[{"related_material":{"record":[{"id":"2957","relation":"later_version","status":"public"}]},"type":"technical_report","year":"2011","date_updated":"2023-02-23T11:05:53Z","pubrep_id":"20","day":"11","citation":{"ieee":"K. Chatterjee and M. Tracol, Decidable problems for probabilistic automata on infinite words. IST Austria, 2011.","short":"K. Chatterjee, M. Tracol, Decidable Problems for Probabilistic Automata on Infinite Words, IST Austria, 2011.","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","mla":"Chatterjee, Krishnendu, and Mathieu Tracol. Decidable Problems for Probabilistic Automata on Infinite Words. IST Austria, 2011, doi:10.15479/AT:IST-2011-0004.","ista":"Chatterjee K, Tracol M. 2011. Decidable problems for probabilistic automata on infinite words, IST Austria, 30p.","ama":"Chatterjee K, Tracol M. 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."},"file":[{"access_level":"open_access","content_type":"application/pdf","date_created":"2018-12-12T11:54:23Z","creator":"system","file_id":"5545","relation":"main_file","file_size":570827,"checksum":"f5a0f664fadc335990f5fcf138df19f1","file_name":"IST-2011-004_IST-2011-0004.pdf","date_updated":"2020-07-14T12:46:40Z"}],"doi":"10.15479/AT:IST-2011-0004","has_accepted_license":"1","month":"04","date_published":"2011-04-11T00:00:00Z","date_created":"2018-12-12T11:39:01Z","oa_version":"Published Version","_id":"5384","language":[{"iso":"eng"}],"ddc":["000","005"],"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"KrCh"}],"page":"30","publisher":"IST Austria","status":"public","title":"Decidable problems for probabilistic automata on infinite words","abstract":[{"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.","lang":"eng"}],"author":[{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","first_name":"Krishnendu"},{"first_name":"Mathieu","last_name":"Tracol","id":"3F54FA38-F248-11E8-B48F-1D18A9856A87","full_name":"Tracol, Mathieu"}],"alternative_title":["IST Austria Technical Report"],"oa":1,"file_date_updated":"2020-07-14T12:46:40Z","publication_identifier":{"issn":["2664-1690"]}},{"author":[{"id":"31E297B6-F248-11E8-B48F-1D18A9856A87","full_name":"Boker, Udi","first_name":"Udi","last_name":"Boker"},{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","first_name":"Krishnendu"},{"first_name":"Thomas A","orcid":"0000−0002−2985−7724","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A"},{"first_name":"Orna","last_name":"Kupferman","full_name":"Kupferman, Orna"}],"oa":1,"status":"public","title":"Temporal specifications with accumulative values","page":"14","publisher":"IST Austria","month":"04","date_created":"2018-12-12T11:39:02Z","date_published":"2011-04-04T00:00:00Z","has_accepted_license":"1","date_updated":"2023-02-23T11:23:41Z","citation":{"chicago":"Boker, Udi, Krishnendu Chatterjee, Thomas A Henzinger, and Orna Kupferman. Temporal Specifications with Accumulative Values. IST Austria, 2011. https://doi.org/10.15479/AT:IST-2011-0003.","ista":"Boker U, Chatterjee K, Henzinger TA, Kupferman O. 2011. Temporal specifications with accumulative values, IST Austria, 14p.","ama":"Boker U, Chatterjee K, Henzinger TA, Kupferman O. Temporal Specifications with Accumulative Values. IST Austria; 2011. doi:10.15479/AT:IST-2011-0003","mla":"Boker, Udi, et al. Temporal Specifications with Accumulative Values. IST Austria, 2011, doi:10.15479/AT:IST-2011-0003.","apa":"Boker, U., Chatterjee, K., Henzinger, T. A., & Kupferman, O. (2011). Temporal specifications with accumulative values. IST Austria. https://doi.org/10.15479/AT:IST-2011-0003","short":"U. Boker, K. Chatterjee, T.A. Henzinger, O. Kupferman, Temporal Specifications with Accumulative Values, IST Austria, 2011.","ieee":"U. Boker, K. Chatterjee, T. A. Henzinger, and O. Kupferman, Temporal specifications with accumulative values. IST Austria, 2011."},"day":"04","file":[{"file_name":"IST-2011-0003_IST-2011-0003.pdf","date_updated":"2020-07-14T12:46:41Z","checksum":"8491d0d48c4911620ecd5350b413c11e","date_created":"2018-12-12T11:53:00Z","file_id":"5461","creator":"system","relation":"main_file","file_size":366281,"access_level":"open_access","content_type":"application/pdf"}],"related_material":{"record":[{"status":"public","relation":"later_version","id":"2038"},{"relation":"later_version","id":"3356","status":"public"}]},"alternative_title":["IST Austria Technical Report"],"file_date_updated":"2020-07-14T12:46:41Z","publication_identifier":{"issn":["2664-1690"]},"ec_funded":1,"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."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"project":[{"call_identifier":"FWF","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering"},{"name":"COMponent-Based Embedded Systems design Techniques","_id":"25EFB36C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"215543"},{"name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"267989"},{"_id":"25F1337C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"214373","name":"Design for Embedded Systems"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"language":[{"iso":"eng"}],"_id":"5385","publication_status":"published","ddc":["000","004"],"oa_version":"Published Version","doi":"10.15479/AT:IST-2011-0003","pubrep_id":"21","year":"2011","type":"technical_report"},{"pubrep_id":"22","date_updated":"2023-02-23T11:22:48Z","file":[{"date_updated":"2020-07-14T12:46:41Z","file_name":"IST-2011-0002_IST-2011-0002.pdf","checksum":"ad64c2add5fe2ad10e9d5c669f3f9526","file_size":26390601,"relation":"main_file","creator":"system","file_id":"5495","date_created":"2018-12-12T11:53:34Z","content_type":"application/pdf","access_level":"open_access"}],"citation":{"ieee":"C. Chen, D. Freedman, and C. Lampert, Enforcing topological constraints in random field image segmentation. IST Austria, 2011.","apa":"Chen, C., Freedman, D., & Lampert, C. (2011). Enforcing topological constraints in random field image segmentation. IST Austria. https://doi.org/10.15479/AT:IST-2011-0002","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. Enforcing Topological Constraints in Random Field Image Segmentation. IST Austria, 2011. https://doi.org/10.15479/AT:IST-2011-0002.","mla":"Chen, Chao, et al. Enforcing Topological Constraints in Random Field Image Segmentation. IST Austria, 2011, doi:10.15479/AT:IST-2011-0002.","ama":"Chen C, Freedman D, Lampert C. Enforcing Topological Constraints in Random Field Image Segmentation. IST Austria; 2011. doi:10.15479/AT:IST-2011-0002","ista":"Chen C, Freedman D, Lampert C. 2011. Enforcing topological constraints in random field image segmentation, IST Austria, 69p."