Functional recycling of C2 domains throughout evolution: A comparative study of synaptotagmin, protein kinase C and phospholipase C by sequence, structural and modelling approaches

The C2 domain is one of the most frequent and widely distributed calcium-binding motifs. Its structure comprises an eight-stranded beta-sandwich with two structural types as if the result of a circular permutation. Combining sequence, structural and modelling information, we have explored, at different levels of granularity, the functional characteristics of several families of C2 domains. At the coarsest level,the similarity correlates with key structural determinants of the C2 domain fold and, at the finest level, with the domain architecture of the proteins containing them, highlighting the functional diversity between the various subfamilies. The functional diversity appears as different conserved surface patches throughout this common fold. In some cases, these patches are related to substrate-binding sites whereas in others they correspond to interfaces of presumably permanent interaction between other domains within the same polypeptide chain. For those related to substrate-binding sites, the predictions overlap with biochemical data in addition to providing some novel observations. For those acting as protein-protein interfaces' our modelling analysis suggests that slight variations between families are a result of not only complementary adaptations in the interfaces involved but also different domain architecture. In the light of the sequence and structural genomic projects, the work presented here shows that modelling approaches along with careful sub-typing of protein families will be a powerful combination for a broader coverage in proteomics. (C) 2003 Elsevier Ltd. All rights reserved.

On systems thinking, systems biology and the in Silico Plant

The recent summary report of a Department of Energy Workshop on Plant Systems Biology (P.V. Minorsky [2003] Plant Physiol 132: 404-409) offered a welcomed advocacy for systems analysis as essential in understanding plant development, growth, and production. The goal of the Workshop was to consider methods for relating the results of molecular research to real-world challenges in plant production for increased food supplies, alternative energy sources, and environmental improvement. The rather surprising feature of this report, however, was that the Workshop largely overlooked the rich history of plant systems analysis extending over nearly 40 years (Sinclair and Seligman, 1996) that has considered exactly those challenges targeted by the Workshop. Past systems research has explored and incorporated biochemical and physiological knowledge into plant simulation models from a number of perspectives. The research has resulted in considerable understanding and insight about how to simulate plant systems and the relative contribution of various factors in influencing plant production. These past activities have contributed directly to research focused on solving the problems of increasing biomass production and crop yields. These modeling approaches are also now providing an avenue to enhance integration of molecular genetic technologies in plant improvement (Hammer et al., 2002).

Regional patterns of agricultural land use and deforestation in Colombia

An expanding human population and associated demands for goods and services continues to exert an increasing pressure on ecological systems. Although the rate of expansion of agricultural lands has slowed since 1960, rapid deforestation still occurs in many tropical countries, including Colombia. However, the location and extent of deforestation and associated ecological impacts within tropical countries is often not well known. The primary aim of this study was to obtain an understanding of the spatial patterns of forest conversion for agricultural land uses in Colombia. We modeled native forest conversion in Colombia at regional and national-levels using logistic regression and classification trees. We investigated the impact of ignoring the regional variability of model parameters, and identified biophysical and socioeconomic factors that best explain the current spatial pattern and inter-regional variation in forest cover. We validated our predictions for the Amazon region using MODIS satellite imagery. The regional-level classification tree that accounted for regional heterogeneity had the greatest discrimination ability. Factors related to accessibility (distance to roads and towns) were related to the presence of forest cover, although this relationship varied regionally. In order to identify areas with a high risk of deforestation, we used predictions from the best model, refined by areas with rural population growth rates of > 2%. We ranked forest ecosystem types in terms of levels of threat of conversion. Our results provide useful inputs to planning for biodiversity conservation in Colombia, by identifying areas and ecosystem types that are vulnerable to deforestation. Several of the predicted deforestation hotspots coincide with areas that are outstanding in terms of biodiversity value.

