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(3) Finally, we consider LTL without the next operator, and establish decidability (NEXPTIME-complete) for all architectures for a fragment that consists of a set of safety assumptions, and a set of guarantees where each guarantee is a safety, reachability, or liveness condition."}],"publist_id":"5835","ec_funded":1,"_id":"1376","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2013","publication_status":"published","title":"Distributed synthesis for LTL fragments","status":"public","publisher":"IEEE","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"author":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu"},{"full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","first_name":"Thomas A","last_name":"Henzinger"},{"first_name":"Jan","last_name":"Otop","id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87","full_name":"Otop, Jan"},{"id":"49704004-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8943-0722","first_name":"Andreas","last_name":"Pavlogiannis","full_name":"Pavlogiannis, Andreas"}],"related_material":{"record":[{"id":"5406","relation":"earlier_version","status":"public"}]},"date_created":"2018-12-11T11:51:40Z","date_updated":"2023-02-23T12:24:53Z","oa_version":"None","month":"12","day":"11","publication":"13th International Conference on Formal Methods in Computer-Aided Design","citation":{"ama":"Chatterjee K, Henzinger TA, Otop J, Pavlogiannis A. Distributed synthesis for LTL fragments. In: 13th International Conference on Formal Methods in Computer-Aided Design. IEEE; 2013:18-25. doi:10.1109/FMCAD.2013.6679386","apa":"Chatterjee, K., Henzinger, T. A., Otop, J., & Pavlogiannis, A. (2013). Distributed synthesis for LTL fragments. In 13th International Conference on Formal Methods in Computer-Aided Design (pp. 18–25). Portland, OR, United States: IEEE. https://doi.org/10.1109/FMCAD.2013.6679386","ieee":"K. Chatterjee, T. A. Henzinger, J. Otop, and A. Pavlogiannis, “Distributed synthesis for LTL fragments,” in 13th International Conference on Formal Methods in Computer-Aided Design, Portland, OR, United States, 2013, pp. 18–25.","ista":"Chatterjee K, Henzinger TA, Otop J, Pavlogiannis A. 2013. Distributed synthesis for LTL fragments. 13th International Conference on Formal Methods in Computer-Aided Design. FMCAD: Formal Methods in Computer-Aided Design, 18–25.","short":"K. Chatterjee, T.A. Henzinger, J. Otop, A. Pavlogiannis, in:, 13th International Conference on Formal Methods in Computer-Aided Design, IEEE, 2013, pp. 18–25.","mla":"Chatterjee, Krishnendu, et al. “Distributed Synthesis for LTL Fragments.” 13th International Conference on Formal Methods in Computer-Aided Design, IEEE, 2013, pp. 18–25, doi:10.1109/FMCAD.2013.6679386.","chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, Jan Otop, and Andreas Pavlogiannis. “Distributed Synthesis for LTL Fragments.” In 13th International Conference on Formal Methods in Computer-Aided Design, 18–25. IEEE, 2013. https://doi.org/10.1109/FMCAD.2013.6679386."},"quality_controlled":"1","project":[{"grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF"},{"name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"},{"call_identifier":"FP7","name":"Quantitative Reactive Modeling","grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"page":"18 - 25","conference":{"location":"Portland, OR, United States","start_date":"2013-10-20","end_date":"2013-10-23","name":"FMCAD: Formal Methods in Computer-Aided Design"},"date_published":"2013-12-11T00:00:00Z","doi":"10.1109/FMCAD.2013.6679386","language":[{"iso":"eng"}]},{"has_accepted_license":"1","publication_identifier":{"issn":["2664-1690"]},"month":"07","day":"08","oa":1,"citation":{"ama":"Chatterjee K, Henzinger TA, Otop J, Pavlogiannis A. Distributed Synthesis for LTL Fragments. IST Austria; 2013. doi:10.15479/AT:IST-2013-130-v1-1","ista":"Chatterjee K, Henzinger TA, Otop J, Pavlogiannis A. 2013. Distributed synthesis for LTL Fragments, IST Austria, 11p.","ieee":"K. Chatterjee, T. A. Henzinger, J. Otop, and A. Pavlogiannis, Distributed synthesis for LTL Fragments. IST Austria, 2013.","apa":"Chatterjee, K., Henzinger, T. A., Otop, J., & Pavlogiannis, A. (2013). Distributed synthesis for LTL Fragments. IST Austria. https://doi.org/10.15479/AT:IST-2013-130-v1-1","mla":"Chatterjee, Krishnendu, et al. Distributed Synthesis for LTL Fragments. IST Austria, 2013, doi:10.15479/AT:IST-2013-130-v1-1.","short":"K. Chatterjee, T.A. Henzinger, J. Otop, A. Pavlogiannis, Distributed Synthesis for LTL Fragments, IST Austria, 2013.","chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, Jan Otop, and Andreas Pavlogiannis. Distributed Synthesis for LTL Fragments. IST Austria, 2013. https://doi.org/10.15479/AT:IST-2013-130-v1-1."},"page":"11","date_published":"2013-07-08T00:00:00Z","doi":"10.15479/AT:IST-2013-130-v1-1","language":[{"iso":"eng"}],"type":"technical_report","alternative_title":["IST Austria Technical Report"],"abstract":[{"text":"We consider the distributed synthesis problem fortemporal logic specifications. Traditionally, the problem has been studied for LTL, and the previous results show that the problem is decidable iff there is no information fork in the architecture. We consider the problem for fragments of LTLand our main results are as follows: (1) We show that the problem is undecidable for architectures with information forks even for the fragment of LTL with temporal operators restricted to next and eventually. (2) For specifications restricted to globally along with non-nested next operators, we establish decidability (in EXPSPACE) for star architectures where the processes receive disjoint inputs, whereas we establish undecidability for architectures containing an information fork-meet structure. (3)Finally, we consider LTL without the next operator, and establish decidability (NEXPTIME-complete) for all architectures for a fragment that consists of a set of safety assumptions, and a set of guarantees where each guarantee is a safety, reachability, or liveness condition.","lang":"eng"}],"file_date_updated":"2020-07-14T12:46:45Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"5406","year":"2013","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"publisher":"IST Austria","status":"public","publication_status":"published","ddc":["005"],"title":"Distributed synthesis for LTL Fragments","related_material":{"record":[{"relation":"later_version","status":"public","id":"1376"}]},"pubrep_id":"130","author":[{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee"},{"full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","first_name":"Thomas A","last_name":"Henzinger"},{"full_name":"Otop, Jan","id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87","last_name":"Otop","first_name":"Jan"},{"full_name":"Pavlogiannis, Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8943-0722","first_name":"Andreas","last_name":"Pavlogiannis"}],"file":[{"file_id":"5540","relation":"main_file","checksum":"855513ebaf6f72228800c5fdb522f93c","date_updated":"2020-07-14T12:46:45Z","date_created":"2018-12-12T11:54:18Z","access_level":"open_access","file_name":"IST-2013-130-v1+1_Distributed_Synthesis.pdf","creator":"system","content_type":"application/pdf","file_size":467895}],"oa_version":"Published Version","date_created":"2018-12-12T11:39:09Z","date_updated":"2023-02-21T17:01:26Z"},{"date_created":"2018-12-12T11:39:10Z","date_updated":"2023-02-23T10:33:11Z","file":[{"checksum":"226bc791124f8d3138379778ce834e86","date_created":"2018-12-12T11:53:16Z","date_updated":"2020-07-14T12:46:46Z","relation":"main_file","file_id":"5477","content_type":"application/pdf","file_size":300481,"creator":"system","access_level":"open_access","file_name":"IST-2013-141-v1+1_main-tech-rpt.pdf"}],"oa_version":"Published Version","author":[{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu"},{"full_name":"Doyen, Laurent","first_name":"Laurent","last_name":"Doyen"},{"full_name":"Nain, Sumit","last_name":"Nain","first_name":"Sumit"},{"full_name":"Vardi, Moshe","first_name":"Moshe","last_name":"Vardi"}],"pubrep_id":"141","related_material":{"record":[{"id":"2213","status":"public","relation":"later_version"}]},"publication_status":"published","ddc":["000","005"],"title":"The complexity of partial-observation stochastic parity games with finite-memory strategies","status":"public","department":[{"_id":"KrCh"}],"publisher":"IST Austria","year":"2013","_id":"5408","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"We consider two-player partial-observation stochastic games where player 1 has partial observation and player 2 has perfect observation. The winning condition we study are omega-regular conditions specified as parity objectives. The qualitative analysis problem given a partial-observation stochastic game and a parity objective asks whether there is a strategy to ensure that the objective is satisfied with probability 1 (resp. positive probability). While the qualitative analysis problems are known to be undecidable even for very special cases of parity objectives, they were shown to be decidable in 2EXPTIME under finite-memory strategies. We improve the complexity and show that the qualitative analysis problems for partial-observation stochastic parity games under finite-memory strategies are \r\nEXPTIME-complete; and also establish optimal (exponential) memory bounds for finite-memory strategies required for qualitative analysis. 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IST Austria, 2013.","apa":"Chatterjee, K., Doyen, L., Nain, S., & Vardi, M. (2013). The complexity of partial-observation stochastic parity games with finite-memory strategies. IST Austria. https://doi.org/10.15479/AT:IST-2013-141-v1-1","ista":"Chatterjee K, Doyen L, Nain S, Vardi M. 2013. The complexity of partial-observation stochastic parity games with finite-memory strategies, IST Austria, 17p.","ama":"Chatterjee K, Doyen L, Nain S, Vardi M. The Complexity of Partial-Observation Stochastic Parity Games with Finite-Memory Strategies. IST Austria; 2013. doi:10.15479/AT:IST-2013-141-v1-1"},"oa":1,"month":"09","day":"12","has_accepted_license":"1","publication_identifier":{"issn":["2664-1690"]}},{"language":[{"iso":"eng"}],"date_published":"2013-07-13T00:00:00Z","oa":1,"citation":{"chicago":"Porsche, Jana. Technical Requirements and Features. IST Austria, 2013.","mla":"Porsche, Jana. Technical Requirements and Features. IST Austria, 2013.","short":"J. Porsche, Technical Requirements and Features, IST Austria, 2013.","ista":"Porsche J. 2013. Technical requirements and features, IST Austria,p.","ieee":"J. Porsche, Technical requirements and features. IST Austria, 2013.","apa":"Porsche, J. (2013). Technical requirements and features. IST Austria.","ama":"Porsche J. Technical Requirements and Features. IST Austria; 2013."},"has_accepted_license":"1","month":"07","day":"13","file":[{"checksum":"9e4f9abf79a56f651f0012a34909880f","date_created":"2018-12-12T11:53:02Z","date_updated":"2020-07-14T12:46:46Z","file_id":"5463","relation":"main_file","creator":"system","content_type":"application/pdf","file_size":90311,"access_level":"open_access","file_name":"IST-2013-135-v1+1_Features.pdf"}],"oa_version":"Published Version","date_created":"2018-12-12T11:39:09Z","date_updated":"2020-07-14T23:07:51Z","pubrep_id":"135","author":[{"full_name":"Porsche, Jana","id":"3252EDC2-F248-11E8-B48F-1D18A9856A87","last_name":"Porsche","first_name":"Jana"}],"publisher":"IST Austria","department":[{"_id":"E-Lib"}],"status":"public","title":"Technical requirements and features","publication_status":"published","ddc":["020"],"_id":"5407","year":"2013","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"This document is created as a part of the project “Repository for Research Data at IST Austria”. It summarises the mandatory features, which need to be fulfilled to provide an institutional repository as a platform and also a service to the scientists at the institute. It also includes optional features, which would be of strong benefit for the scientists and would increase the usage of the repository, and hence the visibility of research at IST Austria."}],"file_date_updated":"2020-07-14T12:46:46Z","type":"report"},{"_id":"5410","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2013","publisher":"IST Austria","department":[{"_id":"KrCh"}],"ddc":["000","005"],"publication_status":"published","status":"public","title":"Automatic generation of alternative starting positions for traditional board games","related_material":{"record":[{"id":"1481","relation":"later_version","status":"public"}]},"pubrep_id":"146","author":[{"first_name":"Umair","last_name":"Ahmed","full_name":"Ahmed, Umair"},{"first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"last_name":"Gulwani","first_name":"Sumit","full_name":"Gulwani, Sumit"}],"oa_version":"Published Version","file":[{"file_size":818189,"content_type":"application/pdf","creator":"system","file_name":"IST-2013-146-v1+1_main.pdf","access_level":"open_access","date_created":"2018-12-12T11:54:06Z","date_updated":"2020-07-14T12:46:46Z","checksum":"409f3aaaf1184e4057b89cbb449dac80","relation":"main_file","file_id":"5528"}],"date_updated":"2023-02-23T10:00:50Z","date_created":"2018-12-12T11:39:10Z","type":"technical_report","alternative_title":["IST Austria Technical Report"],"file_date_updated":"2020-07-14T12:46:46Z","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"}],"oa":1,"citation":{"mla":"Ahmed, Umair, et al. Automatic Generation of Alternative Starting Positions for Traditional Board Games. IST Austria, 2013, doi:10.15479/AT:IST-2013-146-v1-1.","short":"U. Ahmed, K. Chatterjee, S. Gulwani, Automatic Generation of Alternative Starting Positions for Traditional Board Games, IST Austria, 2013.","chicago":"Ahmed, Umair, Krishnendu Chatterjee, and Sumit Gulwani. Automatic Generation of Alternative Starting Positions for Traditional Board Games. IST Austria, 2013. https://doi.org/10.15479/AT:IST-2013-146-v1-1.","ama":"Ahmed U, Chatterjee K, Gulwani S. Automatic Generation of Alternative Starting Positions for Traditional Board Games. IST Austria; 2013. doi:10.15479/AT:IST-2013-146-v1-1","ista":"Ahmed U, Chatterjee K, Gulwani S. 2013. Automatic generation of alternative starting positions for traditional board games, IST Austria, 13p.","ieee":"U. Ahmed, K. Chatterjee, and S. Gulwani, Automatic generation of alternative starting positions for traditional board games. IST Austria, 2013.","apa":"Ahmed, U., Chatterjee, K., & Gulwani, S. (2013). Automatic generation of alternative starting positions for traditional board games. IST Austria. https://doi.org/10.15479/AT:IST-2013-146-v1-1"},"page":"13","doi":"10.15479/AT:IST-2013-146-v1-1","date_published":"2013-12-03T00:00:00Z","language":[{"iso":"eng"}],"has_accepted_license":"1","publication_identifier":{"issn":["2664-1690"]},"month":"12","day":"03"},{"abstract":[{"lang":"eng","text":"We define the model-measuring problem: given a model M and specification φ, what is the maximal distance ρ such that all models M′ within distance ρ from M satisfy (or violate) φ. The model measuring problem presupposes a distance function on models. We concentrate on automatic distance functions, which are defined by weighted automata. The model-measuring problem subsumes several generalizations of the classical model-checking problem, in particular, quantitative model-checking problems that measure the degree of satisfaction of a specification, and robustness problems that measure how much a model can be perturbed without violating the specification. We show that for automatic distance functions, and ω-regular linear-time and branching-time specifications, the model-measuring problem can be solved. We use automata-theoretic model-checking methods for model measuring, replacing the emptiness question for standard word and tree automata by the optimal-weight question for the weighted versions of these automata. We consider weighted automata that accumulate weights by maximizing, summing, discounting, and limit averaging. We give several examples of using the model-measuring problem to compute various notions of robustness and quantitative satisfaction for temporal specifications."}],"type":"conference","alternative_title":["LNCS"],"pubrep_id":"129","oa_version":"Submitted Version","file":[{"date_updated":"2020-07-14T12:45:38Z","date_created":"2018-12-12T10:17:45Z","checksum":"4c04695c4bfdf2119cd4f5d1babc3e8a","relation":"main_file","file_id":"5301","content_type":"application/pdf","file_size":378587,"creator":"system","file_name":"IST-2013-129-v1+1_concur.pdf","access_level":"open_access"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2327","status":"public","ddc":["005","000"],"title":"From model checking to model measuring","intvolume":" 8052","day":"01","has_accepted_license":"1","series_title":"Lecture Notes in Computer Science","date_published":"2013-08-01T00:00:00Z","citation":{"ista":"Henzinger TA, Otop J. 2013. From model checking to model measuring. 8052, 273–287.","ieee":"T. A. Henzinger and J. Otop, “From model checking to model measuring,” vol. 8052. Springer, pp. 273–287, 2013.","apa":"Henzinger, T. A., & Otop, J. (2013). From model checking to model measuring. Presented at the CONCUR: Concurrency Theory, Buenos Aires, Argentina: Springer. https://doi.org/10.1007/978-3-642-40184-8_20","ama":"Henzinger TA, Otop J. From model checking to model measuring. 2013;8052:273-287. doi:10.1007/978-3-642-40184-8_20","chicago":"Henzinger, Thomas A, and Jan Otop. “From Model Checking to Model Measuring.” Lecture Notes in Computer Science. Springer, 2013. https://doi.org/10.1007/978-3-642-40184-8_20.","mla":"Henzinger, Thomas A., and Jan Otop. From Model Checking to Model Measuring. Vol. 8052, Springer, 2013, pp. 273–87, doi:10.1007/978-3-642-40184-8_20.","short":"T.A. Henzinger, J. Otop, 8052 (2013) 273–287."},"page":"273 - 287","file_date_updated":"2020-07-14T12:45:38Z","publist_id":"4599","author":[{"orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A","full_name":"Henzinger, Thomas A"},{"full_name":"Otop, Jan","last_name":"Otop","first_name":"Jan","id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"id":"5417","status":"public","relation":"earlier_version"}]},"date_updated":"2023-02-23T12:25:26Z","date_created":"2018-12-11T11:57:00Z","volume":8052,"year":"2013","publication_status":"published","department":[{"_id":"ToHe"}],"publisher":"Springer","month":"08","conference":{"name":"CONCUR: Concurrency Theory","end_date":"2013-08-30","location":"Buenos Aires, Argentina","start_date":"2013-08-27"},"doi":"10.1007/978-3-642-40184-8_20","language":[{"iso":"eng"}],"oa":1,"quality_controlled":"1"},{"_id":"590","year":"2013","publication_status":"published","title":"Polarization dependent focusing","status":"public","publisher":"OSA","author":[{"full_name":"Schmid, David","first_name":"David","last_name":"Schmid"},{"first_name":"Ting","last_name":"Huang","full_name":"Huang, Ting-Yu"},{"first_name":"Radhika","last_name":"Dirks","full_name":"Dirks, Radhika"},{"full_name":"Onur Hosten","first_name":"Onur","last_name":"Hosten","id":"4C02D85E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2031-204X"},{"full_name":"Kwiat, Paul G","last_name":"Kwiat","first_name":"Paul"}],"date_updated":"2021-01-12T08:05:10Z","date_created":"2018-12-11T11:47:22Z","type":"conference","alternative_title":["Optics InfoBase Conference Papers"],"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"}],"publist_id":"7217","extern":1,"citation":{"mla":"Schmid, David, et al. Polarization Dependent Focusing. OSA, 2013, doi:10.1364/QIM.2013.W6.23.","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. https://doi.org/10.1364/QIM.2013.W6.23.","ama":"Schmid D, Huang T, Dirks R, Hosten O, Kwiat P. Polarization dependent focusing. In: OSA; 2013. doi:10.1364/QIM.2013.W6.23","ista":"Schmid D, Huang T, Dirks R, Hosten O, Kwiat P. 2013. Polarization dependent focusing. QIM: Quantum Information and Measurement, Optics InfoBase Conference Papers, .","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., & Kwiat, P. (2013). Polarization dependent focusing. Presented at the QIM: Quantum Information and Measurement, OSA. https://doi.org/10.1364/QIM.2013.W6.23"},"quality_controlled":0,"conference":{"name":"QIM: Quantum Information and Measurement"},"doi":"10.1364/QIM.2013.W6.23","date_published":"2013-01-01T00:00:00Z","month":"01","day":"01"},{"date_created":"2019-02-05T08:48:24Z","date_updated":"2021-01-12T08:05:15Z","volume":50,"oa_version":"None","author":[{"first_name":"Christopher J.","last_name":"Hillar","full_name":"Hillar, Christopher J."},{"full_name":"Martin del Campo Sanchez, Abraham","id":"4CF47F6A-F248-11E8-B48F-1D18A9856A87","last_name":"Martin del Campo Sanchez","first_name":"Abraham"}],"related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1016/j.jsc.2015.09.002"}]},"status":"public","title":"Finiteness theorems and algorithms for permutation invariant chains of Laurent lattice ideals","publication_status":"published","intvolume":" 50","publisher":"Elsevier","_id":"5920","year":"2013","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","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."}],"type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1016/j.jsc.2012.06.006","date_published":"2013-03-01T00:00:00Z","article_type":"original","quality_controlled":"1","page":"314-334","publication":"Journal of Symbolic Computation","citation":{"chicago":"Hillar, Christopher J., and Abraham Martin del Campo Sanchez. “Finiteness Theorems and Algorithms for Permutation Invariant Chains of Laurent Lattice Ideals.” Journal of Symbolic Computation. Elsevier, 2013. https://doi.org/10.1016/j.jsc.2012.06.006.","mla":"Hillar, Christopher J., and Abraham Martin del Campo Sanchez. “Finiteness Theorems and Algorithms for Permutation Invariant Chains of Laurent Lattice Ideals.” Journal of Symbolic Computation, vol. 50, Elsevier, 2013, pp. 314–34, doi:10.1016/j.jsc.2012.06.006.","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.","ieee":"C. J. Hillar and A. Martin del Campo Sanchez, “Finiteness theorems and algorithms for permutation invariant chains of Laurent lattice ideals,” Journal of Symbolic Computation, vol. 50. Elsevier, pp. 314–334, 2013.","apa":"Hillar, C. J., & Martin del Campo Sanchez, A. (2013). Finiteness theorems and algorithms for permutation invariant chains of Laurent lattice ideals. Journal of Symbolic Computation. Elsevier. https://doi.org/10.1016/j.jsc.2012.06.006","ama":"Hillar CJ, Martin del Campo Sanchez A. Finiteness theorems and algorithms for permutation invariant chains of Laurent lattice ideals. Journal of Symbolic Computation. 2013;50:314-334. doi:10.1016/j.jsc.2012.06.006"},"day":"01","month":"03","article_processing_charge":"No","publication_identifier":{"issn":["0747-7171"]}},{"volume":21,"date_updated":"2021-01-12T08:05:12Z","date_created":"2018-12-11T11:47:22Z","author":[{"full_name":"Schmid, David","first_name":"David","last_name":"Schmid"},{"last_name":"Huang","first_name":"Ting","full_name":"Huang, Ting-Yu"},{"full_name":"Hazrat, Shiraz","last_name":"Hazrat","first_name":"Shiraz"},{"full_name":"Dirks, Radhika","last_name":"Dirks","first_name":"Radhika"},{"full_name":"Onur Hosten","id":"4C02D85E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2031-204X","first_name":"Onur","last_name":"Hosten"},{"last_name":"Quint","first_name":"Stephan","full_name":"Quint, Stephan"},{"full_name":"Thian, Dickson","last_name":"Thian","first_name":"Dickson"},{"full_name":"Kwiat, Paul G","last_name":"Kwiat","first_name":"Paul"}],"intvolume":" 21","publisher":"Optical Society of America","status":"public","title":"Adjustable and robust methods for polarization-dependent focusing","publication_status":"published","_id":"591","year":"2013","extern":1,"issue":"13","publist_id":"7218","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."}],"type":"journal_article","doi":"10.1364/OE.21.015538","date_published":"2013-07-01T00:00:00Z","page":"15538 - 15552","quality_controlled":0,"citation":{"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.","apa":"Schmid, D., Huang, T., Hazrat, S., Dirks, R., Hosten, O., Quint, S., … Kwiat, P. (2013). Adjustable and robust methods for polarization-dependent focusing. Optics Express. Optical Society of America. https://doi.org/10.1364/OE.21.015538","ieee":"D. Schmid et al., “Adjustable and robust methods for polarization-dependent focusing,” Optics Express, vol. 21, no. 13. Optical Society of America, pp. 15538–15552, 2013.","ama":"Schmid D, Huang T, Hazrat S, et al. Adjustable and robust methods for polarization-dependent focusing. Optics Express. 2013;21(13):15538-15552. doi:10.1364/OE.21.015538","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.” Optics Express. Optical Society of America, 2013. https://doi.org/10.1364/OE.21.015538.","mla":"Schmid, David, et al. “Adjustable and Robust Methods for Polarization-Dependent Focusing.” Optics Express, vol. 21, no. 13, Optical Society of America, 2013, pp. 15538–52, doi:10.1364/OE.21.015538.","short":"D. Schmid, T. Huang, S. Hazrat, R. Dirks, O. Hosten, S. Quint, D. Thian, P. Kwiat, Optics Express 21 (2013) 15538–15552."},"publication":"Optics Express","day":"01","month":"07"},{"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3604726/","open_access":"1"}],"citation":{"apa":"Bernecky, C., & Cramer, P. (2013). Struggling to let go: A non-coding RNA directs its own extension and destruction. EMBO Journal. Wiley-Blackwell. https://doi.org/10.1038/emboj.2013.36","ieee":"C. Bernecky and P. Cramer, “Struggling to let go: A non-coding RNA directs its own extension and destruction,” EMBO Journal, vol. 32, no. 6. Wiley-Blackwell, pp. 771–772, 2013.","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. EMBO Journal. 2013;32(6):771-772. doi:10.1038/emboj.2013.36","chicago":"Bernecky, Carrie, and Patrick Cramer. “Struggling to Let Go: A Non-Coding RNA Directs Its Own Extension and Destruction.” EMBO Journal. Wiley-Blackwell, 2013. https://doi.org/10.1038/emboj.2013.36.","short":"C. Bernecky, P. Cramer, EMBO Journal 32 (2013) 771–772.","mla":"Bernecky, Carrie, and Patrick Cramer. “Struggling to Let Go: A Non-Coding RNA Directs Its Own Extension and Destruction.” EMBO Journal, vol. 32, no. 6, Wiley-Blackwell, 2013, pp. 771–72, doi:10.1038/emboj.2013.36."},"oa":1,"publication":"EMBO Journal","page":"771 - 772","date_published":"2013-03-20T00:00:00Z","doi":"10.1038/emboj.2013.36","language":[{"iso":"eng"}],"article_processing_charge":"No","month":"03","day":"20","_id":"595","year":"2013","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 32","publisher":"Wiley-Blackwell","publication_status":"published","title":"Struggling to let go: A non-coding RNA directs its own extension and destruction","status":"public","author":[{"full_name":"Bernecky, Carrie A","orcid":"0000-0003-0893-7036","id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87","last_name":"Bernecky","first_name":"Carrie A"},{"full_name":"Cramer, Patrick","first_name":"Patrick","last_name":"Cramer"}],"oa_version":"None","volume":32,"date_updated":"2021-01-12T08:05:20Z","date_created":"2018-12-11T11:47:23Z","type":"journal_article","publist_id":"7207","issue":"6","extern":"1"},{"intvolume":" 9","title":"Cross-modulation of homeostatic responses to temperature, oxygen and carbon dioxide in C. elegans","ddc":["570"],"status":"public","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"6128","file":[{"checksum":"299b6321be79931c7c17c5db6e69c711","date_updated":"2020-07-14T12:47:20Z","date_created":"2019-03-19T15:14:51Z","relation":"main_file","file_id":"6129","file_size":4499039,"content_type":"application/pdf","creator":"kschuh","access_level":"open_access","file_name":"2013_PLOS_Kodama-Namba.PDF"}],"oa_version":"Published Version","type":"journal_article","issue":"12","abstract":[{"lang":"eng","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."}],"citation":{"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. PLoS Genetics. 2013;9(12). doi:10.1371/journal.pgen.1004011","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.","apa":"Kodama-Namba, E., Fenk, L. A., Bretscher, A. J., Gross, E., Busch, K. E., & de Bono, M. (2013). Cross-modulation of homeostatic responses to temperature, oxygen and carbon dioxide in C. elegans. PLoS Genetics. Public Library of Science (PLoS). https://doi.org/10.1371/journal.pgen.1004011","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,” PLoS Genetics, vol. 9, no. 12. Public Library of Science (PLoS), 2013.","mla":"Kodama-Namba, Eiji, et al. “Cross-Modulation of Homeostatic Responses to Temperature, Oxygen and Carbon Dioxide in C. Elegans.” PLoS Genetics, vol. 9, no. 12, e1004011, Public Library of Science (PLoS), 2013, doi:10.1371/journal.pgen.1004011.","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.” PLoS Genetics. Public Library of Science (PLoS), 2013. https://doi.org/10.1371/journal.pgen.1004011."},"publication":"PLoS Genetics","date_published":"2013-12-19T00:00:00Z","has_accepted_license":"1","day":"19","publisher":"Public Library of Science (PLoS)","publication_status":"published","pmid":1,"year":"2013","volume":9,"date_created":"2019-03-19T14:58:51Z","date_updated":"2021-01-12T08:06:15Z","author":[{"full_name":"Kodama-Namba, Eiji","first_name":"Eiji","last_name":"Kodama-Namba"},{"full_name":"Fenk, Lorenz A.","first_name":"Lorenz A.","last_name":"Fenk"},{"full_name":"Bretscher, Andrew J.","last_name":"Bretscher","first_name":"Andrew J."},{"last_name":"Gross","first_name":"Einav","full_name":"Gross, Einav"},{"first_name":"K. Emanuel","last_name":"Busch","full_name":"Busch, K. Emanuel"},{"full_name":"de Bono, Mario","last_name":"de Bono","first_name":"Mario","orcid":"0000-0001-8347-0443","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87"}],"article_number":"e1004011","extern":"1","license":"https://creativecommons.org/licenses/by/4.0/","file_date_updated":"2020-07-14T12:47:20Z","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["24385919"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1371/journal.pgen.1004011","publication_identifier":{"issn":["1553-7404"]},"month":"12"},{"publisher":"Oxford University Press","publication_status":"published","pmid":1,"year":"2013","volume":41,"date_created":"2019-03-19T15:17:40Z","date_updated":"2021-01-12T08:06:16Z","author":[{"full_name":"Chen, Changchun","first_name":"Changchun","last_name":"Chen"},{"last_name":"Fenk","first_name":"Lorenz A.","full_name":"Fenk, Lorenz A."},{"first_name":"Mario","last_name":"de Bono","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8347-0443","full_name":"de Bono, Mario"}],"article_number":"e193","extern":"1","file_date_updated":"2020-07-14T12:47:20Z","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"pmid":["24013562"]},"language":[{"iso":"eng"}],"doi":"10.1093/nar/gkt805","publication_identifier":{"issn":["1362-4962","0305-1048"]},"month":"11","intvolume":" 41","ddc":["570"],"title":"Efficient genome editing in Caenorhabditis elegans by CRISPR-targeted homologous recombination","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"6130","file":[{"file_id":"6131","relation":"main_file","checksum":"0f1f127cefd043cb922b292e1cd16f02","date_created":"2019-03-19T15:25:42Z","date_updated":"2020-07-14T12:47:20Z","access_level":"open_access","file_name":"2013_OUP_Chen.pdf","creator":"kschuh","content_type":"application/pdf","file_size":340225}],"oa_version":"Published Version","type":"journal_article","issue":"20","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"}],"citation":{"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.” Nucleic Acids Research, vol. 41, no. 20, e193, Oxford University Press, 2013, doi:10.1093/nar/gkt805.","chicago":"Chen, Changchun, Lorenz A. Fenk, and Mario de Bono. “Efficient Genome Editing in Caenorhabditis Elegans by CRISPR-Targeted Homologous Recombination.” Nucleic Acids Research. Oxford University Press, 2013. https://doi.org/10.1093/nar/gkt805.","ama":"Chen C, Fenk LA, de Bono M. Efficient genome editing in Caenorhabditis elegans by CRISPR-targeted homologous recombination. Nucleic Acids Research. 2013;41(20). doi:10.1093/nar/gkt805","apa":"Chen, C., Fenk, L. A., & de Bono, M. (2013). Efficient genome editing in Caenorhabditis elegans by CRISPR-targeted homologous recombination. Nucleic Acids Research. Oxford University Press. https://doi.org/10.1093/nar/gkt805","ieee":"C. Chen, L. A. Fenk, and M. de Bono, “Efficient genome editing in Caenorhabditis elegans by CRISPR-targeted homologous recombination,” Nucleic Acids Research, vol. 41, no. 20. Oxford University Press, 2013.","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."},"publication":"Nucleic Acids Research","date_published":"2013-11-01T00:00:00Z","has_accepted_license":"1","day":"01"},{"month":"08","publication_identifier":{"issn":["0027-8424","1091-6490"]},"language":[{"iso":"eng"}],"doi":"10.1073/pnas.1217428110","quality_controlled":"1","external_id":{"pmid":["23940325"]},"oa":1,"extern":"1","file_date_updated":"2020-07-14T12:47:20Z","date_updated":"2021-01-12T08:06:16Z","date_created":"2019-03-20T14:05:06Z","volume":110,"author":[{"last_name":"Couto","first_name":"A.","full_name":"Couto, A."},{"full_name":"Oda, S.","last_name":"Oda","first_name":"S."},{"last_name":"Nikolaev","first_name":"V. O.","full_name":"Nikolaev, V. O."},{"full_name":"Soltesz, Z.","first_name":"Z.","last_name":"Soltesz"},{"full_name":"de Bono, Mario","orcid":"0000-0001-8347-0443","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","last_name":"de Bono","first_name":"Mario"}],"publication_status":"published","publisher":"Proceedings of the National Academy of Sciences","year":"2013","pmid":1,"day":"27","has_accepted_license":"1","date_published":"2013-08-27T00:00:00Z","page":"E3301-E3310","publication":"Proceedings of the National Academy of Sciences","citation":{"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.” Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences, 2013. https://doi.org/10.1073/pnas.1217428110.","short":"A. Couto, S. Oda, V.O. Nikolaev, Z. Soltesz, M. de Bono, Proceedings of the National Academy of Sciences 110 (2013) E3301–E3310.","mla":"Couto, A., et al. “In Vivo Genetic Dissection of O2-Evoked CGMP Dynamics in a Caenorhabditis Elegans Gas Sensor.” Proceedings of the National Academy of Sciences, vol. 110, no. 35, Proceedings of the National Academy of Sciences, 2013, pp. E3301–10, doi:10.1073/pnas.1217428110.","apa":"Couto, A., Oda, S., Nikolaev, V. O., 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. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1217428110","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,” Proceedings of the National Academy of Sciences, 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.","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. Proceedings of the National Academy of Sciences. 2013;110(35):E3301-E3310. doi:10.1073/pnas.1217428110"},"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."}],"issue":"35","type":"journal_article","file":[{"file_id":"6134","relation":"main_file","date_created":"2019-03-20T14:07:53Z","date_updated":"2020-07-14T12:47:20Z","checksum":"3ee28a694f74a49f0d098970ae391a91","file_name":"2013_PNAS_Couto.pdf","access_level":"open_access","creator":"kschuh","content_type":"application/pdf","file_size":2198763}],"oa_version":"Published Version","status":"public","ddc":["570"],"title":"In vivo genetic dissection of O2-evoked cGMP dynamics in a Caenorhabditis elegans gas sensor","intvolume":" 110","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"6133"},{"extern":"1","issue":"6","abstract":[{"lang":"eng","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."}],"type":"journal_article","volume":29,"oa_version":"None","date_updated":"2021-01-12T08:06:17Z","date_created":"2019-03-20T14:17:42Z","author":[{"full_name":"Rodriguez, Miriam","last_name":"Rodriguez","first_name":"Miriam"},{"first_name":"L. Basten","last_name":"Snoek","full_name":"Snoek, L. Basten"},{"last_name":"de Bono","first_name":"Mario","orcid":"0000-0001-8347-0443","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","full_name":"de Bono, Mario"},{"full_name":"Kammenga, Jan E.","last_name":"Kammenga","first_name":"Jan E."}],"intvolume":" 29","publisher":"Elsevier","publication_status":"published","status":"public","title":"Worms under stress: C. elegans stress response and its relevance to complex human disease and aging","year":"2013","_id":"6135","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["0168-9525"]},"day":"01","month":"06","language":[{"iso":"eng"}],"doi":"10.1016/j.tig.2013.01.010","date_published":"2013-06-01T00:00:00Z","page":"367-374","quality_controlled":"1","citation":{"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.” Trends in Genetics. Elsevier, 2013. https://doi.org/10.1016/j.tig.2013.01.010.","mla":"Rodriguez, Miriam, et al. “Worms under Stress: C. Elegans Stress Response and Its Relevance to Complex Human Disease and Aging.” Trends in Genetics, vol. 29, no. 6, Elsevier, 2013, pp. 367–74, doi:10.1016/j.tig.2013.01.010.","short":"M. Rodriguez, L.B. Snoek, M. de Bono, J.E. Kammenga, Trends in Genetics 29 (2013) 367–374.","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.","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,” Trends in Genetics, vol. 29, no. 6. Elsevier, pp. 367–374, 2013.","apa":"Rodriguez, M., Snoek, L. B., de Bono, M., & Kammenga, J. E. (2013). Worms under stress: C. elegans stress response and its relevance to complex human disease and aging. Trends in Genetics. Elsevier. https://doi.org/10.1016/j.tig.2013.01.010","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. Trends in Genetics. 2013;29(6):367-374. doi:10.1016/j.tig.2013.01.010"},"publication":"Trends in Genetics"},{"extern":"1","type":"book_chapter","author":[{"first_name":"Mario","last_name":"de Bono","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8347-0443","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."}],"oa_version":"None","date_updated":"2021-01-12T08:06:16Z","date_created":"2019-03-20T13:54:05Z","year":"2013","_id":"6132","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publisher":"Walter de Gruyter","editor":[{"last_name":"Hegemann","first_name":"Peter","full_name":"Hegemann, Peter"},{"first_name":"Stephan","last_name":"Sigrist","full_name":"Sigrist, Stephan"}],"title":"Optogenetic actuation, inhibition, modulation and readout for neuronal networks generating behavior in the nematode Caenorhabditis elegans","publication_status":"published","status":"public","publication_identifier":{"isbn":["9783110270723; 9783110270716"]},"month":"08","day":"28","date_published":"2013-08-28T00:00:00Z","language":[{"iso":"eng"}],"citation":{"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.","apa":"de Bono, M., Schafer, W. R., & Gottschalk, A. (2013). Optogenetic actuation, inhibition, modulation and readout for neuronal networks generating behavior in the nematode Caenorhabditis elegans. In P. Hegemann & S. Sigrist (Eds.), Optogenetics (pp. 61–78). Walter de Gruyter.","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 Optogenetics, P. Hegemann and S. Sigrist, Eds. Walter de Gruyter, 2013, pp. 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. Optogenetics. Walter de Gruyter; 2013:61-78.","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 Optogenetics, edited by Peter Hegemann and Stephan Sigrist, 61–78. Walter de Gruyter, 2013.","mla":"de Bono, Mario, et al. “Optogenetic Actuation, Inhibition, Modulation and Readout for Neuronal Networks Generating Behavior in the Nematode Caenorhabditis Elegans.” Optogenetics, edited by Peter Hegemann and Stephan Sigrist, Walter de Gruyter, 2013, pp. 61–78.","short":"M. de Bono, W.R. Schafer, A. Gottschalk, in:, P. Hegemann, S. Sigrist (Eds.), Optogenetics, Walter de Gruyter, 2013, pp. 61–78."},"publication":"Optogenetics","page":"61-78","quality_controlled":"1"},{"author":[{"first_name":"Tze-Chia","last_name":"Lin","full_name":"Lin, Tze-Chia"},{"full_name":"Cole, Jacqueline M.","first_name":"Jacqueline M.","last_name":"Cole"},{"last_name":"Higginbotham","first_name":"Andrew P","orcid":"0000-0003-2607-2363","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","full_name":"Higginbotham, Andrew P"},{"full_name":"Edwards, Alison J.","last_name":"Edwards","first_name":"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"},{"full_name":"Clays, Koen","first_name":"Koen","last_name":"Clays"},{"first_name":"O-Pil","last_name":"Kwon","full_name":"Kwon, O-Pil"}],"date_created":"2019-05-03T09:40:31Z","date_updated":"2021-01-12T08:07:17Z","volume":117,"oa_version":"None","_id":"6370","year":"2013","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publication_status":"published","title":"Molecular origins of the high-performance nonlinear optical susceptibility in a phenolic polyene chromophore: Electron density distributions, hydrogen bonding, and ab initio calculations","status":"public","publisher":"American Chemical Society (ACS)","intvolume":" 117","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"}],"issue":"18","extern":"1","type":"journal_article","date_published":"2013-05-09T00:00:00Z","doi":"10.1021/jp400648q","language":[{"iso":"eng"}],"publication":"The Journal of Physical Chemistry C","citation":{"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.” The Journal of Physical Chemistry C, vol. 117, no. 18, American Chemical Society (ACS), 2013, pp. 9416–30, doi:10.1021/jp400648q.","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.” The Journal of Physical Chemistry C. American Chemical Society (ACS), 2013. https://doi.org/10.1021/jp400648q.","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. The Journal of Physical Chemistry C. 2013;117(18):9416-9430. doi:10.1021/jp400648q","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.","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. The Journal of Physical Chemistry C. American Chemical Society (ACS). https://doi.org/10.1021/jp400648q","ieee":"T.-C. Lin 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,” The Journal of Physical Chemistry C, vol. 117, no. 18. American Chemical Society (ACS), pp. 9416–9430, 2013."},"quality_controlled":"1","page":"9416-9430","day":"09","month":"05","publication_identifier":{"issn":["1932-7447","1932-7455"]}},{"citation":{"chicago":"Henzinger, Thomas A, Hannes Payer, and Ali Sezgin. Replacing Competition with Cooperation to Achieve Scalable Lock-Free FIFO Queues . IST Austria, 2013. https://doi.org/10.15479/AT:IST-2013-124-v1-1.","short":"T.A. Henzinger, H. Payer, A. Sezgin, Replacing Competition with Cooperation to Achieve Scalable Lock-Free FIFO Queues , IST Austria, 2013.","mla":"Henzinger, Thomas A., et al. Replacing Competition with Cooperation to Achieve Scalable Lock-Free FIFO Queues . IST Austria, 2013, doi:10.15479/AT:IST-2013-124-v1-1.","ieee":"T. A. Henzinger, H. Payer, and A. Sezgin, Replacing competition with cooperation to achieve scalable lock-free FIFO queues . IST Austria, 2013.","apa":"Henzinger, T. A., Payer, H., & Sezgin, A. (2013). Replacing competition with cooperation to achieve scalable lock-free FIFO queues . IST Austria. https://doi.org/10.15479/AT:IST-2013-124-v1-1","ista":"Henzinger TA, Payer H, Sezgin A. 2013. Replacing competition with cooperation to achieve scalable lock-free FIFO queues , IST Austria, 23p.","ama":"Henzinger TA, Payer H, Sezgin A. Replacing Competition with Cooperation to Achieve Scalable Lock-Free FIFO Queues . IST Austria; 2013. doi:10.15479/AT:IST-2013-124-v1-1"},"oa":1,"page":"23","doi":"10.15479/AT:IST-2013-124-v1-1","date_published":"2013-06-13T00:00:00Z","language":[{"iso":"eng"}],"month":"06","day":"13","publication_identifier":{"issn":["2664-1690"]},"has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"6440","year":"2013","title":"Replacing competition with cooperation to achieve scalable lock-free FIFO queues ","ddc":["000","005"],"publication_status":"published","status":"public","publisher":"IST Austria","department":[{"_id":"ToHe"}],"author":[{"full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","first_name":"Thomas A","last_name":"Henzinger"},{"full_name":"Payer, Hannes","first_name":"Hannes","last_name":"Payer"},{"full_name":"Sezgin, Ali","last_name":"Sezgin","first_name":"Ali","id":"4C7638DA-F248-11E8-B48F-1D18A9856A87"}],"pubrep_id":"124","date_created":"2019-05-13T14:13:27Z","date_updated":"2020-07-14T23:06:19Z","oa_version":"Published Version","file":[{"file_name":"2013_TechRep_Henzinger.pdf","access_level":"open_access","content_type":"application/pdf","file_size":549684,"creator":"dernst","relation":"main_file","file_id":"6441","date_created":"2019-05-13T14:11:39Z","date_updated":"2020-07-14T12:47:30Z","checksum":"a219ba4eada6cd62befed52262ee15d4"}],"type":"technical_report","alternative_title":["IST Austria Technical Report"],"file_date_updated":"2020-07-14T12:47:30Z","abstract":[{"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.","lang":"eng"}]},{"file_date_updated":"2020-07-14T12:47:40Z","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","extern":"1","year":"2013","publication_status":"published","publisher":"Image Processing On Line","author":[{"first_name":"Marco","last_name":"Mondelli","id":"27EB676C-8706-11E9-9510-7717E6697425","orcid":"0000-0002-3242-7020","full_name":"Mondelli, Marco"}],"date_updated":"2021-01-12T08:08:56Z","date_created":"2019-08-05T12:30:38Z","volume":3,"month":"07","publication_identifier":{"issn":["2105-1232"]},"oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)"},"quality_controlled":"1","doi":"10.5201/ipol.2013.53","language":[{"iso":"eng"}],"type":"journal_article","abstract":[{"lang":"eng","text":"The paper presents an algorithm that applies a stack filter simulating the Mean Curvature Motion equation via a finite difference scheme."}],"_id":"6768","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"A finite difference scheme for the stack filter simulating the MCM","status":"public","ddc":["510"],"intvolume":" 3","oa_version":"Published Version","file":[{"file_id":"6769","relation":"main_file","date_updated":"2020-07-14T12:47:40Z","date_created":"2019-08-05T12:33:40Z","checksum":"83b7d429bc248c6c461229d3504fb139","file_name":"2013_IPOL_Mondelli.pdf","access_level":"open_access","creator":"dernst","file_size":4306158,"content_type":"application/pdf"}],"day":"11","has_accepted_license":"1","publication":"Image Processing On Line","citation":{"chicago":"Mondelli, Marco. “A Finite Difference Scheme for the Stack Filter Simulating the MCM.” Image Processing On Line. Image Processing On Line, 2013. https://doi.org/10.5201/ipol.2013.53.","mla":"Mondelli, Marco. “A Finite Difference Scheme for the Stack Filter Simulating the MCM.” Image Processing On Line, vol. 3, Image Processing On Line, 2013, pp. 68–111, doi:10.5201/ipol.2013.53.","short":"M. Mondelli, Image Processing On Line 3 (2013) 68–111.","ista":"Mondelli M. 2013. A finite difference scheme for the stack filter simulating the MCM. Image Processing On Line. 3, 68–111.","ieee":"M. Mondelli, “A finite difference scheme for the stack filter simulating the MCM,” Image Processing On Line, vol. 3. Image Processing On Line, pp. 68–111, 2013.","apa":"Mondelli, M. (2013). A finite difference scheme for the stack filter simulating the MCM. Image Processing On Line. Image Processing On Line. https://doi.org/10.5201/ipol.2013.53","ama":"Mondelli M. A finite difference scheme for the stack filter simulating the MCM. Image Processing On Line. 2013;3:68-111. doi:10.5201/ipol.2013.53"},"article_type":"original","page":"68-111","date_published":"2013-07-11T00:00:00Z"},{"scopus_import":1,"series_title":"Lecture Notes in Computer Science","day":"01","citation":{"chicago":"Chatterjee, Krishnendu, and Yaron Velner. “Hyperplane Separation Technique for Multidimensional Mean-Payoff Games.” Lecture Notes in Computer Science. Springer, 2013. https://doi.org/10.1007/978-3-642-40184-8_35.","short":"K. Chatterjee, Y. Velner, 8052 (2013) 500–515.","mla":"Chatterjee, Krishnendu, and Yaron Velner. Hyperplane Separation Technique for Multidimensional Mean-Payoff Games. Vol. 8052, Springer, 2013, pp. 500–15, doi:10.1007/978-3-642-40184-8_35.","ieee":"K. Chatterjee and Y. Velner, “Hyperplane separation technique for multidimensional mean-payoff games,” vol. 8052. Springer, pp. 500–515, 2013.","apa":"Chatterjee, K., & Velner, Y. (2013). Hyperplane separation technique for multidimensional mean-payoff games. Presented at the CONCUR: Concurrency Theory, Buenos Aires, Argentinia: Springer. https://doi.org/10.1007/978-3-642-40184-8_35","ista":"Chatterjee K, Velner Y. 2013. Hyperplane separation technique for multidimensional mean-payoff games. 