[{"article_processing_charge":"No","year":"2012","status":"public","language":[{"iso":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","pubrep_id":"180","place":"Berlin, Heidelberg","oa_version":"None","quality_controlled":"1","has_accepted_license":"1","series_title":"LNCS","oa":1,"volume":7561,"doi":"10.1007/978-3-642-33386-6_10","project":[{"name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989","call_identifier":"FP7"}],"publication":"Automated Technology for Verification and Analysis","type":"book_chapter","intvolume":"      7561","ddc":["005"],"publication_identifier":{"eissn":["1611-3349"],"issn":["0302-9743"],"isbn":["9783642333859","9783642333866"]},"author":[{"last_name":"Gupta","first_name":"Ashutosh","full_name":"Gupta, Ashutosh"}],"file_date_updated":"2020-07-14T12:47:10Z","conference":{"start_date":"2012-10-03","end_date":"2012-10-06","location":"Thiruvananthapuram, Kerala, India","name":"ATVA 2012"},"page":"107-121","date_updated":"2023-09-05T14:15:29Z","ec_funded":1,"title":"Improved Single Pass Algorithms for Resolution Proof Reduction","date_published":"2012-01-01T00:00:00Z","_id":"5745","citation":{"ista":"Gupta A. 2012.Improved Single Pass Algorithms for Resolution Proof Reduction. In: Automated Technology for Verification and Analysis. vol. 7561, 107–121.","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>","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>.","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>."},"publication_status":"published","date_created":"2018-12-18T13:01:46Z","publisher":"Springer Berlin Heidelberg","department":[{"_id":"ToHe"}],"file":[{"date_updated":"2020-07-14T12:47:10Z","checksum":"68415837a315de3cc4d120f6019d752c","access_level":"open_access","relation":"main_file","file_id":"5746","file_size":465502,"creator":"dernst","file_name":"2012_ATVA_Gupta.pdf","date_created":"2018-12-18T13:07:35Z","content_type":"application/pdf"}]},{"oa_version":"Published Version","quality_controlled":"1","has_accepted_license":"1","month":"05","year":"2012","status":"public","language":[{"iso":"eng"}],"day":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1016/j.protcy.2012.05.134","publication":"Procedia Technology","oa":1,"volume":4,"author":[{"last_name":"Biswas","id":"3C2B033E-F248-11E8-B48F-1D18A9856A87","first_name":"Ranita","full_name":"Biswas, Ranita","orcid":"0000-0002-5372-7890"},{"last_name":"Sil","full_name":"Sil, Jaya","first_name":"Jaya"}],"file_date_updated":"2020-07-14T12:47:12Z","page":"820-824","abstract":[{"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). ","lang":"eng"}],"date_updated":"2021-01-12T08:03:43Z","type":"journal_article","intvolume":"         4","ddc":["000"],"publication_identifier":{"issn":["2212-0173"]},"publisher":"Elsevier","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"file":[{"file_id":"5863","file_size":305426,"creator":"dernst","checksum":"ba0185986b151d8c11201f48cd505ceb","date_updated":"2020-07-14T12:47:12Z","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_name":"2012_Procedia_Biswas.pdf","date_created":"2019-01-21T07:28:06Z"}],"title":"An Improved Canny Edge Detection Algorithm Based on Type-2 Fuzzy Sets","date_published":"2012-05-01T00:00:00Z","_id":"5839","extern":"1","publication_status":"published","citation":{"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>.","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>.","short":"R. Biswas, J. Sil, Procedia Technology 4 (2012) 820–824.","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>","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.","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>","ista":"Biswas R, Sil J. 2012. An Improved Canny Edge Detection Algorithm Based on Type-2 Fuzzy Sets. Procedia Technology. 4, 820–824."},"date_created":"2019-01-17T11:54:21Z"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"7208","day":"13","article_processing_charge":"No","language":[{"iso":"eng"}],"status":"public","intvolume":"       417","type":"journal_article","year":"2012","month":"04","date_updated":"2021-01-12T08:05:21Z","abstract":[{"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.","lang":"eng"}],"page":"387 - 394","issue":"5","author":[{"last_name":"Bernecky","id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0893-7036","first_name":"Carrie A","full_name":"Bernecky, Carrie A"},{"full_name":"Taatjes, Dylan","first_name":"Dylan","last_name":"Taatjes"}],"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4582759/"}],"oa_version":"None","citation":{"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.","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.","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>","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>","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>.","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>.","short":"C. Bernecky, D. Taatjes, Journal of Molecular Biology 417 (2012) 387–394."},"publication_status":"published","date_created":"2018-12-11T11:47:24Z","extern":"1","_id":"596","date_published":"2012-04-13T00:00:00Z","oa":1,"volume":417,"title":"Activator-mediator binding stabilizes RNA polymerase II orientation within the human mediator-RNA polymerase II-TFIIF assembly","publication":"Journal of Molecular Biology","publisher":"Elsevier","doi":"10.1016/j.jmb.2012.02.014"},{"_id":"6136","extern":"1","date_published":"2012-03-04T00:00:00Z","title":"Tonic signaling from O2 sensors sets neural circuit activity and behavioral state","publication_status":"published","citation":{"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.","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>.","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>","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":"2019-03-20T14:23:30Z","publisher":"Springer Nature","intvolume":"        15","type":"journal_article","publication_identifier":{"issn":["1097-6256","1546-1726"]},"issue":"4","author":[{"last_name":"Busch","first_name":"Karl Emanuel","full_name":"Busch, Karl Emanuel"},{"last_name":"Laurent","full_name":"Laurent, Patrick","first_name":"Patrick"},{"last_name":"Soltesz","full_name":"Soltesz, Zoltan","first_name":"Zoltan"},{"last_name":"Murphy","first_name":"Robin Joseph","full_name":"Murphy, Robin Joseph"},{"full_name":"Faivre, Olivier","first_name":"Olivier","last_name":"Faivre"},{"last_name":"Hedwig","full_name":"Hedwig, Berthold","first_name":"Berthold"},{"full_name":"Thomas, Martin","first_name":"Martin","last_name":"Thomas"},{"last_name":"Smith","full_name":"Smith, Heather L","first_name":"Heather L"},{"first_name":"Mario","full_name":"de Bono, Mario","orcid":"0000-0001-8347-0443","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","last_name":"de Bono"}],"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3564487/","open_access":"1"}],"date_updated":"2021-01-12T08:06:17Z","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."}],"page":"581-591","oa":1,"volume":15,"doi":"10.1038/nn.3061","publication":"Nature Neuroscience","status":"public","year":"2012","language":[{"iso":"eng"}],"month":"03","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","day":"04","pmid":1,"oa_version":"Submitted Version","external_id":{"pmid":["22388961"]},"quality_controlled":"1"},{"date_updated":"2023-10-16T09:41:31Z","abstract":[{"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.","lang":"eng"}],"article_type":"original","page":"63-78","issue":"1","main_file_link":[{"url":"http://mi.mathnet.ru/eng/jmag525","open_access":"1"}],"author":[{"id":"2A77D7A2-F248-11E8-B48F-1D18A9856A87","last_name":"Pausinger","orcid":"0000-0002-8379-3768","full_name":"Pausinger, Florian","first_name":"Florian"}],"acknowledgement":"This work is supported by the Austrian Science Fund (FWF), Project P22025-N18.