Biomedical subjects

Tetsuo Shibuya

Publications and source records attributed to Tetsuo Shibuya.

7 recordsLinked to original sources

PubMed2005

Keratinocyte growth factor receptor expression in normal colorectal epithelial cells and differentiated type of colorectal cancer.

The keratinocyte growth factor receptor, also known as KGFR/FGFR2 IIIb, is mainly localized in epithelial cells and participates in the proliferation of these cells. In the present study, we attempted to clarify the expression and role of KGFR in human colorectal cancer. The KGFR protein was detected in several colorectal cancer cell lines. Immuno-histochemically, KGFR was expressed on the luminal surface of epithelial cells in normal colorectal tissues. KGFR was expressed in 35 of 56 (62.5%) colorectal cancer patients and localized at the center of the cancer nests. Cytokeratin 20 (CK 20) colocalized with KGFR. In contrast, Ki-67 localized at the periphery of the cancer nests. Clinicopathologically, a high level of KGFR expression was associated with well-differentiated histological type (p<0.0001) and shallow wall invasion (p<0.0174). These findings indicate that KGFR may play important roles in the differentiation of normal colorectal epithelial cells and establishment of the well-differentiated histological type of colorectal cancer cells.

Aged↗

PubMed2004

Efficient filtering methods for clustering cDNAs with spliced sequence alignment.

MOTIVATION: Clustering sequences of a full-length cDNA library into alternative splice form candidates is a very important problem. RESULTS: We developed a new efficient algorithm to cluster sequences of a full-length cDNA library into alternative splice form candidates. Current clustering algorithms for cDNAs tend to produce too many clusters containing incorrect splice form candidates. Our algorithm is based on a spliced sequence alignment algorithm that considers splice sites. The spliced sequence alignment algorithm is a variant of an ordinary dynamic programming algorithm, which requires O(nm) time for checking a pair of sequences where n and m are the lengths of the two sequences. Since the time bound is too large to perform all-pair comparison for a large set of sequences, we developed new techniques to reduce the computation time without affecting the accuracy of the output clusters. Our algorithm was applied to 21 076 mouse cDNA sequences of the FANTOM 1.10 database to examine its performance and accuracy. In these experiments, we achieved about 2-12-fold speedup against a method using only a traditional hash-based technique. Moreover, without using any information of the mouse genome sequence data or any gene data in public databases, we succeeded in listing 87-89% of all the clusters that biologists have annotated manually. AVAILABILITY: We provide a web service for cDNA clustering located at https://access.obigrid.org/ibm/cluspa/, for which registration for the OBIGrid (http://www.obigrid.org) is required.

Algorithms↗

PubMed2004

Cure of intractable pancreatic fistula by subcutaneous fistulojejunostomy.

Fistulojejunostomy was performed at the subcutaneous level in two patients with intractable pancreatic fistula that occurred after surgery for cancer of the ampulla of Vater and carcinoma of the lower bile duct. The treatment yielded mostly satisfactory results, though one patient incurred postoperative wound dehiscence, which was healed with conservative measures. Compared with conventional procedures, this method is technically easy to perform, as it does not involve surgical separation of the fistula up to a site deep within the abdominal cavity, rarely results in side injury, and poses few potential risks of cicatricial stenosis of the fistular lumen, because blood supply to the fistula is preserved. Subcutaneous fistulojejunostomy is considered to be recommendable for pancreatic fistulas that occur long after surgery and which are stenosed at the site of the pancreatojejunal stenosis and thus require surgical treatment.

Aged↗

PubMed2003

Reevaluation of human cytomegalovirus coding potential.

