Network topology and the evolution of dynamics in an artificial genetic regulatory network model created by whole genome duplication and divergence

Topological measures of large-scale complex networks are applied to a specific artificial regulatory network model created through a whole genome duplication and divergence mechanism. This class of networks share topological features with natural transcriptional regulatory networks. Specifically, these networks display scale-free and small-world topology and possess subgraph distributions similar to those of natural networks. Thus, the topologies inherent in natural networks may be in part due to their method of creation rather than being exclusively shaped by subsequent evolution under selection. The evolvability of the dynamics of these networks is also examined by evolving networks in simulation to obtain three simple types of output dynamics. The networks obtained from this process show a wide variety of topologies and numbers of genes indicating that it is relatively easy to evolve these classes of dynamics in this model. (c) 2006 Elsevier Ireland Ltd. All rights reserved.

The use of heparan sulfate to augment fracture repair in a rat fracture model

Fracture healing is a complex process regulated by numerous growth and adhesive factors expressed at specific stages during healing. The naturally occurring, cell surface-expressed sugar, heparan sulfate (HS), is known to bind to and potentiate the effects of many classes of growth factors, and as such, may be a potential candidate therapy for enhancing bone repair. This study investigated the local application of bone-derived HS in the repair of rat femoral fractures. After 2 weeks, there was a significant increase in the callus size of rats administered with 5 mu g HS compared to the control and 50 mu g HS groups, presumably due to increased trabecular bone volume rather than increased cartilage production. In addition, 5 mu g HS increased the expression of ALP, Runx2, FGF-1, IGF-II, TGF-beta 1, and VEGF. It is hypothesized that these increases resulted from changes in HS-mediated receptor/ligand interactions that increase local growth factor production to augment bone formation. The findings of this study demonstrate the anabolic potential of HS in bone repair by recruiting and enhancing the production of endogenous growth factors at the site of injury. (c) 2006 Orthopaedic Research Society.

Yield criterion of porous materials subjected to complex stress states

Finite-element simulations are used to obtain many thousands of yield points for porous materials with arbitrary void-volume fractions with spherical voids arranged in simple cubic, body-centred cubic and face-centred cubic three-dimensional arrays. Multi-axial stress states are explored. We show that the data may be fitted by a yield function which is similar to the Gurson-Tvergaard-Needleman (GTN) form, but which also depends on the determinant of the stress tensor, and all additional parameters may be expressed in terms of standard GTN-like parameters. The dependence of these parameters on the void-volume fraction is found. (c) 2006 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

A complex systems approach to the value of ecological resources

A theory of value sits at the core of every school of economic thought and directs the allocation of resources to competing uses. Ecological resources complicate the modem neoclassical approach to determining value due to their complex nature, considerable non-market values and the difficulty in assigning property rights. Application of the market model through economic valuation only provides analytical solutions based on virtual markets, and neither the demand nor supply-side techniques of valuation can adequately consider the complex set of biophysical and ecological relations that lead to the provision of ecosystem goods and services. This paper sets out a conceptual framework for a complex systems approach to the value of ecological resources. This approach is based on there being both an intrinsic quality of ecological resources and a subjective evaluation by the consumer. Both elements are necessary for economic value. This conceptual framework points the way towards a theory of value that incorporates both elements, so has implications for principles by which ecological resources can be allocated. (c) 2005 Elsevier B.V. All rights reserved.

Imitating the neighbours: vocal dialect matching in a mimic-model system

Vocal mimicry provides a unique system for investigating song learning and cultural evolution in birds. Male lyrebirds produce complex vocal displays that include extensive and accurate mimicry of many other bird species. We recorded and analysed the songs of the Albert's lyrebird (Menura alberti) and its most commonly imitated model species, the satin bowerbird (Ptilonorhynchus violaceus), at six sites in southeast Queensland, Australia. We show that each population of lyrebirds faithfully reproduces the song of the local population of bowerbirds. Within a population, lyrebirds show less variation in song structure than the available variation in the songs of the models. These results provide the first quantitative evidence for dialect matching in the songs of two species that have no direct ecological relationship.

