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Management of the research group on logic for biological pattern formation

Administrative Group

Project AreaFrom molecules, cells to organs : trans-hierarchical logic for higher-order pattern and structures
Project/Area Number 22127001
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

Principal Investigator

TAKEDA Hiroyuki  東京大学, 理学(系)研究科(研究院), 教授 (80179647)

Co-Investigator(Kenkyū-buntansha) 上野 直人  基礎生物学研究所, 形態形成研究部門, 教授 (40221105)
Co-Investigator(Renkei-kenkyūsha) KONDO Shigeru  大阪大学, 大学院生命機能研究科, 教授 (10252503)
OGURA Toshihiko  東北大学, 加齢医学研究所, 教授 (60273851)
MATSUMOTO Takeo  名古屋工業大学, 大学院工学研究科, 教授 (30209639)
MATSUNO Kenji  東京理科大学, 基礎工学部, 教授 (60318227)
SAWA Hitoshi  独立行政法人理化学研究所, 細胞運命研究チーム, チームリーダー (80222024)
UENO Naoto  基礎生物学研究所, 形態形成研究部門, 教授 (40221105)
Project Period (FY) 2010-04-01 – 2016-03-31
Project Status Completed (Fiscal Year 2015)
Budget Amount *help
¥51,480,000 (Direct Cost: ¥39,600,000、Indirect Cost: ¥11,880,000)
Fiscal Year 2014: ¥11,570,000 (Direct Cost: ¥8,900,000、Indirect Cost: ¥2,670,000)
Fiscal Year 2013: ¥10,140,000 (Direct Cost: ¥7,800,000、Indirect Cost: ¥2,340,000)
Fiscal Year 2012: ¥10,660,000 (Direct Cost: ¥8,200,000、Indirect Cost: ¥2,460,000)
Fiscal Year 2011: ¥10,530,000 (Direct Cost: ¥8,100,000、Indirect Cost: ¥2,430,000)
Fiscal Year 2010: ¥8,580,000 (Direct Cost: ¥6,600,000、Indirect Cost: ¥1,980,000)
Keywords器官形成 / 体軸形成 / 数理モデル / 力学的パラメータ / パターン形成 / 力学的パラメーター
Outline of Final Research Achievements

In a multi-cellular organism, groups of cells produce higher-order patterns and structures during development. To explore this order formation, we need logics that explain the processes of trans-hierarchy from the level of molecules and cells to entire organs. In our research group, we examined the logic for organogenesis and pattern formation by introducing mathematical modeling and as-set-unknown parameters relating to physical properties of cells such as force and deformation. To facilitate intimate collaboration among wet biologists, theoretical biologists and engineers specializing in measuring physical properties of cells and tissues, the stirring committee provided various supports such as annual grant meetings, research camps and technical seminars.

Report

(6 results)
  • 2015 Final Research Report ( PDF )
  • 2014 Annual Research Report
  • 2013 Annual Research Report
  • 2012 Annual Research Report
  • 2011 Annual Research Report
  • 2010 Annual Research Report

Research Products

(54 results)

All 2016 2015 2014 2013 2012 2011 Other

All Int'l Joint Research (1 results) Journal Article (24 results) (of which Peer Reviewed: 24 results,  Open Access: 13 results,  Acknowledgement Compliant: 13 results) Presentation (23 results) (of which Int'l Joint Research: 5 results,  Invited: 9 results) Remarks (4 results) Funded Workshop (2 results)

  • [Int'l Joint Research] Mechanobiology Institute, NUS(シンガポール)

    • Related Report
      2014 Annual Research Report
  • [Journal Article] Development of the pancreas in medaka, Oryzias latipes, from embryo to adult2015

    • Author(s)
      Takayoshi Otsuka, Tatsuya Tsukahara & Takeda, H.
    • Journal Title

      Dev Growth Differ.

