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759 results on '"Shiroishi, Toshihiko"'

1. Improving laboratory animal genetic reporting: LAG-R guidelines.

Author

Teboul, Lydia, Amos-Landgraf, James, Benavides, Fernando, Birling, Marie-Christine, Brown, Steve, Bryda, Elizabeth, Bunton-Stasyshyn, Rosie, Chin, Hsian-Jean, Crispo, Martina, Delerue, Fabien, Dobbie, Michael, Franklin, Craig, Fuchtbauer, Ernst-Martin, Gao, Xiang, Golzio, Christelle, Haffner, Rebecca, Hérault, Yann, Hrabe de Angelis, Martin, Lloyd, Kevin, Magnuson, Terry, Montoliu, Lluis, Murray, Stephen, Nam, Ki-Hoan, Nutter, Lauryl, Pailhoux, Eric, Pardo Manuel de Villena, Fernando, Peterson, Kevin, Reinholdt, Laura, Sedlacek, Radislav, Seong, Je, Shiroishi, Toshihiko, Smith, Cynthia, Takeo, Toru, Tinsley, Louise, Vilotte, Jean-Luc, Warming, Søren, Wells, Sara, Whitelaw, C, Yoshiki, Atsushi, and Pavlovic, Guillaume

Subjects
Animals, Animals, Laboratory, Guidelines as Topic, Reproducibility of Results, Research Design, Animal Experimentation, Biomedical Research
Abstract

The biomedical research community addresses reproducibility challenges in animal studies through standardized nomenclature, improved experimental design, transparent reporting, data sharing, and centralized repositories. The ARRIVE guidelines outline documentation standards for laboratory animals in experiments, but genetic information is often incomplete. To remedy this, we propose the Laboratory Animal Genetic Reporting (LAG-R) framework. LAG-R aims to document animals genetic makeup in scientific publications, providing essential details for replication and appropriate model use. While verifying complete genetic compositions may be impractical, better reporting and validation efforts enhance reliability of research. LAG-R standardization will bolster reproducibility, peer review, and overall scientific rigor.

Published
2024

2. Analysis of genome-wide knockout mouse database identifies candidate ciliopathy genes

Author

Higgins, Kendall, Moore, Bret A, Berberovic, Zorana, Adissu, Hibret A, Eskandarian, Mohammad, Flenniken, Ann M, Shao, Andy, Imai, Denise M, Clary, Dave, Lanoue, Louise, Newbigging, Susan, Nutter, Lauryl MJ, Adams, David J, Bosch, Fatima, Braun, Robert E, Brown, Steve DM, Dickinson, Mary E, Dobbie, Michael, Flicek, Paul, Gao, Xiang, Galande, Sanjeev, Grobler, Anne, Heaney, Jason D, Herault, Yann, de Angelis, Martin Hrabe, Chin, Hsian-Jean Genie, Mammano, Fabio, Qin, Chuan, Shiroishi, Toshihiko, Sedlacek, Radislav, Seong, J-K, Xu, Ying, Lloyd, KC Kent, McKerlie, Colin, and Moshiri, Ala

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Biomedical and Clinical Sciences, Genetics, Biotechnology, Rare Diseases, 2.1 Biological and endogenous factors, Mice, Animals, Mice, Knockout, Ciliopathies, Gene Knockout Techniques, Cilia, Databases, Factual, Nerve Tissue Proteins, Cell Cycle Proteins, IMPC Consortium
Abstract

We searched a database of single-gene knockout (KO) mice produced by the International Mouse Phenotyping Consortium (IMPC) to identify candidate ciliopathy genes. We first screened for phenotypes in mouse lines with both ocular and renal or reproductive trait abnormalities. The STRING protein interaction tool was used to identify interactions between known cilia gene products and those encoded by the genes in individual knockout mouse strains in order to generate a list of "candidate ciliopathy genes." From this list, 32 genes encoded proteins predicted to interact with known ciliopathy proteins. Of these, 25 had no previously described roles in ciliary pathobiology. Histological and morphological evidence of phenotypes found in ciliopathies in knockout mouse lines are presented as examples (genes Abi2, Wdr62, Ap4e1, Dync1li1, and Prkab1). Phenotyping data and descriptions generated on IMPC mouse line are useful for mechanistic studies, target discovery, rare disease diagnosis, and preclinical therapeutic development trials. Here we demonstrate the effective use of the IMPC phenotype data to uncover genes with no previous role in ciliary biology, which may be clinically relevant for identification of novel disease genes implicated in ciliopathies.