Organisational learning - a critical systems thinking discipline

Original Paper European Journal of Information Systems (2001) 10, 135–146; doi:10.1057/palgrave.ejis.3000394 Organisational learning—a critical systems thinking discipline P Panagiotidis1,3 and J S Edwards2,4 1Deloitte and Touche, Athens, Greece 2Aston Business School, Aston University, Aston Triangle, Birmingham, B4 7ET, UK Correspondence: Dr J S Edwards, Aston Business School, Aston University, Aston Triangle, Birmingham, B4 7ET, UK. E-mail: j.s.edwards@aston.ac.uk 3Petros Panagiotidis is Manager responsible for the Process and Systems Integrity Services of Deloitte and Touche in Athens, Greece. He has a BSc in Business Administration and an MSc in Management Information Systems from Western International University, Phoenix, Arizona, USA; an MSc in Business Systems Analysis and Design from City University, London, UK; and a PhD degree from Aston University, Birmingham, UK. His doctorate was in Business Systems Analysis and Design. His principal interests now are in the ERP/DSS field, where he serves as project leader and project risk managment leader in the implementation of SAP and JD Edwards/Cognos in various major clients in the telecommunications and manufacturing sectors. In addition, he is responsible for the development and application of knowledge management systems and activity-based costing systems. 4John S Edwards is Senior Lecturer in Operational Research and Systems at Aston Business School, Birmingham, UK. He holds MA and PhD degrees (in mathematics and operational research respectively) from Cambridge University. His principal research interests are in knowledge management and decision support, especially methods and processes for system development. He has written more than 30 research papers on these topics, and two books, Building Knowledge-based Systems and Decision Making with Computers, both published by Pitman. Current research work includes the effect of scale of operations on knowledge management, interfacing expert systems with simulation models, process modelling in law and legal services, and a study of the use of artifical intelligence techniques in management accounting. Top of pageAbstract This paper deals with the application of critical systems thinking in the domain of organisational learning and knowledge management. Its viewpoint is that deep organisational learning only takes place when the business systems' stakeholders reflect on their actions and thus inquire about their purpose(s) in relation to the business system and the other stakeholders they perceive to exist. This is done by reflecting both on the sources of motivation and/or deception that are contained in their purpose, and also on the sources of collective motivation and/or deception that are contained in the business system's purpose. The development of an organisational information system that captures, manages and institutionalises meaningful information—a knowledge management system—cannot be separated from organisational learning practices, since it should be the result of these very practices. Although Senge's five disciplines provide a useful starting-point in looking at organisational learning, we argue for a critical systems approach, instead of an uncritical Systems Dynamics one that concentrates only on the organisational learning practices. We proceed to outline a methodology called Business Systems Purpose Analysis (BSPA) that offers a participatory structure for team and organisational learning, upon which the stakeholders can take legitimate action that is based on the force of the better argument. In addition, the organisational learning process in BSPA leads to the development of an intrinsically motivated information organisational system that allows for the institutionalisation of the learning process itself in the form of an organisational knowledge management system. This could be a specific application, or something as wide-ranging as an Enterprise Resource Planning (ERP) implementation. Examples of the use of BSPA in two ERP implementations are presented.

Higher-order co-occurrences for exploratory point pattern analysis and decision tree clustering on spatial data

Analyzing geographical patterns by collocating events, objects or their attributes has a long history in surveillance and monitoring, and is particularly applied in environmental contexts, such as ecology or epidemiology. The identification of patterns or structures at some scales can be addressed using spatial statistics, particularly marked point processes methodologies. Classification and regression trees are also related to this goal of finding "patterns" by deducing the hierarchy of influence of variables on a dependent outcome. Such variable selection methods have been applied to spatial data, but, often without explicitly acknowledging the spatial dependence. Many methods routinely used in exploratory point pattern analysis are2nd-order statistics, used in a univariate context, though there is also a wide literature on modelling methods for multivariate point pattern processes. This paper proposes an exploratory approach for multivariate spatial data using higher-order statistics built from co-occurrences of events or marks given by the point processes. A spatial entropy measure, derived from these multinomial distributions of co-occurrences at a given order, constitutes the basis of the proposed exploratory methods. © 2010 Elsevier Ltd.