      Volume: 57 Pages: 557-569

    • DOI

      10.1111/dgd.12237

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] G protein-coupled receptors Flop1 and Flop2 inhibit Wnt/β-catenin signaling and are essential for head formation in Xenopus.2015

    • Author(s)
      Miyagi, A., Negishi, T., Yamamoto, T.S., and Ueno, N.
    • Journal Title

      Developmental Biology

      Volume: 407 Pages: 131-144

    • DOI

      10.1016/j.ydbio.2015.08.001

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Phosphorylation-dependent ubiquitination of paraxial protocadherin (PAPC) controls gastrulation cell movements.2015

    • Author(s)
      Kai, M., Ueno, N. and Kinoshita, N.
    • Journal Title

      PLoS One

      Volume: 10

    • DOI

      10.1371/journal.pone.0115111

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] The medaka dhc2 mutant reveals conserved and distinct mechanisms of Hedgehog signaling in teleosts.2015

    • Author(s)
      Yamamoto, T., Tsukahara, T., Ishiguro, T., Hagiwara, H., Taira, M. & Takeda, H.
    • Journal Title

      BMC Developmental Biology

      Volume: 15 Pages: 9-9

    • DOI

      10.1186/s12861-015-0057-x

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Large hypomethylated domains serve as strong repressive machinery for key developmental genes in vertebrates2014

    • Author(s)
      Nakamura, R., Tsukahara, T., Qu, W., Ichikawa, K., Otsuka, T., Ogoshi, K., Saito, T.L., Matsushima, K., Sugano, S., Hashimoto, S., Suzuki, Y., Morishita, S. & Takeda, H.
    • Journal Title

      Development

      Volume: 141 Pages: 2568-2580

    • DOI

      10.1242/dev.108548

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Six1 is a key regulator of the developmental and evolutionary architecture of sensory neurons in craniates2014

    • Author(s)
      H. Yajima, M. Suzuki, H. Ochi, K. Ikeda, S. Sato, K. Yamamura, H. Ogino, N. Ueno and K. Kawakami
    • Journal Title

      BMC Biology

      Volume: 12 Pages: 12-40

    • DOI

      10.1186/1741-7007-12-40

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Left-right asymmetry is formed in individual cells by intrinsic cell chirality2014

    • Author(s)
      Hatori, R., Ando, T., Sasamura, T., Nakazawa, N., Nakamura, M., Taniguchi, K., Hozumi, S., Kikuta, J., Ishii, M., *Matsuno, K.
    • Journal Title

      Developmental biology

      Volume: 133 Pages: 482-495

    • DOI

      10.1016/j.ydbio.2013.07.023

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Estimation of the mechanical connection between apical stress fibers and the nucleus in vascular smooth muscle cells cultured on a substrate2014

    • Author(s)
      Nagayama K, Yamazaki S, Yahiro Y, Matsumoto T.
    • Journal Title

      Journal of Biomechanics

      Volume: 47 Pages: 1422-1429

    • DOI

      10.1016/j.jbiomech.2014.01.042

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] In vitro analysis suggests that difference in cell movement during direct interaction can generate various pigment patterns in vivo2014

    • Author(s)
      Yamanaka H, Kondo S
    • Journal Title

      PNAS

      Volume: 111 Pages: 1867-72

    • DOI

      10.1073/pnas.1315416111

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Involvement of Delta–Notch signaling in zebrafish adult pigment stripe patterning2014

    • Author(s)
      Hamada H, Watanabe M, Lau HE, Nishida T, Hasegawa T, Parichy DM, Kondo S, Parichy DM, Kondo S
    • Journal Title

      Development

      Volume: 141 Pages: 318-24

    • DOI

      10.1242/dev.099804

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Haemodynamically dependent valvulogenesis of zebrafish heart is mediated by flow-dependent expression of miR-212013

    • Author(s)
      Banjo T, Grajcarek J, Yoshino D, Osada H, Miyasaka KY, Kida YS, Ueki Y, Nagayama K Kawakami K, Matsumoto T, Sato M, Ogura T
    • Journal Title

      Nature Commun

      Volume: 4,1978 Pages: 1-11

    • DOI

      10.1038/ncomms2978

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Trunk exoskeleton in teleosts is mesodermal in origin.2013

    • Author(s)
      Atsuko Shimada
    • Journal Title

      Nat Commun

      Volume: 4 Pages: 1639-1639

    • DOI

      10.1038/ncomms2643

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Modular development of the teleost trunk along the dorsoventral axis and zic1/zic4 as selector genes in the dorsal module.2013

    • Author(s)
      Toru Kawanishi
    • Journal Title

      Development

      Volume: 140 Pages: 1486-1496

    • DOI

      10.1242/dev.088567

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Rescue of Notch signaling in cells incapable of GDP-L-fucose synthesis by gap junction transfer of GDP-L-fucose in Drosophila2012

    • Author(s)
      Ayukawa, T., Matsumoto, K., Ishikawa, HO., Ishino, A., Yamakawa, T., Aoyama, N., Suzuki, T., Matsuno. K.
    • Journal Title

      Proc Natl Acad Sci U S A.

