研究者詳細 - 森田　瑞樹

論文 - 森田　瑞樹

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Impact of Sensor-Axis Combinations on Machine Learning Accuracy for Human Activity Recognition Using Accelerometer Data in Clinical Settings 査読国際誌

Takahiro Yamane, Moeka Kimura, Mizuki Morita

Physical Activity and Health 9 ( 1 ) 95 - 109 2025年5月

担当区分：最終著者,　責任著者記述言語：英語掲載種別：研究論文（学術雑誌）出版者・発行元：Ubiquity Press, Ltd.

Background: Identifying patient activity during symptom onset is crucial in conditions such as chronic obstructive pulmonary disease (COPD) or arrhythmia. Accelerometer data can aid in this process; however, minimal data requirements are preferable. This study aimed to determine the minimum number of axes required to accurately recognize activities related to COPD or arrhythmia.Methods: Thirty healthy participants wore a 9-axis accelerometer in five positions and performed nine activities. Machine learning-based activity recognition was conducted using 9-, 6-, and 3-axis data from the nondominant wrist or chest, as these two positions demonstrated high recognition accuracy in our previous study.Results: For the nondominant wrist, the accuracy of recognizing activities such as lying in the supine position, standing, eating, and running was comparable for the 3-axis acceleration and 9-axis data. For the chest, the accuracy of recognizing activities such as lying in the supine position, standing, sitting, using the restroom, and ascending or descending stairs was comparable for 6-axis (combined acceleration and magnetometer) and 9-axis data.Conclusions: The findings suggest that 3-axis acceleration data for the nondominant wrist and 6-axis combined acceleration and magnetometer data for the chest lead to high activity recognition accuracy.

DOI： 10.5334/paah.441

Clinical-level screening of sleep apnea syndrome with single-lead ECG alone is achievable using machine learning with appropriate time windows 査読国際誌

Takahiro Yamane, Masanori Fujii, Mizuki Morita

Sleep and Breathing 29 ( 2 ) 156 2025年4月

担当区分：最終著者,　責任著者記述言語：英語掲載種別：研究論文（学術雑誌）出版者・発行元：Springer Science and Business Media LLC

Purpose: To establish a simple and noninvasive screening test for sleep apnea (SA) that imposes less burden on potential patients. The specific objective of this study was to verify the effectiveness of past and future single-lead electrocardiogram (ECG) data from SA occurrence sites in improving the estimation accuracy of SA and sleep apnea syndrome (SAS) using machine learning.
Methods: The Apnea-ECG dataset comprising 70 ECG recordings was used to construct various machine-learning models. The time window size was adjusted based on the accuracy of SA detection, and the performance of SA detection and SAS diagnosis (apnea‒hypopnea index ≥ 5 was considered SAS) was compared.
Results: Using ECG data from a few minutes before and after the occurrence of SAs improved the estimation accuracy of SA and SAS in all machine learning models. The optimal range of the time window and achieved accuracy for SAS varied by model; however, the sensitivity ranged from 95.7 to 100%, and the specificity ranged from 91.7 to 100%.
Conclusions: ECG data from a few minutes before and after SA occurrence were effective in SA detection and SAS diagnosis, confirming that SA is a continuous phenomenon and that SA affects heart function over a few minutes before and after SA occurrence. Screening tests for SAS, using data obtained from single-lead ECGs with appropriate past and future time windows, should be performed with clinical-level accuracy.

DOI： 10.1007/s11325-025-03316-0

その他リンク： https://link.springer.com/article/10.1007/s11325-025-03316-0/fulltext.html

Application of Nine-Axis Accelerometer-Based Recognition of Daily Activities in Clinical Examination 査読国際誌

Takahiro Yamane, Moeka Kimura, Mizuki Morita

Physical Activity and Health 8 ( 1 ) 29 - 46 2024年3月

Tri-Axial Accelerometer-Based Recognition of Daily Activities Causing Shortness of Breath in COPD Patients 査読国際誌

Takahiro Yamane, Yuu Yamasaki, Wakana Nakashima, Mizuki Morita

Physical Activity and Health 7 ( 1 ) 64 - 75 2023年2月

Trial of sportswear type ECG sensor device for cardiac safety management during marathon running 査読国際誌

Takahiro Yamane, Kazuya Hirano, Kenta Hirai, Daiki Ousaka, Noriko Sakano, Mizuki Morita, Susumu Oozawa, Shingo Kasahara

Advanced Biomedical Engineering 11 151 - 161 2022年8月

担当区分：責任著者記述言語：英語掲載種別：研究論文（学術雑誌）出版者・発行元：Japanese Society for Medical and Biological Engineering (JSMBE)

Cardiac arrest has been reported during participation in several sports. Of these sports, marathon running is a particularly popular sport but imposes high cardiac load. Indeed, its popularity has been growing worldwide. Risk of cardiac arrest during marathon races is also expected to increase. Several studies have recorded electrocardiographic (ECG) information during marathon races to protect athletes from cardiac arrest. Although evaluable ECG data have been obtained and analyzed, cost-effectiveness of the system, data quality, and clinical significance remain inadequate. This report is the first to describe an economical electrocardiograph built into a T-shirt for use during marathon race. Twenty healthy runners aged 20 to 59 years (mean 36 years) wore the ECG device while running. The ECG data were monitored and analyzed to assess the observed frequencies of specified arrhythmias and the sections of the marathon in which the arrhythmias occurred. Of the ECG data obtained from 14 runners who completed the full marathon, six ECG datasets were evaluable. In some runners, there was inadequate contact between the electrode and body surface or poor Bluetooth connection between the ECG wireless transmitter and smartphone. Regarding arrhythmia analysis, all evaluable data that were analyzed showed some rhythm fluctuations. In conclusion, this economical T-shirt type ECG sensor provided evaluable ECG data during marathon races, although the evaluable rate was not high. The data were used to analyze specified arrhythmias, but some difficulties were encountered. The ECG sensor did not function properly because of a system error. The ECG sensor was not adequately moistened to record ECGs accurately. Moreover, some runners chose an unsuitable shirt size, which impaired the stability and strength of the electrode–skin contact. These shortcomings produced noise in the ECG data, which made it difficult to analyze arrhythmias. The next step will be to solve these problems and acquire data from a large number of runners.

