[{"day":"11","month":"04","publication_identifier":{"issn":["2664-1690"]},"has_accepted_license":"1","date_published":"2011-04-11T00:00:00Z","doi":"10.15479/AT:IST-2011-0004","language":[{"iso":"eng"}],"oa":1,"citation":{"short":"K. Chatterjee, M. Tracol, Decidable Problems for Probabilistic Automata on Infinite Words, IST Austria, 2011.","mla":"Chatterjee, Krishnendu, and Mathieu Tracol. Decidable Problems for Probabilistic Automata on Infinite Words. IST Austria, 2011, doi:10.15479/AT:IST-2011-0004.","chicago":"Chatterjee, Krishnendu, and Mathieu Tracol. Decidable Problems for Probabilistic Automata on Infinite Words. IST Austria, 2011. https://doi.org/10.15479/AT:IST-2011-0004.","ama":"Chatterjee K, Tracol M. Decidable Problems for Probabilistic Automata on Infinite Words. IST Austria; 2011. doi:10.15479/AT:IST-2011-0004","apa":"Chatterjee, K., & Tracol, M. (2011). Decidable problems for probabilistic automata on infinite words. IST Austria. https://doi.org/10.15479/AT:IST-2011-0004","ieee":"K. Chatterjee and M. Tracol, Decidable problems for probabilistic automata on infinite words. IST Austria, 2011.","ista":"Chatterjee K, Tracol M. 2011. Decidable problems for probabilistic automata on infinite words, IST Austria, 30p."},"page":"30","abstract":[{"lang":"eng","text":"We consider probabilistic automata on infinite words with acceptance defined by parity conditions. We consider three qualitative decision problems: (i) the positive decision problem asks whether there is a word that is accepted with positive probability; (ii) the almost decision problem asks whether there is a word that is accepted with probability 1; and (iii) the limit decision problem asks whether for every ε > 0 there is a word that is accepted with probability at least 1 − ε. We unify and generalize several decidability results for probabilistic automata over infinite words, and identify a robust (closed under union and intersection) subclass of probabilistic automata for which all the qualitative decision problems are decidable for parity conditions. We also show that if the input words are restricted to lasso shape words, then the positive and almost problems are decidable for all probabilistic automata with parity conditions."}],"file_date_updated":"2020-07-14T12:46:40Z","type":"technical_report","alternative_title":["IST Austria Technical Report"],"author":[{"first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"full_name":"Tracol, Mathieu","id":"3F54FA38-F248-11E8-B48F-1D18A9856A87","last_name":"Tracol","first_name":"Mathieu"}],"related_material":{"record":[{"relation":"later_version","status":"public","id":"2957"}]},"pubrep_id":"20","date_updated":"2023-02-23T11:05:53Z","date_created":"2018-12-12T11:39:01Z","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"IST-2011-004_IST-2011-0004.pdf","content_type":"application/pdf","file_size":570827,"creator":"system","relation":"main_file","file_id":"5545","checksum":"f5a0f664fadc335990f5fcf138df19f1","date_created":"2018-12-12T11:54:23Z","date_updated":"2020-07-14T12:46:40Z"}],"_id":"5384","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2011","title":"Decidable problems for probabilistic automata on infinite words","publication_status":"published","ddc":["000","005"],"status":"public","publisher":"IST Austria","department":[{"_id":"KrCh"}]},{"scopus_import":"1","month":"07","day":"22","article_processing_charge":"No","publication_identifier":{"eisbn":["978-1-4577-0395-9"],"isbn":["978-1-4577-0394-2"]},"quality_controlled":"1","page":"2089 - 2096","publication":"CVPR: Computer Vision and Pattern Recognition","citation":{"mla":"Chen, Chao, et al. “Enforcing Topological Constraints in Random Field Image Segmentation.” CVPR: Computer Vision and Pattern Recognition, IEEE, 2011, pp. 2089–96, doi:10.1109/CVPR.2011.5995503.","short":"C. Chen, D. Freedman, C. Lampert, in:, CVPR: Computer Vision and Pattern Recognition, IEEE, 2011, pp. 2089–2096.","chicago":"Chen, Chao, Daniel Freedman, and Christoph Lampert. “Enforcing Topological Constraints in Random Field Image Segmentation.” In CVPR: Computer Vision and Pattern Recognition, 2089–96. IEEE, 2011. https://doi.org/10.1109/CVPR.2011.5995503.","ama":"Chen C, Freedman D, Lampert C. Enforcing topological constraints in random field image segmentation. In: CVPR: Computer Vision and Pattern Recognition. IEEE; 2011:2089-2096. doi:10.1109/CVPR.2011.5995503","ista":"Chen C, Freedman D, Lampert C. 2011. Enforcing topological constraints in random field image segmentation. CVPR: Computer Vision and Pattern Recognition. CVPR: Conference on Computer Vision and Pattern Recognition, 2089–2096.","apa":"Chen, C., Freedman, D., & Lampert, C. (2011). Enforcing topological constraints in random field image segmentation. In CVPR: Computer Vision and Pattern Recognition (pp. 2089–2096). Colorado Springs, CO, United States: IEEE. https://doi.org/10.1109/CVPR.2011.5995503","ieee":"C. Chen, D. Freedman, and C. Lampert, “Enforcing topological constraints in random field image segmentation,” in CVPR: Computer Vision and Pattern Recognition, Colorado Springs, CO, United States, 2011, pp. 2089–2096."},"language":[{"iso":"eng"}],"conference":{"end_date":"2011-06-25","location":"Colorado Springs, CO, United States","start_date":"2011-06-20","name":"CVPR: Conference on Computer Vision and Pattern Recognition"},"date_published":"2011-07-22T00:00:00Z","doi":"10.1109/CVPR.2011.5995503","type":"conference","abstract":[{"text":"We introduce TopoCut: a new way to integrate knowledge about topological properties (TPs) into random field image segmentation model. Instead of including TPs as additional constraints during minimization of the energy function, we devise an efficient algorithm for modifying the unary potentials such that the resulting segmentation is guaranteed with the desired properties. Our method is more flexible in the sense that it handles more topology constraints than previous methods, which were only able to enforce pairwise or global connectivity. In particular, our method is very fast, making it for the first time possible to enforce global topological properties in practical image segmentation tasks.","lang":"eng"}],"publist_id":"3294","status":"public","publication_status":"published","title":"Enforcing topological constraints in random field image segmentation","department":[{"_id":"HeEd"},{"_id":"ChLa"}],"publisher":"IEEE","_id":"3336","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2011","acknowledgement":"The first author is supported by the Austrian Science Fund (FWF) grant No. P20134-N13. The authors would like to thank Sebastian Nowozin for helpful discussions.","date_updated":"2023-02-23T12:23:56Z","date_created":"2018-12-11T12:02:45Z","oa_version":"None","author":[{"last_name":"Chen","first_name":"Chao","id":"3E92416E-F248-11E8-B48F-1D18A9856A87","full_name":"Chen, Chao"},{"full_name":"Freedman, Daniel","first_name":"Daniel","last_name":"Freedman"},{"full_name":"Lampert, Christoph","last_name":"Lampert","first_name":"Christoph","orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"id":"5386","relation":"earlier_version","status":"public"}]}},{"oa_version":"None","volume":6803,"date_created":"2018-12-11T12:02:40Z","date_updated":"2023-02-23T12:23:48Z","related_material":{"record":[{"id":"5383","status":"public","relation":"earlier_version"}]},"author":[{"full_name":"Wies, Thomas","last_name":"Wies","first_name":"Thomas","id":"447BFB88-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Muñiz, Marco","last_name":"Muñiz","first_name":"Marco"},{"last_name":"Kuncak","first_name":"Viktor","full_name":"Kuncak, Viktor"}],"department":[{"_id":"ToHe"}],"intvolume":" 6803","publisher":"Springer","publication_status":"published","status":"public","title":"An efficient decision procedure for imperative tree data structures","_id":"3323","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","year":"2011","publist_id":"3312","abstract":[{"text":"We present a new decidable logic called TREX for expressing constraints about imperative tree data structures. In particular, TREX supports a transitive closure operator that can express reachability constraints, which often appear in data structure invariants. We show that our logic is closed under weakest precondition computation, which enables its use for automated software verification. We further show that satisfiability of formulas in TREX is decidable in NP. The low complexity makes it an attractive alternative to more expensive logics such as monadic second-order logic (MSOL) over trees, which have been traditionally used for reasoning about tree data structures.","lang":"eng"}],"alternative_title":["LNAI "],"type":"conference","language":[{"iso":"eng"}],"doi":"10.1007/978-3-642-22438-6_36","date_published":"2011-07-19T00:00:00Z","conference":{"name":"CADE 23: Automated Deduction ","location":"Wrocław, Poland","start_date":"2011-07-31","end_date":"2011-08-05"},"page":"476 - 491","quality_controlled":"1","citation":{"ista":"Wies T, Muñiz M, Kuncak V. 2011. An efficient decision procedure for imperative tree data structures. CADE 23: Automated Deduction , LNAI , vol. 6803, 476–491.","apa":"Wies, T., Muñiz, M., & Kuncak, V. (2011). An efficient decision procedure for imperative tree data structures (Vol. 6803, pp. 476–491). Presented at the CADE 23: Automated Deduction , Wrocław, Poland: Springer. https://doi.org/10.1007/978-3-642-22438-6_36","ieee":"T. Wies, M. Muñiz, and V. Kuncak, “An efficient decision procedure for imperative tree data structures,” presented at the CADE 23: Automated Deduction , Wrocław, Poland, 2011, vol. 6803, pp. 476–491.","ama":"Wies T, Muñiz M, Kuncak V. An efficient decision procedure for imperative tree data structures. In: Vol 6803. Springer; 2011:476-491. doi:10.1007/978-3-642-22438-6_36","chicago":"Wies, Thomas, Marco Muñiz, and Viktor Kuncak. “An Efficient Decision Procedure for Imperative Tree Data Structures,” 6803:476–91. Springer, 2011. https://doi.org/10.1007/978-3-642-22438-6_36.","mla":"Wies, Thomas, et al. An Efficient Decision Procedure for Imperative Tree Data Structures. Vol. 6803, Springer, 2011, pp. 476–91, doi:10.1007/978-3-642-22438-6_36.","short":"T. Wies, M. Muñiz, V. Kuncak, in:, Springer, 2011, pp. 476–491."},"day":"19","month":"07","scopus_import":1},{"project":[{"call_identifier":"FP7","name":"Quantitative Reactive Modeling","grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425"},{"grant_number":"S11402-N23","_id":"25F5A88A-B435-11E9-9278-68D0E5697425","name":"Moderne Concurrency Paradigms","call_identifier":"FWF"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"},{"call_identifier":"FP7","name":"Design for Embedded Systems","grant_number":"214373","_id":"25F1337C-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","oa":1,"language":[{"iso":"eng"}],"doi":"10.1007/978-3-642-22110-1_20","conference":{"location":"Snowbird, USA","start_date":"2011-07-14","end_date":"2011-07-20","name":"CAV: Computer Aided Verification"},"month":"04","publisher":"Springer","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"editor":[{"first_name":"Ganesh","last_name":"Gopalakrishnan","full_name":"Gopalakrishnan, Ganesh"},{"last_name":"Qadeer","first_name":"Shaz","full_name":"Qadeer, Shaz"}],"publication_status":"published","year":"2011","volume":6806,"date_created":"2018-12-11T12:02:55Z","date_updated":"2023-02-23T12:24:01Z","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"5388"}]},"author":[{"id":"4DCBEFFE-F248-11E8-B48F-1D18A9856A87","last_name":"Cerny","first_name":"Pavol","full_name":"Cerny, Pavol"},{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A"},{"last_name":"Radhakrishna","first_name":"Arjun","id":"3B51CAC4-F248-11E8-B48F-1D18A9856A87","full_name":"Radhakrishna, Arjun"},{"first_name":"Rohit","last_name":"Singh","full_name":"Singh, Rohit"}],"publist_id":"3247","ec_funded":1,"file_date_updated":"2020-07-14T12:46:10Z","page":"243 - 259","citation":{"ama":"Cerny P, Chatterjee K, Henzinger TA, Radhakrishna A, Singh R. Quantitative synthesis for concurrent programs. In: Gopalakrishnan G, Qadeer S, eds. Vol 6806. Springer; 2011:243-259. doi:10.1007/978-3-642-22110-1_20","ieee":"P. Cerny, K. Chatterjee, T. A. Henzinger, A. Radhakrishna, and R. Singh, “Quantitative synthesis for concurrent programs,” presented at the CAV: Computer Aided Verification, Snowbird, USA, 2011, vol. 6806, pp. 243–259.","apa":"Cerny, P., Chatterjee, K., Henzinger, T. A., Radhakrishna, A., & Singh, R. (2011). Quantitative synthesis for concurrent programs. In G. Gopalakrishnan & S. Qadeer (Eds.) (Vol. 6806, pp. 243–259). Presented at the CAV: Computer Aided Verification, Snowbird, USA: Springer. https://doi.org/10.1007/978-3-642-22110-1_20","ista":"Cerny P, Chatterjee K, Henzinger TA, Radhakrishna A, Singh R. 2011. Quantitative synthesis for concurrent programs. CAV: Computer Aided Verification, LNCS, vol. 6806, 243–259.","short":"P. Cerny, K. Chatterjee, T.A. Henzinger, A. Radhakrishna, R. Singh, in:, G. Gopalakrishnan, S. Qadeer (Eds.), Springer, 2011, pp. 243–259.","mla":"Cerny, Pavol, et al. Quantitative Synthesis for Concurrent Programs. Edited by Ganesh Gopalakrishnan and Shaz Qadeer, vol. 6806, Springer, 2011, pp. 243–59, doi:10.1007/978-3-642-22110-1_20.","chicago":"Cerny, Pavol, Krishnendu Chatterjee, Thomas A Henzinger, Arjun Radhakrishna, and Rohit Singh. “Quantitative Synthesis for Concurrent Programs.” edited by Ganesh Gopalakrishnan and Shaz Qadeer, 6806:243–59. Springer, 2011. https://doi.org/10.1007/978-3-642-22110-1_20."},"date_published":"2011-04-21T00:00:00Z","has_accepted_license":"1","article_processing_charge":"No","day":"21","intvolume":" 6806","ddc":["000","004"],"title":"Quantitative synthesis for concurrent programs","status":"public","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"3366","oa_version":"Submitted Version","file":[{"date_created":"2018-12-12T10:15:51Z","date_updated":"2020-07-14T12:46:10Z","checksum":"c033689355f45742dc7c99b5af13ce7a","file_id":"5174","relation":"main_file","creator":"system","file_size":508946,"content_type":"application/pdf","file_name":"IST-2012-76-v1+1_Quantitative_synthesis_for_concurrent_programs.pdf","access_level":"open_access"}],"pubrep_id":"76","alternative_title":["LNCS"],"type":"conference","abstract":[{"lang":"eng","text":"We present an algorithmic method for the quantitative, performance-aware synthesis of concurrent programs. The input consists of a nondeterministic partial program and of a parametric performance model. The nondeterminism allows the programmer to omit which (if any) synchronization construct is used at a particular program location. The performance model, specified as a weighted automaton, can capture system architectures by assigning different costs to actions such as locking, context switching, and memory and cache accesses. The quantitative synthesis problem is to automatically resolve the nondeterminism of the partial program so that both correctness is guaranteed and performance is optimal. As is standard for shared memory concurrency, correctness is formalized "specification free", in particular as race freedom or deadlock freedom. For worst-case (average-case) performance, we show that the problem can be reduced to 2-player graph games (with probabilistic transitions) with quantitative objectives. While we show, using game-theoretic methods, that the synthesis problem is Nexp-complete, we present an algorithmic method and an implementation that works efficiently for concurrent programs and performance models of practical interest. We have implemented a prototype tool and used it to synthesize finite-state concurrent programs that exhibit different programming patterns, for several performance models representing different architectures. 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In system design, the parity objective is used to encode ω-regular specifications, and the mean-payoff and energy objectives can be used to model quantitative resource constraints. The energy condition re- quires that the resource level never drops below 0, and the mean-payoff condi- tion requires that the limit-average value of the resource consumption is within a threshold. While these two (energy and mean-payoff) classical conditions are equivalent for two-player games, we show that they differ for MDPs. We show that the problem of deciding whether a state is almost-sure winning (i.e., winning with probability 1) in energy parity MDPs is in NP ∩ coNP, while for mean- payoff parity MDPs, the problem is solvable in polynomial time, improving a recent PSPACE bound."}],"citation":{"ama":"Chatterjee K, Doyen L. Energy and mean-payoff parity Markov Decision Processes. In: Vol 6907. Springer; 2011:206-218. doi:10.1007/978-3-642-22993-0_21","ieee":"K. Chatterjee and L. Doyen, “Energy and mean-payoff parity Markov Decision Processes,” presented at the MFCS: Mathematical Foundations of Computer Science, Warsaw, Poland, 2011, vol. 6907, pp. 206–218.","apa":"Chatterjee, K., & Doyen, L. (2011). Energy and mean-payoff parity Markov Decision Processes (Vol. 6907, pp. 206–218). Presented at the MFCS: Mathematical Foundations of Computer Science, Warsaw, Poland: Springer. https://doi.org/10.1007/978-3-642-22993-0_21","ista":"Chatterjee K, Doyen L. 2011. Energy and mean-payoff parity Markov Decision Processes. MFCS: Mathematical Foundations of Computer Science, LNCS, vol. 6907, 206–218.","short":"K. Chatterjee, L. Doyen, in:, Springer, 2011, pp. 206–218.","mla":"Chatterjee, Krishnendu, and Laurent Doyen. Energy and Mean-Payoff Parity Markov Decision Processes. Vol. 6907, Springer, 2011, pp. 206–18, doi:10.1007/978-3-642-22993-0_21.","chicago":"Chatterjee, Krishnendu, and Laurent Doyen. “Energy and Mean-Payoff Parity Markov Decision Processes,” 6907:206–18. Springer, 2011. https://doi.org/10.1007/978-3-642-22993-0_21."},"page":"206 - 218","date_published":"2011-09-28T00:00:00Z","scopus_import":1,"day":"28"},{"date_created":"2018-12-12T11:39:02Z","date_updated":"2023-02-23T11:23:11Z","file":[{"file_name":"IST-2011-0001_IST-2011-0001.pdf","access_level":"open_access","creator":"system","file_size":329976,"content_type":"application/pdf","file_id":"5458","relation":"main_file","date_created":"2018-12-12T11:52:57Z","date_updated":"2020-07-14T12:46:41Z","checksum":"824d6c70e6d3feb3e836b009e0b3cf73"}],"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"},{"first_name":"Laurent","last_name":"Doyen","full_name":"Doyen, Laurent"}],"pubrep_id":"23","related_material":{"record":[{"relation":"later_version","status":"public","id":"3345"}]},"ddc":["000","005"],"status":"public","publication_status":"published","title":"Energy and mean-payoff parity Markov decision processes","department":[{"_id":"KrCh"}],"publisher":"IST Austria","year":"2011","_id":"5387","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2020-07-14T12:46:41Z","abstract":[{"lang":"eng","text":"We consider Markov Decision Processes (MDPs) with mean-payoff parity and energy parity objectives. In system design, the parity objective is used to encode ω-regular specifications, and the mean-payoff and energy objectives can be used to model quantitative resource constraints. The energy condition re- quires that the resource level never drops below 0, and the mean-payoff condi- tion requires that the limit-average value of the resource consumption is within a threshold. While these two (energy and mean-payoff) classical conditions are equivalent for two-player games, we show that they differ for MDPs. We show that the problem of deciding whether a state is almost-sure winning (i.e., winning with probability 1) in energy parity MDPs is in NP ∩ coNP, while for mean- payoff parity MDPs, the problem is solvable in polynomial time, improving a recent PSPACE bound."}],"alternative_title":["IST Austria Technical Report"],"type":"technical_report","language":[{"iso":"eng"}],"doi":"10.15479/AT:IST-2011-0001","date_published":"2011-02-16T00:00:00Z","page":"20","citation":{"ista":"Chatterjee K, Doyen L. 2011. Energy and mean-payoff parity Markov decision processes, IST Austria, 20p.","ieee":"K. Chatterjee and L. Doyen, Energy and mean-payoff parity Markov decision processes. IST Austria, 2011.","apa":"Chatterjee, K., & Doyen, L. (2011). Energy and mean-payoff parity Markov decision processes. IST Austria. https://doi.org/10.15479/AT:IST-2011-0001","ama":"Chatterjee K, Doyen L. Energy and Mean-Payoff Parity Markov Decision Processes. IST Austria; 2011. doi:10.15479/AT:IST-2011-0001","chicago":"Chatterjee, Krishnendu, and Laurent Doyen. Energy and Mean-Payoff Parity Markov Decision Processes. IST Austria, 2011. https://doi.org/10.15479/AT:IST-2011-0001.","mla":"Chatterjee, Krishnendu, and Laurent Doyen. Energy and Mean-Payoff Parity Markov Decision Processes. IST Austria, 2011, doi:10.15479/AT:IST-2011-0001.","short":"K. Chatterjee, L. Doyen, Energy and Mean-Payoff Parity Markov Decision Processes, IST Austria, 2011."},"oa":1,"day":"16","month":"02","has_accepted_license":"1","publication_identifier":{"issn":["2664-1690"]}},{"doi":"10.1038/474170a","date_published":"2011-06-08T00:00:00Z","publication":"Nature","citation":{"ama":"Hosten O. Quantum physics: How to catch a wave. Nature. 2011;474(7350):170-171. doi:10.1038/474170a","ieee":"O. Hosten, “Quantum physics: How to catch a wave,” Nature, vol. 474, no. 7350. Nature Publishing Group, pp. 170–171, 2011.","apa":"Hosten, O. (2011). Quantum physics: How to catch a wave. Nature. Nature Publishing Group. https://doi.org/10.1038/474170a","ista":"Hosten O. 2011. Quantum physics: How to catch a wave. Nature. 474(7350), 170–171.","short":"O. Hosten, Nature 474 (2011) 170–171.","mla":"Hosten, Onur. “Quantum Physics: How to Catch a Wave.” Nature, vol. 474, no. 7350, Nature Publishing Group, 2011, pp. 170–71, doi:10.1038/474170a.","chicago":"Hosten, Onur. “Quantum Physics: How to Catch a Wave.” Nature. Nature Publishing Group, 2011. https://doi.org/10.1038/474170a."},"quality_controlled":0,"page":"170 - 171","month":"06","day":"08","author":[{"full_name":"Onur Hosten","first_name":"Onur","last_name":"Hosten","id":"4C02D85E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2031-204X"}],"date_created":"2018-12-11T11:47:18Z","date_updated":"2021-01-12T08:03:34Z","volume":474,"year":"2011","_id":"580","publication_status":"published","title":"Quantum physics: How to catch a wave","status":"public","intvolume":" 474","publisher":"Nature Publishing Group","publist_id":"7224","issue":"7350","extern":1,"type":"journal_article"},{"title":"Methods towards achieving precise birefringent focusing","publication_status":"published","status":"public","publisher":"OSA","_id":"585","year":"2011","date_updated":"2021-01-12T08:03:44Z","date_created":"2018-12-11T11:47:20Z","author":[{"last_name":"Schmid","first_name":"David","full_name":"Schmid, David"},{"full_name":"Hazrat, Shiraz","last_name":"Hazrat","first_name":"Shiraz"},{"first_name":"Radhika","last_name":"Rangarajan","full_name":"Rangarajan, Radhika"},{"full_name":"Onur Hosten","id":"4C02D85E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2031-204X","first_name":"Onur","last_name":"Hosten"},{"full_name":"Quint, Stephan","first_name":"Stephan","last_name":"Quint"},{"last_name":"Kwiat","first_name":"Paul","full_name":"Kwiat, Paul G"}],"alternative_title":["Optics InfoBase Conference Papers"],"type":"conference","extern":1,"abstract":[{"text":"We present two independent schemes for the precise focusing of orthogonal polarizations of light at arbitrary relative locations. The first scheme uses a polarization Sagnac interferometer, the second a set of three birefringent elements.\n\n","lang":"eng"}],"publist_id":"7220","quality_controlled":0,"citation":{"ama":"Schmid D, Hazrat S, Rangarajan R, Hosten O, Quint S, Kwiat P. Methods towards achieving precise birefringent focusing. In: OSA; 2011. doi:10.1364/CLEO_AT.2011.JThB130","ieee":"D. Schmid, S. Hazrat, R. Rangarajan, O. Hosten, S. Quint, and P. Kwiat, “Methods towards achieving precise birefringent focusing,” presented at the QELS: Quantum Electronics and Laser Science, 2011.","apa":"Schmid, D., Hazrat, S., Rangarajan, R., Hosten, O., Quint, S., & Kwiat, P. (2011). Methods towards achieving precise birefringent focusing. Presented at the QELS: Quantum Electronics and Laser Science, OSA. https://doi.org/10.1364/CLEO_AT.2011.JThB130","ista":"Schmid D, Hazrat S, Rangarajan R, Hosten O, Quint S, Kwiat P. 2011. Methods towards achieving precise birefringent focusing. QELS: Quantum Electronics and Laser Science, Optics InfoBase Conference Papers, .","short":"D. Schmid, S. Hazrat, R. Rangarajan, O. Hosten, S. Quint, P. Kwiat, in:, OSA, 2011.","mla":"Schmid, David, et al. Methods towards Achieving Precise Birefringent Focusing. OSA, 2011, doi:10.1364/CLEO_AT.2011.JThB130.","chicago":"Schmid, David, Shiraz Hazrat, Radhika Rangarajan, Onur Hosten, Stephan Quint, and Paul Kwiat. “Methods towards Achieving Precise Birefringent Focusing.” OSA, 2011. https://doi.org/10.1364/CLEO_AT.2011.JThB130."},"conference":{"name":"QELS: Quantum Electronics and Laser Science"},"doi":"10.1364/CLEO_AT.2011.JThB130","date_published":"2011-01-01T00:00:00Z","month":"01","day":"01"},{"type":"journal_article","publist_id":"7223","issue":"6","abstract":[{"lang":"eng","text":"We demonstrate a Raman laser using cold Rb87 atoms as the gain medium in a high-finesse optical cavity. We observe robust continuous wave lasing in the atypical regime where single atoms can considerably affect the cavity field. Consequently, we discover unusual lasing threshold behavior in the system causing jumps in lasing power, and propose a model to explain the effect. We also measure the intermode laser linewidth, and observe values as low as 80Hz. The tunable gain properties of this laser suggest multiple directions for future research."}],"extern":1,"year":"2011","_id":"586","intvolume":" 107","publisher":"American Physical Society","status":"public","title":"Raman lasing with a cold atom gain medium in a high-finesse optical cavity","publication_status":"published","author":[{"last_name":"Vrijsen","first_name":"Geert","full_name":"Vrijsen, Geert"},{"full_name":"Onur Hosten","id":"4C02D85E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2031-204X","first_name":"Onur","last_name":"Hosten"},{"full_name":"Lee, Jongmin","last_name":"Lee","first_name":"Jongmin"},{"full_name":"Bernon, Simon","first_name":"Simon","last_name":"Bernon"},{"first_name":"Mark","last_name":"Kasevich","full_name":"Kasevich, Mark A"}],"volume":107,"date_created":"2018-12-11T11:47:20Z","date_updated":"2021-01-12T08:05:05Z","month":"08","day":"04","citation":{"ama":"Vrijsen G, Hosten O, Lee J, Bernon S, Kasevich M. Raman lasing with a cold atom gain medium in a high-finesse optical cavity. Physical Review Letters. 2011;107(6). doi:10.1103/PhysRevLett.107.063904","ieee":"G. Vrijsen, O. Hosten, J. Lee, S. Bernon, and M. Kasevich, “Raman lasing with a cold atom gain medium in a high-finesse optical cavity,” Physical Review Letters, vol. 107, no. 6. American Physical Society, 2011.","apa":"Vrijsen, G., Hosten, O., Lee, J., Bernon, S., & Kasevich, M. (2011). Raman lasing with a cold atom gain medium in a high-finesse optical cavity. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.107.063904","ista":"Vrijsen G, Hosten O, Lee J, Bernon S, Kasevich M. 2011. Raman lasing with a cold atom gain medium in a high-finesse optical cavity. Physical Review Letters. 107(6).","short":"G. Vrijsen, O. Hosten, J. Lee, S. Bernon, M. Kasevich, Physical Review Letters 107 (2011).","mla":"Vrijsen, Geert, et al. “Raman Lasing with a Cold Atom Gain Medium in a High-Finesse Optical Cavity.” Physical Review Letters, vol. 107, no. 6, American Physical Society, 2011, doi:10.1103/PhysRevLett.107.063904.","chicago":"Vrijsen, Geert, Onur Hosten, Jongmin Lee, Simon Bernon, and Mark Kasevich. “Raman Lasing with a Cold Atom Gain Medium in a High-Finesse Optical Cavity.” Physical Review Letters. American Physical Society, 2011. https://doi.org/10.1103/PhysRevLett.107.063904."},"publication":"Physical Review Letters","quality_controlled":0,"doi":"10.1103/PhysRevLett.107.063904","date_published":"2011-08-04T00:00:00Z"},{"extern":"1","abstract":[{"lang":"eng","text":"The macromolecular assembly required to initiate transcription of protein-coding genes, known as the Pre-Initiation Complex (PIC), consists of multiple protein complexes and is approximately 3.5 MDa in size. At the heart of this assembly is the Mediator complex, which helps regulate PIC activity and interacts with the RNA polymerase II (pol II) enzyme. The structure of the human Mediator-pol II interface is not well-characterized, whereas attempts to structurally define the Mediator-pol II interaction in yeast have relied on incomplete assemblies of Mediator and/or pol II and have yielded inconsistent interpretations. We have assembled the complete, 1.9 MDa human Mediator-pol II-TFIIF complex from purified components and have characterized its structural organization using cryo-electron microscopy and single-particle reconstruction techniques. The orientation of pol II within this assembly was determined by crystal structure docking and further validated with projection matching experiments, allowing the structural organization of the entire human PIC to be envisioned. Significantly, pol II orientation within the Mediator-pol II-TFIIF assembly can be reconciled with past studies that determined the location of other PIC components relative to pol II itself. Pol II surfaces required for interacting with TFIIB, TFIIE, and promoter DNA (i.e., the pol II cleft) are exposed within the Mediator-pol II-TFIIF structure; RNA exit is unhindered along the RPB4/7 subunits; upstream and downstream DNA is accessible for binding additional factors; and no major structural re-organization is necessary to accommodate the large, multi-subunit TFIIH or TFIID complexes. The data also reveal how pol II binding excludes Mediator-CDK8 subcomplex interactions and provide a structural basis for Mediator-dependent control of PIC assembly and function. Finally, parallel structural analysis of Mediator-pol II complexes lacking TFIIF reveal that TFIIF plays a key role in stabilizing pol II orientation within the assembly."}],"issue":"3","publist_id":"7209","type":"journal_article","date_updated":"2021-01-12T08:05:25Z","date_created":"2018-12-11T11:47:24Z","oa_version":"None","volume":9,"author":[{"orcid":"0000-0003-0893-7036","id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87","last_name":"Bernecky","first_name":"Carrie A","full_name":"Bernecky, Carrie A"},{"last_name":"Grob","first_name":"Patricia","full_name":"Grob, Patricia"},{"first_name":"Christopher","last_name":"Ebmeier","full_name":"Ebmeier, Christopher"},{"full_name":"Nogales, Eva","last_name":"Nogales","first_name":"Eva"},{"full_name":"Taatjes, Dylan","first_name":"Dylan","last_name":"Taatjes"}],"publication_status":"published","status":"public","title":"Molecular architecture of the human Mediator-RNA polymerase II-TFIIF assembly","publisher":"Public Library of Science","intvolume":" 9","_id":"597","year":"2011","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","month":"03","article_processing_charge":"No","language":[{"iso":"eng"}],"doi":"10.1371/journal.pbio.1000603","date_published":"2011-03-01T00:00:00Z","publication":"PLoS Biology","citation":{"chicago":"Bernecky, Carrie, Patricia Grob, Christopher Ebmeier, Eva Nogales, and Dylan Taatjes. “Molecular Architecture of the Human Mediator-RNA Polymerase II-TFIIF Assembly.” PLoS Biology. Public Library of Science, 2011. https://doi.org/10.1371/journal.pbio.1000603.","mla":"Bernecky, Carrie, et al. “Molecular Architecture of the Human Mediator-RNA Polymerase II-TFIIF Assembly.” PLoS Biology, vol. 9, no. 3, Public Library of Science, 2011, doi:10.1371/journal.pbio.1000603.","short":"C. Bernecky, P. Grob, C. Ebmeier, E. Nogales, D. Taatjes, PLoS Biology 9 (2011).","ista":"Bernecky C, Grob P, Ebmeier C, Nogales E, Taatjes D. 2011. Molecular architecture of the human Mediator-RNA polymerase II-TFIIF assembly. PLoS Biology. 9(3).","apa":"Bernecky, C., Grob, P., Ebmeier, C., Nogales, E., & Taatjes, D. (2011). Molecular architecture of the human Mediator-RNA polymerase II-TFIIF assembly. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.1000603","ieee":"C. Bernecky, P. Grob, C. Ebmeier, E. Nogales, and D. Taatjes, “Molecular architecture of the human Mediator-RNA polymerase II-TFIIF assembly,” PLoS Biology, vol. 9, no. 3. Public Library of Science, 2011.","ama":"Bernecky C, Grob P, Ebmeier C, Nogales E, Taatjes D. Molecular architecture of the human Mediator-RNA polymerase II-TFIIF assembly. PLoS Biology. 