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Development of a graphical model and a tolerance region for the assessment of physiological process and ecological diversity

Research Project

Project/Area Number 25280006
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypePartial Multi-year Fund
Section一般
Research Field Statistical science
Research InstitutionThe University of Tokyo

Principal Investigator

Kishino Hirohisa  東京大学, 農学生命科学研究科, 教授 (00141987)

Co-Investigator(Kenkyū-buntansha) Kitada Shuichi  東京海洋大学, 海洋科学技術研究科, 教授 (10262338)
Project Period (FY) 2013-04-01 – 2016-03-31
Project Status Completed (Fiscal Year 2015)
Budget Amount *help
¥17,030,000 (Direct Cost: ¥13,100,000、Indirect Cost: ¥3,930,000)
Fiscal Year 2015: ¥5,590,000 (Direct Cost: ¥4,300,000、Indirect Cost: ¥1,290,000)
Fiscal Year 2014: ¥5,590,000 (Direct Cost: ¥4,300,000、Indirect Cost: ¥1,290,000)
Fiscal Year 2013: ¥5,850,000 (Direct Cost: ¥4,500,000、Indirect Cost: ¥1,350,000)
Keywords医薬生物・ゲノム解析 / 生体と生態系の健全性 / 遺伝子ネットワーク / 分子系統樹 / リスク評価 / 医薬生物・ゲノム統計解析 / 影響評価手法
Outline of Final Research Achievements

First, we developed a method that constructs the entropy-based maximal core connected subgraph of gene expression profiles. The analysis of the expression profiles at the early developmental stage of Atlantic salmon showed that the resultant graph makes it easy to understand the key players and their interactions. Second, we defined two complementary tolerance intervals. The coverage probability of the standard tolerance interval is at least the pre-specified level, whereas that of the complementary tolerance interval is at most the specified level. With the two complementary tolerance intervals, we developed a statistical procedure to test a target population includes a pre-specified amount of outliers with respect to the reference population. Third, we developed a new index of community diversity. By comparing the species sampling proportion with the value estimated assuming random sampling, it measures phylogenetic skew of member species.

Report

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

    (55 results)

All 2016 2015 2014 2013

All Journal Article (21 results) (of which Int'l Joint Research: 6 results,  Peer Reviewed: 21 results,  Open Access: 11 results,  Acknowledgement Compliant: 10 results) Presentation (34 results) (of which Int'l Joint Research: 1 results,  Invited: 8 results)

  • [Journal Article] Grouping substitution types into different relaxed molecular clocks2016

    • Author(s)
      Lee, H-J., Kishino, H., Rodrigue, N., and Thorne, J. L.
    • Journal Title

      Philosophical Transactions of Royal Society B

      Volume: accepted

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] Assessment of the network of protected areas for birds in Taiwan with regard to functional and phylogenetic diversity2016

    • Author(s)
      Chen, H., Nagai, S., and Kishino, H.
    • Journal Title

      Pacific Conservation Biology

      Volume: 22 Issue: 1 Pages: 61-71

    • DOI

      10.1071/pc15046

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] Hypothesis testing of inclusion of the tolerance interval for the assessment of food safety2015

    • Author(s)
      Chen, H. and Kishino, H.
    • Journal Title

      PLoS ONE

      Volume: 10(10) Issue: 10 Pages: e0141117-e0141117

    • DOI

      10.1371/journal.pone.0141117

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] Global pattern of phylogenetic species composition of shark and its conservation priority2015

    • Author(s)
      Chen, H. and Kishino, H.
    • Journal Title

      Ecology and Evolution

      Volume: 5(19) Issue: 19 Pages: 4455-4465

    • DOI

      10.1002/ece3.1724

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] A Bayesian hierarchical ANOVA model of stochastic seasonality for Diodon Holocanthus in northern Taiwan2015

    • Author(s)
      Chen, H., Shao, K-T., and Kishino, H.
    • Journal Title

      the Journal of Marine Science and Technology

      Volume: accepted

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] 関係式のモデリングと誤差のモデリング2015

    • Author(s)
      岸野洋久
    • Journal Title

      日本生態学会誌

      Volume: 65 Pages: 187-196

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Viruses Roll the Dice: The Stochastic Behavior of Viral Genome Molecules Accelerates Viral Adaptation at the Cell and Tissue Levels2015

    • Author(s)
      Miyashita S., Ishibashi K., Kishino H. and Ishikawa M.
    • Journal Title

      PLOS Biology

      Volume: 13 Issue: 3 Pages: e1002094-e1002094

    • DOI

      10.1371/journal.pbio.1002094

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Phylogenetic skew: an index of community diversity.2015

    • Author(s)
      Chen, H., Shao, K-T., and Kishino, H.
    • Journal Title

      Molecular Ecology.

