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1. Pattern Matching and Discourse Processing in Information Extraction from Japanese Text

Author

Kitani, T., Eriguchi, Y., and Hara, M.

Subjects
Computer Science - Artificial Intelligence
Abstract

Information extraction is the task of automatically picking up information of interest from an unconstrained text. Information of interest is usually extracted in two steps. First, sentence level processing locates relevant pieces of information scattered throughout the text; second, discourse processing merges coreferential information to generate the output. In the first step, pieces of information are locally identified without recognizing any relationships among them. A key word search or simple pattern search can achieve this purpose. The second step requires deeper knowledge in order to understand relationships among separately identified pieces of information. Previous information extraction systems focused on the first step, partly because they were not required to link up each piece of information with other pieces. To link the extracted pieces of information and map them onto a structured output format, complex discourse processing is essential. This paper reports on a Japanese information extraction system that merges information using a pattern matcher and discourse processor. Evaluation results show a high level of system performance which approaches human performance., Comment: See http://www.jair.org/ for any accompanying files

Published
1994

6. Modeling Transposition of the Great Arteries with Patient-Specific Induced Pluripotent Stem Cells

Author

Ontoria-Oviedo I, Földes G, Tejedor S, Panadero J, Kitani T, Vázquez A, Wu JC, Harding SE, and Sepúlveda P

Subjects
Notch signaling pathway, angiogenesis, great arteries transposition, iPSC, endothelial cells
Abstract

The dextro-transposition of the great arteries (d-TGA) is one of the most common congenital heart diseases. To identify biological processes that could be related to the development of d-TGA, we established induced pluripotent stem cell (iPSC) lines from two patients with d-TGA and from two healthy subjects (as controls) and differentiated them into endothelial cells (iPSC-ECs). iPSC-EC transcriptome profiling and bioinformatics analysis revealed differences in the expression level of genes involved in circulatory system and animal organ development. iPSC-ECs from patients with d-TGA showed impaired ability to develop tubular structures in an in vitro capillary-like tube formation assay, and interactome studies revealed downregulation of biological processes related to Notch signaling, circulatory system development and angiogenesis, pointing to alterations in vascular structure development. Our study provides an iPSC-based cellular model to investigate the etiology of d-TGA.

Published
2021

14. Stimulation of Ca^<2+>/calmodulin-dependent protein kinase phosphatase by polycations

Author

Kameshita, I, Kitani, T, Okuno, S, Takeuchi, M, and Fujisawa, H

Abstract

Elsevier, Ishida, A. ; Kameshita, I. ; Kitani, T. ; Okuno, S. ; Takeuchi, M. ; Fujisawa, H., ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS, 408(2), 2002, 229-238, Ca^/calmodulin-dependent protein kinase phosphatase (CaMKPase) dephosphorylates and regulates multifunctional Ca^/calmodulin-dependent protein kinases (CaMKs). One of the prominent features of CaMKPase is stimulation of phosphatase activity by polycations such as poly--lysine (poly(Lys)). Using various polycations, basicity and molecular weight of the polymer proved to be important for the stimulation. Surface plasmon resonance (SPR) analysis showed that CaMKIV(T196D), which mimics CaMKPase substrate, and CaMKPase could form tight complexes with poly(Lys). Pull-down binding experiments suggested that the formation of a tightly associated ternary complex consisting of CaMKPase, poly(Lys), and phosphorylated CaMKIV is essential for stimulation. Dilution experiments also supported this contention. Poly(Lys) failed to stimulate a CaMKPase mutant in which a Glu cluster corresponding to residues 101–109 in the N-terminal domain was deleted, and the mutant could not interact with poly(Lys) in the presence of Mn^. Thus, the Glu cluster appeared to be the binding site for polycations and to play a pivotal role in the polycation stimulation of CaMKPase activity.

Published
2002

15. Substrate specificity of Ca(2+)/calmodulin-dependent protein kinase phosphatase: kinetic studies using synthetic phosphopeptides as model substrates

Author

Shigeri, Y, Tatsu, Y, Endo, Y, Kameshita, I, Okuno, S, Kitani, T, Takeuchi, M, Yumoto, N, and Fujisawa, H