8052, 500–515.","ama":"Chatterjee K, Velner Y. Hyperplane separation technique for multidimensional mean-payoff games. 2013;8052:500-515. doi:10.1007/978-3-642-40184-8_35"},"page":"500 - 515","date_published":"2013-08-01T00:00:00Z","type":"conference","alternative_title":["LNCS"],"abstract":[{"text":"Two-player games on graphs are central in many problems in formal verification and program analysis such as synthesis and verification of open systems. In this work, we consider both finite-state game graphs, and recursive game graphs (or pushdown game graphs) that model the control flow of sequential programs with recursion. The objectives we study are multidimensional mean-payoff objectives, where the goal of player 1 is to ensure that the mean-payoff is non-negative in all dimensions. In pushdown games two types of strategies are relevant: (1) global strategies, that depend on the entire global history; and (2) modular strategies, that have only local memory and thus do not depend on the context of invocation. Our main contributions are as follows: (1) We show that finite-state multidimensional mean-payoff games can be solved in polynomial time if the number of dimensions and the maximal absolute value of the weights are fixed; whereas if the number of dimensions is arbitrary, then the problem is known to be coNP-complete. (2) We show that pushdown graphs with multidimensional mean-payoff objectives can be solved in polynomial time. For both (1) and (2) our algorithms are based on hyperplane separation technique. (3) For pushdown games under global strategies both one and multidimensional mean-payoff objectives problems are known to be undecidable, and we show that under modular strategies the multidimensional problem is also undecidable; under modular strategies the one-dimensional problem is NP-complete. We show that if the number of modules, the number of exits, and the maximal absolute value of the weights are fixed, then pushdown games under modular strategies with one-dimensional mean-payoff objectives can be solved in polynomial time, and if either the number of exits or the number of modules is unbounded, then the problem is NP-hard. (4) Finally we show that a fixed parameter tractable algorithm for finite-state multidimensional mean-payoff games or pushdown games under modular strategies with one-dimensional mean-payoff objectives would imply the fixed parameter tractability of parity games.","lang":"eng"}],"_id":"2329","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Hyperplane separation technique for multidimensional mean-payoff games","status":"public","intvolume":" 8052","oa_version":"Preprint","month":"08","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1210.3141"}],"oa":1,"external_id":{"arxiv":["1210.3141"]},"quality_controlled":"1","project":[{"grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory","call_identifier":"FWF"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"conference":{"end_date":"2013-08-30","start_date":"2013-08-27","location":"Buenos Aires, Argentinia","name":"CONCUR: Concurrency Theory"},"doi":"10.1007/978-3-642-40184-8_35","language":[{"iso":"eng"}],"ec_funded":1,"publist_id":"4597","year":"2013","publication_status":"published","publisher":"Springer","department":[{"_id":"KrCh"}],"author":[{"last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"},{"last_name":"Velner","first_name":"Yaron","full_name":"Velner, Yaron"}],"related_material":{"record":[{"id":"717","status":"public","relation":"later_version"}]},"date_created":"2018-12-11T11:57:01Z","date_updated":"2023-02-23T13:00:42Z","volume":8052},{"publication":"Nature Materials","citation":{"ama":"Ottakam Thotiyl MM, Freunberger SA, Peng Z, Chen Y, Liu Z, Bruce PG. A stable cathode for the aprotic Li–O2 battery. Nature Materials. 2013;12(11):1050-1056. doi:10.1038/nmat3737","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,” Nature Materials, vol. 12, no. 11. Springer Nature, pp. 1050–1056, 2013.","apa":"Ottakam Thotiyl, M. M., Freunberger, S. A., Peng, Z., Chen, Y., Liu, Z., & Bruce, P. G. (2013). A stable cathode for the aprotic Li–O2 battery. Nature Materials. Springer Nature. https://doi.org/10.1038/nmat3737","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.","mla":"Ottakam Thotiyl, Muhammed M., et al. “A Stable Cathode for the Aprotic Li–O2 Battery.” Nature Materials, vol. 12, no. 11, Springer Nature, 2013, pp. 1050–56, doi:10.1038/nmat3737.","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.” Nature Materials. Springer Nature, 2013. https://doi.org/10.1038/nmat3737."},"article_type":"original","quality_controlled":"1","page":"1050-1056","date_published":"2013-09-01T00:00:00Z","doi":"10.1038/nmat3737","language":[{"iso":"eng"}],"day":"01","month":"09","article_processing_charge":"No","publication_identifier":{"issn":["1476-1122","1476-4660"]},"year":"2013","_id":"7306","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"A stable cathode for the aprotic Li–O2 battery","publication_status":"published","intvolume":" 12","publisher":"Springer Nature","author":[{"full_name":"Ottakam Thotiyl, Muhammed M.","last_name":"Ottakam Thotiyl","first_name":"Muhammed M."},{"last_name":"Freunberger","first_name":"Stefan Alexander","orcid":"0000-0003-2902-5319","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","full_name":"Freunberger, Stefan Alexander"},{"full_name":"Peng, Zhangquan","last_name":"Peng","first_name":"Zhangquan"},{"first_name":"Yuhui","last_name":"Chen","full_name":"Chen, Yuhui"},{"full_name":"Liu, Zheng","first_name":"Zheng","last_name":"Liu"},{"first_name":"Peter G.","last_name":"Bruce","full_name":"Bruce, Peter G."}],"date_updated":"2021-01-12T08:12:55Z","date_created":"2020-01-15T12:18:29Z","oa_version":"None","volume":12,"type":"journal_article","abstract":[{"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.","lang":"eng"}],"issue":"11","extern":"1"},{"day":"12","month":"05","article_processing_charge":"No","publication_identifier":{"issn":["1755-4330","1755-4349"]},"quality_controlled":"1","article_type":"original","page":"489-494","publication":"Nature Chemistry","citation":{"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.” Nature Chemistry, vol. 5, no. 6, Springer Nature, 2013, pp. 489–94, doi:10.1038/nchem.1646.","chicago":"Chen, Yuhui, Stefan Alexander Freunberger, Zhangquan Peng, Olivier Fontaine, and Peter G. Bruce. “Charging a Li–O2 Battery Using a Redox Mediator.” Nature Chemistry. Springer Nature, 2013. https://doi.org/10.1038/nchem.1646.","ama":"Chen Y, Freunberger SA, Peng Z, Fontaine O, Bruce PG. Charging a Li–O2 battery using a redox mediator. Nature Chemistry. 2013;5(6):489-494. doi:10.1038/nchem.1646","ieee":"Y. Chen, S. A. Freunberger, Z. Peng, O. Fontaine, and P. G. Bruce, “Charging a Li–O2 battery using a redox mediator,” Nature Chemistry, vol. 5, no. 6. Springer Nature, pp. 489–494, 2013.","apa":"Chen, Y., Freunberger, S. A., Peng, Z., Fontaine, O., & Bruce, P. G. (2013). Charging a Li–O2 battery using a redox mediator. Nature Chemistry. Springer Nature. https://doi.org/10.1038/nchem.1646","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."},"language":[{"iso":"eng"}],"doi":"10.1038/nchem.1646","date_published":"2013-05-12T00:00:00Z","type":"journal_article","extern":"1","abstract":[{"lang":"eng","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."}],"issue":"6","publication_status":"published","title":"Charging a Li–O2 battery using a redox mediator","status":"public","publisher":"Springer Nature","intvolume":" 5","year":"2013","_id":"7307","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T08:12:56Z","date_created":"2020-01-15T12:18:43Z","oa_version":"None","volume":5,"author":[{"last_name":"Chen","first_name":"Yuhui","full_name":"Chen, Yuhui"},{"orcid":"0000-0003-2902-5319","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","last_name":"Freunberger","first_name":"Stefan Alexander","full_name":"Freunberger, Stefan Alexander"},{"first_name":"Zhangquan","last_name":"Peng","full_name":"Peng, Zhangquan"},{"last_name":"Fontaine","first_name":"Olivier","full_name":"Fontaine, Olivier"},{"full_name":"Bruce, Peter G.","first_name":"Peter G.","last_name":"Bruce"}]},{"issue":"7","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"}],"type":"journal_article","oa_version":"None","_id":"7596","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 25","status":"public","title":"Arabidopsis casein kinase1 proteins CK1.3 and CK1.4 phosphorylate cryptochrome2 to regulate blue light signaling","article_processing_charge":"No","day":"26","date_published":"2013-08-26T00:00:00Z","citation":{"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. The Plant Cell. 2013;25(7):2618-2632. doi:10.1105/tpc.113.114322","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.","apa":"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. American Society of Plant Biologists. https://doi.org/10.1105/tpc.113.114322","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,” The Plant Cell, 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.” The Plant Cell, vol. 25, no. 7, American Society of Plant Biologists, 2013, pp. 2618–32, doi:10.1105/tpc.113.114322.","short":"S. Tan, C. Dai, H.-T. Liu, H.-W. Xue, The Plant Cell 25 (2013) 2618–2632.","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.” The Plant Cell. American Society of Plant Biologists, 2013. https://doi.org/10.1105/tpc.113.114322."},"publication":"The Plant Cell","page":"2618-2632","article_type":"original","extern":"1","author":[{"id":"2DE75584-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0471-8285","first_name":"Shutang","last_name":"Tan","full_name":"Tan, Shutang"},{"first_name":"C.","last_name":"Dai","full_name":"Dai, C."},{"last_name":"Liu","first_name":"H.-T.","full_name":"Liu, H.-T."},{"first_name":"H.-W.","last_name":"Xue","full_name":"Xue, H.-W."}],"volume":25,"date_updated":"2021-01-12T08:14:24Z","date_created":"2020-03-21T16:06:55Z","pmid":1,"year":"2013","publisher":"American Society of Plant Biologists","publication_status":"published","publication_identifier":{"issn":["1040-4651","1532-298X"]},"month":"08","doi":"10.1105/tpc.113.114322","language":[{"iso":"eng"}],"external_id":{"pmid":["23897926"]},"quality_controlled":"1"},{"oa_version":"None","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"7595","intvolume":" 45","status":"public","title":"Arabidopsis inositol 1,3,4-trisphosphate 5/6 kinase 2 is required for seed coat development","issue":"7","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."}],"type":"journal_article","date_published":"2013-07-01T00:00:00Z","citation":{"short":"Y. Tang, S. Tan, H. Xue, Acta Biochimica et Biophysica Sinica 45 (2013) 549–560.","mla":"Tang, Yong, et al. “Arabidopsis Inositol 1,3,4-Trisphosphate 5/6 Kinase 2 Is Required for Seed Coat Development.” Acta Biochimica et Biophysica Sinica, vol. 45, no. 7, Oxford University Press, 2013, pp. 549–60, doi:10.1093/abbs/gmt039.","chicago":"Tang, Yong, Shutang Tan, and Hongwei Xue. “Arabidopsis Inositol 1,3,4-Trisphosphate 5/6 Kinase 2 Is Required for Seed Coat Development.” Acta Biochimica et Biophysica Sinica. Oxford University Press, 2013. https://doi.org/10.1093/abbs/gmt039.","ama":"Tang Y, Tan S, Xue H. Arabidopsis inositol 1,3,4-trisphosphate 5/6 kinase 2 is required for seed coat development. Acta Biochimica et Biophysica Sinica. 2013;45(7):549-560. doi:10.1093/abbs/gmt039","ieee":"Y. Tang, S. Tan, and H. Xue, “Arabidopsis inositol 1,3,4-trisphosphate 5/6 kinase 2 is required for seed coat development,” Acta Biochimica et Biophysica Sinica, vol. 45, no. 7. Oxford University Press, pp. 549–560, 2013.","apa":"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. Oxford University Press. https://doi.org/10.1093/abbs/gmt039","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."},"publication":"Acta Biochimica et Biophysica Sinica","page":"549-560","article_type":"original","article_processing_charge":"No","day":"01","author":[{"first_name":"Yong","last_name":"Tang","full_name":"Tang, Yong"},{"full_name":"Tan, Shutang","first_name":"Shutang","last_name":"Tan","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0471-8285"},{"full_name":"Xue, Hongwei","last_name":"Xue","first_name":"Hongwei"}],"volume":45,"date_updated":"2021-01-12T08:14:23Z","date_created":"2020-03-21T16:06:36Z","pmid":1,"year":"2013","publisher":"Oxford University Press","publication_status":"published","extern":"1","doi":"10.1093/abbs/gmt039","language":[{"iso":"eng"}],"external_id":{"pmid":["23595027"]},"quality_controlled":"1","publication_identifier":{"issn":["1745-7270","1672-9145"]},"month":"07"},{"month":"01","day":"01","article_processing_charge":"No","citation":{"chicago":"Alistarh, Dan-Adrian, James Aspnes, George Giakkoupis, and Philipp Woelfel. “Randomized Loose Renaming in O(Loglogn) Time,” 200–209. ACM, 2013. https://doi.org/10.1145/2484239.2484240.","short":"D.-A. Alistarh, J. Aspnes, G. Giakkoupis, P. Woelfel, in:, ACM, 2013, pp. 200–209.","mla":"Alistarh, Dan-Adrian, et al. Randomized Loose Renaming in O(Loglogn) Time. ACM, 2013, pp. 200–09, doi:10.1145/2484239.2484240.","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.","apa":"Alistarh, D.-A., Aspnes, J., Giakkoupis, G., & Woelfel, P. (2013). Randomized loose renaming in O(loglogn) time (pp. 200–209). Presented at the PODC: Principles of Distributed Computing, ACM. https://doi.org/10.1145/2484239.2484240","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.","ama":"Alistarh D-A, Aspnes J, Giakkoupis G, Woelfel P. Randomized loose renaming in O(loglogn) time. In: ACM; 2013:200-209. doi:10.1145/2484239.2484240"},"page":"200 - 209","conference":{"name":"PODC: Principles of Distributed Computing"},"date_published":"2013-01-01T00:00:00Z","doi":"10.1145/2484239.2484240","language":[{"iso":"eng"}],"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"}],"publist_id":"6889","extern":"1","_id":"765","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.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2013","title":"Randomized loose renaming in O(loglogn) time","publication_status":"published","status":"public","publisher":"ACM","author":[{"last_name":"Alistarh","first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","full_name":"Alistarh, Dan-Adrian"},{"full_name":"Aspnes, James","last_name":"Aspnes","first_name":"James"},{"full_name":"Giakkoupis, George","last_name":"Giakkoupis","first_name":"George"},{"full_name":"Woelfel, Philipp","first_name":"Philipp","last_name":"Woelfel"}],"date_created":"2018-12-11T11:48:23Z","date_updated":"2023-02-23T13:13:14Z","oa_version":"None"},{"date_created":"2020-04-30T11:00:15Z","date_updated":"2021-01-12T08:15:14Z","volume":22,"oa_version":"None","author":[{"full_name":"Robinson, Matthew Richard","orcid":"0000-0001-8982-8813","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","last_name":"Robinson","first_name":"Matthew Richard"},{"full_name":"Santure, Anna W.","first_name":"Anna W.","last_name":"Santure"},{"full_name":"DeCauwer, Isabelle","last_name":"DeCauwer","first_name":"Isabelle"},{"full_name":"Sheldon, Ben C.","last_name":"Sheldon","first_name":"Ben C."},{"first_name":"Jon","last_name":"Slate","full_name":"Slate, Jon"}],"publication_status":"published","status":"public","title":"Partitioning of genetic variation across the genome using multimarker methods in a wild bird population","publisher":"Wiley","intvolume":" 22","year":"2013","_id":"7745","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","abstract":[{"lang":"eng","text":"The underlying basis of genetic variation in quantitative traits, in terms of the number of causal variants and the size of their effects, is largely unknown in natural populations. The expectation is that complex quantitative trait variation is attributable to many, possibly interacting, causal variants, whose effects may depend upon the sex, age and the environment in which they are expressed. A recently developed methodology in animal breeding derives a value of relatedness among individuals from high‐density genomic marker data, to estimate additive genetic variance within livestock populations. Here, we adapt and test the effectiveness of these methods to partition genetic variation for complex traits across genomic regions within ecological study populations where individuals have varying degrees of relatedness. We then apply this approach for the first time to a natural population and demonstrate that genetic variation in wing length in the great tit (Parus major) reflects contributions from multiple genomic regions. We show that a polygenic additive mode of gene action best describes the patterns observed, and we find no evidence of dosage compensation for the sex chromosome. Our results suggest that most of the genomic regions that influence wing length have the same effects in both sexes. We found a limited amount of genetic variance in males that is attributed to regions that have no effects in females, which could facilitate the sexual dimorphism observed for this trait. Although this exploratory work focuses on one complex trait, the methodology is generally applicable to any trait for any laboratory or wild population, paving the way for investigating sex‐, age‐ and environment‐specific genetic effects and thus the underlying genetic architecture of phenotype in biological study systems."}],"issue":"15","type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1111/mec.12375","date_published":"2013-08-01T00:00:00Z","article_type":"original","quality_controlled":"1","page":"3963-3980","publication":"Molecular Ecology","citation":{"chicago":"Robinson, Matthew Richard, Anna W. Santure, Isabelle DeCauwer, Ben C. Sheldon, and Jon Slate. “Partitioning of Genetic Variation across the Genome Using Multimarker Methods in a Wild Bird Population.” Molecular Ecology. Wiley, 2013. https://doi.org/10.1111/mec.12375.","short":"M.R. Robinson, A.W. Santure, I. DeCauwer, B.C. Sheldon, J. Slate, Molecular Ecology 22 (2013) 3963–3980.","mla":"Robinson, Matthew Richard, et al. “Partitioning of Genetic Variation across the Genome Using Multimarker Methods in a Wild Bird Population.” Molecular Ecology, vol. 22, no. 15, Wiley, 2013, pp. 3963–80, doi:10.1111/mec.12375.","apa":"Robinson, M. R., Santure, A. W., DeCauwer, I., Sheldon, B. C., & Slate, J. (2013). Partitioning of genetic variation across the genome using multimarker methods in a wild bird population. Molecular Ecology. Wiley. https://doi.org/10.1111/mec.12375","ieee":"M. R. Robinson, A. W. Santure, I. DeCauwer, B. C. Sheldon, and J. Slate, “Partitioning of genetic variation across the genome using multimarker methods in a wild bird population,” Molecular Ecology, vol. 22, no. 15. Wiley, pp. 3963–3980, 2013.","ista":"Robinson MR, Santure AW, DeCauwer I, Sheldon BC, Slate J. 2013. Partitioning of genetic variation across the genome using multimarker methods in a wild bird population. Molecular Ecology. 22(15), 3963–3980.","ama":"Robinson MR, Santure AW, DeCauwer I, Sheldon BC, Slate J. Partitioning of genetic variation across the genome using multimarker methods in a wild bird population. Molecular Ecology. 2013;22(15):3963-3980. doi:10.1111/mec.12375"},"month":"08","day":"01","article_processing_charge":"No","publication_identifier":{"issn":["0962-1083"]}},{"date_updated":"2021-01-12T08:15:14Z","date_created":"2020-04-30T11:00:32Z","oa_version":"None","volume":22,"author":[{"full_name":"Santure, Anna W.","first_name":"Anna W.","last_name":"Santure"},{"last_name":"De Cauwer","first_name":"Isabelle","full_name":"De Cauwer, Isabelle"},{"last_name":"Robinson","first_name":"Matthew Richard","orcid":"0000-0001-8982-8813","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","full_name":"Robinson, Matthew Richard"},{"full_name":"Poissant, Jocelyn","last_name":"Poissant","first_name":"Jocelyn"},{"first_name":"Ben C.","last_name":"Sheldon","full_name":"Sheldon, Ben C."},{"first_name":"Jon","last_name":"Slate","full_name":"Slate, Jon"}],"title":"Genomic dissection of variation in clutch size and egg mass in a wild great tit (Parus major) population","status":"public","publication_status":"published","publisher":"Wiley","intvolume":" 22","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"7746","year":"2013","extern":"1","abstract":[{"text":"Clutch size and egg mass are life history traits that have been extensively studied in wild bird populations, as life history theory predicts a negative trade‐off between them, either at the phenotypic or at the genetic level. Here, we analyse the genomic architecture of these heritable traits in a wild great tit (Parus major) population, using three marker‐based approaches – chromosome partitioning, quantitative trait locus (QTL) mapping and a genome‐wide association study (GWAS). The variance explained by each great tit chromosome scales with predicted chromosome size, no location in the genome contains genome‐wide significant QTL, and no individual SNPs are associated with a large proportion of phenotypic variation, all of which may suggest that variation in both traits is due to many loci of small effect, located across the genome. There is no evidence that any regions of the genome contribute significantly to both traits, which combined with a small, nonsignificant negative genetic covariance between the traits, suggests the absence of genetic constraints on the independent evolution of these traits. Our findings support the hypothesis that variation in life history traits in natural populations is likely to be determined by many loci of small effect spread throughout the genome, which are subject to continued input of variation by mutation and migration, although we cannot exclude the possibility of an additional input of major effect genes influencing either trait.","lang":"eng"}],"issue":"15","type":"journal_article","language":[{"iso":"eng"}],"date_published":"2013-08-01T00:00:00Z","doi":"10.1111/mec.12376","quality_controlled":"1","article_type":"original","page":"3949-3962","publication":"Molecular Ecology","citation":{"ama":"Santure AW, De Cauwer I, Robinson MR, Poissant J, Sheldon BC, Slate J. Genomic dissection of variation in clutch size and egg mass in a wild great tit (Parus major) population. Molecular Ecology. 2013;22(15):3949-3962. doi:10.1111/mec.12376","ista":"Santure AW, De Cauwer I, Robinson MR, Poissant J, Sheldon BC, Slate J. 2013. Genomic dissection of variation in clutch size and egg mass in a wild great tit (Parus major) population. Molecular Ecology. 22(15), 3949–3962.","apa":"Santure, A. W., De Cauwer, I., Robinson, M. R., Poissant, J., Sheldon, B. C., & Slate, J. (2013). Genomic dissection of variation in clutch size and egg mass in a wild great tit (Parus major) population. Molecular Ecology. Wiley. https://doi.org/10.1111/mec.12376","ieee":"A. W. Santure, I. De Cauwer, M. R. Robinson, J. Poissant, B. C. Sheldon, and J. Slate, “Genomic dissection of variation in clutch size and egg mass in a wild great tit (Parus major) population,” Molecular Ecology, vol. 22, no. 15. Wiley, pp. 3949–3962, 2013.","mla":"Santure, Anna W., et al. “Genomic Dissection of Variation in Clutch Size and Egg Mass in a Wild Great Tit (Parus Major) Population.” Molecular Ecology, vol. 22, no. 15, Wiley, 2013, pp. 3949–62, doi:10.1111/mec.12376.","short":"A.W. Santure, I. De Cauwer, M.R. Robinson, J. Poissant, B.C. Sheldon, J. Slate, Molecular Ecology 22 (2013) 3949–3962.","chicago":"Santure, Anna W., Isabelle De Cauwer, Matthew Richard Robinson, Jocelyn Poissant, Ben C. Sheldon, and Jon Slate. “Genomic Dissection of Variation in Clutch Size and Egg Mass in a Wild Great Tit (Parus Major) Population.” Molecular Ecology. Wiley, 2013. https://doi.org/10.1111/mec.12376."},"day":"01","month":"08","publication_identifier":{"issn":["0962-1083"]},"article_processing_charge":"No"},{"date_created":"2020-04-30T11:00:49Z","date_updated":"2021-01-12T08:15:15Z","volume":16,"oa_version":"None","author":[{"first_name":"Matthew Richard","last_name":"Robinson","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","orcid":"0000-0001-8982-8813","full_name":"Robinson, Matthew Richard"},{"full_name":"Beckerman, Andrew P.","first_name":"Andrew P.","last_name":"Beckerman"}],"title":"Quantifying multivariate plasticity: Genetic variation in resource acquisition drives plasticity in resource allocation to components of life history","publication_status":"published","status":"public","intvolume":" 16","publisher":"Wiley","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"7747","year":"2013","extern":"1","abstract":[{"text":"Acquisition and allocation of resources are central to life‐history theory. However, empirical work typically focuses only on allocation despite the fact that relationships between fitness components may be governed by differences in the ability of individuals to acquire resources across environments. Here, we outline a statistical framework to partition the genetic basis of multivariate plasticity into independent axes of genetic variation, and quantify for the first time, the extent to which specific traits drive multitrait genotype–environment interactions. Our framework generalises to analyses of plasticity, growth and ageing. We apply this approach to a unique, large‐scale, multivariate study of acquisition, allocation and plasticity in the life history of the cricket, Gryllus firmus. We demonstrate that resource acquisition and allocation are genetically correlated, and that plasticity in trade‐offs between allocation to components of fitness is 90% dependent on genetic variance for total resource acquisition. These results suggest that genotype–environment effects for resource acquisition can maintain variation in life‐history components that are typically observed in the wild.","lang":"eng"}],"issue":"3","type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1111/ele.12047","date_published":"2013-03-01T00:00:00Z","article_type":"original","quality_controlled":"1","page":"281-290","publication":"Ecology Letters","citation":{"ama":"Robinson MR, Beckerman AP. Quantifying multivariate plasticity: Genetic variation in resource acquisition drives plasticity in resource allocation to components of life history. Ecology Letters. 2013;16(3):281-290. doi:10.1111/ele.12047","apa":"Robinson, M. R., & Beckerman, A. P. (2013). Quantifying multivariate plasticity: Genetic variation in resource acquisition drives plasticity in resource allocation to components of life history. Ecology Letters. Wiley. https://doi.org/10.1111/ele.12047","ieee":"M. R. Robinson and A. P. Beckerman, “Quantifying multivariate plasticity: Genetic variation in resource acquisition drives plasticity in resource allocation to components of life history,” Ecology Letters, vol. 16, no. 3. Wiley, pp. 281–290, 2013.","ista":"Robinson MR, Beckerman AP. 2013. Quantifying multivariate plasticity: Genetic variation in resource acquisition drives plasticity in resource allocation to components of life history. Ecology Letters. 16(3), 281–290.","short":"M.R. Robinson, A.P. Beckerman, Ecology Letters 16 (2013) 281–290.","mla":"Robinson, Matthew Richard, and Andrew P. Beckerman. “Quantifying Multivariate Plasticity: Genetic Variation in Resource Acquisition Drives Plasticity in Resource Allocation to Components of Life History.” Ecology Letters, vol. 16, no. 3, Wiley, 2013, pp. 281–90, doi:10.1111/ele.12047.","chicago":"Robinson, Matthew Richard, and Andrew P. Beckerman. “Quantifying Multivariate Plasticity: Genetic Variation in Resource Acquisition Drives Plasticity in Resource Allocation to Components of Life History.” Ecology Letters. Wiley, 2013. https://doi.org/10.1111/ele.12047."},"day":"01","month":"03","publication_identifier":{"issn":["1461-023X"]},"article_processing_charge":"No"},{"_id":"7775","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2013","publication_status":"published","status":"public","title":"Stability of jammed packings II: The transverse length scale","intvolume":" 9","publisher":"Royal Society of Chemistry","author":[{"full_name":"Schoenholz, Samuel S.","last_name":"Schoenholz","first_name":"Samuel S."},{"first_name":"Carl Peter","last_name":"Goodrich","id":"EB352CD2-F68A-11E9-89C5-A432E6697425","orcid":"0000-0002-1307-5074","full_name":"Goodrich, Carl Peter"},{"full_name":"Kogan, Oleg","last_name":"Kogan","first_name":"Oleg"},{"first_name":"Andrea J.","last_name":"Liu","full_name":"Liu, Andrea J."},{"first_name":"Sidney R.","last_name":"Nagel","full_name":"Nagel, Sidney R."}],"date_updated":"2021-01-12T08:15:27Z","date_created":"2020-04-30T11:43:58Z","volume":9,"oa_version":"None","article_number":"11000","type":"journal_article","abstract":[{"text":"As a function of packing fraction at zero temperature and applied stress, an amorphous packing of spheres exhibits a jamming transition where the system is sensitive to boundary conditions even in the thermodynamic limit. Upon further compression, the system should become insensitive to boundary conditions provided it is sufficiently large. Here we explore the linear response to a large class of boundary perturbations in 2 and 3 dimensions. We consider each finite packing with periodic-boundary conditions as the basis of an infinite square or cubic lattice and study properties of vibrational modes at arbitrary wave vector. We find that the stability of such modes can be understood in terms of a competition between plane waves and the anomalous vibrational modes associated with the jamming transition; infinitesimal boundary perturbations become irrelevant for systems that are larger than a length scale that characterizes the transverse excitations. This previously identified length diverges at the jamming transition.","lang":"eng"}],"issue":"46","extern":"1","publication":"Soft Matter","citation":{"ista":"Schoenholz SS, Goodrich CP, Kogan O, Liu AJ, Nagel SR. 2013. Stability of jammed packings II: The transverse length scale. Soft Matter. 9(46), 11000.","ieee":"S. S. Schoenholz, C. P. Goodrich, O. Kogan, A. J. Liu, and S. R. Nagel, “Stability of jammed packings II: The transverse length scale,” Soft Matter, vol. 9, no. 46. Royal Society of Chemistry, 2013.","apa":"Schoenholz, S. S., Goodrich, C. P., Kogan, O., Liu, A. J., & Nagel, S. R. (2013). Stability of jammed packings II: The transverse length scale. Soft Matter. Royal Society of Chemistry. https://doi.org/10.1039/c3sm51096d","ama":"Schoenholz SS, Goodrich CP, Kogan O, Liu AJ, Nagel SR. Stability of jammed packings II: The transverse length scale. Soft Matter. 2013;9(46). doi:10.1039/c3sm51096d","chicago":"Schoenholz, Samuel S., Carl Peter Goodrich, Oleg Kogan, Andrea J. Liu, and Sidney R. Nagel. “Stability of Jammed Packings II: The Transverse Length Scale.” Soft Matter. Royal Society of Chemistry, 2013. https://doi.org/10.1039/c3sm51096d.","mla":"Schoenholz, Samuel S., et al. “Stability of Jammed Packings II: The Transverse Length Scale.” Soft Matter, vol. 9, no. 46, 11000, Royal Society of Chemistry, 2013, doi:10.1039/c3sm51096d.","short":"S.S. Schoenholz, C.P. Goodrich, O. Kogan, A.J. Liu, S.R. Nagel, Soft Matter 9 (2013)."},"article_type":"original","quality_controlled":"1","date_published":"2013-10-08T00:00:00Z","doi":"10.1039/c3sm51096d","language":[{"iso":"eng"}],"day":"08","month":"10","article_processing_charge":"No","publication_identifier":{"issn":["1744-683X","1744-6848"]}},{"language":[{"iso":"eng"}],"doi":"10.1039/c3sm51095f","date_published":"2013-10-08T00:00:00Z","article_type":"original","quality_controlled":"1","publication":"Soft Matter","citation":{"ama":"Goodrich CP, Ellenbroek WG, Liu AJ. Stability of jammed packings I: The rigidity length scale. Soft Matter. 2013;9(46). doi:10.1039/c3sm51095f","ista":"Goodrich CP, Ellenbroek WG, Liu AJ. 2013. Stability of jammed packings I: The rigidity length scale. Soft Matter. 9(46), 10993.","apa":"Goodrich, C. P., Ellenbroek, W. G., & Liu, A. J. (2013). Stability of jammed packings I: The rigidity length scale. Soft Matter. Royal Society of Chemistry. https://doi.org/10.1039/c3sm51095f","ieee":"C. P. Goodrich, W. G. Ellenbroek, and A. J. Liu, “Stability of jammed packings I: The rigidity length scale,” Soft Matter, vol. 9, no. 46. Royal Society of Chemistry, 2013.","mla":"Goodrich, Carl Peter, et al. “Stability of Jammed Packings I: The Rigidity Length Scale.” Soft Matter, vol. 9, no. 46, 10993, Royal Society of Chemistry, 2013, doi:10.1039/c3sm51095f.","short":"C.P. Goodrich, W.G. Ellenbroek, A.J. Liu, Soft Matter 9 (2013).","chicago":"Goodrich, Carl Peter, Wouter G. Ellenbroek, and Andrea J. Liu. “Stability of Jammed Packings I: The Rigidity Length Scale.” Soft Matter. Royal Society of Chemistry, 2013. https://doi.org/10.1039/c3sm51095f."},"day":"08","month":"10","publication_identifier":{"issn":["1744-683X","1744-6848"]},"article_processing_charge":"No","date_updated":"2021-01-12T08:15:27Z","date_created":"2020-04-30T11:43:42Z","volume":9,"oa_version":"None","author":[{"last_name":"Goodrich","first_name":"Carl Peter","orcid":"0000-0002-1307-5074","id":"EB352CD2-F68A-11E9-89C5-A432E6697425","full_name":"Goodrich, Carl Peter"},{"full_name":"Ellenbroek, Wouter G.","last_name":"Ellenbroek","first_name":"Wouter G."},{"full_name":"Liu, Andrea J.","first_name":"Andrea J.","last_name":"Liu"}],"publication_status":"published","title":"Stability of jammed packings I: The rigidity length scale","status":"public","intvolume":" 9","publisher":"Royal Society of Chemistry","_id":"7774","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2013","extern":"1","abstract":[{"text":"In 2005, Wyart et al. [Europhys. Lett., 2005, 72, 486] showed that the low frequency vibrational properties of jammed amorphous sphere packings can be understood in terms of a length scale, called l*, that diverges as the system becomes marginally unstable. Despite the tremendous success of this theory, it has been difficult to connect the counting argument that defines l* to other length scales that diverge near the jamming transition. We present an alternate derivation of l* based on the onset of rigidity. This phenomenological approach reveals the physical mechanism underlying the length scale and is relevant to a range of systems for which the original argument breaks down. It also allows us to present the first direct numerical measurement of l*.","lang":"eng"}],"issue":"46","article_number":"10993","type":"journal_article"},{"publication_status":"published","publisher":"Frontiers Media","year":"2013","pmid":1,"date_updated":"2021-01-12T08:16:38Z","date_created":"2020-06-25T13:23:50Z","volume":7,"author":[{"full_name":"Vogels, Tim P","last_name":"Vogels","first_name":"Tim P","orcid":"0000-0003-3295-6181","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425"},{"full_name":"Froemke, R. C.","first_name":"R. C.","last_name":"Froemke"},{"last_name":"Doyon","first_name":"N.","full_name":"Doyon, N."},{"last_name":"Gilson","first_name":"M.","full_name":"Gilson, M."},{"full_name":"Haas, J. S.","first_name":"J. S.","last_name":"Haas"},{"first_name":"R.","last_name":"Liu","full_name":"Liu, R."},{"first_name":"A.","last_name":"Maffei","full_name":"Maffei, A."},{"last_name":"Miller","first_name":"P.","full_name":"Miller, P."},{"full_name":"Wierenga, C. J.","last_name":"Wierenga","first_name":"C. J."},{"full_name":"Woodin, M. A.","first_name":"M. A.","last_name":"Woodin"},{"last_name":"Zenke","first_name":"F.","full_name":"Zenke, F."},{"full_name":"Sprekeler, H.","first_name":"H.","last_name":"Sprekeler"}],"article_number":"119","license":"https://creativecommons.org/licenses/by/3.0/","extern":"1","file_date_updated":"2020-07-16T11:23:40Z","quality_controlled":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode","name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)","short":"CC BY (3.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"pmid":["23882186"]},"language":[{"iso":"eng"}],"doi":"10.3389/fncir.2013.00119","month":"07","publication_identifier":{"eissn":["1662-5110"]},"ddc":["570"],"title":"Inhibitory synaptic plasticity: Spike timing-dependence and putative network function","status":"public","intvolume":" 7","_id":"8030","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"date_updated":"2020-07-16T11:23:40Z","date_created":"2020-07-16T11:23:40Z","checksum":"9c321cb12977d84048712eefa7f0c497","success":1,"relation":"main_file","file_id":"8123","file_size":1530469,"content_type":"application/pdf","creator":"cziletti","file_name":"2013_FrontNeurCirc_Vogels.pdf","access_level":"open_access"}],"type":"journal_article","abstract":[{"lang":"eng","text":"While the plasticity of excitatory synaptic connections in the brain has been widely studied, the plasticity of inhibitory connections is much less understood. Here, we present recent experimental and theoretical findings concerning the rules of spike timing-dependent inhibitory plasticity and their putative network function. This is a summary of a workshop at the COSYNE conference 2012."}],"article_type":"original","publication":"Frontiers in Neural Circuits","citation":{"mla":"Vogels, Tim P., et al. “Inhibitory Synaptic Plasticity: Spike Timing-Dependence and Putative Network Function.” Frontiers in Neural Circuits, vol. 7, 119, Frontiers Media, 2013, doi:10.3389/fncir.2013.00119.","short":"T.P. Vogels, R.C. Froemke, N. Doyon, M. Gilson, J.S. Haas, R. Liu, A. Maffei, P. Miller, C.J. Wierenga, M.A. Woodin, F. Zenke, H. Sprekeler, Frontiers in Neural Circuits 7 (2013).","chicago":"Vogels, Tim P, R. C. Froemke, N. Doyon, M. Gilson, J. S. Haas, R. Liu, A. Maffei, et al. “Inhibitory Synaptic Plasticity: Spike Timing-Dependence and Putative Network Function.” Frontiers in Neural Circuits. Frontiers Media, 2013. https://doi.org/10.3389/fncir.2013.00119.","ama":"Vogels TP, Froemke RC, Doyon N, et al. Inhibitory synaptic plasticity: Spike timing-dependence and putative network function. Frontiers in Neural Circuits. 2013;7. doi:10.3389/fncir.2013.00119","ista":"Vogels TP, Froemke RC, Doyon N, Gilson M, Haas JS, Liu R, Maffei A, Miller P, Wierenga CJ, Woodin MA, Zenke F, Sprekeler H. 2013. Inhibitory synaptic plasticity: Spike timing-dependence and putative network function. Frontiers in Neural Circuits. 7, 119.","apa":"Vogels, T. P., Froemke, R. C., Doyon, N., Gilson, M., Haas, J. S., Liu, R., … Sprekeler, H. (2013). Inhibitory synaptic plasticity: Spike timing-dependence and putative network function. Frontiers in Neural Circuits. Frontiers Media. https://doi.org/10.3389/fncir.2013.00119","ieee":"T. P. Vogels et al., “Inhibitory synaptic plasticity: Spike timing-dependence and putative network function,” Frontiers in Neural Circuits, vol. 7. Frontiers Media, 2013."},"date_published":"2013-07-18T00:00:00Z","day":"18","has_accepted_license":"1","article_processing_charge":"No"},{"date_created":"2018-12-11T11:48:38Z","date_updated":"2021-01-12T08:16:57Z","volume":126,"author":[{"full_name":"Steffen, Anika","last_name":"Steffen","first_name":"Anika"},{"full_name":"Ladwein, Markus","last_name":"Ladwein","first_name":"Markus"},{"first_name":"Georgi A","last_name":"Dimchev","id":"38C393BE-F248-11E8-B48F-1D18A9856A87","full_name":"Georgi Dimchev"},{"first_name":"Anke","last_name":"Hein","full_name":"Hein, Anke"},{"first_name":"Lisa","last_name":"Schwenkmezger","full_name":"Schwenkmezger, Lisa"},{"last_name":"Arens","first_name":"Stefan","full_name":"Arens, Stefan"},{"first_name":"Kathrin","last_name":"Ladwein","full_name":"Ladwein, Kathrin I"},{"last_name":"Holleboom","first_name":"J.","full_name":"Holleboom, J. Margit"},{"id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078","first_name":"Florian","last_name":"Schur","full_name":"Florian Schur"},{"last_name":"Small","first_name":"John","full_name":"Small, John V"},{"first_name":"Janett","last_name":"Schwarz","full_name":"Schwarz, Janett"},{"first_name":"Ralf","last_name":"Gerhard","full_name":"Gerhard, Ralf"},{"full_name":"Faix, Jan","last_name":"Faix","first_name":"Jan"},{"first_name":"Theresia","last_name":"Stradal","full_name":"Stradal, Theresia E"},{"full_name":"Brakebusch, Cord H","first_name":"Cord","last_name":"Brakebusch"},{"last_name":"Rottner","first_name":"Klemens","full_name":"Rottner, Klemens"}],"title":"Rac function is crucial for cell migration but is not required for spreading and focal adhesion formation","status":"public","publication_status":"published","publisher":"Company of Biologists","intvolume":" 126","_id":"811","year":"2013","acknowledgement":"This work was supported in part by the Deutsche Forschungsgemeinschaft [grants within programs SFB621 to K.R., and FOR629 and SFB629 to T.E.B.S.]. Deposited in PMC for immediate release.\nWe thank Brigitte Denker and Gerd Landsberg for excellent technical assistance. We are grateful to Robert Geffers (HZI Braunschweig, Germany) for microarray analyses and to Mirko Himmel (UKE Hamburg, Germany) for valuable advice on FRAP analysis.","extern":1,"abstract":[{"text":"Cell migration is commonly accompanied by protrusion of membrane ruffles and lamellipodia. In two-dimensional migration, protrusion of these thin sheets of cytoplasm is considered relevant to both exploration of new space and initiation of nascent adhesion to the substratum. Lamellipodium formation can be potently stimulated by Rho GTPases of the Rac subfamily, but alsoby RhoG or Cdc42. Here we describe viable fibroblast cell lines geneticallydeficient for Rac1 that lack detectable levels of Rac2 and Rac3. Rac-deficient cells were devoid of apparent lamellipodia, but these structures were restored by expression of either Rac subfamily member, but not by Cdc42 or RhoG. Cells deficient in Rac showed strong reduction in wound closure and random cell migration and a notable loss of sensitivity to a chemotactic gradient. Despite these defects, Rac-deficient cells were able to spread, formed filopodia and established focal adhesions. Spreading in these cells was achieved by the extension of filopodia followed by the advancement of cytoplasmic veils between them. The number and size of focal adhesions as well as their intensity were largely unaffected by genetic removal of Rac1. However, Rac deficiency increased the mobility of different components in focal adhesions, potentially explaining how Rac - although not essential - can contribute to focal adhesion assembly. Together, our data demonstrate that Rac signaling is essential for lamellipodium protrusion and for efficient cell migration, but not for spreading or filopodium formation. Our findings also suggest that Rac GTPases are crucial to the establishment or maintenance of polarity in chemotactic migration.","lang":"eng"}],"publist_id":"6840","issue":"20","type":"journal_article","date_published":"2013-01-01T00:00:00Z","doi":"10.1242/jcs.118232","quality_controlled":0,"page":"4572 - 4588","publication":"Journal of Cell Science","citation":{"ama":"Steffen A, Ladwein M, Dimchev GA, et al. Rac function is crucial for cell migration but is not required for spreading and focal adhesion formation. Journal of Cell Science. 2013;126(20):4572-4588. doi:10.1242/jcs.118232","ieee":"A. Steffen et al., “Rac function is crucial for cell migration but is not required for spreading and focal adhesion formation,” Journal of Cell Science, vol. 126, no. 20. Company of Biologists, pp. 4572–4588, 2013.","apa":"Steffen, A., Ladwein, M., Dimchev, G. A., Hein, A., Schwenkmezger, L., Arens, S., … Rottner, K. (2013). Rac function is crucial for cell migration but is not required for spreading and focal adhesion formation. Journal of Cell Science. Company of Biologists. https://doi.org/10.1242/jcs.118232","ista":"Steffen A, Ladwein M, Dimchev GA, Hein A, Schwenkmezger L, Arens S, Ladwein K, Holleboom J, Schur FK, Small J, Schwarz J, Gerhard R, Faix J, Stradal T, Brakebusch C, Rottner K. 2013. Rac function is crucial for cell migration but is not required for spreading and focal adhesion formation. Journal of Cell Science. 126(20), 4572–4588.","short":"A. Steffen, M. Ladwein, G.A. Dimchev, A. Hein, L. Schwenkmezger, S. Arens, K. Ladwein, J. Holleboom, F.K. Schur, J. Small, J. Schwarz, R. Gerhard, J. Faix, T. Stradal, C. Brakebusch, K. Rottner, Journal of Cell Science 126 (2013) 4572–4588.","mla":"Steffen, Anika, et al. “Rac Function Is Crucial for Cell Migration but Is Not Required for Spreading and Focal Adhesion Formation.” Journal of Cell Science, vol. 126, no. 20, Company of Biologists, 2013, pp. 4572–88, doi:10.1242/jcs.118232.","chicago":"Steffen, Anika, Markus Ladwein, Georgi A Dimchev, Anke Hein, Lisa Schwenkmezger, Stefan Arens, Kathrin Ladwein, et al. “Rac Function Is Crucial for Cell Migration but Is Not Required for Spreading and Focal Adhesion Formation.” Journal of Cell Science. Company of Biologists, 2013. https://doi.org/10.1242/jcs.118232."},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"day":"01","month":"01"},{"publication":"Molecular Biology of the Cell","citation":{"ama":"Koestler S, Steffen A, Nemethova M, et al. Arp2/3 complex is essential for actin network treadmilling as well as for targeting of capping protein and cofilin. Molecular Biology of the Cell. 2013;24(18):2861-2875. doi:10.1091/mbc.E12-12-0857","ista":"Koestler S, Steffen A, Nemethova M, Winterhoff M, Luo N, Holleboom J, Krupp J, Jacob S, Vinzenz M, Schur FK, Schlüter K, Gunning P, Winkler C, Schmeiser C, Faix J, Stradal T, Small J, Rottner K. 2013. Arp2/3 complex is essential for actin network treadmilling as well as for targeting of capping protein and cofilin. Molecular Biology of the Cell. 24(18), 2861–2875.","ieee":"S. Koestler et al., “Arp2/3 complex is essential for actin network treadmilling as well as for targeting of capping protein and cofilin,” Molecular Biology of the Cell, vol. 24, no. 18. American Society for Biology, pp. 2861–2875, 2013.","apa":"Koestler, S., Steffen, A., Nemethova, M., Winterhoff, M., Luo, N., Holleboom, J., … Rottner, K. (2013). Arp2/3 complex is essential for actin network treadmilling as well as for targeting of capping protein and cofilin. Molecular Biology of the Cell. American Society for Biology. https://doi.org/10.1091/mbc.E12-12-0857","mla":"Koestler, Stefan, et al. “Arp2/3 Complex Is Essential for Actin Network Treadmilling as Well as for Targeting of Capping Protein and Cofilin.” Molecular Biology of the Cell, vol. 24, no. 18, American Society for Biology, 2013, pp. 2861–75, doi:10.1091/mbc.E12-12-0857.","short":"S. Koestler, A. Steffen, M. Nemethova, M. Winterhoff, N. Luo, J. Holleboom, J. Krupp, S. Jacob, M. Vinzenz, F.K. Schur, K. Schlüter, P. Gunning, C. Winkler, C. Schmeiser, J. Faix, T. Stradal, J. Small, K. Rottner, Molecular Biology of the Cell 24 (2013) 2861–2875.","chicago":"Koestler, Stefan, Anika Steffen, Maria Nemethova, Moritz Winterhoff, Ningning Luo, J. Holleboom, Jessica Krupp, et al. “Arp2/3 Complex Is Essential for Actin Network Treadmilling as Well as for Targeting of Capping Protein and Cofilin.” Molecular Biology of the Cell. American Society for Biology, 2013. https://doi.org/10.1091/mbc.E12-12-0857."