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2. Chapter 2 Established and Emerging Techniques for Characterising the Formation, Structure and Performance of Calcified Structures under Ocean Acidification

Author

Fitzer, Susan C., Bin San Chan, Vera, Meng, Yuan, Chandra Rajan, Kanmani, Suzuki, Michio, Not, Christelle, Toyofuku, Takashi, and Fal, Laura

Subjects
Structures, techniques, ocean acidification, Earth Sciences, Geography, Environment, Planning
Abstract

Ocean acidification (OA) is the decline in seawater pH and saturation levels of calcium carbonate (CaCO3) minerals that has led to concerns for calcifying organisms such as corals, oysters and mussels because of the adverse effects of OA on their biomineralisation, shells and skeletons. A range of cellular biology, geochemistry and materials science approaches have been used to explore biomineralisation. These techniques have revealed that responses to seawater acidification can be highly variable among species, yet the underlying mechanisms remain largely unresolved. To assess the impacts of global OA, researchers will need to apply a range of tools developed across disciplines, many of which are emerging and have not yet been used in this context. This review outlines techniques that could be applied to study OA-induced alterations in the mechanisms of biomineralisation and their ultimate effects on shells and skeletons. We illustrate how to characterise, quantify and monitor the process of biomineralisation in the context of global climate change and OA. We highlight the basic principles, as well as the advantages and disadvantages, of established, emerging and future techniques for OA researchers. A combination of these techniques will enable a holistic approach and better understanding of the potential impact of OA on biomineralisation and its consequences for marine calcifiers and associated ecosystems.

Published
2019

4. Subcortical volumetric alterations in four major psychiatric disorders: a mega-analysis study of 5604 subjects and a volumetric data-driven approach for classification.

Author

Okada, Naohiro, Fukunaga, Masaki, Miura, Kenichiro, Nemoto, Kiyotaka, Matsumoto, Junya, Hashimoto, Naoki, Kiyota, Masahiro, Morita, Kentaro, Koshiyama, Daisuke, Ohi, Kazutaka, Takahashi, Tsutomu, Koeda, Michihiko, Yamamori, Hidenaga, Fujimoto, Michiko, Yasuda, Yuka, Hasegawa, Naomi, Narita, Hisashi, Yokoyama, Satoshi, Mishima, Ryo, Kawashima, Takahiko, Kobayashi, Yuko, Sasabayashi, Daiki, Harada, Kenichiro, Yamamoto, Maeri, Hirano, Yoji, Itahashi, Takashi, Nakataki, Masahito, Hashimoto, Ryu-Ichiro, Tha, Khin, Koike, Shinsuke, Matsubara, Toshio, Okada, Go, Jahanshad, Neda, Yoshimura, Reiji, Abe, Osamu, Onitsuka, Toshiaki, Watanabe, Yoshiyuki, Matsuo, Koji, Yamasue, Hidenori, Okamoto, Yasumasa, Suzuki, Michio, Turner, Jessica, Thompson, Paul, Ozaki, Norio, Kasai, Kiyoto, Hashimoto, Ryota, and Van Erp, Theodorus

Subjects
Humans, Schizophrenia, Depressive Disorder, Major, Bipolar Disorder, Female, Male, Magnetic Resonance Imaging, Adult, Neuroimaging, Brain, Autism Spectrum Disorder, Middle Aged, Mental Disorders, Organ Size
Abstract

Differential diagnosis is sometimes difficult in practical psychiatric settings, in terms of using the current diagnostic system based on presenting symptoms and signs. The creation of a novel diagnostic system using objective biomarkers is expected to take place. Neuroimaging studies and others reported that subcortical brain structures are the hubs for various psycho-behavioral functions, while there are so far no neuroimaging data-driven clinical criteria overcoming limitations of the current diagnostic system, which would reflect cognitive/social functioning. Prior to the main analysis, we conducted a large-scale multisite study of subcortical volumetric and lateralization alterations in schizophrenia, bipolar disorder, major depressive disorder, and autism spectrum disorder using T1-weighted images of 5604 subjects (3078 controls and 2526 patients). We demonstrated larger lateral ventricles volume in schizophrenia, bipolar disorder, and major depressive disorder, smaller hippocampus volume in schizophrenia and bipolar disorder, and schizophrenia-specific smaller amygdala, thalamus, and accumbens volumes and larger caudate, putamen, and pallidum volumes. In addition, we observed a leftward alteration of lateralization for pallidum volume specifically in schizophrenia. Moreover, as our main objective, we clustered the 5,604 subjects based on subcortical volumes, and explored whether data-driven clustering results can explain cognitive/social functioning in the subcohorts. We showed a four-biotype classification, namely extremely (Brain Biotype [BB] 1) and moderately smaller limbic regions (BB2), larger basal ganglia (BB3), and normal volumes (BB4), being associated with cognitive/social functioning. Specifically, BB1 and BB2-3 were associated with severe and mild cognitive/social impairment, respectively, while BB4 was characterized by normal cognitive/social functioning. Our results may lead to the future creation of novel biological data-driven psychiatric diagnostic criteria, which may be expected to be useful for prediction or therapeutic selection.

