[{"oa":1,"publisher":"IST Austria","ddc":["000"],"file_date_updated":"2020-07-14T12:46:46Z","has_accepted_license":"1","department":[{"_id":"KrCh"}],"page":"12","status":"public","date_created":"2018-12-12T11:39:10Z","alternative_title":["IST Austria Technical Report"],"_id":"5409","title":"Edit distance for timed automata","date_updated":"2024-10-21T06:02:53Z","file":[{"relation":"main_file","content_type":"application/pdf","checksum":"0f7633081ba8299c543322f0ad08571f","file_name":"IST-2013-144-v1+1_main.pdf","file_size":336377,"date_created":"2018-12-12T11:53:08Z","file_id":"5469","creator":"system","date_updated":"2020-07-14T12:46:46Z","access_level":"open_access"}],"day":"30","type":"technical_report","publication_identifier":{"issn":["2664-1690"]},"date_published":"2013-10-30T00:00:00Z","abstract":[{"text":"The edit distance between two (untimed) traces is the minimum cost of a sequence of edit operations (insertion, deletion, or substitution) needed to transform one trace to the other. Edit distances have been extensively studied in the untimed setting, and form the basis for approximate matching of sequences in different domains such as coding theory, parsing, and speech recognition. \r\nIn this paper, we lift the study of edit distances from untimed languages to the timed setting. We define an edit distance between timed words which incorporates both the edit distance between the untimed words and the absolute difference in timestamps. Our edit distance between two timed words is computable in polynomial time. Further, we show that the edit distance between a timed word and a timed language generated by a timed automaton, defined as the edit distance between the word and the closest word in the language, is PSPACE-complete. While computing the edit distance between two timed automata is undecidable, we show that the approximate version, where we decide if the edit distance between two timed automata is either less than a given parameter or more than delta away from the parameter, for delta>0, can be solved in exponential space and is EXPSPACE-hard. Our definitions and techniques can be generalized to the setting of hybrid systems, and we show analogous decidability results for rectangular automata.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","publication_status":"published","year":"2013","language":[{"iso":"eng"}],"author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"},{"orcid":"0000-0003-4783-0389","id":"3B699956-F248-11E8-B48F-1D18A9856A87","full_name":"Ibsen-Jensen, Rasmus","last_name":"Ibsen-Jensen","first_name":"Rasmus"},{"full_name":"Majumdar, Rupak","first_name":"Rupak","last_name":"Majumdar"}],"citation":{"short":"K. Chatterjee, R. Ibsen-Jensen, R. Majumdar, Edit Distance for Timed Automata, IST Austria, 2013.","chicago":"Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, and Rupak Majumdar. <i>Edit Distance for Timed Automata</i>. IST Austria, 2013. <a href=\"https://doi.org/10.15479/AT:IST-2013-144-v1-1\">https://doi.org/10.15479/AT:IST-2013-144-v1-1</a>.","ista":"Chatterjee K, Ibsen-Jensen R, Majumdar R. 2013. Edit distance for timed automata, IST Austria, 12p.","ieee":"K. Chatterjee, R. Ibsen-Jensen, and R. Majumdar, <i>Edit distance for timed automata</i>. IST Austria, 2013.","apa":"Chatterjee, K., Ibsen-Jensen, R., &#38; Majumdar, R. (2013). <i>Edit distance for timed automata</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2013-144-v1-1\">https://doi.org/10.15479/AT:IST-2013-144-v1-1</a>","mla":"Chatterjee, Krishnendu, et al. <i>Edit Distance for Timed Automata</i>. IST Austria, 2013, doi:<a href=\"https://doi.org/10.15479/AT:IST-2013-144-v1-1\">10.15479/AT:IST-2013-144-v1-1</a>.","ama":"Chatterjee K, Ibsen-Jensen R, Majumdar R. <i>Edit Distance for Timed Automata</i>. IST Austria; 2013. doi:<a href=\"https://doi.org/10.15479/AT:IST-2013-144-v1-1\">10.15479/AT:IST-2013-144-v1-1</a>"},"month":"10","pubrep_id":"144","doi":"10.15479/AT:IST-2013-144-v1-1","related_material":{"record":[{"id":"2216","relation":"later_version","status":"public"}]}},{"oa":1,"publisher":"IST Austria","ddc":["000","005"],"has_accepted_license":"1","file_date_updated":"2020-07-14T12:46:46Z","page":"13","department":[{"_id":"KrCh"}],"status":"public","date_created":"2018-12-12T11:39:10Z","alternative_title":["IST Austria Technical Report"],"_id":"5410","date_updated":"2025-05-19T11:10:16Z","title":"Automatic generation of alternative starting positions for traditional board games","day":"03","file":[{"date_updated":"2020-07-14T12:46:46Z","access_level":"open_access","date_created":"2018-12-12T11:54:06Z","file_size":818189,"file_id":"5528","creator":"system","checksum":"409f3aaaf1184e4057b89cbb449dac80","file_name":"IST-2013-146-v1+1_main.pdf","relation":"main_file","content_type":"application/pdf"}],"publication_identifier":{"issn":["2664-1690"]},"type":"technical_report","abstract":[{"text":"Board games, like Tic-Tac-Toe and CONNECT-4, play an important role not only in development of mathematical and logical skills, but also in emotional and social development. In this paper, we address the problem of generating targeted starting positions for such games. This can facilitate new approaches for bringing novice players to mastery, and also leads to discovery of interesting game variants. \r\nOur approach generates starting states of varying hardness levels for player 1 in a two-player board game, given rules of the board game, the desired number of steps required for player 1 to win, and the expertise levels of the two players. Our approach leverages symbolic methods and iterative simulation to efficiently search the extremely large state space. We present experimental results that include discovery of states of varying hardness levels for several simple grid-based board games. Also, the presence of such states for standard game variants like Tic-Tac-Toe on board size 4x4 opens up new games to be played that have not been played for ages since the default start state is heavily biased. ","lang":"eng"}],"date_published":"2013-12-03T00:00:00Z","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","year":"2013","language":[{"iso":"eng"}],"author":[{"full_name":"Ahmed, Umair","first_name":"Umair","last_name":"Ahmed"},{"last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Gulwani","first_name":"Sumit","full_name":"Gulwani, Sumit"}],"citation":{"ista":"Ahmed U, Chatterjee K, Gulwani S. 2013. Automatic generation of alternative starting positions for traditional board games, IST Austria, 13p.","chicago":"Ahmed, Umair, Krishnendu Chatterjee, and Sumit Gulwani. <i>Automatic Generation of Alternative Starting Positions for Traditional Board Games</i>. IST Austria, 2013. <a href=\"https://doi.org/10.15479/AT:IST-2013-146-v1-1\">https://doi.org/10.15479/AT:IST-2013-146-v1-1</a>.","short":"U. Ahmed, K. Chatterjee, S. Gulwani, Automatic Generation of Alternative Starting Positions for Traditional Board Games, IST Austria, 2013.","mla":"Ahmed, Umair, et al. <i>Automatic Generation of Alternative Starting Positions for Traditional Board Games</i>. IST Austria, 2013, doi:<a href=\"https://doi.org/10.15479/AT:IST-2013-146-v1-1\">10.15479/AT:IST-2013-146-v1-1</a>.","ieee":"U. Ahmed, K. Chatterjee, and S. Gulwani, <i>Automatic generation of alternative starting positions for traditional board games</i>. IST Austria, 2013.","apa":"Ahmed, U., Chatterjee, K., &#38; Gulwani, S. (2013). <i>Automatic generation of alternative starting positions for traditional board games</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2013-146-v1-1\">https://doi.org/10.15479/AT:IST-2013-146-v1-1</a>","ama":"Ahmed U, Chatterjee K, Gulwani S. <i>Automatic Generation of Alternative Starting Positions for Traditional Board Games</i>. IST Austria; 2013. doi:<a href=\"https://doi.org/10.15479/AT:IST-2013-146-v1-1\">10.15479/AT:IST-2013-146-v1-1</a>"},"month":"12","pubrep_id":"146","doi":"10.15479/AT:IST-2013-146-v1-1","related_material":{"record":[{"relation":"later_version","status":"public","id":"1481"}]}},{"date_created":"2018-12-18T13:10:21Z","status":"public","date_updated":"2025-07-10T11:52:57Z","day":"01","series_title":"CAV","type":"book_chapter","publication":"Computer Aided Verification","ec_funded":1,"publisher":"Springer Berlin Heidelberg","file_date_updated":"2020-07-14T12:47:10Z","page":"174-190","volume":8044,"project":[{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Reactive Modeling","grant_number":"267989"},{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"}],"pubrep_id":"195","doi":"10.1007/978-3-642-39799-8_11","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"scopus_import":"1","intvolume":"      8044","place":"Berlin, Heidelberg","quality_controlled":"1","_id":"5747","title":"Automatic Linearizability Proofs of Concurrent Objects with Cooperating Updates","file":[{"date_updated":"2020-07-14T12:47:10Z","access_level":"open_access","file_size":236480,"date_created":"2018-12-18T13:13:33Z","file_id":"5748","creator":"dernst","checksum":"a901cc6b71db08b61c0d4c0cbacc6287","file_name":"2013_CAV_Dragoi.pdf","relation":"main_file","content_type":"application/pdf"}],"publication_identifier":{"isbn":["9783642397981"],"eisbn":["9783642397998"],"issn":["0302-9743"],"eissn":["1611-3349"]},"oa":1,"ddc":["005"],"has_accepted_license":"1","department":[{"_id":"ToHe"}],"conference":{"name":"CAV: Computer Aided Verification","end_date":"2013-07-19","start_date":"2013-07-13","location":"Saint Petersburg, Russia"},"author":[{"full_name":"Dragoi, Cezara","last_name":"Dragoi","first_name":"Cezara","id":"2B2B5ED0-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Ashutosh","last_name":"Gupta","full_name":"Gupta, Ashutosh","id":"335E5684-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Thomas A","last_name":"Henzinger","full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724"}],"citation":{"ama":"Dragoi C, Gupta A, Henzinger TA. Automatic Linearizability Proofs of Concurrent Objects with Cooperating Updates. In: <i>Computer Aided Verification</i>. Vol 8044. CAV. Berlin, Heidelberg: Springer Berlin Heidelberg; 