New tools for self-organised pattern formation

Position-dependent gene expression is a critical aspect of the development and behaviour of multicellular organisms. It requires a complex series of interactions to occur between different cell types in addition to intracellular signalling cascades. We used Escherichia coli to study the properties of an artificial signalling system at the interface between two expanding cell populations. We genetically engineered one population to produce a diffusible acyl-homoserine lactone (AHL) signal, and another population to respond to it. Our experiments demonstrate how such a signal can be used to reproducibly generate simple visible patterns with high accuracy in swimming agar. The producing and responding cassettes of two such signalling systems can be linked to produce a symmetric interface for bidirectional communication that can be used to visualise molecular logic. Intracellular feedback between these two cassettes would then create a framework for self-organised patterning of higher complexity. Adapting the experiments of Basu et al. (Basu et al., 2005) using cell motility, rather than a differential response to AHL concentrations as a way to define zones of response, we noted how the interaction of sender and receiver cell populations on a swimming plate could lead to complex pattern formation. Equipping highly motile strains such as E. coli MC1000 with AHL-mediated auto-inducing systems based on Vibrio fischeri luxI/luxR and Pseudomonas aeruginosa lasI/lasR cassettes would allow the amplification of a response to an AHL signal and its propagation. We designed and synthesised codon-optimised auto-inducing luxI/R and lasI/R cassettes as optimal gene expression is crucial for the generation of robust patterns. We still have to complete and test the entire genetic circuitry, although by modelling the system we were able to demonstrate its feasibility. © 2007 The Institution of Engineering and Technology.

New evidence for the origin and behaviour of deep ocean 'crusts'

In situ tests in deep waterWest African clays show crust-like shear strengths within the top few metres of sediment. Typical strength profiles show su rising from mud-line to 10 kPa to 15 kPa before dropping back to normally consolidated strengths of 3 kPa to 4 kPa by 1.5m to 2m depth. A Cam-shear device is used to better understand the mechanical behaviour of undisturbed crust samples under pipelines. Extremely variable peak and residual shear strengths are observed for a range of pipeline consolidation stresses and test shear rates, with residual strengths approximating zero. ESEM of undisturbed samples and wet-sieved samples from various core depths show the presence of numerous randomly-located groups of invertebrate faecal pellets. It is therefore proposed that the cause of strength variability during shear testing and, indeed, of the crust's origin, is the presence of random groups of faecal pellets within the sediment. © 2011 Taylor & Francis Group, London.

Use of contexts in language model interpolation and adaptation

Language models (LMs) are often constructed by building multiple individual component models that are combined using context independent interpolation weights. By tuning these weights, using either perplexity or discriminative approaches, it is possible to adapt LMs to a particular task. This paper investigates the use of context dependent weighting in both interpolation and test-time adaptation of language models. Depending on the previous word contexts, a discrete history weighting function is used to adjust the contribution from each component model. As this dramatically increases the number of parameters to estimate, robust weight estimation schemes are required. Several approaches are described in this paper. The first approach is based on MAP estimation where interpolation weights of lower order contexts are used as smoothing priors. The second approach uses training data to ensure robust estimation of LM interpolation weights. This can also serve as a smoothing prior for MAP adaptation. A normalized perplexity metric is proposed to handle the bias of the standard perplexity criterion to corpus size. A range of schemes to combine weight information obtained from training data and test data hypotheses are also proposed to improve robustness during context dependent LM adaptation. In addition, a minimum Bayes' risk (MBR) based discriminative training scheme is also proposed. An efficient weighted finite state transducer (WFST) decoding algorithm for context dependent interpolation is also presented. The proposed technique was evaluated using a state-of-the-art Mandarin Chinese broadcast speech transcription task. Character error rate (CER) reductions up to 7.3 relative were obtained as well as consistent perplexity improvements. © 2012 Elsevier Ltd. All rights reserved.

System Dynamics and Scenario Planning: Implementation Challenges

In this paper we discuss key implementation challenges of a systems approach that combines System Dynamics, Scenario Planning and Qualitative Data Analysis methods in tackling a complex problem. We present the methods and the underlying framework. We then detail the main difficulties encountered in designing and planning the Scenario Planning workshop and how they were overcome, such as finding and involving the stakeholders and customising the process to fit within timing constraints. After presenting the results from this application, we argue that the consultants or system analysts need to engage with the stakeholders as process facilitators and not as system experts in order to gain commitment, trust and to improve information sharing. They also need be ready to adapt their tools and processes as well as their own thinking for more effective complex problem solving.

Transient natural ventilation of a space with localised heating

The natural ventilation of a well-mixed, pre-heated room with a point source of heating, and openings at the base and roof is investigated. The transient draining associated with the room being warmer than the exterior combined with the convective ow produced by the point source of heat leads to a fascinating series of transient ow regimes as the system evolves to the two-layer steady-state regime described by Linden, Lane-Ser_ and Smeed [1]. As the room begins to ventilate, a turbulent plume rises from the point source of heat to the ceiling, and typically forms a deepening layer of hot air. However, with a weak heat source, then at some point the ascending plume will intrude beneath the layer of original uid. Otherwise, the ascending plume always reaches the top of the room as the system evolves to a steady state. We develop a simpli_ed model of the transient evolution and test this with some new laboratory experiments. We conclude with a discussion of the implications of our results for real buildings.