Published
2023

5. Cerebral cortical structural alteration patterns across four major psychiatric disorders in 5549 individuals.

Author

Matsumoto, Junya, Fukunaga, Masaki, Miura, Kenichiro, Nemoto, Kiyotaka, Okada, Naohiro, Hashimoto, Naoki, Morita, Kentaro, Koshiyama, Daisuke, Ohi, Kazutaka, Takahashi, Tsutomu, Koeda, Michihiko, Yamamori, Hidenaga, Fujimoto, Michiko, Yasuda, Yuka, Ito, Satsuki, Yamazaki, Ryuichi, Hasegawa, Naomi, Narita, Hisashi, Yokoyama, Satoshi, Mishima, Ryo, Miyata, Jun, Kobayashi, Yuko, Sasabayashi, Daiki, Harada, Kenichiro, Yamamoto, Maeri, Hirano, Yoji, Itahashi, Takashi, Nakataki, Masahito, Hashimoto, Ryu-Ichiro, Tha, Khin, Koike, Shinsuke, Matsubara, Toshio, Okada, Go, Yoshimura, Reiji, Abe, Osamu, Turner, Jessica, Jahanshad, Neda, Thompson, Paul, Onitsuka, Toshiaki, Watanabe, Yoshiyuki, Matsuo, Koji, Yamasue, Hidenori, Okamoto, Yasumasa, Suzuki, Michio, Ozaki, Norio, Kasai, Kiyoto, Hashimoto, Ryota, and Van Erp, Theodorus

Subjects
Humans, Depressive Disorder, Major, Autism Spectrum Disorder, Bipolar Disorder, Mental Disorders, Cerebral Cortex, Magnetic Resonance Imaging
Abstract

According to the operational diagnostic criteria, psychiatric disorders such as schizophrenia (SZ), bipolar disorder (BD), major depressive disorder (MDD), and autism spectrum disorder (ASD) are classified based on symptoms. While its cluster of symptoms defines each of these psychiatric disorders, there is also an overlap in symptoms between the disorders. We hypothesized that there are also similarities and differences in cortical structural neuroimaging features among these psychiatric disorders. T1-weighted magnetic resonance imaging scans were performed for 5,549 subjects recruited from 14 sites. Effect sizes were determined using a linear regression model within each protocol, and these effect sizes were meta-analyzed. The similarity of the differences in cortical thickness and surface area of each disorder group was calculated using cosine similarity, which was calculated from the effect sizes of each cortical regions. The thinnest cortex was found in SZ, followed by BD and MDD. The cosine similarity values between disorders were 0.943 for SZ and BD, 0.959 for SZ and MDD, and 0.943 for BD and MDD, which indicated that a common pattern of cortical thickness alterations was found among SZ, BD, and MDD. Additionally, a generally smaller cortical surface area was found in SZ and MDD than in BD, and the effect was larger in SZ. The cosine similarity values between disorders were 0.945 for SZ and MDD, 0.867 for SZ and ASD, and 0.811 for MDD and ASD, which indicated a common pattern of cortical surface area alterations among SZ, MDD, and ASD. Patterns of alterations in cortical thickness and surface area were revealed in the four major psychiatric disorders. To our knowledge, this is the first report of a cross-disorder analysis conducted on four major psychiatric disorders. Cross-disorder brain imaging research can help to advance our understanding of the pathogenesis of psychiatric disorders and common symptoms.

