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2,350 results on '"Okada, Takashi"'

7. LONRF2 is a protein quality control ubiquitin ligase whose deficiency causes late-onset neurological deficits

Author

Li, Dan, Johmura, Yoshikazu, Morimoto, Satoru, Doi, Miyuki, Nakanishi, Keiko, Ozawa, Manabu, Tsunekawa, Yuji, Inoue-Yamauchi, Akane, Naruse, Hiroya, Matsukawa, Takashi, Takeshita, Yukio, Suzuki, Naoki, Aoki, Masashi, Nishiyama, Ayumi, Zeng, Xin, Konishi, Chieko, Suzuki, Narumi, Nishiyama, Atsuya, Harris, Alexander Stephen, Morita, Mariko, Yamaguchi, Kiyoshi, Furukawa, Yoichi, Nakai, Kenta, Tsuji, Shoji, Yamazaki, Satoshi, Yamanashi, Yuji, Shimada, Shoichi, Okada, Takashi, Okano, Hideyuki, Toda, Tatsushi, and Nakanishi, Makoto

Published
2023
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10. Oxytocin-induced increases in cytokines and clinical effect on the core social features of autism: Analyses of RCT datasets

Author

Wakuda, Tomoyasu, Benner, Seico, Uemura, Yukari, Nishimura, Tomoko, Kojima, Masaki, Kuroda, Miho, Matsumoto, Kaori, Kanai, Chieko, Inada, Naoko, Harada, Taeko, Kameno, Yosuke, Munesue, Toshio, Inoue, Jun, Umemura, Kazuo, Yamauchi, Aya, Ogawa, Nanayo, Kushima, Itaru, Suyama, Satoshi, Saito, Takuya, Hamada, Junko, Kano, Yukiko, Honda, Nami, Kikuchi, Saya, Seto, Moe, Tomita, Hiroaki, Miyoshi, Noriko, Matsumoto, Megumi, Kawaguchi, Yuko, Kanai, Koji, Ikeda, Manabu, Nakamura, Itta, Isomura, Shuichi, Hirano, Yoji, Onitsuka, Toshiaki, Ozaki, Norio, Kosaka, Hirotaka, Okada, Takashi, Kuwabara, Hitoshi, and Yamasue, Hidenori

Published
2024
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11. Dynamic sampling bias and overdispersion induced by skewed offspring distributions

Author

Okada, Takashi and Hallatschek, Oskar

Subjects
Quantitative Biology - Populations and Evolution, Physics - Biological Physics
Abstract

Natural populations often show enhanced genetic drift consistent with a strong skew in their offspring number distribution. The skew arises because the variability of family sizes is either inherently strong or amplified by population expansions, leading to so-called `jackpot' events. The resulting allele frequency fluctuations are large and, therefore, challenge standard models of population genetics, which assume sufficiently narrow offspring distributions. While the neutral dynamics backward in time can be readily analyzed using coalescent approaches, we still know little about the effect of broad offspring distributions on the dynamics forward in time, especially with selection. Here, we employ an exact asymptotic analysis combined with a scaling hypothesis to demonstrate that over-dispersed frequency trajectories emerge from the competition of conventional forces, such as selection or mutations, with an emerging time-dependent sampling bias against the minor allele. The sampling bias arises from the characteristic time-dependence of the largest sampled family size within each allelic type. Using this insight, we establish simple scaling relations for allele frequency fluctuations, fixation probabilities, extinction times, and the site frequency spectra that arise when offspring numbers are distributed according to a power law $~n^{-(1+\alpha)}$. To demonstrate that this coarse-grained model captures a wide variety of non-equilibrium dynamics, we validate our results in traveling waves, where the phenomenon of 'gene surfing' can produce any exponent $1<\alpha <2$. We argue that the concept of a dynamic sampling bias is useful generally to develop both intuition and statistical tests for the unusual dynamics of populations with skewed offspring distributions, which can confound commonly used tests for selection or demographic history., Comment: 39 pages, 22 Figures; v2: Figure 5 is replaced

