[{"date_created":"2018-12-12T11:38:59Z","doi":"10.15479/AT:IST-2012-0001","page":"21","_id":"5378","department":[{"_id":"KrCh"}],"publisher":"IST Austria","file":[{"file_id":"5489","date_created":"2018-12-12T11:53:28Z","creator":"system","relation":"main_file","checksum":"ec8d1857cc7095d3de5107a0162ced37","date_updated":"2020-07-14T12:46:39Z","content_type":"application/pdf","file_name":"IST-2012-0001_IST-2012-0001.pdf","file_size":394256,"access_level":"open_access"}],"citation":{"ista":"Chatterjee K, Chaubal S, Kamath P. 2012. Faster algorithms for alternating refinement relations, IST Austria, 21p.","ieee":"K. Chatterjee, S. Chaubal, and P. Kamath, <i>Faster algorithms for alternating refinement relations</i>. IST Austria, 2012.","apa":"Chatterjee, K., Chaubal, S., &#38; Kamath, P. (2012). <i>Faster algorithms for alternating refinement relations</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2012-0001\">https://doi.org/10.15479/AT:IST-2012-0001</a>","mla":"Chatterjee, Krishnendu, et al. <i>Faster Algorithms for Alternating Refinement Relations</i>. IST Austria, 2012, doi:<a href=\"https://doi.org/10.15479/AT:IST-2012-0001\">10.15479/AT:IST-2012-0001</a>.","ama":"Chatterjee K, Chaubal S, Kamath P. <i>Faster Algorithms for Alternating Refinement Relations</i>. IST Austria; 2012. doi:<a href=\"https://doi.org/10.15479/AT:IST-2012-0001\">10.15479/AT:IST-2012-0001</a>","short":"K. Chatterjee, S. Chaubal, P. Kamath, Faster Algorithms for Alternating Refinement Relations, IST Austria, 2012.","chicago":"Chatterjee, Krishnendu, Siddhesh Chaubal, and Pritish Kamath. <i>Faster Algorithms for Alternating Refinement Relations</i>. IST Austria, 2012. <a href=\"https://doi.org/10.15479/AT:IST-2012-0001\">https://doi.org/10.15479/AT:IST-2012-0001</a>."},"title":"Faster algorithms for alternating refinement relations","status":"public","type":"technical_report","pubrep_id":"14","month":"07","oa_version":"Published Version","day":"04","related_material":{"record":[{"id":"497","relation":"later_version","status":"public"}]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"year":"2012","publication_status":"published","oa":1,"ddc":["000","005"],"date_updated":"2023-02-23T12:21:38Z","publication_identifier":{"issn":["2664-1690"]},"file_date_updated":"2020-07-14T12:46:39Z","has_accepted_license":"1","alternative_title":["IST Austria Technical Report"],"author":[{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee"},{"last_name":"Chaubal","first_name":"Siddhesh","full_name":"Chaubal, Siddhesh"},{"full_name":"Kamath, Pritish","first_name":"Pritish","last_name":"Kamath"}],"abstract":[{"lang":"eng","text":"One central issue in the formal design and analysis of reactive systems is the notion of refinement that asks whether all behaviors of the implementation is allowed by the specification. The local interpretation of behavior leads to the notion of simulation. Alternating transition systems (ATSs) provide a general model for composite reactive systems, and the simulation relation for ATSs is known as alternating simulation. The simulation relation for fair transition systems is called fair simulation. In this work our main contributions are as follows: (1) We present an improved algorithm for fair simulation with Büchi fairness constraints; our algorithm requires O(n3 · m) time as compared to the previous known O(n6)-time algorithm, where n is the number of states and m is the number of transitions. (2) We present a game based algorithm for alternating simulation that requires O(m2)-time as compared to the previous known O((n · m)2)-time algorithm, where n is the number of states and m is the size of transition relation. (3) We present an iterative algorithm for alternating simulation that matches the time complexity of the game based algorithm, but is more space efficient than the game based algorithm."}],"date_published":"2012-07-04T00:00:00Z"},{"month":"07","oa_version":"Published Version","year":"2012","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"23","related_material":{"record":[{"status":"public","relation":"earlier_version","id":"3124"}]},"oa":1,"publication_status":"published","publication_identifier":{"issn":["2664-1690"]},"ddc":["000"],"date_updated":"2023-02-23T11:13:22Z","has_accepted_license":"1","file_date_updated":"2020-07-14T12:46:44Z","alternative_title":["IST Austria Technical Report"],"author":[{"id":"476A2FD6-F248-11E8-B48F-1D18A9856A87","full_name":"Korc, Filip","last_name":"Korc","first_name":"Filip"},{"last_name":"Kolmogorov","first_name":"Vladimir","full_name":"Kolmogorov, Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Lampert, Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887","last_name":"Lampert","first_name":"Christoph"}],"date_published":"2012-07-23T00:00:00Z","abstract":[{"lang":"eng","text":"We consider the problem of inference in agraphical model with binary variables. While in theory it is arguably preferable to compute marginal probabilities, in practice researchers often use MAP inference due to the availability of efficient discrete optimization algorithms. We bridge the gap between the two approaches by introducing the Discrete  Marginals technique in which approximate marginals are obtained by minimizing an objective function with unary and pair-wise terms over a discretized domain. This allows the use of techniques originally devel-oped for MAP-MRF inference and learning. We explore two ways to set up the objective function - by discretizing the Bethe free energy and by learning it  from training data. Experimental results show that for certain types of graphs a learned function can out-perform the  Bethe approximation. We also establish a link between the Bethe free energy and submodular functions."}],"doi":"10.15479/AT:IST-2012-0003","date_created":"2018-12-12T11:39:06Z","_id":"5396","page":"13","department":[{"_id":"VlKo"},{"_id":"ChLa"}],"citation":{"ista":"Korc F, Kolmogorov V, Lampert C. 2012. Approximating marginals using discrete energy minimization, IST Austria, 13p.","ieee":"F. Korc, V. Kolmogorov, and C. Lampert, <i>Approximating marginals using discrete energy minimization</i>. IST Austria, 2012.","mla":"Korc, Filip, et al. <i>Approximating Marginals Using Discrete Energy Minimization</i>. IST Austria, 2012, doi:<a href=\"https://doi.org/10.15479/AT:IST-2012-0003\">10.15479/AT:IST-2012-0003</a>.","apa":"Korc, F., Kolmogorov, V., &#38; Lampert, C. (2012). <i>Approximating marginals using discrete energy minimization</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2012-0003\">https://doi.org/10.15479/AT:IST-2012-0003</a>","short":"F. Korc, V. Kolmogorov, C. Lampert, Approximating Marginals Using Discrete Energy Minimization, IST Austria, 2012.","ama":"Korc F, Kolmogorov V, Lampert C. <i>Approximating Marginals Using Discrete Energy Minimization</i>. IST Austria; 2012. doi:<a href=\"https://doi.org/10.15479/AT:IST-2012-0003\">10.15479/AT:IST-2012-0003</a>","chicago":"Korc, Filip, Vladimir Kolmogorov, and Christoph Lampert. <i>Approximating Marginals Using Discrete Energy Minimization</i>. IST Austria, 2012. <a href=\"https://doi.org/10.15479/AT:IST-2012-0003\">https://doi.org/10.15479/AT:IST-2012-0003</a>."},"file":[{"file_size":618744,"access_level":"open_access","file_name":"IST-2012-0003_IST-2012-0003.pdf","content_type":"application/pdf","date_updated":"2020-07-14T12:46:44Z","relation":"main_file","checksum":"7e0ba85ad123b13223aaf6cdde2d288c","creator":"system","date_created":"2018-12-12T11:53:29Z","file_id":"5490"}],"publisher":"IST Austria","title":"Approximating marginals using discrete energy minimization","pubrep_id":"36","type":"technical_report","status":"public"},{"_id":"5398","date_created":"2018-12-12T11:39:06Z","department":[{"_id":"E-Lib"}],"publisher":"IST Austria","file":[{"access_level":"open_access","file_size":238544,"file_name":"IST-2012-103-v1+1_Actual_state_of_research_data_@_IST_Austria.pdf","content_type":"application/pdf","date_updated":"2020-07-14T12:46:44Z","relation":"main_file","checksum":"e0a7c041eea1ca4b70ab6f9ec5177f4e","date_created":"2018-12-12T11:53:11Z","creator":"system","file_id":"5472"}],"citation":{"mla":"Porsche, Jana. <i>Actual State of Research Data @ ISTAustria</i>. IST Austria, 2012.","apa":"Porsche, J. (2012). <i>Actual state of research data @ ISTAustria</i>. IST Austria.","ama":"Porsche J. <i>Actual State of Research Data @ ISTAustria</i>. IST Austria; 2012.","chicago":"Porsche, Jana. <i>Actual State of Research Data @ ISTAustria</i>. IST Austria, 2012.","short":"J. Porsche, Actual State of Research Data @ ISTAustria, IST Austria, 2012.","ista":"Porsche J. 2012. Actual state of research data @ ISTAustria, IST Austria,p.","ieee":"J. Porsche, <i>Actual state of research data @ ISTAustria</i>. IST Austria, 2012."