Classification and comparison of ligand-binding sites derived from grid-mapped knowledge-based potentials

We describe the application of knowledge-based potentials implemented in the MOE program to compare the ligand-binding sites of several proteins. The binding probabilities for a polar and a hydrophobic probe are calculated on a grid to allow easy comparison of binding sites of superimposed related proteins. The method is fast and simple enough to simultaneously use structural information of multiple proteins of a target family. The method can be used to rapidly cluster proteins into subfamilies according to the similarity of hydrophobic and polar fields of their ligand-binding sites. Regions of the binding site which are common within a protein family can be identified and analysed for the design of family-targeted libraries or those which differ for improvement of ligand selectivity. The field-based hierarchical clustering is demonstrated for three protein families: the ligand-binding domains of nuclear receptors, the ATP-binding sites of protein kinases and the substrate binding sites of proteases. More detailed comparisons are presented for serine proteases of the chymotrypsin family, for the peroxisome proliferator-activated receptor subfamily of nuclear receptors and for progesterone and androgen receptor. The results are in good accordance with structure-based analysis and highlight important differences of the binding sites, which have been also described in the literature.     

From the field to the web: implementing best-practice recommendations in documentary linguistics

New methods of documenting languages with digital technologies has led to a multitude of different formats that are difficult to reuse over time. To overcome the problems surrounding the portability of digital language documentation, linguists are in the process of formulating best-practice recommendations to increase the likelihood of their work's long-term survival. This paper describes the implementation of a comprehensive set of current best-practice recommendations pertaining to content, format, discovery, access, citation, preservation, and rights in the context of the language documentation efforts of the Texas German Dialect Project. This project is different from others in that it is not primarily concerned with digitizing and archiving existing recordings. Instead, the archive it is creating is the end-result of a research project whose workflow begins with data-collection in the filed and ends with depositing digitized and annotated language materials in a web-accessible digital archive of Texas German. This paper shows how a number of conflicting best-practice recommendations can be resolved, thereby satisfying the diverse needs of academic research, teaching, and outreach to the community. As such, the results reported here are an important contribution to the search for strategies guaranteeing the long-term survival of digital language documentation resources.

Coordination components for collaborative virtual environments

This paper deals with the behavior of virtual environments from the collaboration point-of-view, in which actors (human or virtual beings) interact and collaborate by means of interdependent tasks. In this sense, actors may realize tasks that are dependent on tasks performed by other actors, while the interdependencies between tasks (through resource management and temporal relations) delineate the overall behavior of a virtual environment. Our main goal is to propose an approach for the coordination of those behaviors. Initially a generic study of possible interdependencies between collaborative tasks is presented, followed by the formal modeling (using Petri Nets) of coordination mechanisms for those dependencies. In order to implement such mechanisms, an architecture of reusable and pluggable coordination components is also introduced. These components are used in an implementation of a multi-user videogame. The presented approach is a concrete step to create virtual societies of actors that collaborate to reach common goals without the risk of getting involved in conflicting or repetitive tasks.     

Critical success factors revisited: success and failure cases of information systems for senior executives

The literature suggests the existence of critical success factors (CSFs) for the development of information systems that support senior executives. Our study of six organizations gives evidence for this notion of CSFs. The study further shows an interesting pattern, namely that companies either “get it right”, and essentially succeed on all CSFs, or “get it completely wrong”, that is, fall short on each of the CSFs. Among the six cases for which data were collected through in-depth interviews with company executives, three organizations seemed to manage all the CSFs properly, while two others managed all CSFs poorly. Only one organization showed a mixed scorecard, managing some factors well and some not so well. At the completion of the study, this organization could neither be judged as a success, nor as a failure. This dichotomy between success and failure cases suggests the existence of an even smaller set of “meta-success” factors. Based on our findings, we speculate that these “meta-success” factors are “championship”, “availability of resources”, and “link to organization objectives”.     

Will virtual education initiatives succeed?

The use of information technology to enhance teaching and learning processes has been practiced for a number of years now. However, the rapid growth in the use of the Internet has led to a new dimension in interactive and collaborative learning anytime and anyplace dynamically. With the explosion of “virtual education initiatives”, the question of the feasibility and success criteria for such projects quickly arises. To address the question in an organized way, we propose a project assessment based on critical success factors. Hence, in this article, we draw on a widely recognized critical success factor framework. We (slightly) adjust the framework to fit the special characteristics of virtual education initiatives, and apply to one case study, namely the virtual education initiative at the Faculty of Business at the City University of Hong Kong. The results suggest that the past success of the case is due to the adherence to the large majority of critical success factors. However, it also outlines some areas of concern. The paper concludes with a discussion on the strength and limitations of virtual learning environment as well as future directions. This revised version was published online in July 2006 with corrections to the Cover Date.     

