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2. Hydrodynamic Equations for a system with translational and rotational dynamics

Author

Yoshimori, Akira and Das, Shankar P.

Subjects
Condensed Matter - Statistical Mechanics
Abstract

We obtain the equations of fluctuating hydrodynamics for many-particle systems whose microscopic units have both translational and rotational motion. The orientational dynamics of each element are studied in terms of the rotational Brownian motion of a corresponding fixed-length director ${\bf u}$. The time evolution of a set of collective densities $\{\hat{\psi}\}$ is obtained as an exact representation of the corresponding microscopic dynamics. For the Smoluchowski dynamics, noise in the Langevin equation for the director ${\bf u}$ is multiplicative. We obtain that the equation of motion for the collective number-density has two different forms, respectively, for the I\"{t}o and Stratonvich interpretation of the multiplicative noise in the ${\bf u}$-equation. Without the ${\bf u}$ variable, both reduce to the Standard Dean-Kawasaki form. Next, we average the microscopic equations for the collective densities $\{\hat{\psi}\}$ (which are, at this stage, a collection of Dirac delta functions) over phase space variables and obtain a corresponding set of stochastic partial differential equations for the coarse-grained densities $\{\psi\}$ with smooth spatial and temporal dependence. The coarse-grained equations of motion for the collective densities $\{\psi\}$ constitute the fluctuating non-linear hydrodynamics for the fluid with both rotational and translational dynamics. From the stationary solution of the corresponding Fokker-Planck equation, we obtain a free energy functional ${\cal F}[\psi]$ and demonstrate the relation between the ${\cal F}[\psi]$s for different levels of the FNH descriptions with its corresponding set of $\{\psi\}$., Comment: 45 pages

Published
2025

3. Age-dependent risk for thromboembolism in atrial fibrillation: The Fushimi AF registry

Author

Masahiro Esato, Yoshimori An, Hisashi Ogawa, Hiromichi Wada, Koji Hasegawa, Hikari Tsuji, Mitsuru Abe, and Masaharu Akao

Subjects
Atrial fibrillation, Thromboembolism, Age subgroups, Diseases of the circulatory (Cardiovascular) system, RC666-701
Abstract

Background: The risk for thromboembolism depending on the different age subgroups in patients with atrial fibrillation (AF) has not been fully elucidated. Methods: The Fushimi AF Registry is a community-based prospective survey of patients with AF in Fushimi-ku, Kyoto. Follow-up data were available for 4,466 patients by the end of 2019. Clinical determinants and the description of variables which interact and lead to the incidence of thromboembolism (the composite of ischemic stroke and systemic embolism [SE]) were identified in overall population and in age subgroups (≤64, 65–74, and ≥ 75 years). Results: A total of 314 patients developed thromboembolism during the median follow-up of 1,610 days (1.56 per 100 person-years). The independent determinants were age advance (per 10 years, hazard ratio [HR]: 1.51, 95% confidence interval [CI]: 1.22–1.86, P

Published
2022
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4. Ischemic Stroke in Acute Decompensated Heart Failure: From the KCHF Registry

Author

Moritake Iguchi, Takao Kato, Hidenori Yaku, Takeshi Morimoto, Yasutaka Inuzuka, Yodo Tamaki, Neiko Ozasa, Erika Yamamoto, Yusuke Yoshikawa, Takeshi Kitai, Yasuhiro Hamatani, Yugo Yamashita, Nobutoyo Masunaga, Hisashi Ogawa, Mitsuru Ishii, Yoshimori An, Ryoji Taniguchi, Masashi Kato, Mamoru Takahashi, Toshikazu Jinnai, Tomoyuki Ikeda, Kazuya Nagao, Takafumi Kawai, Akihiro Komasa, Ryusuke Nishikawa, Yuichi Kawase, Takashi Morinaga, Mitsunori Kawato, Yuta Seko, Mamoru Toyofuku, Yutaka Furukawa, Kenji Ando, Kazushige Kadota, Mitsuru Abe, Masaharu Akao, Yukihito Sato, Koichiro Kuwahara, and Takeshi Kimura

Subjects
acute heart failure, B‐type natriuretic peptide, ischemic stroke, N‐terminal pro B‐type natriuretic peptide, Diseases of the circulatory (Cardiovascular) system, RC666-701
Abstract

Background Heart failure (HF) is a known risk factor for ischemic stroke, but data regarding ischemic stroke during hospitalization for acute decompensated HF (ADHF) are limited. Methods and Results We analyzed the data from a multicenter registry (Kyoto Congestive Heart Failure [KCHF] Registry) that enrolled 4056 consecutive patients with ADHF in Japan (mean age, 78 years; men, 2238 patients [55%]; acute coronary syndrome [ACS], 239 patients [5.9%]). We investigated the incidence and predictors of ischemic stroke during hospitalization for ADHF. During the hospitalization, 63 patients (1.6%) developed ischemic stroke. The median interval from admission to the onset of ischemic stroke was 7 [interquartile range: 2–14] days, and the most common underlying cause was cardioembolism (64%). Men (OR, 1.87; 95%CI, 1.11–3.24), ACS (OR, 2.31; 95%CI, 1.01–4.93), absence of prior HF hospitalization (OR, 2.21; 95%CI, 1.24–4.21), and high B‐type natriuretic peptide (BNP)/N‐terminal proBNP (NT‐proBNP) levels (above the median) at admission (OR, 3.15; 95%CI, 1.84–5.60) were independently associated with ischemic stroke. In patients without ACS, the independent risk factors for ischemic stroke were fully consistent with those in the main analysis. Higher quartiles of BNP/NT‐proBNP levels were significantly associated with higher incidence of ischemic stroke (P for trend,

Published
2021
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5. Ostial atresia of the coronary sinus in patients with supraventricular arrhythmias

