[{"title":"Genome amplification and cellular senescence are hallmarks of human placenta development","publication_status":"published","external_id":{"isi":["000449328500025"]},"abstract":[{"lang":"eng","text":"Genome amplification and cellular senescence are commonly associated with pathological processes. While physiological roles for polyploidization and senescence have been described in mouse development, controversy exists over their significance in humans. Here, we describe tetraploidization and senescence as phenomena of normal human placenta development. During pregnancy, placental extravillous trophoblasts (EVTs) invade the pregnant endometrium, termed decidua, to establish an adapted microenvironment required for the developing embryo. This process is critically dependent on continuous cell proliferation and differentiation, which is thought to follow the classical model of cell cycle arrest prior to terminal differentiation. Strikingly, flow cytometry and DNAseq revealed that EVT formation is accompanied with a genome-wide polyploidization, independent of mitotic cycles. DNA replication in these cells was analysed by a fluorescent cell-cycle indicator reporter system, cell cycle marker expression and EdU incorporation. Upon invasion into the decidua, EVTs widely lose their replicative potential and enter a senescent state characterized by high senescence-associated (SA) β-galactosidase activity, induction of a SA secretory phenotype as well as typical metabolic alterations. Furthermore, we show that the shift from endocycle-dependent genome amplification to growth arrest is disturbed in androgenic complete hydatidiform moles (CHM), a hyperplastic pregnancy disorder associated with increased risk of developing choriocarinoma. Senescence is decreased in CHM-EVTs, accompanied by exacerbated endoreduplication and hyperploidy. We propose induction of cellular senescence as a ploidy-limiting mechanism during normal human placentation and unravel a link between excessive polyploidization and reduced senescence in CHM."}],"license":"https://creativecommons.org/licenses/by/4.0/","article_processing_charge":"No","volume":14,"author":[{"full_name":"Velicky, Philipp","id":"39BDC62C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2340-7431","first_name":"Philipp","last_name":"Velicky"},{"last_name":"Meinhardt","first_name":"Gudrun","full_name":"Meinhardt, Gudrun"},{"full_name":"Plessl, Kerstin","first_name":"Kerstin","last_name":"Plessl"},{"full_name":"Vondra, Sigrid","last_name":"Vondra","first_name":"Sigrid"},{"full_name":"Weiss, Tamara","first_name":"Tamara","last_name":"Weiss"},{"first_name":"Peter","last_name":"Haslinger","full_name":"Haslinger, Peter"},{"first_name":"Thomas","last_name":"Lendl","full_name":"Lendl, Thomas"},{"full_name":"Aumayr, Karin","last_name":"Aumayr","first_name":"Karin"},{"first_name":"Mario","last_name":"Mairhofer","full_name":"Mairhofer, Mario"},{"full_name":"Zhu, Xiaowei","first_name":"Xiaowei","last_name":"Zhu"},{"first_name":"Birgit","last_name":"Schütz","full_name":"Schütz, Birgit"},{"full_name":"Hannibal, Roberta L.","last_name":"Hannibal","first_name":"Roberta L."},{"full_name":"Lindau, Robert","first_name":"Robert","last_name":"Lindau"},{"last_name":"Weil","first_name":"Beatrix","full_name":"Weil, Beatrix"},{"first_name":"Jan","last_name":"Ernerudh","full_name":"Ernerudh, Jan"},{"full_name":"Neesen, Jürgen","last_name":"Neesen","first_name":"Jürgen"},{"full_name":"Egger, Gerda","first_name":"Gerda","last_name":"Egger"},{"last_name":"Mikula","first_name":"Mario","full_name":"Mikula, Mario"},{"full_name":"Röhrl, Clemens","last_name":"Röhrl","first_name":"Clemens"},{"first_name":"Alexander E.","last_name":"Urban","full_name":"Urban, Alexander E."},{"full_name":"Baker, Julie","first_name":"Julie","last_name":"Baker"},{"last_name":"Knöfler","first_name":"Martin","full_name":"Knöfler, Martin"},{"last_name":"Pollheimer","first_name":"Jürgen","full_name":"Pollheimer, Jürgen"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","ddc":["570"],"has_accepted_license":"1","quality_controlled":"1","file":[{"creator":"kschuh","date_created":"2019-02-14T13:14:35Z","content_type":"application/pdf","file_name":"2018_PLOS_Velicky.pdf","access_level":"open_access","relation":"main_file","checksum":"34aa9a5972f61889c19f18be8ee787a0","file_size":4592947,"date_updated":"2020-07-14T12:47:15Z","file_id":"6000"}],"publication":"PLOS Genetics","publication_identifier":{"issn":["1553-7404"]},"doi":"10.1371/journal.pgen.1007698","issue":"10","article_number":"e1007698","date_created":"2019-02-14T13:07:45Z","year":"2018","date_updated":"2023-09-19T14:31:43Z","publisher":"Public Library of Science","department":[{"_id":"JoDa"}],"date_published":"2018-10-12T00:00:00Z","month":"10","language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:47:15Z","oa":1,"isi":1,"scopus_import":"1","_id":"5998","type":"journal_article","oa_version":"Published Version","intvolume":"        14","citation":{"ama":"Velicky P, Meinhardt G, Plessl K, et al. Genome amplification and cellular senescence are hallmarks of human placenta development. <i>PLOS Genetics</i>. 2018;14(10). doi:<a href=\"https://doi.org/10.1371/journal.pgen.1007698\">10.1371/journal.pgen.1007698</a>","ista":"Velicky P, Meinhardt G, Plessl K, Vondra S, Weiss T, Haslinger P, Lendl T, Aumayr K, Mairhofer M, Zhu X, Schütz B, Hannibal RL, Lindau R, Weil B, Ernerudh J, Neesen J, Egger G, Mikula M, Röhrl C, Urban AE, Baker J, Knöfler M, Pollheimer J. 2018. Genome amplification and cellular senescence are hallmarks of human placenta development. PLOS Genetics. 14(10), e1007698.","short":"P. Velicky, G. Meinhardt, K. Plessl, S. Vondra, T. Weiss, P. Haslinger, T. Lendl, K. Aumayr, M. Mairhofer, X. Zhu, B. Schütz, R.L. Hannibal, R. Lindau, B. Weil, J. Ernerudh, J. Neesen, G. Egger, M. Mikula, C. Röhrl, A.E. Urban, J. Baker, M. Knöfler, J. Pollheimer, PLOS Genetics 14 (2018).","ieee":"P. Velicky <i>et al.</i>, “Genome amplification and cellular senescence are hallmarks of human placenta development,” <i>PLOS Genetics</i>, vol. 14, no. 10. Public Library of Science, 2018.","mla":"Velicky, Philipp, et al. “Genome Amplification and Cellular Senescence Are Hallmarks of Human Placenta Development.” <i>PLOS Genetics</i>, vol. 14, no. 10, e1007698, Public Library of Science, 2018, doi:<a href=\"https://doi.org/10.1371/journal.pgen.1007698\">10.1371/journal.pgen.1007698</a>.","apa":"Velicky, P., Meinhardt, G., Plessl, K., Vondra, S., Weiss, T., Haslinger, P., … Pollheimer, J. (2018). Genome amplification and cellular senescence are hallmarks of human placenta development. <i>PLOS Genetics</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pgen.1007698\">https://doi.org/10.1371/journal.pgen.1007698</a>","chicago":"Velicky, Philipp, Gudrun Meinhardt, Kerstin Plessl, Sigrid Vondra, Tamara Weiss, Peter Haslinger, Thomas Lendl, et al. “Genome Amplification and Cellular Senescence Are Hallmarks of Human Placenta Development.” <i>PLOS Genetics</i>. Public Library of Science, 2018. <a href=\"https://doi.org/10.1371/journal.pgen.1007698\">https://doi.org/10.1371/journal.pgen.1007698</a>."},"day":"12","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"}},{"oa":1,"isi":1,"publisher":"Oxford University Press","arxiv":1,"department":[{"_id":"TaHa"}],"date_updated":"2023-09-19T14:37:19Z","language":[{"iso":"eng"}],"month":"05","date_published":"2018-05-01T00:00:00Z","type":"journal_article","oa_version":"Preprint","intvolume":"       116","_id":"5999","scopus_import":"1","citation":{"ista":"Yang Y, Zhao G. 2018. The cohomological Hall algebra of a preprojective algebra. Proceedings of the London Mathematical Society. 116(5), 1029–1074.","ama":"Yang Y, Zhao G. The cohomological Hall algebra of a preprojective algebra. <i>Proceedings of the London Mathematical Society</i>. 2018;116(5):1029-1074. doi:<a href=\"https://doi.org/10.1112/plms.12111\">10.1112/plms.12111</a>","ieee":"Y. Yang and G. Zhao, “The cohomological Hall algebra of a preprojective algebra,” <i>Proceedings of the London Mathematical Society</i>, vol. 116, no. 5. Oxford University Press, pp. 1029–1074, 2018.","short":"Y. Yang, G. Zhao, Proceedings of the London Mathematical Society 116 (2018) 1029–1074.","mla":"Yang, Yaping, and Gufang Zhao. “The Cohomological Hall Algebra of a Preprojective Algebra.” <i>Proceedings of the London Mathematical Society</i>, vol. 116, no. 5, Oxford University Press, 2018, pp. 1029–74, doi:<a href=\"https://doi.org/10.1112/plms.12111\">10.1112/plms.12111</a>.","chicago":"Yang, Yaping, and Gufang Zhao. “The Cohomological Hall Algebra of a Preprojective Algebra.” <i>Proceedings of the London Mathematical Society</i>. Oxford University Press, 2018. <a href=\"https://doi.org/10.1112/plms.12111\">https://doi.org/10.1112/plms.12111</a>.","apa":"Yang, Y., &#38; Zhao, G. (2018). The cohomological Hall algebra of a preprojective algebra. <i>Proceedings of the London Mathematical Society</i>. Oxford University Press. <a href=\"https://doi.org/10.1112/plms.12111\">https://doi.org/10.1112/plms.12111</a>"},"day":"01","status":"public","abstract":[{"text":"We introduce for each quiver Q and each algebraic oriented cohomology theory A, the cohomological Hall algebra (CoHA) of Q, as the A-homology of the moduli of representations of the preprojective algebra of Q. This generalizes the K-theoretic Hall algebra of commuting varieties defined by Schiffmann-Vasserot. When A is the Morava K-theory, we show evidence that this algebra is a candidate for Lusztig's reformulated conjecture on modular representations of algebraic groups.\r\nWe construct an action of the preprojective CoHA on the A-homology of Nakajima quiver varieties. We compare this with the action of the Borel subalgebra of Yangian when A is the intersection theory. We also give a shuffle algebra description of this CoHA in terms of the underlying formal group law of A. As applications, we obtain a shuffle description of the Yangian. ","lang":"eng"}],"external_id":{"isi":["000431506400001"],"arxiv":["1407.7994"]},"publication_status":"published","page":"1029-1074","article_processing_charge":"No","title":"The cohomological Hall algebra of a preprojective algebra","volume":116,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"first_name":"Yaping","last_name":"Yang","full_name":"Yang, Yaping"},{"first_name":"Gufang","last_name":"Zhao","full_name":"Zhao, Gufang","id":"2BC2AC5E-F248-11E8-B48F-1D18A9856A87"}],"quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/1407.7994","open_access":"1"}],"year":"2018","date_created":"2019-02-14T13:14:22Z","publication":"Proceedings of the London Mathematical Society","issue":"5","publication_identifier":{"issn":["0024-6115"]},"doi":"10.1112/plms.12111"},{"year":"2018","date_created":"2019-02-14T13:40:53Z","issue":"3","publication_identifier":{"issn":["0003-9527"],"eissn":["1432-0673"]},"doi":"10.1007/s00205-018-1232-6","publication":"Archive for Rational Mechanics and Analysis","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1511.05935"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"id":"4197AD04-F248-11E8-B48F-1D18A9856A87","full_name":"Napiórkowski, Marcin M","first_name":"Marcin M","last_name":"Napiórkowski"},{"last_name":"Reuvers","first_name":"Robin","full_name":"Reuvers, Robin"},{"full_name":"Solovej, Jan Philip","first_name":"Jan Philip","last_name":"Solovej"}],"volume":229,"page":"1037-1090","article_processing_charge":"No","abstract":[{"lang":"eng","text":"The Bogoliubov free energy functional is analysed. The functional serves as a model of a translation-invariant Bose gas at positive temperature. We prove the existence of minimizers in the case of repulsive interactions given by a sufficiently regular two-body potential. Furthermore, we prove the existence of a phase transition in this model and provide its phase diagram."