Extending a model of shift-work tolerance

The present study contributes to theory and practice through the development of a model of shift-work tolerance with the potential to indicate interventions that reduce nurses' intention toward turnover and increase job satisfaction in hospital-based settings. Survey data from 1257 nurses were used to conduct structural equation modeling that examine the direct and indirect effects of supervisor and colleague support, team identity, team climate, and control over working environment on time-based work/life conflict, psychological well-being, physical symptoms, job satisfaction, and turnover intention. The analysis of the proposed model revealed a good fit The chi-square difference test was non-significant (χ2(26)=338.56), the fit indices were high (CFI=.923, NFI=.918, and NNFI=.868), the distribution of residuals was symmetric and approached zero, the average standardized residual was low (AASR=.04), and the standardized RMR was .072. In terms of the predictor variable, the final model explained 48% of the variance in turnover intention. The data revealed considerable evidence of both direct effects on adjustment and complex indirect links between levels of adjustment and work-related social support, team identity, team climate, and control. Nurses with high supervisor and coworker support experienced more positive team climates, identified more strongly with their team, and increased their perceptions of control over their work environment. This in turn lowered their appraisals of their time-based work/life conflict, which consequently increased their psychological well-being and job satisfaction and reduced their physical health symptoms and turnover intention. The type of shift schedule worked by the nurses influenced levels of turnover intention, control over work environment, time-based work/life conflict, and physical symptoms.

A Bethe ansatz solvable model for superpositions of Cooper pairs and condensed molecular bosons

We introduce a general Hamiltonian describing coherent superpositions of Cooper pairs and condensed molecular bosons. For particular choices of the coupling parameters, the model is integrable. One integrable manifold, as well as the Bethe ansatz solution, was found by Dukelsky et al. [J. Dukelsky, G.G. Dussel, C. Esebbag, S. Pittel, Phys. Rev. Lett. 93 (2004) 050403]. Here we show that there is a second integrable manifold, established using the boundary quantum inverse scattering method. In this manner we obtain the exact solution by means of the algebraic Bethe ansatz. In the case where the Cooper pair energies are degenerate we examine the relationship between the spectrum of these integrable Hamiltonians and the quasi-exactly solvable spectrum of particular Schrodinger operators. For the solution we derive here the potential of the Schrodinger operator is given in terms of hyperbolic functions. For the solution derived by Dukelsky et al., loc. cit. the potential is sextic and the wavefunctions obey PT-symmetric boundary conditions. This latter case provides a novel example of an integrable Hermitian Hamiltonian acting on a Fock space whose states map into a Hilbert space of PE-symmetric wavefunctions defined on a contour in the complex plane. (c) 2006 Elsevier B.V. All rights reserved.

Investigating the use of sweet sorghum as a model for sugar accumulation in sugarcane

This paper outlines a current investigation of sugar accumulation in sweet sorghum to assist in understanding and simplifying this complex trait in sugarcane. A recombinant inbred line (RIL) sorghum population, between a sweet and a grain sorghum, has been developed and phenotyped for various morphological and agronomic traits related to grain yield, biomass and stem sugar content. A genetic linkage map will be constructed for the sweet sorghum population with the objective of identifying genomic regions associated with sucrose accumulation in sweet sorghum. This will lead to further work, including comparative mapping in sugarcane, to identify the extent to which sweet sorghum can be used as a model for investigating sugar accumulation in sugarcane.

Model-Driven safety evaluation with state-event-based component failure annotations

Over the past years, the paradigm of component-based software engineering has been established in the construction of complex mission-critical systems. Due to this trend, there is a practical need for techniques that evaluate critical properties (such as safety, reliability, availability or performance) of these systems. In this paper, we review several high-level techniques for the evaluation of safety properties for component-based systems and we propose a new evaluation model (State Event Fault Trees) that extends safety analysis towards a lower abstraction level. This model possesses a state-event semantics and strong encapsulation, which is especially useful for the evaluation of component-based software systems. Finally, we compare the techniques and give suggestions for their combined usage