Author

Ken‐ichi Hiroshima, Masahiko Goya, Michio Nagashima, Masato Fukunaga, Masatsugu Ohe, Yoshimori An, Yu Makihara, Kentaro Hayashi, and Kenji Ando

Subjects
coronary sinus, occlusion of the coronary sinus ostium, ostial atresia, persistent left superior vena cava, supraventricular tachycardia, Diseases of the circulatory (Cardiovascular) system, RC666-701
Abstract

Abstract Of 3577 patients with supraventricular arrhythmias, 3 demonstrated an atresia of the coronary sinus (CS) ostium. Two patients had the accessory pathways. One had atrial fibrillation. No unroofed CS or apparent persistent left superior vena cava was observed. Venous drainage through a small cardiac vein located on the lateral portion of the tricuspid annulus was observed in all patients. Those cases demonstrated that the incidence of ostial atresia of the CS was 0.084%. Accessory pathways were often accompanied by this anomaly. An abnormal venous orifice located on the lateral tricuspid annulus often functioned as the drainage of the CS flow.

Published
2019
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6. Clinical Features and Prognosis in Patients with Atrial Fibrillation and Prior Stroke: Comparing the Fushimi and Darlington AF Registries

Author

Hisashi Ogawa, Keitaro Senoo, Yoshimori An, Alena Shantsila, Eduard Shantsila, Deirdre A. Lane, Andreas Wolff, Masaharu Akao, and Gregory Y.H. Lip

Subjects
Atrial fibrillation, Previous stroke, Secondary prevention, Observational, Japan, United Kingdom, Medicine, Medicine (General), R5-920
Abstract

Background: Ethnic differences in clinical characteristics, stroke risk profiles and outcomes among atrial fibrillation (AF) patients may exist. We therefore compared AF patients with previous stroke from Japan and the United Kingdom (UK). Methods: We compared clinical characteristics, stroke risk and outcomes among AF patients from the Fushimi AF registry who had experienced a previous stroke (Japan; n = 688; 19.7%) and the Darlington AF registry (UK; n = 428; 19.0%). Results: AF patients with previous stroke in Fushimi were significantly younger (76.8 and 79.6 years of age in Fushimi and Darlington; p

Published
2017
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7. Mortality and predictors of appropriate implantable cardioverter defibrillator therapy in Japanese patients with Multicenter Automatic Defibrillator Implantation Trial II criteria

Author

Yoshimori An, MD, Kenji Ando, MD, Yoshimitsu Soga, MD, Akihiro Nomura, MD, Michio Nagashima, MD, Kentaro Hayashi, MD, Yu Makihara, MD, Masato Fukunaga, MD, Ken-ichi Hiroshima, MD, Masakiyo Nobuyoshi, MD, and Masahiko Goya, MD

Subjects
Implantable cardioverter defibrillator, Primary prevention, Ventricular tachyarrhythmia, Diseases of the circulatory (Cardiovascular) system, RC666-701
Abstract

Background: Data regarding long-term mortality and factors influencing appropriate therapies in Japanese patients with implantable cardioverter defibrillators (ICD), who satisfy the Multicenter Automatic Defibrillator Implantation Trial II (MADIT II) criteria for primary prevention, remain scarce. Methods: A total of 118 consecutive patients who underwent ICD implantation without any prior ventricular arrhythmic event, from January 2000 to December 2012, were enrolled based on the MADIT II criteria: left ventricular ejection fraction (LVEF) of ≤30% with ischemic heart disease and at least 4 weeks after a myocardial infarction. We investigated the mortality and factors influencing appropriate ICD therapies in this population. Results: The mean age was 69±10 years, and the mean LVEF was 25.1±4.5%. During the median follow up of 1406 days, the mortality rate was 20%, and the incidence of appropriate ICD therapy was 37% at 3 years. Multivariate analysis by using Cox regression model showed that left ventricular diastolic diameter ≥60 mm (hazard ratio [HR], 2.31; 95% confidence interval [CI], 1.07–5.38; P=0.033) and the presence of non-sustained ventricular tachycardia (NSVT) before implantation (HR, 2.26; 95% CI, 1.17-4.39; P=0.015) were independent predictors of appropriate ICD therapy. Conclusions: The mortality and incidence of appropriate ICD therapy were 20% and 37%, respectively, at 3 years in Japanese patients who met the MADIT II criteria during ICD implantation for primary prevention of sudden cardiac death. The presence of NSVT and dilated left ventricle independently predicted the incidence of appropriate ICD therapy after implantation.

Published
2017
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11. Impact of catheter ablation of ventricular tachycardia in patients with prior myocardial infarctions

Author

Masato Fukunaga, MD, Masahiko Goya, MD, Kenichi Hiroshima, MD, Kentaro Hayashi, MD, Masatsugu Ohe, MD, Yu Makihara, MD, Michio Nagashima, MD, Yoshimori An, MD, Shinichi Shirai, MD, Kenji Ando, MD, Hiroyoshi Yokoi, MD, and Masashi Iwabuchi, MD

Subjects
Catheter ablation, Ventricular tachycardia, Prior myocardial infarction, Endpoint, Delayed potential, Diseases of the circulatory (Cardiovascular) system, RC666-701
Abstract

Background: Catheter ablation can reduce episodes of ventricular tachycardia (VT) after myocardial infarction (MI). However, the optimal endpoint of the ablation procedure remains unclear. Methods: Fifty-one consecutive patients who received catheter ablation for VT after MI were included. The procedures targeted the isthmus of all the induced, sustained VTs. When the patients with induced VTs were hemodynamically stable, radiofrequency energy was delivered at the mid-diastolic potential recording site during VT. When the patients with VTs were hemodynamically unstable, the critical channel was identified at the delayed potential recording site, showing a good pace map, with a long stimulus-QRS interval. We delivered radiofrequency energy along the identified isthmus and across the exit of the circuit. Results: At the end of the procedure, all VTs became non-inducible in 30 patients (59%) and some VTs were inducible in 21 patients (41%). During a mean of 40±29 months of follow-up, no VT or ventricular fibrillation recurred in 24 patients (80%) in the non-inducible group and in 12 patients (57%) in the inducible group, respectively (P=0.03). The identification of the channel during VT mapping tended to associate with no recurrence, although the difference was not statistically significant (P=0.2). Fourteen patients (27%) died during the follow-up period, mostly due to non-cardiac causes. Conclusions: The catheter ablation targeting the isthmus of prior-MIVT and non-inducibility at the end of the procedure can provide a satisfactory follow-up result.