2013:174-190. doi:<a href=\"https://doi.org/10.1007/978-3-642-39799-8_11\">10.1007/978-3-642-39799-8_11</a>","ieee":"C. Dragoi, A. Gupta, and T. A. Henzinger, “Automatic Linearizability Proofs of Concurrent Objects with Cooperating Updates,” in <i>Computer Aided Verification</i>, vol. 8044, Berlin, Heidelberg: Springer Berlin Heidelberg, 2013, pp. 174–190.","apa":"Dragoi, C., Gupta, A., &#38; Henzinger, T. A. (2013). Automatic Linearizability Proofs of Concurrent Objects with Cooperating Updates. In <i>Computer Aided Verification</i> (Vol. 8044, pp. 174–190). Berlin, Heidelberg: Springer Berlin Heidelberg. <a href=\"https://doi.org/10.1007/978-3-642-39799-8_11\">https://doi.org/10.1007/978-3-642-39799-8_11</a>","mla":"Dragoi, Cezara, et al. “Automatic Linearizability Proofs of Concurrent Objects with Cooperating Updates.” <i>Computer Aided Verification</i>, vol. 8044, Springer Berlin Heidelberg, 2013, pp. 174–90, doi:<a href=\"https://doi.org/10.1007/978-3-642-39799-8_11\">10.1007/978-3-642-39799-8_11</a>.","chicago":"Dragoi, Cezara, Ashutosh Gupta, and Thomas A Henzinger. “Automatic Linearizability Proofs of Concurrent Objects with Cooperating Updates.” In <i>Computer Aided Verification</i>, 8044:174–90. CAV. Berlin, Heidelberg: Springer Berlin Heidelberg, 2013. <a href=\"https://doi.org/10.1007/978-3-642-39799-8_11\">https://doi.org/10.1007/978-3-642-39799-8_11</a>.","short":"C. Dragoi, A. Gupta, T.A. Henzinger, in:, Computer Aided Verification, Springer Berlin Heidelberg, Berlin, Heidelberg, 2013, pp. 174–190.","ista":"Dragoi C, Gupta A, Henzinger TA. 2013.Automatic Linearizability Proofs of Concurrent Objects with Cooperating Updates. In: Computer Aided Verification. vol. 8044, 174–190."},"month":"08","date_published":"2013-08-01T00:00:00Z","oa_version":"None","publication_status":"published","year":"2013"},{"author":[{"full_name":"Schmid, David","last_name":"Schmid","first_name":"David"},{"full_name":"Huang, Ting-Yu","first_name":"Ting","last_name":"Huang"},{"full_name":"Dirks, Radhika","first_name":"Radhika","last_name":"Dirks"},{"full_name":"Onur Hosten","last_name":"Hosten","first_name":"Onur","id":"4C02D85E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2031-204X"},{"full_name":"Kwiat, Paul G","first_name":"Paul","last_name":"Kwiat"}],"doi":"10.1364/QIM.2013.W6.23","citation":{"ista":"Schmid D, Huang T, Dirks R, Hosten O, Kwiat P. 2013. Polarization dependent focusing. QIM: Quantum Information and Measurement, Optics InfoBase Conference Papers, .","short":"D. Schmid, T. Huang, R. Dirks, O. Hosten, P. Kwiat, in:, OSA, 2013.","chicago":"Schmid, David, Ting Huang, Radhika Dirks, Onur Hosten, and Paul Kwiat. “Polarization Dependent Focusing.” OSA, 2013. <a href=\"https://doi.org/10.1364/QIM.2013.W6.23\">https://doi.org/10.1364/QIM.2013.W6.23</a>.","mla":"Schmid, David, et al. <i>Polarization Dependent Focusing</i>. OSA, 2013, doi:<a href=\"https://doi.org/10.1364/QIM.2013.W6.23\">10.1364/QIM.2013.W6.23</a>.","ieee":"D. Schmid, T. Huang, R. Dirks, O. Hosten, and P. Kwiat, “Polarization dependent focusing,” presented at the QIM: Quantum Information and Measurement, 2013.","apa":"Schmid, D., Huang, T., Dirks, R., Hosten, O., &#38; Kwiat, P. (2013). Polarization dependent focusing. Presented at the QIM: Quantum Information and Measurement, OSA. <a href=\"https://doi.org/10.1364/QIM.2013.W6.23\">https://doi.org/10.1364/QIM.2013.W6.23</a>","ama":"Schmid D, Huang T, Dirks R, Hosten O, Kwiat P. Polarization dependent focusing. In: OSA; 2013. doi:<a href=\"https://doi.org/10.1364/QIM.2013.W6.23\">10.1364/QIM.2013.W6.23</a>"},"month":"01","publication_status":"published","year":"2013","abstract":[{"text":"We present two methods of creating two orthogonally-polarized focal points at customizable relative locations. These schemes may be critical for enhancing entanglement sources and other applications.","lang":"eng"}],"date_published":"2013-01-01T00:00:00Z","quality_controlled":0,"alternative_title":["Optics InfoBase Conference Papers"],"date_created":"2018-12-11T11:47:22Z","status":"public","day":"01","type":"conference","_id":"590","title":"Polarization dependent focusing","date_updated":"2021-01-12T08:05:10Z","publisher":"OSA","conference":{"name":"QIM: Quantum Information and Measurement"},"publist_id":"7217","extern":1},{"volume":21,"author":[{"full_name":"Schmid, David","last_name":"Schmid","first_name":"David"},{"full_name":"Huang, Ting-Yu","last_name":"Huang","first_name":"Ting"},{"first_name":"Shiraz","last_name":"Hazrat","full_name":"Hazrat, Shiraz"},{"full_name":"Dirks, Radhika","first_name":"Radhika","last_name":"Dirks"},{"id":"4C02D85E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2031-204X","first_name":"Onur","last_name":"Hosten","full_name":"Onur Hosten"},{"first_name":"Stephan","last_name":"Quint","full_name":"Quint, Stephan"},{"full_name":"Thian, Dickson","first_name":"Dickson","last_name":"Thian"},{"last_name":"Kwiat","first_name":"Paul","full_name":"Kwiat, Paul G"}],"issue":"13","citation":{"chicago":"Schmid, David, Ting Huang, Shiraz Hazrat, Radhika Dirks, Onur Hosten, Stephan Quint, Dickson Thian, and Paul Kwiat. “Adjustable and Robust Methods for Polarization-Dependent Focusing.” <i>Optics Express</i>. Optical Society of America, 2013. <a href=\"https://doi.org/10.1364/OE.21.015538\">https://doi.org/10.1364/OE.21.015538</a>.","short":"D. Schmid, T. Huang, S. Hazrat, R. Dirks, O. Hosten, S. Quint, D. Thian, P. Kwiat, Optics Express 21 (2013) 15538–15552.","ista":"Schmid D, Huang T, Hazrat S, Dirks R, Hosten O, Quint S, Thian D, Kwiat P. 2013. Adjustable and robust methods for polarization-dependent focusing. Optics Express. 21(13), 15538–15552.","ieee":"D. Schmid <i>et al.</i>, “Adjustable and robust methods for polarization-dependent focusing,” <i>Optics Express</i>, vol. 21, no. 13. Optical Society of America, pp. 15538–15552, 2013.","apa":"Schmid, D., Huang, T., Hazrat, S., Dirks, R., Hosten, O., Quint, S., … Kwiat, P. (2013). Adjustable and robust methods for polarization-dependent focusing. <i>Optics Express</i>. Optical Society of America. <a href=\"https://doi.org/10.1364/OE.21.015538\">https://doi.org/10.1364/OE.21.015538</a>","mla":"Schmid, David, et al. “Adjustable and Robust Methods for Polarization-Dependent Focusing.” <i>Optics Express</i>, vol. 21, no. 13, Optical Society of America, 2013, pp. 15538–52, doi:<a href=\"https://doi.org/10.1364/OE.21.015538\">10.1364/OE.21.015538</a>.","ama":"Schmid D, Huang T, Hazrat S, et al. Adjustable and robust methods for polarization-dependent focusing. <i>Optics Express</i>. 2013;21(13):15538-15552. doi:<a href=\"https://doi.org/10.1364/OE.21.015538\">10.1364/OE.21.015538</a>"},"month":"07","doi":"10.1364/OE.21.015538","date_published":"2013-07-01T00:00:00Z","abstract":[{"lang":"eng","text":"We present two methods for the precise independent focusing of orthogonal linear polarizations of light at arbitrary relative locations. Our first scheme uses a displaced lens in a polarization Sagnac interferometer to provide adjustable longitudinal and lateral focal displacements via simple geometry; the second uses uniaxial crystals to achieve the same effect in a compact collinear setup. We develop the theoretical applications and limitations of our schemes, and provide experimental confirmation of our calculations."}],"publication_status":"published","year":"2013","date_created":"2018-12-11T11:47:22Z","status":"public","intvolume":"        21","quality_controlled":0,"_id":"591","title":"Adjustable and robust methods for polarization-dependent focusing","date_updated":"2021-01-12T08:05:12Z","day":"01","type":"journal_article","publication":"Optics Express","publisher":"Optical Society of America","extern":1,"page":"15538 - 15552","publist_id":"7218"},{"extern":"1","main_file_link":[{"url":"https://doi.org/10.1016/j.jsc.2012.06.006","open_access":"1"}],"oa":1,"publication_identifier":{"issn":["0747-7171"]},"title":"Finiteness theorems and algorithms for permutation invariant chains of Laurent lattice ideals","_id":"5920","quality_controlled":"1","intvolume":"        50","article_type":"original","year":"2013","oa_version":"Published Version","publication_status":"published","date_published":"2013-03-01T00:00:00Z","OA_place":"publisher","related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1016/j.jsc.2015.09.002"}]},"month":"03","citation":{"ama":"Hillar CJ, Martin del Campo Sanchez A. Finiteness theorems and algorithms for permutation invariant chains of Laurent lattice ideals. <i>Journal of Symbolic Computation</i>. 2013;50:314-334. doi:<a href=\"https://doi.org/10.1016/j.jsc.2012.06.006\">10.1016/j.jsc.2012.06.006</a>","ieee":"C. J. Hillar and A. Martin del Campo Sanchez, “Finiteness theorems and algorithms for permutation invariant chains of Laurent lattice ideals,” <i>Journal of Symbolic Computation</i>, vol. 50. Elsevier, pp. 314–334, 2013.","apa":"Hillar, C. J., &#38; Martin del Campo Sanchez, A. (2013). Finiteness theorems and algorithms for permutation invariant chains of Laurent lattice ideals. <i>Journal of Symbolic Computation</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jsc.2012.06.006\">https://doi.org/10.1016/j.jsc.2012.06.006</a>","mla":"Hillar, Christopher J., and Abraham Martin del Campo Sanchez. “Finiteness Theorems and Algorithms for Permutation Invariant Chains of Laurent Lattice Ideals.” <i>Journal of Symbolic Computation</i>, vol. 50, Elsevier, 2013, pp. 314–34, doi:<a href=\"https://doi.org/10.1016/j.jsc.2012.06.006\">10.1016/j.jsc.2012.06.006</a>.","chicago":"Hillar, Christopher J., and Abraham Martin del Campo Sanchez. “Finiteness Theorems and Algorithms for Permutation Invariant Chains of Laurent Lattice Ideals.” <i>Journal of Symbolic Computation</i>. Elsevier, 2013. <a href=\"https://doi.org/10.1016/j.jsc.2012.06.006\">https://doi.org/10.1016/j.jsc.2012.06.006</a>.","short":"C.J. Hillar, A. Martin del Campo Sanchez, Journal of Symbolic Computation 50 (2013) 314–334.","ista":"Hillar CJ, Martin del Campo Sanchez A. 2013. Finiteness theorems and algorithms for permutation invariant chains of Laurent lattice ideals. Journal of Symbolic Computation. 