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344 results on '"Masuya, Hiroshi"'

1. Large Slope Disaster at Hakusan District in Japan and Estimation of Risk by Rockfall

Author

Masuya, Hiroshi, Fuji, Takanari, Kurihashi, Yusuke, di Prisco, Marco, Series Editor, Chen, Sheng-Hong, Series Editor, Vayas, Ioannis, Series Editor, Kumar Shukla, Sanjay, Series Editor, Sharma, Anuj, Series Editor, Kumar, Nagesh, Series Editor, Wang, Chien Ming, Series Editor, Cui, Zhen-Dong, Series Editor, Duc Long, Phung, editor, and Dung, Nguyen Tien, editor

Published
2024
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2. Antibiotic-dependent instability of homeostatic plasticity for growth and environmental load

Author

Okada, Shunnosuke, Inabu, Yudai, Miyamoto, Hirokuni, Suzuki, Kenta, Kato, Tamotsu, Kurotani, Atsushi, Taguchi, Yutaka, Fujino, Ryoichi, Shiotsuka, Yuji, Etoh, Tetsuji, Tsuji, Naoko, Matsuura, Makiko, Tsuboi, Arisa, Saito, Akira, Masuya, Hiroshi, Kikuchi, Jun, Ohno, Hiroshi, and Takahashi, Hideyuki

Subjects
Quantitative Biology - Quantitative Methods
Abstract

Reducing antibiotic usage in livestock animals has become an urgent issue worldwide to prevent antimicrobial resistance. Here, abuse of chlortetracycline (CTC), a versatile antibacterial agent, on the performance, blood components, fecal microbiota, and organic acid concentration in calves was investigated. Japanese Black calves were fed milk replacer containing CTC at 10 g/kg (CON) or 0 g/kg (EXP). Growth performance was not affected by CTC administration. However, CTC administration altered the correlation between fecal organic acids and bacterial genera. Machine learning methods such as association analysis, linear discriminant analysis, and energy landscape analysis revealed that CTC administration affected according to certain rules the population of various types of fecal bacteria. It is particularly interesting that the population of several methane-producing bacteria was high in the CON, and that of Lachnospiraceae, a butyrate-producing bacteria, was high in the EXP at 60 d of age. Furthermore, statistical causal inference based on machine learning data estimated that CTC treatment affects the entire intestinal environment, inhibiting butyrate production for growth and biological defense, which may be attributed to methanogens in feces. Thus, these observations highlight the multiple harmful impacts of antibiotics on intestinal health and the potential production of greenhouse gas in the calves.

Published
2022
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3. Estimation of symbiotic bacterial structure in a sustainable seagrass ecosystem on recycled management

Author

Miyamoto, Hirokuni, Kawachi, Nobuhiro, Kurotani, Atsushi, Moriya, Shigeharu, Suda, Wataru, Suzuki, Kenta, Matsuura, Makiko, Tsuji, Naoko, Nakaguma, Teruno, Ishii, Chitose, Tsuboi, Arisa, Shindo, Chie, Kato, Tamotsu, Udagawa, Motoaki, Satoh, Takashi, Wada, Satoshi, Masuya, Hiroshi, Miyamoto, Hisashi, Ohno, Hiroshi, and Kikuchi, Jun

Subjects
Quantitative Biology - Populations and Evolution
Abstract

Seagrass meadows play an essential role in blue carbon and aquatic ecosystem services. However, methods for the flourishing of seagrass are still being explored. Here, data from 49 public coastal surveys on the distribution of seagrass and seaweed around the onshore aquaculture facilities are revalidated, and an exceptional area where the seagrass Zostera marina thrives was found. The bacterial population there showed an apparent decrease in the pathogen candidates belonging to the order Flavobacteriales. Moreover, structure equation modeling and a linear non-Gaussian acyclic model based on the machine learning data estimated an optimal symbiotic bacterial group candidate for seagrass growth as follows: the Lachnospiraceae and Ruminococcaceae families as gut-inhabitant bacteria, Rhodobacteraceae as photosynthetic bacteria, and Desulfobulbaceae as cable bacteria modulating oxygen or nitrate reduction and oxidation of sulfide. These observations confer a novel perspective on the seagrass symbiotic bacterial structures critical for blue carbon and low-pathogenic marine ecosystems in aquaculture., Comment: 54 pages, 3 figures, 16 supporting information

Published
2022
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5. Estimation of silent phenotypes of calf antibiotic dysbiosis