Published
2022

3. The Deep Genome Project

Author

Lloyd, KC Kent, Adams, David J, Baynam, Gareth, Beaudet, Arthur L, Bosch, Fatima, Boycott, Kym M, Braun, Robert E, Caulfield, Mark, Cohn, Ronald, Dickinson, Mary E, Dobbie, Michael S, Flenniken, Ann M, Flicek, Paul, Galande, Sanjeev, Gao, Xiang, Grobler, Anne, Heaney, Jason D, Herault, Yann, de Angelis, Martin Hrabě, Lupski, James R, Lyonnet, Stanislas, Mallon, Ann-Marie, Mammano, Fabio, MacRae, Calum A, McInnes, Roderick, McKerlie, Colin, Meehan, Terrence F, Murray, Stephen A, Nutter, Lauryl MJ, Obata, Yuichi, Parkinson, Helen, Pepper, Michael S, Sedlacek, Radislav, Seong, Je Kyung, Shiroishi, Toshihiko, Smedley, Damian, Tocchini-Valentini, Glauco, Valle, David, Wang, Chi-Kuang Leo, Wells, Sara, White, Jacqueline, Wurst, Wolfgang, Xu, Ying, and Brown, Steve DM

Subjects
Animals, Genes, Genome, Humans, Mice, Mutation, Phenotype, Proteins, Environmental Sciences, Biological Sciences, Information and Computing Sciences, Bioinformatics
Published
2020

8. Use of spurious correlation for multiplicity adjustment

Author

Ninomiya, Yoshiyuki, Kuriki, Satoshi, Shiroishi, Toshihiko, and Takada, Toyoyuki

Subjects
Statistics - Methodology
Abstract

We consider one of the most basic multiple testing problems that compares expectations of multivariate data among several groups. As a test statistic, a conventional (approximate) $t$-statistic is considered, and we determine its rejection region using a common rejection limit. When there are unknown correlations among test statistics, the multiplicity adjusted $p$-values are dependent on the unknown correlations. They are usually replaced with their estimates that are always consistent under any hypothesis. In this paper, we propose the use of estimates, which are not necessarily consistent and are referred to as spurious correlations, in order to improve statistical power. Through simulation studies, we verify that the proposed method asymptotically controls the family-wise error rate and clearly provides higher statistical power than existing methods. In addition, the proposed and existing methods are applied to a real multiple testing problem that compares quantitative traits among groups of mice and the results are compared.

