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1. Nanoscale defect evaluation framework combining real-time transmission electron microscopy and integrated machine learning-particle filter estimation

Author

Sasaki, K., Muramatsu, M., Hirayama, K., Endo, K., and Murayama, M.

Subjects
Multidisciplinary, flow, image
Abstract

Observation of dynamic processes by transmission electron microscopy (TEM) is an attractive technique to experimentally analyze materials' nanoscale phenomena and understand the microstructure-properties relationships in nanoscale. Even if spatial and temporal resolutions of real-time TEM increase significantly, it is still difficult to say that the researchers quantitatively evaluate the dynamic behavior of defects. Images in TEM video are a two-dimensional projection of three-dimensional space phenomena, thus missing information must be existed that makes image's uniquely accurate interpretation challenging. Therefore, even though they are still a clustering high-dimensional data and can be compressed to two-dimensional, conventional statistical methods for analyzing images may not be powerful enough to track nanoscale behavior by removing various artifacts associated with experiment; and automated and unbiased processing tools for such big-data are becoming mission-critical to discover knowledge about unforeseen behavior. We have developed a method to quantitative image analysis framework to resolve these problems, in which machine learning and particle filter estimation are uniquely combined. The quantitative and automated measurement of the dislocation velocity in an Fe-31Mn-3Al-3Si autunitic steel subjected to the tensile deformation was performed to validate the framework, and an intermittent motion of the dislocations was quantitatively analyzed. The framework is successfully classifying, identifying and tracking nanoscale objects; these are not able to be accurately implemented by the conventional mean-path based analysis. JST CREST [JPMJCR1994]; Nanoscale Characterization and Fabrication Laboratory (NCFL), Institute for Critical Technology and Applied Science (ICTAS), Virginia Tech; NSF [ECCS 1542100,, ECCS 2025151]; US Department of Energy, Office of Science, Office of Basic Energy Sciences [DE-FG02-06ER15786]; JSPS KAKENHI [19H02029, 20H02479] Published version M. Muramatsu and M. Murayama greatly appreciate the financial support by the JST CREST (JPMJCR1994). The authors also would like to express their special acknowledgement to Prof. Nobuhiro Tsuji (Kyoto University) and Chang-Yu Hung (Virginia Tech) for supporting results interpretation and data collection. This study was partly supported by Nanoscale Characterization and Fabrication Laboratory (NCFL), Institute for Critical Technology and Applied Science (ICTAS), Virginia Tech and used shared facilities at the Virginia Tech National Center for Earth and Environmental Nanotechnology Infrastructure (NanoEarth), a member of the National Nanotechnology Coordinated Infrastructure (NNCI), supported by NSF (ECCS 1542100, ECCS 2025151). M. Murayama acknowledges financial support from the US Department of Energy, Office of Science, Office of Basic Energy Sciences under Award #DE-FG02-06ER15786 for technical development of TEM in-situ deformation, and JSPS KAKENHI Grant Numbers 19H02029 & 20H02479.

Published
2022
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2. Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network

