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Directed acyclic graph kernels for structural RNA analysis.

ABSTRACT: BACKGROUND: Recent discoveries of a large variety of important roles for non-coding RNAs (ncRNAs) have been reported by numerous researchers. In order to analyze ncRNAs by kernel methods including support vector machines, we propose stem kernels as an extension of string kernels for measuring the similarities between two RNA sequences from the viewpoint of secondary structures. However, applying stem kernels directly to large data sets of ncRNAs is impractical due to their computational complexity. RESULTS: We have developed a new technique based on directed acyclic graphs (DAGs) derived from base-pairing probability matrices of RNA sequences that significantly increases the computation speed of stem kernels. Furthermore, we propose profile-profile stem kernels for multiple alignments of RNA sequences which utilize base-pairing probability matrices for multiple alignments instead of those for individual sequences. Our kernels outperformed the existing methods with respect to the detection of known ncRNAs and kernel hierarchical clustering. CONCLUSION: Stem kernels can be utilized as a reliable similarity measure of structural RNAs, and can be used in various kernel-based applications.

SUBMITTER: Sato K

PROVIDER: S-EPMC2515856 | biostudies-literature | 2008

REPOSITORIES: biostudies-literature

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Directed acyclic graph kernels for structural RNA analysis.

Sato Kengo K Mituyama Toutai T Asai Kiyoshi K Sakakibara Yasubumi Y

BMC bioinformatics 20080722

<h4>Background</h4>Recent discoveries of a large variety of important roles for non-coding RNAs (ncRNAs) have been reported by numerous researchers. In order to analyze ncRNAs by kernel methods including support vector machines, we propose stem kernels as an extension of string kernels for measuring the similarities between two RNA sequences from the viewpoint of secondary structures. However, applying stem kernels directly to large data sets of ncRNAs is impractical due to their computational c ...[more]

PMID: 18647390

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Project description:BackgroundHigh tibial osteotomy (HTO) is increasingly used in young and physically active patients with knee osteoarthritis. These patients have high expectations, including return to sport (RTS). By retaining native knee structures, a return to highly knee-demanding activities seems possible. However, evidence on patient-related outcomes, including RTS, is sparse. Also, time to RTS has never been described. Furthermore, prognostic factors for RTS after HTO have never been investigated. These data may further justify HTO as a surgical alternative to knee arthroplasty.PurposeTo investigate the extent and timing of RTS after HTO in the largest cohort investigated for RTS to date and to identify prognostic factors for successful RTS.Study designCase-control study; Level of evidence, 3.MethodsConsecutive patients with HTO, operated on between 2012 and 2015, received a questionnaire. First, pre- and postoperative sports participation questions were asked. Also, time to RTS, sports level and frequency, impact level, the presymptomatic and postoperative Tegner activity score (1-10; higher is more active), and the postoperative Lysholm score (0-100; higher is better) were collected. Finally, prognostic factors for RTS were analyzed using a logistic regression model. Covariates were selected based on univariate analysis and a directed acyclic graph.ResultsWe included 340 eligible patients of whom 294 sufficiently completed the questionnaire. The mean follow-up was 3.7 years (± 1.0 years). Out of 256 patients participating in sports preoperatively, 210 patients (82%) returned to sport postoperatively, of whom 158 (75%) returned within 6 months. We observed a shift to participation in lower-impact activities, although 44% of reported sports activities at final follow-up were intermediate- or high-impact sports. The median Tegner score decreased from 5.0 (interquartile range [IQR], 4.0-6.0) presymptomatically to 4.0 (IQR, 3.0-4.0) at follow-up (P < .001). The mean Lysholm score at follow-up was 68 (SD, ± 22). No significant differences were found between patients with varus or valgus osteoarthritis. The strongest prognostic factor for RTS was continued sports participation in the year before surgery (odds ratio, 2.81; 95% CI, 1.37-5.76).ConclusionMore than 8 of 10 patients returned to sport after HTO. Continued preoperative sports participation was associated with a successful RTS. Future studies need to identify additional prognostic factors.

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Directed acyclic graph kernels for structural RNA analysis.

Publications

Directed acyclic graph kernels for structural RNA analysis.

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