DOI： 10.14326/abe.11.151

Initial evaluation of a novel electrocardiography sensor-embedded fabric wear during a full marathon 査読国際誌

Daiki Ousaka, Kenta Hirai, Noriko Sakano, Mizuki Morita, Madoka Haruna, Kazuya Hirano, Takahiro Yamane, Akira Teraoka, Kazuo Sanou, Susumu Oozawa, Shingo Kasahara

Heart and Vessels 37 ( 3 ) 443 - 450 2022年3月

Multiple cancer type classification by small RNA expression profiles with plasma samples from multiple facilities 査読国際誌

Kuno Suzuki, Hideyoshi Igata, Motoki Abe, Yusuke Yamamoto, small RNA based cancer classification project

Cancer Science 113 ( 6 ) 2144 - 2166 2022年2月

Predicting Anesthetic Infusion Events Using Machine Learning 査読国際誌

Naoki Miyaguchi, Koh Takeuchi, Hisashi Kashima, Mizuki Morita, Hiroshi Morimatsu

Scientific Reports 11 ( 1 ) 23648 - 23648 2021年11月

The Data Use Ontology to streamline responsible access to human biomedical datasets 査読国際共著国際誌

Jonathan Lawson, Moran N. Cabili, Giselle Kerry, Tiffany Boughtwood, Adrian Thorogood, Pinar Alper, Sarion R. Bowers, Rebecca R. Boyles, Anthony J. Brookes, Matthew Brush, Tony Burdett, Hayley Clissold, Stacey Donnelly, Stephanie O.M. Dyke, Mallory A. Freeberg, Melissa A. Haendel, Chihiro Hata, Petr Holub, Francis Jeanson, Aina Jene, Minae Kawashima, Shuichi Kawashima, Melissa Konopko, Irene Kyomugisha, Haoyuan Li, Mikael Linden, Laura Lyman Rodriguez, Mizuki Morita, Nicola Mulder, Jean Muller, Satoshi Nagaie, Jamal Nasir, Soichi Ogishima, Vivian Ota Wang, Laura D. Paglione, Ravi N. Pandya, Helen Parkinson, Anthony A. Philippakis, Fabian Prasser, Jordi Rambla, Kathy Reinold, Gregory A. Rushton, Andrea Saltzman, Gary Saunders, Heidi J. Sofia, John D. Spalding, Morris A. Swertz, Ilia Tulchinsky, Esther J. van Enckevort, Susheel Varma, Craig Voisin, Natsuko Yamamoto, Chisato Yamasaki, Lyndon Zass, Jaime M. Guidry Auvil, Tommi H. Nyrönen, Mélanie Courtot

Cell Genomics 1 ( 2 ) 100028 - 100028 2021年11月

Simple Wearable Device to Reduce Stress When Delivering a Speech without Pre-Training 査読国際誌

Takahiro Yamane, Yuma Nakadoi, Mina Takagi, Mizuki Morita

Healthcare Informatics Research 27 ( 3 ) 231 - 240 2021年7月

担当区分：最終著者,　責任著者記述言語：英語掲載種別：研究論文（学術雑誌）出版者・発行元：Korean Society of Medical Informatics

DOI： 10.4258/hir.2021.27.3.231

その他リンク： https://www.webofscience.com/wos/woscc/full-record/WOS:000684600200008

パンデミックへの備えとしての医療資材の循環備蓄：モデル化とシミュレーション査読

森田瑞樹

統合科学 1 17 - 20 2021年3月

担当区分：筆頭著者,　最終著者,　責任著者記述言語：日本語掲載種別：研究論文（大学，研究機関等紀要）

感染症の世界的な大流行（パンデミック）が発生すると，マスク，消毒液，個人保護具などの医療資材の需要が平時の生産能力を超えるため，必要量を確保することが一時的に困難になる。このような事態に備えるためには備蓄が必要となる。しかし，パンデミックは発生頻度が低く，いつ発生するか予測できないため，パンデミックの際に備蓄した医療資材が古くなっている可能性がある。本稿では，備蓄した医療資材が消費期限を過ぎることを防ぐ工夫として「循環備蓄（ローリングストック）」を提案し，循環備蓄のモデル化とそれに基づいたシミュレーションを示す。これを，循環備蓄用の倉庫の設計，感染症の流行開始における医療資材の減少のモニタリング，医療資材の生産能力が増強された後の備蓄量の回復過程のモニタリングに適用する例を示す。

DOI： 10.18926/interdisciplinary/61886

遠隔での見守りのための機器・サービスの調査と訪問看護での利用を想定した分類査読

坂本年生, 平田晶奈, 森田瑞樹

統合科学 1 47 - 63 2021年3月

De-identifying free text of Japanese electronic health records 査読国際誌

Kohei Kajiyama, Hiromasa Horiguchi, Takashi Okumura, Mizuki Morita, Yoshinobu Kano

Journal of Biomedical Semantics 11 ( 1 ) 11 - 11 2020年9月

DV200 index for assessing RNA integrity in next-generation sequencing 査読国際誌

Takehiro Matsubara, Junichi Soh, Mizuki Morita, Takahiro Uwabo, Shuta Tomida, Toshiyoshi Fujiwara, Susumu Kanazawa, Shinichi Toyooka, Akira Hirasawa

BioMed Research International 2020 9349132 2020年2月

Search for Therapeutic Agents for Cardiac Arrest Using a Drug Discovery Tool and Large-Scale Medical Information Database 査読国際誌

Yoshito Zamami, Takahiro Niimura, Toshihiro Koyama, Yuta Shigemi, Yuki Izawa-Ishizawa, Mizuki Morita, Ayako Ohshima, Keisaku Harada, Toru Imai, Hiromi Hagiwara, Naoto Okada, Mitsuhiro Goda, Kenshi Takechi, Masayuki Chuma, Yutaka Kondo, Koichiro Tsuchiya, Shiro Hinotsu, Mitsunobu R Kano, Keisuke Ishizawa

