Protein sequence threading, the alignment problem, and a two-step strategy

Conventionally, protein structure prediction via threading relies on some nonoptimal method to align a protein sequence to each member of a library of known structures. We show how a score function (force field) can be modified so as to allow the direct application of a dynamic programming algorithm to the problem. This involves an approximation whose damage can be minimized by an optimization process during score function parameter determination. The method is compared to sequence to structure alignments using a more conventional pair-wise score function and the frozen approximation. The new method produces results comparable to the frozen approximation, but is faster and has fewer adjustable parameters. It is also free of memory of the template's original amino acid sequence, and does not suffer from a problem of nonconvergence, which can be shown to occur with the frozen approximation. Alignments generated by the simplified score function can then be ranked using a second score function with the approximations removed. (C) 1999 John Wiley & Sons, Inc.

Organisational learning and knowledge acquisition. A case study of internationalising manufacturers of wood-based prefabricated buildings

The study investigates organisational learning and knowledge acquisition of wood-based prefabricated building manufacturers. This certain group of case companies was chosen, because their management and their employees generally have a strong manufacturing and engineering background, while the housing sector is characterised by national norms, regulations, as well as local building styles. Considering this setting, it was investigated, how the case companies develop organisational learning capabilities, acquire and transfer knowledge for their internationalisation. The theoretical framework of this study constitutes the knowledge-based conceptualisation of internationalisation, which combines the traditional internationalisation process, as well as the international new venture perspective based on their commonalities in the knowledge-based view of the firm. Different theories of internationalisation, including the network-perspective, were outlined and a framework on organisational learning and knowledge acquisition was established. The empirical research followed a qualitative approach, deploying a multiple-case study with five case companies from Austria, Finland and Germany. In the study, the development of the wood-based prefabricated building industry and of the case companies are described, and the motives, facilitators and challenges for foreign expansion, as well as the companies’ internationalisation approaches are compared. Different methods of how companies facilitate the knowledge-exchange or learn about new markets are also outlined. Experience, market knowledge and personal contacts are considered essential for the internationalisation process. The major finding of the study is that it is not necessary to acquire the market knowledge internally in a slow process as proposed by the Uppsala model. In four cases companies engaged knowledge in symbiotic relations with local business partners. Thereby, the building manufacturers contribute their design and production capabilities, and in return, their local partners provide them with knowledge about the market and local regulations; while they manage the sales and construction operations. Thus, the study provides strong evidence for the propositions of network perspective. One case company developed the knowledge internally in a gradual process: it entered the market sequentially with several business lines, showing an increasing level of complexity. In both of the observed strategies, single-loop and double-loop learning processes occurred.

Modelling an expert GIS system based on knowledge to evaluate oil spill environmental sensitivity

Oil spills cause great damage to coastal habitats, especially when rapid and suitable response measures are not taken. Establishing high priority areas is fundamental for the operation of response teams. Under this context and considering the need for keeping all geographical information up-to-date for emergencial use, the present study proposes employing a decision tree coupled with a knowledge-based approach using GIS to assign oil sensitivity indices to Brazilian coastal habitats. The modelled system works based on rules set by the official standards of Brazilian Federal Environment Organ. We tested it on one of the littoral regions of Brazil where transportation of petroleum is most intense: the coast of the municipalities of Sao Sebastiao and Caraguatatuba in the northern littoral of São Paulo state, Brazil. The system automatically ranked the littoral sensitivity index of the study area habitats according to geographical conditions during summer and winter; since index ranks of some habitats varied between these seasons because of sediment alterations. The obtained results illustrate the great potential of the proposed system in generating ESI maps and in aiding response teams during emergency operations. (C) 2009 Elsevier Ltd. All rights reserved.