},"quality_controlled":0,"page":"2861 - 2875","doi":"10.1091/mbc.E12-12-0857","date_published":"2013-09-15T00:00:00Z","day":"15","month":"09","_id":"812","acknowledgement":"This work was supported in part by Deutsche Forschungsgemeinschaft Grants RO2414/3-1 (to K.R.) and FA330/6-1 (to J.F.), Austrian \nScience Fund Projects FWF 1516-B09 and FWF P21292-B09 (to J.V.S.), the Vienna Science and Technology Fund (WWTF, to \nJ.V.S. and C.S.), and Australian National Health and Medical \nResearch Council Grant APP1004175 (to P.W.G.). We thank J. Adams, \nR. Chisholm, A. Hall, L. Machesky, H. G. Mannherz, D. Schafer, and \nR. Wedlich-Söldner for expression constructs and B. Denker, \nP. Hagendorff, and G. Landsberg for technical assistance.","year":"2013","publication_status":"published","status":"public","title":"Arp2/3 complex is essential for actin network treadmilling as well as for targeting of capping protein and cofilin","publisher":"American Society for Biology","intvolume":" 24","author":[{"first_name":"Stefan","last_name":"Koestler","full_name":"Koestler, Stefan A"},{"first_name":"Anika","last_name":"Steffen","full_name":"Steffen, Anika"},{"first_name":"Maria","last_name":"Nemethova","id":"34E27F1C-F248-11E8-B48F-1D18A9856A87","full_name":"Maria Nemethova"},{"full_name":"Winterhoff, Moritz","last_name":"Winterhoff","first_name":"Moritz"},{"last_name":"Luo","first_name":"Ningning","full_name":"Luo, Ningning"},{"last_name":"Holleboom","first_name":"J.","full_name":"Holleboom, J. Margit"},{"full_name":"Krupp, Jessica","first_name":"Jessica","last_name":"Krupp"},{"full_name":"Jacob, Sonja","first_name":"Sonja","last_name":"Jacob"},{"last_name":"Vinzenz","first_name":"Marlene","full_name":"Vinzenz, Marlene"},{"first_name":"Florian","last_name":"Schur","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078","full_name":"Florian Schur"},{"full_name":"Schlüter, Kai","first_name":"Kai","last_name":"Schlüter"},{"full_name":"Gunning, Peter W","last_name":"Gunning","first_name":"Peter"},{"first_name":"Christoph","last_name":"Winkler","full_name":"Winkler, Christoph"},{"full_name":"Schmeiser, Christian","last_name":"Schmeiser","first_name":"Christian"},{"full_name":"Faix, Jan","last_name":"Faix","first_name":"Jan"},{"first_name":"Theresia","last_name":"Stradal","full_name":"Stradal, Theresia E"},{"full_name":"Small, John V","last_name":"Small","first_name":"John"},{"full_name":"Rottner, Klemens","last_name":"Rottner","first_name":"Klemens"}],"date_updated":"2021-01-12T08:17:00Z","date_created":"2018-12-11T11:48:38Z","volume":24,"type":"journal_article","abstract":[{"text":"Lamellipodia are sheet-like protrusions formed during migration or phagocytosis and comprise a network of actin filaments. Filament formation in this network is initiated by nucleation/branching through the actin-related protein 2/3 (Arp2/3) complex downstream of its activator, suppressor of cAMP receptor/WASP-family verprolin homologous (Scar/WAVE), but the relative relevance of Arp2/3-mediated branching versus actin filament elongation is unknown. Here we use instantaneous interference with Arp2/3 complex function in live fibroblasts with established lamellipodia. This allows direct examination of both the fate of elongating filaments upon instantaneous suppression of Arp2/3 complex activity and the consequences of this treatment on the dynamics of other lamellipodial regulators. We show that Arp2/3 complex is an essential organizer of treadmilling actin filament arrays but has little effect on the net rate of actin filament turnover at the cell periphery. In addition, Arp2/3 complex serves as key upstream factor for the recruitment of modulators of lamellipodia formation such as capping protein or cofilin. Arp2/3 complex is thus decisive for filament organization and geometry within the network not only by generating branches and novel filament ends, but also by directing capping or severing activities to the lamellipodium. Arp2/3 complex is also crucial to lamellipodia-based migration of keratocytes.","lang":"eng"}],"publist_id":"6841","issue":"18","extern":1},{"citation":{"ama":"Schur FK, Hagen W, De Marco A, Briggs J. Determination of protein structure at 8.5Å resolution using cryo-electron tomography and sub-tomogram averaging. Journal of Structural Biology. 2013;184(3):394-400. doi:10.1016/j.jsb.2013.10.015","ista":"Schur FK, Hagen W, De Marco A, Briggs J. 2013. Determination of protein structure at 8.5Å resolution using cryo-electron tomography and sub-tomogram averaging. Journal of Structural Biology. 184(3), 394–400.","apa":"Schur, F. K., Hagen, W., De Marco, A., & Briggs, J. (2013). Determination of protein structure at 8.5Å resolution using cryo-electron tomography and sub-tomogram averaging. Journal of Structural Biology. Academic Press. https://doi.org/10.1016/j.jsb.2013.10.015","ieee":"F. K. Schur, W. Hagen, A. De Marco, and J. Briggs, “Determination of protein structure at 8.5Å resolution using cryo-electron tomography and sub-tomogram averaging,” Journal of Structural Biology, vol. 184, no. 3. Academic Press, pp. 394–400, 2013.","mla":"Schur, Florian KM, et al. “Determination of Protein Structure at 8.5Å Resolution Using Cryo-Electron Tomography and Sub-Tomogram Averaging.” Journal of Structural Biology, vol. 184, no. 3, Academic Press, 2013, pp. 394–400, doi:10.1016/j.jsb.2013.10.015.","short":"F.K. Schur, W. Hagen, A. De Marco, J. Briggs, Journal of Structural Biology 184 (2013) 394–400.","chicago":"Schur, Florian KM, Wim Hagen, Alex De Marco, and John Briggs. “Determination of Protein Structure at 8.5Å Resolution Using Cryo-Electron Tomography and Sub-Tomogram Averaging.” Journal of Structural Biology. Academic Press, 2013. https://doi.org/10.1016/j.jsb.2013.10.015."},"publication":"Journal of Structural Biology","page":"394 - 400","quality_controlled":0,"date_published":"2013-12-01T00:00:00Z","doi":"10.1016/j.jsb.2013.10.015","month":"12","day":"01","_id":"810","year":"2013","acknowledgement":"The M-PMV ΔPro CANC tubes imaged in this study were a kind gift from Pavel Ulbrich and Tomas Ruml, Institute of Chemical Technology, Prague. The cryo-EM grids were prepared by Tanmay Bharat. This study was technically supported by EMBL’s IT services unit and by Frank Thommen. We thank Martin Schorb and Svetlana Dodonova for discussions and advice; Khanh Huy Bui for advice and scripts to streamline tomogram reconstruction; and Giulia Zanetti, Tanmay Bharat, and Martin Beck for comments on the manuscript. This study was supported by Deutsche Forschungsgemeinschaft grant BR 3635/2-1 to JAGB.","publisher":"Academic Press","intvolume":" 184","title":"Determination of protein structure at 8.5Å resolution using cryo-electron tomography and sub-tomogram averaging","publication_status":"published","status":"public","author":[{"last_name":"Schur","first_name":"Florian","orcid":"0000-0003-4790-8078","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","full_name":"Florian Schur"},{"full_name":"Hagen, Wim J","first_name":"Wim","last_name":"Hagen"},{"full_name":"De Marco, Alex","first_name":"Alex","last_name":"De Marco"},{"full_name":"Briggs, John A","first_name":"John","last_name":"Briggs"}],"volume":184,"date_created":"2018-12-11T11:48:37Z","date_updated":"2021-01-12T08:16:54Z","type":"journal_article","publist_id":"6839","issue":"3","abstract":[{"lang":"eng","text":"Cryo-electron tomography combined with image processing by sub-tomogram averaging is unique in its power to resolve the structures of proteins and macromolecular complexes in situ. Limitations of the method, including the low signal to noise ratio within individual images from cryo-tomographic datasets and difficulties in determining the defocus at which the data was collected, mean that to date the very best structures obtained by sub-tomogram averaging are limited to a resolution of approximately 15. Å. Here, by optimizing data collection and defocus determination steps, we have determined the structure of assembled Mason-Pfizer monkey virus Gag protein using sub-tomogram averaging to a resolution of 8.5. Å. At this resolution alpha-helices can be directly and clearly visualized. These data demonstrate for the first time that high-resolution structural information can be obtained from cryo-electron tomograms using sub-tomogram averaging. Sub-tomogram averaging has the potential to allow detailed studies of unsolved and biologically relevant structures under biologically relevant conditions."}],"extern":1},{"article_number":"307","file_date_updated":"2020-08-10T13:45:19Z","extern":"1","pmid":1,"year":"2013","publisher":"Springer Nature","publication_status":"published","author":[{"first_name":"Branka","last_name":"Petricevic","full_name":"Petricevic, Branka"},{"first_name":"Johannes","last_name":"Laengle","full_name":"Laengle, Johannes"},{"full_name":"Singer, Josef","last_name":"Singer","first_name":"Josef"},{"full_name":"Sachet, Monika","last_name":"Sachet","first_name":"Monika"},{"orcid":"0000-0002-8777-3502","id":"36432834-F248-11E8-B48F-1D18A9856A87","last_name":"Fazekas","first_name":"Judit","full_name":"Fazekas, Judit"},{"full_name":"Steger, Guenther","first_name":"Guenther","last_name":"Steger"},{"full_name":"Bartsch, Rupert","first_name":"Rupert","last_name":"Bartsch"},{"last_name":"Jensen-Jarolim","first_name":"Erika","full_name":"Jensen-Jarolim, Erika"},{"last_name":"Bergmann","first_name":"Michael","full_name":"Bergmann, Michael"}],"volume":11,"date_updated":"2022-08-25T14:52:39Z","date_created":"2020-08-10T11:54:34Z","publication_identifier":{"issn":["1479-5876"]},"month":"12","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode","name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)","short":"CC BY (3.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["24330813"]},"oa":1,"quality_controlled":"1","doi":"10.1186/1479-5876-11-307","language":[{"iso":"eng"}],"type":"journal_article","abstract":[{"lang":"eng","text":"Background: Monoclonal antibodies (mAb), such as trastuzumab are a valuable addition to breast cancer therapy.\r\nData obtained from neoadjuvant settings revealed that antibody-dependent cell-mediated cytotoxicity (ADCC) is a\r\nmajor mechanism of action for the mAb trastuzumab. Conflicting results still call into question whether disease\r\nprogression, prolonged treatment or concomitant chemotherapy influences ADCC and related immunological\r\nphenomena.\r\nMethods: We analyzed the activity of ADCC and antibody-dependent cell-mediated phagocytosis (ADCP) of\r\nperipheral blood mononuclear cells (PBMCs) from human epidermal growth factor receptor 2 (HER2/neu) positive\r\nbreast cancer patients receiving trastuzumab therapy either in an adjuvant (n = 13) or metastatic (n = 15) setting as\r\nwell as from trastuzumab treatment-naive (t-naive) HER2/neu negative patients (n = 15). PBMCs from healthy volunteers\r\n(n = 24) were used as controls. ADCC and ADCP activity was correlated with the expression of antibody binding\r\nFc-gamma receptor (FcγR)I (CD64), FcγRII (CD32) and FcγRIII (CD16) on CD14+ (monocytes) and CD56+ (NK) cells, as well as the expression of CD107a+ (LAMP-1) on CD56+ cells and the total amount of CD4+CD25+FOXP3+ (Treg) cells. In metastatic patients, markers were correlated with progression-free survival (PFS).\r\nResults: ADCC activity was significantly down regulated in metastatic, adjuvant and t-naive patient cohorts as compared to healthy controls. Reduced ADCC activity was inversely correlated with the expression of CD107a on CD56+\r\ncells in adjuvant patients. ADCC and ADCP activity of the patient cohorts were similar, regardless of treatment duration\r\nor additional chemotherapy. PFS in metastatic patients inversely correlated with the number of peripheral Treg cells.\r\nConclusion: The reduction of ADCC in patients as compared to healthy controls calls for adjuvant strategies, such as\r\nimmune-enhancing agents, to improve the activity of trastuzumab. However, efficacy of trastuzumab-specific ADCC\r\nand ADCP appears not to be affected by treatment duration, disease progression or concomitant chemotherapy. This\r\nfinding supports the application of trastuzumab at any stage of the disease."}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"8245","intvolume":" 11","ddc":["570"],"title":"Trastuzumab mediates antibody-dependent cell-mediated cytotoxicity and phagocytosis to the same extent in both adjuvant and metastatic HER2/neu breast cancer patients","status":"public","oa_version":"None","file":[{"file_id":"8247","relation":"main_file","date_created":"2020-08-10T13:45:19Z","date_updated":"2020-08-10T13:45:19Z","success":1,"file_name":"2013_JoTM_Petricevic.pdf","access_level":"open_access","creator":"dernst","file_size":777311,"content_type":"application/pdf"}],"has_accepted_license":"1","article_processing_charge":"No","day":"12","citation":{"ieee":"B. Petricevic et al., “Trastuzumab mediates antibody-dependent cell-mediated cytotoxicity and phagocytosis to the same extent in both adjuvant and metastatic HER2/neu breast cancer patients,” Journal of Translational Medicine, vol. 11. Springer Nature, 2013.","apa":"Petricevic, B., Laengle, J., Singer, J., Sachet, M., Singer, J., Steger, G., … Bergmann, M. (2013). Trastuzumab mediates antibody-dependent cell-mediated cytotoxicity and phagocytosis to the same extent in both adjuvant and metastatic HER2/neu breast cancer patients. Journal of Translational Medicine. Springer Nature. https://doi.org/10.1186/1479-5876-11-307","ista":"Petricevic B, Laengle J, Singer J, Sachet M, Singer J, Steger G, Bartsch R, Jensen-Jarolim E, Bergmann M. 2013. Trastuzumab mediates antibody-dependent cell-mediated cytotoxicity and phagocytosis to the same extent in both adjuvant and metastatic HER2/neu breast cancer patients. Journal of Translational Medicine. 11, 307.","ama":"Petricevic B, Laengle J, Singer J, et al. Trastuzumab mediates antibody-dependent cell-mediated cytotoxicity and phagocytosis to the same extent in both adjuvant and metastatic HER2/neu breast cancer patients. Journal of Translational Medicine. 2013;11. doi:10.1186/1479-5876-11-307","chicago":"Petricevic, Branka, Johannes Laengle, Josef Singer, Monika Sachet, Judit Singer, Guenther Steger, Rupert Bartsch, Erika Jensen-Jarolim, and Michael Bergmann. “Trastuzumab Mediates Antibody-Dependent Cell-Mediated Cytotoxicity and Phagocytosis to the Same Extent in Both Adjuvant and Metastatic HER2/Neu Breast Cancer Patients.” Journal of Translational Medicine. Springer Nature, 2013. https://doi.org/10.1186/1479-5876-11-307.","short":"B. Petricevic, J. Laengle, J. Singer, M. Sachet, J. Singer, G. Steger, R. Bartsch, E. Jensen-Jarolim, M. Bergmann, Journal of Translational Medicine 11 (2013).","mla":"Petricevic, Branka, et al. “Trastuzumab Mediates Antibody-Dependent Cell-Mediated Cytotoxicity and Phagocytosis to the Same Extent in Both Adjuvant and Metastatic HER2/Neu Breast Cancer Patients.” Journal of Translational Medicine, vol. 11, 307, Springer Nature, 2013, doi:10.1186/1479-5876-11-307."},"publication":"Journal of Translational Medicine","date_published":"2013-12-12T00:00:00Z"},{"year":"2013","publication_status":"published","publisher":"Frontiers Research Foundation","department":[{"_id":"EvBe"}],"author":[{"full_name":"O'Brien, José","last_name":"O'Brien","first_name":"José"},{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","first_name":"Eva","last_name":"Benková","full_name":"Benková, Eva"}],"date_updated":"2021-01-12T08:17:50Z","date_created":"2018-12-11T11:48:43Z","volume":4,"article_number":"451","file_date_updated":"2020-07-14T12:48:11Z","publist_id":"6821","ec_funded":1,"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":"1","project":[{"name":"Hormonal cross-talk in plant organogenesis","call_identifier":"FP7","_id":"253FCA6A-B435-11E9-9278-68D0E5697425","grant_number":"207362"}],"doi":"10.3389/fpls.2013.00451","language":[{"iso":"eng"}],"month":"11","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"827","status":"public","title":"Cytokinin cross talking during biotic and abiotic stress responses","ddc":["580"],"intvolume":" 4","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"5903","date_updated":"2020-07-14T12:48:11Z","date_created":"2019-01-31T10:40:38Z","checksum":"fdc25ddd1bf9a99b99f662cdbafeddd4","file_name":"2013_FrontiersPlant_OBrien.pdf","access_level":"open_access","file_size":953299,"content_type":"application/pdf","creator":"dernst"}],"type":"journal_article","abstract":[{"lang":"eng","text":"As sessile organisms, plants have to be able to adapt to a continuously changing environment. Plants that perceive some of these changes as stress signals activate signaling pathways to modulate their development and to enable them to survive. The complex responses to environmental cues are to a large extent mediated by plant hormones that together orchestrate the final plant response. The phytohormone cytokinin is involved in many plant developmental processes. Recently, it has been established that cytokinin plays an important role in stress responses, but does not act alone. Indeed, the hormonal control of plant development and stress adaptation is the outcome of a complex network of multiple synergistic and antagonistic interactions between various hormones. Here, we review the recent findings on the cytokinin function as part of this hormonal network. We focus on the importance of the crosstalk between cytokinin and other hormones, such as abscisic acid, jasmonate, salicylic acid, ethylene, and auxin in the modulation of plant development and stress adaptation. Finally, the impact of the current research in the biotechnological industry will be discussed."}],"publication":"Frontiers in Plant Science","citation":{"chicago":"O’Brien, José, and Eva Benková. “Cytokinin Cross Talking during Biotic and Abiotic Stress Responses.” Frontiers in Plant Science. Frontiers Research Foundation, 2013. https://doi.org/10.3389/fpls.2013.00451.","short":"J. O’Brien, E. Benková, Frontiers in Plant Science 4 (2013).","mla":"O’Brien, José, and Eva Benková. “Cytokinin Cross Talking during Biotic and Abiotic Stress Responses.” Frontiers in Plant Science, vol. 4, 451, Frontiers Research Foundation, 2013, doi:10.3389/fpls.2013.00451.","apa":"O’Brien, J., & Benková, E. (2013). Cytokinin cross talking during biotic and abiotic stress responses. Frontiers in Plant Science. Frontiers Research Foundation. https://doi.org/10.3389/fpls.2013.00451","ieee":"J. O’Brien and E. Benková, “Cytokinin cross talking during biotic and abiotic stress responses,” Frontiers in Plant Science, vol. 4. Frontiers Research Foundation, 2013.","ista":"O’Brien J, Benková E. 2013. Cytokinin cross talking during biotic and abiotic stress responses. Frontiers in Plant Science. 4, 451.","ama":"O’Brien J, Benková E. Cytokinin cross talking during biotic and abiotic stress responses. Frontiers in Plant Science. 2013;4. doi:10.3389/fpls.2013.00451"},"date_published":"2013-11-19T00:00:00Z","scopus_import":1,"day":"19","has_accepted_license":"1"},{"publication":"Frontiers in Plant Science","citation":{"ista":"Cuesta C, Wabnik KT, Benková E. 2013. Systems approaches to study root architecture dynamics. Frontiers in Plant Science. 4, 537.","ieee":"C. Cuesta, K. T. Wabnik, and E. Benková, “Systems approaches to study root architecture dynamics,” Frontiers in Plant Science, vol. 4. Frontiers Research Foundation, 2013.","apa":"Cuesta, C., Wabnik, K. T., & Benková, E. (2013). Systems approaches to study root architecture dynamics. Frontiers in Plant Science. Frontiers Research Foundation. https://doi.org/10.3389/fpls.2013.00537","ama":"Cuesta C, Wabnik KT, Benková E. Systems approaches to study root architecture dynamics. Frontiers in Plant Science. 2013;4. doi:10.3389/fpls.2013.00537","chicago":"Cuesta, Candela, Krzysztof T Wabnik, and Eva Benková. “Systems Approaches to Study Root Architecture Dynamics.” Frontiers in Plant Science. Frontiers Research Foundation, 2013. https://doi.org/10.3389/fpls.2013.00537.","mla":"Cuesta, Candela, et al. “Systems Approaches to Study Root Architecture Dynamics.” Frontiers in Plant Science, vol. 4, 537, Frontiers Research Foundation, 2013, doi:10.3389/fpls.2013.00537.","short":"C. Cuesta, K.T. Wabnik, E. Benková, Frontiers in Plant Science 4 (2013)."},"date_published":"2013-12-26T00:00:00Z","scopus_import":1,"day":"26","has_accepted_license":"1","_id":"828","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Systems approaches to study root architecture dynamics","ddc":["580"],"intvolume":" 4","file":[{"file_size":710835,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2013_FrontiersPlant_Cuesta.pdf","checksum":"0185b3c4d7df9a94bd3ce5a66d213506","date_updated":"2020-07-14T12:48:11Z","date_created":"2019-01-31T10:36:43Z","relation":"main_file","file_id":"5902"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"text":"The plant root system is essential for providing anchorage to the soil, supplying minerals and water, and synthesizing metabolites. It is a dynamic organ modulated by external cues such as environmental signals, water and nutrients availability, salinity and others. Lateral roots (LRs) are initiated from the primary root post-embryonically, after which they progress through discrete developmental stages which can be independently controlled, providing a high level of plasticity during root system formation. Within this review, main contributions are presented, from the classical forward genetic screens to the more recent high-throughput approaches, combined with computer model predictions, dissecting how LRs and thereby root system architecture is established and developed.","lang":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","project":[{"call_identifier":"FP7","name":"Hormonal cross-talk in plant organogenesis","grant_number":"207362","_id":"253FCA6A-B435-11E9-9278-68D0E5697425"}],"doi":"10.3389/fpls.2013.00537","language":[{"iso":"eng"}],"month":"12","year":"2013","publication_status":"published","publisher":"Frontiers Research Foundation","department":[{"_id":"EvBe"}],"author":[{"full_name":"Cuesta, Candela","orcid":"0000-0003-1923-2410","id":"33A3C818-F248-11E8-B48F-1D18A9856A87","last_name":"Cuesta","first_name":"Candela"},{"full_name":"Wabnik, Krzysztof T","last_name":"Wabnik","first_name":"Krzysztof T","orcid":"0000-0001-7263-0560","id":"4DE369A4-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","last_name":"Benková","first_name":"Eva","full_name":"Benková, Eva"}],"date_updated":"2021-01-12T08:17:52Z","date_created":"2018-12-11T11:48:43Z","volume":4,"article_number":"537","file_date_updated":"2020-07-14T12:48:11Z","publist_id":"6820","ec_funded":1},{"language":[{"iso":"eng"}],"doi":"10.1111/tpj.12309","quality_controlled":"1","external_id":{"pmid":["23941199"]},"month":"09","volume":76,"date_updated":"2022-03-21T07:17:26Z","date_created":"2018-12-11T11:48:44Z","author":[{"full_name":"Galbiati, Francesca","last_name":"Galbiati","first_name":"Francesca"},{"full_name":"Sinha Roy, Dola","last_name":"Sinha Roy","first_name":"Dola"},{"full_name":"Simonini, Sara","last_name":"Simonini","first_name":"Sara"},{"full_name":"Cucinotta, Mara","last_name":"Cucinotta","first_name":"Mara"},{"last_name":"Ceccato","first_name":"Luca","full_name":"Ceccato, Luca"},{"orcid":"0000-0003-1923-2410","id":"33A3C818-F248-11E8-B48F-1D18A9856A87","last_name":"Cuesta","first_name":"Candela","full_name":"Cuesta, Candela"},{"first_name":"Mária","last_name":"Šimášková","full_name":"Šimášková, Mária"},{"last_name":"Benková","first_name":"Eva","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Benková, Eva"},{"first_name":"Yuri","last_name":"Kamiuchi","full_name":"Kamiuchi, Yuri"},{"full_name":"Aida, Mitsuhiro","last_name":"Aida","first_name":"Mitsuhiro"},{"full_name":"Weijers, Dolf","first_name":"Dolf","last_name":"Weijers"},{"full_name":"Simon, Rüdiger","last_name":"Simon","first_name":"Rüdiger"},{"last_name":"Masiero","first_name":"Simona","full_name":"Masiero, Simona"},{"last_name":"Colombo","first_name":"Lucia","full_name":"Colombo, Lucia"}],"publisher":"Wiley-Blackwell","publication_status":"published","pmid":1,"year":"2013","acknowledgement":"The project and F.G. were supported by the CARIPLO Foundation (project 2009-2990) and COST (European Cooperation in Science and Technology) action HAPRECI (Harnessing Plant Reproduction for Crop Improvement). E.B. and C.C. were supported by the European Research Council through a ‘Starting Independent Research’ grant (ERC-2007-Stg-207362-HCPO). We thank A.P. MacCabe (Consejo Superior de Investigaciones Científicas, Valencia, Spain) for critical reading of the manuscript.","extern":"1","publist_id":"6818","date_published":"2013-09-19T00:00:00Z","page":"446 - 455","article_type":"original","citation":{"short":"F. Galbiati, D. Sinha Roy, S. Simonini, M. Cucinotta, L. Ceccato, C. Cuesta, M. Šimášková, E. Benková, Y. Kamiuchi, M. Aida, D. Weijers, R. Simon, S. Masiero, L. Colombo, The Plant Journal for Cell and Molecular Biology 76 (2013) 446–455.","mla":"Galbiati, Francesca, et al. “An Integrative Model of the Control of Ovule Primordia Formation.” The Plant Journal for Cell and Molecular Biology, vol. 76, no. 3, Wiley-Blackwell, 2013, pp. 446–55, doi:10.1111/tpj.12309.","chicago":"Galbiati, Francesca, Dola Sinha Roy, Sara Simonini, Mara Cucinotta, Luca Ceccato, Candela Cuesta, Mária Šimášková, et al. “An Integrative Model of the Control of Ovule Primordia Formation.” The Plant Journal for Cell and Molecular Biology. Wiley-Blackwell, 2013. https://doi.org/10.1111/tpj.12309.","ama":"Galbiati F, Sinha Roy D, Simonini S, et al. An integrative model of the control of ovule primordia formation. The Plant journal for cell and molecular biology. 2013;76(3):446-455. doi:10.1111/tpj.12309","apa":"Galbiati, F., Sinha Roy, D., Simonini, S., Cucinotta, M., Ceccato, L., Cuesta, C., … Colombo, L. (2013). An integrative model of the control of ovule primordia formation. The Plant Journal for Cell and Molecular Biology. Wiley-Blackwell. https://doi.org/10.1111/tpj.12309","ieee":"F. Galbiati et al., “An integrative model of the control of ovule primordia formation,” The Plant journal for cell and molecular biology, vol. 76, no. 3. Wiley-Blackwell, pp. 446–455, 2013.","ista":"Galbiati F, Sinha Roy D, Simonini S, Cucinotta M, Ceccato L, Cuesta C, Šimášková M, Benková E, Kamiuchi Y, Aida M, Weijers D, Simon R, Masiero S, Colombo L. 2013. An integrative model of the control of ovule primordia formation. The Plant journal for cell and molecular biology. 76(3), 446–455."},"publication":"The Plant journal for cell and molecular biology","article_processing_charge":"No","day":"19","scopus_import":"1","oa_version":"None","intvolume":" 76","title":"An integrative model of the control of ovule primordia formation","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"830","issue":"3","abstract":[{"lang":"eng","text":"Upon hormonal signaling, ovules develop as lateral organs from the placenta. Ovule numbers ultimately determine the number of seeds that develop, and thereby contribute to the final seed yield in crop plants. We demonstrate here that CUP-SHAPED COTYLEDON 1 (CUC1), CUC2 and AINTEGUMENTA (ANT) have additive effects on ovule primordia formation. We show that expression of the CUC1 and CUC2 genes is required to redundantly regulate expression of PINFORMED1 (PIN1), which in turn is required for ovule primordia formation. Furthermore, our results suggest that the auxin response factor MONOPTEROS (MP/ARF5) may directly bind ANT, CUC1 and CUC2 and promote their transcription. Based on our findings, we propose an integrative model to describe the molecular mechanisms of the early stages of ovule development."}],"type":"journal_article"},{"day":"22","month":"10","publication":"Molecular Systems Biology","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)"},"citation":{"ama":"Péret B, Middleton A, French A, et al. Sequential induction of auxin efflux and influx carriers regulates lateral root emergence. Molecular Systems Biology. 2013;9. doi:10.1038/msb.2013.43","ieee":"B. Péret et al., “Sequential induction of auxin efflux and influx carriers regulates lateral root emergence,” Molecular Systems Biology, vol. 9. Nature Publishing Group, 2013.","apa":"Péret, B., Middleton, A., French, A., Larrieu, A., Bishopp, A., Njo, M., … Bennett, M. (2013). Sequential induction of auxin efflux and influx carriers regulates lateral root emergence. Molecular Systems Biology. Nature Publishing Group. https://doi.org/10.1038/msb.2013.43","ista":"Péret B, Middleton A, French A, Larrieu A, Bishopp A, Njo M, Wells D, Porco S, Mellor N, Band L, Casimiro I, Kleine Vehn J, Vanneste S, Sairanen I, Mallet R, Sandberg G, Ljung K, Beeckman T, Benková E, Friml J, Kramer E, King J, De Smet I, Pridmore T, Owen M, Bennett M. 2013. Sequential induction of auxin efflux and influx carriers regulates lateral root emergence. Molecular Systems Biology. 9.","short":"B. Péret, A. Middleton, A. French, A. Larrieu, A. Bishopp, M. Njo, D. Wells, S. Porco, N. Mellor, L. Band, I. Casimiro, J. Kleine Vehn, S. Vanneste, I. Sairanen, R. Mallet, G. Sandberg, K. Ljung, T. Beeckman, E. Benková, J. Friml, E. Kramer, J. King, I. De Smet, T. Pridmore, M. Owen, M. Bennett, Molecular Systems Biology 9 (2013).","mla":"Péret, Benjamin, et al. “Sequential Induction of Auxin Efflux and Influx Carriers Regulates Lateral Root Emergence.” Molecular Systems Biology, vol. 9, Nature Publishing Group, 2013, doi:10.1038/msb.2013.43.","chicago":"Péret, Benjamin, Alistair Middleton, Andrew French, Antoine Larrieu, Anthony Bishopp, Maria Njo, Darren Wells, et al. “Sequential Induction of Auxin Efflux and Influx Carriers Regulates Lateral Root Emergence.” Molecular Systems Biology. Nature Publishing Group, 2013. https://doi.org/10.1038/msb.2013.43."},"quality_controlled":0,"date_published":"2013-10-22T00:00:00Z","doi":"10.1038/msb.2013.43","type":"journal_article","abstract":[{"text":"In Arabidopsis, lateral roots originate from pericycle cells deep within the primary root. New lateral root primordia (LRP) have to emerge through several overlaying tissues. Here, we report that auxin produced in new LRP is transported towards the outer tissues where it triggers cell separation by inducing both the auxin influx carrier LAX3 and cell-wall enzymes. LAX3 is expressed in just two cell files overlaying new LRP. To understand how this striking pattern of LAX3 expression is regulated, we developed a mathematical model that captures the network regulating its expression and auxin transport within realistic three-dimensional cell and tissue geometries. Our model revealed that, for the LAX3 spatial expression to be robust to natural variations in root tissue geometry, an efflux carrier is required--later identified to be PIN3. To prevent LAX3 from being transiently expressed in multiple cell files, PIN3 and LAX3 must be induced consecutively, which we later demonstrated to be the case. Our study exemplifies how mathematical models can be used to direct experiments to elucidate complex developmental processes.","lang":"eng"}],"publist_id":"6817","extern":1,"_id":"831","year":"2013","acknowledgement":"This work was supported by an FEBS Long‐Term Fellowship (BP), an Intra‐European Fellowship for Career Development under the 7th framework of the European Commission (IEF‐2008‐220506 to BP), an EMBO Long‐Term Fellowship (BP), an European Reintegration Grant under the 7th framework of the European Commission (ERG‐2010‐276662 to BP) and the Swedish Research Council (VR 621‐2010‐5720 to IS, GS and KL). AMM, APF, AL, LRB, SP, NM, DMW, MO, JRK and MJB acknowledge the support of the Biotechnology and Biological Sciences Research Council (BBSRC) and Engineering and Physical Sciences Research Council (EPSRC) funding to the Centre for Plant Integrative Biology (CPIB); BBSRC Professorial Research Fellowship funding to DMW and MJB; Belgian Scientific policy (BELSPO contract MARS) to TB and MJB. We thank Bert de Rybel for his help in Multisite Gateway cloning.","status":"public","publication_status":"published","title":"Sequential induction of auxin efflux and influx carriers regulates lateral root emergence","publisher":"Nature Publishing Group","intvolume":" 9","author":[{"last_name":"Péret","first_name":"Benjamin","full_name":"Péret, Benjamin"},{"last_name":"Middleton","first_name":"Alistair","full_name":"Middleton, Alistair M"},{"full_name":"French, Andrew P","last_name":"French","first_name":"Andrew"},{"last_name":"Larrieu","first_name":"Antoine","full_name":"Larrieu, Antoine"},{"full_name":"Bishopp, Anthony","last_name":"Bishopp","first_name":"Anthony"},{"last_name":"Njo","first_name":"Maria","full_name":"Njo, Maria"},{"full_name":"Wells, Darren M","last_name":"Wells","first_name":"Darren"},{"full_name":"Porco, Silvana","first_name":"Silvana","last_name":"Porco"},{"first_name":"Nathan","last_name":"Mellor","full_name":"Mellor, Nathan"},{"full_name":"Band, Leah R","last_name":"Band","first_name":"Leah"},{"full_name":"Casimiro, Ilda","last_name":"Casimiro","first_name":"Ilda"},{"first_name":"Jürgen","last_name":"Kleine Vehn","full_name":"Kleine-Vehn, Jürgen"},{"last_name":"Vanneste","first_name":"Steffen","full_name":"Vanneste, Steffen"},{"last_name":"Sairanen","first_name":"Ilkka","full_name":"Sairanen, Ilkka"},{"full_name":"Mallet, Romain","first_name":"Romain","last_name":"Mallet"},{"first_name":"Göran","last_name":"Sandberg","full_name":"Sandberg, Göran"},{"full_name":"Ljung, Karin","last_name":"Ljung","first_name":"Karin"},{"full_name":"Beeckman, Tom","last_name":"Beeckman","first_name":"Tom"},{"last_name":"Benková","first_name":"Eva","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Eva Benková"},{"full_name":"Jirí Friml","first_name":"Jirí","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"},{"last_name":"Kramer","first_name":"Eric","full_name":"Kramer, Eric"},{"full_name":"King, John R","last_name":"King","first_name":"John"},{"last_name":"De Smet","first_name":"Ive","full_name":"De Smet, Ive"},{"full_name":"Pridmore, Tony","last_name":"Pridmore","first_name":"Tony"},{"last_name":"Owen","first_name":"Markus","full_name":"Owen, Markus"},{"full_name":"Bennett, Malcolm J","last_name":"Bennett","first_name":"Malcolm"}],"date_created":"2018-12-11T11:48:44Z","date_updated":"2021-01-12T08:18:03Z","volume":9},{"day":"09","month":"10","publication_identifier":{"issn":["0925-2738","1573-5001"]},"article_processing_charge":"No","keyword":["Spectroscopy","Biochemistry"],"language":[{"iso":"eng"}],"doi":"10.1007/s10858-013-9787-x","date_published":"2013-10-09T00:00:00Z","quality_controlled":"1","article_type":"original","page":"263-280","publication":"Journal of Biomolecular NMR","citation":{"ista":"Haller JD, Schanda P. 2013. Amplitudes and time scales of picosecond-to-microsecond motion in proteins studied by solid-state NMR: a critical evaluation of experimental approaches and application to crystalline ubiquitin. Journal of Biomolecular NMR. 57(3), 263–280.","apa":"Haller, J. D., & Schanda, P. (2013). Amplitudes and time scales of picosecond-to-microsecond motion in proteins studied by solid-state NMR: a critical evaluation of experimental approaches and application to crystalline ubiquitin. Journal of Biomolecular NMR. Springer Nature. https://doi.org/10.1007/s10858-013-9787-x","ieee":"J. D. Haller and P. Schanda, “Amplitudes and time scales of picosecond-to-microsecond motion in proteins studied by solid-state NMR: a critical evaluation of experimental approaches and application to crystalline ubiquitin,” Journal of Biomolecular NMR, vol. 57, no. 3. Springer Nature, pp. 263–280, 2013.","ama":"Haller JD, Schanda P. Amplitudes and time scales of picosecond-to-microsecond motion in proteins studied by solid-state NMR: a critical evaluation of experimental approaches and application to crystalline ubiquitin. Journal of Biomolecular NMR. 2013;57(3):263-280. doi:10.1007/s10858-013-9787-x","chicago":"Haller, Jens D., and Paul Schanda. “Amplitudes and Time Scales of Picosecond-to-Microsecond Motion in Proteins Studied by Solid-State NMR: A Critical Evaluation of Experimental Approaches and Application to Crystalline Ubiquitin.” Journal of Biomolecular NMR. Springer Nature, 2013. https://doi.org/10.1007/s10858-013-9787-x.","mla":"Haller, Jens D., and Paul Schanda. “Amplitudes and Time Scales of Picosecond-to-Microsecond Motion in Proteins Studied by Solid-State NMR: A Critical Evaluation of Experimental Approaches and Application to Crystalline Ubiquitin.” Journal of Biomolecular NMR, vol. 57, no. 3, Springer Nature, 2013, pp. 263–80, doi:10.1007/s10858-013-9787-x.","short":"J.D. Haller, P. Schanda, Journal of Biomolecular NMR 57 (2013) 263–280."},"extern":"1","abstract":[{"text":"Solid-state NMR provides insight into protein motion over time scales ranging from picoseconds to seconds. While in solution state the methodology to measure protein dynamics is well established, there is currently no such consensus protocol for measuring dynamics in solids. In this article, we perform a detailed investigation of measurement protocols for fast motions, i.e. motions ranging from picoseconds to a few microseconds, which is the range covered by dipolar coupling and relaxation experiments. We perform a detailed theoretical investigation how dipolar couplings and relaxation data can provide information about amplitudes and time scales of local motion. We show that the measurement of dipolar couplings is crucial for obtaining accurate motional parameters, while systematic errors are found when only relaxation data are used. Based on this realization, we investigate how the REDOR experiment can provide such data in a very accurate manner. We identify that with accurate rf calibration, and explicit consideration of rf field inhomogeneities, one can obtain highly accurate absolute order parameters. We then perform joint model-free analyses of 6 relaxation data sets and dipolar couplings, based on previously existing, as well as new data sets on microcrystalline ubiquitin. We show that nanosecond motion can be detected primarily in loop regions, and compare solid-state data to solution-state relaxation and RDC analyses. The protocols investigated here will serve as a useful basis towards the establishment of a routine protocol for the characterization of ps–μs motions in proteins by solid-state NMR.","lang":"eng"}],"issue":"3","type":"journal_article","date_updated":"2021-01-12T08:19:26Z","date_created":"2020-09-18T10:09:05Z","volume":57,"oa_version":"None","author":[{"full_name":"Haller, Jens D.","first_name":"Jens D.","last_name":"Haller"},{"id":"7B541462-FAF6-11E9-A490-E8DFE5697425","orcid":"0000-0002-9350-7606","first_name":"Paul","last_name":"Schanda","full_name":"Schanda, Paul"}],"title":"Amplitudes and time scales of picosecond-to-microsecond motion in proteins studied by solid-state NMR: a critical evaluation of experimental approaches and application to crystalline ubiquitin","status":"public","publication_status":"published","intvolume":" 57","publisher":"Springer Nature","_id":"8461","year":"2013","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"day":"09","month":"08","publication_identifier":{"issn":["0022-2836"]},"article_processing_charge":"No","keyword":["Molecular Biology"],"date_published":"2013-08-09T00:00:00Z","doi":"10.1016/j.jmb.2013.04.028","language":[{"iso":"eng"}],"publication":"Journal of Molecular Biology","citation":{"ieee":"E. Rennella et al., “Oligomeric states along the folding pathways of β2-microglobulin: Kinetics, thermodynamics, and structure,” Journal of Molecular Biology, vol. 425, no. 15. Elsevier, pp. 2722–2736, 2013.","apa":"Rennella, E., Cutuil, T., Schanda, P., Ayala, I., Gabel, F., Forge, V., … Brutscher, B. (2013). Oligomeric states along the folding pathways of β2-microglobulin: Kinetics, thermodynamics, and structure. Journal of Molecular Biology. Elsevier. https://doi.org/10.1016/j.jmb.2013.04.028","ista":"Rennella E, Cutuil T, Schanda P, Ayala I, Gabel F, Forge V, Corazza A, Esposito G, Brutscher B. 2013. Oligomeric states along the folding pathways of β2-microglobulin: Kinetics, thermodynamics, and structure. Journal of Molecular Biology. 425(15), 2722–2736.","ama":"Rennella E, Cutuil T, Schanda P, et al. Oligomeric states along the folding pathways of β2-microglobulin: Kinetics, thermodynamics, and structure. Journal of Molecular Biology. 2013;425(15):2722-2736. doi:10.1016/j.jmb.2013.04.028","chicago":"Rennella, E., T. Cutuil, Paul Schanda, I. Ayala, F. Gabel, V. Forge, A. Corazza, G. Esposito, and B. Brutscher. “Oligomeric States along the Folding Pathways of Β2-Microglobulin: Kinetics, Thermodynamics, and Structure.” Journal of Molecular Biology. Elsevier, 2013. https://doi.org/10.1016/j.jmb.2013.04.028.","short":"E. Rennella, T. Cutuil, P. Schanda, I. Ayala, F. Gabel, V. Forge, A. Corazza, G. Esposito, B. Brutscher, Journal of Molecular Biology 425 (2013) 2722–2736.","mla":"Rennella, E., et al. “Oligomeric States along the Folding Pathways of Β2-Microglobulin: Kinetics, Thermodynamics, and Structure.” Journal of Molecular Biology, vol. 425, no. 15, Elsevier, 2013, pp. 2722–36, doi:10.1016/j.jmb.2013.04.028."},"article_type":"original","quality_controlled":"1","page":"2722-2736","abstract":[{"lang":"eng","text":"The transition of proteins from their soluble functional state to amyloid fibrils and aggregates is associated with the onset of several human diseases. Protein aggregation often requires some structural reshaping and the subsequent formation of intermolecular contacts. Therefore, the study of the conformation of excited protein states and their ability to form oligomers is of primary importance for understanding the molecular basis of amyloid fibril formation. Here, we investigated the oligomerization processes that occur along the folding of the amyloidogenic human protein β2-microglobulin. The combination of real-time two-dimensional NMR data with real-time small-angle X-ray scattering measurements allowed us to derive thermodynamic and kinetic information on protein oligomerization of different conformational states populated along the folding pathways. In particular, we could demonstrate that a long-lived folding intermediate (I-state) has a higher propensity to oligomerize compared to the native state. Our data agree well with a simple five-state kinetic model that involves only monomeric and dimeric species. The dimers have an elongated shape with the dimerization interface located at the apical side of β2-microglobulin close to Pro32, the residue that has a trans conformation in the I-state and a cis conformation in the native (N) state. Our experimental data suggest that partial unfolding in the apical half of the protein close to Pro32 leads to an excited state conformation with enhanced propensity for oligomerization. This excited state becomes more populated in the transient I-state due to the destabilization of the native conformation by the trans-Pro32 configuration."}],"issue":"15","extern":"1","type":"journal_article","author":[{"full_name":"Rennella, E.","last_name":"Rennella","first_name":"E."},{"first_name":"T.","last_name":"Cutuil","full_name":"Cutuil, T."},{"id":"7B541462-FAF6-11E9-A490-E8DFE5697425","orcid":"0000-0002-9350-7606","first_name":"Paul","last_name":"Schanda","full_name":"Schanda, Paul"},{"first_name":"I.","last_name":"Ayala","full_name":"Ayala, I."},{"full_name":"Gabel, F.","last_name":"Gabel","first_name":"F."},{"full_name":"Forge, V.","first_name":"V.","last_name":"Forge"},{"full_name":"Corazza, A.","first_name":"A.","last_name":"Corazza"},{"full_name":"Esposito, G.","last_name":"Esposito","first_name":"G."},{"last_name":"Brutscher","first_name":"B.","full_name":"Brutscher, B."}],"date_created":"2020-09-18T10:09:12Z","date_updated":"2022-08-25T14:56:24Z","volume":425,"oa_version":"None","year":"2013","_id":"8462","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","title":"Oligomeric states along the folding pathways of β2-microglobulin: Kinetics, thermodynamics, and structure","status":"public","publication_status":"published","intvolume":" 425","publisher":"Elsevier"},{"date_published":"2013-05-30T00:00:00Z","doi":"10.1038/nature12220","page":"E2 - E3","quality_controlled":0,"citation":{"ama":"Breen M, Kemena C, Vlasov P, Notredame C, Kondrashov F. Breen et al. reply. Nature. 2013;497(7451):E2-E3. doi:10.1038/nature12220","ieee":"M. Breen, C. Kemena, P. Vlasov, C. Notredame, and F. Kondrashov, “Breen et al. reply,” Nature, vol. 497, no. 7451. Nature Publishing Group, pp. E2–E3, 2013.","apa":"Breen, M., Kemena, C., Vlasov, P., Notredame, C., & Kondrashov, F. (2013). Breen et al. reply. Nature. Nature Publishing Group. https://doi.org/10.1038/nature12220","ista":"Breen M, Kemena C, Vlasov P, Notredame C, Kondrashov F. 2013. Breen et al. reply. Nature. 497(7451), E2–E3.","short":"M. Breen, C. Kemena, P. Vlasov, C. Notredame, F. Kondrashov, Nature 497 (2013) E2–E3.","mla":"Breen, Michael, et al. “Breen et Al. Reply.” Nature, vol. 497, no. 7451, Nature Publishing Group, 2013, pp. E2–3, doi:10.1038/nature12220.","chicago":"Breen, Michael, Carsten Kemena, Peter Vlasov, Cédric Notredame, and Fyodor Kondrashov. “Breen et Al. Reply.” Nature. Nature Publishing Group, 2013. https://doi.org/10.1038/nature12220."},"publication":"Nature","month":"05","day":"30","volume":497,"date_updated":"2021-01-12T08:21:40Z","date_created":"2018-12-11T11:49:05Z","author":[{"last_name":"Breen","first_name":"Michael","full_name":"Breen, Michael S"},{"last_name":"Kemena","first_name":"Carsten","full_name":"Kemena, Carsten"},{"last_name":"Vlasov","first_name":"Peter","full_name":"Vlasov, Peter K"},{"first_name":"Cédric","last_name":"Notredame","full_name":"Notredame, Cédric"},{"full_name":"Fyodor Kondrashov","orcid":"0000-0001-8243-4694","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","last_name":"Kondrashov","first_name":"Fyodor"}],"publisher":"Nature Publishing Group","intvolume":" 497","publication_status":"published","title":"Breen et al. reply","status":"public","year":"2013","_id":"899","extern":1,"publist_id":"6747","issue":"7451","abstract":[{"lang":"eng","text":"Understanding fitness landscapes, a conceptual depiction of the genotype-to-phenotype relationship, is crucial to many areas of biology. Two aspects of fitness landscapes are the focus of contemporary studies of molecular evolution. First, the local shape of the fitness landscape defined by the contribution of individual alleles to fitness that is independent of all genetic interactions. Second, the global, multidimensional fitness landscape shape determined by how interactions between alleles at different loci change each other’s fitness impact, or epistasis. In explaining the high amino-acid usage (u), we focused on the global shape of the fitness landscape, ignoring the perturbations at individual sites."}],"type":"journal_article"},{"day":"01","month":"08","article_processing_charge":"No","publication_identifier":{"issn":["0749-6419"]},"scopus_import":"1","language":[{"iso":"eng"}],"date_published":"2013-08-01T00:00:00Z","doi":"10.1016/j.ijplas.2013.01.006","quality_controlled":"1","article_type":"original","page":"65-79","publication":"International Journal of Plasticity","citation":{"mla":"Cheng, Bingqing, and Alfonso H. W. Ngan. “The Crystal Structures of Sintered Copper Nanoparticles: A Molecular Dynamics Study.” International Journal of Plasticity, vol. 47, Elsevier, 2013, pp. 65–79, doi:10.1016/j.ijplas.2013.01.006.","short":"B. Cheng, A.H.W. Ngan, International Journal of Plasticity 47 (2013) 65–79.","chicago":"Cheng, Bingqing, and Alfonso H.W. Ngan. “The Crystal Structures of Sintered Copper Nanoparticles: A Molecular Dynamics Study.” International Journal of Plasticity. Elsevier, 2013. https://doi.org/10.1016/j.ijplas.2013.01.006.","ama":"Cheng B, Ngan AHW. The crystal structures of sintered copper nanoparticles: A molecular dynamics study. International Journal of Plasticity. 2013;47:65-79. doi:10.1016/j.ijplas.2013.01.006","ista":"Cheng B, Ngan AHW. 2013. The crystal structures of sintered copper nanoparticles: A molecular dynamics study. International Journal of Plasticity. 47, 65–79.","apa":"Cheng, B., & Ngan, A. H. W. (2013). The crystal structures of sintered copper nanoparticles: A molecular dynamics study. International Journal of Plasticity. Elsevier. https://doi.org/10.1016/j.ijplas.2013.01.006","ieee":"B. Cheng and A. H. W. Ngan, “The crystal structures of sintered copper nanoparticles: A molecular dynamics study,” International Journal of Plasticity, vol. 47. Elsevier, pp. 65–79, 2013."},"extern":"1","abstract":[{"lang":"eng","text":"The coalescence of nano-crystals during sintering is often found to result in interesting crystalline structures such as multi-fold twins, and yet the plasticity mechanism accompanying their formation is unclear. In this work, the sintering behavior of two unsupported copper nanoparticles initially at room temperature is investigated by molecular dynamics simulations under the constant-energy ensemble. The results reveal that once the two nanoparticles are brought into contact, they often go through drastic structural changes with the inter-particle grain boundary quickly eliminated, and single- and multi-fold twinning occurs frequently in the coalesced product. Whereas the formation of single twins is found to be via the more usual mechanism of emission of Shockley partials on {1 1 1} planes, the formation of fivefold twins, however, takes place via a novel dislocation-free mechanism involving a series of shear and rigid-body rotation processes caused by elastic waves with amplitudes not corresponding to any allowable Burgers vector in the fcc lattice. Such a lattice-wave, dislocation-free twinning mechanism has never been reported before."