Published
2023

6. Identification and Estimation of Production Function with Unobserved Heterogeneity

Author

Kasahara, Hiroyuki, Schrimpf, Paul, and Suzuki, Michio

Subjects
Economics - Econometrics
Abstract

This paper examines the nonparametric identifiability of production functions, considering firm heterogeneity beyond Hicks-neutral technology terms. We propose a finite mixture model to account for unobserved heterogeneity in production technology and productivity growth processes. Our analysis demonstrates that the production function for each latent type can be nonparametrically identified using four periods of panel data, relying on assumptions similar to those employed in existing literature on production function and panel data identification. By analyzing Japanese plant-level panel data, we uncover significant disparities in estimated input elasticities and productivity growth processes among latent types within narrowly defined industries. We further show that neglecting unobserved heterogeneity in input elasticities may lead to substantial and systematic bias in the estimation of productivity growth.

Published
2023

9. Increased structural covariance of cortical measures in individuals with an at-risk mental state

Author

Sasabayashi, Daiki, Tsugawa, Sakiko, Nakajima, Shinichiro, Takahashi, Tsutomu, Takayanagi, Yoichiro, Koike, Shinsuke, Katagiri, Naoyuki, Katsura, Masahiro, Furuichi, Atsushi, Mizukami, Yuko, Nishiyama, Shimako, Kobayashi, Haruko, Yuasa, Yusuke, Tsujino, Naohisa, Sakuma, Atsushi, Ohmuro, Noriyuki, Sato, Yutaro, Tomimoto, Kazuho, Okada, Naohiro, Tada, Mariko, Suga, Motomu, Maikusa, Norihide, Plitman, Eric, Wannan, Cassandra M.J., Zalesky, Andrew, Chakravarty, Mallar, Noguchi, Kyo, Yamasue, Hidenori, Matsumoto, Kazunori, Nemoto, Takahiro, Tomita, Hiroaki, Mizuno, Masafumi, Kasai, Kiyoto, and Suzuki, Michio

Published
2025
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14. Neuroanatomical heterogeneity and homogeneity in individuals at clinical high risk for psychosis

Author

Baldwin, Helen, Radua, Joaquim, Antoniades, Mathilde, Haas, Shalaila S, Frangou, Sophia, Agartz, Ingrid, Allen, Paul, Andreassen, Ole A, Atkinson, Kimberley, Bachman, Peter, Baeza, Inmaculada, Bartholomeusz, Cali F, Chee, Michael WL, Colibazzi, Tiziano, Cooper, Rebecca E, Corcoran, Cheryl M, Cropley, Vanessa L, Ebdrup, Bjørn H, Fortea, Adriana, Glenthøj, Louise Birkedal, Hamilton, Holly K, Haut, Kristen M, Hayes, Rebecca A, He, Ying, Heekeren, Karsten, Kaess, Michael, Kasai, Kiyoto, Katagiri, Naoyuki, Kim, Minah, Kindler, Jochen, Klaunig, Mallory J, Koike, Shinsuke, Koppel, Alex, Kristensen, Tina D, Bin Kwak, Yoo, Kwon, Jun Soo, Lawrie, Stephen M, Lebedeva, Irina, Lee, Jimmy, Lin, Ashleigh, Loewy, Rachel L, Mathalon, Daniel H, Michel, Chantal, Mizrahi, Romina, Møller, Paul, Nelson, Barnaby, Nemoto, Takahiro, Nordholm, Dorte, Omelchenko, Maria A, Pantelis, Christos, Raghava, Jayachandra M, Røssberg, Jan I, Rössler, Wulf, Salisbury, Dean F, Sasabayashi, Daiki, Schall, Ulrich, Smigielski, Lukasz, Sugranyes, Gisela, Suzuki, Michio, Takahashi, Tsutomu, Tamnes, Christian K, Tang, Jinsong, Theodoridou, Anastasia, Thomopoulos, Sophia I, Tomyshev, Alexander S, Uhlhaas, Peter J, Værnes, Tor G, van Amelsvoort, Therese AMJ, Van Erp, Theo GM, Waltz, James A, Westlye, Lars T, Wood, Stephen J, Zhou, Juan H, McGuire, Philip, Thompson, Paul M, Jalbrzikowski, Maria, Hernaus, Dennis, and Fusar-Poli, Paolo

