%% Theory of Computing
%% File: v009a001.bib
%% Publication date: January 21, 2013
%% Authors: Nathaniel Bryans, Ehsan Chiniforooshan, David Doty, Lila Kari, and Shinnosuke Seki
%
@preamble{"\newcommand{\sortsilent}[1]{}"}

@string{acm      = "ACM Press"}
@string{ieee     = "IEEE Comp. Soc. Press"}
@string{springer = "Springer"}

@string{SIAMJComput="SIAM J. Comput."}
@string{tcs      = "Theoret. Comput. Sci."}

@string{Algorithmica="Algorithmica"}
@string{jcss="J. Comput. System Sci."}

@string{stoc00="Proc. 32nd STOC"}
@string{stoc01="Proc. 33rd STOC"}
@string{stoc02="Proc. 34th STOC"}

@string{focs80="Proc. 21st FOCS"}
@string{focs09="Proc. 50th FOCS"}

@string{soda=" Ann. ACM-SIAM Symp. on Discrete Algorithms"}
@string{soda04="Proc. 15th" # soda  # " (SODA'04)"}
@string{soda06="Proc. 17th" # soda  # " (SODA'06)"}
@string{soda10="Proc. 21st" # soda  # " (SODA'10)"}
@string{soda11="Proc. 22nd" # soda  # " (SODA'11)"}

@string{icalp=" Internat. Colloq. on Automata, Languages and Programming"}
@string{icalp08= "Proc. 35th" # icalp # " (ICALP'08)"}
@string{icalp09= "Proc. 36th" # icalp # " (ICALP'09)"}
@string{icalp12= "Proc. 39th" # icalp # " (ICALP'12)"}

@string{stacs=" Symp. Theoretical Aspects of Comp. Sci."}
@string{stacs11= "Proc. 28th" # stacs  # " (STACS'11)"}


@inproceedings{ks06,
title = {Reducing tile complexity for self-assembly through temperature programming},
author = {Ming-Yang Kao and Robert T. Schweller},
crossref = {psoda06},
bibsource = {DBLP, http://dblp.uni-trier.de},
pages = {571-580},
doi = {10.1145/1109557.1109620},
}


@article{ddfirss07,
title = {Staged Self-Assembly: Nanomanufacture of Arbitrary Shapes with ${O}(1)$ Glues},
author = {Erik D. Demaine and Martin L. Demaine and S{\'a}ndor P. Fekete and Mashhood Ishaque and Eynat Rafalin and Robert T. Schweller and Diane L. Souvaine},
note = {Preliminary version in \href{http://dx.doi.org/10.1007/978-3-540-77962-9_1}{DNA'07}},
journal = {Natural Computing},
number = {3},
volume = {7},
year = {2008},
bibsource = {DBLP, http://dblp.uni-trier.de},
pages = {347-370},
doi = {10.1007/s11047-008-9073-0},
}
%
@inproceedings{ddfirss07-conference,
title = {Staged Self-Assembly: Nanomanufacture of Arbitrary Shapes with ${O}(1)$ Glues},
author = {Erik D. Demaine and Martin L. Demaine and S{\'a}ndor P. Fekete and Mashhood Ishaque and Eynat Rafalin and Robert T. Schweller and Diane L. Souvaine},
booktitle = {13th Internat. Meet. DNA Computing (DNA'07)},
publisher = springer,
year = {2007},
bibsource = {DBLP, http://dblp.uni-trier.de},
pages = {1-14},
doi = {10.1007/978-3-540-77962-9\_1},
}
%
@book{gareyjohnson79,
title = {Computers and Intractability},
author = {Michael R. Garey and David S. Johnson},
publisher = {W. H. Freeman},
address = {New York},
year = {1979},
}
%
@book{arora2009computational,
title = {Computational Complexity: A Modern Approach},
author = {Sanjeev Arora and Boaz Barak},
publisher = {Cambridge University Press},
year = {2009},
} 
%
@article{fujharparwinmur07,
title = {Toward Reliable Algorithmic Self-Assembly of {DNA} Tiles: A Fixed-Width Cellular Automaton Pattern},
author = {Kenichi Fujibayashi and Rizal Hariadi and Sung Ha Park and Erik Winfree and Satoshi Murata},
journal = {Nano Letters},
number = {7},
volume = {8},
year = {2008},
pages = {1791--1797},
doi = {10.1021/nl0722830},
}