},"type":"report","status":"public","pubrep_id":"103","title":"Actual state of research data @ ISTAustria","day":"12","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2012","language":[{"iso":"eng"}],"month":"11","oa_version":"Published Version","date_updated":"2020-07-14T23:04:49Z","ddc":["020"],"publication_status":"published","oa":1,"has_accepted_license":"1","file_date_updated":"2020-07-14T12:46:44Z","abstract":[{"text":"This document is created as a part of the project “Repository for Research Data on IST Austria”. It summarises the actual state of research data at IST Austria, based on survey results. It supports the choice of appropriate software, which would best fit the requirements of their users, the researchers.","lang":"eng"}],"date_published":"2012-11-12T00:00:00Z","author":[{"first_name":"Jana","last_name":"Porsche","id":"3252EDC2-F248-11E8-B48F-1D18A9856A87","full_name":"Porsche, Jana"}]},{"project":[{"name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"267989"}],"date_created":"2018-12-18T13:01:46Z","publisher":"Springer Berlin Heidelberg","file":[{"content_type":"application/pdf","date_updated":"2020-07-14T12:47:10Z","file_size":465502,"access_level":"open_access","file_name":"2012_ATVA_Gupta.pdf","file_id":"5746","checksum":"68415837a315de3cc4d120f6019d752c","relation":"main_file","date_created":"2018-12-18T13:07:35Z","creator":"dernst"}],"series_title":"LNCS","language":[{"iso":"eng"}],"year":"2012","publication":"Automated Technology for Verification and Analysis","ec_funded":1,"file_date_updated":"2020-07-14T12:47:10Z","volume":7561,"date_published":"2012-01-01T00:00:00Z","author":[{"first_name":"Ashutosh","last_name":"Gupta","full_name":"Gupta, Ashutosh"}],"page":"107-121","_id":"5745","intvolume":"      7561","doi":"10.1007/978-3-642-33386-6_10","department":[{"_id":"ToHe"}],"place":"Berlin, Heidelberg","quality_controlled":"1","article_processing_charge":"No","citation":{"ista":"Gupta A. 2012.Improved Single Pass Algorithms for Resolution Proof Reduction. In: Automated Technology for Verification and Analysis. vol. 7561, 107–121.","ieee":"A. Gupta, “Improved Single Pass Algorithms for Resolution Proof Reduction,” in <i>Automated Technology for Verification and Analysis</i>, vol. 7561, Berlin, Heidelberg: Springer Berlin Heidelberg, 2012, pp. 107–121.","ama":"Gupta A. Improved Single Pass Algorithms for Resolution Proof Reduction. In: <i>Automated Technology for Verification and Analysis</i>. Vol 7561. LNCS. Berlin, Heidelberg: Springer Berlin Heidelberg; 2012:107-121. doi:<a href=\"https://doi.org/10.1007/978-3-642-33386-6_10\">10.1007/978-3-642-33386-6_10</a>","short":"A. Gupta, in:, Automated Technology for Verification and Analysis, Springer Berlin Heidelberg, Berlin, Heidelberg, 2012, pp. 107–121.","chicago":"Gupta, Ashutosh. “Improved Single Pass Algorithms for Resolution Proof Reduction.” In <i>Automated Technology for Verification and Analysis</i>, 7561:107–21. LNCS. Berlin, Heidelberg: Springer Berlin Heidelberg, 2012. <a href=\"https://doi.org/10.1007/978-3-642-33386-6_10\">https://doi.org/10.1007/978-3-642-33386-6_10</a>.","apa":"Gupta, A. (2012). Improved Single Pass Algorithms for Resolution Proof Reduction. In <i>Automated Technology for Verification and Analysis</i> (Vol. 7561, pp. 107–121). Berlin, Heidelberg: Springer Berlin Heidelberg. <a href=\"https://doi.org/10.1007/978-3-642-33386-6_10\">https://doi.org/10.1007/978-3-642-33386-6_10</a>","mla":"Gupta, Ashutosh. “Improved Single Pass Algorithms for Resolution Proof Reduction.” <i>Automated Technology for Verification and Analysis</i>, vol. 7561, Springer Berlin Heidelberg, 2012, pp. 107–21, doi:<a href=\"https://doi.org/10.1007/978-3-642-33386-6_10\">10.1007/978-3-642-33386-6_10</a>."},"type":"book_chapter","status":"public","pubrep_id":"180","title":"Improved Single Pass Algorithms for Resolution Proof Reduction","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"None","date_updated":"2023-09-05T14:15:29Z","ddc":["005"],"publication_identifier":{"isbn":["9783642333859","9783642333866"],"eissn":["1611-3349"],"issn":["0302-9743"]},"publication_status":"published","oa":1,"conference":{"location":"Thiruvananthapuram, Kerala, India","end_date":"2012-10-06","start_date":"2012-10-03","name":"ATVA 2012"},"has_accepted_license":"1"},{"date_published":"2012-05-01T00:00:00Z","volume":4,"abstract":[{"lang":"eng","text":"Canny's edge detection algorithm is a classical and robust method for edge detection in gray-scale images. The two \r\nsignificant features of this method are introduction of NMS (Non-Maximum Suppression) and double thresholding of \r\nthe  gradient  image.  Due  to  poor  illumination,  the  region  boundaries  in  an  image  may  become  vague,  creating  \r\nuncertainties  in  the  gradient  image.  In  this  paper,  we  have  proposed  an  algorithm  based  on  the  concept  of  type-2  fuzzy  sets  to  handle  uncertainties  that  automatically  selects  the  threshold  values  needed  to  segment  the  gradient image using classical Canny’s edge detection algorithm. The results show that our algorithm works significantly well on different benchmark images as well as medical images (hand radiography images). "}],"author":[{"full_name":"Biswas, Ranita","id":"3C2B033E-F248-11E8-B48F-1D18A9856A87","first_name":"Ranita","last_name":"Biswas","orcid":"0000-0002-5372-7890"},{"full_name":"Sil, Jaya","last_name":"Sil","first_name":"Jaya"}],"file_date_updated":"2020-07-14T12:47:12Z","language":[{"iso":"eng"}],"year":"2012","day":"01","publication":"Procedia Technology","file":[{"file_id":"5863","creator":"dernst","date_created":"2019-01-21T07:28:06Z","relation":"main_file","checksum":"ba0185986b151d8c11201f48cd505ceb","date_updated":"2020-07-14T12:47:12Z","content_type":"application/pdf","file_name":"2012_Procedia_Biswas.pdf","access_level":"open_access","file_size":305426}],"publisher":"Elsevier","date_created":"2019-01-17T11:54:21Z","has_accepted_license":"1","publication_identifier":{"issn":["2212-0173"]},"ddc":["000"],"date_updated":"2021-01-12T08:03:43Z","oa":1,"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"05","oa_version":"Published Version","type":"journal_article","status":"public","tmp":{"short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"title":"An Improved Canny Edge Detection Algorithm Based on Type-2 Fuzzy Sets","citation":{"ieee":"R. Biswas and J. Sil, “An Improved Canny Edge Detection Algorithm Based on Type-2 Fuzzy Sets,” <i>Procedia Technology</i>, vol. 4. Elsevier, pp. 820–824, 2012.","ista":"Biswas R, Sil J. 2012. An Improved Canny Edge Detection Algorithm Based on Type-2 Fuzzy Sets. Procedia Technology. 4, 820–824.","apa":"Biswas, R., &#38; Sil, J. (2012). An Improved Canny Edge Detection Algorithm Based on Type-2 Fuzzy Sets. <i>Procedia Technology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.protcy.2012.05.134\">https://doi.org/10.1016/j.protcy.2012.05.134</a>","mla":"Biswas, Ranita, and Jaya Sil. “An Improved Canny Edge Detection Algorithm Based on Type-2 Fuzzy Sets.” <i>Procedia Technology</i>, vol. 4, Elsevier, 2012, pp. 820–24, doi:<a href=\"https://doi.org/10.1016/j.protcy.2012.05.134\">10.1016/j.protcy.2012.05.134</a>.","chicago":"Biswas, Ranita, and Jaya Sil. “An Improved Canny Edge Detection Algorithm Based on Type-2 Fuzzy Sets.” <i>Procedia Technology</i>. Elsevier, 2012. <a href=\"https://doi.org/10.1016/j.protcy.2012.05.134\">https://doi.org/10.1016/j.protcy.2012.05.134</a>.","ama":"Biswas R, Sil J. An Improved Canny Edge Detection Algorithm Based on Type-2 Fuzzy Sets. <i>Procedia Technology</i>. 2012;4:820-824. doi:<a href=\"https://doi.org/10.1016/j.protcy.2012.05.134\">10.1016/j.protcy.2012.05.134</a>","short":"R. Biswas, J. Sil, Procedia Technology 4 (2012) 820–824."},"extern":"1","quality_controlled":"1","intvolume":"         4","page":"820-824","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","_id":"5839","doi":"10.1016/j.protcy.2012.05.134"},{"title":"Activator-mediator binding stabilizes RNA polymerase II orientation within the human mediator-RNA polymerase II-TFIIF assembly","type":"journal_article","status":"public","publisher":"Elsevier","article_processing_charge":"No","citation":{"mla":"Bernecky, Carrie, and Dylan Taatjes. “Activator-Mediator Binding Stabilizes RNA Polymerase II Orientation within the Human Mediator-RNA Polymerase II-TFIIF Assembly.” <i>Journal of Molecular Biology</i>, vol. 417, no. 5, Elsevier, 2012, pp. 387–94, doi:<a href=\"https://doi.org/10.1016/j.jmb.2012.02.014\">10.1016/j.jmb.2012.02.014</a>.","apa":"Bernecky, C., &#38; Taatjes, D. (2012). Activator-mediator binding stabilizes RNA polymerase II orientation within the human mediator-RNA polymerase II-TFIIF assembly. <i>Journal of Molecular Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jmb.2012.02.014\">https://doi.org/10.1016/j.jmb.2012.02.014</a>","short":"C. Bernecky, D. Taatjes, Journal of Molecular Biology 417 (2012) 387–394.","ama":"Bernecky C, Taatjes D. Activator-mediator binding stabilizes RNA polymerase II orientation within the human mediator-RNA polymerase II-TFIIF assembly. <i>Journal of Molecular Biology</i>. 2012;417(5):387-394. doi:<a href=\"https://doi.org/10.1016/j.jmb.2012.02.014\">10.1016/j.jmb.2012.02.014</a>","chicago":"Bernecky, Carrie, and Dylan Taatjes. “Activator-Mediator Binding Stabilizes RNA Polymerase II Orientation within the Human Mediator-RNA Polymerase II-TFIIF Assembly.” <i>Journal of Molecular Biology</i>. Elsevier, 2012. <a href=\"https://doi.org/10.1016/j.jmb.2012.02.014\">https://doi.org/10.1016/j.jmb.2012.02.014</a>.","ieee":"C. Bernecky and D. Taatjes, “Activator-mediator binding stabilizes RNA polymerase II orientation within the human mediator-RNA polymerase II-TFIIF assembly,” <i>Journal of Molecular Biology</i>, vol. 417, no. 5. Elsevier, pp. 387–394, 2012.","ista":"Bernecky C, Taatjes D. 2012. Activator-mediator binding stabilizes RNA polymerase II orientation within the human mediator-RNA polymerase II-TFIIF assembly. Journal of Molecular Biology. 417(5), 387–394."},"extern":"1","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4582759/","open_access":"1"}],"date_created":"2018-12-11T11:47:24Z","doi":"10.1016/j.jmb.2012.02.014","page":"387 - 394","_id":"596","intvolume":"       417","author":[{"full_name":"Bernecky, Carrie A","id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0893-7036","first_name":"Carrie A","last_name":"Bernecky"},{"last_name":"Taatjes","first_name":"Dylan","full_name":"Taatjes, Dylan"}],"volume":417,"abstract":[{"lang":"eng","text":"The human Mediator complex controls RNA polymerase II (pol II) function in ways that remain incompletely understood. Activator-Mediator binding alters Mediator structure, and these activator-induced structural shifts appear to play key roles in regulating transcription. A recent cryo-electron microscopy (EM) analysis revealed that pol II adopted a stable orientation within a Mediator-pol II-TFIIF assembly in which Mediator was bound to the activation domain of viral protein 16 (VP16). Whereas TFIIF was shown to be important for orienting pol II within this assembly, the potential role of the activator was not assessed. To determine how activator binding might affect pol II orientation, we isolated human Mediator-pol II-TFIIF complexes in which Mediator was not bound to an activator. Cryo-EM analysis of this assembly, coupled with pol II crystal structure docking, revealed that pol II binds Mediator at the same general location; however, in contrast to VP16-bound Mediator, pol II does not appear to stably orient in the absence of an activator. Variability in pol II orientation might be important mechanistically, perhaps to enable sense and antisense transcription at human promoters. Because Mediator interacts extensively with pol II, these results suggest that Mediator structural shifts induced by activator binding help stably orient pol II prior to transcription initiation."