Author

Grapotte M., Saraswat M., Bessiere C., Menichelli C., Ramilowski J. A., Severin J., Hayashizaki Y., Itoh M., Tagami M., Murata M., Kojima-Ishiyama M., Noma S., Noguchi S., Kasukawa T., Hasegawa A., Suzuki H., Nishiyori-Sueki H., Frith M. C., Abugessaisa I., Aitken S., Aken B. L., Alam I., Alam T., Alasiri R., Alhendi A. M. N., Alinejad-Rokny H., Alvarez M. J., Andersson R., Arakawa T., Araki M., Arbel T., Archer J., Archibald A. L., Arner E., Arner P., Asai K., Ashoor H., Astrom G., Babina M., Baillie J. K., Bajic V. B., Bajpai A., Baker S., Baldarelli R. M., Balic A., Bansal M., Batagov A. O., Batzoglou S., Beckhouse A. G., Beltrami A. P., Beltrami C. A., Bertin N., Bhattacharya S., Bickel P. J., Blake J. A., Blanchette M., Bodega B., Bonetti A., Bono H., Bornholdt J., Bttcher M., Bougouffa S., Boyd M., Breda J., Brombacher F., Brown J. B., Bult C. J., Burroughs A. M., Burt D. W., Busch A., Caglio G., Califano A., Cameron C. J., Cannistraci C. V., Carbone A., Carlisle A. J., Carninci P., Carter K. W., Cesselli D., Chang J. -C., Chen J. C., Chen Y., Chierici M., Christodoulou J., Ciani Y., Clark E. L., Coskun M., Dalby M., Dalla E., Daub C. O., Davis C. A., de Hoon M. J. L., de Rie D., Denisenko E., Deplancke B., Detmar M., Deviatiiarov R., Di Bernardo D., Diehl A. D., Dieterich L. C., Dimont E., Djebali S., Dohi T., Dostie J., Drablos F., Edge A. S. B., Edinger M., Ehrlund A., Ekwall K., Elofsson A., Endoh M., Enomoto H., Enomoto S., Faghihi M., Fagiolini M., Farach-Carson M. C., Faulkner G. J., Favorov A., Fernandes A. M., Ferrai C., Forrest A. R. R., Forrester L. M., Forsberg M., Fort A., Francescatto M., Freeman T. C., Frith M., Fukuda S., Funayama M., Furlanello C., Furuno M., Furusawa C., Gao H., Gazova I., Gebhard C., Geier F., Geijtenbeek T. B. H., Ghosh S., Ghosheh Y., Gingeras T. R., Gojobori T., Goldberg T., Goldowitz D., Gough J., Greco D., Gruber A. J., Guhl S., Guigo R., Guler R., Gusev O., Gustincich S., Ha T. J., Haberle V., Hale P., Hallstrom B. M., Hamada M., Handoko L., Hara M., Harbers M., Harrow J., Harshbarger J., Hase T., Hashimoto K., Hatano T., Hattori N., Hayashi R., Herlyn M., Hettne K., Heutink P., Hide W., Hitchens K. J., Sui S. H., 't Hoen P. A. C., Hon C. C., Hori F., Horie M., Horimoto K., Horton P., Hou R., Huang E., Huang Y., Hugues R., Hume D., Ienasescu H., Iida K., Ikawa T., Ikemura T., Ikeo K., Inoue N., Ishizu Y., Ito Y., Ivshina A. V., Jankovic B. R., Jenjaroenpun P., Johnson R., Jorgensen M., Jorjani H., Joshi A., Jurman G., Kaczkowski B., Kai C., Kaida K., Kajiyama K., Kaliyaperumal R., Kaminuma E., Kanaya T., Kaneda H., Kapranov P., Kasianov A. S., Katayama T., Kato S., Kawaguchi S., Kawai J., Kawaji H., Kawamoto H., Kawamura Y. I., Kawasaki S., Kawashima T., Kempfle J. S., Kenna T. J., Kere J., Khachigian L., Kiryu H., Kishima M., Kitajima H., Kitamura T., Kitano H., Klaric E., Klepper K., Klinken S. P., Kloppmann E., Knox A. J., Kodama Y., Kogo Y., Kojima M., Kojima S., Komatsu N., Komiyama H., Kono T., Koseki H., Koyasu S., Kratz A., Kukalev A., Kulakovskiy I., Kundaje A., Kunikata H., Kuo R., Kuo T., Kuraku S., Kuznetsov V. A., Kwon T. J., Larouche M., Lassmann T., Law A., Le-Cao K. -A., Lecellier C. -H., Lee W., Lenhard B., Lennartsson A., Li K., Li R., Lilje B., Lipovich L., Lizio M., Lopez G., Magi S., Mak G. K., Makeev V., Manabe R., Mandai M., Mar J., Maruyama K., Maruyama T., Mason E., Mathelier A., Matsuda H., Medvedeva Y. A., Meehan T. F., Mejhert N., Meynert A., Mikami N., Minoda A., Miura H., Miyagi Y., Miyawaki A., Mizuno Y., Morikawa H., Morimoto M., Morioka M., Morishita S., Moro K., Motakis E., Motohashi H., Mukarram A. K., Mummery C. L., Mungall C. J., Murakawa Y., Muramatsu M., Nagasaka K., Nagase T., Nakachi Y., Nakahara F., Nakai K., Nakamura K., Nakamura Y., Nakazawa T., Nason G. P., Nepal C., Nguyen Q. H., Nielsen L. K., Nishida K., Nishiguchi K. M., Nishiyori H., Nitta K., Notredame C., Ogishima S., Ohkura N., Ohno H., Ohshima M., Ohtsu T., Okada Y., Okada-Hatakeyama M., Okazaki Y., Oksvold P., Orlando V., Ow G. S., Ozturk M., Pachkov M., Paparountas T., Parihar S. P., Park S. -J., Pascarella G., Passier R., Persson H., Philippens I. H., Piazza S., Plessy C., Pombo A., Ponten F., Poulain S., Poulsen T. M., Pradhan S., Prezioso C., Pridans C., Qin X. -Y., Quackenbush J., Rackham O., Ramilowski J., Ravasi T., Rehli M., Rennie S., Rito T., Rizzu P., Robert C., Roos M., Rost B., Roudnicky F., Roy R., Rye M. B., Sachenkova O., Saetrom P., Sai H., Saiki S., Saito M., Saito A., Sakaguchi S., Sakai M., Sakaue S., Sakaue-Sawano A., Sandelin A., Sano H., Sasamoto Y., Sato H., Saxena A., Saya H., Schafferhans A., Schmeier S., Schmidl C., Schmocker D., Schneider C., Schueler M., Schultes E. A., Schulze-Tanzil G., Semple C. A., Seno S., Seo W., Sese J., Sheng G., Shi J., Shimoni Y., Shin J. W., SimonSanchez J., Sivertsson A., Sjostedt E., Soderhall C., Laurent G. S., Stoiber M. H., Sugiyama D., Summers K. M., Suzuki A. M., Suzuki K., Suzuki M., Suzuki N., Suzuki T., Swanson D. J., Swoboda R. K., Taguchi A., Takahashi H., Takahashi M., Takamochi K., Takeda S., Takenaka Y., Tam K. T., Tanaka H., Tanaka R., Tanaka Y., Tang D., Taniuchi I., Tanzer A., Tarui H., Taylor M. S., Terada A., Terao Y., Testa A. C., Thomas M., Thongjuea S., Tomii K., Triglia E. T., Toyoda H., Tsang H. G., Tsujikawa M., Uhlen M., Valen E., van de Wetering M., van Nimwegen E., Velmeshev D., Verardo R., Vitezic M., Vitting-Seerup K., von Feilitzen K., Voolstra C. R., Vorontsov I. E., Wahlestedt C., Wasserman W. W., Watanabe K., Watanabe S., Wells C. A., Winteringham L. N., Wolvetang E., Yabukami H., Yagi K., Yamada T., Yamaguchi Y., Yamamoto M., Yamamoto Y., Yamanaka Y., Yano K., Yasuzawa K., Yatsuka Y., Yo M., Yokokura S., Yoneda M., Yoshida E., Yoshida Y., Yoshihara M., Young R., Young R. S., Yu N. Y., Yumoto N., Zabierowski S. E., Zhang P. G., Zucchelli S., Zwahlen M., Chatelain C., Brehelin L., Grapotte, M., Saraswat, M., Bessiere, C., Menichelli, C., Ramilowski, J. A., Severin, J., Hayashizaki, Y., Itoh, M., Tagami, M., Murata, M., Kojima-Ishiyama, M., Noma, S., Noguchi, S., Kasukawa, T., Hasegawa, A., Suzuki, H., Nishiyori-Sueki, H., Frith, M. C., Abugessaisa, I., Aitken, S., Aken, B. L., Alam, I., Alam, T., Alasiri, R., Alhendi, A. M. N., Alinejad-Rokny, H., Alvarez, M. J., Andersson, R., Arakawa, T., Araki, M., Arbel, T., Archer, J., Archibald, A. L., Arner, E., Arner, P., Asai, K., Ashoor, H., Astrom, G., Babina, M., Baillie, J. K., Bajic, V. B., Bajpai, A., Baker, S., Baldarelli, R. M., Balic, A., Bansal, M., Batagov, A. O., Batzoglou, S., Beckhouse, A. G., Beltrami, A. P., Beltrami, C. A., Bertin, N., Bhattacharya, S., Bickel, P. J., Blake, J. A., Blanchette, M., Bodega, B., Bonetti, A., Bono, H., Bornholdt, J., Bttcher, M., Bougouffa, S., Boyd, M., Breda, J., Brombacher, F., Brown, J. B., Bult, C. J., Burroughs, A. M., Burt, D. W., Busch, A., Caglio, G., Califano, A., Cameron, C. J., Cannistraci, C. V., Carbone, A., Carlisle, A. J., Carninci, P., Carter, K. W., Cesselli, D., Chang, J. -C., Chen, J. C., Chen, Y., Chierici, M., Christodoulou, J., Ciani, Y., Clark, E. L., Coskun, M., Dalby, M., Dalla, E., Daub, C. O., Davis, C. A., de