@inproceedings{adchgohu01,
title = {Running time and program size for self-assembled squares},
author = {Leonard M. Adleman and Qi Cheng and Ashish Goel and Ming-Deh A. Huang},
crossref = {pstoc01},
bibsource = {DBLP, http://dblp.uni-trier.de},
pages = {740-748},
doi = {10.1145/380752.380881},
}
%
@article{origamilithographynaturenano2009,
title = {Placement and orientation of individual {DNA} shapes on lithographically patterned surfaces},
author = {Ryan J. Kershner and Luisa D. Bozano and Christine M. Micheel and Albert M. Hung and Ann R. Fornof and Jennifer N. Cha and Charles T. Rettner and Marco Bersani and Jane Frommer and Paul W. K. Rothemund and Gregory M. Wallraff},
journal = {Nature Nanotechnology},
volume = {3},
number = {9},
year = {2009},
pages = {557-561},
doi = {10.1038/nnano.2009.220},
}
%
@inproceedings{beckerrr06,
title = {Self-assemblying Classes of Shapes with a Minimum Number of Tiles, and in Optimal Time},
author = {Florent Becker and Ivan Rapaport and {\'E}ric R{\'e}mila},
booktitle = {26th Internat. Conf. Foundations of Software Technology and Theoretical Computer Science (FSTTCS'06)},
year = {2006},
bibsource = {DBLP, http://dblp.uni-trier.de},
pages = {45-56},
doi = {10.1007/11944836\_7},
}
%
@phdthesis{winf98,
title = {Algorithmic Self-Assembly of {D}{N}{A}},
author = {Erik Winfree},
school = {California Institute of Technology},
year = {1998},
} 
@inproceedings{brychidotkarsek11,
title = {The Power of Nondeterminism in Self-Assembly},
author = {Nathaniel Bryans and Ehsan Chiniforooshan and David Doty and Lila Kari and Shinnosuke Seki},
crossref = {psoda11},
bibsource = {DBLP, http://dblp.uni-trier.de},
pages = {590-602},
eprint = {acm:2133082},
}
%
@article{seem82,
title = {Nucleic-acid junctions and lattices},
author = {Nadrian C. Seeman},
journal = {Journal of Theoretical Biology},
volume = {99},
number = {2},
year = {1982},
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} 
%
@inproceedings{patitztas,
title = {Simulation of Self-Assembly in the Abstract Tile Assembly Model with {I}{S}{U} {T}{A}{S}},
author = {Matthew J. Patitz},
publisher = {Sciencetechnica},
booktitle = {6th Ann. Conf. Foundations of Nanoscience (FNANO'09)},
year = {2009},
pages = {209--219},
eprint = {arxiv:1101.5151},
}
%
@article{manstasto10,
title = {Two Lower Bounds for Self-assemblies at Temperature 1},
author = "{\sortsilent{Manuch}J{\'a}n Ma\v{n}uch, Ladislav Stacho, and
            Christine Stoll}",
journal = {J. Computational Biology},
number = {6},
volume = {17},
year = {2010},
pages = {841-852},
note = {Preliminary versions in \href{http://dx.doi.org/10.1145/1529282.1529453}{SAC'09} and \href{http://dx.doi.org/10.1109/ICBBE.2009.5163719}{ICBBE'09}},
doi = {10.1089/cmb.2009.0067},
} 
%
@inproceedings{manstasto10-conference-sac,
title = {Two lower bounds for self-assemblies at temperature 1},
author = {Ma\v{n}uch, J{\'a}n and Ladislav Stacho and Christine Stoll},
booktitle = {Proc. 2009 ACM Symp. Applied Computing (SAC'09)},
year = {2009},
bibsource = {DBLP, http://dblp.uni-trier.de},
pages = {808-809},
doi = {10.1145/1529282.1529453},
}
%
@inproceedings{manstasto10-conference-icbbe,
title = {Two lower bounds for self-assemblies at temperature 1},
author = {J{\'a}n Ma\v{n}uch and Ladislav Stacho and Christine Stoll},
booktitle={3rd Internat. Conf. Bioinformatics and Biomedical Engineering (ICBBE'09)},
year = {2009},
bibsource = {DBLP, http://dblp.uni-trier.de},
pages={1-4},
doi={10.1109/ICBBE.2009.5163719},
}