}],"date_published":"2012-04-13T00:00:00Z","issue":"5","oa":1,"publication_status":"published","date_updated":"2021-01-12T08:05:21Z","publication":"Journal of Molecular Biology","oa_version":"None","month":"04","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"13","publist_id":"7208","language":[{"iso":"eng"}],"year":"2012"},{"publication":"Nature Neuroscience","language":[{"iso":"eng"}],"year":"2012","day":"04","author":[{"first_name":"Karl Emanuel","last_name":"Busch","full_name":"Busch, Karl Emanuel"},{"last_name":"Laurent","first_name":"Patrick","full_name":"Laurent, Patrick"},{"last_name":"Soltesz","first_name":"Zoltan","full_name":"Soltesz, Zoltan"},{"first_name":"Robin Joseph","last_name":"Murphy","full_name":"Murphy, Robin Joseph"},{"first_name":"Olivier","last_name":"Faivre","full_name":"Faivre, Olivier"},{"full_name":"Hedwig, Berthold","first_name":"Berthold","last_name":"Hedwig"},{"first_name":"Martin","last_name":"Thomas","full_name":"Thomas, Martin"},{"full_name":"Smith, Heather L","last_name":"Smith","first_name":"Heather L"},{"orcid":"0000-0001-8347-0443","first_name":"Mario","last_name":"de Bono","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","full_name":"de Bono, Mario"}],"date_published":"2012-03-04T00:00:00Z","abstract":[{"lang":"eng","text":"Tonic receptors convey stimulus duration and intensity and are implicated in homeostatic control. However, how tonic homeostatic signals are generated and how they reconfigure neural circuits and modify animal behavior is poorly understood. Here we show that Caenorhabditis elegans O2-sensing neurons are tonic receptors that continuously signal ambient [O2] to set the animal's behavioral state. Sustained signaling relied on a Ca2+ relay involving L-type voltage-gated Ca2+ channels, the ryanodine and the inositol-1,4,5-trisphosphate receptors. Tonic activity evoked continuous neuropeptide release, which helps elicit the enduring behavioral state associated with high [O2]. Sustained O2 receptor signaling was propagated to downstream neural circuits, including the hub interneuron RMG. O2 receptors evoked similar locomotory states at particular O2 concentrations, regardless of previous d[O2]/dt. However, a phasic component of the URX receptors' response to high d[O2]/dt, as well as tonic-to-phasic transformations in downstream interneurons, enabled transient reorientation movements shaped by d[O2]/dt. Our results highlight how tonic homeostatic signals can generate both transient and enduring behavioral change."}],"volume":15,"issue":"4","date_created":"2019-03-20T14:23:30Z","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3564487/","open_access":"1"}],"pmid":1,"publisher":"Springer Nature","oa":1,"publication_status":"published","publication_identifier":{"issn":["1097-6256","1546-1726"]},"date_updated":"2021-01-12T08:06:17Z","month":"03","oa_version":"Submitted Version","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","external_id":{"pmid":["22388961"]},"doi":"10.1038/nn.3061","intvolume":"        15","_id":"6136","page":"581-591","title":"Tonic signaling from O2 sensors sets neural circuit activity and behavioral state","type":"journal_article","status":"public","extern":"1","citation":{"mla":"Busch, Karl Emanuel, et al. “Tonic Signaling from O2 Sensors Sets Neural Circuit Activity and Behavioral State.” <i>Nature Neuroscience</i>, vol. 15, no. 4, Springer Nature, 2012, pp. 581–91, doi:<a href=\"https://doi.org/10.1038/nn.3061\">10.1038/nn.3061</a>.","apa":"Busch, K. E., Laurent, P., Soltesz, Z., Murphy, R. J., Faivre, O., Hedwig, B., … de Bono, M. (2012). Tonic signaling from O2 sensors sets neural circuit activity and behavioral state. <i>Nature Neuroscience</i>. Springer Nature. <a href=\"https://doi.org/10.1038/nn.3061\">https://doi.org/10.1038/nn.3061</a>","chicago":"Busch, Karl Emanuel, Patrick Laurent, Zoltan Soltesz, Robin Joseph Murphy, Olivier Faivre, Berthold Hedwig, Martin Thomas, Heather L Smith, and Mario de Bono. “Tonic Signaling from O2 Sensors Sets Neural Circuit Activity and Behavioral State.” <i>Nature Neuroscience</i>. Springer Nature, 2012. <a href=\"https://doi.org/10.1038/nn.3061\">https://doi.org/10.1038/nn.3061</a>.","short":"K.E. Busch, P. Laurent, Z. Soltesz, R.J. Murphy, O. Faivre, B. Hedwig, M. Thomas, H.L. Smith, M. de Bono, Nature Neuroscience 15 (2012) 581–591.","ama":"Busch KE, Laurent P, Soltesz Z, et al. Tonic signaling from O2 sensors sets neural circuit activity and behavioral state. <i>Nature Neuroscience</i>. 2012;15(4):581-591. doi:<a href=\"https://doi.org/10.1038/nn.3061\">10.1038/nn.3061</a>","ieee":"K. E. Busch <i>et al.</i>, “Tonic signaling from O2 sensors sets neural circuit activity and behavioral state,” <i>Nature Neuroscience</i>, vol. 15, no. 4. Springer Nature, pp. 581–591, 2012.","ista":"Busch KE, Laurent P, Soltesz Z, Murphy RJ, Faivre O, Hedwig B, Thomas M, Smith HL, de Bono M. 2012. Tonic signaling from O2 sensors sets neural circuit activity and behavioral state. Nature Neuroscience. 15(4), 581–591."}},{"date_created":"2019-06-27T08:16:56Z","article_type":"original","scopus_import":"1","main_file_link":[{"url":"http://mi.mathnet.ru/eng/jmag525","open_access":"1"}],"publisher":"B. Verkin Institute for Low Temperature Physics and Engineering","year":"2012","language":[{"iso":"eng"}],"day":"01","publication":"Journal of Mathematical Physics, Analysis, Geometry","date_published":"2012-01-01T00:00:00Z","volume":8,"abstract":[{"lang":"eng","text":"First we note that the best polynomial approximation to vertical bar x vertical bar on the set, which consists of an interval on the positive half-axis and a point on the negative half-axis, can be given by means of the classical Chebyshev polynomials. Then we explore the cases when a solution of the related problem on two intervals can be given in elementary functions."}],"author":[{"orcid":"0000-0002-8379-3768","first_name":"Florian","last_name":"Pausinger","id":"2A77D7A2-F248-11E8-B48F-1D18A9856A87","full_name":"Pausinger, Florian"}],"issue":"1","department":[{"_id":"HeEd"}],"quality_controlled":"1","acknowledgement":"This work is supported by the Austrian Science Fund (FWF), Project P22025-N18.\r\n","intvolume":"         8","page":"63-78","_id":"6588","external_id":{"isi":["000301173600004"]},"type":"journal_article","status":"public","title":"Elementary solutions of the Bernstein problem on two intervals","isi":1,"article_processing_charge":"No","citation":{"ista":"Pausinger F. 2012. Elementary solutions of the Bernstein problem on two intervals. Journal of Mathematical Physics, Analysis, Geometry. 8(1), 63–78.","ieee":"F. Pausinger, “Elementary solutions of the Bernstein problem on two intervals,” <i>Journal of Mathematical Physics, Analysis, Geometry</i>, vol. 8, no. 1. B. Verkin Institute for Low Temperature Physics and Engineering, pp. 63–78, 2012.","ama":"Pausinger F. Elementary solutions of the Bernstein problem on two intervals. <i>Journal of Mathematical Physics, Analysis, Geometry</i>. 2012;8(1):63-78.","chicago":"Pausinger, Florian. “Elementary Solutions of the Bernstein Problem on Two Intervals.” <i>Journal of Mathematical Physics, Analysis, Geometry</i>. B. Verkin Institute for Low Temperature Physics and Engineering, 2012.","short":"F. Pausinger, Journal of Mathematical Physics, Analysis, Geometry 8 (2012) 63–78.","mla":"Pausinger, Florian. “Elementary Solutions of the Bernstein Problem on Two Intervals.” <i>Journal of Mathematical Physics, Analysis, Geometry</i>, vol. 8, no. 1, B. Verkin Institute for Low Temperature Physics and Engineering, 2012, pp. 63–78.","apa":"Pausinger, F. (2012). Elementary solutions of the Bernstein problem on two intervals. <i>Journal of Mathematical Physics, Analysis, Geometry</i>. B. Verkin Institute for Low Temperature Physics and Engineering."},"publication_identifier":{"issn":["1812-9471"]},"date_updated":"2023-10-16T09:41:31Z","publication_status":"published","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"01","oa_version":"Published Version"},{"status":"public","type":"journal_article","title":"Prym varieties of spectral covers","citation":{"mla":"Hausel, Tamás, and Christian Pauly. “Prym Varieties of Spectral Covers.” <i>Geometry and Topology</i>, vol. 16, no. 3, University of Warwick, 2012, pp. 1609–38, doi:<a href=\"https://doi.org/10.2140/gt.2012.16.1609\">10.2140/gt.2012.16.1609</a>.","apa":"Hausel, T., &#38; Pauly, C. (2012). Prym varieties of spectral covers. <i>Geometry and Topology</i>. University of Warwick. <a href=\"https://doi.org/10.2140/gt.2012.16.1609\">https://doi.org/10.2140/gt.2012.16.1609</a>","short":"T. Hausel, C. Pauly, Geometry and Topology 16 (2012) 1609–1638.","chicago":"Hausel, Tamás, and Christian Pauly. “Prym Varieties of Spectral Covers.” <i>Geometry and Topology</i>. University of Warwick, 2012. <a href=\"https://doi.org/10.2140/gt.2012.16.1609\">https://doi.org/10.2140/gt.2012.16.1609</a>.","ama":"Hausel T, Pauly C. Prym varieties of spectral covers. <i>Geometry and Topology</i>. 