Approximating the Set of Local Minima in Partial RNA Folding Landscapes

Motivation: We study a stochastic method for approximating the set of local minima in partial RNA folding landscapes associated with a bounded-distance neighbourhood of folding conformations. The conformations are limited to RNA secondary structures without pseudoknots. The method aims at exploring partial energy landscapes pL induced by folding simulations and their underlying neighbourhood relations. It combines an approximation of the number of local optima devised by Garnier and Kallel (2002) with a run-time estimation for identifying sets of local optima established by Reeves and Eremeev (2004).

Results: The method is tested on nine sequences of length between 50 nt and 400 nt, which allows us to compare the results with data generated by RNAsubopt and subsequent barrier tree calculations. On the nine sequences, the method captures on average 92% of local minima with settings designed for a target of 95%. The run-time of the heuristic can be estimated by O(n2D?ln?), where n is the sequence length, ? is the number of local minima in the partial landscape pL under consideration and D is the maximum number of steepest descent steps in attraction basins associated with pL.

Catalysing open innovation through publicly funded R&D: A Comparison of University and Company-based research centres

Public funding of university and company-based R&D centres of excellence is widespread both in core and more peripheral regions. What is less well-known is whether these R&D centres can catalyse multi-directional, multi-actor and iterative innovation. Based on data from a real-time monitoring study, this article explores the development of 18 R&D centres’ external connections. University-based R&D centres establish more new connections than company-based centres and are more likely to be interacting with small or micro-firms. However, there is a general bias towards links with larger firms; micro, small and medium-sized enterprises also are less likely to be involved in collaborative R&D with research centres than other types of relationships. The results suggest the potential for R&D centres to act as a catalyst for open innovation but emphasise the need to ensure that the focus of the R&D being conducted is relevant to the needs of smaller firms.

Imported and translated landscapes: Buenos Aires nineteenth-century waterfront parks

The study of urban and landscape history has recently questioned the peripheral condition of certain areas and re-examined them as valuable parts of an international network . In such a framework cities are not only recipients of foreign influences but active agents in their own urban transformations. Meanwhile, the regeneration of urban waterfronts appears increasingly in the spotlight globally , but the re-use of the waterfront as public space began more than a century ago.

Buenos Aires is an example of a ‘peripheral’ city, in which waterfront parks at the end of the nineteenth century were the product of international influences combined with local conditions, needs and expertise. Buenos Aires developed a continuous increase and diversity of leisure waterfront space, making it different from most European or ‘central’ cities. This paper will analyse the process of translation of landscape design on Buenos Aires’ waterfront while outlining the significance of waterfront parks to the city and its growing urban population.

Microscopic theory for random processes in weakly-coupled open systems

In order to relate macroscopic random motion (described e.g. by Langevin-type theories) to microscopic dynamics, we have undertaken the derivation of a Fokker-Planck-type equation from first microscopic principles. Both subsystems are subject to an external force field. Explicit expressions for the diffusion and drift coefficients are obtained, in terms of the field.

Open access gastroscopy--3 year experience of a new service

We have audited the first 3 yr of a new open access gastroscopy service in the Royal Victoria Hospital, Belfast to assess service demands, patient demography and diagnostic trends. Over 3 yr there were 1872 referrals (800 from fundholding general practitioners), 8.8 per cent were non attenders and 5.4 per cent cancelled appointments. Endoscopic diagnostic categories showed no significant change over the 3 yr, 39 per cent non ulcer dyspepsia, 35 per cent gastro-oesophageal reflux disease (GORD), 17 per cent peptic ulcer disease (PUD), 6 per cent GORD and PUD, 1 per cent gastric erosions and 0.8 per cent carcinoma.

The OpenPMU Platform for Open Source Phasor Measurements

OpenPMU is an open platform for the development of phasor measurement unit (PMU) technology. A need has been identified for an open-source alternative to commercial PMU devices tailored to the needs of the university researcher and for enabling the development of new synchrophasor instruments from this foundation. OpenPMU achieves this through open-source hardware design specifications and software source code, allowing duplicates of the OpenPMU to be fabricated under open-source licenses. This paper presents the OpenPMU device based on the Labview development environment. The device is performance tested according to the IEEE C37.118.1 standard. Compatibility with the IEEE C37.118.2 messaging format is achieved through middleware which is readily adaptable to other PMU projects or applications. Improvements have been made to the original design to increase its flexibility. A new modularized architecture for the OpenPMU is presented using an open messaging format which the authors propose is adopted as a platform for PMU research.

Communicating open systems

Just as conventional institutions are organisational structures for coordinating the activities of multiple interacting individuals, electronic institutions provide a computational analogue for coordinating the activities of multiple interacting software agents. In this paper, we argue that open multi-agent systems can be effectively designed and implemented as electronic institutions, for which we provide a comprehensive computational model. More specifically, the paper provides an operational semantics for electronic institutions, specifying the essential data structures, the state representation and the key operations necessary to implement them. We specify the agent workflow structure that is the core component of such electronic institutions and particular instantiations of knowledge representation languages that support the institutional model. In so doing, we provide the first formal account of the electronic institution concept in a rigorous and unambiguous way.

BAILII, Legal Education and Open Access to Law

The British and Irish Legal Information Institute (BAILII) entered the online legal information landscape in 2001 with charitable status as a provider of UK and European judgments, and has over the past decade or so moved from a system quickly put together with any materials which could be found, to a system which provides a core resource to professionals in law. In this article we provide an overview for the law teacher of the system’s first years and we then look at whether usage in law schools has matched that of the professional, how the JISC funded Open Law project enabled development for law students, and where we might go in the future as part of the Legal Information Institute collective which operates under the ‘Free Access to Law’ banner.
As members of the Open Law team who sought funding, carried out the research and implemented the project, it seems to us that the project was generally successful. Our indications were that prior to Open Law the use of BAILII by students was low – it was not readily found or discussed by lecturers, was difficult to use, and generally less user friendly than it could have been. The changes implemented by Open Law appear to have changed that position considerably. However, our findings also indicate that there is much work to do to re-energise digital legal information as a legal education research field.