Published
2016
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12. Lead extractions in patients with cardiac implantable electronic device infections: Single center experience

Author

Masahiko Goya, MD, Michio Nagashima, MD, Ken-ichi Hiroshima, MD, Kentaro Hayashi, MD, Yu Makihara, MD, Masato Fukunaga, MD, Yoshimori An, MD, Masatsugu Ohe, MD, So-ichiro Yamazato, MD, Ko-ichiro Sonoda, MD, Kennosuke Yamashita, MD, Kouji Katayama, Tomoaki Ito, Harushi Niu, Kenji Ando, MD, Hiroyoshi Yokoi, MD, and Masashi Iwabuchi, MD

Subjects
Lead extraction, Laser, Pacemaker, Defibrillator, Infection, Diseases of the circulatory (Cardiovascular) system, RC666-701
Abstract

Background: Lead extraction using laser sheaths is performed mainly for cardiac implantable electronic device (CIED) infections. However, there are few reports concerning the management of CIED infections in Japan. Methods and results: Lead extraction procedures were performed in 183 patients targeting 450 leads (atrial leads: 170, ventricular: 181, implantable cardioverter-defibrillators (ICDs): 79, and coronary sinus: 20). One hundred twenty patients (65.6%) presented with pocket infections without the presentation of an endovascular infection. Blood cultures were positive at least once in 63 patients (34.4%). Complete procedure success was achieved for 437 leads (97.1%) while partial removal occurred in nine, and failure in four leads. Major complications directly related to the procedure occurred in five patients (2.7%). Two of the four patients with a cardiac tamponade required a surgical repair. All patients received intravenous antibiotics, at least, one week after the procedure. Pocket or systemic infections were successfully controlled in 181 patients (98.9%). Coagulase-negative staphylococci (30.1%) and Staphylococcus aureus (37.1%) were the most common causes of CIED infections. Conclusion: The current status of CIED infections in Japan seems to be similar to that previously reported from foreign countries. The optimal treatment of CIED infections involves the complete explantation of all hardware, followed by antibiotic therapy.

Published
2016
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13. Radiofrequency ablation of ventricular premature contraction originating from a native coronary cusp after transcatheter aortic valve replacement

Author

Shota Tohoku, Kenichi Hiroshima, Shoichi Kuramitsu, Michio Nagashima, Masato Fukunaga, Yoshimori An, and Kenji Ando

Subjects
Diseases of the circulatory (Cardiovascular) system, RC666-701
Abstract

We describe a case of radiofrequency ablation of ventricular premature contraction (VPC) originating from the left ventricular outflow tract after transcatheter aortic valve replacement. The VPC origin was the native aortic valve annulus between the left and right coronary cusps. Radiofrequency ablation was successfully performed by manipulating the ablation catheter from the gap between the sinotubular junction and implanted valve. Keywords: Radiofrequency ablation, Transcatheter aortic valve replacement, Ventricular premature contraction, Ventricular arrhythmia

Published
2017
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14. Long-term outcomes of catheter ablation of ventricular tachycardia in patients with structural heart disease

Author

Masahiko Goya, MD, Masato Fukunaga, MD, Ken-ichi Hiroshima, MD, Kentaro Hayashi, MD, Yu Makihara, MD, Michio Nagashima, MD, Yoshimori An, MD, Seiji Ohe, MD, Kennosuke Yamashita, MD, Kenji Ando, MD, Hiroyoshi Yokoi, MD, Masashi Iwabuchi, MD, Kouji Katayama, Tomoaki Ito, and Harushi Niu

Subjects
Catheter ablation, Ventricular tachycardia, Remote myocardial infarction, Dilated cardiomyopathy, Arrhythmogenic right ventricular dysplasia/cardiomyopathy, Diseases of the circulatory (Cardiovascular) system, RC666-701
Abstract

Background: Catheter ablation of ventricular tachycardia (VT) is feasible. However, the long-term outcomes for different underlying diseases have not been well defined. Methods: Eighty-eight consecutive patients who underwent catheter ablation of VT using a three-dimensional mapping system were analyzed. The primary endpoint was any VT or ventricular fibrillation (VF) recurrence. Secondary endpoints were a composite of death or any VT/VF recurrence. Underlying heart diseases were remote myocardial infarction (remote MI) in 51 patients and non-ischemic cardiomyopathy in 37 (arrhythmogenic right ventricular cardiomyopathy [ARVC] in 18 patients, and dilated cardiomyopathy [NIDCM] in 19). Results: Acute success was achieved in 82 of 88 (93%) patients. During a follow-up period of 39.2±4.6 months, VT recurred in 26 of 87 (30%), and VT/VF recurrence or death occurred in 39 of 87 (45%) patients. ARVC had better outcomes than NIDCM for the primary (p

Published
2015
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15. 3D T1rho sequences with FASE, UTE, and MAPSS acquisitions for knee evaluation

Author

Bae, Won C, Malis, Vadim, Kassai, Yoshimori, and Miyazaki, Mitsue

Subjects
Biomedical and Clinical Sciences, Clinical Sciences, Biomedical Imaging, Bioengineering, Clinical Research, Musculoskeletal, Humans, Sepharose, Imaging, Three-Dimensional, Knee Joint, Magnetic Resonance Imaging, Tibia, MRI, Osteoarthritis, Cartilage, Meniscus, Clinical sciences
Abstract

