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.

Organic Matter Dynamics in the Wet Tropics Under Different Sugarcane Residue Management Regimes

Retention of sugarcane leaves and tops on the soil surface after harvesting has almost completely replaced pre- and post-harvest burning of crop residues in the Australian sugar industry. Since its introduction around 25 years ago, residue retention has increased soil organic matter to improve soil fertility as well as improve harvest flexibility and reduce erosion. However, in the wet tropics residue retention also poses potential problems of prolonged waterlogging, and late-season release of nitrogen which can reduce sugar content of the crop. The objective of this project is to examine the management of sugarcane residues in the wet tropics using a systems approach. Subsidiary objectives are (a) to improve understanding of nitrogen cycling in Australian sugarcane soils in the wet tropics, and (b) to identify ways to manage crop residues to retain their advantages and limit their disadvantages. Project objectives will be addressed using several approaches. Historic farm production data recorded by sugar mills in the wet tropics will be analysed to determine the effect of residue burning or retention on crop yield and sugar content. The impact of climate on soil processes will be highlighed by development of an index of nitrogen mineralisation using the Agricultural Production Systems Simulator (APSIM) model. Increased understanding of nitrogen cycling in Australian sugarcane soils and management of crop residues will be gained through a field experiment recently established in the Australian wet tropics. From this experiment the decomposition and nitrogen dynamics of residues placed on the soil surface and incorporated will be compared. The effect of differences in temperature, soil water content and pH will be further examined on these soils under glasshouse conditions. Preliminary results show a high ammonium to nitrate ratio in tropics soils, which may be due to low rates of nitrification that increase the retention of nitrogen in a form (ammonium) that is less subject to leaching. Further results will be presented at Congress.

Stimuli of varying spatial scale induce gamma activity with distinct temporal characteristics in human visual cortex

Gamma activity to stationary grating stimuli was studied non-invasively using MEG recordings in humans. Using a spatial filtering technique, we localized gamma activity to primary visual cortex. We tested the hypothesis that spatial frequency properties of visual stimuli may be related to the temporal frequency characteristics of the associated cortical responses. We devised a method to assess temporal frequency differences between stimulus-related responses that typically exhibit complex spectral shapes. We applied this methodology to either single-trial (induced) or time-averaged (evoked) responses in four frequency ranges (0-40, 20-60, 40-80 and 60-100 Hz) and two time windows (either the entire duration of stimulus presentation or the first second following stimulus onset). Our results suggest that stimuli of varying spatial frequency induce responses that exhibit significantly different temporal frequency characteristics. These effects were particularly accentuated for induced responses in the classical gamma frequency band (20-60 Hz) analyzed over the entire duration of stimulus presentation. Strikingly, examining the first second of the responses following stimulus onset resulted in significant loss in stimulus specificity, suggesting that late signal components contain functionally relevant information. These findings advocate a functional role of gamma activity in sensory representation. We suggest that stimulus specific frequency characteristics of MEG signals can be mapped to processes of neuronal synchronization within the framework of coupled dynamical systems.

A new entropy measure based on the Renyi entropy rate using Gaussian kernels

The concept of entropy rate is well defined in dynamical systems theory but is impossible to apply it directly to finite real world data sets. With this in mind, Pincus developed Approximate Entropy (ApEn), which uses ideas from Eckmann and Ruelle to create a regularity measure based on entropy rate that can be used to determine the influence of chaotic behaviour in a real world signal. However, this measure was found not to be robust and so an improved formulation known as the Sample Entropy (SampEn) was created by Richman and Moorman to address these issues. We have developed a new, related, regularity measure which is not based on the theory provided by Eckmann and Ruelle and proves a more well-behaved measure of complexity than the previous measures whilst still retaining a low computational cost.

Amplitude response of a unilaterally constrained nonlinear micromechanical resonator

Dynamical systems that involve impacts frequently arise in engineering. This Letter reports a study of such a system at microscale that consists of a nonlinear resonator operating with an unilateral impact. The microresonators were fabricated on silicon-on-insulator wafers by using a one-mask process and then characterised by using the capacitively driving and sensing method. Numerical results concerning the dynamics of this vibro-impact system were verified by the experiments. Bifurcation analysis was used to provide a qualitative scenario of the system steady-state solutions as a function of both the amplitude and the frequency of the external driving sinusoidal voltage. The results show that the amplitude of resonant peak is levelled off owing to the impact effect and that the bandwidth of impacting is dependent upon the nonlinearity and the operating conditions.

