Locating previously unknown patterns in data-mining results: a dual data- and knowledge-mining method

BACKGROUND: Data mining can be utilized to automate analysis of substantial amounts of data produced in many organizations. However, data mining produces large numbers of rules and patterns, many of which are not useful. Existing methods for pruning uninteresting patterns have only begun to automate the knowledge acquisition step (which is required for subjective measures of interestingness), hence leaving a serious bottleneck. In this paper we propose a method for automatically acquiring knowledge to shorten the pattern list by locating the novel and interesting ones. METHODS: The dual-mining method is based on automatically comparing the strength of patterns mined from a database with the strength of equivalent patterns mined from a relevant knowledgebase. When these two estimates of pattern strength do not match, a high "surprise score" is assigned to the pattern, identifying the pattern as potentially interesting. The surprise score captures the degree of novelty or interestingness of the mined pattern. In addition, we show how to compute p values for each surprise score, thus filtering out noise and attaching statistical significance. RESULTS: We have implemented the dual-mining method using scripts written in Perl and R. We applied the method to a large patient database and a biomedical literature citation knowledgebase. The system estimated association scores for 50,000 patterns, composed of disease entities and lab results, by querying the database and the knowledgebase. It then computed the surprise scores by comparing the pairs of association scores. Finally, the system estimated statistical significance of the scores. CONCLUSION: The dual-mining method eliminates more than 90% of patterns with strong associations, thus identifying them as uninteresting. We found that the pruning of patterns using the surprise score matched the biomedical evidence in the 100 cases that were examined by hand. The method automates the acquisition of knowledge, thus reducing dependence on the knowledge elicited from human expert, which is usually a rate-limiting step

Herbal therapy associated with antibiotic therapy: potentiation of the antibiotic activity against methicillin – resistant Staphylococcus aureus by Turnera ulmifolia L

<p>Abstract</p> <p>Background</p> <p><it>Staphylococcus </it>genus is widely spread in nature being part of the indigenous microbiota of skin and mucosa of animal and birds. Some <it>Staphylococcus </it>species are frequently recognized as etiological agents of many animal and human opportunistic infections This is the first report testing the antibiotic resistance-modifying activity of <it>Turnera ulmifolia </it>against methicillin-resistant <it>Staphylococcus aureus </it>– MRSA strain.</p> <p>Methods</p> <p>In this study an ethanol extract of <it>Turnera ulmifolia </it>L. and chlorpromazine were tested for their antimicrobial activity alone or in combination with aminoglycosides against an MRSA strain.</p> <p>Results</p> <p>The synergism of the ethanol extract and aminoglycosides were verified using microdillution method. A synergistic effect of this extract on gentamicin and kanamycin was demonstrated. Similarly, a potentiating effect of chlorpromazine on kanamycin, gentamicin and neomycin, indicating the involvement of an efflux system in the resistance to these aminoglycosides.</p> <p>Conclusion</p> <p>It is therefore suggested that extracts from <it>Turnera ulmifolia </it>could be used as a source of plant-derived natural products with resistance-modifying activity, constituting a new weapon against the problem of bacterial resistance to antibiotics demonstrated in MRSA strains.</p

Comparison of proton channel, phagocyte oxidase, and respiratory burst levels between human eosinophil and neutrophil granulocytes.

Robust production of reactive oxygen species (ROS) by phagocyte NADPH oxidase (phox) during the respiratory burst (RB) is a characteristic feature of eosinophil and neutrophil granulocytes. In these cells the voltage-gated proton channel (Hv1) is now considered as an ancillary subunit of the phox needed for intense ROS production. Multiple sources reported that the expression of phox subunits and RB is more intensive in eosinophils than in neutrophils. In most of these studies the eosinophils were not isolated from healthy individuals, and a comparative analysis of Hv1 expression had never been carried out. We performed a systematic comparison of the levels of essential phox subunits, Hv1 expression and ROS producing capacity between eosinophils and neutrophils of healthy individuals. The expression of phox components was similar, whereas the amount of Hv1 was approximately 10-fold greater in eosinophils. Furthermore, Hv1 expression correlated with Nox2 expression only in eosinophils. Additionally, in confocal microscopy experiments co-accumulation of Hv1 and Nox2 at the cell periphery was observed in resting eosinophils but not in neutrophils. While phorbol-12-myristate-13-acetate-induced peak extracellular ROS release was approximately 1.7-fold greater in eosinophils, oxygen consumption studies indicated that the maximal intensity of the RB is only approximately 1.4-fold greater in eosinophils. Our data reinforce that eosinophils, unlike neutrophils, generate ROS predominantly extracellularly. In contrast to previous works we have found that the two granulocyte types display very similar phox subunit expression and RB capacity. The large difference in Hv1 expression suggests that its support to intense ROS production is more important at the cell surface

Long Distance Movements and Disjunct Spatial Use of Harbor Seals (Phoca vitulina) in the Inland Waters of the Pacific Northwest

BACKGROUND: Worldwide, adult harbor seals (Phoca vitulina) typically limit their movements and activity to <50 km from their primary haul-out site. As a result, the ecological impact of harbor seals is viewed as limited to relatively small spatial scales. Harbor seals in the Pacific Northwest are believed to remain <30 km from their primary haul-out site, one of several contributing factors to the current stock designation. However, movement patterns within the region are not well understood because previous studies have used radio-telemetry, which has range limitations. Our objective was to use satellite-telemetry to determine the regional spatial scale of movements. METHODOLOGY/PRINCIPAL FINDINGS: Satellite tags were deployed on 20 adult seals (n=16 males and 4 females) from two rocky reefs and a mudflat-bay during April-May 2007. Standard filtering algorithms were used to remove outliers, resulting in an average (± SD) of 693 (± 377) locations per seal over 110 (± 32) days. A particle filter was implemented to interpolate locations temporally and decrease erroneous locations on land. Minimum over-water distances were calculated between filtered locations and each seal's capture site to show movement of seals over time relative to their capture site, and we estimated utilization distributions from kernel density analysis to reflect spatial use. Eight males moved >100 km from their capture site at least once, two of which traveled round trip to and from the Pacific coast, a total distance >400 km. Disjunct spatial use patterns observed provide new insight into general harbor seal behavior. CONCLUSIONS/SIGNIFICANCE: Long-distance movements and disjunct spatial use of adult harbor seals have not been reported for the study region and are rare worldwide in such a large proportion of tagged individuals. Thus, the ecological influence of individual seals may reach farther than previously assumed

The use and limits of ITS data in the analysis of intraspecific variation in Passiflora L. (Passifloraceae)

The discovery and characterization of informative intraspecific genetic markers is fundamental for evolutionary and conservation genetics studies. Here, we used nuclear ribosomal ITS sequences to access intraspecific genetic diversity in 23 species of the genus Passiflora L. Some degree of variation was detected in 21 of these. The Passiflora and Decaloba (DC.) Rchb. subgenera showed significant differences in the sizes of the two ITS regions and in GC content, which can be related to reproductive characteristics of species in these subgenera. Furthermore, clear geographical patterns in the spatial distribution of sequence types were identified in six species. The results indicate that ITS may be a useful tool for the evaluation of intraspecific genetic variation in Passiflora