@article{solwin07,
title = {Complexity of Self-Assembled Shapes},
author = {David Soloveichik and Erik Winfree},
note = {Preliminary version in \href{http://dx.doi.org/10.1007/11493785_30}{DNA'04}},
journal = SIAMJComput,
number = {6},
volume = {36},
year = {2007},
bibsource = {DBLP, http://dblp.uni-trier.de},
pages = {1544-1569},
doi = {10.1137/S0097539704446712},
}
%
@inproceedings{solwin07-conference,
title = {Complexity of Self-assembled Shapes},
author = {David Soloveichik and Erik Winfree},
booktitle = {10th Internat. Workshop DNA Computing (DNA'04)},
publisher = springer,
year = {2004},
bibsource = {DBLP, http://dblp.uni-trier.de},
pages = {344-354},
doi = {10.1007/11493785\_30},
}
@inproceedings{fupatschshe12,
title = {Self-assembly with Geometric Tiles},
author = {Bin Fu and Matthew J. Patitz and Robert T. Schweller and Robert Sheline},
booktitle = icalp12,
year = {2012},
bibsource = {DBLP, http://dblp.uni-trier.de},
pages = {714-725},
doi = {10.1007/978-3-642-31594-7\_60},
}


@article{dot10,
title = {Randomized Self-Assembly for Exact Shapes},
author = {David Doty},
note = {Preliminary version in \href{http://dx.doi.org/10.1109/FOCS.2009.13}{FOCS'09}},
journal = SIAMJComput,
number = {8},
volume = {39},
year = {2010},
bibsource = {DBLP, http://dblp.uni-trier.de},
pages = {3521-3552},
doi = {10.1137/090779152},
}
%
@inproceedings{dot10-conference,
title = {Randomized Self-Assembly for Exact Shapes},
author = {David Doty},
crossref = {pfocs09},
bibsource = {DBLP, http://dblp.uni-trier.de},
pages = {85-94},
doi = {10.1109/FOCS.2009.13},
}
@inproceedings{sekiokuno2012,
title = {On the Behavior of Tile Assembly System at High Temperatures},
author = {Shinnosuke Seki and Yasushi Okuno},
booktitle = {8th Conf. Computability in Europe, (CiE'12)},
publisher = springer,
year = {2012},
bibsource = {DBLP, http://dblp.uni-trier.de},
pages = {549-559},
doi = {10.1007/978-3-642-30870-3\_55},
}
@article{fortune79,
title = {A Note on Sparse Complete Sets},
author = {Steven Fortune},
journal = SIAMJComput,
number = {3},
volume = {8},
year = {1979},
bibsource = {DBLP, http://dblp.uni-trier.de},
pages = {431-433},
doi = {10.1137/0208034},
}
@inproceedings{kaoschs08,
title = {Randomized Self-assembly for Approximate Shapes},
author = {Ming-Yang Kao and Robert T. Schweller},
booktitle = icalp08,
publisher = springer,
year = {2008},
bibsource = {DBLP, http://dblp.uni-trier.de},
pages = {370-384},
doi = {10.1007/978-3-540-70575-8\_31},
}
%
@article{chagoprei12,
title = {Tile Complexity of Linear Assemblies},
author = {Harish Chandran and Nikhil Gopalkrishnan and John H. Reif},
journal = SIAMJComput,
note = {Preliminary version in \href{http://dx.doi.org/10.1007/978-3-642-02927-1_21}{ICALP'09}},
volume = {41},
number = {4},
year = {2012},
pages = {1051-1073},
doi = {10.1137/110822487},
}
%
@inproceedings{chagoprei12-conference,
title = {The Tile Complexity of Linear Assemblies},
author = {Harish Chandran and Nikhil Gopalkrishnan and John H. Reif},
booktitle = icalp09,
publisher = springer,
year = {2009},
bibsource = {DBLP, http://dblp.uni-trier.de},
pages = {235-253},
doi = {10.1007/978-3-642-02927-1\_21},
}
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title = {The Polynomial-Time Hierarchy},
author = {Larry J. Stockmeyer},
journal = tcs,
number = {1},
volume = {3},
year = {1976},
bibsource = {DBLP, http://dblp.uni-trier.de},
pages = {1-22},
doi = {10.1016/0304-3975(76)90061-X},
}
%
@article{liuparreilab04,
title = {{DNA} nanotubes self-assembled from triple-crossover tiles as templates for conductive nanowires},
author = {Dage Liu and Sung Ha Park and John H. Reif and Thomas H. LaBean},
publisher = {National Academy of Sciences},
journal = {Proc. Nat. Acad. Sci.},
number = {3},
volume = {101},
year = {2004},
pages = {717-722},
doi = {10.1073/pnas.0305860101},
}
%
@article{yanparfinreilab03,
title = {{DNA}-templated self-assembly of protein arrays and highly conductive nanowires},
author = {Hao Yan and Sung Ha Park and Gleb Finkelstein and John H. Reif and Thomas H. LaBean},
publisher = {AAAS},
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year = {2003},
pages = {1882-1884},
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}