Abstract

This is a pre-copy-editing, author-produced PDF of an article accepted for publication in Journal of Biochemistry following peer review. The definitive publisher-authenticated version Oxford University Press, Journal of Biochemistry, 129(5), 2001, 745-753 is available online at: http://jb.oxfordjournals.org/cgi/content/abstract/129/5/745. author, Ca(2+)/calmodulin-dependent protein kinase phosphatase (CaMKPase) dephosphorylates and regulates multifunctional Ca(2+)/calmodulin-dependent protein kinases. In order to elucidate the mechanism of substrate recognition by CaMKPase, we chemically synthesized a variety of phosphopeptide analogs and carried out kinetic analysis using them as CaMKPase substrates. This is the first report using systematically synthesized phosphopeptides as substrates for kinetic studies on substrate specificities of protein Ser/Thr phosphatases. CaMKPase was shown to be a protein Ser/Thr phosphatase having a strong preference for a phospho-Thr residue. A Pro residue adjacent to the dephosphorylation site on the C-terminal side and acidic clusters around the dephosphorylation site had detrimental effects on dephosphorylation by CaMKPase. Deletion analysis of a model substrate peptide revealed that the minimal length of the substrate peptide was only 2 to 3 amino acid residues including the dephosphorylation site. The residues on the C-terminal side of the dephosphorylation site were not essential for dephosphorylation, whereas the residue adjacent to the dephosphorylation site on the N-terminal side was essential. Ala-scanning analysis suggested that CaMKPase did not recognize a specific motif around the dephosphorylation site. Myosin light chain phosphorylated by protein kinase C and Erk2 phosphorylated by MEK1 were poor substrates for CaMKPase, while a synthetic phosphopeptide corresponding to the sequence around the phosphorylation site of the former was not dephosphorylated by CaMKPase but that of the latter was fairly good substrate. These data suggest that substrate specificity of CaMKPase is determined by higher-order structure of the substrate protein rather than by the primary structure around its dephosphorylation site. Use of phosphopeptide substrates also revealed that poly-L-lysine, an activator for CaMKPase, activated the enzyme mainly through increase in the V(max) values.

Published
2001

19. Lack of effects of oxolinic acid on spermatogenesis in young adult and aged Wistar rats

Author

Shin-ichi Katsuda, Takenaka A, Yuji Kurokawa, Kazuyoshi Taya, Kayoko Kudoh, Kitani T, Akira Maekawa, and Midori Yoshida

Subjects
Male, medicine.medical_specialty, Aging, Time Factors, Anti-Infective Agents, Urinary, Biology, Toxicology, Internal medicine, Oxolinic acid, Testis, medicine, Animals, Rats, Wistar, Spermatogenesis, Testosterone, Antibacterial agent, Leydig cell, Dose-Response Relationship, Drug, Oxolinic Acid, Leydig Cells, General Medicine, Luteinizing Hormone, Seminiferous Tubules, Rats, Endocrinology, medicine.anatomical_structure, Seminiferous tubule, Toxicity, Luteinizing hormone, Cell Division, Food Science, medicine.drug
Abstract

Prolonged treatment with oxolinic acid is known to elevate serum luteinizing hormone (LH) levels, resulting in induction of Leydig cell tumors in rats. In a carcinogenicity study of the compound, tubular atrophy of the testis was also increased, suggesting that oxolinic acid might affect spermatogenesis. The present study was therefore performed using rats of different ages with a particular focus on seminiferous tubule alteration and its relation to Leydig cell proliferation. Young adult (7 weeks of age) and aged (52 weeks of age) males of the Wistar strain were administered oxolinic acid at dietary concentrations of 0 (basal diet), 300, 1000 or 3000 ppm for 4 (all groups), 13 (0 and 3000 ppm groups), 26 (0 and 3000 ppm groups), or 52 weeks (0 and 3000 ppm groups of aged rats). Serum LH levels were elevated in both young adult and aged animals treated with 3000 ppm at most examined time points. While testosterone levels were also increased at the early time points in young adult, this was not the case in older animals. Elevation of the incidences of foci and/or focal hyperplasia of Leydig cells was noted but was only slight limited to aged rats treated with 3000 ppm after 26 weeks. Furthermore, it did not appear to be related to seminiferous tubular alteration. No treatment-related histopathological abnormalities could be detected in any treatment group, and morphometrical stage analysis of spermatogenesis conducted for the control and 3000 ppm-treated groups demonstrated no lesions. These results provide strong evidence that prolonged oxolinic treatment does not directly induce testicular toxicity or altered spermatogenesis in either young adult or aged rats, except for slight increase of Leydig cell proliferative lesions caused by elevated serum LH levels. Aged rats might have higher sensitivity than young adults to the effects of oxolinic acid on proliferative lesions of Leydig cells.