Hoon, M. J. L., de Rie, D., Denisenko, E., Deplancke, B., Detmar, M., Deviatiiarov, R., Di Bernardo, D., Diehl, A. D., Dieterich, L. C., Dimont, E., Djebali, S., Dohi, T., Dostie, J., Drablos, F., Edge, A. S. B., Edinger, M., Ehrlund, A., Ekwall, K., Elofsson, A., Endoh, M., Enomoto, H., Enomoto, S., Faghihi, M., Fagiolini, M., Farach-Carson, M. C., Faulkner, G. J., Favorov, A., Fernandes, A. M., Ferrai, C., Forrest, A. R. R., Forrester, L. M., Forsberg, M., Fort, A., Francescatto, M., Freeman, T. C., Frith, M., Fukuda, S., Funayama, M., Furlanello, C., Furuno, M., Furusawa, C., Gao, H., Gazova, I., Gebhard, C., Geier, F., Geijtenbeek, T. B. H., Ghosh, S., Ghosheh, Y., Gingeras, T. R., Gojobori, T., Goldberg, T., Goldowitz, D., Gough, J., Greco, D., Gruber, A. J., Guhl, S., Guigo, R., Guler, R., Gusev, O., Gustincich, S., Ha, T. J., Haberle, V., Hale, P., Hallstrom, B. M., Hamada, M., Handoko, L., Hara, M., Harbers, M., Harrow, J., Harshbarger, J., Hase, T., Hashimoto, K., Hatano, T., Hattori, N., Hayashi, R., Herlyn, M., Hettne, K., Heutink, P., Hide, W., Hitchens, K. J., Sui, S. H., 't Hoen, P. A. C., Hon, C. C., Hori, F., Horie, M., Horimoto, K., Horton, P., Hou, R., Huang, E., Huang, Y., Hugues, R., Hume, D., Ienasescu, H., Iida, K., Ikawa, T., Ikemura, T., Ikeo, K., Inoue, N., Ishizu, Y., Ito, Y., Ivshina, A. V., Jankovic, B. R., Jenjaroenpun, P., Johnson, R., Jorgensen, M., Jorjani, H., Joshi, A., Jurman, G., Kaczkowski, B., Kai, C., Kaida, K., Kajiyama, K., Kaliyaperumal, R., Kaminuma, E., Kanaya, T., Kaneda, H., Kapranov, P., Kasianov, A. S., Katayama, T., Kato, S., Kawaguchi, S., Kawai, J., Kawaji, H., Kawamoto, H., Kawamura, Y. I., Kawasaki, S., Kawashima, T., Kempfle, J. S., Kenna, T. J., Kere, J., Khachigian, L., Kiryu, H., Kishima, M., Kitajima, H., Kitamura, T., Kitano, H., Klaric, E., Klepper, K., Klinken, S. P., Kloppmann, E., Knox, A. J., Kodama, Y., Kogo, Y., Kojima, M., Kojima, S., Komatsu, N., Komiyama, H., Kono, T., Koseki, H., Koyasu, S., Kratz, A., Kukalev, A., Kulakovskiy, I., Kundaje, A., Kunikata, H., Kuo, R., Kuo, T., Kuraku, S., Kuznetsov, V. A., Kwon, T. J., Larouche, M., Lassmann, T., Law, A., Le-Cao, K. -A., Lecellier, C. -H., Lee, W., Lenhard, B., Lennartsson, A., Li, K., Li, R., Lilje, B., Lipovich, L., Lizio, M., Lopez, G., Magi, S., Mak, G. K., Makeev, V., Manabe, R., Mandai, M., Mar, J., Maruyama, K., Maruyama, T., Mason, E., Mathelier, A., Matsuda, H., Medvedeva, Y. A., Meehan, T. F., Mejhert, N., Meynert, A., Mikami, N., Minoda, A., Miura, H., Miyagi, Y., Miyawaki, A., Mizuno, Y., Morikawa, H., Morimoto, M., Morioka, M., Morishita, S., Moro, K., Motakis, E., Motohashi, H., Mukarram, A. K., Mummery, C. L., Mungall, C. J., Murakawa, Y., Muramatsu, M., Nagasaka, K., Nagase, T., Nakachi, Y., Nakahara, F., Nakai, K., Nakamura, K., Nakamura, Y., Nakazawa, T., Nason, G. P., Nepal, C., Nguyen, Q. H., Nielsen, L. K., Nishida, K., Nishiguchi, K. M., Nishiyori, H., Nitta, K., Notredame, C., Ogishima, S., Ohkura, N., Ohno, H., Ohshima, M., Ohtsu, T., Okada, Y., Okada-Hatakeyama, M., Okazaki, Y., Oksvold, P., Orlando, V., Ow, G. S., Ozturk, M., Pachkov, M., Paparountas, T., Parihar, S. P., Park, S. -J., Pascarella, G., Passier, R., Persson, H., Philippens, I. H., Piazza, S., Plessy, C., Pombo, A., Ponten, F., Poulain, S., Poulsen, T. M., Pradhan, S., Prezioso, C., Pridans, C., Qin, X. -Y., Quackenbush, J., Rackham, O., Ramilowski, J., Ravasi, T., Rehli, M., Rennie, S., Rito, T., Rizzu, P., Robert, C., Roos, M., Rost, B., Roudnicky, F., Roy, R., Rye, M. B., Sachenkova, O., Saetrom, P., Sai, H., Saiki, S., Saito, M., Saito, A., Sakaguchi, S., Sakai, M., Sakaue, S., Sakaue-Sawano, A., Sandelin, A., Sano, H., Sasamoto, Y., Sato, H., Saxena, A., Saya, H., Schafferhans, A., Schmeier, S., Schmidl, C., Schmocker, D., Schneider, C., Schueler, M., Schultes, E. A., Schulze-Tanzil, G., Semple, C. A., Seno, S., Seo, W., Sese, J., Sheng, G., Shi, J., Shimoni, Y., Shin, J. W., Simonsanchez, J., Sivertsson, A., Sjostedt, E., Soderhall, C., Laurent, G. S., Stoiber, M. H., Sugiyama, D., Summers, K. M., Suzuki, A. M., Suzuki, K., Suzuki, M., Suzuki, N., Suzuki, T., Swanson, D. J., Swoboda, R. K., Taguchi, A., Takahashi, H., Takahashi, M., Takamochi, K., Takeda, S., Takenaka, Y., Tam, K. T., Tanaka, H., Tanaka, R., Tanaka, Y., Tang, D., Taniuchi, I., Tanzer, A., Tarui, H., Taylor, M. S., Terada, A., Terao, Y., Testa, A. C., Thomas, M., Thongjuea, S., Tomii, K., Triglia, E. T., Toyoda, H., Tsang, H. G., Tsujikawa, M., Uhlen, M., Valen, E., van de Wetering, M., van Nimwegen, E., Velmeshev, D., Verardo, R., Vitezic, M., Vitting-Seerup, K., von Feilitzen, K., Voolstra, C. R., Vorontsov, I. E., Wahlestedt, C., Wasserman, W. W., Watanabe, K., Watanabe, S., Wells, C. A., Winteringham, L. N., Wolvetang, E., Yabukami, H., Yagi, K., Yamada, T., Yamaguchi, Y., Yamamoto, M., Yamamoto, Y., Yamanaka, Y., Yano, K., Yasuzawa, K., Yatsuka, Y., Yo, M., Yokokura, S., Yoneda, M., Yoshida, E., Yoshida, Y., Yoshihara, M., Young, R., Young, R. S., Yu, N. Y., Yumoto, N., Zabierowski, S. E., Zhang, P. G., Zucchelli, S., Zwahlen, M., Chatelain, C., Brehelin, L., Institute of Biotechnology, Biosciences, Institut de Génétique Moléculaire de Montpellier (IGMM), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Computationnelle (IBC), Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Méthodes et Algorithmes pour la Bioinformatique (MAB), Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier (LIRMM), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), RIKEN Center for Integrative Medical Sciences [Yokohama] (RIKEN IMS), RIKEN - Institute of Physical and Chemical Research [Japon] (RIKEN), National Institute of Advanced Industrial Science and Technology (AIST), SANOFI Recherche, University of British Columbia (UBC), Experimental Immunology, Infectious diseases, AII - Infectious diseases, Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), and Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Montpellier (UM)