Published
2021
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13. Structural reduction of chemical reaction networks based on topology

Author

Hirono, Yuji, Okada, Takashi, Miyazaki, Hiroyasu, and Hidaka, Yoshimasa

Subjects
Quantitative Biology - Molecular Networks, Physics - Biological Physics
Abstract

We develop a model-independent reduction method of chemical reaction systems based on the stoichiometry, which determines their network topology. A subnetwork can be eliminated systematically to give a reduced system with fewer degrees of freedom. This subnetwork removal is accompanied by rewiring of the network, which is prescribed by the Schur complement of the stoichiometric matrix. Using homology and cohomology groups to characterize the topology of chemical reaction networks, we can track the changes of the network topology induced by the reduction through the changes in those groups. We prove that, when certain topological conditions are met, the steady-state chemical concentrations and reaction rates of the reduced system are ensured to be the same as those of the original system. This result holds regardless of the modeling of the reactions, namely chemical kinetics, since the conditions only involve topological information. This is advantageous because the details of reaction kinetics and parameter values are difficult to identify in many practical situations. The method allows us to reduce a reaction network while preserving its original steady-state properties, thereby complex reaction systems can be studied efficiently. We demonstrate the reduction method in hypothetical networks and the central carbon metabolism of Escherichia coli., Comment: 49 pages, 7 figures; ver 2: published version

Published
2021
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21. Identifying Viral Vector Characteristics by Nanopore Sensing

Author

Tsutsui, Makusu, primary, Wada, Mikako, additional, Arima, Akihide, additional, Tsunekawa, Yuji, additional, Sasaki, Takako, additional, Sakamoto, Kenji, additional, Yokota, Kazumichi, additional, Baba, Yoshinobu, additional, Kawai, Tomoji, additional, and Okada, Takashi, additional

Published
2024
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31. Exome sequencing analysis of Japanese autism spectrum disorder case-control sample supports an increased burden of synaptic function-related genes

Author

Kimura, Hiroki, Nakatochi, Masahiro, Aleksic, Branko, Guevara, James, Toyama, Miho, Hayashi, Yu, Kato, Hidekazu, Kushima, Itaru, Morikawa, Mako, Ishizuka, Kanako, Okada, Takashi, Tsurusaki, Yoshinori, Fujita, Atsushi, Miyake, Noriko, Ogi, Tomoo, Takata, Atsushi, Matsumoto, Naomichi, Buxbaum, Joseph, Ozaki, Norio, and Sebat, Jonathan

Published
2022
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33. Identification of ultra-rare disruptive variants in voltage-gated calcium channel-encoding genes in Japanese samples of schizophrenia and autism spectrum disorder

Author

Wang, Chenyao, Horigane, Shin-ichiro, Wakamori, Minoru, Ueda, Shuhei, Kawabata, Takeshi, Fujii, Hajime, Kushima, Itaru, Kimura, Hiroki, Ishizuka, Kanako, Nakamura, Yukako, Iwayama, Yoshimi, Ikeda, Masashi, Iwata, Nakao, Okada, Takashi, Aleksic, Branko, Mori, Daisuke, Yoshida, Takashi, Bito, Haruhiko, Yoshikawa, Takeo, Takemoto-Kimura, Sayaka, and Ozaki, Norio

Published
2022
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35. Structural Bifurcation Analysis in Chemical Reaction Networks

Author

Okada, Takashi, Tsai, Je-Chiang, and Mochizuki, Atsushi

Subjects
Quantitative Biology - Molecular Networks, Mathematics - Dynamical Systems, Physics - Biological Physics
Abstract