Sustainable production of biologically active molecules of marine based origin

The marine environment offers both economic and scientific potential which are relatively untapped from a biotechnological point of view. These environments whilst harsh are ironically fragile and dependent on a harmonious life form balance. Exploitation of natural resources by exhaustive wild harvesting has obvious negative environmental consequences. From a European industry perspective marine organisms are a largely underutilised resource. This is not due to lack of interest but due to a lack of choice the industry faces for cost competitive, sustainable and environmentally conscientious product alternatives. Knowledge of the biotechnological potential of marine organisms together with the development of sustainable systems for their cultivation, processing and utilisation are essential. In 2010, the European Commission recognised this need and funded a collaborative RTD/SME project under the Framework 7-Knowledge Based Bio-Economy (KBBE) Theme 2 Programme 'Sustainable culture of marine microorganisms, algae and/or invertebrates for high value added products'. The scope of that project entitled 'Sustainable Production of Biologically Active Molecules of Marine Based Origin' (BAMMBO) is outlined. Although the Union is a global leader in many technologies, it faces increasing competition from traditional rivals and emerging economies alike and must therefore improve its innovation performance. For this reason innovation is placed at the heart of a European Horizon 2020 Strategy wherein the challenge is to connect economic performance to eco performance. This article provides a synopsis of the research activities of the BAMMBO project as they fit within the wider scope of sustainable environmentally conscientious marine resource exploitation for high-value biomolecules. © 2013 Elsevier B.V.

Managing a World Heritage Site: Potentials and limitations of transdisciplinary approaches

Balancing the frequently conflicting priorities of conservation and economic development poses a challenge to management of the Swiss Alps Jungfrau- Aletsch World Heritage Site (WHS). This is a complex societal problem that calls for a knowledge-based solution. This in turn requires a transdisciplinary research framework in which problems are defined and solved cooperatively by actors from the scientific community and the life-world. In this article we re-examine studies carried out in the region of the Swiss Alps Jungfrau-Aletsch WHS, covering three key issues prevalent in transdisciplinary settings: integration of stakeholders into participatory processes; perceptions and positions; and negotiability and implementation. In the case of the Swiss Alps Jungfrau-Aletsch WHS the transdisciplinary setting created a situation of mutual learning among stakeholders from different levels and backgrounds. However, the studies showed that the benefits of such processes of mutual learning are continuously at risk of being diminished by the power play inherent in participatory approaches.

Managing a World Heritage Site – Potentials and Limitations of Transdisciplinary Approaches

Management of the World Heritage Site Swiss Alps Jungfrau-Aletsch is challenged by the interplay of conservation and economic development. This is a situation where a knowledge-based solution is sought for a complex societal problem. This sets the frame for transdisciplinary research where the problem is defined and solved cooperatively by actors from science and the life-world. In this paper we re-examine studies carried out in the region of the WHS Jungfrau-Aletsch and reveal the issue of integration into participation, the issue of perceptions and positions as well as the issue of negotiability and implementation as key issues prevalent in transdisciplinary settings. The transdisciplinary setting in the case of the WHS Jungfrau-Aletsch constructs a situation of mutual learning among stakeholders from different levels and backgrounds. However, the positive effects of mutual learning are continuously challenged by the power play inherent in participatory approaches.

Modeling Commercial Knowledge to Develop Advanced Agent-based Marketplaces for E-commerce

This paper argues about the utility of advanced knowledge-based techniques to develop web-based applications that help consumers in finding products within marketplaces in e-commerce. In particular, we describe the idea of model-based approach to develop a shopping agent that dynamically configures a product according to the needs and preferences of customers. Finally, the paper summarizes the advantages provided by this approach.

Simulation based knowledge elicitation:effect of visual representation and model parameters

Since much knowledge is tacit, eliciting knowledge is a common bottleneck during the development of knowledge-based systems. Visual interactive simulation (VIS) has been proposed as a means for eliciting experts’ decision-making by getting them to interact with a visual simulation of the real system in which they work. In order to explore the effectiveness and efficiency of VIS based knowledge elicitation, an experiment has been carried out with decision-makers in a Ford Motor Company engine assembly plant. The model properties under investigation were the level of visual representation (2-dimensional, 2½-dimensional and 3-dimensional) and the model parameter settings (unadjusted and adjusted to represent more uncommon and extreme situations). The conclusion from the experiment is that using a 2-dimensional representation with adjusted parameter settings provides the better simulation-based means for eliciting knowledge, at least for the case modelled.