2011;9(3). doi:10.1371/journal.pbio.1000603"}},{"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":["21437263"]},"oa":1,"quality_controlled":"1","doi":"10.1371/journal.pgen.1001341","language":[{"iso":"eng"}],"publication_identifier":{"issn":["1553-7404"]},"month":"03","pmid":1,"year":"2011","publisher":"Public Library of Science","publication_status":"published","author":[{"first_name":"Fausto","last_name":"Arellano-Carbajal","full_name":"Arellano-Carbajal, Fausto"},{"full_name":"Briseño-Roa, Luis","first_name":"Luis","last_name":"Briseño-Roa"},{"full_name":"Couto, Africa","first_name":"Africa","last_name":"Couto"},{"first_name":"Benny H. H.","last_name":"Cheung","full_name":"Cheung, Benny H. H."},{"full_name":"Labouesse, Michel","first_name":"Michel","last_name":"Labouesse"},{"last_name":"de Bono","first_name":"Mario","orcid":"0000-0001-8347-0443","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","full_name":"de Bono, Mario"}],"volume":7,"date_updated":"2021-01-12T08:06:19Z","date_created":"2019-03-20T15:08:23Z","article_number":"e1001341","file_date_updated":"2020-07-14T12:47:20Z","license":"https://creativecommons.org/licenses/by/4.0/","extern":"1","citation":{"ista":"Arellano-Carbajal F, Briseño-Roa L, Couto A, Cheung BHH, Labouesse M, de Bono M. 2011. Macoilin, a conserved nervous system–specific ER membrane protein that regulates neuronal excitability. PLoS Genetics. 7(3), e1001341.","apa":"Arellano-Carbajal, F., Briseño-Roa, L., Couto, A., Cheung, B. H. H., Labouesse, M., & de Bono, M. (2011). Macoilin, a conserved nervous system–specific ER membrane protein that regulates neuronal excitability. PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1001341","ieee":"F. Arellano-Carbajal, L. Briseño-Roa, A. Couto, B. H. H. Cheung, M. Labouesse, and M. de Bono, “Macoilin, a conserved nervous system–specific ER membrane protein that regulates neuronal excitability,” PLoS Genetics, vol. 7, no. 3. Public Library of Science, 2011.","ama":"Arellano-Carbajal F, Briseño-Roa L, Couto A, Cheung BHH, Labouesse M, de Bono M. Macoilin, a conserved nervous system–specific ER membrane protein that regulates neuronal excitability. PLoS Genetics. 2011;7(3). doi:10.1371/journal.pgen.1001341","chicago":"Arellano-Carbajal, Fausto, Luis Briseño-Roa, Africa Couto, Benny H. H. Cheung, Michel Labouesse, and Mario de Bono. “Macoilin, a Conserved Nervous System–Specific ER Membrane Protein That Regulates Neuronal Excitability.” PLoS Genetics. Public Library of Science, 2011. https://doi.org/10.1371/journal.pgen.1001341.","mla":"Arellano-Carbajal, Fausto, et al. “Macoilin, a Conserved Nervous System–Specific ER Membrane Protein That Regulates Neuronal Excitability.” PLoS Genetics, vol. 7, no. 3, e1001341, Public Library of Science, 2011, doi:10.1371/journal.pgen.1001341.","short":"F. Arellano-Carbajal, L. Briseño-Roa, A. Couto, B.H.H. Cheung, M. Labouesse, M. de Bono, PLoS Genetics 7 (2011)."},"publication":"PLoS Genetics","date_published":"2011-03-17T00:00:00Z","has_accepted_license":"1","day":"17","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"6140","intvolume":" 7","title":"Macoilin, a conserved nervous system–specific ER membrane protein that regulates neuronal excitability","status":"public","ddc":["570"],"file":[{"checksum":"c609b2ce616d7dafbb617ec5d022f1ea","date_created":"2019-03-20T15:18:11Z","date_updated":"2020-07-14T12:47:20Z","file_id":"6141","relation":"main_file","creator":"kschuh","content_type":"application/pdf","file_size":5625063,"access_level":"open_access","file_name":"2011_PLOS_Arellano-Carbajal.PDF"}],"oa_version":"Published Version","type":"journal_article","issue":"3","abstract":[{"lang":"eng","text":"Genome sequence comparisons have highlighted many novel gene families that are conserved across animal phyla but whose biological function is unknown. Here, we functionally characterize a member of one such family, the macoilins. Macoilins are characterized by several highly conserved predicted transmembrane domains towards the N-terminus and by coiled-coil regions C-terminally. They are found throughout Eumetazoa but not in other organisms. Mutants for the single Caenorhabditis elegans macoilin, maco-1, exhibit a constellation of behavioral phenotypes, including defects in aggregation, O2 responses, and swimming. MACO-1 protein is expressed broadly and specifically in the nervous system and localizes to the rough endoplasmic reticulum; it is excluded from dendrites and axons. Apart from subtle synapse defects, nervous system development appears wild-type in maco-1 mutants. However, maco-1 animals are resistant to the cholinesterase inhibitor aldicarb and sensitive to levamisole, suggesting pre-synaptic defects. Using in vivo imaging, we show that macoilin is required to evoke Ca2+ transients, at least in some neurons: in maco-1 mutants the O2-sensing neuron PQR is unable to generate a Ca2+ response to a rise in O2. By genetically disrupting neurotransmission, we show that pre-synaptic input is not necessary for PQR to respond to O2, indicating that the response is mediated by cell-intrinsic sensory transduction and amplification. Disrupting the sodium leak channels NCA-1/NCA-2, or the N-,P/Q,R-type voltage-gated Ca2+ channels, also fails to disrupt Ca2+ responses in the PQR cell body to O2 stimuli. By contrast, mutations in egl-19, which encodes the only Caenorhabditis elegans L-type voltage-gated Ca2+ channel α1 subunit, recapitulate the Ca2+ response defect we see in maco-1 mutants, although we do not see defects in localization of EGL-19. Together, our data suggest that macoilin acts in the ER to regulate assembly or traffic of ion channels or ion channel regulators."}]},{"day":"20","page":"20672-20677","citation":{"chicago":"Milward, K., K. E. Busch, R. J. Murphy, Mario de Bono, and B. Olofsson. “Neuronal and Molecular Substrates for Optimal Foraging in Caenorhabditis Elegans.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2011. https://doi.org/10.1073/pnas.1106134109.","mla":"Milward, K., et al. “Neuronal and Molecular Substrates for Optimal Foraging in Caenorhabditis Elegans.” Proceedings of the National Academy of Sciences, vol. 108, no. 51, National Academy of Sciences, 2011, pp. 20672–77, doi:10.1073/pnas.1106134109.","short":"K. Milward, K.E. Busch, R.J. Murphy, M. de Bono, B. Olofsson, Proceedings of the National Academy of Sciences 108 (2011) 20672–20677.","ista":"Milward K, Busch KE, Murphy RJ, de Bono M, Olofsson B. 2011. Neuronal and molecular substrates for optimal foraging in Caenorhabditis elegans. Proceedings of the National Academy of Sciences. 108(51), 20672–20677.","ieee":"K. Milward, K. E. Busch, R. J. Murphy, M. de Bono, and B. Olofsson, “Neuronal and molecular substrates for optimal foraging in Caenorhabditis elegans,” Proceedings of the National Academy of Sciences, vol. 108, no. 51. National Academy of Sciences, pp. 20672–20677, 2011.","apa":"Milward, K., Busch, K. E., Murphy, R. J., de Bono, M., & Olofsson, B. (2011). Neuronal and molecular substrates for optimal foraging in Caenorhabditis elegans. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.1106134109","ama":"Milward K, Busch KE, Murphy RJ, de Bono M, Olofsson B. Neuronal and molecular substrates for optimal foraging in Caenorhabditis elegans. Proceedings of the National Academy of Sciences. 2011;108(51):20672-20677. doi:10.1073/pnas.1106134109"},"publication":"Proceedings of the National Academy of Sciences","date_published":"2011-12-20T00:00:00Z","type":"journal_article","issue":"51","abstract":[{"lang":"eng","text":"Variation in food quality and abundance requires animals to decide whether to stay on a poor food patch or leave in search of better food. An important question in behavioral ecology asks when is it optimal for an animal to leave a food patch it is depleting. Although optimal foraging is central to evolutionary success, the neural and molecular mechanisms underlying it are poorly understood. Here we investigate the neuronal basis for adaptive food-leaving behavior in response to resource depletion in Caenorhabditis elegans, and identify several of the signaling pathways involved. The ASE neurons, previously implicated in salt chemoattraction, promote food-leaving behavior via a cGMP pathway as food becomes limited. High ambient O2 promotes food-leaving via the O2-sensing neurons AQR, PQR, and URX. Ectopic activation of these neurons using channelrhodopsin is sufficient to induce high food-leaving behavior. In contrast, the neuropeptide receptor NPR-1, which regulates social behavior on food, acts in the ASE neurons, the nociceptive ASH neurons, and in the RMG interneuron to repress food-leaving. Finally, we show that neuroendocrine signaling by TGF-β/DAF-7 and neuronal insulin signaling are necessary for adaptive food-leaving behavior. We suggest that animals integrate information about their nutritional state with ambient oxygen and gustatory stimuli to formulate optimal foraging strategies."}],"intvolume":" 108","status":"public","title":"Neuronal and molecular substrates for optimal foraging in Caenorhabditis elegans","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"6137","oa_version":"Submitted Version","publication_identifier":{"issn":["0027-8424","1091-6490"]},"month":"12","quality_controlled":"1","oa":1,"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3251049/","open_access":"1"}],"external_id":{"pmid":["22135454"]},"language":[{"iso":"eng"}],"doi":"10.1073/pnas.1106134109","extern":"1","publisher":"National Academy of Sciences","publication_status":"published","pmid":1,"year":"2011","volume":108,"date_created":"2019-03-20T14:30:06Z","date_updated":"2021-01-12T08:06:18Z","author":[{"full_name":"Milward, K.","first_name":"K.","last_name":"Milward"},{"full_name":"Busch, K. E.","first_name":"K. E.","last_name":"Busch"},{"first_name":"R. J.","last_name":"Murphy","full_name":"Murphy, R. J."},{"full_name":"de Bono, Mario","last_name":"de Bono","first_name":"Mario","orcid":"0000-0001-8347-0443","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Olofsson","first_name":"B.","full_name":"Olofsson, B."}]},{"file_date_updated":"2020-07-14T12:47:20Z","extern":"1","author":[{"full_name":"Bretscher, Andrew Jonathan","first_name":"Andrew Jonathan","last_name":"Bretscher"},{"full_name":"Kodama-Namba, Eiji","first_name":"Eiji","last_name":"Kodama-Namba"},{"last_name":"Busch","first_name":"Karl Emanuel","full_name":"Busch, Karl Emanuel"},{"last_name":"Murphy","first_name":"Robin Joseph","full_name":"Murphy, Robin Joseph"},{"last_name":"Soltesz","first_name":"Zoltan","full_name":"Soltesz, Zoltan"},{"full_name":"Laurent, Patrick","first_name":"Patrick","last_name":"Laurent"},{"full_name":"de Bono, Mario","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8347-0443","first_name":"Mario","last_name":"de Bono"}],"date_updated":"2021-01-12T08:06:18Z","date_created":"2019-03-20T15:01:41Z","volume":69,"year":"2011","pmid":1,"publication_status":"published","publisher":"Elsevier BV","month":"03","publication_identifier":{"issn":["0896-6273"]},"doi":"10.1016/j.neuron.2011.02.023","language":[{"iso":"eng"}],"external_id":{"pmid":["21435556"]},"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","issue":"6","type":"journal_article","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2011_Cell_Bretscher.pdf","content_type":"application/pdf","file_size":2448332,"creator":"kschuh","relation":"main_file","file_id":"6139","checksum":"547cffd123f4c508ae927c9244b8f92a","date_created":"2019-03-20T15:06:32Z","date_updated":"2020-07-14T12:47:20Z"}],"_id":"6138","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","title":"Temperature, oxygen, and salt-sensing neurons in C. elegans are carbon dioxide sensors that control avoidance behavior","ddc":["570"],"status":"public","intvolume":" 69","day":"24","has_accepted_license":"1","date_published":"2011-03-24T00:00:00Z","publication":"Neuron","citation":{"chicago":"Bretscher, Andrew Jonathan, Eiji Kodama-Namba, Karl Emanuel Busch, Robin Joseph Murphy, Zoltan Soltesz, Patrick Laurent, and Mario de Bono. “Temperature, Oxygen, and Salt-Sensing Neurons in C. Elegans Are Carbon Dioxide Sensors That Control Avoidance Behavior.” Neuron. Elsevier BV, 2011. https://doi.org/10.1016/j.neuron.2011.02.023.","short":"A.J. Bretscher, E. Kodama-Namba, K.E. Busch, R.J. Murphy, Z. Soltesz, P. Laurent, M. de Bono, Neuron 69 (2011) 1099–1113.","mla":"Bretscher, Andrew Jonathan, et al. “Temperature, Oxygen, and Salt-Sensing Neurons in C. Elegans Are Carbon Dioxide Sensors That Control Avoidance Behavior.” Neuron, vol. 69, no. 6, Elsevier BV, 2011, pp. 1099–113, doi:10.1016/j.neuron.2011.02.023.","apa":"Bretscher, A. J., Kodama-Namba, E., Busch, K. E., Murphy, R. J., Soltesz, Z., Laurent, P., & de Bono, M. (2011). Temperature, oxygen, and salt-sensing neurons in C. elegans are carbon dioxide sensors that control avoidance behavior. Neuron. Elsevier BV. https://doi.org/10.1016/j.neuron.2011.02.023","ieee":"A. J. Bretscher et al., “Temperature, oxygen, and salt-sensing neurons in C. elegans are carbon dioxide sensors that control avoidance behavior,” Neuron, vol. 69, no. 6. Elsevier BV, pp. 1099–1113, 2011.","ista":"Bretscher AJ, Kodama-Namba E, Busch KE, Murphy RJ, Soltesz Z, Laurent P, de Bono M. 2011. Temperature, oxygen, and salt-sensing neurons in C. elegans are carbon dioxide sensors that control avoidance behavior. Neuron. 69(6), 1099–1113.","ama":"Bretscher AJ, Kodama-Namba E, Busch KE, et al. Temperature, oxygen, and salt-sensing neurons in C. elegans are carbon dioxide sensors that control avoidance behavior. Neuron. 2011;69(6):1099-1113. doi:10.1016/j.neuron.2011.02.023"},"page":"1099-1113"},{"quality_controlled":"1","page":"25675-25686","publication":"Journal of Biological Chemistry","citation":{"chicago":"Baranova, Natalia S., Erik Nilebäck, F. Michael Haller, David C. Briggs, Sofia Svedhem, Anthony J. Day, and Ralf P. Richter. “The Inflammation-Associated Protein TSG-6 Cross-Links Hyaluronan via Hyaluronan-Induced TSG-6 Oligomers.” Journal of Biological Chemistry. American Society for Biochemistry & Molecular Biology, 2011. https://doi.org/10.1074/jbc.m111.247395.","mla":"Baranova, Natalia S., et al. “The Inflammation-Associated Protein TSG-6 Cross-Links Hyaluronan via Hyaluronan-Induced TSG-6 Oligomers.” Journal of Biological Chemistry, vol. 286, no. 29, American Society for Biochemistry & Molecular Biology, 2011, pp. 25675–86, doi:10.1074/jbc.m111.247395.","short":"N.S. Baranova, E. Nilebäck, F.M. Haller, D.C. Briggs, S. Svedhem, A.J. Day, R.P. Richter, Journal of Biological Chemistry 286 (2011) 25675–25686.","ista":"Baranova NS, Nilebäck E, Haller FM, Briggs DC, Svedhem S, Day AJ, Richter RP. 2011. The inflammation-associated protein TSG-6 cross-links hyaluronan via hyaluronan-induced TSG-6 oligomers. Journal of Biological Chemistry. 286(29), 25675–25686.","apa":"Baranova, N. S., Nilebäck, E., Haller, F. M., Briggs, D. C., Svedhem, S., Day, A. J., & Richter, R. P. (2011). The inflammation-associated protein TSG-6 cross-links hyaluronan via hyaluronan-induced TSG-6 oligomers. Journal of Biological Chemistry. American Society for Biochemistry & Molecular Biology. https://doi.org/10.1074/jbc.m111.247395","ieee":"N. S. Baranova et al., “The inflammation-associated protein TSG-6 cross-links hyaluronan via hyaluronan-induced TSG-6 oligomers,” Journal of Biological Chemistry, vol. 286, no. 29. American Society for Biochemistry & Molecular Biology, pp. 25675–25686, 2011.","ama":"Baranova NS, Nilebäck E, Haller FM, et al. The inflammation-associated protein TSG-6 cross-links hyaluronan via hyaluronan-induced TSG-6 oligomers. Journal of Biological Chemistry. 2011;286(29):25675-25686. doi:10.1074/jbc.m111.247395"},"oa":1,"main_file_link":[{"open_access":"1","url":"http://www.jbc.org/content/286/29/25675.full.pdf"}],"language":[{"iso":"eng"}],"doi":"10.1074/jbc.m111.247395","date_published":"2011-07-22T00:00:00Z","month":"07","day":"22","publication_identifier":{"issn":["0021-9258","1083-351X"]},"publication_status":"published","title":"The inflammation-associated protein TSG-6 cross-links hyaluronan via hyaluronan-induced TSG-6 oligomers","status":"public","publisher":"American Society for Biochemistry & Molecular Biology","intvolume":" 286","year":"2011","_id":"6298","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T08:06:58Z","date_created":"2019-04-11T20:57:43Z","volume":286,"oa_version":"Published Version","author":[{"first_name":"Natalia","last_name":"Baranova","id":"38661662-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3086-9124","full_name":"Baranova, Natalia"},{"full_name":"Nilebäck, Erik","last_name":"Nilebäck","first_name":"Erik"},{"full_name":"Haller, F. Michael","first_name":"F. Michael","last_name":"Haller"},{"last_name":"Briggs","first_name":"David C.","full_name":"Briggs, David C."},{"full_name":"Svedhem, Sofia","first_name":"Sofia","last_name":"Svedhem"},{"last_name":"Day","first_name":"Anthony J.","full_name":"Day, Anthony J."},{"full_name":"Richter, Ralf P.","last_name":"Richter","first_name":"Ralf P."}],"type":"journal_article","extern":"1","abstract":[{"lang":"eng","text":"Tumor necrosis factor-stimulated gene-6 (TSG-6) is a hyalu-ronan (HA)-binding protein that plays important roles ininflammation and ovulation. TSG-6-mediated cross-linking ofHA has been proposed as a functional mechanism (e.g.for regu-lating leukocyte adhesion), but direct evidence for cross-linkingis lacking, and we know very little about its impact on HA ultra-structure. Here we used films of polymeric and oligomeric HAchains, end-grafted to a solid support, and a combination ofsurface-sensitive biophysical techniques to quantify the bindingof TSG-6 into HA films and to correlate binding to morpholog-ical changes. We find that full-length TSG-6 binds with pro-nounced positive cooperativity and demonstrate that it cancross-link HA at physiologically relevant concentrations. Ourdata indicate that cooperative binding of full-length TSG-6arises from HA-induced protein oligomerization and that theTSG-6 oligomers act as cross-linkers. In contrast, the HA-bind-ing domain of TSG-6 (the Link module) alone binds withoutpositive cooperativity and weaker than the full-length protein.Both the Link module and full-length TSG-6 condensed andrigidified HA films, and the degree of condensation scaled withthe affinity between the TSG-6 constructs and HA. We proposethat condensation is the result of protein-mediated HA cross-linking. Our findings firmly establish that TSG-6 is a potent HAcross-linking agent and might hence have important implica-tions for the mechanistic understanding of the biological func-tion of TSG-6 (e.g.in inflammation)."}],"issue":"29"},{"oa_version":"Published Version","status":"public","title":"Noise underlies switching behavior of the bacterial flagellum","intvolume":" 101","_id":"6496","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"We report the switching behavior of the full bacterial flagellum system that includes the filament and the motor in wild-type Escherichia coli cells. In sorting the motor behavior by the clockwise bias, we find that the distributions of the clockwise (CW) and counterclockwise (CCW) intervals are either exponential or nonexponential with long tails. At low bias, CW intervals are exponentially distributed and CCW intervals exhibit long tails. At intermediate CW bias (0.5) both CW and CCW intervals are mainly exponentially distributed. A simple model suggests that these two distinct switching behaviors are governed by the presence of signaling noise within the chemotaxis network. Low noise yields exponentially distributed intervals, whereas large noise yields nonexponential behavior with long tails. These drastically different motor statistics may play a role in optimizing bacterial behavior for a wide range of environmental conditions.","lang":"eng"}],"issue":"10","type":"journal_article","date_published":"2011-11-16T00:00:00Z","page":"2336-2340","publication":"Biophysical Journal","citation":{"ama":"Park H, Oikonomou P, Guet CC, Cluzel P. Noise underlies switching behavior of the bacterial flagellum. Biophysical Journal. 2011;101(10):2336-2340. doi:10.1016/j.bpj.2011.09.040","ista":"Park H, Oikonomou P, Guet CC, Cluzel P. 2011. Noise underlies switching behavior of the bacterial flagellum. Biophysical Journal. 101(10), 2336–2340.","apa":"Park, H., Oikonomou, P., Guet, C. C., & Cluzel, P. (2011). Noise underlies switching behavior of the bacterial flagellum. Biophysical Journal. Elsevier. https://doi.org/10.1016/j.bpj.2011.09.040","ieee":"H. Park, P. Oikonomou, C. C. Guet, and P. Cluzel, “Noise underlies switching behavior of the bacterial flagellum,” Biophysical Journal, vol. 101, no. 10. Elsevier, pp. 2336–2340, 2011.","mla":"Park, Heungwon, et al. “Noise Underlies Switching Behavior of the Bacterial Flagellum.” Biophysical Journal, vol. 101, no. 10, Elsevier, 2011, pp. 2336–40, doi:10.1016/j.bpj.2011.09.040.","short":"H. Park, P. Oikonomou, C.C. Guet, P. Cluzel, Biophysical Journal 101 (2011) 2336–2340.","chicago":"Park, Heungwon, Panos Oikonomou, Calin C Guet, and Philippe Cluzel. “Noise Underlies Switching Behavior of the Bacterial Flagellum.” Biophysical Journal. Elsevier, 2011. https://doi.org/10.1016/j.bpj.2011.09.040."},"day":"16","article_processing_charge":"No","scopus_import":"1","date_updated":"2021-04-16T11:54:49Z","date_created":"2019-05-28T11:54:29Z","volume":101,"author":[{"full_name":"Park, Heungwon","last_name":"Park","first_name":"Heungwon"},{"last_name":"Oikonomou","first_name":"Panos","full_name":"Oikonomou, Panos"},{"full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","last_name":"Guet","first_name":"Calin C"},{"first_name":"Philippe","last_name":"Cluzel","full_name":"Cluzel, Philippe"}],"publication_status":"published","department":[{"_id":"CaGu"}],"publisher":"Elsevier","year":"2011","pmid":1,"language":[{"iso":"eng"}],"doi":"10.1016/j.bpj.2011.09.040","quality_controlled":"1","oa":1,"external_id":{"pmid":["22098731"]},"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3218319/","open_access":"1"}],"month":"11","publication_identifier":{"issn":["0006-3495"]}},{"abstract":[{"text":"This article refers to algorithms based on finite difference schemes for computing mean and affine curvature evolutions of digital images, introduced by Alvarez and Morel [L. Alvarez, J.M. Morel, “Formalization and computational aspects of image analysis”, Acta Numerica, pp. 159, 1994]. We discuss consistency, stability and convergence. Our analysis focuses on some possible choices of the parameters, choices that generate multiple variants in the implementations. Meaningful visual examples on how the algorithms actually work are provided.","lang":"eng"}],"type":"journal_article","file":[{"file_id":"6751","relation":"main_file","checksum":"910710811224c633202791e0c217d05d","date_created":"2019-08-01T06:34:21Z","date_updated":"2020-07-14T12:47:39Z","access_level":"open_access","file_name":"2011_IPOL_Mondelli.pdf","creator":"dernst","file_size":2793903,"content_type":"application/pdf"}],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"6749","ddc":["000"],"status":"public","title":"Finite difference schemes for MCM and AMSS","intvolume":" 1","day":"13","has_accepted_license":"1","date_published":"2011-09-13T00:00:00Z","publication":"Image Processing On Line","citation":{"mla":"Mondelli, Marco, and Adina Ciomaga. “Finite Difference Schemes for MCM and AMSS.” Image Processing On Line, vol. 1, IPOL Image Processing On Line, 2011, pp. 127–77, doi:10.5201/ipol.2011.cm_fds.","short":"M. Mondelli, A. Ciomaga, Image Processing On Line 1 (2011) 127–177.","chicago":"Mondelli, Marco, and Adina Ciomaga. “Finite Difference Schemes for MCM and AMSS.” Image Processing On Line. IPOL Image Processing On Line, 2011. https://doi.org/10.5201/ipol.2011.cm_fds.","ama":"Mondelli M, Ciomaga A. Finite difference schemes for MCM and AMSS. Image Processing On Line. 2011;1:127-177. doi:10.5201/ipol.2011.cm_fds","ista":"Mondelli M, Ciomaga A. 2011. Finite difference schemes for MCM and AMSS. Image Processing On Line. 1, 127–177.","apa":"Mondelli, M., & Ciomaga, A. (2011). Finite difference schemes for MCM and AMSS. Image Processing On Line. IPOL Image Processing On Line. https://doi.org/10.5201/ipol.2011.cm_fds","ieee":"M. Mondelli and A. Ciomaga, “Finite difference schemes for MCM and AMSS,” Image Processing On Line, vol. 1. IPOL Image Processing On Line, pp. 127–177, 2011."},"page":"127-177","file_date_updated":"2020-07-14T12:47:39Z","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","extern":"1","author":[{"full_name":"Mondelli, Marco","id":"27EB676C-8706-11E9-9510-7717E6697425","orcid":"0000-0002-3242-7020","first_name":"Marco","last_name":"Mondelli"},{"last_name":"Ciomaga","first_name":"Adina","full_name":"Ciomaga, Adina"}],"date_updated":"2021-01-12T08:08:50Z","date_created":"2019-07-31T09:44:24Z","volume":1,"year":"2011","publication_status":"published","publisher":"IPOL Image Processing On Line","month":"09","publication_identifier":{"issn":["2105-1232"]},"doi":"10.5201/ipol.2011.cm_fds","language":[{"iso":"eng"}],"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"},{"year":"2011","_id":"6767","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Editura Universitãtii „Alexandru Ioan Cuza” Iasi","publication_status":"published","title":"On finite difference schemes for curvature motions","status":"public","author":[{"full_name":"Mondelli, Marco","orcid":"0000-0002-3242-7020","id":"27EB676C-8706-11E9-9510-7717E6697425","last_name":"Mondelli","first_name":"Marco"},{"last_name":"Ciomaga","first_name":"Adina","full_name":"Ciomaga, Adina"}],"oa_version":"None","date_created":"2019-08-05T12:20:58Z","date_updated":"2021-01-12T08:08:56Z","type":"conference","abstract":[{"lang":"eng","text":"In the present paper we give a thorough analysis of two finite difference schemes for the Mean Curvature Motion and its affine variant, the Affine Morphological Scale Space, schemes introduced in the Image Processing framework. This analysis brings in a series of parameters that allow us to compute an accurate discrete evolution of curvature motions.\r\nThe choice of these parameters is based on intrinsic geometric properties of the evolution equations for linear, radial and elliptical functions. In the last part we present several examples, underlining the main advantages of the algorithms (the removal of pixelization effects and JPEG artifacts) as well as their major drawbacks (absence of contrast invariance and grid dependence). A detailed explanatory report, the ANSI C implementations and an on-line demo can be found at http://www.ipol.im/."}],"extern":"1","citation":{"short":"M. Mondelli, A. Ciomaga, in:, Proceedings of the International Student Conference on Pure and Applied Mathematics, Editura Universitãtii „Alexandru Ioan Cuza” Iasi, 2011, pp. 137–156.","mla":"Mondelli, Marco, and Adina Ciomaga. “On Finite Difference Schemes for Curvature Motions.” Proceedings of the International Student Conference on Pure and Applied Mathematics, Editura Universitãtii „Alexandru Ioan Cuza” Iasi, 2011, pp. 137–56, doi:10.13140/2.1.1862.4646.","chicago":"Mondelli, Marco, and Adina Ciomaga. “On Finite Difference Schemes for Curvature Motions.” In Proceedings of the International Student Conference on Pure and Applied Mathematics, 137–56. Editura Universitãtii „Alexandru Ioan Cuza” Iasi, 2011. https://doi.org/10.13140/2.1.1862.4646.","ama":"Mondelli M, Ciomaga A. On finite difference schemes for curvature motions. In: Proceedings of the International Student Conference on Pure and Applied Mathematics. Editura Universitãtii „Alexandru Ioan Cuza” Iasi; 2011:137-156. doi:10.13140/2.1.1862.4646","apa":"Mondelli, M., & Ciomaga, A. (2011). On finite difference schemes for curvature motions. In Proceedings of the International Student Conference on Pure and Applied Mathematics (pp. 137–156). Iasi, Romania: Editura Universitãtii „Alexandru Ioan Cuza” Iasi. https://doi.org/10.13140/2.1.1862.4646","ieee":"M. Mondelli and A. Ciomaga, “On finite difference schemes for curvature motions,” in Proceedings of the International Student Conference on Pure and Applied Mathematics, Iasi, Romania, 2011, pp. 137–156.","ista":"Mondelli M, Ciomaga A. 2011. On finite difference schemes for curvature motions. Proceedings of the International Student Conference on Pure and Applied Mathematics. ISCOPAM: International Student Conference on Pure and Applied Mathematics, 137–156."},"publication":"Proceedings of the International Student Conference on Pure and Applied Mathematics","page":"137-156","quality_controlled":"1","date_published":"2011-01-01T00:00:00Z","doi":"10.13140/2.1.1862.4646","conference":{"name":"ISCOPAM: International Student Conference on Pure and Applied Mathematics","end_date":"2010-07-16","location":"Iasi, Romania","start_date":"2010-07-12"},"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["978-973-703-602-5"]},"month":"01","day":"01"},{"day":"21","month":"02","publication_identifier":{"issn":["0953-8984","1361-648X"]},"article_processing_charge":"No","quality_controlled":"1","article_type":"original","publication":"Journal of Physics: Condensed Matter","citation":{"mla":"Salje, E. K. H., et al. “Determination of Iron Sites and the Amount of Amorphization in Radiation-Damaged Titanite (CaSiTiO5).” Journal of Physics: Condensed Matter, vol. 23, no. 10, 105402, IOP Publishing, 2011, doi:10.1088/0953-8984/23/10/105402.","short":"E.K.H. Salje, D.J. Safarik, R.D. Taylor, M.P. Pasternak, K.A. Modic, L.A. Groat, J.C. Lashley, Journal of Physics: Condensed Matter 23 (2011).","chicago":"Salje, E K H, D J Safarik, R D Taylor, M P Pasternak, Kimberly A Modic, L A Groat, and J C Lashley. “Determination of Iron Sites and the Amount of Amorphization in Radiation-Damaged Titanite (CaSiTiO5).” Journal of Physics: Condensed Matter. IOP Publishing, 2011. https://doi.org/10.1088/0953-8984/23/10/105402.","ama":"Salje EKH, Safarik DJ, Taylor RD, et al. Determination of iron sites and the amount of amorphization in radiation-damaged titanite (CaSiTiO5). Journal of Physics: Condensed Matter. 2011;23(10). doi:10.1088/0953-8984/23/10/105402","ista":"Salje EKH, Safarik DJ, Taylor RD, Pasternak MP, Modic KA, Groat LA, Lashley JC. 2011. Determination of iron sites and the amount of amorphization in radiation-damaged titanite (CaSiTiO5). Journal of Physics: Condensed Matter. 23(10), 105402.","ieee":"E. K. H. Salje et al., “Determination of iron sites and the amount of amorphization in radiation-damaged titanite (CaSiTiO5),” Journal of Physics: Condensed Matter, vol. 23, no. 10. IOP Publishing, 2011.","apa":"Salje, E. K. H., Safarik, D. J., Taylor, R. D., Pasternak, M. P., Modic, K. A., Groat, L. A., & Lashley, J. C. (2011). Determination of iron sites and the amount of amorphization in radiation-damaged titanite (CaSiTiO5). Journal of Physics: Condensed Matter. IOP Publishing. https://doi.org/10.1088/0953-8984/23/10/105402"},"language":[{"iso":"eng"}],"date_published":"2011-02-21T00:00:00Z","doi":"10.1088/0953-8984/23/10/105402","article_number":"105402","type":"journal_article","extern":"1","abstract":[{"text":"Iron is a ubiquitous impurity in metamict (radiation-damaged and partially amorphized) materials such as titanite (CaSiTiO5). Using 57Fe Mössbauer spectroscopy we find that iron in metamict titanite is partitioned between amorphous and crystalline regions based on valence. Trivalent iron exists in the crystalline titanite matrix whereas divalent iron exists almost exclusively in radiation-amorphized regions. We find that the relative abundances of the oxidation states correlate with the volume fraction of amorphous and crystalline regions. Our data also show that oxidation of iron proceeds along with the recrystallization of the amorphized regions. Recrystallization is confirmed to occur over the range 700 °C < T < 925 °C, and no further structural changes are observed at higher temperatures. It is surprising that our Mössbauer measurements show divalent iron to be surrounded by titanite with a high degree of short-range structural order in the amorphized regions. This observation is fundamentally different from other metamict materials such as zircon (ZrSiO4), where amorphized regions show no short-range order.","lang":"eng"}],"issue":"10","title":"Determination of iron sites and the amount of amorphization in radiation-damaged titanite (CaSiTiO5)","publication_status":"published","status":"public","intvolume":" 23","publisher":"IOP Publishing","year":"2011","_id":"7076","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2019-11-19T13:39:30Z","date_updated":"2021-01-12T08:11:43Z","volume":23,"oa_version":"None","author":[{"first_name":"E K H","last_name":"Salje","full_name":"Salje, E K H"},{"full_name":"Safarik, D J","last_name":"Safarik","first_name":"D J"},{"full_name":"Taylor, R D","first_name":"R D","last_name":"Taylor"},{"first_name":"M P","last_name":"Pasternak","full_name":"Pasternak, M P"},{"full_name":"Modic, Kimberly A","first_name":"Kimberly A","last_name":"Modic","id":"13C26AC0-EB69-11E9-87C6-5F3BE6697425","orcid":"0000-0001-9760-3147"},{"full_name":"Groat, L A","last_name":"Groat","first_name":"L A"},{"full_name":"Lashley, J C","first_name":"J C","last_name":"Lashley"}]},{"article_processing_charge":"No","publication_identifier":{"issn":["0925-8388"]},"day":"03","month":"02","language":[{"iso":"eng"}],"doi":"10.1016/j.jallcom.2010.10.187","date_published":"2011-02-03T00:00:00Z","page":"1544-1549","quality_controlled":"1","article_type":"original","citation":{"ieee":"J. Capps et al., “The effect of Ag concentration on the structural, electrical and thermal transport behavior of Pb:Te:Ag:Se mixtures and improvement of thermoelectric performance via Cu doping,” Journal of Alloys and Compounds, vol. 509, no. 5. Elsevier, pp. 1544–1549, 2011.","apa":"Capps, J., Ma, B., Drye, T., Nucklos, C., Lindsey, S., Rhodes, D., … Drymiotis, F. (2011). The effect of Ag concentration on the structural, electrical and thermal transport behavior of Pb:Te:Ag:Se mixtures and improvement of thermoelectric performance via Cu doping. Journal of Alloys and Compounds. Elsevier. https://doi.org/10.1016/j.jallcom.2010.10.187","ista":"Capps J, Ma B, Drye T, Nucklos C, Lindsey S, Rhodes D, Zhang Q, Modic KA, Cawthorne S, Drymiotis F. 2011. The effect of Ag concentration on the structural, electrical and thermal transport behavior of Pb:Te:Ag:Se mixtures and improvement of thermoelectric performance via Cu doping. Journal of Alloys and Compounds. 