Subjects
0301 basic medicine, General Physics and Astronomy, Genome, Mice, 0302 clinical medicine, Transcription (biology), Promoter Regions, Genetic, Transcription Initiation, Genetic, 0303 health sciences, Multidisciplinary, 1184 Genetics, developmental biology, physiology, High-Throughput Nucleotide Sequencing, Neurodegenerative Diseases, 222 Other engineering and technologies, Genomics, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], humanities, Enhancer Elements, Genetic, Microsatellite Repeat, Transcription Initiation Site, Sequence motif, Transcription Initiation, Human, Enhancer Elements, Neural Networks, Science, 610 Medicine & health, Computational biology, Biology, Article, General Biochemistry, Genetics and Molecular Biology, Promoter Regions, 03 medical and health sciences, Computer, Deep Learning, Tandem repeat, Genetic, Clinical Research, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Machine learning, Genetics, Animals, Humans, Polymorphism, Enhancer, Transcriptomics, Gene, A549 Cell, 030304 developmental biology, Polymorphism, Genetic, Neurodegenerative Disease, Base Sequence, Animal, Genome, Human, Human Genome, Computational Biology, Promoter, General Chemistry, 113 Computer and information sciences, Cap analysis gene expression, 030104 developmental biology, [SDV.GEN.GH]Life Sciences [q-bio]/Genetics/Human genetics, Cardiovascular and Metabolic Diseases, A549 Cells, Minion, Generic health relevance, 3111 Biomedicine, Neural Networks, Computer, 610 Medizin und Gesundheit, 030217 neurology & neurosurgery, FANTOM consortium, Microsatellite Repeats
Abstract