}],"publication_status":"published","external_id":{"arxiv":["1511.05935"],"isi":["000435367300003"]},"title":"The Bogoliubov free energy functional I: Existence of minimizers and phase diagram","day":"01","status":"public","citation":{"mla":"Napiórkowski, Marcin M., et al. “The Bogoliubov Free Energy Functional I: Existence of Minimizers and Phase Diagram.” <i>Archive for Rational Mechanics and Analysis</i>, vol. 229, no. 3, Springer Nature, 2018, pp. 1037–90, doi:<a href=\"https://doi.org/10.1007/s00205-018-1232-6\">10.1007/s00205-018-1232-6</a>.","apa":"Napiórkowski, M. M., Reuvers, R., &#38; Solovej, J. P. (2018). The Bogoliubov free energy functional I: Existence of minimizers and phase diagram. <i>Archive for Rational Mechanics and Analysis</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00205-018-1232-6\">https://doi.org/10.1007/s00205-018-1232-6</a>","chicago":"Napiórkowski, Marcin M, Robin Reuvers, and Jan Philip Solovej. “The Bogoliubov Free Energy Functional I: Existence of Minimizers and Phase Diagram.” <i>Archive for Rational Mechanics and Analysis</i>. Springer Nature, 2018. <a href=\"https://doi.org/10.1007/s00205-018-1232-6\">https://doi.org/10.1007/s00205-018-1232-6</a>.","ama":"Napiórkowski MM, Reuvers R, Solovej JP. The Bogoliubov free energy functional I: Existence of minimizers and phase diagram. <i>Archive for Rational Mechanics and Analysis</i>. 2018;229(3):1037-1090. doi:<a href=\"https://doi.org/10.1007/s00205-018-1232-6\">10.1007/s00205-018-1232-6</a>","ista":"Napiórkowski MM, Reuvers R, Solovej JP. 2018. The Bogoliubov free energy functional I: Existence of minimizers and phase diagram. Archive for Rational Mechanics and Analysis. 229(3), 1037–1090.","ieee":"M. M. Napiórkowski, R. Reuvers, and J. P. Solovej, “The Bogoliubov free energy functional I: Existence of minimizers and phase diagram,” <i>Archive for Rational Mechanics and Analysis</i>, vol. 229, no. 3. Springer Nature, pp. 1037–1090, 2018.","short":"M.M. Napiórkowski, R. Reuvers, J.P. Solovej, Archive for Rational Mechanics and Analysis 229 (2018) 1037–1090."},"project":[{"_id":"25C878CE-B435-11E9-9278-68D0E5697425","grant_number":"P27533_N27","call_identifier":"FWF","name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems"}],"intvolume":"       229","oa_version":"Preprint","type":"journal_article","_id":"6002","scopus_import":"1","isi":1,"oa":1,"month":"09","language":[{"iso":"eng"}],"date_published":"2018-09-01T00:00:00Z","arxiv":1,"department":[{"_id":"RoSe"}],"publisher":"Springer Nature","date_updated":"2025-04-15T08:26:15Z"},{"title":"State of the art on stylized fabrication","external_id":{"isi":["000437272800019"]},"publication_status":"published","abstract":[{"text":"Digital fabrication devices are powerful tools for creating tangible reproductions of 3D digital models. Most available printing technologies aim at producing an accurate copy of a tridimensional shape. However, fabrication technologies can also be used to create a stylistic representation of a digital shape. We refer to this class of methods as ‘stylized fabrication methods’. These methods abstract geometric and physical features of a given shape to create an unconventional representation, to produce an optical illusion or to devise a particular interaction with the fabricated model. In this state‐of‐the‐art report, we classify and overview this broad and emerging class of approaches and also propose possible directions for future research.","lang":"eng"}],"article_processing_charge":"No","page":"325-342","volume":37,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"orcid":"0000-0001-6511-9385","id":"49876194-F248-11E8-B48F-1D18A9856A87","full_name":"Bickel, Bernd","first_name":"Bernd","last_name":"Bickel"},{"first_name":"Paolo","last_name":"Cignoni","full_name":"Cignoni, Paolo"},{"full_name":"Malomo, Luigi","last_name":"Malomo","first_name":"Luigi"},{"last_name":"Pietroni","first_name":"Nico","full_name":"Pietroni, Nico"}],"ddc":["004"],"has_accepted_license":"1","quality_controlled":"1","file":[{"file_size":6209349,"date_updated":"2020-07-14T12:47:15Z","access_level":"open_access","relation":"main_file","checksum":"d2bbe5c658d8159fbe9016a4f5e82b19","file_id":"6004","creator":"kschuh","file_name":"StylizedFabricationSTAR-Personal.pdf","content_type":"application/pdf","date_created":"2019-02-14T14:09:28Z"}],"publication":"Computer Graphics Forum","doi":"10.1111/cgf.13327","publication_identifier":{"issn":["0167-7055"]},"issue":"6","date_created":"2019-02-14T13:52:25Z","year":"2018","date_updated":"2025-04-14T07:28:57Z","publisher":"Wiley","department":[{"_id":"BeBi"}],"date_published":"2018-09-01T00:00:00Z","month":"09","language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:47:15Z","oa":1,"isi":1,"scopus_import":"1","_id":"6003","type":"journal_article","oa_version":"Submitted Version","intvolume":"        37","project":[{"call_identifier":"H2020","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","_id":"24F9549A-B435-11E9-9278-68D0E5697425","grant_number":"715767"}],"citation":{"ieee":"B. Bickel, P. Cignoni, L. Malomo, and N. Pietroni, “State of the art on stylized fabrication,” <i>Computer Graphics Forum</i>, vol. 37, no. 6. Wiley, pp. 325–342, 2018.","short":"B. Bickel, P. Cignoni, L. Malomo, N. Pietroni, Computer Graphics Forum 37 (2018) 325–342.","ama":"Bickel B, Cignoni P, Malomo L, Pietroni N. State of the art on stylized fabrication. <i>Computer Graphics Forum</i>. 2018;37(6):325-342. doi:<a href=\"https://doi.org/10.1111/cgf.13327\">10.1111/cgf.13327</a>","ista":"Bickel B, Cignoni P, Malomo L, Pietroni N. 2018. State of the art on stylized fabrication. Computer Graphics Forum. 37(6), 325–342.","chicago":"Bickel, Bernd, Paolo Cignoni, Luigi Malomo, and Nico Pietroni. “State of the Art on Stylized Fabrication.” <i>Computer Graphics Forum</i>. Wiley, 2018. <a href=\"https://doi.org/10.1111/cgf.13327\">https://doi.org/10.1111/cgf.13327</a>.","apa":"Bickel, B., Cignoni, P., Malomo, L., &#38; Pietroni, N. (2018). State of the art on stylized fabrication. <i>Computer Graphics Forum</i>. Wiley. <a href=\"https://doi.org/10.1111/cgf.13327\">https://doi.org/10.1111/cgf.13327</a>","mla":"Bickel, Bernd, et al. “State of the Art on Stylized Fabrication.” <i>Computer Graphics Forum</i>, vol. 37, no. 6, Wiley, 2018, pp. 325–42, doi:<a href=\"https://doi.org/10.1111/cgf.13327\">10.1111/cgf.13327</a>."},"pubrep_id":"1051","status":"public","day":"01","ec_funded":1},{"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"day":"01","status":"public","alternative_title":["LIPIcs"],"project":[{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","call_identifier":"FWF","name":"Formal methods for the design and analysis of complex systems"},{"name":"Formal Methods meets Algorithmic Game Theory","call_identifier":"FWF","grant_number":"M02369","_id":"264B3912-B435-11E9-9278-68D0E5697425"}],"citation":{"mla":"Avni, Guy, et al. <i>Timed Network Games with Clocks</i>. Vol. 117, 23, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, doi:<a href=\"https://doi.org/10.4230/LIPICS.MFCS.2018.23\">10.4230/LIPICS.MFCS.2018.23</a>.","chicago":"Avni, Guy, Shibashis Guha, and Orna Kupferman. “Timed Network Games with Clocks,” Vol. 117. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. <a href=\"https://doi.org/10.4230/LIPICS.MFCS.2018.23\">https://doi.org/10.4230/LIPICS.MFCS.2018.23</a>.","apa":"Avni, G., Guha, S., &#38; Kupferman, O. (2018). Timed network games with clocks (Vol. 117). Presented at the MFCS: Mathematical Foundations of Computer Science, Liverpool, United Kingdom: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPICS.MFCS.2018.23\">https://doi.org/10.4230/LIPICS.MFCS.2018.23</a>","ista":"Avni G, Guha S, Kupferman O. 2018. Timed network games with clocks. MFCS: Mathematical Foundations of Computer Science, LIPIcs, vol. 117, 23.","ama":"Avni G, Guha S, Kupferman O. Timed network games with clocks. In: Vol 117. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018. doi:<a href=\"https://doi.org/10.4230/LIPICS.MFCS.2018.23\">10.4230/LIPICS.MFCS.2018.23</a>","short":"G. Avni, S. Guha, O. Kupferman, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018.","ieee":"G. Avni, S. Guha, and O. Kupferman, “Timed network games with clocks,” presented at the MFCS: Mathematical Foundations of Computer Science, Liverpool, United Kingdom, 2018, vol. 117."},"type":"conference","oa_version":"Published Version","intvolume":"       117","_id":"6005","scopus_import":"1","oa":1,"file_date_updated":"2020-07-14T12:47:15Z","department":[{"_id":"ToHe"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","date_updated":"2025-07-10T12:01:59Z","month":"08","language":[{"iso":"eng"}],"date_published":"2018-08-01T00:00:00Z","article_number":"23","year":"2018","date_created":"2019-02-14T14:12:09Z","publication_identifier":{"issn":["1868-8969"]},"doi":"10.4230/LIPICS.MFCS.2018.23","quality_controlled":"1","file":[{"file_id":"6007","access_level":"open_access","relation":"main_file","checksum":"41ab2ae9b63f5eb49fa995250c0ba128","date_updated":"2020-07-14T12:47:15Z","file_size":542889,"date_created":"2019-02-14T14:22:04Z","content_type":"application/pdf","file_name":"2018_LIPIcs_Avni.pdf","creator":"dernst"}],"ddc":["000"],"conference":{"name":"MFCS: Mathematical Foundations of Computer Science","start_date":"2018-08-27","end_date":"2018-08-31","location":"Liverpool, United Kingdom"},"has_accepted_license":"1","volume":117,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Guy","last_name":"Avni","full_name":"Avni, Guy","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5588-8287"},{"full_name":"Guha, Shibashis","last_name":"Guha","first_name":"Shibashis"},{"full_name":"Kupferman, Orna","last_name":"Kupferman","first_name":"Orna"}],"related_material":{"record":[{"id":"963","relation":"earlier_version","status":"public"}]},"abstract":[{"text":"Network games are widely used as a model for selfish resource-allocation problems. In the classicalmodel, each player selects a path connecting her source and target vertices. The cost of traversingan edge depends on theload; namely, number of players that traverse it. Thus, it abstracts the factthat different users may use a resource at different times and for different durations, which playsan important role in determining the costs of the users in reality. For example, when transmittingpackets in a communication network, routing traffic in a road network, or processing a task in aproduction system, actual sharing and congestion of resources crucially depends on time.In [13], we introducedtimed network games, which add a time component to network games.Each vertexvin the network is associated with a cost function, mapping the load onvto theprice that a player pays for staying invfor one time unit with this load.  Each edge in thenetwork is guarded by the time intervals in which it can be traversed, which forces the players tospend time in the vertices. In this work we significantly extend the way time can be referred toin timed network games. In the model we study, the network is equipped withclocks, and, as intimed automata, edges are guarded by constraints on the values of the clocks, and their traversalmay involve a reset of some clocks. We argue that the stronger model captures many realisticnetworks.  