[{"issue":"6","abstract":[{"lang":"eng","text":"The CLE (CLAVATA3/Embryo Surrounding Region-related) peptides are small secreted signaling peptides that are primarily involved in the regulation of stem cell homeostasis in different plant meristems. Particularly, the characterization of the CLE41-PXY/TDR signaling pathway has greatly advanced our understanding on the potential roles of CLE peptides in vascular development and wood formation. Nevertheless, our knowledge on this gene family in a tree species is limited. In a recent study, we reported on a systematically investigation of the CLE gene family in Populus trichocarpa . The potential roles of PtCLE genes were studied by comparative analysis and transcriptional pro fi ling. Among fi fty PtCLE members, many PtCLE proteins share identical CLE motifs or contain the same CLE motif as that of AtCLEs, while PtCLE genes exhibited either comparable or distinct expression patterns comparing to their Arabidopsis counterparts. These fi ndings indicate the existence of both functional conservation and functional divergence between PtCLEs and their AtCLE orthologues. Our results provide valuable resources for future functional investigations of these critical signaling molecules in woody plants. "}],"type":"journal_article","oa_version":"Submitted Version","_id":"510","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 11","title":"The CLE gene family in Populus trichocarpa","status":"public","article_processing_charge":"No","day":"02","scopus_import":"1","date_published":"2016-06-02T00:00:00Z","citation":{"ista":"Liu Z, Yang N, Lv Y, Pan L, Lv S, Han H, Wang G. 2016. The CLE gene family in Populus trichocarpa. Plant Signaling & Behavior. 11(6), e1191734.","ieee":"Z. Liu et al., “The CLE gene family in Populus trichocarpa,” Plant Signaling & Behavior, vol. 11, no. 6. Taylor & Francis, 2016.","apa":"Liu, Z., Yang, N., Lv, Y., Pan, L., Lv, S., Han, H., & Wang, G. (2016). The CLE gene family in Populus trichocarpa. Plant Signaling & Behavior. Taylor & Francis. https://doi.org/10.1080/15592324.2016.1191734","ama":"Liu Z, Yang N, Lv Y, et al. The CLE gene family in Populus trichocarpa. Plant Signaling & Behavior. 2016;11(6). doi:10.1080/15592324.2016.1191734","chicago":"Liu, Zhijun, Nan Yang, Yanting Lv, Lixia Pan, Shuo Lv, Huibin Han, and Guodong Wang. “The CLE Gene Family in Populus Trichocarpa.” Plant Signaling & Behavior. Taylor & Francis, 2016. https://doi.org/10.1080/15592324.2016.1191734.","mla":"Liu, Zhijun, et al. “The CLE Gene Family in Populus Trichocarpa.” Plant Signaling & Behavior, vol. 11, no. 6, e1191734, Taylor & Francis, 2016, doi:10.1080/15592324.2016.1191734.","short":"Z. Liu, N. Yang, Y. Lv, L. Pan, S. Lv, H. Han, G. Wang, Plant Signaling & Behavior 11 (2016)."},"publication":"Plant Signaling & Behavior","publist_id":"7308","article_number":"e1191734","author":[{"first_name":"Zhijun","last_name":"Liu","full_name":"Liu, Zhijun"},{"first_name":"Nan","last_name":"Yang","full_name":"Yang, Nan"},{"full_name":"Lv, Yanting","first_name":"Yanting","last_name":"Lv"},{"first_name":"Lixia","last_name":"Pan","full_name":"Pan, Lixia"},{"first_name":"Shuo","last_name":"Lv","full_name":"Lv, Shuo"},{"last_name":"Han","first_name":"Huibin","id":"31435098-F248-11E8-B48F-1D18A9856A87","full_name":"Han, Huibin"},{"last_name":"Wang","first_name":"Guodong","full_name":"Wang, Guodong"}],"volume":11,"date_created":"2018-12-11T11:46:53Z","date_updated":"2023-10-17T11:13:40Z","year":"2016","acknowledgement":"We are grateful to Dr. Long (Laboratoire de Reproduction et Developpement des Plantes,CNRS,INRA,ENSLyon,UCBL,Universite de Lyon,France)for critical reading of the article. Work in our group is supported by the National Natural Science Foundation of China (31271575; 31200902), the Fundamental Research Funds for the Central Univ ersities (GK201103005), the Specialized Research Fund for the Doctoral Program of Higher Education from the Ministry of Education of China (20120202120009), the Scientific Research Foundation for the Returned Overseas Chinese Scholars, State Education Ministry, and the Natural Science Basic Research Plan in Shaanxi Province of China (2014JM3064). ","publisher":"Taylor & Francis","department":[{"_id":"JiFr"}],"publication_status":"published","month":"06","doi":"10.1080/15592324.2016.1191734","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4973754/"}],"oa":1,"quality_controlled":"1"},{"abstract":[{"text":"Linking classical microwave electrical circuits to the optical telecommunication band is at the core of modern communication. Future quantum information networks will require coherent microwave-to-optical conversion to link electronic quantum processors and memories via low-loss optical telecommunication networks. Efficient conversion can be achieved with electro-optical modulators operating at the single microwave photon level. In the standard electro-optic modulation scheme, this is impossible because both up- and down-converted sidebands are necessarily present. Here, we demonstrate true single-sideband up- or down-conversion in a triply resonant whispering gallery mode resonator by explicitly addressing modes with asymmetric free spectral range. Compared to previous experiments, we show a 3 orders of magnitude improvement of the electro-optical conversion efficiency, reaching 0.1% photon number conversion for a 10 GHz microwave tone at 0.42 mW of optical pump power. The presented scheme is fully compatible with existing superconducting 3D circuit quantum electrodynamics technology and can be used for nonclassical state conversion and communication. Our conversion bandwidth is larger than 1 MHz and is not fundamentally limited.","lang":"eng"}],"issue":"6","type":"journal_article","oa_version":"Published Version","_id":"1263","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Efficient microwave to optical photon conversion: An electro-optical realization","intvolume":" 3","day":"20","article_processing_charge":"No","scopus_import":"1","date_published":"2016-06-20T00:00:00Z","publication":"Optica","citation":{"mla":"Rueda, Alfredo, et al. “Efficient Microwave to Optical Photon Conversion: An Electro-Optical Realization.” Optica, vol. 3, no. 6, Optica Publishing Group, 2016, pp. 597–604, doi:10.1364/OPTICA.3.000597.","short":"A. Rueda, F. Sedlmeir, M. Collodo, U. Vogl, B. Stiller, G. Schunk, D. Strekalov, C. Marquardt, J.M. Fink, O. Painter, G. Leuchs, H. Schwefel, Optica 3 (2016) 597–604.","chicago":"Rueda, Alfredo, Florian Sedlmeir, Michele Collodo, Ulrich Vogl, Birgit Stiller, Gerhard Schunk, Dmitry Strekalov, et al. “Efficient Microwave to Optical Photon Conversion: An Electro-Optical Realization.” Optica. Optica Publishing Group, 2016. https://doi.org/10.1364/OPTICA.3.000597.","ama":"Rueda A, Sedlmeir F, Collodo M, et al. Efficient microwave to optical photon conversion: An electro-optical realization. Optica. 2016;3(6):597-604. doi:10.1364/OPTICA.3.000597","ista":"Rueda A, Sedlmeir F, Collodo M, Vogl U, Stiller B, Schunk G, Strekalov D, Marquardt C, Fink JM, Painter O, Leuchs G, Schwefel H. 2016. Efficient microwave to optical photon conversion: An electro-optical realization. Optica. 3(6), 597–604.","ieee":"A. Rueda et al., “Efficient microwave to optical photon conversion: An electro-optical realization,” Optica, vol. 3, no. 6. Optica Publishing Group, pp. 597–604, 2016.","apa":"Rueda, A., Sedlmeir, F., Collodo, M., Vogl, U., Stiller, B., Schunk, G., … Schwefel, H. (2016). Efficient microwave to optical photon conversion: An electro-optical realization. Optica. Optica Publishing Group. https://doi.org/10.1364/OPTICA.3.000597"},"page":"597 - 604","publist_id":"6061","author":[{"full_name":"Rueda, Alfredo","last_name":"Rueda","first_name":"Alfredo"},{"first_name":"Florian","last_name":"Sedlmeir","full_name":"Sedlmeir, Florian"},{"last_name":"Collodo","first_name":"Michele","full_name":"Collodo, Michele"},{"first_name":"Ulrich","last_name":"Vogl","full_name":"Vogl, Ulrich"},{"last_name":"Stiller","first_name":"Birgit","full_name":"Stiller, Birgit"},{"first_name":"Gerhard","last_name":"Schunk","full_name":"Schunk, Gerhard"},{"last_name":"Strekalov","first_name":"Dmitry","full_name":"Strekalov, Dmitry"},{"full_name":"Marquardt, Christoph","last_name":"Marquardt","first_name":"Christoph"},{"id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8112-028X","first_name":"Johannes M","last_name":"Fink","full_name":"Fink, Johannes M"},{"full_name":"Painter, Oskar","last_name":"Painter","first_name":"Oskar"},{"last_name":"Leuchs","first_name":"Gerd","full_name":"Leuchs, Gerd"},{"last_name":"Schwefel","first_name":"Harald","full_name":"Schwefel, Harald"}],"date_updated":"2023-10-17T12:17:15Z","date_created":"2018-12-11T11:51:01Z","volume":3,"year":"2016","acknowledgement":"Alexander von Humboldt Foundation; Studienstiftung des Deutschen Volkes. We would like to acknowledge our stimulating discussions with Konrad Lehnert and Alessandro Pitanti.","publication_status":"published","publisher":"Optica Publishing Group","department":[{"_id":"JoFi"}],"month":"06","doi":"10.1364/OPTICA.3.000597","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://doi.org/10.1364/OPTICA.3.000597","open_access":"1"}],"oa":1,"quality_controlled":"1"},{"language":[{"iso":"eng"}],"doi":"10.1364/OL.41.004621","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}],"quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/1609.02863","open_access":"1"}],"oa":1,"month":"10","volume":41,"date_updated":"2023-10-17T12:16:24Z","date_created":"2018-12-11T11:51:09Z","author":[{"full_name":"Midya, Bikashkali","last_name":"Midya","first_name":"Bikashkali","id":"456187FC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Konotop, Vladimir","last_name":"Konotop","first_name":"Vladimir"}],"department":[{"_id":"MiLe"}],"publisher":"Optica Publishing Group","publication_status":"published","acknowledgement":"The research of B.M. is supported by the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant No. [291734].","year":"2016","ec_funded":1,"publist_id":"6029","date_published":"2016-10-15T00:00:00Z","page":"4621 - 4624","citation":{"mla":"Midya, Bikashkali, and Vladimir Konotop. “Modes and Exceptional Points in Waveguides with Impedance Boundary Conditions.” Optics Letters, vol. 41, no. 20, Optica Publishing Group, 2016, pp. 4621–24, doi:10.1364/OL.41.004621.","short":"B. Midya, V. Konotop, Optics Letters 41 (2016) 4621–4624.","chicago":"Midya, Bikashkali, and Vladimir Konotop. “Modes and Exceptional Points in Waveguides with Impedance Boundary Conditions.” Optics Letters. Optica Publishing Group, 2016. https://doi.org/10.1364/OL.41.004621.","ama":"Midya B, Konotop V. Modes and exceptional points in waveguides with impedance boundary conditions. Optics Letters. 2016;41(20):4621-4624. doi:10.1364/OL.41.004621","ista":"Midya B, Konotop V. 2016. Modes and exceptional points in waveguides with impedance boundary conditions. Optics Letters. 41(20), 4621–4624.","ieee":"B. Midya and V. Konotop, “Modes and exceptional points in waveguides with impedance boundary conditions,” Optics Letters, vol. 41, no. 20. Optica Publishing Group, pp. 4621–4624, 2016.","apa":"Midya, B., & Konotop, V. (2016). Modes and exceptional points in waveguides with impedance boundary conditions. Optics Letters. Optica Publishing Group. https://doi.org/10.1364/OL.41.004621"},"publication":"Optics Letters","article_processing_charge":"No","day":"15","scopus_import":"1","oa_version":"Preprint","intvolume":" 41","status":"public","title":"Modes and exceptional points in waveguides with impedance boundary conditions","_id":"1287","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"20","abstract":[{"lang":"eng","text":"A planar waveguide with an impedance boundary, composed of nonperfect metallic plates, and with passive or active dielectric filling, is considered. We show the possibility of selective mode guiding and amplification when a homogeneous pump is added to the dielectric and analyze differences in TE and TM mode propagation. Such a non-conservative system is also shown to feature exceptional points for specific and experimentally tunable parameters, which are described for a particular case of transparent dielectric."}],"type":"journal_article"},{"external_id":{"pmid":["27649687"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","doi":"10.1038/srep33754","language":[{"iso":"eng"}],"month":"09","pmid":1,"year":"2016","acknowledgement":"We wish to thank Prof. Ewa U. Kurczyńska for initiation of this work and valuable advices. We thank Martine De Cock for help in preparing the manuscript. This work was supported by the European Research Council (project ERC-2011-StG-20101109-PSDP), the European Social Fund (CZ.1.07/2.3.00/20.0043), and the Czech Science Foundation GAČR (GA13-40637 S) to J.F., (GA 13-39982S) to E.B. and E.M. and in part by the European Regional Development Fund (project “CEITEC, Central European Institute of Technology”, CZ.1.05/1.1.00/02.0068).","department":[{"_id":"EvBe"},{"_id":"JiFr"}],"publisher":"Nature Publishing Group","publication_status":"published","related_material":{"record":[{"id":"545","relation":"later_version","status":"public"}]},"author":[{"last_name":"Mazur","first_name":"Ewa","full_name":"Mazur, Ewa"},{"full_name":"Benková, Eva","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","last_name":"Benková","first_name":"Eva"},{"first_name":"Jirí","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí"}],"volume":6,"date_created":"2018-12-11T11:51:05Z","date_updated":"2024-02-12T12:03:42Z","article_number":"33754","publist_id":"6042","file_date_updated":"2020-07-14T12:44:42Z","license":"https://creativecommons.org/licenses/by/4.0/","citation":{"ama":"Mazur E, Benková E, Friml J. Vascular cambium regeneration and vessel formation in wounded inflorescence stems of Arabidopsis. Scientific Reports. 2016;6. doi:10.1038/srep33754","ieee":"E. Mazur, E. Benková, and J. Friml, “Vascular cambium regeneration and vessel formation in wounded inflorescence stems of Arabidopsis,” Scientific Reports, vol. 6. Nature Publishing Group, 2016.","apa":"Mazur, E., Benková, E., & Friml, J. (2016). Vascular cambium regeneration and vessel formation in wounded inflorescence stems of Arabidopsis. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/srep33754","ista":"Mazur E, Benková E, Friml J. 2016. Vascular cambium regeneration and vessel formation in wounded inflorescence stems of Arabidopsis. Scientific Reports. 6, 33754.","short":"E. Mazur, E. Benková, J. Friml, Scientific Reports 6 (2016).","mla":"Mazur, Ewa, et al. “Vascular Cambium Regeneration and Vessel Formation in Wounded Inflorescence Stems of Arabidopsis.” Scientific Reports, vol. 6, 33754, Nature Publishing Group, 2016, doi:10.1038/srep33754.","chicago":"Mazur, Ewa, Eva Benková, and Jiří Friml. “Vascular Cambium Regeneration and Vessel Formation in Wounded Inflorescence Stems of Arabidopsis.” Scientific Reports. Nature Publishing Group, 2016. https://doi.org/10.1038/srep33754."},"publication":"Scientific Reports","date_published":"2016-09-21T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"21","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1274","intvolume":" 6","ddc":["581"],"title":"Vascular cambium regeneration and vessel formation in wounded inflorescence stems of Arabidopsis","status":"public","pubrep_id":"692","file":[{"file_id":"5008","relation":"main_file","date_updated":"2020-07-14T12:44:42Z","date_created":"2018-12-12T10:13:25Z","checksum":"ee371fbc9124ad93157a95829264e4fe","file_name":"IST-2016-692-v1+1_srep33754.pdf","access_level":"open_access","creator":"system","file_size":2895147,"content_type":"application/pdf"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"Synchronized tissue polarization during regeneration or de novo vascular tissue formation is a plant-specific example of intercellular communication and coordinated development. According to the canalization hypothesis, the plant hormone auxin serves as polarizing signal that mediates directional channel formation underlying the spatio-temporal vasculature patterning. A necessary part of canalization is a positive feedback between auxin signaling and polarity of the intercellular auxin flow. The cellular and molecular mechanisms of this process are still poorly understood, not the least, because of a lack of a suitable model system. We show that the main genetic model plant, Arabidopsis (Arabidopsis thaliana) can be used to study the canalization during vascular cambium regeneration and new vasculature formation. We monitored localized auxin responses, directional auxin-transport channels formation, and establishment of new vascular cambium polarity during regenerative processes after stem wounding. The increased auxin response above and around the wound preceded the formation of PIN1 auxin transporter-marked channels from the primarily homogenous tissue and the transient, gradual changes in PIN1 localization preceded the polarity of newly formed vascular tissue. Thus, Arabidopsis is a useful model for studies of coordinated tissue polarization and vasculature formation after wounding allowing for genetic and mechanistic dissection of the canalization hypothesis."}]},{"abstract":[{"text":"This article provides an introduction to the role of microRNAs in the nervous system and outlines their potential involvement in the pathophysiology of schizophrenia, which is hypothesized to arise owing to environmental factors and genetic predisposition.","lang":"eng"}],"issue":"4","type":"journal_article","pubrep_id":"981","oa_version":"Submitted Version","file":[{"file_name":"IST-2018-981-v1+1_YNP150011_annotatedproof_FINAL.pdf","access_level":"open_access","creator":"system","file_size":601679,"content_type":"application/pdf","file_id":"5278","relation":"main_file","date_created":"2018-12-12T10:17:24Z","date_updated":"2020-07-14T12:44:41Z","checksum":"649aee381f30f7ef7e9efa912d41c2e3"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1253","ddc":["576","610"],"status":"public","title":"How MicroRNAs Are involved in splitting the mind","intvolume":" 73","day":"01","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_published":"2016-04-01T00:00:00Z","publication":"JAMA Psychiatry","citation":{"mla":"Tsai, Lihuei, and Sandra Siegert. “How MicroRNAs Are Involved in Splitting the Mind.” JAMA Psychiatry, vol. 73, no. 4, American Medical Association, 2016, pp. 409–10, doi:10.1001/jamapsychiatry.2015.3144.","short":"L. Tsai, S. Siegert, JAMA Psychiatry 73 (2016) 409–410.","chicago":"Tsai, Lihuei, and Sandra Siegert. “How MicroRNAs Are Involved in Splitting the Mind.” JAMA Psychiatry. American Medical Association, 2016. https://doi.org/10.1001/jamapsychiatry.2015.3144.","ama":"Tsai L, Siegert S. How MicroRNAs Are involved in splitting the mind. JAMA Psychiatry. 2016;73(4):409-410. doi:10.1001/jamapsychiatry.2015.3144","ista":"Tsai L, Siegert S. 2016. How MicroRNAs Are involved in splitting the mind. JAMA Psychiatry. 73(4), 409–410.","apa":"Tsai, L., & Siegert, S. (2016). How MicroRNAs Are involved in splitting the mind. JAMA Psychiatry. American Medical Association. https://doi.org/10.1001/jamapsychiatry.2015.3144","ieee":"L. Tsai and S. Siegert, “How MicroRNAs Are involved in splitting the mind,” JAMA Psychiatry, vol. 73, no. 4. American Medical Association, pp. 409–410, 2016."},"page":"409 - 410","file_date_updated":"2020-07-14T12:44:41Z","publist_id":"6074","author":[{"last_name":"Tsai","first_name":"Lihuei","full_name":"Tsai, Lihuei"},{"full_name":"Siegert, Sandra","orcid":"0000-0001-8635-0877","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","last_name":"Siegert","first_name":"Sandra"}],"date_created":"2018-12-11T11:50:58Z","date_updated":"2024-02-14T12:07:22Z","volume":73,"year":"2016","pmid":1,"publication_status":"published","department":[{"_id":"SaSi"}],"publisher":"American Medical Association","month":"04","publication_identifier":{"issn":["2168-622X"]},"doi":"10.1001/jamapsychiatry.2015.3144","language":[{"iso":"eng"}],"external_id":{"pmid":["26963490"]},"oa":1,"quality_controlled":"1"},{"type":"technical_report","alternative_title":["IST Austria Technical Report"],"_id":"5452","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","ddc":["000"],"title":"Arbitrarily strong amplifiers of natural selection","pubrep_id":"750","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"IST-2017-728-v2+1_main.pdf","creator":"system","file_size":811558,"content_type":"application/pdf","file_id":"5460","relation":"main_file","checksum":"58e895f26c82f560c0f0989bf8b08599","date_updated":"2020-07-14T12:46:59Z","date_created":"2018-12-12T11:52:59Z"}],"day":"30","article_processing_charge":"No","has_accepted_license":"1","citation":{"short":"A. Pavlogiannis, J. Tkadlec, K. Chatterjee, M. Nowak, Arbitrarily Strong Amplifiers of Natural Selection, IST Austria, 2016.","mla":"Pavlogiannis, Andreas, et al. Arbitrarily Strong Amplifiers of Natural Selection. IST Austria, 2016, doi:10.15479/AT:IST-2017-728-v2-1.","chicago":"Pavlogiannis, Andreas, Josef Tkadlec, Krishnendu Chatterjee, and Martin Nowak. Arbitrarily Strong Amplifiers of Natural Selection. IST Austria, 2016. https://doi.org/10.15479/AT:IST-2017-728-v2-1.","ama":"Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak M. Arbitrarily Strong Amplifiers of Natural Selection. IST Austria; 2016. doi:10.15479/AT:IST-2017-728-v2-1","apa":"Pavlogiannis, A., Tkadlec, J., Chatterjee, K., & Nowak, M. (2016). Arbitrarily strong amplifiers of natural selection. IST Austria. https://doi.org/10.15479/AT:IST-2017-728-v2-1","ieee":"A. Pavlogiannis, J. Tkadlec, K. Chatterjee, and M. Nowak, Arbitrarily strong amplifiers of natural selection. IST Austria, 2016.","ista":"Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak M. 2016. Arbitrarily strong amplifiers of natural selection, IST Austria, 32p."},"page":"32","date_published":"2016-12-30T00:00:00Z","file_date_updated":"2020-07-14T12:46:59Z","ec_funded":1,"year":"2016","publication_status":"published","department":[{"_id":"KrCh"}],"publisher":"IST Austria","author":[{"full_name":"Pavlogiannis, Andreas","first_name":"Andreas","last_name":"Pavlogiannis","id":"49704004-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8943-0722"},{"full_name":"Tkadlec, Josef","orcid":"0000-0002-1097-9684","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","last_name":"Tkadlec","first_name":"Josef"},{"first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"first_name":"Martin","last_name":"Nowak","full_name":"Nowak, Martin"}],"related_material":{"record":[{"id":"5453","relation":"later_version","status":"public"},{"id":"5559","status":"public","relation":"popular_science"}]},"date_updated":"2024-02-21T13:48:42Z","date_created":"2018-12-12T11:39:25Z","month":"12","publication_identifier":{"issn":["2664-1690"]},"oa":1,"project":[{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"}],"doi":"10.15479/AT:IST-2017-728-v2-1","language":[{"iso":"eng"}]},{"date_published":"2016-02-19T00:00:00Z","doi":"10.15479/AT:ISTA:34","tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"oa":1,"citation":{"ieee":"T. Ellis and D. Field, “Flower colour data and phylogeny (NEXUS) files.” Institute of Science and Technology Austria, 2016.","apa":"Ellis, T., & Field, D. (2016). Flower colour data and phylogeny (NEXUS) files. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:34","ista":"Ellis T, Field D. 2016. Flower colour data and phylogeny (NEXUS) files, Institute of Science and Technology Austria, 10.15479/AT:ISTA:34.","ama":"Ellis T, Field D. Flower colour data and phylogeny (NEXUS) files. 2016. doi:10.15479/AT:ISTA:34","chicago":"Ellis, Thomas, and David Field. “Flower Colour Data and Phylogeny (NEXUS) Files.” Institute of Science and Technology Austria, 2016. https://doi.org/10.15479/AT:ISTA:34.","short":"T. Ellis, D. Field, (2016).","mla":"Ellis, Thomas, and David Field. Flower Colour Data and Phylogeny (NEXUS) Files. Institute of Science and Technology Austria, 2016, doi:10.15479/AT:ISTA:34."},"has_accepted_license":"1","article_processing_charge":"No","day":"19","month":"02","related_material":{"record":[{"relation":"research_paper","status":"public","id":"1382"}]},"author":[{"id":"3153D6D4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8511-0254","first_name":"Thomas","last_name":"Ellis","full_name":"Ellis, Thomas"},{"last_name":"Field","first_name":"David","orcid":"0000-0002-4014-8478","id":"419049E2-F248-11E8-B48F-1D18A9856A87","full_name":"Field, David"}],"oa_version":"Published Version","file":[{"date_created":"2018-12-12T13:02:27Z","date_updated":"2020-07-14T12:47:00Z","checksum":"950f85b80427d357bfeff09608ba02e9","relation":"main_file","file_id":"5594","file_size":4468543,"content_type":"application/zip","creator":"system","file_name":"IST-2016-34-v1+1_tellis_flower_colour_data.zip","access_level":"open_access"}],"date_created":"2018-12-12T12:31:29Z","date_updated":"2024-02-21T13:49:54Z","year":"2016","_id":"5550","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"NiBa"}],"publisher":"Institute of Science and Technology Austria","ddc":["576"],"status":"public","title":"Flower colour data and phylogeny (NEXUS) files","publist_id":"5828","file_date_updated":"2020-07-14T12:47:00Z","abstract":[{"text":"We collected flower colour information on species in the tribe Antirrhineae from taxonomic literature. We also retreived molecular data from GenBank for as many of these species as possible to estimate phylogenetic relationships among these taxa. We then used the R package 'diversitree' to examine patterns of evolutionary transitions between anthocyanin and yellow pigmentation across the phylogeny.\r\n\r\nFor full details of the methods see:\r\nEllis TJ and Field DL \"Repeated gains in yellow and anthocyanin pigmentation in flower colour transitions in the Antirrhineae”, Annals of Botany (in press)","lang":"eng"}],"type":"research_data","datarep_id":"34"},{"author":[{"first_name":"Robert","last_name":"Hauschild","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9843-3522","full_name":"Hauschild, Robert"}],"file":[{"file_name":"IST-2016-44-v1+1_migrationAnalyzer.zip","access_level":"open_access","content_type":"application/zip","file_size":20692,"creator":"system","relation":"main_file","file_id":"5621","date_updated":"2020-07-14T12:47:02Z","date_created":"2018-12-12T13:03:03Z","checksum":"9f96cddbcd4ed689f48712ffe234d5e5"}],"oa_version":"Published Version","date_created":"2018-12-12T12:31:31Z","date_updated":"2024-02-21T13:50:06Z","year":"2016","_id":"5555","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Institute of Science and Technology Austria","department":[{"_id":"Bio"}],"status":"public","ddc":["570"],"title":"Fiji script to determine average speed and direction of migration of cells","abstract":[{"lang":"eng","text":"This FIJI script calculates the population average of the migration speed as a function of time of all cells from wide field microscopy movies."}],"file_date_updated":"2020-07-14T12:47:02Z","type":"research_data","datarep_id":"44","doi":"10.15479/AT:ISTA:44","date_published":"2016-07-08T00:00:00Z","citation":{"mla":"Hauschild, Robert. Fiji Script to Determine Average Speed and Direction of Migration of Cells. Institute of Science and Technology Austria, 2016, doi:10.15479/AT:ISTA:44.","short":"R. Hauschild, (2016).","chicago":"Hauschild, Robert. “Fiji Script to Determine Average Speed and Direction of Migration of Cells.” Institute of Science and Technology Austria, 2016. https://doi.org/10.15479/AT:ISTA:44.","ama":"Hauschild R. Fiji script to determine average speed and direction of migration of cells. 2016. doi:10.15479/AT:ISTA:44","ista":"Hauschild R. 2016. Fiji script to determine average speed and direction of migration of cells, Institute of Science and Technology Austria, 10.15479/AT:ISTA:44.","ieee":"R. Hauschild, “Fiji script to determine average speed and direction of migration of cells.” Institute of Science and Technology Austria, 2016.","apa":"Hauschild, R. (2016). Fiji script to determine average speed and direction of migration of cells. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:44"},"tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"oa":1,"has_accepted_license":"1","article_processing_charge":"No","day":"08","month":"07","keyword":["cell migration","wide field microscopy","FIJI"]},{"article_processing_charge":"No","has_accepted_license":"1","day":"20","month":"09","keyword":["discrete tomography"],"doi":"10.15479/AT:ISTA:46","date_published":"2016-09-20T00:00:00Z","tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"oa":1,"citation":{"mla":"Swoboda, Paul. Synthetic Discrete Tomography Problems. Institute of Science and Technology Austria, 2016, doi:10.15479/AT:ISTA:46.","short":"P. Swoboda, (2016).","chicago":"Swoboda, Paul. “Synthetic Discrete Tomography Problems.” Institute of Science and Technology Austria, 2016. https://doi.org/10.15479/AT:ISTA:46.","ama":"Swoboda P. Synthetic discrete tomography problems. 2016. doi:10.15479/AT:ISTA:46","ista":"Swoboda P. 2016. Synthetic discrete tomography problems, Institute of Science and Technology Austria, 10.15479/AT:ISTA:46.","apa":"Swoboda, P. (2016). Synthetic discrete tomography problems. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:46","ieee":"P. Swoboda, “Synthetic discrete tomography problems.” Institute of Science and Technology Austria, 2016."},"abstract":[{"text":"Small synthetic discrete tomography problems.\r\nSizes are 32x32, 64z64 and 256x256.\r\nProjection angles are 2, 4, and 6.\r\nNumber of labels are 3 and 5.","lang":"eng"}],"file_date_updated":"2020-07-14T12:47:02Z","type":"research_data","datarep_id":"46","file":[{"relation":"main_file","file_id":"5645","date_created":"2018-12-12T13:05:19Z","date_updated":"2020-07-14T12:47:02Z","checksum":"aa5a16a0dc888da7186fb8fc45e88439","file_name":"IST-2016-46-v1+1_discrete_tomography_synthetic.zip","access_level":"open_access","file_size":36058401,"content_type":"application/zip","creator":"system"}],"oa_version":"Published Version","date_created":"2018-12-12T12:31:31Z","date_updated":"2024-02-21T13:50:21Z","contributor":[{"contributor_type":"data_collector","last_name":"Kuske","first_name":"Jan"}],"author":[{"full_name":"Swoboda, Paul","id":"446560C6-F248-11E8-B48F-1D18A9856A87","last_name":"Swoboda","first_name":"Paul"}],"publisher":"Institute of Science and Technology Austria","department":[{"_id":"VlKo"}],"status":"public","ddc":["006"],"title":"Synthetic discrete tomography problems","_id":"5557","year":"2016","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"doi":"10.15479/AT:ISTA:th_640","supervisor":[{"full_name":"Wojtan, Christopher J","orcid":"0000-0001-6646-5546","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","last_name":"Wojtan","first_name":"Christopher J"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"month":"07","publication_identifier":{"issn":["2663-337X"]},"year":"2016","acknowledgement":"First and foremost I would like to thank Chris. I have been incredibly lucky to have\r\nyou as my advisor. Your integrity and aspiration to do the right thing in all walks of\r\nlife is something I admire and aspire to. I also really appreciate the fact that when\r\nworking with you it felt like we were equals. I think we had a very synergetic work\r\nrelationship: I learned immensely from you, but I dare say that you learned a few\r\nthings from me as well. ;)\r\nNext, I would like to thank my amazing committee. Hao, it was a fantastic\r\nexperience working with you. You showed me how to persevere and keep morale\r\nhigh when things were looking the most bleak before the deadline. You are an\r\nincredible motivator and super fun to be around! Vladimir, thanks for the shared\r\nlunches and the poker games. Sorry for not bringing them back when I got busy.\r\nAlso, sorry for embarrassing you by asking about your guitar playing that one\r\ntime. You really are quite awesome! Nils, one of the friendliest and most humble\r\npeople you will meet and a top notch researcher to boot! Thank you for joining\r\nmy committee late!\r\nI would also like to acknowledge the Visual Computing group at IST Austria\r\nfrom whom I have learned so much. The excellent discussions we had in reading\r\ngroups and research meetings really helped me become a better researcher!\r\nNext, I would like to thank all the amazing people that I met during my PhD\r\nstudies, both at IST Austria, in Vienna and elsewhere. ","publication_status":"published","department":[{"_id":"ChWo"}],"publisher":"Institute of Science and Technology Austria","author":[{"orcid":"0000-0002-4417-3224","id":"439F0C8C-F248-11E8-B48F-1D18A9856A87","last_name":"Bojsen-Hansen","first_name":"Morten","full_name":"Bojsen-Hansen, Morten"}],"related_material":{"record":[{"relation":"other","status":"public","id":"5558"}]},"date_updated":"2024-02-21T13:50:48Z","date_created":"2018-12-11T11:50:16Z","file_date_updated":"2018-12-12T10:13:02Z","publist_id":"6238","citation":{"chicago":"Bojsen-Hansen, Morten. “Tracking, Correcting and Absorbing Water Surface Waves.” Institute of Science and Technology Austria, 2016. https://doi.org/10.15479/AT:ISTA:th_640.","mla":"Bojsen-Hansen, Morten. Tracking, Correcting and Absorbing Water Surface Waves. Institute of Science and Technology Austria, 2016, doi:10.15479/AT:ISTA:th_640.","short":"M. Bojsen-Hansen, Tracking, Correcting and Absorbing Water Surface Waves, Institute of Science and Technology Austria, 2016.","ista":"Bojsen-Hansen M. 2016. Tracking, correcting and absorbing water surface waves. Institute of Science and Technology Austria.","ieee":"M. Bojsen-Hansen, “Tracking, correcting and absorbing water surface waves,” Institute of Science and Technology Austria, 2016.","apa":"Bojsen-Hansen, M. (2016). Tracking, correcting and absorbing water surface waves. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_640","ama":"Bojsen-Hansen M. Tracking, correcting and absorbing water surface waves. 2016. doi:10.15479/AT:ISTA:th_640"},"page":"114","date_published":"2016-07-15T00:00:00Z","day":"15","has_accepted_license":"1","article_processing_charge":"No","_id":"1122","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Tracking, correcting and absorbing water surface waves","status":"public","ddc":["004","005","006","532","621"],"oa_version":"Published Version","file":[{"relation":"main_file","file_id":"4982","date_updated":"2018-12-12T10:13:02Z","date_created":"2018-12-12T10:13:02Z","access_level":"open_access","file_name":"IST-2016-640-v1+1_2016_Bojsen-Hansen_TCaAWSW.pdf","content_type":"application/pdf","file_size":13869345,"creator":"system"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"text":"Computer graphics is an extremely exciting field for two reasons. On the one hand,\r\nthere is a healthy injection of pragmatism coming from the visual effects industry\r\nthat want robust algorithms that work so they can produce results at an increasingly\r\nfrantic pace. On the other hand, they must always try to push the envelope and\r\nachieve the impossible to wow their audiences in the next blockbuster, which means\r\nthat the industry has not succumb to conservatism, and there is plenty of room to\r\ntry out new and crazy ideas if there is a chance that it will pan into something\r\nuseful.\r\nWater simulation has been in visual effects for decades, however it still remains\r\nextremely challenging because of its high computational cost and difficult artdirectability.\r\nThe work in this thesis tries to address some of these difficulties.\r\nSpecifically, we make the following three novel contributions to the state-of-the-art\r\nin water simulation for visual effects.\r\nFirst, we develop the first algorithm that can convert any sequence of closed\r\nsurfaces in time into a moving triangle mesh. State-of-the-art methods at the time\r\ncould only handle surfaces with fixed connectivity, but we are the first to be able to\r\nhandle surfaces that merge and split apart. This is important for water simulation\r\npractitioners, because it allows them to convert splashy water surfaces extracted\r\nfrom particles or simulated using grid-based level sets into triangle meshes that can\r\nbe either textured and enhanced with extra surface dynamics as a post-process.\r\nWe also apply our algorithm to other phenomena that merge and split apart, such\r\nas morphs and noisy reconstructions of human performances.\r\nSecond, we formulate a surface-based energy that measures the deviation of a\r\nwater surface froma physically valid state. Such discrepancies arise when there is a\r\nmismatch in the degrees of freedom between the water surface and the underlying\r\nphysics solver. This commonly happens when practitioners use a moving triangle\r\nmesh with a grid-based physics solver, or when high-resolution grid-based surfaces\r\nare combined with low-resolution physics. Following the direction of steepest\r\ndescent on our surface-based energy, we can either smooth these artifacts or turn\r\nthem into high-resolution waves by interpreting the energy as a physical potential.\r\nThird, we extend state-of-the-art techniques in non-reflecting boundaries to handle spatially and time-varying background flows. This allows a novel new\r\nworkflow where practitioners can re-simulate part of an existing simulation, such\r\nas removing a solid obstacle, adding a new splash or locally changing the resolution.\r\nSuch changes can easily lead to new waves in the re-simulated region that would\r\nreflect off of the new simulation boundary, effectively ruining the illusion of a\r\nseamless simulation boundary between the existing and new simulations. Our\r\nnon-reflecting boundaries makes sure that such waves are absorbed.","lang":"eng"}]},{"file_date_updated":"2020-07-14T12:44:48Z","publist_id":"5809","author":[{"full_name":"Ellis, Thomas","first_name":"Thomas","last_name":"Ellis","id":"3153D6D4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8511-0254"}],"related_material":{"record":[{"status":"public","relation":"popular_science","id":"5553"},{"relation":"popular_science","status":"public","id":"5551"},{"id":"5552","status":"public","relation":"popular_science"}]},"date_created":"2018-12-11T11:51:47Z","date_updated":"2024-02-21T13:51:39Z","year":"2016","acknowledgement":"I am indebted to many people for their support during my PhD, but I particularly wish to thank Nick Barton for his guidance and intuition, and for encouraging me to take the time to look beyond the immediate topic of my PhD to understand the broader context. I am also especially grateful to David Field his bottomless patience, invaluable advice on experimental design, analysis and scientific writing, and for tireless work on the population surveys and genomic work without most of my thesis could not have happened. \r\n\r\nIt has been a pleasure to work with the combined strengths of the groups at The John Innes Centre, University of Toulouse and IST Austria. Thanks to Enrico Coen and his group for hosting me in Norwich in 2011 and especially for setting up the tag experiment. \r\n\r\nI thank David Field, Desmond Bradley and Maria Clara Melo-Hurtado for organising field collections, as well as Monique Burrus and Christophe Andalo and a large number of volunteers for their e ff orts helping with the field work. Furthermore I thank Coline Jaworski for providing seeds and for her input into the design of the experimental arrays, and Matthew Couchman for maintaining the database of. \r\n\r\nIn addition to those mentioned above, I am grateful to Melinda Pickup, Spencer Barrett, and four anonymous reviewers for their insightful comments on sections of this manuscript. I also thank Jana Porsche for her e ff orts in tracking down the more obscure references for chapter 5, and Jon Bollback for his advice about the analysis. \r\n\r\nI am indebted to Jon Ågren for his patience whilst I finished this thesis, and to Sylvia Cremer and Magnus Nordborg for taking the time to read and evaluate the thesis given a shorter deadline than was fair. \r\n\r\nA very positive aspect of my PhD has been the supportive atmosphere of IST. In particular, I have come to appreciate the enormous support from our group assistants Nicole Hotzy, Julia Asimakis, Christine Ostermann and Jerneja Beslagic. I also thank Christian Chaloupka and Stefan Hipfinger for their enthusiasm and readiness to help where possible in setting up our greenhouse and experiments. ","publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"NiBa"}],"month":"02","publication_identifier":{"issn":["2663-337X"]},"doi":"10.15479/AT:ISTA:TH_526 ","supervisor":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton","full_name":"Barton, Nicholas H"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"oa":1,"abstract":[{"text":"Hybrid zones represent evolutionary laboratories, where recombination brings together alleles in combinations which have not previously been tested by selection. This provides an excellent opportunity to test the effect of molecular variation on fitness, and how this variation is able to spread through populations in a natural context. The snapdragon Antirrhinum majus is polymorphic in the wild for two loci controlling the distribution of yellow and magenta floral pigments. Where the yellow A. m. striatum and the magenta A. m. pseudomajus meet along a valley in the Spanish Pyrenees they form a stable hybrid zone Alleles at these loci recombine to give striking transgressive variation for flower colour. The sharp transition in phenotype over ~1km implies strong selection maintaining the hybrid zone. An indirect assay of pollinator visitation in the field found that pollinators forage in a positive-frequency dependent manner on Antirrhinum, matching previous data on fruit set. Experimental arrays and paternity analysis of wild-pollinated seeds demonstrated assortative mating for pigmentation alleles, and that pollinator behaviour alone is sufficient to explain this pattern. Selection by pollinators should be sufficiently strong to maintain the hybrid zone, although other mechanisms may be at work. At a broader scale I examined evolutionary transitions between yellow and anthocyanin pigmentation in the tribe Antirrhinae, and found that selection has acted strate that pollinators are a major determinant of reproductive success and mating patterns in wild Antirrhinum.","lang":"eng"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"pubrep_id":"526","file":[{"file_name":"IST-2016-526-v1+1_Ellis_signed_thesis.pdf","access_level":"open_access","file_size":11928241,"content_type":"application/pdf","creator":"system","relation":"main_file","file_id":"5106","date_created":"2018-12-12T10:14:51Z","date_updated":"2020-07-14T12:44:48Z","checksum":"a89b17ff27cf92c9a15f6b3d46bd7e53"}],"oa_version":"Published Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"1398","status":"public","title":"The role of pollinator-mediated selection in the maintenance of a flower color polymorphism in an Antirrhinum majus hybrid zone","ddc":["576"],"day":"18","article_processing_charge":"No","has_accepted_license":"1","date_published":"2016-02-18T00:00:00Z","citation":{"short":"T. Ellis, The Role of Pollinator-Mediated Selection in the Maintenance of a Flower Color Polymorphism in an Antirrhinum Majus Hybrid Zone, Institute of Science and Technology Austria, 2016.","mla":"Ellis, Thomas. The Role of Pollinator-Mediated Selection in the Maintenance of a Flower Color Polymorphism in an Antirrhinum Majus Hybrid Zone. Institute of Science and Technology Austria, 2016, doi:10.15479/AT:ISTA:TH_526 .","chicago":"Ellis, Thomas. “The Role of Pollinator-Mediated Selection in the Maintenance of a Flower Color Polymorphism in an Antirrhinum Majus Hybrid Zone.” Institute of Science and Technology Austria, 2016. https://doi.org/10.15479/AT:ISTA:TH_526 .","ama":"Ellis T. The role of pollinator-mediated selection in the maintenance of a flower color polymorphism in an Antirrhinum majus hybrid zone. 2016. doi:10.15479/AT:ISTA:TH_526 ","ieee":"T. Ellis, “The role of pollinator-mediated selection in the maintenance of a flower color polymorphism in an Antirrhinum majus hybrid zone,” Institute of Science and Technology Austria, 2016.","apa":"Ellis, T. (2016). The role of pollinator-mediated selection in the maintenance of a flower color polymorphism in an Antirrhinum majus hybrid zone. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:TH_526 ","ista":"Ellis T. 2016. The role of pollinator-mediated selection in the maintenance of a flower color polymorphism in an Antirrhinum majus hybrid zone. Institute of Science and Technology Austria."},"page":"130"},{"oa":1,"language":[{"iso":"eng"}],"supervisor":[{"full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240"}],"degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"month":"07","publisher":"Institute of Science and Technology Austria","department":[{"_id":"NiBa"}],"publication_status":"published","year":"2016","acknowledgement":"This PhD thesis may not have been completed without the help and care I received from some peo- ple during my PhD life. I am especially grateful to Tiago Paixao, Gasper Tkacik, Nick Barton, not only for their scientific advices but also for their patience and support. I thank Calin Guet and Jonathan Bollback for allowing me to “play around” in their labs and get some experience on experimental evolution. I thank Magdalena Steinrueck and Fabienne Jesse for collaborating and sharing their experimental data with me. I thank Johannes Jaeger for reviewing my thesis. I thank all members of Barton group (aka bartonians) for their feedback, and all workers of IST Austria for making the best working conditions. Lastly, I thank two special women, Nejla Sag ̆lam and Setenay Dog ̆an, for their continuous support and encouragement. I truly had a great chance of having right people around me.","date_updated":"2024-02-21T13:50:34Z","date_created":"2018-12-11T11:50:19Z","related_material":{"record":[{"id":"1666","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"research_data","id":"5554"}]},"author":[{"last_name":"Tugrul","first_name":"Murat","orcid":"0000-0002-8523-0758","id":"37C323C6-F248-11E8-B48F-1D18A9856A87","full_name":"Tugrul, Murat"}],"publist_id":"6229","file_date_updated":"2021-02-22T11:45:20Z","page":"89","citation":{"ieee":"M. Tugrul, “Evolution of transcriptional regulatory sequences,” Institute of Science and Technology Austria, 2016.","apa":"Tugrul, M. (2016). Evolution of transcriptional regulatory sequences. Institute of Science and Technology Austria.","ista":"Tugrul M. 2016. Evolution of transcriptional regulatory sequences. Institute of Science and Technology Austria.","ama":"Tugrul M. Evolution of transcriptional regulatory sequences. 2016.","chicago":"Tugrul, Murat. “Evolution of Transcriptional Regulatory Sequences.” Institute of Science and Technology Austria, 2016.","short":"M. Tugrul, Evolution of Transcriptional Regulatory Sequences, Institute of Science and Technology Austria, 2016.","mla":"Tugrul, Murat. Evolution of Transcriptional Regulatory Sequences. Institute of Science and Technology Austria, 2016."},"date_published":"2016-07-01T00:00:00Z","has_accepted_license":"1","article_processing_charge":"No","day":"01","ddc":["576"],"title":"Evolution of transcriptional regulatory sequences","status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"1131","file":[{"access_level":"closed","file_name":"Tugrul_thesis_w_signature_page.pdf","content_type":"application/pdf","file_size":3695257,"creator":"dernst","relation":"main_file","file_id":"6810","checksum":"66cb61a59943e4fb7447c6a86be5ef51","date_updated":"2019-08-13T08:53:52Z","date_created":"2019-08-13T08:53:52Z"},{"relation":"main_file","file_id":"9182","date_updated":"2021-02-22T11:45:20Z","date_created":"2021-02-22T11:45:20Z","checksum":"293e388d70563760f6b24c3e66283dda","success":1,"file_name":"2016_Tugrul_Thesis.pdf","access_level":"open_access","content_type":"application/pdf","file_size":3880811,"creator":"dernst"}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"lang":"eng","text":"Evolution of gene regulation is important for phenotypic evolution and diversity. Sequence-specific binding of regulatory proteins is one of the key regulatory mechanisms determining gene expression. Although there has been intense interest in evolution of regulatory binding sites in the last decades, a theoretical understanding is far from being complete. In this thesis, I aim at a better understanding of the evolution of transcriptional regulatory binding sequences by using biophysical and population genetic models.\r\nIn the first part of the thesis, I discuss how to formulate the evolutionary dynamics of binding se- quences in a single isolated binding site and in promoter/enhancer regions. I develop a theoretical framework bridging between a thermodynamical model for transcription and a mutation-selection-drift model for monomorphic populations. I mainly address the typical evolutionary rates, and how they de- pend on biophysical parameters (e.g. binding length and specificity) and population genetic parameters (e.g. population size and selection strength).\r\nIn the second part of the thesis, I analyse empirical data for a better evolutionary and biophysical understanding of sequence-specific binding of bacterial RNA polymerase. First, I infer selection on regulatory and non-regulatory binding sites of RNA polymerase in the E. coli K12 genome. Second, I infer the chemical potential of RNA polymerase, an important but unknown physical parameter defining the threshold energy for strong binding. Furthermore, I try to understand the relation between the lac promoter sequence diversity and the LacZ activity variation among 20 bacterial isolates by constructing a simple but biophysically motivated gene expression model. Lastly, I lay out a statistical framework to predict adaptive point mutations in de novo promoter evolution in a selection experiment."}]},{"keyword":["paternity assignment","pedigree","matting patterns","assortative mating","Antirrhinum majus","frequency-dependent selection","plant-pollinator interaction"],"article_processing_charge":"No","has_accepted_license":"1","day":"19","month":"02","oa":1,"tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"citation":{"chicago":"Field, David, and Thomas Ellis. “Inference of Mating Patterns among Wild Snapdragons in a Natural Hybrid Zone in 2012.” Institute of Science and Technology Austria, 2016. https://doi.org/10.15479/AT:ISTA:37.","mla":"Field, David, and Thomas Ellis. Inference of Mating Patterns among Wild Snapdragons in a Natural Hybrid Zone in 2012. Institute of Science and Technology Austria, 2016, doi:10.15479/AT:ISTA:37.","short":"D. Field, T. Ellis, (2016).","ista":"Field D, Ellis T. 2016. Inference of mating patterns among wild snapdragons in a natural hybrid zone in 2012, Institute of Science and Technology Austria, 10.15479/AT:ISTA:37.","ieee":"D. Field and T. Ellis, “Inference of mating patterns among wild snapdragons in a natural hybrid zone in 2012.” Institute of Science and Technology Austria, 2016.","apa":"Field, D., & Ellis, T. (2016). Inference of mating patterns among wild snapdragons in a natural hybrid zone in 2012. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:37","ama":"Field D, Ellis T. Inference of mating patterns among wild snapdragons in a natural hybrid zone in 2012. 2016. doi:10.15479/AT:ISTA:37"},"date_published":"2016-02-19T00:00:00Z","doi":"10.15479/AT:ISTA:37","type":"research_data","datarep_id":"37","abstract":[{"text":"Genotypic, phenotypic and demographic data for 2128 wild snapdragons and 1127 open-pollinated progeny from a natural hybrid zone, collected as part of Tom Ellis' PhD thesis (submitted) February 2016).\r\n\r\nTissue samples were sent to LGC Genomics in Berlin for DNA extraction, and genotyping at 70 SNP markers by KASPR genotyping. 29 of these SNPs failed to amplify reliably, and have been removed from this dataset.\r\n\r\nOther data were retreived from an online database of this population at www.antspec.org.","lang":"eng"}],"file_date_updated":"2020-07-14T12:47:01Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"5553","year":"2016","department":[{"_id":"NiBa"}],"publisher":"Institute of Science and Technology Austria","status":"public","ddc":["576"],"title":"Inference of mating patterns among wild snapdragons in a natural hybrid zone in 2012","related_material":{"record":[{"id":"1398","status":"public","relation":"research_paper"}]},"contributor":[{"contributor_type":"project_manager","last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"author":[{"first_name":"David","last_name":"Field","id":"419049E2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4014-8478","full_name":"Field, David"},{"last_name":"Ellis","first_name":"Thomas","orcid":"0000-0002-8511-0254","id":"3153D6D4-F248-11E8-B48F-1D18A9856A87","full_name":"Ellis, Thomas"}],"oa_version":"Published Version","file":[{"file_id":"5620","relation":"main_file","date_created":"2018-12-12T13:03:02Z","date_updated":"2020-07-14T12:47:01Z","checksum":"4ae751b1fa4897fa216241f975a57313","file_name":"IST-2016-37-v1+1_paternity_archive.zip","access_level":"open_access","creator":"system","content_type":"application/zip","file_size":132808}],"date_created":"2018-12-12T12:31:30Z","date_updated":"2024-02-21T13:51:14Z"},{"month":"02","day":"19","has_accepted_license":"1","article_processing_charge":"No","citation":{"apa":"Ellis, T. (2016). Data on pollinator observations and offpsring phenotypes. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:35","ieee":"T. Ellis, “Data on pollinator observations and offpsring phenotypes.” Institute of Science and Technology Austria, 2016.","ista":"Ellis T. 2016. Data on pollinator observations and offpsring phenotypes, Institute of Science and Technology Austria, 10.15479/AT:ISTA:35.","ama":"Ellis T. Data on pollinator observations and offpsring phenotypes. 2016. doi:10.15479/AT:ISTA:35","chicago":"Ellis, Thomas. “Data on Pollinator Observations and Offpsring Phenotypes.” Institute of Science and Technology Austria, 2016. https://doi.org/10.15479/AT:ISTA:35.","short":"T. Ellis, (2016).","mla":"Ellis, Thomas. Data on Pollinator Observations and Offpsring Phenotypes. Institute of Science and Technology Austria, 2016, doi:10.15479/AT:ISTA:35."},"tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"oa":1,"doi":"10.15479/AT:ISTA:35","date_published":"2016-02-19T00:00:00Z","datarep_id":"35","type":"research_data","abstract":[{"lang":"eng","text":"Data from array experiments investigating pollinator behaviour on snapdragons in controlled conditions, and their effect on plant mating. Data were collected as part of Tom Ellis' PhD thesis , submitted February 2016.\r\n\r\nWe placed a total of 36 plants in a grid inside a closed organza tent, with a single hive of commercially bred bumblebees (Bombus hortorum). We used only the yellow-flowered Antirrhinum majus striatum and the magenta-flowered Antirrhinum majus pseudomajus, at ratios of 6:36, 12:24, 18:18, 24:12 and 30:6.\r\n\r\nAfter 24 hours to learn how to deal with snapdragons, I observed pollinators foraging on plants, and recorded the transitions between plants. Thereafter seeds on plants were allowed to develops. A sample of these were grown to maturity when their flower colour could be determined, and they were scored as yellow, magenta, or hybrid."