}],"type":"journal_article","date_updated":"2023-02-23T14:04:30Z","date_created":"2021-07-15T14:27:44Z","volume":47,"oa_version":"None","author":[{"last_name":"Cheng","first_name":"Bingqing","orcid":"0000-0002-3584-9632","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","full_name":"Cheng, Bingqing"},{"full_name":"Ngan, Alfonso H.W.","first_name":"Alfonso H.W.","last_name":"Ngan"}],"status":"public","publication_status":"published","title":"The crystal structures of sintered copper nanoparticles: A molecular dynamics study","publisher":"Elsevier","intvolume":" 47","_id":"9674","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","year":"2013"},{"language":[{"iso":"eng"}],"doi":"10.1016/j.commatsci.2013.03.014","date_published":"2013-06-01T00:00:00Z","page":"1-11","quality_controlled":"1","article_type":"original","citation":{"mla":"Cheng, Bingqing, and Alfonso H. W. Ngan. “The Sintering and Densification Behaviour of Many Copper Nanoparticles: A Molecular Dynamics Study.” Computational Materials Science, vol. 74, Elsevier, 2013, pp. 1–11, doi:10.1016/j.commatsci.2013.03.014.","short":"B. Cheng, A.H.W. Ngan, Computational Materials Science 74 (2013) 1–11.","chicago":"Cheng, Bingqing, and Alfonso H.W. Ngan. “The Sintering and Densification Behaviour of Many Copper Nanoparticles: A Molecular Dynamics Study.” Computational Materials Science. Elsevier, 2013. https://doi.org/10.1016/j.commatsci.2013.03.014.","ama":"Cheng B, Ngan AHW. The sintering and densification behaviour of many copper nanoparticles: A molecular dynamics study. Computational Materials Science. 2013;74:1-11. doi:10.1016/j.commatsci.2013.03.014","ista":"Cheng B, Ngan AHW. 2013. The sintering and densification behaviour of many copper nanoparticles: A molecular dynamics study. Computational Materials Science. 74, 1–11.","apa":"Cheng, B., & Ngan, A. H. W. (2013). The sintering and densification behaviour of many copper nanoparticles: A molecular dynamics study. Computational Materials Science. Elsevier. https://doi.org/10.1016/j.commatsci.2013.03.014","ieee":"B. Cheng and A. H. W. Ngan, “The sintering and densification behaviour of many copper nanoparticles: A molecular dynamics study,” Computational Materials Science, vol. 74. Elsevier, pp. 1–11, 2013."},"publication":"Computational Materials Science","article_processing_charge":"No","publication_identifier":{"issn":["0927-0256"]},"day":"01","month":"06","scopus_import":"1","volume":74,"oa_version":"None","date_created":"2021-07-16T06:46:38Z","date_updated":"2023-02-23T14:04:35Z","author":[{"orcid":"0000-0002-3584-9632","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","last_name":"Cheng","first_name":"Bingqing","full_name":"Cheng, Bingqing"},{"full_name":"Ngan, Alfonso H.W.","last_name":"Ngan","first_name":"Alfonso H.W."}],"publisher":"Elsevier","intvolume":" 74","publication_status":"published","title":"The sintering and densification behaviour of many copper nanoparticles: A molecular dynamics study","status":"public","year":"2013","_id":"9676","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","extern":"1","abstract":[{"text":"Despite its relevance to a range of technological applications including nanocrystalline material fabrication, the sintering mechanisms of nanoparticles have not been well understood. It has been recognized that extrapolation from understanding of macro-particle sintering is unreliable for the nano-particle size regime. In this work, the sintering behaviour of copper nanoparticles under periodic boundary conditions at different temperatures and pressures was investigated by Molecular Dynamics simulations. It was found that smaller particle sizes, higher temperature and higher external pressure facilitate densification. Through a comparison with a two-sphere model, the governing mechanisms for many nanoparticles sintered at low temperature (T⩽900K) were identified to be a variety of plasticity processes including dislocation, twinning and even amorphization at the contact neck regions, due to the presence of high stresses.","lang":"eng"}],"type":"journal_article"},{"type":"journal_article","extern":1,"issue":"2","publist_id":"6429","abstract":[{"lang":"eng","text":"We study the stability of the normal state in a mesoscopic NSN junction biased by a constant voltage V with respect to the formation of the superconducting order. Using the linearized time-dependent Ginzburg-Landau equation, we obtain the temperature dependence of the instability line, V inst(T), where nucleation of superconductivity takes place. For sufficiently low biases, a stationary symmetric superconducting state emerges below the instability line. For higher biases, the normal phase is destroyed by the formation of a nonstationary bimodal state with two superconducting nuclei localized near the opposite terminals. The low-temperature and large-voltage behavior of the instability line is highly sensitive to the details of the inelastic relaxation mechanism in the wire. Therefore, experimental studies of Vinst(T) in NSN junctions may be used as an effective tool to access the parameters of the inelastic relaxation in the normal state."}],"intvolume":" 87","publisher":"American Physical Society","publication_status":"published","status":"public","title":"Onset of superconductivity in a voltage-biased normal-superconducting-normal microbridge","_id":"971","year":"2013","acknowledgement":"We are grateful to M. V. Feigel'man, A. Kamenev, T. M. Klapwijk, J. P. Pekola, V. V. Ryazanov, J. C. W. Song, and D. Y. Vodolazov for discussions.","volume":87,"date_created":"2018-12-11T11:49:28Z","date_updated":"2021-01-12T08:22:20Z","author":[{"full_name":"Maksym Serbyn","last_name":"Serbyn","first_name":"Maksym","orcid":"0000-0002-2399-5827","id":"47809E7E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Mikhail","last_name":"Skvortsov","full_name":"Skvortsov, Mikhail A"}],"month":"01","day":"02","quality_controlled":0,"citation":{"short":"M. Serbyn, M. Skvortsov, Physical Review B - Condensed Matter and Materials Physics 87 (2013).","mla":"Serbyn, Maksym, and Mikhail Skvortsov. “Onset of Superconductivity in a Voltage-Biased Normal-Superconducting-Normal Microbridge.” Physical Review B - Condensed Matter and Materials Physics, vol. 87, no. 2, American Physical Society, 2013, doi:10.1103/PhysRevB.87.020501.","chicago":"Serbyn, Maksym, and Mikhail Skvortsov. “Onset of Superconductivity in a Voltage-Biased Normal-Superconducting-Normal Microbridge.” Physical Review B - Condensed Matter and Materials Physics. American Physical Society, 2013. https://doi.org/10.1103/PhysRevB.87.020501.","ama":"Serbyn M, Skvortsov M. Onset of superconductivity in a voltage-biased normal-superconducting-normal microbridge. Physical Review B - Condensed Matter and Materials Physics. 2013;87(2). doi:10.1103/PhysRevB.87.020501","ieee":"M. Serbyn and M. Skvortsov, “Onset of superconductivity in a voltage-biased normal-superconducting-normal microbridge,” Physical Review B - Condensed Matter and Materials Physics, vol. 87, no. 2. American Physical Society, 2013.","apa":"Serbyn, M., & Skvortsov, M. (2013). Onset of superconductivity in a voltage-biased normal-superconducting-normal microbridge. Physical Review B - Condensed Matter and Materials Physics. American Physical Society. https://doi.org/10.1103/PhysRevB.87.020501","ista":"Serbyn M, Skvortsov M. 2013. Onset of superconductivity in a voltage-biased normal-superconducting-normal microbridge. Physical Review B - Condensed Matter and Materials Physics. 87(2)."},"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1208.6004","open_access":"1"}],"publication":"Physical Review B - Condensed Matter and Materials Physics","doi":"10.1103/PhysRevB.87.020501","date_published":"2013-01-02T00:00:00Z"},{"year":"2013","_id":"972","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"American Association for the Advancement of Science","intvolume":" 341","status":"public","publication_status":"published","title":"Observation of dirac node formation and mass acquisition in a topological crystalline insulator","author":[{"first_name":"Yoshinori","last_name":"Okada","full_name":"Okada, Yoshinori"},{"full_name":"Serbyn, Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827","first_name":"Maksym","last_name":"Serbyn"},{"full_name":"Lin, Hsin","last_name":"Lin","first_name":"Hsin"},{"last_name":"Walkup","first_name":"Daniel","full_name":"Walkup, Daniel"},{"last_name":"Zhou","first_name":"Wenwen","full_name":"Zhou, Wenwen"},{"last_name":"Dhital","first_name":"Chetan","full_name":"Dhital, Chetan"},{"last_name":"Neupane","first_name":"Madhab","full_name":"Neupane, Madhab"},{"first_name":"Suyang","last_name":"Xu","full_name":"Xu, Suyang"},{"full_name":"Wang, Yungjui","first_name":"Yungjui","last_name":"Wang"},{"last_name":"Sankar","first_name":"Raman","full_name":"Sankar, Raman"},{"first_name":"Fangcheng","last_name":"Chou","full_name":"Chou, Fangcheng"},{"first_name":"Arun","last_name":"Bansil","full_name":"Bansil, Arun"},{"first_name":"Md","last_name":"Hasan","full_name":"Hasan, Md"},{"full_name":"Wilson, Stephen","first_name":"Stephen","last_name":"Wilson"},{"last_name":"Fu","first_name":"Liang","full_name":"Fu, Liang"},{"last_name":"Madhavan","first_name":"Vidya","full_name":"Madhavan, Vidya"}],"oa_version":"Preprint","volume":341,"date_created":"2018-12-11T11:49:29Z","date_updated":"2021-01-12T08:22:20Z","type":"journal_article","publist_id":"6430","issue":"6153","abstract":[{"lang":"eng","text":"In topological crystalline insulators (TCIs), topology and crystal symmetry intertwine to create surface states with distinct characteristics. The breaking of crystal symmetry in TCIs is predicted to impart mass to the massless Dirac fermions. Here, we report high-resolution scanning tunneling microscopy studies of a TCI, Pb1-xSnxSe that reveal the coexistence of zero-mass Dirac fermions protected by crystal symmetry with massive Dirac fermions consistent with crystal symmetry breaking. In addition, we show two distinct regimes of the Fermi surface topology separated by a Van-Hove singularity at the Lifshitz transition point. Our work paves the way for engineering the Dirac band gap and realizing interaction-driven topological quantum phenomena in TCIs."}],"extern":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1305.2823"}],"citation":{"apa":"Okada, Y., Serbyn, M., Lin, H., Walkup, D., Zhou, W., Dhital, C., … Madhavan, V. (2013). Observation of dirac node formation and mass acquisition in a topological crystalline insulator. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.1239451","ieee":"Y. Okada et al., “Observation of dirac node formation and mass acquisition in a topological crystalline insulator,” Science, vol. 341, no. 6153. American Association for the Advancement of Science, pp. 1496–1499, 2013.","ista":"Okada Y, Serbyn M, Lin H, Walkup D, Zhou W, Dhital C, Neupane M, Xu S, Wang Y, Sankar R, Chou F, Bansil A, Hasan M, Wilson S, Fu L, Madhavan V. 2013. Observation of dirac node formation and mass acquisition in a topological crystalline insulator. Science. 341(6153), 1496–1499.","ama":"Okada Y, Serbyn M, Lin H, et al. Observation of dirac node formation and mass acquisition in a topological crystalline insulator. Science. 2013;341(6153):1496-1499. doi:10.1126/science.1239451","chicago":"Okada, Yoshinori, Maksym Serbyn, Hsin Lin, Daniel Walkup, Wenwen Zhou, Chetan Dhital, Madhab Neupane, et al. “Observation of Dirac Node Formation and Mass Acquisition in a Topological Crystalline Insulator.” Science. American Association for the Advancement of Science, 2013. https://doi.org/10.1126/science.1239451.","short":"Y. Okada, M. Serbyn, H. Lin, D. Walkup, W. Zhou, C. Dhital, M. Neupane, S. Xu, Y. Wang, R. Sankar, F. Chou, A. Bansil, M. Hasan, S. Wilson, L. Fu, V. Madhavan, Science 341 (2013) 1496–1499.","mla":"Okada, Yoshinori, et al. “Observation of Dirac Node Formation and Mass Acquisition in a Topological Crystalline Insulator.” Science, vol. 341, no. 6153, American Association for the Advancement of Science, 2013, pp. 1496–99, doi:10.1126/science.1239451."},"external_id":{"arxiv":["1305.2823"]},"oa":1,"publication":"Science","page":"1496 - 1499","quality_controlled":"1","doi":"10.1126/science.1239451","date_published":"2013-01-01T00:00:00Z","language":[{"iso":"eng"}],"month":"01","day":"01"},{"citation":{"ama":"Serbyn M, Papić Z, Abanin D. Universal slow growth of entanglement in interacting strongly disordered systems. Physical Review Letters. 2013;110(26). doi:10.1103/PhysRevLett.110.260601","apa":"Serbyn, M., Papić, Z., & Abanin, D. (2013). Universal slow growth of entanglement in interacting strongly disordered systems. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.110.260601","ieee":"M. Serbyn, Z. Papić, and D. Abanin, “Universal slow growth of entanglement in interacting strongly disordered systems,” Physical Review Letters, vol. 110, no. 26. American Physical Society, 2013.","ista":"Serbyn M, Papić Z, Abanin D. 2013. Universal slow growth of entanglement in interacting strongly disordered systems. Physical Review Letters. 110(26).","short":"M. Serbyn, Z. Papić, D. Abanin, Physical Review Letters 110 (2013).","mla":"Serbyn, Maksym, et al. “Universal Slow Growth of Entanglement in Interacting Strongly Disordered Systems.” Physical Review Letters, vol. 110, no. 26, American Physical Society, 2013, doi:10.1103/PhysRevLett.110.260601.","chicago":"Serbyn, Maksym, Zlatko Papić, and Dmitry Abanin. “Universal Slow Growth of Entanglement in Interacting Strongly Disordered Systems.” Physical Review Letters. American Physical Society, 2013. https://doi.org/10.1103/PhysRevLett.110.260601."},"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1304.4605"}],"publication":"Physical Review Letters","quality_controlled":0,"date_published":"2013-06-28T00:00:00Z","doi":"10.1103/PhysRevLett.110.260601","month":"06","day":"28","_id":"975","acknowledgement":"We would like to thank E. Altman and J. Moore for useful comments on the manuscript. This research was supported in part by Perimeter Institute for Theoretical Physics. Research at Perimeter Institute is supported by the Government of Canada through Industry Canada and by the Province of Ontario through the Ministry of Economic Development & Innovation. Z. P. was supported by DOE Grant No. DE-SC0002140. The simulations presented in this article were performed on computational resources supported by the High Performance Computing Center (PICSciE) at Princeton University.","year":"2013","intvolume":" 110","publisher":"American Physical Society","title":"Universal slow growth of entanglement in interacting strongly disordered systems","publication_status":"published","status":"public","author":[{"full_name":"Maksym Serbyn","last_name":"Serbyn","first_name":"Maksym","orcid":"0000-0002-2399-5827","id":"47809E7E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Papić, Zlatko","first_name":"Zlatko","last_name":"Papić"},{"first_name":"Dmitry","last_name":"Abanin","full_name":"Abanin, Dmitry A"}],"volume":110,"date_updated":"2021-01-12T08:22:22Z","date_created":"2018-12-11T11:49:29Z","type":"journal_article","issue":"26","publist_id":"6426","abstract":[{"lang":"eng","text":"Recent numerical work by Bardarson, Pollmann, and Moore revealed a slow, logarithmic in time, growth of the entanglement entropy for initial product states in a putative many-body localized phase. We show that this surprising phenomenon results from the dephasing due to exponentially small interaction-induced corrections to the eigenenergies of different states. For weak interactions, we find that the entanglement entropy grows as ξln (Vt/), where V is the interaction strength, and ξ is the single-particle localization length. The saturated value of the entanglement entropy at long times is determined by the participation ratios of the initial state over the eigenstates of the subsystem. Our work shows that the logarithmic entanglement growth is a universal phenomenon characteristic of the many-body localized phase in any number of spatial dimensions, and reveals a broad hierarchy of dephasing time scales present in such a phase."}],"extern":1},{"doi":"10.1371/journal.pone.0080814.s001","date_published":"2013-12-12T00:00:00Z","citation":{"ama":"Zagorsky B, Reiter J, Chatterjee K, Nowak M. Forgiver triumphs in alternating prisoner’s dilemma . 2013. doi:10.1371/journal.pone.0080814.s001","ieee":"B. Zagorsky, J. Reiter, K. Chatterjee, and M. Nowak, “Forgiver triumphs in alternating prisoner’s dilemma .” Public Library of Science, 2013.","apa":"Zagorsky, B., Reiter, J., Chatterjee, K., & Nowak, M. (2013). Forgiver triumphs in alternating prisoner’s dilemma . Public Library of Science. https://doi.org/10.1371/journal.pone.0080814.s001","ista":"Zagorsky B, Reiter J, Chatterjee K, Nowak M. 2013. Forgiver triumphs in alternating prisoner’s dilemma , Public Library of Science, 10.1371/journal.pone.0080814.s001.","short":"B. Zagorsky, J. Reiter, K. Chatterjee, M. Nowak, (2013).","mla":"Zagorsky, Benjamin, et al. Forgiver Triumphs in Alternating Prisoner’s Dilemma . Public Library of Science, 2013, doi:10.1371/journal.pone.0080814.s001.","chicago":"Zagorsky, Benjamin, Johannes Reiter, Krishnendu Chatterjee, and Martin Nowak. “Forgiver Triumphs in Alternating Prisoner’s Dilemma .” Public Library of Science, 2013. https://doi.org/10.1371/journal.pone.0080814.s001."},"article_processing_charge":"No","day":"12","month":"12","oa_version":"Published Version","date_updated":"2023-02-23T10:34:39Z","date_created":"2021-07-28T15:45:07Z","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"2247"}]},"author":[{"first_name":"Benjamin","last_name":"Zagorsky","full_name":"Zagorsky, Benjamin"},{"full_name":"Reiter, Johannes","last_name":"Reiter","first_name":"Johannes","orcid":"0000-0002-0170-7353","id":"4A918E98-F248-11E8-B48F-1D18A9856A87"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"},{"last_name":"Nowak","first_name":"Martin","full_name":"Nowak, Martin"}],"department":[{"_id":"KrCh"}],"publisher":"Public Library of Science","status":"public","title":"Forgiver triumphs in alternating prisoner's dilemma ","_id":"9749","year":"2013","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","abstract":[{"lang":"eng","text":"Cooperative behavior, where one individual incurs a cost to help another, is a wide spread phenomenon. Here we study direct reciprocity in the context of the alternating Prisoner's Dilemma. We consider all strategies that can be implemented by one and two-state automata. We calculate the payoff matrix of all pairwise encounters in the presence of noise. We explore deterministic selection dynamics with and without mutation. Using different error rates and payoff values, we observe convergence to a small number of distinct equilibria. Two of them are uncooperative strict Nash equilibria representing always-defect (ALLD) and Grim. The third equilibrium is mixed and represents a cooperative alliance of several strategies, dominated by a strategy which we call Forgiver. Forgiver cooperates whenever the opponent has cooperated; it defects once when the opponent has defected, but subsequently Forgiver attempts to re-establish cooperation even if the opponent has defected again. Forgiver is not an evolutionarily stable strategy, but the alliance, which it rules, is asymptotically stable. For a wide range of parameter values the most commonly observed outcome is convergence to the mixed equilibrium, dominated by Forgiver. Our results show that although forgiving might incur a short-term loss it can lead to a long-term gain. Forgiveness facilitates stable cooperation in the presence of exploitation and noise."}],"type":"research_data_reference"},{"month":"02","quality_controlled":"1","acknowledged_ssus":[{"_id":"ScienComp"}],"language":[{"iso":"eng"}],"doi":"10.1111/mec.12165","publist_id":"3788","publication_status":"published","department":[{"_id":"NiBa"}],"publisher":"Wiley-Blackwell","year":"2013","acknowledgement":"This study has made use of the computational resources provided by IST Austria and the Edinburgh Compute and Data Facility (ECDF; http://www.ecdf.ed.ac.uk). The ECDF is partially supported by the eDIKT initiative (http://www.edikt.org.uk). S.A. acknowledges financial support by IST Austria, the Janggen-Pöhn Foundation, St. Gallen, the Roche Research Foundation, Basel, the University of Edinburgh in the form of a Torrance Studentship, and the Austrian Science Fund (FWF P21305-N13).","date_created":"2018-12-11T12:00:28Z","date_updated":"2023-02-23T14:07:19Z","volume":22,"author":[{"id":"2D35326E-F248-11E8-B48F-1D18A9856A87","last_name":"Aeschbacher","first_name":"Simon","full_name":"Aeschbacher, Simon"},{"last_name":"Futschik","first_name":"Andreas","full_name":"Futschik, Andreas"},{"full_name":"Beaumont, Mark","first_name":"Mark","last_name":"Beaumont"}],"related_material":{"record":[{"status":"public","relation":"research_data","id":"9758"}]},"scopus_import":1,"day":"01","page":"987 - 1002","publication":"Molecular Ecology","citation":{"chicago":"Aeschbacher, Simon, Andreas Futschik, and Mark Beaumont. “Approximate Bayesian Computation for Modular Inference Problems with Many Parameters: The Example of Migration Rates. .” Molecular Ecology. Wiley-Blackwell, 2013. https://doi.org/10.1111/mec.12165.","short":"S. Aeschbacher, A. Futschik, M. Beaumont, Molecular Ecology 22 (2013) 987–1002.","mla":"Aeschbacher, Simon, et al. “Approximate Bayesian Computation for Modular Inference Problems with Many Parameters: The Example of Migration Rates. .” Molecular Ecology, vol. 22, no. 4, Wiley-Blackwell, 2013, pp. 987–1002, doi:10.1111/mec.12165.","ieee":"S. Aeschbacher, A. Futschik, and M. Beaumont, “Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates. ,” Molecular Ecology, vol. 22, no. 4. Wiley-Blackwell, pp. 987–1002, 2013.","apa":"Aeschbacher, S., Futschik, A., & Beaumont, M. (2013). Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates. . Molecular Ecology. Wiley-Blackwell. https://doi.org/10.1111/mec.12165","ista":"Aeschbacher S, Futschik A, Beaumont M. 2013. Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates. . Molecular Ecology. 22(4), 987–1002.","ama":"Aeschbacher S, Futschik A, Beaumont M. Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates. . Molecular Ecology. 2013;22(4):987-1002. doi:10.1111/mec.12165"},"date_published":"2013-02-01T00:00:00Z","type":"journal_article","abstract":[{"text":"We propose a two-step procedure for estimating multiple migration rates in an approximate Bayesian computation (ABC) framework, accounting for global nuisance parameters. The approach is not limited to migration, but generally of interest for inference problems with multiple parameters and a modular structure (e.g. independent sets of demes or loci). We condition on a known, but complex demographic model of a spatially subdivided population, motivated by the reintroduction of Alpine ibex (Capra ibex) into Switzerland. In the first step, the global parameters ancestral mutation rate and male mating skew have been estimated for the whole population in Aeschbacher et al. (Genetics 2012; 192: 1027). In the second step, we estimate in this study the migration rates independently for clusters of demes putatively connected by migration. For large clusters (many migration rates), ABC faces the problem of too many summary statistics. We therefore assess by simulation if estimation per pair of demes is a valid alternative. We find that the trade-off between reduced dimensionality for the pairwise estimation on the one hand and lower accuracy due to the assumption of pairwise independence on the other depends on the number of migration rates to be inferred: the accuracy of the pairwise approach increases with the number of parameters, relative to the joint estimation approach. To distinguish between low and zero migration, we perform ABC-type model comparison between a model with migration and one without. Applying the approach to microsatellite data from Alpine ibex, we find no evidence for substantial gene flow via migration, except for one pair of demes in one direction.","lang":"eng"}],"issue":"4","title":"Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates. ","status":"public","intvolume":" 22","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2944","oa_version":"None"},{"day":"01","month":"01","date_published":"2013-01-01T00:00:00Z","doi":"10.1186/1756-0500-6-310","language":[{"iso":"eng"}],"publication":"BMC Research Notes","citation":{"ama":"Derelle R, Kondrashov F, Arkhipov V, et al. Color differences among feral pigeons (Columba livia) are not attributable to sequence variation in the coding region of the melanocortin-1 receptor gene MC1R. BMC Research Notes. 2013;6(1). doi:10.1186/1756-0500-6-310","ista":"Derelle R, Kondrashov F, Arkhipov V, Corbel H, Frantz A, Gasparini J, Jacquin L, Jacob G, Thibault S, Baudry E. 2013. Color differences among feral pigeons (Columba livia) are not attributable to sequence variation in the coding region of the melanocortin-1 receptor gene MC1R. BMC Research Notes. 6(1).","apa":"Derelle, R., Kondrashov, F., Arkhipov, V., Corbel, H., Frantz, A., Gasparini, J., … Baudry, E. (2013). Color differences among feral pigeons (Columba livia) are not attributable to sequence variation in the coding region of the melanocortin-1 receptor gene MC1R. BMC Research Notes. BioMed Central. https://doi.org/10.1186/1756-0500-6-310","ieee":"R. Derelle et al., “Color differences among feral pigeons (Columba livia) are not attributable to sequence variation in the coding region of the melanocortin-1 receptor gene MC1R,” BMC Research Notes, vol. 6, no. 1. BioMed Central, 2013.","mla":"Derelle, Romain, et al. “Color Differences among Feral Pigeons (Columba Livia) Are Not Attributable to Sequence Variation in the Coding Region of the Melanocortin-1 Receptor Gene MC1R.” BMC Research Notes, vol. 6, no. 1, BioMed Central, 2013, doi:10.1186/1756-0500-6-310.","short":"R. Derelle, F. Kondrashov, V. Arkhipov, H. Corbel, A. Frantz, J. Gasparini, L. Jacquin, G. Jacob, S. Thibault, E. Baudry, BMC Research Notes 6 (2013).","chicago":"Derelle, Romain, Fyodor Kondrashov, Vladimir Arkhipov, Hélène Corbel, Adrien Frantz, Julien Gasparini, Lisa Jacquin, Gwenaël Jacob, Sophie Thibault, and Emmanuelle Baudry. “Color Differences among Feral Pigeons (Columba Livia) Are Not Attributable to Sequence Variation in the Coding Region of the Melanocortin-1 Receptor Gene MC1R.” BMC Research Notes. BioMed Central, 2013. https://doi.org/10.1186/1756-0500-6-310."},"abstract":[{"text":"Background: Genetic variation at the melanocortin-1 receptor (MC1R) gene is correlated with melanin color variation in many birds. Feral pigeons (Columba livia) show two major melanin-based colorations: a red coloration due to pheomelanic pigment and a black coloration due to eumelanic pigment. Furthermore, within each color type, feral pigeons display continuous variation in the amount of melanin pigment present in the feathers, with individuals varying from pure white to a full dark melanic color. Coloration is highly heritable and it has been suggested that it is under natural or sexual selection, or both. Our objective was to investigate whether MC1R allelic variants are associated with plumage color in feral pigeons. Findings. We sequenced 888 bp of the coding sequence of MC1R among pigeons varying both in the type, eumelanin or pheomelanin, and the amount of melanin in their feathers. We detected 10 non-synonymous substitutions and 2 synonymous substitution but none of them were associated with a plumage type. It remains possible that non-synonymous substitutions that influence coloration are present in the short MC1R fragment that we did not sequence but this seems unlikely because we analyzed the entire functionally important region of the gene. Conclusions: Our results show that color differences among feral pigeons are probably not attributable to amino acid variation at the MC1R locus. Therefore, variation in regulatory regions of MC1R or variation in other genes may be responsible for the color polymorphism of feral pigeons.","lang":"eng"}],"issue":"1","publist_id":"6752","extern":"1","type":"journal_article","author":[{"first_name":"Romain","last_name":"Derelle","full_name":"Derelle, Romain"},{"id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694","first_name":"Fyodor","last_name":"Kondrashov","full_name":"Kondrashov, Fyodor"},{"full_name":"Arkhipov, Vladimir","last_name":"Arkhipov","first_name":"Vladimir"},{"full_name":"Corbel, Hélène","last_name":"Corbel","first_name":"Hélène"},{"last_name":"Frantz","first_name":"Adrien","full_name":"Frantz, Adrien"},{"first_name":"Julien","last_name":"Gasparini","full_name":"Gasparini, Julien"},{"first_name":"Lisa","last_name":"Jacquin","full_name":"Jacquin, Lisa"},{"full_name":"Jacob, Gwenaël","first_name":"Gwenaël","last_name":"Jacob"},{"first_name":"Sophie","last_name":"Thibault","full_name":"Thibault, Sophie"},{"first_name":"Emmanuelle","last_name":"Baudry","full_name":"Baudry, Emmanuelle"}],"date_created":"2018-12-11T11:49:04Z","date_updated":"2021-01-12T08:21:25Z","volume":6,"oa_version":"None","_id":"894","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2013","acknowledgement":"Romain Derelle was supported by grant from Plan Nacional 004302 BFU2012-31329. Fyodor A Kondrashov was supported by grants HHMI (Howard Hughes Medical Institute) 003803 and EMBO 003691 EUI-EURYIP-2011-4320.","status":"public","title":"Color differences among feral pigeons (Columba livia) are not attributable to sequence variation in the coding region of the melanocortin-1 receptor gene MC1R","publication_status":"published","intvolume":" 6","publisher":"BioMed Central"},{"keyword":["Multidisciplinary"],"scopus_import":"1","day":"22","article_processing_charge":"No","article_type":"original","page":"936-940","publication":"Science","citation":{"chicago":"Palacci, Jérémie A, S. Sacanna, A. P. Steinberg, D. J. Pine, and P. M. Chaikin. “Living Crystals of Light-Activated Colloidal Surfers.” Science. American Association for the Advancement of Science , 2013. https://doi.org/10.1126/science.1230020.","short":"J.A. Palacci, S. Sacanna, A.P. Steinberg, D.J. Pine, P.M. Chaikin, Science 339 (2013) 936–940.","mla":"Palacci, Jérémie A., et al. “Living Crystals of Light-Activated Colloidal Surfers.” Science, vol. 339, no. 6122, American Association for the Advancement of Science , 2013, pp. 936–40, doi:10.1126/science.1230020.","ieee":"J. A. Palacci, S. Sacanna, A. P. Steinberg, D. J. Pine, and P. M. Chaikin, “Living crystals of light-activated colloidal surfers,” Science, vol. 339, no. 6122. American Association for the Advancement of Science , pp. 936–940, 2013.","apa":"Palacci, J. A., Sacanna, S., Steinberg, A. P., Pine, D. J., & Chaikin, P. M. (2013). Living crystals of light-activated colloidal surfers. Science. American Association for the Advancement of Science . https://doi.org/10.1126/science.1230020","ista":"Palacci JA, Sacanna S, Steinberg AP, Pine DJ, Chaikin PM. 2013. Living crystals of light-activated colloidal surfers. Science. 339(6122), 936–940.","ama":"Palacci JA, Sacanna S, Steinberg AP, Pine DJ, Chaikin PM. Living crystals of light-activated colloidal surfers. Science. 2013;339(6122):936-940. doi:10.1126/science.1230020"},"date_published":"2013-02-22T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"Spontaneous formation of colonies of bacteria or flocks of birds are examples of self-organization in active living matter. Here, we demonstrate a form of self-organization from nonequilibrium driving forces in a suspension of synthetic photoactivated colloidal particles. They lead to two-dimensional \"living crystals,\" which form, break, explode, and re-form elsewhere. The dynamic assembly results from a competition between self-propulsion of particles and an attractive interaction induced respectively by osmotic and phoretic effects and activated by light. We measured a transition from normal to giant-number fluctuations. Our experiments are quantitatively described by simple numerical simulations. We show that the existence of the living crystals is intrinsically related to the out-of-equilibrium collisions of the self-propelled particles."}],"issue":"6122","status":"public","title":"Living crystals of light-activated colloidal surfers","intvolume":" 339","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"9055","oa_version":"None","month":"02","publication_identifier":{"issn":["0036-8075"],"eissn":["1095-9203"]},"quality_controlled":"1","external_id":{"pmid":["23371555"]},"language":[{"iso":"eng"}],"doi":"10.1126/science.1230020","extern":"1","publication_status":"published","publisher":"American Association for the Advancement of Science ","year":"2013","pmid":1,"date_updated":"2022-08-25T14:57:43Z","date_created":"2021-02-01T14:37:29Z","volume":339,"author":[{"first_name":"Jérémie A","last_name":"Palacci","id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d","orcid":"0000-0002-7253-9465","full_name":"Palacci, Jérémie A"},{"full_name":"Sacanna, S.","first_name":"S.","last_name":"Sacanna"},{"last_name":"Steinberg","first_name":"A. P.","full_name":"Steinberg, A. P."},{"full_name":"Pine, D. J.","first_name":"D. J.","last_name":"Pine"},{"first_name":"P. M.","last_name":"Chaikin","full_name":"Chaikin, P. M."}]},{"date_published":"2013-09-01T00:00:00Z","page":"25 - 30","quality_controlled":0,"oa":1,"citation":{"mla":"Arkhipov, Vladimir, et al. “Birds of Mys Shmidta, North Chukotka, Russia.” Forktail, no. 29, Oriental Bird Club, 2013, pp. 25–30.","short":"V. Arkhipov, T. Noah, S. Koschkar, F. Kondrashov, Forktail (2013) 25–30.","chicago":"Arkhipov, Vladimir, T Noah, Steffen Koschkar, and Fyodor Kondrashov. “Birds of Mys Shmidta, North Chukotka, Russia.” Forktail. Oriental Bird Club, 2013.","ama":"Arkhipov V, Noah T, Koschkar S, Kondrashov F. Birds of Mys Shmidta, north Chukotka, Russia. Forktail. 2013;(29):25-30.","ista":"Arkhipov V, Noah T, Koschkar S, Kondrashov F. 2013. Birds of Mys Shmidta, north Chukotka, Russia. Forktail. (29), 25–30.","apa":"Arkhipov, V., Noah, T., Koschkar, S., & Kondrashov, F. (2013). Birds of Mys Shmidta, north Chukotka, Russia. Forktail. Oriental Bird Club.","ieee":"V. Arkhipov, T. Noah, S. Koschkar, and F. Kondrashov, “Birds of Mys Shmidta, north Chukotka, Russia,” Forktail, no. 29. Oriental Bird Club, pp. 25–30, 2013."},"main_file_link":[{"open_access":"1","url":"http://orientalbirdclub.org/forktail29/"}],"publication":"Forktail","day":"01","month":"09","date_updated":"2021-01-12T08:21:48Z","date_created":"2018-12-11T11:49:07Z","author":[{"first_name":"Vladimir","last_name":"Arkhipov","full_name":"Arkhipov, Vladimir Y"},{"first_name":"T","last_name":"Noah","full_name":"Noah T"},{"full_name":"Koschkar, Steffen","first_name":"Steffen","last_name":"Koschkar"},{"full_name":"Fyodor Kondrashov","orcid":"0000-0001-8243-4694","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","last_name":"Kondrashov","first_name":"Fyodor"}],"publisher":"Oriental Bird Club","title":"Birds of Mys Shmidta, north Chukotka, Russia","status":"public","publication_status":"published","acknowledgement":"We thank Natalya Kveten and Oksana Makarova, heads of administrations of Mys Shmidta and Ryrkaypiy for hospitality and for help with organising our excursions. Warm thanks too to Pavel Tomkovich for useful comments on local birds and ornithological literature. We are very grateful to The David and Lucile Packard Foundation for the support to Birds Russia’s Spoon-billed Sandpiper conservation programme in 2011 and to Evgeny Syroechkovsky Jr, the leader of the Spoon-billed Sandpiper conservation team in Russia.","_id":"905","year":"2013","extern":1,"publist_id":"6741","issue":"29","abstract":[{"text":"A survey of avifauna was carried out in the Mys Shmidta area, north Chukotka, Russia from 8 June to 12 July 2011. A total of 90 species was recorded in the area, which together with literature data made a final list of 104 species. For several species this area is beyond the northern, north-eastern or north-western limits of their known distribution. We collected new data for 19 globally or locally threatened species. Tundra Swan Cygnus columbianus, Emperor Goose Anser canagica, American Golden Plover Pluvialis dominica, Western Sandpiper Calidris mauri, Semipalmated Sandpiper C. pusilla, Northern House Martin Delichon urbica and Barn Swallow Hirundo rustica were all confirmed to be breeding. Breeding of Brent Goose Branta bernicla nigricans, Spectacled Eider Somateria fischeri and Steller's Eider Polysticta stelleri was judged to be 'very likely'. There was no evidence for breeding of Ross's Gull Rhodostethia rosea despite several records. Two Eurasian Dotterels Eudromias morinellus were recorded displaying for the first time in the area, but the status of the species is unclear. The area is important for Snowy Owl Nyctea scandiaca, and as moulting grounds for Emperor Goose. Canada Goose Branta canadensis, Baikal Teal Anas formosa, Bar-tailed Godwit Limosa lapponica, Slaty-backed Gull Larus schistisagus, Thayer's Gull L. thayeri, Black-headed Gull L. ridibundus, White-tailed Eagle Haliaeetus albicilla, Steller's Sea Eagle H. pelagicus, Osprey Pandion haliaetus, Arctic Warbler Phylloscopus borealis and House Sparrow Passer domesticus are more likely to be rare vagrants or migrants. An observation of a Pine Siskin Carduelis pinus is the first record for Eurasia.","lang":"eng"}],"type":"journal_article"},{"author":[{"full_name":"Melet, Angélique","last_name":"Melet","first_name":"Angélique"},{"first_name":"Maxim","last_name":"Nikurashin","full_name":"Nikurashin, Maxim"},{"orcid":"0000-0001-5836-5350","id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b","last_name":"Muller","first_name":"Caroline J","full_name":"Muller, Caroline J"},{"full_name":"Falahat, S.","last_name":"Falahat","first_name":"S."},{"full_name":"Nycander, Jonas","last_name":"Nycander","first_name":"Jonas"},{"full_name":"Timko, Patrick G.","last_name":"Timko","first_name":"Patrick G."},{"last_name":"Arbic","first_name":"Brian K.","full_name":"Arbic, Brian K."},{"full_name":"Goff, John A.","first_name":"John A.","last_name":"Goff"}],"volume":118,"date_created":"2021-02-15T15:11:39Z","date_updated":"2022-01-24T13:46:15Z","year":"2013","publisher":"American Geophysical Union","publication_status":"published","extern":"1","doi":"10.1002/2013jc009212","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://doi.org/10.1002/2013JC009212","open_access":"1"}],"oa":1,"quality_controlled":"1","publication_identifier":{"issn":["2169-9275"]},"month":"11","oa_version":"Published Version","_id":"9153","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","intvolume":" 118","status":"public","title":"Internal tide generation by abyssal hills using analytical theory","issue":"11","abstract":[{"text":"Internal tide driven mixing plays a key role in sustaining the deep ocean stratification and meridional overturning circulation. Internal tides can be generated by topographic horizontal scales ranging from hundreds of meters to tens of kilometers. State of the art topographic products barely resolve scales smaller than ∼10 km in the deep ocean. On these scales abyssal hills dominate ocean floor roughness. The impact of abyssal hill roughness on internal‐tide generation is evaluated in this study. The conversion of M2 barotropic to baroclinic tidal energy is calculated based on linear wave theory both in real and spectral space using the Shuttle Radar Topography Mission SRTM30_PLUS bathymetric product at 1/120° resolution with and without the addition of synthetic abyssal hill roughness. Internal tide generation by abyssal hills integrates to 0.1 TW globally or 0.03 TW when the energy flux is empirically corrected for supercritical slope (i.e., ∼10% of the energy flux due to larger topographic scales resolved in standard products in both cases). The abyssal hill driven energy conversion is dominated by mid‐ocean ridges, where abyssal hill roughness is large. Focusing on two regions located over the Mid‐Atlantic Ridge and the East Pacific Rise, it is shown that regionally linear theory predicts an increase of the energy flux due to abyssal hills of up to 100% or 60% when an empirical correction for supercritical slopes is attempted. Therefore, abyssal hills, unresolved in state of the art topographic products, can have a strong impact on internal tide generation, especially over mid‐ocean ridges.","lang":"eng"}],"type":"journal_article","date_published":"2013-11-07T00:00:00Z","citation":{"ista":"Melet A, Nikurashin M, Muller CJ, Falahat S, Nycander J, Timko PG, Arbic BK, Goff JA. 2013. Internal tide generation by abyssal hills using analytical theory. Journal of Geophysical Research: Oceans. 118(11), 6303–6318.","apa":"Melet, A., Nikurashin, M., Muller, C. J., Falahat, S., Nycander, J., Timko, P. G., … Goff, J. A. (2013). Internal tide generation by abyssal hills using analytical theory. Journal of Geophysical Research: Oceans. American Geophysical Union. https://doi.org/10.1002/2013jc009212","ieee":"A. Melet et al., “Internal tide generation by abyssal hills using analytical theory,” Journal of Geophysical Research: Oceans, vol. 118, no. 11. American Geophysical Union, pp. 6303–6318, 2013.","ama":"Melet A, Nikurashin M, Muller CJ, et al. Internal tide generation by abyssal hills using analytical theory. Journal of Geophysical Research: Oceans. 2013;118(11):6303-6318. doi:10.1002/2013jc009212","chicago":"Melet, Angélique, Maxim Nikurashin, Caroline J Muller, S. Falahat, Jonas Nycander, Patrick G. Timko, Brian K. Arbic, and John A. Goff. “Internal Tide Generation by Abyssal Hills Using Analytical Theory.” Journal of Geophysical Research: Oceans. American Geophysical Union, 2013. https://doi.org/10.1002/2013jc009212.","mla":"Melet, Angélique, et al. “Internal Tide Generation by Abyssal Hills Using Analytical Theory.” Journal of Geophysical Research: Oceans, vol. 118, no. 11, American Geophysical Union, 2013, pp. 6303–18, doi:10.1002/2013jc009212.","short":"A. Melet, M. Nikurashin, C.J. Muller, S. Falahat, J. Nycander, P.G. Timko, B.K. Arbic, J.A. Goff, Journal of Geophysical Research: Oceans 118 (2013) 6303–6318."},"publication":"Journal of Geophysical Research: Oceans","page":"6303-6318","article_type":"original","article_processing_charge":"No","day":"07"},{"article_processing_charge":"No","day":"15","keyword":["Atmospheric Science"],"date_published":"2013-07-15T00:00:00Z","citation":{"ama":"Muller CJ. Impact of convective organization on the response of tropical precipitation extremes to warming. Journal of Climate. 2013;26(14):5028-5043. doi:10.1175/jcli-d-12-00655.1","ista":"Muller CJ. 2013. Impact of convective organization on the response of tropical precipitation extremes to warming. Journal of Climate. 26(14), 5028–5043.","apa":"Muller, C. J. (2013). Impact of convective organization on the response of tropical precipitation extremes to warming. Journal of Climate. American Meteorological Society. https://doi.org/10.1175/jcli-d-12-00655.1","ieee":"C. J. Muller, “Impact of convective organization on the response of tropical precipitation extremes to warming,” Journal of Climate, vol. 26, no. 14. American Meteorological Society, pp. 5028–5043, 2013.","mla":"Muller, Caroline J. “Impact of Convective Organization on the Response of Tropical Precipitation Extremes to Warming.” Journal of Climate, vol. 26, no. 14, American Meteorological Society, 2013, pp. 5028–43, doi:10.1175/jcli-d-12-00655.1.","short":"C.J. Muller, Journal of Climate 26 (2013) 5028–5043.","chicago":"Muller, Caroline J. “Impact of Convective Organization on the Response of Tropical Precipitation Extremes to Warming.” Journal of Climate. American Meteorological Society, 2013. https://doi.org/10.1175/jcli-d-12-00655.1."},"publication":"Journal of Climate","page":"5028-5043","article_type":"original","issue":"14","abstract":[{"lang":"eng","text":"In this study the response of tropical precipitation extremes to warming in organized convection is examined using a cloud-resolving model. Vertical shear is imposed to organize the convection into squall lines. Earlier studies show that in disorganized convection, the fractional increase of precipitation extremes is similar to that of surface water vapor, which is substantially smaller than the increase in column water vapor. It has been suggested that organized convection could lead to stronger amplifications.\r\nRegardless of the strength of the shear, amplifications of precipitation extremes in the cloud-resolving simulations are comparable to those of surface water vapor and are substantially less than increases in column water vapor. The results without shear and with critical shear, for which the squall lines are perpendicular to the shear, are surprisingly similar with a fractional rate of increase of precipitation extremes slightly smaller than that of surface water vapor. Interestingly, the dependence on shear is nonmonotonic, and stronger supercritical shear yields larger rates, close to or slightly larger than surface humidity.\r\nA scaling is used to evaluate the thermodynamic and dynamic contributions to precipitation extreme changes. To first order, they are dominated by the thermodynamic component, which has the same magnitude for all shears, close to the change in surface water vapor. The dynamic contribution plays a secondary role and tends to weaken extremes without shear and with critical shear, while it strengthens extremes with supercritical shear. These different dynamic contributions for different shears are due to different responses of convective mass fluxes in individual updrafts to warming."}],"type":"journal_article","oa_version":"Published Version","_id":"9154","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","intvolume":" 26","status":"public","title":"Impact of convective organization on the response of tropical precipitation extremes to warming","publication_identifier":{"issn":["0894-8755","1520-0442"]},"month":"07","doi":"10.1175/jcli-d-12-00655.1","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"url":"https://doi.org/10.1175/JCLI-D-12-00655.1","open_access":"1"}],"quality_controlled":"1","extern":"1","author":[{"orcid":"0000-0001-5836-5350","id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b","last_name":"Muller","first_name":"Caroline J","full_name":"Muller, Caroline J"}],"volume":26,"date_created":"2021-02-15T15:26:39Z","date_updated":"2022-01-24T13:46:41Z","year":"2013","publisher":"American Meteorological Society","publication_status":"published"},{"publication_identifier":{"eissn":["15205126"],"issn":["00027863"]},"month":"10","language":[{"iso":"eng"}],"doi":"10.1021/ja406090s","quality_controlled":"1","oa":1,"external_id":{"arxiv":["1310.5724"],"pmid":["24131488"]},"main_file_link":[{"url":"https://arxiv.org/abs/1310.5724","open_access":"1"}],"extern":"1","volume":135,"date_updated":"2021-02-22T10:10:41Z","date_created":"2021-02-18T14:31:26Z","author":[{"full_name":"Palacci, Jérémie A","first_name":"Jérémie A","last_name":"Palacci","id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d","orcid":"0000-0002-7253-9465"},{"last_name":"Sacanna","first_name":"Stefano","full_name":"Sacanna, Stefano"},{"last_name":"Vatchinsky","first_name":"Adrian","full_name":"Vatchinsky, Adrian"},{"first_name":"Paul M.","last_name":"Chaikin","full_name":"Chaikin, Paul M."},{"last_name":"Pine","first_name":"David J.","full_name":"Pine, David J."