50, 314–334."},"author":[{"first_name":"Christopher J.","last_name":"Hillar","full_name":"Hillar, Christopher J."},{"full_name":"Martin del Campo Sanchez, Abraham","last_name":"Martin del Campo Sanchez","first_name":"Abraham","id":"4CF47F6A-F248-11E8-B48F-1D18A9856A87"}],"page":"314-334","publisher":"Elsevier","publication":"Journal of Symbolic Computation","type":"journal_article","day":"01","date_updated":"2025-05-20T06:30:08Z","date_created":"2019-02-05T08:48:24Z","status":"public","language":[{"iso":"eng"}],"OA_type":"free access","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","abstract":[{"lang":"eng","text":"We study chains of lattice ideals that are invariant under a symmetric group action. In our setting, the ambient rings for these ideals are polynomial rings which are increasing in (Krull) dimension. Thus, these chains will fail to stabilize in the traditional commutative algebra sense. However, we prove a theorem which says that “up to the action of the group”, these chains locally stabilize. We also give an algorithm, which we have implemented in software, for explicitly constructing these stabilization generators for a family of Laurent toric ideals involved in applications to algebraic statistics. We close with several open problems and conjectures arising from our theoretical and computational investigations."}],"doi":"10.1016/j.jsc.2012.06.006","volume":50},{"oa":1,"publication":"EMBO Journal","publisher":"Wiley-Blackwell","page":"771 - 772","publist_id":"7207","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3604726/"}],"extern":"1","intvolume":"        32","status":"public","date_created":"2018-12-11T11:47:23Z","day":"20","type":"journal_article","_id":"595","title":"Struggling to let go: A non-coding RNA directs its own extension and destruction","date_updated":"2021-01-12T08:05:20Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"None","publication_status":"published","year":"2013","date_published":"2013-03-20T00:00:00Z","article_processing_charge":"No","language":[{"iso":"eng"}],"volume":32,"author":[{"id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0893-7036","full_name":"Bernecky, Carrie A","first_name":"Carrie A","last_name":"Bernecky"},{"full_name":"Cramer, Patrick","last_name":"Cramer","first_name":"Patrick"}],"doi":"10.1038/emboj.2013.36","citation":{"short":"C. Bernecky, P. Cramer, EMBO Journal 32 (2013) 771–772.","chicago":"Bernecky, Carrie, and Patrick Cramer. “Struggling to Let Go: A Non-Coding RNA Directs Its Own Extension and Destruction.” <i>EMBO Journal</i>. Wiley-Blackwell, 2013. <a href=\"https://doi.org/10.1038/emboj.2013.36\">https://doi.org/10.1038/emboj.2013.36</a>.","ista":"Bernecky C, Cramer P. 2013. Struggling to let go: A non-coding RNA directs its own extension and destruction. EMBO Journal. 32(6), 771–772.","ama":"Bernecky C, Cramer P. Struggling to let go: A non-coding RNA directs its own extension and destruction. <i>EMBO Journal</i>. 2013;32(6):771-772. doi:<a href=\"https://doi.org/10.1038/emboj.2013.36\">10.1038/emboj.2013.36</a>","apa":"Bernecky, C., &#38; Cramer, P. (2013). Struggling to let go: A non-coding RNA directs its own extension and destruction. <i>EMBO Journal</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1038/emboj.2013.36\">https://doi.org/10.1038/emboj.2013.36</a>","ieee":"C. Bernecky and P. Cramer, “Struggling to let go: A non-coding RNA directs its own extension and destruction,” <i>EMBO Journal</i>, vol. 32, no. 6. Wiley-Blackwell, pp. 771–772, 2013.","mla":"Bernecky, Carrie, and Patrick Cramer. “Struggling to Let Go: A Non-Coding RNA Directs Its Own Extension and Destruction.” <i>EMBO Journal</i>, vol. 32, no. 6, Wiley-Blackwell, 2013, pp. 771–72, doi:<a href=\"https://doi.org/10.1038/emboj.2013.36\">10.1038/emboj.2013.36</a>."},"issue":"6","month":"03"},{"abstract":[{"text":"Different interoceptive systems must be integrated to ensure that multiple homeostatic insults evoke appropriate behavioral and physiological responses. Little is known about how this is achieved. Using C. elegans, we dissect cross-modulation between systems that monitor temperature, O2 and CO2. CO2 is less aversive to animals acclimated to 15°C than those grown at 22°C. This difference requires the AFD neurons, which respond to both temperature and CO2 changes. CO2 evokes distinct AFD Ca2+ responses in animals acclimated at 15°C or 22°C. Mutants defective in synaptic transmission can reprogram AFD CO2 responses according to temperature experience, suggesting reprogramming occurs cell autonomously. AFD is exquisitely sensitive to CO2. Surprisingly, gradients of 0.01% CO2/second evoke very different Ca2+ responses from gradients of 0.04% CO2/second. Ambient O2 provides further contextual modulation of CO2 avoidance. At 21% O2 tonic signalling from the O2-sensing neuron URX inhibits CO2 avoidance. This inhibition can be graded according to O2 levels. In a natural wild isolate, a switch from 21% to 19% O2 is sufficient to convert CO2 from a neutral to an aversive cue. This sharp tuning is conferred partly by the neuroglobin GLB-5. The modulatory effects of O2 on CO2 avoidance involve the RIA interneurons, which are post-synaptic to URX and exhibit CO2-evoked Ca2+ responses. Ambient O2 and acclimation temperature act combinatorially to modulate CO2 responsiveness. Our work highlights the integrated architecture of homeostatic responses in C. elegans.","lang":"eng"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","article_number":"e1004011","language":[{"iso":"eng"}],"volume":9,"external_id":{"pmid":["24385919"]},"doi":"10.1371/journal.pgen.1004011","publication":"PLoS Genetics","publisher":"Public Library of Science (PLoS)","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file_date_updated":"2020-07-14T12:47:20Z","pmid":1,"status":"public","date_created":"2019-03-19T14:58:51Z","date_updated":"2021-01-12T08:06:15Z","day":"19","type":"journal_article","date_published":"2013-12-19T00:00:00Z","oa_version":"Published Version","publication_status":"published","year":"2013","author":[{"full_name":"Kodama-Namba, Eiji","last_name":"Kodama-Namba","first_name":"Eiji"},{"full_name":"Fenk, Lorenz A.","first_name":"Lorenz A.","last_name":"Fenk"},{"last_name":"Bretscher","first_name":"Andrew J.","full_name":"Bretscher, Andrew J."},{"full_name":"Gross, Einav","last_name":"Gross","first_name":"Einav"},{"last_name":"Busch","first_name":"K. Emanuel","full_name":"Busch, K. Emanuel"},{"id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8347-0443","first_name":"Mario","last_name":"de Bono","full_name":"de Bono, Mario"}],"issue":"12","citation":{"mla":"Kodama-Namba, Eiji, et al. “Cross-Modulation of Homeostatic Responses to Temperature, Oxygen and Carbon Dioxide in C. Elegans.” <i>PLoS Genetics</i>, vol. 9, no. 12, e1004011, Public Library of Science (PLoS), 2013, doi:<a href=\"https://doi.org/10.1371/journal.pgen.1004011\">10.1371/journal.pgen.1004011</a>.","ieee":"E. Kodama-Namba, L. A. Fenk, A. J. Bretscher, E. Gross, K. E. Busch, and M. de Bono, “Cross-modulation of homeostatic responses to temperature, oxygen and carbon dioxide in C. elegans,” <i>PLoS Genetics</i>, vol. 9, no. 12. Public Library of Science (PLoS), 2013.","apa":"Kodama-Namba, E., Fenk, L. A., Bretscher, A. J., Gross, E., Busch, K. E., &#38; de Bono, M. (2013). Cross-modulation of homeostatic responses to temperature, oxygen and carbon dioxide in C. elegans. <i>PLoS Genetics</i>. Public Library of Science (PLoS). <a href=\"https://doi.org/10.1371/journal.pgen.1004011\">https://doi.org/10.1371/journal.pgen.1004011</a>","ama":"Kodama-Namba E, Fenk LA, Bretscher AJ, Gross E, Busch KE, de Bono M. Cross-modulation of homeostatic responses to temperature, oxygen and carbon dioxide in C. elegans. <i>PLoS Genetics</i>. 2013;9(12). doi:<a href=\"https://doi.org/10.1371/journal.pgen.1004011\">10.1371/journal.pgen.1004011</a>","ista":"Kodama-Namba E, Fenk LA, Bretscher AJ, Gross E, Busch KE, de Bono M. 2013. Cross-modulation of homeostatic responses to temperature, oxygen and carbon dioxide in C. elegans. PLoS Genetics. 9(12), e1004011.","short":"E. Kodama-Namba, L.A. Fenk, A.J. Bretscher, E. Gross, K.E. Busch, M. de Bono, PLoS Genetics 9 (2013).","chicago":"Kodama-Namba, Eiji, Lorenz A. Fenk, Andrew J. Bretscher, Einav Gross, K. Emanuel Busch, and Mario de Bono. “Cross-Modulation of Homeostatic Responses to Temperature, Oxygen and Carbon Dioxide in C. Elegans.” <i>PLoS Genetics</i>. Public Library of Science (PLoS), 2013. <a href=\"https://doi.org/10.1371/journal.pgen.1004011\">https://doi.org/10.1371/journal.pgen.1004011</a>."},"month":"12","oa":1,"ddc":["570"],"has_accepted_license":"1","extern":"1","intvolume":"         9","quality_controlled":"1","_id":"6128","title":"Cross-modulation of homeostatic responses to temperature, oxygen and carbon dioxide in C. elegans","file":[{"file_id":"6129","file_size":4499039,"date_created":"2019-03-19T15:14:51Z","creator":"kschuh","date_updated":"2020-07-14T12:47:20Z","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_name":"2013_PLOS_Kodama-Namba.PDF","checksum":"299b6321be79931c7c17c5db6e69c711"}],"publication_identifier":{"issn":["1553-7404"]}},{"author":[{"full_name":"Chen, Changchun","last_name":"Chen","first_name":"Changchun"},{"full_name":"Fenk, Lorenz A.","first_name":"Lorenz A.","last_name":"Fenk"},{"orcid":"0000-0001-8347-0443","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","last_name":"de Bono","first_name":"Mario","full_name":"de Bono, Mario"}],"issue":"20","citation":{"ista":"Chen C, Fenk LA, de Bono M. 2013. Efficient genome editing in Caenorhabditis elegans by CRISPR-targeted homologous recombination. Nucleic Acids Research. 