Published
2016

9. Extensive identification of genes involved in congenital and structural heart disorders and cardiomyopathy

Author

Spielmann, Nadine, Miller, Gregor, Oprea, Tudor I., Hsu, Chih-Wei, Fobo, Gisela, Frishman, Goar, Montrone, Corinna, Haseli Mashhadi, Hamed, Mason, Jeremy, Munoz Fuentes, Violeta, Leuchtenberger, Stefanie, Ruepp, Andreas, Wagner, Matias, Westphal, Dominik S., Wolf, Cordula, Görlach, Agnes, Sanz-Moreno, Adrián, Cho, Yi-Li, Teperino, Raffaele, Brandmaier, Stefan, Sharma, Sapna, Galter, Isabella Rikarda, Östereicher, Manuela A., Zapf, Lilly, Mayer-Kuckuk, Philipp, Rozman, Jan, Teboul, Lydia, Bunton-Stasyshyn, Rosie K. A., Cater, Heather, Stewart, Michelle, Christou, Skevoulla, Westerberg, Henrik, Willett, Amelia M., Wotton, Janine M., Roper, Willson B., Christiansen, Audrey E., Ward, Christopher S., Heaney, Jason D., Reynolds, Corey L., Prochazka, Jan, Bower, Lynette, Clary, David, Selloum, Mohammed, Bou About, Ghina, Wendling, Olivia, Jacobs, Hugues, Leblanc, Sophie, Meziane, Hamid, Sorg, Tania, Audain, Enrique, Gilly, Arthur, Rayner, Nigel W., Hitz, Marc-Phillip, Zeggini, Eleftheria, Wolf, Eckhard, Sedlacek, Radislav, Murray, Steven A., Svenson, Karen L., Braun, Robert E., White, Jaqueline K., Kelsey, Lois, Gao, Xiang, Shiroishi, Toshihiko, Xu, Ying, Seong, Je Kyung, Mammano, Fabio, Tocchini-Valentini, Glauco P., Beaudet, Arthur L., Meehan, Terrence F., Parkinson, Helen, Smedley, Damian, Mallon, Ann-Marie, Wells, Sara E., Grallert, Harald, Wurst, Wolfgang, Marschall, Susan, Fuchs, Helmut, Brown, Steve D. M., Flenniken, Ann M., Nutter, Lauryl M. J., McKerlie, Colin, Herault, Yann, Lloyd, K. C. Kent, Dickinson, Mary E., Gailus-Durner, Valerie, and Hrabe de Angelis, Martin

Published
2022
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11. Publisher Correction: Extensive identification of genes involved in congenital and structural heart disorders and cardiomyopathy

Author

Spielmann, Nadine, Miller, Gregor, Oprea, Tudor I., Hsu, Chih-Wei, Fobo, Gisela, Frishman, Goar, Montrone, Corinna, Haseli Mashhadi, Hamed, Mason, Jeremy, Munoz Fuentes, Violeta, Leuchtenberger, Stefanie, Ruepp, Andreas, Wagner, Matias, Westphal, Dominik S., Wolf, Cordula, Görlach, Agnes, Sanz-Moreno, Adrián, Cho, Yi-Li, Teperino, Raffaele, Brandmaier, Stefan, Sharma, Sapna, Galter, Isabella Rikarda, Östereicher, Manuela A., Zapf, Lilly, Mayer-Kuckuk, Philipp, Rozman, Jan, Teboul, Lydia, Bunton-Stasyshyn, Rosie K. A., Cater, Heather, Stewart, Michelle, Christou, Skevoulla, Westerberg, Henrik, Willett, Amelia M., Wotton, Janine M., Roper, Willson B., Christiansen, Audrey E., Ward, Christopher S., Heaney, Jason D., Reynolds, Corey L., Prochazka, Jan, Bower, Lynette, Clary, David, Selloum, Mohammed, Bou About, Ghina, Wendling, Olivia, Jacobs, Hugues, Leblanc, Sophie, Meziane, Hamid, Sorg, Tania, Audain, Enrique, Gilly, Arthur, Rayner, Nigel W., Hitz, Marc-Phillip, Zeggini, Eleftheria, Wolf, Eckhard, Sedlacek, Radislav, Murray, Steven A., Svenson, Karen L., Braun, Robert E., White, Jaqueline K., Kelsey, Lois, Gao, Xiang, Shiroishi, Toshihiko, Xu, Ying, Seong, Je Kyung, Mammano, Fabio, Tocchini-Valentini, Glauco P., Beaudet, Arthur L., Meehan, Terrence F., Parkinson, Helen, Smedley, Damian, Mallon, Ann-Marie, Wells, Sara E., Grallert, Harald, Wurst, Wolfgang, Marschall, Susan, Fuchs, Helmut, Brown, Steve D. M., Flenniken, Ann M., Nutter, Lauryl M. J., McKerlie, Colin, Herault, Yann, Lloyd, K. C. Kent, Dickinson, Mary E., Gailus-Durner, Valerie, and Hrabe de Angelis, Martin