}],"publisher":"American Chemical Society","publication_status":"published","pmid":1,"year":"2013","article_processing_charge":"No","day":"30","keyword":["Colloid and Surface Chemistry","Biochemistry","General Chemistry","Catalysis"],"scopus_import":"1","date_published":"2013-10-30T00:00:00Z","page":"15978-15981","article_type":"original","citation":{"mla":"Palacci, Jérémie A., et al. “Photoactivated Colloidal Dockers for Cargo Transportation.” Journal of the American Chemical Society, vol. 135, no. 43, American Chemical Society, 2013, pp. 15978–81, doi:10.1021/ja406090s.","short":"J.A. Palacci, S. Sacanna, A. Vatchinsky, P.M. Chaikin, D.J. Pine, Journal of the American Chemical Society 135 (2013) 15978–15981.","chicago":"Palacci, Jérémie A, Stefano Sacanna, Adrian Vatchinsky, Paul M. Chaikin, and David J. Pine. “Photoactivated Colloidal Dockers for Cargo Transportation.” Journal of the American Chemical Society. American Chemical Society, 2013. https://doi.org/10.1021/ja406090s.","ama":"Palacci JA, Sacanna S, Vatchinsky A, Chaikin PM, Pine DJ. Photoactivated colloidal dockers for cargo transportation. Journal of the American Chemical Society. 2013;135(43):15978-15981. doi:10.1021/ja406090s","ista":"Palacci JA, Sacanna S, Vatchinsky A, Chaikin PM, Pine DJ. 2013. Photoactivated colloidal dockers for cargo transportation. Journal of the American Chemical Society. 135(43), 15978–15981.","ieee":"J. A. Palacci, S. Sacanna, A. Vatchinsky, P. M. Chaikin, and D. J. Pine, “Photoactivated colloidal dockers for cargo transportation,” Journal of the American Chemical Society, vol. 135, no. 43. American Chemical Society, pp. 15978–15981, 2013.","apa":"Palacci, J. A., Sacanna, S., Vatchinsky, A., Chaikin, P. M., & Pine, D. J. (2013). Photoactivated colloidal dockers for cargo transportation. Journal of the American Chemical Society. American Chemical Society. https://doi.org/10.1021/ja406090s"},"publication":"Journal of the American Chemical Society","issue":"43","abstract":[{"lang":"eng","text":"We introduce a self-propelled colloidal hematite docker that can be steered to a small particle cargo many times its size, dock, transport the cargo to a remote location, and then release it. The self-propulsion and docking are reversible and activated by visible light. The docker can be steered either by a weak uniform magnetic field or by nanoscale tracks in a textured substrate. The light-activated motion and docking originate from osmotic/phoretic particle transport in a concentration gradient of fuel, hydrogen peroxide, induced by the photocatalytic activity of the hematite. The docking mechanism is versatile and can be applied to various materials and shapes. The hematite dockers are simple single-component particles and are synthesized in bulk quantities. This system opens up new possibilities for designing complex micrometer-size factories as well as new biomimetic systems."}],"type":"journal_article","oa_version":"Preprint","intvolume":" 135","status":"public","title":"Photoactivated colloidal dockers for cargo transportation","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","_id":"9167"},{"_id":"921","year":"2013","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"This work was supported by National Science Foundation (NSF) Grant DMS-1068869 and by the NSF Center for Theoretical Biological Physics (Grant NSF PHY-0822283).\r\nWe acknowledge useful discussions with Eshel Ben-Jacob and Assaf Zaritsky. ","intvolume":" 110","publisher":"National Academy of Sciences","publication_status":"published","status":"public","title":"Alignment of cellular motility forces with tissue flow as a mechanism for efficient wound healing","author":[{"full_name":"Basan, Markus","last_name":"Basan","first_name":"Markus"},{"first_name":"Jens","last_name":"Elgeti","full_name":"Elgeti, Jens"},{"first_name":"Edouard B","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B"},{"full_name":"Rappel, Wouter","last_name":"Rappel","first_name":"Wouter"},{"full_name":"Levine, Herbert","first_name":"Herbert","last_name":"Levine"}],"volume":110,"oa_version":"None","date_created":"2018-12-11T11:49:12Z","date_updated":"2021-01-12T08:21:55Z","type":"journal_article","issue":"7","publist_id":"6518","abstract":[{"lang":"eng","text":"Recent experiments have shown that spreading epithelial sheets exhibit a long-range coordination of motility forces that leads to a buildup of tension in the tissue, which may enhance cell division and the speed of wound healing. Furthermore, the edges of these epithelial sheets commonly show finger-like protrusions whereas the bulk often displays spontaneous swirls of motile cells. To explain these experimental observations, we propose a simple flocking-type mechanism, in which cells tend to align their motility forceswith their velocity. Implementing this idea in amechanical tissue simulation, the proposed model gives rise to efficient spreading and can explain the experimentally observed long-range alignment of motility forces in highly disordered patterns, as well as the buildup of tensile stress throughout the tissue. Our model also qualitatively reproduces the dependence of swirl size and swirl velocity on cell density reported in experiments and exhibits an undulation instability at the edge of the spreading tissue commonly observed in vivo. Finally, we study the dependence of colony spreading speed on important physical and biological parameters and derive simple scaling relations that show that coordination of motility forces leads to an improvement of the wound healing process for realistic tissue parameters."}],"extern":"1","citation":{"apa":"Basan, M., Elgeti, J., Hannezo, E. B., Rappel, W., & Levine, H. (2013). Alignment of cellular motility forces with tissue flow as a mechanism for efficient wound healing. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1219937110","ieee":"M. Basan, J. Elgeti, E. B. Hannezo, W. Rappel, and H. Levine, “Alignment of cellular motility forces with tissue flow as a mechanism for efficient wound healing,” PNAS, vol. 110, no. 7. National Academy of Sciences, pp. 2452–2459, 2013.","ista":"Basan M, Elgeti J, Hannezo EB, Rappel W, Levine H. 2013. Alignment of cellular motility forces with tissue flow as a mechanism for efficient wound healing. PNAS. 110(7), 2452–2459.","ama":"Basan M, Elgeti J, Hannezo EB, Rappel W, Levine H. Alignment of cellular motility forces with tissue flow as a mechanism for efficient wound healing. PNAS. 2013;110(7):2452-2459. doi:10.1073/pnas.1219937110","chicago":"Basan, Markus, Jens Elgeti, Edouard B Hannezo, Wouter Rappel, and Herbert Levine. “Alignment of Cellular Motility Forces with Tissue Flow as a Mechanism for Efficient Wound Healing.” PNAS. National Academy of Sciences, 2013. https://doi.org/10.1073/pnas.1219937110.","short":"M. Basan, J. Elgeti, E.B. Hannezo, W. Rappel, H. Levine, PNAS 110 (2013) 2452–2459.","mla":"Basan, Markus, et al. “Alignment of Cellular Motility Forces with Tissue Flow as a Mechanism for Efficient Wound Healing.” PNAS, vol. 110, no. 7, National Academy of Sciences, 2013, pp. 2452–59, doi:10.1073/pnas.1219937110."},"publication":"PNAS","page":"2452 - 2459","doi":"10.1073/pnas.1219937110","date_published":"2013-02-12T00:00:00Z","language":[{"iso":"eng"}],"article_processing_charge":"No","month":"02","day":"12"},{"scopus_import":"1","article_processing_charge":"No","day":"28","citation":{"chicago":"Zemach, Assaf, M. Yvonne Kim, Ping-Hung Hsieh, Devin Coleman-Derr, Leor Eshed-Williams, Ka Thao, Stacey L. Harmer, and Daniel Zilberman. “The Arabidopsis Nucleosome Remodeler DDM1 Allows DNA Methyltransferases to Access H1-Containing Heterochromatin.” Cell. Elsevier, 2013. https://doi.org/10.1016/j.cell.2013.02.033.","short":"A. Zemach, M.Y. Kim, P.-H. Hsieh, D. Coleman-Derr, L. Eshed-Williams, K. Thao, S.L. Harmer, D. Zilberman, Cell 153 (2013) 193–205.","mla":"Zemach, Assaf, et al. “The Arabidopsis Nucleosome Remodeler DDM1 Allows DNA Methyltransferases to Access H1-Containing Heterochromatin.” Cell, vol. 153, no. 1, Elsevier, 2013, pp. 193–205, doi:10.1016/j.cell.2013.02.033.","ieee":"A. Zemach et al., “The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin,” Cell, vol. 153, no. 1. Elsevier, pp. 193–205, 2013.","apa":"Zemach, A., Kim, M. Y., Hsieh, P.-H., Coleman-Derr, D., Eshed-Williams, L., Thao, K., … Zilberman, D. (2013). The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin. Cell. Elsevier. https://doi.org/10.1016/j.cell.2013.02.033","ista":"Zemach A, Kim MY, Hsieh P-H, Coleman-Derr D, Eshed-Williams L, Thao K, Harmer SL, Zilberman D. 2013. The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin. Cell. 153(1), 193–205.","ama":"Zemach A, Kim MY, Hsieh P-H, et al. The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin. Cell. 2013;153(1):193-205. doi:10.1016/j.cell.2013.02.033"},"publication":"Cell","page":"193-205","article_type":"original","date_published":"2013-03-28T00:00:00Z","type":"journal_article","issue":"1","abstract":[{"text":"Nucleosome remodelers of the DDM1/Lsh family are required for DNA methylation of transposable elements, but the reason for this is unknown. How DDM1 interacts with other methylation pathways, such as small-RNA-directed DNA methylation (RdDM), which is thought to mediate plant asymmetric methylation through DRM enzymes, is also unclear. Here, we show that most asymmetric methylation is facilitated by DDM1 and mediated by the methyltransferase CMT2 separately from RdDM. We find that heterochromatic sequences preferentially require DDM1 for DNA methylation and that this preference depends on linker histone H1. RdDM is instead inhibited by heterochromatin and absolutely requires the nucleosome remodeler DRD1. Together, DDM1 and RdDM mediate nearly all transposon methylation and collaborate to repress transposition and regulate the methylation and expression of genes. Our results indicate that DDM1 provides DNA methyltransferases access to H1-containing heterochromatin to allow stable silencing of transposable elements in cooperation with the RdDM pathway.","lang":"eng"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"9459","intvolume":" 153","status":"public","title":"The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin","oa_version":"Published Version","publication_identifier":{"issn":["0092-8674"],"eissn":["1097-4172"]},"month":"03","external_id":{"pmid":["23540698"]},"main_file_link":[{"url":"https://doi.org/10.1016/j.cell.2013.02.033","open_access":"1"}],"oa":1,"quality_controlled":"1","doi":"10.1016/j.cell.2013.02.033","language":[{"iso":"eng"}],"extern":"1","pmid":1,"year":"2013","publisher":"Elsevier","department":[{"_id":"DaZi"}],"publication_status":"published","author":[{"full_name":"Zemach, Assaf","last_name":"Zemach","first_name":"Assaf"},{"full_name":"Kim, M. Yvonne","last_name":"Kim","first_name":"M. Yvonne"},{"last_name":"Hsieh","first_name":"Ping-Hung","full_name":"Hsieh, Ping-Hung"},{"full_name":"Coleman-Derr, Devin","last_name":"Coleman-Derr","first_name":"Devin"},{"first_name":"Leor","last_name":"Eshed-Williams","full_name":"Eshed-Williams, Leor"},{"last_name":"Thao","first_name":"Ka","full_name":"Thao, Ka"},{"full_name":"Harmer, Stacey L.","last_name":"Harmer","first_name":"Stacey L."},{"full_name":"Zilberman, Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","orcid":"0000-0002-0123-8649","first_name":"Daniel","last_name":"Zilberman"}],"volume":153,"date_updated":"2021-12-14T08:25:35Z","date_created":"2021-06-04T12:23:28Z"},{"publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"month":"05","doi":"10.1073/pnas.1306164110","language":[{"iso":"eng"}],"oa":1,"external_id":{"pmid":["23613580"]},"main_file_link":[{"url":"https://doi.org/10.1073/pnas.1306164110","open_access":"1"}],"quality_controlled":"1","extern":"1","author":[{"last_name":"Rodrigues","first_name":"Jessica A.","full_name":"Rodrigues, Jessica A."},{"last_name":"Ruan","first_name":"Randy","full_name":"Ruan, Randy"},{"full_name":"Nishimura, Toshiro","first_name":"Toshiro","last_name":"Nishimura"},{"full_name":"Sharma, Manoj K.","first_name":"Manoj K.","last_name":"Sharma"},{"full_name":"Sharma, Rita","first_name":"Rita","last_name":"Sharma"},{"full_name":"Ronald, Pamela C","last_name":"Ronald","first_name":"Pamela C"},{"full_name":"Fischer, Robert L.","first_name":"Robert L.","last_name":"Fischer"},{"last_name":"Zilberman","first_name":"Daniel","orcid":"0000-0002-0123-8649","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","full_name":"Zilberman, Daniel"}],"volume":110,"date_updated":"2021-12-14T08:26:44Z","date_created":"2021-06-07T07:31:02Z","pmid":1,"year":"2013","publisher":"National Academy of Sciences","department":[{"_id":"DaZi"}],"publication_status":"published","article_processing_charge":"No","day":"07","scopus_import":"1","keyword":["Multidisciplinary"],"date_published":"2013-05-07T00:00:00Z","citation":{"ama":"Rodrigues JA, Ruan R, Nishimura T, et al. Imprinted expression of genes and small RNA is associated with localized hypomethylation of the maternal genome in rice endosperm. Proceedings of the National Academy of Sciences. 2013;110(19):7934-7939. doi:10.1073/pnas.1306164110","ieee":"J. A. Rodrigues et al., “Imprinted expression of genes and small RNA is associated with localized hypomethylation of the maternal genome in rice endosperm,” Proceedings of the National Academy of Sciences, vol. 110, no. 19. National Academy of Sciences, pp. 7934–7939, 2013.","apa":"Rodrigues, J. A., Ruan, R., Nishimura, T., Sharma, M. K., Sharma, R., Ronald, P. C., … Zilberman, D. (2013). Imprinted expression of genes and small RNA is associated with localized hypomethylation of the maternal genome in rice endosperm. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.1306164110","ista":"Rodrigues JA, Ruan R, Nishimura T, Sharma MK, Sharma R, Ronald PC, Fischer RL, Zilberman D. 2013. Imprinted expression of genes and small RNA is associated with localized hypomethylation of the maternal genome in rice endosperm. Proceedings of the National Academy of Sciences. 110(19), 7934–7939.","short":"J.A. Rodrigues, R. Ruan, T. Nishimura, M.K. Sharma, R. Sharma, P.C. Ronald, R.L. Fischer, D. Zilberman, Proceedings of the National Academy of Sciences 110 (2013) 7934–7939.","mla":"Rodrigues, Jessica A., et al. “Imprinted Expression of Genes and Small RNA Is Associated with Localized Hypomethylation of the Maternal Genome in Rice Endosperm.” Proceedings of the National Academy of Sciences, vol. 110, no. 19, National Academy of Sciences, 2013, pp. 7934–39, doi:10.1073/pnas.1306164110.","chicago":"Rodrigues, Jessica A., Randy Ruan, Toshiro Nishimura, Manoj K. Sharma, Rita Sharma, Pamela C Ronald, Robert L. Fischer, and Daniel Zilberman. “Imprinted Expression of Genes and Small RNA Is Associated with Localized Hypomethylation of the Maternal Genome in Rice Endosperm.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2013. https://doi.org/10.1073/pnas.1306164110."},"publication":"Proceedings of the National Academy of Sciences","page":"7934-7939","article_type":"original","issue":"19","abstract":[{"lang":"eng","text":"Arabidopsis thaliana endosperm, a transient tissue that nourishes the embryo, exhibits extensive localized DNA demethylation on maternally inherited chromosomes. Demethylation mediates parent-of-origin–specific (imprinted) gene expression but is apparently unnecessary for the extensive accumulation of maternally biased small RNA (sRNA) molecules detected in seeds. Endosperm DNA in the distantly related monocots rice and maize is likewise locally hypomethylated, but whether this hypomethylation is generally parent-of-origin specific is unknown. Imprinted expression of sRNA also remains uninvestigated in monocot seeds. Here, we report high-coverage sequencing of the Kitaake rice cultivar that enabled us to show that localized hypomethylation in rice endosperm occurs solely on the maternal genome, preferring regions of high DNA accessibility. Maternally expressed imprinted genes are enriched for hypomethylation at putative promoter regions and transcriptional termini and paternally expressed genes at promoters and gene bodies, mirroring our recent results in A. thaliana. However, unlike in A. thaliana, rice endosperm sRNA populations are dominated by specific strong sRNA-producing loci, and imprinted 24-nt sRNAs are expressed from both parental genomes and correlate with hypomethylation. Overlaps between imprinted sRNA loci and imprinted genes expressed from opposite alleles suggest that sRNAs may regulate genomic imprinting. Whereas sRNAs in seedling tissues primarily originate from small class II (cut-and-paste) transposable elements, those in endosperm are more uniformly derived, including sequences from other transposon classes, as well as genic and intergenic regions. Our data indicate that the endosperm exhibits a unique pattern of sRNA expression and suggest that localized hypomethylation of maternal endosperm DNA is conserved in flowering plants."}],"type":"journal_article","oa_version":"Published Version","_id":"9481","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","intvolume":" 110","title":"Imprinted expression of genes and small RNA is associated with localized hypomethylation of the maternal genome in rice endosperm","status":"public"},{"quality_controlled":"1","oa":1,"external_id":{"pmid":["23635145"]},"main_file_link":[{"url":"https://pubmed.ncbi.nlm.nih.gov/23635145/","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.1063/1.4802025","publication_identifier":{"eissn":["1089-7690"],"issn":["0021-9606"]},"month":"04","publisher":"AIP Publishing","publication_status":"published","pmid":1,"year":"2013","volume":138,"date_created":"2021-07-15T09:27:58Z","date_updated":"2021-08-09T12:35:34Z","author":[{"id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","orcid":"0000-0002-3584-9632","first_name":"Bingqing","last_name":"Cheng","full_name":"Cheng, Bingqing"},{"last_name":"Ngan","first_name":"Alfonso H. W.","full_name":"Ngan, Alfonso H. W."}],"article_number":"164314","extern":"1","article_type":"original","citation":{"ama":"Cheng B, Ngan AHW. Thermally induced solid-solid structural transition of copper nanoparticles through direct geometrical conversion. The Journal of Chemical Physics. 2013;138(16). doi:10.1063/1.4802025","ieee":"B. Cheng and A. H. W. Ngan, “Thermally induced solid-solid structural transition of copper nanoparticles through direct geometrical conversion,” The Journal of Chemical Physics, vol. 138, no. 16. AIP Publishing, 2013.","apa":"Cheng, B., & Ngan, A. H. W. (2013). Thermally induced solid-solid structural transition of copper nanoparticles through direct geometrical conversion. The Journal of Chemical Physics. AIP Publishing. https://doi.org/10.1063/1.4802025","ista":"Cheng B, Ngan AHW. 2013. Thermally induced solid-solid structural transition of copper nanoparticles through direct geometrical conversion. The Journal of Chemical Physics. 138(16), 164314.","short":"B. Cheng, A.H.W. Ngan, The Journal of Chemical Physics 138 (2013).","mla":"Cheng, Bingqing, and Alfonso H. W. Ngan. “Thermally Induced Solid-Solid Structural Transition of Copper Nanoparticles through Direct Geometrical Conversion.” The Journal of Chemical Physics, vol. 138, no. 16, 164314, AIP Publishing, 2013, doi:10.1063/1.4802025.","chicago":"Cheng, Bingqing, and Alfonso H. W. Ngan. “Thermally Induced Solid-Solid Structural Transition of Copper Nanoparticles through Direct Geometrical Conversion.” The Journal of Chemical Physics. AIP Publishing, 2013. https://doi.org/10.1063/1.4802025."},"publication":"The Journal of Chemical Physics","date_published":"2013-04-28T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"28","intvolume":" 138","status":"public","title":"Thermally induced solid-solid structural transition of copper nanoparticles through direct geometrical conversion","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","_id":"9663","oa_version":"Submitted Version","type":"journal_article","issue":"16","abstract":[{"lang":"eng","text":"Molecular dynamics simulations of small Cu nanoparticles using three different interatomic potentials at rising temperature indicate that small nanoparticles can undergo solid-solid structural transitions through a direct geometrical conversion route. The direct geometrical conversion can happen for cuboctahedral nanoparticles, which turn into an icosahedra shape: one diagonal of the square faces contracts, and the faces are folded along the diagonal to give rise to two equilateral triangles. The transition is a kinetic process that cannot be fully explained through an energetic point of view. It has low activation energy and fast reaction time in the simulations. The transition mechanism is via the transmission of shear waves initiated from the particle surface and does not involve dislocation activity."}]},{"extern":"1","abstract":[{"lang":"eng","text":"In this work, we simulate the response of two Cu nanoparticles colliding at different approaching rates at room temperature by MD. For small nanospheres, the formation of single twins is favored at high approach rates, whereas larger nanospheres mainly deform by dislocation slip. For small nanocubes with large {100} flat surfaces, however, a dislocation-free direct geometrical conversion process that leads to five-fold twinning dominates except at highly retarded approaching rates. For larger nanocubes, single twin formation is the governing plasticity mechanism. The probability for plastic deformation by dislocation slip or twinning is attributed to the abundance of surface steps, which act as sites for dislocation nucleation."}],"type":"journal_article","date_created":"2021-07-19T09:04:36Z","date_updated":"2023-02-23T14:04:51Z","volume":585,"oa_version":"None","author":[{"full_name":"Cheng, Bingqing","orcid":"0000-0002-3584-9632","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","last_name":"Cheng","first_name":"Bingqing"},{"first_name":"Alfonso H.W.","last_name":"Ngan","full_name":"Ngan, Alfonso H.W."}],"publication_status":"published","status":"public","title":"Crystal plasticity of Cu nanocrystals during collision","publisher":"Elsevier","intvolume":" 585","year":"2013","_id":"9682","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","day":"15","month":"11","article_processing_charge":"No","publication_identifier":{"issn":["0921-5093"]},"scopus_import":"1","language":[{"iso":"eng"}],"date_published":"2013-11-15T00:00:00Z","doi":"10.1016/j.msea.2013.07.065","quality_controlled":"1","article_type":"original","page":"326-334","publication":"Materials Science and Engineering: A","citation":{"apa":"Cheng, B., & Ngan, A. H. W. (2013). Crystal plasticity of Cu nanocrystals during collision. Materials Science and Engineering: A. Elsevier. https://doi.org/10.1016/j.msea.2013.07.065","ieee":"B. Cheng and A. H. W. Ngan, “Crystal plasticity of Cu nanocrystals during collision,” Materials Science and Engineering: A, vol. 585. Elsevier, pp. 326–334, 2013.","ista":"Cheng B, Ngan AHW. 2013. Crystal plasticity of Cu nanocrystals during collision. Materials Science and Engineering: A. 585, 326–334.","ama":"Cheng B, Ngan AHW. Crystal plasticity of Cu nanocrystals during collision. Materials Science and Engineering: A. 2013;585:326-334. doi:10.1016/j.msea.2013.07.065","chicago":"Cheng, Bingqing, and Alfonso H.W. Ngan. “Crystal Plasticity of Cu Nanocrystals during Collision.” Materials Science and Engineering: A. Elsevier, 2013. https://doi.org/10.1016/j.msea.2013.07.065.","short":"B. Cheng, A.H.W. Ngan, Materials Science and Engineering: A 585 (2013) 326–334.","mla":"Cheng, Bingqing, and Alfonso H. W. Ngan. “Crystal Plasticity of Cu Nanocrystals during Collision.” Materials Science and Engineering: A, vol. 585, Elsevier, 2013, pp. 326–34, doi:10.1016/j.msea.2013.07.065."}},{"year":"2013","_id":"970","acknowledgement":"We thank Pablo Jarillo-Herrero, Leonardo Campos, and Thiti Taychatanapat for attracting our attention to the problem of biased trilayer graphene, and for many helpful discussions.","intvolume":" 87","publisher":"American Physical Society","status":"public","title":"New Dirac points and multiple Landau level crossings in biased trilayer graphene","publication_status":"published","author":[{"first_name":"Maksym","last_name":"Serbyn","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827","full_name":"Maksym Serbyn"},{"full_name":"Abanin, Dmitry A","last_name":"Abanin","first_name":"Dmitry"}],"volume":87,"date_updated":"2021-01-12T08:22:20Z","date_created":"2018-12-11T11:49:28Z","type":"journal_article","publist_id":"6428","issue":"11","abstract":[{"text":"Recently a new high-mobility Dirac material, trilayer graphene, was realized experimentally. The band structure of ABA-stacked trilayer graphene consists of a monolayer-like and a bilayer-like pair of bands. Here we study electronic properties of ABA-stacked trilayer graphene biased by a perpendicular electric field. We find that the combination of the bias and trigonal warping gives rise to a set of new Dirac points: In each valley, seven species of Dirac fermions with small masses of order of a few meV emerge. The positions and masses of the emergent Dirac fermions are tunable by bias, and one group of Dirac fermions becomes massless at a certain bias value. Therefore, in contrast to bilayer graphene, the conductivity at the neutrality point is expected to show nonmonotonic behavior, becoming of the order of a few e2/h when some Dirac masses vanish. Further, we analyze the evolution of the Landau level spectrum as a function of bias. The emergence of new Dirac points in the band structure translates into new threefold-degenerate groups of Landau levels. This leads to an anomalous quantum Hall effect, in which some quantum Hall steps have a height of 3e2/h. At an intermediate bias, the degeneracies of all Landau levels get lifted, and in this regime all quantum Hall plateaus are spaced by e2/h. Finally, we show that the pattern of Landau level crossings is very sensitive to certain band structure parameters, and can therefore provide a useful tool for determining their precise values.","lang":"eng"}],"extern":1,"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1212.6251"}],"citation":{"ama":"Serbyn M, Abanin D. New Dirac points and multiple Landau level crossings in biased trilayer graphene. Physical Review B - Condensed Matter and Materials Physics. 2013;87(11). doi:10.1103/PhysRevB.87.115422","ista":"Serbyn M, Abanin D. 2013. New Dirac points and multiple Landau level crossings in biased trilayer graphene. Physical Review B - Condensed Matter and Materials Physics. 87(11).","apa":"Serbyn, M., & Abanin, D. (2013). New Dirac points and multiple Landau level crossings in biased trilayer graphene. Physical Review B - Condensed Matter and Materials Physics. American Physical Society. https://doi.org/10.1103/PhysRevB.87.115422","ieee":"M. Serbyn and D. Abanin, “New Dirac points and multiple Landau level crossings in biased trilayer graphene,” Physical Review B - Condensed Matter and Materials Physics, vol. 87, no. 11. American Physical Society, 2013.","mla":"Serbyn, Maksym, and Dmitry Abanin. “New Dirac Points and Multiple Landau Level Crossings in Biased Trilayer Graphene.” Physical Review B - Condensed Matter and Materials Physics, vol. 87, no. 11, American Physical Society, 2013, doi:10.1103/PhysRevB.87.115422.","short":"M. Serbyn, D. Abanin, Physical Review B - Condensed Matter and Materials Physics 87 (2013).","chicago":"Serbyn, Maksym, and Dmitry Abanin. “New Dirac Points and Multiple Landau Level Crossings in Biased Trilayer Graphene.” Physical Review B - Condensed Matter and Materials Physics. American Physical Society, 2013. https://doi.org/10.1103/PhysRevB.87.115422."},"publication":"Physical Review B - Condensed Matter and Materials Physics","quality_controlled":0,"doi":"10.1103/PhysRevB.87.115422","date_published":"2013-03-18T00:00:00Z","day":"18","month":"03"},{"abstract":[{"lang":"eng","text":"We construct a complete set of local integrals of motion that characterize the many-body localized (MBL) phase. Our approach relies on the assumption that local perturbations act locally on the eigenstates in the MBL phase, which is supported by numerical simulations of the random-field XXZ spin chain. We describe the structure of the eigenstates in the MBL phase and discuss the implications of local conservation laws for its nonequilibrium quantum dynamics. We argue that the many-body localization can be used to protect coherence in the system by suppressing relaxation between eigenstates with different local integrals of motion."}],"issue":"12","publist_id":"6424","extern":1,"type":"journal_article","author":[{"last_name":"Serbyn","first_name":"Maksym","orcid":"0000-0002-2399-5827","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","full_name":"Maksym Serbyn"},{"first_name":"Zlatko","last_name":"Papić","full_name":"Papić, Zlatko"},{"full_name":"Abanin, Dmitry A","first_name":"Dmitry","last_name":"Abanin"}],"date_updated":"2021-01-12T08:22:21Z","date_created":"2018-12-11T11:49:29Z","volume":111,"_id":"973","year":"2013","acknowledgement":"We thank J. Moore for useful discussions. Research at Perimeter Institute is supported by the Government of Canada through Industry Canada and by the Province of Ontario through the Ministry of Economic Development & Innovation. Z. P. was supported by DOE Grant No. DE-SC0002140. M. S. was supported by the National Science Foundation under Grant No. DMR-1104498. The simulations presented in this article were performed on computational resources supported by the High Performance Computing Center (PICSciE) at Princeton University.","status":"public","publication_status":"published","title":"Local conservation laws and the structure of the many body localized states","intvolume":" 111","publisher":"American Physical Society","day":"17","month":"09","doi":"10.1103/PhysRevLett.111.127201","date_published":"2013-09-17T00:00:00Z","publication":"Physical Review Letters","main_file_link":[{"url":"https://arxiv.org/abs/1305.5554","open_access":"1"}],"citation":{"chicago":"Serbyn, Maksym, Zlatko Papić, and Dmitry Abanin. “Local Conservation Laws and the Structure of the Many Body Localized States.” Physical Review Letters. American Physical Society, 2013. https://doi.org/10.1103/PhysRevLett.111.127201.","mla":"Serbyn, Maksym, et al. “Local Conservation Laws and the Structure of the Many Body Localized States.” Physical Review Letters, vol. 111, no. 12, American Physical Society, 2013, doi:10.1103/PhysRevLett.111.127201.","short":"M. Serbyn, Z. Papić, D. Abanin, Physical Review Letters 111 (2013).","ista":"Serbyn M, Papić Z, Abanin D. 2013. Local conservation laws and the structure of the many body localized states. Physical Review Letters. 111(12).","ieee":"M. Serbyn, Z. Papić, and D. Abanin, “Local conservation laws and the structure of the many body localized states,” Physical Review Letters, vol. 111, no. 12. American Physical Society, 2013.","apa":"Serbyn, M., Papić, Z., & Abanin, D. (2013). Local conservation laws and the structure of the many body localized states. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.111.127201","ama":"Serbyn M, Papić Z, Abanin D. Local conservation laws and the structure of the many body localized states. Physical Review Letters. 2013;111(12). doi:10.1103/PhysRevLett.111.127201"},"oa":1,"quality_controlled":0},{"day":"19","month":"07","doi":"10.1103/PhysRevB.88.024419","date_published":"2013-07-19T00:00:00Z","language":[{"iso":"eng"}],"publication":"Physical Review B - Condensed Matter and Materials Physics","external_id":{"arxiv":["1212.5179"]},"citation":{"apa":"Serbyn, M., Senthil, T., & Lee, P. (2013). Overscreened Kondo fixed point in S=1 spin liquid. Physical Review B - Condensed Matter and Materials Physics. American Physical Society. https://doi.org/10.1103/PhysRevB.88.024419","ieee":"M. Serbyn, T. Senthil, and P. Lee, “Overscreened Kondo fixed point in S=1 spin liquid,” Physical Review B - Condensed Matter and Materials Physics, vol. 88, no. 2. American Physical Society, 2013.","ista":"Serbyn M, Senthil T, Lee P. 2013. Overscreened Kondo fixed point in S=1 spin liquid. Physical Review B - Condensed Matter and Materials Physics. 88(2).","ama":"Serbyn M, Senthil T, Lee P. Overscreened Kondo fixed point in S=1 spin liquid. Physical Review B - Condensed Matter and Materials Physics. 2013;88(2). doi:10.1103/PhysRevB.88.024419","chicago":"Serbyn, Maksym, Todadri Senthil, and Patrick Lee. “Overscreened Kondo Fixed Point in S=1 Spin Liquid.” Physical Review B - Condensed Matter and Materials Physics. American Physical Society, 2013. https://doi.org/10.1103/PhysRevB.88.024419.","short":"M. Serbyn, T. Senthil, P. Lee, Physical Review B - Condensed Matter and Materials Physics 88 (2013).","mla":"Serbyn, Maksym, et al. “Overscreened Kondo Fixed Point in S=1 Spin Liquid.” Physical Review B - Condensed Matter and Materials Physics, vol. 88, no. 2, American Physical Society, 2013, doi:10.1103/PhysRevB.88.024419."},"main_file_link":[{"url":"https://arxiv.org/abs/1212.5179","open_access":"1"}],"oa":1,"quality_controlled":"1","abstract":[{"text":"We propose a possible realization of the overscreened Kondo impurity problem by a magnetic s=1/2 impurity embedded in a two-dimensional S=1 U(1) spin liquid with a Fermi surface. This problem contains an interesting interplay between non-Fermi-liquid behavior induced by a U(1) gauge field coupled to fermions and a non-Fermi-liquid fixed point in the overscreened Kondo problem. Using a large-N expansion together with an expansion in the dynamical exponent of the gauge field, we find that the coupling to the gauge field leads to weak but observable changes in the physical properties of the system at the overscreened Kondo fixed point. We discuss the extrapolation of this result to a physical case and argue that the realization of overscreened Kondo physics could lead to observations of effects due to gauge fields.","lang":"eng"}],"publist_id":"6425","issue":"2","extern":"1","type":"journal_article","author":[{"full_name":"Serbyn, Maksym","first_name":"Maksym","last_name":"Serbyn","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827"},{"last_name":"Senthil","first_name":"Todadri","full_name":"Senthil, Todadri"},{"last_name":"Lee","first_name":"Patrick","full_name":"Lee, Patrick"}],"date_created":"2018-12-11T11:49:29Z","date_updated":"2021-01-12T08:22:21Z","volume":88,"oa_version":"Preprint","_id":"974","year":"2013","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","publication_status":"published","title":"Overscreened Kondo fixed point in S=1 spin liquid","publisher":"American Physical Society","intvolume":" 88"},{"volume":13,"date_created":"2018-12-11T11:56:46Z","date_updated":"2023-02-23T14:07:06Z","related_material":{"record":[{"id":"9753","status":"public","relation":"research_data"}]},"author":[{"id":"35A7A418-F248-11E8-B48F-1D18A9856A87","last_name":"Tragust","first_name":"Simon","full_name":"Tragust, Simon"},{"id":"3DC97C8E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1832-8883","first_name":"Line V","last_name":"Ugelvig","full_name":"Ugelvig, Line V"},{"last_name":"Chapuisat","first_name":"Michel","full_name":"Chapuisat, Michel"},{"full_name":"Heinze, Jürgen","first_name":"Jürgen","last_name":"Heinze"},{"id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2193-3868","first_name":"Sylvia","last_name":"Cremer","full_name":"Cremer, Sylvia"}],"department":[{"_id":"SyCr"}],"publisher":"BioMed Central","publication_status":"published","acknowledgement":"The study was funded by the European Research Council (Marie Curie ERG 036569) and Marie Curie IEF 302204 to LVU\r\nCC BY 2.0\r\n","year":"2013","ec_funded":1,"publist_id":"4647","file_date_updated":"2020-07-14T12:45:37Z","article_number":"225","language":[{"iso":"eng"}],"doi":"10.1186/1471-2148-13-225","project":[{"grant_number":"243071","_id":"25DC711C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Social Vaccination in Ant Colonies: from Individual Mechanisms to Society Effects"},{"name":"Host-Parasite Coevolution","grant_number":"CR-118/3-1","_id":"25DAF0B2-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"month":"10","oa_version":"Published Version","file":[{"checksum":"c16ef36f2a10786a7885e19c4528d707","date_created":"2018-12-12T10:13:41Z","date_updated":"2020-07-14T12:45:37Z","file_id":"5026","relation":"main_file","creator":"system","file_size":281736,"content_type":"application/pdf","access_level":"open_access","file_name":"IST-2016-402-v1+1_1471-2148-13-225.pdf"}],"pubrep_id":"402","intvolume":" 13","status":"public","title":"Pupal cocoons affect sanitary brood care and limit fungal infections in ant colonies","ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2284","issue":"1","abstract":[{"lang":"eng","text":"Background: The brood of ants and other social insects is highly susceptible to pathogens, particularly those that penetrate the soft larval and pupal cuticle. We here test whether the presence of a pupal cocoon, which occurs in some ant species but not in others, affects the sanitary brood care and fungal infection patterns after exposure to the entomopathogenic fungus Metarhizium brunneum. We use a) a comparative approach analysing four species with either naked or cocooned pupae and b) a within-species analysis of a single ant species, in which both pupal types co-exist in the same colony. Results: We found that the presence of a cocoon did not compromise fungal pathogen detection by the ants and that species with cocooned pupae increased brood grooming after pathogen exposure. All tested ant species further removed brood from their nests, which was predominantly expressed towards larvae and naked pupae treated with the live fungal pathogen. In contrast, cocooned pupae exposed to live fungus were not removed at higher rates than cocooned pupae exposed to dead fungus or a sham control. Consistent with this, exposure to the live fungus caused high numbers of infections and fungal outgrowth in larvae and naked pupae, but not in cocooned pupae. Moreover, the ants consistently removed the brood prior to fungal outgrowth, ensuring a clean brood chamber. Conclusion: Our study suggests that the pupal cocoon has a protective effect against fungal infection, causing an adaptive change in sanitary behaviours by the ants. It further demonstrates that brood removal-originally described for honeybees as "hygienic behaviour"-is a widespread sanitary behaviour in ants, which likely has important implications on disease dynamics in social insect colonies."}],"type":"journal_article","date_published":"2013-10-14T00:00:00Z","citation":{"short":"S. Tragust, L.V. Ugelvig, M. Chapuisat, J. Heinze, S. Cremer, BMC Evolutionary Biology 13 (2013).","mla":"Tragust, Simon, et al. “Pupal Cocoons Affect Sanitary Brood Care and Limit Fungal Infections in Ant Colonies.” BMC Evolutionary Biology, vol. 13, no. 1, 225, BioMed Central, 2013, doi:10.1186/1471-2148-13-225.","chicago":"Tragust, Simon, Line V Ugelvig, Michel Chapuisat, Jürgen Heinze, and Sylvia Cremer. “Pupal Cocoons Affect Sanitary Brood Care and Limit Fungal Infections in Ant Colonies.” BMC Evolutionary Biology. BioMed Central, 2013. https://doi.org/10.1186/1471-2148-13-225.","ama":"Tragust S, Ugelvig LV, Chapuisat M, Heinze J, Cremer S. Pupal cocoons affect sanitary brood care and limit fungal infections in ant colonies. BMC Evolutionary Biology. 2013;13(1). doi:10.1186/1471-2148-13-225","ieee":"S. Tragust, L. V. Ugelvig, M. Chapuisat, J. Heinze, and S. Cremer, “Pupal cocoons affect sanitary brood care and limit fungal infections in ant colonies,” BMC Evolutionary Biology, vol. 13, no. 1. BioMed Central, 2013.","apa":"Tragust, S., Ugelvig, L. V., Chapuisat, M., Heinze, J., & Cremer, S. (2013). Pupal cocoons affect sanitary brood care and limit fungal infections in ant colonies. BMC Evolutionary Biology. BioMed Central. https://doi.org/10.1186/1471-2148-13-225","ista":"Tragust S, Ugelvig LV, Chapuisat M, Heinze J, Cremer S. 2013. Pupal cocoons affect sanitary brood care and limit fungal infections in ant colonies. BMC Evolutionary Biology. 13(1), 225."},"publication":"BMC Evolutionary Biology","has_accepted_license":"1","day":"14","scopus_import":1},{"publist_id":"4667","file_date_updated":"2020-07-14T12:45:36Z","article_number":"e1003344","volume":9,"date_created":"2018-12-11T11:56:43Z","date_updated":"2023-02-23T14:07:04Z","related_material":{"record":[{"id":"9752","status":"public","relation":"research_data"}]},"author":[{"first_name":"Kristina","last_name":"Simmons","full_name":"Simmons, Kristina"},{"first_name":"Jason","last_name":"Prentice","full_name":"Prentice, Jason"},{"first_name":"Gasper","last_name":"Tkacik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","full_name":"Tkacik, Gasper"},{"full_name":"Homann, Jan","last_name":"Homann","first_name":"Jan"},{"full_name":"Yee, Heather","last_name":"Yee","first_name":"Heather"},{"full_name":"Palmer, Stephanie","first_name":"Stephanie","last_name":"Palmer"},{"last_name":"Nelson","first_name":"Philip","full_name":"Nelson, Philip"},{"last_name":"Balasubramanian","first_name":"Vijay","full_name":"Balasubramanian, Vijay"}],"publisher":"Public Library of Science","department":[{"_id":"GaTk"}],"publication_status":"published","year":"2013","month":"12","language":[{"iso":"eng"}],"doi":"10.1371/journal.pcbi.1003344","quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"issue":"12","abstract":[{"text":"Redundancies and correlations in the responses of sensory neurons may seem to waste neural resources, but they can also carry cues about structured stimuli and may help the brain to correct for response errors. To investigate the effect of stimulus structure on redundancy in retina, we measured simultaneous responses from populations of retinal ganglion cells presented with natural and artificial stimuli that varied greatly in correlation structure; these stimuli and recordings are publicly available online. Responding to spatio-temporally structured stimuli such as natural movies, pairs of ganglion cells were modestly more correlated than in response to white noise checkerboards, but they were much less correlated than predicted by a non-adapting functional model of retinal response. Meanwhile, responding to stimuli with purely spatial correlations, pairs of ganglion cells showed increased correlations consistent with a static, non-adapting receptive field and nonlinearity. We found that in response to spatio-temporally correlated stimuli, ganglion cells had faster temporal kernels and tended to have stronger surrounds. These properties of individual cells, along with gain changes that opposed changes in effective contrast at the ganglion cell input, largely explained the pattern of pairwise correlations across stimuli where receptive field measurements were possible.","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","file":[{"file_name":"IST-2016-410-v1+1_journal.pcbi.1003344.pdf","access_level":"open_access","file_size":3115568,"content_type":"application/pdf","creator":"system","relation":"main_file","file_id":"5089","date_updated":"2020-07-14T12:45:36Z","date_created":"2018-12-12T10:14:36Z","checksum":"46722afc4f7eabb0831165d9c1b171ad"}],"pubrep_id":"410","intvolume":" 9","status":"public","title":"Transformation of stimulus correlations by the retina","ddc":["570"],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"2277","has_accepted_license":"1","day":"05","scopus_import":1,"date_published":"2013-12-05T00:00:00Z","citation":{"ista":"Simmons K, Prentice J, Tkačik G, Homann J, Yee H, Palmer S, Nelson P, Balasubramanian V. 2013. Transformation of stimulus correlations by the retina. PLoS Computational Biology. 9(12), e1003344.","ieee":"K. Simmons et al., “Transformation of stimulus correlations by the retina,” PLoS Computational Biology, vol. 9, no. 12. Public Library of Science, 2013.","apa":"Simmons, K., Prentice, J., Tkačik, G., Homann, J., Yee, H., Palmer, S., … Balasubramanian, V. (2013). Transformation of stimulus correlations by the retina. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1003344","ama":"Simmons K, Prentice J, Tkačik G, et al. Transformation of stimulus correlations by the retina. PLoS Computational Biology. 2013;9(12). doi:10.1371/journal.pcbi.1003344","chicago":"Simmons, Kristina, Jason Prentice, Gašper Tkačik, Jan Homann, Heather Yee, Stephanie Palmer, Philip Nelson, and Vijay Balasubramanian. “Transformation of Stimulus Correlations by the Retina.” PLoS Computational Biology. Public Library of Science, 2013. https://doi.org/10.1371/journal.pcbi.1003344.","mla":"Simmons, Kristina, et al. “Transformation of Stimulus Correlations by the Retina.” PLoS Computational Biology, vol. 9, no. 12, e1003344, Public Library of Science, 2013, doi:10.1371/journal.pcbi.1003344.","short":"K. Simmons, J. Prentice, G. Tkačik, J. Homann, H. Yee, S. Palmer, P. Nelson, V. Balasubramanian, PLoS Computational Biology 9 (2013)."},"publication":"PLoS Computational Biology"},{"related_material":{"record":[{"id":"2170","relation":"used_in_publication","status":"public"}]},"author":[{"full_name":"Hearn, Jack","last_name":"Hearn","first_name":"Jack"},{"full_name":"Stone, Graham","first_name":"Graham","last_name":"Stone"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton","full_name":"Barton, Nicholas H"},{"full_name":"Lohse, Konrad","first_name":"Konrad","last_name":"Lohse"},{"full_name":"Bunnefeld, Lynsey","first_name":"Lynsey","last_name":"Bunnefeld"}],"oa_version":"Published Version","date_created":"2021-07-30T08:31:22Z","date_updated":"2023-02-23T10:31:17Z","_id":"9754","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","year":"2013","publisher":"Dryad","department":[{"_id":"NiBa"}],"title":"Data from: Likelihood-based inference of population history from low coverage de novo genome assemblies","status":"public","abstract":[{"lang":"eng","text":"Short-read sequencing technologies have in principle made it feasible to draw detailed inferences about the recent history of any organism. In practice, however, this remains challenging due to the difficulty of genome assembly in most organisms and the lack of statistical methods powerful enough to discriminate among recent, non-equilibrium histories. We address both the assembly and inference challenges. We develop a bioinformatic pipeline for generating outgroup-rooted alignments of orthologous sequence blocks from de novo low-coverage short-read data for a small number of genomes, and show how such sequence blocks can be used to fit explicit models of population divergence and admixture in a likelihood framework. To illustrate our approach, we reconstruct the Pleistocene history of an oak-feeding insect (the oak gallwasp Biorhiza pallida) which, in common with many other taxa, was restricted during Pleistocene ice ages to a longitudinal series of southern refugia spanning theWestern Palaearctic. Our analysis of sequence blocks sampled from a single genome from each of three major glacial refugia reveals support for an unexpected history dominated by recent admixture. Despite the fact that 80% of the genome is affected by admixture during the last glacial cycle, we are able to infer the deeper divergence history of these populations. These inferences are robust to variation in block length, mutation model, and the sampling location of individual genomes within refugia. This combination of de novo assembly and numerical likelihood calculation provides a powerful framework for estimating recent population history that can be applied to any organism without the need for prior genetic resources."}],"type":"research_data_reference","doi":"10.5061/dryad.r3r60","date_published":"2013-10-01T00:00:00Z","main_file_link":[{"url":"https://doi.org/10.5061/dryad.r3r60","open_access":"1"}],"oa":1,"citation":{"mla":"Hearn, Jack, et al. Data from: Likelihood-Based Inference of Population History from Low Coverage de Novo Genome Assemblies. Dryad, 2013, doi:10.5061/dryad.r3r60.","short":"J. Hearn, G. Stone, N.H. Barton, K. Lohse, L. Bunnefeld, (2013).","chicago":"Hearn, Jack, Graham Stone, Nicholas H Barton, Konrad Lohse, and Lynsey Bunnefeld. “Data from: Likelihood-Based Inference of Population History from Low Coverage de Novo Genome Assemblies.” Dryad, 2013. https://doi.org/10.5061/dryad.r3r60.","ama":"Hearn J, Stone G, Barton NH, Lohse K, Bunnefeld L. Data from: Likelihood-based inference of population history from low coverage de novo genome assemblies. 