[{"has_accepted_license":"1","oa":1,"oa_version":"Published Version","status":"public","alternative_title":["IST Austria Technical Report"],"language":[{"iso":"eng"}],"related_material":{"record":[{"status":"public","id":"2038","relation":"later_version"},{"status":"public","id":"3356","relation":"later_version"}]},"ec_funded":1,"page":"14","publisher":"IST Austria","date_published":"2011-04-04T00:00:00Z","publication_status":"published","year":"2011","publication_identifier":{"issn":["2664-1690"]},"title":"Temporal specifications with accumulative values","type":"technical_report","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["000","004"],"file":[{"checksum":"8491d0d48c4911620ecd5350b413c11e","access_level":"open_access","creator":"system","content_type":"application/pdf","relation":"main_file","date_created":"2018-12-12T11:53:00Z","file_size":366281,"file_name":"IST-2011-0003_IST-2011-0003.pdf","date_updated":"2020-07-14T12:46:41Z","file_id":"5461"}],"abstract":[{"lang":"eng","text":"There is recently a significant effort to add quantitative objectives to formal verification and synthesis. We introduce and investigate the extension of temporal logics with quantitative atomic assertions, aiming for a general and flexible framework for quantitative-oriented specifications. In the heart of quantitative objectives lies the accumulation of values along a computation. It is either the accumulated summation, as with the energy objectives, or the accumulated average, as with the mean-payoff objectives. We investigate the extension of temporal logics with the prefix-accumulation assertions Sum(v) ≥ c and Avg(v) ≥ c, where v is a numeric variable of the system, c is a constant rational number, and Sum(v) and Avg(v) denote the accumulated sum and average of the values of v from the beginning of the computation up to the current point of time. We also allow the path-accumulation assertions LimInfAvg(v) ≥ c and LimSupAvg(v) ≥ c, referring to the average value along an entire computation. We study the border of decidability for extensions of various temporal logics. In particular, we show that extending the fragment of CTL that has only the EX, EF, AX, and AG temporal modalities by prefix-accumulation assertions and extending LTL with path-accumulation assertions, result in temporal logics whose model-checking problem is decidable. The extended logics allow to significantly extend the currently known energy and mean-payoff objectives. Moreover, the prefix-accumulation assertions may be refined with “controlled-accumulation”, allowing, for example, to specify constraints on the average waiting time between a request and a grant. On the negative side, we show that the fragment we point to is, in a sense, the maximal logic whose extension with prefix-accumulation assertions permits a decidable model-checking procedure. Extending a temporal logic that has the EG or EU modalities, and in particular CTL and LTL, makes the problem undecidable."}],"doi":"10.15479/AT:IST-2011-0003","file_date_updated":"2020-07-14T12:46:41Z","date_created":"2018-12-12T11:39:02Z","_id":"5385","author":[{"full_name":"Boker, Udi","last_name":"Boker","id":"31E297B6-F248-11E8-B48F-1D18A9856A87","first_name":"Udi"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger"},{"first_name":"Orna","last_name":"Kupferman","full_name":"Kupferman, Orna"}],"date_updated":"2023-02-23T11:23:41Z","day":"04","month":"04","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"project":[{"grant_number":"S 11407_N23","call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"grant_number":"215543","call_identifier":"FP7","name":"COMponent-Based Embedded Systems design Techniques","_id":"25EFB36C-B435-11E9-9278-68D0E5697425"},{"name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989","call_identifier":"FP7"},{"name":"Design for Embedded Systems","_id":"25F1337C-B435-11E9-9278-68D0E5697425","grant_number":"214373","call_identifier":"FP7"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"pubrep_id":"21","citation":{"short":"U. Boker, K. Chatterjee, T.A. Henzinger, O. Kupferman, Temporal Specifications with Accumulative Values, IST Austria, 2011.","apa":"Boker, U., Chatterjee, K., Henzinger, T. A., &#38; Kupferman, O. (2011). <i>Temporal specifications with accumulative values</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2011-0003\">https://doi.org/10.15479/AT:IST-2011-0003</a>","mla":"Boker, Udi, et al. <i>Temporal Specifications with Accumulative Values</i>. IST Austria, 2011, doi:<a href=\"https://doi.org/10.15479/AT:IST-2011-0003\">10.15479/AT:IST-2011-0003</a>.","ama":"Boker U, Chatterjee K, Henzinger TA, Kupferman O. <i>Temporal Specifications with Accumulative Values</i>. IST Austria; 2011. doi:<a href=\"https://doi.org/10.15479/AT:IST-2011-0003\">10.15479/AT:IST-2011-0003</a>","chicago":"Boker, Udi, Krishnendu Chatterjee, Thomas A Henzinger, and Orna Kupferman. <i>Temporal Specifications with Accumulative Values</i>. IST Austria, 2011. <a href=\"https://doi.org/10.15479/AT:IST-2011-0003\">https://doi.org/10.15479/AT:IST-2011-0003</a>.","ista":"Boker U, Chatterjee K, Henzinger TA, Kupferman O. 2011. Temporal specifications with accumulative values, IST Austria, 14p.","ieee":"U. Boker, K. Chatterjee, T. A. Henzinger, and O. Kupferman, <i>Temporal specifications with accumulative values</i>. IST Austria, 2011."}},{"author":[{"id":"3E92416E-F248-11E8-B48F-1D18A9856A87","last_name":"Chen","first_name":"Chao","full_name":"Chen, Chao"},{"last_name":"Freedman","first_name":"Daniel","full_name":"Freedman, Daniel"},{"orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph","first_name":"Christoph","last_name":"Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87"}],"publisher":"IST Austria","page":"69","publication_status":"published","publication_identifier":{"issn":["2664-1690"]},"year":"2011","date_updated":"2023-02-23T11:22:48Z","date_published":"2011-03-28T00:00:00Z","oa_version":"Published Version","status":"public","has_accepted_license":"1","file_date_updated":"2020-07-14T12:46:41Z","oa":1,"related_material":{"record":[{"relation":"later_version","status":"public","id":"3336"}]},"language":[{"iso":"eng"}],"alternative_title":["IST Austria Technical Report"],"date_created":"2018-12-12T11:39:02Z","_id":"5386","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"}],"pubrep_id":"22","citation":{"ieee":"C. Chen, D. Freedman, and C. Lampert, <i>Enforcing topological constraints in random field image segmentation</i>. IST Austria, 2011.","apa":"Chen, C., Freedman, D., &#38; Lampert, C. (2011). <i>Enforcing topological constraints in random field image segmentation</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2011-0002\">https://doi.org/10.15479/AT:IST-2011-0002</a>","mla":"Chen, Chao, et al. <i>Enforcing Topological Constraints in Random Field Image Segmentation</i>. IST Austria, 2011, doi:<a href=\"https://doi.org/10.15479/AT:IST-2011-0002\">10.15479/AT:IST-2011-0002</a>.","short":"C. Chen, D. Freedman, C. Lampert, Enforcing Topological Constraints in Random Field Image Segmentation, IST Austria, 2011.","chicago":"Chen, Chao, Daniel Freedman, and Christoph Lampert. <i>Enforcing Topological Constraints in Random Field Image Segmentation</i>. IST Austria, 2011. <a href=\"https://doi.org/10.15479/AT:IST-2011-0002\">https://doi.org/10.15479/AT:IST-2011-0002</a>.","ama":"Chen C, Freedman D, Lampert C. <i>Enforcing Topological Constraints in Random Field Image Segmentation</i>. IST Austria; 2011. doi:<a href=\"https://doi.org/10.15479/AT:IST-2011-0002\">10.15479/AT:IST-2011-0002</a>","ista":"Chen C, Freedman D, Lampert C. 2011. Enforcing topological constraints in random field image segmentation, IST Austria, 69p."