\r\n","publication_identifier":{"issn":["1812-9471"]},"type":"journal_article","intvolume":"         8","department":[{"_id":"HeEd"}],"publisher":"B. Verkin Institute for Low Temperature Physics and Engineering","date_created":"2019-06-27T08:16:56Z","publication_status":"published","citation":{"ista":"Pausinger F. 2012. Elementary solutions of the Bernstein problem on two intervals. Journal of Mathematical Physics, Analysis, Geometry. 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.","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.","short":"F. Pausinger, Journal of Mathematical Physics, Analysis, Geometry 8 (2012) 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.","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."},"date_published":"2012-01-01T00:00:00Z","_id":"6588","title":"Elementary solutions of the Bernstein problem on two intervals","external_id":{"isi":["000301173600004"]},"quality_controlled":"1","scopus_import":"1","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","year":"2012","status":"public","language":[{"iso":"eng"}],"article_processing_charge":"No","month":"01","isi":1,"publication":"Journal of Mathematical Physics, Analysis, Geometry","volume":8,"oa":1},{"volume":109,"oa":1,"arxiv":1,"publication":"Physical Review Letters","keyword":["general physics and astronomy"],"doi":"10.1103/physrevlett.109.188101","pmid":1,"day":"31","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","month":"10","status":"public","year":"2012","language":[{"iso":"eng"}],"article_processing_charge":"No","quality_controlled":"1","external_id":{"arxiv":["1206.3528"],"pmid":["23215334"]},"oa_version":"Preprint","scopus_import":"1","date_created":"2021-11-29T14:08:00Z","citation":{"ista":"Šarić A, Cacciuto A. 2012. Mechanism of membrane tube formation induced by adhesive nanocomponents. Physical Review Letters. 109(18), 188101.","ama":"Šarić A, Cacciuto A. Mechanism of membrane tube formation induced by adhesive nanocomponents. <i>Physical Review Letters</i>. 2012;109(18). doi:<a href=\"https://doi.org/10.1103/physrevlett.109.188101\">10.1103/physrevlett.109.188101</a>","ieee":"A. Šarić and A. Cacciuto, “Mechanism of membrane tube formation induced by adhesive nanocomponents,” <i>Physical Review Letters</i>, vol. 109, no. 18. American Physical Society, 2012.","apa":"Šarić, A., &#38; Cacciuto, A. (2012). Mechanism of membrane tube formation induced by adhesive nanocomponents. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevlett.109.188101\">https://doi.org/10.1103/physrevlett.109.188101</a>","mla":"Šarić, Anđela, and Angelo Cacciuto. “Mechanism of Membrane Tube Formation Induced by Adhesive Nanocomponents.” <i>Physical Review Letters</i>, vol. 109, no. 18, 188101, American Physical Society, 2012, doi:<a href=\"https://doi.org/10.1103/physrevlett.109.188101\">10.1103/physrevlett.109.188101</a>.","chicago":"Šarić, Anđela, and Angelo Cacciuto. “Mechanism of Membrane Tube Formation Induced by Adhesive Nanocomponents.” <i>Physical Review Letters</i>. American Physical Society, 2012. <a href=\"https://doi.org/10.1103/physrevlett.109.188101\">https://doi.org/10.1103/physrevlett.109.188101</a>.","short":"A. Šarić, A. Cacciuto, Physical Review Letters 109 (2012)."},"publication_status":"published","title":"Mechanism of membrane tube formation induced by adhesive nanocomponents","extern":"1","_id":"10387","date_published":"2012-10-31T00:00:00Z","publisher":"American Physical Society","publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]},"intvolume":"       109","type":"journal_article","article_type":"original","article_number":"188101","abstract":[{"lang":"eng","text":"We report numerical simulations of membrane tubulation driven by large colloidal particles. Using Monte Carlo simulations we study how the process depends on particle size and binding strength, and present accurate free energy calculations to sort out how tube formation compares with the competing budding process. We find that tube formation is a result of the collective behavior of the particles adhering on the surface, and it occurs for binding strengths that are smaller than those required for budding. We also find that long linear aggregates of particles forming on the membrane surface act as nucleation seeds for tubulation by lowering the free energy barrier associated to the process."}],"date_updated":"2021-11-29T14:29:25Z","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1206.3528"}],"author":[{"id":"bf63d406-f056-11eb-b41d-f263a6566d8b","last_name":"Šarić","orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela","first_name":"Anđela"},{"last_name":"Cacciuto","first_name":"Angelo","full_name":"Cacciuto, Angelo"}],"issue":"18"},{"day":"14","pmid":1,"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","month":"03","article_processing_charge":"No","year":"2012","language":[{"iso":"eng"}],"status":"public","quality_controlled":"1","external_id":{"pmid":["22540513"],"arxiv":["1201.0036"]},"oa_version":"Preprint","scopus_import":"1","oa":1,"volume":108,"publication":"Physical Review Letters","arxiv":1,"doi":"10.1103/physrevlett.108.118101","keyword":["general physics and astronomy"],"publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]},"type":"journal_article","intvolume":"       108","article_type":"original","article_number":"118101","abstract":[{"lang":"eng","text":"Using computer simulations, we show that lipid membranes can mediate linear aggregation of spherical nanoparticles binding to it for a wide range of biologically relevant bending rigidities. This result is in net contrast with the isotropic aggregation of nanoparticles on fluid interfaces or the expected clustering of isotropic insertions in biological membranes. We present a phase diagram indicating where linear aggregation is expected and compute explicitly the free-energy barriers associated with linear and isotropic aggregation. Finally, we provide simple scaling arguments to explain this phenomenology."}],"date_updated":"2021-11-29T15:12:13Z","acknowledgement":"This work was supported by the National Science Foundation under Career Grant No. DMR-0846426.\r\n","author":[{"last_name":"Šarić","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","first_name":"Anđela","full_name":"Šarić, Anđela","orcid":"0000-0002-7854-2139"},{"full_name":"Cacciuto, Angelo","first_name":"Angelo","last_name":"Cacciuto"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1201.0036"}],"issue":"11","citation":{"short":"A. Šarić, A. Cacciuto, Physical Review Letters 108 (2012).","chicago":"Šarić, Anđela, and Angelo Cacciuto. “Fluid Membranes Can Drive Linear Aggregation of Adsorbed Spherical Nanoparticles.” <i>Physical Review Letters</i>. American Physical Society, 2012. <a href=\"https://doi.org/10.1103/physrevlett.108.118101\">https://doi.org/10.1103/physrevlett.108.118101</a>.","mla":"Šarić, Anđela, and Angelo Cacciuto. “Fluid Membranes Can Drive Linear Aggregation of Adsorbed Spherical Nanoparticles.” <i>Physical Review Letters</i>, vol. 108, no. 11, 118101, American Physical Society, 2012, doi:<a href=\"https://doi.org/10.1103/physrevlett.108.118101\">10.1103/physrevlett.108.118101</a>.","apa":"Šarić, A., &#38; Cacciuto, A. (2012). Fluid membranes can drive linear aggregation of adsorbed spherical nanoparticles. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevlett.108.118101\">https://doi.org/10.1103/physrevlett.108.118101</a>","ama":"Šarić A, Cacciuto A. Fluid membranes can drive linear aggregation of adsorbed spherical nanoparticles. <i>Physical Review Letters</i>. 