41(20), e193.","chicago":"Chen, Changchun, Lorenz A. Fenk, and Mario de Bono. “Efficient Genome Editing in Caenorhabditis Elegans by CRISPR-Targeted Homologous Recombination.” <i>Nucleic Acids Research</i>. Oxford University Press, 2013. <a href=\"https://doi.org/10.1093/nar/gkt805\">https://doi.org/10.1093/nar/gkt805</a>.","short":"C. Chen, L.A. Fenk, M. de Bono, Nucleic Acids Research 41 (2013).","mla":"Chen, Changchun, et al. “Efficient Genome Editing in Caenorhabditis Elegans by CRISPR-Targeted Homologous Recombination.” <i>Nucleic Acids Research</i>, vol. 41, no. 20, e193, Oxford University Press, 2013, doi:<a href=\"https://doi.org/10.1093/nar/gkt805\">10.1093/nar/gkt805</a>.","ieee":"C. Chen, L. A. Fenk, and M. de Bono, “Efficient genome editing in Caenorhabditis elegans by CRISPR-targeted homologous recombination,” <i>Nucleic Acids Research</i>, vol. 41, no. 20. Oxford University Press, 2013.","apa":"Chen, C., Fenk, L. A., &#38; de Bono, M. (2013). Efficient genome editing in Caenorhabditis elegans by CRISPR-targeted homologous recombination. <i>Nucleic Acids Research</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/nar/gkt805\">https://doi.org/10.1093/nar/gkt805</a>","ama":"Chen C, Fenk LA, de Bono M. Efficient genome editing in Caenorhabditis elegans by CRISPR-targeted homologous recombination. <i>Nucleic Acids Research</i>. 2013;41(20). doi:<a href=\"https://doi.org/10.1093/nar/gkt805\">10.1093/nar/gkt805</a>"},"month":"11","date_published":"2013-11-01T00:00:00Z","oa_version":"Published Version","publication_status":"published","year":"2013","intvolume":"        41","quality_controlled":"1","_id":"6130","title":"Efficient genome editing in Caenorhabditis elegans by CRISPR-targeted homologous recombination","file":[{"file_id":"6131","date_created":"2019-03-19T15:25:42Z","file_size":340225,"creator":"kschuh","date_updated":"2020-07-14T12:47:20Z","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_name":"2013_OUP_Chen.pdf","checksum":"0f1f127cefd043cb922b292e1cd16f02"}],"publication_identifier":{"issn":["1362-4962","0305-1048"]},"oa":1,"ddc":["570"],"has_accepted_license":"1","extern":"1","volume":41,"external_id":{"pmid":["24013562"]},"doi":"10.1093/nar/gkt805","abstract":[{"text":"Cas9 is an RNA-guided double-stranded DNA nuclease that participates in clustered regularly interspaced short palindromic repeats (CRISPR)-mediated adaptive immunity in prokaryotes. CRISPR–Cas9 has recently been used to generate insertion and deletion mutations in Caenorhabditis elegans, but not to create tailored changes (knock-ins). We show that the CRISPR–CRISPR-associated (Cas) system can be adapted for efficient and precise editing of the C. elegans genome. The targeted double-strand breaks generated by CRISPR are substrates for transgene-instructed gene conversion. This allows customized changes in the C. elegans genome by homologous recombination: sequences contained in the repair template (the transgene) are copied by gene conversion into the genome. The possibility to edit the C. elegans genome at selected locations will facilitate the systematic study of gene function in this widely used model organism.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"e193","language":[{"iso":"eng"}],"status":"public","date_created":"2019-03-19T15:17:40Z","date_updated":"2021-01-12T08:06:16Z","day":"01","type":"journal_article","publication":"Nucleic Acids Research","publisher":"Oxford University Press","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file_date_updated":"2020-07-14T12:47:20Z","pmid":1},{"date_created":"2019-03-20T13:54:05Z","status":"public","quality_controlled":"1","_id":"6132","date_updated":"2021-01-12T08:06:16Z","title":"Optogenetic actuation, inhibition, modulation and readout for neuronal networks generating behavior in the nematode Caenorhabditis elegans","day":"28","type":"book_chapter","publication_identifier":{"isbn":["9783110270723; 9783110270716"]},"publication":"Optogenetics","publisher":"Walter de Gruyter","extern":"1","page":"61-78","editor":[{"last_name":"Hegemann","first_name":"Peter","full_name":"Hegemann, Peter"},{"full_name":"Sigrist, Stephan","last_name":"Sigrist","first_name":"Stephan"}],"author":[{"orcid":"0000-0001-8347-0443","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","last_name":"de Bono","first_name":"Mario","full_name":"de Bono, Mario"},{"full_name":"Schafer, W.R.","first_name":"W.R.","last_name":"Schafer"},{"full_name":"Gottschalk, A.","last_name":"Gottschalk","first_name":"A."}],"citation":{"short":"M. de Bono, W.R. Schafer, A. Gottschalk, in:, P. Hegemann, S. Sigrist (Eds.), Optogenetics, Walter de Gruyter, 2013, pp. 61–78.","chicago":"Bono, Mario de, W.R. Schafer, and A. Gottschalk. “Optogenetic Actuation, Inhibition, Modulation and Readout for Neuronal Networks Generating Behavior in the Nematode Caenorhabditis Elegans.” In <i>Optogenetics</i>, edited by Peter Hegemann and Stephan Sigrist, 61–78. Walter de Gruyter, 2013.","ista":"de Bono M, Schafer WR, Gottschalk A. 2013.Optogenetic actuation, inhibition, modulation and readout for neuronal networks generating behavior in the nematode Caenorhabditis elegans. In: Optogenetics. , 61–78.","ama":"de Bono M, Schafer WR, Gottschalk A. Optogenetic actuation, inhibition, modulation and readout for neuronal networks generating behavior in the nematode Caenorhabditis elegans. In: Hegemann P, Sigrist S, eds. <i>Optogenetics</i>. Walter de Gruyter; 2013:61-78.","ieee":"M. de Bono, W. R. Schafer, and A. Gottschalk, “Optogenetic actuation, inhibition, modulation and readout for neuronal networks generating behavior in the nematode Caenorhabditis elegans,” in <i>Optogenetics</i>, P. Hegemann and S. Sigrist, Eds. Walter de Gruyter, 2013, pp. 61–78.","apa":"de Bono, M., Schafer, W. R., &#38; Gottschalk, A. (2013). Optogenetic actuation, inhibition, modulation and readout for neuronal networks generating behavior in the nematode Caenorhabditis elegans. In P. Hegemann &#38; S. Sigrist (Eds.), <i>Optogenetics</i> (pp. 61–78). Walter de Gruyter.","mla":"de Bono, Mario, et al. “Optogenetic Actuation, Inhibition, Modulation and Readout for Neuronal Networks Generating Behavior in the Nematode Caenorhabditis Elegans.” <i>Optogenetics</i>, edited by Peter Hegemann and Stephan Sigrist, Walter de Gruyter, 2013, pp. 61–78."},"month":"08","date_published":"2013-08-28T00:00:00Z","oa_version":"None","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publication_status":"published","year":"2013","language":[{"iso":"eng"}]},{"date_published":"2013-08-27T00:00:00Z","oa_version":"Published Version","publication_status":"published","year":"2013","author":[{"full_name":"Couto, A.","first_name":"A.","last_name":"Couto"},{"last_name":"Oda","first_name":"S.","full_name":"Oda, S."},{"last_name":"Nikolaev","first_name":"V. O.","full_name":"Nikolaev, V. O."},{"last_name":"Soltesz","first_name":"Z.","full_name":"Soltesz, Z."},{"last_name":"de Bono","first_name":"Mario","full_name":"de Bono, Mario","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8347-0443"}],"issue":"35","citation":{"ama":"Couto A, Oda S, Nikolaev VO, Soltesz Z, de Bono M. In vivo genetic dissection of O2-evoked cGMP dynamics in a Caenorhabditis elegans gas sensor. <i>Proceedings of the National Academy of Sciences</i>. 2013;110(35):E3301-E3310. doi:<a href=\"https://doi.org/10.1073/pnas.1217428110\">10.1073/pnas.1217428110</a>","mla":"Couto, A., et al. “In Vivo Genetic Dissection of O2-Evoked CGMP Dynamics in a Caenorhabditis Elegans Gas Sensor.” <i>Proceedings of the National Academy of Sciences</i>, vol. 110, no. 35, Proceedings of the National Academy of Sciences, 2013, pp. E3301–10, doi:<a href=\"https://doi.org/10.1073/pnas.1217428110\">10.1073/pnas.1217428110</a>.","apa":"Couto, A., Oda, S., Nikolaev, V. O., Soltesz, Z., &#38; de Bono, M. (2013). In vivo genetic dissection of O2-evoked cGMP dynamics in a Caenorhabditis elegans gas sensor. <i>Proceedings of the National Academy of Sciences</i>. Proceedings of the National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1217428110\">https://doi.org/10.1073/pnas.1217428110</a>","ieee":"A. Couto, S. Oda, V. O. Nikolaev, Z. Soltesz, and M. de Bono, “In vivo genetic dissection of O2-evoked cGMP dynamics in a Caenorhabditis elegans gas sensor,” <i>Proceedings of the National Academy of Sciences</i>, vol. 110, no. 35. Proceedings of the National Academy of Sciences, pp. E3301–E3310, 2013.","ista":"Couto A, Oda S, Nikolaev VO, Soltesz Z, de Bono M. 2013. In vivo genetic dissection of O2-evoked cGMP dynamics in a Caenorhabditis elegans gas sensor. Proceedings of the National Academy of Sciences. 110(35), E3301–E3310.","chicago":"Couto, A., S. Oda, V. O. Nikolaev, Z. Soltesz, and Mario de Bono. “In Vivo Genetic Dissection of O2-Evoked CGMP Dynamics in a Caenorhabditis Elegans Gas Sensor.” <i>Proceedings of the National Academy of Sciences</i>. Proceedings of the National Academy of Sciences, 2013. <a href=\"https://doi.org/10.1073/pnas.1217428110\">https://doi.org/10.1073/pnas.1217428110</a>.","short":"A. Couto, S. Oda, V.O. Nikolaev, Z. Soltesz, M. de Bono, Proceedings of the National Academy of Sciences 110 (2013) E3301–E3310."},"month":"08","oa":1,"ddc":["570"],"has_accepted_license":"1","extern":"1","intvolume":"       110","quality_controlled":"1","_id":"6133","title":"In vivo genetic dissection of O2-evoked cGMP dynamics in a Caenorhabditis elegans gas sensor","file":[{"creator":"kschuh","file_id":"6134","file_size":2198763,"date_created":"2019-03-20T14:07:53Z","access_level":"open_access","date_updated":"2020-07-14T12:47:20Z","content_type":"application/pdf","relation":"main_file","file_name":"2013_PNAS_Couto.pdf","checksum":"3ee28a694f74a49f0d098970ae391a91"}],"publication_identifier":{"issn":["0027-8424","1091-6490"]},"abstract":[{"lang":"eng","text":"cGMP signaling is widespread in the nervous system. However, it has proved difficult to visualize and genetically probe endogenously evoked cGMP dynamics in neurons in vivo. Here, we combine cGMP and Ca2+ biosensors to image and dissect a cGMP signaling network in a Caenorhabditis elegans oxygen-sensing neuron. We show that a rise in O2 can evoke a tonic increase in cGMP that requires an atypical O2-binding soluble guanylate cyclase and that is sustained until oxygen levels fall. Increased cGMP leads to a sustained Ca2+ response in the neuron that depends on cGMP-gated ion channels. Elevated levels of cGMP and Ca2+ stimulate competing negative feedback loops that shape cGMP dynamics. Ca2+-dependent negative feedback loops, including activation of phosphodiesterase-1 (PDE-1), dampen the rise of cGMP. A different negative feedback loop, mediated by phosphodiesterase-2 (PDE-2) and stimulated by cGMP-dependent kinase (PKG), unexpectedly promotes cGMP accumulation following a rise in O2, apparently by keeping in check gating of cGMP channels and limiting activation of Ca2+-dependent negative feedback loops. Simultaneous imaging of Ca2+ and cGMP suggests that cGMP levels can rise close to cGMP channels while falling elsewhere. O2-evoked cGMP and Ca2+ responses are highly reproducible when the same neuron in an individual animal is stimulated repeatedly, suggesting that cGMP transduction has high intrinsic reliability. However, responses vary substantially across individuals, despite animals being genetically identical and similarly reared. This variability may reflect stochastic differences in expression of cGMP signaling components. Our work provides in vivo insights into the architecture of neuronal cGMP signaling."