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Development and application of analysis methodology for next generation human omics

Planned Research

Project AreaTransomic Analysis of Metabolic Adaptation
Project/Area Number 17H06307
Research Category

Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)

Allocation TypeSingle-year Grants
Review Section Biological Sciences
Research InstitutionThe University of Tokyo (2019-2021)
Tokyo Medical and Dental University (2017-2018)

Principal Investigator

Tsunoda Tatsuhiko  東京大学, 大学院理学系研究科(理学部), 教授 (10273468)

Co-Investigator(Kenkyū-buntansha) 重水 大智  国立研究開発法人国立長寿医療研究センター, メディカルゲノムセンター, 部長 (70617464)
Project Period (FY) 2017-06-30 – 2022-03-31
Project Status Completed (Fiscal Year 2021)
Budget Amount *help
¥101,920,000 (Direct Cost: ¥78,400,000、Indirect Cost: ¥23,520,000)
Fiscal Year 2021: ¥20,020,000 (Direct Cost: ¥15,400,000、Indirect Cost: ¥4,620,000)
Fiscal Year 2020: ¥20,020,000 (Direct Cost: ¥15,400,000、Indirect Cost: ¥4,620,000)
Fiscal Year 2019: ¥20,020,000 (Direct Cost: ¥15,400,000、Indirect Cost: ¥4,620,000)
Fiscal Year 2018: ¥20,020,000 (Direct Cost: ¥15,400,000、Indirect Cost: ¥4,620,000)
Fiscal Year 2017: ¥21,840,000 (Direct Cost: ¥16,800,000、Indirect Cost: ¥5,040,000)
Keywordsトランスオミクス / 代謝アダプテーション / オミクス解析 / XX
Outline of Final Research Achievements

To capture the whole picture and behavior leading to diseases by metabolic adaptation, it is necessary to integrate multi-omics data across the omics layers. In this study, we arranged trans-omics statistical analysis methods based on knowledge-based, causal-hierarchical, and integrated methods, and analyzed omics data to decipher trans-omics and systematically and comprehensively clarify changes in metabolic states in diseases and living organisms. As a result, we derived a new original methodology based on deep learning and conducted trans-omics analysis of diabetes, Alzheimer's disease, cancer immunity and tumor-microenvironment using clinical samples and model animals to discover novel genes, pathways, interactions, new sub-classes and their underlying mechanisms across humans and mice.

Academic Significance and Societal Importance of the Research Achievements

本研究により、オミクスの多階層データを繋ぐ方法論の基礎を築いた。知識型、因果・階層型、統合型という柱を基本とし、中でも特に派生した深層学習によるオミクス解析の方法論の進展は、世界でも唯一無二である。また組織検体からゲノムや遺伝子発現などのプロファイルからがん微小環境をトランスオミクス解析し、免疫編集を解明した。本研究を基盤とし、個体レベルのネットワーク再構築により、糖代謝疾患などの多因子疾患やがん転移などの環境適応の全体像の解明、薬剤の動的な選択などのプレシジョン医療の基盤の形成、複数の創薬標的分子のネットワークによる同定、そして新規治療法開発に繋がることが期待できる。

Report

(6 results)
  • 2021 Annual Research Report   Final Research Report ( PDF )
  • 2020 Annual Research Report
  • 2019 Annual Research Report
  • 2018 Annual Research Report
  • 2017 Annual Research Report

Research Products

(63 results)

All 2022 2021 2020 2019 2018 2017 Other

All Int'l Joint Research (11 results) Journal Article (20 results) (of which Int'l Joint Research: 16 results,  Peer Reviewed: 19 results,  Open Access: 15 results) Presentation (27 results) (of which Int'l Joint Research: 17 results,  Invited: 27 results) Book (1 results) Remarks (4 results)

  • [Int'l Joint Research] University of the South Pacific(フィジー)

    • Related Report
      2021 Annual Research Report
  • [Int'l Joint Research] Griffith University(オーストラリア)

    • Related Report
      2021 Annual Research Report
  • [Int'l Joint Research] University of the South Pacific(フィジー)

    • Related Report
      2020 Annual Research Report
  • [Int'l Joint Research] Griffith University(オーストラリア)

    • Related Report
      2020 Annual Research Report
  • [Int'l Joint Research] University of the South Pacific(フィジー)