2012;108(11). doi:<a href=\"https://doi.org/10.1103/physrevlett.108.118101\">10.1103/physrevlett.108.118101</a>","ieee":"A. Šarić and A. Cacciuto, “Fluid membranes can drive linear aggregation of adsorbed spherical nanoparticles,” <i>Physical Review Letters</i>, vol. 108, no. 11. American Physical Society, 2012.","ista":"Šarić A, Cacciuto A. 2012. Fluid membranes can drive linear aggregation of adsorbed spherical nanoparticles. Physical Review Letters. 108(11), 118101."},"publication_status":"published","date_created":"2021-11-29T14:30:05Z","title":"Fluid membranes can drive linear aggregation of adsorbed spherical nanoparticles","_id":"10388","date_published":"2012-03-14T00:00:00Z","extern":"1","publisher":"American Physical Society"},{"month":"05","article_processing_charge":"No","language":[{"iso":"eng"}],"status":"public","year":"2012","day":"25","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"6334","oa_version":"Preprint","external_id":{"arxiv":["1201.1008"]},"oa":1,"volume":108,"doi":"10.1103/PhysRevLett.108.215302","publication":"Physical Review Letters","arxiv":1,"type":"journal_article","intvolume":"       108","author":[{"first_name":"Manfred","full_name":"Mark, Manfred","last_name":"Mark"},{"last_name":"Haller","first_name":"Elmar","full_name":"Haller, Elmar"},{"last_name":"Lauber","first_name":"Katharina","full_name":"Lauber, Katharina"},{"last_name":"Danzl","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","first_name":"Johann G","full_name":"Danzl, Johann G","orcid":"0000-0001-8559-3973"},{"last_name":"Janisch","first_name":"Alexander","full_name":"Janisch, Alexander"},{"last_name":"Büchler","full_name":"Büchler, Hans","first_name":"Hans"},{"last_name":"Daley","full_name":"Daley, Andrew","first_name":"Andrew"},{"last_name":"Nägerl","first_name":"Hanns","full_name":"Nägerl, Hanns"}],"main_file_link":[{"url":"https://arxiv.org/abs/1201.1008","open_access":"1"}],"acknowledgement":"We are indebted to R. Grimm for generous support. We thank J. von Stecher, P. Johnson, and E. Tiesinga for fruitful discussions. We gratefully acknowledge funding by the Austrian Science Fund (FWF) within Project No. I153-N16 and within the framework of the European Science Foundation (ESF) EuroQUASAR collective research project QuDeGPM, and by the European Research Council (ERC) under Project No. 278417.","issue":"21","abstract":[{"lang":"eng","text":"We prepare and study a metastable attractive Mott-insulator state formed with bosonic atoms in a three-dimensional optical lattice. Starting from a Mott insulator with Cs atoms at weak repulsive interactions, we use a magnetic Feshbach resonance to tune the interactions to large attractive values and produce a metastable state pinned by attractive interactions with a lifetime on the order of 10 s. We probe the (de)excitation spectrum via lattice modulation spectroscopy, measuring the interaction dependence of two- and three-body bound-state energies. As a result of increased on-site three-body loss we observe resonance broadening and suppression of tunneling processes that produce three-body occupation."}],"date_updated":"2021-01-12T06:47:58Z","title":"Preparation and spectroscopy of a metastable mott-insulator state with attractive interactions","date_published":"2012-05-25T00:00:00Z","extern":"1","_id":"1056","citation":{"ista":"Mark M, Haller E, Lauber K, Danzl JG, Janisch A, Büchler H, Daley A, Nägerl H. 2012. Preparation and spectroscopy of a metastable mott-insulator state with attractive interactions. Physical Review Letters. 108(21).","ama":"Mark M, Haller E, Lauber K, et al. Preparation and spectroscopy of a metastable mott-insulator state with attractive interactions. <i>Physical Review Letters</i>. 2012;108(21). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.108.215302\">10.1103/PhysRevLett.108.215302</a>","ieee":"M. Mark <i>et al.</i>, “Preparation and spectroscopy of a metastable mott-insulator state with attractive interactions,” <i>Physical Review Letters</i>, vol. 108, no. 21. American Physical Society, 2012.","apa":"Mark, M., Haller, E., Lauber, K., Danzl, J. G., Janisch, A., Büchler, H., … Nägerl, H. (2012). Preparation and spectroscopy of a metastable mott-insulator state with attractive interactions. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.108.215302\">https://doi.org/10.1103/PhysRevLett.108.215302</a>","chicago":"Mark, Manfred, Elmar Haller, Katharina Lauber, Johann G Danzl, Alexander Janisch, Hans Büchler, Andrew Daley, and Hanns Nägerl. “Preparation and Spectroscopy of a Metastable Mott-Insulator State with Attractive Interactions.” <i>Physical Review Letters</i>. American Physical Society, 2012. <a href=\"https://doi.org/10.1103/PhysRevLett.108.215302\">https://doi.org/10.1103/PhysRevLett.108.215302</a>.","mla":"Mark, Manfred, et al. “Preparation and Spectroscopy of a Metastable Mott-Insulator State with Attractive Interactions.” <i>Physical Review Letters</i>, vol. 108, no. 21, American Physical Society, 2012, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.108.215302\">10.1103/PhysRevLett.108.215302</a>.","short":"M. Mark, E. Haller, K. Lauber, J.G. Danzl, A. Janisch, H. Büchler, A. Daley, H. Nägerl, Physical Review Letters 108 (2012)."},"publication_status":"published","date_created":"2018-12-11T11:49:55Z","publisher":"American Physical Society"},{"oa_version":"Published Version","quality_controlled":"1","article_processing_charge":"No","status":"public","language":[{"iso":"eng"}],"year":"2012","month":"02","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","alternative_title":["Bulletin of the American Physical Society"],"day":"01","publication":"APS March Meeting 2012","oa":1,"volume":57,"issue":"1","main_file_link":[{"open_access":"1","url":"https://meetings.aps.org/Meeting/MAR12/Event/167014"}],"author":[{"full_name":"Polshyn, Hryhoriy","first_name":"Hryhoriy","orcid":"0000-0001-8223-8896","last_name":"Polshyn","id":"edfc7cb1-526e-11ec-b05a-e6ecc27e4e48"},{"first_name":"Raffi","full_name":"Budakian, Raffi","last_name":"Budakian"}],"acknowledgement":"This work was supported by the Center for Emergent Superconductivity, an Energy Frontier Research Center funded by the U.S. DOE, Office of Science, under Award No. DE-AC0298CH1088.","date_updated":"2022-02-08T10:48:01Z","conference":{"name":"APS: American Physical Society","location":"Boston, MA, United States","end_date":"2012-03-02","start_date":"2012-02-27"},"article_number":"X21.00008","abstract":[{"text":"The goal of this work is to study the superconducting coherence length in the fluctuation regime in cuprate superconductors. In this work we present cantilever torque magnetometry measurements of micron-size BSCCO flakes patterned with arrays of nanometer scale rings or holes. Using ultrasensitive dynamic torque magnetometry, oscillations in magnetization are observed near Tc as a function of the applied magnetic flux threading the array. Special effort was made to detect the oscillations in magnetization at temperatures above Tc, where the Nernst effect and magnetization measurements suggest the possibility of pairing. To constrain the magnitude of the coherence length in the fluctuation regime, we will present the dependence of the amplitude of the h/2e period oscillations as a function of temperature and hole size.","lang":"eng"}],"intvolume":"        57","type":"conference","publication_identifier":{"issn":["0003-0503"]},"publisher":"American Physical Society","_id":"10750","date_published":"2012-02-01T00:00:00Z","extern":"1","title":"Cantilever torque magnetometry study of multiply connected