Frontiers in pharmacology 10 1257 - 1257 2019年11月

記述言語：英語掲載種別：研究論文（学術雑誌）

The survival rate of cardiac arrest patients is less than 10%; therefore, development of a therapeutic strategy that improves their prognosis is necessary. Herein, we searched data collected from medical facilities throughout Japan for drugs that improve the survival rate of cardiac arrest patients. Candidate drugs, which could improve the prognosis of cardiac arrest patients, were extracted using "TargetMine," a drug discovery tool. We investigated whether the candidate drugs were among the drugs administered within 1 month after cardiac arrest in data of cardiac arrest cases obtained from the Japan Medical Data Center. Logistic regression analysis was performed, with the explanatory variables being the presence or absence of the administration of those candidate drugs that were administered to ≥10 patients and the objective variable being the "survival discharge." Adjusted odds ratios for survival discharge were calculated using propensity scores for drugs that significantly improved the proportion of survival discharge; the influence of covariates, such as patient background, medical history, and treatment factors, was excluded by the inverse probability-of-treatment weighted method. Using the search strategy, we extracted 165 drugs with vasodilator activity as candidate drugs. Drugs not approved in Japan, oral medicines, and external medicines were excluded. Then, we investigated whether the candidate drugs were administered to the 2,227 cardiac arrest patients included in this study. The results of the logistic regression analysis showed that three (isosorbide dinitrate, nitroglycerin, and nicardipine) of seven drugs that were administered to ≥10 patients showed significant association with improvement in the proportion of survival discharge. Further analyses using propensity scores revealed that the adjusted odds ratios for survival discharge for patients administered isosorbide dinitrate, nitroglycerin, and nicardipine were 3.35, 5.44, and 4.58, respectively. Thus, it can be suggested that isosorbide dinitrate, nitroglycerin, and nicardipine could be novel therapeutic agents for improving the prognosis of cardiac arrest patients.

DOI： 10.3389/fphar.2019.01257

Challenges in Building and Maintaining Rare Disease Patient Registries: Results of a Questionnaire Survey in Japan at 2012

Mizuki Morita, Soichi Ogishima

medRxiv 19004770 2019年8月

A new approach to prevent critical cardiac accidents in athletes by real-time electrocardiographic tele-monitoring system: Initial trial in full marathon 査読国際誌

Daiki Ousaka, Noriko Sakano, Mizuki Morita, Takayuki Shuku, Kazuo Sanou, Shingo Kasahara, Susumu Oozawa

Journal of Cardiology Cases 20 ( 1 ) 35 - 38 2019年5月

Tweet Classification Toward Twitter-Based Disease Surveillance: New Data, Methods, and Evaluations 査読国際誌

Shoko Wakamiya, Mizuki Morita, Yoshinobu Kano, Tomoko Ohkuma, Eiji Aramaki

Journal of Medical Internet Research 21 ( 2 ) e12783 2019年2月

Change Detection in Vital Signs Associated with Impending Death for Homecare Patients Using a Pressure-Sensing Mat 査読国際誌

Takayuki Shuku, Noriko Sakano, Mizuki Morita, Shingo Kasahara

European Journal for Biomedical Informatics 14 ( 1 ) 52 - 57 2018年2月

Medical Attitudes Survey for Female Dystrophinopathy Carriers in Japan 査読国際誌

Michio Kobayashi, Tomoyuki Hatakeyama, Masatoshi Ishizaki, Katsuhito Adachi, Mizuki Morita, Naohiro Yonemoto, Tsuyoshi Matsumura, Itaru Toyoshima, En Kimura

Internal Medicine 57 ( 16 ) 2325 - 2332 2018年

記述言語：英語掲載種別：研究論文（学術雑誌）出版者・発行元：JAPAN SOC INTERNAL MEDICINE

Objective This study attempted to clarify the current status of female dystrophinopathy carriers, including the numbers of patients, the status of genetic screening, the status of counseling. physicians' understanding. and barriers to registration.Methods We sent out questionnaires to 402 physicians registered in the Remudy dystrophinopathy registry. The total number of responses received was 130 (response rate: 32%).Result In total, 1,212 cases of Duchenne muscular dystrophy, 365 cases of Becker muscular dystrophy, and 132 cases of female dystrophinopathy with a confirmed genetic mutation were encountered, and genetic testing was performed in the mother in 137, 23, and 12 cases, respectively. With respect to the risk of the onset of health problems, 25% of physicians always explained, 29% usually explained, 29% sometimes explained, and 13% never explained the risk to the mothers and female siblings of dystrophinopathy patients. The most common reason for not explaining the risk was a lack of knowledge/information. Thirty-five percent were familiar with the guidelines for testing the heart function of carriers.Conclusion Fewer mothers of dystrophinopathy patients have undergone genetic testing in Japan than in other countries. A significant portion of doctors did not explain the risks of health problems due to a lack of knowledge. We hope this survey will lead to an increased discussion of female dystrophinopathy patients.