}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"volume":110,"external_id":{"pmid":["23940325"]},"doi":"10.1073/pnas.1217428110","publication":"Proceedings of the National Academy of Sciences","publisher":"Proceedings of the National Academy of Sciences","file_date_updated":"2020-07-14T12:47:20Z","pmid":1,"page":"E3301-E3310","date_created":"2019-03-20T14:05:06Z","status":"public","date_updated":"2021-01-12T08:06:16Z","day":"27","type":"journal_article"},{"language":[{"iso":"eng"}],"year":"2013","publication_status":"published","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa_version":"None","date_published":"2013-06-01T00:00:00Z","abstract":[{"text":"Many organisms have stress response pathways, components of which share homology with players in complex human disease pathways. Research on stress response in the nematode worm Caenorhabditis elegans has provided detailed insights into the genetic and molecular mechanisms underlying complex human diseases. In this review we focus on four different types of environmental stress responses – heat shock, oxidative stress, hypoxia, and osmotic stress – and on how these can be used to study the genetics of complex human diseases. All four types of responses involve the genetic machineries that underlie a number of complex human diseases such as cancer and neurodegenerative diseases, including Alzheimer's and Parkinson's. We highlight the types of stress response experiments required to detect the genes and pathways underlying human disease and suggest that studying stress biology in worms can be translated to understanding human disease and provide potential targets for drug discovery.","lang":"eng"}],"doi":"10.1016/j.tig.2013.01.010","month":"06","issue":"6","citation":{"ama":"Rodriguez M, Snoek LB, de Bono M, Kammenga JE. Worms under stress: C. elegans stress response and its relevance to complex human disease and aging. <i>Trends in Genetics</i>. 2013;29(6):367-374. doi:<a href=\"https://doi.org/10.1016/j.tig.2013.01.010\">10.1016/j.tig.2013.01.010</a>","mla":"Rodriguez, Miriam, et al. “Worms under Stress: C. Elegans Stress Response and Its Relevance to Complex Human Disease and Aging.” <i>Trends in Genetics</i>, vol. 29, no. 6, Elsevier, 2013, pp. 367–74, doi:<a href=\"https://doi.org/10.1016/j.tig.2013.01.010\">10.1016/j.tig.2013.01.010</a>.","ieee":"M. Rodriguez, L. B. Snoek, M. de Bono, and J. E. Kammenga, “Worms under stress: C. elegans stress response and its relevance to complex human disease and aging,” <i>Trends in Genetics</i>, vol. 29, no. 6. Elsevier, pp. 367–374, 2013.","apa":"Rodriguez, M., Snoek, L. B., de Bono, M., &#38; Kammenga, J. E. (2013). Worms under stress: C. elegans stress response and its relevance to complex human disease and aging. <i>Trends in Genetics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.tig.2013.01.010\">https://doi.org/10.1016/j.tig.2013.01.010</a>","ista":"Rodriguez M, Snoek LB, de Bono M, Kammenga JE. 2013. Worms under stress: C. elegans stress response and its relevance to complex human disease and aging. Trends in Genetics. 29(6), 367–374.","short":"M. Rodriguez, L.B. Snoek, M. de Bono, J.E. Kammenga, Trends in Genetics 29 (2013) 367–374.","chicago":"Rodriguez, Miriam, L. Basten Snoek, Mario de Bono, and Jan E. Kammenga. “Worms under Stress: C. Elegans Stress Response and Its Relevance to Complex Human Disease and Aging.” <i>Trends in Genetics</i>. Elsevier, 2013. <a href=\"https://doi.org/10.1016/j.tig.2013.01.010\">https://doi.org/10.1016/j.tig.2013.01.010</a>."},"author":[{"full_name":"Rodriguez, Miriam","last_name":"Rodriguez","first_name":"Miriam"},{"last_name":"Snoek","first_name":"L. Basten","full_name":"Snoek, L. Basten"},{"first_name":"Mario","last_name":"de Bono","full_name":"de Bono, Mario","orcid":"0000-0001-8347-0443","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jan E.","last_name":"Kammenga","full_name":"Kammenga, Jan E."}],"volume":29,"page":"367-374","extern":"1","publisher":"Elsevier","publication":"Trends in Genetics","type":"journal_article","publication_identifier":{"issn":["0168-9525"]},"day":"01","date_updated":"2021-01-12T08:06:17Z","title":"Worms under stress: C. elegans stress response and its relevance to complex human disease and aging","_id":"6135","quality_controlled":"1","intvolume":"        29","date_created":"2019-03-20T14:17:42Z","status":"public"},{"doi":"10.1021/jp400648q","issue":"18","citation":{"short":"T.-C. Lin, J.M. Cole, A.P. Higginbotham, A.J. Edwards, R.O. Piltz, J. Pérez-Moreno, J.-Y. Seo, S.-C. Lee, K. Clays, O.-P. Kwon, The Journal of Physical Chemistry C 117 (2013) 9416–9430.","chicago":"Lin, Tze-Chia, Jacqueline M. Cole, Andrew P Higginbotham, Alison J. Edwards, Ross O. Piltz, Javier Pérez-Moreno, Ji-Youn Seo, Seung-Chul Lee, Koen Clays, and O-Pil Kwon. “Molecular Origins of the High-Performance Nonlinear Optical Susceptibility in a Phenolic Polyene Chromophore: Electron Density Distributions, Hydrogen Bonding, and Ab Initio Calculations.” <i>The Journal of Physical Chemistry C</i>. American Chemical Society (ACS), 2013. <a href=\"https://doi.org/10.1021/jp400648q\">https://doi.org/10.1021/jp400648q</a>.","ista":"Lin T-C, Cole JM, Higginbotham AP, Edwards AJ, Piltz RO, Pérez-Moreno J, Seo J-Y, Lee S-C, Clays K, Kwon O-P. 2013. Molecular origins of the high-performance nonlinear optical susceptibility in a phenolic polyene chromophore: Electron density distributions, hydrogen bonding, and ab initio calculations. The Journal of Physical Chemistry C. 117(18), 9416–9430.","ieee":"T.-C. Lin <i>et al.</i>, “Molecular origins of the high-performance nonlinear optical susceptibility in a phenolic polyene chromophore: Electron density distributions, hydrogen bonding, and ab initio calculations,” <i>The Journal of Physical Chemistry C</i>, vol. 117, no. 18. American Chemical Society (ACS), pp. 9416–9430, 2013.","apa":"Lin, T.-C., Cole, J. M., Higginbotham, A. P., Edwards, A. J., Piltz, R. O., Pérez-Moreno, J., … Kwon, O.-P. (2013). Molecular origins of the high-performance nonlinear optical susceptibility in a phenolic polyene chromophore: Electron density distributions, hydrogen bonding, and ab initio calculations. <i>The Journal of Physical Chemistry C</i>. American Chemical Society (ACS). <a href=\"https://doi.org/10.1021/jp400648q\">https://doi.org/10.1021/jp400648q</a>","mla":"Lin, Tze-Chia, et al. “Molecular Origins of the High-Performance Nonlinear Optical Susceptibility in a Phenolic Polyene Chromophore: Electron Density Distributions, Hydrogen Bonding, and Ab Initio Calculations.” <i>The Journal of Physical Chemistry C</i>, vol. 117, no. 18, American Chemical Society (ACS), 2013, pp. 9416–30, doi:<a href=\"https://doi.org/10.1021/jp400648q\">10.1021/jp400648q</a>.","ama":"Lin T-C, Cole JM, Higginbotham AP, et al. Molecular origins of the high-performance nonlinear optical susceptibility in a phenolic polyene chromophore: Electron density distributions, hydrogen bonding, and ab initio calculations. <i>The Journal of Physical Chemistry C</i>. 2013;117(18):9416-9430. doi:<a href=\"https://doi.org/10.1021/jp400648q\">10.1021/jp400648q</a>"},"month":"05","volume":117,"author":[{"full_name":"Lin, Tze-Chia","last_name":"Lin","first_name":"Tze-Chia"},{"full_name":"Cole, Jacqueline M.","last_name":"Cole","first_name":"Jacqueline M."},{"full_name":"Higginbotham, Andrew P","first_name":"Andrew P","last_name":"Higginbotham","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2607-2363"},{"last_name":"Edwards","first_name":"Alison J.","full_name":"Edwards, Alison J."