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Approximating Tree Edit Distance through String Edit Distance for Binary Tree Codes

100%

Aratsu T. , Hirata K. , Kuboyama T.

2010

tom Vol. 101, nr 3

157-171

This article proposes an approximation of the tree edit distance through the string edit distance for binary tree codes, instead of for Euler strings introduced by Akutsu (2006). Here, a binary tree code is a string obtained by traversing a binary tree representation with two kinds of dummy nodes of a tree in preorder. Then, we show that σ/2≤τ≤(h+1)σ+h, where τ is the tree edit distance between trees, and is the string edit distance between their binary tree codes and h is the minimum height of the trees.

Segmental Mapping and Distance for Rooted Labeled Ordered Trees

100%

Kan T. , Higuchi S. , Hirata K.

Fundamenta Informaticae

2014

tom Vol. 132, nr 4

461--483

In this paper, as variations of a Tai mapping between rooted labeled ordered trees (trees, for short), we introduce a segmentalmapping to preserve the parent-children relationship as possible, and also top-down segmengal and bottom-up segmental mappings as the segmental mappings that contain the pair of the roots and the pair of the leaves, respectively. Then, we show that these mappings provide a new hierarchy for the variations of the Tai mapping in addition to a well-known one, in particular, the top-down segmental mapping coincides with a top-down mapping. Also we show that both segmental and bottom-up segmental distances as the minimumcosts of segmental and bottom-up segmental mappings are metrics. Next, we design algorithms to compute the segmental and the bottom-up segmental distances in quadratic time and space. Finally, we give experimental results for the segmental distance.

Effects of Clostridium perfringens enterotoxin via claudin-4 on normal human pancreatic duct epithelial cells and cancer cells

63%

Yamaguchi H. , Kojima T. , Ito T. , Kyuno D. , Kimura Y. , Imamura M. , Hirata K. , Sawada N.

Cellular and Molecular Biology Letters

2011

tom 16

nr 3

The tight junction protein claudin-4 is frequently overexpressed in pancreatic cancer, and is also a receptor for Clostridium perfringens enterotoxin (CPE). The cytotoxic effects of CPE are thought to be useful as a novel therapeutic tool for pancreatic cancer. However, the responses to CPE via claudin-4 remain unknown in normal human pancreatic duct epithelial (HPDE) cells. We introduced the human telomerase reverse transcriptase (hTERT) gene into HPDE cells in primary culture as a model of normal HPDE cells in vitro. hTERT-HPDE cells treated with or without 10% FBS and pancreatic cancer cell lines PANC-1, BXPC3, HPAF-II and HPAC were treated with CPE. In Western blotting, the expression of claudin-4 protein in hTERT-HPDE cells treated with 10% FBS was as high as it was in all of the pancreatic cancer cell lines. In hTERT-HPDE cells with or without 10% FBS, cytotoxicity was not observed at any concentration of CPE, whereas in all pancreatic cancer cell lines, CPE had a dose-dependent cytotoxic effect. In hTERT-HPDE cells with 10% FBS, claudin-4 was localized in the apical-most regions, where there are tight junction areas, in which in all pancreatic cancer cell lines claudin-4 was found not only in the apical-most regions but also at basolateral membranes. In hTERT-HPDE cells with 10% FBS after treatment with CPE, downregulation of barrier function and claudin-4 expression at the membranes was observed. In HPAC cells, the sensitivity to CPE was significantly decreased by knockdown of claudin-4 expression using siRNA compared to the control. These findings suggest that, in normal HPDE cells, the lack of toxicity of CPE was probably due to the localization of claudin-4, which is different from that of pancreatic cancer cells. hTERT-HPDE cells in this culture system may be a useful model of normal HPDE cells not only for physiological regulation of claudin-4 expression but also for developing safer and more effective therapeutic methods targeting claudin-4 in pancreatic cancer.