},"doi":"10.15479/AT:IST-2011-0002","title":"Enforcing topological constraints in random field image segmentation","type":"technical_report","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"28","month":"03","department":[{"_id":"ChLa"}],"ddc":["000"],"file":[{"content_type":"application/pdf","creator":"system","access_level":"open_access","checksum":"ad64c2add5fe2ad10e9d5c669f3f9526","relation":"main_file","date_created":"2018-12-12T11:53:34Z","file_size":26390601,"file_id":"5495","file_name":"IST-2011-0002_IST-2011-0002.pdf","date_updated":"2020-07-14T12:46:41Z"}]},{"doi":"10.15479/AT:IST-2011-0001","citation":{"apa":"Chatterjee, K., &#38; Doyen, L. (2011). <i>Energy and mean-payoff parity Markov decision processes</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2011-0001\">https://doi.org/10.15479/AT:IST-2011-0001</a>","mla":"Chatterjee, Krishnendu, and Laurent Doyen. <i>Energy and Mean-Payoff Parity Markov Decision Processes</i>. IST Austria, 2011, doi:<a href=\"https://doi.org/10.15479/AT:IST-2011-0001\">10.15479/AT:IST-2011-0001</a>.","short":"K. Chatterjee, L. Doyen, Energy and Mean-Payoff Parity Markov Decision Processes, IST Austria, 2011.","ama":"Chatterjee K, Doyen L. <i>Energy and Mean-Payoff Parity Markov Decision Processes</i>. IST Austria; 2011. doi:<a href=\"https://doi.org/10.15479/AT:IST-2011-0001\">10.15479/AT:IST-2011-0001</a>","chicago":"Chatterjee, Krishnendu, and Laurent Doyen. <i>Energy and Mean-Payoff Parity Markov Decision Processes</i>. IST Austria, 2011. <a href=\"https://doi.org/10.15479/AT:IST-2011-0001\">https://doi.org/10.15479/AT:IST-2011-0001</a>.","ista":"Chatterjee K, Doyen L. 2011. Energy and mean-payoff parity Markov decision processes, IST Austria, 20p.","ieee":"K. Chatterjee and L. Doyen, <i>Energy and mean-payoff parity Markov decision processes</i>. IST Austria, 2011."},"pubrep_id":"23","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."}],"ddc":["000","005"],"file":[{"relation":"main_file","date_created":"2018-12-12T11:52:57Z","checksum":"824d6c70e6d3feb3e836b009e0b3cf73","access_level":"open_access","creator":"system","content_type":"application/pdf","date_updated":"2020-07-14T12:46:41Z","file_name":"IST-2011-0001_IST-2011-0001.pdf","file_id":"5458","file_size":329976}],"department":[{"_id":"KrCh"}],"month":"02","day":"16","type":"technical_report","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Energy and mean-payoff parity Markov decision processes","date_published":"2011-02-16T00:00:00Z","date_updated":"2023-02-23T11:23:11Z","publication_status":"published","year":"2011","publication_identifier":{"issn":["2664-1690"]},"page":"20","publisher":"IST Austria","author":[{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"last_name":"Doyen","first_name":"Laurent","full_name":"Doyen, Laurent"}],"_id":"5387","date_created":"2018-12-12T11:39:02Z","alternative_title":["IST Austria Technical Report"],"related_material":{"record":[{"status":"public","id":"3345","relation":"later_version"}]},"language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:46:41Z","oa":1,"has_accepted_license":"1","status":"public","oa_version":"Published Version"},{"publication":"Nature","citation":{"ista":"Hosten O. 2011. Quantum physics: How to catch a wave. Nature. 474(7350), 170–171.","ama":"Hosten O. Quantum physics: How to catch a wave. <i>Nature</i>. 2011;474(7350):170-171. doi:<a href=\"https://doi.org/10.1038/474170a\">10.1038/474170a</a>","chicago":"Hosten, Onur. “Quantum Physics: How to Catch a Wave.” <i>Nature</i>. Nature Publishing Group, 2011. <a href=\"https://doi.org/10.1038/474170a\">https://doi.org/10.1038/474170a</a>.","short":"O. Hosten, Nature 474 (2011) 170–171.","apa":"Hosten, O. (2011). Quantum physics: How to catch a wave. <i>Nature</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/474170a\">https://doi.org/10.1038/474170a</a>","mla":"Hosten, Onur. “Quantum Physics: How to Catch a Wave.” <i>Nature</i>, vol. 474, no. 7350, Nature Publishing Group, 2011, pp. 170–71, doi:<a href=\"https://doi.org/10.1038/474170a\">10.1038/474170a</a>.","ieee":"O. Hosten, “Quantum physics: How to catch a wave,” <i>Nature</i>, vol. 474, no. 7350. Nature Publishing Group, pp. 170–171, 2011."},"doi":"10.1038/474170a","type":"journal_article","day":"08","title":"Quantum physics: How to catch a wave","intvolume":"       474","month":"06","author":[{"full_name":"Onur Hosten","orcid":"0000-0002-2031-204X","first_name":"Onur","id":"4C02D85E-F248-11E8-B48F-1D18A9856A87","last_name":"Hosten"}],"publisher":"Nature Publishing Group","quality_controlled":0,"page":"170 - 171","date_updated":"2021-01-12T08:03:34Z","year":"2011","publication_status":"published","date_published":"2011-06-08T00:00:00Z","status":"public","extern":1,"publist_id":"7224","issue":"7350","volume":474,"_id":"580","date_created":"2018-12-11T11:47:18Z"},{"month":"01","title":"Methods towards achieving precise birefringent focusing","day":"01","type":"conference","conference":{"name":"QELS: Quantum Electronics and Laser Science"},"doi":"10.1364/CLEO_AT.2011.JThB130","citation":{"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.","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, .","ama":"Schmid D, Hazrat S, Rangarajan R, Hosten O, Quint S, Kwiat P. Methods towards achieving precise birefringent focusing. In: OSA; 2011. doi:<a href=\"https://doi.org/10.1364/CLEO_AT.2011.JThB130\">10.1364/CLEO_AT.2011.JThB130</a>","chicago":"Schmid, David, Shiraz Hazrat, Radhika Rangarajan, Onur Hosten, Stephan Quint, and Paul Kwiat. “Methods towards Achieving Precise Birefringent Focusing.” OSA, 2011. <a href=\"https://doi.org/10.1364/CLEO_AT.2011.JThB130\">https://doi.org/10.1364/CLEO_AT.2011.JThB130</a>.","apa":"Schmid, D., Hazrat, S., Rangarajan, R., Hosten, O., Quint, S., &#38; Kwiat, P. (2011). Methods towards achieving precise birefringent focusing. Presented at the QELS: Quantum Electronics and Laser Science, OSA. <a href=\"https://doi.org/10.1364/CLEO_AT.2011.JThB130\">https://doi.org/10.1364/CLEO_AT.2011.JThB130</a>","short":"D. Schmid, S. Hazrat, R. Rangarajan, O. Hosten, S. Quint, P. Kwiat, in:, OSA, 2011.","mla":"Schmid, David, et al. <i>Methods towards Achieving Precise Birefringent Focusing</i>. OSA, 2011, doi:<a href=\"https://doi.org/10.1364/CLEO_AT.2011.JThB130\">10.1364/CLEO_AT.2011.JThB130</a>."