      Volume: 24 Issue: 4 Pages: 759-770

    • DOI

      10.1111/mec.13064

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Bayesian inference of baseline fertility and treatment effects via a crop yield-fertility model.2014

    • Author(s)
      Chen, H., Yamagishi, J., and Kishino, H.
    • Journal Title

      PLoS ONE.

      Volume: 9 (11) Issue: 11 Pages: e112785-e112785

    • DOI

      10.1371/journal.pone.0112785

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Model-based tolerance intervals derived from cumulative historical composition data: Application for substantial equivalence assessment of a genetically modified crop.2014

    • Author(s)
      Hong, B., Fisher, T., Sult, T., Maxwell, C., Mickelson, J., Kishino, H., and Locke, M.
    • Journal Title

      Journal of Agricultural and Food Chemistry.

      Volume: 62 Issue: 40 Pages: 9916-9926

    • DOI

      10.1021/jf502158q

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Archaeal β diversity patterns under the seafloor along geochemical gradients.2014

    • Author(s)
      Koyano,H., Tsubouchi, T., Kishino, H., and Akutsu, T.
    • Journal Title

      Journal of Geophysical Research G.

      Volume: 119 Issue: 9 Pages: 1770-1788

    • DOI

      10.1002/2014jg002676

    • NAID

      120005623238

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Genetic effects of marine stock enhancement : a case study based on the highly piscivorous Japanese Spanish mackerel.2014

    • Author(s)
      Nakajima K, Kitada S, Habara Y, Sano S, Yokoyama E, Sugaya T, Iwamoto A, Kishino H, Hamasaki K
    • Journal Title

      Canadian Journal of Fisheries and Aquatic Sciences

      Volume: 71 Issue: 2 Pages: 301-314

    • DOI

      10.1139/cjfas-2013-0418

    • Related Report
      2014 Annual Research Report 2013 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Comprehensive Comparison of Self-Administered Questionnaires for Measuring Quantitative Autistic Traits in Adults2014

    • Author(s)
      Takeshi Nishiyama, Masako Suzuki, Katsunori Adachi, Satoshi Sumi,Kensuke Okada, Hirohisa Kishino, Saeko Sakai, Yoko Kamio, Masayo Kojima, Sadao Suzuki, Stephen M. Kanne
    • Journal Title

      Journal of Autism and Developmental Disorders

      Volume: 44 Issue: 5 Pages: 993-1007

    • DOI

      10.1007/s10803-013-2020-7

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Reproduction of an alien Ruditapes clam (Bivalvia: Veneridae) on recreational clam-gathering grounds in Tokyo Bay, Japan.2014

    • Author(s)
      Hamasaki, K., Ishibashi, Y., and Kitada, S.
    • Journal Title

      Molluscan Research

      Volume: 34 Issue: 1 Pages: 24-61

    • DOI

      10.1080/13235818.2013.862145

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Japanese chum salmon stock enhancement: Current perspective and future challenges2014

    • Author(s)
      Kitada, S.
    • Journal Title

      Fishery Science

      Volume: 80 Issue: 2 Pages: 237-249

    • DOI

      10.1007/s12562-013-0692-8

    • NAID

      40020038504

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Molecular and morphological evidence of hybridization between native Ruditapes philippinarum and the introduced Ruditapes form in Japan2013

    • Author(s)
      Kitada S, Fujikake C, Asakura Y; Yuki H, Nakajima K, Vargas K M, Kawashima S, Hamasaki K, Kishino H
    • Journal Title

      Conservation Genetics

      Volume: 14 (3) Issue: 3 Pages: 717-733

    • DOI

      10.1007/s10592-013-0467-x

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Fractional parentage analysis and a scale-free reproductive network of brown trout.2013

    • Author(s)
      Koyano, H., Serbezov, D., Kishino, H., and Schweder, T.
    • Journal Title

      Journal of Theoretical Biology.