509(5), 1544–1549.","ama":"Capps J, Ma B, Drye T, et al. The effect of Ag concentration on the structural, electrical and thermal transport behavior of Pb:Te:Ag:Se mixtures and improvement of thermoelectric performance via Cu doping. Journal of Alloys and Compounds. 2011;509(5):1544-1549. doi:10.1016/j.jallcom.2010.10.187","chicago":"Capps, J., B. Ma, T. Drye, C. Nucklos, S. Lindsey, D. Rhodes, Q. Zhang, Kimberly A Modic, S. Cawthorne, and F. Drymiotis. “The Effect of Ag Concentration on the Structural, Electrical and Thermal Transport Behavior of Pb:Te:Ag:Se Mixtures and Improvement of Thermoelectric Performance via Cu Doping.” Journal of Alloys and Compounds. Elsevier, 2011. https://doi.org/10.1016/j.jallcom.2010.10.187.","short":"J. Capps, B. Ma, T. Drye, C. Nucklos, S. Lindsey, D. Rhodes, Q. Zhang, K.A. Modic, S. Cawthorne, F. Drymiotis, Journal of Alloys and Compounds 509 (2011) 1544–1549.","mla":"Capps, J., et al. “The Effect of Ag Concentration on the Structural, Electrical and Thermal Transport Behavior of Pb:Te:Ag:Se Mixtures and Improvement of Thermoelectric Performance via Cu Doping.” Journal of Alloys and Compounds, vol. 509, no. 5, Elsevier, 2011, pp. 1544–49, doi:10.1016/j.jallcom.2010.10.187."},"publication":"Journal of Alloys and Compounds","extern":"1","issue":"5","abstract":[{"lang":"eng","text":"Pb, Te, Ag and Se, when reacted in a 1:1:x:1 (x = 1.9, 2.0, 2.01) molar ratio, form a two phase composite which consists of a phase which crystallizes in the fcc cubic PbSe structure and a phase that crystallizes in the Ag2Te structure. In this article, we demonstrate that by varying the Ag concentration, we can manipulate which variant of the Ag2Te structure stabilizes at room temperature (monoclinic α-Ag2Te or cubic β-Ag1.9Te) and can consequently manipulate the electrical and thermal transport behavior of the composite and hence the thermoelectric performance. Additionally, we show that Cu-doping results in an overall improvement in thermoelectric performance. Our results suggest that formation of composites is a viable path for achieving a phonon-glass-electron-crystal (PGEC) alloy."}],"type":"journal_article","volume":509,"oa_version":"None","date_updated":"2021-01-12T08:11:44Z","date_created":"2019-11-19T13:45:37Z","author":[{"first_name":"J.","last_name":"Capps","full_name":"Capps, J."},{"full_name":"Ma, B.","last_name":"Ma","first_name":"B."},{"first_name":"T.","last_name":"Drye","full_name":"Drye, T."},{"full_name":"Nucklos, C.","last_name":"Nucklos","first_name":"C."},{"first_name":"S.","last_name":"Lindsey","full_name":"Lindsey, S."},{"first_name":"D.","last_name":"Rhodes","full_name":"Rhodes, D."},{"first_name":"Q.","last_name":"Zhang","full_name":"Zhang, Q."},{"orcid":"0000-0001-9760-3147","id":"13C26AC0-EB69-11E9-87C6-5F3BE6697425","last_name":"Modic","first_name":"Kimberly A","full_name":"Modic, Kimberly A"},{"last_name":"Cawthorne","first_name":"S.","full_name":"Cawthorne, S."},{"first_name":"F.","last_name":"Drymiotis","full_name":"Drymiotis, F."}],"publisher":"Elsevier","intvolume":" 509","status":"public","publication_status":"published","title":"The effect of Ag concentration on the structural, electrical and thermal transport behavior of Pb:Te:Ag:Se mixtures and improvement of thermoelectric performance via Cu doping","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"7077","year":"2011"},{"type":"journal_article","extern":"1","issue":"1","abstract":[{"lang":"eng","text":"Li-ion batteries have transformed portable electronics and will play a key role in the electrification of transport. However, the highest energy storage possible for Li-ion batteries is insufficient for the long-term needs of society, for example, extended-range electric vehicles. To go beyond the horizon of Li-ion batteries is a formidable challenge; there are few options. Here we consider two: Li–air (O2) and Li–S. The energy that can be stored in Li–air (based on aqueous or non-aqueous electrolytes) and Li–S cells is compared with Li-ion; the operation of the cells is discussed, as are the significant hurdles that will have to be overcome if such batteries are to succeed. Fundamental scientific advances in understanding the reactions occurring in the cells as well as new materials are key to overcoming these obstacles. The potential benefits of Li–air and Li–S justify the continued research effort that will be needed."}],"intvolume":" 11","publisher":"Springer Nature","status":"public","title":"Li–O2 and Li–S batteries with high energy storage","publication_status":"published","_id":"7313","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2011","oa_version":"None","volume":11,"date_updated":"2021-01-12T08:12:59Z","date_created":"2020-01-15T12:20:01Z","related_material":{"link":[{"url":"https://doi.org/10.1038/nmat3237","relation":"erratum"}]},"author":[{"first_name":"Peter G.","last_name":"Bruce","full_name":"Bruce, Peter G."},{"full_name":"Freunberger, Stefan Alexander","last_name":"Freunberger","first_name":"Stefan Alexander","orcid":"0000-0003-2902-5319","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425"},{"last_name":"Hardwick","first_name":"Laurence J.","full_name":"Hardwick, Laurence J."},{"full_name":"Tarascon, Jean-Marie","last_name":"Tarascon","first_name":"Jean-Marie"}],"article_processing_charge":"No","publication_identifier":{"issn":["1476-1122","1476-4660"]},"day":"15","month":"12","page":"19-29","article_type":"original","quality_controlled":"1","citation":{"ista":"Bruce PG, Freunberger SA, Hardwick LJ, Tarascon J-M. 2011. Li–O2 and Li–S batteries with high energy storage. Nature Materials. 11(1), 19–29.","apa":"Bruce, P. G., Freunberger, S. A., Hardwick, L. J., & Tarascon, J.-M. (2011). Li–O2 and Li–S batteries with high energy storage. Nature Materials. Springer Nature. https://doi.org/10.1038/nmat3191","ieee":"P. G. Bruce, S. A. Freunberger, L. J. Hardwick, and J.-M. Tarascon, “Li–O2 and Li–S batteries with high energy storage,” Nature Materials, vol. 11, no. 1. Springer Nature, pp. 19–29, 2011.","ama":"Bruce PG, Freunberger SA, Hardwick LJ, Tarascon J-M. Li–O2 and Li–S batteries with high energy storage. Nature Materials. 2011;11(1):19-29. doi:10.1038/nmat3191","chicago":"Bruce, Peter G., Stefan Alexander Freunberger, Laurence J. Hardwick, and Jean-Marie Tarascon. “Li–O2 and Li–S Batteries with High Energy Storage.” Nature Materials. Springer Nature, 2011. https://doi.org/10.1038/nmat3191.","mla":"Bruce, Peter G., et al. “Li–O2 and Li–S Batteries with High Energy Storage.” Nature Materials, vol. 11, no. 1, Springer Nature, 2011, pp. 19–29, doi:10.1038/nmat3191.","short":"P.G. Bruce, S.A. Freunberger, L.J. Hardwick, J.-M. Tarascon, Nature Materials 11 (2011) 19–29."},"publication":"Nature Materials","language":[{"iso":"eng"}],"date_published":"2011-12-15T00:00:00Z","doi":"10.1038/nmat3191"},{"abstract":[{"lang":"eng","text":"The electrolyte is one of the greatest challenges facing the development of the non‐aqueous Li–O2 battery. Although ether‐based electrolytes do from Li2O2 on the first discharge, it is shown by various techniques that they also decompose and that decomposition increases while Li2O2 decreases on cycling (see picture). Thus, these electrolytes are not suitable. "}],"issue":"37","extern":"1","type":"journal_article","author":[{"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":"Yuhui","last_name":"Chen","full_name":"Chen, Yuhui"},{"last_name":"Drewett","first_name":"Nicholas E.","full_name":"Drewett, Nicholas E."},{"last_name":"Hardwick","first_name":"Laurence J.","full_name":"Hardwick, Laurence J."},{"first_name":"Fanny","last_name":"Bardé","full_name":"Bardé, Fanny"},{"first_name":"Peter G.","last_name":"Bruce","full_name":"Bruce, Peter G."}],"date_created":"2020-01-15T12:20:19Z","date_updated":"2021-01-12T08:12:59Z","oa_version":"None","volume":50,"_id":"7314","year":"2011","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"The Lithium-Oxygen battery with ether-based electrolytes","publication_status":"published","intvolume":" 50","publisher":"Wiley","day":"05","month":"09","article_processing_charge":"No","publication_identifier":{"issn":["1433-7851"]},"doi":"10.1002/anie.201102357","date_published":"2011-09-05T00:00:00Z","language":[{"iso":"eng"}],"publication":"Angewandte Chemie International Edition","citation":{"short":"S.A. Freunberger, Y. Chen, N.E. Drewett, L.J. Hardwick, F. Bardé, P.G. Bruce, Angewandte Chemie International Edition 50 (2011) 8609–8613.","mla":"Freunberger, Stefan Alexander, et al. “The Lithium-Oxygen Battery with Ether-Based Electrolytes.” Angewandte Chemie International Edition, vol. 50, no. 37, Wiley, 2011, pp. 8609–13, doi:10.1002/anie.201102357.","chicago":"Freunberger, Stefan Alexander, Yuhui Chen, Nicholas E. Drewett, Laurence J. Hardwick, Fanny Bardé, and Peter G. Bruce. “The Lithium-Oxygen Battery with Ether-Based Electrolytes.” Angewandte Chemie International Edition. Wiley, 2011. https://doi.org/10.1002/anie.201102357.","ama":"Freunberger SA, Chen Y, Drewett NE, Hardwick LJ, Bardé F, Bruce PG. The Lithium-Oxygen battery with ether-based electrolytes. Angewandte Chemie International Edition. 2011;50(37):8609-8613. doi:10.1002/anie.201102357","ieee":"S. A. Freunberger, Y. Chen, N. E. Drewett, L. J. Hardwick, F. Bardé, and P. G. Bruce, “The Lithium-Oxygen battery with ether-based electrolytes,” Angewandte Chemie International Edition, vol. 50, no. 37. Wiley, pp. 8609–8613, 2011.","apa":"Freunberger, S. A., Chen, Y., Drewett, N. E., Hardwick, L. J., Bardé, F., & Bruce, P. G. (2011). The Lithium-Oxygen battery with ether-based electrolytes. Angewandte Chemie International Edition. Wiley. https://doi.org/10.1002/anie.201102357","ista":"Freunberger SA, Chen Y, Drewett NE, Hardwick LJ, Bardé F, Bruce PG. 2011. The Lithium-Oxygen battery with ether-based electrolytes. Angewandte Chemie International Edition. 50(37), 8609–8613."},"article_type":"original","quality_controlled":"1","page":"8609-8613"},{"date_created":"2020-01-15T12:20:54Z","date_updated":"2021-01-12T08:13:00Z","volume":14,"oa_version":"None","author":[{"full_name":"Trahey, L.","last_name":"Trahey","first_name":"L."},{"full_name":"Johnson, C. S.","last_name":"Johnson","first_name":"C. S."},{"full_name":"Vaughey, J. T.","last_name":"Vaughey","first_name":"J. T."},{"first_name":"S.-H.","last_name":"Kang","full_name":"Kang, S.-H."},{"first_name":"L. J.","last_name":"Hardwick","full_name":"Hardwick, L. J."},{"full_name":"Freunberger, Stefan Alexander","last_name":"Freunberger","first_name":"Stefan Alexander","orcid":"0000-0003-2902-5319","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425"},{"full_name":"Bruce, P. G.","last_name":"Bruce","first_name":"P. G."},{"full_name":"Thackeray, M. M.","first_name":"M. M.","last_name":"Thackeray"}],"status":"public","title":"Activated Lithium-Metal-Oxides as catalytic electrodes for Li–O2 cells","publication_status":"published","intvolume":" 14","publisher":"The Electrochemical Society","_id":"7317","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2011","extern":"1","abstract":[{"text":"Lithium-metal oxides with a high formal Li2O content, such as Li5FeO4 (5Li2O•Fe2O3) and a Li2MnO3•LiFeO2 composite ({Li2O•MnO2}•{Li2O•Fe2O3}) have been explored as electrocatalysts for primary and rechargeable Li-O2 cells. Activation occurs predominantly by Li2O removal, either electrochemically or chemically by acid-treatment. Superior electrochemical behavior is obtained if activation occurs by acid-treatment; Li2MnO3•LiFeO2 catalysts provide 2516 mAh/g (carbon) corresponding to 931 mAh/g (electrocatalyst + carbon) during the initial discharge. The reaction is reasonably reversible during the early cycles. The approach has implications for designing electrocatalysts that participate through electrochemical Li2O extraction/reformation reactions, offering exceptionally high capacities.","lang":"eng"}],"issue":"5","article_number":"A64","type":"journal_article","language":[{"iso":"eng"}],"date_published":"2011-03-02T00:00:00Z","doi":"10.1149/1.3555366","article_type":"original","quality_controlled":"1","publication":"Electrochemical and Solid-State Letters","citation":{"apa":"Trahey, L., Johnson, C. S., Vaughey, J. T., Kang, S.-H., Hardwick, L. J., Freunberger, S. A., … Thackeray, M. M. (2011). Activated Lithium-Metal-Oxides as catalytic electrodes for Li–O2 cells. Electrochemical and Solid-State Letters. The Electrochemical Society. https://doi.org/10.1149/1.3555366","ieee":"L. Trahey et al., “Activated Lithium-Metal-Oxides as catalytic electrodes for Li–O2 cells,” Electrochemical and Solid-State Letters, vol. 14, no. 5. The Electrochemical Society, 2011.","ista":"Trahey L, Johnson CS, Vaughey JT, Kang S-H, Hardwick LJ, Freunberger SA, Bruce PG, Thackeray MM. 2011. Activated Lithium-Metal-Oxides as catalytic electrodes for Li–O2 cells. Electrochemical and Solid-State Letters. 14(5), A64.","ama":"Trahey L, Johnson CS, Vaughey JT, et al. Activated Lithium-Metal-Oxides as catalytic electrodes for Li–O2 cells. Electrochemical and Solid-State Letters. 2011;14(5). doi:10.1149/1.3555366","chicago":"Trahey, L., C. S. Johnson, J. T. Vaughey, S.-H. Kang, L. J. Hardwick, Stefan Alexander Freunberger, P. G. Bruce, and M. M. Thackeray. “Activated Lithium-Metal-Oxides as Catalytic Electrodes for Li–O2 Cells.” Electrochemical and Solid-State Letters. The Electrochemical Society, 2011. https://doi.org/10.1149/1.3555366.","short":"L. Trahey, C.S. Johnson, J.T. Vaughey, S.-H. Kang, L.J. Hardwick, S.A. Freunberger, P.G. Bruce, M.M. Thackeray, Electrochemical and Solid-State Letters 14 (2011).","mla":"Trahey, L., et al. “Activated Lithium-Metal-Oxides as Catalytic Electrodes for Li–O2 Cells.” Electrochemical and Solid-State Letters, vol. 14, no. 5, A64, The Electrochemical Society, 2011, doi:10.1149/1.3555366."},"month":"03","day":"02","publication_identifier":{"issn":["1099-0062"]},"article_processing_charge":"No"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"7316","year":"2011","publisher":"ACS","intvolume":" 133","title":"Reactions in the rechargeable Lithium–O2 battery with alkyl carbonate electrolytes","publication_status":"published","status":"public","author":[{"orcid":"0000-0003-2902-5319","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","last_name":"Freunberger","first_name":"Stefan Alexander","full_name":"Freunberger, Stefan Alexander"},{"full_name":"Chen, Yuhui","last_name":"Chen","first_name":"Yuhui"},{"last_name":"Peng","first_name":"Zhangquan","full_name":"Peng, Zhangquan"},{"last_name":"Griffin","first_name":"John M.","full_name":"Griffin, John M."},{"full_name":"Hardwick, Laurence J.","first_name":"Laurence J.","last_name":"Hardwick"},{"full_name":"Bardé, Fanny","first_name":"Fanny","last_name":"Bardé"},{"first_name":"Petr","last_name":"Novák","full_name":"Novák, Petr"},{"full_name":"Bruce, Peter G.","last_name":"Bruce","first_name":"Peter G."}],"oa_version":"None","volume":133,"date_updated":"2021-01-12T08:13:00Z","date_created":"2020-01-15T12:20:43Z","type":"journal_article","issue":"20","abstract":[{"text":"The nonaqueous rechargeable lithium–O2 battery containing an alkyl carbonate electrolyte discharges by formation of C3H6(OCO2Li)2, Li2CO3, HCO2Li, CH3CO2Li, CO2, and H2O at the cathode, due to electrolyte decomposition. Charging involves oxidation of C3H6(OCO2Li)2, Li2CO3, HCO2Li, CH3CO2Li accompanied by CO2 and H2O evolution. Mechanisms are proposed for the reactions on discharge and charge. The different pathways for discharge and charge are consistent with the widely observed voltage gap in Li–O2 cells. Oxidation of C3H6(OCO2Li)2 involves terminal carbonate groups leaving behind the OC3H6O moiety that reacts to form a thick gel on the Li anode. Li2CO3, HCO2Li, CH3CO2Li, and C3H6(OCO2Li)2 accumulate in the cathode on cycling correlating with capacity fading and cell failure. The latter is compounded by continuous consumption of the electrolyte on each discharge.","lang":"eng"}],"extern":"1","citation":{"chicago":"Freunberger, Stefan Alexander, Yuhui Chen, Zhangquan Peng, John M. Griffin, Laurence J. Hardwick, Fanny Bardé, Petr Novák, and Peter G. Bruce. “Reactions in the Rechargeable Lithium–O2 Battery with Alkyl Carbonate Electrolytes.” Journal of the American Chemical Society. ACS, 2011. https://doi.org/10.1021/ja2021747.","short":"S.A. Freunberger, Y. Chen, Z. Peng, J.M. Griffin, L.J. Hardwick, F. Bardé, P. Novák, P.G. Bruce, Journal of the American Chemical Society 133 (2011) 8040–8047.","mla":"Freunberger, Stefan Alexander, et al. “Reactions in the Rechargeable Lithium–O2 Battery with Alkyl Carbonate Electrolytes.” Journal of the American Chemical Society, vol. 133, no. 20, ACS, 2011, pp. 8040–47, doi:10.1021/ja2021747.","ieee":"S. A. Freunberger et al., “Reactions in the rechargeable Lithium–O2 battery with alkyl carbonate electrolytes,” Journal of the American Chemical Society, vol. 133, no. 20. ACS, pp. 8040–8047, 2011.","apa":"Freunberger, S. A., Chen, Y., Peng, Z., Griffin, J. M., Hardwick, L. J., Bardé, F., … Bruce, P. G. (2011). Reactions in the rechargeable Lithium–O2 battery with alkyl carbonate electrolytes. Journal of the American Chemical Society. ACS. https://doi.org/10.1021/ja2021747","ista":"Freunberger SA, Chen Y, Peng Z, Griffin JM, Hardwick LJ, Bardé F, Novák P, Bruce PG. 2011. Reactions in the rechargeable Lithium–O2 battery with alkyl carbonate electrolytes. Journal of the American Chemical Society. 133(20), 8040–8047.","ama":"Freunberger SA, Chen Y, Peng Z, et al. Reactions in the rechargeable Lithium–O2 battery with alkyl carbonate electrolytes. Journal of the American Chemical Society. 2011;133(20):8040-8047. doi:10.1021/ja2021747"},"publication":"Journal of the American Chemical Society","page":"8040-8047","article_type":"original","quality_controlled":"1","date_published":"2011-04-27T00:00:00Z","doi":"10.1021/ja2021747","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0002-7863","1520-5126"]},"article_processing_charge":"No","day":"27","month":"04"},{"article_processing_charge":"No","publication_identifier":{"issn":["1433-7851"]},"month":"07","day":"04","citation":{"ista":"Peng Z, Freunberger SA, Hardwick LJ, Chen Y, Giordani V, Bardé F, Novák P, Graham D, Tarascon J-M, Bruce PG. 2011. Oxygen reactions in a non-aqueous Li+ electrolyte. Angewandte Chemie International Edition. 50(28), 6351–6355.","ieee":"Z. Peng et al., “Oxygen reactions in a non-aqueous Li+ electrolyte,” Angewandte Chemie International Edition, vol. 50, no. 28. Wiley, pp. 6351–6355, 2011.","apa":"Peng, Z., Freunberger, S. A., Hardwick, L. J., Chen, Y., Giordani, V., Bardé, F., … Bruce, P. G. (2011). Oxygen reactions in a non-aqueous Li+ electrolyte. Angewandte Chemie International Edition. Wiley. https://doi.org/10.1002/anie.201100879","ama":"Peng Z, Freunberger SA, Hardwick LJ, et al. Oxygen reactions in a non-aqueous Li+ electrolyte. Angewandte Chemie International Edition. 2011;50(28):6351-6355. doi:10.1002/anie.201100879","chicago":"Peng, Zhangquan, Stefan Alexander Freunberger, Laurence J. Hardwick, Yuhui Chen, Vincent Giordani, Fanny Bardé, Petr Novák, Duncan Graham, Jean-Marie Tarascon, and Peter G. Bruce. “Oxygen Reactions in a Non-Aqueous Li+ Electrolyte.” Angewandte Chemie International Edition. Wiley, 2011. https://doi.org/10.1002/anie.201100879.","mla":"Peng, Zhangquan, et al. “Oxygen Reactions in a Non-Aqueous Li+ Electrolyte.” Angewandte Chemie International Edition, vol. 50, no. 28, Wiley, 2011, pp. 6351–55, doi:10.1002/anie.201100879.","short":"Z. Peng, S.A. Freunberger, L.J. Hardwick, Y. Chen, V. Giordani, F. Bardé, P. Novák, D. Graham, J.-M. Tarascon, P.G. Bruce, Angewandte Chemie International Edition 50 (2011) 6351–6355."},"publication":"Angewandte Chemie International Edition","page":"6351-6355","article_type":"original","doi":"10.1002/anie.201100879","date_published":"2011-07-04T00:00:00Z","language":[{"iso":"eng"}],"type":"journal_article","issue":"28","abstract":[{"text":"Spectroscopic data (see picture) provide direct evidence that in non‐aqueous Li+ electrolyte, O2 is reduced to O2−, which then forms LiO2 on the electrode surface which disproportionates to Li2O2. On charging, Li2O2 decomposes directly, in a one‐step reaction to evolve O2 and does not pass through LiO2 as an intermediate. ","lang":"eng"}],"extern":"1","_id":"7315","year":"2011","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 50","publisher":"Wiley","status":"public","title":"Oxygen reactions in a non-aqueous Li+ electrolyte","publication_status":"published","author":[{"full_name":"Peng, Zhangquan","last_name":"Peng","first_name":"Zhangquan"},{"full_name":"Freunberger, Stefan Alexander","last_name":"Freunberger","first_name":"Stefan Alexander","orcid":"0000-0003-2902-5319","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425"},{"first_name":"Laurence J.","last_name":"Hardwick","full_name":"Hardwick, Laurence J."},{"first_name":"Yuhui","last_name":"Chen","full_name":"Chen, Yuhui"},{"full_name":"Giordani, Vincent","last_name":"Giordani","first_name":"Vincent"},{"last_name":"Bardé","first_name":"Fanny","full_name":"Bardé, Fanny"},{"last_name":"Novák","first_name":"Petr","full_name":"Novák, Petr"},{"first_name":"Duncan","last_name":"Graham","full_name":"Graham, Duncan"},{"full_name":"Tarascon, Jean-Marie","last_name":"Tarascon","first_name":"Jean-Marie"},{"full_name":"Bruce, Peter G.","first_name":"Peter G.","last_name":"Bruce"}],"oa_version":"None","volume":50,"date_created":"2020-01-15T12:20:31Z","date_updated":"2021-01-12T08:12:59Z"},{"extern":"1","abstract":[{"text":"Synchronous distributed algorithms are easier to design and prove correct than algorithms that tolerate asynchrony. Yet, in the real world, networks experience asynchrony and other timing anomalies. In this paper, we address the question of how to efficiently transform an algorithm that relies on synchronization into an algorithm that tolerates asynchronous executions. We introduce a transformation technique from synchronous algorithms to indulgent algorithms [1], which induces only a constant overhead in terms of time complexity in well-behaved executions. Our technique is based on a new abstraction we call an asynchrony detector, which the participating processes implement collectively. The resulting transformation works for a large class of colorless tasks, including consensus and set agreement. Interestingly, we also show that our technique is relevant for colored tasks, by applying it to the renaming problem, to obtain the first indulgent renaming algorithm.","lang":"eng"}],"publist_id":"6898","alternative_title":["LNCS"],"type":"conference","date_created":"2018-12-11T11:48:20Z","date_updated":"2023-02-23T13:11:09Z","oa_version":"None","volume":"6522 LNCS","author":[{"full_name":"Alistarh, Dan-Adrian","first_name":"Dan-Adrian","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X"},{"last_name":"Gilbert","first_name":"Seth","full_name":"Gilbert, Seth"},{"last_name":"Guerraoui","first_name":"Rachid","full_name":"Guerraoui, Rachid"},{"full_name":"Travers, Corentin","last_name":"Travers","first_name":"Corentin"}],"title":"Generating fast indulgent algorithms","status":"public","publication_status":"published","publisher":"Springer","_id":"757","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"The authors would like to thank Prof. Hagit Attiya and Nikola\r\nKneˇ\r\nzevi ́\r\nc for their help on previous drafts of this paper, and the anonymous reviewers\r\nfor their useful feedback.","year":"2011","day":"01","month":"01","article_processing_charge":"No","language":[{"iso":"eng"}],"conference":{"name":"ICDCN: International Conference on Distributed Computing and Networking"},"date_published":"2011-01-01T00:00:00Z","doi":"10.1007/978-3-642-17679-1_4","page":"41 - 52","citation":{"apa":"Alistarh, D.-A., Gilbert, S., Guerraoui, R., & Travers, C. (2011). Generating fast indulgent algorithms (Vol. 6522 LNCS, pp. 41–52). Presented at the ICDCN: International Conference on Distributed Computing and Networking, Springer. https://doi.org/10.1007/978-3-642-17679-1_4","ieee":"D.-A. Alistarh, S. Gilbert, R. Guerraoui, and C. Travers, “Generating fast indulgent algorithms,” presented at the ICDCN: International Conference on Distributed Computing and Networking, 2011, vol. 6522 LNCS, pp. 41–52.","ista":"Alistarh D-A, Gilbert S, Guerraoui R, Travers C. 2011. Generating fast indulgent algorithms. ICDCN: International Conference on Distributed Computing and Networking, LNCS, vol. 6522 LNCS, 41–52.","ama":"Alistarh D-A, Gilbert S, Guerraoui R, Travers C. Generating fast indulgent algorithms. In: Vol 6522 LNCS. Springer; 2011:41-52. doi:10.1007/978-3-642-17679-1_4","chicago":"Alistarh, Dan-Adrian, Seth Gilbert, Rachid Guerraoui, and Corentin Travers. “Generating Fast Indulgent Algorithms,” 6522 LNCS:41–52. Springer, 2011. https://doi.org/10.1007/978-3-642-17679-1_4.","short":"D.-A. Alistarh, S. Gilbert, R. Guerraoui, C. Travers, in:, Springer, 2011, pp. 41–52.","mla":"Alistarh, Dan-Adrian, et al. Generating Fast Indulgent Algorithms. Vol. 6522 LNCS, Springer, 2011, pp. 41–52, doi:10.1007/978-3-642-17679-1_4."}},{"type":"conference","extern":"1","abstract":[{"text":"We study the complexity of renaming, a fundamental problem in distributed computing in which a set of processes need to pick distinct names from a given namespace. We prove an individual lower bound of Ω(k) process steps for deterministic renaming into any namespace of size sub-exponential in k, where k is the number of participants. This bound is tight: it draws an exponential separation between deterministic and randomized solutions, and implies new tight bounds for deterministic fetch-and-increment registers, queues and stacks. The proof of the bound is interesting in its own right, for it relies on the first reduction from renaming to another fundamental problem in distributed computing: mutual exclusion. We complement our individual bound with a global lower bound of Ω(k log (k/c)) on the total step complexity of renaming into a namespace of size ck, for any c ≥ 1. This applies to randomized algorithms against a strong adversary, and helps derive new global lower bounds for randomized approximate counter and fetch-and-increment implementations, all tight within logarithmic factors.","lang":"eng"}],"publist_id":"6895","publication_status":"published","title":"The complexity of renaming","status":"public","publisher":"IEEE","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"759","acknowledgement":"The authors would like to thank Hagit Attiya and Keren\r\nCensor-Hillel for discussions and feedback on earlier versions of this paper, and the anonymous reviewers for their\r\nvery useful suggestions.","year":"2011","date_updated":"2023-02-23T13:11:40Z","date_created":"2018-12-11T11:48:21Z","oa_version":"None","author":[{"last_name":"Alistarh","first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","full_name":"Alistarh, Dan-Adrian"},{"first_name":"James","last_name":"Aspnes","full_name":"Aspnes, James"},{"last_name":"Gilbert","first_name":"Seth","full_name":"Gilbert, Seth"},{"last_name":"Guerraoui","first_name":"Rachid","full_name":"Guerraoui, Rachid"}],"month":"01","day":"01","article_processing_charge":"No","page":"718 - 727","citation":{"mla":"Alistarh, Dan-Adrian, et al. The Complexity of Renaming. IEEE, 2011, pp. 718–27, doi:10.1109/FOCS.2011.66.","short":"D.-A. Alistarh, J. Aspnes, S. Gilbert, R. Guerraoui, in:, IEEE, 2011, pp. 718–727.","chicago":"Alistarh, Dan-Adrian, James Aspnes, Seth Gilbert, and Rachid Guerraoui. “The Complexity of Renaming,” 718–27. IEEE, 2011. https://doi.org/10.1109/FOCS.2011.66.","ama":"Alistarh D-A, Aspnes J, Gilbert S, Guerraoui R. The complexity of renaming. In: IEEE; 2011:718-727. doi:10.1109/FOCS.2011.66","ista":"Alistarh D-A, Aspnes J, Gilbert S, Guerraoui R. 2011. The complexity of renaming. FOCS: Foundations of Computer Science, 718–727.","ieee":"D.-A. Alistarh, J. Aspnes, S. Gilbert, and R. Guerraoui, “The complexity of renaming,” presented at the FOCS: Foundations of Computer Science, 2011, pp. 718–727.","apa":"Alistarh, D.-A., Aspnes, J., Gilbert, S., & Guerraoui, R. (2011). The complexity of renaming (pp. 718–727). Presented at the FOCS: Foundations of Computer Science, IEEE. https://doi.org/10.1109/FOCS.2011.66"},"language":[{"iso":"eng"}],"conference":{"name":"FOCS: Foundations of Computer Science"},"date_published":"2011-01-01T00:00:00Z","doi":"10.1109/FOCS.2011.66"},{"acknowledgement":"We would like to thank Hagit Attiya, Rachid Guerraoui\r\nand Prasad Jayanti for useful discussions and support. We\r\nwould also like to thank the anonymous reviewers for many\r\nuseful comments.","_id":"761","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2011","publisher":"ACM","title":"Optimal-time adaptive strong renaming, with applications to counting","publication_status":"published","status":"public","author":[{"full_name":"Alistarh, Dan-Adrian","first_name":"Dan-Adrian","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X"},{"full_name":"Aspnes, James","last_name":"Aspnes","first_name":"James"},{"full_name":"Censor Hillel, Keren","last_name":"Censor Hillel","first_name":"Keren"},{"full_name":"Gilbert, Seth","first_name":"Seth","last_name":"Gilbert"},{"last_name":"Zadimoghaddam","first_name":"Morteza","full_name":"Zadimoghaddam, Morteza"}],"oa_version":"None","date_updated":"2023-02-23T13:12:17Z","date_created":"2018-12-11T11:48:22Z","type":"conference","publist_id":"6897","abstract":[{"text":"We give two new randomized algorithms for strong renaming, both of which work against an adaptive adversary in asynchronous shared memory. The first uses repeated sampling over a sequence of arrays of decreasing size to assign unique names to each of n processes with step complexity O(log3 n). The second transforms any sorting network into a strong adaptive renaming protocol, with an expected cost equal to the depth of the sorting network. Using an AKS sorting network, this gives a strong adaptive renaming algorithm with step complexity O(log k), where k is the contention in the current execution. We show this to be optimal based on a classic lower bound of Jayanti. We also show that any such strong renaming protocol can be used to build a monotone-consistent counter with logarithmic step complexity (at the cost of adding a max register) or a linearizable fetch-and-increment register (at the cost of increasing the step complexity by a logarithmic factor).","lang":"eng"}],"extern":"1","citation":{"apa":"Alistarh, D.-A., Aspnes, J., Censor Hillel, K., Gilbert, S., & Zadimoghaddam, M. (2011). Optimal-time adaptive strong renaming, with applications to counting (pp. 239–248). Presented at the PODC: Principles of Distributed Computing, ACM. https://doi.org/10.1145/1993806.1993850","ieee":"D.