The addition of clocks breaks the techniques we developed in [13] and we developnew techniques in order to show that positive results on classic network games carry over to thestronger timed setting.","lang":"eng"}],"publication_status":"published","article_processing_charge":"No","title":"Timed network games with clocks"},{"project":[{"_id":"264B3912-B435-11E9-9278-68D0E5697425","grant_number":"M02369","call_identifier":"FWF","name":"Formal Methods meets Algorithmic Game Theory"},{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF"},{"call_identifier":"FWF","name":"Formal methods for the design and analysis of complex systems","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211"}],"citation":{"short":"G. Avni, S. Guha, O. Kupferman, Games 9 (2018).","ieee":"G. Avni, S. Guha, and O. Kupferman, “An abstraction-refinement methodology for reasoning about network games,” <i>Games</i>, vol. 9, no. 3. MDPI, 2018.","ama":"Avni G, Guha S, Kupferman O. An abstraction-refinement methodology for reasoning about network games. <i>Games</i>. 2018;9(3). doi:<a href=\"https://doi.org/10.3390/g9030039\">10.3390/g9030039</a>","ista":"Avni G, Guha S, Kupferman O. 2018. An abstraction-refinement methodology for reasoning about network games. Games. 9(3), 39.","apa":"Avni, G., Guha, S., &#38; Kupferman, O. (2018). An abstraction-refinement methodology for reasoning about network games. <i>Games</i>. MDPI. <a href=\"https://doi.org/10.3390/g9030039\">https://doi.org/10.3390/g9030039</a>","chicago":"Avni, Guy, Shibashis Guha, and Orna Kupferman. “An Abstraction-Refinement Methodology for Reasoning about Network Games.” <i>Games</i>. MDPI, 2018. <a href=\"https://doi.org/10.3390/g9030039\">https://doi.org/10.3390/g9030039</a>.","mla":"Avni, Guy, et al. “An Abstraction-Refinement Methodology for Reasoning about Network Games.” <i>Games</i>, vol. 9, no. 3, 39, MDPI, 2018, doi:<a href=\"https://doi.org/10.3390/g9030039\">10.3390/g9030039</a>."},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"day":"01","status":"public","file_date_updated":"2020-07-14T12:47:16Z","oa":1,"date_updated":"2025-07-10T11:49:38Z","department":[{"_id":"ToHe"}],"publisher":"MDPI","date_published":"2018-09-01T00:00:00Z","month":"09","language":[{"iso":"eng"}],"type":"journal_article","oa_version":"Published Version","intvolume":"         9","scopus_import":"1","_id":"6006","quality_controlled":"1","file":[{"file_size":505155,"date_updated":"2020-07-14T12:47:16Z","access_level":"open_access","relation":"main_file","checksum":"749d65ca4ce74256a029d9644a1b1cb0","file_id":"6008","creator":"kschuh","content_type":"application/pdf","file_name":"2018_MDPI_Avni.pdf","date_created":"2019-02-14T14:20:31Z"}],"ddc":["004"],"has_accepted_license":"1","article_number":"39","date_created":"2019-02-14T14:17:54Z","year":"2018","publication":"Games","publication_identifier":{"issn":["2073-4336"]},"doi":"10.3390/g9030039","issue":"3","publication_status":"published","abstract":[{"text":"Network games (NGs) are played on directed graphs and are extensively used in network design and analysis. Search problems for NGs include finding special strategy profiles such as a Nash equilibrium and a globally-optimal solution. The networks modeled by NGs may be huge. In formal verification, abstraction has proven to be an extremely effective technique for reasoning about systems with big and even infinite state spaces. We describe an abstraction-refinement methodology for reasoning about NGs. Our methodology is based on an abstraction function that maps the state space of an NG to a much smaller state space. We search for a global optimum and a Nash equilibrium by reasoning on an under- and an over-approximation defined on top of this smaller state space. When the approximations are too coarse to find such profiles, we refine the abstraction function. We extend the abstraction-refinement methodology to labeled networks, where the objectives of the players are regular languages. Our experimental results demonstrate the effectiveness of the methodology. ","lang":"eng"}],"article_processing_charge":"No","title":"An abstraction-refinement methodology for reasoning about network games","volume":9,"author":[{"last_name":"Avni","first_name":"Guy","full_name":"Avni, Guy","orcid":"0000-0001-5588-8287","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Guha, Shibashis","first_name":"Shibashis","last_name":"Guha"},{"first_name":"Orna","last_name":"Kupferman","full_name":"Kupferman, Orna"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","related_material":{"record":[{"id":"1003","relation":"earlier_version","status":"public"}]}},{"abstract":[{"lang":"eng","text":"The optic tectum (TeO), or superior colliculus, is a multisensory midbrain center that organizes spatially orienting responses to relevant stimuli. To define the stimulus with the highest priority at each moment, a network of reciprocal connections between the TeO and the isthmi promotes competition between concurrent tectal inputs. In the avian midbrain, the neurons mediating enhancement and suppression of tectal inputs are located in separate isthmic nuclei, facilitating the analysis of the neural processes that mediate competition. A specific subset of radial neurons in the intermediate tectal layers relay retinal inputs to the isthmi, but at present it is unclear whether separate neurons innervate individual nuclei or a single neural type sends a common input to several of them. In this study, we used in vitro neural tracing and cell-filling experiments in chickens to show that single neurons innervate, via axon collaterals, the three nuclei that comprise the isthmotectal network. This demonstrates that the input signals representing the strength of the incoming stimuli are simultaneously relayed to the mechanisms promoting both enhancement and suppression of the input signals. By performing in vivo recordings in anesthetized chicks, we also show that this common input generates synchrony between both antagonistic mechanisms, demonstrating that activity enhancement and suppression are closely coordinated. From a computational point of view, these results suggest that these tectal neurons constitute integrative nodes that combine inputs from different sources to drive in parallel several concurrent neural processes, each performing complementary functions within the network through different firing patterns and connectivity."}],"external_id":{"pmid":["30026198"],"isi":["000440982000020"]},"publication_status":"published","page":"E7615-E7623","article_processing_charge":"No","title":"“Shepherd’s crook” neurons drive and synchronize the enhancing and suppressive mechanisms of the midbrain stimulus selection network","volume":115,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"full_name":"Garrido-Charad, Florencia","last_name":"Garrido-Charad","first_name":"Florencia"},{"first_name":"Tomas A","last_name":"Vega Zuniga","full_name":"Vega Zuniga, Tomas A","id":"2E7C4E78-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Cristián","last_name":"Gutiérrez-Ibáñez","full_name":"Gutiérrez-Ibáñez, Cristián"},{"last_name":"Fernandez","first_name":"Pedro","full_name":"Fernandez, Pedro"},{"full_name":"López-Jury, Luciana","first_name":"Luciana","last_name":"López-Jury"},{"last_name":"González-Cabrera","first_name":"Cristian","full_name":"González-Cabrera, Cristian"},{"first_name":"Harvey J.","last_name":"Karten","full_name":"Karten, Harvey J."},{"last_name":"Luksch","first_name":"Harald","full_name":"Luksch, Harald"},{"first_name":"Gonzalo J.","last_name":"Marín","full_name":"Marín, Gonzalo J."}],"pmid":1,"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/30026198"}],"year":"2018","date_created":"2019-02-14T14:33:34Z","publication":"Proceedings of the National Academy of Sciences","issue":"32","doi":"10.1073/pnas.1804517115","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"oa":1,"isi":1,"publisher":"National Academy of Sciences","department":[{"_id":"MaJö"}],"date_updated":"2023-09-19T14:35:36Z","language":[{"iso":"eng"}],"month":"08","date_published":"2018-08-07T00:00:00Z","type":"journal_article","intvolume":"       115","oa_version":"Submitted Version","_id":"6010","scopus_import":"1","citation":{"mla":"Garrido-Charad, Florencia, et al. ““Shepherd’s Crook” Neurons Drive and Synchronize the Enhancing and Suppressive Mechanisms of the Midbrain Stimulus Selection Network.” <i>Proceedings of the National Academy of Sciences</i>, vol. 115, no. 32, National Academy of Sciences, 2018, pp. E7615–23, doi:<a href=\"https://doi.org/10.1073/pnas.1804517115\">10.1073/pnas.1804517115</a>.","apa":"Garrido-Charad, F., Vega Zuniga, T. A., Gutiérrez-Ibáñez, C., Fernandez, P., López-Jury, L., González-Cabrera, C., … Marín, G. J. (2018). “Shepherd’s crook” neurons drive and synchronize the enhancing and suppressive mechanisms of the midbrain stimulus selection network. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1804517115\">https://doi.org/10.1073/pnas.1804517115</a>","chicago":"Garrido-Charad, Florencia, Tomas A Vega Zuniga, Cristián Gutiérrez-Ibáñez, Pedro Fernandez, Luciana López-Jury, Cristian González-Cabrera, Harvey J. Karten, Harald Luksch, and Gonzalo J. Marín. ““Shepherd’s Crook” Neurons Drive and Synchronize the Enhancing and Suppressive Mechanisms of the Midbrain Stimulus Selection Network.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2018. <a href=\"https://doi.org/10.1073/pnas.1804517115\">https://doi.org/10.1073/pnas.1804517115</a>.","ista":"Garrido-Charad F, Vega Zuniga TA, Gutiérrez-Ibáñez C, Fernandez P, López-Jury L, González-Cabrera C, Karten HJ, Luksch H, Marín GJ. 2018. “Shepherd’s crook” neurons drive and synchronize the enhancing and suppressive mechanisms of the midbrain stimulus selection network. Proceedings of the National Academy of Sciences. 115(32), E7615–E7623.","ama":"Garrido-Charad F, Vega Zuniga TA, Gutiérrez-Ibáñez C, et al. “Shepherd’s crook” neurons drive and synchronize the enhancing and suppressive mechanisms of the midbrain stimulus selection network. <i>Proceedings of the National Academy of Sciences</i>. 2018;115(32):E7615-E7623. doi:<a href=\"https://doi.org/10.1073/pnas.1804517115\">10.1073/pnas.1804517115</a>","short":"F. Garrido-Charad, T.A. Vega Zuniga, C. Gutiérrez-Ibáñez, P. Fernandez, L. López-Jury, C. González-Cabrera, H.J. Karten, H. Luksch, G.J. Marín, Proceedings of the National Academy of Sciences 115 (2018) E7615–E7623.","ieee":"F. Garrido-Charad <i>et al.</i>, ““Shepherd’s crook” neurons drive and synchronize the enhancing and suppressive mechanisms of the midbrain stimulus selection network,” <i>Proceedings of the National Academy of Sciences</i>, vol. 115, no. 32. National Academy of Sciences, pp. E7615–E7623, 2018."