},"day":"28","related_material":{"record":[{"id":"3336","relation":"later_version","status":"public"}]},"year":"2011","type":"technical_report","month":"03","oa_version":"Published Version","date_created":"2018-12-12T11:39:02Z","date_published":"2011-03-28T00:00:00Z","doi":"10.15479/AT:IST-2011-0002","has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"ChLa"}],"publisher":"IST Austria","page":"69","publication_status":"published","ddc":["000"],"language":[{"iso":"eng"}],"_id":"5386","alternative_title":["IST Austria Technical Report"],"author":[{"id":"3E92416E-F248-11E8-B48F-1D18A9856A87","full_name":"Chen, Chao","last_name":"Chen","first_name":"Chao"},{"full_name":"Freedman, Daniel","first_name":"Daniel","last_name":"Freedman"},{"id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","full_name":"Lampert, Christoph","first_name":"Christoph","orcid":"0000-0001-8622-7887","last_name":"Lampert"}],"publication_identifier":{"issn":["2664-1690"]},"oa":1,"file_date_updated":"2020-07-14T12:46:41Z","status":"public","abstract":[{"lang":"eng","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."}],"title":"Enforcing topological constraints in random field image segmentation"},{"status":"public","title":"Energy and mean-payoff parity Markov decision processes","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."}],"author":[{"orcid":"0000-0002-4561-241X","last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Laurent","last_name":"Doyen","full_name":"Doyen, Laurent"}],"alternative_title":["IST Austria Technical Report"],"publication_identifier":{"issn":["2664-1690"]},"oa":1,"file_date_updated":"2020-07-14T12:46:41Z","ddc":["000","005"],"publication_status":"published","_id":"5387","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"KrCh"}],"publisher":"IST Austria","page":"20","doi":"10.15479/AT:IST-2011-0001","has_accepted_license":"1","month":"02","oa_version":"Published Version","date_created":"2018-12-12T11:39:02Z","date_published":"2011-02-16T00:00:00Z","related_material":{"record":[{"status":"public","id":"3345","relation":"later_version"}]},"year":"2011","type":"technical_report","pubrep_id":"23","date_updated":"2023-02-23T11:23:11Z","file":[{"file_name":"IST-2011-0001_IST-2011-0001.pdf","date_updated":"2020-07-14T12:46:41Z","checksum":"824d6c70e6d3feb3e836b009e0b3cf73","date_created":"2018-12-12T11:52:57Z","file_size":329976,"relation":"main_file","file_id":"5458","creator":"system","access_level":"open_access","content_type":"application/pdf"}],"day":"16","citation":{"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","short":"K. Chatterjee, L. Doyen, Energy and Mean-Payoff Parity Markov Decision Processes, IST Austria, 2011.","mla":"Chatterjee, Krishnendu, and Laurent Doyen. Energy and Mean-Payoff Parity Markov Decision Processes. IST Austria, 2011, doi:10.15479/AT:IST-2011-0001.","ista":"Chatterjee K, Doyen L. 2011. Energy and mean-payoff parity Markov decision processes, IST Austria, 20p.","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."}},{"quality_controlled":"1","page":"20672-20677","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3251049/"}],"publisher":"National Academy of Sciences","publication":"Proceedings of the National Academy of Sciences","intvolume":" 108","issue":"51","oa":1,"author":[{"last_name":"Milward","first_name":"K.","full_name":"Milward, K."},{"full_name":"Busch, K. E.","first_name":"K. E.","last_name":"Busch"},{"full_name":"Murphy, R. J.","first_name":"R. J.","last_name":"Murphy"},{"full_name":"de Bono, Mario","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8347-0443","last_name":"de Bono","first_name":"Mario"},{"last_name":"Olofsson","first_name":"B.","full_name":"Olofsson, B."}],"title":"Neuronal and molecular substrates for optimal foraging in Caenorhabditis elegans","status":"public","citation":{"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","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,” Proceedings of the National Academy of Sciences, vol. 108, no. 51. National Academy of Sciences, pp. 20672–20677, 2011.","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","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.” Proceedings of the National Academy of Sciences, vol. 108, no. 51, National Academy of Sciences, 2011, pp. 20672–77, doi:10.1073/pnas.1106134109.","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."},"day":"20","date_updated":"2021-01-12T08:06:18Z","date_published":"2011-12-20T00:00:00Z","date_created":"2019-03-20T14:30:06Z","month":"12","volume":108,"external_id":{"pmid":["22135454"]},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"_id":"6137","publication_status":"published","publication_identifier":{"issn":["0027-8424","1091-6490"]},"abstract":[{"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.","lang":"eng"}],"extern":"1","type":"journal_article","year":"2011","oa_version":"Submitted Version","pmid":1,"doi":"10.1073/pnas.1106134109"},{"date_published":"2011-03-24T00:00:00Z","date_created":"2019-03-20T15:01:41Z","month":"03","has_accepted_license":"1","volume":69,"file":[{"content_type":"application/pdf","access_level":"open_access","file_size":2448332,"file_id":"6139","relation":"main_file","creator":"kschuh","date_created":"2019-03-20T15:06:32Z","checksum":"547cffd123f4c508ae927c9244b8f92a","date_updated":"2020-07-14T12:47:20Z","file_name":"2011_Cell_Bretscher.pdf"}],"day":"24","citation":{"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.","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.","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.","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","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."