposure estimated by the induced exposure technique. Results show that night-time influence increases crash risks of motorcycles particularly during merging and diverging manoeuvres on expressways, and turning manoeuvres at intersections. Riders appear to exercise more care while riding on wet road surfaces particularly during night. Many hazardous interactions at intersections tend to be related to the failure of drivers to notice a motorcycle as well as to judge correctly the speed/distance of an oncoming motorcycle. Road side conflicts due to stopping/waiting vehicles and interactions with opposing traffic on undivided roads have been found to be as detrimental factors on motorcycle safety along arterial, main and local roads away from intersections. Based on the findings of this study, several targeted countermeasures in the form of legislations, rider training, and safety awareness programmes have been recommended.

Bayesian hierarchical analysis on crash prediction models

Traditional crash prediction models, such as generalized linear regression models, are incapable of taking into account the multilevel data structure, which extensively exists in crash data. Disregarding the possible within-group correlations can lead to the production of models giving unreliable and biased estimates of unknowns. This study innovatively proposes a -level hierarchy, viz. (Geographic region level – Traffic site level – Traffic crash level – Driver-vehicle unit level – Vehicle-occupant level) Time level, to establish a general form of multilevel data structure in traffic safety analysis. To properly model the potential cross-group heterogeneity due to the multilevel data structure, a framework of Bayesian hierarchical models that explicitly specify multilevel structure and correctly yield parameter estimates is introduced and recommended. The proposed method is illustrated in an individual-severity analysis of intersection crashes using the Singapore crash records. This study proved the importance of accounting for the within-group correlations and demonstrated the flexibilities and effectiveness of the Bayesian hierarchical method in modeling multilevel structure of traffic crash data.