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title = {Complete Sets and the Polynomial-Time Hierarchy},
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journal = tcs,
number = {1},
volume = {3},
year = {1976},
bibsource = {DBLP, http://dblp.uni-trier.de},
pages = {23-33},
doi = {10.1016/0304-3975(76)90062-1},
}
%
@misc{schwellerpersonalcommunicationpnsa,
title = {Personal communication},
author = {Robert T. Schweller},
url = {http://faculty.utpa.edu/rtschweller/papers/TheGap.pdf},
note = {\url{http://faculty.utpa.edu/rtschweller/papers/TheGap.pdf}},
year = {2011},
}
%
@article{dotcacm,
title = {Theory of Algorithmic Self-Assembly},
author = {David Doty},
url = {http://www.dna.caltech.edu/~ddoty/papers/tasa.pdf},
journal = {Comm. ACM},
year = {2012},
volume = {55},
number = {12},
pages = {78-88},
doi = {10.1145/2380656.2380675},
} 
%
@article{barschrotwin09,
title = {An Information-Bearing Seed for Nucleating Algorithmic Self-Assembly},
author = {Robert D. Barish and Rebecca Schulman and Paul W. K. Rothemund and Erik Winfree},
journal = {Proc. Nat. Acad. Sci.},
number = {15},
volume = {106},
year = {2009},
pages = {6054--6059},
doi = {10.1073/pnas.0808736106},
}
%
@article{park2006finite,
title = {{Finite-Size, Fully Addressable {DNA} Tile Lattices Formed by Hierarchical Assembly Procedures}},
author = {Sung Ha Park and Constantin Pistol and Sang Jung Ahn and John H. Reif and Alvin R. Lebeck and Chris Dwyer and Thomas H. LaBean},
journal = {Angewandte Chemie International Edition},
volume = {45},
number = {5},
year = {2006},
publisher = {WILEY-VCH Verlag},
doi = {10.1002/anie.200503797},
pages = {735--739},
}

@article{mahaney82,
title = {Sparse Complete Sets of {NP}: Solution of a Conjecture of {B}erman and {H}artmanis},
author = {Stephen R. Mahaney},
note = {Preliminary version in \href{http://dx.doi.org/10.1109/SFCS.1980.40}{FOCS'80}},
journal = jcss,
number = {2},
volume = {25},
year = {1982},
bibsource = {DBLP, http://dblp.uni-trier.de},
pages = {130-143},
doi = {10.1016/0022-0000(82)90002-2},
}
%
@inproceedings{mahaney82-conference,
title = {Sparse Complete Sets for {NP}: Solution of a Conjecture of {B}erman and {H}artmanis},
author = {Stephen R. Mahaney},
crossref = {pfocs80},
bibsource = {DBLP, http://dblp.uni-trier.de},
pages = {54-60},
doi = {10.1109/SFCS.1980.40},
}
%
@techreport{adle99,
title = {Towards a Mathematical Theory of Self-Assembly},
author = {Leonard M. Adleman},
year = {2000},
institution = {University of Southern California},
} 
@article{jlsat1,
title = {Limitations of self-assembly at temperature 1},
author = {David Doty and Matthew J. Patitz and Scott M. Summers},
journal = tcs,
number = {1-2},
volume = {412},
year = {2011},
bibsource = {DBLP, http://dblp.uni-trier.de},
pages = {145-158},
note = {Preliminary version in \href{http://link.springer.com/chapter/10.1007\%2F978-3-642-10604-0_4}{DNA'09}},
doi = {10.1016/j.tcs.2010.08.023},
}