Published
2022
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13. Sparse principal component regression for generalized linear models

Author

Kawano, Shuichi, Fujisawa, Hironori, Takada, Toyoyuki, and Shiroishi, Toshihiko

Subjects
Statistics - Machine Learning, Statistics - Methodology
Abstract

Principal component regression (PCR) is a widely used two-stage procedure: principal component analysis (PCA), followed by regression in which the selected principal components are regarded as new explanatory variables in the model. Note that PCA is based only on the explanatory variables, so the principal components are not selected using the information on the response variable. In this paper, we propose a one-stage procedure for PCR in the framework of generalized linear models. The basic loss function is based on a combination of the regression loss and PCA loss. An estimate of the regression parameter is obtained as the minimizer of the basic loss function with a sparse penalty. We call the proposed method sparse principal component regression for generalized linear models (SPCR-glm). Taking the two loss function into consideration simultaneously, SPCR-glm enables us to obtain sparse principal component loadings that are related to a response variable. However, a combination of loss functions may cause a parameter identification problem, but this potential problem is avoided by virtue of the sparse penalty. Thus, the sparse penalty plays two roles in this method. The parameter estimation procedure is proposed using various update algorithms with the coordinate descent algorithm. We apply SPCR-glm to two real datasets, doctor visits data and mouse consomic strain data. SPCR-glm provides more easily interpretable principal component (PC) scores and clearer classification on PC plots than the usual PCA., Comment: 29 pages

Published
2016
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15. Type specimens, taxonomic history, and genetic analysis of the Japanese dancing mouse or waltzer, Mus wagneri variety rotans Droogleever Fortuyn, 1912 (Mammalia, Muridae)

Author

Cruz, M. (Mónica), Bergmans, Wim, Takada, Toyoyuki, Shiroishi, Toshihiko, Yoshiki, Atsushi, Cruz, M. (Mónica), Bergmans, Wim, Takada, Toyoyuki, Shiroishi, Toshihiko, and Yoshiki, Atsushi

Abstract

In the present paper, the existence and location of the type series of the Japanese dancing mouse or waltzer, Mus wagneri variety rotans Droogleever Fortuyn, 1912, are established, and a lectotype is designated. Available type specimens are measured, and some morphological parameters, sex, and general condition of the specimens are recorded. A literature survey was conducted, and an attempt is made to clarify the position of M. wagneri variety rotans in the taxonomy of Mus. A genetic analysis suggests that the type series of the Japanese dancing mouse represent a crossbred, or derivation of a crossbred, between the original Japanese dancing mouse of Mus musculus molossinus Temminck 1844 origin and European fancy or laboratory mice of Mus musculus domesticus Schwarz & Schwarz, 1943 origin. Much of their genome was replaced and occupied by Mus musculus domesticus type genome, probably through extensive breeding with European mice.

Published
2024
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17. Sparse principal component regression with adaptive loading

Author

Kawano, Shuichi, Fujisawa, Hironori, Takada, Toyoyuki, and Shiroishi, Toshihiko

Subjects
Statistics - Machine Learning, Statistics - Methodology, 62H25, 62J07
Abstract

Principal component regression (PCR) is a two-stage procedure that selects some principal components and then constructs a regression model regarding them as new explanatory variables. Note that the principal components are obtained from only explanatory variables and not considered with the response variable. To address this problem, we propose the sparse principal component regression (SPCR) that is a one-stage procedure for PCR. SPCR enables us to adaptively obtain sparse principal component loadings that are related to the response variable and select the number of principal components simultaneously. SPCR can be obtained by the convex optimization problem for each of parameters with the coordinate descent algorithm. Monte Carlo simulations and real data analyses are performed to illustrate the effectiveness of SPCR., Comment: 24 pages

Published
2014
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19. Type specimens, taxonomic history, and genetic analysis of the Japanese dancing mouse or waltzer, Mus wagneri variety rotans Droogleever Fortuyn, 1912 (Mammalia, Muridae).