BSCCO arrays near Tc","citation":{"ista":"Polshyn H, Budakian R. 2012. Cantilever torque magnetometry study of multiply connected BSCCO arrays near Tc. APS March Meeting 2012. APS: American Physical Society, Bulletin of the American Physical Society, vol. 57, X21.00008.","ama":"Polshyn H, Budakian R. Cantilever torque magnetometry study of multiply connected BSCCO arrays near Tc. In: <i>APS March Meeting 2012</i>. Vol 57. American Physical Society; 2012.","ieee":"H. Polshyn and R. Budakian, “Cantilever torque magnetometry study of multiply connected BSCCO arrays near Tc,” in <i>APS March Meeting 2012</i>, Boston, MA, United States, 2012, vol. 57, no. 1.","apa":"Polshyn, H., &#38; Budakian, R. (2012). Cantilever torque magnetometry study of multiply connected BSCCO arrays near Tc. In <i>APS March Meeting 2012</i> (Vol. 57). Boston, MA, United States: American Physical Society.","chicago":"Polshyn, Hryhoriy, and Raffi Budakian. “Cantilever Torque Magnetometry Study of Multiply Connected BSCCO Arrays near Tc.” In <i>APS March Meeting 2012</i>, Vol. 57. American Physical Society, 2012.","mla":"Polshyn, Hryhoriy, and Raffi Budakian. “Cantilever Torque Magnetometry Study of Multiply Connected BSCCO Arrays near Tc.” <i>APS March Meeting 2012</i>, vol. 57, no. 1, X21.00008, American Physical Society, 2012.","short":"H. Polshyn, R. Budakian, in:, APS March Meeting 2012, American Physical Society, 2012."},"publication_status":"published","date_created":"2022-02-08T10:39:08Z"},{"quality_controlled":"1","external_id":{"pmid":["22984074"]},"has_accepted_license":"1","oa_version":"Published Version","scopus_import":"1","day":"14","pmid":1,"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","month":"09","article_processing_charge":"No","year":"2012","language":[{"iso":"eng"}],"status":"public","publication":"Science","doi":"10.1126/science.1224839","oa":1,"volume":337,"article_type":"original","page":"1360-1364","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_updated":"2021-12-14T08:28:51Z","author":[{"first_name":"Christian A.","full_name":"Ibarra, Christian A.","last_name":"Ibarra"},{"full_name":"Feng, Xiaoqi","first_name":"Xiaoqi","last_name":"Feng"},{"full_name":"Schoft, Vera K.","first_name":"Vera K.","last_name":"Schoft"},{"last_name":"Hsieh","first_name":"Tzung-Fu","full_name":"Hsieh, Tzung-Fu"},{"first_name":"Rie","full_name":"Uzawa, Rie","last_name":"Uzawa"},{"last_name":"Rodrigues","full_name":"Rodrigues, Jessica A.","first_name":"Jessica A."},{"last_name":"Zemach","first_name":"Assaf","full_name":"Zemach, Assaf"},{"first_name":"Nina","full_name":"Chumak, Nina","last_name":"Chumak"},{"last_name":"Machlicova","full_name":"Machlicova, Adriana","first_name":"Adriana"},{"last_name":"Nishimura","first_name":"Toshiro","full_name":"Nishimura, Toshiro"},{"full_name":"Rojas, Denisse","first_name":"Denisse","last_name":"Rojas"},{"last_name":"Fischer","first_name":"Robert L.","full_name":"Fischer, Robert L."},{"last_name":"Tamaru","full_name":"Tamaru, Hisashi","first_name":"Hisashi"},{"id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","last_name":"Zilberman","orcid":"0000-0002-0123-8649","full_name":"Zilberman, Daniel","first_name":"Daniel"}],"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4034762/","open_access":"1"}],"issue":"6100","ddc":["580"],"publication_identifier":{"eissn":["1095-9203"],"issn":["0036-8075"]},"intvolume":"       337","type":"journal_article","publisher":"American Association for the Advancement of Science","department":[{"_id":"DaZi"}],"citation":{"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.","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>.","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>.","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>","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.","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>"},"publication_status":"published","date_created":"2021-06-04T07:51:31Z","title":"Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes","extern":"1","_id":"9451","date_published":"2012-09-14T00:00:00Z"},{"external_id":{"pmid":["23071449"]},"quality_controlled":"1","scopus_import":"1","oa_version":"Published Version","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","pmid":1,"day":"11","language":[{"iso":"eng"}],"status":"public","year":"2012","article_processing_charge":"No","month":"10","publication":"PLoS Genetics","doi":"10.1371/journal.pgen.1002988","volume":8,"oa":1,"date_updated":"2021-12-14T08:29:57Z","article_type":"original","abstract":[{"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.","lang":"eng"}],"article_number":"e1002988","issue":"10","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1371/journal.pgen.1002988"}],"author":[{"last_name":"Coleman-Derr","first_name":"Devin","full_name":"Coleman-Derr, Devin"},{"orcid":"0000-0002-0123-8649","first_name":"Daniel","full_name":"Zilberman, Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","last_name":"Zilberman"}],"publication_identifier":{"eissn":["1553-7404"],"issn":["1553-7390"]},"type":"journal_article","intvolume":"         8","department":[{"_id":"DaZi"}],"publisher":"Public Library of Science","date_created":"2021-06-07T10:55:27Z","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.","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>.","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>.","short":"D. Coleman-Derr, D. Zilberman, PLoS Genetics 8 (2012).","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.","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>","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>"},"publication_status":"published","_id":"9497","date_published":"2012-10-11T00:00:00Z","extern":"1","title":"Deposition of histone variant H2A.Z within gene bodies regulates responsive genes"},{"publication_identifier":{"issn":["1553-7390"],"eissn":["1553-7404"]},"type":"journal_article","intvolume":"         8","date_updated":"2021-12-14T08:31:14Z","article_number":"e1002512","article_type":"original","abstract":[{"lang":"eng","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."}],"issue":"3","author":[{"last_name":"Kim","full_name":"Kim, Sang Yeol","first_name":"Sang Yeol"},{"first_name":"Jungeun","full_name":"Lee, Jungeun","last_name":"Lee"},{"first_name":"Leor","full_name":"Eshed-Williams, Leor","last_name":"Eshed-Williams"},{"full_name":"Zilberman, Daniel","first_name":"Daniel","orcid":"0000-0002-0123-8649","last_name":"Zilberman","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1"},{"last_name":"Sung","full_name":"Sung, Z. Renee","first_name":"Z. Renee"}],"main_file_link":[{"url":"https://doi.org/10.1371/journal.pgen.1002512","open_access":"1"}],"publication_status":"published","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.","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>","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>.","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>.","short":"S.Y. Kim, J. Lee, L. Eshed-Williams, D. Zilberman, Z.R. Sung, PLoS Genetics 8 (2012)."},"date_created":"2021-06-07T11:07:56Z","_id":"9499","extern":"1","date_published":"2012-03-22T00:00:00Z","title":"EMF1 and PRC2 cooperate to repress key regulators of Arabidopsis development","publisher":"Public Library of Science","department":[{"_id":"DaZi"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","day":"22","pmid":1,"article_processing_charge":"No","language":[{"iso":"eng"}],"status":"public","year":"2012","month":"03","external_id":{"pmid":["22457632"]},"quality_controlled":"1","scopus_import":"1","oa_version":"Published Version","oa":1,"volume":8,"publication":"PLoS Genetics","doi":"10.1371/journal.pgen.1002512"},{"author":[{"last_name":"Coleman-Derr","first_name":"D.","full_name":"Coleman-Derr, D."