      Volume: 109(38) Pages: 15318-15323

    • DOI

      10.1073/pnas.1202369109

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Changing clothes easily: connexin41.8 regulates skin pattern variation2012

    • Author(s)
      Watanabe, m., Kondo, S.
    • Journal Title

      Pigment Cell & Melanoma Research

      Volume: 25(3) Pages: 326-30

    • DOI

      10.1111/j.1755-148x.2012.00984.x

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Deficient Notch signaling associated with neurogenic pecanex is compensated for by the unfolded protein response in Drosophila2012

    • Author(s)
      Tomoko Yamakawa, Kenta Yamada, Takeshi Sasamura, Naotaka Nakazawa, Maiko Kanai, Emiko Suzuki, Mark E.Fortini, Kenji Matsuno
    • Journal Title

      Development

      Volume: 139 Pages: 558-567

    • DOI

      10.1242/dev.073858

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Multiple functions of PBRM-1/Polybromo- and LET-526/Osa-containing chromatin remodeling complexes in C.elegans development2012

    • Author(s)
      Shibata Y, Uchida M, Takeshita H, Nishiwaki K., Sawa H
    • Journal Title

      Dev.Biol.

      Volume: 361 Pages: 349-357

    • DOI

      10.1016/j.ydbio.2011.10.035

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] The medaka zic1/zic4 mutant provides molecular insights into teleost caudal fin evolution.2012

    • Author(s)
      Yuuta Moriyama
    • Journal Title

      Current biology (pub;ished on line at 3/1 2012)

      Volume: 21 Pages: 601-601

    • DOI

      10.1016/j.cub.2012.01.063

    • Related Report
      2012 Annual Research Report 2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Pigment pattern formation by contact-dependent depolarization2012

    • Author(s)
      Inaba, M.
    • Journal Title

      Science

      Volume: 335 Pages: 677-677

    • DOI

      10.1126/science.1212821

    • Related Report
      2012 Annual Research Report 2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Dynamic Changes of Traction Force at Focal Adhesions during Macroscopic Cell Stretching Using an Elastic Micropillar Substrate: Tensional Homeostasis of Aortic Smooth Muscle Cells2012

    • Author(s)
      Nagayama, K., Adachi, A., Matsumoto, T.
    • Journal Title

      JBSE

      Volume: 7(2) Issue: 2 Pages: 130-140

    • DOI

      10.1299/jbse.7.130

    • NAID

      130002066897

    • ISSN
      1880-9863
    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Cell movements of the deep layer of non-neural ectoderm underlie complete neural tube closure in Xenopus2012

    • Author(s)
      Morita, H.
    • Journal Title

      Development

      Volume: 139 Pages: 1417-1426

    • DOI

      10.1242/dev.073239

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Chirality in Planar cell shape contributes to left-right asymmetric epithelial morphogenesis2011

    • Author(s)
      Kiicniro Tanigucni, Reo Maeda, Tadashi Ando, Takashi Okumura, Naotaka Nakazawa, Ryo Hatori, Mitsutoshi Nakamura, Shunya Hozumi, Hiroo Fujiwara, Kenji Matsuno
    • Journal Title

      Science

      Volume: 333 Pages: 339-341

    • DOI

      10.1126/science.1200940

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Wnt regulates spindle asymmetry to generate asymmetric nuclear β-catenin in C. elegans2011

    • Author(s)
      Sugioka, K.
    • Journal Title

      Cell

      Volume: 146 Pages: 942-954

    • DOI

      10.1016/j.cell.2011.07.043

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Heterogeneous Response of Traction Force at Focal Adhesions of Vascular Smooth Muscle Cells Subjected to Macroscopic Stretch on a Micropillar Substrate2011

    • Author(s)
      Nagayama, K.
    • Journal Title

      J Biomech

      Volume: 44 Pages: 2699-2705

    • DOI

      10.1016/j.jbiomech.2011.07.023

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Presentation] Deciphering the genetic code for the vertebrate pluripotent epigenome‐Insights from the medaka genome2016