Published
2002

20. Relationship between eyed-egg percentage and levels of cortisol and thyroid hormone in masu salmon Oncorhynchus masou

Author

Mingist, M., Kitani, T., Koide, N., Ueda, H., Mingist, M., Kitani, T., Koide, N., and Ueda, H.

Abstract

This study investigated a possible cause of the low eyed-egg percentage that has occurred recently in pond-reared masu salmon Oncorhynchus masou, at the Kumaishi Fish Hatchery Station, Hokkaido, Japan. Serum cortisol levels of masu salmon during the spawning period were compared between individuals from Kumaishi and those from another station (Mori). Cortisol, thyroxine (T4) and triiodothyronine (T3) hormones were also measured in eyed eggs and their levels were compared to the eyed-egg percentage. Serum cortisol levels were significantly higher at Kumaishi than at Mori. There was a good relationship between serum cortisol and fertilized eggs cortisol levels. As cortisol levels in both ovulated females and in the eyed eggs increased, the eyed-egg percentage decreased, indicating a highly significant negative relationship between cortisol levels and eyed-egg percentage. In contrast, as the T3 and T4 levels in eyed eggs increased, the eyed-egg percentage increased. The consistently high cortisol level in serum and eyed eggs observed at Kumaishi may have had a significant effect in lowering the eyed-egg percentage.