},{"first_name":"Daniel","full_name":"Zilberman, Daniel","orcid":"0000-0002-0123-8649","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","last_name":"Zilberman"}],"main_file_link":[{"url":"https://doi.org/10.1101/sqb.2012.77.014944","open_access":"1"}],"date_updated":"2021-12-14T08:33:09Z","abstract":[{"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.","lang":"eng"}],"article_type":"review","page":"147-154","type":"journal_article","intvolume":"        77","publication_identifier":{"issn":["0091-7451"],"eissn":["1943-4456"]},"publisher":"Cold Spring Harbor Laboratory Press","department":[{"_id":"DaZi"}],"_id":"9535","extern":"1","date_published":"2012-12-18T00:00:00Z","title":"DNA methylation, H2A.Z, and the regulation of constitutive expression","citation":{"short":"D. Coleman-Derr, D. Zilberman, Cold Spring Harbor Symposia on Quantitative Biology 77 (2012) 147–154.","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>.","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>","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>","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.","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."},"publication_status":"published","date_created":"2021-06-08T13:01:23Z","scopus_import":"1","oa_version":"Published Version","external_id":{"pmid":["23250988"]},"quality_controlled":"1","article_processing_charge":"No","status":"public","year":"2012","language":[{"iso":"eng"}],"month":"12","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","day":"18","pmid":1,"doi":"10.1101/sqb.2012.77.014944","publication":"Cold Spring Harbor Symposia on Quantitative Biology","oa":1,"volume":77},{"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."}],"quality_controlled":0,"date_updated":"2021-01-12T08:22:18Z","author":[{"last_name":"Bieri","full_name":"Bieri, Samuel","first_name":"Samuel"},{"id":"47809E7E-F248-11E8-B48F-1D18A9856A87","last_name":"Serbyn","first_name":"Maksym","full_name":"Maksym Serbyn","orcid":"0000-0002-2399-5827"},{"full_name":"Senthil, Todadri S","first_name":"Todadri","last_name":"Senthil"},{"first_name":"Patrick","full_name":"Lee, Patrick","last_name":"Lee"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1208.3231"}],"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).","issue":"22","day":"13","publist_id":"6431","month":"12","intvolume":"        86","type":"journal_article","year":"2012","status":"public","publication":"Physical Review B - Condensed Matter and Materials Physics","publisher":"American Physical Society","doi":"10.1103/PhysRevB.86.224409","date_created":"2018-12-11T11:49:27Z","publication_status":"published","citation":{"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>.","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).","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>","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.","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>","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)."},"volume":86,"title":"Paired chiral spin liquid with a Fermi surface in S=1 model on the triangular lattice","oa":1,"extern":1,"_id":"966","date_published":"2012-12-13T00:00:00Z"},{"department":[{"_id":"SyCr"}],"doi":"10.5061/dryad.sv37s","publisher":"Dryad","date_created":"2021-07-30T08:39:13Z","citation":{"apa":"Konrad, M., Vyleta, M., Theis, F., Stock, M., Klatt, M., Drescher, V., … Cremer, S. (2012). Data from: Social transfer of pathogenic fungus promotes active immunisation in ant colonies. Dryad. <a href=\"https://doi.org/10.5061/dryad.sv37s\">https://doi.org/10.5061/dryad.sv37s</a>","ama":"Konrad M, Vyleta M, Theis F, et al. Data from: Social transfer of pathogenic fungus promotes active immunisation in ant colonies. 2012. doi:<a href=\"https://doi.org/10.5061/dryad.sv37s\">10.5061/dryad.sv37s</a>","ieee":"M. Konrad <i>et al.</i>, “Data from: Social transfer of pathogenic fungus promotes active immunisation in ant colonies.” Dryad, 2012.","short":"M. Konrad, M. Vyleta, F. Theis, M. Stock, M. Klatt, V. Drescher, C. Marr, L.V. Ugelvig, S. Cremer, (2012).","mla":"Konrad, Matthias, et al. <i>Data from: Social Transfer of Pathogenic Fungus Promotes Active Immunisation in Ant Colonies</i>. Dryad, 2012, doi:<a href=\"https://doi.org/10.5061/dryad.sv37s\">10.5061/dryad.sv37s</a>.","chicago":"Konrad, Matthias, Meghan Vyleta, Fabian Theis, Miriam Stock, Martina Klatt, Verena Drescher, Carsten Marr, Line V Ugelvig, and Sylvia Cremer. “Data from: Social Transfer of Pathogenic Fungus Promotes Active Immunisation in Ant Colonies.” Dryad, 2012. <a href=\"https://doi.org/10.5061/dryad.sv37s\">https://doi.org/10.5061/dryad.sv37s</a>.","ista":"Konrad M, Vyleta M, Theis F, Stock M, Klatt M, Drescher V, Marr C, Ugelvig LV, Cremer S. 2012. Data from: Social transfer of pathogenic fungus promotes active immunisation in ant colonies, Dryad, <a href=\"https://doi.org/10.5061/dryad.sv37s\">10.5061/dryad.sv37s</a>."},"date_published":"2012-09-27T00:00:00Z","_id":"9755","title":"Data from: Social transfer of pathogenic fungus promotes active immunisation in ant colonies","oa":1,"date_updated":"2023-02-23T11:18:41Z","abstract":[{"lang":"eng","text":"Due to the omnipresent risk of epidemics, insect societies have evolved sophisticated disease defences at the individual and colony level. An intriguing yet little understood phenomenon is that social contact to pathogen-exposed individuals reduces susceptibility of previously naive nestmates to this pathogen. We tested whether such social immunisation in Lasius ants against the entomopathogenic fungus Metarhizium anisopliae is based on active upregulation of the immune system of nestmates following contact to an infectious individual or passive protection via transfer of immune effectors among group members—that is, active versus passive immunisation. We found no evidence for involvement of passive immunisation via transfer of antimicrobials among colony members. Instead, intensive allogrooming behaviour between naive and pathogen-exposed ants before fungal conidia firmly attached to their cuticle suggested passage of the pathogen from the exposed individuals to their nestmates. By tracing fluorescence-labelled conidia we indeed detected frequent pathogen transfer to the nestmates, where they caused low-level infections as revealed by growth of small numbers of fungal colony forming units from their dissected body content. These infections rarely led to death, but instead promoted an enhanced ability to inhibit fungal growth and an active upregulation of immune genes involved in antifungal defences (defensin and prophenoloxidase, PPO). Contrarily, there was no upregulation of the gene cathepsin L, which is associated with antibacterial and antiviral defences, and we found no increased antibacterial activity of nestmates of fungus-exposed ants. This indicates that social immunisation after fungal exposure is specific, similar to recent findings for individual-level immune priming in invertebrates. Epidemiological modeling further suggests that active social immunisation is adaptive, as it leads to faster elimination of the disease and lower death rates than passive immunisation. Interestingly, humans have also utilised the protective effect of low-level infections to fight smallpox by intentional transfer of low pathogen doses (“variolation” or “inoculation”)."