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Application of new methods of statistical analysis to functional movements of biomolecules

Research Project

Project/Area Number 25610105
Research Category

Grant-in-Aid for Challenging Exploratory Research

Allocation TypeMulti-year Fund
Research Field Mathematical physics/Fundamental condensed matter physics
Research InstitutionNara Women's University

Principal Investigator

Toda Mikito  奈良女子大学, 自然科学系, 准教授 (70197896)

Co-Investigator(Kenkyū-buntansha) Takami Toshiya  大分大学, 工学部, 教授 (10270472)
Fukumizu Kenji  統計数理研究所, 数理推論研究系, 教授 (60311362)
Fujisaki Hiroshi  日本医科大学, 医学部, 准教授 (60573243)
Project Period (FY) 2013-04-01 – 2016-03-31
Project Status Completed (Fiscal Year 2015)
Budget Amount *help
¥4,030,000 (Direct Cost: ¥3,100,000、Indirect Cost: ¥930,000)
Fiscal Year 2015: ¥1,170,000 (Direct Cost: ¥900,000、Indirect Cost: ¥270,000)
Fiscal Year 2014: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000)
Fiscal Year 2013: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000)
Keywords時系列解析 / ウェーブレット変換 / 次元縮約 / 生体分子 / 機能発現 / 反応動力学 / 相空間構造 / 主成分解析 / 正準相関解析 / 情報縮約 / 集団運動 / 大自由度力学系 / 非平衡統計力学 / 統計科学 / ウエーブレット解析 / ウエーブレット変換 / 動的相関 / 頑健性 / 天然変性タンパク質 / 統計的因果推論
Outline of Final Research Achievements

Understanding molecular function is a challenging problem. In particular, functional processes are rare events, we need to develop a new methodology for dimensional reduction for time series data in large dimensional space. In order to attack these problems, we combine achievements of recent progress in data analysis such as wavelet transformations, trend analysis and kernel methods. We also rely on recent results of nonlinear science such as phase space geometry of reaction dynamics. We apply these methods to analyze model systems of reaction dynamics, Fermi-Pasta-Ulam coupled oscillator system and proteins.

Report

(4 results)
  • 2015 Annual Research Report   Final Research Report ( PDF )
  • 2014 Research-status Report
  • 2013 Research-status Report
  • Research Products

    (60 results)

All 2016 2015 2014 2013 Other

All Journal Article (11 results) (of which Peer Reviewed: 10 results,  Open Access: 4 results,  Acknowledgement Compliant: 6 results) Presentation (49 results) (of which Int'l Joint Research: 4 results,  Invited: 15 results)

  • [Journal Article] Mechanism and Experimental Observability of Global Switching Between Reactive and Nonreactive Coordinates at High Total Energies2015

    • Author(s)
      H. Teramoto, M. Toda, H. Kono, M.Takahashi, T. Komatsuzaki
    • Journal Title

      Physical Review Letters

      Volume: 115 Issue: 9 Pages: 093003-093003

    • DOI

      10.1103/physrevlett.115.093003

    • NAID

      120005853086

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Breakdown Mechanisms of Normally Hyperbolic Invariant Manifolds2015

    • Author(s)
      H. Teramoto, M. Toda, T. Komatsuzaki
    • Journal Title

      Nonlinearity

      Volume: 28 Issue: 8 Pages: 2677-2698

    • DOI

      10.1088/0951-7715/28/8/2677

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] A coarse graining method to extract cooperative modes of water molecules2015

    • Author(s)
      H. Teramoto, M.Toda, T.Komatsuzaki
    • Journal Title

      Advances in Science, Technology and Environmentology

      Volume: 11 Pages: 7-11

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Understandings of chemical reaction dynamics in terms of dynamical systems theory2015

    • Author(s)
      Hiroshi Teramoto, Mikito Toda, Tamiki Komatsuzaki
    • Journal Title

      AIP Conference Proceedings

      Volume: 1702 Pages: 1-4

    • DOI

      10.1063/1.4938850

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed
  • [Journal Article] A network structure of emotional interactions in an electronic bulletin board2015