}],"file_date_updated":"2020-07-14T12:47:01Z","title":"Data on pollinator observations and offpsring phenotypes","status":"public","publisher":"Institute of Science and Technology Austria","department":[{"_id":"NiBa"}],"_id":"5551","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2016","date_updated":"2024-02-21T13:51:27Z","date_created":"2018-12-12T12:31:29Z","file":[{"file_size":32775,"content_type":"application/zip","creator":"system","access_level":"open_access","file_name":"IST-2016-35-v1+1_array_data.zip","checksum":"aa3eb85d52b110cd192aa23147c4d4f3","date_created":"2018-12-12T13:05:12Z","date_updated":"2020-07-14T12:47:01Z","relation":"main_file","file_id":"5640"}],"oa_version":"Published Version","author":[{"id":"3153D6D4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8511-0254","first_name":"Thomas","last_name":"Ellis","full_name":"Ellis, Thomas"}],"contributor":[{"first_name":"David","last_name":"Field","id":"419049E2-F248-11E8-B48F-1D18A9856A87"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton"}],"related_material":{"record":[{"status":"public","relation":"research_paper","id":"1398"}]}},{"status":"public","title":"Pollinator visitation data for wild Antirrhinum majus plants, with phenotypic and frequency data.","publisher":"Institute of Science and Technology Austria","department":[{"_id":"NiBa"}],"_id":"5552","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2016","date_updated":"2024-02-21T13:51:40Z","date_created":"2018-12-12T12:31:30Z","oa_version":"Published Version","file":[{"file_id":"5625","relation":"main_file","checksum":"cbc61b523d4d475a04a737d50dc470ef","date_updated":"2020-07-14T12:47:01Z","date_created":"2018-12-12T13:03:07Z","access_level":"open_access","file_name":"IST-2016-36-v1+1_tag_assay_archive.zip","creator":"system","file_size":44905,"content_type":"application/zip"}],"author":[{"full_name":"Ellis, Thomas","first_name":"Thomas","last_name":"Ellis","id":"3153D6D4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8511-0254"}],"related_material":{"record":[{"relation":"research_paper","status":"public","id":"1398"}]},"contributor":[{"id":"419049E2-F248-11E8-B48F-1D18A9856A87","first_name":"David","last_name":"Field"},{"first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240"}],"datarep_id":"36","type":"research_data","abstract":[{"lang":"eng","text":"Data on pollinator visitation to wild snapdragons in a natural hybrid zone, collected as part of Tom Ellis' PhD thesis (submitted February 2016).\r\n\r\nSnapdragon flowers have a mouth-like structure which pollinators must open to access nectar. We placed 5mm cellophane tags in these mouths, which are held in place by the pressure of the flower until a pollinator visits. When she opens the flower, the tag drops out, and one can infer a visit. We surveyed plants over multiple days in 2010, 2011 and 2012.\r\n\r\nAlso included are data on phenotypic and demographic variables which may be explanatory variables for pollinator visitation."}],"file_date_updated":"2020-07-14T12:47:01Z","citation":{"mla":"Ellis, Thomas. Pollinator Visitation Data for Wild Antirrhinum Majus Plants, with Phenotypic and Frequency Data. Institute of Science and Technology Austria, 2016, doi:10.15479/AT:ISTA:36.","short":"T. Ellis, (2016).","chicago":"Ellis, Thomas. “Pollinator Visitation Data for Wild Antirrhinum Majus Plants, with Phenotypic and Frequency Data.” Institute of Science and Technology Austria, 2016. https://doi.org/10.15479/AT:ISTA:36.","ama":"Ellis T. Pollinator visitation data for wild Antirrhinum majus plants, with phenotypic and frequency data. 2016. doi:10.15479/AT:ISTA:36","ista":"Ellis T. 2016. Pollinator visitation data for wild Antirrhinum majus plants, with phenotypic and frequency data., Institute of Science and Technology Austria, 10.15479/AT:ISTA:36.","apa":"Ellis, T. (2016). Pollinator visitation data for wild Antirrhinum majus plants, with phenotypic and frequency data. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:36","ieee":"T. Ellis, “Pollinator visitation data for wild Antirrhinum majus plants, with phenotypic and frequency data.” Institute of Science and Technology Austria, 2016."},"oa":1,"doi":"10.15479/AT:ISTA:36","date_published":"2016-02-19T00:00:00Z","day":"19","month":"02","article_processing_charge":"No","has_accepted_license":"1"},{"_id":"5554","year":"2016","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Institute of Science and Technology Austria","department":[{"_id":"NiBa"},{"_id":"JoBo"}],"status":"public","title":"Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase","contributor":[{"id":"2C023F40-F248-11E8-B48F-1D18A9856A87","last_name":"Steinrück","contributor_type":"researcher","first_name":"Magdalena"},{"last_name":"Jesse","contributor_type":"researcher","first_name":"Fabienne","id":"4C8C26A4-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"id":"1131","status":"public","relation":"used_in_publication"}]},"author":[{"full_name":"Tugrul, Murat","last_name":"Tugrul","first_name":"Murat","orcid":"0000-0002-8523-0758","id":"37C323C6-F248-11E8-B48F-1D18A9856A87"}],"oa_version":"Published Version","file":[{"checksum":"1fc0a10bb7ce110fcb5e1fbe3cf0c4e2","date_updated":"2020-07-14T12:47:01Z","date_created":"2018-12-12T13:03:08Z","relation":"main_file","file_id":"5626","content_type":"application/zip","file_size":1123495,"creator":"system","access_level":"open_access","file_name":"IST-2016-43-v1+1_DATA_MTugrul_PhDThesis_Chapter3.zip"}],"date_updated":"2024-02-21T13:50:34Z","date_created":"2018-12-12T12:31:30Z","type":"research_data","datarep_id":"43","abstract":[{"text":"The data stored here is used in Murat Tugrul's PhD thesis (Chapter 3), which is related to the evolution of bacterial RNA polymerase binding.\r\nMagdalena Steinrueck (PhD Student in Calin Guet's group at IST Austria) performed the experiments and created the data on de novo promoter evolution. Fabienne Jesse (PhD Student in Jon Bollback's group at IST Austria) performed the experiments and created the data on lac promoter evolution.","lang":"eng"}],"file_date_updated":"2020-07-14T12:47:01Z","tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"oa":1,"citation":{"chicago":"Tugrul, Murat. “Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase.” Institute of Science and Technology Austria, 2016. https://doi.org/10.15479/AT:ISTA:43.","short":"M. Tugrul, (2016).","mla":"Tugrul, Murat. Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase. Institute of Science and Technology Austria, 2016, doi:10.15479/AT:ISTA:43.","apa":"Tugrul, M. (2016). Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:43","ieee":"M. Tugrul, “Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase.” Institute of Science and Technology Austria, 2016.","ista":"Tugrul M. 2016. Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase, Institute of Science and Technology Austria, 10.15479/AT:ISTA:43.","ama":"Tugrul M. Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase. 2016. doi:10.15479/AT:ISTA:43"},"doi":"10.15479/AT:ISTA:43","date_published":"2016-05-12T00:00:00Z","keyword":["RNAP binding","de novo promoter evolution","lac promoter"],"has_accepted_license":"1","article_processing_charge":"No","day":"12","month":"05"},{"department":[{"_id":"ChWo"}],"publisher":"Institute of Science and Technology Austria","ddc":["004"],"status":"public","title":"Tracking, Correcting and Absorbing Water Surface Waves","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"5558","year":"2016","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"5589","date_created":"2018-12-12T13:02:18Z","date_updated":"2020-07-14T12:47:02Z","checksum":"5b1b256ad796fbddb4b7729f5e45e444","file_name":"IST-2016-48-v1+1_2016_Bojsen-Hansen_TCaAWSW.tar.bz2","access_level":"open_access","content_type":"application/x-bzip2","file_size":55237885,"creator":"system"}],"date_created":"2018-12-12T12:31:31Z","date_updated":"2024-02-21T13:50:48Z","related_material":{"record":[{"id":"1122","status":"public","relation":"other"}]},"pubrep_id":"640","author":[{"last_name":"Bojsen-Hansen","first_name":"Morten","orcid":"0000-0002-4417-3224","id":"439F0C8C-F248-11E8-B48F-1D18A9856A87","full_name":"Bojsen-Hansen, Morten"}],"type":"research_data","datarep_id":"48","publist_id":"6238","abstract":[{"text":"PhD thesis LaTeX source code","lang":"eng"}],"file_date_updated":"2020-07-14T12:47:02Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"citation":{"ama":"Bojsen-Hansen M. Tracking, Correcting and Absorbing Water Surface Waves. 2016. doi:10.15479/AT:ISTA:48","apa":"Bojsen-Hansen, M. (2016). Tracking, Correcting and Absorbing Water Surface Waves. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:48","ieee":"M. Bojsen-Hansen, “Tracking, Correcting and Absorbing Water Surface Waves.” Institute of Science and Technology Austria, 2016.","ista":"Bojsen-Hansen M. 2016. Tracking, Correcting and Absorbing Water Surface Waves, Institute of Science and Technology Austria, 10.15479/AT:ISTA:48.","short":"M. Bojsen-Hansen, (2016).","mla":"Bojsen-Hansen, Morten. Tracking, Correcting and Absorbing Water Surface Waves. Institute of Science and Technology Austria, 2016, doi:10.15479/AT:ISTA:48.","chicago":"Bojsen-Hansen, Morten. “Tracking, Correcting and Absorbing Water Surface Waves.” Institute of Science and Technology Austria, 2016. https://doi.org/10.15479/AT:ISTA:48."},"oa":1,"doi":"10.15479/AT:ISTA:48","date_published":"2016-09-23T00:00:00Z","has_accepted_license":"1","article_processing_charge":"No","day":"23","month":"09"},{"date_published":"2016-08-25T00:00:00Z","doi":"10.15479/AT:ISTA:45","oa":1,"tmp":{"short":"CC BY-SA (4.0)","image":"/images/cc_by_sa.png","name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode"},"citation":{"ama":"Lukacisin M, Landon M, Jajoo R. MATLAB analysis code for “Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.” 2016. doi:10.15479/AT:ISTA:45","ieee":"M. Lukacisin, M. Landon, and R. Jajoo, “MATLAB analysis code for ‘Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.’” Institute of Science and Technology Austria, 2016.","apa":"Lukacisin, M., Landon, M., & Jajoo, R. (2016). MATLAB analysis code for “Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:45","ista":"Lukacisin M, Landon M, Jajoo R. 2016. MATLAB analysis code for ‘Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:45.","short":"M. Lukacisin, M. Landon, R. Jajoo, (2016).","mla":"Lukacisin, Martin, et al. MATLAB Analysis Code for “Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.” Institute of Science and Technology Austria, 2016, doi:10.15479/AT:ISTA:45.","chicago":"Lukacisin, Martin, Matthieu Landon, and Rishi Jajoo. “MATLAB Analysis Code for ‘Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.’” Institute of Science and Technology Austria, 2016. https://doi.org/10.15479/AT:ISTA:45."},"month":"08","day":"25","article_processing_charge":"No","has_accepted_license":"1","keyword":["transcription","pausing","backtracking","polymerase","RNA","NET-seq","nucleosome","basepairing"],"date_updated":"2024-02-21T13:51:53Z","date_created":"2018-12-12T12:31:31Z","oa_version":"Published Version","file":[{"file_size":296722548,"content_type":"application/zip","creator":"system","file_name":"IST-2016-45-v1+1_PaperCode.zip","access_level":"open_access","date_updated":"2020-07-14T12:47:02Z","date_created":"2018-12-12T13:02:58Z","checksum":"ee697f2b1ade4dc14d6ac0334dd832ab","relation":"main_file","file_id":"5616"}],"author":[{"full_name":"Lukacisin, Martin","orcid":"0000-0001-6549-4177","id":"298FFE8C-F248-11E8-B48F-1D18A9856A87","last_name":"Lukacisin","first_name":"Martin"},{"last_name":"Landon","first_name":"Matthieu","full_name":"Landon, Matthieu"},{"last_name":"Jajoo","first_name":"Rishi","full_name":"Jajoo, Rishi"}],"related_material":{"record":[{"id":"8431","relation":"used_in_publication","status":"deleted"},{"id":"1029","relation":"research_paper","status":"public"}]},"ddc":["571"],"title":"MATLAB analysis code for 'Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast'","status":"public","department":[{"_id":"ToBo"}],"publisher":"Institute of Science and Technology Austria","_id":"5556","year":"2016","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","license":"https://creativecommons.org/licenses/by-sa/4.0/","abstract":[{"lang":"eng","text":"MATLAB code and processed datasets available for reproducing the results in: \r\nLukačišin, M.*, Landon, M.*, Jajoo, R*. (2016) Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.\r\n*equal contributions"}],"file_date_updated":"2020-07-14T12:47:02Z","datarep_id":"45","type":"research_data"},{"date_created":"2024-03-26T10:42:21Z","date_updated":"2024-03-27T08:23:11Z","volume":9905,"author":[{"first_name":"S. N.","last_name":"Zhang","full_name":"Zhang, S. N."},{"first_name":"M.","last_name":"Feroci","full_name":"Feroci, M."},{"full_name":"Santangelo, A.","last_name":"Santangelo","first_name":"A."},{"last_name":"Dong","first_name":"Y. W.","full_name":"Dong, Y. W."},{"full_name":"Feng, H.","first_name":"H.","last_name":"Feng"},{"last_name":"Lu","first_name":"F. J.","full_name":"Lu, F. J."},{"full_name":"Nandra, K.","last_name":"Nandra","first_name":"K."},{"full_name":"Wang, Z. S.","last_name":"Wang","first_name":"Z. 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F."},{"full_name":"Zampa, G.","last_name":"Zampa","first_name":"G."},{"full_name":"Zampa, N.","last_name":"Zampa","first_name":"N."},{"full_name":"Zdziarski, A.","first_name":"A.","last_name":"Zdziarski"},{"full_name":"Zhang, C.","last_name":"Zhang","first_name":"C."},{"full_name":"Zhang, C. L.","last_name":"Zhang","first_name":"C. L."},{"first_name":"L.","last_name":"Zhang","full_name":"Zhang, L."},{"full_name":"Zhang, X.","last_name":"Zhang","first_name":"X."},{"last_name":"Zhang","first_name":"Z.","full_name":"Zhang, Z."},{"full_name":"Zhang, W. D.","first_name":"W. D.","last_name":"Zhang"},{"full_name":"Zheng, S. J.","first_name":"S. J.","last_name":"Zheng"},{"full_name":"Zhou, P.","first_name":"P.","last_name":"Zhou"},{"first_name":"X. L.","last_name":"Zhou","full_name":"Zhou, X. L."}],"publication_status":"published","publisher":"SPIE","year":"2016","extern":"1","article_number":"99051Q ","language":[{"iso":"eng"}],"doi":"10.1117/12.2232034","quality_controlled":"1","oa":1,"external_id":{"arxiv":["1607.08823"]},"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.1607.08823","open_access":"1"}],"month":"07","publication_identifier":{"issn":["0277-786X"]},"oa_version":"Preprint","status":"public","title":"eXTP: Enhanced X-ray timing and polarization mission","intvolume":" 9905","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"15245","abstract":[{"lang":"eng","text":"eXTP is a science mission designed to study the state of matter under extreme conditions of density, gravity and magnetism. Primary goals are the determination of the equation of state of matter at supra-nuclear density, the measurement of QED effects in highly magnetized star, and the study of accretion in the strong-field regime of gravity. Primary targets include isolated and binary neutron stars, strong magnetic field systems like magnetars, and stellar-mass and supermassive black holes. The mission carries a unique and unprecedented suite of state-of-the-art scientific instruments enabling for the first time ever the simultaneous spectral-timing-polarimetry studies of cosmic sources in the energy range from 0.5-30 keV (and beyond). Key elements of the payload are: the Spectroscopic Focusing Array (SFA) - a set of 11 X-ray optics for a total effective area of ∼0.9 m2 and 0.6 m2 at 2 keV and 6 keV respectively, equipped with Silicon Drift Detectors offering <180 eV spectral resolution; the Large Area Detector (LAD) - a deployable set of 640 Silicon Drift Detectors, for a total effective area of ∼3.4 m2, between 6 and 10 keV, and spectral resolution better than 250 eV; the Polarimetry Focusing Array (PFA) - a set of 2 X-ray telescope, for a total effective area of 250 cm2 at 2 keV, equipped with imaging gas pixel photoelectric polarimeters; the Wide Field Monitor (WFM) - a set of 3 coded mask wide field units, equipped with position-sensitive Silicon Drift Detectors, each covering a 90 degrees x 90 degrees field of view. The eXTP international consortium includes major institutions of the Chinese Academy of Sciences and Universities in China, as well as major institutions in several European countries and the United States. The predecessor of eXTP, the XTP mission concept, has been selected and funded as one of the so-called background missions in the Strategic Priority Space Science Program of the Chinese Academy of Sciences since 2011. The strong European participation has significantly enhanced the scientific capabilities of eXTP. The planned launch date of the mission is earlier than 2025."}],"type":"conference","date_published":"2016-07-01T00:00:00Z","publication":"Proceedings of the SPIE","citation":{"chicago":"Zhang, S. N., M. Feroci, A. Santangelo, Y. W. Dong, H. Feng, F. J. Lu, K. Nandra, et al. “EXTP: Enhanced X-Ray Timing and Polarization Mission.” In Proceedings of the SPIE, Vol. 9905. SPIE, 2016. https://doi.org/10.1117/12.2232034.","short":"S.N. Zhang, M. Feroci, A. Santangelo, Y.W. Dong, H. Feng, F.J. Lu, K. Nandra, Z.S. Wang, S. Zhang, E. Bozzo, S. Brandt, A. De Rosa, L.J. Gou, M. Hernanz, M. van der Klis, X.D. Li, Y. Liu, P. Orleanski, G. Pareschi, M. Pohl, J. Poutanen, J.L. Qu, S. Schanne, L. Stella, P. Uttley, A. Watts, R.X. Xu, W.F. Yu, J.J.M. in ’t Zand, S. Zane, L. Alvarez, L. Amati, L. Baldini, C. Bambi, S. Basso, S. Bhattacharyya, R. Bellazzini, T. Belloni, P. Bellutti, S. Bianchi, A. Brez, M. Bursa, V. Burwitz, C. Budtz-Jørgensen, I. Caiazzo, R. Campana, X.L. Cao, P. Casella, C.Y. Chen, L. Chen, T. Chen, Y. Chen, Y. Chen, Y.P. Chen, M. Civitani, F. Coti Zelati, W. Cui, W.W. Cui, Z.G. Dai, E. Del Monte, D. de Martino, S. Di Cosimo, S. Diebold, M. Dovciak, I. Donnarumma, V. Doroshenko, P. Esposito, Y. Evangelista, Y. Favre, P. Friedrich, F. Fuschino, J.L. Galvez, Z.L. Gao, M.Y. Ge, O. Gevin, D. Goetz, D.W. Han, J. Heyl, J. Horak, W. Hu, F. Huang, Q.S. Huang, R. Hudec, D. Huppenkothen, G.L. Israel, A. Ingram, V. Karas, D. Karelin, P.A. Jenke, L. Ji, S. Korpela, D. Kunneriath, C. Labanti, G. Li, X. Li, Z.S. Li, E.W. Liang, O. Limousin, L. Lin, Z.X. Ling, H.B. Liu, H.W. Liu, Z. Liu, B. Lu, N. Lund, D. Lai, B. Luo, T. Luo, B. Ma, S. Mahmoodifar, M. Marisaldi, A. Martindale, N. Meidinger, Y.P. Men, M. Michalska, R. Mignani, M. Minuti, S. Motta, F. Muleri, J. Neilsen, M. Orlandini, A.T. Pan, A. Patruno, E. Perinati, A. Picciotto, C. Piemonte, M. Pinchera, A. Rachevski, M. Rapisarda, N. Rea, E.M.R. Rossi, A. Rubini, G. Sala, X.W. Shu, C. Sgro, Z.X. Shen, P. Soffitta, L.M. Song, G. Spandre, G. Stratta, T.E. Strohmayer, L. Sun, J. Svoboda, G. Tagliaferri, C. Tenzer, T. Hong, R. Taverna, G. Torok, R. Turolla, S. Vacchi, J. Wang, D. Walton, K. Wang, J.F. Wang, R.J. Wang, Y.F. Wang, S.S. Weng, J. Wilms, B. Winter, X. Wu, X.F. Wu, S.L. Xiong, Y.P. Xu, Y.Q. Xue, Z. Yan, S. Yang, X. Yang, Y.J. Yang, F. Yuan, W.M. Yuan, Y.F. Yuan, G. Zampa, N. Zampa, A. Zdziarski, C. Zhang, C.L. Zhang, L. Zhang, X. Zhang, Z. Zhang, W.D. Zhang, S.J. Zheng, P. Zhou, X.L. Zhou, in:, Proceedings of the SPIE, SPIE, 2016.","mla":"Zhang, S. N., et al. “EXTP: Enhanced X-Ray Timing and Polarization Mission.” Proceedings of the SPIE, vol. 9905, 99051Q, SPIE, 2016, doi:10.1117/12.2232034.","apa":"Zhang, S. N., Feroci, M., Santangelo, A., Dong, Y. W., Feng, H., Lu, F. J., … Zhou, X. L. (2016). eXTP: Enhanced X-ray timing and polarization mission. In Proceedings of the SPIE (Vol. 9905). SPIE. https://doi.org/10.1117/12.2232034","ieee":"S. N. Zhang et al., “eXTP: Enhanced X-ray timing and polarization mission,” in Proceedings of the SPIE, 2016, vol. 9905.","ista":"Zhang SN et al. 2016. eXTP: Enhanced X-ray timing and polarization mission. Proceedings of the SPIE. vol. 9905, 99051Q.","ama":"Zhang SN, Feroci M, Santangelo A, et al. eXTP: Enhanced X-ray timing and polarization mission. In: Proceedings of the SPIE. Vol 9905. SPIE; 2016. doi:10.1117/12.2232034"},"day":"01","article_processing_charge":"No","scopus_import":"1"},{"language":[{"iso":"eng"}],"doi":"10.1016/j.cell.2016.11.013","project":[{"grant_number":"F03523","_id":"25473368-B435-11E9-9278-68D0E5697425","name":"Transmembrane Transporters in Health and Disease","call_identifier":"FWF"}],"quality_controlled":"1","oa":1,"month":"12","volume":167,"date_updated":"2024-03-28T23:30:12Z","date_created":"2018-12-11T11:50:35Z","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"395"}]},"author":[{"full_name":"Tarlungeanu, Dora-Clara","id":"2ABCE612-F248-11E8-B48F-1D18A9856A87","first_name":"Dora-Clara","last_name":"Tarlungeanu"},{"full_name":"Deliu, Elena","id":"37A40D7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7370-5293","first_name":"Elena","last_name":"Deliu"},{"id":"4C66542E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9033-9096","first_name":"Christoph","last_name":"Dotter","full_name":"Dotter, Christoph"},{"full_name":"Kara, Majdi","first_name":"Majdi","last_name":"Kara"},{"last_name":"Janiesch","first_name":"Philipp","full_name":"Janiesch, Philipp"},{"full_name":"Scalise, Mariafrancesca","first_name":"Mariafrancesca","last_name":"Scalise"},{"full_name":"Galluccio, Michele","first_name":"Michele","last_name":"Galluccio"},{"last_name":"Tesulov","first_name":"Mateja","full_name":"Tesulov, Mateja"},{"first_name":"Emanuela","last_name":"Morelli","id":"3F4D1282-F248-11E8-B48F-1D18A9856A87","full_name":"Morelli, Emanuela"},{"first_name":"Fatma","last_name":"Sönmez","full_name":"Sönmez, Fatma"},{"last_name":"Bilgüvar","first_name":"Kaya","full_name":"Bilgüvar, Kaya"},{"first_name":"Ryuichi","last_name":"Ohgaki","full_name":"Ohgaki, Ryuichi"},{"full_name":"Kanai, Yoshikatsu","first_name":"Yoshikatsu","last_name":"Kanai"},{"full_name":"Johansen, Anide","first_name":"Anide","last_name":"Johansen"},{"first_name":"Seham","last_name":"Esharif","full_name":"Esharif, Seham"},{"last_name":"Ben Omran","first_name":"Tawfeg","full_name":"Ben Omran, Tawfeg"},{"full_name":"Topcu, Meral","first_name":"Meral","last_name":"Topcu"},{"full_name":"Schlessinger, Avner","first_name":"Avner","last_name":"Schlessinger"},{"full_name":"Indiveri, Cesare","first_name":"Cesare","last_name":"Indiveri"},{"first_name":"Kent","last_name":"Duncan","full_name":"Duncan, Kent"},{"full_name":"Caglayan, Ahmet","last_name":"Caglayan","first_name":"Ahmet"},{"full_name":"Günel, Murat","first_name":"Murat","last_name":"Günel"},{"last_name":"Gleeson","first_name":"Joseph","full_name":"Gleeson, Joseph"},{"full_name":"Novarino, Gaia","first_name":"Gaia","last_name":"Novarino","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7673-7178"}],"department":[{"_id":"GaNo"}],"publisher":"Cell Press","publication_status":"published","acknowledgement":"This work was supported by NICHD (P01HD070494) and SFARI (grant 275275) to J.G.G., and FWF (SFB35_3523) to G.N.\r\nWe thank A.C. Manzano, Mike Liu, and F. Marr for technical assistance, and R. Shigemoto and the IST Austria Electron Microscopy (EM) Facility for assistance. We acknowledge support from CIDR for genome-wide SNP analysis (X01HG008823) and Broad Institute Center for Mendelian Disorders (UM1HG008900 to D. MacArthur), the Yale Center for Mendelian Disorders (U54HG006504 to M.G.), the Gregory M. Kiez and Mehmet Kutman Foundation (M.G.), Italian Ministry of Instruction University and Research (PON01_00937 to C.I.), and NIH (R01-GM108911 to A.S.). This work was supported by NICHD (P01HD070494) and SFARI (grant 275275) to J.G.G., and FWF (SFB35_3523) to G.N.\r\n\r\n#EMFacility","year":"2016","publist_id":"6170","file_date_updated":"2020-07-14T12:44:37Z","date_published":"2016-12-01T00:00:00Z","page":"1481 - 1494","article_type":"original","citation":{"chicago":"Tarlungeanu, Dora-Clara, Elena Deliu, Christoph Dotter, Majdi Kara, Philipp Janiesch, Mariafrancesca Scalise, Michele Galluccio, et al. “Impaired Amino Acid Transport at the Blood Brain Barrier Is a Cause of Autism Spectrum Disorder.” Cell. Cell Press, 2016. https://doi.org/10.1016/j.cell.2016.11.013.","mla":"Tarlungeanu, Dora-Clara, et al. “Impaired Amino Acid Transport at the Blood Brain Barrier Is a Cause of Autism Spectrum Disorder.” Cell, vol. 167, no. 6, Cell Press, 2016, pp. 1481–94, doi:10.1016/j.cell.2016.11.013.","short":"D.-C. Tarlungeanu, E. Deliu, C. Dotter, M. Kara, P. Janiesch, M. Scalise, M. Galluccio, M. Tesulov, E. Morelli, F. Sönmez, K. Bilgüvar, R. Ohgaki, Y. Kanai, A. Johansen, S. Esharif, T. Ben Omran, M. Topcu, A. Schlessinger, C. Indiveri, K. Duncan, A. Caglayan, M. Günel, J. Gleeson, G. Novarino, Cell 167 (2016) 1481–1494.","ista":"Tarlungeanu D-C, Deliu E, Dotter C, Kara M, Janiesch P, Scalise M, Galluccio M, Tesulov M, Morelli E, Sönmez F, Bilgüvar K, Ohgaki R, Kanai Y, Johansen A, Esharif S, Ben Omran T, Topcu M, Schlessinger A, Indiveri C, Duncan K, Caglayan A, Günel M, Gleeson J, Novarino G. 2016. Impaired amino acid transport at the blood brain barrier is a cause of autism spectrum disorder. Cell. 167(6), 1481–1494.","apa":"Tarlungeanu, D.-C., Deliu, E., Dotter, C., Kara, M., Janiesch, P., Scalise, M., … Novarino, G. (2016). Impaired amino acid transport at the blood brain barrier is a cause of autism spectrum disorder. Cell. Cell Press. https://doi.org/10.1016/j.cell.2016.11.013","ieee":"D.-C. Tarlungeanu et al., “Impaired amino acid transport at the blood brain barrier is a cause of autism spectrum disorder,” Cell, vol. 167, no. 6. Cell Press, pp. 1481–1494, 2016.","ama":"Tarlungeanu D-C, Deliu E, Dotter C, et al. Impaired amino acid transport at the blood brain barrier is a cause of autism spectrum disorder. Cell. 2016;167(6):1481-1494. doi:10.1016/j.cell.2016.11.013"},"publication":"Cell","article_processing_charge":"No","has_accepted_license":"1","day":"01","scopus_import":"1","oa_version":"Submitted Version","file":[{"file_name":"IST-2017-771-v1+1_Tarlungeanu_et_al._Final_edited.pdf","access_level":"open_access","content_type":"application/pdf","file_size":73907957,"creator":"system","relation":"main_file","file_id":"5030","date_created":"2018-12-12T10:13:44Z","date_updated":"2020-07-14T12:44:37Z","checksum":"7fe01ab12a6610d3db421e0136db2f77"}],"pubrep_id":"771","intvolume":" 167","status":"public","title":"Impaired amino acid transport at the blood brain barrier is a cause of autism spectrum disorder","ddc":["576","616"],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"1183","issue":"6","abstract":[{"text":"Autism spectrum disorders (ASD) are a group of genetic disorders often overlapping with other neurological conditions. We previously described abnormalities in the branched-chain amino acid (BCAA) catabolic pathway as a cause of ASD. Here, we show that the solute carrier transporter 7a5 (SLC7A5), a large neutral amino acid transporter localized at the blood brain barrier (BBB), has an essential role in maintaining normal levels of brain BCAAs. In mice, deletion of Slc7a5 from the endothelial cells of the BBB leads to atypical brain amino acid profile, abnormal mRNA translation, and severe neurological abnormalities. Furthermore, we identified several patients with autistic traits and motor delay carrying deleterious homozygous mutations in the SLC7A5 gene. Finally, we demonstrate that BCAA intracerebroventricular administration ameliorates abnormal behaviors in adult mutant mice. Our data elucidate a neurological syndrome defined by SLC7A5 mutations and support an essential role for the BCAA in human brain function.","lang":"eng"}],"type":"journal_article"},{"date_published":"2016-10-24T00:00:00Z","publication":"Nature Cell Biology","citation":{"ama":"Leithner AF, Eichner A, Müller J, et al. Diversified actin protrusions promote environmental exploration but are dispensable for locomotion of leukocytes. Nature Cell Biology. 2016;18:1253-1259. doi:10.1038/ncb3426","ieee":"A. F. Leithner et al., “Diversified actin protrusions promote environmental exploration but are dispensable for locomotion of leukocytes,” Nature Cell Biology, vol. 18. Nature Publishing Group, pp. 1253–1259, 2016.","apa":"Leithner, A. F., Eichner, A., Müller, J., Reversat, A., Brown, M., Schwarz, J., … Sixt, M. K. (2016). Diversified actin protrusions promote environmental exploration but are dispensable for locomotion of leukocytes. Nature Cell Biology. Nature Publishing Group. https://doi.org/10.1038/ncb3426","ista":"Leithner AF, Eichner A, Müller J, Reversat A, Brown M, Schwarz J, Merrin J, De Gorter D, Schur FK, Bayerl J, de Vries I, Wieser S, Hauschild R, Lai F, Moser M, Kerjaschki D, Rottner K, Small V, Stradal T, Sixt MK. 2016. Diversified actin protrusions promote environmental exploration but are dispensable for locomotion of leukocytes. Nature Cell Biology. 18, 1253–1259.","short":"A.F. Leithner, A. Eichner, J. Müller, A. Reversat, M. Brown, J. Schwarz, J. Merrin, D. De Gorter, F.K. Schur, J. Bayerl, I. de Vries, S. Wieser, R. Hauschild, F. Lai, M. Moser, D. Kerjaschki, K. Rottner, V. Small, T. Stradal, M.K. Sixt, Nature Cell Biology 18 (2016) 1253–1259.","mla":"Leithner, Alexander F., et al. “Diversified Actin Protrusions Promote Environmental Exploration but Are Dispensable for Locomotion of Leukocytes.” Nature Cell Biology, vol. 18, Nature Publishing Group, 2016, pp. 1253–59, doi:10.1038/ncb3426.","chicago":"Leithner, Alexander F, Alexander Eichner, Jan Müller, Anne Reversat, Markus Brown, Jan Schwarz, Jack Merrin, et al. “Diversified Actin Protrusions Promote Environmental Exploration but Are Dispensable for Locomotion of Leukocytes.” Nature Cell Biology. Nature Publishing Group, 2016. https://doi.org/10.1038/ncb3426."},"article_type":"original","page":"1253 - 1259","day":"24","has_accepted_license":"1","article_processing_charge":"No","scopus_import":1,"file":[{"creator":"dernst","content_type":"application/pdf","file_size":4433280,"file_name":"2018_NatureCell_Leithner.pdf","access_level":"open_access","date_created":"2020-05-14T16:33:46Z","date_updated":"2020-07-14T12:44:43Z","checksum":"e1411cb7c99a2d9089c178a6abef25e7","file_id":"7844","relation":"main_file"}],"oa_version":"Submitted Version","_id":"1321","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"status":"public","title":"Diversified actin protrusions promote environmental exploration but are dispensable for locomotion of leukocytes","intvolume":" 18","abstract":[{"text":"Most migrating cells extrude their front by the force of actin polymerization. Polymerization requires an initial nucleation step, which is mediated by factors establishing either parallel filaments in the case of filopodia or branched filaments that form the branched lamellipodial network. Branches are considered essential for regular cell motility and are initiated by the Arp2/3 complex, which in turn is activated by nucleation-promoting factors of the WASP and WAVE families. Here we employed rapid amoeboid crawling leukocytes and found that deletion of the WAVE complex eliminated actin branching and thus lamellipodia formation. The cells were left with parallel filaments at the leading edge, which translated, depending on the differentiation status of the cell, into a unipolar pointed cell shape or cells with multiple filopodia. Remarkably, unipolar cells migrated with increased speed and enormous directional persistence, while they were unable to turn towards chemotactic gradients. Cells with multiple filopodia retained chemotactic activity but their migration was progressively impaired with increasing geometrical complexity of the extracellular environment. These findings establish that diversified leading edge protrusions serve as explorative structures while they slow down actual locomotion.","lang":"eng"}],"type":"journal_article","doi":"10.1038/ncb3426","acknowledged_ssus":[{"_id":"SSU"}],"language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)"},"quality_controlled":"1","project":[{"grant_number":"281556","_id":"25A603A2-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Cytoskeletal force generation and force transduction of migrating leukocytes (EU)"}],"month":"10","author":[{"full_name":"Leithner, Alexander F","first_name":"Alexander F","last_name":"Leithner","id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1073-744X"},{"last_name":"Eichner","first_name":"Alexander","id":"4DFA52AE-F248-11E8-B48F-1D18A9856A87","full_name":"Eichner, Alexander"},{"last_name":"Müller","first_name":"Jan","id":"AD07FDB4-0F61-11EA-8158-C4CC64CEAA8D","full_name":"Müller, Jan"},{"last_name":"Reversat","first_name":"Anne","orcid":"0000-0003-0666-8928","id":"35B76592-F248-11E8-B48F-1D18A9856A87","full_name":"Reversat, Anne"},{"id":"3DAB9AFC-F248-11E8-B48F-1D18A9856A87","first_name":"Markus","last_name":"Brown","full_name":"Brown, Markus"},{"id":"346C1EC6-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","last_name":"Schwarz","full_name":"Schwarz, Jan"},{"full_name":"Merrin, Jack","id":"4515C308-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5145-4609","first_name":"Jack","last_name":"Merrin"},{"full_name":"De Gorter, David","first_name":"David","last_name":"De Gorter"},{"full_name":"Schur, Florian","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078","first_name":"Florian","last_name":"Schur"},{"full_name":"Bayerl, Jonathan","last_name":"Bayerl","first_name":"Jonathan"},{"id":"4C7D837E-F248-11E8-B48F-1D18A9856A87","last_name":"De Vries","first_name":"Ingrid","full_name":"De Vries, Ingrid"},{"full_name":"Wieser, Stefan","id":"355AA5A0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2670-2217","first_name":"Stefan","last_name":"Wieser"},{"orcid":"0000-0001-9843-3522","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","last_name":"Hauschild","first_name":"Robert","full_name":"Hauschild, Robert"},{"full_name":"Lai, Frank","first_name":"Frank","last_name":"Lai"},{"full_name":"Moser, Markus","first_name":"Markus","last_name":"Moser"},{"full_name":"Kerjaschki, Dontscho","last_name":"Kerjaschki","first_name":"Dontscho"},{"last_name":"Rottner","first_name":"Klemens","full_name":"Rottner, Klemens"},{"full_name":"Small, Victor","first_name":"Victor","last_name":"Small"},{"full_name":"Stradal, Theresia","first_name":"Theresia","last_name":"Stradal"},{"first_name":"Michael K","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K"}],"related_material":{"record":[{"id":"323","relation":"dissertation_contains","status":"public"}]},"date_created":"2018-12-11T11:51:21Z","date_updated":"2024-03-28T23:30:16Z","volume":18,"acknowledgement":"This work was supported by the German Research Foundation (DFG) Priority Program SP 1464 to T.E.B.S. and M.S., and European Research Council (ERC GA 281556) and Human Frontiers Program grants to M.S.\r\nService Units of IST Austria for excellent technical support.","year":"2016","publication_status":"published","department":[{"_id":"MiSi"},{"_id":"NanoFab"},{"_id":"Bio"}],"publisher":"Nature Publishing Group","file_date_updated":"2020-07-14T12:44:43Z","ec_funded":1,"publist_id":"5949","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/"},{"acknowledged_ssus":[{"_id":"SSU"}],"language":[{"iso":"eng"}],"doi":"10.1016/j.celrep.2016.06.036","quality_controlled":"1","project":[{"grant_number":"T 560-B17","_id":"2529486C-B435-11E9-9278-68D0E5697425","name":"Cell- and Tissue Mechanics in Zebrafish Germ Layer Formation","call_identifier":"FWF"},{"name":"Cell Cortex and Germ Layer Formation in Zebrafish Gastrulation","call_identifier":"FWF","_id":"2527D5CC-B435-11E9-9278-68D0E5697425","grant_number":"I 812-B12"},{"call_identifier":"FP7","name":"Microbial Ion Channels for Synthetic Neurobiology","_id":"25548C20-B435-11E9-9278-68D0E5697425","grant_number":"303564"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"month":"07","date_created":"2018-12-11T11:50:08Z","date_updated":"2024-03-28T23:30:26Z","volume":16,"author":[{"orcid":"0000-0002-6453-8075","id":"3BED66BE-F248-11E8-B48F-1D18A9856A87","last_name":"Sako","first_name":"Keisuke","full_name":"Sako, Keisuke"},{"full_name":"Pradhan, Saurabh","last_name":"Pradhan","first_name":"Saurabh"},{"id":"419EECCC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2676-3367","first_name":"Vanessa","last_name":"Barone","full_name":"Barone, Vanessa"},{"first_name":"Álvaro","last_name":"Inglés Prieto","id":"2A9DB292-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5409-8571","full_name":"Inglés Prieto, Álvaro"},{"full_name":"Mueller, Patrick","last_name":"Mueller","first_name":"Patrick"},{"last_name":"Ruprecht","first_name":"Verena","orcid":"0000-0003-4088-8633","id":"4D71A03A-F248-11E8-B48F-1D18A9856A87","full_name":"Ruprecht, Verena"},{"full_name":"Capek, Daniel","id":"31C42484-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5199-9940","first_name":"Daniel","last_name":"Capek"},{"first_name":"Sanjeev","last_name":"Galande","full_name":"Galande, Sanjeev"},{"first_name":"Harald L","last_name":"Janovjak","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8023-9315","full_name":"Janovjak, Harald L"},{"full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","first_name":"Carl-Philipp J"}],"related_material":{"record":[{"id":"961","relation":"dissertation_contains","status":"public"},{"status":"public","relation":"dissertation_contains","id":"50"}]},"publication_status":"published","publisher":"Cell Press","department":[{"_id":"CaHe"},{"_id":"HaJa"}],"year":"2016","acknowledgement":"We are grateful to members of the C.-P.H. and H.J. labs for discussions, R. Hauschild and the different Scientific Service Units at IST Austria for technical help, M. Dravecka for performing initial experiments, A. Schier for reading an earlier version of the manuscript, K.W. Rogers for technical help, and C. Hill, A. Bruce, and L. Solnica-Krezel for sending plasmids. This work was supported by grants from the Austrian Science Foundation (FWF): (T560-B17) and (I 812-B12) to V.R. and C.-P.H., and from the European Union (EU FP7): (6275) to H.J. A.I.-P. is supported by a Ramon Areces fellowship.","file_date_updated":"2018-12-12T10:11:04Z","publist_id":"6275","ec_funded":1,"date_published":"2016-07-19T00:00:00Z","page":"866 - 877","publication":"Cell Reports","citation":{"short":"K. Sako, S. Pradhan, V. Barone, Á. Inglés Prieto, P. Mueller, V. Ruprecht, D. Capek, S. Galande, H.L. Janovjak, C.-P.J. Heisenberg, Cell Reports 16 (2016) 866–877.","mla":"Sako, Keisuke, et al. “Optogenetic Control of Nodal Signaling Reveals a Temporal Pattern of Nodal Signaling Regulating Cell Fate Specification during Gastrulation.” Cell Reports, vol. 16, no. 3, Cell Press, 2016, pp. 866–77, doi:10.1016/j.celrep.2016.06.036.","chicago":"Sako, Keisuke, Saurabh Pradhan, Vanessa Barone, Álvaro Inglés Prieto, Patrick Mueller, Verena Ruprecht, Daniel Capek, Sanjeev Galande, Harald L Janovjak, and Carl-Philipp J Heisenberg. “Optogenetic Control of Nodal Signaling Reveals a Temporal Pattern of Nodal Signaling Regulating Cell Fate Specification during Gastrulation.” Cell Reports. Cell Press, 2016. https://doi.org/10.1016/j.celrep.2016.06.036.","ama":"Sako K, Pradhan S, Barone V, et al. Optogenetic control of nodal signaling reveals a temporal pattern of nodal signaling regulating cell fate specification during gastrulation. Cell Reports. 2016;16(3):866-877. doi:10.1016/j.celrep.2016.06.036","apa":"Sako, K., Pradhan, S., Barone, V., Inglés Prieto, Á., Mueller, P., Ruprecht, V., … Heisenberg, C.-P. J. (2016). Optogenetic control of nodal signaling reveals a temporal pattern of nodal signaling regulating cell fate specification during gastrulation. Cell Reports. Cell Press. https://doi.org/10.1016/j.celrep.2016.06.036","ieee":"K. Sako et al., “Optogenetic control of nodal signaling reveals a temporal pattern of nodal signaling regulating cell fate specification during gastrulation,” Cell Reports, vol. 16, no. 3. Cell Press, pp. 866–877, 2016.","ista":"Sako K, Pradhan S, Barone V, Inglés Prieto Á, Mueller P, Ruprecht V, Capek D, Galande S, Janovjak HL, Heisenberg C-PJ. 2016. Optogenetic control of nodal signaling reveals a temporal pattern of nodal signaling regulating cell fate specification during gastrulation. Cell Reports. 16(3), 866–877."},"day":"19","has_accepted_license":"1","scopus_import":1,"file":[{"file_id":"4857","relation":"main_file","date_updated":"2018-12-12T10:11:04Z","date_created":"2018-12-12T10:11:04Z","file_name":"IST-2017-754-v1+1_1-s2.0-S2211124716307768-main.pdf","access_level":"open_access","creator":"system","content_type":"application/pdf","file_size":3921947}],"oa_version":"Published Version","pubrep_id":"754","title":"Optogenetic control of nodal signaling reveals a temporal pattern of nodal signaling regulating cell fate specification during gastrulation","ddc":["570","576"],"status":"public","intvolume":" 16","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","_id":"1100","abstract":[{"lang":"eng","text":"During metazoan development, the temporal pattern of morphogen signaling is critical for organizing cell fates in space and time. Yet, tools for temporally controlling morphogen signaling within the embryo are still scarce. Here, we developed a photoactivatable Nodal receptor to determine how the temporal pattern of Nodal signaling affects cell fate specification during zebrafish gastrulation. By using this receptor to manipulate the duration of Nodal signaling in vivo by light, we show that extended Nodal signaling within the organizer promotes prechordal plate specification and suppresses endoderm differentiation. Endoderm differentiation is suppressed by extended Nodal signaling inducing expression of the transcriptional repressor goosecoid (gsc) in prechordal plate progenitors, which in turn restrains Nodal signaling from upregulating the endoderm differentiation gene sox17 within these cells. Thus, optogenetic manipulation of Nodal signaling identifies a critical role of Nodal signaling duration for organizer cell fate specification during gastrulation."}],"issue":"3","type":"journal_article"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1437","title":"Algorithms for algebraic path properties in concurrent systems of constant treewidth components","status":"public","oa_version":"Preprint","type":"conference","alternative_title":["POPL"],"abstract":[{"text":"We study algorithmic questions for concurrent systems where the transitions are labeled from a complete, closed semiring, and path properties are algebraic with semiring operations. The algebraic path properties can model dataflow analysis problems, the shortest path problem, and many other natural problems that arise in program analysis. We consider that each component of the concurrent system is a graph with constant treewidth, a property satisfied by the controlflow graphs of most programs. We allow for multiple possible queries, which arise naturally in demand driven dataflow analysis. The study of multiple queries allows us to consider the tradeoff between the resource usage of the one-time preprocessing and for each individual query. The traditional approach constructs the product graph of all components and applies the best-known graph algorithm on the product. In this approach, even the answer to a single query requires the transitive closure (i.e., the results of all possible queries), which provides no room for tradeoff between preprocessing and query time. Our main contributions are algorithms that significantly improve the worst-case running time of the traditional approach, and provide various tradeoffs depending on the number of queries. For example, in a concurrent system of two components, the traditional approach requires hexic time in the worst case for answering one query as well as computing the transitive closure, whereas we show that with one-time preprocessing in almost cubic time, each subsequent query can be answered in at most linear time, and even the transitive closure can be computed in almost quartic time. Furthermore, we establish conditional optimality results showing that the worst-case running time of our algorithms cannot be improved without achieving major breakthroughs in graph algorithms (i.e., improving the worst-case bound for the shortest path problem in general graphs). Preliminary experimental results show that our algorithms perform favorably on several benchmarks.","lang":"eng"}],"citation":{"ama":"Chatterjee K, Goharshady AK, Ibsen-Jensen R, Pavlogiannis A. Algorithms for algebraic path properties in concurrent systems of constant treewidth components. In: Vol 20-22. ACM; 2016:733-747. doi:10.1145/2837614.2837624","ista":"Chatterjee K, Goharshady AK, Ibsen-Jensen R, Pavlogiannis A. 2016. Algorithms for algebraic path properties in concurrent systems of constant treewidth components. POPL: Principles of Programming Languages, POPL, vol. 20–22, 733–747.","ieee":"K. Chatterjee, A. K. Goharshady, R. Ibsen-Jensen, and A. Pavlogiannis, “Algorithms for algebraic path properties in concurrent systems of constant treewidth components,” presented at the POPL: Principles of Programming Languages, St. Petersburg, FL, USA, 2016, vol. 20–22, pp. 733–747.","apa":"Chatterjee, K., Goharshady, A. K., Ibsen-Jensen, R., & Pavlogiannis, A. (2016). Algorithms for algebraic path properties in concurrent systems of constant treewidth components (Vol. 20–22, pp. 733–747). Presented at the POPL: Principles of Programming Languages, St. Petersburg, FL, USA: ACM. https://doi.org/10.1145/2837614.2837624","mla":"Chatterjee, Krishnendu, et al. Algorithms for Algebraic Path Properties in Concurrent Systems of Constant Treewidth Components. Vol. 20–22, ACM, 2016, pp. 733–47, doi:10.1145/2837614.2837624.","short":"K. Chatterjee, A.K. Goharshady, R. Ibsen-Jensen, A. Pavlogiannis, in:, ACM, 2016, pp. 733–747.","chicago":"Chatterjee, Krishnendu, Amir Kafshdar Goharshady, Rasmus Ibsen-Jensen, and Andreas Pavlogiannis. “Algorithms for Algebraic Path Properties in Concurrent Systems of Constant Treewidth Components,” 20–22:733–47. ACM, 2016. https://doi.org/10.1145/2837614.2837624."},"page":"733 - 747","date_published":"2016-01-11T00:00:00Z","scopus_import":1,"day":"11","year":"2016","department":[{"_id":"KrCh"}],"publisher":"ACM","publication_status":"published","related_material":{"record":[{"status":"public","relation":"earlier_version","id":"5441"},{"id":"5442","status":"public","relation":"earlier_version"},{"relation":"dissertation_contains","status":"public","id":"821"},{"id":"6009","relation":"later_version","status":"public"},{"id":"8934","relation":"dissertation_contains","status":"public"}]},"author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"},{"full_name":"Goharshady, Amir","last_name":"Goharshady","first_name":"Amir","orcid":"0000-0003-1702-6584","id":"391365CE-F248-11E8-B48F-1D18A9856A87"},{"id":"3B699956-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4783-0389","first_name":"Rasmus","last_name":"Ibsen-Jensen","full_name":"Ibsen-Jensen, Rasmus"},{"full_name":"Pavlogiannis, Andreas","last_name":"Pavlogiannis","first_name":"Andreas","orcid":"0000-0002-8943-0722","id":"49704004-F248-11E8-B48F-1D18A9856A87"}],"volume":"20-22","date_created":"2018-12-11T11:52:01Z","date_updated":"2024-03-28T23:30:33Z","ec_funded":1,"publist_id":"5761","oa":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1510.07565"}],"external_id":{"arxiv":["1510.07565"]},"project":[{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"}],"quality_controlled":"1","doi":"10.1145/2837614.2837624","conference":{"end_date":"2016-01-22","start_date":"2016-01-20","location":"St. Petersburg, FL, USA","name":"POPL: Principles of Programming Languages"},"language":[{"iso":"eng"}],"month":"01"},{"month":"07","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1604.07169"}],"oa":1,"project":[{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF"},{"name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"},{"call_identifier":"FP7","name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989"}],"quality_controlled":"1","doi":"10.1007/978-3-319-41528-4_1","conference":{"name":"CAV: Computer Aided Verification","end_date":"2016-07-23","location":"Toronto, Canada","start_date":"2016-07-17"},"language":[{"iso":"eng"}],"publist_id":"5824","ec_funded":1,"year":"2016","department":[{"_id":"KrCh"}],"publisher":"Springer","publication_status":"published","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"8934"}]},"author":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu"},{"full_name":"Fu, Hongfei","first_name":"Hongfei","last_name":"Fu","id":"3AAD03D6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Amir","last_name":"Goharshady","id":"391365CE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1702-6584","full_name":"Goharshady, Amir"}],"volume":9779,"date_updated":"2024-03-28T23:30:33Z","date_created":"2018-12-11T11:51:43Z","scopus_import":1,"day":"01","citation":{"ama":"Chatterjee K, Fu H, Goharshady AK. Termination analysis of probabilistic programs through Positivstellensatz’s. In: Vol 9779. Springer; 2016:3-22. doi:10.1007/978-3-319-41528-4_1","ista":"Chatterjee K, Fu H, Goharshady AK. 2016. Termination analysis of probabilistic programs through Positivstellensatz’s. CAV: Computer Aided Verification, LNCS, vol. 9779, 3–22.","ieee":"K. Chatterjee, H. Fu, and A. K. Goharshady, “Termination analysis of probabilistic programs through Positivstellensatz’s,” presented at the CAV: Computer Aided Verification, Toronto, Canada, 2016, vol. 9779, pp. 3–22.","apa":"Chatterjee, K., Fu, H., & Goharshady, A. K. (2016). Termination analysis of probabilistic programs through Positivstellensatz’s (Vol. 9779, pp. 3–22). Presented at the CAV: Computer Aided Verification, Toronto, Canada: Springer. https://doi.org/10.1007/978-3-319-41528-4_1","mla":"Chatterjee, Krishnendu, et al. Termination Analysis of Probabilistic Programs through Positivstellensatz’s. Vol. 9779, Springer, 2016, pp. 3–22, doi:10.1007/978-3-319-41528-4_1.","short":"K. Chatterjee, H. Fu, A.K. Goharshady, in:, Springer, 2016, pp. 3–22.","chicago":"Chatterjee, Krishnendu, Hongfei Fu, and Amir Kafshdar Goharshady. “Termination Analysis of Probabilistic Programs through Positivstellensatz’s,” 9779:3–22. Springer, 2016. https://doi.org/10.1007/978-3-319-41528-4_1."},"page":"3 - 22","date_published":"2016-07-01T00:00:00Z","type":"conference","alternative_title":["LNCS"],"abstract":[{"text":"We consider nondeterministic probabilistic programs with the most basic liveness property of termination. We present efficient methods for termination analysis of nondeterministic probabilistic programs with polynomial guards and assignments. Our approach is through synthesis of polynomial ranking supermartingales, that on one hand significantly generalizes linear ranking supermartingales and on the other hand is a counterpart of polynomial ranking-functions for proving termination of nonprobabilistic programs. The approach synthesizes polynomial ranking-supermartingales through Positivstellensatz's, yielding an efficient method which is not only sound, but also semi-complete over a large subclass of programs. We show experimental results to demonstrate that our approach can handle several classical programs with complex polynomial guards and assignments, and can synthesize efficient quadratic ranking-supermartingales when a linear one does not exist even for simple affine programs.","lang":"eng"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1386","intvolume":" 9779","title":"Termination analysis of probabilistic programs through Positivstellensatz's","status":"public","oa_version":"Preprint"},{"date_published":"2015-03-01T00:00:00Z","citation":{"chicago":"Polshyn, Hryhoriy, Can Zhang, Tyler Naibert, James Eckstein, and Raffi Budakian. “Study of Fe (Se, Te) Micron-Sized Rings by Magnetic Force Microscopy.” In APS March Meeting 2015, Vol. 60. American Physical Society, 2015.","mla":"Polshyn, Hryhoriy, et al. “Study of Fe (Se, Te) Micron-Sized Rings by Magnetic Force Microscopy.” APS March Meeting 2015, vol. 60, no. 1, G16.00009, American Physical Society, 2015.","short":"H. Polshyn, C. Zhang, T. Naibert, J. Eckstein, R. Budakian, in:, APS March Meeting 2015, American Physical Society, 2015.","ista":"Polshyn H, Zhang C, Naibert T, Eckstein J, Budakian R. 2015. Study of Fe (Se, Te) micron-sized rings by magnetic force microscopy. APS March Meeting 2015. APS: American Physical Society, Bulletin of the American Physical Society, vol. 60, G16.00009.","apa":"Polshyn, H., Zhang, C., Naibert, T., Eckstein, J., & Budakian, R. (2015). Study of Fe (Se, Te) micron-sized rings by magnetic force microscopy. In APS March Meeting 2015 (Vol. 60). San Antonio, TX, United States: American Physical Society.","ieee":"H. Polshyn, C. Zhang, T. Naibert, J. Eckstein, and R. Budakian, “Study of Fe (Se, Te) micron-sized rings by magnetic force microscopy,” in APS March Meeting 2015, San Antonio, TX, United States, 2015, vol. 60, no. 1.","ama":"Polshyn H, Zhang C, Naibert T, Eckstein J, Budakian R. Study of Fe (Se, Te) micron-sized rings by magnetic force microscopy. In: APS March Meeting 2015. Vol 60. American Physical Society; 2015."},"publication":"APS March Meeting 2015","article_processing_charge":"No","day":"01","oa_version":"Published Version","intvolume":" 60","title":"Study of Fe (Se, Te) micron-sized rings by magnetic force microscopy","status":"public","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"10748","issue":"1","abstract":[{"lang":"eng","text":"The study of fluxoid states and fluxoid dynamics in mesoscopic iron-based superconducting rings is valuable for characterizing the basic properties of the superconductor, and may also provide important insight into the superconducting paring symmetry. We report the fabrications of micron-sized rings and disks from thin films of Fe(Se, Te) grown by molecular beam epitaxy. In order to study fluxoid states in rings we developed a custom-tailored version of magnetic force microscopy (MFM). This technique has a number of qualitative advantages for working with mesoscopic superconducting samples in comparison to the conventional MFM and other imaging techniques. We observed metastable fluxoid states in rings of different sizes. Thermally activated fluxoid dynamics of these states was studied and modeled. In addition, we found different regimes of interaction between Fe(Se, Te) ring and MFM tip which are explained. Possibilities of the existence of exotic vortex states and proposals for experiments to test the symmetry of the superconducting order parameter in iron based superconductors are analyzed."}],"alternative_title":["Bulletin of the American Physical Society"],"type":"conference","language":[{"iso":"eng"}],"conference":{"name":"APS: American Physical Society","start_date":"2015-03-02","location":"San Antonio, TX, United States","end_date":"2015-03-06"},"quality_controlled":"1","main_file_link":[{"url":"https://meetings.aps.org/Meeting/MAR15/Event/238442","open_access":"1"}],"oa":1,"publication_identifier":{"issn":["0003-0503"]},"month":"03","volume":60,"date_created":"2022-02-08T10:17:09Z","date_updated":"2022-02-08T10:42:53Z","author":[{"first_name":"Hryhoriy","last_name":"Polshyn","id":"edfc7cb1-526e-11ec-b05a-e6ecc27e4e48","orcid":"0000-0001-8223-8896","full_name":"Polshyn, Hryhoriy"},{"first_name":"Can","last_name":"Zhang","full_name":"Zhang, Can"},{"full_name":"Naibert, Tyler","last_name":"Naibert","first_name":"Tyler"},{"full_name":"Eckstein, James","first_name":"James","last_name":"Eckstein"},{"last_name":"Budakian","first_name":"Raffi","full_name":"Budakian, Raffi"}],"publisher":"American Physical Society","publication_status":"published","year":"2015","extern":"1","article_number":"G16.00009"},{"scopus_import":"1","keyword":["General Environmental Science"],"has_accepted_license":"1","article_processing_charge":"No","day":"10","citation":{"ama":"Parise F, Lygeros J, Ruess J. Bayesian inference for stochastic individual-based models of ecological systems: a pest control simulation study. Frontiers in Environmental Science. 