}],"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"3242"}]},"author":[{"full_name":"Konrad, Matthias","first_name":"Matthias","last_name":"Konrad","id":"46528076-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Vyleta","id":"418901AA-F248-11E8-B48F-1D18A9856A87","full_name":"Vyleta, Meghan","first_name":"Meghan"},{"full_name":"Theis, Fabian","first_name":"Fabian","last_name":"Theis"},{"full_name":"Stock, Miriam","first_name":"Miriam","id":"42462816-F248-11E8-B48F-1D18A9856A87","last_name":"Stock"},{"full_name":"Klatt, Martina","first_name":"Martina","id":"E60F29C6-E9AE-11E9-AF6E-D190C7302F38","last_name":"Klatt"},{"full_name":"Drescher, Verena","first_name":"Verena","last_name":"Drescher"},{"first_name":"Carsten","full_name":"Marr, Carsten","last_name":"Marr"},{"last_name":"Ugelvig","id":"3DC97C8E-F248-11E8-B48F-1D18A9856A87","first_name":"Line V","full_name":"Ugelvig, Line V","orcid":"0000-0003-1832-8883"},{"full_name":"Cremer, Sylvia","first_name":"Sylvia","orcid":"0000-0002-2193-3868","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","last_name":"Cremer"}],"oa_version":"Published Version","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.sv37s"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","day":"27","year":"2012","status":"public","type":"research_data_reference","article_processing_charge":"No","month":"09"},{"department":[{"_id":"SyCr"}],"doi":"10.5061/dryad.61649","publisher":"Dryad","title":"Data from: Ants disinfect fungus-exposed brood by oral uptake and spread of their poison","oa":1,"date_published":"2012-12-14T00:00:00Z","_id":"9757","date_created":"2021-07-30T12:31:31Z","citation":{"mla":"Tragust, Simon, et al. <i>Data from: Ants Disinfect Fungus-Exposed Brood by Oral Uptake and Spread of Their Poison</i>. Dryad, 2012, doi:<a href=\"https://doi.org/10.5061/dryad.61649\">10.5061/dryad.61649</a>.","chicago":"Tragust, Simon, Barbara Mitteregger, Vanessa Barone, Matthias Konrad, Line V Ugelvig, and Sylvia Cremer. “Data from: Ants Disinfect Fungus-Exposed Brood by Oral Uptake and Spread of Their Poison.” Dryad, 2012. <a href=\"https://doi.org/10.5061/dryad.61649\">https://doi.org/10.5061/dryad.61649</a>.","short":"S. Tragust, B. Mitteregger, V. Barone, M. Konrad, L.V. Ugelvig, S. Cremer, (2012).","ama":"Tragust S, Mitteregger B, Barone V, Konrad M, Ugelvig LV, Cremer S. Data from: Ants disinfect fungus-exposed brood by oral uptake and spread of their poison. 2012. doi:<a href=\"https://doi.org/10.5061/dryad.61649\">10.5061/dryad.61649</a>","ieee":"S. Tragust, B. Mitteregger, V. Barone, M. Konrad, L. V. Ugelvig, and S. Cremer, “Data from: Ants disinfect fungus-exposed brood by oral uptake and spread of their poison.” Dryad, 2012.","apa":"Tragust, S., Mitteregger, B., Barone, V., Konrad, M., Ugelvig, L. V., &#38; Cremer, S. (2012). Data from: Ants disinfect fungus-exposed brood by oral uptake and spread of their poison. Dryad. <a href=\"https://doi.org/10.5061/dryad.61649\">https://doi.org/10.5061/dryad.61649</a>","ista":"Tragust S, Mitteregger B, Barone V, Konrad M, Ugelvig LV, Cremer S. 2012. Data from: Ants disinfect fungus-exposed brood by oral uptake and spread of their poison, Dryad, <a href=\"https://doi.org/10.5061/dryad.61649\">10.5061/dryad.61649</a>."},"oa_version":"Published Version","author":[{"full_name":"Tragust, Simon","first_name":"Simon","id":"35A7A418-F248-11E8-B48F-1D18A9856A87","last_name":"Tragust"},{"last_name":"Mitteregger","id":"479DDAAC-E9CD-11E9-9B5F-82450873F7A1","first_name":"Barbara","full_name":"Mitteregger, Barbara"},{"full_name":"Barone, Vanessa","first_name":"Vanessa","orcid":"0000-0003-2676-3367","last_name":"Barone","id":"419EECCC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Konrad, Matthias","first_name":"Matthias","last_name":"Konrad","id":"46528076-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Ugelvig","id":"3DC97C8E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1832-8883","full_name":"Ugelvig, Line V","first_name":"Line V"},{"last_name":"Cremer","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2193-3868","full_name":"Cremer, Sylvia","first_name":"Sylvia"}],"main_file_link":[{"url":"https://doi.org/10.5061/dryad.61649","open_access":"1"}],"related_material":{"record":[{"id":"2926","status":"public","relation":"used_in_publication"}]},"abstract":[{"lang":"eng","text":"To fight infectious diseases, host immune defences are employed at multiple levels. Sanitary behaviour, such as pathogen avoidance and removal, acts as a first line of defence to prevent infection [1] before activation of the physiological immune system. Insect societies have evolved a wide range of collective hygiene measures and intensive health care towards pathogen-exposed group members [2]. One of the most common behaviours is allogrooming, in which nestmates remove infectious particles from the body surfaces of exposed individuals [3]. Here we show that, in invasive garden ants, grooming of fungus-exposed brood is effective beyond the sheer mechanical removal of fungal conidiospores as it also includes chemical disinfection through the application of poison produced by the ants themselves. Formic acid is the main active component of the poison. It inhibits fungal growth of conidiospores remaining on the brood surface after grooming and also those collected in the mouth of the grooming ant. This dual function is achieved by uptake of the poison droplet into the mouth through acidopore self-grooming and subsequent application onto the infectious brood via brood grooming. This extraordinary behaviour extends current understanding of grooming and the establishment of social immunity in insect societies."}],"date_updated":"2023-02-23T11:04:28Z","month":"12","status":"public","type":"research_data_reference","year":"2012","article_processing_charge":"No","day":"14","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf"},{"related_material":{"record":[{"relation":"used_in_publication","id":"2944","status":"public"}]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.274b1"}],"oa_version":"Published Version","author":[{"full_name":"Aeschbacher, Simon","first_name":"Simon","last_name":"Aeschbacher","id":"2D35326E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Futschik","full_name":"Futschik, Andreas","first_name":"Andreas"},{"full_name":"Beaumont, Mark","first_name":"Mark","last_name":"Beaumont"}],"date_updated":"2023-02-23T11:05:19Z","abstract":[{"lang":"eng","text":"We propose a two-step procedure for estimating multiple migration rates in an approximate Bayesian computation (ABC) framework, accounting for global nuisance parameters. The approach is not limited to migration, but generally of interest for inference problems with multiple parameters and a modular structure (e.g. independent sets of demes or loci). We condition on a known, but complex demographic model of a spatially subdivided population, motivated by the reintroduction of Alpine ibex (Capra ibex) into Switzerland. In the first step, the global parameters ancestral mutation rate and male mating skew have been estimated for the whole population in Aeschbacher et al. (Genetics 2012; 192: 1027). In the second step, we estimate in this study the migration rates independently for clusters of demes putatively connected by migration. For large clusters (many migration rates), ABC faces the problem of too many summary statistics. We therefore assess by simulation if estimation per pair of demes is a valid alternative. We find that the trade-off between reduced dimensionality for the pairwise estimation on the one hand and lower accuracy due to the assumption of pairwise independence on the other depends on the number of migration rates to be inferred: the accuracy of the pairwise approach increases with the number of parameters, relative to the joint estimation approach. To distinguish between low and zero migration, we perform ABC-type model comparison between a model with migration and one without. Applying the approach to microsatellite data from Alpine ibex, we find no evidence for substantial gene flow via migration, except for one pair of demes in one direction."