2012;16(3):1609-1638. doi:<a href=\"https://doi.org/10.2140/gt.2012.16.1609\">10.2140/gt.2012.16.1609</a>","ista":"Hausel T, Pauly C. 2012. Prym varieties of spectral covers. Geometry and Topology. 16(3), 1609–1638.","ieee":"T. Hausel and C. Pauly, “Prym varieties of spectral covers,” <i>Geometry and Topology</i>, vol. 16, no. 3. University of Warwick, pp. 1609–1638, 2012."},"extern":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1012.4748"}],"publisher":"University of Warwick","quality_controlled":0,"intvolume":"        16","_id":"1471","page":"1609 - 1638","date_created":"2018-12-11T11:52:13Z","doi":"10.2140/gt.2012.16.1609","date_published":"2012-08-01T00:00:00Z","volume":16,"abstract":[{"lang":"eng","text":"Given a possibly reducible and non-reduced spectral cover π: X → C over a smooth projective complex curve C we determine the group of connected components of the Prym variety Prym(X/C). As an immediate application we show that the finite group of n-torsion points of the Jacobian of C acts trivially on the cohomology of the twisted SL n-Higgs moduli space up to the degree which is predicted by topological mirror symmetry. In particular this yields a new proof of a result of Harder-Narasimhan, showing that this finite group acts trivially on the cohomology of the twisted SL n stable bundle moduli space."}],"author":[{"first_name":"Tamas","last_name":"Hausel","id":"4A0666D8-F248-11E8-B48F-1D18A9856A87","full_name":"Tamas Hausel"},{"last_name":"Pauly","first_name":"Christian","full_name":"Pauly, Christian"}],"issue":"3","date_updated":"2021-01-12T06:50:58Z","publication_status":"published","oa":1,"year":"2012","publist_id":"5726","day":"01","month":"08","publication":"Geometry and Topology"},{"date_published":"2012-05-01T00:00:00Z","abstract":[{"text":"For G = GL 2, PGL 2, SL 2 we prove that the perverse filtration associated with the Hitchin map on the rational cohomology of the moduli space of twisted G-Higgs bundles on a compact Riemann surface C agrees with the weight filtration on the rational cohomology of the twisted G character variety of C when the cohomologies are identified via non-Abelian Hodge theory. The proof is accomplished by means of a study of the topology of the Hitchin map over the locus of integral spectral curves.","lang":"eng"}],"volume":175,"author":[{"full_name":"De Cataldo, Mark A","last_name":"De Cataldo","first_name":"Mark"},{"id":"4A0666D8-F248-11E8-B48F-1D18A9856A87","full_name":"Tamas Hausel","last_name":"Hausel","first_name":"Tamas"},{"first_name":"Luca","last_name":"Migliorini","full_name":"Migliorini, Luca"}],"issue":"3","date_updated":"2021-01-12T06:50:59Z","publication_status":"published","oa":1,"year":"2012","day":"01","publist_id":"5727","publication":"Annals of Mathematics","month":"05","type":"journal_article","status":"public","title":"Topology of hitchin systems and Hodge theory of character varieties: The case A 1","extern":1,"citation":{"apa":"De Cataldo, M., Hausel, T., &#38; Migliorini, L. (2012). Topology of hitchin systems and Hodge theory of character varieties: The case A 1. <i>Annals of Mathematics</i>. Princeton University Press. <a href=\"https://doi.org/10.4007/annals.2012.175.3.7\">https://doi.org/10.4007/annals.2012.175.3.7</a>","mla":"De Cataldo, Mark, et al. “Topology of Hitchin Systems and Hodge Theory of Character Varieties: The Case A 1.” <i>Annals of Mathematics</i>, vol. 175, no. 3, Princeton University Press, 2012, pp. 1329–407, doi:<a href=\"https://doi.org/10.4007/annals.2012.175.3.7\">10.4007/annals.2012.175.3.7</a>.","short":"M. De Cataldo, T. Hausel, L. Migliorini, Annals of Mathematics 175 (2012) 1329–1407.","ama":"De Cataldo M, Hausel T, Migliorini L. Topology of hitchin systems and Hodge theory of character varieties: The case A 1. <i>Annals of Mathematics</i>. 2012;175(3):1329-1407. doi:<a href=\"https://doi.org/10.4007/annals.2012.175.3.7\">10.4007/annals.2012.175.3.7</a>","chicago":"De Cataldo, Mark, Tamás Hausel, and Luca Migliorini. “Topology of Hitchin Systems and Hodge Theory of Character Varieties: The Case A 1.” <i>Annals of Mathematics</i>. Princeton University Press, 2012. <a href=\"https://doi.org/10.4007/annals.2012.175.3.7\">https://doi.org/10.4007/annals.2012.175.3.7</a>.","ieee":"M. De Cataldo, T. Hausel, and L. Migliorini, “Topology of hitchin systems and Hodge theory of character varieties: The case A 1,” <i>Annals of Mathematics</i>, vol. 175, no. 3. Princeton University Press, pp. 1329–1407, 2012.","ista":"De Cataldo M, Hausel T, Migliorini L. 2012. Topology of hitchin systems and Hodge theory of character varieties: The case A 1. Annals of Mathematics. 175(3), 1329–1407."},"main_file_link":[{"url":"http://arxiv.org/abs/1004.1420","open_access":"1"}],"publisher":"Princeton University Press","quality_controlled":0,"acknowledgement":"Mark Andrea A. de Cataldo was partially supported by N.S.A. and N.S.F. Tamás Hausel was supported by a Royal Society University Research Fellowship. Luca Migliorini was partially supported by PRIN 2007 project \"Spazi di moduli e teoria di Lie\"","intvolume":"       175","_id":"1472","page":"1329 - 1407","doi":"10.4007/annals.2012.175.3.7","date_created":"2018-12-11T11:52:13Z"},{"date_published":"2012-06-08T00:00:00Z","abstract":[{"text":"Little is known about the stability of trophic relationships in complex natural communities over evolutionary timescales. Here, we use sequence data from 18 nuclear loci to reconstruct and compare the intraspecific histories of major Pleistocene refugial populations in the Middle East, the Balkans and Iberia in a guild of four Chalcid parasitoids (Cecidostiba fungosa, C. semifascia, Hobbya stenonota and Mesopolobus amaenus) all attacking Cynipid oak galls. We develop a likelihood method to numerically estimate models of divergence between three populations from multilocus data. We investigate the power of this framework on simulated data, and - using triplet alignments of intronic loci - quantify the support for all possible divergence relationships between refugial populations in the four parasitoids. Although an East to West order of population divergence has highest support in all but one species, we cannot rule out alternative population tree topologies. Comparing the estimated times of population splits between species, we find that one species, M. amaenus, has a significantly older history than the rest of the guild and must have arrived in central Europe at least one glacial cycle prior to other guild members. This suggests that although all four species may share a common origin in the East, they expanded westwards into Europe at different times.","lang":"eng"}],"author":[{"first_name":"Konrad","last_name":"Lohse","full_name":"Lohse, Konrad"},{"full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","last_name":"Barton","first_name":"Nicholas H"},{"first_name":"Graham","last_name":"Stone","full_name":"Stone, Graham"},{"last_name":"Melika","first_name":"George","full_name":"Melika, George"}],"ddc":["570"],"date_updated":"2025-05-28T11:56:58Z","oa":1,"year":"2012","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"2968"}]},"day":"08","oa_version":"Published Version","month":"06","type":"research_data_reference","status":"public","tmp":{"name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","image":"/images/cc_0.png"},"title":"Data from: A likelihood-based comparison of population histories in a parasitoid guild","article_processing_charge":"No","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.0g0fs"}],"citation":{"ista":"Lohse K, Barton NH, Stone G, Melika G. 2012. Data from: A likelihood-based comparison of population histories in a parasitoid guild, Dryad, <a href=\"https://doi.org/10.5061/DRYAD.0G0FS\">10.5061/DRYAD.0G0FS</a>.","ieee":"K. Lohse, N. H. Barton, G. Stone, and G. Melika, “Data from: A likelihood-based comparison of population histories in a parasitoid guild.” Dryad, 2012.","short":"K. Lohse, N.H. Barton, G. Stone, G. Melika, (2012).","chicago":"Lohse, Konrad, Nicholas H Barton, Graham Stone, and George Melika. “Data from: A Likelihood-Based Comparison of Population Histories in a Parasitoid Guild.” Dryad, 2012. <a href=\"https://doi.org/10.5061/DRYAD.0G0FS\">https://doi.org/10.5061/DRYAD.0G0FS</a>.","ama":"Lohse K, Barton NH, Stone G, Melika G. Data from: A likelihood-based comparison of population histories in a parasitoid guild. 2012. doi:<a href=\"https://doi.org/10.5061/DRYAD.0G0FS\">10.5061/DRYAD.0G0FS</a>","mla":"Lohse, Konrad, et al. <i>Data from: A Likelihood-Based Comparison of Population Histories in a Parasitoid Guild</i>. Dryad, 2012, doi:<a href=\"https://doi.org/10.5061/DRYAD.0G0FS\">10.5061/DRYAD.0G0FS</a>.","apa":"Lohse, K., Barton, N. H., Stone, G., &#38; Melika, G. (2012). Data from: A likelihood-based comparison of population histories in a parasitoid guild. Dryad. <a href=\"https://doi.org/10.5061/DRYAD.0G0FS\">https://doi.org/10.5061/DRYAD.0G0FS</a>"},"publisher":"Dryad","department":[{"_id":"NiBa"}],"_id":"13075","doi":"10.5061/DRYAD.0G0FS","date_created":"2023-05-23T17:01:02Z"},{"status":"public","type":"conference","title":"Conditional model checking: A technique to pass information between verifiers","citation":{"short":"D. Beyer, T.A. Henzinger, M. Keremoglu, P. Wendler, in:, Proceedings of the ACM SIGSOFT 20th International Symposium on the Foundations of Software Engineering, ACM, 2012.","chicago":"Beyer, Dirk, Thomas A Henzinger, Mehmet Keremoglu, and Philipp Wendler. “Conditional Model Checking: A Technique to Pass Information between Verifiers.” In <i>Proceedings of the ACM SIGSOFT 20th International Symposium on the Foundations of Software Engineering</i>. ACM, 2012. <a href=\"https://doi.org/10.1145/2393596.2393664\">https://doi.org/10.1145/2393596.2393664</a>.","ama":"Beyer D, Henzinger TA, Keremoglu M, Wendler P. Conditional model checking: A technique to pass information between verifiers. In: <i>Proceedings of the ACM SIGSOFT 20th International Symposium on the Foundations of Software Engineering</i>. ACM; 2012. doi:<a href=\"https://doi.org/10.1145/2393596.2393664\">10.1145/2393596.2393664</a>","mla":"Beyer, Dirk, et al. “Conditional Model Checking: A Technique to Pass Information between Verifiers.” <i>Proceedings of the ACM SIGSOFT 20th International Symposium on the Foundations of Software Engineering</i>, 57, ACM, 2012, doi:<a href=\"https://doi.org/10.1145/2393596.2393664\">10.1145/2393596.2393664</a>.","apa":"Beyer, D., Henzinger, T. A., Keremoglu, M., &#38; Wendler, P. (2012). Conditional model checking: A technique to pass information between verifiers. In <i>Proceedings of the ACM SIGSOFT 20th International Symposium on the Foundations of Software Engineering</i>. Cary, NC, USA: ACM. <a href=\"https://doi.org/10.1145/2393596.2393664\">https://doi.org/10.1145/2393596.2393664</a>","ieee":"D. Beyer, T. A. Henzinger, M. Keremoglu, and P. Wendler, “Conditional model checking: A technique to pass information between verifiers,” in <i>Proceedings of the ACM SIGSOFT 20th International Symposium on the Foundations of Software Engineering</i>, Cary, NC, USA, 2012.","ista":"Beyer D, Henzinger TA, Keremoglu M, Wendler P. 2012. Conditional model checking: A technique to pass information between verifiers. Proceedings of the ACM SIGSOFT 20th International Symposium on the Foundations of Software Engineering. FSE: Foundations of Software Engineering, 57."