},"date_updated":"2021-01-12T08:06:18Z","oa":1,"author":[{"last_name":"Bretscher","first_name":"Andrew Jonathan","full_name":"Bretscher, Andrew Jonathan"},{"last_name":"Kodama-Namba","first_name":"Eiji","full_name":"Kodama-Namba, Eiji"},{"full_name":"Busch, Karl Emanuel","last_name":"Busch","first_name":"Karl Emanuel"},{"full_name":"Murphy, Robin Joseph","first_name":"Robin Joseph","last_name":"Murphy"},{"full_name":"Soltesz, Zoltan","last_name":"Soltesz","first_name":"Zoltan"},{"last_name":"Laurent","first_name":"Patrick","full_name":"Laurent, Patrick"},{"last_name":"de Bono","orcid":"0000-0001-8347-0443","first_name":"Mario","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","full_name":"de Bono, Mario"}],"title":"Temperature, oxygen, and salt-sensing neurons in C. elegans are carbon dioxide sensors that control avoidance behavior","status":"public","publisher":"Elsevier BV","page":"1099-1113","quality_controlled":"1","intvolume":" 69","publication":"Neuron","issue":"6","oa_version":"Published Version","pmid":1,"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.1016/j.neuron.2011.02.023","year":"2011","type":"journal_article","publication_identifier":{"issn":["0896-6273"]},"file_date_updated":"2020-07-14T12:47:20Z","extern":"1","external_id":{"pmid":["21435556"]},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"publication_status":"published","language":[{"iso":"eng"}],"_id":"6138"},{"file_date_updated":"2020-07-14T12:47:20Z","publication_identifier":{"issn":["1553-7404"]},"abstract":[{"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.","lang":"eng"}],"extern":"1","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","external_id":{"pmid":["21437263"]},"_id":"6140","language":[{"iso":"eng"}],"ddc":["570"],"publication_status":"published","pmid":1,"oa_version":"Published Version","doi":"10.1371/journal.pgen.1001341","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"year":"2011","type":"journal_article","author":[{"full_name":"Arellano-Carbajal, Fausto","first_name":"Fausto","last_name":"Arellano-Carbajal"},{"first_name":"Luis","last_name":"Briseño-Roa","full_name":"Briseño-Roa, Luis"},{"first_name":"Africa","last_name":"Couto","full_name":"Couto, Africa"},{"full_name":"Cheung, Benny H. H.","last_name":"Cheung","first_name":"Benny H. H."},{"full_name":"Labouesse, Michel","last_name":"Labouesse","first_name":"Michel"},{"orcid":"0000-0001-8347-0443","last_name":"de Bono","first_name":"Mario","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","full_name":"de Bono, Mario"}],"oa":1,"status":"public","title":"Macoilin, a conserved nervous system–specific ER membrane protein that regulates neuronal excitability","article_number":"e1001341","publication":"PLoS Genetics","intvolume":" 7","quality_controlled":"1","publisher":"Public Library of Science","issue":"3","month":"03","date_published":"2011-03-17T00:00:00Z","date_created":"2019-03-20T15:08:23Z","volume":7,"has_accepted_license":"1","date_updated":"2021-01-12T08:06:19Z","day":"17","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.","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","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.","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.","short":"F. Arellano-Carbajal, L. Briseño-Roa, A. Couto, B.H.H. Cheung, M. Labouesse, M. de Bono, PLoS Genetics 7 (2011).","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."},"file":[{"relation":"main_file","creator":"kschuh","file_id":"6141","file_size":5625063,"date_created":"2019-03-20T15:18:11Z","content_type":"application/pdf","access_level":"open_access","date_updated":"2020-07-14T12:47:20Z","file_name":"2011_PLOS_Arellano-Carbajal.PDF","checksum":"c609b2ce616d7dafbb617ec5d022f1ea"}]},{"date_updated":"2021-01-12T08:06:58Z","citation":{"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.","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.","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.","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","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.","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."},"day":"22","type":"journal_article","year":"2011","month":"07","oa_version":"Published Version","date_published":"2011-07-22T00:00:00Z","date_created":"2019-04-11T20:57:43Z","volume":286,"doi":"10.1074/jbc.m111.247395","intvolume":" 286","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"Journal of Biological Chemistry","publisher":"American Society for Biochemistry & Molecular Biology","page":"25675-25686","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"http://www.jbc.org/content/286/29/25675.full.pdf"}],"publication_status":"published","_id":"6298","language":[{"iso":"eng"}],"issue":"29","author":[{"first_name":"Natalia","orcid":"0000-0002-3086-9124","last_name":"Baranova","id":"38661662-F248-11E8-B48F-1D18A9856A87","full_name":"Baranova, Natalia"},{"first_name":"Erik","last_name":"Nilebäck","full_name":"Nilebäck, Erik"},{"full_name":"Haller, F. Michael","first_name":"F. Michael","last_name":"Haller"},{"full_name":"Briggs, David C.","first_name":"David C.","last_name":"Briggs"},{"first_name":"Sofia","last_name":"Svedhem","full_name":"Svedhem, Sofia"},{"first_name":"Anthony J.","last_name":"Day","full_name":"Day, Anthony J."},{"first_name":"Ralf P.","last_name":"Richter","full_name":"Richter, Ralf P."}],"publication_identifier":{"issn":["0021-9258","1083-351X"]},"oa":1,"status":"public","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)."}],"title":"The inflammation-associated protein TSG-6 cross-links hyaluronan via hyaluronan-induced TSG-6 oligomers"},{"department":[{"_id":"CaGu"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"pmid":["22098731"]},"publication_status":"published","language":[{"iso":"eng"}],"_id":"6496","article_processing_charge":"No","publication_identifier":{"issn":["0006-3495"]},"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"}],"scopus_import":"1","type":"journal_article","year":"2011","pmid":1,"oa_version":"Published Version","doi":"10.1016/j.bpj.2011.09.040","intvolume":" 101","publication":"Biophysical Journal","publisher":"Elsevier","quality_controlled":"1","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3218319/","open_access":"1"}],"page":"2336-2340","issue":"10","author":[{"last_name":"Park","first_name":"Heungwon","full_name":"Park, Heungwon"},{"full_name":"Oikonomou, Panos","last_name":"Oikonomou","first_name":"Panos"},{"orcid":"0000-0001-6220-2052","last_name":"Guet","first_name":"Calin C","full_name":"Guet, Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Cluzel, Philippe","last_name":"Cluzel","first_name":"Philippe"}],"oa":1,"status":"public","title":"Noise underlies switching behavior of the bacterial flagellum","date_updated":"2021-04-16T11:54:49Z","citation":{"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.","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. Biophysical Journal. 