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Augmenting Suffix Trees, with Applications [chapter]

Yossi Matias, S. Muthukrishnan, Süleyman Cenk Sahinalp, Jacob Ziv
<span title="">1998</span> <i title="Springer Berlin Heidelberg"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/2w3awgokqne6te4nvlofavy5a4" style="color: black;">Lecture Notes in Computer Science</a> </i> &nbsp;
Our algorithms rely on augmenting the su x tree, a fundamental data structure in string algorithmics. The augmentations are nontrivial and they form the technical crux of this paper.  ...  Information retrieval and data compression are the two main application areas where the rich theory of string algorithmics plays a fundamental role.  ...  In our applications too, we augment the su x tree with extra edges and additional information.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/3-540-68530-8_6">doi:10.1007/3-540-68530-8_6</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/jeqww6w4nfbyfbd3fmy2oqg5iy">fatcat:jeqww6w4nfbyfbd3fmy2oqg5iy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20060917144659/http://theory.stanford.edu/~matias/papers/esa98.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/31/6e/316e0666ef4849155e0a28798e9c163ad0e9cd55.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/3-540-68530-8_6"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> springer.com </button> </a>

Generalized suffix trees for biological sequence data: applications and implementation

Bieganski, Riedl, Cartis, Retzel
<span title="">1994</span> <i title="IEEE Comput. Soc. Press"> Proceedings of the Twenty-Seventh Hawaii International Conference on System Sciences HICSS-94 </i> &nbsp;
This paper addresses applications of sujjix trees and generalized suffix trees (GSTs) to biological sequence data analysis.  ...  We define a basic set of suffix tree and GST operations needed to support sequence data analysis.  ...  FIGURE 9 . 9 A suffix tree for the sequence ACACTT augmented with prefix pointers.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1109/hicss.1994.323593">doi:10.1109/hicss.1994.323593</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ocsqocmthjbndoawy7fpdhk6ua">fatcat:ocsqocmthjbndoawy7fpdhk6ua</a> </span>
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A Suffix Tree Or Not a Suffix Tree? [chapter]

Tatiana Starikovskaya, Hjalte Wedel Vildhøj
<span title="">2015</span> <i title="Springer International Publishing"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/2w3awgokqne6te4nvlofavy5a4" style="color: black;">Lecture Notes in Computer Science</a> </i> &nbsp;
Such general suffix trees have many applications and are for example needed to allow efficient updates when suffix trees are built online.  ...  ., is there a string S whose suffix tree has the same topological structure as τ ? We place no restrictions on S, in particular we do not require that S ends with a unique symbol.  ...  We replace the original problem with the following one: Can τ be augmented to become a $-suffix tree?  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/978-3-319-19315-1_30">doi:10.1007/978-3-319-19315-1_30</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/bnckjfkztnavznoxjmmrmxhgre">fatcat:bnckjfkztnavznoxjmmrmxhgre</a> </span>
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A Suffix Tree Or Not A Suffix Tree? [article]

Tatiana Starikovskaya, Hjalte Wedel Vildhøj
<span title="2014-09-01">2014</span> <i > arXiv </i> &nbsp; <span class="release-stage" >pre-print</span>
Such general suffix trees have many applications and are for example needed to allow efficient updates when suffix trees are built online.  ...  ., is there a string S whose suffix tree has the same topological structure as τ? We place no restrictions on S, in particular we do not require that S ends with a unique symbol.  ...  We replace the original problem with the following one: Can τ be augmented to become a $-suffix tree?  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/1403.1364v3">arXiv:1403.1364v3</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/imjk6a2kwra33dmrarhqzlfame">fatcat:imjk6a2kwra33dmrarhqzlfame</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20191021085702/https://arxiv.org/pdf/1403.1364v3.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/69/e2/69e2c2b77d310d26791c231141b6e61e17d7ebea.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/1403.1364v3" title="arxiv.org access"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> arxiv.org </button> </a>

Most Recent Match Queries in On-Line Suffix Trees (with appendix) [article]

N. Jesper Larsson
<span title="2014-07-14">2014</span> <i > arXiv </i> &nbsp; <span class="release-stage" >pre-print</span>
We present augmentations to Ukkonen's suffix tree construction algorithm for optimal-time queries, maintaining indexing time within a logarithmic factor in the size of the indexed string.  ...  A suffix tree is able to efficiently locate a pattern in an indexed string, but not in general the most recent copy of the pattern in an online stream, which is desirable in some applications.  ...  Our augmentations of the suffix tree in itself do not alter its structure, and consequently, existing techniques for augmenting the suffix tree algorithm for to index a sliding window in O(1) amortized  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/1403.0800v3">arXiv:1403.0800v3</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/r66zopb3hvfqlgx53mbxap6uae">fatcat:r66zopb3hvfqlgx53mbxap6uae</a> </span>
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A suffix tree or not a suffix tree?