添付ファイル： advpub_0163-17.pdf

DOI： 10.2169/internalmedicine.0163-17

Effects of Cold Ischemia on RNA Stability and Quality of Lung Tissues Based on Standard PREanalytical Code Categorization 査読国際誌

Takehiro Matsubara, Shuta Tomida, Junichi Soh, Takahiro Uwabo, Yoshiko Mori, Mizuki Morita, Yasutomo Nasu, Susumu Kanazawa, Shinichi Toyooka

Biopreservation and Biobanking 15 ( 5 ) 484 - 486 2017年10月

MedNLPDoc: Japanese Shared Task for Clinical NLP 査読国際誌

Eiji Aramaki, Yoshinobu Kano, Tomoko Ohkuma, Mizuki Morita

Proceedings of the Clinical Natural Language Processing Workshop at the 26th International Conference on Computational Linguistics (COLING 2016) 13 - 16 2016年12月

Overview of the NTCIR-12 MedNLPDoc Task. 査読

Eiji Aramaki, Mizuki Morita, Yoshinobu Kano, Tomoko Ohkuma

Proceedings of the 12th NTCIR Conference on Evaluation of Information Access Technologies, National Center of Sciences, Tokyo, Japan, June 7-10, 2016 2016年

Antitumor effect of afatinib, as a human epidermal growth factor receptor 2-targeted therapy, in lung cancers harboring HER2 oncogene alterations 査読国際誌

Ken Suzawa, Shinichi Toyooka, Masakiyo Sakaguchi, Mizuki Morita, Hiromasa Yamamoto, Shuta Tomida, Tomoaki Ohtsuka, Mototsugu Watanabe, Shinsuke Hashida, Yuho Maki, Junichi Soh, Hiroaki Asano, Kazunori Tsukuda, Shinichiro Miyoshi

Cancer Science 107 ( 1 ) 45 - 52 2015年11月

記述言語：英語掲載種別：研究論文（学術雑誌）出版者・発行元：WILEY

Human epidermal growth factor receptor 2 (HER2) is a member of the HER family of proteins containing four receptor tyrosine kinases. It plays an important role in the pathogenesis of certain human cancers. In non-small-cell lung cancer (NSCLC), HER2 amplification or mutations have been reported. However, little is known about the benefit of HER2-targeted therapy for NSCLCs harboring HER2 alterations. In this study, we investigated the antitumor effect of afatinib, an irreversible epidermal growth factor receptor (EGFR)-HER2 dual inhibitor, in lung cancers harboring HER2 oncogene alterations, including novel HER2 mutations in the transmembrane domain, which we recently identified. Normal bronchial epithelial cells, BEAS-2B, ectopically overexpressing wild-type HER2 or mutants (A775insYVMA, G776VC, G776LC, P780insGSP, V659E, and G660D) showed constitutive autophosphorylation of HER2 and activation of downstream signaling. They were sensitive to afatinib, but insensitive to gefitinib. Furthermore, we examined the antitumor activity of afatinib and gefitinib in several NSCLC cell lines, and investigated the association between their genetic alterations and sensitivity to afatinib treatment. In HER2-altered NSCLC cells (H2170, Calu-3, and H1781), afatinib downregulated the phosphorylation of HER2 and EGFR as well as their downstream signaling, and induced an antiproliferative effect through G(1) arrest and apoptotic cell death. In contrast, HER2- or EGFR-non-dependent NSCLC cells were insensitive to afatinib. In addition, these effects were confirmed in vivo by using a xenograft mouse model of HER2-altered lung cancer cells. Our results suggest that afatinib is a therapeutic option as a HER2-targeted therapy for NSCLC harboring HER2 amplification or mutations.

DOI： 10.1111/cas.12845

MDP環境モデルを使った心不全臨床データの分析

城真範, 森田瑞樹, 神嶌敏弘, 橋田浩一, 赤穂昭太郎, 麻生英樹, 荒牧英治, 興梠貴英, 合原一幸, 小室一成, 永井良三

生産研究 67 ( 3 ) 281 - 285 2015年5月

Implementation of linked data in the life sciences at BioHackathon 2011 査読

Kiyoko F. Aoki-Kinoshita, Akira R. Kinjo, Mizuki Morita, Yoshinobu Igarashi, Yi-an Chen, Yasumasa Shigemoto, Takatomo Fujisawa, Yukie Akune, Takeo Katoda, Anna Kokubu, Takaaki Mori, Mitsuteru Nakao, Shuichi Kawashima, Shinobu Okamoto, Toshiaki Katayama, Soichi Ogishima

Journal of Biomedical Semantics 6 3 2015年1月

記述言語：英語掲載種別：研究論文（学術雑誌）出版者・発行元：BMC

Background: Linked Data has gained some attention recently in the life sciences as an effective way to provide and share data. As a part of the Semantic Web, data are linked so that a person or machine can explore the web of data. Resource Description Framework (RDF) is the standard means of implementing Linked Data. In the process of generating RDF data, not only are data simply linked to one another, the links themselves are characterized by ontologies, thereby allowing the types of links to be distinguished. Although there is a high labor cost to define an ontology for data providers, the merit lies in the higher level of interoperability with data analysis and visualization software. This increase in interoperability facilitates the multi-faceted retrieval of data, and the appropriate data can be quickly extracted and visualized. Such retrieval is usually performed using the SPARQL (SPARQL Protocol and RDF Query Language) query language, which is used to query RDF data stores. For the database provider, such interoperability will surely lead to an increase in the number of users.Results: This manuscript describes the experiences and discussions shared among participants of the week-long BioHackathon 2011 who went through the development of RDF representations of their own data and developed specific RDF and SPARQL use cases. Advice regarding considerations to take when developing RDF representations of their data are provided for bioinformaticians considering making data available and interoperable.Conclusions: Participants of the BioHackathon 2011 were able to produce RDF representations of their data and gain a better understanding of the requirements for producing such data in a period of just five days. We summarize the work accomplished with the hope that it will be useful for researchers involved in developing laboratory databases or data analysis, and those who are considering such technologies as RDF and Linked Data.