},"abstract":[{"lang":"eng","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"}],"alternative_title":["Optics InfoBase Conference Papers"],"date_created":"2018-12-11T11:47:20Z","_id":"585","publist_id":"7220","status":"public","extern":1,"date_published":"2011-01-01T00:00:00Z","publication_status":"published","year":"2011","date_updated":"2021-01-12T08:03:44Z","quality_controlled":0,"publisher":"OSA","author":[{"full_name":"Schmid, David","last_name":"Schmid","first_name":"David"},{"full_name":"Hazrat, Shiraz","last_name":"Hazrat","first_name":"Shiraz"},{"first_name":"Radhika","last_name":"Rangarajan","full_name":"Rangarajan, Radhika"},{"orcid":"0000-0002-2031-204X","full_name":"Onur Hosten","first_name":"Onur","last_name":"Hosten","id":"4C02D85E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Quint, Stephan","first_name":"Stephan","last_name":"Quint"},{"full_name":"Kwiat, Paul G","last_name":"Kwiat","first_name":"Paul"}]},{"date_created":"2018-12-11T11:47:20Z","_id":"586","status":"public","extern":1,"volume":107,"issue":"6","publist_id":"7223","year":"2011","publication_status":"published","date_updated":"2021-01-12T08:05:05Z","date_published":"2011-08-04T00:00:00Z","quality_controlled":0,"publisher":"American Physical Society","author":[{"last_name":"Vrijsen","first_name":"Geert","full_name":"Vrijsen, Geert"},{"orcid":"0000-0002-2031-204X","full_name":"Onur Hosten","first_name":"Onur","last_name":"Hosten","id":"4C02D85E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Lee, Jongmin","first_name":"Jongmin","last_name":"Lee"},{"full_name":"Bernon, Simon","first_name":"Simon","last_name":"Bernon"},{"full_name":"Kasevich, Mark A","first_name":"Mark","last_name":"Kasevich"}],"month":"08","intvolume":"       107","title":"Raman lasing with a cold atom gain medium in a high-finesse optical cavity","day":"04","type":"journal_article","citation":{"mla":"Vrijsen, Geert, et al. “Raman Lasing with a Cold Atom Gain Medium in a High-Finesse Optical Cavity.” <i>Physical Review Letters</i>, vol. 107, no. 6, American Physical Society, 2011, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.107.063904\">10.1103/PhysRevLett.107.063904</a>.","apa":"Vrijsen, G., Hosten, O., Lee, J., Bernon, S., &#38; Kasevich, M. (2011). Raman lasing with a cold atom gain medium in a high-finesse optical cavity. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.107.063904\">https://doi.org/10.1103/PhysRevLett.107.063904</a>","short":"G. Vrijsen, O. Hosten, J. Lee, S. Bernon, M. Kasevich, Physical Review Letters 107 (2011).","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. <i>Physical Review Letters</i>. 2011;107(6). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.107.063904\">10.1103/PhysRevLett.107.063904</a>","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).","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.” <i>Physical Review Letters</i>. American Physical Society, 2011. <a href=\"https://doi.org/10.1103/PhysRevLett.107.063904\">https://doi.org/10.1103/PhysRevLett.107.063904</a>.","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,” <i>Physical Review Letters</i>, vol. 107, no. 6. American Physical Society, 2011."},"doi":"10.1103/PhysRevLett.107.063904","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."}],"publication":"Physical Review Letters"},{"date_updated":"2021-01-12T08:05:25Z","year":"2011","publication_status":"published","date_published":"2011-03-01T00:00:00Z","author":[{"id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87","last_name":"Bernecky","first_name":"Carrie A","full_name":"Bernecky, Carrie A","orcid":"0000-0003-0893-7036"},{"last_name":"Grob","first_name":"Patricia","full_name":"Grob, Patricia"},{"full_name":"Ebmeier, Christopher","first_name":"Christopher","last_name":"Ebmeier"},{"last_name":"Nogales","first_name":"Eva","full_name":"Nogales, Eva"},{"full_name":"Taatjes, Dylan","last_name":"Taatjes","first_name":"Dylan"}],"publisher":"Public Library of Science","article_processing_charge":"No","_id":"597","language":[{"iso":"eng"}],"date_created":"2018-12-11T11:47:24Z","extern":"1","status":"public","oa_version":"None","issue":"3","publist_id":"7209","volume":9,"citation":{"chicago":"Bernecky, Carrie, Patricia Grob, Christopher Ebmeier, Eva Nogales, and Dylan Taatjes. “Molecular Architecture of the Human Mediator-RNA Polymerase II-TFIIF Assembly.” <i>PLoS Biology</i>. Public Library of Science, 2011. <a href=\"https://doi.org/10.1371/journal.pbio.1000603\">https://doi.org/10.1371/journal.pbio.1000603</a>.","ama":"Bernecky C, Grob P, Ebmeier C, Nogales E, Taatjes D. Molecular architecture of the human Mediator-RNA polymerase II-TFIIF assembly. <i>PLoS Biology</i>. 2011;9(3). doi:<a href=\"https://doi.org/10.1371/journal.pbio.1000603\">10.1371/journal.pbio.1000603</a>","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).","mla":"Bernecky, Carrie, et al. “Molecular Architecture of the Human Mediator-RNA Polymerase II-TFIIF Assembly.” <i>PLoS Biology</i>, vol. 9, no. 3, Public Library of Science, 2011, doi:<a href=\"https://doi.org/10.1371/journal.pbio.1000603\">10.1371/journal.pbio.1000603</a>.","apa":"Bernecky, C., Grob, P., Ebmeier, C., Nogales, E., &#38; Taatjes, D. (2011). Molecular architecture of the human Mediator-RNA polymerase II-TFIIF assembly. <i>PLoS Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.1000603\">https://doi.org/10.1371/journal.pbio.1000603</a>","short":"C. Bernecky, P. Grob, C. Ebmeier, E. Nogales, D. Taatjes, PLoS Biology 9 (2011).","ieee":"C. Bernecky, P. Grob, C. Ebmeier, E. Nogales, and D. Taatjes, “Molecular architecture of the human Mediator-RNA polymerase II-TFIIF assembly,” <i>PLoS Biology</i>, vol. 9, no. 3. Public Library of Science, 2011."},"doi":"10.1371/journal.pbio.1000603","abstract":[{"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.","lang":"eng"}],"publication":"PLoS Biology","month":"03","type":"journal_article","day":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Molecular architecture of the human Mediator-RNA polymerase II-TFIIF assembly","intvolume":"         9"},{"author":[{"full_name":"Milward, K.","first_name":"K.","last_name":"Milward"},{"first_name":"K. E.","last_name":"Busch","full_name":"Busch, K. E."},{"full_name":"Murphy, R. J.","first_name":"R. J.","last_name":"Murphy"},{"last_name":"de Bono","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","first_name":"Mario","orcid":"0000-0001-8347-0443","full_name":"de Bono, Mario"},{"full_name":"Olofsson, B.","first_name":"B.","last_name":"Olofsson"}],"date_updated":"2021-01-12T08:06:18Z","issue":"51","volume":108,"_id":"6137","date_created":"2019-03-20T14:30:06Z","external_id":{"pmid":["22135454"]},"citation":{"ama":"Milward K, Busch KE, Murphy RJ, de Bono M, Olofsson B. Neuronal and molecular substrates for optimal foraging in Caenorhabditis elegans. <i>Proceedings of the National Academy of Sciences</i>. 2011;108(51):20672-20677. doi:<a href=\"https://doi.org/10.1073/pnas.1106134109\">10.1073/pnas.1106134109</a>","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.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2011. <a href=\"https://doi.org/10.1073/pnas.1106134109\">https://doi.org/10.1073/pnas.1106134109</a>.","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.","mla":"Milward, K., et al. “Neuronal and Molecular Substrates for Optimal Foraging in Caenorhabditis Elegans.” <i>Proceedings of the National Academy of Sciences</i>, vol. 108, no. 51, National Academy of Sciences, 2011, pp. 20672–77, doi:<a href=\"https://doi.org/10.1073/pnas.1106134109\">10.1073/pnas.1106134109</a>.","apa":"Milward, K., Busch, K. E., Murphy, R. J., de Bono, M., &#38; Olofsson, B. (2011). Neuronal and molecular substrates for optimal foraging in Caenorhabditis elegans. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1106134109\">https://doi.org/10.1073/pnas.1106134109</a>","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.","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,” <i>Proceedings of the National Academy of Sciences</i>, vol. 108, no. 51. National Academy of Sciences, pp. 20672–20677, 2011."