Subjects
Serious Mental Illness, Prevention, Biomedical Imaging, Mental Health, Clinical Research, Neurosciences, Brain, Humans, Magnetic Resonance Imaging, Psychotic Disorders, ENIGMA Clinical High Risk for Psychosis Working Group, Clinical Sciences, Public Health and Health Services, Psychology
Abstract

Individuals at Clinical High Risk for Psychosis (CHR-P) demonstrate heterogeneity in clinical profiles and outcome features. However, the extent of neuroanatomical heterogeneity in the CHR-P state is largely undetermined. We aimed to quantify the neuroanatomical heterogeneity in structural magnetic resonance imaging measures of cortical surface area (SA), cortical thickness (CT), subcortical volume (SV), and intracranial volume (ICV) in CHR-P individuals compared with healthy controls (HC), and in relation to subsequent transition to a first episode of psychosis. The ENIGMA CHR-P consortium applied a harmonised analysis to neuroimaging data across 29 international sites, including 1579 CHR-P individuals and 1243 HC, offering the largest pooled CHR-P neuroimaging dataset to date. Regional heterogeneity was indexed with the Variability Ratio (VR) and Coefficient of Variation (CV) ratio applied at the group level. Personalised estimates of heterogeneity of SA, CT and SV brain profiles were indexed with the novel Person-Based Similarity Index (PBSI), with two complementary applications. First, to assess the extent of within-diagnosis similarity or divergence of neuroanatomical profiles between individuals. Second, using a normative modelling approach, to assess the 'normativeness' of neuroanatomical profiles in individuals at CHR-P. CHR-P individuals demonstrated no greater regional heterogeneity after applying FDR corrections. However, PBSI scores indicated significantly greater neuroanatomical divergence in global SA, CT and SV profiles in CHR-P individuals compared with HC. Normative PBSI analysis identified 11 CHR-P individuals (0.70%) with marked deviation (>1.5 SD) in SA, 118 (7.47%) in CT and 161 (10.20%) in SV. Psychosis transition was not significantly associated with any measure of heterogeneity. Overall, our examination of neuroanatomical heterogeneity within the CHR-P state indicated greater divergence in neuroanatomical profiles at an individual level, irrespective of psychosis conversion. Further large-scale investigations are required of those who demonstrate marked deviation.

Published
2022

25. Cross-Disorder Analysis of Genic and Regulatory Copy Number Variations in Bipolar Disorder, Schizophrenia, and Autism Spectrum Disorder

Author

Kushima, Itaru, Nakatochi, Masahiro, Aleksic, Branko, Okada, Takashi, Kimura, Hiroki, Kato, Hidekazu, Morikawa, Mako, Inada, Toshiya, Ishizuka, Kanako, Torii, Youta, Nakamura, Yukako, Tanaka, Satoshi, Imaeda, Miho, Takahashi, Nagahide, Yamamoto, Maeri, Iwamoto, Kunihiro, Nawa, Yoshihiro, Ogawa, Nanayo, Iritani, Shuji, Hayashi, Yu, Lo, Tzuyao, Otgonbayar, Gantsooj, Furuta, Sho, Iwata, Nakao, Ikeda, Masashi, Saito, Takeo, Ninomiya, Kohei, Okochi, Tomo, Hashimoto, Ryota, Yamamori, Hidenaga, Yasuda, Yuka, Fujimoto, Michiko, Miura, Kenichiro, Itokawa, Masanari, Arai, Makoto, Miyashita, Mitsuhiro, Toriumi, Kazuya, Ohi, Kazutaka, Shioiri, Toshiki, Kitaichi, Kiyoyuki, Someya, Toshiyuki, Watanabe, Yuichiro, Egawa, Jun, Takahashi, Tsutomu, Suzuki, Michio, Sasaki, Tsukasa, Tochigi, Mamoru, Nishimura, Fumichika, Yamasue, Hidenori, Kuwabara, Hitoshi, Wakuda, Tomoyasu, Kato, Takahiro A., Kanba, Shigenobu, Horikawa, Hideki, Usami, Masahide, Kodaira, Masaki, Watanabe, Kyota, Yoshikawa, Takeo, Toyota, Tomoko, Yokoyama, Shigeru, Munesue, Toshio, Kimura, Ryo, Funabiki, Yasuko, Kosaka, Hirotaka, Jung, Minyoung, Kasai, Kiyoto, Ikegame, Tempei, Jinde, Seiichiro, Numata, Shusuke, Kinoshita, Makoto, Kato, Tadafumi, Kakiuchi, Chihiro, Yamakawa, Kazuhiro, Suzuki, Toshimitsu, Hashimoto, Naoki, Ishikawa, Shuhei, Yamagata, Bun, Nio, Shintaro, Murai, Toshiya, Son, Shuraku, Kunii, Yasuto, Yabe, Hirooki, Inagaki, Masumi, Goto, Yu-ichi, Okumura, Yuto, Ito, Tomoya, Arioka, Yuko, Mori, Daisuke, and Ozaki, Norio