-A. Alistarh, J. Aspnes, K. Censor Hillel, S. Gilbert, and M. Zadimoghaddam, “Optimal-time adaptive strong renaming, with applications to counting,” presented at the PODC: Principles of Distributed Computing, 2011, pp. 239–248.","ista":"Alistarh D-A, Aspnes J, Censor Hillel K, Gilbert S, Zadimoghaddam M. 2011. Optimal-time adaptive strong renaming, with applications to counting. PODC: Principles of Distributed Computing, 239–248.","ama":"Alistarh D-A, Aspnes J, Censor Hillel K, Gilbert S, Zadimoghaddam M. Optimal-time adaptive strong renaming, with applications to counting. In: ACM; 2011:239-248. doi:10.1145/1993806.1993850","chicago":"Alistarh, Dan-Adrian, James Aspnes, Keren Censor Hillel, Seth Gilbert, and Morteza Zadimoghaddam. “Optimal-Time Adaptive Strong Renaming, with Applications to Counting,” 239–48. ACM, 2011. https://doi.org/10.1145/1993806.1993850.","short":"D.-A. Alistarh, J. Aspnes, K. Censor Hillel, S. Gilbert, M. Zadimoghaddam, in:, ACM, 2011, pp. 239–248.","mla":"Alistarh, Dan-Adrian, et al. Optimal-Time Adaptive Strong Renaming, with Applications to Counting. ACM, 2011, pp. 239–48, doi:10.1145/1993806.1993850."},"page":"239 - 248","doi":"10.1145/1993806.1993850","date_published":"2011-01-01T00:00:00Z","conference":{"name":"PODC: Principles of Distributed Computing"},"language":[{"iso":"eng"}],"article_processing_charge":"No","day":"01","month":"01"},{"type":"conference","alternative_title":["LNCS"],"publist_id":"6896","abstract":[{"lang":"eng","text":"A randomized implementation is given of a test-and-set register with O(log log n) individual step complexity and O(n) total step complexity against an oblivious adversary. The implementation is linearizable and multi-shot, and shows an exponential complexity improvement over previous solutions designed to work against a strong adversary."}],"extern":"1","acknowledgement":"The work of Dan Alistarh was supported by the NCCR MICS Project. The work of James Aspnes was supported in part by NSF grant CCF-0916389.","_id":"760","year":"2011","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Springer","publication_status":"published","status":"public","title":"Sub-logarithmic test-and-set against a weak adversary","author":[{"id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian","last_name":"Alistarh","full_name":"Alistarh, Dan-Adrian"},{"last_name":"Aspnes","first_name":"James","full_name":"Aspnes, James"}],"volume":"6950 LNCS","oa_version":"None","date_updated":"2023-02-23T13:12:01Z","date_created":"2018-12-11T11:48:21Z","article_processing_charge":"No","month":"01","day":"01","citation":{"chicago":"Alistarh, Dan-Adrian, and James Aspnes. “Sub-Logarithmic Test-and-Set against a Weak Adversary,” 6950 LNCS:97–109. Springer, 2011. https://doi.org/10.1007/978-3-642-24100-0_7.","mla":"Alistarh, Dan-Adrian, and James Aspnes. Sub-Logarithmic Test-and-Set against a Weak Adversary. Vol. 6950 LNCS, Springer, 2011, pp. 97–109, doi:10.1007/978-3-642-24100-0_7.","short":"D.-A. Alistarh, J. Aspnes, in:, Springer, 2011, pp. 97–109.","ista":"Alistarh D-A, Aspnes J. 2011. Sub-logarithmic test-and-set against a weak adversary. DISC: Distributed Computing, LNCS, vol. 6950 LNCS, 97–109.","ieee":"D.-A. Alistarh and J. Aspnes, “Sub-logarithmic test-and-set against a weak adversary,” presented at the DISC: Distributed Computing, 2011, vol. 6950 LNCS, pp. 97–109.","apa":"Alistarh, D.-A., & Aspnes, J. (2011). Sub-logarithmic test-and-set against a weak adversary (Vol. 6950 LNCS, pp. 97–109). Presented at the DISC: Distributed Computing, Springer. https://doi.org/10.1007/978-3-642-24100-0_7","ama":"Alistarh D-A, Aspnes J. Sub-logarithmic test-and-set against a weak adversary. In: Vol 6950 LNCS. Springer; 2011:97-109. doi:10.1007/978-3-642-24100-0_7"},"page":"97 - 109","date_published":"2011-01-01T00:00:00Z","doi":"10.1007/978-3-642-24100-0_7","conference":{"name":"DISC: Distributed Computing"},"language":[{"iso":"eng"}]},{"volume":22,"oa_version":"None","date_updated":"2021-01-12T08:15:16Z","date_created":"2020-04-30T11:01:43Z","author":[{"full_name":"Robinson, Matthew Richard","first_name":"Matthew Richard","last_name":"Robinson","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","orcid":"0000-0001-8982-8813"}],"publisher":"Oxford University Press","intvolume":" 22","publication_status":"published","title":"Understanding intrasexual competition and sexual selection requires an evolutionary ecology framework","status":"public","year":"2011","_id":"7750","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","issue":"6","type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1093/beheco/arr110","date_published":"2011-11-01T00:00:00Z","page":"1143-1144","article_type":"original","quality_controlled":"1","citation":{"chicago":"Robinson, Matthew Richard. “Understanding Intrasexual Competition and Sexual Selection Requires an Evolutionary Ecology Framework.” Behavioral Ecology. Oxford University Press, 2011. https://doi.org/10.1093/beheco/arr110.","short":"M.R. Robinson, Behavioral Ecology 22 (2011) 1143–1144.","mla":"Robinson, Matthew Richard. “Understanding Intrasexual Competition and Sexual Selection Requires an Evolutionary Ecology Framework.” Behavioral Ecology, vol. 22, no. 6, Oxford University Press, 2011, pp. 1143–44, doi:10.1093/beheco/arr110.","apa":"Robinson, M. R. (2011). Understanding intrasexual competition and sexual selection requires an evolutionary ecology framework. Behavioral Ecology. Oxford University Press. https://doi.org/10.1093/beheco/arr110","ieee":"M. R. Robinson, “Understanding intrasexual competition and sexual selection requires an evolutionary ecology framework,” Behavioral Ecology, vol. 22, no. 6. Oxford University Press, pp. 1143–1144, 2011.","ista":"Robinson MR. 2011. Understanding intrasexual competition and sexual selection requires an evolutionary ecology framework. Behavioral Ecology. 22(6), 1143–1144.","ama":"Robinson MR. Understanding intrasexual competition and sexual selection requires an evolutionary ecology framework. Behavioral Ecology. 2011;22(6):1143-1144. doi:10.1093/beheco/arr110"},"publication":"Behavioral Ecology","article_processing_charge":"No","publication_identifier":{"issn":["1465-7279","1045-2249"]},"day":"01","month":"11"},{"extern":"1","pmid":1,"year":"2011","publisher":"Society for Neuroscience","publication_status":"published","author":[{"full_name":"Woodruff, A. R.","last_name":"Woodruff","first_name":"A. R."},{"full_name":"McGarry, L. M.","last_name":"McGarry","first_name":"L. M."},{"id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","orcid":"0000-0003-3295-6181","first_name":"Tim P","last_name":"Vogels","full_name":"Vogels, Tim P"},{"full_name":"Inan, M.","last_name":"Inan","first_name":"M."},{"first_name":"S. A.","last_name":"Anderson","full_name":"Anderson, S. A."},{"full_name":"Yuste, R.","last_name":"Yuste","first_name":"R."}],"volume":31,"date_updated":"2021-01-12T08:16:36Z","date_created":"2020-06-25T13:09:49Z","publication_identifier":{"issn":["0270-6474","1529-2401"]},"month":"12","oa":1,"external_id":{"pmid":["22159102"]},"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4071969/","open_access":"1"}],"quality_controlled":"1","doi":"10.1523/jneurosci.3894-11.2011","language":[{"iso":"eng"}],"type":"journal_article","issue":"49","abstract":[{"text":"Chandelier (axoaxonic) cells (ChCs) are a distinct group of GABAergic interneurons that innervate the axon initial segments of pyramidal cells. However, their circuit role and the function of their clearly defined anatomical specificity remain unclear. Recent work has demonstrated that chandelier cells can produce depolarizing GABAergic PSPs, occasionally driving postsynaptic targets to spike. On the other hand, other work suggests that ChCs are hyperpolarizing and may have an inhibitory role. These disparate functional effects may reflect heterogeneity among ChCs. Here, using brain slices from transgenic mouse strains, we first demonstrate that, across different neocortical areas and genetic backgrounds, upper Layer 2/3 ChCs belong to a single electrophysiologically and morphologically defined population, extensively sampling Layer 1 inputs with asymmetric dendrites. Consistent with being a single cell type, we find electrical coupling between ChCs. We then investigate the effect of chandelier cell activation on pyramidal neuron spiking in several conditions, ranging from the resting membrane potential to stimuli designed to approximate in vivo membrane potential dynamics. We find that under quiescent conditions, chandelier cells are capable of both promoting and inhibiting spike generation, depending on the postsynaptic membrane potential. However, during in vivo-like membrane potential fluctuations, the dominant postsynaptic effect was a strong inhibition. Thus, neocortical chandelier cells, even from within a homogeneous population, appear to play a dual role in the circuit, helping to activate quiescent pyramidal neurons, while at the same time inhibiting active ones.","lang":"eng"}],"_id":"8025","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","intvolume":" 31","status":"public","title":"State-dependent function of neocortical chandelier cells","oa_version":"Published Version","article_processing_charge":"No","day":"7","citation":{"chicago":"Woodruff, A. R., L. M. McGarry, Tim P Vogels, M. Inan, S. A. Anderson, and R. Yuste. “State-Dependent Function of Neocortical Chandelier Cells.” Journal of Neuroscience. Society for Neuroscience, 2011. https://doi.org/10.1523/jneurosci.3894-11.2011.","mla":"Woodruff, A. R., et al. “State-Dependent Function of Neocortical Chandelier Cells.” Journal of Neuroscience, vol. 31, no. 49, Society for Neuroscience, 2011, pp. 17872–86, doi:10.1523/jneurosci.3894-11.2011.","short":"A.R. Woodruff, L.M. McGarry, T.P. Vogels, M. Inan, S.A. Anderson, R. Yuste, Journal of Neuroscience 31 (2011) 17872–17886.","ista":"Woodruff AR, McGarry LM, Vogels TP, Inan M, Anderson SA, Yuste R. 2011. State-dependent function of neocortical chandelier cells. Journal of Neuroscience. 31(49), 17872–17886.","apa":"Woodruff, A. R., McGarry, L. M., Vogels, T. P., Inan, M., Anderson, S. A., & Yuste, R. (2011). State-dependent function of neocortical chandelier cells. Journal of Neuroscience. Society for Neuroscience. https://doi.org/10.1523/jneurosci.3894-11.2011","ieee":"A. R. Woodruff, L. M. McGarry, T. P. Vogels, M. Inan, S. A. Anderson, and R. Yuste, “State-dependent function of neocortical chandelier cells,” Journal of Neuroscience, vol. 31, no. 49. Society for Neuroscience, pp. 17872–17886, 2011.","ama":"Woodruff AR, McGarry LM, Vogels TP, Inan M, Anderson SA, Yuste R. State-dependent function of neocortical chandelier cells. Journal of Neuroscience. 2011;31(49):17872-17886. doi:10.1523/jneurosci.3894-11.2011"},"publication":"Journal of Neuroscience","page":"17872-17886","article_type":"original","date_published":"2011-12-07T00:00:00Z"},{"scopus_import":"1","article_processing_charge":"No","day":"16","page":"1569-1573","article_type":"original","citation":{"mla":"Vogels, Tim P., et al. “Inhibitory Plasticity Balances Excitation and Inhibition in Sensory Pathways and Memory Networks.” Science, vol. 334, no. 6062, American Association for the Advancement of Science, 2011, pp. 1569–73, doi:10.1126/science.1211095.","short":"T.P. Vogels, H. Sprekeler, F. Zenke, C. Clopath, W. Gerstner, Science 334 (2011) 1569–1573.","chicago":"Vogels, Tim P, H. Sprekeler, F. Zenke, C. Clopath, and W. Gerstner. “Inhibitory Plasticity Balances Excitation and Inhibition in Sensory Pathways and Memory Networks.” Science. American Association for the Advancement of Science, 2011. https://doi.org/10.1126/science.1211095.","ama":"Vogels TP, Sprekeler H, Zenke F, Clopath C, Gerstner W. Inhibitory plasticity balances excitation and inhibition in sensory pathways and memory networks. Science. 2011;334(6062):1569-1573. doi:10.1126/science.1211095","ista":"Vogels TP, Sprekeler H, Zenke F, Clopath C, Gerstner W. 2011. Inhibitory plasticity balances excitation and inhibition in sensory pathways and memory networks. Science. 334(6062), 1569–1573.","ieee":"T. P. Vogels, H. Sprekeler, F. Zenke, C. Clopath, and W. Gerstner, “Inhibitory plasticity balances excitation and inhibition in sensory pathways and memory networks,” Science, vol. 334, no. 6062. American Association for the Advancement of Science, pp. 1569–1573, 2011.","apa":"Vogels, T. P., Sprekeler, H., Zenke, F., Clopath, C., & Gerstner, W. (2011). Inhibitory plasticity balances excitation and inhibition in sensory pathways and memory networks. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.1211095"},"publication":"Science","date_published":"2011-12-16T00:00:00Z","type":"journal_article","issue":"6062","abstract":[{"text":"Cortical neurons receive balanced excitatory and inhibitory synaptic currents. Such a balance could be established and maintained in an experience-dependent manner by synaptic plasticity at inhibitory synapses. We show that this mechanism provides an explanation for the sparse firing patterns observed in response to natural stimuli and fits well with a recently observed interaction of excitatory and inhibitory receptive field plasticity. The introduction of inhibitory plasticity in suitable recurrent networks provides a homeostatic mechanism that leads to asynchronous irregular network states. Further, it can accommodate synaptic memories with activity patterns that become indiscernible from the background state but can be reactivated by external stimuli. Our results suggest an essential role of inhibitory plasticity in the formation and maintenance of functional cortical circuitry.","lang":"eng"}],"intvolume":" 334","title":"Inhibitory plasticity balances excitation and inhibition in sensory pathways and memory networks","status":"public","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","_id":"8074","oa_version":"None","publication_identifier":{"issn":["0036-8075","1095-9203"]},"month":"12","quality_controlled":"1","external_id":{"pmid":["22075724"]},"language":[{"iso":"eng"}],"doi":"10.1126/science.1211095","extern":"1","publisher":"American Association for the Advancement of Science","publication_status":"published","pmid":1,"year":"2011","volume":334,"date_updated":"2021-06-02T14:57:22Z","date_created":"2020-06-30T13:26:17Z","related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1126/science.336.6083.802-c"}]},"author":[{"full_name":"Vogels, Tim P","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","orcid":"0000-0003-3295-6181","first_name":"Tim P","last_name":"Vogels"},{"first_name":"H.","last_name":"Sprekeler","full_name":"Sprekeler, H."},{"full_name":"Zenke, F.","last_name":"Zenke","first_name":"F."},{"full_name":"Clopath, C.","first_name":"C.","last_name":"Clopath"},{"first_name":"W.","last_name":"Gerstner","full_name":"Gerstner, W."}]},{"author":[{"full_name":"Schanda, Paul","first_name":"Paul","last_name":"Schanda","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","orcid":"0000-0002-9350-7606"},{"first_name":"Beat H.","last_name":"Meier","full_name":"Meier, Beat H."},{"full_name":"Ernst, Matthias","first_name":"Matthias","last_name":"Ernst"}],"oa_version":"None","volume":210,"date_created":"2020-09-18T10:10:50Z","date_updated":"2021-01-12T08:19:29Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"8469","year":"2011","publisher":"Elsevier","intvolume":" 210","title":"Accurate measurement of one-bond H–X heteronuclear dipolar couplings in MAS solid-state NMR","status":"public","publication_status":"published","issue":"2","abstract":[{"text":"The accurate experimental determination of dipolar-coupling constants for one-bond heteronuclear dipolar couplings in solids is a key for the quantification of the amplitudes of motional processes. Averaging of the dipolar coupling reports on motions on time scales up to the inverse of the coupling constant, in our case tens of microseconds. Combining dipolar-coupling derived order parameters that characterize the amplitudes of the motion with relaxation data leads to a more precise characterization of the dynamical parameters and helps to disentangle the amplitudes and the time scales of the motional processes, which impact relaxation rates in a highly correlated way. Here. we describe and characterize an improved experimental protocol – based on REDOR – to measure these couplings in perdeuterated proteins with a reduced sensitivity to experimental missettings. Because such effects are presently the dominant source of systematic errors in experimental dipolar-coupling measurements, these compensated experiments should help to significantly improve the precision of such data. A detailed comparison with other commonly used pulse sequences (T-MREV, phase-inverted CP,R18 5/2, and R18 7/1) is provided.","lang":"eng"}],"extern":"1","type":"journal_article","doi":"10.1016/j.jmr.2011.03.015","date_published":"2011-06-01T00:00:00Z","language":[{"iso":"eng"}],"citation":{"chicago":"Schanda, Paul, Beat H. Meier, and Matthias Ernst. “Accurate Measurement of One-Bond H–X Heteronuclear Dipolar Couplings in MAS Solid-State NMR.” Journal of Magnetic Resonance. Elsevier, 2011. https://doi.org/10.1016/j.jmr.2011.03.015.","mla":"Schanda, Paul, et al. “Accurate Measurement of One-Bond H–X Heteronuclear Dipolar Couplings in MAS Solid-State NMR.” Journal of Magnetic Resonance, vol. 210, no. 2, Elsevier, 2011, pp. 246–59, doi:10.1016/j.jmr.2011.03.015.","short":"P. Schanda, B.H. Meier, M. Ernst, Journal of Magnetic Resonance 210 (2011) 246–259.","ista":"Schanda P, Meier BH, Ernst M. 2011. Accurate measurement of one-bond H–X heteronuclear dipolar couplings in MAS solid-state NMR. Journal of Magnetic Resonance. 210(2), 246–259.","ieee":"P. Schanda, B. H. Meier, and M. Ernst, “Accurate measurement of one-bond H–X heteronuclear dipolar couplings in MAS solid-state NMR,” Journal of Magnetic Resonance, vol. 210, no. 2. Elsevier, pp. 246–259, 2011.","apa":"Schanda, P., Meier, B. H., & Ernst, M. (2011). Accurate measurement of one-bond H–X heteronuclear dipolar couplings in MAS solid-state NMR. Journal of Magnetic Resonance. Elsevier. https://doi.org/10.1016/j.jmr.2011.03.015","ama":"Schanda P, Meier BH, Ernst M. Accurate measurement of one-bond H–X heteronuclear dipolar couplings in MAS solid-state NMR. Journal of Magnetic Resonance. 2011;210(2):246-259. doi:10.1016/j.jmr.2011.03.015"},"publication":"Journal of Magnetic Resonance","page":"246-259","article_type":"original","quality_controlled":"1","publication_identifier":{"issn":["1090-7807"]},"article_processing_charge":"No","day":"01","month":"06","keyword":["Nuclear and High Energy Physics","Biophysics","Biochemistry","Condensed Matter Physics"]},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"8470","year":"2011","intvolume":" 12","publisher":"Wiley","status":"public","title":"A proton-detected 4D solid-state NMR experiment for protein structure determination","publication_status":"published","author":[{"full_name":"Huber, Matthias","first_name":"Matthias","last_name":"Huber"},{"last_name":"Hiller","first_name":"Sebastian","full_name":"Hiller, Sebastian"},{"full_name":"Schanda, Paul","orcid":"0000-0002-9350-7606","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","last_name":"Schanda","first_name":"Paul"},{"full_name":"Ernst, Matthias","last_name":"Ernst","first_name":"Matthias"},{"full_name":"Böckmann, Anja","last_name":"Böckmann","first_name":"Anja"},{"full_name":"Verel, René","first_name":"René","last_name":"Verel"},{"full_name":"Meier, Beat H.","last_name":"Meier","first_name":"Beat H."}],"volume":12,"oa_version":"None","date_updated":"2021-01-12T08:19:30Z","date_created":"2020-09-18T10:10:56Z","type":"journal_article","issue":"5","abstract":[{"lang":"eng","text":"Adding a new dimension: 4D or 3D proton‐detected spectra of perdeuterated protein samples with 1H labelled amides and methyl groups permit collecting unambiguous distance restraints with high sensitivity and determining protein structure by solid‐state NMR (see picture)."}],"extern":"1","citation":{"mla":"Huber, Matthias, et al. “A Proton-Detected 4D Solid-State NMR Experiment for Protein Structure Determination.” ChemPhysChem, vol. 12, no. 5, Wiley, 2011, pp. 915–18, doi:10.1002/cphc.201100062.","short":"M. Huber, S. Hiller, P. Schanda, M. Ernst, A. Böckmann, R. Verel, B.H. Meier, ChemPhysChem 12 (2011) 915–918.","chicago":"Huber, Matthias, Sebastian Hiller, Paul Schanda, Matthias Ernst, Anja Böckmann, René Verel, and Beat H. Meier. “A Proton-Detected 4D Solid-State NMR Experiment for Protein Structure Determination.” ChemPhysChem. Wiley, 2011. https://doi.org/10.1002/cphc.201100062.","ama":"Huber M, Hiller S, Schanda P, et al. A proton-detected 4D solid-state NMR experiment for protein structure determination. ChemPhysChem. 2011;12(5):915-918. doi:10.1002/cphc.201100062","ista":"Huber M, Hiller S, Schanda P, Ernst M, Böckmann A, Verel R, Meier BH. 2011. A proton-detected 4D solid-state NMR experiment for protein structure determination. ChemPhysChem. 12(5), 915–918.","ieee":"M. Huber et al., “A proton-detected 4D solid-state NMR experiment for protein structure determination,” ChemPhysChem, vol. 12, no. 5. Wiley, pp. 915–918, 2011.","apa":"Huber, M., Hiller, S., Schanda, P., Ernst, M., Böckmann, A., Verel, R., & Meier, B. H. (2011). A proton-detected 4D solid-state NMR experiment for protein structure determination. ChemPhysChem. Wiley. https://doi.org/10.1002/cphc.201100062"},"publication":"ChemPhysChem","page":"915-918","article_type":"original","quality_controlled":"1","date_published":"2011-02-15T00:00:00Z","doi":"10.1002/cphc.201100062","language":[{"iso":"eng"}],"keyword":["Physical and Theoretical Chemistry","Atomic and Molecular Physics","and Optics"],"publication_identifier":{"issn":["1439-4235"]},"article_processing_charge":"No","day":"15","month":"02"},{"type":"journal_article","issue":"46","abstract":[{"text":"Nonsymmetric motion: Solid‐state NMR measurements of dipolar coupling tensors provide insight into protein dynamics. The hitherto ignored asymmetry of the dipolar coupling tensor contains valuable information about motional asymmetry, which was used in the first direct site‐resolved measurement of such tensors. Important motions such as rotamer jumps can now be directly detected in the solid state.","lang":"eng"}],"extern":"1","_id":"8464","year":"2011","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Wiley","intvolume":" 50","publication_status":"published","title":"Solid-state NMR measurements of asymmetric dipolar couplings provide insight into protein side-chain motion","status":"public","related_material":{"link":[{"url":"https://doi.org/10.1002/anie.201206663","relation":"erratum"}]},"author":[{"first_name":"Paul","last_name":"Schanda","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","orcid":"0000-0002-9350-7606","full_name":"Schanda, Paul"},{"full_name":"Huber, Matthias","first_name":"Matthias","last_name":"Huber"},{"last_name":"Boisbouvier","first_name":"Jérôme","full_name":"Boisbouvier, Jérôme"},{"full_name":"Meier, Beat H.","last_name":"Meier","first_name":"Beat H."},{"first_name":"Matthias","last_name":"Ernst","full_name":"Ernst, Matthias"}],"volume":50,"oa_version":"None","date_created":"2020-09-18T10:09:40Z","date_updated":"2021-01-12T08:19:27Z","article_processing_charge":"No","publication_identifier":{"issn":["1433-7851"]},"month":"09","day":"14","citation":{"ista":"Schanda P, Huber M, Boisbouvier J, Meier BH, Ernst M. 2011. Solid-state NMR measurements of asymmetric dipolar couplings provide insight into protein side-chain motion. Angewandte Chemie International Edition. 50(46), 11005–11009.","ieee":"P. Schanda, M. Huber, J. Boisbouvier, B. H. Meier, and M. Ernst, “Solid-state NMR measurements of asymmetric dipolar couplings provide insight into protein side-chain motion,” Angewandte Chemie International Edition, vol. 50, no. 46. Wiley, pp. 11005–11009, 2011.","apa":"Schanda, P., Huber, M., Boisbouvier, J., Meier, B. H., & Ernst, M. (2011). Solid-state NMR measurements of asymmetric dipolar couplings provide insight into protein side-chain motion. Angewandte Chemie International Edition. Wiley. https://doi.org/10.1002/anie.201103944","ama":"Schanda P, Huber M, Boisbouvier J, Meier BH, Ernst M. Solid-state NMR measurements of asymmetric dipolar couplings provide insight into protein side-chain motion. Angewandte Chemie International Edition. 2011;50(46):11005-11009. doi:10.1002/anie.201103944","chicago":"Schanda, Paul, Matthias Huber, Jérôme Boisbouvier, Beat H. Meier, and Matthias Ernst. “Solid-State NMR Measurements of Asymmetric Dipolar Couplings Provide Insight into Protein Side-Chain Motion.” Angewandte Chemie International Edition. Wiley, 2011. https://doi.org/10.1002/anie.201103944.","mla":"Schanda, Paul, et al. “Solid-State NMR Measurements of Asymmetric Dipolar Couplings Provide Insight into Protein Side-Chain Motion.” Angewandte Chemie International Edition, vol. 50, no. 46, Wiley, 2011, pp. 11005–09, doi:10.1002/anie.201103944.","short":"P. Schanda, M. Huber, J. Boisbouvier, B.H. Meier, M. Ernst, Angewandte Chemie International Edition 50 (2011) 11005–11009."},"publication":"Angewandte Chemie International Edition","page":"11005-11009","article_type":"original","quality_controlled":"1","doi":"10.1002/anie.201103944","date_published":"2011-09-14T00:00:00Z","language":[{"iso":"eng"}]},{"month":"10","day":"25","publication_identifier":{"issn":["0925-2738","1573-5001"]},"article_processing_charge":"No","quality_controlled":"1","article_type":"original","page":"477-485","publication":"Journal of Biomolecular NMR","citation":{"mla":"Lalli, Daniela, et al. “Three-Dimensional Deuterium-Carbon Correlation Experiments for High-Resolution Solid-State MAS NMR Spectroscopy of Large Proteins.” Journal of Biomolecular NMR, vol. 51, no. 4, Springer Nature, 2011, pp. 477–85, doi:10.1007/s10858-011-9578-1.","short":"D. Lalli, P. Schanda, A. Chowdhury, J. Retel, M. Hiller, V.A. Higman, L. Handel, V. Agarwal, B. Reif, B. van Rossum, Ü. Akbey, H. Oschkinat, Journal of Biomolecular NMR 51 (2011) 477–485.","chicago":"Lalli, Daniela, Paul Schanda, Anup Chowdhury, Joren Retel, Matthias Hiller, Victoria A. Higman, Lieselotte Handel, et al. “Three-Dimensional Deuterium-Carbon Correlation Experiments for High-Resolution Solid-State MAS NMR Spectroscopy of Large Proteins.” Journal of Biomolecular NMR. Springer Nature, 2011. https://doi.org/10.1007/s10858-011-9578-1.","ama":"Lalli D, Schanda P, Chowdhury A, et al. Three-dimensional deuterium-carbon correlation experiments for high-resolution solid-state MAS NMR spectroscopy of large proteins. Journal of Biomolecular NMR. 2011;51(4):477-485. doi:10.1007/s10858-011-9578-1","ista":"Lalli D, Schanda P, Chowdhury A, Retel J, Hiller M, Higman VA, Handel L, Agarwal V, Reif B, van Rossum B, Akbey Ü, Oschkinat H. 2011. Three-dimensional deuterium-carbon correlation experiments for high-resolution solid-state MAS NMR spectroscopy of large proteins. Journal of Biomolecular NMR. 51(4), 477–485.","apa":"Lalli, D., Schanda, P., Chowdhury, A., Retel, J., Hiller, M., Higman, V. A., … Oschkinat, H. (2011). Three-dimensional deuterium-carbon correlation experiments for high-resolution solid-state MAS NMR spectroscopy of large proteins. Journal of Biomolecular NMR. Springer Nature. https://doi.org/10.1007/s10858-011-9578-1","ieee":"D. Lalli et al., “Three-dimensional deuterium-carbon correlation experiments for high-resolution solid-state MAS NMR spectroscopy of large proteins,” Journal of Biomolecular NMR, vol. 51, no. 4. Springer Nature, pp. 477–485, 2011."},"language":[{"iso":"eng"}],"date_published":"2011-10-25T00:00:00Z","doi":"10.1007/s10858-011-9578-1","type":"journal_article","extern":"1","issue":"4","status":"public","publication_status":"published","title":"Three-dimensional deuterium-carbon correlation experiments for high-resolution solid-state MAS NMR spectroscopy of large proteins","publisher":"Springer Nature","intvolume":" 51","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"8468","year":"2011","date_created":"2020-09-18T10:10:43Z","date_updated":"2021-01-12T08:19:29Z","volume":51,"oa_version":"None","author":[{"full_name":"Lalli, Daniela","first_name":"Daniela","last_name":"Lalli"},{"first_name":"Paul","last_name":"Schanda","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","orcid":"0000-0002-9350-7606","full_name":"Schanda, Paul"},{"first_name":"Anup","last_name":"Chowdhury","full_name":"Chowdhury, Anup"},{"first_name":"Joren","last_name":"Retel","full_name":"Retel, Joren"},{"first_name":"Matthias","last_name":"Hiller","full_name":"Hiller, Matthias"},{"full_name":"Higman, Victoria A.","last_name":"Higman","first_name":"Victoria A."},{"full_name":"Handel, Lieselotte","first_name":"Lieselotte","last_name":"Handel"},{"full_name":"Agarwal, Vipin","last_name":"Agarwal","first_name":"Vipin"},{"first_name":"Bernd","last_name":"Reif","full_name":"Reif, Bernd"},{"first_name":"Barth","last_name":"van Rossum","full_name":"van Rossum, Barth"},{"full_name":"Akbey, Ümit","last_name":"Akbey","first_name":"Ümit"},{"last_name":"Oschkinat","first_name":"Hartmut","full_name":"Oschkinat, Hartmut"}]},{"volume":6,"date_created":"2018-12-11T11:49:02Z","date_updated":"2021-01-12T08:21:18Z","author":[{"full_name":"Koblik, Evgeniy A","last_name":"Koblik","first_name":"Evgeniy"},{"first_name":"Yaroslav","last_name":"Red'Kin","full_name":"Red'Kin, Yaroslav A"},{"first_name":"Margarita","last_name":"Meer","full_name":"Meer, Margarita S"},{"full_name":"Derelle, Romain","last_name":"Derelle","first_name":"Romain"},{"full_name":"Golenkina, Sofia A","first_name":"Sofia","last_name":"Golenkina"},{"full_name":"Fyodor Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694","first_name":"Fyodor","last_name":"Kondrashov"},{"first_name":"Vladimir","last_name":"Arkhipov","full_name":"Arkhipov, Vladimir Y"}],"intvolume":" 6","publisher":"Public Library of Science","publication_status":"published","title":"Acrocephalus orinus: A case of Mistaken identity","status":"public","acknowledgement":"The work was supported by the Plan Nacional grant number BFU2009-09271 from the Spanish Ministry of Science and Innovation.\nWe extend our thanks to A.M. Peklo and I.V. Fadeev for granting us access to ornithological collections, to V.S. Shishkin, M.V. Kalyakin, R.D. Kashkarov, O.V. Belyalov and V.M. Loskot for valuable insights and to L. Svensson for extensive feedback on the manuscript. We thank E.I. Rogaev for access to ancient DNA facility.\n","_id":"890","year":"2011","extern":1,"issue":"4","publist_id":"6760","abstract":[{"lang":"eng","text":"Recent discovery of the Large-billed Reed Warbler (Acrocephalus orinus) in museums and in the wild significantly expanded our knowledge of its morphological traits and genetic variability, and revealed new data on geographical distribution of the breeding grounds, migration routes and wintering locations of this species. It is now certain that A. orinus is breeding in Central Asia; however, the precise area of distribution remains unclear. The difficulty in the further study of this species lies in the small number of known specimens, with only 13 currently available in museums, and in the relative uncertainty of the breeding area and habitat of this species. Following morphological and genetic analyses from Svensson, et al, we describe 14 new A. orinus specimens from collections of Zoological Museums of the former USSR from the territory of Central Asian states. All of these specimens were erroneously labeled as Blyth's Reed Warbler (A. dumetorum), which is thought to be a breeding species in these areas. The 14 new A. orinus specimens were collected during breeding season while most of the 85 A. dumetorum specimens from the same area were collected during the migration period. Our data indicate that the Central Asian territory previously attributed as breeding grounds of A. dumetorum is likely to constitute the breeding territory of A. orinus. This rare case of a re-description of the breeding territory of a lost species emphasizes the importance of maintenance of museum collections around the world. If the present data on the breeding grounds of A. orinus are confirmed with field observations and collections, the literature on the biology of A. dumetorum from the southern part of its range may have to be reconsidered."}],"type":"journal_article","doi":"10.1371/journal.pone.0017716","date_published":"2011-01-01T00:00:00Z","quality_controlled":0,"citation":{"ama":"Koblik E, Red’Kin Y, Meer M, et al. Acrocephalus orinus: A case of Mistaken identity. PLoS One. 2011;6(4). doi:10.1371/journal.pone.0017716","apa":"Koblik, E., Red’Kin, Y., Meer, M., Derelle, R., Golenkina, S., Kondrashov, F., & Arkhipov, V. (2011). Acrocephalus orinus: A case of Mistaken identity. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0017716","ieee":"E. Koblik et al., “Acrocephalus orinus: A case of Mistaken identity,” PLoS One, vol. 6, no. 4. Public Library of Science, 2011.","ista":"Koblik E, Red’Kin Y, Meer M, Derelle R, Golenkina S, Kondrashov F, Arkhipov V. 2011. Acrocephalus orinus: A case of Mistaken identity. PLoS One. 6(4).","short":"E. Koblik, Y. Red’Kin, M. Meer, R. Derelle, S. Golenkina, F. Kondrashov, V. Arkhipov, PLoS One 6 (2011).","mla":"Koblik, Evgeniy, et al. “Acrocephalus Orinus: A Case of Mistaken Identity.” PLoS One, vol. 6, no. 4, Public Library of Science, 2011, doi:10.1371/journal.pone.0017716.","chicago":"Koblik, Evgeniy, Yaroslav Red’Kin, Margarita Meer, Romain Derelle, Sofia Golenkina, Fyodor Kondrashov, and Vladimir Arkhipov. “Acrocephalus Orinus: A Case of Mistaken Identity.” PLoS One. Public Library of Science, 2011. https://doi.org/10.1371/journal.pone.0017716."},"publication":"PLoS One","day":"01","month":"01"},{"type":"journal_article","publist_id":"7964","issue":"5","abstract":[{"text":"A popular method for generating micron-sized aerosols is to submerge ultrasonic (ω ∼ MHz) piezoelectric oscillators in a water bath. The submerged oscillator atomizes the fluid, creating droplets with radii proportional to the wavelength of the standing wave at the fluid surface. Classical theory for the Faraday instability predicts a parametric instability driving a capillary wave at the subharmonic (ω / 2) frequency. For many applications it is desirable to reduce the size of the droplets; however, using higher frequency oscillators becomes impractical beyond a few MHz. Observations are presented that demonstrate that smaller droplets may also be created by increasing the driving amplitude of the oscillator, and that this effect becomes more pronounced for large driving frequencies. It is shown that these observations are consistent with a transition from droplets associated with subharmonic (ω/2) capillary waves to harmonic (ω) capillary waves induced by larger driving frequencies and amplitudes, as predicted by a stability analysis of the capillary waves.","lang":"eng"}],"extern":"1","pmid":1,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"90","year":"2011","publisher":"Acoustical Society of America","intvolume":" 130","title":"Evidence of the harmonic Faraday instability in ultrasonic atomization experiments with a deep, inviscid fluid","publication_status":"published","status":"public","author":[{"full_name":"Higginbotham, Andrew P","first_name":"Andrew P","last_name":"Higginbotham","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2607-2363"},{"last_name":"Guillen","first_name":"A","full_name":"Guillen, A"},{"full_name":"Jones, Nick","last_name":"Jones","first_name":"Nick"},{"full_name":"Donnelly, Tom","first_name":"Tom","last_name":"Donnelly"},{"full_name":"Bernoff, Andrew","last_name":"Bernoff","first_name":"Andrew"}],"oa_version":"None","volume":130,"date_created":"2018-12-11T11:44:34Z","date_updated":"2021-01-12T08:21:44Z","month":"11","day":"16","citation":{"ama":"Higginbotham AP, Guillen A, Jones N, Donnelly T, Bernoff A. Evidence of the harmonic Faraday instability in ultrasonic atomization experiments with a deep, inviscid fluid. Journal of the Acoustical Society of America. 2011;130(5):2694-2699. doi:10.1121/1.3643816","apa":"Higginbotham, A. P., Guillen, A., Jones, N., Donnelly, T., & Bernoff, A. (2011). Evidence of the harmonic Faraday instability in ultrasonic atomization experiments with a deep, inviscid fluid. Journal of the Acoustical Society of America. Acoustical Society of America. https://doi.org/10.1121/1.3643816","ieee":"A. P. Higginbotham, A. Guillen, N. Jones, T. Donnelly, and A. Bernoff, “Evidence of the harmonic Faraday instability in ultrasonic atomization experiments with a deep, inviscid fluid,” Journal of the Acoustical Society of America, vol. 130, no. 5. Acoustical Society of America, pp. 2694–2699, 2011.","ista":"Higginbotham AP, Guillen A, Jones N, Donnelly T, Bernoff A. 2011. Evidence of the harmonic Faraday instability in ultrasonic atomization experiments with a deep, inviscid fluid. Journal of the Acoustical Society of America. 130(5), 2694–2699.","short":"A.P. Higginbotham, A. Guillen, N. Jones, T. Donnelly, A. Bernoff, Journal of the Acoustical Society of America 130 (2011) 2694–2699.","mla":"Higginbotham, Andrew P., et al. “Evidence of the Harmonic Faraday Instability in Ultrasonic Atomization Experiments with a Deep, Inviscid Fluid.” Journal of the Acoustical Society of America, vol. 130, no. 5, Acoustical Society of America, 2011, pp. 2694–99, doi:10.1121/1.3643816.","chicago":"Higginbotham, Andrew P, A Guillen, Nick Jones, Tom Donnelly, and Andrew Bernoff. “Evidence of the Harmonic Faraday Instability in Ultrasonic Atomization Experiments with a Deep, Inviscid Fluid.” Journal of the Acoustical Society of America. Acoustical Society of America, 2011. https://doi.org/10.1121/1.3643816."},"external_id":{"pmid":[" 22087897"]},"publication":"Journal of the Acoustical Society of America","page":"2694 - 2699","quality_controlled":"1","doi":"10.1121/1.3643816","date_published":"2011-11-16T00:00:00Z","language":[{"iso":"eng"}]},{"abstract":[{"lang":"eng","text":"A cloud-resolving model is used to investigate the effect of warming on high percentiles of precipitation (precipitation extremes) in the idealized setting of radiative-convective equilibrium. While this idealized setting does not allow for several factors that influence precipitation in the tropics, it does allow for an evaluation of the response of precipitation extremes to warming in simulations with resolved rather than parameterized convection. The methodology developed should also be applicable to less idealized simulations.\r\n\r\nModeled precipitation extremes are found to increase in magnitude in response to an increase in sea surface temperature. A dry static energy budget is used to relate the changes in precipitation extremes to changes in atmospheric temperature, vertical velocity, and precipitation efficiency. To first order, the changes in precipitation extremes are captured by changes in the mean temperature structure of the atmosphere. Changes in vertical velocities play a secondary role and tend to weaken the strength of precipitation extremes, despite an intensification of updraft velocities in the upper troposphere. The influence of changes in condensate transports on precipitation extremes is quantified in terms of a precipitation efficiency; it does not change greatly with warming.\r\n\r\nTropical precipitation extremes have previously been found to increase at a greater fractional rate than the amount of atmospheric water vapor in observations of present-day variability and in some climate model simulations with parameterized convection. But the fractional increases in precipitation extremes in the cloud-resolving simulations are comparable in magnitude to those in surface water vapor concentrations (owing to a partial cancellation between dynamical and thermodynamical changes), and are substantially less than the fractional increases in column water vapor."}],"issue":"11","type":"journal_article","oa_version":"Published Version","title":"Intensification of precipitation extremes with warming in a cloud-resolving model","status":"public","intvolume":" 24","_id":"9144","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","day":"01","article_processing_charge":"No","keyword":["Atmospheric Science"],"date_published":"2011-06-01T00:00:00Z","article_type":"original","page":"2784-2800","publication":"Journal of Climate","citation":{"ama":"Muller CJ, O’Gorman PA, Back LE. Intensification of precipitation extremes with warming in a cloud-resolving model. Journal of Climate. 2011;24(11):2784-2800. doi:10.1175/2011jcli3876.1","ista":"Muller CJ, O’Gorman PA, Back LE. 2011. Intensification of precipitation extremes with warming in a cloud-resolving model. Journal of Climate. 24(11), 2784–2800.","apa":"Muller, C. J., O’Gorman, P. A., & Back, L. E. (2011). Intensification of precipitation extremes with warming in a cloud-resolving model. Journal of Climate. American Meteorological Society. https://doi.org/10.1175/2011jcli3876.1","ieee":"C. J. Muller, P. A. O’Gorman, and L. E. Back, “Intensification of precipitation extremes with warming in a cloud-resolving model,” Journal of Climate, vol. 24, no. 11. American Meteorological Society, pp. 2784–2800, 2011.","mla":"Muller, Caroline J., et al. “Intensification of Precipitation Extremes with Warming in a Cloud-Resolving Model.” Journal of Climate, vol. 24, no. 11, American Meteorological Society, 2011, pp. 2784–800, doi:10.1175/2011jcli3876.1.","short":"C.J. Muller, P.A. O’Gorman, L.E. Back, Journal of Climate 24 (2011) 2784–2800.","chicago":"Muller, Caroline J, Paul A. O’Gorman, and Larissa E. Back. “Intensification of Precipitation Extremes with Warming in a Cloud-Resolving Model.” Journal of Climate. American Meteorological Society, 2011. https://doi.org/10.1175/2011jcli3876.1."},"extern":"1","date_updated":"2022-01-24T13:52:46Z","date_created":"2021-02-15T14:39:57Z","volume":24,"author":[{"full_name":"Muller, Caroline J","last_name":"Muller","first_name":"Caroline J","orcid":"0000-0001-5836-5350","id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b"},{"last_name":"O’Gorman","first_name":"Paul A.","full_name":"O’Gorman, Paul A."},{"full_name":"Back, Larissa E.","first_name":"Larissa E.","last_name":"Back"}],"publication_status":"published","publisher":"American Meteorological Society","year":"2011","month":"06","publication_identifier":{"eissn":["1520-0442"],"issn":["0894-8755"]},"language":[{"iso":"eng"}],"doi":"10.1175/2011jcli3876.1","quality_controlled":"1","main_file_link":[{"url":"https://doi.org/10.1175/2011JCLI3876.1","open_access":"1"}],"oa":1},{"date_updated":"2022-01-24T13:52:11Z","date_created":"2021-02-15T14:39:29Z","volume":1,"oa_version":"None","author":[{"full_name":"Muller, Caroline J","orcid":"0000-0001-5836-5350","id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b","last_name":"Muller","first_name":"Caroline J"},{"first_name":"P. A.","last_name":"O’Gorman","full_name":"O’Gorman, P. A."}],"title":"An energetic perspective on the regional response of precipitation to climate change","status":"public","publication_status":"published","intvolume":" 1","publisher":"Springer Nature","year":"2011","_id":"9143","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","extern":"1","abstract":[{"lang":"eng","text":"Understanding and predicting the response of the hydrological cycle to climate change is a major challenge with important societal implications. Much progress has been made in understanding the response of global average precipitation by considering the energy balances of the atmosphere and the surface1,2,3,4,5,6. This energetic perspective reveals that changes in temperature, greenhouse gases, aerosols, solar forcing and cloud feedbacks can all affect the global average rate of precipitation5,7,8,9,10,11. Local precipitation changes have conventionally been analysed using the water vapour budget, but here we show that the energetic approach can be extended to local changes in precipitation by including changes in horizontal energy transport. In simulations of twenty-first century climate change, this energy transport accounts for much of the spatial variability in precipitation change. We show that changes in radiative and surface sensible heat fluxes are a guide to the local precipitation response over land and at large scales, but not at small scales over the ocean, where cloud and water vapour radiative feedbacks dampen the response. The energetic approach described here helps bridge the gap between our understanding of global and regional precipitation changes. It could be applied to better understand the response of regional precipitation to different radiative forcings, including geo-engineering schemes, as well as to understand the differences between the fast and slow responses of regional precipitation to such forcings."}],"issue":"5","type":"journal_article","language":[{"iso":"eng"}],"date_published":"2011-07-24T00:00:00Z","doi":"10.1038/nclimate1169","quality_controlled":"1","article_type":"original","page":"266-271","publication":"Nature Climate Change","citation":{"short":"C.J. Muller, P.A. O’Gorman, Nature Climate Change 1 (2011) 266–271.","mla":"Muller, Caroline J., and P. A. O’Gorman. “An Energetic Perspective on the Regional Response of Precipitation to Climate Change.” Nature Climate Change, vol. 1, no. 5, Springer Nature, 2011, pp. 266–71, doi:10.1038/nclimate1169.","chicago":"Muller, Caroline J, and P. A. O’Gorman. “An Energetic Perspective on the Regional Response of Precipitation to Climate Change.” Nature Climate Change. Springer Nature, 2011. https://doi.org/10.1038/nclimate1169.","ama":"Muller CJ, O’Gorman PA. An energetic perspective on the regional response of precipitation to climate change. Nature Climate Change. 2011;1(5):266-271. doi:10.1038/nclimate1169","apa":"Muller, C. J., & O’Gorman, P. A. (2011). An energetic perspective on the regional response of precipitation to climate change. Nature Climate Change. Springer Nature. https://doi.org/10.1038/nclimate1169","ieee":"C. J. Muller and P. A. O’Gorman, “An energetic perspective on the regional response of precipitation to climate change,” Nature Climate Change, vol. 1, no. 5. Springer Nature, pp. 266–271, 2011.","ista":"Muller CJ, O’Gorman PA. 2011. An energetic perspective on the regional response of precipitation to climate change. Nature Climate Change. 1(5), 266–271."},"month":"07","day":"24","article_processing_charge":"No","publication_identifier":{"issn":["1758-678X","1758-6798"]}},{"abstract":[{"lang":"eng","text":"The conserved role of Notch signaling in controlling intestinal cell fate specification and homeostasis has been extensively studied. Nevertheless, the precise identity of the cells in which Notch signaling is active and the role of different Notch receptor paralogues in the intestine remain ambiguous, due to the lack of reliable tools to investigate Notch expression and function in vivo. We generated a new series of transgenic mice that allowed us, by lineage analysis, to formally prove that Notch1 and Notch2 are specifically expressed in crypt stem cells. In addition, a novel Notch reporter mouse, Hes1-EmGFP SAT, demonstrated exclusive Notch activity in crypt stem cells and absorptive progenitors. This roster of knock-in and reporter mice represents a valuable resource to functionally explore the Notch pathway in vivo in virtually all tissues."}],"issue":"10","type":"journal_article","oa_version":"Published Version","file":[{"file_name":"2011_PLOS1_Fre.PDF","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":2860615,"file_id":"6401","relation":"main_file","date_created":"2019-05-10T11:20:26Z","date_updated":"2020-07-14T12:48:15Z","checksum":"b4e864125dfcb9fa57a9e01688838081"}],"_id":"923","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","ddc":["570"],"title":"Notch lineages and activity in intestinal stem cells determined by a new set of knock in mice","intvolume":" 6","day":"03","has_accepted_license":"1","date_published":"2011-10-03T00:00:00Z","publication":"PLoS One","citation":{"short":"S. Fré, E.B. Hannezo, S. Šale, M. Huyghe, D. Lafkas, H. Kissel, A. Louvi, J. Greve, D. Louvard, S. Artavanis Tsakonas, PLoS One 6 (2011).","mla":"Fré, Silvia, et al. “Notch Lineages and Activity in Intestinal Stem Cells Determined by a New Set of Knock in Mice.” PLoS One, vol. 6, no. 10, e25785, Public Library of Science, 2011, doi:10.1371/journal.pone.0025785.","chicago":"Fré, Silvia, Edouard B Hannezo, Sanja Šale, Mathilde Huyghe, Daniel Lafkas, Holger Kissel, Angeliki Louvi, Jeffrey Greve, Daniel Louvard, and Spyros Artavanis Tsakonas. “Notch Lineages and Activity in Intestinal Stem Cells Determined by a New Set of Knock in Mice.” PLoS One. Public Library of Science, 2011. https://doi.org/10.1371/journal.pone.0025785.","ama":"Fré S, Hannezo EB, Šale S, et al. Notch lineages and activity in intestinal stem cells determined by a new set of knock in mice. PLoS One. 2011;6(10). doi:10.1371/journal.pone.0025785","apa":"Fré, S., Hannezo, E. B., Šale, S., Huyghe, M., Lafkas, D., Kissel, H., … Artavanis Tsakonas, S. (2011). Notch lineages and activity in intestinal stem cells determined by a new set of knock in mice. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0025785","ieee":"S. Fré et al., “Notch lineages and activity in intestinal stem cells determined by a new set of knock in mice,” PLoS One, vol. 6, no. 10. Public Library of Science, 2011.","ista":"Fré S, Hannezo EB, Šale S, Huyghe M, Lafkas D, Kissel H, Louvi A, Greve J, Louvard D, Artavanis Tsakonas S. 2011. Notch lineages and activity in intestinal stem cells determined by a new set of knock in mice. PLoS One. 6(10), e25785."},"file_date_updated":"2020-07-14T12:48:15Z","publist_id":"6520","extern":"1","article_number":"e25785","author":[{"full_name":"Fré, Silvia","last_name":"Fré","first_name":"Silvia"},{"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":"Šale, Sanja","last_name":"Šale","first_name":"Sanja"},{"first_name":"Mathilde","last_name":"Huyghe","full_name":"Huyghe, Mathilde"},{"last_name":"Lafkas","first_name":"Daniel","full_name":"Lafkas, Daniel"},{"last_name":"Kissel","first_name":"Holger","full_name":"Kissel, Holger"},{"last_name":"Louvi","first_name":"Angeliki","full_name":"Louvi, Angeliki"},{"last_name":"Greve","first_name":"Jeffrey","full_name":"Greve, Jeffrey"},{"first_name":"Daniel","last_name":"Louvard","full_name":"Louvard, Daniel"},{"full_name":"Artavanis Tsakonas, Spyros","last_name":"Artavanis Tsakonas","first_name":"Spyros"}],"date_updated":"2021-01-12T08:21:56Z","date_created":"2018-12-11T11:49:13Z","volume":6,"year":"2011","publication_status":"published","publisher":"Public Library of Science","month":"10","doi":"10.1371/journal.pone.0025785","language":[{"iso":"eng"}],"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"},{"extern":"1","author":[{"full_name":"Hsieh, Tzung-Fu","first_name":"Tzung-Fu","last_name":"Hsieh"},{"first_name":"Juhyun","last_name":"Shin","full_name":"Shin, Juhyun"},{"last_name":"Uzawa","first_name":"Rie","full_name":"Uzawa, Rie"},{"full_name":"Silva, Pedro","first_name":"Pedro","last_name":"Silva"},{"full_name":"Cohen, Stephanie","last_name":"Cohen","first_name":"Stephanie"},{"full_name":"Bauer, Matthew J.","last_name":"Bauer","first_name":"Matthew J."},{"full_name":"Hashimoto, Meryl","first_name":"Meryl","last_name":"Hashimoto"},{"full_name":"Kirkbride, Ryan C.","first_name":"Ryan C.","last_name":"Kirkbride"},{"last_name":"Harada","first_name":"John J.","full_name":"Harada, John J."},{"full_name":"Zilberman, Daniel","first_name":"Daniel","last_name":"Zilberman","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","orcid":"0000-0002-0123-8649"},{"full_name":"Fischer, Robert L.","first_name":"Robert L.","last_name":"Fischer"}],"volume":108,"date_updated":"2021-12-14T08:33:49Z","date_created":"2021-06-07T07:40:38Z","pmid":1,"year":"2011","department":[{"_id":"DaZi"}],"publisher":"National Academy of Sciences","publication_status":"published","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"month":"02","doi":"10.1073/pnas.1019273108","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1073/pnas.1019273108"}],"external_id":{"pmid":["21257907"]},"quality_controlled":"1","issue":"5","abstract":[{"text":"Imprinted genes are expressed primarily or exclusively from either the maternal or paternal allele, a phenomenon that occurs in flowering plants and mammals. Flowering plant imprinted gene expression has been described primarily in endosperm, a terminal nutritive tissue consumed by the embryo during seed development or after germination. Imprinted expression in Arabidopsis thaliana endosperm is orchestrated by differences in cytosine DNA methylation between the paternal and maternal genomes as well as by Polycomb group proteins. Currently, only 11 imprinted A. thaliana genes are known. Here, we use extensive sequencing of cDNA libraries to identify 9 paternally expressed and 34 maternally expressed imprinted genes in A. thaliana endosperm that are regulated by the DNA-demethylating glycosylase DEMETER, the DNA methyltransferase MET1, and/or the core Polycomb group protein FIE. These genes encode transcription factors, proteins involved in hormone signaling, components of the ubiquitin protein degradation pathway, regulators of histone and DNA methylation, and small RNA pathway proteins. We also identify maternally expressed genes that may be regulated by unknown mechanisms or deposited from maternal tissues. We did not detect any imprinted genes in the embryo. Our results show that imprinted gene expression is an extensive mechanistically complex phenomenon that likely affects multiple aspects of seed development.","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"9483","intvolume":" 108","status":"public","title":"Regulation of imprinted gene expression in Arabidopsis endosperm","article_processing_charge":"No","day":"01","scopus_import":"1","date_published":"2011-02-01T00:00:00Z","citation":{"ista":"Hsieh T-F, Shin J, Uzawa R, Silva P, Cohen S, Bauer MJ, Hashimoto M, Kirkbride RC, Harada JJ, Zilberman D, Fischer RL. 2011. Regulation of imprinted gene expression in Arabidopsis endosperm. Proceedings of the National Academy of Sciences. 108(5), 1755–1762.","apa":"Hsieh, T.-F., Shin, J., Uzawa, R., Silva, P., Cohen, S., Bauer, M. J., … Fischer, R. L. (2011). Regulation of imprinted gene expression in Arabidopsis endosperm. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.1019273108","ieee":"T.-F. Hsieh et al., “Regulation of imprinted gene expression in Arabidopsis endosperm,” Proceedings of the National Academy of Sciences, vol. 108, no. 5. National Academy of Sciences, pp. 1755–1762, 2011.","ama":"Hsieh T-F, Shin J, Uzawa R, et al. Regulation of imprinted gene expression in Arabidopsis endosperm. Proceedings of the National Academy of Sciences. 2011;108(5):1755-1762. doi:10.1073/pnas.1019273108","chicago":"Hsieh, Tzung-Fu, Juhyun Shin, Rie Uzawa, Pedro Silva, Stephanie Cohen, Matthew J. Bauer, Meryl Hashimoto, et al. “Regulation of Imprinted Gene Expression in Arabidopsis Endosperm.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2011. https://doi.org/10.1073/pnas.1019273108.","mla":"Hsieh, Tzung-Fu, et al. “Regulation of Imprinted Gene Expression in Arabidopsis Endosperm.” Proceedings of the National Academy of Sciences, vol. 108, no. 5, National Academy of Sciences, 2011, pp. 1755–62, doi:10.1073/pnas.1019273108.","short":"T.-F. Hsieh, J. Shin, R. Uzawa, P. Silva, S. Cohen, M.J. Bauer, M. Hashimoto, R.C. Kirkbride, J.J. Harada, D. Zilberman, R.L. Fischer, Proceedings of the National Academy of Sciences 108 (2011) 1755–1762."},"publication":"Proceedings of the National Academy of Sciences","page":"1755-1762","article_type":"original"},{"extern":1,"abstract":[{"lang":"eng","text":"Motivated by recent experiments on the material Ba3NiSb 2O9, we consider a spin-one quantum antiferromagnet on a triangular lattice with the Heisenberg bilinear and biquadratic exchange interactions and a single-ion anisotropy. Using a fermionic "triplon" representation for spins, we study the phase diagram within mean-field theory. In addition to a fully gapped spin-liquid ground state, we find a state where one gapless triplon mode with a Fermi surface coexists with d+id topological pairing of the other triplons. Despite the existence of a Fermi surface, this ground state has fully gapped bulk spin excitations. Such a state has linear in-temperature specific heat and constant in-plane spin susceptibility, with an unusually high Wilson ratio."}],"issue":"18","publist_id":"6432","type":"journal_article","date_created":"2018-12-11T11:49:27Z","date_updated":"2021-01-12T08:22:18Z","volume":84,"author":[{"full_name":"Maksym Serbyn","orcid":"0000-0002-2399-5827","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","last_name":"Serbyn","first_name":"Maksym"},{"first_name":"Todadri","last_name":"Senthil","full_name":"Senthil, Todadri S"},{"full_name":"Lee, Patrick","last_name":"Lee","first_name":"Patrick"}],"status":"public","title":"Exotic S=1 spin-liquid state with fermionic excitations on the triangular lattice","publication_status":"published","intvolume":" 84","publisher":"American Physical Society","_id":"967","year":"2011","day":"03","month":"11","doi":"10.1103/PhysRevB.84.180403","date_published":"2011-11-03T00:00:00Z","quality_controlled":0,"publication":"Physical Review B - Condensed Matter and Materials Physics","oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1108.3070","open_access":"1"}],"citation":{"ista":"Serbyn M, Senthil T, Lee P. 2011. Exotic S=1 spin-liquid state with fermionic excitations on the triangular lattice. Physical Review B - Condensed Matter and Materials Physics. 84(18).","apa":"Serbyn, M., Senthil, T., & Lee, P. (2011). Exotic S=1 spin-liquid state with fermionic excitations on the triangular lattice. Physical Review B - Condensed Matter and Materials Physics. American Physical Society. https://doi.org/10.1103/PhysRevB.84.180403","ieee":"M. Serbyn, T. Senthil, and P. Lee, “Exotic S=1 spin-liquid state with fermionic excitations on the triangular lattice,” Physical Review B - Condensed Matter and Materials Physics, vol. 84, no. 18. American Physical Society, 2011.","ama":"Serbyn M, Senthil T, Lee P. Exotic S=1 spin-liquid state with fermionic excitations on the triangular lattice. Physical Review B - Condensed Matter and Materials Physics. 2011;84(18). doi:10.1103/PhysRevB.84.180403","chicago":"Serbyn, Maksym, Todadri Senthil, and Patrick Lee. “Exotic S=1 Spin-Liquid State with Fermionic Excitations on the Triangular Lattice.” Physical Review B - Condensed Matter and Materials Physics. American Physical Society, 2011. https://doi.org/10.1103/PhysRevB.84.180403.","mla":"Serbyn, Maksym, et al. “Exotic S=1 Spin-Liquid State with Fermionic Excitations on the Triangular Lattice.” Physical Review B - Condensed Matter and Materials Physics, vol. 84, no. 18, American Physical Society, 2011, doi:10.1103/PhysRevB.84.180403.","short":"M. Serbyn, T. Senthil, P. Lee, Physical Review B - Condensed Matter and Materials Physics 84 (2011)."}},{"day":"19","month":"01","date_published":"2011-01-19T00:00:00Z","doi":"10.1103/PhysRevB.83.024506","quality_controlled":0,"citation":{"ama":"Serbyn M, Lee P. Isotope effect on the superfluid density in conventional and high-temperature superconductors. Physical Review B - Condensed Matter and Materials Physics. 2011;83(2). doi:10.1103/PhysRevB.83.024506","ista":"Serbyn M, Lee P. 2011. Isotope effect on the superfluid density in conventional and high-temperature superconductors. Physical Review B - Condensed Matter and Materials Physics. 83(2).","ieee":"M. Serbyn and P. Lee, “Isotope effect on the superfluid density in conventional and high-temperature superconductors,” Physical Review B - Condensed Matter and Materials Physics, vol. 83, no. 2. American Physical Society, 2011.","apa":"Serbyn, M., & Lee, P. (2011). Isotope effect on the superfluid density in conventional and high-temperature superconductors. Physical Review B - Condensed Matter and Materials Physics. American Physical Society. https://doi.org/10.1103/PhysRevB.83.024506","mla":"Serbyn, Maksym, and Patrick Lee. “Isotope Effect on the Superfluid Density in Conventional and High-Temperature Superconductors.” Physical Review B - Condensed Matter and Materials Physics, vol. 83, no. 2, American Physical Society, 2011, doi:10.1103/PhysRevB.83.024506.","short":"M. Serbyn, P. Lee, Physical Review B - Condensed Matter and Materials Physics 83 (2011).","chicago":"Serbyn, Maksym, and Patrick Lee. “Isotope Effect on the Superfluid Density in Conventional and High-Temperature Superconductors.” Physical Review B - Condensed Matter and Materials Physics. American Physical Society, 2011. https://doi.org/10.1103/PhysRevB.83.024506."},"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1009.2429","open_access":"1"}],"publication":"Physical Review B - Condensed Matter and Materials Physics","extern":1,"publist_id":"6434","issue":"2","abstract":[{"text":"We investigate the isotope effect on the London penetration depth of a superconductor which measures n S/m*, the ratio of superfluid density to effective mass. We use a simplified model of electrons weakly coupled to a single phonon frequency ω E, but assume that the energy gap Δ does not have any isotope effect. Nevertheless, we find an isotope effect for n S/m* which is significant if Δ is sufficiently large that it becomes comparable to ω E, a regime of interest to high-T c cuprate superconductors and possibly other families of unconventional superconductors with relatively high T c. Our model is too simple to describe the cuprates and it gives the wrong sign of the isotope effect when compared with experiment, but it is a proof of principle that the isotope effect exists for n S/m* in materials where the pairing gap and T c are not of phonon origin and have no isotope effect.","lang":"eng"}],"type":"journal_article","volume":83,"date_created":"2018-12-11T11:49:28Z","date_updated":"2021-01-12T08:22:19Z","author":[{"full_name":"Maksym Serbyn","last_name":"Serbyn","first_name":"Maksym","orcid":"0000-0002-2399-5827","id":"47809E7E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Patrick","last_name":"Lee","full_name":"Lee, Patrick"}],"intvolume":" 83","publisher":"American Physical Society","title":"Isotope effect on the superfluid density in conventional and high-temperature superconductors","status":"public","publication_status":"published","_id":"969","year":"2011"},{"publisher":"Elsevier","intvolume":" 405","status":"public","publication_status":"published","title":"Probing water accessibility in HET-s(218–289) amyloid fibrils by solid-state NMR","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"8471","year":"2011","volume":405,"oa_version":"None","date_updated":"2021-01-12T08:19:30Z","date_created":"2020-09-18T10:11:03Z","author":[{"first_name":"Hélène","last_name":"Van Melckebeke","full_name":"Van Melckebeke, Hélène"},{"id":"7B541462-FAF6-11E9-A490-E8DFE5697425","orcid":"0000-0002-9350-7606","first_name":"Paul","last_name":"Schanda","full_name":"Schanda, Paul"},{"full_name":"Gath, Julia","last_name":"Gath","first_name":"Julia"},{"full_name":"Wasmer, Christian","first_name":"Christian","last_name":"Wasmer"},{"full_name":"Verel, René","first_name":"René","last_name":"Verel"},{"first_name":"Adam","last_name":"Lange","full_name":"Lange, Adam"},{"full_name":"Meier, Beat H.","first_name":"Beat H.","last_name":"Meier"},{"full_name":"Böckmann, Anja","first_name":"Anja","last_name":"Böckmann"}],"type":"journal_article","extern":"1","issue":"3","abstract":[{"lang":"eng","text":"Despite the importance of protein fibrils in the context of conformational diseases, information on their structure is still sparse. Hydrogen/deuterium exchange measurements of backbone amide protons allow the identification hydrogen-bonding patterns and reveal pertinent information on the amyloid β-sheet architecture. However, they provide only little information on the identity of residues exposed to solvent or buried inside the fibril core. NMR spectroscopy is a potent method for identifying solvent-accessible residues in proteins via observation of polarization transfer between chemically exchanging side-chain protons and water protons. We show here that the combined use of highly deuterated samples and fast magic-angle spinning greatly attenuates unwanted spin diffusion and allows identification of polarization exchange with the solvent in a site-specific manner. We apply this measurement protocol to HET-s(218–289) prion fibrils under different conditions (including physiological pH, where protofibrils assemble together into thicker fibrils) and demonstrate that each protofibril of HET-s(218–289), is surrounded by water, thus excluding the existence of extended dry interfibril contacts. We also show that exchangeable side-chain protons inside the hydrophobic core of HET-s(218–289) do not exchange over time intervals of weeks to months. The experiments proposed in this study can provide insight into the detailed structural features of amyloid fibrils in general."}],"page":"765-772","article_type":"original","quality_controlled":"1","citation":{"ama":"Van Melckebeke H, Schanda P, Gath J, et al. Probing water accessibility in HET-s(218–289) amyloid fibrils by solid-state NMR. Journal of Molecular Biology. 2011;405(3):765-772. doi:10.1016/j.jmb.2010.11.004","ista":"Van Melckebeke H, Schanda P, Gath J, Wasmer C, Verel R, Lange A, Meier BH, Böckmann A. 2011. Probing water accessibility in HET-s(218–289) amyloid fibrils by solid-state NMR. Journal of Molecular Biology. 