@article{jssadst,
title = {Strict self-assembly of discrete {S}ierpinski triangles},
author = {James I. Lathrop and Jack H. Lutz and Scott M. Summers},
note = {Preliminary version in \href{http://dx.doi.org/10.1007/978-3-540-73001-9_47}{CiE'07}},
journal = tcs,
number = {4-5},
volume = {410},
year = {2009},
bibsource = {DBLP, http://dblp.uni-trier.de},
pages = {384-405},
doi = {10.1016/j.tcs.2008.09.062},
}
%
@inproceedings{jssadst-conference,
title = {Strict Self-assembly of Discrete {S}ierpinski Triangles},
author = {James I. Lathrop and Jack H. Lutz and Scott M. Summers},
booktitle = {3rd Conf. Computability in Europe, (CiE'07)},
year = {2007},
bibsource = {DBLP, http://dblp.uni-trier.de},
pages = {455-464},
doi = {10.1007/978-3-540-73001-9\_47},
}
%
@article{ropawi04,
title = {Algorithmic Self-Assembly of {DNA} {S}ierpinski Triangles},
author = {Paul W. K. Rothemund and Nick Papadakis and Erik Winfree},
journal = {PLoS Biology},
number = {12},
volume = {2},
year = {2004},
pages = {2041--2053},
doi = {10.1371/journal.pbio.0020424},
}
%
@article{schuma02a,
title = {Completeness in the Polynomial-Time Hierarchy: Part {I}: {A} Compendium},
author = {Marcus Schaefer and Christopher Umans},
journal = {SIGACTN: SIGACT News (ACM Special Interest Group on Automata and Computability Theory)},
number = {3},
volume = {33},
year = {2002},
pages = {32--49},
doi = {10.1145/582475.582484},
}
%
@inproceedings{wang63,
title = {Dominoes and the {AEA} case of the decision problem},
author = {Hao Wang},
publisher = {Polytechnic Press of Polytechnic Inst. of Brooklyn, Brooklyn, N.Y.},
booktitle = {Proc. Symp. Mathem. Theory of Automata (MTA'62)},
year = {1963},
pages = {23-55},
} 
%
@misc{constantine10personal,
title = {Personal Communication},
author = {Constantine Evans},
} 
@article{agks05,
title = {Complexities for Generalized Models of Self-Assembly},
author = {Gagan Aggarwal and Qi Cheng and Michael H. Goldwasser and Ming-Yang Kao and Pablo Moisset de Espan{\'e}s and Robert T. Schweller},
note = {Preliminary version in \href{http://dl.acm.org/citation.cfm?id=982792.982926}{SODA'04}},
journal = SIAMJComput,
number = {6},
volume = {34},
year = {2005},
bibsource = {DBLP, http://dblp.uni-trier.de},
pages = {1493-1515},
doi = {10.1137/S0097539704445202},
}
%
@inproceedings{agks05-conference,
title = {Complexities for generalized models of self-assembly},
author = {Gagan Aggarwal and Michael H. Goldwasser and Ming-Yang Kao and Robert T. Schweller},
crossref = {psoda04},
bibsource = {DBLP, http://dblp.uni-trier.de},
pages = {880-889},
eprint = {acm:982792.982926},
}


@article{carbonnanotubesnaturenano2010,
title = {Self-assembly of carbon nanotubes into two-dimensional geometries using {DNA} origami templates},
author = {Hareem T. Maune and Si-Ping Han and Robert D. Barish and Marc Bockrath and William A. Goddard III and Paul W. K. Rothemund and Erik Winfree},
journal = {Nature Nanotechnology},
volume = {5},
number = {1},
year = {2010},
pages = {61-66},
doi = {10.1038/nnano.2009.311},
}