Published
2007

22. Clinical Nephrology - Epidemiology II

Author

Agnes, H., primary, Kalman, P., additional, Jozsef, A., additional, Henrik, B., additional, Mucsi, I., additional, Kamata, K., additional, Sano, T., additional, Naito, S., additional, Okamoto, T., additional, Okina, C., additional, Kamata, M., additional, Murano, J., additional, Kobayashi, K., additional, Uchida, M., additional, Aoyama, T., additional, Takeuchi, Y., additional, Nagaba, Y., additional, Sakamoto, H., additional, Torino, C., additional, Panuccio, V., additional, Clementi, A., additional, Garozzo, M., additional, Bonanno, G., additional, Boito, R., additional, Natale, G., additional, Cicchetti, T., additional, Chippari, A., additional, Logozzo, D., additional, Alati, G., additional, Cassani, S., additional, Sellaro, A., additional, D'arrigo, G., additional, Tripepi, G., additional, Roberta, A., additional, Postorino, M., additional, Mallamaci, F., additional, Zoccali, C., additional, Buonanno, E., additional, Brancaccio, S., additional, Fimiani, V., additional, Napolitano, P., additional, Spadola, R., additional, Morrone, L., additional, DI Iorio, B., additional, Russo, D., additional, Betriu, A., additional, Martinez-Alonso, M., additional, Vidal, T., additional, Valdivielso, J., additional, Fernandez, E., additional, Bernadette, F., additional, Jean-Baptiste, B., additional, Frimat, L., additional, Madala, N. D., additional, Thusi, G. P., additional, Sibisi, N., additional, Mazibuko, B. G., additional, Assounga, A. G. H., additional, Tsai, N.-C., additional, Wang, H.-H., additional, Chen, Y.-C., additional, Hung, C.-C., additional, Hwang, S.-J., additional, Chen, H.-C., additional, Branco, P., additional, Adragao, T., additional, Birne, R., additional, Martins, A. R., additional, Vizinho, R., additional, Gaspar, A., additional, Grilo, M. J., additional, Barata, J. D., additional, Bonhorst, D., additional, Adragao, P., additional, Kim, J. S., additional, Yang, J. W., additional, Kim, M. K., additional, Choi, S. O., additional, Han, B. G., additional, Nathalie, N., additional, Sunny, E., additional, Glorieux, G., additional, Daniela, B., additional, Fellype, B., additional, Sophie, L., additional, Horst D, L., additional, Ziad, M., additional, Raymond, V., additional, Yanai, M., additional, Okada, K., additional, Takeuchi, K., additional, Nitta, K., additional, Takahashi, S., additional, Morena, M., additional, Jaussent, I., additional, Halkovich, A., additional, Dupuy, A.-M., additional, Bargnoux, A.-S., additional, Chenine, L., additional, Leray-Moragues, H., additional, Klouche, K., additional, Vernhet, H., additional, Canaud, B., additional, Cristol, J.-P., additional, Shutov, A., additional, Serov, V., additional, Kuznetsova, J., additional, Menzorov, M., additional, Serova, D., additional, Petrescu, L., additional, Zugravu, A., additional, Capusa, C., additional, Stancu, S., additional, Cinca, S., additional, Anghel, C., additional, Timofte, D., additional, Medrihan, L., additional, Ionescu, D., additional, Mircescu, G., additional, Hsu, T.-W., additional, Kuo, K.-L., additional, Hung, S.-C., additional, Tarng, D.-C., additional, Lee, S., additional, Kim, I., additional, Lee, D., additional, Rhee, H., additional, Song, S., additional, Seong, E., additional, Kwak, I., additional, Holzmann, M., additional, Gardell, C., additional, Jeppsson, A., additional, Sartipy, U., additional, Solak, Y., additional, Yilmaz, M. I., additional, Caglar, K., additional, Saglam, M., additional, Yaman, H., additional, Sonmez, A., additional, Unal, H. U., additional, Gok, M., additional, Gaipov, A., additional, Kayrak, M., additional, Eyileten, T., additional, Turk, S., additional, Vural, A., additional, DI Lullo, L., additional, Floccari, F., additional, Rivera, R., additional, Granata, A., additional, D'amelio, A., additional, Logias, F., additional, Otranto, G., additional, Malaguti, M., additional, Santoboni, A., additional, Fiorini, F., additional, Connor, T., additional, Oygar, D., additional, Nitsch, D., additional, Gale, D., additional, Steenkamp, R., additional, Neild, G. H., additional, Maxwell, P., additional, Louise Hogsbro, I., additional, Redal-Baigorri, B., additional, Sautenet, B., additional, Halimi, J. M., additional, Caille, A., additional, Goupille, P., additional, Giraudeau, B., additional, Oguz, Y., additional, Yenicesu, M., additional, Cetinkaya, H., additional, Ishimoto, Y., additional, Ohki, T., additional, Sugahara, M., additional, Kanemitsu, T., additional, Kobayashi, M., additional, Uchida, L., additional, Kotera, N., additional, Tanaka, S., additional, Sugimoto, T., additional, Mise, N., additional, Miyazaki, N., additional, Matsumoto, J., additional, Murata, I., additional, Yoshida, G., additional, Morishita, K., additional, Ushikoshi, H., additional, Nishigaki, K., additional, Ogura, S., additional, Minatoguchi, S., additional, Harvey, R., additional, Ala, A., additional, Banerjee, D., additional, Farmer, C., additional, Irving, J., additional, Hobbs, H., additional, Wheeler, T., additional, Klebe, B., additional, Stevens, P., additional, Selim, G., additional, Stojceva-Taneva, O., additional, Tozija, L., additional, Stojcev, N., additional, Gelev, S., additional, Dzekova-Vidimliski, P., additional, Pavleska, S., additional, Sikole, A., additional, Qureshi, A. R., additional, Evans, M., additional, Stendahl, M., additional, Prutz, K. G., additional, Elinder, C. G., additional, Tamagaki, K., additional, Kado, H., additional, Nakata, M., additional, Kitani, T., additional, Ota, N., additional, Ishida, R., additional, Matsuoka, E., additional, Shiotsu, Y., additional, Ishida, M., additional, Mori, Y., additional, Christelle, M., additional, Rognant, N., additional, Evelyne, D., additional, Sophie, F., additional, Laurent, J., additional, Maurice, L., additional, Silverwood, R., additional, Pierce, M., additional, Kuh, D., additional, Savage, C., additional, Ferro, C., additional, Moniek, D. G., additional, De