2011;101(10):2336-2340. doi:10.1016/j.bpj.2011.09.040","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.","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","short":"H. Park, P. Oikonomou, C.C. Guet, P. Cluzel, Biophysical Journal 101 (2011) 2336–2340.","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."},"day":"16","month":"11","date_published":"2011-11-16T00:00:00Z","date_created":"2019-05-28T11:54:29Z","volume":101},{"publist_id":"5728","doi":"10.1215/00127094-1444258","volume":160,"date_published":"2011-01-01T00:00:00Z","date_created":"2018-12-11T11:52:11Z","month":"01","type":"journal_article","year":"2011","citation":{"ama":"Hausel T, Letellier E, Rodríguez Villegas F. Arithmetic harmonic analysis on character and quiver varieties. Duke Mathematical Journal. 2011;160(2):323-400. doi:10.1215/00127094-1444258","ista":"Hausel T, Letellier E, Rodríguez Villegas F. 2011. Arithmetic harmonic analysis on character and quiver varieties. Duke Mathematical Journal. 160(2), 323–400.","mla":"Hausel, Tamás, et al. “Arithmetic Harmonic Analysis on Character and Quiver Varieties.” Duke Mathematical Journal, vol. 160, no. 2, Duke University Press, 2011, pp. 323–400, doi:10.1215/00127094-1444258.","chicago":"Hausel, Tamás, Emmanuel Letellier, and Fernando Rodríguez Villegas. “Arithmetic Harmonic Analysis on Character and Quiver Varieties.” Duke Mathematical Journal. Duke University Press, 2011. https://doi.org/10.1215/00127094-1444258.","short":"T. Hausel, E. Letellier, F. Rodríguez Villegas, Duke Mathematical Journal 160 (2011) 323–400.","apa":"Hausel, T., Letellier, E., & Rodríguez Villegas, F. (2011). Arithmetic harmonic analysis on character and quiver varieties. Duke Mathematical Journal. Duke University Press. https://doi.org/10.1215/00127094-1444258","ieee":"T. Hausel, E. Letellier, and F. Rodríguez Villegas, “Arithmetic harmonic analysis on character and quiver varieties,” Duke Mathematical Journal, vol. 160, no. 2. Duke University Press, pp. 323–400, 2011."},"day":"01","date_updated":"2021-01-12T06:50:56Z","abstract":[{"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).","lang":"eng"}],"title":"Arithmetic harmonic analysis on character and quiver varieties","extern":1,"status":"public","oa":1,"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.","author":[{"id":"4A0666D8-F248-11E8-B48F-1D18A9856A87","full_name":"Tamas Hausel","first_name":"Tamas","last_name":"Hausel"},{"first_name":"Emmanuel","last_name":"Letellier","full_name":"Letellier, Emmanuel"},{"first_name":"Fernando","last_name":"Rodríguez Villegas","full_name":"Rodríguez Villegas, Fernando"}],"issue":"2","_id":"1467","publication_status":"published","page":"323 - 400","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/0810.2076"}],"quality_controlled":0,"publisher":"Duke University Press","publication":"Duke Mathematical Journal","intvolume":" 160"},{"status":"public","title":"Mapping backbone and side-chain interactions in the transition state of a coupled protein folding and binding reaction","author":[{"last_name":"Bachmann","first_name":"Annett","full_name":"Bachmann, Annett"},{"full_name":"Wildemann, Dirk","last_name":"Wildemann","first_name":"Dirk"},{"first_name":"Florian M","last_name":"Praetorius","id":"dfec9381-4341-11ee-8fd8-faa02bba7d62","full_name":"Praetorius, Florian M"},{"last_name":"Fischer","first_name":"Gunter","full_name":"Fischer, Gunter"},{"last_name":"Kiefhaber","first_name":"Thomas","full_name":"Kiefhaber, Thomas"}],"oa":1,"issue":"10","intvolume":" 108","publication":"PNAS","publisher":"Proceedings of the National Academy of Sciences","page":"3952-3957","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1073/pnas.1012668108"}],"keyword":["Multidisciplinary"],"article_type":"original","volume":108,"month":"01","date_published":"2011-01-12T00:00:00Z","date_created":"2023-09-06T12:54:36Z","date_updated":"2023-11-07T11:50:29Z","citation":{"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.","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.","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","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.","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.","short":"A. Bachmann, D. Wildemann, F.M. Praetorius, G. Fischer, T. Kiefhaber, PNAS 108 (2011) 3952–3957.","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"},"day":"12","extern":"1","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."}],"article_processing_charge":"No","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"publication_status":"published","_id":"14305","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"pmid":["21325613"]},"doi":"10.1073/pnas.1012668108","pmid":1,"oa_version":"Published Version","scopus_import":"1","year":"2011","type":"journal_article"},{"_id":"9144","language":[{"iso":"eng"}],"publication_status":"published","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","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."}],"extern":"1","publication_identifier":{"issn":["0894-8755"],"eissn":["1520-0442"]},"article_processing_charge":"No","year":"2011","type":"journal_article","doi":"10.1175/2011jcli3876.1","oa_version":"Published Version","issue":"11","page":"2784-2800","keyword":["Atmospheric Science"],"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1175/2011JCLI3876.1"}],"publisher":"American Meteorological Society","publication":"Journal of Climate","intvolume":" 24","title":"Intensification of precipitation extremes with warming in a cloud-resolving model","status":"public","oa":1,"author":[{"id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b","full_name":"Muller, Caroline J","first_name":"Caroline J","orcid":"0000-0001-5836-5350","last_name":"Muller"},{"full_name":"O’Gorman, Paul A.","last_name":"O’Gorman","first_name":"Paul A."