2015;3. doi:10.3389/fenvs.2015.00042","ista":"Parise F, Lygeros J, Ruess J. 2015. Bayesian inference for stochastic individual-based models of ecological systems: a pest control simulation study. Frontiers in Environmental Science. 3, 42.","ieee":"F. Parise, J. Lygeros, and J. Ruess, “Bayesian inference for stochastic individual-based models of ecological systems: a pest control simulation study,” Frontiers in Environmental Science, vol. 3. Frontiers, 2015.","apa":"Parise, F., Lygeros, J., & Ruess, J. (2015). Bayesian inference for stochastic individual-based models of ecological systems: a pest control simulation study. Frontiers in Environmental Science. Frontiers. https://doi.org/10.3389/fenvs.2015.00042","mla":"Parise, Francesca, et al. “Bayesian Inference for Stochastic Individual-Based Models of Ecological Systems: A Pest Control Simulation Study.” Frontiers in Environmental Science, vol. 3, 42, Frontiers, 2015, doi:10.3389/fenvs.2015.00042.","short":"F. Parise, J. Lygeros, J. Ruess, Frontiers in Environmental Science 3 (2015).","chicago":"Parise, Francesca, John Lygeros, and Jakob Ruess. “Bayesian Inference for Stochastic Individual-Based Models of Ecological Systems: A Pest Control Simulation Study.” Frontiers in Environmental Science. Frontiers, 2015. https://doi.org/10.3389/fenvs.2015.00042."},"publication":"Frontiers in Environmental Science","article_type":"original","date_published":"2015-06-10T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"Mathematical models are of fundamental importance in the understanding of complex population dynamics. For instance, they can be used to predict the population evolution starting from different initial conditions or to test how a system responds to external perturbations. For this analysis to be meaningful in real applications, however, it is of paramount importance to choose an appropriate model structure and to infer the model parameters from measured data. While many parameter inference methods are available for models based on deterministic ordinary differential equations, the same does not hold for more detailed individual-based models. Here we consider, in particular, stochastic models in which the time evolution of the species abundances is described by a continuous-time Markov chain. These models are governed by a master equation that is typically difficult to solve. Consequently, traditional inference methods that rely on iterative evaluation of parameter likelihoods are computationally intractable. The aim of this paper is to present recent advances in parameter inference for continuous-time Markov chain models, based on a moment closure approximation of the parameter likelihood, and to investigate how these results can help in understanding, and ultimately controlling, complex systems in ecology. Specifically, we illustrate through an agricultural pest case study how parameters of a stochastic individual-based model can be identified from measured data and how the resulting model can be used to solve an optimal control problem in a stochastic setting. In particular, we show how the matter of determining the optimal combination of two different pest control methods can be formulated as a chance constrained optimization problem where the control action is modeled as a state reset, leading to a hybrid system formulation."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"10794","intvolume":" 3","status":"public","title":"Bayesian inference for stochastic individual-based models of ecological systems: a pest control simulation study","ddc":["000","570"],"oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2015_FrontiersEnvironmScience_Parise.pdf","creator":"dernst","file_size":1371201,"content_type":"application/pdf","file_id":"10795","relation":"main_file","success":1,"checksum":"26c222487564e1be02a11d688d6f769d","date_created":"2022-02-25T11:55:26Z","date_updated":"2022-02-25T11:55:26Z"}],"publication_identifier":{"issn":["2296-665X"]},"month":"06","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","doi":"10.3389/fenvs.2015.00042","language":[{"iso":"eng"}],"article_number":"42","ec_funded":1,"file_date_updated":"2022-02-25T11:55:26Z","acknowledgement":"The authors would like to acknowledge contributions from Baptiste Mottet who performed preliminary analysis regarding parameter inference for the considered case study in a student project (Mottet, 2014/2015).\r\nThe research leading to these results has received funding from the People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme (FP7/2007-2013) under REA grant agreement No. [291734] and from SystemsX under the project SignalX.","year":"2015","publisher":"Frontiers","department":[{"_id":"ToHe"},{"_id":"GaTk"}],"publication_status":"published","author":[{"full_name":"Parise, Francesca","last_name":"Parise","first_name":"Francesca"},{"full_name":"Lygeros, John","first_name":"John","last_name":"Lygeros"},{"full_name":"Ruess, Jakob","first_name":"Jakob","last_name":"Ruess","id":"4A245D00-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1615-3282"}],"volume":3,"date_updated":"2022-02-25T11:59:23Z","date_created":"2022-02-25T11:42:25Z"},{"publication_identifier":{"issn":["1934-5909"]},"month":"12","language":[{"iso":"eng"}],"doi":"10.1016/j.stem.2015.09.001","quality_controlled":"1","external_id":{"pmid":["26456686"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.stem.2015.09.001"}],"oa":1,"extern":"1","volume":17,"date_updated":"2022-07-18T08:44:21Z","date_created":"2022-04-07T07:49:51Z","author":[{"full_name":"Mertens, Jerome","first_name":"Jerome","last_name":"Mertens"},{"last_name":"Paquola","first_name":"Apuã C.M.","full_name":"Paquola, Apuã C.M."},{"full_name":"Ku, Manching","first_name":"Manching","last_name":"Ku"},{"full_name":"Hatch, Emily","first_name":"Emily","last_name":"Hatch"},{"full_name":"Böhnke, Lena","first_name":"Lena","last_name":"Böhnke"},{"last_name":"Ladjevardi","first_name":"Shauheen","full_name":"Ladjevardi, Shauheen"},{"full_name":"McGrath, Sean","first_name":"Sean","last_name":"McGrath"},{"first_name":"Benjamin","last_name":"Campbell","full_name":"Campbell, Benjamin"},{"full_name":"Lee, Hyungjun","first_name":"Hyungjun","last_name":"Lee"},{"full_name":"Herdy, Joseph R.","last_name":"Herdy","first_name":"Joseph R."},{"first_name":"J. Tiago","last_name":"Gonçalves","full_name":"Gonçalves, J. Tiago"},{"last_name":"Toda","first_name":"Tomohisa","full_name":"Toda, Tomohisa"},{"last_name":"Kim","first_name":"Yongsung","full_name":"Kim, Yongsung"},{"full_name":"Winkler, Jürgen","first_name":"Jürgen","last_name":"Winkler"},{"full_name":"Yao, Jun","last_name":"Yao","first_name":"Jun"},{"full_name":"HETZER, Martin W","orcid":"0000-0002-2111-992X","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","last_name":"HETZER","first_name":"Martin W"},{"first_name":"Fred H.","last_name":"Gage","full_name":"Gage, Fred H."}],"publisher":"Elsevier","publication_status":"published","pmid":1,"year":"2015","article_processing_charge":"No","day":"03","keyword":["Cell Biology","Genetics","Molecular Medicine"],"scopus_import":"1","date_published":"2015-12-03T00:00:00Z","page":"705-718","article_type":"original","citation":{"chicago":"Mertens, Jerome, Apuã C.M. Paquola, Manching Ku, Emily Hatch, Lena Böhnke, Shauheen Ladjevardi, Sean McGrath, et al. “Directly Reprogrammed Human Neurons Retain Aging-Associated Transcriptomic Signatures and Reveal Age-Related Nucleocytoplasmic Defects.” Cell Stem Cell. Elsevier, 2015. https://doi.org/10.1016/j.stem.2015.09.001.","mla":"Mertens, Jerome, et al. “Directly Reprogrammed Human Neurons Retain Aging-Associated Transcriptomic Signatures and Reveal Age-Related Nucleocytoplasmic Defects.” Cell Stem Cell, vol. 17, no. 6, Elsevier, 2015, pp. 705–18, doi:10.1016/j.stem.2015.09.001.","short":"J. Mertens, A.C.M. Paquola, M. Ku, E. Hatch, L. Böhnke, S. Ladjevardi, S. McGrath, B. Campbell, H. Lee, J.R. Herdy, J.T. Gonçalves, T. Toda, Y. Kim, J. Winkler, J. Yao, M. Hetzer, F.H. Gage, Cell Stem Cell 17 (2015) 705–718.","ista":"Mertens J, Paquola ACM, Ku M, Hatch E, Böhnke L, Ladjevardi S, McGrath S, Campbell B, Lee H, Herdy JR, Gonçalves JT, Toda T, Kim Y, Winkler J, Yao J, Hetzer M, Gage FH. 2015. Directly reprogrammed human neurons retain aging-associated transcriptomic signatures and reveal age-related nucleocytoplasmic defects. Cell Stem Cell. 17(6), 705–718.","ieee":"J. Mertens et al., “Directly reprogrammed human neurons retain aging-associated transcriptomic signatures and reveal age-related nucleocytoplasmic defects,” Cell Stem Cell, vol. 17, no. 6. Elsevier, pp. 705–718, 2015.","apa":"Mertens, J., Paquola, A. C. M., Ku, M., Hatch, E., Böhnke, L., Ladjevardi, S., … Gage, F. H. (2015). Directly reprogrammed human neurons retain aging-associated transcriptomic signatures and reveal age-related nucleocytoplasmic defects. Cell Stem Cell. Elsevier. https://doi.org/10.1016/j.stem.2015.09.001","ama":"Mertens J, Paquola ACM, Ku M, et al. Directly reprogrammed human neurons retain aging-associated transcriptomic signatures and reveal age-related nucleocytoplasmic defects. Cell Stem Cell. 2015;17(6):705-718. doi:10.1016/j.stem.2015.09.001"},"publication":"Cell Stem Cell","issue":"6","abstract":[{"text":"Aging is a major risk factor for many human diseases, and in vitro generation of human neurons is an attractive approach for modeling aging-related brain disorders. However, modeling aging in differentiated human neurons has proved challenging. We generated neurons from human donors across a broad range of ages, either by iPSC-based reprogramming and differentiation or by direct conversion into induced neurons (iNs). While iPSCs and derived neurons did not retain aging-associated gene signatures, iNs displayed age-specific transcriptional profiles and revealed age-associated decreases in the nuclear transport receptor RanBP17. We detected an age-dependent loss of nucleocytoplasmic compartmentalization (NCC) in donor fibroblasts and corresponding iNs and found that reduced RanBP17 impaired NCC in young cells, while iPSC rejuvenation restored NCC in aged cells. These results show that iNs retain important aging-related signatures, thus allowing modeling of the aging process in vitro, and they identify impaired NCC as an important factor in human aging.","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","intvolume":" 17","title":"Directly reprogrammed human neurons retain aging-associated transcriptomic signatures and reveal age-related nucleocytoplasmic defects","status":"public","_id":"11079","user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd"},{"user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","_id":"11077","intvolume":" 29","title":"The nucleoporin Nup153 regulates embryonic stem cell pluripotency through gene silencing","status":"public","oa_version":"Published Version","type":"journal_article","issue":"12","abstract":[{"text":"Nucleoporins (Nups) are a family of proteins best known as the constituent building blocks of nuclear pore complexes (NPCs), membrane-embedded channels that mediate nuclear transport across the nuclear envelope. Recent evidence suggests that several Nups have additional roles in controlling the activation and silencing of developmental genes; however, the mechanistic details of these functions remain poorly understood. Here, we show that depletion of Nup153 in mouse embryonic stem cells (mESCs) causes the derepression of developmental genes and induction of early differentiation. This loss of stem cell identity is not associated with defects in the nuclear import of key pluripotency factors. Rather, Nup153 binds around the transcriptional start site (TSS) of developmental genes and mediates the recruitment of the polycomb-repressive complex 1 (PRC1) to a subset of its target loci. Our results demonstrate a chromatin-associated role of Nup153 in maintaining stem cell pluripotency by functioning in mammalian epigenetic gene silencing.","lang":"eng"}],"citation":{"ama":"Jacinto FV, Benner C, Hetzer M. The nucleoporin Nup153 regulates embryonic stem cell pluripotency through gene silencing. Genes & Development. 2015;29(12):1224-1238. doi:10.1101/gad.260919.115","ista":"Jacinto FV, Benner C, Hetzer M. 2015. The nucleoporin Nup153 regulates embryonic stem cell pluripotency through gene silencing. Genes & Development. 29(12), 1224–1238.","ieee":"F. V. Jacinto, C. Benner, and M. Hetzer, “The nucleoporin Nup153 regulates embryonic stem cell pluripotency through gene silencing,” Genes & Development, vol. 29, no. 12. Cold Spring Harbor Laboratory, pp. 1224–1238, 2015.","apa":"Jacinto, F. V., Benner, C., & Hetzer, M. (2015). The nucleoporin Nup153 regulates embryonic stem cell pluripotency through gene silencing. Genes & Development. Cold Spring Harbor Laboratory. https://doi.org/10.1101/gad.260919.115","mla":"Jacinto, Filipe V., et al. “The Nucleoporin Nup153 Regulates Embryonic Stem Cell Pluripotency through Gene Silencing.” Genes & Development, vol. 29, no. 12, Cold Spring Harbor Laboratory, 2015, pp. 1224–38, doi:10.1101/gad.260919.115.","short":"F.V. Jacinto, C. Benner, M. Hetzer, Genes & Development 29 (2015) 1224–1238.","chicago":"Jacinto, Filipe V., Chris Benner, and Martin Hetzer. “The Nucleoporin Nup153 Regulates Embryonic Stem Cell Pluripotency through Gene Silencing.” Genes & Development. Cold Spring Harbor Laboratory, 2015. https://doi.org/10.1101/gad.260919.115."},"publication":"Genes & Development","page":"1224-1238","article_type":"original","date_published":"2015-06-16T00:00:00Z","scopus_import":"1","keyword":["Developmental Biology","Genetics"],"article_processing_charge":"No","day":"16","pmid":1,"year":"2015","publisher":"Cold Spring Harbor Laboratory","publication_status":"published","author":[{"full_name":"Jacinto, Filipe V.","last_name":"Jacinto","first_name":"Filipe V."},{"full_name":"Benner, Chris","first_name":"Chris","last_name":"Benner"},{"id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","orcid":"0000-0002-2111-992X","first_name":"Martin W","last_name":"HETZER","full_name":"HETZER, Martin W"}],"volume":29,"date_updated":"2022-07-18T08:43:51Z","date_created":"2022-04-07T07:49:31Z","extern":"1","external_id":{"pmid":["26080816"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/gad.260919.115"}],"oa":1,"quality_controlled":"1","doi":"10.1101/gad.260919.115","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1549-5477"],"issn":["0890-9369"]},"month":"06"},{"month":"09","publication_identifier":{"issn":["2405-4712"]},"language":[{"iso":"eng"}],"doi":"10.1016/j.cels.2015.08.012","quality_controlled":"1","main_file_link":[{"url":"https://doi.org/10.1016/j.cels.2015.08.012","open_access":"1"}],"oa":1,"external_id":{"pmid":["27135913"]},"extern":"1","date_updated":"2022-07-18T08:44:07Z","date_created":"2022-04-07T07:49:39Z","volume":1,"author":[{"last_name":"Ori","first_name":"Alessandro","full_name":"Ori, Alessandro"},{"last_name":"Toyama","first_name":"Brandon H.","full_name":"Toyama, Brandon H."},{"first_name":"Michael S.","last_name":"Harris","full_name":"Harris, Michael S."},{"full_name":"Bock, Thomas","last_name":"Bock","first_name":"Thomas"},{"full_name":"Iskar, Murat","last_name":"Iskar","first_name":"Murat"},{"first_name":"Peer","last_name":"Bork","full_name":"Bork, Peer"},{"full_name":"Ingolia, Nicholas T.","first_name":"Nicholas T.","last_name":"Ingolia"},{"first_name":"Martin W","last_name":"HETZER","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","orcid":"0000-0002-2111-992X","full_name":"HETZER, Martin W"},{"last_name":"Beck","first_name":"Martin","full_name":"Beck, Martin"}],"publication_status":"published","publisher":"Elsevier","year":"2015","pmid":1,"day":"23","article_processing_charge":"No","keyword":["Cell Biology","Histology","Pathology and Forensic Medicine"],"scopus_import":"1","date_published":"2015-09-23T00:00:00Z","article_type":"original","page":"P224-237","publication":"Cell Systems","citation":{"ama":"Ori A, Toyama BH, Harris MS, et al. Integrated transcriptome and proteome analyses reveal organ-specific proteome deterioration in old rats. Cell Systems. 2015;1(3):P224-237. doi:10.1016/j.cels.2015.08.012","apa":"Ori, A., Toyama, B. H., Harris, M. S., Bock, T., Iskar, M., Bork, P., … Beck, M. (2015). Integrated transcriptome and proteome analyses reveal organ-specific proteome deterioration in old rats. Cell Systems. Elsevier. https://doi.org/10.1016/j.cels.2015.08.012","ieee":"A. Ori et al., “Integrated transcriptome and proteome analyses reveal organ-specific proteome deterioration in old rats,” Cell Systems, vol. 1, no. 3. Elsevier, pp. P224-237, 2015.","ista":"Ori A, Toyama BH, Harris MS, Bock T, Iskar M, Bork P, Ingolia NT, Hetzer M, Beck M. 2015. Integrated transcriptome and proteome analyses reveal organ-specific proteome deterioration in old rats. Cell Systems. 1(3), P224-237.","short":"A. Ori, B.H. Toyama, M.S. Harris, T. Bock, M. Iskar, P. Bork, N.T. Ingolia, M. Hetzer, M. Beck, Cell Systems 1 (2015) P224-237.","mla":"Ori, Alessandro, et al. “Integrated Transcriptome and Proteome Analyses Reveal Organ-Specific Proteome Deterioration in Old Rats.” Cell Systems, vol. 1, no. 3, Elsevier, 2015, pp. P224-237, doi:10.1016/j.cels.2015.08.012.","chicago":"Ori, Alessandro, Brandon H. Toyama, Michael S. Harris, Thomas Bock, Murat Iskar, Peer Bork, Nicholas T. Ingolia, Martin Hetzer, and Martin Beck. “Integrated Transcriptome and Proteome Analyses Reveal Organ-Specific Proteome Deterioration in Old Rats.” Cell Systems. Elsevier, 2015. https://doi.org/10.1016/j.cels.2015.08.012."},"abstract":[{"lang":"eng","text":"Aging is associated with the decline of protein, cell, and organ function. Here, we use an integrated approach to characterize gene expression, bulk translation, and cell biology in the brains and livers of young and old rats. We identify 468 differences in protein abundance between young and old animals. The majority are a consequence of altered translation output, that is, the combined effect of changes in transcript abundance and translation efficiency. In addition, we identify 130 proteins whose overall abundance remains unchanged but whose sub-cellular localization, phosphorylation state, or splice-form varies. While some protein-level differences appear to be a generic property of the rats’ chronological age, the majority are specific to one organ. These may be a consequence of the organ’s physiology or the chronological age of the cells within the tissue. Taken together, our study provides an initial view of the proteome at the molecular, sub-cellular, and organ level in young and old rats."}],"issue":"3","type":"journal_article","oa_version":"Published Version","title":"Integrated transcriptome and proteome analyses reveal organ-specific proteome deterioration in old rats","status":"public","intvolume":" 1","_id":"11078","user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd"},{"oa_version":"Published Version","status":"public","title":"Nuclear pore proteins and the control of genome functions","intvolume":" 29","_id":"11076","user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","abstract":[{"text":"Nuclear pore complexes (NPCs) are composed of several copies of ∼30 different proteins called nucleoporins (Nups). NPCs penetrate the nuclear envelope (NE) and regulate the nucleocytoplasmic trafficking of macromolecules. Beyond this vital role, NPC components influence genome functions in a transport-independent manner. Nups play an evolutionarily conserved role in gene expression regulation that, in metazoans, extends into the nuclear interior. Additionally, in proliferative cells, Nups play a crucial role in genome integrity maintenance and mitotic progression. Here we discuss genome-related functions of Nups and their impact on essential DNA metabolism processes such as transcription, chromosome duplication, and segregation.","lang":"eng"}],"issue":"4","type":"journal_article","date_published":"2015-02-01T00:00:00Z","article_type":"original","page":"337-349","publication":"Genes & Development","citation":{"short":"A. Ibarra, M. Hetzer, Genes & Development 29 (2015) 337–349.","mla":"Ibarra, Arkaitz, and Martin Hetzer. “Nuclear Pore Proteins and the Control of Genome Functions.” Genes & Development, vol. 29, no. 4, Cold Spring Harbor Laboratory, 2015, pp. 337–49, doi:10.1101/gad.256495.114.","chicago":"Ibarra, Arkaitz, and Martin Hetzer. “Nuclear Pore Proteins and the Control of Genome Functions.” Genes & Development. Cold Spring Harbor Laboratory, 2015. https://doi.org/10.1101/gad.256495.114.","ama":"Ibarra A, Hetzer M. Nuclear pore proteins and the control of genome functions. Genes & Development. 2015;29(4):337-349. doi:10.1101/gad.256495.114","ieee":"A. Ibarra and M. Hetzer, “Nuclear pore proteins and the control of genome functions,” Genes & Development, vol. 29, no. 4. Cold Spring Harbor Laboratory, pp. 337–349, 2015.","apa":"Ibarra, A., & Hetzer, M. (2015). Nuclear pore proteins and the control of genome functions. Genes & Development. Cold Spring Harbor Laboratory. https://doi.org/10.1101/gad.256495.114","ista":"Ibarra A, Hetzer M. 2015. Nuclear pore proteins and the control of genome functions. Genes & Development. 29(4), 337–349."},"day":"01","article_processing_charge":"No","keyword":["Developmental Biology","Genetics"],"scopus_import":"1","date_updated":"2022-07-18T08:43:20Z","date_created":"2022-04-07T07:49:21Z","volume":29,"author":[{"full_name":"Ibarra, Arkaitz","first_name":"Arkaitz","last_name":"Ibarra"},{"first_name":"Martin W","last_name":"HETZER","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","orcid":"0000-0002-2111-992X","full_name":"HETZER, Martin W"}],"publication_status":"published","publisher":"Cold Spring Harbor Laboratory","year":"2015","pmid":1,"extern":"1","language":[{"iso":"eng"}],"doi":"10.1101/gad.256495.114","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/gad.256495.114"}],"oa":1,"external_id":{"pmid":["25691464"]},"month":"02","publication_identifier":{"issn":["0890-9369"],"eissn":["1549-5477"]}},{"article_type":"original","page":"1502-1504","publication":"Cell","citation":{"chicago":"Hatch, Emily M., and Martin Hetzer. “Linking Micronuclei to Chromosome Fragmentation.” Cell. Elsevier, 2015. https://doi.org/10.1016/j.cell.2015.06.005.","short":"E.M. Hatch, M. Hetzer, Cell 161 (2015) 1502–1504.","mla":"Hatch, Emily M., and Martin Hetzer. “Linking Micronuclei to Chromosome Fragmentation.” Cell, vol. 161, no. 7, Elsevier, 2015, pp. 1502–04, doi:10.1016/j.cell.2015.06.005.","ieee":"E. M. Hatch and M. Hetzer, “Linking micronuclei to chromosome fragmentation,” Cell, vol. 161, no. 7. Elsevier, pp. 1502–1504, 2015.","apa":"Hatch, E. M., & Hetzer, M. (2015). Linking micronuclei to chromosome fragmentation. Cell. Elsevier. https://doi.org/10.1016/j.cell.2015.06.005","ista":"Hatch EM, Hetzer M. 2015. Linking micronuclei to chromosome fragmentation. Cell. 161(7), 1502–1504.","ama":"Hatch EM, Hetzer M. Linking micronuclei to chromosome fragmentation. Cell. 2015;161(7):1502-1504. doi:10.1016/j.cell.2015.06.005"},"date_published":"2015-06-18T00:00:00Z","keyword":["General Biochemistry","Genetics and Molecular Biology"],"scopus_import":"1","day":"18","article_processing_charge":"No","title":"Linking micronuclei to chromosome fragmentation","status":"public","intvolume":" 161","_id":"11073","user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"Human cancer cells bear complex chromosome rearrangements that can be potential drivers of cancer development. However, the molecular mechanisms underlying these rearrangements have been unclear. Zhang et al. use a new technique combining live-cell imaging and single-cell sequencing to demonstrate that chromosomes mis-segregated to micronuclei frequently undergo chromothripsis-like rearrangements in the subsequent cell cycle."}],"issue":"7","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.cell.2015.06.005"}],"oa":1,"external_id":{"pmid":["26091034"]},"language":[{"iso":"eng"}],"doi":"10.1016/j.cell.2015.06.005","month":"06","publication_identifier":{"issn":["0092-8674"]},"publication_status":"published","publisher":"Elsevier","year":"2015","pmid":1,"date_updated":"2022-07-18T08:34:33Z","date_created":"2022-04-07T07:48:49Z","volume":161,"author":[{"last_name":"Hatch","first_name":"Emily M.","full_name":"Hatch, Emily M."},{"orcid":"0000-0002-2111-992X","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","last_name":"HETZER","first_name":"Martin W","full_name":"HETZER, Martin W"}],"extern":"1"},{"publication_identifier":{"issn":["0960-9822"]},"month":"05","quality_controlled":"1","oa":1,"external_id":{"pmid":["25989073"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.cub.2015.02.033"}],"language":[{"iso":"eng"}],"doi":"10.1016/j.cub.2015.02.033","extern":"1","publisher":"Elsevier","publication_status":"published","pmid":1,"year":"2015","volume":25,"date_created":"2022-04-07T07:49:00Z","date_updated":"2022-07-18T08:34:34Z","author":[{"full_name":"Hatch, Emily M.","first_name":"Emily M.","last_name":"Hatch"},{"full_name":"HETZER, Martin W","orcid":"0000-0002-2111-992X","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","last_name":"HETZER","first_name":"Martin W"}],"keyword":["General Agricultural and Biological Sciences","General Biochemistry","Genetics and Molecular Biology"],"scopus_import":"1","article_processing_charge":"No","day":"18","page":"PR397-R399","article_type":"original","citation":{"ista":"Hatch EM, Hetzer M. 2015. Chromothripsis. Current Biology. 25(10), PR397-R399.","ieee":"E. M. Hatch and M. Hetzer, “Chromothripsis,” Current Biology, vol. 25, no. 10. Elsevier, pp. PR397-R399, 2015.","apa":"Hatch, E. M., & Hetzer, M. (2015). Chromothripsis. Current Biology. Elsevier. https://doi.org/10.1016/j.cub.2015.02.033","ama":"Hatch EM, Hetzer M. Chromothripsis. Current Biology. 2015;25(10):PR397-R399. doi:10.1016/j.cub.2015.02.033","chicago":"Hatch, Emily M., and Martin Hetzer. “Chromothripsis.” Current Biology. Elsevier, 2015. https://doi.org/10.1016/j.cub.2015.02.033.","mla":"Hatch, Emily M., and Martin Hetzer. “Chromothripsis.” Current Biology, vol. 25, no. 10, Elsevier, 2015, pp. PR397-R399, doi:10.1016/j.cub.2015.02.033.","short":"E.M. Hatch, M. Hetzer, Current Biology 25 (2015) PR397-R399."},"publication":"Current Biology","date_published":"2015-05-18T00:00:00Z","type":"journal_article","issue":"10","intvolume":" 25","title":"Chromothripsis","status":"public","_id":"11074","user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","oa_version":"Published Version"},{"external_id":{"arxiv":["1504.01734"]},"main_file_link":[{"url":"https://arxiv.org/abs/1504.01734","open_access":"1"}],"oa":1,"quality_controlled":"1","doi":"10.1088/0004-637X/808/2/139","language":[{"iso":"eng"}],"month":"07","publication_identifier":{"eissn":["1538-4357"],"issn":["0004-637X"]},"year":"2015","acknowledgement":"We thank the anonymous reviewer for useful and constructive comments and suggestions which greatly improved the quality and clarity of our work. D.S. acknowledges financial support from the Netherlands Organisation for Scientific research (NWO) through a Veni fellowship, from FCT through a FCT Investigator Starting Grant and Start-up Grant (IF/01154/2012/CP0189/CT0010), from FCT grant UID/FIS/04434/2013, and from LSF and LKBF. J.M. acknowledges the award of a Huygens PhD fellowship. H.R. acknowledges support from the ERC Advanced Investigator program NewClusters 321271. The authors thank Mark Dijkstra, Bhaskar Agarwal, Jarrett Johnson, Andrea Ferrara, Jarle Brinchmann, Rebecca Bowler, George Becker, Emma Curtis-Lake, Milos Milosavljevic, Raffaella Schneider, Paul Shapiro, and Erik Zackrisson for interesting, stimulating and helpful discussions. The authors are extremely grateful to ESO for the award of ESO DDT time (294.A-5018 and 294.A-5039) which allowed the spectroscopic confirmation of both sources and the detailed investigation of their nature. Observations are also based on data from W.M. Keck Observatory. The W.M. Keck Observatory is operated as a scientific partnership of Caltech, the University of California and the National Aeronautics and Space Administration. Based on observations obtained with MegaPrime/Megacam, a joint project of CFHT and CEA/IRFU, at the Canada–France–Hawaii Telescope (CFHT) which is operated by the National Research Council (NRC) of Canada, the Institut National des Science de lUnivers of the Centre National de la Recherche Scientifique (CNRS) of France, and the University of Hawaii. This work is based in part on data products produced at Terapix available at the Canadian Astronomy Data Centre as part of the Canada–France–Hawaii Telescope Legacy Survey, a collaborative project of NRC and CNRS. Based on data products from observations made with ESO Telescopes at the La Silla Paranal Observatory under ESO programme IDs 294.A-5018, 294.A-5039, and 179.A-2005, and on data products produced by TERAPIX and the Cambridge Astronomy Survey Unit on behalf of the UltraVISTA consortium. The authors acknowledge the award of service time (SW2014b20) on the William Herschel Telescope (WHT). WHT and its service programme are operated on the island of La Palma by the Isaac Newton Group in the Spanish Observatorio del Roque de los Muchachos of the Instituto de Astrofisica de Canarias.","publication_status":"published","publisher":"IOP Publishing","author":[{"last_name":"Sobral","first_name":"David","full_name":"Sobral, David"},{"last_name":"Matthee","first_name":"Jorryt J","orcid":"0000-0003-2871-127X","id":"7439a258-f3c0-11ec-9501-9df22fe06720","full_name":"Matthee, Jorryt J"},{"full_name":"Darvish, Behnam","first_name":"Behnam","last_name":"Darvish"},{"last_name":"Schaerer","first_name":"Daniel","full_name":"Schaerer, Daniel"},{"full_name":"Mobasher, Bahram","last_name":"Mobasher","first_name":"Bahram"},{"last_name":"Röttgering","first_name":"Huub","full_name":"Röttgering, Huub"},{"full_name":"Santos, Sérgio","first_name":"Sérgio","last_name":"Santos"},{"full_name":"Hemmati, Shoubaneh","last_name":"Hemmati","first_name":"Shoubaneh"}],"date_updated":"2022-08-18T10:30:13Z","date_created":"2022-07-07T09:00:58Z","volume":808,"extern":"1","publication":"The Astrophysical Journal","citation":{"short":"D. Sobral, J.J. Matthee, B. Darvish, D. Schaerer, B. Mobasher, H. Röttgering, S. Santos, S. Hemmati, The Astrophysical Journal 808 (2015) 139.","mla":"Sobral, David, et al. “Evidence for PopIII-like Stellar Populations in the Most Luminous Lyα Emitters at the Epoch of Reionisation: Spectroscopic Confirmation.” The Astrophysical Journal, vol. 808, no. 2, IOP Publishing, 2015, p. 139, doi:10.1088/0004-637X/808/2/139.","chicago":"Sobral, David, Jorryt J Matthee, Behnam Darvish, Daniel Schaerer, Bahram Mobasher, Huub Röttgering, Sérgio Santos, and Shoubaneh Hemmati. “Evidence for PopIII-like Stellar Populations in the Most Luminous Lyα Emitters at the Epoch of Reionisation: Spectroscopic Confirmation.” The Astrophysical Journal. IOP Publishing, 2015. https://doi.org/10.1088/0004-637X/808/2/139.","ama":"Sobral D, Matthee JJ, Darvish B, et al. Evidence for PopIII-like stellar populations in the most luminous Lyα emitters at the epoch of reionisation: Spectroscopic confirmation. The Astrophysical Journal. 2015;808(2):139. doi:10.1088/0004-637X/808/2/139","ieee":"D. Sobral et al., “Evidence for PopIII-like stellar populations in the most luminous Lyα emitters at the epoch of reionisation: Spectroscopic confirmation,” The Astrophysical Journal, vol. 808, no. 2. IOP Publishing, p. 139, 2015.","apa":"Sobral, D., Matthee, J. J., Darvish, B., Schaerer, D., Mobasher, B., Röttgering, H., … Hemmati, S. (2015). Evidence for PopIII-like stellar populations in the most luminous Lyα emitters at the epoch of reionisation: Spectroscopic confirmation. The Astrophysical Journal. IOP Publishing. https://doi.org/10.1088/0004-637X/808/2/139","ista":"Sobral D, Matthee JJ, Darvish B, Schaerer D, Mobasher B, Röttgering H, Santos S, Hemmati S. 2015. Evidence for PopIII-like stellar populations in the most luminous Lyα emitters at the epoch of reionisation: Spectroscopic confirmation. The Astrophysical Journal. 808(2), 139."},"article_type":"original","page":"139","date_published":"2015-07-28T00:00:00Z","scopus_import":"1","keyword":["Space and Planetary Science","Astronomy and Astrophysics","dark ages","reionization","first stars – early universe – galaxies: evolution"],"day":"28","article_processing_charge":"No","_id":"11519","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Evidence for PopIII-like stellar populations in the most luminous Lyα emitters at the epoch of reionisation: Spectroscopic confirmation","status":"public","intvolume":" 808","oa_version":"Preprint","type":"journal_article","abstract":[{"text":"Faint Lyα emitters become increasingly rarer toward the reionization epoch (z ∼ 6–7). However, observations from a very large (∼5 deg2) Lyα narrow-band survey at z = 6.6 show that this is not the case for the most luminous emitters, capable of ionizing their own local bubbles. Here we present follow-up observations of the two most luminous Lyα candidates in the COSMOS field: “MASOSA” and “CR7.” We used X-SHOOTER, SINFONI, and FORS2 on the Very Large Telescope, and DEIMOS on Keck, to confirm both candidates beyond any doubt. We find redshifts of z = 6.541 and z = 6.604 for “MASOSA” and “CR7,” respectively. MASOSA has a strong detection in Lyα with a line width of 386 ± 30 km s−1 (FWHM) and with very high EW0 (>200 Å), but undetected in the continuum, implying very low stellar mass and a likely young, metal-poor stellar population. “CR7,” with an observed Lyα luminosity of 1043.92±0.05 erg s−1 is the most luminous Lyα emitter ever found at z > 6 and is spatially extended (∼16 kpc). “CR7” reveals a narrow Lyα line with 266 ± 15 km s−1 FWHM, being detected in the near-infrared (NIR) (rest-frame UV; β = −2.3 ± 0.1) and in IRAC/Spitzer. We detect a narrow He II 1640 Å emission line (6σ, FWHM = 130 ± 30 km s−1 ) in CR7 which can explain the clear excess seen in the J-band photometry (EW0 ∼ 80 Å). We find no other emission lines from the UV to the NIR in our X-SHOOTER spectra (He II/O III] 1663 Å > 3 and He II/C III] 1908 Å > 2.5). We conclude that CR7 is best explained by a combination of a PopIII-like population, which dominates the rest-frame UV and the nebular emission, and a more normal stellar population, which presumably dominates the mass. Hubble Space Telescope/WFC3 observations show that the light is indeed spatially separated between a very blue component, coincident with Lyα and He II emission, and two red components (∼5 kpc away), which dominate the mass. Our findings are consistent with theoretical predictions of a PopIII wave, with PopIII star formation migrating away from the original sites of star formation.","lang":"eng"}],"issue":"2"},{"language":[{"iso":"eng"}],"doi":"10.1093/mnras/stv1076","quality_controlled":"1","oa":1,"external_id":{"arxiv":["1502.06602"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1502.06602"}],"publication_identifier":{"eissn":["1365-2966"],"issn":["0035-8711"]},"month":"08","volume":451,"date_updated":"2022-08-19T08:23:18Z","date_created":"2022-07-14T09:02:22Z","author":[{"full_name":"Sobral, D.","last_name":"Sobral","first_name":"D."},{"last_name":"Matthee","first_name":"Jorryt J","orcid":"0000-0003-2871-127X","id":"7439a258-f3c0-11ec-9501-9df22fe06720","full_name":"Matthee, Jorryt J"},{"first_name":"P. N.","last_name":"Best","full_name":"Best, P. N."},{"full_name":"Smail, I.","first_name":"I.","last_name":"Smail"},{"full_name":"Khostovan, A. A.","last_name":"Khostovan","first_name":"A. A."},{"full_name":"Milvang-Jensen, B.","first_name":"B.","last_name":"Milvang-Jensen"},{"last_name":"Kim","first_name":"J.-W.","full_name":"Kim, J.-W."},{"last_name":"Stott","first_name":"J.","full_name":"Stott, J."},{"last_name":"Calhau","first_name":"J.","full_name":"Calhau, J."},{"full_name":"Nayyeri, H.","last_name":"Nayyeri","first_name":"H."},{"last_name":"Mobasher","first_name":"B.","full_name":"Mobasher, B."}],"publisher":"Oxford University Press","publication_status":"published","year":"2015","acknowledgement":"The authors wish to thank the anonymous reviewer for many helpful comments and suggestions which greatly improved the clarity and quality of this work. DS acknowledges financial support from the Netherlands Organization for Scientific research (NWO) through a Veni fellowship, from FCT through an FCT Investigator Starting Grant and Start-up Grant (IF/01154/2012/CP0189/CT0010), from FCT grant PEst-OE/FIS/UI2751/2014, and from LSF and LKBF. JM acknowledges the award of a Huygens PhD fellowship. PNB is grateful for support from STFC. IRS acknowledges support from STFC, a Leverhulme Fellowship, the ERC Advanced Investigator programme DUSTYGAL and a Royal Society/Wolfson Merit Award. BMJ acknowledges support from the ERC-StG grant EGGS-278202. The Dark Cosmology Centre is funded by the DNRF. The Dark Cosmology Centre is funded by the DNRF. JWK acknowledges support from the National Research Foundation of Korea (NRF) grant, no. 2008-0060544, funded by the Korea government (MSIP). JPS acknowledges support from STFC (ST/I001573/1). JC acknowledges support from the FCT-IF grant IF/01154/2012/CP0189/CT0010. The work was only possible due to OPTICON/FP7 and the invaluable access that it granted to the CFHT telescope. We would also like to acknowledge the excellent work done by CFHT staff in conducting the observations in service mode, and on delivering truly excellent data. We are also tremendously thankful to Kentaro Aoki for the incredible support while observing at Subaru with FMOS, and also to the Keck staff for the help with the observations with MOSFIRE. This work is based on observations obtained with WIRCam on the CFHT, OPTICON programme 2011B/029, 2012A019 and 2012B/016. Based on observations made with ESO telescopes at the La Silla Paranal Observatory under programmes IDs 60.A-9460 (data can be accessed through the ESO data archive), 087.A 0337 and 089.A-0965. Based on observations done with FMOS on Subaru under programme S14A-084, and on MOSFIRE/Keck observations under programme U066M. Part of the data on which this analysis is based are available from Sobral et al. (2013a). Dedicated to the memory of C. M. Sobral (1953-2014).","extern":"1","date_published":"2015-08-11T00:00:00Z","page":"2303-2323","article_type":"original","citation":{"ama":"Sobral D, Matthee JJ, Best PN, et al. CF-HiZELS, an ∼10 deg2 emission-line survey with spectroscopic follow-up: Hα, [O III] + Hβ and [O II] luminosity functions at z = 0.8, 1.4 and 2.2 . Monthly Notices of the Royal Astronomical Society. 2015;451(3):2303-2323. doi:10.1093/mnras/stv1076","ista":"Sobral D, Matthee JJ, Best PN, Smail I, Khostovan AA, Milvang-Jensen B, Kim J-W, Stott J, Calhau J, Nayyeri H, Mobasher B. 2015. CF-HiZELS, an ∼10 deg2 emission-line survey with spectroscopic follow-up: Hα, [O III] + Hβ and [O II] luminosity functions at z = 0.8, 1.4 and 2.2 . Monthly Notices of the Royal Astronomical Society. 451(3), 2303–2323.","ieee":"D. Sobral et al., “CF-HiZELS, an ∼10 deg2 emission-line survey with spectroscopic follow-up: Hα, [O III] + Hβ and [O II] luminosity functions at z = 0.8, 1.4 and 2.2 ,” Monthly Notices of the Royal Astronomical Society, vol. 451, no. 3. Oxford University Press, pp. 2303–2323, 2015.","apa":"Sobral, D., Matthee, J. J., Best, P. N., Smail, I., Khostovan, A. A., Milvang-Jensen, B., … Mobasher, B. (2015). CF-HiZELS, an ∼10 deg2 emission-line survey with spectroscopic follow-up: Hα, [O III] + Hβ and [O II] luminosity functions at z = 0.8, 1.4 and 2.2 . Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/stv1076","mla":"Sobral, D., et al. “CF-HiZELS, an ∼10 Deg2 Emission-Line Survey with Spectroscopic Follow-up: Hα, [O III] + Hβ and [O II] Luminosity Functions at z = 0.8, 1.4 and 2.2 .” Monthly Notices of the Royal Astronomical Society, vol. 451, no. 3, Oxford University Press, 2015, pp. 2303–23, doi:10.1093/mnras/stv1076.","short":"D. Sobral, J.J. Matthee, P.N. Best, I. Smail, A.A. Khostovan, B. Milvang-Jensen, J.-W. Kim, J. Stott, J. Calhau, H. Nayyeri, B. Mobasher, Monthly Notices of the Royal Astronomical Society 451 (2015) 2303–2323.","chicago":"Sobral, D., Jorryt J Matthee, P. N. Best, I. Smail, A. A. Khostovan, B. Milvang-Jensen, J.-W. Kim, et al. “CF-HiZELS, an ∼10 Deg2 Emission-Line Survey with Spectroscopic Follow-up: Hα, [O III] + Hβ and [O II] Luminosity Functions at z = 0.8, 1.4 and 2.2 .” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2015. https://doi.org/10.1093/mnras/stv1076."},"publication":"Monthly Notices of the Royal Astronomical Society","article_processing_charge":"No","day":"11","keyword":["Space and Planetary Science","Astronomy and Astrophysics","galaxies: evolution","galaxies: formation","galaxies: luminosity function","mass function","cosmology: observations","early Universe","large-scale structure of Universe"],"scopus_import":"1","oa_version":"Preprint","intvolume":" 451","title":"CF-HiZELS, an ∼10 deg2 emission-line survey with spectroscopic follow-up: Hα, [O III] + Hβ and [O II] luminosity functions at z = 0.8, 1.4 and 2.2 ","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"11580","issue":"3","abstract":[{"text":"We present results from the largest contiguous narrow-band survey in the near-infrared. We have used the wide-field infrared camera/Canada–France–Hawaii Telescope and the lowOH2 filter (1.187 ± 0.005 μm) to survey ≈10 deg2 of contiguous extragalactic sky in the SA22 field. A total of ∼6000 candidate emission-line galaxies are found. We use deep ugrizJK data to obtain robust photometric redshifts. We combine our data with the High-redshift(Z) Emission Line Survey (HiZELS), explore spectroscopic surveys (VVDS, VIPERS) and obtain our own spectroscopic follow-up with KMOS, FMOS and MOSFIRE to derive large samples of high-redshift emission-line selected galaxies: 3471 Hα emitters at z = 0.8, 1343 [O III] + Hβ emitters at z = 1.4 and 572 [O II] emitters at z = 2.2. We probe comoving volumes of >106 Mpc3 and find significant overdensities, including an 8.5σ (spectroscopically confirmed) overdensity of Hα emitters at z = 0.81. We derive Hα, [O III] + Hβ and [O II] luminosity functions at z = 0.8, 1.4, 2.2, respectively, and present implications for future surveys such as Euclid. Our uniquely large volumes/areas allow us to subdivide the samples in thousands of randomized combinations of areas and provide a robust empirical measurement of sample/cosmic variance. We show that surveys for star-forming/emission-line galaxies at a depth similar to ours can only overcome cosmic-variance (errors <10 per cent) if they are based on volumes >5 × 105 Mpc3; errors on L* and ϕ* due to sample (cosmic) variance on surveys probing ∼104 and ∼105 Mpc3 are typically very high: ∼300 and ∼40–60 per cent, respectively.","lang":"eng"}],"type":"journal_article"},{"abstract":[{"text":"Using wide-field narrow-band surveys, we provide a new measurement of the z = 6.6 Lymanα emitter (LAE) luminosity function (LF), which constraints the bright end for the first time. We use a combination of archival narrow-band NB921 data in UDS and new NB921 measurements in SA22 and COSMOS/UltraVISTA, all observed with the Subaru telescope, with a total area of ∼5 deg2. We exclude lower redshift interlopers by using broad-band optical and near-infrared photometry and also exclude three supernovae with data split over multiple epochs. Combining the UDS and COSMOS samples, we find no evolution of the bright end of the Lyα LF between z = 5.7 and 6.6, which is supported by spectroscopic follow-up, and conclude that sources with Himiko-like luminosity are not as rare as previously thought, with number densities of ∼1.5 × 10−5 Mpc−3. Combined with our wide-field SA22 measurements, our results indicate a non-Schechter-like bright end of the LF at z = 6.6 and a different evolution of observed faint and bright LAEs, overcoming cosmic variance. This differential evolution is also seen in the spectroscopic follow-up of UV-selected galaxies and is now also confirmed for LAEs, and we argue that it may be an effect of reionization. Using a toy model, we show that such differential evolution of the LF is expected, since brighter sources are able to ionize their surroundings earlier, such that Lyα photons are able to escape. Our targets are excellent candidates for detailed follow-up studies and provide the possibility to give a unique view on the earliest stages in the formation of galaxies and reionization process.","lang":"eng"}],"issue":"1","type":"journal_article","oa_version":"Preprint","_id":"11581","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Identification of the brightest Lyα emitters at z = 6.6: implications for the evolution of the luminosity function in the reionization era","intvolume":" 451","day":"21","article_processing_charge":"No","scopus_import":"1","keyword":["Space and Planetary Science","Astronomy and Astrophysics"],"date_published":"2015-07-21T00:00:00Z","publication":"Monthly Notices of the Royal Astronomical Society","citation":{"ieee":"J. J. Matthee, D. Sobral, S. Santos, H. Röttgering, B. Darvish, and B. Mobasher, “Identification of the brightest Lyα emitters at z = 6.6: implications for the evolution of the luminosity function in the reionization era,” Monthly Notices of the Royal Astronomical Society, vol. 451, no. 1. Oxford University Press, pp. 400–417, 2015.","apa":"Matthee, J. J., Sobral, D., Santos, S., Röttgering, H., Darvish, B., & Mobasher, B. (2015). Identification of the brightest Lyα emitters at z = 6.6: implications for the evolution of the luminosity function in the reionization era. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/stv947","ista":"Matthee JJ, Sobral D, Santos S, Röttgering H, Darvish B, Mobasher B. 2015. Identification of the brightest Lyα emitters at z = 6.6: implications for the evolution of the luminosity function in the reionization era. Monthly Notices of the Royal Astronomical Society. 451(1), 400–417.","ama":"Matthee JJ, Sobral D, Santos S, Röttgering H, Darvish B, Mobasher B. Identification of the brightest Lyα emitters at z = 6.6: implications for the evolution of the luminosity function in the reionization era. Monthly Notices of the Royal Astronomical Society. 2015;451(1):400-417. doi:10.1093/mnras/stv947","chicago":"Matthee, Jorryt J, David Sobral, Sérgio Santos, Huub Röttgering, Behnam Darvish, and Bahram Mobasher. “Identification of the Brightest Lyα Emitters at z = 6.6: Implications for the Evolution of the Luminosity Function in the Reionization Era.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2015. https://doi.org/10.1093/mnras/stv947.","short":"J.J. Matthee, D. Sobral, S. Santos, H. Röttgering, B. Darvish, B. Mobasher, Monthly Notices of the Royal Astronomical Society 451 (2015) 400–417.","mla":"Matthee, Jorryt J., et al. “Identification of the Brightest Lyα Emitters at z = 6.6: Implications for the Evolution of the Luminosity Function in the Reionization Era.” Monthly Notices of the Royal Astronomical Society, vol. 451, no. 1, Oxford University Press, 2015, pp. 400–17, doi:10.1093/mnras/stv947."},"article_type":"original","page":"400-417","extern":"1","author":[{"full_name":"Matthee, Jorryt J","last_name":"Matthee","first_name":"Jorryt J","orcid":"0000-0003-2871-127X","id":"7439a258-f3c0-11ec-9501-9df22fe06720"},{"full_name":"Sobral, David","last_name":"Sobral","first_name":"David"},{"full_name":"Santos, Sérgio","last_name":"Santos","first_name":"Sérgio"},{"last_name":"Röttgering","first_name":"Huub","full_name":"Röttgering, Huub"},{"last_name":"Darvish","first_name":"Behnam","full_name":"Darvish, Behnam"},{"full_name":"Mobasher, Bahram","last_name":"Mobasher","first_name":"Bahram"}],"date_created":"2022-07-14T11:57:03Z","date_updated":"2022-08-19T08:25:25Z","volume":451,"acknowledgement":"We thank the anonymous referee for the comments and suggestions which have improved the quality of this work. We thank Masami Ouchi for his useful comments on an earlier version of this paper. JM acknowledges the support of a Huygens PhD fellowship from Leiden University and is thankful for the hospitality of the Center for Astronomy and Astrophysics of the University of Lisbon where part of this research has been done. DS acknowledges financial support from the Netherlands Organization for Scientific research (NWO) through a Veni fellowship, from FCT through a FCT Investigator Starting Grant and Start-up Grant (IF/01154/2012/CP0189/CT0010) and from FCT grant PEstOE/FIS/UI2751/2014. HR acknowledges support from the ERC Advanced Investigator programme NewClusters 321271. We acknowledge the award of ESO DDT time (294.A-5018) for providing the possibility of a timely publication of this work.\r\nBased on observations with the Subaru Telescope (Programme IDs: our observations: S14A-086; archival: S05B-027, S06A-025, S06B-010, S07A-013, S07B-008, S08B-008 and S09A-017) and the W.M. Keck Observatory. The Subaru telescope is operated by the National Astronomical Observatory of Japan. The W.M. Keck Observatory is operated as a scientific partnership among the California Institute of Technology, the University of California and the National Aeronautics and Space Administration. Based on observations made with ESO Telescopes at the La Silla Paranal Observatory under programme ID 294.A-5018. Based on observations obtained with MegaPrime/Megacam, a joint project of CFHT and CEA/IRFU, at the Canada–France-Hawaii Telescope (CFHT) which is operated by the National Research Council (NRC) of Canada, the Institut National des Science de l’Univers of the Centre National de la Recherche Scientifique (CNRS) of France, and the University of Hawaii. This work is based in part on data products produced at Terapix available at the Canadian Astronomy Data Centre as part of the CFHT Legacy Survey, a collaborative project of NRC and CNRS. Based on data products from observations made with ESO Telescopes at the La Silla Paranal Observatory under ESO programme ID 179.A-2005 and on data products produced by TERAPIX and the Cambridge Astronomy Survey Unit on behalf of the UltraVISTA consortium.\r\nIn addition to the CFHT-LS and COSMOS-UltraVISTA surveys, we are grateful for the excellent data sets from the UKIRT-DXS, SXDF and S-COSMOS survey teams, without these legacy surveys, this research would have been impossible. We have benefited greatly from the public available programming language PYTHON, including the NUMPY, MATPLOTLIB, PYFITS, SCIPY and ASTROPY packages, the astronomical imaging tools SEXTRACTOR, SWARP and SCAMP and the indispensable TOPCAT analysis tool (Taylor 2013)","year":"2015","publication_status":"published","publisher":"Oxford University Press","month":"07","publication_identifier":{"eissn":["1365-2966"],"issn":["0035-8711"]},"doi":"10.1093/mnras/stv947","language":[{"iso":"eng"}],"external_id":{"arxiv":["1502.07355"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1502.07355"}],"quality_controlled":"1"},{"date_published":"2015-11-01T00:00:00Z","publication":"Monthly Notices of the Royal Astronomical Society","citation":{"chicago":"Pallottini, A., A. Ferrara, F. Pacucci, S. Gallerani, S. Salvadori, R. Schneider, D. Schaerer, D. Sobral, and Jorryt J Matthee. “The Brightest Lyα Emitter: Pop III or Black Hole?” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2015. https://doi.org/10.1093/mnras/stv1795.","short":"A. Pallottini, A. Ferrara, F. Pacucci, S. Gallerani, S. Salvadori, R. Schneider, D. Schaerer, D. Sobral, J.J. Matthee, Monthly Notices of the Royal Astronomical Society 453 (2015) 2465–2470.","mla":"Pallottini, A., et al. “The Brightest Lyα Emitter: Pop III or Black Hole?” Monthly Notices of the Royal Astronomical Society, vol. 453, no. 3, Oxford University Press, 2015, pp. 2465–70, doi:10.1093/mnras/stv1795.","apa":"Pallottini, A., Ferrara, A., Pacucci, F., Gallerani, S., Salvadori, S., Schneider, R., … Matthee, J. J. (2015). The brightest Lyα emitter: Pop III or black hole? Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/stv1795","ieee":"A. Pallottini et al., “The brightest Lyα emitter: Pop III or black hole?,” Monthly Notices of the Royal Astronomical Society, vol. 453, no. 3. Oxford University Press, pp. 2465–2470, 2015.","ista":"Pallottini A, Ferrara A, Pacucci F, Gallerani S, Salvadori S, Schneider R, Schaerer D, Sobral D, Matthee JJ. 2015. The brightest Lyα emitter: Pop III or black hole? Monthly Notices of the Royal Astronomical Society. 453(3), 2465–2470.","ama":"Pallottini A, Ferrara A, Pacucci F, et al. The brightest Lyα emitter: Pop III or black hole? Monthly Notices of the Royal Astronomical Society. 2015;453(3):2465-2470. doi:10.1093/mnras/stv1795"},"article_type":"original","page":"2465-2470","day":"01","article_processing_charge":"No","scopus_import":"1","keyword":["Space and Planetary Science","Astronomy and Astrophysics","black hole physics","stars: Population III","galaxies: high-redshift"],"oa_version":"Preprint","_id":"11579","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"The brightest Lyα emitter: Pop III or black hole?","status":"public","intvolume":" 453","abstract":[{"text":"CR7 is the brightest z = 6.6 Ly α emitter (LAE) known to date, and spectroscopic follow-up by Sobral et al. suggests that CR7 might host Population (Pop) III stars. We examine this interpretation using cosmological hydrodynamical simulations. Several simulated galaxies show the same ‘Pop III wave’ pattern observed in CR7. However, to reproduce the extreme CR7 Ly α/He II1640 line luminosities (Lα/HeII) a top-heavy initial mass function and a massive ( ≳ 107 M⊙) Pop III burst with age ≲ 2 Myr are required. Assuming that the observed properties of Ly α and He II emission are typical for Pop III, we predict that in the COSMOS/UDS/SA22 fields, 14 out of the 30 LAEs at z = 6.6 with Lα > 1043.3 erg s−1 should also host Pop III stars producing an observable LHeII≳1042.7ergs−1. As an alternate explanation, we explore the possibility that CR7 is instead powered by accretion on to a direct collapse black hole. Our model predicts Lα, LHeII, and X-ray luminosities that are in agreement with the observations. In any case, the observed properties of CR7 indicate that this galaxy is most likely powered by sources formed from pristine gas. We propose that further X-ray observations can distinguish between the two above scenarios.","lang":"eng"}],"issue":"3","type":"journal_article","doi":"10.1093/mnras/stv1795","language":[{"iso":"eng"}],"external_id":{"arxiv":["1506.07173"]},"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1506.07173","open_access":"1"}],"quality_controlled":"1","month":"11","publication_identifier":{"eissn":["1365-2966"],"issn":["0035-8711"]},"author":[{"last_name":"Pallottini","first_name":"A.","full_name":"Pallottini, A."},{"first_name":"A.","last_name":"Ferrara","full_name":"Ferrara, A."},{"first_name":"F.","last_name":"Pacucci","full_name":"Pacucci, F."},{"full_name":"Gallerani, S.","last_name":"Gallerani","first_name":"S."},{"last_name":"Salvadori","first_name":"S.","full_name":"Salvadori, S."},{"first_name":"R.","last_name":"Schneider","full_name":"Schneider, R."},{"last_name":"Schaerer","first_name":"D.","full_name":"Schaerer, D."