In living cells, chemical reactions form a complex network. Complicated dynamics arising from such networks are the origins of biological functions. We propose a novel mathematical method to analyze bifurcation behaviors of a reaction system from the network structure alone. The whole network is decomposed into subnetworks based on "buffering structures". For each subnetwork, the bifurcation condition is studied independently, and the parameters that can induce bifurcations and the chemicals that can exhibit bifurcations are determined. We demonstrate our theory using hypothetical and real networks., Comment: 29 pages, 12 figures. v2: FIG S4 corrected

Published
2017
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36. Ligand-concentration sensitivity of a multi-state receptor

Author

Okada, Takashi

Subjects
Physics - Biological Physics, Quantitative Biology - Molecular Networks, Quantitative Biology - Subcellular Processes
Abstract

Biological sensory systems generally operate out of equilibrium, which often leads to their improved performance. Here, we study the sensitivity of ligand concentration for a general receptor model, which is generally in the non-equilibrium stationary state, in the framework of a stochastic diffusion equation. We derived a general formula of the maximum sensitivity. Specifically, the sensitivity is limited universally by the Berg-Purcell limit [Biophys. J ., 1977], regardless of whether the receptor is in an equilibrium or non-equilibrium state., Comment: 5 pages, 4 figures

Published
2017

37. Sensitivity and Network Topology in Chemical Reaction Systems

Author

Okada, Takashi and Mochizuki, Atsushi

Subjects
Quantitative Biology - Molecular Networks, Physics - Biological Physics, Quantitative Biology - Subcellular Processes
Abstract

In living cells, biochemical reactions are catalyzed by specific enzymes and connect to one another by sharing substrates and products, forming complex networks. In our previous studies, we established a framework determining the responses to enzyme perturbations only from network topology, and then proved a theorem, called the law of localization, explaining response patterns in terms of network topology. In this paper, we generalize these results to reaction networks with conserved concentrations, which allows us to study any reaction systems. We also propose novel network characteristics quantifying robustness. We compare E. coli metabolic network with randomly rewired networks, and find that the robustness of the E. coli network is significantly higher than that of the random networks., Comment: 14 pages, 13 figures

Published
2017
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38. Psychiatric comorbidities of attention deficit/hyperactivity disorder in Japan: a nationwide population-based study.

Author

Okada, Takashi, Sotodate, Takuma, Ogasawara-Shimizu, Mari, and Nishigaki, Nobuhiro

Subjects
PEOPLE with mental illness, AUTISM spectrum disorders, MENTAL illness, SLEEP disorders, PSYCHIATRIC diagnosis
Abstract

Introduction: This study aimed to estimate prevalence and incidence of attention deficit/hyperactivity disorder (ADHD) and comorbid relationships between ADHD and other psychiatric disorders in Japan. Methods: Using the real-world JMDC Claims Database, we conducted a cross-sectional study (analysis years 2017–2021) and retrospective cohort study (observation 2 years before/after the initial ADHD diagnosis; data collection 2005–2021; enrollment 2017–2019). Patients were male or female, aged 0–57 years. Cross-sectional study patients had an ADHD or other psychiatric disorder diagnosis (with or without medication) and were continuously registered in each analysis year; retrospective study patients had an ADHD diagnosis and ≥2 years' observation before and after diagnosis. Endpoints were annual prevalence and incidence of ADHD in Japan, prevalence and risk ratio of each psychiatric comorbidity in patients with ADHD, prevalence and risk ratios of ADHD in patients with each psychiatric comorbidity, and prevalence of psychiatric disorders before/after the initial ADHD diagnosis. Results: ADHD prevalence in children/adolescents and adults increased each year from 2017 to 2021. Prevalence in boys was 3.5–4.1 times higher than in girls. Prevalence in adults was lower than in children/adolescents, with a small sex difference. ADHD was highly comorbid with various psychiatric disorders. In 2019, the most common comorbidity in children/adolescents with ADHD was autism spectrum disorder (ASD; 54.4%); in adults, it was mood disorders (60.9%). ADHD prevalence in patients with various psychiatric disorders was higher than in the control population. ADHD prevalence was highest in patients with oppositional defiance disorder among both children/adolescents and adults (77.2% and 69.2%, respectively). In the retrospective cohort study (N = 14,940), the most common psychiatric disorders diagnosed prior to ADHD diagnosis were ASD in children/adolescents (33.9% of patients), and mood disorders and sleep disorders in adults (36.9% and 23.8% of patients, respectively). Discussion: ADHD was comorbid with various psychiatric disorders in Japan. In children and adolescents with ADHD, ASD was often diagnosed prior to ADHD. Psychiatric disorders, especially mood disorders and sleep disorders, were frequently diagnosed prior to the initial ADHD diagnosis in adults. The likelihood of comorbid ADHD should be considered when diagnosing adult patients with psychiatric disorders. [ABSTRACT FROM AUTHOR]