Using the Cap Analysis of Gene Expression (CAGE) technology, the FANTOM5 consortium provided one of the most comprehensive maps of transcription start sites (TSSs) in several species. Strikingly, ~72% of them could not be assigned to a specific gene and initiate at unconventional regions, outside promoters or enhancers. Here, we probe these unassigned TSSs and show that, in all species studied, a significant fraction of CAGE peaks initiate at microsatellites, also called short tandem repeats (STRs). To confirm this transcription, we develop Cap Trap RNA-seq, a technology which combines cap trapping and long read MinION sequencing. We train sequence-based deep learning models able to predict CAGE signal at STRs with high accuracy. These models unveil the importance of STR surrounding sequences not only to distinguish STR classes, but also to predict the level of transcription initiation. Importantly, genetic variants linked to human diseases are preferentially found at STRs with high transcription initiation level, supporting the biological and clinical relevance of transcription initiation at STRs. Together, our results extend the repertoire of non-coding transcription associated with DNA tandem repeats and complexify STR polymorphism., Nature Communications, 12 (1), ISSN:2041-1723

Published
2020
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3. Supplementary Material for: L-Type Voltage-Dependent Calcium Channel Alpha Subunit 1C Is a Novel Candidate Gene Associated with Secondary Hyperparathyroidism: An Application of Haplotype-Based Analysis for Multiple Linked Single Nucleotide Polymorphisms

Author

Yokoyama, K., Urashima, M., Ohkido, I., Kono, T., Yoshida, T., Muramatsu, M., Niu, T., and Hosoya, T.

Abstract

Background and Methods: We conducted a large-scale case-control study that explored the association of 358 single nucleotide polymorphisms (SNPs) in 185 patients with end-stage renal disease. A variety of SNPs were recognized as significant in simple association studies. In addition, haplotype analysis identified the gene for the alpha 1C subunit of the voltage-dependent L-type calcium channel (CACNA1C) as having a significant association with secondary hyperparathyroidism (intact parathyroid hormone level >200 pg/ml) among 61 haplotypes. Since CACNA1C is a relatively large molecule, we examined 84 SNP markers from the CACNA1C region located on chromosome 12 by haplotype case-control association analysis. Results: Sixteen SNPs of 14 genes were significant according to allelic and/or genotypic studies (p < 0.05 by Fisher’s exact test). Three different SNPs were from the CACNA1C gene. Next, we performed haplotype-based association testing with a focus on the CACNA1C region, revealing an odds ratio (OR) of 1.63 and 95% confidence interval (CI) of 1.05–2.52. The second major haplotype with a frequency of 27% was also significant and acted as a protective haplotype (p = 0.022 by Fisher’s exact test, with an OR of 0.55 and 95% CI of 0.33–0.90). Conclusion: These results suggest that CACNA1C may be associated with secondary hyperparathyroidism. In addition, the haplotype-based approach may be useful to screen for key molecules associated with complex traits.