},{"full_name":"Sobral, D.","first_name":"D.","last_name":"Sobral"},{"first_name":"Jorryt J","last_name":"Matthee","id":"7439a258-f3c0-11ec-9501-9df22fe06720","orcid":"0000-0003-2871-127X","full_name":"Matthee, Jorryt J"}],"date_created":"2022-07-14T08:58:36Z","date_updated":"2022-08-19T08:19:23Z","volume":453,"year":"2015","acknowledgement":"SS acknowledges support from the Netherlands Organization for Scientific research (NWO), VENI grant 639.041.233. RS acknowledges support from the European Research Council under the European Union (FP/2007-2013)/ERC grant agreement no. 306476. DS acknowledges (i) financial support from the NWO through a Veni fellowship and (ii) funding from FCT through a FCT Investigator Starting Grant and Start-up Grant (IF/01154/2012/CP0189/CT0010) and from FCT grant PEstOE/FIS/UI2751/2014.","publication_status":"published","publisher":"Oxford University Press","extern":"1"},{"article_number":"2","extern":"1","publication_status":"published","publisher":"Association for Computing Machinery","year":"2015","date_created":"2022-07-27T11:54:56Z","date_updated":"2023-02-09T10:03:35Z","volume":4,"author":[{"first_name":"Riccardo","last_name":"Colini-Baldeschi","full_name":"Colini-Baldeschi, Riccardo"},{"first_name":"Stefano","last_name":"Leonardi","full_name":"Leonardi, Stefano"},{"full_name":"Henzinger, Monika H","orcid":"0000-0002-5008-6530","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","last_name":"Henzinger","first_name":"Monika H"},{"first_name":"Martin","last_name":"Starnberger","full_name":"Starnberger, Martin"}],"month":"12","publication_identifier":{"eissn":["2167-8383"],"issn":["2167-8375"]},"quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"http://eprints.cs.univie.ac.at/3510/"}],"language":[{"iso":"eng"}],"doi":"10.1145/2818357","type":"journal_article","abstract":[{"lang":"eng","text":"We study multiple keyword sponsored search auctions with budgets. Each keyword has multiple ad slots with a click-through rate. The bidders have additive valuations, which are linear in the click-through rates, and budgets, which are restricting their overall payments. Additionally, the number of slots per keyword assigned to a bidder is bounded.\r\n\r\nWe show the following results: (1) We give the first mechanism for multiple keywords, where click-through rates differ among slots. Our mechanism is incentive compatible in expectation, individually rational in expectation, and Pareto optimal. (2) We study the combinatorial setting, where each bidder is only interested in a subset of the keywords. We give an incentive compatible, individually rational, Pareto-optimal, and deterministic mechanism for identical click-through rates. (3) We give an impossibility result for incentive compatible, individually rational, Pareto-optimal, and deterministic mechanisms for bidders with diminishing marginal valuations."}],"issue":"1","status":"public","title":"On multiple keyword sponsored search auctions with budgets","intvolume":" 4","_id":"11668","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version","keyword":["Algorithms","Economics","Clinching ascending auction","auctions with budgets","Sponsored search auctions"],"scopus_import":"1","day":"05","article_processing_charge":"No","article_type":"original","publication":"ACM Transactions on Economics and Computation","citation":{"apa":"Colini-Baldeschi, R., Leonardi, S., Henzinger, M. H., & Starnberger, M. (2015). On multiple keyword sponsored search auctions with budgets. ACM Transactions on Economics and Computation. Association for Computing Machinery. https://doi.org/10.1145/2818357","ieee":"R. Colini-Baldeschi, S. Leonardi, M. H. Henzinger, and M. Starnberger, “On multiple keyword sponsored search auctions with budgets,” ACM Transactions on Economics and Computation, vol. 4, no. 1. Association for Computing Machinery, 2015.","ista":"Colini-Baldeschi R, Leonardi S, Henzinger MH, Starnberger M. 2015. On multiple keyword sponsored search auctions with budgets. ACM Transactions on Economics and Computation. 4(1), 2.","ama":"Colini-Baldeschi R, Leonardi S, Henzinger MH, Starnberger M. On multiple keyword sponsored search auctions with budgets. ACM Transactions on Economics and Computation. 2015;4(1). doi:10.1145/2818357","chicago":"Colini-Baldeschi, Riccardo, Stefano Leonardi, Monika H Henzinger, and Martin Starnberger. “On Multiple Keyword Sponsored Search Auctions with Budgets.” ACM Transactions on Economics and Computation. Association for Computing Machinery, 2015. https://doi.org/10.1145/2818357.","short":"R. Colini-Baldeschi, S. Leonardi, M.H. Henzinger, M. Starnberger, ACM Transactions on Economics and Computation 4 (2015).","mla":"Colini-Baldeschi, Riccardo, et al. “On Multiple Keyword Sponsored Search Auctions with Budgets.” ACM Transactions on Economics and Computation, vol. 4, no. 1, 2, Association for Computing Machinery, 2015, doi:10.1145/2818357."},"date_published":"2015-12-05T00:00:00Z"},{"publication_identifier":{"eissn":["2167-8383"],"issn":["2167-8375"]},"month":"12","doi":"10.1145/2818351","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1209.6448"}],"external_id":{"arxiv":["1209.6448"]},"oa":1,"quality_controlled":"1","extern":"1","article_number":"4","author":[{"last_name":"Dütting","first_name":"Paul","full_name":"Dütting, Paul"},{"id":"540c9bbd-f2de-11ec-812d-d04a5be85630","orcid":"0000-0002-5008-6530","first_name":"Monika H","last_name":"Henzinger","full_name":"Henzinger, Monika H"},{"full_name":"Starnberger, Martin","first_name":"Martin","last_name":"Starnberger"}],"volume":4,"date_updated":"2022-09-09T12:08:37Z","date_created":"2022-07-27T12:09:15Z","year":"2015","publisher":"Association for Computing Machinery","publication_status":"published","article_processing_charge":"No","day":"05","scopus_import":"1","keyword":["Algorithmic game theory","auction theory","Clinching auction","Pareto optimality","Budget limits"],"date_published":"2015-12-05T00:00:00Z","citation":{"chicago":"Dütting, Paul, Monika H Henzinger, and Martin Starnberger. “Auctions for Heterogeneous Items and Budget Limits.” ACM Transactions on Economics and Computation. Association for Computing Machinery, 2015. https://doi.org/10.1145/2818351.","mla":"Dütting, Paul, et al. “Auctions for Heterogeneous Items and Budget Limits.” ACM Transactions on Economics and Computation, vol. 4, no. 1, 4, Association for Computing Machinery, 2015, doi:10.1145/2818351.","short":"P. Dütting, M.H. Henzinger, M. Starnberger, ACM Transactions on Economics and Computation 4 (2015).","ista":"Dütting P, Henzinger MH, Starnberger M. 2015. Auctions for heterogeneous items and budget limits. ACM Transactions on Economics and Computation. 4(1), 4.","ieee":"P. Dütting, M. H. Henzinger, and M. Starnberger, “Auctions for heterogeneous items and budget limits,” ACM Transactions on Economics and Computation, vol. 4, no. 1. Association for Computing Machinery, 2015.","apa":"Dütting, P., Henzinger, M. H., & Starnberger, M. (2015). Auctions for heterogeneous items and budget limits. ACM Transactions on Economics and Computation. Association for Computing Machinery. https://doi.org/10.1145/2818351","ama":"Dütting P, Henzinger MH, Starnberger M. Auctions for heterogeneous items and budget limits. ACM Transactions on Economics and Computation. 2015;4(1). doi:10.1145/2818351"},"publication":"ACM Transactions on Economics and Computation","article_type":"original","issue":"1","abstract":[{"lang":"eng","text":"We study individual rational, Pareto-optimal, and incentive compatible mechanisms for auctions with heterogeneous items and budget limits. We consider settings with multiunit demand and additive valuations. For single-dimensional valuations we prove a positive result for randomized mechanisms, and a negative result for deterministic mechanisms. While the positive result allows for private budgets, the negative result is for public budgets. For multidimensional valuations and public budgets we prove an impossibility result that applies to deterministic and randomized mechanisms. Taken together this shows the power of randomization in certain settings with heterogeneous items, but it also shows its limitations."}],"type":"journal_article","oa_version":"Preprint","_id":"11669","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 4","status":"public","title":"Auctions for heterogeneous items and budget limits"},{"day":"09","article_processing_charge":"No","scopus_import":"1","date_published":"2015-12-09T00:00:00Z","page":"230–243","publication":"11th International Conference on Web and Internet Economics","citation":{"ama":"Cheung YK, Henzinger MH, Hoefer M, Starnberger M. Combinatorial auctions with conflict-based externalities. In: 11th International Conference on Web and Internet Economics. Vol 9470. Springer Nature; 2015:230–243. doi:10.1007/978-3-662-48995-6_17","apa":"Cheung, Y. K., Henzinger, M. H., Hoefer, M., & Starnberger, M. (2015). Combinatorial auctions with conflict-based externalities. In 11th International Conference on Web and Internet Economics (Vol. 9470, pp. 230–243). Amsterdam, Netherlands: Springer Nature. https://doi.org/10.1007/978-3-662-48995-6_17","ieee":"Y. K. Cheung, M. H. Henzinger, M. Hoefer, and M. Starnberger, “Combinatorial auctions with conflict-based externalities,” in 11th International Conference on Web and Internet Economics, Amsterdam, Netherlands, 2015, vol. 9470, pp. 230–243.","ista":"Cheung YK, Henzinger MH, Hoefer M, Starnberger M. 2015. Combinatorial auctions with conflict-based externalities. 11th International Conference on Web and Internet Economics. WINE: International Conference on Web and Internet Economics, LNCS, vol. 9470, 230–243.","short":"Y.K. Cheung, M.H. Henzinger, M. Hoefer, M. Starnberger, in:, 11th International Conference on Web and Internet Economics, Springer Nature, 2015, pp. 230–243.","mla":"Cheung, Yun Kuen, et al. “Combinatorial Auctions with Conflict-Based Externalities.” 11th International Conference on Web and Internet Economics, vol. 9470, Springer Nature, 2015, pp. 230–243, doi:10.1007/978-3-662-48995-6_17.","chicago":"Cheung, Yun Kuen, Monika H Henzinger, Martin Hoefer, and Martin Starnberger. “Combinatorial Auctions with Conflict-Based Externalities.” In 11th International Conference on Web and Internet Economics, 9470:230–243. Springer Nature, 2015. https://doi.org/10.1007/978-3-662-48995-6_17."},"abstract":[{"text":"Combinatorial auctions (CA) are a well-studied area in algorithmic mechanism design. However, contrary to the standard model, empirical studies suggest that a bidder’s valuation often does not depend solely on the goods assigned to him. For instance, in adwords auctions an advertiser might not want his ads to be displayed next to his competitors’ ads. In this paper, we propose and analyze several natural graph-theoretic models that incorporate such negative externalities, in which bidders form a directed conflict graph with maximum out-degree Δ. We design algorithms and truthful mechanisms for social welfare maximization that attain approximation ratios depending on Δ.\r\n\r\nFor CA, our results are twofold: (1) A lottery that eliminates conflicts by discarding bidders/items independent of the bids. It allows to apply any truthful 𝛼-approximation mechanism for conflict-free valuations and yields an 𝒪(𝛼Δ)-approximation mechanism. (2) For fractionally sub-additive valuations, we design a rounding algorithm via a novel combination of a semi-definite program and a linear program, resulting in a cone program; the approximation ratio is 𝒪((ΔloglogΔ)/logΔ). The ratios are almost optimal given existing hardness results.\r\n\r\nFor adwords auctions, we present several algorithms for the most relevant scenario when the number of items is small. In particular, we design a truthful mechanism with approximation ratio 𝑜(Δ) when the number of items is only logarithmic in the number of bidders.","lang":"eng"}],"alternative_title":["LNCS"],"type":"conference","oa_version":"Preprint","status":"public","title":"Combinatorial auctions with conflict-based externalities","intvolume":" 9470","_id":"11774","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"12","publication_identifier":{"issn":["0302-9743"],"eisbn":["9783662489956"],"isbn":["9783662489949"]},"language":[{"iso":"eng"}],"conference":{"start_date":"2015-12-09","location":"Amsterdam, Netherlands","end_date":"2015-12-12","name":"WINE: International Conference on Web and Internet Economics"},"doi":"10.1007/978-3-662-48995-6_17","quality_controlled":"1","external_id":{"arxiv":["1509.09147"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.1509.09147"}],"extern":"1","date_created":"2022-08-08T13:54:32Z","date_updated":"2023-02-10T09:08:30Z","volume":9470,"author":[{"first_name":"Yun Kuen","last_name":"Cheung","full_name":"Cheung, Yun Kuen"},{"full_name":"Henzinger, Monika H","orcid":"0000-0002-5008-6530","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","last_name":"Henzinger","first_name":"Monika H"},{"first_name":"Martin","last_name":"Hoefer","full_name":"Hoefer, Martin"},{"full_name":"Starnberger, Martin","first_name":"Martin","last_name":"Starnberger"}],"publication_status":"published","publisher":"Springer Nature","year":"2015"},{"oa_version":"Preprint","title":"Ad exchange: Envy-free auctions with mediators","status":"public","intvolume":" 9470","_id":"11773","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Ad exchanges are an emerging platform for trading advertisement slots on the web with billions of dollars revenue per year. Every time a user visits a web page, the publisher of that web page can ask an ad exchange to auction off the ad slots on this page to determine which advertisements are shown at which price. Due to the high volume of traffic, ad networks typically act as mediators for individual advertisers at ad exchanges. If multiple advertisers in an ad network are interested in the ad slots of the same auction, the ad network might use a “local” auction to resell the obtained ad slots among its advertisers.\r\n\r\nIn this work we want to deepen the theoretical understanding of these new markets by analyzing them from the viewpoint of combinatorial auctions. Prior work studied mostly single-item auctions, while we allow the advertisers to express richer preferences over multiple items. We develop a game-theoretic model for the entanglement of the central auction at the ad exchange with the local auctions at the ad networks. We consider the incentives of all three involved parties and suggest a three-party competitive equilibrium, an extension of the Walrasian equilibrium that ensures envy-freeness for all participants. We show the existence of a three-party competitive equilibrium and a polynomial-time algorithm to find one for gross-substitute bidder valuations."}],"alternative_title":["LNCS"],"type":"conference","date_published":"2015-12-09T00:00:00Z","page":"104–117","publication":"11th International Conference on Web and Internet Economics","citation":{"ista":"Ben-Zwi O, Henzinger MH, Loitzenbauer V. 2015. Ad exchange: Envy-free auctions with mediators. 11th International Conference on Web and Internet Economics. WINE: International Conference on Web and Internet Economics, LNCS, vol. 9470, 104–117.","ieee":"O. Ben-Zwi, M. H. Henzinger, and V. Loitzenbauer, “Ad exchange: Envy-free auctions with mediators,” in 11th International Conference on Web and Internet Economics, Amsterdam, Netherlands, 2015, vol. 9470, pp. 104–117.","apa":"Ben-Zwi, O., Henzinger, M. H., & Loitzenbauer, V. (2015). Ad exchange: Envy-free auctions with mediators. In 11th International Conference on Web and Internet Economics (Vol. 9470, pp. 104–117). Amsterdam, Netherlands: Springer Nature. https://doi.org/10.1007/978-3-662-48995-6_8","ama":"Ben-Zwi O, Henzinger MH, Loitzenbauer V. Ad exchange: Envy-free auctions with mediators. In: 11th International Conference on Web and Internet Economics. Vol 9470. Springer Nature; 2015:104–117. doi:10.1007/978-3-662-48995-6_8","chicago":"Ben-Zwi, Oren, Monika H Henzinger, and Veronika Loitzenbauer. “Ad Exchange: Envy-Free Auctions with Mediators.” In 11th International Conference on Web and Internet Economics, 9470:104–117. Springer Nature, 2015. https://doi.org/10.1007/978-3-662-48995-6_8.","mla":"Ben-Zwi, Oren, et al. “Ad Exchange: Envy-Free Auctions with Mediators.” 11th International Conference on Web and Internet Economics, vol. 9470, Springer Nature, 2015, pp. 104–117, doi:10.1007/978-3-662-48995-6_8.","short":"O. Ben-Zwi, M.H. Henzinger, V. Loitzenbauer, in:, 11th International Conference on Web and Internet Economics, Springer Nature, 2015, pp. 104–117."},"day":"09","article_processing_charge":"No","scopus_import":"1","date_updated":"2023-02-10T09:06:23Z","date_created":"2022-08-08T13:33:56Z","volume":9470,"author":[{"last_name":"Ben-Zwi","first_name":"Oren","full_name":"Ben-Zwi, Oren"},{"full_name":"Henzinger, Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","orcid":"0000-0002-5008-6530","first_name":"Monika H","last_name":"Henzinger"},{"first_name":"Veronika","last_name":"Loitzenbauer","full_name":"Loitzenbauer, Veronika"}],"publication_status":"published","publisher":"Springer Nature","year":"2015","extern":"1","language":[{"iso":"eng"}],"conference":{"location":"Amsterdam, Netherlands","start_date":"2015-09-09","end_date":"2015-09-12","name":"WINE: International Conference on Web and Internet Economics"},"doi":"10.1007/978-3-662-48995-6_8","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.1604.05562"}],"external_id":{"arxiv":["1604.05562"]},"oa":1,"month":"12","publication_identifier":{"isbn":["9783662489949"],"eisbn":["9783662489956"],"issn":["0302-9743"]}},{"abstract":[{"lang":"eng","text":"Recently we presented the first algorithm for maintaining the set of nodes reachable from a source node in a directed graph that is modified by edge deletions with 𝑜(𝑚𝑛) total update time, where 𝑚 is the number of edges and 𝑛 is the number of nodes in the graph [Henzinger et al. STOC 2014]. The algorithm is a combination of several different algorithms, each for a different 𝑚 vs. 𝑛 trade-off. For the case of 𝑚=Θ(𝑛1.5) the running time is 𝑂(𝑛2.47), just barely below 𝑚𝑛=Θ(𝑛2.5). In this paper we simplify the previous algorithm using new algorithmic ideas and achieve an improved running time of 𝑂̃ (min(𝑚7/6𝑛2/3,𝑚3/4𝑛5/4+𝑜(1),𝑚2/3𝑛4/3+𝑜(1)+𝑚3/7𝑛12/7+𝑜(1))). This gives, e.g., 𝑂(𝑛2.36) for the notorious case 𝑚=Θ(𝑛1.5). We obtain the same upper bounds for the problem of maintaining the strongly connected components of a directed graph undergoing edge deletions. Our algorithms are correct with high probabililty against an oblivious adversary."}],"type":"conference","alternative_title":["LNCS"],"oa_version":"Preprint","_id":"11785","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Improved algorithms for decremental single-source reachability on directed graphs","status":"public","intvolume":" 9134","day":"01","article_processing_charge":"No","scopus_import":"1","date_published":"2015-01-01T00:00:00Z","publication":"42nd International Colloquium on Automata, Languages and Programming","citation":{"short":"M.H. Henzinger, S. Krinninger, D. Nanongkai, in:, 42nd International Colloquium on Automata, Languages and Programming, Springer Nature, 2015, pp. 725–736.","mla":"Henzinger, Monika H., et al. “Improved Algorithms for Decremental Single-Source Reachability on Directed Graphs.” 42nd International Colloquium on Automata, Languages and Programming, vol. 9134, Springer Nature, 2015, pp. 725–36, doi:10.1007/978-3-662-47672-7_59.","chicago":"Henzinger, Monika H, Sebastian Krinninger, and Danupon Nanongkai. “Improved Algorithms for Decremental Single-Source Reachability on Directed Graphs.” In 42nd International Colloquium on Automata, Languages and Programming, 9134:725–36. Springer Nature, 2015. https://doi.org/10.1007/978-3-662-47672-7_59.","ama":"Henzinger MH, Krinninger S, Nanongkai D. Improved algorithms for decremental single-source reachability on directed graphs. In: 42nd International Colloquium on Automata, Languages and Programming. Vol 9134. Springer Nature; 2015:725-736. doi:10.1007/978-3-662-47672-7_59","ieee":"M. H. Henzinger, S. Krinninger, and D. Nanongkai, “Improved algorithms for decremental single-source reachability on directed graphs,” in 42nd International Colloquium on Automata, Languages and Programming, Kyoto, Japan, 2015, vol. 9134, pp. 725–736.","apa":"Henzinger, M. H., Krinninger, S., & Nanongkai, D. (2015). Improved algorithms for decremental single-source reachability on directed graphs. In 42nd International Colloquium on Automata, Languages and Programming (Vol. 9134, pp. 725–736). Kyoto, Japan: Springer Nature. https://doi.org/10.1007/978-3-662-47672-7_59","ista":"Henzinger MH, Krinninger S, Nanongkai D. 2015. Improved algorithms for decremental single-source reachability on directed graphs. 42nd International Colloquium on Automata, Languages and Programming. ICALP: International Colloquium on Automata, Languages, and Programming, LNCS, vol. 9134, 725–736."},"page":"725 - 736","extern":"1","author":[{"id":"540c9bbd-f2de-11ec-812d-d04a5be85630","orcid":"0000-0002-5008-6530","first_name":"Monika H","last_name":"Henzinger","full_name":"Henzinger, Monika H"},{"full_name":"Krinninger, Sebastian","first_name":"Sebastian","last_name":"Krinninger"},{"first_name":"Danupon","last_name":"Nanongkai","full_name":"Nanongkai, Danupon"}],"date_created":"2022-08-11T08:51:32Z","date_updated":"2023-02-10T09:10:26Z","volume":9134,"year":"2015","publication_status":"published","publisher":"Springer Nature","month":"01","publication_identifier":{"issn":["0302-9743"],"isbn":["9783662476710"]},"conference":{"location":"Kyoto, Japan","start_date":"2015-07-06","end_date":"2015-07-10","name":"ICALP: International Colloquium on Automata, Languages, and Programming"},"doi":"10.1007/978-3-662-47672-7_59","language":[{"iso":"eng"}],"external_id":{"arxiv":["1612.03856"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1612.03856"}],"quality_controlled":"1"},{"main_file_link":[{"url":"https://arxiv.org/abs/1412.6466","open_access":"1"}],"external_id":{"arxiv":["1412.6466"]},"oa":1,"quality_controlled":"1","doi":"10.1007/978-3-662-47672-7_58","conference":{"location":"Kyoto, Japan","start_date":"2015-07-06","end_date":"2015-07-10","name":"ICALP: International Colloquium on Automata, Languages, and Programming"},"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0302-9743"],"isbn":["9783662476710"]},"month":"07","year":"2015","publisher":"Springer Nature","publication_status":"published","author":[{"last_name":"Henzinger","first_name":"Monika H","orcid":"0000-0002-5008-6530","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","full_name":"Henzinger, Monika H"},{"full_name":"Krinninger, Sebastian","first_name":"Sebastian","last_name":"Krinninger"},{"first_name":"Veronika","last_name":"Loitzenbauer","full_name":"Loitzenbauer, Veronika"}],"volume":9134,"date_updated":"2023-02-10T09:21:47Z","date_created":"2022-08-11T09:38:34Z","extern":"1","citation":{"ieee":"M. H. Henzinger, S. Krinninger, and V. Loitzenbauer, “Finding 2-edge and 2-vertex strongly connected components in quadratic time,” in 2nd International Colloquium on Automata, Languages and Programming, Kyoto, Japan, 2015, vol. 9134, pp. 713–724.","apa":"Henzinger, M. H., Krinninger, S., & Loitzenbauer, V. (2015). Finding 2-edge and 2-vertex strongly connected components in quadratic time. In 2nd International Colloquium on Automata, Languages and Programming (Vol. 9134, pp. 713–724). Kyoto, Japan: Springer Nature. https://doi.org/10.1007/978-3-662-47672-7_58","ista":"Henzinger MH, Krinninger S, Loitzenbauer V. 2015. Finding 2-edge and 2-vertex strongly connected components in quadratic time. 2nd International Colloquium on Automata, Languages and Programming. ICALP: International Colloquium on Automata, Languages, and Programming, LNCS, vol. 9134, 713–724.","ama":"Henzinger MH, Krinninger S, Loitzenbauer V. Finding 2-edge and 2-vertex strongly connected components in quadratic time. In: 2nd International Colloquium on Automata, Languages and Programming. Vol 9134. Springer Nature; 2015:713-724. doi:10.1007/978-3-662-47672-7_58","chicago":"Henzinger, Monika H, Sebastian Krinninger, and Veronika Loitzenbauer. “Finding 2-Edge and 2-Vertex Strongly Connected Components in Quadratic Time.” In 2nd International Colloquium on Automata, Languages and Programming, 9134:713–24. Springer Nature, 2015. https://doi.org/10.1007/978-3-662-47672-7_58.","short":"M.H. Henzinger, S. Krinninger, V. Loitzenbauer, in:, 2nd International Colloquium on Automata, Languages and Programming, Springer Nature, 2015, pp. 713–724.","mla":"Henzinger, Monika H., et al. “Finding 2-Edge and 2-Vertex Strongly Connected Components in Quadratic Time.” 2nd International Colloquium on Automata, Languages and Programming, vol. 9134, Springer Nature, 2015, pp. 713–24, doi:10.1007/978-3-662-47672-7_58."},"publication":"2nd International Colloquium on Automata, Languages and Programming","page":"713 - 724","date_published":"2015-07-06T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"06","_id":"11787","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 9134","status":"public","title":"Finding 2-edge and 2-vertex strongly connected components in quadratic time","oa_version":"Preprint","type":"conference","alternative_title":["LNCS"],"abstract":[{"lang":"eng","text":"We present faster algorithms for computing the 2-edge and 2-vertex strongly connected components of a directed graph. While in undirected graphs the 2-edge and 2-vertex connected components can be found in linear time, in directed graphs with m edges and n vertices only rather simple O(m n)-time algorithms were known. We use a hierarchical sparsification technique to obtain algorithms that run in time 𝑂(𝑛2). For 2-edge strongly connected components our algorithm gives the first running time improvement in 20 years. Additionally we present an 𝑂(𝑚2/log𝑛)-time algorithm for 2-edge strongly connected components, and thus improve over the O(m n) running time also when 𝑚=𝑂(𝑛). Our approach extends to k-edge and k-vertex strongly connected components for any constant k with a running time of 𝑂(𝑛2log𝑛) for k-edge-connectivity and 𝑂(𝑛3) for k-vertex-connectivity."}]},{"date_published":"2015-01-01T00:00:00Z","page":"156–167","citation":{"ama":"Dvořák W, Henzinger MH. Online ad assignment with an ad exchange. In: 12th International Workshop of Approximation and Online Algorithms. Vol 8952. Springer Nature; 2015:156–167. doi:10.1007/978-3-319-18263-6_14","ista":"Dvořák W, Henzinger MH. 2015. Online ad assignment with an ad exchange. 12th International Workshop of Approximation and Online Algorithms. WAOA: International Workshop on Approximation and Online Algorithms, LNCS, vol. 8952, 156–167.","apa":"Dvořák, W., & Henzinger, M. H. (2015). Online ad assignment with an ad exchange. In 12th International Workshop of Approximation and Online Algorithms (Vol. 8952, pp. 156–167). Wroclaw, Poland: Springer Nature. https://doi.org/10.1007/978-3-319-18263-6_14","ieee":"W. Dvořák and M. H. Henzinger, “Online ad assignment with an ad exchange,” in 12th International Workshop of Approximation and Online Algorithms, Wroclaw, Poland, 2015, vol. 8952, pp. 156–167.","mla":"Dvořák, Wolfgang, and Monika H. Henzinger. “Online Ad Assignment with an Ad Exchange.” 12th International Workshop of Approximation and Online Algorithms, vol. 8952, Springer Nature, 2015, pp. 156–167, doi:10.1007/978-3-319-18263-6_14.","short":"W. Dvořák, M.H. Henzinger, in:, 12th International Workshop of Approximation and Online Algorithms, Springer Nature, 2015, pp. 156–167.","chicago":"Dvořák, Wolfgang, and Monika H Henzinger. “Online Ad Assignment with an Ad Exchange.” In 12th International Workshop of Approximation and Online Algorithms, 8952:156–167. Springer Nature, 2015. https://doi.org/10.1007/978-3-319-18263-6_14."},"publication":"12th International Workshop of Approximation and Online Algorithms","article_processing_charge":"No","day":"01","scopus_import":"1","oa_version":"Preprint","intvolume":" 8952","status":"public","title":"Online ad assignment with an ad exchange","_id":"11788","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Ad exchanges are becoming an increasingly popular way to sell advertisement slots on the internet. An ad exchange is basically a spot market for ad impressions. A publisher who has already signed contracts reserving advertisement impressions on his pages can choose between assigning a new ad impression for a new page view to a contracted advertiser or to sell it at an ad exchange. This leads to an online revenue maximization problem for the publisher. Given a new impression to sell decide whether (a) to assign it to a contracted advertiser and if so to which one or (b) to sell it at the ad exchange and if so at which reserve price. We make no assumptions about the distribution of the advertiser valuations that participate in the ad exchange and show that there exists a simple primal-dual based online algorithm, whose lower bound for the revenue converges to 𝑅𝐴𝐷𝑋+𝑅𝐴(1−1/𝑒), where 𝑅𝐴𝐷𝑋 is the revenue that the optimum algorithm achieves from the ad exchange and 𝑅𝐴 is the revenue that the optimum algorithm achieves from the contracted advertisers.","lang":"eng"}],"alternative_title":["LNCS"],"type":"conference","language":[{"iso":"eng"}],"doi":"10.1007/978-3-319-18263-6_14","conference":{"name":"WAOA: International Workshop on Approximation and Online Algorithms","end_date":"2014-09-12","start_date":"2014-09-11","location":"Wroclaw, Poland"},"quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1604.05603"}],"external_id":{"arxiv":["1604.05603"]},"publication_identifier":{"issn":["0302-9743"]},"month":"01","volume":8952,"date_updated":"2023-02-10T09:26:06Z","date_created":"2022-08-11T09:43:32Z","author":[{"full_name":"Dvořák, Wolfgang","first_name":"Wolfgang","last_name":"Dvořák"},{"last_name":"Henzinger","first_name":"Monika H","orcid":"0000-0002-5008-6530","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","full_name":"Henzinger, Monika H"}],"publisher":"Springer Nature","publication_status":"published","year":"2015","extern":"1"},{"scopus_import":"1","article_processing_charge":"No","day":"01","citation":{"mla":"Bhattacharya, Sayan, et al. “Design of Dynamic Algorithms via Primal-Dual Method.” 42nd International Colloquium on Automata, Languages and Programming, vol. 9134, Springer Nature, 2015, pp. 206–18, doi:10.1007/978-3-662-47672-7_17.","short":"S. Bhattacharya, M.H. Henzinger, G.F. Italiano, in:, 42nd International Colloquium on Automata, Languages and Programming, Springer Nature, 2015, pp. 206–218.","chicago":"Bhattacharya, Sayan, Monika H Henzinger, and Giuseppe F. Italiano. “Design of Dynamic Algorithms via Primal-Dual Method.” In 42nd International Colloquium on Automata, Languages and Programming, 9134:206–18. Springer Nature, 2015. https://doi.org/10.1007/978-3-662-47672-7_17.","ama":"Bhattacharya S, Henzinger MH, Italiano GF. Design of dynamic algorithms via primal-dual method. In: 42nd International Colloquium on Automata, Languages and Programming. Vol 9134. Springer Nature; 2015:206-218. doi:10.1007/978-3-662-47672-7_17","ista":"Bhattacharya S, Henzinger MH, Italiano GF. 2015. Design of dynamic algorithms via primal-dual method. 42nd International Colloquium on Automata, Languages and Programming. ICALP: International Colloquium on Automata, Languages, and Programming, LNCS, vol. 9134, 206–218.","ieee":"S. Bhattacharya, M. H. Henzinger, and G. F. Italiano, “Design of dynamic algorithms via primal-dual method,” in 42nd International Colloquium on Automata, Languages and Programming, Kyoto, Japan, 2015, vol. 9134, pp. 206–218.","apa":"Bhattacharya, S., Henzinger, M. H., & Italiano, G. F. (2015). Design of dynamic algorithms via primal-dual method. In 42nd International Colloquium on Automata, Languages and Programming (Vol. 9134, pp. 206–218). Kyoto, Japan: Springer Nature. https://doi.org/10.1007/978-3-662-47672-7_17"},"publication":"42nd International Colloquium on Automata, Languages and Programming","page":"206 - 218","date_published":"2015-01-01T00:00:00Z","type":"conference","alternative_title":["LNCS"],"abstract":[{"lang":"eng","text":"In this paper, we develop a dynamic version of the primal-dual method for optimization problems, and apply it to obtain the following results. (1) For the dynamic set-cover problem, we maintain an 𝑂(𝑓2)-approximately optimal solution in 𝑂(𝑓⋅log(𝑚+𝑛)) amortized update time, where 𝑓 is the maximum “frequency” of an element, 𝑛 is the number of sets, and 𝑚 is the maximum number of elements in the universe at any point in time. (2) For the dynamic 𝑏-matching problem, we maintain an 𝑂(1)-approximately optimal solution in 𝑂(log3𝑛) amortized update time, where 𝑛 is the number of nodes in the graph."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"11786","intvolume":" 9134","title":"Design of dynamic algorithms via primal-dual method","status":"public","oa_version":"Preprint","publication_identifier":{"isbn":["9783662476710"],"issn":["0302-9743"]},"month":"01","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1604.05337"}],"oa":1,"external_id":{"arxiv":["1604.05337"]},"quality_controlled":"1","doi":"10.1007/978-3-662-47672-7_17","conference":{"end_date":"2015-07-10","start_date":"2015-07-06","location":"Kyoto, Japan","name":"ICALP: International Colloquium on Automata, Languages, and Programming"},"language":[{"iso":"eng"}],"extern":"1","year":"2015","publisher":"Springer Nature","publication_status":"published","author":[{"first_name":"Sayan","last_name":"Bhattacharya","full_name":"Bhattacharya, Sayan"},{"last_name":"Henzinger","first_name":"Monika H","orcid":"0000-0002-5008-6530","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","full_name":"Henzinger, Monika H"},{"last_name":"Italiano","first_name":"Giuseppe F.","full_name":"Italiano, Giuseppe F."}],"volume":9134,"date_updated":"2023-02-10T09:13:31Z","date_created":"2022-08-11T09:28:49Z"},{"month":"01","publication_identifier":{"eissn":["2041-210X"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"pmid":["25893087"]},"quality_controlled":"1","doi":"10.1111/2041-210x.12299","language":[{"iso":"eng"}],"file_date_updated":"2022-08-16T06:52:53Z","extern":"1","year":"2015","pmid":1,"publication_status":"published","publisher":"Wiley","author":[{"first_name":"Olga","last_name":"Chernomor","full_name":"Chernomor, Olga"},{"last_name":"Minh","first_name":"Bui Quang","full_name":"Minh, Bui Quang"},{"full_name":"Forest, Félix","last_name":"Forest","first_name":"Félix"},{"full_name":"Klaere, Steffen","first_name":"Steffen","last_name":"Klaere"},{"full_name":"Ingram, Travis","first_name":"Travis","last_name":"Ingram"},{"last_name":"Henzinger","first_name":"Monika H","orcid":"0000-0002-5008-6530","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","full_name":"Henzinger, Monika H"},{"full_name":"von Haeseler, Arndt","first_name":"Arndt","last_name":"von Haeseler"}],"date_created":"2022-08-16T06:43:49Z","date_updated":"2023-02-17T09:30:08Z","volume":6,"scopus_import":"1","day":"01","has_accepted_license":"1","article_processing_charge":"No","publication":"Methods in Ecology and Evolution","citation":{"ama":"Chernomor O, Minh BQ, Forest F, et al. Split diversity in constrained conservation prioritization using integer linear programming. Methods in Ecology and Evolution. 2015;6(1):83-91. doi:10.1111/2041-210x.12299","ista":"Chernomor O, Minh BQ, Forest F, Klaere S, Ingram T, Henzinger MH, von Haeseler A. 2015. Split diversity in constrained conservation prioritization using integer linear programming. Methods in Ecology and Evolution. 6(1), 83–91.","ieee":"O. Chernomor et al., “Split diversity in constrained conservation prioritization using integer linear programming,” Methods in Ecology and Evolution, vol. 6, no. 1. Wiley, pp. 83–91, 2015.","apa":"Chernomor, O., Minh, B. Q., Forest, F., Klaere, S., Ingram, T., Henzinger, M. H., & von Haeseler, A. (2015). Split diversity in constrained conservation prioritization using integer linear programming. Methods in Ecology and Evolution. Wiley. https://doi.org/10.1111/2041-210x.12299","mla":"Chernomor, Olga, et al. “Split Diversity in Constrained Conservation Prioritization Using Integer Linear Programming.” Methods in Ecology and Evolution, vol. 6, no. 1, Wiley, 2015, pp. 83–91, doi:10.1111/2041-210x.12299.","short":"O. Chernomor, B.Q. Minh, F. Forest, S. Klaere, T. Ingram, M.H. Henzinger, A. von Haeseler, Methods in Ecology and Evolution 6 (2015) 83–91.","chicago":"Chernomor, Olga, Bui Quang Minh, Félix Forest, Steffen Klaere, Travis Ingram, Monika H Henzinger, and Arndt von Haeseler. “Split Diversity in Constrained Conservation Prioritization Using Integer Linear Programming.” Methods in Ecology and Evolution. Wiley, 2015. https://doi.org/10.1111/2041-210x.12299."},"article_type":"original","page":"83-91","date_published":"2015-01-01T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"Phylogenetic diversity (PD) is a measure of biodiversity based on the evolutionary history of species. Here, we discuss several optimization problems related to the use of PD, and the more general measure split diversity (SD), in conservation prioritization.\r\nDepending on the conservation goal and the information available about species, one can construct optimization routines that incorporate various conservation constraints. We demonstrate how this information can be used to select sets of species for conservation action. Specifically, we discuss the use of species' geographic distributions, the choice of candidates under economic pressure, and the use of predator–prey interactions between the species in a community to define viability constraints.\r\nDespite such optimization problems falling into the area of NP hard problems, it is possible to solve them in a reasonable amount of time using integer programming. We apply integer linear programming to a variety of models for conservation prioritization that incorporate the SD measure.\r\nWe exemplarily show the results for two data sets: the Cape region of South Africa and a Caribbean coral reef community. Finally, we provide user-friendly software at http://www.cibiv.at/software/pda."}],"issue":"1","_id":"11845","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"title":"Split diversity in constrained conservation prioritization using integer linear programming","status":"public","intvolume":" 6","oa_version":"Published Version","file":[{"file_size":411415,"content_type":"application/pdf","creator":"asandaue","file_name":"2015_MethodsInEcologyAndEvolutionChernomor.pdf","access_level":"open_access","date_created":"2022-08-16T06:52:53Z","date_updated":"2022-08-16T06:52:53Z","checksum":"880e78f09f0ac99cb351c48dc97623b6","success":1,"relation":"main_file","file_id":"11846"}]},{"language":[{"iso":"eng"}],"doi":"10.1145/2746539.2746609","date_published":"2015-06-14T00:00:00Z","conference":{"name":"STOC: Symposium on Theory of Computing","end_date":"2015-06-17","start_date":"2015-06-14","location":"Portland, OR, United States"},"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1511.06773"}],"external_id":{"arxiv":["1511.06773"]},"citation":{"chicago":"Henzinger, Monika H, Sebastian Krinninger, Danupon Nanongkai, and Thatchaphol Saranurak. “Unifying and Strengthening Hardness for Dynamic Problems via the Online Matrix-Vector Multiplication Conjecture.” In 47th Annual ACM Symposium on Theory of Computing. Association for Computing Machinery, 2015. https://doi.org/10.1145/2746539.2746609.","mla":"Henzinger, Monika H., et al. “Unifying and Strengthening Hardness for Dynamic Problems via the Online Matrix-Vector Multiplication Conjecture.” 47th Annual ACM Symposium on Theory of Computing, 21–30, Association for Computing Machinery, 2015, doi:10.1145/2746539.2746609.","short":"M.H. Henzinger, S. Krinninger, D. Nanongkai, T. Saranurak, in:, 47th Annual ACM Symposium on Theory of Computing, Association for Computing Machinery, 2015.","ista":"Henzinger MH, Krinninger S, Nanongkai D, Saranurak T. 2015. Unifying and strengthening hardness for dynamic problems via the online matrix-vector multiplication conjecture. 47th Annual ACM Symposium on Theory of Computing. STOC: Symposium on Theory of Computing, 21–30.","apa":"Henzinger, M. H., Krinninger, S., Nanongkai, D., & Saranurak, T. (2015). Unifying and strengthening hardness for dynamic problems via the online matrix-vector multiplication conjecture. In 47th Annual ACM Symposium on Theory of Computing. Portland, OR, United States: Association for Computing Machinery. https://doi.org/10.1145/2746539.2746609","ieee":"M. H. Henzinger, S. Krinninger, D. Nanongkai, and T. Saranurak, “Unifying and strengthening hardness for dynamic problems via the online matrix-vector multiplication conjecture,” in 47th Annual ACM Symposium on Theory of Computing, Portland, OR, United States, 2015.","ama":"Henzinger MH, Krinninger S, Nanongkai D, Saranurak T. Unifying and strengthening hardness for dynamic problems via the online matrix-vector multiplication conjecture. In: 47th Annual ACM Symposium on Theory of Computing. Association for Computing Machinery; 2015. doi:10.1145/2746539.2746609"},"oa":1,"publication":"47th Annual ACM Symposium on Theory of Computing","article_processing_charge":"No","publication_identifier":{"issn":["0737.8017"],"isbn":["978-145033536-2"]},"day":"14","month":"06","scopus_import":"1","oa_version":"Preprint","date_created":"2022-08-16T09:31:21Z","date_updated":"2023-02-17T11:09:54Z","author":[{"last_name":"Henzinger","first_name":"Monika H","orcid":"0000-0002-5008-6530","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","full_name":"Henzinger, Monika H"},{"last_name":"Krinninger","first_name":"Sebastian","full_name":"Krinninger, Sebastian"},{"first_name":"Danupon","last_name":"Nanongkai","full_name":"Nanongkai, Danupon"},{"first_name":"Thatchaphol","last_name":"Saranurak","full_name":"Saranurak, Thatchaphol"}],"publisher":"Association for Computing Machinery","title":"Unifying and strengthening hardness for dynamic problems via the online matrix-vector multiplication conjecture","publication_status":"published","status":"public","year":"2015","_id":"11868","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","abstract":[{"lang":"eng","text":"Consider the following Online Boolean Matrix-Vector Multiplication problem: We are given an n x n matrix M and will receive n column-vectors of size n, denoted by v1, ..., vn, one by one. After seeing each vector vi, we have to output the product Mvi before we can see the next vector. A naive algorithm can solve this problem using O(n3) time in total, and its running time can be slightly improved to O(n3/log2 n) [Williams SODA'07]. We show that a conjecture that there is no truly subcubic (O(n3-ε)) time algorithm for this problem can be used to exhibit the underlying polynomial time hardness shared by many dynamic problems. For a number of problems, such as subgraph connectivity, Pagh's problem, d-failure connectivity, decremental single-source shortest paths, and decremental transitive closure, this conjecture implies tight hardness results. Thus, proving or disproving this conjecture will be very interesting as it will either imply several tight unconditional lower bounds or break through a common barrier that blocks progress with these problems. This conjecture might also be considered as strong evidence against any further improvement for these problems since refuting it will imply a major breakthrough for combinatorial Boolean matrix multiplication and other long-standing problems if the term \"combinatorial algorithms\" is interpreted as \"Strassen-like algorithms\" [Ballard et al. SPAA'11].\r\n\r\nThe conjecture also leads to hardness results for problems that were previously based on diverse problems and conjectures -- such as 3SUM, combinatorial Boolean matrix multiplication, triangle detection, and multiphase -- thus providing a uniform way to prove polynomial hardness results for dynamic algorithms; some of the new proofs are also simpler or even become trivial. The conjecture also leads to stronger and new, non-trivial, hardness results, e.g., for the fully-dynamic densest subgraph and diameter problems."}],"type":"conference","article_number":"21-30"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"11869","year":"2015","publisher":"Association for Computing Machinery","title":"Space- and time-efficient algorithm for maintaining dense subgraphs on one-pass dynamic streams","status":"public","publication_status":"published","author":[{"full_name":"Bhattacharya, Sayan","last_name":"Bhattacharya","first_name":"Sayan"},{"full_name":"Henzinger, Monika H","orcid":"0000-0002-5008-6530","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","last_name":"Henzinger","first_name":"Monika H"},{"full_name":"Nanongkai, Danupon","last_name":"Nanongkai","first_name":"Danupon"},{"full_name":"Tsourakakis, Charalampos","last_name":"Tsourakakis","first_name":"Charalampos"}],"oa_version":"Preprint","date_updated":"2023-02-17T11:17:03Z","date_created":"2022-08-16T09:36:48Z","type":"conference","abstract":[{"lang":"eng","text":"While in many graph mining applications it is crucial to handle a stream of updates efficiently in terms of both time and space, not much was known about achieving such type of algorithm. In this paper we study this issue for a problem which lies at the core of many graph mining applications called densest subgraph problem. We develop an algorithm that achieves time- and space-efficiency for this problem simultaneously. It is one of the first of its kind for graph problems to the best of our knowledge.\r\n\r\nGiven an input graph, the densest subgraph is the subgraph that maximizes the ratio between the number of edges and the number of nodes. For any ε>0, our algorithm can, with high probability, maintain a (4+ε)-approximate solution under edge insertions and deletions using ~O(n) space and ~O(1) amortized time per update; here, $n$ is the number of nodes in the graph and ~O hides the O(polylog_{1+ε} n) term. The approximation ratio can be improved to (2+ε) with more time. It can be extended to a (2+ε)-approximation sublinear-time algorithm and a distributed-streaming algorithm. Our algorithm is the first streaming algorithm that can maintain the densest subgraph in one pass. Prior to this, no algorithm could do so even in the special case of an incremental stream and even when there is no time restriction. The previously best algorithm in this setting required O(log n) passes [BahmaniKV12]. The space required by our algorithm is tight up to a polylogarithmic factor."}],"extern":"1","citation":{"short":"S. Bhattacharya, M.H. Henzinger, D. Nanongkai, C. Tsourakakis, in:, 47th Annual ACM Symposium on Theory of Computing, Association for Computing Machinery, 2015, pp. 173–182.","mla":"Bhattacharya, Sayan, et al. “Space- and Time-Efficient Algorithm for Maintaining Dense Subgraphs on One-Pass Dynamic Streams.” 47th Annual ACM Symposium on Theory of Computing, Association for Computing Machinery, 2015, pp. 173–82, doi:10.1145/2746539.2746592.","chicago":"Bhattacharya, Sayan, Monika H Henzinger, Danupon Nanongkai, and Charalampos Tsourakakis. “Space- and Time-Efficient Algorithm for Maintaining Dense Subgraphs on One-Pass Dynamic Streams.” In 47th Annual ACM Symposium on Theory of Computing, 173–82. Association for Computing Machinery, 2015. https://doi.org/10.1145/2746539.2746592.","ama":"Bhattacharya S, Henzinger MH, Nanongkai D, Tsourakakis C. Space- and time-efficient algorithm for maintaining dense subgraphs on one-pass dynamic streams. In: 47th Annual ACM Symposium on Theory of Computing. Association for Computing Machinery; 2015:173-182. doi:10.1145/2746539.2746592","apa":"Bhattacharya, S., Henzinger, M. H., Nanongkai, D., & Tsourakakis, C. (2015). Space- and time-efficient algorithm for maintaining dense subgraphs on one-pass dynamic streams. In 47th Annual ACM Symposium on Theory of Computing (pp. 173–182). Portland, OR, United States: Association for Computing Machinery. https://doi.org/10.1145/2746539.2746592","ieee":"S. Bhattacharya, M. H. Henzinger, D. Nanongkai, and C. Tsourakakis, “Space- and time-efficient algorithm for maintaining dense subgraphs on one-pass dynamic streams,” in 47th Annual ACM Symposium on Theory of Computing, Portland, OR, United States, 2015, pp. 173–182.","ista":"Bhattacharya S, Henzinger MH, Nanongkai D, Tsourakakis C. 2015. Space- and time-efficient algorithm for maintaining dense subgraphs on one-pass dynamic streams. 47th Annual ACM Symposium on Theory of Computing. STOC: Symposium on Theory of Computing, 173–182."},"external_id":{"arxiv":["1504.02268"]},"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1504.02268","open_access":"1"}],"publication":"47th Annual ACM Symposium on Theory of Computing","page":"173 - 182","quality_controlled":"1","date_published":"2015-06-01T00:00:00Z","doi":"10.1145/2746539.2746592","conference":{"end_date":"2015-06-17","start_date":"2015-06-14","location":"Portland, OR, United States","name":"STOC: Symposium on Theory of Computing"},"language":[{"iso":"eng"}],"scopus_import":"1","publication_identifier":{"isbn":["978-145033536-2"],"issn":["0737-8017"]},"article_processing_charge":"No","month":"06","day":"01"},{"publication":"32nd International Symposium on Theoretical Aspects of Computer Science","citation":{"chicago":"Bhattacharya, Sayan, Wolfgang Dvorák, Monika H Henzinger, and Martin Starnberger. “Welfare Maximization with Friends-of-Friends Network Externalities.” In 32nd International Symposium on Theoretical Aspects of Computer Science, 30:90–102. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015. https://doi.org/10.4230/LIPICS.STACS.2015.90.","mla":"Bhattacharya, Sayan, et al. “Welfare Maximization with Friends-of-Friends Network Externalities.” 32nd International Symposium on Theoretical Aspects of Computer Science, vol. 30, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015, pp. 90–102, doi:10.4230/LIPICS.STACS.2015.90.","short":"S. Bhattacharya, W. Dvorák, M.H. Henzinger, Martin Starnberger, in:, 32nd International Symposium on Theoretical Aspects of Computer Science, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015, pp. 90–102.","ista":"Bhattacharya S, Dvorák W, Henzinger MH, Starnberger Martin. 2015. Welfare maximization with friends-of-friends network externalities. 32nd International Symposium on Theoretical Aspects of Computer Science. STACS: Symposium on Theoretical Aspects of Computer Science, LIPIcs, vol. 30, 90–102.","apa":"Bhattacharya, S., Dvorák, W., Henzinger, M. H., & Starnberger, Martin. (2015). Welfare maximization with friends-of-friends network externalities. In 32nd International Symposium on Theoretical Aspects of Computer Science (Vol. 30, pp. 90–102). Garching, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.STACS.2015.90","ieee":"S. Bhattacharya, W. Dvorák, M. H. Henzinger, and Martin Starnberger, “Welfare maximization with friends-of-friends network externalities,” in 32nd International Symposium on Theoretical Aspects of Computer Science, Garching, Germany, 2015, vol. 30, pp. 90–102.","ama":"Bhattacharya S, Dvorák W, Henzinger MH, Starnberger Martin. Welfare maximization with friends-of-friends network externalities. In: 32nd International Symposium on Theoretical Aspects of Computer Science. Vol 30. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2015:90-102. doi:10.4230/LIPICS.STACS.2015.90"},"page":"90-102","date_published":"2015-02-26T00:00:00Z","scopus_import":"1","day":"26","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"11837","status":"public","title":"Welfare maximization with friends-of-friends network externalities","intvolume":" 30","oa_version":"Published Version","type":"conference","alternative_title":["LIPIcs"],"abstract":[{"text":"Online social networks allow the collection of large amounts of data about the influence between users connected by a friendship-like relationship. When distributing items among agents forming a social network, this information allows us to exploit network externalities that each agent receives from his neighbors that get the same item. In this paper we consider Friends-of-Friends (2-hop) network externalities, i.e., externalities that not only depend on the neighbors that get the same item but also on neighbors of neighbors. For these externalities we study a setting where multiple different items are assigned to unit-demand agents. Specifically, we study the problem of welfare maximization under different types of externality functions. Let n be the number of agents and m be the number of items. Our contributions are the following: (1) We show that welfare maximization is APX-hard; we show that even for step functions with 2-hop (and also with 1-hop) externalities it is NP-hard to approximate social welfare better than (1-1/e). (2) On the positive side we present (i) an O(sqrt n)-approximation algorithm for general concave externality functions,\r\n(ii) an O(\\log m)-approximation algorithm for linear externality functions, and (iii) an (1-1/e)\\frac{1}{6}-approximation algorithm for 2-hop step function externalities. We also improve the result from [6] for 1-hop step function externalities by giving a (1-1/e)/2-approximation algorithm.","lang":"eng"}],"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.4230/LIPICS.STACS.2015.90"}],"quality_controlled":"1","conference":{"name":"STACS: Symposium on Theoretical Aspects of Computer Science","location":"Garching, Germany","start_date":"2015-03-04","end_date":"2015-03-07"},"doi":"10.4230/LIPICS.STACS.2015.90","language":[{"iso":"eng"}],"month":"02","publication_identifier":{"issn":["1868-8969"],"isbn":["978-3-939897-78-1"]},"year":"2015","publication_status":"published","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","author":[{"full_name":"Bhattacharya, Sayan","first_name":"Sayan","last_name":"Bhattacharya"},{"full_name":"Dvorák, Wolfgang","first_name":"Wolfgang","last_name":"Dvorák"},{"orcid":"0000-0002-5008-6530","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","last_name":"Henzinger","first_name":"Monika H","full_name":"Henzinger, Monika H"},{"last_name":"Starnberger","first_name":" Martin","full_name":"Starnberger, Martin"}],"related_material":{"record":[{"relation":"later_version","status":"public","id":"11903"}]},"date_created":"2022-08-12T11:39:40Z","date_updated":"2023-02-21T16:32:37Z","volume":30,"extern":"1"},{"extern":"1","year":"2015","publication_status":"published","publisher":"Elsevier","author":[{"last_name":"Henzinger","first_name":"Monika H","orcid":"0000-0002-5008-6530","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","full_name":"Henzinger, Monika H"},{"first_name":"Veronika","last_name":"Loitzenbauer","full_name":"Loitzenbauer, Veronika"}],"date_updated":"2023-02-17T14:50:04Z","date_created":"2022-08-17T09:06:53Z","volume":573,"month":"03","publication_identifier":{"issn":["0304-3975"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.tcs.2015.01.033"}],"oa":1,"quality_controlled":"1","doi":"10.1016/j.tcs.2015.01.033","language":[{"iso":"eng"}],"type":"journal_article","abstract":[{"lang":"eng","text":"We consider auctions of indivisible items to unit-demand bidders with budgets. This setting was suggested as an expressive model for single sponsored search auctions. Prior work presented mechanisms that compute bidder-optimal outcomes and are truthful for a restricted set of inputs, i.e., inputs in so-called general position. This condition is easily violated. We provide the first mechanism that is truthful in expectation for all inputs and achieves for each bidder no worse utility than the bidder-optimal outcome. Additionally we give a complete characterization for which inputs mechanisms that compute bidder-optimal outcomes are truthful."