},"day":"07","status":"public"},{"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1703.01678"}],"conference":{"location":"Stockholm, Sweden","end_date":"2018-07-15","name":"ICML: International Conference on Machine Learning","start_date":"2018-07-10"},"quality_controlled":"1","publication":"Proceedings of the 35 th International Conference on Machine Learning","date_created":"2019-02-14T14:51:57Z","year":"2018","title":"Data-dependent stability of stochastic gradient descent","article_processing_charge":"No","page":"2815-2824","publication_status":"published","external_id":{"arxiv":["1703.01678"],"isi":["000683379202095"]},"abstract":[{"lang":"eng","text":"We establish a data-dependent notion of algorithmic stability for Stochastic Gradient Descent (SGD), and employ it to develop novel generalization bounds. This is in contrast to previous distribution-free algorithmic stability results for SGD which depend on the worst-case constants. By virtue of the data-dependent argument, our bounds provide new insights into learning with SGD on convex and non-convex problems. In the convex case, we show that the bound on the generalization error depends on the risk at the initialization point. In the non-convex case, we prove that the expected curvature of the objective function around the initialization point has crucial influence on the generalization error. In both cases, our results suggest a simple data-driven strategy to stabilize SGD by pre-screening its initialization. As a corollary, our results allow us to show optimistic generalization bounds that exhibit fast convergence rates for SGD subject to a vanishing empirical risk and low noise of stochastic gradient. "}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Kuzborskij, Ilja","first_name":"Ilja","last_name":"Kuzborskij"},{"full_name":"Lampert, Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887","first_name":"Christoph","last_name":"Lampert"}],"volume":80,"citation":{"ista":"Kuzborskij I, Lampert C. 2018. Data-dependent stability of stochastic gradient descent. Proceedings of the 35 th International Conference on Machine Learning. ICML: International Conference on Machine Learning vol. 80, 2815–2824.","ama":"Kuzborskij I, Lampert C. Data-dependent stability of stochastic gradient descent. In: <i>Proceedings of the 35 Th International Conference on Machine Learning</i>. Vol 80. ML Research Press; 2018:2815-2824.","ieee":"I. Kuzborskij and C. Lampert, “Data-dependent stability of stochastic gradient descent,” in <i>Proceedings of the 35 th International Conference on Machine Learning</i>, Stockholm, Sweden, 2018, vol. 80, pp. 2815–2824.","short":"I. Kuzborskij, C. Lampert, in:, Proceedings of the 35 Th International Conference on Machine Learning, ML Research Press, 2018, pp. 2815–2824.","mla":"Kuzborskij, Ilja, and Christoph Lampert. “Data-Dependent Stability of Stochastic Gradient Descent.” <i>Proceedings of the 35 Th International Conference on Machine Learning</i>, vol. 80, ML Research Press, 2018, pp. 2815–24.","apa":"Kuzborskij, I., &#38; Lampert, C. (2018). Data-dependent stability of stochastic gradient descent. In <i>Proceedings of the 35 th International Conference on Machine Learning</i> (Vol. 80, pp. 2815–2824). Stockholm, Sweden: ML Research Press.","chicago":"Kuzborskij, Ilja, and Christoph Lampert. “Data-Dependent Stability of Stochastic Gradient Descent.” In <i>Proceedings of the 35 Th International Conference on Machine Learning</i>, 80:2815–24. ML Research Press, 2018."},"project":[{"_id":"2532554C-B435-11E9-9278-68D0E5697425","grant_number":"308036","call_identifier":"FP7","name":"Lifelong Learning of Visual Scene Understanding"}],"status":"public","day":"01","ec_funded":1,"date_published":"2018-02-01T00:00:00Z","month":"02","language":[{"iso":"eng"}],"date_updated":"2025-04-15T07:10:23Z","arxiv":1,"publisher":"ML Research Press","department":[{"_id":"ChLa"}],"isi":1,"oa":1,"scopus_import":"1","_id":"6011","intvolume":"        80","oa_version":"Preprint","type":"conference"},{"citation":{"ieee":"S. Sahoo, C. Lampert, and G. S. Martius, “Learning equations for extrapolation and control,” in <i>Proceedings of the 35th International Conference on Machine Learning</i>, Stockholm, Sweden, 2018, vol. 80, pp. 4442–4450.","short":"S. Sahoo, C. Lampert, G.S. Martius, in:, Proceedings of the 35th International Conference on Machine Learning, ML Research Press, 2018, pp. 4442–4450.","ista":"Sahoo S, Lampert C, Martius GS. 2018. Learning equations for extrapolation and control. Proceedings of the 35th International Conference on Machine Learning. ICML: International Conference on Machine Learning vol. 80, 4442–4450.","ama":"Sahoo S, Lampert C, Martius GS. Learning equations for extrapolation and control. In: <i>Proceedings of the 35th International Conference on Machine Learning</i>. Vol 80. ML Research Press; 2018:4442-4450.","chicago":"Sahoo, Subham, Christoph Lampert, and Georg S Martius. “Learning Equations for Extrapolation and Control.” In <i>Proceedings of the 35th International Conference on Machine Learning</i>, 80:4442–50. ML Research Press, 2018.","apa":"Sahoo, S., Lampert, C., &#38; Martius, G. S. (2018). Learning equations for extrapolation and control. In <i>Proceedings of the 35th International Conference on Machine Learning</i> (Vol. 80, pp. 4442–4450). Stockholm, Sweden: ML Research Press.","mla":"Sahoo, Subham, et al. “Learning Equations for Extrapolation and Control.” <i>Proceedings of the 35th International Conference on Machine Learning</i>, vol. 80, ML Research Press, 2018, pp. 4442–50."},"project":[{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"ec_funded":1,"status":"public","day":"01","isi":1,"oa":1,"language":[{"iso":"eng"}],"month":"02","date_published":"2018-02-01T00:00:00Z","arxiv":1,"department":[{"_id":"ChLa"}],"publisher":"ML Research Press","date_updated":"2025-04-15T06:50:24Z","oa_version":"Preprint","intvolume":"        80","type":"conference","_id":"6012","scopus_import":"1","quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/1806.07259","open_access":"1"}],"conference":{"end_date":"2018-07-15","location":"Stockholm, Sweden","start_date":"2018-07-10","name":"ICML: International Conference on Machine Learning"},"year":"2018","date_created":"2019-02-14T15:21:07Z","publication":"Proceedings of the 35th International Conference on Machine Learning","page":"4442-4450","article_processing_charge":"No","abstract":[{"lang":"eng","text":"We present an approach to identify concise equations from data using a shallow neural network approach. In contrast to ordinary black-box regression, this approach allows understanding functional relations and generalizing them from observed data to unseen parts of the parameter space. We show how to extend the class of learnable equations for a recently proposed equation learning network to include divisions, and we improve the learning and model selection strategy to be useful for challenging real-world data. For systems governed by analytical expressions, our method can in many cases identify the true underlying equation and extrapolate to unseen domains. We demonstrate its effectiveness by experiments on a cart-pendulum system, where only 2 random rollouts are required to learn the forward dynamics and successfully achieve the swing-up task."}],"publication_status":"published","external_id":{"isi":["000683379204058"],"arxiv":["1806.07259"]},"title":"Learning equations for extrapolation and control","author":[{"last_name":"Sahoo","first_name":"Subham","full_name":"Sahoo, Subham"},{"first_name":"Christoph","last_name":"Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph"},{"first_name":"Georg S","last_name":"Martius","full_name":"Martius, Georg S","id":"3A276B68-F248-11E8-B48F-1D18A9856A87"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":80,"related_material":{"link":[{"url":"https://ist.ac.at/en/news/first-machine-learning-method-capable-of-accurate-extrapolation/","relation":"press_release","description":"News on IST Homepage"}]}},{"related_material":{"record":[{"id":"1192","relation":"earlier_version","status":"public"}]},"volume":15,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"id":"3B32BAA8-F248-11E8-B48F-1D18A9856A87","full_name":"Kazda, Alexandr","first_name":"Alexandr","last_name":"Kazda"},{"id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","full_name":"Kolmogorov, Vladimir","first_name":"Vladimir","last_name":"Kolmogorov"},{"id":"3CB3BC06-F248-11E8-B48F-1D18A9856A87","full_name":"Rolinek, Michal","last_name":"Rolinek","first_name":"Michal"}],"title":"Even delta-matroids and the complexity of planar boolean CSPs","publication_status":"published","external_id":{"isi":["000468036500007"],"arxiv":["1602.03124"]},"abstract":[{"lang":"eng","text":"The main result of this article is a generalization of the classical blossom algorithm for finding perfect matchings. Our algorithm can efficiently solve Boolean CSPs where each variable appears in exactly two constraints (we call it edge CSP) and all constraints are even Δ-matroid relations (represented by lists of tuples). As a consequence of this, we settle the complexity classification of planar Boolean CSPs started by Dvorak and Kupec. Using a reduction to even Δ-matroids, we then extend the tractability result to larger classes of Δ-matroids that we call efficiently coverable. It properly includes classes that were known to be tractable before, namely, co-independent, compact, local, linear, and binary, with the following caveat:We represent Δ-matroids by lists of tuples, while the last two use a representation by matrices. Since an n ×n matrix can represent exponentially many tuples, our tractability result is not strictly stronger than the known algorithm for linear and binary Δ-matroids."}],"article_processing_charge":"No","publication":"ACM Transactions on Algorithms","doi":"10.1145/3230649","issue":"2","article_number":"22","date_created":"2019-02-17T22:59:25Z","year":"2018","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1602.03124"}],"quality_controlled":"1","scopus_import":"1","_id":"6032","type":"journal_article","oa_version":"Preprint","intvolume":"        15","article_type":"original","date_updated":"2025-06-04T08:46:58Z","department":[{"_id":"VlKo"}],"publisher":"ACM","arxiv":1,"date_published":"2018-12-01T00:00:00Z","language":[{"iso":"eng"}],"month":"12","oa":1,"isi":1,"status":"public","day":"01","ec_funded":1,"project":[{"call_identifier":"FP7","name":"Discrete Optimization in Computer Vision: Theory and Practice","_id":"25FBA906-B435-11E9-9278-68D0E5697425","grant_number":"616160"}],"citation":{"apa":"Kazda, A., Kolmogorov, V., &#38; Rolinek, M. (2018). Even delta-matroids and the complexity of planar boolean CSPs. <i>ACM Transactions on Algorithms</i>. ACM. <a href=\"https://doi.org/10.1145/3230649\">https://doi.org/10.1145/3230649</a>","chicago":"Kazda, Alexandr, Vladimir Kolmogorov, and Michal Rolinek. “Even Delta-Matroids and the Complexity of Planar Boolean CSPs.” <i>ACM Transactions on Algorithms</i>. ACM, 2018. <a href=\"https://doi.org/10.1145/3230649\">https://doi.org/10.1145/3230649</a>.","mla":"Kazda, Alexandr, et al. “Even Delta-Matroids and the Complexity of Planar Boolean CSPs.” <i>ACM Transactions on Algorithms</i>, vol. 15, no. 2, 22, ACM, 2018, doi:<a href=\"https://doi.org/10.1145/3230649\">10.1145/3230649</a>.","short":"A. Kazda, V. Kolmogorov, M. Rolinek, ACM Transactions on Algorithms 15 (2018).","ieee":"A. Kazda, V. Kolmogorov, and M. Rolinek, “Even delta-matroids and the complexity of planar boolean CSPs,” <i>ACM Transactions on Algorithms</i>, vol. 15, no. 2. ACM, 2018.","ama":"Kazda A, Kolmogorov V, Rolinek M. Even delta-matroids and the complexity of planar boolean CSPs. <i>ACM Transactions on Algorithms</i>. 2018;15(2). doi:<a href=\"https://doi.org/10.1145/3230649\">10.1145/3230649</a>","ista":"Kazda A, Kolmogorov V, Rolinek M. 2018. Even delta-matroids and the complexity of planar boolean CSPs. ACM Transactions on Algorithms. 15(2), 22."