},"department":[{"_id":"ToHe"}],"quality_controlled":"1","acknowledgement":"This  research  was  supported  by  the  Canadian  NSERC grant   RGPIN   341819-07,    the   ERC   Advanced   Grant QUAREM, and the Austrian Science Fund NFN RiSE.","_id":"1384","doi":"10.1145/2393596.2393664","article_number":"57","date_updated":"2021-01-12T06:50:18Z","conference":{"location":"Cary, NC, USA","start_date":"2012-11-11","name":"FSE: Foundations of Software Engineering","end_date":"2012-11-16"},"oa":1,"publication_status":"published","publist_id":"5826","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","month":"11","oa_version":"Preprint","scopus_import":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1109.6926"}],"publisher":"ACM","date_created":"2018-12-11T11:51:42Z","project":[{"grant_number":"267989","call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling"},{"grant_number":"S 11407_N23","call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425"}],"date_published":"2012-11-01T00:00:00Z","abstract":[{"text":"Software model checking, as an undecidable problem, has three possible outcomes: (1) the program satisfies the specification, (2) the program does not satisfy the specification, and (3) the model checker fails. The third outcome usually manifests itself in a space-out, time-out, or one component of the verification tool giving up; in all of these failing cases, significant computation is performed by the verification tool before the failure, but no result is reported. We propose to reformulate the model-checking problem as follows, in order to have the verification tool report a summary of the performed work even in case of failure: given a program and a specification, the model checker returns a condition Ψ - usually a state predicate - such that the program satisfies the specification under the condition Ψ - that is, as long as the program does not leave the states in which Ψ is satisfied. In our experiments, we investigated as one major application of conditional model checking the sequential combination of model checkers with information passing. We give the condition that one model checker produces, as input to a second conditional model checker, such that the verification problem for the second is restricted to the part of the state space that is not covered by the condition, i.e., the second model checker works on the problems that the first model checker could not solve. Our experiments demonstrate that repeated application of conditional model checkers, passing information from one model checker to the next, can significantly improve the verification results and performance, i.e., we can now verify programs that we could not verify before.","lang":"eng"}],"author":[{"full_name":"Beyer, Dirk","last_name":"Beyer","first_name":"Dirk"},{"orcid":"0000−0002−2985−7724","first_name":"Thomas A","last_name":"Henzinger","full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Keremoglu, Mehmet","last_name":"Keremoglu","first_name":"Mehmet"},{"full_name":"Wendler, Philipp","first_name":"Philipp","last_name":"Wendler"}],"ec_funded":1,"language":[{"iso":"eng"}],"year":"2012","day":"01","publication":"Proceedings of the ACM SIGSOFT 20th International Symposium on the Foundations of Software Engineering"},{"publication":"Physical Review Letters","day":"29","year":"2012","language":[{"iso":"eng"}],"issue":"26","author":[{"full_name":"Theurkauff, I.","first_name":"I.","last_name":"Theurkauff"},{"first_name":"C.","last_name":"Cottin-Bizonne","full_name":"Cottin-Bizonne, C."},{"last_name":"Palacci","first_name":"Jérémie A","orcid":"0000-0002-7253-9465","id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d","full_name":"Palacci, Jérémie A"},{"last_name":"Ybert","first_name":"C.","full_name":"Ybert, C."},{"first_name":"L.","last_name":"Bocquet","full_name":"Bocquet, L."}],"abstract":[{"text":"In this Letter, we explore experimentally the phase behavior of a dense active suspension of self-propelled colloids. In addition to a solidlike and gaslike phase observed for high and low densities, a novel cluster phase is reported at intermediate densities. This takes the form of a stationary assembly of dense aggregates—resulting from a permanent dynamical merging and separation of active colloids—whose average size grows with activity as a linear function of the self-propelling velocity. While different possible scenarios can be considered to account for these observations—such as a generic velocity weakening instability recently put forward—we show that the experimental results are reproduced mathematically by a chemotactic aggregation mechanism, originally introduced to account for bacterial aggregation and accounting here for diffusiophoretic chemical interaction between colloidal swimmers.","lang":"eng"}],"volume":108,"date_published":"2012-06-29T00:00:00Z","article_type":"letter_note","date_created":"2021-01-19T10:26:59Z","publisher":"American Physical Society ","pmid":1,"main_file_link":[{"url":"https://arxiv.org/abs/1202.6264","open_access":"1"}],"scopus_import":"1","month":"06","oa_version":"Preprint","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","oa":1,"publication_status":"published","date_updated":"2023-02-23T13:46:45Z","publication_identifier":{"issn":["00319007"],"eissn":["10797114"]},"arxiv":1,"article_number":"268303","doi":"10.1103/physrevlett.108.268303","external_id":{"pmid":["23005020"],"arxiv":["1202.6264"]},"_id":"9014","intvolume":"       108","quality_controlled":"1","extern":"1","article_processing_charge":"No","citation":{"mla":"Theurkauff, I., et al. “Dynamic Clustering in Active Colloidal Suspensions with Chemical Signaling.” <i>Physical Review Letters</i>, vol. 108, no. 26, 268303, American Physical Society , 2012, doi:<a href=\"https://doi.org/10.1103/physrevlett.108.268303\">10.1103/physrevlett.108.268303</a>.","apa":"Theurkauff, I., Cottin-Bizonne, C., Palacci, J. A., Ybert, C., &#38; Bocquet, L. (2012). Dynamic clustering in active colloidal suspensions with chemical signaling. <i>Physical Review Letters</i>. American Physical Society . <a href=\"https://doi.org/10.1103/physrevlett.108.268303\">https://doi.org/10.1103/physrevlett.108.268303</a>","ama":"Theurkauff I, Cottin-Bizonne C, Palacci JA, Ybert C, Bocquet L. Dynamic clustering in active colloidal suspensions with chemical signaling. <i>Physical Review Letters</i>. 2012;108(26). doi:<a href=\"https://doi.org/10.1103/physrevlett.108.268303\">10.1103/physrevlett.108.268303</a>","short":"I. Theurkauff, C. Cottin-Bizonne, J.A. Palacci, C. Ybert, L. Bocquet, Physical Review Letters 108 (2012).","chicago":"Theurkauff, I., C. Cottin-Bizonne, Jérémie A Palacci, C. Ybert, and L. Bocquet. “Dynamic Clustering in Active Colloidal Suspensions with Chemical Signaling.” <i>Physical Review Letters</i>. American Physical Society , 2012. <a href=\"https://doi.org/10.1103/physrevlett.108.268303\">https://doi.org/10.1103/physrevlett.108.268303</a>.","ista":"Theurkauff I, Cottin-Bizonne C, Palacci JA, Ybert C, Bocquet L. 2012. Dynamic clustering in active colloidal suspensions with chemical signaling. Physical Review Letters. 108(26), 268303.","ieee":"I. Theurkauff, C. Cottin-Bizonne, J. A. Palacci, C. Ybert, and L. Bocquet, “Dynamic clustering in active colloidal suspensions with chemical signaling,” <i>Physical Review Letters</i>, vol. 108, no. 26. American Physical Society , 2012."},"title":"Dynamic clustering in active colloidal suspensions with chemical signaling","type":"journal_article","status":"public"},{"oa":1,"publication_status":"published","date_updated":"2022-01-24T13:49:41Z","publication_identifier":{"issn":["0022-4928","1520-0469"]},"month":"08","oa_version":"Published Version","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","title":"Detailed investigation of the self-aggregation of convection in cloud-resolving simulations","status":"public","type":"journal_article","article_processing_charge":"No","citation":{"apa":"Muller, C. J., &#38; Held, I. M. (2012). Detailed investigation of the self-aggregation of convection in cloud-resolving simulations. <i>Journal of the Atmospheric Sciences</i>. American Meteorological Society. <a href=\"https://doi.org/10.1175/jas-d-11-0257.1\">https://doi.org/10.1175/jas-d-11-0257.1</a>","mla":"Muller, Caroline J., and Isaac M. Held. “Detailed Investigation of the Self-Aggregation of Convection in Cloud-Resolving Simulations.” <i>Journal of the Atmospheric Sciences</i>, vol. 69, no. 8, American Meteorological Society, 2012, pp. 2551–65, doi:<a href=\"https://doi.org/10.1175/jas-d-11-0257.1\">10.1175/jas-d-11-0257.1</a>.","short":"C.J. Muller, I.M. Held, Journal of the Atmospheric Sciences 69 (2012) 2551–2565.","chicago":"Muller, Caroline J, and Isaac M. Held. “Detailed Investigation of the Self-Aggregation of Convection in Cloud-Resolving Simulations.” <i>Journal of the Atmospheric Sciences</i>. American Meteorological Society, 2012. <a href=\"https://doi.org/10.1175/jas-d-11-0257.1\">https://doi.org/10.1175/jas-d-11-0257.1</a>.","ama":"Muller CJ, Held IM. Detailed investigation of the self-aggregation of convection in cloud-resolving simulations. <i>Journal of the Atmospheric Sciences</i>. 