Author

Okada, Shunnosuke, Inabu, Yudai, Miyamoto, Hirokuni, Suzuki, Kenta, Kato, Tamotsu, Kurotani, Atsushi, Taguchi, Yutaka, Fujino, Ryoichi, Shiotsuka, Yuji, Etoh, Tetsuji, Tsuji, Naoko, Matsuura, Makiko, Tsuboi, Arisa, Saito, Akira, Masuya, Hiroshi, Kikuchi, Jun, Nagasawa, Yuya, Hirose, Aya, Hayashi, Tomohito, Ohno, Hiroshi, and Takahashi, Hideyuki

Published
2023
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6. Development of Semantic Web-based Imaging Database for Biological Morphome

Author

Kume, Satoshi, Masuya, Hiroshi, Maeda, Mitsuyo, Suga, Mitsuo, Kataoka, Yosky, and Kobayashi, Norio

Subjects
Quantitative Biology - Quantitative Methods, Computer Science - Artificial Intelligence, Computer Science - Computer Vision and Pattern Recognition, Computer Science - Databases, Electrical Engineering and Systems Science - Image and Video Processing
Abstract

We introduce the RIKEN Microstructural Imaging Metadatabase, a semantic web-based imaging database in which image metadata are described using the Resource Description Framework (RDF) and detailed biological properties observed in the images can be represented as Linked Open Data. The metadata are used to develop a large-scale imaging viewer that provides a straightforward graphical user interface to visualise a large microstructural tiling image at the gigabyte level. We applied the database to accumulate comprehensive microstructural imaging data produced by automated scanning electron microscopy. As a result, we have successfully managed vast numbers of images and their metadata, including the interpretation of morphological phenotypes occurring in sub-cellular components and biosamples captured in the images. We also discuss advanced utilisation of morphological imaging data that can be promoted by this database.

Published
2021
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7. Development of an Ontology for an Integrated Image Analysis Platform to enable Global Sharing of Microscopy Imaging Data

Author

Kume, Satoshi, Masuya, Hiroshi, Kataoka, Yosky, and Kobayashi, Norio

Subjects
Computer Science - Digital Libraries, Electrical Engineering and Systems Science - Image and Video Processing, Quantitative Biology - Quantitative Methods
Abstract

Imaging data is one of the most important fundamentals in the current life sciences. We aimed to construct an ontology to describe imaging metadata as a data schema of the integrated database for optical and electron microscopy images combined with various bio-entities. To realise this, we applied Resource Description Framework (RDF) to an Open Microscopy Environment (OME) data model, which is the de facto standard to describe optical microscopy images and experimental data. We translated the XML-based OME metadata into the base concept of RDF schema as a trial of developing microscopy ontology. In this ontology, we propose 18 upper-level concepts including missing concepts in OME such as electron microscopy, phenotype data, biosample, and imaging conditions.

Published
2021

15. Identification of genetic elements in metabolism by high-throughput mouse phenotyping

Author

Rozman, Jan, Rathkolb, Birgit, Oestereicher, Manuela A, Schütt, Christine, Ravindranath, Aakash Chavan, Leuchtenberger, Stefanie, Sharma, Sapna, Kistler, Martin, Willershäuser, Monja, Brommage, Robert, Meehan, Terrence F, Mason, Jeremy, Haselimashhadi, Hamed, IMPC Consortium, Hough, Tertius, Mallon, Ann-Marie, Wells, Sara, Santos, Luis, Lelliott, Christopher J, White, Jacqueline K, Sorg, Tania, Champy, Marie-France, Bower, Lynette R, Reynolds, Corey L, Flenniken, Ann M, Murray, Stephen A, Nutter, Lauryl MJ, Svenson, Karen L, West, David, Tocchini-Valentini, Glauco P, Beaudet, Arthur L, Bosch, Fatima, Braun, Robert B, Dobbie, Michael S, Gao, Xiang, Herault, Yann, Moshiri, Ala, Moore, Bret A, Kent Lloyd, KC, McKerlie, Colin, Masuya, Hiroshi, Tanaka, Nobuhiko, Flicek, Paul, Parkinson, Helen E, Sedlacek, Radislav, Seong, Je Kyung, Wang, Chi-Kuang Leo, Moore, Mark, Brown, Steve D, Tschöp, Matthias H, Wurst, Wolfgang, Klingenspor, Martin, Wolf, Eckhard, Beckers, Johannes, Machicao, Fausto, Peter, Andreas, Staiger, Harald, Häring, Hans-Ulrich, Grallert, Harald, Campillos, Monica, Maier, Holger, Fuchs, Helmut, Gailus-Durner, Valerie, Werner, Thomas, and Hrabe de Angelis, Martin