    • Author(s)
      Hiroyuki Takeda
    • Organizer
      3rd Medaka Strategic Meeting and 17th Australia & New Zealand Zebrafish Metting
    • Place of Presentation
      メルボルン(オーストラリア)
    • Year and Date
      2016-02-03
    • Related Report
      2014 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Sequence-based logic for the vertebrate pluripotent epigenome2015

    • Author(s)
      Hiroyuki Takeda
    • Organizer
      4th International Symposium of the mathematics on Chromatin Live dynamics
    • Place of Presentation
      JMSアステールプラザ(広島県広島市)
    • Year and Date
      2015-12-01
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] 器官形成におけるカルシウムダイナミクス2015

    • Author(s)
      上野直人
    • Organizer
      第13回糖鎖科学コンソーシアムシンポジウム
    • Place of Presentation
      ウインクあいち(愛知県名古屋市)
    • Year and Date
      2015-10-19
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] Cell and Tissue Dynamics of Neural Tube Formation.2015

    • Author(s)
      Naoto Ueno, Makoto Suzuki, Hiroshi Koyama and Yasuhiro Inoue.
    • Organizer
      iCeMS International Symposium
    • Place of Presentation
      京都大学(京都府京都市)
    • Year and Date
      2015-09-23
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] Calcium Dynamics Shapes the Neural Tube.2015

    • Author(s)
      Naoto Ueno and Makoto Suzuki
    • Organizer
      he 3rd Asia-Pacific Developmental Biology Conference
    • Place of Presentation
      西安(中国)
    • Year and Date
      2015-09-13
    • Related Report
      2014 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Genomics and epigenomics in fish genomes2015

    • Author(s)
      Hiroyuki Takeda
    • Organizer
      The 7th Internatinal Symposium of Integrative
    • Place of Presentation
      蘭州(中国)
    • Year and Date
      2015-08-25
    • Related Report
      2014 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Prepatterning of Developmental Gene Expression in Vertebrates - interplay between genetic and epigenetic mechanisms2015

    • Author(s)
      Hiroyuki Takeda
    • Organizer
      UT -NTU Joint Symposium - Frontier of Biological Sciences
    • Place of Presentation
      台北(台湾)
    • Year and Date
      2015-03-09
    • Related Report
      2014 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Logic of the epigenetic code in the vertebrate genome2015

    • Author(s)
      Hiroyuki Takeda
    • Organizer
      Finnish-Japanese joint symposium on Morphogenesis and Signaling.
    • Place of Presentation
      ヘルシンキ(フィンランド)
    • Year and Date
      2015-03-04
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] Vertebrate PCP and nose morphogenesis2015

    • Author(s)
      Naoto Ueno
    • Organizer
      Finnish-Japanese joint symposium on Morphogenesis and Signaling.
    • Place of Presentation
      ヘルシンキ(フィンランド)
    • Year and Date
      2015-03-03
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] Cell chirality derives the left-right directional torsions Drosophila gut2014

    • Author(s)
      松野健二
    • Organizer
      MBI-Japan Joint Symposium2014
    • Place of Presentation
      National University of Singapore
    • Year and Date
      2014-12-03
    • Related Report
      2013 Annual Research Report
  • [Presentation] Engineering approaches toward estimation of stress and strain distributions in Xenopus laevis embryos2014

    • Author(s)
      松本健郎
    • Organizer
      MBI-Japan Joint Symposium2014
    • Place of Presentation
      National University of Singapore
    • Year and Date
      2014-12-03
    • Related Report
      2013 Annual Research Report
  • [Presentation] Cell Chirality Induces Mechanical Force Driving the Left-Right Directional Rotations of the Gut in Drosophila2014

    • Author(s)
      松野健二
    • Organizer
      Force in Development
    • Place of Presentation
      岡崎カンファレンスセンター(愛知県岡崎市)
    • Year and Date
      2014-11-18
    • Related Report
      2013 Annual Research Report
  • [Presentation] Establishment of robust compartments in fish somites along the dorsoventral axis2014

    • Author(s)
      武田洋幸
    • Organizer
      Force in Development
    • Place of Presentation
      岡崎カンファレンスセンター(愛知県岡崎市)
    • Year and Date
      2014-11-18
    • Related Report
      2013 Annual Research Report
  • [Presentation] Biomechanical analyses of Xenopus laevis embryo: Toward estimation of stress and strain distributions during morphogenesis2014