Simulation of air traffic controllers' behaviour using the operator choice model

The Operator Choice Model (OCM) was developed to model the behaviour of operators attending to complex tasks involving interdependent concurrent activities, such as in Air Traffic Control (ATC). The purpose of the OCM is to provide a flexible framework for modelling and simulation that can be used for quantitative analyses in human reliability assessment, comparison between human computer interaction (HCI) designs, and analysis of operator workload. The OCM virtual operator is essentially a cycle of four processes: Scan Classify Decide Action Perform Action. Once a cycle is complete, the operator will return to the Scan process. It is also possible to truncate a cycle and return to Scan after each of the processes. These processes are described using Continuous Time Probabilistic Automata (CTPA). The details of the probability and timing models are specific to the domain of application, and need to be specified using domain experts. We are building an application of the OCM for use in ATC. In order to develop a realistic model we are calibrating the probability and timing models that comprise each process using experimental data from a series of experiments conducted with student subjects. These experiments have identified the factors that influence perception and decision making in simplified conflict detection and resolution tasks. This paper presents an application of the OCM approach to a simple ATC conflict detection experiment. The aim is to calibrate the OCM so that its behaviour resembles that of the experimental subjects when it is challenged with the same task. Its behaviour should also interpolate when challenged with scenarios similar to those used to calibrate it. The approach illustrated here uses logistic regression to model the classifications made by the subjects. This model is fitted to the calibration data, and provides an extrapolation to classifications in scenarios outside of the calibration data. A simple strategy is used to calibrate the timing component of the model, and the results for reaction times are compared between the OCM and the student subjects. While this approach to timing does not capture the full complexity of the reaction time distribution seen in the data from the student subjects, the mean and the tail of the distributions are similar.

A hierarchical latent variable model for data visualization

Visualization has proven to be a powerful and widely-applicable tool the analysis and interpretation of data. Most visualization algorithms aim to find a projection from the data space down to a two-dimensional visualization space. However, for complex data sets living in a high-dimensional space it is unlikely that a single two-dimensional projection can reveal all of the interesting structure. We therefore introduce a hierarchical visualization algorithm which allows the complete data set to be visualized at the top level, with clusters and sub-clusters of data points visualized at deeper levels. The algorithm is based on a hierarchical mixture of latent variable models, whose parameters are estimated using the expectation-maximization algorithm. We demonstrate the principle of the approach first on a toy data set, and then apply the algorithm to the visualization of a synthetic data set in 12 dimensions obtained from a simulation of multi-phase flows in oil pipelines and to data in 36 dimensions derived from satellite images.

Causality and synchronisation in complex systems with applications to neuroscience

This thesis presents an investigation, of synchronisation and causality, motivated by problems in computational neuroscience. The thesis addresses both theoretical and practical signal processing issues regarding the estimation of interdependence from a set of multivariate data generated by a complex underlying dynamical system. This topic is driven by a series of problems in neuroscience, which represents the principal background motive behind the material in this work. The underlying system is the human brain and the generative process of the data is based on modern electromagnetic neuroimaging methods . In this thesis, the underlying functional of the brain mechanisms are derived from the recent mathematical formalism of dynamical systems in complex networks. This is justified principally on the grounds of the complex hierarchical and multiscale nature of the brain and it offers new methods of analysis to model its emergent phenomena. A fundamental approach to study the neural activity is to investigate the connectivity pattern developed by the brain’s complex network. Three types of connectivity are important to study: 1) anatomical connectivity refering to the physical links forming the topology of the brain network; 2) effective connectivity concerning with the way the neural elements communicate with each other using the brain’s anatomical structure, through phenomena of synchronisation and information transfer; 3) functional connectivity, presenting an epistemic concept which alludes to the interdependence between data measured from the brain network. The main contribution of this thesis is to present, apply and discuss novel algorithms of functional connectivities, which are designed to extract different specific aspects of interaction between the underlying generators of the data. Firstly, a univariate statistic is developed to allow for indirect assessment of synchronisation in the local network from a single time series. This approach is useful in inferring the coupling as in a local cortical area as observed by a single measurement electrode. Secondly, different existing methods of phase synchronisation are considered from the perspective of experimental data analysis and inference of coupling from observed data. These methods are designed to address the estimation of medium to long range connectivity and their differences are particularly relevant in the context of volume conduction, that is known to produce spurious detections of connectivity. Finally, an asymmetric temporal metric is introduced in order to detect the direction of the coupling between different regions of the brain. The method developed in this thesis is based on a machine learning extensions of the well known concept of Granger causality. The thesis discussion is developed alongside examples of synthetic and experimental real data. The synthetic data are simulations of complex dynamical systems with the intention to mimic the behaviour of simple cortical neural assemblies. They are helpful to test the techniques developed in this thesis. The real datasets are provided to illustrate the problem of brain connectivity in the case of important neurological disorders such as Epilepsy and Parkinson’s disease. The methods of functional connectivity in this thesis are applied to intracranial EEG recordings in order to extract features, which characterize underlying spatiotemporal dynamics before during and after an epileptic seizure and predict seizure location and onset prior to conventional electrographic signs. The methodology is also applied to a MEG dataset containing healthy, Parkinson’s and dementia subjects with the scope of distinguishing patterns of pathological from physiological connectivity.