}},{"date_created":"2018-12-11T11:47:27Z","year":"2018","doi":"10.1016/j.anihpc.2017.11.004","issue":"5","publication":"Annales de l'Institut Henri Poincare (C) Non Linear Analysis","quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/1607.00268","open_access":"1"}],"author":[{"last_name":"Duerinckx","first_name":"Mitia","full_name":"Duerinckx, Mitia"},{"orcid":"0000-0002-0479-558X","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","full_name":"Fischer, Julian L","first_name":"Julian L","last_name":"Fischer"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","volume":35,"article_processing_charge":"No","page":"1267-1319","publication_status":"published","external_id":{"isi":["000437975500005"],"arxiv":["1607.00268"]},"abstract":[{"text":"We establish the existence of a global solution for a new family of fluid-like equations, which are obtained in certain regimes in as the mean-field evolution of the supercurrent density in a (2D section of a) type-II superconductor with pinning and with imposed electric current. We also consider general vortex-sheet initial data, and investigate the uniqueness and regularity properties of the solution. For some choice of parameters, the equation under investigation coincides with the so-called lake equation from 2D shallow water fluid dynamics, and our analysis then leads to a new existence result for rough initial data.","lang":"eng"}],"title":"Well-posedness for mean-field evolutions arising in superconductivity","day":"01","status":"public","citation":{"chicago":"Duerinckx, Mitia, and Julian L Fischer. “Well-Posedness for Mean-Field Evolutions Arising in Superconductivity.” <i>Annales de l’Institut Henri Poincare (C) Non Linear Analysis</i>. Elsevier, 2018. <a href=\"https://doi.org/10.1016/j.anihpc.2017.11.004\">https://doi.org/10.1016/j.anihpc.2017.11.004</a>.","apa":"Duerinckx, M., &#38; Fischer, J. L. (2018). Well-posedness for mean-field evolutions arising in superconductivity. <i>Annales de l’Institut Henri Poincare (C) Non Linear Analysis</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.anihpc.2017.11.004\">https://doi.org/10.1016/j.anihpc.2017.11.004</a>","mla":"Duerinckx, Mitia, and Julian L. Fischer. “Well-Posedness for Mean-Field Evolutions Arising in Superconductivity.” <i>Annales de l’Institut Henri Poincare (C) Non Linear Analysis</i>, vol. 35, no. 5, Elsevier, 2018, pp. 1267–319, doi:<a href=\"https://doi.org/10.1016/j.anihpc.2017.11.004\">10.1016/j.anihpc.2017.11.004</a>.","short":"M. Duerinckx, J.L. Fischer, Annales de l’Institut Henri Poincare (C) Non Linear Analysis 35 (2018) 1267–1319.","ieee":"M. Duerinckx and J. L. Fischer, “Well-posedness for mean-field evolutions arising in superconductivity,” <i>Annales de l’Institut Henri Poincare (C) Non Linear Analysis</i>, vol. 35, no. 5. Elsevier, pp. 1267–1319, 2018.","ama":"Duerinckx M, Fischer JL. Well-posedness for mean-field evolutions arising in superconductivity. <i>Annales de l’Institut Henri Poincare (C) Non Linear Analysis</i>. 2018;35(5):1267-1319. doi:<a href=\"https://doi.org/10.1016/j.anihpc.2017.11.004\">10.1016/j.anihpc.2017.11.004</a>","ista":"Duerinckx M, Fischer JL. 2018. Well-posedness for mean-field evolutions arising in superconductivity. Annales de l’Institut Henri Poincare (C) Non Linear Analysis. 35(5), 1267–1319."},"oa_version":"Submitted Version","intvolume":"        35","acknowledgement":"The work of the author is supported by F.R.S.-FNRS ( Fonds de la Recherche Scientifique - FNRS ) through a Research Fellowship.\r\n\r\n","type":"journal_article","publist_id":"7199","scopus_import":"1","_id":"606","isi":1,"oa":1,"date_published":"2018-08-01T00:00:00Z","language":[{"iso":"eng"}],"month":"08","date_updated":"2023-09-19T10:39:09Z","department":[{"_id":"JuFi"}],"arxiv":1,"publisher":"Elsevier"},{"citation":{"ama":"Bodova K, Haskovec J, Markowich P. Well posedness and maximum entropy approximation for the dynamics of quantitative traits. <i>Physica D: Nonlinear Phenomena</i>. 2018;376-377:108-120. doi:<a href=\"https://doi.org/10.1016/j.physd.2017.10.015\">10.1016/j.physd.2017.10.015</a>","ista":"Bodova K, Haskovec J, Markowich P. 2018. Well posedness and maximum entropy approximation for the dynamics of quantitative traits. Physica D: Nonlinear Phenomena. 376–377, 108–120.","ieee":"K. Bodova, J. Haskovec, and P. Markowich, “Well posedness and maximum entropy approximation for the dynamics of quantitative traits,” <i>Physica D: Nonlinear Phenomena</i>, vol. 376–377. Elsevier, pp. 108–120, 2018.","short":"K. Bodova, J. Haskovec, P. Markowich, Physica D: Nonlinear Phenomena 376–377 (2018) 108–120.","mla":"Bodova, Katarina, et al. “Well Posedness and Maximum Entropy Approximation for the Dynamics of Quantitative Traits.” <i>Physica D: Nonlinear Phenomena</i>, vol. 376–377, Elsevier, 2018, pp. 108–20, doi:<a href=\"https://doi.org/10.1016/j.physd.2017.10.015\">10.1016/j.physd.2017.10.015</a>.","apa":"Bodova, K., Haskovec, J., &#38; Markowich, P. (2018). Well posedness and maximum entropy approximation for the dynamics of quantitative traits. <i>Physica D: Nonlinear Phenomena</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.physd.2017.10.015\">https://doi.org/10.1016/j.physd.2017.10.015</a>","chicago":"Bodova, Katarina, Jan Haskovec, and Peter Markowich. “Well Posedness and Maximum Entropy Approximation for the Dynamics of Quantitative Traits.” <i>Physica D: Nonlinear Phenomena</i>. Elsevier, 2018. <a href=\"https://doi.org/10.1016/j.physd.2017.10.015\">https://doi.org/10.1016/j.physd.2017.10.015</a>."},"status":"public","day":"01","publisher":"Elsevier","arxiv":1,"department":[{"_id":"NiBa"},{"_id":"GaTk"}],"date_updated":"2024-10-09T20:58:45Z","month":"08","language":[{"iso":"eng"}],"date_published":"2018-08-01T00:00:00Z","oa":1,"isi":1,"_id":"607","scopus_import":"1","publist_id":"7198","acknowledgement":"JH and PM are funded by KAUST baseline funds and grant no. 1000000193 .\r\nWe thank Nicholas Barton (IST Austria) for his useful comments and suggestions. \r\n\r\n","type":"journal_article","oa_version":"Submitted Version","main_file_link":[{"url":"https://arxiv.org/abs/1704.08757","open_access":"1"}],"quality_controlled":"1","corr_author":"1","publication":"Physica D: Nonlinear Phenomena","doi":"10.1016/j.physd.2017.10.015","year":"2018","date_created":"2018-12-11T11:47:28Z","title":"Well posedness and maximum entropy approximation for the dynamics of quantitative traits","abstract":[{"lang":"eng","text":"We study the Fokker-Planck equation derived in the large system limit of the Markovian process describing the dynamics of quantitative traits. The Fokker-Planck equation is posed on a bounded domain and its transport and diffusion coefficients vanish on the domain's boundary. We first argue that, despite this degeneracy, the standard no-flux boundary condition is valid. We derive the weak formulation of the problem and prove the existence and uniqueness of its solutions by constructing the corresponding contraction semigroup on a suitable function space. Then, we prove that for the parameter regime with high enough mutation rate the problem exhibits a positive spectral gap, which implies exponential convergence to equilibrium.Next, we provide a simple derivation of the so-called Dynamic Maximum Entropy (DynMaxEnt) method for approximation of observables (moments) of the Fokker-Planck solution, which can be interpreted as a nonlinear Galerkin approximation. The limited applicability of the DynMaxEnt method inspires us to introduce its modified version that is valid for the whole range of admissible parameters. Finally, we present several numerical experiments to demonstrate the performance of both the original and modified DynMaxEnt methods. We observe that in the parameter regimes where both methods are valid, the modified one exhibits slightly better approximation properties compared to the original one."}],"external_id":{"isi":["000437962900012"],"arxiv":["1704.08757"]},"publication_status":"published","page":"108-120","article_processing_charge":"No","volume":"376-377","author":[{"id":"2BA24EA0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7214-0171","full_name":"Bodova, Katarina","first_name":"Katarina","last_name":"Bodova"},{"first_name":"Jan","last_name":"Haskovec","full_name":"Haskovec, Jan"},{"first_name":"Peter","last_name":"Markowich","full_name":"Markowich, Peter"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"article_type":"original","oa_version":"Published Version","intvolume":"       712","type":"journal_article","publist_id":"7197","_id":"608","scopus_import":"1","isi":1,"oa":1,"language":[{"iso":"eng"}],"month":"02","date_published":"2018-02-15T00:00:00Z","publisher":"Elsevier","department":[{"_id":"ToHe"}],"date_updated":"2026-06-18T18:58:53Z","ec_funded":1,"day":"15","status":"public","citation":{"ista":"Avni G, Kupferman O. 2018. Synthesis from component libraries with costs. Theoretical Computer Science. 712, 50–72.","ama":"Avni G, Kupferman O. Synthesis from component libraries with costs. <i>Theoretical Computer Science</i>. 2018;712:50-72. doi:<a href=\"https://doi.org/10.1016/j.tcs.2017.11.001\">10.1016/j.tcs.2017.11.001</a>","short":"G. Avni, O. Kupferman, Theoretical Computer Science 712 (2018) 50–72.","ieee":"G. Avni and O. Kupferman, “Synthesis from component libraries with costs,” <i>Theoretical Computer Science</i>, vol. 712. Elsevier, pp. 50–72, 2018.","mla":"Avni, Guy, and Orna Kupferman. “Synthesis from Component Libraries with Costs.” <i>Theoretical Computer Science</i>, vol. 712, Elsevier, 2018, pp. 50–72, doi:<a href=\"https://doi.org/10.1016/j.tcs.2017.11.001\">10.1016/j.tcs.2017.11.001</a>.","apa":"Avni, G., &#38; Kupferman, O. (2018). Synthesis from component libraries with costs. <i>Theoretical Computer Science</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.tcs.2017.11.001\">https://doi.org/10.1016/j.tcs.2017.11.001</a>","chicago":"Avni, Guy, and Orna Kupferman. “Synthesis from Component Libraries with Costs.” <i>Theoretical Computer Science</i>. Elsevier, 2018. <a href=\"https://doi.org/10.1016/j.tcs.2017.11.001\">https://doi.org/10.1016/j.tcs.2017.11.001</a>."},"project":[{"name":"Quantitative Reactive Modeling","call_identifier":"FP7","grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425"},{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF"},{"grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"Formal methods for the design and analysis of complex systems","call_identifier":"FWF"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Avni, Guy","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5588-8287","first_name":"Guy","last_name":"Avni"},{"full_name":"Kupferman, Orna","last_name":"Kupferman","first_name":"Orna"}],"volume":712,"page":"50 - 72","article_processing_charge":"No","abstract":[{"text":"Synthesis is the automated construction of a system from its specification. In real life, hardware and software systems are rarely constructed from scratch. Rather, a system is typically constructed from a library of components. Lustig and Vardi formalized this intuition and studied LTL synthesis from component libraries. In real life, designers seek optimal systems. In this paper we add optimality considerations to the setting. We distinguish between quality considerations (for example, size - the smaller a system is, the better it is), and pricing (for example, the payment to the company who manufactured the component). We study the problem of designing systems with minimal quality-cost and price. A key point is that while the quality cost is individual - the choices of a designer are independent of choices made by other designers that use the same library, pricing gives rise to a resource-allocation game - designers that use the same component share its price, with the share being proportional to the number of uses (a component can be used several times in a design). We study both closed and open settings, and in both we solve the problem of finding an optimal design. In a setting with multiple designers, we also study the game-theoretic problems of the induced resource-allocation game.","lang":"eng"}],"external_id":{"isi":["000424959200003"]},"publication_status":"published","title":"Synthesis from component libraries with costs","year":"2018","date_created":"2018-12-11T11:47:28Z","doi":"10.1016/j.tcs.2017.11.001","publication":"Theoretical Computer Science","corr_author":"1","quality_controlled":"1","main_file_link":[{"url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.636.4529","open_access":"1"}],"ddc":["000"]},{"article_processing_charge":"No","page":"131 - 134","external_id":{"arxiv":["1509.06286"]},"publication_status":"published","abstract":[{"lang":"eng","text":"We prove that there is no strongly regular graph (SRG) with parameters (460; 153; 32; 60). The proof is based on a recent lower bound on the number of 4-cliques in a SRG and some applications of Euclidean representation of SRGs. "}],"oa":1,"date_published":"2018-05-23T00:00:00Z","title":"There is no strongly regular graph with