NeMo: Network Module identification in Cytoscape

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NeMo: Network Module identification in Cytoscape

Abstract Background As the size of the known human interactome grows, biologists increasingly rely on computational tools to identify patterns that represent protein complexes and pathways. Previous studies have shown that densely connected network components frequently correspond to community structure and functionally related modules. In this work, we present a novel method to identify densely connected and bipartite network modules based on a log odds score for shared neighbours. Results To evaluate the performance of our method (NeMo), we compare it to other widely used tools for community detection including kMetis, MCODE, and spectral clustering. We test these methods on a collection of synthetically constructed networks and the set of MIPS human complexes. We apply our method to the CXC chemokine pathway and find a high scoring functional module of 12 disconnected phospholipase isoforms. Conclusion We present a novel method that combines a unique neighbour-sharing score with hierarchical agglomerative clustering to identify diverse network communities. The approach is unique in that we identify both dense network and dense bipartite network structures in a single approach. Our results suggest that the performance of NeMo is better than or competitive with leading approaches on both real and synthetic datasets. We minimize model complexity and generalization error in the Bayesian spirit by integrating out nuisance parameters. An implementation of our method is freely available for download as a plugin to Cytoscape through our website and through Cytoscape itself.</p

Direct comparisons of commercial weight-loss programs on weight, waist circumference, and blood pressure: a systematic review

Abstract Background Obesity is common in the U.S. and many individuals turn to commercial programs to lose weight. Our objective was to directly compare weight loss, waist circumference, and systolic and diastolic blood pressure (SBP, DBP) outcomes between commercially available weight-loss programs. Methods We conducted a systematic review by searching MEDLINE and the Cochrane Database of Systematic Reviews from inception to November 2014 and by using references identified by commercial programs. We included randomized, controlled trials (RCTs) of at least 12 weeks duration that reported comparisons with other commercial weight-loss programs. Two reviewers extracted information on mean change in weight, waist circumference, SBP and DBP and assessed risk of bias. Results We included seven articles representing three RCTs. Curves participants lost 1.8 kg (95%CI: 0.1, 3.5 kg) more than Weight Watchers in one comparison. There was no statistically significant difference in waist circumference change among the included programs. The mean reduction in SBP for SlimFast participants was 4.5 mmHg (95%CI: 0.4, 8.6 mmHg) more than that of Atkins participants in one comparison. There was no significant difference in mean DBP changes among programs. Conclusions There is limited evidence that any one of the commercial weight-loss programs has superior results for mean weight change, mean waist circumference change, or mean blood pressure change

Additional file 1: of Direct comparisons of commercial weight-loss programs on weight, waist circumference, and blood pressure: a systematic review

Table S1. PRISMA Checklist. Table S2. Electronic Search Strategy. Table S3. Study Eligibility Criteria. Figure S1. Summary of evidence search and selection. *Other exclusions included trials with ineligible study designs (retrospective case series, RCT < 12 weeks duration, etc.) or ineligible programs (not available in the US, etc.). **Ineligible commercial programs include those that use medications or supplements, modified specifically for the study, unavailable in the U.S., or available only to special populations like active duty military or veteran. Abbreviations: CDSR – Cochrane Database of Systematic Reviews; RCT – randomized controlled trial. (DOC 1403 kb