Subjects
Biochemistry and Cell Biology, Bioinformatics and Computational Biology, Genetics, Biological Sciences, Nutrition, Human Genome, Aetiology, 2.1 Biological and endogenous factors, Animals, Area Under Curve, Basal Metabolism, Blood Glucose, Body Weight, Diabetes Mellitus, Type 2, Gene Regulatory Networks, Genome-Wide Association Study, High-Throughput Screening Assays, Humans, Metabolic Diseases, Mice, Mice, Knockout, Obesity, Oxygen Consumption, Phenotype, Triglycerides, IMPC Consortium
Abstract

Metabolic diseases are a worldwide problem but the underlying genetic factors and their relevance to metabolic disease remain incompletely understood. Genome-wide research is needed to characterize so-far unannotated mammalian metabolic genes. Here, we generate and analyze metabolic phenotypic data of 2016 knockout mouse strains under the aegis of the International Mouse Phenotyping Consortium (IMPC) and find 974 gene knockouts with strong metabolic phenotypes. 429 of those had no previous link to metabolism and 51 genes remain functionally completely unannotated. We compared human orthologues of these uncharacterized genes in five GWAS consortia and indeed 23 candidate genes are associated with metabolic disease. We further identify common regulatory elements in promoters of candidate genes. As each regulatory element is composed of several transcription factor binding sites, our data reveal an extensive metabolic phenotype-associated network of co-regulated genes. Our systematic mouse phenotype analysis thus paves the way for full functional annotation of the genome.

Published
2018

18. Prevalence of sexual dimorphism in mammalian phenotypic traits

Author

Karp, Natasha A, Mason, Jeremy, Beaudet, Arthur L, Benjamini, Yoav, Bower, Lynette, Braun, Robert E, Brown, Steve DM, Chesler, Elissa J, Dickinson, Mary E, Flenniken, Ann M, Fuchs, Helmut, Angelis, Martin Hrabe de, Gao, Xiang, Guo, Shiying, Greenaway, Simon, Heller, Ruth, Herault, Yann, Justice, Monica J, Kurbatova, Natalja, Lelliott, Christopher J, Lloyd, KC Kent, Mallon, Ann-Marie, Mank, Judith E, Masuya, Hiroshi, McKerlie, Colin, Meehan, Terrence F, Mott, Richard F, Murray, Stephen A, Parkinson, Helen, Ramirez-Solis, Ramiro, Santos, Luis, Seavitt, John R, Smedley, Damian, Sorg, Tania, Speak, Anneliese O, Steel, Karen P, Svenson, Karen L, Wakana, Shigeharu, West, David, Wells, Sara, Westerberg, Henrik, Yaacoby, Shay, and White, Jacqueline K

Subjects
Biological Psychology, Biological Sciences, Biomedical and Clinical Sciences, Psychology, Genetics, Animals, Body Weight, Female, Genes, Modifier, Genotype, Mammals, Mice, Phenotype, Quantitative Trait, Heritable, Sex Characteristics, International Mouse Phenotyping Consortium
Abstract

The role of sex in biomedical studies has often been overlooked, despite evidence of sexually dimorphic effects in some biological studies. Here, we used high-throughput phenotype data from 14,250 wildtype and 40,192 mutant mice (representing 2,186 knockout lines), analysed for up to 234 traits, and found a large proportion of mammalian traits both in wildtype and mutants are influenced by sex. This result has implications for interpreting disease phenotypes in animal models and humans.

Published
2017

21. Applying the ARRIVE Guidelines to an In Vivo Database.

Author

Karp, Natasha A, Meehan, Terry F, Morgan, Hugh, Mason, Jeremy C, Blake, Andrew, Kurbatova, Natalja, Smedley, Damian, Jacobsen, Julius, Mott, Richard F, Iyer, Vivek, Matthews, Peter, Melvin, David G, Wells, Sara, Flenniken, Ann M, Masuya, Hiroshi, Wakana, Shigeharu, White, Jacqueline K, Lloyd, KC Kent, Reynolds, Corey L, Paylor, Richard, West, David B, Svenson, Karen L, Chesler, Elissa J, de Angelis, Martin Hrabě, Tocchini-Valentini, Glauco P, Sorg, Tania, Herault, Yann, Parkinson, Helen, Mallon, Ann-Marie, and Brown, Steve DM

Subjects
Animals, Mice, Animal Experimentation, Phenotype, Guidelines as Topic, Databases as Topic, Developmental Biology, Biological Sciences, Agricultural and Veterinary Sciences, Medical and Health Sciences
Abstract