},{"full_name":"Piltz, Ross O.","first_name":"Ross O.","last_name":"Piltz"},{"last_name":"Pérez-Moreno","first_name":"Javier","full_name":"Pérez-Moreno, Javier"},{"full_name":"Seo, Ji-Youn","first_name":"Ji-Youn","last_name":"Seo"},{"last_name":"Lee","first_name":"Seung-Chul","full_name":"Lee, Seung-Chul"},{"last_name":"Clays","first_name":"Koen","full_name":"Clays, Koen"},{"full_name":"Kwon, O-Pil","first_name":"O-Pil","last_name":"Kwon"}],"language":[{"iso":"eng"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publication_status":"published","oa_version":"None","year":"2013","date_published":"2013-05-09T00:00:00Z","abstract":[{"text":"The molecular and supramolecular origins of the superior nonlinear optical (NLO) properties observed in the organic phenolic triene material, OH1 (2-(3-(4-hydroxystyryl)-5,5-dimethylcyclohex-2-enylidene)malononitrile), are presented. The molecular charge-transfer distribution is topographically mapped, demonstrating that a uniformly delocalized passive electronic medium facilitates the charge-transfer between the phenolic electron donor and the cyano electron acceptors which lie at opposite ends of the molecule. Its ability to act as a “push–pull” π-conjugated molecule is quantified, relative to similar materials, by supporting empirical calculations; these include bond-length alternation and harmonic-oscillator stabilization energy (HOSE) tests. Such tests, together with frontier molecular orbital considerations, reveal that OH1 can exist readily in its aromatic (neutral) or quinoidal (charge-separated) state, thereby overcoming the “nonlinearity-thermal stability trade-off”. The HOSE calculation also reveals a correlation between the quinoidal resonance contribution to the overall structure of OH1 and the UV–vis absorption peak wavelength in the wider family of configurationally locked polyene framework materials. Solid-state tensorial coefficients of the molecular dipole, polarizability, and the first hyperpolarizability for OH1 are derived from the first-, second-, and third-order electronic moments of the experimental charge-density distribution. The overall solid-state molecular dipole moment is compared with those from gas-phase calculations, revealing that crystal field effects are very significant in OH1. The solid-state hyperpolarizability derived from this charge-density study affords good agreement with gas-phase calculations as well as optical measurements based on hyper-Rayleigh scattering (HRS) and electric-field-induced second harmonic (EFISH) generation. This lends support to the further use of charge-density studies to calculate solid-state hyperpolarizability coefficients in other organic NLO materials. Finally, this charge-density study is also employed to provide an advanced classification of hydrogen bonds in OH1, which requires more stringent criteria than those from conventional structure analysis. As a result, only the strongest OH···NC interaction is so classified as a true hydrogen bond. Indeed, it is this electrostatic interaction that influences the molecular charge transfer: the other four, weaker, nonbonded contacts nonetheless affect the crystal packing. Overall, the establishment of these structure–property relationships lays a blueprint for designing further, more NLO efficient, materials in this industrially leading organic family of compounds.","lang":"eng"}],"day":"09","type":"journal_article","publication_identifier":{"issn":["1932-7447","1932-7455"]},"_id":"6370","title":"Molecular origins of the high-performance nonlinear optical susceptibility in a phenolic polyene chromophore: Electron density distributions, hydrogen bonding, and ab initio calculations","date_updated":"2021-01-12T08:07:17Z","quality_controlled":"1","date_created":"2019-05-03T09:40:31Z","intvolume":"       117","status":"public","page":"9416-9430","extern":"1","publication":"The Journal of Physical Chemistry C","publisher":"American Chemical Society (ACS)"},{"day":"13","file":[{"file_size":549684,"date_created":"2019-05-13T14:11:39Z","file_id":"6441","creator":"dernst","date_updated":"2020-07-14T12:47:30Z","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"a219ba4eada6cd62befed52262ee15d4","file_name":"2013_TechRep_Henzinger.pdf"}],"type":"technical_report","publication_identifier":{"issn":["2664-1690"]},"_id":"6440","date_updated":"2020-07-14T23:06:19Z","title":"Replacing competition with cooperation to achieve scalable lock-free FIFO queues ","alternative_title":["IST Austria Technical Report"],"status":"public","date_created":"2019-05-13T14:13:27Z","department":[{"_id":"ToHe"}],"page":"23","ddc":["000","005"],"has_accepted_license":"1","file_date_updated":"2020-07-14T12:47:30Z","oa":1,"publisher":"IST Austria","doi":"10.15479/AT:IST-2013-124-v1-1","citation":{"ama":"Henzinger TA, Payer H, Sezgin A. <i>Replacing Competition with Cooperation to Achieve Scalable Lock-Free FIFO Queues </i>. IST Austria; 2013. doi:<a href=\"https://doi.org/10.15479/AT:IST-2013-124-v1-1\">10.15479/AT:IST-2013-124-v1-1</a>","mla":"Henzinger, Thomas A., et al. <i>Replacing Competition with Cooperation to Achieve Scalable Lock-Free FIFO Queues </i>. IST Austria, 2013, doi:<a href=\"https://doi.org/10.15479/AT:IST-2013-124-v1-1\">10.15479/AT:IST-2013-124-v1-1</a>.","ieee":"T. A. Henzinger, H. Payer, and A. Sezgin, <i>Replacing competition with cooperation to achieve scalable lock-free FIFO queues </i>. IST Austria, 2013.","apa":"Henzinger, T. A., Payer, H., &#38; Sezgin, A. (2013). <i>Replacing competition with cooperation to achieve scalable lock-free FIFO queues </i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2013-124-v1-1\">https://doi.org/10.15479/AT:IST-2013-124-v1-1</a>","ista":"Henzinger TA, Payer H, Sezgin A. 2013. Replacing competition with cooperation to achieve scalable lock-free FIFO queues , IST Austria, 23p.","chicago":"Henzinger, Thomas A, Hannes Payer, and Ali Sezgin. <i>Replacing Competition with Cooperation to Achieve Scalable Lock-Free FIFO Queues </i>. IST Austria, 2013. <a href=\"https://doi.org/10.15479/AT:IST-2013-124-v1-1\">https://doi.org/10.15479/AT:IST-2013-124-v1-1</a>.","short":"T.A. Henzinger, H. Payer, A. Sezgin, Replacing Competition with Cooperation to Achieve Scalable Lock-Free FIFO Queues , IST Austria, 2013."},"pubrep_id":"124","month":"06","author":[{"full_name":"Henzinger, Thomas A","last_name":"Henzinger","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724"},{"full_name":"Payer, Hannes","first_name":"Hannes","last_name":"Payer"},{"id":"4C7638DA-F248-11E8-B48F-1D18A9856A87","full_name":"Sezgin, Ali","first_name":"Ali","last_name":"Sezgin"}],"language":[{"iso":"eng"}],"oa_version":"Published Version","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2013","date_published":"2013-06-13T00:00:00Z","abstract":[{"lang":"eng","text":"In order to guarantee that each method of a data structure updates the logical state exactly once, al-most all non-blocking implementations employ Compare-And-Swap (CAS) based synchronization. For FIFO  queue  implementations  this  translates  into  concurrent  enqueue  or  dequeue  methods competing among themselves to update the same variable, the tail or the head, respectively, leading to high contention and poor scalability. Recent non-blocking queue implementations try to alleviate high contentionby increasing the number of contention points, all the while using CAS-based synchronization. Furthermore, obtaining a wait-free implementation with competition is achieved by additional synchronization which leads to further degradation of performance.In this paper we formalize the notion of competitiveness of a synchronizing statement which can beused as a measure for the scalability of concurrent implementations.  We present a new queue implementation, the Speculative Pairing (SP) queue, which, as we show, decreases competitiveness by using Fetch-And-Increment (FAI) instead of CAS. We prove that the SP queue is linearizable and lock-free.We also show that replacing CAS with FAI leads to wait-freedom for dequeue methods without an adverse effect on performance.  In fact, our experiments suggest that the SP queue can perform and scale better than the state-of-the-art queue implementations."}]},{"language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"The paper presents an algorithm that applies a stack filter simulating the Mean Curvature Motion equation via a finite difference scheme.","lang":"eng"}],"doi":"10.5201/ipol.2013.53","volume":3,"page":"68-111","file_date_updated":"2020-07-14T12:47:40Z","publication":"Image Processing On Line","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA (4.0)","image":"/images/cc_by_nc_sa.png"},"publisher":"Image Processing On Line","day":"11","type":"journal_article","date_updated":"2021-01-12T08:08:56Z","date_created":"2019-08-05T12:30:38Z","status":"public","article_type":"original","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","oa_version":"Published Version","publication_status":"published","year":"2013","date_published":"2013-07-11T00:00:00Z","citation":{"mla":"Mondelli, Marco. “A Finite Difference Scheme for the Stack Filter Simulating the MCM.” <i>Image Processing On Line</i>, vol. 3, Image Processing On Line, 2013, pp. 68–111, doi:<a href=\"https://doi.org/10.5201/ipol.2013.53\">10.5201/ipol.2013.53</a>.","apa":"Mondelli, M. (2013). A finite difference scheme for the stack filter simulating the MCM. <i>Image Processing On Line</i>. Image Processing On Line. <a href=\"https://doi.org/10.5201/ipol.2013.53\">https://doi.org/10.5201/ipol.2013.53</a>","ieee":"M. Mondelli, “A finite difference scheme for the stack filter simulating the MCM,” <i>Image Processing On Line</i>, vol. 3. Image Processing On Line, pp. 68–111, 2013.","ama":"Mondelli M. A finite difference scheme for the stack filter simulating the MCM. <i>Image Processing On Line</i>. 2013;3:68-111. doi:<a href=\"https://doi.org/10.5201/ipol.2013.53\">10.5201/ipol.2013.53</a>","ista":"Mondelli M. 2013. A finite difference scheme for the stack filter simulating the MCM. Image Processing On Line. 3, 68–111.","short":"M. Mondelli, Image Processing On Line 3 (2013) 68–111.","chicago":"Mondelli, Marco. “A Finite Difference Scheme for the Stack Filter Simulating the MCM.” <i>Image Processing On Line</i>. Image Processing On Line, 2013. <a href=\"https://doi.org/10.5201/ipol.2013.53\">https://doi.org/10.5201/ipol.2013.53</a>."