The Bio-Dictionary-based Gene Finder was used to reassess the coding potential of the AD169 laboratory strain of human cytomegalovirus and sequences in the Toledo strain that are missing in the laboratory strain of the virus. The gene-finder algorithm assesses the potential of an ORF to encode a protein based on matches to a database of amino acid patterns derived from a large collection of proteins. The algorithm was used to score all human cytomegalovirus ORFs with the potential to encode polypeptides >/=50 aa in length. As a further test for functionality, the genomes of the chimpanzee, rhesus, and murine cytomegaloviruses were searched for orthologues of the predicted human cytomegalovirus ORFs. The analysis indicates that 37 previously annotated ORFs ought to be discarded, and at least nine previously unrecognized ORFs with relatively strong coding potential should be added. Thus, the human cytomegalovirus genome appears to contain approximately 192 unique ORFs with the potential to encode a protein. Support for several of the predictions of our in silico analysis was obtained by sequencing several domains within a clinical isolate of human cytomegalovirus.

Algorithms↗

PubMed2003

The web server of IBM's Bioinformatics and Pattern Discovery group.

We herein present and discuss the services and content which are available on the web server of IBM's Bioinformatics and Pattern Discovery group. The server is operational around the clock and provides access to a variety of methods that have been published by the group's members and collaborators. The available tools correspond to applications ranging from the discovery of patterns in streams of events and the computation of multiple sequence alignments, to the discovery of genes in nucleic acid sequences and the interactive annotation of amino acid sequences. Additionally, annotations for more than 70 archaeal, bacterial, eukaryotic and viral genomes are available on-line and can be searched interactively. The tools and code bundles can be accessed beginning at http://cbcsrv.watson.ibm.com/Tspd.html whereas the genomics annotations are available at http://cbcsrv.watson.ibm.com/Annotations/.

Computational Biology↗

PubMed2002

Dictionary-driven prokaryotic gene finding.

Gene identification, also known as gene finding or gene recognition, is among the important problems of molecular biology that have been receiving increasing attention with the advent of large scale sequencing projects. Previous strategies for solving this problem can be categorized into essentially two schools of thought: one school employs sequence composition statistics, whereas the other relies on database similarity searches. In this paper, we propose a new gene identification scheme that combines the best characteristics from each of these two schools. In particular, our method determines gene candidates among the ORFs that can be identified in a given DNA strand through the use of the Bio-Dictionary, a database of patterns that covers essentially all of the currently available sample of the natural protein sequence space. Our approach relies entirely on the use of redundant patterns as the agents on which the presence or absence of genes is predicated and does not employ any additional evidence, e.g. ribosome-binding site signals. The Bio-Dictionary Gene Finder (BDGF), the algorithm's implementation, is a single computational engine able to handle the gene identification task across distinct archaeal and bacterial genomes. The engine exhibits performance that is characterized by simultaneous very high values of sensitivity and specificity, and a high percentage of correctly predicted start sites. Using a collection of patterns derived from an old (June 2000) release of the Swiss-Prot/TrEMBL database that contained 451 602 proteins and fragments, we demonstrate our method's generality and capabilities through an extensive analysis of 17 complete archaeal and bacterial genomes. Examples of previously unreported genes are also shown and discussed in detail.

Algorithms↗

PubMed2002

Metachronous adenocarcinoma occurring at a colostomy site after abdominoperineal resection for rectal carcinoma.

Carcinomas rarely occur at the site of a colostomy. A 73-year-old man underwent abdominoperineal resection (Miles' surgical procedure) for rectal carcinoma in September 1988. He did not return to the hospital until September 1995, when he was admitted with stricture of the stoma. Neither tumor nor ulcer was detected at the stoma. The tip of the doctor's little finger was able to pass through the stoma, and manual expanding alleviated the stricture. The patient did not return to the hospital again until August 1996, at age 81 years, when he visited the hospital because of complete stricture of the stoma. A biopsy revealed an adenomatous carcinoma, but the results of various examinations suggested no metastasis. A portion of the intestine, including the stoma and surrounding skin, was resected, and a new stoma was created in the descending colon. We report this rare carcinoma occurring at the site of a colostomy, and we review the literature.

Adenocarcinoma↗