Detecting and correcting errors in ruled-based expert systems : an integration of empirical and explanation-based learning

In this paper, we argue that techniques proposed for combining empirical and explanation-based learning methods can also be used to detect errors in rule-based expert systems, to isolate the blame for these errors to a small number of rules and suggest revisions to the rules to eliminate these errors. We demonstrate that FOCL, an extension to Quinlan's FOIL program, can learn in spite of an incorrect domain theory (e.g., a knowledge base of an expert system that contains some erroneous rules). A prototype knowledge acquisition tool, KR-FOCL, has been constructed that can utilize a trace of FOCL to suggest revisions to a rule base

An information-based approach to integrating empirical and explanation-based learning

We describe a new approach to integrating explanation-based and empirical learning methods for learning relational concepts. The approach uses an information-based heuristic to evaluate components of a hypothesis that are proposed either by explanation-based or empirical methods. Providing domain knowledge to the integrated system can decrease the amount of search required during learning and increase the accuracy of learned concepts, even when the domain knowledge is incorrect and incomplete and there is noise in the training data

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Cell-Free Rolling Mediated by L-Selectin and Sialyl Lewis\u3csup\u3ex\u3c/sup\u3e Reveals the Shear Threshold Effect

The selectin family of adhesion molecules mediates attachment and rolling of neutrophils to stimulated endothelial cells. This step of the inflammatory response is a prerequisite to firm attachment and extravasation. We have reported that microspheres coated with sialyl Lewisx (sLex) interact specifically and roll over E-selectin and P-selectin substrates (Brunk et al., 1996; Rodgers et al., 2000). This paper extends the use of the cell-free system to the study of the interactions between L-selectin and sLex under flow. We find that sLex microspheres specifically interact with and roll on L-selectin substrates. Rolling velocity increases with wall shear stress and decreases with increasing L-selectin density. Rolling velocities are fast, between 25 and 225 μm/s, typical of L-selectin interactions. The variability of rolling velocity, quantified by the variance in rolling velocity, scales linearly with rolling velocity. Rolling flux varies with both wall shear stress and L-selectin site density. At a density of L-selectin of 800 sites/μm2, the rolling flux of sLex coated microspheres goes through a clear maximum with respect to shear stress at 0.7 dyne/cm2. This behavior, in which the maintenance and promotion of rolling interactions on selectins requires shear stress above a threshold value, is known as the shear threshold effect. We found that the magnitude of the effect is greatest at an L-selectin density of 800 sites/μm2 and gradually diminishes with increasing L-selectin site density. Our study is the first to reveal the shear threshold effect with a cell free system and the first to show the dependence of the shear threshold effect on L-selectin site density in a reconstituted system. Our ability to recreate the shear threshold effect in a cell-free system strongly suggests the origin of the effect is in the physical chemistry of L-selectin interaction with its ligand, and largely eliminates cellular features such as deformability or topography as its cause

A large-scale proteogenomics study of apicomplexan pathogens-Toxoplasma gondii and Neospora caninum

Proteomics data can supplement genome annotation efforts, for example being used to confirm gene models or correct gene annotation errors. Here, we present a large‐scale proteogenomics study of two important apicomplexan pathogens: Toxoplasma gondii and Neospora caninum. We queried proteomics data against a panel of official and alternate gene models generated directly from RNASeq data, using several newly generated and some previously published MS datasets for this meta‐analysis. We identified a total of 201 996 and 39 953 peptide‐spectrum matches for T. gondii and N. caninum, respectively, at a 1% peptide FDR threshold. This equated to the identification of 30 494 distinct peptide sequences and 2921 proteins (matches to official gene models) for T. gondii, and 8911 peptides/1273 proteins for N. caninum following stringent protein‐level thresholding. We have also identified 289 and 140 loci for T. gondii and N. caninum, respectively, which mapped to RNA‐Seq‐derived gene models used in our analysis and apparently absent from the official annotation (release 10 from EuPathDB) of these species. We present several examples in our study where the RNA‐Seq evidence can help in correction of the current gene model and can help in discovery of potential new genes

The Long Shadow of Senescence: Age Impacts Survival and Territory Defense in Loons

Senescence, increased mortality that occurs among animals of advanced age, impacts behavior and ecology in many avian species. We investigated actuarial, reproductive, and behavioral senescence using capture, marking, and resighting data from a 26-year study of common loons (Gavia immer). Territorial residents of both sexes exhibited high annual survival (0.94) until their mid 20s, at which point survival fell to 0.76 and 0.77 in males and females, respectively. Sexual symmetry in actuarial senescence is somewhat surprising in this species, because males make a substantially greater investment in territory defense and chick-rearing and because males engage in lethal contests for territory ownership. Survival of displaced breeders (0.80) was lower than that of territorial residents in both young and old individuals. Old males and females also experienced slightly higher annual probability of eviction (0.16 for males; 0.17 for females) than prime-aged breeders (0.13 for both sexes), indicating senescence in territory defense. Prime-aged males reclaimed territories at a high rate (0.49), in contrast to females of the same age (0.33). However, old males resettled with success (0.35) similar to old females (0.31), suggesting that males decline in competitive ability as they age. Nonetheless males, but not females, showed an apparent increase in breeding success over the entire lifetime, a possible indication that very old males make a terminal investment in reproductive output at the cost of survival

Patterns of richness across forest beetle communities—A methodological comparison of observed and estimated species numbers

Abstract Species richness is a frequently used measure of biodiversity. The compilation of a complete species list is an often unattainable goal. Estimators of species richness have been developed to overcome this problem. While the use of these estimators is becoming increasingly popular, working with the observed number of species is still common practice. To assess whether patterns of beetle communities based on observed numbers may be compared among each other, we compared patterns from observed and estimated numbers of species for beetle communities in the canopy of the Leipzig floodplain forest. These patterns were species richness and the number of shared species among three tree species and two canopy strata. We tested the applicability of the asymptotic Chao1 estimator and the estimate provided by the nonasymptotic rarefaction–extrapolation method for all tree species and both upper canopy and lower canopy. In the majority of cases, the ranking patterns of species richness for host tree species and strata were the same for the observed and estimated number of species. The ranking patterns of the number of species shared among host tree species and strata, however, were significantly different between observed and estimated values. Our results indicate that the observed number of species under‐represents species richness and the number of shared species. However, ranking comparisons of published patterns based on the number of observed species may be acceptable for species richness but likely not reliable for the number of shared species. Further studies are needed to corroborate this conclusion. We encourage to use estimators and to provide open access to data to allow comparative assessments