Author

Cruz, Mónica, Bergmans, Wim, Takada, Toyoyuki, Shiroishi, Toshihiko, and Yoshiki, Atsushi

Subjects
MAMMALS, LABORATORY mice, MICE, MURIDAE
Abstract

In the present paper, the existence and location of the type series of the Japanese dancing mouse or waltzer, Mus wagneri variety rotans Droogleever Fortuyn, 1912, are established, and a lectotype is designated. Available type specimens are measured, and some morphological parameters, sex, and general condition of the specimens are recorded. A literature survey was conducted, and an attempt is made to clarify the position of M. wagneri variety rotans in the taxonomy of Mus. A genetic analysis suggests that the type series of the Japanese dancing mouse represent a crossbred, or derivation of a crossbred, between the original Japanese dancing mouse of Mus musculus molossinus Temminck 1844 origin and European fancy or laboratory mice of Mus musculus domesticus Schwarz & Schwarz, 1943 origin. Much of their genome was replaced and occupied by Mus musculus domesticus type genome, probably through extensive breeding with European mice. [ABSTRACT FROM AUTHOR]

Published
2024
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24. Functional Annotation of Mouse Genome Sequences

Author

Nadeau, Joseph H., Balling, Rudi, Barsh, Greg, Beier, David, Brown, S. D. M., Bucan, Maja, Camper, Sally, Carlson, George, Copeland, Neal, Eppig, Janan, Fletcher, Colin, Frankel, Wayne N., Ganten, Detlev, Goldowitz, Dan, Goodnow, Chris, Guenet, Jean-Louis, Hicks, Geoff, de Angelis, Martin Hrabe, Jackson, Ian, Jacob, Howard J., Jenkins, Nancy, Johnson, Dabney, Justice, Monica, Kay, Steve, Kingsley, David, Lehrach, Hans, Magnuson, Terry, Meisler, Miriam, Poustka, AnneMarie, Rinchik, Eugene M., Rossant, Janet, Russell, Lee B., Schimenti, John, Shiroishi, Toshihiko, Skarnes, William C., Soriano, Phil, Stanford, William, Takahashi, Joseph S., Wurst, Wolfgang, and Zimmer, Andreas

Published
2001

28. Caspase-1 initiates apoptosis in the absence of gasdermin D

Author

Tsuchiya, Kohsuke, Nakajima, Shinsuke, Hosojima, Shoko, Thi Nguyen, Dinh, Hattori, Tsuyoshi, Manh Le, Thuong, Hori, Osamu, Mahib, Mamunur Rashid, Yamaguchi, Yoshifumi, Miura, Masayuki, Kinoshita, Takeshi, Kushiyama, Hiroko, Sakurai, Mayumi, Shiroishi, Toshihiko, and Suda, Takashi

Published
2019
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31. Phenotype Detection in Morphological Mutant Mice Using Deformation Features

Author

Roy, Sharmili, Liang, Xi, Kitamoto, Asanobu, Tamura, Masaru, Shiroishi, Toshihiko, Brown, Michael S., 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, Nierstrasz, Oscar, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Sudan, Madhu, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Vardi, Moshe Y., Series editor, Weikum, Gerhard, Series editor, Mori, Kensaku, editor, Sakuma, Ichiro, editor, Sato, Yoshinobu, editor, Barillot, Christian, editor, and Navab, Nassir, editor

Published
2013
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32. Two Loci Contribute to Age-Related Hearing Loss Resistance in the Japanese Wild-Derived Inbred MSM/Ms Mice

Author

Yasuda, Shumpei P., primary, Miyasaka, Yuki, additional, Hou, Xuehan, additional, Obara, Yo, additional, Shitara, Hiroshi, additional, Seki, Yuta, additional, Matsuoka, Kunie, additional, Takahashi, Ai, additional, Wakai, Eri, additional, Hibino, Hiroshi, additional, Takada, Toyoyuki, additional, Shiroishi, Toshihiko, additional, Kominami, Ryo, additional, and Kikkawa, Yoshiaki, additional