Published
2017
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4. Changes in the distribution pattern of gelatin-binding protein of 28 kDa (adiponectin) in myocardial remodelling after ischaemic injury

Author

Kinji Ito, Matsuo Taniyama, Toshiharu Ishii, Lijun Zhang, Yuri Akishima, Nam-Ho Choi-Miura, Muramatsu M, Motowo Tomita, Yoda-Murakami M, Motoko Ishihara, Yukio Ishikawa, and Yoshikiyo Akasaka

Subjects
Pathology, medicine.medical_specialty, Histology, biology, business.industry, Infarction, Granulation tissue, General Medicine, medicine.disease, Pathology and Forensic Medicine, Fibronectin, Lesion, Type IV collagen, medicine.anatomical_structure, biology.protein, Medicine, Immunohistochemistry, Myocardial infarction, medicine.symptom, business, Immunostaining
Abstract

Aims: Gelatin-binding protein of 28 kDa (GBP28) is a collagen-like plasma protein having a binding capacity with collagens. We investigated GBP28 role on myocardial remodelling as well as the diagnostic significance of GBP28 immunostaining in myocardial infarction. Methods and results: Myocardial tissues obtained from 47 autopsied hearts with infarction were immunostained with antibodies against GBP28, fibronectin, type III and IV collagens, and prolyl 4-hydroxylase. GBP28 was distributed in interstitium of infarcted lesions at an early stage. GBP28 was linearly found both along the border with vital myocardium and at the periphery of surviving cardiomyocyte around the lesion at granulative stage. However, it was not observed in the scar. GBP28 distribution patterns were similar to those of fibronectin in infarcted lesions and those of type IV collagen at the periphery of cardiomyocyte. Type III collagen was not recognized in the early-stage lesion but increased along with scar maturation. Prolyl 4-hydroxylase was found in surviving cardiomyocytes around the lesion during all stages and in interstitial cells appeared in granulation tissue. Conclusion: GBP28 plays a role as a scaffold of newly formed collagen in myocardial remodelling after ischaemic injury, and GBP28 immunostaining may assist in a diagnosis of healing stage.

Published
2002
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5. Cancer-associated myofibroblasts possess various factors to promote endometrial tumor progression

Author

Akira Orimo, Tomioka Y, Shimizu Y, Sato M, Oigawa S, Kamata K, Nogi Y, Inoue S, Takahashi M, Hata T, and Muramatsu M

Subjects
Adult, Vascular Endothelial Growth Factor Receptor-1, Estrogen Receptor alpha, Receptor Protein-Tyrosine Kinases, Cell Cycle Proteins, Muscle, Smooth, Middle Aged, Hypoxia-Inducible Factor 1, alpha Subunit, Immunohistochemistry, Endometrial Neoplasms, Ki-67 Antigen, Receptors, Vascular Endothelial Growth Factor, Receptors, Estrogen, Proliferating Cell Nuclear Antigen, Proto-Oncogene Proteins, Humans, Female, Receptors, Growth Factor, Growth Substances, Aged, Transcription Factors
Abstract

Myofibroblastic invasion associated with malignant epithelial cells of endometrial cancer as well as other cancers is often found in the interstitium. To assess the myofibroblastic-epithelial interaction, frozen sections from a total of 10 endometrial cancers with or without invasive myofibroblasts were immunohistochemically examined. Interestingly, the invasive myofibroblasts adjacent to malignant epithelial cells showed frequently intensive positive staining of several growth factors such as vascular endothelial growth factor (VEGF), insulin-like growth factor I, and epidermal growth factor, the cognate receptors such as Fetal liver kinase-1/Kinase Insert Domain-containing receptor/VEGF receptor-2, fms-like tyrosine kinase-1/VEGF receptor-1, and epidermal growth factor receptor, several cell cycle regulators such as cyclins and cyclin dependent kinases, and estrogen receptor alpha. Moreover, we indicated that the majority of the myofibroblasts as well as cancer epithelial cells are proliferating because of their positive staining of proliferating cell nuclear antigen and Ki-67. Furthermore, the myofibroblasts were also positive of hypoxia-inducible factor 1 alpha, which is a marker protein of hypoxia, probably followed by activation of VEGF-Flk-1 and VEGF-fms-like tyrosine kinase-1 signals, which could initiate angiogenesis. These findings suggest directly that the myofibroblasts might participate in the progression of tumor cells in terms of cancer cell growth stimulation and also activated initiation of angiogenesis.

Published
2001

6. [X-linked sideroblastic anemia]

Author

Muramatsu M, Usuki K, Koji Izutsu, Yamaguchi Y, Iki S, Furuyama K, Kondo M, and Urabe A

Subjects
Adult, Male, X Chromosome, Genetic Linkage, Humans, Anemia, Sideroblastic, Pedigree
Abstract

A 20-year-old man presented with microcytic hypochromic anemia (hemoglobin: 9.3 g/dl, MCV: 82.0 fl, MCHC: 29.5 g/dl) and dimorphism RBCs in circulating blood (RDW: 26.8%). Ringed sideroblasts accounted for 29.5% of bone marrow erythroblasts. Iron overload was also observed. Because the patient had a clear family history of anemia, he was given a diagnosis of X-linked sideroblastic anemia. The activity of delta-aminolevulinic acid synthase (ALAS) in bone marrow erythroblasts was low. However, we did not detect mutation of the gene for ALAS. The patient has responded well to a treatment regimen consisting of oral vitamin B6, Fe-chelation therapy, and phlebotomy.

Published
1999

7. Genome Symbols in the Triticeae (Poaceae)

Author

Wang, R. R-C., von Bothmer, R., Dvorak, J., Fedak, G., Linde-Laursen, I., and Muramatsu, M.