    • Related Report
      2019 Annual Research Report
  • [Int'l Joint Research] Griffith University(オーストラリア)

    • Related Report
      2019 Annual Research Report
  • [Int'l Joint Research] Imperial College London(英国)

    • Related Report
      2018 Annual Research Report
  • [Int'l Joint Research] EISBM(フランス)

    • Related Report
      2018 Annual Research Report
  • [Int'l Joint Research] University of the South Pacific(フィジー)

    • Related Report
      2018 Annual Research Report
  • [Int'l Joint Research] Morgan State University(米国)

    • Related Report
      2018 Annual Research Report
  • [Int'l Joint Research] Griffith University(オーストラリア)

    • Related Report
      2018 Annual Research Report
  • [Journal Article] Immune subtypes and neoantigen-related immune evasion in advanced colorectal cancer2022

    • Author(s)
      Sugawara Toshitaka、Miya Fuyuki、Ishikawa Toshiaki、Lysenko Artem、Nishino Jo、Kamatani Takashi、Takemoto Akira、Boroevich Keith A.、Kakimi Kazuhiro、Kinugasa Yusuke、Tanabe Minoru、Tsunoda Tatsuhiko
    • Journal Title

      iScience

      Volume: 25 Pages: 103740-103740

    • DOI

      10.1016/j.isci.2022.103740

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] DeepFeature: feature selection in nonimage data using convolutional neural network2021

    • Author(s)
      Sharma Alok、Lysenko Artem、Boroevich Keith A、Vans Edwin、Tsunoda Tatsuhiko
    • Journal Title

      Briefings in Bioinformatics

      Volume: 22

    • DOI

      10.1093/bib/bbab297

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Forecasting the spread of COVID-19 using LSTM network2021

    • Author(s)
      Kumar Shiu、Sharma Ronesh、Tsunoda Tatsuhiko、Kumarevel Thirumananseri、Sharma Alok
    • Journal Title

      BMC Bioinformatics

      Volume: 22

    • DOI

      10.1186/s12859-021-04224-2

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] 生活習慣病のトランスオミクス解析2021

    • Author(s)
      柚木克之、小鍛冶俊也、角田達彦、黒田真也
    • Journal Title

      医学のあゆみ

      Volume: 278 Pages: 501-509

    • Related Report
      2021 Annual Research Report
  • [Journal Article] Deep Learning Approach for Automated Detection of Myopic Maculopathy and Pathologic Myopia in Fundus Images2021

    • Author(s)
      DU Ran、Xie Shiqi、Fang Yuxin、Igarashi-Yokoi Tae、Moriyama Muka、Ogata Satoko、Tsunoda Tatsuhiko、Kamatani Takashi、Yamamoto Shinji、Cheng Ching-Yu、Saw Seang-Mei、Ting Daniel、Wong Tien Y.、Ohno-Matsui Kyoko
    • Journal Title

      Ophthalmology Retina

      Volume: -

    • DOI

      10.1016/j.oret.2021.02.006

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Single-stranded and double-stranded DNA-binding protein prediction using HMM profiles2021

    • Author(s)
      Sharma Ronesh、Kumar Shiu、Tsunoda Tatsuhiko、Kumarevel Thirumananseri、Sharma Alok
    • Journal Title

      Analytical Biochemistry

      Volume: 612 Pages: 113954-113954

    • DOI

      10.1016/j.ab.2020.113954

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] RAM-PGK: Prediction of Lysine Phosphoglycerylation Based on Residue Adjacency Matrix2020

    • Author(s)
      Chandra Abel Avitesh、Sharma Alok、Dehzangi Abdollah、Tsunoda Tatushiko
    • Journal Title

      Genes

      Volume: 11 Pages: 1524-1524

    • DOI

      10.3390/genes11121524

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] PupStruct: Prediction of Pupylated Lysine Residues Using Structural Properties of Amino Acids2020

    • Author(s)
      Singh Vineet、Sharma Alok、Dehzangi Abdollah、Tsunoda Tatushiko
    • Journal Title

      Genes

      Volume: 11 Pages: 1431-1431

    • DOI

      10.3390/genes11121431

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Clinical usefulness of multigene screening with phenotype-driven bioinformatics analysis for the diagnosis of patients with monogenic diabetes or severe insulin resistance2020

    • Author(s)
      Hosoe Jun, ... Fujiwara Toyofumi et al.
    • Journal Title

      Diabetes Res Clin Pract.