405(3), 765–772.","apa":"Van Melckebeke, H., Schanda, P., Gath, J., Wasmer, C., Verel, R., Lange, A., … Böckmann, A. (2011). Probing water accessibility in HET-s(218–289) amyloid fibrils by solid-state NMR. Journal of Molecular Biology. Elsevier. https://doi.org/10.1016/j.jmb.2010.11.004","ieee":"H. Van Melckebeke et al., “Probing water accessibility in HET-s(218–289) amyloid fibrils by solid-state NMR,” Journal of Molecular Biology, vol. 405, no. 3. Elsevier, pp. 765–772, 2011.","mla":"Van Melckebeke, Hélène, et al. “Probing Water Accessibility in HET-s(218–289) Amyloid Fibrils by Solid-State NMR.” Journal of Molecular Biology, vol. 405, no. 3, Elsevier, 2011, pp. 765–72, doi:10.1016/j.jmb.2010.11.004.","short":"H. Van Melckebeke, P. Schanda, J. Gath, C. Wasmer, R. Verel, A. Lange, B.H. Meier, A. Böckmann, Journal of Molecular Biology 405 (2011) 765–772.","chicago":"Van Melckebeke, Hélène, Paul Schanda, Julia Gath, Christian Wasmer, René Verel, Adam Lange, Beat H. Meier, and Anja Böckmann. “Probing Water Accessibility in HET-s(218–289) Amyloid Fibrils by Solid-State NMR.” Journal of Molecular Biology. Elsevier, 2011. https://doi.org/10.1016/j.jmb.2010.11.004."},"publication":"Journal of Molecular Biology","language":[{"iso":"eng"}],"date_published":"2011-01-21T00:00:00Z","doi":"10.1016/j.jmb.2010.11.004","publication_identifier":{"issn":["0022-2836"]},"article_processing_charge":"No","day":"21","month":"01"},{"type":"journal_article","abstract":[{"text":"The classical principle of least action says that orbits of mechanical systems extremize action; an important subclass are those orbits that minimize action. In this paper we utilize this principle along with Aubry-Mather theory to construct (Birkhoff) regions of instability for a certain three-body problem, given by a Hamiltonian system of 2 degrees of freedom. We believe that these methods can be applied to construct instability regions for a variety of Hamiltonian systems with 2 degrees of freedom. The Hamiltonian model we consider describes dynamics of a Sun-Jupiter-comet system, and under some simplifying assumptions, we show the existence of instabilities for the orbit of the comet. In particular, we show that a comet which starts close to an orbit in the shape of an ellipse of eccentricity e=0.66 can increase in eccentricity up to e=0.96. In the sequels to this paper, we extend the result to beyond e=1 and show the existence of ejection orbits. Such orbits are initially well within the range of our solar system. This might give an indication of why most objects rotating around the Sun in our solar system have relatively low eccentricity.","lang":"eng"}],"issue":"2","extern":"1","_id":"8505","year":"2011","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","publication_status":"published","title":"Destruction of invariant curves in the restricted circular planar three-body problem by using comparison of action","publisher":"Duke University Press","intvolume":" 159","author":[{"full_name":"Galante, Joseph","last_name":"Galante","first_name":"Joseph"},{"last_name":"Kaloshin","first_name":"Vadim","orcid":"0000-0002-6051-2628","id":"FE553552-CDE8-11E9-B324-C0EBE5697425","full_name":"Kaloshin, Vadim"}],"date_updated":"2021-01-12T08:19:45Z","date_created":"2020-09-18T10:47:41Z","oa_version":"None","volume":159,"keyword":["General Mathematics"],"day":"04","month":"08","publication_identifier":{"issn":["0012-7094"]},"article_processing_charge":"No","publication":"Duke Mathematical Journal","citation":{"mla":"Galante, Joseph, and Vadim Kaloshin. “Destruction of Invariant Curves in the Restricted Circular Planar Three-Body Problem by Using Comparison of Action.” Duke Mathematical Journal, vol. 159, no. 2, Duke University Press, 2011, pp. 275–327, doi:10.1215/00127094-1415878.","short":"J. Galante, V. Kaloshin, Duke Mathematical Journal 159 (2011) 275–327.","chicago":"Galante, Joseph, and Vadim Kaloshin. “Destruction of Invariant Curves in the Restricted Circular Planar Three-Body Problem by Using Comparison of Action.” Duke Mathematical Journal. Duke University Press, 2011. https://doi.org/10.1215/00127094-1415878.","ama":"Galante J, Kaloshin V. Destruction of invariant curves in the restricted circular planar three-body problem by using comparison of action. Duke Mathematical Journal. 2011;159(2):275-327. doi:10.1215/00127094-1415878","ista":"Galante J, Kaloshin V. 2011. Destruction of invariant curves in the restricted circular planar three-body problem by using comparison of action. Duke Mathematical Journal. 159(2), 275–327.","ieee":"J. Galante and V. Kaloshin, “Destruction of invariant curves in the restricted circular planar three-body problem by using comparison of action,” Duke Mathematical Journal, vol. 159, no. 2. Duke University Press, pp. 275–327, 2011.","apa":"Galante, J., & Kaloshin, V. (2011). Destruction of invariant curves in the restricted circular planar three-body problem by using comparison of action. Duke Mathematical Journal. Duke University Press. https://doi.org/10.1215/00127094-1415878"},"quality_controlled":"1","article_type":"original","page":"275-327","doi":"10.1215/00127094-1415878","date_published":"2011-08-04T00:00:00Z","language":[{"iso":"eng"}]},{"month":"03","day":"14","date_published":"2011-03-14T00:00:00Z","doi":"10.1002/9780470619902.ch4","citation":{"ama":"Kondrashov F. Gene Dosage and Duplication. In: Evolution after Gene Duplication. Wiley-Blackwell; 2011:57-76. doi:10.1002/9780470619902.ch4","apa":"Kondrashov, F. (2011). Gene Dosage and Duplication. In Evolution after Gene Duplication (pp. 57–76). Wiley-Blackwell. https://doi.org/10.1002/9780470619902.ch4","ieee":"F. Kondrashov, “Gene Dosage and Duplication,” in Evolution after Gene Duplication, Wiley-Blackwell, 2011, pp. 57–76.","ista":"Kondrashov F. 2011.Gene Dosage and Duplication. In: Evolution after Gene Duplication. , 57–76.","short":"F. Kondrashov, in:, Evolution after Gene Duplication, Wiley-Blackwell, 2011, pp. 57–76.","mla":"Kondrashov, Fyodor. “Gene Dosage and Duplication.” Evolution after Gene Duplication, Wiley-Blackwell, 2011, pp. 57–76, doi:10.1002/9780470619902.ch4.","chicago":"Kondrashov, Fyodor. “Gene Dosage and Duplication.” In Evolution after Gene Duplication, 57–76. Wiley-Blackwell, 2011. https://doi.org/10.1002/9780470619902.ch4."},"publication":"Evolution after Gene Duplication","page":"57 - 76","quality_controlled":0,"publist_id":"6766","extern":1,"type":"book_chapter","author":[{"last_name":"Kondrashov","first_name":"Fyodor","orcid":"0000-0001-8243-4694","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","full_name":"Fyodor Kondrashov"}],"date_created":"2018-12-11T11:49:00Z","date_updated":"2021-01-12T08:21:08Z","year":"2011","_id":"881","publisher":"Wiley-Blackwell","publication_status":"published","status":"public","title":"Gene Dosage and Duplication"},{"author":[{"first_name":"Thomas","last_name":"Angelini","full_name":"Angelini, Thomas"},{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561","first_name":"Edouard B","last_name":"Hannezo","full_name":"Hannezo, Edouard B"},{"first_name":"Xavier","last_name":"Trepatc","full_name":"Trepatc, Xavier"},{"full_name":"Marquez, Manuel","first_name":"Manuel","last_name":"Marquez"},{"last_name":"Fredberg","first_name":"Jeffrey","full_name":"Fredberg, Jeffrey"},{"last_name":"Weitz","first_name":"David","full_name":"Weitz, David"}],"date_created":"2018-12-11T11:49:12Z","date_updated":"2021-01-12T08:21:54Z","oa_version":"None","volume":108,"year":"2011","_id":"919","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","status":"public","title":"Glass-like dynamics of collective cell migration","publisher":"PNAS","intvolume":" 108","abstract":[{"text":"Collective cell migration in tissues occurs throughout embryonic development, during wound healing, and in cancerous tumor invasion, yet most detailed knowledge of cell migration comes from single-cell studies. As single cells migrate, the shape of the cell body fluctuates dramatically through cyclic processes of extension, adhesion, and retraction, accompanied by erratic changes in migration direction. Within confluent cell layers, such subcellular motions must be coupled between neighbors, yet the influence of these subcellular motions on collective migration is not known. Here we study motion within a confluent epithelial cell sheet, simultaneously measuring collective migration and subcellular motions, covering a broad range of length scales, time scales, and cell densities. At large length scales and time scales collective migration slows as cell density rises, yet the fastest cells move in large, multicell groups whose scale grows with increasing cell density. This behavior has an intriguing analogy to dynamic heterogeneities found in particulate systems as they become more crowded and approach a glass transition. In addition we find a diminishing self-diffusivity of short-wavelength motions within the cell layer, and growing peaks in the vibrational density of states associated with cooperative cell-shape fluctuations. Both of these observations are also intriguingly reminiscent of a glass transition. Thus, these results provide a broad and suggestive analogy between cell motion within a confluent layer and the dynamics of supercooled colloidal and molecular fluids approaching a glass transition.","lang":"eng"}],"issue":"12","publist_id":"6522","extern":"1","type":"journal_article","doi":"10.1073/pnas.1010059108","date_published":"2011-03-22T00:00:00Z","language":[{"iso":"eng"}],"publication":"Proceedings of the National Academy of Sciences of the United States of America","citation":{"mla":"Angelini, Thomas, et al. “Glass-like Dynamics of Collective Cell Migration.” Proceedings of the National Academy of Sciences of the United States of America, vol. 108, no. 12, PNAS, 2011, pp. 4714–19, doi:10.1073/pnas.1010059108.","short":"T. Angelini, E.B. Hannezo, X. Trepatc, M. Marquez, J. Fredberg, D. Weitz, Proceedings of the National Academy of Sciences of the United States of America 108 (2011) 4714–4719.","chicago":"Angelini, Thomas, Edouard B Hannezo, Xavier Trepatc, Manuel Marquez, Jeffrey Fredberg, and David Weitz. “Glass-like Dynamics of Collective Cell Migration.” Proceedings of the National Academy of Sciences of the United States of America. PNAS, 2011. https://doi.org/10.1073/pnas.1010059108.","ama":"Angelini T, Hannezo EB, Trepatc X, Marquez M, Fredberg J, Weitz D. Glass-like dynamics of collective cell migration. Proceedings of the National Academy of Sciences of the United States of America. 2011;108(12):4714-4719. doi:10.1073/pnas.1010059108","ista":"Angelini T, Hannezo EB, Trepatc X, Marquez M, Fredberg J, Weitz D. 2011. Glass-like dynamics of collective cell migration. Proceedings of the National Academy of Sciences of the United States of America. 108(12), 4714–4719.","ieee":"T. Angelini, E. B. Hannezo, X. Trepatc, M. Marquez, J. Fredberg, and D. Weitz, “Glass-like dynamics of collective cell migration,” Proceedings of the National Academy of Sciences of the United States of America, vol. 108, no. 12. PNAS, pp. 4714–4719, 2011.","apa":"Angelini, T., Hannezo, E. B., Trepatc, X., Marquez, M., Fredberg, J., & Weitz, D. (2011). Glass-like dynamics of collective cell migration. Proceedings of the National Academy of Sciences of the United States of America. PNAS. https://doi.org/10.1073/pnas.1010059108"},"quality_controlled":"1","page":"4714 - 4719","month":"03","day":"22"},{"publication":"Physical Review Letters","citation":{"ama":"Hannezo EB, Prost J, Joanny J. Instabilities of monolayered epithelia Shape and structure of villi and crypts. Physical Review Letters. 2011;107(7). doi:10.1103/PhysRevLett.107.078104","ieee":"E. B. Hannezo, J. Prost, and J. Joanny, “Instabilities of monolayered epithelia Shape and structure of villi and crypts,” Physical Review Letters, vol. 107, no. 7. American Physical Society, 2011.","apa":"Hannezo, E. B., Prost, J., & Joanny, J. (2011). Instabilities of monolayered epithelia Shape and structure of villi and crypts. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.107.078104","ista":"Hannezo EB, Prost J, Joanny J. 2011. Instabilities of monolayered epithelia Shape and structure of villi and crypts. Physical Review Letters. 107(7).","short":"E.B. Hannezo, J. Prost, J. Joanny, Physical Review Letters 107 (2011).","mla":"Hannezo, Edouard B., et al. “Instabilities of Monolayered Epithelia Shape and Structure of Villi and Crypts.” Physical Review Letters, vol. 107, no. 7, American Physical Society, 2011, doi:10.1103/PhysRevLett.107.078104.","chicago":"Hannezo, Edouard B, Jacques Prost, and Jean Joanny. “Instabilities of Monolayered Epithelia Shape and Structure of Villi and Crypts.” Physical Review Letters. American Physical Society, 2011. https://doi.org/10.1103/PhysRevLett.107.078104."},"date_published":"2011-08-11T00:00:00Z","doi":"10.1103/PhysRevLett.107.078104","language":[{"iso":"eng"}],"month":"08","day":"11","article_processing_charge":"No","year":"2011","_id":"918","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"We thank S. Fre and M. Huygue for discussion and for showing us in vivo samples and A. Bergès for help with the manuscript.","title":"Instabilities of monolayered epithelia Shape and structure of villi and crypts","publication_status":"published","status":"public","intvolume":" 107","publisher":"American Physical Society","author":[{"full_name":"Hannezo, Edouard B","first_name":"Edouard B","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561"},{"last_name":"Prost","first_name":"Jacques","full_name":"Prost, Jacques"},{"full_name":"Joanny, Jean","last_name":"Joanny","first_name":"Jean"}],"date_updated":"2021-01-12T08:21:54Z","date_created":"2018-12-11T11:49:11Z","oa_version":"None","volume":107,"type":"journal_article","abstract":[{"text":"We study theoretically the shapes of a dividing epithelial monolayer of cells lying on top of an elastic stroma. The negative tension created by cell division provokes a buckling instability at a finite wave vector leading to the formation of periodic arrays of villi and crypts. The instability is similar to the buckling of a metallic plate under compression. We use the results to rationalize the various structures of the intestinal lining observed in vivo. Taking into account the coupling between cell division and local curvature, we obtain different patterns of villi and crypts, which could explain the different morphologies of the small intestine and the colon.","lang":"eng"}],"publist_id":"6521","issue":"7","extern":"1"},{"extern":"1","pmid":1,"year":"2011","department":[{"_id":"DaZi"}],"publisher":"Elsevier","publication_status":"published","author":[{"full_name":"Zilberman, Daniel","orcid":"0000-0002-0123-8649","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","last_name":"Zilberman","first_name":"Daniel"}],"volume":20,"date_updated":"2021-12-14T08:34:37Z","date_created":"2021-06-08T06:23:39Z","publication_identifier":{"eissn":["1878-1551"],"issn":["1534-5807"]},"month":"06","main_file_link":[{"url":"https://doi.org/10.1016/j.devcel.2011.05.018","open_access":"1"}],"external_id":{"pmid":["21664571"]},"oa":1,"quality_controlled":"1","doi":"10.1016/j.devcel.2011.05.018","language":[{"iso":"eng"}],"type":"other_academic_publication","issue":"6","abstract":[{"text":"Little is known about chromatin remodeling events immediately after fertilization. A recent report by Autran et al. (2011) in Cell now shows that chromatin regulatory pathways that silence transposable elements are responsible for global delayed activation of gene expression in the early Arabidopsis embryo.","lang":"eng"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"9522","intvolume":" 20","status":"public","title":"Balancing parental contributions in plant embryonic gene activation","oa_version":"Published Version","article_processing_charge":"No","day":"14","citation":{"ieee":"D. Zilberman, Balancing parental contributions in plant embryonic gene activation, vol. 20, no. 6. Elsevier, 2011, pp. 735–736.","apa":"Zilberman, D. (2011). Balancing parental contributions in plant embryonic gene activation. Developmental Cell (Vol. 20, pp. 735–736). Elsevier. https://doi.org/10.1016/j.devcel.2011.05.018","ista":"Zilberman D. 2011. Balancing parental contributions in plant embryonic gene activation, Elsevier,p.","ama":"Zilberman D. Balancing Parental Contributions in Plant Embryonic Gene Activation. Vol 20. Elsevier; 2011:735-736. doi:10.1016/j.devcel.2011.05.018","chicago":"Zilberman, Daniel. Balancing Parental Contributions in Plant Embryonic Gene Activation. Developmental Cell. Vol. 20. Elsevier, 2011. https://doi.org/10.1016/j.devcel.2011.05.018.","short":"D. Zilberman, Balancing Parental Contributions in Plant Embryonic Gene Activation, Elsevier, 2011.","mla":"Zilberman, Daniel. “Balancing Parental Contributions in Plant Embryonic Gene Activation.” Developmental Cell, vol. 20, no. 6, Elsevier, 2011, pp. 735–36, doi:10.1016/j.devcel.2011.05.018."},"publication":"Developmental Cell","page":"735-736","date_published":"2011-06-14T00:00:00Z"},{"volume":6854,"date_created":"2021-07-11T22:01:19Z","date_updated":"2021-08-12T13:53:17Z","author":[{"first_name":"Rocio","last_name":"Gonzalez-Diaz","full_name":"Gonzalez-Diaz, Rocio"},{"full_name":"Ion, Adrian","last_name":"Ion","first_name":"Adrian","id":"29F89302-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Jimenez, Maria Jose","last_name":"Jimenez","first_name":"Maria Jose"},{"full_name":"Poyatos, Regina","last_name":"Poyatos","first_name":"Regina"}],"department":[{"_id":"HeEd"}],"publisher":"Springer Nature","publication_status":"published","year":"2011","language":[{"iso":"eng"}],"doi":"10.1007/978-3-642-23672-3_35","conference":{"location":"Seville, Spain","start_date":"2011-08-29","end_date":"2011-08-31","name":"CAIP: International Conference on Computer Analysis of Images and Patterns"},"quality_controlled":"1","oa":1,"main_file_link":[{"url":"http://hdl.handle.net/11441/30766","open_access":"1"}],"publication_identifier":{"isbn":["9783642236716"],"eissn":["16113349"],"issn":["03029743"]},"month":"08","oa_version":"Published Version","intvolume":" 6854","status":"public","title":"Incremental-decremental algorithm for computing AT-models and persistent homology","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","_id":"9648","abstract":[{"lang":"eng","text":"In this paper, we establish a correspondence between the incremental algorithm for computing AT-models [8,9] and the one for computing persistent homology [6,14,15]. We also present a decremental algorithm for computing AT-models that allows to extend the persistence computation to a wider setting. Finally, we show how to combine incremental and decremental techniques for persistent homology computation."}],"alternative_title":["LNCS"],"type":"conference","date_published":"2011-08-01T00:00:00Z","page":"286-293","citation":{"apa":"Gonzalez-Diaz, R., Ion, A., Jimenez, M. J., & Poyatos, R. (2011). Incremental-decremental algorithm for computing AT-models and persistent homology. In Computer Analysis of Images and Patterns (Vol. 6854, pp. 286–293). Seville, Spain: Springer Nature. https://doi.org/10.1007/978-3-642-23672-3_35","ieee":"R. Gonzalez-Diaz, A. Ion, M. J. Jimenez, and R. Poyatos, “Incremental-decremental algorithm for computing AT-models and persistent homology,” in Computer Analysis of Images and Patterns, Seville, Spain, 2011, vol. 6854, pp. 286–293.","ista":"Gonzalez-Diaz R, Ion A, Jimenez MJ, Poyatos R. 2011. Incremental-decremental algorithm for computing AT-models and persistent homology. Computer Analysis of Images and Patterns. CAIP: International Conference on Computer Analysis of Images and Patterns, LNCS, vol. 6854, 286–293.","ama":"Gonzalez-Diaz R, Ion A, Jimenez MJ, Poyatos R. Incremental-decremental algorithm for computing AT-models and persistent homology. In: Computer Analysis of Images and Patterns. Vol 6854. Springer Nature; 2011:286-293. doi:10.1007/978-3-642-23672-3_35","chicago":"Gonzalez-Diaz, Rocio, Adrian Ion, Maria Jose Jimenez, and Regina Poyatos. “Incremental-Decremental Algorithm for Computing AT-Models and Persistent Homology.” In Computer Analysis of Images and Patterns, 6854:286–93. Springer Nature, 2011. https://doi.org/10.1007/978-3-642-23672-3_35.","short":"R. Gonzalez-Diaz, A. Ion, M.J. Jimenez, R. Poyatos, in:, Computer Analysis of Images and Patterns, Springer Nature, 2011, pp. 286–293.","mla":"Gonzalez-Diaz, Rocio, et al. “Incremental-Decremental Algorithm for Computing AT-Models and Persistent Homology.” Computer Analysis of Images and Patterns, vol. 6854, Springer Nature, 2011, pp. 286–93, doi:10.1007/978-3-642-23672-3_35."},"publication":"Computer Analysis of Images and Patterns","article_processing_charge":"No","day":"01","scopus_import":"1"},{"volume":106,"date_updated":"2021-01-12T08:22:19Z","date_created":"2018-12-11T11:49:27Z","author":[{"orcid":"0000-0002-2399-5827","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","last_name":"Serbyn","first_name":"Maksym","full_name":"Maksym Serbyn"},{"first_name":"Mikhail","last_name":"Skvortsov","full_name":"Skvortsov, Mikhail A"},{"first_name":"Andrei","last_name":"Varlamov","full_name":"Varlamov, Andrei A"},{"full_name":"Galitski, Victor M","first_name":"Victor","last_name":"Galitski"}],"intvolume":" 106","publisher":"American Physical Society","title":"Serbyn et al. Reply:","status":"public","publication_status":"published","year":"2011","_id":"968","extern":1,"publist_id":"6433","issue":"13","abstract":[{"lang":"eng","text":"A Reply to the Comment by Andrei Sergeev, M. Reizer, and V. Mitin."}],"type":"journal_article","doi":"10.1103/PhysRevLett.106.139702","date_published":"2011-04-01T00:00:00Z","quality_controlled":0,"citation":{"ama":"Serbyn M, Skvortsov M, Varlamov A, Galitski V. Serbyn et al. Reply: Physical Review Letters. 2011;106(13). doi:10.1103/PhysRevLett.106.139702","ista":"Serbyn M, Skvortsov M, Varlamov A, Galitski V. 2011. Serbyn et al. Reply: Physical Review Letters. 106(13).","apa":"Serbyn, M., Skvortsov, M., Varlamov, A., & Galitski, V. (2011). Serbyn et al. Reply: Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.106.139702","ieee":"M. Serbyn, M. Skvortsov, A. Varlamov, and V. Galitski, “Serbyn et al. Reply:,” Physical Review Letters, vol. 106, no. 13. American Physical Society, 2011.","mla":"Serbyn, Maksym, et al. “Serbyn et Al. Reply:” Physical Review Letters, vol. 106, no. 13, American Physical Society, 2011, doi:10.1103/PhysRevLett.106.139702.","short":"M. Serbyn, M. Skvortsov, A. Varlamov, V. Galitski, Physical Review Letters 106 (2011).","chicago":"Serbyn, Maksym, Mikhail Skvortsov, Andrei Varlamov, and Victor Galitski. “Serbyn et Al. Reply:” Physical Review Letters. American Physical Society, 2011. https://doi.org/10.1103/PhysRevLett.106.139702."},"publication":"Physical Review Letters","day":"01","month":"04"},{"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","_id":"3395","title":"Effect of oceanographic barriers and overfishing on the population genetic structure of the European spiny lobster Palinurus elephas","status":"public","intvolume":" 104","oa_version":"None","type":"journal_article","abstract":[{"lang":"eng","text":"Defining population structure and genetic diversity levels is of the utmost importance for developing efficient conservation strategies. Overfishing has caused mean annual catches of the European spiny lobster (Palinurus elephas) to decrease alarmingly along its distribution area. In this context, there is a need for comprehensive studies aiming to evaluate the genetic health of the exploited populations. The present study is based on a set of ten nuclear markers amplified in 331 individuals from ten different localities covering most of P. elephas distribution area. Samples from Atlantic and Mediterranean basins showed small but significant differences, indicating that P. elephas populations do not behave as a single panmictic unit but form two partially-overlapping groups. Despite intense overfishing, our dataset did not recover a recent bottleneck signal, and instead showed a large and stable historical effective size. This result could be accounted for by specific life-history traits (reproduction and longevity) and the limitations of molecular markers in covering recent timescales for nontemporal samples. The findings of the present study emphasize the need to integrate information on effective population sizes and life-history parameters when evaluating population connectivity levels from genetic data."}],"issue":"2","publication":"Biological Journal of the Linnean Society","citation":{"ista":"Palero F, Abello P, Macpherson E, Beaumont M, Pascual M. 2011. Effect of oceanographic barriers and overfishing on the population genetic structure of the European spiny lobster Palinurus elephas. Biological Journal of the Linnean Society. 104(2), 407–418.","apa":"Palero, F., Abello, P., Macpherson, E., Beaumont, M., & Pascual, M. (2011). Effect of oceanographic barriers and overfishing on the population genetic structure of the European spiny lobster Palinurus elephas. Biological Journal of the Linnean Society. Wiley-Blackwell. https://doi.org/10.1111/j.1095-8312.2011.01728.x","ieee":"F. Palero, P. Abello, E. Macpherson, M. Beaumont, and M. Pascual, “Effect of oceanographic barriers and overfishing on the population genetic structure of the European spiny lobster Palinurus elephas,” Biological Journal of the Linnean Society, vol. 104, no. 2. Wiley-Blackwell, pp. 407–418, 2011.","ama":"Palero F, Abello P, Macpherson E, Beaumont M, Pascual M. Effect of oceanographic barriers and overfishing on the population genetic structure of the European spiny lobster Palinurus elephas. Biological Journal of the Linnean Society. 2011;104(2):407-418. doi:10.1111/j.1095-8312.2011.01728.x","chicago":"Palero, Ferran, Pere Abello, Enrique Macpherson, Mark Beaumont, and Marta Pascual. “Effect of Oceanographic Barriers and Overfishing on the Population Genetic Structure of the European Spiny Lobster Palinurus Elephas.” Biological Journal of the Linnean Society. Wiley-Blackwell, 2011. https://doi.org/10.1111/j.1095-8312.2011.01728.x.","mla":"Palero, Ferran, et al. “Effect of Oceanographic Barriers and Overfishing on the Population Genetic Structure of the European Spiny Lobster Palinurus Elephas.” Biological Journal of the Linnean Society, vol. 104, no. 2, Wiley-Blackwell, 2011, pp. 407–18, doi:10.1111/j.1095-8312.2011.01728.x.","short":"F. Palero, P. Abello, E. Macpherson, M. Beaumont, M. Pascual, Biological Journal of the Linnean Society 104 (2011) 407–418."},"page":"407 - 418","date_published":"2011-09-14T00:00:00Z","scopus_import":"1","day":"14","article_processing_charge":"No","acknowledgement":"This work was supported by a pre-doctoral fellowship awarded by the Autonomous Government of Catalonia to F.P. (2006FIC-00082). Research was funded by projects FBBVA-BIOCON 08-187/09, CGL2006-13423, and CTM2007-66635. The authors are part of the research group 2009SGR-636, 2009SGR-655, and 2009SGR-1364 of the Generalitat de Catalunya. F.P. acknowledges EU-Synthesys grant (GB-TAF-4474).","year":"2011","publication_status":"published","publisher":"Wiley-Blackwell","department":[{"_id":"NiBa"}],"author":[{"id":"3F0E2A22-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0343-8329","first_name":"Ferran","last_name":"Palero","full_name":"Palero, Ferran"},{"full_name":"Abello, Pere","first_name":"Pere","last_name":"Abello"},{"full_name":"Macpherson, Enrique","first_name":"Enrique","last_name":"Macpherson"},{"full_name":"Beaumont, Mark","first_name":"Mark","last_name":"Beaumont"},{"full_name":"Pascual, Marta","last_name":"Pascual","first_name":"Marta"}],"related_material":{"record":[{"status":"public","relation":"research_data","id":"9762"}]},"date_created":"2018-12-11T12:03:06Z","date_updated":"2023-02-23T14:07:31Z","volume":104,"publist_id":"3212","quality_controlled":"1","doi":"10.1111/j.1095-8312.2011.01728.x","language":[{"iso":"eng"}],"month":"09"},{"abstract":[{"text":"Defining population structure and genetic diversity levels is of the utmost importance for developing efficient conservation strategies. Overfishing has caused mean annual catches of the European spiny lobster (Palinurus elephas) to decrease alarmingly along its distribution area. In this context, there is a need for comprehensive studies to evaluate the genetic health of the exploited populations. The present work is based on a set of 10 nuclear markers amplified in 331 individuals from 10 different localities covering most of P. elephas distribution area. Samples from Atlantic and Mediterranean basins showed small but significant differences, indicating that P. elephas populations do not behave as a single panmictic unit but form two partially-overlapping groups. Despite intense overfishing, our dataset did not recover a recent bottleneck signal, and showed a large and stable historical effective size instead. This result could be accounted for by specific life history traits (reproduction and longevity) and the limitations of molecular markers in covering very recent timescales for non temporal samples. Our study emphasizes the necessity of integrating information on effective population sizes and life history parameters when evaluating population connectivity levels from genetic data.","lang":"eng"}],"type":"research_data_reference","oa_version":"Published Version","date_created":"2021-08-02T07:11:19Z","date_updated":"2023-02-23T11:25:25Z","related_material":{"record":[{"id":"3395","relation":"used_in_publication","status":"public"}]},"author":[{"full_name":"Palero, Ferran","last_name":"Palero","first_name":"Ferran","orcid":"0000-0002-0343-8329","id":"3F0E2A22-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Abello, Pere","first_name":"Pere","last_name":"Abello"},{"first_name":"Enrique","last_name":"Macpherson","full_name":"Macpherson, Enrique"},{"first_name":"Mark","last_name":"Beaumont","full_name":"Beaumont, Mark"},{"full_name":"Pascual, Marta","first_name":"Marta","last_name":"Pascual"}],"publisher":"IST Austria","department":[{"_id":"NiBa"}],"status":"public","title":"Data from: Effect of oceanographic barriers and overfishing on the population genetic structure of the European spiny lobster (Palinurus elephas)","year":"2011","_id":"9762","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","article_processing_charge":"No","day":"12","month":"05","date_published":"2011-05-12T00:00:00Z","doi":"10.5061/dryad.299h8","oa":1,"main_file_link":[{"url":"https://doi.org/10.5061/dryad.299h8","open_access":"1"}],"citation":{"ama":"Palero F, Abello P, Macpherson E, Beaumont M, Pascual M. Data from: Effect of oceanographic barriers and overfishing on the population genetic structure of the European spiny lobster (Palinurus elephas). 2011. doi:10.5061/dryad.299h8","ieee":"F. Palero, P. Abello, E. Macpherson, M. Beaumont, and M. Pascual, “Data from: Effect of oceanographic barriers and overfishing on the population genetic structure of the European spiny lobster (Palinurus elephas).” IST Austria, 2011.","apa":"Palero, F., Abello, P., Macpherson, E., Beaumont, M., & Pascual, M. (2011). Data from: Effect of oceanographic barriers and overfishing on the population genetic structure of the European spiny lobster (Palinurus elephas). IST Austria. https://doi.org/10.5061/dryad.299h8","ista":"Palero F, Abello P, Macpherson E, Beaumont M, Pascual M. 2011. Data from: Effect of oceanographic barriers and overfishing on the population genetic structure of the European spiny lobster (Palinurus elephas), IST Austria, 10.5061/dryad.299h8.","short":"F. Palero, P. Abello, E. Macpherson, M. Beaumont, M. Pascual, (2011).","mla":"Palero, Ferran, et al. Data from: Effect of Oceanographic Barriers and Overfishing on the Population Genetic Structure of the European Spiny Lobster (Palinurus Elephas). IST Austria, 2011, doi:10.5061/dryad.299h8.","chicago":"Palero, Ferran, Pere Abello, Enrique Macpherson, Mark Beaumont, and Marta Pascual. “Data from: Effect of Oceanographic Barriers and Overfishing on the Population Genetic Structure of the European Spiny Lobster (Palinurus Elephas).” IST Austria, 2011. https://doi.org/10.5061/dryad.299h8."