},"day":"20","intvolume":"       108","month":"12","pmid":1,"page":"20672-20677","publisher":"National Academy of Sciences","quality_controlled":"1","date_published":"2011-12-20T00:00:00Z","year":"2011","publication_status":"published","publication_identifier":{"issn":["0027-8424","1091-6490"]},"oa":1,"status":"public","extern":"1","oa_version":"Submitted Version","language":[{"iso":"eng"}],"publication":"Proceedings of the National Academy of Sciences","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."}],"doi":"10.1073/pnas.1106134109","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3251049/","open_access":"1"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","type":"journal_article","title":"Neuronal and molecular substrates for optimal foraging in Caenorhabditis elegans"},{"author":[{"full_name":"Bretscher, Andrew Jonathan","last_name":"Bretscher","first_name":"Andrew Jonathan"},{"first_name":"Eiji","last_name":"Kodama-Namba","full_name":"Kodama-Namba, Eiji"},{"last_name":"Busch","first_name":"Karl Emanuel","full_name":"Busch, Karl Emanuel"},{"last_name":"Murphy","first_name":"Robin Joseph","full_name":"Murphy, Robin Joseph"},{"first_name":"Zoltan","last_name":"Soltesz","full_name":"Soltesz, Zoltan"},{"first_name":"Patrick","last_name":"Laurent","full_name":"Laurent, Patrick"},{"first_name":"Mario","last_name":"de Bono","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8347-0443","full_name":"de Bono, Mario"}],"date_updated":"2021-01-12T08:06:18Z","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"volume":69,"issue":"6","file_date_updated":"2020-07-14T12:47:20Z","date_created":"2019-03-20T15:01:41Z","_id":"6138","external_id":{"pmid":["21435556"]},"citation":{"ieee":"A. J. Bretscher <i>et al.</i>, “Temperature, oxygen, and salt-sensing neurons in C. elegans are carbon dioxide sensors that control avoidance behavior,” <i>Neuron</i>, 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. <i>Neuron</i>. 2011;69(6):1099-1113. doi:<a href=\"https://doi.org/10.1016/j.neuron.2011.02.023\">10.1016/j.neuron.2011.02.023</a>","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.” <i>Neuron</i>. Elsevier BV, 2011. <a href=\"https://doi.org/10.1016/j.neuron.2011.02.023\">https://doi.org/10.1016/j.neuron.2011.02.023</a>.","apa":"Bretscher, A. J., Kodama-Namba, E., Busch, K. E., Murphy, R. J., Soltesz, Z., Laurent, P., &#38; de Bono, M. (2011). Temperature, oxygen, and salt-sensing neurons in C. elegans are carbon dioxide sensors that control avoidance behavior. <i>Neuron</i>. Elsevier BV. <a href=\"https://doi.org/10.1016/j.neuron.2011.02.023\">https://doi.org/10.1016/j.neuron.2011.02.023</a>","mla":"Bretscher, Andrew Jonathan, et al. “Temperature, Oxygen, and Salt-Sensing Neurons in C. Elegans Are Carbon Dioxide Sensors That Control Avoidance Behavior.” <i>Neuron</i>, vol. 69, no. 6, Elsevier BV, 2011, pp. 1099–113, doi:<a href=\"https://doi.org/10.1016/j.neuron.2011.02.023\">10.1016/j.neuron.2011.02.023</a>.","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."},"intvolume":"        69","day":"24","pmid":1,"month":"03","page":"1099-1113","quality_controlled":"1","publisher":"Elsevier BV","date_published":"2011-03-24T00:00:00Z","publication_identifier":{"issn":["0896-6273"]},"publication_status":"published","year":"2011","has_accepted_license":"1","oa":1,"oa_version":"Published Version","extern":"1","status":"public","language":[{"iso":"eng"}],"publication":"Neuron","doi":"10.1016/j.neuron.2011.02.023","title":"Temperature, oxygen, and salt-sensing neurons in C. elegans are carbon dioxide sensors that control avoidance behavior","type":"journal_article","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","file":[{"relation":"main_file","date_created":"2019-03-20T15:06:32Z","creator":"kschuh","access_level":"open_access","content_type":"application/pdf","checksum":"547cffd123f4c508ae927c9244b8f92a","file_id":"6139","file_name":"2011_Cell_Bretscher.pdf","date_updated":"2020-07-14T12:47:20Z","file_size":2448332}],"ddc":["570"]},{"oa_version":"Published Version","status":"public","extern":"1","has_accepted_license":"1","oa":1,"language":[{"iso":"eng"}],"article_number":"e1001341","quality_controlled":"1","publisher":"Public Library of Science","publication_status":"published","publication_identifier":{"issn":["1553-7404"]},"year":"2011","date_published":"2011-03-17T00:00:00Z","title":"Macoilin, a conserved nervous system–specific ER membrane protein that regulates neuronal excitability","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","type":"journal_article","file":[{"date_created":"2019-03-20T15:18:11Z","relation":"main_file","access_level":"open_access","creator":"kschuh","content_type":"application/pdf","checksum":"c609b2ce616d7dafbb617ec5d022f1ea","file_id":"6141","date_updated":"2020-07-14T12:47:20Z","file_name":"2011_PLOS_Arellano-Carbajal.PDF","file_size":5625063}],"ddc":["570"],"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."}],"publication":"PLoS Genetics","doi":"10.1371/journal.pgen.1001341","volume":7,"issue":"3","file_date_updated":"2020-07-14T12:47:20Z","date_created":"2019-03-20T15:08:23Z","_id":"6140","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"},{"last_name":"Couto","first_name":"Africa","full_name":"Couto, Africa"},{"full_name":"Cheung, Benny H. H.","first_name":"Benny H. H.","last_name":"Cheung"},{"full_name":"Labouesse, Michel","last_name":"Labouesse","first_name":"Michel"},{"full_name":"de Bono, Mario","orcid":"0000-0001-8347-0443","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","last_name":"de Bono","first_name":"Mario"}],"date_updated":"2021-01-12T08:06:19Z","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"intvolume":"         7","day":"17","pmid":1,"month":"03","external_id":{"pmid":["21437263"]},"citation":{"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,” <i>PLoS Genetics</i>, vol. 7, no. 3. Public Library of Science, 2011.","short":"F. Arellano-Carbajal, L. Briseño-Roa, A. Couto, B.H.H. Cheung, M. Labouesse, M. de Bono, PLoS Genetics 7 (2011).","mla":"Arellano-Carbajal, Fausto, et al. “Macoilin, a Conserved Nervous System–Specific ER Membrane Protein That Regulates Neuronal Excitability.” <i>PLoS Genetics</i>, vol. 7, no. 3, e1001341, Public Library of Science, 2011, doi:<a href=\"https://doi.org/10.1371/journal.pgen.1001341\">10.1371/journal.pgen.1001341</a>.","apa":"Arellano-Carbajal, F., Briseño-Roa, L., Couto, A., Cheung, B. H. H., Labouesse, M., &#38; de Bono, M. (2011). Macoilin, a conserved nervous system–specific ER membrane protein that regulates neuronal excitability. <i>PLoS Genetics</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pgen.1001341\">https://doi.org/10.1371/journal.pgen.1001341</a>","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.","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.” <i>PLoS Genetics</i>. Public Library of Science, 2011. <a href=\"https://doi.org/10.1371/journal.pgen.1001341\">https://doi.org/10.1371/journal.pgen.1001341</a>.","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. <i>PLoS Genetics</i>. 2011;7(3). doi:<a href=\"https://doi.org/10.1371/journal.pgen.1001341\">10.1371/journal.pgen.1001341</a>"}},{"_id":"6298","language":[{"iso":"eng"}],"date_created":"2019-04-11T20:57:43Z","extern":"1","status":"public","oa_version":"Published Version","issue":"29","oa":1,"volume":286,"date_updated":"2021-01-12T08:06:58Z","publication_identifier":{"issn":["0021-9258","1083-351X"]},"publication_status":"published","year":"2011","date_published":"2011-07-22T00:00:00Z","author":[{"full_name":"Baranova, Natalia","orcid":"0000-0002-3086-9124","first_name":"Natalia","id":"38661662-F248-11E8-B48F-1D18A9856A87","last_name":"Baranova"},{"last_name":"Nilebäck","first_name":"Erik","full_name":"Nilebäck, Erik"},{"full_name":"Haller, F. Michael","last_name":"Haller","first_name":"F. Michael"},{"full_name":"Briggs, David C.","last_name":"Briggs","first_name":"David C."