2013. doi:10.5061/dryad.r3r60","ista":"Hearn J, Stone G, Barton NH, Lohse K, Bunnefeld L. 2013. Data from: Likelihood-based inference of population history from low coverage de novo genome assemblies, Dryad, 10.5061/dryad.r3r60.","ieee":"J. Hearn, G. Stone, N. H. Barton, K. Lohse, and L. Bunnefeld, “Data from: Likelihood-based inference of population history from low coverage de novo genome assemblies.” Dryad, 2013.","apa":"Hearn, J., Stone, G., Barton, N. H., Lohse, K., & Bunnefeld, L. (2013). Data from: Likelihood-based inference of population history from low coverage de novo genome assemblies. Dryad. https://doi.org/10.5061/dryad.r3r60"},"article_processing_charge":"No","day":"01","month":"10"},{"volume":87,"date_updated":"2021-01-12T08:22:22Z","date_created":"2018-12-11T11:49:30Z","author":[{"full_name":"Maksym Serbyn","first_name":"Maksym","last_name":"Serbyn","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827"},{"first_name":"Patrick","last_name":"Lee","full_name":"Lee, Patrick"}],"publisher":"American Physical Society","intvolume":" 87","status":"public","title":"Spinon-phonon interaction in algebraic spin liquids","publication_status":"published","_id":"976","year":"2013","acknowledgement":"M. S. is grateful to X.-G. Wen, L. Levitov, M. Metlitski, K. Michaeli, K.-T. Chen, and A. Potter for many useful discussions. We acknowledge support by Grant No. NSF DMR 1104498. We acknowledge the hospitality of KITP, where final stages of this project were completed.","extern":1,"issue":"17","publist_id":"6427","abstract":[{"text":"Motivated by a search for experimental probes to access the physics of fractionalized excitations called spinons in spin liquids, we study the interaction of spinons with lattice vibrations. We consider the case of algebraic spin liquid, when spinons have fermionic statistics and a Dirac-like dispersion. We establish the general procedure for deriving spinon-phonon interactions, which is based on symmetry considerations. The procedure is illustrated for four different algebraic spin liquids: π-flux and staggered-flux phases on a square lattice, π-flux phase on a kagome lattice, and zero-flux phase on a honeycomb lattice. Although the low-energy description is similar for all these phases, different underlying symmetry groups lead to a distinct form of spinon-phonon interaction Hamiltonian. The explicit form of the spinon-phonon interaction is used to estimate the attenuation of ultrasound in an algebraic spin liquid. The prospects of the sound attenuation as a probe of spinons are discussed.","lang":"eng"}],"type":"journal_article","date_published":"2013-05-22T00:00:00Z","doi":"10.1103/PhysRevB.87.174424","quality_controlled":0,"citation":{"chicago":"Serbyn, Maksym, and Patrick Lee. “Spinon-Phonon Interaction in Algebraic Spin Liquids.” Physical Review B - Condensed Matter and Materials Physics. American Physical Society, 2013. https://doi.org/10.1103/PhysRevB.87.174424.","short":"M. Serbyn, P. Lee, Physical Review B - Condensed Matter and Materials Physics 87 (2013).","mla":"Serbyn, Maksym, and Patrick Lee. “Spinon-Phonon Interaction in Algebraic Spin Liquids.” Physical Review B - Condensed Matter and Materials Physics, vol. 87, no. 17, American Physical Society, 2013, doi:10.1103/PhysRevB.87.174424.","apa":"Serbyn, M., & Lee, P. (2013). Spinon-phonon interaction in algebraic spin liquids. Physical Review B - Condensed Matter and Materials Physics. American Physical Society. https://doi.org/10.1103/PhysRevB.87.174424","ieee":"M. Serbyn and P. Lee, “Spinon-phonon interaction in algebraic spin liquids,” Physical Review B - Condensed Matter and Materials Physics, vol. 87, no. 17. American Physical Society, 2013.","ista":"Serbyn M, Lee P. 2013. Spinon-phonon interaction in algebraic spin liquids. Physical Review B - Condensed Matter and Materials Physics. 87(17).","ama":"Serbyn M, Lee P. Spinon-phonon interaction in algebraic spin liquids. Physical Review B - Condensed Matter and Materials Physics. 2013;87(17). doi:10.1103/PhysRevB.87.174424"},"main_file_link":[{"url":"https://arxiv.org/abs/1303.0772","open_access":"1"}],"oa":1,"publication":"Physical Review B - Condensed Matter and Materials Physics","month":"05","day":"22"},{"extern":"1","year":"2013","publication_status":"published","publisher":"Copernicus GmbH","author":[{"first_name":"A. F.","last_name":"Lutz","full_name":"Lutz, A. F."},{"full_name":"Immerzeel, W. W.","last_name":"Immerzeel","first_name":"W. W."},{"first_name":"A.","last_name":"Gobiet","full_name":"Gobiet, A."},{"full_name":"Pellicciotti, Francesca","first_name":"Francesca","last_name":"Pellicciotti","id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70"},{"last_name":"Bierkens","first_name":"M. F. P.","full_name":"Bierkens, M. F. P."}],"date_created":"2023-02-20T08:17:05Z","date_updated":"2023-02-24T08:19:48Z","volume":17,"month":"09","publication_identifier":{"issn":["1607-7938"]},"oa":1,"main_file_link":[{"url":"https://doi.org/10.5194/hess-17-3661-2013","open_access":"1"}],"quality_controlled":"1","doi":"10.5194/hess-17-3661-2013","language":[{"iso":"eng"}],"type":"journal_article","abstract":[{"text":"Central Asian water resources largely depend on melt water generated in the Pamir and Tien Shan mountain ranges. To estimate future water availability in this region, it is necessary to use climate projections to estimate the future glacier extent and volume. In this study, we evaluate the impact of uncertainty in climate change projections on the future glacier extent in the Amu and Syr Darya river basins. To this end we use the latest climate change projections generated for the upcoming IPCC report (CMIP5) and, for comparison, projections used in the fourth IPCC assessment (CMIP3). With these projections we force a regionalized glacier mass balance model, and estimate changes in the basins' glacier extent as a function of the glacier size distribution in the basins and projected temperature and precipitation. This glacier mass balance model is specifically developed for implementation in large scale hydrological models, where the spatial resolution does not allow for simulating individual glaciers and data scarcity is an issue. Although the CMIP5 ensemble results in greater regional warming than the CMIP3 ensemble and the range in projections for temperature as well as precipitation is wider for the CMIP5 than for the CMIP3, the spread in projections of future glacier extent in Central Asia is similar for both ensembles. This is because differences in temperature rise are small during periods of maximum melt (July–September) while differences in precipitation change are small during the period of maximum accumulation (October–February). However, the model uncertainty due to parameter uncertainty is high, and has roughly the same importance as uncertainty in the climate projections. Uncertainty about the size of the decline in glacier extent remains large, making estimates of future Central Asian glacier evolution and downstream water availability uncertain.","lang":"eng"}],"issue":"9","_id":"12638","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Comparison of climate change signals in CMIP3 and CMIP5 multi-model ensembles and implications for Central Asian glaciers","status":"public","intvolume":" 17","oa_version":"Published Version","scopus_import":"1","keyword":["General Earth and Planetary Sciences","General Engineering","General Environmental Science"],"day":"01","article_processing_charge":"No","publication":"Hydrology and Earth System Sciences","citation":{"ista":"Lutz AF, Immerzeel WW, Gobiet A, Pellicciotti F, Bierkens MFP. 2013. Comparison of climate change signals in CMIP3 and CMIP5 multi-model ensembles and implications for Central Asian glaciers. Hydrology and Earth System Sciences. 17(9), 3661–3677.","ieee":"A. F. Lutz, W. W. Immerzeel, A. Gobiet, F. Pellicciotti, and M. F. P. Bierkens, “Comparison of climate change signals in CMIP3 and CMIP5 multi-model ensembles and implications for Central Asian glaciers,” Hydrology and Earth System Sciences, vol. 17, no. 9. Copernicus GmbH, pp. 3661–3677, 2013.","apa":"Lutz, A. F., Immerzeel, W. W., Gobiet, A., Pellicciotti, F., & Bierkens, M. F. P. (2013). Comparison of climate change signals in CMIP3 and CMIP5 multi-model ensembles and implications for Central Asian glaciers. Hydrology and Earth System Sciences. Copernicus GmbH. https://doi.org/10.5194/hess-17-3661-2013","ama":"Lutz AF, Immerzeel WW, Gobiet A, Pellicciotti F, Bierkens MFP. Comparison of climate change signals in CMIP3 and CMIP5 multi-model ensembles and implications for Central Asian glaciers. Hydrology and Earth System Sciences. 2013;17(9):3661-3677. doi:10.5194/hess-17-3661-2013","chicago":"Lutz, A. F., W. W. Immerzeel, A. Gobiet, Francesca Pellicciotti, and M. F. P. Bierkens. “Comparison of Climate Change Signals in CMIP3 and CMIP5 Multi-Model Ensembles and Implications for Central Asian Glaciers.” Hydrology and Earth System Sciences. Copernicus GmbH, 2013. https://doi.org/10.5194/hess-17-3661-2013.","mla":"Lutz, A. F., et al. “Comparison of Climate Change Signals in CMIP3 and CMIP5 Multi-Model Ensembles and Implications for Central Asian Glaciers.” Hydrology and Earth System Sciences, vol. 17, no. 9, Copernicus GmbH, 2013, pp. 3661–77, doi:10.5194/hess-17-3661-2013.","short":"A.F. Lutz, W.W. Immerzeel, A. Gobiet, F. Pellicciotti, M.F.P. Bierkens, Hydrology and Earth System Sciences 17 (2013) 3661–3677."},"article_type":"original","page":"3661-3677","date_published":"2013-09-01T00:00:00Z"},{"type":"journal_article","issue":"9","abstract":[{"lang":"eng","text":"In the headwater catchments of the main Asian rivers, glaciohydrological models are a useful tool to anticipate impacts of climatic changes. However, the reliability of their projections strongly depends on the quality and quantity of data that are available for parameter estimation, model calibration and validation, as well as on the accuracy of climate change projections. In this study the physically oriented, glaciohydrological model TOPKAPI-ETH is used to simulate future changes in snow, glacier, and runoff from the Hunza River Basin in northern Pakistan. Three key sources of model uncertainty in future runoff projections are compared: model parameters, climate projections, and natural climate variability. A novel approach, applicable also to ungauged catchments, is used to determine which model parameters and model components significantly affect the overall model uncertainty. We show that the model is capable of reproducing streamflow and glacier mass balances, but that all analyzed sources of uncertainty significantly affect the reliability of future projections, and that their effect is variable in time and in space. The effect of parametric uncertainty often exceeds the impact of climate uncertainty and natural climate variability, especially in heavily glacierized subcatchments. The results of the uncertainty analysis allow detailed recommendations on network design and the timing and location of field measurements, which could efficiently help to reduce model uncertainty in the future."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12639","intvolume":" 49","title":"Sources of uncertainty in modeling the glaciohydrological response of a Karakoram watershed to climate change","status":"public","oa_version":"Published Version","scopus_import":"1","keyword":["Water Science and Technology"],"article_processing_charge":"No","day":"01","citation":{"chicago":"Ragettli, S., Francesca Pellicciotti, R. Bordoy, and W. W. Immerzeel. “Sources of Uncertainty in Modeling the Glaciohydrological Response of a Karakoram Watershed to Climate Change.” Water Resources Research. American Geophysical Union, 2013. https://doi.org/10.1002/wrcr.20450.","short":"S. Ragettli, F. Pellicciotti, R. Bordoy, W.W. Immerzeel, Water Resources Research 49 (2013) 6048–6066.","mla":"Ragettli, S., et al. “Sources of Uncertainty in Modeling the Glaciohydrological Response of a Karakoram Watershed to Climate Change.” Water Resources Research, vol. 49, no. 9, American Geophysical Union, 2013, pp. 6048–66, doi:10.1002/wrcr.20450.","ieee":"S. Ragettli, F. Pellicciotti, R. Bordoy, and W. W. Immerzeel, “Sources of uncertainty in modeling the glaciohydrological response of a Karakoram watershed to climate change,” Water Resources Research, vol. 49, no. 9. American Geophysical Union, pp. 6048–6066, 2013.","apa":"Ragettli, S., Pellicciotti, F., Bordoy, R., & Immerzeel, W. W. (2013). Sources of uncertainty in modeling the glaciohydrological response of a Karakoram watershed to climate change. Water Resources Research. American Geophysical Union. https://doi.org/10.1002/wrcr.20450","ista":"Ragettli S, Pellicciotti F, Bordoy R, Immerzeel WW. 2013. Sources of uncertainty in modeling the glaciohydrological response of a Karakoram watershed to climate change. Water Resources Research. 49(9), 6048–6066.","ama":"Ragettli S, Pellicciotti F, Bordoy R, Immerzeel WW. Sources of uncertainty in modeling the glaciohydrological response of a Karakoram watershed to climate change. Water Resources Research. 2013;49(9):6048-6066. doi:10.1002/wrcr.20450"},"publication":"Water Resources Research","page":"6048-6066","article_type":"original","date_published":"2013-03-01T00:00:00Z","extern":"1","year":"2013","publisher":"American Geophysical Union","publication_status":"published","author":[{"full_name":"Ragettli, S.","last_name":"Ragettli","first_name":"S."},{"first_name":"Francesca","last_name":"Pellicciotti","id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70","full_name":"Pellicciotti, Francesca"},{"full_name":"Bordoy, R.","last_name":"Bordoy","first_name":"R."},{"first_name":"W. W.","last_name":"Immerzeel","full_name":"Immerzeel, W. W."}],"volume":49,"date_created":"2023-02-20T08:17:12Z","date_updated":"2023-02-24T08:16:19Z","publication_identifier":{"issn":["0043-1397"]},"month":"03","main_file_link":[{"url":"https://doi.org/10.1002/wrcr.20450","open_access":"1"}],"oa":1,"quality_controlled":"1","doi":"10.1002/wrcr.20450","language":[{"iso":"eng"}]},{"year":"2013","publication_status":"published","publisher":"Wiley","author":[{"first_name":"S.","last_name":"Ragettli","full_name":"Ragettli, S."},{"full_name":"Cortés, G.","last_name":"Cortés","first_name":"G."},{"full_name":"McPhee, J.","first_name":"J.","last_name":"McPhee"},{"id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70","first_name":"Francesca","last_name":"Pellicciotti","full_name":"Pellicciotti, Francesca"}],"date_created":"2023-02-20T08:16:39Z","date_updated":"2023-02-24T08:48:40Z","volume":28,"extern":"1","quality_controlled":"1","doi":"10.1002/hyp.10055","language":[{"iso":"eng"}],"month":"09","publication_identifier":{"issn":["0885-6087"]},"_id":"12633","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"An evaluation of approaches for modelling hydrological processes in high-elevation, glacierized Andean watersheds","intvolume":" 28","oa_version":"None","type":"journal_article","abstract":[{"lang":"eng","text":"We use two hydrological models of varying complexity to study the Juncal River Basin in the Central Andes of Chile with the aim to understand the degree of conceptualization and the spatial structure that are needed to model present and future streamflows. We use a conceptual semi-distributed model based on elevation bands [Water Evaluation and Planning (WEAP)], frequently used for water management, and a physically oriented, fully distributed model [Topographic Kinematic Wave Approximation and Integration ETH Zurich (TOPKAPI-ETH)] developed for research purposes mainly. We evaluate the ability of the two models to reproduce the key hydrological processes in the basin with emphasis on snow accumulation and melt, streamflow and the relationships between internal processes. Both models are capable of reproducing observed runoff and the evolution of Moderate-resolution Imaging Spectroradiometer snow cover adequately. In spite of WEAP's simple and conceptual approach for modelling snowmelt and its lack of glacier representation and snow gravitational redistribution as well as a proper routing algorithm, this model can reproduce historical data with a similar goodness of fit as the more complex TOPKAPI-ETH. We show that the performance of both models can be improved by using measured precipitation gradients of higher temporal resolution. In contrast to the good performance of the conceptual model for the present climate, however, we demonstrate that the simplifications in WEAP lead to error compensation, which results in different predictions in simulated melt and runoff for a potentially warmer future climate. TOPKAPI-ETH, using a more physical representation of processes, depends less on calibration and thus is less subject to a compensation of errors through different model components. Our results show that data obtained locally in ad hoc short-term field campaigns are needed to complement data extrapolated from long-term records for simulating changes in the water cycle of high-elevation catchments but that these data can only be efficiently used by a model applying a spatially distributed physical representation of hydrological processes."}],"issue":"23","publication":"Hydrological Processes","citation":{"ista":"Ragettli S, Cortés G, McPhee J, Pellicciotti F. 2013. An evaluation of approaches for modelling hydrological processes in high-elevation, glacierized Andean watersheds. Hydrological Processes. 28(23), 5674–5695.","apa":"Ragettli, S., Cortés, G., McPhee, J., & Pellicciotti, F. (2013). An evaluation of approaches for modelling hydrological processes in high-elevation, glacierized Andean watersheds. Hydrological Processes. Wiley. https://doi.org/10.1002/hyp.10055","ieee":"S. Ragettli, G. Cortés, J. McPhee, and F. Pellicciotti, “An evaluation of approaches for modelling hydrological processes in high-elevation, glacierized Andean watersheds,” Hydrological Processes, vol. 28, no. 23. Wiley, pp. 5674–5695, 2013.","ama":"Ragettli S, Cortés G, McPhee J, Pellicciotti F. An evaluation of approaches for modelling hydrological processes in high-elevation, glacierized Andean watersheds. Hydrological Processes. 2013;28(23):5674-5695. doi:10.1002/hyp.10055","chicago":"Ragettli, S., G. Cortés, J. McPhee, and Francesca Pellicciotti. “An Evaluation of Approaches for Modelling Hydrological Processes in High-Elevation, Glacierized Andean Watersheds.” Hydrological Processes. Wiley, 2013. https://doi.org/10.1002/hyp.10055.","mla":"Ragettli, S., et al. “An Evaluation of Approaches for Modelling Hydrological Processes in High-Elevation, Glacierized Andean Watersheds.” Hydrological Processes, vol. 28, no. 23, Wiley, 2013, pp. 5674–95, doi:10.1002/hyp.10055.","short":"S. Ragettli, G. Cortés, J. McPhee, F. Pellicciotti, Hydrological Processes 28 (2013) 5674–5695."},"article_type":"original","page":"5674-5695","date_published":"2013-09-06T00:00:00Z","scopus_import":"1","keyword":["Water Science and Technology"],"day":"06","article_processing_charge":"No"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"9520","intvolume":" 24","title":"A conversation across generations: Soma-germ cell crosstalk in plants","status":"public","oa_version":"Published Version","type":"journal_article","issue":"3","abstract":[{"lang":"eng","text":"Plants undergo alternation of generation in which reproductive cells develop in the plant body (\"sporophytic generation\") and then differentiate into a multicellular gamete-forming \"gametophytic generation.\" Different populations of helper cells assist in this transgenerational journey, with somatic tissues supporting early development and single nurse cells supporting gametogenesis. New data reveal a two-way relationship between early reproductive cells and their helpers involving complex epigenetic and signaling networks determining cell number and fate. Later, the egg cell plays a central role in specifying accessory cells, whereas in both gametophytes, companion cells contribute non-cell-autonomously to the epigenetic landscape of the gamete genomes."}],"citation":{"ama":"Feng X, Zilberman D, Dickinson H. A conversation across generations: Soma-germ cell crosstalk in plants. Developmental Cell. 2013;24(3):215-225. doi:10.1016/j.devcel.2013.01.014","ista":"Feng X, Zilberman D, Dickinson H. 2013. A conversation across generations: Soma-germ cell crosstalk in plants. Developmental Cell. 24(3), 215–225.","ieee":"X. Feng, D. Zilberman, and H. Dickinson, “A conversation across generations: Soma-germ cell crosstalk in plants,” Developmental Cell, vol. 24, no. 3. Elsevier, pp. 215–225, 2013.","apa":"Feng, X., Zilberman, D., & Dickinson, H. (2013). A conversation across generations: Soma-germ cell crosstalk in plants. Developmental Cell. Elsevier. https://doi.org/10.1016/j.devcel.2013.01.014","mla":"Feng, Xiaoqi, et al. “A Conversation across Generations: Soma-Germ Cell Crosstalk in Plants.” Developmental Cell, vol. 24, no. 3, Elsevier, 2013, pp. 215–25, doi:10.1016/j.devcel.2013.01.014.","short":"X. Feng, D. Zilberman, H. Dickinson, Developmental Cell 24 (2013) 215–225.","chicago":"Feng, Xiaoqi, Daniel Zilberman, and Hugh Dickinson. “A Conversation across Generations: Soma-Germ Cell Crosstalk in Plants.” Developmental Cell. Elsevier, 2013. https://doi.org/10.1016/j.devcel.2013.01.014."},"publication":"Developmental Cell","page":"215-225","article_type":"review","date_published":"2013-02-11T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"11","pmid":1,"year":"2013","publisher":"Elsevier","department":[{"_id":"DaZi"},{"_id":"XiFe"}],"publication_status":"published","author":[{"full_name":"Feng, Xiaoqi","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","orcid":"0000-0002-4008-1234","first_name":"Xiaoqi","last_name":"Feng"},{"id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","orcid":"0000-0002-0123-8649","first_name":"Daniel","last_name":"Zilberman","full_name":"Zilberman, Daniel"},{"last_name":"Dickinson","first_name":"Hugh","full_name":"Dickinson, Hugh"}],"volume":24,"date_created":"2021-06-08T06:14:50Z","date_updated":"2023-05-08T11:00:59Z","extern":"1","oa":1,"external_id":{"pmid":["23410937"]},"main_file_link":[{"url":"https://doi.org/10.1016/j.devcel.2013.01.014","open_access":"1"}],"quality_controlled":"1","doi":"10.1016/j.devcel.2013.01.014","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1878-1551"],"issn":["1534-5807"]},"month":"02"},{"date_created":"2023-08-01T09:47:17Z","date_updated":"2023-08-08T07:47:35Z","volume":24,"author":[{"full_name":"Ely, Tal","first_name":"Tal","last_name":"Ely"},{"first_name":"Sanjib","last_name":"Das","full_name":"Das, Sanjib"},{"first_name":"Wenjie","last_name":"Li","full_name":"Li, Wenjie"},{"last_name":"Kundu","first_name":"Pintu","full_name":"Kundu, Pintu"},{"last_name":"Tirosh","first_name":"Einat","full_name":"Tirosh, Einat"},{"full_name":"Cahen, David","first_name":"David","last_name":"Cahen"},{"last_name":"Vilan","first_name":"Ayelet","full_name":"Vilan, Ayelet"},{"full_name":"Klajn, Rafal","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","first_name":"Rafal","last_name":"Klajn"}],"publication_status":"published","publisher":"Georg Thieme Verlag","year":"2013","extern":"1","language":[{"iso":"eng"}],"doi":"10.1055/s-0033-1340087","quality_controlled":"1","month":"10","publication_identifier":{"issn":["0936-5214"],"eissn":["1437-2096"]},"oa_version":"None","status":"public","title":"Photocontrol of electrical conductance with a nonsymmetrical azobenzene dithiol","intvolume":" 24","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13405","abstract":[{"text":"We report a method for preparing electrode–molecule–electrode junctions that incorporate nonsymmetrical azobenzene dithiols. Our approach is based on sequential deprotection of thiol moieties originally carrying two different protecting groups. The azobenzene derivatives retained their switching properties within monolayers and permitted the photocontrol of electrical conductance.","lang":"eng"}],"issue":"18","type":"journal_article","date_published":"2013-10-22T00:00:00Z","article_type":"original","page":"2370-2374","publication":"Synlett","citation":{"apa":"Ely, T., Das, S., Li, W., Kundu, P., Tirosh, E., Cahen, D., … Klajn, R. (2013). Photocontrol of electrical conductance with a nonsymmetrical azobenzene dithiol. Synlett. Georg Thieme Verlag. https://doi.org/10.1055/s-0033-1340087","ieee":"T. Ely et al., “Photocontrol of electrical conductance with a nonsymmetrical azobenzene dithiol,” Synlett, vol. 24, no. 18. Georg Thieme Verlag, pp. 2370–2374, 2013.","ista":"Ely T, Das S, Li W, Kundu P, Tirosh E, Cahen D, Vilan A, Klajn R. 2013. Photocontrol of electrical conductance with a nonsymmetrical azobenzene dithiol. Synlett. 24(18), 2370–2374.","ama":"Ely T, Das S, Li W, et al. Photocontrol of electrical conductance with a nonsymmetrical azobenzene dithiol. Synlett. 2013;24(18):2370-2374. doi:10.1055/s-0033-1340087","chicago":"Ely, Tal, Sanjib Das, Wenjie Li, Pintu Kundu, Einat Tirosh, David Cahen, Ayelet Vilan, and Rafal Klajn. “Photocontrol of Electrical Conductance with a Nonsymmetrical Azobenzene Dithiol.” Synlett. Georg Thieme Verlag, 2013. https://doi.org/10.1055/s-0033-1340087.","short":"T. Ely, S. Das, W. Li, P. Kundu, E. Tirosh, D. Cahen, A. Vilan, R. Klajn, Synlett 24 (2013) 2370–2374.","mla":"Ely, Tal, et al. “Photocontrol of Electrical Conductance with a Nonsymmetrical Azobenzene Dithiol.” Synlett, vol. 24, no. 18, Georg Thieme Verlag, 2013, pp. 2370–74, doi:10.1055/s-0033-1340087."},"day":"22","article_processing_charge":"No","keyword":["Organic Chemistry"],"scopus_import":"1"},{"extern":"1","volume":25,"date_updated":"2023-08-08T07:49:36Z","date_created":"2023-08-01T09:47:30Z","author":[{"full_name":"Das, Sanjib","last_name":"Das","first_name":"Sanjib"},{"first_name":"Priyadarshi","last_name":"Ranjan","full_name":"Ranjan, Priyadarshi"},{"full_name":"Maiti, Pradipta Sankar","first_name":"Pradipta Sankar","last_name":"Maiti"},{"full_name":"Singh, Gurvinder","last_name":"Singh","first_name":"Gurvinder"},{"first_name":"Gregory","last_name":"Leitus","full_name":"Leitus, Gregory"},{"full_name":"Klajn, Rafal","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","first_name":"Rafal","last_name":"Klajn"}],"publisher":"Wiley","publication_status":"published","pmid":1,"year":"2013","publication_identifier":{"issn":["0935-9648"]},"month":"01","language":[{"iso":"eng"}],"doi":"10.1002/adma.201201734","quality_controlled":"1","external_id":{"pmid":["22933327"]},"issue":"3","abstract":[{"text":"Dual-responsive nanoparticles are designed by functionalizing magnetic cores with light-responsive ligands. These materials respond to both light and magnetic fields and can be assembled into various higher-order structures, depending on the relative contributions of these two stimuli.","lang":"eng"}],"type":"journal_article","oa_version":"None","intvolume":" 25","title":"Dual-responsive nanoparticles and their self-assembly","status":"public","_id":"13406","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","day":"18","keyword":["Mechanical Engineering","Mechanics of Materials","General Materials Science"],"scopus_import":"1","date_published":"2013-01-18T00:00:00Z","page":"422-426","article_type":"original","citation":{"mla":"Das, Sanjib, et al. “Dual-Responsive Nanoparticles and Their Self-Assembly.” Advanced Materials, vol. 25, no. 3, Wiley, 2013, pp. 422–26, doi:10.1002/adma.201201734.","short":"S. Das, P. Ranjan, P.S. Maiti, G. Singh, G. Leitus, R. Klajn, Advanced Materials 25 (2013) 422–426.","chicago":"Das, Sanjib, Priyadarshi Ranjan, Pradipta Sankar Maiti, Gurvinder Singh, Gregory Leitus, and Rafal Klajn. “Dual-Responsive Nanoparticles and Their Self-Assembly.” Advanced Materials. Wiley, 2013. https://doi.org/10.1002/adma.201201734.","ama":"Das S, Ranjan P, Maiti PS, Singh G, Leitus G, Klajn R. Dual-responsive nanoparticles and their self-assembly. Advanced Materials. 2013;25(3):422-426. doi:10.1002/adma.201201734","ista":"Das S, Ranjan P, Maiti PS, Singh G, Leitus G, Klajn R. 2013. Dual-responsive nanoparticles and their self-assembly. Advanced Materials. 25(3), 422–426.","apa":"Das, S., Ranjan, P., Maiti, P. S., Singh, G., Leitus, G., & Klajn, R. (2013). Dual-responsive nanoparticles and their self-assembly. Advanced Materials. Wiley. https://doi.org/10.1002/adma.201201734","ieee":"S. Das, P. Ranjan, P. S. Maiti, G. Singh, G. Leitus, and R. Klajn, “Dual-responsive nanoparticles and their self-assembly,” Advanced Materials, vol. 25, no. 3. Wiley, pp. 422–426, 2013."},"publication":"Advanced Materials"},{"doi":"10.1103/PhysRevLett.110.018701","language":[{"iso":"eng"}],"external_id":{"arxiv":["0806.2694"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","month":"01","author":[{"last_name":"Stephens","first_name":"Greg","full_name":"Stephens, Greg"},{"full_name":"Mora, Thierry","first_name":"Thierry","last_name":"Mora"},{"full_name":"Tkacik, Gasper","first_name":"Gasper","last_name":"Tkacik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455"},{"full_name":"Bialek, William","first_name":"William","last_name":"Bialek"}],"volume":110,"date_created":"2018-12-11T12:00:19Z","date_updated":"2023-09-04T11:47:51Z","year":"2013","acknowledgement":"This work was supported in part by NSF Grants No. IIS-0613435, No. IBN-0344678, and No. PHY-0957573, by NIH Grant No. T32 MH065214, by the Human Frontier Science Program, and by the Swartz Foundation.\r\nCC BY 3.0\r\n","publisher":"American Physical Society","department":[{"_id":"GaTk"}],"publication_status":"published","publist_id":"3829","file_date_updated":"2020-07-14T12:45:53Z","article_number":"018701","date_published":"2013-01-02T00:00:00Z","citation":{"ama":"Stephens G, Mora T, Tkačik G, Bialek W. Statistical thermodynamics of natural images. Physical Review Letters. 2013;110(1). doi:10.1103/PhysRevLett.110.018701","ieee":"G. Stephens, T. Mora, G. Tkačik, and W. Bialek, “Statistical thermodynamics of natural images,” Physical Review Letters, vol. 110, no. 1. American Physical Society, 2013.","apa":"Stephens, G., Mora, T., Tkačik, G., & Bialek, W. (2013). Statistical thermodynamics of natural images. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.110.018701","ista":"Stephens G, Mora T, Tkačik G, Bialek W. 2013. Statistical thermodynamics of natural images. Physical Review Letters. 110(1), 018701.","short":"G. Stephens, T. Mora, G. Tkačik, W. Bialek, Physical Review Letters 110 (2013).","mla":"Stephens, Greg, et al. “Statistical Thermodynamics of Natural Images.” Physical Review Letters, vol. 110, no. 1, 018701, American Physical Society, 2013, doi:10.1103/PhysRevLett.110.018701.","chicago":"Stephens, Greg, Thierry Mora, Gašper Tkačik, and William Bialek. “Statistical Thermodynamics of Natural Images.” Physical Review Letters. American Physical Society, 2013. https://doi.org/10.1103/PhysRevLett.110.018701."},"publication":"Physical Review Letters","article_type":"original","has_accepted_license":"1","article_processing_charge":"No","day":"02","pubrep_id":"401","file":[{"file_id":"5366","relation":"main_file","checksum":"72bfbc2094c4680e8a8a6bed668cd06d","date_created":"2018-12-12T10:18:44Z","date_updated":"2020-07-14T12:45:53Z","access_level":"open_access","file_name":"IST-2016-401-v1+1_1281.full.pdf","creator":"system","content_type":"application/pdf","file_size":416965}],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2914","intvolume":" 110","title":"Statistical thermodynamics of natural images","ddc":["530"],"status":"public","issue":"1","abstract":[{"text":"The scale invariance of natural images suggests an analogy to the statistical mechanics of physical systems at a critical point. Here we examine the distribution of pixels in small image patches and show how to construct the corresponding thermodynamics. We find evidence for criticality in a diverging specific heat, which corresponds to large fluctuations in how "surprising" we find individual images, and in the quantitative form of the entropy vs energy. We identify special image configurations as local energy minima and show that average patches within each basin are interpretable as lines and edges in all orientations.","lang":"eng"}],"type":"journal_article"},{"oa_version":"None","intvolume":" 1013","status":"public","title":"Live Cell Imaging of Chemotactic Dendritic Cell Migration in Explanted Mouse Ear Preparations","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"10900","abstract":[{"text":"Leukocyte migration through the interstitial space is crucial for the maintenance of tolerance and immunity. The main cues for leukocyte trafficking are chemokines thought to directionally guide these cells towards their targets. However, model systems that facilitate quantification of chemokine-guided leukocyte migration in vivo are uncommon. Here we describe an ex vivo crawl-in assay using explanted mouse ears that allows the visualization of chemokine-dependent dendritic cell (DC) motility in the dermal interstitium in real time. We present methods for the preparation of mouse ear sheets and their use in multidimensional confocal imaging experiments to monitor and analyze the directional migration of fluorescently labelled DCs through the dermis and into afferent lymphatic vessels. The assay provides a more physiological approach to study leukocyte migration than in vitro three-dimensional (3D) or 2-dimensional (2D) migration assays such as collagen gels and transwell assays.","lang":"eng"}],"alternative_title":["Methods in Molecular Biology"],"type":"book_chapter","date_published":"2013-04-03T00:00:00Z","page":"215-226","citation":{"short":"M. Weber, M.K. Sixt, in:, A. Cardona, E. Ubogu (Eds.), Chemokines, Humana Press, Totowa, NJ, 2013, pp. 215–226.","mla":"Weber, Michele, and Michael K. Sixt. “Live Cell Imaging of Chemotactic Dendritic Cell Migration in Explanted Mouse Ear Preparations.” Chemokines, edited by Astrid Cardona and Eroboghene Ubogu, vol. 1013, Humana Press, 2013, pp. 215–26, doi:10.1007/978-1-62703-426-5_14.","chicago":"Weber, Michele, and Michael K Sixt. “Live Cell Imaging of Chemotactic Dendritic Cell Migration in Explanted Mouse Ear Preparations.” In Chemokines, edited by Astrid Cardona and Eroboghene Ubogu, 1013:215–26. MIMB. Totowa, NJ: Humana Press, 2013. https://doi.org/10.1007/978-1-62703-426-5_14.","ama":"Weber M, Sixt MK. Live Cell Imaging of Chemotactic Dendritic Cell Migration in Explanted Mouse Ear Preparations. In: Cardona A, Ubogu E, eds. Chemokines. Vol 1013. MIMB. Totowa, NJ: Humana Press; 2013:215-226. doi:10.1007/978-1-62703-426-5_14","ieee":"M. Weber and M. K. Sixt, “Live Cell Imaging of Chemotactic Dendritic Cell Migration in Explanted Mouse Ear Preparations,” in Chemokines, vol. 1013, A. Cardona and E. Ubogu, Eds. Totowa, NJ: Humana Press, 2013, pp. 215–226.","apa":"Weber, M., & Sixt, M. K. (2013). Live Cell Imaging of Chemotactic Dendritic Cell Migration in Explanted Mouse Ear Preparations. In A. Cardona & E. Ubogu (Eds.), Chemokines (Vol. 1013, pp. 215–226). Totowa, NJ: Humana Press. https://doi.org/10.1007/978-1-62703-426-5_14","ista":"Weber M, Sixt MK. 2013.Live Cell Imaging of Chemotactic Dendritic Cell Migration in Explanted Mouse Ear Preparations. In: Chemokines. Methods in Molecular Biology, vol. 1013, 215–226."},"publication":"Chemokines","article_processing_charge":"No","day":"03","series_title":"MIMB","scopus_import":"1","volume":1013,"date_created":"2022-03-21T07:47:41Z","date_updated":"2023-09-05T13:15:33Z","author":[{"full_name":"Weber, Michele","id":"3A3FC708-F248-11E8-B48F-1D18A9856A87","first_name":"Michele","last_name":"Weber"},{"full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","first_name":"Michael K","last_name":"Sixt"}],"publisher":"Humana Press","editor":[{"full_name":"Cardona, Astrid","first_name":"Astrid","last_name":"Cardona"},{"full_name":"Ubogu, Eroboghene","last_name":"Ubogu","first_name":"Eroboghene"}],"department":[{"_id":"MiSi"}],"publication_status":"published","pmid":1,"acknowledgement":"We would like to thank Alexander Eichner and Ingrid de Vries for discussion and critical reading of the manuscript, and Mary Frank for assistance with the recording of videos and images in Fig. 1. M.S. is supported through funding from the German Research Foundation (DFG). M.W. acknowledges the Alexander von Humboldt Foundation for funding.","year":"2013","place":"Totowa, NJ","language":[{"iso":"eng"}],"doi":"10.1007/978-1-62703-426-5_14","quality_controlled":"1","external_id":{"pmid":["23625502"]},"publication_identifier":{"eissn":["1940-6029"],"isbn":["9781627034258"],"issn":["1064-3745"],"eisbn":["9781627034265"]},"month":"04"},{"project":[{"name":"Quantitative Reactive Modeling","call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","call_identifier":"FWF","name":"Rigorous Systems Engineering"}],"quality_controlled":"1","oa":1,"language":[{"iso":"eng"}],"doi":"10.1007/978-3-642-39799-8_11","conference":{"end_date":"2013-07-19","start_date":"2013-07-13","location":"Saint Petersburg, Russia","name":"CAV 2013"},"publication_identifier":{"eissn":["1611-3349"],"isbn":["9783642397981","9783642397998"],"issn":["0302-9743"]},"publisher":"Springer Berlin Heidelberg","department":[{"_id":"ToHe"}],"publication_status":"published","year":"2013","volume":8044,"date_updated":"2023-09-05T14:16:07Z","date_created":"2018-12-18T13:10:21Z","author":[{"full_name":"Dragoi, Cezara","last_name":"Dragoi","first_name":"Cezara","id":"2B2B5ED0-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Ashutosh","last_name":"Gupta","id":"335E5684-F248-11E8-B48F-1D18A9856A87","full_name":"Gupta, Ashutosh"},{"full_name":"Henzinger, Thomas A","first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724"}],"place":"Berlin, Heidelberg","ec_funded":1,"file_date_updated":"2020-07-14T12:47:10Z","page":"174-190","citation":{"ama":"Dragoi C, Gupta A, Henzinger TA. Automatic Linearizability Proofs of Concurrent Objects with Cooperating Updates. In: Computer Aided Verification. Vol 8044. CAV. Berlin, Heidelberg: Springer Berlin Heidelberg; 2013:174-190. doi:10.1007/978-3-642-39799-8_11","apa":"Dragoi, C., Gupta, A., & Henzinger, T. A. (2013). Automatic Linearizability Proofs of Concurrent Objects with Cooperating Updates. In Computer Aided Verification (Vol. 8044, pp. 174–190). Berlin, Heidelberg: Springer Berlin Heidelberg. https://doi.org/10.1007/978-3-642-39799-8_11","ieee":"C. Dragoi, A. Gupta, and T. A. Henzinger, “Automatic Linearizability Proofs of Concurrent Objects with Cooperating Updates,” in Computer Aided Verification, vol. 8044, Berlin, Heidelberg: Springer 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.","short":"C. Dragoi, A. Gupta, T.A. Henzinger, in:, Computer Aided Verification, Springer Berlin Heidelberg, Berlin, Heidelberg, 2013, pp. 174–190.","mla":"Dragoi, Cezara, et al. “Automatic Linearizability Proofs of Concurrent Objects with Cooperating Updates.” Computer Aided Verification, vol. 8044, Springer Berlin Heidelberg, 2013, pp. 174–90, doi:10.1007/978-3-642-39799-8_11.","chicago":"Dragoi, Cezara, Ashutosh Gupta, and Thomas A Henzinger. “Automatic Linearizability Proofs of Concurrent Objects with Cooperating Updates.” In Computer Aided Verification, 8044:174–90. CAV. Berlin, Heidelberg: Springer Berlin Heidelberg, 2013. https://doi.org/10.1007/978-3-642-39799-8_11."},"publication":"Computer Aided Verification","date_published":"2013-01-01T00:00:00Z","series_title":"CAV","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","intvolume":" 8044","ddc":["005"],"status":"public","title":"Automatic Linearizability Proofs of Concurrent Objects with Cooperating Updates","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"5747","file":[{"creator":"dernst","file_size":236480,"content_type":"application/pdf","file_name":"2013_CAV_Dragoi.pdf","access_level":"open_access","date_created":"2018-12-18T13:13:33Z","date_updated":"2020-07-14T12:47:10Z","checksum":"a901cc6b71db08b61c0d4c0cbacc6287","file_id":"5748","relation":"main_file"}],"oa_version":"None","pubrep_id":"195","type":"book_chapter"},{"series_title":"LNCS","scopus_import":"1","day":"15","article_processing_charge":"No","page":"214-225","publication":"7th International Conference on Language and Automata Theory and Applications","citation":{"chicago":"Chatterjee, Krishnendu, Siddhesh Chaubal, and Sasha Rubin. “How to Travel between Languages.” In 7th International Conference on Language and Automata Theory and Applications, 7810:214–25. LNCS. Berlin, Heidelberg: Springer Nature, 2013. https://doi.org/10.1007/978-3-642-37064-9_20.","short":"K. Chatterjee, S. Chaubal, S. Rubin, in:, 7th International Conference on Language and Automata Theory and Applications, Springer Nature, Berlin, Heidelberg, 2013, pp. 214–225.","mla":"Chatterjee, Krishnendu, et al. “How to Travel between Languages.” 7th International Conference on Language and Automata Theory and Applications, vol. 7810, Springer Nature, 2013, pp. 214–25, doi:10.1007/978-3-642-37064-9_20.","apa":"Chatterjee, K., Chaubal, S., & Rubin, S. (2013). How to travel between languages. In 7th International Conference on Language and Automata Theory and Applications (Vol. 7810, pp. 214–225). Berlin, Heidelberg: Springer Nature. https://doi.org/10.1007/978-3-642-37064-9_20","ieee":"K. Chatterjee, S. Chaubal, and S. Rubin, “How to travel between languages,” in 7th International Conference on Language and Automata Theory and Applications, Bilbao, Spain, 2013, vol. 7810, pp. 214–225.","ista":"Chatterjee K, Chaubal S, Rubin S. 2013. How to travel between languages. 7th International Conference on Language and Automata Theory and Applications. LATA: Conference on Language and Automata Theory and ApplicationsLNCS, LNCS, vol. 7810, 214–225.","ama":"Chatterjee K, Chaubal S, Rubin S. How to travel between languages. In: 7th International Conference on Language and Automata Theory and Applications. Vol 7810. LNCS. Berlin, Heidelberg: Springer Nature; 2013:214-225. doi:10.1007/978-3-642-37064-9_20"},"date_published":"2013-04-15T00:00:00Z","alternative_title":["LNCS"],"type":"conference","abstract":[{"lang":"eng","text":"We consider how to edit strings from a source language so that the edited strings belong to a target language, where the languages are given as deterministic finite automata. Non-streaming (or offline) transducers perform edits given the whole source string. We show that the class of deterministic one-pass transducers with registers along with increment and min operation suffices for computing optimal edit distance, whereas the same class of transducers without the min operation is not sufficient. Streaming (or online) transducers perform edits as the letters of the source string are received. We present a polynomial time algorithm for the partial-repair problem that given a bound α asks for the construction of a deterministic streaming transducer (if one exists) that ensures that the ‘maximum fraction’ η of the strings of the source language are edited, within cost α, to the target language."}],"status":"public","title":"How to travel between languages","intvolume":" 7810","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"10902","oa_version":"None","month":"04","publication_identifier":{"eissn":["1611-3349"],"isbn":["9783642370632"],"eisbn":["9783642370649"],"issn":["0302-9743"]},"quality_controlled":"1","project":[{"_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF"},{"grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Game Theory"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"language":[{"iso":"eng"}],"conference":{"end_date":"2013-04-05","start_date":"2013-04-02","location":"Bilbao, Spain","name":"LATA: Conference on Language and Automata Theory and Applications"},"doi":"10.1007/978-3-642-37064-9_20","place":"Berlin, Heidelberg","ec_funded":1,"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"KrCh"}],"acknowledgement":"The research was supported by Austrian Science Fund (FWF) Grant No P 23499-N23, FWF NFN Grant No S11407-N23 (RiSE), ERC Start grant (279307: Graph Games), and Microsoft faculty fellows award. Thanks to Gabriele Puppis for suggesting the problem of identifying a deterministic transducer to compute the optimal cost, and to Martin Chmelik for his comments on the introduction.","year":"2013","date_updated":"2023-09-05T15:10:38Z","date_created":"2022-03-21T07:56:21Z","volume":7810,"author":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu"},{"full_name":"Chaubal, Siddhesh","last_name":"Chaubal","first_name":"Siddhesh"},{"full_name":"Rubin, Sasha","id":"2EC51194-F248-11E8-B48F-1D18A9856A87","first_name":"Sasha","last_name":"Rubin"}]},{"series_title":"LNCS","scopus_import":"1","article_processing_charge":"No","day":"01","page":"182-183","citation":{"chicago":"Edelsbrunner, Herbert. “Persistent Homology in Image Processing.” In Graph-Based Representations in Pattern Recognition, 7877:182–83. LNCS. Berlin, Heidelberg: Springer Nature, 2013. https://doi.org/10.1007/978-3-642-38221-5_19.","mla":"Edelsbrunner, Herbert. “Persistent Homology in Image Processing.” Graph-Based Representations in Pattern Recognition, vol. 7877, Springer Nature, 2013, pp. 182–83, doi:10.1007/978-3-642-38221-5_19.","short":"H. Edelsbrunner, in:, Graph-Based Representations in Pattern Recognition, Springer Nature, Berlin, Heidelberg, 2013, pp. 182–183.","ista":"Edelsbrunner H. 2013. Persistent homology in image processing. Graph-Based Representations in Pattern Recognition. GbRPR: Graph-based Representations in Pattern RecognitionLNCS vol. 7877, 182–183.","apa":"Edelsbrunner, H. (2013). Persistent homology in image processing. In Graph-Based Representations in Pattern Recognition (Vol. 7877, pp. 182–183). Berlin, Heidelberg: Springer Nature. https://doi.org/10.1007/978-3-642-38221-5_19","ieee":"H. Edelsbrunner, “Persistent homology in image processing,” in Graph-Based Representations in Pattern Recognition, Vienna, Austria, 2013, vol. 7877, pp. 182–183.","ama":"Edelsbrunner H. Persistent homology in image processing. In: Graph-Based Representations in Pattern Recognition. Vol 7877. LNCS. Berlin, Heidelberg: Springer Nature; 2013:182-183. doi:10.1007/978-3-642-38221-5_19"},"publication":"Graph-Based Representations in Pattern Recognition","date_published":"2013-06-01T00:00:00Z","type":"conference","abstract":[{"text":"Taking images is an efficient way to collect data about the physical world. It can be done fast and in exquisite detail. By definition, image processing is the field that concerns itself with the computation aimed at harnessing the information contained in images [10]. This talk is concerned with topological information. Our main thesis is that persistent homology [5] is a useful method to quantify and summarize topological information, building a bridge that connects algebraic topology with applications. We provide supporting evidence for this thesis by touching upon four technical developments in the overlap between persistent homology and image processing.","lang":"eng"}],"intvolume":" 7877","title":"Persistent homology in image processing","status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"10897","oa_version":"None","publication_identifier":{"isbn":["9783642382208"],"eissn":["1611-3349"],"eisbn":["9783642382215"],"issn":["0302-9743"]},"month":"06","project":[{"name":"Topological Complex Systems","call_identifier":"FP7","_id":"255D761E-B435-11E9-9278-68D0E5697425","grant_number":"318493"}],"quality_controlled":"1","language":[{"iso":"eng"}],"doi":"10.1007/978-3-642-38221-5_19","conference":{"end_date":"2013-05-17","start_date":"2013-05-15","location":"Vienna, Austria","name":"GbRPR: Graph-based Representations in Pattern Recognition"},"place":"Berlin, Heidelberg","ec_funded":1,"publisher":"Springer Nature","department":[{"_id":"HeEd"}],"publication_status":"published","year":"2013","acknowledgement":"This research is partially supported by the European Science Foundation (ESF) under the Research Network Programme, the European Union under the Toposys Project FP7-ICT-318493-STREP, the Russian Government under the Mega Project 11.G34.31.0053.","volume":7877,"date_created":"2022-03-21T07:30:33Z","date_updated":"2023-09-05T15:10:20Z","author":[{"orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner","first_name":"Herbert","full_name":"Edelsbrunner, Herbert"}]},{"article_processing_charge":"No","has_accepted_license":"1","day":"05","date_published":"2013-09-05T00:00:00Z","citation":{"short":"D. Zufferey, Analysis of Dynamic Message Passing Programs, Institute of Science and Technology Austria, 2013.","mla":"Zufferey, Damien. Analysis of Dynamic Message Passing Programs. Institute of Science and Technology Austria, 2013, doi:10.15479/at:ista:1405.","chicago":"Zufferey, Damien. “Analysis of Dynamic Message Passing Programs.” Institute of Science and Technology Austria, 2013. https://doi.org/10.15479/at:ista:1405.","ama":"Zufferey D. Analysis of dynamic message passing programs. 