DOI： 10.1186/2041-1480-6-3

患者／クライエント／当事者による記録を活かす意見交換会の活動報告査読

荒牧英治, 荒木健治, 石井保志, 上松幸一, 北嶋志保, 熊谷晋一郎, 櫻井公恵, 瀬戸山陽子, 高橋由光, 冨井美子, 堀里子, 西舘澄人, 森田瑞樹, 矢島弘士, 和田恵美子, 則のぞみ, 島本裕美子

医療情報学 34 ( 4 ) 197 - 200 2014年9月

患者中心の情報管理とそれを可能にする新しいインフォームドコンセント招待

森田瑞樹

情報管理 57 ( 1 ) 3 - 11 2014年4月

記述言語：日本語出版者・発行元：科学技術振興機構

遺伝情報をはじめとした私たちの医療・健康情報は，利活用することで個人および公共の双方にとって利益をもたらすものであると同時に，機微性の高い情報でありその扱いには慎重さが求められる。そのため，それらは医療機関や研究機関において厳重に管理されている。しかし近年，医療・健康情報を取り巻く状況には大きな変化が起こっており，新しい考え方が必要である。これはまた，患者や一般市民が自分自身の個人情報をコントロールできる範囲を広げ，同時に，患者や一般市民による医学研究への関与を深める可能性を秘めている。こうした状況の変化を踏まえつつ，ダイナミックコンセントと呼ばれる比較的新しいインフォームドコンセントの方法を中心に，患者・一般市民による医療・健康情報の管理について概観する。

DOI： 10.1241/johokanri.57.3

BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains. 査読

Toshiaki Katayama, Mark D Wilkinson, Kiyoko F Aoki-Kinoshita, Shuichi Kawashima, Yasunori Yamamoto, Atsuko Yamaguchi, Shinobu Okamoto, Shin Kawano, Jin-Dong Kim, Yue Wang, Hongyan Wu, Yoshinobu Kano, Hiromasa Ono, Hidemasa Bono, Simon Kocbek, Jan Aerts, Yukie Akune, Erick Antezana, Kazuharu Arakawa, Bruno Aranda, Joachim Baran, Jerven Bolleman, Raoul JP Bonnal, Pier Luigi Buttigieg, Matthew P Campbell, Yi-an Chen, Hirokazu Chiba, Peter JA Cock, K Bretonnel Cohen, Alexandru Constantin, Geraint Duck, Michel Dumontier, Takatomo Fujisawa, Toyofumi Fujiwara, Naohisa Goto, Robert Hoehndorf, Yoshinobu Igarashi, Hidetoshi Itaya, Maori Ito, Wataru Iwasaki, Matúš Kalaš, Takeo Katoda, Taehong Kim, Anna Kokubu, Yusuke Komiyama, Masaaki Kotera, Camille Laibe, Hilmar Lapp, Thomas Lütteke, M Scott Marshall, Takaaki Mori, Hiroshi Mori, Mizuki Morita, Katsuhiko Murakami, Mitsuteru Nakao, Hisashi Narimatsu, Hiroyo Nishide, Yosuke Nishimura, Johan Nystrom-Persson, Soichi Ogishima, Yasunobu Okamura, Shujiro Okuda, Kazuki Oshita, Nicki H Packer, Pjotr Prins, Rene Ranzinger, Philippe Rocca-Serra, Susanna Sansone, Hiromichi Sawaki, Sung-Ho Shin, Andrea Splendiani, Francesco Strozzi, Shu Tadaka, Philip Toukach, Ikuo Uchiyama, Masahito Umezaki, Rutger Vos, Patricia L Whetzel, Issaku Yamada, Chisato Yamasaki, Riu Yamashita, William S York, Christian M Zmasek, Shoko Kawamoto, Toshihisa Takagi

Journal of Biomedical Semantics 5 5 2014年2月

Arresting Treatment Patterns for Individual Patients in Clinical Big Data: An Exploratory Procedure.

Mizuki Morita, Masanori Shiro, Shotaro Akaho, Hideki Asoh, Toshihiro Kamishima, Eiji Aramaki, Kôiti Hasida, Takahide Kohro

2014 AAAI Spring Symposia 2014年

Comparing Social Media and Search Activity as Social Sensors for the Detection of Influenza 査読

Mizuki Morita, Sachiko Maskawa, Eiji Aramaki

Proceedings of the 5th International Symposium on Language in Biology and Medicine (LBM2013) 75 - 79 2013年12月

患者と医師が使う言葉の違い : 闘病記の医学的な応用に向けて(<特集>パーソナルデータに基づく気付きの創発)

荒牧英治, 増川佐知子, 宮部真衣, 森田瑞樹

人工知能学会誌 28 ( 6 ) 857 - 861 2013年11月

A Word in a Dictionary is used by Numerous Users 査読

Eiji Aramaki, Sachiko Maskawa, Mai Miyabe, Mizuki Morita, Sachi Yasuda

Proceedings of the 6th International Joint Conference on Natural Language Processing (IJCNLP 2013) 874 - 877 2013年10月

Toxygates: interactive toxicity analysis on a hybrid microarray and linked data platform 査読国際誌

Johan Nystroem-Persson, Yoshinobu Igarashi, Maori Ito, Mizuki Morita, Noriyuki Nakatsu, Hiroshi Yamada, Kenji Mizuguchi

Bioinformatics 29 ( 23 ) 3080 - 3086 2013年9月

記述言語：英語掲載種別：研究論文（学術雑誌）出版者・発行元：OXFORD UNIV PRESS

Motivation: In early stage drug development, it is desirable to assess the toxicity of compounds as quickly as possible. Biomarker genes can help predict whether a candidate drug will adversely affect a given individual, but they are often difficult to discover. In addition, the mechanism of toxicity of many drugs and common compounds is not yet well understood. The Japanese Toxicogenomics Project provides a large database of systematically collected microarray samples from rats (liver, kidney and primary hepatocytes) and human cells (primary hepatocytes) after exposure to 170 different compounds in different dosages and at different time intervals. However, until now, no intuitive user interface has been publically available, making it time consuming and difficult for individual researchers to explore the data.
Results: We present Toxygates, a user-friendly integrated analysis platform for this database. Toxygates combines a large microarray dataset with the ability to fetch semantic linked data, such as pathways, compound-protein interactions and orthologs, on demand. It can also perform pattern-based compound ranking with respect to the expression values of a set of relevant candidate genes. By using Toxygates, users can freely interrogate the transcriptome's response to particular compounds and conditions, which enables deep exploration of toxicity mechanisms.