Goeij, M., additional, Nynke, H., additional, Gurbey, O., additional, Joris, R., additional, Friedo, D., additional, Clayton, P., additional, Grace, B., additional, Cass, A., additional, Mcdonald, S., additional, Lorenzo, V., additional, Martin Conde, M., additional, Dusso, A., additional, Valdivielso, J. M., additional, Roggeri, D. P., additional, Cannella, G., additional, Cozzolino, M., additional, Mazzaferro, S., additional, Messa, P., additional, Brancaccio, D., additional, De Souza Faria, R., additional, Fernandes, N., additional, Lovisi, J., additional, Moura Marta, M., additional, Reboredo, M., additional, Do Vale Pinheiro, B., additional, Bastos, M., additional, Hundt, F., additional, Pabst, S., additional, Hammerstingl, C., additional, Gerhardt, T., additional, Skowasch, D., additional, Woitas, R., additional, Lopes, A. A., additional, Silva, L. F., additional, Matos, C. M., additional, Martins, M. S., additional, Silva, F. A., additional, Lopes, G. B., additional, Pizzarelli, F., additional, Dattolo, P., additional, Michelassi, S., additional, Rossi, C., additional, Bandinelli, S., additional, Mieth, M., additional, Mass, R., additional, Ferrucci, L., additional, Parisi, S., additional, Arduino, S., additional, Attini, R., additional, Fassio, F., additional, Biolcati, M., additional, Pagano, A., additional, Bossotti, C., additional, Ferraresi, M., additional, Gaglioti, P., additional, Todros, T., additional, Piccoli, G. B., additional, Salgado, T. M., additional, Arguello, B., additional, Benrimoj, S. I., additional, Fernandez-Llimos, F., additional, Bailey, P., additional, Tomson, C., additional, Ben-Shlomo, Y., additional, Santoro, A., additional, Rucci, P., additional, Mandreoli, M., additional, Caruso, F., additional, Corradini, M., additional, Flachi, M., additional, Gibertoni, D., additional, Rigotti, A., additional, Russo, G., additional, Fantini, M., additional, Mahapatra, H. S., additional, Choudhury, S., additional, Buxi, G., additional, Sharma, N., additional, Gupta, Y., additional, Sekhar, V., additional, Yanagisawa, N., additional, Ando, M., additional, Ajisawa, A., additional, Tsuchiya, K., additional, Janusz, O., additional, Mikolaj, M., additional, Jacek, M., additional, Boleslaw, R., additional, Prakash, S., additional, Coffin, R., additional, Schold, J., additional, Einstadter, D., additional, Stark, S., additional, Rodgers, D., additional, Howard, M., additional, Sehgal, A., additional, Palmer, S., additional, Tong, A., additional, Manns, B., additional, Craig, J., additional, Ruospo, M., additional, Gargano, L., additional, Strippoli, G., additional, Vecchio, M., additional, Petruzzi, M., additional, De Benedictis, M., additional, Pellegrini, F., additional, Ohno, Y., additional, Ishimura, E., additional, Naganuma, T., additional, Kondo, K., additional, Fukushima, W., additional, Mui, K., additional, Inaba, M., additional, Hirota, Y., additional, Sun, X., additional, Jiang, S., additional, Gu, H., additional, Chen, Y., additional, XI, C., additional, Qiao, X., additional, Chen, X., additional, Daher, E., additional, Junior, G. S., additional, Jacinto, C. N., additional, Pimentel, R. S., additional, Aguiar, G. B. R., additional, Lima, C. B., additional, Borges, R. C., additional, Mota, L. P. C., additional, Melo, J. V. L., additional, Melo, S. A., additional, Canamary, V. T., additional, Alves, M., additional, Araujo, S. M. H. A., additional, Huang, Y. K., additional, Rogacev, K., additional, Cremers, B., additional, Zawada, A., additional, Seiler, S., additional, Binder, N., additional, Ege, P., additional, Grosse-Dunker, G., additional, Heisel, I., additional, Hornof, F., additional, Jeken, J., additional, Rebling, N., additional, Ulrich, C., additional, Scheller, B., additional, Bohm, M., additional, Fliser, D., additional, Heine, G. H., additional, Robinson, B., additional, Wang, M., additional, Bieber, B., additional, Fluck, R., additional, Kerr, P. G., additional, Wikstrom, B., additional, Krishnan, M., additional, Nissenson, A., additional, Pisoni, R. L., additional, Mykleset, S., additional, Osthus, T. B., additional, Waldum, B., additional, Os, I., additional, Buttigieg, J., additional, Cassar, A., additional, Farrugia Agius, J., additional, Hara, M., additional, Yamato, M., additional, Yasuda, K., additional, and Sasaki, K., additional

Published
2012
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23. Brain regions involved in fatigue sensation: Reduced acetylcarnitine uptake into the brain

Author

Kuratsune, H, Yamaguti, K, Lindh, G, Evengård, B, Haberg, G, Matsumura, K, Iwase, M, Onoe, H, Takahashi, M, Machii, T, Kanakura, U, Kitani, T, Långström, B, Watanabe, Y, Kuratsune, H, Yamaguti, K, Lindh, G, Evengård, B, Haberg, G, Matsumura, K, Iwase, M, Onoe, H, Takahashi, M, Machii, T, Kanakura, U, Kitani, T, Långström, B, and Watanabe, Y

Published
2002

44. Low levels of serum acylcarnitine in chronic fatigue syndrome and chronic hepatitis type C, but not seen in other diseases.

Author

Kuratsune, H, primary, Yamaguti, K, additional, Lindh, G, additional, Evengard, B, additional, Takahashi, M, additional, Machii, T, additional, Matsumura, K, additional, Takaishi, J, additional, Kawata, S, additional, Långström, B, additional, Kanakura, Y, additional, Kitani, T, additional, and Watanabe, Y, additional

Published
1998
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