PurposeFor biochemical evaluation of soft tissues of the knee, T1rho magnetic resonance imaging (MRI) has been proposed. Purpose of this study was to compare three T1rho sequences based on fast advanced spin echo (FASE), ultrashort echo time (UTE), and magnetization-prepared angle-modulated partitioned k-space spoiled gradient echo snapshots (MAPSS) acquisitions for the knee evaluation.Materials and methodsWe developed two T1rho sequences using 3D FASE or 3D radial UTE acquisitions. 3D MAPSS T1rho was provided by the manufacturer. Agarose phantoms with varying concentrations were imaged. Additionally, bilateral knees of asymptomatic subjects were imaged sagittally. T1rho values of the phantoms and 4 regions of interest (ROI) of the knees (i.e., anterior and posterior meniscus, femoral and tibial cartilage) were determined.ResultsIn phantoms, all T1rho values monotonically decreased with increasing agarose concentration. 3D MAPSS T1rho values of 51, 34, and 38 ms were found for 2, 3, and 4% agarose, respectively, similar to published values on another platform. In the knee, the raw images were detailed with good contrast. Cartilage and meniscus T1rho values varied with the pulse sequence, being the lowest in the 3D UTE T1rho sequence. Comparing different ROIs, menisci generally had lower T1rho values compared to cartilage, as expected in healthy knees.ConclusionWe have successfully developed and implemented the new T1rho sequences and validated them using agarose phantoms and volunteer knees. All sequences were optimized to be clinically feasible (~ 5 min or less) and yielded satisfactory image quality and T1rho values consistent with the literature.

Published
2023

17. Next questions in autophagy

Author

Cuervo, Ana Maria, Elazar, Zvulun, Evans, Chantell, Ge, Liang, Hansen, Malene, Jäättelä, Marja, Liang, Jin Rui (Amos), Loos, Ben, Mizushima, Noboru, Simon, Anna Katharina, Tooze, Sharon, Yoshimori, Tamotsu, and Nakamura, Shuhei

Published
2024
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18. Lung T2* mapping using 3D ultrashort TE with tight intervals δTE

Author

Malis, Vadim, Kassai, Yoshimori, Vucevic, Diana, Bae, Won C, Ohno, Yoshiharu, Yen, Andrew, and Miyazaki, Mitsue

Subjects
Lung, Clinical Research, bi-exponential model, lung T-2*, short and long T-2 components, ultrashort TE, lung T 2 * $$ {\mathrm{T}}_2^{\ast } $$, short and long T2 components, Biomedical Engineering, Nuclear Medicine & Medical Imaging
Abstract

PurposeTo develop 3D ultrashort-TE (UTE) sequences with tight TE intervals (δTE), allowing for accurate T2*$$ {\mathrm{T}}_2^{\ast } $$ mapping of lungs under free breathing.MethodsWe have implemented a four-echo UTE sequence with δTE (

Published
2023

21. Usefulness of Higher Order of System-Size Correction for Diffusion Coefficients of Macromolecules: A Molecular Dynamics Study

Author

Iwashita, Tomoya, Nagao, Masaaki, Yoshimori, Akira, Terazima, Masahide, and Akiyama, Ryo

Subjects
Physics - Chemical Physics, Condensed Matter - Soft Condensed Matter, Physics - Biological Physics
Abstract

Yeh and Hummer's simplified estimation method has often been adopted to obtain diffusion coefficients for solute molecules using molecular dynamic simulation. However, the simplified formula is not necessarily valid when a small basic cell is used. Therefore, we conducted molecular dynamics simulations of aqueous protein solution to estimate the diffusion coefficient for the infinite dilution limit. We confirmed a deviation from the simplified formula in the simulation data and rationalized the discrepancy based on the unsimplified formula., Comment: 20pages, 5figures

Published
2022
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22. Aliphatic and Olefinic Fat Suppression in the Orbit Using Polarity-altered Spectral and Spatial Selective Acquisition (PASTA) with Opposed Phase

Author

Malis, Vadim, Bae, Won C, Yamamoto, Asako, Kassai, Yoshimori, McDonald, Marin A, and Miyazaki, Mitsue

Subjects
Space Sciences, Physical Sciences, Neurosciences, aliphatic and olefinic fat, fat suppression, orbit, polarity altered spectral and spatial acquisition, unsaturated and saturated chemical shift opposed phase
Abstract

PurposeFatty acid composition of the orbit makes it challenging to achieve complete fat suppression during orbit MR imaging. Implementation of a fat suppression technique capable of suppressing signals from saturated (aliphatic) and unsaturated (olefinic or protons at double-bonded carbon sites) fat would improve the visualization of an optical nerve. Furthermore, the ability to semi-quantify the fractions of aliphatic and olefinic fat may potentially provide valuable information in assessing orbit pathology.MethodsA phantom study was conducted on various oil samples on a clinical 3 Tesla scanner. The imaging protocol included three 2D fast spin echo (FSE) sequences: in-phase, polarity-altered spectral and spatial selective acquisition (PASTA), and a combination of PASTA with opposed phase in olefinic and aliphatic chemical shift. The results were validated against high-resolution 11.7T NMR and compared with images acquired with spectral attenuated inversion recovery (SPAIR) and chemical shift selective (CHESS) fat suppression techniques. In-vivo data were acquired on eight healthy subjects and were compared with the prior histological studies.ResultsPASTA with opposed phase achieved complete suppression of fat signals in the orbits and provided images of well-delineated optical nerves and muscles in all subjects. The olefinic fat fraction in the olive, walnut, and fish oil phantoms at 3T was found to be 5.0%, 11.2%, and 12.8%, respectively, whereas 11.7T NMR provides the following olefinic fat fractions: 6.0% for olive, 11.5% for walnut, and 12.6% for fish oils. For the in-vivo study, on average, olefinic fat accounted for 9.9% ± 3.8% of total fat while the aliphatic fat fraction was 90.1% ± 3.8%, in the normal orbits.ConclusionWe have introduced a new fat suppression technique using PASTA with opposed phase and applied it to human orbits. The purposed method achieves an excellent orbital fat suppression and the quantification of aliphatic and olefinic fat signals.