Tatiana Starikovskaya, Hjalte Wedel Vildhøj
<span title="">2015</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/usw2n4yaarcurchx7i4on2iqea" style="color: black;">Journal of Discrete Algorithms</a> </i> &nbsp;
Such general suffix trees have many applications and are for example needed to allow efficient updates when suffix trees are built online.  ...  ., is there a string S whose suffix tree has the same topological structure as τ ? We place no restrictions on S, in particular we do not require that S ends with a unique symbol.  ...  We replace the original problem with the following one: Can τ be augmented to become a $-suffix tree?  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.jda.2015.01.005">doi:10.1016/j.jda.2015.01.005</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/fkknsewu7veenpjakkl4ixyasm">fatcat:fkknsewu7veenpjakkl4ixyasm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20171120121331/https://core.ac.uk/download/pdf/33131240.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/ad/b3/adb32da1b3b168f7cffc41d5d3f56f7e5692e309.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.jda.2015.01.005"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a>

Tackling the Augmentative Puzzle in Turkish

Utku Türk
<span title="2020-12-29">2020</span> <i title="Linguistic Society of America"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/abhhoaa4s5fm5poecy3pvectgq" style="color: black;">Proceedings of the Workshop on Turkic and Languages in Contact with Turkic</a> </i> &nbsp;
This paper deals with the suffix -cIk in Turkish, and argues that the suffix -cIk has an augmentative meaning, as well as a diminutive meaning which has been mentioned in the literature extensively.  ...  I also show strict categorical selection properties for the diminutive and augmentative suffix: The augmentative one can only be attached to adjectival bases that express negative orderings.  ...  In section 4, I offer my analysis of AUGMENTATIVE formations with necessary lexical items and trees and show derivational steps. 3 create an ungrammatical utterance when they are suffixed with -CIk.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3765/ptu.v5i1.4771">doi:10.3765/ptu.v5i1.4771</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/sshpnbiyr5dixm5hnmzxrxbvni">fatcat:sshpnbiyr5dixm5hnmzxrxbvni</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210213133108/https://journals.linguisticsociety.org/proceedings/index.php/tu/article/download/4771/4471" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/0d/d5/0dd59f34854ddbd0ea937bd9264073ea8539a032.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3765/ptu.v5i1.4771"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a>

Engineering Small Space Dictionary Matching [article]

Shoshana Marcus Dina Sokol
<span title="2013-01-28">2013</span> <i > arXiv </i> &nbsp; <span class="release-stage" >pre-print</span>
We use the compressed suffix tree as the underlying data structure of our algorithm, thus, the working space of our algorithm is proportional to the optimal compression of the dictionary.  ...  We also contribute a succinct tool for performing constant-time lowest marked ancestor queries on a tree that is succinctly encoded as a sequence of balanced parentheses, with linear time preprocessing  ...  Acknowledgements The authors would like to thank Simon Gog for his help installing and working with the Succinct Data Structures Library.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/1301.6428v1">arXiv:1301.6428v1</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/5k34y7ew2jb5fbgvpu2xj7snn4">fatcat:5k34y7ew2jb5fbgvpu2xj7snn4</a> </span>
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Multidimensional Incremental Parsing: Current Status and Future Directions

Anas Boubas
<span title="">2014</span> <i title="EJournal Publishing"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/dvpgeslokng5hpqcame34jtsc4" style="color: black;">International Journal of Information and Electronics Engineering</a> </i> &nbsp;
We aim with this work to spur interest in the research community to further investigate MDIP.  ...  For this, a suffix tree can be constructed. Each node in the tree represents a suffix, with the root node being the empty symbol.  ...  The dictionary is augmented with all possible codewords that can grow from along any possible without violating the suffixing order.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.7763/ijiee.2014.v4.449">doi:10.7763/ijiee.2014.v4.449</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/5a6vdsvkwrgzhn2l2u723dornm">fatcat:5a6vdsvkwrgzhn2l2u723dornm</a> </span>
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Minimal Suffix and Rotation of a Substring in Optimal Time

Tomasz Kociumaka, Marc Herbstritt
<span title="2016-06-24">2016</span> <i > <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/cpozivjjrjdjbodfq76vaaxdpm" style="color: black;">Annual Symposium on Combinatorial Pattern Matching</a> </i> &nbsp;
We combine them with further algorithmic and combinatorial tools, such as fusion trees and the notion of order isomorphism of strings.  ...  For a text of length n given in advance, the substring minimal suffix queries ask to determine the lexicographically minimal non-empty suffix of a substring specified by the location of its occurrence  ...  Acknowledgements I would like to thank the remaining co-authors of [4] , collaboration with whom on earlier results about minimal and maximal suffixes sparked some of my ideas used in this paper.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.4230/lipics.cpm.2016.28">doi:10.4230/lipics.cpm.2016.28</a> <a target="_blank" rel="external noopener" href="https://dblp.org/rec/conf/cpm/Kociumaka16.html">dblp:conf/cpm/Kociumaka16</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/5ecfttqb4rcqraxd6ezwipepxq">fatcat:5ecfttqb4rcqraxd6ezwipepxq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20220123040542/https://drops.dagstuhl.de/opus/volltexte/2016/6062/pdf/LIPIcs-CPM-2016-28.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/a4/a0/a4a0c84d2b370d0d15dad5964b4ffe2afbca1d0d.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.4230/lipics.cpm.2016.28"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Suffix trees for very large genomic sequences