Published
2022
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33. Generation of Rac1 conditional mutant mice by Cre/loxP system

Author

Suzuki, Dai, Yamada, Atsushi, Amano, Takanori, Kimura, Ayako, Yasuhara, Rika, Sakahara, Mizuho, Tamura, Masaru, Tsumaki, Noriyuki, Takeda, Shu, Nakamura, Masanori, Shiroishi, Toshihiko, Aiba, Atsu, Kamijo, Ryutaro, Shioda, Seiji, editor, Homma, Ikuo, editor, and Kato, Nobumasa, editor

Published
2009
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36. Insights into Mus musculus Population Structure across Eurasia Revealed by Whole-Genome Analysis

Author

Fujiwara, Kazumichi, Kawai, Yosuke, Takada, Toyoyuki, Shiroishi, Toshihiko, Saitou, Naruya, Suzuki, Hitoshi, Osada, Naoki, Fujiwara, Kazumichi, Kawai, Yosuke, Takada, Toyoyuki, Shiroishi, Toshihiko, Saitou, Naruya, Suzuki, Hitoshi, and Osada, Naoki

Abstract

For more than 100 years, house mice (Mus musculus) have been used as a key animal model in biomedical research. House mice are genetically diverse, yet their genetic background at the global level has not been fully understood. Previous studies have suggested that they originated in South Asia and diverged into three major subspecies, almost simultaneously, approximately 110,000-500,000 years ago; however, they have spread across the world with the migration of modern humans in prehistoric and historic times (similar to 10,000 years ago to the present day) and have undergone secondary contact, which has complicated the genetic landscape of wild house mice. In this study, we sequenced the whole-genome sequences of 98 wild house mice collected from Eurasia, particularly East Asia, Southeast Asia, and South Asia. Although wild house mice were found to consist of three major genetic groups corresponding to the three major subspecies, individuals representing admixtures between subspecies were more prevalent in East Asia than has been previously recognized. Furthermore, several samples exhibited an incongruent pattern of genealogies between mitochondrial and autosomal genomes. Using samples that likely retained the original genetic components of subspecies with the least admixture, we estimated the pattern and timing of divergence among the subspecies. The estimated divergence time of the three subspecies was 187,000-226,000 years ago. These results will help us to understand the genetic diversity of wild mice on a global scale, and the findings will be particularly useful in future biomedical and evolutionary studies involving laboratory mice established from such wild mice.

Published
2022

42. 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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43. 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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48. Asian Mouse Mutagenesis Resource Association (AMMRA): mouse genetics and laboratory animal resources in the Asia Pacific

Author

Chin, Hsian-Jean, Dobbie, Michael S., Gao, Xiang, Hennessy, James E., Nam, Ki-Hoan, Seong, Je Kyung, Shiroishi, Toshihiko, Takeo, Toru, Yoshiki, Atsushi, Zao, Jing, Wang, Chi-Kuang Leo, Chin, Hsian-Jean, Dobbie, Michael S., Gao, Xiang, Hennessy, James E., Nam, Ki-Hoan, Seong, Je Kyung, Shiroishi, Toshihiko, Takeo, Toru, Yoshiki, Atsushi, Zao, Jing, and Wang, Chi-Kuang Leo

Abstract

The Asian Mouse Mutagenesis Resource Association (AMMRA) is a non-profit organization consisting of major resource and research institutions with rodent expertise from within the Asia Pacific region. For more than a decade, aiming to support biomedical research and stimulate international collaboration, AMMRA has always been a friendly and passionate ally of Asian and Australian member institutions devoted to sharing knowledge, exchanging resources, and promoting biomedical research. AMMRA is also missioned to global connection by working closely with the consortiums such as the International Mouse Phenotyping Consortium and the International Mouse Strain Resource. This review discusses the emergence of AMMRA and outlines its many roles and responsibilities in promoting, assisting, enriching research, and ultimately enhancing global life science research quality. © 2021, The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.

Published
2021

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