      Volume: 169 Pages: 108461-108461

    • DOI

      10.1016/j.diabres.2020.108461

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Predicting protein-peptide binding sites with a deep convolutional neural network2020

    • Author(s)
      Wardah Wafaa、Dehzangi Abdollah、Taherzadeh Ghazaleh、Rashid Mahmood A.、Khan M.G.M.、Tsunoda Tatsuhiko、Sharma Alok
    • Journal Title

      Journal of Theoretical Biology

      Volume: 496 Pages: 110278-110278

    • DOI

      10.1016/j.jtbi.2020.110278

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Multiple Myeloma DREAM Challenge reveals epigenetic regulator PHF19 as marker of aggressive disease2020

    • Author(s)
      Mason Mike J.、Multiple Myeloma DREAM Consortium (including Lysenko, Artem)、et al.
    • Journal Title

      Leukemia

      Volume: - Pages: 1866-1874

    • DOI

      10.1038/s41375-020-0742-z

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Quantification of multicellular colonization in tumor metastasis using exome‐sequencing data2020

    • Author(s)
      Nishino Jo、Watanabe Shuichi、Miya Fuyuki、Kamatani Takashi、Sugawara Toshitaka、Boroevich Keith A.、Tsunoda Tatsuhiko
    • Journal Title

      International Journal of Cancer

      Volume: 146 Pages: 2488-2497

    • DOI

      10.1002/ijc.32910

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Bigram-PGK: phosphoglycerylation prediction using the technique of bigram probabilities of position specific scoring matrix2019

    • Author(s)
      Chandra Abel、Sharma Alok、Dehzangi Abdollah、Shigemizu Daichi、Tsunoda Tatsuhiko
    • Journal Title

      BMC Molecular and Cell Biology

      Volume: 20 Pages: 57-57

    • DOI

      10.1186/s12860-019-0240-1

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] A comparison of machine learning classifiers for dementia with Lewy bodies using miRNA expression data2019

    • Author(s)
      Shigemizu Daichi、Akiyama Shintaro、Asanomi Yuya、Boroevich Keith A.、Sharma Alok、Tsunoda Tatsuhiko、Sakurai Takashi、Ozaki Kouichi、Ochiya Takahiro、Niida Shumpei
    • Journal Title

      BMC Medical Genomics

      Volume: 12 Pages: 150-150

    • DOI

      10.1186/s12920-019-0607-3

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] DeepInsight: A methodology to transform a non-image data to an image for convolution neural network architecture2019

    • Author(s)
      Sharma Alok、Vans Edwin、Shigemizu Daichi、Boroevich Keith A.、Tsunoda Tatsuhiko
    • Journal Title

      Scientific Reports

      Volume: 9 Pages: 11399-11399

    • DOI

      10.1038/s41598-019-47765-6

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] EvolStruct-Phogly: incorporating structural properties and evolutionary information from profile bigrams for the phosphoglycerylation prediction2019

    • Author(s)
      Chandra Abel Avitesh、Sharma Alok、Dehzangi Abdollah、Tsunoda Tatushiko
    • Journal Title

      BMC Genomics

      Volume: 19 Pages: 984-984

    • DOI

      10.1186/s12864-018-5383-5

    • Related Report
      2019 Annual Research Report 2018 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Navigating the disease landscape: knowledge representations for contextualizing molecular signatures.2019

    • Author(s)
      Mansoor Saqi, Artem Lysenko, Yi-Ke Guo, Tatsuhiko Tsunoda, Charles Auffray
    • Journal Title

      Briefings in Bioinformatics

      Volume: - Pages: 609-623

    • DOI

      10.1093/bib/bby025

    • Related Report
      2018 Annual Research Report 2017 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] PhoglyStruct: Prediction of phosphoglycerylated lysine residues using structural properties of amino acids2018

    • Author(s)
      Chandra Abel、Sharma Alok、Dehzangi Abdollah、Ranganathan Shoba、Jokhan Anjeela、Chou Kuo-Chen、Tsunoda Tatsuhiko
    • Journal Title

      Scientific Reports

      Volume: 8 Pages: 17923-17923

    • DOI

      10.1038/s41598-018-36203-8

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] An integrative machine learning approach for prediction of toxicity-related drug safety2018