},{"full_name":"Back, Larissa E.","last_name":"Back","first_name":"Larissa E."}],"day":"01","citation":{"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","short":"C.J. Muller, P.A. O’Gorman, L.E. Back, Journal of Climate 24 (2011) 2784–2800.","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.","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.","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.","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","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."},"date_updated":"2022-01-24T13:52:46Z","volume":24,"article_type":"original","date_published":"2011-06-01T00:00:00Z","date_created":"2021-02-15T14:39:57Z","month":"06"},{"file_date_updated":"2020-07-14T12:48:15Z","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"}],"extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"923","language":[{"iso":"eng"}],"ddc":["570"],"publication_status":"published","oa_version":"Published Version","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.1371/journal.pone.0025785","publist_id":"6520","type":"journal_article","year":"2011","oa":1,"author":[{"first_name":"Silvia","last_name":"Fré","full_name":"Fré, Silvia"},{"first_name":"Edouard B","last_name":"Hannezo","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","full_name":"Hannezo, Edouard B"},{"first_name":"Sanja","last_name":"Šale","full_name":"Šale, Sanja"},{"full_name":"Huyghe, Mathilde","first_name":"Mathilde","last_name":"Huyghe"},{"full_name":"Lafkas, Daniel","first_name":"Daniel","last_name":"Lafkas"},{"first_name":"Holger","last_name":"Kissel","full_name":"Kissel, Holger"},{"last_name":"Louvi","first_name":"Angeliki","full_name":"Louvi, Angeliki"},{"first_name":"Jeffrey","last_name":"Greve","full_name":"Greve, Jeffrey"},{"last_name":"Louvard","first_name":"Daniel","full_name":"Louvard, Daniel"},{"full_name":"Artavanis Tsakonas, Spyros","first_name":"Spyros","last_name":"Artavanis Tsakonas"}],"title":"Notch lineages and activity in intestinal stem cells determined by a new set of knock in mice","article_number":"e25785","status":"public","quality_controlled":"1","publisher":"Public Library of Science","publication":"PLoS One","intvolume":" 6","issue":"10","date_created":"2018-12-11T11:49:13Z","date_published":"2011-10-03T00:00:00Z","month":"10","has_accepted_license":"1","volume":6,"citation":{"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.","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.","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. PLoS One. 2011;6(10). doi: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.","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","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)."},"day":"03","file":[{"date_created":"2019-05-10T11:20:26Z","file_size":2860615,"relation":"main_file","creator":"dernst","file_id":"6401","access_level":"open_access","content_type":"application/pdf","file_name":"2011_PLOS1_Fre.PDF","date_updated":"2020-07-14T12:48:15Z","checksum":"b4e864125dfcb9fa57a9e01688838081"}],"date_updated":"2021-01-12T08:21:56Z"},{"issue":"5","quality_controlled":"1","page":"1755-1762","main_file_link":[{"url":"https://doi.org/10.1073/pnas.1019273108","open_access":"1"}],"publisher":"National Academy of Sciences","publication":"Proceedings of the National Academy of Sciences","intvolume":" 108","title":"Regulation of imprinted gene expression in Arabidopsis endosperm","status":"public","oa":1,"author":[{"full_name":"Hsieh, Tzung-Fu","first_name":"Tzung-Fu","last_name":"Hsieh"},{"full_name":"Shin, Juhyun","first_name":"Juhyun","last_name":"Shin"},{"full_name":"Uzawa, Rie","last_name":"Uzawa","first_name":"Rie"},{"first_name":"Pedro","last_name":"Silva","full_name":"Silva, Pedro"},{"last_name":"Cohen","first_name":"Stephanie","full_name":"Cohen, Stephanie"},{"first_name":"Matthew J.","last_name":"Bauer","full_name":"Bauer, Matthew J."},{"last_name":"Hashimoto","first_name":"Meryl","full_name":"Hashimoto, Meryl"},{"last_name":"Kirkbride","first_name":"Ryan C.","full_name":"Kirkbride, Ryan C."},{"first_name":"John J.","last_name":"Harada","full_name":"Harada, John J."},{"last_name":"Zilberman","orcid":"0000-0002-0123-8649","first_name":"Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","full_name":"Zilberman, Daniel"},{"full_name":"Fischer, Robert L.","first_name":"Robert L.","last_name":"Fischer"}],"citation":{"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.","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.","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.","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.","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.","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"},"day":"01","date_updated":"2021-12-14T08:33:49Z","volume":108,"article_type":"original","date_published":"2011-02-01T00:00:00Z","date_created":"2021-06-07T07:40:38Z","month":"02","language":[{"iso":"eng"}],"_id":"9483","publication_status":"published","external_id":{"pmid":["21257907"]},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","department":[{"_id":"DaZi"}],"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."}],"extern":"1","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"article_processing_charge":"No","year":"2011","type":"journal_article","scopus_import":"1","doi":"10.1073/pnas.1019273108","oa_version":"Published Version","pmid":1},{"day":"14","citation":{"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","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.","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.","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","ieee":"D. Zilberman, Balancing parental contributions in plant embryonic gene activation, vol. 20, no. 6. Elsevier, 2011, pp. 735–736."