}},{"type":"conference","extern":"1","abstract":[{"text":"Segmentation is the process of partitioning digital images into meaningful regions. The analysis of biological high content images often requires segmentation as a first step. We propose ilastik as an easy-to-use tool which allows the user without expertise in image processing to perform segmentation and classification in a unified way. ilastik learns from labels provided by the user through a convenient mouse interface. Based on these labels, ilastik infers a problem specific segmentation. A random forest classifier is used in the learning step, in which each pixel's neighborhood is characterized by a set of generic (nonlinear) features. ilastik supports up to three spatial plus one spectral dimension and makes use of all dimensions in the feature calculation. ilastik provides realtime feedback that enables the user to interactively refine the segmentation result and hence further fine-tune the classifier. An uncertainty measure guides the user to ambiguous regions in the images. Real time performance is achieved by multi-threading which fully exploits the capabilities of modern multi-core machines. Once a classifier has been trained on a set of representative images, it can be exported and used to automatically process a very large number of images (e.g. using the CellProfiler pipeline). ilastik is an open source project and released under the BSD license at www.ilastik.org.","lang":"eng"}],"publisher":"Institute of Electrical and Electronics Engineers","department":[{"_id":"Bio"}],"title":"Ilastik: Interactive learning and segmentation toolkit","publication_status":"published","status":"public","_id":"9943","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","year":"2011","oa_version":"Preprint","date_created":"2021-08-19T11:49:58Z","date_updated":"2023-02-23T14:13:38Z","author":[{"full_name":"Sommer, Christoph M","first_name":"Christoph M","last_name":"Sommer","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1216-9105"},{"full_name":"Straehle, Christoph","last_name":"Straehle","first_name":"Christoph"},{"full_name":"Köthe, Ullrich","first_name":"Ullrich","last_name":"Köthe"},{"full_name":"Hamprecht, Fred A.","first_name":"Fred A.","last_name":"Hamprecht"}],"keyword":["image segmentation","biomedical imaging","three dimensional displays","neurons","retina","observers","image color analysis"],"publication_identifier":{"issn":["1945-7928"],"eissn":["1945-8452"],"isbn":["978-1-4244-4127-3"]},"article_processing_charge":"No","month":"06","day":"09","quality_controlled":"1","oa":1,"main_file_link":[{"url":"https://www.researchgate.net/publication/224241106_Ilastik_Interactive_learning_and_segmentation_toolkit","open_access":"1"}],"citation":{"mla":"Sommer, Christoph M., et al. “Ilastik: Interactive Learning and Segmentation Toolkit.” 2011 IEEE International Symposium on Biomedical Imaging: From Nano to Micro, Institute of Electrical and Electronics Engineers, 2011, doi:10.1109/isbi.2011.5872394.","short":"C.M. Sommer, C. Straehle, U. Köthe, F.A. Hamprecht, in:, 2011 IEEE International Symposium on Biomedical Imaging: From Nano to Micro, Institute of Electrical and Electronics Engineers, 2011.","chicago":"Sommer, Christoph M, Christoph Straehle, Ullrich Köthe, and Fred A. Hamprecht. “Ilastik: Interactive Learning and Segmentation Toolkit.” In 2011 IEEE International Symposium on Biomedical Imaging: From Nano to Micro. Institute of Electrical and Electronics Engineers, 2011. https://doi.org/10.1109/isbi.2011.5872394.","ama":"Sommer CM, Straehle C, Köthe U, Hamprecht FA. Ilastik: Interactive learning and segmentation toolkit. In: 2011 IEEE International Symposium on Biomedical Imaging: From Nano to Micro. Institute of Electrical and Electronics Engineers; 2011. doi:10.1109/isbi.2011.5872394","ista":"Sommer CM, Straehle C, Köthe U, Hamprecht FA. 2011. Ilastik: Interactive learning and segmentation toolkit. 2011 IEEE International Symposium on Biomedical Imaging: from Nano to Micro. ISBI: International Symposium on Biomedical Imaging.","apa":"Sommer, C. M., Straehle, C., Köthe, U., & Hamprecht, F. A. (2011). Ilastik: Interactive learning and segmentation toolkit. In 2011 IEEE International Symposium on Biomedical Imaging: from Nano to Micro. Chicago, Illinois, USA: Institute of Electrical and Electronics Engineers. https://doi.org/10.1109/isbi.2011.5872394","ieee":"C. M. Sommer, C. Straehle, U. Köthe, and F. A. Hamprecht, “Ilastik: Interactive learning and segmentation toolkit,” in 2011 IEEE International Symposium on Biomedical Imaging: from Nano to Micro, Chicago, Illinois, USA, 2011."},"publication":"2011 IEEE International Symposium on Biomedical Imaging: from Nano to Micro","language":[{"iso":"eng"}],"doi":"10.1109/isbi.2011.5872394","date_published":"2011-06-09T00:00:00Z","conference":{"end_date":"2011-04-02","location":"Chicago, Illinois, USA","start_date":"2011-03-30","name":"ISBI: International Symposium on Biomedical Imaging"}},{"article_processing_charge":"No","day":"01","series_title":"LNIP","scopus_import":"1","date_published":"2011-06-01T00:00:00Z","page":"215-224","citation":{"ista":"Artner NM, Ion A, Kropatsch WG. 2011. Spatio-temporal extraction of articulated models in a graph pyramid. Graph-Based Representations in Pattern Recognition. GbRPR: Graph-based Representations in Pattern RecognitionLNIP, LNCS, vol. 6658, 215–224.","ieee":"N. M. Artner, A. Ion, and W. G. Kropatsch, “Spatio-temporal extraction of articulated models in a graph pyramid,” in Graph-Based Representations in Pattern Recognition, Münster, Germany, 2011, vol. 6658, pp. 215–224.","apa":"Artner, N. M., Ion, A., & Kropatsch, W. G. (2011). Spatio-temporal extraction of articulated models in a graph pyramid. In X. Jiang, M. Ferrer, & A. Torsello (Eds.), Graph-Based Representations in Pattern Recognition (Vol. 6658, pp. 215–224). Berlin, Heidelberg: Springer. https://doi.org/10.1007/978-3-642-20844-7_22","ama":"Artner NM, Ion A, Kropatsch WG. Spatio-temporal extraction of articulated models in a graph pyramid. In: Jiang X, Ferrer M, Torsello A, eds. Graph-Based Representations in Pattern Recognition. Vol 6658. LNIP. Berlin, Heidelberg: Springer; 2011:215-224. doi:10.1007/978-3-642-20844-7_22","chicago":"Artner, Nicole M., Adrian Ion, and Walter G. Kropatsch. “Spatio-Temporal Extraction of Articulated Models in a Graph Pyramid.” In Graph-Based Representations in Pattern Recognition, edited by Xiaoyi Jiang, Miquel Ferrer, and Andrea Torsello, 6658:215–24. LNIP. Berlin, Heidelberg: Springer, 2011. https://doi.org/10.1007/978-3-642-20844-7_22.","mla":"Artner, Nicole M., et al. “Spatio-Temporal Extraction of Articulated Models in a Graph Pyramid.” Graph-Based Representations in Pattern Recognition, edited by Xiaoyi Jiang et al., vol. 6658, Springer, 2011, pp. 215–24, doi:10.1007/978-3-642-20844-7_22.","short":"N.M. Artner, A. Ion, W.G. Kropatsch, in:, X. Jiang, M. Ferrer, A. Torsello (Eds.), Graph-Based Representations in Pattern Recognition, Springer, Berlin, Heidelberg, 2011, pp. 215–224."},"publication":"Graph-Based Representations in Pattern Recognition","abstract":[{"text":"This paper presents a method to create a model of an articulated object using the planar motion in an initialization video. The model consists of rigid parts connected by points of articulation. The rigid parts are described by the positions of salient feature-points tracked throughout the video. Following a filtering step that identifies points that belong to different objects, rigid parts are found by a grouping process in a graph pyramid. Valid articulation points are selected by verifying multiple hypotheses for each pair of parts.","lang":"eng"}],"alternative_title":["LNCS"],"type":"conference","oa_version":"None","intvolume":" 6658","status":"public","title":"Spatio-temporal extraction of articulated models in a graph pyramid","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"10907","publication_identifier":{"issn":["0302-9743"],"eisbn":["9783642208447"],"eissn":["1611-3349"],"isbn":["9783642208430"]},"month":"06","language":[{"iso":"eng"}],"doi":"10.1007/978-3-642-20844-7_22","conference":{"name":"GbRPR: Graph-based Representations in Pattern Recognition","end_date":"2011-05-20","start_date":"2011-05-18","location":"Münster, Germany"},"quality_controlled":"1","place":"Berlin, Heidelberg","volume":6658,"date_created":"2022-03-21T08:08:35Z","date_updated":"2023-09-05T14:10:15Z","author":[{"last_name":"Artner","first_name":"Nicole M.","full_name":"Artner, Nicole M."},{"id":"29F89302-F248-11E8-B48F-1D18A9856A87","first_name":"Adrian","last_name":"Ion","full_name":"Ion, Adrian"},{"full_name":"Kropatsch, Walter G.","first_name":"Walter G.","last_name":"Kropatsch"}],"publisher":"Springer","department":[{"_id":"HeEd"}],"editor":[{"full_name":"Jiang, Xiaoyi","first_name":"Xiaoyi","last_name":"Jiang"},{"first_name":"Miquel","last_name":"Ferrer","full_name":"Ferrer, Miquel"},{"full_name":"Torsello, Andrea","last_name":"Torsello","first_name":"Andrea"}],"publication_status":"published","acknowledgement":"This work has been partially supported by the Austrian Science Fund under grants S9103-N13 and P18716-N13.","year":"2011"},{"author":[{"id":"F44D762E-4F9D-11E9-B64C-9EB26CEFFB5F","first_name":"Kathrin","last_name":"Schumann","full_name":"Schumann, Kathrin"}],"date_updated":"2023-09-07T11:31:48Z","date_created":"2018-12-11T12:02:24Z","year":"2011","acknowledgement":"I would like to express my sincere gratitude to the following people who made with their continuous support and encouragement this thesis possible: First, I want to thank Prof. Dr. Michael Sixt for his excellent supervision and mentoring, especially for the nice, relaxed working atmosphere, a lot of brilliant ideas and the freedom to work in my own way.\r\n\r\nProf. Dr. Reinhard Fässler for his constant support of the Sixt lab and for providing excellent working conditions. \r\n\r\nProf. Dr. Sanjiv Luther and Prof. Dr. Tobias Bollenbach for agreeing to be member of my thesis committee and to evaluate my work.\r\n\r\nDr. Walther Göhring, Carmen Schmitz, the Recombinant Protein Production core facility and the animal care takers for providing the “infrastructure” for this thesis. \r\n\r\nProf. Dr. Daniel Legler, Markus Bruckner and Dr. Julien Polleux for very fruitful collaborations and discussions.\r\n\r\nMy labmates for their help, a lot of discussions and to make the Sixt lab to a convenient place to work : Karin Hirsch, Tim Lämmeramnn, Holger Pflicke, Jörg Renkawitz, Michele Weber and Alexander Eichner All members of the Department of Molecular Medicine for their help. Especially I want to thank Sarah Schmidt, Karin Hirsch and Raphael Ruppert for their friendship, nice chats and their uncensored point of view. ","department":[{"_id":"MiSi"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","publist_id":"3371","file_date_updated":"2021-02-22T11:24:30Z","language":[{"iso":"eng"}],"supervisor":[{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","first_name":"Michael K","last_name":"Sixt","full_name":"Sixt, Michael K"}],"degree_awarded":"PhD","oa":1,"publication_identifier":{"issn":["2663-337X"]},"month":"03","pubrep_id":"11","oa_version":"Published Version","file":[{"creator":"dernst","content_type":"application/pdf","file_size":4487708,"file_name":"2011_Thesis_Kathrin_Schumann.pdf","access_level":"closed","date_created":"2019-03-26T08:12:21Z","date_updated":"2020-07-14T12:46:06Z","checksum":"e69eee6252660f0b694a2ea8923ddc72","file_id":"6177","relation":"main_file"},{"access_level":"open_access","file_name":"2011_Thesis_Schumann_noS.pdf","creator":"dernst","file_size":4313127,"content_type":"application/pdf","file_id":"9175","relation":"main_file","success":1,"checksum":"71727d63f424b5b446f68f4b87ecadc0","date_updated":"2021-02-22T11:24:30Z","date_created":"2021-02-22T11:24:30Z"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"3275","ddc":["570","579"],"title":"The role of chemotactic gradients in dendritic cell migration","status":"public","abstract":[{"lang":"eng","text":"Chemokines organize immune cell trafficking by inducing either directed (tactic) or random (kinetic) migration and by activating integrins in order to support surface adhesion (haptic). Beyond that the same chemokines can establish clearly defined functional areas in secondary lymphoid organs. Until now it is unclear how chemokines can fulfill such diverse functions. One decisive prerequisite to explain these capacities is to know how chemokines are presented in tissue. In theory chemokines could occur either soluble or immobilized, and could be distributed either homogenously or as a concentration gradient. To dissect if and how the presenting mode of chemokines influences immune cells, I tested the response of dendritic cells (DCs) to differentially displayed chemokines. DCs are antigen presenting cells that reside in the periphery and migrate into draining lymph nodes (LNs) once exposed to inflammatory stimuli to activate naïve T cells. DCs are guided to and within the LN by the chemokine receptor CCR7, which has two ligands, the chemokines CCL19 and CCL21. Both CCR7 ligands are expressed by fibroblastic reticular cells in the LN, but differ in their ability to bind to heparan sulfate residues. CCL21 has a highly charged C-terminal extension, which mediates binding to anionic surfaces, whereas CCL19 is lacking such residues and likely distributes as a soluble molecule. This study shows that surface-bound CCL21 causes random, haptokinetic DC motility, which is confined to the chemokine coated area by insideout activation of β2 integrins that mediate cell binding to the surface. CCL19 on the other hand forms concentration gradients which trigger directional, chemotactic movement, but no surface adhesion. In addition DCs can actively manipulate this system by recruiting and activating serine proteases on their surfaces, which create - by proteolytically removing the adhesive C-terminus - a solubilized variant of CCL21 that functionally resembles CCL19. By generating a CCL21 concentration gradient DCs establish a positive feedback loop to recruit further DCs from the periphery to the CCL21 coated region. In addition DCs can sense chemotactic gradients as well as immobilized haptokinetic fields at the same time and integrate these signals. The result is chemotactically biased haptokinesis - directional migration confined to a chemokine coated track or area - which could explain the dynamic but spatially tightly controlled swarming leukocyte locomotion patterns that have been observed in lymphatic organs by intravital microscopists. The finding that DCs can approach soluble cues in a non-adhesive manner while they attach to surfaces coated with immobilized cues raises the question how these cells transmit intracellular forces to the environment, especially in the non-adherent migration mode. In order to migrate, cells have to generate and transmit force to the extracellular substrate. Force transmission is the prerequisite to procure an expansion of the leading edge and a forward motion of the whole cell body. In the current conceptions actin polymerization at the leading edge is coupled to extracellular ligands via the integrin family of transmembrane receptors, which allows the transmission of intracellular force. Against the paradigm of force transmission during migration, leukocytes, like DCs, are able to migrate in threedimensional environments without using integrin transmembrane receptors (Lämmermann et al., 2008). This reflects the biological function of leukocytes, as they can invade almost all tissues, whereby their migration has to be independent from the extracellular environment. How the cells can achieve this is unclear. For this study I examined DC migration in a defined threedimensional environment and highlighted actin-dynamics with the probe Lifeact-GFP. The result was that chemotactic DCs can switch between integrin-dependent and integrin- independent locomotion and can thereby adapt to the adhesive properties of their environment. If the cells are able to couple their actin cytoskeleton to the substrate, actin polymerization is entirely converted into protrusion. Without coupling the actin cortex undergoes slippage and retrograde actin flow can be observed. But retrograde actin flow can be completely compensated by higher actin polymerization rate keeping the migration velocity and the shape of the cells unaltered. Mesenchymal cells like fibroblast cannot balance the loss of adhesive interaction, cannot protrude into open space and, therefore, strictly depend on integrinmediated force coupling. This leukocyte specific phenomenon of “adaptive force transmission” endows these cells with the unique ability to transit and invade almost every type of tissue. "}],"type":"dissertation","alternative_title":["ISTA Thesis"],"date_published":"2011-03-01T00:00:00Z","citation":{"ama":"Schumann K. The role of chemotactic gradients in dendritic cell migration. 2011.","ieee":"K. Schumann, “The role of chemotactic gradients in dendritic cell migration,” Institute of Science and Technology Austria, 2011.","apa":"Schumann, K. (2011). The role of chemotactic gradients in dendritic cell migration. Institute of Science and Technology Austria.","ista":"Schumann K. 2011. The role of chemotactic gradients in dendritic cell migration. Institute of Science and Technology Austria.","short":"K. Schumann, The Role of Chemotactic Gradients in Dendritic Cell Migration, Institute of Science and Technology Austria, 2011.","mla":"Schumann, Kathrin. The Role of Chemotactic Gradients in Dendritic Cell Migration. Institute of Science and Technology Austria, 2011.","chicago":"Schumann, Kathrin. “The Role of Chemotactic Gradients in Dendritic Cell Migration.” Institute of Science and Technology Austria, 2011."},"page":"141","article_processing_charge":"No","has_accepted_license":"1","day":"01"},{"alternative_title":["ISTA Thesis"],"type":"dissertation","publist_id":"3373","title":"Mechanics of adhesion and de‐adhesion in zebrafish germ layer progenitors","publication_status":"published","status":"public","department":[{"_id":"CaHe"}],"publisher":"Institute of Science and Technology Austria","_id":"3273","year":"2011","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_updated":"2023-09-07T11:30:16Z","date_created":"2018-12-11T12:02:23Z","oa_version":"None","author":[{"full_name":"Maître, Jean-Léon","last_name":"Maître","first_name":"Jean-Léon","orcid":"0000-0002-3688-1474","id":"48F1E0D8-F248-11E8-B48F-1D18A9856A87"}],"month":"12","day":"12","publication_identifier":{"issn":["2663-337X"]},"article_processing_charge":"No","citation":{"chicago":"Maître, Jean-Léon. “Mechanics of Adhesion and De‐adhesion in Zebrafish Germ Layer Progenitors.” Institute of Science and Technology Austria, 2011.","mla":"Maître, Jean-Léon. Mechanics of Adhesion and De‐adhesion in Zebrafish Germ Layer Progenitors. Institute of Science and Technology Austria, 2011.","short":"J.-L. Maître, Mechanics of Adhesion and De‐adhesion in Zebrafish Germ Layer Progenitors, Institute of Science and Technology Austria, 2011.","ista":"Maître J-L. 2011. Mechanics of adhesion and de‐adhesion in zebrafish germ layer progenitors. Institute of Science and Technology Austria.","apa":"Maître, J.-L. (2011). Mechanics of adhesion and de‐adhesion in zebrafish germ layer progenitors. Institute of Science and Technology Austria.","ieee":"J.-L. Maître, “Mechanics of adhesion and de‐adhesion in zebrafish germ layer progenitors,” Institute of Science and Technology Austria, 2011.","ama":"Maître J-L. Mechanics of adhesion and de‐adhesion in zebrafish germ layer progenitors. 2011."},"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"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"date_published":"2011-12-12T00:00:00Z"},{"type":"conference","alternative_title":["LNCS"],"abstract":[{"text":"We construct efficient authentication protocols and message-authentication codes (MACs) whose security can be reduced to the learning parity with noise (LPN) problem. Despite a large body of work - starting with the HB protocol of Hopper and Blum in 2001 - until now it was not even known how to construct an efficient authentication protocol from LPN which is secure against man-in-the-middle (MIM) attacks. A MAC implies such a (two-round) protocol. © 2011 International Association for Cryptologic Research","lang":"eng"}],"publist_id":"3442","extern":"1","acknowledgement":"The European Regional Development Fund (ERDF),Guardtime,Qualcomm,Swedbank","_id":"3238","year":"2011","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publication_status":"published","title":"Efficient authentication from hard learning problems","status":"public","publisher":"Springer","intvolume":" 6632","author":[{"full_name":"Kiltz, Eike","last_name":"Kiltz","first_name":"Eike"},{"full_name":"Pietrzak, Krzysztof Z","last_name":"Pietrzak","first_name":"Krzysztof Z","orcid":"0000-0002-9139-1654","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Cash, David","last_name":"Cash","first_name":"David"},{"last_name":"Jain","first_name":"Abhishek","full_name":"Jain, Abhishek"},{"first_name":"Daniele","last_name":"Venturi","full_name":"Venturi, Daniele"}],"related_material":{"record":[{"id":"1187","status":"public","relation":"later_version"}]},"date_updated":"2023-09-20T11:20:57Z","date_created":"2018-12-11T12:02:11Z","oa_version":"None","volume":6632,"month":"05","day":"01","citation":{"mla":"Kiltz, Eike, et al. Efficient Authentication from Hard Learning Problems. Vol. 6632, Springer, 2011, pp. 7–26, doi:10.1007/978-3-642-20465-4_3.","short":"E. Kiltz, K.Z. Pietrzak, D. Cash, A. Jain, D. Venturi, in:, Springer, 2011, pp. 7–26.","chicago":"Kiltz, Eike, Krzysztof Z Pietrzak, David Cash, Abhishek Jain, and Daniele Venturi. “Efficient Authentication from Hard Learning Problems,” 6632:7–26. Springer, 2011. https://doi.org/10.1007/978-3-642-20465-4_3.","ama":"Kiltz E, Pietrzak KZ, Cash D, Jain A, Venturi D. Efficient authentication from hard learning problems. In: Vol 6632. Springer; 2011:7-26. doi:10.1007/978-3-642-20465-4_3","ista":"Kiltz E, Pietrzak KZ, Cash D, Jain A, Venturi D. 2011. Efficient authentication from hard learning problems. EUROCRYPT: Theory and Applications of Cryptographic Techniques, LNCS, vol. 6632, 7–26.","apa":"Kiltz, E., Pietrzak, K. Z., Cash, D., Jain, A., & Venturi, D. (2011). Efficient authentication from hard learning problems (Vol. 6632, pp. 7–26). Presented at the EUROCRYPT: Theory and Applications of Cryptographic Techniques, Tallinn, Estonia: Springer. https://doi.org/10.1007/978-3-642-20465-4_3","ieee":"E. Kiltz, K. Z. Pietrzak, D. Cash, A. Jain, and D. Venturi, “Efficient authentication from hard learning problems,” presented at the EUROCRYPT: Theory and Applications of Cryptographic Techniques, Tallinn, Estonia, 2011, vol. 6632, pp. 7–26."},"quality_controlled":"1","page":"7 - 26","conference":{"end_date":"2011-05-19","location":"Tallinn, Estonia","start_date":"2011-05-15","name":"EUROCRYPT: Theory and Applications of Cryptographic Techniques"},"doi":"10.1007/978-3-642-20465-4_3","date_published":"2011-05-01T00:00:00Z","language":[{"iso":"eng"}]},{"article_processing_charge":"No","day":"01","scopus_import":"1","date_published":"2011-09-01T00:00:00Z","citation":{"ista":"Soriano S, Hons M, Schumann K, Kumar V, Dennier T, Lyck R, Sixt MK, Stein J. 2011. In vivo analysis of uropod function during physiological T cell trafficking. Journal of Immunology. 187(5), 2356–2364.","ieee":"S. Soriano et al., “In vivo analysis of uropod function during physiological T cell trafficking,” Journal of Immunology, vol. 187, no. 5. American Association of Immunologists, pp. 2356–2364, 2011.","apa":"Soriano, S., Hons, M., Schumann, K., Kumar, V., Dennier, T., Lyck, R., … Stein, J. (2011). In vivo analysis of uropod function during physiological T cell trafficking. Journal of Immunology. American Association of Immunologists. https://doi.org/10.4049/jimmunol.1100935","ama":"Soriano S, Hons M, Schumann K, et al. In vivo analysis of uropod function during physiological T cell trafficking. Journal of Immunology. 2011;187(5):2356-2364. doi:10.4049/jimmunol.1100935","chicago":"Soriano, Silvia, Miroslav Hons, Kathrin Schumann, Varsha Kumar, Timo Dennier, Ruth Lyck, Michael K Sixt, and Jens Stein. “In Vivo Analysis of Uropod Function during Physiological T Cell Trafficking.” Journal of Immunology. American Association of Immunologists, 2011. https://doi.org/10.4049/jimmunol.1100935.","mla":"Soriano, Silvia, et al. “In Vivo Analysis of Uropod Function during Physiological T Cell Trafficking.” Journal of Immunology, vol. 187, no. 5, American Association of Immunologists, 2011, pp. 2356–64, doi:10.4049/jimmunol.1100935.","short":"S. Soriano, M. Hons, K. Schumann, V. Kumar, T. Dennier, R. Lyck, M.K. Sixt, J. Stein, Journal of Immunology 187 (2011) 2356–2364."},"publication":"Journal of Immunology","page":"2356 - 2364","article_type":"original","issue":"5","abstract":[{"text":"Migrating lymphocytes acquire a polarized phenotype with a leading and a trailing edge, or uropod. Although in vitro experiments in cell lines or activated primary cell cultures have established that Rho-p160 coiled-coil kinase (ROCK)-myosin II-mediated uropod contractility is required for integrin de-adhesion on two-dimensional surfaces and nuclear propulsion through narrow pores in three-dimensional matrices, less is known about the role of these two events during the recirculation of primary, nonactivated lymphocytes. Using pharmacological antagonists of ROCK and myosin II, we report that inhibition of uropod contractility blocked integrin-independent mouse T cell migration through narrow, but not large, pores in vitro. T cell crawling on chemokine-coated endothelial cells under shear was severely impaired by ROCK inhibition, whereas transendothelial migration was only reduced through endothelial cells with high, but not low, barrier properties. Using three-dimensional thick-tissue imaging and dynamic two-photon microscopy of T cell motility in lymphoid tissue, we demonstrated a significant role for uropod contractility in intraluminal crawling and transendothelial migration through lymph node, but not bone marrow, endothelial cells. Finally, we demonstrated that ICAM-1, but not anatomical constraints or integrin-independent interactions, reduced parenchymal motility of inhibitor-treated T cells within the dense lymphoid microenvironment, thus assigning context-dependent roles for uropod contraction during lymphocyte recirculation.","lang":"eng"}],"type":"journal_article","oa_version":"None","_id":"3392","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 187","status":"public","title":"In vivo analysis of uropod function during physiological T cell trafficking","publication_identifier":{"issn":["0022-1767"],"eissn":["1550-6606"]},"month":"09","doi":"10.4049/jimmunol.1100935","language":[{"iso":"eng"}],"quality_controlled":"1","publist_id":"3215","author":[{"last_name":"Soriano","first_name":"Silvia","full_name":"Soriano, Silvia"},{"full_name":"Hons, Miroslav","first_name":"Miroslav","last_name":"Hons","orcid":"0000-0002-6625-3348"},{"full_name":"Schumann, Kathrin","first_name":"Kathrin","last_name":"Schumann"},{"full_name":"Kumar, Varsha","last_name":"Kumar","first_name":"Varsha"},{"first_name":"Timo","last_name":"Dennier","full_name":"Dennier, Timo"},{"last_name":"Lyck","first_name":"Ruth","full_name":"Lyck, Ruth"},{"full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","first_name":"Michael K"},{"last_name":"Stein","first_name":"Jens","full_name":"Stein, Jens"}],"volume":187,"date_updated":"2023-10-10T13:14:59Z","date_created":"2018-12-11T12:03:04Z","year":"2011","publisher":"American Association of Immunologists","department":[{"_id":"MiSi"}],"publication_status":"published"},{"abstract":[{"lang":"eng","text":"We study multi-label prediction for structured output sets, a problem that occurs, for example, in object detection in images, secondary structure prediction in computational biology, and graph matching with symmetries. Conventional multilabel classification techniques are typically not applicable in this situation, because they require explicit enumeration of the label set, which is infeasible in case of structured outputs. Relying on techniques originally designed for single-label structured prediction, in particular structured support vector machines, results in reduced prediction accuracy, or leads to infeasible optimization problems. In this work we derive a maximum-margin training formulation for multi-label structured prediction that remains computationally tractable while achieving high prediction accuracy. It also shares most beneficial properties with single-label maximum-margin approaches, in particular formulation as a convex optimization problem, efficient working set training, and PAC-Bayesian generalization bounds."}],"publist_id":"3522","type":"conference","date_updated":"2023-10-17T11:47:35Z","date_created":"2018-12-11T12:01:45Z","oa_version":"None","author":[{"full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","last_name":"Lampert","first_name":"Christoph"}],"related_material":{"record":[{"id":"3322","relation":"later_version","status":"public"}]},"title":"Maximum margin multi-label structured prediction","publication_status":"published","status":"public","department":[{"_id":"ChLa"}],"publisher":"Neural Information Processing Systems","_id":"3163","year":"2011","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","day":"01","month":"12","scopus_import":1,"language":[{"iso":"eng"}],"conference":{"name":"NIPS: Neural Information Processing Systems","location":"Granada, Spain","start_date":"2011-12-12","end_date":"2011-12-14"},"date_published":"2011-12-01T00:00:00Z","quality_controlled":"1","citation":{"ama":"Lampert C. Maximum margin multi-label structured prediction. In: Neural Information Processing Systems; 2011.","ieee":"C. Lampert, “Maximum margin multi-label structured prediction,” presented at the NIPS: Neural Information Processing Systems, Granada, Spain, 2011.","apa":"Lampert, C. (2011). Maximum margin multi-label structured prediction. Presented at the NIPS: Neural Information Processing Systems, Granada, Spain: Neural Information Processing Systems.","ista":"Lampert C. 2011. Maximum margin multi-label structured prediction. NIPS: Neural Information Processing Systems.","short":"C. Lampert, in:, Neural Information Processing Systems, 2011.","mla":"Lampert, Christoph. Maximum Margin Multi-Label Structured Prediction. Neural Information Processing Systems, 2011.","chicago":"Lampert, Christoph. “Maximum Margin Multi-Label Structured Prediction.” Neural Information Processing Systems, 2011."}},{"publist_id":"3313","abstract":[{"lang":"eng","text":"We study multi-label prediction for structured output spaces, a problem that occurs, for example, in object detection in images, secondary structure prediction in computational biology, and graph matching with symmetries. Conventional multi-label classification techniques are typically not applicable in this situation, because they require explicit enumeration of the label space, which is infeasible in case of structured outputs. Relying on techniques originally designed for single- label structured prediction, in particular structured support vector machines, results in reduced prediction accuracy, or leads to infeasible optimization problems. In this work we derive a maximum-margin training formulation for multi-label structured prediction that remains computationally tractable while achieving high prediction accuracy. It also shares most beneficial properties with single-label maximum-margin approaches, in particular a formulation as a convex optimization problem, efficient working set training, and PAC-Bayesian generalization bounds."}],"type":"conference_poster","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"3163"}]},"author":[{"full_name":"Lampert, Christoph","last_name":"Lampert","first_name":"Christoph","orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87"}],"oa_version":"None","date_created":"2018-12-11T12:02:40Z","date_updated":"2023-10-17T11:47:36Z","_id":"3322","year":"2011","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"ChLa"}],"publisher":"Neural Information Processing Systems Foundation","title":"Maximum margin multi label structured prediction","publication_status":"published","status":"public","article_processing_charge":"No","day":"13","month":"12","date_published":"2011-12-13T00:00:00Z","language":[{"iso":"eng"}],"citation":{"mla":"Lampert, Christoph. “Maximum Margin Multi Label Structured Prediction.” NIPS: Neural Information Processing Systems, Neural Information Processing Systems Foundation, 2011.","short":"C. Lampert, Maximum Margin Multi Label Structured Prediction, Neural Information Processing Systems Foundation, 2011.","chicago":"Lampert, Christoph. Maximum Margin Multi Label Structured Prediction. NIPS: Neural Information Processing Systems. Neural Information Processing Systems Foundation, 2011.","ama":"Lampert C. Maximum Margin Multi Label Structured Prediction. Neural Information Processing Systems Foundation; 2011.","ista":"Lampert C. 2011. Maximum margin multi label structured prediction, Neural Information Processing Systems Foundation,p.","ieee":"C. Lampert, Maximum margin multi label structured prediction. Neural Information Processing Systems Foundation, 2011.","apa":"Lampert, C. (2011). Maximum margin multi label structured prediction. NIPS: Neural Information Processing Systems. Neural Information Processing Systems Foundation."