DOI： 10.1093/bioinformatics/btt531

マイノリティのための情報処理 -難病支援を題材に- 招待

森田瑞樹, 荒牧英治

情報処理 54 ( 8 ) 834 - 840 2013年7月

記述言語：日本語掲載種別：研究論文（学術雑誌）出版者・発行元：一般社団法人情報処理学会

インターネットと情報処理技術によって人間社会におけるロングテールである社会的マイノリティの支援のあり方が変わりつつある.本稿では,社会的マイノリティのひとつとして難病を取り上げ,本邦における難病患者が,現在どのような問題を抱えているかを概観する.同時に,難病患者を取りまず状況を改善するために,現在,どのような情報処理の取り組みがなされ,また,今後,どのような支援が望まれているかを解説する.

Online population-based patient registry to collect and share health-related data of rare disease patients

Mizuki Morita, Soichi Ogishima, Kunihiro Nishimura, Eiji Aramaki, Tateo Ito

AAAI Spring Symposium - Technical Report SS-13-03 65 - 66 2013年

掲載種別：研究論文（国際会議プロシーディングス）

Rare diseases, those affecting few patients, are in fact neglected diseases that demand special concern and care. We are constructing an online system to collect health-related data and complaints from rare-disease patients to share that information with stakeholders, thereby facilitating the development of new or improved drugs, treatments, and policies and enhancing the quality of life (QOL) for patients with such diseases. The system will also track and monitor the physical states and conditions of patients, which will facilitate the management of their QOL and improve communication with health professionals. Copyright © 2013 Association for the Advancement of Artificial Intelligence.

Overview of the NTCIR-10 MedNLP Task. 査読

Mizuki Morita, Yoshinobu Kano, Tomoko Ohkuma, Mai Miyabe, Eiji Aramaki

Proceedings of the 10th NTCIR Conference on Evaluation of Information Access Technologies, NTCIR-10, National Center of Sciences, Tokyo, Japan, June 18-21, 2013 2013年

文章分類と疾患モデルの融合によるソーシャルメディアからの感染症把握査読

荒牧英治, 増川佐知子, 森田瑞樹

自然言語処理 19 ( 5 ) 419 - 435 2012年12月

記述言語：日本語掲載種別：研究論文（学術雑誌）

近年，ウェブの情報を用いて，感染症などの疾病状態を監視するシステムに注目が集まっている．本研究では，ソーシャルメディアを用いたインフルエンザ・サーベイランスに注目する．これまでの多くのシステムは，単純な単語の頻度情報をもとに患者の状態を調査するというものであった．しかし，この方法では，実際に疾患にかかっていない場合の発言を収集してしまう恐れがある．また，そもそも，医療者でない個人の自発的な発言の集計が，必ずしもインフルエンザの流行と一致するとは限らない．本研究では，前者の問題に対応するため，発言者が実際にインフルエンザにかかっているもののみを抽出し集計を行う．後者の問題に対して，発言と流行の時間的なずれを吸収するための感染症モデルを提案する．実験においては，Twitter の発言を材料にしたインフルエンザ流行の推定値は，感染症情報センターの患者数と相関係数 0.910 という高い相関を示し，その有効性を示した．本研究により，ソーシャルメディア上の情報をそのまま用いるのではなく，文章分類や疾患モデルと組み合わせて用いることで，さらに精度を向上できることが示された．

DOI： 10.5715/jnlp.19.419

Blind prediction of quaternary structures of homo-oligomeric proteins from amino acid sequences based on templates 査読

Mizuki Morita, Masanori Kakuta, Kentaro Shimizu, Shugo Nakamura

Journal of Proteome Science & Computational Biology 1 1 2012年4月

Sagace: A web-based search engine for biomedical databases in Japan 査読

Mizuki Morita, Yoshinobu Igarashi, Maori Ito, Yi-An Chen, Chioko Nagao, Yuki Sakaguchi, Ryuichi Sakate, Tohru Masui, Kenji Mizuguchi

BMC Research Notes 5 604 2012年

記述言語：英語掲載種別：研究論文（学術雑誌）

Background: In the big data era, biomedical research continues to generate a large amount of data, and the generated information is often stored in a database and made publicly available. Although combining data from multiple databases should accelerate further studies, the current number of life sciences databases is too large to grasp features and contents of each database. Findings. We have developed Sagace, a web-based search engine that enables users to retrieve information from a range of biological databases (such as gene expression profiles and proteomics data) and biological resource banks (such as mouse models of disease and cell lines). With Sagace, users can search more than 300 databases in Japan. Sagace offers features tailored to biomedical research, including manually tuned ranking, a faceted navigation to refine search results, and rich snippets constructed with retrieved metadata for each database entry. Conclusions: Sagace will be valuable for experts who are involved in biomedical research and drug development in both academia and industry. Sagace is freely available at. © 2012 Morita et al.
licensee BioMed Central Ltd.

DOI： 10.1186/1756-0500-5-604

Influenza patients are invisible in the web: Traditional model still improves the state-of-the-art web based influenza surveillance

Eiji Aramaki, Sachiko Maskawa, Mizuki Morita

AAAI Spring Symposium - Technical Report SS-12-05 5 - 8 2012年

掲載種別：研究論文（国際会議プロシーディングス）

Although web-based information extraction systems draw much attention, most of such systems assume that the web directly reflects the real world. For instance, Google flu trend, which is one of the-state-of-the-art influenza surveillance systems, relies on the basic idea that the amount of the influenza related search queries directly correlates with the number of the influenza patients. However, the real patients suffering from influenza symptoms are invisible in the web, because they do not use Internet. Considering this gap, this paper employs an infectious model, assuming that a potential patient utilizes Internet at the first sign of flu. The proposed model improves two types of the state-of-the-art systems, Google based system (from 0.837 correlation to 0.928) and Twitter based system (from 0.898 correlation to 0.918). This study demonstrated that a simple model could easily improve the web-based surveillance. Copyright © 2012, Association for the Advancement of Artificial Intelligence. All rights reserved.