2012;69(8):2551-2565. doi:<a href=\"https://doi.org/10.1175/jas-d-11-0257.1\">10.1175/jas-d-11-0257.1</a>","ieee":"C. J. Muller and I. M. Held, “Detailed investigation of the self-aggregation of convection in cloud-resolving simulations,” <i>Journal of the Atmospheric Sciences</i>, vol. 69, no. 8. American Meteorological Society, pp. 2551–2565, 2012.","ista":"Muller CJ, Held IM. 2012. Detailed investigation of the self-aggregation of convection in cloud-resolving simulations. Journal of the Atmospheric Sciences. 69(8), 2551–2565."},"extern":"1","quality_controlled":"1","doi":"10.1175/jas-d-11-0257.1","page":"2551-2565","_id":"9142","intvolume":"        69","author":[{"id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b","full_name":"Muller, Caroline J","last_name":"Muller","first_name":"Caroline J","orcid":"0000-0001-5836-5350"},{"last_name":"Held","first_name":"Isaac M.","full_name":"Held, Isaac M."}],"abstract":[{"lang":"eng","text":"In models of radiative–convective equilibrium it is known that convection can spontaneously aggregate into one single localized moist region if the domain is large enough. The large changes in the mean climate state and radiative fluxes accompanying this self-aggregation raise questions as to what simulations at lower resolutions with parameterized convection, in similar homogeneous geometries, should be expected to produce to be considered successful in mimicking a cloud-resolving model.\r\nThe authors investigate this self-aggregation in a nonrotating, three-dimensional cloud-resolving model on a square domain without large-scale forcing. It is found that self-aggregation is sensitive not only to the domain size, but also to the horizontal resolution. With horizontally homogeneous initial conditions, convective aggregation only occurs on domains larger than about 200km and with resolutions coarser than about 2km in the model examined. The system exhibits hysteresis, so that with aggregated initial conditions, convection remains aggregated even at our finest resolution, 500m, as long as the domain is greater than 200–300km.\r\nThe sensitivity of self-aggregation to resolution and domain size in this model is due to the sensitivity of the distribution of low clouds to these two parameters. Indeed, the mechanism responsible for the aggregation of convection is the dynamical response to the longwave radiative cooling from low clouds. Strong longwave cooling near cloud top in dry regions forces downward motion, which by continuity generates inflow near cloud top and near-surface outflow from dry regions. This circulation results in the net export of moist static energy from regions with low moist static energy, yielding a positive feedback."}],"volume":69,"date_published":"2012-08-01T00:00:00Z","issue":"8","keyword":["Atmospheric Science"],"publication":"Journal of the Atmospheric Sciences","day":"01","year":"2012","language":[{"iso":"eng"}],"publisher":"American Meteorological Society","main_file_link":[{"url":"https://doi.org/10.1175/JAS-D-11-0257.1","open_access":"1"}],"article_type":"original","date_created":"2021-02-15T14:39:03Z"},{"doi":"10.1103/PhysRevLett.109.018101","date_created":"2018-12-11T11:49:13Z","external_id":{"arxiv":["1207.1516"]},"_id":"922","intvolume":"       109","title":"Mechanical instabilities of biological tubes","type":"journal_article","status":"public","publisher":"American Physical Society","citation":{"ama":"Hannezo EB, Prost J, Joanny J. Mechanical instabilities of biological tubes. <i>Physical Review Letters</i>. 2012;109(1). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.109.018101\">10.1103/PhysRevLett.109.018101</a>","short":"E.B. Hannezo, J. Prost, J. Joanny, Physical Review Letters 109 (2012).","chicago":"Hannezo, Edouard B, Jacques Prost, and Jean Joanny. “Mechanical Instabilities of Biological Tubes.” <i>Physical Review Letters</i>. American Physical Society, 2012. <a href=\"https://doi.org/10.1103/PhysRevLett.109.018101\">https://doi.org/10.1103/PhysRevLett.109.018101</a>.","mla":"Hannezo, Edouard B., et al. “Mechanical Instabilities of Biological Tubes.” <i>Physical Review Letters</i>, vol. 109, no. 1, American Physical Society, 2012, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.109.018101\">10.1103/PhysRevLett.109.018101</a>.","apa":"Hannezo, E. B., Prost, J., &#38; Joanny, J. (2012). Mechanical instabilities of biological tubes. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.109.018101\">https://doi.org/10.1103/PhysRevLett.109.018101</a>","ista":"Hannezo EB, Prost J, Joanny J. 2012. Mechanical instabilities of biological tubes. Physical Review Letters. 109(1).","ieee":"E. B. Hannezo, J. Prost, and J. Joanny, “Mechanical instabilities of biological tubes,” <i>Physical Review Letters</i>, vol. 109, no. 1. American Physical Society, 2012."},"extern":"1","article_processing_charge":"No","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1207.1516"}],"oa":1,"publication_status":"published","date_updated":"2021-01-12T08:21:56Z","month":"07","publication":"Physical Review Letters","oa_version":"Preprint","publist_id":"6519","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"03","language":[{"iso":"eng"}],"year":"2012","author":[{"first_name":"Edouard B","last_name":"Hannezo","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","full_name":"Hannezo, Edouard B"},{"full_name":"Prost, Jacques","last_name":"Prost","first_name":"Jacques"},{"full_name":"Joanny, Jean","last_name":"Joanny","first_name":"Jean"}],"abstract":[{"text":"We study theoretically the morphologies of biological tubes affected by various pathologies. When epithelial cells grow, the negative tension produced by their division provokes a buckling instability. Several shapes are investigated: varicose, dilated, sinuous, or sausagelike. They are all found in pathologies of tracheal, renal tubes, or arteries. The final shape depends crucially on the mechanical parameters of the tissues: Young's modulus, wall-to-lumen ratio, homeostatic pressure. We argue that since tissues must be in quasistatic mechanical equilibrium, abnormal shapes convey information as to what causes the pathology. We calculate a phase diagram of tubular instabilities which could be a helpful guide for investigating the underlying genetic regulation.","lang":"eng"}],"volume":109,"date_published":"2012-07-03T00:00:00Z","arxiv":1,"issue":"1"},{"has_accepted_license":"1","oa_version":"Published Version","month":"09","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication_status":"published","oa":1,"ddc":["580"],"date_updated":"2021-12-14T08:28:51Z","publication_identifier":{"eissn":["1095-9203"],"issn":["0036-8075"]},"extern":"1","citation":{"apa":"Ibarra, C. A., Feng, X., Schoft, V. K., Hsieh, T.-F., Uzawa, R., Rodrigues, J. A., … Zilberman, D. (2012). Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.1224839\">https://doi.org/10.1126/science.1224839</a>","mla":"Ibarra, Christian A., et al. “Active DNA Demethylation in Plant Companion Cells Reinforces Transposon Methylation in Gametes.” <i>Science</i>, vol. 337, no. 6100, American Association for the Advancement of Science, 2012, pp. 1360–64, doi:<a href=\"https://doi.org/10.1126/science.1224839\">10.1126/science.1224839</a>.","short":"C.A. Ibarra, X. Feng, V.K. Schoft, T.-F. Hsieh, R. Uzawa, J.A. Rodrigues, A. Zemach, N. Chumak, A. Machlicova, T. Nishimura, D. Rojas, R.L. Fischer, H. Tamaru, D. Zilberman, Science 337 (2012) 1360–1364.","chicago":"Ibarra, Christian A., Xiaoqi Feng, Vera K. Schoft, Tzung-Fu Hsieh, Rie Uzawa, Jessica A. Rodrigues, Assaf Zemach, et al. “Active DNA Demethylation in Plant Companion Cells Reinforces Transposon Methylation in Gametes.” <i>Science</i>. American Association for the Advancement of Science, 2012. <a href=\"https://doi.org/10.1126/science.1224839\">https://doi.org/10.1126/science.1224839</a>.","ama":"Ibarra CA, Feng X, Schoft VK, et al. Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes. <i>Science</i>. 2012;337(6100):1360-1364. doi:<a href=\"https://doi.org/10.1126/science.1224839\">10.1126/science.1224839</a>","ista":"Ibarra CA, Feng X, Schoft VK, Hsieh T-F, Uzawa R, Rodrigues JA, Zemach A, Chumak N, Machlicova A, Nishimura T, Rojas D, Fischer RL, Tamaru H, Zilberman D. 2012. Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes. Science. 337(6100), 1360–1364.","ieee":"C. A. Ibarra <i>et al.</i>, “Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes,” <i>Science</i>, vol. 337, no. 6100. American Association for the Advancement of Science, pp. 1360–1364, 2012."},"article_processing_charge":"No","title":"Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes","status":"public","type":"journal_article","doi":"10.1126/science.1224839","external_id":{"pmid":["22984074"]},"_id":"9451","page":"1360-1364","intvolume":"       337","quality_controlled":"1","department":[{"_id":"DaZi"}],"issue":"6100","author":[{"first_name":"Christian A.","last_name":"Ibarra","full_name":"Ibarra, Christian A."},{"full_name":"Feng, Xiaoqi","last_name":"Feng","first_name":"Xiaoqi"},{"full_name":"Schoft, Vera K.","last_name":"Schoft","first_name":"Vera K."},{"last_name":"Hsieh","first_name":"Tzung-Fu","full_name":"Hsieh, Tzung-Fu"},{"last_name":"Uzawa","first_name":"Rie","full_name":"Uzawa, Rie"},{"first_name":"Jessica A.","last_name":"Rodrigues","full_name":"Rodrigues, Jessica A."