}],"_id":"11901","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Truthful unit-demand auctions with budgets revisited","intvolume":" 573","oa_version":"None","scopus_import":"1","day":"30","article_processing_charge":"No","publication":"Theoretical Computer Science","citation":{"ieee":"M. H. Henzinger and V. Loitzenbauer, “Truthful unit-demand auctions with budgets revisited,” Theoretical Computer Science, vol. 573. Elsevier, pp. 1–15, 2015.","apa":"Henzinger, M. H., & Loitzenbauer, V. (2015). Truthful unit-demand auctions with budgets revisited. Theoretical Computer Science. Elsevier. https://doi.org/10.1016/j.tcs.2015.01.033","ista":"Henzinger MH, Loitzenbauer V. 2015. Truthful unit-demand auctions with budgets revisited. Theoretical Computer Science. 573, 1–15.","ama":"Henzinger MH, Loitzenbauer V. Truthful unit-demand auctions with budgets revisited. Theoretical Computer Science. 2015;573:1-15. doi:10.1016/j.tcs.2015.01.033","chicago":"Henzinger, Monika H, and Veronika Loitzenbauer. “Truthful Unit-Demand Auctions with Budgets Revisited.” Theoretical Computer Science. Elsevier, 2015. https://doi.org/10.1016/j.tcs.2015.01.033.","short":"M.H. Henzinger, V. Loitzenbauer, Theoretical Computer Science 573 (2015) 1–15.","mla":"Henzinger, Monika H., and Veronika Loitzenbauer. “Truthful Unit-Demand Auctions with Budgets Revisited.” Theoretical Computer Science, vol. 573, Elsevier, 2015, pp. 1–15, doi:10.1016/j.tcs.2015.01.033."},"article_type":"original","page":"1-15","date_published":"2015-03-30T00:00:00Z"},{"month":"02","language":[{"iso":"eng"}],"doi":"10.1103/PhysRevLett.114.055503","quality_controlled":"1","external_id":{"arxiv":["1408.1607"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1408.1607"}],"oa":1,"extern":"1","publist_id":"7933","article_number":"055503","date_created":"2018-12-11T11:44:44Z","date_updated":"2021-01-12T06:49:07Z","volume":114,"author":[{"id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2299-3176","first_name":"Scott R","last_name":"Waitukaitis","full_name":"Waitukaitis, Scott R"},{"full_name":"Menaut, Rémi","first_name":"Rémi","last_name":"Menaut"},{"full_name":"Chen, Bryan","first_name":"Bryan","last_name":"Chen"},{"last_name":"Van Hecke","first_name":"Martin","full_name":"Van Hecke, Martin"}],"publication_status":"published","publisher":"American Physical Society","year":"2015","acknowledgement":"B. G. C. acknowledges support from FOM, and S. W. and M. v. H. acknowledge support from NWO.","day":"04","date_published":"2015-02-04T00:00:00Z","publication":"APS Physics, Physical Review Letters","citation":{"chicago":"Waitukaitis, Scott R, Rémi Menaut, Bryan Chen, and Martin Van Hecke. “Origami Multistability: From Single Vertices to Metasheets.” APS Physics, Physical Review Letters. American Physical Society, 2015. https://doi.org/10.1103/PhysRevLett.114.055503.","mla":"Waitukaitis, Scott R., et al. “Origami Multistability: From Single Vertices to Metasheets.” APS Physics, Physical Review Letters, vol. 114, no. 5, 055503, American Physical Society, 2015, doi:10.1103/PhysRevLett.114.055503.","short":"S.R. Waitukaitis, R. Menaut, B. Chen, M. Van Hecke, APS Physics, Physical Review Letters 114 (2015).","ista":"Waitukaitis SR, Menaut R, Chen B, Van Hecke M. 2015. Origami multistability: From single vertices to metasheets. APS Physics, Physical Review Letters. 114(5), 055503.","apa":"Waitukaitis, S. R., Menaut, R., Chen, B., & Van Hecke, M. (2015). Origami multistability: From single vertices to metasheets. APS Physics, Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.114.055503","ieee":"S. R. Waitukaitis, R. Menaut, B. Chen, and M. Van Hecke, “Origami multistability: From single vertices to metasheets,” APS Physics, Physical Review Letters, vol. 114, no. 5. American Physical Society, 2015.","ama":"Waitukaitis SR, Menaut R, Chen B, Van Hecke M. Origami multistability: From single vertices to metasheets. APS Physics, Physical Review Letters. 2015;114(5). doi:10.1103/PhysRevLett.114.055503"},"abstract":[{"text":"We show that the simplest building blocks of origami-based materials - rigid, degree-four vertices - are generically multistable. The existence of two distinct branches of folding motion emerging from the flat state suggests at least bistability, but we show how nonlinearities in the folding motions allow generic vertex geometries to have as many as five stable states. In special geometries with collinear folds and symmetry, more branches emerge leading to as many as six stable states. Tuning the fold energy parameters, we show how monostability is also possible. Finally, we show how to program the stability features of a single vertex into a periodic fold tessellation. The resulting metasheets provide a previously unanticipated functionality - tunable and switchable shape and size via multistability.","lang":"eng"}],"issue":"5","type":"journal_article","oa_version":"Preprint","title":"Origami multistability: From single vertices to metasheets","status":"public","intvolume":" 114","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"121"},{"date_updated":"2021-01-12T06:50:18Z","date_created":"2018-12-11T11:51:42Z","volume":1,"author":[{"full_name":"Yu, Luo","last_name":"Yu","first_name":"Luo"},{"full_name":"Scholl, Stefan","first_name":"Stefan","last_name":"Scholl"},{"first_name":"Anett","last_name":"Doering","full_name":"Doering, Anett"},{"first_name":"Zhang","last_name":"Yi","full_name":"Yi, Zhang"},{"first_name":"Niloufer","last_name":"Irani","full_name":"Irani, Niloufer"},{"first_name":"Simone","last_name":"Di Rubbo","full_name":"Di Rubbo, Simone"},{"full_name":"Neumetzler, Lutz","last_name":"Neumetzler","first_name":"Lutz"},{"first_name":"Praveen","last_name":"Krishnamoorthy","full_name":"Krishnamoorthy, Praveen"},{"full_name":"Van Houtte, Isabelle","last_name":"Van Houtte","first_name":"Isabelle"},{"first_name":"Evelien","last_name":"Mylle","full_name":"Mylle, Evelien"},{"full_name":"Bischoff, Volker","last_name":"Bischoff","first_name":"Volker"},{"full_name":"Vernhettes, Samantha","first_name":"Samantha","last_name":"Vernhettes"},{"full_name":"Winne, Johan","first_name":"Johan","last_name":"Winne"},{"first_name":"Jirí","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí"},{"last_name":"Stierhof","first_name":"York","full_name":"Stierhof, York"},{"first_name":"Karin","last_name":"Schumacher","full_name":"Schumacher, Karin"},{"full_name":"Persson, Staffan","last_name":"Persson","first_name":"Staffan"},{"full_name":"Russinova, Eugenia","first_name":"Eugenia","last_name":"Russinova"}],"publication_status":"published","department":[{"_id":"JiFr"}],"publisher":"Nature Publishing Group","year":"2015","pmid":1,"publist_id":"5827","article_number":"15094","language":[{"iso":"eng"}],"doi":"10.1038/nplants.2015.94","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4905525/"}],"oa":1,"external_id":{"pmid":["27250258"]},"month":"07","oa_version":"Submitted Version","status":"public","title":"V-ATPase activity in the TGN/EE is required for exocytosis and recycling in Arabidopsis","intvolume":" 1","_id":"1383","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"In plants, vacuolar H+-ATPase (V-ATPase) activity acidifies both the trans-Golgi network/early endosome (TGN/EE) and the vacuole. This dual V-ATPase function has impeded our understanding of how the pH homeostasis within the plant TGN/EE controls exo- and endocytosis. Here, we show that the weak V-ATPase mutant deetiolated3 (det3) displayed a pH increase in the TGN/EE, but not in the vacuole, strongly impairing secretion and recycling of the brassinosteroid receptor and the cellulose synthase complexes to the plasma membrane, in contrast to mutants lacking tonoplast-localized V-ATPase activity only. The brassinosteroid insensitivity and the cellulose deficiency defects in det3 were tightly correlated with reduced Golgi and TGN/EE motility. Thus, our results provide strong evidence that acidification of the TGN/EE, but not of the vacuole, is indispensable for functional secretion and recycling in plants."}],"issue":"7","type":"journal_article","date_published":"2015-07-06T00:00:00Z","article_type":"original","publication":"Nature Plants","citation":{"ama":"Yu L, Scholl S, Doering A, et al. V-ATPase activity in the TGN/EE is required for exocytosis and recycling in Arabidopsis. Nature Plants. 2015;1(7). doi:10.1038/nplants.2015.94","apa":"Yu, L., Scholl, S., Doering, A., Yi, Z., Irani, N., Di Rubbo, S., … Russinova, E. (2015). V-ATPase activity in the TGN/EE is required for exocytosis and recycling in Arabidopsis. Nature Plants. Nature Publishing Group. https://doi.org/10.1038/nplants.2015.94","ieee":"L. Yu et al., “V-ATPase activity in the TGN/EE is required for exocytosis and recycling in Arabidopsis,” Nature Plants, vol. 1, no. 7. Nature Publishing Group, 2015.","ista":"Yu L, Scholl S, Doering A, Yi Z, Irani N, Di Rubbo S, Neumetzler L, Krishnamoorthy P, Van Houtte I, Mylle E, Bischoff V, Vernhettes S, Winne J, Friml J, Stierhof Y, Schumacher K, Persson S, Russinova E. 2015. V-ATPase activity in the TGN/EE is required for exocytosis and recycling in Arabidopsis. Nature Plants. 1(7), 15094.","short":"L. Yu, S. Scholl, A. Doering, Z. Yi, N. Irani, S. Di Rubbo, L. Neumetzler, P. Krishnamoorthy, I. Van Houtte, E. Mylle, V. Bischoff, S. Vernhettes, J. Winne, J. Friml, Y. Stierhof, K. Schumacher, S. Persson, E. Russinova, Nature Plants 1 (2015).","mla":"Yu, Luo, et al. “V-ATPase Activity in the TGN/EE Is Required for Exocytosis and Recycling in Arabidopsis.” Nature Plants, vol. 1, no. 7, 15094, Nature Publishing Group, 2015, doi:10.1038/nplants.2015.94.","chicago":"Yu, Luo, Stefan Scholl, Anett Doering, Zhang Yi, Niloufer Irani, Simone Di Rubbo, Lutz Neumetzler, et al. “V-ATPase Activity in the TGN/EE Is Required for Exocytosis and Recycling in Arabidopsis.” Nature Plants. Nature Publishing Group, 2015. https://doi.org/10.1038/nplants.2015.94."},"day":"06","article_processing_charge":"No","scopus_import":1},{"title":"Lifelong learning with non-i.i.d. tasks","status":"public","intvolume":" 2015","_id":"1425","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa_version":"None","alternative_title":["Advances in Neural Information Processing Systems"],"type":"conference","abstract":[{"lang":"eng","text":"In this work we aim at extending the theoretical foundations of lifelong learning. Previous work analyzing this scenario is based on the assumption that learning tasks are sampled i.i.d. from a task environment or limited to strongly constrained data distributions. Instead, we study two scenarios when lifelong learning is possible, even though the observed tasks do not form an i.i.d. sample: first, when they are sampled from the same environment, but possibly with dependencies, and second, when the task environment is allowed to change over time in a consistent way. In the first case we prove a PAC-Bayesian theorem that can be seen as a direct generalization of the analogous previous result for the i.i.d. case. For the second scenario we propose to learn an inductive bias in form of a transfer procedure. We present a generalization bound and show on a toy example how it can be used to identify a beneficial transfer algorithm."}],"page":"1540 - 1548","citation":{"short":"A. Pentina, C. Lampert, in:, Neural Information Processing Systems, 2015, pp. 1540–1548.","mla":"Pentina, Anastasia, and Christoph Lampert. Lifelong Learning with Non-i.i.d. Tasks. Vol. 2015, Neural Information Processing Systems, 2015, pp. 1540–48.","chicago":"Pentina, Anastasia, and Christoph Lampert. “Lifelong Learning with Non-i.i.d. Tasks,” 2015:1540–48. Neural Information Processing Systems, 2015.","ama":"Pentina A, Lampert C. Lifelong learning with non-i.i.d. tasks. In: Vol 2015. Neural Information Processing Systems; 2015:1540-1548.","apa":"Pentina, A., & Lampert, C. (2015). Lifelong learning with non-i.i.d. tasks (Vol. 2015, pp. 1540–1548). Presented at the NIPS: Neural Information Processing Systems, Montreal, Canada: Neural Information Processing Systems.","ieee":"A. Pentina and C. Lampert, “Lifelong learning with non-i.i.d. tasks,” presented at the NIPS: Neural Information Processing Systems, Montreal, Canada, 2015, vol. 2015, pp. 1540–1548.","ista":"Pentina A, Lampert C. 2015. Lifelong learning with non-i.i.d. tasks. NIPS: Neural Information Processing Systems, Advances in Neural Information Processing Systems, vol. 2015, 1540–1548."},"date_published":"2015-01-01T00:00:00Z","scopus_import":1,"day":"01","publication_status":"published","department":[{"_id":"ChLa"}],"publisher":"Neural Information Processing Systems","year":"2015","date_updated":"2021-01-12T06:50:39Z","date_created":"2018-12-11T11:51:57Z","volume":2015,"author":[{"id":"42E87FC6-F248-11E8-B48F-1D18A9856A87","first_name":"Anastasia","last_name":"Pentina","full_name":"Pentina, Anastasia"},{"full_name":"Lampert, Christoph","first_name":"Christoph","last_name":"Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887"}],"publist_id":"5781","ec_funded":1,"quality_controlled":"1","project":[{"name":"Lifelong Learning of Visual Scene Understanding","call_identifier":"FP7","grant_number":"308036","_id":"2532554C-B435-11E9-9278-68D0E5697425"}],"main_file_link":[{"open_access":"1","url":"http://papers.nips.cc/paper/6007-lifelong-learning-with-non-iid-tasks"}],"oa":1,"language":[{"iso":"eng"}],"conference":{"start_date":"2015-12-07","location":"Montreal, Canada","end_date":"2015-12-12","name":"NIPS: Neural Information Processing Systems"},"month":"01"},{"date_created":"2018-12-11T11:51:56Z","date_updated":"2021-01-12T06:50:38Z","volume":28,"oa_version":"Submitted Version","author":[{"full_name":"Kwitt, Roland","last_name":"Kwitt","first_name":"Roland"},{"orcid":"0000-0002-8871-5814","id":"4700A070-F248-11E8-B48F-1D18A9856A87","last_name":"Huber","first_name":"Stefan","full_name":"Huber, Stefan"},{"full_name":"Niethammer, Marc","first_name":"Marc","last_name":"Niethammer"},{"last_name":"Lin","first_name":"Weili","full_name":"Lin, Weili"},{"last_name":"Bauer","first_name":"Ulrich","orcid":"0000-0002-9683-0724","id":"2ADD483A-F248-11E8-B48F-1D18A9856A87","full_name":"Bauer, Ulrich"}],"status":"public","publication_status":"published","title":"Statistical topological data analysis-A kernel perspective","publisher":"Neural Information Processing Systems","department":[{"_id":"HeEd"}],"intvolume":" 28","_id":"1424","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"This work was partially supported by the Austrian Science FUnd, project no. KLI 00012.","year":"2015","abstract":[{"text":"We consider the problem of statistical computations with persistence diagrams, a summary representation of topological features in data. These diagrams encode persistent homology, a widely used invariant in topological data analysis. While several avenues towards a statistical treatment of the diagrams have been explored recently, we follow an alternative route that is motivated by the success of methods based on the embedding of probability measures into reproducing kernel Hilbert spaces. In fact, a positive definite kernel on persistence diagrams has recently been proposed, connecting persistent homology to popular kernel-based learning techniques such as support vector machines. However, important properties of that kernel enabling a principled use in the context of probability measure embeddings remain to be explored. Our contribution is to close this gap by proving universality of a variant of the original kernel, and to demonstrate its effective use in twosample hypothesis testing on synthetic as well as real-world data.","lang":"eng"}],"publist_id":"5782","alternative_title":["Advances in Neural Information Processing Systems"],"type":"conference","language":[{"iso":"eng"}],"conference":{"end_date":"2015-12-12","location":"Montreal, Canada","start_date":"2015-12-07","name":"NIPS: Neural Information Processing Systems"},"date_published":"2015-12-01T00:00:00Z","quality_controlled":"1","page":"3070 - 3078","oa":1,"main_file_link":[{"url":"https://papers.nips.cc/paper/5887-statistical-topological-data-analysis-a-kernel-perspective","open_access":"1"}],"citation":{"mla":"Kwitt, Roland, et al. Statistical Topological Data Analysis-A Kernel Perspective. Vol. 28, Neural Information Processing Systems, 2015, pp. 3070–78.","short":"R. Kwitt, S. Huber, M. Niethammer, W. Lin, U. Bauer, in:, Neural Information Processing Systems, 2015, pp. 3070–3078.","chicago":"Kwitt, Roland, Stefan Huber, Marc Niethammer, Weili Lin, and Ulrich Bauer. “Statistical Topological Data Analysis-A Kernel Perspective,” 28:3070–78. Neural Information Processing Systems, 2015.","ama":"Kwitt R, Huber S, Niethammer M, Lin W, Bauer U. Statistical topological data analysis-A kernel perspective. In: Vol 28. Neural Information Processing Systems; 2015:3070-3078.","ista":"Kwitt R, Huber S, Niethammer M, Lin W, Bauer U. 2015. Statistical topological data analysis-A kernel perspective. NIPS: Neural Information Processing Systems, Advances in Neural Information Processing Systems, vol. 28, 3070–3078.","ieee":"R. Kwitt, S. Huber, M. Niethammer, W. Lin, and U. Bauer, “Statistical topological data analysis-A kernel perspective,” presented at the NIPS: Neural Information Processing Systems, Montreal, Canada, 2015, vol. 28, pp. 3070–3078.","apa":"Kwitt, R., Huber, S., Niethammer, M., Lin, W., & Bauer, U. (2015). Statistical topological data analysis-A kernel perspective (Vol. 28, pp. 3070–3078). Presented at the NIPS: Neural Information Processing Systems, Montreal, Canada: Neural Information Processing Systems."},"day":"01","month":"12"},{"_id":"1430","year":"2015","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","publication_status":"published","title":"First steps towards a runtime comparison of natural and artificial evolution","publisher":"ACM","department":[{"_id":"NiBa"},{"_id":"CaGu"}],"author":[{"full_name":"Paixao, Tiago","first_name":"Tiago","last_name":"Paixao","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2361-3953"},{"first_name":"Dirk","last_name":"Sudholt","full_name":"Sudholt, Dirk"},{"full_name":"Heredia, Jorge","last_name":"Heredia","first_name":"Jorge"},{"full_name":"Trubenova, Barbora","first_name":"Barbora","last_name":"Trubenova","id":"42302D54-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6873-2967"}],"date_updated":"2021-01-12T06:50:41Z","date_created":"2018-12-11T11:51:58Z","oa_version":"Preprint","type":"conference","abstract":[{"lang":"eng","text":"Evolutionary algorithms (EAs) form a popular optimisation paradigm inspired by natural evolution. In recent years the field of evolutionary computation has developed a rigorous analytical theory to analyse their runtime on many illustrative problems. Here we apply this theory to a simple model of natural evolution. In the Strong Selection Weak Mutation (SSWM) evolutionary regime the time between occurrence of new mutations is much longer than the time it takes for a new beneficial mutation to take over the population. In this situation, the population only contains copies of one genotype and evolution can be modelled as a (1+1)-type process where the probability of accepting a new genotype (improvements or worsenings) depends on the change in fitness. We present an initial runtime analysis of SSWM, quantifying its performance for various parameters and investigating differences to the (1+1) EA. We show that SSWM can have a moderate advantage over the (1+1) EA at crossing fitness valleys and study an example where SSWM outperforms the (1+1) EA by taking advantage of information on the fitness gradient."}],"ec_funded":1,"publist_id":"5768","publication":"Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation","citation":{"ista":"Paixao T, Sudholt D, Heredia J, Trubenova B. 2015. First steps towards a runtime comparison of natural and artificial evolution. Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation. GECCO: Genetic and evolutionary computation conference, 1455–1462.","apa":"Paixao, T., Sudholt, D., Heredia, J., & Trubenova, B. (2015). First steps towards a runtime comparison of natural and artificial evolution. In Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation (pp. 1455–1462). Madrid, Spain: ACM. https://doi.org/10.1145/2739480.2754758","ieee":"T. Paixao, D. Sudholt, J. Heredia, and B. Trubenova, “First steps towards a runtime comparison of natural and artificial evolution,” in Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation, Madrid, Spain, 2015, pp. 1455–1462.","ama":"Paixao T, Sudholt D, Heredia J, Trubenova B. First steps towards a runtime comparison of natural and artificial evolution. In: Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation. ACM; 2015:1455-1462. doi:10.1145/2739480.2754758","chicago":"Paixao, Tiago, Dirk Sudholt, Jorge Heredia, and Barbora Trubenova. “First Steps towards a Runtime Comparison of Natural and Artificial Evolution.” In Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation, 1455–62. ACM, 2015. https://doi.org/10.1145/2739480.2754758.","mla":"Paixao, Tiago, et al. “First Steps towards a Runtime Comparison of Natural and Artificial Evolution.” Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation, ACM, 2015, pp. 1455–62, doi:10.1145/2739480.2754758.","short":"T. Paixao, D. Sudholt, J. Heredia, B. Trubenova, in:, Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation, ACM, 2015, pp. 1455–1462."},"oa":1,"main_file_link":[{"url":"http://arxiv.org/abs/1504.06260","open_access":"1"}],"quality_controlled":"1","page":"1455 - 1462","project":[{"grant_number":"618091","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","call_identifier":"FP7"}],"conference":{"name":"GECCO: Genetic and evolutionary computation conference","end_date":"2015-07-15","start_date":"2015-07-11","location":"Madrid, Spain"},"doi":"10.1145/2739480.2754758","date_published":"2015-07-11T00:00:00Z","language":[{"iso":"eng"}],"scopus_import":1,"month":"07","day":"11"},{"author":[{"full_name":"Ferrara, Anna","first_name":"Anna","last_name":"Ferrara"},{"full_name":"Fuchsbauer, Georg","id":"46B4C3EE-F248-11E8-B48F-1D18A9856A87","last_name":"Fuchsbauer","first_name":"Georg"},{"full_name":"Liu, Bin","last_name":"Liu","first_name":"Bin"},{"last_name":"Warinschi","first_name":"Bogdan","full_name":"Warinschi, Bogdan"}],"oa_version":"Submitted Version","date_created":"2018-12-11T11:52:14Z","date_updated":"2021-01-12T06:50:59Z","_id":"1474","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2015","department":[{"_id":"KrPi"}],"publisher":"IEEE","publication_status":"published","status":"public","title":"Policy privacy in cryptographic access control","ec_funded":1,"publist_id":"5722","abstract":[{"lang":"eng","text":"Cryptographic access control offers selective access to encrypted data via a combination of key management and functionality-rich cryptographic schemes, such as attribute-based encryption. Using this approach, publicly available meta-data may inadvertently leak information on the access policy that is enforced by cryptography, which renders cryptographic access control unusable in settings where this information is highly sensitive. We begin to address this problem by presenting rigorous definitions for policy privacy in cryptographic access control. For concreteness we set our results in the model of Role-Based Access Control (RBAC), where we identify and formalize several different flavors of privacy, however, our framework should serve as inspiration for other models of access control. Based on our insights we propose a new system which significantly improves on the privacy properties of state-of-the-art constructions. Our design is based on a novel type of privacy-preserving attribute-based encryption, which we introduce and show how to instantiate. We present our results in the context of a cryptographic RBAC system by Ferrara et al. (CSF'13), which uses cryptography to control read access to files, while write access is still delegated to trusted monitors. We give an extension of the construction that permits cryptographic control over write access. Our construction assumes that key management uses out-of-band channels between the policy enforcer and the users but eliminates completely the need for monitoring read/write access to the data."}],"type":"conference","date_published":"2015-09-04T00:00:00Z","doi":"10.1109/CSF.2015.11","conference":{"name":"CSF: Computer Security Foundations","start_date":"2015-07-13","location":"Verona, Italy","end_date":"2015-07-17"},"language":[{"iso":"eng"}],"main_file_link":[{"url":"http://epubs.surrey.ac.uk/808055/","open_access":"1"}],"citation":{"ista":"Ferrara A, Fuchsbauer G, Liu B, Warinschi B. 2015. Policy privacy in cryptographic access control. CSF: Computer Security Foundations, 46–60.","ieee":"A. Ferrara, G. Fuchsbauer, B. Liu, and B. Warinschi, “Policy privacy in cryptographic access control,” presented at the CSF: Computer Security Foundations, Verona, Italy, 2015, pp. 46–60.","apa":"Ferrara, A., Fuchsbauer, G., Liu, B., & Warinschi, B. (2015). Policy privacy in cryptographic access control (pp. 46–60). Presented at the CSF: Computer Security Foundations, Verona, Italy: IEEE. https://doi.org/10.1109/CSF.2015.11","ama":"Ferrara A, Fuchsbauer G, Liu B, Warinschi B. Policy privacy in cryptographic access control. In: IEEE; 2015:46-60. doi:10.1109/CSF.2015.11","chicago":"Ferrara, Anna, Georg Fuchsbauer, Bin Liu, and Bogdan Warinschi. “Policy Privacy in Cryptographic Access Control,” 46–60. IEEE, 2015. https://doi.org/10.1109/CSF.2015.11.","mla":"Ferrara, Anna, et al. Policy Privacy in Cryptographic Access Control. IEEE, 2015, pp. 46–60, doi:10.1109/CSF.2015.11.","short":"A. Ferrara, G. Fuchsbauer, B. Liu, B. Warinschi, in:, IEEE, 2015, pp. 46–60."},"oa":1,"page":"46-60","project":[{"grant_number":"259668","_id":"258C570E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Provable Security for Physical Cryptography"}],"quality_controlled":"1","article_processing_charge":"No","month":"09","day":"04"},{"date_published":"2015-01-01T00:00:00Z","publication":"Asterisque","citation":{"mla":"Hausel, Tamás, and Fernando Rodríguez Villegas. “Cohomology of Large Semiprojective Hyperkähler Varieties.” Asterisque, vol. 2015, no. 370, Societe Mathematique de France, 2015, pp. 113–56.","short":"T. Hausel, F. Rodríguez Villegas, Asterisque 2015 (2015) 113–156.","chicago":"Hausel, Tamás, and Fernando Rodríguez Villegas. “Cohomology of Large Semiprojective Hyperkähler Varieties.” Asterisque. Societe Mathematique de France, 2015.","ama":"Hausel T, Rodríguez Villegas F. Cohomology of large semiprojective hyperkähler varieties. Asterisque. 2015;2015(370):113-156.","ista":"Hausel T, Rodríguez Villegas F. 2015. Cohomology of large semiprojective hyperkähler varieties. Asterisque. 2015(370), 113–156.","apa":"Hausel, T., & Rodríguez Villegas, F. (2015). Cohomology of large semiprojective hyperkähler varieties. Asterisque. Societe Mathematique de France.","ieee":"T. Hausel and F. Rodríguez Villegas, “Cohomology of large semiprojective hyperkähler varieties,” Asterisque, vol. 2015, no. 370. Societe Mathematique de France, pp. 113–156, 2015."},"oa":1,"main_file_link":[{"url":"http://arxiv.org/abs/1309.4914","open_access":"1"}],"quality_controlled":0,"page":"113 - 156","day":"01","month":"01","author":[{"full_name":"Tamas Hausel","first_name":"Tamas","last_name":"Hausel","id":"4A0666D8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Rodríguez Villegas","first_name":"Fernando","full_name":"Rodríguez Villegas, Fernando"}],"date_created":"2018-12-11T11:52:13Z","date_updated":"2021-01-12T06:50:59Z","volume":2015,"year":"2015","_id":"1473","status":"public","title":"Cohomology of large semiprojective hyperkähler varieties","publication_status":"published","intvolume":" 2015","publisher":"Societe Mathematique de France","abstract":[{"lang":"eng","text":"In this paper we survey geometric and arithmetic techniques to study the cohomology of semiprojective hyperkähler manifolds including toric hyperkähler varieties, Nakajima quiver varieties and moduli spaces of Higgs bundles on Riemann surfaces. The resulting formulae for their Poincaré polynomials are combinatorial and representation theoretical in nature. In particular we will look at their Betti numbers and will establish some results and state some expectations on their asymptotic shape."}],"issue":"370","publist_id":"5723","extern":1,"type":"review"},{"type":"conference","abstract":[{"lang":"eng","text":"Topological data analysis offers a rich source of valuable information to study vision problems. Yet, so far we lack a theoretically sound connection to popular kernel-based learning techniques, such as kernel SVMs or kernel PCA. In this work, we establish such a connection by designing a multi-scale kernel for persistence diagrams, a stable summary representation of topological features in data. We show that this kernel is positive definite and prove its stability with respect to the 1-Wasserstein distance. Experiments on two benchmark datasets for 3D shape classification/retrieval and texture recognition show considerable performance gains of the proposed method compared to an alternative approach that is based on the recently introduced persistence landscapes."}],"publist_id":"5709","_id":"1483","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2015","publication_status":"published","status":"public","title":"A stable multi-scale kernel for topological machine learning","publisher":"IEEE","department":[{"_id":"HeEd"}],"author":[{"full_name":"Reininghaus, Jan","last_name":"Reininghaus","first_name":"Jan","id":"4505473A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Huber","first_name":"Stefan","orcid":"0000-0002-8871-5814","id":"4700A070-F248-11E8-B48F-1D18A9856A87","full_name":"Huber, Stefan"},{"first_name":"Ulrich","last_name":"Bauer","id":"2ADD483A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9683-0724","full_name":"Bauer, Ulrich"},{"first_name":"Roland","last_name":"Kwitt","full_name":"Kwitt, Roland"}],"date_updated":"2021-01-12T06:51:03Z","date_created":"2018-12-11T11:52:17Z","oa_version":"Preprint","scopus_import":1,"day":"14","month":"10","publication_identifier":{"eisbn":["978-1-4673-6964-0 "]},"citation":{"ama":"Reininghaus J, Huber S, Bauer U, Kwitt R. A stable multi-scale kernel for topological machine learning. In: IEEE; 2015:4741-4748. doi:10.1109/CVPR.2015.7299106","ieee":"J. Reininghaus, S. Huber, U. Bauer, and R. Kwitt, “A stable multi-scale kernel for topological machine learning,” presented at the CVPR: Computer Vision and Pattern Recognition, Boston, MA, USA, 2015, pp. 4741–4748.","apa":"Reininghaus, J., Huber, S., Bauer, U., & Kwitt, R. (2015). A stable multi-scale kernel for topological machine learning (pp. 4741–4748). Presented at the CVPR: Computer Vision and Pattern Recognition, Boston, MA, USA: IEEE. https://doi.org/10.1109/CVPR.2015.7299106","ista":"Reininghaus J, Huber S, Bauer U, Kwitt R. 2015. A stable multi-scale kernel for topological machine learning. CVPR: Computer Vision and Pattern Recognition, 4741–4748.","short":"J. Reininghaus, S. Huber, U. Bauer, R. Kwitt, in:, IEEE, 2015, pp. 4741–4748.","mla":"Reininghaus, Jan, et al. A Stable Multi-Scale Kernel for Topological Machine Learning. IEEE, 2015, pp. 4741–48, doi:10.1109/CVPR.2015.7299106.","chicago":"Reininghaus, Jan, Stefan Huber, Ulrich Bauer, and Roland Kwitt. “A Stable Multi-Scale Kernel for Topological Machine Learning,” 4741–48. IEEE, 2015. https://doi.org/10.1109/CVPR.2015.7299106."},"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1412.6821"}],"oa":1,"page":"4741 - 4748","conference":{"name":"CVPR: Computer Vision and Pattern Recognition","end_date":"2015-06-12","start_date":"2015-06-07","location":"Boston, MA, USA"},"date_published":"2015-10-14T00:00:00Z","doi":"10.1109/CVPR.2015.7299106","language":[{"iso":"eng"}]},{"month":"01","publication_identifier":{"isbn":["978-3-939897-80-4 "]},"quality_controlled":"1","project":[{"call_identifier":"FP7","name":"Quantitative Reactive Modeling","grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425"},{"name":"Moderne Concurrency Paradigms","call_identifier":"FWF","_id":"25F5A88A-B435-11E9-9278-68D0E5697425","grant_number":"S11402-N23"},{"name":"The Wittgenstein Prize","call_identifier":"FWF","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"language":[{"iso":"eng"}],"conference":{"start_date":"2015-05-03","location":"Asilomar, CA, United States","end_date":"2015-05-06","name":"SNAPL: Summit oN Advances in Programming Languages"},"doi":"10.4230/LIPIcs.SNAPL.2015.90","file_date_updated":"2020-07-14T12:44:58Z","ec_funded":1,"publist_id":"5681","publication_status":"published","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","department":[{"_id":"ToHe"}],"year":"2015","date_created":"2018-12-11T11:52:22Z","date_updated":"2020-08-11T10:09:14Z","volume":32,"author":[{"id":"2B2B5ED0-F248-11E8-B48F-1D18A9856A87","last_name":"Dragoi","first_name":"Cezara","full_name":"Dragoi, Cezara"},{"full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","first_name":"Thomas A","last_name":"Henzinger"},{"full_name":"Zufferey, Damien","first_name":"Damien","last_name":"Zufferey","id":"4397AC76-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3197-8736"}],"series_title":"Leibniz International Proceedings in Informatics","scopus_import":1,"day":"01","has_accepted_license":"1","page":"90 - 102","citation":{"ama":"Dragoi C, Henzinger TA, Zufferey D. The need for language support for fault-tolerant distributed systems. 2015;32:90-102. doi:10.4230/LIPIcs.SNAPL.2015.90","ista":"Dragoi C, Henzinger TA, Zufferey D. 2015. The need for language support for fault-tolerant distributed systems. 32, 90–102.","apa":"Dragoi, C., Henzinger, T. A., & Zufferey, D. (2015). The need for language support for fault-tolerant distributed systems. Presented at the SNAPL: Summit oN Advances in Programming Languages, Asilomar, CA, United States: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.SNAPL.2015.90","ieee":"C. Dragoi, T. A. Henzinger, and D. Zufferey, “The need for language support for fault-tolerant distributed systems,” vol. 32. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, pp. 90–102, 2015.","mla":"Dragoi, Cezara, et al. The Need for Language Support for Fault-Tolerant Distributed Systems. Vol. 32, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015, pp. 90–102, doi:10.4230/LIPIcs.SNAPL.2015.90.","short":"C. Dragoi, T.A. Henzinger, D. Zufferey, 32 (2015) 90–102.","chicago":"Dragoi, Cezara, Thomas A Henzinger, and Damien Zufferey. “The Need for Language Support for Fault-Tolerant Distributed Systems.” Leibniz International Proceedings in Informatics. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015. https://doi.org/10.4230/LIPIcs.SNAPL.2015.90."},"date_published":"2015-01-01T00:00:00Z","alternative_title":["LIPIcs"],"type":"conference","abstract":[{"text":"Fault-tolerant distributed algorithms play an important role in many critical/high-availability applications. These algorithms are notoriously difficult to implement correctly, due to asynchronous communication and the occurrence of faults, such as the network dropping messages or computers crashing. Nonetheless there is surprisingly little language and verification support to build distributed systems based on fault-tolerant algorithms. In this paper, we present some of the challenges that a designer has to overcome to implement a fault-tolerant distributed system. Then we review different models that have been proposed to reason about distributed algorithms and sketch how such a model can form the basis for a domain-specific programming language. Adopting a high-level programming model can simplify the programmer's life and make the code amenable to automated verification, while still compiling to efficiently executable code. We conclude by summarizing the current status of an ongoing language design and implementation project that is based on this idea.","lang":"eng"}],"title":"The need for language support for fault-tolerant distributed systems","ddc":["005"],"status":"public","intvolume":" 32","_id":"1498","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"file_id":"5050","relation":"main_file","date_updated":"2020-07-14T12:44:58Z","date_created":"2018-12-12T10:14:02Z","checksum":"cf5e94baa89a2dc4c5de01abc676eda8","file_name":"IST-2016-499-v1+1_9.pdf","access_level":"open_access","creator":"system","content_type":"application/pdf","file_size":489362}],"pubrep_id":"499"},{"month":"07","quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"language":[{"iso":"eng"}],"doi":"10.1093/nar/gkv727","article_number":"e146","publist_id":"5682","file_date_updated":"2020-07-14T12:44:58Z","department":[{"_id":"GaNo"}],"publisher":"Oxford University Press","publication_status":"published","year":"2015","acknowledgement":"Austrian Science Fund [FWF P25185-B22, FWF F4302- B09, FWFW1207-B09]. Funding for open access charge: Austrian Science Fund.\r\nWe thank Florian Breitwieser for advice during the early stages of this project. High-throughput sequencing was conducted by the Biomedical Sequencing Facility (BSF) at CeMM in Vienna.","volume":43,"date_created":"2018-12-11T11:52:22Z","date_updated":"2021-01-12T06:51:09Z","author":[{"first_name":"Daniel","last_name":"Andergassen","full_name":"Andergassen, Daniel"},{"full_name":"Dotter, Christoph","first_name":"Christoph","last_name":"Dotter","id":"4C66542E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kulinski, Tomasz","first_name":"Tomasz","last_name":"Kulinski"},{"full_name":"Guenzl, Philipp","last_name":"Guenzl","first_name":"Philipp"},{"full_name":"Bammer, Philipp","last_name":"Bammer","first_name":"Philipp"},{"full_name":"Barlow, Denise","last_name":"Barlow","first_name":"Denise"},{"last_name":"Pauler","first_name":"Florian","full_name":"Pauler, Florian"},{"full_name":"Hudson, Quanah","last_name":"Hudson","first_name":"Quanah"}],"scopus_import":1,"has_accepted_license":"1","day":"21","citation":{"short":"D. Andergassen, C. Dotter, T. Kulinski, P. Guenzl, P. Bammer, D. Barlow, F. Pauler, Q. Hudson, Nucleic Acids Research 43 (2015).","mla":"Andergassen, Daniel, et al. “Allelome.PRO, a Pipeline to Define Allele-Specific Genomic Features from High-Throughput Sequencing Data.” Nucleic Acids Research, vol. 43, no. 21, e146, Oxford University Press, 2015, doi:10.1093/nar/gkv727.","chicago":"Andergassen, Daniel, Christoph Dotter, Tomasz Kulinski, Philipp Guenzl, Philipp Bammer, Denise Barlow, Florian Pauler, and Quanah Hudson. “Allelome.PRO, a Pipeline to Define Allele-Specific Genomic Features from High-Throughput Sequencing Data.” Nucleic Acids Research. Oxford University Press, 2015. https://doi.org/10.1093/nar/gkv727.","ama":"Andergassen D, Dotter C, Kulinski T, et al. Allelome.PRO, a pipeline to define allele-specific genomic features from high-throughput sequencing data. Nucleic Acids Research. 2015;43(21). doi:10.1093/nar/gkv727","ieee":"D. Andergassen et al., “Allelome.PRO, a pipeline to define allele-specific genomic features from high-throughput sequencing data,” Nucleic Acids Research, vol. 43, no. 21. Oxford University Press, 2015.","apa":"Andergassen, D., Dotter, C., Kulinski, T., Guenzl, P., Bammer, P., Barlow, D., … Hudson, Q. (2015). Allelome.PRO, a pipeline to define allele-specific genomic features from high-throughput sequencing data. Nucleic Acids Research. Oxford University Press. https://doi.org/10.1093/nar/gkv727","ista":"Andergassen D, Dotter C, Kulinski T, Guenzl P, Bammer P, Barlow D, Pauler F, Hudson Q. 2015. Allelome.PRO, a pipeline to define allele-specific genomic features from high-throughput sequencing data. Nucleic Acids Research. 43(21), e146."},"publication":"Nucleic Acids Research","date_published":"2015-07-21T00:00:00Z","type":"journal_article","issue":"21","abstract":[{"text":"Detecting allelic biases from high-throughput sequencing data requires an approach that maximises sensitivity while minimizing false positives. Here, we present Allelome.PRO, an automated user-friendly bioinformatics pipeline, which uses high-throughput sequencing data from reciprocal crosses of two genetically distinct mouse strains to detect allele-specific expression and chromatin modifications. Allelome.PRO extends approaches used in previous studies that exclusively analyzed imprinted expression to give a complete picture of the ‘allelome’ by automatically categorising the allelic expression of all genes in a given cell type into imprinted, strain-biased, biallelic or non-informative. Allelome.PRO offers increased sensitivity to analyze lowly expressed transcripts, together with a robust false discovery rate empirically calculated from variation in the sequencing data. We used RNA-seq data from mouse embryonic fibroblasts from F1 reciprocal crosses to determine a biologically relevant allelic ratio cutoff, and define for the first time an entire allelome. Furthermore, we show that Allelome.PRO detects differential enrichment of H3K4me3 over promoters from ChIP-seq data validating the RNA-seq results. This approach can be easily extended to analyze histone marks of active enhancers, or transcription factor binding sites and therefore provides a powerful tool to identify candidate cis regulatory elements genome wide.","lang":"eng"}],"intvolume":" 43","status":"public","title":"Allelome.PRO, a pipeline to define allele-specific genomic features from high-throughput sequencing data","ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1497","file":[{"file_name":"2015_NucleicAcidsRes_Andergassen.pdf","access_level":"open_access","content_type":"application/pdf","file_size":6863297,"creator":"dernst","relation":"main_file","file_id":"5768","date_updated":"2020-07-14T12:44:58Z","date_created":"2018-12-20T14:18:57Z","checksum":"385b83854fd0eb2e4f386867da2823e2"}],"oa_version":"Published Version"},{"doi":"10.4230/LIPIcs.CONCUR.2015.142","conference":{"name":"CONCUR: Concurrency Theory","start_date":"2015-09-01","location":"Madrid, Spain","end_date":"2015-09-04"},"language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"project":[{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989","call_identifier":"FP7","name":"Quantitative Reactive Modeling"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","call_identifier":"FWF"},{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"}],"quality_controlled":"1","month":"01","author":[{"last_name":"Kretinsky","first_name":"Jan","orcid":"0000-0002-8122-2881","id":"44CEF464-F248-11E8-B48F-1D18A9856A87","full_name":"Kretinsky, Jan"},{"full_name":"Larsen, Kim","last_name":"Larsen","first_name":"Kim"},{"full_name":"Laursen, Simon","last_name":"Laursen","first_name":"Simon"},{"last_name":"Srba","first_name":"Jiří","full_name":"Srba, Jiří"}],"volume":42,"date_updated":"2021-01-12T06:51:10Z","date_created":"2018-12-11T11:52:22Z","acknowledgement":"The research leading to these results has received funding from the European Union Seventh Framework Programme (FP7/2007-2013) under grant agreement 601148 (CASSTING), EU FP7 FET project SENSATION, Sino-Danish Basic Research Center IDAE4CPS, the European Research Council (ERC) under grant agreement 267989 (QUAREM), the Austrian Science Fund (FWF) project S11402-N23 (RiSE) and Z211-N23 (Wittgenstein Award), the Czech Science Foundation under grant agreement P202/12/G061, and People Programme (Marie Curie Actions) of the European Union’s Seventh Framework\r\nProgramme (FP7/2007-2013) REA Grant No 291734.","year":"2015","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"publication_status":"published","ec_funded":1,"publist_id":"5680","file_date_updated":"2020-07-14T12:44:58Z","date_published":"2015-01-01T00:00:00Z","citation":{"ama":"Kretinsky J, Larsen K, Laursen S, Srba J. Polynomial time decidability of weighted synchronization under partial observability. In: Vol 42. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2015:142-154. doi:10.4230/LIPIcs.CONCUR.2015.142","ieee":"J. Kretinsky, K. Larsen, S. Laursen, and J. Srba, “Polynomial time decidability of weighted synchronization under partial observability,” presented at the CONCUR: Concurrency Theory, Madrid, Spain, 2015, vol. 42, pp. 142–154.","apa":"Kretinsky, J., Larsen, K., Laursen, S., & Srba, J. (2015). Polynomial time decidability of weighted synchronization under partial observability (Vol. 42, pp. 142–154). Presented at the CONCUR: Concurrency Theory, Madrid, Spain: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.CONCUR.2015.142","ista":"Kretinsky J, Larsen K, Laursen S, Srba J. 2015. Polynomial time decidability of weighted synchronization under partial observability. CONCUR: Concurrency Theory, LIPIcs, vol. 42, 142–154.","short":"J. Kretinsky, K. Larsen, S. Laursen, J. Srba, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015, pp. 142–154.","mla":"Kretinsky, Jan, et al. Polynomial Time Decidability of Weighted Synchronization under Partial Observability. Vol. 42, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015, pp. 142–54, doi:10.4230/LIPIcs.CONCUR.2015.142.","chicago":"Kretinsky, Jan, Kim Larsen, Simon Laursen, and Jiří Srba. “Polynomial Time Decidability of Weighted Synchronization under Partial Observability,” 42:142–54. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015. https://doi.org/10.4230/LIPIcs.CONCUR.2015.142."},"page":"142 - 154","has_accepted_license":"1","day":"01","scopus_import":1,"pubrep_id":"498","oa_version":"Published Version","file":[{"date_updated":"2020-07-14T12:44:58Z","date_created":"2018-12-12T10:08:12Z","checksum":"49eb5021caafaabe5356c65b9c5f8c9c","relation":"main_file","file_id":"4672","file_size":623563,"content_type":"application/pdf","creator":"system","file_name":"IST-2016-498-v1+1_32.pdf","access_level":"open_access"}],"_id":"1499","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 42","status":"public","ddc":["000","003"],"title":"Polynomial time decidability of weighted synchronization under partial observability","abstract":[{"text":"We consider weighted automata with both positive and negative integer weights on edges and\r\nstudy the problem of synchronization using adaptive strategies that may only observe whether\r\nthe current weight-level is negative or nonnegative. We show that the synchronization problem is decidable in polynomial time for deterministic weighted automata.","lang":"eng"}],"type":"conference","alternative_title":["LIPIcs"]},{"type":"conference","abstract":[{"lang":"eng","text":"Motivated by biological questions, we study configurations of equal-sized disks in the Euclidean plane that neither pack nor cover. Measuring the quality by the probability that a random point lies in exactly one disk, we show that the regular hexagonal grid gives the maximum among lattice configurations. "}],"ec_funded":1,"publist_id":"5684","status":"public","publication_status":"published","title":"Relaxed disk packing","publisher":"Queen's University","department":[{"_id":"HeEd"}],"_id":"1495","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","year":"2015","date_updated":"2021-01-12T06:51:09Z","date_created":"2018-12-11T11:52:21Z","volume":"2015-August","oa_version":"Submitted Version","author":[{"last_name":"Edelsbrunner","first_name":"Herbert","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","full_name":"Edelsbrunner, Herbert"},{"first_name":"Mabel","last_name":"Iglesias Ham","id":"41B58C0C-F248-11E8-B48F-1D18A9856A87","full_name":"Iglesias Ham, Mabel"},{"full_name":"Kurlin, Vitaliy","first_name":"Vitaliy","last_name":"Kurlin"}],"scopus_import":1,"month":"08","day":"01","quality_controlled":"1","page":"128-135","project":[{"call_identifier":"FP7","name":"Topological Complex Systems","_id":"255D761E-B435-11E9-9278-68D0E5697425","grant_number":"318493"}],"publication":"Proceedings of the 27th Canadian Conference on Computational Geometry","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1505.03402"}],"oa":1,"citation":{"ama":"Edelsbrunner H, Iglesias Ham M, Kurlin V. Relaxed disk packing. In: Proceedings of the 27th Canadian Conference on Computational Geometry. Vol 2015-August. Queen’s University; 2015:128-135.","apa":"Edelsbrunner, H., Iglesias Ham, M., & Kurlin, V. (2015). Relaxed disk packing. In Proceedings of the 27th Canadian Conference on Computational Geometry (Vol. 2015–August, pp. 128–135). Ontario, Canada: Queen’s University.","ieee":"H. Edelsbrunner, M. Iglesias Ham, and V. Kurlin, “Relaxed disk packing,” in Proceedings of the 27th Canadian Conference on Computational Geometry, Ontario, Canada, 2015, vol. 2015–August, pp. 128–135.","ista":"Edelsbrunner H, Iglesias Ham M, Kurlin V. 2015. Relaxed disk packing. Proceedings of the 27th Canadian Conference on Computational Geometry. CCCG: Canadian Conference on Computational Geometry vol. 2015–August, 128–135.","short":"H. Edelsbrunner, M. Iglesias Ham, V. Kurlin, in:, Proceedings of the 27th Canadian Conference on Computational Geometry, Queen’s University, 2015, pp. 128–135.","mla":"Edelsbrunner, Herbert, et al. “Relaxed Disk Packing.” Proceedings of the 27th Canadian Conference on Computational Geometry, vol. 2015–August, Queen’s University, 2015, pp. 128–35.","chicago":"Edelsbrunner, Herbert, Mabel Iglesias Ham, and Vitaliy Kurlin. “Relaxed Disk Packing.” In Proceedings of the 27th Canadian Conference on Computational Geometry, 2015–August:128–35. Queen’s University, 2015."},"language":[{"iso":"eng"}],"conference":{"end_date":"2015-08-12","start_date":"2015-08-10","location":"Ontario, Canada","name":"CCCG: Canadian Conference on Computational Geometry"},"date_published":"2015-08-01T00:00:00Z"},{"author":[{"full_name":"Bao, Zhigang","orcid":"0000-0003-3036-1475","id":"442E6A6C-F248-11E8-B48F-1D18A9856A87","last_name":"Bao","first_name":"Zhigang"},{"last_name":"Lin","first_name":"Liang","full_name":"Lin, Liang"},{"last_name":"Pan","first_name":"Guangming","full_name":"Pan, Guangming"},{"last_name":"Zhou","first_name":"Wang","full_name":"Zhou, Wang"}],"volume":43,"oa_version":"Published Version","date_updated":"2021-01-12T06:51:14Z","date_created":"2018-12-11T11:52:24Z","_id":"1504","year":"2015","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 43","publisher":"Institute of Mathematical Statistics","status":"public","title":"Spectral statistics of large dimensional spearman s rank correlation matrix and its application","publication_status":"published","publist_id":"5674","issue":"6","abstract":[{"text":"Let Q = (Q1, . . . , Qn) be a random vector drawn from the uniform distribution on the set of all n! permutations of {1, 2, . . . , n}. Let Z = (Z1, . . . , Zn), where Zj is the mean zero variance one random variable obtained by centralizing and normalizing Qj , j = 1, . . . , n. Assume that Xi , i = 1, . . . ,p are i.i.d. copies of 1/√ p Z and X = Xp,n is the p × n random matrix with Xi as its ith row. Then Sn = XX is called the p × n Spearman's rank correlation matrix which can be regarded as a high dimensional extension of the classical nonparametric statistic Spearman's rank correlation coefficient between two independent random variables. In this paper, we establish a CLT for the linear spectral statistics of this nonparametric random matrix model in the scenario of high dimension, namely, p = p(n) and p/n→c ∈ (0,∞) as n→∞.We propose a novel evaluation scheme to estimate the core quantity in Anderson and Zeitouni's cumulant method in [Ann. Statist. 36 (2008) 2553-2576] to bypass the so-called joint cumulant summability. In addition, we raise a two-step comparison approach to obtain the explicit formulae for the mean and covariance functions in the CLT. Relying on this CLT, we then construct a distribution-free statistic to test complete independence for components of random vectors. Owing to the nonparametric property, we can use this test on generally distributed random variables including the heavy-tailed ones.","lang":"eng"}],"extern":"1","type":"journal_article","doi":"10.1214/15-AOS1353","date_published":"2015-12-01T00:00:00Z","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1312.5119"}],"citation":{"short":"Z. Bao, L. Lin, G. Pan, W. Zhou, Annals of Statistics 43 (2015) 2588–2623.","mla":"Bao, Zhigang, et al. “Spectral Statistics of Large Dimensional Spearman s Rank Correlation Matrix and Its Application.” Annals of Statistics, vol. 43, no. 6, Institute of Mathematical Statistics, 2015, pp. 2588–623, doi:10.1214/15-AOS1353.","chicago":"Bao, Zhigang, Liang Lin, Guangming Pan, and Wang Zhou. “Spectral Statistics of Large Dimensional Spearman s Rank Correlation Matrix and Its Application.” Annals of Statistics. Institute of Mathematical Statistics, 2015. https://doi.org/10.1214/15-AOS1353.","ama":"Bao Z, Lin L, Pan G, Zhou W. Spectral statistics of large dimensional spearman s rank correlation matrix and its application. Annals of Statistics. 2015;43(6):2588-2623. doi:10.1214/15-AOS1353","apa":"Bao, Z., Lin, L., Pan, G., & Zhou, W. (2015). Spectral statistics of large dimensional spearman s rank correlation matrix and its application. Annals of Statistics. Institute of Mathematical Statistics. https://doi.org/10.1214/15-AOS1353","ieee":"Z. Bao, L. Lin, G. Pan, and W. Zhou, “Spectral statistics of large dimensional spearman s rank correlation matrix and its application,” Annals of Statistics, vol. 43, no. 6. Institute of Mathematical Statistics, pp. 2588–2623, 2015.","ista":"Bao Z, Lin L, Pan G, Zhou W. 2015. Spectral statistics of large dimensional spearman s rank correlation matrix and its application. Annals of Statistics. 43(6), 2588–2623."},"publication":"Annals of Statistics","page":"2588 - 2623","quality_controlled":"1","month":"12","day":"01"},{"author":[{"last_name":"Sadel","first_name":"Christian","orcid":"0000-0001-8255-3968","id":"4760E9F8-F248-11E8-B48F-1D18A9856A87","full_name":"Sadel, Christian"}],"date_created":"2018-12-11T11:52:24Z","date_updated":"2021-01-12T06:51:13Z","volume":35,"oa_version":"Preprint","year":"2015","_id":"1503","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"A Herman-Avila-Bochi formula for higher-dimensional pseudo-unitary and Hermitian-symplectic-cocycles","publication_status":"published","status":"public","intvolume":" 35","publisher":"Cambridge University Press","abstract":[{"text":"A Herman-Avila-Bochi type formula is obtained for the average sum of the top d Lyapunov exponents over a one-parameter family of double-struck G-cocycles, where double-struck G is the group that leaves a certain, non-degenerate Hermitian form of signature (c, d) invariant. The generic example of such a group is the pseudo-unitary group U(c, d) or, in the case c = d, the Hermitian-symplectic group HSp(2d) which naturally appears for cocycles related to Schrödinger operators. In the case d = 1, the formula for HSp(2d) cocycles reduces to the Herman-Avila-Bochi formula for SL(2, ℝ) cocycles.","lang":"eng"}],"issue":"5","publist_id":"5675","extern":"1","type":"journal_article","date_published":"2015-03-14T00:00:00Z","doi":"10.1017/etds.2013.103","language":[{"iso":"eng"}],"publication":"Ergodic Theory and Dynamical Systems","oa":1,"citation":{"ama":"Sadel C. A Herman-Avila-Bochi formula for higher-dimensional pseudo-unitary and Hermitian-symplectic-cocycles. Ergodic Theory and Dynamical Systems. 