Published
2023

23. Genetic Risk Stratification of Primary Open-Angle Glaucoma in Japanese Individuals

Author

Matsuda, Koichi, Yamanashi, Yuji, Furukawa, Yoichi, Morisaki, Takayuki, Okada, Yukinori, Murakami, Yoshinori, Muto, Kaori, Nagai, Akiko, Nakamura, Yusuke, Obara, Wataru, Yamaji, Ken, Takahashi, Kazuhisa, Asai, Satoshi, Takahashi, Yasuo, Higashiue, Shinichi, Kobayashi, Shuzo, Yamaguchi, Hiroki, Nagata, Yasunobu, Wakita, Satoshi, Nito, Chikako, Iwasaki, Yu-Ki, Murayama, Shigeo, Yoshimori, Kozo, Miki, Yoshio, Obata, Daisuke, Higashiyama, Masahiko, Masumoto, Akihide, Koga, Yoshinobu, Koretsune, Yukihiro, Aihara, Makoto, Sakata, Rei, Kashiwagi, Kenji, Mabuchi, Fumihiko, Kawase, Kazuhide, Iwata, Takeshi, Tsujikawa, Motokazu, Nishiguchi, Koji M., Akiyama, Masato, Tamiya, Gen, Fujiwara, Kohta, Shiga, Yukihiro, Yokoyama, Yu, Hashimoto, Kazuki, Sato, Masataka, Sato, Kota, Narita, Akira, Hashimoto, Sawako, Ueda, Emi, Furuta, Yoshihiko, Hata, Jun, Miyake, Masahiro, Ikeda, Hanako O., Suda, Kenji, Numa, Shogo, Mori, Yuki, Morino, Kazuya, Murakami, Yusuke, Shimokawa, Sakurako, Nakamura, Shun, Yawata, Nobuyo, Fujisawa, Kimihiko, Yamana, Satoshi, Mori, Kenichiro, Ikeda, Yasuhiro, Miyata, Kazunori, Mori, Keisuke, Ogino, Ken, Koyanagi, Yoshito, Kamatani, Yoichiro, Ninomiya, Toshiharu, Sonoda, Koh-Hei, and Nakazawa, Toru

Published
2024
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28. Quantification of escape from X chromosome inactivation with single-cell omics data reveals heterogeneity across cell types and tissues