Higher-order co-occurrences for exploratory point pattern analysis and decision tree clustering on spatial data

Analyzing geographical patterns by collocating events, objects or their attributes has a long history in surveillance and monitoring, and is particularly applied in environmental contexts, such as ecology or epidemiology. The identification of patterns or structures at some scales can be addressed using spatial statistics, particularly marked point processes methodologies. Classification and regression trees are also related to this goal of finding "patterns" by deducing the hierarchy of influence of variables on a dependent outcome. Such variable selection methods have been applied to spatial data, but, often without explicitly acknowledging the spatial dependence. Many methods routinely used in exploratory point pattern analysis are2nd-order statistics, used in a univariate context, though there is also a wide literature on modelling methods for multivariate point pattern processes. This paper proposes an exploratory approach for multivariate spatial data using higher-order statistics built from co-occurrences of events or marks given by the point processes. A spatial entropy measure, derived from these multinomial distributions of co-occurrences at a given order, constitutes the basis of the proposed exploratory methods. © 2010 Elsevier Ltd.

Computer integrated manufacturing (CIM) and the principle of business control

In response to the increasing international competitiveness, many manufacturing businesses are rethinking their management strategies and philosophies towards achieving a computer integrated environment. The explosive growth in Advanced Manufacturing Technology (AMI) has resulted in the formation of functional "Islands of Automation" such as Computer Aided Design (CAD), Computer Aided Manufacturing (CAM), Computer Aided Process Planning (CAPP) and Manufacturing Resources Planning (MRPII). This has resulted in an environment which has focussed areas of excellence and poor overall efficiency, co-ordination and control. The main role of Computer Integrated Manufacturing (CIM) is to integrate these islands of automation and develop a totally integrated and controlled environment. However, the various perceptions of CIM, although developing, remain focussed on a very narrow integration scope and have consequently resulted in mere linked islands of automation with little improvement in overall co-ordination and control. This thesis, that is the research described within, develops and examines a more holistic view of CIM, which is based on the integration of various business elements. One particular business element, namely control, has been shown to have a multi-facetted and underpinning relationship with the CIM philosophy. This relationship impacts various CIM system design aspects including the CIM business analysis and modelling technique, the specification of systems integration requirements, the CIM system architectural form and the degree of business redesign. The research findings show that fundamental changes to CIM system design are required; these are incorporated in a generic CIM design methodology. The affect and influence of this holistic view of CIM on a manufacturing business has been evaluated through various industrial case study applications. Based on the evidence obtained, it has been concluded that this holistic, control based approach to CIM can provide a greatly improved means of achieving a totally integrated and controlled business environment. This generic CIM methodology will therefore make a significant contribution to the planning, modelling, design and development of future CIM systems.

Linking finite-element analysis and computer-aided drafting processes

The aim of this research was to investigate the integration of computer-aided drafting and finite-element analysis in a linked computer-aided design procedure and to develop the necessary software. The Be'zier surface patch for surface representation was used to bridge the gap between the rather separate fields of drafting and finite-element analysis because the surfaces are defined by analytical functions which allow systematic and controlled variation of the shape and provide continuous derivatives up to any required degree. The objectives of this research were achieved by establishing : (i) A package which interpretes the engineering drawings of plate and shell structures and prepares the Be'zier net necessary for surface representation. (ii) A general purpose stand-alone meshed-surface modelling package for surface representation of plates and shells using the Be'zier surface patch technique. (iii) A translator which adapts the geometric description of plate and shell structures as given by the meshed-surface modeller to the form needed by the finite-element analysis package. The translator was extended to suit fan impellers by taking advantage of their sectorial symmetry. The linking processes were carried out for simple test structures, simplified and actual fan impellers to verify the flexibility and usefulness of the linking technique adopted. Finite-element results for thin plate and shell structures showed excellent agreement with those obtained by other investigators while results for the simplified and actual fan impellers also showed good agreement with those obtained in an earlier investigation where finite-element analysis input data were manually prepared. Some extensions of this work have also been discussed.