parameters (460; 153; 32; 60)","month":"05","language":[{"iso":"eng"}],"date_updated":"2021-01-12T08:06:06Z","publisher":"Springer","department":[{"_id":"TaHa"}],"arxiv":1,"author":[{"full_name":"Bondarenko, Andriy","first_name":"Andriy","last_name":"Bondarenko"},{"id":"388D3134-F248-11E8-B48F-1D18A9856A87","full_name":"Mellit, Anton","last_name":"Mellit","first_name":"Anton"},{"full_name":"Prymak, Andriy","last_name":"Prymak","first_name":"Andriy"},{"first_name":"Danylo","last_name":"Radchenko","full_name":"Radchenko, Danylo"},{"last_name":"Viazovska","first_name":"Maryna","full_name":"Viazovska, Maryna"}],"oa_version":"Preprint","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","extern":"1","type":"book_chapter","publist_id":"7993","_id":"61","citation":{"apa":"Bondarenko, A., Mellit, A., Prymak, A., Radchenko, D., &#38; Viazovska, M. (2018). There is no strongly regular graph with parameters (460; 153; 32; 60). In <i>Contemporary Computational Mathematics</i> (pp. 131–134). Springer. <a href=\"https://doi.org/10.1007/978-3-319-72456-0_7\">https://doi.org/10.1007/978-3-319-72456-0_7</a>","chicago":"Bondarenko, Andriy, Anton Mellit, Andriy Prymak, Danylo Radchenko, and Maryna Viazovska. “There Is No Strongly Regular Graph with Parameters (460; 153; 32; 60).” In <i>Contemporary Computational Mathematics</i>, 131–34. Springer, 2018. <a href=\"https://doi.org/10.1007/978-3-319-72456-0_7\">https://doi.org/10.1007/978-3-319-72456-0_7</a>.","mla":"Bondarenko, Andriy, et al. “There Is No Strongly Regular Graph with Parameters (460; 153; 32; 60).” <i>Contemporary Computational Mathematics</i>, Springer, 2018, pp. 131–34, doi:<a href=\"https://doi.org/10.1007/978-3-319-72456-0_7\">10.1007/978-3-319-72456-0_7</a>.","short":"A. Bondarenko, A. Mellit, A. Prymak, D. Radchenko, M. Viazovska, in:, Contemporary Computational Mathematics, Springer, 2018, pp. 131–134.","ieee":"A. Bondarenko, A. Mellit, A. Prymak, D. Radchenko, and M. Viazovska, “There is no strongly regular graph with parameters (460; 153; 32; 60),” in <i>Contemporary Computational Mathematics</i>, Springer, 2018, pp. 131–134.","ama":"Bondarenko A, Mellit A, Prymak A, Radchenko D, Viazovska M. There is no strongly regular graph with parameters (460; 153; 32; 60). In: <i>Contemporary Computational Mathematics</i>. Springer; 2018:131-134. doi:<a href=\"https://doi.org/10.1007/978-3-319-72456-0_7\">10.1007/978-3-319-72456-0_7</a>","ista":"Bondarenko A, Mellit A, Prymak A, Radchenko D, Viazovska M. 2018.There is no strongly regular graph with parameters (460; 153; 32; 60). In: Contemporary Computational Mathematics. , 131–134."},"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1509.06286"}],"date_created":"2018-12-11T11:44:25Z","year":"2018","doi":"10.1007/978-3-319-72456-0_7","publication":"Contemporary Computational Mathematics","day":"23","status":"public"},{"date_created":"2019-03-19T12:41:33Z","year":"2018","publication_identifier":{"issn":["0027-8424","1091-6490"]},"doi":"10.1073/pnas.1714610115","issue":"29","publication":"Proceedings of the National Academy of Sciences","quality_controlled":"1","file":[{"file_id":"6110","file_size":1567765,"date_updated":"2020-07-14T12:47:19Z","access_level":"open_access","relation":"main_file","checksum":"5e81665377441cdd8d99ab952c534319","content_type":"application/pdf","file_name":"2018_PNAS_Laurent.pdf","date_created":"2019-03-19T13:01:58Z","creator":"kschuh"}],"has_accepted_license":"1","ddc":["570"],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Laurent, Patrick","first_name":"Patrick","last_name":"Laurent"},{"full_name":"Ch’ng, QueeLim","last_name":"Ch’ng","first_name":"QueeLim"},{"first_name":"Maëlle","last_name":"Jospin","full_name":"Jospin, Maëlle"},{"first_name":"Changchun","last_name":"Chen","full_name":"Chen, Changchun"},{"first_name":"Ramiro","last_name":"Lorenzo","full_name":"Lorenzo, Ramiro"},{"id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8347-0443","full_name":"de Bono, Mario","last_name":"de Bono","first_name":"Mario"}],"extern":"1","volume":115,"pmid":1,"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","page":"E6890-E6899","external_id":{"pmid":["29959203"]},"publication_status":"published","abstract":[{"lang":"eng","text":"Neuropeptides are ubiquitous modulators of behavior and physiology. They are packaged in specialized secretory organelles called dense core vesicles (DCVs) that are released upon neural stimulation. Unlike synaptic vesicles, which can be recycled and refilled close to release sites, DCVs must be replenished by de novo synthesis in the cell body. Here, we dissect DCV cell biology in vivo in a Caenorhabditis elegans sensory neuron whose tonic activity we can control using a natural stimulus. We express fluorescently tagged neuropeptides in the neuron and define parameters that describe their subcellular distribution. We measure these parameters at high and low neural activity in 187 mutants defective in proteins implicated in membrane traffic, neuroendocrine secretion, and neuronal or synaptic activity. Using unsupervised hierarchical clustering methods, we analyze these data and identify 62 groups of genes with similar mutant phenotypes. We explore the function of a subset of these groups. We recapitulate many previous findings, validating our paradigm. We uncover a large battery of proteins involved in recycling DCV membrane proteins, something hitherto poorly explored. We show that the unfolded protein response promotes DCV production, which may contribute to intertissue communication of stress. We also find evidence that different mechanisms of priming and exocytosis may operate at high and low neural activity. Our work provides a defined framework to study DCV biology at different neural activity levels."}],"title":"Genetic dissection of neuropeptide cell biology at high and low activity in a defined sensory neuron","tmp":{"short":"CC BY-NC-ND (4.0)","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","image":"/images/cc_by_nc_nd.png"},"status":"public","day":"17","citation":{"mla":"Laurent, Patrick, et al. “Genetic Dissection of Neuropeptide Cell Biology at High and Low Activity in a Defined Sensory Neuron.” <i>Proceedings of the National Academy of Sciences</i>, vol. 115, no. 29, National Academy of Sciences, 2018, pp. E6890–99, doi:<a href=\"https://doi.org/10.1073/pnas.1714610115\">10.1073/pnas.1714610115</a>.","apa":"Laurent, P., Ch’ng, Q., Jospin, M., Chen, C., Lorenzo, R., &#38; de Bono, M. (2018). Genetic dissection of neuropeptide cell biology at high and low activity in a defined sensory neuron. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1714610115\">https://doi.org/10.1073/pnas.1714610115</a>","chicago":"Laurent, Patrick, QueeLim Ch’ng, Maëlle Jospin, Changchun Chen, Ramiro Lorenzo, and Mario de Bono. “Genetic Dissection of Neuropeptide Cell Biology at High and Low Activity in a Defined Sensory Neuron.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2018. <a href=\"https://doi.org/10.1073/pnas.1714610115\">https://doi.org/10.1073/pnas.1714610115</a>.","ista":"Laurent P, Ch’ng Q, Jospin M, Chen C, Lorenzo R, de Bono M. 2018. Genetic dissection of neuropeptide cell biology at high and low activity in a defined sensory neuron. Proceedings of the National Academy of Sciences. 115(29), E6890–E6899.","ama":"Laurent P, Ch’ng Q, Jospin M, Chen C, Lorenzo R, de Bono M. Genetic dissection of neuropeptide cell biology at high and low activity in a defined sensory neuron. <i>Proceedings of the National Academy of Sciences</i>. 2018;115(29):E6890-E6899. doi:<a href=\"https://doi.org/10.1073/pnas.1714610115\">10.1073/pnas.1714610115</a>","ieee":"P. Laurent, Q. Ch’ng, M. Jospin, C. Chen, R. Lorenzo, and M. de Bono, “Genetic dissection of neuropeptide cell biology at high and low activity in a defined sensory neuron,” <i>Proceedings of the National Academy of Sciences</i>, vol. 115, no. 29. National Academy of Sciences, pp. E6890–E6899, 2018.","short":"P. Laurent, Q. Ch’ng, M. Jospin, C. Chen, R. Lorenzo, M. de Bono, Proceedings of the National Academy of Sciences 115 (2018) E6890–E6899."},"oa_version":"Published Version","intvolume":"       115","type":"journal_article","_id":"6109","file_date_updated":"2020-07-14T12:47:19Z","oa":1,"date_published":"2018-07-17T00:00:00Z","language":[{"iso":"eng"}],"month":"07","date_updated":"2021-01-12T08:06:09Z","publisher":"National Academy of Sciences"},{"oa":1,"file_date_updated":"2020-07-14T12:47:19Z","month":"06","language":[{"iso":"eng"}],"date_published":"2018-06-07T00:00:00Z","publisher":"Public Library of Science","date_updated":"2021-01-12T08:06:11Z","intvolume":"        14","oa_version":"Published Version","type":"journal_article","_id":"6111","citation":{"chicago":"McLachlan, Ian G., Isabel Beets, Mario de Bono, and Maxwell G. Heiman. “A Neuronal MAP Kinase Constrains Growth of a Caenorhabditis Elegans Sensory Dendrite throughout the Life of the Organism.” <i>PLOS Genetics</i>. Public Library of Science, 2018. <a href=\"https://doi.org/10.1371/journal.pgen.1007435\">https://doi.org/10.1371/journal.pgen.1007435</a>.","apa":"McLachlan, I. G., Beets, I., de Bono, M., &#38; Heiman, M. G. (2018). A neuronal MAP kinase constrains growth of a Caenorhabditis elegans sensory dendrite throughout the life of the organism. <i>PLOS Genetics</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pgen.1007435\">https://doi.org/10.1371/journal.pgen.1007435</a>","mla":"McLachlan, Ian G., et al. “A Neuronal MAP Kinase Constrains Growth of a Caenorhabditis Elegans Sensory Dendrite throughout the Life of the Organism.” <i>PLOS Genetics</i>, vol. 14, no. 6, e1007435, Public Library of Science, 2018, doi:<a href=\"https://doi.org/10.1371/journal.pgen.1007435\">10.1371/journal.pgen.1007435</a>.","ieee":"I. G. McLachlan, I. Beets, M. de Bono, and M. G. Heiman, “A neuronal MAP kinase constrains growth of a Caenorhabditis elegans sensory dendrite throughout the life of the organism,” <i>PLOS Genetics</i>, vol. 14, no. 6. Public Library of Science, 2018.","short":"I.G. McLachlan, I. Beets, M. de Bono, M.G. Heiman, PLOS Genetics 14 (2018).","ista":"McLachlan IG, Beets I, de Bono M, Heiman MG. 2018. A neuronal MAP kinase constrains growth of a Caenorhabditis elegans sensory dendrite throughout the life of the organism. PLOS Genetics. 14(6), e1007435.","ama":"McLachlan IG, Beets I, de Bono M, Heiman MG. A neuronal MAP kinase constrains growth of a Caenorhabditis elegans sensory dendrite throughout the life of the organism. <i>PLOS Genetics</i>. 2018;14(6). doi:<a href=\"https://doi.org/10.1371/journal.pgen.1007435\">10.1371/journal.pgen.1007435</a>"},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"day":"07","status":"public","abstract":[{"lang":"eng","text":"Neurons develop elaborate morphologies that provide a model for understanding cellular architecture. By studying C. elegans sensory dendrites, we previously identified genes that act to promote the extension of ciliated sensory dendrites during embryogenesis. Interestingly, the nonciliated dendrite of the oxygen-sensing neuron URX is not affected by these genes, suggesting it develops through a distinct mechanism. Here, we use a visual forward genetic screen to identify mutants that affect URX dendrite morphogenesis. We find that disruption of the MAP kinase MAPK-15 or the βH-spectrin SMA-1 causes a phenotype opposite to what we had seen before: dendrites extend normally during embryogenesis but begin to overgrow as the animals reach adulthood, ultimately extending up to 150% of their normal length. SMA-1 is broadly expressed and acts non-cell-autonomously, while MAPK-15 is expressed in many sensory neurons including URX and acts cell-autonomously. MAPK-15 acts at the time of overgrowth, localizes at the dendrite ending, and requires its kinase activity, suggesting it acts locally in time and space to constrain dendrite growth. Finally, we find that the oxygen-sensing guanylate cyclase GCY-35, which normally localizes at the dendrite ending, is localized throughout the overgrown region, and that overgrowth can be suppressed by overexpressing GCY-35 or by genetically mimicking elevated cGMP signaling. These results suggest that overgrowth may correspond to expansion of a sensory compartment at the dendrite ending, reminiscent of the remodeling of sensory cilia or dendritic spines. Thus, in contrast to established pathways that promote dendrite growth during early development, our results reveal a distinct mechanism that constrains dendrite growth throughout the life of the animal, possibly by controlling the size of a sensory compartment at the dendrite ending."