},"date_updated":"2021-12-14T08:34:37Z","date_created":"2021-06-08T06:23:39Z","date_published":"2011-06-14T00:00:00Z","month":"06","volume":20,"publisher":"Elsevier","quality_controlled":"1","page":"735-736","main_file_link":[{"url":"https://doi.org/10.1016/j.devcel.2011.05.018","open_access":"1"}],"intvolume":" 20","publication":"Developmental Cell","issue":"6","oa":1,"author":[{"full_name":"Zilberman, Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","first_name":"Daniel","last_name":"Zilberman","orcid":"0000-0002-0123-8649"}],"title":"Balancing parental contributions in plant embryonic gene activation","status":"public","year":"2011","type":"other_academic_publication","oa_version":"Published Version","pmid":1,"doi":"10.1016/j.devcel.2011.05.018","external_id":{"pmid":["21664571"]},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","department":[{"_id":"DaZi"}],"publication_status":"published","_id":"9522","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1878-1551"],"issn":["1534-5807"]},"article_processing_charge":"No","extern":"1","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"}]},{"month":"08","date_published":"2011-08-01T00:00:00Z","date_created":"2021-07-11T22:01:19Z","volume":6854,"date_updated":"2021-08-12T13:53:17Z","day":"01","citation":{"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.","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","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.","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.","short":"R. Gonzalez-Diaz, A. Ion, M.J. Jimenez, R. Poyatos, in:, Computer Analysis of Images and Patterns, Springer Nature, 2011, pp. 286–293.","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."},"conference":{"name":"CAIP: International Conference on Computer Analysis of Images and Patterns","location":"Seville, Spain","start_date":"2011-08-29","end_date":"2011-08-31"},"author":[{"first_name":"Rocio","last_name":"Gonzalez-Diaz","full_name":"Gonzalez-Diaz, Rocio"},{"full_name":"Ion, Adrian","id":"29F89302-F248-11E8-B48F-1D18A9856A87","last_name":"Ion","first_name":"Adrian"},{"full_name":"Jimenez, Maria Jose","last_name":"Jimenez","first_name":"Maria Jose"},{"first_name":"Regina","last_name":"Poyatos","full_name":"Poyatos, Regina"}],"oa":1,"status":"public","title":"Incremental-decremental algorithm for computing AT-models and persistent homology","intvolume":" 6854","publication":"Computer Analysis of Images and Patterns","publisher":"Springer Nature","page":"286-293","quality_controlled":"1","main_file_link":[{"url":"http://hdl.handle.net/11441/30766","open_access":"1"}],"oa_version":"Published Version","doi":"10.1007/978-3-642-23672-3_35","scopus_import":"1","year":"2011","type":"conference","article_processing_charge":"No","alternative_title":["LNCS"],"publication_identifier":{"issn":["03029743"],"isbn":["9783642236716"],"eissn":["16113349"]},"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."}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","department":[{"_id":"HeEd"}],"publication_status":"published","_id":"9648","language":[{"iso":"eng"}]},{"publisher":"American Physical Society","quality_controlled":0,"main_file_link":[{"url":"https://arxiv.org/abs/1108.3070","open_access":"1"}],"intvolume":" 84","publication":"Physical Review B - Condensed Matter and Materials Physics","issue":"18","publication_status":"published","_id":"967","oa":1,"author":[{"full_name":"Maksym Serbyn","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","first_name":"Maksym","last_name":"Serbyn","orcid":"0000-0002-2399-5827"},{"full_name":"Senthil, Todadri S","last_name":"Senthil","first_name":"Todadri"},{"full_name":"Lee, Patrick","first_name":"Patrick","last_name":"Lee"}],"extern":1,"title":"Exotic S=1 spin-liquid state with fermionic excitations on the triangular lattice","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."}],"status":"public","citation":{"short":"M. Serbyn, T. Senthil, P. Lee, Physical Review B - Condensed Matter and Materials Physics 84 (2011).","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","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).","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.","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."},"day":"03","date_updated":"2021-01-12T08:22:18Z","year":"2011","type":"journal_article","date_published":"2011-11-03T00:00:00Z","date_created":"2018-12-11T11:49:27Z","month":"11","volume":84,"publist_id":"6432","doi":"10.1103/PhysRevB.84.180403"},{"citation":{"ieee":"A. Šarić and A. Cacciuto, “Soft elastic surfaces as a platform for particle self-assembly,” Soft Matter, vol. 7, no. 18. Royal Society of Chemistry, 2011.","apa":"Šarić, A., & Cacciuto, A. (2011). Soft elastic surfaces as a platform for particle self-assembly. Soft Matter. Royal Society of Chemistry. https://doi.org/10.1039/c1sm05773a","short":"A. Šarić, A. Cacciuto, Soft Matter 7 (2011).","mla":"Šarić, Anđela, and Angelo Cacciuto. “Soft Elastic Surfaces as a Platform for Particle Self-Assembly.” Soft Matter, vol. 7, no. 18, 8324, Royal Society of Chemistry, 2011, doi:10.1039/c1sm05773a.","ama":"Šarić A, Cacciuto A. Soft elastic surfaces as a platform for particle self-assembly. Soft Matter. 2011;7(18). doi:10.1039/c1sm05773a","ista":"Šarić A, Cacciuto A. 2011. Soft elastic surfaces as a platform for particle self-assembly. Soft Matter. 7(18), 8324.","chicago":"Šarić, Anđela, and Angelo Cacciuto. “Soft Elastic Surfaces as a Platform for Particle Self-Assembly.” Soft Matter. Royal Society of Chemistry, 2011. https://doi.org/10.1039/c1sm05773a."},"day":"08","date_updated":"2021-11-29T15:12:10Z","date_created":"2021-11-29T14:33:18Z","date_published":"2011-08-08T00:00:00Z","month":"08","article_type":"original","volume":7,"main_file_link":[{"url":"https://arxiv.org/abs/1106.2995","open_access":"1"}],"keyword":["condensed matter physics","general chemistry"],"quality_controlled":"1","publisher":"Royal Society of Chemistry","publication":"Soft Matter","intvolume":" 7","issue":"18","oa":1,"author":[{"first_name":"Anđela","last_name":"Šarić","orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b"},{"first_name":"Angelo","last_name":"Cacciuto","full_name":"Cacciuto, Angelo"}],"title":"Soft elastic surfaces as a platform for particle self-assembly","article_number":"8324","status":"public","type":"journal_article","year":"2011","arxiv":1,"scopus_import":"1","oa_version":"Preprint","doi":"10.1039/c1sm05773a","external_id":{"arxiv":["1106.2995"]},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"10389","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["1744-683X"],"eissn":["1744-6848"]},"article_processing_charge":"No","acknowledgement":"This work was supported by the National