Spectral pattern, grouping, and the pitches of complex tones and their components

Harmonically related components are typically heard as a unified entity with a rich timbre and a pitch corresponding to the fundamental frequency. Mistuning a component generally has four consequences: (i) the global pitch of the complex shifts in the same direction as the mistuning; (ii) the component makes a reduced contribution to global pitch; (iii) the component is heard out as a separate sound with a pure timbre; (iv) its pitch differs from that of a pure tone of equal frequency in a small but systematic way. Local interactions between neighbouring components cannot explain these effects; instead they are usually explained in terms of the global operation of a single harmonic-template mechanism. However, several observations indicate that separate mechanisms govern the selection of spectral components for perceptual fusion and for the computation of global pitch. First, an increase in mistuning causes a harmonic to be heard out before it begins to be excluded from the computation of global pitch. Second, a single even harmonic added to an odd-harmonic complex is typically more salient than its odd neighbours. Third, the mistuning of a component in frequency-shifted stimuli, or stimuli with a moderate spectral stretch, results in changes in salience and component pitch like those seen for harmonic stimuli. Fourth, the global pitch of frequency-shifted stimuli is predicted well by the weighted fit of a harmonic template, but, with the exception of the lowest component, the fusion of individual partials for shifted stimuli is best predicted by the common pattern of spectral spacing. Fifth, our sensitivity to spectral pattern is surprisingly resistant to random variations in component spacing induced by applying mistunings to several harmonics at once. These findings are evaluated in the context of an autocorrelogram model of the proposed pitch/grouping dissociation. © S. Hirzel Verlag · EAA.

Development of an in-vitro model system to investigate the mechanism of muscle protein catabolism induced by proteolysis-inducing factor

The mechanism of muscle protein catabolism induced by proteolysis-inducing factor, produced by cachexia-inducing murine and human tumours has been studied in vitro using C2C12 myoblasts and myotubes. In both myoblasts and myotubes protein degradation was enhanced by proteolysis-inducing factor after 24 h incubation. In myoblasts this followed a bell-shaped dose-response curve with maximal effects at a proteolysis-inducing factor concentration between 2 and 4 nM, while in myotubes increased protein degradation was seen at all concentrations of proteolysis-inducing factor up to 10 nM, again with a maximum of 4 nM proteolysis-inducing factor. Protein degradation induced by proteolysis-inducing factor was completely attenuated in the presence of cycloheximide (1 μM), suggesting a requirement for new protein synthesis. In both myoblasts and myotubes protein degradation was accompanied by an increased expression of the α-type subunits of the 20S proteasome as well as functional activity of the proteasome, as determined by the 'chymotrypsin-like' enzyme activity. There was also an increased expression of the 19S regulatory complex as well as the ubiquitin-conjugating enzyme (E214k), and in myotubes a decrease in myosin expression was seen with increasing concentrations of proteolysis-inducing factor. These results show that proteolysis-inducing factor co-ordinately upregulates both ubiquitin conjugation and proteasome activity in both myoblasts and myotubes and may play an important role in the muscle wasting seen in cancer cachexia. © 2002 Cancer Research UK.

Examining the strategy development process through the lens of complex adaptive systems theory

The development of strategy remains a debate for academics and a concern for practitioners. Published research has focused on producing models for strategy development and on studying how strategy is developed in organisations. The Operational Research literature has highlighted the importance of considering complexity within strategic decision making; but little has been done to link strategy development with complexity theories, despite organisations and organisational environments becoming increasingly more complex. We review the dominant streams of strategy development and complexity theories. Our theoretical investigation results in the first conceptual framework which links an established Strategic Operational Research model, the Strategy Development Process model, with complexity via Complex Adaptive Systems theory. We present preliminary findings from the use of this conceptual framework applied to a longitudinal, in-depth case study, to demonstrate the advantages of using this integrated conceptual model. Our research shows that the conceptual model proposed provides rich data and allows for a more holistic examination of the strategy development process. © 2012 Operational Research Society Ltd. All rights reserved.