Author

Charoensawan, Varodom, Hon, Chung-Chau, Majumder, Partha P., Matangkasombut, Ponpan, Park, Woong-Yang, Prabhakar, Shyam, Shin, Jay W., Carninci, Piero, Chambers, John C., Loh, Marie, Pithukpakorn, Manop, Suktitipat, Bhoom, Yamamoto, Kazuhiko, Rajagopalan, Deepa, Rayan, Nirmala Arul, Sankaran, Shvetha, Chantaraamporn, Juthamard, Chatterjee, Ankita, Ghosh, Supratim, Han, Kyung Yeon, Jevapatarakul, Damita, Nguantad, Sarintip, Sarkar, Sumanta, Thungsatianpun, Narita, Abe, Mai, Furukawa, Seiko, Inoue, Gyo, Myouzen, Keiko, Oh, Jin-Mi, Suzuki, Akari, Ando, Yoshinari, Kojima, Miki, Kouno, Tsukasa, Lim, Jinyeong, Maitra, Arindam, Tan, Le Min, Venkatesh, Prasanna Nori, Choi, Murim, Park, Jong-Eun, Buyamin, Eliora Violain, Kock, Kian Hong, Xuan Lin, Quy Xiao, Moody, Jonathan, Sonthalia, Radhika, Ishigaki, Kazuyoshi, Nakano, Masahiro, Okada, Yukinori, Tomofuji, Yoshihiko, Ho Namkoong, Edahiro, Ryuya, Takano, Tomomi, Nishihara, Hiroshi, Shirai, Yuya, Sonehara, Kyuto, Tanaka, Hiromu, Azekawa, Shuhei, Mikami, Yohei, Lee, Ho, Hasegawa, Takanori, Okudela, Koji, Okuzaki, Daisuke, Motooka, Daisuke, Kanai, Masahiro, Naito, Tatsuhiko, Yamamoto, Kenichi, Wang, Qingbo S., Saiki, Ryunosuke, Ishihara, Rino, Matsubara, Yuta, Hamamoto, Junko, Hayashi, Hiroyuki, Yoshimura, Yukihiro, Tachikawa, Natsuo, Yanagita, Emmy, Hyugaji, Takayoshi, Shimizu, Eigo, Katayama, Kotoe, Kato, Yasuhiro, Morita, Takayoshi, Takahashi, Kazuhisa, Harada, Norihiro, Naito, Toshio, Hiki, Makoto, Matsushita, Yasushi, Takagi, Haruhi, Aoki, Ryousuke, Nakamura, Ai, Harada, Sonoko, Sasano, Hitoshi, Kabata, Hiroki, Masaki, Katsunori, Kamata, Hirofumi, Ikemura, Shinnosuke, Chubachi, Shotaro, Okamori, Satoshi, Terai, Hideki, Morita, Atsuho, Asakura, Takanori, Sasaki, Junichi, Morisaki, Hiroshi, Uwamino, Yoshifumi, Nanki, Kosaku, Uchida, Sho, Uno, Shunsuke, Nishimura, Tomoyasu, Ishiguro, Takashi, Isono, Taisuke, Shibata, Shun, Matsui, Yuma, Hosoda, Chiaki, Takano, Kenji, Nishida, Takashi, Kobayashi, Yoichi, Takaku, Yotaro, Takayanagi, Noboru, Ueda, Soichiro, Tada, Ai, Miyawaki, Masayoshi, Yamamoto, Masaomi, Yoshida, Eriko, Hayashi, Reina, Nagasaka, Tomoki, Arai, Sawako, Kaneko, Yutaro, Sasaki, Kana, Tagaya, Etsuko, Kawana, Masatoshi, Arimura, Ken, Takahashi, Kunihiko, Anzai, Tatsuhiko, Ito, Satoshi, Endo, Akifumi, Uchimura, Yuji, Miyazaki, Yasunari, Honda, Takayuki, Tateishi, Tomoya, Tohda, Shuji, Ichimura, Naoya, Sonobe, Kazunari, Sassa, Chihiro Tani, Nakajima, Jun, Nakano, Yasushi, Nakajima, Yukiko, Anan, Ryusuke, Arai, Ryosuke, Kurihara, Yuko, Harada, Yuko, Nishio, Kazumi, Ueda, Tetsuya, Azuma, Masanori, Saito, Ryuichi, Sado, Toshikatsu, Miyazaki, Yoshimune, Sato, Ryuichi, Haruta, Yuki, Nagasaki, Tadao, Yasui, Yoshinori, Hasegawa, Yoshinori, Mutoh, Yoshikazu, Kimura, Tomoki, Sato, Tomonori, Takei, Reoto, Hagimoto, Satoshi, Noguchi, Yoichiro, Yamano, Yasuhiko, Sasano, Hajime, Ota, Sho, Nakamori, Yasushi, Yoshiya, Kazuhisa, Saito, Fukuki, Yoshihara, Tomoyuki, Wada, Daiki, Iwamura, Hiromu, Kanayama, Syuji, Maruyama, Shuhei, Yoshiyama, Takashi, Ohta, Ken, Kokuto, Hiroyuki, Ogata, Hideo, Tanaka, Yoshiaki, Arakawa, Kenichi, Shimoda, Masafumi, Osawa, Takeshi, Tateno, Hiroki, Hase, Isano, Yoshida, Shuichi, Suzuki, Shoji, Kawada, Miki, Horinouchi, Hirohisa, Saito, Fumitake, Mitamura, Keiko, Hagihara, Masao, Ochi, Junichi, Uchida, Tomoyuki, Baba, Rie, Arai, Daisuke, Ogura, Takayuki, Takahashi, Hidenori, Hagiwara, Shigehiro, Nagao, Genta, Konishi, Shunichiro, Nakachi, Ichiro, Murakami, Koji, Yamada, Mitsuhiro, Sugiura, Hisatoshi, Sano, Hirohito, Matsumoto, Shuichiro, Kimura, Nozomu, Ono, Yoshinao, Baba, Hiroaki, Suzuki, Yusuke, Nakayama, Sohei, Masuzawa, Keita, Namba, Shinichi, Suzuki, Ken, Naito, Yoko, Liu, Yu-Chen, Takuwa, Ayako, Sugihara, Fuminori, Wing, James B., Sakakibara, Shuhei, Hizawa, Nobuyuki, Shiroyama, Takayuki, Miyawaki, Satoru, Kawamura, Yusuke, Nakayama, Akiyoshi, Matsuo, Hirotaka, Yuichi, Maeda, Nii, Takuro, Noda, Yoshimi, Niitsu, Takayuki, Adachi, Yuichi, Enomoto, Takatoshi, Amiya, Saori, Hara, Reina, Yamaguchi, Yuta, Murakami, Teruaki, Kuge, Tomoki, Matsumoto, Kinnosuke, Yamamoto, Yuji, Yamamoto, Makoto, Yoneda, Midori, Kishikawa, Toshihiro, Yamada, Shuhei, Kawabata, Shuhei, Kijima, Noriyuki, Takagaki, Masatoshi, Sasa, Noah, Ueno, Yuya, Suzuki, Motoyuki, Takemoto, Norihiko, Eguchi, Hirotaka, Fukusumi, Takahito, Imai, Takao, Fukushima, Munehisa, Kishima, Haruhiko, Inohara, Hidenori, Tomono, Kazunori, Kato, Kazuto, Takahashi, Meiko, Matsuda, Fumihiko, Hirata, Haruhiko, Takeda, Yoshito, Koh, Hidefumi, Manabe, Tadashi, Funatsu, Yohei, Ito, Fumimaro, Fukui, Takahiro, Shinozuka, Keisuke, Kohashi, Sumiko, Miyazaki, Masatoshi, Shoko, Tomohisa, Kojima, Mitsuaki, Adachi, Tomohiro, Ishikawa, Motonao, Takahashi, Kenichiro, Inoue, Takashi, Hirano, Toshiyuki, Kobayashi, Keigo, Takaoka, Hatsuyo, Watanabe, Kazuyoshi, Miyazawa, Naoki, Kimura, Yasuhiro, Sado, Reiko, Sugimoto, Hideyasu, Kamiya, Akane, Kuwahara, Naota, Fujiwara, Akiko, Matsunaga, Tomohiro, Sato, Yoko, Okada, Takenori, Hirai, Yoshihiro, Kawashima, Hidetoshi, Narita, Atsuya, Niwa, Kazuki, Sekikawa, Yoshiyuki, Nishi, Koichi, Nishitsuji, Masaru, Tani, Mayuko, Suzuki, Junya, Nakatsumi, Hiroki, Ogura, Takashi, Kitamura, Hideya, Hagiwara, Eri, Murohashi, Kota, Okabayashi, Hiroko, Mochimaru, Takao, Nukaga, Shigenari, Satomi, Ryosuke, Oyamada, Yoshitaka, Mori, Nobuaki, Baba, Tomoya, Fukui, Yasutaka, Odate, Mitsuru, Mashimo, Shuko, Makino, Yasushi, Yagi, Kazuma, Hashiguchi, Mizuha, Kagyo, Junko, Shiomi, Tetsuya, Fuke, Satoshi, Saito, Hiroshi, Tsuchida, Tomoya, Fujitani, Shigeki, Takita, Mumon, Morikawa, Daiki, Yoshida, Toru, Izumo, Takehiro, Inomata, Minoru, Kuse, Naoyuki, Awano, Nobuyasu, Tone, Mari, Ito, Akihiro, Nakamura, Yoshihiko, Hoshino, Kota, Maruyama, Junichi, Ishikura, Hiroyasu, Takata, Tohru, Odani, Toshio, Amishima, Masaru, Hattori, Takeshi, Shichinohe, Yasuo, Kagaya, Takashi, Kita, Toshiyuki, Ohta, Kazuhide, Sakagami, Satoru, Koshida, Kiyoshi, Hayashi, Kentaro, Shimizu, Tetsuo, Kozu, Yutaka, Hiranuma, Hisato, Gon, Yasuhiro, Izumi, Namiki, Nagata, Kaoru, Ueda, Ken, Taki, Reiko, Hanada, Satoko, Kawamura, Kodai, Ichikado, Kazuya, Nishiyama, Kenta, Muranaka, Hiroyuki, Nakamura, Kazunori, Hashimoto, Naozumi, Wakahara, Keiko, Koji, Sakamoto, Omote, Norihito, Ando, Akira, Kodama, Nobuhiro, Kaneyama, Yasunari, Shunsuke, Maeda, Kuraki, Takashige, Matsumoto, Takemasa, Yokote, Koutaro, Nakada, Taka-Aki, Abe, Ryuzo, Oshima, Taku, Shimada, Tadanaga, Harada, Masahiro, Takahashi, Takeshi, Ono, Hiroshi, Sakurai, Toshihiro, Shibusawa, Takayuki, Kimizuka, Yoshifumi, Kawana, Akihiko, Sano, Tomoya, Watanabe, Chie, Suematsu, Ryohei, Sageshima, Hisako, Yoshifuji, Ayumi, Ito, Kazuto, Takahashi, Saeko, Ishioka, Kota, Nakamura, Morio, Masuda, Makoto, Wakabayashi, Aya, Watanabe, Hiroki, Ueda, Suguru, Nishikawa, Masanori, Chihara, Yusuke, Takeuchi, Mayumi, Onoi, Keisuke, Shinozuka, Jun, Sueyoshi, Atsushi, Nagasaki, Yoji, Okamoto, Masaki, Ishihara, Sayoko, Shimo, Masatoshi, Tokunaga, Yoshihisa, Kusaka, Yu, Ohba, Takehiko, Isogai, Susumu, Ogawa, Aki, Inoue, Takuya, Fukuyama, Satoru, Eriguchi, Yoshihiro, Yonekawa, Akiko, Kan-o, Keiko, Matsumoto, Koichiro, Kanaoka, Kensuke, Ihara, Shoichi, Komuta, Kiyoshi, Inoue, Yoshiaki, Chiba, Shigeru, Yamagata, Kunihiro, Hiramatsu, Yuji, Kai, Hirayasu, Asano, Koichiro, Oguma, Tsuyoshi, Ito, Yoko, Hashimoto, Satoru, Yamasaki, Masaki, Kasamatsu, Yu, Komase, Yuko, Hida, Naoya, Tsuburai, Takahiro, Oyama, Baku, Takada, Minoru, Kanda, Hidenori, Kitagawa, Yuichiro, Fukuta, Tetsuya, Miyake, Takahito, Yoshida, Shozo, Ogura, Shinji, Abe, Shinji, Kono, Yuta, Togashi, Yuki, Takoi, Hiroyuki, Kikuchi, Ryota, Ogawa, Shinichi, Ogata, Tomouki, Ishihara, Shoichiro, Kanehiro, Arihiko, Ozaki, Shinji, Fuchimoto, Yasuko, Wada, Sae, Fujimoto, Nobukazu, Nishiyama, Kei, Terashima, Mariko, Beppu, Satoru, Yoshida, Kosuke, Narumoto, Osamu, Nagai, Hideaki, Ooshima, Nobuharu, Motegi, Mitsuru, Umeda, Akira, Miyagawa, Kazuya, Shimada, Hisato, Endo, Mayu, Ohira, Yoshiyuki, Watanabe, Masafumi, Inoue, Sumito, Igarashi, Akira, Sato, Masamichi, Sagara, Hironori, Tanaka, Akihiko, Ohta, Shin, Kimura, Tomoyuki, Shibata, Yoko, Tanino, Yoshinori, Nikaido, Takefumi, Minemura, Hiroyuki, Sato, Yuki, Yamada, Yuichiro, Hashino, Takuya, Shinoki, Masato, Iwagoe, Hajime, Takahashi, Hiroshi, Fujii, Kazuhiko, Kishi, Hiroto, Kanai, Masayuki, Imamura, Tomonori, Yamashita, Tatsuya, Yatomi, Masakiyo, Maeno, Toshitaka, Hayashi, Shinichi, Takahashi, Mai, Kuramochi, Mizuki, Kamimaki, Isamu, Tominaga, Yoshiteru, Ishii, Tomoo, Utsugi, Mitsuyoshi, Ono, Akihiro, Tanaka, Toru, Kashiwada, Takeru, Fujita, Kazue, Saito, Yoshinobu, Seike, Masahiro, Watanabe, Hiroko, Matsuse, Hiroto, Kodaka, Norio, Nakano, Chihiro, Oshio, Takeshi, Hirouchi, Takatomo, Makino, Shohei, Egi, Moritoki, Omae, Yosuke, Nannya, Yasuhito, Ueno, Takafumi, Katayama, Kazuhiko, Ai, Masumi, Fukui, Yoshinori, Kumanogoh, Atsushi, Sato, Toshiro, Hasegawa, Naoki, Tokunaga, Katsushi, Ishii, Makoto, Koike, Ryuji, Kitagawa, Yuko, Kimura, Akinori, Imoto, Seiya, Miyano, Satoru, Ogawa, Seishi, Kanai, Takanori, Fukunaga, Koichi, Takeshima, Yusuke, Tanaka, Kentaro, Koichi Matsuda, Yamanashi, Yuji, Furukawa, Yoichi, Morisaki, Takayuki, Murakami, Yoshinori, Kamatani, Yoichiro, Muto, Kaori, Nagai, Akiko, Nakamura, Yusuke, Obara, Wataru, Yamaji, Ken, Asai, Satoshi, Takahashi, Yasuo, Higashiue, Shinichi, Kobayashi, Shuzo, Yamaguchi, Hiroki, Nagata, Yasunobu, Wakita, Satoshi, Nito, Chikako, Iwasaki, Yu-ki, Murayama, Shigeo, Yoshimori, Kozo, Miki, Yoshio, Obata, Daisuke, Higashiyama, Masahiko, Masumoto, Akihide, Koga, Yoshinobu, Koretsune, Yukihiro, Yata, Tomohiro, Ogawa, Kotaro, Namkoong, Ho, Okuno, Tatsusada, Liu, Boxiang, Matsuda, Koichi, and Mochizuki, Hideki