},"publication":"NIPS: Neural Information Processing Systems"},{"author":[{"first_name":"Sebastian","last_name":"Nowozin","full_name":"Nowozin, Sebastian"},{"full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","last_name":"Lampert","first_name":"Christoph"}],"volume":6,"date_updated":"2023-10-17T11:52:46Z","date_created":"2018-12-11T12:02:39Z","year":"2011","publisher":"Now Publishers","department":[{"_id":"ChLa"}],"publication_status":"published","publist_id":"3315","file_date_updated":"2020-07-14T12:46:07Z","doi":"10.1561/0600000033","language":[{"iso":"eng"}],"oa":1,"quality_controlled":"1","month":"05","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2011_CompGraphicsVision_Nowozin.pdf","content_type":"application/pdf","file_size":3745064,"creator":"dernst","relation":"main_file","file_id":"7837","checksum":"f1043ef389f1558e2a226bb51568511f","date_created":"2020-05-14T14:34:47Z","date_updated":"2020-07-14T12:46:07Z"}],"_id":"3320","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 6","title":"Structured learning and prediction in computer vision","ddc":["000"],"status":"public","issue":"3-4","abstract":[{"text":"Powerful statistical models that can be learned efficiently from large amounts of data are currently revolutionizing computer vision. These models possess a rich internal structure reflecting task-specific relations and constraints. This monograph introduces the reader to the most popular classes of structured models in computer vision. Our focus is discrete undirected graphical models which we cover in detail together with a description of algorithms for both probabilistic inference and maximum a posteriori inference. We discuss separately recently successful techniques for prediction in general structured models. In the second part of this monograph we describe methods for parameter learning where we distinguish the classic maximum likelihood based methods from the more recent prediction-based parameter learning methods. We highlight developments to enhance current models and discuss kernelized models and latent variable models. To make the monograph more practical and to provide links to further study we provide examples of successful application of many methods in the computer vision literature.","lang":"eng"}],"type":"journal_article","date_published":"2011-05-23T00:00:00Z","citation":{"ama":"Nowozin S, Lampert C. Structured learning and prediction in computer vision. Foundations and Trends in Computer Graphics and Vision. 2011;6(3-4):185-365. doi:10.1561/0600000033","apa":"Nowozin, S., & Lampert, C. (2011). Structured learning and prediction in computer vision. Foundations and Trends in Computer Graphics and Vision. Now Publishers. https://doi.org/10.1561/0600000033","ieee":"S. Nowozin and C. Lampert, “Structured learning and prediction in computer vision,” Foundations and Trends in Computer Graphics and Vision, vol. 6, no. 3–4. Now Publishers, pp. 185–365, 2011.","ista":"Nowozin S, Lampert C. 2011. Structured learning and prediction in computer vision. Foundations and Trends in Computer Graphics and Vision. 6(3–4), 185–365.","short":"S. Nowozin, C. Lampert, Foundations and Trends in Computer Graphics and Vision 6 (2011) 185–365.","mla":"Nowozin, Sebastian, and Christoph Lampert. “Structured Learning and Prediction in Computer Vision.” Foundations and Trends in Computer Graphics and Vision, vol. 6, no. 3–4, Now Publishers, 2011, pp. 185–365, doi:10.1561/0600000033.","chicago":"Nowozin, Sebastian, and Christoph Lampert. “Structured Learning and Prediction in Computer Vision.” Foundations and Trends in Computer Graphics and Vision. Now Publishers, 2011. https://doi.org/10.1561/0600000033."},"publication":"Foundations and Trends in Computer Graphics and Vision","page":"185 - 365","article_type":"original","has_accepted_license":"1","article_processing_charge":"No","day":"23","scopus_import":"1"},{"month":"01","day":"01","article_processing_charge":"No","scopus_import":"1","language":[{"iso":"eng"}],"conference":{"name":"ICML: International Conference on Machine Learning","start_date":"2011-06-28","location":"Bellevue, United States","end_date":"2011-07-02"},"date_published":"2011-01-01T00:00:00Z","page":"425 - 432","citation":{"ama":"Quadrianto N, Lampert C. Learning multi-view neighborhood preserving projections. In: ML Research Press; 2011:425-432.","apa":"Quadrianto, N., & Lampert, C. (2011). Learning multi-view neighborhood preserving projections (pp. 425–432). Presented at the ICML: International Conference on Machine Learning, Bellevue, United States: ML Research Press.","ieee":"N. Quadrianto and C. Lampert, “Learning multi-view neighborhood preserving projections,” presented at the ICML: International Conference on Machine Learning, Bellevue, United States, 2011, pp. 425–432.","ista":"Quadrianto N, Lampert C. 2011. Learning multi-view neighborhood preserving projections. ICML: International Conference on Machine Learning, 425–432.","short":"N. Quadrianto, C. Lampert, in:, ML Research Press, 2011, pp. 425–432.","mla":"Quadrianto, Novi, and Christoph Lampert. Learning Multi-View Neighborhood Preserving Projections. ML Research Press, 2011, pp. 425–32.","chicago":"Quadrianto, Novi, and Christoph Lampert. “Learning Multi-View Neighborhood Preserving Projections,” 425–32. ML Research Press, 2011."},"abstract":[{"lang":"eng","text":"We address the problem of metric learning for multi-view data, namely the construction of embedding projections from data in different representations into a shared feature space, such that the Euclidean distance in this space provides a meaningful within-view as well as between-view similarity. Our motivation stems from the problem of cross-media retrieval tasks, where the availability of a joint Euclidean distance function is a pre-requisite to allow fast, in particular hashing-based, nearest neighbor queries. We formulate an objective function that expresses the intuitive concept that matching samples are mapped closely together in the output space, whereas non-matching samples are pushed apart, no matter in which view they are available. The resulting optimization problem is not convex, but it can be decomposed explicitly into a convex and a concave part, thereby allowing efficient optimization using the convex-concave procedure. Experiments on an image retrieval task show that nearest-neighbor based cross-view retrieval is indeed possible, and the proposed technique improves the retrieval accuracy over baseline techniques."}],"publist_id":"3316","type":"conference","date_updated":"2023-10-17T11:59:50Z","date_created":"2018-12-11T12:02:39Z","oa_version":"None","author":[{"full_name":"Quadrianto, Novi","last_name":"Quadrianto","first_name":"Novi"},{"full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","last_name":"Lampert","first_name":"Christoph"}],"status":"public","publication_status":"published","title":"Learning multi-view neighborhood preserving projections","publisher":"ML Research Press","department":[{"_id":"ChLa"}],"year":"2011","_id":"3319","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"3373","intvolume":" 36","status":"public","title":"Measuring the complete force field of an optical trap","oa_version":"Published Version","type":"journal_article","issue":"7","abstract":[{"lang":"eng","text":"The use of optical traps to measure or apply forces on the molecular level requires a precise knowledge of the trapping force field. Close to the trap center, this field is typically approximated as linear in the displacement of the trapped microsphere. However, applications demanding high forces at low laser intensities can probe the light-microsphere interaction beyond the linear regime. Here, we measured the full nonlinear force and displacement response of an optical trap in two dimensions using a dual-beam optical trap setup with back-focal-plane photodetection. We observed a substantial stiffening of the trap beyond the linear regime that depends on microsphere size, in agreement with Mie theory calculations. Surprisingly, we found that the linear detection range for forces exceeds the one for displacement by far. Our approach allows for a complete calibration of an optical trap."}],"citation":{"ista":"Jahnel M, Behrndt M, Jannasch A, Schaeffer E, Grill S. 2011. Measuring the complete force field of an optical trap. Optics Letters. 36(7), 1260–1262.","apa":"Jahnel, M., Behrndt, M., Jannasch, A., Schaeffer, E., & Grill, S. (2011). Measuring the complete force field of an optical trap. Optics Letters. Optica Publishing Group. https://doi.org/10.1364/OL.36.001260","ieee":"M. Jahnel, M. Behrndt, A. Jannasch, E. Schaeffer, and S. Grill, “Measuring the complete force field of an optical trap,” Optics Letters, vol. 36, no. 7. Optica Publishing Group, pp. 1260–1262, 2011.","ama":"Jahnel M, Behrndt M, Jannasch A, Schaeffer E, Grill S. Measuring the complete force field of an optical trap. Optics Letters. 2011;36(7):1260-1262. doi:10.1364/OL.36.001260","chicago":"Jahnel, Marcus, Martin Behrndt, Anita Jannasch, Erik Schaeffer, and Stephan Grill. “Measuring the Complete Force Field of an Optical Trap.” Optics Letters. Optica Publishing Group, 2011. https://doi.org/10.1364/OL.36.001260.","mla":"Jahnel, Marcus, et al. “Measuring the Complete Force Field of an Optical Trap.” Optics Letters, vol. 36, no. 7, Optica Publishing Group, 2011, pp. 1260–62, doi:10.1364/OL.36.001260.","short":"M. Jahnel, M. Behrndt, A. Jannasch, E. Schaeffer, S. Grill, Optics Letters 36 (2011) 1260–1262."},"publication":"Optics Letters","page":"1260 - 1262","date_published":"2011-03-30T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"30","year":"2011","publisher":"Optica Publishing Group","department":[{"_id":"CaHe"}],"publication_status":"published","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"1403"}]},"author":[{"last_name":"Jahnel","first_name":"Marcus","full_name":"Jahnel, Marcus"},{"id":"3ECECA3A-F248-11E8-B48F-1D18A9856A87","last_name":"Behrndt","first_name":"Martin","full_name":"Behrndt, Martin"},{"last_name":"Jannasch","first_name":"Anita","full_name":"Jannasch, Anita"},{"full_name":"Schaeffer, Erik","first_name":"Erik","last_name":"Schaeffer"},{"last_name":"Grill","first_name":"Stephan","full_name":"Grill, Stephan"}],"volume":36,"date_updated":"2023-10-17T12:16:58Z","date_created":"2018-12-11T12:02:58Z","publist_id":"3234","oa":1,"main_file_link":[{"open_access":"1","url":"https://www.osapublishing.org/ol/abstract.cfm?uri=ol-36-7-1260"}],"quality_controlled":"1","doi":"10.1364/OL.36.001260","language":[{"iso":"eng"}],"month":"03"},{"publist_id":"3232","ec_funded":1,"publication_status":"published","department":[{"_id":"NiBa"}],"publisher":"The Royal Society","year":"2011","pmid":1,"date_created":"2018-12-11T12:02:58Z","date_updated":"2023-10-18T06:39:05Z","volume":8,"author":[{"id":"2A181218-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5985-7653","first_name":"Harold","last_name":"de Vladar","full_name":"de Vladar, Harold"},{"full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240"}],"month":"05","quality_controlled":"1","project":[{"call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation","_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152"}],"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3061091/"}],"external_id":{"pmid":["21084341"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1098/rsif.2010.0438","type":"journal_article","abstract":[{"lang":"eng","text":"By exploiting an analogy between population genetics and statistical mechanics, we study the evolution of a polygenic trait under stabilizing selection, mutation and genetic drift. This requires us to track only four macroscopic variables, instead of the distribution of all the allele frequencies that influence the trait. These macroscopic variables are the expectations of: the trait mean and its square, the genetic variance, and of a measure of heterozygosity, and are derived from a generating function that is in turn derived by maximizing an entropy measure. These four macroscopics are enough to accurately describe the dynamics of the trait mean and of its genetic variance (and in principle of any other quantity). Unlike previous approaches that were based on an infinite series of moments or cumulants, which had to be truncated arbitrarily, our calculations provide a well-defined approximation procedure. We apply the framework to abrupt and gradual changes in the optimum, as well as to changes in the strength of stabilizing selection. Our approximations are surprisingly accurate, even for systems with as few as five loci. We find that when the effects of drift are included, the expected genetic variance is hardly altered by directional selection, even though it fluctuates in any particular instance. We also find hysteresis, showing that even after averaging over the microscopic variables, the macroscopic trajectories retain a memory of the underlying genetic states."}],"issue":"58","title":"The statistical mechanics of a polygenic character under stabilizing selection mutation and drift","status":"public","intvolume":" 8","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"3375","oa_version":"Submitted Version","scopus_import":"1","day":"01","article_processing_charge":"No","article_type":"original","page":"720 - 739","publication":"Journal of the Royal Society Interface","citation":{"mla":"de Vladar, Harold, and Nicholas H. Barton. “The Statistical Mechanics of a Polygenic Character under Stabilizing Selection Mutation and Drift.” Journal of the Royal Society Interface, vol. 8, no. 58, The Royal Society, 2011, pp. 720–39, doi:10.1098/rsif.2010.0438.","short":"H. de Vladar, N.H. Barton, Journal of the Royal Society Interface 8 (2011) 720–739.","chicago":"Vladar, Harold de, and Nicholas H Barton. “The Statistical Mechanics of a Polygenic Character under Stabilizing Selection Mutation and Drift.” Journal of the Royal Society Interface. The Royal Society, 2011. https://doi.org/10.1098/rsif.2010.0438.","ama":"de Vladar H, Barton NH. The statistical mechanics of a polygenic character under stabilizing selection mutation and drift. Journal of the Royal Society Interface. 2011;8(58):720-739. doi:10.1098/rsif.2010.0438","ista":"de Vladar H, Barton NH. 2011. The statistical mechanics of a polygenic character under stabilizing selection mutation and drift. Journal of the Royal Society Interface. 8(58), 720–739.","ieee":"H. de Vladar and N. H. Barton, “The statistical mechanics of a polygenic character under stabilizing selection mutation and drift,” Journal of the Royal Society Interface, vol. 8, no. 58. The Royal Society, pp. 720–739, 2011.","apa":"de Vladar, H., & Barton, N. H. (2011). The statistical mechanics of a polygenic character under stabilizing selection mutation and drift. Journal of the Royal Society Interface. The Royal Society. https://doi.org/10.1098/rsif.2010.0438"},"date_published":"2011-05-01T00:00:00Z"},{"title":"Spatial waves of advance with bistable dynamics: Cytoplasmic and genetic analogues of Allee effects","status":"public","ddc":["570"],"intvolume":" 178","_id":"3393","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version","file":[{"creator":"system","content_type":"application/pdf","file_size":629130,"access_level":"open_access","file_name":"IST-2016-554-v1+1_BartonTurelli2011_copy.pdf","checksum":"7fd22a2ef3321a6fca6a439b3be5d8f4","date_updated":"2020-07-14T12:46:11Z","date_created":"2018-12-12T10:08:31Z","file_id":"4692","relation":"main_file"}],"pubrep_id":"554","type":"journal_article","abstract":[{"lang":"eng","text":"Unlike unconditionally advantageous “Fisherian” variants that tend to spread throughout a species range once introduced anywhere, “bistable” variants, such as chromosome translocations, have two alternative stable frequencies, absence and (near) fixation. Analogous to populations with Allee effects, bistable variants tend to increase locally only once they become sufficiently common, and their spread depends on their rate of increase averaged over all frequencies. Several proposed manipulations of insect populations, such as using Wolbachia or “engineered underdominance” to suppress vector-borne diseases, produce bistable rather than Fisherian dynamics. We synthesize and extend theoretical analyses concerning three features of their spatial behavior: rate of spread, conditions to initiate spread from a localized introduction, and wave stopping caused by variation in population densities or dispersal rates. Unlike Fisherian variants, bistable variants tend to spread spatially only for particular parameter combinations and initial conditions. Wave initiation requires introduction over an extended region, while subsequent spatial spread is slower than for Fisherian waves and can easily be halted by local spatial inhomogeneities. We present several new results, including robust sufficient conditions to initiate (and stop) spread, using a one-parameter cubic approximation applicable to several models. The results have both basic and applied implications."}],"issue":"3","article_type":"original","page":"E48 - E75","publication":"American Naturalist","citation":{"mla":"Barton, Nicholas H., and Michael Turelli. “Spatial Waves of Advance with Bistable Dynamics: Cytoplasmic and Genetic Analogues of Allee Effects.” American Naturalist, vol. 178, no. 3, The University of Chicago Press, 2011, pp. E48–75, doi:10.1086/661246.","short":"N.H. Barton, M. Turelli, American Naturalist 178 (2011) E48–E75.","chicago":"Barton, Nicholas H, and Michael Turelli. “Spatial Waves of Advance with Bistable Dynamics: Cytoplasmic and Genetic Analogues of Allee Effects.” American Naturalist. The University of Chicago Press, 2011. https://doi.org/10.1086/661246.","ama":"Barton NH, Turelli M. Spatial waves of advance with bistable dynamics: Cytoplasmic and genetic analogues of Allee effects. American Naturalist. 2011;178(3):E48-E75. doi:10.1086/661246","ista":"Barton NH, Turelli M. 2011. Spatial waves of advance with bistable dynamics: Cytoplasmic and genetic analogues of Allee effects. American Naturalist. 178(3), E48–E75.","apa":"Barton, N. H., & Turelli, M. (2011). Spatial waves of advance with bistable dynamics: Cytoplasmic and genetic analogues of Allee effects. American Naturalist. The University of Chicago Press. https://doi.org/10.1086/661246","ieee":"N. H. Barton and M. Turelli, “Spatial waves of advance with bistable dynamics: Cytoplasmic and genetic analogues of Allee effects,” American Naturalist, vol. 178, no. 3. The University of Chicago Press, pp. E48–E75, 2011."},"date_published":"2011-09-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"No","has_accepted_license":"1","publication_status":"published","publisher":"The University of Chicago Press","department":[{"_id":"NiBa"}],"year":"2011","date_updated":"2023-10-18T08:01:43Z","date_created":"2018-12-11T12:03:05Z","volume":178,"author":[{"first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"},{"last_name":"Turelli","first_name":"Michael","full_name":"Turelli, Michael"}],"file_date_updated":"2020-07-14T12:46:11Z","publist_id":"3214","quality_controlled":"1","oa":1,"language":[{"iso":"eng"}],"doi":"10.1086/661246","month":"09","publication_identifier":{"eissn":["1537-5323"],"issn":["0003-0147"]}},{"abstract":[{"lang":"eng","text":"Understanding the mechanism of protein folding requires a detailed knowledge of the structural properties of the barriers separating unfolded from native conformations. The S-peptide from ribonuclease S forms its α-helical structure only upon binding to the folded S-protein. We characterized the transition state for this binding-induced folding reaction at high resolution by determining the effect of site-specific backbone thioxylation and side-chain modifications on the kinetics and thermodynamics of the reaction, which allows us to monitor formation of backbone hydrogen bonds and side-chain interactions in the transition state. The experiments reveal that α-helical structure in the S-peptide is absent in the transition state of binding. Recognition between the unfolded S-peptide and the S-protein is mediated by loosely packed hydrophobic side-chain interactions in two well defined regions on the S-peptide. Close packing and helix formation occurs rapidly after binding. Introducing hydrophobic residues at positions outside the recognition region can drastically slow down association."}],"issue":"10","type":"journal_article","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14305","title":"Mapping backbone and side-chain interactions in the transition state of a coupled protein folding and binding reaction","status":"public","intvolume":" 108","day":"12","article_processing_charge":"No","scopus_import":"1","keyword":["Multidisciplinary"],"date_published":"2011-01-12T00:00:00Z","publication":"PNAS","citation":{"apa":"Bachmann, A., Wildemann, D., Praetorius, F. M., Fischer, G., & Kiefhaber, T. (2011). Mapping backbone and side-chain interactions in the transition state of a coupled protein folding and binding reaction. PNAS. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1012668108","ieee":"A. Bachmann, D. Wildemann, F. M. Praetorius, G. Fischer, and T. Kiefhaber, “Mapping backbone and side-chain interactions in the transition state of a coupled protein folding and binding reaction,” PNAS, vol. 108, no. 10. Proceedings of the National Academy of Sciences, pp. 3952–3957, 2011.","ista":"Bachmann A, Wildemann D, Praetorius FM, Fischer G, Kiefhaber T. 2011. Mapping backbone and side-chain interactions in the transition state of a coupled protein folding and binding reaction. PNAS. 108(10), 3952–3957.","ama":"Bachmann A, Wildemann D, Praetorius FM, Fischer G, Kiefhaber T. Mapping backbone and side-chain interactions in the transition state of a coupled protein folding and binding reaction. PNAS. 2011;108(10):3952-3957. doi:10.1073/pnas.1012668108","chicago":"Bachmann, Annett, Dirk Wildemann, Florian M Praetorius, Gunter Fischer, and Thomas Kiefhaber. “Mapping Backbone and Side-Chain Interactions in the Transition State of a Coupled Protein Folding and Binding Reaction.” PNAS. Proceedings of the National Academy of Sciences, 2011. https://doi.org/10.1073/pnas.1012668108.","short":"A. Bachmann, D. Wildemann, F.M. Praetorius, G. Fischer, T. Kiefhaber, PNAS 108 (2011) 3952–3957.","mla":"Bachmann, Annett, et al. “Mapping Backbone and Side-Chain Interactions in the Transition State of a Coupled Protein Folding and Binding Reaction.” PNAS, vol. 108, no. 10, Proceedings of the National Academy of Sciences, 2011, pp. 3952–57, doi:10.1073/pnas.1012668108."},"article_type":"original","page":"3952-3957","extern":"1","author":[{"full_name":"Bachmann, Annett","last_name":"Bachmann","first_name":"Annett"},{"full_name":"Wildemann, Dirk","first_name":"Dirk","last_name":"Wildemann"},{"full_name":"Praetorius, Florian M","first_name":"Florian M","last_name":"Praetorius","id":"dfec9381-4341-11ee-8fd8-faa02bba7d62"},{"last_name":"Fischer","first_name":"Gunter","full_name":"Fischer, Gunter"},{"full_name":"Kiefhaber, Thomas","last_name":"Kiefhaber","first_name":"Thomas"}],"date_updated":"2023-11-07T11:50:29Z","date_created":"2023-09-06T12:54:36Z","volume":108,"year":"2011","pmid":1,"publication_status":"published","publisher":"Proceedings of the National Academy of Sciences","month":"01","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"doi":"10.1073/pnas.1012668108","language":[{"iso":"eng"}],"external_id":{"pmid":["21325613"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1073/pnas.1012668108"}],"quality_controlled":"1"},{"type":"journal_article","extern":"1","abstract":[{"text":"During assembly of the Drosophila olfactory circuit, projection neuron (PN) dendrites prepattern the developing antennal lobe before the arrival of axons from their presynaptic partners, the adult olfactory receptor neurons (ORNs). We previously found that levels of transmembrane Semaphorin-1a, which acts as a receptor, instruct PN dendrite targeting along the dorsolateral-ventromedial axis. Here we show that two secreted semaphorins, Sema-2a and Sema-2b, provide spatial cues for PN dendrite targeting. Sema-2a and Sema-2b proteins are distributed in gradients opposing the Sema-1a protein gradient, and Sema-1a binds to Sema-2a-expressing cells. In Sema-2a and Sema-2b double mutants, PN dendrites that normally target dorsolaterally in the antennal lobe mistarget ventromedially, phenocopying cell-autonomous Sema-1a removal from these PNs. Cell ablation, cell-specific knockdown, and rescue experiments indicate that secreted semaphorins from degenerating larval ORN axons direct dendrite targeting. Thus, a degenerating brain structure instructs the wiring of a developing circuit through the repulsive action of secreted semaphorins.","lang":"eng"}],"issue":"5","publication_status":"published","status":"public","title":"Secreted semaphorins from degenerating larval ORN axons direct adult projection neuron dendrite targeting","intvolume":" 72","publisher":"Elsevier","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"7701","year":"2011","date_created":"2020-04-30T10:36:12Z","date_updated":"2024-01-31T10:13:39Z","volume":72,"oa_version":"None","author":[{"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"},{"first_name":"Ya-Hui","last_name":"Chou","full_name":"Chou, Ya-Hui"},{"last_name":"Wu","first_name":"Zhuhao","full_name":"Wu, Zhuhao"},{"last_name":"Joo","first_name":"William","full_name":"Joo, William"},{"last_name":"Komiyama","first_name":"Takaki","full_name":"Komiyama, Takaki"},{"first_name":"Christopher J.","last_name":"Potter","full_name":"Potter, Christopher J."},{"full_name":"Kolodkin, Alex L.","first_name":"Alex L.","last_name":"Kolodkin"},{"last_name":"Garcia","first_name":"K. Christopher","full_name":"Garcia, K. Christopher"},{"full_name":"Luo, Liqun","last_name":"Luo","first_name":"Liqun"}],"day":"08","month":"12","publication_identifier":{"issn":["0896-6273"]},"article_processing_charge":"No","quality_controlled":"1","article_type":"original","page":"734-747","publication":"Neuron","citation":{"chicago":"Sweeney, Lora B., Ya-Hui Chou, Zhuhao Wu, William Joo, Takaki Komiyama, Christopher J. Potter, Alex L. Kolodkin, K. Christopher Garcia, and Liqun Luo. “Secreted Semaphorins from Degenerating Larval ORN Axons Direct Adult Projection Neuron Dendrite Targeting.” Neuron. Elsevier, 2011. https://doi.org/10.1016/j.neuron.2011.09.026.","mla":"Sweeney, Lora B., et al. “Secreted Semaphorins from Degenerating Larval ORN Axons Direct Adult Projection Neuron Dendrite Targeting.” Neuron, vol. 72, no. 5, Elsevier, 2011, pp. 734–47, doi:10.1016/j.neuron.2011.09.026.","short":"L.B. Sweeney, Y.-H. Chou, Z. Wu, W. Joo, T. Komiyama, C.J. Potter, A.L. Kolodkin, K.C. Garcia, L. Luo, Neuron 72 (2011) 734–747.","ista":"Sweeney LB, Chou Y-H, Wu Z, Joo W, Komiyama T, Potter CJ, Kolodkin AL, Garcia KC, Luo L. 2011. Secreted semaphorins from degenerating larval ORN axons direct adult projection neuron dendrite targeting. Neuron. 72(5), 734–747.","apa":"Sweeney, L. B., Chou, Y.-H., Wu, Z., Joo, W., Komiyama, T., Potter, C. J., … Luo, L. (2011). Secreted semaphorins from degenerating larval ORN axons direct adult projection neuron dendrite targeting. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2011.09.026","ieee":"L. B. Sweeney et al., “Secreted semaphorins from degenerating larval ORN axons direct adult projection neuron dendrite targeting,” Neuron, vol. 72, no. 5. Elsevier, pp. 734–747, 2011.","ama":"Sweeney LB, Chou Y-H, Wu Z, et al. Secreted semaphorins from degenerating larval ORN axons direct adult projection neuron dendrite targeting. Neuron. 2011;72(5):734-747. doi:10.1016/j.neuron.2011.09.026"},"language":[{"iso":"eng"}],"doi":"10.1016/j.neuron.2011.09.026","date_published":"2011-12-08T00:00:00Z"},{"language":[{"iso":"eng"}],"doi":"10.1016/j.neuron.2011.02.050","date_published":"2011-04-28T00:00:00Z","page":"281-298","article_type":"original","quality_controlled":"1","citation":{"mla":"Wu, Zhuhao, et al. “A Combinatorial Semaphorin Code Instructs the Initial Steps of Sensory Circuit Assembly in the Drosophila CNS.” Neuron, vol. 70, no. 2, Elsevier, 2011, pp. 281–98, doi:10.1016/j.neuron.2011.02.050.","short":"Z. Wu, L.B. Sweeney, J.C. Ayoob, K. Chak, B.J. Andreone, T. Ohyama, R. Kerr, L. Luo, M. Zlatic, A.L. Kolodkin, Neuron 70 (2011) 281–298.","chicago":"Wu, Zhuhao, Lora B. Sweeney, Joseph C. Ayoob, Kayam Chak, Benjamin J. Andreone, Tomoko Ohyama, Rex Kerr, Liqun Luo, Marta Zlatic, and Alex L. Kolodkin. “A Combinatorial Semaphorin Code Instructs the Initial Steps of Sensory Circuit Assembly in the Drosophila CNS.” Neuron. Elsevier, 2011. https://doi.org/10.1016/j.neuron.2011.02.050.","ama":"Wu Z, Sweeney LB, Ayoob JC, et al. A combinatorial semaphorin code instructs the initial steps of sensory circuit assembly in the Drosophila CNS. Neuron. 2011;70(2):281-298. doi:10.1016/j.neuron.2011.02.050","ista":"Wu Z, Sweeney LB, Ayoob JC, Chak K, Andreone BJ, Ohyama T, Kerr R, Luo L, Zlatic M, Kolodkin AL. 2011. A combinatorial semaphorin code instructs the initial steps of sensory circuit assembly in the Drosophila CNS. Neuron. 70(2), 281–298.","apa":"Wu, Z., Sweeney, L. B., Ayoob, J. C., Chak, K., Andreone, B. J., Ohyama, T., … Kolodkin, A. L. (2011). A combinatorial semaphorin code instructs the initial steps of sensory circuit assembly in the Drosophila CNS. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2011.02.050","ieee":"Z. Wu et al., “A combinatorial semaphorin code instructs the initial steps of sensory circuit assembly in the Drosophila CNS,” Neuron, vol. 70, no. 2. Elsevier, pp. 281–298, 2011."},"publication":"Neuron","article_processing_charge":"No","publication_identifier":{"issn":["0896-6273"]},"day":"28","month":"04","oa_version":"None","volume":70,"date_updated":"2024-01-31T10:14:29Z","date_created":"2020-04-30T10:36:30Z","author":[{"last_name":"Wu","first_name":"Zhuhao","full_name":"Wu, Zhuhao"},{"full_name":"Sweeney, Lora Beatrice Jaeger","last_name":"Sweeney","first_name":"Lora Beatrice Jaeger","orcid":"0000-0001-9242-5601","id":"56BE8254-C4F0-11E9-8E45-0B23E6697425"},{"full_name":"Ayoob, Joseph C.","last_name":"Ayoob","first_name":"Joseph C."},{"last_name":"Chak","first_name":"Kayam","full_name":"Chak, Kayam"},{"full_name":"Andreone, Benjamin J.","first_name":"Benjamin J.","last_name":"Andreone"},{"first_name":"Tomoko","last_name":"Ohyama","full_name":"Ohyama, Tomoko"},{"full_name":"Kerr, Rex","last_name":"Kerr","first_name":"Rex"},{"full_name":"Luo, Liqun","first_name":"Liqun","last_name":"Luo"},{"first_name":"Marta","last_name":"Zlatic","full_name":"Zlatic, Marta"},{"full_name":"Kolodkin, Alex L.","last_name":"Kolodkin","first_name":"Alex L."}],"intvolume":" 70","publisher":"Elsevier","title":"A combinatorial semaphorin code instructs the initial steps of sensory circuit assembly in the Drosophila CNS","status":"public","publication_status":"published","_id":"7702","year":"2011","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","issue":"2","abstract":[{"text":"Longitudinal axon fascicles within the Drosophila embryonic CNS provide connections between body segments and are required for coordinated neural signaling along the anterior-posterior axis. We show here that establishment of select CNS longitudinal tracts and formation of precise mechanosensory afferent innervation to the same CNS region are coordinately regulated by the secreted semaphorins Sema-2a and Sema-2b. Both Sema-2a and Sema-2b utilize the same neuronal receptor, plexin B (PlexB), but serve distinct guidance functions. Localized Sema-2b attraction promotes the initial assembly of a subset of CNS longitudinal projections and subsequent targeting of chordotonal sensory afferent axons to these same longitudinal connectives, whereas broader Sema-2a repulsion serves to prevent aberrant innervation. In the absence of Sema-2b or PlexB, chordotonal afferent connectivity within the CNS is severely disrupted, resulting in specific larval behavioral deficits. These results reveal that distinct semaphorin-mediated guidance functions converge at PlexB and are critical for functional neural circuit assembly.","lang":"eng"}],"type":"journal_article"}]