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Articles by Y Murakami
Total Records ( 6 ) for Y Murakami
  R. V Spriggs , Y Murakami , H Nakamura and S. Jones

Motivation: All eukaryotic proteomes are characterized by a significant percentage of proteins of unknown function. Comp-utational function prediction methods are therefore essential as initial steps in the function annotation process. This article describes an annotation method (PiRaNhA) for the prediction of RNA-binding residues (RBRs) from protein sequence information. A series of sequence properties (position specific scoring matrices, interface propensities, predicted accessibility and hydrophobicity) are used to train a support vector machine. This method is then evaluated for its potential to be applied to RNA-binding function prediction at the level of the complete protein.

Results: The 5-fold cross-validation of PiRaNhA on a dataset of 81 RNA-binding proteins achieves a Matthews Correlation Coefficient (MCC) of 0.50 and accuracy of 87.2%. When used to predict RBRs in 42 proteins not used in training, PiRaNhA achieves an MCC of 0.41 and accuracy of 84.5%. Decision values from the PiRaNhA predictions were used in a second SVM to make predictions of RNA-binding function at the protein level, achieving an MCC of 0.53 and accuracy of 76.1%. The PiRaNhA RBR predictions allow experimentalists to perform more targeted experiments for function annotation; and the prediction of RNA-binding function at the protein level shows promise for proteome-wide annotations.

Availability and Implementation: Freely available on the web at or

Contact:[email protected].

Supplementary Information: Supplementary data are available at the Bioinformatics online.

  F Hosoi , H Izumi , A Kawahara , Y Murakami , H Kinoshita , M Kage , K Nishio , K Kohno , M Kuwano and M. Ono

N-myc downstream regulated gene 1 (NDRG1)/Cap43 expression is a predictive marker of good prognosis in patients with pancreatic cancer as we reported previously. In this study, NDRG1/Cap43 decreased the expression of various chemoattractants, including CXC chemokines for inflammatory cells, and the recruitment of macrophages and neutrophils with suppression of both angiogenesis and growth in mouse xenograft models. We further found that NDRG1/Cap43 induced nuclear factor-B (NF-B) signaling attenuation through marked decreases in inhibitor of B kinase (IKK) β expression and IB phosphorylation. Decreased IKKβ expression in cells overexpressing NDRG1/Cap43 resulted in reduction of both nuclear translocation of p65 and p50 and their binding to the NF-B motif. The introduction of an exogenous IKKβ gene restored NDRG1/Cap43-suppressed expression of melanoma growth-stimulating activity /CXCL1, epithelial-derived neutrophil activating protein-78/CXCL5, interleukin-8/CXCL8 and vascular endothelial growth factor-A, accompanied by increased phosphorylation of IB in NDRG1/Cap43-expressing cells. In patients with pancreatic cancer, NDRG1/Cap43 expression levels were also inversely correlated with the number of infiltrating macrophages in the tumor stroma. This study suggests a novel mechanism by which NDRG1/Cap43 modulates tumor angiogenesis/growth and infiltration of macrophages/neutrophils through attenuation of NF-B signaling. [Cancer Res 2009;69(12):4983–91]

  T Yamada , H Doppalapudi , H. T McElderry , T Okada , Y Murakami , Y Inden , Y Yoshida , N Yoshida , T Murohara , A. E Epstein , V. J Plumb , S. H Litovsky and G. N. Kay

Idiopathic ventricular arrhythmias (VAs) can originate from the left ventricular papillary muscles (PAMs). This study investigated the electrophysiological characteristics of these VAs and their relevance for the results of catheter ablation.

Methods and Results—

We studied 19 patients who underwent successful catheter ablation of idiopathic VAs originating from the anterior (n=7) and posterior PAMs (n=12). Although an excellent pace map was obtained at the first ablation site in 17 patients, radiofrequency ablation at that site failed to eliminate the VAs, and radiofrequency lesions in a relatively wide area around that site were required to completely eliminate the VAs in all patients. Radiofrequency current with an irrigated or nonirrigated 8-mm-tip ablation catheter was required to achieve a lasting ablation of the PAM VA origins. During 42% of the PAM VAs, a sharp ventricular prepotential was recorded at the successful ablation site. In 9 (47%) patients, PAM VAs exhibited multiple QRS morphologies, with subtle, but distinguishable differences occurring spontaneously and after the ablation. In 7 (78%) of those patients, radiofrequency lesions on both sides of the PAMs where pacing could reproduce an excellent match to the 2 different QRS morphologies of the VAs were required to completely eliminate the VAs.


Radiofrequency catheter ablation of idiopathic PAM VAs is challenging probably because the VA origin is located relatively deep beneath the endocardium of the PAMs. PAM VAs often exhibit multiple QRS morphologies, which may be caused by a single origin with preferential conduction resulting from the complex structure of the PAMs.

  T Matsuda , T Fujii , Y Sano , S. e Kudo , Y Oda , M Igarashi , H Iishi , Y Murakami , H Ishikawa , T Shimoda , K Kaneko and S. Yoshida

The National Polyp Study is used as the basis of recommendations for colonoscopic surveillance after polypectomy, establishing an interval of 3 years after removal of newly diagnosed adenomas. The aim of this retrospective cohort study was to estimate the incidence of advanced neoplasia after initial colonoscopy and compare the differences among risk groups.


Patients over 40 years who were referred for initial colonoscopy at six institutes were selected. They were classified into four groups based on the initial colonoscopy: A, patients without any adenoma; B, with adenomas of <6 mm only; C, with adenomas of ≥6 mm; D, with any intramucosal cancer. The index lesion (IL) at follow-up colonoscopy was defined as large adenoma ≥10 mm, intramucosal/invasive cancer.


A total of 5309 patients were enrolled in this study. Overall, median follow-up period was 5.1 years. The numbers of eligible patients in the various subgroups were A, 2006; B, 1655; C, 1123; D, 525. A total of 379 ILs were newly diagnosed during follow-up colonoscopy. The cumulative incidence of ILs in each group was A, 2.6%; B, 6.7%; C, 13.4%; and D, 12.6%.


Patients with any adenomas >6 mm or intramucosal cancer at the initial colonoscopy have a higher risk of advanced neoplasia during follow-up colonoscopy.

  D Shindo , K Takahashi , Y Murakami , K Yamazaki , S Deguchi , H Suga and Y. Kondo

The double-probe piezodriving specimen holder that was recently developed by some of the present authors is modified to introduce a laser irradiation port in one of its two arms. As a result, the new specimen holder consists of a piezodriving probe and a laser irradiation port, both of which can be three-dimensionally controlled by using piezoelectric elements and micrometers. While the piezodriving probe interacts with the specimen set in the holder in several ways, the laser beam causes photo-induced phenomena to occur. By performing electron holography using the new specimen holder, we demonstrate that it is possible to evaluate the change in the electric field resulting from the discharging effect of laser irradiation on organic photoconductors.

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