}],"external_id":{"pmid":["29879119"]},"publication_status":"published","title":"A neuronal MAP kinase constrains growth of a Caenorhabditis elegans sensory dendrite throughout the life of the organism","extern":"1","author":[{"last_name":"McLachlan","first_name":"Ian G.","full_name":"McLachlan, Ian G."},{"full_name":"Beets, Isabel","last_name":"Beets","first_name":"Isabel"},{"full_name":"de Bono, Mario","orcid":"0000-0001-8347-0443","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","last_name":"de Bono","first_name":"Mario"},{"first_name":"Maxwell G.","last_name":"Heiman","full_name":"Heiman, Maxwell G."}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","volume":14,"pmid":1,"quality_controlled":"1","file":[{"date_created":"2019-03-19T13:18:01Z","file_name":"2018_PLOS_McLachlan.pdf","content_type":"application/pdf","creator":"kschuh","file_id":"6112","relation":"main_file","checksum":"622036b945365dbc575bea2768aa9bc8","access_level":"open_access","date_updated":"2020-07-14T12:47:19Z","file_size":13011506}],"has_accepted_license":"1","ddc":["570"],"year":"2018","date_created":"2019-03-19T13:09:28Z","article_number":"e1007435","issue":"6","doi":"10.1371/journal.pgen.1007435","publication_identifier":{"issn":["1553-7404"]},"publication":"PLOS Genetics"},{"citation":{"apa":"Pull, C., Ugelvig, L. V., Wiesenhofer, F., Grasse, A. V., Tragust, S., Schmitt, T., … Cremer, S. (2018). Destructive disinfection of infected brood prevents systemic disease spread in ant colonies. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.32073\">https://doi.org/10.7554/eLife.32073</a>","chicago":"Pull, Christopher, Line V Ugelvig, Florian Wiesenhofer, Anna V Grasse, Simon Tragust, Thomas Schmitt, Mark Brown, and Sylvia Cremer. “Destructive Disinfection of Infected Brood Prevents Systemic Disease Spread in Ant Colonies.” <i>ELife</i>. eLife Sciences Publications, 2018. <a href=\"https://doi.org/10.7554/eLife.32073\">https://doi.org/10.7554/eLife.32073</a>.","mla":"Pull, Christopher, et al. “Destructive Disinfection of Infected Brood Prevents Systemic Disease Spread in Ant Colonies.” <i>ELife</i>, vol. 7, e32073, eLife Sciences Publications, 2018, doi:<a href=\"https://doi.org/10.7554/eLife.32073\">10.7554/eLife.32073</a>.","short":"C. Pull, L.V. Ugelvig, F. Wiesenhofer, A.V. Grasse, S. Tragust, T. Schmitt, M. Brown, S. Cremer, ELife 7 (2018).","ieee":"C. Pull <i>et al.</i>, “Destructive disinfection of infected brood prevents systemic disease spread in ant colonies,” <i>eLife</i>, vol. 7. eLife Sciences Publications, 2018.","ama":"Pull C, Ugelvig LV, Wiesenhofer F, et al. Destructive disinfection of infected brood prevents systemic disease spread in ant colonies. <i>eLife</i>. 2018;7. doi:<a href=\"https://doi.org/10.7554/eLife.32073\">10.7554/eLife.32073</a>","ista":"Pull C, Ugelvig LV, Wiesenhofer F, Grasse AV, Tragust S, Schmitt T, Brown M, Cremer S. 2018. Destructive disinfection of infected brood prevents systemic disease spread in ant colonies. eLife. 7, e32073."},"project":[{"call_identifier":"FP7","name":"Social Vaccination in Ant Colonies: from Individual Mechanisms to Society Effects","_id":"25DC711C-B435-11E9-9278-68D0E5697425","grant_number":"243071"},{"grant_number":"302004","_id":"25DDF0F0-B435-11E9-9278-68D0E5697425","name":"Collective disease defence and pathogen detection abilities in ant societies: a chemo-neuro-immunological approach","call_identifier":"FP7"}],"pubrep_id":"978","status":"public","day":"09","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ec_funded":1,"date_published":"2018-01-09T00:00:00Z","language":[{"iso":"eng"}],"month":"01","date_updated":"2026-04-08T14:19:10Z","department":[{"_id":"SyCr"}],"publisher":"eLife Sciences Publications","isi":1,"file_date_updated":"2020-07-14T12:47:20Z","oa":1,"publist_id":"7188","scopus_import":"1","_id":"616","oa_version":"Published Version","intvolume":"         7","type":"journal_article","has_accepted_license":"1","ddc":["570","590"],"corr_author":"1","quality_controlled":"1","file":[{"file_name":"IST-2018-978-v1+1_elife-32073-v1.pdf","content_type":"application/pdf","date_created":"2018-12-12T10:10:43Z","creator":"system","file_id":"4832","date_updated":"2020-07-14T12:47:20Z","file_size":1435585,"access_level":"open_access","checksum":"540f941e8d3530a9441e4affd94f07d7","relation":"main_file"}],"doi":"10.7554/eLife.32073","publication":"eLife","date_created":"2018-12-11T11:47:31Z","year":"2018","article_number":"e32073","title":"Destructive disinfection of infected brood prevents systemic disease spread in ant colonies","article_processing_charge":"Yes","external_id":{"isi":["000419601300001"]},"publication_status":"published","abstract":[{"lang":"eng","text":"Social insects protect their colonies from infectious disease through collective defences that result in social immunity. In ants, workers first try to prevent infection of colony members. Here, we show that if this fails and a pathogen establishes an infection, ants employ an efficient multicomponent behaviour − &quot;destructive disinfection&quot; − to prevent further spread of disease through the colony. Ants specifically target infected pupae during the pathogen's non-contagious incubation period, relying on chemical 'sickness cues' emitted by pupae. They then remove the pupal cocoon, perforate its cuticle and administer antimicrobial poison, which enters the body and prevents pathogen replication from the inside out. Like the immune system of a body that specifically targets and eliminates infected cells, this social immunity measure sacrifices infected brood to stop the pathogen completing its lifecycle, thus protecting the rest of the colony. Hence, the same principles of disease defence apply at different levels of biological organisation."}],"related_material":{"record":[{"id":"819","relation":"dissertation_contains","status":"public"}]},"author":[{"full_name":"Pull, Christopher","id":"3C7F4840-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1122-3982","last_name":"Pull","first_name":"Christopher"},{"id":"3DC97C8E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1832-8883","full_name":"Ugelvig, Line V","last_name":"Ugelvig","first_name":"Line V"},{"first_name":"Florian","last_name":"Wiesenhofer","id":"39523C54-F248-11E8-B48F-1D18A9856A87","full_name":"Wiesenhofer, Florian"},{"full_name":"Grasse, Anna V","id":"406F989C-F248-11E8-B48F-1D18A9856A87","last_name":"Grasse","first_name":"Anna V"},{"last_name":"Tragust","first_name":"Simon","full_name":"Tragust, Simon","id":"35A7A418-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Schmitt","first_name":"Thomas","full_name":"Schmitt, Thomas"},{"full_name":"Brown, Mark","first_name":"Mark","last_name":"Brown"},{"first_name":"Sylvia","last_name":"Cremer","full_name":"Cremer, Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2193-3868"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","volume":7},{"citation":{"mla":"Kutzer, Megan, et al. “Genotype and Diet Affect Resistance, Survival, and Fecundity but Not Fecundity Tolerance.” <i>Journal of Evolutionary Biology</i>, vol. 31, no. 1, Wiley, 2018, pp. 159–71, doi:<a href=\"https://doi.org/10.1111/jeb.13211\">10.1111/jeb.13211</a>.","apa":"Kutzer, M., Kurtz, J., &#38; Armitage, S. (2018). Genotype and diet affect resistance, survival, and fecundity but not fecundity tolerance. <i>Journal of Evolutionary Biology</i>. Wiley. <a href=\"https://doi.org/10.1111/jeb.13211\">https://doi.org/10.1111/jeb.13211</a>","chicago":"Kutzer, Megan, Joachim Kurtz, and Sophie Armitage. “Genotype and Diet Affect Resistance, Survival, and Fecundity but Not Fecundity Tolerance.” <i>Journal of Evolutionary Biology</i>. Wiley, 2018. <a href=\"https://doi.org/10.1111/jeb.13211\">https://doi.org/10.1111/jeb.13211</a>.","ama":"Kutzer M, Kurtz J, Armitage S. Genotype and diet affect resistance, survival, and fecundity but not fecundity tolerance. <i>Journal of Evolutionary Biology</i>. 2018;31(1):159-171. doi:<a href=\"https://doi.org/10.1111/jeb.13211\">10.1111/jeb.13211</a>","ista":"Kutzer M, Kurtz J, Armitage S. 2018. Genotype and diet affect resistance, survival, and fecundity but not fecundity tolerance. Journal of Evolutionary Biology. 31(1), 159–171.","ieee":"M. Kutzer, J. Kurtz, and S. Armitage, “Genotype and diet affect resistance, survival, and fecundity but not fecundity tolerance,” <i>Journal of Evolutionary Biology</i>, vol. 31, no. 1. Wiley, pp. 159–171, 2018.","short":"M. Kutzer, J. Kurtz, S. Armitage, Journal of Evolutionary Biology 31 (2018) 159–171."},"status":"public","day":"01","isi":1,"oa":1,"language":[{"iso":"eng"}],"month":"01","date_published":"2018-01-01T00:00:00Z","publisher":"Wiley","department":[{"_id":"SyCr"}],"date_updated":"2026-06-18T19:00:18Z","article_type":"original","oa_version":"Published Version","intvolume":"        31","type":"journal_article","acknowledgement":"We would like to thank Susann Wicke for performing the genome-wide SNP/indel analyses, as well as Veronica Alves, Kevin Ferro, Momir Futo, Barbara Hasert, Dafne Maximo, Nora Schulz, Marlene Sroka, and Barth Wieczorek for technical help. We thank Brian Lazzaro for the L. lactis strain and Bruno Lemaitre for the Pseudomonas entomophila strain. We would like to thank two anonymous reviewers for their helpful comments. We are grateful to the Deutsche Forschungsgemeinschaft (DFG) priority programme 1399 ‘Host parasite coevolution’ for funding this project (AR 872/1-1). ","publist_id":"7187","_id":"617","scopus_import":"1","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1111/jeb.13211"}],"ddc":["570"],"year":"2018","date_created":"2018-12-11T11:47:31Z","issue":"1","doi":"10.1111/jeb.13211","publication_identifier":{"eissn":["1420-9101"],"issn":["1010-061X"]},"publication":"Journal of Evolutionary Biology","page":"159  - 171","article_processing_charge":"No","abstract":[{"lang":"eng","text":"Insects are exposed to a variety of potential pathogens in their environment, many of which can severely impact fitness and health. Consequently, hosts have evolved resistance and tolerance strategies to suppress or cope with infections. Hosts utilizing resistance improve fitness by clearing or reducing pathogen loads, and hosts utilizing tolerance reduce harmful fitness effects per pathogen load. To understand variation in, and selective pressures on, resistance and tolerance, we asked to what degree they are shaped by host genetic background, whether plasticity in these responses depends upon dietary environment, and whether there are interactions between these two factors. Females from ten wild-type Drosophila melanogaster genotypes were kept on high- or low-protein (yeast) diets and infected with one of two opportunistic bacterial pathogens, Lactococcus lactis or Pseudomonas entomophila. We measured host resistance as the inverse of bacterial load in the early infection phase. The relationship (slope) between fly fecundity and individual-level bacteria load provided our fecundity tolerance measure. Genotype and dietary yeast determined host fecundity and strongly affected survival after infection with pathogenic P. entomophila. There was considerable genetic variation in host resistance, a commonly found phenomenon resulting from for example varying resistance costs or frequency-dependent selection. Despite this variation and the reproductive cost of higher P. entomophila loads, fecundity tolerance did not vary across genotypes. The absence of genetic variation in tolerance may suggest that at this early infection stage, fecundity tolerance is fixed or that any evolved tolerance mechanisms are not expressed under these infection conditions."