},{"last_name":"Svedhem","first_name":"Sofia","full_name":"Svedhem, Sofia"},{"full_name":"Day, Anthony J.","last_name":"Day","first_name":"Anthony J."},{"full_name":"Richter, Ralf P.","last_name":"Richter","first_name":"Ralf P."}],"publisher":"American Society for Biochemistry & Molecular Biology","quality_controlled":"1","page":"25675-25686","month":"07","type":"journal_article","day":"22","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"       286","title":"The inflammation-associated protein TSG-6 cross-links hyaluronan via hyaluronan-induced TSG-6 oligomers","main_file_link":[{"url":"http://www.jbc.org/content/286/29/25675.full.pdf","open_access":"1"}],"citation":{"apa":"Baranova, N. S., Nilebäck, E., Haller, F. M., Briggs, D. C., Svedhem, S., Day, A. J., &#38; Richter, R. P. (2011). The inflammation-associated protein TSG-6 cross-links hyaluronan via hyaluronan-induced TSG-6 oligomers. <i>Journal of Biological Chemistry</i>. American Society for Biochemistry &#38; Molecular Biology. <a href=\"https://doi.org/10.1074/jbc.m111.247395\">https://doi.org/10.1074/jbc.m111.247395</a>","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.","mla":"Baranova, Natalia S., et al. “The Inflammation-Associated Protein TSG-6 Cross-Links Hyaluronan via Hyaluronan-Induced TSG-6 Oligomers.” <i>Journal of Biological Chemistry</i>, vol. 286, no. 29, American Society for Biochemistry &#38; Molecular Biology, 2011, pp. 25675–86, doi:<a href=\"https://doi.org/10.1074/jbc.m111.247395\">10.1074/jbc.m111.247395</a>.","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.” <i>Journal of Biological Chemistry</i>. American Society for Biochemistry &#38; Molecular Biology, 2011. <a href=\"https://doi.org/10.1074/jbc.m111.247395\">https://doi.org/10.1074/jbc.m111.247395</a>.","ama":"Baranova NS, Nilebäck E, Haller FM, et al. The inflammation-associated protein TSG-6 cross-links hyaluronan via hyaluronan-induced TSG-6 oligomers. <i>Journal of Biological Chemistry</i>. 2011;286(29):25675-25686. doi:<a href=\"https://doi.org/10.1074/jbc.m111.247395\">10.1074/jbc.m111.247395</a>","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.","ieee":"N. S. Baranova <i>et al.</i>, “The inflammation-associated protein TSG-6 cross-links hyaluronan via hyaluronan-induced TSG-6 oligomers,” <i>Journal of Biological Chemistry</i>, vol. 286, no. 29. American Society for Biochemistry &#38; Molecular Biology, pp. 25675–25686, 2011."},"doi":"10.1074/jbc.m111.247395","abstract":[{"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).","lang":"eng"}],"publication":"Journal of Biological Chemistry"},{"article_processing_charge":"No","language":[{"iso":"eng"}],"oa_version":"Published Version","status":"public","oa":1,"publication_status":"published","year":"2011","publication_identifier":{"issn":["0006-3495"]},"date_published":"2011-11-16T00:00:00Z","quality_controlled":"1","publisher":"Elsevier","page":"2336-2340","title":"Noise underlies switching behavior of the bacterial flagellum","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3218319/"}],"doi":"10.1016/j.bpj.2011.09.040","abstract":[{"lang":"eng","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."}],"publication":"Biophysical Journal","date_created":"2019-05-28T11:54:29Z","_id":"6496","volume":101,"issue":"10","date_updated":"2021-04-16T11:54:49Z","author":[{"first_name":"Heungwon","last_name":"Park","full_name":"Park, Heungwon"},{"full_name":"Oikonomou, Panos","last_name":"Oikonomou","first_name":"Panos"},{"orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C","first_name":"Calin C","last_name":"Guet","id":"47F8433E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Cluzel, Philippe","last_name":"Cluzel","first_name":"Philippe"}],"pmid":1,"department":[{"_id":"CaGu"}],"month":"11","intvolume":"       101","day":"16","citation":{"apa":"Park, H., Oikonomou, P., Guet, C. C., &#38; Cluzel, P. (2011). Noise underlies switching behavior of the bacterial flagellum. <i>Biophysical Journal</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.bpj.2011.09.040\">https://doi.org/10.1016/j.bpj.2011.09.040</a>","short":"H. Park, P. Oikonomou, C.C. Guet, P. Cluzel, Biophysical Journal 101 (2011) 2336–2340.","mla":"Park, Heungwon, et al. “Noise Underlies Switching Behavior of the Bacterial Flagellum.” <i>Biophysical Journal</i>, vol. 101, no. 10, Elsevier, 2011, pp. 2336–40, doi:<a href=\"https://doi.org/10.1016/j.bpj.2011.09.040\">10.1016/j.bpj.2011.09.040</a>.","ista":"Park H, Oikonomou P, Guet CC, Cluzel P. 2011. Noise underlies switching behavior of the bacterial flagellum. Biophysical Journal. 101(10), 2336–2340.","ama":"Park H, Oikonomou P, Guet CC, Cluzel P. Noise underlies switching behavior of the bacterial flagellum. <i>Biophysical Journal</i>. 2011;101(10):2336-2340. doi:<a href=\"https://doi.org/10.1016/j.bpj.2011.09.040\">10.1016/j.bpj.2011.09.040</a>","chicago":"Park, Heungwon, Panos Oikonomou, Calin C Guet, and Philippe Cluzel. “Noise Underlies Switching Behavior of the Bacterial Flagellum.” <i>Biophysical Journal</i>. Elsevier, 2011. <a href=\"https://doi.org/10.1016/j.bpj.2011.09.040\">https://doi.org/10.1016/j.bpj.2011.09.040</a>.","ieee":"H. Park, P. Oikonomou, C. C. Guet, and P. Cluzel, “Noise underlies switching behavior of the bacterial flagellum,” <i>Biophysical Journal</i>, vol. 101, no. 10. Elsevier, pp. 2336–2340, 2011."},"scopus_import":"1","external_id":{"pmid":["22098731"]}},{"status":"public","extern":1,"oa":1,"issue":"2","publist_id":"5728","volume":160,"acknowledgement":"Hausel’s work was supported by National Science Foundation grants DMS-0305505 and DMS-0604775, by an Alfred Sloan Fellowship, and by a Royal Society University Research Fellowship. Letellier’s work supported by Agence Nationale de la Recherche grant ANR-09-JCJC-0102-01.\nRodriguez-Villegas’s work supported by National Science Foundation grant DMS-0200605, by an FRA from the University of Texas at Austin, by EPSRC grant EP/G027110/1, by visiting fellowships at All Souls and Wadham Colleges in Oxford, and by a Research Scholarship from the Clay Mathematical Institute.","_id":"1467","date_created":"2018-12-11T11:52:11Z","publisher":"Duke University Press","author":[{"first_name":"Tamas","last_name":"Hausel","id":"4A0666D8-F248-11E8-B48F-1D18A9856A87","full_name":"Tamas Hausel"},{"full_name":"Letellier, Emmanuel","first_name":"Emmanuel","last_name":"Letellier"},{"full_name":"Rodríguez Villegas, Fernando","last_name":"Rodríguez Villegas","first_name":"Fernando"}],"quality_controlled":0,"page":"323 - 400","date_updated":"2021-01-12T06:50:56Z","publication_status":"published","year":"2011","date_published":"2011-01-01T00:00:00Z","day":"01","type":"journal_article","title":"Arithmetic harmonic analysis on character and quiver varieties","intvolume":"       160","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/0810.2076"}],"month":"01","abstract":[{"lang":"eng","text":"We propose a general conjecture for the mixed Hodge polynomial of the generic character varieties of representations of the fundamental group of a Riemann surface of genus g to GLn(C) with fixed generic semisimple conjugacy classes at k punctures. This conjecture generalizes the Cauchy identity for Macdonald polynomials and is a common generalization of two formulas that we prove in this paper. The first is a formula for the E-polynomial of these character varieties which we obtain using the character table of GLn(Fq). We use this formula to compute the Euler characteristic of character varieties. The second formula gives the Poincaré polynomial of certain associated quiver varieties which we obtain using the character table of gln(Fq). In the last main result we prove that the Poincaré polynomials of the quiver varieties equal certain multiplicities in the tensor product of irreducible characters of GLn(Fq). As a consequence we find a curious connection between Kac-Moody algebras associated with comet-shaped, and typically wild, quivers and the representation theory of GLn(Fq)."