    • Author(s)
      H.Adachi, M.Toda
    • Journal Title

      Proceeding of Social Modeling and Simulations + Econophysics Colloquium

      Volume: no volume Pages: 311-322

    • DOI

      10.1007/978-3-319-20591-5_28

    • ISBN
      9783319205908, 9783319205915
    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] A new method to improve validity range of Lie canonical perturbation theory: with a central focus on a concept of non‐blow‐up region2014

    • Author(s)
      Hiroshi Teramoto, Mikito Toda, Tamiki Komatsuzaki
    • Journal Title

      Theoretical Chemistry Account

      Volume: 133 Issue: 11

    • DOI

      10.1007/s00214-014-1571-9

    • NAID

      120005650128

    • Related Report
      2014 Research-status Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] タンパク質分子の構造ダイナミクス:ウェーブレット変換による解析2014

    • Author(s)
      鎌田真由美、戸田幹人
    • Journal Title

      統計数理

      Volume: 62 Pages: 203-220

    • NAID

      120006020825

    • Related Report
      2014 Research-status Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Spatio-temporal Hierarchy in the Dynamics of a Minimalist Protein Model2013

    • Author(s)
      Yasuhiro Matsunaga, Akinori Baba, Chun Biu Li, John Straub, Mikito Toda, Tamiki Komatsuzaki, R. Berry
    • Journal Title

      The Journal of Chemical Physics

      Volume: 139 Issue: 21 Pages: 215101-215101

    • DOI

      10.1063/1.4834415

    • NAID

      120005385312

    • Related Report
      2013 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Measuring dynamical randomness of quantum chaos by statistics of Schmidt eigenvalues2013

    • Author(s)
      H. Kubotani, S. Adachi and M. Toda
    • Journal Title

      Physical Review E

      Volume: 87 Issue: 6

    • DOI

      10.1103/physreve.87.062921

    • Related Report
      2013 Research-status Report
    • Peer Reviewed
  • [Journal Article] Fluctuations of Healthy and Unhealthy Heartbeat Intervals2013

    • Author(s)
      Boon Leong Lan and Mikito Toda
    • Journal Title

      Europhysics Letters

      Volume: Vol.102 Issue: 1 Pages: 18002-18002

    • DOI

      10.1209/0295-5075/102/18002

    • Related Report
      2013 Research-status Report
    • Peer Reviewed
  • [Journal Article] 大自由度系の集団運動抽出に向けた問題提起:化学反応動力学の観点から2013

    • Author(s)
      寺本央、戸田幹人、小松崎民樹
    • Journal Title

      数理解析研究所講究録

      Volume: 1827 Pages: 154-170

    • Related Report
      2013 Research-status Report
  • [Presentation] 結合振動子系における多様な動的現象の解析32016

    • Author(s)
      森田紗代、戸田幹人
    • Organizer
      日本物理学会年会
    • Place of Presentation
      東北学院大学
    • Year and Date
      2016-03-20
    • Related Report
      2015 Annual Research Report
  • [Presentation] Fermi-Pasta-Ulam結合振動子系における動的緩和現象の解析42016

    • Author(s)
      神戸舞、冨士香奈、戸田幹人
    • Organizer
      日本物理学会年会
    • Place of Presentation
      東北学院大学
    • Year and Date
      2016-03-20
    • Related Report
      2015 Annual Research Report
  • [Presentation] Dynamical Reaction Theory Beyond Conventional Statistical Reaction Theory2015

    • Author(s)
      Mikito Toda
    • Organizer
      Workshop on "Theory of Gas Phase Scattering and Reactivity for Astrophysics"
    • Place of Presentation
      Max-Planck Institute for Extraterrestrial Physics, Munchen, Germany
    • Year and Date
      2015-11-27
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 大自由度力学系の特徴集出2015

