Biomedical subjects

Taku Kudo

Publications and source records attributed to Taku Kudo.

3 recordsLinked to original sources

PubMed2006

Mining frequent stem patterns from unaligned RNA sequences.

MOTIVATION: In detection of non-coding RNAs, it is often necessary to identify the secondary structure motifs from a set of putative RNA sequences. Most of the existing algorithms aim to provide the best motif or few good motifs, but biologists often need to inspect all the possible motifs thoroughly. RESULTS: Our method RNAmine employs a graph theoretic representation of RNA sequences and detects all the possible motifs exhaustively using a graph mining algorithm. The motif detection problem boils down to finding frequently appearing patterns in a set of directed and labeled graphs. In the tasks of common secondary structure prediction and local motif detection from long sequences, our method performed favorably both in accuracy and in efficiency with the state-of-the-art methods such as CMFinder. AVAILABILITY: The software is available upon request.

Algorithms↗

PubMed2004

Use of morphological analysis in protein name recognition.

Protein name recognition aims to detect each and every protein names appearing in a PubMed abstract. The task is not simple, as the graphic word boundary (space separator) assumed in conventional preprocessing does not necessarily coincide with the protein name boundary. Such boundary disagreement caused by tokenization ambiguity has usually been ignored in conventional preprocessing of general English. In this paper, we argue that boundary disagreement poses serious limitations in biomedical English text processing, not to mention protein name recognition. Our key idea for dealing with the boundary disagreement is to apply techniques used in Japanese morphological analysis where there are no word boundaries. Having evaluated the proposed method with GENIA corpus 3.02, we obtain F-measure of 69.01 on a strict criterion and 79.32 on a relaxed criterion. The result is comparable to other published work in protein name recognition, without resorting to manually prepared ad hoc feature engineering. Further, compared to the conventional preprocessing, the use of morphological analysis as preprocessing improves the performance of protein name recognition and reduces the execution time.

Abstracting and Indexing↗

PubMed2002

A new serum antibody test kit (E plate) for evaluation of Helicobacter pylori eradication.

OBJECTIVE: Serological antibody test have been widely performed to detect the presence of H. pylori, but they have not been used to evaluate the status of H. pylori after eradication. In this study we evaluated the diagnostic accuracy of a new serological test kit (E-plate) after eradication. METHOD: Eradication of H. pylori was performed in 100 patients by proton pump inhibitor (PPI)+amoxicillin (AMPC)+clarithromycin (CAM) or PPI+AMPC therapy. Evaluation of H. pylori was done by culture, histology and rapid urease test before, and 8 weeks after, the treatment. Serological tests were also performed before and after treatment using the E plate. Cure was defined as no evidence of H. pylori at 8 weeks after the treatment. Receiver operating characteristic (ROC) analysis was performed to determine the ideal cut-off value for percentage change in the serological test. RESULT: Success was obtained in 73 patients, failure in 20 patients and there were 7 dropouts. Serological test value was significantly decreased after treatment (44.3 +/- 29.6 U/ ml) compared to before treatment (94.8 +/- 73.2 U/ml) in the successful cases. In contrast, those with no significant change after treatment (62.7 +/- 31.3 U/ml) compared to before treatment (72.9 +/- 47.7 U/ml) were considered as failure cases. ROC analysis revealed that cut-off values of a 20%, 30%, and 40% decrease on E plate result yielded a sensitivity of 95.5%, 92.4%, 71.2% and a specificity of 73.3%, 84.2%, 94.7%, respectively. CONCLUSION: The new E plate serological test kit for H. pylori was useful for distinguishing success from failure 8 weeks after completion of eradication therapy for H. pylori.

2-Pyridinylmethylsulfinylbenzimidazoles↗