Bayesian online algorithms for learning in discrete Hidden Markov Models

We propose and analyze two different Bayesian online algorithms for learning in discrete Hidden Markov Models and compare their performance with the already known Baldi-Chauvin Algorithm. Using the Kullback-Leibler divergence as a measure of generalization we draw learning curves in simplified situations for these algorithms and compare their performances.

Variational inference for diffusion processes

Diffusion processes are a family of continuous-time continuous-state stochastic processes that are in general only partially observed. The joint estimation of the forcing parameters and the system noise (volatility) in these dynamical systems is a crucial, but non-trivial task, especially when the system is nonlinear and multimodal. We propose a variational treatment of diffusion processes, which allows us to compute type II maximum likelihood estimates of the parameters by simple gradient techniques and which is computationally less demanding than most MCMC approaches. We also show how a cheap estimate of the posterior over the parameters can be constructed based on the variational free energy.

Computer integrated system for form-roll manufacture

Computer integrated manufacture has brought about great advances in manufacturing technology and its recognition is world wide. Cold roll forming of thin-walled sections, and in particular the design and manufacture of form-rolls, the special tooling used in the cold roll forming process, is but one such area where computer integrated manufacture can make a positive contribution. The work reported in this thesis, concerned with the development of an integrated manufacturing system for assisting the design and manufacture of form-rolls, was undertaken in collaboration with a leading manufacturer of thin-walled sections. A suit of computer programs, written in FORTRAN 77, have been developed to provide computer aids for every aspect of work in form-roll design and manufacture including cost estimation and stock control aids. The first phase of the development programme dealt with the establishment of CAD facilities for form-roll design, comprising the design of the finished section, the flower pattern, the roll design and the interactive roll editor program. Concerning the CAM facilities, dealt with in the second phase, an expert system roll machining processor and a general post-processor have been developed for considering the roll geometry and automatically generating NC tape programs for any required CNC lathe system. These programs have been successfully implemented, as an integrated manufacturing software system, on the VAX 11/750 super-minicomputer with graphics facilities for displaying drawings interactively on the terminal screen. The development of the integrated system has been found beneficial in all aspects of form-roll design and manufacture. Design and manufacturing lead times have been reduced by several weeks, quality has improved considerably and productivity has increased. The work has also demonstrated the promising nature of the expert systems approach to computer integrated manufacture.

Obstacles and solutions to maximising urban biodiversity throughout the lifecycles of major developments in England

Thus far, achieving net biodiversity gains through major urban developments has been neither common nor straightforward - despite the presence of incentives, regulatory contexts, and ubiquitous practical guidance tools. A diverse set of obstructions, occurring within different spatial, temporal and actor hierarchies, are experienced by practitioners and render the realisation of maximised biodiversity, a rarity. This research aims to illuminate why this is so, and what needs to be changed to rectify the situation. To determine meaningful findings and conclusions, capable of assisting applied contexts and accommodating a diverse range of influences, a ‘systems approach’ was adopted. This approach led to the use of a multi-strategy research methodology, to identify the key obstructions and solutions to protecting and enhancing biodiversity - incorporating the following methods: action research, a questionnaire to local government ecologists, interviews and personal communications with leading players, and literature reviews. Nevertheless, ‘case studies’ are the predominant research method, the focus being a ‘nested’ case study looking at strategic issues of the largest regeneration area in Europe ‘the Thames Gateway’, and the largest individual mixeduse mega-development in the UK (at the time of planning consent) ‘Eastern Quarry 2’ - set within the Gateway. A further key case study, focussing on the Central Riverside development in Sheffield, identifies the merits of competition and partnership. The nested cases, theories and findings show that the strategic scale - generally relating to governance and prioritisation - impacts heavily upon individual development sites. It also enables the identification of various processes, mechanisms and issues at play on the individual development sites, which primarily relate to project management, planning processes, skills and transdisciplinary working, innovative urban biodiversity design capabilities, incentives, organisational cultures, and socio-ecological resilience. From these findings a way forward is mapped, spanning aspects from strategic governance to detailed project management.