    • Author(s)
      戸田幹人
    • Organizer
      ワークショップ「大自由度分子系における化学反応機序の理解と制御」
    • Place of Presentation
      北海道大学
    • Year and Date
      2015-11-01
    • Related Report
      2015 Annual Research Report
    • Invited
  • [Presentation] 大自由度力学系の集団運動2015

    • Author(s)
      戸田幹人
    • Organizer
      研究会「非線形現象の捉え方」
    • Place of Presentation
      福岡工業大学セミナーハウス
    • Year and Date
      2015-10-10
    • Related Report
      2015 Annual Research Report
    • Invited
  • [Presentation] Fermi-Pasta-Ulam結合振動子系における動的緩和現象の解析32015

    • Author(s)
      神戸舞、冨士香奈、戸田幹人
    • Organizer
      日本物理学会秋季大会
    • Place of Presentation
      関西大学
    • Year and Date
      2015-09-17
    • Related Report
      2015 Annual Research Report
  • [Presentation] 特異点論を用いた非断熱交差の安定性と分岐の解析2015

    • Author(s)
      寺本央、戸田幹人、小松崎民樹
    • Organizer
      日本物理学会秋季大会
    • Place of Presentation
      関西大学
    • Year and Date
      2015-09-16
    • Related Report
      2015 Annual Research Report
  • [Presentation] Geometry and Dynamics in systems of more than 2 dof2015

    • Author(s)
      Mikito Toda
    • Organizer
      Workshop on "Geometry of Chemical Reaction Dynamics in Gas and Condensed Phases"
    • Place of Presentation
      Telluride Science Research Center
    • Year and Date
      2015-08-05
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Dynamical reaction theory from micro to macro through mesoscopic levels2015

    • Author(s)
      Mikito Toda
    • Organizer
      R. Stephen Berry Tribute Symposium
    • Place of Presentation
      Telluride Science Research Center
    • Year and Date
      2015-06-25
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Time-frequency approach to molecular dynamics simulation of proteins2015

    • Author(s)
      Mikito Toda
    • Organizer
      Workshop on "The Complexity of Dynamics and Kinetics from Single Molecules to Cells"
    • Place of Presentation
      Telluride Science Research Center
    • Year and Date
      2015-06-18
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] A Global Dynamical Switching of a Reaction Coordinate and its Experimental Observability2015

    • Author(s)
      寺本央、戸田幹人、小松崎民樹
    • Organizer
      第31回化学反応討論会
    • Place of Presentation
      北海道大学
    • Year and Date
      2015-06-03
    • Related Report
      2015 Annual Research Report
  • [Presentation] 非線形動力学に依拠した情報発掘法の開拓と生体分子への応用2015

    • Author(s)
      戸田幹人
    • Organizer
      第5回物質・デバイス領域共同研究拠点報告会
    • Place of Presentation
      九州大学
    • Year and Date
      2015-04-20
    • Related Report
      2015 Annual Research Report
  • [Presentation] Fermi-Pasta-Ulam結合振動子系における動的緩和現象の解析22015

    • Author(s)
      神戸舞,戸田幹人
    • Organizer
      日本物理学会年会
    • Place of Presentation
      早稲田大学(東京都)
    • Year and Date
      2015-03-22
    • Related Report
      2014 Research-status Report
  • [Presentation] 非平衡分子動力学を用いた生体分子内のエネルギー移動の解析2015

    • Author(s)
      藤崎弘士,古田忠臣,戸田幹人
    • Organizer
      日本物理学会年会
    • Place of Presentation
      早稲田大学(東京都)
    • Year and Date
      2015-03-21
    • Related Report
      2014 Research-status Report
  • [Presentation] 大自由度力学系における振動エネルギー移動の解析2015

    • Author(s)
      櫛田茉実,冨士香奈,藤崎弘士,戸田幹人
    • Organizer
      日本物理学会年会
    • Place of Presentation
      早稲田大学(東京都)
    • Year and Date
      2015-03-21
    • Related Report
      2014 Research-status Report
  • [Presentation] 結合振動子系における多様な動的現象の解析22015