Published
2022
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28. Thalamic and striato-pallidal volumes in schizophrenia patients and individuals at risk for psychosis: A multi-atlas segmentation study

Author

Takahashi, Tsutomu, Tsugawa, Sakiko, Nakajima, Shinichiro, Plitman, Eric, Chakravarty, M. Mallar, Masuda, Fumi, Wada, Masataka, Kurose, Shin, Ochi, Ryo, Matsushita, Karin, Sasabayashi, Daiki, Nakamura, Mihoko, Nishikawa, Yumiko, Takayanagi, Yoichiro, Nishiyama, Shimako, Higuchi, Yuko, Mizukami, Yuko, Furuichi, Atsushi, Kido, Mikio, Hashimoto, Ryota, Noguchi, Kyo, Fujii, Shinya, Mimura, Masaru, Noda, Yoshihiro, and Suzuki, Michio

Published
2022
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38. Gross anatomical features of the insular cortex in affective disorders.

Author

Takahashi, Tsutomu, Sasabayashi, Daiki, Yücel, Murat, Whittle, Sarah, Suzuki, Michio, Pantelis, Christos, Malhi, Gin S., and Allen, Nicholas B.

Subjects
INSULAR cortex, MENTAL depression, AFFECTIVE disorders, MAGNETIC resonance imaging, BIPOLAR disorder
Abstract

Introduction: The number of insular gyri is elevated in patients with schizophrenia. Thus, it has potential as a marker of early neurodevelopmental abnormalities. However, currently it remains unclear whether patients with other neuropsychiatric disorders, such as affective disorders, also have this gross brain anatomical feature. Materials and methods: The macroscopic features of the insular cortex in 26 patients with bipolar disorder (BD), 56 with major depressive disorder (MDD), and control subjects for each clinical group (24 for BD and 33 for MDD) were assessed using magnetic resonance imaging. Results: The number of short insular gyri was higher in BD patients than in matched controls bilaterally with well-developed accessory and middle short gyri. Furthermore, the left middle short gyrus was more developed in MDD patients than in matched controls, and was weakly associated with the severity of depressive symptoms. Discussion: The present results indicate that changes in the gross morphology of the insular cortex in BD and MDD is a potential vulnerability factor associated with their neurodevelopmental pathologies, and may also contribute to the severity of symptoms in MDD. [ABSTRACT FROM AUTHOR]

Published
2024
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39. Structure‐Guided Discovery of a Potent Inhibitor of the Ferric Citrate Binding Protein FecB in Vibrio Bacteria.

Author

Jiang, Jinyan, Okuda, Suguru, Itoh, Hideaki, Okamoto, Ken, Nakanishi, Hiromi, Suzuki, Michio, Lu, Peng, and Nagata, Koji

Subjects
VIRTUAL high-throughput screening (Drug development), VIBRIO alginolyticus, BACTERIAL growth, CARRIER proteins, IRON ions
Abstract

Infections caused by Gram‐negative bacteria present a significant risk to human health worldwide. Novel strategies are needed to deal with the challenge caused by drug‐resistant bacteria. Here, we report a new approach to combat infections by targeting iron‐binding proteins to suppress bacterial growth. We investigated the function of the conserved periplasmic binding protein FecB from Vibrio alginolyticus. FecB was known to play a crucial role in the bacterial growth and to relate with biofilm formation. We then solved the crystal structures and elucidated the binding mechanism of FecB with ferric ion chelated by citrate. The results indicated that FecB binds weakly to one citrate molecule and strongly to the Fe3+‐(citrate)2 complex. Based on these results, a structure‐based virtual screening approach was conducted against FecB to identify small molecules that block ferric citrate uptake. Further evaluations in vivo and in vitro demonstrated that salvianolic acid C significantly suppressed bacterial growth, indicating that targeting bacterial nutrient absorption is a promising strategy for identifying potential antibacterial drugs. [ABSTRACT FROM AUTHOR]

Published
2024
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40. Midline brain structures in adult Niemann-Pick type C disease: a cross-sectional study.