The Animal Research: Reporting of In Vivo Experiments (ARRIVE) guidelines were developed to address the lack of reproducibility in biomedical animal studies and improve the communication of research findings. While intended to guide the preparation of peer-reviewed manuscripts, the principles of transparent reporting are also fundamental for in vivo databases. Here, we describe the benefits and challenges of applying the guidelines for the International Mouse Phenotyping Consortium (IMPC), whose goal is to produce and phenotype 20,000 knockout mouse strains in a reproducible manner across ten research centres. In addition to ensuring the transparency and reproducibility of the IMPC, the solutions to the challenges of applying the ARRIVE guidelines in the context of IMPC will provide a resource to help guide similar initiatives in the future.

Published
2015

23. Development of Semantic Web-Based Imaging Database for Biological Morphome

Author

Kume, Satoshi, Masuya, Hiroshi, Maeda, Mitsuyo, Suga, Mitsuo, Kataoka, Yosky, Kobayashi, Norio, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Wang, Zhe, editor, Turhan, Anni-Yasmin, editor, Wang, Kewen, editor, and Zhang, Xiaowang, editor

Published
2017
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24. Semantic Graph Analysis for Federated LOD Surfing in Life Sciences

Author

Yamaguchi, Atsuko, Kozaki, Kouji, Yamamoto, Yasunori, Masuya, Hiroshi, Kobayashi, Norio, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Wang, Zhe, editor, Turhan, Anni-Yasmin, editor, Wang, Kewen, editor, and Zhang, Xiaowang, editor

Published
2017
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27. Computational estimation of sediment symbiotic bacterial structures of seagrasses overgrowing downstream of onshore aquaculture

Author

Miyamoto, Hirokuni, primary, Kawachi, Nobuhiro, additional, Kurotani, Atsushi, additional, Moriya, Shigeharu, additional, Suda, Wataru, additional, Suzuki, Kenta, additional, Matsuura, Makiko, additional, Tsuji, Naoko, additional, Nakaguma, Teruno, additional, Ishii, Chitose, additional, Tsuboi, Arisa, additional, Shindo, Chie, additional, Kato, Tamotsu, additional, Udagawa, Motoaki, additional, Satoh, Takashi, additional, Wada, Satoshi, additional, Masuya, Hiroshi, additional, Miyamoto, Hisashi, additional, Ohno, Hiroshi, additional, and Kikuchi, Jun, additional

Published
2023
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28. Semantic Data Acquisition by Traversing Class–Class Relationships Over Linked Open Data

Author

Yamaguchi, Atsuko, Kozaki, Kouji, Lenz, Kai, Yamamoto, Yasunori, Masuya, Hiroshi, Kobayashi, Norio, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Li, Yuan-Fang, editor, Hu, Wei, editor, Dong, Jin Song, editor, Antoniou, Grigoris, editor, Wang, Zhe, editor, Sun, Jun, editor, and Liu, Yang, editor

Published
2016
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29. RIKEN MetaDatabase: A Database Platform as a Microcosm of Linked Open Data Cloud in the Life Sciences

Author

Kobayashi, Norio, Lenz, Kai, Masuya, Hiroshi, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Li, Yuan-Fang, editor, Hu, Wei, editor, Dong, Jin Song, editor, Antoniou, Grigoris, editor, Wang, Zhe, editor, Sun, Jun, editor, and Liu, Yang, editor

Published
2016
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36. Development of Linked Open Data for Bioresources

Author

Masuya, Hiroshi, Takatsuki, Terue, Makita, Yuko, Yoshida, Yuko, Mochizuki, Yoshiki, Kobayashi, Norio, Yoshiki, Atsushi, Nakamura, Yukio, Toyoda, Tetsuro, Obata, Yuichi, Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Doug, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Takeda, Hideaki, editor, Qu, Yuzhong, editor, Mizoguchi, Riichiro, editor, and Kitamura, Yoshinobu, editor

Published
2013
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40. Principles and application of LIMS in mouse clinics

Author

Maier, Holger, Schütt, Christine, Steinkamp, Ralph, Hurt, Anja, Schneltzer, Elida, Gormanns, Philipp, Lengger, Christoph, Griffiths, Mark, Melvin, David, Agrawal, Neha, Alcantara, Rafael, Evans, Arthur, Gannon, David, Holroyd, Simon, Kipp, Christian, Raj, Navis Pretheeba, Richardson, David, LeBlanc, Sophie, Vasseur, Laurent, Masuya, Hiroshi, Kobayashi, Kimio, Suzuki, Tomohiro, Tanaka, Nobuhiko, Wakana, Shigeharu, Walling, Alison, Clary, David, Gallegos, Juan, Fuchs, Helmut, de Angelis, Martin Hrabě, and Gailus-Durner, Valerie