},{"full_name":"Zemach, Assaf","last_name":"Zemach","first_name":"Assaf"},{"first_name":"Nina","last_name":"Chumak","full_name":"Chumak, Nina"},{"full_name":"Machlicova, Adriana","first_name":"Adriana","last_name":"Machlicova"},{"full_name":"Nishimura, Toshiro","last_name":"Nishimura","first_name":"Toshiro"},{"last_name":"Rojas","first_name":"Denisse","full_name":"Rojas, Denisse"},{"full_name":"Fischer, Robert L.","first_name":"Robert L.","last_name":"Fischer"},{"full_name":"Tamaru, Hisashi","last_name":"Tamaru","first_name":"Hisashi"},{"first_name":"Daniel","last_name":"Zilberman","orcid":"0000-0002-0123-8649","full_name":"Zilberman, Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1"}],"volume":337,"abstract":[{"text":"The Arabidopsis thaliana central cell, the companion cell of the egg, undergoes DNA demethylation before fertilization, but the targeting preferences, mechanism, and biological significance of this process remain unclear. Here, we show that active DNA demethylation mediated by the DEMETER DNA glycosylase accounts for all of the demethylation in the central cell and preferentially targets small, AT-rich, and nucleosome-depleted euchromatic transposable elements. The vegetative cell, the companion cell of sperm, also undergoes DEMETER-dependent demethylation of similar sequences, and lack of DEMETER in vegetative cells causes reduced small RNA–directed DNA methylation of transposons in sperm. Our results demonstrate that demethylation in companion cells reinforces transposon methylation in plant gametes and likely contributes to stable silencing of transposable elements across generations.","lang":"eng"}],"date_published":"2012-09-14T00:00:00Z","publication":"Science","day":"14","year":"2012","language":[{"iso":"eng"}],"publisher":"American Association for the Advancement of Science","pmid":1,"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4034762/","open_access":"1"}],"scopus_import":"1","date_created":"2021-06-04T07:51:31Z","article_type":"original"},{"article_number":"e1002988","month":"10","oa_version":"Published Version","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication_status":"published","oa":1,"publication_identifier":{"issn":["1553-7390"],"eissn":["1553-7404"]},"date_updated":"2021-12-14T08:29:57Z","citation":{"ista":"Coleman-Derr D, Zilberman D. 2012. Deposition of histone variant H2A.Z within gene bodies regulates responsive genes. PLoS Genetics. 8(10), e1002988.","ieee":"D. Coleman-Derr and D. Zilberman, “Deposition of histone variant H2A.Z within gene bodies regulates responsive genes,” <i>PLoS Genetics</i>, vol. 8, no. 10. Public Library of Science, 2012.","apa":"Coleman-Derr, D., &#38; Zilberman, D. (2012). Deposition of histone variant H2A.Z within gene bodies regulates responsive genes. <i>PLoS Genetics</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pgen.1002988\">https://doi.org/10.1371/journal.pgen.1002988</a>","mla":"Coleman-Derr, Devin, and Daniel Zilberman. “Deposition of Histone Variant H2A.Z within Gene Bodies Regulates Responsive Genes.” <i>PLoS Genetics</i>, vol. 8, no. 10, e1002988, Public Library of Science, 2012, doi:<a href=\"https://doi.org/10.1371/journal.pgen.1002988\">10.1371/journal.pgen.1002988</a>.","chicago":"Coleman-Derr, Devin, and Daniel Zilberman. “Deposition of Histone Variant H2A.Z within Gene Bodies Regulates Responsive Genes.” <i>PLoS Genetics</i>. Public Library of Science, 2012. <a href=\"https://doi.org/10.1371/journal.pgen.1002988\">https://doi.org/10.1371/journal.pgen.1002988</a>.","short":"D. Coleman-Derr, D. Zilberman, PLoS Genetics 8 (2012).","ama":"Coleman-Derr D, Zilberman D. Deposition of histone variant H2A.Z within gene bodies regulates responsive genes. <i>PLoS Genetics</i>. 2012;8(10). doi:<a href=\"https://doi.org/10.1371/journal.pgen.1002988\">10.1371/journal.pgen.1002988</a>"},"article_processing_charge":"No","extern":"1","title":"Deposition of histone variant H2A.Z within gene bodies regulates responsive genes","status":"public","type":"journal_article","external_id":{"pmid":["23071449"]},"doi":"10.1371/journal.pgen.1002988","intvolume":"         8","_id":"9497","quality_controlled":"1","department":[{"_id":"DaZi"}],"issue":"10","author":[{"last_name":"Coleman-Derr","first_name":"Devin","full_name":"Coleman-Derr, Devin"},{"orcid":"0000-0002-0123-8649","last_name":"Zilberman","first_name":"Daniel","full_name":"Zilberman, Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1"}],"date_published":"2012-10-11T00:00:00Z","abstract":[{"lang":"eng","text":"The regulation of eukaryotic chromatin relies on interactions between many epigenetic factors, including histone modifications, DNA methylation, and the incorporation of histone variants. H2A.Z, one of the most conserved but enigmatic histone variants that is enriched at the transcriptional start sites of genes, has been implicated in a variety of chromosomal processes. Recently, we reported a genome-wide anticorrelation between H2A.Z and DNA methylation, an epigenetic hallmark of heterochromatin that has also been found in the bodies of active genes in plants and animals. Here, we investigate the basis of this anticorrelation using a novel h2a.z loss-of-function line in Arabidopsis thaliana. Through genome-wide bisulfite sequencing, we demonstrate that loss of H2A.Z in Arabidopsis has only a minor effect on the level or profile of DNA methylation in genes, and we propose that the global anticorrelation between DNA methylation and H2A.Z is primarily caused by the exclusion of H2A.Z from methylated DNA. RNA sequencing and genomic mapping of H2A.Z show that H2A.Z enrichment across gene bodies, rather than at the TSS, is correlated with lower transcription levels and higher measures of gene responsiveness. Loss of H2A.Z causes misregulation of many genes that are disproportionately associated with response to environmental and developmental stimuli. We propose that H2A.Z deposition in gene bodies promotes variability in levels and patterns of gene expression, and that a major function of genic DNA methylation is to exclude H2A.Z from constitutively expressed genes."}],"volume":8,"publication":"PLoS Genetics","language":[{"iso":"eng"}],"year":"2012","day":"11","pmid":1,"main_file_link":[{"url":"https://doi.org/10.1371/journal.pgen.1002988","open_access":"1"}],"publisher":"Public Library of Science","scopus_import":"1","date_created":"2021-06-07T10:55:27Z","article_type":"original"},{"author":[{"full_name":"Kim, Sang Yeol","first_name":"Sang Yeol","last_name":"Kim"},{"first_name":"Jungeun","last_name":"Lee","full_name":"Lee, Jungeun"},{"first_name":"Leor","last_name":"Eshed-Williams","full_name":"Eshed-Williams, Leor"},{"orcid":"0000-0002-0123-8649","last_name":"Zilberman","first_name":"Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","full_name":"Zilberman, Daniel"},{"first_name":"Z. Renee","last_name":"Sung","full_name":"Sung, Z. Renee"}],"date_published":"2012-03-22T00:00:00Z","abstract":[{"text":"EMBRYONIC FLOWER1 (EMF1) is a plant-specific gene crucial to Arabidopsis vegetative development. Loss of function mutants in the EMF1 gene mimic the phenotype caused by mutations in Polycomb Group protein (PcG) genes, which encode epigenetic repressors that regulate many aspects of eukaryotic development. In Arabidopsis, Polycomb Repressor Complex 2 (PRC2), made of PcG proteins, catalyzes trimethylation of lysine 27 on histone H3 (H3K27me3) and PRC1-like proteins catalyze H2AK119 ubiquitination. Despite functional similarity to PcG proteins, EMF1 lacks sequence homology with known PcG proteins; thus, its role in the PcG mechanism is unclear. To study the EMF1 functions and its mechanism of action, we performed genome-wide mapping of EMF1 binding and H3K27me3 modification sites in Arabidopsis seedlings. The EMF1 binding pattern is similar to that of H3K27me3 modification on the chromosomal and genic level. ChIPOTLe peak finding and clustering analyses both show that the highly trimethylated genes also have high enrichment levels of EMF1 binding, termed EMF1_K27 genes. EMF1 interacts with regulatory genes, which are silenced to allow vegetative growth, and with genes specifying cell fates during growth and differentiation. H3K27me3 marks not only these genes but also some genes that are involved in endosperm development and maternal effects. Transcriptome analysis, coupled with the H3K27me3 pattern, of EMF1_K27 genes in emf1 and PRC2 mutants showed that EMF1 represses gene activities via diverse mechanisms and plays a novel role in the PcG mechanism.","lang":"eng"}],"volume":8,"issue":"3","publication":"PLoS Genetics","language":[{"iso":"eng"}],"year":"2012","day":"22","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1371/journal.pgen.1002512"}],"pmid":1,"publisher":"Public Library of Science","article_type":"original","date_created":"2021-06-07T11:07:56Z","article_number":"e1002512","publication_status":"published","oa":1,"publication_identifier":{"issn":["1553-7390"],"eissn":["1553-7404"]},"date_updated":"2021-12-14T08:31:14Z","oa_version":"Published Version","month":"03","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","title":"EMF1 and PRC2 cooperate to repress key regulators of Arabidopsis development","status":"public","type":"journal_article","article_processing_charge":"No","citation":{"ista":"Kim SY, Lee J, Eshed-Williams L, Zilberman D, Sung ZR. 2012. EMF1 and PRC2 cooperate to repress key regulators of Arabidopsis development. PLoS Genetics. 