An automated approach to network features of protein structure ensembles

Network theory applied to protein structures provides insights into numerous problems of biological relevance. The explosion in structural data available from PDB and simulations establishes a need to introduce a standalone-efficient program that assembles network concepts/parameters under one hood in an automated manner. Herein, we discuss the development/application of an exhaustive, user-friendly, standalone program package named PSN-Ensemble, which can handle structural ensembles generated through molecular dynamics (MD) simulation/NMR studies or from multiple X-ray structures. The novelty in network construction lies in the explicit consideration of side-chain interactions among amino acids. The program evaluates network parameters dealing with topological organization and long-range allosteric communication. The introduction of a flexible weighing scheme in terms of residue pairwise cross-correlation/interaction energy in PSN-Ensemble brings in dynamical/chemical knowledge into the network representation. Also, the results are mapped on a graphical display of the structure, allowing an easy access of network analysis to a general biological community. The potential of PSN-Ensemble toward examining structural ensemble is exemplified using MD trajectories of an ubiquitin-conjugating enzyme (UbcH5b). Furthermore, insights derived from network parameters evaluated using PSN-Ensemble for single-static structures of active/inactive states of 2-adrenergic receptor and the ternary tRNA complexes of tyrosyl tRNA synthetases (from organisms across kingdoms) are discussed. PSN-Ensemble is freely available from http://vishgraph.mbu.iisc.ernet.in/PSN-Ensemble/psn_index.html.

A new adaptive marine policy toolbox to support ecosystem-based approach to management

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An approach to functional synthesis of solutions in mechanical conceptual design. Part III: Spatial configuration

These three papers describe an approach to the synthesis of solutions to a class of mechanical design problems; these involve transmission and transformation of mechanical forces and motion, and can be described by a set of inputs and outputs. The approach involves (1) identifying a set of primary functional elements and rules of combining them, and (2) developing appropriate representations and reasoning procedures for synthesising solution concepts using these elements and their combination rules; these synthesis procedures can produce an exhaustive set of solution concepts, in terms of their topological as well as spatial configurations, to a given design problem. This paper (Part III) describes a constraint propagation procedure which, using a knowledge base of spatial information about a set of primary functional elements, can produce possible spatial configurations of solution concepts generated in Part II.

A structured modelling approach to simulating dynamic behaviours in complex organisations

This article reports a case study application of a systematic approach to modelling complex organisations, centred on simulation modelling (SM). The approach leads to populated instances of complementary model types, in ways that systematically capture, validate and facilitate various uses of organisational understandings, knowledge and data normally distributed amongst multiple knowledge holders. The model-driven approach to decision making enables improved manufacturing responsiveness. Literature on modelling technologies relevant to manufacturing systems organisation design and change is presented, as is literature on production planning and control. This provides a rationale for the development of a new modelling methodology which combines the use of enterprise, causal loop and SM. Subsequently, this article describes how in the case of a specific manufacturing enterprise the combined modelling techniques have informed the choice of alternative production planning and control policies. An example enterprise model of a capacitor manufacturing company is illustrated as derivative causal-loop models that structure and enable the design and use of a general purpose simulation model.

Enhanced integrated modelling approach to reconfiguring manufacturing enterprises

Dynamism and uncertainty are real challenges for present day manufacturing enterprises (MEs). Reasons include: an increasing demand for customisation, reduced time to market, shortened product life cycles and globalisation. MEs can reduce competitive pressure by becoming reconfigurable and change-capable. However, modern manufacturing philosophies, including agile and lean, must complement the application of reconfigurable manufacturing paradigms. Choosing and applying the best philosophies and techniques is very difficult as most MEs deploy complex and unique configurations of processes and resource systems, and seek economies of scope and scale in respect of changing and distinctive product flows. It follows that systematic methods of achieving model driven reconfiguration and interoperation of component based manufacturing systems are required to design, engineer and change future MEs. This thesis, titled Enhanced Integrated Modelling Approach to Reconfiguring Manufacturing Enterprises , introduces the development and prototyping a model-driven environment for the design, engineering, optimisation and control of the reconfiguration of MEs with an embedded capability to handle various types of change. The thesis describes a novel systematic approach, namely enhanced integrated modelling approach (EIMA), in which coherent sets of integrated models are created that facilitates the engineering of MEs especially their production planning and control (PPC) systems. The developed environment supports the engineering of common types of strategic, tactical and operational processes found in many MEs. The EIMA is centred on the ISO standardised CIMOSA process modelling approach. Early study led to the development of simulation models during which various CIMOSA shortcomings were observed, especially in its support for aspects of ME dynamism. A need was raised to structure and create semantically enriched models hence forming an enhanced integrated modelling environment. The thesis also presents three industrial case examples: (1) Ford Motor Company; (2) Bradgate Furniture Manufacturing Company; and (3) ACM Bearings Company. In order to understand the system prior to realisation of any PPC strategy, multiple process segments of any target organisation need to be modelled. Coherent multi-perspective case study models are presented that have facilitated process reengineering and associated resource system configuration. Such models have a capability to enable PPC decision making processes in support of the reconfiguration of MEs. During these case studies, capabilities of a number of software tools were exploited such as Arena®, Simul8®, Plant Simulation®, MS Visio®, and MS Excel®. Case study results demonstrated effectiveness of the concepts related to the EIMA. The research has resulted in new contributions to knowledge in terms of new understandings, concepts and methods in following ways: (1) a structured model driven integrated approach to the design, optimisation and control of future reconfiguration of MEs. The EIMA is an enriched and generic process modelling approach with capability to represent both static and dynamic aspects of an ME; and (2) example application cases showing benefits in terms of reduction in lead time, cost and resource load and in terms of improved responsiveness of processes and resource systems with a special focus on PPC; (3) identification and industrial application of a new key performance indicator (KPI) known as P3C the measuring and monitoring of which can aid in enhancing reconfigurability and responsiveness of MEs; and (4) an enriched modelling concept framework (E-MUNE) to capture requirements of static and dynamic aspects of MEs where the conceptual framework has the capability to be extended and modified according to the requirements. The thesis outlines key areas outlining a need for future research into integrated modelling approaches, interoperation and updating mechanisms of partial models in support of the reconfiguration of MEs.

