MoSuMo: A Semantic Web service to generate electrostatic potentials across solvent excluded protein surfaces and binding pockets

Investigations of molecular interactions can benefit from knowledge of the regions that correspond to binding sites and electrostatic potentials across molecular surfaces. In support of simulations aimed at a coarser level of granularity than molecular dynamics, we have developed MoSuMo, a SADI-based Semantic Web service for generating molecular surfaces from a set of 3D atomic coordinates. MoSuMo's service input requires a Protein Data Bank (PDB) identifier from which it obtains the PDB entry and for which it generates electrostatic potentials as vertex values across a geometric mesh that represents the molecular surface. Service inputs and outputs are specified as restrictions on classes from the Semanticscience Integrated Ontology (SIO), which is formalized using the Web Ontology Language (OWL). Binding sites containing their ligands are identified and described as sub-collections of surface vertices. Thus, MoSuMo provides a semantic web service for investigating molecular interactions including visualization.     

Robust skeletonization using the discrete λ-medial axis

Medial axes and skeletons are notoriously sensitive to contour irregularities. This lack of stability is a serious problem for applications in e.g. shape analysis and recognition. In 2005, Chazal and Lieutier introduced the λ-medial axis as a new concept for computing the medial axis of a shape subject to single parameter filtering. The λ-medial axis is stable under small shape perturbations, as proved by these authors. In this article, a discrete λ-medial axis (DLMA) is introduced and compared with the recently introduced integer medial axis (GIMA). We show that DLMA provides measurably better results than GIMA, with regard to stability and sensibility to rotations. We give efficient algorithms to compute the DLMA, and we also introduce a variant of the DLMA which may be computed in linear-time.     

A linear translation from CTL* to the first-order modal μ -calculus

The modal μ-calculus is a very expressive temporal logic. In particular, logics such as LTL, CTL and CTL* can be translated into the modal μ-calculus, although existing translations of LTL and CTL* are at least exponential in size. We show that an existing simple first-order extension of the modal μ-calculus allows for a linear translation from LTL. Furthermore, we show that solving the translated formulae is as efficient as the best known methods to solve LTL formulae directly.     

Network State Estimation and Prediction for Real-Time Traffic Management

Advanced Traveler Information Systems (ATIS) and Advanced Traffic Management Systems (ATMS) have the potential to contribute to the solution of the traffic congestion problem. DynaMIT is a real-time system that can be used to generate guidance for travelers. The main principle on which DynaMIT is based is that information should be consistent, and user optimal. Consistency implies that the traffic conditions experienced by the travelers are consistent with the condition assumed in generating the guidance. To generate consistent user optimal information, DynaMIT performs two main functions: state estimation and prediction. A demand simulator and a supply simulator interact to perform these tasks. A case study demonstrates the value of the system.     

The role of algorithm and result comprehensibility of automated scheduling on complacency

Several studies have stressed that even expert operators who are aware of a machine's limits could adopt its proposals without questioning them (i.e., the complacency phenomenon). In production scheduling for manufacturing, this is a significant problem, as it is often suggested that the machine be allowed to build the production schedule, confining the human role to that of rescheduling. This article evaluates the characteristics of scheduling algorithms on human rescheduling performance, the quality of which was related to complacency. It is suggested that scheduling algorithms be characterized as having result comprehensibility (the result respects the scheduler's expectations in terms of the discourse rules of the information display) or algorithm comprehensibility (the complexity of the algorithm hides some important constraints). The findings stress, on the one hand, that result comprehensibility is necessary to achieve good production performance and to limit complacency. On the other hand, algorithm comprehensibility leads to poor performance due to the very high cost of understanding the algorithm. © 2008 Wiley Periodicals, Inc.     

A multi-level, multi-theory perspective of information technology implementation

Abstract.  Much of information technology (IT) implementation research has focused on individuals' acceptance of IT by examining their behaviour when faced with new IT and the antecedents of these behaviours. As they are frequently undertaken within a project framework, IT implementations also entail the application of project management practices in order to be successful. Based on the premise that antecedents of lower level theories are frequently determined by the outcomes of a higher level theory, the present paper illustrates how organizational-level decisions, examined from the perspective of economics theories, can help explain the antecedents of project risk management at the project and individual levels. To do so, the paper describes an IT implementation effort which went through three phases; the first two of which were abandoned versions of the same project. An organizational-level analysis of the case from an economics perspective and its project-level analysis from a risk management perspective show how organizational-level decisions influenced the antecedents at the project and individual levels, providing a more complete understanding of the IT implementation in question, an understanding which neither a theory approach nor a level perspective could provide on its own.     

Occupational health problems and injuries among Quebec's physical educators

The purpose of this study was to describe the traumatology of teaching physical education (PE) and to document the causes and mechanisms of injuries in this occupation. Our sample was composed of 314 physical educators (PEs) teaching at three school levels (primary school, secondary school and college) who responded to a questionnaire survey. The results showed a 0.55 rate of recent lesion per teacher per year (0.65 for women and 0.51 for men). A total of 37.6% of subjects were affected by a lesion during the last year at work. Subjects with a higher weekly frequency of leisure physical activities or endurance activities (five times and more) were less affected by chronic lesions as well as those who frequently practiced aerobic physical activities. Prevalence of chronic injuries was higher in older teachers. Our results confirm that the rate of lesions in this group of workers is high, and that school level and respondent age may influence the rate of lesion and the characteristics of risk factors. In particular, the effect of ageing and teaching specialization on the incidence of occupational problems in PEs warrants further research. Given the relatively high rate of injuries among PE teachers, we suggest that it is necessary to further explore preventive strategies to reduce occupational risk in these workers. In particular, prophylactic physical activity outside of work may represent such a strategy since PEs more active outside their work have lower chronic injury prevalence. PEs gave long periods of standing the highest rating for movements or positions most likely to cause them occupational injuries. It can thus be suggested to find ways to reduce standing position sustained for long periods.     

Property Testing of Regular Tree Languages

We consider the edit distance with moves on the class of words and the class of ordered trees. We first exhibit a simple tester for the class of regular languages on words and generalize it to the class of ranked and unranked regular trees. We also show that this distance problem is -complete on ordered trees. A preliminary version of this paper appeared in Proceedings of 31st International Colloquium on Automata, Languages and Programming, volume 3142 of Lecture Notes in Computer Science, pages 932–944, Springer, 2005. Work supported by ACI Sécurité Informatique: VERA of the French Ministry of research.     

Extension of the decidability of the marked PCP to instances with unique blocks

In the Post Correspondence Problem (PCP) an instance (h,g)$(h,g)$ consists of two morphisms h$h$ and g$g$, and the problem is to determine whether or not there exists a nonempty word w$w$ such that h(w)=g(w)$h\left(w\right)=g\left(w\right)$. Here we prove that the PCP is decidable for instances with unique blocks using the decidability of the marked PCP. Also, we show that it is decidable whether an instance satisfying the uniqueness condition for continuations has an infinite solution. These results establish a new and larger class of decidable instances of the PCP, including the class of marked instances.