Published
2024
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42. Law of localization in chemical reaction networks

Author

Okada, Takashi and Mochizuki, Atsushi

Subjects
Quantitative Biology - Molecular Networks, Mathematics - Dynamical Systems, Physics - Biological Physics, Quantitative Biology - Subcellular Processes
Abstract

In living cells, chemical reactions are connected by sharing their products and substrates, and form complex networks, e.g. metabolic pathways. Here we developed a theory to predict the sensitivity, i.e. the responses of concentrations and fluxes to perturbations of enzymes, from network structure alone. Responses turn out to exhibit two characteristic patterns, $localization$ and $hierarchy$. We present a general theorem connecting sensitivity with network topology that explains these characteristic patterns. Our results imply that network topology is an origin of biological robustness. Finally, we suggest a strategy to determine real networks from experimental measurements., Comment: 18 pages 5 figures; v2: minor corrections (accepted for publication in Physical Review Letters)

Published
2016
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46. Patterns of change in regulatory modules of chemical reaction systems induced by network modification

Author

Hishida, Atsuki, Okada, Takashi, Mochizuki, Atsushi, Hishida, Atsuki, Okada, Takashi, and Mochizuki, Atsushi

Abstract

Cellular functions are realized through the dynamics of chemical reaction networks formed by thousands of chemical reactions. Numerical studies have empirically demonstrated that small differences in network structures among species or tissues can cause substantial changes in dynamics. However, a general principle for behavior changes in response to network structure modifications is not known. The chemical reaction system possesses substructures called buffering structures, which are characterized by a certain topological index being zero. It was proven that the steady-state response to modulation of reaction parameters inside a buffering structure is localized in the buffering structure. In this study, we developed a method to systematically identify the loss or creation of buffering structures induced by the addition of a single degradation reaction from network structure alone. This makes it possible to predict the qualitative and macroscopic changes in regulation that will be caused by the network modification. This method was applied to two reaction systems: the central metabolic system and the mitogen-activated protein kinases signal transduction system. Our method enables identification of reactions that are important for biological functions in living systems.

Published
2024

47. Hybrid Wheat and Abiotic Stress

Author

Okada, Takashi, Whitford, Ryan, Ramawat, Kishan Gopal, Series Editor, Rajpal, Vijay Rani, editor, Sehgal, Deepmala, editor, Kumar, Avinash, editor, and Raina, S.N., editor

Published
2019
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49. Applications and Limitations of Equilibrium Density Gradient Analytical Ultracentrifugation for the Quantitative Characterization of Adeno-Associated Virus Vectors

Author

Hirohata, Kiichi, primary, Yamaguchi, Yuki, additional, Maruno, Takahiro, additional, Shibuya, Risa, additional, Torisu, Tetsuo, additional, Onishi, Takayuki, additional, Chono, Hideto, additional, Mineno, Junichi, additional, Yuzhe, Yuan, additional, Higashiyama, Kiyoko, additional, Masumi-Koizumi, Kyoko, additional, Uchida, Kazuhisa, additional, Yamamoto, Takenori, additional, Uchida, Eriko, additional, Okada, Takashi, additional, and Uchiyama, Susumu, additional

Published
2024
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