Author

Walterfang, Mark, Takahashi, Tsutomu, Di Biase, Maria A., Cropley, Vanessa L., Sasabayashi, Daiki, Suzuki, Michio, Velakoulis, Dennis, and Pantelis, Christos

Subjects
MAGNETIC resonance imaging, BRAIN anatomy, MAGNETIC resonance, PSYCHOSES, GANGLIOSIDES
Abstract

Objective: A range of neuropathological changes occur in the brains of individuals with adult Niemann-Pick type C disease (NPC), a recessive disorder of cholesterol trafficking that results in accumulation of cholesterol and gangliosides in lysosomes, particularly in neurons. One of the most significant regions of grey matter loss occurs in the thalami, which abut the midline. What is not known is whether these are neurodevelopmental in origin well prior to symptomatic onset. We aimed to examine other markers of midline developmental anomalies in adults with NPC. Method: We examined the size of adhesio interthalamica (AI) and cavum septum pellucidum (CSP) (if present) in nine individuals diagnosed with NPC and nine healthy comparison subjects, matched for age and gender, using a 3T magnetic resonance volumetric sequence and measured the length of the AI and CSP in mm. Results: We found that 5/9 NPC patients and 0/9 controls had a missing AI. AI length was significantly shorter in the patient group. No subject in other group had a large CSP, and CSP length did not differ. Duration of illness showed a trend to a negative correlation with AI length in patients. Conclusions: Our findings suggest that adult NPC patients show some markers of early neurodevelopmental disturbance, matching findings seen in psychotic disorders. The differences in AI, but not CSP, suggest neurodevelopmental change may occur early in gestation rather than post-partum. The relationship with duration of illness suggests that there may be atrophy over time in these structures, consistent with prior analyses of grey matter regions in NPC. [ABSTRACT FROM AUTHOR]

Published
2024
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44. Prediction of psychotic disorder in individuals with clinical high-risk state by multimodal machine-learning: A preliminary study

Author

Takayanagi, Yoichiro, primary, Sasabayashi, Daiki, additional, Takahashi, Tsutomu, additional, Higuchi, Yuko, additional, Nishiyama, Shimako, additional, Tateno, Takahiro, additional, Mizukami, Yuko, additional, Akasaki, Yukiko, additional, Furuichi, Atsushi, additional, Kobayashi, Haruko, additional, Takayanagi, Mizuho, additional, Noguchi, Kyo, additional, Tsujii, Noa, additional, and Suzuki, Michio, additional

Published
2024
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48. Structural and Functional Analysis of the Amorphous Calcium Carbonate-Binding Protein Paramyosin in the Shell of the Pearl Oyster, Pinctada fucata

Author

Futagawa, Kei, primary, Ikeda, Haruka, additional, Negishi, Lumi, additional, Kurumizaka, Hitoshi, additional, Yamamoto, Ayame, additional, Furihata, Kazuo, additional, Ito, Yutaka, additional, Ikeya, Teppei, additional, Nagata, Koji, additional, Funabara, Daisuke, additional, and Suzuki, Michio, additional

Published
2024
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49. The components of the AhR‐molecular chaperone complex differ depending on whether the ligands are toxic or non‐toxic

Author

Narita, Yukihiko, primary, Tamura, Arisa, additional, Hatakeyama, Shiori, additional, Uemura, Seiya, additional, Miura, Atsuko, additional, Haga, Asami, additional, Tsuji, Noriko, additional, Fujie, Nozomi, additional, Izumi, Yukina, additional, Sugawara, Taku, additional, Otaka, Michiro, additional, Okamoto, Ken, additional, Lu, Peng, additional, Okuda, Suguru, additional, Suzuki, Michio, additional, Nagata, Koji, additional, Shimizu, Hiroaki, additional, and Itoh, Hideaki, additional

Published
2024
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