Subjects
nuclear genome symbols, Psathyrostachys, genome symbols, triticeae (poaceae), Life Sciences, Hordeum murinum, Hordeum pusillum
Abstract

A system for the application of nuclear genome symbols in the tribe Triticeae is proposed. It is based mainly on prevailing symbols. In agreement with this, the system uses individual upper case letters as symbols in the first place. Since the number of basic nuclear genomes in the Triticeae exceeds the number of single letters in the Roman alphabet, some basic genomes are designated with an upper case letter followed by a lower case letter, e.g. Ns for the genome of Psathyrostachys. Superscripts in small letters are used when modified versions of a basic genome are referred to, e.g. HP for the genome found in Hordeum pusillum. Unknown or equivocally identified genomes are designated by X followed by a lower case letter, e.g. Xu for Hordeum murinum. Underline of the relevant genome symbol can be used to indicate the origin of the cytoplasm.

Published
1994

11. Advances in phase-stepping real-time holography using photorefractive sillenite crystals

Author

Marcos Gesualdi, Barbosa, E. A., Muramatsu, M., Universidade do Vale do Paraiba, Universidade Estadual Paulista (UNESP), and Universidade de São Paulo (USP)

Subjects
Phase shifting, Interferometry, Holography
Abstract

Made available in DSpace on 2022-04-28T18:55:17Z (GMT). No. of bitstreams: 0 Previous issue date: 2006-01-01 This work presents a review of recent developments in phase-stepping real-time holographic interferometry with photorefractive sillenite crystals. Quantitative results are shown in micro-rotation, micro-displacement, and microdeformation measurements, and in wave-optics and surface analysis as well. The phase stepping was carried out in a four-frame process and the resulting phase map was unwrapped by applying a sin/cos filter. The experimental results are in good agreement with the ones obtained through other means, showing the promising potentialities of phase-stepping real-time holographic interferometry for in situ visualisation, monitoring and analysis in non-destructive testing. Institute de Pesquisa e Desenolvimento Universidade do Vale do Paraiba, Av. Shishima Hifumi, 2911, Sao Jose dos Campos - SP Laboratório de Óptica Aplicada Faculdade de Tecnologia de São Paulo CEETEPS-UNESP, Pça Cel Fernando Prestes, 30, CEP 01124 060, São Paulo - SP Instituto de Fisica Universidade de São Paulo Cid. Universitaria, Rua do Matão, Travessa R, 187, CEP 05508-900, Sao Paulo - SP Laboratório de Óptica Aplicada Faculdade de Tecnologia de São Paulo CEETEPS-UNESP, Pça Cel Fernando Prestes, 30, CEP 01124 060, São Paulo - SP

12. Identification of an enhancer responsible for tumor marker gene expression by means of transgenic rats

Author

Suzuki, T., Imagawa, M., Hirabayashi, M., Yuki, A., Koji Hisatake, Nomura, K., Kitagawa, T., and Muramatsu, M.

Subjects
Chloramphenicol O-Acetyltransferase, Male, Base Sequence, Molecular Sequence Data, Restriction Mapping, Gene Expression Regulation, Enzymologic, Rats, Animals, Genetically Modified, Gene Expression Regulation, Neoplastic, Isoenzymes, Enhancer Elements, Genetic, Liver Neoplasms, Experimental, Liver, Reference Values, Biomarkers, Tumor, Animals, Diethylnitrosamine, Glutathione Transferase
Abstract

The glutathione transferase P (GST-P) gene is known for its specific expression during chemical hepatocarcinogenesis of the rat and is used as a tumor marker for hepatocellular carcinoma. We have shown recently that the upstream 2.9-kb region of the GST-P gene is sufficient for conferring tumor-specific expression of the gene in vivo (S. Morimura et al., Proc. Natl. Acad. Sci. USA, 90: 2065-2068, 1993). To further identify crucial sequence elements regulating the unique expression of this gene, we have established six independent lines of transgenic rats bearing distinct areas of the GST-P gene that are connected to the chloramphenicol acetyltransferase coding region and analyzed changes of the chloramphenicol acetyltransferase activity during the course of chemical hepatocarcinogenesis. We demonstrate here that the enhancer, glutathione transferase P enhancer I, that is located 2.5 kb upstream of the GST-P gene is required and sufficient for its tumor-specific expression of the gene among other controlling elements. This approach to transgene expression could be used to define other enhancers, the activity of which is dependent on cellular changes such as carcinogenesis, development, and differentiation.

15. Recent progress and future plan of heavy-ion radiotherapy facility, HIMAC

Author

Noda, K., Furukawa, T., Hara, Y., Inaniwa, T., Iwata, Y., Katagiri, K., Kanematsu, N., Kitagawa, A., Kota Mizushima, Mori, S., Murakami, T., Muramatsu, M., Nakao, M., Noda, A., Sato, S., Shirai, T., Takada, E., and Takei, Y.

Abstract

The carbon-ion radiotherapy (RT) with HIMAC has been conducted since 1994, and the accumulated treatment number exceeded 9,000 in May 2014. During the last two decades, NIRS has developed both the accelerator and beam-delivery technologies related to the carbon-ion RT, which has brought several carbon-ion RT facilities in Japan. At present, NIRS has developed a carbon-ion rotating gantry with the superconducting technology to be operated from 2016. As the future plan, NIRS has developed a direct acceleration system of positron-emission beams for verification on an irradiation field, and NIRS also just starts a design study of a superconducting synchrotron ring for carbon-ion RT.

16. Remodelación ósea a través del Modelo de Stanford

Author

Henry Figueredo Losada, González-Fernández, V., Batista-Aguiar, J., Muramatsu, M., and Felipe-Garmendia, Á M.