}],"publication":"Duke Mathematical Journal","citation":{"mla":"Hausel, Tamás, et al. “Arithmetic Harmonic Analysis on Character and Quiver Varieties.” <i>Duke Mathematical Journal</i>, vol. 160, no. 2, Duke University Press, 2011, pp. 323–400, doi:<a href=\"https://doi.org/10.1215/00127094-1444258\">10.1215/00127094-1444258</a>.","short":"T. Hausel, E. Letellier, F. Rodríguez Villegas, Duke Mathematical Journal 160 (2011) 323–400.","apa":"Hausel, T., Letellier, E., &#38; Rodríguez Villegas, F. (2011). Arithmetic harmonic analysis on character and quiver varieties. <i>Duke Mathematical Journal</i>. Duke University Press. <a href=\"https://doi.org/10.1215/00127094-1444258\">https://doi.org/10.1215/00127094-1444258</a>","ama":"Hausel T, Letellier E, Rodríguez Villegas F. Arithmetic harmonic analysis on character and quiver varieties. <i>Duke Mathematical Journal</i>. 2011;160(2):323-400. doi:<a href=\"https://doi.org/10.1215/00127094-1444258\">10.1215/00127094-1444258</a>","ista":"Hausel T, Letellier E, Rodríguez Villegas F. 2011. Arithmetic harmonic analysis on character and quiver varieties. Duke Mathematical Journal. 160(2), 323–400.","chicago":"Hausel, Tamás, Emmanuel Letellier, and Fernando Rodríguez Villegas. “Arithmetic Harmonic Analysis on Character and Quiver Varieties.” <i>Duke Mathematical Journal</i>. Duke University Press, 2011. <a href=\"https://doi.org/10.1215/00127094-1444258\">https://doi.org/10.1215/00127094-1444258</a>.","ieee":"T. Hausel, E. Letellier, and F. Rodríguez Villegas, “Arithmetic harmonic analysis on character and quiver varieties,” <i>Duke Mathematical Journal</i>, vol. 160, no. 2. Duke University Press, pp. 323–400, 2011."},"doi":"10.1215/00127094-1444258"},{"volume":108,"issue":"10","date_created":"2023-09-06T12:54:36Z","_id":"14305","article_type":"original","author":[{"first_name":"Annett","last_name":"Bachmann","full_name":"Bachmann, Annett"},{"full_name":"Wildemann, Dirk","first_name":"Dirk","last_name":"Wildemann"},{"full_name":"Praetorius, Florian M","id":"dfec9381-4341-11ee-8fd8-faa02bba7d62","last_name":"Praetorius","first_name":"Florian M"},{"full_name":"Fischer, Gunter","first_name":"Gunter","last_name":"Fischer"},{"full_name":"Kiefhaber, Thomas","first_name":"Thomas","last_name":"Kiefhaber"}],"keyword":["Multidisciplinary"],"date_updated":"2023-11-07T11:50:29Z","intvolume":"       108","day":"12","pmid":1,"month":"01","external_id":{"pmid":["21325613"]},"scopus_import":"1","citation":{"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,” <i>PNAS</i>, 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.","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.” <i>PNAS</i>. Proceedings of the National Academy of Sciences, 2011. <a href=\"https://doi.org/10.1073/pnas.1012668108\">https://doi.org/10.1073/pnas.1012668108</a>.","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. <i>PNAS</i>. 2011;108(10):3952-3957. doi:<a href=\"https://doi.org/10.1073/pnas.1012668108\">10.1073/pnas.1012668108</a>","apa":"Bachmann, A., Wildemann, D., Praetorius, F. M., Fischer, G., &#38; Kiefhaber, T. (2011). Mapping backbone and side-chain interactions in the transition state of a coupled protein folding and binding reaction. <i>PNAS</i>. Proceedings of the National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1012668108\">https://doi.org/10.1073/pnas.1012668108</a>","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.” <i>PNAS</i>, vol. 108, no. 10, Proceedings of the National Academy of Sciences, 2011, pp. 3952–57, doi:<a href=\"https://doi.org/10.1073/pnas.1012668108\">10.1073/pnas.1012668108</a>."},"oa":1,"oa_version":"Published Version","extern":"1","status":"public","language":[{"iso":"eng"}],"article_processing_charge":"No","page":"3952-3957","quality_controlled":"1","publisher":"Proceedings of the National Academy of Sciences","date_published":"2011-01-12T00:00:00Z","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"publication_status":"published","year":"2011","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1073/pnas.1012668108"}],"title":"Mapping backbone and side-chain interactions in the transition state of a coupled protein folding and binding reaction","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","publication":"PNAS","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."}],"doi":"10.1073/pnas.1012668108"},{"citation":{"ieee":"C. J. Muller and P. A. O’Gorman, “An energetic perspective on the regional response of precipitation to climate change,” <i>Nature Climate Change</i>, vol. 1, no. 5. Springer Nature, pp. 266–271, 2011.","chicago":"Muller, Caroline J, and P. A. O’Gorman. “An Energetic Perspective on the Regional Response of Precipitation to Climate Change.” <i>Nature Climate Change</i>. Springer Nature, 2011. <a href=\"https://doi.org/10.1038/nclimate1169\">https://doi.org/10.1038/nclimate1169</a>.","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.","ama":"Muller CJ, O’Gorman PA. An energetic perspective on the regional response of precipitation to climate change. <i>Nature Climate Change</i>. 2011;1(5):266-271. doi:<a href=\"https://doi.org/10.1038/nclimate1169\">10.1038/nclimate1169</a>","short":"C.J. Muller, P.A. O’Gorman, Nature Climate Change 1 (2011) 266–271.","apa":"Muller, C. J., &#38; O’Gorman, P. A. (2011). An energetic perspective on the regional response of precipitation to climate change. <i>Nature Climate Change</i>. Springer Nature. <a href=\"https://doi.org/10.1038/nclimate1169\">https://doi.org/10.1038/nclimate1169</a>","mla":"Muller, Caroline J., and P. A. O’Gorman. “An Energetic Perspective on the Regional Response of Precipitation to Climate Change.” <i>Nature Climate Change</i>, vol. 1, no. 5, Springer Nature, 2011, pp. 266–71, doi:<a href=\"https://doi.org/10.1038/nclimate1169\">10.1038/nclimate1169</a>."},"doi":"10.1038/nclimate1169","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."}],"publication":"Nature Climate Change","month":"07","type":"journal_article","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","day":"24","title":"An energetic perspective on the regional response of precipitation to climate change","intvolume":"         1","date_updated":"2022-01-24T13:52:11Z","publication_status":"published","publication_identifier":{"issn":["1758-678X","1758-6798"]},"year":"2011","date_published":"2011-07-24T00:00:00Z","publisher":"Springer Nature","author":[{"orcid":"0000-0001-5836-5350","full_name":"Muller, Caroline J","first_name":"Caroline J","last_name":"Muller","id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b"},{"first_name":"P. A.","last_name":"O’Gorman","full_name":"O’Gorman, P. A."