Multi-colour switching of polymer stabilized chiral nematic liquid crystal devices

We have fabricated a series of polymer stabilized chiral nematic test cells for use as flexoelectro-optic devices. The devices fabricated were based on commercial chiral nematic mixtures which were polymer stabilized so as to enhance the uniformity and stability of the uniform lying helix texture in the cells. During fabrication and test procedures a series of unusual scattering states have been observed within the devices at different viewing angles. The observations made so far indicate that the properties of the scattering state lies somewhere between the focal conic texture and the Grandjean or planar texture and that the devices exhibit both a helical pitch selective reflection and scattering effect. What is even more dramatic is that the wavelength selectivity of the scattering effect can be tuned by an applied field. In addition, we show that it is possible to achieve good uniform lying helix textures from such devices. Moreover, we show that in certain cases the spontaneous alignment of the helix in the plane of the device opens up the possibility of a new mode of switching. Flexoelectric, Redshift, Coloured scattering, Liquid crystal, Polymer-stabilized liquid-crystal;.

Building more sustainable solutions in production-consumption systems: the case of food for people with reduced access

In new product development, the ability to integrate different dimensions of sustainability at a value chain level is still a complex, problematic goal. As product-service approaches are increasingly enabling the introduction of more sustainable paths, this paper describes the authors' experience thus far when building insights into conditions for the implementation of integrated solutions in a process of co-development and testing in real life conditions, which are driven by a social need focusing on food for people with reduced access. Throughout this process, which brought together producers, consumers and other stakeholders to design and test industrialised, sustainable solutions, empirical evidence demonstrates feasibility and usefulness of the approach and insight into the conditions for implementing interactive, comprehensive multi-stakeholder processes in real life situations. In addition, results show that the delivery of innovative solutions enabled to offer social added value, economic profits and environmental improvements under specific experimental conditions. © 2006 Elsevier Ltd. All rights reserved.

A validation of commercial flow solver performance on hybridised octree meshes

In recent years we have been developing a meshing system which is aimed at eliminating the bottleneck represented by building meshes for real-world, complex turbomachinery configurations. This system is based on a rapid octree meshing technology which is then made conformal to the bodies present. The objective of this paper is to demonstrate that this class of mesh is not only very fast to produce but also fit-for-purpose in the sense that simulations generated with third-party commercial flow solvers like Fluent have the same accuracy as those performed on more conventional meshes. A range of standard examples and test cases will be presented. Copyright © 2011 by ASME.

Insight into differences in nanoindentation properties of bone.

Nanoindentation provides the ideal framework to determine mechanical properties of bone at the tissue scale without being affected by the size, shape, and porosity of the bone. However, the values of tissue level mechanical properties vary significantly between studies. Since the differences in the bone sample, hydration state, and test parameters complicate direct comparisons across the various studies, these discrepancies in values cannot be compared directly. The objective of the current study is to evaluate and compare mechanical properties of the same bones using a broad range of testing parameters. Wild type C56BL6 mice tibiae were embedded following different processes and tested in dry and rehydrated conditions. Spherical and Berkovich indenter probes were used, and data analysis was considered within the elasto-plastic (Oliver-Pharr), viscoelastic and visco-elastic-plastic frameworks. The mean values of plane strain modulus varied significantly depending on the hydration state, probe geometry and analysis method. Indentations in dry bone analyzed using a visco-elastic-plastic approach gave values of 34 GPa. After rehydrating the same bones and indenting them with a spherical tip and utilizing a viscoelastic analysis, the mean modulus value was 4 GPa, nearly an order of magnitude smaller. Results suggest that the hydration state, probe geometry and the limitations and assumptions of each analysis method influence significantly the measured mechanical properties. This is the first time that such a systematic study has been carried out and it has been concluded that the discrepancies in the mechanical properties of bone measured by nanoindentation found in the literature should not be attributed only to the differences between the bones themselves, but also to the testing and analysis protocols.

Distribution matching for transduction

Many transductive inference algorithms assume that distributions over training and test estimates should be related, e.g. by providing a large margin of separation on both sets. We use this idea to design a transduction algorithm which can be used without modification for classification, regression, and structured estimation. At its heart we exploit the fact that for a good learner the distributions over the outputs on training and test sets should match. This is a classical two-sample problem which can be solved efficiently in its most general form by using distance measures in Hilbert Space. It turns out that a number of existing heuristics can be viewed as special cases of our approach.

Code-specific policy gradient rules for spiking neurons

Although it is widely believed that reinforcement learning is a suitable tool for describing behavioral learning, the mechanisms by which it can be implemented in networks of spiking neurons are not fully understood. Here, we show that different learning rules emerge from a policy gradient approach depending on which features of the spike trains are assumed to influence the reward signals, i.e., depending on which neural code is in effect. We use the framework of Williams (1992) to derive learning rules for arbitrary neural codes. For illustration, we present policy-gradient rules for three different example codes - a spike count code, a spike timing code and the most general "full spike train" code - and test them on simple model problems. In addition to classical synaptic learning, we derive learning rules for intrinsic parameters that control the excitability of the neuron. The spike count learning rule has structural similarities with established Bienenstock-Cooper-Munro rules. If the distribution of the relevant spike train features belongs to the natural exponential family, the learning rules have a characteristic shape that raises interesting prediction problems.