Lipid recognition propensities of amino acids in membrane proteins from atomic resolution data 査読

Mizuki Morita, AVSK M. Katta, Shandar Ahmad, Takaharu Mori, Yuji Sugita, Kenji Mizuguchi

BMC Biophysics 4 ( 1 ) 21 2011年12月

記述言語：英語掲載種別：研究論文（学術雑誌）

Background: Protein-lipid interactions play essential roles in the conformational stability and biological functions of membrane proteins. However, few of the previous computational studies have taken into account the atomic details of protein-lipid interactions explicitly.Results: To gain an insight into the molecular mechanisms of the recognition of lipid molecules by membrane proteins, we investigated amino acid propensities in membrane proteins for interacting with the head and tail groups of lipid molecules. We observed a common pattern of lipid tail-amino acid interactions in two different data sources, crystal structures and molecular dynamics simulations. These interactions are largely explained by general lipophilicity, whereas the preferences for lipid head groups vary among individual proteins. We also found that membrane and water-soluble proteins utilize essentially an identical set of amino acids for interacting with lipid head and tail groups.Conclusions: We showed that the lipophilicity of amino acid residues determines the amino acid preferences for lipid tail groups in both membrane and water-soluble proteins, suggesting that tightly-bound lipid molecules and lipids in the annular shell interact with membrane proteins in a similar manner. In contrast, interactions between lipid head groups and amino acids showed a more variable pattern, apparently constrained by each protein's specific molecular function. © 2011 Morita et al
licensee BioMed Central Ltd.

DOI： 10.1186/2046-1682-4-21

Twitter Catches The Flu: Detecting Influenza Epidemics using Twitter Streams 査読

Eiji Aramaki, Sachiko Maskawa, Mizuki Morita

Proceedings of the 2011 Conference on Empirical Methods in Natural Language Processing (EMNLP 2011) 1568 - 1576 2011年7月

BUDDY-system: A web site for constructing a dataset of protein pairs between ligand-bound and unbound states 査読

Mizuki Morita, Tohru Terada, Shugo Nakamura, Kentaro Shimizu

BMC Research Notes 4 143 2011年

記述言語：英語掲載種別：研究論文（学術雑誌）

Background: Elucidating molecular recognition by proteins, such as in enzyme-substrate and receptor-ligand interactions, is a key to understanding biological phenomena. To delineate these protein interactions, it is important to perform structural bioinformatics studies relevant to molecular recognition. Such studies require a dataset of protein structure pairs between ligand-bound and unbound states. In many studies, the same well-designed and high-quality dataset has been used repeatedly, which has spurred the development of subsequent relevant research. Using previously constructed datasets, researchers are able to fairly compare obtained results with those of other studies
in addition, much effort and time is saved. Therefore, it is important to construct a refined dataset that will appeal to many researchers. However, constructing such datasets is not a trivial task. Findings. We have developed the BUDDY-system, a web site designed to support the building of a dataset comprising pairs of protein structures between ligand-bound and unbound states, which are widely used in various areas associated with molecular recognition. In addition to constructing a dataset, the BUDDY-system also allows the user to search for ligand-bound protein structures by its unbound state or by its ligand
and to search for ligands by a particular receptor protein. Conclusions: The BUDDY-system receives input from the user as a single entry or a dataset consisting of a list of ligand-bound state protein structures, unbound state protein structures, or ligands and returns to the user a list of protein structure pairs between the ligand-bound and the corresponding unbound states. This web site is designed for researchers who are involved not only in structural bioinformatics but also in experimental studies. The BUDDY-system is freely available on the web. © 2011 Morita et al
licensee BioMed Central Ltd.

DOI： 10.1186/1756-0500-4-143

Prediction of carbohydrate-binding proteins from sequences using support vector machines 査読

Seizi Someya, Masanori Kakuta, Mizuki Morita, Kazuya Sumikoshi, Wei Cao, Zhenyi Ge, Osamu Hirose, Shugo Nakamura, Tohru Terada, Kentaro Shimizu

Advances in Bioinformatics 2010 289301 2010年

記述言語：英語掲載種別：研究論文（学術雑誌）

Carbohydrate-binding proteins are proteins that can interact with sugar chains but do not modify them. They are involved in many physiological functions, and we have developed a method for predicting them from their amino acid sequences. Our method is based on support vector machines (SVMs). We first clarified the definition of carbohydrate-binding proteins and then constructed positive and negative datasets with which the SVMs were trained. By applying the leave-one-out test to these datasets, our method delivered 0.92 of the area under the receiver operating characteristic (ROC) curve. We also examined two amino acid grouping methods that enable effective learning of sequence patterns and evaluated the performance of these methods. When we applied our method in combination with the homology-based prediction method to the annotated human genome database, H-invDB, we found that the true positive rate of prediction was improved. © 2010 Seizi Someya et al.

DOI： 10.1155/2010/289301

Structural bases of GM1 gangliosidosis and Morquio B disease 査読国際誌

Mizuki Morita, Seiji Saito, Kazuyoshi Ikeda, Kazuki Ohno, Kanako Sugawara, Toshihiro Suzuki, Tadayasu Togawa, Hitoshi Sakuraba

Journal of Human Genetics 54 ( 9 ) 510 - 515 2009年9月

記述言語：英語掲載種別：研究論文（学術雑誌）出版者・発行元：Nature Publishing Group

Allelic mutations of the lysosomal beta-galactosidase gene cause heterogeneous clinical phenotypes, such as GM1 gangliosidosis and Morquio B disease, the former being further classified into three variants, namely infantile, juvenile and adult forms; and heterogeneous biochemical phenotypes were shown in these forms. We tried to elucidate the bases of these diseases from a structural viewpoint. We first constructed a three-dimensional structural model of human beta-galactosidase by means of homology modeling. The human beta-galactosidase consists of three domains, such as, a TIM barrel fold domain, which functions as a catalytic domain, and two galactose-binding domain-like fold domains. We then constructed structural models of representative mutant beta-galactosidase proteins (G123R, R201C, I51T and Y83H) and predicted the structural change associated with each phenotype by calculating the number of affected atoms, determining the root-mean-square deviation and the solvent-accessible surface area, and by color imaging. The results show that there is a good correlation between the structural changes caused by amino-acid substitutions in the beta-galactosidase molecule, as well as biochemical and clinical phenotypes in these representative cases. Protein structural study is useful for elucidating the bases of these diseases. Journal Human Genetics (2009) 54, 510-515; doi:10.1038/jhg.2009.70; published online 31 July 2009

