Assignment methods for incidence calculus

Incidence calculus is a mechanism for probabilistic reasoning in which sets of possible worlds, called incidences, are associated with axioms, and probabilities are then associated with these sets. Inference rules are used to deduce bounds on the incidence of formulae which are not axioms, and bounds for the probability of such a formula can then be obtained. In practice an assignment of probabilities directly to axioms may be given, and it is then necessary to find an assignment of incidence which will reproduce these probabilities. We show that this task of assigning incidences can be viewed as a tree searching problem, and two techniques for performing this research are discussed. One of these is a new proposal involving a depth first search, while the other incorporates a random element. A Prolog implementation of these methods has been developed. The two approaches are compared for efficiency and the significance of their results are discussed. Finally we discuss a new proposal for applying techniques from linear programming to incidence calculus.

A comprehensive comparison between generalized incidence calculus and Dempster-Shafer theory of evidence.

Dealing with uncertainty problems in intelligent systems has attracted a lot of attention in the AI community. Quite a few techniques have been proposed. Among them, the Dempster-Shafer theory of evidence (DS theory) has been widely appreciated. In DS theory, Dempster's combination rule plays a major role. However, it has been pointed out that the application domains of the rule are rather limited and the application of the theory sometimes gives unexpected results. We have previously explored the problem with Dempster's combination rule and proposed an alternative combination mechanism in generalized incidence calculus. In this paper we give a comprehensive comparison between generalized incidence calculus and the Dempster-Shafer theory of evidence. We first prove that these two theories have the same ability in representing evidence and combining DS-independent evidence. We then show that the new approach can deal with some dependent situations while Dempster's combination rule cannot. Various examples in the paper show the ways of using generalized incidence calculus in expert systems.

Constructing probabilistic ATMS using extended incidence calculus

This paper discusses the relations between extended incidence calculus and assumption-based truth maintenance systems (ATMSs). We first prove that managing labels for statements (nodes) in an ATMS is equivalent to producing incidence sets of these statements in extended incidence calculus. We then demonstrate that the justification set for a node is functionally equivalent to the implication relation set for the same node in extended incidence calculus. As a consequence, extended incidence calculus can provide justifications for an ATMS, because implication relation sets are discovered by the system automatically. We also show that extended incidence calculus provides a theoretical basis for constructing a probabilistic ATMS by associating proper probability distributions on assumptions. In this way, we can not only produce labels for all nodes in the system, but also calculate the probability of any of such nodes in it. The nogood environments can also be obtained automatically. Therefore, extended incidence calculus and the ATMS are equivalent in carrying out inferences at both the symbolic level and the numerical level. This extends a result due to Laskey and Lehner.

Modelling the impact of antibiotic use and infection control practices on the incidence of hospital-acquired methicillin-resistant Staphylococcus aureus: a time-series analysis

Objectives: Methicillin-resistant Staphylococcus aureus (MRSA) is a major nosocomial pathogen worldwide. A wide range of factors have been suggested to influence the spread of MRSA. The objective of this study was to evaluate the effect of antimicrobial drug use and infection control practices on nosocomial MRSA incidence in a 426-bed general teaching hospital in Northern Ireland.

Methods: The present research involved the retrospective collection of monthly data on the usage of antibiotics and on infection control practices within the hospital over a 5 year period (January 2000–December 2004). A multivariate ARIMA (time-series analysis) model was built to relate MRSA incidence with antibiotic use and infection control practices.

Results: Analysis of the 5 year data set showed that temporal variations in MRSA incidence followed temporal variations in the use of fluoroquinolones, third-generation cephalosporins, macrolides and amoxicillin/clavulanic acid (coefficients = 0.005, 0.03, 0.002 and 0.003, respectively, with various time lags). Temporal relationships were also observed between MRSA incidence and infection control practices, i.e. the number of patients actively screened for MRSA (coefficient = -0.007), the use of alcohol-impregnated wipes (coefficient = -0.0003) and the bulk orders of alcohol-based handrub (coefficients = -0.04 and -0.08), with increased infection control activity being associated with decreased MRSA incidence, and between MRSA incidence and the number of new patients admitted with MRSA (coefficient = 0.22). The model explained 78.4% of the variance in the monthly incidence of MRSA.

Conclusions: The results of this study confirm the value of infection control policies as well as suggest the usefulness of restricting the use of certain antimicrobial classes to control MRSA.

High incidence of cryptic repeated elements in microsatellite flanking regions of galatheid genomes and its evolutionary implications

During the development of PCR primer sets for icrosatellite marker loci from enriched genomic libraries for three squat lobster species from Galatheidae (Decapoda: Anomura); Munida rugosa (Fabricius, 1775), M. sarsi (Huus, 1935), and Galathea strigosa (Linnaeus, 1761) (collectively known as squat lobsters), a number of unforeseen problems were encountered. These included PCR amplification failure, lack of amplification consistency, and the amplification of multiple fragments. Careful examination of microsatellite containing sequences revealed the existence of cryptic repeated elements on presumed unique flanking regions. BLAST analysis of these and other VNTR containing sequences (N 5 252) indicates that these cryptic elements can be grouped into families based upon sequence similarities. The unique features characterising these families suggest that different molecular mechanisms are involved. Of particular relevance is the association of microsatellites with mobile elements. This is the first reported observation of this phenomenon in crustaceans, and it also helps to explain why microsatellite primer development in galatheids has been relatively unsuccessful to date. We suggest a number of steps that can be used to identify similar problems in microsatellite marker development for other species, and also alternative approaches for both marker development and for the study of molecular evolution of species characterised by complex genome organisation. More specifically, we argue that new generation sequencing methodologies, which capitalise on parallel and multiplexed sequencing may pave the way forward for future crustacean research.