}],"type":"research_data_reference","status":"public","year":"2012","article_processing_charge":"No","month":"11","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","day":"14","department":[{"_id":"NiBa"}],"publisher":"Dryad","doi":"10.5061/dryad.274b1","date_published":"2012-11-14T00:00:00Z","_id":"9758","title":"Data from: Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates","oa":1,"date_created":"2021-07-30T12:36:39Z","citation":{"ista":"Aeschbacher S, Futschik A, Beaumont M. 2012. Data from: Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates, Dryad, <a href=\"https://doi.org/10.5061/dryad.274b1\">10.5061/dryad.274b1</a>.","apa":"Aeschbacher, S., Futschik, A., &#38; Beaumont, M. (2012). Data from: Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates. Dryad. <a href=\"https://doi.org/10.5061/dryad.274b1\">https://doi.org/10.5061/dryad.274b1</a>","ama":"Aeschbacher S, Futschik A, Beaumont M. Data from: Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates. 2012. doi:<a href=\"https://doi.org/10.5061/dryad.274b1\">10.5061/dryad.274b1</a>","ieee":"S. Aeschbacher, A. Futschik, and M. Beaumont, “Data from: Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates.” Dryad, 2012.","short":"S. Aeschbacher, A. Futschik, M. Beaumont, (2012).","mla":"Aeschbacher, Simon, et al. <i>Data from: Approximate Bayesian Computation for Modular Inference Problems with Many Parameters: The Example of Migration Rates</i>. Dryad, 2012, doi:<a href=\"https://doi.org/10.5061/dryad.274b1\">10.5061/dryad.274b1</a>.","chicago":"Aeschbacher, Simon, Andreas Futschik, and Mark Beaumont. “Data from: Approximate Bayesian Computation for Modular Inference Problems with Many Parameters: The Example of Migration Rates.” Dryad, 2012. <a href=\"https://doi.org/10.5061/dryad.274b1\">https://doi.org/10.5061/dryad.274b1</a>."}},{"project":[{"name":"Synaptic Mechanisms of Neuronal Network Function","_id":"25BC64A8-B435-11E9-9278-68D0E5697425","grant_number":"JO_780/A5"},{"grant_number":"SFB-TR3-TP10B","name":"Glutamaterge synaptische Übertragung und Plastizität in hippocampalen Mikroschaltkreisen","_id":"25BDE9A4-B435-11E9-9278-68D0E5697425"}],"doi":"10.1038/nrn3125","publication":"Nature Reviews Neuroscience","volume":13,"oa":1,"scopus_import":1,"oa_version":"Submitted Version","has_accepted_license":"1","quality_controlled":"1","status":"public","language":[{"iso":"eng"}],"year":"2012","month":"01","pubrep_id":"820","publist_id":"3322","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","department":[{"_id":"PeJo"}],"publisher":"Nature Publishing Group","file":[{"relation":"main_file","access_level":"open_access","date_updated":"2020-07-14T12:46:07Z","checksum":"4c1c86b2f6e4e1562f5bb800b457ea9f","creator":"system","file_size":314246,"file_id":"4931","date_created":"2018-12-12T10:12:13Z","file_name":"IST-2017-820-v1+1_17463_3_art_file_109404_ltmxbw.pdf","content_type":"application/pdf"},{"content_type":"application/pdf","date_created":"2018-12-12T10:12:14Z","file_name":"IST-2017-820-v1+2_17463_3_figure_109402_ltmwlp.pdf","file_size":1840216,"file_id":"4932","creator":"system","access_level":"open_access","relation":"main_file","date_updated":"2020-07-14T12:46:07Z","checksum":"bceb2efdd49d115f4dde8486bc1be3f2"}],"_id":"3317","date_published":"2012-01-01T00:00:00Z","title":"Nanodomain coupling between Ca(2+) channels and sensors of exocytosis at fast mammalian synapses","date_created":"2018-12-11T12:02:38Z","publication_status":"published","citation":{"apa":"Eggermann, E., Bucurenciu, I., Goswami, S., &#38; Jonas, P. M. (2012). Nanodomain coupling between Ca(2+) channels and sensors of exocytosis at fast mammalian synapses. <i>Nature Reviews Neuroscience</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nrn3125\">https://doi.org/10.1038/nrn3125</a>","ama":"Eggermann E, Bucurenciu I, Goswami S, Jonas PM. Nanodomain coupling between Ca(2+) channels and sensors of exocytosis at fast mammalian synapses. <i>Nature Reviews Neuroscience</i>. 2012;13(1):7-21. doi:<a href=\"https://doi.org/10.1038/nrn3125\">10.1038/nrn3125</a>","ieee":"E. Eggermann, I. Bucurenciu, S. Goswami, and P. M. Jonas, “Nanodomain coupling between Ca(2+) channels and sensors of exocytosis at fast mammalian synapses,” <i>Nature Reviews Neuroscience</i>, vol. 13, no. 1. Nature Publishing Group, pp. 7–21, 2012.","short":"E. Eggermann, I. Bucurenciu, S. Goswami, P.M. Jonas, Nature Reviews Neuroscience 13 (2012) 7–21.","mla":"Eggermann, Emmanuel, et al. “Nanodomain Coupling between Ca(2+) Channels and Sensors of Exocytosis at Fast Mammalian Synapses.” <i>Nature Reviews Neuroscience</i>, vol. 13, no. 1, Nature Publishing Group, 2012, pp. 7–21, doi:<a href=\"https://doi.org/10.1038/nrn3125\">10.1038/nrn3125</a>.","chicago":"Eggermann, Emmanuel, Iancu Bucurenciu, Sarit Goswami, and Peter M Jonas. “Nanodomain Coupling between Ca(2+) Channels and Sensors of Exocytosis at Fast Mammalian Synapses.” <i>Nature Reviews Neuroscience</i>. Nature Publishing Group, 2012. <a href=\"https://doi.org/10.1038/nrn3125\">https://doi.org/10.1038/nrn3125</a>.","ista":"Eggermann E, Bucurenciu I, Goswami S, Jonas PM. 2012. Nanodomain coupling between Ca(2+) channels and sensors of exocytosis at fast mammalian synapses. Nature Reviews Neuroscience. 13(1), 7–21."},"file_date_updated":"2020-07-14T12:46:07Z","issue":"1","acknowledgement":"Work of the authors was funded by grants of the Deutsche Forschungsgemeinschaft to P.J. (grants SFB 780/A5, TR 3/B10 and the Leibniz programme), a European Research Council Advanced grant to P.J. and a Swiss National Foundation fellowship to E.E.\r\nWe thank D. Tsien and E. Neher for their comments on this Review, J. Guzmán and A. Pernía-Andrade for reading earlier versions and E. Kramberger for perfect editorial support. We apologize that owing to space constraints, not all relevant papers could be cited.\r\n","author":[{"id":"34DACA34-E9AE-11E9-849C-D35BD8ADC20C","last_name":"Eggermann","first_name":"Emmanuel","full_name":"Eggermann, Emmanuel"},{"first_name":"Iancu","full_name":"Bucurenciu, Iancu","id":"4BD1D872-E9AE-11E9-9EE9-8BF4597A9E2A","last_name":"Bucurenciu"},{"first_name":"Sarit","full_name":"Goswami, Sarit","last_name":"Goswami","id":"3A578F32-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Peter M","full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","last_name":"Jonas"}],"date_updated":"2021-01-12T07:42:36Z","page":"7 - 21","abstract":[{"text":"The physical distance between presynaptic Ca2+ channels and the Ca2+ sensors that trigger exocytosis of neurotransmitter-containing vesicles is a key determinant of the signalling properties of synapses in the nervous system. Recent functional analysis indicates that in some fast central synapses, transmitter release is triggered by a small number of Ca2+ channels that are coupled to Ca2+ sensors at the nanometre scale. Molecular analysis suggests that this tight coupling is generated by protein–protein interactions involving Ca2+ channels, Ca2+ sensors and various other synaptic proteins. Nanodomain coupling has several functional advantages, as it increases the efficacy, speed and energy efficiency of synaptic transmission.","lang":"eng"}],"intvolume":"        13","type":"journal_article","ddc":["570"]},{"year":"2012","type":"journal_article","intvolume":"        