    • Author(s)
      松本健郎
    • Organizer
      Force in Development
    • Place of Presentation
      岡崎カンファレンスセンター(愛知県岡崎市)
    • Year and Date
      2014-11-18
    • Related Report
      2013 Annual Research Report
  • [Presentation] Ca2+ dynamics during neural tube formation of Xenopus2014

    • Author(s)
      上野直人
    • Organizer
      Force in Development
    • Place of Presentation
      岡崎カンファレンスセンター(愛知県岡崎市)
    • Year and Date
      2014-11-17
    • Related Report
      2013 Annual Research Report
  • [Presentation] Hemodynamic Forces as a Regulator of Cardiogenesis and Circulatory Homeostasis2014

    • Author(s)
      小椋利彦
    • Organizer
      Force in Development
    • Place of Presentation
      岡崎カンファレンスセンター(愛知県岡崎市)
    • Year and Date
      2014-11-17
    • Related Report
      2013 Annual Research Report
  • [Presentation] epigenetic regulation of key developmental genes - A genome-wide approach in the medaka genome2014

    • Author(s)
      Hiroyuki Takeda
    • Organizer
      2nd Strategical Meeting for Medaka Research
    • Place of Presentation
      セビリア(スぺイン)
    • Year and Date
      2014-04-11
    • Related Report
      2014 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Epijenetic regulation of key developmental genes in the medaka genome: Large DNA hypomethylated domains as a robust repression platform in pluripotent cells2014

    • Author(s)
      武田洋幸
    • Organizer
      6th Asia oceania Zebrafish Meeting HKUST, Hong Kong
    • Place of Presentation
      香港(中国)
    • Year and Date
      2014-01-21
    • Related Report
      2013 Annual Research Report
  • [Presentation] 新しいメカノバイオロジーのために‐医学/生物学的意義と融合的研究の重要性‐2013

    • Author(s)
      小椋利彦
    • Organizer
      第36回日本分子生物学会年会
    • Place of Presentation
      神戸国際会議場(兵庫県神戸市)
    • Year and Date
      2013-12-04
    • Related Report
      2013 Annual Research Report
  • [Presentation] 平面内細胞極性の数理モデル2012

    • Author(s)
      秋山正和
    • Organizer
      応用数学合同研究集会2012
    • Place of Presentation
      龍谷大学(滋賀)
    • Related Report
      2012 Annual Research Report
  • [Presentation] From molecules and cells to organs : trans-hierarchical logic for higher-order pattern and structures2011

    • Author(s)
      Takeda, H.
    • Organizer
      JSDB-GFE Joint meeting of Developmental Biology
    • Place of Presentation
      ドレスデン(ドイツ)
    • Related Report
      2010 Annual Research Report
  • [Presentation] Casting Genetic Light on Morphological Diversity in the Fish Body Shape

    • Author(s)
      Takeda, H.
    • Organizer
      22nd Pacific Science Congress.
    • Place of Presentation
      Kuala Lumpur, Malaysia
    • Related Report
      2011 Annual Research Report
    • Invited
  • [Presentation] “波”が生み出す多彩な生命機能

    • Author(s)
      近藤 滋
    • Organizer
      第89回日本生理学会大会
    • Place of Presentation
      長野県松本文化会館(松本市)
    • Related Report
      2011 Annual Research Report
    • Invited
  • [Remarks] ミクロからマクロへ階層を超える秩序形成のロジック

    • URL

      http://www.morphologic.jp/

    • Related Report
      2014 Annual Research Report 2013 Annual Research Report
  • [Remarks] ミクロからマクロへ階層を超える秩序形成のロジック

    • URL

      http://www.morphologic.jp

    • Related Report
      2012 Annual Research Report
  • [Remarks] ミクロからマクロへ階層を超える秩序形成のロジック

    • URL

      http://www.morphologic.jp

    • Related Report
      2011 Annual Research Report
  • [Remarks]

    • URL

      http://www.morphologic.jp/

    • Related Report
      2010 Annual Research Report
  • [Funded Workshop] シンガポール国立大学合同シンポジウム2014

    • Place of Presentation
      シンガポール(シンガポール)
    • Year and Date
      2014-12-02
    • Related Report
      2014 Annual Research Report
  • [Funded Workshop] Force in Development2014

    • Place of Presentation
      岡崎カンファレンスセンター(愛知県岡崎市)
    • Year and Date
      2014-11-17
    • Related Report
      2014 Annual Research Report

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Published: 2010-08-22   Modified: 2019-07-29  

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