An experimental study of Quartets MaxCut and other supertree methods

<p>Abstract</p> <p>Background</p> <p>Supertree methods represent one of the major ways by which the Tree of Life can be estimated, but despite many recent algorithmic innovations, matrix representation with parsimony (MRP) remains the main algorithmic supertree method.</p> <p>Results</p> <p>We evaluated the performance of several supertree methods based upon the Quartets MaxCut (QMC) method of Snir and Rao and showed that two of these methods usually outperform MRP and five other supertree methods that we studied, under many realistic model conditions. However, the QMC-based methods have scalability issues that may limit their utility on large datasets. We also observed that taxon sampling impacted supertree accuracy, with poor results obtained when all of the source trees were only sparsely sampled. Finally, we showed that the popular optimality criterion of minimizing the total topological distance of the supertree to the source trees is only weakly correlated with supertree topological accuracy. Therefore evaluating supertree methods on biological datasets is problematic.</p> <p>Conclusions</p> <p>Our results show that supertree methods that improve upon MRP are possible, and that an effort should be made to produce scalable and robust implementations of the most accurate supertree methods. Also, because topological accuracy depends upon taxon sampling strategies, attempts to construct very large phylogenetic trees using supertree methods should consider the selection of source tree datasets, as well as supertree methods. Finally, since supertree topological error is only weakly correlated with the supertree's topological distance to its source trees, development and testing of supertree methods presents methodological challenges.</p

Successful prevention of the transmission of vancomycin-resistant enterococci in a Brazilian public teaching hospital

INTRODUCTION: Vancomycin-resistant enterococci (VRE) can colonize or cause infections in high-risk patients and contaminate the environment. Our objective was to describe theepidemiological investigation of an outbreak of VRE, the interventions made, and their impact on its control. METHODS: We conducted a retrospective, descriptive, non-comparative study by reviewing the charts of patients with a VRE-positive culture in the University Hospital of Campinas State University, comprising 380 beds, 40 of which were in intensive care units (ICUs), who were admitted from February 2008-January 2009. Interventions were divided into educational activity, reviewing the workflow processes, engineering measures, and administrative procedures. RESULTS: There were 150 patients, 139 (92.7%) colonized and 11 (7.3%) infected. Seventy-three percent were cared for in non-ICUs (p = 0.028). Infection was more frequent in patients with a central-line (p = 0.043), mechanical ventilation (p = 0.013), urinary catheter (p = 0.049), or surgical drain (p = 0.049). Vancomycin, metronidazole, ciprofloxacin, and third-generation cephalosporin were previously used by 47 (31.3%), 31 (20.7%), 24 (16%), and 24 (16%) patients, respectively. Death was more frequent in infected (73%) than in colonized (17%) patients (p < 0.001). After the interventions, the attack rate fell from 1.49 to 0.33 (p < 0.001). CONCLUSIONS: Classical risk factors for VRE colonization or infection, e.g., being cared for in an ICU and previous use of vancomycin, were not found in this study. The conjunction of an educational program, strict adhesion to contact precautions, and reinforcement of environmental cleaning were able to prevent the dissemination of VRE