2013. doi:10.15479/at:ista:1405","ieee":"D. Zufferey, “Analysis of dynamic message passing programs,” Institute of Science and Technology Austria, 2013.","apa":"Zufferey, D. (2013). Analysis of dynamic message passing programs. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:1405","ista":"Zufferey D. 2013. Analysis of dynamic message passing programs. Institute of Science and Technology Austria."},"page":"134","abstract":[{"lang":"eng","text":"Motivated by the analysis of highly dynamic message-passing systems, i.e. unbounded thread creation, mobility, etc. we present a framework for the analysis of depth-bounded systems. Depth-bounded systems are one of the most expressive known fragment of the π-calculus for which interesting verification problems are still decidable. Even though they are infinite state systems depth-bounded systems are well-structured, thus can be analyzed algorithmically. We give an interpretation of depth-bounded systems as graph-rewriting systems. This gives more flexibility and ease of use to apply depth-bounded systems to other type of systems like shared memory concurrency.\r\n\r\nFirst, we develop an adequate domain of limits for depth-bounded systems, a prerequisite for the effective representation of downward-closed sets. Downward-closed sets are needed by forward saturation-based algorithms to represent potentially infinite sets of states. Then, we present an abstract interpretation framework to compute the covering set of well-structured transition systems. Because, in general, the covering set is not computable, our abstraction over-approximates the actual covering set. Our abstraction captures the essence of acceleration based-algorithms while giving up enough precision to ensure convergence. We have implemented the analysis in the PICASSO tool and show that it is accurate in practice. Finally, we build some further analyses like termination using the covering set as starting point."}],"type":"dissertation","alternative_title":["ISTA Thesis"],"file":[{"access_level":"open_access","file_name":"2013_Zufferey_thesis_final.pdf","creator":"dernst","content_type":"application/pdf","file_size":1514906,"file_id":"9176","relation":"main_file","success":1,"checksum":"ed2d7b52933d134e8dc69d569baa284e","date_updated":"2021-02-22T11:28:36Z","date_created":"2021-02-22T11:28:36Z"},{"date_updated":"2021-11-17T13:47:58Z","date_created":"2021-11-16T14:42:52Z","checksum":"cecc4c4b14225bee973d32e3dba91a55","relation":"main_file","file_id":"10298","file_size":1378313,"content_type":"application/pdf","creator":"cchlebak","file_name":"2013_Zufferey_thesis_final_pdfa.pdf","access_level":"closed"}],"oa_version":"Published Version","_id":"1405","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","ddc":["000"],"status":"public","title":"Analysis of dynamic message passing programs","publication_identifier":{"issn":["2663-337X"]},"month":"09","doi":"10.15479/at:ista:1405","language":[{"iso":"eng"}],"degree_awarded":"PhD","supervisor":[{"last_name":"Henzinger","first_name":"Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A"}],"oa":1,"main_file_link":[{"url":"http://dzufferey.github.io/files/2013_thesis.pdf"}],"project":[{"call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"},{"name":"Quantitative Reactive Modeling","call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989"}],"ec_funded":1,"publist_id":"5802","file_date_updated":"2021-11-17T13:47:58Z","related_material":{"record":[{"id":"2847","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"3251"},{"id":"4361","relation":"part_of_dissertation","status":"public"}]},"author":[{"first_name":"Damien","last_name":"Zufferey","id":"4397AC76-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3197-8736","full_name":"Zufferey, Damien"}],"date_updated":"2023-09-07T11:36:37Z","date_created":"2018-12-11T11:51:50Z","acknowledgement":"This work was supported in part by the Austrian Science Fund NFN RiSE (Rigorous Systems Engineering) and by the ERC Advanced Grant QUAREM (Quantitative Reactve Modeling).\r\nChapter 2, 3, and 4 are joint work with Thomas A. Henzinger and Thomas Wies. Chapter 2 was published in FoSSaCS 2010 as “Forward Analysis of Depth-Bounded Processes” [112]. Chapter 3 was published in VMCAI 2012 as “Ideal Abstractions for Well-Structured Transition Systems” [114]. Chap- ter 5.1 is joint work with Kshitij Bansal, Eric Koskinen, and Thomas Wies. It was published in TACAS 2013 as “Structural Counter Abstraction” [13]. The author’s contribution in this part is mostly related to the implementation. The theory required to understand the method and its implementation is quickly recalled to make the thesis self-contained, but should not be considered as a contribution. For the details of the methods, we refer the reader to the orig- inal publication [13] and the corresponding technical report [14]. Chapter 5.2 is ongoing work with Shahram Esmaeilsabzali, Rupak Majumdar, and Thomas Wies. I also would like to thank the people who supported over the past 4 years. My advisor Thomas A. Henzinger who gave me a lot of freedom to work on projects I was interested in. My collaborators, especially Thomas Wies with whom I worked since the beginning. The members of my thesis committee, Viktor Kun- cak and Rupak Majumdar, who also agreed to advise me. Simon Aeschbacher, Pavol Cerny, Cezara Dragoi, Arjun Radhakrishna, my family, friends and col- leagues who created an enjoyable environment. ","year":"2013","publisher":"Institute of Science and Technology Austria","department":[{"_id":"ToHe"},{"_id":"GradSch"}],"publication_status":"published"},{"abstract":[{"text":"Depth-Bounded Systems form an expressive class of well-structured transition systems. They can model a wide range of concurrent infinite-state systems including those with dynamic thread creation, dynamically changing communication topology, and complex shared heap structures. We present the first method to automatically prove fair termination of depth-bounded systems. Our method uses a numerical abstraction of the system, which we obtain by systematically augmenting an over-approximation of the system’s reachable states with a finite set of counters. This numerical abstraction can be analyzed with existing termination provers. What makes our approach unique is the way in which it exploits the well-structuredness of the analyzed system. We have implemented our work in a prototype tool and used it to automatically prove liveness properties of complex concurrent systems, including nonblocking algorithms such as Treiber’s stack and several distributed processes. Many of these examples are beyond the scope of termination analyses that are based on traditional counter abstractions.","lang":"eng"}],"alternative_title":["LNCS"],"type":"conference","oa_version":"Submitted Version","intvolume":" 7795","status":"public","title":"Structural Counter Abstraction","_id":"2847","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","series_title":"Lecture Notes in Computer Science","scopus_import":1,"date_published":"2013-03-01T00:00:00Z","page":"62 - 77","citation":{"chicago":"Bansal, Kshitij, Eric Koskinen, Thomas Wies, and Damien Zufferey. “Structural Counter Abstraction.” Edited by Nir Piterman and Scott Smolka. Lecture Notes in Computer Science. Springer, 2013. https://doi.org/10.1007/978-3-642-36742-7_5.","short":"K. Bansal, E. Koskinen, T. Wies, D. Zufferey, 7795 (2013) 62–77.","mla":"Bansal, Kshitij, et al. Structural Counter Abstraction. Edited by Nir Piterman and Scott Smolka, vol. 7795, Springer, 2013, pp. 62–77, doi:10.1007/978-3-642-36742-7_5.","apa":"Bansal, K., Koskinen, E., Wies, T., & Zufferey, D. (2013). Structural Counter Abstraction. (N. Piterman & S. Smolka, Eds.). Presented at the TACAS: Tools and Algorithms for the Construction and Analysis of Systems, Rome, Italy: Springer. https://doi.org/10.1007/978-3-642-36742-7_5","ieee":"K. Bansal, E. Koskinen, T. Wies, and D. Zufferey, “Structural Counter Abstraction,” vol. 7795. Springer, pp. 62–77, 2013.","ista":"Bansal K, Koskinen E, Wies T, Zufferey D. 2013. Structural Counter Abstraction (eds. N. Piterman & S. Smolka). 7795, 62–77.","ama":"Bansal K, Koskinen E, Wies T, Zufferey D. Structural Counter Abstraction. Piterman N, Smolka S, eds. 2013;7795:62-77. doi:10.1007/978-3-642-36742-7_5"},"publist_id":"3947","ec_funded":1,"volume":7795,"date_updated":"2023-09-07T11:36:36Z","date_created":"2018-12-11T11:59:54Z","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"1405"}]},"author":[{"first_name":"Kshitij","last_name":"Bansal","full_name":"Bansal, Kshitij"},{"full_name":"Koskinen, Eric","last_name":"Koskinen","first_name":"Eric"},{"id":"447BFB88-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas","last_name":"Wies","full_name":"Wies, Thomas"},{"last_name":"Zufferey","first_name":"Damien","orcid":"0000-0002-3197-8736","id":"4397AC76-F248-11E8-B48F-1D18A9856A87","full_name":"Zufferey, Damien"}],"department":[{"_id":"ToHe"}],"publisher":"Springer","editor":[{"first_name":"Nir","last_name":"Piterman","full_name":"Piterman, Nir"},{"first_name":"Scott","last_name":"Smolka","full_name":"Smolka, Scott"}],"publication_status":"published","year":"2013","month":"03","language":[{"iso":"eng"}],"doi":"10.1007/978-3-642-36742-7_5","conference":{"end_date":"2013-03-24","location":"Rome, Italy","start_date":"2013-03-16","name":"TACAS: Tools and Algorithms for the Construction and Analysis of Systems"},"project":[{"call_identifier":"FP7","name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989"},{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering"}],"quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"http://arise.or.at/pubpdf/Structural_Counter_Abstraction.pdf"}]},{"publist_id":"5801","abstract":[{"lang":"eng","text":"Epithelial spreading is a critical part of various developmental and wound repair processes. Here we use zebrafish epiboly as a model system to study the cellular and molecular mechanisms underlying the spreading of epithelial sheets. During zebrafish epiboly the enveloping cell layer (EVL), a simple squamous epithelium, spreads over the embryo to eventually cover the entire yolk cell by the end of gastrulation. The EVL leading edge is anchored through tight junctions to the yolk syncytial layer (YSL), where directly adjacent to the EVL margin a contractile actomyosin ring is formed that is thought to drive EVL epiboly. The prevalent view in the field was that the contractile ring exerts a pulling force on the EVL margin, which pulls the EVL towards the vegetal pole. However, how this force is generated and how it affects EVL morphology still remains elusive. Moreover, the cellular mechanisms mediating the increase in EVL surface area, while maintaining tissue integrity and function are still unclear. Here we show that the YSL actomyosin ring pulls on the EVL margin by two distinct force-generating mechanisms. One mechanism is based on contraction of the ring around its circumference, as previously proposed. The second mechanism is based on actomyosin retrogade flows, generating force through resistance against the substrate. The latter can function at any epiboly stage even in situations where the contraction-based mechanism is unproductive. Additionally, we demonstrate that during epiboly the EVL is subjected to anisotropic tension, which guides the orientation of EVL cell division along the main axis (animal-vegetal) of tension. The influence of tension in cell division orientation involves cell elongation and requires myosin-2 activity for proper spindle alignment. Strikingly, we reveal that tension-oriented cell divisions release anisotropic tension within the EVL and that in the absence of such divisions, EVL cells undergo ectopic fusions. We conclude that forces applied to the EVL by the action of the YSL actomyosin ring generate a tension anisotropy in the EVL that orients cell divisions, which in turn limit tissue tension increase thereby facilitating tissue spreading."}],"alternative_title":["ISTA Thesis"],"type":"dissertation","oa_version":"None","date_updated":"2023-09-07T11:36:07Z","date_created":"2018-12-11T11:51:50Z","author":[{"full_name":"Campinho, Pedro","orcid":"0000-0002-8526-5416","id":"3AFBBC42-F248-11E8-B48F-1D18A9856A87","last_name":"Campinho","first_name":"Pedro"}],"department":[{"_id":"CaHe"}],"publisher":"Institute of Science and Technology Austria","title":"Mechanics of zebrafish epiboly: Tension-oriented cell divisions limit anisotropic tissue tension in epithelial spreading","publication_status":"published","status":"public","year":"2013","_id":"1406","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication_identifier":{"issn":["2663-337X"]},"article_processing_charge":"No","month":"10","day":"01","language":[{"iso":"eng"}],"degree_awarded":"PhD","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"supervisor":[{"full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","last_name":"Heisenberg"}],"date_published":"2013-10-01T00:00:00Z","page":"123","citation":{"ama":"Campinho P. Mechanics of zebrafish epiboly: Tension-oriented cell divisions limit anisotropic tissue tension in epithelial spreading. 2013.","ista":"Campinho P. 2013. Mechanics of zebrafish epiboly: Tension-oriented cell divisions limit anisotropic tissue tension in epithelial spreading. Institute of Science and Technology Austria.","ieee":"P. Campinho, “Mechanics of zebrafish epiboly: Tension-oriented cell divisions limit anisotropic tissue tension in epithelial spreading,” Institute of Science and Technology Austria, 2013.","apa":"Campinho, P. (2013). Mechanics of zebrafish epiboly: Tension-oriented cell divisions limit anisotropic tissue tension in epithelial spreading. Institute of Science and Technology Austria.","mla":"Campinho, Pedro. Mechanics of Zebrafish Epiboly: Tension-Oriented Cell Divisions Limit Anisotropic Tissue Tension in Epithelial Spreading. Institute of Science and Technology Austria, 2013.","short":"P. Campinho, Mechanics of Zebrafish Epiboly: Tension-Oriented Cell Divisions Limit Anisotropic Tissue Tension in Epithelial Spreading, Institute of Science and Technology Austria, 2013.","chicago":"Campinho, Pedro. “Mechanics of Zebrafish Epiboly: Tension-Oriented Cell Divisions Limit Anisotropic Tissue Tension in Epithelial Spreading.” Institute of Science and Technology Austria, 2013."}},{"related_material":{"record":[{"relation":"research_data","status":"public","id":"9749"},{"id":"1400","status":"public","relation":"dissertation_contains"}]},"author":[{"last_name":"Zagorsky","first_name":"Benjamin","full_name":"Zagorsky, Benjamin"},{"full_name":"Reiter, Johannes","orcid":"0000-0002-0170-7353","id":"4A918E98-F248-11E8-B48F-1D18A9856A87","last_name":"Reiter","first_name":"Johannes"},{"first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"full_name":"Nowak, Martin","first_name":"Martin","last_name":"Nowak"}],"volume":8,"date_updated":"2023-09-07T11:40:43Z","date_created":"2018-12-11T11:56:33Z","year":"2013","department":[{"_id":"KrCh"}],"publisher":"Public Library of Science","publication_status":"published","publist_id":"4702","ec_funded":1,"file_date_updated":"2020-07-14T12:45:34Z","article_number":"e80814","doi":"10.1371/journal.pone.0080814","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"project":[{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"},{"name":"Rigorous Systems Engineering","call_identifier":"FWF","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"quality_controlled":"1","month":"12","pubrep_id":"409","oa_version":"Published Version","file":[{"date_updated":"2020-07-14T12:45:34Z","date_created":"2018-12-12T10:11:15Z","checksum":"808e8b9e6e89658bee4ffbbfac1bd19d","relation":"main_file","file_id":"4868","content_type":"application/pdf","file_size":1050042,"creator":"system","file_name":"IST-2016-409-v1+1_journal.pone.0080814.pdf","access_level":"open_access"}],"_id":"2247","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 8","status":"public","title":"Forgiver triumphs in alternating prisoner's dilemma ","ddc":["000"],"issue":"12","abstract":[{"text":"Cooperative behavior, where one individual incurs a cost to help another, is a wide spread phenomenon. Here we study direct reciprocity in the context of the alternating Prisoner's Dilemma. We consider all strategies that can be implemented by one and two-state automata. We calculate the payoff matrix of all pairwise encounters in the presence of noise. We explore deterministic selection dynamics with and without mutation. Using different error rates and payoff values, we observe convergence to a small number of distinct equilibria. Two of them are uncooperative strict Nash equilibria representing always-defect (ALLD) and Grim. The third equilibrium is mixed and represents a cooperative alliance of several strategies, dominated by a strategy which we call Forgiver. Forgiver cooperates whenever the opponent has cooperated; it defects once when the opponent has defected, but subsequently Forgiver attempts to re-establish cooperation even if the opponent has defected again. Forgiver is not an evolutionarily stable strategy, but the alliance, which it rules, is asymptotically stable. For a wide range of parameter values the most commonly observed outcome is convergence to the mixed equilibrium, dominated by Forgiver. Our results show that although forgiving might incur a short-term loss it can lead to a long-term gain. Forgiveness facilitates stable cooperation in the presence of exploitation and noise.","lang":"eng"}],"type":"journal_article","date_published":"2013-12-12T00:00:00Z","citation":{"ama":"Zagorsky B, Reiter J, Chatterjee K, Nowak M. Forgiver triumphs in alternating prisoner’s dilemma . PLoS One. 2013;8(12). doi:10.1371/journal.pone.0080814","ista":"Zagorsky B, Reiter J, Chatterjee K, Nowak M. 2013. Forgiver triumphs in alternating prisoner’s dilemma . PLoS One. 8(12), e80814.","ieee":"B. Zagorsky, J. Reiter, K. Chatterjee, and M. Nowak, “Forgiver triumphs in alternating prisoner’s dilemma ,” PLoS One, vol. 8, no. 12. Public Library of Science, 2013.","apa":"Zagorsky, B., Reiter, J., Chatterjee, K., & Nowak, M. (2013). Forgiver triumphs in alternating prisoner’s dilemma . PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0080814","mla":"Zagorsky, Benjamin, et al. “Forgiver Triumphs in Alternating Prisoner’s Dilemma .” PLoS One, vol. 8, no. 12, e80814, Public Library of Science, 2013, doi:10.1371/journal.pone.0080814.","short":"B. Zagorsky, J. Reiter, K. Chatterjee, M. Nowak, PLoS One 8 (2013).","chicago":"Zagorsky, Benjamin, Johannes Reiter, Krishnendu Chatterjee, and Martin Nowak. “Forgiver Triumphs in Alternating Prisoner’s Dilemma .” PLoS One. Public Library of Science, 2013. https://doi.org/10.1371/journal.pone.0080814."},"publication":"PLoS One","has_accepted_license":"1","day":"12","scopus_import":1},{"intvolume":" 6","status":"public","title":"The effect of one additional driver mutation on tumor progression","ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2858","oa_version":"Published Version","file":[{"file_name":"IST-2016-415-v1+1_Reiter_et_al-2013-Evolutionary_Applications.pdf","access_level":"open_access","file_size":1172037,"content_type":"application/pdf","creator":"system","relation":"main_file","file_id":"5173","date_created":"2018-12-12T10:15:50Z","date_updated":"2020-07-14T12:45:51Z","checksum":"e2955b3889f8a823c3d5a72cb16f8957"}],"pubrep_id":"415","type":"journal_article","issue":"1","abstract":[{"lang":"eng","text":"Tumor growth is caused by the acquisition of driver mutations, which enhance the net reproductive rate of cells. Driver mutations may increase cell division, reduce cell death, or allow cells to overcome density-limiting effects. We study the dynamics of tumor growth as one additional driver mutation is acquired. Our models are based on two-type branching processes that terminate in either tumor disappearance or tumor detection. In our first model, both cell types grow exponentially, with a faster rate for cells carrying the additional driver. We find that the additional driver mutation does not affect the survival probability of the lesion, but can substantially reduce the time to reach the detectable size if the lesion is slow growing. In our second model, cells lacking the additional driver cannot exceed a fixed carrying capacity, due to density limitations. In this case, the time to detection depends strongly on this carrying capacity. Our model provides a quantitative framework for studying tumor dynamics during different stages of progression. We observe that early, small lesions need additional drivers, while late stage metastases are only marginally affected by them. These results help to explain why additional driver mutations are typically not detected in fast-growing metastases."}],"page":"34 - 45","citation":{"ista":"Reiter J, Božić I, Allen B, Chatterjee K, Nowak M. 2013. The effect of one additional driver mutation on tumor progression. Evolutionary Applications. 6(1), 34–45.","apa":"Reiter, J., Božić, I., Allen, B., Chatterjee, K., & Nowak, M. (2013). The effect of one additional driver mutation on tumor progression. Evolutionary Applications. Wiley-Blackwell. https://doi.org/10.1111/eva.12020","ieee":"J. Reiter, I. Božić, B. Allen, K. Chatterjee, and M. Nowak, “The effect of one additional driver mutation on tumor progression,” Evolutionary Applications, vol. 6, no. 1. Wiley-Blackwell, pp. 34–45, 2013.","ama":"Reiter J, Božić I, Allen B, Chatterjee K, Nowak M. The effect of one additional driver mutation on tumor progression. Evolutionary Applications. 2013;6(1):34-45. doi:10.1111/eva.12020","chicago":"Reiter, Johannes, Ivana Božić, Benjamin Allen, Krishnendu Chatterjee, and Martin Nowak. “The Effect of One Additional Driver Mutation on Tumor Progression.” Evolutionary Applications. Wiley-Blackwell, 2013. https://doi.org/10.1111/eva.12020.","mla":"Reiter, Johannes, et al. “The Effect of One Additional Driver Mutation on Tumor Progression.” Evolutionary Applications, vol. 6, no. 1, Wiley-Blackwell, 2013, pp. 34–45, doi:10.1111/eva.12020.","short":"J. Reiter, I. Božić, B. Allen, K. Chatterjee, M. Nowak, Evolutionary Applications 6 (2013) 34–45."},"publication":"Evolutionary Applications","date_published":"2013-01-01T00:00:00Z","scopus_import":1,"has_accepted_license":"1","day":"01","publisher":"Wiley-Blackwell","department":[{"_id":"KrCh"}],"publication_status":"published","year":"2013","volume":6,"date_created":"2018-12-11T11:59:58Z","date_updated":"2023-09-07T11:40:43Z","related_material":{"record":[{"id":"1400","status":"public","relation":"dissertation_contains"}]},"author":[{"first_name":"Johannes","last_name":"Reiter","id":"4A918E98-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0170-7353","full_name":"Reiter, Johannes"},{"first_name":"Ivana","last_name":"Božić","full_name":"Božić, Ivana"},{"first_name":"Benjamin","last_name":"Allen","id":"135B5B70-E9D2-11E9-BD74-BB415DA2B523","full_name":"Allen, Benjamin"},{"first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"full_name":"Nowak, Martin","first_name":"Martin","last_name":"Nowak"}],"publist_id":"3931","ec_funded":1,"file_date_updated":"2020-07-14T12:45:51Z","project":[{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Game Theory"}],"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1111/eva.12020","month":"01"},{"scopus_import":1,"has_accepted_license":"1","day":"25","citation":{"mla":"Božić, Ivana, et al. “Evolutionary Dynamics of Cancer in Response to Targeted Combination Therapy.” ELife, vol. 2, e00747, eLife Sciences Publications, 2013, doi:10.7554/eLife.00747.","short":"I. Božić, J. Reiter, B. Allen, T. Antal, K. Chatterjee, P. Shah, Y. Moon, A. Yaqubie, N. Kelly, D. Le, E. Lipson, P. Chapman, L. Diaz, B. Vogelstein, M. Nowak, ELife 2 (2013).","chicago":"Božić, Ivana, Johannes Reiter, Benjamin Allen, Tibor Antal, Krishnendu Chatterjee, Preya Shah, Yo Moon, et al. “Evolutionary Dynamics of Cancer in Response to Targeted Combination Therapy.” ELife. eLife Sciences Publications, 2013. https://doi.org/10.7554/eLife.00747.","ama":"Božić I, Reiter J, Allen B, et al. Evolutionary dynamics of cancer in response to targeted combination therapy. eLife. 2013;2. doi:10.7554/eLife.00747","ista":"Božić I, Reiter J, Allen B, Antal T, Chatterjee K, Shah P, Moon Y, Yaqubie A, Kelly N, Le D, Lipson E, Chapman P, Diaz L, Vogelstein B, Nowak M. 2013. Evolutionary dynamics of cancer in response to targeted combination therapy. eLife. 2, e00747.","apa":"Božić, I., Reiter, J., Allen, B., Antal, T., Chatterjee, K., Shah, P., … Nowak, M. (2013). Evolutionary dynamics of cancer in response to targeted combination therapy. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.00747","ieee":"I. Božić et al., “Evolutionary dynamics of cancer in response to targeted combination therapy,” eLife, vol. 2. eLife Sciences Publications, 2013."},"publication":"eLife","date_published":"2013-06-25T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"In solid tumors, targeted treatments can lead to dramatic regressions, but responses are often short-lived because resistant cancer cells arise. The major strategy proposed for overcoming resistance is combination therapy. We present a mathematical model describing the evolutionary dynamics of lesions in response to treatment. We first studied 20 melanoma patients receiving vemurafenib. We then applied our model to an independent set of pancreatic, colorectal, and melanoma cancer patients with metastatic disease. We find that dual therapy results in long-term disease control for most patients, if there are no single mutations that cause cross-resistance to both drugs; in patients with large disease burden, triple therapy is needed. We also find that simultaneous therapy with two drugs is much more effective than sequential therapy. Our results provide realistic expectations for the efficacy of new drug combinations and inform the design of trials for new cancer therapeutics."}],"intvolume":" 2","ddc":["570","610"],"status":"public","title":"Evolutionary dynamics of cancer in response to targeted combination therapy","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2816","file":[{"file_size":3358321,"content_type":"application/pdf","creator":"system","access_level":"open_access","file_name":"IST-2013-134-v1+1_e00747.full.pdf","checksum":"2c38c47815eacd8fa66cb8b404cf7c61","date_created":"2018-12-12T10:12:48Z","date_updated":"2020-07-14T12:45:49Z","relation":"main_file","file_id":"4967"}],"oa_version":"Published Version","pubrep_id":"134","month":"06","quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"language":[{"iso":"eng"}],"doi":"10.7554/eLife.00747","article_number":"e00747","publist_id":"3985","file_date_updated":"2020-07-14T12:45:49Z","publisher":"eLife Sciences Publications","department":[{"_id":"KrCh"}],"publication_status":"published","year":"2013","volume":2,"date_created":"2018-12-11T11:59:45Z","date_updated":"2023-09-07T11:40:43Z","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"1400"}]},"author":[{"full_name":"Božić, Ivana","first_name":"Ivana","last_name":"Božić"},{"full_name":"Reiter, Johannes","last_name":"Reiter","first_name":"Johannes","orcid":"0000-0002-0170-7353","id":"4A918E98-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Allen, Benjamin","first_name":"Benjamin","last_name":"Allen"},{"full_name":"Antal, Tibor","last_name":"Antal","first_name":"Tibor"},{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu"},{"full_name":"Shah, Preya","last_name":"Shah","first_name":"Preya"},{"first_name":"Yo","last_name":"Moon","full_name":"Moon, Yo"},{"first_name":"Amin","last_name":"Yaqubie","full_name":"Yaqubie, Amin"},{"first_name":"Nicole","last_name":"Kelly","full_name":"Kelly, Nicole"},{"first_name":"Dung","last_name":"Le","full_name":"Le, Dung"},{"full_name":"Lipson, Evan","last_name":"Lipson","first_name":"Evan"},{"full_name":"Chapman, Paul","first_name":"Paul","last_name":"Chapman"},{"first_name":"Luis","last_name":"Diaz","full_name":"Diaz, Luis"},{"last_name":"Vogelstein","first_name":"Bert","full_name":"Vogelstein, Bert"},{"first_name":"Martin","last_name":"Nowak","full_name":"Nowak, Martin"}]},{"scopus_import":1,"series_title":"Lecture Notes in Computer Science","day":"01","citation":{"ieee":"J. Reiter, I. Božić, K. Chatterjee, and M. Nowak, “TTP: Tool for tumor progression,” in Proceedings of 25th Int. Conf. on Computer Aided Verification, St. Petersburg, Russia, 2013, vol. 8044, pp. 101–106.","apa":"Reiter, J., Božić, I., Chatterjee, K., & Nowak, M. (2013). TTP: Tool for tumor progression. In Proceedings of 25th Int. Conf. on Computer Aided Verification (Vol. 8044, pp. 101–106). St. Petersburg, Russia: Springer. https://doi.org/10.1007/978-3-642-39799-8_6","ista":"Reiter J, Božić I, Chatterjee K, Nowak M. 2013. TTP: Tool for tumor progression. Proceedings of 25th Int. Conf. on Computer Aided Verification. CAV: Computer Aided VerificationLecture Notes in Computer Science, LNCS, vol. 8044, 101–106.","ama":"Reiter J, Božić I, Chatterjee K, Nowak M. TTP: Tool for tumor progression. In: Proceedings of 25th Int. Conf. on Computer Aided Verification. Vol 8044. Lecture Notes in Computer Science. Springer; 2013:101-106. doi:10.1007/978-3-642-39799-8_6","chicago":"Reiter, Johannes, Ivana Božić, Krishnendu Chatterjee, and Martin Nowak. “TTP: Tool for Tumor Progression.” In Proceedings of 25th Int. Conf. on Computer Aided Verification, 8044:101–6. Lecture Notes in Computer Science. Springer, 2013. https://doi.org/10.1007/978-3-642-39799-8_6.","short":"J. Reiter, I. Božić, K. Chatterjee, M. Nowak, in:, Proceedings of 25th Int. Conf. on Computer Aided Verification, Springer, 2013, pp. 101–106.","mla":"Reiter, Johannes, et al. “TTP: Tool for Tumor Progression.” Proceedings of 25th Int. Conf. on Computer Aided Verification, vol. 8044, Springer, 2013, pp. 101–06, doi:10.1007/978-3-642-39799-8_6."},"publication":"Proceedings of 25th Int. Conf. on Computer Aided Verification","page":"101 - 106","date_published":"2013-01-01T00:00:00Z","type":"conference","alternative_title":["LNCS"],"abstract":[{"text":"In this work we present a flexible tool for tumor progression, which simulates the evolutionary dynamics of cancer. Tumor progression implements a multi-type branching process where the key parameters are the fitness landscape, the mutation rate, and the average time of cell division. The fitness of a cancer cell depends on the mutations it has accumulated. The input to our tool could be any fitness landscape, mutation rate, and cell division time, and the tool produces the growth dynamics and all relevant statistics.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2000","intvolume":" 8044","title":"TTP: Tool for tumor progression","status":"public","oa_version":"Preprint","month":"01","external_id":{"arxiv":["1303.5251"]},"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1303.5251","open_access":"1"}],"project":[{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"quality_controlled":"1","doi":"10.1007/978-3-642-39799-8_6","conference":{"start_date":"2013-07-13","location":"St. Petersburg, Russia","end_date":"2013-07-19","name":"CAV: Computer Aided Verification"},"language":[{"iso":"eng"}],"publist_id":"5077","ec_funded":1,"year":"2013","publisher":"Springer","department":[{"_id":"KrCh"}],"publication_status":"published","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"5399"},{"id":"1400","relation":"dissertation_contains","status":"public"}]},"author":[{"last_name":"Reiter","first_name":"Johannes","orcid":"0000-0002-0170-7353","id":"4A918E98-F248-11E8-B48F-1D18A9856A87","full_name":"Reiter, Johannes"},{"full_name":"Božić, Ivana","last_name":"Božić","first_name":"Ivana"},{"last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"},{"last_name":"Nowak","first_name":"Martin","full_name":"Nowak, Martin"}],"volume":8044,"date_created":"2018-12-11T11:55:08Z","date_updated":"2023-09-07T11:40:43Z"},{"page":"951 - 967","citation":{"ama":"Cerny P, Henzinger TA, Radhakrishna A, Ryzhyk L, Tarrach T. Efficient synthesis for concurrency by semantics-preserving transformations. In: Vol 8044. Springer; 2013:951-967. doi:10.1007/978-3-642-39799-8_68","ieee":"P. Cerny, T. A. Henzinger, A. Radhakrishna, L. Ryzhyk, and T. Tarrach, “Efficient synthesis for concurrency by semantics-preserving transformations,” presented at the CAV: Computer Aided Verification, St. Petersburg, Russia, 2013, vol. 8044, pp. 951–967.","apa":"Cerny, P., Henzinger, T. A., Radhakrishna, A., Ryzhyk, L., & Tarrach, T. (2013). Efficient synthesis for concurrency by semantics-preserving transformations (Vol. 8044, pp. 951–967). Presented at the CAV: Computer Aided Verification, St. Petersburg, Russia: Springer. https://doi.org/10.1007/978-3-642-39799-8_68","ista":"Cerny P, Henzinger TA, Radhakrishna A, Ryzhyk L, Tarrach T. 2013. Efficient synthesis for concurrency by semantics-preserving transformations. CAV: Computer Aided Verification, LNCS, vol. 8044, 951–967.","short":"P. Cerny, T.A. Henzinger, A. Radhakrishna, L. Ryzhyk, T. Tarrach, in:, Springer, 2013, pp. 951–967.","mla":"Cerny, Pavol, et al. Efficient Synthesis for Concurrency by Semantics-Preserving Transformations. Vol. 8044, Springer, 2013, pp. 951–67, doi:10.1007/978-3-642-39799-8_68.","chicago":"Cerny, Pavol, Thomas A Henzinger, Arjun Radhakrishna, Leonid Ryzhyk, and Thorsten Tarrach. “Efficient Synthesis for Concurrency by Semantics-Preserving Transformations,” 8044:951–67. Springer, 2013. https://doi.org/10.1007/978-3-642-39799-8_68."},"date_published":"2013-07-01T00:00:00Z","scopus_import":1,"has_accepted_license":"1","day":"01","intvolume":" 8044","status":"public","ddc":["000","004"],"title":"Efficient synthesis for concurrency by semantics-preserving transformations","_id":"2445","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version","file":[{"date_updated":"2020-07-14T12:45:40Z","date_created":"2018-12-12T10:15:37Z","checksum":"70c70ca5487faba82262c63e1b678a27","file_id":"5158","relation":"main_file","creator":"system","file_size":365548,"content_type":"application/pdf","file_name":"IST-2014-199-v1+1_cav2013-final.pdf","access_level":"open_access"}],"pubrep_id":"199","alternative_title":["LNCS"],"type":"conference","abstract":[{"lang":"eng","text":"We develop program synthesis techniques that can help programmers fix concurrency-related bugs. We make two new contributions to synthesis for concurrency, the first improving the efficiency of the synthesized code, and the second improving the efficiency of the synthesis procedure itself. The first contribution is to have the synthesis procedure explore a variety of (sequential) semantics-preserving program transformations. Classically, only one such transformation has been considered, namely, the insertion of synchronization primitives (such as locks). Based on common manual bug-fixing techniques used by Linux device-driver developers, we explore additional, more efficient transformations, such as the reordering of independent instructions. The second contribution is to speed up the counterexample-guided removal of concurrency bugs within the synthesis procedure by considering partial-order traces (instead of linear traces) as counterexamples. A partial-order error trace represents a set of linear (interleaved) traces of a concurrent program all of which lead to the same error. By eliminating a partial-order error trace, we eliminate in a single iteration of the synthesis procedure all linearizations of the partial-order trace. We evaluated our techniques on several simplified examples of real concurrency bugs that occurred in Linux device drivers."}],"project":[{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989","name":"Quantitative Reactive Modeling","call_identifier":"FP7"},{"call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","oa":1,"language":[{"iso":"eng"}],"doi":"10.1007/978-3-642-39799-8_68","conference":{"name":"CAV: Computer Aided Verification","end_date":"2013-07-19","start_date":"2013-07-13","location":"St. Petersburg, Russia"},"month":"07","publisher":"Springer","department":[{"_id":"ToHe"}],"publication_status":"published","year":"2013","volume":8044,"date_updated":"2023-09-07T11:57:01Z","date_created":"2018-12-11T11:57:42Z","related_material":{"record":[{"id":"1130","relation":"dissertation_contains","status":"public"}]},"author":[{"id":"4DCBEFFE-F248-11E8-B48F-1D18A9856A87","last_name":"Cerny","first_name":"Pavol","full_name":"Cerny, Pavol"},{"last_name":"Henzinger","first_name":"Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A"},{"id":"3B51CAC4-F248-11E8-B48F-1D18A9856A87","first_name":"Arjun","last_name":"Radhakrishna","full_name":"Radhakrishna, Arjun"},{"last_name":"Ryzhyk","first_name":"Leonid","full_name":"Ryzhyk, Leonid"},{"full_name":"Tarrach, Thorsten","last_name":"Tarrach","first_name":"Thorsten","orcid":"0000-0003-4409-8487","id":"3D6E8F2C-F248-11E8-B48F-1D18A9856A87"}],"ec_funded":1,"publist_id":"4458","file_date_updated":"2020-07-14T12:45:40Z"},{"date_published":"2013-01-07T00:00:00Z","page":"76 - 82","citation":{"mla":"Tragust, Simon, et al. “Ants Disinfect Fungus-Exposed Brood by Oral Uptake and Spread of Their Poison.” Current Biology, vol. 23, no. 1, Cell Press, 2013, pp. 76–82, doi:10.1016/j.cub.2012.11.034.","short":"S. Tragust, B. Mitteregger, V. Barone, M. Konrad, L.V. Ugelvig, S. Cremer, Current Biology 23 (2013) 76–82.","chicago":"Tragust, Simon, Barbara Mitteregger, Vanessa Barone, Matthias Konrad, Line V Ugelvig, and Sylvia Cremer. “Ants Disinfect Fungus-Exposed Brood by Oral Uptake and Spread of Their Poison.” Current Biology. Cell Press, 2013. https://doi.org/10.1016/j.cub.2012.11.034.","ama":"Tragust S, Mitteregger B, Barone V, Konrad M, Ugelvig LV, Cremer S. Ants disinfect fungus-exposed brood by oral uptake and spread of their poison. Current Biology. 2013;23(1):76-82. doi:10.1016/j.cub.2012.11.034","ista":"Tragust S, Mitteregger B, Barone V, Konrad M, Ugelvig LV, Cremer S. 2013. Ants disinfect fungus-exposed brood by oral uptake and spread of their poison. Current Biology. 23(1), 76–82.","ieee":"S. Tragust, B. Mitteregger, V. Barone, M. Konrad, L. V. Ugelvig, and S. Cremer, “Ants disinfect fungus-exposed brood by oral uptake and spread of their poison,” Current Biology, vol. 23, no. 1. Cell Press, pp. 76–82, 2013.","apa":"Tragust, S., Mitteregger, B., Barone, V., Konrad, M., Ugelvig, L. V., & Cremer, S. (2013). Ants disinfect fungus-exposed brood by oral uptake and spread of their poison. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2012.11.034"},"publication":"Current Biology","day":"07","scopus_import":1,"oa_version":"None","intvolume":" 23","title":"Ants disinfect fungus-exposed brood by oral uptake and spread of their poison","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2926","issue":"1","abstract":[{"text":"To fight infectious diseases, host immune defenses are employed at multiple levels. Sanitary behavior, such as pathogen avoidance and removal, acts as a first line of defense to prevent infection [1] before activation of the physiological immune system. Insect societies have evolved a wide range of collective hygiene measures and intensive health care toward pathogen-exposed group members [2]. One of the most common behaviors is allogrooming, in which nestmates remove infectious particles from the body surfaces of exposed individuals [3]. Here we show that, in invasive garden ants, grooming of fungus-exposed brood is effective beyond the sheer mechanical removal of fungal conidiospores; it also includes chemical disinfection through the application of poison produced by the ants themselves. Formic acid is the main active component of the poison. It inhibits fungal growth of conidiospores remaining on the brood surface after grooming and also those collected in the mouth of the grooming ant. This dual function is achieved by uptake of the poison droplet into the mouth through acidopore self-grooming and subsequent application onto the infectious brood via brood grooming. This extraordinary behavior extends the current understanding of grooming and the establishment of social immunity in insect societies.","lang":"eng"}],"type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1016/j.cub.2012.11.034","project":[{"_id":"25DAF0B2-B435-11E9-9278-68D0E5697425","grant_number":"CR-118/3-1","name":"Host-Parasite Coevolution"},{"grant_number":"243071","_id":"25DC711C-B435-11E9-9278-68D0E5697425","name":"Social Vaccination in Ant Colonies: from Individual Mechanisms to Society Effects","call_identifier":"FP7"},{"name":"Pathogen Detectors Collective disease defence and pathogen detection abilities in ant societies: a chemo-neuro-immunological approach","call_identifier":"FP7","_id":"25DDF0F0-B435-11E9-9278-68D0E5697425","grant_number":"302004"}],"quality_controlled":"1","month":"01","volume":23,"date_updated":"2023-09-07T12:05:08Z","date_created":"2018-12-11T12:00:23Z","related_material":{"record":[{"id":"9757","status":"public","relation":"research_data"},{"status":"public","relation":"dissertation_contains","id":"961"}]},"author":[{"last_name":"Tragust","first_name":"Simon","id":"35A7A418-F248-11E8-B48F-1D18A9856A87","full_name":"Tragust, Simon"},{"first_name":"Barbara","last_name":"Mitteregger","id":"479DDAAC-E9CD-11E9-9B5F-82450873F7A1","full_name":"Mitteregger, Barbara"},{"first_name":"Vanessa","last_name":"Barone","id":"419EECCC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2676-3367","full_name":"Barone, Vanessa"},{"first_name":"Matthias","last_name":"Konrad","id":"46528076-F248-11E8-B48F-1D18A9856A87","full_name":"Konrad, Matthias"},{"full_name":"Ugelvig, Line V","orcid":"0000-0003-1832-8883","id":"3DC97C8E-F248-11E8-B48F-1D18A9856A87","last_name":"Ugelvig","first_name":"Line V"},{"full_name":"Cremer, Sylvia","first_name":"Sylvia","last_name":"Cremer","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2193-3868"}],"department":[{"_id":"SyCr"},{"_id":"CaHe"}],"publisher":"Cell Press","publication_status":"published","year":"2013","acknowledgement":"Funding for this project was obtained by the German Research Foundation (DFG, to S.C.) and the European Research Council (ERC, through an ERC-Starting Grant to S.C. and an Individual Marie Curie IEF fellowship to L.V.U.).\r\nWe thank Jørgen Eilenberg, Bernhardt Steinwender, Miriam Stock, and Meghan L. Vyleta for the fungal strain and its characterization; Volker Witte for chemical information; Eva Sixt for ant drawings; and Robert Hauschild for help with image analysis. We further thank Martin Kaltenpoth, Michael Sixt, Jürgen Heinze, and Joachim Ruther for discussion and Daria Siekhaus, Sophie A.O. Armitage, and Leila Masri for comments on the manuscript. \r\n","publist_id":"3811","ec_funded":1},{"doi":"10.1109/LICS.2013.39","conference":{"end_date":"2013-06-28","location":"New Orleans, LA, United States","start_date":"2013-06-25","name":"LICS: Logic in Computer Science"},"language":[{"iso":"eng"}],"main_file_link":[{"url":"http://arxiv.org/abs/1305.4103","open_access":"1"}],"external_id":{"arxiv":["1305.4103"]},"oa":1,"project":[{"call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407","name":"Game Theory","call_identifier":"FWF"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","month":"08","related_material":{"record":[{"id":"1294","status":"public","relation":"later_version"}]},"author":[{"first_name":"Tomáš","last_name":"Brázdil","full_name":"Brázdil, Tomáš"},{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu"},{"first_name":"Vojtěch","last_name":"Forejt","full_name":"Forejt, Vojtěch"},{"first_name":"Antonín","last_name":"Kučera","full_name":"Kučera, Antonín"}],"date_created":"2018-12-11T11:56:53Z","date_updated":"2023-09-20T11:15:30Z","year":"2013","publisher":"IEEE","department":[{"_id":"KrCh"}],"publication_status":"published","publist_id":"4622","ec_funded":1,"date_published":"2013-08-01T00:00:00Z","citation":{"ama":"Brázdil T, Chatterjee K, Forejt V, Kučera A. Trading performance for stability in Markov decision processes. In: 28th Annual ACM/IEEE Symposium. IEEE; 2013:331-340. doi:10.1109/LICS.2013.39","ista":"Brázdil T, Chatterjee K, Forejt V, Kučera A. 2013. Trading performance for stability in Markov decision processes. 28th Annual ACM/IEEE Symposium. LICS: Logic in Computer Science, 331–340.","ieee":"T. Brázdil, K. Chatterjee, V. Forejt, and A. Kučera, “Trading performance for stability in Markov decision processes,” in 28th Annual ACM/IEEE Symposium, New Orleans, LA, United States, 2013, pp. 331–340.","apa":"Brázdil, T., Chatterjee, K., Forejt, V., & Kučera, A. (2013). Trading performance for stability in Markov decision processes. In 28th Annual ACM/IEEE Symposium (pp. 331–340). New Orleans, LA, United States: IEEE. https://doi.org/10.1109/LICS.2013.39","mla":"Brázdil, Tomáš, et al. “Trading Performance for Stability in Markov Decision Processes.” 28th Annual ACM/IEEE Symposium, IEEE, 2013, pp. 331–40, doi:10.1109/LICS.2013.39.","short":"T. Brázdil, K. Chatterjee, V. Forejt, A. Kučera, in:, 28th Annual ACM/IEEE Symposium, IEEE, 2013, pp. 331–340.","chicago":"Brázdil, Tomáš, Krishnendu Chatterjee, Vojtěch Forejt, and Antonín Kučera. “Trading Performance for Stability in Markov Decision Processes.” In 28th Annual ACM/IEEE Symposium, 331–40. IEEE, 2013. https://doi.org/10.1109/LICS.2013.39."},"publication":"28th Annual ACM/IEEE Symposium","page":"331 - 340","day":"01","scopus_import":1,"oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2305","status":"public","title":"Trading performance for stability in Markov decision processes","abstract":[{"lang":"eng","text":"We study the complexity of central controller synthesis problems for finite-state Markov decision processes, where the objective is to optimize both the expected mean-payoff performance of the system and its stability. e argue that the basic theoretical notion of expressing the stability in terms of the variance of the mean-payoff (called global variance in our paper) is not always sufficient, since it ignores possible instabilities on respective runs. For this reason we propose alernative definitions of stability, which we call local and hybrid variance, and which express how rewards on each run deviate from the run's own mean-payoff and from the expected mean-payoff, respectively. We show that a strategy ensuring both the expected mean-payoff and the variance below given bounds requires randomization and memory, under all the above semantics of variance. We then look at the problem of determining whether there is a such a strategy. For the global variance, we show that the problem is in PSPACE, and that the answer can be approximated in pseudo-polynomial time. For the hybrid variance, the analogous decision problem is in NP, and a polynomial-time approximating algorithm also exists. For local variance, we show that the decision problem is in NP. Since the overall performance can be traded for stability (and vice versa), we also present algorithms for approximating the associated Pareto curve in all the three cases. Finally, we study a special case of the decision problems, where we require a given expected mean-payoff together with zero variance. Here we show that the problems can be all solved in polynomial time."