},"month":"07","author":[{"first_name":"Marco","last_name":"Mondelli","full_name":"Mondelli, Marco","orcid":"0000-0002-3242-7020","id":"27EB676C-8706-11E9-9510-7717E6697425"}],"extern":"1","ddc":["510"],"has_accepted_license":"1","oa":1,"file":[{"file_name":"2013_IPOL_Mondelli.pdf","checksum":"83b7d429bc248c6c461229d3504fb139","content_type":"application/pdf","relation":"main_file","access_level":"open_access","date_updated":"2020-07-14T12:47:40Z","creator":"dernst","file_id":"6769","date_created":"2019-08-05T12:33:40Z","file_size":4306158}],"publication_identifier":{"issn":["2105-1232"]},"_id":"6768","title":"A finite difference scheme for the stack filter simulating the MCM","quality_controlled":"1","intvolume":"         3"},{"extern":"1","page":"1050-1056","publisher":"Springer Nature","publication":"Nature Materials","title":"A stable cathode for the aprotic Li–O2 battery","date_updated":"2021-01-12T08:12:55Z","_id":"7306","type":"journal_article","publication_identifier":{"issn":["1476-1122","1476-4660"]},"day":"01","status":"public","date_created":"2020-01-15T12:18:29Z","intvolume":"        12","quality_controlled":"1","language":[{"iso":"eng"}],"article_type":"original","article_processing_charge":"No","abstract":[{"lang":"eng","text":"Rechargeable lithium–air (O2) batteries are receiving intense interest because their high theoretical specific energy exceeds that of lithium-ion batteries. If the Li–O2 battery is ever to succeed, highly reversible formation/decomposition of Li2O2 must take place at the cathode on cycling. However, carbon, used ubiquitously as the basis of the cathode, decomposes during Li2O2 oxidation on charge and actively promotes electrolyte decomposition on cycling. Replacing carbon with a nanoporous gold cathode, when in contact with a dimethyl sulphoxide-based electrolyte, does seem to demonstrate better stability. However, nanoporous gold is not a suitable cathode; its high mass destroys the key advantage of Li–O2 over Li ion (specific energy), it is too expensive and too difficult to fabricate. Identifying a suitable cathode material for the Li–O2 cell is one of the greatest challenges at present. Here we show that a TiC-based cathode reduces greatly side reactions (arising from the electrolyte and electrode degradation) compared with carbon and exhibits better reversible formation/decomposition of Li2O2 even than nanoporous gold (>98% capacity retention after 100 cycles, compared with 95% for nanoporous gold); it is also four times lighter, of lower cost and easier to fabricate. The stability may originate from the presence of TiO2 (along with some TiOC) on the surface of TiC. In contrast to carbon or nanoporous gold, TiC seems to represent a more viable, stable, cathode for aprotic Li–O2 cells."}],"date_published":"2013-09-01T00:00:00Z","year":"2013","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"None","publication_status":"published","month":"09","citation":{"ista":"Ottakam Thotiyl MM, Freunberger SA, Peng Z, Chen Y, Liu Z, Bruce PG. 2013. A stable cathode for the aprotic Li–O2 battery. Nature Materials. 12(11), 1050–1056.","short":"M.M. Ottakam Thotiyl, S.A. Freunberger, Z. Peng, Y. Chen, Z. Liu, P.G. Bruce, Nature Materials 12 (2013) 1050–1056.","chicago":"Ottakam Thotiyl, Muhammed M., Stefan Alexander Freunberger, Zhangquan Peng, Yuhui Chen, Zheng Liu, and Peter G. Bruce. “A Stable Cathode for the Aprotic Li–O2 Battery.” <i>Nature Materials</i>. Springer Nature, 2013. <a href=\"https://doi.org/10.1038/nmat3737\">https://doi.org/10.1038/nmat3737</a>.","mla":"Ottakam Thotiyl, Muhammed M., et al. “A Stable Cathode for the Aprotic Li–O2 Battery.” <i>Nature Materials</i>, vol. 12, no. 11, Springer Nature, 2013, pp. 1050–56, doi:<a href=\"https://doi.org/10.1038/nmat3737\">10.1038/nmat3737</a>.","apa":"Ottakam Thotiyl, M. M., Freunberger, S. A., Peng, Z., Chen, Y., Liu, Z., &#38; Bruce, P. G. (2013). A stable cathode for the aprotic Li–O2 battery. <i>Nature Materials</i>. Springer Nature. <a href=\"https://doi.org/10.1038/nmat3737\">https://doi.org/10.1038/nmat3737</a>","ieee":"M. M. Ottakam Thotiyl, S. A. Freunberger, Z. Peng, Y. Chen, Z. Liu, and P. G. Bruce, “A stable cathode for the aprotic Li–O2 battery,” <i>Nature Materials</i>, vol. 12, no. 11. Springer Nature, pp. 1050–1056, 2013.","ama":"Ottakam Thotiyl MM, Freunberger SA, Peng Z, Chen Y, Liu Z, Bruce PG. A stable cathode for the aprotic Li–O2 battery. <i>Nature Materials</i>. 2013;12(11):1050-1056. doi:<a href=\"https://doi.org/10.1038/nmat3737\">10.1038/nmat3737</a>"},"issue":"11","doi":"10.1038/nmat3737","author":[{"first_name":"Muhammed M.","last_name":"Ottakam Thotiyl","full_name":"Ottakam Thotiyl, Muhammed M."},{"orcid":"0000-0003-2902-5319","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","full_name":"Freunberger, Stefan Alexander","last_name":"Freunberger","first_name":"Stefan Alexander"},{"full_name":"Peng, Zhangquan","last_name":"Peng","first_name":"Zhangquan"},{"full_name":"Chen, Yuhui","last_name":"Chen","first_name":"Yuhui"},{"full_name":"Liu, Zheng","first_name":"Zheng","last_name":"Liu"},{"full_name":"Bruce, Peter G.","first_name":"Peter G.","last_name":"Bruce"}],"volume":12},{"oa_version":"None","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","year":"2013","date_published":"2013-05-12T00:00:00Z","abstract":[{"text":"The non-aqueous Li–air (O2) battery is receiving intense interest because its theoretical specific energy exceeds that of Li-ion batteries. Recharging the Li–O2 battery depends on oxidizing solid lithium peroxide (Li2O2), which is formed on discharge within the porous cathode. However, transporting charge between Li2O2 particles and the solid electrode surface is at best very difficult and leads to voltage polarization on charging, even at modest rates. This is a significant problem facing the non-aqueous Li–O2 battery. Here we show that incorporation of a redox mediator, tetrathiafulvalene (TTF), enables recharging at rates that are impossible for the cell in the absence of the mediator. On charging, TTF is oxidized to TTF+ at the cathode surface; TTF+ in turn oxidizes the solid Li2O2, which results in the regeneration of TTF. The mediator acts as an electron–hole transfer agent that permits efficient oxidation of solid Li2O2. The cell with the mediator demonstrated 100 charge/discharge cycles.","lang":"eng"}],"article_processing_charge":"No","article_type":"original","language":[{"iso":"eng"}],"volume":5,"author":[{"full_name":"Chen, Yuhui","last_name":"Chen","first_name":"Yuhui"},{"orcid":"0000-0003-2902-5319","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","full_name":"Freunberger, Stefan Alexander","last_name":"Freunberger","first_name":"Stefan Alexander"},{"full_name":"Peng, Zhangquan","first_name":"Zhangquan","last_name":"Peng"},{"first_name":"Olivier","last_name":"Fontaine","full_name":"Fontaine, Olivier"},{"last_name":"Bruce","first_name":"Peter G.","full_name":"Bruce, Peter G."}],"doi":"10.1038/nchem.1646","citation":{"ista":"Chen Y, Freunberger SA, Peng Z, Fontaine O, Bruce PG. 2013. Charging a Li–O2 battery using a redox mediator. Nature Chemistry. 5(6), 489–494.","chicago":"Chen, Yuhui, Stefan Alexander Freunberger, Zhangquan Peng, Olivier Fontaine, and Peter G. Bruce. “Charging a Li–O2 Battery Using a Redox Mediator.” <i>Nature Chemistry</i>. Springer Nature, 2013. <a href=\"https://doi.org/10.1038/nchem.1646\">https://doi.org/10.1038/nchem.1646</a>.","short":"Y. Chen, S.A. Freunberger, Z. Peng, O. Fontaine, P.G. Bruce, Nature Chemistry 5 (2013) 489–494.","mla":"Chen, Yuhui, et al. “Charging a Li–O2 Battery Using a Redox Mediator.” <i>Nature Chemistry</i>, vol. 5, no. 6, Springer Nature, 2013, pp. 489–94, doi:<a href=\"https://doi.org/10.1038/nchem.1646\">10.1038/nchem.1646</a>.","apa":"Chen, Y., Freunberger, S. A., Peng, Z., Fontaine, O., &#38; Bruce, P. G. (2013). Charging a Li–O2 battery using a redox mediator. <i>Nature Chemistry</i>. Springer Nature. <a href=\"https://doi.org/10.1038/nchem.1646\">https://doi.org/10.1038/nchem.1646</a>","ieee":"Y. Chen, S. A. Freunberger, Z. Peng, O. Fontaine, and P. G. Bruce, “Charging a Li–O2 battery using a redox mediator,” <i>Nature Chemistry</i>, vol. 5, no. 6. Springer Nature, pp. 489–494, 2013.","ama":"Chen Y, Freunberger SA, Peng Z, Fontaine O, Bruce PG. Charging a Li–O2 battery using a redox mediator. <i>Nature Chemistry</i>. 2013;5(6):489-494. doi:<a href=\"https://doi.org/10.1038/nchem.1646\">10.1038/nchem.1646</a>"},"issue":"6","month":"05","publication":"Nature Chemistry","publisher":"Springer Nature","page":"489-494","extern":"1","quality_controlled":"1","status":"public","date_created":"2020-01-15T12:18:43Z","intvolume":"         5","day":"12","type":"journal_article","publication_identifier":{"issn":["1755-4330","1755-4349"]},"_id":"7307","title":"Charging a Li–O2 battery using a redox mediator","date_updated":"2021-01-12T08:12:56Z"},{"page":"549-560","pmid":1,"publisher":"Oxford University Press","publication":"Acta Biochimica et Biophysica Sinica","type":"journal_article","day":"01","date_updated":"2021-01-12T08:14:23Z","status":"public","date_created":"2020-03-21T16:06:36Z","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","abstract":[{"lang":"eng","text":"Inositol 1,3,4-trisphosphate 5/6 kinase (ITPK) phosphorylates inositol 1,3,4-trisphosphate to form inositol 1,3,4,5-tetrakisphosphate and inositol 1,3,4,6-tetrakisphosphate which can be finally transferred to inositol hexaphosphate (IP6) and play important roles during plant growth and development. There are 4 putative ITPK members in Arabidopsis. Expression pattern analysis showed that ITPK2 is constitutively expressed in various tissues. A T-DNA knockout mutant of ITPK2 was identified and scanning electron microscopy (SEM) analysis showed that the epidermis structure of seed coat was irregularly formed in seeds of itpk2-1 mutant, resulting in the increased permeability of seed coat to tetrazolium salts. Further analysis by gas chromatography coupled with mass spectrometry of lipid polyester monomers in cell wall confirmed a dramatic decrease in composition of suberin and cutin, which relate to the permeability of seed coat and the formation of which is accompanied with seed coat development. These results indicate that ITPK2 plays an essential role in seed coat development and lipid polyester barrier formation."}],"doi":"10.1093/abbs/gmt039","external_id":{"pmid":["23595027"]},"volume":45,"extern":"1","publication_identifier":{"issn":["1745-7270","1672-9145"]},"title":"Arabidopsis inositol 1,3,4-trisphosphate 5/6 kinase 2 is required for seed coat development","_id":"7595","quality_controlled":"1","intvolume":"        45","article_type":"original","year":"2013","publication_status":"published","oa_version":"None","date_published":"2013-07-01T00:00:00Z","month":"07","issue":"7","citation":{"mla":"Tang, Yong, et al. “Arabidopsis Inositol 1,3,4-Trisphosphate 5/6 Kinase 2 Is Required for Seed Coat Development.” <i>Acta Biochimica et Biophysica Sinica</i>, vol. 45, no. 7, Oxford University Press, 2013, pp. 549–60, doi:<a href=\"https://doi.org/10.1093/abbs/gmt039\">10.1093/abbs/gmt039</a>.","ieee":"Y. Tang, S. Tan, and H. Xue, “Arabidopsis inositol 1,3,4-trisphosphate 5/6 kinase 2 is required for seed coat development,” <i>Acta Biochimica et Biophysica Sinica</i>, vol. 45, no. 7. Oxford University Press, pp. 549–560, 2013.","apa":"Tang, Y., Tan, S., &#38; Xue, H. (2013). Arabidopsis inositol 1,3,4-trisphosphate 5/6 kinase 2 is required for seed coat development. <i>Acta Biochimica et Biophysica Sinica</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/abbs/gmt039\">https://doi.org/10.1093/abbs/gmt039</a>","ama":"Tang Y, Tan S, Xue H. Arabidopsis inositol 1,3,4-trisphosphate 5/6 kinase 2 is required for seed coat development. <i>Acta Biochimica et Biophysica Sinica</i>. 