Marina Barsky, Ulrike Stege, Alex Thomo, Chris Upton
<span title="">2009</span> <i title="ACM Press"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/6g37zvjwwrhv3dizi6ffue642m" style="color: black;">Proceeding of the 18th ACM conference on Information and knowledge management - CIKM &#39;09</a> </i> &nbsp;
Unfortunately, when it comes to the use of suffix trees in real-life applications, the current methods for constructing suffix trees do not scale for large inputs.  ...  As a proof of concept, we show that our method allows to build the suffix tree for 12GB of real DNA sequences in 26 hours on a single machine with 2GB of RAM.  ...  The suffix tree of X can be constructed given its suffix array SA augmented with an LCP information.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1145/1645953.1646134">doi:10.1145/1645953.1646134</a> <a target="_blank" rel="external noopener" href="https://dblp.org/rec/conf/cikm/BarskySTU09.html">dblp:conf/cikm/BarskySTU09</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/h6w3pi6fmvdutgvug6arovqnlu">fatcat:h6w3pi6fmvdutgvug6arovqnlu</a> </span>
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The Myriad Virtues of Subword Trees [chapter]

Alberto Apostolico
<span title="">1985</span> <i title="Springer Berlin Heidelberg"> Combinatorial Algorithms on Words </i> &nbsp;
The data structures developed in this endeavor are variously referred to as B-trees. position ,trees, suffix (or prefix) trees, su bword trees, repetition finders, directed acyclic word graphs,-etc.  ...  Several nontrivial applications of subword trees have been developed since their first appearance. Some stich applications depart considerably from the original motivations.  ...  However. it seems to be an interesting open question whether there are words whose minimal augmented suffix trees do in fact attain that bound.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/978-3-642-82456-2_6">doi:10.1007/978-3-642-82456-2_6</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/kquz5mvsdffttnglhfm4u4ujaa">fatcat:kquz5mvsdffttnglhfm4u4ujaa</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180719071037/https://docs.lib.purdue.edu/cgi/viewcontent.cgi?article=1458&amp;context=cstech" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/e4/85/e4856de037a93d3cb5091fff055122c1b77d099e.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/978-3-642-82456-2_6"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> springer.com </button> </a>

Fast Algorithm for Partial Covers in Words [article]

Tomasz Kociumaka, Jakub Radoszewski, Wojciech Rytter, Solon P. Pissis, Tomasz Waleń
<span title="2013-12-31">2013</span> <i > arXiv </i> &nbsp; <span class="release-stage" >pre-print</span>
By-Products of Cover Suffix Tree In this section we present two additional applications of the Cover Suffix Tree.  ...  Then, each node of the augmented tree is annotated with two integer values.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/1401.0163v1">arXiv:1401.0163v1</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/lkxdizlbuvcchowaeb3l2bnyv4">fatcat:lkxdizlbuvcchowaeb3l2bnyv4</a> </span>
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Efficient implementation of suffix trees

Arne Andersson, Stefan Nilsson
<span title="">1995</span> <i title="Wiley"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/afve5b3tavbfzch46mdtazbqla" style="color: black;">Software, Practice &amp; Experience</a> </i> &nbsp;
We study the problem of string searching using the traditional approach of storing all unique substrings of the text in a suffix tree.  ...  The methods of path compression, level compression and data compression are combined to build a simple, compact and efficient implementation of a suffix tree.  ...  Since the augmented suffix array has a large space overhead, another method that combines a suffix array with a bucket array was suggested for practical use.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/spe.4380250203">doi:10.1002/spe.4380250203</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/jlkzx6vzwjeorhzjwxbjrh3kq4">fatcat:jlkzx6vzwjeorhzjwxbjrh3kq4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20070208080839/http://cs.ubc.ca:80/rr/proceedings/spe91-95/spe/vol25/issue2/spe935aa.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/7c/bf/7cbfa58e22eb01b88a8136b3ed1a47139e309020.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/spe.4380250203"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> wiley.com </button> </a>

On-Line Construction of Position Heaps [chapter]

Gregory Kucherov
<span title="">2011</span> <i title="Springer Berlin Heidelberg"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/2w3awgokqne6te4nvlofavy5a4" style="color: black;">Lecture Notes in Computer Science</a> </i> &nbsp;
Our construction is based on classic suffix pointers and resembles the Ukkonen's algorithm for suffix trees [Ukk95].  ...  Using suffix pointers, the position heap can be extended into the augmented position heap that allows for a linear-time string matching algorithm [EMOW11].  ...  Among them, suffix tree and suffix array are most widely used structures, providing efficient solutions for a wide range of applications [CR94, Gus97] .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/978-3-642-24583-1_32">doi:10.1007/978-3-642-24583-1_32</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/zt6mbmfd5vhllckmph6dss23va">fatcat:zt6mbmfd5vhllckmph6dss23va</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190305112406/https://core.ac.uk/download/pdf/48341683.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/31/0d/310daa9142b156340cdffa61b86b6b8a615bdcae.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/978-3-642-24583-1_32"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> springer.com </button> </a>
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