Service level management with agent technology

This paper outlines a generic evaluation methodology for multimedia and real time applications. It concentrates on the application layer and the service aspect. Principles of software evaluation for quality assessment and measurement for networked services and distributed applications are used to present a specific method for measuring important characteristics. The method and the measurement procedure allow comparison of the actual characteristics of service quality with the required characteristics and thresholds. The proof of concepts will be made by the implementation of quality measurement agents following the approach outlined in this paper. Our approach of performing service level management (SLM) with agent technology is distributed, slim, minimizable to the maximum, independent in its methodology and offers comparable, objective results.     

A multi-start iterated local search with tabu list and path relinking for the two-echelon location-routing problem

The two-echelon location-routing problem (LRP-2E) is raised by the design of transportation networks with two types of trips: first-level trips serving from one main depot a set of satellite depots, to be located, and second-level trips supplying customers from these satellites. In the proposed multi-start iterated local search (MS-ILS), three greedy randomized heuristics are used cyclically to get initial solutions. Each ILS run alternates between two search spaces: LRP-2E solutions, and travelling salesman (TSP) tours covering the main depot and the customers. The number of iterations allotted to a run is reduced whenever a known solution (stored in a tabu list) is revisited. MS-ILS can be reinforced by a path-relinking procedure (PR), used internally for intensification, as post-optimization, or both. On two sets with 24 and 30 LRP-2E instances, MS-ILS outperforms on average two GRASP algorithms and adding PR brings a further improvement. Our metaheuristic also surpasses a tabu search on 30 instances for a more general problem with several main depots. It is still effective on a particular case, the capacitated location-routing problem (CLRP): In a comparison with four published metaheuristics, only one (LRGTS, Prins et al., 2007) does better.     

New method for selectivity enhancement of SiC field effect gas sensors for quantification of NO x

A silicon carbide based enhancement type metal insulator field effect transistor with porous gate metallization has been investigated as a total NO _x sensor operated in a temperature cycling mode. This operating mode is quite new for gas sensors based on the field effect but promising results have been reported earlier. Based on static investigations we have developed a suitable T-cycle optimized for NO _x detection and quantification in a mixture of typical exhaust gases (CO, C₂H₄, and NH₃). Significant features describing the shape of the sensor response have been extracted and evaluated with multivariate statistics (e.g. linear discriminant analysis) allowing quantification of NO _x . Additional cleaning-cycles every 30?min improve the stability of the sensor further. With this kind of advanced signal processing the influence of sensor drift and cross sensitivity to ambient gases can be reduced effectively. Measurements have proven that different concentrations of NO _x can be detected even in a changing mixture of other typical exhaust gases under dry and humid conditions. In addition to that, unknown concentrations of NO _x can be detected based on a small set of training data. It can be concluded that the performance of GasFETs for NO _x determination can be enhanced considerably with temperature cycling and appropriate signal processing.     

Local search methods for efficient router nodes placement in wireless mesh networks

Wireless Mesh Networks (WMNs) are an important networking infrastructure for providing cost-efficient broadband wireless connectivity to a group of users. WMNs are increasingly being used in urban, metropolitan and municipal area networks for deployment of medical, transport, surveillance systems, etc. The performance and operability of WMNs largely depends on placement of mesh routers nodes in the geographical area to achieve network connectivity and stability. The objective is to find an optimal and robust topology of the mesh router network to support intelligent telecommunication services to clients such as adaptive and flexible wireless Internet access, mobile data, voice, video in addition to supporting other preferred client services. In this work, we propose and evaluate local search methods for intelligent placement of mesh routers in WMNs with a two fold objective: maximizing the size of the giant component in the network and user coverage. Given a grid area where to distribute a given number of mesh router nodes, which can have different radio coverage, and a number of fixed clients a priori distributed in the given area, local search methods explore different local movements and incrementally improve the quality of the router nodes placement in terms of network connectivity and user coverage. We have experimentally evaluated the proposed local search methods through a benchmark of generated instances of varying sizes. Moreover, different distributions of mesh clients (Uniform, Normal, Exponential and Weibull) are used. The experimental evaluation showed the good performance of local search methods for optimizing network connectivity and user coverage in WMNs.