      Volume: 336 Pages: 717-733

    • DOI

      10.1016/j.jtbi.2013.06.038

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Plasmodium falciparum mitochondrial genetic diversity exhibits isolation-by-distance patterns supporting a sub-Saharan African origin.2013

    • Author(s)
      Tanabe K, Jombart T, Horibe S, Palacpac N, Honma H, Tachibana S, Nakamura M, Horii T, Kishinod H, Mita T*.
    • Journal Title

      Mitochondrion

      Volume: 13 Issue: 6 Pages: 630-636

    • DOI

      10.1016/j.mito.2013.08.008

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] A cross-species socio-emotional behaviour development revealed by a multivariate analysis2013

    • Author(s)
      小柴満美子、白川由佳、三村喬生、妹尾綾、狩野源太、中村俊
    • Journal Title

      Scientific Reports

      Volume: Vol.3 Issue: 1 Pages: 1-7

    • DOI

      10.1038/srep02630

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Spatial distribution of selection pressure on a protein based on the hierarchical Bayesian model2013

    • Author(s)
      Teruaki Watabe and Hirohisa Kishino
    • Journal Title

      Molecular Biology and Evolution

      Volume: 30 Issue: 12 Pages: 2714-2722

    • DOI

      10.1093/molbev/mst151

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Ecological interactions between hatchery and wild fish: A case study based on the highly piscivorous Japanese Spanish mackerel2013

    • Author(s)
      Nakajima K , Yamazaki H, Takemori H, Obata y Iwamoto A, Hamasaki K, Kitada S
    • Journal Title

      Aquaculture Environment Interactions

      Volume: 3 (3) Issue: 3 Pages: 231-243

    • DOI

      10.3354/aei00065

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Presentation] Assessment of protected area networks for bird biodiversity in Taiwan2016

    • Author(s)
      Chen, H., Nagai, S., and Kishino, H.
    • Organizer
      日本生態学会
    • Place of Presentation
      仙台国際センター(宮城県仙台市)
    • Year and Date
      2016-03-20
    • Related Report
      2015 Annual Research Report
  • [Presentation] シミュレーションと系統解析から探る、淡水魚の朝鮮半島からの侵入と拡散2016

    • Author(s)
      谷口昇二・岡崎登志夫・岸野洋久
    • Organizer
      日本生態学会
    • Place of Presentation
      仙台国際センター(宮城県仙台市)
    • Year and Date
      2016-03-20
    • Related Report
      2015 Annual Research Report
  • [Presentation] 分子系統樹と個体ベースシミュレーションによる移入淡水魚の拡散と置き換わりの推定2016

    • Author(s)
      谷口昇二・岡崎登志夫・岸野洋久
    • Organizer
      日本計量生物学会
    • Place of Presentation
      統計数理研究所(東京都立川市)
    • Year and Date
      2016-03-18
    • Related Report
      2015 Annual Research Report
  • [Presentation] On the adaptive mutations on the viral genomes and genetic diversity of communities2016

    • Author(s)
      Kishino, H.
    • Organizer
      Invited seminar
    • Place of Presentation
      重慶大学(中国重慶市)
    • Year and Date
      2016-03-10
    • Related Report
      2015 Annual Research Report
    • Invited
  • [Presentation] Spatio-temporal modeling to measure viral adaptation and community diversity2015

    • Author(s)
      Kishino, H.
    • Organizer
      Invited seminar
    • Place of Presentation
      リンツ大学(オーストリア、リンツ)
    • Year and Date
      2015-11-26
    • Related Report
      2015 Annual Research Report
    • Invited
  • [Presentation] On the adaptive mutations on the viral genomes and genetic diversity of communities2015

    • Author(s)
      Kishino, H.
    • Organizer
      Invited seminar
    • Place of Presentation
      ウイーン集団遺伝研究科(オーストリア、ウイーン)
    • Year and Date
      2015-11-24
    • Related Report
      2015 Annual Research Report
    • Invited
  • [Presentation] 日本進化学会学会賞・木村賞受賞講演2015

    • Author(s)
      岸野洋久
    • Organizer
      日本進化学会
    • Place of Presentation
      中央大学(東京都文京区)
    • Year and Date
      2015-08-20
    • Related Report
      2015 Annual Research Report
    • Invited
  • [Presentation] Genetic interactions between hatchery and wild fish: Japanese chum salmon perspectives2015

    • Author(s)
      Kitada, S., Miyakoshi, Y., Nakamichi, R., and Kishino, H.
    • Organizer
      the American Fisheries Society
    • Place of Presentation
      オレゴンコンベンションセンター(アメリカ、ポートランド)
    • Year and Date
      2015-08-16
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research
  • [Presentation] The Core gene expression cascade during the early developmental process identifies genetic mechanisms for salmonids captive breeding2015