A New Approach to Media Cluster Research: Bringing the Human Factor back into Scope

This paper is part of a collaborative project being undertaken by the three leading universities of Brussels, VUB, ULB and USL-B supported by Innnoviris. The project called Media Clusters Brussels - MCB - started in October 2014 with the goal to analyze the development of a Media Park around the two public broadcasters at the site of Reyers in Brussels being host of a media cluster in the capital city. Not only policymakers but also many authors recognized in the last decade that the media industry is characterized from a geographical point of view by a heavy concentration to a limited number of large cities, where media clusters have emerged (Karlsson & Picard, 2011). The common assumption about media clusters is that locating inside a regional agglomeration of related actors brings advantages for these firms. Especially, the interrelations and interactions between the actors on a social level matter for the shape and efficiency of the agglomerations (Picard, 2008). However, even though the importance of the actors and their interrelations has been a common assumption, many authors solely focus on the macro-economical aspects of the clusters. Within this paper, we propose to realize a socio-economical analysis of media clusters to make informed decisions in the development and so, bring the social (human) factor back into scope. Therefore, this article focuses on the development of a novel valuable framework, the so-called 7P framework with a multilevel and interdisciplinary approach, which includes three aspects, which have been identified as emerging success-factors of media clusters: partnerships, (media) professionals and positive spillovers.

An Enactive Approach to the Design of New Tangible Musical Instruments

In this paper, we propose a theoretical framework for the design of tangible interfaces for musical expression. The main insight for the proposed approach is the importance and utility of familiar sensorimotor experiences for the creation of engaging and playable new musical instruments. In particular, we suggest exploiting the commonalities between different natural interactions by varying the auditory response or tactile details of the instrument within certain limits. Using this principle, devices for classes of sounds such as coarse grain collision interactions or friction interactions can be designed. The designs we propose retain the familiar tactile aspect of the interaction so that the performer can take advantage of tacit knowledge gained through experiences with such phenomena in the real world.

A novel approach to dynamic modelling of polymer extrusion for improved process control

Polymer extrusion is a complex process and the availability of good dynamic models is key for improved system operation. Previous modelling attempts have failed adequately to capture the non-linearities of the process or prove too complex for control applications. This work presents a novel approach to the problem by the modelling of extrusion viscosity and pressure, adopting a grey box modelling technique that combines mechanistic knowledge with empirical data using a genetic algorithm approach. The models are shown to outperform those of a much higher order generated by a conventional black box technique while providing insight into the underlying processes at work within the extruder.

A meta-heuristic approach to parallel code generation

The efficient generation of parallel code for multi-processor environments, is a large and complicated issue. Attempts to address this problem have always resulted in significant input from users. Because of constraints on user knowledge and time, the automation of the process is a promising and practically important research area. In recent years heuristic approaches have been used to capture available knowledge and make it available for the parallelisation process. Here, the introduction of a novel approach of neural network techniques is combined with an expert system technique to enhance the availability of knowledge to aid in the automatic generation of parallel code.

Reflective analysis of a mixed-methods approach to study the experiences of young people leaving care in Romania.

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An interprofessional approach to improving paediatric medication safety.

BACKGROUND: Safe drug prescribing and administration are essential elements within undergraduate healthcare curricula, but medication errors, especially in paediatric practice, continue to compromise patient safety. In this area of clinical care, collective responsibility, team working and communication between health professionals have been identified as key elements in safe clinical practice. To date, there is limited research evidence as to how best to deliver teaching and learning of these competencies to practitioners of the future.

METHODS: An interprofessional workshop to facilitate learning of knowledge, core competencies, communication and team working skills in paediatric drug prescribing and administration at undergraduate level was developed and evaluated. The practical, ward-based workshop was delivered to 4th year medical and 3rd year nursing students and evaluated using a pre and post workshop questionnaire with open-ended response questions.

RESULTS: Following the workshop, students reported an increase in their knowledge and awareness of paediatric medication safety and the causes of medication errors (p < 0.001), with the greatest increase noted among medical students. Highly significant changes in students' attitudes to shared learning were observed, indicating that safe medication practice is learnt more effectively with students from other healthcare disciplines. Qualitative data revealed that students' participation in the workshop improved communication and teamworking skills, and led to greater awareness of the role of other healthcare professionals.

CONCLUSION: This study has helped bridge the knowledge-skills gap, demonstrating how an interprofessional approach to drug prescribing and administration has the potential to improve quality and safety within healthcare.

Network biology: a direct approach to study biological function

In this paper we discuss the dualism of gene networks and their role in systems biology. We argue that gene networks ( 1) can serve as a conceptual framework, forming a fundamental level of a phenomenological description, and ( 2) are a means to represent and analyze data. The latter point does not only allow a systems analysis but is even amenable for a direct approach to study biological function. Here we focus on the clarity of our main arguments and conceptual meaning of gene networks, rather than the causal inference of gene networks from data. (C) 2010 John Wiley & Sons, Inc. WIREs Syst Biol Med 2011 3 379-391 DOI: 10.1002/wsbm.134