    • Author(s)
      森田紗代,戸田幹人
    • Organizer
      日本物理学会年会
    • Place of Presentation
      早稲田大学(東京都)
    • Year and Date
      2015-03-21
    • Related Report
      2014 Research-status Report
  • [Presentation] SNSの発言間における参照関係と感情表現のネットワーク2015

    • Author(s)
      足立遥、戸田幹人
    • Organizer
      日本物理学会年会
    • Place of Presentation
      早稲田大学(東京都)
    • Year and Date
      2015-03-21
    • Related Report
      2014 Research-status Report
  • [Presentation] Understandings of Chemical Reaction Dynamics in terms of Dynamical System Theory2015

    • Author(s)
      Hiroshi Teramoto, Mikito Toda and Tamiki Komatsuzaki
    • Organizer
      Computational Chemistry (CC) Symposium in ICCMSE 2015
    • Place of Presentation
      Athens(Greece)
    • Year and Date
      2015-03-20
    • Related Report
      2014 Research-status Report
    • Invited
  • [Presentation] 大自由度系における振動エネルギー移動の解析2015

    • Author(s)
      戸田幹人
    • Organizer
      Workshop on Dynamical Systems and Computation 2015
    • Place of Presentation
      北海道大学(北海道札幌市)
    • Year and Date
      2015-03-05
    • Related Report
      2014 Research-status Report
  • [Presentation] Time series analysis using wavelets to extract collective motion of proteins2015

    • Author(s)
      Mikito Toda
    • Organizer
      Spectroscopy and Dynamics of Molecules and Clusters 2015 (SDMC2015)
    • Place of Presentation
      Nainital( India)
    • Year and Date
      2015-02-22
    • Related Report
      2014 Research-status Report
    • Invited
  • [Presentation] SNSにおける感情の伝播現象に関する研究~投稿の参照関係に基づく感情語ネットワークの特性~2015

    • Author(s)
      足立遥、戸田幹人
    • Organizer
      第6回テキストマイニング・シンポジウム
    • Place of Presentation
      ティーオージー会議室(大阪府大阪市)
    • Year and Date
      2015-02-05
    • Related Report
      2014 Research-status Report
  • [Presentation] SNSにおける感情表現とその相互作用関係の抽出2015

    • Author(s)
      足立遥、戸田幹人
    • Organizer
      第220回自然言語処理研究会(情報処理学会)
    • Place of Presentation
      九州大学(福岡県福岡市)
    • Year and Date
      2015-01-19
    • Related Report
      2014 Research-status Report
  • [Presentation] 大自由度力学系に対する時系列解析:ウエーブレット変換を用いた試み2014

    • Author(s)
      戸田幹人
    • Organizer
      環瀬戸内応用数理研究部会シンポジウム
    • Place of Presentation
      加計学園国際学術交流センター(岡山県倉敷市)
    • Year and Date
      2014-12-05
    • Related Report
      2014 Research-status Report
  • [Presentation] A network structure of emotional interactions in an electronic bulletin board2014

    • Author(s)
      Haruka Adachi, Mikito Toda
    • Organizer
      Social Modeling and Simulations + Econophysics Colloquium 2014
    • Place of Presentation
      神戸ポートアイランドセンター(兵庫県神戸市)
    • Year and Date
      2014-11-04
    • Related Report
      2014 Research-status Report
  • [Presentation] Time series analysis of the protein SNase : its dynamics and function2014

    • Author(s)
      Kana Fuji, Mikito Toda
    • Organizer
      Japan-Slovenia Seminar on Nonlinear Science (Kansai 2014)
    • Place of Presentation
      奈良女子大学(奈良県奈良市)
    • Year and Date
      2014-10-29
    • Related Report
      2014 Research-status Report
  • [Presentation] 正準変換摂動理論の有効領域の拡張法とそれによる振動子間の非線形共鳴によるエネルギー移動の解明2014

    • Author(s)
      寺本 央、戸田幹人、小松崎民樹
    • Organizer
      日本物理学会
    • Place of Presentation
      中部大学(愛知県春日井市)
    • Year and Date
      2014-09-09
    • Related Report
      2014 Research-status Report
  • [Presentation] Fermi-Pasta-Ulam結合振動子系における動的緩和現象の解析2014