Science Foundation under Career Grant No. DMR-0846426. We thank Josep C. Pàmies and William L. Miller for helpful discussions.","abstract":[{"text":"We perform numerical simulations to study self-assembly of nanoparticles mediated by an elastic planar surface. We show how the nontrivial elastic response to deformations of these surfaces leads to anisotropic interactions between the particles resulting in aggregates having different geometrical features. The morphology of the patterns can be controlled by the mechanical properties of the surface and the strength of the particle adhesion. We use simple scaling arguments to understand the formation of the different structures, and we show how the adhering particles can cause the underlying elastic substrate to wrinkle if two of its opposite edges are clamped. Finally, we discuss the implications of our results and suggest how elastic surfaces could be used in nanofabrication.","lang":"eng"}],"extern":"1"},{"publisher":"IOP Publishing Ltd.","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1011.0179"}],"intvolume":" 264","publication":"Journal of Physics: Conference Series","issue":"1","oa":1,"author":[{"first_name":"Hanns","last_name":"Nägerl","full_name":"Nägerl, Hanns"},{"last_name":"Mark","first_name":"Manfred","full_name":"Mark, Manfred"},{"last_name":"Haller","first_name":"Elmar","full_name":"Haller, Elmar"},{"last_name":"Gustavsson","first_name":"Mattias","full_name":"Gustavsson, Mattias"},{"full_name":"Hart, Russell","last_name":"Hart","first_name":"Russell"},{"last_name":"Danzl","orcid":"0000-0001-8559-3973","first_name":"Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","full_name":"Danzl, Johann G"}],"title":"Ultracold and dense samples of ground-state molecules in lattice potentials","status":"public","day":"01","citation":{"mla":"Nägerl, Hanns, et al. “Ultracold and Dense Samples of Ground-State Molecules in Lattice Potentials.” Journal of Physics: Conference Series, vol. 264, no. 1, IOP Publishing Ltd., 2011, doi:10.1088/1742-6596/264/1/012015.","ista":"Nägerl H, Mark M, Haller E, Gustavsson M, Hart R, Danzl JG. 2011. Ultracold and dense samples of ground-state molecules in lattice potentials. Journal of Physics: Conference Series. 264(1).","ama":"Nägerl H, Mark M, Haller E, Gustavsson M, Hart R, Danzl JG. Ultracold and dense samples of ground-state molecules in lattice potentials. Journal of Physics: Conference Series. 2011;264(1). doi:10.1088/1742-6596/264/1/012015","chicago":"Nägerl, Hanns, Manfred Mark, Elmar Haller, Mattias Gustavsson, Russell Hart, and Johann G Danzl. “Ultracold and Dense Samples of Ground-State Molecules in Lattice Potentials.” Journal of Physics: Conference Series. IOP Publishing Ltd., 2011. https://doi.org/10.1088/1742-6596/264/1/012015.","ieee":"H. Nägerl, M. Mark, E. Haller, M. Gustavsson, R. Hart, and J. G. Danzl, “Ultracold and dense samples of ground-state molecules in lattice potentials,” Journal of Physics: Conference Series, vol. 264, no. 1. IOP Publishing Ltd., 2011.","short":"H. Nägerl, M. Mark, E. Haller, M. Gustavsson, R. Hart, J.G. Danzl, Journal of Physics: Conference Series 264 (2011).","apa":"Nägerl, H., Mark, M., Haller, E., Gustavsson, M., Hart, R., & Danzl, J. G. (2011). Ultracold and dense samples of ground-state molecules in lattice potentials. Journal of Physics: Conference Series. IOP Publishing Ltd. https://doi.org/10.1088/1742-6596/264/1/012015"},"date_updated":"2021-01-12T06:47:54Z","date_created":"2018-12-11T11:49:52Z","date_published":"2011-01-01T00:00:00Z","month":"01","volume":264,"external_id":{"arxiv":["1011.0179"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","_id":"1048","language":[{"iso":"eng"}],"article_processing_charge":"No","acknowledgement":"We thank H. Ritsch, N. Bouloufa, O. Dulieu, J. Aldegunde, J. M. Hutson, H. Salami, T. Bergeman, S. D ̈urr, and K. Bergmann for valuable discussions and H. Telle, H. Schnatz, B. Lipphardt, and J. Alnis for sharing technical expertise. We are indebted to R. Grimm for generous support. We gratefully acknowledge funding by the Austrian Ministry of Science and\r\nResearch (Bundesministerium f ̈ur Wissenschaft und Forschung) and the Austrian Science Fund\r\n(Fonds zur F ̈orderung der wissenschaftlichen Forschung) in the form of a START prize grant\r\nand by the European Science Foundation within the framework of the EuroQUASAR collective\r\nresearch project QuDeGPM (Project I 153-N16) and within the framework of the EuroQUAM\r\ncollective research project QuDipMol (Project I 124-N16). R.H. was supported by a Marie Curie\r\nInternational Incoming Fellowship within the 7th European Community Framework Programme","extern":"1","abstract":[{"text":"We produce an ultracold and dense sample of rovibronic ground state Cs 2 molecules close to the regime of quantum degeneracy, in a single hyperfine level, in the presence of an optical lattice. The molecules are individually trapped, in the motional ground state of an optical lattice well, with a lifetime of 8 s. For preparation, we start with a zero-temperature atomic Mott-insulator state with optimized double-site occupancy and efficiently associate weakly-bound dimer molecules on a Feshbach resonance. Despite extremely weak Franck-Condon wavefunction overlap, the molecules are subsequently transferred with >50% efficiency to the rovibronic ground state by a stimulated four-photon process. Our results present a crucial step towards the generation of Bose-Einstein condensates of ground-state molecules and, when suitably generalized to polar heteronuclear molecules such as RbCs, the realization of dipolar many-body quantum-gas phases in periodic potentials.","lang":"eng"}],"year":"2011","type":"journal_article","arxiv":1,"oa_version":"Preprint","doi":"10.1088/1742-6596/264/1/012015","publist_id":"6340"},{"volume":83,"month":"03","date_created":"2018-12-11T11:49:53Z","date_published":"2011-03-28T00:00:00Z","date_updated":"2021-01-12T06:47:55Z","citation":{"mla":"Bai, Jianmei, et al. “Global Analysis of Data on the Spin-Orbit-Coupled A 1Σu+ and b 3Πu Inf States of Cs2.” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 83, no. 3, American Physical Society, 2011, doi:10.1103/PhysRevA.83.032514.","ama":"Bai J, Ahmed E, Beser B, et al. Global analysis of data on the spin-orbit-coupled A 1Σu+ and b 3Πu inf states of Cs2. Physical Review A - Atomic, Molecular, and Optical Physics. 