    • Author(s)
      Lysenko Artem、Sharma Alok、Boroevich Keith A、Tsunoda Tatsuhiko
    • Journal Title

      Life Science Alliance

      Volume: 1 Pages: 1-14

    • DOI

      10.26508/lsa.201800098

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Integrated analysis of human genetic association study and mouse transcriptome suggests LBH and SHF genes as novel susceptible genes for amyloid-β accumulation in Alzheimer's disease.2018

    • Author(s)
      Yamaguchi-Kabata Y, Morihara T, Ohara T, Ninomiya T, Takahashi A, Akatsu H, Hashizume Y, Hayashi N, Shigemizu D, Boroevich KA, Ikeda M, Kubo M, Takeda M, Tsunoda T.
    • Journal Title

      Human Genetics

      Volume: 37(6-7) Pages: 132-146

    • DOI

      10.1007/s00439-018-1906-z

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Presentation] ゲノム医科学を推進するデータ駆動型研究2021

    • Author(s)
      角田達彦
    • Organizer
      AMED「脳とこころ」疾患メカプロジェクト進捗報告会
    • Related Report
      2021 Annual Research Report
    • Invited
  • [Presentation] ゲノム医科学を推進する深層学習と数理科学2021

    • Author(s)
      角田達彦
    • Organizer
      第25回日本がん分子標的治療学会学術集会・シンポジウム2 「AI」
    • Related Report
      2021 Annual Research Report
    • Invited
  • [Presentation] 生物情報科学の視点から行うがん研究 ~DNA, RNA, 病理画像を用いた免疫環境解析や多領域解析を中心に~2021

    • Author(s)
      鎌谷高志
    • Organizer
      第19回関東骨軟部腫瘍の基礎を語る会
    • Related Report
      2021 Annual Research Report
    • Invited
  • [Presentation] 新たな知によるゲノム医科学2021

    • Author(s)
      角田 達彦
    • Organizer
      東京大学ゲノム医科学研究機構2020年度シンポジウム
    • Related Report
      2020 Annual Research Report
    • Invited
  • [Presentation] Exploring etiologies, sub-classification, and risk prediction of diseases based on big-data analysis of clinical and whole omics data in medicine2021

    • Author(s)
      Tatsuhiko Tsunoda
    • Organizer
      ERCIM-JST Joint Symposium on Big Data and Artificial Intelligence. 2021
    • Related Report
      2020 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Exploring etiologies, sub-classification, and risk prediction of diseases based on big-data analysis of clinical and whole omics data in medicine2021

    • Author(s)
      Tatsuhiko Tsunoda
    • Organizer
      CREST International Symposium on Big Data Application 2021
    • Related Report
      2020 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 深層学習が拓く新たなゲノム医科学2021

    • Author(s)
      角田 達彦
    • Organizer
      第16回日本がん分子標的治療学会TRワークショップ
    • Related Report
      2020 Annual Research Report
    • Invited
  • [Presentation] Personalized Cancer Medicine with Heterogeneity and Immunological Analysis2020

    • Author(s)
      Tatsuhiko Tsunoda
    • Organizer
      CREST International Symposium on Big Data Application
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 全ゲノム解析による糖尿病などの疾患の発症や治療・予後予測に向けて2019

    • Author(s)
      角田 達彦
    • Organizer
      AI医療活用研究会
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] Data-driven Medical Sciences with Omic Analysis2019

    • Author(s)
      Tatsuhiko Tsunoda
    • Organizer
      Moonshot International Symposium
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Medical Big Data Analysis for Precision Medicine.2019

    • Author(s)
      Tatsuhiko Tsunoda
    • Organizer
      CREST Joint International Symposium for Big Data
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Cancer heterogeneity and immunology for precision medicine.2019

    • Author(s)
      Tatsuhiko Tsunoda
    • Organizer
      CREST International Symposium on Big Data Application
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Omic Big Data Analysis Drives Precision Medicine.2018

    • Author(s)
      Tatsuhiko Tsunoda
    • Organizer
      The 8th Annual Translational Bioinformatics Conference/2018 Annual Conference of Korean Society for Bioinformatics
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Omic analysis with AI drives precision medicine.2018