2015;35(5):1582-1591. doi:10.1017/etds.2013.103","ieee":"C. Sadel, “A Herman-Avila-Bochi formula for higher-dimensional pseudo-unitary and Hermitian-symplectic-cocycles,” Ergodic Theory and Dynamical Systems, vol. 35, no. 5. Cambridge University Press, pp. 1582–1591, 2015.","apa":"Sadel, C. (2015). A Herman-Avila-Bochi formula for higher-dimensional pseudo-unitary and Hermitian-symplectic-cocycles. Ergodic Theory and Dynamical Systems. Cambridge University Press. https://doi.org/10.1017/etds.2013.103","ista":"Sadel C. 2015. A Herman-Avila-Bochi formula for higher-dimensional pseudo-unitary and Hermitian-symplectic-cocycles. Ergodic Theory and Dynamical Systems. 35(5), 1582–1591.","short":"C. Sadel, Ergodic Theory and Dynamical Systems 35 (2015) 1582–1591.","mla":"Sadel, Christian. “A Herman-Avila-Bochi Formula for Higher-Dimensional Pseudo-Unitary and Hermitian-Symplectic-Cocycles.” Ergodic Theory and Dynamical Systems, vol. 35, no. 5, Cambridge University Press, 2015, pp. 1582–91, doi:10.1017/etds.2013.103.","chicago":"Sadel, Christian. “A Herman-Avila-Bochi Formula for Higher-Dimensional Pseudo-Unitary and Hermitian-Symplectic-Cocycles.” Ergodic Theory and Dynamical Systems. Cambridge University Press, 2015. https://doi.org/10.1017/etds.2013.103."},"main_file_link":[{"url":"https://arxiv.org/abs/1307.8414","open_access":"1"}],"quality_controlled":"1","page":"1582 - 1591","month":"03","day":"14"},{"pubrep_id":"503","oa_version":"Published Version","file":[{"checksum":"49eb5021caafaabe5356c65b9c5f8c9c","date_updated":"2020-07-14T12:44:59Z","date_created":"2018-12-12T10:13:19Z","relation":"main_file","file_id":"5001","content_type":"application/pdf","file_size":623563,"creator":"system","access_level":"open_access","file_name":"IST-2016-503-v1+1_32.pdf"}],"_id":"1510","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 34","title":"On computability and triviality of well groups","ddc":["510"],"status":"public","abstract":[{"lang":"eng","text":"The concept of well group in a special but important case captures homological properties of the zero set of a continuous map f from K to R^n on a compact space K that are invariant with respect to perturbations of f. The perturbations are arbitrary continuous maps within L_infty distance r from f for a given r > 0. The main drawback of the approach is that the computability of well groups was shown only when dim K = n or n = 1. Our contribution to the theory of well groups is twofold: on the one hand we improve on the computability issue, but on the other hand we present a range of examples where the well groups are incomplete invariants, that is, fail to capture certain important robust properties of the zero set. For the first part, we identify a computable subgroup of the well group that is obtained by cap product with the pullback of the orientation of R^n by f. In other words, well groups can be algorithmically approximated from below. When f is smooth and dim K < 2n-2, our approximation of the (dim K-n)th well group is exact. For the second part, we find examples of maps f, f' from K to R^n with all well groups isomorphic but whose perturbations have different zero sets. We discuss on a possible replacement of the well groups of vector valued maps by an invariant of a better descriptive power and computability status. "}],"type":"conference","alternative_title":["LIPIcs"],"date_published":"2015-06-11T00:00:00Z","citation":{"ieee":"P. Franek and M. Krcál, “On computability and triviality of well groups,” presented at the SoCG: Symposium on Computational Geometry, Eindhoven, Netherlands, 2015, vol. 34, pp. 842–856.","apa":"Franek, P., & Krcál, M. (2015). On computability and triviality of well groups (Vol. 34, pp. 842–856). Presented at the SoCG: Symposium on Computational Geometry, Eindhoven, Netherlands: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.SOCG.2015.842","ista":"Franek P, Krcál M. 2015. On computability and triviality of well groups. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 34, 842–856.","ama":"Franek P, Krcál M. On computability and triviality of well groups. In: Vol 34. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2015:842-856. doi:10.4230/LIPIcs.SOCG.2015.842","chicago":"Franek, Peter, and Marek Krcál. “On Computability and Triviality of Well Groups,” 34:842–56. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015. https://doi.org/10.4230/LIPIcs.SOCG.2015.842.","short":"P. Franek, M. Krcál, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015, pp. 842–856.","mla":"Franek, Peter, and Marek Krcál. On Computability and Triviality of Well Groups. Vol. 34, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015, pp. 842–56, doi:10.4230/LIPIcs.SOCG.2015.842."},"page":"842 - 856","has_accepted_license":"1","day":"11","scopus_import":1,"related_material":{"record":[{"id":"1408","relation":"later_version","status":"public"}]},"author":[{"full_name":"Franek, Peter","id":"473294AE-F248-11E8-B48F-1D18A9856A87","first_name":"Peter","last_name":"Franek"},{"id":"33E21118-F248-11E8-B48F-1D18A9856A87","last_name":"Krcál","first_name":"Marek","full_name":"Krcál, Marek"}],"volume":34,"date_created":"2018-12-11T11:52:26Z","date_updated":"2023-02-21T17:02:57Z","year":"2015","department":[{"_id":"UlWa"},{"_id":"HeEd"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","publication_status":"published","ec_funded":1,"publist_id":"5667","file_date_updated":"2020-07-14T12:44:59Z","doi":"10.4230/LIPIcs.SOCG.2015.842","conference":{"start_date":"2015-06-22","location":"Eindhoven, Netherlands","end_date":"2015-06-25","name":"SoCG: Symposium on Computational Geometry"},"language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}],"quality_controlled":"1","month":"06"},{"doi":"10.1214/14-AOS1281","date_published":"2015-02-01T00:00:00Z","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1304.5690"}],"oa":1,"citation":{"short":"Z. Bao, G. Pan, W. Zhou, Annals of Statistics 43 (2015) 382–421.","mla":"Bao, Zhigang, et al. “Universality for the Largest Eigenvalue of Sample Covariance Matrices with General Population.” Annals of Statistics, vol. 43, no. 1, Institute of Mathematical Statistics, 2015, pp. 382–421, doi:10.1214/14-AOS1281.","chicago":"Bao, Zhigang, Guangming Pan, and Wang Zhou. “Universality for the Largest Eigenvalue of Sample Covariance Matrices with General Population.” Annals of Statistics. Institute of Mathematical Statistics, 2015. https://doi.org/10.1214/14-AOS1281.","ama":"Bao Z, Pan G, Zhou W. Universality for the largest eigenvalue of sample covariance matrices with general population. Annals of Statistics. 2015;43(1):382-421. doi:10.1214/14-AOS1281","ieee":"Z. Bao, G. Pan, and W. Zhou, “Universality for the largest eigenvalue of sample covariance matrices with general population,” Annals of Statistics, vol. 43, no. 1. Institute of Mathematical Statistics, pp. 382–421, 2015.","apa":"Bao, Z., Pan, G., & Zhou, W. (2015). Universality for the largest eigenvalue of sample covariance matrices with general population. Annals of Statistics. Institute of Mathematical Statistics. https://doi.org/10.1214/14-AOS1281","ista":"Bao Z, Pan G, Zhou W. 2015. Universality for the largest eigenvalue of sample covariance matrices with general population. Annals of Statistics. 43(1), 382–421."},"publication":"Annals of Statistics","page":"382 - 421","quality_controlled":"1","month":"02","day":"01","author":[{"full_name":"Bao, Zhigang","first_name":"Zhigang","last_name":"Bao","id":"442E6A6C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3036-1475"},{"full_name":"Pan, Guangming","first_name":"Guangming","last_name":"Pan"},{"full_name":"Zhou, Wang","first_name":"Wang","last_name":"Zhou"}],"oa_version":"Preprint","volume":43,"date_created":"2018-12-11T11:52:25Z","date_updated":"2021-01-12T06:51:14Z","_id":"1505","acknowledgement":"B.Z. was supported in part by NSFC Grant 11071213, ZJNSF Grant R6090034 and SRFDP Grant 20100101110001. P.G. was supported in part by the Ministry of Education, Singapore, under Grant ARC 14/11. Z.W. was supported in part by the Ministry of Education, Singapore, under Grant ARC 14/11, and by a Grant R-155-000-131-112 at the National University of Singapore\r\n","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2015","publisher":"Institute of Mathematical Statistics","department":[{"_id":"LaEr"}],"intvolume":" 43","title":"Universality for the largest eigenvalue of sample covariance matrices with general population","publication_status":"published","status":"public","publist_id":"5672","issue":"1","abstract":[{"lang":"eng","text":"This paper is aimed at deriving the universality of the largest eigenvalue of a class of high-dimensional real or complex sample covariance matrices of the form W N =Σ 1/2XX∗Σ 1/2 . Here, X = (xij )M,N is an M× N random matrix with independent entries xij , 1 ≤ i M,≤ 1 ≤ j ≤ N such that Exij = 0, E|xij |2 = 1/N . On dimensionality, we assume that M = M(N) and N/M → d ε (0, ∞) as N ∞→. For a class of general deterministic positive-definite M × M matrices Σ , under some additional assumptions on the distribution of xij 's, we show that the limiting behavior of the largest eigenvalue of W N is universal, via pursuing a Green function comparison strategy raised in [Probab. Theory Related Fields 154 (2012) 341-407, Adv. Math. 229 (2012) 1435-1515] by Erd″os, Yau and Yin for Wigner matrices and extended by Pillai and Yin [Ann. Appl. Probab. 24 (2014) 935-1001] to sample covariance matrices in the null case (&Epsi = I ). Consequently, in the standard complex case (Ex2 ij = 0), combing this universality property and the results known for Gaussian matrices obtained by El Karoui in [Ann. Probab. 35 (2007) 663-714] (nonsingular case) and Onatski in [Ann. Appl. Probab. 18 (2008) 470-490] (singular case), we show that after an appropriate normalization the largest eigenvalue of W N converges weakly to the type 2 Tracy-Widom distribution TW2 . Moreover, in the real case, we show that whenΣ is spiked with a fixed number of subcritical spikes, the type 1 Tracy-Widom limit TW1 holds for the normalized largest eigenvalue of W N , which extends a result of Féral and Péché in [J. Math. Phys. 50 (2009) 073302] to the scenario of nondiagonal Σ and more generally distributed X . In summary, we establish the Tracy-Widom type universality for the largest eigenvalue of generally distributed sample covariance matrices under quite light assumptions on &Sigma . Applications of these limiting results to statistical signal detection and structure recognition of separable covariance matrices are also discussed."}],"type":"journal_article"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1508","year":"2015","department":[{"_id":"LaEr"}],"intvolume":" 17","publisher":"European Mathematical Society","publication_status":"published","status":"public","title":"Gap universality of generalized Wigner and β ensembles","author":[{"full_name":"Erdös, László","orcid":"0000-0001-5366-9603","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","last_name":"Erdös","first_name":"László"},{"first_name":"Horng","last_name":"Yau","full_name":"Yau, Horng"}],"oa_version":"Preprint","volume":17,"date_created":"2018-12-11T11:52:26Z","date_updated":"2021-01-12T06:51:15Z","type":"journal_article","publist_id":"5669","issue":"8","abstract":[{"text":"We consider generalized Wigner ensembles and general β-ensembles with analytic potentials for any β ≥ 1. The recent universality results in particular assert that the local averages of consecutive eigenvalue gaps in the bulk of the spectrum are universal in the sense that they coincide with those of the corresponding Gaussian β-ensembles. In this article, we show that local averaging is not necessary for this result, i.e. we prove that the single gap distributions in the bulk are universal. In fact, with an additional step, our result can be extended to any C4(ℝ) potential.","lang":"eng"}],"citation":{"mla":"Erdös, László, and Horng Yau. “Gap Universality of Generalized Wigner and β Ensembles.” Journal of the European Mathematical Society, vol. 17, no. 8, European Mathematical Society, 2015, pp. 1927–2036, doi:10.4171/JEMS/548.","short":"L. Erdös, H. Yau, Journal of the European Mathematical Society 17 (2015) 1927–2036.","chicago":"Erdös, László, and Horng Yau. “Gap Universality of Generalized Wigner and β Ensembles.” Journal of the European Mathematical Society. European Mathematical Society, 2015. https://doi.org/10.4171/JEMS/548.","ama":"Erdös L, Yau H. Gap universality of generalized Wigner and β ensembles. Journal of the European Mathematical Society. 2015;17(8):1927-2036. doi:10.4171/JEMS/548","ista":"Erdös L, Yau H. 2015. Gap universality of generalized Wigner and β ensembles. Journal of the European Mathematical Society. 17(8), 1927–2036.","apa":"Erdös, L., & Yau, H. (2015). Gap universality of generalized Wigner and β ensembles. Journal of the European Mathematical Society. European Mathematical Society. https://doi.org/10.4171/JEMS/548","ieee":"L. Erdös and H. Yau, “Gap universality of generalized Wigner and β ensembles,” Journal of the European Mathematical Society, vol. 17, no. 8. European Mathematical Society, pp. 1927–2036, 2015."},"oa":1,"main_file_link":[{"url":"http://arxiv.org/abs/1211.3786","open_access":"1"}],"publication":"Journal of the European Mathematical Society","page":"1927 - 2036","quality_controlled":"1","doi":"10.4171/JEMS/548","date_published":"2015-08-01T00:00:00Z","language":[{"iso":"eng"}],"scopus_import":1,"day":"01","month":"08"},{"language":[{"iso":"eng"}],"date_published":"2015-08-01T00:00:00Z","doi":"10.3150/14-BEJ615","page":"1600 - 1628","quality_controlled":"1","main_file_link":[{"url":"http://arxiv.org/abs/1208.5823","open_access":"1"}],"citation":{"ama":"Bao Z, Pan G, Zhou W. The logarithmic law of random determinant. Bernoulli. 2015;21(3):1600-1628. doi:10.3150/14-BEJ615","apa":"Bao, Z., Pan, G., & Zhou, W. (2015). The logarithmic law of random determinant. Bernoulli. Bernoulli Society for Mathematical Statistics and Probability. https://doi.org/10.3150/14-BEJ615","ieee":"Z. Bao, G. Pan, and W. Zhou, “The logarithmic law of random determinant,” Bernoulli, vol. 21, no. 3. Bernoulli Society for Mathematical Statistics and Probability, pp. 1600–1628, 2015.","ista":"Bao Z, Pan G, Zhou W. 2015. The logarithmic law of random determinant. Bernoulli. 21(3), 1600–1628.","short":"Z. Bao, G. Pan, W. Zhou, Bernoulli 21 (2015) 1600–1628.","mla":"Bao, Zhigang, et al. “The Logarithmic Law of Random Determinant.” Bernoulli, vol. 21, no. 3, Bernoulli Society for Mathematical Statistics and Probability, 2015, pp. 1600–28, doi:10.3150/14-BEJ615.","chicago":"Bao, Zhigang, Guangming Pan, and Wang Zhou. “The Logarithmic Law of Random Determinant.” Bernoulli. Bernoulli Society for Mathematical Statistics and Probability, 2015. https://doi.org/10.3150/14-BEJ615."},"oa":1,"publication":"Bernoulli","day":"01","month":"08","volume":21,"oa_version":"Preprint","date_updated":"2021-01-12T06:51:14Z","date_created":"2018-12-11T11:52:25Z","author":[{"full_name":"Bao, Zhigang","id":"442E6A6C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3036-1475","first_name":"Zhigang","last_name":"Bao"},{"first_name":"Guangming","last_name":"Pan","full_name":"Pan, Guangming"},{"last_name":"Zhou","first_name":"Wang","full_name":"Zhou, Wang"}],"department":[{"_id":"LaEr"}],"publisher":"Bernoulli Society for Mathematical Statistics and Probability","intvolume":" 21","title":"The logarithmic law of random determinant","status":"public","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1506","year":"2015","publist_id":"5671","issue":"3","abstract":[{"lang":"eng","text":"Consider the square random matrix An = (aij)n,n, where {aij:= a(n)ij , i, j = 1, . . . , n} is a collection of independent real random variables with means zero and variances one. Under the additional moment condition supn max1≤i,j ≤n Ea4ij <∞, we prove Girko's logarithmic law of det An in the sense that as n→∞ log | detAn| ? (1/2) log(n-1)! d/→√(1/2) log n N(0, 1)."}],"type":"journal_article"},{"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":"1","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"}],"doi":"10.1093/gbe/evv215","language":[{"iso":"eng"}],"month":"12","year":"2015","publication_status":"published","publisher":"Oxford University Press","department":[{"_id":"BeVi"}],"author":[{"first_name":"Arka","last_name":"Pal","id":"6AAB2240-CA9A-11E9-9C1A-D9D1E5697425","full_name":"Pal, Arka"},{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","first_name":"Beatriz","last_name":"Vicoso","full_name":"Vicoso, Beatriz"}],"date_created":"2018-12-11T11:52:27Z","date_updated":"2021-01-12T06:51:18Z","volume":7,"file_date_updated":"2020-07-14T12:45:00Z","publist_id":"5664","ec_funded":1,"publication":"Genome Biology and Evolution","citation":{"ama":"Pal A, Vicoso B. The X chromosome of hemipteran insects: Conservation, dosage compensation and sex-biased expression. Genome Biology and Evolution. 2015;7(12):3259-3268. doi:10.1093/gbe/evv215","ieee":"A. Pal and B. Vicoso, “The X chromosome of hemipteran insects: Conservation, dosage compensation and sex-biased expression,” Genome Biology and Evolution, vol. 7, no. 12. Oxford University Press, pp. 3259–3268, 2015.","apa":"Pal, A., & Vicoso, B. (2015). The X chromosome of hemipteran insects: Conservation, dosage compensation and sex-biased expression. Genome Biology and Evolution. Oxford University Press. https://doi.org/10.1093/gbe/evv215","ista":"Pal A, Vicoso B. 2015. The X chromosome of hemipteran insects: Conservation, dosage compensation and sex-biased expression. Genome Biology and Evolution. 7(12), 3259–3268.","short":"A. Pal, B. Vicoso, Genome Biology and Evolution 7 (2015) 3259–3268.","mla":"Pal, Arka, and Beatriz Vicoso. “The X Chromosome of Hemipteran Insects: Conservation, Dosage Compensation and Sex-Biased Expression.” Genome Biology and Evolution, vol. 7, no. 12, Oxford University Press, 2015, pp. 3259–68, doi:10.1093/gbe/evv215.","chicago":"Pal, Arka, and Beatriz Vicoso. “The X Chromosome of Hemipteran Insects: Conservation, Dosage Compensation and Sex-Biased Expression.” Genome Biology and Evolution. Oxford University Press, 2015. https://doi.org/10.1093/gbe/evv215."},"page":"3259 - 3268","date_published":"2015-12-01T00:00:00Z","scopus_import":1,"day":"01","has_accepted_license":"1","article_processing_charge":"No","_id":"1513","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"title":"The X chromosome of hemipteran insects: Conservation, dosage compensation and sex-biased expression","status":"public","intvolume":" 7","pubrep_id":"496","file":[{"content_type":"application/pdf","file_size":858027,"creator":"system","file_name":"IST-2016-496-v1+1_Genome_Biol_Evol-2015-Pal-3259-68.pdf","access_level":"open_access","date_updated":"2020-07-14T12:45:00Z","date_created":"2018-12-12T10:17:29Z","checksum":"2b56b8c2e2a1d4cc3c9cb8daba26dd9b","relation":"main_file","file_id":"5284"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"Insects of the order Hemiptera (true bugs) use a wide range of mechanisms of sex determination, including genetic sex determination, paternal genome elimination, and haplodiploidy. Genetic sex determination, the prevalent mode, is generally controlled by a pair of XY sex chromosomes or by an XX/X0 system, but different configurations that include additional sex chromosomes are also present. Although this diversity of sex determining systems has been extensively studied at the cytogenetic level, only the X chromosome of the model pea aphid Acyrthosiphon pisum has been analyzed at the genomic level, and little is known about X chromosome biology in the rest of the order.\r\n\r\nIn this study, we take advantage of published DNA- and RNA-seq data from three additional Hemiptera species to perform a comparative analysis of the gene content and expression of the X chromosome throughout this clade. We find that, despite showing evidence of dosage compensation, the X chromosomes of these species show female-biased expression, and a deficit of male-biased genes, in direct contrast to the pea aphid X. We further detect an excess of shared gene content between these very distant species, suggesting that despite the diversity of sex determining systems, the same chromosomal element is used as the X throughout a large portion of the order. "}],"issue":"12"},{"author":[{"first_name":"Matthias","last_name":"Erbar","full_name":"Erbar, Matthias"},{"id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0845-1338","first_name":"Jan","last_name":"Maas","full_name":"Maas, Jan"},{"full_name":"Renger, Michiel","first_name":"Michiel","last_name":"Renger"}],"volume":20,"date_created":"2018-12-11T11:52:29Z","date_updated":"2021-01-12T06:51:19Z","year":"2015","department":[{"_id":"JaMa"}],"publisher":"Institute of Mathematical Statistics","publication_status":"published","publist_id":"5660","file_date_updated":"2020-07-14T12:45:00Z","article_number":"89","doi":"10.1214/ECP.v20-4315","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":"1","month":"11","pubrep_id":"494","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"4828","checksum":"135741c17d3e1547ca696b6fbdcd559c","date_updated":"2020-07-14T12:45:00Z","date_created":"2018-12-12T10:10:39Z","access_level":"open_access","file_name":"IST-2016-494-v1+1_4315-23820-1-PB.pdf","content_type":"application/pdf","file_size":230525,"creator":"system"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1517","intvolume":" 20","ddc":["519"],"title":"From large deviations to Wasserstein gradient flows in multiple dimensions","status":"public","abstract":[{"lang":"eng","text":"We study the large deviation rate functional for the empirical distribution of independent Brownian particles with drift. In one dimension, it has been shown by Adams, Dirr, Peletier and Zimmer that this functional is asymptotically equivalent (in the sense of Γ-convergence) to the Jordan-Kinderlehrer-Otto functional arising in the Wasserstein gradient flow structure of the Fokker-Planck equation. In higher dimensions, part of this statement (the lower bound) has been recently proved by Duong, Laschos and Renger, but the upper bound remained open, since the proof of Duong et al relies on regularity properties of optimal transport maps that are restricted to one dimension. In this note we present a new proof of the upper bound, thereby generalising the result of Adams et al to arbitrary dimensions.\r\n"}],"type":"journal_article","date_published":"2015-11-29T00:00:00Z","citation":{"ama":"Erbar M, Maas J, Renger M. From large deviations to Wasserstein gradient flows in multiple dimensions. Electronic Communications in Probability. 2015;20. doi:10.1214/ECP.v20-4315","ista":"Erbar M, Maas J, Renger M. 2015. From large deviations to Wasserstein gradient flows in multiple dimensions. Electronic Communications in Probability. 20, 89.","apa":"Erbar, M., Maas, J., & Renger, M. (2015). From large deviations to Wasserstein gradient flows in multiple dimensions. Electronic Communications in Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/ECP.v20-4315","ieee":"M. Erbar, J. Maas, and M. Renger, “From large deviations to Wasserstein gradient flows in multiple dimensions,” Electronic Communications in Probability, vol. 20. Institute of Mathematical Statistics, 2015.","mla":"Erbar, Matthias, et al. “From Large Deviations to Wasserstein Gradient Flows in Multiple Dimensions.” Electronic Communications in Probability, vol. 20, 89, Institute of Mathematical Statistics, 2015, doi:10.1214/ECP.v20-4315.","short":"M. Erbar, J. Maas, M. Renger, Electronic Communications in Probability 20 (2015).","chicago":"Erbar, Matthias, Jan Maas, and Michiel Renger. “From Large Deviations to Wasserstein Gradient Flows in Multiple Dimensions.” Electronic Communications in Probability. Institute of Mathematical Statistics, 2015. https://doi.org/10.1214/ECP.v20-4315."},"publication":"Electronic Communications in Probability","has_accepted_license":"1","day":"29","scopus_import":1},{"type":"journal_article","issue":"5","abstract":[{"lang":"eng","text":"Evolutionary biologists have an array of powerful theoretical techniques that can accurately predict changes in the genetic composition of populations. Changes in gene frequencies and genetic associations between loci can be tracked as they respond to a wide variety of evolutionary forces. However, it is often less clear how to decompose these various forces into components that accurately reflect the underlying biology. Here, we present several issues that arise in the definition and interpretation of selection and selection coefficients, focusing on insights gained through the examination of selection coefficients in multilocus notation. Using this notation, we discuss how its flexibility-which allows different biological units to be identified as targets of selection-is reflected in the interpretation of the coefficients that the notation generates. In many situations, it can be difficult to agree on whether loci can be considered to be under "direct" versus "indirect" selection, or to quantify this selection. We present arguments for what the terms direct and indirect selection might best encompass, considering a range of issues, from viability and sexual selection to kin selection. We show how multilocus notation can discriminate between direct and indirect selection, and describe when it can do so."}],"_id":"1519","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 69","ddc":["570"],"status":"public","title":"The interpretation of selection coefficients","pubrep_id":"560","oa_version":"Submitted Version","file":[{"access_level":"open_access","file_name":"IST-2016-560-v1+1_Interpreting_ML_coefficients_11.2.15_App.pdf","creator":"system","content_type":"application/pdf","file_size":188872,"file_id":"4822","relation":"main_file","checksum":"fd8d23f476bc194419929b72ca265c02","date_updated":"2020-07-14T12:45:00Z","date_created":"2018-12-12T10:10:34Z"},{"file_id":"4823","relation":"main_file","checksum":"b774911e70044641d556e258efcb52ef","date_created":"2018-12-12T10:10:35Z","date_updated":"2020-07-14T12:45:00Z","access_level":"open_access","file_name":"IST-2016-560-v1+2_Interpreting_ML_coefficients_11.2.15_mainText.pdf","creator":"system","content_type":"application/pdf","file_size":577415}],"scopus_import":1,"has_accepted_license":"1","day":"19","citation":{"apa":"Barton, N. H., & Servedio, M. (2015). The interpretation of selection coefficients. Evolution. Wiley. https://doi.org/10.1111/evo.12641","ieee":"N. H. Barton and M. Servedio, “The interpretation of selection coefficients,” Evolution, vol. 69, no. 5. Wiley, pp. 1101–1112, 2015.","ista":"Barton NH, Servedio M. 2015. The interpretation of selection coefficients. Evolution. 69(5), 1101–1112.","ama":"Barton NH, Servedio M. The interpretation of selection coefficients. Evolution. 2015;69(5):1101-1112. doi:10.1111/evo.12641","chicago":"Barton, Nicholas H, and Maria Servedio. “The Interpretation of Selection Coefficients.” Evolution. Wiley, 2015. https://doi.org/10.1111/evo.12641.","short":"N.H. Barton, M. Servedio, Evolution 69 (2015) 1101–1112.","mla":"Barton, Nicholas H., and Maria Servedio. “The Interpretation of Selection Coefficients.” Evolution, vol. 69, no. 5, Wiley, 2015, pp. 1101–12, doi:10.1111/evo.12641."},"publication":"Evolution","page":"1101 - 1112","date_published":"2015-03-19T00:00:00Z","publist_id":"5656","ec_funded":1,"file_date_updated":"2020-07-14T12:45:00Z","year":"2015","department":[{"_id":"NiBa"}],"publisher":"Wiley","publication_status":"published","author":[{"first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"},{"full_name":"Servedio, Maria","last_name":"Servedio","first_name":"Maria"}],"volume":69,"date_created":"2018-12-11T11:52:29Z","date_updated":"2021-01-12T06:51:20Z","month":"03","oa":1,"project":[{"_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152","call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation"}],"quality_controlled":"1","doi":"10.1111/evo.12641","language":[{"iso":"eng"}]},{"has_accepted_license":"1","article_processing_charge":"No","day":"12","scopus_import":1,"date_published":"2015-11-12T00:00:00Z","citation":{"mla":"Bauer, Bruno, et al. “Arbeitsgruppe „Nationale Strategie“ Des Open Access Network Austria OANA.” VÖB Mitteilungen, vol. 68, no. 3, Verein Österreichischer Bibliothekare, 2015, pp. 580–607, doi:10.5281/zenodo.33178.","short":"B. Bauer, G. Blechl, C. Bock, P. Danowski, A. Ferus, A. Graschopf, T. König, K. Mayer, F. Reckling, K. Rieck, P. Seitz, H. Stöger, E. Welzig, VÖB Mitteilungen 68 (2015) 580–607.","chicago":"Bauer, Bruno, Guido Blechl, Christoph Bock, Patrick Danowski, Andreas Ferus, Anton Graschopf, Thomas König, et al. “Arbeitsgruppe „Nationale Strategie“ Des Open Access Network Austria OANA.” VÖB Mitteilungen. Verein Österreichischer Bibliothekare, 2015. https://doi.org/10.5281/zenodo.33178.","ama":"Bauer B, Blechl G, Bock C, et al. Arbeitsgruppe „Nationale Strategie“ des Open Access Network Austria OANA. VÖB Mitteilungen. 2015;68(3):580-607. doi:10.5281/zenodo.33178","ista":"Bauer B, Blechl G, Bock C, Danowski P, Ferus A, Graschopf A, König T, Mayer K, Reckling F, Rieck K, Seitz P, Stöger H, Welzig E. 2015. Arbeitsgruppe „Nationale Strategie“ des Open Access Network Austria OANA. VÖB Mitteilungen. 68(3), 580–607.","ieee":"B. Bauer et al., “Arbeitsgruppe „Nationale Strategie“ des Open Access Network Austria OANA,” VÖB Mitteilungen, vol. 68, no. 3. Verein Österreichischer Bibliothekare, pp. 580–607, 2015.","apa":"Bauer, B., Blechl, G., Bock, C., Danowski, P., Ferus, A., Graschopf, A., … Welzig, E. (2015). Arbeitsgruppe „Nationale Strategie“ des Open Access Network Austria OANA. VÖB Mitteilungen. Verein Österreichischer Bibliothekare. https://doi.org/10.5281/zenodo.33178"},"publication":"VÖB Mitteilungen","page":"580 - 607","article_type":"original","issue":"3","abstract":[{"text":"Based on 16 recommendations, efforts should be made to achieve the following goal: By 2025, all scholarly publication activity in Austria should be Open Access. In other words, the final versions of all scholarly publications resulting from the support of public resources must be freely accessible on the Internet without delay (Gold Open Access). The resources required to meet this obligation shall be provided to the authors, or the cost of the publication venues shall be borne directly by the research organisations.","lang":"eng"}],"type":"journal_article","pubrep_id":"720","oa_version":"Published Version","file":[{"date_updated":"2020-07-14T12:45:00Z","date_created":"2018-12-12T10:17:59Z","checksum":"a495fe253bbc7615b1d60e9e85c94408","file_id":"5317","relation":"main_file","creator":"system","file_size":931707,"content_type":"application/pdf","file_name":"IST-2016-720-v1+1_OANA_OA-Empfehlungen_12-11-2015.pdf","access_level":"open_access"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1525","intvolume":" 68","status":"public","ddc":["020"],"title":"Arbeitsgruppe „Nationale Strategie“ des Open Access Network Austria OANA","month":"11","doi":"10.5281/zenodo.33178","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","publist_id":"5648","file_date_updated":"2020-07-14T12:45:00Z","author":[{"last_name":"Bauer","first_name":"Bruno","full_name":"Bauer, Bruno"},{"last_name":"Blechl","first_name":"Guido","full_name":"Blechl, Guido"},{"first_name":"Christoph","last_name":"Bock","full_name":"Bock, Christoph"},{"full_name":"Danowski, Patrick","last_name":"Danowski","first_name":"Patrick","orcid":"0000-0002-6026-4409","id":"2EBD1598-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Ferus, Andreas","last_name":"Ferus","first_name":"Andreas"},{"full_name":"Graschopf, Anton","last_name":"Graschopf","first_name":"Anton"},{"full_name":"König, Thomas","last_name":"König","first_name":"Thomas"},{"full_name":"Mayer, Katja","last_name":"Mayer","first_name":"Katja"},{"full_name":"Reckling, Falk","first_name":"Falk","last_name":"Reckling"},{"full_name":"Rieck, Katharina","last_name":"Rieck","first_name":"Katharina"},{"full_name":"Seitz, Peter","first_name":"Peter","last_name":"Seitz"},{"full_name":"Stöger, Herwig","first_name":"Herwig","last_name":"Stöger"},{"full_name":"Welzig, Elvira","last_name":"Welzig","first_name":"Elvira"}],"volume":68,"date_updated":"2021-01-12T06:51:22Z","date_created":"2018-12-11T11:52:31Z","year":"2015","department":[{"_id":"E-Lib"}],"publisher":"Verein Österreichischer Bibliothekare","publication_status":"published"},{"abstract":[{"text":"Many stochastic models of biochemical reaction networks contain some chemical species for which the number of molecules that are present in the system can only be finite (for instance due to conservation laws), but also other species that can be present in arbitrarily large amounts. The prime example of such networks are models of gene expression, which typically contain a small and finite number of possible states for the promoter but an infinite number of possible states for the amount of mRNA and protein. One of the main approaches to analyze such models is through the use of equations for the time evolution of moments of the chemical species. Recently, a new approach based on conditional moments of the species with infinite state space given all the different possible states of the finite species has been proposed. It was argued that this approach allows one to capture more details about the full underlying probability distribution with a smaller number of equations. Here, I show that the result that less moments provide more information can only stem from an unnecessarily complicated description of the system in the classical formulation. The foundation of this argument will be the derivation of moment equations that describe the complete probability distribution over the finite state space but only low-order moments over the infinite state space. I will show that the number of equations that is needed is always less than what was previously claimed and always less than the number of conditional moment equations up to the same order. To support these arguments, a symbolic algorithm is provided that can be used to derive minimal systems of unconditional moment equations for models with partially finite state space. ","lang":"eng"}],"issue":"24","type":"journal_article","pubrep_id":"593","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"4641","date_updated":"2020-07-14T12:45:01Z","date_created":"2018-12-12T10:07:43Z","checksum":"838657118ae286463a2b7737319f35ce","file_name":"IST-2016-593-v1+1_Minimal_moment_equations.pdf","access_level":"open_access","file_size":605355,"content_type":"application/pdf","creator":"system"}],"_id":"1539","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["000"],"title":"Minimal moment equations for stochastic models of biochemical reaction networks with partially finite state space","status":"public","intvolume":" 143","day":"22","has_accepted_license":"1","scopus_import":1,"date_published":"2015-12-22T00:00:00Z","publication":"Journal of Chemical Physics","citation":{"ama":"Ruess J. Minimal moment equations for stochastic models of biochemical reaction networks with partially finite state space. Journal of Chemical Physics. 2015;143(24). doi:10.1063/1.4937937","apa":"Ruess, J. (2015). Minimal moment equations for stochastic models of biochemical reaction networks with partially finite state space. Journal of Chemical Physics. American Institute of Physics. https://doi.org/10.1063/1.4937937","ieee":"J. Ruess, “Minimal moment equations for stochastic models of biochemical reaction networks with partially finite state space,” Journal of Chemical Physics, vol. 143, no. 24. American Institute of Physics, 2015.","ista":"Ruess J. 2015. Minimal moment equations for stochastic models of biochemical reaction networks with partially finite state space. Journal of Chemical Physics. 143(24), 244103.","short":"J. Ruess, Journal of Chemical Physics 143 (2015).","mla":"Ruess, Jakob. “Minimal Moment Equations for Stochastic Models of Biochemical Reaction Networks with Partially Finite State Space.” Journal of Chemical Physics, vol. 143, no. 24, 244103, American Institute of Physics, 2015, doi:10.1063/1.4937937.","chicago":"Ruess, Jakob. “Minimal Moment Equations for Stochastic Models of Biochemical Reaction Networks with Partially Finite State Space.” Journal of Chemical Physics. American Institute of Physics, 2015. https://doi.org/10.1063/1.4937937."},"file_date_updated":"2020-07-14T12:45:01Z","ec_funded":1,"publist_id":"5632","article_number":"244103","author":[{"orcid":"0000-0003-1615-3282","id":"4A245D00-F248-11E8-B48F-1D18A9856A87","last_name":"Ruess","first_name":"Jakob","full_name":"Ruess, Jakob"}],"date_created":"2018-12-11T11:52:36Z","date_updated":"2021-01-12T06:51:28Z","volume":143,"year":"2015","publication_status":"published","department":[{"_id":"ToHe"},{"_id":"GaTk"}],"publisher":"American Institute of Physics","month":"12","doi":"10.1063/1.4937937","language":[{"iso":"eng"}],"oa":1,"quality_controlled":"1","project":[{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989","call_identifier":"FP7","name":"Quantitative Reactive Modeling"},{"name":"Rigorous Systems Engineering","call_identifier":"FWF","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211"},{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"}]},{"publisher":"Nature Publishing Group","department":[{"_id":"JiFr"}],"publication_status":"published","year":"2015","volume":6,"date_updated":"2021-01-12T06:51:26Z","date_created":"2018-12-11T11:52:34Z","author":[{"full_name":"Wang, Hongzhe","first_name":"Hongzhe","last_name":"Wang"},{"full_name":"Yang, Kezhen","first_name":"Kezhen","last_name":"Yang"},{"full_name":"Zou, Junjie","last_name":"Zou","first_name":"Junjie"},{"last_name":"Zhu","first_name":"Lingling","full_name":"Zhu, Lingling"},{"first_name":"Zidian","last_name":"Xie","full_name":"Xie, Zidian"},{"full_name":"Morita, Miyoterao","last_name":"Morita","first_name":"Miyoterao"},{"full_name":"Tasaka, Masao","first_name":"Masao","last_name":"Tasaka"},{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jirí","full_name":"Friml, Jirí"},{"full_name":"Grotewold, Erich","first_name":"Erich","last_name":"Grotewold"},{"full_name":"Beeckman, Tom","first_name":"Tom","last_name":"Beeckman"},{"last_name":"Vanneste","first_name":"Steffen","full_name":"Vanneste, Steffen"},{"first_name":"Fred","last_name":"Sack","full_name":"Sack, Fred"},{"full_name":"Le, Jie","first_name":"Jie","last_name":"Le"}],"article_number":"8822","publist_id":"5637","ec_funded":1,"file_date_updated":"2020-07-14T12:45:01Z","project":[{"grant_number":"282300","_id":"25716A02-B435-11E9-9278-68D0E5697425","name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7"}],"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"language":[{"iso":"eng"}],"doi":"10.1038/ncomms9822","month":"11","intvolume":" 6","status":"public","ddc":["570"],"title":"Transcriptional regulation of PIN genes by FOUR LIPS and MYB88 during Arabidopsis root gravitropism","_id":"1534","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"IST-2016-485-v1+1_ncomms9822.pdf","creator":"system","content_type":"application/pdf","file_size":1852268,"file_id":"5259","relation":"main_file","checksum":"3c06735fc7cd7e482ca830cbd26001bf","date_created":"2018-12-12T10:17:07Z","date_updated":"2020-07-14T12:45:01Z"}],"pubrep_id":"485","type":"journal_article","abstract":[{"text":"PIN proteins are auxin export carriers that direct intercellular auxin flow and in turn regulate many aspects of plant growth and development including responses to environmental changes. The Arabidopsis R2R3-MYB transcription factor FOUR LIPS (FLP) and its paralogue MYB88 regulate terminal divisions during stomatal development, as well as female reproductive development and stress responses. Here we show that FLP and MYB88 act redundantly but differentially in regulating the transcription of PIN3 and PIN7 in gravity-sensing cells of primary and lateral roots. On the one hand, FLP is involved in responses to gravity stimulation in primary roots, whereas on the other, FLP and MYB88 function complementarily in establishing the gravitropic set-point angles of lateral roots. Our results support a model in which FLP and MYB88 expression specifically determines the temporal-spatial patterns of PIN3 and PIN7 transcription that are closely associated with their preferential functions during root responses to gravity.","lang":"eng"}],"citation":{"ama":"Wang H, Yang K, Zou J, et al. Transcriptional regulation of PIN genes by FOUR LIPS and MYB88 during Arabidopsis root gravitropism. Nature Communications. 2015;6. doi:10.1038/ncomms9822","ieee":"H. Wang et al., “Transcriptional regulation of PIN genes by FOUR LIPS and MYB88 during Arabidopsis root gravitropism,” Nature Communications, vol. 6. Nature Publishing Group, 2015.","apa":"Wang, H., Yang, K., Zou, J., Zhu, L., Xie, Z., Morita, M., … Le, J. (2015). Transcriptional regulation of PIN genes by FOUR LIPS and MYB88 during Arabidopsis root gravitropism. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms9822","ista":"Wang H, Yang K, Zou J, Zhu L, Xie Z, Morita M, Tasaka M, Friml J, Grotewold E, Beeckman T, Vanneste S, Sack F, Le J. 2015. Transcriptional regulation of PIN genes by FOUR LIPS and MYB88 during Arabidopsis root gravitropism. Nature Communications. 6, 8822.","short":"H. Wang, K. Yang, J. Zou, L. Zhu, Z. Xie, M. Morita, M. Tasaka, J. Friml, E. Grotewold, T. Beeckman, S. Vanneste, F. Sack, J. Le, Nature Communications 6 (2015).","mla":"Wang, Hongzhe, et al. “Transcriptional Regulation of PIN Genes by FOUR LIPS and MYB88 during Arabidopsis Root Gravitropism.” Nature Communications, vol. 6, 8822, Nature Publishing Group, 2015, doi:10.1038/ncomms9822.","chicago":"Wang, Hongzhe, Kezhen Yang, Junjie Zou, Lingling Zhu, Zidian Xie, Miyoterao Morita, Masao Tasaka, et al. “Transcriptional Regulation of PIN Genes by FOUR LIPS and MYB88 during Arabidopsis Root Gravitropism.” Nature Communications. Nature Publishing Group, 2015. https://doi.org/10.1038/ncomms9822."},"publication":"Nature Communications","date_published":"2015-11-18T00:00:00Z","scopus_import":1,"has_accepted_license":"1","day":"18"},{"quality_controlled":"1","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"}],"external_id":{"pmid":["26085136"]},"oa":1,"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4491780/"}],"language":[{"iso":"eng"}],"doi":"10.1073/pnas.1423947112","month":"06","publication_status":"published","publisher":"National Academy of Sciences","department":[{"_id":"ToHe"},{"_id":"GaTk"}],"acknowledgement":"J.R., F.P., and J.L. acknowledge support from the European Commission under the Network of Excellence HYCON2 (highly-complex and networked control systems) and SystemsX.ch under the SignalX Project. J.R. acknowledges support from the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme FP7/2007-2013 under REA (Research Executive Agency) Grant 291734. M.K. acknowledges support from Human Frontier Science Program Grant RP0061/2011 (www.hfsp.org). ","year":"2015","pmid":1,"date_created":"2018-12-11T11:52:36Z","date_updated":"2021-01-12T06:51:27Z","volume":112,"author":[{"id":"4A245D00-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1615-3282","first_name":"Jakob","last_name":"Ruess","full_name":"Ruess, Jakob"},{"first_name":"Francesca","last_name":"Parise","full_name":"Parise, Francesca"},{"full_name":"Milias Argeitis, Andreas","first_name":"Andreas","last_name":"Milias Argeitis"},{"first_name":"Mustafa","last_name":"Khammash","full_name":"Khammash, Mustafa"},{"full_name":"Lygeros, John","last_name":"Lygeros","first_name":"John"}],"ec_funded":1,"publist_id":"5633","page":"8148 - 8153","publication":"PNAS","citation":{"ista":"Ruess J, Parise F, Milias Argeitis A, Khammash M, Lygeros J. 2015. Iterative experiment design guides the characterization of a light-inducible gene expression circuit. PNAS. 112(26), 8148–8153.","ieee":"J. Ruess, F. Parise, A. Milias Argeitis, M. Khammash, and J. Lygeros, “Iterative experiment design guides the characterization of a light-inducible gene expression circuit,” PNAS, vol. 112, no. 26. National Academy of Sciences, pp. 8148–8153, 2015.","apa":"Ruess, J., Parise, F., Milias Argeitis, A., Khammash, M., & Lygeros, J. (2015). Iterative experiment design guides the characterization of a light-inducible gene expression circuit. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1423947112","ama":"Ruess J, Parise F, Milias Argeitis A, Khammash M, Lygeros J. Iterative experiment design guides the characterization of a light-inducible gene expression circuit. PNAS. 2015;112(26):8148-8153. doi:10.1073/pnas.1423947112","chicago":"Ruess, Jakob, Francesca Parise, Andreas Milias Argeitis, Mustafa Khammash, and John Lygeros. “Iterative Experiment Design Guides the Characterization of a Light-Inducible Gene Expression Circuit.” PNAS. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1423947112.","mla":"Ruess, Jakob, et al. “Iterative Experiment Design Guides the Characterization of a Light-Inducible Gene Expression Circuit.” PNAS, vol. 112, no. 26, National Academy of Sciences, 2015, pp. 8148–53, doi:10.1073/pnas.1423947112.","short":"J. Ruess, F. Parise, A. Milias Argeitis, M. Khammash, J. Lygeros, PNAS 112 (2015) 8148–8153."},"date_published":"2015-06-30T00:00:00Z","scopus_import":1,"day":"30","status":"public","title":"Iterative experiment design guides the characterization of a light-inducible gene expression circuit","intvolume":" 112","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1538","oa_version":"Submitted Version","type":"journal_article","abstract":[{"lang":"eng","text":"Systems biology rests on the idea that biological complexity can be better unraveled through the interplay of modeling and experimentation. However, the success of this approach depends critically on the informativeness of the chosen experiments, which is usually unknown a priori. Here, we propose a systematic scheme based on iterations of optimal experiment design, flow cytometry experiments, and Bayesian parameter inference to guide the discovery process in the case of stochastic biochemical reaction networks. To illustrate the benefit of our methodology, we apply it to the characterization of an engineered light-inducible gene expression circuit in yeast and compare the performance of the resulting model with models identified from nonoptimal experiments. In particular, we compare the parameter posterior distributions and the precision to which the outcome of future experiments can be predicted. Moreover, we illustrate how the identified stochastic model can be used to determine light induction patterns that make either the average amount of protein or the variability in a population of cells follow a desired profile. Our results show that optimal experiment design allows one to derive models that are accurate enough to precisely predict and regulate the protein expression in heterogeneous cell populations over extended periods of time."}],"issue":"26"},{"type":"journal_article","issue":"2","abstract":[{"lang":"eng","text":"Neuronal and neuroendocrine L-type calcium channels (Cav1.2, Cav1.3) open readily at relatively low membrane potentials and allow Ca2+ to enter the cells near resting potentials. In this way, Cav1.2 and Cav1.3 shape the action potential waveform, contribute to gene expression, synaptic plasticity, neuronal differentiation, hormone secretion and pacemaker activity. In the chromaffin cells (CCs) of the adrenal medulla, Cav1.3 is highly expressed and is shown to support most of the pacemaking current that sustains action potential (AP) firings and part of the catecholamine secretion. Cav1.3 forms Ca2+-nanodomains with the fast inactivating BK channels and drives the resting SK currents. These latter set the inter-spike interval duration between consecutive spikes during spontaneous firing and the rate of spike adaptation during sustained depolarizations. Cav1.3 plays also a primary role in the switch from “tonic” to “burst” firing that occurs in mouse CCs when either the availability of voltage-gated Na channels (Nav) is reduced or the β2 subunit featuring the fast inactivating BK channels is deleted. Here, we discuss the functional role of these “neuronlike” firing modes in CCs and how Cav1.3 contributes to them. The open issue is to understand how these novel firing patterns are adapted to regulate the quantity of circulating catecholamines during resting condition or in response to acute and chronic stress."}],"intvolume":" 8","status":"public","title":"Cav1.3 channels as key regulators of neuron-like firings and catecholamine release in chromaffin cells","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1535","oa_version":"Submitted Version","scopus_import":1,"article_processing_charge":"No","day":"01","page":"149 - 161","article_type":"original","citation":{"ista":"Vandael DH, Marcantoni A, Carbone E. 2015. Cav1.3 channels as key regulators of neuron-like firings and catecholamine release in chromaffin cells. Current Molecular Pharmacology. 8(2), 149–161.","ieee":"D. H. Vandael, A. Marcantoni, and E. Carbone, “Cav1.3 channels as key regulators of neuron-like firings and catecholamine release in chromaffin cells,” Current Molecular Pharmacology, vol. 8, no. 2. Bentham Science Publishers, pp. 149–161, 2015.","apa":"Vandael, D. H., Marcantoni, A., & Carbone, E. (2015). Cav1.3 channels as key regulators of neuron-like firings and catecholamine release in chromaffin cells. Current Molecular Pharmacology. Bentham Science Publishers. https://doi.org/10.2174/1874467208666150507105443","ama":"Vandael DH, Marcantoni A, Carbone E. Cav1.3 channels as key regulators of neuron-like firings and catecholamine release in chromaffin cells. Current Molecular Pharmacology. 2015;8(2):149-161. doi:10.2174/1874467208666150507105443","chicago":"Vandael, David H, Andrea Marcantoni, and Emilio Carbone. “Cav1.3 Channels as Key Regulators of Neuron-like Firings and Catecholamine Release in Chromaffin Cells.” Current Molecular Pharmacology. Bentham Science Publishers, 2015. https://doi.org/10.2174/1874467208666150507105443.","mla":"Vandael, David H., et al. “Cav1.3 Channels as Key Regulators of Neuron-like Firings and Catecholamine Release in Chromaffin Cells.” Current Molecular Pharmacology, vol. 8, no. 2, Bentham Science Publishers, 2015, pp. 149–61, doi:10.2174/1874467208666150507105443.","short":"D.H. Vandael, A. Marcantoni, E. Carbone, Current Molecular Pharmacology 8 (2015) 149–161."},"publication":"Current Molecular Pharmacology","date_published":"2015-10-01T00:00:00Z","publist_id":"5636","department":[{"_id":"PeJo"}],"publisher":"Bentham Science Publishers","publication_status":"published","pmid":1,"acknowledgement":"This work was supported by the Italian MIUR (PRIN 2010/2011 project 2010JFYFY2) and the University of Torino.","year":"2015","volume":8,"date_updated":"2021-01-12T06:51:26Z","date_created":"2018-12-11T11:52:35Z","author":[{"last_name":"Vandael","first_name":"David H","orcid":"0000-0001-7577-1676","id":"3AE48E0A-F248-11E8-B48F-1D18A9856A87","full_name":"Vandael, David H"},{"first_name":"Andrea","last_name":"Marcantoni","full_name":"Marcantoni, Andrea"},{"last_name":"Carbone","first_name":"Emilio","full_name":"Carbone, Emilio"}],"month":"10","quality_controlled":"1","oa":1,"external_id":{"pmid":["25966692"]},"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5384372/"}],"language":[{"iso":"eng"}],"doi":"10.2174/1874467208666150507105443"},{"month":"10","doi":"10.1016/j.jtbi.2015.07.011","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"project":[{"_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","grant_number":"618091","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","call_identifier":"FP7"},{"grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation"}],"quality_controlled":"1","publist_id":"5629","ec_funded":1,"file_date_updated":"2020-07-14T12:45:01Z","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","author":[{"full_name":"Paixao, Tiago","last_name":"Paixao","first_name":"Tiago","orcid":"0000-0003-2361-3953","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Badkobeh, Golnaz","last_name":"Badkobeh","first_name":"Golnaz"},{"first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"},{"first_name":"Doğan","last_name":"Çörüş","full_name":"Çörüş, Doğan"},{"full_name":"Dang, Duccuong","first_name":"Duccuong","last_name":"Dang"},{"last_name":"Friedrich","first_name":"Tobias","full_name":"Friedrich, Tobias"},{"last_name":"Lehre","first_name":"Per","full_name":"Lehre, Per"},{"full_name":"Sudholt, Dirk","first_name":"Dirk","last_name":"Sudholt"},{"first_name":"Andrew","last_name":"Sutton","full_name":"Sutton, Andrew"},{"full_name":"Trubenova, Barbora","orcid":"0000-0002-6873-2967","id":"42302D54-F248-11E8-B48F-1D18A9856A87","last_name":"Trubenova","first_name":"Barbora"}],"volume":383,"date_updated":"2021-01-12T06:51:29Z","date_created":"2018-12-11T11:52:37Z","year":"2015","department":[{"_id":"NiBa"},{"_id":"CaGu"}],"publisher":"Elsevier","publication_status":"published","has_accepted_license":"1","day":"21","scopus_import":1,"date_published":"2015-10-21T00:00:00Z","citation":{"chicago":"Paixao, Tiago, Golnaz Badkobeh, Nicholas H Barton, Doğan Çörüş, Duccuong Dang, Tobias Friedrich, Per Lehre, Dirk Sudholt, Andrew Sutton, and Barbora Trubenova. “Toward a Unifying Framework for Evolutionary Processes.” Journal of Theoretical Biology. Elsevier, 2015. https://doi.org/10.1016/j.jtbi.2015.07.011.","mla":"Paixao, Tiago, et al. “Toward a Unifying Framework for Evolutionary Processes.” Journal of Theoretical Biology, vol. 383, Elsevier, 2015, pp. 28–43, doi:10.1016/j.jtbi.2015.07.011.","short":"T. Paixao, G. Badkobeh, N.H. Barton, D. Çörüş, D. Dang, T. Friedrich, P. Lehre, D. Sudholt, A. Sutton, B. Trubenova, Journal of Theoretical Biology 383 (2015) 28–43.","ista":"Paixao T, Badkobeh G, Barton NH, Çörüş D, Dang D, Friedrich T, Lehre P, Sudholt D, Sutton A, Trubenova B. 2015. Toward a unifying framework for evolutionary processes. Journal of Theoretical Biology. 383, 28–43.","apa":"Paixao, T., Badkobeh, G., Barton, N. H., Çörüş, D., Dang, D., Friedrich, T., … Trubenova, B. (2015). Toward a unifying framework for evolutionary processes. Journal of Theoretical Biology. Elsevier. https://doi.org/10.1016/j.jtbi.2015.07.011","ieee":"T. Paixao et al., “Toward a unifying framework for evolutionary processes,” Journal of Theoretical Biology, vol. 383. Elsevier, pp. 28–43, 2015.","ama":"Paixao T, Badkobeh G, Barton NH, et al. Toward a unifying framework for evolutionary processes. Journal of Theoretical Biology. 