@article{dnarobotnature2010,
title = {Molecular Robots Guided by Prescriptive Landscapes},
author = {Kyle Lund and Anthony T. Manzo and Nadine Dabby and Nicole Micholotti and Alexander Johnson-Buck and Jeanetter Nangreave and Steven Taylor and Renjun Pei and Milan N. Stojanovic and Nils G. Walter and Erik Winfree and Hao Yan},
journal = {Nature},
volume = {465},
number = {7295},
year = {2010},
pages = {206-210},
doi = {10.1038/nature09012},
}

@article{sum09,
title = {Reducing Tile Complexity for the Self-assembly of Scaled Shapes Through Temperature Programming},
author = {Scott M. Summers},
journal = Algorithmica,
number = {1-2},
volume = {63},
year = {2012},
bibsource = {DBLP, http://dblp.uni-trier.de},
pages = {117-136},
doi = {10.1007/s00453-011-9522-5},
}

@inproceedings{rnasesoda2010,
title = {Shape Replication through Self-Assembly and {RN}ase Enzymes},
author = {Zachary Abel and Nadia Benbernou and Mirela Damian and Erik D. Demaine and Martin L. Demaine and Robin Y. Flatland and Scott D. Kominers and Robert T. Schweller},
crossref = {psoda10},
bibsource = {DBLP, http://dblp.uni-trier.de},
pages = {1045-1064},
eprint = {acm:1873601.1873686},
}
%
@inproceedings{dempatschsum2010rnase,
title = {Self-Assembly of Arbitrary Shapes Using {RNA}se Enzymes: Meeting the {K}olmogorov Bound with Small Scale Factor},
author = {Erik D. Demaine and Matthew J. Patitz and Robert T. Schweller and Scott M. Summers},
booktitle = stacs11,
year = {2011},
bibsource = {DBLP, http://dblp.uni-trier.de},
pages = {201-212},
doi = {10.4230/LIPIcs.STACS.2011.201},
}
%
@article{park2004electronic,
title = {{Electronic Nanostructures Templated on Self-Assembled {DNA} Scaffolds}},
author = {Sung Ha Park and Hao Yan and John H. Reif and Thomas H. LaBean and Gleb Finkelstein},
publisher = {Institute of Physics Publishing},
journal = {Nanotechnology},
volume = {15},
number = {10},
year = {2004},
pages = {S525--S527},
doi = {10.1088/0957-4484/15/10/005},
}

@article{jccsa,
title = {Computability and Complexity in Self-assembly},
author = {James I. Lathrop and Jack H. Lutz and Matthew J. Patitz and Scott M. Summers},
note = {Preliminary version in \href{http://dx.doi.org/10.1007/978-3-540-69407-6_38}{CiE'08}},
journal = {Theory of Computing Systems},
number = {3},
volume = {48},
year = {2011},
bibsource = {DBLP, http://dblp.uni-trier.de},
pages = {617-647},
doi = {10.1007/s00224-010-9252-0},
}
%
@inproceedings{jccsa-conference,
title = {Computability and Complexity in Self-assembly},
author = {James I. Lathrop and Jack H. Lutz and Matthew J. Patitz and Scott M. Summers},
booktitle = {4th Conf. Computability in Europe (CiE'08)},
publisher = springer,
year = {2008},
bibsource = {DBLP, http://dblp.uni-trier.de},
pages = {349-358},
doi = {10.1007/978-3-540-69407-6\_38},
}
%
@article{wang61,
title = {Proving Theorems by Pattern Recognition -- {II}},
author = {Hao Wang},
journal = {The Bell System Technical Journal},
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volume = {XL},
year = {1961},
pages = {1-41},
} 
@inproceedings{rotwin00,
title = {The program-size complexity of self-assembled squares (extended abstract)},
author = {Paul W. K. Rothemund and Erik Winfree},
crossref = {pstoc00},
bibsource = {DBLP, http://dblp.uni-trier.de},
pages = {459-468},
doi = {10.1145/335305.335358},
}
%
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