}],"type":"conference"},{"language":[{"iso":"eng"}],"date_published":"2013-04-01T00:00:00Z","doi":"10.1145/2461328.2461356","conference":{"name":"HSCC: Hybrid Systems - Computation and Control","end_date":"2013-04-11","location":"Philadelphia, PA, United States","start_date":"2013-04-08"},"project":[{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF"},{"grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Game Theory"},{"grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"page":"163 - 172","quality_controlled":"1","citation":{"ama":"Chatterjee K, Kößler A, Schmid U. Automated analysis of real-time scheduling using graph games. In: Proceedings of the 16th International Conference on Hybrid Systems: Computation and Control. ACM; 2013:163-172. doi:10.1145/2461328.2461356","ista":"Chatterjee K, Kößler A, Schmid U. 2013. Automated analysis of real-time scheduling using graph games. Proceedings of the 16th International conference on Hybrid systems: Computation and control. HSCC: Hybrid Systems - Computation and Control, 163–172.","ieee":"K. Chatterjee, A. Kößler, and U. Schmid, “Automated analysis of real-time scheduling using graph games,” in Proceedings of the 16th International conference on Hybrid systems: Computation and control, Philadelphia, PA, United States, 2013, pp. 163–172.","apa":"Chatterjee, K., Kößler, A., & Schmid, U. (2013). Automated analysis of real-time scheduling using graph games. In Proceedings of the 16th International conference on Hybrid systems: Computation and control (pp. 163–172). Philadelphia, PA, United States: ACM. https://doi.org/10.1145/2461328.2461356","mla":"Chatterjee, Krishnendu, et al. “Automated Analysis of Real-Time Scheduling Using Graph Games.” Proceedings of the 16th International Conference on Hybrid Systems: Computation and Control, ACM, 2013, pp. 163–72, doi:10.1145/2461328.2461356.","short":"K. Chatterjee, A. Kößler, U. Schmid, in:, Proceedings of the 16th International Conference on Hybrid Systems: Computation and Control, ACM, 2013, pp. 163–172.","chicago":"Chatterjee, Krishnendu, Alexander Kößler, and Ulrich Schmid. “Automated Analysis of Real-Time Scheduling Using Graph Games.” In Proceedings of the 16th International Conference on Hybrid Systems: Computation and Control, 163–72. ACM, 2013. https://doi.org/10.1145/2461328.2461356."},"publication":"Proceedings of the 16th International conference on Hybrid systems: Computation and control","publication_identifier":{"isbn":["978-1-4503-1567-8 "]},"month":"04","day":"01","scopus_import":1,"oa_version":"None","date_created":"2018-12-11T11:59:46Z","date_updated":"2023-09-27T12:52:38Z","related_material":{"record":[{"relation":"later_version","status":"public","id":"738"}]},"author":[{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"first_name":"Alexander","last_name":"Kößler","full_name":"Kößler, Alexander"},{"full_name":"Schmid, Ulrich","first_name":"Ulrich","last_name":"Schmid"}],"publisher":"ACM","department":[{"_id":"KrCh"}],"status":"public","publication_status":"published","title":"Automated analysis of real-time scheduling using graph games","year":"2013","_id":"2820","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ec_funded":1,"publist_id":"3981","abstract":[{"lang":"eng","text":"In this paper, we introduce the powerful framework of graph games for the analysis of real-time scheduling with firm deadlines. We introduce a novel instance of a partial-observation game that is suitable for this purpose, and prove decidability of all the involved decision problems. We derive a graph game that allows the automated computation of the competitive ratio (along with an optimal witness algorithm for the competitive ratio) and establish an NP-completeness proof for the graph game problem. For a given on-line algorithm, we present polynomial time solution for computing (i) the worst-case utility; (ii) the worst-case utility ratio w.r.t. a clairvoyant off-line algorithm; and (iii) the competitive ratio. A major strength of the proposed approach lies in its flexibility w.r.t. incorporating additional constraints on the adversary and/or the algorithm, including limited maximum or average load, finiteness of periods of overload, etc., which are easily added by means of additional instances of standard objective functions for graph games. "}],"type":"conference"},{"intvolume":" 28","status":"public","title":"Inference algorithms for pattern-based CRFs on sequence data","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2272","oa_version":"Submitted Version","alternative_title":["JMLR"],"type":"conference","issue":"3","abstract":[{"lang":"eng","text":"We consider Conditional Random Fields (CRFs) with pattern-based potentials defined on a chain. In this model the energy of a string (labeling) x1...xn is the sum of terms over intervals [i,j] where each term is non-zero only if the substring xi...xj equals a prespecified pattern α. Such CRFs can be naturally applied to many sequence tagging problems.\r\nWe present efficient algorithms for the three standard inference tasks in a CRF, namely computing (i) the partition function, (ii) marginals, and (iii) computing the MAP. Their complexities are respectively O(nL), O(nLℓmax) and O(nLmin{|D|,log(ℓmax+1)}) where L is the combined length of input patterns, ℓmax is the maximum length of a pattern, and D is the input alphabet. This improves on the previous algorithms of (Ye et al., 2009) whose complexities are respectively O(nL|D|), O(n|Γ|L2ℓ2max) and O(nL|D|), where |Γ| is the number of input patterns.\r\nIn addition, we give an efficient algorithm for sampling. Finally, we consider the case of non-positive weights. (Komodakis & Paragios, 2009) gave an O(nL) algorithm for computing the MAP. We present a modification that has the same worst-case complexity but can beat it in the best case. "}],"page":"145 - 153","citation":{"chicago":"Takhanov, Rustem, and Vladimir Kolmogorov. “Inference Algorithms for Pattern-Based CRFs on Sequence Data.” In ICML’13 Proceedings of the 30th International Conference on International, 28:145–53. ML Research Press, 2013.","short":"R. Takhanov, V. Kolmogorov, in:, ICML’13 Proceedings of the 30th International Conference on International, ML Research Press, 2013, pp. 145–153.","mla":"Takhanov, Rustem, and Vladimir Kolmogorov. “Inference Algorithms for Pattern-Based CRFs on Sequence Data.” ICML’13 Proceedings of the 30th International Conference on International, vol. 28, no. 3, ML Research Press, 2013, pp. 145–53.","ieee":"R. Takhanov and V. Kolmogorov, “Inference algorithms for pattern-based CRFs on sequence data,” in ICML’13 Proceedings of the 30th International Conference on International, Atlanta, GA, USA, 2013, vol. 28, no. 3, pp. 145–153.","apa":"Takhanov, R., & Kolmogorov, V. (2013). Inference algorithms for pattern-based CRFs on sequence data. In ICML’13 Proceedings of the 30th International Conference on International (Vol. 28, pp. 145–153). Atlanta, GA, USA: ML Research Press.","ista":"Takhanov R, Kolmogorov V. 2013. Inference algorithms for pattern-based CRFs on sequence data. ICML’13 Proceedings of the 30th International Conference on International. ICML: International Conference on Machine Learning, JMLR, vol. 28, 145–153.","ama":"Takhanov R, Kolmogorov V. Inference algorithms for pattern-based CRFs on sequence data. In: ICML’13 Proceedings of the 30th International Conference on International. Vol 28. ML Research Press; 2013:145-153."},"publication":"ICML'13 Proceedings of the 30th International Conference on International","date_published":"2013-06-01T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"01","department":[{"_id":"VlKo"}],"publisher":"ML Research Press","publication_status":"published","year":"2013","volume":28,"date_updated":"2023-10-17T09:51:32Z","date_created":"2018-12-11T11:56:41Z","related_material":{"record":[{"status":"public","relation":"later_version","id":"1794"}]},"author":[{"full_name":"Takhanov, Rustem","last_name":"Takhanov","first_name":"Rustem","id":"2CCAC26C-F248-11E8-B48F-1D18A9856A87"},{"id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","last_name":"Kolmogorov","first_name":"Vladimir","full_name":"Kolmogorov, Vladimir"}],"publist_id":"4672","quality_controlled":"1","main_file_link":[{"url":"http://proceedings.mlr.press/v28/takhanov13.pdf?CFID=105472548&CFTOKEN=5c5859b5d97b4439-27B4AC58-BA92-A964-B598CAACEE6CC515","open_access":"1"}],"oa":1,"language":[{"iso":"eng"}],"conference":{"name":"ICML: International Conference on Machine Learning","start_date":"2013-06-16","location":"Atlanta, GA, USA","end_date":"2013-06-21"},"month":"06"},{"intvolume":" 8","status":"public","title":"ZIFL1.1 transporter modulates polar auxin transport by stabilizing membrane abundance of multiple PINs in Arabidopsis root tip","_id":"2448","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version","type":"journal_article","issue":"10","abstract":[{"lang":"eng","text":"Cell-to-cell directional flow of the phytohormone auxin is primarily established by polar localization of the PIN auxin transporters, a process tightly regulated at multiple levels by auxin itself. We recently reported that, in the context of strong auxin flows, activity of the vacuolar ZIFL1.1 transporter is required for fine-tuning of polar auxin transport rates in the Arabidopsis root. In particular, ZIFL1.1 function protects plasma-membrane stability of the PIN2 carrier in epidermal root tip cells under conditions normally triggering PIN2 degradation. Here, we show that ZIFL1.1 activity at the root tip also promotes PIN1 plasma-membrane abundance in central cylinder cells, thus supporting the notion that ZIFL1.1 acts as a general positive modulator of polar auxin transport in roots."}],"article_type":"original","citation":{"ieee":"E. Remy, P. Baster, J. Friml, and P. Duque, “ZIFL1.1 transporter modulates polar auxin transport by stabilizing membrane abundance of multiple PINs in Arabidopsis root tip,” Plant Signaling & Behavior, vol. 8, no. 10. Taylor & Francis, 2013.","apa":"Remy, E., Baster, P., Friml, J., & Duque, P. (2013). ZIFL1.1 transporter modulates polar auxin transport by stabilizing membrane abundance of multiple PINs in Arabidopsis root tip. Plant Signaling & Behavior. Taylor & Francis. https://doi.org/10.4161/psb.25688","ista":"Remy E, Baster P, Friml J, Duque P. 2013. ZIFL1.1 transporter modulates polar auxin transport by stabilizing membrane abundance of multiple PINs in Arabidopsis root tip. Plant Signaling & Behavior. 8(10), e25688.","ama":"Remy E, Baster P, Friml J, Duque P. ZIFL1.1 transporter modulates polar auxin transport by stabilizing membrane abundance of multiple PINs in Arabidopsis root tip. Plant Signaling & Behavior. 2013;8(10). doi:10.4161/psb.25688","chicago":"Remy, Estelle, Pawel Baster, Jiří Friml, and Paula Duque. “ZIFL1.1 Transporter Modulates Polar Auxin Transport by Stabilizing Membrane Abundance of Multiple PINs in Arabidopsis Root Tip.” Plant Signaling & Behavior. Taylor & Francis, 2013. https://doi.org/10.4161/psb.25688.","short":"E. Remy, P. Baster, J. Friml, P. Duque, Plant Signaling & Behavior 8 (2013).","mla":"Remy, Estelle, et al. “ZIFL1.1 Transporter Modulates Polar Auxin Transport by Stabilizing Membrane Abundance of Multiple PINs in Arabidopsis Root Tip.” Plant Signaling & Behavior, vol. 8, no. 10, e25688, Taylor & Francis, 2013, doi:10.4161/psb.25688."},"publication":"Plant Signaling & Behavior","date_published":"2013-07-10T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"10","publisher":"Taylor & Francis","department":[{"_id":"JiFr"}],"publication_status":"published","pmid":1,"year":"2013","volume":8,"date_created":"2018-12-11T11:57:43Z","date_updated":"2023-10-17T11:15:14Z","author":[{"full_name":"Remy, Estelle","last_name":"Remy","first_name":"Estelle"},{"full_name":"Baster, Pawel","first_name":"Pawel","last_name":"Baster","id":"3028BD74-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jirí"},{"last_name":"Duque","first_name":"Paula","full_name":"Duque, Paula"}],"article_number":"e25688","publist_id":"4455","ec_funded":1,"project":[{"_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300","name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7"}],"quality_controlled":"1","external_id":{"pmid":["23857365"]},"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4091088/","open_access":"1"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.4161/psb.25688","month":"07"},{"publist_id":"3939","department":[{"_id":"CaGu"}],"publisher":"The Royal Society","publication_status":"published","pmid":1,"year":"2013","volume":280,"date_updated":"2023-10-18T06:43:23Z","date_created":"2018-12-11T11:59:56Z","related_material":{"record":[{"id":"9751","status":"public","relation":"research_data"}]},"author":[{"last_name":"Refardt","first_name":"Dominik","full_name":"Refardt, Dominik"},{"last_name":"Bergmiller","first_name":"Tobias","orcid":"0000-0001-5396-4346","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","full_name":"Bergmiller, Tobias"},{"last_name":"Kümmerli","first_name":"Rolf","full_name":"Kümmerli, Rolf"}],"publication_identifier":{"eissn":["1471-2954"]},"month":"05","quality_controlled":"1","external_id":{"pmid":["23516238"]},"oa":1,"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3619501/"}],"language":[{"iso":"eng"}],"doi":"10.1098/rspb.2012.3035","type":"journal_article","issue":"1759","abstract":[{"text":"High relatedness among interacting individuals has generally been considered a precondition for the evolution of altruism. However, kin-selection theory also predicts the evolution of altruism when relatedness is low, as long as the cost of the altruistic act is minor compared with its benefit. Here, we demonstrate evidence for a low-cost altruistic act in bacteria. We investigated Escherichia coli responding to the attack of an obligately lytic phage by committing suicide in order to prevent parasite transmission to nearby relatives. We found that bacterial suicide provides large benefits to survivors at marginal costs to committers. The cost of suicide was low, because infected cells are moribund, rapidly dying upon phage infection, such that no more opportunity for reproduction remains. As a consequence of its marginal cost, host suicide was selectively favoured even when relatedness between committers and survivors approached zero. Altogether, our findings demonstrate that low-cost suicide can evolve with ease, represents an effective host-defence strategy, and seems to be widespread among microbes. Moreover, low-cost suicide might also occur in higher organisms as exemplified by infected social insect workers leaving the colony to die in isolation.","lang":"eng"}],"intvolume":" 280","title":"Altruism can evolve when relatedness is low: Evidence from bacteria committing suicide upon phage infection","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2853","oa_version":"Submitted Version","scopus_import":"1","article_processing_charge":"No","day":"22","article_type":"original","citation":{"ama":"Refardt D, Bergmiller T, Kümmerli R. Altruism can evolve when relatedness is low: Evidence from bacteria committing suicide upon phage infection. Proceedings of the Royal Society of London Series B Biological Sciences. 2013;280(1759). doi:10.1098/rspb.2012.3035","apa":"Refardt, D., Bergmiller, T., & Kümmerli, R. (2013). Altruism can evolve when relatedness is low: Evidence from bacteria committing suicide upon phage infection. Proceedings of the Royal Society of London Series B Biological Sciences. The Royal Society. https://doi.org/10.1098/rspb.2012.3035","ieee":"D. Refardt, T. Bergmiller, and R. Kümmerli, “Altruism can evolve when relatedness is low: Evidence from bacteria committing suicide upon phage infection,” Proceedings of the Royal Society of London Series B Biological Sciences, vol. 280, no. 1759. The Royal Society, 2013.","ista":"Refardt D, Bergmiller T, Kümmerli R. 2013. Altruism can evolve when relatedness is low: Evidence from bacteria committing suicide upon phage infection. Proceedings of the Royal Society of London Series B Biological Sciences. 280(1759).","short":"D. Refardt, T. Bergmiller, R. Kümmerli, Proceedings of the Royal Society of London Series B Biological Sciences 280 (2013).","mla":"Refardt, Dominik, et al. “Altruism Can Evolve When Relatedness Is Low: Evidence from Bacteria Committing Suicide upon Phage Infection.” Proceedings of the Royal Society of London Series B Biological Sciences, vol. 280, no. 1759, The Royal Society, 2013, doi:10.1098/rspb.2012.3035.","chicago":"Refardt, Dominik, Tobias Bergmiller, and Rolf Kümmerli. “Altruism Can Evolve When Relatedness Is Low: Evidence from Bacteria Committing Suicide upon Phage Infection.” Proceedings of the Royal Society of London Series B Biological Sciences. The Royal Society, 2013. https://doi.org/10.1098/rspb.2012.3035."},"publication":"Proceedings of the Royal Society of London Series B Biological Sciences","date_published":"2013-05-22T00:00:00Z"},{"type":"research_data_reference","abstract":[{"lang":"eng","text":"High relatedness among interacting individuals has generally been considered a precondition for the evolution of altruism. However, kin-selection theory also predicts the evolution of altruism when relatedness is low, as long as the cost of the altruistic act is minor compared to its benefit. Here, we demonstrate evidence for a low-cost altruistic act in bacteria. We investigated Escherichia coli responding to the attack of an obligately lytic phage by committing suicide in order to prevent parasite transmission to nearby relatives. We found that bacterial suicide provides large benefits to survivors at marginal costs to committers. The cost of suicide was low because infected cells are moribund, rapidly dying upon phage infection, such that no more opportunity for reproduction remains. As a consequence of its marginal cost, host suicide was selectively favoured even when relatedness between committers and survivors approached zero. Altogether, our findings demonstrate that low-cost suicide can evolve with ease, represents an effective host-defence strategy, and seems to be widespread among microbes. Moreover, low-cost suicide might also occur in higher organisms as exemplified by infected social insect workers leaving the colony to die in isolation."}],"department":[{"_id":"CaGu"}],"publisher":"Dryad","status":"public","title":"Data from: Altruism can evolve when relatedness is low: evidence from bacteria committing suicide upon phage infection","year":"2013","_id":"9751","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","oa_version":"Published Version","date_updated":"2023-10-18T06:43:22Z","date_created":"2021-07-30T08:08:09Z","related_material":{"record":[{"id":"2853","status":"public","relation":"used_in_publication"}]},"author":[{"full_name":"Refardt, Dominik","first_name":"Dominik","last_name":"Refardt"},{"full_name":"Bergmiller, Tobias","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5396-4346","first_name":"Tobias","last_name":"Bergmiller"},{"last_name":"Kümmerli","first_name":"Rolf","full_name":"Kümmerli, Rolf"}],"article_processing_charge":"No","day":"21","month":"03","oa":1,"citation":{"short":"D. Refardt, T. Bergmiller, R. Kümmerli, (2013).","mla":"Refardt, Dominik, et al. Data from: Altruism Can Evolve When Relatedness Is Low: Evidence from Bacteria Committing Suicide upon Phage Infection. Dryad, 2013, doi:10.5061/dryad.b1q2n.","chicago":"Refardt, Dominik, Tobias Bergmiller, and Rolf Kümmerli. “Data from: Altruism Can Evolve When Relatedness Is Low: Evidence from Bacteria Committing Suicide upon Phage Infection.” Dryad, 2013. https://doi.org/10.5061/dryad.b1q2n.","ama":"Refardt D, Bergmiller T, Kümmerli R. Data from: Altruism can evolve when relatedness is low: evidence from bacteria committing suicide upon phage infection. 2013. doi:10.5061/dryad.b1q2n","ieee":"D. Refardt, T. Bergmiller, and R. Kümmerli, “Data from: Altruism can evolve when relatedness is low: evidence from bacteria committing suicide upon phage infection.” Dryad, 2013.","apa":"Refardt, D., Bergmiller, T., & Kümmerli, R. (2013). Data from: Altruism can evolve when relatedness is low: evidence from bacteria committing suicide upon phage infection. Dryad. https://doi.org/10.5061/dryad.b1q2n","ista":"Refardt D, Bergmiller T, Kümmerli R. 2013. Data from: Altruism can evolve when relatedness is low: evidence from bacteria committing suicide upon phage infection, Dryad, 10.5061/dryad.b1q2n."},"main_file_link":[{"url":"https://doi.org/10.5061/dryad.b1q2n","open_access":"1"}],"date_published":"2013-03-21T00:00:00Z","doi":"10.5061/dryad.b1q2n"},{"month":"05","day":"22","article_processing_charge":"No","publication_identifier":{"issn":["0896-6273"]},"doi":"10.1016/j.neuron.2013.03.022","date_published":"2013-05-22T00:00:00Z","language":[{"iso":"eng"}],"publication":"Neuron","citation":{"short":"W.J. Joo, L.B. Sweeney, L. Liang, L. Luo, Neuron 78 (2013) 673–686.","mla":"Joo, William J., et al. “Linking Cell Fate, Trajectory Choice, and Target Selection: Genetic Analysis of Sema-2b in Olfactory Axon Targeting.” Neuron, vol. 78, no. 4, Elsevier, 2013, pp. 673–86, doi:10.1016/j.neuron.2013.03.022.","chicago":"Joo, William J., Lora B. Sweeney, Liang Liang, and Liqun Luo. “Linking Cell Fate, Trajectory Choice, and Target Selection: Genetic Analysis of Sema-2b in Olfactory Axon Targeting.” Neuron. Elsevier, 2013. https://doi.org/10.1016/j.neuron.2013.03.022.","ama":"Joo WJ, Sweeney LB, Liang L, Luo L. Linking cell fate, trajectory choice, and target selection: Genetic analysis of sema-2b in olfactory axon targeting. Neuron. 2013;78(4):673-686. doi:10.1016/j.neuron.2013.03.022","apa":"Joo, W. J., Sweeney, L. B., Liang, L., & Luo, L. (2013). Linking cell fate, trajectory choice, and target selection: Genetic analysis of sema-2b in olfactory axon targeting. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2013.03.022","ieee":"W. J. Joo, L. B. Sweeney, L. Liang, and L. Luo, “Linking cell fate, trajectory choice, and target selection: Genetic analysis of sema-2b in olfactory axon targeting,” Neuron, vol. 78, no. 4. Elsevier, pp. 673–686, 2013.","ista":"Joo WJ, Sweeney LB, Liang L, Luo L. 2013. Linking cell fate, trajectory choice, and target selection: Genetic analysis of sema-2b in olfactory axon targeting. Neuron. 78(4), 673–686."},"article_type":"original","quality_controlled":"1","page":"673-686","abstract":[{"text":"Neural circuit assembly requires selection of specific cell fates, axonal trajectories, and synaptic targets. By analyzing the function of a secreted semaphorin, Sema-2b, in Drosophila olfactory receptor neuron (ORN) development, we identified multiple molecular and cellular mechanisms that link these events. Notch signaling limits Sema-2b expression to ventromedial ORN classes, within which Sema-2b cell-autonomously sensitizes ORN axons to external semaphorins. Central-brain-derived Sema-2a and Sema-2b attract Sema-2b-expressing axons to the ventromedial trajectory. In addition, Sema-2b/PlexB-mediated axon-axon interactions consolidate this trajectory choice and promote ventromedial axon-bundle formation. Selecting the correct developmental trajectory is ultimately essential for proper target choice. These findings demonstrate that Sema-2b couples ORN axon guidance to postsynaptic target neuron dendrite patterning well before the final target selection phase, and exemplify how a single guidance molecule can drive consecutive stages of neural circuit assembly with the help of sophisticated spatial and temporal regulation.","lang":"eng"}],"issue":"4","extern":"1","type":"journal_article","author":[{"full_name":"Joo, William J.","first_name":"William J.","last_name":"Joo"},{"full_name":"Sweeney, Lora Beatrice Jaeger","orcid":"0000-0001-9242-5601","id":"56BE8254-C4F0-11E9-8E45-0B23E6697425","last_name":"Sweeney","first_name":"Lora Beatrice Jaeger"},{"full_name":"Liang, Liang","last_name":"Liang","first_name":"Liang"},{"first_name":"Liqun","last_name":"Luo","full_name":"Luo, Liqun"}],"date_created":"2020-04-30T13:19:59Z","date_updated":"2024-01-31T10:15:25Z","oa_version":"None","volume":78,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"7785","year":"2013","status":"public","publication_status":"published","title":"Linking cell fate, trajectory choice, and target selection: Genetic analysis of sema-2b in olfactory axon targeting","publisher":"Elsevier","intvolume":" 78"},{"date_created":"2018-12-11T11:56:42Z","date_updated":"2024-03-20T08:31:49Z","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"5197","checksum":"37b61637b62fc079d9141c59d9f1a94f","date_created":"2018-12-12T10:16:11Z","date_updated":"2020-07-14T12:45:36Z","access_level":"open_access","file_name":"IST-2016-671-v1+1_796.pdf","content_type":"application/pdf","file_size":405870,"creator":"system"}],"author":[{"full_name":"Dziembowski, Stefan","first_name":"Stefan","last_name":"Dziembowski"},{"full_name":"Faust, Sebastian","first_name":"Sebastian","last_name":"Faust"},{"full_name":"Kolmogorov, Vladimir","first_name":"Vladimir","last_name":"Kolmogorov","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Krzysztof Z","last_name":"Pietrzak","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654","full_name":"Pietrzak, Krzysztof Z"}],"pubrep_id":"671","related_material":{"record":[{"relation":"later_version","status":"public","id":"1675"}]},"publication_status":"published","title":"Proofs of Space","status":"public","ddc":["530"],"publisher":"IST Austria","department":[{"_id":"VlKo"},{"_id":"KrPi"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2274","year":"2013","abstract":[{"lang":"eng","text":"Proofs of work (PoW) have been suggested by Dwork and Naor (Crypto'92) as protection to a shared resource. The basic idea is to ask the service requestor to dedicate some non-trivial amount of computational work to every request. The original applications included prevention of spam and protection against denial of service attacks. More recently, PoWs have been used to prevent double spending in the Bitcoin digital currency system.\r\n\r\nIn this work, we put forward an alternative concept for PoWs -- so-called proofs of space (PoS), where a service requestor must dedicate a significant amount of disk space as opposed to computation. We construct secure PoS schemes in the random oracle model, using graphs with high "pebbling complexity" and Merkle hash-trees. "}],"file_date_updated":"2020-07-14T12:45:36Z","publist_id":"4670","type":"report","language":[{"iso":"eng"}],"date_published":"2013-11-28T00:00:00Z","citation":{"chicago":"Dziembowski, Stefan, Sebastian Faust, Vladimir Kolmogorov, and Krzysztof Z Pietrzak. Proofs of Space. IST Austria, 2013.","mla":"Dziembowski, Stefan, et al. Proofs of Space. IST Austria, 2013.","short":"S. Dziembowski, S. Faust, V. Kolmogorov, K.Z. Pietrzak, Proofs of Space, IST Austria, 2013.","ista":"Dziembowski S, Faust S, Kolmogorov V, Pietrzak KZ. 2013. Proofs of Space, IST Austria,p.","apa":"Dziembowski, S., Faust, S., Kolmogorov, V., & Pietrzak, K. Z. (2013). Proofs of Space. IST Austria.","ieee":"S. Dziembowski, S. Faust, V. Kolmogorov, and K. Z. Pietrzak, Proofs of Space. IST Austria, 2013.","ama":"Dziembowski S, Faust S, Kolmogorov V, Pietrzak KZ. Proofs of Space. IST Austria; 2013."},"oa":1,"day":"28","month":"11","has_accepted_license":"1","scopus_import":1},{"keyword":["Molecular Biology","Biotechnology"],"scopus_import":"1","day":"20","article_processing_charge":"No","article_type":"original","publication":"Molecular BioSystems","citation":{"chicago":"Woehrmann, Marcos H., Walter M. Bray, James K. Durbin, Sean C. Nisam, Alicia K. Michael, Emerson Glassey, Joshua M. Stuart, and R. Scott Lokey. “Large-Scale Cytological Profiling for Functional Analysis of Bioactive Compounds.” Molecular BioSystems. Royal Society of Chemistry, 2013. https://doi.org/10.1039/c3mb70245f.","mla":"Woehrmann, Marcos H., et al. “Large-Scale Cytological Profiling for Functional Analysis of Bioactive Compounds.” Molecular BioSystems, vol. 9, no. 11, 2604, Royal Society of Chemistry, 2013, doi:10.1039/c3mb70245f.","short":"M.H. Woehrmann, W.M. Bray, J.K. Durbin, S.C. Nisam, A.K. Michael, E. Glassey, J.M. Stuart, R.S. Lokey, Molecular BioSystems 9 (2013).","ista":"Woehrmann MH, Bray WM, Durbin JK, Nisam SC, Michael AK, Glassey E, Stuart JM, Lokey RS. 2013. Large-scale cytological profiling for functional analysis of bioactive compounds. Molecular BioSystems. 9(11), 2604.","ieee":"M. H. Woehrmann et al., “Large-scale cytological profiling for functional analysis of bioactive compounds,” Molecular BioSystems, vol. 9, no. 11. Royal Society of Chemistry, 2013.","apa":"Woehrmann, M. H., Bray, W. M., Durbin, J. K., Nisam, S. C., Michael, A. K., Glassey, E., … Lokey, R. S. (2013). Large-scale cytological profiling for functional analysis of bioactive compounds. Molecular BioSystems. Royal Society of Chemistry. https://doi.org/10.1039/c3mb70245f","ama":"Woehrmann MH, Bray WM, Durbin JK, et al. Large-scale cytological profiling for functional analysis of bioactive compounds. Molecular BioSystems. 2013;9(11). doi:10.1039/c3mb70245f"},"date_published":"2013-08-20T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"Cytological profiling (CP) is an unbiased image-based screening technique that uses automated microscopy and image analysis to profile compounds based on numerous quantifiable phenotypic features. We used CP to evaluate a library of nearly 500 compounds with documented mechanisms of action (MOAs) spanning a wide range of biological pathways. We developed informatics techniques for generating dosage-independent phenotypic “fingerprints” for each compound, and for quantifying the likelihood that a compound's CP fingerprint corresponds to its annotated MOA. We identified groups of features that distinguish classes with closely related phenotypes, such as microtubule poisons vs. HSP90 inhibitors, and DNA synthesis vs. proteasome inhibitors. We tested several cases in which cytological profiles indicated novel mechanisms, including a tyrphostin kinase inhibitor involved in mitochondrial uncoupling, novel microtubule poisons, and a nominal PPAR-gamma ligand that acts as a proteasome inhibitor, using independent biochemical assays to confirm the MOAs predicted by the CP signatures. We also applied maximal-information statistics to identify correlations between cytological features and kinase inhibitory activities by combining the CP fingerprints of 24 kinase inhibitors with published data on their specificities against a diverse panel of kinases. The resulting analysis suggests a strategy for probing the biological functions of specific kinases by compiling cytological data from inhibitors of varying specificities."}],"issue":"11","title":"Large-scale cytological profiling for functional analysis of bioactive compounds","status":"public","intvolume":" 9","_id":"15162","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"None","month":"08","publication_identifier":{"eissn":["1742-2051"],"issn":["1742-206X"]},"quality_controlled":"1","language":[{"iso":"eng"}],"doi":"10.1039/c3mb70245f","article_number":"2604","extern":"1","publication_status":"published","publisher":"Royal Society of Chemistry","year":"2013","date_created":"2024-03-21T07:58:57Z","date_updated":"2024-03-25T11:45:46Z","volume":9,"author":[{"full_name":"Woehrmann, Marcos H.","first_name":"Marcos H.","last_name":"Woehrmann"},{"full_name":"Bray, Walter M.","first_name":"Walter M.","last_name":"Bray"},{"full_name":"Durbin, James K.","first_name":"James K.","last_name":"Durbin"},{"first_name":"Sean C.","last_name":"Nisam","full_name":"Nisam, Sean C."},{"last_name":"Michael","first_name":"Alicia Kathleen","id":"6437c950-2a03-11ee-914d-d6476dd7b75c","full_name":"Michael, Alicia Kathleen"},{"first_name":"Emerson","last_name":"Glassey","full_name":"Glassey, Emerson"},{"full_name":"Stuart, Joshua M.","first_name":"Joshua M.","last_name":"Stuart"},{"last_name":"Lokey","first_name":"R. Scott","full_name":"Lokey, R. Scott"}]},{"article_processing_charge":"No","day":"31","keyword":["general physics and astronomy"],"scopus_import":"1","date_published":"2012-10-31T00:00:00Z","article_type":"original","citation":{"ama":"Šarić A, Cacciuto A. Mechanism of membrane tube formation induced by adhesive nanocomponents. Physical Review Letters. 2012;109(18). doi:10.1103/physrevlett.109.188101","apa":"Šarić, A., & Cacciuto, A. (2012). Mechanism of membrane tube formation induced by adhesive nanocomponents. Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.109.188101","ieee":"A. Šarić and A. Cacciuto, “Mechanism of membrane tube formation induced by adhesive nanocomponents,” Physical Review Letters, vol. 109, no. 18. American Physical Society, 2012.","ista":"Šarić A, Cacciuto A. 2012. Mechanism of membrane tube formation induced by adhesive nanocomponents. Physical Review Letters. 109(18), 188101.","short":"A. Šarić, A. Cacciuto, Physical Review Letters 109 (2012).","mla":"Šarić, Anđela, and Angelo Cacciuto. “Mechanism of Membrane Tube Formation Induced by Adhesive Nanocomponents.” Physical Review Letters, vol. 109, no. 18, 188101, American Physical Society, 2012, doi:10.1103/physrevlett.109.188101.","chicago":"Šarić, Anđela, and Angelo Cacciuto. “Mechanism of Membrane Tube Formation Induced by Adhesive Nanocomponents.” Physical Review Letters. American Physical Society, 2012. https://doi.org/10.1103/physrevlett.109.188101."},"publication":"Physical Review Letters","issue":"18","abstract":[{"text":"We report numerical simulations of membrane tubulation driven by large colloidal particles. Using Monte Carlo simulations we study how the process depends on particle size and binding strength, and present accurate free energy calculations to sort out how tube formation compares with the competing budding process. We find that tube formation is a result of the collective behavior of the particles adhering on the surface, and it occurs for binding strengths that are smaller than those required for budding. We also find that long linear aggregates of particles forming on the membrane surface act as nucleation seeds for tubulation by lowering the free energy barrier associated to the process.","lang":"eng"}],"type":"journal_article","oa_version":"Preprint","intvolume":" 109","status":"public","title":"Mechanism of membrane tube formation induced by adhesive nanocomponents","_id":"10387","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]},"month":"10","language":[{"iso":"eng"}],"doi":"10.1103/physrevlett.109.188101","quality_controlled":"1","external_id":{"pmid":["23215334"],"arxiv":["1206.3528"]},"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1206.3528","open_access":"1"}],"extern":"1","article_number":"188101","volume":109,"date_created":"2021-11-29T14:08:00Z","date_updated":"2021-11-29T14:29:25Z","author":[{"full_name":"Šarić, Anđela","last_name":"Šarić","first_name":"Anđela","orcid":"0000-0002-7854-2139","id":"bf63d406-f056-11eb-b41d-f263a6566d8b"},{"last_name":"Cacciuto","first_name":"Angelo","full_name":"Cacciuto, Angelo"}],"publisher":"American Physical Society","publication_status":"published","pmid":1,"year":"2012"},{"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"10388","status":"public","title":"Fluid membranes can drive linear aggregation of adsorbed spherical nanoparticles","intvolume":" 108","oa_version":"Preprint","type":"journal_article","abstract":[{"lang":"eng","text":"Using computer simulations, we show that lipid membranes can mediate linear aggregation of spherical nanoparticles binding to it for a wide range of biologically relevant bending rigidities. This result is in net contrast with the isotropic aggregation of nanoparticles on fluid interfaces or the expected clustering of isotropic insertions in biological membranes. We present a phase diagram indicating where linear aggregation is expected and compute explicitly the free-energy barriers associated with linear and isotropic aggregation. Finally, we provide simple scaling arguments to explain this phenomenology."}],"issue":"11","publication":"Physical Review Letters","citation":{"mla":"Šarić, Anđela, and Angelo Cacciuto. “Fluid Membranes Can Drive Linear Aggregation of Adsorbed Spherical Nanoparticles.” Physical Review Letters, vol. 108, no. 11, 118101, American Physical Society, 2012, doi:10.1103/physrevlett.108.118101.","short":"A. Šarić, A. Cacciuto, Physical Review Letters 108 (2012).","chicago":"Šarić, Anđela, and Angelo Cacciuto. “Fluid Membranes Can Drive Linear Aggregation of Adsorbed Spherical Nanoparticles.” Physical Review Letters. American Physical Society, 2012. https://doi.org/10.1103/physrevlett.108.118101.","ama":"Šarić A, Cacciuto A. Fluid membranes can drive linear aggregation of adsorbed spherical nanoparticles. Physical Review Letters. 2012;108(11). doi:10.1103/physrevlett.108.118101","ista":"Šarić A, Cacciuto A. 2012. Fluid membranes can drive linear aggregation of adsorbed spherical nanoparticles. Physical Review Letters. 108(11), 118101.","apa":"Šarić, A., & Cacciuto, A. (2012). Fluid membranes can drive linear aggregation of adsorbed spherical nanoparticles. Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.108.118101","ieee":"A. Šarić and A. Cacciuto, “Fluid membranes can drive linear aggregation of adsorbed spherical nanoparticles,” Physical Review Letters, vol. 108, no. 11. American Physical Society, 2012."},"article_type":"original","date_published":"2012-03-14T00:00:00Z","scopus_import":"1","keyword":["general physics and astronomy"],"day":"14","article_processing_charge":"No","acknowledgement":"This work was supported by the National Science Foundation under Career Grant No. DMR-0846426.\r\n","year":"2012","pmid":1,"publication_status":"published","publisher":"American Physical Society","author":[{"full_name":"Šarić, Anđela","last_name":"Šarić","first_name":"Anđela","orcid":"0000-0002-7854-2139","id":"bf63d406-f056-11eb-b41d-f263a6566d8b"},{"full_name":"Cacciuto, Angelo","last_name":"Cacciuto","first_name":"Angelo"}],"date_updated":"2021-11-29T15:12:13Z","date_created":"2021-11-29T14:30:05Z","volume":108,"article_number":"118101","extern":"1","external_id":{"arxiv":["1201.0036"],"pmid":["22540513"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1201.0036"}],"quality_controlled":"1","doi":"10.1103/physrevlett.108.118101","language":[{"iso":"eng"}],"month":"03","publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]}},{"author":[{"last_name":"Erne","first_name":"Barbara","full_name":"Erne, Barbara"},{"full_name":"Graff, Mareike","last_name":"Graff","first_name":"Mareike"},{"full_name":"Klemm, Wolfram","last_name":"Klemm","first_name":"Wolfram"},{"id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8559-3973","first_name":"Johann G","last_name":"Danzl","full_name":"Danzl, Johann G"},{"last_name":"Leschber","first_name":"Gunda","full_name":"Leschber, Gunda"}],"oa_version":"None","volume":380,"date_updated":"2021-01-12T06:47:57Z","date_created":"2018-12-11T11:49:54Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1055","year":"2012","acknowledgement":"We thank the interdisciplinary team at the ELK Berlin Chest Hospital.","publisher":"Elsevier","intvolume":" 380","title":"Bulla in the lung","publication_status":"published","status":"public","publist_id":"6333","issue":"9849","abstract":[{"text":"In July, 2011, a 32-year-old man presented with thoracic pain radiating to the left arm and upper dorsum, shortness of breath, and palpitations. He had had upper back tension for 6 months. Medical history was unremarkable apart from moderate nicotine use (two pack-years). Echocardiography, electrocardiography, and laboratory tests were unremarkable, excluding a cardiac event. CT of the chest after chest radiography showed a large bulla of 16 cm diameter in the right hemithorax (figure A). We did not detect radiological evidence of underlying pulmonary disease. The bulla wall was unremarkable and no structures were seen within the bulla.","lang":"eng"}],"extern":"1","type":"journal_article","date_published":"2012-10-01T00:00:00Z","doi":"10.1016/S0140-6736(12)60690-4","language":[{"iso":"eng"}],"citation":{"ieee":"B. Erne, M. Graff, W. Klemm, J. G. Danzl, and G. Leschber, “Bulla in the lung,” The Lancet, vol. 380, no. 9849. Elsevier, 2012.","apa":"Erne, B., Graff, M., Klemm, W., Danzl, J. G., & Leschber, G. (2012). Bulla in the lung. The Lancet. Elsevier. https://doi.org/10.1016/S0140-6736(12)60690-4","ista":"Erne B, Graff M, Klemm W, Danzl JG, Leschber G. 2012. Bulla in the lung. The Lancet. 380(9849).","ama":"Erne B, Graff M, Klemm W, Danzl JG, Leschber G. Bulla in the lung. The Lancet. 2012;380(9849). doi:10.1016/S0140-6736(12)60690-4","chicago":"Erne, Barbara, Mareike Graff, Wolfram Klemm, Johann G Danzl, and Gunda Leschber. “Bulla in the Lung.” The Lancet. Elsevier, 2012. https://doi.org/10.1016/S0140-6736(12)60690-4.","short":"B. Erne, M. Graff, W. Klemm, J.G. Danzl, G. Leschber, The Lancet 380 (2012).","mla":"Erne, Barbara, et al. “Bulla in the Lung.” The Lancet, vol. 380, no. 9849, Elsevier, 2012, doi:10.1016/S0140-6736(12)60690-4."},"publication":"The Lancet","article_processing_charge":"No","month":"10","day":"01"},{"article_processing_charge":"No","month":"05","day":"25","external_id":{"arxiv":["1201.1008"]},"citation":{"apa":"Mark, M., Haller, E., Lauber, K., Danzl, J. G., Janisch, A., Büchler, H., … Nägerl, H. (2012). Preparation and spectroscopy of a metastable mott-insulator state with attractive interactions. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.108.215302","ieee":"M. Mark et al., “Preparation and spectroscopy of a metastable mott-insulator state with attractive interactions,” Physical Review Letters, vol. 108, no. 21. American Physical Society, 2012.","ista":"Mark M, Haller E, Lauber K, Danzl JG, Janisch A, Büchler H, Daley A, Nägerl H. 2012. Preparation and spectroscopy of a metastable mott-insulator state with attractive interactions. Physical Review Letters. 108(21).","ama":"Mark M, Haller E, Lauber K, et al. Preparation and spectroscopy of a metastable mott-insulator state with attractive interactions. Physical Review Letters. 2012;108(21). doi:10.1103/PhysRevLett.108.215302","chicago":"Mark, Manfred, Elmar Haller, Katharina Lauber, Johann G Danzl, Alexander Janisch, Hans Büchler, Andrew Daley, and Hanns Nägerl. “Preparation and Spectroscopy of a Metastable Mott-Insulator State with Attractive Interactions.” Physical Review Letters. American Physical Society, 2012. https://doi.org/10.1103/PhysRevLett.108.215302.","short":"M. Mark, E. Haller, K. Lauber, J.G. Danzl, A. Janisch, H. Büchler, A. Daley, H. Nägerl, Physical Review Letters 108 (2012).","mla":"Mark, Manfred, et al. “Preparation and Spectroscopy of a Metastable Mott-Insulator State with Attractive Interactions.” Physical Review Letters, vol. 108, no. 21, American Physical Society, 2012, doi:10.1103/PhysRevLett.108.215302."},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1201.1008"}],"oa":1,"publication":"Physical Review Letters","language":[{"iso":"eng"}],"date_published":"2012-05-25T00:00:00Z","doi":"10.1103/PhysRevLett.108.215302","type":"journal_article","extern":"1","publist_id":"6334","issue":"21","abstract":[{"text":"We prepare and study a metastable attractive Mott-insulator state formed with bosonic atoms in a three-dimensional optical lattice. Starting from a Mott insulator with Cs atoms at weak repulsive interactions, we use a magnetic Feshbach resonance to tune the interactions to large attractive values and produce a metastable state pinned by attractive interactions with a lifetime on the order of 10 s. We probe the (de)excitation spectrum via lattice modulation spectroscopy, measuring the interaction dependence of two- and three-body bound-state energies. As a result of increased on-site three-body loss we observe resonance broadening and suppression of tunneling processes that produce three-body occupation.","lang":"eng"}],"intvolume":" 108","publisher":"American Physical Society","publication_status":"published","title":"Preparation and spectroscopy of a metastable mott-insulator state with attractive interactions","status":"public","_id":"1056","acknowledgement":"We are indebted to R. Grimm for generous support. We thank J. von Stecher, P. Johnson, and E. Tiesinga for fruitful discussions. We gratefully acknowledge funding by the Austrian Science Fund (FWF) within Project No. I153-N16 and within the framework of the European Science Foundation (ESF) EuroQUASAR collective research project QuDeGPM, and by the European Research Council (ERC) under Project No. 278417.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2012","volume":108,"oa_version":"Preprint","date_created":"2018-12-11T11:49:55Z","date_updated":"2021-01-12T06:47:58Z","author":[{"first_name":"Manfred","last_name":"Mark","full_name":"Mark, Manfred"},{"full_name":"Haller, Elmar","last_name":"Haller","first_name":"Elmar"},{"full_name":"Lauber, Katharina","last_name":"Lauber","first_name":"Katharina"},{"full_name":"Danzl, Johann G","first_name":"Johann G","last_name":"Danzl","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8559-3973"},{"first_name":"Alexander","last_name":"Janisch","full_name":"Janisch, Alexander"},{"full_name":"Büchler, Hans","last_name":"Büchler","first_name":"Hans"},{"full_name":"Daley, Andrew","first_name":"Andrew","last_name":"Daley"},{"last_name":"Nägerl","first_name":"Hanns","full_name":"Nägerl, Hanns"}]},{"extern":"1","article_number":"X21.00008","author":[{"full_name":"Polshyn, Hryhoriy","first_name":"Hryhoriy","last_name":"Polshyn","id":"edfc7cb1-526e-11ec-b05a-e6ecc27e4e48","orcid":"0000-0001-8223-8896"},{"full_name":"Budakian, Raffi","last_name":"Budakian","first_name":"Raffi"}],"date_created":"2022-02-08T10:39:08Z","date_updated":"2022-02-08T10:48:01Z","volume":57,"acknowledgement":"This work was supported by the Center for Emergent Superconductivity, an Energy Frontier Research Center funded by the U.S. DOE, Office of Science, under Award No. DE-AC0298CH1088.","year":"2012","publication_status":"published","publisher":"American Physical Society","month":"02","publication_identifier":{"issn":["0003-0503"]},"conference":{"name":"APS: American Physical Society","start_date":"2012-02-27","location":"Boston, MA, United States","end_date":"2012-03-02"},"language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"url":"https://meetings.aps.org/Meeting/MAR12/Event/167014","open_access":"1"}],"quality_controlled":"1","abstract":[{"text":"The goal of this work is to study the superconducting coherence length in the fluctuation regime in cuprate superconductors. In this work we present cantilever torque magnetometry measurements of micron-size BSCCO flakes patterned with arrays of nanometer scale rings or holes. Using ultrasensitive dynamic torque magnetometry, oscillations in magnetization are observed near Tc as a function of the applied magnetic flux threading the array. Special effort was made to detect the oscillations in magnetization at temperatures above Tc, where the Nernst effect and magnetization measurements suggest the possibility of pairing. To constrain the magnitude of the coherence length in the fluctuation regime, we will present the dependence of the amplitude of the h/2e period oscillations as a function of temperature and hole size.","lang":"eng"}],"issue":"1","type":"conference","alternative_title":["Bulletin of the American Physical Society"],"oa_version":"Published Version","_id":"10750","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","status":"public","title":"Cantilever torque magnetometry study of multiply connected BSCCO arrays near Tc","intvolume":" 57","day":"01","article_processing_charge":"No","date_published":"2012-02-01T00:00:00Z","publication":"APS March Meeting 2012","citation":{"short":"H. Polshyn, R. Budakian, in:, APS March Meeting 2012, American Physical Society, 2012.","mla":"Polshyn, Hryhoriy, and Raffi Budakian. “Cantilever Torque Magnetometry Study of Multiply Connected BSCCO Arrays near Tc.” APS March Meeting 2012, vol. 57, no. 1, X21.00008, American Physical Society, 2012.","chicago":"Polshyn, Hryhoriy, and Raffi Budakian. “Cantilever Torque Magnetometry Study of Multiply Connected BSCCO Arrays near Tc.” In APS March Meeting 2012, Vol. 57. American Physical Society, 2012.","ama":"Polshyn H, Budakian R. Cantilever torque magnetometry study of multiply connected BSCCO arrays near Tc. In: APS March Meeting 2012. Vol 57. American Physical Society; 2012.","ieee":"H. Polshyn and R. Budakian, “Cantilever torque magnetometry study of multiply connected BSCCO arrays near Tc,” in APS March Meeting 2012, Boston, MA, United States, 2012, vol. 57, no. 1.","apa":"Polshyn, H., & Budakian, R. (2012). Cantilever torque magnetometry study of multiply connected BSCCO arrays near Tc. In APS March Meeting 2012 (Vol. 57). Boston, MA, United States: American Physical Society.","ista":"Polshyn H, Budakian R. 2012. Cantilever torque magnetometry study of multiply connected BSCCO arrays near Tc. APS March Meeting 2012. APS: American Physical Society, Bulletin of the American Physical Society, vol. 57, X21.00008."}}]