2015;383:28-43. doi:10.1016/j.jtbi.2015.07.011"},"publication":" Journal of Theoretical Biology","page":"28 - 43","abstract":[{"lang":"eng","text":"The theory of population genetics and evolutionary computation have been evolving separately for nearly 30 years. Many results have been independently obtained in both fields and many others are unique to its respective field. We aim to bridge this gap by developing a unifying framework for evolutionary processes that allows both evolutionary algorithms and population genetics models to be cast in the same formal framework. The framework we present here decomposes the evolutionary process into its several components in order to facilitate the identification of similarities between different models. In particular, we propose a classification of evolutionary operators based on the defining properties of the different components. We cast several commonly used operators from both fields into this common framework. Using this, we map different evolutionary and genetic algorithms to different evolutionary regimes and identify candidates with the most potential for the translation of results between the fields. This provides a unified description of evolutionary processes and represents a stepping stone towards new tools and results to both fields. "}],"type":"journal_article","pubrep_id":"483","file":[{"file_name":"IST-2016-483-v1+1_1-s2.0-S0022519315003409-main.pdf","access_level":"open_access","creator":"system","content_type":"application/pdf","file_size":595307,"file_id":"5244","relation":"main_file","date_created":"2018-12-12T10:16:53Z","date_updated":"2020-07-14T12:45:01Z","checksum":"33b60ecfea60764756a9ee9df5eb65ca"}],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1542","intvolume":" 383","title":"Toward a unifying framework for evolutionary processes","ddc":["570"],"status":"public"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1546","title":"Nanoscale distribution of presynaptic Ca2+ channels and its impact on vesicular release during development","ddc":["570"],"status":"public","intvolume":" 85","pubrep_id":"482","file":[{"date_created":"2018-12-12T10:15:47Z","date_updated":"2020-07-14T12:45:01Z","checksum":"725f4d5be2dbb44b283ce722645ef37d","relation":"main_file","file_id":"5170","content_type":"application/pdf","file_size":3080111,"creator":"system","file_name":"IST-2016-482-v1+1_1-s2.0-S0896627314010472-main.pdf","access_level":"open_access"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"text":"Synaptic efficacy and precision are influenced by the coupling of voltage-gated Ca2+ channels (VGCCs) to vesicles. But because the topography of VGCCs and their proximity to vesicles is unknown, a quantitative understanding of the determinants of vesicular release at nanometer scale is lacking. To investigate this, we combined freeze-fracture replica immunogold labeling of Cav2.1 channels, local [Ca2+] imaging, and patch pipette perfusion of EGTA at the calyx of Held. Between postnatal day 7 and 21, VGCCs formed variable sized clusters and vesicular release became less sensitive to EGTA, whereas fixed Ca2+ buffer properties remained constant. Experimentally constrained reaction-diffusion simulations suggest that Ca2+ sensors for vesicular release are located at the perimeter of VGCC clusters (<30nm) and predict that VGCC number per cluster determines vesicular release probability without altering release time course. This "perimeter release model" provides a unifying framework accounting for developmental changes in both synaptic efficacy and time course.","lang":"eng"}],"issue":"1","publication":"Neuron","citation":{"ieee":"Y. Nakamura et al., “Nanoscale distribution of presynaptic Ca2+ channels and its impact on vesicular release during development,” Neuron, vol. 85, no. 1. Elsevier, pp. 145–158, 2015.","apa":"Nakamura, Y., Harada, H., Kamasawa, N., Matsui, K., Rothman, J., Shigemoto, R., … Takahashi, T. (2015). Nanoscale distribution of presynaptic Ca2+ channels and its impact on vesicular release during development. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2014.11.019","ista":"Nakamura Y, Harada H, Kamasawa N, Matsui K, Rothman J, Shigemoto R, Silver RA, Digregorio D, Takahashi T. 2015. Nanoscale distribution of presynaptic Ca2+ channels and its impact on vesicular release during development. Neuron. 85(1), 145–158.","ama":"Nakamura Y, Harada H, Kamasawa N, et al. Nanoscale distribution of presynaptic Ca2+ channels and its impact on vesicular release during development. Neuron. 2015;85(1):145-158. doi:10.1016/j.neuron.2014.11.019","chicago":"Nakamura, Yukihiro, Harumi Harada, Naomi Kamasawa, Ko Matsui, Jason Rothman, Ryuichi Shigemoto, R Angus Silver, David Digregorio, and Tomoyuki Takahashi. “Nanoscale Distribution of Presynaptic Ca2+ Channels and Its Impact on Vesicular Release during Development.” Neuron. Elsevier, 2015. https://doi.org/10.1016/j.neuron.2014.11.019.","short":"Y. Nakamura, H. Harada, N. Kamasawa, K. Matsui, J. Rothman, R. Shigemoto, R.A. Silver, D. Digregorio, T. Takahashi, Neuron 85 (2015) 145–158.","mla":"Nakamura, Yukihiro, et al. “Nanoscale Distribution of Presynaptic Ca2+ Channels and Its Impact on Vesicular Release during Development.” Neuron, vol. 85, no. 1, Elsevier, 2015, pp. 145–58, doi:10.1016/j.neuron.2014.11.019."},"page":"145 - 158","date_published":"2015-01-07T00:00:00Z","scopus_import":1,"day":"07","has_accepted_license":"1","year":"2015","acknowledgement":"This work was supported by the Core Research for Evolutional Science and Technology (CREST) of Japan Science and Technology Agency to T.T. and R.S.; by the funding provided by Okinawa Institute of Science and Technology (OIST) to T.T. and Y.N.; by JSPS Core-to-Core Program, A. Advanced Networks to T.T.; by the Grant-in-Aid for Young Scientists from the Japanese Ministry of Education, Culture, Sports, Science and Technology (#23700474) to Y.N.; by the Centre National de la Recherche Scientifique through the Actions Thematiques et Initatives sur Programme, Fondation Fyssen, Fondation pour la Recherche Medicale, Federation pour la Recherche sur le Cerveau, Agence Nationale de la Recherche (ANR-2007-Neuro-008-01 and ANR-2010-BLAN-1411-01) to D.D. and Y.N.; and by the European Commission Coordination Action ENINET (LSHM-CT-2005-19063) to D.D. and R.A.S. R.A.S. and J.S.R. were funded by Wellcome Trust Senior (064413) and Principal (095667) Research Fellowship and an ERC advance grant (294667) to RAS.","publication_status":"published","department":[{"_id":"RySh"}],"publisher":"Elsevier","author":[{"full_name":"Nakamura, Yukihiro","last_name":"Nakamura","first_name":"Yukihiro"},{"full_name":"Harada, Harumi","orcid":"0000-0001-7429-7896","id":"2E55CDF2-F248-11E8-B48F-1D18A9856A87","last_name":"Harada","first_name":"Harumi"},{"full_name":"Kamasawa, Naomi","last_name":"Kamasawa","first_name":"Naomi"},{"full_name":"Matsui, Ko","first_name":"Ko","last_name":"Matsui"},{"last_name":"Rothman","first_name":"Jason","full_name":"Rothman, Jason"},{"full_name":"Shigemoto, Ryuichi","first_name":"Ryuichi","last_name":"Shigemoto","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444"},{"last_name":"Silver","first_name":"R Angus","full_name":"Silver, R Angus"},{"full_name":"Digregorio, David","last_name":"Digregorio","first_name":"David"},{"full_name":"Takahashi, Tomoyuki","first_name":"Tomoyuki","last_name":"Takahashi"}],"date_updated":"2021-01-12T06:51:31Z","date_created":"2018-12-11T11:52:39Z","volume":85,"file_date_updated":"2020-07-14T12:45:01Z","publist_id":"5625","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","doi":"10.1016/j.neuron.2014.11.019","language":[{"iso":"eng"}],"month":"01"},{"publication_status":"published","publisher":"Academic Press","department":[{"_id":"MaLo"}],"year":"2015","pmid":1,"date_created":"2018-12-11T11:52:38Z","date_updated":"2021-01-12T06:51:30Z","volume":128,"author":[{"first_name":"Phuong","last_name":"Nguyen","full_name":"Nguyen, Phuong"},{"first_name":"Christine","last_name":"Field","full_name":"Field, Christine"},{"first_name":"Aaron","last_name":"Groen","full_name":"Groen, Aaron"},{"full_name":"Mitchison, Timothy","last_name":"Mitchison","first_name":"Timothy"},{"last_name":"Loose","first_name":"Martin","orcid":"0000-0001-7309-9724","id":"462D4284-F248-11E8-B48F-1D18A9856A87","full_name":"Loose, Martin"}],"publist_id":"5627","quality_controlled":"1","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4578691/","open_access":"1"}],"external_id":{"pmid":["25997350"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1016/bs.mcb.2015.01.007","month":"04","title":"Using supported bilayers to study the spatiotemporal organization of membrane-bound proteins","status":"public","intvolume":" 128","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1544","oa_version":"Submitted Version","type":"book_chapter","abstract":[{"lang":"eng","text":"Cell division in prokaryotes and eukaryotes is commonly initiated by the well-controlled binding of proteins to the cytoplasmic side of the cell membrane. However, a precise characterization of the spatiotemporal dynamics of membrane-bound proteins is often difficult to achieve in vivo. Here, we present protocols for the use of supported lipid bilayers to rebuild the cytokinetic machineries of cells with greatly different dimensions: the bacterium Escherichia coli and eggs of the vertebrate Xenopus laevis. Combined with total internal reflection fluorescence microscopy, these experimental setups allow for precise quantitative analyses of membrane-bound proteins. The protocols described to obtain glass-supported membranes from bacterial and vertebrate lipids can be used as starting points for other reconstitution experiments. We believe that similar biochemical assays will be instrumental to study the biochemistry and biophysics underlying a variety of complex cellular tasks, such as signaling, vesicle trafficking, and cell motility."}],"page":"223 - 241","publication":"Building a Cell from its Components Parts","citation":{"ama":"Nguyen P, Field C, Groen A, Mitchison T, Loose M. Using supported bilayers to study the spatiotemporal organization of membrane-bound proteins. In: Building a Cell from Its Components Parts. Vol 128. Academic Press; 2015:223-241. doi:10.1016/bs.mcb.2015.01.007","apa":"Nguyen, P., Field, C., Groen, A., Mitchison, T., & Loose, M. (2015). Using supported bilayers to study the spatiotemporal organization of membrane-bound proteins. In Building a Cell from its Components Parts (Vol. 128, pp. 223–241). Academic Press. https://doi.org/10.1016/bs.mcb.2015.01.007","ieee":"P. Nguyen, C. Field, A. Groen, T. Mitchison, and M. Loose, “Using supported bilayers to study the spatiotemporal organization of membrane-bound proteins,” in Building a Cell from its Components Parts, vol. 128, Academic Press, 2015, pp. 223–241.","ista":"Nguyen P, Field C, Groen A, Mitchison T, Loose M. 2015.Using supported bilayers to study the spatiotemporal organization of membrane-bound proteins. In: Building a Cell from its Components Parts. vol. 128, 223–241.","short":"P. Nguyen, C. Field, A. Groen, T. Mitchison, M. Loose, in:, Building a Cell from Its Components Parts, Academic Press, 2015, pp. 223–241.","mla":"Nguyen, Phuong, et al. “Using Supported Bilayers to Study the Spatiotemporal Organization of Membrane-Bound Proteins.” Building a Cell from Its Components Parts, vol. 128, Academic Press, 2015, pp. 223–41, doi:10.1016/bs.mcb.2015.01.007.","chicago":"Nguyen, Phuong, Christine Field, Aaron Groen, Timothy Mitchison, and Martin Loose. “Using Supported Bilayers to Study the Spatiotemporal Organization of Membrane-Bound Proteins.” In Building a Cell from Its Components Parts, 128:223–41. Academic Press, 2015. https://doi.org/10.1016/bs.mcb.2015.01.007."},"date_published":"2015-04-08T00:00:00Z","scopus_import":1,"day":"08"},{"issue":"6","abstract":[{"text":"Reciprocal coevolution between host and pathogen is widely seen as a major driver of evolution and biological innovation. Yet, to date, the underlying genetic mechanisms and associated trait functions that are unique to rapid coevolutionary change are generally unknown. We here combined experimental evolution of the bacterial biocontrol agent Bacillus thuringiensis and its nematode host Caenorhabditis elegans with large-scale phenotyping, whole genome analysis, and functional genetics to demonstrate the selective benefit of pathogen virulence and the underlying toxin genes during the adaptation process. We show that: (i) high virulence was specifically favoured during pathogen–host coevolution rather than pathogen one-sided adaptation to a nonchanging host or to an environment without host; (ii) the pathogen genotype BT-679 with known nematocidal toxin genes and high virulence specifically swept to fixation in all of the independent replicate populations under coevolution but only some under one-sided adaptation; (iii) high virulence in the BT-679-dominated populations correlated with elevated copy numbers of the plasmid containing the nematocidal toxin genes; (iv) loss of virulence in a toxin-plasmid lacking BT-679 isolate was reconstituted by genetic reintroduction or external addition of the toxins.We conclude that sustained coevolution is distinct from unidirectional selection in shaping the pathogen's genome and life history characteristics. To our knowledge, this study is the first to characterize the pathogen genes involved in coevolutionary adaptation in an animal host–pathogen interaction system.","lang":"eng"}],"type":"journal_article","pubrep_id":"481","file":[{"creator":"system","content_type":"application/pdf","file_size":3468956,"file_name":"IST-2016-481-v1+1_journal.pbio.1002169.pdf","access_level":"open_access","date_updated":"2020-07-14T12:45:02Z","date_created":"2018-12-12T10:14:13Z","checksum":"30dee7a2c11ed09f2f5634655c0146f8","file_id":"5063","relation":"main_file"}],"oa_version":"Published Version","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1551","intvolume":" 13","ddc":["570"],"title":"Host–pathogen coevolution: The selective advantage of Bacillus thuringiensis virulence and its cry toxin genes","status":"public","has_accepted_license":"1","day":"04","scopus_import":1,"date_published":"2015-06-04T00:00:00Z","citation":{"ista":"El Masri L, Branca A, Sheppard A, Papkou A, Laehnemann D, Guenther P, Prahl S, Saebelfeld M, Hollensteiner J, Liesegang H, Brzuszkiewicz E, Daniel R, Michiels N, Schulte R, Kurtz J, Rosenstiel P, Telschow A, Bornberg Bauer E, Schulenburg H. 2015. Host–pathogen coevolution: The selective advantage of Bacillus thuringiensis virulence and its cry toxin genes. PLoS Biology. 13(6), 1–30.","ieee":"L. El Masri et al., “Host–pathogen coevolution: The selective advantage of Bacillus thuringiensis virulence and its cry toxin genes,” PLoS Biology, vol. 13, no. 6. Public Library of Science, pp. 1–30, 2015.","apa":"El Masri, L., Branca, A., Sheppard, A., Papkou, A., Laehnemann, D., Guenther, P., … Schulenburg, H. (2015). Host–pathogen coevolution: The selective advantage of Bacillus thuringiensis virulence and its cry toxin genes. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.1002169","ama":"El Masri L, Branca A, Sheppard A, et al. Host–pathogen coevolution: The selective advantage of Bacillus thuringiensis virulence and its cry toxin genes. PLoS Biology. 2015;13(6):1-30. doi:10.1371/journal.pbio.1002169","chicago":"El Masri, Leila, Antoine Branca, Anna Sheppard, Andrei Papkou, David Laehnemann, Patrick Guenther, Swantje Prahl, et al. “Host–Pathogen Coevolution: The Selective Advantage of Bacillus Thuringiensis Virulence and Its Cry Toxin Genes.” PLoS Biology. Public Library of Science, 2015. https://doi.org/10.1371/journal.pbio.1002169.","mla":"El Masri, Leila, et al. “Host–Pathogen Coevolution: The Selective Advantage of Bacillus Thuringiensis Virulence and Its Cry Toxin Genes.” PLoS Biology, vol. 13, no. 6, Public Library of Science, 2015, pp. 1–30, doi:10.1371/journal.pbio.1002169.","short":"L. El Masri, A. Branca, A. Sheppard, A. Papkou, D. Laehnemann, P. Guenther, S. Prahl, M. Saebelfeld, J. Hollensteiner, H. Liesegang, E. Brzuszkiewicz, R. Daniel, N. Michiels, R. Schulte, J. Kurtz, P. Rosenstiel, A. Telschow, E. Bornberg Bauer, H. Schulenburg, PLoS Biology 13 (2015) 1–30."},"publication":"PLoS Biology","page":"1 - 30","ec_funded":1,"publist_id":"5620","file_date_updated":"2020-07-14T12:45:02Z","author":[{"first_name":"Leila","last_name":"El Masri","id":"349A6E66-F248-11E8-B48F-1D18A9856A87","full_name":"El Masri, Leila"},{"last_name":"Branca","first_name":"Antoine","full_name":"Branca, Antoine"},{"full_name":"Sheppard, Anna","last_name":"Sheppard","first_name":"Anna"},{"last_name":"Papkou","first_name":"Andrei","full_name":"Papkou, Andrei"},{"full_name":"Laehnemann, David","last_name":"Laehnemann","first_name":"David"},{"full_name":"Guenther, Patrick","last_name":"Guenther","first_name":"Patrick"},{"full_name":"Prahl, Swantje","first_name":"Swantje","last_name":"Prahl"},{"full_name":"Saebelfeld, Manja","first_name":"Manja","last_name":"Saebelfeld"},{"full_name":"Hollensteiner, Jacqueline","first_name":"Jacqueline","last_name":"Hollensteiner"},{"full_name":"Liesegang, Heiko","last_name":"Liesegang","first_name":"Heiko"},{"last_name":"Brzuszkiewicz","first_name":"Elzbieta","full_name":"Brzuszkiewicz, Elzbieta"},{"full_name":"Daniel, Rolf","last_name":"Daniel","first_name":"Rolf"},{"full_name":"Michiels, Nico","last_name":"Michiels","first_name":"Nico"},{"full_name":"Schulte, Rebecca","last_name":"Schulte","first_name":"Rebecca"},{"first_name":"Joachim","last_name":"Kurtz","full_name":"Kurtz, Joachim"},{"last_name":"Rosenstiel","first_name":"Philip","full_name":"Rosenstiel, Philip"},{"first_name":"Arndt","last_name":"Telschow","full_name":"Telschow, Arndt"},{"first_name":"Erich","last_name":"Bornberg Bauer","full_name":"Bornberg Bauer, Erich"},{"full_name":"Schulenburg, Hinrich","last_name":"Schulenburg","first_name":"Hinrich"}],"volume":13,"date_updated":"2021-01-12T06:51:33Z","date_created":"2018-12-11T11:52:40Z","year":"2015","acknowledgement":"We are very grateful for funding from the German Science Foundation (DFG) to HS (SCHU 1415/8, SCHU 1415/9), PR (RO 2994/3), EBB (BO 2544/7), HL (LI 1690/2), AT (TE 976/2), RDS (SCHU 2522/1), JK (KU 1929/4); from the Kiel Excellence Cluster Inflammation at Interfaces to HS and PR; and from the ISTFELLOW program (Co-fund Marie Curie Actions of the European Commission) to LM.","department":[{"_id":"SyCr"}],"publisher":"Public Library of Science","publication_status":"published","month":"06","doi":"10.1371/journal.pbio.1002169","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1"},{"pubrep_id":"839","oa_version":"Submitted Version","file":[{"content_type":"application/pdf","file_size":1919655,"creator":"system","file_name":"IST-2017-839-v1+1_mckenzie.pdf","access_level":"open_access","date_created":"2018-12-12T10:11:02Z","date_updated":"2020-07-14T12:45:01Z","checksum":"bd1bfdf2423a0c3b6e7cabfa8b44bc0f","relation":"main_file","file_id":"4854"}],"_id":"1549","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Flipping the photoswitch: Ion channels under light control","status":"public","ddc":["571","576"],"intvolume":" 869","abstract":[{"lang":"eng","text":"Nature has incorporated small photochromic molecules, colloquially termed 'photoswitches', in photoreceptor proteins to sense optical cues in photo-taxis and vision. While Nature's ability to employ light-responsive functionalities has long been recognized, it was not until recently that scientists designed, synthesized and applied synthetic photochromes to manipulate many of which open rapidly and locally in their native cell types, biological processes with the temporal and spatial resolution of light. Ion channels in particular have come to the forefront of proteins that can be put under the designer control of synthetic photochromes. Photochromic ion channel controllers are comprised of three classes, photochromic soluble ligands (PCLs), photochromic tethered ligands (PTLs) and photochromic crosslinkers (PXs), and in each class ion channel functionality is controlled through reversible changes in photochrome structure. By acting as light-dependent ion channel agonists, antagonist or modulators, photochromic controllers effectively converted a wide range of ion channels, including voltage-gated ion channels, 'leak channels', tri-, tetra- and pentameric ligand-gated ion channels, and temperaturesensitive ion channels, into man-made photoreceptors. Control by photochromes can be reversible, unlike in the case of 'caged' compounds, and non-invasive with high spatial precision, unlike pharmacology and electrical manipulation. Here, we introduce design principles of emerging photochromic molecules that act on ion channels and discuss the impact that these molecules are beginning to have on ion channel biophysics and neuronal physiology."}],"type":"book_chapter","date_published":"2015-09-18T00:00:00Z","publication":"Novel chemical tools to study ion channel biology","citation":{"chicago":"Mckenzie, Catherine, Inmaculada Sanchez-Romero, and Harald L Janovjak. “Flipping the Photoswitch: Ion Channels under Light Control.” In Novel Chemical Tools to Study Ion Channel Biology, 869:101–17. Advances in Experimental Medicine and Biology. Springer, 2015. https://doi.org/10.1007/978-1-4939-2845-3_6.","short":"C. Mckenzie, I. Sanchez-Romero, H.L. Janovjak, in:, Novel Chemical Tools to Study Ion Channel Biology, Springer, 2015, pp. 101–117.","mla":"Mckenzie, Catherine, et al. “Flipping the Photoswitch: Ion Channels under Light Control.” Novel Chemical Tools to Study Ion Channel Biology, vol. 869, Springer, 2015, pp. 101–17, doi:10.1007/978-1-4939-2845-3_6.","apa":"Mckenzie, C., Sanchez-Romero, I., & Janovjak, H. L. (2015). Flipping the photoswitch: Ion channels under light control. In Novel chemical tools to study ion channel biology (Vol. 869, pp. 101–117). Springer. https://doi.org/10.1007/978-1-4939-2845-3_6","ieee":"C. Mckenzie, I. Sanchez-Romero, and H. L. Janovjak, “Flipping the photoswitch: Ion channels under light control,” in Novel chemical tools to study ion channel biology, vol. 869, Springer, 2015, pp. 101–117.","ista":"Mckenzie C, Sanchez-Romero I, Janovjak HL. 2015.Flipping the photoswitch: Ion channels under light control. In: Novel chemical tools to study ion channel biology. vol. 869, 101–117.","ama":"Mckenzie C, Sanchez-Romero I, Janovjak HL. Flipping the photoswitch: Ion channels under light control. In: Novel Chemical Tools to Study Ion Channel Biology. Vol 869. Advances in Experimental Medicine and Biology. Springer; 2015:101-117. doi:10.1007/978-1-4939-2845-3_6"},"page":"101 - 117","day":"18","has_accepted_license":"1","scopus_import":1,"series_title":"Advances in Experimental Medicine and Biology","author":[{"id":"3EEDE19A-F248-11E8-B48F-1D18A9856A87","first_name":"Catherine","last_name":"Mckenzie","full_name":"Mckenzie, Catherine"},{"id":"3D9C5D30-F248-11E8-B48F-1D18A9856A87","last_name":"Sanchez Romero","first_name":"Inmaculada","full_name":"Sanchez Romero, Inmaculada"},{"orcid":"0000-0002-8023-9315","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","last_name":"Janovjak","first_name":"Harald L","full_name":"Janovjak, Harald L"}],"date_updated":"2021-01-12T06:51:32Z","date_created":"2018-12-11T11:52:39Z","volume":869,"year":"2015","publication_status":"published","publisher":"Springer","department":[{"_id":"HaJa"}],"file_date_updated":"2020-07-14T12:45:01Z","publist_id":"5622","doi":"10.1007/978-1-4939-2845-3_6","language":[{"iso":"eng"}],"oa":1,"quality_controlled":"1","month":"09","publication_identifier":{"isbn":["978-1-4939-2844-6"]}},{"month":"12","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4651099/","open_access":"1"}],"oa":1,"external_id":{"pmid":["26386058"]},"quality_controlled":"1","doi":"10.1128/AEM.02051-15","language":[{"iso":"eng"}],"publist_id":"5623","pmid":1,"year":"2015","department":[{"_id":"SyCr"}],"publisher":"American Society for Microbiology","publication_status":"published","author":[{"full_name":"Milutinovic, Barbara","id":"2CDC32B8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8214-4758","first_name":"Barbara","last_name":"Milutinovic"},{"first_name":"Christina","last_name":"Höfling","full_name":"Höfling, Christina"},{"first_name":"Momir","last_name":"Futo","full_name":"Futo, Momir"},{"full_name":"Scharsack, Jörn","last_name":"Scharsack","first_name":"Jörn"},{"first_name":"Joachim","last_name":"Kurtz","full_name":"Kurtz, Joachim"}],"volume":81,"date_created":"2018-12-11T11:52:39Z","date_updated":"2021-01-12T06:51:31Z","scopus_import":1,"day":"01","citation":{"ista":"Milutinovic B, Höfling C, Futo M, Scharsack J, Kurtz J. 2015. Infection of Tribolium castaneum with Bacillus thuringiensis: Quantification of bacterial replication within cadavers, transmission via cannibalism, and inhibition of spore germination. Applied and Environmental Microbiology. 81(23), 8135–8144.","apa":"Milutinovic, B., Höfling, C., Futo, M., Scharsack, J., & Kurtz, J. (2015). Infection of Tribolium castaneum with Bacillus thuringiensis: Quantification of bacterial replication within cadavers, transmission via cannibalism, and inhibition of spore germination. Applied and Environmental Microbiology. American Society for Microbiology. https://doi.org/10.1128/AEM.02051-15","ieee":"B. Milutinovic, C. Höfling, M. Futo, J. Scharsack, and J. Kurtz, “Infection of Tribolium castaneum with Bacillus thuringiensis: Quantification of bacterial replication within cadavers, transmission via cannibalism, and inhibition of spore germination,” Applied and Environmental Microbiology, vol. 81, no. 23. American Society for Microbiology, pp. 8135–8144, 2015.","ama":"Milutinovic B, Höfling C, Futo M, Scharsack J, Kurtz J. Infection of Tribolium castaneum with Bacillus thuringiensis: Quantification of bacterial replication within cadavers, transmission via cannibalism, and inhibition of spore germination. Applied and Environmental Microbiology. 2015;81(23):8135-8144. doi:10.1128/AEM.02051-15","chicago":"Milutinovic, Barbara, Christina Höfling, Momir Futo, Jörn Scharsack, and Joachim Kurtz. “Infection of Tribolium Castaneum with Bacillus Thuringiensis: Quantification of Bacterial Replication within Cadavers, Transmission via Cannibalism, and Inhibition of Spore Germination.” Applied and Environmental Microbiology. American Society for Microbiology, 2015. https://doi.org/10.1128/AEM.02051-15.","mla":"Milutinovic, Barbara, et al. “Infection of Tribolium Castaneum with Bacillus Thuringiensis: Quantification of Bacterial Replication within Cadavers, Transmission via Cannibalism, and Inhibition of Spore Germination.” Applied and Environmental Microbiology, vol. 81, no. 23, American Society for Microbiology, 2015, pp. 8135–44, doi:10.1128/AEM.02051-15.","short":"B. Milutinovic, C. Höfling, M. Futo, J. Scharsack, J. Kurtz, Applied and Environmental Microbiology 81 (2015) 8135–8144."},"publication":"Applied and Environmental Microbiology","page":"8135 - 8144","date_published":"2015-12-01T00:00:00Z","type":"journal_article","issue":"23","abstract":[{"text":"Reproduction within a host and transmission to the next host are crucial for the virulence and fitness of pathogens. Nevertheless, basic knowledge about such parameters is often missing from the literature, even for well-studied bacteria, such as Bacillus thuringiensis, an endospore-forming insect pathogen, which infects its hosts via the oral route. To characterize bacterial replication success, we made use of an experimental oral infection system for the red flour beetle Tribolium castaneum and developed a flow cytometric assay for the quantification of both spore ingestion by the individual beetle larvae and the resulting spore load after bacterial replication and resporulation within cadavers. On average, spore numbers increased 460-fold, showing that Bacillus thuringiensis grows and replicates successfully in insect cadavers. By inoculating cadaver-derived spores and spores from bacterial stock cultures into nutrient medium, we next investigated outgrowth characteristics of vegetative cells and found that cadaver- derived bacteria showed reduced growth compared to bacteria from the stock cultures. Interestingly, this reduced growth was a consequence of inhibited spore germination, probably originating from the host and resulting in reduced host mortality in subsequent infections by cadaver-derived spores. Nevertheless, we further showed that Bacillus thuringiensis transmission was possible via larval cannibalism when no other food was offered. These results contribute to our understanding of the ecology of Bacillus thuringiensis as an insect pathogen.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1548","intvolume":" 81","title":"Infection of Tribolium castaneum with Bacillus thuringiensis: Quantification of bacterial replication within cadavers, transmission via cannibalism, and inhibition of spore germination","status":"public","oa_version":"Submitted Version"},{"day":"02","scopus_import":1,"date_published":"2015-09-02T00:00:00Z","page":"989 - 998","citation":{"ama":"Mayer C, Jaglin X, Cobbs L, et al. Clonally related forebrain interneurons disperse broadly across both functional areas and structural boundaries. Neuron. 2015;87(5):989-998. doi:10.1016/j.neuron.2015.07.011","apa":"Mayer, C., Jaglin, X., Cobbs, L., Bandler, R., Streicher, C., Cepko, C., … Fishell, G. (2015). Clonally related forebrain interneurons disperse broadly across both functional areas and structural boundaries. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2015.07.011","ieee":"C. Mayer et al., “Clonally related forebrain interneurons disperse broadly across both functional areas and structural boundaries,” Neuron, vol. 87, no. 5. Elsevier, pp. 989–998, 2015.","ista":"Mayer C, Jaglin X, Cobbs L, Bandler R, Streicher C, Cepko C, Hippenmeyer S, Fishell G. 2015. Clonally related forebrain interneurons disperse broadly across both functional areas and structural boundaries. Neuron. 87(5), 989–998.","short":"C. Mayer, X. Jaglin, L. Cobbs, R. Bandler, C. Streicher, C. Cepko, S. Hippenmeyer, G. Fishell, Neuron 87 (2015) 989–998.","mla":"Mayer, Christian, et al. “Clonally Related Forebrain Interneurons Disperse Broadly across Both Functional Areas and Structural Boundaries.” Neuron, vol. 87, no. 5, Elsevier, 2015, pp. 989–98, doi:10.1016/j.neuron.2015.07.011.","chicago":"Mayer, Christian, Xavier Jaglin, Lucy Cobbs, Rachel Bandler, Carmen Streicher, Constance Cepko, Simon Hippenmeyer, and Gord Fishell. “Clonally Related Forebrain Interneurons Disperse Broadly across Both Functional Areas and Structural Boundaries.” Neuron. Elsevier, 2015. https://doi.org/10.1016/j.neuron.2015.07.011."},"publication":"Neuron","issue":"5","abstract":[{"lang":"eng","text":"The medial ganglionic eminence (MGE) gives rise to the majority of mouse forebrain interneurons. Here, we examine the lineage relationship among MGE-derived interneurons using a replication-defective retroviral library containing a highly diverse set of DNA barcodes. Recovering the barcodes from the mature progeny of infected progenitor cells enabled us to unambiguously determine their respective lineal relationship. We found that clonal dispersion occurs across large areas of the brain and is not restricted by anatomical divisions. As such, sibling interneurons can populate the cortex, hippocampus striatum, and globus pallidus. The majority of interneurons appeared to be generated from asymmetric divisions of MGE progenitor cells, followed by symmetric divisions within the subventricular zone. Altogether, our findings uncover that lineage relationships do not appear to determine interneuron allocation to particular regions. As such, it is likely that clonally related interneurons have considerable flexibility as to the particular forebrain circuits to which they can contribute."}],"type":"journal_article","oa_version":"Submitted Version","intvolume":" 87","status":"public","title":"Clonally related forebrain interneurons disperse broadly across both functional areas and structural boundaries","_id":"1550","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"09","language":[{"iso":"eng"}],"doi":"10.1016/j.neuron.2015.07.011","quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4560602/"}],"external_id":{"pmid":["26299473"]},"publist_id":"5621","volume":87,"date_updated":"2021-01-12T06:51:32Z","date_created":"2018-12-11T11:52:40Z","author":[{"first_name":"Christian","last_name":"Mayer","full_name":"Mayer, Christian"},{"full_name":"Jaglin, Xavier","last_name":"Jaglin","first_name":"Xavier"},{"last_name":"Cobbs","first_name":"Lucy","full_name":"Cobbs, Lucy"},{"full_name":"Bandler, Rachel","last_name":"Bandler","first_name":"Rachel"},{"first_name":"Carmen","last_name":"Streicher","id":"36BCB99C-F248-11E8-B48F-1D18A9856A87","full_name":"Streicher, Carmen"},{"full_name":"Cepko, Constance","last_name":"Cepko","first_name":"Constance"},{"full_name":"Hippenmeyer, Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061","first_name":"Simon","last_name":"Hippenmeyer"},{"full_name":"Fishell, Gord","first_name":"Gord","last_name":"Fishell"}],"department":[{"_id":"SiHi"}],"publisher":"Elsevier","publication_status":"published","pmid":1,"acknowledgement":"Research in the G.F. laboratory is supported by NIH (NS 081297, MH095147, and P01NS074972) and the Simons Foundation. Research in the S.H. laboratory is supported by the European Union (FP7-CIG618444). C.M. is supported by EMBO ALTF (1295-2012). X.H.J. is supported by EMBO (ALTF 303-2010) and HFSP (LT000078/2011-L).\r\n\r\n","year":"2015"},{"type":"journal_article","abstract":[{"text":"Let G be a graph on the vertex set V(G) = {x1,…,xn} with the edge set E(G), and let R = K[x1,…, xn] be the polynomial ring over a field K. Two monomial ideals are associated to G, the edge ideal I(G) generated by all monomials xixj with {xi,xj} ∈ E(G), and the vertex cover ideal IG generated by monomials ∏xi∈Cxi for all minimal vertex covers C of G. A minimal vertex cover of G is a subset C ⊂ V(G) such that each edge has at least one vertex in C and no proper subset of C has the same property. Indeed, the vertex cover ideal of G is the Alexander dual of the edge ideal of G. In this paper, for an unmixed bipartite graph G we consider the lattice of vertex covers LG and we explicitly describe the minimal free resolution of the ideal associated to LG which is exactly the vertex cover ideal of G. Then we compute depth, projective dimension, regularity and extremal Betti numbers of R/I(G) in terms of the associated lattice.","lang":"eng"}],"issue":"3","title":"Resolution of unmixed bipartite graphs","status":"public","intvolume":" 52","_id":"1547","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","scopus_import":1,"day":"31","page":"977 - 986","publication":"Bulletin of the Korean Mathematical Society","citation":{"ama":"Mohammadi F, Moradi S. Resolution of unmixed bipartite graphs. Bulletin of the Korean Mathematical Society. 2015;52(3):977-986. doi:10.4134/BKMS.2015.52.3.977","ista":"Mohammadi F, Moradi S. 2015. Resolution of unmixed bipartite graphs. Bulletin of the Korean Mathematical Society. 52(3), 977–986.","ieee":"F. Mohammadi and S. Moradi, “Resolution of unmixed bipartite graphs,” Bulletin of the Korean Mathematical Society, vol. 52, no. 3. Korean Mathematical Society, pp. 977–986, 2015.","apa":"Mohammadi, F., & Moradi, S. (2015). Resolution of unmixed bipartite graphs. Bulletin of the Korean Mathematical Society. Korean Mathematical Society. https://doi.org/10.4134/BKMS.2015.52.3.977","mla":"Mohammadi, Fatemeh, and Somayeh Moradi. “Resolution of Unmixed Bipartite Graphs.” Bulletin of the Korean Mathematical Society, vol. 52, no. 3, Korean Mathematical Society, 2015, pp. 977–86, doi:10.4134/BKMS.2015.52.3.977.","short":"F. Mohammadi, S. Moradi, Bulletin of the Korean Mathematical Society 52 (2015) 977–986.","chicago":"Mohammadi, Fatemeh, and Somayeh Moradi. “Resolution of Unmixed Bipartite Graphs.” Bulletin of the Korean Mathematical Society. Korean Mathematical Society, 2015. https://doi.org/10.4134/BKMS.2015.52.3.977."},"date_published":"2015-05-31T00:00:00Z","publist_id":"5624","publication_status":"published","department":[{"_id":"CaUh"}],"publisher":"Korean Mathematical Society","year":"2015","date_created":"2018-12-11T11:52:39Z","date_updated":"2021-01-12T06:51:31Z","volume":52,"author":[{"id":"2C29581E-F248-11E8-B48F-1D18A9856A87","first_name":"Fatemeh","last_name":"Mohammadi","full_name":"Mohammadi, Fatemeh"},{"last_name":"Moradi","first_name":"Somayeh","full_name":"Moradi, Somayeh"}],"month":"05","publication_identifier":{"eissn":["2234-3016"]},"quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/0901.3015"}],"language":[{"iso":"eng"}],"doi":"10.4134/BKMS.2015.52.3.977"},{"date_published":"2015-08-01T00:00:00Z","page":"4631 - 4642","citation":{"chicago":"Jia, Yuebin, Huiyu Tian, Hongjiang Li, Qianqian Yu, Lei Wang, Jiří Friml, and Zhaojun Ding. “The Arabidopsis Thaliana Elongator Complex Subunit 2 Epigenetically Affects Root Development.” Journal of Experimental Botany. Oxford University Press, 2015. https://doi.org/10.1093/jxb/erv230.","short":"Y. Jia, H. Tian, H. Li, Q. Yu, L. Wang, J. Friml, Z. Ding, Journal of Experimental Botany 66 (2015) 4631–4642.","mla":"Jia, Yuebin, et al. “The Arabidopsis Thaliana Elongator Complex Subunit 2 Epigenetically Affects Root Development.” Journal of Experimental Botany, vol. 66, no. 15, Oxford University Press, 2015, pp. 4631–42, doi:10.1093/jxb/erv230.","ieee":"Y. Jia et al., “The Arabidopsis thaliana elongator complex subunit 2 epigenetically affects root development,” Journal of Experimental Botany, vol. 66, no. 15. Oxford University Press, pp. 4631–4642, 2015.","apa":"Jia, Y., Tian, H., Li, H., Yu, Q., Wang, L., Friml, J., & Ding, Z. (2015). The Arabidopsis thaliana elongator complex subunit 2 epigenetically affects root development. Journal of Experimental Botany. Oxford University Press. https://doi.org/10.1093/jxb/erv230","ista":"Jia Y, Tian H, Li H, Yu Q, Wang L, Friml J, Ding Z. 2015. The Arabidopsis thaliana elongator complex subunit 2 epigenetically affects root development. Journal of Experimental Botany. 66(15), 4631–4642.","ama":"Jia Y, Tian H, Li H, et al. The Arabidopsis thaliana elongator complex subunit 2 epigenetically affects root development. Journal of Experimental Botany. 2015;66(15):4631-4642. doi:10.1093/jxb/erv230"},"publication":"Journal of Experimental Botany","has_accepted_license":"1","day":"01","scopus_import":1,"file":[{"access_level":"open_access","file_name":"IST-2016-480-v1+1_J._Exp._Bot.-2015-Jia-4631-42.pdf","creator":"system","file_size":7753043,"content_type":"application/pdf","file_id":"5051","relation":"main_file","checksum":"257919be0ce3d306185d3891ad7acf39","date_created":"2018-12-12T10:14:02Z","date_updated":"2020-07-14T12:45:02Z"}],"oa_version":"Published Version","pubrep_id":"480","intvolume":" 66","title":"The Arabidopsis thaliana elongator complex subunit 2 epigenetically affects root development","status":"public","ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1556","issue":"15","abstract":[{"lang":"eng","text":"The elongator complex subunit 2 (ELP2) protein, one subunit of an evolutionarily conserved histone acetyltransferase complex, has been shown to participate in leaf patterning, plant immune and abiotic stress responses in Arabidopsis thaliana. Here, its role in root development was explored. Compared to the wild type, the elp2 mutant exhibited an accelerated differentiation of its root stem cells and cell division was more active in its quiescent centre (QC). The key transcription factors responsible for maintaining root stem cell and QC identity, such as AP2 transcription factors PLT1 (PLETHORA1) and PLT2 (PLETHORA2), GRAS transcription factors such as SCR (SCARECROW) and SHR (SHORT ROOT) and WUSCHEL-RELATED HOMEOBOX5 transcription factor WOX5, were all strongly down-regulated in the mutant. On the other hand, expression of the G2/M transition activator CYCB1 was substantially induced in elp2. The auxin efflux transporters PIN1 and PIN2 showed decreased protein levels and PIN1 also displayed mild polarity alterations in elp2, which resulted in a reduced auxin content in the root tip. Either the acetylation or methylation level of each of these genes differed between the mutant and the wild type, suggesting that the ELP2 regulation of root development involves the epigenetic modification of a range of transcription factors and other developmental regulators."}],"type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1093/jxb/erv230","quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"month":"08","volume":66,"date_updated":"2021-01-12T06:51:35Z","date_created":"2018-12-11T11:52:42Z","author":[{"last_name":"Jia","first_name":"Yuebin","full_name":"Jia, Yuebin"},{"full_name":"Tian, Huiyu","first_name":"Huiyu","last_name":"Tian"},{"orcid":"0000-0001-5039-9660","id":"33CA54A6-F248-11E8-B48F-1D18A9856A87","last_name":"Li","first_name":"Hongjiang","full_name":"Li, Hongjiang"},{"first_name":"Qianqian","last_name":"Yu","full_name":"Yu, Qianqian"},{"full_name":"Wang, Lei","first_name":"Lei","last_name":"Wang"},{"full_name":"Friml, Jirí","last_name":"Friml","first_name":"Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Ding, Zhaojun","last_name":"Ding","first_name":"Zhaojun"}],"publisher":"Oxford University Press","department":[{"_id":"JiFr"}],"publication_status":"published","year":"2015","publist_id":"5615","file_date_updated":"2020-07-14T12:45:02Z"},{"_id":"1555","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 14","ddc":["510"],"title":"Rich bifurcation structure in a two patch vaccination model","status":"public","oa_version":"Published Version","type":"journal_article","issue":"2","abstract":[{"text":"We show that incorporating spatial dispersal of individuals into a simple vaccination epidemic model may give rise to a model that exhibits rich dynamical behavior. Using an SIVS (susceptible-infected-vaccinated-susceptible) model as a basis, we describe the spread of an infectious disease in a population split into two regions. In each subpopulation, both forward and backward bifurcations can occur. This implies that for disconnected regions the two-patch system may admit several steady states. We consider traveling between the regions and investigate the impact of spatial dispersal of individuals on the model dynamics. We establish conditions for the existence of multiple nontrivial steady states in the system, and we study the structure of the equilibria. The mathematical analysis reveals an unusually rich dynamical behavior, not normally found in the simple epidemic models. In addition to the disease-free equilibrium, eight endemic equilibria emerge from backward transcritical and saddle-node bifurcation points, forming an interesting bifurcation diagram. Stability of steady states, their bifurcations, and the global dynamics are investigated with analytical tools, numerical simulations, and rigorous set-oriented numerical computations.","lang":"eng"}],"citation":{"chicago":"Knipl, Diána, Pawel Pilarczyk, and Gergely Röst. “Rich Bifurcation Structure in a Two Patch Vaccination Model.” SIAM Journal on Applied Dynamical Systems. Society for Industrial and Applied Mathematics , 2015. https://doi.org/10.1137/140993934.","short":"D. Knipl, P. Pilarczyk, G. Röst, SIAM Journal on Applied Dynamical Systems 14 (2015) 980–1017.","mla":"Knipl, Diána, et al. “Rich Bifurcation Structure in a Two Patch Vaccination Model.” SIAM Journal on Applied Dynamical Systems, vol. 14, no. 2, Society for Industrial and Applied Mathematics , 2015, pp. 980–1017, doi:10.1137/140993934.","apa":"Knipl, D., Pilarczyk, P., & Röst, G. (2015). Rich bifurcation structure in a two patch vaccination model. SIAM Journal on Applied Dynamical Systems. Society for Industrial and Applied Mathematics . https://doi.org/10.1137/140993934","ieee":"D. Knipl, P. Pilarczyk, and G. Röst, “Rich bifurcation structure in a two patch vaccination model,” SIAM Journal on Applied Dynamical Systems, vol. 14, no. 2. Society for Industrial and Applied Mathematics , pp. 980–1017, 2015.","ista":"Knipl D, Pilarczyk P, Röst G. 2015. Rich bifurcation structure in a two patch vaccination model. SIAM Journal on Applied Dynamical Systems. 14(2), 980–1017.","ama":"Knipl D, Pilarczyk P, Röst G. Rich bifurcation structure in a two patch vaccination model. SIAM Journal on Applied Dynamical Systems. 2015;14(2):980-1017. doi:10.1137/140993934"},"publication":"SIAM Journal on Applied Dynamical Systems","page":"980 - 1017","article_type":"original","date_published":"2015-01-01T00:00:00Z","scopus_import":1,"article_processing_charge":"No","day":"01","year":"2015","acknowledgement":"Institute of Science and Technology Austria, Am Campus 1, 3400 Klosterneuburg, Austria (pawel.pilarczyk@ist.ac.at). This author’s work was partially supported by the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement 622033, by Fundo Europeu de Desenvolvimento Regional (FEDER) through COMPETE—Programa Operacional Factores de Competitividade (POFC), by the Portuguese national funds through Funda ̧caoparaaCiˆencia e a Tecnologia (FCT) in the framework of the research project FCOMP-01-0124-FEDER-010645 (ref. FCT PTDC/MAT/098871/2008), and by European Research Council through StG 259559 in the framework of the EPIDELAY project.","publisher":"Society for Industrial and Applied Mathematics ","department":[{"_id":"HeEd"}],"publication_status":"published","author":[{"full_name":"Knipl, Diána","last_name":"Knipl","first_name":"Diána"},{"full_name":"Pilarczyk, Pawel","last_name":"Pilarczyk","first_name":"Pawel","id":"3768D56A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Röst, Gergely","first_name":"Gergely","last_name":"Röst"}],"volume":14,"date_updated":"2021-01-12T06:51:34Z","date_created":"2018-12-11T11:52:42Z","ec_funded":1,"publist_id":"5616","oa":1,"main_file_link":[{"open_access":"1","url":"http://discovery.ucl.ac.uk/1473750/1/99393.pdf"}],"project":[{"_id":"255F06BE-B435-11E9-9278-68D0E5697425","grant_number":"622033","call_identifier":"FP7","name":"Persistent Homology - Images, Data and Maps"}],"quality_controlled":"1","doi":"10.1137/140993934","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1536-0040"]},"month":"01"},{"month":"12","language":[{"iso":"eng"}],"doi":"10.1073/pnas.1511366112","quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4697423/"}],"external_id":{"pmid":["26644569"]},"publist_id":"5612","date_updated":"2021-01-12T06:51:36Z","date_created":"2018-12-11T11:52:43Z","volume":112,"author":[{"orcid":"0000-0003-4783-0389","id":"3B699956-F248-11E8-B48F-1D18A9856A87","last_name":"Ibsen-Jensen","first_name":"Rasmus","full_name":"Ibsen-Jensen, Rasmus"},{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee"},{"last_name":"Nowak","first_name":"Martin","full_name":"Nowak, Martin"}],"publication_status":"published","department":[{"_id":"KrCh"}],"publisher":"National Academy of Sciences","year":"2015","pmid":1,"day":"22","scopus_import":1,"date_published":"2015-12-22T00:00:00Z","page":"15636 - 15641","publication":"PNAS","citation":{"ista":"Ibsen-Jensen R, Chatterjee K, Nowak M. 2015. Computational complexity of ecological and evolutionary spatial dynamics. PNAS. 112(51), 15636–15641.","ieee":"R. Ibsen-Jensen, K. Chatterjee, and M. Nowak, “Computational complexity of ecological and evolutionary spatial dynamics,” PNAS, vol. 112, no. 51. National Academy of Sciences, pp. 15636–15641, 2015.","apa":"Ibsen-Jensen, R., Chatterjee, K., & Nowak, M. (2015). Computational complexity of ecological and evolutionary spatial dynamics. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1511366112","ama":"Ibsen-Jensen R, Chatterjee K, Nowak M. Computational complexity of ecological and evolutionary spatial dynamics. PNAS. 2015;112(51):15636-15641. doi:10.1073/pnas.1511366112","chicago":"Ibsen-Jensen, Rasmus, Krishnendu Chatterjee, and Martin Nowak. “Computational Complexity of Ecological and Evolutionary Spatial Dynamics.” PNAS. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1511366112.","mla":"Ibsen-Jensen, Rasmus, et al. “Computational Complexity of Ecological and Evolutionary Spatial Dynamics.” PNAS, vol. 112, no. 51, National Academy of Sciences, 2015, pp. 15636–41, doi:10.1073/pnas.1511366112.","short":"R. Ibsen-Jensen, K. Chatterjee, M. Nowak, PNAS 112 (2015) 15636–15641."},"abstract":[{"text":"There are deep, yet largely unexplored, connections between computer science and biology. Both disciplines examine how information proliferates in time and space. Central results in computer science describe the complexity of algorithms that solve certain classes of problems. An algorithm is deemed efficient if it can solve a problem in polynomial time, which means the running time of the algorithm is a polynomial function of the length of the input. There are classes of harder problems for which the fastest possible algorithm requires exponential time. Another criterion is the space requirement of the algorithm. There is a crucial distinction between algorithms that can find a solution, verify a solution, or list several distinct solutions in given time and space. The complexity hierarchy that is generated in this way is the foundation of theoretical computer science. Precise complexity results can be notoriously difficult. The famous question whether polynomial time equals nondeterministic polynomial time (i.e., P = NP) is one of the hardest open problems in computer science and all of mathematics. Here, we consider simple processes of ecological and evolutionary spatial dynamics. The basic question is: What is the probability that a new invader (or a new mutant)will take over a resident population?We derive precise complexity results for a variety of scenarios. We therefore show that some fundamental questions in this area cannot be answered by simple equations (assuming that P is not equal to NP).","lang":"eng"}],"issue":"51","type":"journal_article","oa_version":"Submitted Version","title":"Computational complexity of ecological and evolutionary spatial dynamics","status":"public","intvolume":" 112","_id":"1559","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"day":"26","scopus_import":1,"date_published":"2015-02-26T00:00:00Z","page":"207 - 210","citation":{"chicago":"Liao, Cheyang, Wouter Smet, Géraldine Brunoud, Saiko Yoshida, Teva Vernoux, and Dolf Weijers. “Reporters for Sensitive and Quantitative Measurement of Auxin Response.” Nature Methods. Nature Publishing Group, 2015. https://doi.org/10.1038/nmeth.3279.","mla":"Liao, Cheyang, et al. “Reporters for Sensitive and Quantitative Measurement of Auxin Response.” Nature Methods, vol. 12, no. 3, Nature Publishing Group, 2015, pp. 207–10, doi:10.1038/nmeth.3279.","short":"C. Liao, W. Smet, G. Brunoud, S. Yoshida, T. Vernoux, D. Weijers, Nature Methods 12 (2015) 207–210.","ista":"Liao C, Smet W, Brunoud G, Yoshida S, Vernoux T, Weijers D. 2015. Reporters for sensitive and quantitative measurement of auxin response. Nature Methods. 12(3), 207–210.","apa":"Liao, C., Smet, W., Brunoud, G., Yoshida, S., Vernoux, T., & Weijers, D. (2015). Reporters for sensitive and quantitative measurement of auxin response. Nature Methods. Nature Publishing Group. https://doi.org/10.1038/nmeth.3279","ieee":"C. Liao, W. Smet, G. Brunoud, S. Yoshida, T. Vernoux, and D. Weijers, “Reporters for sensitive and quantitative measurement of auxin response,” Nature Methods, vol. 12, no. 3. Nature Publishing Group, pp. 207–210, 2015.","ama":"Liao C, Smet W, Brunoud G, Yoshida S, Vernoux T, Weijers D. Reporters for sensitive and quantitative measurement of auxin response. Nature Methods. 2015;12(3):207-210. doi:10.1038/nmeth.3279"},"publication":"Nature Methods","issue":"3","abstract":[{"lang":"eng","text":"The visualization of hormonal signaling input and output is key to understanding how multicellular development is regulated. The plant signaling molecule auxin triggers many growth and developmental responses, but current tools lack the sensitivity or precision to visualize these. We developed a set of fluorescent reporters that allow sensitive and semiquantitative readout of auxin responses at cellular resolution in Arabidopsis thaliana. These generic tools are suitable for any transformable plant species."}],"type":"journal_article","oa_version":"Submitted Version","intvolume":" 12","status":"public","title":"Reporters for sensitive and quantitative measurement of auxin response","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1554","month":"02","language":[{"iso":"eng"}],"doi":"10.1038/nmeth.3279","quality_controlled":"1","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4344836/","open_access":"1"}],"oa":1,"external_id":{"pmid":["25643149"]},"publist_id":"5617","volume":12,"date_updated":"2021-01-12T06:51:34Z","date_created":"2018-12-11T11:52:41Z","author":[{"full_name":"Liao, Cheyang","last_name":"Liao","first_name":"Cheyang"},{"first_name":"Wouter","last_name":"Smet","full_name":"Smet, Wouter"},{"first_name":"Géraldine","last_name":"Brunoud","full_name":"Brunoud, Géraldine"},{"first_name":"Saiko","last_name":"Yoshida","id":"2E46069C-F248-11E8-B48F-1D18A9856A87","full_name":"Yoshida, Saiko"},{"first_name":"Teva","last_name":"Vernoux","full_name":"Vernoux, Teva"},{"full_name":"Weijers, Dolf","last_name":"Weijers","first_name":"Dolf"}],"publisher":"Nature Publishing Group","department":[{"_id":"JiFr"}],"publication_status":"published","pmid":1,"year":"2015"},{"month":"11","language":[{"iso":"eng"}],"doi":"10.1113/JP271078","quality_controlled":"1","oa":1,"external_id":{"pmid":["26282459"]},"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4650409/","open_access":"1"}],"publist_id":"5606","volume":593,"date_created":"2018-12-11T11:52:45Z","date_updated":"2021-01-12T06:51:38Z","author":[{"last_name":"Gavello","first_name":"Daniela","full_name":"Gavello, Daniela"},{"first_name":"David H","last_name":"Vandael","id":"3AE48E0A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7577-1676","full_name":"Vandael, David H"},{"first_name":"Sara","last_name":"Gosso","full_name":"Gosso, Sara"},{"last_name":"Carbone","first_name":"Emilio","full_name":"Carbone, Emilio"},{"full_name":"Carabelli, Valentina","last_name":"Carabelli","first_name":"Valentina"}],"department":[{"_id":"PeJo"}],"publisher":"Wiley-Blackwell","publication_status":"published","pmid":1,"year":"2015","acknowledgement":"This work was supported by the Compagnia di San Paolo Foundation ‘Neuroscience Program’ to VC and ‘Progetto di Ateneo 2011-13’ to EC.\r\nWe thank Dr Claudio Franchino for cell preparation and for providing excellent technical support.","day":"15","scopus_import":1,"date_published":"2015-11-15T00:00:00Z","page":"4835 - 4853","citation":{"ieee":"D. Gavello, D. H. Vandael, S. Gosso, E. Carbone, and V. Carabelli, “Dual action of leptin on rest-firing and stimulated catecholamine release via phosphoinositide 3-kinase-riven BK channel up-regulation in mouse chromaffin cells,” Journal of Physiology, vol. 593, no. 22. Wiley-Blackwell, pp. 4835–4853, 2015.","apa":"Gavello, D., Vandael, D. H., Gosso, S., Carbone, E., & Carabelli, V. (2015). Dual action of leptin on rest-firing and stimulated catecholamine release via phosphoinositide 3-kinase-riven BK channel up-regulation in mouse chromaffin cells. Journal of Physiology. Wiley-Blackwell. https://doi.org/10.1113/JP271078","ista":"Gavello D, Vandael DH, Gosso S, Carbone E, Carabelli V. 2015. Dual action of leptin on rest-firing and stimulated catecholamine release via phosphoinositide 3-kinase-riven BK channel up-regulation in mouse chromaffin cells. Journal of Physiology. 593(22), 4835–4853.","ama":"Gavello D, Vandael DH, Gosso S, Carbone E, Carabelli V. Dual action of leptin on rest-firing and stimulated catecholamine release via phosphoinositide 3-kinase-riven BK channel up-regulation in mouse chromaffin cells. Journal of Physiology. 