47","status":"public","language":[{"iso":"eng"}],"month":"03","publist_id":"3303","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","day":"01","scopus_import":1,"issue":"3","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1104.1510"}],"author":[{"first_name":"Michael","full_name":"Kerber, Michael","orcid":"0000-0002-8030-9299","last_name":"Kerber","id":"36E4574A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Michael","full_name":"Sagraloff, Michael","last_name":"Sagraloff"}],"oa_version":"Preprint","date_updated":"2021-01-12T07:42:43Z","quality_controlled":"1","page":"239 - 258","abstract":[{"lang":"eng","text":"Computing the topology of an algebraic plane curve C means computing a combinatorial graph that is isotopic to C and thus represents its topology in R2. We prove that, for a polynomial of degree n with integer coefficients bounded by 2ρ, the topology of the induced curve can be computed with  bit operations ( indicates that we omit logarithmic factors). Our analysis improves the previous best known complexity bounds by a factor of n2. The improvement is based on new techniques to compute and refine isolating intervals for the real roots of polynomials, and on the consequent amortized analysis of the critical fibers of the algebraic curve."}],"_id":"3331","date_published":"2012-03-01T00:00:00Z","volume":47,"title":"A worst case bound for topology computation of algebraic curves","oa":1,"date_created":"2018-12-11T12:02:43Z","publication_status":"published","citation":{"ieee":"M. Kerber and M. Sagraloff, “A worst case bound for topology computation of algebraic curves,” <i> Journal of Symbolic Computation</i>, vol. 47, no. 3. Elsevier, pp. 239–258, 2012.","ama":"Kerber M, Sagraloff M. A worst case bound for topology computation of algebraic curves. <i> Journal of Symbolic Computation</i>. 2012;47(3):239-258. doi:<a href=\"https://doi.org/10.1016/j.jsc.2011.11.001\">10.1016/j.jsc.2011.11.001</a>","apa":"Kerber, M., &#38; Sagraloff, M. (2012). A worst case bound for topology computation of algebraic curves. <i> Journal of Symbolic Computation</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jsc.2011.11.001\">https://doi.org/10.1016/j.jsc.2011.11.001</a>","mla":"Kerber, Michael, and Michael Sagraloff. “A Worst Case Bound for Topology Computation of Algebraic Curves.” <i> Journal of Symbolic Computation</i>, vol. 47, no. 3, Elsevier, 2012, pp. 239–58, doi:<a href=\"https://doi.org/10.1016/j.jsc.2011.11.001\">10.1016/j.jsc.2011.11.001</a>.","chicago":"Kerber, Michael, and Michael Sagraloff. “A Worst Case Bound for Topology Computation of Algebraic Curves.” <i> Journal of Symbolic Computation</i>. Elsevier, 2012. <a href=\"https://doi.org/10.1016/j.jsc.2011.11.001\">https://doi.org/10.1016/j.jsc.2011.11.001</a>.","short":"M. Kerber, M. Sagraloff,  Journal of Symbolic Computation 47 (2012) 239–258.","ista":"Kerber M, Sagraloff M. 2012. A worst case bound for topology computation of algebraic curves.  Journal of Symbolic Computation. 47(3), 239–258."},"department":[{"_id":"HeEd"}],"doi":"10.1016/j.jsc.2011.11.001","publisher":"Elsevier","publication":" Journal of Symbolic Computation"},{"oa":1,"volume":7213,"arxiv":1,"doi":"10.1007/978-3-642-28729-9_18","project":[{"call_identifier":"FWF","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"grant_number":"S 11407_N23","call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"3284","alternative_title":["LNCS"],"day":"22","language":[{"iso":"eng"}],"status":"public","year":"2012","month":"03","external_id":{"arxiv":["1107.2009"]},"quality_controlled":"1","scopus_import":1,"related_material":{"record":[{"relation":"earlier_version","id":"5382","status":"public"}]},"oa_version":"Preprint","publication_status":"published","citation":{"short":"K. Chatterjee, in:, Springer, 2012, pp. 270–285.","chicago":"Chatterjee, Krishnendu. “Robustness of Structurally Equivalent Concurrent Parity Games,” 7213:270–85. Springer, 2012. <a href=\"https://doi.org/10.1007/978-3-642-28729-9_18\">https://doi.org/10.1007/978-3-642-28729-9_18</a>.","mla":"Chatterjee, Krishnendu. <i>Robustness of Structurally Equivalent Concurrent Parity Games</i>. Vol. 7213, Springer, 2012, pp. 270–85, doi:<a href=\"https://doi.org/10.1007/978-3-642-28729-9_18\">10.1007/978-3-642-28729-9_18</a>.","apa":"Chatterjee, K. (2012). Robustness of structurally equivalent concurrent parity games (Vol. 7213, pp. 270–285). Presented at the FoSSaCS: Foundations of Software Science and Computation Structures, Tallinn, Estonia: Springer. <a href=\"https://doi.org/10.1007/978-3-642-28729-9_18\">https://doi.org/10.1007/978-3-642-28729-9_18</a>","ama":"Chatterjee K. Robustness of structurally equivalent concurrent parity games. In: Vol 7213. Springer; 2012:270-285. doi:<a href=\"https://doi.org/10.1007/978-3-642-28729-9_18\">10.1007/978-3-642-28729-9_18</a>","ieee":"K. Chatterjee, “Robustness of structurally equivalent concurrent parity games,” presented at the FoSSaCS: Foundations of Software Science and Computation Structures, Tallinn, Estonia, 2012, vol. 7213, pp. 270–285.","ista":"Chatterjee K. 2012. Robustness of structurally equivalent concurrent parity games. FoSSaCS: Foundations of Software Science and Computation Structures, LNCS, vol. 7213, 270–285."},"date_created":"2018-12-11T12:02:46Z","date_published":"2012-03-22T00:00:00Z","_id":"3341","title":"Robustness of structurally equivalent concurrent parity games","ec_funded":1,"publisher":"Springer","department":[{"_id":"KrCh"}],"intvolume":"      7213","type":"conference","date_updated":"2023-02-23T12:23:46Z","conference":{"start_date":"2012-03-24","end_date":"2012-04-01","location":"Tallinn, Estonia","name":"FoSSaCS: Foundations of Software Science and Computation Structures"},"abstract":[{"text":"We consider two-player stochastic games played on a finite state space for an infinite number of rounds. The games are concurrent: in each round, the two players (player 1 and player 2) choose their moves independently and simultaneously; the current state and the two moves determine a probability distribution over the successor states. We also consider the important special case of turn-based stochastic games where players make moves in turns, rather than concurrently. We study concurrent games with \\omega-regular winning conditions specified as parity objectives. The value for player 1 for a parity objective is the maximal probability with which the player can guarantee the satisfaction of the objective against all strategies of the opponent. We study the problem of continuity and robustness of the value function in concurrent and turn-based stochastic parity gameswith respect to imprecision in the transition probabilities. We present quantitative bounds on the difference of the value function (in terms of the imprecision of the transition probabilities) and show the value continuity for structurally equivalent concurrent games (two games are structurally equivalent if the support of the transition function is same and the probabilities differ). We also show robustness of optimal strategies for structurally equivalent turn-based stochastic parity games. Finally we show that the value continuity property breaks without the structurally equivalent assumption (even for Markov chains) and show that our quantitative bound is asymptotically optimal. Hence our results are tight (the assumption is both necessary and sufficient) and optimal (our quantitative bound is asymptotically optimal).","lang":"eng"}],"page":"270 - 285","author":[{"last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu"}],"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1107.2009"}]}]