    • Author(s)
      Nakamichi, R., Kishino, H., and Kitada, S.
    • Organizer
      the American Fisheries Society
    • Place of Presentation
      オレゴンコンベンションセンター(アメリカ、ポートランド)
    • Year and Date
      2015-08-16
    • Related Report
      2015 Annual Research Report
  • [Presentation] Global pattern of phylogenetic species composition of shark and its conservation priority2015

    • Author(s)
      陳虹諺・岸野洋久
    • Organizer
      日本水産学会
    • Place of Presentation
      東京海洋大(東京都港区)
    • Year and Date
      2015-03-27 – 2015-03-31
    • Related Report
      2014 Annual Research Report
  • [Presentation] Algal bloom and its phylogenetic aggregation2015

    • Author(s)
      陳虹諺・長井敏・漆崎慎吾・山本圭吾・及川寛・安池元重・中村洋路・田邉晶史・本郷悠貴・藤原篤志・岸野洋久
    • Organizer
      日本水産学会
    • Place of Presentation
      東京海洋大(東京都港区)
    • Year and Date
      2015-03-27 – 2015-03-31
    • Related Report
      2014 Annual Research Report
  • [Presentation] 経験ベイズFSTは高遺伝子流動海産魚類の微細な集団構造を明らかにする2015

    • Author(s)
      北田修一・中道礼一郎・岸野洋久
    • Organizer
      日本水産学会
    • Place of Presentation
      東京海洋大(東京都港区)
    • Year and Date
      2015-03-27 – 2015-03-31
    • Related Report
      2014 Annual Research Report
  • [Presentation] ベニザケの産卵回帰における遺伝子発現ネットワークと上流/下流産卵群の環境適応の系統差2015

    • Author(s)
      中道礼一郎・岸野洋久・北田修一
    • Organizer
      日本水産学会
    • Place of Presentation
      東京海洋大(東京都港区)
    • Year and Date
      2015-03-27 – 2015-03-31
    • Related Report
      2014 Annual Research Report
  • [Presentation] Measuring genetic diversity of populations and communities2015

    • Author(s)
      Kishino, H.
    • Organizer
      Invited seminar at Southwest University, China
    • Place of Presentation
      西南大学(中国重慶市)
    • Year and Date
      2015-03-18
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] Algal bloom and its phylogenetic aggregation2015

    • Author(s)
      陳虹諺・長井敏・漆崎慎吾・山本圭吾・及川寛・安池元重・中村洋路・田邉晶史・本郷悠貴・藤原篤志・岸野洋久
    • Organizer
      日本計量生物学会
    • Place of Presentation
      京都大学(京都府京都市)
    • Year and Date
      2015-03-12 – 2015-03-13
    • Related Report
      2014 Annual Research Report
  • [Presentation] Statistical modeling to measure selection and adaptation2014

    • Author(s)
      Kishino, H.
    • Organizer
      Invited seminar
    • Place of Presentation
      国立台湾大学(台湾台北市)
    • Year and Date
      2014-11-25
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] Hypothesis testing of inclusion of the tolerance interval.2014

    • Author(s)
      陳虹諺・岸野洋久
    • Organizer
      統計関連学会連合
    • Place of Presentation
      東京大(東京都文京区)
    • Year and Date
      2014-09-13 – 2014-09-16
    • Related Report
      2014 Annual Research Report
  • [Presentation] インフルエンザヘマグルチニンタンパク質上における選択圧の分布と変遷の検出2014

    • Author(s)
      渡部輝明・岸野洋久
    • Organizer
      日本進化学会
    • Place of Presentation
      高槻現代劇場(大阪府高槻市)
    • Year and Date
      2014-08-21 – 2014-08-24
    • Related Report
      2014 Annual Research Report
  • [Presentation] A high phylogenetic skew of sharks in the tropical sea2014

    • Author(s)
      陳虹諺・岸野洋久
    • Organizer
      日本進化学会
    • Place of Presentation
      高槻現代劇場(大阪府高槻市)
    • Year and Date
      2014-08-21 – 2014-08-24
    • Related Report
      2014 Annual Research Report
  • [Presentation] Baseline fertility connects crop yield and soil2014

    • Author(s)
      Chen, H-Y., Yamagishi, J., and Kishino, H.
    • Organizer
      International Biometric Society
    • Place of Presentation
      Florence, Italy
    • Year and Date
      2014-07-06 – 2014-07-11
    • Related Report
      2014 Annual Research Report
  • [Presentation] Phylogenetic skew: A new index of community diversity.2014