DOI： 10.1038/jhg.2009.70

Added mass effect on immobilizations of proteins on a 27 MHz quartz crystal microbalance in aqueous solution 査読

Hiroyuki Furusawa, Tomomitsu Ozeki, Mizuki Morita, Yoshio Okahata

Analytical Chemistry 81 ( 6 ) 2268 - 2273 2009年3月

記述言語：英語掲載種別：研究論文（学術雑誌）出版者・発行元：6

During the immobilization process of proteins onto an Au-surface of a 27 MHz quartz crystal microbalance (QCM) in aqueous solutions, apparent large frequency changes (ΔFwater) were observed compared with those in the air phase (ΔFair) due to the interaction with surrounding water of proteins. On the basis of an energy-transfer model for the QCM, the apparent added mass in the aqueous solution [(-ΔF water)/(-ΔFair) - 1] could be explained by frictional forces at the interface of proteins with aqueous solutions. When [(-ΔFwater)/(-ΔFair) -1] values for various proteins were plotted against values relating to the friction (antimobility), such as values of the molecular weight divided by the sedimentation coefficient (Mw/s), the inverse of the diffusion coefficient (1/D), and the volume divided by the surface area (volume/surface area) apparent radius) of proteins, there were good linear correlations. Thus, observations of the larger ΔF water than ΔFair for protein immobilizations on the QCM can be simply explained by the friction effect at the interface between proteins and the aqueous solution. Thus, QCM would be a mass sensor based on mechanical oscillation motion even in aqueous solutions.

DOI： 10.1021/ac802412t

Highly accurate method for ligand-binding site prediction in unbound state (apo) protein structures 査読国際誌

Mizuki Morita, Shugo Nakamura, Kentaro Shimizu

Proteins: Structure, Function, and Bioinformatics 73 ( 2 ) 468 - 479 2008年11月

担当区分：筆頭著者記述言語：英語掲載種別：研究論文（学術雑誌）出版者・発行元：Wiley-Liss

This article describes a new method for predicting ligand-binding sites of proteins. The method involves calculating the van der Waals interaction energy between a protein and probes placed on the protein surface, and then clustering the probes with attractive interaction to find the energetically most favorable locus. In 80% (28/35) of the test cases, the ligand-binding site was successfully predicted on a ligand-bound protein structure, and in 77% (27/35) was successfully predicted on an unbound structure. Our method was used to successfully predict ligand-binding sites unaffected by induced-fit as long as its scales were not very large, and it contributed to a significant improvement in prediction with unbound state protein structures. This represents a significant advance over conventional methods in detecting ligand-binding sites on uncharacterized proteins. Moreover, our method can predict ligand-binding sites with a narrower locus than those achieved using conventional methods.

DOI： 10.1002/prot.22067

Hydration and energy dissipation measurements of biomolecules on a piezoelectric quartz oscillator by admittance analyses 査読国際誌

Tomomitsu Ozeki, Mizuki Morita, Hiroshi Yoshimine, Hiroyuki Furusawa, Yoshio Okahata

Analytical Chemistry 79 ( 1 ) 79 - 88 2007年1月

記述言語：英語掲載種別：研究論文（学術雑誌）出版者・発行元：American Chemical Society

By using a 27-MHz piezoelectric quartz oscillator connected with a vector network analyzer, we obtained resonance frequency decreases (-Delta F-water) and energy dissipation increases (Delta D-water) during binding of biotinylated bovine serum albumin, biotinylated ssDNA, biotinylated dsDNA, and biotinylated pullulan to a NeutrAvidin-immobilized 27-MHz quartz crystal microbalance (QCM) plate in aqueous solution, as well as in the wet air phase (98% humidity, -Delta F-wet and Delta D-wet) and in the dry air phase (-Delta F-air and Delta D-air). -Delta F-water indicates the total mass of the molecule, bound water, and vibrated water in aqueous solutions. -Delta F-wet indicates the total mass of the molecule and bound water. -Delta F-air simply shows the real mass of the molecule on the QCM. In terms of results, (-Delta F-wet)/(-Delta F-air) values indicated the bound water ratios per unit biomolecular mass were on the order of pullulan (2.1-2.2) > DNAs = proteins (1.4-1.6) > polystyrene (1.0). The (-Delta F-water)/(-Delta F-air) values indicated the hydrodynamic water (bound and vibrated water) ratios per unit biomolecular mass were on the order of dsDNA (6.5) > ssDNA = pullulan (3.5-4.4) > proteins (2.4-2.5) > polystyrene (1.0). Energy dissipation parameters per unit mass in water (Delta D-water/(-Delta F-air)) were on the order of pullulan > dsDNA > ssDNA > proteins > polystyrene. Energy dissipation in the wet and dry air phases (Delta D-wet and Delta D-air) were negligibly small, which indicates even these biomolecules act as elastic membranes in the air phase (without aqueous solution). We obtained a good linear relationship between [(-Delta F-water)/(-Delta F-air) - 1], which is indicative of hydration and Delta D-water/(-Delta F-air) of proteins. The aforementioned values suggest that the energy dissipation of proteins was mainly caused by hydration and that proteins themselves are elastic molecules without energy dissipation in aqueous solutions. On the contrary, plots in cases of denatured proteins, DNAs, and pullulans were relatively deviant toward the large hydration and energy dissipation from the theoretical line as perfect elastic materials, meaning that the large energy dissipation occurs because of viscoelastic properties of denatured proteins, linear DNAs, and pullulans in the water phase, in addition to energy dissipation due to the hydration of molecules. These two parameters could characterize various biomolecules with structural properties in aqueous solutions.

DOI： 10.1021/ac060873x

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