Subjects
Bone remodelling, Remodelación ósea, lcsh:Mechanical engineering and machinery, Jacob´s model, biomecánica, elementos finitos, biomechanic, lcsh:TJ1-1570, finite elements method
Abstract

El material óseo es radicalmente distinto a cualquier otro material tratado por la mecánica clásica, su estructura es heterogénea y anisótropa, y sus propiedades mecánicas varían no solo entre distintos individuos, sino también, para un mismo hueso En los tratamientos e intervenciones quirúrgicas donde está presente la readaptación, el crecimiento inducido del hueso puede ser modelado mediante el empleo de los criterios de remodelación ósea interna propuesto por algunos autores (Cowin y R. Huiskes, R. Carter, Doblare y García, Jacob y Beaupré y otros).En este trabajo se toma el modelo de remodelación ósea propuesto por Jacob (1994) y se implementa con la utilización del programa Abaqus 6.4 utilizando una subrutina de usuario (UMAT), se aplico a un modelo 2D de hueso genérico con un sistema de cargas para comprobar los efectos de la remodelación y las variaciones de los valores de densidad. Como parte del trabajo fueron creados dos programas para el procesamiento de los datos, para un análisis de resultados fuera del visualizador del Abaqus, logrando una apreciación cualitativamente y cuantitativamente de los resultados. The bone material is radically different to any other material tried by the classic mechanics, its structure is heterogeneous and anisótropic, and its mechanical properties not vary alone among different individuals, but also, for oneself bone In the medical treatments and surgical interventions where it is present the readaptation, the induced growth of the bone can be modeled by means of the employment of the approaches of remodeling bone intern proposed by some authors (Cowin and R. Huiskes, R. Crankcase, I will Doblare & García, Jacob & Beaupré and other).In this work it takes the pattern of bone remodelling proposed by Jacob (1994) and it is implemented with the use of the software Abaqus using user's subroutine (UMAT), its applies a model 2D of generic bone with a system of loads to check the effects of the remodelling and the variations of the values of density. As part of the work two software were created for the prosecution of the data, for an analysis of results outside of the visualizador of the Abaqus, achieving a qualitative and quantitative appreciation of the result.

17. Development for new carbon cancer-therapy facility and future plan of HIMAC

Author

Noda, K., Fujisawa, T., Furukawa, T., Iwata, Y., Kanai, T., Kanazawa, M., Kanematsu, N., Kitagawa, A., Kobayashi, Y., Komori, M., Minohara, S., Murakami, T., Muramatsu, M., Sato, S., Takada, E., Torikoshi, M., Yoshida, K., Yamada, S., Sato, Y., Mutsumi Tashiro, Yusa, K., Kobayashi, C., Shibuya, S., Takahashi, O., and Tsubuku, H.

23. Site-directed mutagenesis of human glutathione transferase P1-1: Spectral, kinetic, and structural properties of Cys-47 and Lys-54 mutants

Author

Lo Bello, M., Battistoni, A., Mazzetti, A. P., Board, P. G., Muramatsu, M., Federici, G., and Giorgio Ricci

Subjects
Protein Conformation, glutathione transferase, amino acid sequence, amino acid substitution, article, enzyme kinetics, enzyme specificity, enzyme structure, human, priority journal, site directed mutagenesis, Base Sequence, Cysteine, Enzyme Stability, Glutathione Transferase, Human, Hydrolysis, Isoenzymes, Kinetics, Lysine, Molecular Sequence Data, Mutagenesis, Site-Directed, Oligodeoxyribonucleotides, Spectrophotometry, Ultraviolet, Support, Non-U.S. Gov't, Site-Directed, Settore BIO/10, Non-U.S. Gov't, Ultraviolet, Mutagenesis, Spectrophotometry, Support

24. An electro-chemo-mechanical analysis of solid oxide fuel cell considering evolution of microstructure in porous electrode using phase-field method

Author

Muramatsu, M., Takase, S., Keiji Yashiro, Kawada, T., and Terada, K.

Subjects
Finite element method, Solid Oxide Fuel Cells, Potential Simulation, Stress Analysis, Microstructure, Elements finits, Mètode dels, Coupled problems (Complex systems) -- Numerical solutions, Matemàtiques i estadística::Anàlisi numèrica::Mètodes en elements finits [Àrees temàtiques de la UPC]
Abstract

For the numerical simulation of oxygen potential distributions in Solid Oxide Fuel Cell (SOFC), the time-evolution of the anode microstructure is reflected in the macroscopic electrical conductivities and the amount of triple-phase boundaries. Once the oxygen potential distributions are determined, the time-variation of the reduction-induced strains due to nonstoichiometry of oxide materials is calculated along with the thermal strains. These strains cause the macroscopic stresses in mutually constrained components. Thus, the capability of the proposed method is demonstrated in characterizing the aging degradation of the macroscopic electro-chemo-mechanical behavior of SOFC that is caused by the Nisintering in cermet microstructures during long-period control.

25. Nomenclature for human glutathione transferases [1]

Author

Mannervik, B., Awasthi, Y. C., Board, P. G., Hayes, J. D., Di Ilio, C., Ketterer, B., Listowsky, I., Morgenstern, R., Muramatsu, M., William Pearson, Pickett, C. B., Sato, K., Widersten, M., and Wolf, C. R.

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