}],"publication_status":"published","external_id":{"isi":["000419307000014"],"pmid":["29150962"]},"title":"Genotype and diet affect resistance, survival, and fecundity but not fecundity tolerance","author":[{"last_name":"Kutzer","first_name":"Megan","id":"29D0B332-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8696-6978","full_name":"Kutzer, Megan"},{"last_name":"Kurtz","first_name":"Joachim","full_name":"Kurtz, Joachim"},{"full_name":"Armitage, Sophie","first_name":"Sophie","last_name":"Armitage"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":31,"pmid":1},{"doi":"10.48550/arXiv.1804.07752","publication":"arXiv","day":"20","status":"public","year":"2018","date_created":"2019-03-28T09:20:06Z","ec_funded":1,"article_number":"1804.07752","main_file_link":[{"url":"https://arxiv.org/abs/1804.07752","open_access":"1"}],"citation":{"ieee":"J. Alt, L. Erdös, and T. H. Krüger, “The Dyson equation with linear self-energy: Spectral bands, edges and  cusps,” <i>arXiv</i>. .","short":"J. Alt, L. Erdös, T.H. Krüger, ArXiv (n.d.).","ama":"Alt J, Erdös L, Krüger TH. The Dyson equation with linear self-energy: Spectral bands, edges and  cusps. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.1804.07752\">10.48550/arXiv.1804.07752</a>","ista":"Alt J, Erdös L, Krüger TH. The Dyson equation with linear self-energy: Spectral bands, edges and  cusps. arXiv, 1804.07752.","chicago":"Alt, Johannes, László Erdös, and Torben H Krüger. “The Dyson Equation with Linear Self-Energy: Spectral Bands, Edges and  Cusps.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.1804.07752\">https://doi.org/10.48550/arXiv.1804.07752</a>.","apa":"Alt, J., Erdös, L., &#38; Krüger, T. H. (n.d.). The Dyson equation with linear self-energy: Spectral bands, edges and  cusps. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.1804.07752\">https://doi.org/10.48550/arXiv.1804.07752</a>","mla":"Alt, Johannes, et al. “The Dyson Equation with Linear Self-Energy: Spectral Bands, Edges and  Cusps.” <i>ArXiv</i>, 1804.07752, doi:<a href=\"https://doi.org/10.48550/arXiv.1804.07752\">10.48550/arXiv.1804.07752</a>."},"project":[{"name":"Random matrices, universality and disordered quantum systems","call_identifier":"FP7","grant_number":"338804","_id":"258DCDE6-B435-11E9-9278-68D0E5697425"}],"related_material":{"record":[{"id":"14694","relation":"later_version","status":"public"},{"status":"public","id":"149","relation":"dissertation_contains"}]},"_id":"6183","oa_version":"Preprint","author":[{"last_name":"Alt","first_name":"Johannes","id":"36D3D8B6-F248-11E8-B48F-1D18A9856A87","full_name":"Alt, Johannes"},{"id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5366-9603","full_name":"Erdös, László","last_name":"Erdös","first_name":"László"},{"last_name":"Krüger","first_name":"Torben H","full_name":"Krüger, Torben H","orcid":"0000-0002-4821-3297","id":"3020C786-F248-11E8-B48F-1D18A9856A87"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"preprint","acknowledgement":"Partially funded by ERC Advanced Grant RANMAT No. 338804.\r\nPartially supported by the Hausdorff Center for Mathematics.\r\n","month":"04","title":"The Dyson equation with linear self-energy: Spectral bands, edges and  cusps","language":[{"iso":"eng"}],"date_published":"2018-04-20T00:00:00Z","arxiv":1,"department":[{"_id":"LaEr"}],"date_updated":"2026-04-08T14:11:36Z","article_processing_charge":"No","oa":1,"abstract":[{"lang":"eng","text":"We study the unique solution $m$ of the Dyson equation \\[ -m(z)^{-1} = z - a\r\n+ S[m(z)] \\] on a von Neumann algebra $\\mathcal{A}$ with the constraint\r\n$\\mathrm{Im}\\,m\\geq 0$. Here, $z$ lies in the complex upper half-plane, $a$ is\r\na self-adjoint element of $\\mathcal{A}$ and $S$ is a positivity-preserving\r\nlinear operator on $\\mathcal{A}$. We show that $m$ is the Stieltjes transform\r\nof a compactly supported $\\mathcal{A}$-valued measure on $\\mathbb{R}$. Under\r\nsuitable assumptions, we establish that this measure has a uniformly\r\n$1/3$-H\\\"{o}lder continuous density with respect to the Lebesgue measure, which\r\nis supported on finitely many intervals, called bands. In fact, the density is\r\nanalytic inside the bands with a square-root growth at the edges and internal\r\ncubic root cusps whenever the gap between two bands vanishes. The shape of\r\nthese singularities is universal and no other singularity may occur. We give a\r\nprecise asymptotic description of $m$ near the singular points. These\r\nasymptotics generalize the analysis at the regular edges given in the companion\r\npaper on the Tracy-Widom universality for the edge eigenvalue statistics for\r\ncorrelated random matrices [arXiv:1804.07744] and they play a key role in the\r\nproof of the Pearcey universality at the cusp for Wigner-type matrices\r\n[arXiv:1809.03971,arXiv:1811.04055]. We also extend the finite dimensional band\r\nmass formula from [arXiv:1804.07744] to the von Neumann algebra setting by\r\nshowing that the spectral mass of the bands is topologically rigid under\r\ndeformations and we conclude that these masses are quantized in some important\r\ncases."}],"external_id":{"arxiv":["1804.07752"]},"publication_status":"draft"},{"citation":{"apa":"Shabazi, A., Kinnison, J., Vescovi, R., Du, M., Hill, R., Jösch, M. A., … Scheirer, W. (2018). Flexible learning-free segmentation and reconstruction of neural volumes. <i>Scientific Reports</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41598-018-32628-3\">https://doi.org/10.1038/s41598-018-32628-3</a>","chicago":"Shabazi, Ali, Jeffery Kinnison, Rafael Vescovi, Ming Du, Robert Hill, Maximilian A Jösch, Marc Takeno, et al. “Flexible Learning-Free Segmentation and Reconstruction of Neural Volumes.” <i>Scientific Reports</i>. Nature Publishing Group, 2018. <a href=\"https://doi.org/10.1038/s41598-018-32628-3\">https://doi.org/10.1038/s41598-018-32628-3</a>.","mla":"Shabazi, Ali, et al. “Flexible Learning-Free Segmentation and Reconstruction of Neural Volumes.” <i>Scientific Reports</i>, vol. 8, no. 1, 14247, Nature Publishing Group, 2018, doi:<a href=\"https://doi.org/10.1038/s41598-018-32628-3\">10.1038/s41598-018-32628-3</a>.","short":"A. Shabazi, J. Kinnison, R. Vescovi, M. Du, R. Hill, M.A. Jösch, M. Takeno, H. Zeng, N. Da Costa, J. Grutzendler, N. Kasthuri, W. Scheirer, Scientific Reports 8 (2018).","ieee":"A. Shabazi <i>et al.</i>, “Flexible learning-free segmentation and reconstruction of neural volumes,” <i>Scientific Reports</i>, vol. 8, no. 1. Nature Publishing Group, 2018.","ista":"Shabazi A, Kinnison J, Vescovi R, Du M, Hill R, Jösch MA, Takeno M, Zeng H, Da Costa N, Grutzendler J, Kasthuri N, Scheirer W. 2018. Flexible learning-free segmentation and reconstruction of neural volumes. Scientific Reports. 8(1), 14247.","ama":"Shabazi A, Kinnison J, Vescovi R, et al. Flexible learning-free segmentation and reconstruction of neural volumes. <i>Scientific Reports</i>. 2018;8(1). doi:<a href=\"https://doi.org/10.1038/s41598-018-32628-3\">10.1038/s41598-018-32628-3</a>"},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","day":"24","oa":1,"file_date_updated":"2020-07-14T12:47:24Z","isi":1,"publisher":"Nature Publishing Group","department":[{"_id":"MaJö"}],"date_updated":"2023-09-11T14:02:55Z","language":[{"iso":"eng"}],"month":"09","date_published":"2018-09-24T00:00:00Z","acknowledgement":"Equipment was generously donated by the NVIDIA Corporation, and made available by the National Science Foundation (NSF) through grant #CNS-1629914. This research used resources of the Argonne Leadership Computing Facility, which is a DOE Office of Science User Facility supported under Contract DE-AC02-06CH11357.","type":"journal_article","article_type":"original","oa_version":"Published Version","intvolume":"         8","_id":"62","scopus_import":"1","publist_id":"7992","quality_controlled":"1","file":[{"file_id":"5699","access_level":"open_access","checksum":"1a14ae0666b82fbaa04bef110e3f6bf2","relation":"main_file","date_updated":"2020-07-14T12:47:24Z","file_size":4141645,"date_created":"2018-12-17T12:22:24Z","content_type":"application/pdf","file_name":"2018_ScientificReports_Shahbazi.pdf","creator":"dernst"}],"ddc":["570"],"has_accepted_license":"1","article_number":"14247","year":"2018","date_created":"2018-12-11T11:44:25Z","publication":"Scientific Reports","issue":"1","doi":"10.1038/s41598-018-32628-3","abstract":[{"lang":"eng","text":"Imaging is a dominant strategy for data collection in neuroscience, yielding stacks of images that often scale to gigabytes of data for a single experiment. Machine learning algorithms from computer vision can serve as a pair of virtual eyes that tirelessly processes these images, automatically detecting and identifying microstructures. Unlike learning methods, our Flexible Learning-free Reconstruction of Imaged Neural volumes (FLoRIN) pipeline exploits structure-specific contextual clues and requires no training. This approach generalizes across different modalities, including serially-sectioned scanning electron microscopy (sSEM) of genetically labeled and contrast enhanced processes, spectral confocal reflectance (SCoRe) microscopy, and high-energy synchrotron X-ray microtomography (μCT) of large tissue volumes. We deploy the FLoRIN pipeline on newly published and novel mouse datasets, demonstrating the high biological fidelity of the pipeline’s reconstructions. FLoRIN reconstructions are of sufficient quality for preliminary biological study, for example examining the distribution and morphology of cells or extracting single axons from functional data. Compared to existing supervised learning methods, FLoRIN is one to two orders of magnitude faster and produces high-quality reconstructions that are tolerant to noise and artifacts, as is shown qualitatively and quantitatively."}],"external_id":{"isi":["000445336600015"]},"publication_status":"published","article_processing_charge":"No","title":"Flexible learning-free segmentation and reconstruction of neural volumes","volume":8,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"full_name":"Shabazi, Ali","first_name":"Ali","last_name":"Shabazi"},{"last_name":"Kinnison","first_name":"Jeffery","full_name":"Kinnison, Jeffery"},{"last_name":"Vescovi","first_name":"Rafael","full_name":"Vescovi, Rafael"},{"first_name":"Ming","last_name":"Du","full_name":"Du, Ming"},{"last_name":"Hill","first_name":"Robert","full_name":"Hill, Robert"},{"last_name":"Jösch","first_name":"Maximilian A","full_name":"Jösch, Maximilian A","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3937-1330"},{"last_name":"Takeno","first_name":"Marc","full_name":"Takeno, Marc"},{"full_name":"Zeng, Hongkui","first_name":"Hongkui","last_name":"Zeng"},{"full_name":"Da Costa, Nuno","last_name":"Da Costa","first_name":"Nuno"},{"first_name":"Jaime","last_name":"Grutzendler","full_name":"Grutzendler, Jaime"},{"full_name":"Kasthuri, Narayanan","last_name":"Kasthuri","first_name":"Narayanan"},{"full_name":"Scheirer, Walter","last_name":"Scheirer","first_name":"Walter"}],"related_material":{"link":[{"url":"http://doi.org/10.1038/s41598-018-36220-7","relation":"erratum"}]}}]