8(3), e1002512.","ieee":"S. Y. Kim, J. Lee, L. Eshed-Williams, D. Zilberman, and Z. R. Sung, “EMF1 and PRC2 cooperate to repress key regulators of Arabidopsis development,” <i>PLoS Genetics</i>, vol. 8, no. 3. Public Library of Science, 2012.","apa":"Kim, S. Y., Lee, J., Eshed-Williams, L., Zilberman, D., &#38; Sung, Z. R. (2012). EMF1 and PRC2 cooperate to repress key regulators of Arabidopsis development. <i>PLoS Genetics</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pgen.1002512\">https://doi.org/10.1371/journal.pgen.1002512</a>","mla":"Kim, Sang Yeol, et al. “EMF1 and PRC2 Cooperate to Repress Key Regulators of Arabidopsis Development.” <i>PLoS Genetics</i>, vol. 8, no. 3, e1002512, Public Library of Science, 2012, doi:<a href=\"https://doi.org/10.1371/journal.pgen.1002512\">10.1371/journal.pgen.1002512</a>.","short":"S.Y. Kim, J. Lee, L. Eshed-Williams, D. Zilberman, Z.R. Sung, PLoS Genetics 8 (2012).","ama":"Kim SY, Lee J, Eshed-Williams L, Zilberman D, Sung ZR. EMF1 and PRC2 cooperate to repress key regulators of Arabidopsis development. <i>PLoS Genetics</i>. 2012;8(3). doi:<a href=\"https://doi.org/10.1371/journal.pgen.1002512\">10.1371/journal.pgen.1002512</a>","chicago":"Kim, Sang Yeol, Jungeun Lee, Leor Eshed-Williams, Daniel Zilberman, and Z. Renee Sung. “EMF1 and PRC2 Cooperate to Repress Key Regulators of Arabidopsis Development.” <i>PLoS Genetics</i>. Public Library of Science, 2012. <a href=\"https://doi.org/10.1371/journal.pgen.1002512\">https://doi.org/10.1371/journal.pgen.1002512</a>."},"extern":"1","quality_controlled":"1","department":[{"_id":"DaZi"}],"external_id":{"pmid":["22457632"]},"doi":"10.1371/journal.pgen.1002512","intvolume":"         8","_id":"9499"},{"publication_identifier":{"eissn":["1943-4456"],"issn":["0091-7451"]},"date_updated":"2021-12-14T08:33:09Z","oa":1,"publication_status":"published","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","oa_version":"Published Version","month":"12","department":[{"_id":"DaZi"}],"quality_controlled":"1","intvolume":"        77","page":"147-154","_id":"9535","external_id":{"pmid":["23250988"]},"doi":"10.1101/sqb.2012.77.014944","status":"public","type":"journal_article","title":"DNA methylation, H2A.Z, and the regulation of constitutive expression","citation":{"ista":"Coleman-Derr D, Zilberman D. 2012. DNA methylation, H2A.Z, and the regulation of constitutive expression. Cold Spring Harbor Symposia on Quantitative Biology. 77, 147–154.","ieee":"D. Coleman-Derr and D. Zilberman, “DNA methylation, H2A.Z, and the regulation of constitutive expression,” <i>Cold Spring Harbor Symposia on Quantitative Biology</i>, vol. 77. Cold Spring Harbor Laboratory Press, pp. 147–154, 2012.","apa":"Coleman-Derr, D., &#38; Zilberman, D. (2012). DNA methylation, H2A.Z, and the regulation of constitutive expression. <i>Cold Spring Harbor Symposia on Quantitative Biology</i>. Cold Spring Harbor Laboratory Press. <a href=\"https://doi.org/10.1101/sqb.2012.77.014944\">https://doi.org/10.1101/sqb.2012.77.014944</a>","mla":"Coleman-Derr, D., and Daniel Zilberman. “DNA Methylation, H2A.Z, and the Regulation of Constitutive Expression.” <i>Cold Spring Harbor Symposia on Quantitative Biology</i>, vol. 77, Cold Spring Harbor Laboratory Press, 2012, pp. 147–54, doi:<a href=\"https://doi.org/10.1101/sqb.2012.77.014944\">10.1101/sqb.2012.77.014944</a>.","chicago":"Coleman-Derr, D., and Daniel Zilberman. “DNA Methylation, H2A.Z, and the Regulation of Constitutive Expression.” <i>Cold Spring Harbor Symposia on Quantitative Biology</i>. Cold Spring Harbor Laboratory Press, 2012. <a href=\"https://doi.org/10.1101/sqb.2012.77.014944\">https://doi.org/10.1101/sqb.2012.77.014944</a>.","short":"D. Coleman-Derr, D. Zilberman, Cold Spring Harbor Symposia on Quantitative Biology 77 (2012) 147–154.","ama":"Coleman-Derr D, Zilberman D. DNA methylation, H2A.Z, and the regulation of constitutive expression. <i>Cold Spring Harbor Symposia on Quantitative Biology</i>. 2012;77:147-154. doi:<a href=\"https://doi.org/10.1101/sqb.2012.77.014944\">10.1101/sqb.2012.77.014944</a>"},"article_processing_charge":"No","extern":"1","year":"2012","language":[{"iso":"eng"}],"day":"18","publication":"Cold Spring Harbor Symposia on Quantitative Biology","date_published":"2012-12-18T00:00:00Z","abstract":[{"lang":"eng","text":"The most well-studied function of DNA methylation in eukaryotic cells is the transcriptional silencing of genes and transposons. More recent results showed that many eukaryotes methylate the bodies of genes as well and that this methylation correlates with transcriptional activity rather than repression. The purpose of gene body methylation remains mysterious, but is potentially related to the histone variant H2A.Z. Studies in plants and animals have shown that the genome-wide distributions of H2A.Z and DNA methylation are strikingly anticorrelated. Furthermore, we and other investigators have shown that this relationship is likely to be the result of an ancient but unknown mechanism by which DNA methylation prevents the incorporation of H2A.Z. Recently, we discovered strong correlations between the presence of H2A.Z within gene bodies, the degree to which a gene's expression varies across tissue types or environmental conditions, and transcriptional misregulation in an h2a.z mutant. We propose that one basal function of gene body methylation is the establishment of constitutive expression patterns within housekeeping genes by excluding H2A.Z from their bodies."}],"volume":77,"author":[{"last_name":"Coleman-Derr","first_name":"D.","full_name":"Coleman-Derr, D."},{"first_name":"Daniel","last_name":"Zilberman","orcid":"0000-0002-0123-8649","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","full_name":"Zilberman, Daniel"}],"date_created":"2021-06-08T13:01:23Z","article_type":"review","scopus_import":"1","pmid":1,"main_file_link":[{"url":"https://doi.org/10.1101/sqb.2012.77.014944","open_access":"1"}],"publisher":"Cold Spring Harbor Laboratory Press"},{"doi":"10.1103/PhysRevB.86.224409","date_created":"2018-12-11T11:49:27Z","_id":"966","intvolume":"        86","acknowledgement":"We thank Kuang-Ting Chen, Rebecca Flint, Dmitri Ivanov, Z.-X. Liu, Tai-Kai Ng, Lara Thompson, Tamás Tóth, and Fa Wang for helpful discussions. T.S. is supported by NSF DMR 1005434. P.A.L. is supported by NSF DMR 1104498. S.B. acknowledges support from the Swiss National Science Foundation (SNSF).","quality_controlled":0,"publisher":"American Physical Society","citation":{"ista":"Bieri S, Serbyn M, Senthil T, Lee P. 2012. Paired chiral spin liquid with a Fermi surface in S=1 model on the triangular lattice. Physical Review B - Condensed Matter and Materials Physics. 86(22).","ieee":"S. Bieri, M. Serbyn, T. Senthil, and P. Lee, “Paired chiral spin liquid with a Fermi surface in S=1 model on the triangular lattice,” <i>Physical Review B - Condensed Matter and Materials Physics</i>, vol. 86, no. 22. American Physical Society, 2012.","ama":"Bieri S, Serbyn M, Senthil T, Lee P. Paired chiral spin liquid with a Fermi surface in S=1 model on the triangular lattice. <i>Physical Review B - Condensed Matter and Materials Physics</i>. 2012;86(22). doi:<a href=\"https://doi.org/10.1103/PhysRevB.86.224409\">10.1103/PhysRevB.86.224409</a>","chicago":"Bieri, Samuel, Maksym Serbyn, Todadri Senthil, and Patrick Lee. “Paired Chiral Spin Liquid with a Fermi Surface in S=1 Model on the Triangular Lattice.” <i>Physical Review B - Condensed Matter and Materials Physics</i>. American Physical Society, 2012. <a href=\"https://doi.org/10.1103/PhysRevB.86.224409\">https://doi.org/10.1103/PhysRevB.86.224409</a>.","short":"S. Bieri, M. Serbyn, T. Senthil, P. Lee, Physical Review B - Condensed Matter and Materials Physics 86 (2012).","apa":"Bieri, S., Serbyn, M., Senthil, T., &#38; Lee, P. (2012). Paired chiral spin liquid with a Fermi surface in S=1 model on the triangular lattice. <i>Physical Review B - Condensed Matter and Materials Physics</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevB.86.224409\">https://doi.org/10.1103/PhysRevB.86.224409</a>","mla":"Bieri, Samuel, et al. “Paired Chiral Spin Liquid with a Fermi Surface in S=1 Model on the Triangular Lattice.” <i>Physical Review B - Condensed Matter and Materials Physics</i>, vol. 86, no. 22, American Physical Society, 2012, doi:<a href=\"https://doi.org/10.1103/PhysRevB.86.224409\">10.1103/PhysRevB.86.224409</a>."},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1208.3231"}],"extern":1,"title":"Paired chiral spin liquid with a Fermi surface in S=1 model on the triangular lattice","status":"public","type":"journal_article","month":"12","publication":"Physical Review B - Condensed Matter and Materials Physics","day":"13","publist_id":"6431","year":"2012","publication_status":"published","oa":1,"date_updated":"2021-01-12T08:22:18Z","issue":"22","author":[{"last_name":"Bieri","first_name":"Samuel","full_name":"Bieri, Samuel"},{"orcid":"0000-0002-2399-5827","last_name":"Serbyn","first_name":"Maksym","full_name":"Maksym Serbyn","id":"47809E7E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Senthil","first_name":"Todadri","full_name":"Senthil, Todadri S"},{"full_name":"Lee, Patrick","last_name":"Lee","first_name":"Patrick"}],"abstract":[{"lang":"eng","text":"Motivated by recent experiments on Ba3NiSb2O 9, we investigate possible quantum spin liquid ground states for spin S=1 Heisenberg models on the triangular lattice. We use variational Monte Carlo techniques to calculate the energies of microscopic spin liquid wave functions where spin is represented by three flavors of fermionic spinon operators. These energies are compared with the energies of various competing three-sublattice ordered states. Our approach shows that the antiferromagnetic Heisenberg model with biquadratic term and single-ion anisotropy does not have a low-temperature spin liquid phase. However, for an SU(3)-invariant model with sufficiently strong ring-exchange terms, we find a paired chiral quantum spin liquid with a Fermi surface of deconfined spinons that is stable against all types of ordering patterns we considered. We discuss the physics of this exotic spin liquid state in relation to the recent experiment and suggest new ways to test this scenario."}],"volume":86,"date_published":"2012-12-13T00:00:00Z"}]