}],"article_type":"original","quality_controlled":"1","page":"266-271","article_processing_charge":"No","_id":"9143","language":[{"iso":"eng"}],"date_created":"2021-02-15T14:39:29Z","status":"public","extern":"1","oa_version":"None","issue":"5","volume":1},{"day":"01","intvolume":"        24","month":"06","citation":{"ieee":"C. J. Muller, P. A. O’Gorman, and L. E. Back, “Intensification of precipitation extremes with warming in a cloud-resolving model,” <i>Journal of Climate</i>, vol. 24, no. 11. American Meteorological Society, pp. 2784–2800, 2011.","chicago":"Muller, Caroline J, Paul A. O’Gorman, and Larissa E. Back. “Intensification of Precipitation Extremes with Warming in a Cloud-Resolving Model.” <i>Journal of Climate</i>. American Meteorological Society, 2011. <a href=\"https://doi.org/10.1175/2011jcli3876.1\">https://doi.org/10.1175/2011jcli3876.1</a>.","ama":"Muller CJ, O’Gorman PA, Back LE. Intensification of precipitation extremes with warming in a cloud-resolving model. <i>Journal of Climate</i>. 2011;24(11):2784-2800. doi:<a href=\"https://doi.org/10.1175/2011jcli3876.1\">10.1175/2011jcli3876.1</a>","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.","short":"C.J. Muller, P.A. O’Gorman, L.E. Back, Journal of Climate 24 (2011) 2784–2800.","apa":"Muller, C. J., O’Gorman, P. A., &#38; Back, L. E. (2011). Intensification of precipitation extremes with warming in a cloud-resolving model. <i>Journal of Climate</i>. American Meteorological Society. <a href=\"https://doi.org/10.1175/2011jcli3876.1\">https://doi.org/10.1175/2011jcli3876.1</a>","mla":"Muller, Caroline J., et al. “Intensification of Precipitation Extremes with Warming in a Cloud-Resolving Model.” <i>Journal of Climate</i>, vol. 24, no. 11, American Meteorological Society, 2011, pp. 2784–800, doi:<a href=\"https://doi.org/10.1175/2011jcli3876.1\">10.1175/2011jcli3876.1</a>."},"issue":"11","volume":24,"_id":"9144","date_created":"2021-02-15T14:39:57Z","author":[{"first_name":"Caroline J","last_name":"Muller","id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b","orcid":"0000-0001-5836-5350","full_name":"Muller, Caroline J"},{"full_name":"O’Gorman, Paul A.","first_name":"Paul A.","last_name":"O’Gorman"},{"last_name":"Back","first_name":"Larissa E.","full_name":"Back, Larissa E."}],"keyword":["Atmospheric Science"],"article_type":"original","date_updated":"2022-01-24T13:52:46Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","type":"journal_article","title":"Intensification of precipitation extremes with warming in a cloud-resolving model","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1175/2011JCLI3876.1"}],"abstract":[{"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.","lang":"eng"}],"publication":"Journal of Climate","doi":"10.1175/2011jcli3876.1","status":"public","extern":"1","oa_version":"Published Version","oa":1,"article_processing_charge":"No","language":[{"iso":"eng"}],"publisher":"American Meteorological Society","quality_controlled":"1","page":"2784-2800","publication_identifier":{"eissn":["1520-0442"],"issn":["0894-8755"]},"publication_status":"published","year":"2011","date_published":"2011-06-01T00:00:00Z"},{"language":[{"iso":"eng"}],"date_created":"2018-12-11T11:49:11Z","_id":"918","article_processing_charge":"No","volume":107,"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.","issue":"7","publist_id":"6521","oa_version":"None","extern":"1","status":"public","date_published":"2011-08-11T00:00:00Z","year":"2011","publication_status":"published","date_updated":"2021-01-12T08:21:54Z","publisher":"American Physical Society","author":[{"last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B"},{"first_name":"Jacques","last_name":"Prost","full_name":"Prost, Jacques"},{"last_name":"Joanny","first_name":"Jean","full_name":"Joanny, Jean"}],"month":"08","intvolume":"       107","title":"Instabilities of monolayered epithelia Shape and structure of villi and crypts","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"11","type":"journal_article","doi":"10.1103/PhysRevLett.107.078104","citation":{"ieee":"E. B. Hannezo, J. Prost, and J. Joanny, “Instabilities of monolayered epithelia Shape and structure of villi and crypts,” <i>Physical Review Letters</i>, vol. 107, no. 7. American Physical Society, 2011.","short":"E.B. Hannezo, J. Prost, J. Joanny, Physical Review Letters 107 (2011).","apa":"Hannezo, E. B., Prost, J., &#38; Joanny, J. (2011). Instabilities of monolayered epithelia Shape and structure of villi and crypts. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.107.078104\">https://doi.org/10.1103/PhysRevLett.107.078104</a>","mla":"Hannezo, Edouard B., et al. “Instabilities of Monolayered Epithelia Shape and Structure of Villi and Crypts.” <i>Physical Review Letters</i>, vol. 107, no. 7, American Physical Society, 2011, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.107.078104\">10.1103/PhysRevLett.107.078104</a>.","ista":"Hannezo EB, Prost J, Joanny J. 2011. Instabilities of monolayered epithelia Shape and structure of villi and crypts. Physical Review Letters. 107(7).","chicago":"Hannezo, Edouard B, Jacques Prost, and Jean Joanny. “Instabilities of Monolayered Epithelia Shape and Structure of Villi and Crypts.” <i>Physical Review Letters</i>. American Physical Society, 2011. <a href=\"https://doi.org/10.1103/PhysRevLett.107.078104\">https://doi.org/10.1103/PhysRevLett.107.078104</a>.","ama":"Hannezo EB, Prost J, Joanny J. Instabilities of monolayered epithelia Shape and structure of villi and crypts. <i>Physical Review Letters</i>. 2011;107(7). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.107.078104\">10.1103/PhysRevLett.107.078104</a>"},"publication":"Physical Review Letters","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"}]},{"publication":"Proceedings of the National Academy of Sciences of the United States of America","abstract":[{"lang":"eng","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."}],"doi":"10.1073/pnas.1010059108","citation":{"ieee":"T. Angelini, E. B. Hannezo, X. Trepatc, M. Marquez, J. Fredberg, and D. Weitz, “Glass-like dynamics of collective cell migration,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 108, no. 12. PNAS, pp. 4714–4719, 2011.","apa":"Angelini, T., Hannezo, E. B., Trepatc, X., Marquez, M., Fredberg, J., &#38; Weitz, D. (2011). Glass-like dynamics of collective cell migration. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. PNAS. <a href=\"https://doi.org/10.1073/pnas.1010059108\">https://doi.org/10.1073/pnas.1010059108</a>","mla":"Angelini, Thomas, et al. “Glass-like Dynamics of Collective Cell Migration.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 108, no. 12, PNAS, 2011, pp. 4714–19, doi:<a href=\"https://doi.org/10.1073/pnas.1010059108\">10.1073/pnas.1010059108</a>.","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.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. PNAS, 2011. <a href=\"https://doi.org/10.1073/pnas.1010059108\">https://doi.org/10.1073/pnas.1010059108</a>.","ama":"Angelini T, Hannezo EB, Trepatc X, Marquez M, Fredberg J, Weitz D. Glass-like dynamics of collective cell migration. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2011;108(12):4714-4719. doi:<a href=\"https://doi.org/10.1073/pnas.1010059108\">10.1073/pnas.1010059108</a>","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."