    • Author(s)
      Tatsuhiko Tsunoda
    • Organizer
      The 5th RIKEN-KI/SciLifeLab Joint Symposium
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Trans-omic and Trans-species Analysis Drives Precision Medicine.2018

    • Author(s)
      Tatsuhiko Tsunoda
    • Organizer
      The 41st Annual Meeting of the Molecular Biology Society of Japan
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Trans-omic Analysis Strategy for Precision Medicine.2018

    • Author(s)
      Tatsuhiko Tsunoda
    • Organizer
      The 2nd International Symposium for Trans-Omics
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Public Big Data Accelerate Medical Science Research.2018

    • Author(s)
      Tatsuhiko Tsunoda
    • Organizer
      Symposium “Public database and application for medicine in Japan and Asia”, The 63rd Annual Meeting of the Japan Society of Human Genetics
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Exploring etiologies, sub-classification, and risk prediction of diseases based on big-data analysis of clinical and whole omics data in medicine.2018

    • Author(s)
      Tatsuhiko Tsunoda
    • Organizer
      CREST International Symposium on Big Data Application
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] ゲノム医科学の進展とプレシジョン医療の推進.2018

    • Author(s)
      角田 達彦
    • Organizer
      東北メディカルメガバンク第16回ゲノム・オミックス連携推進セミナー
    • Related Report
      2018 Annual Research Report
    • Invited
  • [Presentation] 臨床研究におけるビッグデータの活用.2018

    • Author(s)
      角田 達彦
    • Organizer
      臨床研究統計コース, 統計数理研究所
    • Related Report
      2018 Annual Research Report
    • Invited
  • [Presentation] Exploring etiologies, sub-classification, and risk prediction of diseases based on big-data analysis of clinical and whole omics data in medicine2017

    • Author(s)
      Tatsuhiko Tsunoda
    • Organizer
      CREST Big Data Fields Joint Meeting
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Trans-omic analysis drives precision medicine2017

    • Author(s)
      Tatsuhiko Tsunoda
    • Organizer
      The 1st International Symposium for Trans-Omics
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Multi-omic analysis for precision cancer medicine2017

    • Author(s)
      Tatsuhiko Tsunoda
    • Organizer
      DNA sequencing technologies and their application in practice WS
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Omic analysis drives precision medicine2017

    • Author(s)
      Tatsuhiko Tsunoda
    • Organizer
      International Conference for Precision Cancer Medicine
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Multiomics and clinical analysis of cancer2017

    • Author(s)
      Tatsuhiko Tsunoda
    • Organizer
      CREST International Symposium on Big Data Application
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 医学・医療ビッグデータによるマルチオミックス解析2017

    • Author(s)
      角田 達彦
    • Organizer
      東京医科歯科大学‐早稲田大学連携ワークショップ
    • Related Report
      2017 Annual Research Report
    • Invited
  • [Presentation] オミックス解析によるゲノム医療の新たな展開2017

    • Author(s)
      角田 達彦
    • Organizer
      第 8 回生物統計ネットワークシンポジウム
    • Related Report
      2017 Annual Research Report
    • Invited
  • [Book] 遺伝統計学と疾患ゲノムデータ解析(2章ー10「GWASをトランスオミクスで読み解く」)2018

    • Author(s)
      柚木克之、角田達彦、黒田真也(岡田随象 編)
    • Total Pages
      10
    • Publisher
      株式会社 メディカル ドゥ
    • ISBN
      9784944157631
    • Related Report
      2017 Annual Research Report
  • [Remarks] 代謝統合オミクス

    • URL

      http://transomics.umin.jp

    • Related Report
      2021 Annual Research Report 2020 Annual Research Report 2019 Annual Research Report
  • [Remarks] 東京大学 角田研究室(日本語版)

    • URL

      http://mesm.bs.s.u-tokyo.ac.jp

    • Related Report
      2021 Annual Research Report
  • [Remarks] 東京大学 角田研究室(英語版)

    • URL

      http://mesm.bs.s.u-tokyo.ac.jp/index_Eng.html

    • Related Report
      2021 Annual Research Report
  • [Remarks] 東京大学 角田研究室

    • URL

      http://mesm.bs.s.u-tokyo.ac.jp

    • Related Report
      2020 Annual Research Report 2019 Annual Research Report

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Published: 2017-07-04   Modified: 2023-01-30  

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