    • Author(s)
      神戸舞,戸田幹人
    • Organizer
      日本物理学会
    • Place of Presentation
      中部大学(愛知県春日井市)
    • Year and Date
      2014-09-08
    • Related Report
      2014 Research-status Report
  • [Presentation] 結合振動子系における多様な動的現象の解析2014

    • Author(s)
      森田紗代,戸田幹人
    • Organizer
      日本物理学会
    • Place of Presentation
      中部大学(愛知県春日井市)
    • Year and Date
      2014-09-08
    • Related Report
      2014 Research-status Report
  • [Presentation] 大自由度力学系におけるエネルギー移動の解析32014

    • Author(s)
      櫛田茉実,冨士香奈,戸田幹人,藤崎弘士
    • Organizer
      日本物理学会
    • Place of Presentation
      中部大学(愛知県春日井市)
    • Year and Date
      2014-09-08
    • Related Report
      2014 Research-status Report
  • [Presentation] Chemical Ratchet: a possible mechanism to break the detailed balance2014

    • Author(s)
      Mikito Toda
    • Organizer
      Workshop "What kinds of dynamical feature can we extract from data?"
    • Place of Presentation
      ニセコ町民センター(北海道ニセコ町)
    • Year and Date
      2014-08-27
    • Related Report
      2014 Research-status Report
  • [Presentation] Reaction Coordinate Switching Mechanism, on the Possibility of Its Experimental Verification and Its Quantum Manifestation2014

    • Author(s)
      Hiroshi Teramoto, Mikito Toda and Tamiki Komatsuzaki
    • Organizer
      The 10th AIMS (American Institute of Mathematical Science) Conference on Dynamical Systems, Differential Equations and Applications Special Session 113
    • Place of Presentation
      Madrid(Spain)
    • Year and Date
      2014-07-08
    • Related Report
      2014 Research-status Report
    • Invited
  • [Presentation] Time Series Analysis using Wavelet To Extract Collective Behavior of Proteins2014

    • Author(s)
      Mikito Toda
    • Organizer
      Let's face chaos through nonlinear science
    • Place of Presentation
      Maribor( Slovenia)
    • Year and Date
      2014-07-04
    • Related Report
      2014 Research-status Report
    • Invited
  • [Presentation] 生体分子と水の過渡的な集団運動の抽出2014

    • Author(s)
      寺本 央、戸田幹人、小松崎民樹
    • Organizer
      第17回理論化学討論会
    • Place of Presentation
      名古屋大学(愛知県名古屋市)
    • Year and Date
      2014-05-22
    • Related Report
      2014 Research-status Report
  • [Presentation] 生体分子と水の過渡的な協同運動の抽出

    • Author(s)
      寺本央,戸田幹人,小松崎民樹
    • Organizer
      日本物理学会年会
    • Place of Presentation
      東海大学
    • Related Report
      2013 Research-status Report
  • [Presentation] 核酸分解酵素Staphylococcal nucleaseの分子動力学に対する時系列解析 活性低下における水、リガンド、ループの関係性

    • Author(s)
      冨士香奈,藤崎弘士,古田忠臣,芝るみ,山口真理子,戸田幹人
    • Organizer
      日本物理学会年会
    • Place of Presentation
      東海大学
    • Related Report
      2013 Research-status Report
  • [Presentation] シグナル伝達に関与するPDZドメインの分子動力学データに対する時系列解析4

    • Author(s)
      岸田直子,藤崎弘士,戸田幹人
    • Organizer
      日本物理学会年会
    • Place of Presentation
      東海大学
    • Related Report
      2013 Research-status Report
  • [Presentation] 大自由度力学系におけるエネルギー移動の解析2

    • Author(s)
      櫛田茉実,冨士香奈,戸田幹人
    • Organizer
      日本物理学会年会
    • Place of Presentation
      東海大学
    • Related Report
      2013 Research-status Report
  • [Presentation] タンパク質シニョリンの構造変化パスサンプリングII