},"type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"22","intvolume":"       108","title":"Glass-like dynamics of collective cell migration","month":"03","page":"4714 - 4719","publisher":"PNAS","author":[{"full_name":"Angelini, Thomas","last_name":"Angelini","first_name":"Thomas"},{"last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B"},{"full_name":"Trepatc, Xavier","last_name":"Trepatc","first_name":"Xavier"},{"full_name":"Marquez, Manuel","last_name":"Marquez","first_name":"Manuel"},{"first_name":"Jeffrey","last_name":"Fredberg","full_name":"Fredberg, Jeffrey"},{"last_name":"Weitz","first_name":"David","full_name":"Weitz, David"}],"quality_controlled":"1","date_published":"2011-03-22T00:00:00Z","date_updated":"2021-01-12T08:21:54Z","year":"2011","publication_status":"published","publist_id":"6522","issue":"12","volume":108,"status":"public","extern":"1","oa_version":"None","_id":"919","language":[{"iso":"eng"}],"date_created":"2018-12-11T11:49:12Z"},{"month":"10","day":"03","intvolume":"         6","citation":{"ieee":"S. Fré <i>et al.</i>, “Notch lineages and activity in intestinal stem cells determined by a new set of knock in mice,” <i>PLoS One</i>, vol. 6, no. 10. Public Library of Science, 2011.","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.” <i>PLoS One</i>. Public Library of Science, 2011. <a href=\"https://doi.org/10.1371/journal.pone.0025785\">https://doi.org/10.1371/journal.pone.0025785</a>.","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.","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. <i>PLoS One</i>. 2011;6(10). doi:<a href=\"https://doi.org/10.1371/journal.pone.0025785\">10.1371/journal.pone.0025785</a>","mla":"Fré, Silvia, et al. “Notch Lineages and Activity in Intestinal Stem Cells Determined by a New Set of Knock in Mice.” <i>PLoS One</i>, vol. 6, no. 10, e25785, Public Library of Science, 2011, doi:<a href=\"https://doi.org/10.1371/journal.pone.0025785\">10.1371/journal.pone.0025785</a>.","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).","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. <i>PLoS One</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0025785\">https://doi.org/10.1371/journal.pone.0025785</a>"},"_id":"923","date_created":"2018-12-11T11:49:13Z","issue":"10","file_date_updated":"2020-07-14T12:48:15Z","volume":6,"date_updated":"2021-01-12T08:21:56Z","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"author":[{"last_name":"Fré","first_name":"Silvia","full_name":"Fré, Silvia"},{"full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","last_name":"Hannezo","first_name":"Edouard B"},{"first_name":"Sanja","last_name":"Šale","full_name":"Šale, Sanja"},{"full_name":"Huyghe, Mathilde","first_name":"Mathilde","last_name":"Huyghe"},{"first_name":"Daniel","last_name":"Lafkas","full_name":"Lafkas, Daniel"},{"full_name":"Kissel, Holger","last_name":"Kissel","first_name":"Holger"},{"last_name":"Louvi","first_name":"Angeliki","full_name":"Louvi, Angeliki"},{"full_name":"Greve, Jeffrey","first_name":"Jeffrey","last_name":"Greve"},{"full_name":"Louvard, Daniel","first_name":"Daniel","last_name":"Louvard"},{"first_name":"Spyros","last_name":"Artavanis Tsakonas","full_name":"Artavanis Tsakonas, Spyros"}],"ddc":["570"],"file":[{"date_created":"2019-05-10T11:20:26Z","relation":"main_file","checksum":"b4e864125dfcb9fa57a9e01688838081","creator":"dernst","content_type":"application/pdf","access_level":"open_access","file_name":"2011_PLOS1_Fre.PDF","date_updated":"2020-07-14T12:48:15Z","file_id":"6401","file_size":2860615}],"type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Notch lineages and activity in intestinal stem cells determined by a new set of knock in mice","doi":"10.1371/journal.pone.0025785","publication":"PLoS One","abstract":[{"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.","lang":"eng"}],"article_number":"e25785","language":[{"iso":"eng"}],"oa":1,"publist_id":"6520","has_accepted_license":"1","extern":"1","status":"public","oa_version":"Published Version","date_published":"2011-10-03T00:00:00Z","publication_status":"published","year":"2011","publisher":"Public Library of Science","quality_controlled":"1"},{"scopus_import":"1","citation":{"ieee":"T.-F. Hsieh <i>et al.</i>, “Regulation of imprinted gene expression in Arabidopsis endosperm,” <i>Proceedings of the National Academy of Sciences</i>, vol. 108, no. 5. National Academy of Sciences, pp. 1755–1762, 2011.","mla":"Hsieh, Tzung-Fu, et al. “Regulation of Imprinted Gene Expression in Arabidopsis Endosperm.” <i>Proceedings of the National Academy of Sciences</i>, vol. 108, no. 5, National Academy of Sciences, 2011, pp. 1755–62, doi:<a href=\"https://doi.org/10.1073/pnas.1019273108\">10.1073/pnas.1019273108</a>.","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. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1019273108\">https://doi.org/10.1073/pnas.1019273108</a>","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.","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.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2011. <a href=\"https://doi.org/10.1073/pnas.1019273108\">https://doi.org/10.1073/pnas.1019273108</a>.","ama":"Hsieh T-F, Shin J, Uzawa R, et al. Regulation of imprinted gene expression in Arabidopsis endosperm. <i>Proceedings of the National Academy of Sciences</i>. 2011;108(5):1755-1762. doi:<a href=\"https://doi.org/10.1073/pnas.1019273108\">10.1073/pnas.1019273108</a>","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."},"external_id":{"pmid":["21257907"]},"pmid":1,"department":[{"_id":"DaZi"}],"month":"02","intvolume":"       108","day":"01","date_updated":"2021-12-14T08:33:49Z","author":[{"full_name":"Hsieh, Tzung-Fu","last_name":"Hsieh","first_name":"Tzung-Fu"},{"full_name":"Shin, Juhyun","last_name":"Shin","first_name":"Juhyun"},{"last_name":"Uzawa","first_name":"Rie","full_name":"Uzawa, Rie"},{"full_name":"Silva, Pedro","first_name":"Pedro","last_name":"Silva"},{"first_name":"Stephanie","last_name":"Cohen","full_name":"Cohen, Stephanie"},{"full_name":"Bauer, Matthew J.","first_name":"Matthew J.","last_name":"Bauer"},{"first_name":"Meryl","last_name":"Hashimoto","full_name":"Hashimoto, Meryl"},{"first_name":"Ryan C.","last_name":"Kirkbride","full_name":"Kirkbride, Ryan C."},{"full_name":"Harada, John J.","first_name":"John J.","last_name":"Harada"},{"first_name":"Daniel","last_name":"Zilberman","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","orcid":"0000-0002-0123-8649","full_name":"Zilberman, Daniel"},{"full_name":"Fischer, Robert L.","last_name":"Fischer","first_name":"Robert L."}],"article_type":"original","date_created":"2021-06-07T07:40:38Z","_id":"9483","volume":108,"issue":"5","doi":"10.1073/pnas.1019273108","publication":"Proceedings of the National Academy of Sciences","abstract":[{"lang":"eng","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."}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1073/pnas.1019273108"}],"title":"Regulation of imprinted gene expression in Arabidopsis endosperm","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","type":"journal_article","date_published":"2011-02-01T00:00:00Z","year":"2011","publication_status":"published","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"page":"1755-1762","quality_controlled":"1","publisher":"National Academy of Sciences","language":[{"iso":"eng"}],"article_processing_charge":"No","oa":1,"oa_version":"Published Version","status":"public","extern":"1"}]