Published
2024
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41. Beth Levine in memoriam

Author

An, Zhenyi, Ballabio, Andrea, Bennett, Lynda, Boya, Patricia, Cecconi, Francesco, Chiang, Wei-Chung, Codogno, Patrice, Colombo, Maria Isabel, Cuervo, Ana Maria, Debnath, Jayanta, Deretic, Vojo, Dikic, Ivan, Dionne, Keith, Dong, Xiaonan, Elazar, Zvulun, Galluzzi, Lorenzo, Gentile, Frank, Griffin, Diane E, Hansen, Malene, Hardwick, J Marie, He, Congcong, Huang, Shu-Yi, Hurley, James, Jackson, William T, Jozefiak, Cindy, Kitsis, Richard N, Klionsky, Daniel J, Kroemer, Guido, Meijer, Alfred J, Melendez, Alicia, Melino, Gerry, Mizushima, Noboru, Murphy, Leon O, Nixon, Ralph, Orvedahl, Anthony, Pattingre, Sophie, Piacentini, Mauro, Reggiori, Fulvio, Ross, Theodora, Rubinsztein, David C, Ryan, Kevin, Sadoshima, Junichi, Schreiber, Stuart L, Scott, Frederick, Sebti, Salwa, Shiloh, Michael, Shoji, Sanae, Simonsen, Anne, Smith, Haley, Sumpter, Kathryn M, Thompson, Craig B, Thorburn, Andrew, Thumm, Michael, Tooze, Sharon, Vaccaro, Maria I, Virgin, Herbert W, Wang, Fei, White, Eileen, Xavier, Ramnik J, Yoshimori, Tamotsu, Yuan, Junying, Yue, Zhenyu, and Zhong, Qing

Subjects
Biochemistry and Cell Biology, Biological Sciences, Biochemistry & Molecular Biology, Biochemistry and cell biology
Published
2020

42. Structural basis for autophagy inhibition by the human Rubicon–Rab7 complex

Author

Bhargava, Hersh K, Tabata, Keisuke, Byck, Jordan M, Hamasaki, Maho, Farrell, Daniel P, Anishchenko, Ivan, DiMaio, Frank, Im, Young Jun, Yoshimori, Tamotsu, and Hurley, James H

Subjects
Biochemistry and Cell Biology, Medicinal and Biomolecular Chemistry, Chemical Sciences, Biological Sciences, Rare Diseases, Orphan Drug, Autophagy, Autophagy-Related Proteins, Crystallography, X-Ray, HeLa Cells, Humans, Models, Molecular, Protein Binding, Protein Domains, rab GTP-Binding Proteins, rab7 GTP-Binding Proteins, autophagy, Rab GTPase, crystal structure, Hela Cells
Abstract

Rubicon is a potent negative regulator of autophagy and a potential target for autophagy-inducing therapeutics. Rubicon-mediated inhibition of autophagy requires the interaction of the C-terminal Rubicon homology (RH) domain of Rubicon with Rab7-GTP. Here we report the 2.8-Å crystal structure of the Rubicon RH domain in complex with Rab7-GTP. Our structure reveals a fold for the RH domain built around four zinc clusters. The switch regions of Rab7 insert into pockets on the surface of the RH domain in a mode that is distinct from those of other Rab-effector complexes. Rubicon residues at the dimer interface are required for Rubicon and Rab7 to colocalize in living cells. Mutation of Rubicon RH residues in the Rab7-binding site restores efficient autophagic flux in the presence of overexpressed Rubicon, validating the Rubicon RH domain as a promising therapeutic target.

Published
2020

48. The P4‐ATPase Drs2 interacts with and stabilizes the multisubunit tethering complex TRAPPIII in yeast

Author

Pazos, Irene, Puig‐Tintó, Marta, Betancur, Laura, Cordero, Jorge, Jiménez‐Menéndez, Nereida, Abella, Marc, Hernández, Altair C, Duran, Ana G, Adachi‐Fernández, Emi, Belmonte‐Mateos, Carla, Sabido‐Bozo, Susana, Tosi, Sébastien, Nezu, Akiko, Oliva, Baldomero, Colombelli, Julien, Graham, Todd R, Yoshimori, Tamotsu, Muñiz, Manuel, Hamasaki, Maho, and Gallego, Oriol

Published
2023
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