2013;45(7):549-560. doi:<a href=\"https://doi.org/10.1093/abbs/gmt039\">10.1093/abbs/gmt039</a>","ista":"Tang Y, Tan S, Xue H. 2013. Arabidopsis inositol 1,3,4-trisphosphate 5/6 kinase 2 is required for seed coat development. Acta Biochimica et Biophysica Sinica. 45(7), 549–560.","chicago":"Tang, Yong, Shutang Tan, and Hongwei Xue. “Arabidopsis Inositol 1,3,4-Trisphosphate 5/6 Kinase 2 Is Required for Seed Coat Development.” <i>Acta Biochimica et Biophysica Sinica</i>. Oxford University Press, 2013. <a href=\"https://doi.org/10.1093/abbs/gmt039\">https://doi.org/10.1093/abbs/gmt039</a>.","short":"Y. Tang, S. Tan, H. Xue, Acta Biochimica et Biophysica Sinica 45 (2013) 549–560."},"author":[{"full_name":"Tang, Yong","last_name":"Tang","first_name":"Yong"},{"orcid":"0000-0002-0471-8285","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","full_name":"Tan, Shutang","last_name":"Tan","first_name":"Shutang"},{"full_name":"Xue, Hongwei","first_name":"Hongwei","last_name":"Xue"}]},{"pmid":1,"page":"2618-2632","publication":"The Plant Cell","publisher":"American Society of Plant Biologists","date_updated":"2021-01-12T08:14:24Z","day":"26","type":"journal_article","status":"public","date_created":"2020-03-21T16:06:55Z","language":[{"iso":"eng"}],"abstract":[{"text":"Casein kinase1 (CK1) plays crucial roles in regulating growth and development via phosphorylating various substrates throughout the eukaryote kingdom. Blue light is crucial for normal growth of both plants and animals, and blue light receptor cryptochrome2 (CRY2) undergoes blue light–dependent phosphorylation and degradation in planta. To study the function of plant CK1s, systematic genetic analysis showed that deficiency of two paralogous Arabidopsis thaliana CK1s, CK1.3 and CK1.4, caused shortened hypocotyls, especially under blue light, while overexpression of either CK1.3 or CK1.4 resulted in the insensitive response to blue light and delayed flowering under long-day conditions. CK1.3 or CK1.4 act dependently on CRY2, and overexpression of CK1.3 or CK1.4 significantly suppresses the hypersensitive response to blue light by CRY2 overexpression. Biochemical studies showed that CK1.3 and CK1.4 directly phosphorylate CRY2 at Ser-587 and Thr-603 in vitro and negatively regulate CRY2 stability in planta, which are stimulated by blue light, further confirming the crucial roles of CK1.3 and CK1.4 in blue light responses through phosphorylating CRY2. Interestingly, expression of CK1.3 and CK1.4 is stimulated by blue light and feedback regulated by CRY2-mediated signaling. These results provide direct evidence for CRY2 phosphorylation and informative clues on the mechanisms of CRY2-mediated light responses.","lang":"eng"}],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"pmid":["23897926"]},"doi":"10.1105/tpc.113.114322","volume":25,"extern":"1","_id":"7596","title":"Arabidopsis casein kinase1 proteins CK1.3 and CK1.4 phosphorylate cryptochrome2 to regulate blue light signaling","publication_identifier":{"issn":["1040-4651","1532-298X"]},"intvolume":"        25","quality_controlled":"1","article_type":"original","date_published":"2013-08-26T00:00:00Z","oa_version":"None","publication_status":"published","year":"2013","issue":"7","citation":{"chicago":"Tan, Shutang, C. Dai, H.-T. Liu, and H.-W. Xue. “Arabidopsis Casein Kinase1 Proteins CK1.3 and CK1.4 Phosphorylate Cryptochrome2 to Regulate Blue Light Signaling.” <i>The Plant Cell</i>. American Society of Plant Biologists, 2013. <a href=\"https://doi.org/10.1105/tpc.113.114322\">https://doi.org/10.1105/tpc.113.114322</a>.","short":"S. Tan, C. Dai, H.-T. Liu, H.-W. Xue, The Plant Cell 25 (2013) 2618–2632.","ista":"Tan S, Dai C, Liu H-T, Xue H-W. 2013. Arabidopsis casein kinase1 proteins CK1.3 and CK1.4 phosphorylate cryptochrome2 to regulate blue light signaling. The Plant Cell. 25(7), 2618–2632.","ama":"Tan S, Dai C, Liu H-T, Xue H-W. Arabidopsis casein kinase1 proteins CK1.3 and CK1.4 phosphorylate cryptochrome2 to regulate blue light signaling. <i>The Plant Cell</i>. 2013;25(7):2618-2632. doi:<a href=\"https://doi.org/10.1105/tpc.113.114322\">10.1105/tpc.113.114322</a>","apa":"Tan, S., Dai, C., Liu, H.-T., &#38; Xue, H.-W. (2013). Arabidopsis casein kinase1 proteins CK1.3 and CK1.4 phosphorylate cryptochrome2 to regulate blue light signaling. <i>The Plant Cell</i>. American Society of Plant Biologists. <a href=\"https://doi.org/10.1105/tpc.113.114322\">https://doi.org/10.1105/tpc.113.114322</a>","ieee":"S. Tan, C. Dai, H.-T. Liu, and H.-W. Xue, “Arabidopsis casein kinase1 proteins CK1.3 and CK1.4 phosphorylate cryptochrome2 to regulate blue light signaling,” <i>The Plant Cell</i>, vol. 25, no. 7. American Society of Plant Biologists, pp. 2618–2632, 2013.","mla":"Tan, Shutang, et al. “Arabidopsis Casein Kinase1 Proteins CK1.3 and CK1.4 Phosphorylate Cryptochrome2 to Regulate Blue Light Signaling.” <i>The Plant Cell</i>, vol. 25, no. 7, American Society of Plant Biologists, 2013, pp. 2618–32, doi:<a href=\"https://doi.org/10.1105/tpc.113.114322\">10.1105/tpc.113.114322</a>."},"month":"08","author":[{"first_name":"Shutang","last_name":"Tan","full_name":"Tan, Shutang","orcid":"0000-0002-0471-8285","id":"2DE75584-F248-11E8-B48F-1D18A9856A87"},{"first_name":"C.","last_name":"Dai","full_name":"Dai, C."},{"first_name":"H.-T.","last_name":"Liu","full_name":"Liu, H.-T."},{"first_name":"H.-W.","last_name":"Xue","full_name":"Xue, H.-W."}]},{"publisher":"ACM","extern":"1","acknowledgement":"Dan Alistarh - This author was supported by the SNF Postdoctoral Fellows Program, NSF grant CCF-1217921, DoE ASCR grant\r\nER26116/DE-SC0008923,  and  by  grants  from  the  Oracle\r\nand Intel corporations.\r\nJames Aspnes - Supported in part by NSF grant CCF-0916389.\r\nGeorge Giakkoupis - This work was funded in part by INRIA Associate Team\r\nRADCON, and ERC Starting Grant GOSSPLE 204742.\r\nPhilipp Woelfel - This research was undertaken, in part, thanks to funding\r\nfrom the Canada Research Chairs program and the HP Labs\r\nInnovation Research Program.","page":"200 - 209","publist_id":"6889","conference":{"name":"PODC: Principles of Distributed Computing"},"status":"public","date_created":"2018-12-11T11:48:23Z","_id":"765","title":"Randomized loose renaming in O(loglogn) time","date_updated":"2023-02-23T13:13:14Z","day":"01","type":"conference","abstract":[{"text":"Renaming is a classic distributed coordination task in which a set of processes must pick distinct identifiers from a small namespace. In this paper, we consider the time complexity of this problem when the namespace is linear in the number of participants, a variant known as loose renaming. We give a non-adaptive algorithm with O(log log n) (individual) step complexity, where n is a known upper bound on contention, and an adaptive algorithm with step complexity O((log log k)2), where k is the actual contention in the execution. We also present a variant of the adaptive algorithm which requires O(k log log k) total process steps. All upper bounds hold with high probability against a strong adaptive adversary. We complement the algorithms with an ω(log log n) expected time lower bound on the complexity of randomized renaming using test-and-set operations and linear space. The result is based on a new coupling technique, and is the first to apply to non-adaptive randomized renaming. Since our algorithms use O(n) test-and-set objects, our results provide matching bounds on the cost of loose renaming in this setting.","lang":"eng"}],"date_published":"2013-01-01T00:00:00Z","article_processing_charge":"No","oa_version":"None","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","year":"2013","language":[{"iso":"eng"}],"author":[{"full_name":"Alistarh, Dan-Adrian","first_name":"Dan-Adrian","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X"},{"full_name":"Aspnes, James","last_name":"Aspnes","first_name":"James"},{"full_name":"Giakkoupis, George","first_name":"George","last_name":"Giakkoupis"},{"last_name":"Woelfel","first_name":"Philipp","full_name":"Woelfel, Philipp"}],"citation":{"apa":"Alistarh, D.-A., Aspnes, J., Giakkoupis, G., &#38; Woelfel, P. (2013). Randomized loose renaming in O(loglogn) time (pp. 200–209). Presented at the PODC: Principles of Distributed Computing, ACM. <a href=\"https://doi.org/10.1145/2484239.2484240\">https://doi.org/10.1145/2484239.2484240</a>","ieee":"D.-A. Alistarh, J. Aspnes, G. Giakkoupis, and P. Woelfel, “Randomized loose renaming in O(loglogn) time,” presented at the PODC: Principles of Distributed Computing, 2013, pp. 200–209.","mla":"Alistarh, Dan-Adrian, et al. <i>Randomized Loose Renaming in O(Loglogn) Time</i>. ACM, 2013, pp. 200–09, doi:<a href=\"https://doi.org/10.1145/2484239.2484240\">10.1145/2484239.2484240</a>.","ama":"Alistarh D-A, Aspnes J, Giakkoupis G, Woelfel P. Randomized loose renaming in O(loglogn) time. In: ACM; 2013:200-209. doi:<a href=\"https://doi.org/10.1145/2484239.2484240\">10.1145/2484239.2484240</a>","short":"D.-A. Alistarh, J. Aspnes, G. Giakkoupis, P. Woelfel, in:, ACM, 2013, pp. 200–209.","chicago":"Alistarh, Dan-Adrian, James Aspnes, George Giakkoupis, and Philipp Woelfel. “Randomized Loose Renaming in O(Loglogn) Time,” 200–209. ACM, 2013. <a href=\"https://doi.org/10.1145/2484239.2484240\">https://doi.org/10.1145/2484239.2484240</a>.","ista":"Alistarh D-A, Aspnes J, Giakkoupis G, Woelfel P. 2013. Randomized loose renaming in O(loglogn) time. PODC: Principles of Distributed Computing, 200–209."},"month":"01","doi":"10.1145/2484239.2484240"}]