Knowledge Construction Technology through Hypermedia-Based Intelligent Conversational Channel

There have been multifarious approaches in building expert knowledge in medical or engineering field through expert system, case-based reasoning, model-based reasoning and also a large-scale knowledge-based system. The intriguing factors with these approaches are mainly the choices of reasoning mechanism, ontology, knowledge representation, elicitation and modeling. In our study, we argue that the knowledge construction through hypermedia-based community channel is an effective approach in constructing expert’s knowledge. We define that the knowledge can be represented as in the simplest form such as stories to the most complex ones such as on-the-job type of experiences. The current approaches of encoding experiences require expert’s knowledge to be acquired and represented in rules, cases or causal model. We differentiate the two types of knowledge which are the content knowledge and socially-derivable knowledge. The latter is described as knowledge that is earned through social interaction. Intelligent Conversational Channel is the system that supports the building and sharing on this type of knowledge.

Expert system for the assessment of power transformer insulation condition based on type-2 fuzzy logic systems

An efficient expert system for the power transformer condition assessment is presented in this paper. Through the application of Duval`s triangle and the method of the gas ratios a first assessment of the transformer condition is obtained in the form of a dissolved gas analysis (DGA) diagnosis according IEC 60599. As a second step, a knowledge mining procedure is performed, by conducting surveys whose results are fed into a first Type-2 Fuzzy Logic System (T2-FLS), in order to initially evaluate the condition of the equipment taking only the results of dissolved gas analysis into account. The output of this first T2-FLS is used as the input of a second T2-FLS, which additionally weighs up the condition of the paper-oil system. The output of this last T2-FLS is given in terms of words easily understandable by the maintenance personnel. The proposed assessing methodology has been validated for several cases of transformers in service. (C) 2010 Elsevier Ltd. All rights reserved.

Protein fold recognition score functions: Unusual construction strategies

We describe two ways of optimizing score functions for protein sequence to structure threading. The first method adjusts parameters to improve sequence to structure alignment. The second adjusts parameters so as to improve a score function's ability to rank alignments calculated in the first score function. Unlike those functions known as knowledge-based force fields, the resulting parameter sets do not rely on Boltzmann statistics, have no claim to representing free energies and are purely constructions for recognizing protein folds. The methods give a small improvement, but suggest that functions can be profitably optimized for very specific aspects of protein fold recognition, Proteins 1999;36:454-461. (C) 1999 Wiley-Liss, Inc.

Phenomenological turbulence and innovation in knowledge systems

Most considerations of knowledge management focus on corporations and, until recently, considered knowledge to be objective, stable, and asocial. In this paper we wish to move the focus away from corporations, and examine knowledge and national innovation systems. We argue that the knowledge systems in which innovation takes place are phenomenologically turbulent, a state not made explicit in the change, innovation and socio-economic studies of knowledge literature, and that this omission poses a serious limitation to the successful analysis of innovation and knowledge systems. To address this lack we suggest that three evolutionary processes must be considered: self-referencing, self-transformation and self-organisation. These processes, acting simultaneously, enable system cohesion, radical innovation and adaptation. More specifically, we argue that in knowledge-based economies the high levels of phenomenological turbulence drives these processes. Finally, we spell out important policy principles that derive from these processes.

The European challenge of KMN and innovation: a skills and competence portfolio for knowledge worker in SME's

Versão editor: http://www.isegi.unl.pt/docentes/acorreia/documentos/European_Challenge_KM_Innovation_2004.pdf

TINSEL – a web-based intelligent tutoring system on electrical installation design

This paper presents a project consisting on the development of an Intelligent Tutoring System, for training and support concerning the development of electrical installation projects to be used by electrical engineers, technicians and students. One of the major goals of this project is to devise a teaching model based on Intelligent Tutoring techniques, considering not only academic knowledge but also other types of more empirical knowledge, able to achieve successfully the training of electrical installation design.