Published
2015
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41. Chemical-Mediated Microbial Interactions Can Reduce the Effectiveness of Time-Series-Based Inference of Ecological Interaction Networks

Author

Suzuki, Kenta, primary, Abe, Masato S., additional, Kumakura, Daiki, additional, Nakaoka, Shinji, additional, Fujiwara, Fuki, additional, Miyamoto, Hirokuni, additional, Nakaguma, Teruno, additional, Okada, Mashiro, additional, Sakurai, Kengo, additional, Shimizu, Shohei, additional, Iwata, Hiroyoshi, additional, Masuya, Hiroshi, additional, Nihei, Naoto, additional, and Ichihashi, Yasunori, additional

Published
2022
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42. A Potential Symbiotic Sediment Bacterial Structure That Contributes to Seagrass Growth Downstream of Onshore Aquaculture

Author

Miyamoto, Hirokuni, primary, Kawachi, Nobuhiro, additional, Kurotani, Atsushi, additional, Moriya, Shigeharu, additional, Suda, Wataru, additional, Suzuki, Kenta, additional, Matsuura, Makiko, additional, Tsuji, Naoko, additional, Nakaguma, Teruno, additional, Ishii, Chitose, additional, Tsuboi, Arisa, additional, Shindo, Chie, additional, Kato, Tamotsu, additional, Udagawa, Motoaki, additional, Satoh, Takashi, additional, Wada, Satoshi, additional, Masuya, Hiroshi, additional, Miyamoto, Hisashi, additional, Ohno, Hiroshi, additional, and Kikuchi, Jun, additional

Published
2022
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46. MoG+: a database of genomic variations across three mouse subspecies for biomedical research

Author

Takada, Toyoyuki, primary, Fukuta, Kentaro, additional, Usuda, Daiki, additional, Kushida, Tatsuya, additional, Kondo, Shinji, additional, Kawamoto, Shoko, additional, Yoshiki, Atsushi, additional, Obata, Yuichi, additional, Fujiyama, Asao, additional, Toyoda, Atsushi, additional, Noguchi, Hideki, additional, Shiroishi, Toshihiko, additional, and Masuya, Hiroshi, additional

Published
2021
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48. Long-term Application of Carbon Fiber Composite Cable Tendon in the Prestressed Concrete Bridge-Shinmiya Bridge in Japan

Author

Nguyen Hue Thi, Masuya Hiroshi, Ha Tuan Minh, Fukada Saiji, Hanaoka Daishin, Kobayashi Kazuhiro, and Koida Eiji

Subjects
Engineering (General). Civil engineering (General), TA1-2040
Abstract

Carbon fiber reinforced plastic (Carbon Fiber Composite Cable, CFCC) has the outstanding features in comparison with regular steel. In October 1988, CFCC was applied as the tensioning material in main girders of new Shinmiya Bridge in Ishikawa, Japan. This was the first bridge in Japan and in the world, which CFCC tendons were used in the prestressed concrete bridge to counter salt damage. To investigate the serviceability and durability of the main girders and CFCC, three full-scale test girders were fabricated in 1988. At the same time, a bending experiment was conducted on one girder to investigate the ultimate behavior, load carrying capacity of the PC girder, as well the strain behavior of the CFCC. Besides, two PC girders were placed next to the main girders of the bridge in the same conditions. One of them was used for a destructive test after six years of the construction time (1994). In this study, another test specimen that was exposed to the actual corrosive environment after nearly 30 years was subjected to a destructive test by bending load. The load carrying capacity of the girder was clarified, and the durability of the PC girders using CFCC tendon was confirmed.

Published
2018
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49. Mouse resources at the RIKEN BioResource Research Center and the National BioResource Project core facility in Japan

Author

Mizuno-Iijima, Saori, primary, Nakashiba, Toshiaki, additional, Ayabe, Shinya, additional, Nakata, Hatsumi, additional, Ike, Fumio, additional, Hiraiwa, Noriko, additional, Mochida, Keiji, additional, Ogura, Atsuo, additional, Masuya, Hiroshi, additional, Kawamoto, Shoko, additional, Tamura, Masaru, additional, Obata, Yuichi, additional, Shiroishi, Toshihiko, additional, and Yoshiki, Atsushi, additional

Published
2021
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