2011;83(3). doi:10.1103/PhysRevA.83.032514","ista":"Bai J, Ahmed E, Beser B, Guan Y, Kotochigova S, Lyyra M, Ashman S, Wolfe C, Huennekens J, Xie F, Li D, Li L, Tamanis M, Ferber R, Drozdova A, Pazyuk E, Stolyarov A, Danzl JG, Nägerl H, Bouloufa N, Dulieu O, Amiot C, Salami H, Bergeman T. 2011. Global analysis of data on the spin-orbit-coupled A 1Σu+ and b 3Πu inf states of Cs2. Physical Review A - Atomic, Molecular, and Optical Physics. 83(3).","chicago":"Bai, Jianmei, Ergin Ahmed, Bediha Beser, Yafei Guan, Svetlana Kotochigova, Marjatta Lyyra, Seth Ashman, et al. “Global Analysis of Data on the Spin-Orbit-Coupled A 1Σu+ and b 3Πu Inf States of Cs2.” Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society, 2011. https://doi.org/10.1103/PhysRevA.83.032514.","ieee":"J. Bai et al., “Global analysis of data on the spin-orbit-coupled A 1Σu+ and b 3Πu inf states of Cs2,” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 83, no. 3. American Physical Society, 2011.","short":"J. Bai, E. Ahmed, B. Beser, Y. Guan, S. Kotochigova, M. Lyyra, S. Ashman, C. Wolfe, J. Huennekens, F. Xie, D. Li, L. Li, M. Tamanis, R. Ferber, A. Drozdova, E. Pazyuk, A. Stolyarov, J.G. Danzl, H. Nägerl, N. Bouloufa, O. Dulieu, C. Amiot, H. Salami, T. Bergeman, Physical Review A - Atomic, Molecular, and Optical Physics 83 (2011).","apa":"Bai, J., Ahmed, E., Beser, B., Guan, Y., Kotochigova, S., Lyyra, M., … Bergeman, T. (2011). Global analysis of data on the spin-orbit-coupled A 1Σu+ and b 3Πu inf states of Cs2. Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society. https://doi.org/10.1103/PhysRevA.83.032514"},"day":"28","status":"public","title":"Global analysis of data on the spin-orbit-coupled A 1Σu+ and b 3Πu inf states of Cs2","author":[{"first_name":"Jianmei","last_name":"Bai","full_name":"Bai, Jianmei"},{"last_name":"Ahmed","first_name":"Ergin","full_name":"Ahmed, Ergin"},{"full_name":"Beser, Bediha","last_name":"Beser","first_name":"Bediha"},{"full_name":"Guan, Yafei","first_name":"Yafei","last_name":"Guan"},{"full_name":"Kotochigova, Svetlana","first_name":"Svetlana","last_name":"Kotochigova"},{"first_name":"Marjatta","last_name":"Lyyra","full_name":"Lyyra, Marjatta"},{"full_name":"Ashman, Seth","first_name":"Seth","last_name":"Ashman"},{"full_name":"Wolfe, Christopher","first_name":"Christopher","last_name":"Wolfe"},{"last_name":"Huennekens","first_name":"John","full_name":"Huennekens, John"},{"last_name":"Xie","first_name":"Feng","full_name":"Xie, Feng"},{"first_name":"Dan","last_name":"Li","full_name":"Li, Dan"},{"last_name":"Li","first_name":"Li","full_name":"Li, Li"},{"full_name":"Tamanis, Maris","first_name":"Maris","last_name":"Tamanis"},{"first_name":"Ruvin","last_name":"Ferber","full_name":"Ferber, Ruvin"},{"first_name":"Anastasia","last_name":"Drozdova","full_name":"Drozdova, Anastasia"},{"full_name":"Pazyuk, Elena","last_name":"Pazyuk","first_name":"Elena"},{"first_name":"Andrey","last_name":"Stolyarov","full_name":"Stolyarov, Andrey"},{"full_name":"Danzl, Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","first_name":"Johann G","orcid":"0000-0001-8559-3973","last_name":"Danzl"},{"last_name":"Nägerl","first_name":"Hanns","full_name":"Nägerl, Hanns"},{"first_name":"Nadia","last_name":"Bouloufa","full_name":"Bouloufa, Nadia"},{"last_name":"Dulieu","first_name":"Olivier","full_name":"Dulieu, Olivier"},{"full_name":"Amiot, Claude","last_name":"Amiot","first_name":"Claude"},{"first_name":"Houssam","last_name":"Salami","full_name":"Salami, Houssam"},{"first_name":"Thomas","last_name":"Bergeman","full_name":"Bergeman, Thomas"}],"oa":1,"issue":"3","intvolume":" 83","publication":" Physical Review A - Atomic, Molecular, and Optical Physics","publisher":"American Physical Society","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1101.5412"}],"publist_id":"6339","doi":"10.1103/PhysRevA.83.032514","oa_version":"Preprint","type":"journal_article","year":"2011","arxiv":1,"extern":"1","abstract":[{"lang":"eng","text":"We present experimentally derived potential curves 1?and spin-orbit interaction functions for the strongly perturbed AΣu+ 3?and bΠu states of the cesium dimer. The results are based on data from several sources. Laser-induced fluorescence Fourier transform spectroscopy (LIF FTS) was used some time ago in the Laboratoire Aimé Cotton primarily to study the XΣg+ state. More recent work at Tsinghua University provides information from moderate 3?resolution spectroscopy on the lowest levels of the bΠ0u± state as well as additional high-resolution data. From Innsbruck University, we have precision data obtained with cold Cs2 molecules. Recent data from Temple University was obtained using the optical-optical double resonance polarization spectroscopy technique, and finally, a group at the University of Latvia has added additional LIF FTS data. In the Hamiltonian matrix, we have used analytic potentials (the expanded Morse oscillator form) with both finite-difference (FD) coupled-channel and discrete variable representation (DVR) calculations of the term values. Fitted diagonal and off-diagonal spin-orbit functions are obtained and compared with ab initio results from Temple and Moscow State universities."}],"acknowledgement":"The work in Temple University was supported by NSF grant no. PHY-0855502. S.K. acknowledges support from AFOSR and from NSF grant no. PHY-1005453. S.A., C.M., and J.H. were supported by NSF grants no. PHY-0652938 and PHY-0968898. The work at Stony Brook was supported by NSF grants no. PHY-0652459 and PHY-0968905. The work in Tsinghua University was supported by NSFC of China, under grant no. 20773072. The Moscow team thanks the Russian Foundation for Basic Researches by the grant no. 10-03-00195 and MSU Priority Direction 2.3. M.T. and R.F. are grateful to Ilze Klincare, Olga Nikolayeva, and Artis Kruzins for their help in spectra analysis, as well as appreciate the support from the ESF 2009/0223/1DP/1.1.1.2.0/09/APIA/VIAA/008 project.","article_processing_charge":"No","publication_status":"published","_id":"1050","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"arxiv":["1101.5412"]}}]