2015;593(22):4835-4853. doi:10.1113/JP271078","chicago":"Gavello, Daniela, David H Vandael, Sara Gosso, Emilio Carbone, and Valentina Carabelli. “Dual Action of Leptin on Rest-Firing and Stimulated Catecholamine Release via Phosphoinositide 3-Kinase-Riven BK Channel up-Regulation in Mouse Chromaffin Cells.” Journal of Physiology. Wiley-Blackwell, 2015. https://doi.org/10.1113/JP271078.","short":"D. Gavello, D.H. Vandael, S. Gosso, E. Carbone, V. Carabelli, Journal of Physiology 593 (2015) 4835–4853.","mla":"Gavello, Daniela, et al. “Dual Action of Leptin on Rest-Firing and Stimulated Catecholamine Release via Phosphoinositide 3-Kinase-Riven BK Channel up-Regulation in Mouse Chromaffin Cells.” Journal of Physiology, vol. 593, no. 22, Wiley-Blackwell, 2015, pp. 4835–53, doi:10.1113/JP271078."},"publication":"Journal of Physiology","issue":"22","abstract":[{"lang":"eng","text":"Leptin is an adipokine produced by the adipose tissue regulating body weight through its appetite-suppressing effect. Besides being expressed in the hypothalamus and hippocampus, leptin receptors (ObRs) are also present in chromaffin cells of the adrenal medulla. In the present study, we report the effect of leptin on mouse chromaffin cell (MCC) functionality, focusing on cell excitability and catecholamine secretion. Acute application of leptin (1 nm) on spontaneously firing MCCs caused a slowly developing membrane hyperpolarization followed by complete blockade of action potential (AP) firing. This inhibitory effect at rest was abolished by the BK channel blocker paxilline (1 μm), suggesting the involvement of BK potassium channels. Single-channel recordings in 'perforated microvesicles' confirmed that leptin increased BK channel open probability without altering its unitary conductance. BK channel up-regulation was associated with the phosphoinositide 3-kinase (PI3K) signalling cascade because the PI3K specific inhibitor wortmannin (100 nm) fully prevented BK current increase. We also tested the effect of leptin on evoked AP firing and Ca2+-driven exocytosis. Although leptin preserves well-adapted AP trains of lower frequency, APs are broader and depolarization-evoked exocytosis is increased as a result of the larger size of the ready-releasable pool and higher frequency of vesicle release. The kinetics and quantal size of single secretory events remained unaltered. Leptin had no effect on firing and secretion in db-/db- mice lacking the ObR gene, confirming its specificity. In conclusion, leptin exhibits a dual action on MCC activity. It dampens AP firing at rest but preserves AP firing and increases catecholamine secretion during sustained stimulation, highlighting the importance of the adipo-adrenal axis in the leptin-mediated increase of sympathetic tone and catecholamine release."}],"type":"journal_article","oa_version":"Submitted Version","intvolume":" 593","status":"public","title":"Dual action of leptin on rest-firing and stimulated catecholamine release via phosphoinositide 3-kinase-riven BK channel up-regulation in mouse chromaffin cells","_id":"1565","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"language":[{"iso":"eng"}],"doi":"10.3389/fncom.2015.00145","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"}],"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"month":"11","volume":9,"date_created":"2018-12-11T11:52:45Z","date_updated":"2021-01-12T06:51:37Z","author":[{"first_name":"Matthieu","last_name":"Gilson","full_name":"Gilson, Matthieu"},{"id":"3933349E-F248-11E8-B48F-1D18A9856A87","last_name":"Savin","first_name":"Cristina","full_name":"Savin, Cristina"},{"full_name":"Zenke, Friedemann","first_name":"Friedemann","last_name":"Zenke"}],"department":[{"_id":"GaTk"}],"publisher":"Frontiers Research Foundation","publication_status":"published","year":"2015","publist_id":"5607","ec_funded":1,"file_date_updated":"2020-07-14T12:45:02Z","article_number":"145","date_published":"2015-11-30T00:00:00Z","citation":{"chicago":"Gilson, Matthieu, Cristina Savin, and Friedemann Zenke. “Editorial: Emergent Neural Computation from the Interaction of Different Forms of Plasticity.” Frontiers in Computational Neuroscience. Frontiers Research Foundation, 2015. https://doi.org/10.3389/fncom.2015.00145.","mla":"Gilson, Matthieu, et al. “Editorial: Emergent Neural Computation from the Interaction of Different Forms of Plasticity.” Frontiers in Computational Neuroscience, vol. 9, no. 11, 145, Frontiers Research Foundation, 2015, doi:10.3389/fncom.2015.00145.","short":"M. Gilson, C. Savin, F. Zenke, Frontiers in Computational Neuroscience 9 (2015).","ista":"Gilson M, Savin C, Zenke F. 2015. Editorial: Emergent neural computation from the interaction of different forms of plasticity. Frontiers in Computational Neuroscience. 9(11), 145.","apa":"Gilson, M., Savin, C., & Zenke, F. (2015). Editorial: Emergent neural computation from the interaction of different forms of plasticity. Frontiers in Computational Neuroscience. Frontiers Research Foundation. https://doi.org/10.3389/fncom.2015.00145","ieee":"M. Gilson, C. Savin, and F. Zenke, “Editorial: Emergent neural computation from the interaction of different forms of plasticity,” Frontiers in Computational Neuroscience, vol. 9, no. 11. Frontiers Research Foundation, 2015.","ama":"Gilson M, Savin C, Zenke F. Editorial: Emergent neural computation from the interaction of different forms of plasticity. Frontiers in Computational Neuroscience. 2015;9(11). doi:10.3389/fncom.2015.00145"},"publication":"Frontiers in Computational Neuroscience","has_accepted_license":"1","day":"30","scopus_import":1,"oa_version":"Published Version","file":[{"checksum":"cea73b6d3ef1579f32da10b82f4de4fd","date_created":"2018-12-12T10:12:09Z","date_updated":"2020-07-14T12:45:02Z","relation":"main_file","file_id":"4927","file_size":187038,"content_type":"application/pdf","creator":"system","access_level":"open_access","file_name":"IST-2016-479-v1+1_fncom-09-00145.pdf"}],"pubrep_id":"479","intvolume":" 9","ddc":["570"],"status":"public","title":"Editorial: Emergent neural computation from the interaction of different forms of plasticity","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1564","issue":"11","type":"journal_article"},{"scopus_import":1,"has_accepted_license":"1","day":"18","citation":{"short":"Q. Chen, Y. Liu, S. Maere, E. Lee, G. Van Isterdael, Z. Xie, W. Xuan, J. Lucas, V. Vassileva, S. Kitakura, P. Marhavý, K.T. Wabnik, N. Geldner, E. Benková, J. Le, H. Fukaki, E. Grotewold, C. Li, J. Friml, F. Sack, T. Beeckman, S. Vanneste, Nature Communications 6 (2015).","mla":"Chen, Qian, et al. “A Coherent Transcriptional Feed-Forward Motif Model for Mediating Auxin-Sensitive PIN3 Expression during Lateral Root Development.” Nature Communications, vol. 6, 8821, Nature Publishing Group, 2015, doi:10.1038/ncomms9821.","chicago":"Chen, Qian, Yang Liu, Steven Maere, Eunkyoung Lee, Gert Van Isterdael, Zidian Xie, Wei Xuan, et al. “A Coherent Transcriptional Feed-Forward Motif Model for Mediating Auxin-Sensitive PIN3 Expression during Lateral Root Development.” Nature Communications. Nature Publishing Group, 2015. https://doi.org/10.1038/ncomms9821.","ama":"Chen Q, Liu Y, Maere S, et al. A coherent transcriptional feed-forward motif model for mediating auxin-sensitive PIN3 expression during lateral root development. Nature Communications. 2015;6. doi:10.1038/ncomms9821","apa":"Chen, Q., Liu, Y., Maere, S., Lee, E., Van Isterdael, G., Xie, Z., … Vanneste, S. (2015). A coherent transcriptional feed-forward motif model for mediating auxin-sensitive PIN3 expression during lateral root development. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms9821","ieee":"Q. Chen et al., “A coherent transcriptional feed-forward motif model for mediating auxin-sensitive PIN3 expression during lateral root development,” Nature Communications, vol. 6. Nature Publishing Group, 2015.","ista":"Chen Q, Liu Y, Maere S, Lee E, Van Isterdael G, Xie Z, Xuan W, Lucas J, Vassileva V, Kitakura S, Marhavý P, Wabnik KT, Geldner N, Benková E, Le J, Fukaki H, Grotewold E, Li C, Friml J, Sack F, Beeckman T, Vanneste S. 2015. A coherent transcriptional feed-forward motif model for mediating auxin-sensitive PIN3 expression during lateral root development. Nature Communications. 6, 8821."},"publication":"Nature Communications","date_published":"2015-11-18T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"Multiple plant developmental processes, such as lateral root development, depend on auxin distribution patterns that are in part generated by the PIN-formed family of auxin-efflux transporters. Here we propose that AUXIN RESPONSE FACTOR7 (ARF7) and the ARF7-regulated FOUR LIPS/MYB124 (FLP) transcription factors jointly form a coherent feed-forward motif that mediates the auxin-responsive PIN3 transcription in planta to steer the early steps of lateral root formation. This regulatory mechanism might endow the PIN3 circuitry with a temporal 'memory' of auxin stimuli, potentially maintaining and enhancing the robustness of the auxin flux directionality during lateral root development. The cooperative action between canonical auxin signalling and other transcription factors might constitute a general mechanism by which transcriptional auxin-sensitivity can be regulated at a tissue-specific level."}],"_id":"1574","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 6","ddc":["580"],"title":"A coherent transcriptional feed-forward motif model for mediating auxin-sensitive PIN3 expression during lateral root development","status":"public","pubrep_id":"477","oa_version":"Published Version","file":[{"file_name":"IST-2016-477-v1+1_ncomms9821.pdf","access_level":"open_access","file_size":1701815,"content_type":"application/pdf","creator":"system","relation":"main_file","file_id":"5085","date_updated":"2020-07-14T12:45:02Z","date_created":"2018-12-12T10:14:32Z","checksum":"8ff5c108899b548806e1cb7a302fe76d"}],"month":"11","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":"1","doi":"10.1038/ncomms9821","language":[{"iso":"eng"}],"article_number":"8821","publist_id":"5597","file_date_updated":"2020-07-14T12:45:02Z","year":"2015","acknowledgement":"of the European Research Council (project ERC-2011-StG-20101109-PSDP) (to J.F.), a FEBS long-term fellowship (to P.M.) ","department":[{"_id":"EvBe"},{"_id":"JiFr"}],"publisher":"Nature Publishing Group","publication_status":"published","author":[{"full_name":"Chen, Qian","last_name":"Chen","first_name":"Qian"},{"last_name":"Liu","first_name":"Yang","full_name":"Liu, Yang"},{"first_name":"Steven","last_name":"Maere","full_name":"Maere, Steven"},{"first_name":"Eunkyoung","last_name":"Lee","full_name":"Lee, Eunkyoung"},{"first_name":"Gert","last_name":"Van Isterdael","full_name":"Van Isterdael, Gert"},{"full_name":"Xie, Zidian","last_name":"Xie","first_name":"Zidian"},{"full_name":"Xuan, Wei","last_name":"Xuan","first_name":"Wei"},{"first_name":"Jessica","last_name":"Lucas","full_name":"Lucas, Jessica"},{"first_name":"Valya","last_name":"Vassileva","full_name":"Vassileva, Valya"},{"full_name":"Kitakura, Saeko","first_name":"Saeko","last_name":"Kitakura"},{"full_name":"Marhavy, Peter","orcid":"0000-0001-5227-5741","id":"3F45B078-F248-11E8-B48F-1D18A9856A87","last_name":"Marhavy","first_name":"Peter"},{"last_name":"Wabnik","first_name":"Krzysztof T","orcid":"0000-0001-7263-0560","id":"4DE369A4-F248-11E8-B48F-1D18A9856A87","full_name":"Wabnik, Krzysztof T"},{"full_name":"Geldner, Niko","last_name":"Geldner","first_name":"Niko"},{"orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","last_name":"Benková","first_name":"Eva","full_name":"Benková, Eva"},{"first_name":"Jie","last_name":"Le","full_name":"Le, Jie"},{"full_name":"Fukaki, Hidehiro","last_name":"Fukaki","first_name":"Hidehiro"},{"full_name":"Grotewold, Erich","first_name":"Erich","last_name":"Grotewold"},{"last_name":"Li","first_name":"Chuanyou","full_name":"Li, Chuanyou"},{"first_name":"Jirí","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí"},{"full_name":"Sack, Fred","last_name":"Sack","first_name":"Fred"},{"full_name":"Beeckman, Tom","last_name":"Beeckman","first_name":"Tom"},{"last_name":"Vanneste","first_name":"Steffen","full_name":"Vanneste, Steffen"}],"volume":6,"date_created":"2018-12-11T11:52:48Z","date_updated":"2021-01-12T06:51:42Z"},{"scopus_import":1,"day":"25","has_accepted_license":"1","publication":"Nature Communications","citation":{"chicago":"Chabaud, Mélanie, Mélina Heuzé, Marine Bretou, Pablo Vargas, Paolo Maiuri, Paola Solanes, Mathieu Maurin, et al. “Cell Migration and Antigen Capture Are Antagonistic Processes Coupled by Myosin II in Dendritic Cells.” Nature Communications. Nature Publishing Group, 2015. https://doi.org/10.1038/ncomms8526.","short":"M. Chabaud, M. Heuzé, M. Bretou, P. Vargas, P. Maiuri, P. Solanes, M. Maurin, E. Terriac, M. Le Berre, D. Lankar, T. Piolot, R. Adelstein, Y. Zhang, M.K. Sixt, J. Jacobelli, O. Bénichou, R. Voituriez, M. Piel, A. Lennon Duménil, Nature Communications 6 (2015).","mla":"Chabaud, Mélanie, et al. “Cell Migration and Antigen Capture Are Antagonistic Processes Coupled by Myosin II in Dendritic Cells.” Nature Communications, vol. 6, 7526, Nature Publishing Group, 2015, doi:10.1038/ncomms8526.","apa":"Chabaud, M., Heuzé, M., Bretou, M., Vargas, P., Maiuri, P., Solanes, P., … Lennon Duménil, A. (2015). Cell migration and antigen capture are antagonistic processes coupled by myosin II in dendritic cells. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms8526","ieee":"M. Chabaud et al., “Cell migration and antigen capture are antagonistic processes coupled by myosin II in dendritic cells,” Nature Communications, vol. 6. Nature Publishing Group, 2015.","ista":"Chabaud M, Heuzé M, Bretou M, Vargas P, Maiuri P, Solanes P, Maurin M, Terriac E, Le Berre M, Lankar D, Piolot T, Adelstein R, Zhang Y, Sixt MK, Jacobelli J, Bénichou O, Voituriez R, Piel M, Lennon Duménil A. 2015. Cell migration and antigen capture are antagonistic processes coupled by myosin II in dendritic cells. Nature Communications. 6, 7526.","ama":"Chabaud M, Heuzé M, Bretou M, et al. Cell migration and antigen capture are antagonistic processes coupled by myosin II in dendritic cells. Nature Communications. 2015;6. doi:10.1038/ncomms8526"},"date_published":"2015-06-25T00:00:00Z","type":"journal_article","abstract":[{"text":"The immune response relies on the migration of leukocytes and on their ability to stop in precise anatomical locations to fulfil their task. How leukocyte migration and function are coordinated is unknown. Here we show that in immature dendritic cells, which patrol their environment by engulfing extracellular material, cell migration and antigen capture are antagonistic. This antagonism results from transient enrichment of myosin IIA at the cell front, which disrupts the back-to-front gradient of the motor protein, slowing down locomotion but promoting antigen capture. We further highlight that myosin IIA enrichment at the cell front requires the MHC class II-associated invariant chain (Ii). Thus, by controlling myosin IIA localization, Ii imposes on dendritic cells an intermittent antigen capture behaviour that might facilitate environment patrolling. We propose that the requirement for myosin II in both cell migration and specific cell functions may provide a general mechanism for their coordination in time and space.","lang":"eng"}],"status":"public","title":"Cell migration and antigen capture are antagonistic processes coupled by myosin II in dendritic cells","ddc":["570"],"intvolume":" 6","_id":"1575","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"content_type":"application/pdf","file_size":4530215,"creator":"system","file_name":"IST-2016-476-v1+1_ncomms8526.pdf","access_level":"open_access","date_updated":"2020-07-14T12:45:02Z","date_created":"2018-12-12T10:11:58Z","checksum":"bae12e86be2adb28253f890b8bba8315","relation":"main_file","file_id":"4915"}],"oa_version":"Published Version","pubrep_id":"476","month":"06","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1038/ncomms8526","article_number":"7526","file_date_updated":"2020-07-14T12:45:02Z","publist_id":"5596","publication_status":"published","publisher":"Nature Publishing Group","department":[{"_id":"MiSi"}],"year":"2015","acknowledgement":"M.C. and M.L.H. were supported by fellowships from the Fondation pour la Recherche Médicale and the Association pour la Recherche contre le Cancer, respectively. This work was funded by grants from the City of Paris and the European Research Council to A.-M.L.-D. (Strapacemi 243103), the Association Nationale pour la Recherche (ANR-09-PIRI-0027-PCVI) and the InnaBiosanté foundation (Micemico) to A.-M.L.-D., M.P. and R.V., and the DCBIOL Labex from the French Government (ANR-10-IDEX-0001-02-PSL* and ANR-11-LABX-0043). The super-resolution SIM microscope was funded through an ERC Advanced Investigator Grant (250367) to Edith Heard (CNRS UMR3215/Inserm U934, Institut Curie).","date_created":"2018-12-11T11:52:48Z","date_updated":"2021-01-12T06:51:42Z","volume":6,"author":[{"last_name":"Chabaud","first_name":"Mélanie","full_name":"Chabaud, Mélanie"},{"first_name":"Mélina","last_name":"Heuzé","full_name":"Heuzé, Mélina"},{"full_name":"Bretou, Marine","first_name":"Marine","last_name":"Bretou"},{"first_name":"Pablo","last_name":"Vargas","full_name":"Vargas, Pablo"},{"last_name":"Maiuri","first_name":"Paolo","full_name":"Maiuri, Paolo"},{"last_name":"Solanes","first_name":"Paola","full_name":"Solanes, Paola"},{"full_name":"Maurin, Mathieu","first_name":"Mathieu","last_name":"Maurin"},{"full_name":"Terriac, Emmanuel","last_name":"Terriac","first_name":"Emmanuel"},{"first_name":"Maël","last_name":"Le Berre","full_name":"Le Berre, Maël"},{"first_name":"Danielle","last_name":"Lankar","full_name":"Lankar, Danielle"},{"full_name":"Piolot, Tristan","first_name":"Tristan","last_name":"Piolot"},{"full_name":"Adelstein, Robert","first_name":"Robert","last_name":"Adelstein"},{"full_name":"Zhang, Yingfan","first_name":"Yingfan","last_name":"Zhang"},{"full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","first_name":"Michael K","last_name":"Sixt"},{"full_name":"Jacobelli, Jordan","last_name":"Jacobelli","first_name":"Jordan"},{"full_name":"Bénichou, Olivier","last_name":"Bénichou","first_name":"Olivier"},{"full_name":"Voituriez, Raphaël","first_name":"Raphaël","last_name":"Voituriez"},{"full_name":"Piel, Matthieu","last_name":"Piel","first_name":"Matthieu"},{"last_name":"Lennon Duménil","first_name":"Ana","full_name":"Lennon Duménil, Ana"}]},{"day":"17","scopus_import":1,"date_published":"2015-02-17T00:00:00Z","citation":{"mla":"Doyle, Siamsa, et al. “An Early Secretory Pathway Mediated by Gnom-like 1 and Gnom Is Essential for Basal Polarity Establishment in Arabidopsis Thaliana.” PNAS, vol. 112, no. 7, National Academy of Sciences, 2015, pp. E806–15, doi:10.1073/pnas.1424856112.","short":"S. Doyle, A. Haegera, T. Vain, A. Rigala, C. Viotti, M. Łangowskaa, Q. Maa, J. Friml, N. Raikhel, G. Hickse, S. Robert, PNAS 112 (2015) E806–E815.","chicago":"Doyle, Siamsa, Ash Haegera, Thomas Vain, Adeline Rigala, Corrado Viotti, Małgorzata Łangowskaa, Qian Maa, et al. “An Early Secretory Pathway Mediated by Gnom-like 1 and Gnom Is Essential for Basal Polarity Establishment in Arabidopsis Thaliana.” PNAS. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1424856112.","ama":"Doyle S, Haegera A, Vain T, et al. An early secretory pathway mediated by gnom-like 1 and gnom is essential for basal polarity establishment in Arabidopsis thaliana. PNAS. 2015;112(7):E806-E815. doi:10.1073/pnas.1424856112","ista":"Doyle S, Haegera A, Vain T, Rigala A, Viotti C, Łangowskaa M, Maa Q, Friml J, Raikhel N, Hickse G, Robert S. 2015. An early secretory pathway mediated by gnom-like 1 and gnom is essential for basal polarity establishment in Arabidopsis thaliana. PNAS. 112(7), E806–E815.","ieee":"S. Doyle et al., “An early secretory pathway mediated by gnom-like 1 and gnom is essential for basal polarity establishment in Arabidopsis thaliana,” PNAS, vol. 112, no. 7. National Academy of Sciences, pp. E806–E815, 2015.","apa":"Doyle, S., Haegera, A., Vain, T., Rigala, A., Viotti, C., Łangowskaa, M., … Robert, S. (2015). An early secretory pathway mediated by gnom-like 1 and gnom is essential for basal polarity establishment in Arabidopsis thaliana. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1424856112"},"publication":"PNAS","page":"E806 - E815","issue":"7","abstract":[{"lang":"eng","text":"Spatial regulation of the plant hormone indole-3-acetic acid (IAA, or auxin) is essential for plant development. Auxin gradient establishment is mediated by polarly localized auxin transporters, including PIN-FORMED (PIN) proteins. Their localization and abundance at the plasma membrane are tightly regulated by endomembrane machinery, especially the endocytic and recycling pathways mediated by the ADP ribosylation factor guanine nucleotide exchange factor (ARF-GEF) GNOM. We assessed the role of the early secretory pathway in establishing PIN1 polarity in Arabidopsis thaliana by pharmacological and genetic approaches. We identified the compound endosidin 8 (ES8), which selectively interferes with PIN1 basal polarity without altering the polarity of apical proteins. ES8 alters the auxin distribution pattern in the root and induces a strong developmental phenotype, including reduced root length. The ARF-GEF- defective mutants gnom-like 1 ( gnl1-1) and gnom ( van7) are significantly resistant to ES8. The compound does not affect recycling or vacuolar trafficking of PIN1 but leads to its intracellular accumulation, resulting in loss of PIN1 basal polarity at the plasma membrane. Our data confirm a role for GNOM in endoplasmic reticulum (ER) - Golgi trafficking and reveal that a GNL1/GNOM-mediated early secretory pathway selectively regulates PIN1 basal polarity establishment in a manner essential for normal plant development."}],"type":"journal_article","oa_version":"Published Version","_id":"1569","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 112","status":"public","title":"An early secretory pathway mediated by gnom-like 1 and gnom is essential for basal polarity establishment in Arabidopsis thaliana","month":"02","doi":"10.1073/pnas.1424856112","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4343110/"}],"oa":1,"project":[{"name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300"}],"quality_controlled":"1","ec_funded":1,"publist_id":"5602","author":[{"full_name":"Doyle, Siamsa","first_name":"Siamsa","last_name":"Doyle"},{"full_name":"Haegera, Ash","last_name":"Haegera","first_name":"Ash"},{"first_name":"Thomas","last_name":"Vain","full_name":"Vain, Thomas"},{"full_name":"Rigala, Adeline","first_name":"Adeline","last_name":"Rigala"},{"last_name":"Viotti","first_name":"Corrado","full_name":"Viotti, Corrado"},{"last_name":"Łangowskaa","first_name":"Małgorzata","full_name":"Łangowskaa, Małgorzata"},{"last_name":"Maa","first_name":"Qian","full_name":"Maa, Qian"},{"full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jirí"},{"first_name":"Natasha","last_name":"Raikhel","full_name":"Raikhel, Natasha"},{"last_name":"Hickse","first_name":"Glenn","full_name":"Hickse, Glenn"},{"full_name":"Robert, Stéphanie","last_name":"Robert","first_name":"Stéphanie"}],"volume":112,"date_updated":"2021-01-12T06:51:39Z","date_created":"2018-12-11T11:52:46Z","year":"2015","acknowledgement":"This work was supported by Vetenskapsrådet and Vinnova (Verket för Innovationssystemet) (S.M.D., T.V., M.Ł., and S.R.), Knut och Alice Wallenbergs Stiftelse (S.M.D., A.R., and C.V.), Kempestiftelserna (A.H. and Q.M.), Carl Tryggers Stiftelse för Vetenskaplig Forskning (Q.M.), European Research Council Grant ERC-2011-StG-20101109-PSDP (to J.F.), US Department of Energy Grant DE-FG02-02ER15295 (to N.V.R.), and National Science Foundation Grant MCB-0817916 (to N.V.R. and G.R.H.). ","publisher":"National Academy of Sciences","department":[{"_id":"JiFr"}],"publication_status":"published"},{"publist_id":"5601","ec_funded":1,"date_updated":"2021-01-12T06:51:40Z","date_created":"2018-12-11T11:52:47Z","volume":112,"author":[{"first_name":"Ralf","last_name":"Der","full_name":"Der, Ralf"},{"full_name":"Martius, Georg S","id":"3A276B68-F248-11E8-B48F-1D18A9856A87","last_name":"Martius","first_name":"Georg S"}],"publication_status":"published","department":[{"_id":"ChLa"},{"_id":"GaTk"}],"publisher":"National Academy of Sciences","year":"2015","pmid":1,"month":"11","language":[{"iso":"eng"}],"doi":"10.1073/pnas.1508400112","quality_controlled":"1","project":[{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"}],"oa":1,"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4653169/","open_access":"1"}],"external_id":{"pmid":["26504200"]},"abstract":[{"text":"Grounding autonomous behavior in the nervous system is a fundamental challenge for neuroscience. In particular, self-organized behavioral development provides more questions than answers. Are there special functional units for curiosity, motivation, and creativity? This paper argues that these features can be grounded in synaptic plasticity itself, without requiring any higher-level constructs. We propose differential extrinsic plasticity (DEP) as a new synaptic rule for self-learning systems and apply it to a number of complex robotic systems as a test case. Without specifying any purpose or goal, seemingly purposeful and adaptive rhythmic behavior is developed, displaying a certain level of sensorimotor intelligence. These surprising results require no systemspecific modifications of the DEP rule. They rather arise from the underlying mechanism of spontaneous symmetry breaking,which is due to the tight brain body environment coupling. The new synaptic rule is biologically plausible and would be an interesting target for neurobiological investigation. We also argue that this neuronal mechanism may have been a catalyst in natural evolution.","lang":"eng"}],"issue":"45","type":"journal_article","oa_version":"Submitted Version","status":"public","title":"Novel plasticity rule can explain the development of sensorimotor intelligence","intvolume":" 112","_id":"1570","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"10","scopus_import":1,"date_published":"2015-11-10T00:00:00Z","page":"E6224 - E6232","publication":"PNAS","citation":{"chicago":"Der, Ralf, and Georg S Martius. “Novel Plasticity Rule Can Explain the Development of Sensorimotor Intelligence.” PNAS. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1508400112.","short":"R. Der, G.S. Martius, PNAS 112 (2015) E6224–E6232.","mla":"Der, Ralf, and Georg S. Martius. “Novel Plasticity Rule Can Explain the Development of Sensorimotor Intelligence.” PNAS, vol. 112, no. 45, National Academy of Sciences, 2015, pp. E6224–32, doi:10.1073/pnas.1508400112.","apa":"Der, R., & Martius, G. S. (2015). Novel plasticity rule can explain the development of sensorimotor intelligence. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1508400112","ieee":"R. Der and G. S. Martius, “Novel plasticity rule can explain the development of sensorimotor intelligence,” PNAS, vol. 112, no. 45. National Academy of Sciences, pp. E6224–E6232, 2015.","ista":"Der R, Martius GS. 2015. Novel plasticity rule can explain the development of sensorimotor intelligence. PNAS. 112(45), E6224–E6232.","ama":"Der R, Martius GS. Novel plasticity rule can explain the development of sensorimotor intelligence. PNAS. 2015;112(45):E6224-E6232. doi:10.1073/pnas.1508400112"}},{"type":"journal_article","issue":"1","publist_id":"5599","abstract":[{"text":"We consider the quantum ferromagnetic Heisenberg model in three dimensions, for all spins S ≥ 1/2. We rigorously prove the validity of the spin-wave approximation for the excitation spectrum, at the level of the first non-trivial contribution to the free energy at low temperatures. Our proof comes with explicit, constructive upper and lower bounds on the error term. It uses in an essential way the bosonic formulation of the model in terms of the Holstein-Primakoff representation. In this language, the model describes interacting bosons with a hard-core on-site repulsion and a nearest-neighbor attraction. This attractive interaction makes the lower bound on the free energy particularly tricky: the key idea there is to prove a differential inequality for the two-particle density, which is thereby shown to be smaller than the probability density of a suitably weighted two-particle random process on the lattice.\r\n","lang":"eng"}],"_id":"1572","year":"2015","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 339","publisher":"Springer","department":[{"_id":"RoSe"}],"title":"Validity of the spin-wave approximation for the free energy of the Heisenberg ferromagnet","status":"public","publication_status":"published","author":[{"full_name":"Correggi, Michele","first_name":"Michele","last_name":"Correggi"},{"full_name":"Giuliani, Alessandro","first_name":"Alessandro","last_name":"Giuliani"},{"full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","last_name":"Seiringer","first_name":"Robert"}],"oa_version":"Preprint","volume":339,"date_created":"2018-12-11T11:52:47Z","date_updated":"2021-01-12T06:51:41Z","scopus_import":1,"month":"06","day":"23","citation":{"chicago":"Correggi, Michele, Alessandro Giuliani, and Robert Seiringer. “Validity of the Spin-Wave Approximation for the Free Energy of the Heisenberg Ferromagnet.” Communications in Mathematical Physics. Springer, 2015. https://doi.org/10.1007/s00220-015-2402-0.","mla":"Correggi, Michele, et al. “Validity of the Spin-Wave Approximation for the Free Energy of the Heisenberg Ferromagnet.” Communications in Mathematical Physics, vol. 339, no. 1, Springer, 2015, pp. 279–307, doi:10.1007/s00220-015-2402-0.","short":"M. Correggi, A. Giuliani, R. Seiringer, Communications in Mathematical Physics 339 (2015) 279–307.","ista":"Correggi M, Giuliani A, Seiringer R. 2015. Validity of the spin-wave approximation for the free energy of the Heisenberg ferromagnet. Communications in Mathematical Physics. 339(1), 279–307.","apa":"Correggi, M., Giuliani, A., & Seiringer, R. (2015). Validity of the spin-wave approximation for the free energy of the Heisenberg ferromagnet. Communications in Mathematical Physics. Springer. https://doi.org/10.1007/s00220-015-2402-0","ieee":"M. Correggi, A. Giuliani, and R. Seiringer, “Validity of the spin-wave approximation for the free energy of the Heisenberg ferromagnet,” Communications in Mathematical Physics, vol. 339, no. 1. Springer, pp. 279–307, 2015.","ama":"Correggi M, Giuliani A, Seiringer R. Validity of the spin-wave approximation for the free energy of the Heisenberg ferromagnet. Communications in Mathematical Physics. 2015;339(1):279-307. doi:10.1007/s00220-015-2402-0"},"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1312.7873"}],"oa":1,"publication":"Communications in Mathematical Physics","page":"279 - 307","quality_controlled":"1","doi":"10.1007/s00220-015-2402-0","date_published":"2015-06-23T00:00:00Z","language":[{"iso":"eng"}]},{"oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1573","intvolume":" 68","title":"Unconditional uniqueness for the cubic gross pitaevskii hierarchy via quantum de finetti","status":"public","issue":"10","abstract":[{"lang":"eng","text":"We present a new, simpler proof of the unconditional uniqueness of solutions to the cubic Gross-Pitaevskii hierarchy in ℝ3. One of the main tools in our analysis is the quantum de Finetti theorem. Our uniqueness result is equivalent to the one established in the celebrated works of Erdos, Schlein, and Yau."}],"type":"journal_article","date_published":"2015-10-01T00:00:00Z","citation":{"ama":"Chen T, Hainzl C, Pavlović N, Seiringer R. Unconditional uniqueness for the cubic gross pitaevskii hierarchy via quantum de finetti. Communications on Pure and Applied Mathematics. 2015;68(10):1845-1884. doi:10.1002/cpa.21552","apa":"Chen, T., Hainzl, C., Pavlović, N., & Seiringer, R. (2015). Unconditional uniqueness for the cubic gross pitaevskii hierarchy via quantum de finetti. Communications on Pure and Applied Mathematics. Wiley. https://doi.org/10.1002/cpa.21552","ieee":"T. Chen, C. Hainzl, N. Pavlović, and R. Seiringer, “Unconditional uniqueness for the cubic gross pitaevskii hierarchy via quantum de finetti,” Communications on Pure and Applied Mathematics, vol. 68, no. 10. Wiley, pp. 1845–1884, 2015.","ista":"Chen T, Hainzl C, Pavlović N, Seiringer R. 2015. Unconditional uniqueness for the cubic gross pitaevskii hierarchy via quantum de finetti. Communications on Pure and Applied Mathematics. 68(10), 1845–1884.","short":"T. Chen, C. Hainzl, N. Pavlović, R. Seiringer, Communications on Pure and Applied Mathematics 68 (2015) 1845–1884.","mla":"Chen, Thomas, et al. “Unconditional Uniqueness for the Cubic Gross Pitaevskii Hierarchy via Quantum de Finetti.” Communications on Pure and Applied Mathematics, vol. 68, no. 10, Wiley, 2015, pp. 1845–84, doi:10.1002/cpa.21552.","chicago":"Chen, Thomas, Christian Hainzl, Nataša Pavlović, and Robert Seiringer. “Unconditional Uniqueness for the Cubic Gross Pitaevskii Hierarchy via Quantum de Finetti.” Communications on Pure and Applied Mathematics. Wiley, 2015. https://doi.org/10.1002/cpa.21552."},"publication":"Communications on Pure and Applied Mathematics","page":"1845 - 1884","day":"01","scopus_import":1,"author":[{"first_name":"Thomas","last_name":"Chen","full_name":"Chen, Thomas"},{"first_name":"Christian","last_name":"Hainzl","full_name":"Hainzl, Christian"},{"full_name":"Pavlović, Nataša","first_name":"Nataša","last_name":"Pavlović"},{"orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","last_name":"Seiringer","first_name":"Robert","full_name":"Seiringer, Robert"}],"volume":68,"date_created":"2018-12-11T11:52:48Z","date_updated":"2021-01-12T06:51:41Z","year":"2015","department":[{"_id":"RoSe"}],"publisher":"Wiley","publication_status":"published","publist_id":"5598","doi":"10.1002/cpa.21552","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"url":"http://arxiv.org/abs/1307.3168","open_access":"1"}],"project":[{"_id":"26450934-B435-11E9-9278-68D0E5697425","name":"NSERC Postdoctoral fellowship"}],"quality_controlled":"1","month":"10"},{"day":"17","has_accepted_license":"1","article_processing_charge":"No","scopus_import":1,"date_published":"2015-12-17T00:00:00Z","article_type":"original","page":"430 - 443","publication":"Neuroscience","citation":{"ama":"Brenes O, Vandael DH, Carbone E, Montarolo P, Ghirardi M. Knock-down of synapsin alters cell excitability and action potential waveform by potentiating BK and voltage gated Ca2 currents in Helix serotonergic neurons. Neuroscience. 2015;311:430-443. doi:10.1016/j.neuroscience.2015.10.046","ista":"Brenes O, Vandael DH, Carbone E, Montarolo P, Ghirardi M. 2015. Knock-down of synapsin alters cell excitability and action potential waveform by potentiating BK and voltage gated Ca2 currents in Helix serotonergic neurons. Neuroscience. 311, 430–443.","apa":"Brenes, O., Vandael, D. H., Carbone, E., Montarolo, P., & Ghirardi, M. (2015). Knock-down of synapsin alters cell excitability and action potential waveform by potentiating BK and voltage gated Ca2 currents in Helix serotonergic neurons. Neuroscience. Elsevier. https://doi.org/10.1016/j.neuroscience.2015.10.046","ieee":"O. Brenes, D. H. Vandael, E. Carbone, P. Montarolo, and M. Ghirardi, “Knock-down of synapsin alters cell excitability and action potential waveform by potentiating BK and voltage gated Ca2 currents in Helix serotonergic neurons,” Neuroscience, vol. 311. Elsevier, pp. 430–443, 2015.","mla":"Brenes, Oscar, et al. “Knock-down of Synapsin Alters Cell Excitability and Action Potential Waveform by Potentiating BK and Voltage Gated Ca2 Currents in Helix Serotonergic Neurons.” Neuroscience, vol. 311, Elsevier, 2015, pp. 430–43, doi:10.1016/j.neuroscience.2015.10.046.","short":"O. Brenes, D.H. Vandael, E. Carbone, P. Montarolo, M. Ghirardi, Neuroscience 311 (2015) 430–443.","chicago":"Brenes, Oscar, David H Vandael, Emilio Carbone, Pier Montarolo, and Mirella Ghirardi. “Knock-down of Synapsin Alters Cell Excitability and Action Potential Waveform by Potentiating BK and Voltage Gated Ca2 Currents in Helix Serotonergic Neurons.” Neuroscience. Elsevier, 2015. https://doi.org/10.1016/j.neuroscience.2015.10.046."},"abstract":[{"text":"Synapsins (Syns) are an evolutionarily conserved family of presynaptic proteins crucial for the fine-tuning of synaptic function. A large amount of experimental evidences has shown that Syns are involved in the development of epileptic phenotypes and several mutations in Syn genes have been associated with epilepsy in humans and animal models. Syn mutations induce alterations in circuitry and neurotransmitter release, differentially affecting excitatory and inhibitory synapses, thus causing an excitation/inhibition imbalance in network excitability toward hyperexcitability that may be a determinant with regard to the development of epilepsy. Another approach to investigate epileptogenic mechanisms is to understand how silencing Syn affects the cellular behavior of single neurons and is associated with the hyperexcitable phenotypes observed in epilepsy. Here, we examined the functional effects of antisense-RNA inhibition of Syn expression on individually identified and isolated serotonergic cells of the Helix land snail. We found that Helix synapsin silencing increases cell excitability characterized by a slightly depolarized resting membrane potential, decreases the rheobase, reduces the threshold for action potential (AP) firing and increases the mean and instantaneous firing rates, with respect to control cells. The observed increase of Ca2+ and BK currents in Syn-silenced cells seems to be related to changes in the shape of the AP waveform. These currents sustain the faster spiking in Syn-deficient cells by increasing the after hyperpolarization and limiting the Na+ and Ca2+ channel inactivation during repetitive firing. This in turn speeds up the depolarization phase by reaching the AP threshold faster. Our results provide evidence that Syn silencing increases intrinsic cell excitability associated with increased Ca2+ and Ca2+-dependent BK currents in the absence of excitatory or inhibitory inputs.","lang":"eng"}],"type":"journal_article","file":[{"file_id":"7849","relation":"main_file","date_created":"2020-05-15T06:50:20Z","date_updated":"2020-07-14T12:45:02Z","checksum":"af2c4c994718c7be417eba0dc746aac9","file_name":"2015_Neuroscience_Brenes.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":5563015}],"oa_version":"Submitted Version","title":"Knock-down of synapsin alters cell excitability and action potential waveform by potentiating BK and voltage gated Ca2 currents in Helix serotonergic neurons","status":"public","ddc":["570"],"intvolume":" 311","_id":"1580","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"12","language":[{"iso":"eng"}],"doi":"10.1016/j.neuroscience.2015.10.046","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"file_date_updated":"2020-07-14T12:45:02Z","publist_id":"5591","date_created":"2018-12-11T11:52:50Z","date_updated":"2021-01-12T06:51:44Z","volume":311,"author":[{"last_name":"Brenes","first_name":"Oscar","full_name":"Brenes, Oscar"},{"first_name":"David H","last_name":"Vandael","id":"3AE48E0A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7577-1676","full_name":"Vandael, David H"},{"first_name":"Emilio","last_name":"Carbone","full_name":"Carbone, Emilio"},{"full_name":"Montarolo, Pier","last_name":"Montarolo","first_name":"Pier"},{"first_name":"Mirella","last_name":"Ghirardi","full_name":"Ghirardi, Mirella"}],"publication_status":"published","department":[{"_id":"PeJo"}],"publisher":"Elsevier","year":"2015"},{"citation":{"short":"A. Carvalho, B. Vicoso, C. Russo, B. Swenor, A. Clark, PNAS 112 (2015) 12450–12455.","mla":"Carvalho, Antonio, et al. “Birth of a New Gene on the Y Chromosome of Drosophila Melanogaster.” PNAS, vol. 112, no. 40, National Academy of Sciences, 2015, pp. 12450–55, doi:10.1073/pnas.1516543112.","chicago":"Carvalho, Antonio, Beatriz Vicoso, Claudia Russo, Bonnielin Swenor, and Andrew Clark. “Birth of a New Gene on the Y Chromosome of Drosophila Melanogaster.” PNAS. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1516543112.","ama":"Carvalho A, Vicoso B, Russo C, Swenor B, Clark A. Birth of a new gene on the Y chromosome of Drosophila melanogaster. PNAS. 2015;112(40):12450-12455. doi:10.1073/pnas.1516543112","ieee":"A. Carvalho, B. Vicoso, C. Russo, B. Swenor, and A. Clark, “Birth of a new gene on the Y chromosome of Drosophila melanogaster,” PNAS, vol. 112, no. 40. National Academy of Sciences, pp. 12450–12455, 2015.","apa":"Carvalho, A., Vicoso, B., Russo, C., Swenor, B., & Clark, A. (2015). Birth of a new gene on the Y chromosome of Drosophila melanogaster. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1516543112","ista":"Carvalho A, Vicoso B, Russo C, Swenor B, Clark A. 2015. Birth of a new gene on the Y chromosome of Drosophila melanogaster. PNAS. 112(40), 12450–12455."},"publication":"PNAS","page":"12450 - 12455","article_type":"original","date_published":"2015-10-06T00:00:00Z","scopus_import":1,"article_processing_charge":"No","day":"06","_id":"1577","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 112","status":"public","title":"Birth of a new gene on the Y chromosome of Drosophila melanogaster","oa_version":"Published Version","type":"journal_article","issue":"40","abstract":[{"text":"Contrary to the pattern seen in mammalian sex chromosomes, where most Y-linked genes have X-linked homologs, the Drosophila X and Y chromosomes appear to be unrelated. Most of the Y-linked genes have autosomal paralogs, so autosome-to-Y transposition must be the main source of Drosophila Y-linked genes. Here we show how these genes were acquired. We found a previously unidentified gene (flagrante delicto Y, FDY) that originated from a recent duplication of the autosomal gene vig2 to the Y chromosome of Drosophila melanogaster. Four contiguous genes were duplicated along with vig2, but they became pseudogenes through the accumulation of deletions and transposable element insertions, whereas FDY remained functional, acquired testis-specific expression, and now accounts for ∼20% of the vig2-like mRNA in testis. FDY is absent in the closest relatives of D. melanogaster, and DNA sequence divergence indicates that the duplication to the Y chromosome occurred ∼2 million years ago. Thus, FDY provides a snapshot of the early stages of the establishment of a Y-linked gene and demonstrates how the Drosophila Y has been accumulating autosomal genes.","lang":"eng"}],"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4603513/","open_access":"1"}],"oa":1,"external_id":{"pmid":["26385968"]},"quality_controlled":"1","doi":"10.1073/pnas.1516543112","language":[{"iso":"eng"}],"month":"10","pmid":1,"acknowledgement":"This work was supported by grants from Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), FAPERJ, and CAPES (to A.B.C.), and National Institutes of Health Grant R01 GM64590 (to A.G.C. and A.B.C.).\r\nWe thank M. Vibranovski, C. Bergman, and the Berkeley Drosophila Genome Project for access to unpublished data; M. Vibranovski, R. Hoskins, S. Celniker, C. Kennedy, J. Carlson, S. Galasinski, B. Wakimoto, J. Yasuhara, G. Sutton, M. Kuhner, J. Felsenstein, and C. Santos for help in various steps of the work; and B. Bitner-Mathe, R. Ventura, the members of the A.B.C. and A.G.C. laboratories, and two reviewers for many valuable comments on the manuscript.","year":"2015","publisher":"National Academy of Sciences","department":[{"_id":"BeVi"}],"publication_status":"published","author":[{"first_name":"Antonio","last_name":"Carvalho","full_name":"Carvalho, Antonio"},{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","first_name":"Beatriz","last_name":"Vicoso","full_name":"Vicoso, Beatriz"},{"full_name":"Russo, Claudia","first_name":"Claudia","last_name":"Russo"},{"full_name":"Swenor, Bonnielin","first_name":"Bonnielin","last_name":"Swenor"},{"last_name":"Clark","first_name":"Andrew","full_name":"Clark, Andrew"}],"volume":112,"date_created":"2018-12-11T11:52:49Z","date_updated":"2021-01-12T06:51:43Z","publist_id":"5594"},{"date_updated":"2021-01-12T06:51:43Z","date_created":"2018-12-11T11:52:50Z","volume":367,"author":[{"last_name":"Brooks","first_name":"Christopher","full_name":"Brooks, Christopher"},{"full_name":"Martin Del Campo Sanchez, Abraham","first_name":"Abraham","last_name":"Martin Del Campo Sanchez","id":"4CF47F6A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Sottile, Frank","first_name":"Frank","last_name":"Sottile"}],"publication_status":"published","department":[{"_id":"CaUh"}],"publisher":"American Mathematical Society","year":"2015","acknowledgement":"This research was supported in part by NSF grant DMS-915211 and the Institut Mittag-Leffler.\r\n","publist_id":"5592","language":[{"iso":"eng"}],"doi":"10.1090/S0002-9947-2014-06192-8","quality_controlled":"1","main_file_link":[{"url":"http://arxiv.org/abs/1207.4280","open_access":"1"}],"oa":1,"month":"06","oa_version":"Preprint","title":"Galois groups of Schubert problems of lines are at least alternating","status":"public","intvolume":" 367","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1579","abstract":[{"lang":"eng","text":"We show that the Galois group of any Schubert problem involving lines in projective space contains the alternating group. This constitutes the largest family of enumerative problems whose Galois groups have been largely determined. Using a criterion of Vakil and a special position argument due to Schubert, our result follows from a particular inequality among Kostka numbers of two-rowed tableaux. In most cases, a combinatorial injection proves the inequality. For the remaining cases, we use the Weyl integral formulas to obtain an integral formula for these Kostka numbers. This rewrites the inequality as an integral, which we estimate to establish the inequality."}],"issue":"6","type":"journal_article","date_published":"2015-06-01T00:00:00Z","page":"4183 - 4206","publication":"Transactions of the American Mathematical Society","citation":{"apa":"Brooks, C., Martin del Campo Sanchez, A., & Sottile, F. (2015). Galois groups of Schubert problems of lines are at least alternating. Transactions of the American Mathematical Society. American Mathematical Society. https://doi.org/10.1090/S0002-9947-2014-06192-8","ieee":"C. Brooks, A. Martin del Campo Sanchez, and F. Sottile, “Galois groups of Schubert problems of lines are at least alternating,” Transactions of the American Mathematical Society, vol. 367, no. 6. American Mathematical Society, pp. 4183–4206, 2015.","ista":"Brooks C, Martin del Campo Sanchez A, Sottile F. 2015. Galois groups of Schubert problems of lines are at least alternating. Transactions of the American Mathematical Society. 367(6), 4183–4206.","ama":"Brooks C, Martin del Campo Sanchez A, Sottile F. Galois groups of Schubert problems of lines are at least alternating. Transactions of the American Mathematical Society. 2015;367(6):4183-4206. doi:10.1090/S0002-9947-2014-06192-8","chicago":"Brooks, Christopher, Abraham Martin del Campo Sanchez, and Frank Sottile. “Galois Groups of Schubert Problems of Lines Are at Least Alternating.” Transactions of the American Mathematical Society. American Mathematical Society, 2015. https://doi.org/10.1090/S0002-9947-2014-06192-8.","short":"C. Brooks, A. Martin del Campo Sanchez, F. Sottile, Transactions of the American Mathematical Society 367 (2015) 4183–4206.","mla":"Brooks, Christopher, et al. “Galois Groups of Schubert Problems of Lines Are at Least Alternating.” Transactions of the American Mathematical Society, vol. 367, no. 6, American Mathematical Society, 2015, pp. 4183–206, doi:10.1090/S0002-9947-2014-06192-8."},"day":"01","article_processing_charge":"No","scopus_import":1},{"month":"12","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1038/srep18589","article_number":"18589","publist_id":"5582","file_date_updated":"2020-07-14T12:45:03Z","publisher":"Nature Publishing Group","department":[{"_id":"BjHo"}],"publication_status":"published","year":"2015","volume":5,"date_updated":"2021-01-12T06:51:48Z","date_created":"2018-12-11T11:52:53Z","author":[{"full_name":"Altmeyer, Sebastian","id":"2EE67FDC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5964-0203","first_name":"Sebastian","last_name":"Altmeyer"},{"first_name":"Younghae","last_name":"Do","full_name":"Do, Younghae"},{"first_name":"Ying","last_name":"Lai","full_name":"Lai, Ying"}],"scopus_import":1,"has_accepted_license":"1","day":"21","article_type":"original","citation":{"ama":"Altmeyer S, Do Y, Lai Y. Magnetic field induced flow pattern reversal in a ferrofluidic Taylor-Couette system. Scientific Reports. 2015;5. doi:10.1038/srep18589","ieee":"S. Altmeyer, Y. Do, and Y. Lai, “Magnetic field induced flow pattern reversal in a ferrofluidic Taylor-Couette system,” Scientific Reports, vol. 5. Nature Publishing Group, 2015.","apa":"Altmeyer, S., Do, Y., & Lai, Y. (2015). Magnetic field induced flow pattern reversal in a ferrofluidic Taylor-Couette system. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/srep18589","ista":"Altmeyer S, Do Y, Lai Y. 2015. Magnetic field induced flow pattern reversal in a ferrofluidic Taylor-Couette system. Scientific Reports. 5, 18589.","short":"S. Altmeyer, Y. Do, Y. Lai, Scientific Reports 5 (2015).","mla":"Altmeyer, Sebastian, et al. “Magnetic Field Induced Flow Pattern Reversal in a Ferrofluidic Taylor-Couette System.” Scientific Reports, vol. 5, 18589, Nature Publishing Group, 2015, doi:10.1038/srep18589.","chicago":"Altmeyer, Sebastian, Younghae Do, and Ying Lai. “Magnetic Field Induced Flow Pattern Reversal in a Ferrofluidic Taylor-Couette System.” Scientific Reports. Nature Publishing Group, 2015. https://doi.org/10.1038/srep18589."},"publication":"Scientific Reports","date_published":"2015-12-21T00:00:00Z","type":"journal_article","abstract":[{"text":"We investigate the dynamics of ferrofluidic wavy vortex flows in the counter-rotating Taylor-Couette system, with a focus on wavy flows with a mixture of the dominant azimuthal modes. Without external magnetic field flows are stable and pro-grade with respect to the rotation of the inner cylinder. More complex behaviors can arise when an axial or a transverse magnetic field is applied. Depending on the direction and strength of the field, multi-stable wavy states and bifurcations can occur. We uncover the phenomenon of flow pattern reversal as the strength of the magnetic field is increased through a critical value. In between the regimes of pro-grade and retrograde flow rotations, standing waves with zero angular velocities can emerge. A striking finding is that, under a transverse magnetic field, a second reversal in the flow pattern direction can occur, where the flow pattern evolves into pro-grade rotation again from a retrograde state. Flow reversal is relevant to intriguing phenomena in nature such as geomagnetic reversal. Our results suggest that, in ferrofluids, flow pattern reversal can be induced by varying a magnetic field in a controlled manner, which can be realized in laboratory experiments with potential applications in the development of modern fluid devices.","lang":"eng"}],"intvolume":" 5","ddc":["530","540"],"title":"Magnetic field induced flow pattern reversal in a ferrofluidic Taylor-Couette system","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1589","oa_version":"Published Version","file":[{"creator":"system","file_size":2771236,"content_type":"application/pdf","access_level":"open_access","file_name":"IST-2016-472-v1+1_srep18589.pdf","checksum":"927e151674347661ce36eae2818dafdc","date_updated":"2020-07-14T12:45:03Z","date_created":"2018-12-12T10:13:49Z","file_id":"5036","relation":"main_file"}],"pubrep_id":"472"},{"publist_id":"5587","file_date_updated":"2020-07-14T12:45:03Z","publisher":"Elsevier","department":[{"_id":"HeEd"}],"publication_status":"published","year":"2015","volume":48,"date_created":"2018-12-11T11:52:51Z","date_updated":"2023-02-23T10:05:22Z","related_material":{"record":[{"status":"public","relation":"other","id":"1582"}]},"author":[{"last_name":"Biedl","first_name":"Therese","full_name":"Biedl, Therese"},{"full_name":"Held, Martin","last_name":"Held","first_name":"Martin"},{"orcid":"0000-0002-8871-5814","id":"4700A070-F248-11E8-B48F-1D18A9856A87","last_name":"Huber","first_name":"Stefan","full_name":"Huber, Stefan"},{"first_name":"Dominik","last_name":"Kaaser","full_name":"Kaaser, Dominik"},{"full_name":"Palfrader, Peter","first_name":"Peter","last_name":"Palfrader"}],"month":"07","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1016/j.comgeo.2015.01.004","type":"journal_article","issue":"5","abstract":[{"lang":"eng","text":"We investigate weighted straight skeletons from a geometric, graph-theoretical, and combinatorial point of view. We start with a thorough definition and shed light on some ambiguity issues in the procedural definition. We investigate the geometry, combinatorics, and topology of faces and the roof model, and we discuss in which cases a weighted straight skeleton is connected. Finally, we show that the weighted straight skeleton of even a simple polygon may be non-planar and may contain cycles, and we discuss under which restrictions on the weights and/or the input polygon the weighted straight skeleton still behaves similar to its unweighted counterpart. In particular, we obtain a non-procedural description and a linear-time construction algorithm for the straight skeleton of strictly convex polygons with arbitrary weights."}],"intvolume":" 48","title":"Reprint of: Weighted straight skeletons in the plane","status":"public","ddc":["000"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1584","oa_version":"Published Version","file":[{"file_id":"5292","relation":"main_file","checksum":"5b33719a86f7f4c8e5dc62c1b6893f49","date_updated":"2020-07-14T12:45:03Z","date_created":"2018-12-12T10:17:36Z","access_level":"open_access","file_name":"IST-2016-475-v1+1_1-s2.0-S092577211500005X-main.pdf","creator":"system","file_size":508379,"content_type":"application/pdf"}],"pubrep_id":"475","scopus_import":1,"has_accepted_license":"1","day":"01","page":"429 - 442","citation":{"chicago":"Biedl, Therese, Martin Held, Stefan Huber, Dominik Kaaser, and Peter Palfrader. “Reprint of: Weighted Straight Skeletons in the Plane.” Computational Geometry: Theory and Applications. Elsevier, 2015. https://doi.org/10.1016/j.comgeo.2015.01.004.","short":"T. Biedl, M. Held, S. Huber, D. Kaaser, P. Palfrader, Computational Geometry: Theory and Applications 48 (2015) 429–442.","mla":"Biedl, Therese, et al. “Reprint of: Weighted Straight Skeletons in the Plane.” Computational Geometry: Theory and Applications, vol. 48, no. 5, Elsevier, 2015, pp. 429–42, doi:10.1016/j.comgeo.2015.01.004.","apa":"Biedl, T., Held, M., Huber, S., Kaaser, D., & Palfrader, P. (2015). Reprint of: Weighted straight skeletons in the plane. Computational Geometry: Theory and Applications. Elsevier. https://doi.org/10.1016/j.comgeo.2015.01.004","ieee":"T. Biedl, M. Held, S. Huber, D. Kaaser, and P. Palfrader, “Reprint of: Weighted straight skeletons in the plane,” Computational Geometry: Theory and Applications, vol. 48, no. 5. Elsevier, pp. 429–442, 2015.","ista":"Biedl T, Held M, Huber S, Kaaser D, Palfrader P. 2015. Reprint of: Weighted straight skeletons in the plane. Computational Geometry: Theory and Applications. 48(5), 429–442.","ama":"Biedl T, Held M, Huber S, Kaaser D, Palfrader P. Reprint of: Weighted straight skeletons in the plane. Computational Geometry: Theory and Applications. 2015;48(5):429-442. doi:10.1016/j.comgeo.2015.01.004"},"publication":"Computational Geometry: Theory and Applications","date_published":"2015-07-01T00:00:00Z"}]