    • Author(s)
      Chen, H-Y., Shao, K-T., and Kishino, H.
    • Organizer
      the joint annual meeting of the Society for the Study of Evolution (SSE), the Society of Systematic Biologists (SSB), and the American Society of Naturalists (ASN).
    • Place of Presentation
      Raleigh, USA.
    • Year and Date
      2014-06-20 – 2014-06-24
    • Related Report
      2014 Annual Research Report
  • [Presentation] ベースライン肥沃度は作物収量と土壌を結び付ける.2014

    • Author(s)
      陳虹諺・山岸順子・岸野洋久
    • Organizer
      日本計量生物学会
    • Place of Presentation
      統計数理研究所(東京都立川市)
    • Year and Date
      2014-05-23 – 2014-05-24
    • Related Report
      2014 Annual Research Report
  • [Presentation] Distribution of positive selection and divergence times2014

    • Author(s)
      Kishino, H.
    • Organizer
      Masami Hasegawa's memorial workshop
    • Place of Presentation
      Fudan University (Shanghai, China)
    • Related Report
      2013 Annual Research Report
  • [Presentation] 関係式のモデリングと誤差のモデリング2014

    • Author(s)
      岸野洋久
    • Organizer
      日本生態学会
    • Place of Presentation
      広島国際会議場(広島県広島市)
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] A new index of effective community size2014

    • Author(s)
      陳虹諺,岸野洋久
    • Organizer
      日本生態学会
    • Place of Presentation
      広島国際会議場(広島県広島市)
    • Related Report
      2013 Annual Research Report
  • [Presentation] タイセイヨウサケの初期発生における遺伝子発現ネットワークにみられる養殖の影響2014

    • Author(s)
      中道礼一郎,岸野洋久,北田修一
    • Organizer
      日本水産学会
    • Place of Presentation
      北海道大学(北海道函館市)
    • Related Report
      2013 Annual Research Report
  • [Presentation] Baseline fertility connects crop yield and soil2014

    • Author(s)
      陳虹諺,岸野洋久
    • Organizer
      日本作物学会
    • Place of Presentation
      千葉大学(千葉県千葉市)
    • Related Report
      2013 Annual Research Report
  • [Presentation] サケ科魚類の生活史における遺伝子発現コアネットワーク:最大エントロピー法による極大連結有向グラフの推定2013

    • Author(s)
      中道礼一郎,岸野洋久,北田修一
    • Organizer
      日本計量生物学会
    • Place of Presentation
      パルセいいざか(福島県福島市)
    • Related Report
      2013 Annual Research Report
  • [Presentation] 魚群集構造に見る系統学的多様性の頑健性2013

    • Author(s)
      陳虹諺,岸野洋久
    • Organizer
      日本計量生物学会
    • Place of Presentation
      パルセいいざか(福島県福島市)
    • Related Report
      2013 Annual Research Report
  • [Presentation] Spatial distribution of selection pressure on a protein based on the hierarchical Bayesian model2013

    • Author(s)
      Watabe, T. and Kishino, H.
    • Organizer
      Society for Molecular Biology and Evolution
    • Place of Presentation
      Hyatt Regency Chicago (Chicago, USA)
    • Related Report
      2013 Annual Research Report
  • [Presentation] 世界古細菌群集の配列・環境地図2013

    • Author(s)
      柏村卓朗,岸野洋久
    • Organizer
      日本進化学会
    • Place of Presentation
      筑波大学(茨城県つくば市)
    • Related Report
      2013 Annual Research Report
  • [Presentation] Effective community size and the effect of weighted species sampling2013

    • Author(s)
      陳虹諺,岸野洋久
    • Organizer
      日本進化学会
    • Place of Presentation
      筑波大学(茨城県つくば市)
    • Related Report
      2013 Annual Research Report
  • [Presentation] Spatiotemporal modeling to measure the effects of mutations and selection pressures2013

    • Author(s)
      Kishino, H., Watabe, T. , Nakamichi, R., and Kitada, S.
    • Organizer
      International Statistical Institute
    • Place of Presentation
      Hong Kong Convention and Exhibition Centre (Hong Kong, China)
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] A new index of effective community size2013

    • Author(s)
      陳虹諺,岸野洋久
    • Organizer
      統計関連学会連合
    • Place of Presentation
      大阪大学(大阪府吹田市)
    • Related Report
      2013 Annual Research Report

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Published: 2013-05-21   Modified: 2019-07-29  

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