    • Author(s)
      藤崎弘士,冨士香奈,戸田幹人
    • Organizer
      日本物理学会年会
    • Place of Presentation
      東海大学
    • Related Report
      2013 Research-status Report
  • [Presentation] Dimensional reduction for molecular dynamics of proteins

    • Author(s)
      Mikito Toda
    • Organizer
      Workshop on Lagrangian Coherent Structures and Dynamical Systems
    • Place of Presentation
      北海道大学
    • Related Report
      2013 Research-status Report
    • Invited
  • [Presentation] 生体分子の分子動力学で探る集団運動

    • Author(s)
      戸田幹人
    • Organizer
      京都大学数理解析研究所研究集会「ランダム力学系理論とその応用」
    • Place of Presentation
      京都大学
    • Related Report
      2013 Research-status Report
    • Invited
  • [Presentation] The analysis of energy transfer in Chaotic Dynamical Systems

    • Author(s)
      Mami Kushida, Kana Fuji, Mikito Toda
    • Organizer
      Biophysical Society of Japan
    • Place of Presentation
      名古屋大学
    • Related Report
      2013 Research-status Report
  • [Presentation] Time-series analysis of molecular dynamics: Conformational change and dynamics of collective behavior

    • Author(s)
      Kana Fuji, Masakazu Sekijima, Hiroshi Fujisaki, Mikito Toda
    • Organizer
      Biophysical Society of Japan
    • Place of Presentation
      名古屋大学
    • Related Report
      2013 Research-status Report
  • [Presentation] 生体分子の分子動力学に対する時系列解析 集団運動の揺らぎと構造変化の関係を探る IV

    • Author(s)
      冨士香奈,関嶋政和,藤崎弘士,戸田幹人
    • Organizer
      日本物理学会
    • Place of Presentation
      徳島大学
    • Related Report
      2013 Research-status Report
  • [Presentation] タンパク質シニョリンの構造変化パスサンプリング

    • Author(s)
      藤崎弘士,冨士香奈,戸田幹人
    • Organizer
      日本物理学会
    • Place of Presentation
      徳島大学
    • Related Report
      2013 Research-status Report
  • [Presentation] シグナル伝達に関与するPDZドメインの分子動力学に対する時系列解析3

    • Author(s)
      岸田直子,藤崎弘士,戸田幹人
    • Organizer
      日本物理学会
    • Place of Presentation
      徳島大学
    • Related Report
      2013 Research-status Report
  • [Presentation] 大自由度力学系におけるエネルギー移動の解析

    • Author(s)
      櫛田茉実,冨士香奈,戸田幹人
    • Organizer
      日本物理学会
    • Place of Presentation
      徳島大学
    • Related Report
      2013 Research-status Report
  • [Presentation] 生体分子の分子動力学データに対するウエーブレット変換を用いた時系列解析

    • Author(s)
      戸田幹人、鎌田真由美
    • Organizer
      日本生物物理学会北海道支部講演会
    • Place of Presentation
      北海道大学
    • Related Report
      2013 Research-status Report
    • Invited
  • [Presentation] Analysis of motion features using wavelet for molecular dynamics simulation of proteins

    • Author(s)
      Mikito Toda, Mayumi Kamada
    • Organizer
      Telluride Summer workshop "The Complexity of Dynamics and Kinetics in Many Dimensions "
    • Place of Presentation
      Telluride Science Research Center, Telluride Colorado, USA
    • Related Report
      2013 Research-status Report
    • Invited
  • [Presentation] Future prospects of the dynamical theory of reactions

    • Author(s)
      Mikito Toda
    • Organizer
      Telluride workshop "Geometry of Chemical Reaction Dynamics in Gas and Condensed Phases"
    • Place of Presentation
      Telluride Science Research Center, Telluride Colorado, USA
    • Related Report
      2013 Research-status Report
    • Invited

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Published: 2014-07-25   Modified: 2019-07-29  

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